diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
index ea717e7edccbdebe98166eb0c88073477f3e307a..b2463c75f099d6f0cd06ed83a5ec6a55fc7ae2f8 100644
--- a/.github/workflows/api.yaml
+++ b/.github/workflows/api.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -18,6 +20,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -55,15 +58,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/bioblend.yaml b/.github/workflows/bioblend.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f0da9f2ed0e673fb0f19f3efa827608c358ca630
--- /dev/null
+++ b/.github/workflows/bioblend.yaml
@@ -0,0 +1,80 @@
+name: BioBlend Tests
+on:
+  pull_request:
+    paths:
+      - .github/workflows/bioblend.yaml
+      - lib/galaxy/schema/**
+      - lib/galaxy/webapps/galaxy/api/**
+      - lib/galaxy/webapps/galaxy/services/**
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres
+        # Provide the password for postgres
+        env:
+          POSTGRES_PASSWORD: postgres
+        # Set health checks to wait until postgres has started
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    strategy:
+      fail-fast: false
+      matrix:
+        tox_env: [py313]
+        galaxy_python_version: ["3.8"]
+    steps:
+      - name: Checkout Galaxy
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          path: galaxy
+      - name: Checkout Bioblend
+        uses: actions/checkout@v4
+        with:
+          repository: galaxyproject/bioblend
+          path: bioblend
+      - name: Cache pip dir
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.tox_env }}
+      - name: Calculate Python version for BioBlend from tox_env
+        id: get_bioblend_python_version
+        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
+      - name: Set up Python for BioBlend
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
+      - name: Install tox
+        run: |
+          python3 -m pip install --upgrade pip setuptools
+          python3 -m pip install 'tox>=1.8.0'
+      - name: Set up Python for Galaxy
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.galaxy_python_version }}
+      - name: Run tests
+        env:
+          PGPASSWORD: postgres
+          PGPORT: 5432
+          PGHOST: localhost
+        run: |
+          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
+          createdb -U postgres galaxy
+          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
+          ./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}
+      - name: The job has failed
+        if: ${{ failure() }}
+        run: |
+          cat galaxy/*.log
diff --git a/.github/workflows/build_container_image.yaml b/.github/workflows/build_container_image.yaml
index 53a4a285a73d2c5acc2accb55ad4295afdadaa5f..dbff3546e9ae79fb4458da7bddf04abbfa017455 100644
--- a/.github/workflows/build_container_image.yaml
+++ b/.github/workflows/build_container_image.yaml
@@ -10,8 +10,67 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 jobs:
+  ghcrbuild:
+    name: Build container image for GHCR
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
+      - name: Set outputs
+        id: commit
+        run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT
+      - name: Set branch name
+        id: branch
+        run: |
+          if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then
+            echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then
+            echo "name=dev" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then
+            echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT
+          fi
+        shell: bash
+      - name: Extract metadata for container image
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=raw,value=${{steps.branch.outputs.name}}
+      - name: Build args
+        id: buildargs
+        run: |
+            echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT 
+            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          platforms: linux/amd64
+
+      - name: Login to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push container image to ghcr
+        uses: docker/build-push-action@v4
+        with:
+          build-args: |
+              GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }}
+              BUILD_DATE=${{ steps.buildargs.outputs.builddate }}
+              IMAGE_TAG=${{ steps.branch.outputs.name }}
+          file: .k8s_ci.Dockerfile
+          push: true
+          context: .
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64
+
   build:
-    name: Build container image
+    name: Build container image for Galaxy repos
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
@@ -58,3 +117,4 @@ jobs:
         uses: actions-hub/docker@master
         with:
           args: push galaxy/galaxy-min:${{ steps.branch.outputs.name }}
+
diff --git a/.github/workflows/check_test_class_names.yaml b/.github/workflows/check_test_class_names.yaml
index 1d73f57af374332c9c4aaf8673cc4b24fbee04f1..33bf31877177f0f607312585a25860f81d8049d2 100644
--- a/.github/workflows/check_test_class_names.yaml
+++ b/.github/workflows/check_test_class_names.yaml
@@ -5,6 +5,9 @@ on:
       - '.ci/check_test_class_names.sh'
       - 'lib/galaxy_test/**'
       - 'test/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
@@ -17,11 +20,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
         run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt
       - name: Run tests
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index a4cb056311a5beadd60fac600e576f0de8e07cca..bbacec3a450b65d1533f33b09c06cafa0c2197d9 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -19,7 +19,9 @@ on:
     branches: [ dev ]
   schedule:
     - cron: '16 6 * * 0'
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   analyze:
     name: Analyze
diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 23848f81c014bf5d5dcdef91bfc3c07f08439f61..0a1928e69861e8b842e291f69196acf415b613bc 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -44,12 +46,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache venv dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Move test data
         run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
       - name: Install planemo
@@ -64,7 +62,7 @@ jobs:
       - name: Lint converters
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
-          planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}"
+          planemo lint --skip CitationsMissing,HelpEmpty,HelpMissing --report_level warn "${TOOL_ARRAY[@]}"
       - name: Run tests
         run: |
           mapfile -t TOOL_ARRAY < tool_list.txt
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
index f9ac963071ac745c3ebf59cbda865771033aa79b..3dbae9898f4f34e992eb5d59379fcd714a515c8f 100644
--- a/.github/workflows/cwl_conformance.yaml
+++ b/.github/workflows/cwl_conformance.yaml
@@ -4,10 +4,14 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
 concurrency:
@@ -46,20 +50,17 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
       - name: Run tests
         run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
         working-directory: 'galaxy root'
diff --git a/.github/workflows/db_indexes.yaml b/.github/workflows/db_indexes.yaml
index cc5ec407b5d4819b23f9498f79f6a534f618ea56..f74c7d5f63e228bed68a0fbf2746c0a2b55d1d0c 100644
--- a/.github/workflows/db_indexes.yaml
+++ b/.github/workflows/db_indexes.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -45,16 +47,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml
index 56530f565278189bf8afe95db235f88f2ac936e4..2401107eb32517ccb950a1c2f6d69ed8c513e59a 100644
--- a/.github/workflows/dependencies.yaml
+++ b/.github/workflows/dependencies.yaml
@@ -8,29 +8,31 @@ jobs:
     name: Update dependencies
     if: github.repository_owner == 'galaxyproject'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v4
+      # Install Python 3.8 for update_lint_requirements.sh
+      # Install Python 3.9 (as default) to allow `uv lock` to generate metadata for rucio-clients
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: |
+            3.8
+            3.9
       - name: Update dependencies
-        run: | 
-          python -m venv .venv
-          make update-dependencies
+        run: make update-dependencies
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:
           author: galaxybot <galaxybot@users.noreply.github.com>
           token: ${{ secrets.GALAXYBOT_PAT }}
-          commit-message: Update Python dependencies
+          commit-message: |
+            Update Python dependencies
+
+            by running `make update-dependencies`.
           branch: dev_auto_update_dependencies
           delete-branch: true
           push-to-fork: galaxybot/galaxy
           title: Update Python dependencies
-          body: Run `make update-dependencies`.
+          body: by running `make update-dependencies`.
           labels: |
             area/dependencies
             kind/enhancement
diff --git a/.github/workflows/deployment.yaml b/.github/workflows/deployment.yaml
index 6e6506e9fdf89ac184f07f60633c1f07af583930..281b60beb071d234abca8e939292dc19c4701454 100644
--- a/.github/workflows/deployment.yaml
+++ b/.github/workflows/deployment.yaml
@@ -20,10 +20,6 @@ on:
         - all
         - api
         - selenium
-      branch:
-        description: 'Branch of code to run from'
-        default: 'dev'
-        type: string        
       debug:
         required: true
         description: 'Run deployment tests with debug mode on'
@@ -41,11 +37,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - uses: nanasess/setup-chromedriver@v2
       - name: Run tests
         run: bash ./test/deployment/usegalaxystar.bash
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 77a01f531907e58c15cacbf91145f45a0e930d8a..742d5b6a0048e9700fcd9eb7f905de1e5f183f39 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -32,11 +34,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
         run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
       - name: Add Google Analytics to doc/source/conf.py
diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
index bc487ab9ec327cccc55219f0ae17f40b97575c91..c874344fe6d006d85dfb1d0196cac92f95facef0 100644
--- a/.github/workflows/first_startup.yaml
+++ b/.github/workflows/first_startup.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   YARN_INSTALL_OPTS: --frozen-lockfile
 concurrency:
@@ -23,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}
@@ -40,16 +42,12 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework_tools.yaml
similarity index 88%
rename from .github/workflows/framework.yaml
rename to .github/workflows/framework_tools.yaml
index dcc5e7614b15b10a629edadab1005e0f02cbb951..167afcdc45b8982311bdb76403b3c8c535a9f1be 100644
--- a/.github/workflows/framework.yaml
+++ b/.github/workflows/framework_tools.yaml
@@ -1,15 +1,17 @@
-name: Framework tests
+name: Tool framework tests
 on:
   push:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -51,22 +53,19 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-tools
       - name: Run tests
-        run: ./run_tests.sh --coverage --framework
+        run: ./run_tests.sh --coverage --framework-tools
         working-directory: 'galaxy root'
       - uses: codecov/codecov-action@v3
         with:
diff --git a/.github/workflows/framework_workflows.yaml b/.github/workflows/framework_workflows.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..018463833e22af398a9de0cdc2653c5f7a1bd330
--- /dev/null
+++ b/.github/workflows/framework_workflows.yaml
@@ -0,0 +1,77 @@
+name: Workflow framework tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_WORKFLOW_AFTER_RERUN: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8']
+    services:
+      postgres:
+        image: postgres:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v4
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v4
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-workflows
+      - name: Run tests
+        run: ./run_tests.sh --coverage --framework-workflows
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v3
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: Framework test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_workflows_tests.html'
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 0dc78ef4bb1c1e411975df4f7f5c9f3922e84fce..1bdc5b58cf9a77d62022243c5abb61ea8fc0685c 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -25,7 +27,7 @@ concurrency:
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -76,16 +78,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
index 414446b5d827951b126e870bd49c89b48a70343e..73488daea60ddb7885d7cbb498ceada964cfd4a7 100644
--- a/.github/workflows/integration_selenium.yaml
+++ b/.github/workflows/integration_selenium.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -54,15 +56,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index fc03fde8c3a9ddbf7301c90f2f9245532b04ce83..37d337fb95febef33a5f35103805de734721b430 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
@@ -32,15 +32,15 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: |
+            ${{ env.LINT_PATH }}
+            ${{ env.TYPE_PATH }}
+            ${{ env.CORE_PATH }}
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:
@@ -55,4 +55,6 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
+        with:
+          version: "24.8.0"  # last version supporting Python 3.8
       - uses: isort/isort-action@v1
diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml
index 4269db840770159f6da35f0a33154ab59ef55666..9aa656bd20e1c34846af46e5f867338039c0dce9 100644
--- a/.github/workflows/lint_openapi_schema.yml
+++ b/.github/workflows/lint_openapi_schema.yml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -20,28 +22,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
       - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/maintenance_bot.yaml b/.github/workflows/maintenance_bot.yaml
index 1daa3898769d0a4697e64c26d8e362882f03e7ef..b45dd2b87c7a45ad3578599b7a2686c740f53994 100644
--- a/.github/workflows/maintenance_bot.yaml
+++ b/.github/workflows/maintenance_bot.yaml
@@ -12,7 +12,7 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     env:
-      MILESTONE_NUMBER: 27
+      MILESTONE_NUMBER: 29
     steps:
       - name: Get latest pull request labels
         id: get_pr_labels
diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 4d33cc3febd733a67b2a2b350257a48996f269ec..0d4eed74c0e02f03e055858c33d7db07791772b8 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -28,15 +30,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:
@@ -44,6 +43,8 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6  # https://github.com/eWaterCycle/setup-apptainer/pull/68
       - name: Install tox
         run: pip install tox
       - name: Run tests
diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index 0a3050cbcb6b77ada165c16345afb3cdaf1c75d2..b0639ca433406c0d1f6a594641dffb2551537c44 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -21,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}
@@ -34,24 +36,15 @@ jobs:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
-      - name: Get full Python version
-        id: full-python-version
-        shell: bash
-        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
         uses: actions/cache@v4
-        id: pip-cache
         with:
           path: ~/Library/Caches/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-      - name: Cache tox env
-        uses: actions/cache@v4
-        with:
-          path: .tox
-          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
-      - name: Install miniconda  # use this job to test using Python from a conda environment
+      - name: Install miniforge  # use this job to test using Python from a conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-version: latest
           activate-environment: ''
       - name: Restore client cache
         uses: actions/cache@v4
diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml
index 45413a608f190b32c65b103adae49da3abc9ab54..ecfdc7452464acb8bc759996ec6de7e224d76c3c 100644
--- a/.github/workflows/performance.yaml
+++ b/.github/workflows/performance.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -50,15 +52,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/pr-title-update.yml b/.github/workflows/pr-title-update.yml
new file mode 100644
index 0000000000000000000000000000000000000000..8ffd54a45da423c5125599c8e97d877deff656ec
--- /dev/null
+++ b/.github/workflows/pr-title-update.yml
@@ -0,0 +1,29 @@
+name: Update PR title
+
+on:
+  pull_request_target:
+    types: [opened, edited, reopened]
+
+jobs:
+  update-title:
+    if: github.event.action != 'edited' || github.event.changes.base.ref.from != ''
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Update PR title
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          TARGET_BRANCH: "${{ github.base_ref }}"
+          PR_TITLE: "${{ github.event.pull_request.title }}"
+          REPO: "${{ github.repository }}"
+        run: |
+          VERSION=$(echo $TARGET_BRANCH | grep -oP '^release_\K\d+.\d+$' || true)
+          NEW_TITLE=$(echo "$PR_TITLE" | sed -E "s/\[[0-9]+\.[0-9]+\] //")
+          if [[ -n "$VERSION" ]]; then
+            NEW_TITLE="[$VERSION] $NEW_TITLE"
+          fi
+          if [[ "$NEW_TITLE" != "$PR_TITLE" ]]; then
+            gh pr edit $PR_NUMBER --repo "$REPO" --title "$NEW_TITLE"
+          fi
diff --git a/.github/workflows/publish_artifacts.yaml b/.github/workflows/publish_artifacts.yaml
index dded5d1086eb0d76868c55078baf331ad85144fa..e4bc8f6118f8fc38148ab0396a6ec4440a9ae0ac 100644
--- a/.github/workflows/publish_artifacts.yaml
+++ b/.github/workflows/publish_artifacts.yaml
@@ -1,26 +1,48 @@
 name: Publish release artifacts
 on:
-    release:
-      types: [released, prereleased]
+  release:
+    types: [released, prereleased]
 jobs:
-  build-and-publish:
+  build-and-publish-pypi:
     if: github.repository_owner == 'galaxyproject'
-    name: build-and-publish
+    name: Build and Publish to PyPI
     runs-on: ubuntu-latest
     strategy:
         matrix:
             python-version: ['3.8']
     steps:
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/checkout@v4
       - name: Install script dependencies
         run: pip install galaxy-release-util
-      - name: Build and publish
+      - name: Build and publish to PyPI
         run: |
           galaxy-release-util build-and-upload --no-confirm
         env:
             TWINE_USERNAME: __token__
             TWINE_PASSWORD: ${{ github.event.release.prerelease && secrets.PYPI_TEST_TOKEN || secrets.PYPI_MAIN_TOKEN }}
             TWINE_REPOSITORY_URL: ${{ github.event.release.prerelease && 'https://test.pypi.org/legacy/' || 'https://upload.pypi.org/legacy/' }}
+
+  build-and-publish-npm:
+    if: github.repository_owner == 'galaxyproject'
+    name: Build and Publish to NPM
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'client/yarn.lock'
+          registry-url: 'https://registry.npmjs.org'
+      - name: build client
+        run: yarn && yarn build-production
+        working-directory: 'client'
+      - name: publish client
+        if: "!github.event.release.prerelease"
+        run: npm publish --provenance --access public
+        working-directory: 'client'
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml
index d2a730549837f7a7a04b04f49d2f32aa92dd2f35..f0285ff468f6f93a6bacd887eabca78c16c507cb 100644
--- a/.github/workflows/reports_startup.yaml
+++ b/.github/workflows/reports_startup.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
 env:
   YARN_INSTALL_OPTS: --frozen-lockfile
 concurrency:
@@ -18,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     defaults:
       run:
         shell: bash -l {0}
@@ -35,16 +37,12 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
index 3c3d9126cbb524183ddee4ae33b83f2959ddb3d5..8ea022cad9d7e27359879426b2a9b026c214df31 100644
--- a/.github/workflows/selenium.yaml
+++ b/.github/workflows/selenium.yaml
@@ -3,9 +3,11 @@ on:
   push:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
+      - 'packages/**'
   schedule:
     # Run at midnight UTC every Tuesday
     - cron: '0 0 * * 2'
@@ -59,15 +61,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml
index da5e092118dc88c620da5ee34a1050cba9d6d1b2..f38f05846e747638a797bd93c682fa9ba3b51f03 100644
--- a/.github/workflows/test_galaxy_packages.yaml
+++ b/.github/workflows/test_galaxy_packages.yaml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:
@@ -31,11 +31,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
       - name: Install tox
diff --git a/.github/workflows/test_galaxy_packages_for_pulsar.yaml b/.github/workflows/test_galaxy_packages_for_pulsar.yaml
index 3ce8c2f3beceadadf5d0f7e6513b55f3a3ae58cc..5f54f7fd31adc7387eb484eee8cffcadeab5e974 100644
--- a/.github/workflows/test_galaxy_packages_for_pulsar.yaml
+++ b/.github/workflows/test_galaxy_packages_for_pulsar.yaml
@@ -16,7 +16,7 @@ concurrency:
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04  # Python 3.7 is not available via setup-python on ubuntu >=24.04
     strategy:
       fail-fast: false
       matrix:
@@ -28,11 +28,8 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
       - name: Install ffmpeg
diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml
index df121215d9f1112ff1fa0e088070aa7586e455f3..46ba1b38956175204639e8d136ee8f6fece52238 100644
--- a/.github/workflows/toolshed.yaml
+++ b/.github/workflows/toolshed.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   TOOL_SHED_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
@@ -21,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:
@@ -45,16 +47,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        id: pip-cache
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml
index dbb9b21587c716e2381f9aa9c4498f1463dcc2ed..9c106bfd4613bc62a07635f1423393534d348d6d 100644
--- a/.github/workflows/unit-postgres.yaml
+++ b/.github/workflows/unit-postgres.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/postgres?client_encoding=utf8'  # using postgres as the db
 concurrency:
@@ -44,15 +46,12 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
index 33b2857ddeee1c3a1a3678ac1cb31f4cd6a2f70b..bf41453d740a37cc263cf7d8d356cdb2f2c0d1c1 100644
--- a/.github/workflows/unit.yaml
+++ b/.github/workflows/unit.yaml
@@ -5,11 +5,13 @@ on:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
       - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -20,28 +22,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.12']
+        python-version: ['3.8', '3.13']
     steps:
       - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
       - uses: actions/setup-node@v4
         with:
           node-version: '18.12.1'
           cache: 'yarn'
           cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: 'galaxy root/requirements.txt'
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
-      - name: Cache pip dir
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache tox env
         uses: actions/cache@v4
         with:
diff --git a/.gitignore b/.gitignore
index d40861441c6a3d23739e4fc59dccd99d62980a37..330502b43a5ea6fee170a2e07e66184e44db27eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -153,6 +153,7 @@ doc/build
 doc/schema.md
 doc/source/admin/config_logging_default_yaml.rst
 doc/source/dev/schema.md
+doc/source/dev/plantuml.jar
 client/docs/dist
 
 # Webpack stats
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3d8f4c947fd81c39c59eae6a38209d4152175fc0..065b2a47fe7d0d3a1a8bf55e0278717f83696052 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -9,8 +9,8 @@ variables:
   CONTAINER_GALAXY_URL: "${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}"
   CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"
   CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"
-  GALAXY_VERSION_PYTHON: 24.1.dev5+ornl
-  GALAXY_VERSION_DOCKER: 24.1.dev5.ornl
+  GALAXY_VERSION_PYTHON: 24.2.dev0+ornl
+  GALAXY_VERSION_DOCKER: 24.2.dev0.ornl
 
 # This import is for the func_rse_docker_* functions
 before_script:
diff --git a/Makefile b/Makefile
index bd3422297aad91cfda6d488e745bd574174bde51..64d649ebf188d71642be1a2ae88fa6e96aa1e84c 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
 VENV?=.venv
 # Source virtualenv to execute command (darker, sphinx, twine, etc...)
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
-RELEASE_CURR:=24.1
+RELEASE_CURR:=25.0
 RELEASE_UPSTREAM:=upstream
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
@@ -186,6 +186,9 @@ else
 	$(IN_VENV) cd client && yarn install $(YARN_INSTALL_OPTS)
 endif
 
+format-xsd:
+	xmllint --format --output galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
+	mv galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
 
 build-api-schema:
 	$(IN_VENV) python scripts/dump_openapi_schema.py _schema.yaml
@@ -196,8 +199,8 @@ remove-api-schema:
 	rm _shed_schema.yaml
 
 update-client-api-schema: client-node-deps build-api-schema
-	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_schema.yaml > src/api/schema/schema.ts && npx prettier --write src/api/schema/schema.ts
-	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_shed_schema.yaml > ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && npx prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
+	$(IN_VENV) cd client && npx openapi-typescript ../_schema.yaml > src/api/schema/schema.ts && npx prettier --write src/api/schema/schema.ts
+	$(IN_VENV) cd client && npx openapi-typescript ../_shed_schema.yaml > ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && npx prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
 	$(MAKE) remove-api-schema
 
 lint-api-schema: build-api-schema
diff --git a/README.rst b/README.rst
index 17e11d9ff09869d5503d9022c6a888aa113fefa4..6c4fb522c003ceb7da2007fc8ede154c72030c4b 100644
--- a/README.rst
+++ b/README.rst
@@ -24,7 +24,7 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.8 . To check your Python version, run:
+Galaxy requires Python 3.8 or higher. To check your Python version, run:
 
 .. code:: console
 
diff --git a/SECURITY.md b/SECURITY.md
index 2b30ab9b1106512291f5c9f6ffa1dd3b626c1f5d..22f1b73cc79b3adff123eea05ae10780d196acef 100644
--- a/SECURITY.md
+++ b/SECURITY.md
@@ -16,8 +16,7 @@ The following branches or releases receive security support:
 
 - Development on the `dev` branch, hosted on GitHub, which will become the next release of Galaxy
 - Releases within the past 12 months.
-  - E.g. 16.04 will receive support until 2017-04. As the month changes to 2017-05 it will become unsupported.
-- There are currently no plans for Long Term Support (LTS) releases.
+  - E.g. 24.0 will receive support for a full year, at which point 25.0 will be available.
 
 For unsupported branches:
 
@@ -41,7 +40,7 @@ These are only examples. The security team will provide a severity classificatio
 
 ## Notification of Vulnerabilities
 
-For high severity issues, we will notify [the list of public Galaxy owners](https://lists.galaxyproject.org/listinfo/galaxy-public-servers) with:
+For high severity issues, we will notify [the list of public Galaxy owners](https://lists.galaxyproject.org/lists/galaxy-public-servers.lists.galaxyproject.org/) with:
 
 - A description of the issue
 - List of supported versions that are affected
diff --git a/client/.eslintrc.js b/client/.eslintrc.js
index 8a7dd383bd66db88bccf8513cb4879ec62db3d53..a2ade17c292b63c55f3c8b8f7c1fb4e794a1e284 100644
--- a/client/.eslintrc.js
+++ b/client/.eslintrc.js
@@ -82,6 +82,11 @@ const baseRules = {
     "import/first": "error",
     "import/newline-after-import": "error",
     "import/no-duplicates": "error",
+
+    "@typescript-eslint/consistent-type-imports": [
+        "error",
+        { prefer: "type-imports", fixStyle: "inline-type-imports" },
+    ],
 };
 
 const baseExtends = [
diff --git a/client/docs/querying-the-api.md b/client/docs/querying-the-api.md
index 63dc48b873eac5ba98ce2367e46a19f7ac881814..40360e44aea18abbe81585e98ed120dd329de3e9 100644
--- a/client/docs/querying-the-api.md
+++ b/client/docs/querying-the-api.md
@@ -24,44 +24,105 @@ If there is no Composable for the API endpoint you are using, try using a (Pinia
 
 ### Direct API Calls
 
--   If the type of data you are querying should not be cached, or you just need to update or create new data, you can use the API directly. Make sure to use the **Fetcher** (see below) instead of Axios, as it provides a type-safe interface to the API along with some extra benefits.
+-   If the type of data you are querying should not be cached, or you just need to update or create new data, you can use the API directly. Make sure to use the **GalaxyApi client** (see below) instead of Axios, as it provides a type-safe interface to the API along with some extra benefits.
 
-## 2. Prefer Fetcher over Axios (when possible)
+## 2. Prefer **GalaxyApi client** over Axios (when possible)
 
--   **Use Fetcher with OpenAPI Specs**: If there is an OpenAPI spec for the API endpoint you are using (in other words, there is a FastAPI route defined in Galaxy), always use the Fetcher. It will provide you with a type-safe interface to the API.
+-   **Use **GalaxyApi client** with OpenAPI Specs**: If there is an OpenAPI spec for the API endpoint you are using (in other words, there is a FastAPI route defined in Galaxy), always use the GalaxyApi client. It will provide you with a type-safe interface to the API.
 
 **Do**
 
-```typescript
-import { fetcher } from "@/api/schema";
-const datasetsFetcher = fetcher.path("/api/dataset/{id}").method("get").create();
+```ts
+import { ref, onMounted } from "vue";
 
-const { data: dataset } = await datasetsFetcher({ id: "testID" });
+import { GalaxyApi, type HDADetailed } from "@/api";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+interface Props {
+    datasetId: string;
+}
+
+const props = defineProps<Props>();
+
+const datasetDetails = ref<HDADetailed>();
+const errorMessage = ref<string>();
+
+async function loadDatasetDetails() {
+    // Your IDE will provide you with autocompletion for the route and all the parameters
+    const { data, error } = await GalaxyApi().GET("/api/datasets/{dataset_id}", {
+        params: {
+            path: {
+                dataset_id: props.datasetId,
+            },
+            query: { view: "detailed" },
+        },
+    });
+
+    if (error) {
+        // Handle error here. For example, you can display a message to the user.
+        errorMessage.value = errorMessageAsString(error);
+        // Make sure to return here, otherwise `data` will be undefined
+        return;
+    }
+
+    // Use `data` here. We are casting it to HDADetailed to help the type inference because
+    // we requested the "detailed" view and this endpoint returns different types depending
+    // on the view. In general, the correct type will be inferred automatically using the
+    // API schema so you don't need to (and shouldn't) cast it.
+    datasetDetails.value = data as HDADetailed;
+}
+
+onMounted(() => {
+    loadDatasetDetails();
+});
 ```
 
 **Don't**
 
-```js
+```ts
+import { ref, onMounted } from "vue";
+
 import axios from "axios";
 import { getAppRoot } from "onload/loadConfig";
-import { rethrowSimple } from "utils/simple-error";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+interface Props {
+    datasetId: string;
+}
+
+const props = defineProps<Props>();
+
+const datasetDetails = ref<HDADetailed>();
+const errorMessage = ref<string>();
 
-async getDataset(datasetId) {
+async function loadDatasetDetails() {
+    // You need to construct the URL yourself
     const url = `${getAppRoot()}api/datasets/${datasetId}`;
+    // You are forced to use a try-catch block to handle errors
+    // and you may forget to do so.
     try {
-        const response = await axios.get(url);
-        return response.data;
+        // This is not type-safe and cannot detect changes in the API schema.
+        const response = await axios.get(url, {
+            // You need to know the API parameters, no type inference here.
+            params: { view: "detailed" },
+        });
+        // In this case, you need to cast the response to the correct type
+        // (as in the previous example), but you will also have to do it in the general
+        // case because there is no type inference.
+        datasetDetails = response.data as HDADetailed;
     } catch (e) {
-        rethrowSimple(e);
+        errorMessage.value = errorMessageAsString(error);
     }
 }
 
-const dataset = await getDataset("testID");
+onMounted(() => {
+    loadDatasetDetails();
+});
 ```
 
 > **Reason**
 >
-> The `fetcher` class provides a type-safe interface to the API, and is already configured to use the correct base URL and error handling.
+> The `GalaxyApi client` function provides a type-safe interface to the API, and is already configured to use the correct base URL. In addition, it will force you to handle errors properly, and will provide you with a type-safe response object. It uses `openapi-fetch` and you can find more information about it [here](https://openapi-ts.dev/openapi-fetch/).
 
 ## 3. Where to put your API queries?
 
@@ -79,8 +140,8 @@ If so, you should consider putting the query in a Store. If not, you should cons
 
 If so, you should consider putting it under src/api/<resource>.ts and exporting it from there. This will allow you to reuse the query in multiple places specially if you need to do some extra processing of the data. Also it will help to keep track of what parts of the API are being used and where.
 
-### Should I use the `fetcher` directly or should I write a wrapper function?
+### Should I use the `GalaxyApi client` directly or should I write a wrapper function?
 
--   If you **don't need to do any extra processing** of the data, you can use the `fetcher` directly.
--   If you **need to do some extra processing**, you should consider writing a wrapper function. Extra processing can be anything from transforming the data to adding extra parameters to the query or omitting some of them, handling conditional types in response data, etc.
--   Using a **wrapper function** will help in case we decide to replace the `fetcher` with something else in the future (as we are doing now with _Axios_).
+-   If you **don't need to do any additional processing** of the data, you **should** use the `GalaxyApi client` directly.
+-   If you **need to do some additional processing**, then consider writing a wrapper function. Additional processing can be anything from transforming the data to adding extra parameters to the query, providing useful defaults, handling conditional types in response data, etc.
+-   In any case, please try to avoid modeling your own types if you can use the ones defined in the OpenAPI spec (client/src/api/schema/schema.ts). This will help to keep the codebase consistent and avoid duplication of types or API specification drifting.
diff --git a/client/docs/unit-testing/writing-tests.md b/client/docs/unit-testing/writing-tests.md
index 9a49db6c510a37832147f93f5fc5b42a6fedfae4..830f8f27c9f90257b5b18ccc9fb7df1037864f57 100644
--- a/client/docs/unit-testing/writing-tests.md
+++ b/client/docs/unit-testing/writing-tests.md
@@ -67,3 +67,50 @@ describe("some module you wrote", () => {
 
 We have created some [common helpers for common testing
 scenarios](https://github.com/galaxyproject/galaxy/blob/dev/client/tests/jest/helpers.js).
+
+### Mocking API calls
+
+When testing components that make API calls, you should use [**Mock Service Worker**](https://mswjs.io/docs/getting-started/) in combination with [**openapi-msw**](https://github.com/christoph-fricke/openapi-msw?tab=readme-ov-file#openapi-msw).
+
+If you want to know more about why MSW is a good choice for mocking API calls, you can read [this article](https://mswjs.io/docs/philosophy).
+
+If your component makes an API call, for example to get a particular history, you can mock the response of the API call using the `useServerMock` composable in your test file.
+
+```ts
+import { useServerMock } from "@/api/client/__mocks__";
+
+const { server, http } = useServerMock();
+
+describe("MyComponent", () => {
+    it("should do something with the history", async () => {
+        // Mock the response of the API call
+        server.use(
+            http.get("/api/histories/{history_id}", ({ params, query, response }) => {
+                // You can use logic to return different responses based on the request
+                if (query.get("view") === "detailed") {
+                    return response(200).json(TEST_HISTORY_DETAILED);
+                }
+
+                // Or simulate an error
+                if (params.history_id === "must-fail") {
+                    return response("5XX").json(EXPECTED_500_ERROR, { status: 500 });
+                }
+
+                return response(200).json(TEST_HISTORY_SUMMARY);
+            })
+        );
+
+        // Your test code here
+    });
+});
+```
+
+Using this approach, it will ensure the type safety of the API calls and the responses. If you need to mock API calls that are not defined in the OpenAPI specs, you can use the `http.untyped` variant to mock any API route. Or define an untyped response for a specific route with `HttpResponse`. See the example below:
+
+```ts
+const catchAll = http.untyped.all("/resource/*", ({ params }) => {
+    return HttpResponse.json(/* ... */);
+});
+```
+
+For more information on how to use `openapi-msw`, you can check the [official documentation](https://github.com/christoph-fricke/openapi-msw?tab=readme-ov-file#handling-unknown-paths).
diff --git a/client/gulpfile.js b/client/gulpfile.js
index 873bae0c0bd880615124ea0b3462189389c2bae8..f16b5eb8485401b73aca3cda83cd07ac6cb2b142 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -1,10 +1,11 @@
 const path = require("path");
-const fs = require("fs");
+const fs = require("fs-extra");
 const del = require("del");
 const { src, dest, series, parallel, watch } = require("gulp");
 const child_process = require("child_process");
 const { globSync } = require("glob");
 const buildIcons = require("./icons/build_icons");
+const xml2js = require("xml2js");
 
 /*
  * We'll want a flexible glob down the road, but for now there are no
@@ -14,22 +15,19 @@ const buildIcons = require("./icons/build_icons");
 const STATIC_PLUGIN_BUILD_IDS = [
     "annotate_image",
     "chiraviz",
-    "cytoscape",
     "drawrna",
     "editor",
     "example",
+    "fits_graph_viewer",
     "fits_image_viewer",
     "h5web",
     "heatmap/heatmap_default",
     "hyphyvision",
     "jqplot/jqplot_bar",
     "media_player",
-    "msa",
     "mvpapp",
-    "ngl",
     "nora",
     "nvd3/nvd3_bar",
-    "openlayers",
     "openseadragon",
     "PCA_3Dplot",
     "phylocanvas",
@@ -37,11 +35,16 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "scatterplot",
     "tiffviewer",
     "ts_visjs",
-    "venn",
 ];
+const INSTALL_PLUGIN_BUILD_IDS = ["cytoscape", "ngl", "msa", "openlayers", "venn", "vizarr"]; // todo: derive from XML
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
 
+const failOnError =
+    process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR && process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR !== "0"
+        ? true
+        : false;
+
 const PATHS = {
     nodeModules: "./node_modules",
     stagedLibraries: {
@@ -57,11 +60,6 @@ const PATHS = {
     },
 };
 
-const failOnError =
-    process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR && process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR !== "0"
-        ? true
-        : false;
-
 PATHS.pluginBaseDir =
     (process.env.GALAXY_PLUGIN_PATH && process.env.GALAXY_PLUGIN_PATH !== "None"
         ? process.env.GALAXY_PLUGIN_PATH
@@ -162,6 +160,8 @@ function buildPlugins(callback, forceRebuild) {
             console.log(`No changes detected for ${pluginName}`);
         } else {
             console.log(`Installing Dependencies for ${pluginName}`);
+
+            // Else we call yarn install and yarn build
             child_process.spawnSync(
                 "yarn",
                 ["install", "--production=false", "--network-timeout=300000", "--check-files"],
@@ -205,6 +205,64 @@ function buildPlugins(callback, forceRebuild) {
     return callback();
 }
 
+async function installPlugins(callback) {
+    // iterate through install_plugin_build_ids, identify xml files and install dependencies
+    for (const plugin_name of INSTALL_PLUGIN_BUILD_IDS) {
+        const pluginDir = path.join(PATHS.pluginBaseDir, `visualizations/${plugin_name}`);
+        const xmlPath = path.join(pluginDir, `config/${plugin_name}.xml`);
+        // Check if the file exists
+        if (fs.existsSync(xmlPath)) {
+            await installDependenciesFromXML(xmlPath, pluginDir);
+        } else {
+            console.error(`XML file not found: ${xmlPath}`);
+        }
+    }
+    return callback();
+}
+
+// Function to parse the XML and install dependencies
+async function installDependenciesFromXML(xmlPath, pluginDir) {
+    try {
+        const pluginXML = fs.readFileSync(xmlPath);
+        const parsedXML = await xml2js.parseStringPromise(pluginXML);
+        const requirements = parsedXML.visualization.requirements[0].requirement;
+
+        const installPromises = requirements.map(async (dep) => {
+            const { type: reqType, package: pkgName, version } = dep.$;
+
+            if (reqType === "npm" && pkgName && version) {
+                try {
+                    const installResult = child_process.spawnSync(
+                        "npm",
+                        ["install", "--silent", "--no-save", "--prefix .", `${pkgName}@${version}`],
+                        {
+                            cwd: pluginDir,
+                            stdio: "inherit",
+                            shell: true,
+                        }
+                    );
+
+                    if (installResult.status === 0) {
+                        await fs.copy(
+                            path.join(pluginDir, "node_modules", pkgName, "static"),
+                            path.join(pluginDir, "static")
+                        );
+                        console.log(`Installed package ${pkgName}@${version} in ${pluginDir}`);
+                    } else {
+                        console.error(`Error installing package ${pkgName}@${version} in ${pluginDir}`);
+                    }
+                } catch (err) {
+                    console.error(`Error handling package ${pkgName}@${version} in ${pluginDir}:`, err);
+                }
+            }
+        });
+
+        await Promise.all(installPromises);
+    } catch (err) {
+        console.error(`Error processing XML file ${xmlPath}:`, err);
+    }
+}
+
 function forceBuildPlugins(callback) {
     return buildPlugins(callback, true);
 }
@@ -214,8 +272,8 @@ function cleanPlugins() {
 }
 
 const client = parallel(fonts, stageLibs, icons);
-const plugins = series(buildPlugins, cleanPlugins, stagePlugins);
-const pluginsRebuild = series(forceBuildPlugins, cleanPlugins, stagePlugins);
+const plugins = series(buildPlugins, installPlugins, cleanPlugins, stagePlugins);
+const pluginsRebuild = series(forceBuildPlugins, installPlugins, cleanPlugins, stagePlugins);
 
 function watchPlugins() {
     const BUILD_PLUGIN_WATCH_GLOB = [
@@ -229,3 +287,4 @@ module.exports.plugins = plugins;
 module.exports.pluginsRebuild = pluginsRebuild;
 module.exports.watchPlugins = watchPlugins;
 module.exports.default = parallel(client, plugins);
+module.exports.installPlugins = installPlugins;
diff --git a/client/openapi_to_schema.mjs b/client/openapi_to_schema.mjs
deleted file mode 100644
index d85b349f096d51a3fd83e90b5638a63ef30a8959..0000000000000000000000000000000000000000
--- a/client/openapi_to_schema.mjs
+++ /dev/null
@@ -1,21 +0,0 @@
-// this is a helper script that fixes const values
-// upstream fix in https://github.com/drwpow/openapi-typescript/pull/1014
-import openapiTS from "openapi-typescript";
-
-const inputFilePath = process.argv[2];
-
-const localPath = new URL(inputFilePath, import.meta.url);
-openapiTS(localPath, {
-    transform(schemaObject, metadata) {
-        if ("const" in schemaObject) {
-            const constType = typeof schemaObject.const;
-            switch (constType) {
-                case "number":
-                case "boolean":
-                    return `${schemaObject.const}`;
-                default:
-                    return `"${schemaObject.const}"`;
-            }
-        }
-    },
-}).then((output) => console.log(output));
diff --git a/client/package.json b/client/package.json
index ed153282c5ac68b682c8e15f4c1392ea9f19f6ef..de12b9f71852ffb2bbf4c0edca156342d052a681 100644
--- a/client/package.json
+++ b/client/package.json
@@ -42,7 +42,7 @@
     "@popperjs/core": "^2.11.8",
     "@sentry/browser": "^7.74.1",
     "@sentry/vue": "^7.114.0",
-    "@types/jest": "^29.5.6",
+    "@types/jest": "^29.5.12",
     "@vueuse/core": "^10.5.0",
     "@vueuse/math": "^10.9.0",
     "assert": "^2.1.0",
@@ -62,9 +62,11 @@
     "dom-to-image": "^2.6.0",
     "dompurify": "^3.0.6",
     "dumpmeta-webpack-plugin": "^0.2.0",
+    "echarts": "^5.5.1",
     "elkjs": "^0.8.2",
     "file-saver": "^2.0.5",
     "flush-promises": "^1.0.2",
+    "font-awesome-6": "npm:@fortawesome/free-solid-svg-icons@6",
     "glob": "^10.3.10",
     "handsontable": "^4.0.0",
     "hsluv": "^1.0.1",
@@ -81,15 +83,14 @@
     "markdown-it": "^13.0.2",
     "markdown-it-regexp": "^0.4.0",
     "object-hash": "^3.0.0",
-    "openapi-typescript": "^6.1.0",
-    "openapi-typescript-fetch": "^1.1.3",
+    "openapi-fetch": "^0.10.6",
     "pinia": "^2.1.7",
     "popper.js": "^1.16.1",
     "pretty-bytes": "^6.1.1",
     "pyre-to-regexp": "^0.0.6",
     "querystring-es3": "^0.2.1",
     "regenerator-runtime": "^0.14.0",
-    "requirejs": "2.3.6",
+    "requirejs": "2.3.7",
     "rxjs": "^7.8.1",
     "rxjs-spy": "^8.0.2",
     "rxjs-spy-devtools-plugin": "^0.0.4",
@@ -101,7 +102,11 @@
     "tus-js-client": "^3.1.1",
     "underscore": "^1.13.6",
     "util": "^0.12.5",
+    "vega": "^5.30.0",
+    "vega-embed": "^6.26.0",
+    "vega-lite": "^5.21.0",
     "vue": "^2.7.14",
+    "vue-echarts": "^7.0.3",
     "vue-infinite-scroll": "^2.0.2",
     "vue-multiselect": "^2.1.7",
     "vue-observe-visibility": "^1.0.0",
@@ -142,7 +147,7 @@
     "@babel/preset-typescript": "^7.23.2",
     "@cerner/duplicate-package-checker-webpack-plugin": "^2.3.0",
     "@pinia/testing": "0.1.3",
-    "@testing-library/jest-dom": "^6.1.4",
+    "@testing-library/jest-dom": "^6.4.8",
     "@types/d3": "^7.4.2",
     "@types/dompurify": "^3.0.2",
     "@types/jquery": "^3.5.24",
@@ -172,15 +177,21 @@
     "eslint-plugin-vue": "^9.17.0",
     "eslint-plugin-vuejs-accessibility": "^2.2.0",
     "expose-loader": "^4.1.0",
+    "fake-indexeddb": "^6.0.0",
+    "fs-extra": "^11.2.0",
     "gulp": "^4.0.2",
     "ignore-loader": "^0.1.2",
     "imports-loader": "^4.0.1",
     "jest": "^29.7.0",
     "jest-environment-jsdom": "^29.7.0",
+    "jest-fixed-jsdom": "^0.0.2",
     "jest-location-mock": "^2.0.0",
     "jsdom-worker": "^0.3.0",
     "json-loader": "^0.5.7",
     "mini-css-extract-plugin": "^2.7.6",
+    "msw": "^2.3.4",
+    "openapi-msw": "^0.7.0",
+    "openapi-typescript": "^7.3.0",
     "postcss-loader": "^7.3.3",
     "prettier": "^2.8.8",
     "process": "^0.11.10",
@@ -189,7 +200,7 @@
     "sass-loader": "^13.3.2",
     "store": "^2.0.12",
     "style-loader": "^3.3.3",
-    "ts-jest": "^29.1.1",
+    "ts-jest": "^29.2.3",
     "ts-loader": "^9.5.0",
     "tsconfig-paths-webpack-plugin": "^4.1.0",
     "typescript": "^5.2.2",
@@ -200,6 +211,7 @@
     "webpack-dev-server": "^4.15.1",
     "webpack-merge": "^5.10.0",
     "xml-js": "^1.6.11",
+    "xml2js": "^0.6.2",
     "yaml-jest": "^1.2.0",
     "yaml-loader": "^0.8.0"
   },
diff --git a/client/src/api/client/__mocks__/index.ts b/client/src/api/client/__mocks__/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..573116ce03b36e5c08f3c8fc91ef466143803dc8
--- /dev/null
+++ b/client/src/api/client/__mocks__/index.ts
@@ -0,0 +1,68 @@
+import { HttpResponse } from "msw";
+import { setupServer } from "msw/node";
+import { createOpenApiHttp } from "openapi-msw";
+
+import { type GalaxyApiPaths } from "@/api/schema";
+
+export { HttpResponse };
+
+function createApiClientMock() {
+    return createOpenApiHttp<GalaxyApiPaths>({ baseUrl: window.location.origin });
+}
+
+let http: ReturnType<typeof createApiClientMock>;
+let server: ReturnType<typeof setupServer>;
+
+/**
+ * Returns a `server` instance that can be used to mock the Galaxy API server
+ * and make requests to the Galaxy API using the OpenAPI schema.
+ *
+ * It is an instance of Mock Service Worker (MSW) server (https://github.com/mswjs/msw).
+ * And the `http` object is an instance of OpenAPI-MSW (https://github.com/christoph-fricke/openapi-msw)
+ * that add support for full type inference from OpenAPI schema definitions.
+ */
+export function useServerMock() {
+    if (!server) {
+        server = setupServer();
+        http = createApiClientMock();
+    }
+
+    beforeAll(() => {
+        // Enable API mocking before all the tests.
+        server.listen({
+            onUnhandledRequest: (request) => {
+                const method = request.method.toLowerCase();
+                const apiPath = request.url.replace(window.location.origin, "");
+                const errorMessage = `
+No request handler found for ${request.method} ${request.url}.
+
+Make sure you have added a request handler for this request in your tests.
+
+Example:
+
+const { server, http } = useServerMock();
+server.use(
+    http.${method}('${apiPath}', ({ response }) => {
+        return response(200).json({});
+    })
+);
+                `;
+                throw new Error(errorMessage);
+            },
+        });
+    });
+
+    afterEach(() => {
+        // Reset the request handlers between each test.
+        // This way the handlers we add on a per-test basis
+        // do not leak to other, irrelevant tests.
+        server.resetHandlers();
+    });
+
+    afterAll(() => {
+        // Finally, disable API mocking after the tests are done.
+        server.close();
+    });
+
+    return { server, http };
+}
diff --git a/client/src/api/client/index.ts b/client/src/api/client/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3de48773d64b8502081740f5c068e65f86048730
--- /dev/null
+++ b/client/src/api/client/index.ts
@@ -0,0 +1,32 @@
+import createClient from "openapi-fetch";
+
+import { type GalaxyApiPaths } from "@/api/schema";
+import { getAppRoot } from "@/onload/loadConfig";
+
+function getBaseUrl() {
+    const isTest = process.env.NODE_ENV === "test";
+    return isTest ? window.location.origin : getAppRoot(undefined, true);
+}
+
+function apiClientFactory() {
+    return createClient<GalaxyApiPaths>({ baseUrl: getBaseUrl() });
+}
+
+export type GalaxyApiClient = ReturnType<typeof apiClientFactory>;
+
+let client: GalaxyApiClient;
+
+/**
+ * Returns the Galaxy API client.
+ *
+ * It can be used to make requests to the Galaxy API using the OpenAPI schema.
+ *
+ * See: https://openapi-ts.dev/openapi-fetch/
+ */
+export function GalaxyApi(): GalaxyApiClient {
+    if (!client) {
+        client = apiClientFactory();
+    }
+
+    return client;
+}
diff --git a/client/src/api/client/serverMock.test.ts b/client/src/api/client/serverMock.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e65b65b60f1a4a2a42ad7ad22841ca2d20c1bcb6
--- /dev/null
+++ b/client/src/api/client/serverMock.test.ts
@@ -0,0 +1,107 @@
+import { type HistoryDetailed, type HistorySummary, type MessageException } from "@/api";
+import { GalaxyApi } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
+
+const TEST_HISTORY_SUMMARY: HistorySummary = {
+    model_class: "History",
+    id: "test",
+    name: "Test History",
+    archived: false,
+    deleted: false,
+    purged: false,
+    published: false,
+    update_time: "2021-09-01T00:00:00",
+    count: 0,
+    annotation: "Test History Annotation",
+    tags: [],
+    url: "/api/histories/test",
+};
+
+const TEST_HISTORY_DETAILED: HistoryDetailed = {
+    ...TEST_HISTORY_SUMMARY,
+    create_time: "2021-09-01T00:00:00",
+    contents_url: "/api/histories/test/contents",
+    importable: false,
+    slug: "testSlug",
+    size: 0,
+    user_id: "userID",
+    username_and_slug: "username/slug",
+    state: "ok",
+    empty: true,
+    hid_counter: 0,
+    genome_build: null,
+    state_ids: {},
+    state_details: {},
+};
+
+const EXPECTED_500_ERROR: MessageException = { err_code: 500, err_msg: "Internal Server Error" };
+
+// Mock the server responses
+const { server, http } = useServerMock();
+server.use(
+    http.get("/api/histories/{history_id}", ({ params, query, response }) => {
+        if (query.get("view") === "detailed") {
+            return response(200).json(TEST_HISTORY_DETAILED);
+        }
+        if (params.history_id === "must-fail") {
+            return response("5XX").json(EXPECTED_500_ERROR, { status: 500 });
+        }
+        return response(200).json(TEST_HISTORY_SUMMARY);
+    })
+);
+
+describe("useServerMock", () => {
+    it("mocks the Galaxy Server", async () => {
+        {
+            const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+                params: {
+                    path: { history_id: "test" },
+                    query: { view: "summary" },
+                },
+            });
+
+            expect(error).toBeUndefined();
+
+            expect(data).toBeDefined();
+            expect(data).toEqual(TEST_HISTORY_SUMMARY);
+        }
+
+        {
+            const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+                params: {
+                    path: { history_id: "test" },
+                    query: { view: "detailed" },
+                },
+            });
+
+            expect(error).toBeUndefined();
+
+            expect(data).toBeDefined();
+            expect(data).toEqual(TEST_HISTORY_DETAILED);
+        }
+
+        {
+            const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+                params: {
+                    path: { history_id: "must-fail" },
+                },
+            });
+
+            expect(error).toBeDefined();
+            expect(error).toEqual(EXPECTED_500_ERROR);
+
+            expect(data).toBeUndefined();
+        }
+
+        {
+            const { data, error } = await GalaxyApi().GET("/api/configuration");
+
+            expect(data).toBeUndefined();
+
+            expect(error).toBeDefined();
+            expect(`${JSON.stringify(error)}`).toContain(
+                "Make sure you have added a request handler for this request in your tests."
+            );
+        }
+    });
+});
diff --git a/client/src/api/configTemplates.ts b/client/src/api/configTemplates.ts
index 51b21382c50544fcbf755ea511b2e7d74c84845d..ec987c7eb3a74e4bc21770ed419d44436facc83f 100644
--- a/client/src/api/configTemplates.ts
+++ b/client/src/api/configTemplates.ts
@@ -1,4 +1,6 @@
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema";
+
+export type CreateInstancePayload = components["schemas"]["CreateInstancePayload"];
 
 export type Instance =
     | components["schemas"]["UserFileSourceModel"]
@@ -10,13 +12,18 @@ export type TemplateVariable =
     | components["schemas"]["TemplateVariablePathComponent"]
     | components["schemas"]["TemplateVariableBoolean"];
 export type TemplateSecret = components["schemas"]["TemplateSecret"];
-export type VariableValueType = (string | boolean | number) | undefined;
-export type VariableData = { [key: string]: VariableValueType };
-export type SecretData = { [key: string]: string };
+export type VariableData = CreateInstancePayload["variables"];
+export type VariableValueType = VariableData[keyof VariableData];
+export type SecretData = CreateInstancePayload["secrets"];
 
 export type PluginAspectStatus = components["schemas"]["PluginAspectStatus"];
 export type PluginStatus = components["schemas"]["PluginStatus"];
 
+export type UpgradeInstancePayload = components["schemas"]["UpgradeInstancePayload"];
+export type TestUpgradeInstancePayload = components["schemas"]["TestUpgradeInstancePayload"];
+export type UpdateInstancePayload = components["schemas"]["UpdateInstancePayload"];
+export type TestUpdateInstancePayload = components["schemas"]["TestUpdateInstancePayload"];
+
 export interface TemplateSummary {
     description: string | null;
     hidden?: boolean;
diff --git a/client/src/api/datasetCollections.ts b/client/src/api/datasetCollections.ts
index cc45c5811cf7a7b7d852fc2f9b1b1dbe00ef8527..f659ec4982c41a46fa3d33889071dda519a28096 100644
--- a/client/src/api/datasetCollections.ts
+++ b/client/src/api/datasetCollections.ts
@@ -1,16 +1,20 @@
-import { CollectionEntry, DCESummary, HDCADetailed, HDCASummary, isHDCA } from "@/api";
-import { fetcher } from "@/api/schema";
+import { type CollectionEntry, type DCESummary, GalaxyApi, type HDCADetailed, type HDCASummary, isHDCA } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 const DEFAULT_LIMIT = 50;
 
-const getCollectionDetails = fetcher.path("/api/dataset_collections/{id}").method("get").create();
-
 /**
  * Fetches the details of a collection.
  * @param params.id The ID of the collection (HDCA) to fetch.
  */
 export async function fetchCollectionDetails(params: { id: string }): Promise<HDCADetailed> {
-    const { data } = await getCollectionDetails({ id: params.id });
+    const { data, error } = await GalaxyApi().GET("/api/dataset_collections/{id}", {
+        params: { path: params },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
     return data as HDCADetailed;
 }
 
@@ -19,15 +23,19 @@ export async function fetchCollectionDetails(params: { id: string }): Promise<HD
  * @param params.id The ID of the collection (HDCA) to fetch.
  */
 export async function fetchCollectionSummary(params: { id: string }): Promise<HDCASummary> {
-    const { data } = await getCollectionDetails({ id: params.id, view: "collection" });
+    const { data, error } = await GalaxyApi().GET("/api/dataset_collections/{id}", {
+        params: {
+            path: params,
+            query: { view: "collection" },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
     return data as HDCASummary;
 }
 
-const getCollectionContents = fetcher
-    .path("/api/dataset_collections/{hdca_id}/contents/{parent_id}")
-    .method("get")
-    .create();
-
 export async function fetchCollectionElements(params: {
     /** The ID of the top level HDCA that associates this collection with the History it belongs to. */
     hdcaId: string;
@@ -38,13 +46,16 @@ export async function fetchCollectionElements(params: {
     /** The maximum number of elements to fetch. */
     limit?: number;
 }): Promise<DCESummary[]> {
-    const { data } = await getCollectionContents({
-        instance_type: "history",
-        hdca_id: params.hdcaId,
-        parent_id: params.collectionId,
-        offset: params.offset,
-        limit: params.limit,
+    const { data, error } = await GalaxyApi().GET("/api/dataset_collections/{hdca_id}/contents/{parent_id}", {
+        params: {
+            path: { hdca_id: params.hdcaId, parent_id: params.collectionId },
+            query: { instance_type: "history", offset: params.offset, limit: params.limit },
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
     return data;
 }
 
@@ -65,14 +76,3 @@ export async function fetchElementsFromCollection(params: {
         limit: params.limit ?? DEFAULT_LIMIT,
     });
 }
-
-export const fetchCollectionAttributes = fetcher
-    .path("/api/dataset_collections/{id}/attributes")
-    .method("get")
-    .create();
-
-const postCopyCollection = fetcher.path("/api/dataset_collections/{id}/copy").method("post").create();
-export async function copyCollection(id: string, dbkey: string): Promise<Record<string, never>> {
-    const { data } = await postCopyCollection({ id, dbkey });
-    return data;
-}
diff --git a/client/src/api/datasets.ts b/client/src/api/datasets.ts
index c6096ea18f651392649e53840100114a52069bc9..6b8f0606537c0aaf1d2abd778ac027a41f350e28 100644
--- a/client/src/api/datasets.ts
+++ b/client/src/api/datasets.ts
@@ -1,86 +1,80 @@
 import axios from "axios";
-import type { FetchArgType } from "openapi-typescript-fetch";
 
-import { HDADetailed } from "@/api";
-import { components, fetcher } from "@/api/schema";
+import { type components, GalaxyApi, type GalaxyApiPaths, type HDADetailed } from "@/api";
 import { withPrefix } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
 
-export const datasetsFetcher = fetcher.path("/api/datasets").method("get").create();
-
-type GetDatasetsApiOptions = FetchArgType<typeof datasetsFetcher>;
-type GetDatasetsQuery = Pick<GetDatasetsApiOptions, "limit" | "offset">;
-// custom interface for how we use getDatasets
-interface GetDatasetsOptions extends GetDatasetsQuery {
-    sortBy?: string;
-    sortDesc?: boolean;
-    query?: string;
-}
+export async function fetchDatasetDetails(params: { id: string }): Promise<HDADetailed> {
+    const { data, error } = await GalaxyApi().GET("/api/datasets/{dataset_id}", {
+        params: {
+            path: {
+                dataset_id: params.id,
+            },
+            query: { view: "detailed" },
+        },
+    });
 
-/** Datasets request helper **/
-export async function getDatasets(options: GetDatasetsOptions = {}) {
-    const params: GetDatasetsApiOptions = {};
-    if (options.sortBy) {
-        const sortPrefix = options.sortDesc ? "-dsc" : "-asc";
-        params.order = `${options.sortBy}${sortPrefix}`;
-    }
-    if (options.limit) {
-        params.limit = options.limit;
-    }
-    if (options.offset) {
-        params.offset = options.offset;
+    if (error) {
+        rethrowSimple(error);
     }
-    if (options.query) {
-        params.q = ["name-contains"];
-        params.qv = [options.query];
-    }
-    const { data } = await datasetsFetcher(params);
-    return data;
-}
-
-export const fetchDataset = fetcher.path("/api/datasets/{dataset_id}").method("get").create();
-
-export const fetchDatasetStorage = fetcher.path("/api/datasets/{dataset_id}/storage").method("get").create();
-
-export async function fetchDatasetDetails(params: { id: string }): Promise<HDADetailed> {
-    const { data } = await fetchDataset({ dataset_id: params.id, view: "detailed" });
-    // We know that the server will return a DatasetDetails object because of the view parameter
-    // but the type system doesn't, so we have to cast it.
-    return data as unknown as HDADetailed;
+    return data as HDADetailed;
 }
 
-const updateDataset = fetcher.path("/api/datasets/{dataset_id}").method("put").create();
-
 export async function undeleteDataset(datasetId: string) {
-    const { data } = await updateDataset({
-        dataset_id: datasetId,
-        type: "dataset",
-        deleted: false,
+    const { data, error } = await GalaxyApi().PUT("/api/datasets/{dataset_id}", {
+        params: {
+            path: { dataset_id: datasetId },
+        },
+        body: {
+            deleted: false,
+        },
     });
+    if (error) {
+        rethrowSimple(error);
+    }
     return data;
 }
 
-const deleteDataset = fetcher.path("/api/datasets/{dataset_id}").method("delete").create();
-
 export async function purgeDataset(datasetId: string) {
-    const { data } = await deleteDataset({ dataset_id: datasetId, purge: true });
+    const { data, error } = await GalaxyApi().DELETE("/api/datasets/{dataset_id}", {
+        params: {
+            path: { dataset_id: datasetId },
+            query: { purge: true },
+        },
+    });
+    if (error) {
+        rethrowSimple(error);
+    }
     return data;
 }
 
-const datasetCopy = fetcher.path("/api/histories/{history_id}/contents/{type}s").method("post").create();
-type HistoryContentsArgs = FetchArgType<typeof datasetCopy>;
+type CopyDatasetParamsType = GalaxyApiPaths["/api/histories/{history_id}/contents/{type}s"]["post"]["parameters"];
+type CopyDatasetBodyType = components["schemas"]["CreateHistoryContentPayload"];
+
 export async function copyDataset(
-    datasetId: HistoryContentsArgs["content"],
-    historyId: HistoryContentsArgs["history_id"],
-    type: HistoryContentsArgs["type"] = "dataset",
-    source: HistoryContentsArgs["source"] = "hda"
+    datasetId: CopyDatasetBodyType["content"],
+    historyId: CopyDatasetParamsType["path"]["history_id"],
+    type: CopyDatasetParamsType["path"]["type"] = "dataset",
+    source: CopyDatasetBodyType["source"] = "hda"
 ) {
-    const response = await datasetCopy({
-        history_id: historyId,
-        type,
-        source: source,
-        content: datasetId,
+    const { data, error } = await GalaxyApi().POST("/api/histories/{history_id}/contents/{type}s", {
+        params: {
+            path: { history_id: historyId, type },
+        },
+        body: {
+            source,
+            content: datasetId,
+            // TODO: Investigate. These should be optional, but the API requires explicit null values?
+            type,
+            copy_elements: null,
+            hide_source_items: null,
+            instance_type: null,
+        },
     });
-    return response.data;
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
 }
 
 export function getCompositeDatasetLink(historyDatasetId: string, path: string) {
@@ -88,10 +82,12 @@ export function getCompositeDatasetLink(historyDatasetId: string, path: string)
 }
 
 export type DatasetExtraFiles = components["schemas"]["DatasetExtraFiles"];
-export const fetchDatasetExtraFiles = fetcher.path("/api/datasets/{dataset_id}/extra_files").method("get").create();
 
 export async function fetchDatasetAttributes(datasetId: string) {
     const { data } = await axios.get(withPrefix(`/dataset/get_edit?dataset_id=${datasetId}`));
 
     return data;
 }
+
+export type HistoryContentType = components["schemas"]["HistoryContentType"];
+export type HistoryContentSource = components["schemas"]["HistoryContentSource"];
diff --git a/client/src/api/datatypes.ts b/client/src/api/datatypes.ts
index fde4da5b529be3e29c0aef26655962afc1f0f188..0b6d30a71c6057166f1288e8215316b40c5c554b 100644
--- a/client/src/api/datatypes.ts
+++ b/client/src/api/datatypes.ts
@@ -1,13 +1,3 @@
-import { fetcher } from "@/api/schema";
+import { type components } from "@/api";
 
-export const datatypesFetcher = fetcher.path("/api/datatypes").method("get").create();
-
-export const edamFormatsFetcher = fetcher.path("/api/datatypes/edam_formats/detailed").method("get").create();
-export const edamDataFetcher = fetcher.path("/api/datatypes/edam_data/detailed").method("get").create();
-
-const typesAndMappingsFetcher = fetcher.path("/api/datatypes/types_and_mapping").method("get").create();
-
-export async function fetchDatatypesAndMappings(upload_only = true) {
-    const { data } = await typesAndMappingsFetcher({ upload_only });
-    return data;
-}
+export type CompositeFileInfo = components["schemas"]["CompositeFileInfo"];
diff --git a/client/src/api/dbKeys.ts b/client/src/api/dbKeys.ts
index ec152513788392dcf224c5fa195b32b7f829050b..9becc5f4af5c60baaf4fde5e52e4495cbd8a938e 100644
--- a/client/src/api/dbKeys.ts
+++ b/client/src/api/dbKeys.ts
@@ -3,6 +3,13 @@
  * but now it is used to get the list of more generic "dbkeys".
  */
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
-export const dbKeysFetcher = fetcher.path("/api/genomes").method("get").create();
+export async function getDbKeys() {
+    const { data, error } = await GalaxyApi().GET("/api/genomes");
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
diff --git a/client/src/api/fileSources.ts b/client/src/api/fileSources.ts
index 68935db4573f0d600fe8aea7d4090f7c34440815..eb984b938e8f47778e90c87ce647e5b286393eec 100644
--- a/client/src/api/fileSources.ts
+++ b/client/src/api/fileSources.ts
@@ -4,3 +4,4 @@ export type FileSourceTemplateSummary = components["schemas"]["FileSourceTemplat
 export type FileSourceTemplateSummaries = FileSourceTemplateSummary[];
 
 export type UserFileSourceModel = components["schemas"]["UserFileSourceModel"];
+export type FileSourceTypes = UserFileSourceModel["type"];
diff --git a/client/src/api/forms.ts b/client/src/api/forms.ts
deleted file mode 100644
index 04f19169d5a143368abd66c2a079728e94cabebe..0000000000000000000000000000000000000000
--- a/client/src/api/forms.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-import { fetcher } from "@/api/schema";
-
-export const deleteForm = fetcher.path("/api/forms/{id}").method("delete").create();
-export const undeleteForm = fetcher.path("/api/forms/{id}/undelete").method("post").create();
diff --git a/client/src/api/groups.ts b/client/src/api/groups.ts
deleted file mode 100644
index e795ccfdbf476020f2bb6163f55267005dc537b8..0000000000000000000000000000000000000000
--- a/client/src/api/groups.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-import axios from "axios";
-
-import { components, fetcher } from "@/api/schema";
-
-type GroupModel = components["schemas"]["GroupModel"];
-export async function getAllGroups(): Promise<GroupModel[]> {
-    const { data } = await axios.get("/api/groups");
-    return data;
-}
-
-export const deleteGroup = fetcher.path("/api/groups/{group_id}").method("delete").create();
-export const purgeGroup = fetcher.path("/api/groups/{group_id}/purge").method("post").create();
-export const undeleteGroup = fetcher.path("/api/groups/{group_id}/undelete").method("post").create();
diff --git a/client/src/api/histories.archived.ts b/client/src/api/histories.archived.ts
index 518ab55a72a73c6df3481080170decf70940d590..e580a94207ffc7a2453a6b08d83d7d0b97236595 100644
--- a/client/src/api/histories.archived.ts
+++ b/client/src/api/histories.archived.ts
@@ -1,13 +1,13 @@
-import type { FetchArgType } from "openapi-typescript-fetch";
-
-import { type components, fetcher } from "@/api/schema";
+import { type components, GalaxyApi, type GalaxyApiPaths } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export type ArchivedHistorySummary = components["schemas"]["ArchivedHistorySummary"];
 export type ArchivedHistoryDetailed = components["schemas"]["ArchivedHistoryDetailed"];
-export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];
+export type AnyArchivedHistory = ArchivedHistorySummary | ArchivedHistoryDetailed;
 
-type GetArchivedHistoriesParams = FetchArgType<typeof getArchivedHistories>;
-type SerializationOptions = Pick<GetArchivedHistoriesParams, "view" | "keys">;
+type MaybeArchivedHistoriesQueryParams = GalaxyApiPaths["/api/histories/archived"]["get"]["parameters"]["query"];
+type ArchivedHistoriesQueryParams = Exclude<MaybeArchivedHistoriesQueryParams, undefined>;
+type SerializationOptions = Pick<ArchivedHistoriesQueryParams, "view" | "keys">;
 
 interface FilterOptions {
     query?: string;
@@ -26,97 +26,44 @@ interface SortingOptions {
 interface GetArchivedHistoriesOptions extends FilterOptions, PaginationOptions, SortingOptions, SerializationOptions {}
 
 interface ArchivedHistoriesResult {
-    histories: ArchivedHistorySummary[] | ArchivedHistoryDetailed[];
+    histories: AnyArchivedHistory[];
     totalMatches: number;
 }
 
 const DEFAULT_PAGE_SIZE = 10;
 
-const getArchivedHistories = fetcher.path("/api/histories/archived").method("get").create();
-
 /**
  * Get a list of archived histories.
  */
-export async function fetchArchivedHistories(
-    options: GetArchivedHistoriesOptions = {}
-): Promise<ArchivedHistoriesResult> {
+export async function fetchArchivedHistories(options: GetArchivedHistoriesOptions): Promise<ArchivedHistoriesResult> {
     const params = optionsToApiParams(options);
-    const { data, headers } = await getArchivedHistories(params);
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    const { response, data, error } = await GalaxyApi().GET("/api/histories/archived", {
+        params: {
+            query: params,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     if (params.view === "detailed") {
         return {
             histories: data as ArchivedHistoryDetailed[],
             totalMatches,
         };
     }
+
     return {
         histories: data as ArchivedHistorySummary[],
         totalMatches,
     };
 }
 
-const postArchiveHistory = fetcher.path("/api/histories/{history_id}/archive").method("post").create();
-
-/**
- * Archive a history.
- * @param historyId The history to archive
- * @param archiveExportId The optional archive export record to associate. This can be used to restore a snapshot copy of the history in the future.
- * @param purgeHistory Whether to purge the history after archiving. Can only be used in combination with an archive export record.
- * @returns The archived history summary.
- */
-export async function archiveHistory(
-    historyId: string,
-    archiveExportId?: string,
-    purgeHistory?: boolean
-): Promise<ArchivedHistorySummary> {
-    const { data } = await postArchiveHistory({
-        history_id: historyId,
-        archive_export_id: archiveExportId,
-        purge_history: purgeHistory,
-    });
-    return data as ArchivedHistorySummary;
-}
-
-const putUnarchiveHistory = fetcher
-    .path("/api/histories/{history_id}/archive/restore")
-    .method("put")
-    // @ts-ignore: workaround for optional query parameters in PUT. More info here https://github.com/ajaishankar/openapi-typescript-fetch/pull/55
-    .create({ force: undefined });
-
-/**
- * Unarchive/restore a history.
- * @param historyId The history to unarchive.
- * @param force Whether to force un-archiving for purged histories.
- * @returns The restored history summary.
- */
-export async function unarchiveHistory(historyId: string, force?: boolean): Promise<ArchivedHistorySummary> {
-    const { data } = await putUnarchiveHistory({ history_id: historyId, force });
-    return data as ArchivedHistorySummary;
-}
-
-const reimportHistoryFromStore = fetcher.path("/api/histories/from_store_async").method("post").create();
-
-/**
- * Reimport an archived history as a new copy from the associated export record.
- *
- * @param archivedHistory The archived history to reimport. It must have an associated export record.
- * @returns The async task result summary to track the reimport progress.
- */
-export async function reimportArchivedHistoryFromExportRecord(
-    archivedHistory: ArchivedHistorySummary
-): Promise<AsyncTaskResultSummary> {
-    if (!archivedHistory.export_record_data) {
-        throw new Error("The archived history does not have an associated export record.");
-    }
-    const { data } = await reimportHistoryFromStore({
-        model_store_format: archivedHistory.export_record_data.model_store_format,
-        store_content_uri: archivedHistory.export_record_data.target_uri,
-    });
-    return data as AsyncTaskResultSummary;
-}
-
-function optionsToApiParams(options: GetArchivedHistoriesOptions): GetArchivedHistoriesParams {
-    const params: GetArchivedHistoriesParams = {};
+function optionsToApiParams(options: GetArchivedHistoriesOptions): ArchivedHistoriesQueryParams {
+    const params: ArchivedHistoriesQueryParams = {};
     if (options.query) {
         params.q = ["name-contains"];
         params.qv = [options.query];
diff --git a/client/src/api/histories.export.ts b/client/src/api/histories.export.ts
index 8a8e11f6a8be445b4e5b9e15d618e399f3456ce8..19f54919b68340d6b931947510d8e3f0414edc81 100644
--- a/client/src/api/histories.export.ts
+++ b/client/src/api/histories.export.ts
@@ -1,17 +1,7 @@
-import type { components } from "@/api/schema";
-import { fetcher } from "@/api/schema";
-import {
-    type ExportRecord,
-    ExportRecordModel,
-    type ObjectExportTaskResponse,
-} from "@/components/Common/models/exportRecordModel";
+import { GalaxyApi, type ModelStoreFormat, type ObjectExportTaskResponse } from "@/api";
+import { type ExportRecord, ExportRecordModel } from "@/components/Common/models/exportRecordModel";
 import { DEFAULT_EXPORT_PARAMS } from "@/composables/shortTermStorage";
-
-type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
-
-const _getExportRecords = fetcher.path("/api/histories/{history_id}/exports").method("get").create();
-const _exportToFileSource = fetcher.path("/api/histories/{history_id}/write_store").method("post").create();
-const _importFromStoreAsync = fetcher.path("/api/histories/from_store_async").method("post").create();
+import { rethrowSimple } from "@/utils/simple-error";
 
 /**
  * A list of objects with the available export formats IDs and display names.
@@ -28,17 +18,20 @@ export const AVAILABLE_EXPORT_FORMATS: { id: ModelStoreFormat; name: string }[]
  * @returns a promise with a list of export records associated with the given history.
  */
 export async function fetchHistoryExportRecords(historyId: string) {
-    const response = await _getExportRecords(
-        {
-            history_id: historyId,
-        },
-        {
-            headers: {
-                Accept: "application/vnd.galaxy.task.export+json",
+    const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}/exports", {
+        params: {
+            path: { history_id: historyId },
+            header: {
+                accept: "application/vnd.galaxy.task.export+json",
             },
-        }
-    );
-    return response.data.map((item: unknown) => new ExportRecordModel(item as ObjectExportTaskResponse));
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    return data.map((item) => new ExportRecordModel(item as ObjectExportTaskResponse));
 }
 
 /**
@@ -47,7 +40,7 @@ export async function fetchHistoryExportRecords(historyId: string) {
  * @param exportDirectory the output directory in the file source
  * @param fileName the name of the output archive
  * @param exportParams additional parameters to configure the export
- * @returns A promise with the request response
+ * @returns A promise with the async task response that can be used to track the export progress.
  */
 export async function exportHistoryToFileSource(
     historyId: string,
@@ -57,24 +50,42 @@ export async function exportHistoryToFileSource(
 ) {
     const exportDirectoryUri = `${exportDirectory}/${fileName}.${exportParams.modelStoreFormat}`;
 
-    return _exportToFileSource({
-        history_id: historyId,
-        target_uri: exportDirectoryUri,
-        model_store_format: exportParams.modelStoreFormat as ModelStoreFormat,
-        include_files: exportParams.includeFiles,
-        include_deleted: exportParams.includeDeleted,
-        include_hidden: exportParams.includeHidden,
+    const { data, error } = await GalaxyApi().POST("/api/histories/{history_id}/write_store", {
+        params: {
+            path: { history_id: historyId },
+        },
+        body: {
+            target_uri: exportDirectoryUri,
+            model_store_format: exportParams.modelStoreFormat,
+            include_files: exportParams.includeFiles,
+            include_deleted: exportParams.includeDeleted,
+            include_hidden: exportParams.includeHidden,
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    return data;
 }
 
 /**
  * Imports a new history using the information stored in the given export record.
  * @param record The export record to be imported
- * @returns A promise with the request response
+ * @returns A promise with the async task response that can be used to track the import progress.
  */
 export async function reimportHistoryFromRecord(record: ExportRecord) {
-    return _importFromStoreAsync({
-        store_content_uri: record.importUri,
-        model_store_format: record.modelStoreFormat,
+    const { data, error } = await GalaxyApi().POST("/api/histories/from_store_async", {
+        body: {
+            store_content_uri: record.importUri,
+            model_store_format: record.modelStoreFormat,
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    return data;
 }
diff --git a/client/src/api/histories.ts b/client/src/api/histories.ts
index ef0aeaa5df0b9e58516545af191a672a569dd19d..ed10bb8efb1f03c76a39f7756ad5d87701d976f0 100644
--- a/client/src/api/histories.ts
+++ b/client/src/api/histories.ts
@@ -1,16 +1,3 @@
-import { fetcher } from "@/api/schema";
+import { type components } from "@/api";
 
-export const historiesFetcher = fetcher.path("/api/histories").method("get").create();
-export const archivedHistoriesFetcher = fetcher.path("/api/histories/archived").method("get").create();
-export const deleteHistory = fetcher.path("/api/histories/{history_id}").method("delete").create();
-export const deleteHistories = fetcher.path("/api/histories/batch/delete").method("put").create();
-export const undeleteHistory = fetcher.path("/api/histories/deleted/{history_id}/undelete").method("post").create();
-export const undeleteHistories = fetcher.path("/api/histories/batch/undelete").method("put").create();
-export const publishedHistoriesFetcher = fetcher.path("/api/histories/published").method("get").create();
-export const historyFetcher = fetcher.path("/api/histories/{history_id}").method("get").create();
-export const updateHistoryItemsInBulk = fetcher
-    .path("/api/histories/{history_id}/contents/bulk")
-    .method("put")
-    .create();
-export const sharing = fetcher.path("/api/histories/{history_id}/sharing").method("get").create();
-export const enableLink = fetcher.path("/api/histories/{history_id}/enable_link_access").method("put").create();
+export type HistoryContentsResult = components["schemas"]["HistoryContentsResult"];
diff --git a/client/src/api/index.test.ts b/client/src/api/index.test.ts
index 42b666b2f03fcad9d597ff2574d92e71a4f17a6c..6d82145560ef34ab0343c2053862f5a33368d5c9 100644
--- a/client/src/api/index.test.ts
+++ b/client/src/api/index.test.ts
@@ -1,10 +1,11 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
+
 import {
     type AnonymousUser,
     type AnyHistory,
     type HistorySummary,
     type HistorySummaryExtended,
     isRegisteredUser,
-    type User,
     userOwnsHistory,
 } from ".";
 
@@ -12,16 +13,12 @@ const REGISTERED_USER_ID = "fake-user-id";
 const ANOTHER_USER_ID = "another-fake-user-id";
 const ANONYMOUS_USER_ID = null;
 
-const REGISTERED_USER: User = {
-    id: REGISTERED_USER_ID,
-    email: "test@mail.test",
-    tags_used: [],
-    isAnonymous: false,
-    total_disk_usage: 0,
-};
+const REGISTERED_USER = getFakeRegisteredUser({ id: REGISTERED_USER_ID });
 
 const ANONYMOUS_USER: AnonymousUser = {
     isAnonymous: true,
+    total_disk_usage: 0,
+    nice_total_disk_usage: "0.0 bytes",
 };
 
 const SESSIONLESS_USER = null;
diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index d1dbc8854bbbe3162697805b71c34179a68568c0..b83042dd69964302d1c9e8d0e5140bdc8d327ad1 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -1,12 +1,22 @@
 /** Contains type alias and definitions related to Galaxy API models. */
 
-import { components } from "@/api/schema";
+import { GalaxyApi } from "@/api/client";
+import { type components, type GalaxyApiPaths } from "@/api/schema";
+
+export { type components, GalaxyApi, type GalaxyApiPaths };
 
 /**
  * Contains minimal information about a History.
  */
 export type HistorySummary = components["schemas"]["HistorySummary"];
 
+/**
+ * Represents the possible values for the `sort_by` parameter when querying histories.
+ * We can not extract this from the schema for an unknown reason.
+ * The desired solution would be: `GalaxyApiPaths["/api/histories"]["get"]["parameters"]["query"]["sort_by"]`.
+ */
+export type HistorySortByLiteral = "create_time" | "name" | "update_time" | "username" | undefined;
+
 /**
  * Contains minimal information about a History with additional content stats.
  * This is a subset of information that can be relatively frequently updated after
@@ -128,6 +138,14 @@ export interface DCECollection extends DCESummary {
     object: DCObject;
 }
 
+/**
+ * DatasetCollectionElement specific type for datasets.
+ */
+export interface DCEDataset extends DCESummary {
+    element_type: "hda";
+    object: HDAObject;
+}
+
 /**
  * Contains summary information about a HDCA (HistoryDatasetCollectionAssociation).
  *
@@ -148,6 +166,8 @@ export type HDCADetailed = components["schemas"]["HDCADetailed"];
  */
 export type DCObject = components["schemas"]["DCObject"];
 
+export type HDAObject = components["schemas"]["HDAObject"];
+
 export type DatasetCollectionAttributes = components["schemas"]["DatasetCollectionAttributesResult"];
 
 export type ConcreteObjectStoreModel = components["schemas"]["ConcreteObjectStoreModel"];
@@ -174,12 +194,16 @@ export type CollectionEntry = HDCASummary | SubCollection;
 /**
  * Returns true if the given entry is a top level HDCA and false for sub-collections.
  */
-export function isHDCA(entry?: CollectionEntry): entry is HDCASummary {
+export function isHDCA(entry?: HistoryItemSummary | CollectionEntry): entry is HDCASummary {
     return (
         entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset_collection"
     );
 }
 
+export function isDCE(item: object): item is DCESummary {
+    return item && "element_type" in item;
+}
+
 /**
  * Returns true if the given element of a collection is a DatasetCollection.
  */
@@ -187,6 +211,13 @@ export function isCollectionElement(element: DCESummary): element is DCECollecti
     return element.element_type === "dataset_collection";
 }
 
+/**
+ * Returns true if the given element of a collection is a Dataset.
+ */
+export function isDatasetElement(element: DCESummary): element is DCEDataset {
+    return element.element_type === "hda";
+}
+
 /**
  * Returns true if the given dataset entry is an instance of DatasetDetails.
  */
@@ -215,36 +246,31 @@ export function isHistoryItem(item: object): item is HistoryItemSummary {
     return item && "history_content_type" in item;
 }
 
-type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
+type RegisteredUserModel = components["schemas"]["DetailedUserModel"];
+type AnonymousUserModel = components["schemas"]["AnonUserModel"];
+type UserModel = RegisteredUserModel | AnonymousUserModel;
 
-/** Represents a registered user.**/
-export interface User extends QuotaUsageResponse {
-    id: string;
-    email: string;
-    tags_used: string[];
+export interface RegisteredUser extends RegisteredUserModel {
     isAnonymous: false;
-    is_admin?: boolean;
-    username?: string;
 }
 
-export interface AnonymousUser {
-    id?: string;
+export interface AnonymousUser extends AnonymousUserModel {
     isAnonymous: true;
-    is_admin?: false;
-    username?: string;
 }
 
-export type GenericUser = User | AnonymousUser;
-
 /** Represents any user, including anonymous users or session-less (null) users.**/
-export type AnyUser = GenericUser | null;
+export type AnyUser = RegisteredUser | AnonymousUser | null;
+
+export function isRegisteredUser(user: AnyUser | UserModel): user is RegisteredUser {
+    return user !== null && "email" in user;
+}
 
-export function isRegisteredUser(user: AnyUser): user is User {
-    return user !== null && !user?.isAnonymous;
+export function isAnonymousUser(user: AnyUser | UserModel): user is AnonymousUser {
+    return user !== null && !isRegisteredUser(user);
 }
 
-export function isAnonymousUser(user: AnyUser): user is AnonymousUser {
-    return user !== null && user.isAnonymous;
+export function isAdminUser(user: AnyUser | UserModel): user is RegisteredUser {
+    return isRegisteredUser(user) && user.is_admin;
 }
 
 export function userOwnsHistory(user: AnyUser, history: AnyHistory) {
@@ -274,3 +300,16 @@ export type DatasetTransform = {
     action: "to_posix_lines" | "spaces_to_tabs" | "datatype_groom";
     datatype_ext: "bam" | "qname_sorted.bam" | "qname_input_sorted.bam" | "isa-tab" | "isa-json";
 };
+
+/**
+ * Base type for all exceptions returned by the API.
+ */
+export type MessageException = components["schemas"]["MessageExceptionModel"];
+
+export type StoreExportPayload = components["schemas"]["StoreExportPayload"];
+export type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
+export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
+export type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
+export type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];
+
+export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];
diff --git a/client/src/api/invocations.ts b/client/src/api/invocations.ts
index 2196f9a9254ea82e348de87df93d4a75c7aaa2cf..935fa7463bff70862744a5e0d3aa7dc00bac66be 100644
--- a/client/src/api/invocations.ts
+++ b/client/src/api/invocations.ts
@@ -1,65 +1,14 @@
-import axios from "axios";
-
-import { getAppRoot } from "@/onload";
-
-import { ApiResponse, components, fetcher } from "./schema";
+import { type components } from "./schema";
 
 export type WorkflowInvocationElementView = components["schemas"]["WorkflowInvocationElementView"];
 export type WorkflowInvocationCollectionView = components["schemas"]["WorkflowInvocationCollectionView"];
 export type InvocationJobsSummary = components["schemas"]["InvocationJobsResponse"];
 export type InvocationStep = components["schemas"]["InvocationStep"];
+export type InvocationMessage = components["schemas"]["InvocationMessageResponseUnion"];
 
 export type StepJobSummary =
     | components["schemas"]["InvocationStepJobsResponseStepModel"]
     | components["schemas"]["InvocationStepJobsResponseJobModel"]
     | components["schemas"]["InvocationStepJobsResponseCollectionJobsModel"];
 
-export const invocationsFetcher = fetcher.path("/api/invocations").method("get").create();
-
-export const stepJobsSummaryFetcher = fetcher
-    .path("/api/invocations/{invocation_id}/step_jobs_summary")
-    .method("get")
-    .create();
-
-export type WorkflowInvocation = WorkflowInvocationElementView | WorkflowInvocationCollectionView;
-
-export interface WorkflowInvocationJobsSummary {
-    id: string;
-}
-
-export interface WorkflowInvocationStep {
-    id: string;
-}
-
-export async function invocationForJob(params: { jobId: string }): Promise<WorkflowInvocation | null> {
-    const { data } = await axios.get(`${getAppRoot()}api/invocations?job_id=${params.jobId}`);
-    if (data.length > 0) {
-        return data[0] as WorkflowInvocation;
-    } else {
-        return null;
-    }
-}
-
-// TODO: Replace these provisional functions with fetchers after https://github.com/galaxyproject/galaxy/pull/16707 is merged
-export async function fetchInvocationDetails(params: { id: string }): Promise<ApiResponse<WorkflowInvocation>> {
-    const { data } = await axios.get(`${getAppRoot()}api/invocations/${params.id}`);
-    return {
-        data,
-    } as ApiResponse<WorkflowInvocation>;
-}
-
-export async function fetchInvocationJobsSummary(params: {
-    id: string;
-}): Promise<ApiResponse<WorkflowInvocationJobsSummary>> {
-    const { data } = await axios.get(`${getAppRoot()}api/invocations/${params.id}/jobs_summary`);
-    return {
-        data,
-    } as ApiResponse<WorkflowInvocationJobsSummary>;
-}
-
-export async function fetchInvocationStep(params: { id: string }): Promise<ApiResponse<WorkflowInvocationStep>> {
-    const { data } = await axios.get(`${getAppRoot()}api/invocations/steps/${params.id}`);
-    return {
-        data,
-    } as ApiResponse<WorkflowInvocationStep>;
-}
+export type WorkflowInvocation = components["schemas"]["WorkflowInvocationResponse"];
diff --git a/client/src/api/jobs.ts b/client/src/api/jobs.ts
index 289a440e0fd9f7f823f8cb9bb230063b522716be..31e9801ddfdd12d127d632651be5ba55f625c891 100644
--- a/client/src/api/jobs.ts
+++ b/client/src/api/jobs.ts
@@ -1,21 +1,9 @@
-import { components, fetcher } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 export type JobDestinationParams = components["schemas"]["JobDestinationParams"];
-
-export const getJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
-
-export const jobLockStatus = fetcher.path("/api/job_lock").method("get").create();
-export const jobLockUpdate = fetcher.path("/api/job_lock").method("put").create();
-
-export const fetchJobDestinationParams = fetcher.path("/api/jobs/{job_id}/destination_params").method("get").create();
-
-export const jobsFetcher = fetcher.path("/api/jobs").method("get").create();
-
 export type ShowFullJobResponse = components["schemas"]["ShowFullJobResponse"];
+export type JobBaseModel = components["schemas"]["JobBaseModel"];
 export type JobDetails = components["schemas"]["ShowFullJobResponse"] | components["schemas"]["EncodedJobDetails"];
-export const fetchJobDetails = fetcher.path("/api/jobs/{job_id}").method("get").create();
-
 export type JobInputSummary = components["schemas"]["JobInputSummary"];
-export const fetchJobCommonProblems = fetcher.path("/api/jobs/{job_id}/common_problems").method("get").create();
-
-export const postJobErrorReport = fetcher.path("/api/jobs/{job_id}/error").method("post").create();
+export type JobDisplayParametersSummary = components["schemas"]["JobDisplayParametersSummary"];
+export type JobMetric = components["schemas"]["JobMetric"];
diff --git a/client/src/api/landings.ts b/client/src/api/landings.ts
new file mode 100644
index 0000000000000000000000000000000000000000..03bbfc01d84058bbaf1b2af6fe94f213d4959ddc
--- /dev/null
+++ b/client/src/api/landings.ts
@@ -0,0 +1,4 @@
+import { type components } from "@/api/schema";
+
+export type ClaimLandingPayload = components["schemas"]["ClaimLandingPayload"];
+export type WorkflowLandingRequest = components["schemas"]["WorkflowLandingRequest"];
diff --git a/client/src/api/notifications.broadcast.ts b/client/src/api/notifications.broadcast.ts
index cbea28ada102831e38401dde67e6ae3d80250ef0..170de0619443780ec5bdd086a9c5a845cbe81579 100644
--- a/client/src/api/notifications.broadcast.ts
+++ b/client/src/api/notifications.broadcast.ts
@@ -1,29 +1,43 @@
-import { type components, fetcher } from "@/api/schema";
+import { GalaxyApi, type GalaxyApiPaths } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
-type BroadcastNotificationResponse = components["schemas"]["BroadcastNotificationResponse"];
+// TODO: Move these functions to broadcastStore and refactor other calls to go through the store
 
-const broadcastFetcher = fetcher.path("/api/notifications/broadcast/{notification_id}").method("get").create();
-export async function fetchBroadcast(id: string): Promise<BroadcastNotificationResponse> {
-    const { data } = await broadcastFetcher({ notification_id: id });
+export async function fetchAllBroadcasts() {
+    const { data, error } = await GalaxyApi().GET("/api/notifications/broadcast");
+    if (error) {
+        rethrowSimple(error);
+    }
     return data;
 }
 
-const broadcastsFetcher = fetcher.path("/api/notifications/broadcast").method("get").create();
-export async function fetchAllBroadcasts(): Promise<BroadcastNotificationResponse[]> {
-    const { data } = await broadcastsFetcher({});
-    return data;
-}
+type CreateBroadcastNotificationRequestBody =
+    GalaxyApiPaths["/api/notifications/broadcast"]["post"]["requestBody"]["content"]["application/json"];
+export async function createBroadcast(broadcast: CreateBroadcastNotificationRequestBody) {
+    const { data, error } = await GalaxyApi().POST("/api/notifications/broadcast", {
+        body: broadcast,
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
 
-const postBroadcast = fetcher.path("/api/notifications/broadcast").method("post").create();
-type BroadcastNotificationCreateRequest = components["schemas"]["BroadcastNotificationCreateRequest"];
-export async function createBroadcast(broadcast: BroadcastNotificationCreateRequest) {
-    const { data } = await postBroadcast(broadcast);
     return data;
 }
 
-const putBroadcast = fetcher.path("/api/notifications/broadcast/{notification_id}").method("put").create();
-type NotificationBroadcastUpdateRequest = components["schemas"]["NotificationBroadcastUpdateRequest"];
-export async function updateBroadcast(id: string, broadcast: NotificationBroadcastUpdateRequest) {
-    const { data } = await putBroadcast({ notification_id: id, ...broadcast });
+type UpdateBroadcastNotificationRequestBody =
+    GalaxyApiPaths["/api/notifications/broadcast/{notification_id}"]["put"]["requestBody"]["content"]["application/json"];
+export async function updateBroadcast(id: string, broadcast: UpdateBroadcastNotificationRequestBody) {
+    const { data, error } = await GalaxyApi().PUT("/api/notifications/broadcast/{notification_id}", {
+        params: {
+            path: { notification_id: id },
+        },
+        body: broadcast,
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     return data;
 }
diff --git a/client/src/api/notifications.preferences.ts b/client/src/api/notifications.preferences.ts
deleted file mode 100644
index 8509d7cd269139e64d520ade8d8eda84075fccb1..0000000000000000000000000000000000000000
--- a/client/src/api/notifications.preferences.ts
+++ /dev/null
@@ -1,23 +0,0 @@
-import { type components, fetcher } from "@/api/schema";
-
-type UserNotificationPreferences = components["schemas"]["UserNotificationPreferences"];
-
-export interface UserNotificationPreferencesExtended extends UserNotificationPreferences {
-    supportedChannels: string[];
-}
-
-const getNotificationsPreferences = fetcher.path("/api/notifications/preferences").method("get").create();
-export async function getNotificationsPreferencesFromServer(): Promise<UserNotificationPreferencesExtended> {
-    const { data, headers } = await getNotificationsPreferences({});
-    return {
-        ...data,
-        supportedChannels: headers.get("supported-channels")?.split(",") ?? [],
-    };
-}
-
-type UpdateUserNotificationPreferencesRequest = components["schemas"]["UpdateUserNotificationPreferencesRequest"];
-const updateNotificationsPreferences = fetcher.path("/api/notifications/preferences").method("put").create();
-export async function updateNotificationsPreferencesOnServer(request: UpdateUserNotificationPreferencesRequest) {
-    const { data } = await updateNotificationsPreferences(request);
-    return data;
-}
diff --git a/client/src/api/notifications.ts b/client/src/api/notifications.ts
index b5724618e3a5648cdcc28d416ed259fa5cd39fe1..ea35af9e3582b72e5059a7e5308cf0c525f20006 100644
--- a/client/src/api/notifications.ts
+++ b/client/src/api/notifications.ts
@@ -1,6 +1,9 @@
-import { type components, fetcher } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 export type BaseUserNotification = components["schemas"]["UserNotificationResponse"];
+export type UserNotificationPreferences = components["schemas"]["UserNotificationPreferences"]["preferences"];
+export type NotificationChannel = keyof components["schemas"]["NotificationChannelSettings"];
+export type NotificationCategory = components["schemas"]["PersonalNotificationCategory"];
 
 export interface MessageNotification extends BaseUserNotification {
     category: "message";
@@ -12,61 +15,26 @@ export interface SharedItemNotification extends BaseUserNotification {
     content: components["schemas"]["NewSharedItemNotificationContent"];
 }
 
-export type UserNotification = MessageNotification | SharedItemNotification;
-
-export type NotificationChanges = components["schemas"]["UserNotificationUpdateRequest"];
-
-export type UserNotificationsBatchUpdateRequest = components["schemas"]["UserNotificationsBatchUpdateRequest"];
-
-export type NotificationVariants = components["schemas"]["NotificationVariant"];
-
-export type NewSharedItemNotificationContentItemType =
-    components["schemas"]["NewSharedItemNotificationContent"]["item_type"];
-
-type UserNotificationUpdateRequest = components["schemas"]["UserNotificationUpdateRequest"];
-
-export type NotificationCreateRequest = components["schemas"]["NotificationCreateRequest"];
-
-type NotificationResponse = components["schemas"]["NotificationResponse"];
+type NotificationCreateData = components["schemas"]["NotificationCreateData"];
 
-const getNotification = fetcher.path("/api/notifications/{notification_id}").method("get").create();
-
-export async function loadNotification(id: string): Promise<NotificationResponse> {
-    const { data } = await getNotification({ notification_id: id });
-    return data;
-}
-
-const postNotification = fetcher.path("/api/notifications").method("post").create();
-
-export async function sendNotification(notification: NotificationCreateRequest) {
-    const { data } = await postNotification(notification);
-    return data;
+export interface MessageNotificationCreateData extends NotificationCreateData {
+    category: "message";
+    content: components["schemas"]["MessageNotificationContent"];
 }
 
-const putNotification = fetcher.path("/api/notifications/{notification_id}").method("put").create();
+export type NotificationCreateRequest = components["schemas"]["NotificationCreateRequest"];
 
-export async function updateNotification(id: string, notification: UserNotificationUpdateRequest) {
-    const { data } = await putNotification({ notification_id: id, ...notification });
-    return data;
+export interface MessageNotificationCreateRequest extends NotificationCreateRequest {
+    notification: MessageNotificationCreateData;
 }
 
-const getNotifications = fetcher.path("/api/notifications").method("get").create();
-
-export async function loadNotificationsFromServer(): Promise<UserNotification[]> {
-    const { data } = await getNotifications({});
-    return data as UserNotification[];
-}
+export type UserNotification = MessageNotification | SharedItemNotification;
 
-const putBatchNotifications = fetcher.path("/api/notifications").method("put").create();
+export type NotificationChanges = components["schemas"]["UserNotificationUpdateRequest"];
 
-export async function updateBatchNotificationsOnServer(request: UserNotificationsBatchUpdateRequest) {
-    const { data } = await putBatchNotifications(request);
-    return data;
-}
+export type UserNotificationsBatchUpdateRequest = components["schemas"]["UserNotificationsBatchUpdateRequest"];
 
-const getNotificationStatus = fetcher.path("/api/notifications/status").method("get").create();
+export type NotificationVariants = components["schemas"]["NotificationVariant"];
 
-export async function loadNotificationsStatus(since: Date) {
-    const { data } = await getNotificationStatus({ since: since.toISOString().replace("Z", "") });
-    return data;
-}
+export type NewSharedItemNotificationContentItemType =
+    components["schemas"]["NewSharedItemNotificationContent"]["item_type"];
diff --git a/client/src/api/objectStores.templates.ts b/client/src/api/objectStores.templates.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0bc65dde204aa55693867290cc443ba485b6720a
--- /dev/null
+++ b/client/src/api/objectStores.templates.ts
@@ -0,0 +1,4 @@
+import type { components } from "@/api/schema";
+
+export type ObjectStoreTemplateSummary = components["schemas"]["ObjectStoreTemplateSummary"];
+export type ObjectStoreTemplateSummaries = ObjectStoreTemplateSummary[];
diff --git a/client/src/api/objectStores.ts b/client/src/api/objectStores.ts
index b6c1f6c59f7d1320ffc89370e4cc4bdeebde9cbe..376d75d8e54abffdf4a51f94c5055686987e2ea5 100644
--- a/client/src/api/objectStores.ts
+++ b/client/src/api/objectStores.ts
@@ -1,37 +1,57 @@
-import { fetcher } from "@/api/schema";
-import type { components } from "@/api/schema/schema";
+import { type components, GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export type UserConcreteObjectStore = components["schemas"]["UserConcreteObjectStoreModel"];
 
-export type ObjectStoreTemplateType = "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
-
-const getObjectStores = fetcher.path("/api/object_stores").method("get").create();
+export type ObjectStoreTemplateType = components["schemas"]["UserConcreteObjectStoreModel"]["type"];
 
 export async function getSelectableObjectStores() {
-    const { data } = await getObjectStores({ selectable: true });
+    const { data, error } = await GalaxyApi().GET("/api/object_stores", {
+        params: {
+            query: { selectable: true },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     return data;
 }
 
-const getObjectStore = fetcher.path("/api/object_stores/{object_store_id}").method("get").create();
-const getUserObjectStoreInstance = fetcher
-    .path("/api/object_store_instances/{user_object_store_id}")
-    .method("get")
-    .create();
-
 export async function getObjectStoreDetails(id: string) {
     if (id.startsWith("user_objects://")) {
         const userObjectStoreId = id.substring("user_objects://".length);
-        const { data } = await getUserObjectStoreInstance({ user_object_store_id: userObjectStoreId });
+
+        const { data, error } = await GalaxyApi().GET("/api/object_store_instances/{uuid}", {
+            params: { path: { uuid: userObjectStoreId } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
         return data;
     } else {
-        const { data } = await getObjectStore({ object_store_id: id });
+        const { data, error } = await GalaxyApi().GET("/api/object_stores/{object_store_id}", {
+            params: { path: { object_store_id: id } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
         return data;
     }
 }
 
-const updateObjectStoreFetcher = fetcher.path("/api/datasets/{dataset_id}/object_store_id").method("put").create();
-
 export async function updateObjectStore(datasetId: string, objectStoreId: string) {
-    const { data } = await updateObjectStoreFetcher({ dataset_id: datasetId, object_store_id: objectStoreId });
-    return data;
+    const { error } = await GalaxyApi().PUT("/api/datasets/{dataset_id}/object_store_id", {
+        params: { path: { dataset_id: datasetId } },
+        body: { object_store_id: objectStoreId },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
 }
diff --git a/client/src/api/pages.ts b/client/src/api/pages.ts
deleted file mode 100644
index 89e89d2e8940ef6440be591dc9cceb699320617c..0000000000000000000000000000000000000000
--- a/client/src/api/pages.ts
+++ /dev/null
@@ -1,9 +0,0 @@
-import { fetcher } from "@/api/schema";
-
-/** Page request helper **/
-const deletePageById = fetcher.path("/api/pages/{id}").method("delete").create();
-export async function deletePage(itemId: string): Promise<void> {
-    await deletePageById({
-        id: itemId,
-    });
-}
diff --git a/client/src/api/quotas.ts b/client/src/api/quotas.ts
deleted file mode 100644
index f164fcf80632a5751b190954f4fa95def21dd6c5..0000000000000000000000000000000000000000
--- a/client/src/api/quotas.ts
+++ /dev/null
@@ -1,5 +0,0 @@
-import { fetcher } from "@/api/schema";
-
-export const deleteQuota = fetcher.path("/api/quotas/{id}").method("delete").create();
-export const purgeQuota = fetcher.path("/api/quotas/{id}/purge").method("post").create();
-export const undeleteQuota = fetcher.path("/api/quotas/deleted/{id}/undelete").method("post").create();
diff --git a/client/src/api/remoteFiles.ts b/client/src/api/remoteFiles.ts
index ff149655c0375cb1c49cf8c8b1a35bcacceaf38e..5b014a75199f3d2f353c5737a6f00777b0a1b150 100644
--- a/client/src/api/remoteFiles.ts
+++ b/client/src/api/remoteFiles.ts
@@ -1,5 +1,5 @@
-import type { components } from "@/api/schema";
-import { fetcher } from "@/api/schema/fetcher";
+import { type components, GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 /** The browsing mode:
  * - `file` - allows to select files or directories contained in a source (default)
@@ -28,24 +28,30 @@ export interface FilterFileSourcesOptions {
     exclude?: FileSourcePluginKind[];
 }
 
-const remoteFilesPluginsFetcher = fetcher.path("/api/remote_files/plugins").method("get").create();
-
 /**
  * Get the list of available file sources from the server that can be browsed.
  * @param options The options to filter the file sources.
  * @returns The list of available (browsable) file sources from the server.
  */
 export async function fetchFileSources(options: FilterFileSourcesOptions = {}): Promise<BrowsableFilesSourcePlugin[]> {
-    const { data } = await remoteFilesPluginsFetcher({
-        browsable_only: true,
-        include_kind: options.include,
-        exclude_kind: options.exclude,
+    const { data, error } = await GalaxyApi().GET("/api/remote_files/plugins", {
+        params: {
+            query: {
+                browsable_only: true,
+                include_kind: options.include,
+                exclude_kind: options.exclude,
+            },
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    // Since we specified browsable_only in the query, we can safely cast the data to the expected type.
     return data as BrowsableFilesSourcePlugin[];
 }
 
-export const remoteFilesFetcher = fetcher.path("/api/remote_files").method("get").create();
-
 export interface BrowseRemoteFilesResult {
     entries: RemoteEntry[];
     totalMatches: number;
@@ -71,28 +77,28 @@ export async function browseRemoteFiles(
     query?: string,
     sortBy?: string
 ): Promise<BrowseRemoteFilesResult> {
-    const { data, headers } = await remoteFilesFetcher({
-        target: uri,
-        recursive: isRecursive,
-        writeable,
-        limit,
-        offset,
-        query,
-        sort_by: sortBy,
+    const { response, data, error } = await GalaxyApi().GET("/api/remote_files", {
+        params: {
+            query: {
+                format: "uri",
+                target: uri,
+                recursive: isRecursive,
+                writeable,
+                limit,
+                offset,
+                query,
+                sort_by: sortBy,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
-    return { entries: data as RemoteEntry[], totalMatches };
-}
 
-const createEntry = fetcher.path("/api/remote_files").method("post").create();
+    if (error) {
+        rethrowSimple(error);
+    }
 
-/**
- * Create a new entry (directory/record) on the given file source URI.
- * @param uri The file source URI to create the entry in.
- * @param name The name of the entry to create.
- * @returns The created entry details.
- */
-export async function createRemoteEntry(uri: string, name: string): Promise<CreatedEntry> {
-    const { data } = await createEntry({ target: uri, name: name });
-    return data;
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
+
+    // Since we specified format=uri in the query, we can safely cast the data to the expected type.
+    const entries = data as RemoteEntry[];
+    return { entries, totalMatches };
 }
diff --git a/client/src/api/roles.ts b/client/src/api/roles.ts
deleted file mode 100644
index 4667ca53a2b5bf1a5b491ed0710569bc0fb290a5..0000000000000000000000000000000000000000
--- a/client/src/api/roles.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-import { fetcher } from "@/api/schema";
-
-const getRoles = fetcher.path("/api/roles").method("get").create();
-export async function getAllRoles() {
-    const { data } = await getRoles({});
-    return data;
-}
-
-export const deleteRole = fetcher.path("/api/roles/{id}").method("delete").create();
-export const purgeRole = fetcher.path("/api/roles/{id}/purge").method("post").create();
-export const undeleteRole = fetcher.path("/api/roles/{id}/undelete").method("post").create();
diff --git a/client/src/api/schema/__mocks__/fetcher.ts b/client/src/api/schema/__mocks__/fetcher.ts
deleted file mode 100644
index 56c8a56ed3ef6b3e0e6f4661c5a26caa967650a4..0000000000000000000000000000000000000000
--- a/client/src/api/schema/__mocks__/fetcher.ts
+++ /dev/null
@@ -1,95 +0,0 @@
-import type { paths } from "@/api/schema";
-
-jest.mock("@/api/schema", () => ({
-    fetcher: mockFetcher,
-}));
-
-jest.mock("@/api/schema/fetcher", () => ({
-    fetcher: mockFetcher,
-}));
-
-type Path = keyof paths;
-type Method = "get" | "post" | "put" | "delete";
-
-interface MockValue {
-    path: Path | RegExp;
-    method: Method;
-    value: any;
-}
-
-const mockValues: MockValue[] = [];
-
-function getMockReturn(path: Path, method: Method, args: any[]) {
-    for (let i = mockValues.length - 1; i >= 0; i--) {
-        const matchPath = mockValues[i]!.path;
-        const matchMethod = mockValues[i]!.method;
-        const value = mockValues[i]!.value;
-
-        const getValue = () => {
-            if (typeof value === "function") {
-                return value(...args);
-            } else {
-                return value;
-            }
-        };
-
-        if (matchMethod !== method) {
-            continue;
-        }
-
-        if (typeof matchPath === "string") {
-            if (matchPath === path) {
-                return getValue();
-            }
-        } else {
-            if (path.match(matchPath)) {
-                return getValue();
-            }
-        }
-    }
-
-    // if no mock has been setup, never resolve API request
-    return new Promise(() => {});
-}
-
-function setMockReturn(path: Path | RegExp, method: Method, value: any) {
-    mockValues.push({
-        path,
-        method,
-        value,
-    });
-}
-
-/**
- * Mock implementation for the fetcher found in `@/api/schema/fetcher`
- *
- * You need to call `jest.mock("@/api/schema")` and/or `jest.mock("@/api/schema/fetcher")`
- * (depending on what module the file you are testing imported)
- * in order for this mock to take effect.
- *
- * To specify return values for the mock, use
- * `mockFetcher.path(...).method(...).mock(desiredReturnValue)`
- * This will cause any use of fetcher on the same path and method to receive the contents of `desiredReturnValue`.
- *
- * If this return value is a function, it will be ran and passed the parameters passed to the fetcher, and it's result returned.
- *
- * `path(...)` can take a `RegExp`, in which case any path matching the Regular Expression with a fitting method will be used.
- *
- * If multiple mock paths match a path, the latest defined will be used.
- *
- * `clearMocks()` can be used to reset all mock return values set with `.mock()`
- */
-export const mockFetcher = {
-    path: (path: Path | RegExp) => ({
-        method: (method: Method) => ({
-            // prettier-ignore
-            create: () => async (...args: any[]) => getMockReturn(path as Path, method, args),
-            mock: (mockReturn: any) => setMockReturn(path, method, mockReturn),
-        }),
-    }),
-    clearMocks: () => {
-        mockValues.length = 0;
-    },
-};
-
-export const fetcher = mockFetcher;
diff --git a/client/src/api/schema/__mocks__/index.ts b/client/src/api/schema/__mocks__/index.ts
deleted file mode 100644
index d498943ddefa7361641f6312cfa5554840581b9f..0000000000000000000000000000000000000000
--- a/client/src/api/schema/__mocks__/index.ts
+++ /dev/null
@@ -1 +0,0 @@
-export { fetcher, mockFetcher } from "./fetcher";
diff --git a/client/src/api/schema/fetcher.ts b/client/src/api/schema/fetcher.ts
deleted file mode 100644
index bb60436dd4f3913c9f672569f531a2730430f36d..0000000000000000000000000000000000000000
--- a/client/src/api/schema/fetcher.ts
+++ /dev/null
@@ -1,21 +0,0 @@
-import type { ApiResponse, Middleware } from "openapi-typescript-fetch";
-import { Fetcher } from "openapi-typescript-fetch";
-
-import { getAppRoot } from "@/onload/loadConfig";
-import { rethrowSimple } from "@/utils/simple-error";
-
-import type { paths } from "./schema";
-
-export { ApiResponse };
-
-const rethrowSimpleMiddleware: Middleware = async (url, init, next) => {
-    try {
-        const response = await next(url, init);
-        return response;
-    } catch (e) {
-        rethrowSimple(e);
-    }
-};
-
-export const fetcher = Fetcher.for<paths>();
-fetcher.configure({ baseUrl: getAppRoot(undefined, true), use: [rethrowSimpleMiddleware] });
diff --git a/client/src/api/schema/index.ts b/client/src/api/schema/index.ts
index d931cad37dd6d077bf85bbe158cc9b5e49624840..7adf8ad41bb7c901461d7cb61182b2e6becd34ab 100644
--- a/client/src/api/schema/index.ts
+++ b/client/src/api/schema/index.ts
@@ -1,2 +1,3 @@
-export { type ApiResponse, fetcher } from "./fetcher";
-export type { components, operations, paths } from "./schema";
+import { type components, type paths as GalaxyApiPaths } from "./schema";
+
+export { type components, type GalaxyApiPaths };
diff --git a/client/src/api/schema/mockFetcher.test.ts b/client/src/api/schema/mockFetcher.test.ts
deleted file mode 100644
index e4eddd5a3f581e9b8c979fbff11d7888e58ae8a9..0000000000000000000000000000000000000000
--- a/client/src/api/schema/mockFetcher.test.ts
+++ /dev/null
@@ -1,42 +0,0 @@
-import { fetcher } from "@/api/schema";
-
-import { mockFetcher } from "./__mocks__/fetcher";
-
-jest.mock("@/api/schema");
-
-mockFetcher.path("/api/configuration").method("get").mock("CONFIGURATION");
-
-mockFetcher
-    .path(/^.*\/histories\/.*$/)
-    .method("get")
-    .mock("HISTORY");
-
-mockFetcher
-    .path(/\{history_id\}/)
-    .method("put")
-    .mock((param: { history_id: string }) => `param:${param.history_id}`);
-
-describe("mockFetcher", () => {
-    it("mocks fetcher", async () => {
-        {
-            const fetch = fetcher.path("/api/configuration").method("get").create();
-            const value = await fetch({});
-
-            expect(value).toEqual("CONFIGURATION");
-        }
-
-        {
-            const fetch = fetcher.path("/api/histories/deleted").method("get").create();
-            const value = await fetch({});
-
-            expect(value).toEqual("HISTORY");
-        }
-
-        {
-            const fetchHistory = fetcher.path("/api/histories/{history_id}/exports").method("put").create();
-            const value = await fetchHistory({ history_id: "test" });
-
-            expect(value).toEqual("param:test");
-        }
-    });
-});
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index ce8d68a8db65f27a1949927febb400b8a6e59769..5c1ee689893038e62053503d0296e30e581c86fc 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -5,131 +5,383 @@
 
 export interface paths {
     "/api/authenticate/baseauth": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns returns an API key for authenticated user based on BaseAuth headers. */
         get: operations["get_api_key_api_authenticate_baseauth_get"];
-    };
-    "/api/cloud/storage/get": {
-        /**
-         * Gets given objects from a given cloud-based bucket to a Galaxy history.
-         * @deprecated
-         */
-        post: operations["get_api_cloud_storage_get_post"];
-    };
-    "/api/cloud/storage/send": {
-        /**
-         * Sends given dataset(s) in a given history to a given cloud-based bucket.
-         * @deprecated
-         */
-        post: operations["send_api_cloud_storage_send_post"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/chat": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        /**
+         * Query
+         * @description We're off to ask the wizard
+         */
+        post: operations["query_api_chat_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/chat/{job_id}/feedback": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        /**
+         * Feedback
+         * @description Provide feedback on the chatbot response.
+         */
+        put: operations["feedback_api_chat__job_id__feedback_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return an object containing exposable configuration settings
          * @description Return an object containing exposable configuration settings.
          *
-         * A more complete list is returned if the user is an admin.
-         * Pass in `view` and a comma-seperated list of keys to control which
-         * configuration settings are returned.
+         *     A more complete list is returned if the user is an admin.
+         *     Pass in `view` and a comma-seperated list of keys to control which
+         *     configuration settings are returned.
          */
         get: operations["index_api_configuration_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration/decode/{encoded_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Decode a given id
          * @description Decode a given id.
          */
         get: operations["decode_id_api_configuration_decode__encoded_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration/dynamic_tool_confs": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return dynamic tool configuration files
          * @description Return dynamic tool configuration files.
          */
         get: operations["dynamic_tool_confs_api_configuration_dynamic_tool_confs_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration/encode/{decoded_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Encode a given id
          * @description Decode a given id.
          */
         get: operations["encode_id_api_configuration_encode__decoded_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration/tool_lineages": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return tool lineages for tools that have them
          * @description Return tool lineages for tools that have them.
          */
         get: operations["tool_lineages_api_configuration_tool_lineages_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/configuration/toolbox": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Reload the Galaxy toolbox (but not individual tools)
          * @description Reload the Galaxy toolbox (but not individual tools).
          */
         put: operations["reload_toolbox_api_configuration_toolbox_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collection_element/{dce_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Content */
         get: operations["content_api_dataset_collection_element__dce_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Create a new dataset collection instance. */
         post: operations["create_api_dataset_collections_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{hdca_id}/contents/{parent_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns direct child contents of indicated dataset collection parent ID. */
         get: operations["contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns detailed information about the given collection. */
         get: operations["show_api_dataset_collections__id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}/attributes": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns `dbkey`/`extension` attributes for all the collection elements. */
         get: operations["attributes_api_dataset_collections__id__attributes_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}/copy": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Copy the given collection datasets to a new collection using a new `dbkey` attribute. */
         post: operations["copy_api_dataset_collections__id__copy_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}/download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Download the content of a dataset collection as a `zip` archive.
          * @description Download the content of a history dataset collection as a `zip` archive
-         * while maintaining approximate collection structure.
+         *     while maintaining approximate collection structure.
          */
         get: operations["dataset_collections__download"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}/prepare_download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Prepare an short term storage object that the collection will be downloaded to.
          * @description The history dataset collection will be written as a `zip` archive to the
-         * returned short term storage object. Progress tracking this file's creation
-         * can be tracked with the short_term_storage API.
+         *     returned short term storage object. Progress tracking this file's creation
+         *     can be tracked with the short_term_storage API.
          */
         post: operations["prepare_collection_download_api_dataset_collections__id__prepare_download_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/dataset_collections/{id}/suitable_converters": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns a list of applicable converters for all datatypes in the given collection. */
         get: operations["suitable_converters_api_dataset_collections__id__suitable_converters_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Search datasets or collections using a query system. */
         get: operations["index_api_datasets_get"];
+        put?: never;
+        post?: never;
         /**
          * Deletes or purges a batch of datasets.
          * @description Deletes or purges a batch of datasets.
-         * **Warning**: only the ownership of the datasets (and upload state for HDAs) is checked,
-         * no other checks or restrictions are made.
+         *     **Warning**: only the ownership of the datasets (and upload state for HDAs) is checked,
+         *     no other checks or restrictions are made.
          */
         delete: operations["delete_batch_api_datasets_delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays information about and/or content of a dataset.
-         * @description **Note**: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters
-         * and return different kinds of responses, the documentation here will be limited.
-         * To get more information please check the source code.
+         * @description **Note**: Due to the multipurpose nature of this endpoint, which can receive a wide variety of parameters
+         *     and return different kinds of responses, the documentation here will be limited.
+         *     To get more information please check the source code.
          */
         get: operations["show_api_datasets__dataset_id__get"];
         /**
@@ -137,229 +389,672 @@ export interface paths {
          * @description Updates the values for the history content item with the given ``ID``.
          */
         put: operations["datasets__update_dataset"];
+        post?: never;
         /**
          * Delete the history dataset content with the given ``ID``.
          * @description Delete the history content with the given ``ID`` and path specified type.
          *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
+         *     **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
         delete: operations["datasets__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/content/{content_type}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Retrieve information about the content of a dataset. */
         get: operations["get_structured_content_api_datasets__dataset_id__content__content_type__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/converted": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return a a map with all the existing converted datasets associated with this instance.
          * @description Return a map of `<converted extension> : <converted id>` containing all the *existing* converted datasets.
          */
         get: operations["converted_api_datasets__dataset_id__converted_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/converted/{ext}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return information about datasets made by converting this dataset to a new format.
          * @description Return information about datasets made by converting this dataset to a new format.
          *
-         * If there is no existing converted dataset for the format in `ext`, one will be created.
+         *     If there is no existing converted dataset for the format in `ext`, one will be created.
          *
-         * **Note**: `view` and `keys` are also available to control the serialization of the dataset.
+         *     **Note**: `view` and `keys` are also available to control the serialization of the dataset.
          */
         get: operations["converted_ext_api_datasets__dataset_id__converted__ext__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/extra_files": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get the list of extra files/directories associated with a dataset. */
         get: operations["extra_files_api_datasets__dataset_id__extra_files_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/get_content_as_text": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns dataset content as Text. */
         get: operations["get_content_as_text_api_datasets__dataset_id__get_content_as_text_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/hash": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Compute dataset hash for dataset and update model */
         put: operations["compute_hash_api_datasets__dataset_id__hash_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/inheritance_chain": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** For internal use, this endpoint may change without warning. */
         get: operations["show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/metrics": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return job metrics for specified job.
          * @deprecated
          */
         get: operations["get_metrics_api_datasets__dataset_id__metrics_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/object_store_id": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Update an object store ID for a dataset you own. */
         put: operations["datasets__update_object_store_id"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/parameters_display": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Resolve parameters as a list for nested display.
          * @deprecated
          * @description Resolve parameters as a list for nested display.
-         * This API endpoint is unstable and tied heavily to Galaxy's JS client code,
-         * this endpoint will change frequently.
+         *     This API endpoint is unstable and tied heavily to Galaxy's JS client code,
+         *     this endpoint will change frequently.
          */
         get: operations["resolve_parameters_display_api_datasets__dataset_id__parameters_display_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/permissions": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set permissions of the given history dataset to the given role ids.
          * @description Set permissions of the given history dataset to the given role ids.
          */
         put: operations["update_permissions_api_datasets__dataset_id__permissions_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{dataset_id}/storage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Display user-facing storage details related to the objectstore a dataset resides in. */
         get: operations["show_storage_api_datasets__dataset_id__storage_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{history_content_id}/display": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays (preview) or downloads dataset content.
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         get: operations["display_api_datasets__history_content_id__display_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
         /**
          * Check if dataset content can be previewed or downloaded.
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         head: operations["display_api_datasets__history_content_id__display_head"];
+        patch?: never;
+        trace?: never;
     };
     "/api/datasets/{history_content_id}/metadata_file": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns the metadata file associated with this history item. */
         get: operations["datasets__get_metadata_file"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
         /** Check if metadata file can be downloaded. */
         head: operations["get_metadata_file_datasets_api_datasets__history_content_id__metadata_file_head"];
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Lists all available data types
          * @description Gets the list of all available data types.
          */
         get: operations["index_api_datatypes_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/converters": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the list of all installed converters
          * @description Gets the list of all installed converters.
          */
         get: operations["converters_api_datatypes_converters_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/edam_data": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a dictionary/map of datatypes and EDAM data
          * @description Gets a map of datatypes and their corresponding EDAM data.
          */
         get: operations["edam_data_api_datatypes_edam_data_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/edam_data/detailed": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a dictionary of datatypes and EDAM data details
          * @description Gets a map of datatypes and their corresponding EDAM data.
-         * EDAM data contains the EDAM iri, label, and definition.
+         *     EDAM data contains the EDAM iri, label, and definition.
          */
         get: operations["edam_data_detailed_api_datatypes_edam_data_detailed_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/edam_formats": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a dictionary/map of datatypes and EDAM formats
          * @description Gets a map of datatypes and their corresponding EDAM formats.
          */
         get: operations["edam_formats_api_datatypes_edam_formats_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/edam_formats/detailed": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a dictionary of datatypes and EDAM format details
          * @description Gets a map of datatypes and their corresponding EDAM formats.
-         * EDAM formats contain the EDAM iri, label, and definition.
+         *     EDAM formats contain the EDAM iri, label, and definition.
          */
         get: operations["edam_formats_detailed_api_datatypes_edam_formats_detailed_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/mapping": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns mappings for data types and their implementing classes
          * @description Gets mappings for data types.
          */
         get: operations["mapping_api_datatypes_mapping_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/sniffers": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the list of all installed sniffers
          * @description Gets the list of all installed data type sniffers.
          */
         get: operations["sniffers_api_datatypes_sniffers_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/datatypes/types_and_mapping": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns all the data types extensions and their mappings
          * @description Combines the datatype information from (/api/datatypes) and the
-         * mapping information from (/api/datatypes/mapping) into a single
-         * response.
+         *     mapping information from (/api/datatypes/mapping) into a single
+         *     response.
          */
         get: operations["types_and_mapping_api_datatypes_types_and_mapping_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/display_applications": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the list of display applications.
          * @description Returns the list of display applications.
          */
         get: operations["display_applications_index_api_display_applications_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/display_applications/reload": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Reloads the list of display applications.
          * @description Reloads the list of display applications.
          */
         post: operations["display_applications_reload_api_display_applications_reload_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/drs_download/{object_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Download */
         get: operations["download_api_drs_download__object_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/file_source_instances": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a list of persisted file source instances defined by the requesting user. */
         get: operations["file_sources__instances_index"];
+        put?: never;
         /** Create a user-bound file source. */
         post: operations["file_sources__create_instance"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/file_source_instances/test": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Test payload for creating user-bound file source. */
         post: operations["file_sources__test_new_instance_configuration"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
-    "/api/file_source_instances/{user_file_source_id}": {
+    "/api/file_source_instances/{uuid}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a persisted user file source instance. */
         get: operations["file_sources__instances_get"];
         /** Update or upgrade user file source instance. */
         put: operations["file_sources__instances_update"];
+        post?: never;
         /** Purge user file source instance. */
         delete: operations["file_sources__instances_purge"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/file_source_instances/{uuid}/test": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Test a file source instance and return status. */
+        get: operations["file_sources__instances_test_instance"];
+        put?: never;
+        /** Test updating or upgrading user file source instance. */
+        post: operations["file_sources__test_instances_update"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/file_source_templates": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a list of file source templates available to build user defined file sources from */
         get: operations["file_sources__templates_index"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/file_source_templates/{template_id}/{template_version}/oauth2": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Template Oauth2 */
+        get: operations["file_sources__template_oauth2"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/folders/{folder_id}/contents": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a list of a folder's contents (files and sub-folders) with additional metadata about the folder.
          * @description Returns a list of a folder's contents (files and sub-folders).
          *
-         * Additional metadata for the folder is provided in the response as a separate object containing data
-         * for breadcrumb path building, permissions and other folder's details.
+         *     Additional metadata for the folder is provided in the response as a separate object containing data
+         *     for breadcrumb path building, permissions and other folder's details.
          *
-         * *Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).
+         *     *Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).
          *
-         * **Security note**:
-         * - Accessing a library folder or sub-folder requires only access to the parent library.
-         * - Deleted folders can only be accessed by admins or users with `MODIFY` permission.
-         * - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.
+         *     **Security note**:
+         *     - Accessing a library folder or sub-folder requires only access to the parent library.
+         *     - Deleted folders can only be accessed by admins or users with `MODIFY` permission.
+         *     - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.
          */
         get: operations["index_api_folders__folder_id__contents_get"];
+        put?: never;
         /** Creates a new library file from an existing HDA/HDCA. */
         post: operations["add_history_datasets_to_library_api_folders__folder_id__contents_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/folders/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays information about a particular library folder.
          * @description Returns detailed information about the library folder with the given ID.
@@ -380,94 +1075,279 @@ export interface paths {
          * @description Marks the specified library folder as deleted (or undeleted).
          */
         delete: operations["delete_api_folders__id__delete"];
+        options?: never;
+        head?: never;
         /**
          * Update
          * @description Updates the information of an existing library folder.
          */
         patch: operations["update_api_folders__id__patch"];
+        trace?: never;
     };
     "/api/folders/{id}/permissions": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Gets the current or available permissions of a particular library folder.
          * @description Gets the current or available permissions of a particular library.
-         * The results can be paginated and additionally filtered by a query.
+         *     The results can be paginated and additionally filtered by a query.
          */
         get: operations["get_permissions_api_folders__id__permissions_get"];
+        put?: never;
         /**
          * Sets the permissions to manage a library folder.
          * @description Sets the permissions to manage a library folder.
          */
         post: operations["set_permissions_api_folders__id__permissions_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/forms/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        post?: never;
         /** Delete */
         delete: operations["delete_api_forms__id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/forms/{id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Undelete */
         post: operations["undelete_api_forms__id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/ftp_files": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays remote files available to the user. Please use /api/remote_files instead.
          * @deprecated
          * @description Lists all remote files available to the user from different sources.
          *
-         * The total count of files and directories is returned in the 'total_matches' header.
+         *     The total count of files and directories is returned in the 'total_matches' header.
          */
         get: operations["index_api_ftp_files_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/genomes": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return a list of installed genomes */
         get: operations["index_api_genomes_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/genomes/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return information about build <id> */
         get: operations["show_api_genomes__id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/genomes/{id}/indexes": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return all available indexes for a genome id for provided type */
         get: operations["indexes_api_genomes__id__indexes_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/genomes/{id}/sequences": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return raw sequence data */
         get: operations["sequences_api_genomes__id__sequences_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays a collection (list) of groups. */
         get: operations["index_api_groups_get"];
+        put?: never;
         /** Creates a new group. */
         post: operations["create_api_groups_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays information about a group. */
         get: operations["show_group_api_groups__group_id__get"];
         /** Modifies a group. */
         put: operations["update_api_groups__group_id__put"];
+        post?: never;
         /** Delete */
         delete: operations["delete_api_groups__group_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/purge": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Purge */
         post: operations["purge_api_groups__group_id__purge_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/roles": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays a collection (list) of groups. */
         get: operations["group_roles_api_groups__group_id__roles_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/roles/{role_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays information about a group role. */
         get: operations["group_role_api_groups__group_id__roles__role_id__get"];
         /** Adds a role to a group */
         put: operations["update_api_groups__group_id__roles__role_id__put"];
+        post?: never;
         /** Removes a role from a group */
         delete: operations["delete_api_groups__group_id__roles__role_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Undelete */
         post: operations["undelete_api_groups__group_id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/user/{user_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays information about a group user.
          * @description Displays information about a group user.
@@ -476,25 +1356,49 @@ export interface paths {
         /**
          * Adds a user to a group
          * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Adds a user to a group
+         *     Adds a user to a group
          */
         put: operations["update_api_groups__group_id__user__user_id__put"];
+        post?: never;
         /**
          * Removes a user from a group
          * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Removes a user from a group
+         *     Removes a user from a group
          */
         delete: operations["delete_api_groups__group_id__user__user_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays a collection (list) of groups.
          * @description GET /api/groups/{encoded_group_id}/users
-         * Displays a collection (list) of groups.
+         *     Displays a collection (list) of groups.
          */
         get: operations["group_users_api_groups__group_id__users_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/groups/{group_id}/users/{user_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays information about a group user.
          * @description Displays information about a group user.
@@ -503,145 +1407,374 @@ export interface paths {
         /**
          * Adds a user to a group
          * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Adds a user to a group
+         *     Adds a user to a group
          */
         put: operations["update_api_groups__group_id__users__user_id__put"];
+        post?: never;
         /**
          * Removes a user from a group
          * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Removes a user from a group
+         *     Removes a user from a group
          */
         delete: operations["delete_api_groups__group_id__users__user_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/help/forum/search": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Search the Galaxy Help forum.
          * @description Search the Galaxy Help forum using the Discourse API.
          *
-         * **Note**: This endpoint is for **INTERNAL USE ONLY** and is not part of the public Galaxy API.
+         *     **Note**: This endpoint is for **INTERNAL USE ONLY** and is not part of the public Galaxy API.
          */
         get: operations["search_forum_api_help_forum_search_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns histories available to the current user. */
         get: operations["index_api_histories_get"];
+        put?: never;
         /**
          * Creates a new history.
          * @description The new history can also be copied form a existing history or imported from an archive or URL.
          */
         post: operations["create_api_histories_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/archived": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get a list of all archived histories for the current user.
          * @description Get a list of all archived histories for the current user.
          *
-         * Archived histories are histories are not part of the active histories of the user but they can be accessed using this endpoint.
+         *     Archived histories are histories are not part of the active histories of the user but they can be accessed using this endpoint.
          */
         get: operations["get_archived_histories_api_histories_archived_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/batch/delete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Marks several histories with the given IDs as deleted. */
         put: operations["batch_delete_api_histories_batch_delete_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/batch/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Marks several histories with the given IDs as undeleted. */
         put: operations["batch_undelete_api_histories_batch_undelete_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/count": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns number of histories for the current user. */
         get: operations["count_api_histories_count_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/deleted": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns deleted histories for the current user. */
         get: operations["index_deleted_api_histories_deleted_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/deleted/{history_id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Restores a deleted history with the given ID (that hasn't been purged). */
         post: operations["undelete_api_histories_deleted__history_id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/from_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Create histories from a model store. */
         post: operations["create_from_store_api_histories_from_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/from_store_async": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Launch a task to create histories from a model store. */
         post: operations["create_from_store_async_api_histories_from_store_async_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/most_recently_used": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns the most recently used history of the user. */
         get: operations["show_recent_api_histories_most_recently_used_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/published": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return all histories that are published. */
         get: operations["published_api_histories_published_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/shared_with_me": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return all histories that are shared with the current user. */
         get: operations["shared_with_me_api_histories_shared_with_me_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns the history with the given ID. */
         get: operations["history_api_histories__history_id__get"];
         /** Updates the values for the history with the given ID. */
         put: operations["update_api_histories__history_id__put"];
+        post?: never;
         /** Marks the history with the given ID as deleted. */
         delete: operations["delete_api_histories__history_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/archive": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Archive a history.
          * @description Marks the given history as 'archived' and returns the history.
          *
-         * Archiving a history will remove it from the list of active histories of the user but it will still be
-         * accessible via the `/api/histories/{id}` or the `/api/histories/archived` endpoints.
+         *     Archiving a history will remove it from the list of active histories of the user but it will still be
+         *     accessible via the `/api/histories/{id}` or the `/api/histories/archived` endpoints.
          *
-         * Associating an export record:
+         *     Associating an export record:
          *
-         * - Optionally, an export record (containing information about a recent snapshot of the history) can be associated with the
-         * archived history by providing an `archive_export_id` in the payload. The export record must belong to the history and
-         * must be in the ready state.
-         * - When associating an export record, the history can be purged after it has been archived using the `purge_history` flag.
+         *     - Optionally, an export record (containing information about a recent snapshot of the history) can be associated with the
+         *     archived history by providing an `archive_export_id` in the payload. The export record must belong to the history and
+         *     must be in the ready state.
+         *     - When associating an export record, the history can be purged after it has been archived using the `purge_history` flag.
          *
-         * If the history is already archived, this endpoint will return a 409 Conflict error, indicating that the history is already archived.
-         * If the history was not purged after it was archived, you can restore it using the `/api/histories/{id}/archive/restore` endpoint.
+         *     If the history is already archived, this endpoint will return a 409 Conflict error, indicating that the history is already archived.
+         *     If the history was not purged after it was archived, you can restore it using the `/api/histories/{id}/archive/restore` endpoint.
          */
         post: operations["archive_history_api_histories__history_id__archive_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/archive/restore": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Restore an archived history.
          * @description Restores an archived history and returns it.
          *
-         * Restoring an archived history will add it back to the list of active histories of the user (unless it was purged).
+         *     Restoring an archived history will add it back to the list of active histories of the user (unless it was purged).
          *
-         * **Warning**: Please note that histories that are associated with an archive export might be purged after export, so un-archiving them
-         * will not restore the datasets that were in the history before it was archived. You will need to import back the archive export
-         * record to restore the history and its datasets as a new copy. See `/api/histories/from_store_async` for more information.
+         *     **Warning**: Please note that histories that are associated with an archive export might be purged after export, so un-archiving them
+         *     will not restore the datasets that were in the history before it was archived. You will need to import back the archive export
+         *     record to restore the history and its datasets as a new copy. See `/api/histories/from_store_async` for more information.
          */
         put: operations["restore_archived_history_api_histories__history_id__archive_restore_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/citations": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return all the citations for the tools used to produce the datasets in the history. */
         get: operations["citations_api_histories__history_id__citations_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the contents of the given history.
          * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
          *
-         * - The contents can be filtered and queried using the appropriate parameters.
-         * - The amount of information returned for each item can be customized.
+         *     - The contents can be filtered and queried using the appropriate parameters.
+         *     - The amount of information returned for each item can be customized.
          *
-         * **Note**: Anonymous users are allowed to get their current history contents.
+         *     **Note**: Anonymous users are allowed to get their current history contents.
          */
         get: operations["history_contents__index"];
         /**
          * Batch update specific properties of a set items contained in the given History.
          * @description Batch update specific properties of a set items contained in the given History.
          *
-         * If you provide an invalid/unknown property key the request will not fail, but no changes
-         * will be made to the items.
+         *     If you provide an invalid/unknown property key the request will not fail, but no changes
+         *     will be made to the items.
          */
         put: operations["update_batch_api_histories__history_id__contents_put"];
         /**
@@ -650,78 +1783,218 @@ export interface paths {
          * @description Create a new `HDA` or `HDCA` in the given History.
          */
         post: operations["history_contents__create"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/archive": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Build and return a compressed archive of the selected history contents.
          * @description Build and return a compressed archive of the selected history contents.
          *
-         * **Note**: this is a volatile endpoint and settings and behavior may change.
+         *     **Note**: this is a volatile endpoint and settings and behavior may change.
          */
         get: operations["history_contents__archive"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/archive/{filename}.{format}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Build and return a compressed archive of the selected history contents.
          * @description Build and return a compressed archive of the selected history contents.
          *
-         * **Note**: this is a volatile endpoint and settings and behavior may change.
+         *     **Note**: this is a volatile endpoint and settings and behavior may change.
          */
         get: operations["history_contents__archive_named"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/bulk": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Executes an operation on a set of items contained in the given History.
          * @description Executes an operation on a set of items contained in the given History.
          *
-         * The items to be processed can be explicitly set or determined by a dynamic query.
+         *     The items to be processed can be explicitly set or determined by a dynamic query.
          */
         put: operations["bulk_operation_api_histories__history_id__contents_bulk_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/dataset_collections/{id}/download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Download the content of a dataset collection as a `zip` archive.
          * @description Download the content of a history dataset collection as a `zip` archive
-         * while maintaining approximate collection structure.
+         *     while maintaining approximate collection structure.
          */
         get: operations["history_contents__download_collection"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/datasets/{id}/materialize": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Materialize a deferred dataset into real, usable dataset. */
         post: operations["materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{dataset_id}/permissions": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set permissions of the given history dataset to the given role ids.
          * @description Set permissions of the given history dataset to the given role ids.
          */
         put: operations["update_permissions_api_histories__history_id__contents__dataset_id__permissions_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{history_content_id}/display": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays (preview) or downloads dataset content.
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         get: operations["history_contents_display_api_histories__history_id__contents__history_content_id__display_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
         /**
          * Check if dataset content can be previewed or downloaded.
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         head: operations["history_contents_display_api_histories__history_id__contents__history_content_id__display_head"];
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{history_content_id}/extra_files": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get the list of extra files/directories associated with a dataset. */
         get: operations["extra_files_history_api_histories__history_id__contents__history_content_id__extra_files_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{history_content_id}/metadata_file": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns the metadata file associated with this history item. */
         get: operations["history_contents__get_metadata_file"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{history_content_id}/tags": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tags based on history_content_id */
         get: operations["index_api_histories__history_id__contents__history_content_id__tags_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{history_content_id}/tags/{tag_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tag based on history_content_id */
         get: operations["show_api_histories__history_id__contents__history_content_id__tags__tag_name__get"];
         /** Update tag based on history_content_id */
@@ -730,14 +2003,24 @@ export interface paths {
         post: operations["create_api_histories__history_id__contents__history_content_id__tags__tag_name__post"];
         /** Delete tag based on history_content_id */
         delete: operations["delete_api_histories__history_id__contents__history_content_id__tags__tag_name__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
          * @deprecated
          * @description Return detailed information about an `HDA` or `HDCA` within a history.
          *
-         * **Note**: Anonymous users are allowed to get their current history contents.
+         *     **Note**: Anonymous users are allowed to get their current history contents.
          */
         get: operations["history_contents__show_legacy"];
         /**
@@ -746,44 +2029,80 @@ export interface paths {
          * @description Updates the values for the history content item with the given ``ID``.
          */
         put: operations["history_contents__update_legacy"];
+        post?: never;
         /**
          * Delete the history dataset with the given ``ID``.
          * @description Delete the history content with the given ``ID`` and query specified type (defaults to dataset).
          *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
+         *     **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
         delete: operations["history_contents__delete_legacy"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{id}/validate": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Validates the metadata associated with a dataset within a History.
          * @description Validates the metadata associated with a dataset within a History.
          */
         put: operations["validate_api_histories__history_id__contents__id__validate_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{type}s": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the contents of the given history filtered by type.
          * @description Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
          *
-         * - The contents can be filtered and queried using the appropriate parameters.
-         * - The amount of information returned for each item can be customized.
+         *     - The contents can be filtered and queried using the appropriate parameters.
+         *     - The amount of information returned for each item can be customized.
          *
-         * **Note**: Anonymous users are allowed to get their current history contents.
+         *     **Note**: Anonymous users are allowed to get their current history contents.
          */
         get: operations["history_contents__index_typed"];
+        put?: never;
         /**
          * Create a new `HDA` or `HDCA` in the given History.
          * @description Create a new `HDA` or `HDCA` in the given History.
          */
         post: operations["history_contents__create_typed"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{type}s/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return detailed information about a specific HDA or HDCA with the given `ID` within a history.
          * @description Return detailed information about an `HDA` or `HDCA` within a history.
          *
-         * **Note**: Anonymous users are allowed to get their current history contents.
+         *     **Note**: Anonymous users are allowed to get their current history contents.
          */
         get: operations["history_contents__show"];
         /**
@@ -791,68 +2110,170 @@ export interface paths {
          * @description Updates the values for the history content item with the given ``ID``.
          */
         put: operations["history_contents__update_typed"];
+        post?: never;
         /**
          * Delete the history content with the given ``ID`` and path specified type.
          * @description Delete the history content with the given ``ID`` and path specified type.
          *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
+         *     **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
         delete: operations["history_contents__delete_typed"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{type}s/{id}/jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return detailed information about an `HDA` or `HDCAs` jobs.
          * @description Return detailed information about an `HDA` or `HDCAs` jobs.
          *
-         * **Warning**: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
+         *     **Warning**: We allow anyone to fetch job state information about any object they
+         *     can guess an encoded ID for - it isn't considered protected data. This keeps
+         *     polling IDs as part of state calculation for large histories and collections as
+         *     efficient as possible.
          */
         get: operations["show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{type}s/{id}/prepare_store_download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Prepare a dataset or dataset collection for export-style download. */
         post: operations["prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents/{type}s/{id}/write_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Prepare a dataset or dataset collection for export-style download and write to supplied URI. */
         post: operations["write_store_api_histories__history_id__contents__type_s__id__write_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/contents_from_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Create contents from store.
          * @description Create history contents from model store.
-         * Input can be a tarfile created with build_objects script distributed
-         * with galaxy-data, from an exported history with files stripped out,
-         * or hand-crafted JSON dictionary.
+         *     Input can be a tarfile created with build_objects script distributed
+         *     with galaxy-data, from an exported history with files stripped out,
+         *     or hand-crafted JSON dictionary.
          */
         post: operations["create_from_store_api_histories__history_id__contents_from_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/custom_builds_metadata": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns meta data for custom builds. */
         get: operations["get_custom_builds_metadata_api_histories__history_id__custom_builds_metadata_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/disable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item inaccessible by a URL link.
          * @description Makes this item inaccessible by a URL link and return the current sharing status.
          */
         put: operations["disable_link_access_api_histories__history_id__disable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/enable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item accessible by a URL link.
          * @description Makes this item accessible by a URL link and return the current sharing status.
          */
         put: operations["enable_link_access_api_histories__history_id__enable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/exports": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get previous history exports.
          * @description By default the legacy job-based history exports (jeha) are returned.
          *
-         * Change the `accept` content type header to return the new task-based history exports.
+         *     Change the `accept` content type header to return the new task-based history exports.
          */
         get: operations["get_history_exports_api_histories__history_id__exports_get"];
         /**
@@ -860,85 +2281,214 @@ export interface paths {
          * @deprecated
          * @description This will start a job to create a history export archive.
          *
-         * Calling this endpoint multiple times will return the 202 status code until the archive
-         * has been completely generated and is ready to download. When ready, it will return
-         * the 200 status code along with the download link information.
+         *     Calling this endpoint multiple times will return the 202 status code until the archive
+         *     has been completely generated and is ready to download. When ready, it will return
+         *     the 200 status code along with the download link information.
          *
-         * If the history will be exported to a `directory_uri`, instead of returning the download
-         * link information, the Job ID will be returned so it can be queried to determine when
-         * the file has been written.
+         *     If the history will be exported to a `directory_uri`, instead of returning the download
+         *     link information, the Job ID will be returned so it can be queried to determine when
+         *     the file has been written.
          *
-         * **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
-         * `/api/histories/{id}/write_store` instead.
+         *     **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
+         *     `/api/histories/{id}/write_store` instead.
          */
         put: operations["archive_export_api_histories__history_id__exports_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/exports/{jeha_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * If ready and available, return raw contents of exported history as a downloadable archive.
          * @deprecated
          * @description See ``PUT /api/histories/{id}/exports`` to initiate the creation
-         * of the history export - when ready, that route will return 200 status
-         * code (instead of 202) and this route can be used to download the archive.
+         *     of the history export - when ready, that route will return 200 status
+         *     code (instead of 202) and this route can be used to download the archive.
          *
-         * **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
-         * `/api/histories/{id}/write_store` instead.
+         *     **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
+         *     `/api/histories/{id}/write_store` instead.
          */
         get: operations["history_archive_download_api_histories__history_id__exports__jeha_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.
          * @description Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.
          *
-         * **Warning**: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
+         *     **Warning**: We allow anyone to fetch job state information about any object they
+         *     can guess an encoded ID for - it isn't considered protected data. This keeps
+         *     polling IDs as part of state calculation for large histories and collections as
+         *     efficient as possible.
          */
         get: operations["index_jobs_summary_api_histories__history_id__jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/materialize": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Materialize a deferred library or HDA dataset into real, usable dataset in specified history. */
         post: operations["materialize_to_history_api_histories__history_id__materialize_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/prepare_store_download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Return a short term storage token to monitor download of the history. */
         post: operations["prepare_store_download_api_histories__history_id__prepare_store_download_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/publish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item public and accessible by a URL link.
          * @description Makes this item publicly available by a URL link and return the current sharing status.
          */
         put: operations["publish_api_histories__history_id__publish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/share_with_users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Share this item with specific users.
          * @description Shares this item with specific users and return the current sharing status.
          */
         put: operations["share_with_users_api_histories__history_id__share_with_users_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/sharing": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get the current sharing status of the given item.
          * @description Return the sharing status of the item.
          */
         get: operations["sharing_api_histories__history_id__sharing_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/slug": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set a new slug for this shared item.
          * @description Sets a new slug to access this item by URL. The new slug must be unique.
          */
         put: operations["set_slug_api_histories__history_id__slug_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/tags": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tags based on history_id */
         get: operations["index_api_histories__history_id__tags_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/tags/{tag_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tag based on history_id */
         get: operations["show_api_histories__history_id__tags__tag_name__get"];
         /** Update tag based on history_id */
@@ -947,72 +2497,258 @@ export interface paths {
         post: operations["create_api_histories__history_id__tags__tag_name__post"];
         /** Delete tag based on history_id */
         delete: operations["delete_api_histories__history_id__tags__tag_name__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/unpublish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Removes this item from the published list.
          * @description Removes this item from the published list and return the current sharing status.
          */
         put: operations["unpublish_api_histories__history_id__unpublish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/histories/{history_id}/write_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Prepare history for export-style download and write to supplied URI. */
         post: operations["write_store_api_histories__history_id__write_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get the list of a user's workflow invocations. */
         get: operations["index_invocations_api_invocations_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/from_store": {
-        /**
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        /**
          * Create Invocations From Store
          * @description Create invocation(s) from a supplied model store.
          */
         post: operations["create_invocations_from_store_api_invocations_from_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/steps/{step_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show details of workflow invocation step. */
         get: operations["step_api_invocations_steps__step_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get detailed description of a workflow invocation. */
         get: operations["show_invocation_api_invocations__invocation_id__get"];
+        put?: never;
+        post?: never;
         /** Cancel the specified workflow invocation. */
         delete: operations["cancel_invocation_api_invocations__invocation_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated across all current jobs of the workflow invocation.
          * @description Warning: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
+         *     can guess an encoded ID for - it isn't considered protected data. This keeps
+         *     polling IDs as part of state calculation for large histories and collections as
+         *     efficient as possible.
          */
         get: operations["invocation_jobs_summary_api_invocations__invocation_id__jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/invocations/{invocation_id}/metrics": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get Invocation Metrics */
+        get: operations["get_invocation_metrics_api_invocations__invocation_id__metrics_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/prepare_store_download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Prepare a workflow invocation export-style download. */
         post: operations["prepare_store_download_api_invocations__invocation_id__prepare_store_download_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/report": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get JSON summarizing invocation for reporting. */
         get: operations["show_invocation_report_api_invocations__invocation_id__report_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/report.pdf": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get PDF summarizing invocation for reporting. */
         get: operations["show_invocation_report_pdf_api_invocations__invocation_id__report_pdf_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/invocations/{invocation_id}/request": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get a description modeling an API request to invoke this workflow - this is recreated and will be more specific in some ways than the initial creation request. */
+        get: operations["invocation_as_request_api_invocations__invocation_id__request_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/step_jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated per step of the workflow invocation.
          * @description Warning: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
+         *     can guess an encoded ID for - it isn't considered protected data. This keeps
+         *     polling IDs as part of state calculation for large histories and collections as
+         *     efficient as possible.
          */
         get: operations["invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/steps/{step_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Show details of workflow invocation step.
          * @description An alias for `GET /api/invocations/steps/{step_id}`. `invocation_id` is ignored.
@@ -1020,12 +2756,37 @@ export interface paths {
         get: operations["invocation_step_api_invocations__invocation_id__steps__step_id__get"];
         /** Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc. */
         put: operations["update_invocation_step_api_invocations__invocation_id__steps__step_id__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/invocations/{invocation_id}/write_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Prepare a workflow invocation export-style download and write to supplied URI. */
         post: operations["write_store_api_invocations__invocation_id__write_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/job_lock": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Job Lock Status
          * @description Get job lock status.
@@ -1036,152 +2797,515 @@ export interface paths {
          * @description Set job lock status.
          */
         put: operations["update_job_lock_api_job_lock_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Index */
         get: operations["index_api_jobs_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/search": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Return jobs for current user
          * @description This method is designed to scan the list of previously run jobs and find records of jobs that had
-         * the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply
-         * recycle the old results.
+         *     the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply
+         *     recycle the old results.
          */
         post: operations["search_jobs_api_jobs_search_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return dictionary containing description of job data. */
         get: operations["show_job_api_jobs__job_id__get"];
+        put?: never;
+        post?: never;
         /** Cancels specified job */
         delete: operations["cancel_job_api_jobs__job_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/common_problems": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Check inputs and job for common potential problems to aid in error reporting */
         get: operations["check_common_problems_api_jobs__job_id__common_problems_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/jobs/{job_id}/console_output": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**
+         * Returns STDOUT and STDERR from the tool running in a specific job.
+         * @description Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
+         *     of where to start reading stdout/stderr. The length parameters control how much
+         *     stdout/stderr is read.
+         */
+        get: operations["get_console_output_api_jobs__job_id__console_output_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/destination_params": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return destination parameters for specified job. */
         get: operations["destination_params_job_api_jobs__job_id__destination_params_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/error": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Submits a bug report via the API. */
         post: operations["report_error_api_jobs__job_id__error_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/jobs/{job_id}/finish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        /** Finished a job regardless of execution status (ie early job finish) */
+        put: operations["finish_job_api_jobs__job_id__finish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/inputs": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns input datasets created by a job. */
         get: operations["get_inputs_api_jobs__job_id__inputs_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/metrics": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return job metrics for specified job. */
         get: operations["get_metrics_api_jobs__job_id__metrics_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/oidc-tokens": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get a fresh OIDC token
          * @description Allows remote job running mechanisms to get a fresh OIDC token that can be used on remote side to authorize user. It is not meant to represent part of Galaxy's stable, user facing API
          */
         get: operations["get_token_api_jobs__job_id__oidc_tokens_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/outputs": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns output datasets created by a job. */
         get: operations["get_outputs_api_jobs__job_id__outputs_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/parameters_display": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Resolve parameters as a list for nested display.
          * @description Resolve parameters as a list for nested display.
-         * This API endpoint is unstable and tied heavily to Galaxy's JS client code,
-         * this endpoint will change frequently.
+         *     This API endpoint is unstable and tied heavily to Galaxy's JS client code,
+         *     this endpoint will change frequently.
          */
         get: operations["resolve_parameters_display_api_jobs__job_id__parameters_display_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/jobs/{job_id}/resume": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Resumes a paused job. */
         put: operations["resume_paused_job_api_jobs__job_id__resume_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/libraries": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a list of summary data for all libraries.
          * @description Returns a list of summary data for all libraries.
          */
         get: operations["index_api_libraries_get"];
+        put?: never;
         /**
          * Creates a new library and returns its summary information.
          * @description Creates a new library and returns its summary information. Currently, only admin users can create libraries.
          */
         post: operations["create_api_libraries_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/libraries/deleted": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns a list of summary data for all libraries marked as deleted.
          * @description Returns a list of summary data for all libraries marked as deleted.
          */
         get: operations["index_deleted_api_libraries_deleted_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/libraries/from_store": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Create libraries from a model store. */
         post: operations["create_from_store_api_libraries_from_store_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/libraries/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns summary information about a particular library.
          * @description Returns summary information about a particular library.
          */
         get: operations["show_api_libraries__id__get"];
+        put?: never;
+        post?: never;
         /**
          * Marks the specified library as deleted (or undeleted).
          * @description Marks the specified library as deleted (or undeleted).
-         * Currently, only admin users can delete or restore libraries.
+         *     Currently, only admin users can delete or restore libraries.
          */
         delete: operations["delete_api_libraries__id__delete"];
+        options?: never;
+        head?: never;
         /**
          * Updates the information of an existing library.
          * @description Updates the information of an existing library.
          */
         patch: operations["update_api_libraries__id__patch"];
+        trace?: never;
     };
     "/api/libraries/{id}/permissions": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Gets the current or available permissions of a particular library.
          * @description Gets the current or available permissions of a particular library.
-         * The results can be paginated and additionally filtered by a query.
+         *     The results can be paginated and additionally filtered by a query.
          */
         get: operations["get_permissions_api_libraries__id__permissions_get"];
+        put?: never;
         /**
          * Sets the permissions to access and manipulate a library.
          * @description Sets the permissions to access and manipulate a library.
          */
         post: operations["set_permissions_api_libraries__id__permissions_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/libraries/{library_id}/contents": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**
+         * Return a list of library files and folders.
+         * @deprecated
+         * @description This endpoint is deprecated. Please use GET /api/folders/{folder_id}/contents instead.
+         */
+        get: operations["index_api_libraries__library_id__contents_get"];
+        put?: never;
+        /**
+         * Create a new library file or folder.
+         * @deprecated
+         * @description This endpoint is deprecated. Please use POST /api/folders/{folder_id} or POST /api/folders/{folder_id}/contents instead.
+         */
+        post: operations["create_form_api_libraries__library_id__contents_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/libraries/{library_id}/contents/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**
+         * Return a library file or folder.
+         * @deprecated
+         * @description This endpoint is deprecated. Please use GET /api/libraries/datasets/{library_id} instead.
+         */
+        get: operations["library_content_api_libraries__library_id__contents__id__get"];
+        /**
+         * Update a library file or folder.
+         * @deprecated
+         * @description This endpoint is deprecated. Please use PATCH /api/libraries/datasets/{library_id} instead.
+         */
+        put: operations["update_api_libraries__library_id__contents__id__put"];
+        post?: never;
+        /**
+         * Delete a library file or folder.
+         * @deprecated
+         * @description This endpoint is deprecated. Please use DELETE /api/libraries/datasets/{library_id} instead.
+         */
+        delete: operations["delete_api_libraries__library_id__contents__id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/licenses": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Lists all available SPDX licenses
          * @description Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/).
          */
         get: operations["index_api_licenses_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/licenses/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Gets the SPDX license metadata associated with the short identifier
          * @description Returns the license metadata associated with the given
-         * [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).
+         *     [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).
          */
         get: operations["get_api_licenses__id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/metrics": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Records a collection of metrics.
          * @description Record any metrics sent and return some status object.
          */
         post: operations["create_api_metrics_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the list of notifications associated with the user.
          * @description Anonymous users cannot receive personal notifications, only broadcasted notifications.
          *
-         * You can use the `limit` and `offset` parameters to paginate through the notifications.
+         *     You can use the `limit` and `offset` parameters to paginate through the notifications.
          */
         get: operations["get_user_notifications_api_notifications_get"];
         /** Updates a list of notifications with the requested values in a single request. */
@@ -1193,31 +3317,53 @@ export interface paths {
         post: operations["send_notification_api_notifications_post"];
         /** Deletes a list of notifications received by the user in a single request. */
         delete: operations["delete_user_notifications_api_notifications_delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications/broadcast": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns all currently active broadcasted notifications.
          * @description Only Admin users can access inactive notifications (scheduled or recently expired).
          */
         get: operations["get_all_broadcasted_api_notifications_broadcast_get"];
+        put?: never;
         /**
          * Broadcasts a notification to every user in the system.
          * @description Broadcasted notifications are a special kind of notification that are always accessible to all users, including anonymous users.
-         * They are typically used to display important information such as maintenance windows or new features.
-         * These notifications are displayed differently from regular notifications, usually in a banner at the top or bottom of the page.
+         *     They are typically used to display important information such as maintenance windows or new features.
+         *     These notifications are displayed differently from regular notifications, usually in a banner at the top or bottom of the page.
          *
-         * Broadcasted notifications can include action links that are displayed as buttons.
-         * This allows users to easily perform tasks such as filling out surveys, accepting legal agreements, or accessing new tutorials.
+         *     Broadcasted notifications can include action links that are displayed as buttons.
+         *     This allows users to easily perform tasks such as filling out surveys, accepting legal agreements, or accessing new tutorials.
          *
-         * Some key features of broadcasted notifications include:
-         * - They are not associated with a specific user, so they cannot be deleted or marked as read.
-         * - They can be scheduled to be displayed in the future or to expire after a certain time.
-         * - By default, broadcasted notifications are published immediately and expire six months after publication.
-         * - Only admins can create, edit, reschedule, or expire broadcasted notifications as needed.
+         *     Some key features of broadcasted notifications include:
+         *     - They are not associated with a specific user, so they cannot be deleted or marked as read.
+         *     - They can be scheduled to be displayed in the future or to expire after a certain time.
+         *     - By default, broadcasted notifications are published immediately and expire six months after publication.
+         *     - Only admins can create, edit, reschedule, or expire broadcasted notifications as needed.
          */
         post: operations["broadcast_notification_api_notifications_broadcast_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications/broadcast/{notification_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the information of a specific broadcasted notification.
          * @description Only Admin users can access inactive notifications (scheduled or recently expired).
@@ -1228,209 +3374,555 @@ export interface paths {
          * @description Only Admins can update broadcasted notifications. This is useful to reschedule, edit or expire broadcasted notifications.
          */
         put: operations["update_broadcasted_notification_api_notifications_broadcast__notification_id__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications/preferences": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the current user's preferences for notifications.
          * @description Anonymous users cannot have notification preferences. They will receive only broadcasted notifications.
          *
-         * - The settings will contain all possible channels, but the client should only show the ones that are really supported by the server.
-         *   The supported channels are returned in the `supported-channels` header.
+         *     - The settings will contain all possible channels, but the client should only show the ones that are really supported by the server.
+         *       The supported channels are returned in the `supported-channels` header.
          */
         get: operations["get_notification_preferences_api_notifications_preferences_get"];
         /**
          * Updates the user's preferences for notifications.
          * @description Anonymous users cannot have notification preferences. They will receive only broadcasted notifications.
          *
-         * - Can be used to completely enable/disable notifications for a particular type (category)
-         * or to enable/disable a particular channel on each category.
+         *     - Can be used to completely enable/disable notifications for a particular type (category)
+         *     or to enable/disable a particular channel on each category.
          */
         put: operations["update_notification_preferences_api_notifications_preferences_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications/status": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Returns the current status summary of the user's notifications since a particular date.
          * @description Anonymous users cannot receive personal notifications, only broadcasted notifications.
          */
         get: operations["get_notifications_status_api_notifications_status_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/notifications/{notification_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays information about a notification received by the user. */
         get: operations["show_notification_api_notifications__notification_id__get"];
         /** Updates the state of a notification received by the user. */
         put: operations["update_user_notification_api_notifications__notification_id__put"];
+        post?: never;
         /**
          * Deletes a notification received by the user.
          * @description When a notification is deleted, it is not immediately removed from the database, but marked as deleted.
          *
-         * - It will not be returned in the list of notifications, but admins can still access it as long as it is not expired.
-         * - It will be eventually removed from the database by a background task after the expiration time.
-         * - Deleted notifications will be permanently deleted when the expiration time is reached.
+         *     - It will not be returned in the list of notifications, but admins can still access it as long as it is not expired.
+         *     - It will be eventually removed from the database by a background task after the expiration time.
+         *     - Deleted notifications will be permanently deleted when the expiration time is reached.
          */
         delete: operations["delete_user_notification_api_notifications__notification_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/object_store_instances": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a list of persisted object store instances defined by the requesting user. */
         get: operations["object_stores__instances_index"];
+        put?: never;
         /** Create a user-bound object store. */
         post: operations["object_stores__create_instance"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/object_store_instances/test": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Test payload for creating user-bound object store. */
         post: operations["object_stores__test_new_instance_configuration"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
-    "/api/object_store_instances/{user_object_store_id}": {
+    "/api/object_store_instances/{uuid}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a persisted user object store instance. */
         get: operations["object_stores__instances_get"];
         /** Update or upgrade user object store instance. */
         put: operations["object_stores__instances_update"];
+        post?: never;
         /** Purge user object store instance. */
         delete: operations["object_stores__instances_purge"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/object_store_instances/{uuid}/test": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get a persisted user object store instance. */
+        get: operations["object_stores__instances_test_instance"];
+        put?: never;
+        /** Test updating or upgrading user object source instance. */
+        post: operations["object_stores__test_instances_update"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/object_store_templates": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a list of object store templates available to build user defined object stores from */
         get: operations["object_stores__templates_index"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/object_stores": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get a list of (currently only concrete) object stores configured with this Galaxy instance. */
         get: operations["index_api_object_stores_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/object_stores/{object_store_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get information about a concrete object store configured with Galaxy. */
         get: operations["show_info_api_object_stores__object_store_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Lists all Pages viewable by the user.
          * @description Get a list with summary information of all Pages available to the user.
          */
         get: operations["index_api_pages_get"];
+        put?: never;
         /**
          * Create a page and return summary information.
          * @description Get a list with details of all Pages available to the user.
          */
         post: operations["create_api_pages_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return a page summary and the content of the last revision.
          * @description Return summary information about a specific Page and the content of the last revision.
          */
         get: operations["show_api_pages__id__get"];
+        put?: never;
+        post?: never;
         /**
          * Marks the specific Page as deleted.
          * @description Marks the Page with the given ID as deleted.
          */
         delete: operations["delete_api_pages__id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}.pdf": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return a PDF document of the last revision of the Page.
          * @description Return a PDF document of the last revision of the Page.
          *
-         * This feature may not be available in this Galaxy.
+         *     This feature may not be available in this Galaxy.
          */
         get: operations["show_pdf_api_pages__id__pdf_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/disable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item inaccessible by a URL link.
          * @description Makes this item inaccessible by a URL link and return the current sharing status.
          */
         put: operations["disable_link_access_api_pages__id__disable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/enable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item accessible by a URL link.
          * @description Makes this item accessible by a URL link and return the current sharing status.
          */
         put: operations["enable_link_access_api_pages__id__enable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/prepare_download": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Return a PDF document of the last revision of the Page.
          * @description Return a STS download link for this page to be downloaded as a PDF.
          *
-         * This feature may not be available in this Galaxy.
+         *     This feature may not be available in this Galaxy.
          */
         post: operations["prepare_pdf_api_pages__id__prepare_download_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/publish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item public and accessible by a URL link.
          * @description Makes this item publicly available by a URL link and return the current sharing status.
          */
         put: operations["publish_api_pages__id__publish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/share_with_users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Share this item with specific users.
          * @description Shares this item with specific users and return the current sharing status.
          */
         put: operations["share_with_users_api_pages__id__share_with_users_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/sharing": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get the current sharing status of the given Page.
          * @description Return the sharing status of the item.
          */
         get: operations["sharing_api_pages__id__sharing_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/slug": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set a new slug for this shared item.
          * @description Sets a new slug to access this item by URL. The new slug must be unique.
          */
         put: operations["set_slug_api_pages__id__slug_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Undelete the specific Page.
          * @description Marks the Page with the given ID as undeleted.
          */
         put: operations["undelete_api_pages__id__undelete_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/pages/{id}/unpublish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Removes this item from the published list.
          * @description Removes this item from the published list and return the current sharing status.
          */
         put: operations["unpublish_api_pages__id__unpublish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays a list with information of quotas that are currently active.
          * @description Displays a list with information of quotas that are currently active.
          */
         get: operations["index_api_quotas_get"];
+        put?: never;
         /**
          * Creates a new quota.
          * @description Creates a new quota.
          */
         post: operations["create_api_quotas_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas/deleted": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays a list with information of quotas that have been deleted.
          * @description Displays a list with information of quotas that have been deleted.
          */
         get: operations["index_deleted_api_quotas_deleted_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas/deleted/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays details on a particular quota that has been deleted.
          * @description Displays details on a particular quota that has been deleted.
          */
         get: operations["deleted_quota_api_quotas_deleted__id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas/deleted/{id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /**
          * Restores a previously deleted quota.
          * @description Restores a previously deleted quota.
          */
         post: operations["undelete_api_quotas_deleted__id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays details on a particular active quota.
          * @description Displays details on a particular active quota.
@@ -1441,460 +3933,1488 @@ export interface paths {
          * @description Updates an existing quota.
          */
         put: operations["update_api_quotas__id__put"];
+        post?: never;
         /**
          * Deletes an existing quota.
          * @description Deletes an existing quota.
          */
         delete: operations["delete_api_quotas__id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/quotas/{id}/purge": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Purges a previously deleted quota. */
         post: operations["purge_api_quotas__id__purge_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/remote_files": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Displays remote files available to the user.
          * @description Lists all remote files available to the user from different sources.
          *
-         * The total count of files and directories is returned in the 'total_matches' header.
+         *     The total count of files and directories is returned in the 'total_matches' header.
          */
         get: operations["index_api_remote_files_get"];
+        put?: never;
         /**
          * Creates a new entry (directory/record) on the remote files source.
          * @description Creates a new entry on the remote files source.
          */
         post: operations["create_entry_api_remote_files_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/remote_files/plugins": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Display plugin information for each of the gxfiles:// URI targets available.
          * @description Display plugin information for each of the gxfiles:// URI targets available.
          */
         get: operations["plugins_api_remote_files_plugins_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/roles": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Index */
         get: operations["index_api_roles_get"];
+        put?: never;
         /** Create */
         post: operations["create_api_roles_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/roles/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show */
         get: operations["show_api_roles__id__get"];
+        put?: never;
+        post?: never;
         /** Delete */
         delete: operations["delete_api_roles__id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/roles/{id}/purge": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Purge */
         post: operations["purge_api_roles__id__purge_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/roles/{id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Undelete */
         post: operations["undelete_api_roles__id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/short_term_storage/{storage_request_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Serve the staged download specified by request ID. */
         get: operations["serve_api_short_term_storage__storage_request_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/short_term_storage/{storage_request_id}/ready": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Determine if specified storage request ID is ready for download. */
         get: operations["is_ready_api_short_term_storage__storage_request_id__ready_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/datasets": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        post?: never;
         /**
          * Purges a set of datasets by ID from disk. The datasets must be owned by the user.
          * @description **Warning**: This operation cannot be undone. All objects will be deleted permanently from the disk.
          */
         delete: operations["cleanup_datasets_api_storage_datasets_delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/datasets/discarded": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns discarded datasets owned by the given user. The results can be paginated. */
         get: operations["discarded_datasets_api_storage_datasets_discarded_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/datasets/discarded/summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns information with the total storage space taken by discarded datasets owned by the given user. */
         get: operations["discarded_datasets_summary_api_storage_datasets_discarded_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/histories": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        post?: never;
         /**
          * Purges a set of histories by ID. The histories must be owned by the user.
          * @description **Warning**: This operation cannot be undone. All objects will be deleted permanently from the disk.
          */
         delete: operations["cleanup_histories_api_storage_histories_delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/histories/archived": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns archived histories owned by the given user that are not purged. The results can be paginated. */
         get: operations["archived_histories_api_storage_histories_archived_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/histories/archived/summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns information with the total storage space taken by non-purged archived histories associated with the given user. */
         get: operations["archived_histories_summary_api_storage_histories_archived_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/histories/discarded": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns all discarded histories associated with the given user. */
         get: operations["discarded_histories_api_storage_histories_discarded_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/storage/histories/discarded/summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns information with the total storage space taken by discarded histories associated with the given user. */
         get: operations["discarded_histories_summary_api_storage_histories_discarded_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tags": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Apply a new set of tags to an item.
          * @description Replaces the tags associated with an item with the new ones specified in the payload.
          *
-         * - The previous tags will be __deleted__.
-         * - If no tags are provided in the request body, the currently associated tags will also be __deleted__.
+         *     - The previous tags will be __deleted__.
+         *     - If no tags are provided in the request body, the currently associated tags will also be __deleted__.
          */
         put: operations["update_api_tags_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tasks/{task_id}/state": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Determine state of task ID */
         get: operations["state_api_tasks__task_id__state_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_data": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Lists all available data tables
          * @description Get the list of all available data tables.
          */
         get: operations["index_api_tool_data_get"];
+        put?: never;
         /** Import a data manager bundle */
         post: operations["create_api_tool_data_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_data/{table_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get details of a given data table
          * @description Get details of a given tool data table.
          */
         get: operations["show_api_tool_data__table_name__get"];
+        put?: never;
+        post?: never;
         /**
          * Removes an item from a data table
          * @description Removes an item from a data table and reloads it to return its updated details.
          */
         delete: operations["delete_api_tool_data__table_name__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_data/{table_name}/fields/{field_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get information about a particular field in a tool data table
          * @description Reloads a data table and return its details.
          */
         get: operations["show_field_api_tool_data__table_name__fields__field_name__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get information about a particular field in a tool data table
          * @description Download a file associated with the data table field.
          */
         get: operations["download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_data/{table_name}/reload": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Reloads a tool data table
          * @description Reloads a data table and return its details.
          */
         get: operations["reload_api_tool_data__table_name__reload_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_shed_repositories": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Lists installed tool shed repositories. */
         get: operations["index_api_tool_shed_repositories_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_shed_repositories/check_for_updates": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Check for updates to the specified repository, or all installed repositories. */
         get: operations["check_for_updates_api_tool_shed_repositories_check_for_updates_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tool_shed_repositories/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show installed tool shed repository. */
         get: operations["show_api_tool_shed_repositories__id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tools/fetch": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Upload files to Galaxy */
         post: operations["fetch_form_api_tools_fetch_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tours": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Index
          * @description Return list of available tours.
          */
         get: operations["index_api_tours_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/tours/{tour_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Show
          * @description Return a tour definition.
          */
         get: operations["show_api_tours__tour_id__get"];
+        put?: never;
         /**
          * Update Tour
          * @description Return a tour definition.
          */
         post: operations["update_tour_api_tours__tour_id__post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get Users
          * @description Return a collection of users. Filters will only work if enabled in config or user is admin.
          */
         get: operations["get_users_api_users_get"];
+        put?: never;
         /** Create a new Galaxy user. Only admins can create users for now. */
         post: operations["create_user_api_users_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/current/recalculate_disk_usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Triggers a recalculation of the current user disk usage.
          * @description This route will be removed in a future version.
          *
-         * Please use `/api/users/current/recalculate_disk_usage` instead.
+         *     Please use `/api/users/current/recalculate_disk_usage` instead.
          */
         put: operations["recalculate_disk_usage_api_users_current_recalculate_disk_usage_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/deleted": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get Deleted Users
          * @description Return a collection of deleted users. Only admins can see deleted users.
          */
         get: operations["get_deleted_users_api_users_deleted_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/deleted/{user_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return information about a deleted user. Only admins can see deleted users. */
         get: operations["get_deleted_user_api_users_deleted__user_id__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/deleted/{user_id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Restore a deleted user. Only admins can restore users. */
         post: operations["undelete_user_api_users_deleted__user_id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/recalculate_disk_usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Triggers a recalculation of the current user disk usage.
          * @deprecated
          * @description This route will be removed in a future version.
          *
-         * Please use `/api/users/current/recalculate_disk_usage` instead.
+         *     Please use `/api/users/current/recalculate_disk_usage` instead.
          */
         put: operations["recalculate_disk_usage_api_users_recalculate_disk_usage_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return information about a specified or the current user. Only admin can see deleted or other users */
         get: operations["get_user_api_users__user_id__get"];
         /** Update the values of a user. Only admin can update others. */
         put: operations["update_user_api_users__user_id__put"];
+        post?: never;
         /** Delete a user. Only admins can delete others or purge users. */
         delete: operations["delete_user_api_users__user_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/api_key": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return the user's API key */
         get: operations["get_or_create_api_key_api_users__user_id__api_key_get"];
+        put?: never;
         /** Create a new API key for the user */
         post: operations["create_api_key_api_users__user_id__api_key_post"];
         /** Delete the current API key of the user */
         delete: operations["delete_api_key_api_users__user_id__api_key_delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/api_key/detailed": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return the user's API key with extra information. */
         get: operations["get_api_key_detailed_api_users__user_id__api_key_detailed_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/beacon": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return information about beacon share settings
          * @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
          */
         get: operations["get_beacon_settings_api_users__user_id__beacon_get"];
+        put?: never;
         /**
          * Change beacon setting
          * @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
          */
         post: operations["set_beacon_settings_api_users__user_id__beacon_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/custom_builds": {
-        /** Returns collection of custom builds. */
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**  Returns collection of custom builds. */
         get: operations["get_custom_builds_api_users__user_id__custom_builds_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/custom_builds/{key}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Add new custom build. */
         put: operations["add_custom_builds_api_users__user_id__custom_builds__key__put"];
+        post?: never;
         /** Delete a custom build */
         delete: operations["delete_custom_build_api_users__user_id__custom_builds__key__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/favorites/{object_type}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Add the object to user's favorites */
         put: operations["set_favorite_api_users__user_id__favorites__object_type__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/favorites/{object_type}/{object_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        post?: never;
         /** Remove the object from user's favorites */
         delete: operations["remove_favorite_api_users__user_id__favorites__object_type___object_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/objectstore_usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return the user's object store usage summary broken down by object store ID */
         get: operations["get_user_objectstore_usage_api_users__user_id__objectstore_usage_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/recalculate_disk_usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Triggers a recalculation of the current user disk usage. */
         put: operations["recalculate_disk_usage_by_user_id_api_users__user_id__recalculate_disk_usage_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/users/{user_id}/roles": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**
+         * Get User Roles
+         * @description Return a list of roles associated with this user. Only admins can see user roles.
+         */
+        get: operations["get_user_roles_api_users__user_id__roles_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/send_activation_email": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Sends activation email to user. */
         post: operations["send_activation_email_api_users__user_id__send_activation_email_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/theme/{theme}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Set the user's theme choice */
         put: operations["set_theme_api_users__user_id__theme__theme__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return the user's quota usage summary broken down by quota source */
         get: operations["get_user_usage_api_users__user_id__usage_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/users/{user_id}/usage/{label}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Return the user's quota usage summary for a given quota source label */
         get: operations["get_user_usage_for_label_api_users__user_id__usage__label__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/version": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return Galaxy version information: major/minor version, optional extra info
          * @description Return Galaxy version information: major/minor version, optional extra info.
          */
         get: operations["version_api_version_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Returns visualizations for the current user. */
         get: operations["index_api_visualizations_get"];
-    };
+        put?: never;
+        /**
+         * Create a new visualization.
+         * @description Creates a new visualization using the given payload and does not require the import_id field.
+         *     If import_id given, it imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload.
+         */
+        post: operations["create_api_visualizations_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/visualizations/{id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /**
+         * Get a visualization by ID.
+         * @description Return the visualization.
+         */
+        get: operations["show_api_visualizations__id__get"];
+        /** Update a visualization. */
+        put: operations["update_api_visualizations__id__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/visualizations/{id}/disable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item inaccessible by a URL link.
          * @description Makes this item inaccessible by a URL link and return the current sharing status.
          */
         put: operations["disable_link_access_api_visualizations__id__disable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/enable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item accessible by a URL link.
          * @description Makes this item accessible by a URL link and return the current sharing status.
          */
         put: operations["enable_link_access_api_visualizations__id__enable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/publish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item public and accessible by a URL link.
          * @description Makes this item publicly available by a URL link and return the current sharing status.
          */
         put: operations["publish_api_visualizations__id__publish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/share_with_users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Share this item with specific users.
          * @description Shares this item with specific users and return the current sharing status.
          */
         put: operations["share_with_users_api_visualizations__id__share_with_users_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/sharing": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get the current sharing status of the given Visualization.
          * @description Return the sharing status of the item.
          */
         get: operations["sharing_api_visualizations__id__sharing_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/slug": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set a new slug for this shared item.
          * @description Sets a new slug to access this item by URL. The new slug must be unique.
          */
         put: operations["set_slug_api_visualizations__id__slug_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/visualizations/{id}/unpublish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Removes this item from the published list.
          * @description Removes this item from the published list and return the current sharing status.
          */
         put: operations["unpublish_api_visualizations__id__unpublish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/whoami": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Return information about the current authenticated user
          * @description Return information about the current authenticated user.
          */
         get: operations["whoami_api_whoami_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/workflow_landings": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        /** Create Landing */
+        post: operations["create_landing_api_workflow_landings_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/workflow_landings/{uuid}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get Landing */
+        get: operations["get_landing_api_workflow_landings__uuid__get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/api/workflow_landings/{uuid}/claim": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
+        /** Claim Landing */
+        post: operations["claim_landing_api_workflow_landings__uuid__claim_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Lists stored workflows viewable by the user.
          * @description Lists stored workflows viewable by the user.
          */
         get: operations["index_api_workflows_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/menu": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get workflows present in the tools panel. */
         get: operations["get_workflow_menu_api_workflows_menu_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Displays information needed to run a workflow. */
         get: operations["show_workflow_api_workflows__workflow_id__get"];
+        put?: never;
+        post?: never;
         /** Add the deleted flag to a workflow. */
         delete: operations["delete_workflow_api_workflows__workflow_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/counts": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get state counts for accessible workflow. */
         get: operations["workflows__invocation_counts"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/disable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item inaccessible by a URL link.
          * @description Makes this item inaccessible by a URL link and return the current sharing status.
          */
         put: operations["disable_link_access_api_workflows__workflow_id__disable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/enable_link_access": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item accessible by a URL link.
          * @description Makes this item accessible by a URL link and return the current sharing status.
          */
         put: operations["enable_link_access_api_workflows__workflow_id__enable_link_access_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get the list of a user's workflow invocations. */
         get: operations["index_invocations_api_workflows__workflow_id__invocations_get"];
+        put?: never;
         /** Schedule the workflow specified by `workflow_id` to run. */
         post: operations["Invoke_workflow_api_workflows__workflow_id__invocations_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get detailed description of a workflow invocation.
          * @description An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__get"];
+        put?: never;
+        post?: never;
         /**
          * Cancel the specified workflow invocation.
          * @description An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` is ignored.
          */
         delete: operations["cancel_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated across all current jobs of the workflow invocation.
          * @description An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. `workflow_id` is ignored.
          */
         get: operations["workflow_invocation_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}/report": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get JSON summarizing invocation for reporting.
          * @description An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_report_api_workflows__workflow_id__invocations__invocation_id__report_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get PDF summarizing invocation for reporting.
          * @description An alias for `GET /api/invocations/{invocation_id}/report.pdf`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_report_pdf_api_workflows__workflow_id__invocations__invocation_id__report_pdf_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated per step of the workflow invocation.
          * @description An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. `workflow_id` is ignored.
          */
         get: operations["workflow_invocation_step_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__step_jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Show details of workflow invocation step.
          * @description An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` and `invocation_id` are ignored.
@@ -1905,44 +5425,134 @@ export interface paths {
          * @description An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` is ignored.
          */
         put: operations["update_workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/publish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Makes this item public and accessible by a URL link.
          * @description Makes this item publicly available by a URL link and return the current sharing status.
          */
         put: operations["publish_api_workflows__workflow_id__publish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/refactor": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /** Updates the workflow stored with the given ID. */
         put: operations["refactor_api_workflows__workflow_id__refactor_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/share_with_users": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Share this item with specific users.
          * @description Shares this item with specific users and return the current sharing status.
          */
         put: operations["share_with_users_api_workflows__workflow_id__share_with_users_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/sharing": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get the current sharing status of the given item.
          * @description Return the sharing status of the item.
          */
         get: operations["sharing_api_workflows__workflow_id__sharing_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/slug": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Set a new slug for this shared item.
          * @description Sets a new slug to access this item by URL. The new slug must be unique.
          */
         put: operations["set_slug_api_workflows__workflow_id__slug_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/tags": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tags based on workflow_id */
         get: operations["index_api_workflows__workflow_id__tags_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/tags/{tag_name}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Show tag based on workflow_id */
         get: operations["show_api_workflows__workflow_id__tags__tag_name__get"];
         /** Update tag based on workflow_id */
@@ -1951,77 +5561,189 @@ export interface paths {
         post: operations["create_api_workflows__workflow_id__tags__tag_name__post"];
         /** Delete tag based on workflow_id */
         delete: operations["delete_api_workflows__workflow_id__tags__tag_name__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/undelete": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
+        put?: never;
         /** Remove the deleted flag from a workflow. */
         post: operations["undelete_workflow_api_workflows__workflow_id__undelete_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/unpublish": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        get?: never;
         /**
          * Removes this item from the published list.
          * @description Removes this item from the published list and return the current sharing status.
          */
         put: operations["unpublish_api_workflows__workflow_id__unpublish_put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get the list of a user's workflow invocations.
          * @deprecated
          */
         get: operations["index_invocations_api_workflows__workflow_id__usage_get"];
+        put?: never;
         /**
          * Schedule the workflow specified by `workflow_id` to run.
          * @deprecated
          */
         post: operations["Invoke_workflow_api_workflows__workflow_id__usage_post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get detailed description of a workflow invocation.
          * @deprecated
          * @description An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__get"];
+        put?: never;
+        post?: never;
         /**
          * Cancel the specified workflow invocation.
          * @deprecated
          * @description An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` is ignored.
          */
         delete: operations["cancel_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__delete"];
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}/jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated across all current jobs of the workflow invocation.
          * @deprecated
          * @description An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. `workflow_id` is ignored.
          */
         get: operations["workflow_invocation_jobs_summary_api_workflows__workflow_id__usage__invocation_id__jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}/report": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get JSON summarizing invocation for reporting.
          * @deprecated
          * @description An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_report_api_workflows__workflow_id__usage__invocation_id__report_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}/report.pdf": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get PDF summarizing invocation for reporting.
          * @deprecated
          * @description An alias for `GET /api/invocations/{invocation_id}/report.pdf`. `workflow_id` is ignored.
          */
         get: operations["show_workflow_invocation_report_pdf_api_workflows__workflow_id__usage__invocation_id__report_pdf_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}/step_jobs_summary": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Get job state summary info aggregated per step of the workflow invocation.
          * @deprecated
          * @description An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. `workflow_id` is ignored.
          */
         get: operations["workflow_invocation_step_jobs_summary_api_workflows__workflow_id__usage__invocation_id__step_jobs_summary_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/usage/{invocation_id}/steps/{step_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /**
          * Show details of workflow invocation step.
          * @deprecated
@@ -2034,31 +5756,102 @@ export interface paths {
          * @description An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` is ignored.
          */
         put: operations["update_workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__put"];
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/api/workflows/{workflow_id}/versions": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** List all versions of a workflow. */
         get: operations["show_versions_api_workflows__workflow_id__versions_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/ga4gh/drs/v1/objects/{object_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get Object */
         get: operations["get_object_ga4gh_drs_v1_objects__object_id__get"];
+        put?: never;
         /** Get Object */
         post: operations["get_object_ga4gh_drs_v1_objects__object_id__post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/ga4gh/drs/v1/objects/{object_id}/access/{access_id}": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Get Access Url */
         get: operations["get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__get"];
+        put?: never;
         /** Get Access Url */
         post: operations["get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__post"];
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
     "/ga4gh/drs/v1/service-info": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
         /** Service Info */
         get: operations["service_info_ga4gh_drs_v1_service_info_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
+    "/oauth2_callback": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Callback entry point for remote resource responses with OAuth2 authorization codes */
+        get: operations["oauth2_callback_oauth2_callback_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
     };
 }
-
 export type webhooks = Record<string, never>;
-
 export interface components {
     schemas: {
         /** APIKeyModel */
@@ -2134,22 +5927,21 @@ export interface components {
         /** AddInputAction */
         AddInputAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "add_input";
             /** Collection Type */
             collection_type?: string | null;
             /** Default */
-            default?: Record<string, never> | null;
+            default?: unknown | null;
             /** Label */
             label?: string | null;
             /**
              * Optional
              * @default false
              */
-            optional?: boolean | null;
+            optional: boolean | null;
             position?: components["schemas"]["Position"] | null;
             /** Restrict On Connections */
             restrict_on_connections?: boolean | null;
@@ -2164,14 +5956,13 @@ export interface components {
          * AddStepAction
          * @description Add a new action to the workflow.
          *
-         * After the workflow is updated, an order_index will be assigned
-         * and this step may cause other steps to have their output_index
-         * adjusted.
+         *     After the workflow is updated, an order_index will be assigned
+         *     and this step may cause other steps to have their output_index
+         *     adjusted.
          */
         AddStepAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "add_step";
@@ -2201,7 +5992,7 @@ export interface components {
              * Quota percent
              * @description Percentage of the storage quota applicable to the user.
              */
-            quota_percent?: Record<string, never>;
+            quota_percent?: number | null;
             /**
              * Total disk usage
              * @description Size of all non-purged, unique datasets of the user in bytes.
@@ -2220,7 +6011,7 @@ export interface components {
              * @description Whether to purge the history after archiving it. It requires an `archive_export_id` to be set.
              * @default false
              */
-            purge_history?: boolean;
+            purge_history: boolean;
         };
         /** ArchivedHistoryDetailed */
         ArchivedHistoryDetailed: {
@@ -2265,7 +6056,7 @@ export interface components {
              * @description TODO
              * @default ?
              */
-            genome_build?: string | null;
+            genome_build: string | null;
             /**
              * History ID
              * @example 0123456789ABCDEF
@@ -2323,14 +6114,14 @@ export interface components {
              * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
              */
             state_details: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             };
             /**
              * State IDs
              * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.
              */
             state_ids: {
-                [key: string]: string[] | undefined;
+                [key: string]: string[];
             };
             tags: components["schemas"]["TagCollection"];
             /**
@@ -2527,29 +6318,95 @@ export interface components {
              * All Datasets
              * @default true
              */
-            all_datasets?: Record<string, never>;
+            all_datasets: unknown;
             /** Archive File */
-            archive_file?: Record<string, never>;
+            archive_file?: unknown;
             /** Archive Source */
-            archive_source?: Record<string, never>;
+            archive_source?: unknown;
             /**
              * Archive Type
              * @default url
              */
-            archive_type?: Record<string, never>;
+            archive_type: unknown;
             /** History Id */
-            history_id?: Record<string, never>;
+            history_id?: unknown;
             /** Name */
-            name?: Record<string, never>;
+            name?: unknown;
+        };
+        /** Body_create_form_api_libraries__library_id__contents_post */
+        Body_create_form_api_libraries__library_id__contents_post: {
+            /** Create Type */
+            create_type: unknown;
+            /**
+             * Dbkey
+             * @default ?
+             */
+            dbkey: unknown;
+            /** Extended Metadata */
+            extended_metadata?: unknown;
+            /** File Type */
+            file_type?: unknown;
+            /** Files */
+            files?: string[] | null;
+            /**
+             * Filesystem Paths
+             * @default
+             */
+            filesystem_paths: unknown;
+            /** Folder Id */
+            folder_id: unknown;
+            /** From Hda Id */
+            from_hda_id?: unknown;
+            /** From Hdca Id */
+            from_hdca_id?: unknown;
+            /**
+             * Ldda Message
+             * @default
+             */
+            ldda_message: unknown;
+            /**
+             * Link Data Only
+             * @default copy_files
+             */
+            link_data_only: unknown;
+            /**
+             * Roles
+             * @default
+             */
+            roles: unknown;
+            /**
+             * Server Dir
+             * @default
+             */
+            server_dir: unknown;
+            /**
+             * Tag Using Filenames
+             * @default false
+             */
+            tag_using_filenames: unknown;
+            /**
+             * Tags
+             * @default []
+             */
+            tags: unknown;
+            /** Upload Files */
+            upload_files?: unknown;
+            /**
+             * Upload Option
+             * @default upload_file
+             */
+            upload_option: unknown;
+            /** Uuid */
+            uuid?: unknown;
         };
         /** Body_fetch_form_api_tools_fetch_post */
         Body_fetch_form_api_tools_fetch_post: {
             /** Files */
             files?: string[] | null;
             /** History Id */
-            history_id: Record<string, never>;
+            history_id: unknown;
             /** Targets */
-            targets: Record<string, never>;
+            targets: unknown;
         };
         /** BroadcastNotificationContent */
         BroadcastNotificationContent: {
@@ -2559,12 +6416,10 @@ export interface components {
              */
             action_links?: components["schemas"]["ActionLink"][] | null;
             /**
-             * Category
-             * @default broadcast
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
-            category?: "broadcast";
+            category: "broadcast";
             /**
              * Message
              * @description The message of the notification (supports Markdown).
@@ -2587,7 +6442,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            category?: "broadcast";
+            category: "broadcast";
             /**
              * Content
              * @description The content of the broadcast notification. Broadcast notifications are displayed prominently to all users and can contain action links to redirect the user to a specific page.
@@ -2630,7 +6485,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            category?: "broadcast";
+            category: "broadcast";
             content: components["schemas"]["BroadcastNotificationContent"];
             /**
              * Create time
@@ -2708,12 +6563,12 @@ export interface components {
             /**
              * @description Features supported by this file source.
              * @default {
-             *   "pagination": false,
-             *   "search": false,
-             *   "sorting": false
-             * }
+             *       "pagination": false,
+             *       "search": false,
+             *       "sorting": false
+             *     }
              */
-            supports?: components["schemas"]["FilesSourceSupports"];
+            supports: components["schemas"]["FilesSourceSupports"];
             /**
              * Type
              * @description The type of the plugin.
@@ -2763,6 +6618,20 @@ export interface components {
              */
             type: "change_dbkey";
         };
+        /** ChatPayload */
+        ChatPayload: {
+            /**
+             * Context
+             * @description The context for the chatbot.
+             * @default
+             */
+            context: string | null;
+            /**
+             * Query
+             * @description The query to be sent to the chatbot.
+             */
+            query: string;
+        };
         /** CheckForUpdatesResponse */
         CheckForUpdatesResponse: {
             /**
@@ -2787,11 +6656,16 @@ export interface components {
             /**
              * Type
              * @description The digest method used to create the checksum.
-             * The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA Named Information Hash Algorithm Registry]. Other values MAY be used, as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
-             * GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future. Until then, if implementers do choose such an algorithm (e.g. because it's implemented by their storage provider), they SHOULD use an existing standard `type` value such as `md5`, `etag`, `crc32c`, `trunc512`, or `sha1`.
+             *     The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA Named Information Hash Algorithm Registry]. Other values MAY be used, as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
+             *     GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future. Until then, if implementers do choose such an algorithm (e.g. because it's implemented by their storage provider), they SHOULD use an existing standard `type` value such as `md5`, `etag`, `crc32c`, `trunc512`, or `sha1`.
              */
             type: string;
         };
+        /** ClaimLandingPayload */
+        ClaimLandingPayload: {
+            /** Client Secret */
+            client_secret?: string | null;
+        };
         /** CleanableItemsSummary */
         CleanableItemsSummary: {
             /**
@@ -2810,85 +6684,6 @@ export interface components {
             /** Item Ids */
             item_ids: string[];
         };
-        /** CloudDatasets */
-        CloudDatasets: {
-            /**
-             * Authentication ID
-             * @description The ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations via `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define a new authorization.
-             * @example 0123456789ABCDEF
-             */
-            authz_id: string;
-            /**
-             * Bucket
-             * @description The name of a bucket to which data should be sent (e.g., a bucket name on AWS S3).
-             */
-            bucket: string;
-            /**
-             * Objects
-             * @description A list of dataset IDs belonging to the specified history that should be sent to the given bucket. If not provided, Galaxy sends all the datasets belonging the specified history.
-             */
-            dataset_ids?: string[] | null;
-            /**
-             * History ID
-             * @description The ID of history from which the object should be downloaded
-             * @example 0123456789ABCDEF
-             */
-            history_id: string;
-            /**
-             * Spaces to tabs
-             * @description A boolean value. If set to 'True', and an object with same name of the dataset to be sent already exist in the bucket, Galaxy replaces the existing object with the dataset to be sent. If set to 'False', Galaxy appends datetime to the dataset name to prevent overwriting an existing object.
-             * @default false
-             */
-            overwrite_existing?: boolean | null;
-        };
-        /** CloudDatasetsResponse */
-        CloudDatasetsResponse: {
-            /**
-             * Bucket
-             * @description The name of bucket to which the listed datasets are queued to be sent
-             */
-            bucket_name: string;
-            /**
-             * Failed datasets
-             * @description The datasets for which Galaxy failed to create (and queue) send job
-             */
-            failed_dataset_labels: string[];
-            /**
-             * Send datasets
-             * @description The datasets for which Galaxy succeeded to create (and queue) send job
-             */
-            sent_dataset_labels: string[];
-        };
-        /** CloudObjects */
-        CloudObjects: {
-            /**
-             * Authentication ID
-             * @description The ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations via `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define a new authorization.
-             * @example 0123456789ABCDEF
-             */
-            authz_id: string;
-            /**
-             * Bucket
-             * @description The name of a bucket from which data should be fetched from (e.g., a bucket name on AWS S3).
-             */
-            bucket: string;
-            /**
-             * History ID
-             * @description The ID of history to which the object should be received to.
-             * @example 0123456789ABCDEF
-             */
-            history_id: string;
-            /**
-             * Input arguments
-             * @description A summary of the input arguments, which is optional and will default to {}.
-             */
-            input_args?: components["schemas"]["InputArguments"] | null;
-            /**
-             * Objects
-             * @description A list of the names of objects to be fetched.
-             */
-            objects: string[];
-        };
         /** CollectionElementIdentifier */
         CollectionElementIdentifier: {
             /**
@@ -2931,12 +6726,18 @@ export interface components {
         CompositeDataElement: {
             /** Md5 */
             MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
              * Auto Decompress
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             composite: components["schemas"]["CompositeItems"];
@@ -2946,12 +6747,12 @@ export interface components {
              * Dbkey
              * @default ?
              */
-            dbkey?: string;
+            dbkey: string;
             /**
              * Deferred
              * @default false
              */
-            deferred?: boolean;
+            deferred: boolean;
             /** Description */
             description?: string | null;
             elements_from?: components["schemas"]["ElementsFromType"] | null;
@@ -2959,20 +6760,23 @@ export interface components {
              * Ext
              * @default auto
              */
-            ext?: string;
+            ext: string;
             extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
             /** Info */
             info?: string | null;
+            /** Metadata */
+            metadata?: Record<string, never> | null;
             /** Name */
-            name?: string | number | number | boolean | null;
+            name?: string | number | boolean | null;
             /**
              * Space To Tab
              * @default false
              */
-            space_to_tab?: boolean;
+            space_to_tab: boolean;
             /**
-             * Src
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             src: "composite";
@@ -2982,7 +6786,7 @@ export interface components {
              * To Posix Lines
              * @default false
              */
-            to_posix_lines?: boolean;
+            to_posix_lines: boolean;
         };
         /** CompositeFileInfo */
         CompositeFileInfo: {
@@ -3038,7 +6842,7 @@ export interface components {
              * @description Hash function name to use to compute dataset hashes.
              * @default MD5
              */
-            hash_function?: components["schemas"]["HashFunctionNameEnum"] | null;
+            hash_function: components["schemas"]["HashFunctionNameEnum"] | null;
         };
         /** ConcreteObjectStoreModel */
         ConcreteObjectStoreModel: {
@@ -3072,8 +6876,7 @@ export interface components {
         /** ConnectAction */
         ConnectAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "connect";
@@ -3111,11 +6914,11 @@ export interface components {
          * ConvertedDatasetsMap
          * @description Map of `file extension` -> `converted dataset encoded id`
          * @example {
-         *   "csv": "dataset_id"
-         * }
+         *       "csv": "dataset_id"
+         *     }
          */
         ConvertedDatasetsMap: {
-            [key: string]: string | undefined;
+            [key: string]: string;
         };
         /** CreateEntryPayload */
         CreateEntryPayload: {
@@ -3148,10 +6951,11 @@ export interface components {
             /**
              * Content
              * @description Depending on the `source` it can be:
-             * - The encoded id from the library dataset
-             * - The encoded id from the library folder
-             * - The encoded id from the HDA
-             * - The encoded id from the HDCA
+             *     - The encoded id from the library dataset
+             *     - The encoded id from the library folder
+             *     - The encoded id from the HDA
+             *     - The encoded id from the HDCA
+             *
              */
             content?: string | null;
             /**
@@ -3159,7 +6963,7 @@ export interface components {
              * @description If the source is a collection, whether to copy child HDAs into the target history as well. Prior to the galaxy release 23.1 this defaulted to false.
              * @default true
              */
-            copy_elements?: boolean | null;
+            copy_elements: boolean | null;
             /**
              * DBKey
              * @description TODO
@@ -3180,7 +6984,7 @@ export interface components {
              * @description Whether to mark the original HDAs as hidden.
              * @default false
              */
-            hide_source_items?: boolean | null;
+            hide_source_items: boolean | null;
             /**
              * History Id
              * @description The ID of the history that will contain the collection. Required if `instance_type=history`.
@@ -3191,7 +6995,7 @@ export interface components {
              * @description The type of the instance, either `history` (default) or `library`.
              * @default history
              */
-            instance_type?: ("history" | "library") | null;
+            instance_type: ("history" | "library") | null;
             /**
              * Name
              * @description The name of the new collection.
@@ -3207,8 +7011,9 @@ export interface components {
              * @description The type of content to be created in the history.
              * @default dataset
              */
-            type?: components["schemas"]["HistoryContentType"] | null;
-            [key: string]: unknown | undefined;
+            type: components["schemas"]["HistoryContentType"] | null;
+        } & {
+            [key: string]: unknown;
         };
         /** CreateHistoryFromStore */
         CreateHistoryFromStore: {
@@ -3226,15 +7031,17 @@ export interface components {
             name: string;
             /** Secrets */
             secrets: {
-                [key: string]: string | undefined;
+                [key: string]: string;
             };
             /** Template Id */
             template_id: string;
             /** Template Version */
             template_version: number;
+            /** Uuid */
+            uuid?: string | null;
             /** Variables */
             variables: {
-                [key: string]: (string | boolean | number) | undefined;
+                [key: string]: string | boolean | number;
             };
         };
         /** CreateInvocationsFromStorePayload */
@@ -3249,19 +7056,19 @@ export interface components {
              * Legacy Job State
              * @deprecated
              * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
+             *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+             *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+             *             are not the mapped over step outputs but the individual job outputs.
              * @default false
              */
-            legacy_job_state?: boolean;
+            legacy_job_state: boolean;
             model_store_format?: components["schemas"]["ModelStoreFormat"] | null;
             /**
              * Include step details
              * @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary
              * @default false
              */
-            step_details?: boolean;
+            step_details: boolean;
             /** Store Content Uri */
             store_content_uri?: string | null;
             /** Store Dict */
@@ -3297,7 +7104,7 @@ export interface components {
              * @description The new message attribute of the LDDA created.
              * @default
              */
-            ldda_message?: string | null;
+            ldda_message: string | null;
         };
         /** CreateLibraryFolderPayload */
         CreateLibraryFolderPayload: {
@@ -3306,7 +7113,7 @@ export interface components {
              * @description A detailed description of the library folder.
              * @default
              */
-            description?: string | null;
+            description: string | null;
             /**
              * Name
              * @description The name of the library folder.
@@ -3320,7 +7127,7 @@ export interface components {
              * @description A detailed description of the Library.
              * @default
              */
-            description?: string | null;
+            description: string | null;
             /**
              * Name
              * @description The name of the Library.
@@ -3331,7 +7138,7 @@ export interface components {
              * @description A short text describing the contents of the Library.
              * @default
              */
-            synopsis?: string | null;
+            synopsis: string | null;
         };
         /** CreateMetricsPayload */
         CreateMetricsPayload: {
@@ -3339,7 +7146,7 @@ export interface components {
              * List of metrics to be recorded.
              * @default []
              */
-            metrics?: components["schemas"]["Metric"][];
+            metrics: components["schemas"]["Metric"][];
         };
         /** CreateNewCollectionPayload */
         CreateNewCollectionPayload: {
@@ -3353,7 +7160,7 @@ export interface components {
              * @description Whether to create a copy of the source HDAs for the new collection.
              * @default true
              */
-            copy_elements?: boolean | null;
+            copy_elements: boolean | null;
             /**
              * Element Identifiers
              * @description List of elements that should be in the new collection.
@@ -3369,7 +7176,7 @@ export interface components {
              * @description Whether to mark the original HDAs as hidden.
              * @default false
              */
-            hide_source_items?: boolean | null;
+            hide_source_items: boolean | null;
             /**
              * History Id
              * @description The ID of the history that will contain the collection. Required if `instance_type=history`.
@@ -3380,7 +7187,7 @@ export interface components {
              * @description The type of the instance, either `history` (default) or `library`.
              * @default history
              */
-            instance_type?: ("history" | "library") | null;
+            instance_type: ("history" | "library") | null;
             /**
              * Name
              * @description The name of the new collection.
@@ -3399,13 +7206,13 @@ export interface components {
              * @description Raw text contents of the last page revision (type dependent on content_format).
              * @default
              */
-            content?: string | null;
+            content: string | null;
             /**
              * Content format
              * @description Either `markdown` or `html`.
              * @default html
              */
-            content_format?: components["schemas"]["PageContentFormat"];
+            content_format: components["schemas"]["PageContentFormat"];
             /**
              * Workflow invocation ID
              * @description Encoded ID used by workflow generated reports.
@@ -3421,7 +7228,8 @@ export interface components {
              * @description The name of the page.
              */
             title: string;
-            [key: string]: unknown | undefined;
+        } & {
+            [key: string]: unknown;
         };
         /** CreateQuotaParams */
         CreateQuotaParams: {
@@ -3435,7 +7243,7 @@ export interface components {
              * @description Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. None is equivalent to ``no``.
              * @default no
              */
-            default?: components["schemas"]["DefaultQuotaValues"];
+            default: components["schemas"]["DefaultQuotaValues"];
             /**
              * Description
              * @description Detailed text description for this Quota.
@@ -3446,13 +7254,13 @@ export interface components {
              * @description A list of group IDs or names to associate with this quota.
              * @default []
              */
-            in_groups?: string[] | null;
+            in_groups: string[] | null;
             /**
              * Users
              * @description A list of user IDs or user emails to associate with this quota.
              * @default []
              */
-            in_users?: string[] | null;
+            in_users: string[] | null;
             /**
              * Name
              * @description The name of the quota. This must be unique within a Galaxy instance.
@@ -3463,7 +7271,7 @@ export interface components {
              * @description Quotas can have one of three `operations`:- `=` : The quota is exactly the amount specified- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions
              * @default =
              */
-            operation?: components["schemas"]["QuotaOperation"];
+            operation: components["schemas"]["QuotaOperation"];
             /**
              * Quota Source Label
              * @description If set, quota source label to apply this quota operation to. Otherwise, the default quota is used.
@@ -3507,6 +7315,31 @@ export interface components {
              */
             url: string;
         };
+        /**
+         * CreateType
+         * @enum {string}
+         */
+        CreateType: "file" | "folder" | "collection";
+        /** CreateWorkflowLandingRequestPayload */
+        CreateWorkflowLandingRequestPayload: {
+            /** Client Secret */
+            client_secret?: string | null;
+            /**
+             * Public
+             * @description If workflow landing request is public anyone with the uuid can use the landing request. If not public the request must be claimed before use and additional verification might occur.
+             * @default false
+             */
+            public: boolean;
+            /** Request State */
+            request_state?: Record<string, never> | null;
+            /** Workflow Id */
+            workflow_id: string;
+            /**
+             * Workflow Target Type
+             * @enum {string}
+             */
+            workflow_target_type: "stored_workflow" | "workflow" | "trs_url";
+        };
         /** CreatedEntryResponse */
         CreatedEntryResponse: {
             /**
@@ -3578,48 +7411,200 @@ export interface components {
              */
             username: string;
         };
-        /** CustomBuildCreationPayload */
-        CustomBuildCreationPayload: {
+        /** CustomArchivedHistoryView */
+        CustomArchivedHistoryView: {
             /**
-             * Length type
-             * @description The type of the len file.
+             * Annotation
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
              */
-            "len|type": components["schemas"]["CustomBuildLenType"];
+            annotation?: string | null;
             /**
-             * Length value
-             * @description The content of the length file.
+             * Archived
+             * @description Whether this item has been archived and is no longer active.
              */
-            "len|value": string;
+            archived?: boolean | null;
             /**
-             * Name
-             * @description The name of the custom build.
+             * Contents Active
+             * @description Contains the number of active, deleted or hidden items in a History.
              */
-            name: string;
-        };
-        /**
-         * CustomBuildLenType
-         * @enum {string}
-         */
-        CustomBuildLenType: "file" | "fasta" | "text";
-        /** CustomBuildModel */
-        CustomBuildModel: {
+            contents_active?: components["schemas"]["HistoryActiveContentCounts"] | null;
             /**
-             * Count
-             * @description The number of chromosomes/contigs.
+             * Contents States
+             * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
              */
-            count?: string | null;
+            contents_states?: {
+                [key: string]: number;
+            } | null;
             /**
-             * Fasta
-             * @description The primary id of the fasta file from a history.
+             * Contents URL
+             * @description The relative URL to access the contents of this History.
              */
-            fasta?: string | null;
+            contents_url?: string | null;
             /**
-             * ID
-             * @description The ID of the custom build.
+             * Count
+             * @description The number of items in the history.
              */
-            id: string;
+            count?: number | null;
             /**
-             * Length
+             * Create Time
+             * @description The time and date this item was created.
+             */
+            create_time?: string | null;
+            /**
+             * Deleted
+             * @description Whether this item is marked as deleted.
+             */
+            deleted?: boolean | null;
+            /**
+             * Export Record Data
+             * @description The export record data associated with this archived history. Used to recover the history.
+             */
+            export_record_data?: components["schemas"]["ExportRecordData"] | null;
+            /**
+             * Genome Build
+             * @description TODO
+             */
+            genome_build?: string | null;
+            /**
+             * History ID
+             * @example 0123456789ABCDEF
+             */
+            id?: string;
+            /**
+             * Importable
+             * @description Whether this History can be imported by other users with a shared link.
+             */
+            importable?: boolean | null;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             */
+            model_class?: "History";
+            /**
+             * Name
+             * @description The name of the history.
+             */
+            name?: string | null;
+            /**
+             * Nice Size
+             * @description The total size of the contents of this history in a human-readable format.
+             */
+            nice_size?: string | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store new datasets in this history.
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Published
+             * @description Whether this resource is currently publicly available to all users.
+             */
+            published?: boolean | null;
+            /**
+             * Purged
+             * @description Whether this item has been permanently removed.
+             */
+            purged?: boolean | null;
+            /**
+             * Size
+             * @description The total size of the contents of this history in bytes.
+             */
+            size?: number | null;
+            /**
+             * Slug
+             * @description Part of the URL to uniquely identify this History by link in a readable way.
+             */
+            slug?: string | null;
+            /**
+             * State
+             * @description The current state of the History based on the states of the datasets it contains.
+             */
+            state?: components["schemas"]["DatasetState"] | null;
+            /**
+             * State Counts
+             * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
+             */
+            state_details?: {
+                [key: string]: number;
+            } | null;
+            /**
+             * State IDs
+             * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.
+             */
+            state_ids?: {
+                [key: string]: string[];
+            } | null;
+            tags?: components["schemas"]["TagCollection"] | null;
+            /**
+             * Update Time
+             * @description The last time and date this item was updated.
+             */
+            update_time?: string | null;
+            /**
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
+             */
+            url?: string | null;
+            /**
+             * User ID
+             * @description The encoded ID of the user that owns this History.
+             */
+            user_id?: string | null;
+            /**
+             * Username
+             * @description Owner of the history
+             */
+            username?: string | null;
+            /**
+             * Username and slug
+             * @description The relative URL in the form of /u/{username}/h/{slug}
+             */
+            username_and_slug?: string | null;
+        };
+        /** CustomBuildCreationPayload */
+        CustomBuildCreationPayload: {
+            /**
+             * Length type
+             * @description The type of the len file.
+             */
+            "len|type": components["schemas"]["CustomBuildLenType"];
+            /**
+             * Length value
+             * @description The content of the length file.
+             */
+            "len|value": string;
+            /**
+             * Name
+             * @description The name of the custom build.
+             */
+            name: string;
+        };
+        /**
+         * CustomBuildLenType
+         * @enum {string}
+         */
+        CustomBuildLenType: "file" | "fasta" | "text";
+        /** CustomBuildModel */
+        CustomBuildModel: {
+            /**
+             * Count
+             * @description The number of chromosomes/contigs.
+             */
+            count?: string | null;
+            /**
+             * Fasta
+             * @description The primary id of the fasta file from a history.
+             */
+            fasta?: string | null;
+            /**
+             * ID
+             * @description The ID of the custom build.
+             */
+            id: string;
+            /**
+             * Length
              * @description The primary id of the len file.
              * @example 0123456789ABCDEF
              */
@@ -3645,8 +7630,9 @@ export interface components {
             /**
              * Fasta HDAs
              * @description A list of label/value pairs with all the datasets of type `FASTA` contained in the History.
-             *  - `label` is item position followed by the name of the dataset.
-             *  - `value` is the encoded database ID of the dataset.
+             *      - `label` is item position followed by the name of the dataset.
+             *      - `value` is the encoded database ID of the dataset.
+             *
              */
             fasta_hdas: components["schemas"]["LabelValuePair"][];
             /**
@@ -3677,7 +7663,7 @@ export interface components {
              * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
              */
             contents_states?: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             } | null;
             /**
              * Contents URL
@@ -3765,14 +7751,14 @@ export interface components {
              * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
              */
             state_details?: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             } | null;
             /**
              * State IDs
              * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.
              */
             state_ids?: {
-                [key: string]: string[] | undefined;
+                [key: string]: string[];
             } | null;
             tags?: components["schemas"]["TagCollection"] | null;
             /**
@@ -3872,7 +7858,7 @@ export interface components {
              * @description The summary information of each of the elements inside the dataset collection.
              * @default []
              */
-            elements?: components["schemas"]["DCESummary"][];
+            elements: components["schemas"]["DCESummary"][];
             /**
              * Dataset Collection ID
              * @example 0123456789ABCDEF
@@ -3898,7 +7884,7 @@ export interface components {
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Destination */
             destination:
                 | components["schemas"]["HdaDestination"]
@@ -3922,7 +7908,7 @@ export interface components {
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Destination */
             destination:
                 | components["schemas"]["HdaDestination"]
@@ -3954,19 +7940,19 @@ export interface components {
              * @description A list of roles that can access the dataset. The user has to **have all these roles** in order to access this dataset. Users without access permission **cannot** have other permissions on this dataset. If there are no access roles set on the dataset it is considered **unrestricted**.
              * @default []
              */
-            access_dataset_roles?: string[][];
+            access_dataset_roles: string[][];
             /**
              * Manage Roles
              * @description A list of roles that can manage permissions on the dataset. Users with **any** of these roles can manage permissions of this dataset. If you remove yourself you will lose the ability to manage this dataset unless you are an admin.
              * @default []
              */
-            manage_dataset_roles?: string[][];
+            manage_dataset_roles: string[][];
             /**
              * Modify Roles
              * @description A list of roles that can modify the library item. This is a library related permission. User with **any** of these roles can modify name, metadata, and other information about this library item.
              * @default []
              */
-            modify_item_roles?: string[][];
+            modify_item_roles: string[][];
         };
         /** DatasetCollectionAttributesResult */
         DatasetCollectionAttributesResult: {
@@ -4073,6 +8059,11 @@ export interface components {
              */
             name: string;
         };
+        /**
+         * DatasetPermissionAction
+         * @enum {string}
+         */
+        DatasetPermissionAction: "set_permissions" | "make_private" | "remove_restrictions";
         /**
          * DatasetPermissions
          * @description Role-based permissions for accessing and managing a dataset.
@@ -4083,13 +8074,13 @@ export interface components {
              * @description The set of roles (encoded IDs) that can access this dataset.
              * @default []
              */
-            access?: string[];
+            access: string[];
             /**
              * Management
              * @description The set of roles (encoded IDs) that can manage this dataset.
              * @default []
              */
-            manage?: string[];
+            manage: string[];
         };
         /** DatasetSource */
         DatasetSource: {
@@ -4113,7 +8104,7 @@ export interface components {
              * Transform
              * @description The transformations applied to the dataset source.
              */
-            transform?: Record<string, never>[] | null;
+            transform?: unknown[] | null;
         };
         /** DatasetSourceId */
         DatasetSourceId: {
@@ -4149,9 +8140,8 @@ export interface components {
             | "setting_metadata"
             | "failed_metadata"
             | "deferred"
-/** ndip_todo: is this a right place?      */
-            | "stopped"
-            | "discarded";
+            | "discarded"
+            | "stopped";
         /** DatasetStorageDetails */
         DatasetStorageDetails: {
             /**
@@ -4207,47 +8197,6 @@ export interface components {
              */
             sources: Record<string, never>[];
         };
-        /** DatasetSummary */
-        DatasetSummary: {
-            /**
-             * Create Time
-             * @description The time and date this item was created.
-             */
-            create_time: string | null;
-            /** Deleted */
-            deleted: boolean;
-            /** File Size */
-            file_size: number;
-            /**
-             * Id
-             * @example 0123456789ABCDEF
-             */
-            id: string;
-            /** Purgable */
-            purgable: boolean;
-            /** Purged */
-            purged: boolean;
-            /**
-             * State
-             * @description The current state of this dataset.
-             */
-            state: components["schemas"]["DatasetState"];
-            /** Total Size */
-            total_size: number;
-            /**
-             * Update Time
-             * @description The last time and date this item was updated.
-             */
-            update_time: string | null;
-            /**
-             * UUID
-             * Format: uuid4
-             * @description Universal unique identifier for this dataset.
-             */
-            uuid: string;
-        };
-        /** DatasetSummaryList */
-        DatasetSummaryList: components["schemas"]["DatasetSummary"][];
         /** DatasetTextContentDetails */
         DatasetTextContentDetails: {
             /**
@@ -4316,7 +8265,7 @@ export interface components {
              * @description If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel
              * @default false
              */
-            display_in_upload?: boolean;
+            display_in_upload: boolean;
             /**
              * Extension
              * @description The data type’s Dataset file extension
@@ -4364,7 +8313,7 @@ export interface components {
          * @default {}
          */
         DatatypesEDAMDetailsDict: {
-            [key: string]: components["schemas"]["DatatypeEDAMDetails"] | undefined;
+            [key: string]: components["schemas"]["DatatypeEDAMDetails"];
         };
         /** DatatypesMap */
         DatatypesMap: {
@@ -4373,18 +8322,16 @@ export interface components {
              * @description Dictionary mapping datatype's classes with their base classes
              */
             class_to_classes: {
-                [key: string]:
-                    | {
-                          [key: string]: boolean | undefined;
-                      }
-                    | undefined;
+                [key: string]: {
+                    [key: string]: boolean;
+                };
             };
             /**
              * Extension Map
              * @description Dictionary mapping datatype's extensions with implementation classes
              */
             ext_to_class_name: {
-                [key: string]: string | undefined;
+                [key: string]: string;
             };
         };
         /** DefaultQuota */
@@ -4399,8 +8346,9 @@ export interface components {
             /**
              * Type
              * @description The type of the default quota. Either one of:
-             *  - `registered`: the associated quota will affect registered users.
-             *  - `unregistered`: the associated quota will affect unregistered users.
+             *      - `registered`: the associated quota will affect registered users.
+             *      - `unregistered`: the associated quota will affect unregistered users.
+             *
              */
             type: components["schemas"]["DefaultQuotaTypes"];
         };
@@ -4426,7 +8374,7 @@ export interface components {
              * @description Whether to permanently delete from disk the specified datasets. *Warning*: this is a destructive operation.
              * @default false
              */
-            purge?: boolean | null;
+            purge: boolean | null;
         };
         /** DeleteDatasetBatchResult */
         DeleteDatasetBatchResult: {
@@ -4453,7 +8401,7 @@ export interface components {
              * @description Whether to definitely remove this history from disk.
              * @default false
              */
-            purge?: boolean;
+            purge: boolean;
         };
         /** DeleteHistoryContentPayload */
         DeleteHistoryContentPayload: {
@@ -4462,25 +8410,25 @@ export interface components {
              * @description Whether to remove the dataset from storage. Datasets will only be removed from storage once all HDAs or LDDAs that refer to this datasets are deleted.
              * @default false
              */
-            purge?: boolean;
+            purge: boolean;
             /**
              * Recursive
              * @description When deleting a dataset collection, whether to also delete containing datasets.
              * @default false
              */
-            recursive?: boolean;
+            recursive: boolean;
             /**
              * Stop Job
              * @description Whether to stop the creating job if all the job's outputs are deleted.
              * @default false
              */
-            stop_job?: boolean;
+            stop_job: boolean;
         };
         /**
          * DeleteHistoryContentResult
          * @description Contains minimum information about the deletion state of a history item.
          *
-         * Can also contain any other properties of the item.
+         *     Can also contain any other properties of the item.
          */
         DeleteHistoryContentResult: {
             /**
@@ -4507,7 +8455,7 @@ export interface components {
              * @description Whether to definitely remove this history from disk.
              * @default false
              */
-            purge?: boolean;
+            purge: boolean;
         };
         /** DeleteJobPayload */
         DeleteJobPayload: {
@@ -4532,7 +8480,7 @@ export interface components {
              * @description Whether to also purge the Quota after deleting it.
              * @default false
              */
-            purge?: boolean;
+            purge: boolean;
         };
         /** DeletedCustomBuild */
         DeletedCustomBuild: {
@@ -4594,12 +8542,12 @@ export interface components {
              * Quota in bytes
              * @description Quota applicable to the user in bytes.
              */
-            quota_bytes: Record<string, never>;
+            quota_bytes?: number | null;
             /**
              * Quota percent
              * @description Percentage of the storage quota applicable to the user.
              */
-            quota_percent?: Record<string, never>;
+            quota_percent?: number | null;
             /**
              * Tags used
              * @description Tags used by the user
@@ -4619,8 +8567,7 @@ export interface components {
         /** DisconnectAction */
         DisconnectAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "disconnect";
@@ -4649,7 +8596,7 @@ export interface components {
         };
         /** DisplayApplication */
         DisplayApplication: {
-            /** Filename */
+            /** Filename  */
             filename_: string;
             /** Id */
             id: string;
@@ -4665,7 +8612,7 @@ export interface components {
             /**
              * Access Methods
              * @description The list of access methods that can be used to fetch the `DrsObject`.
-             * Required for single blobs; optional for bundles.
+             *     Required for single blobs; optional for bundles.
              */
             access_methods?: components["schemas"]["AccessMethod"][] | null;
             /**
@@ -4676,30 +8623,30 @@ export interface components {
             /**
              * Checksums
              * @description The checksum of the `DrsObject`. At least one checksum must be provided.
-             * For blobs, the checksum is computed over the bytes in the blob.
-             * For bundles, the checksum is computed over a sorted concatenation of the checksums of its top-level contained objects (not recursive, names not included). The list of checksums is sorted alphabetically (hex-code) before concatenation and a further checksum is performed on the concatenated checksum value.
-             * For example, if a bundle contains blobs with the following checksums:
-             * md5(blob1) = 72794b6d
-             * md5(blob2) = 5e089d29
-             * Then the checksum of the bundle is:
-             * md5( concat( sort( md5(blob1), md5(blob2) ) ) )
-             * = md5( concat( sort( 72794b6d, 5e089d29 ) ) )
-             * = md5( concat( 5e089d29, 72794b6d ) )
-             * = md5( 5e089d2972794b6d )
-             * = f7a29a04
+             *     For blobs, the checksum is computed over the bytes in the blob.
+             *     For bundles, the checksum is computed over a sorted concatenation of the checksums of its top-level contained objects (not recursive, names not included). The list of checksums is sorted alphabetically (hex-code) before concatenation and a further checksum is performed on the concatenated checksum value.
+             *     For example, if a bundle contains blobs with the following checksums:
+             *     md5(blob1) = 72794b6d
+             *     md5(blob2) = 5e089d29
+             *     Then the checksum of the bundle is:
+             *     md5( concat( sort( md5(blob1), md5(blob2) ) ) )
+             *     = md5( concat( sort( 72794b6d, 5e089d29 ) ) )
+             *     = md5( concat( 5e089d29, 72794b6d ) )
+             *     = md5( 5e089d2972794b6d )
+             *     = f7a29a04
              */
             checksums: components["schemas"]["Checksum"][];
             /**
              * Contents
              * @description If not set, this `DrsObject` is a single blob.
-             * If set, this `DrsObject` is a bundle containing the listed `ContentsObject` s (some of which may be further nested).
+             *     If set, this `DrsObject` is a bundle containing the listed `ContentsObject` s (some of which may be further nested).
              */
             contents?: components["schemas"]["ContentsObject"][] | null;
             /**
              * Created Time
              * Format: date-time
              * @description Timestamp of content creation in RFC3339.
-             * (This is the creation time of the underlying content, not of the JSON object.)
+             *     (This is the creation time of the underlying content, not of the JSON object.)
              */
             created_time: string;
             /**
@@ -4720,19 +8667,19 @@ export interface components {
             /**
              * Name
              * @description A string that can be used to name a `DrsObject`.
-             * This string is made up of uppercase and lowercase letters, decimal digits, hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable filenames].
+             *     This string is made up of uppercase and lowercase letters, decimal digits, hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable filenames].
              */
             name?: string | null;
             /**
              * Self Uri
              * @description A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object.
-             * The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around.  For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.
+             *     The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around.  For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the `self_uri` presents you with a hostname and properly encoded DRS ID for use in subsequent `access` endpoint calls.
              */
             self_uri: string;
             /**
              * Size
              * @description For blobs, the blob size in bytes.
-             * For bundles, the cumulative size, in bytes, of items in the `contents` field.
+             *     For bundles, the cumulative size, in bytes, of items in the `contents` field.
              */
             size: number;
             /**
@@ -4743,7 +8690,7 @@ export interface components {
             /**
              * Version
              * @description A string representing a version.
-             * (Some systems may use checksum, a RFC3339 timestamp, or an incrementing version number.)
+             *     (Some systems may use checksum, a RFC3339 timestamp, or an incrementing version number.)
              */
             version?: string | null;
         };
@@ -4883,8 +8830,8 @@ export interface components {
              * @description Dictionary mapping all the tool inputs (by name) to the corresponding data references.
              * @default {}
              */
-            inputs?: {
-                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
+            inputs: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"];
             };
             /**
              * Job Runner Name
@@ -4902,22 +8849,22 @@ export interface components {
              * Output collections
              * @default {}
              */
-            output_collections?: {
-                [key: string]: components["schemas"]["EncodedHdcaSourceId"] | undefined;
+            output_collections: {
+                [key: string]: components["schemas"]["EncodedHdcaSourceId"];
             };
             /**
              * Outputs
              * @description Dictionary mapping all the tool outputs (by name) to the corresponding data references.
              * @default {}
              */
-            outputs?: {
-                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
+            outputs: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"];
             };
             /**
              * Parameters
              * @description Object containing all the parameters of the tool associated with this job. The specific parameters depend on the tool itself.
              */
-            params: Record<string, never>;
+            params: unknown;
             /**
              * State
              * @description Current state of the job.
@@ -4939,6 +8886,11 @@ export interface components {
              * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
              */
             user_email?: string | null;
+            /**
+             * User Id
+             * @description User ID of user that ran this job
+             */
+            user_id?: string | null;
         };
         /** EncodedJobParameterHistoryItem */
         EncodedJobParameterHistoryItem: {
@@ -4979,19 +8931,19 @@ export interface components {
              * @description Whether to export as gzip archive.
              * @default true
              */
-            gzip?: boolean | null;
+            gzip: boolean | null;
             /**
              * Include Deleted
              * @description Whether to include deleted datasets in the exported archive.
              * @default false
              */
-            include_deleted?: boolean | null;
+            include_deleted: boolean | null;
             /**
              * Include Hidden
              * @description Whether to include hidden datasets in the exported archive.
              * @default false
              */
-            include_hidden?: boolean | null;
+            include_hidden: boolean | null;
         };
         /** ExportObjectMetadata */
         ExportObjectMetadata: {
@@ -5036,24 +8988,24 @@ export interface components {
              * @description Include file contents for deleted datasets (if include_files is True).
              * @default false
              */
-            include_deleted?: boolean;
+            include_deleted: boolean;
             /**
              * Include Files
              * @description include materialized files in export when available
              * @default true
              */
-            include_files?: boolean;
+            include_files: boolean;
             /**
              * Include hidden
              * @description Include file contents for hidden datasets (if include_files is True).
              * @default false
              */
-            include_hidden?: boolean;
+            include_hidden: boolean;
             /**
              * @description format of model store to export
              * @default tar.gz
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
+            model_store_format: components["schemas"]["ModelStoreFormat"];
             /**
              * Target URI
              * @description Galaxy Files URI to write mode store content to.
@@ -5079,7 +9031,7 @@ export interface components {
              * @description Prevent Galaxy from checking for a single file in a directory and re-interpreting the archive
              * @default true
              */
-            fuzzy_root?: boolean | null;
+            fuzzy_root: boolean | null;
             /** Items From */
             items_from?: string | null;
             src: components["schemas"]["Src"];
@@ -5092,8 +9044,7 @@ export interface components {
         /** ExtractInputAction */
         ExtractInputAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "extract_input";
@@ -5106,8 +9057,7 @@ export interface components {
         /** ExtractUntypedParameter */
         ExtractUntypedParameter: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "extract_untyped_parameter";
@@ -5154,18 +9104,35 @@ export interface components {
                 | components["schemas"]["HdcaDataItemsFromTarget"]
                 | components["schemas"]["FtpImportTarget"]
             )[];
-            [key: string]: unknown | undefined;
+        } & {
+            [key: string]: unknown;
+        };
+        /** FetchDatasetHash */
+        FetchDatasetHash: {
+            /**
+             * Hash Function
+             * @enum {string}
+             */
+            hash_function: "MD5" | "SHA-1" | "SHA-256" | "SHA-512";
+            /** Hash Value */
+            hash_value: string;
         };
         /** FileDataElement */
         FileDataElement: {
             /** Md5 */
             MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
              * Auto Decompress
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             /** Created From Basename */
@@ -5174,12 +9141,12 @@ export interface components {
              * Dbkey
              * @default ?
              */
-            dbkey?: string;
+            dbkey: string;
             /**
              * Deferred
              * @default false
              */
-            deferred?: boolean;
+            deferred: boolean;
             /** Description */
             description?: string | null;
             elements_from?: components["schemas"]["ElementsFromType"] | null;
@@ -5187,20 +9154,21 @@ export interface components {
              * Ext
              * @default auto
              */
-            ext?: string;
+            ext: string;
             extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
             /** Info */
             info?: string | null;
             /** Name */
-            name?: string | number | number | boolean | null;
+            name?: string | number | boolean | null;
             /**
              * Space To Tab
              * @default false
              */
-            space_to_tab?: boolean;
+            space_to_tab: boolean;
             /**
-             * Src
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             src: "files";
@@ -5210,13 +9178,12 @@ export interface components {
              * To Posix Lines
              * @default false
              */
-            to_posix_lines?: boolean;
+            to_posix_lines: boolean;
         };
         /** FileDefaultsAction */
         FileDefaultsAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "fill_defaults";
@@ -5269,8 +9236,7 @@ export interface components {
             state: components["schemas"]["DatasetState"];
             tags: components["schemas"]["TagCollection"];
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "file";
@@ -5291,7 +9257,7 @@ export interface components {
              * Hidden
              * @default false
              */
-            hidden?: boolean;
+            hidden: boolean;
             /** Id */
             id: string;
             /** Name */
@@ -5302,7 +9268,7 @@ export interface components {
              * Type
              * @enum {string}
              */
-            type: "ftp" | "posix" | "s3fs" | "azure";
+            type: "ftp" | "posix" | "s3fs" | "azure" | "onedata" | "webdav" | "dropbox" | "googledrive";
             /** Variables */
             variables?:
                 | (
@@ -5316,7 +9282,7 @@ export interface components {
              * Version
              * @default 0
              */
-            version?: number;
+            version: number;
         };
         /** FilesSourcePlugin */
         FilesSourcePlugin: {
@@ -5353,12 +9319,12 @@ export interface components {
             /**
              * @description Features supported by this file source.
              * @default {
-             *   "pagination": false,
-             *   "search": false,
-             *   "sorting": false
-             * }
+             *       "pagination": false,
+             *       "search": false,
+             *       "sorting": false
+             *     }
              */
-            supports?: components["schemas"]["FilesSourceSupports"];
+            supports: components["schemas"]["FilesSourceSupports"];
             /**
              * Type
              * @description The type of the plugin.
@@ -5390,25 +9356,24 @@ export interface components {
              * @description Whether this file source supports server-side pagination.
              * @default false
              */
-            pagination?: boolean;
+            pagination: boolean;
             /**
              * Search
              * @description Whether this file source supports server-side search.
              * @default false
              */
-            search?: boolean;
+            search: boolean;
             /**
              * Sorting
              * @description Whether this file source supports server-side sorting.
              * @default false
              */
-            sorting?: boolean;
+            sorting: boolean;
         };
         /** FillStepDefaultsAction */
         FillStepDefaultsAction: {
             /**
-             * Action Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             action_type: "fill_step_defaults";
@@ -5434,7 +9399,7 @@ export interface components {
              * @description A detailed description of the library folder.
              * @default
              */
-            description?: string | null;
+            description: string | null;
             /**
              * Id
              * @example 0123456789ABCDEF
@@ -5443,8 +9408,7 @@ export interface components {
             /** Name */
             name: string;
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "folder";
@@ -5459,12 +9423,18 @@ export interface components {
         FtpImportElement: {
             /** Md5 */
             MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
              * Auto Decompress
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             /** Created From Basename */
@@ -5473,12 +9443,12 @@ export interface components {
              * Dbkey
              * @default ?
              */
-            dbkey?: string;
+            dbkey: string;
             /**
              * Deferred
              * @default false
              */
-            deferred?: boolean;
+            deferred: boolean;
             /** Description */
             description?: string | null;
             elements_from?: components["schemas"]["ElementsFromType"] | null;
@@ -5486,22 +9456,23 @@ export interface components {
              * Ext
              * @default auto
              */
-            ext?: string;
+            ext: string;
             extra_files?: components["schemas"]["ExtraFiles"] | null;
             /** Ftp Path */
             ftp_path: string;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
             /** Info */
             info?: string | null;
             /** Name */
-            name?: string | number | number | boolean | null;
+            name?: string | number | boolean | null;
             /**
              * Space To Tab
              * @default false
              */
-            space_to_tab?: boolean;
+            space_to_tab: boolean;
             /**
-             * Src
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             src: "ftp_import";
@@ -5511,7 +9482,7 @@ export interface components {
              * To Posix Lines
              * @default false
              */
-            to_posix_lines?: boolean;
+            to_posix_lines: boolean;
         };
         /** FtpImportTarget */
         FtpImportTarget: {
@@ -5520,7 +9491,7 @@ export interface components {
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             destination: components["schemas"]["HdcaDestination"];
@@ -5549,12 +9520,12 @@ export interface components {
              * role IDs
              * @default []
              */
-            role_ids?: string[];
+            role_ids: string[];
             /**
              * user IDs
              * @default []
              */
-            user_ids?: string[];
+            user_ids: string[];
         };
         /**
          * GroupListResponse
@@ -5706,6 +9677,11 @@ export interface components {
              * @description TODO
              */
             api_type?: "file" | null;
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**
@@ -5823,7 +9799,7 @@ export interface components {
              * Metadata
              * @description The metadata associated with this dataset.
              */
-            metadata?: Record<string, never> | null;
+            metadata?: unknown | null;
             /**
              * Miscellaneous Blurb
              * @description TODO
@@ -5924,7 +9900,8 @@ export interface components {
              * @description The collection of visualizations that can be applied to this dataset.
              */
             visualizations?: components["schemas"]["Visualization"][] | null;
-            [key: string]: unknown | undefined;
+        } & {
+            [key: string]: unknown;
         };
         /**
          * HDADetailed
@@ -5949,7 +9926,12 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            api_type?: "file";
+            api_type: "file";
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**
@@ -6028,7 +10010,7 @@ export interface components {
              * @description TODO
              * @default ?
              */
-            genome_build?: string | null;
+            genome_build: string | null;
             /**
              * Hashes
              * @description The list of hashes associated with this dataset.
@@ -6039,7 +10021,7 @@ export interface components {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              * @default hda
              */
-            hda_ldda?: components["schemas"]["DatasetSourceType"];
+            hda_ldda: components["schemas"]["DatasetSourceType"];
             /**
              * HID
              * @description The index position of this item in the History.
@@ -6071,7 +10053,7 @@ export interface components {
              * Metadata
              * @description The metadata associated with this dataset.
              */
-            metadata?: Record<string, never> | null;
+            metadata?: unknown | null;
             /**
              * Miscellaneous Blurb
              * @description TODO
@@ -6137,7 +10119,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            type?: "file";
+            type: "file";
             /**
              * Type - ID
              * @description The type and the encoded ID of this item. Used for caching.
@@ -6273,7 +10255,7 @@ export interface components {
              * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
              * @default hda
              */
-            hda_ldda?: components["schemas"]["DatasetSourceType"];
+            hda_ldda: components["schemas"]["DatasetSourceType"];
             /**
              * History ID
              * @example 0123456789ABCDEF
@@ -6300,7 +10282,8 @@ export interface components {
             state: components["schemas"]["DatasetState"];
             /** Tags */
             tags: string[];
-            [key: string]: unknown | undefined;
+        } & {
+            [key: string]: unknown;
         };
         /**
          * HDASummary
@@ -6335,7 +10318,7 @@ export interface components {
              * @description TODO
              * @default ?
              */
-            genome_build?: string | null;
+            genome_build: string | null;
             /**
              * HID
              * @description The index position of this item in the History.
@@ -6401,31 +10384,167 @@ export interface components {
              */
             visible: boolean;
         };
-        /**
-         * HDCADetailed
-         * @description History Dataset Collection Association detailed information.
-         */
-        HDCADetailed: {
+        /** HDCACustom */
+        HDCACustom: {
             /**
              * Dataset Collection ID
              * @example 0123456789ABCDEF
              */
-            collection_id: string;
+            collection_id?: string;
             /**
              * Collection Type
              * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
              */
-            collection_type: string;
+            collection_type?: string | null;
             /**
              * Contents URL
              * @description The relative URL to access the contents of this History.
              */
-            contents_url: string;
+            contents_url?: string | null;
             /**
              * Create Time
              * @description The time and date this item was created.
              */
-            create_time: string | null;
+            create_time?: string | null;
+            /**
+             * Deleted
+             * @description Whether this item is marked as deleted.
+             */
+            deleted?: boolean | null;
+            /**
+             * Element Count
+             * @description The number of elements contained in the dataset collection. It may be None or undefined if the collection could not be populated.
+             */
+            element_count?: number | null;
+            /**
+             * Elements
+             * @description The summary information of each of the elements inside the dataset collection.
+             */
+            elements?: components["schemas"]["DCESummary"][] | null;
+            /**
+             * Elements Datatypes
+             * @description A set containing all the different element datatypes in the collection.
+             */
+            elements_datatypes?: string[] | null;
+            /**
+             * HID
+             * @description The index position of this item in the History.
+             */
+            hid?: number | null;
+            /**
+             * History Content Type
+             * @description This is always `dataset_collection` for dataset collections.
+             */
+            history_content_type?: "dataset_collection" | null;
+            /**
+             * History ID
+             * @example 0123456789ABCDEF
+             */
+            history_id?: string;
+            /**
+             * Id
+             * @example 0123456789ABCDEF
+             */
+            id?: string;
+            /**
+             * Implicit Collection Jobs Id
+             * @description Encoded ID for the ICJ object describing the collection of jobs corresponding to this collection
+             */
+            implicit_collection_jobs_id?: string | null;
+            /**
+             * Job Source ID
+             * @description The encoded ID of the Job that produced this dataset collection. Used to track the state of the job.
+             */
+            job_source_id?: string | null;
+            /**
+             * Job Source Type
+             * @description The type of job (model class) that produced this dataset collection. Used to track the state of the job.
+             */
+            job_source_type?: components["schemas"]["JobSourceType"] | null;
+            /**
+             * Job State Summary
+             * @description Overview of the job states working inside the dataset collection.
+             */
+            job_state_summary?: components["schemas"]["HDCJobStateSummary"] | null;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             */
+            model_class?: "HistoryDatasetCollectionAssociation";
+            /**
+             * Name
+             * @description The name of the item.
+             */
+            name?: string | null;
+            /**
+             * Populated
+             * @description Whether the dataset collection elements (and any subcollections elements) were successfully populated.
+             */
+            populated?: boolean | null;
+            /**
+             * Populated State
+             * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated.
+             */
+            populated_state?: components["schemas"]["DatasetCollectionPopulatedState"] | null;
+            /**
+             * Populated State Message
+             * @description Optional message with further information in case the population of the dataset collection failed.
+             */
+            populated_state_message?: string | null;
+            tags?: components["schemas"]["TagCollection"] | null;
+            /**
+             * Type
+             * @description This is always `collection` for dataset collections.
+             */
+            type?: "collection" | null;
+            /**
+             * Type - ID
+             * @description The type and the encoded ID of this item. Used for caching.
+             */
+            type_id?: string | null;
+            /**
+             * Update Time
+             * @description The last time and date this item was updated.
+             */
+            update_time?: string | null;
+            /**
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
+             */
+            url?: string | null;
+            /**
+             * Visible
+             * @description Whether this item is visible or hidden to the user by default.
+             */
+            visible?: boolean | null;
+        };
+        /**
+         * HDCADetailed
+         * @description History Dataset Collection Association detailed information.
+         */
+        HDCADetailed: {
+            /**
+             * Dataset Collection ID
+             * @example 0123456789ABCDEF
+             */
+            collection_id: string;
+            /**
+             * Collection Type
+             * @description The type of the collection, can be `list`, `paired`, or define subcollections using `:` as separator like `list:paired` or `list:list`.
+             */
+            collection_type: string;
+            /**
+             * Contents URL
+             * @description The relative URL to access the contents of this History.
+             */
+            contents_url: string;
+            /**
+             * Create Time
+             * @description The time and date this item was created.
+             */
+            create_time: string | null;
             /**
              * Deleted
              * @description Whether this item is marked as deleted.
@@ -6441,7 +10560,7 @@ export interface components {
              * @description The summary information of each of the elements inside the dataset collection.
              * @default []
              */
-            elements?: components["schemas"]["DCESummary"][];
+            elements: components["schemas"]["DCESummary"][];
             /**
              * Elements Datatypes
              * @description A set containing all the different element datatypes in the collection.
@@ -6524,7 +10643,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            type?: "collection";
+            type: "collection";
             /**
              * Type - ID
              * @description The type and the encoded ID of this item. Used for caching.
@@ -6582,6 +10701,11 @@ export interface components {
              * @description The number of elements contained in the dataset collection. It may be None or undefined if the collection could not be populated.
              */
             element_count?: number | null;
+            /**
+             * Elements Datatypes
+             * @description A set containing all the different element datatypes in the collection.
+             */
+            elements_datatypes: string[];
             /**
              * HID
              * @description The index position of this item in the History.
@@ -6649,7 +10773,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            type?: "collection";
+            type: "collection";
             /**
              * Type - ID
              * @description The type and the encoded ID of this item. Used for caching.
@@ -6682,90 +10806,85 @@ export interface components {
              * @description Total number of jobs associated with a dataset collection.
              * @default 0
              */
-            all_jobs?: number;
+            all_jobs: number;
             /**
              * Deleted jobs
              * @description Number of jobs in the `deleted` state.
              * @default 0
              */
-            deleted?: number;
+            deleted: number;
             /**
              * Deleted new jobs
              * @description Number of jobs in the `deleted_new` state.
              * @default 0
              */
-            deleted_new?: number;
+            deleted_new: number;
             /**
              * Jobs with errors
              * @description Number of jobs in the `error` state.
              * @default 0
              */
-            error?: number;
+            error: number;
             /**
              * Failed jobs
              * @description Number of jobs in the `failed` state.
              * @default 0
              */
-            failed?: number;
+            failed: number;
             /**
              * New jobs
              * @description Number of jobs in the `new` state.
              * @default 0
              */
-            new?: number;
+            new: number;
             /**
              * OK jobs
              * @description Number of jobs in the `ok` state.
              * @default 0
              */
-            ok?: number;
+            ok: number;
             /**
              * Paused jobs
              * @description Number of jobs in the `paused` state.
              * @default 0
              */
-            paused?: number;
+            paused: number;
             /**
              * Queued jobs
              * @description Number of jobs in the `queued` state.
              * @default 0
              */
-            queued?: number;
+            queued: number;
             /**
              * Resubmitted jobs
              * @description Number of jobs in the `resubmitted` state.
              * @default 0
              */
-            resubmitted?: number;
+            resubmitted: number;
             /**
              * Running jobs
              * @description Number of jobs in the `running` state.
              * @default 0
              */
-            running?: number;
+            running: number;
             /**
              * Skipped jobs
              * @description Number of jobs that were skipped due to conditional workflow step execution.
              * @default 0
              */
-            skipped?: number;
+            skipped: number;
             /**
              * Upload jobs
              * @description Number of jobs in the `upload` state.
              * @default 0
              */
-            upload?: number;
+            upload: number;
             /**
              * Waiting jobs
              * @description Number of jobs in the `waiting` state.
              * @default 0
              */
-            waiting?: number;
-        };
-        /** HTTPValidationError */
-        HTTPValidationError: {
-            /** Detail */
-            detail?: components["schemas"]["ValidationError"][];
+            waiting: number;
         };
         /**
          * HashFunctionNameEnum
@@ -6782,8 +10901,7 @@ export interface components {
         /** HdaDestination */
         HdaDestination: {
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "hdas";
@@ -6795,7 +10913,7 @@ export interface components {
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             destination: components["schemas"]["HdcaDestination"];
@@ -6821,7 +10939,7 @@ export interface components {
              * @description Decompress compressed data before sniffing?
              * @default false
              */
-            auto_decompress?: boolean;
+            auto_decompress: boolean;
             /** Collection Type */
             collection_type?: string | null;
             destination: components["schemas"]["HdcaDestination"];
@@ -6857,21 +10975,21 @@ export interface components {
          * @description Model for a category in the help forum.
          */
         HelpForumCategory: {
-            [key: string]: unknown | undefined;
+            [key: string]: unknown;
         };
         /**
          * HelpForumGroup
          * @description Model for a group in the help forum.
          */
         HelpForumGroup: {
-            [key: string]: unknown | undefined;
+            [key: string]: unknown;
         };
         /**
          * HelpForumGroupedSearchResult
          * @description Model for a grouped search result.
          */
         HelpForumGroupedSearchResult: {
-            [key: string]: unknown | undefined;
+            [key: string]: unknown;
         };
         /**
          * HelpForumPost
@@ -6882,17 +11000,17 @@ export interface components {
              * Avatar Template
              * @description The avatar template of the user.
              */
-            avatar_template: string;
+            avatar_template: string | null;
             /**
              * Blurb
              * @description The blurb of the post.
              */
-            blurb: string;
+            blurb: string | null;
             /**
              * Created At
              * @description The creation date of the post.
              */
-            created_at: string;
+            created_at: string | null;
             /**
              * Id
              * @description The ID of the post.
@@ -6902,34 +11020,35 @@ export interface components {
              * Like Count
              * @description The number of likes of the post.
              */
-            like_count: number;
+            like_count: number | null;
             /**
              * Name
              * @description The name of the post.
              */
-            name: string;
+            name: string | null;
             /**
              * Post Number
              * @description The post number of the post.
              */
-            post_number: number;
+            post_number: number | null;
             /**
              * Topic Id
              * @description The ID of the topic of the post.
              */
-            topic_id: number;
+            topic_id: number | null;
             /**
              * Username
              * @description The username of the post author.
              */
-            username: string;
-            [key: string]: unknown | undefined;
+            username: string | null;
+        } & {
+            [key: string]: unknown;
         };
         /**
          * HelpForumSearchResponse
          * @description Response model for the help search API endpoint.
          *
-         * This model is based on the Discourse API response for the search endpoint.
+         *     This model is based on the Discourse API response for the search endpoint.
          */
         HelpForumSearchResponse: {
             /**
@@ -6970,7 +11089,7 @@ export interface components {
          * @description Model for a tag in the help forum.
          */
         HelpForumTag: {
-            [key: string]: unknown | undefined;
+            [key: string]: unknown;
         };
         /**
          * HelpForumTopic
@@ -6981,7 +11100,7 @@ export interface components {
              * Archetype
              * @description The archetype of the topic.
              */
-            archetype: Record<string, never>;
+            archetype: unknown;
             /**
              * Archived
              * @description Whether the topic is archived.
@@ -7076,7 +11195,7 @@ export interface components {
              * Tags Descriptions
              * @description The descriptions of the tags of the topic.
              */
-            tags_descriptions?: Record<string, never> | null;
+            tags_descriptions?: unknown | null;
             /**
              * Title
              * @description The title of the topic.
@@ -7103,7 +11222,7 @@ export interface components {
          * @description Model for a user in the help forum.
          */
         HelpForumUser: {
-            [key: string]: unknown | undefined;
+            [key: string]: unknown;
         };
         /**
          * HistoryActiveContentCounts
@@ -7194,13 +11313,14 @@ export interface components {
         /**
          * HistoryContentsResult
          * @description List of history content items.
-         * Can contain different views and kinds of items.
+         *     Can contain different views and kinds of items.
          */
         HistoryContentsResult: (
             | components["schemas"]["HDACustom"]
             | components["schemas"]["HDADetailed"]
             | components["schemas"]["HDASummary"]
             | components["schemas"]["HDAInaccessible"]
+            | components["schemas"]["HDCACustom"]
             | components["schemas"]["HDCADetailed"]
             | components["schemas"]["HDCASummary"]
         )[];
@@ -7218,6 +11338,7 @@ export interface components {
                 | components["schemas"]["HDADetailed"]
                 | components["schemas"]["HDASummary"]
                 | components["schemas"]["HDAInaccessible"]
+                | components["schemas"]["HDCACustom"]
                 | components["schemas"]["HDCADetailed"]
                 | components["schemas"]["HDCASummary"]
             )[];
@@ -7268,7 +11389,7 @@ export interface components {
              * @description TODO
              * @default ?
              */
-            genome_build?: string | null;
+            genome_build: string | null;
             /**
              * History ID
              * @example 0123456789ABCDEF
@@ -7326,14 +11447,14 @@ export interface components {
              * @description A dictionary keyed to possible dataset states and valued with the number of datasets in this history that have those states.
              */
             state_details: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             };
             /**
              * State IDs
              * @description A dictionary keyed to possible dataset states and valued with lists containing the ids of each HDA in that state.
              */
             state_ids: {
-                [key: string]: string[] | undefined;
+                [key: string]: string[];
             };
             tags: components["schemas"]["TagCollection"];
             /**
@@ -7464,9 +11585,7 @@ export interface components {
              */
             id: string;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
+             * @description The name of the database model class. (enum property replaced by openapi-typescript)
              * @enum {string}
              */
             model: "ImplicitCollectionJobs";
@@ -7480,8 +11599,8 @@ export interface components {
              * @description A dictionary of job states and the number of jobs in that state.
              * @default {}
              */
-            states?: {
-                [key: string]: number | undefined;
+            states: {
+                [key: string]: number;
             };
         };
         /** ImportToolDataBundle */
@@ -7499,8 +11618,7 @@ export interface components {
              */
             id: string;
             /**
-             * src
-             * @description Indicates that the tool data should be resolved from a dataset.
+             * @description Indicates that the tool data should be resolved from a dataset. (enum property replaced by openapi-typescript)
              * @enum {string}
              */
             src: "hda" | "ldda";
@@ -7508,9 +11626,7 @@ export interface components {
         /** ImportToolDataBundleUriSource */
         ImportToolDataBundleUriSource: {
             /**
-             * src
-             * @description Indicates that the tool data should be resolved by a URI.
-             * @constant
+             * @description Indicates that the tool data should be resolved by a URI. (enum property replaced by openapi-typescript)
              * @enum {string}
              */
             src: "uri";
@@ -7520,33 +11636,6 @@ export interface components {
              */
             uri: string;
         };
-        /** InputArguments */
-        InputArguments: {
-            /**
-             * Database Key
-             * @description Sets the database key of the objects being fetched to Galaxy.
-             * @default ?
-             */
-            dbkey?: string | null;
-            /**
-             * File Type
-             * @description Sets the Galaxy datatype (e.g., `bam`) for the objects being fetched to Galaxy. See the following link for a complete list of Galaxy data types: https://galaxyproject.org/learn/datatypes/.
-             * @default auto
-             */
-            file_type?: string | null;
-            /**
-             * Spaces to tabs
-             * @description A boolean value ('true' or 'false') that sets if spaces should be converted to tab in the objects being fetched to Galaxy. Applicable only if `to_posix_lines` is True
-             * @default false
-             */
-            space_to_tab?: boolean | null;
-            /**
-             * POSIX line endings
-             * @description A boolean value ('true' or 'false'); if 'Yes', converts universal line endings to POSIX line endings. Set to 'False' if you upload a gzip, bz2 or zip archive containing a binary file.
-             * @default Yes
-             */
-            to_posix_lines?: "Yes" | boolean | null;
-        };
         /** InputDataCollectionStep */
         InputDataCollectionStep: {
             /**
@@ -7564,7 +11653,7 @@ export interface components {
              * @description A dictionary containing information about the inputs connected to this workflow step.
              */
             input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
+                [key: string]: components["schemas"]["InputStep"];
             };
             /**
              * Tool ID
@@ -7575,15 +11664,14 @@ export interface components {
              * Tool Inputs
              * @description TODO
              */
-            tool_inputs?: Record<string, never>;
+            tool_inputs?: unknown;
             /**
              * Tool Version
              * @description The version of the tool associated with this step.
              */
             tool_version?: string | null;
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "data_collection_input";
@@ -7607,7 +11695,7 @@ export interface components {
              * @description A dictionary containing information about the inputs connected to this workflow step.
              */
             input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
+                [key: string]: components["schemas"]["InputStep"];
             };
             /**
              * Tool ID
@@ -7618,15 +11706,14 @@ export interface components {
              * Tool Inputs
              * @description TODO
              */
-            tool_inputs?: Record<string, never>;
+            tool_inputs?: unknown;
             /**
              * Tool Version
              * @description The version of the tool associated with this step.
              */
             tool_version?: string | null;
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "data_input";
@@ -7650,7 +11737,7 @@ export interface components {
              * @description A dictionary containing information about the inputs connected to this workflow step.
              */
             input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
+                [key: string]: components["schemas"]["InputStep"];
             };
             /**
              * Tool ID
@@ -7661,15 +11748,14 @@ export interface components {
              * Tool Inputs
              * @description TODO
              */
-            tool_inputs?: Record<string, never>;
+            tool_inputs?: unknown;
             /**
              * Tool Version
              * @description The version of the tool associated with this step.
              */
             tool_version?: string | null;
             /**
-             * Type
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             type: "parameter_input";
@@ -7752,7 +11838,7 @@ export interface components {
              * Error Message
              * @default Installation error message, the empty string means no error was recorded
              */
-            error_message?: string;
+            error_message: string;
             /**
              * ID
              * @description Encoded ID of the install tool shed repository.
@@ -7802,8 +11888,7 @@ export interface components {
              */
             history_id: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "history_deleted";
@@ -7811,8 +11896,7 @@ export interface components {
         /** InvocationCancellationReviewFailedResponse */
         InvocationCancellationReviewFailedResponse: {
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "cancelled_on_review";
@@ -7825,8 +11909,7 @@ export interface components {
         /** InvocationCancellationUserRequestResponse */
         InvocationCancellationUserRequestResponse: {
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "user_request";
@@ -7839,8 +11922,7 @@ export interface components {
              */
             output_name: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "workflow_output_not_found";
@@ -7861,8 +11943,7 @@ export interface components {
              */
             hdca_id: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "collection_failed";
@@ -7886,8 +11967,7 @@ export interface components {
              */
             hda_id: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "dataset_failed";
@@ -7905,8 +11985,7 @@ export interface components {
              */
             details?: string | null;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "expression_evaluation_failed";
@@ -7930,8 +12009,7 @@ export interface components {
              */
             job_id: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "job_failed";
@@ -7951,8 +12029,7 @@ export interface components {
             /** Tool or module output name that was referenced but not produced */
             output_name: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "output_not_found";
@@ -7970,8 +12047,7 @@ export interface components {
              */
             details: string;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "when_not_boolean";
@@ -7981,6 +12057,21 @@ export interface components {
              */
             workflow_step_id: number;
         };
+        /** InvocationFailureWorkflowParameterInvalidResponse */
+        InvocationFailureWorkflowParameterInvalidResponse: {
+            /**
+             * Details
+             * @description Message raised by validator
+             */
+            details: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            reason: "workflow_parameter_invalid";
+            /** Workflow parameter step that failed validation */
+            workflow_step_id: number;
+        };
         /** InvocationInput */
         InvocationInput: {
             /**
@@ -8016,7 +12107,7 @@ export interface components {
              * Parameter value
              * @description Value of the input parameter.
              */
-            parameter_value: Record<string, never>;
+            parameter_value: unknown;
             /**
              * Workflow step ID
              * @description The encoded ID of the workflow step associated with the input parameter.
@@ -8048,9 +12139,22 @@ export interface components {
              * @description The states of all the jobs related to the Invocation.
              */
             states: {
-                [key: string]: number | undefined;
-            };
-        };
+                [key: string]: number;
+            };
+        };
+        InvocationMessageResponseUnion:
+            | components["schemas"]["InvocationCancellationReviewFailedResponse"]
+            | components["schemas"]["InvocationCancellationHistoryDeletedResponse"]
+            | components["schemas"]["InvocationCancellationUserRequestResponse"]
+            | components["schemas"]["InvocationFailureDatasetFailedResponse"]
+            | components["schemas"]["InvocationFailureCollectionFailedResponse"]
+            | components["schemas"]["InvocationFailureJobFailedResponse"]
+            | components["schemas"]["InvocationFailureOutputNotFoundResponse"]
+            | components["schemas"]["InvocationFailureExpressionEvaluationFailedResponse"]
+            | components["schemas"]["InvocationFailureWhenNotBooleanResponse"]
+            | components["schemas"]["InvocationUnexpectedFailureResponse"]
+            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"]
+            | components["schemas"]["InvocationFailureWorkflowParameterInvalidResponse"];
         /** InvocationOutput */
         InvocationOutput: {
             /**
@@ -8168,7 +12272,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            render_format?: "markdown";
+            render_format: "markdown";
             /**
              * Title
              * @description The name of the report.
@@ -8199,7 +12303,14 @@ export interface components {
          * InvocationState
          * @enum {string}
          */
-        InvocationState: "new" | "ready" | "scheduled" | "cancelled" | "cancelling" | "failed";
+        InvocationState:
+            | "new"
+            | "requires_materialization"
+            | "ready"
+            | "scheduled"
+            | "cancelled"
+            | "cancelling"
+            | "failed";
         /**
          * InvocationStep
          * @description Information about workflow invocation step
@@ -8227,7 +12338,7 @@ export interface components {
              * @description Jobs associated with the workflow invocation step.
              * @default []
              */
-            jobs?: components["schemas"]["JobBaseModel"][];
+            jobs: components["schemas"]["JobBaseModel"][];
             /**
              * Model class
              * @description The name of the database model class.
@@ -8245,16 +12356,16 @@ export interface components {
              * @description The dataset collection outputs of the workflow invocation step.
              * @default {}
              */
-            output_collections?: {
-                [key: string]: components["schemas"]["InvocationStepCollectionOutput"] | undefined;
+            output_collections: {
+                [key: string]: components["schemas"]["InvocationStepCollectionOutput"];
             };
             /**
              * Outputs
              * @description The outputs of the workflow invocation step.
              * @default {}
              */
-            outputs?: {
-                [key: string]: components["schemas"]["InvocationStepOutput"] | undefined;
+            outputs: {
+                [key: string]: components["schemas"]["InvocationStepOutput"];
             };
             /**
              * State of the invocation step
@@ -8300,7 +12411,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            src?: "hdca";
+            src: "hdca";
         };
         /** InvocationStepJobsResponseCollectionJobsModel */
         InvocationStepJobsResponseCollectionJobsModel: {
@@ -8326,7 +12437,7 @@ export interface components {
              * @description The states of all the jobs related to the Invocation.
              */
             states: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             };
         };
         /** InvocationStepJobsResponseJobModel */
@@ -8353,7 +12464,7 @@ export interface components {
              * @description The states of all the jobs related to the Invocation.
              */
             states: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             };
         };
         /** InvocationStepJobsResponseStepModel */
@@ -8380,7 +12491,7 @@ export interface components {
              * @description The states of all the jobs related to the Invocation.
              */
             states: {
-                [key: string]: number | undefined;
+                [key: string]: number;
             };
         };
         /** InvocationStepOutput */
@@ -8398,7 +12509,7 @@ export interface components {
              * @constant
              * @enum {string}
              */
-            src?: "hda";
+            src: "hda";
             /**
              * UUID
              * @description Universal unique identifier of the workflow step output dataset.
@@ -8418,8 +12529,7 @@ export interface components {
              */
             details?: string | null;
             /**
-             * Reason
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
             reason: "unexpected_failure";
@@ -8444,26 +12554,27 @@ export interface components {
              * @description Indicates if tool state corrections are allowed for workflow invocation.
              * @default false
              */
-            allow_tool_state_corrections?: boolean | null;
+            allow_tool_state_corrections: boolean | null;
             /**
              * Batch
              * @description Indicates if the workflow is invoked as a batch.
              * @default false
              */
-            batch?: boolean | null;
+            batch: boolean | null;
             /**
-             * Dataset Map
-             * @description TODO
+             * Legacy Dataset Map
+             * @deprecated
+             * @description An older alternative to specifying inputs using database IDs, do not use this and use inputs instead
              * @default {}
              */
-            ds_map?: {
-                [key: string]: Record<string, never> | undefined;
+            ds_map: {
+                [key: string]: Record<string, never>;
             } | null;
             /**
              * Effective Outputs
              * @description TODO
              */
-            effective_outputs?: Record<string, never> | null;
+            effective_outputs?: unknown | null;
             /**
              * History
              * @description The encoded history id - passed exactly like this 'hist_id=...' -  into which to import. Or the name of the new history into which to import.
@@ -8476,12 +12587,12 @@ export interface components {
             history_id?: string | null;
             /**
              * Inputs
-             * @description TODO
+             * @description Specify values for formal inputs to the workflow
              */
             inputs?: Record<string, never> | null;
             /**
              * Inputs By
-             * @description How inputs maps to inputs (datasets/collections) to workflows steps.
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
              */
             inputs_by?: string | null;
             /**
@@ -8489,13 +12600,13 @@ export interface components {
              * @description True when fetching by Workflow ID, False when fetching by StoredWorkflow ID
              * @default false
              */
-            instance?: boolean | null;
+            instance: boolean | null;
             /**
              * Legacy
              * @description Indicating if to use legacy workflow invocation.
              * @default false
              */
-            legacy?: boolean | null;
+            legacy: boolean | null;
             /**
              * New History Name
              * @description The name of the new history into which to import.
@@ -8506,68 +12617,63 @@ export interface components {
              * @description Indicates if the workflow invocation should not be added to the history.
              * @default false
              */
-            no_add_to_history?: boolean | null;
+            no_add_to_history: boolean | null;
             /**
-             * Parameters
-             * @description The raw parameters for the workflow invocation.
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead.
              * @default {}
              */
-            parameters?: Record<string, never> | null;
+            parameters: Record<string, never> | null;
             /**
-             * Parameters Normalized
-             * @description Indicates if parameters are already normalized for workflow invocation.
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
              * @default false
              */
-            parameters_normalized?: boolean | null;
+            parameters_normalized: boolean | null;
             /**
              * Preferred Intermediate Object Store ID
-             * @description The ID of the ? object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_intermediate_object_store_id?: string | null;
             /**
              * Preferred Object Store ID
-             * @description The ID of the object store that should be used to store new datasets in this history.
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_object_store_id?: string | null;
             /**
              * Preferred Outputs Object Store ID
-             * @description The ID of the object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
              */
             preferred_outputs_object_store_id?: string | null;
             /**
              * Replacement Parameters
-             * @description TODO
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
              * @default {}
              */
-            replacement_params?: Record<string, never> | null;
+            replacement_params: Record<string, never> | null;
             /**
              * Require Exact Tool Versions
              * @description If true, exact tool versions are required for workflow invocation.
              * @default true
              */
-            require_exact_tool_versions?: boolean | null;
+            require_exact_tool_versions: boolean | null;
             /**
              * Resource Parameters
-             * @description TODO
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
              * @default {}
              */
-            resource_params?: Record<string, never> | null;
+            resource_params: Record<string, never> | null;
             /**
              * Scheduler
              * @description Scheduler to use for workflow invocation.
              */
             scheduler?: string | null;
-            /**
-             * Step Parameters
-             * @description TODO
-             */
-            step_parameters?: Record<string, never> | null;
             /**
              * Use cached job
              * @description Indicated whether to use a cached job for workflow invocation.
              * @default false
              */
-            use_cached_job?: boolean | null;
+            use_cached_job: boolean | null;
             /**
              * Version
              * @description The version of the workflow to invoke.
@@ -8680,6 +12786,24 @@ export interface components {
              */
             update_time: string;
         };
+        /** JobConsoleOutput */
+        JobConsoleOutput: {
+            /**
+             * Job State
+             * @description The current job's state
+             */
+            state?: components["schemas"]["JobState"] | null;
+            /**
+             * STDERR
+             * @description Tool STDERR from job.
+             */
+            stderr?: string | null;
+            /**
+             * STDOUT
+             * @description Tool STDOUT from job.
+             */
+            stdout?: string | null;
+        };
         /** JobDestinationParams */
         JobDestinationParams: {
             /**
@@ -8697,7 +12821,8 @@ export interface components {
              * @description ID assigned to submitted job by external job running system
              */
             "Runner Job ID"?: string | null;
-            [key: string]: unknown | undefined;
+        } & {
+            [key: string]: unknown;
         };
         /** JobDisplayParametersSummary */
         JobDisplayParametersSummary: {
@@ -8711,7 +12836,7 @@ export interface components {
              * @description Dictionary mapping all the tool outputs (by name) with the corresponding dataset information in a nested format.
              */
             outputs: {
-                [key: string]: components["schemas"]["JobOutput"][] | undefined;
+                [key: string]: components["schemas"]["JobOutput"][];
             };
             /**
              * Parameters
@@ -8891,12 +13016,12 @@ export interface components {
         /**
          * JobMetric
          * @example {
-         *   "name": "start_epoch",
-         *   "plugin": "core",
-         *   "raw_value": "1614261340.0000000",
-         *   "title": "Job Start Time",
-         *   "value": "2021-02-25 14:55:40"
-         * }
+         *       "name": "start_epoch",
+         *       "plugin": "core",
+         *       "raw_value": "1614261340.0000000",
+         *       "title": "Job Start Time",
+         *       "value": "2021-02-25 14:55:40"
+         *     }
          */
         JobMetric: {
             /**
@@ -8937,7 +13062,7 @@ export interface components {
              * Output label
              * @description The output label
              */
-            label: Record<string, never>;
+            label: unknown;
             /**
              * Dataset
              * @description The associated dataset.
@@ -8979,8 +13104,7 @@ export interface components {
              * @description The values of the job parameter
              */
             value?:
-                | components["schemas"]["EncodedJobParameterHistoryItem"][]
-                | number
+                | (components["schemas"]["EncodedJobParameterHistoryItem"] | null)[]
                 | number
                 | boolean
                 | string
@@ -9020,9 +13144,7 @@ export interface components {
              */
             id: string;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
+             * @description The name of the database model class. (enum property replaced by openapi-typescript)
              * @enum {string}
              */
             model: "Job";
@@ -9036,8 +13158,8 @@ export interface components {
              * @description A dictionary of job states and the number of jobs in that state.
              * @default {}
              */
-            states?: {
-                [key: string]: number | undefined;
+            states: {
+                [key: string]: number;
             };
         };
         /**
@@ -9136,6 +13258,11 @@ export interface components {
              */
             value: string;
         };
+        /**
+         * LandingRequestState
+         * @enum {string}
+         */
+        LandingRequestState: "unclaimed" | "claimed";
         /** LegacyLibraryPermissionsPayload */
         LegacyLibraryPermissionsPayload: {
             /**
@@ -9143,25 +13270,25 @@ export interface components {
              * @description A list of role encoded IDs defining roles that should have access permission on the library.
              * @default []
              */
-            LIBRARY_ACCESS_in?: string[] | string | null;
+            LIBRARY_ACCESS_in: string[] | string | null;
             /**
              * Manage IDs
              * @description A list of role encoded IDs defining roles that should have manage permission on the library.
              * @default []
              */
-            LIBRARY_ADD_in?: string[] | string | null;
+            LIBRARY_ADD_in: string[] | string | null;
             /**
              * Modify IDs
              * @description A list of role encoded IDs defining roles that should have modify permission on the library.
              * @default []
              */
-            LIBRARY_MANAGE_in?: string[] | string | null;
+            LIBRARY_MANAGE_in: string[] | string | null;
             /**
              * Add IDs
              * @description A list of role encoded IDs defining roles that should be able to add items to the library.
              * @default []
              */
-            LIBRARY_MODIFY_in?: string[] | string | null;
+            LIBRARY_MODIFY_in: string[] | string | null;
         };
         /** LibraryAvailablePermissions */
         LibraryAvailablePermissions: {
@@ -9177,7 +13304,7 @@ export interface components {
             page_limit: number;
             /**
              * Roles
-             * @description A list available roles that can be assigned to a particular permission.
+             * @description A list containing available roles that can be assigned to a particular permission.
              */
             roles: components["schemas"]["BasicRoleModel"][];
             /**
@@ -9186,15312 +13313,22347 @@ export interface components {
              */
             total: number;
         };
-        /** LibraryCurrentPermissions */
-        LibraryCurrentPermissions: {
+        /** LibraryContentsCollectionCreatePayload */
+        LibraryContentsCollectionCreatePayload: {
+            /** the type of collection to create */
+            collection_type: string;
             /**
-             * Access Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which have access to the Library.
+             * Copy Elements
+             * @description if True, copy the elements into the collection
+             * @default false
              */
-            access_library_role_list: string[][];
+            copy_elements: boolean;
+            /** @description the type of item to create */
+            create_type: components["schemas"]["CreateType"];
+            /** list of dictionaries containing the element identifiers for the collection */
+            element_identifiers: Record<string, never>[];
             /**
-             * Add Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library.
+             * Extended Metadata
+             * @description sub-dictionary containing any extended metadata to associate with the item
              */
-            add_library_item_role_list: string[][];
+            extended_metadata?: Record<string, never> | null;
             /**
-             * Manage Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library.
+             * Folder Id
+             * @description the encoded id of the parent folder of the new item
+             * @example 0123456789ABCDEF
              */
-            manage_library_role_list: string[][];
+            folder_id: string;
             /**
-             * Modify Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library.
+             * From Hda Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDA to copy into the library
              */
-            modify_library_role_list: string[][];
-        };
-        /** LibraryDestination */
-        LibraryDestination: {
+            from_hda_id?: string | null;
             /**
-             * Description
-             * @description Description for library to create
+             * From Hdca Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDCA to copy into the library
              */
-            description?: string | null;
+            from_hdca_id?: string | null;
             /**
-             * Name
-             * @description Must specify a library name
+             * Hide Source Items
+             * @description if True, hide the source items in the collection
+             * @default false
              */
-            name: string;
+            hide_source_items: boolean;
             /**
-             * Synopsis
-             * @description Description for library to create
+             * Ldda Message
+             * @description the new message attribute of the LDDA created
+             * @default
              */
-            synopsis?: string | null;
+            ldda_message: string;
+            /** the name of the collection */
+            name?: string | null;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Tag Using Filenames
+             * @description create tags on datasets using the file's original name
+             * @default false
              */
-            type: "library";
-        };
-        /** LibraryFolderContentsIndexResult */
-        LibraryFolderContentsIndexResult: {
-            /** Folder Contents */
-            folder_contents: (
-                | components["schemas"]["FileLibraryFolderItem"]
-                | components["schemas"]["FolderLibraryFolderItem"]
-            )[];
-            metadata: components["schemas"]["LibraryFolderMetadata"];
-        };
-        /** LibraryFolderCurrentPermissions */
-        LibraryFolderCurrentPermissions: {
+            tag_using_filenames: boolean;
             /**
-             * Add Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library folder.
+             * Tags
+             * @description create the given list of tags on datasets
+             * @default []
              */
-            add_library_item_role_list: string[][];
+            tags: string[];
             /**
-             * Manage Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library folder.
+             * @deprecated
+             * @description the method to use for uploading files
+             * @default upload_file
              */
-            manage_folder_role_list: string[][];
+            upload_option: components["schemas"]["UploadOption"];
+        };
+        /** LibraryContentsCreateDatasetCollectionResponse */
+        LibraryContentsCreateDatasetCollectionResponse: components["schemas"]["LibraryContentsCreateDatasetResponse"][];
+        /** LibraryContentsCreateDatasetResponse */
+        LibraryContentsCreateDatasetResponse: {
+            /** Created From Basename */
+            created_from_basename: string | null;
+            /** Data Type */
+            data_type: string;
+            /** Deleted */
+            deleted: boolean;
+            /** File Ext */
+            file_ext: string;
+            /** File Name */
+            file_name: string;
+            /** File Size */
+            file_size: number;
+            /** Genome Build */
+            genome_build: string;
+            /** Hda Ldda */
+            hda_ldda: string;
+            /** Id */
+            id: string;
+            /** Library Dataset Id */
+            library_dataset_id: string;
+            /** Misc Blurb */
+            misc_blurb: string | null;
+            /** Misc Info */
+            misc_info: string | null;
             /**
-             * Modify Role List
-             * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library folder.
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            modify_folder_role_list: string[][];
+            model_class: "LibraryDatasetDatasetAssociation";
+            /** Name */
+            name: string;
+            /** Parent Library Id */
+            parent_library_id: string;
+            /** State */
+            state: string;
+            /** Update Time */
+            update_time: string;
+            /** Uuid */
+            uuid: string;
+            /** Visible */
+            visible: boolean;
+        } & {
+            [key: string]: unknown;
         };
-        /** LibraryFolderDestination */
-        LibraryFolderDestination: {
+        /** LibraryContentsCreateFileListResponse */
+        LibraryContentsCreateFileListResponse: components["schemas"]["LibraryContentsCreateFileResponse"][];
+        /** LibraryContentsCreateFileResponse */
+        LibraryContentsCreateFileResponse: {
             /**
-             * Library Folder Id
+             * Id
              * @example 0123456789ABCDEF
              */
-            library_folder_id: string;
+            id: string;
+            /** Name */
+            name: string;
+            /** Url */
+            url: string;
+        };
+        /** LibraryContentsCreateFolderListResponse */
+        LibraryContentsCreateFolderListResponse: components["schemas"]["LibraryContentsCreateFolderResponse"][];
+        /** LibraryContentsCreateFolderResponse */
+        LibraryContentsCreateFolderResponse: {
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Id
+             * @example 0123456789ABCDEF
              */
-            type: "library_folder";
+            id: string;
+            /** Name */
+            name: string;
+            /** Url */
+            url: string;
         };
-        /** LibraryFolderDetails */
-        LibraryFolderDetails: {
+        /** LibraryContentsDeletePayload */
+        LibraryContentsDeletePayload: {
             /**
-             * Deleted
-             * @description Whether this folder is marked as deleted.
+             * Purge
+             * @description if True, purge the library dataset
+             * @default false
              */
+            purge: boolean;
+        };
+        /** LibraryContentsDeleteResponse */
+        LibraryContentsDeleteResponse: {
+            /** Deleted */
             deleted: boolean;
             /**
-             * Description
-             * @description A detailed description of the library folder.
-             * @default
+             * Id
+             * @example 0123456789ABCDEF
              */
-            description?: string | null;
+            id: string;
+        };
+        /** LibraryContentsFileCreatePayload */
+        LibraryContentsFileCreatePayload: {
+            /** @description the type of item to create */
+            create_type: components["schemas"]["CreateType"];
             /**
-             * Genome Build
-             * @description TODO
+             * database key
              * @default ?
              */
-            genome_build?: string | null;
-            /**
-             * ID
-             * @description Encoded ID of the library folder.
-             * @example 0123456789ABCDEF
-             */
-            id: string;
+            dbkey: string | unknown[];
             /**
-             * Item Count
-             * @description A detailed description of the library folder.
+             * Extended Metadata
+             * @description sub-dictionary containing any extended metadata to associate with the item
              */
-            item_count: number;
+            extended_metadata?: Record<string, never> | null;
+            /** file type */
+            file_type?: string | null;
             /**
-             * Path
-             * @description The list of folder names composing the path to this folder.
-             * @default []
+             * Filesystem Paths
+             * @description (only if upload_option is 'upload_paths' and the user is an admin) file paths on the Galaxy server to upload to the library, one file per line
+             * @default
              */
-            library_path?: string[];
+            filesystem_paths: string;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Folder Id
+             * @description the encoded id of the parent folder of the new item
+             * @example 0123456789ABCDEF
              */
-            model_class: "LibraryFolder";
+            folder_id: string;
             /**
-             * Name
-             * @description The name of the library folder.
+             * From Hda Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDA to copy into the library
              */
-            name: string;
+            from_hda_id?: string | null;
             /**
-             * Parent Folder ID
-             * @description Encoded ID of the parent folder. Empty if it's the root folder.
+             * From Hdca Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDCA to copy into the library
              */
-            parent_id?: string | null;
+            from_hdca_id?: string | null;
             /**
-             * Parent Library ID
-             * @description Encoded ID of the Library this folder belongs to.
-             * @example 0123456789ABCDEF
+             * Ldda Message
+             * @description the new message attribute of the LDDA created
+             * @default
              */
-            parent_library_id: string;
+            ldda_message: string;
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * @description (only when upload_option is 'upload_directory' or 'upload_paths').Setting to 'link_to_files' symlinks instead of copying the files
+             * @default copy_files
              */
-            update_time: string;
-        };
-        /** LibraryFolderMetadata */
-        LibraryFolderMetadata: {
-            /** Can Add Library Item */
-            can_add_library_item: boolean;
-            /** Can Modify Folder */
-            can_modify_folder: boolean;
-            /** Folder Description */
-            folder_description: string;
-            /** Folder Name */
-            folder_name: string;
-            /** Full Path */
-            full_path: unknown[][];
+            link_data_only: components["schemas"]["LinkDataOnly"];
             /**
-             * Parent Library Id
-             * @example 0123456789ABCDEF
+             * user selected roles
+             * @default
              */
-            parent_library_id: string;
-            /** Total Rows */
-            total_rows: number;
-        };
-        /**
-         * LibraryFolderPermissionAction
-         * @constant
-         * @enum {string}
-         */
-        LibraryFolderPermissionAction: "set_permissions";
-        /** LibraryFolderPermissionsPayload */
-        LibraryFolderPermissionsPayload: {
+            roles: string;
             /**
-             * Action
-             * @description Indicates what action should be performed on the library folder.
+             * Server Dir
+             * @description (only if upload_option is 'upload_directory') relative path of the subdirectory of Galaxy ``library_import_dir`` (if admin) or ``user_library_import_dir`` (if non-admin) to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded.
+             * @default
              */
-            action?: components["schemas"]["LibraryFolderPermissionAction"] | null;
+            server_dir: string;
             /**
-             * Add IDs
-             * @description A list of role encoded IDs defining roles that should be able to add items to the library.
-             * @default []
+             * Tag Using Filenames
+             * @description create tags on datasets using the file's original name
+             * @default false
              */
-            "add_ids[]"?: string[] | string | null;
+            tag_using_filenames: boolean;
             /**
-             * Manage IDs
-             * @description A list of role encoded IDs defining roles that should have manage permission on the library.
+             * Tags
+             * @description create the given list of tags on datasets
              * @default []
              */
-            "manage_ids[]"?: string[] | string | null;
+            tags: string[];
+            /** list of the uploaded files */
+            upload_files?: Record<string, never>[] | null;
             /**
-             * Modify IDs
-             * @description A list of role encoded IDs defining roles that should have modify permission on the library.
-             * @default []
+             * @deprecated
+             * @description the method to use for uploading files
+             * @default upload_file
              */
-            "modify_ids[]"?: string[] | string | null;
+            upload_option: components["schemas"]["UploadOption"];
+            /** UUID of the dataset to upload */
+            uuid?: string | null;
+        } & {
+            [key: string]: unknown;
         };
-        /** LibraryLegacySummary */
-        LibraryLegacySummary: {
+        /** LibraryContentsFolderCreatePayload */
+        LibraryContentsFolderCreatePayload: {
+            /** @description the type of item to create */
+            create_type: components["schemas"]["CreateType"];
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * description of the folder to create
+             * @default
              */
-            create_time: string;
+            description: string;
             /**
-             * Deleted
-             * @description Whether this Library has been deleted.
+             * Extended Metadata
+             * @description sub-dictionary containing any extended metadata to associate with the item
              */
-            deleted: boolean;
+            extended_metadata?: Record<string, never> | null;
             /**
-             * Description
-             * @description A detailed description of the Library.
-             * @default
+             * Folder Id
+             * @description the encoded id of the parent folder of the new item
+             * @example 0123456789ABCDEF
              */
-            description?: string | null;
+            folder_id: string;
             /**
-             * ID
-             * @description Encoded ID of the Library.
-             * @example 0123456789ABCDEF
+             * From Hda Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDA to copy into the library
              */
-            id: string;
+            from_hda_id?: string | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * From Hdca Id
+             * @description (only if create_type is 'file') the encoded id of an accessible HDCA to copy into the library
              */
-            model_class: "Library";
+            from_hdca_id?: string | null;
             /**
-             * Name
-             * @description The name of the Library.
+             * Ldda Message
+             * @description the new message attribute of the LDDA created
+             * @default
              */
-            name: string;
+            ldda_message: string;
             /**
-             * Root Folder ID
-             * @description Encoded ID of the Library's base folder.
-             * @example 0123456789ABCDEF
+             * name of the folder to create
+             * @default
              */
-            root_folder_id: string;
+            name: string;
             /**
-             * Description
-             * @description A short text describing the contents of the Library.
+             * Tag Using Filenames
+             * @description create tags on datasets using the file's original name
+             * @default false
              */
-            synopsis?: string | null;
-        };
-        /**
-         * LibraryPermissionAction
-         * @enum {string}
-         */
-        LibraryPermissionAction: "set_permissions" | "remove_restrictions";
-        /**
-         * LibraryPermissionScope
-         * @enum {string}
-         */
-        LibraryPermissionScope: "current" | "available";
-        /** LibraryPermissionsPayload */
-        LibraryPermissionsPayload: {
+            tag_using_filenames: boolean;
             /**
-             * Access IDs
-             * @description A list of role encoded IDs defining roles that should have access permission on the library.
+             * Tags
+             * @description create the given list of tags on datasets
              * @default []
              */
-            "access_ids[]"?: string[] | string | null;
+            tags: string[];
             /**
-             * Action
-             * @description Indicates what action should be performed on the Library.
+             * @deprecated
+             * @description the method to use for uploading files
+             * @default upload_file
              */
-            action?: components["schemas"]["LibraryPermissionAction"] | null;
-            /**
-             * Add IDs
-             * @description A list of role encoded IDs defining roles that should be able to add items to the library.
-             * @default []
-             */
-            "add_ids[]"?: string[] | string | null;
-            /**
-             * Manage IDs
-             * @description A list of role encoded IDs defining roles that should have manage permission on the library.
-             * @default []
-             */
-            "manage_ids[]"?: string[] | string | null;
+            upload_option: components["schemas"]["UploadOption"];
+        };
+        /** LibraryContentsIndexDatasetResponse */
+        LibraryContentsIndexDatasetResponse: {
             /**
-             * Modify IDs
-             * @description A list of role encoded IDs defining roles that should have modify permission on the library.
-             * @default []
+             * Id
+             * @example 0123456789ABCDEF
              */
-            "modify_ids[]"?: string[] | string | null;
+            id: string;
+            /** Name */
+            name: string;
+            /** Type */
+            type: string;
+            /** Url */
+            url: string;
         };
-        /** LibrarySummary */
-        LibrarySummary: {
+        /** LibraryContentsIndexFolderResponse */
+        LibraryContentsIndexFolderResponse: {
             /**
-             * Can User Add
-             * @description Whether the current user can add contents to this Library.
+             * Id
+             * @example 0123456789ABCDEF
              */
-            can_user_add: boolean;
+            id: string;
+            /** Name */
+            name: string;
+            /** Type */
+            type: string;
+            /** Url */
+            url: string;
+        };
+        /** LibraryContentsIndexListResponse */
+        LibraryContentsIndexListResponse: (
+            | components["schemas"]["LibraryContentsIndexFolderResponse"]
+            | components["schemas"]["LibraryContentsIndexDatasetResponse"]
+        )[];
+        /** LibraryContentsShowDatasetResponse */
+        LibraryContentsShowDatasetResponse: {
+            /** Created From Basename */
+            created_from_basename: string | null;
+            /** Data Type */
+            data_type: string;
+            /** Date Uploaded */
+            date_uploaded: string;
+            /** File Ext */
+            file_ext: string;
+            /** File Name */
+            file_name: string;
+            /** File Size */
+            file_size: number;
             /**
-             * Can User Manage
-             * @description Whether the current user can manage the Library and its contents.
+             * Folder Id
+             * @example 0123456789ABCDEF
              */
-            can_user_manage: boolean;
+            folder_id: string;
+            /** Genome Build */
+            genome_build: string | null;
             /**
-             * Can User Modify
-             * @description Whether the current user can modify this Library.
+             * Id
+             * @example 0123456789ABCDEF
              */
-            can_user_modify: boolean;
+            id: string;
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Ldda Id
+             * @example 0123456789ABCDEF
              */
-            create_time: string;
+            ldda_id: string;
+            /** Message */
+            message: string | null;
+            /** Misc Blurb */
+            misc_blurb: string | null;
+            /** Misc Info */
+            misc_info: string | null;
             /**
-             * Create Time Pretty
-             * @description Nice time representation of the creation date.
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            create_time_pretty: string;
+            model_class: "LibraryDataset";
+            /** Name */
+            name: string;
             /**
-             * Deleted
-             * @description Whether this Library has been deleted.
+             * Parent Library Id
+             * @example 0123456789ABCDEF
              */
+            parent_library_id: string;
+            /** Peek */
+            peek: string | null;
+            /** State */
+            state: string;
+            tags: components["schemas"]["TagCollection"];
+            /** Update Time */
+            update_time: string;
+            /** Uploaded By */
+            uploaded_by: string | null;
+            /** Uuid */
+            uuid: string;
+        } & {
+            [key: string]: unknown;
+        };
+        /** LibraryContentsShowFolderResponse */
+        LibraryContentsShowFolderResponse: {
+            /** Deleted */
             deleted: boolean;
+            /** Description */
+            description: string;
+            /** Genome Build */
+            genome_build: string | null;
             /**
-             * Description
-             * @description A detailed description of the Library.
-             * @default
-             */
-            description?: string | null;
-            /**
-             * ID
-             * @description Encoded ID of the Library.
+             * Id
              * @example 0123456789ABCDEF
              */
             id: string;
+            /** Item Count */
+            item_count: number;
+            /** Library Path */
+            library_path: string[];
             /**
              * Model class
              * @description The name of the database model class.
              * @constant
              * @enum {string}
              */
-            model_class: "Library";
-            /**
-             * Name
-             * @description The name of the Library.
-             */
+            model_class: "LibraryFolder";
+            /** Name */
             name: string;
+            /** Parent Id */
+            parent_id: string | null;
             /**
-             * Public
-             * @description Whether this Library has been deleted.
-             */
-            public: boolean;
-            /**
-             * Root Folder ID
-             * @description Encoded ID of the Library's base folder.
+             * Parent Library Id
              * @example 0123456789ABCDEF
              */
-            root_folder_id: string;
+            parent_library_id: string;
+            /** Update Time */
+            update_time: string;
+        };
+        /** LibraryCurrentPermissions */
+        LibraryCurrentPermissions: {
             /**
-             * Description
-             * @description A short text describing the contents of the Library.
+             * Access Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which have access to the Library.
              */
-            synopsis?: string | null;
-        };
-        /**
-         * LibrarySummaryList
-         * @default []
-         */
-        LibrarySummaryList: components["schemas"]["LibrarySummary"][];
-        /** LicenseMetadataModel */
-        LicenseMetadataModel: {
+            access_library_role_list: string[][];
             /**
-             * Details URL
-             * Format: uri
-             * @description URL to the SPDX json details for this license
+             * Add Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library.
              */
-            detailsUrl: string;
+            add_library_item_role_list: string[][];
             /**
-             * Deprecated License
-             * @description True if the entire license is deprecated
+             * Manage Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library.
              */
-            isDeprecatedLicenseId: boolean;
+            manage_library_role_list: string[][];
             /**
-             * OSI approved
-             * @description Indicates if the [OSI](https://opensource.org/) has approved the license
+             * Modify Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library.
              */
-            isOsiApproved: boolean;
+            modify_library_role_list: string[][];
+        };
+        /** LibraryDestination */
+        LibraryDestination: {
             /**
-             * Identifier
-             * @description SPDX Identifier
+             * Description
+             * @description Description for library to create
              */
-            licenseId: string;
+            description?: string | null;
             /**
              * Name
-             * @description Full name of the license
+             * @description Must specify a library name
              */
             name: string;
             /**
-             * Recommended
-             * @description True if this license is recommended to be used
+             * Synopsis
+             * @description Description for library to create
              */
-            recommended: boolean;
+            synopsis?: string | null;
             /**
-             * Reference
-             * @description Reference to the HTML format for the license file
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            reference: string;
+            type: "library";
+        };
+        /** LibraryFolderContentsIndexResult */
+        LibraryFolderContentsIndexResult: {
+            /** Folder Contents */
+            folder_contents: (
+                | components["schemas"]["FileLibraryFolderItem"]
+                | components["schemas"]["FolderLibraryFolderItem"]
+            )[];
+            metadata: components["schemas"]["LibraryFolderMetadata"];
+        };
+        /** LibraryFolderCurrentPermissions */
+        LibraryFolderCurrentPermissions: {
             /**
-             * Reference number
-             * @description *Deprecated* - this field is generated and is no longer in use
+             * Add Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can add items to the Library folder.
              */
-            referenceNumber: number;
+            add_library_item_role_list: string[][];
             /**
-             * Reference URLs
-             * @description Cross reference URL pointing to additional copies of the license
+             * Manage Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can manage the Library folder.
              */
-            seeAlso: string[];
+            manage_folder_role_list: string[][];
             /**
-             * SPDX URL
-             * Format: uri
+             * Modify Role List
+             * @description A list containing pairs of role names and corresponding encoded IDs which can modify the Library folder.
              */
-            spdxUrl: string;
+            modify_folder_role_list: string[][];
+        };
+        /** LibraryFolderDestination */
+        LibraryFolderDestination: {
             /**
-             * URL
-             * Format: uri
-             * @description License URL
+             * Library Folder Id
+             * @example 0123456789ABCDEF
              */
-            url: string;
+            library_folder_id: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "library_folder";
         };
-        /**
-         * LimitedUserModel
-         * @description This is used when config options (expose_user_name and expose_user_email) are in place.
-         */
-        LimitedUserModel: {
-            /** Email */
-            email?: string | null;
+        /** LibraryFolderDetails */
+        LibraryFolderDetails: {
+            /**
+             * Deleted
+             * @description Whether this folder is marked as deleted.
+             */
+            deleted: boolean;
+            /**
+             * Description
+             * @description A detailed description of the library folder.
+             * @default
+             */
+            description: string | null;
+            /**
+             * Genome Build
+             * @description TODO
+             * @default ?
+             */
+            genome_build: string | null;
             /**
              * ID
-             * @description Encoded ID of the user
+             * @description Encoded ID of the library folder.
              * @example 0123456789ABCDEF
              */
             id: string;
-            /** Username */
-            username?: string | null;
-        };
-        /** Link */
-        Link: {
-            /** Name */
-            name: string;
-        };
-        /**
-         * ListJstreeResponse
-         * @deprecated
-         * @description List of files in Jstree format.
-         * @default []
-         */
-        ListJstreeResponse: Record<string, never>[];
-        /**
-         * ListUriResponse
-         * @description List of directories and files.
-         * @default []
-         */
-        ListUriResponse: (components["schemas"]["RemoteFile"] | components["schemas"]["RemoteDirectory"])[];
-        /**
-         * MandatoryNotificationCategory
-         * @description These notification categories cannot be opt-out by the user.
-         *
-         * The user will always receive notifications from these categories.
-         * @constant
-         * @enum {string}
-         */
-        MandatoryNotificationCategory: "broadcast";
-        /** MaterializeDatasetInstanceAPIRequest */
-        MaterializeDatasetInstanceAPIRequest: {
             /**
-             * Content
-             * @description Depending on the `source` it can be:
-             * - The encoded id of the source library dataset
-             * - The encoded id of the HDA
-             *
-             * @example 0123456789ABCDEF
+             * Item Count
+             * @description A detailed description of the library folder.
              */
-            content: string;
+            item_count: number;
             /**
-             * Source
-             * @description The source of the content. Can be other history element to be copied or library elements.
+             * Path
+             * @description The list of folder names composing the path to this folder.
+             * @default []
              */
-            source: components["schemas"]["DatasetSourceType"];
-        };
-        /** MessageNotificationContent */
-        MessageNotificationContent: {
+            library_path: string[];
             /**
-             * Category
-             * @default message
+             * Model class
+             * @description The name of the database model class.
              * @constant
              * @enum {string}
              */
-            category?: "message";
+            model_class: "LibraryFolder";
             /**
-             * Message
-             * @description The message of the notification (supports Markdown).
+             * Name
+             * @description The name of the library folder.
              */
-            message: string;
+            name: string;
             /**
-             * Subject
-             * @description The subject of the notification.
+             * Parent Folder ID
+             * @description Encoded ID of the parent folder. Empty if it's the root folder.
              */
-            subject: string;
-        };
-        /**
-         * MetadataFile
-         * @description Metadata file associated with a dataset.
-         */
-        MetadataFile: {
+            parent_id?: string | null;
             /**
-             * Download URL
-             * @description The URL to download this item from the server.
+             * Parent Library ID
+             * @description Encoded ID of the Library this folder belongs to.
+             * @example 0123456789ABCDEF
              */
-            download_url: string;
+            parent_library_id: string;
             /**
-             * File Type
-             * @description TODO
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
              */
-            file_type: string;
+            update_time: string;
         };
-        /** Metric */
-        Metric: {
-            /**
-             * Arguments
-             * @description A JSON string containing an array of extra data.
-             */
-            args: string;
-            /**
-             * Level
-             * @description An integer representing the metric's log level.
-             */
-            level: number;
-            /**
-             * Namespace
-             * @description Label indicating the source of the metric.
-             */
-            namespace: string;
+        /** LibraryFolderMetadata */
+        LibraryFolderMetadata: {
+            /** Can Add Library Item */
+            can_add_library_item: boolean;
+            /** Can Modify Folder */
+            can_modify_folder: boolean;
+            /** Folder Description */
+            folder_description: string;
+            /** Folder Name */
+            folder_name: string;
+            /** Full Path */
+            full_path: [string, string][];
             /**
-             * Timestamp
-             * @description The timestamp in ISO format.
+             * Parent Library Id
+             * @example 0123456789ABCDEF
              */
-            time: string;
+            parent_library_id: string;
+            /** Total Rows */
+            total_rows: number;
         };
         /**
-         * ModelStoreFormat
-         * @description Available types of model stores for export.
+         * LibraryFolderPermissionAction
+         * @constant
          * @enum {string}
          */
-        ModelStoreFormat: "tgz" | "tar" | "tar.gz" | "bag.zip" | "bag.tar" | "bag.tgz" | "rocrate.zip" | "bco.json";
-        /** NestedElement */
-        NestedElement: {
-            /** Md5 */
-            MD5?: string | null;
+        LibraryFolderPermissionAction: "set_permissions";
+        /** LibraryFolderPermissionsPayload */
+        LibraryFolderPermissionsPayload: {
             /**
-             * Auto Decompress
-             * @description Decompress compressed data before sniffing?
-             * @default false
+             * Action
+             * @description Indicates what action should be performed on the library folder.
              */
-            auto_decompress?: boolean;
-            /** Collection Type */
-            collection_type?: string | null;
-            /** Created From Basename */
-            created_from_basename?: string | null;
+            action?: components["schemas"]["LibraryFolderPermissionAction"] | null;
             /**
-             * Dbkey
-             * @default ?
+             * Add IDs
+             * @description A list of role encoded IDs defining roles that should be able to add items to the library.
+             * @default []
              */
-            dbkey?: string;
+            "add_ids[]": string[] | string | null;
             /**
-             * Deferred
-             * @default false
+             * Manage IDs
+             * @description A list of role encoded IDs defining roles that should have manage permission on the library.
+             * @default []
              */
-            deferred?: boolean;
-            /** Description */
-            description?: string | null;
-            /** Elements */
-            elements: (
-                | (
-                      | components["schemas"]["FileDataElement"]
-                      | components["schemas"]["PastedDataElement"]
-                      | components["schemas"]["UrlDataElement"]
-                      | components["schemas"]["PathDataElement"]
-                      | components["schemas"]["ServerDirElement"]
-                      | components["schemas"]["FtpImportElement"]
-                      | components["schemas"]["CompositeDataElement"]
-                  )
-                | components["schemas"]["NestedElement"]
-            )[];
-            elements_from?: components["schemas"]["ElementsFromType"] | null;
+            "manage_ids[]": string[] | string | null;
             /**
-             * Ext
-             * @default auto
+             * Modify IDs
+             * @description A list of role encoded IDs defining roles that should have modify permission on the library.
+             * @default []
              */
-            ext?: string;
-            extra_files?: components["schemas"]["ExtraFiles"] | null;
-            /** Info */
-            info?: string | null;
-            /** Name */
-            name?: string | number | number | boolean | null;
+            "modify_ids[]": string[] | string | null;
+        };
+        /** LibraryLegacySummary */
+        LibraryLegacySummary: {
             /**
-             * Space To Tab
-             * @default false
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            space_to_tab?: boolean;
-            /** Tags */
-            tags?: string[] | null;
+            create_time: string;
             /**
-             * To Posix Lines
-             * @default false
+             * Deleted
+             * @description Whether this Library has been deleted.
              */
-            to_posix_lines?: boolean;
-        };
-        /** NewSharedItemNotificationContent */
-        NewSharedItemNotificationContent: {
+            deleted: boolean;
             /**
-             * Category
-             * @default new_shared_item
-             * @constant
-             * @enum {string}
+             * Description
+             * @description A detailed description of the Library.
+             * @default
              */
-            category?: "new_shared_item";
+            description: string | null;
             /**
-             * Item name
-             * @description The name of the shared item.
+             * ID
+             * @description Encoded ID of the Library.
+             * @example 0123456789ABCDEF
              */
-            item_name: string;
+            id: string;
             /**
-             * Item type
-             * @description The type of the shared item.
+             * Model class
+             * @description The name of the database model class.
+             * @constant
              * @enum {string}
              */
-            item_type: "history" | "workflow" | "visualization" | "page";
+            model_class: "Library";
             /**
-             * Owner name
-             * @description The name of the owner of the shared item.
+             * Name
+             * @description The name of the Library.
              */
-            owner_name: string;
+            name: string;
             /**
-             * Slug
-             * @description The slug of the shared item. Used for the link to the item.
+             * Root Folder ID
+             * @description Encoded ID of the Library's base folder.
+             * @example 0123456789ABCDEF
              */
-            slug: string;
+            root_folder_id: string;
+            /**
+             * Description
+             * @description A short text describing the contents of the Library.
+             */
+            synopsis?: string | null;
         };
         /**
-         * NotificationBroadcastUpdateRequest
-         * @description A notification update request specific for broadcasting.
+         * LibraryPermissionAction
+         * @enum {string}
          */
-        NotificationBroadcastUpdateRequest: {
+        LibraryPermissionAction: "set_permissions" | "remove_restrictions";
+        /**
+         * LibraryPermissionScope
+         * @enum {string}
+         */
+        LibraryPermissionScope: "current" | "available";
+        /** LibraryPermissionsPayload */
+        LibraryPermissionsPayload: {
             /**
-             * Content
-             * @description The content of the broadcast notification. Broadcast notifications are displayed prominently to all users and can contain action links to redirect the user to a specific page.
+             * Access IDs
+             * @description A list of role encoded IDs defining roles that should have access permission on the library.
+             * @default []
              */
-            content?: components["schemas"]["BroadcastNotificationContent"] | null;
+            "access_ids[]": string[] | string | null;
             /**
-             * Expiration time
-             * @description The time when the notification should expire. By default it will expire after 6 months. Expired notifications will be permanently deleted.
+             * Action
+             * @description Indicates what action should be performed on the Library.
              */
-            expiration_time?: string | null;
+            action?: components["schemas"]["LibraryPermissionAction"] | null;
             /**
-             * Publication time
-             * @description The time when the notification should be published. Notifications can be created and then scheduled to be published at a later time.
+             * Add IDs
+             * @description A list of role encoded IDs defining roles that should be able to add items to the library.
+             * @default []
              */
-            publication_time?: string | null;
+            "add_ids[]": string[] | string | null;
             /**
-             * Source
-             * @description The source of the notification. Represents the agent that created the notification.
-             */
-            source?: string | null;
-            /**
-             * Variant
-             * @description The variant of the notification. Used to express the importance of the notification.
-             */
-            variant?: components["schemas"]["NotificationVariant"] | null;
-        };
-        /**
-         * NotificationCategorySettings
-         * @description The settings for a notification category.
-         */
-        NotificationCategorySettings: {
-            /**
-             * Channels
-             * @description The channels that the user wants to receive notifications from for this category.
-             * @default {
-             *   "email": true,
-             *   "push": true
-             * }
-             */
-            channels?: components["schemas"]["NotificationChannelSettings"];
-            /**
-             * Enabled
-             * @description Whether the user wants to receive notifications for this category.
-             * @default true
-             */
-            enabled?: boolean;
-        };
-        /**
-         * NotificationChannelSettings
-         * @description The settings for each channel of a notification category.
-         */
-        NotificationChannelSettings: {
-            /**
-             * Email
-             * @description Whether the user wants to receive email notifications for this category. This setting will be ignored unless the server supports asynchronous tasks.
-             * @default true
+             * Manage IDs
+             * @description A list of role encoded IDs defining roles that should have manage permission on the library.
+             * @default []
              */
-            email?: boolean;
+            "manage_ids[]": string[] | string | null;
             /**
-             * Push
-             * @description Whether the user wants to receive push notifications in the browser for this category.
-             * @default true
+             * Modify IDs
+             * @description A list of role encoded IDs defining roles that should have modify permission on the library.
+             * @default []
              */
-            push?: boolean;
+            "modify_ids[]": string[] | string | null;
         };
-        /**
-         * NotificationCreateData
-         * @description Basic common fields for all notification create requests.
-         */
-        NotificationCreateData: {
+        /** LibrarySummary */
+        LibrarySummary: {
             /**
-             * Category
-             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
+             * Can User Add
+             * @description Whether the current user can add contents to this Library.
              */
-            category:
-                | components["schemas"]["MandatoryNotificationCategory"]
-                | components["schemas"]["PersonalNotificationCategory"];
+            can_user_add: boolean;
             /**
-             * Content
-             * @description The content of the notification. The structure depends on the category.
+             * Can User Manage
+             * @description Whether the current user can manage the Library and its contents.
              */
-            content:
-                | components["schemas"]["MessageNotificationContent"]
-                | components["schemas"]["NewSharedItemNotificationContent"]
-                | components["schemas"]["BroadcastNotificationContent"];
+            can_user_manage: boolean;
             /**
-             * Expiration time
-             * @description The time when the notification should expire. By default it will expire after 6 months. Expired notifications will be permanently deleted.
+             * Can User Modify
+             * @description Whether the current user can modify this Library.
              */
-            expiration_time?: string | null;
+            can_user_modify: boolean;
             /**
-             * Publication time
-             * @description The time when the notification should be published. Notifications can be created and then scheduled to be published at a later time.
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            publication_time?: string | null;
+            create_time: string;
             /**
-             * Source
-             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
+             * Create Time Pretty
+             * @description Nice time representation of the creation date.
              */
-            source: string;
+            create_time_pretty: string;
             /**
-             * Variant
-             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
+             * Deleted
+             * @description Whether this Library has been deleted.
              */
-            variant: components["schemas"]["NotificationVariant"];
-        };
-        /** NotificationCreateRequest */
-        NotificationCreateRequest: {
+            deleted: boolean;
             /**
-             * Notification
-             * @description The notification to create. The structure depends on the category.
+             * Description
+             * @description A detailed description of the Library.
+             * @default
              */
-            notification: components["schemas"]["NotificationCreateData"];
+            description: string | null;
             /**
-             * Recipients
-             * @description The recipients of the notification. Can be a combination of users, groups and roles.
+             * ID
+             * @description Encoded ID of the Library.
+             * @example 0123456789ABCDEF
              */
-            recipients: components["schemas"]["NotificationRecipientsRequest"];
-        };
-        /** NotificationCreatedResponse */
-        NotificationCreatedResponse: {
+            id: string;
             /**
-             * Notification
-             * @description The notification that was created. The structure depends on the category.
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            notification: components["schemas"]["NotificationResponse"];
+            model_class: "Library";
             /**
-             * Total notifications sent
-             * @description The total number of notifications that were sent to the recipients.
+             * Name
+             * @description The name of the Library.
              */
-            total_notifications_sent: number;
-        };
-        /** NotificationRecipientsRequest */
-        NotificationRecipientsRequest: {
+            name: string;
             /**
-             * Group IDs
-             * @description The list of encoded group IDs of the groups that should receive the notification.
-             * @default []
+             * Public
+             * @description Whether this Library has been deleted.
              */
-            group_ids?: string[];
+            public: boolean;
             /**
-             * Role IDs
-             * @description The list of encoded role IDs of the roles that should receive the notification.
-             * @default []
+             * Root Folder ID
+             * @description Encoded ID of the Library's base folder.
+             * @example 0123456789ABCDEF
              */
-            role_ids?: string[];
+            root_folder_id: string;
             /**
-             * User IDs
-             * @description The list of encoded user IDs of the users that should receive the notification.
-             * @default []
+             * Description
+             * @description A short text describing the contents of the Library.
              */
-            user_ids?: string[];
+            synopsis?: string | null;
         };
         /**
-         * NotificationResponse
-         * @description Basic common fields for all notification responses.
+         * LibrarySummaryList
+         * @default []
          */
-        NotificationResponse: {
-            /**
-             * Category
-             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
-             */
-            category:
-                | components["schemas"]["MandatoryNotificationCategory"]
-                | components["schemas"]["PersonalNotificationCategory"];
+        LibrarySummaryList: components["schemas"]["LibrarySummary"][];
+        /** LicenseMetadataModel */
+        LicenseMetadataModel: {
             /**
-             * Content
-             * @description The content of the notification. The structure depends on the category.
+             * Details URL
+             * Format: uri
+             * @description URL to the SPDX json details for this license
              */
-            content:
-                | components["schemas"]["MessageNotificationContent"]
-                | components["schemas"]["NewSharedItemNotificationContent"]
-                | components["schemas"]["BroadcastNotificationContent"];
+            detailsUrl: string;
             /**
-             * Create time
-             * Format: date-time
-             * @description The time when the notification was created.
+             * Deprecated License
+             * @description True if the entire license is deprecated
              */
-            create_time: string;
+            isDeprecatedLicenseId: boolean;
             /**
-             * Expiration time
-             * @description The time when the notification will expire. If not set, the notification will never expire. Expired notifications will be permanently deleted.
+             * OSI approved
+             * @description Indicates if the [OSI](https://opensource.org/) has approved the license
              */
-            expiration_time?: string | null;
+            isOsiApproved: boolean;
             /**
-             * ID
-             * @description The encoded ID of the notification.
-             * @example 0123456789ABCDEF
+             * Identifier
+             * @description SPDX Identifier
              */
-            id: string;
+            licenseId: string;
             /**
-             * Publication time
-             * Format: date-time
-             * @description The time when the notification was published. Notifications can be created and then published at a later time.
+             * Name
+             * @description Full name of the license
              */
-            publication_time: string;
+            name: string;
             /**
-             * Source
-             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
+             * Recommended
+             * @description True if this license is recommended to be used
              */
-            source: string;
+            recommended: boolean;
             /**
-             * Update time
-             * Format: date-time
-             * @description The time when the notification was last updated.
+             * Reference
+             * @description Reference to the HTML format for the license file
              */
-            update_time: string;
+            reference: string;
             /**
-             * Variant
-             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
+             * Reference number
+             * @description *Deprecated* - this field is generated and is no longer in use
              */
-            variant: components["schemas"]["NotificationVariant"];
-        };
-        /**
-         * NotificationStatusSummary
-         * @description A summary of the notification status for a user. Contains only updates since a particular timestamp.
-         */
-        NotificationStatusSummary: {
+            referenceNumber: number;
             /**
-             * Broadcasts
-             * @description The list of updated broadcasts.
+             * Reference URLs
+             * @description Cross reference URL pointing to additional copies of the license
              */
-            broadcasts: components["schemas"]["BroadcastNotificationResponse"][];
+            seeAlso: string[];
             /**
-             * Notifications
-             * @description The list of updated notifications for the user.
+             * SPDX URL
+             * Format: uri
              */
-            notifications: components["schemas"]["UserNotificationResponse"][];
+            spdxUrl: string;
             /**
-             * Total unread count
-             * @description The total number of unread notifications for the user.
+             * URL
+             * Format: uri
+             * @description License URL
              */
-            total_unread_count: number;
+            url: string;
         };
         /**
-         * NotificationVariant
-         * @description The notification variant communicates the intent or relevance of the notification.
-         * @enum {string}
+         * LimitedUserModel
+         * @description This is used when config options (expose_user_name and expose_user_email) are in place.
          */
-        NotificationVariant: "info" | "warning" | "urgent";
-        /** NotificationsBatchRequest */
-        NotificationsBatchRequest: {
+        LimitedUserModel: {
+            /** Email */
+            email?: string | null;
             /**
-             * Notification IDs
-             * @description The list of encoded notification IDs of the notifications that should be updated.
+             * ID
+             * @description Encoded ID of the user
+             * @example 0123456789ABCDEF
              */
-            notification_ids: string[];
+            id: string;
+            /** Username */
+            username?: string | null;
+        };
+        /** Link */
+        Link: {
+            /** Name */
+            name: string;
         };
         /**
-         * NotificationsBatchUpdateResponse
-         * @description The response of a batch update request.
+         * LinkDataOnly
+         * @enum {string}
          */
-        NotificationsBatchUpdateResponse: {
-            /**
-             * Updated count
-             * @description The number of notifications that were updated.
-             */
-            updated_count: number;
-        };
-        /** ObjectExportTaskResponse */
-        ObjectExportTaskResponse: {
-            /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
-             */
-            create_time: string;
-            export_metadata?: components["schemas"]["ExportObjectMetadata"] | null;
+        LinkDataOnly: "copy_files" | "link_to_files";
+        /**
+         * ListJstreeResponse
+         * @deprecated
+         * @description List of files in Jstree format.
+         * @default []
+         */
+        ListJstreeResponse: unknown[];
+        /**
+         * ListUriResponse
+         * @description List of directories and files.
+         * @default []
+         */
+        ListUriResponse: (components["schemas"]["RemoteFile"] | components["schemas"]["RemoteDirectory"])[];
+        /**
+         * MandatoryNotificationCategory
+         * @description These notification categories cannot be opt-out by the user.
+         *
+         *     The user will always receive notifications from these categories.
+         * @constant
+         * @enum {string}
+         */
+        MandatoryNotificationCategory: "broadcast";
+        /** MaterializeDatasetInstanceAPIRequest */
+        MaterializeDatasetInstanceAPIRequest: {
             /**
-             * ID
-             * @description The encoded database ID of the export request.
+             * Content
+             * @description Depending on the `source` it can be:
+             *     - The encoded id of the source library dataset
+             *     - The encoded id of the HDA
+             *
              * @example 0123456789ABCDEF
              */
-            id: string;
+            content: string;
             /**
-             * Preparing
-             * @description Whether the archive is currently being built or in preparation.
+             * Source
+             * @description The source of the content. Can be other history element to be copied or library elements.
              */
-            preparing: boolean;
+            source: components["schemas"]["DatasetSourceType"];
+        };
+        /** MessageExceptionModel */
+        MessageExceptionModel: {
+            /** Err Code */
+            err_code: number;
+            /** Err Msg */
+            err_msg: string;
+        };
+        /** MessageNotificationContent */
+        MessageNotificationContent: {
             /**
-             * Ready
-             * @description Whether the export has completed successfully and the archive is ready
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            ready: boolean;
+            category: "message";
             /**
-             * Task ID
-             * Format: uuid4
-             * @description The identifier of the task processing the export.
+             * Message
+             * @description The message of the notification (supports Markdown).
              */
-            task_uuid: string;
+            message: string;
             /**
-             * Up to Date
-             * @description False, if a new export archive should be generated.
+             * Subject
+             * @description The subject of the notification.
              */
-            up_to_date: boolean;
+            subject: string;
         };
-        /** ObjectStoreTemplateSummaries */
-        ObjectStoreTemplateSummaries: components["schemas"]["ObjectStoreTemplateSummary"][];
-        /** ObjectStoreTemplateSummary */
-        ObjectStoreTemplateSummary: {
-            /** Badges */
-            badges: components["schemas"]["BadgeDict"][];
-            /** Description */
-            description: string | null;
-            /**
-             * Hidden
-             * @default false
-             */
-            hidden?: boolean;
-            /** Id */
-            id: string;
-            /** Name */
-            name: string | null;
-            /** Secrets */
-            secrets?: components["schemas"]["TemplateSecret"][] | null;
+        /**
+         * MetadataFile
+         * @description Metadata file associated with a dataset.
+         */
+        MetadataFile: {
             /**
-             * Type
-             * @enum {string}
+             * Download URL
+             * @description The URL to download this item from the server.
              */
-            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
-            /** Variables */
-            variables?:
-                | (
-                      | components["schemas"]["TemplateVariableString"]
-                      | components["schemas"]["TemplateVariableInteger"]
-                      | components["schemas"]["TemplateVariablePathComponent"]
-                      | components["schemas"]["TemplateVariableBoolean"]
-                  )[]
-                | null;
+            download_url: string;
             /**
-             * Version
-             * @default 0
+             * File Type
+             * @description TODO
              */
-            version?: number;
+            file_type: string;
         };
-        /** OutputReferenceByLabel */
-        OutputReferenceByLabel: {
+        /** Metric */
+        Metric: {
             /**
-             * Label
-             * @description The unique label of the step being referenced.
+             * Arguments
+             * @description A JSON string containing an array of extra data.
              */
-            label: string;
+            args: string;
             /**
-             * Output Name
-             * @description The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.
-             * @default output
+             * Level
+             * @description An integer representing the metric's log level.
              */
-            output_name?: string | null;
-        };
-        /** OutputReferenceByOrderIndex */
-        OutputReferenceByOrderIndex: {
+            level: number;
             /**
-             * Order Index
-             * @description The order_index of the step being referenced. The order indices of a workflow start at 0.
+             * Namespace
+             * @description Label indicating the source of the metric.
              */
-            order_index: number;
+            namespace: string;
             /**
-             * Output Name
-             * @description The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.
-             * @default output
+             * Timestamp
+             * @description The timestamp in ISO format.
              */
-            output_name?: string | null;
+            time: string;
         };
         /**
-         * PageContentFormat
+         * ModelStoreFormat
+         * @description Available types of model stores for export.
          * @enum {string}
          */
-        PageContentFormat: "markdown" | "html";
-        /** PageDetails */
-        PageDetails: {
+        ModelStoreFormat: "tgz" | "tar" | "tar.gz" | "bag.zip" | "bag.tar" | "bag.tgz" | "rocrate.zip" | "bco.json";
+        /** NestedElement */
+        NestedElement: {
+            /** Md5 */
+            MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
-             * Content
-             * @description Raw text contents of the last page revision (type dependent on content_format).
-             * @default
+             * Auto Decompress
+             * @description Decompress compressed data before sniffing?
+             * @default false
              */
-            content?: string | null;
+            auto_decompress: boolean;
+            /** Collection Type */
+            collection_type?: string | null;
+            /** Created From Basename */
+            created_from_basename?: string | null;
             /**
-             * Content format
-             * @description Either `markdown` or `html`.
-             * @default html
+             * Dbkey
+             * @default ?
              */
-            content_format?: components["schemas"]["PageContentFormat"];
+            dbkey: string;
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Deferred
+             * @default false
              */
-            create_time: string;
+            deferred: boolean;
+            /** Description */
+            description?: string | null;
+            /** Elements */
+            elements: (
+                | (
+                      | components["schemas"]["FileDataElement"]
+                      | components["schemas"]["PastedDataElement"]
+                      | components["schemas"]["UrlDataElement"]
+                      | components["schemas"]["PathDataElement"]
+                      | components["schemas"]["ServerDirElement"]
+                      | components["schemas"]["FtpImportElement"]
+                      | components["schemas"]["CompositeDataElement"]
+                  )
+                | components["schemas"]["NestedElement"]
+            )[];
+            elements_from?: components["schemas"]["ElementsFromType"] | null;
             /**
-             * Deleted
-             * @description Whether this Page has been deleted.
+             * Ext
+             * @default auto
              */
-            deleted: boolean;
+            ext: string;
+            extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
+            /** Info */
+            info?: string | null;
+            /** Name */
+            name?: string | number | boolean | null;
             /**
-             * Encoded email
-             * @description The encoded email of the user.
+             * Space To Tab
+             * @default false
              */
-            email_hash: string;
+            space_to_tab: boolean;
+            /** Tags */
+            tags?: string[] | null;
             /**
-             * Galaxy Version
-             * @description The version of Galaxy this object was generated with.
+             * To Posix Lines
+             * @default false
              */
-            generate_time?: string | null;
+            to_posix_lines: boolean;
+        };
+        /** NewSharedItemNotificationContent */
+        NewSharedItemNotificationContent: {
             /**
-             * Galaxy Version
-             * @description The version of Galaxy this object was generated with.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            generate_version?: string | null;
+            category: "new_shared_item";
             /**
-             * ID
-             * @description Encoded ID of the Page.
-             * @example 0123456789ABCDEF
+             * Item name
+             * @description The name of the shared item.
              */
-            id: string;
+            item_name: string;
             /**
-             * Importable
-             * @description Whether this Page can be imported.
+             * Item type
+             * @description The type of the shared item.
+             * @enum {string}
              */
-            importable: boolean;
+            item_type: "history" | "workflow" | "visualization" | "page";
             /**
-             * Latest revision ID
-             * @description The encoded ID of the last revision of this Page.
-             * @example 0123456789ABCDEF
+             * Owner name
+             * @description The name of the owner of the shared item.
              */
-            latest_revision_id: string;
+            owner_name: string;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Slug
+             * @description The slug of the shared item. Used for the link to the item.
              */
-            model_class: "Page";
+            slug: string;
+        };
+        /**
+         * NotificationBroadcastUpdateRequest
+         * @description A notification update request specific for broadcasting.
+         */
+        NotificationBroadcastUpdateRequest: {
             /**
-             * Published
-             * @description Whether this Page has been published.
+             * Content
+             * @description The content of the broadcast notification. Broadcast notifications are displayed prominently to all users and can contain action links to redirect the user to a specific page.
              */
-            published: boolean;
+            content?: components["schemas"]["BroadcastNotificationContent"] | null;
             /**
-             * List of revisions
-             * @description The history with the encoded ID of each revision of the Page.
+             * Expiration time
+             * @description The time when the notification should expire. By default it will expire after 6 months. Expired notifications will be permanently deleted.
              */
-            revision_ids: string[];
+            expiration_time?: string | null;
             /**
-             * Identifier
-             * @description The title slug for the page URL, must be unique.
+             * Publication time
+             * @description The time when the notification should be published. Notifications can be created and then scheduled to be published at a later time.
              */
-            slug: string;
-            tags: components["schemas"]["TagCollection"];
+            publication_time?: string | null;
             /**
-             * Title
-             * @description The name of the page.
+             * Source
+             * @description The source of the notification. Represents the agent that created the notification.
              */
-            title: string;
+            source?: string | null;
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Variant
+             * @description The variant of the notification. Used to express the importance of the notification.
              */
-            update_time: string;
+            variant?: components["schemas"]["NotificationVariant"] | null;
+        };
+        /**
+         * NotificationCategorySettings
+         * @description The settings for a notification category.
+         */
+        NotificationCategorySettings: {
             /**
-             * Username
-             * @description The name of the user owning this Page.
+             * Channels
+             * @description The channels that the user wants to receive notifications from for this category.
+             * @default {
+             *       "email": true,
+             *       "push": true
+             *     }
              */
-            username: string;
-            [key: string]: unknown | undefined;
+            channels: components["schemas"]["NotificationChannelSettings"];
+            /**
+             * Enabled
+             * @description Whether the user wants to receive notifications for this category.
+             * @default true
+             */
+            enabled: boolean;
         };
-        /** PageSummary */
-        PageSummary: {
+        /**
+         * NotificationChannelSettings
+         * @description The settings for each channel of a notification category.
+         */
+        NotificationChannelSettings: {
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Email
+             * @description Whether the user wants to receive email notifications for this category. This setting will be ignored unless the server supports asynchronous tasks.
+             * @default true
              */
-            create_time: string;
+            email: boolean;
             /**
-             * Deleted
-             * @description Whether this Page has been deleted.
+             * Push
+             * @description Whether the user wants to receive push notifications in the browser for this category.
+             * @default true
              */
-            deleted: boolean;
+            push: boolean;
+        };
+        /**
+         * NotificationCreateData
+         * @description Basic common fields for all notification create requests.
+         */
+        NotificationCreateData: {
             /**
-             * Encoded email
-             * @description The encoded email of the user.
+             * Category
+             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
              */
-            email_hash: string;
+            category:
+                | components["schemas"]["MandatoryNotificationCategory"]
+                | components["schemas"]["PersonalNotificationCategory"];
             /**
-             * ID
-             * @description Encoded ID of the Page.
-             * @example 0123456789ABCDEF
+             * Content
+             * @description The content of the notification. The structure depends on the category.
              */
-            id: string;
+            content:
+                | components["schemas"]["MessageNotificationContent"]
+                | components["schemas"]["NewSharedItemNotificationContent"]
+                | components["schemas"]["BroadcastNotificationContent"];
             /**
-             * Importable
-             * @description Whether this Page can be imported.
+             * Expiration time
+             * @description The time when the notification should expire. By default it will expire after 6 months. Expired notifications will be permanently deleted.
              */
-            importable: boolean;
+            expiration_time?: string | null;
             /**
-             * Latest revision ID
-             * @description The encoded ID of the last revision of this Page.
-             * @example 0123456789ABCDEF
+             * Publication time
+             * @description The time when the notification should be published. Notifications can be created and then scheduled to be published at a later time.
              */
-            latest_revision_id: string;
+            publication_time?: string | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Source
+             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
              */
-            model_class: "Page";
+            source: string;
             /**
-             * Published
-             * @description Whether this Page has been published.
+             * Variant
+             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
              */
-            published: boolean;
+            variant: components["schemas"]["NotificationVariant"];
+        };
+        /** NotificationCreateRequest */
+        NotificationCreateRequest: {
             /**
-             * List of revisions
-             * @description The history with the encoded ID of each revision of the Page.
+             * Notification
+             * @description The notification to create. The structure depends on the category.
              */
-            revision_ids: string[];
+            notification: components["schemas"]["NotificationCreateData"];
             /**
-             * Identifier
-             * @description The title slug for the page URL, must be unique.
+             * Recipients
+             * @description The recipients of the notification. Can be a combination of users, groups and roles.
              */
-            slug: string;
-            tags: components["schemas"]["TagCollection"];
+            recipients: components["schemas"]["NotificationRecipientsRequest"];
+        };
+        /** NotificationCreatedResponse */
+        NotificationCreatedResponse: {
             /**
-             * Title
-             * @description The name of the page.
+             * Notification
+             * @description The notification that was created. The structure depends on the category.
              */
-            title: string;
+            notification: components["schemas"]["NotificationResponse"];
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Total notifications sent
+             * @description The total number of notifications that were sent to the recipients.
              */
-            update_time: string;
+            total_notifications_sent: number;
+        };
+        /** NotificationRecipientsRequest */
+        NotificationRecipientsRequest: {
             /**
-             * Username
-             * @description The name of the user owning this Page.
+             * Group IDs
+             * @description The list of encoded group IDs of the groups that should receive the notification.
+             * @default []
              */
-            username: string;
+            group_ids: string[];
+            /**
+             * Role IDs
+             * @description The list of encoded role IDs of the roles that should receive the notification.
+             * @default []
+             */
+            role_ids: string[];
+            /**
+             * User IDs
+             * @description The list of encoded user IDs of the users that should receive the notification.
+             * @default []
+             */
+            user_ids: string[];
         };
         /**
-         * PageSummaryList
-         * @default []
+         * NotificationResponse
+         * @description Basic common fields for all notification responses.
          */
-        PageSummaryList: components["schemas"]["PageSummary"][];
-        /** PastedDataElement */
-        PastedDataElement: {
-            /** Md5 */
-            MD5?: string | null;
+        NotificationResponse: {
             /**
-             * Auto Decompress
-             * @description Decompress compressed data before sniffing?
-             * @default false
+             * Category
+             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
              */
-            auto_decompress?: boolean;
-            /** Collection Type */
-            collection_type?: string | null;
-            /** Created From Basename */
-            created_from_basename?: string | null;
+            category:
+                | components["schemas"]["MandatoryNotificationCategory"]
+                | components["schemas"]["PersonalNotificationCategory"];
             /**
-             * Dbkey
-             * @default ?
+             * Content
+             * @description The content of the notification. The structure depends on the category.
              */
-            dbkey?: string;
+            content:
+                | components["schemas"]["MessageNotificationContent"]
+                | components["schemas"]["NewSharedItemNotificationContent"]
+                | components["schemas"]["BroadcastNotificationContent"];
             /**
-             * Deferred
-             * @default false
+             * Create time
+             * Format: date-time
+             * @description The time when the notification was created.
              */
-            deferred?: boolean;
-            /** Description */
-            description?: string | null;
-            elements_from?: components["schemas"]["ElementsFromType"] | null;
+            create_time: string;
             /**
-             * Ext
-             * @default auto
+             * Expiration time
+             * @description The time when the notification will expire. If not set, the notification will never expire. Expired notifications will be permanently deleted.
              */
-            ext?: string;
-            extra_files?: components["schemas"]["ExtraFiles"] | null;
-            /** Info */
-            info?: string | null;
-            /** Name */
-            name?: string | number | number | boolean | null;
+            expiration_time?: string | null;
             /**
-             * Paste Content
-             * @description Content to upload
+             * ID
+             * @description The encoded ID of the notification.
+             * @example 0123456789ABCDEF
              */
-            paste_content: string | number | number | boolean;
+            id: string;
             /**
-             * Space To Tab
-             * @default false
+             * Publication time
+             * Format: date-time
+             * @description The time when the notification was published. Notifications can be created and then published at a later time.
              */
-            space_to_tab?: boolean;
+            publication_time: string;
             /**
-             * Src
-             * @constant
-             * @enum {string}
-             */
-            src: "pasted";
-            /** Tags */
-            tags?: string[] | null;
-            /**
-             * To Posix Lines
-             * @default false
+             * Source
+             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
              */
-            to_posix_lines?: boolean;
-        };
-        /** PathDataElement */
-        PathDataElement: {
-            /** Md5 */
-            MD5?: string | null;
+            source: string;
             /**
-             * Auto Decompress
-             * @description Decompress compressed data before sniffing?
-             * @default false
+             * Update time
+             * Format: date-time
+             * @description The time when the notification was last updated.
              */
-            auto_decompress?: boolean;
-            /** Collection Type */
-            collection_type?: string | null;
-            /** Created From Basename */
-            created_from_basename?: string | null;
+            update_time: string;
             /**
-             * Dbkey
-             * @default ?
+             * Variant
+             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
              */
-            dbkey?: string;
+            variant: components["schemas"]["NotificationVariant"];
+        };
+        /**
+         * NotificationStatusSummary
+         * @description A summary of the notification status for a user. Contains only updates since a particular timestamp.
+         */
+        NotificationStatusSummary: {
             /**
-             * Deferred
-             * @default false
+             * Broadcasts
+             * @description The list of updated broadcasts.
              */
-            deferred?: boolean;
-            /** Description */
-            description?: string | null;
-            elements_from?: components["schemas"]["ElementsFromType"] | null;
+            broadcasts: components["schemas"]["BroadcastNotificationResponse"][];
             /**
-             * Ext
-             * @default auto
+             * Notifications
+             * @description The list of updated notifications for the user.
              */
-            ext?: string;
-            extra_files?: components["schemas"]["ExtraFiles"] | null;
-            /** Info */
-            info?: string | null;
-            /** Link Data Only */
-            link_data_only?: boolean | null;
-            /** Name */
-            name?: string | number | number | boolean | null;
-            /** Path */
-            path: string;
+            notifications: components["schemas"]["UserNotificationResponse"][];
             /**
-             * Space To Tab
-             * @default false
+             * Total unread count
+             * @description The total number of unread notifications for the user.
              */
-            space_to_tab?: boolean;
+            total_unread_count: number;
+        };
+        /**
+         * NotificationVariant
+         * @description The notification variant communicates the intent or relevance of the notification.
+         * @enum {string}
+         */
+        NotificationVariant: "info" | "warning" | "urgent";
+        /** NotificationsBatchRequest */
+        NotificationsBatchRequest: {
             /**
-             * Src
-             * @constant
-             * @enum {string}
+             * Notification IDs
+             * @description The list of encoded notification IDs of the notifications that should be updated.
              */
-            src: "path";
-            /** Tags */
-            tags?: string[] | null;
+            notification_ids: string[];
+        };
+        /**
+         * NotificationsBatchUpdateResponse
+         * @description The response of a batch update request.
+         */
+        NotificationsBatchUpdateResponse: {
             /**
-             * To Posix Lines
-             * @default false
+             * Updated count
+             * @description The number of notifications that were updated.
              */
-            to_posix_lines?: boolean;
+            updated_count: number;
         };
-        /** PauseStep */
-        PauseStep: {
+        /** OAuth2Info */
+        OAuth2Info: {
+            /** Authorize Url */
+            authorize_url: string;
+        };
+        /** ObjectExportTaskResponse */
+        ObjectExportTaskResponse: {
             /**
-             * Annotation
-             * @description An annotation to provide details or to help understand the purpose and usage of this item.
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            annotation: string | null;
+            create_time: string;
+            export_metadata?: components["schemas"]["ExportObjectMetadata"] | null;
             /**
              * ID
-             * @description The identifier of the step. It matches the index order of the step inside the workflow.
+             * @description The encoded database ID of the export request.
+             * @example 0123456789ABCDEF
              */
-            id: number;
+            id: string;
             /**
-             * Input Steps
-             * @description A dictionary containing information about the inputs connected to this workflow step.
+             * Preparing
+             * @description Whether the archive is currently being built or in preparation.
              */
-            input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
-            };
+            preparing: boolean;
             /**
-             * Tool ID
-             * @description The unique name of the tool associated with this step.
+             * Ready
+             * @description Whether the export has completed successfully and the archive is ready
              */
-            tool_id?: string | null;
+            ready: boolean;
             /**
-             * Tool Inputs
-             * @description TODO
+             * Task ID
+             * Format: uuid4
+             * @description The identifier of the task processing the export.
              */
-            tool_inputs?: Record<string, never>;
+            task_uuid: string;
             /**
-             * Tool Version
-             * @description The version of the tool associated with this step.
+             * Up to Date
+             * @description False, if a new export archive should be generated.
              */
-            tool_version?: string | null;
+            up_to_date: boolean;
+        };
+        /** ObjectStoreTemplateSummaries */
+        ObjectStoreTemplateSummaries: components["schemas"]["ObjectStoreTemplateSummary"][];
+        /** ObjectStoreTemplateSummary */
+        ObjectStoreTemplateSummary: {
+            /** Badges */
+            badges: components["schemas"]["BadgeDict"][];
+            /** Description */
+            description: string | null;
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean;
+            /** Id */
+            id: string;
+            /** Name */
+            name: string | null;
+            /** Secrets */
+            secrets?: components["schemas"]["TemplateSecret"][] | null;
             /**
              * Type
-             * @constant
              * @enum {string}
              */
-            type: "pause";
-            /** When */
-            when: string | null;
-        };
-        /** Person */
-        Person: {
-            /** Address */
-            address?: string | null;
-            /** Alternate Name */
-            alternateName?: string | null;
+            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3" | "onedata";
+            /** Variables */
+            variables?:
+                | (
+                      | components["schemas"]["TemplateVariableString"]
+                      | components["schemas"]["TemplateVariableInteger"]
+                      | components["schemas"]["TemplateVariablePathComponent"]
+                      | components["schemas"]["TemplateVariableBoolean"]
+                  )[]
+                | null;
             /**
-             * Class
-             * @default Person
+             * Version
+             * @default 0
              */
-            class?: string;
-            /** Email */
-            email?: string | null;
-            /** Family Name */
-            familyName?: string | null;
-            /** Fax Number */
-            faxNumber?: string | null;
-            /** Given Name */
-            givenName?: string | null;
+            version: number;
+        };
+        /** OutputReferenceByLabel */
+        OutputReferenceByLabel: {
             /**
-             * Honorific Prefix
-             * @description Honorific Prefix (e.g. Dr/Mrs/Mr)
+             * Label
+             * @description The unique label of the step being referenced.
              */
-            honorificPrefix?: string | null;
+            label: string;
             /**
-             * Honorific Suffix
-             * @description Honorific Suffix (e.g. M.D.)
+             * Output Name
+             * @description The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.
+             * @default output
              */
-            honorificSuffix?: string | null;
+            output_name: string | null;
+        };
+        /** OutputReferenceByOrderIndex */
+        OutputReferenceByOrderIndex: {
             /**
-             * Identifier
-             * @description Identifier (typically an orcid.org ID)
+             * Order Index
+             * @description The order_index of the step being referenced. The order indices of a workflow start at 0.
              */
-            identifier?: string | null;
-            /** Image URL */
-            image?: string | null;
-            /** Job Title */
-            jobTitle?: string | null;
+            order_index: number;
             /**
-             * Name
-             * @description The name of the creator.
+             * Output Name
+             * @description The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.
+             * @default output
              */
-            name?: string | null;
-            /** Telephone */
-            telephone?: string | null;
-            /** URL */
-            url?: string | null;
+            output_name: string | null;
         };
         /**
-         * PersonalNotificationCategory
-         * @description These notification categories can be opt-out by the user and will be
-         * displayed in the notification preferences.
+         * PageContentFormat
          * @enum {string}
          */
-        PersonalNotificationCategory: "message" | "new_shared_item";
-        /** PluginAspectStatus */
-        PluginAspectStatus: {
-            /** Message */
-            message: string;
+        PageContentFormat: "markdown" | "html";
+        /** PageDetails */
+        PageDetails: {
             /**
-             * State
-             * @enum {string}
+             * Content
+             * @description Raw text contents of the last page revision (type dependent on content_format).
+             * @default
              */
-            state: "ok" | "not_ok" | "unknown";
-        };
-        /**
-         * PluginKind
-         * @description Enum to distinguish between different kinds or categories of plugins.
-         * @enum {string}
-         */
-        PluginKind: "rfs" | "drs" | "rdm" | "stock";
-        /** PluginStatus */
-        PluginStatus: {
-            connection?: components["schemas"]["PluginAspectStatus"] | null;
-            template_definition: components["schemas"]["PluginAspectStatus"];
-            template_settings?: components["schemas"]["PluginAspectStatus"] | null;
-        };
-        /** Position */
-        Position: {
-            /** Left */
-            left: number;
-            /** Top */
-            top: number;
-        };
-        /** PrepareStoreDownloadPayload */
-        PrepareStoreDownloadPayload: {
-            /**
-             * Bco Merge History Metadata
-             * @description When reading tags/annotations to generate BCO object include history metadata.
-             * @default false
-             */
-            bco_merge_history_metadata?: boolean;
+            content: string | null;
             /**
-             * Bco Override Algorithmic Error
-             * @description Override algorithmic error for 'error domain' when generating BioCompute object.
+             * Content format
+             * @description Either `markdown` or `html`.
+             * @default html
              */
-            bco_override_algorithmic_error?: {
-                [key: string]: string | undefined;
-            } | null;
+            content_format: components["schemas"]["PageContentFormat"];
             /**
-             * Bco Override Empirical Error
-             * @description Override empirical error for 'error domain' when generating BioCompute object.
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            bco_override_empirical_error?: {
-                [key: string]: string | undefined;
-            } | null;
+            create_time: string;
             /**
-             * Bco Override Environment Variables
-             * @description Override environment variables for 'execution_domain' when generating BioCompute object.
+             * Deleted
+             * @description Whether this Page has been deleted.
              */
-            bco_override_environment_variables?: {
-                [key: string]: string | undefined;
-            } | null;
+            deleted: boolean;
             /**
-             * Bco Override Xref
-             * @description Override xref for 'description domain' when generating BioCompute object.
+             * Encoded email
+             * @description The encoded email of the user.
              */
-            bco_override_xref?: components["schemas"]["XrefItem"][] | null;
+            email_hash: string;
             /**
-             * Include deleted
-             * @description Include file contents for deleted datasets (if include_files is True).
-             * @default false
+             * Galaxy Version
+             * @description The version of Galaxy this object was generated with.
              */
-            include_deleted?: boolean;
+            generate_time?: string | null;
             /**
-             * Include Files
-             * @description include materialized files in export when available
-             * @default true
+             * Galaxy Version
+             * @description The version of Galaxy this object was generated with.
              */
-            include_files?: boolean;
+            generate_version?: string | null;
             /**
-             * Include hidden
-             * @description Include file contents for hidden datasets (if include_files is True).
-             * @default false
+             * ID
+             * @description Encoded ID of the Page.
+             * @example 0123456789ABCDEF
              */
-            include_hidden?: boolean;
+            id: string;
             /**
-             * @description format of model store to export
-             * @default tar.gz
+             * Importable
+             * @description Whether this Page can be imported.
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
-        };
-        /** QuotaDetails */
-        QuotaDetails: {
+            importable: boolean;
             /**
-             * Bytes
-             * @description The amount, expressed in bytes, of this Quota.
+             * Latest revision ID
+             * @description The encoded ID of the last revision of this Page.
+             * @example 0123456789ABCDEF
              */
-            bytes: number;
+            latest_revision_id: string;
             /**
-             * Default
-             * @description A list indicating which types of default user quotas, if any, are associated with this quota.
-             * @default []
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            default?: components["schemas"]["DefaultQuota"][];
+            model_class: "Page";
             /**
-             * Description
-             * @description Detailed text description for this Quota.
+             * Published
+             * @description Whether this Page has been published.
              */
-            description: string;
+            published: boolean;
             /**
-             * Display Amount
-             * @description Human-readable representation of the `amount` field.
+             * List of revisions
+             * @description The history with the encoded ID of each revision of the Page.
              */
-            display_amount: string;
+            revision_ids: string[];
             /**
-             * Groups
-             * @description A list of specific groups of users associated with this quota.
-             * @default []
+             * Identifier
+             * @description The title slug for the page URL, must be unique.
              */
-            groups?: components["schemas"]["GroupQuota"][];
+            slug: string;
+            tags: components["schemas"]["TagCollection"];
             /**
-             * ID
-             * @description The `encoded identifier` of the quota.
-             * @example 0123456789ABCDEF
+             * Title
+             * @description The name of the page.
              */
-            id: string;
+            title: string;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
              */
-            model_class: "Quota";
+            update_time: string;
             /**
-             * Name
-             * @description The name of the quota. This must be unique within a Galaxy instance.
+             * Username
+             * @description The name of the user owning this Page.
              */
-            name: string;
+            username: string;
+        } & {
+            [key: string]: unknown;
+        };
+        /** PageSummary */
+        PageSummary: {
             /**
-             * Operation
-             * @description Quotas can have one of three `operations`:- `=` : The quota is exactly the amount specified- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions
-             * @default =
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            operation?: components["schemas"]["QuotaOperation"];
+            create_time: string;
             /**
-             * Quota Source Label
-             * @description Quota source label
+             * Deleted
+             * @description Whether this Page has been deleted.
              */
-            quota_source_label?: string | null;
+            deleted: boolean;
             /**
-             * Users
-             * @description A list of specific users associated with this quota.
-             * @default []
+             * Encoded email
+             * @description The encoded email of the user.
              */
-            users?: components["schemas"]["UserQuota"][];
-        };
-        /** QuotaModel */
-        QuotaModel: {
-            /** Enabled */
-            enabled: boolean;
-            /** Source */
-            source?: string | null;
-        };
-        /**
-         * QuotaOperation
-         * @enum {string}
-         */
-        QuotaOperation: "=" | "+" | "-";
-        /**
-         * QuotaSummary
-         * @description Contains basic information about a Quota
-         */
-        QuotaSummary: {
+            email_hash: string;
             /**
              * ID
-             * @description The `encoded identifier` of the quota.
+             * @description Encoded ID of the Page.
              * @example 0123456789ABCDEF
              */
             id: string;
+            /**
+             * Importable
+             * @description Whether this Page can be imported.
+             */
+            importable: boolean;
+            /**
+             * Latest revision ID
+             * @description The encoded ID of the last revision of this Page.
+             * @example 0123456789ABCDEF
+             */
+            latest_revision_id: string;
             /**
              * Model class
              * @description The name of the database model class.
              * @constant
              * @enum {string}
              */
-            model_class: "Quota";
+            model_class: "Page";
             /**
-             * Name
-             * @description The name of the quota. This must be unique within a Galaxy instance.
+             * Published
+             * @description Whether this Page has been published.
              */
-            name: string;
+            published: boolean;
             /**
-             * Quota Source Label
-             * @description Quota source label
+             * List of revisions
+             * @description The history with the encoded ID of each revision of the Page.
              */
-            quota_source_label?: string | null;
+            revision_ids: string[];
             /**
-             * URL
-             * @deprecated
-             * @description The relative URL to get this particular Quota details from the rest API.
+             * Identifier
+             * @description The title slug for the page URL, must be unique.
              */
-            url: string;
-        };
-        /**
-         * QuotaSummaryList
-         * @default []
-         */
-        QuotaSummaryList: components["schemas"]["QuotaSummary"][];
-        /** RefactorActionExecution */
-        RefactorActionExecution: {
-            /** Action */
-            action:
-                | components["schemas"]["AddInputAction"]
-                | components["schemas"]["AddStepAction"]
-                | components["schemas"]["ConnectAction"]
-                | components["schemas"]["DisconnectAction"]
-                | components["schemas"]["ExtractInputAction"]
-                | components["schemas"]["ExtractUntypedParameter"]
-                | components["schemas"]["FileDefaultsAction"]
-                | components["schemas"]["FillStepDefaultsAction"]
-                | components["schemas"]["UpdateAnnotationAction"]
-                | components["schemas"]["UpdateCreatorAction"]
-                | components["schemas"]["UpdateNameAction"]
-                | components["schemas"]["UpdateLicenseAction"]
-                | components["schemas"]["UpdateOutputLabelAction"]
-                | components["schemas"]["UpdateReportAction"]
-                | components["schemas"]["UpdateStepLabelAction"]
-                | components["schemas"]["UpdateStepPositionAction"]
-                | components["schemas"]["UpgradeSubworkflowAction"]
-                | components["schemas"]["UpgradeToolAction"]
-                | components["schemas"]["UpgradeAllStepsAction"]
-                | components["schemas"]["RemoveUnlabeledWorkflowOutputs"];
-            /** Messages */
-            messages: components["schemas"]["RefactorActionExecutionMessage"][];
-        };
-        /** RefactorActionExecutionMessage */
-        RefactorActionExecutionMessage: {
+            slug: string;
+            tags: components["schemas"]["TagCollection"];
             /**
-             * From Order Index
-             * @description For dropped connections these optional attributes refer to the output
-             * side of the connection that was dropped.
+             * Title
+             * @description The name of the page.
              */
-            from_order_index?: number | null;
+            title: string;
             /**
-             * From Step Label
-             * @description For dropped connections these optional attributes refer to the output
-             * side of the connection that was dropped.
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
              */
-            from_step_label?: string | null;
+            update_time: string;
             /**
-             * Input Name
-             * @description If this message is about an input to a step,
-             * this field describes the target input name. $The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input').
+             * Username
+             * @description The name of the user owning this Page.
              */
-            input_name?: string | null;
-            /** Message */
-            message: string;
-            message_type: components["schemas"]["RefactorActionExecutionMessageTypeEnum"];
+            username: string;
+        };
+        /**
+         * PageSummaryList
+         * @default []
+         */
+        PageSummaryList: components["schemas"]["PageSummary"][];
+        /** PastedDataElement */
+        PastedDataElement: {
+            /** Md5 */
+            MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
-             * Order Index
-             * @description Reference to the step the message refers to. $
-             *
-             * Messages don't have to be bound to a step, but if they are they will
-             * have a step_label and order_index included in the execution message.
-             * These are the label and order_index before applying the refactoring,
-             * the result of applying the action may change one or both of these.
-             * If connections are dropped this step reference will refer to the
-             * step with the previously connected input.
+             * Auto Decompress
+             * @description Decompress compressed data before sniffing?
+             * @default false
              */
-            order_index?: number | null;
+            auto_decompress: boolean;
+            /** Collection Type */
+            collection_type?: string | null;
+            /** Created From Basename */
+            created_from_basename?: string | null;
             /**
-             * Output Label
-             * @description If the message_type is workflow_output_drop_forced, this is the output label dropped.
+             * Dbkey
+             * @default ?
              */
-            output_label?: string | null;
+            dbkey: string;
             /**
-             * Output Name
-             * @description If this message is about an output to a step,
-             * this field describes the target output name. The output name as defined by the workflow module corresponding to the step being referenced.
+             * Deferred
+             * @default false
              */
-            output_name?: string | null;
+            deferred: boolean;
+            /** Description */
+            description?: string | null;
+            elements_from?: components["schemas"]["ElementsFromType"] | null;
             /**
-             * Step Label
-             * @description Reference to the step the message refers to. $
-             *
-             * Messages don't have to be bound to a step, but if they are they will
-             * have a step_label and order_index included in the execution message.
-             * These are the label and order_index before applying the refactoring,
-             * the result of applying the action may change one or both of these.
-             * If connections are dropped this step reference will refer to the
-             * step with the previously connected input.
+             * Ext
+             * @default auto
              */
-            step_label?: string | null;
-        };
-        /**
-         * RefactorActionExecutionMessageTypeEnum
-         * @enum {string}
-         */
-        RefactorActionExecutionMessageTypeEnum:
-            | "tool_version_change"
-            | "tool_state_adjustment"
-            | "connection_drop_forced"
-            | "workflow_output_drop_forced";
-        /** RefactorRequest */
-        RefactorRequest: {
-            /** Actions */
-            actions: (
-                | components["schemas"]["AddInputAction"]
-                | components["schemas"]["AddStepAction"]
-                | components["schemas"]["ConnectAction"]
-                | components["schemas"]["DisconnectAction"]
-                | components["schemas"]["ExtractInputAction"]
-                | components["schemas"]["ExtractUntypedParameter"]
-                | components["schemas"]["FileDefaultsAction"]
-                | components["schemas"]["FillStepDefaultsAction"]
-                | components["schemas"]["UpdateAnnotationAction"]
-                | components["schemas"]["UpdateCreatorAction"]
-                | components["schemas"]["UpdateNameAction"]
-                | components["schemas"]["UpdateLicenseAction"]
-                | components["schemas"]["UpdateOutputLabelAction"]
-                | components["schemas"]["UpdateReportAction"]
-                | components["schemas"]["UpdateStepLabelAction"]
-                | components["schemas"]["UpdateStepPositionAction"]
-                | components["schemas"]["UpgradeSubworkflowAction"]
-                | components["schemas"]["UpgradeToolAction"]
-                | components["schemas"]["UpgradeAllStepsAction"]
-                | components["schemas"]["RemoveUnlabeledWorkflowOutputs"]
-            )[];
+            ext: string;
+            extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
+            /** Info */
+            info?: string | null;
+            /** Name */
+            name?: string | number | boolean | null;
             /**
-             * Dry Run
-             * @default false
+             * Paste Content
+             * @description Content to upload
              */
-            dry_run?: boolean;
+            paste_content: string | number | boolean;
             /**
-             * Style
-             * @default export
+             * Space To Tab
+             * @default false
              */
-            style?: string;
-        };
-        /** RefactorResponse */
-        RefactorResponse: {
-            /** Action Executions */
-            action_executions: components["schemas"]["RefactorActionExecution"][];
-            /** Dry Run */
-            dry_run: boolean;
-            /** Workflow */
-            workflow: string;
-        };
-        /** ReloadFeedback */
-        ReloadFeedback: {
-            /** Failed */
-            failed: (string | null)[];
-            /** Message */
-            message: string;
-            /** Reloaded */
-            reloaded: (string | null)[];
-        };
-        /** RemoteDirectory */
-        RemoteDirectory: {
+            space_to_tab: boolean;
             /**
-             * Class
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
-            class: "Directory";
+            src: "pasted";
+            /** Tags */
+            tags?: string[] | null;
             /**
-             * Name
-             * @description The name of the entry.
+             * To Posix Lines
+             * @default false
              */
-            name: string;
+            to_posix_lines: boolean;
+        };
+        /** PathDataElement */
+        PathDataElement: {
+            /** Md5 */
+            MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
-             * Path
-             * @description The path of the entry.
+             * Auto Decompress
+             * @description Decompress compressed data before sniffing?
+             * @default false
              */
-            path: string;
+            auto_decompress: boolean;
+            /** Collection Type */
+            collection_type?: string | null;
+            /** Created From Basename */
+            created_from_basename?: string | null;
             /**
-             * URI
-             * @description The URI of the entry.
+             * Dbkey
+             * @default ?
              */
-            uri: string;
-        };
-        /** RemoteFile */
-        RemoteFile: {
+            dbkey: string;
             /**
-             * Class
-             * @constant
-             * @enum {string}
+             * Deferred
+             * @default false
              */
-            class: "File";
+            deferred: boolean;
+            /** Description */
+            description?: string | null;
+            elements_from?: components["schemas"]["ElementsFromType"] | null;
             /**
-             * Creation time
-             * @description The creation time of the file.
+             * Ext
+             * @default auto
              */
-            ctime: string;
+            ext: string;
+            extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
+            /** Info */
+            info?: string | null;
+            /** Link Data Only */
+            link_data_only?: boolean | null;
+            /** Name */
+            name?: string | number | boolean | null;
+            /** Path */
+            path: string;
             /**
-             * Name
-             * @description The name of the entry.
+             * Space To Tab
+             * @default false
              */
-            name: string;
+            space_to_tab: boolean;
             /**
-             * Path
-             * @description The path of the entry.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            path: string;
+            src: "path";
+            /** Tags */
+            tags?: string[] | null;
             /**
-             * Size
-             * @description The size of the file in bytes.
+             * To Posix Lines
+             * @default false
              */
-            size: number;
+            to_posix_lines: boolean;
+        };
+        /** PauseStep */
+        PauseStep: {
             /**
-             * URI
-             * @description The URI of the entry.
+             * Annotation
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
              */
-            uri: string;
-        };
-        /**
-         * RemoteFilesDisableMode
-         * @enum {string}
-         */
-        RemoteFilesDisableMode: "folders" | "files";
-        /**
-         * RemoteFilesFormat
-         * @enum {string}
-         */
-        RemoteFilesFormat: "flat" | "jstree" | "uri";
-        /** RemoteUserCreationPayload */
-        RemoteUserCreationPayload: {
+            annotation: string | null;
             /**
-             * Email
-             * @description Email of the user
+             * ID
+             * @description The identifier of the step. It matches the index order of the step inside the workflow.
              */
-            remote_user_email: string;
-        };
-        /** RemoveUnlabeledWorkflowOutputs */
-        RemoveUnlabeledWorkflowOutputs: {
+            id: number;
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Input Steps
+             * @description A dictionary containing information about the inputs connected to this workflow step.
              */
-            action_type: "remove_unlabeled_workflow_outputs";
-        };
-        /** Report */
-        Report: {
-            /** Markdown */
-            markdown: string;
-        };
-        /** ReportJobErrorPayload */
-        ReportJobErrorPayload: {
+            input_steps: {
+                [key: string]: components["schemas"]["InputStep"];
+            };
             /**
-             * History Dataset Association ID
-             * @description The History Dataset Association ID related to the error.
-             * @example 0123456789ABCDEF
+             * Tool ID
+             * @description The unique name of the tool associated with this step.
              */
-            dataset_id: string;
+            tool_id?: string | null;
             /**
-             * Email
-             * @description Email address for communication with the user. Only required for anonymous users.
+             * Tool Inputs
+             * @description TODO
              */
-            email?: string | null;
+            tool_inputs?: unknown;
             /**
-             * Message
-             * @description The optional message sent with the error report.
+             * Tool Version
+             * @description The version of the tool associated with this step.
              */
-            message?: string | null;
-        };
-        /**
-         * RequestDataType
-         * @description Particular pieces of information that can be requested for a dataset.
-         * @enum {string}
-         */
-        RequestDataType:
-            | "state"
-            | "converted_datasets_state"
-            | "data"
-            | "features"
-            | "raw_data"
-            | "track_config"
-            | "genome_data"
-            | "in_use_state";
-        /**
-         * Requirement
-         * @description Available types of job sources (model classes) that produce dataset collections.
-         * @enum {string}
-         */
-        Requirement: "logged_in" | "new_history" | "admin";
-        /** RoleDefinitionModel */
-        RoleDefinitionModel: {
-            /**
-             * Description
-             * @description Description of the role
-             */
-            description: string;
+            tool_version?: string | null;
             /**
-             * Group IDs
-             * @default []
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            group_ids?: string[] | null;
+            type: "pause";
+            /** When */
+            when: string | null;
+        };
+        /** Person */
+        Person: {
+            /** Address */
+            address?: string | null;
+            /** Alternate Name */
+            alternateName?: string | null;
             /**
-             * Name
-             * @description Name of the role
+             * Class
+             * @default Person
              */
-            name: string;
+            class: string;
+            /** Email */
+            email?: string | null;
+            /** Family Name */
+            familyName?: string | null;
+            /** Fax Number */
+            faxNumber?: string | null;
+            /** Given Name */
+            givenName?: string | null;
             /**
-             * User IDs
-             * @default []
+             * Honorific Prefix
+             * @description Honorific Prefix (e.g. Dr/Mrs/Mr)
              */
-            user_ids?: string[] | null;
-        };
-        /** RoleListResponse */
-        RoleListResponse: components["schemas"]["RoleModelResponse"][];
-        /** RoleModelResponse */
-        RoleModelResponse: {
-            /** Description */
-            description: string | null;
+            honorificPrefix?: string | null;
             /**
-             * ID
-             * @description Encoded ID of the role
-             * @example 0123456789ABCDEF
+             * Honorific Suffix
+             * @description Honorific Suffix (e.g. M.D.)
              */
-            id: string;
+            honorificSuffix?: string | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Identifier
+             * @description Identifier (typically an orcid.org ID)
              */
-            model_class: "Role";
+            identifier?: string | null;
+            /** Image URL */
+            image?: string | null;
+            /** Job Title */
+            jobTitle?: string | null;
             /**
              * Name
-             * @description Name of the role
-             */
-            name: string;
-            /**
-             * Type
-             * @description Type or category of the role
+             * @description The name of the creator.
              */
-            type: string;
+            name?: string | null;
+            /** Telephone */
+            telephone?: string | null;
+            /** URL */
+            url?: string | null;
+        };
+        /**
+         * PersonalNotificationCategory
+         * @description These notification categories can be opt-out by the user and will be
+         *     displayed in the notification preferences.
+         * @enum {string}
+         */
+        PersonalNotificationCategory: "message" | "new_shared_item";
+        /** PluginAspectStatus */
+        PluginAspectStatus: {
+            /** Message */
+            message: string;
             /**
-             * URL
-             * @deprecated
-             * @description The relative URL to access this item.
+             * State
+             * @enum {string}
              */
-            url: string;
+            state: "ok" | "not_ok" | "unknown";
         };
-        /** RootModel[Dict[str, int]] */
-        RootModel_Dict_str__int__: {
-            [key: string]: number | undefined;
+        /**
+         * PluginKind
+         * @description Enum to distinguish between different kinds or categories of plugins.
+         * @enum {string}
+         */
+        PluginKind: "rfs" | "drs" | "rdm" | "stock";
+        /** PluginStatus */
+        PluginStatus: {
+            connection?: components["schemas"]["PluginAspectStatus"] | null;
+            oauth2_access_token_generation?: components["schemas"]["PluginAspectStatus"] | null;
+            template_definition: components["schemas"]["PluginAspectStatus"];
+            template_settings?: components["schemas"]["PluginAspectStatus"] | null;
         };
-        /** SearchJobsPayload */
-        SearchJobsPayload: {
+        /** Position */
+        Position: {
+            /** Left */
+            left: number;
+            /** Top */
+            top: number;
+        };
+        /** PrepareStoreDownloadPayload */
+        PrepareStoreDownloadPayload: {
             /**
-             * Inputs
-             * @description The inputs of the job.
+             * Bco Merge History Metadata
+             * @description When reading tags/annotations to generate BCO object include history metadata.
+             * @default false
              */
-            inputs: Record<string, never>;
+            bco_merge_history_metadata: boolean;
             /**
-             * State
-             * @description Current state of the job.
+             * Bco Override Algorithmic Error
+             * @description Override algorithmic error for 'error domain' when generating BioCompute object.
              */
-            state?: components["schemas"]["JobState"] | null;
+            bco_override_algorithmic_error?: {
+                [key: string]: string;
+            } | null;
             /**
-             * Tool ID
-             * @description The tool ID related to the job.
+             * Bco Override Empirical Error
+             * @description Override empirical error for 'error domain' when generating BioCompute object.
              */
-            tool_id: string;
-            [key: string]: unknown | undefined;
-        };
-        /** ServerDirElement */
-        ServerDirElement: {
-            /** Md5 */
-            MD5?: string | null;
+            bco_override_empirical_error?: {
+                [key: string]: string;
+            } | null;
             /**
-             * Auto Decompress
-             * @description Decompress compressed data before sniffing?
-             * @default false
+             * Bco Override Environment Variables
+             * @description Override environment variables for 'execution_domain' when generating BioCompute object.
              */
-            auto_decompress?: boolean;
-            /** Collection Type */
-            collection_type?: string | null;
-            /** Created From Basename */
-            created_from_basename?: string | null;
+            bco_override_environment_variables?: {
+                [key: string]: string;
+            } | null;
             /**
-             * Dbkey
-             * @default ?
+             * Bco Override Xref
+             * @description Override xref for 'description domain' when generating BioCompute object.
              */
-            dbkey?: string;
+            bco_override_xref?: components["schemas"]["XrefItem"][] | null;
             /**
-             * Deferred
+             * Include deleted
+             * @description Include file contents for deleted datasets (if include_files is True).
              * @default false
              */
-            deferred?: boolean;
-            /** Description */
-            description?: string | null;
-            elements_from?: components["schemas"]["ElementsFromType"] | null;
+            include_deleted: boolean;
             /**
-             * Ext
-             * @default auto
+             * Include Files
+             * @description include materialized files in export when available
+             * @default true
              */
-            ext?: string;
-            extra_files?: components["schemas"]["ExtraFiles"] | null;
-            /** Info */
-            info?: string | null;
-            /** Link Data Only */
-            link_data_only?: boolean | null;
-            /** Name */
-            name?: string | number | number | boolean | null;
-            /** Server Dir */
-            server_dir: string;
+            include_files: boolean;
             /**
-             * Space To Tab
+             * Include hidden
+             * @description Include file contents for hidden datasets (if include_files is True).
              * @default false
              */
-            space_to_tab?: boolean;
-            /**
-             * Src
-             * @constant
-             * @enum {string}
-             */
-            src: "server_dir";
-            /** Tags */
-            tags?: string[] | null;
+            include_hidden: boolean;
             /**
-             * To Posix Lines
-             * @default false
+             * @description format of model store to export
+             * @default tar.gz
              */
-            to_posix_lines?: boolean;
+            model_store_format: components["schemas"]["ModelStoreFormat"];
         };
-        /** Service */
-        Service: {
+        /** QuotaDetails */
+        QuotaDetails: {
             /**
-             * Contacturl
-             * @description URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).
+             * Bytes
+             * @description The amount, expressed in bytes, of this Quota.
              */
-            contactUrl?: string | null;
+            bytes: number;
             /**
-             * Createdat
-             * @description Timestamp describing when the service was first deployed and available (RFC 3339 format)
+             * Default
+             * @description A list indicating which types of default user quotas, if any, are associated with this quota.
+             * @default []
              */
-            createdAt?: string | null;
+            default: components["schemas"]["DefaultQuota"][];
             /**
              * Description
-             * @description Description of the service. Should be human readable and provide information about the service.
+             * @description Detailed text description for this Quota.
              */
-            description?: string | null;
+            description: string;
             /**
-             * Documentationurl
-             * @description URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.
+             * Display Amount
+             * @description Human-readable representation of the `amount` field.
              */
-            documentationUrl?: string | null;
+            display_amount: string;
             /**
-             * Environment
-             * @description Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.
+             * Groups
+             * @description A list of specific groups of users associated with this quota.
+             * @default []
              */
-            environment?: string | null;
+            groups: components["schemas"]["GroupQuota"][];
             /**
-             * Id
-             * @description Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.
+             * ID
+             * @description The `encoded identifier` of the quota.
+             * @example 0123456789ABCDEF
              */
             id: string;
             /**
-             * Name
-             * @description Name of this service. Should be human readable.
-             */
-            name: string;
-            /** @description Organization providing the service */
-            organization: components["schemas"]["galaxy__schema__drs__Organization"];
-            type: components["schemas"]["ServiceType"];
-            /**
-             * Updatedat
-             * @description Timestamp describing when the service was last updated (RFC 3339 format)
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            updatedAt?: string | null;
+            model_class: "Quota";
             /**
-             * Version
-             * @description Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.
+             * Name
+             * @description The name of the quota. This must be unique within a Galaxy instance.
              */
-            version: string;
-        };
-        /** ServiceType */
-        ServiceType: {
+            name: string;
             /**
-             * Artifact
-             * @description Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.
+             * Operation
+             * @description Quotas can have one of three `operations`:- `=` : The quota is exactly the amount specified- `+` : The amount specified will be added to the amounts of the user's other associated quota definitions- `-` : The amount specified will be subtracted from the amounts of the user's other associated quota definitions
+             * @default =
              */
-            artifact: string;
+            operation: components["schemas"]["QuotaOperation"];
             /**
-             * Group
-             * @description Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).
+             * Quota Source Label
+             * @description Quota source label
              */
-            group: string;
+            quota_source_label?: string | null;
             /**
-             * Version
-             * @description Version of the API or specification. GA4GH specifications use semantic versioning.
+             * Users
+             * @description A list of specific users associated with this quota.
+             * @default []
              */
-            version: string;
+            users: components["schemas"]["UserQuota"][];
         };
-        /** SetSlugPayload */
-        SetSlugPayload: {
-            /**
-             * New Slug
-             * @description The slug that will be used to access this shared item.
-             */
-            new_slug: string;
+        /** QuotaModel */
+        QuotaModel: {
+            /** Enabled */
+            enabled: boolean;
+            /** Source */
+            source?: string | null;
         };
-        /** ShareHistoryExtra */
-        ShareHistoryExtra: {
-            /**
-             * Accessible Count
-             * @description The number of datasets in the history that are public or accessible by all the target users.
-             * @default 0
-             */
-            accessible_count?: number;
-            /**
-             * Can Change
-             * @description A collection of datasets that are not accessible by one or more of the target users and that can be made accessible for others by the user sharing the history.
-             * @default []
-             */
-            can_change?: components["schemas"]["HDABasicInfo"][];
+        /**
+         * QuotaOperation
+         * @enum {string}
+         */
+        QuotaOperation: "=" | "+" | "-";
+        /**
+         * QuotaSummary
+         * @description Contains basic information about a Quota
+         */
+        QuotaSummary: {
             /**
-             * Can Share
-             * @description Indicates whether the resource can be directly shared or requires further actions.
-             * @default false
+             * ID
+             * @description The `encoded identifier` of the quota.
+             * @example 0123456789ABCDEF
              */
-            can_share?: boolean;
+            id: string;
             /**
-             * Cannot Change
-             * @description A collection of datasets that are not accessible by one or more of the target users and that cannot be made accessible for others by the user sharing the history.
-             * @default []
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            cannot_change?: components["schemas"]["HDABasicInfo"][];
-        };
-        /** ShareHistoryWithStatus */
-        ShareHistoryWithStatus: {
+            model_class: "Quota";
             /**
-             * Encoded Email
-             * @description Encoded owner email.
+             * Name
+             * @description The name of the quota. This must be unique within a Galaxy instance.
              */
-            email_hash?: string | null;
+            name: string;
             /**
-             * Errors
-             * @description Collection of messages indicating that the resource was not shared with some (or all users) due to an error.
-             * @default []
+             * Quota Source Label
+             * @description Quota source label
              */
-            errors?: string[];
+            quota_source_label?: string | null;
             /**
-             * Extra
-             * @description Optional extra information about this shareable resource that may be of interest. The contents of this field depend on the particular resource.
+             * URL
+             * @deprecated
+             * @description The relative URL to get this particular Quota details from the rest API.
              */
-            extra: components["schemas"]["ShareHistoryExtra"];
+            url: string;
+        };
+        /**
+         * QuotaSummaryList
+         * @default []
+         */
+        QuotaSummaryList: components["schemas"]["QuotaSummary"][];
+        /** RefactorActionExecution */
+        RefactorActionExecution: {
+            /** Action */
+            action:
+                | components["schemas"]["AddInputAction"]
+                | components["schemas"]["AddStepAction"]
+                | components["schemas"]["ConnectAction"]
+                | components["schemas"]["DisconnectAction"]
+                | components["schemas"]["ExtractInputAction"]
+                | components["schemas"]["ExtractUntypedParameter"]
+                | components["schemas"]["FileDefaultsAction"]
+                | components["schemas"]["FillStepDefaultsAction"]
+                | components["schemas"]["UpdateAnnotationAction"]
+                | components["schemas"]["UpdateCreatorAction"]
+                | components["schemas"]["UpdateNameAction"]
+                | components["schemas"]["UpdateLicenseAction"]
+                | components["schemas"]["UpdateOutputLabelAction"]
+                | components["schemas"]["UpdateReportAction"]
+                | components["schemas"]["UpdateStepLabelAction"]
+                | components["schemas"]["UpdateStepPositionAction"]
+                | components["schemas"]["UpgradeSubworkflowAction"]
+                | components["schemas"]["UpgradeToolAction"]
+                | components["schemas"]["UpgradeAllStepsAction"]
+                | components["schemas"]["RemoveUnlabeledWorkflowOutputs"];
+            /** Messages */
+            messages: components["schemas"]["RefactorActionExecutionMessage"][];
+        };
+        /** RefactorActionExecutionMessage */
+        RefactorActionExecutionMessage: {
             /**
-             * ID
-             * @description The encoded ID of the resource to be shared.
-             * @example 0123456789ABCDEF
+             * From Order Index
+             * @description For dropped connections these optional attributes refer to the output
+             *     side of the connection that was dropped.
              */
-            id: string;
+            from_order_index?: number | null;
             /**
-             * Importable
-             * @description Whether this resource can be published using a link.
+             * From Step Label
+             * @description For dropped connections these optional attributes refer to the output
+             *     side of the connection that was dropped.
              */
-            importable: boolean;
+            from_step_label?: string | null;
             /**
-             * Published
-             * @description Whether this resource is currently published.
+             * Input Name
+             * @description If this message is about an input to a step,
+             *     this field describes the target input name. $The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input').
              */
-            published: boolean;
+            input_name?: string | null;
+            /** Message */
+            message: string;
+            message_type: components["schemas"]["RefactorActionExecutionMessageTypeEnum"];
             /**
-             * Title
-             * @description The title or name of the resource.
+             * Order Index
+             * @description Reference to the step the message refers to. $
+             *
+             *     Messages don't have to be bound to a step, but if they are they will
+             *     have a step_label and order_index included in the execution message.
+             *     These are the label and order_index before applying the refactoring,
+             *     the result of applying the action may change one or both of these.
+             *     If connections are dropped this step reference will refer to the
+             *     step with the previously connected input.
+             *
              */
-            title: string;
+            order_index?: number | null;
             /**
-             * Username
-             * @description The owner's username.
+             * Output Label
+             * @description If the message_type is workflow_output_drop_forced, this is the output label dropped.
              */
-            username?: string | null;
+            output_label?: string | null;
             /**
-             * Username and slug
-             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
+             * Output Name
+             * @description If this message is about an output to a step,
+             *     this field describes the target output name. The output name as defined by the workflow module corresponding to the step being referenced.
+             *
              */
-            username_and_slug?: string | null;
+            output_name?: string | null;
             /**
-             * Users shared with
-             * @description The list of encoded ids for users the resource has been shared.
-             * @default []
+             * Step Label
+             * @description Reference to the step the message refers to. $
+             *
+             *     Messages don't have to be bound to a step, but if they are they will
+             *     have a step_label and order_index included in the execution message.
+             *     These are the label and order_index before applying the refactoring,
+             *     the result of applying the action may change one or both of these.
+             *     If connections are dropped this step reference will refer to the
+             *     step with the previously connected input.
+             *
              */
-            users_shared_with?: components["schemas"]["UserEmail"][];
+            step_label?: string | null;
         };
-        /** ShareWithExtra */
-        ShareWithExtra: {
+        /**
+         * RefactorActionExecutionMessageTypeEnum
+         * @enum {string}
+         */
+        RefactorActionExecutionMessageTypeEnum:
+            | "tool_version_change"
+            | "tool_state_adjustment"
+            | "connection_drop_forced"
+            | "workflow_output_drop_forced";
+        /** RefactorRequest */
+        RefactorRequest: {
+            /** Actions */
+            actions: (
+                | components["schemas"]["AddInputAction"]
+                | components["schemas"]["AddStepAction"]
+                | components["schemas"]["ConnectAction"]
+                | components["schemas"]["DisconnectAction"]
+                | components["schemas"]["ExtractInputAction"]
+                | components["schemas"]["ExtractUntypedParameter"]
+                | components["schemas"]["FileDefaultsAction"]
+                | components["schemas"]["FillStepDefaultsAction"]
+                | components["schemas"]["UpdateAnnotationAction"]
+                | components["schemas"]["UpdateCreatorAction"]
+                | components["schemas"]["UpdateNameAction"]
+                | components["schemas"]["UpdateLicenseAction"]
+                | components["schemas"]["UpdateOutputLabelAction"]
+                | components["schemas"]["UpdateReportAction"]
+                | components["schemas"]["UpdateStepLabelAction"]
+                | components["schemas"]["UpdateStepPositionAction"]
+                | components["schemas"]["UpgradeSubworkflowAction"]
+                | components["schemas"]["UpgradeToolAction"]
+                | components["schemas"]["UpgradeAllStepsAction"]
+                | components["schemas"]["RemoveUnlabeledWorkflowOutputs"]
+            )[];
             /**
-             * Can Share
-             * @description Indicates whether the resource can be directly shared or requires further actions.
+             * Dry Run
              * @default false
              */
-            can_share?: boolean;
-        };
-        /** ShareWithPayload */
-        ShareWithPayload: {
-            /**
-             * Share Option
-             * @description User choice for sharing resources which its contents may be restricted:
-             *  - None: The user did not choose anything yet or no option is needed.
-             *  - make_public: The contents of the resource will be made publicly accessible.
-             *  - make_accessible_to_shared: This will automatically create a new `sharing role` allowing protected contents to be accessed only by the desired users.
-             *  - no_changes: This won't change the current permissions for the contents. The user which this resource will be shared may not be able to access all its contents.
-             */
-            share_option?: components["schemas"]["SharingOptions"] | null;
+            dry_run: boolean;
             /**
-             * User Identifiers
-             * @description A collection of encoded IDs (or email addresses) of users that this resource will be shared with.
+             * Style
+             * @default export
              */
-            user_ids: (string | string)[];
+            style: string;
         };
-        /** ShareWithStatus */
-        ShareWithStatus: {
-            /**
-             * Encoded Email
-             * @description Encoded owner email.
-             */
-            email_hash?: string | null;
-            /**
-             * Errors
-             * @description Collection of messages indicating that the resource was not shared with some (or all users) due to an error.
-             * @default []
+        /** RefactorResponse */
+        RefactorResponse: {
+            /** Action Executions */
+            action_executions: components["schemas"]["RefactorActionExecution"][];
+            /** Dry Run */
+            dry_run: boolean;
+            /** Workflow */
+            workflow: string;
+        };
+        /** ReloadFeedback */
+        ReloadFeedback: {
+            /** Failed */
+            failed: (string | null)[];
+            /** Message */
+            message: string;
+            /** Reloaded */
+            reloaded: (string | null)[];
+        };
+        /** RemoteDirectory */
+        RemoteDirectory: {
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            errors?: string[];
+            class: "Directory";
             /**
-             * Extra
-             * @description Optional extra information about this shareable resource that may be of interest. The contents of this field depend on the particular resource.
+             * Name
+             * @description The name of the entry.
              */
-            extra?: components["schemas"]["ShareWithExtra"] | null;
+            name: string;
             /**
-             * ID
-             * @description The encoded ID of the resource to be shared.
-             * @example 0123456789ABCDEF
+             * Path
+             * @description The path of the entry.
              */
-            id: string;
+            path: string;
             /**
-             * Importable
-             * @description Whether this resource can be published using a link.
+             * URI
+             * @description The URI of the entry.
              */
-            importable: boolean;
+            uri: string;
+        };
+        /** RemoteFile */
+        RemoteFile: {
             /**
-             * Published
-             * @description Whether this resource is currently published.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            published: boolean;
+            class: "File";
             /**
-             * Title
-             * @description The title or name of the resource.
+             * Creation time
+             * @description The creation time of the file.
              */
-            title: string;
+            ctime: string;
             /**
-             * Username
-             * @description The owner's username.
+             * Name
+             * @description The name of the entry.
              */
-            username?: string | null;
+            name: string;
             /**
-             * Username and slug
-             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
+             * Path
+             * @description The path of the entry.
              */
-            username_and_slug?: string | null;
+            path: string;
             /**
-             * Users shared with
-             * @description The list of encoded ids for users the resource has been shared.
-             * @default []
+             * Size
+             * @description The size of the file in bytes.
+             */
+            size: number;
+            /**
+             * URI
+             * @description The URI of the entry.
              */
-            users_shared_with?: components["schemas"]["UserEmail"][];
+            uri: string;
         };
         /**
-         * SharingOptions
-         * @description Options for sharing resources that may have restricted access to all or part of their contents.
+         * RemoteFilesDisableMode
          * @enum {string}
          */
-        SharingOptions: "make_public" | "make_accessible_to_shared" | "no_changes";
-        /** SharingStatus */
-        SharingStatus: {
+        RemoteFilesDisableMode: "folders" | "files";
+        /**
+         * RemoteFilesFormat
+         * @enum {string}
+         */
+        RemoteFilesFormat: "flat" | "jstree" | "uri";
+        /** RemoteUserCreationPayload */
+        RemoteUserCreationPayload: {
             /**
-             * Encoded Email
-             * @description Encoded owner email.
+             * Email
+             * @description Email of the user
              */
-            email_hash?: string | null;
+            remote_user_email: string;
+        };
+        /** RemoveUnlabeledWorkflowOutputs */
+        RemoveUnlabeledWorkflowOutputs: {
             /**
-             * ID
-             * @description The encoded ID of the resource to be shared.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            action_type: "remove_unlabeled_workflow_outputs";
+        };
+        /** Report */
+        Report: {
+            /** Markdown */
+            markdown: string;
+        };
+        /** ReportJobErrorPayload */
+        ReportJobErrorPayload: {
+            /**
+             * History Dataset Association ID
+             * @description The History Dataset Association ID related to the error.
              * @example 0123456789ABCDEF
              */
-            id: string;
+            dataset_id: string;
             /**
-             * Importable
-             * @description Whether this resource can be published using a link.
+             * Email
+             * @description Email address for communication with the user. Only required for anonymous users.
              */
-            importable: boolean;
+            email?: string | null;
             /**
-             * Published
-             * @description Whether this resource is currently published.
+             * Message
+             * @description The optional message sent with the error report.
              */
-            published: boolean;
+            message?: string | null;
+        };
+        /**
+         * RequestDataType
+         * @description Particular pieces of information that can be requested for a dataset.
+         * @enum {string}
+         */
+        RequestDataType:
+            | "state"
+            | "converted_datasets_state"
+            | "data"
+            | "features"
+            | "raw_data"
+            | "track_config"
+            | "genome_data"
+            | "in_use_state";
+        /**
+         * Requirement
+         * @description Available types of job sources (model classes) that produce dataset collections.
+         * @enum {string}
+         */
+        Requirement: "logged_in" | "new_history" | "admin";
+        /** RoleDefinitionModel */
+        RoleDefinitionModel: {
             /**
-             * Title
-             * @description The title or name of the resource.
+             * Description
+             * @description Description of the role
              */
-            title: string;
+            description: string;
             /**
-             * Username
-             * @description The owner's username.
+             * Group IDs
+             * @default []
              */
-            username?: string | null;
+            group_ids: string[] | null;
             /**
-             * Username and slug
-             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
+             * Name
+             * @description Name of the role
              */
-            username_and_slug?: string | null;
+            name: string;
             /**
-             * Users shared with
-             * @description The list of encoded ids for users the resource has been shared.
+             * User IDs
              * @default []
              */
-            users_shared_with?: components["schemas"]["UserEmail"][];
+            user_ids: string[] | null;
         };
-        /** ShortTermStoreExportPayload */
-        ShortTermStoreExportPayload: {
-            /** Duration */
-            duration?: number | number | null;
+        /** RoleListResponse */
+        RoleListResponse: components["schemas"]["RoleModelResponse"][];
+        /** RoleModelResponse */
+        RoleModelResponse: {
+            /** Description */
+            description: string | null;
             /**
-             * Include deleted
-             * @description Include file contents for deleted datasets (if include_files is True).
-             * @default false
+             * ID
+             * @description Encoded ID of the role
+             * @example 0123456789ABCDEF
              */
-            include_deleted?: boolean;
+            id: string;
             /**
-             * Include Files
-             * @description include materialized files in export when available
-             * @default true
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            include_files?: boolean;
+            model_class: "Role";
             /**
-             * Include hidden
-             * @description Include file contents for hidden datasets (if include_files is True).
-             * @default false
+             * Name
+             * @description Name of the role
              */
-            include_hidden?: boolean;
+            name: string;
             /**
-             * @description format of model store to export
-             * @default tar.gz
+             * Type
+             * @description Type or category of the role
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
+            type: string;
             /**
-             * Short Term Storage Request Id
-             * Format: uuid
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
              */
-            short_term_storage_request_id: string;
+            url: string;
         };
-        /** ShowFullJobResponse */
-        ShowFullJobResponse: {
+        /** RootModel[Dict[str, int]] */
+        RootModel_Dict_str__int__: {
+            [key: string]: number;
+        };
+        /** SearchJobsPayload */
+        SearchJobsPayload: {
             /**
-             * Command Line
-             * @description The command line produced by the job. Users can see this value if allowed in the configuration, administrator can always see this value.
+             * Inputs
+             * @description The inputs of the job.
              */
-            command_line?: string | null;
+            inputs: Record<string, never>;
             /**
-             * Command Version
-             * @description Tool version indicated during job execution.
+             * State
+             * @description Current state of the job.
              */
-            command_version?: string | null;
+            state?: components["schemas"]["JobState"] | null;
             /**
-             * Copied from Job-ID
-             * @description Reference to cached job if job execution was cached.
+             * Tool ID
+             * @description The tool ID related to the job.
              */
-            copied_from_job_id?: string | null;
+            tool_id: string;
+        } & {
+            [key: string]: unknown;
+        };
+        /** ServerDirElement */
+        ServerDirElement: {
+            /** Md5 */
+            MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Auto Decompress
+             * @description Decompress compressed data before sniffing?
+             * @default false
              */
-            create_time: string;
+            auto_decompress: boolean;
+            /** Collection Type */
+            collection_type?: string | null;
+            /** Created From Basename */
+            created_from_basename?: string | null;
             /**
-             * Job dependencies
-             * @description The dependencies of the job.
+             * Dbkey
+             * @default ?
              */
-            dependencies?: Record<string, never>[] | null;
+            dbkey: string;
             /**
-             * Exit Code
-             * @description The exit code returned by the tool. Can be unset if the job is not completed yet.
+             * Deferred
+             * @default false
              */
-            exit_code?: number | null;
+            deferred: boolean;
+            /** Description */
+            description?: string | null;
+            elements_from?: components["schemas"]["ElementsFromType"] | null;
             /**
-             * External ID
-             * @description The job id used by the external job runner (Condor, Pulsar, etc.). Only administrator can see this value.
+             * Ext
+             * @default auto
              */
-            external_id?: string | null;
+            ext: string;
+            extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
+            /** Info */
+            info?: string | null;
+            /** Link Data Only */
+            link_data_only?: boolean | null;
+            /** Name */
+            name?: string | number | boolean | null;
+            /** Server Dir */
+            server_dir: string;
             /**
-             * Galaxy Version
-             * @description The (major) version of Galaxy used to create this job.
+             * Space To Tab
+             * @default false
              */
-            galaxy_version?: string | null;
+            space_to_tab: boolean;
             /**
-             * Job Handler
-             * @description The job handler process assigned to handle this job. Only administrator can see this value.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            handler?: string | null;
+            src: "server_dir";
+            /** Tags */
+            tags?: string[] | null;
             /**
-             * History ID
-             * @description The encoded ID of the history associated with this item.
+             * To Posix Lines
+             * @default false
              */
-            history_id?: string | null;
+            to_posix_lines: boolean;
+        };
+        /** Service */
+        Service: {
             /**
-             * Job ID
-             * @example 0123456789ABCDEF
+             * Contacturl
+             * @description URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).
              */
-            id: string;
+            contactUrl?: string | null;
             /**
-             * Inputs
-             * @description Dictionary mapping all the tool inputs (by name) to the corresponding data references.
-             * @default {}
+             * Createdat
+             * @description Timestamp describing when the service was first deployed and available (RFC 3339 format)
              */
-            inputs?: {
-                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
-            };
+            createdAt?: string | null;
             /**
-             * Job Messages
-             * @description List with additional information and possible reasons for a failed job.
+             * Description
+             * @description Description of the service. Should be human readable and provide information about the service.
              */
-            job_messages?: Record<string, never>[] | null;
+            description?: string | null;
             /**
-             * Job Metrics
-             * @description Collections of metrics provided by `JobInstrumenter` plugins on a particular job. Only administrators can see these metrics.
+             * Documentationurl
+             * @description URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.
              */
-            job_metrics?: components["schemas"]["JobMetricCollection"] | null;
+            documentationUrl?: string | null;
             /**
-             * Job Runner Name
-             * @description Name of the job runner plugin that handles this job. Only administrator can see this value.
+             * Environment
+             * @description Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.
              */
-            job_runner_name?: string | null;
+            environment?: string | null;
             /**
-             * Job Standard Error
-             * @description The captured standard error of the job execution.
+             * Id
+             * @description Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.
              */
-            job_stderr?: string | null;
+            id: string;
             /**
-             * Job Standard Output
-             * @description The captured standard output of the job execution.
+             * Name
+             * @description Name of this service. Should be human readable.
              */
-            job_stdout?: string | null;
+            name: string;
+            /** @description Organization providing the service */
+            organization: components["schemas"]["galaxy__schema__drs__Organization"];
+            type: components["schemas"]["ServiceType"];
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Updatedat
+             * @description Timestamp describing when the service was last updated (RFC 3339 format)
              */
-            model_class: "Job";
+            updatedAt?: string | null;
             /**
-             * Output collections
-             * @default {}
+             * Version
+             * @description Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.
              */
-            output_collections?: {
-                [key: string]: components["schemas"]["EncodedHdcaSourceId"] | undefined;
-            };
+            version: string;
+        };
+        /** ServiceType */
+        ServiceType: {
             /**
-             * Outputs
-             * @description Dictionary mapping all the tool outputs (by name) to the corresponding data references.
-             * @default {}
+             * Artifact
+             * @description Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.
              */
-            outputs?: {
-                [key: string]: components["schemas"]["EncodedDatasetJobInfo"] | undefined;
-            };
+            artifact: string;
             /**
-             * Parameters
-             * @description Object containing all the parameters of the tool associated with this job. The specific parameters depend on the tool itself.
+             * Group
+             * @description Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).
              */
-            params: Record<string, never>;
+            group: string;
             /**
-             * State
-             * @description Current state of the job.
+             * Version
+             * @description Version of the API or specification. GA4GH specifications use semantic versioning.
              */
-            state: components["schemas"]["JobState"];
+            version: string;
+        };
+        /** SetSlugPayload */
+        SetSlugPayload: {
             /**
-             * Standard Error
-             * @description Combined tool and job standard error streams.
+             * New Slug
+             * @description The slug that will be used to access this shared item.
              */
-            stderr?: string | null;
+            new_slug: string;
+        };
+        /** ShareHistoryExtra */
+        ShareHistoryExtra: {
             /**
-             * Standard Output
-             * @description Combined tool and job standard output streams.
+             * Accessible Count
+             * @description The number of datasets in the history that are public or accessible by all the target users.
+             * @default 0
              */
-            stdout?: string | null;
+            accessible_count: number;
             /**
-             * Tool ID
-             * @description Identifier of the tool that generated this job.
+             * Can Change
+             * @description A collection of datasets that are not accessible by one or more of the target users and that can be made accessible for others by the user sharing the history.
+             * @default []
              */
-            tool_id: string;
+            can_change: components["schemas"]["HDABasicInfo"][];
             /**
-             * Tool Standard Error
-             * @description The captured standard error of the tool executed by the job.
+             * Can Share
+             * @description Indicates whether the resource can be directly shared or requires further actions.
+             * @default false
              */
-            tool_stderr?: string | null;
+            can_share: boolean;
             /**
-             * Tool Standard Output
-             * @description The captured standard output of the tool executed by the job.
+             * Cannot Change
+             * @description A collection of datasets that are not accessible by one or more of the target users and that cannot be made accessible for others by the user sharing the history.
+             * @default []
              */
-            tool_stdout?: string | null;
+            cannot_change: components["schemas"]["HDABasicInfo"][];
+        };
+        /** ShareHistoryWithStatus */
+        ShareHistoryWithStatus: {
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Encoded Email
+             * @description Encoded owner email.
              */
-            update_time: string;
+            email_hash?: string | null;
             /**
-             * User Email
-             * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
+             * Errors
+             * @description Collection of messages indicating that the resource was not shared with some (or all users) due to an error.
+             * @default []
              */
-            user_email?: string | null;
-        };
-        /**
-         * Src
-         * @enum {string}
-         */
-        Src: "url" | "pasted" | "files" | "path" | "composite" | "ftp_import" | "server_dir";
-        /** StepReferenceByLabel */
-        StepReferenceByLabel: {
+            errors: string[];
             /**
-             * Label
-             * @description The unique label of the step being referenced.
+             * Extra
+             * @description Optional extra information about this shareable resource that may be of interest. The contents of this field depend on the particular resource.
              */
-            label: string;
-        };
-        /** StepReferenceByOrderIndex */
-        StepReferenceByOrderIndex: {
+            extra: components["schemas"]["ShareHistoryExtra"];
             /**
-             * Order Index
-             * @description The order_index of the step being referenced. The order indices of a workflow start at 0.
+             * ID
+             * @description The encoded ID of the resource to be shared.
+             * @example 0123456789ABCDEF
              */
-            order_index: number;
-        };
-        /** StorageItemCleanupError */
-        StorageItemCleanupError: {
-            /** Error */
-            error: string;
+            id: string;
             /**
-             * Item Id
-             * @example 0123456789ABCDEF
+             * Importable
+             * @description Whether this resource can be published using a link.
              */
-            item_id: string;
-        };
-        /** StorageItemsCleanupResult */
-        StorageItemsCleanupResult: {
-            /** Errors */
-            errors: components["schemas"]["StorageItemCleanupError"][];
-            /** Success Item Count */
-            success_item_count: number;
-            /** Total Free Bytes */
-            total_free_bytes: number;
-            /** Total Item Count */
-            total_item_count: number;
-        };
-        /** StoreExportPayload */
-        StoreExportPayload: {
+            importable: boolean;
             /**
-             * Include deleted
-             * @description Include file contents for deleted datasets (if include_files is True).
-             * @default false
+             * Published
+             * @description Whether this resource is currently published.
              */
-            include_deleted?: boolean;
+            published: boolean;
             /**
-             * Include Files
-             * @description include materialized files in export when available
-             * @default true
+             * Title
+             * @description The title or name of the resource.
              */
-            include_files?: boolean;
+            title: string;
             /**
-             * Include hidden
-             * @description Include file contents for hidden datasets (if include_files is True).
-             * @default false
+             * Username
+             * @description The owner's username.
              */
-            include_hidden?: boolean;
+            username?: string | null;
             /**
-             * @description format of model store to export
-             * @default tar.gz
+             * Username and slug
+             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
-        };
-        /** StoredItem */
-        StoredItem: {
-            /**
-             * Id
-             * @example 0123456789ABCDEF
-             */
-            id: string;
-            /** Name */
-            name: string;
-            /** Size */
-            size: number;
-            /** Type */
-            type: "history" | "dataset";
+            username_and_slug?: string | null;
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Users shared with
+             * @description The list of encoded ids for users the resource has been shared.
+             * @default []
              */
-            update_time: string;
+            users_shared_with: components["schemas"]["UserEmail"][];
         };
-        /**
-         * StoredItemOrderBy
-         * @description Available options for sorting Stored Items results.
-         * @enum {string}
-         */
-        StoredItemOrderBy: "name-asc" | "name-dsc" | "size-asc" | "size-dsc" | "update_time-asc" | "update_time-dsc";
-        /** StoredWorkflowDetailed */
-        StoredWorkflowDetailed: {
-            /**
-             * Annotation
-             * @description An annotation to provide details or to help understand the purpose and usage of this item.
-             */
-            annotation: string | null;
+        /** ShareWithExtra */
+        ShareWithExtra: {
             /**
-             * Annotations
-             * @description An list of annotations to provide details or to help understand the purpose and usage of this workflow.
+             * Can Share
+             * @description Indicates whether the resource can be directly shared or requires further actions.
+             * @default false
              */
-            annotations?: string[] | null;
+            can_share: boolean;
+        };
+        /** ShareWithPayload */
+        ShareWithPayload: {
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Share Option
+             * @description User choice for sharing resources which its contents may be restricted:
+             *      - None: The user did not choose anything yet or no option is needed.
+             *      - make_public: The contents of the resource will be made publicly accessible.
+             *      - make_accessible_to_shared: This will automatically create a new `sharing role` allowing protected contents to be accessed only by the desired users.
+             *      - no_changes: This won't change the current permissions for the contents. The user which this resource will be shared may not be able to access all its contents.
+             *
              */
-            create_time: string;
+            share_option?: components["schemas"]["SharingOptions"] | null;
             /**
-             * Creator
-             * @description Additional information about the creator (or multiple creators) of this workflow.
+             * User Identifiers
+             * @description A collection of encoded IDs (or email addresses) of users that this resource will be shared with.
              */
-            creator?:
-                | (components["schemas"]["Person"] | components["schemas"]["galaxy__schema__schema__Organization"])[]
-                | null;
+            user_ids: string[];
+        };
+        /** ShareWithStatus */
+        ShareWithStatus: {
             /**
-             * Deleted
-             * @description Whether this item is marked as deleted.
+             * Encoded Email
+             * @description Encoded owner email.
              */
-            deleted: boolean;
+            email_hash?: string | null;
             /**
-             * Email Hash
-             * @description The hash of the email of the creator of this workflow
+             * Errors
+             * @description Collection of messages indicating that the resource was not shared with some (or all users) due to an error.
+             * @default []
              */
-            email_hash: string | null;
+            errors: string[];
             /**
-             * Hidden
-             * @description TODO
+             * Extra
+             * @description Optional extra information about this shareable resource that may be of interest. The contents of this field depend on the particular resource.
              */
-            hidden: boolean;
+            extra?: components["schemas"]["ShareWithExtra"] | null;
             /**
-             * Id
+             * ID
+             * @description The encoded ID of the resource to be shared.
              * @example 0123456789ABCDEF
              */
             id: string;
             /**
              * Importable
-             * @description Indicates if the workflow is importable by the current user.
+             * @description Whether this resource can be published using a link.
              */
-            importable: boolean | null;
+            importable: boolean;
             /**
-             * Inputs
-             * @description A dictionary containing information about all the inputs of the workflow.
-             * @default {}
+             * Published
+             * @description Whether this resource is currently published.
              */
-            inputs?: {
-                [key: string]: components["schemas"]["WorkflowInput"] | undefined;
-            };
+            published: boolean;
             /**
-             * Latest workflow UUID
-             * @description TODO
+             * Title
+             * @description The title or name of the resource.
              */
-            latest_workflow_uuid?: string | null;
+            title: string;
             /**
-             * License
-             * @description SPDX Identifier of the license associated with this workflow.
+             * Username
+             * @description The owner's username.
              */
-            license?: string | null;
+            username?: string | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Username and slug
+             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
              */
-            model_class: "StoredWorkflow";
+            username_and_slug?: string | null;
             /**
-             * Name
-             * @description The name of the history.
+             * Users shared with
+             * @description The list of encoded ids for users the resource has been shared.
+             * @default []
              */
-            name: string;
+            users_shared_with: components["schemas"]["UserEmail"][];
+        };
+        /**
+         * SharingOptions
+         * @description Options for sharing resources that may have restricted access to all or part of their contents.
+         * @enum {string}
+         */
+        SharingOptions: "make_public" | "make_accessible_to_shared" | "no_changes";
+        /** SharingStatus */
+        SharingStatus: {
             /**
-             * Number of Steps
-             * @description The number of steps that make up this workflow.
+             * Encoded Email
+             * @description Encoded owner email.
              */
-            number_of_steps?: number | null;
+            email_hash?: string | null;
             /**
-             * Owner
-             * @description The name of the user who owns this workflow.
+             * ID
+             * @description The encoded ID of the resource to be shared.
+             * @example 0123456789ABCDEF
              */
-            owner: string;
+            id: string;
+            /**
+             * Importable
+             * @description Whether this resource can be published using a link.
+             */
+            importable: boolean;
             /**
              * Published
-             * @description Whether this workflow is currently publicly available to all users.
+             * @description Whether this resource is currently published.
              */
             published: boolean;
             /**
-             * Show in Tool Panel
-             * @description Whether to display this workflow in the Tools Panel.
+             * Title
+             * @description The title or name of the resource.
              */
-            show_in_tool_panel?: boolean | null;
+            title: string;
             /**
-             * Slug
-             * @description The slug of the workflow.
+             * Username
+             * @description The owner's username.
              */
-            slug: string | null;
+            username?: string | null;
             /**
-             * Source Metadata
-             * @description The source metadata of the workflow.
+             * Username and slug
+             * @description The relative URL in the form of /u/{username}/{resource_single_char}/{slug}
              */
-            source_metadata: Record<string, never> | null;
+            username_and_slug?: string | null;
             /**
-             * Steps
-             * @description A dictionary with information about all the steps of the workflow.
-             * @default {}
+             * Users shared with
+             * @description The list of encoded ids for users the resource has been shared.
+             * @default []
              */
-            steps?: {
-                [key: string]:
-                    | (
-                          | components["schemas"]["InputDataStep"]
-                          | components["schemas"]["InputDataCollectionStep"]
-                          | components["schemas"]["InputParameterStep"]
-                          | components["schemas"]["PauseStep"]
-                          | components["schemas"]["ToolStep"]
-                          | components["schemas"]["SubworkflowStep"]
-                      )
-                    | undefined;
-            };
-            tags: components["schemas"]["TagCollection"];
+            users_shared_with: components["schemas"]["UserEmail"][];
+        };
+        /** ShortTermStoreExportPayload */
+        ShortTermStoreExportPayload: {
+            /** Duration */
+            duration?: number | null;
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Include deleted
+             * @description Include file contents for deleted datasets (if include_files is True).
+             * @default false
              */
-            update_time: string;
+            include_deleted: boolean;
             /**
-             * URL
-             * @deprecated
-             * @description The relative URL to access this item.
+             * Include Files
+             * @description include materialized files in export when available
+             * @default true
              */
-            url: string;
+            include_files: boolean;
             /**
-             * Version
-             * @description The version of the workflow represented by an incremental number.
+             * Include hidden
+             * @description Include file contents for hidden datasets (if include_files is True).
+             * @default false
              */
-            version: number;
-        };
-        /** SubworkflowStep */
-        SubworkflowStep: {
+            include_hidden: boolean;
             /**
-             * Annotation
-             * @description An annotation to provide details or to help understand the purpose and usage of this item.
+             * @description format of model store to export
+             * @default tar.gz
              */
-            annotation: string | null;
+            model_store_format: components["schemas"]["ModelStoreFormat"];
             /**
-             * ID
-             * @description The identifier of the step. It matches the index order of the step inside the workflow.
+             * Short Term Storage Request Id
+             * Format: uuid
              */
-            id: number;
+            short_term_storage_request_id: string;
+        };
+        /** ShowFullJobResponse */
+        ShowFullJobResponse: {
             /**
-             * Input Steps
-             * @description A dictionary containing information about the inputs connected to this workflow step.
+             * Command Line
+             * @description The command line produced by the job. Users can see this value if allowed in the configuration, administrator can always see this value.
              */
-            input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
-            };
+            command_line?: string | null;
             /**
-             * Tool ID
-             * @description The unique name of the tool associated with this step.
+             * Command Version
+             * @description Tool version indicated during job execution.
              */
-            tool_id?: string | null;
+            command_version?: string | null;
             /**
-             * Tool Inputs
-             * @description TODO
+             * Copied from Job-ID
+             * @description Reference to cached job if job execution was cached.
              */
-            tool_inputs?: Record<string, never>;
+            copied_from_job_id?: string | null;
             /**
-             * Tool Version
-             * @description The version of the tool associated with this step.
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            tool_version?: string | null;
+            create_time: string;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Job dependencies
+             * @description The dependencies of the job.
              */
-            type: "subworkflow";
-            /** When */
-            when: string | null;
+            dependencies?: unknown[] | null;
             /**
-             * Workflow ID
-             * @description The encoded ID of the workflow that will be run on this step.
-             * @example 0123456789ABCDEF
-             */
-            workflow_id: string;
-        };
-        /** SuitableConverter */
-        SuitableConverter: {
+             * Exit Code
+             * @description The exit code returned by the tool. Can be unset if the job is not completed yet.
+             */
+            exit_code?: number | null;
             /**
-             * Name
-             * @description The name of the converter.
+             * External ID
+             * @description The job id used by the external job runner (Condor, Pulsar, etc.). Only administrator can see this value.
              */
-            name: string;
+            external_id?: string | null;
             /**
-             * Original Type
-             * @description The type to convert from.
+             * Galaxy Version
+             * @description The (major) version of Galaxy used to create this job.
              */
-            original_type: string;
+            galaxy_version?: string | null;
             /**
-             * Target Type
-             * @description The type to convert to.
+             * Job Handler
+             * @description The job handler process assigned to handle this job. Only administrator can see this value.
              */
-            target_type: string;
+            handler?: string | null;
             /**
-             * Tool Id
-             * @description The ID of the tool that can perform the type conversion.
+             * History ID
+             * @description The encoded ID of the history associated with this item.
              */
-            tool_id: string;
-        };
-        /**
-         * SuitableConverters
-         * @description Collection of converters that can be used on a particular dataset collection.
-         */
-        SuitableConverters: components["schemas"]["SuitableConverter"][];
-        /**
-         * SupportedType
-         * @enum {string}
-         */
-        SupportedType: "None" | "BasicAuth" | "BearerAuth" | "PassportAuth";
-        /**
-         * TagCollection
-         * @description Represents the collection of tags associated with an item.
-         */
-        TagCollection: string[];
-        /** TagOperationParams */
-        TagOperationParams: {
-            /** Tags */
-            tags: string[];
-            /** Type */
-            type: "add_tags" | "remove_tags";
-        };
-        /**
-         * TaggableItemClass
-         * @enum {string}
-         */
-        TaggableItemClass:
-            | "History"
-            | "HistoryDatasetAssociation"
-            | "HistoryDatasetCollectionAssociation"
-            | "LibraryDatasetDatasetAssociation"
-            | "Page"
-            | "StoredWorkflow"
-            | "Visualization";
-        /**
-         * TaskState
-         * @description Enum representing the possible states of a task.
-         * @enum {string}
-         */
-        TaskState: "PENDING" | "STARTED" | "RETRY" | "FAILURE" | "SUCCESS";
-        /** TemplateSecret */
-        TemplateSecret: {
-            /** Help */
-            help: string | null;
-            /** Label */
-            label?: string | null;
-            /** Name */
-            name: string;
-        };
-        /** TemplateVariableBoolean */
-        TemplateVariableBoolean: {
+            history_id?: string | null;
             /**
-             * Default
-             * @default false
+             * Job ID
+             * @example 0123456789ABCDEF
              */
-            default?: boolean;
-            /** Help */
-            help: string | null;
-            /** Label */
-            label?: string | null;
-            /** Name */
-            name: string;
+            id: string;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Inputs
+             * @description Dictionary mapping all the tool inputs (by name) to the corresponding data references.
+             * @default {}
              */
-            type: "boolean";
-        };
-        /** TemplateVariableInteger */
-        TemplateVariableInteger: {
+            inputs: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"];
+            };
             /**
-             * Default
-             * @default 0
+             * Job Messages
+             * @description List with additional information and possible reasons for a failed job.
              */
-            default?: number;
-            /** Help */
-            help: string | null;
-            /** Label */
-            label?: string | null;
-            /** Name */
-            name: string;
+            job_messages?: unknown[] | null;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Job Metrics
+             * @description Collections of metrics provided by `JobInstrumenter` plugins on a particular job. Only administrators can see these metrics.
              */
-            type: "integer";
-        };
-        /** TemplateVariablePathComponent */
-        TemplateVariablePathComponent: {
-            /** Default */
-            default?: string | null;
-            /** Help */
-            help: string | null;
-            /** Label */
-            label?: string | null;
-            /** Name */
-            name: string;
+            job_metrics?: components["schemas"]["JobMetricCollection"] | null;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * Job Runner Name
+             * @description Name of the job runner plugin that handles this job. Only administrator can see this value.
              */
-            type: "path_component";
-        };
-        /** TemplateVariableString */
-        TemplateVariableString: {
+            job_runner_name?: string | null;
             /**
-             * Default
-             * @default
+             * Job Standard Error
+             * @description The captured standard error of the job execution.
              */
-            default?: string;
-            /** Help */
-            help: string | null;
-            /** Label */
-            label?: string | null;
-            /** Name */
-            name: string;
+            job_stderr?: string | null;
             /**
-             * Type
+             * Job Standard Output
+             * @description The captured standard output of the job execution.
+             */
+            job_stdout?: string | null;
+            /**
+             * Model class
+             * @description The name of the database model class.
              * @constant
              * @enum {string}
              */
-            type: "string";
-        };
-        /** ToolDataDetails */
-        ToolDataDetails: {
+            model_class: "Job";
             /**
-             * Columns
-             * @description A list of column names
+             * Output collections
+             * @default {}
              */
-            columns: string[];
+            output_collections: {
+                [key: string]: components["schemas"]["EncodedHdcaSourceId"];
+            };
             /**
-             * Fields
-             * @default []
+             * Outputs
+             * @description Dictionary mapping all the tool outputs (by name) to the corresponding data references.
+             * @default {}
              */
-            fields?: string[][];
+            outputs: {
+                [key: string]: components["schemas"]["EncodedDatasetJobInfo"];
+            };
             /**
-             * Model class
-             * @description The name of class modelling this tool data
+             * Parameters
+             * @description Object containing all the parameters of the tool associated with this job. The specific parameters depend on the tool itself.
              */
-            model_class: string;
+            params: unknown;
             /**
-             * Name
-             * @description The name of this tool data entry
+             * State
+             * @description Current state of the job.
              */
-            name: string;
-        };
-        /** ToolDataEntry */
-        ToolDataEntry: {
+            state: components["schemas"]["JobState"];
             /**
-             * Model class
-             * @description The name of class modelling this tool data
+             * Standard Error
+             * @description Combined tool and job standard error streams.
              */
-            model_class: string;
+            stderr?: string | null;
             /**
-             * Name
-             * @description The name of this tool data entry
+             * Standard Output
+             * @description Combined tool and job standard output streams.
              */
-            name: string;
-        };
-        /** ToolDataEntryList */
-        ToolDataEntryList: components["schemas"]["ToolDataEntry"][];
-        /** ToolDataField */
-        ToolDataField: {
+            stdout?: string | null;
             /**
-             * Base directories
-             * @description A list of directories where the data files are stored
+             * Tool ID
+             * @description Identifier of the tool that generated this job.
              */
-            base_dir: string[];
-            /** Fields */
-            fields: {
-                [key: string]: string | undefined;
-            };
+            tool_id: string;
             /**
-             * Files
-             * @description A dictionary of file names and their size in bytes
+             * Tool Standard Error
+             * @description The captured standard error of the tool executed by the job.
              */
-            files: {
-                [key: string]: number | undefined;
-            };
+            tool_stderr?: string | null;
             /**
-             * Fingerprint
-             * @description SHA1 Hash
+             * Tool Standard Output
+             * @description The captured standard output of the tool executed by the job.
              */
-            fingerprint: string;
+            tool_stdout?: string | null;
             /**
-             * Model class
-             * @description The name of class modelling this tool data field
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
              */
-            model_class: string;
+            update_time: string;
             /**
-             * Name
-             * @description The name of the field
+             * User Email
+             * @description The email of the user that owns this job. Only the owner of the job and administrators can see this value.
              */
-            name: string;
-        };
-        /** ToolDataItem */
-        ToolDataItem: {
+            user_email?: string | null;
             /**
-             * Values
-             * @description A `\t` (TAB) separated list of column __contents__. You must specify a value for each of the columns of the data table.
+             * User Id
+             * @description User ID of user that ran this job
              */
-            values: string;
+            user_id?: string | null;
         };
-        /** ToolStep */
-        ToolStep: {
+        /**
+         * Src
+         * @enum {string}
+         */
+        Src: "url" | "pasted" | "files" | "path" | "composite" | "ftp_import" | "server_dir";
+        /** StepReferenceByLabel */
+        StepReferenceByLabel: {
             /**
-             * Annotation
-             * @description An annotation to provide details or to help understand the purpose and usage of this item.
+             * Label
+             * @description The unique label of the step being referenced.
              */
-            annotation: string | null;
+            label: string;
+        };
+        /** StepReferenceByOrderIndex */
+        StepReferenceByOrderIndex: {
             /**
-             * ID
-             * @description The identifier of the step. It matches the index order of the step inside the workflow.
+             * Order Index
+             * @description The order_index of the step being referenced. The order indices of a workflow start at 0.
              */
-            id: number;
+            order_index: number;
+        };
+        /** StorageItemCleanupError */
+        StorageItemCleanupError: {
+            /** Error */
+            error: string;
             /**
-             * Input Steps
-             * @description A dictionary containing information about the inputs connected to this workflow step.
+             * Item Id
+             * @example 0123456789ABCDEF
              */
-            input_steps: {
-                [key: string]: components["schemas"]["InputStep"] | undefined;
-            };
+            item_id: string;
+        };
+        /** StorageItemsCleanupResult */
+        StorageItemsCleanupResult: {
+            /** Errors */
+            errors: components["schemas"]["StorageItemCleanupError"][];
+            /** Success Item Count */
+            success_item_count: number;
+            /** Total Free Bytes */
+            total_free_bytes: number;
+            /** Total Item Count */
+            total_item_count: number;
+        };
+        /** StoreExportPayload */
+        StoreExportPayload: {
             /**
-             * Tool ID
-             * @description The unique name of the tool associated with this step.
+             * Include deleted
+             * @description Include file contents for deleted datasets (if include_files is True).
+             * @default false
              */
-            tool_id?: string | null;
+            include_deleted: boolean;
             /**
-             * Tool Inputs
-             * @description TODO
+             * Include Files
+             * @description include materialized files in export when available
+             * @default true
              */
-            tool_inputs?: Record<string, never>;
+            include_files: boolean;
             /**
-             * Tool Version
-             * @description The version of the tool associated with this step.
+             * Include hidden
+             * @description Include file contents for hidden datasets (if include_files is True).
+             * @default false
              */
-            tool_version?: string | null;
+            include_hidden: boolean;
             /**
-             * Type
-             * @constant
-             * @enum {string}
+             * @description format of model store to export
+             * @default tar.gz
              */
-            type: "tool";
-            /** When */
-            when: string | null;
+            model_store_format: components["schemas"]["ModelStoreFormat"];
         };
-        /** Tour */
-        Tour: {
-            /**
-             * Description
-             * @description Tour description
-             */
-            description: string;
+        /** StoredItem */
+        StoredItem: {
             /**
-             * Identifier
-             * @description Tour identifier
+             * Id
+             * @example 0123456789ABCDEF
              */
             id: string;
-            /**
-             * Name
-             * @description Name of tour
-             */
+            /** Name */
             name: string;
+            /** Size */
+            size: number;
+            /** Type */
+            type: "history" | "dataset";
             /**
-             * Requirements
-             * @description Requirements to run the tour.
-             */
-            requirements: components["schemas"]["Requirement"][];
-            /**
-             * Tags
-             * @description Topic topic tags
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
              */
-            tags: string[];
+            update_time: string;
         };
-        /** TourDetails */
-        TourDetails: {
+        /**
+         * StoredItemOrderBy
+         * @description Available options for sorting Stored Items results.
+         * @enum {string}
+         */
+        StoredItemOrderBy: "name-asc" | "name-dsc" | "size-asc" | "size-dsc" | "update_time-asc" | "update_time-dsc";
+        /** StoredWorkflowDetailed */
+        StoredWorkflowDetailed: {
             /**
-             * Description
-             * @description Tour description
+             * Annotation
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
              */
-            description: string;
+            annotation: string | null;
             /**
-             * Name
-             * @description Name of tour
+             * Annotations
+             * @description An list of annotations to provide details or to help understand the purpose and usage of this workflow.
              */
-            name: string;
+            annotations?: string[] | null;
             /**
-             * Requirements
-             * @description Requirements to run the tour.
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
              */
-            requirements: components["schemas"]["Requirement"][];
+            create_time: string;
             /**
-             * Steps
-             * @description Tour steps
+             * Creator
+             * @description Additional information about the creator (or multiple creators) of this workflow.
              */
-            steps: components["schemas"]["TourStep"][];
+            creator?:
+                | (components["schemas"]["Person"] | components["schemas"]["galaxy__schema__schema__Organization"])[]
+                | null;
             /**
-             * Tags
-             * @description Topic topic tags
+             * Deleted
+             * @description Whether this item is marked as deleted.
              */
-            tags: string[];
+            deleted: boolean;
             /**
-             * Default title
-             * @description Default title for each step
+             * Email Hash
+             * @description The hash of the email of the creator of this workflow
              */
-            title_default?: string | null;
-        };
-        /**
-         * TourList
-         * @default []
-         */
-        TourList: components["schemas"]["Tour"][];
-        /** TourStep */
-        TourStep: {
+            email_hash: string | null;
             /**
-             * Content
-             * @description Text shown to the user
+             * Hidden
+             * @description TODO
              */
-            content?: string | null;
+            hidden: boolean;
             /**
-             * Element
-             * @description CSS selector for the element to be described/clicked
+             * Id
+             * @example 0123456789ABCDEF
              */
-            element?: string | null;
+            id: string;
             /**
-             * Placement
-             * @description Placement of the text box relative to the selected element
+             * Importable
+             * @description Indicates if the workflow is importable by the current user.
              */
-            placement?: string | null;
+            importable: boolean | null;
             /**
-             * Post-click
-             * @description Elements that receive a click() event after the step is shown
+             * Inputs
+             * @description A dictionary containing information about all the inputs of the workflow.
+             * @default {}
              */
-            postclick?: boolean | string[] | null;
+            inputs: {
+                [key: string]: components["schemas"]["WorkflowInput"];
+            };
             /**
-             * Pre-click
-             * @description Elements that receive a click() event before the step is shown
+             * Latest workflow UUID
+             * @description TODO
              */
-            preclick?: boolean | string[] | null;
+            latest_workflow_uuid?: string | null;
             /**
-             * Text-insert
-             * @description Text to insert if element is a text box (e.g. tool search or upload)
+             * License
+             * @description SPDX Identifier of the license associated with this workflow.
              */
-            textinsert?: string | null;
+            license?: string | null;
             /**
-             * Title
-             * @description Title displayed in the header of the step container
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
              */
-            title?: string | null;
-        };
-        /** UndeleteHistoriesPayload */
-        UndeleteHistoriesPayload: {
+            model_class: "StoredWorkflow";
             /**
-             * IDs
-             * @description List of history IDs to be undeleted.
+             * Name
+             * @description The name of the history.
              */
-            ids: string[];
-        };
-        /** UpdateAnnotationAction */
-        UpdateAnnotationAction: {
+            name: string;
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Number of Steps
+             * @description The number of steps that make up this workflow.
              */
-            action_type: "update_annotation";
-            /** Annotation */
-            annotation: string;
-        };
-        /**
-         * UpdateCollectionAttributePayload
-         * @description Contains attributes that can be updated for all elements in a dataset collection.
-         */
-        UpdateCollectionAttributePayload: {
+            number_of_steps?: number | null;
             /**
-             * Dbkey
-             * @description TODO
+             * Owner
+             * @description The name of the user who owns this workflow.
              */
-            dbkey: string;
-        };
-        /**
-         * UpdateContentItem
-         * @description Used for updating a particular history item. All fields are optional.
-         */
-        UpdateContentItem: {
+            owner: string;
             /**
-             * Content Type
-             * @description The type of this item.
+             * Published
+             * @description Whether this workflow is currently publicly available to all users.
              */
-            history_content_type: components["schemas"]["HistoryContentType"];
+            published: boolean;
             /**
-             * Id
-             * @example 0123456789ABCDEF
+             * Show in Tool Panel
+             * @description Whether to display this workflow in the Tools Panel.
              */
-            id: string;
-            [key: string]: unknown | undefined;
-        };
-        /** UpdateCreatorAction */
-        UpdateCreatorAction: {
+            show_in_tool_panel?: boolean | null;
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Slug
+             * @description The slug of the workflow.
              */
-            action_type: "update_creator";
-            /** Creator */
-            creator?: Record<string, never>;
-        };
-        /**
-         * UpdateHistoryContentsBatchPayload
-         * @description Contains property values that will be updated for all the history `items` provided.
-         * @example {
-         *   "items": [
-         *     {
-         *       "history_content_type": "dataset",
-         *       "id": "string"
-         *     }
-         *   ],
-         *   "visible": false
-         * }
-         */
-        UpdateHistoryContentsBatchPayload: {
+            slug: string | null;
             /**
-             * Items
-             * @description A list of content items to update with the changes.
+             * Source Metadata
+             * @description The source metadata of the workflow.
              */
-            items: components["schemas"]["UpdateContentItem"][];
-            [key: string]: unknown | undefined;
+            source_metadata: Record<string, never> | null;
+            /**
+             * Steps
+             * @description A dictionary with information about all the steps of the workflow.
+             * @default {}
+             */
+            steps: {
+                [key: string]:
+                    | components["schemas"]["InputDataStep"]
+                    | components["schemas"]["InputDataCollectionStep"]
+                    | components["schemas"]["InputParameterStep"]
+                    | components["schemas"]["PauseStep"]
+                    | components["schemas"]["ToolStep"]
+                    | components["schemas"]["SubworkflowStep"];
+            };
+            tags: components["schemas"]["TagCollection"];
+            /**
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string;
+            /**
+             * URL
+             * @deprecated
+             * @description The relative URL to access this item.
+             */
+            url: string;
+            /**
+             * Version
+             * @description The version of the workflow represented by an incremental number.
+             */
+            version: number;
         };
-        /**
-         * UpdateHistoryContentsPayload
-         * @description Can contain arbitrary/dynamic fields that will be updated for a particular history item.
-         * @example {
-         *   "annotation": "Test",
-         *   "visible": false
-         * }
-         */
-        UpdateHistoryContentsPayload: {
+        /** SubworkflowStep */
+        SubworkflowStep: {
             /**
              * Annotation
-             * @description A user-defined annotation for this item.
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
              */
-            annotation?: string | null;
+            annotation: string | null;
             /**
-             * Deleted
-             * @description Whether this item is marked as deleted.
+             * ID
+             * @description The identifier of the step. It matches the index order of the step inside the workflow.
              */
-            deleted?: boolean | null;
+            id: number;
             /**
-             * Name
-             * @description The new name of the item.
+             * Input Steps
+             * @description A dictionary containing information about the inputs connected to this workflow step.
              */
-            name?: string | null;
+            input_steps: {
+                [key: string]: components["schemas"]["InputStep"];
+            };
             /**
-             * Tags
-             * @description A list of tags to add to this item.
+             * Tool ID
+             * @description The unique name of the tool associated with this step.
              */
-            tags?: components["schemas"]["TagCollection"] | null;
+            tool_id?: string | null;
             /**
-             * Visible
-             * @description Whether this item is visible in the history.
+             * Tool Inputs
+             * @description TODO
              */
-            visible?: boolean | null;
-            [key: string]: unknown | undefined;
-        };
-        /** UpdateInstancePayload */
-        UpdateInstancePayload: {
-            /** Active */
-            active?: boolean | null;
-            /** Description */
-            description?: string | null;
-            /** Hidden */
-            hidden?: boolean | null;
-            /** Name */
-            name?: string | null;
-            /** Variables */
-            variables?: {
-                [key: string]: (string | boolean | number) | undefined;
-            } | null;
-        };
-        /** UpdateInstanceSecretPayload */
-        UpdateInstanceSecretPayload: {
-            /** Secret Name */
-            secret_name: string;
-            /** Secret Value */
-            secret_value: string;
-        };
-        /** UpdateLibraryFolderPayload */
-        UpdateLibraryFolderPayload: {
+            tool_inputs?: unknown;
             /**
-             * Description
-             * @description The new description of the library folder.
+             * Tool Version
+             * @description The version of the tool associated with this step.
              */
-            description?: string | null;
+            tool_version?: string | null;
             /**
-             * Name
-             * @description The new name of the library folder.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            name?: string | null;
-        };
-        /** UpdateLibraryPayload */
-        UpdateLibraryPayload: {
+            type: "subworkflow";
+            /** When */
+            when: string | null;
             /**
-             * Description
-             * @description A detailed description of the Library. Leave unset to keep the existing.
+             * Workflow ID
+             * @description The encoded ID of the workflow that will be run on this step.
+             * @example 0123456789ABCDEF
              */
-            description?: string | null;
+            workflow_id: string;
+        };
+        /** SuitableConverter */
+        SuitableConverter: {
             /**
              * Name
-             * @description The new name of the Library. Leave unset to keep the existing.
+             * @description The name of the converter.
              */
-            name?: string | null;
+            name: string;
             /**
-             * Synopsis
-             * @description A short text describing the contents of the Library. Leave unset to keep the existing.
+             * Original Type
+             * @description The type to convert from.
              */
-            synopsis?: string | null;
-        };
-        /** UpdateLicenseAction */
-        UpdateLicenseAction: {
+            original_type: string;
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Target Type
+             * @description The type to convert to.
              */
-            action_type: "update_license";
-            /** License */
-            license: string;
-        };
-        /** UpdateNameAction */
-        UpdateNameAction: {
+            target_type: string;
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Tool Id
+             * @description The ID of the tool that can perform the type conversion.
              */
-            action_type: "update_name";
+            tool_id: string;
+        };
+        /**
+         * SuitableConverters
+         * @description Collection of converters that can be used on a particular dataset collection.
+         */
+        SuitableConverters: components["schemas"]["SuitableConverter"][];
+        /**
+         * SupportedType
+         * @enum {string}
+         */
+        SupportedType: "None" | "BasicAuth" | "BearerAuth" | "PassportAuth";
+        /**
+         * TagCollection
+         * @description Represents the collection of tags associated with an item.
+         */
+        TagCollection: string[];
+        /** TagOperationParams */
+        TagOperationParams: {
+            /** Tags */
+            tags: string[];
+            /** Type */
+            type: "add_tags" | "remove_tags";
+        };
+        /**
+         * TaggableItemClass
+         * @enum {string}
+         */
+        TaggableItemClass:
+            | "History"
+            | "HistoryDatasetAssociation"
+            | "HistoryDatasetCollectionAssociation"
+            | "LibraryDatasetDatasetAssociation"
+            | "Page"
+            | "StoredWorkflow"
+            | "Visualization";
+        /**
+         * TaskState
+         * @description Enum representing the possible states of a task.
+         * @enum {string}
+         */
+        TaskState: "PENDING" | "STARTED" | "RETRY" | "FAILURE" | "SUCCESS";
+        /** TemplateSecret */
+        TemplateSecret: {
+            /** Help */
+            help: string | null;
+            /** Label */
+            label?: string | null;
             /** Name */
             name: string;
         };
-        /** UpdateObjectStoreIdPayload */
-        UpdateObjectStoreIdPayload: {
+        /** TemplateVariableBoolean */
+        TemplateVariableBoolean: {
             /**
-             * Object Store Id
-             * @description Object store ID to update to, it must be an object store with the same device ID as the target dataset currently.
+             * Default
+             * @default false
              */
-            object_store_id: string;
-        };
-        /** UpdateOutputLabelAction */
-        UpdateOutputLabelAction: {
+            default: boolean;
+            /** Help */
+            help: string | null;
+            /** Label */
+            label?: string | null;
+            /** Name */
+            name: string;
             /**
-             * Action Type
+             * Type
              * @constant
              * @enum {string}
              */
-            action_type: "update_output_label";
-            /** Output */
-            output:
-                | components["schemas"]["OutputReferenceByOrderIndex"]
-                | components["schemas"]["OutputReferenceByLabel"];
-            /** Output Label */
-            output_label: string;
+            type: "boolean";
         };
-        /** UpdateQuotaParams */
-        UpdateQuotaParams: {
-            /**
-             * Amount
-             * @description Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``)
-             */
-            amount?: string | null;
+        /** TemplateVariableInteger */
+        TemplateVariableInteger: {
             /**
              * Default
-             * @description Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. Calling this method with ``default="no"`` on a non-default quota will throw an error. Not passing this parameter is equivalent to passing ``no``.
+             * @default 0
              */
-            default?: components["schemas"]["DefaultQuotaValues"] | null;
-            /**
-             * Description
-             * @description Detailed text description for this Quota.
-             */
-            description?: string | null;
-            /**
-             * Groups
-             * @description A list of group IDs or names to associate with this quota.
-             */
-            in_groups?: string[] | null;
-            /**
-             * Users
-             * @description A list of user IDs or user emails to associate with this quota.
-             */
-            in_users?: string[] | null;
-            /**
-             * Name
-             * @description The new name of the quota. This must be unique within a Galaxy instance.
-             */
-            name?: string | null;
-            /**
-             * Operation
-             * @description One of (``+``, ``-``, ``=``). If you wish to change this value, you must also provide the ``amount``, otherwise it will not take effect.
-             * @default =
-             */
-            operation?: components["schemas"]["QuotaOperation"];
-        };
-        /** UpdateReportAction */
-        UpdateReportAction: {
-            /**
-             * Action Type
-             * @constant
-             * @enum {string}
-             */
-            action_type: "update_report";
-            report: components["schemas"]["Report"];
-        };
-        /** UpdateStepLabelAction */
-        UpdateStepLabelAction: {
+            default: number;
+            /** Help */
+            help: string | null;
+            /** Label */
+            label?: string | null;
+            /** Name */
+            name: string;
             /**
-             * Action Type
+             * Type
              * @constant
              * @enum {string}
              */
-            action_type: "update_step_label";
-            /**
-             * Label
-             * @description The unique label of the step being referenced.
-             */
-            label: string;
-            /**
-             * Step
-             * @description The target step for this action.
-             */
-            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
+            type: "integer";
         };
-        /** UpdateStepPositionAction */
-        UpdateStepPositionAction: {
+        /** TemplateVariablePathComponent */
+        TemplateVariablePathComponent: {
+            /** Default */
+            default?: string | null;
+            /** Help */
+            help: string | null;
+            /** Label */
+            label?: string | null;
+            /** Name */
+            name: string;
             /**
-             * Action Type
+             * Type
              * @constant
              * @enum {string}
              */
-            action_type: "update_step_position";
-            position_shift: components["schemas"]["Position"];
-            /**
-             * Step
-             * @description The target step for this action.
-             */
-            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
+            type: "path_component";
         };
-        /**
-         * UpdateUserNotificationPreferencesRequest
-         * @description Contains the new notification preferences of a user.
-         */
-        UpdateUserNotificationPreferencesRequest: {
+        /** TemplateVariableString */
+        TemplateVariableString: {
             /**
-             * Preferences
-             * @description The new notification preferences of the user.
+             * Default
+             * @default
              */
-            preferences: {
-                [key: string]: components["schemas"]["NotificationCategorySettings"] | undefined;
-            };
-        };
-        /** UpgradeAllStepsAction */
-        UpgradeAllStepsAction: {
+            default: string;
+            /** Help */
+            help: string | null;
+            /** Label */
+            label?: string | null;
+            /** Name */
+            name: string;
             /**
-             * Action Type
+             * Type
              * @constant
              * @enum {string}
              */
-            action_type: "upgrade_all_steps";
+            type: "string";
         };
-        /** UpgradeInstancePayload */
-        UpgradeInstancePayload: {
+        /** TestUpdateInstancePayload */
+        TestUpdateInstancePayload: {
+            /** Variables */
+            variables?: {
+                [key: string]: string | boolean | number;
+            } | null;
+        };
+        /** TestUpgradeInstancePayload */
+        TestUpgradeInstancePayload: {
             /** Secrets */
             secrets: {
-                [key: string]: string | undefined;
+                [key: string]: string;
             };
             /** Template Version */
             template_version: number;
             /** Variables */
             variables: {
-                [key: string]: (string | boolean | number) | undefined;
+                [key: string]: string | boolean | number;
             };
         };
-        /** UpgradeSubworkflowAction */
-        UpgradeSubworkflowAction: {
+        /** ToolDataDetails */
+        ToolDataDetails: {
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Columns
+             * @description A list of column names
              */
-            action_type: "upgrade_subworkflow";
-            /** Content Id */
-            content_id?: string | null;
+            columns: string[];
             /**
-             * Step
-             * @description The target step for this action.
+             * Fields
+             * @default []
              */
-            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
-        };
-        /** UpgradeToolAction */
-        UpgradeToolAction: {
+            fields: string[][];
             /**
-             * Action Type
-             * @constant
-             * @enum {string}
+             * Model class
+             * @description The name of class modelling this tool data
              */
-            action_type: "upgrade_tool";
+            model_class: string;
             /**
-             * Step
-             * @description The target step for this action.
+             * Name
+             * @description The name of this tool data entry
              */
-            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
-            /** Tool Version */
-            tool_version?: string | null;
+            name: string;
         };
-        /** UrlDataElement */
-        UrlDataElement: {
-            /** Md5 */
-            MD5?: string | null;
+        /** ToolDataEntry */
+        ToolDataEntry: {
             /**
-             * Auto Decompress
-             * @description Decompress compressed data before sniffing?
-             * @default false
+             * Model class
+             * @description The name of class modelling this tool data
              */
-            auto_decompress?: boolean;
-            /** Collection Type */
-            collection_type?: string | null;
-            /** Created From Basename */
-            created_from_basename?: string | null;
+            model_class: string;
             /**
-             * Dbkey
-             * @default ?
+             * Name
+             * @description The name of this tool data entry
              */
-            dbkey?: string;
+            name: string;
+        };
+        /** ToolDataEntryList */
+        ToolDataEntryList: components["schemas"]["ToolDataEntry"][];
+        /** ToolDataField */
+        ToolDataField: {
             /**
-             * Deferred
-             * @default false
+             * Base directories
+             * @description A list of directories where the data files are stored
              */
-            deferred?: boolean;
-            /** Description */
-            description?: string | null;
-            elements_from?: components["schemas"]["ElementsFromType"] | null;
+            base_dir: string[];
+            /** Fields */
+            fields: {
+                [key: string]: string;
+            };
             /**
-             * Ext
-             * @default auto
+             * Files
+             * @description A dictionary of file names and their size in bytes
              */
-            ext?: string;
-            extra_files?: components["schemas"]["ExtraFiles"] | null;
-            /** Info */
-            info?: string | null;
-            /** Name */
-            name?: string | number | number | boolean | null;
+            files: {
+                [key: string]: number;
+            };
             /**
-             * Space To Tab
-             * @default false
+             * Fingerprint
+             * @description SHA1 Hash
              */
-            space_to_tab?: boolean;
+            fingerprint: string;
             /**
-             * Src
-             * @constant
-             * @enum {string}
+             * Model class
+             * @description The name of class modelling this tool data field
              */
-            src: "url";
-            /** Tags */
-            tags?: string[] | null;
+            model_class: string;
             /**
-             * To Posix Lines
-             * @default false
+             * Name
+             * @description The name of the field
              */
-            to_posix_lines?: boolean;
+            name: string;
+        };
+        /** ToolDataItem */
+        ToolDataItem: {
             /**
-             * Url
-             * @description URL to upload
+             * Values
+             * @description A `\t` (TAB) separated list of column __contents__. You must specify a value for each of the columns of the data table.
              */
-            url: string;
+            values: string;
         };
-        /** UserBeaconSetting */
-        UserBeaconSetting: {
+        /** ToolStep */
+        ToolStep: {
             /**
-             * Enabled
-             * @description True if beacon sharing is enabled
+             * Annotation
+             * @description An annotation to provide details or to help understand the purpose and usage of this item.
              */
-            enabled: boolean;
-        };
-        /** UserConcreteObjectStoreModel */
-        UserConcreteObjectStoreModel: {
-            /** Active */
-            active: boolean;
-            /** Badges */
-            badges: components["schemas"]["BadgeDict"][];
-            /** Description */
-            description?: string | null;
-            /** Device */
-            device?: string | null;
-            /** Hidden */
-            hidden: boolean;
-            /** Name */
-            name?: string | null;
-            /** Object Store Id */
-            object_store_id?: string | null;
-            /** Private */
-            private: boolean;
-            /** Purged */
-            purged: boolean;
-            quota: components["schemas"]["QuotaModel"];
-            /** Secrets */
-            secrets: string[];
-            /** Template Id */
-            template_id: string;
-            /** Template Version */
-            template_version: number;
+            annotation: string | null;
             /**
-             * Type
-             * @enum {string}
+             * ID
+             * @description The identifier of the step. It matches the index order of the step inside the workflow.
              */
-            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
+            id: number;
             /**
-             * Uuid
-             * Format: uuid4
+             * Input Steps
+             * @description A dictionary containing information about the inputs connected to this workflow step.
              */
-            uuid: string;
-            /** Variables */
-            variables: {
-                [key: string]: (string | boolean | number) | undefined;
-            } | null;
-        };
-        /** UserCreationPayload */
-        UserCreationPayload: {
+            input_steps: {
+                [key: string]: components["schemas"]["InputStep"];
+            };
             /**
-             * Email
-             * @description Email of the user
+             * Tool ID
+             * @description The unique name of the tool associated with this step.
              */
-            email: string;
+            tool_id?: string | null;
             /**
-             * user_password
-             * @description The password of the user.
+             * Tool Inputs
+             * @description TODO
              */
-            password: string;
+            tool_inputs?: unknown;
             /**
-             * user_name
-             * @description The name of the user.
+             * Tool Version
+             * @description The version of the tool associated with this step.
              */
-            username: string;
-        };
-        /** UserDeletionPayload */
-        UserDeletionPayload: {
+            tool_version?: string | null;
             /**
-             * Purge user
-             * @deprecated
-             * @description Purge the user. Deprecated, please use the `purge` query parameter instead.
-             * @default false
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            purge?: boolean;
+            type: "tool";
+            /** When */
+            when: string | null;
         };
-        /** UserEmail */
-        UserEmail: {
+        /** Tour */
+        Tour: {
             /**
-             * Email
-             * @description The email of the user.
+             * Description
+             * @description Tour description
              */
-            email: string;
+            description: string;
             /**
-             * User ID
-             * @description The encoded ID of the user.
-             * @example 0123456789ABCDEF
+             * Identifier
+             * @description Tour identifier
              */
             id: string;
-        };
-        /** UserFileSourceModel */
-        UserFileSourceModel: {
-            /** Active */
-            active: boolean;
-            /** Description */
-            description: string | null;
-            /** Hidden */
-            hidden: boolean;
-            /** Name */
-            name: string;
-            /** Purged */
-            purged: boolean;
-            /** Secrets */
-            secrets: string[];
-            /** Template Id */
-            template_id: string;
-            /** Template Version */
-            template_version: number;
             /**
-             * Type
-             * @enum {string}
+             * Name
+             * @description Name of tour
              */
-            type: "ftp" | "posix" | "s3fs" | "azure";
-            /** Uri Root */
-            uri_root: string;
+            name: string;
             /**
-             * Uuid
-             * Format: uuid4
+             * Requirements
+             * @description Requirements to run the tour.
              */
-            uuid: string;
-            /** Variables */
-            variables: {
-                [key: string]: (string | boolean | number) | undefined;
-            } | null;
-        };
-        /**
-         * UserModel
-         * @description User in a transaction context.
-         */
-        UserModel: {
+            requirements: components["schemas"]["Requirement"][];
             /**
-             * Active
-             * @description User is active
+             * Tags
+             * @description Topic topic tags
              */
-            active: boolean;
+            tags: string[];
+        };
+        /** TourDetails */
+        TourDetails: {
             /**
-             * Deleted
-             * @description  User is deleted
+             * Description
+             * @description Tour description
              */
-            deleted: boolean;
+            description: string;
             /**
-             * Email
-             * @description Email of the user
+             * Name
+             * @description Name of tour
              */
-            email: string;
+            name: string;
             /**
-             * ID
-             * @description Encoded ID of the user
-             * @example 0123456789ABCDEF
+             * Requirements
+             * @description Requirements to run the tour.
              */
-            id: string;
-            /** Last password change */
-            last_password_change: string | null;
+            requirements: components["schemas"]["Requirement"][];
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Steps
+             * @description Tour steps
              */
-            model_class: "User";
+            steps: components["schemas"]["TourStep"][];
             /**
-             * user_name
-             * @description The name of the user.
+             * Tags
+             * @description Topic topic tags
              */
-            username: string;
-        };
-        /**
-         * UserNotificationListResponse
-         * @description A list of user notifications.
-         */
-        UserNotificationListResponse: components["schemas"]["UserNotificationResponse"][];
-        /**
-         * UserNotificationPreferences
-         * @description Contains the full notification preferences of a user.
-         */
-        UserNotificationPreferences: {
+            tags: string[];
             /**
-             * Preferences
-             * @description The notification preferences of the user.
+             * Default title
+             * @description Default title for each step
              */
-            preferences: {
-                [key: string]: components["schemas"]["NotificationCategorySettings"] | undefined;
-            };
+            title_default?: string | null;
         };
         /**
-         * UserNotificationResponse
-         * @description A notification response specific to the user.
+         * TourList
+         * @default []
          */
-        UserNotificationResponse: {
-            /**
-             * Category
-             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
-             */
-            category: components["schemas"]["PersonalNotificationCategory"];
+        TourList: components["schemas"]["Tour"][];
+        /** TourStep */
+        TourStep: {
             /**
              * Content
-             * @description The content of the notification. The structure depends on the category.
-             */
-            content:
-                | components["schemas"]["MessageNotificationContent"]
-                | components["schemas"]["NewSharedItemNotificationContent"]
-                | components["schemas"]["BroadcastNotificationContent"];
-            /**
-             * Create time
-             * Format: date-time
-             * @description The time when the notification was created.
+             * @description Text shown to the user
              */
-            create_time: string;
+            content?: string | null;
             /**
-             * Deleted
-             * @description Whether the notification is marked as deleted by the user. Deleted notifications don't show up in the notification list.
+             * Element
+             * @description CSS selector for the element to be described/clicked
              */
-            deleted: boolean;
+            element?: string | null;
             /**
-             * Expiration time
-             * @description The time when the notification will expire. If not set, the notification will never expire. Expired notifications will be permanently deleted.
+             * Placement
+             * @description Placement of the text box relative to the selected element
              */
-            expiration_time?: string | null;
+            placement?: string | null;
             /**
-             * ID
-             * @description The encoded ID of the notification.
-             * @example 0123456789ABCDEF
+             * Post-click
+             * @description Elements that receive a click() event after the step is shown
              */
-            id: string;
+            postclick?: boolean | string[] | null;
             /**
-             * Publication time
-             * Format: date-time
-             * @description The time when the notification was published. Notifications can be created and then published at a later time.
+             * Pre-click
+             * @description Elements that receive a click() event before the step is shown
              */
-            publication_time: string;
+            preclick?: boolean | string[] | null;
             /**
-             * Seen time
-             * @description The time when the notification was seen by the user. If not set, the notification was not seen yet.
+             * Text-insert
+             * @description Text to insert if element is a text box (e.g. tool search or upload)
              */
-            seen_time?: string | null;
+            textinsert?: string | null;
             /**
-             * Source
-             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
+             * Title
+             * @description Title displayed in the header of the step container
              */
-            source: string;
+            title?: string | null;
+        };
+        /** UndeleteHistoriesPayload */
+        UndeleteHistoriesPayload: {
             /**
-             * Update time
-             * Format: date-time
-             * @description The time when the notification was last updated.
+             * IDs
+             * @description List of history IDs to be undeleted.
              */
-            update_time: string;
+            ids: string[];
+        };
+        /** UpdateAnnotationAction */
+        UpdateAnnotationAction: {
             /**
-             * Variant
-             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            variant: components["schemas"]["NotificationVariant"];
+            action_type: "update_annotation";
+            /** Annotation */
+            annotation: string;
         };
         /**
-         * UserNotificationUpdateRequest
-         * @description A notification update request specific to the user.
+         * UpdateCollectionAttributePayload
+         * @description Contains attributes that can be updated for all elements in a dataset collection.
          */
-        UserNotificationUpdateRequest: {
+        UpdateCollectionAttributePayload: {
             /**
-             * Deleted
-             * @description Whether the notification should be marked as deleted by the user. If not set, the notification will not be changed.
-             */
-            deleted?: boolean | null;
-            /**
-             * Seen
-             * @description Whether the notification should be marked as seen by the user. If not set, the notification will not be changed.
+             * Dbkey
+             * @description TODO
              */
-            seen?: boolean | null;
+            dbkey: string;
         };
         /**
-         * UserNotificationsBatchUpdateRequest
-         * @description A batch update request specific for user notifications.
+         * UpdateContentItem
+         * @description Used for updating a particular history item. All fields are optional.
          */
-        UserNotificationsBatchUpdateRequest: {
+        UpdateContentItem: {
             /**
-             * Changes
-             * @description The changes that should be applied to the notifications. Only the fields that are set will be changed.
+             * Content Type
+             * @description The type of this item.
              */
-            changes: components["schemas"]["UserNotificationUpdateRequest"];
+            history_content_type: components["schemas"]["HistoryContentType"];
             /**
-             * Notification IDs
-             * @description The list of encoded notification IDs of the notifications that should be updated.
+             * Id
+             * @example 0123456789ABCDEF
              */
-            notification_ids: string[];
-        };
-        /** UserObjectstoreUsage */
-        UserObjectstoreUsage: {
-            /** Object Store Id */
-            object_store_id: string;
-            /** Total Disk Usage */
-            total_disk_usage: number;
+            id: string;
+        } & {
+            [key: string]: unknown;
         };
-        /** UserQuota */
-        UserQuota: {
+        /** UpdateCreatorAction */
+        UpdateCreatorAction: {
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
-            model_class: "UserQuotaAssociation";
-            /**
-             * User
-             * @description Information about a user associated with a quota.
-             */
-            user: components["schemas"]["UserModel"];
-        };
-        /** UserQuotaUsage */
-        UserQuotaUsage: {
-            /** Quota */
-            quota?: string | null;
-            /** Quota Bytes */
-            quota_bytes?: number | null;
-            /** Quota Percent */
-            quota_percent?: number | null;
-            /** Quota Source Label */
-            quota_source_label?: string | null;
-            /** Total Disk Usage */
-            total_disk_usage: number;
-        };
-        /** ValidationError */
-        ValidationError: {
-            /** Location */
-            loc: (string | number)[];
-            /** Message */
-            msg: string;
-            /** Error Type */
-            type: string;
+            action_type: "update_creator";
+            /** Creator */
+            creator?: unknown;
         };
-        /** Visualization */
-        Visualization: Record<string, never>;
-        /** VisualizationSummary */
-        VisualizationSummary: {
-            /**
-             * Annotation
-             * @description The annotation of this Visualization.
-             */
-            annotation?: string | null;
-            /**
-             * Create Time
-             * @description The time and date this item was created.
-             */
-            create_time: string | null;
+        /** UpdateDatasetPermissionsPayload */
+        UpdateDatasetPermissionsPayload: {
+            /** Access Ids[] */
+            "access_ids[]"?: string[] | string | null;
             /**
-             * DbKey
-             * @description The database key of the visualization.
+             * Action
+             * @description Indicates what action should be performed on the dataset.
+             * @default set_permissions
              */
-            dbkey?: string | null;
+            action: components["schemas"]["DatasetPermissionAction"] | null;
+            /** Manage Ids[] */
+            "manage_ids[]"?: string[] | string | null;
+            /** Modify Ids[] */
+            "modify_ids[]"?: string[] | string | null;
+        };
+        /** UpdateDatasetPermissionsPayloadAliasB */
+        UpdateDatasetPermissionsPayloadAliasB: {
             /**
-             * Deleted
-             * @description Whether this Visualization has been deleted.
+             * Access IDs
+             * @description A list of role encoded IDs defining roles that should have access permission on the dataset.
              */
-            deleted: boolean;
+            access?: string[] | string | null;
             /**
-             * ID
-             * @description Encoded ID of the Visualization.
-             * @example 0123456789ABCDEF
+             * Action
+             * @description Indicates what action should be performed on the dataset.
+             * @default set_permissions
              */
-            id: string;
+            action: components["schemas"]["DatasetPermissionAction"] | null;
             /**
-             * Importable
-             * @description Whether this Visualization can be imported.
+             * Manage IDs
+             * @description A list of role encoded IDs defining roles that should have manage permission on the dataset.
              */
-            importable: boolean;
+            manage?: string[] | string | null;
             /**
-             * Published
-             * @description Whether this Visualization has been published.
+             * Modify IDs
+             * @description A list of role encoded IDs defining roles that should have modify permission on the dataset.
              */
-            published: boolean;
+            modify?: string[] | string | null;
+        };
+        /** UpdateDatasetPermissionsPayloadAliasC */
+        UpdateDatasetPermissionsPayloadAliasC: {
             /**
-             * Tags
-             * @description A list of tags to add to this item.
+             * Access IDs
+             * @description A list of role encoded IDs defining roles that should have access permission on the dataset.
              */
-            tags: components["schemas"]["TagCollection"] | null;
+            access_ids?: string[] | string | null;
             /**
-             * Title
-             * @description The name of the visualization.
+             * Action
+             * @description Indicates what action should be performed on the dataset.
+             * @default set_permissions
              */
-            title: string;
+            action: components["schemas"]["DatasetPermissionAction"] | null;
             /**
-             * Type
-             * @description The type of the visualization.
+             * Manage IDs
+             * @description A list of role encoded IDs defining roles that should have manage permission on the dataset.
              */
-            type: string;
+            manage_ids?: string[] | string | null;
             /**
-             * Update Time
-             * @description The last time and date this item was updated.
+             * Modify IDs
+             * @description A list of role encoded IDs defining roles that should have modify permission on the dataset.
              */
-            update_time: string | null;
+            modify_ids?: string[] | string | null;
+        };
+        /**
+         * UpdateHistoryContentsBatchPayload
+         * @description Contains property values that will be updated for all the history `items` provided.
+         * @example {
+         *       "items": [
+         *         {
+         *           "history_content_type": "dataset",
+         *           "id": "string"
+         *         }
+         *       ],
+         *       "visible": false
+         *     }
+         */
+        UpdateHistoryContentsBatchPayload: {
             /**
-             * Username
-             * @description The name of the user owning this Visualization.
+             * Items
+             * @description A list of content items to update with the changes.
              */
-            username: string;
-            [key: string]: unknown | undefined;
+            items: components["schemas"]["UpdateContentItem"][];
+        } & {
+            [key: string]: unknown;
         };
         /**
-         * VisualizationSummaryList
-         * @default []
+         * UpdateHistoryContentsPayload
+         * @description Can contain arbitrary/dynamic fields that will be updated for a particular history item.
+         * @example {
+         *       "annotation": "Test",
+         *       "visible": false
+         *     }
          */
-        VisualizationSummaryList: components["schemas"]["VisualizationSummary"][];
-        /** WorkflowInput */
-        WorkflowInput: {
+        UpdateHistoryContentsPayload: {
             /**
-             * Label
-             * @description Label of the input.
+             * Annotation
+             * @description A user-defined annotation for this item.
              */
-            label: string | null;
+            annotation?: string | null;
             /**
-             * UUID
-             * @description Universal unique identifier of the input.
+             * Deleted
+             * @description Whether this item is marked as deleted.
              */
-            uuid: string | null;
+            deleted?: boolean | null;
             /**
-             * Value
-             * @description TODO
+             * Name
+             * @description The new name of the item.
              */
-            value: Record<string, never> | null;
-        };
-        /** WorkflowInvocationCollectionView */
-        WorkflowInvocationCollectionView: {
+            name?: string | null;
             /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
+             * Tags
+             * @description A list of tags to add to this item.
              */
-            create_time: string;
+            tags?: components["schemas"]["TagCollection"] | null;
             /**
-             * History ID
-             * @description The encoded ID of the history associated with the invocation.
-             * @example 0123456789ABCDEF
+             * Visible
+             * @description Whether this item is visible in the history.
              */
-            history_id: string;
+            visible?: boolean | null;
+        } & {
+            [key: string]: unknown;
+        };
+        /** UpdateHistoryPayload */
+        UpdateHistoryPayload: {
+            /** Annotation */
+            annotation?: string | null;
+            /** Deleted */
+            deleted?: boolean | null;
+            /** Genome Build */
+            genome_build?: string | null;
+            /** Importable */
+            importable?: boolean | null;
+            /** Name */
+            name?: string | null;
+            /** Preferred Object Store Id */
+            preferred_object_store_id?: string | null;
+            /** Published */
+            published?: boolean | null;
+            /** Purged */
+            purged?: boolean | null;
+            tags?: components["schemas"]["TagCollection"] | null;
+        };
+        /** UpdateInstancePayload */
+        UpdateInstancePayload: {
+            /** Active */
+            active?: boolean | null;
+            /** Description */
+            description?: string | null;
+            /** Hidden */
+            hidden?: boolean | null;
+            /** Name */
+            name?: string | null;
+            /** Variables */
+            variables?: {
+                [key: string]: string | boolean | number;
+            } | null;
+        };
+        /** UpdateInstanceSecretPayload */
+        UpdateInstanceSecretPayload: {
+            /** Secret Name */
+            secret_name: string;
+            /** Secret Value */
+            secret_value: string;
+        };
+        /** UpdateLibraryFolderPayload */
+        UpdateLibraryFolderPayload: {
             /**
-             * ID
-             * @description The encoded ID of the workflow invocation.
-             * @example 0123456789ABCDEF
+             * Description
+             * @description The new description of the library folder.
              */
-            id: string;
+            description?: string | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Name
+             * @description The new name of the library folder.
              */
-            model_class: "WorkflowInvocation";
+            name?: string | null;
+        };
+        /** UpdateLibraryPayload */
+        UpdateLibraryPayload: {
             /**
-             * Invocation state
-             * @description State of workflow invocation.
+             * Description
+             * @description A detailed description of the Library. Leave unset to keep the existing.
              */
-            state: components["schemas"]["InvocationState"];
+            description?: string | null;
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * Name
+             * @description The new name of the Library. Leave unset to keep the existing.
              */
-            update_time: string;
+            name?: string | null;
             /**
-             * UUID
-             * @description Universal unique identifier of the workflow invocation.
+             * Synopsis
+             * @description A short text describing the contents of the Library. Leave unset to keep the existing.
              */
-            uuid?: string | string | null;
+            synopsis?: string | null;
+        };
+        /** UpdateLicenseAction */
+        UpdateLicenseAction: {
             /**
-             * Workflow ID
-             * @description The encoded Workflow ID associated with the invocation.
-             * @example 0123456789ABCDEF
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            workflow_id: string;
+            action_type: "update_license";
+            /** License */
+            license: string;
         };
-        /** WorkflowInvocationElementView */
-        WorkflowInvocationElementView: {
-            /**
-             * Create Time
-             * Format: date-time
-             * @description The time and date this item was created.
-             */
-            create_time: string;
+        /** UpdateNameAction */
+        UpdateNameAction: {
             /**
-             * History ID
-             * @description The encoded ID of the history associated with the invocation.
-             * @example 0123456789ABCDEF
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            history_id: string;
+            action_type: "update_name";
+            /** Name */
+            name: string;
+        };
+        /** UpdateObjectStoreIdPayload */
+        UpdateObjectStoreIdPayload: {
             /**
-             * ID
-             * @description The encoded ID of the workflow invocation.
-             * @example 0123456789ABCDEF
+             * Object Store Id
+             * @description Object store ID to update to, it must be an object store with the same device ID as the target dataset currently.
              */
-            id: string;
+            object_store_id: string;
+        };
+        /** UpdateOutputLabelAction */
+        UpdateOutputLabelAction: {
             /**
-             * Input step parameters
-             * @description Input step parameters of the workflow invocation.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            input_step_parameters: {
-                [key: string]: components["schemas"]["InvocationInputParameter"] | undefined;
-            };
+            action_type: "update_output_label";
+            /** Output */
+            output:
+                | components["schemas"]["OutputReferenceByOrderIndex"]
+                | components["schemas"]["OutputReferenceByLabel"];
+            /** Output Label */
+            output_label: string;
+        };
+        /** UpdateQuotaParams */
+        UpdateQuotaParams: {
             /**
-             * Inputs
-             * @description Input datasets/dataset collections of the workflow invocation.
+             * Amount
+             * @description Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``)
              */
-            inputs: {
-                [key: string]: components["schemas"]["InvocationInput"] | undefined;
-            };
+            amount?: string | null;
             /**
-             * Messages
-             * @description A list of messages about why the invocation did not succeed.
+             * Default
+             * @description Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. Calling this method with ``default="no"`` on a non-default quota will throw an error. Not passing this parameter is equivalent to passing ``no``.
              */
-            messages: (
-                | components["schemas"]["InvocationCancellationReviewFailedResponse"]
-                | components["schemas"]["InvocationCancellationHistoryDeletedResponse"]
-                | components["schemas"]["InvocationCancellationUserRequestResponse"]
-                | components["schemas"]["InvocationFailureDatasetFailedResponse"]
-                | components["schemas"]["InvocationFailureCollectionFailedResponse"]
-                | components["schemas"]["InvocationFailureJobFailedResponse"]
-                | components["schemas"]["InvocationFailureOutputNotFoundResponse"]
-                | components["schemas"]["InvocationFailureExpressionEvaluationFailedResponse"]
-                | components["schemas"]["InvocationFailureWhenNotBooleanResponse"]
-                | components["schemas"]["InvocationUnexpectedFailureResponse"]
-                | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"]
-            )[];
+            default?: components["schemas"]["DefaultQuotaValues"] | null;
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
-             * @enum {string}
+             * Description
+             * @description Detailed text description for this Quota.
              */
-            model_class: "WorkflowInvocation";
+            description?: string | null;
             /**
-             * Output collections
-             * @description Output dataset collections of the workflow invocation.
+             * Groups
+             * @description A list of group IDs or names to associate with this quota.
              */
-            output_collections: {
-                [key: string]: components["schemas"]["InvocationOutputCollection"] | undefined;
-            };
+            in_groups?: string[] | null;
             /**
-             * Output values
-             * @description Output values of the workflow invocation.
+             * Users
+             * @description A list of user IDs or user emails to associate with this quota.
              */
-            output_values: Record<string, never>;
+            in_users?: string[] | null;
             /**
-             * Outputs
-             * @description Output datasets of the workflow invocation.
+             * Name
+             * @description The new name of the quota. This must be unique within a Galaxy instance.
              */
-            outputs: {
-                [key: string]: components["schemas"]["InvocationOutput"] | undefined;
-            };
+            name?: string | null;
             /**
-             * Invocation state
-             * @description State of workflow invocation.
+             * Operation
+             * @description One of (``+``, ``-``, ``=``). If you wish to change this value, you must also provide the ``amount``, otherwise it will not take effect.
+             * @default =
              */
-            state: components["schemas"]["InvocationState"];
+            operation: components["schemas"]["QuotaOperation"];
+        };
+        /** UpdateReportAction */
+        UpdateReportAction: {
             /**
-             * Steps
-             * @description Steps of the workflow invocation.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            steps: components["schemas"]["InvocationStep"][];
+            action_type: "update_report";
+            report: components["schemas"]["Report"];
+        };
+        /** UpdateStepLabelAction */
+        UpdateStepLabelAction: {
             /**
-             * Update Time
-             * Format: date-time
-             * @description The last time and date this item was updated.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            update_time: string;
+            action_type: "update_step_label";
             /**
-             * UUID
-             * @description Universal unique identifier of the workflow invocation.
+             * Label
+             * @description The unique label of the step being referenced.
              */
-            uuid?: string | string | null;
+            label: string;
             /**
-             * Workflow ID
-             * @description The encoded Workflow ID associated with the invocation.
-             * @example 0123456789ABCDEF
+             * Step
+             * @description The target step for this action.
              */
-            workflow_id: string;
+            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
         };
-        /** WorkflowInvocationResponse */
-        WorkflowInvocationResponse:
-            | components["schemas"]["WorkflowInvocationElementView"]
-            | components["schemas"]["WorkflowInvocationCollectionView"];
-        /** WorkflowInvocationStateSummary */
-        WorkflowInvocationStateSummary: {
-            /**
-             * Id
-             * @example 0123456789ABCDEF
-             */
-            id: string;
+        /** UpdateStepPositionAction */
+        UpdateStepPositionAction: {
             /**
-             * Model class
-             * @description The name of the database model class.
-             * @constant
+             * @description discriminator enum property added by openapi-typescript
              * @enum {string}
              */
-            model: "WorkflowInvocation";
+            action_type: "update_step_position";
+            position_shift: components["schemas"]["Position"];
             /**
-             * Populated State
-             * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated.
+             * Step
+             * @description The target step for this action.
              */
-            populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
+            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
+        };
+        /**
+         * UpdateUserNotificationPreferencesRequest
+         * @description Contains the new notification preferences of a user.
+         */
+        UpdateUserNotificationPreferencesRequest: {
             /**
-             * States
-             * @description A dictionary of job states and the number of jobs in that state.
-             * @default {}
+             * Preferences
+             * @description The new notification preferences of the user.
              */
-            states?: {
-                [key: string]: number | undefined;
+            preferences: {
+                [key: string]: components["schemas"]["NotificationCategorySettings"];
             };
         };
-        /** WriteInvocationStoreToPayload */
-        WriteInvocationStoreToPayload: {
+        /** UpgradeAllStepsAction */
+        UpgradeAllStepsAction: {
             /**
-             * Bco Merge History Metadata
-             * @description When reading tags/annotations to generate BCO object include history metadata.
-             * @default false
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            bco_merge_history_metadata?: boolean;
+            action_type: "upgrade_all_steps";
+        };
+        /** UpgradeInstancePayload */
+        UpgradeInstancePayload: {
+            /** Secrets */
+            secrets: {
+                [key: string]: string;
+            };
+            /** Template Version */
+            template_version: number;
+            /** Variables */
+            variables: {
+                [key: string]: string | boolean | number;
+            };
+        };
+        /** UpgradeSubworkflowAction */
+        UpgradeSubworkflowAction: {
             /**
-             * Bco Override Algorithmic Error
-             * @description Override algorithmic error for 'error domain' when generating BioCompute object.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            bco_override_algorithmic_error?: {
-                [key: string]: string | undefined;
-            } | null;
+            action_type: "upgrade_subworkflow";
+            /** Content Id */
+            content_id?: string | null;
             /**
-             * Bco Override Empirical Error
-             * @description Override empirical error for 'error domain' when generating BioCompute object.
+             * Step
+             * @description The target step for this action.
              */
-            bco_override_empirical_error?: {
-                [key: string]: string | undefined;
-            } | null;
+            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
+        };
+        /** UpgradeToolAction */
+        UpgradeToolAction: {
             /**
-             * Bco Override Environment Variables
-             * @description Override environment variables for 'execution_domain' when generating BioCompute object.
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            bco_override_environment_variables?: {
-                [key: string]: string | undefined;
-            } | null;
+            action_type: "upgrade_tool";
             /**
-             * Bco Override Xref
-             * @description Override xref for 'description domain' when generating BioCompute object.
+             * Step
+             * @description The target step for this action.
              */
-            bco_override_xref?: components["schemas"]["XrefItem"][] | null;
+            step: components["schemas"]["StepReferenceByOrderIndex"] | components["schemas"]["StepReferenceByLabel"];
+            /** Tool Version */
+            tool_version?: string | null;
+        };
+        /**
+         * UploadOption
+         * @enum {string}
+         */
+        UploadOption: "upload_file" | "upload_paths" | "upload_directory";
+        /** UrlDataElement */
+        UrlDataElement: {
+            /** Md5 */
+            MD5?: string | null;
+            /** Sha-1 */
+            "SHA-1"?: string | null;
+            /** Sha-256 */
+            "SHA-256"?: string | null;
+            /** Sha-512 */
+            "SHA-512"?: string | null;
             /**
-             * Include deleted
-             * @description Include file contents for deleted datasets (if include_files is True).
+             * Auto Decompress
+             * @description Decompress compressed data before sniffing?
              * @default false
              */
-            include_deleted?: boolean;
+            auto_decompress: boolean;
+            /** Collection Type */
+            collection_type?: string | null;
+            /** Created From Basename */
+            created_from_basename?: string | null;
             /**
-             * Include Files
-             * @description include materialized files in export when available
-             * @default true
+             * Dbkey
+             * @default ?
              */
-            include_files?: boolean;
+            dbkey: string;
             /**
-             * Include hidden
-             * @description Include file contents for hidden datasets (if include_files is True).
+             * Deferred
              * @default false
              */
-            include_hidden?: boolean;
+            deferred: boolean;
+            /** Description */
+            description?: string | null;
+            elements_from?: components["schemas"]["ElementsFromType"] | null;
             /**
-             * @description format of model store to export
-             * @default tar.gz
+             * Ext
+             * @default auto
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
-            /**
-             * Target URI
-             * @description Galaxy Files URI to write mode store content to.
-             */
-            target_uri: string;
-        };
-        /** WriteStoreToPayload */
-        WriteStoreToPayload: {
+            ext: string;
+            extra_files?: components["schemas"]["ExtraFiles"] | null;
+            /** Hashes */
+            hashes?: components["schemas"]["FetchDatasetHash"][] | null;
+            /** Info */
+            info?: string | null;
+            /** Name */
+            name?: string | number | boolean | null;
             /**
-             * Include deleted
-             * @description Include file contents for deleted datasets (if include_files is True).
+             * Space To Tab
              * @default false
              */
-            include_deleted?: boolean;
+            space_to_tab: boolean;
             /**
-             * Include Files
-             * @description include materialized files in export when available
-             * @default true
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
              */
-            include_files?: boolean;
+            src: "url";
+            /** Tags */
+            tags?: string[] | null;
             /**
-             * Include hidden
-             * @description Include file contents for hidden datasets (if include_files is True).
+             * To Posix Lines
              * @default false
              */
-            include_hidden?: boolean;
+            to_posix_lines: boolean;
             /**
-             * @description format of model store to export
-             * @default tar.gz
+             * Url
+             * @description URL to upload
              */
-            model_store_format?: components["schemas"]["ModelStoreFormat"];
+            url: string;
+        };
+        /** UserBeaconSetting */
+        UserBeaconSetting: {
             /**
-             * Target URI
-             * @description Galaxy Files URI to write mode store content to.
+             * Enabled
+             * @description True if beacon sharing is enabled
              */
-            target_uri: string;
+            enabled: boolean;
         };
-        /** XrefItem */
-        XrefItem: {
+        /** UserConcreteObjectStoreModel */
+        UserConcreteObjectStoreModel: {
+            /** Active */
+            active: boolean;
+            /** Badges */
+            badges: components["schemas"]["BadgeDict"][];
+            /** Description */
+            description?: string | null;
+            /** Device */
+            device?: string | null;
+            /** Hidden */
+            hidden: boolean;
+            /** Name */
+            name?: string | null;
+            /** Object Store Id */
+            object_store_id?: string | null;
+            /** Private */
+            private: boolean;
+            /** Purged */
+            purged: boolean;
+            quota: components["schemas"]["QuotaModel"];
+            /** Secrets */
+            secrets: string[];
+            /** Template Id */
+            template_id: string;
+            /** Template Version */
+            template_version: number;
             /**
-             * Access Time
-             * Format: date-time
-             * @description Date and time the external reference was accessed
+             * Type
+             * @enum {string}
              */
-            access_time: string;
+            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3" | "onedata";
             /**
-             * Ids
-             * @description List of reference identifiers
+             * Uuid
+             * Format: uuid4
              */
-            ids: string[];
+            uuid: string;
+            /** Variables */
+            variables: {
+                [key: string]: string | boolean | number;
+            } | null;
+        };
+        /** UserCreationPayload */
+        UserCreationPayload: {
             /**
-             * Name
-             * @description Name of external reference
+             * Email
+             * @description Email of the user
              */
-            name: string;
+            email: string;
             /**
-             * Namespace
-             * @description External resource vendor prefix
+             * user_password
+             * @description The password of the user.
              */
-            namespace: string;
+            password: string;
+            /**
+             * user_name
+             * @description The name of the user.
+             */
+            username: string;
         };
-        /** Organization */
-        galaxy__schema__drs__Organization: {
+        /** UserDeletionPayload */
+        UserDeletionPayload: {
             /**
-             * Name
-             * @description Name of the organization responsible for the service
+             * Purge user
+             * @deprecated
+             * @description Purge the user. Deprecated, please use the `purge` query parameter instead.
+             * @default false
+             */
+            purge: boolean;
+        };
+        /** UserEmail */
+        UserEmail: {
+            /**
+             * Email
+             * @description The email of the user.
+             */
+            email: string;
+            /**
+             * User ID
+             * @description The encoded ID of the user.
+             * @example 0123456789ABCDEF
              */
+            id: string;
+        };
+        /** UserFileSourceModel */
+        UserFileSourceModel: {
+            /** Active */
+            active: boolean;
+            /** Description */
+            description: string | null;
+            /** Hidden */
+            hidden: boolean;
+            /** Name */
             name: string;
+            /** Purged */
+            purged: boolean;
+            /** Secrets */
+            secrets: string[];
+            /** Template Id */
+            template_id: string;
+            /** Template Version */
+            template_version: number;
             /**
-             * Url
-             * Format: uri
-             * @description URL of the website of the organization (RFC 3986 format)
+             * Type
+             * @enum {string}
              */
-            url: string;
+            type: "ftp" | "posix" | "s3fs" | "azure" | "onedata" | "webdav" | "dropbox" | "googledrive";
+            /** Uri Root */
+            uri_root: string;
+            /**
+             * Uuid
+             * Format: uuid4
+             */
+            uuid: string;
+            /** Variables */
+            variables: {
+                [key: string]: string | boolean | number;
+            } | null;
+        };
+        /**
+         * UserModel
+         * @description User in a transaction context.
+         */
+        UserModel: {
+            /**
+             * Active
+             * @description User is active
+             */
+            active: boolean;
+            /**
+             * Deleted
+             * @description  User is deleted
+             */
+            deleted: boolean;
+            /**
+             * Email
+             * @description Email of the user
+             */
+            email: string;
+            /**
+             * ID
+             * @description Encoded ID of the user
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /** Last password change */
+            last_password_change: string | null;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "User";
+            /**
+             * user_name
+             * @description The name of the user.
+             */
+            username: string;
+        };
+        /**
+         * UserNotificationListResponse
+         * @description A list of user notifications.
+         */
+        UserNotificationListResponse: components["schemas"]["UserNotificationResponse"][];
+        /**
+         * UserNotificationPreferences
+         * @description Contains the full notification preferences of a user.
+         */
+        UserNotificationPreferences: {
+            /**
+             * Preferences
+             * @description The notification preferences of the user.
+             */
+            preferences: {
+                [key: string]: components["schemas"]["NotificationCategorySettings"];
+            };
+        };
+        /**
+         * UserNotificationResponse
+         * @description A notification response specific to the user.
+         */
+        UserNotificationResponse: {
+            /**
+             * Category
+             * @description The category of the notification. Represents the type of the notification. E.g. 'message' or 'new_shared_item'.
+             */
+            category: components["schemas"]["PersonalNotificationCategory"];
+            /**
+             * Content
+             * @description The content of the notification. The structure depends on the category.
+             */
+            content:
+                | components["schemas"]["MessageNotificationContent"]
+                | components["schemas"]["NewSharedItemNotificationContent"];
+            /**
+             * Create time
+             * Format: date-time
+             * @description The time when the notification was created.
+             */
+            create_time: string;
+            /**
+             * Deleted
+             * @description Whether the notification is marked as deleted by the user. Deleted notifications don't show up in the notification list.
+             */
+            deleted: boolean;
+            /**
+             * Expiration time
+             * @description The time when the notification will expire. If not set, the notification will never expire. Expired notifications will be permanently deleted.
+             */
+            expiration_time?: string | null;
+            /**
+             * ID
+             * @description The encoded ID of the notification.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Publication time
+             * Format: date-time
+             * @description The time when the notification was published. Notifications can be created and then published at a later time.
+             */
+            publication_time: string;
+            /**
+             * Seen time
+             * @description The time when the notification was seen by the user. If not set, the notification was not seen yet.
+             */
+            seen_time?: string | null;
+            /**
+             * Source
+             * @description The source of the notification. Represents the agent that created the notification. E.g. 'galaxy' or 'admin'.
+             */
+            source: string;
+            /**
+             * Update time
+             * Format: date-time
+             * @description The time when the notification was last updated.
+             */
+            update_time: string;
+            /**
+             * Variant
+             * @description The variant of the notification. Represents the intent or relevance of the notification. E.g. 'info' or 'urgent'.
+             */
+            variant: components["schemas"]["NotificationVariant"];
+        };
+        /**
+         * UserNotificationUpdateRequest
+         * @description A notification update request specific to the user.
+         */
+        UserNotificationUpdateRequest: {
+            /**
+             * Deleted
+             * @description Whether the notification should be marked as deleted by the user. If not set, the notification will not be changed.
+             */
+            deleted?: boolean | null;
+            /**
+             * Seen
+             * @description Whether the notification should be marked as seen by the user. If not set, the notification will not be changed.
+             */
+            seen?: boolean | null;
+        };
+        /**
+         * UserNotificationsBatchUpdateRequest
+         * @description A batch update request specific for user notifications.
+         */
+        UserNotificationsBatchUpdateRequest: {
+            /**
+             * Changes
+             * @description The changes that should be applied to the notifications. Only the fields that are set will be changed.
+             */
+            changes: components["schemas"]["UserNotificationUpdateRequest"];
+            /**
+             * Notification IDs
+             * @description The list of encoded notification IDs of the notifications that should be updated.
+             */
+            notification_ids: string[];
+        };
+        /** UserObjectstoreUsage */
+        UserObjectstoreUsage: {
+            /** Object Store Id */
+            object_store_id: string;
+            /** Total Disk Usage */
+            total_disk_usage: number;
+        };
+        /** UserQuota */
+        UserQuota: {
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "UserQuotaAssociation";
+            /**
+             * User
+             * @description Information about a user associated with a quota.
+             */
+            user: components["schemas"]["UserModel"];
+        };
+        /** UserQuotaUsage */
+        UserQuotaUsage: {
+            /** Quota */
+            quota?: string | null;
+            /** Quota Bytes */
+            quota_bytes?: number | null;
+            /** Quota Percent */
+            quota_percent?: number | null;
+            /** Quota Source Label */
+            quota_source_label?: string | null;
+            /** Total Disk Usage */
+            total_disk_usage: number;
+        };
+        /** UserUpdatePayload */
+        UserUpdatePayload: {
+            /**
+             * Active
+             * @description User is active
+             */
+            active?: boolean | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store new datasets in this history.
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Username
+             * @description The name of the user.
+             */
+            username?: string | null;
+        };
+        /** Visualization */
+        Visualization: Record<string, never>;
+        /** VisualizationCreatePayload */
+        VisualizationCreatePayload: {
+            /**
+             * Annotation
+             * @description The annotation of the visualization.
+             */
+            annotation?: string | null;
+            /**
+             * Config
+             * @description The config of the visualization.
+             * @default {}
+             */
+            config: Record<string, never> | null;
+            /**
+             * DbKey
+             * @description The database key of the visualization.
+             */
+            dbkey?: string | null;
+            /**
+             * Slug
+             * @description The slug of the visualization.
+             */
+            slug?: string | null;
+            /**
+             * Title
+             * @description The name of the visualization.
+             * @default Untitled Visualization
+             */
+            title: string | null;
+            /**
+             * Type
+             * @description The type of the visualization.
+             */
+            type: string;
+        };
+        /** VisualizationCreateResponse */
+        VisualizationCreateResponse: {
+            /**
+             * ID
+             * @description Encoded ID of the Visualization.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+        };
+        /** VisualizationPluginResponse */
+        VisualizationPluginResponse: {
+            /**
+             * Description
+             * @description The description of the plugin.
+             */
+            description: string;
+            /**
+             * Embeddable
+             * @description Whether the plugin is embeddable.
+             */
+            embeddable: boolean;
+            /**
+             * Entry Point
+             * @description The entry point of the plugin.
+             */
+            entry_point: Record<string, never>;
+            /**
+             * Groups
+             * @description The groups of the plugin.
+             */
+            groups?: Record<string, never>[] | null;
+            /**
+             * Href
+             * @description The href of the plugin.
+             */
+            href: string;
+            /**
+             * HTML
+             * @description The HTML of the plugin.
+             */
+            html: string;
+            /**
+             * Logo
+             * @description The logo of the plugin.
+             */
+            logo?: string | null;
+            /**
+             * Name
+             * @description The name of the plugin.
+             */
+            name: string;
+            /**
+             * Settings
+             * @description The settings of the plugin.
+             */
+            settings: Record<string, never>[];
+            /**
+             * Specs
+             * @description The specs of the plugin.
+             */
+            specs?: Record<string, never> | null;
+            /**
+             * Target
+             * @description The target of the plugin.
+             */
+            target: string;
+            /**
+             * Title
+             * @description The title of the plugin.
+             */
+            title?: string | null;
+        };
+        /** VisualizationRevisionResponse */
+        VisualizationRevisionResponse: {
+            /**
+             * Config
+             * @description The config of the visualization revision.
+             */
+            config: Record<string, never>;
+            /**
+             * DbKey
+             * @description The database key of the visualization.
+             */
+            dbkey?: string | null;
+            /**
+             * ID
+             * @description Encoded ID of the Visualization Revision.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "VisualizationRevision";
+            /**
+             * Title
+             * @description The name of the visualization revision.
+             */
+            title: string;
+            /**
+             * Visualization ID
+             * @description Encoded ID of the Visualization.
+             * @example 0123456789ABCDEF
+             */
+            visualization_id: string;
+        };
+        /** VisualizationShowResponse */
+        VisualizationShowResponse: {
+            /**
+             * Annotation
+             * @description The annotation of this Visualization.
+             */
+            annotation?: string | null;
+            /**
+             * DbKey
+             * @description The database key of the visualization.
+             */
+            dbkey?: string | null;
+            /**
+             * Email Hash
+             * @description The hash of the email of the user owning this Visualization.
+             */
+            email_hash: string;
+            /**
+             * ID
+             * @description Encoded ID of the Visualization.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Latest Revision
+             * @description The latest revision of this Visualization.
+             */
+            latest_revision: components["schemas"]["VisualizationRevisionResponse"];
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "Visualization";
+            /**
+             * Plugin
+             * @description The plugin of this Visualization.
+             */
+            plugin?: components["schemas"]["VisualizationPluginResponse"] | null;
+            /**
+             * Revisions
+             * @description A list of encoded IDs of the revisions of this Visualization.
+             */
+            revisions: string[];
+            /**
+             * Slug
+             * @description The slug of the visualization.
+             */
+            slug?: string | null;
+            /**
+             * Tags
+             * @description A list of tags to add to this item.
+             */
+            tags?: components["schemas"]["TagCollection"] | null;
+            /**
+             * Title
+             * @description The name of the visualization.
+             */
+            title: string;
+            /**
+             * Type
+             * @description The type of the visualization.
+             */
+            type: string;
+            /**
+             * URL
+             * @description The URL of the visualization.
+             */
+            url: string;
+            /**
+             * User ID
+             * @description The ID of the user owning this Visualization.
+             * @example 0123456789ABCDEF
+             */
+            user_id: string;
+            /**
+             * Username
+             * @description The name of the user owning this Visualization.
+             */
+            username: string;
+        };
+        /** VisualizationSummary */
+        VisualizationSummary: {
+            /**
+             * Annotation
+             * @description The annotation of this Visualization.
+             */
+            annotation?: string | null;
+            /**
+             * Create Time
+             * @description The time and date this item was created.
+             */
+            create_time: string | null;
+            /**
+             * DbKey
+             * @description The database key of the visualization.
+             */
+            dbkey?: string | null;
+            /**
+             * Deleted
+             * @description Whether this Visualization has been deleted.
+             */
+            deleted: boolean;
+            /**
+             * ID
+             * @description Encoded ID of the Visualization.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Importable
+             * @description Whether this Visualization can be imported.
+             */
+            importable: boolean;
+            /**
+             * Published
+             * @description Whether this Visualization has been published.
+             */
+            published: boolean;
+            /**
+             * Tags
+             * @description A list of tags to add to this item.
+             */
+            tags: components["schemas"]["TagCollection"] | null;
+            /**
+             * Title
+             * @description The name of the visualization.
+             */
+            title: string;
+            /**
+             * Type
+             * @description The type of the visualization.
+             */
+            type: string;
+            /**
+             * Update Time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string | null;
+            /**
+             * Username
+             * @description The name of the user owning this Visualization.
+             */
+            username: string;
+        } & {
+            [key: string]: unknown;
+        };
+        /**
+         * VisualizationSummaryList
+         * @default []
+         */
+        VisualizationSummaryList: components["schemas"]["VisualizationSummary"][];
+        /** VisualizationUpdatePayload */
+        VisualizationUpdatePayload: {
+            /**
+             * Config
+             * @description The config of the visualization.
+             * @default {}
+             */
+            config: Record<string, never> | string | null;
+            /**
+             * DbKey
+             * @description The database key of the visualization.
+             */
+            dbkey?: string | null;
+            /**
+             * Deleted
+             * @description Whether this Visualization has been deleted.
+             * @default false
+             */
+            deleted: boolean | null;
+            /**
+             * Title
+             * @description The name of the visualization.
+             */
+            title?: string | null;
+        };
+        /** VisualizationUpdateResponse */
+        VisualizationUpdateResponse: {
+            /**
+             * ID
+             * @description Encoded ID of the Visualization.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Revision
+             * @description Encoded ID of the Visualization Revision.
+             * @example 0123456789ABCDEF
+             */
+            revision: string;
+        };
+        /** WorkflowInput */
+        WorkflowInput: {
+            /**
+             * Label
+             * @description Label of the input.
+             */
+            label: string | null;
+            /**
+             * UUID
+             * @description Universal unique identifier of the input.
+             */
+            uuid: string | null;
+            /**
+             * Value
+             * @description TODO
+             */
+            value: unknown | null;
+        };
+        /** WorkflowInvocationCollectionView */
+        WorkflowInvocationCollectionView: {
+            /**
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
+             */
+            create_time: string;
+            /**
+             * History ID
+             * @description The encoded ID of the history associated with the invocation.
+             * @example 0123456789ABCDEF
+             */
+            history_id: string;
+            /**
+             * ID
+             * @description The encoded ID of the workflow invocation.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "WorkflowInvocation";
+            /**
+             * Invocation state
+             * @description State of workflow invocation.
+             */
+            state: components["schemas"]["InvocationState"];
+            /**
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string;
+            /**
+             * UUID
+             * @description Universal unique identifier of the workflow invocation.
+             */
+            uuid?: string | null;
+            /**
+             * Workflow ID
+             * @description The encoded Workflow ID associated with the invocation.
+             * @example 0123456789ABCDEF
+             */
+            workflow_id: string;
+        };
+        /** WorkflowInvocationElementView */
+        WorkflowInvocationElementView: {
+            /**
+             * Create Time
+             * Format: date-time
+             * @description The time and date this item was created.
+             */
+            create_time: string;
+            /**
+             * History ID
+             * @description The encoded ID of the history associated with the invocation.
+             * @example 0123456789ABCDEF
+             */
+            history_id: string;
+            /**
+             * ID
+             * @description The encoded ID of the workflow invocation.
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * Input step parameters
+             * @description Input step parameters of the workflow invocation.
+             */
+            input_step_parameters: {
+                [key: string]: components["schemas"]["InvocationInputParameter"];
+            };
+            /**
+             * Inputs
+             * @description Input datasets/dataset collections of the workflow invocation.
+             */
+            inputs: {
+                [key: string]: components["schemas"]["InvocationInput"];
+            };
+            /**
+             * Messages
+             * @description A list of messages about why the invocation did not succeed.
+             */
+            messages: components["schemas"]["InvocationMessageResponseUnion"][];
+            /**
+             * Model class
+             * @description The name of the database model class.
+             * @constant
+             * @enum {string}
+             */
+            model_class: "WorkflowInvocation";
+            /**
+             * Output collections
+             * @description Output dataset collections of the workflow invocation.
+             */
+            output_collections: {
+                [key: string]: components["schemas"]["InvocationOutputCollection"];
+            };
+            /**
+             * Output values
+             * @description Output values of the workflow invocation.
+             */
+            output_values: Record<string, never>;
+            /**
+             * Outputs
+             * @description Output datasets of the workflow invocation.
+             */
+            outputs: {
+                [key: string]: components["schemas"]["InvocationOutput"];
+            };
+            /**
+             * Invocation state
+             * @description State of workflow invocation.
+             */
+            state: components["schemas"]["InvocationState"];
+            /**
+             * Steps
+             * @description Steps of the workflow invocation.
+             */
+            steps: components["schemas"]["InvocationStep"][];
+            /**
+             * Update Time
+             * Format: date-time
+             * @description The last time and date this item was updated.
+             */
+            update_time: string;
+            /**
+             * UUID
+             * @description Universal unique identifier of the workflow invocation.
+             */
+            uuid?: string | null;
+            /**
+             * Workflow ID
+             * @description The encoded Workflow ID associated with the invocation.
+             * @example 0123456789ABCDEF
+             */
+            workflow_id: string;
+        };
+        /**
+         * WorkflowInvocationRequestModel
+         * @description Model a workflow invocation request (InvokeWorkflowPayload) for an existing invocation.
+         */
+        WorkflowInvocationRequestModel: {
+            /**
+             * History ID
+             * @description The encoded history id the workflow was run in.
+             */
+            history_id: string;
+            /**
+             * Inputs
+             * @description Values for inputs
+             */
+            inputs: Record<string, never>;
+            /**
+             * Inputs by
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
+             */
+            inputs_by: string;
+            /**
+             * Is instance
+             * @description This API yields a particular workflow instance, newer workflows belonging to the same storedworkflow may have different state.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            instance: true;
+            /**
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead. If these are set, the workflow was not executed in a best-practice fashion and we the resulting invocation request may not fully reflect the executed workflow state.
+             */
+            parameters?: Record<string, never> | null;
+            /**
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            parameters_normalized: true;
+            /**
+             * Preferred Intermediate Object Store ID
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_intermediate_object_store_id?: string | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Preferred Outputs Object Store ID
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
+             */
+            preferred_outputs_object_store_id?: string | null;
+            /**
+             * Replacement Parameters
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
+             * @default {}
+             */
+            replacement_params: Record<string, never> | null;
+            /**
+             * Resource Parameters
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
+             * @default {}
+             */
+            resource_params: Record<string, never> | null;
+            /**
+             * Use cached job
+             * @description Indicated whether to use a cached job for workflow invocation.
+             * @default false
+             */
+            use_cached_job: boolean;
+            /**
+             * Workflow ID
+             * @description The encoded Workflow ID associated with the invocation.
+             */
+            workflow_id: string;
+        };
+        /** WorkflowInvocationResponse */
+        WorkflowInvocationResponse:
+            | components["schemas"]["WorkflowInvocationElementView"]
+            | components["schemas"]["WorkflowInvocationCollectionView"];
+        /** WorkflowInvocationStateSummary */
+        WorkflowInvocationStateSummary: {
+            /**
+             * Id
+             * @example 0123456789ABCDEF
+             */
+            id: string;
+            /**
+             * @description The name of the database model class. (enum property replaced by openapi-typescript)
+             * @enum {string}
+             */
+            model: "WorkflowInvocation";
+            /**
+             * Populated State
+             * @description Indicates the general state of the elements in the dataset collection:- 'new': new dataset collection, unpopulated elements.- 'ok': collection elements populated (HDAs may or may not have errors).- 'failed': some problem populating, won't be populated.
+             */
+            populated_state: components["schemas"]["DatasetCollectionPopulatedState"];
+            /**
+             * States
+             * @description A dictionary of job states and the number of jobs in that state.
+             * @default {}
+             */
+            states: {
+                [key: string]: number;
+            };
+        };
+        /**
+         * WorkflowJobMetric
+         * @example {
+         *       "name": "start_epoch",
+         *       "plugin": "core",
+         *       "raw_value": "1614261340.0000000",
+         *       "title": "Job Start Time",
+         *       "value": "2021-02-25 14:55:40"
+         *     }
+         */
+        WorkflowJobMetric: {
+            /** Job Id */
+            job_id: string;
+            /**
+             * Name
+             * @description The name of the metric variable.
+             */
+            name: string;
+            /**
+             * Plugin
+             * @description The instrumenter plugin that generated this metric.
+             */
+            plugin: string;
+            /**
+             * Raw Value
+             * @description The raw value of the metric as a string.
+             */
+            raw_value: string;
+            /** Step Index */
+            step_index: number;
+            /** Step Label */
+            step_label: string | null;
+            /**
+             * Title
+             * @description A descriptive title for this metric.
+             */
+            title: string;
+            /** Tool Id */
+            tool_id: string;
+            /**
+             * Value
+             * @description The textual representation of the metric value.
+             */
+            value: string;
+        };
+        /** WorkflowLandingRequest */
+        WorkflowLandingRequest: {
+            /** Request State */
+            request_state: Record<string, never>;
+            state: components["schemas"]["LandingRequestState"];
+            /**
+             * UUID
+             * Format: uuid4
+             * @description Universal unique identifier for this dataset.
+             */
+            uuid: string;
+            /** Workflow Id */
+            workflow_id: string;
+            /**
+             * Workflow Target Type
+             * @enum {string}
+             */
+            workflow_target_type: "stored_workflow" | "workflow" | "trs_url";
+        };
+        /** WriteInvocationStoreToPayload */
+        WriteInvocationStoreToPayload: {
+            /**
+             * Bco Merge History Metadata
+             * @description When reading tags/annotations to generate BCO object include history metadata.
+             * @default false
+             */
+            bco_merge_history_metadata: boolean;
+            /**
+             * Bco Override Algorithmic Error
+             * @description Override algorithmic error for 'error domain' when generating BioCompute object.
+             */
+            bco_override_algorithmic_error?: {
+                [key: string]: string;
+            } | null;
+            /**
+             * Bco Override Empirical Error
+             * @description Override empirical error for 'error domain' when generating BioCompute object.
+             */
+            bco_override_empirical_error?: {
+                [key: string]: string;
+            } | null;
+            /**
+             * Bco Override Environment Variables
+             * @description Override environment variables for 'execution_domain' when generating BioCompute object.
+             */
+            bco_override_environment_variables?: {
+                [key: string]: string;
+            } | null;
+            /**
+             * Bco Override Xref
+             * @description Override xref for 'description domain' when generating BioCompute object.
+             */
+            bco_override_xref?: components["schemas"]["XrefItem"][] | null;
+            /**
+             * Include deleted
+             * @description Include file contents for deleted datasets (if include_files is True).
+             * @default false
+             */
+            include_deleted: boolean;
+            /**
+             * Include Files
+             * @description include materialized files in export when available
+             * @default true
+             */
+            include_files: boolean;
+            /**
+             * Include hidden
+             * @description Include file contents for hidden datasets (if include_files is True).
+             * @default false
+             */
+            include_hidden: boolean;
+            /**
+             * @description format of model store to export
+             * @default tar.gz
+             */
+            model_store_format: components["schemas"]["ModelStoreFormat"];
+            /**
+             * Target URI
+             * @description Galaxy Files URI to write mode store content to.
+             */
+            target_uri: string;
+        };
+        /** WriteStoreToPayload */
+        WriteStoreToPayload: {
+            /**
+             * Include deleted
+             * @description Include file contents for deleted datasets (if include_files is True).
+             * @default false
+             */
+            include_deleted: boolean;
+            /**
+             * Include Files
+             * @description include materialized files in export when available
+             * @default true
+             */
+            include_files: boolean;
+            /**
+             * Include hidden
+             * @description Include file contents for hidden datasets (if include_files is True).
+             * @default false
+             */
+            include_hidden: boolean;
+            /**
+             * @description format of model store to export
+             * @default tar.gz
+             */
+            model_store_format: components["schemas"]["ModelStoreFormat"];
+            /**
+             * Target URI
+             * @description Galaxy Files URI to write mode store content to.
+             */
+            target_uri: string;
+        };
+        /** XrefItem */
+        XrefItem: {
+            /**
+             * Access Time
+             * Format: date-time
+             * @description Date and time the external reference was accessed
+             */
+            access_time: string;
+            /**
+             * Ids
+             * @description List of reference identifiers
+             */
+            ids: string[];
+            /**
+             * Name
+             * @description Name of external reference
+             */
+            name: string;
+            /**
+             * Namespace
+             * @description External resource vendor prefix
+             */
+            namespace: string;
+        };
+        /** Organization */
+        galaxy__schema__drs__Organization: {
+            /**
+             * Name
+             * @description Name of the organization responsible for the service
+             */
+            name: string;
+            /**
+             * Url
+             * Format: uri
+             * @description URL of the website of the organization (RFC 3986 format)
+             */
+            url: string;
+        };
+        /** Organization */
+        galaxy__schema__schema__Organization: {
+            /** Address */
+            address?: string | null;
+            /** Alternate Name */
+            alternateName?: string | null;
+            /**
+             * Class
+             * @default Organization
+             */
+            class: string;
+            /** Email */
+            email?: string | null;
+            /** Fax Number */
+            faxNumber?: string | null;
+            /**
+             * Identifier
+             * @description Identifier (typically an orcid.org ID)
+             */
+            identifier?: string | null;
+            /** Image URL */
+            image?: string | null;
+            /**
+             * Name
+             * @description The name of the creator.
+             */
+            name?: string | null;
+            /** Telephone */
+            telephone?: string | null;
+            /** URL */
+            url?: string | null;
+        };
+    };
+    responses: never;
+    parameters: never;
+    requestBodies: never;
+    headers: never;
+    pathItems: never;
+}
+export type $defs = Record<string, never>;
+export interface operations {
+    get_api_key_api_authenticate_baseauth_get: {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["APIKeyResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    query_api_chat_post: {
+        parameters: {
+            query: {
+                job_id: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ChatPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    feedback_api_chat__job_id__feedback_put: {
+        parameters: {
+            query: {
+                feedback: number;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                job_id: string | null;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": number | null;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    index_api_configuration_get: {
+        parameters: {
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Object containing exposable configuration settings */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": Record<string, never>;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    decode_id_api_configuration_decode__encoded_id__get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description Encoded id to be decoded */
+                encoded_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Decoded id */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": {
+                        [key: string]: number;
+                    };
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    dynamic_tool_confs_api_configuration_dynamic_tool_confs_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Dynamic tool configuration files */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": {
+                        [key: string]: string;
+                    }[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    encode_id_api_configuration_encode__decoded_id__get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description Decoded id to be encoded */
+                decoded_id: number;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Encoded id */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": {
+                        [key: string]: string;
+                    };
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    tool_lineages_api_configuration_tool_lineages_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Tool lineages for tools that have them */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": {
+                        [key: string]: Record<string, never>;
+                    }[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    reload_toolbox_api_configuration_toolbox_put: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    content_api_dataset_collection_element__dce_id__get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The encoded ID of the dataset collection element. */
+                dce_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DCESummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    create_api_dataset_collections_post: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateNewCollectionPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["HDCADetailed"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get: {
+        parameters: {
+            query?: {
+                /** @description The type of collection instance. Either `history` (default) or `library`. */
+                instance_type?: "history" | "library";
+                /** @description The maximum number of content elements to return. */
+                limit?: number | null;
+                /** @description The number of content elements that will be skipped before returning. */
+                offset?: number | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                hdca_id: string;
+                /** @description Parent collection ID describing what collection the contents belongs to. */
+                parent_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetCollectionContentElements"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    show_api_dataset_collections__id__get: {
+        parameters: {
+            query?: {
+                /** @description The type of collection instance. Either `history` (default) or `library`. */
+                instance_type?: "history" | "library";
+                /** @description The view of collection instance to return. */
+                view?: string;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json":
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    attributes_api_dataset_collections__id__attributes_get: {
+        parameters: {
+            query?: {
+                /** @description The type of collection instance. Either `history` (default) or `library`. */
+                instance_type?: "history" | "library";
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetCollectionAttributesResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    copy_api_dataset_collections__id__copy_post: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateCollectionAttributePayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    dataset_collections__download: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    prepare_collection_download_api_dataset_collections__id__prepare_download_post: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Short term storage reference for async monitoring of this download. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["AsyncFile"];
+                };
+            };
+            /** @description Required asynchronous tasks required for this operation not available. */
+            501: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    suitable_converters_api_dataset_collections__id__suitable_converters_get: {
+        parameters: {
+            query?: {
+                /** @description The type of collection instance. Either `history` (default) or `library`. */
+                instance_type?: "history" | "library";
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["SuitableConverters"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    index_api_datasets_get: {
+        parameters: {
+            query?: {
+                /** @description Optional identifier of a History. Use it to restrict the search within a particular History. */
+                history_id?: string | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": (
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    delete_batch_api_datasets_delete: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["DeleteDatasetBatchPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DeleteDatasetBatchResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    show_api_datasets__dataset_id__get: {
+        parameters: {
+            query?: {
+                /** @description The type of information about the dataset to be requested. */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                /** @description The type of information about the dataset to be requested. Each of these values may require additional parameters in the request and may return different responses. */
+                data_type?: components["schemas"]["RequestDataType"] | null;
+                /** @description Maximum number of items to return. Currently only applies to `data_type=raw_data` requests */
+                limit?: number | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item. Currently only applies to `data_type=raw_data` requests */
+                offset?: number | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    datasets__update_dataset: {
+        parameters: {
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    datasets__delete: {
+        parameters: {
+            query?: {
+                /**
+                 * @deprecated
+                 * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
+                 */
+                purge?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description When deleting a dataset collection, whether to also delete containing datasets.
+                 */
+                recursive?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to stop the creating job if all outputs of the job have been deleted.
+                 */
+                stop_job?: boolean | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
+            };
+        };
+        responses: {
+            /** @description Request has been executed. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request accepted, processing will finish later. */
+            202: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    get_structured_content_api_datasets__dataset_id__content__content_type__get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+                content_type: components["schemas"]["DatasetContentType"];
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    converted_api_datasets__dataset_id__converted_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["ConvertedDatasetsMap"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    converted_ext_api_datasets__dataset_id__converted__ext__get: {
+        parameters: {
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+                /** @description File extension of the new format to convert this dataset to. */
+                ext: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    extra_files_api_datasets__dataset_id__extra_files_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The encoded database identifier of the dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetExtraFiles"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    get_content_as_text_api_datasets__dataset_id__get_content_as_text_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetTextContentDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    compute_hash_api_datasets__dataset_id__hash_put: {
+        parameters: {
+            query?: {
+                /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ComputeDatasetHashPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
         };
-        /** Organization */
-        galaxy__schema__schema__Organization: {
-            /** Address */
-            address?: string | null;
-            /** Alternate Name */
-            alternateName?: string | null;
-            /**
-             * Class
-             * @default Organization
-             */
-            class?: string;
-            /** Email */
-            email?: string | null;
-            /** Fax Number */
-            faxNumber?: string | null;
-            /**
-             * Identifier
-             * @description Identifier (typically an orcid.org ID)
-             */
-            identifier?: string | null;
-            /** Image URL */
-            image?: string | null;
-            /**
-             * Name
-             * @description The name of the creator.
-             */
-            name?: string | null;
-            /** Telephone */
-            telephone?: string | null;
-            /** URL */
-            url?: string | null;
+    };
+    show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get: {
+        parameters: {
+            query?: {
+                /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetInheritanceChain"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
         };
     };
-    responses: never;
-    parameters: never;
-    requestBodies: never;
-    headers: never;
-    pathItems: never;
-}
-
-export type external = Record<string, never>;
-
-export interface operations {
-    get_api_key_api_authenticate_baseauth_get: {
-        /** Returns returns an API key for authenticated user based on BaseAuth headers. */
+    get_metrics_api_datasets__dataset_id__metrics_get: {
+        parameters: {
+            query?: {
+                /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the dataset */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["APIKeyResponse"];
+                    "application/json": (components["schemas"]["JobMetric"] | null)[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_api_cloud_storage_get_post: {
-        /**
-         * Gets given objects from a given cloud-based bucket to a Galaxy history.
-         * @deprecated
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    datasets__update_object_store_id: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CloudObjects"];
+                "application/json": components["schemas"]["UpdateObjectStoreIdPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetSummaryList"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    send_api_cloud_storage_send_post: {
-        /**
-         * Sends given dataset(s) in a given history to a given cloud-based bucket.
-         * @deprecated
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    resolve_parameters_display_api_datasets__dataset_id__parameters_display_get: {
+        parameters: {
+            query?: {
+                /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the dataset */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["JobDisplayParametersSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    update_permissions_api_datasets__dataset_id__permissions_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CloudDatasets"];
+                "application/json":
+                    | components["schemas"]["UpdateDatasetPermissionsPayload"]
+                    | components["schemas"]["UpdateDatasetPermissionsPayloadAliasB"]
+                    | components["schemas"]["UpdateDatasetPermissionsPayloadAliasC"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetAssociationRoles"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CloudDatasetsResponse"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_configuration_get: {
-        /**
-         * Return an object containing exposable configuration settings
-         * @description Return an object containing exposable configuration settings.
-         *
-         * A more complete list is returned if the user is an admin.
-         * Pass in `view` and a comma-seperated list of keys to control which
-         * configuration settings are returned.
-         */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
+    show_storage_api_datasets__dataset_id__storage_get: {
+        parameters: {
             query?: {
-                view?: string | null;
-                keys?: string | null;
+                /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
+                hda_ldda?: components["schemas"]["DatasetSourceType"];
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                dataset_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DatasetStorageDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    display_api_datasets__history_content_id__display_get: {
+        parameters: {
+            query?: {
+                /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
+                preview?: boolean;
+                /** @description If non-null, get the specified filename from the extra files for this dataset. */
+                filename?: string | null;
+                /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
+                to_ext?: string | null;
+                /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
+                raw?: boolean;
+                /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
+                offset?: number | null;
+                /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes.  */
+                ck_size?: number | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    display_api_datasets__history_content_id__display_head: {
+        parameters: {
+            query?: {
+                /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
+                preview?: boolean;
+                /** @description If non-null, get the specified filename from the extra files for this dataset. */
+                filename?: string | null;
+                /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
+                to_ext?: string | null;
+                /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
+                raw?: boolean;
+                /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
+                offset?: number | null;
+                /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes.  */
+                ck_size?: number | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    datasets__get_metadata_file: {
+        parameters: {
+            query: {
+                /** @description The name of the metadata file to retrieve. */
+                metadata_file: string;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Object containing exposable configuration settings */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    decode_id_api_configuration_decode__encoded_id__get: {
-        /**
-         * Decode a given id
-         * @description Decode a given id.
-         */
+    get_metadata_file_datasets_api_datasets__history_content_id__metadata_file_head: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query: {
+                /** @description The name of the metadata file to retrieve. */
+                metadata_file: string;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description Encoded id to be decoded */
             path: {
-                encoded_id: string;
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Decoded id */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": {
-                        [key: string]: number | undefined;
-                    };
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    dynamic_tool_confs_api_configuration_dynamic_tool_confs_get: {
-        /**
-         * Return dynamic tool configuration files
-         * @description Return dynamic tool configuration files.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+    index_api_datatypes_get: {
+        parameters: {
+            query?: {
+                /** @description Whether to return only the datatype's extension rather than the datatype's details */
+                extension_only?: boolean | null;
+                /** @description Whether to return only datatypes which can be uploaded */
+                upload_only?: boolean | null;
             };
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Dynamic tool configuration files */
+            /** @description List of data types */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": {
-                        [key: string]: string | undefined;
-                    }[];
+                    "application/json": components["schemas"]["DatatypeDetails"][] | string[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    encode_id_api_configuration_encode__decoded_id__get: {
-        /**
-         * Encode a given id
-         * @description Decode a given id.
-         */
+    converters_api_datatypes_converters_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description Decoded id to be encoded */
-            path: {
-                decoded_id: number;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Encoded id */
+            /** @description List of all datatype converters */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": {
-                        [key: string]: string | undefined;
-                    };
+                    "application/json": components["schemas"]["DatatypeConverterList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    tool_lineages_api_configuration_tool_lineages_get: {
-        /**
-         * Return tool lineages for tools that have them
-         * @description Return tool lineages for tools that have them.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
+    edam_data_api_datatypes_edam_data_get: {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Tool lineages for tools that have them */
+            /** @description Dictionary/map of datatypes and EDAM data */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": {
-                        [key: string]: Record<string, never> | undefined;
-                    }[];
+                        [key: string]: string;
+                    };
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    reload_toolbox_api_configuration_toolbox_put: {
-        /**
-         * Reload the Galaxy toolbox (but not individual tools)
-         * @description Reload the Galaxy toolbox (but not individual tools).
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
+    edam_data_detailed_api_datatypes_edam_data_detailed_get: {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Dictionary of EDAM data details containing the EDAM iri, label, and definition */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["DatatypesEDAMDetailsDict"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    content_api_dataset_collection_element__dce_id__get: {
-        /** Content */
+    edam_formats_api_datatypes_edam_formats_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The encoded ID of the dataset collection element. */
-            path: {
-                dce_id: string;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Dictionary/map of datatypes and EDAM formats */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DCESummary"];
+                    "application/json": {
+                        [key: string]: string;
+                    };
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    create_api_dataset_collections_post: {
-        /** Create a new dataset collection instance. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateNewCollectionPayload"];
-            };
+    };
+    edam_formats_detailed_api_datatypes_edam_formats_detailed_get: {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Dictionary of EDAM format details containing the EDAM iri, label, and definition */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HDCADetailed"];
+                    "application/json": components["schemas"]["DatatypesEDAMDetailsDict"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    contents_dataset_collection_api_dataset_collections__hdca_id__contents__parent_id__get: {
-        /** Returns direct child contents of indicated dataset collection parent ID. */
+    mapping_api_datatypes_mapping_get: {
         parameters: {
-            /** @description The type of collection instance. Either `history` (default) or `library`. */
-            /** @description The maximum number of content elements to return. */
-            /** @description The number of content elements that will be skipped before returning. */
-            query?: {
-                instance_type?: "history" | "library";
-                limit?: number | null;
-                offset?: number | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the `HDCA`. */
-            /** @description Parent collection ID describing what collection the contents belongs to. */
-            path: {
-                hdca_id: string;
-                parent_id: string;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Dictionary to map data types with their classes */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetCollectionContentElements"];
+                    "application/json": components["schemas"]["DatatypesMap"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_dataset_collections__id__get: {
-        /** Returns detailed information about the given collection. */
+    sniffers_api_datatypes_sniffers_get: {
         parameters: {
-            /** @description The type of collection instance. Either `history` (default) or `library`. */
-            /** @description The view of collection instance to return. */
-            query?: {
-                instance_type?: "history" | "library";
-                view?: string;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the `HDCA`. */
-            path: {
-                id: string;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description List of datatype sniffers */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": string[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HDCADetailed"] | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    attributes_api_dataset_collections__id__attributes_get: {
-        /** Returns `dbkey`/`extension` attributes for all the collection elements. */
+    types_and_mapping_api_datatypes_types_and_mapping_get: {
         parameters: {
-            /** @description The type of collection instance. Either `history` (default) or `library`. */
             query?: {
-                instance_type?: "history" | "library";
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the `HDCA`. */
-            path: {
-                id: string;
+                /** @description Whether to return only the datatype's extension rather than the datatype's details */
+                extension_only?: boolean | null;
+                /** @description Whether to return only datatypes which can be uploaded */
+                upload_only?: boolean | null;
             };
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Dictionary to map data types with their classes */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetCollectionAttributesResult"];
+                    "application/json": components["schemas"]["DatatypesCombinedMap"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    copy_api_dataset_collections__id__copy_post: {
-        /** Copy the given collection datasets to a new collection using a new `dbkey` attribute. */
+    display_applications_index_api_display_applications_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the `HDCA`. */
-            path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateCollectionAttributePayload"];
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["DisplayApplication"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    dataset_collections__download: {
-        /**
-         * Download the content of a dataset collection as a `zip` archive.
-         * @description Download the content of a history dataset collection as a `zip` archive
-         * while maintaining approximate collection structure.
-         */
+    display_applications_reload_api_display_applications_reload_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the `HDCA`. */
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": {
+                    [key: string]: string[];
+                } | null;
             };
         };
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["ReloadFeedback"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    prepare_collection_download_api_dataset_collections__id__prepare_download_post: {
-        /**
-         * Prepare an short term storage object that the collection will be downloaded to.
-         * @description The history dataset collection will be written as a `zip` archive to the
-         * returned short term storage object. Progress tracking this file's creation
-         * can be tracked with the short_term_storage API.
-         */
+    download_api_drs_download__object_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the `HDCA`. */
             path: {
-                id: string;
+                /** @description The ID of the group */
+                object_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Short term storage reference for async monitoring of this download. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncFile"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Required asynchronous tasks required for this operation not available. */
-            501: never;
         };
     };
-    suitable_converters_api_dataset_collections__id__suitable_converters_get: {
-        /** Returns a list of applicable converters for all datatypes in the given collection. */
+    file_sources__instances_index: {
         parameters: {
-            /** @description The type of collection instance. Either `history` (default) or `library`. */
-            query?: {
-                instance_type?: "history" | "library";
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the `HDCA`. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SuitableConverters"];
+                    "application/json": components["schemas"]["UserFileSourceModel"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_datasets_get: {
-        /** Search datasets or collections using a query system. */
-        parameters?: {
-            /** @description Optional identifier of a History. Use it to restrict the search within a particular History. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            query?: {
-                history_id?: string | null;
-                view?: string | null;
-                keys?: string | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    file_sources__create_instance: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateInstancePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"]
-                    )[];
+                    "application/json": components["schemas"]["UserFileSourceModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_batch_api_datasets_delete: {
-        /**
-         * Deletes or purges a batch of datasets.
-         * @description Deletes or purges a batch of datasets.
-         * **Warning**: only the ownership of the datasets (and upload state for HDAs) is checked,
-         * no other checks or restrictions are made.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    file_sources__test_new_instance_configuration: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["DeleteDatasetBatchPayload"];
+                "application/json": components["schemas"]["CreateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteDatasetBatchResult"];
+                    "application/json": components["schemas"]["PluginStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_datasets__dataset_id__get: {
-        /**
-         * Displays information about and/or content of a dataset.
-         * @description **Note**: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters
-         * and return different kinds of responses, the documentation here will be limited.
-         * To get more information please check the source code.
-         */
+    file_sources__instances_get: {
         parameters: {
-            /** @description The type of information about the dataset to be requested. */
-            /** @description The type of information about the dataset to be requested. Each of these values may require additional parameters in the request and may return different responses. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
-                data_type?: components["schemas"]["RequestDataType"] | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The UUID index for a persisted UserFileSourceStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["UserFileSourceModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    datasets__update_dataset: {
-        /**
-         * Updates the values for the history dataset (HDA) item with the given ``ID``.
-         * @description Updates the values for the history content item with the given ``ID``.
-         */
+    file_sources__instances_update: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
-                dataset_id: string;
+                /** @description The UUID index for a persisted UserFileSourceStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
+                "application/json":
+                    | components["schemas"]["UpdateInstanceSecretPayload"]
+                    | components["schemas"]["UpgradeInstancePayload"]
+                    | components["schemas"]["UpdateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["UserFileSourceModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    datasets__delete: {
-        /**
-         * Delete the history dataset content with the given ``ID``.
-         * @description Delete the history content with the given ``ID`` and path specified type.
-         *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
-         */
+    file_sources__instances_purge: {
         parameters: {
-            /**
-             * @deprecated
-             * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
-             */
-            /**
-             * @deprecated
-             * @description When deleting a dataset collection, whether to also delete containing datasets.
-             */
-            /**
-             * @deprecated
-             * @description Whether to stop the creating job if all outputs of the job have been deleted.
-             */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                purge?: boolean | null;
-                recursive?: boolean | null;
-                stop_job?: boolean | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
-                dataset_id: string;
-            };
-        };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
+                /** @description The UUID index for a persisted UserFileSourceStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Request has been executed. */
-            200: {
-                content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+            /** @description Successful Response */
+            204: {
+                headers: {
+                    [name: string]: unknown;
                 };
+                content?: never;
             };
-            /** @description Request accepted, processing will finish later. */
-            202: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_structured_content_api_datasets__dataset_id__content__content_type__get: {
-        /** Retrieve information about the content of a dataset. */
+    file_sources__instances_test_instance: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
-                content_type: components["schemas"]["DatasetContentType"];
+                /** @description The UUID index for a persisted UserFileSourceStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["PluginStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    converted_api_datasets__dataset_id__converted_get: {
-        /**
-         * Return a a map with all the existing converted datasets associated with this instance.
-         * @description Return a map of `<converted extension> : <converted id>` containing all the *existing* converted datasets.
-         */
+    file_sources__test_instances_update: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The UUID index for a persisted UserFileSourceStore object. */
+                uuid: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json":
+                    | components["schemas"]["TestUpgradeInstancePayload"]
+                    | components["schemas"]["TestUpdateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ConvertedDatasetsMap"];
+                    "application/json": components["schemas"]["PluginStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    converted_ext_api_datasets__dataset_id__converted__ext__get: {
-        /**
-         * Return information about datasets made by converting this dataset to a new format.
-         * @description Return information about datasets made by converting this dataset to a new format.
-         *
-         * If there is no existing converted dataset for the format in `ext`, one will be created.
-         *
-         * **Note**: `view` and `keys` are also available to control the serialization of the dataset.
-         */
+    file_sources__templates_index: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
-            /** @description File extension of the new format to convert this dataset to. */
-            path: {
-                dataset_id: string;
-                ext: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list of the configured file source templates. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"];
+                    "application/json": components["schemas"]["FileSourceTemplateSummaries"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    extra_files_api_datasets__dataset_id__extra_files_get: {
-        /** Get the list of extra files/directories associated with a dataset. */
+    file_sources__template_oauth2: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the dataset. */
             path: {
-                dataset_id: string;
+                /** @description The template ID of the target file source template. */
+                template_id: string;
+                /** @description The template version of the target file source template. */
+                template_version: number;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description OAuth2 authorization url to redirect user to prior to creation. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetExtraFiles"];
+                    "application/json": components["schemas"]["OAuth2Info"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_content_as_text_api_datasets__dataset_id__get_content_as_text_get: {
-        /** Returns dataset content as Text. */
+    index_api_folders__folder_id__contents_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Maximum number of contents to return. */
+                limit?: number;
+                /** @description Return contents from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, contents between position 200-299 will be returned. */
+                offset?: number;
+                /** @description Used to filter the contents. Only the folders and files which name contains this text will be returned. */
+                search_text?: string | null;
+                /** @description Returns also deleted contents. Deleted contents can only be retrieved by Administrators or users with */
+                include_deleted?: boolean | null;
+                /** @description Sort results by specified field. */
+                order_by?: "name" | "description" | "type" | "size" | "update_time";
+                /** @description Sort results in descending order. */
+                sort_desc?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                folder_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The contents of the folder that match the query parameters. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetTextContentDetails"];
+                    "application/json": components["schemas"]["LibraryFolderContentsIndexResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    compute_hash_api_datasets__dataset_id__hash_put: {
-        /** Compute dataset hash for dataset and update model */
+    add_history_datasets_to_library_api_folders__folder_id__contents_post: {
         parameters: {
-            /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                folder_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["ComputeDatasetHashPayload"];
+                "application/json": components["schemas"]["CreateLibraryFilePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_inheritance_chain_api_datasets__dataset_id__inheritance_chain_get: {
-        /** For internal use, this endpoint may change without warning. */
+    show_api_folders__id__get: {
         parameters: {
-            /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetInheritanceChain"];
+                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_metrics_api_datasets__dataset_id__metrics_get: {
-        /**
-         * Return job metrics for specified job.
-         * @deprecated
-         */
+    update_api_folders__id__put: {
         parameters: {
-            /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the dataset */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateLibraryFolderPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (components["schemas"]["JobMetric"] | null)[];
+                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    datasets__update_object_store_id: {
-        /** Update an object store ID for a dataset you own. */
+    create_api_folders__id__post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["UpdateObjectStoreIdPayload"];
+                "application/json": components["schemas"]["CreateLibraryFolderPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    resolve_parameters_display_api_datasets__dataset_id__parameters_display_get: {
-        /**
-         * Resolve parameters as a list for nested display.
-         * @deprecated
-         * @description Resolve parameters as a list for nested display.
-         * This API endpoint is unstable and tied heavily to Galaxy's JS client code,
-         * this endpoint will change frequently.
-         */
+    delete_api_folders__id__delete: {
         parameters: {
-            /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                /** @description Whether to restore a deleted library folder. */
+                undelete?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the dataset */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobDisplayParametersSummary"];
+                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_permissions_api_datasets__dataset_id__permissions_put: {
-        /**
-         * Set permissions of the given history dataset to the given role ids.
-         * @description Set permissions of the given history dataset to the given role ids.
-         */
+    update_api_folders__id__patch: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": Record<string, never>;
+                "application/json": components["schemas"]["UpdateLibraryFolderPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetAssociationRoles"];
+                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_storage_api_datasets__dataset_id__storage_get: {
-        /** Display user-facing storage details related to the objectstore a dataset resides in. */
+    get_permissions_api_folders__id__permissions_get: {
         parameters: {
-            /** @description Whether this dataset belongs to a history (HDA) or a library (LDDA). */
             query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"];
+                /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */
+                scope?: components["schemas"]["LibraryPermissionScope"] | null;
+                /** @description The page number to retrieve when paginating the available roles. */
+                page?: number;
+                /** @description The maximum number of permissions per page when paginating. */
+                page_limit?: number;
+                /** @description Optional search text to retrieve only the roles matching this query. */
+                q?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                dataset_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetStorageDetails"];
+                    "application/json":
+                        | components["schemas"]["LibraryFolderCurrentPermissions"]
+                        | components["schemas"]["LibraryAvailablePermissions"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    display_api_datasets__history_content_id__display_get: {
-        /**
-         * Displays (preview) or downloads dataset content.
-         * @description Streams the dataset for download or the contents preview to be displayed in a browser.
-         */
+    set_permissions_api_folders__id__permissions_post: {
         parameters: {
-            /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description If non-null, get the specified filename from the extra files for this dataset. */
-            /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
-            /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
-            /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
-            /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes. */
             query?: {
-                preview?: boolean;
-                filename?: string | null;
-                to_ext?: string | null;
-                raw?: boolean;
-                offset?: number | null;
-                ck_size?: number | null;
+                /** @description Indicates what action should be performed on the Library. Currently only `set_permissions` is supported. */
+                action?: components["schemas"]["LibraryFolderPermissionAction"] | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                history_content_id: string;
+                /** @description The encoded identifier of the library folder. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["LibraryFolderPermissionsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["LibraryFolderCurrentPermissions"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    display_api_datasets__history_content_id__display_head: {
-        /**
-         * Check if dataset content can be previewed or downloaded.
-         * @description Streams the dataset for download or the contents preview to be displayed in a browser.
-         */
+    delete_api_forms__id__delete: {
         parameters: {
-            /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description If non-null, get the specified filename from the extra files for this dataset. */
-            /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
-            /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
-            /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
-            /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes. */
-            query?: {
-                preview?: boolean;
-                filename?: string | null;
-                to_ext?: string | null;
-                raw?: boolean;
-                offset?: number | null;
-                ck_size?: number | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                history_content_id: string;
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    datasets__get_metadata_file: {
-        /** Returns the metadata file associated with this history item. */
+    undelete_api_forms__id__undelete_post: {
         parameters: {
-            /** @description The name of the metadata file to retrieve. */
-            query: {
-                metadata_file: string;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                history_content_id: string;
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_metadata_file_datasets_api_datasets__history_content_id__metadata_file_head: {
-        /** Check if metadata file can be downloaded. */
+    index_api_ftp_files_get: {
         parameters: {
-            /** @description The name of the metadata file to retrieve. */
-            query: {
-                metadata_file: string;
+            query?: {
+                /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */
+                target?: string;
+                /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
+                format?: components["schemas"]["RemoteFilesFormat"] | null;
+                /** @description Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
+                recursive?: boolean | null;
+                /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+                disable?: components["schemas"]["RemoteFilesDisableMode"] | null;
+                /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
+                writeable?: boolean | null;
+                /** @description Maximum number of entries to return. */
+                limit?: number | null;
+                /** @description Number of entries to skip. */
+                offset?: number | null;
+                /** @description Search query to filter entries by. The syntax could be different depending on the target source. */
+                query?: string | null;
+                /** @description Sort the entries by the specified field. */
+                sort_by?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
-            path: {
-                history_content_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json":
+                        | components["schemas"]["ListUriResponse"]
+                        | components["schemas"]["ListJstreeResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_datatypes_get: {
-        /**
-         * Lists all available data types
-         * @description Gets the list of all available data types.
-         */
-        parameters?: {
-            /** @description Whether to return only the datatype's extension rather than the datatype's details */
-            /** @description Whether to return only datatypes which can be uploaded */
+    index_api_genomes_get: {
+        parameters: {
             query?: {
-                extension_only?: boolean | null;
-                upload_only?: boolean | null;
+                /** @description If true, return genome keys with chromosome lengths */
+                chrom_info?: boolean;
             };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description List of data types */
+            /** @description Installed genomes */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypeDetails"][] | string[];
+                    "application/json": string[][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    converters_api_datatypes_converters_get: {
-        /**
-         * Returns the list of all installed converters
-         * @description Gets the list of all installed converters.
-         */
-        responses: {
-            /** @description List of all datatype converters */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypeConverterList"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    edam_data_api_datatypes_edam_data_get: {
-        /**
-         * Returns a dictionary/map of datatypes and EDAM data
-         * @description Gets a map of datatypes and their corresponding EDAM data.
-         */
+    show_api_genomes__id__get: {
+        parameters: {
+            query?: {
+                /** @description If true, return reference data */
+                reference?: boolean;
+                /** @description Limits size of returned data */
+                num?: number;
+                /** @description Limits size of returned data */
+                chrom?: string;
+                /** @description Limits size of returned data */
+                low?: number;
+                /** @description Limits size of returned data */
+                high?: number;
+                /** @description Format */
+                format?: string;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description Genome ID */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
         responses: {
-            /** @description Dictionary/map of datatypes and EDAM data */
+            /** @description Information about genome build <id> */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": {
-                        [key: string]: string | undefined;
-                    };
+                    "application/json": unknown;
                 };
             };
-        };
-    };
-    edam_data_detailed_api_datatypes_edam_data_detailed_get: {
-        /**
-         * Returns a dictionary of datatypes and EDAM data details
-         * @description Gets a map of datatypes and their corresponding EDAM data.
-         * EDAM data contains the EDAM iri, label, and definition.
-         */
-        responses: {
-            /** @description Dictionary of EDAM data details containing the EDAM iri, label, and definition */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypesEDAMDetailsDict"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    edam_formats_api_datatypes_edam_formats_get: {
-        /**
-         * Returns a dictionary/map of datatypes and EDAM formats
-         * @description Gets a map of datatypes and their corresponding EDAM formats.
-         */
-        responses: {
-            /** @description Dictionary/map of datatypes and EDAM formats */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": {
-                        [key: string]: string | undefined;
-                    };
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    edam_formats_detailed_api_datatypes_edam_formats_detailed_get: {
-        /**
-         * Returns a dictionary of datatypes and EDAM format details
-         * @description Gets a map of datatypes and their corresponding EDAM formats.
-         * EDAM formats contain the EDAM iri, label, and definition.
-         */
+    indexes_api_genomes__id__indexes_get: {
+        parameters: {
+            query?: {
+                /** @description Index type */
+                type?: string;
+                /** @description Format */
+                format?: string;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description Genome ID */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
         responses: {
-            /** @description Dictionary of EDAM format details containing the EDAM iri, label, and definition */
+            /** @description Indexes for a genome id for provided type */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypesEDAMDetailsDict"];
+                    "application/json": unknown;
                 };
             };
-        };
-    };
-    mapping_api_datatypes_mapping_get: {
-        /**
-         * Returns mappings for data types and their implementing classes
-         * @description Gets mappings for data types.
-         */
-        responses: {
-            /** @description Dictionary to map data types with their classes */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypesMap"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    sniffers_api_datatypes_sniffers_get: {
-        /**
-         * Returns the list of all installed sniffers
-         * @description Gets the list of all installed data type sniffers.
-         */
-        responses: {
-            /** @description List of datatype sniffers */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string[];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    types_and_mapping_api_datatypes_types_and_mapping_get: {
-        /**
-         * Returns all the data types extensions and their mappings
-         * @description Combines the datatype information from (/api/datatypes) and the
-         * mapping information from (/api/datatypes/mapping) into a single
-         * response.
-         */
-        parameters?: {
-            /** @description Whether to return only the datatype's extension rather than the datatype's details */
-            /** @description Whether to return only datatypes which can be uploaded */
+    sequences_api_genomes__id__sequences_get: {
+        parameters: {
             query?: {
-                extension_only?: boolean | null;
-                upload_only?: boolean | null;
+                /** @description If true, return reference data */
+                reference?: boolean;
+                /** @description Limits size of returned data */
+                chrom?: string;
+                /** @description Limits size of returned data */
+                low?: number;
+                /** @description Limits size of returned data */
+                high?: number;
+                /** @description Format */
+                format?: string;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
             };
+            path: {
+                /** @description Genome ID */
+                id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Dictionary to map data types with their classes */
+            /** @description Raw sequence data */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatatypesCombinedMap"];
+                    "application/json": unknown;
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    display_applications_index_api_display_applications_get: {
-        /**
-         * Returns the list of display applications.
-         * @description Returns the list of display applications.
-         */
-        responses: {
-            /** @description Successful Response */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DisplayApplication"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    display_applications_reload_api_display_applications_reload_post: {
-        /**
-         * Reloads the list of display applications.
-         * @description Reloads the list of display applications.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    index_api_groups_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
-        requestBody?: {
-            content: {
-                "application/json": {
-                    [key: string]: string[] | undefined;
-                } | null;
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ReloadFeedback"];
+                    "application/json": components["schemas"]["GroupListResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    download_api_drs_download__object_id__get: {
-        /** Download */
+    create_api_groups_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group */
-            path: {
-                object_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["GroupCreatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["GroupListResponse"];
                 };
             };
-        };
-    };
-    file_sources__instances_index: {
-        /** Get a list of persisted file source instances defined by the requesting user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-        };
-        responses: {
-            /** @description Successful Response */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserFileSourceModel"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__create_instance: {
-        /** Create a user-bound file source. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    show_group_api_groups__group_id__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateInstancePayload"];
+            path: {
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserFileSourceModel"];
+                    "application/json": components["schemas"]["GroupResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__test_new_instance_configuration: {
-        /** Test payload for creating user-bound file source. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_api_groups__group_id__put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                group_id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CreateInstancePayload"];
+                "application/json": components["schemas"]["GroupUpdatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["GroupResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["PluginStatus"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__instances_get: {
-        /** Get a persisted user file source instance. */
+    delete_api_groups__group_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
-                user_file_source_id: string;
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserFileSourceModel"];
+                    "application/json": unknown;
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__instances_update: {
-        /** Update or upgrade user file source instance. */
+    purge_api_groups__group_id__purge_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
-                user_file_source_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json":
-                    | components["schemas"]["UpdateInstanceSecretPayload"]
-                    | components["schemas"]["UpgradeInstancePayload"]
-                    | components["schemas"]["UpdateInstancePayload"];
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserFileSourceModel"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__instances_purge: {
-        /** Purge user file source instance. */
+    group_roles_api_groups__group_id__roles_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
-                user_file_source_id: string;
+                /** @description The ID of the group. */
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["GroupRoleListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    file_sources__templates_index: {
-        /** Get a list of file source templates available to build user defined file sources from */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    group_role_api_groups__group_id__roles__role_id__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the role. */
+                role_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A list of the configured file source templates. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["FileSourceTemplateSummaries"];
+                    "application/json": components["schemas"]["GroupRoleResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_folders__folder_id__contents_get: {
-        /**
-         * Returns a list of a folder's contents (files and sub-folders) with additional metadata about the folder.
-         * @description Returns a list of a folder's contents (files and sub-folders).
-         *
-         * Additional metadata for the folder is provided in the response as a separate object containing data
-         * for breadcrumb path building, permissions and other folder's details.
-         *
-         * *Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).
-         *
-         * **Security note**:
-         * - Accessing a library folder or sub-folder requires only access to the parent library.
-         * - Deleted folders can only be accessed by admins or users with `MODIFY` permission.
-         * - Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.
-         */
-        parameters: {
-            /** @description Maximum number of contents to return. */
-            /** @description Return contents from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, contents between position 200-299 will be returned. */
-            /** @description Used to filter the contents. Only the folders and files which name contains this text will be returned. */
-            /** @description Returns also deleted contents. Deleted contents can only be retrieved by Administrators or users with */
-            /** @description Sort results by specified field. */
-            /** @description Sort results in descending order. */
-            query?: {
-                limit?: number;
-                offset?: number;
-                search_text?: string | null;
-                include_deleted?: boolean | null;
-                order_by?: "name" | "description" | "type" | "size" | "update_time";
-                sort_desc?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_api_groups__group_id__roles__role_id__put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                folder_id: string;
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the role. */
+                role_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The contents of the folder that match the query parameters. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderContentsIndexResult"];
+                    "application/json": components["schemas"]["GroupRoleResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    add_history_datasets_to_library_api_folders__folder_id__contents_post: {
-        /** Creates a new library file from an existing HDA/HDCA. */
+    delete_api_groups__group_id__roles__role_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                folder_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateLibraryFilePayload"];
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the role. */
+                role_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["GroupRoleResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_folders__id__get: {
-        /**
-         * Displays information about a particular library folder.
-         * @description Returns detailed information about the library folder with the given ID.
-         */
+    undelete_api_groups__group_id__undelete_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_folders__id__put: {
-        /**
-         * Updates the information of an existing library folder.
-         * @description Updates the information of an existing library folder.
-         */
+    group_user_api_groups__group_id__user__user_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateLibraryFolderPayload"];
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                    "application/json": components["schemas"]["GroupUserResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_folders__id__post: {
-        /**
-         * Create a new library folder underneath the one specified by the ID.
-         * @description Returns detailed information about the newly created library folder.
-         */
+    update_api_groups__group_id__user__user_id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateLibraryFolderPayload"];
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                    "application/json": components["schemas"]["GroupUserResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_folders__id__delete: {
-        /**
-         * Marks the specified library folder as deleted (or undeleted).
-         * @description Marks the specified library folder as deleted (or undeleted).
-         */
+    delete_api_groups__group_id__user__user_id__delete: {
         parameters: {
-            /** @description Whether to restore a deleted library folder. */
-            query?: {
-                undelete?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                    "application/json": components["schemas"]["GroupUserResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_folders__id__patch: {
-        /**
-         * Update
-         * @description Updates the information of an existing library folder.
-         */
+    group_users_api_groups__group_id__users_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateLibraryFolderPayload"];
+                /** @description The ID of the group. */
+                group_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderDetails"];
+                    "application/json": components["schemas"]["GroupUserListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_permissions_api_folders__id__permissions_get: {
-        /**
-         * Gets the current or available permissions of a particular library folder.
-         * @description Gets the current or available permissions of a particular library.
-         * The results can be paginated and additionally filtered by a query.
-         */
+    group_user_api_groups__group_id__users__user_id__get: {
         parameters: {
-            /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */
-            /** @description The page number to retrieve when paginating the available roles. */
-            /** @description The maximum number of permissions per page when paginating. */
-            /** @description Optional search text to retrieve only the roles matching this query. */
-            query?: {
-                scope?: components["schemas"]["LibraryPermissionScope"] | null;
-                page?: number;
-                page_limit?: number;
-                q?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["LibraryFolderCurrentPermissions"]
-                        | components["schemas"]["LibraryAvailablePermissions"];
+                    "application/json": components["schemas"]["GroupUserResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_permissions_api_folders__id__permissions_post: {
-        /**
-         * Sets the permissions to manage a library folder.
-         * @description Sets the permissions to manage a library folder.
-         */
+    update_api_groups__group_id__users__user_id__put: {
         parameters: {
-            /** @description Indicates what action should be performed on the Library. Currently only `set_permissions` is supported. */
-            query?: {
-                action?: components["schemas"]["LibraryFolderPermissionAction"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded identifier of the library folder. */
             path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["LibraryFolderPermissionsPayload"];
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibraryFolderCurrentPermissions"];
+                    "application/json": components["schemas"]["GroupUserResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_forms__id__delete: {
-        /** Delete */
+    delete_api_groups__group_id__users__user_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                id: string;
+                /** @description The ID of the group. */
+                group_id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["GroupUserResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_forms__id__undelete_post: {
-        /** Undelete */
+    search_forum_api_help_forum_search_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query: {
+                /** @description Search query to use for searching the Galaxy Help forum. */
+                query: string;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["HelpForumSearchResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_ftp_files_get: {
-        /**
-         * Displays remote files available to the user. Please use /api/remote_files instead.
-         * @deprecated
-         * @description Lists all remote files available to the user from different sources.
-         *
-         * The total count of files and directories is returned in the 'total_matches' header.
-         */
-        parameters?: {
-            /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */
-            /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
-            /** @description Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
-            /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
-            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
-            /** @description Maximum number of entries to return. */
-            /** @description Number of entries to skip. */
-            /** @description Search query to filter entries by. The syntax could be different depending on the target source. */
-            /** @description Sort the entries by the specified field. */
+    index_api_histories_get: {
+        parameters: {
             query?: {
-                target?: string;
-                format?: components["schemas"]["RemoteFilesFormat"] | null;
-                recursive?: boolean | null;
-                disable?: components["schemas"]["RemoteFilesDisableMode"] | null;
-                writeable?: boolean | null;
+                /** @description The maximum number of items to return. */
                 limit?: number | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
                 offset?: number | null;
-                query?: string | null;
-                sort_by?: string | null;
+                show_own?: boolean;
+                show_published?: boolean;
+                show_shared?: boolean;
+                /** @description Whether to include archived histories. */
+                show_archived?: boolean | null;
+                /** @description Sort index by this specified attribute */
+                sort_by?: "create_time" | "name" | "update_time" | "username";
+                /** @description Sort in descending order? */
+                sort_desc?: boolean;
+                /** @description A mix of free text and GitHub-style tags used to filter the index operation.
+                 *
+                 *     ## Query Structure
+                 *
+                 *     GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+                 *     `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+                 *     *generally* (but not exclusively) corresponds to the name of an attribute on the model
+                 *     being indexed (i.e. a column in the database).
+                 *
+                 *     If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+                 *     generally a partial match will be used to filter the query (i.e. in terms of the implementation
+                 *     this means the database operation `ILIKE` will typically be used).
+                 *
+                 *     Once the tagged filters are extracted from the search query, the remaining text is just
+                 *     used to search various documented attributes of the object.
+                 *
+                 *     ## GitHub-style Tags Available
+                 *
+                 *     `name`
+                 *     : The history's name.
+                 *
+                 *     `annotation`
+                 *     : The history's annotation. (The tag `a` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `tag`
+                 *     : The history's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     ## Free Text
+                 *
+                 *     Free text search terms will be searched against the following attributes of the
+                 *     Historys: `title`, `description`, `slug`, `tag`.
+                 *
+                 *      */
+                search?: string | null;
+                /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */
+                all?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to return only deleted items.
+                 */
+                deleted?: boolean | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["ListUriResponse"]
-                        | components["schemas"]["ListJstreeResponse"];
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_genomes_get: {
-        /** Return a list of installed genomes */
-        parameters?: {
-            /** @description If true, return genome keys with chromosome lengths */
+    create_api_histories_post: {
+        parameters: {
             query?: {
-                chrom_info?: boolean;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/x-www-form-urlencoded": components["schemas"]["Body_create_api_histories_post"];
+            };
         };
         responses: {
-            /** @description Installed genomes */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string[][];
+                    "application/json":
+                        | components["schemas"]["JobImportHistoryResponse"]
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_genomes__id__get: {
-        /** Return information about build <id> */
+    get_archived_histories_api_histories_archived_get: {
         parameters: {
-            /** @description If true, return reference data */
-            /** @description Limits size of returned data */
-            /** @description Limits size of returned data */
-            /** @description Limits size of returned data */
-            /** @description Limits size of returned data */
-            /** @description Format */
             query?: {
-                reference?: boolean;
-                num?: number;
-                chrom?: string;
-                low?: number;
-                high?: number;
-                format?: string;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description Genome ID */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Information about genome build <id> */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": (
+                        | components["schemas"]["CustomArchivedHistoryView"]
+                        | components["schemas"]["ArchivedHistoryDetailed"]
+                        | components["schemas"]["ArchivedHistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    indexes_api_genomes__id__indexes_get: {
-        /** Return all available indexes for a genome id for provided type */
+    batch_delete_api_histories_batch_delete_put: {
         parameters: {
-            /** @description Index type */
-            /** @description Format */
             query?: {
-                type?: string;
-                format?: string;
+                purge?: boolean;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description Genome ID */
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["DeleteHistoriesPayload"];
             };
         };
         responses: {
-            /** @description Indexes for a genome id for provided type */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    sequences_api_genomes__id__sequences_get: {
-        /** Return raw sequence data */
+    batch_undelete_api_histories_batch_undelete_put: {
         parameters: {
-            /** @description If true, return reference data */
-            /** @description Limits size of returned data */
-            /** @description Limits size of returned data */
-            /** @description Limits size of returned data */
-            /** @description Format */
             query?: {
-                reference?: boolean;
-                chrom?: string;
-                low?: number;
-                high?: number;
-                format?: string;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description Genome ID */
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UndeleteHistoriesPayload"];
             };
         };
         responses: {
-            /** @description Raw sequence data */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_groups_get: {
-        /** Displays a collection (list) of groups. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    count_api_histories_count_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupListResponse"];
+                    "application/json": number;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_groups_post: {
-        /** Creates a new group. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    index_deleted_api_histories_deleted_get: {
+        parameters: {
+            query?: {
+                /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */
+                all?: boolean | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["GroupCreatePayload"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupListResponse"];
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_group_api_groups__group_id__get: {
-        /** Displays information about a group. */
+    undelete_api_histories_deleted__history_id__undelete_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                group_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupResponse"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_groups__group_id__put: {
-        /** Modifies a group. */
+    create_from_store_api_histories_from_store_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                group_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["GroupUpdatePayload"];
+                "application/json": components["schemas"]["CreateHistoryFromStore"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupResponse"];
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_groups__group_id__delete: {
-        /** Delete */
+    create_from_store_async_api_histories_from_store_async_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                group_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateHistoryFromStore"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    purge_api_groups__group_id__purge_post: {
-        /** Purge */
+    show_recent_api_histories_most_recently_used_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                group_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    group_roles_api_groups__group_id__roles_get: {
-        /** Displays a collection (list) of groups. */
+    published_api_histories_published_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            path: {
-                group_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupRoleListResponse"];
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    group_role_api_groups__group_id__roles__role_id__get: {
-        /** Displays information about a group role. */
+    shared_with_me_api_histories_shared_with_me_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the role. */
-            path: {
-                group_id: string;
-                role_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupRoleResponse"];
+                    "application/json": (
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_groups__group_id__roles__role_id__put: {
-        /** Adds a role to a group */
+    history_api_histories__history_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the role. */
             path: {
-                group_id: string;
-                role_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupRoleResponse"];
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_groups__group_id__roles__role_id__delete: {
-        /** Removes a role from a group */
+    update_api_histories__history_id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the role. */
             path: {
-                group_id: string;
-                role_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateHistoryPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupRoleResponse"];
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_groups__group_id__undelete_post: {
-        /** Undelete */
+    delete_api_histories__history_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                purge?: boolean;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                group_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["DeleteHistoryPayload"] | null;
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    group_user_api_groups__group_id__user__user_id__get: {
-        /**
-         * Displays information about a group user.
-         * @description Displays information about a group user.
-         */
+    archive_history_api_histories__history_id__archive_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["ArchiveHistoryRequestPayload"] | null;
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json":
+                        | components["schemas"]["CustomArchivedHistoryView"]
+                        | components["schemas"]["ArchivedHistoryDetailed"]
+                        | components["schemas"]["ArchivedHistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_groups__group_id__user__user_id__put: {
-        /**
-         * Adds a user to a group
-         * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Adds a user to a group
-         */
+    restore_archived_history_api_histories__history_id__archive_restore_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description If true, the history will be un-archived even if it has an associated archive export record and was purged. */
+                force?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json":
+                        | components["schemas"]["CustomHistoryView"]
+                        | components["schemas"]["HistoryDetailed"]
+                        | components["schemas"]["HistorySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_groups__group_id__user__user_id__delete: {
-        /**
-         * Removes a user from a group
-         * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Removes a user from a group
-         */
+    citations_api_histories__history_id__citations_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json": unknown[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    group_users_api_groups__group_id__users_get: {
-        /**
-         * Displays a collection (list) of groups.
-         * @description GET /api/groups/{encoded_group_id}/users
-         * Displays a collection (list) of groups.
-         */
+    history_contents__index: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** */
+                v?: string | null;
+                /**
+                 * @deprecated
+                 * @description Legacy name for the `dataset_details` parameter.
+                 */
+                details?: string | null;
+                /**
+                 * @deprecated
+                 * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item.
+                 */
+                ids?: string | null;
+                /**
+                 * @deprecated
+                 * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned.
+                 */
+                types?: string[] | null;
+                /**
+                 * @deprecated
+                 * @description Whether to return deleted or undeleted datasets only. Leave unset for both.
+                 */
+                deleted?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to return visible or hidden datasets only. Leave unset for both.
+                 */
+                visible?: boolean | null;
+                /** @description Whether to return only shareable or not shareable datasets. Leave unset for both. */
+                shareable?: boolean | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+            };
             header?: {
+                /** @description Accept header to determine the response format. Default is 'application/json'. */
+                accept?: "application/json" | "application/vnd.galaxy.history.contents.stats+json";
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
             path: {
-                group_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The contents of the history that match the query. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserListResponse"];
+                    "application/json": components["schemas"]["HistoryContentsResult"];
+                    "application/vnd.galaxy.history.contents.stats+json": components["schemas"]["HistoryContentsWithStatsResult"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    group_user_api_groups__group_id__users__user_id__get: {
-        /**
-         * Displays information about a group user.
-         * @description Displays information about a group user.
-         */
+    update_batch_api_histories__history_id__contents_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateHistoryContentsBatchPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json": components["schemas"]["HistoryContentsResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_groups__group_id__users__user_id__put: {
-        /**
-         * Adds a user to a group
-         * @description PUT /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Adds a user to a group
-         */
+    history_contents__create: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description The type of the target history element. */
+                type?: components["schemas"]["HistoryContentType"] | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateHistoryContentPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"]
+                        | (
+                              | components["schemas"]["HDACustom"]
+                              | components["schemas"]["HDADetailed"]
+                              | components["schemas"]["HDASummary"]
+                              | components["schemas"]["HDAInaccessible"]
+                              | components["schemas"]["HDCACustom"]
+                              | components["schemas"]["HDCADetailed"]
+                              | components["schemas"]["HDCASummary"]
+                          )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_groups__group_id__users__user_id__delete: {
-        /**
-         * Removes a user from a group
-         * @description DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id}
-         * Removes a user from a group
-         */
+    history_contents__archive: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description The name that the Archive will have (defaults to history name). */
+                filename?: string | null;
+                /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */
+                dry_run?: boolean | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group. */
-            /** @description The ID of the user. */
             path: {
-                group_id: string;
-                user_id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["GroupUserResponse"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    search_forum_api_help_forum_search_get: {
-        /**
-         * Search the Galaxy Help forum.
-         * @description Search the Galaxy Help forum using the Discourse API.
-         *
-         * **Note**: This endpoint is for **INTERNAL USE ONLY** and is not part of the public Galaxy API.
-         */
+    history_contents__archive_named: {
         parameters: {
-            /** @description Search query to use for searching the Galaxy Help forum. */
-            query: {
-                query: string;
+            query?: {
+                /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */
+                dry_run?: boolean | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+                /** @description The name that the Archive will have (defaults to history name). */
+                filename: string;
+                /**
+                 * @deprecated
+                 * @description Output format of the archive.
+                 */
+                format: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HelpForumSearchResponse"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_histories_get: {
-        /** Returns histories available to the current user. */
-        parameters?: {
-            /** @description The maximum number of items to return. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description Whether to include archived histories. */
-            /** @description Sort index by this specified attribute */
-            /** @description Sort in descending order? */
-            /**
-             * @description A mix of free text and GitHub-style tags used to filter the index operation.
-             *
-             * ## Query Structure
-             *
-             * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
-             * `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
-             * *generally* (but not exclusively) corresponds to the name of an attribute on the model
-             * being indexed (i.e. a column in the database).
-             *
-             * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
-             * generally a partial match will be used to filter the query (i.e. in terms of the implementation
-             * this means the database operation `ILIKE` will typically be used).
-             *
-             * Once the tagged filters are extracted from the search query, the remaining text is just
-             * used to search various documented attributes of the object.
-             *
-             * ## GitHub-style Tags Available
-             *
-             * `name`
-             * : The history's name.
-             *
-             * `annotation`
-             * : The history's annotation. (The tag `a` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `tag`
-             * : The history's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * ## Free Text
-             *
-             * Free text search terms will be searched against the following attributes of the
-             * Historys: `title`, `description`, `slug`, `tag`.
-             */
-            /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */
-            /**
-             * @deprecated
-             * @description Whether to return only deleted items.
-             */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
+    bulk_operation_api_histories__history_id__contents_bulk_put: {
+        parameters: {
             query?: {
-                limit?: number | null;
-                offset?: number | null;
-                show_own?: boolean;
-                show_published?: boolean;
-                show_shared?: boolean;
-                show_archived?: boolean | null;
-                sort_by?: "create_time" | "name" | "update_time" | "username";
-                sort_desc?: boolean;
-                search?: string | null;
-                all?: boolean | null;
-                deleted?: boolean | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
                 q?: string[] | null;
+                /** @description The value to filter by. */
                 qv?: string[] | null;
-                order?: string | null;
-                view?: string | null;
-                keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["HistoryContentBulkOperationPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": components["schemas"]["HistoryContentBulkOperationResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_histories_post: {
-        /**
-         * Creates a new history.
-         * @description The new history can also be copied form a existing history or imported from an archive or URL.
-         */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    history_contents__download_collection: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody?: {
-            content: {
-                "application/x-www-form-urlencoded": components["schemas"]["Body_create_api_histories_post"];
+            path: {
+                /** @description The ID of the `HDCA`. */
+                id: string;
+                /** @description The encoded database identifier of the History. */
+                history_id: string | null;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["JobImportHistoryResponse"]
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_archived_histories_api_histories_archived_get: {
-        /**
-         * Get a list of all archived histories for the current user.
-         * @description Get a list of all archived histories for the current user.
-         *
-         * Archived histories are histories are not part of the active histories of the user but they can be accessed using this endpoint.
-         */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["ArchivedHistorySummary"]
-                        | components["schemas"]["ArchivedHistoryDetailed"]
-                        | Record<string, never>
-                    )[];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    batch_delete_api_histories_batch_delete_put: {
-        /** Marks several histories with the given IDs as deleted. */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                purge?: boolean;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_permissions_api_histories__history_id__contents__dataset_id__permissions_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                dataset_id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["DeleteHistoriesPayload"];
+                "application/json":
+                    | components["schemas"]["UpdateDatasetPermissionsPayload"]
+                    | components["schemas"]["UpdateDatasetPermissionsPayloadAliasB"]
+                    | components["schemas"]["UpdateDatasetPermissionsPayloadAliasC"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": components["schemas"]["DatasetAssociationRoles"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    batch_undelete_api_histories_batch_undelete_put: {
-        /** Marks several histories with the given IDs as undeleted. */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
+    history_contents_display_api_histories__history_id__contents__history_content_id__display_get: {
+        parameters: {
             query?: {
-                view?: string | null;
-                keys?: string | null;
+                /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
+                preview?: boolean;
+                /** @description If non-null, get the specified filename from the extra files for this dataset. */
+                filename?: string | null;
+                /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
+                to_ext?: string | null;
+                /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
+                raw?: boolean;
+                /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
+                offset?: number | null;
+                /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes.  */
+                ck_size?: number | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UndeleteHistoriesPayload"];
+            path: {
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+                history_id: string | null;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    count_api_histories_count_get: {
-        /** Returns number of histories for the current user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    history_contents_display_api_histories__history_id__contents__history_content_id__display_head: {
+        parameters: {
+            query?: {
+                /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
+                preview?: boolean;
+                /** @description If non-null, get the specified filename from the extra files for this dataset. */
+                filename?: string | null;
+                /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
+                to_ext?: string | null;
+                /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
+                raw?: boolean;
+                /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
+                offset?: number | null;
+                /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes.  */
+                ck_size?: number | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+                history_id: string | null;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": number;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_deleted_api_histories_deleted_get: {
-        /** Returns deleted histories for the current user. */
-        parameters?: {
-            /** @description Whether all histories from other users in this Galaxy should be included. Only admins are allowed to query all histories. */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                all?: boolean | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    extra_files_history_api_histories__history_id__contents__history_content_id__extra_files_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": components["schemas"]["DatasetExtraFiles"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_histories_deleted__history_id__undelete_post: {
-        /** Restores a deleted history with the given ID (that hasn't been purged). */
+    history_contents__get_metadata_file: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
+            query: {
+                /** @description The name of the metadata file to retrieve. */
+                metadata_file: string;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the History Dataset. */
+                history_content_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_from_store_api_histories_from_store_post: {
-        /** Create histories from a model store. */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    index_api_histories__history_id__contents__history_content_id__tags_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateHistoryFromStore"];
+            path: {
+                history_content_id: string;
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["ItemTagsListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_from_store_async_api_histories_from_store_async_post: {
-        /** Launch a task to create histories from a model store. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    show_api_histories__history_id__contents__history_content_id__tags__tag_name__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateHistoryFromStore"];
+            path: {
+                history_content_id: string;
+                tag_name: string;
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["ItemTagsResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_recent_api_histories_most_recently_used_get: {
-        /** Returns the most recently used history of the user. */
-        parameters?: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_api_histories__history_id__contents__history_content_id__tags__tag_name__put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                history_content_id: string;
+                tag_name: string;
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ItemTagsCreatePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    published_api_histories_published_get: {
-        /** Return all histories that are published. */
-        parameters?: {
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    create_api_histories__history_id__contents__history_content_id__tags__tag_name__post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                history_content_id: string;
+                tag_name: string;
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["ItemTagsCreatePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    shared_with_me_api_histories_shared_with_me_get: {
-        /** Return all histories that are shared with the current user. */
-        parameters?: {
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-                view?: string | null;
-                keys?: string | null;
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+        };
+    };
+    delete_api_histories__history_id__contents__history_content_id__tags__tag_name__delete: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                history_content_id: string;
+                tag_name: string;
+                history_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"]
-                    )[];
+                    "application/json": boolean;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_api_histories__history_id__get: {
-        /** Returns the history with the given ID. */
+    history_contents__show_legacy: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
+                /** @description The type of the target history element. */
+                type?: components["schemas"]["HistoryContentType"];
+                /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */
+                fuzzy_count?: number | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_histories__history_id__put: {
-        /** Updates the values for the history with the given ID. */
+    history_contents__update_legacy: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
+                /** @description The type of the target history element. */
+                type?: components["schemas"]["HistoryContentType"];
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": Record<string, never>;
+                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_histories__history_id__delete: {
-        /** Marks the history with the given ID as deleted. */
+    history_contents__delete_legacy: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
-                purge?: boolean;
+                /** @description The type of the target history element. */
+                type?: components["schemas"]["HistoryContentType"];
+                /**
+                 * @deprecated
+                 * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
+                 */
+                purge?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description When deleting a dataset collection, whether to also delete containing datasets.
+                 */
+                recursive?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to stop the creating job if all outputs of the job have been deleted.
+                 */
+                stop_job?: boolean | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
             };
+            cookie?: never;
         };
         requestBody?: {
             content: {
-                "application/json": components["schemas"]["DeleteHistoryPayload"] | null;
+                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
             };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description Request has been executed. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request accepted, processing will finish later. */
+            202: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    archive_history_api_histories__history_id__archive_post: {
-        /**
-         * Archive a history.
-         * @description Marks the given history as 'archived' and returns the history.
-         *
-         * Archiving a history will remove it from the list of active histories of the user but it will still be
-         * accessible via the `/api/histories/{id}` or the `/api/histories/archived` endpoints.
-         *
-         * Associating an export record:
-         *
-         * - Optionally, an export record (containing information about a recent snapshot of the history) can be associated with the
-         * archived history by providing an `archive_export_id` in the payload. The export record must belong to the history and
-         * must be in the ready state.
-         * - When associating an export record, the history can be purged after it has been archived using the `purge_history` flag.
-         *
-         * If the history is already archived, this endpoint will return a 409 Conflict error, indicating that the history is already archived.
-         * If the history was not purged after it was archived, you can restore it using the `/api/histories/{id}/archive/restore` endpoint.
-         */
+    validate_api_histories__history_id__contents__id__validate_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
             };
+            cookie?: never;
         };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["ArchiveHistoryRequestPayload"] | null;
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["ArchivedHistorySummary"]
-                        | components["schemas"]["ArchivedHistoryDetailed"]
-                        | Record<string, never>;
+                    "application/json": Record<string, never>;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    restore_archived_history_api_histories__history_id__archive_restore_put: {
-        /**
-         * Restore an archived history.
-         * @description Restores an archived history and returns it.
-         *
-         * Restoring an archived history will add it back to the list of active histories of the user (unless it was purged).
-         *
-         * **Warning**: Please note that histories that are associated with an archive export might be purged after export, so un-archiving them
-         * will not restore the datasets that were in the history before it was archived. You will need to import back the archive export
-         * record to restore the history and its datasets as a new copy. See `/api/histories/from_store_async` for more information.
-         */
+    history_contents__index_typed: {
         parameters: {
-            /** @description If true, the history will be un-archived even if it has an associated archive export record and was purged. */
             query?: {
-                force?: boolean | null;
+                /** @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** */
+                v?: string | null;
+                /**
+                 * @deprecated
+                 * @description Legacy name for the `dataset_details` parameter.
+                 */
+                details?: string | null;
+                /**
+                 * @deprecated
+                 * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item.
+                 */
+                ids?: string | null;
+                /**
+                 * @deprecated
+                 * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned.
+                 */
+                types?: string[] | null;
+                /**
+                 * @deprecated
+                 * @description Whether to return deleted or undeleted datasets only. Leave unset for both.
+                 */
+                deleted?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to return visible or hidden datasets only. Leave unset for both.
+                 */
+                visible?: boolean | null;
+                /** @description Whether to return only shareable or not shareable datasets. Leave unset for both. */
+                shareable?: boolean | null;
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+                /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
+                q?: string[] | null;
+                /** @description The value to filter by. */
+                qv?: string[] | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
+                order?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description Accept header to determine the response format. Default is 'application/json'. */
+                accept?: "application/json" | "application/vnd.galaxy.history.contents.stats+json";
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The contents of the history that match the query. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["CustomHistoryView"]
-                        | components["schemas"]["HistoryDetailed"]
-                        | components["schemas"]["HistorySummary"];
+                    "application/json": components["schemas"]["HistoryContentsResult"];
+                    "application/vnd.galaxy.history.contents.stats+json": components["schemas"]["HistoryContentsWithStatsResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    citations_api_histories__history_id__citations_get: {
-        /** Return all the citations for the tools used to produce the datasets in the history. */
+    history_contents__create_typed: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateHistoryContentPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>[];
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"]
+                        | (
+                              | components["schemas"]["HDACustom"]
+                              | components["schemas"]["HDADetailed"]
+                              | components["schemas"]["HDASummary"]
+                              | components["schemas"]["HDAInaccessible"]
+                              | components["schemas"]["HDCACustom"]
+                              | components["schemas"]["HDCADetailed"]
+                              | components["schemas"]["HDCASummary"]
+                          )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__index: {
-        /**
-         * Returns the contents of the given history.
-         * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
-         *
-         * - The contents can be filtered and queried using the appropriate parameters.
-         * - The amount of information returned for each item can be customized.
-         *
-         * **Note**: Anonymous users are allowed to get their current history contents.
-         */
+    history_contents__show: {
         parameters: {
-            /** @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** */
-            /**
-             * @deprecated
-             * @description Legacy name for the `dataset_details` parameter.
-             */
-            /**
-             * @deprecated
-             * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item.
-             */
-            /**
-             * @deprecated
-             * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned.
-             */
-            /**
-             * @deprecated
-             * @description Whether to return deleted or undeleted datasets only. Leave unset for both.
-             */
-            /**
-             * @deprecated
-             * @description Whether to return visible or hidden datasets only. Leave unset for both.
-             */
-            /** @description Whether to return only shareable or not shareable datasets. Leave unset for both. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
             query?: {
-                v?: string | null;
-                details?: string | null;
-                ids?: string | null;
-                types?: string[] | null;
-                deleted?: boolean | null;
-                visible?: boolean | null;
-                shareable?: boolean | null;
+                /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */
+                fuzzy_count?: number | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The contents of the history that match the query. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HistoryContentsResult"];
-                    "application/vnd.galaxy.history.contents.stats+json": components["schemas"]["HistoryContentsWithStatsResult"];
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_batch_api_histories__history_id__contents_put: {
-        /**
-         * Batch update specific properties of a set items contained in the given History.
-         * @description Batch update specific properties of a set items contained in the given History.
-         *
-         * If you provide an invalid/unknown property key the request will not fail, but no changes
-         * will be made to the items.
-         */
+    history_contents__update_typed: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["UpdateHistoryContentsBatchPayload"];
+                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HistoryContentsResult"];
+                    "application/json":
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__create: {
-        /**
-         * Create a new `HDA` or `HDCA` in the given History.
-         * @deprecated
-         * @description Create a new `HDA` or `HDCA` in the given History.
-         */
+    history_contents__delete_typed: {
         parameters: {
-            /** @description The type of the target history element. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
-                type?: components["schemas"]["HistoryContentType"] | null;
+                /**
+                 * @deprecated
+                 * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
+                 */
+                purge?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description When deleting a dataset collection, whether to also delete containing datasets.
+                 */
+                recursive?: boolean | null;
+                /**
+                 * @deprecated
+                 * @description Whether to stop the creating job if all outputs of the job have been deleted.
+                 */
+                stop_job?: boolean | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
                 keys?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
-        requestBody: {
+        requestBody?: {
             content: {
-                "application/json": components["schemas"]["CreateHistoryContentPayload"];
+                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
             };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description Request has been executed. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"]
-                        | (
-                              | components["schemas"]["HDACustom"]
-                              | components["schemas"]["HDADetailed"]
-                              | components["schemas"]["HDASummary"]
-                              | components["schemas"]["HDAInaccessible"]
-                              | components["schemas"]["HDCADetailed"]
-                              | components["schemas"]["HDCASummary"]
-                          )[];
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request accepted, processing will finish later. */
+            202: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__archive: {
-        /**
-         * Build and return a compressed archive of the selected history contents.
-         * @description Build and return a compressed archive of the selected history contents.
-         *
-         * **Note**: this is a volatile endpoint and settings and behavior may change.
-         */
+    show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get: {
         parameters: {
-            /** @description The name that the Archive will have (defaults to history name). */
-            /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            query?: {
-                filename?: string | null;
-                dry_run?: boolean | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json":
+                        | components["schemas"]["JobStateSummary"]
+                        | components["schemas"]["ImplicitCollectionJobsStateSummary"]
+                        | components["schemas"]["WorkflowInvocationStateSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__archive_named: {
-        /**
-         * Build and return a compressed archive of the selected history contents.
-         * @description Build and return a compressed archive of the selected history contents.
-         *
-         * **Note**: this is a volatile endpoint and settings and behavior may change.
-         */
+    prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post: {
         parameters: {
-            /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            query?: {
-                dry_run?: boolean | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The name that the Archive will have (defaults to history name). */
-            /**
-             * @deprecated
-             * @description Output format of the archive.
-             */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                filename: string;
-                format: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["StoreExportPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["AsyncFile"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    bulk_operation_api_histories__history_id__contents_bulk_put: {
-        /**
-         * Executes an operation on a set of items contained in the given History.
-         * @description Executes an operation on a set of items contained in the given History.
-         *
-         * The items to be processed can be explicitly set or determined by a dynamic query.
-         */
+    write_store_api_histories__history_id__contents__type_s__id__write_store_post: {
         parameters: {
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            query?: {
-                q?: string[] | null;
-                qv?: string[] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
+                /** @description The ID of the item (`HDA`/`HDCA`) */
+                id: string;
+                /** @description The type of the target history element. */
+                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["HistoryContentBulkOperationPayload"];
+                "application/json": components["schemas"]["WriteStoreToPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HistoryContentBulkOperationResult"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__download_collection: {
-        /**
-         * Download the content of a dataset collection as a `zip` archive.
-         * @description Download the content of a history dataset collection as a `zip` archive
-         * while maintaining approximate collection structure.
-         */
+    create_from_store_api_histories__history_id__contents_from_store_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description View to be passed to the serializer */
+                view?: string | null;
+                /** @description Comma-separated list of keys to be passed to the serializer */
+                keys?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the `HDCA`. */
-            /** @description The encoded database identifier of the History. */
             path: {
-                id: string;
-                history_id: string | null;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateHistoryContentFromStore"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": (
+                        | components["schemas"]["HDACustom"]
+                        | components["schemas"]["HDADetailed"]
+                        | components["schemas"]["HDASummary"]
+                        | components["schemas"]["HDAInaccessible"]
+                        | components["schemas"]["HDCACustom"]
+                        | components["schemas"]["HDCADetailed"]
+                        | components["schemas"]["HDCASummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    materialize_dataset_api_histories__history_id__contents_datasets__id__materialize_post: {
-        /** Materialize a deferred dataset into real, usable dataset. */
+    get_custom_builds_metadata_api_histories__history_id__custom_builds_metadata_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["CustomBuildsMetadataResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_permissions_api_histories__history_id__contents__dataset_id__permissions_put: {
-        /**
-         * Set permissions of the given history dataset to the given role ids.
-         * @description Set permissions of the given history dataset to the given role ids.
-         */
+    disable_link_access_api_histories__history_id__disable_link_access_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                dataset_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": Record<string, never>;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetAssociationRoles"];
+                    "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents_display_api_histories__history_id__contents__history_content_id__display_get: {
-        /**
-         * Displays (preview) or downloads dataset content.
-         * @description Streams the dataset for download or the contents preview to be displayed in a browser.
-         */
+    enable_link_access_api_histories__history_id__enable_link_access_put: {
         parameters: {
-            /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description If non-null, get the specified filename from the extra files for this dataset. */
-            /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
-            /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
-            /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
-            /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes. */
-            query?: {
-                preview?: boolean;
-                filename?: string | null;
-                to_ext?: string | null;
-                raw?: boolean;
-                offset?: number | null;
-                ck_size?: number | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                history_content_id: string;
-                history_id: string | null;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-        };
-    };
-    history_contents_display_api_histories__history_id__contents__history_content_id__display_head: {
-        /**
-         * Check if dataset content can be previewed or downloaded.
-         * @description Streams the dataset for download or the contents preview to be displayed in a browser.
-         */
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    get_history_exports_api_histories__history_id__exports_get: {
         parameters: {
-            /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description If non-null, get the specified filename from the extra files for this dataset. */
-            /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
-            /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
-            /** @description Set this for datatypes that allow chunked display through the display_data method to enable chunking. This specifies a byte offset into the target dataset's display. */
-            /** @description If offset is set, this recommends 'how large' the next chunk should be. This is not respected or interpreted uniformly and should be interpreted as a very loose recommendation. Different datatypes interpret 'largeness' differently - for bam datasets this is a number of lines whereas for tabular datatypes this is interpreted as a number of bytes. */
             query?: {
-                preview?: boolean;
-                filename?: string | null;
-                to_ext?: string | null;
-                raw?: boolean;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
                 offset?: number | null;
-                ck_size?: number | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description Accept header to determine the response format. Default is 'application/json'. */
+                accept?: "application/json" | "application/vnd.galaxy.task.export+json";
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the History Dataset. */
             path: {
-                history_content_id: string;
-                history_id: string | null;
+                /** @description The encoded database identifier of the History. */
+                history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list of history exports */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["JobExportHistoryArchiveListResponse"];
+                    "application/vnd.galaxy.task.export+json": components["schemas"]["ExportTaskListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    extra_files_history_api_histories__history_id__contents__history_content_id__extra_files_get: {
-        /** Get the list of extra files/directories associated with a dataset. */
+    archive_export_api_histories__history_id__exports_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the History Dataset. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                history_content_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["ExportHistoryArchivePayload"] | null;
             };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description Object containing url to fetch export from. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DatasetExtraFiles"];
+                    "application/json":
+                        | components["schemas"]["JobExportHistoryArchiveModel"]
+                        | components["schemas"]["JobIdResponse"];
+                };
+            };
+            /** @description The exported archive file is not ready yet. */
+            202: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__get_metadata_file: {
-        /** Returns the metadata file associated with this history item. */
+    history_archive_download_api_histories__history_id__exports__jeha_id__get: {
         parameters: {
-            /** @description The name of the metadata file to retrieve. */
-            query: {
-                metadata_file: string;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the History Dataset. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                history_content_id: string;
+                /** @description The ID of the specific Job Export History Association or `latest` (default) to download the last generated archive. */
+                jeha_id: string | "latest";
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            /** @description The archive file containing the History. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_histories__history_id__contents__history_content_id__tags_get: {
-        /** Show tags based on history_content_id */
+    index_jobs_summary_api_histories__history_id__jobs_summary_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description A comma-separated list of encoded ids of job summary objects to return - if `ids` is specified types must also be specified and have same length. */
+                ids?: string | null;
+                /** @description A comma-separated list of type of object represented by elements in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. */
+                types?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_content_id: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsListResponse"];
+                    "application/json": (
+                        | components["schemas"]["JobStateSummary"]
+                        | components["schemas"]["ImplicitCollectionJobsStateSummary"]
+                        | components["schemas"]["WorkflowInvocationStateSummary"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_histories__history_id__contents__history_content_id__tags__tag_name__get: {
-        /** Show tag based on history_content_id */
+    materialize_to_history_api_histories__history_id__materialize_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_content_id: string;
-                tag_name: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["MaterializeDatasetInstanceAPIRequest"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_histories__history_id__contents__history_content_id__tags__tag_name__put: {
-        /** Update tag based on history_content_id */
+    prepare_store_download_api_histories__history_id__prepare_store_download_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_content_id: string;
-                tag_name: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["ItemTagsCreatePayload"];
+                "application/json": components["schemas"]["StoreExportPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json": components["schemas"]["AsyncFile"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_histories__history_id__contents__history_content_id__tags__tag_name__post: {
-        /** Create tag based on history_content_id */
+    publish_api_histories__history_id__publish_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_content_id: string;
-                tag_name: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
         };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["ItemTagsCreatePayload"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_histories__history_id__contents__history_content_id__tags__tag_name__delete: {
-        /** Delete tag based on history_content_id */
+    share_with_users_api_histories__history_id__share_with_users_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_content_id: string;
-                tag_name: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ShareWithPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": boolean;
+                    "application/json": components["schemas"]["ShareHistoryWithStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__show_legacy: {
-        /**
-         * Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
-         * @deprecated
-         * @description Return detailed information about an `HDA` or `HDCA` within a history.
-         *
-         * **Note**: Anonymous users are allowed to get their current history contents.
-         */
+    sharing_api_histories__history_id__sharing_get: {
         parameters: {
-            /** @description The type of the target history element. */
-            /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                type?: components["schemas"]["HistoryContentType"];
-                fuzzy_count?: number | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The encoded database identifier of the History. */
             path: {
-                id: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__update_legacy: {
-        /**
-         * Updates the values for the history content item with the given ``ID`` and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
-         * @deprecated
-         * @description Updates the values for the history content item with the given ``ID``.
-         */
+    set_slug_api_histories__history_id__slug_put: {
         parameters: {
-            /** @description The type of the target history element. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                type?: components["schemas"]["HistoryContentType"];
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
+                "application/json": components["schemas"]["SetSlugPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__delete_legacy: {
-        /**
-         * Delete the history dataset with the given ``ID``.
-         * @description Delete the history content with the given ``ID`` and query specified type (defaults to dataset).
-         *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
-         */
+    index_api_histories__history_id__tags_get: {
         parameters: {
-            /** @description The type of the target history element. */
-            /**
-             * @deprecated
-             * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
-             */
-            /**
-             * @deprecated
-             * @description When deleting a dataset collection, whether to also delete containing datasets.
-             */
-            /**
-             * @deprecated
-             * @description Whether to stop the creating job if all outputs of the job have been deleted.
-             */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                type?: components["schemas"]["HistoryContentType"];
-                purge?: boolean | null;
-                recursive?: boolean | null;
-                stop_job?: boolean | null;
-                view?: string | null;
-                keys?: string | null;
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                history_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["ItemTagsListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+        };
+    };
+    show_api_histories__history_id__tags__tag_name__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
                 history_id: string;
-                id: string;
-            };
-        };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
+                tag_name: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Request has been executed. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                    "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Request accepted, processing will finish later. */
-            202: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    validate_api_histories__history_id__contents__id__validate_put: {
-        /**
-         * Validates the metadata associated with a dataset within a History.
-         * @description Validates the metadata associated with a dataset within a History.
-         */
+    update_api_histories__history_id__tags__tag_name__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
             path: {
                 history_id: string;
-                id: string;
+                tag_name: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ItemTagsCreatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["ItemTagsResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__index_typed: {
-        /**
-         * Returns the contents of the given history filtered by type.
-         * @description Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
-         *
-         * - The contents can be filtered and queried using the appropriate parameters.
-         * - The amount of information returned for each item can be customized.
-         *
-         * **Note**: Anonymous users are allowed to get their current history contents.
-         */
+    create_api_histories__history_id__tags__tag_name__post: {
         parameters: {
-            /** @description Only `dev` value is allowed. Set it to use the latest version of this endpoint. **All parameters marked as `deprecated` will be ignored when this parameter is set.** */
-            /**
-             * @deprecated
-             * @description Legacy name for the `dataset_details` parameter.
-             */
-            /**
-             * @deprecated
-             * @description A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the specific datasets will be returned. Also, setting this value will return `all` details of the content item.
-             */
-            /**
-             * @deprecated
-             * @description A list or comma-separated list of kinds of contents to return (currently just `dataset` and `dataset_collection` are available). If unset, all types will be returned.
-             */
-            /**
-             * @deprecated
-             * @description Whether to return deleted or undeleted datasets only. Leave unset for both.
-             */
-            /**
-             * @deprecated
-             * @description Whether to return visible or hidden datasets only. Leave unset for both.
-             */
-            /** @description Whether to return only shareable or not shareable datasets. Leave unset for both. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            /** @description Generally a property name to filter by followed by an (often optional) hyphen and operator string. */
-            /** @description The value to filter by. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma-separated list of values. */
-            query?: {
-                v?: string | null;
-                details?: string | null;
-                ids?: string | null;
-                types?: string[] | null;
-                deleted?: boolean | null;
-                visible?: boolean | null;
-                shareable?: boolean | null;
-                view?: string | null;
-                keys?: string | null;
-                q?: string[] | null;
-                qv?: string[] | null;
-                offset?: number | null;
-                limit?: number | null;
-                order?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The type of the target history element. */
             path: {
                 history_id: string;
-                type: components["schemas"]["HistoryContentType"];
+                tag_name: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["ItemTagsCreatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HistoryContentsResult"]
-                        | components["schemas"]["HistoryContentsWithStatsResult"];
+                    "application/json": components["schemas"]["ItemTagsResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__create_typed: {
-        /**
-         * Create a new `HDA` or `HDCA` in the given History.
-         * @description Create a new `HDA` or `HDCA` in the given History.
-         */
+    delete_api_histories__history_id__tags__tag_name__delete: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The type of the target history element. */
             path: {
                 history_id: string;
-                type: components["schemas"]["HistoryContentType"];
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateHistoryContentPayload"];
+                tag_name: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"]
-                        | (
-                              | components["schemas"]["HDACustom"]
-                              | components["schemas"]["HDADetailed"]
-                              | components["schemas"]["HDASummary"]
-                              | components["schemas"]["HDAInaccessible"]
-                              | components["schemas"]["HDCADetailed"]
-                              | components["schemas"]["HDCASummary"]
-                          )[];
+                    "application/json": boolean;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__show: {
-        /**
-         * Return detailed information about a specific HDA or HDCA with the given `ID` within a history.
-         * @description Return detailed information about an `HDA` or `HDCA` within a history.
-         *
-         * **Note**: Anonymous users are allowed to get their current history contents.
-         */
+    unpublish_api_histories__history_id__unpublish_put: {
         parameters: {
-            /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                fuzzy_count?: number | null;
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The encoded database identifier of the History. */
-            /** @description The type of the target history element. */
             path: {
-                id: string;
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__update_typed: {
-        /**
-         * Updates the values for the history content item with the given ``ID`` and path specified type.
-         * @description Updates the values for the history content item with the given ``ID``.
-         */
+    write_store_api_histories__history_id__write_store_post: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
-            query?: {
-                view?: string | null;
-                keys?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The type of the target history element. */
             path: {
+                /** @description The encoded database identifier of the History. */
                 history_id: string;
-                id: string;
-                type: components["schemas"]["HistoryContentType"];
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["UpdateHistoryContentsPayload"];
+                "application/json": components["schemas"]["WriteStoreToPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_contents__delete_typed: {
-        /**
-         * Delete the history content with the given ``ID`` and path specified type.
-         * @description Delete the history content with the given ``ID`` and path specified type.
-         *
-         * **Note**: Currently does not stop any active jobs for which this dataset is an output.
-         */
+    index_invocations_api_invocations_get: {
         parameters: {
-            /**
-             * @deprecated
-             * @description Whether to remove from disk the target HDA or child HDAs of the target HDCA.
-             */
-            /**
-             * @deprecated
-             * @description When deleting a dataset collection, whether to also delete containing datasets.
-             */
-            /**
-             * @deprecated
-             * @description Whether to stop the creating job if all outputs of the job have been deleted.
-             */
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
-                purge?: boolean | null;
-                recursive?: boolean | null;
-                stop_job?: boolean | null;
+                /** @description Return only invocations for this Workflow ID */
+                workflow_id?: string | null;
+                /** @description Return only invocations for this History ID */
+                history_id?: string | null;
+                /** @description Return only invocations for this Job ID */
+                job_id?: string | null;
+                /** @description Return invocations for this User ID. */
+                user_id?: string | null;
+                /** @description Sort Workflow Invocations by this attribute */
+                sort_by?: components["schemas"]["InvocationSortByEnum"] | null;
+                /** @description Sort in descending order? */
+                sort_desc?: boolean;
+                /** @description Set to false to only include terminal Invocations. */
+                include_terminal?: boolean | null;
+                /** @description Limit the number of invocations to return. */
+                limit?: number | null;
+                /** @description Number of invocations to skip. */
+                offset?: number | null;
+                /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
+                instance?: boolean | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
-                keys?: string | null;
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
+                step_details?: boolean;
+                include_nested_invocations?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The type of the target history element. */
-            path: {
-                history_id: string;
-                id: string;
-                type: components["schemas"]["HistoryContentType"];
-            };
-        };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["DeleteHistoryContentPayload"];
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Request has been executed. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                    "application/json": components["schemas"]["WorkflowInvocationResponse"][];
                 };
             };
-            /** @description Request accepted, processing will finish later. */
-            202: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeleteHistoryContentResult"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_jobs_summary_api_histories__history_id__contents__type_s__id__jobs_summary_get: {
-        /**
-         * Return detailed information about an `HDA` or `HDCAs` jobs.
-         * @description Return detailed information about an `HDA` or `HDCAs` jobs.
-         *
-         * **Warning**: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
-         */
+    create_invocations_from_store_api_invocations_from_store_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The type of the target history element. */
-            path: {
-                history_id: string;
-                id: string;
-                type: components["schemas"]["HistoryContentType"];
-            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateInvocationsFromStorePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["JobStateSummary"]
-                        | components["schemas"]["ImplicitCollectionJobsStateSummary"]
-                        | components["schemas"]["WorkflowInvocationStateSummary"];
+                    "application/json": components["schemas"]["WorkflowInvocationResponse"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    prepare_store_download_api_histories__history_id__contents__type_s__id__prepare_store_download_post: {
-        /** Prepare a dataset or dataset collection for export-style download. */
+    step_api_invocations_steps__step_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The type of the target history element. */
             path: {
-                history_id: string;
-                id: string;
-                type: components["schemas"]["HistoryContentType"];
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["StoreExportPayload"];
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
+                step_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncFile"];
+                    "application/json": components["schemas"]["InvocationStep"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    write_store_api_histories__history_id__contents__type_s__id__write_store_post: {
-        /** Prepare a dataset or dataset collection for export-style download and write to supplied URI. */
+    show_invocation_api_invocations__invocation_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
+                step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
+                legacy_job_state?: boolean;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the item (`HDA`/`HDCA`) */
-            /** @description The type of the target history element. */
             path: {
-                history_id: string;
-                id: string;
-                type: components["schemas"]["HistoryContentType"];
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["WriteStoreToPayload"];
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["WorkflowInvocationResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_from_store_api_histories__history_id__contents_from_store_post: {
-        /**
-         * Create contents from store.
-         * @description Create history contents from model store.
-         * Input can be a tarfile created with build_objects script distributed
-         * with galaxy-data, from an exported history with files stripped out,
-         * or hand-crafted JSON dictionary.
-         */
+    cancel_invocation_api_invocations__invocation_id__delete: {
         parameters: {
-            /** @description View to be passed to the serializer */
-            /** @description Comma-separated list of keys to be passed to the serializer */
             query?: {
-                view?: string | null;
-                keys?: string | null;
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
+                step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
+                legacy_job_state?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateHistoryContentFromStore"];
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["HDACustom"]
-                        | components["schemas"]["HDADetailed"]
-                        | components["schemas"]["HDASummary"]
-                        | components["schemas"]["HDAInaccessible"]
-                        | components["schemas"]["HDCADetailed"]
-                        | components["schemas"]["HDCASummary"]
-                    )[];
+                    "application/json": components["schemas"]["WorkflowInvocationResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_custom_builds_metadata_api_histories__history_id__custom_builds_metadata_get: {
-        /** Returns meta data for custom builds. */
+    invocation_jobs_summary_api_invocations__invocation_id__jobs_summary_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CustomBuildsMetadataResponse"];
+                    "application/json": components["schemas"]["InvocationJobsResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    disable_link_access_api_histories__history_id__disable_link_access_put: {
-        /**
-         * Makes this item inaccessible by a URL link.
-         * @description Makes this item inaccessible by a URL link and return the current sharing status.
-         */
+    get_invocation_metrics_api_invocations__invocation_id__metrics_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["WorkflowJobMetric"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    enable_link_access_api_histories__history_id__enable_link_access_put: {
-        /**
-         * Makes this item accessible by a URL link.
-         * @description Makes this item accessible by a URL link and return the current sharing status.
-         */
+    prepare_store_download_api_invocations__invocation_id__prepare_store_download_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["PrepareStoreDownloadPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["AsyncFile"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_history_exports_api_histories__history_id__exports_get: {
-        /**
-         * Get previous history exports.
-         * @description By default the legacy job-based history exports (jeha) are returned.
-         *
-         * Change the `accept` content type header to return the new task-based history exports.
-         */
+    show_invocation_report_api_invocations__invocation_id__report_get: {
         parameters: {
-            /** @description The maximum number of items to return. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            query?: {
-                limit?: number | null;
-                offset?: number | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A list of history exports */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobExportHistoryArchiveListResponse"];
-                    "application/vnd.galaxy.task.export+json": components["schemas"]["ExportTaskListResponse"];
+                    "application/json": components["schemas"]["InvocationReport"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    archive_export_api_histories__history_id__exports_put: {
-        /**
-         * Start job (if needed) to create history export for corresponding history.
-         * @deprecated
-         * @description This will start a job to create a history export archive.
-         *
-         * Calling this endpoint multiple times will return the 202 status code until the archive
-         * has been completely generated and is ready to download. When ready, it will return
-         * the 200 status code along with the download link information.
-         *
-         * If the history will be exported to a `directory_uri`, instead of returning the download
-         * link information, the Job ID will be returned so it can be queried to determine when
-         * the file has been written.
-         *
-         * **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
-         * `/api/histories/{id}/write_store` instead.
-         */
+    show_invocation_report_pdf_api_invocations__invocation_id__report_pdf_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
-            };
-        };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["ExportHistoryArchivePayload"] | null;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Object containing url to fetch export from. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["JobExportHistoryArchiveModel"]
-                        | components["schemas"]["JobIdResponse"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description The exported archive file is not ready yet. */
-            202: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    history_archive_download_api_histories__history_id__exports__jeha_id__get: {
-        /**
-         * If ready and available, return raw contents of exported history as a downloadable archive.
-         * @deprecated
-         * @description See ``PUT /api/histories/{id}/exports`` to initiate the creation
-         * of the history export - when ready, that route will return 200 status
-         * code (instead of 202) and this route can be used to download the archive.
-         *
-         * **Deprecation notice**: Please use `/api/histories/{id}/prepare_store_download` or
-         * `/api/histories/{id}/write_store` instead.
-         */
+    invocation_as_request_api_invocations__invocation_id__request_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            /** @description The ID of the specific Job Export History Association or `latest` (default) to download the last generated archive. */
             path: {
-                history_id: string;
-                jeha_id: string | "latest";
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The archive file containing the History. */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["WorkflowInvocationRequestModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_jobs_summary_api_histories__history_id__jobs_summary_get: {
-        /**
-         * Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.
-         * @description Return job state summary info for jobs, implicit groups jobs for collections or workflow invocations.
-         *
-         * **Warning**: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
-         */
+    invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get: {
         parameters: {
-            /** @description A comma-separated list of encoded ids of job summary objects to return - if `ids` is specified types must also be specified and have same length. */
-            /** @description A comma-separated list of type of object represented by elements in the `ids` array - any of `Job`, `ImplicitCollectionJob`, or `WorkflowInvocation`. */
-            query?: {
-                ids?: string | null;
-                types?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": (
-                        | components["schemas"]["JobStateSummary"]
-                        | components["schemas"]["ImplicitCollectionJobsStateSummary"]
-                        | components["schemas"]["WorkflowInvocationStateSummary"]
+                        | components["schemas"]["InvocationStepJobsResponseStepModel"]
+                        | components["schemas"]["InvocationStepJobsResponseJobModel"]
+                        | components["schemas"]["InvocationStepJobsResponseCollectionJobsModel"]
                     )[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    materialize_to_history_api_histories__history_id__materialize_post: {
-        /** Materialize a deferred library or HDA dataset into real, usable dataset in specified history. */
+    invocation_step_api_invocations__invocation_id__steps__step_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["MaterializeDatasetInstanceAPIRequest"];
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
+                step_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["InvocationStep"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    prepare_store_download_api_histories__history_id__prepare_store_download_post: {
-        /** Return a short term storage token to monitor download of the history. */
+    update_invocation_step_api_invocations__invocation_id__steps__step_id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
+                step_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["StoreExportPayload"];
+                "application/json": components["schemas"]["InvocationUpdatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
-                content: {
-                    "application/json": components["schemas"]["AsyncFile"];
+                headers: {
+                    [name: string]: unknown;
                 };
-            };
-            /** @description Validation Error */
-            422: {
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["InvocationStep"];
                 };
             };
-        };
-    };
-    publish_api_histories__history_id__publish_put: {
-        /**
-         * Makes this item public and accessible by a URL link.
-         * @description Makes this item publicly available by a URL link and return the current sharing status.
-         */
-        parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The encoded database identifier of the History. */
-            path: {
-                history_id: string;
-            };
-        };
-        responses: {
-            /** @description Successful Response */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    share_with_users_api_histories__history_id__share_with_users_put: {
-        /**
-         * Share this item with specific users.
-         * @description Shares this item with specific users and return the current sharing status.
-         */
+    write_store_api_invocations__invocation_id__write_store_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["ShareWithPayload"];
+                "application/json": components["schemas"]["WriteInvocationStoreToPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ShareHistoryWithStatus"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    sharing_api_histories__history_id__sharing_get: {
-        /**
-         * Get the current sharing status of the given item.
-         * @description Return the sharing status of the item.
-         */
+    job_lock_status_api_job_lock_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            path: {
-                history_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["JobLock"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_slug_api_histories__history_id__slug_put: {
-        /**
-         * Set a new slug for this shared item.
-         * @description Sets a new slug to access this item by URL. The new slug must be unique.
-         */
+    update_job_lock_api_job_lock_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
-            path: {
-                history_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["SetSlugPayload"];
+                "application/json": components["schemas"]["JobLock"];
             };
         };
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["JobLock"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_histories__history_id__tags_get: {
-        /** Show tags based on history_id */
+    index_api_jobs_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description If true, and requester is an admin, will return external job id and user email. This is only available to admins. */
+                user_details?: boolean;
+                /** @description an encoded user id to restrict query to, must be own id if not admin user */
+                user_id?: string | null;
+                /** @description Determines columns to return. Defaults to 'collection'. */
+                view?: components["schemas"]["JobIndexViewEnum"];
+                /** @description Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01') */
+                date_range_min?: string | null;
+                /** @description Limit listing of jobs to those that are updated before specified date (e.g. '2014-01-01') */
+                date_range_max?: string | null;
+                /** @description Limit listing of jobs to those that match the history_id. If none, jobs from any history may be returned. */
+                history_id?: string | null;
+                /** @description Limit listing of jobs to those that match the specified workflow ID. If none, jobs from any workflow (or from no workflows) may be returned. */
+                workflow_id?: string | null;
+                /** @description Limit listing of jobs to those that match the specified workflow invocation ID. If none, jobs from any workflow invocation (or from no workflows) may be returned. */
+                invocation_id?: string | null;
+                /** @description Limit listing of jobs to those that match the specified implicit collection job ID. If none, jobs from any implicit collection execution (or from no implicit collection execution) may be returned. */
+                implicit_collection_jobs_id?: string | null;
+                /** @description Sort results by specified field. */
+                order_by?: components["schemas"]["JobIndexSortByEnum"];
+                /** @description A mix of free text and GitHub-style tags used to filter the index operation.
+                 *
+                 *     ## Query Structure
+                 *
+                 *     GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+                 *     `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+                 *     *generally* (but not exclusively) corresponds to the name of an attribute on the model
+                 *     being indexed (i.e. a column in the database).
+                 *
+                 *     If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+                 *     generally a partial match will be used to filter the query (i.e. in terms of the implementation
+                 *     this means the database operation `ILIKE` will typically be used).
+                 *
+                 *     Once the tagged filters are extracted from the search query, the remaining text is just
+                 *     used to search various documented attributes of the object.
+                 *
+                 *     ## GitHub-style Tags Available
+                 *
+                 *     `user`
+                 *     : The user email of the user that executed the Job. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `tool_id`
+                 *     : The tool ID corresponding to the job. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `runner`
+                 *     : The job runner name used to execute the job. (The tag `r` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions.
+                 *
+                 *     `handler`
+                 *     : The job handler name used to execute the job. (The tag `h` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions.
+                 *
+                 *     ## Free Text
+                 *
+                 *     Free text search terms will be searched against the following attributes of the
+                 *     Jobs: `user`, `tool`, `handler`, `runner`.
+                 *
+                 *      */
+                search?: string | null;
+                /** @description Maximum number of jobs to return. */
+                limit?: number;
+                /** @description Return jobs starting from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be returned. */
+                offset?: number;
+                /** @description A list or comma-separated list of states to filter job query on. If unspecified, jobs of any state may be returned. */
+                state?: string[] | null;
+                /** @description Limit listing of jobs to those that match one of the included tool_ids. If none, all are returned */
+                tool_id?: string[] | null;
+                /** @description Limit listing of jobs to those that match one of the included tool ID sql-like patterns. If none, all are returned */
+                tool_id_like?: string[] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                history_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsListResponse"];
+                    "application/json": (
+                        | components["schemas"]["ShowFullJobResponse"]
+                        | components["schemas"]["EncodedJobDetails"]
+                        | components["schemas"]["JobSummary"]
+                    )[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_histories__history_id__tags__tag_name__get: {
-        /** Show tag based on history_id */
+    search_jobs_api_jobs_search_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                history_id: string;
-                tag_name: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["SearchJobsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json": components["schemas"]["EncodedJobDetails"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_histories__history_id__tags__tag_name__put: {
-        /** Update tag based on history_id */
+    show_job_api_jobs__job_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Show extra information. */
+                full?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_id: string;
-                tag_name: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["ItemTagsCreatePayload"];
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json":
+                        | components["schemas"]["ShowFullJobResponse"]
+                        | components["schemas"]["EncodedJobDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_histories__history_id__tags__tag_name__post: {
-        /** Create tag based on history_id */
+    cancel_job_api_jobs__job_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_id: string;
-                tag_name: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
         requestBody?: {
             content: {
-                "application/json": components["schemas"]["ItemTagsCreatePayload"];
+                "application/json": components["schemas"]["DeleteJobPayload"] | null;
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ItemTagsResponse"];
+                    "application/json": boolean;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_histories__history_id__tags__tag_name__delete: {
-        /** Delete tag based on history_id */
+    check_common_problems_api_jobs__job_id__common_problems_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                history_id: string;
-                tag_name: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": boolean;
+                    "application/json": components["schemas"]["JobInputSummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    unpublish_api_histories__history_id__unpublish_put: {
-        /**
-         * Removes this item from the published list.
-         * @description Removes this item from the published list and return the current sharing status.
-         */
+    get_console_output_api_jobs__job_id__console_output_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query: {
+                stdout_position: number;
+                stdout_length: number;
+                stderr_position: number;
+                stderr_length: number;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["JobConsoleOutput"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    write_store_api_histories__history_id__write_store_post: {
-        /** Prepare history for export-style download and write to supplied URI. */
+    destination_params_job_api_jobs__job_id__destination_params_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the History. */
             path: {
-                history_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["WriteStoreToPayload"];
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["JobDestinationParams"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_invocations_api_invocations_get: {
-        /** Get the list of a user's workflow invocations. */
-        parameters?: {
-            /** @description Return only invocations for this Workflow ID */
-            /** @description Return only invocations for this History ID */
-            /** @description Return only invocations for this Job ID */
-            /** @description Return invocations for this User ID. */
-            /** @description Sort Workflow Invocations by this attribute */
-            /** @description Sort in descending order? */
-            /** @description Set to false to only include terminal Invocations. */
-            /** @description Limit the number of invocations to return. */
-            /** @description Number of invocations to skip. */
-            /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
-            /** @description View to be passed to the serializer */
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            query?: {
-                workflow_id?: string | null;
-                history_id?: string | null;
-                job_id?: string | null;
-                user_id?: string | null;
-                sort_by?: components["schemas"]["InvocationSortByEnum"] | null;
-                sort_desc?: boolean;
-                include_terminal?: boolean | null;
-                limit?: number | null;
-                offset?: number | null;
-                instance?: boolean | null;
-                view?: string | null;
-                step_details?: boolean;
-                include_nested_invocations?: boolean;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    report_error_api_jobs__job_id__error_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the job */
+                job_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ReportJobErrorPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["WorkflowInvocationResponse"][];
+                    "application/json": components["schemas"]["JobErrorSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_invocations_from_store_api_invocations_from_store_post: {
-        /**
-         * Create Invocations From Store
-         * @description Create invocation(s) from a supplied model store.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    finish_job_api_jobs__job_id__finish_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateInvocationsFromStorePayload"];
+            path: {
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["WorkflowInvocationResponse"][];
+                    "application/json": boolean;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    step_api_invocations_steps__step_id__get: {
-        /** Show details of workflow invocation step. */
+    get_inputs_api_jobs__job_id__inputs_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
             path: {
-                step_id: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InvocationStep"];
+                    "application/json": components["schemas"]["JobInputAssociation"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_invocation_api_invocations__invocation_id__get: {
-        /** Get detailed description of a workflow invocation. */
+    get_metrics_api_jobs__job_id__metrics_get: {
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
             query?: {
-                step_details?: boolean;
-                legacy_job_state?: boolean;
+                /**
+                 * @deprecated
+                 * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
+                 */
+                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["WorkflowInvocationResponse"];
+                    "application/json": (components["schemas"]["JobMetric"] | null)[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    cancel_invocation_api_invocations__invocation_id__delete: {
-        /** Cancel the specified workflow invocation. */
+    get_token_api_jobs__job_id__oidc_tokens_get: {
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
-            query?: {
-                step_details?: boolean;
-                legacy_job_state?: boolean;
+            query: {
+                /** @description A key used to authenticate this request as acting on behalf or a job runner for the specified job */
+                job_key: string;
+                /** @description OIDC provider name */
+                provider: string;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["WorkflowInvocationResponse"];
+                    "text/plain": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "text/plain": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "text/plain": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    invocation_jobs_summary_api_invocations__invocation_id__jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated across all current jobs of the workflow invocation.
-         * @description Warning: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
-         */
+    get_outputs_api_jobs__job_id__outputs_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InvocationJobsResponse"];
+                    "application/json": components["schemas"]["JobOutputAssociation"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    prepare_store_download_api_invocations__invocation_id__prepare_store_download_post: {
-        /** Prepare a workflow invocation export-style download. */
+    resolve_parameters_display_api_jobs__job_id__parameters_display_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /**
+                 * @deprecated
+                 * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
+                 */
+                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["PrepareStoreDownloadPayload"];
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncFile"];
+                    "application/json": components["schemas"]["JobDisplayParametersSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_invocation_report_api_invocations__invocation_id__report_get: {
-        /** Get JSON summarizing invocation for reporting. */
+    resume_paused_job_api_jobs__job_id__resume_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
+                /** @description The ID of the job */
+                job_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InvocationReport"];
+                    "application/json": components["schemas"]["JobOutputAssociation"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_invocation_report_pdf_api_invocations__invocation_id__report_pdf_get: {
-        /** Get PDF summarizing invocation for reporting. */
+    index_api_libraries_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Whether to include deleted libraries in the result. */
+                deleted?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            path: {
-                invocation_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["LibrarySummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated per step of the workflow invocation.
-         * @description Warning: We allow anyone to fetch job state information about any object they
-         * can guess an encoded ID for - it isn't considered protected data. This keeps
-         * polling IDs as part of state calculation for large histories and collections as
-         * efficient as possible.
-         */
+    create_api_libraries_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            path: {
-                invocation_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateLibraryPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["InvocationStepJobsResponseStepModel"]
-                        | components["schemas"]["InvocationStepJobsResponseJobModel"]
-                        | components["schemas"]["InvocationStepJobsResponseCollectionJobsModel"]
-                    )[];
+                    "application/json": components["schemas"]["LibrarySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    invocation_step_api_invocations__invocation_id__steps__step_id__get: {
-        /**
-         * Show details of workflow invocation step.
-         * @description An alias for `GET /api/invocations/steps/{step_id}`. `invocation_id` is ignored.
-         */
+    index_deleted_api_libraries_deleted_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
-            path: {
-                invocation_id: string;
-                step_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InvocationStep"];
+                    "application/json": components["schemas"]["LibrarySummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_invocation_step_api_invocations__invocation_id__steps__step_id__put: {
-        /** Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc. */
+    create_from_store_api_libraries_from_store_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
-            path: {
-                invocation_id: string;
-                step_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["InvocationUpdatePayload"];
+                "application/json": components["schemas"]["CreateLibrariesFromStore"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InvocationStep"];
+                    "application/json": components["schemas"]["LibrarySummary"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    write_store_api_invocations__invocation_id__write_store_post: {
-        /** Prepare a workflow invocation export-style download and write to supplied URI. */
+    show_api_libraries__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
             path: {
-                invocation_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["WriteInvocationStoreToPayload"];
+                /** @description The ID of the Library. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["LibrarySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    job_lock_status_api_job_lock_get: {
-        /**
-         * Job Lock Status
-         * @description Get job lock status.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    delete_api_libraries__id__delete: {
+        parameters: {
+            query?: {
+                /** @description Whether to restore a deleted library. */
+                undelete?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Library. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["DeleteLibraryPayload"] | null;
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobLock"];
+                    "application/json": components["schemas"]["LibrarySummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_job_lock_api_job_lock_put: {
-        /**
-         * Update Job Lock
-         * @description Set job lock status.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_api_libraries__id__patch: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Library. */
+                id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["JobLock"];
+                "application/json": components["schemas"]["UpdateLibraryPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobLock"];
+                    "application/json": components["schemas"]["LibrarySummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_jobs_get: {
-        /** Index */
-        parameters?: {
-            /** @description If true, and requester is an admin, will return external job id and user email. This is only available to admins. */
-            /** @description an encoded user id to restrict query to, must be own id if not admin user */
-            /** @description Determines columns to return. Defaults to 'collection'. */
-            /** @description Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01') */
-            /** @description Limit listing of jobs to those that are updated before specified date (e.g. '2014-01-01') */
-            /** @description Limit listing of jobs to those that match the history_id. If none, jobs from any history may be returned. */
-            /** @description Limit listing of jobs to those that match the specified workflow ID. If none, jobs from any workflow (or from no workflows) may be returned. */
-            /** @description Limit listing of jobs to those that match the specified workflow invocation ID. If none, jobs from any workflow invocation (or from no workflows) may be returned. */
-            /** @description Limit listing of jobs to those that match the specified implicit collection job ID. If none, jobs from any implicit collection execution (or from no implicit collection execution) may be returned. */
-            /** @description Sort results by specified field. */
-            /**
-             * @description A mix of free text and GitHub-style tags used to filter the index operation.
-             *
-             * ## Query Structure
-             *
-             * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
-             * `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
-             * *generally* (but not exclusively) corresponds to the name of an attribute on the model
-             * being indexed (i.e. a column in the database).
-             *
-             * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
-             * generally a partial match will be used to filter the query (i.e. in terms of the implementation
-             * this means the database operation `ILIKE` will typically be used).
-             *
-             * Once the tagged filters are extracted from the search query, the remaining text is just
-             * used to search various documented attributes of the object.
-             *
-             * ## GitHub-style Tags Available
-             *
-             * `user`
-             * : The user email of the user that executed the Job. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `tool_id`
-             * : The tool ID corresponding to the job. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `runner`
-             * : The job runner name used to execute the job. (The tag `r` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions.
-             *
-             * `handler`
-             * : The job handler name used to execute the job. (The tag `h` can be used a short hand alias for this tag to filter on this attribute.) This tag is only available for requests using admin keys and/or sessions.
-             *
-             * ## Free Text
-             *
-             * Free text search terms will be searched against the following attributes of the
-             * Jobs: `user`, `tool`, `handler`, `runner`.
-             */
-            /** @description Maximum number of jobs to return. */
-            /** @description Return jobs starting from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, jobs 200-299 will be returned. */
-            /** @description A list or comma-separated list of states to filter job query on. If unspecified, jobs of any state may be returned. */
-            /** @description Limit listing of jobs to those that match one of the included tool_ids. If none, all are returned */
-            /** @description Limit listing of jobs to those that match one of the included tool ID sql-like patterns. If none, all are returned */
+    get_permissions_api_libraries__id__permissions_get: {
+        parameters: {
             query?: {
-                user_details?: boolean;
-                user_id?: string | null;
-                view?: components["schemas"]["JobIndexViewEnum"];
-                date_range_min?: string | string | null;
-                date_range_max?: string | string | null;
-                history_id?: string | null;
-                workflow_id?: string | null;
-                invocation_id?: string | null;
-                implicit_collection_jobs_id?: string | null;
-                order_by?: components["schemas"]["JobIndexSortByEnum"];
-                search?: string | null;
-                limit?: number;
-                offset?: number;
-                state?: string[] | null;
-                tool_id?: string[] | null;
-                tool_id_like?: string[] | null;
+                /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */
+                scope?: components["schemas"]["LibraryPermissionScope"] | null;
+                /** @description Indicates whether the roles available for the library access are requested. */
+                is_library_access?: boolean | null;
+                /** @description The page number to retrieve when paginating the available roles. */
+                page?: number;
+                /** @description The maximum number of permissions per page when paginating. */
+                page_limit?: number;
+                /** @description Optional search text to retrieve only the roles matching this query. */
+                q?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Library. */
+                id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["ShowFullJobResponse"]
-                        | components["schemas"]["EncodedJobDetails"]
-                        | components["schemas"]["JobSummary"]
-                    )[];
+                    "application/json":
+                        | components["schemas"]["LibraryCurrentPermissions"]
+                        | components["schemas"]["LibraryAvailablePermissions"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    search_jobs_api_jobs_search_post: {
-        /**
-         * Return jobs for current user
-         * @description This method is designed to scan the list of previously run jobs and find records of jobs that had
-         * the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply
-         * recycle the old results.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    set_permissions_api_libraries__id__permissions_post: {
+        parameters: {
+            query?: {
+                /** @description Indicates what action should be performed on the Library. */
+                action?: components["schemas"]["LibraryPermissionAction"] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Library. */
+                id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["SearchJobsPayload"];
+                "application/json":
+                    | components["schemas"]["LibraryPermissionsPayload"]
+                    | components["schemas"]["LegacyLibraryPermissionsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["EncodedJobDetails"][];
+                    "application/json":
+                        | components["schemas"]["LibraryLegacySummary"]
+                        | components["schemas"]["LibraryCurrentPermissions"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_job_api_jobs__job_id__get: {
-        /** Return dictionary containing description of job data. */
+    index_api_libraries__library_id__contents_get: {
         parameters: {
-            /** @description Show extra information. */
-            query?: {
-                full?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
             path: {
-                job_id: string;
+                library_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["ShowFullJobResponse"]
-                        | components["schemas"]["EncodedJobDetails"];
+                    "application/json": components["schemas"]["LibraryContentsIndexListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    cancel_job_api_jobs__job_id__delete: {
-        /** Cancels specified job */
+    create_form_api_libraries__library_id__contents_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
             path: {
-                job_id: string;
+                library_id: string;
             };
+            cookie?: never;
         };
-        requestBody?: {
+        requestBody: {
             content: {
-                "application/json": components["schemas"]["DeleteJobPayload"] | null;
+                "multipart/form-data": components["schemas"]["Body_create_form_api_libraries__library_id__contents_post"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": boolean;
+                    "application/json":
+                        | components["schemas"]["LibraryContentsCreateFolderListResponse"]
+                        | components["schemas"]["LibraryContentsCreateFileListResponse"]
+                        | components["schemas"]["LibraryContentsCreateDatasetCollectionResponse"]
+                        | components["schemas"]["LibraryContentsCreateDatasetResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    check_common_problems_api_jobs__job_id__common_problems_get: {
-        /** Check inputs and job for common potential problems to aid in error reporting */
+    library_content_api_libraries__library_id__contents__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
             path: {
-                job_id: string;
+                library_id: string;
+                /** @example F0123456789ABCDEF */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobInputSummary"];
+                    "application/json":
+                        | components["schemas"]["LibraryContentsShowFolderResponse"]
+                        | components["schemas"]["LibraryContentsShowDatasetResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    destination_params_job_api_jobs__job_id__destination_params_get: {
-        /** Return destination parameters for specified job. */
+    update_api_libraries__library_id__contents__id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query: {
+                payload: unknown;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
             path: {
-                job_id: string;
+                library_id: string;
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobDestinationParams"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    report_error_api_jobs__job_id__error_post: {
-        /** Submits a bug report via the API. */
+    delete_api_libraries__library_id__contents__id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
             path: {
-                job_id: string;
+                library_id: string;
+                id: string;
             };
+            cookie?: never;
         };
-        requestBody: {
+        requestBody?: {
             content: {
-                "application/json": components["schemas"]["ReportJobErrorPayload"];
+                "application/json": components["schemas"]["LibraryContentsDeletePayload"] | null;
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobErrorSummary"];
+                    "application/json": components["schemas"]["LibraryContentsDeleteResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_inputs_api_jobs__job_id__inputs_get: {
-        /** Returns input datasets created by a job. */
+    index_api_licenses_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description List of SPDX licenses */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["LicenseMetadataModel"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
-            /** @description The ID of the job */
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    get_api_licenses__id__get: {
+        parameters: {
+            query?: never;
+            header?: never;
             path: {
-                job_id: string;
+                /** @description The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) */
+                id: unknown;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description SPDX license metadata */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobInputAssociation"][];
+                    "application/json": components["schemas"]["LicenseMetadataModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_metrics_api_jobs__job_id__metrics_get: {
-        /** Return job metrics for specified job. */
+    create_api_metrics_post: {
         parameters: {
-            /**
-             * @deprecated
-             * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
-             */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
-            path: {
-                job_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateMetricsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (components["schemas"]["JobMetric"] | null)[];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_token_api_jobs__job_id__oidc_tokens_get: {
-        /**
-         * Get a fresh OIDC token
-         * @description Allows remote job running mechanisms to get a fresh OIDC token that can be used on remote side to authorize user. It is not meant to represent part of Galaxy's stable, user facing API
-         */
+    get_user_notifications_api_notifications_get: {
         parameters: {
-            /** @description A key used to authenticate this request as acting on behalf or a job runner for the specified job */
-            /** @description OIDC provider name */
-            query: {
-                job_key: string;
-                provider: string;
+            query?: {
+                limit?: number | null;
+                offset?: number | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                job_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "text/plain": string;
+                    "application/json": components["schemas"]["UserNotificationListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_outputs_api_jobs__job_id__outputs_get: {
-        /** Returns output datasets created by a job. */
+    update_user_notifications_api_notifications_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
-            path: {
-                job_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UserNotificationsBatchUpdateRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobOutputAssociation"][];
+                    "application/json": components["schemas"]["NotificationsBatchUpdateResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    resolve_parameters_display_api_jobs__job_id__parameters_display_get: {
-        /**
-         * Resolve parameters as a list for nested display.
-         * @description Resolve parameters as a list for nested display.
-         * This API endpoint is unstable and tied heavily to Galaxy's JS client code,
-         * this endpoint will change frequently.
-         */
+    send_notification_api_notifications_post: {
         parameters: {
-            /**
-             * @deprecated
-             * @description Whether this dataset belongs to a history (HDA) or a library (LDDA).
-             */
-            query?: {
-                hda_ldda?: components["schemas"]["DatasetSourceType"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
-            path: {
-                job_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["NotificationCreateRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobDisplayParametersSummary"];
+                    "application/json":
+                        | components["schemas"]["NotificationCreatedResponse"]
+                        | components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    resume_paused_job_api_jobs__job_id__resume_put: {
-        /** Resumes a paused job. */
+    delete_user_notifications_api_notifications_delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the job */
-            path: {
-                job_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["NotificationsBatchRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["JobOutputAssociation"][];
+                    "application/json": components["schemas"]["NotificationsBatchUpdateResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_libraries_get: {
-        /**
-         * Returns a list of summary data for all libraries.
-         * @description Returns a list of summary data for all libraries.
-         */
-        parameters?: {
-            /** @description Whether to include deleted libraries in the result. */
-            query?: {
-                deleted?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    get_all_broadcasted_api_notifications_broadcast_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummaryList"];
+                    "application/json": components["schemas"]["BroadcastNotificationListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_libraries_post: {
-        /**
-         * Creates a new library and returns its summary information.
-         * @description Creates a new library and returns its summary information. Currently, only admin users can create libraries.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    broadcast_notification_api_notifications_broadcast_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CreateLibraryPayload"];
+                "application/json": components["schemas"]["BroadcastNotificationCreateRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummary"];
+                    "application/json": components["schemas"]["NotificationCreatedResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_deleted_api_libraries_deleted_get: {
-        /**
-         * Returns a list of summary data for all libraries marked as deleted.
-         * @description Returns a list of summary data for all libraries marked as deleted.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    get_broadcasted_api_notifications_broadcast__notification_id__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Notification. */
+                notification_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummaryList"];
+                    "application/json": components["schemas"]["BroadcastNotificationResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_from_store_api_libraries_from_store_post: {
-        /** Create libraries from a model store. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    update_broadcasted_notification_api_notifications_broadcast__notification_id__put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Notification. */
+                notification_id: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CreateLibrariesFromStore"];
+                "application/json": components["schemas"]["NotificationBroadcastUpdateRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummary"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_libraries__id__get: {
-        /**
-         * Returns summary information about a particular library.
-         * @description Returns summary information about a particular library.
-         */
+    get_notification_preferences_api_notifications_preferences_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Library. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummary"];
+                    "application/json": components["schemas"]["UserNotificationPreferences"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_libraries__id__delete: {
-        /**
-         * Marks the specified library as deleted (or undeleted).
-         * @description Marks the specified library as deleted (or undeleted).
-         * Currently, only admin users can delete or restore libraries.
-         */
+    update_notification_preferences_api_notifications_preferences_put: {
         parameters: {
-            /** @description Whether to restore a deleted library. */
-            query?: {
-                undelete?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Library. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
-        requestBody?: {
+        requestBody: {
             content: {
-                "application/json": components["schemas"]["DeleteLibraryPayload"] | null;
+                "application/json": components["schemas"]["UpdateUserNotificationPreferencesRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummary"];
+                    "application/json": components["schemas"]["UserNotificationPreferences"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_libraries__id__patch: {
-        /**
-         * Updates the information of an existing library.
-         * @description Updates the information of an existing library.
-         */
+    get_notifications_status_api_notifications_status_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query: {
+                since: string;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Library. */
-            path: {
-                id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateLibraryPayload"];
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LibrarySummary"];
+                    "application/json": components["schemas"]["NotificationStatusSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_permissions_api_libraries__id__permissions_get: {
-        /**
-         * Gets the current or available permissions of a particular library.
-         * @description Gets the current or available permissions of a particular library.
-         * The results can be paginated and additionally filtered by a query.
-         */
+    show_notification_api_notifications__notification_id__get: {
         parameters: {
-            /** @description The scope of the permissions to retrieve. Either the `current` permissions or the `available`. */
-            /** @description Indicates whether the roles available for the library access are requested. */
-            /** @description The page number to retrieve when paginating the available roles. */
-            /** @description The maximum number of permissions per page when paginating. */
-            /** @description Optional search text to retrieve only the roles matching this query. */
-            query?: {
-                scope?: components["schemas"]["LibraryPermissionScope"] | null;
-                is_library_access?: boolean | null;
-                page?: number;
-                page_limit?: number;
-                q?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Library. */
             path: {
-                id: string;
+                /** @description The ID of the Notification. */
+                notification_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["LibraryCurrentPermissions"]
-                        | components["schemas"]["LibraryAvailablePermissions"];
+                    "application/json": components["schemas"]["UserNotificationResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_permissions_api_libraries__id__permissions_post: {
-        /**
-         * Sets the permissions to access and manipulate a library.
-         * @description Sets the permissions to access and manipulate a library.
-         */
+    update_user_notification_api_notifications__notification_id__put: {
         parameters: {
-            /** @description Indicates what action should be performed on the Library. */
-            query?: {
-                action?: components["schemas"]["LibraryPermissionAction"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Library. */
             path: {
-                id: string;
+                /** @description The ID of the Notification. */
+                notification_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json":
-                    | components["schemas"]["LibraryPermissionsPayload"]
-                    | components["schemas"]["LegacyLibraryPermissionsPayload"];
+                "application/json": components["schemas"]["UserNotificationUpdateRequest"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["LibraryLegacySummary"]
-                        | components["schemas"]["LibraryCurrentPermissions"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_licenses_get: {
-        /**
-         * Lists all available SPDX licenses
-         * @description Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/).
-         */
+    delete_user_notification_api_notifications__notification_id__delete: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The ID of the Notification. */
+                notification_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
         responses: {
-            /** @description List of SPDX licenses */
-            200: {
+            /** @description Successful Response */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LicenseMetadataModel"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_api_licenses__id__get: {
-        /**
-         * Gets the SPDX license metadata associated with the short identifier
-         * @description Returns the license metadata associated with the given
-         * [SPDX license short ID](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/).
-         */
+    object_stores__instances_index: {
         parameters: {
-            /** @description The [SPDX license short identifier](https://spdx.github.io/spdx-spec/appendix-I-SPDX-license-list/) */
-            path: {
-                id: Record<string, never>;
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description SPDX license metadata */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["LicenseMetadataModel"];
+                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_metrics_post: {
-        /**
-         * Records a collection of metrics.
-         * @description Record any metrics sent and return some status object.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__create_instance: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CreateMetricsPayload"];
+                "application/json": components["schemas"]["CreateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_user_notifications_api_notifications_get: {
-        /**
-         * Returns the list of notifications associated with the user.
-         * @description Anonymous users cannot receive personal notifications, only broadcasted notifications.
-         *
-         * You can use the `limit` and `offset` parameters to paginate through the notifications.
-         */
-        parameters?: {
-            query?: {
-                limit?: number | null;
-                offset?: number | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__test_new_instance_configuration: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateInstancePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserNotificationListResponse"];
+                    "application/json": components["schemas"]["PluginStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_user_notifications_api_notifications_put: {
-        /** Updates a list of notifications with the requested values in a single request. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__instances_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UserNotificationsBatchUpdateRequest"];
+            path: {
+                /** @description The UUID used to identify a persisted UserObjectStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["NotificationsBatchUpdateResponse"];
+                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    send_notification_api_notifications_post: {
-        /**
-         * Sends a notification to a list of recipients (users, groups or roles).
-         * @description Sends a notification to a list of recipients (users, groups or roles).
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__instances_update: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The UUID used to identify a persisted UserObjectStore object. */
+                uuid: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["NotificationCreateRequest"];
+                "application/json":
+                    | components["schemas"]["UpdateInstanceSecretPayload"]
+                    | components["schemas"]["UpgradeInstancePayload"]
+                    | components["schemas"]["UpdateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["NotificationCreatedResponse"]
-                        | components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_user_notifications_api_notifications_delete: {
-        /** Deletes a list of notifications received by the user in a single request. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__instances_purge: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["NotificationsBatchRequest"];
+            path: {
+                /** @description The UUID used to identify a persisted UserObjectStore object. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["NotificationsBatchUpdateResponse"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_all_broadcasted_api_notifications_broadcast_get: {
-        /**
-         * Returns all currently active broadcasted notifications.
-         * @description Only Admin users can access inactive notifications (scheduled or recently expired).
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__instances_test_instance: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The UUID used to identify a persisted UserObjectStore object. */
+                uuid: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["BroadcastNotificationListResponse"];
+                    "application/json": components["schemas"]["PluginStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    broadcast_notification_api_notifications_broadcast_post: {
-        /**
-         * Broadcasts a notification to every user in the system.
-         * @description Broadcasted notifications are a special kind of notification that are always accessible to all users, including anonymous users.
-         * They are typically used to display important information such as maintenance windows or new features.
-         * These notifications are displayed differently from regular notifications, usually in a banner at the top or bottom of the page.
-         *
-         * Broadcasted notifications can include action links that are displayed as buttons.
-         * This allows users to easily perform tasks such as filling out surveys, accepting legal agreements, or accessing new tutorials.
-         *
-         * Some key features of broadcasted notifications include:
-         * - They are not associated with a specific user, so they cannot be deleted or marked as read.
-         * - They can be scheduled to be displayed in the future or to expire after a certain time.
-         * - By default, broadcasted notifications are published immediately and expire six months after publication.
-         * - Only admins can create, edit, reschedule, or expire broadcasted notifications as needed.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    object_stores__test_instances_update: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The UUID used to identify a persisted UserObjectStore object. */
+                uuid: string;
+            };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["BroadcastNotificationCreateRequest"];
+                "application/json":
+                    | components["schemas"]["TestUpgradeInstancePayload"]
+                    | components["schemas"]["TestUpdateInstancePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["NotificationCreatedResponse"];
+                    "application/json": components["schemas"]["PluginStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_broadcasted_api_notifications_broadcast__notification_id__get: {
-        /**
-         * Returns the information of a specific broadcasted notification.
-         * @description Only Admin users can access inactive notifications (scheduled or recently expired).
-         */
+    object_stores__templates_index: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Notification. */
-            path: {
-                notification_id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list of the configured object store templates. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["BroadcastNotificationResponse"];
+                    "application/json": components["schemas"]["ObjectStoreTemplateSummaries"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_broadcasted_notification_api_notifications_broadcast__notification_id__put: {
-        /**
-         * Updates the state of a broadcasted notification.
-         * @description Only Admins can update broadcasted notifications. This is useful to reschedule, edit or expire broadcasted notifications.
-         */
+    index_api_object_stores_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Restrict index query to user selectable object stores, the current implementation requires this to be true. */
+                selectable?: boolean;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Notification. */
-            path: {
-                notification_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["NotificationBroadcastUpdateRequest"];
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description A list of the configured object stores. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": (
+                        | components["schemas"]["ConcreteObjectStoreModel"]
+                        | components["schemas"]["UserConcreteObjectStoreModel"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_notification_preferences_api_notifications_preferences_get: {
-        /**
-         * Returns the current user's preferences for notifications.
-         * @description Anonymous users cannot have notification preferences. They will receive only broadcasted notifications.
-         *
-         * - The settings will contain all possible channels, but the client should only show the ones that are really supported by the server.
-         *   The supported channels are returned in the `supported-channels` header.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    show_info_api_object_stores__object_store_id__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The concrete object store ID. */
+                object_store_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserNotificationPreferences"];
+                    "application/json": components["schemas"]["ConcreteObjectStoreModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_notification_preferences_api_notifications_preferences_put: {
-        /**
-         * Updates the user's preferences for notifications.
-         * @description Anonymous users cannot have notification preferences. They will receive only broadcasted notifications.
-         *
-         * - Can be used to completely enable/disable notifications for a particular type (category)
-         * or to enable/disable a particular channel on each category.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+    index_api_pages_get: {
+        parameters: {
+            query?: {
+                /** @description Whether to include deleted pages in the result. */
+                deleted?: boolean;
+                limit?: number;
+                offset?: number;
+                /** @description A mix of free text and GitHub-style tags used to filter the index operation.
+                 *
+                 *     ## Query Structure
+                 *
+                 *     GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+                 *     `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+                 *     *generally* (but not exclusively) corresponds to the name of an attribute on the model
+                 *     being indexed (i.e. a column in the database).
+                 *
+                 *     If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+                 *     generally a partial match will be used to filter the query (i.e. in terms of the implementation
+                 *     this means the database operation `ILIKE` will typically be used).
+                 *
+                 *     Once the tagged filters are extracted from the search query, the remaining text is just
+                 *     used to search various documented attributes of the object.
+                 *
+                 *     ## GitHub-style Tags Available
+                 *
+                 *     `title`
+                 *     : The page's title.
+                 *
+                 *     `slug`
+                 *     : The page's slug. (The tag `s` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `tag`
+                 *     : The page's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `user`
+                 *     : The page's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     ## Free Text
+                 *
+                 *     Free text search terms will be searched against the following attributes of the
+                 *     Pages: `title`, `slug`, `tag`, `user`.
+                 *
+                 *      */
+                search?: string | null;
+                show_own?: boolean;
+                show_published?: boolean;
+                show_shared?: boolean;
+                /** @description Sort page index by this specified attribute on the page model */
+                sort_by?: "create_time" | "title" | "update_time" | "username";
+                /** @description Sort in descending order? */
+                sort_desc?: boolean;
+                user_id?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateUserNotificationPreferencesRequest"];
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list with summary page information. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserNotificationPreferences"];
+                    "application/json": components["schemas"]["PageSummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_notifications_status_api_notifications_status_get: {
-        /**
-         * Returns the current status summary of the user's notifications since a particular date.
-         * @description Anonymous users cannot receive personal notifications, only broadcasted notifications.
-         */
+    create_api_pages_post: {
         parameters: {
-            query: {
-                since: string;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreatePagePayload"];
+            };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description The page summary information. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["NotificationStatusSummary"];
+                    "application/json": components["schemas"]["PageSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_notification_api_notifications__notification_id__get: {
-        /** Displays information about a notification received by the user. */
+    show_api_pages__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Notification. */
             path: {
-                notification_id: string;
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The page summary information. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserNotificationResponse"];
+                    "application/json": components["schemas"]["PageDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_user_notification_api_notifications__notification_id__put: {
-        /** Updates the state of a notification received by the user. */
+    delete_api_pages__id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Notification. */
             path: {
-                notification_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UserNotificationUpdateRequest"];
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_user_notification_api_notifications__notification_id__delete: {
-        /**
-         * Deletes a notification received by the user.
-         * @description When a notification is deleted, it is not immediately removed from the database, but marked as deleted.
-         *
-         * - It will not be returned in the list of notifications, but admins can still access it as long as it is not expired.
-         * - It will be eventually removed from the database by a background task after the expiration time.
-         * - Deleted notifications will be permanently deleted when the expiration time is reached.
-         */
+    show_pdf_api_pages__id__pdf_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Notification. */
             path: {
-                notification_id: string;
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description PDF document with the last revision of the page. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/pdf": unknown;
                 };
             };
-        };
-    };
-    object_stores__instances_index: {
-        /** Get a list of persisted object store instances defined by the requesting user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+            /** @description PDF conversion service not available. */
+            501: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
             };
-        };
-        responses: {
-            /** @description Successful Response */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    object_stores__create_instance: {
-        /** Create a user-bound object store. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    disable_link_access_api_pages__id__disable_link_access_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateInstancePayload"];
+            path: {
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    object_stores__test_new_instance_configuration: {
-        /** Test payload for creating user-bound object store. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    enable_link_access_api_pages__id__enable_link_access_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateInstancePayload"];
+            path: {
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["PluginStatus"];
+                    "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    object_stores__instances_get: {
-        /** Get a persisted user object store instance. */
+    prepare_pdf_api_pages__id__prepare_download_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
-                user_object_store_id: string;
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Short term storage reference for async monitoring of this download. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
+                    "application/json": components["schemas"]["AsyncFile"];
+                };
+            };
+            /** @description PDF conversion service not available. */
+            501: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    object_stores__instances_update: {
-        /** Update or upgrade user object store instance. */
+    publish_api_pages__id__publish_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
-                user_object_store_id: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json":
-                    | components["schemas"]["UpdateInstanceSecretPayload"]
-                    | components["schemas"]["UpgradeInstancePayload"]
-                    | components["schemas"]["UpdateInstancePayload"];
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserConcreteObjectStoreModel"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    object_stores__instances_purge: {
-        /** Purge user object store instance. */
+    share_with_users_api_pages__id__share_with_users_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
-                user_object_store_id: string;
-            };
-        };
-        responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
-                content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
-                };
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
-    };
-    object_stores__templates_index: {
-        /** Get a list of object store templates available to build user defined object stores from */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ShareWithPayload"];
             };
         };
         responses: {
-            /** @description A list of the configured object store templates. */
+            /** @description Successful Response */
             200: {
-                content: {
-                    "application/json": components["schemas"]["ObjectStoreTemplateSummaries"];
+                headers: {
+                    [name: string]: unknown;
                 };
-            };
-            /** @description Validation Error */
-            422: {
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["ShareWithStatus"];
                 };
             };
-        };
-    };
-    index_api_object_stores_get: {
-        /** Get a list of (currently only concrete) object stores configured with this Galaxy instance. */
-        parameters?: {
-            /** @description Restrict index query to user selectable object stores, the current implementation requires this to be true. */
-            query?: {
-                selectable?: boolean;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-        };
-        responses: {
-            /** @description A list of the configured object stores. */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["ConcreteObjectStoreModel"]
-                        | components["schemas"]["UserConcreteObjectStoreModel"]
-                    )[];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_info_api_object_stores__object_store_id__get: {
-        /** Get information about a concrete object store configured with Galaxy. */
+    sharing_api_pages__id__sharing_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The concrete object store ID. */
             path: {
-                object_store_id: string;
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ConcreteObjectStoreModel"];
+                    "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    index_api_pages_get: {
-        /**
-         * Lists all Pages viewable by the user.
-         * @description Get a list with summary information of all Pages available to the user.
-         */
-        parameters?: {
-            /** @description Whether to include deleted pages in the result. */
-            /**
-             * @description A mix of free text and GitHub-style tags used to filter the index operation.
-             *
-             * ## Query Structure
-             *
-             * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
-             * `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
-             * *generally* (but not exclusively) corresponds to the name of an attribute on the model
-             * being indexed (i.e. a column in the database).
-             *
-             * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
-             * generally a partial match will be used to filter the query (i.e. in terms of the implementation
-             * this means the database operation `ILIKE` will typically be used).
-             *
-             * Once the tagged filters are extracted from the search query, the remaining text is just
-             * used to search various documented attributes of the object.
-             *
-             * ## GitHub-style Tags Available
-             *
-             * `title`
-             * : The page's title.
-             *
-             * `slug`
-             * : The page's slug. (The tag `s` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `tag`
-             * : The page's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `user`
-             * : The page's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * ## Free Text
-             *
-             * Free text search terms will be searched against the following attributes of the
-             * Pages: `title`, `slug`, `tag`, `user`.
-             */
-            /** @description Sort page index by this specified attribute on the page model */
-            /** @description Sort in descending order? */
-            query?: {
-                deleted?: boolean;
-                limit?: number;
-                offset?: number;
-                search?: string | null;
-                show_own?: boolean;
-                show_published?: boolean;
-                show_shared?: boolean;
-                sort_by?: "create_time" | "title" | "update_time" | "username";
-                sort_desc?: boolean;
-                user_id?: string | null;
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+        };
+    };
+    set_slug_api_pages__id__slug_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the Page. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["SetSlugPayload"];
+            };
         };
         responses: {
-            /** @description A list with summary page information. */
-            200: {
+            /** @description Successful Response */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["PageSummaryList"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_pages_post: {
-        /**
-         * Create a page and return summary information.
-         * @description Get a list with details of all Pages available to the user.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    undelete_api_pages__id__undelete_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreatePagePayload"];
+            path: {
+                /** @description The ID of the Page. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The page summary information. */
-            200: {
+            /** @description Successful Response */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["PageSummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_pages__id__get: {
-        /**
-         * Return a page summary and the content of the last revision.
-         * @description Return summary information about a specific Page and the content of the last revision.
-         */
+    unpublish_api_pages__id__unpublish_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Page. */
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The page summary information. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["PageDetails"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_pages__id__delete: {
-        /**
-         * Marks the specific Page as deleted.
-         * @description Marks the Page with the given ID as deleted.
-         */
+    index_api_quotas_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["QuotaSummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_pdf_api_pages__id__pdf_get: {
-        /**
-         * Return a PDF document of the last revision of the Page.
-         * @description Return a PDF document of the last revision of the Page.
-         *
-         * This feature may not be available in this Galaxy.
-         */
+    create_api_quotas_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateQuotaParams"];
             };
         };
         responses: {
-            /** @description PDF document with the last revision of the page. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/pdf": unknown;
+                    "application/json": components["schemas"]["CreateQuotaResult"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description PDF conversion service not available. */
-            501: never;
         };
     };
-    disable_link_access_api_pages__id__disable_link_access_put: {
-        /**
-         * Makes this item inaccessible by a URL link.
-         * @description Makes this item inaccessible by a URL link and return the current sharing status.
-         */
+    index_deleted_api_quotas_deleted_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["QuotaSummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    enable_link_access_api_pages__id__enable_link_access_put: {
-        /**
-         * Makes this item accessible by a URL link.
-         * @description Makes this item accessible by a URL link and return the current sharing status.
-         */
+    deleted_quota_api_quotas_deleted__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["QuotaDetails"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    prepare_pdf_api_pages__id__prepare_download_post: {
-        /**
-         * Return a PDF document of the last revision of the Page.
-         * @description Return a STS download link for this page to be downloaded as a PDF.
-         *
-         * This feature may not be available in this Galaxy.
-         */
+    undelete_api_quotas_deleted__id__undelete_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Short term storage reference for async monitoring of this download. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncFile"];
+                    "application/json": string;
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description PDF conversion service not available. */
-            501: never;
         };
     };
-    publish_api_pages__id__publish_put: {
-        /**
-         * Makes this item public and accessible by a URL link.
-         * @description Makes this item publicly available by a URL link and return the current sharing status.
-         */
+    quota_api_quotas__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["QuotaDetails"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    share_with_users_api_pages__id__share_with_users_put: {
-        /**
-         * Share this item with specific users.
-         * @description Shares this item with specific users and return the current sharing status.
-         */
+    update_api_quotas__id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["ShareWithPayload"];
+                "application/json": components["schemas"]["UpdateQuotaParams"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ShareWithStatus"];
+                    "application/json": string;
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    sharing_api_pages__id__sharing_get: {
-        /**
-         * Get the current sharing status of the given Page.
-         * @description Return the sharing status of the item.
-         */
+    delete_api_quotas__id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
+        };
+        requestBody?: {
+            content: {
+                "application/json": components["schemas"]["DeleteQuotaPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_slug_api_pages__id__slug_put: {
-        /**
-         * Set a new slug for this shared item.
-         * @description Sets a new slug to access this item by URL. The new slug must be unique.
-         */
+    purge_api_quotas__id__purge_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
             path: {
+                /** @description The ID of the Quota. */
                 id: string;
             };
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["SetSlugPayload"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_pages__id__undelete_put: {
-        /**
-         * Undelete the specific Page.
-         * @description Marks the Page with the given ID as undeleted.
-         */
+    index_api_remote_files_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */
+                target?: string;
+                /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
+                format?: components["schemas"]["RemoteFilesFormat"] | null;
+                /** @description Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
+                recursive?: boolean | null;
+                /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+                disable?: components["schemas"]["RemoteFilesDisableMode"] | null;
+                /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
+                writeable?: boolean | null;
+                /** @description Maximum number of entries to return. */
+                limit?: number | null;
+                /** @description Number of entries to skip. */
+                offset?: number | null;
+                /** @description Search query to filter entries by. The syntax could be different depending on the target source. */
+                query?: string | null;
+                /** @description Sort the entries by the specified field. */
+                sort_by?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description A list with details about the remote files available to the user. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json":
+                        | components["schemas"]["ListUriResponse"]
+                        | components["schemas"]["ListJstreeResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    unpublish_api_pages__id__unpublish_put: {
-        /**
-         * Removes this item from the published list.
-         * @description Removes this item from the published list and return the current sharing status.
-         */
+    create_entry_api_remote_files_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Page. */
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateEntryPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["CreatedEntryResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_quotas_get: {
-        /**
-         * Displays a list with information of quotas that are currently active.
-         * @description Displays a list with information of quotas that are currently active.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    plugins_api_remote_files_plugins_get: {
+        parameters: {
+            query?: {
+                /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
+                browsable_only?: boolean | null;
+                /** @description Whether to return **only** filesources of the specified kind. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
+                include_kind?: components["schemas"]["PluginKind"][] | null;
+                /** @description Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
+                exclude_kind?: components["schemas"]["PluginKind"][] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list with details about each plugin. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["QuotaSummaryList"];
+                    "application/json": components["schemas"]["FilesSourcePluginList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_quotas_post: {
-        /**
-         * Creates a new quota.
-         * @description Creates a new quota.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    index_api_roles_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateQuotaParams"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CreateQuotaResult"];
+                    "application/json": components["schemas"]["RoleListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_deleted_api_quotas_deleted_get: {
-        /**
-         * Displays a list with information of quotas that have been deleted.
-         * @description Displays a list with information of quotas that have been deleted.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    create_api_roles_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["RoleDefinitionModel"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["QuotaSummaryList"];
+                    "application/json": components["schemas"]["RoleModelResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    deleted_quota_api_quotas_deleted__id__get: {
-        /**
-         * Displays details on a particular quota that has been deleted.
-         * @description Displays details on a particular quota that has been deleted.
-         */
+    show_api_roles__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Quota. */
             path: {
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["QuotaDetails"];
+                    "application/json": components["schemas"]["RoleModelResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_quotas_deleted__id__undelete_post: {
-        /**
-         * Restores a previously deleted quota.
-         * @description Restores a previously deleted quota.
-         */
+    delete_api_roles__id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Quota. */
             path: {
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": components["schemas"]["RoleModelResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    quota_api_quotas__id__get: {
-        /**
-         * Displays details on a particular active quota.
-         * @description Displays details on a particular active quota.
-         */
+    purge_api_roles__id__purge_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Quota. */
             path: {
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["QuotaDetails"];
+                    "application/json": components["schemas"]["RoleModelResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_api_quotas__id__put: {
-        /**
-         * Updates an existing quota.
-         * @description Updates an existing quota.
-         */
+    undelete_api_roles__id__undelete_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the Quota. */
             path: {
                 id: string;
             };
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UpdateQuotaParams"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": components["schemas"]["RoleModelResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_quotas__id__delete: {
-        /**
-         * Deletes an existing quota.
-         * @description Deletes an existing quota.
-         */
+    serve_api_short_term_storage__storage_request_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the Quota. */
+            query?: never;
+            header?: never;
             path: {
-                id: string;
-            };
-        };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["DeleteQuotaPayload"];
+                storage_request_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The archive file containing the History. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request was cancelled without an exception condition recorded. */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    purge_api_quotas__id__purge_post: {
-        /** Purges a previously deleted quota. */
+    is_ready_api_short_term_storage__storage_request_id__ready_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The ID of the Quota. */
+            query?: never;
+            header?: never;
             path: {
-                id: string;
+                storage_request_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Boolean indicating if the storage is ready. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": boolean;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_remote_files_get: {
-        /**
-         * Displays remote files available to the user.
-         * @description Lists all remote files available to the user from different sources.
-         *
-         * The total count of files and directories is returned in the 'total_matches' header.
-         */
-        parameters?: {
-            /** @description The source to load datasets from. Possible values: ftpdir, userdir, importdir */
-            /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
-            /** @description Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
-            /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
-            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
-            /** @description Maximum number of entries to return. */
-            /** @description Number of entries to skip. */
-            /** @description Search query to filter entries by. The syntax could be different depending on the target source. */
-            /** @description Sort the entries by the specified field. */
-            query?: {
-                target?: string;
-                format?: components["schemas"]["RemoteFilesFormat"] | null;
-                recursive?: boolean | null;
-                disable?: components["schemas"]["RemoteFilesDisableMode"] | null;
-                writeable?: boolean | null;
-                limit?: number | null;
-                offset?: number | null;
-                query?: string | null;
-                sort_by?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    cleanup_datasets_api_storage_datasets_delete: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CleanupStorageItemsRequest"];
+            };
         };
         responses: {
-            /** @description A list with details about the remote files available to the user. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["ListUriResponse"]
-                        | components["schemas"]["ListJstreeResponse"];
+                    "application/json": components["schemas"]["StorageItemsCleanupResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_entry_api_remote_files_post: {
-        /**
-         * Creates a new entry (directory/record) on the remote files source.
-         * @description Creates a new entry on the remote files source.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    discarded_datasets_api_storage_datasets_discarded_get: {
+        parameters: {
+            query?: {
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
+                order?: components["schemas"]["StoredItemOrderBy"] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CreateEntryPayload"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CreatedEntryResponse"];
+                    "application/json": components["schemas"]["StoredItem"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    plugins_api_remote_files_plugins_get: {
-        /**
-         * Display plugin information for each of the gxfiles:// URI targets available.
-         * @description Display plugin information for each of the gxfiles:// URI targets available.
-         */
-        parameters?: {
-            /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
-            /** @description Whether to return **only** filesources of the specified kind. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
-            /** @description Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
-            query?: {
-                browsable_only?: boolean | null;
-                include_kind?: components["schemas"]["PluginKind"][] | null;
-                exclude_kind?: components["schemas"]["PluginKind"][] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    discarded_datasets_summary_api_storage_datasets_discarded_summary_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A list with details about each plugin. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["FilesSourcePluginList"];
+                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_roles_get: {
-        /** Index */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    cleanup_histories_api_storage_histories_delete: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CleanupStorageItemsRequest"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleListResponse"];
+                    "application/json": components["schemas"]["StorageItemsCleanupResult"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_roles_post: {
-        /** Create */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    archived_histories_api_storage_histories_archived_get: {
+        parameters: {
+            query?: {
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
+                order?: components["schemas"]["StoredItemOrderBy"] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["RoleDefinitionModel"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleModelResponse"];
+                    "application/json": components["schemas"]["StoredItem"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_roles__id__get: {
-        /** Show */
+    archived_histories_summary_api_storage_histories_archived_summary_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleModelResponse"];
+                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_roles__id__delete: {
-        /** Delete */
+    discarded_histories_api_storage_histories_discarded_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
+                order?: components["schemas"]["StoredItemOrderBy"] | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleModelResponse"];
+                    "application/json": components["schemas"]["StoredItem"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    purge_api_roles__id__purge_post: {
-        /** Purge */
+    discarded_histories_summary_api_storage_histories_discarded_summary_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleModelResponse"];
+                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_api_roles__id__undelete_post: {
-        /** Undelete */
+    update_api_tags_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            path: {
-                id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ItemTagsPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["RoleModelResponse"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    serve_api_short_term_storage__storage_request_id__get: {
-        /** Serve the staged download specified by request ID. */
+    state_api_tasks__task_id__state_get: {
         parameters: {
+            query?: never;
+            header?: never;
             path: {
-                storage_request_id: string;
+                task_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The archive file containing the History. */
-            200: never;
-            /** @description Request was cancelled without an exception condition recorded. */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description String indicating task state. */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["TaskState"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    is_ready_api_short_term_storage__storage_request_id__ready_get: {
-        /** Determine if specified storage request ID is ready for download. */
+    index_api_tool_data_get: {
         parameters: {
-            path: {
-                storage_request_id: string;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Boolean indicating if the storage is ready. */
+            /** @description A list with details on individual data tables. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": boolean;
+                    "application/json": components["schemas"]["ToolDataEntryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    cleanup_datasets_api_storage_datasets_delete: {
-        /**
-         * Purges a set of datasets by ID from disk. The datasets must be owned by the user.
-         * @description **Warning**: This operation cannot be undone. All objects will be deleted permanently from the disk.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    create_api_tool_data_post: {
+        parameters: {
+            query?: {
+                tool_data_file_path?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["CleanupStorageItemsRequest"];
+                "application/json": components["schemas"]["ImportToolDataBundle"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["StorageItemsCleanupResult"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    discarded_datasets_api_storage_datasets_discarded_get: {
-        /** Returns discarded datasets owned by the given user. The results can be paginated. */
-        parameters?: {
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
-            query?: {
-                offset?: number | null;
-                limit?: number | null;
-                order?: components["schemas"]["StoredItemOrderBy"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    show_api_tool_data__table_name__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The name of the tool data table */
+                table_name: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A description of the given data table and its content */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["StoredItem"][];
+                    "application/json": components["schemas"]["ToolDataDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    discarded_datasets_summary_api_storage_datasets_discarded_summary_get: {
-        /** Returns information with the total storage space taken by discarded datasets owned by the given user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    delete_api_tool_data__table_name__delete: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The name of the tool data table */
+                table_name: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ToolDataItem"];
+            };
         };
         responses: {
-            /** @description Successful Response */
+            /** @description A description of the affected data table and its content */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                    "application/json": components["schemas"]["ToolDataDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    cleanup_histories_api_storage_histories_delete: {
-        /**
-         * Purges a set of histories by ID. The histories must be owned by the user.
-         * @description **Warning**: This operation cannot be undone. All objects will be deleted permanently from the disk.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    show_field_api_tool_data__table_name__fields__field_name__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CleanupStorageItemsRequest"];
+            path: {
+                /** @description The name of the tool data table */
+                table_name: string;
+                /** @description The name of the tool data table field */
+                field_name: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Information about a data table field */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["StorageItemsCleanupResult"];
+                    "application/json": components["schemas"]["ToolDataField"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    archived_histories_api_storage_histories_archived_get: {
-        /** Returns archived histories owned by the given user that are not purged. The results can be paginated. */
-        parameters?: {
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
-            query?: {
-                offset?: number | null;
-                limit?: number | null;
-                order?: components["schemas"]["StoredItemOrderBy"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The name of the tool data table */
+                table_name: string;
+                /** @description The name of the tool data table field */
+                field_name: string;
+                /** @description The name of a file associated with this data table field */
+                file_name: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Information about a data table field */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["StoredItem"][];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    archived_histories_summary_api_storage_histories_archived_summary_get: {
-        /** Returns information with the total storage space taken by non-purged archived histories associated with the given user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    reload_api_tool_data__table_name__reload_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The name of the tool data table */
+                table_name: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A description of the reloaded data table and its content */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                    "application/json": components["schemas"]["ToolDataDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    discarded_histories_api_storage_histories_discarded_get: {
-        /** Returns all discarded histories associated with the given user. */
-        parameters?: {
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description The maximum number of items to return. */
-            /** @description String containing one of the valid ordering attributes followed by '-asc' or '-dsc' for ascending and descending order respectively. */
+    index_api_tool_shed_repositories_get: {
+        parameters: {
             query?: {
-                offset?: number | null;
-                limit?: number | null;
-                order?: components["schemas"]["StoredItemOrderBy"] | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+                /** @description Filter by repository name. */
+                name?: string | null;
+                /** @description Filter by repository owner. */
+                owner?: string | null;
+                /** @description Filter by changeset revision. */
+                changeset?: string | null;
+                /** @description Filter by whether the repository has been deleted. */
+                deleted?: boolean | null;
+                /** @description Filter by whether the repository has been uninstalled. */
+                uninstalled?: boolean | null;
             };
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A list of installed tool shed repository objects. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["StoredItem"][];
+                    "application/json": components["schemas"]["InstalledToolShedRepository"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    discarded_histories_summary_api_storage_histories_discarded_summary_get: {
-        /** Returns information with the total storage space taken by discarded histories associated with the given user. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    check_for_updates_api_tool_shed_repositories_check_for_updates_get: {
+        parameters: {
+            query?: {
+                id?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description A description of the state and updates message. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CleanableItemsSummary"];
+                    "application/json": components["schemas"]["CheckForUpdatesResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    update_api_tags_put: {
-        /**
-         * Apply a new set of tags to an item.
-         * @description Replaces the tags associated with an item with the new ones specified in the payload.
-         *
-         * - The previous tags will be __deleted__.
-         * - If no tags are provided in the request body, the currently associated tags will also be __deleted__.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["ItemTagsPayload"];
-            };
-        };
-        responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    state_api_tasks__task_id__state_get: {
-        /** Determine state of task ID */
+    show_api_tool_shed_repositories__id__get: {
         parameters: {
+            query?: never;
+            header?: never;
             path: {
-                task_id: string;
+                /** @description The encoded database identifier of the installed Tool Shed Repository. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description String indicating task state. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["TaskState"];
+                    "application/json": components["schemas"]["InstalledToolShedRepository"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    index_api_tool_data_get: {
-        /**
-         * Lists all available data tables
-         * @description Get the list of all available data tables.
-         */
-        responses: {
-            /** @description A list with details on individual data tables. */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ToolDataEntryList"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_tool_data_post: {
-        /** Import a data manager bundle */
-        parameters?: {
-            query?: {
-                tool_data_file_path?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    fetch_form_api_tools_fetch_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["ImportToolDataBundle"];
+                "multipart/form-data": components["schemas"]["Body_fetch_form_api_tools_fetch_post"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_tool_data__table_name__get: {
-        /**
-         * Get details of a given data table
-         * @description Get details of a given tool data table.
-         */
+    index_api_tours_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The name of the tool data table */
-            path: {
-                table_name: string;
-            };
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A description of the given data table and its content */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ToolDataDetails"];
+                    "application/json": components["schemas"]["TourList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_tool_data__table_name__delete: {
-        /**
-         * Removes an item from a data table
-         * @description Removes an item from a data table and reloads it to return its updated details.
-         */
+    show_api_tours__tour_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
-            };
-            /** @description The name of the tool data table */
+            query?: never;
+            header?: never;
             path: {
-                table_name: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["ToolDataItem"];
+                tour_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A description of the affected data table and its content */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ToolDataDetails"];
+                    "application/json": components["schemas"]["TourDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_field_api_tool_data__table_name__fields__field_name__get: {
-        /**
-         * Get information about a particular field in a tool data table
-         * @description Reloads a data table and return its details.
-         */
+    update_tour_api_tours__tour_id__post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The name of the tool data table */
-            /** @description The name of the tool data table field */
             path: {
-                table_name: string;
-                field_name: string;
+                tour_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Information about a data table field */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ToolDataField"];
+                    "application/json": components["schemas"]["TourDetails"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    download_field_file_api_tool_data__table_name__fields__field_name__files__file_name__get: {
-        /**
-         * Get information about a particular field in a tool data table
-         * @description Download a file associated with the data table field.
-         */
+    get_users_api_users_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Indicates if the collection will be about deleted users */
+                deleted?: boolean;
+                /** @description An email address to filter on */
+                f_email?: string | null;
+                /** @description An username address to filter on */
+                f_name?: string | null;
+                /** @description Filter on username OR email */
+                f_any?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The name of the tool data table */
-            /** @description The name of the tool data table field */
-            /** @description The name of a file associated with this data table field */
-            path: {
-                table_name: string;
-                field_name: string;
-                file_name: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Information about a data table field */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": (
+                        | components["schemas"]["UserModel"]
+                        | components["schemas"]["LimitedUserModel"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    reload_api_tool_data__table_name__reload_get: {
-        /**
-         * Reloads a tool data table
-         * @description Reloads a data table and return its details.
-         */
+    create_user_api_users_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The name of the tool data table */
-            path: {
-                table_name: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json":
+                    | components["schemas"]["UserCreationPayload"]
+                    | components["schemas"]["RemoteUserCreationPayload"];
             };
         };
         responses: {
-            /** @description A description of the reloaded data table and its content */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ToolDataDetails"];
+                    "application/json": components["schemas"]["CreatedUserModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_tool_shed_repositories_get: {
-        /** Lists installed tool shed repositories. */
-        parameters?: {
-            /** @description Filter by repository name. */
-            /** @description Filter by repository owner. */
-            /** @description Filter by changeset revision. */
-            /** @description Filter by whether the repository has been deleted. */
-            /** @description Filter by whether the repository has been uninstalled. */
-            query?: {
-                name?: string | null;
-                owner?: string | null;
-                changeset?: string | null;
-                deleted?: boolean | null;
-                uninstalled?: boolean | null;
+    recalculate_disk_usage_api_users_current_recalculate_disk_usage_put: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A list of installed tool shed repository objects. */
+            /** @description The asynchronous task summary to track the task state. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InstalledToolShedRepository"][];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description The background task was submitted but there is no status tracking ID available. */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    check_for_updates_api_tool_shed_repositories_check_for_updates_get: {
-        /** Check for updates to the specified repository, or all installed repositories. */
-        parameters?: {
+    get_deleted_users_api_users_deleted_get: {
+        parameters: {
             query?: {
-                id?: string | null;
+                /** @description An email address to filter on */
+                f_email?: string | null;
+                /** @description An username address to filter on */
+                f_name?: string | null;
+                /** @description Filter on username OR email */
+                f_any?: string | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description A description of the state and updates message. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CheckForUpdatesResponse"];
+                    "application/json": (
+                        | components["schemas"]["UserModel"]
+                        | components["schemas"]["LimitedUserModel"]
+                    )[];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_tool_shed_repositories__id__get: {
-        /** Show installed tool shed repository. */
+    get_deleted_user_api_users_deleted__user_id__get: {
         parameters: {
-            /** @description The encoded database identifier of the installed Tool Shed Repository. */
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
             path: {
-                id: string;
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["InstalledToolShedRepository"];
+                    "application/json":
+                        | components["schemas"]["DetailedUserModel"]
+                        | components["schemas"]["AnonUserModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    fetch_form_api_tools_fetch_post: {
-        /** Upload files to Galaxy */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    undelete_user_api_users_deleted__user_id__undelete_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-        };
-        requestBody: {
-            content: {
-                "multipart/form-data": components["schemas"]["Body_fetch_form_api_tools_fetch_post"];
+            path: {
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["DetailedUserModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    index_api_tours_get: {
-        /**
-         * Index
-         * @description Return list of available tours.
-         */
-        responses: {
-            /** @description Successful Response */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["TourList"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    show_api_tours__tour_id__get: {
-        /**
-         * Show
-         * @description Return a tour definition.
-         */
+    recalculate_disk_usage_api_users_recalculate_disk_usage_put: {
         parameters: {
-            path: {
-                tour_id: string;
+            query?: never;
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The asynchronous task summary to track the task state. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["TourDetails"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                };
+            };
+            /** @description The background task was submitted but there is no status tracking ID available. */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_tour_api_tours__tour_id__post: {
-        /**
-         * Update Tour
-         * @description Return a tour definition.
-         */
+    get_user_api_users__user_id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Indicates if the user is deleted */
+                deleted?: boolean | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
-                tour_id: string;
+                /** @description The ID of the user to get or 'current'. */
+                user_id: string | "current";
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["TourDetails"];
+                    "application/json":
+                        | components["schemas"]["DetailedUserModel"]
+                        | components["schemas"]["AnonUserModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_users_api_users_get: {
-        /**
-         * Get Users
-         * @description Return a collection of users. Filters will only work if enabled in config or user is admin.
-         */
-        parameters?: {
-            /** @description Indicates if the collection will be about deleted users */
-            /** @description An email address to filter on */
-            /** @description An username address to filter on */
-            /** @description Filter on username OR email */
+    update_user_api_users__user_id__put: {
+        parameters: {
             query?: {
-                deleted?: boolean;
-                f_email?: string | null;
-                f_name?: string | null;
-                f_any?: string | null;
+                /** @description Indicates if the user is deleted */
+                deleted?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the user to get or 'current'. */
+                user_id: string | "current";
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UserUpdatePayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["UserModel"]
-                        | components["schemas"]["LimitedUserModel"]
-                    )[];
+                    "application/json": components["schemas"]["DetailedUserModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_user_api_users_post: {
-        /** Create a new Galaxy user. Only admins can create users for now. */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    delete_user_api_users__user_id__delete: {
+        parameters: {
+            query?: {
+                /** @description Whether to definitely remove this user. Only deleted users can be purged. */
+                purge?: boolean;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the user. */
+                user_id: string;
+            };
+            cookie?: never;
         };
-        requestBody: {
+        requestBody?: {
             content: {
-                "application/json":
-                    | components["schemas"]["UserCreationPayload"]
-                    | components["schemas"]["RemoteUserCreationPayload"];
+                "application/json": components["schemas"]["UserDeletionPayload"] | null;
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CreatedUserModel"];
+                    "application/json": components["schemas"]["DetailedUserModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    recalculate_disk_usage_api_users_current_recalculate_disk_usage_put: {
-        /**
-         * Triggers a recalculation of the current user disk usage.
-         * @description This route will be removed in a future version.
-         *
-         * Please use `/api/users/current/recalculate_disk_usage` instead.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    get_or_create_api_key_api_users__user_id__api_key_get: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the user. */
+                user_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The asynchronous task summary to track the task state. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": string;
                 };
             };
-            /** @description The background task was submitted but there is no status tracking ID available. */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_deleted_users_api_users_deleted_get: {
-        /**
-         * Get Deleted Users
-         * @description Return a collection of deleted users. Only admins can see deleted users.
-         */
-        parameters?: {
-            /** @description An email address to filter on */
-            /** @description An username address to filter on */
-            /** @description Filter on username OR email */
-            query?: {
-                f_email?: string | null;
-                f_name?: string | null;
-                f_any?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    create_api_key_api_users__user_id__api_key_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The ID of the user. */
+                user_id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": (
-                        | components["schemas"]["UserModel"]
-                        | components["schemas"]["LimitedUserModel"]
-                    )[];
+                    "application/json": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_deleted_user_api_users_deleted__user_id__get: {
-        /** Return information about a deleted user. Only admins can see deleted users. */
+    delete_api_key_api_users__user_id__api_key_delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["DetailedUserModel"]
-                        | components["schemas"]["AnonUserModel"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    undelete_user_api_users_deleted__user_id__undelete_post: {
-        /** Restore a deleted user. Only admins can restore users. */
+    get_api_key_detailed_api_users__user_id__api_key_detailed_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The API key of the user. */
             200: {
-                content: {
-                    "application/json": components["schemas"]["DetailedUserModel"];
+                headers: {
+                    [name: string]: unknown;
                 };
-            };
-            /** @description Validation Error */
-            422: {
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["APIKeyModel"];
                 };
             };
-        };
-    };
-    recalculate_disk_usage_api_users_recalculate_disk_usage_put: {
-        /**
-         * Triggers a recalculation of the current user disk usage.
-         * @deprecated
-         * @description This route will be removed in a future version.
-         *
-         * Please use `/api/users/current/recalculate_disk_usage` instead.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
-            header?: {
-                "run-as"?: string | null;
+            /** @description The user doesn't have an API key. */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
             };
-        };
-        responses: {
-            /** @description The asynchronous task summary to track the task state. */
-            200: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description The background task was submitted but there is no status tracking ID available. */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_user_api_users__user_id__get: {
-        /** Return information about a specified or the current user. Only admin can see deleted or other users */
+    get_beacon_settings_api_users__user_id__beacon_get: {
         parameters: {
-            /** @description Indicates if the user is deleted */
-            query?: {
-                deleted?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user to get or 'current'. */
             path: {
-                user_id: string | "current";
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json":
-                        | components["schemas"]["DetailedUserModel"]
-                        | components["schemas"]["AnonUserModel"];
+                    "application/json": components["schemas"]["UserBeaconSetting"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    update_user_api_users__user_id__put: {
-        /** Update the values of a user. Only admin can update others. */
+    set_beacon_settings_api_users__user_id__beacon_post: {
         parameters: {
-            /** @description Indicates if the user is deleted */
-            query?: {
-                deleted?: boolean | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user to get or 'current'. */
             path: {
-                user_id: string | "current";
+                /** @description The ID of the user. */
+                user_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": Record<string, never>;
+                "application/json": components["schemas"]["UserBeaconSetting"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DetailedUserModel"];
+                    "application/json": components["schemas"]["UserBeaconSetting"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_user_api_users__user_id__delete: {
-        /** Delete a user. Only admins can delete others or purge users. */
+    get_custom_builds_api_users__user_id__custom_builds_get: {
         parameters: {
-            /** @description Whether to definitely remove this user. Only deleted users can be purged. */
-            query?: {
-                purge?: boolean;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
             };
+            cookie?: never;
         };
-        requestBody?: {
-            content: {
-                "application/json": components["schemas"]["UserDeletionPayload"] | null;
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DetailedUserModel"];
+                    "application/json": components["schemas"]["CustomBuildsCollection"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_or_create_api_key_api_users__user_id__api_key_get: {
-        /** Return the user's API key */
+    add_custom_builds_api_users__user_id__custom_builds__key__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
+                /** @description The key of the custom build to be deleted. */
+                key: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CustomBuildCreationPayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    create_api_key_api_users__user_id__api_key_post: {
-        /** Create a new API key for the user */
+    delete_custom_build_api_users__user_id__custom_builds__key__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
+                /** @description The key of the custom build to be deleted. */
+                key: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": components["schemas"]["DeletedCustomBuild"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_api_key_api_users__user_id__api_key_delete: {
-        /** Delete the current API key of the user */
+    set_favorite_api_users__user_id__favorites__object_type__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
+                /** @description The object type the user wants to favorite */
+                object_type: components["schemas"]["FavoriteObjectType"];
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["FavoriteObject"];
             };
         };
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["FavoriteObjectsSummary"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_api_key_detailed_api_users__user_id__api_key_detailed_get: {
-        /** Return the user's API key with extra information. */
+    remove_favorite_api_users__user_id__favorites__object_type___object_id__delete: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
+                /** @description The object type the user wants to favorite */
+                object_type: components["schemas"]["FavoriteObjectType"];
+                /** @description The ID of an object the user wants to remove from favorites */
+                object_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description The API key of the user. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["APIKeyModel"];
+                    "application/json": components["schemas"]["FavoriteObjectsSummary"];
                 };
             };
-            /** @description The user doesn't have an API key. */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_beacon_settings_api_users__user_id__beacon_get: {
-        /**
-         * Return information about beacon share settings
-         * @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
-         */
+    get_user_objectstore_usage_api_users__user_id__objectstore_usage_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
-                user_id: string;
+                /** @description The ID of the user to get or 'current'. */
+                user_id: string | "current";
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserBeaconSetting"];
+                    "application/json": components["schemas"]["UserObjectstoreUsage"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_beacon_settings_api_users__user_id__beacon_post: {
-        /**
-         * Change beacon setting
-         * @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
-         */
+    recalculate_disk_usage_by_user_id_api_users__user_id__recalculate_disk_usage_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
             };
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["UserBeaconSetting"];
-            };
-        };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description The asynchronous task summary to track the task state. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserBeaconSetting"];
+                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description The background task was submitted but there is no status tracking ID available. */
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_custom_builds_api_users__user_id__custom_builds_get: {
-        /** Returns collection of custom builds. */
+    get_user_roles_api_users__user_id__roles_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["CustomBuildsCollection"];
+                    "application/json": components["schemas"]["RoleListResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    add_custom_builds_api_users__user_id__custom_builds__key__put: {
-        /** Add new custom build. */
+    send_activation_email_api_users__user_id__send_activation_email_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            /** @description The key of the custom build to be deleted. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
-                key: string;
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["CustomBuildCreationPayload"];
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    delete_custom_build_api_users__user_id__custom_builds__key__delete: {
-        /** Delete a custom build */
+    set_theme_api_users__user_id__theme__theme__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            /** @description The key of the custom build to be deleted. */
             path: {
+                /** @description The ID of the user. */
                 user_id: string;
-                key: string;
+                /** @description The theme of the GUI */
+                theme: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["DeletedCustomBuild"];
+                    "application/json": string;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_favorite_api_users__user_id__favorites__object_type__put: {
-        /** Add the object to user's favorites */
+    get_user_usage_api_users__user_id__usage_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            /** @description The object type the user wants to favorite */
             path: {
-                user_id: string;
-                object_type: components["schemas"]["FavoriteObjectType"];
-            };
-        };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["FavoriteObject"];
+                /** @description The ID of the user to get or 'current'. */
+                user_id: string | "current";
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["FavoriteObjectsSummary"];
+                    "application/json": components["schemas"]["UserQuotaUsage"][];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    remove_favorite_api_users__user_id__favorites__object_type___object_id__delete: {
-        /** Remove the object from user's favorites */
+    get_user_usage_for_label_api_users__user_id__usage__label__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            /** @description The object type the user wants to favorite */
-            /** @description The ID of an object the user wants to remove from favorites */
             path: {
-                user_id: string;
-                object_type: components["schemas"]["FavoriteObjectType"];
-                object_id: string;
+                /** @description The ID of the user to get or 'current'. */
+                user_id: string | "current";
+                /** @description The label corresponding to the quota source to fetch usage information about. */
+                label: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["UserQuotaUsage"] | null;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    version_api_version_get: {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Galaxy version information: major/minor version, optional extra info */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": Record<string, never>;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["FavoriteObjectsSummary"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_user_objectstore_usage_api_users__user_id__objectstore_usage_get: {
-        /** Return the user's object store usage summary broken down by object store ID */
+    index_api_visualizations_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description Whether to include deleted visualizations in the result. */
+                deleted?: boolean;
+                /** @description The maximum number of items to return. */
+                limit?: number | null;
+                /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
+                offset?: number | null;
+                user_id?: string | null;
+                show_own?: boolean;
+                show_published?: boolean;
+                show_shared?: boolean;
+                /** @description Sort visualization index by this specified attribute on the visualization model */
+                sort_by?: "create_time" | "title" | "update_time" | "username";
+                /** @description Sort in descending order? */
+                sort_desc?: boolean;
+                /** @description A mix of free text and GitHub-style tags used to filter the index operation.
+                 *
+                 *     ## Query Structure
+                 *
+                 *     GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+                 *     `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+                 *     *generally* (but not exclusively) corresponds to the name of an attribute on the model
+                 *     being indexed (i.e. a column in the database).
+                 *
+                 *     If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+                 *     generally a partial match will be used to filter the query (i.e. in terms of the implementation
+                 *     this means the database operation `ILIKE` will typically be used).
+                 *
+                 *     Once the tagged filters are extracted from the search query, the remaining text is just
+                 *     used to search various documented attributes of the object.
+                 *
+                 *     ## GitHub-style Tags Available
+                 *
+                 *     `title`
+                 *     : The visualization's title.
+                 *
+                 *     `slug`
+                 *     : The visualization's slug. (The tag `s` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `tag`
+                 *     : The visualization's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `user`
+                 *     : The visualization's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     ## Free Text
+                 *
+                 *     Free text search terms will be searched against the following attributes of the
+                 *     Visualizations: `title`, `slug`, `tag`, `type`.
+                 *
+                 *      */
+                search?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user to get or 'current'. */
-            path: {
-                user_id: string | "current";
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserObjectstoreUsage"][];
+                    "application/json": components["schemas"]["VisualizationSummaryList"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    recalculate_disk_usage_by_user_id_api_users__user_id__recalculate_disk_usage_put: {
-        /** Triggers a recalculation of the current user disk usage. */
+    create_api_visualizations_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: {
+                /** @description The encoded database identifier of the Visualization to import. */
+                import_id?: string | null;
+            };
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            path: {
-                user_id: string;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["VisualizationCreatePayload"];
             };
         };
         responses: {
-            /** @description The asynchronous task summary to track the task state. */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["AsyncTaskResultSummary"];
+                    "application/json": components["schemas"]["VisualizationCreateResponse"];
                 };
             };
-            /** @description The background task was submitted but there is no status tracking ID available. */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    send_activation_email_api_users__user_id__send_activation_email_post: {
-        /** Sends activation email to user. */
+    show_api_visualizations__id__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
             path: {
-                user_id: string;
+                /** @description The encoded database identifier of the Visualization. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["VisualizationShowResponse"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_theme_api_users__user_id__theme__theme__put: {
-        /** Set the user's theme choice */
+    update_api_visualizations__id__put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user. */
-            /** @description The theme of the GUI */
             path: {
-                user_id: string;
-                theme: string;
+                /** @description The encoded database identifier of the Visualization. */
+                id: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["VisualizationUpdatePayload"];
             };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": string;
+                    "application/json": components["schemas"]["VisualizationUpdateResponse"] | null;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_user_usage_api_users__user_id__usage_get: {
-        /** Return the user's quota usage summary broken down by quota source */
+    disable_link_access_api_visualizations__id__disable_link_access_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user to get or 'current'. */
             path: {
-                user_id: string | "current";
+                /** @description The encoded database identifier of the Visualization. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserQuotaUsage"][];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    get_user_usage_for_label_api_users__user_id__usage__label__get: {
-        /** Return the user's quota usage summary for a given quota source label */
+    enable_link_access_api_visualizations__id__enable_link_access_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the user to get or 'current'. */
-            /** @description The label corresponding to the quota source to fetch usage information about. */
             path: {
-                user_id: string | "current";
-                label: string;
+                /** @description The encoded database identifier of the Visualization. */
+                id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserQuotaUsage"] | null;
+                    "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-        };
-    };
-    version_api_version_get: {
-        /**
-         * Return Galaxy version information: major/minor version, optional extra info
-         * @description Return Galaxy version information: major/minor version, optional extra info.
-         */
-        responses: {
-            /** @description Galaxy version information: major/minor version, optional extra info */
-            200: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    index_api_visualizations_get: {
-        /** Returns visualizations for the current user. */
-        parameters?: {
-            /** @description Whether to include deleted visualizations in the result. */
-            /** @description The maximum number of items to return. */
-            /** @description Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item */
-            /** @description Sort visualization index by this specified attribute on the visualization model */
-            /** @description Sort in descending order? */
-            /**
-             * @description A mix of free text and GitHub-style tags used to filter the index operation.
-             *
-             * ## Query Structure
-             *
-             * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
-             * `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
-             * *generally* (but not exclusively) corresponds to the name of an attribute on the model
-             * being indexed (i.e. a column in the database).
-             *
-             * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
-             * generally a partial match will be used to filter the query (i.e. in terms of the implementation
-             * this means the database operation `ILIKE` will typically be used).
-             *
-             * Once the tagged filters are extracted from the search query, the remaining text is just
-             * used to search various documented attributes of the object.
-             *
-             * ## GitHub-style Tags Available
-             *
-             * `title`
-             * : The visualization's title.
-             *
-             * `slug`
-             * : The visualization's slug. (The tag `s` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `tag`
-             * : The visualization's tags. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `user`
-             * : The visualization's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * ## Free Text
-             *
-             * Free text search terms will be searched against the following attributes of the
-             * Visualizations: `title`, `slug`, `tag`, `type`.
-             */
-            query?: {
-                deleted?: boolean;
-                limit?: number | null;
-                offset?: number | null;
-                user_id?: string | null;
-                show_own?: boolean;
-                show_published?: boolean;
-                show_shared?: boolean;
-                sort_by?: "create_time" | "title" | "update_time" | "username";
-                sort_desc?: boolean;
-                search?: string | null;
-            };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    publish_api_visualizations__id__publish_put: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The encoded database identifier of the Visualization. */
+                id: string;
+            };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["VisualizationSummaryList"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    disable_link_access_api_visualizations__id__disable_link_access_put: {
-        /**
-         * Makes this item inaccessible by a URL link.
-         * @description Makes this item inaccessible by a URL link and return the current sharing status.
-         */
+    share_with_users_api_visualizations__id__share_with_users_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
             path: {
+                /** @description The encoded database identifier of the Visualization. */
                 id: string;
             };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ShareWithPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["ShareWithStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    enable_link_access_api_visualizations__id__enable_link_access_put: {
-        /**
-         * Makes this item accessible by a URL link.
-         * @description Makes this item accessible by a URL link and return the current sharing status.
-         */
+    sharing_api_visualizations__id__sharing_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
             path: {
+                /** @description The encoded database identifier of the Visualization. */
                 id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    publish_api_visualizations__id__publish_put: {
-        /**
-         * Makes this item public and accessible by a URL link.
-         * @description Makes this item publicly available by a URL link and return the current sharing status.
-         */
+    set_slug_api_visualizations__id__slug_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
             path: {
+                /** @description The encoded database identifier of the Visualization. */
                 id: string;
             };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["SetSlugPayload"];
+            };
         };
         responses: {
             /** @description Successful Response */
-            200: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    share_with_users_api_visualizations__id__share_with_users_put: {
-        /**
-         * Share this item with specific users.
-         * @description Shares this item with specific users and return the current sharing status.
-         */
+    unpublish_api_visualizations__id__unpublish_put: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
             path: {
+                /** @description The encoded database identifier of the Visualization. */
                 id: string;
             };
+            cookie?: never;
         };
-        requestBody: {
-            content: {
-                "application/json": components["schemas"]["ShareWithPayload"];
-            };
-        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["ShareWithStatus"];
+                    "application/json": components["schemas"]["SharingStatus"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    sharing_api_visualizations__id__sharing_get: {
-        /**
-         * Get the current sharing status of the given Visualization.
-         * @description Return the sharing status of the item.
-         */
+    whoami_api_whoami_get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
-            /** @description Successful Response */
+            /** @description Information about the current authenticated user */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["UserModel"] | null;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    set_slug_api_visualizations__id__slug_put: {
-        /**
-         * Set a new slug for this shared item.
-         * @description Sets a new slug to access this item by URL. The new slug must be unique.
-         */
+    create_landing_api_workflow_landings_post: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
-            path: {
-                id: string;
-            };
+            path?: never;
+            cookie?: never;
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["SetSlugPayload"];
+                "application/json": components["schemas"]["CreateWorkflowLandingRequestPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["WorkflowLandingRequest"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
             };
-        };
-        responses: {
-            /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    unpublish_api_visualizations__id__unpublish_put: {
-        /**
-         * Removes this item from the published list.
-         * @description Removes this item from the published list and return the current sharing status.
-         */
+    get_landing_api_workflow_landings__uuid__get: {
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Visualization. */
             path: {
-                id: string;
+                /** @description The UUID used to identify a persisted landing request. */
+                uuid: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["SharingStatus"];
+                    "application/json": components["schemas"]["WorkflowLandingRequest"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
-    whoami_api_whoami_get: {
-        /**
-         * Return information about the current authenticated user
-         * @description Return information about the current authenticated user.
-         */
-        parameters?: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+    claim_landing_api_workflow_landings__uuid__claim_post: {
+        parameters: {
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path: {
+                /** @description The UUID used to identify a persisted landing request. */
+                uuid: string;
+            };
+            cookie?: never;
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["ClaimLandingPayload"] | null;
+            };
         };
         responses: {
-            /** @description Information about the current authenticated user */
+            /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["UserModel"] | null;
+                    "application/json": components["schemas"]["WorkflowLandingRequest"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     index_api_workflows_get: {
-        /**
-         * Lists stored workflows viewable by the user.
-         * @description Lists stored workflows viewable by the user.
-         */
-        parameters?: {
-            /** @description Whether to restrict result to deleted workflows. */
-            /** @description Whether to restrict result to hidden workflows. */
-            /** @description Whether to include a list of missing tools per workflow entry */
-            /** @description In unspecified, default ordering depends on other parameters but generally the user's own workflows appear first based on update time */
-            /** @description Sort in descending order? */
-            /**
-             * @description A mix of free text and GitHub-style tags used to filter the index operation.
-             *
-             * ## Query Structure
-             *
-             * GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
-             * `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
-             * *generally* (but not exclusively) corresponds to the name of an attribute on the model
-             * being indexed (i.e. a column in the database).
-             *
-             * If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
-             * generally a partial match will be used to filter the query (i.e. in terms of the implementation
-             * this means the database operation `ILIKE` will typically be used).
-             *
-             * Once the tagged filters are extracted from the search query, the remaining text is just
-             * used to search various documented attributes of the object.
-             *
-             * ## GitHub-style Tags Available
-             *
-             * `name`
-             * : The stored workflow's name. (The tag `n` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `tag`
-             * : The workflow's tag, if the tag contains a colon an approach will be made to match the key and value of the tag separately. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `user`
-             * : The stored workflow's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
-             *
-             * `is:published`
-             * : Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
-             *
-             * `is:share_with_me`
-             * : Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.
-             *
-             * ## Free Text
-             *
-             * Free text search terms will be searched against the following attributes of the
-             * Stored Workflows: `name`, `tag`, `user`.
-             */
-            /** @description Set this to true to skip joining workflow step counts and optimize the resulting index query. Response objects will not contain step counts. */
+        parameters: {
             query?: {
+                /** @description Whether to restrict result to deleted workflows. */
                 show_deleted?: boolean;
+                /** @description Whether to restrict result to hidden workflows. */
                 show_hidden?: boolean;
+                /** @description Whether to include a list of missing tools per workflow entry */
                 missing_tools?: boolean;
                 show_published?: boolean | null;
                 show_shared?: boolean | null;
+                /** @description In unspecified, default ordering depends on other parameters but generally the user's own workflows appear first based on update time */
                 sort_by?: ("create_time" | "update_time" | "name") | null;
+                /** @description Sort in descending order? */
                 sort_desc?: boolean | null;
                 limit?: number | null;
                 offset?: number | null;
+                /** @description A mix of free text and GitHub-style tags used to filter the index operation.
+                 *
+                 *     ## Query Structure
+                 *
+                 *     GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+                 *     `<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+                 *     *generally* (but not exclusively) corresponds to the name of an attribute on the model
+                 *     being indexed (i.e. a column in the database).
+                 *
+                 *     If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+                 *     generally a partial match will be used to filter the query (i.e. in terms of the implementation
+                 *     this means the database operation `ILIKE` will typically be used).
+                 *
+                 *     Once the tagged filters are extracted from the search query, the remaining text is just
+                 *     used to search various documented attributes of the object.
+                 *
+                 *     ## GitHub-style Tags Available
+                 *
+                 *     `name`
+                 *     : The stored workflow's name. (The tag `n` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `tag`
+                 *     : The workflow's tag, if the tag contains a colon an approach will be made to match the key and value of the tag separately. (The tag `t` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `user`
+                 *     : The stored workflow's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
+                 *
+                 *     `is:published`
+                 *     : Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
+                 *
+                 *     `is:importable`
+                 *     : Include only importable workflows in the final result.
+                 *
+                 *     `is:deleted`
+                 *     : Include only deleted workflows in the final result.
+                 *
+                 *     `is:shared_with_me`
+                 *     : Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.
+                 *
+                 *     `is:bookmarked`
+                 *     : Include only workflows bookmarked by the requesting user.
+                 *
+                 *     ## Free Text
+                 *
+                 *     Free text search terms will be searched against the following attributes of the
+                 *     Stored Workflows: `name`, `tag`, `user`.
+                 *
+                 *      */
                 search?: string | null;
+                /** @description Set this to true to skip joining workflow step counts and optimize the resulting index query. Response objects will not contain step counts. */
                 skip_step_counts?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description A list with summary stored workflow information per viewable entry. */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": Record<string, never>[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     get_workflow_menu_api_workflows_menu_get: {
-        /** Get workflows present in the tools panel. */
-        parameters?: {
-            /** @description Whether to restrict result to deleted workflows. */
-            /** @description Whether to restrict result to hidden workflows. */
-            /** @description Whether to include a list of missing tools per workflow entry */
+        parameters: {
             query?: {
+                /** @description Whether to restrict result to deleted workflows. */
                 show_deleted?: boolean | null;
+                /** @description Whether to restrict result to hidden workflows. */
                 show_hidden?: boolean | null;
+                /** @description Whether to include a list of missing tools per workflow entry */
                 missing_tools?: boolean | null;
                 show_published?: boolean | null;
                 show_shared?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
+            path?: never;
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_api_workflows__workflow_id__get: {
-        /** Displays information needed to run a workflow. */
         parameters: {
-            /** @description Use the legacy workflow format. */
-            /** @description The version of the workflow to fetch. */
             query?: {
                 instance?: boolean | null;
+                /** @description Use the legacy workflow format. */
                 legacy?: boolean | null;
+                /** @description The version of the workflow to fetch. */
                 version?: number | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["StoredWorkflowDetailed"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     delete_workflow_api_workflows__workflow_id__delete: {
-        /** Add the deleted flag to a workflow. */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflows__invocation_counts: {
-        /** Get state counts for accessible workflow. */
         parameters: {
-            /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
             query?: {
+                /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
                 instance?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["RootModel_Dict_str__int__"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     disable_link_access_api_workflows__workflow_id__disable_link_access_put: {
-        /**
-         * Makes this item inaccessible by a URL link.
-         * @description Makes this item inaccessible by a URL link and return the current sharing status.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     enable_link_access_api_workflows__workflow_id__enable_link_access_put: {
-        /**
-         * Makes this item accessible by a URL link.
-         * @description Makes this item accessible by a URL link and return the current sharing status.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     index_invocations_api_workflows__workflow_id__invocations_get: {
-        /** Get the list of a user's workflow invocations. */
         parameters: {
-            /** @description Return only invocations for this History ID */
-            /** @description Return only invocations for this Job ID */
-            /** @description Return invocations for this User ID. */
-            /** @description Sort Workflow Invocations by this attribute */
-            /** @description Sort in descending order? */
-            /** @description Set to false to only include terminal Invocations. */
-            /** @description Limit the number of invocations to return. */
-            /** @description Number of invocations to skip. */
-            /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
-            /** @description View to be passed to the serializer */
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
             query?: {
+                /** @description Return only invocations for this History ID */
                 history_id?: string | null;
+                /** @description Return only invocations for this Job ID */
                 job_id?: string | null;
+                /** @description Return invocations for this User ID. */
                 user_id?: string | null;
+                /** @description Sort Workflow Invocations by this attribute */
                 sort_by?: components["schemas"]["InvocationSortByEnum"] | null;
+                /** @description Sort in descending order? */
                 sort_desc?: boolean;
+                /** @description Set to false to only include terminal Invocations. */
                 include_terminal?: boolean | null;
+                /** @description Limit the number of invocations to return. */
                 limit?: number | null;
+                /** @description Number of invocations to skip. */
                 offset?: number | null;
+                /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
                 instance?: boolean | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     Invoke_workflow_api_workflows__workflow_id__invocations_post: {
-        /** Schedule the workflow specified by `workflow_id` to run. */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The database identifier - UUID or encoded - of the Workflow. */
             path: {
-                workflow_id: string | string | string;
+                /** @description The database identifier - UUID or encoded - of the Workflow. */
+                workflow_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -24501,218 +35663,301 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json":
                         | components["schemas"]["WorkflowInvocationResponse"]
                         | components["schemas"]["WorkflowInvocationResponse"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__get: {
-        /**
-         * Get detailed description of a workflow invocation.
-         * @description An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
             query?: {
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
                 legacy_job_state?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     cancel_workflow_invocation_api_workflows__workflow_id__invocations__invocation_id__delete: {
-        /**
-         * Cancel the specified workflow invocation.
-         * @description An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
             query?: {
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
                 legacy_job_state?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated across all current jobs of the workflow invocation.
-         * @description An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationJobsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_report_api_workflows__workflow_id__invocations__invocation_id__report_get: {
-        /**
-         * Get JSON summarizing invocation for reporting.
-         * @description An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationReport"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_report_pdf_api_workflows__workflow_id__invocations__invocation_id__report_pdf_get: {
-        /**
-         * Get PDF summarizing invocation for reporting.
-         * @description An alias for `GET /api/invocations/{invocation_id}/report.pdf`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_step_jobs_summary_api_workflows__workflow_id__invocations__invocation_id__step_jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated per step of the workflow invocation.
-         * @description An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": (
                         | components["schemas"]["InvocationStepJobsResponseStepModel"]
@@ -24721,66 +35966,90 @@ export interface operations {
                     )[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__get: {
-        /**
-         * Show details of workflow invocation step.
-         * @description An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` and `invocation_id` are ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
                 step_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationStep"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     update_workflow_invocation_step_api_workflows__workflow_id__invocations__invocation_id__steps__step_id__put: {
-        /**
-         * Update state of running workflow step invocation.
-         * @description An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
                 step_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -24790,62 +36059,91 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationStep"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     publish_api_workflows__workflow_id__publish_put: {
-        /**
-         * Makes this item public and accessible by a URL link.
-         * @description Makes this item publicly available by a URL link and return the current sharing status.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     refactor_api_workflows__workflow_id__refactor_put: {
-        /** Updates the workflow stored with the given ID. */
         parameters: {
             query?: {
                 instance?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -24855,32 +36153,45 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["RefactorResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     share_with_users_api_workflows__workflow_id__share_with_users_put: {
-        /**
-         * Share this item with specific users.
-         * @description Shares this item with specific users and return the current sharing status.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -24890,62 +36201,89 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["ShareWithStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     sharing_api_workflows__workflow_id__sharing_get: {
-        /**
-         * Get the current sharing status of the given item.
-         * @description Return the sharing status of the item.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     set_slug_api_workflows__workflow_id__slug_put: {
-        /**
-         * Set a new slug for this shared item.
-         * @description Sets a new slug to access this item by URL. The new slug must be unique.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -24954,79 +36292,131 @@ export interface operations {
         };
         responses: {
             /** @description Successful Response */
-            204: never;
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     index_api_workflows__workflow_id__tags_get: {
-        /** Show tags based on workflow_id */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["ItemTagsListResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_api_workflows__workflow_id__tags__tag_name__get: {
-        /** Show tag based on workflow_id */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
                 workflow_id: string;
                 tag_name: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     update_api_workflows__workflow_id__tags__tag_name__put: {
-        /** Update tag based on workflow_id */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
                 workflow_id: string;
                 tag_name: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -25036,29 +36426,45 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     create_api_workflows__workflow_id__tags__tag_name__post: {
-        /** Create tag based on workflow_id */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
                 workflow_id: string;
                 tag_name: string;
             };
+            cookie?: never;
         };
         requestBody?: {
             content: {
@@ -25068,170 +36474,244 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["ItemTagsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     delete_api_workflows__workflow_id__tags__tag_name__delete: {
-        /** Delete tag based on workflow_id */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
             path: {
                 workflow_id: string;
                 tag_name: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": boolean;
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     undelete_workflow_api_workflows__workflow_id__undelete_post: {
-        /** Remove the deleted flag from a workflow. */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     unpublish_api_workflows__workflow_id__unpublish_put: {
-        /**
-         * Removes this item from the published list.
-         * @description Removes this item from the published list and return the current sharing status.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["SharingStatus"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     index_invocations_api_workflows__workflow_id__usage_get: {
-        /**
-         * Get the list of a user's workflow invocations.
-         * @deprecated
-         */
         parameters: {
-            /** @description Return only invocations for this History ID */
-            /** @description Return only invocations for this Job ID */
-            /** @description Return invocations for this User ID. */
-            /** @description Sort Workflow Invocations by this attribute */
-            /** @description Sort in descending order? */
-            /** @description Set to false to only include terminal Invocations. */
-            /** @description Limit the number of invocations to return. */
-            /** @description Number of invocations to skip. */
-            /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
-            /** @description View to be passed to the serializer */
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
             query?: {
+                /** @description Return only invocations for this History ID */
                 history_id?: string | null;
+                /** @description Return only invocations for this Job ID */
                 job_id?: string | null;
+                /** @description Return invocations for this User ID. */
                 user_id?: string | null;
+                /** @description Sort Workflow Invocations by this attribute */
                 sort_by?: components["schemas"]["InvocationSortByEnum"] | null;
+                /** @description Sort in descending order? */
                 sort_desc?: boolean;
+                /** @description Set to false to only include terminal Invocations. */
                 include_terminal?: boolean | null;
+                /** @description Limit the number of invocations to return. */
                 limit?: number | null;
+                /** @description Number of invocations to skip. */
                 offset?: number | null;
+                /** @description Is provided workflow id for Workflow instead of StoredWorkflow? */
                 instance?: boolean | null;
+                /** @description View to be passed to the serializer */
                 view?: string | null;
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     Invoke_workflow_api_workflows__workflow_id__usage_post: {
-        /**
-         * Schedule the workflow specified by `workflow_id` to run.
-         * @deprecated
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The database identifier - UUID or encoded - of the Workflow. */
             path: {
-                workflow_id: string | string | string;
+                /** @description The database identifier - UUID or encoded - of the Workflow. */
+                workflow_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -25241,224 +36721,301 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json":
                         | components["schemas"]["WorkflowInvocationResponse"]
                         | components["schemas"]["WorkflowInvocationResponse"][];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__get: {
-        /**
-         * Get detailed description of a workflow invocation.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
             query?: {
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
                 legacy_job_state?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     cancel_workflow_invocation_api_workflows__workflow_id__usage__invocation_id__delete: {
-        /**
-         * Cancel the specified workflow invocation.
-         * @deprecated
-         * @description An alias for `DELETE /api/invocations/{invocation_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
-            /**
-             * @description Populate the invocation step state with the job state instead of the invocation step state.
-             *         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
-             *         Partially scheduled steps may provide incomplete information and the listed steps outputs
-             *         are not the mapped over step outputs but the individual job outputs.
-             */
             query?: {
+                /** @description Include details for individual invocation steps and populate a steps attribute in the resulting dictionary. */
                 step_details?: boolean;
+                /** @description Populate the invocation step state with the job state instead of the invocation step state.
+                 *             This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
+                 *             Partially scheduled steps may provide incomplete information and the listed steps outputs
+                 *             are not the mapped over step outputs but the individual job outputs. */
                 legacy_job_state?: boolean;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["WorkflowInvocationResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_jobs_summary_api_workflows__workflow_id__usage__invocation_id__jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated across all current jobs of the workflow invocation.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationJobsResponse"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_report_api_workflows__workflow_id__usage__invocation_id__report_get: {
-        /**
-         * Get JSON summarizing invocation for reporting.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}/report`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationReport"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_workflow_invocation_report_pdf_api_workflows__workflow_id__usage__invocation_id__report_pdf_get: {
-        /**
-         * Get PDF summarizing invocation for reporting.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}/report.pdf`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
-            200: never;
-            /** @description Validation Error */
-            422: {
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content?: never;
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_step_jobs_summary_api_workflows__workflow_id__usage__invocation_id__step_jobs_summary_get: {
-        /**
-         * Get job state summary info aggregated per step of the workflow invocation.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}/step_jobs_summary`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": (
                         | components["schemas"]["InvocationStepJobsResponseStepModel"]
@@ -25467,68 +37024,90 @@ export interface operations {
                     )[];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__get: {
-        /**
-         * Show details of workflow invocation step.
-         * @deprecated
-         * @description An alias for `GET /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` and `invocation_id` are ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
                 step_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationStep"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     update_workflow_invocation_step_api_workflows__workflow_id__usage__invocation_id__steps__step_id__put: {
-        /**
-         * Update state of running workflow step invocation.
-         * @deprecated
-         * @description An alias for `PUT /api/invocations/{invocation_id}/steps/{step_id}`. `workflow_id` is ignored.
-         */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
-            /** @description The encoded database identifier of the Invocation. */
-            /** @description The encoded database identifier of the WorkflowInvocationStep. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
+                /** @description The encoded database identifier of the Invocation. */
                 invocation_id: string;
+                /** @description The encoded database identifier of the WorkflowInvocationStep. */
                 step_id: string;
             };
+            cookie?: never;
         };
         requestBody: {
             content: {
@@ -25538,169 +37117,341 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["InvocationStep"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     show_versions_api_workflows__workflow_id__versions_get: {
-        /** List all versions of a workflow. */
         parameters: {
             query?: {
                 instance?: boolean | null;
             };
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The encoded database identifier of the Stored Workflow. */
             path: {
+                /** @description The encoded database identifier of the Stored Workflow. */
                 workflow_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     get_object_ga4gh_drs_v1_objects__object_id__get: {
-        /** Get Object */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group */
             path: {
+                /** @description The ID of the group */
                 object_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["DrsObject"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     get_object_ga4gh_drs_v1_objects__object_id__post: {
-        /** Get Object */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group */
             path: {
+                /** @description The ID of the group */
                 object_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["DrsObject"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__get: {
-        /** Get Access Url */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group */
-            /** @description The access ID of the access method for objects, unused in Galaxy. */
             path: {
+                /** @description The ID of the group */
                 object_id: string;
+                /** @description The access ID of the access method for objects, unused in Galaxy. */
                 access_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     get_access_url_ga4gh_drs_v1_objects__object_id__access__access_id__post: {
-        /** Get Access Url */
         parameters: {
-            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            query?: never;
             header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
                 "run-as"?: string | null;
             };
-            /** @description The ID of the group */
-            /** @description The access ID of the access method for objects, unused in Galaxy. */
             path: {
+                /** @description The ID of the group */
                 object_id: string;
+                /** @description The access ID of the access method for objects, unused in Galaxy. */
                 access_id: string;
             };
+            cookie?: never;
         };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": Record<string, never>;
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"];
+                    "application/json": components["schemas"]["MessageExceptionModel"];
                 };
             };
         };
     };
     service_info_ga4gh_drs_v1_service_info_get: {
-        /** Service Info */
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown;
+                };
                 content: {
                     "application/json": components["schemas"]["Service"];
                 };
             };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
+    oauth2_callback_oauth2_callback_get: {
+        parameters: {
+            query: {
+                /** @description Base-64 encoded JSON used to route request within Galaxy. */
+                state: string;
+                code?: string | null;
+                error?: string | null;
+            };
+            header?: {
+                /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+                "run-as"?: string | null;
+            };
+            path?: never;
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": unknown;
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
         };
     };
 }
diff --git a/client/src/api/tags.ts b/client/src/api/tags.ts
index fe68ca0da13744f87ebe2a95a08ddb6bbaea795c..2eed2bae0295f8695965013041b0597b27a554ba 100644
--- a/client/src/api/tags.ts
+++ b/client/src/api/tags.ts
@@ -1,13 +1,18 @@
-import { components, fetcher } from "@/api/schema";
+import { type components, GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 type TaggableItemClass = components["schemas"]["TaggableItemClass"];
 
-const putItemTags = fetcher.path("/api/tags").method("put").create();
-
 export async function updateTags(itemId: string, itemClass: TaggableItemClass, itemTags?: string[]): Promise<void> {
-    await putItemTags({
-        item_id: itemId,
-        item_class: itemClass,
-        item_tags: itemTags,
+    const { error } = await GalaxyApi().PUT("/api/tags", {
+        body: {
+            item_id: itemId,
+            item_class: itemClass,
+            item_tags: itemTags,
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
 }
diff --git a/client/src/api/users.ts b/client/src/api/users.ts
index 2b3fca5b279d366f576d65f4b36ae12910e86ad5..a6086985d7a97123f74986b1ff95f2a07da72197 100644
--- a/client/src/api/users.ts
+++ b/client/src/api/users.ts
@@ -1,19 +1,37 @@
-import { fetcher } from "@/api/schema";
-
-export const createApiKey = fetcher.path("/api/users/{user_id}/api_key").method("post").create();
-export const deleteUser = fetcher.path("/api/users/{user_id}").method("delete").create();
-export const fetchQuotaUsages = fetcher.path("/api/users/{user_id}/usage").method("get").create();
-export const fetchObjectStoreUsages = fetcher.path("/api/users/{user_id}/objectstore_usage").method("get").create();
-export const recalculateDiskUsage = fetcher.path("/api/users/current/recalculate_disk_usage").method("put").create();
-export const recalculateDiskUsageByUserId = fetcher
-    .path("/api/users/{user_id}/recalculate_disk_usage")
-    .method("put")
-    .create();
-export const sendActivationEmail = fetcher.path("/api/users/{user_id}/send_activation_email").method("post").create();
-export const undeleteUser = fetcher.path("/api/users/deleted/{user_id}/undelete").method("post").create();
-
-const getUsers = fetcher.path("/api/users").method("get").create();
-export async function getAllUsers() {
-    const { data } = await getUsers({});
-    return data;
+import { GalaxyApi } from "@/api";
+import { toQuotaUsage } from "@/components/User/DiskUsage/Quota/model";
+import { rethrowSimple } from "@/utils/simple-error";
+
+export { type QuotaUsage } from "@/components/User/DiskUsage/Quota/model";
+
+export async function fetchCurrentUserQuotaUsages() {
+    const { data, error } = await GalaxyApi().GET("/api/users/{user_id}/usage", {
+        params: { path: { user_id: "current" } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    return data.map((usage) => toQuotaUsage(usage));
+}
+
+export async function fetchCurrentUserQuotaSourceUsage(quotaSourceLabel?: string | null) {
+    if (!quotaSourceLabel) {
+        quotaSourceLabel = "__null__";
+    }
+
+    const { data, error } = await GalaxyApi().GET("/api/users/{user_id}/usage/{label}", {
+        params: { path: { user_id: "current", label: quotaSourceLabel } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    if (data === null) {
+        return null;
+    }
+
+    return toQuotaUsage(data);
 }
diff --git a/client/src/api/workflows.ts b/client/src/api/workflows.ts
index d040f139cdfc272ac3aabce825912af8b5c6656f..2cc8371d74af3ee836818cd7f3ea36fae31500d5 100644
--- a/client/src/api/workflows.ts
+++ b/client/src/api/workflows.ts
@@ -1,11 +1,16 @@
-import { components, fetcher } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 export type StoredWorkflowDetailed = components["schemas"]["StoredWorkflowDetailed"];
 
-export const workflowsFetcher = fetcher.path("/api/workflows").method("get").create();
-export const workflowFetcher = fetcher.path("/api/workflows/{workflow_id}").method("get").create();
-
-export const invocationCountsFetcher = fetcher.path("/api/workflows/{workflow_id}/counts").method("get").create();
-
-export const sharing = fetcher.path("/api/workflows/{workflow_id}/sharing").method("get").create();
-export const enableLink = fetcher.path("/api/workflows/{workflow_id}/enable_link_access").method("put").create();
+//TODO: replace with generated schema model when available
+export interface WorkflowSummary {
+    name: string;
+    owner: string;
+    [key: string]: unknown;
+    update_time: string;
+    license?: string;
+    tags?: string[];
+    creator?: {
+        [key: string]: unknown;
+    }[];
+}
diff --git a/client/src/components/AboutGalaxy.vue b/client/src/components/AboutGalaxy.vue
index 4c40f4978d064081b993fdd7aedaa69655cd4f54..8dad39ed35b1b2b999100be72419bb79ed155958 100644
--- a/client/src/components/AboutGalaxy.vue
+++ b/client/src/components/AboutGalaxy.vue
@@ -3,6 +3,7 @@
 /* (injected by webpack) */
 
 import { computed } from "vue";
+import { RouterLink } from "vue-router";
 
 import { useConfig } from "@/composables/config";
 import { getAppRoot } from "@/onload/loadConfig";
@@ -28,47 +29,88 @@ const versionUserDocumentationUrl = computed(() => {
 
 <template>
     <div v-if="isConfigLoaded" class="about-galaxy">
-        <Heading h1 :icon="['gxd', 'galaxyLogo']" size="xl">About This Galaxy</Heading>
-        <div>
-            <!-- Galaxy version (detailed), with a link to the release notes -->
-            <Heading h2 separator size="md">Galaxy Version Information</Heading>
-            <p>
-                The Galaxy Server is running version
+        <Heading h1 :icon="['gxd', 'galaxyLogo']" size="lg">Help and Support</Heading>
+        <div class="p-2">
+            <Heading h2 separator size="md">Support</Heading>
+            <div v-if="config.wiki_url">
+                <ExternalLink :href="config.wiki_url">
+                    <strong v-localize>Community Hub</strong>
+                </ExternalLink>
+                <p v-localize>Join our community and explore tutorials on using Galaxy and enhance your skills.</p>
+            </div>
+            <div v-if="config.helpsite_url">
+                <ExternalLink :href="config.helpsite_url">
+                    <strong v-localize>Ask Questions & Find Answers</strong>
+                </ExternalLink>
+                <p v-localize>
+                    Visit the Galaxy Q&A website to find answers to your questions and connect with other users.
+                </p>
+            </div>
+            <div v-if="config.support_url">
+                <ExternalLink :href="config.support_url">
+                    <strong v-localize>Reach Out</strong>
+                </ExternalLink>
+                <p v-localize>Need help or want to teach and learn more about Galaxy? Feel free to reach out to us.</p>
+            </div>
+            <Heading v-localize h2 separator size="md">Help</Heading>
+            <div>
+                <RouterLink to="tours">
+                    <strong v-localize>Interactive Tours</strong>
+                </RouterLink>
+                <p v-localize>Discover and learn about Galaxy with our interactive tours.</p>
+            </div>
+            <div v-if="config.screencasts_url">
+                <ExternalLink :href="config.screencasts_url">
+                    <strong v-localize>Videos and Screencasts</strong>
+                </ExternalLink>
+                <p v-localize>Learn more about Galaxy by watching videos and screencasts.</p>
+            </div>
+            <div v-if="config.citation_url">
+                <ExternalLink :href="config.citation_url">
+                    <strong v-localize>How to Cite Us</strong>
+                </ExternalLink>
+                <p v-localize>View details on how to properly cite Galaxy.</p>
+            </div>
+            <Heading h2 separator size="md">Technical Details</Heading>
+            <div>
+                <!-- Galaxy version (detailed), with a link to the release notes -->
                 <ExternalLink :href="versionUserDocumentationUrl">
-                    <strong> {{ config.version_major }}.{{ config.version_minor }}</strong> </ExternalLink
-                >, and the web client was built on <UtcDate :date="clientBuildDate" mode="pretty" />.
-            </p>
-            <template v-if="config.version_extra">
-                <p>The server also provides the following extra version information</p>
-                <ul>
-                    <li v-for="(value, name, index) in config.version_extra" :key="index">
-                        <strong>{{ name }}</strong>
-                        : {{ value }}
-                    </li>
-                </ul>
-            </template>
-        </div>
-        <div>
-            <Heading h2 separator size="md">Galaxy API Documentation</Heading>
-            <!-- API documentation link -->
-            <p>
-                The Galaxy API is available, and explorable, at
+                    <strong v-localize>Release Notes</strong>
+                </ExternalLink>
+                <p v-localize>
+                    This Galaxy server version is <strong>{{ config.version_major }}.{{ config.version_minor }}</strong
+                    >, and the web client was built on
+                    <strong><UtcDate :date="clientBuildDate" mode="pretty" /></strong>.
+                </p>
+                <template v-if="config.version_extra">
+                    <p v-localize>The server also provides the following extra version information</p>
+                    <ul>
+                        <li v-for="(value, name, index) in config.version_extra" :key="index">
+                            <strong>{{ name }}</strong>
+                            : {{ value }}
+                        </li>
+                    </ul>
+                </template>
+            </div>
+            <div>
                 <ExternalLink :href="apiDocsLink">
-                    {{ apiDocsLink }}
+                    <strong v-localize>API Documentation</strong>
                 </ExternalLink>
-            </p>
-        </div>
-        <div>
-            <Heading h2 separator size="md">License Information</Heading>
-            <p>The Galaxy Software is licensed under <License :license-id="galaxyLicense" /></p>
-        </div>
-        <div v-if="config.terms_url">
-            <!-- Terms, if available.-->
-            <Heading h2 separator size="md">Terms and Conditions</Heading>
-            <p>
-                This Galaxy Server has specified Terms and Conditions that apply to use of the service.
-                <ExternalLink :href="config.terms_url">Review them here.</ExternalLink>
-            </p>
+                <p v-localize>Explore the Galaxy API.</p>
+            </div>
+            <div>
+                <License class="font-weight-bold" :license-id="galaxyLicense" />
+                <p v-localize>The Galaxy Software is licensed under the MIT License.</p>
+            </div>
+            <div v-if="config.terms_url">
+                <!-- Terms, if available.-->
+                <ExternalLink :href="config.terms_url">
+                    <strong v-localize>Terms and Conditions</strong>
+                </ExternalLink>
+                <p v-localize>
+                    This Galaxy Server has specified Terms and Conditions that apply to use of the service.
+                </p>
+            </div>
         </div>
     </div>
 </template>
diff --git a/client/src/components/ActivityBar/ActivityBar.test.js b/client/src/components/ActivityBar/ActivityBar.test.js
index 1fbab6c98cad8f6b67231e46839660a82f756223..8d1b7fc8bfb4d301c18fc3f5f5c30fde42c5a257 100644
--- a/client/src/components/ActivityBar/ActivityBar.test.js
+++ b/client/src/components/ActivityBar/ActivityBar.test.js
@@ -45,7 +45,7 @@ describe("ActivityBar", () => {
 
     beforeEach(async () => {
         const pinia = createTestingPinia({ stubActions: false });
-        activityStore = useActivityStore();
+        activityStore = useActivityStore("default");
         eventStore = useEventStore();
         wrapper = shallowMount(mountTarget, {
             localVue,
diff --git a/client/src/components/ActivityBar/ActivityBar.vue b/client/src/components/ActivityBar/ActivityBar.vue
index 0d9f83fb3d051dc34c2b1f80da49e69f701611cb..d6c727e2b975e5400a90b1af945cb8a7e039c8bf 100644
--- a/client/src/components/ActivityBar/ActivityBar.vue
+++ b/client/src/components/ActivityBar/ActivityBar.vue
@@ -1,11 +1,13 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { faBell, faEllipsisH, faUserCog } from "@fortawesome/free-solid-svg-icons";
+import { watchImmediate } from "@vueuse/core";
 import { storeToRefs } from "pinia";
-import { computed, type Ref, ref, watch } from "vue";
+import { computed, type Ref, ref } from "vue";
 import { useRoute } from "vue-router/composables";
 import draggable from "vuedraggable";
 
 import { useConfig } from "@/composables/config";
-import { useHashedUserId } from "@/composables/hashedUserId";
 import { convertDropData } from "@/stores/activitySetup";
 import { type Activity, useActivityStore } from "@/stores/activityStore";
 import { useEventStore } from "@/stores/eventStore";
@@ -24,6 +26,35 @@ import NotificationsPanel from "@/components/Panels/NotificationsPanel.vue";
 import SettingsPanel from "@/components/Panels/SettingsPanel.vue";
 import ToolPanel from "@/components/Panels/ToolPanel.vue";
 
+const props = withDefaults(
+    defineProps<{
+        defaultActivities?: Activity[];
+        activityBarId?: string;
+        specialActivities?: Activity[];
+        showAdmin?: boolean;
+        optionsTitle?: string;
+        optionsTooltip?: string;
+        optionsHeading?: string;
+        optionsIcon?: IconDefinition;
+        optionsSearchPlaceholder?: string;
+        initialActivity?: string;
+        hidePanel?: boolean;
+    }>(),
+    {
+        defaultActivities: undefined,
+        activityBarId: "default",
+        specialActivities: () => [],
+        showAdmin: true,
+        optionsTitle: "More",
+        optionsHeading: "Additional Activities",
+        optionsIcon: () => faEllipsisH,
+        optionsSearchPlaceholder: "Search Activities",
+        optionsTooltip: "View additional activities",
+        initialActivity: undefined,
+        hidePanel: false,
+    }
+);
+
 // require user to long click before dragging
 const DRAG_DELAY = 50;
 
@@ -32,16 +63,33 @@ const { config, isConfigLoaded } = useConfig();
 const route = useRoute();
 const userStore = useUserStore();
 
-const { hashedUserId } = useHashedUserId();
-
 const eventStore = useEventStore();
-const activityStore = useActivityStore();
+const activityStore = useActivityStore(props.activityBarId);
+
+if (props.initialActivity) {
+    activityStore.toggledSideBar = props.initialActivity;
+}
+
+watchImmediate(
+    () => props.defaultActivities,
+    (defaults) => {
+        if (defaults) {
+            activityStore.overrideDefaultActivities(defaults);
+        } else {
+            activityStore.resetDefaultActivities();
+        }
+    }
+);
+
 const { isAdmin, isAnonymous } = storeToRefs(userStore);
 
-const emit = defineEmits(["dragstart"]);
+const emit = defineEmits<{
+    (e: "dragstart", dragItem: Activity | null): void;
+    (e: "activityClicked", activityId: string): void;
+}>();
 
 // activities from store
-const { activities } = storeToRefs(activityStore);
+const { activities, isSideBarOpen } = storeToRefs(activityStore);
 
 // drag references
 const dragTarget: Ref<EventTarget | null> = ref(null);
@@ -50,13 +98,10 @@ const dragItem: Ref<Activity | null> = ref(null);
 // drag state
 const isDragging = ref(false);
 
-// sync built-in activities with cached activities
-activityStore.sync();
-
 /**
  * Checks if the route of an activity is currently being visited and panels are collapsed
  */
-function isActiveRoute(activityTo: string) {
+function isActiveRoute(activityTo?: string | null) {
     return route.path === activityTo && isActiveSideBar("");
 }
 
@@ -64,16 +109,14 @@ function isActiveRoute(activityTo: string) {
  * Checks if a panel has been expanded
  */
 function isActiveSideBar(menuKey: string) {
-    return userStore.toggledSideBar === menuKey;
+    return activityStore.toggledSideBar === menuKey;
 }
 
-const isSideBarOpen = computed(() => userStore.toggledSideBar !== "");
-
 /**
  * Checks if an activity that has a panel should have the `is-active` prop
  */
 function panelActivityIsActive(activity: Activity) {
-    return isActiveSideBar(activity.id) || (activity.to !== null && isActiveRoute(activity.to));
+    return isActiveSideBar(activity.id) || isActiveRoute(activity.to);
 }
 
 /**
@@ -123,25 +166,41 @@ function onDragOver(evt: MouseEvent) {
 /**
  * Tracks the state of activities which expand or collapse the sidepanel
  */
-function onToggleSidebar(toggle: string = "", to: string | null = null) {
+function toggleSidebar(toggle: string = "", to: string | null = null) {
     // if an activity's dedicated panel/sideBar is already active
     // but the route is different, don't collapse
     if (toggle && to && !(route.path === to) && isActiveSideBar(toggle)) {
         return;
     }
-    userStore.toggleSideBar(toggle);
+    activityStore.toggleSideBar(toggle);
 }
 
-watch(
-    () => hashedUserId.value,
-    () => {
-        activityStore.sync();
+function onActivityClicked(activity: Activity) {
+    if (activity.click) {
+        emit("activityClicked", activity.id);
+    } else {
+        toggleSidebar();
     }
-);
+}
+
+function setActiveSideBar(key: string) {
+    activityStore.toggledSideBar = key;
+}
+
+const canDrag = computed(() => {
+    return isActiveSideBar("settings");
+});
+
+defineExpose({
+    isActiveSideBar,
+    setActiveSideBar,
+});
 </script>
 
 <template>
     <div class="d-flex">
+        <!-- while this warning is correct, it is hiding too many other errors -->
+        <!-- eslint-disable-next-line vuejs-accessibility/no-static-element-interactions -->
         <div
             class="activity-bar d-flex flex-column no-highlight"
             data-description="activity bar"
@@ -152,6 +211,7 @@ watch(
                 <draggable
                     :list="activities"
                     :class="{ 'activity-popper-disabled': isDragging }"
+                    :disabled="!canDrag"
                     :force-fallback="true"
                     chosen-class="activity-chosen-class"
                     :delay="DRAG_DELAY"
@@ -159,49 +219,53 @@ watch(
                     ghost-class="activity-chosen-class"
                     @start="isDragging = true"
                     @end="isDragging = false">
-                    <div v-for="(activity, activityIndex) in activities" :key="activityIndex">
+                    <div
+                        v-for="(activity, activityIndex) in activities"
+                        :key="activityIndex"
+                        :class="{ 'can-drag': canDrag }">
                         <div v-if="activity.visible && (activity.anonymous || !isAnonymous)">
                             <UploadItem
                                 v-if="activity.id === 'upload'"
-                                :id="`activity-${activity.id}`"
+                                :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :title="activity.title"
                                 :tooltip="activity.tooltip" />
                             <InteractiveItem
                                 v-else-if="activity.to && activity.id === 'interactivetools'"
-                                :id="`activity-${activity.id}`"
+                                :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :is-active="isActiveRoute(activity.to)"
                                 :title="activity.title"
                                 :tooltip="activity.tooltip"
                                 :to="activity.to"
-                                @click="onToggleSidebar()" />
+                                @click="toggleSidebar()" />
                             <ActivityItem
-                                v-else-if="
-                                    ['admin', 'tools', 'visualizations', 'multiview', 'invocation'].includes(
-                                        activity.id
-                                    )
-                                "
-                                :id="`activity-${activity.id}`"
+                                v-else-if="activity.id === 'admin' || activity.panel"
+                                :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :is-active="panelActivityIsActive(activity)"
                                 :title="activity.title"
                                 :tooltip="activity.tooltip"
                                 :to="activity.to || ''"
-                                @click="onToggleSidebar(activity.id, activity.to)" />
+                                @click="toggleSidebar(activity.id, activity.to)" />
                             <ActivityItem
-                                v-else-if="activity.to"
-                                :id="`activity-${activity.id}`"
+                                v-else
+                                :id="`${activity.id}`"
                                 :key="activity.id"
+                                :activity-bar-id="props.activityBarId"
                                 :icon="activity.icon"
                                 :is-active="isActiveRoute(activity.to)"
                                 :title="activity.title"
                                 :tooltip="activity.tooltip"
-                                :to="activity.to"
-                                @click="onToggleSidebar()" />
+                                :to="activity.to ?? undefined"
+                                :variant="activity.variant"
+                                @click="onActivityClicked(activity)" />
                         </div>
                     </div>
                 </draggable>
@@ -209,37 +273,72 @@ watch(
             <b-nav v-if="!isAnonymous" vertical class="activity-footer flex-nowrap p-1">
                 <NotificationItem
                     v-if="isConfigLoaded && config.enable_notification_system"
-                    id="activity-notifications"
-                    icon="bell"
+                    id="notifications"
+                    :activity-bar-id="props.activityBarId"
+                    :icon="faBell"
                     :is-active="isActiveSideBar('notifications') || isActiveRoute('/user/notifications')"
                     title="Notifications"
-                    @click="onToggleSidebar('notifications')" />
+                    @click="toggleSidebar('notifications')" />
                 <ActivityItem
-                    id="activity-settings"
-                    icon="cog"
+                    id="settings"
+                    :activity-bar-id="props.activityBarId"
+                    :icon="props.optionsIcon"
                     :is-active="isActiveSideBar('settings')"
-                    title="Settings"
-                    tooltip="Edit preferences"
-                    @click="onToggleSidebar('settings')" />
+                    :title="props.optionsTitle"
+                    :tooltip="props.optionsTooltip"
+                    @click="toggleSidebar('settings')" />
                 <ActivityItem
-                    v-if="isAdmin"
-                    id="activity-admin"
-                    icon="user-cog"
+                    v-if="isAdmin && showAdmin"
+                    id="admin"
+                    :activity-bar-id="props.activityBarId"
+                    :icon="faUserCog"
                     :is-active="isActiveSideBar('admin')"
                     title="Admin"
                     tooltip="Administer this Galaxy"
                     variant="danger"
-                    @click="onToggleSidebar('admin')" />
+                    @click="toggleSidebar('admin')" />
+                <template v-for="activity in props.specialActivities">
+                    <ActivityItem
+                        v-if="activity.panel"
+                        :id="`${activity.id}`"
+                        :key="activity.id"
+                        :activity-bar-id="props.activityBarId"
+                        :icon="activity.icon"
+                        :is-active="panelActivityIsActive(activity)"
+                        :title="activity.title"
+                        :tooltip="activity.tooltip"
+                        :to="activity.to || ''"
+                        :variant="activity.variant"
+                        @click="toggleSidebar(activity.id, activity.to)" />
+                    <ActivityItem
+                        v-else
+                        :id="`${activity.id}`"
+                        :key="activity.id"
+                        :activity-bar-id="props.activityBarId"
+                        :icon="activity.icon"
+                        :is-active="isActiveRoute(activity.to)"
+                        :title="activity.title"
+                        :tooltip="activity.tooltip"
+                        :to="activity.to ?? undefined"
+                        :variant="activity.variant"
+                        @click="onActivityClicked(activity)" />
+                </template>
             </b-nav>
         </div>
-        <FlexPanel v-if="isSideBarOpen" side="left" :collapsible="false">
+        <FlexPanel v-if="isSideBarOpen && !hidePanel" side="left" :collapsible="false">
             <ToolPanel v-if="isActiveSideBar('tools')" />
-            <InvocationsPanel v-else-if="isActiveSideBar('invocation')" />
+            <InvocationsPanel v-else-if="isActiveSideBar('invocation')" :activity-bar-id="props.activityBarId" />
             <VisualizationPanel v-else-if="isActiveSideBar('visualizations')" />
             <MultiviewPanel v-else-if="isActiveSideBar('multiview')" />
             <NotificationsPanel v-else-if="isActiveSideBar('notifications')" />
-            <SettingsPanel v-else-if="isActiveSideBar('settings')" />
+            <SettingsPanel
+                v-else-if="isActiveSideBar('settings')"
+                :activity-bar-id="props.activityBarId"
+                :heading="props.optionsHeading"
+                :search-placeholder="props.optionsSearchPlaceholder"
+                @activityClicked="(id) => emit('activityClicked', id)" />
             <AdminPanel v-else-if="isActiveSideBar('admin')" />
+            <slot name="side-panel" :is-active-side-bar="isActiveSideBar"></slot>
         </FlexPanel>
     </div>
 </template>
@@ -290,4 +389,11 @@ watch(
     overflow-y: auto;
     overflow-x: hidden;
 }
+
+.can-drag {
+    border-radius: 12px;
+    border: 1px;
+    outline: dashed darkgray;
+    outline-offset: -3px;
+}
 </style>
diff --git a/client/src/components/ActivityBar/ActivityItem.test.js b/client/src/components/ActivityBar/ActivityItem.test.js
index d4486230dda9a811564a24f1bd2e1e2e6f25c85e..c1177158befa48d59f801210ac447b988c14b623 100644
--- a/client/src/components/ActivityBar/ActivityItem.test.js
+++ b/client/src/components/ActivityBar/ActivityItem.test.js
@@ -1,3 +1,4 @@
+import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
@@ -12,6 +13,7 @@ describe("ActivityItem", () => {
         wrapper = mount(mountTarget, {
             propsData: {
                 id: "activity-test-id",
+                activityBarId: "activity-bar-test-id",
                 icon: "activity-test-icon",
                 indicator: 0,
                 progressPercentage: 0,
@@ -20,6 +22,7 @@ describe("ActivityItem", () => {
                 to: null,
                 tooltip: "activity-test-tooltip",
             },
+            pinia: createTestingPinia(),
             localVue,
             stubs: {
                 FontAwesomeIcon: true,
@@ -28,8 +31,7 @@ describe("ActivityItem", () => {
     });
 
     it("rendering", async () => {
-        const reference = wrapper.find("[id='activity-test-id']");
-        expect(reference.attributes().id).toBe("activity-test-id");
+        const reference = wrapper.find(".activity-item");
         expect(reference.text()).toBe("activity-test-title");
         expect(reference.find("[icon='activity-test-icon']").exists()).toBeTruthy();
         expect(reference.find(".progress").exists()).toBeFalsy();
@@ -45,7 +47,7 @@ describe("ActivityItem", () => {
     });
 
     it("rendering indicator", async () => {
-        const reference = wrapper.find("[id='activity-test-id']");
+        const reference = wrapper.find(".activity-item");
         const indicatorSelector = "[data-description='activity indicator']";
         const noindicator = reference.find(indicatorSelector);
         expect(noindicator.exists()).toBeFalsy();
diff --git a/client/src/components/ActivityBar/ActivityItem.vue b/client/src/components/ActivityBar/ActivityItem.vue
index 0586a1657f99e32279b19965526c09beb2d3af7d..fa7e67d5e8c0906b5fcaad842cdaca28de82076e 100644
--- a/client/src/components/ActivityBar/ActivityItem.vue
+++ b/client/src/components/ActivityBar/ActivityItem.vue
@@ -1,7 +1,14 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { faQuestion } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import type { Placement } from "@popperjs/core";
+import { computed } from "vue";
 import { useRouter } from "vue-router/composables";
 
+import { type ActivityVariant, useActivityStore } from "@/stores/activityStore";
+import localize from "@/utils/localization";
+
 import TextShort from "@/components/Common/TextShort.vue";
 import Popper from "@/components/Popper/Popper.vue";
 
@@ -14,22 +21,23 @@ interface Option {
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title?: string;
-    icon?: string | object;
+    icon?: IconDefinition;
     indicator?: number;
     isActive?: boolean;
     tooltip?: string;
-    tooltipPlacement?: string;
+    tooltipPlacement?: Placement;
     progressPercentage?: number;
     progressStatus?: string;
     options?: Option[];
     to?: string;
-    variant?: string;
+    variant?: ActivityVariant;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     title: undefined,
-    icon: "question",
+    icon: () => faQuestion,
     indicator: 0,
     isActive: false,
     options: undefined,
@@ -51,41 +59,44 @@ function onClick(evt: MouseEvent): void {
         router.push(props.to);
     }
 }
+
+const store = useActivityStore(props.activityBarId);
+const meta = computed(() => store.metaForId(props.id));
 </script>
 
 <template>
     <Popper reference-is="span" popper-is="span" :placement="tooltipPlacement">
         <template v-slot:reference>
-            <div :id="id" class="activity-item" @click="onClick">
-                <b-nav-item
-                    class="position-relative my-1 p-2"
-                    :class="{ 'nav-item-active': isActive }"
-                    :aria-label="title | l">
-                    <span v-if="progressStatus" class="progress">
-                        <div
-                            class="progress-bar notransition"
-                            :class="{
-                                'bg-danger': progressStatus === 'danger',
-                                'bg-success': progressStatus === 'success',
-                            }"
-                            :style="{
-                                width: `${Math.round(progressPercentage)}%`,
-                            }" />
-                    </span>
-                    <span class="position-relative" :class="`text-${variant}`">
-                        <div class="nav-icon">
-                            <span v-if="indicator > 0" class="nav-indicator" data-description="activity indicator">
-                                {{ Math.min(indicator, 99) }}
-                            </span>
-                            <FontAwesomeIcon :icon="icon" />
-                        </div>
-                        <TextShort v-if="title" :text="title" class="nav-title" />
+            <b-nav-item
+                :id="`activity-${id}`"
+                class="activity-item my-1 p-2"
+                :class="{ 'nav-item-active': isActive }"
+                :link-classes="`variant-${props.variant}`"
+                :aria-label="localize(title)"
+                :disabled="meta?.disabled"
+                @click="onClick">
+                <span v-if="progressStatus" class="progress">
+                    <div
+                        class="progress-bar notransition"
+                        :class="{
+                            'bg-danger': progressStatus === 'danger',
+                            'bg-success': progressStatus === 'success',
+                        }"
+                        :style="{
+                            width: `${Math.round(progressPercentage)}%`,
+                        }" />
+                </span>
+                <div class="nav-icon">
+                    <span v-if="indicator > 0" class="nav-indicator" data-description="activity indicator">
+                        {{ Math.min(indicator, 99) }}
                     </span>
-                </b-nav-item>
-            </div>
+                    <FontAwesomeIcon :icon="icon" />
+                </div>
+                <TextShort v-if="title" :text="title" class="nav-title" />
+            </b-nav-item>
         </template>
         <div class="text-center px-2 py-1">
-            <small v-if="tooltip">{{ tooltip | l }}</small>
+            <small v-if="tooltip">{{ localize(tooltip) }}</small>
             <small v-else>No tooltip available for this item</small>
             <div v-if="options" class="nav-options p-1">
                 <router-link v-for="(option, index) in options" :key="index" :to="option.value">
@@ -101,8 +112,25 @@ function onClick(evt: MouseEvent): void {
 <style scoped lang="scss">
 @import "theme/blue.scss";
 
+.activity-item {
+    position: relative;
+    display: flex;
+    flex-direction: column;
+
+    &:deep(.variant-danger) {
+        color: $brand-danger;
+    }
+
+    &:deep(.variant-disabled) {
+        color: $text-light;
+    }
+}
+
 .nav-icon {
-    @extend .nav-item;
+    position: relative;
+    display: flex;
+    justify-content: center;
+    cursor: pointer;
     font-size: 1rem;
 }
 
@@ -121,13 +149,6 @@ function onClick(evt: MouseEvent): void {
     width: 1.2rem;
 }
 
-.nav-item {
-    display: flex;
-    align-items: center;
-    align-content: center;
-    justify-content: center;
-}
-
 .nav-item-active {
     border-radius: $border-radius-extralarge;
     background: $gray-300;
@@ -143,7 +164,9 @@ function onClick(evt: MouseEvent): void {
 }
 
 .nav-title {
-    @extend .nav-item;
+    position: relative;
+    display: flex;
+    justify-content: center;
     width: 4rem;
     margin-top: 0.5rem;
     font-size: 0.7rem;
diff --git a/client/src/components/ActivityBar/ActivitySettings.test.js b/client/src/components/ActivityBar/ActivitySettings.test.js
index e5555451ec85263b48684094c054b1962d54e56b..d40b3578565080195ed48a74ff76531f070fb374 100644
--- a/client/src/components/ActivityBar/ActivitySettings.test.js
+++ b/client/src/components/ActivityBar/ActivitySettings.test.js
@@ -2,8 +2,9 @@ import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
 import { PiniaVuePlugin } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
+import { nextTick } from "vue";
 
-import { Activities } from "@/stores/activitySetup";
+import { defaultActivities } from "@/stores/activitySetup";
 import { useActivityStore } from "@/stores/activityStore";
 
 import mountTarget from "./ActivitySettings.vue";
@@ -19,7 +20,7 @@ function testActivity(id, newOptions = {}) {
         description: "activity-test-description",
         icon: "activity-test-icon",
         mutable: true,
-        optional: false,
+        optional: true,
         title: "activity-test-title",
         to: null,
         tooltip: "activity-test-tooltip",
@@ -40,38 +41,40 @@ describe("ActivitySettings", () => {
 
     beforeEach(async () => {
         const pinia = createTestingPinia({ stubActions: false });
-        activityStore = useActivityStore();
-        activityStore.sync();
+        activityStore = useActivityStore(undefined);
         wrapper = mount(mountTarget, {
             localVue,
             pinia,
             props: {
                 query: "",
+                activityBarId: undefined,
             },
             stubs: {
-                icon: { template: "<div></div>" },
+                FontAwesomeIcon: { template: "<div></div>" },
             },
         });
+        await activityStore.sync();
     });
 
     it("availability of built-in activities", async () => {
         const items = wrapper.findAll(activityItemSelector);
-        expect(items.length).toBe(Activities.length);
+        const nOptional = defaultActivities.filter((x) => x.optional).length;
+        expect(items.length).toBe(nOptional);
     });
 
-    it("visible but non-optional activity", async () => {
+    it("visible and optional activity", async () => {
         activityStore.setAll([testActivity("1")]);
-        await wrapper.vm.$nextTick();
+        await nextTick();
         const items = wrapper.findAll(activityItemSelector);
         expect(items.length).toBe(1);
-        const pinnedCheckbox = items.at(0).find("[data-icon='thumbtack']");
-        expect(pinnedCheckbox.exists()).toBeTruthy();
-        const pinnedIcon = wrapper.find("[icon='activity-test-icon'");
-        expect(pinnedIcon.exists()).toBeTruthy();
+        const checkbox = items.at(0).find("[title='Hide in Activity Bar']");
+        expect(checkbox.exists()).toBeTruthy();
+        const icon = wrapper.find("[icon='activity-test-icon'");
+        expect(icon.exists()).toBeTruthy();
         expect(activityStore.getAll()[0].visible).toBeTruthy();
-        pinnedCheckbox.trigger("click");
+        checkbox.trigger("click");
         await wrapper.vm.$nextTick();
-        expect(activityStore.getAll()[0].visible).toBeTruthy();
+        expect(activityStore.getAll()[0].visible).toBeFalsy();
     });
 
     it("non-visible but optional activity", async () => {
@@ -84,12 +87,12 @@ describe("ActivitySettings", () => {
         await wrapper.vm.$nextTick();
         const items = wrapper.findAll(activityItemSelector);
         expect(items.length).toBe(1);
-        const hiddenCheckbox = items.at(0).find("[data-icon='square']");
-        expect(hiddenCheckbox.exists()).toBeTruthy();
+        const checkbox = items.at(0).find("[title='Show in Activity Bar']");
+        expect(checkbox.exists()).toBeTruthy();
         expect(activityStore.getAll()[0].visible).toBeFalsy();
-        hiddenCheckbox.trigger("click");
+        checkbox.trigger("click");
         await wrapper.vm.$nextTick();
-        const visibleCheckbox = items.at(0).find("[data-icon='check-square']");
+        const visibleCheckbox = items.at(0).find("[title='Hide in Activity Bar']");
         expect(visibleCheckbox.exists()).toBeTruthy();
         expect(activityStore.getAll()[0].visible).toBeTruthy();
     });
@@ -99,7 +102,7 @@ describe("ActivitySettings", () => {
         await wrapper.vm.$nextTick();
         const items = wrapper.findAll(activityItemSelector);
         expect(items.length).toBe(1);
-        const trash = items.at(0).find("[data-icon='trash']");
+        const trash = items.at(0).find("[data-description='delete activity']");
         expect(trash.exists()).toBeTruthy();
         expect(activityStore.getAll().length).toBe(1);
         trash.trigger("click");
diff --git a/client/src/components/ActivityBar/ActivitySettings.vue b/client/src/components/ActivityBar/ActivitySettings.vue
index 835691d3c0b391cfde7ef0b152cf2d91392d462a..f732252bfd6cf5e7d92516d716a1c38b0724748e 100644
--- a/client/src/components/ActivityBar/ActivitySettings.vue
+++ b/client/src/components/ActivityBar/ActivitySettings.vue
@@ -1,31 +1,29 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faSquare } from "@fortawesome/free-regular-svg-icons";
-import { faCheckSquare, faThumbtack, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { faStar as faStarRegular } from "@fortawesome/free-regular-svg-icons";
+import { faStar, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { storeToRefs } from "pinia";
 import { computed, type ComputedRef } from "vue";
+import { useRouter } from "vue-router/composables";
 
 import { type Activity, useActivityStore } from "@/stores/activityStore";
 
-library.add({
-    faCheckSquare,
-    faSquare,
-    faTrash,
-    faThumbtack,
-});
-
 const props = defineProps<{
+    activityBarId: string;
     query: string;
 }>();
 
-const activityStore = useActivityStore();
-const { activities } = storeToRefs(activityStore);
+const emit = defineEmits<{
+    (e: "activityClicked", activityId: string): void;
+}>();
+
+const activityStore = useActivityStore(props.activityBarId);
+
+const optionalActivities = computed(() => activityStore.activities.filter((a) => a.optional));
 
 const filteredActivities = computed(() => {
     if (props.query?.length > 0) {
         const queryLower = props.query.toLowerCase();
-        const results = activities.value.filter((a: Activity) => {
+        const results = optionalActivities.value.filter((a: Activity) => {
             const attributeValues = [a.title, a.description];
             for (const value of attributeValues) {
                 if (value.toLowerCase().indexOf(queryLower) !== -1) {
@@ -36,7 +34,7 @@ const filteredActivities = computed(() => {
         });
         return results;
     } else {
-        return activities.value;
+        return optionalActivities.value;
     }
 });
 
@@ -44,7 +42,7 @@ const foundActivities: ComputedRef<boolean> = computed(() => {
     return filteredActivities.value.length > 0;
 });
 
-function onClick(activity: Activity) {
+function onFavorite(activity: Activity) {
     if (activity.optional) {
         activity.visible = !activity.visible;
     }
@@ -53,50 +51,78 @@ function onClick(activity: Activity) {
 function onRemove(activity: Activity) {
     activityStore.remove(activity.id);
 }
+
+const router = useRouter();
+
+function executeActivity(activity: Activity) {
+    if (activity.click) {
+        emit("activityClicked", activity.id);
+    }
+
+    if (activity.panel) {
+        activityStore.toggleSideBar(activity.id);
+    }
+
+    if (activity.to) {
+        router.push(activity.to);
+    }
+}
 </script>
 
 <template>
-    <div class="activity-settings rounded no-highlight">
-        <div v-if="foundActivities" class="activity-settings-content">
-            <div v-for="activity in filteredActivities" :key="activity.id">
-                <button class="activity-settings-item p-2 cursor-pointer" @click="onClick(activity)">
-                    <div class="d-flex justify-content-between align-items-start">
-                        <span class="w-100">
-                            <FontAwesomeIcon
-                                v-if="!activity.optional"
-                                class="icon-check mr-1"
-                                icon="fas fa-thumbtack"
-                                fa-fw />
-                            <FontAwesomeIcon
-                                v-else-if="activity.visible"
-                                class="icon-check mr-1"
-                                icon="fas fa-check-square"
-                                fa-fw />
-                            <FontAwesomeIcon v-else class="mr-1" icon="far fa-square" fa-fw />
-                            <span>
-                                <icon class="mr-1" :icon="activity.icon" />
-                                <span v-localize class="font-weight-bold">{{
-                                    activity.title || "No title available"
-                                }}</span>
-                            </span>
+    <div>
+        <div v-if="foundActivities">
+            <button
+                v-for="activity in filteredActivities"
+                :key="activity.id"
+                class="activity-settings-item p-2 cursor-pointer"
+                @click="executeActivity(activity)">
+                <div class="d-flex justify-content-between align-items-start">
+                    <span class="d-flex justify-content-between w-100">
+                        <span>
+                            <FontAwesomeIcon class="mr-1" :icon="activity.icon" />
+                            <span v-localize class="font-weight-bold">{{
+                                activity.title || "No title available"
+                            }}</span>
                         </span>
-                        <b-button
-                            v-if="activity.mutable"
-                            data-description="delete activity"
-                            class="button-delete"
-                            size="sm"
-                            variant="link"
-                            @click.stop="onRemove(activity)">
-                            <FontAwesomeIcon icon="fa-trash" fa-fw />
-                        </b-button>
-                    </div>
-                    <div v-localize class="text-muted">
-                        {{ activity.description || "No description available" }}
-                    </div>
-                </button>
-            </div>
+                        <div>
+                            <BButton
+                                v-if="activity.mutable"
+                                v-b-tooltip.hover
+                                data-description="delete activity"
+                                size="sm"
+                                title="Delete Activity"
+                                variant="link"
+                                @click.stop="onRemove(activity)">
+                                <FontAwesomeIcon :icon="faTrash" fa-fw />
+                            </BButton>
+                            <BButton
+                                v-if="activity.visible"
+                                v-b-tooltip.hover
+                                size="sm"
+                                title="Hide in Activity Bar"
+                                variant="link"
+                                @click.stop="onFavorite(activity)">
+                                <FontAwesomeIcon :icon="faStar" fa-fw />
+                            </BButton>
+                            <BButton
+                                v-else
+                                v-b-tooltip.hover
+                                size="sm"
+                                title="Show in Activity Bar"
+                                variant="link"
+                                @click.stop="onFavorite(activity)">
+                                <FontAwesomeIcon :icon="faStarRegular" fa-fw />
+                            </BButton>
+                        </div>
+                    </span>
+                </div>
+                <div v-localize class="text-muted">
+                    {{ activity.description || "No description available" }}
+                </div>
+            </button>
         </div>
-        <div v-else class="activity-settings-content">
+        <div v-else>
             <b-alert v-localize class="py-1 px-2" show> No matching activities found. </b-alert>
         </div>
     </div>
@@ -105,30 +131,14 @@ function onRemove(activity: Activity) {
 <style lang="scss">
 @import "theme/blue.scss";
 
-.activity-settings {
-    overflow-y: hidden;
-    display: flex;
-    flex-direction: column;
-}
-
-.activity-settings-content {
-    overflow-y: auto;
-}
-
 .activity-settings-item {
     background: none;
     border: none;
     text-align: left;
     transition: none;
     width: 100%;
-
-    .icon-check {
-        color: darken($brand-success, 15%);
-    }
-    .button-delete {
-        background: transparent;
-    }
 }
+
 .activity-settings-item:hover {
     background: $gray-200;
 }
diff --git a/client/src/components/ActivityBar/Items/InteractiveItem.vue b/client/src/components/ActivityBar/Items/InteractiveItem.vue
index 31b9324e93a0dd8f81da11274ff3b79d56f89eba..e6e80ea1d34dd597b7142de9fcfd78756adeef94 100644
--- a/client/src/components/ActivityBar/Items/InteractiveItem.vue
+++ b/client/src/components/ActivityBar/Items/InteractiveItem.vue
@@ -1,10 +1,11 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { storeToRefs } from "pinia";
 import { computed } from "vue";
 
 import { useEntryPointStore } from "@/stores/entryPointStore";
 
-import ActivityItem from "components/ActivityBar/ActivityItem.vue";
+import ActivityItem from "@/components/ActivityBar/ActivityItem.vue";
 
 const { entryPoints } = storeToRefs(useEntryPointStore());
 
@@ -12,13 +13,14 @@ const totalCount = computed(() => entryPoints.value.length);
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
-    icon: string;
+    icon: IconDefinition;
     isActive: boolean;
     to: string;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -26,7 +28,7 @@ const emit = defineEmits<{
 
 const tooltip = computed(() =>
     totalCount.value === 1
-        ? `You currently have 1 active interactive tool`
+        ? "You currently have 1 active interactive tool"
         : `You currently have ${totalCount.value} active interactive tools`
 );
 </script>
@@ -35,6 +37,7 @@ const tooltip = computed(() =>
     <ActivityItem
         v-if="totalCount > 0"
         :id="id"
+        :activity-bar-id="props.activityBarId"
         :icon="icon"
         :indicator="totalCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/NotificationItem.vue b/client/src/components/ActivityBar/Items/NotificationItem.vue
index 84e5a05bcedad4a938b27e3bbd851c8c57b65418..3bd5332c4528ce067b4e96378d88e2c00c754cd7 100644
--- a/client/src/components/ActivityBar/Items/NotificationItem.vue
+++ b/client/src/components/ActivityBar/Items/NotificationItem.vue
@@ -1,21 +1,23 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { storeToRefs } from "pinia";
 import { computed } from "vue";
 
 import { useNotificationsStore } from "@/stores/notificationsStore";
 
-import ActivityItem from "components/ActivityBar/ActivityItem.vue";
+import ActivityItem from "@/components/ActivityBar/ActivityItem.vue";
 
 const { totalUnreadCount } = storeToRefs(useNotificationsStore());
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
-    icon: string;
+    icon: IconDefinition;
     isActive: boolean;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -31,6 +33,7 @@ const tooltip = computed(() =>
 <template>
     <ActivityItem
         :id="id"
+        :activity-bar-id="props.activityBarId"
         :icon="icon"
         :indicator="totalUnreadCount"
         :is-active="isActive"
diff --git a/client/src/components/ActivityBar/Items/UploadItem.vue b/client/src/components/ActivityBar/Items/UploadItem.vue
index e5c2b357d0e7b1223b7ab844d15837bdb8b4d445..c130c4965b217ef2188a6e16d0fb4d90005395e2 100644
--- a/client/src/components/ActivityBar/Items/UploadItem.vue
+++ b/client/src/components/ActivityBar/Items/UploadItem.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { storeToRefs } from "pinia";
 import { onMounted } from "vue";
 
@@ -6,16 +7,17 @@ import { useGlobalUploadModal } from "@/composables/globalUploadModal.js";
 import { useUploadStore } from "@/stores/uploadStore";
 import Query from "@/utils/query-string-parsing.js";
 
-import ActivityItem from "components/ActivityBar/ActivityItem.vue";
+import ActivityItem from "@/components/ActivityBar/ActivityItem.vue";
 
 export interface Props {
     id: string;
+    activityBarId: string;
     title: string;
-    icon: string;
+    icon: IconDefinition;
     tooltip: string;
 }
 
-defineProps<Props>();
+const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "click"): void;
@@ -39,6 +41,7 @@ function onUploadModal() {
 <template>
     <ActivityItem
         :id="id"
+        :activity-bar-id="props.activityBarId"
         :title="title"
         :tooltip="tooltip"
         :icon="icon"
diff --git a/client/src/components/Citation/CitationItem.vue b/client/src/components/Citation/CitationItem.vue
index 82894f285641bb877480bfd957d3ba4e83285609..864dadc112e7a517c1821f05e7329fc206a9090e 100644
--- a/client/src/components/Citation/CitationItem.vue
+++ b/client/src/components/Citation/CitationItem.vue
@@ -4,7 +4,7 @@ import { faExternalLinkAlt } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 
-import { Citation } from ".";
+import { type Citation } from ".";
 
 library.add(faExternalLinkAlt);
 
diff --git a/client/src/components/Collections/CollectionCreatorModal.vue b/client/src/components/Collections/CollectionCreatorModal.vue
new file mode 100644
index 0000000000000000000000000000000000000000..59b3099c53380b84d51e0689b58e7c1fa5a0b836
--- /dev/null
+++ b/client/src/components/Collections/CollectionCreatorModal.vue
@@ -0,0 +1,328 @@
+<script setup lang="ts">
+import { faCheckCircle, faUndo } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BLink, BModal } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import type { HDASummary, HistoryItemSummary, HistorySummary } from "@/api";
+import { createDatasetCollection } from "@/components/History/model/queries";
+import { useCollectionBuilderItemsStore } from "@/stores/collectionBuilderItemsStore";
+import { useHistoryStore } from "@/stores/historyStore";
+import localize from "@/utils/localization";
+import { orList } from "@/utils/strings";
+
+import type { CollectionType, DatasetPair } from "../History/adapters/buildCollectionModal";
+
+import ListCollectionCreator from "./ListCollectionCreator.vue";
+import PairCollectionCreator from "./PairCollectionCreator.vue";
+import PairedListCollectionCreator from "./PairedListCollectionCreator.vue";
+import Heading from "@/components/Common/Heading.vue";
+import GenericItem from "@/components/History/Content/GenericItem.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface Props {
+    historyId: string;
+    showModal: boolean;
+    collectionType: CollectionType;
+    selectedItems?: HistoryItemSummary[];
+    defaultHideSourceItems?: boolean;
+    extensions?: string[];
+    fromRulesInput?: boolean;
+    hideModalOnCreate?: boolean;
+    filterText?: string;
+}
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "created-collection", collection: any): void;
+    (e: "update:show-modal", showModal: boolean): void;
+}>();
+
+/** Computed toggle that handles opening and closing the modal */
+const localShowToggle = computed({
+    get: () => props.showModal,
+    set: (value: boolean) => {
+        emit("update:show-modal", value);
+    },
+});
+
+// Create Collection refs
+const creatingCollection = ref(false);
+const createCollectionError = ref<string | null>(null);
+const createdCollection = ref<any>(null);
+
+// History items variables
+const historyItemsError = ref<string | null>(null);
+const collectionItemsStore = useCollectionBuilderItemsStore();
+const historyStore = useHistoryStore();
+const history = computed(() => historyStore.getHistoryById(props.historyId));
+const historyId = computed(() => props.historyId);
+const localFilterText = computed(() => props.filterText || "");
+const historyUpdateTime = computed(() => history.value?.update_time);
+const isFetchingItems = computed(() => collectionItemsStore.isFetching[localFilterText.value]);
+const historyDatasets = computed(() => {
+    if (collectionItemsStore.cachedDatasetsForFilterText) {
+        return collectionItemsStore.cachedDatasetsForFilterText[localFilterText.value] || [];
+    } else {
+        return [];
+    }
+});
+
+/** Flag for the initial fetch of history items */
+const initialFetch = ref(false);
+
+/** Whether a list of items was selected to create a collection from */
+const fromSelection = computed(() => !!props.selectedItems?.length);
+
+/** Items to create the collection from */
+const creatorItems = computed(() => (fromSelection.value ? props.selectedItems : historyDatasets.value));
+
+watch(
+    () => localShowToggle.value,
+    async (show) => {
+        if (show) {
+            await fetchHistoryDatasets();
+            if (!initialFetch.value) {
+                initialFetch.value = true;
+            }
+        }
+    },
+    { immediate: true }
+);
+
+// Fetch items when history ID or update time changes, only if localShowToggle is true
+watch([historyId, historyUpdateTime, localFilterText], async () => {
+    if (localShowToggle.value) {
+        await fetchHistoryDatasets();
+    }
+});
+
+// If there is a change in `historyDatasets`, but we have selected items, we should update the selected items
+watch(
+    () => historyDatasets.value,
+    (newDatasets) => {
+        if (fromSelection.value) {
+            // find each selected item in the new datasets, and update it
+            props.selectedItems?.forEach((selectedItem) => {
+                const newDataset = newDatasets.find((dataset) => dataset.id === selectedItem.id);
+                if (newDataset) {
+                    Object.assign(selectedItem, newDataset);
+                }
+            });
+        }
+    }
+);
+
+const extensionInTitle = computed<string>(() => {
+    const extensions = props.extensions;
+    if (!extensions || extensions.length == 0 || extensions.indexOf("data") >= 0) {
+        return "";
+    } else {
+        return orList(extensions);
+    }
+});
+
+const modalTitle = computed(() => {
+    if (props.collectionType === "list") {
+        return localize(`Create a list of ${fromSelection.value ? "selected" : ""} ${extensionInTitle.value} datasets`);
+    } else if (props.collectionType === "list:paired") {
+        return localize(
+            `Create a list of ${fromSelection.value ? "selected" : ""} ${extensionInTitle.value} paired datasets`
+        );
+    } else if (props.collectionType === "paired") {
+        return localize(
+            `Create a ${extensionInTitle.value} paired dataset collection ${
+                fromSelection.value ? "from selected items" : ""
+            }`
+        );
+    } else {
+        return localize("Create a collection");
+    }
+});
+
+// Methods
+function createListCollection(elements: HDASummary[], name: string, hideSourceItems: boolean) {
+    const returnedElems = elements.map((element) => ({
+        id: element.id,
+        name: element.name,
+        //TODO: this allows for list:list even if the implementation does not - reconcile
+        src: "src" in element ? element.src : element.history_content_type == "dataset" ? "hda" : "hdca",
+    }));
+    return createHDCA(returnedElems, "list", name, hideSourceItems);
+}
+
+function createListPairedCollection(elements: DatasetPair[], name: string, hideSourceItems: boolean) {
+    const returnedElems = elements.map((pair) => ({
+        collection_type: "paired",
+        src: "new_collection",
+        name: pair.name,
+        element_identifiers: [
+            {
+                name: "forward",
+                id: pair.forward.id,
+                src: "src" in pair.forward ? pair.forward.src : "hda",
+            },
+            {
+                name: "reverse",
+                id: pair.reverse.id,
+                src: "src" in pair.reverse ? pair.reverse.src : "hda",
+            },
+        ],
+    }));
+    return createHDCA(returnedElems, "list:paired", name, hideSourceItems);
+}
+
+function createPairedCollection(elements: DatasetPair, name: string, hideSourceItems: boolean) {
+    const { forward, reverse } = elements;
+    const returnedElems = [
+        { name: "forward", src: "src" in forward ? forward.src : "hda", id: forward.id },
+        { name: "reverse", src: "src" in reverse ? reverse.src : "hda", id: reverse.id },
+    ];
+    return createHDCA(returnedElems, "paired", name, hideSourceItems);
+}
+
+async function createHDCA(
+    element_identifiers: any[],
+    collection_type: CollectionType,
+    name: string,
+    hide_source_items: boolean,
+    options = {}
+) {
+    try {
+        creatingCollection.value = true;
+        const collection = await createDatasetCollection(history.value as HistorySummary, {
+            collection_type,
+            name,
+            hide_source_items,
+            element_identifiers,
+            options,
+        });
+
+        emit("created-collection", collection);
+        createdCollection.value = collection;
+
+        if (props.hideModalOnCreate) {
+            hideModal();
+        }
+    } catch (error) {
+        createCollectionError.value = error as string;
+    } finally {
+        creatingCollection.value = false;
+    }
+}
+
+async function fetchHistoryDatasets() {
+    const { error } = await collectionItemsStore.fetchDatasetsForFiltertext(
+        historyId.value,
+        historyUpdateTime.value,
+        localFilterText.value
+    );
+    if (error) {
+        historyItemsError.value = error;
+        console.error("Error fetching history items:", historyItemsError.value);
+    } else {
+        historyItemsError.value = null;
+    }
+}
+
+function hideModal() {
+    localShowToggle.value = false;
+}
+
+function resetModal() {
+    createCollectionError.value = null;
+    createdCollection.value = null;
+}
+</script>
+
+<template>
+    <BModal
+        id="collection-creator-modal"
+        v-model="localShowToggle"
+        :busy="(fromSelection && isFetchingItems) || creatingCollection"
+        modal-class="ui-modal collection-creator-modal"
+        :hide-footer="!createdCollection && !createCollectionError"
+        ok-only
+        :ok-title="localize('Exit')"
+        ok-variant="secondary"
+        @hidden="resetModal">
+        <template v-slot:modal-header>
+            <Heading class="w-100" size="sm">
+                <div class="d-flex justify-content-between unselectable w-100">
+                    <div>{{ modalTitle }}</div>
+                    <div v-if="!!history">
+                        From history: <b>{{ history.name }}</b>
+                    </div>
+                </div>
+            </Heading>
+        </template>
+        <BAlert v-if="isFetchingItems && !initialFetch" variant="info" show>
+            <LoadingSpan :message="localize('Loading items')" />
+        </BAlert>
+        <BAlert v-else-if="!fromSelection && historyItemsError" variant="danger" show>
+            {{ historyItemsError }}
+        </BAlert>
+        <BAlert v-else-if="creatingCollection" variant="info" show>
+            <LoadingSpan :message="localize('Creating collection')" />
+        </BAlert>
+        <BAlert v-else-if="createCollectionError" variant="danger" show>
+            {{ createCollectionError }}
+            <BLink class="text-decoration-none" @click.stop.prevent="resetModal">
+                <FontAwesomeIcon :icon="faUndo" fixed-width />
+                {{ localize("Try again") }}
+            </BLink>
+        </BAlert>
+        <div v-else-if="createdCollection">
+            <BAlert variant="success" show>
+                <FontAwesomeIcon :icon="faCheckCircle" class="text-success" fixed-width />
+                {{ localize("Collection created successfully.") }}
+                <BLink v-if="!fromSelection" class="text-decoration-none" @click.stop.prevent="resetModal">
+                    <FontAwesomeIcon :icon="faUndo" fixed-width />
+                    {{ localize("Create another collection") }}
+                </BLink>
+            </BAlert>
+
+            <!-- TODO: This is a bit shady, better if we confirm it is a collection type -->
+            <GenericItem :item-id="createdCollection.id" item-src="hdca" />
+        </div>
+        <ListCollectionCreator
+            v-else-if="props.collectionType === 'list'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems || []"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createListCollection"
+            @on-cancel="hideModal" />
+        <PairedListCollectionCreator
+            v-else-if="props.collectionType === 'list:paired'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems || []"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createListPairedCollection"
+            @on-cancel="hideModal" />
+        <PairCollectionCreator
+            v-else-if="props.collectionType === 'paired'"
+            :history-id="props.historyId"
+            :initial-elements="creatorItems || []"
+            :default-hide-source-items="props.defaultHideSourceItems"
+            :from-selection="fromSelection"
+            :extensions="props.extensions"
+            @clicked-create="createPairedCollection"
+            @on-cancel="hideModal" />
+    </BModal>
+</template>
+
+<style lang="scss">
+/** NOTE: Not using `<style scoped> here because these classes are
+`BModal` `body-class` and `content-class` and don't seem to work
+with scoped */
+.collection-creator-modal {
+    .modal-dialog {
+        width: 85%;
+        max-width: 100%;
+    }
+}
+</style>
diff --git a/client/src/components/Collections/ListCollectionCreator.vue b/client/src/components/Collections/ListCollectionCreator.vue
index 5798187943f213c2c7446d167a0ce6f70b5509c6..eeaca575bd56db7304aa2e5b81928fa5a3796358 100644
--- a/client/src/components/Collections/ListCollectionCreator.vue
+++ b/client/src/components/Collections/ListCollectionCreator.vue
@@ -1,43 +1,49 @@
 <script setup lang="ts">
 import "ui/hoverhighlight";
 
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faSortAlphaDown, faUndo } from "@fortawesome/free-solid-svg-icons";
+import { faSquare } from "@fortawesome/free-regular-svg-icons";
+import { faMinus, faSortAlphaDown, faTimes, faUndo } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton } from "bootstrap-vue";
-import { computed, onMounted, ref } from "vue";
+import { BAlert, BButton, BButtonGroup } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
 import draggable from "vuedraggable";
 
-import type { HDCADetailed, HistoryItemSummary } from "@/api";
+import type { HDASummary, HistoryItemSummary } from "@/api";
+import { useConfirmDialog } from "@/composables/confirmDialog";
+import { Toast } from "@/composables/toast";
 import STATES from "@/mvc/dataset/states";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 import localize from "@/utils/localization";
 
+import FormSelectMany from "../Form/Elements/FormSelectMany/FormSelectMany.vue";
+import HelpText from "../Help/HelpText.vue";
 import CollectionCreator from "@/components/Collections/common/CollectionCreator.vue";
 import DatasetCollectionElementView from "@/components/Collections/ListDatasetCollectionElementView.vue";
 
-library.add(faSortAlphaDown, faUndo);
+const NOT_VALID_ELEMENT_MSG: string = localize("is not a valid element for this collection");
 
 interface Props {
-    initialElements: Array<any>;
-    oncancel: () => void;
-    oncreate: () => void;
-    creationFn: (workingElements: any, collectionName: string, hideSourceItems: boolean) => any;
+    historyId: string;
+    initialElements: HistoryItemSummary[];
     defaultHideSourceItems?: boolean;
+    fromSelection?: boolean;
+    extensions?: string[];
 }
 
 const props = defineProps<Props>();
 
 const emit = defineEmits<{
-    (e: "clicked-create", workingElements: any, collectionName: string, hideSourceItems: boolean): void;
+    (e: "clicked-create", workingElements: HDASummary[], collectionName: string, hideSourceItems: boolean): void;
+    (e: "on-cancel"): void;
 }>();
 
 const state = ref("build");
-const originalNamedElements = ref([]);
 const duplicateNames = ref<string[]>([]);
 const invalidElements = ref<string[]>([]);
-const workingElements = ref<HDCADetailed[]>([]);
+const workingElements = ref<HDASummary[]>([]);
 const selectedDatasetElements = ref<string[]>([]);
 const hideSourceItems = ref(props.defaultHideSourceItems || false);
+const atLeastOneElement = ref(true);
 
 const atLeastOneDatasetIsSelected = computed(() => {
     return selectedDatasetElements.value.length > 0;
@@ -54,7 +60,7 @@ const returnInvalidElementsLength = computed(() => {
 const returnInvalidElements = computed(() => {
     return invalidElements.value;
 });
-const noElementsSelected = computed(() => {
+const noInitialElements = computed(() => {
     return props.initialElements.length == 0;
 });
 const showDuplicateError = computed(() => {
@@ -64,17 +70,26 @@ const allElementsAreInvalid = computed(() => {
     return props.initialElements.length == invalidElements.value.length;
 });
 
-/** set up instance vars function */
-function _instanceSetUp() {
-    /** Ids of elements that have been selected by the user - to preserve over renders */
-    selectedDatasetElements.value = [];
-}
+/** If not `fromSelection`, the list of elements that will become the collection */
+const inListElements = ref<HDASummary[]>([]);
+
+// variables for datatype mapping and then filtering
+const datatypesMapperStore = useDatatypesMapperStore();
+const datatypesMapper = computed(() => datatypesMapperStore.datatypesMapper);
+
+/** Are we filtering by datatype? */
+const filterExtensions = computed(() => !!datatypesMapper.value && !!props.extensions?.length);
+
+/** Does `inListElements` have elements with different extensions? */
+const listHasMixedExtensions = computed(() => {
+    const extensions = new Set(inListElements.value.map((e) => e.extension));
+    return extensions.size > 1;
+});
 
 // ----------------------------------------------------------------------- process raw list
 /** set up main data */
 function _elementsSetUp() {
     /** a list of invalid elements and the reasons they aren't valid */
-
     invalidElements.value = [];
 
     //TODO: handle fundamental problem of syncing DOM, views, and list here
@@ -84,21 +99,44 @@ function _elementsSetUp() {
     // copy initial list, sort, add ids if needed
     workingElements.value = JSON.parse(JSON.stringify(props.initialElements.slice(0)));
 
-    _ensureElementIds();
+    // reverse the order of the elements to emulate what we have in the history panel
+    workingElements.value.reverse();
+
+    // for inListElements, reset their values (in order) to datasets from workingElements
+    const inListElementsPrev = inListElements.value;
+    inListElements.value = [];
+    inListElementsPrev.forEach((prevElem) => {
+        const element = workingElements.value.find((e) => e.id === prevElem.id);
+        const problem = _isElementInvalid(prevElem);
+
+        if (element) {
+            inListElements.value.push(element);
+        } else if (problem) {
+            const invalidMsg = `${prevElem.hid}: ${prevElem.name} ${problem} and ${NOT_VALID_ELEMENT_MSG}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Invalid element"));
+        } else {
+            const invalidMsg = `${prevElem.hid}: ${prevElem.name} ${localize("has been removed from the collection")}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Invalid element"));
+        }
+    });
+
+    // _ensureElementIds();
     _validateElements();
     _mangleDuplicateNames();
 }
 
-/** add ids to dataset objs in initial list if none */
-function _ensureElementIds() {
-    workingElements.value.forEach((element) => {
-        if (!Object.prototype.hasOwnProperty.call(element, "id")) {
-            console.warn("Element missing id", element);
-        }
-    });
+// TODO: not sure if this is needed
+// function _ensureElementIds() {
+//     workingElements.value.forEach((element) => {
+//         if (!Object.prototype.hasOwnProperty.call(element, "id")) {
+//             console.warn("Element missing id", element);
+//         }
+//     });
 
-    return workingElements.value;
-}
+//     return workingElements.value;
+// }
 
 // /** separate working list into valid and invalid elements for this collection */
 function _validateElements() {
@@ -116,12 +154,12 @@ function _validateElements() {
 }
 
 /** describe what is wrong with a particular element if anything */
-function _isElementInvalid(element: HistoryItemSummary) {
+function _isElementInvalid(element: HistoryItemSummary): string | null {
     if (element.history_content_type === "dataset_collection") {
         return localize("is a collection, this is not allowed");
     }
 
-    var validState = element.state === STATES.OK || STATES.NOT_READY_STATES.includes(element.state as string);
+    const validState = STATES.VALID_INPUT_STATES.includes(element.state as string);
 
     if (!validState) {
         return localize("has errored, is paused, or is not accessible");
@@ -131,9 +169,32 @@ function _isElementInvalid(element: HistoryItemSummary) {
         return localize("has been deleted or purged");
     }
 
+    // is the element's extension not a subtype of any of the required extensions?
+    if (
+        filterExtensions.value &&
+        element.extension &&
+        !datatypesMapper.value?.isSubTypeOfAny(element.extension, props.extensions!)
+    ) {
+        return localize(`has an invalid format: ${element.extension}`);
+    }
     return null;
 }
 
+/** Show the element's extension next to its name:
+ *  1. If there are no required extensions, so users can avoid creating mixed extension lists.
+ *  2. If the extension is not in the list of required extensions but is a subtype of one of them,
+ *     so users can see that those elements were still included as they are implicitly convertible.
+ */
+function showElementExtension(element: HDASummary) {
+    return (
+        !props.extensions?.length ||
+        (filterExtensions.value &&
+            element.extension &&
+            !props.extensions?.includes(element.extension) &&
+            datatypesMapper.value?.isSubTypeOfAny(element.extension, props.extensions!))
+    );
+}
+
 // /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */
 function _mangleDuplicateNames() {
     var counter = 1;
@@ -152,17 +213,11 @@ function _mangleDuplicateNames() {
     });
 }
 
-function saveOriginalNames() {
-    // Deep copy elements
-    originalNamedElements.value = JSON.parse(JSON.stringify(workingElements.value));
-}
-
-function getOriginalNames() {
-    // Deep copy elements
-    workingElements.value = JSON.parse(JSON.stringify(originalNamedElements.value));
+function changeDatatypeFilter(newFilter: "all" | "datatype" | "ext") {
+    _elementsSetUp();
 }
 
-function elementSelected(e: HDCADetailed) {
+function elementSelected(e: HDASummary) {
     if (!selectedDatasetElements.value.includes(e.id)) {
         selectedDatasetElements.value.push(e.id);
     } else {
@@ -170,8 +225,11 @@ function elementSelected(e: HDCADetailed) {
     }
 }
 
-function elementDiscarded(e: HDCADetailed) {
+function elementDiscarded(e: HDASummary) {
     workingElements.value.splice(workingElements.value.indexOf(e), 1);
+    selectedDatasetElements.value = selectedDatasetElements.value.filter((element) => {
+        return element !== e.id;
+    });
 
     return workingElements.value;
 }
@@ -180,18 +238,38 @@ function clickClearAll() {
     selectedDatasetElements.value = [];
 }
 
-function clickedCreate(collectionName: string) {
+function clickRemoveSelected() {
+    workingElements.value = workingElements.value.filter((element) => {
+        return !selectedDatasetElements.value.includes(element.id);
+    });
+
+    selectedDatasetElements.value = [];
+}
+
+function clickSelectAll() {
+    selectedDatasetElements.value = workingElements.value.map((element) => {
+        return element.id;
+    });
+}
+const { confirm } = useConfirmDialog();
+
+async function clickedCreate(collectionName: string) {
     checkForDuplicates();
 
-    if (state.value !== "error") {
-        emit("clicked-create", workingElements.value, collectionName, hideSourceItems.value);
+    const returnedElements = props.fromSelection ? workingElements.value : inListElements.value;
+    atLeastOneElement.value = returnedElements.length > 0;
 
-        return props
-            .creationFn(workingElements.value, collectionName, hideSourceItems.value)
-            .done(props.oncreate)
-            .fail(() => {
-                state.value = "error";
-            });
+    let confirmed = false;
+    if (!atLeastOneElement.value) {
+        confirmed = await confirm("Are you sure you want to create a list with no datasets?", {
+            title: "Create an empty list",
+            okTitle: "Create",
+            okVariant: "primary",
+        });
+    }
+
+    if (state.value !== "error" && (atLeastOneElement.value || confirmed)) {
+        emit("clicked-create", returnedElements, collectionName, hideSourceItems.value);
     }
 }
 
@@ -215,15 +293,16 @@ function checkForDuplicates() {
 
 /** reset all data to the initial state */
 function reset() {
-    _instanceSetUp();
-    getOriginalNames();
+    /** Ids of elements that have been selected by the user - to preserve over renders */
+    selectedDatasetElements.value = [];
+    _elementsSetUp();
 }
 
 function sortByName() {
     workingElements.value.sort(compareNames);
 }
 
-function compareNames(a: HDCADetailed, b: HDCADetailed) {
+function compareNames(a: HDASummary, b: HDASummary) {
     if (a.name && b.name && a.name < b.name) {
         return -1;
     }
@@ -238,11 +317,55 @@ function onUpdateHideSourceItems(newHideSourceItems: boolean) {
     hideSourceItems.value = newHideSourceItems;
 }
 
-onMounted(() => {
-    _instanceSetUp();
-    _elementsSetUp();
-    saveOriginalNames();
-});
+watch(
+    () => props.initialElements,
+    () => {
+        // for any new/removed elements, add them to working elements
+        _elementsSetUp();
+    },
+    { immediate: true }
+);
+
+watch(
+    () => datatypesMapper.value,
+    async (mapper) => {
+        if (props.extensions?.length && !mapper) {
+            await datatypesMapperStore.createMapper();
+        }
+    },
+    { immediate: true }
+);
+
+function addUploadedFiles(files: HDASummary[]) {
+    const returnedElements = props.fromSelection ? workingElements : inListElements;
+    files.forEach((f) => {
+        const file = props.fromSelection ? f : workingElements.value.find((e) => e.id === f.id);
+        const problem = _isElementInvalid(f);
+        if (file && !returnedElements.value.find((e) => e.id === file.id)) {
+            returnedElements.value.push(file);
+        } else if (problem) {
+            invalidElements.value.push("Uploaded item: " + f.name + "  " + problem);
+            Toast.error(
+                localize(`Dataset ${f.hid}: ${f.name} ${problem} and is an invalid element for this collection`),
+                localize("Uploaded item is invalid")
+            );
+        } else {
+            invalidElements.value.push("Uploaded item: " + f.name + " could not be added to the collection");
+            Toast.error(
+                localize(`Dataset ${f.hid}: ${f.name} could not be added to the collection`),
+                localize("Uploaded item is invalid")
+            );
+        }
+    });
+}
+
+/** find the element in the workingElements array and update its name */
+function renameElement(element: any, name: string) {
+    element = workingElements.value.find((e) => e.id === element.id);
+    if (element) {
+        element.name = name;
+    }
+}
 
 //TODO: issue #9497
 // const removeExtensions = ref(true);
@@ -265,29 +388,13 @@ onMounted(() => {
 
 <template>
     <div class="list-collection-creator">
-        <div v-if="state == 'error'">
+        <div v-if="!showDuplicateError && state == 'error'">
             <BAlert show variant="danger">
-                {{ localize("Galaxy could not be reached and may be updating.  Try again in a few minutes.") }}
+                {{ localize("There was a problem creating the collection.") }}
             </BAlert>
         </div>
         <div v-else>
-            <div v-if="noElementsSelected">
-                <BAlert show variant="warning" dismissible>
-                    {{ localize("No datasets were selected") }}
-                    {{ localize("At least one element is needed for the collection. You may need to") }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ localize("cancel") }}
-                    </a>
-                    {{ localize("and reselect new elements.") }}
-                </BAlert>
-
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ localize("Cancel") }}
-                    </button>
-                </div>
-            </div>
-            <div v-else-if="allElementsAreInvalid">
+            <div v-if="fromSelection && returnInvalidElementsLength">
                 <BAlert show variant="warning" dismissible>
                     {{ localize("The following selections could not be included due to problems:") }}
                     <ul>
@@ -295,194 +402,308 @@ onMounted(() => {
                             {{ problem }}
                         </li>
                     </ul>
-                    {{ localize("At least one element is needed for the collection. You may need to") }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ localize("cancel") }}
-                    </a>
-                    {{ localize("and reselect new elements.") }}
                 </BAlert>
+            </div>
 
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ localize("Cancel") }}
-                    </button>
-                </div>
+            <div v-if="!atLeastOneElement">
+                <BAlert show variant="warning" dismissible @dismissed="atLeastOneElement = true">
+                    {{ localize("At least one element is needed for the list.") }}
+                    <span v-if="fromSelection">
+                        <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                            {{ localize("Cancel") }}
+                        </a>
+                        {{ localize("and reselect new elements.") }}
+                    </span>
+                </BAlert>
             </div>
-            <div v-else>
-                <div v-if="returnInvalidElementsLength">
-                    <BAlert show variant="warning" dismissible>
-                        {{ localize("The following selections could not be included due to problems:") }}
-                        <ul>
-                            <li v-for="problem in returnInvalidElements" :key="problem">
-                                {{ problem }}
-                            </li>
-                        </ul>
-                    </BAlert>
-                </div>
 
-                <div v-if="showDuplicateError">
-                    <BAlert show variant="danger">
+            <div v-if="showDuplicateError">
+                <BAlert show variant="danger">
+                    {{
+                        localize("Collections cannot have duplicated names. The following list names are duplicated: ")
+                    }}
+                    <ol>
+                        <li v-for="name in duplicateNames" :key="name">{{ name }}</li>
+                    </ol>
+                    {{ localize("Please fix these duplicates and try again.") }}
+                </BAlert>
+            </div>
+
+            <CollectionCreator
+                :oncancel="() => emit('on-cancel')"
+                :history-id="props.historyId"
+                :hide-source-items="hideSourceItems"
+                :extensions="extensions"
+                collection-type="list"
+                :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
+                @add-uploaded-files="addUploadedFiles"
+                @on-update-datatype-toggle="changeDatatypeFilter"
+                @onUpdateHideSourceItems="onUpdateHideSourceItems"
+                @clicked-create="clickedCreate">
+                <template v-slot:help-content>
+                    <p>
                         {{
                             localize(
-                                "Collections cannot have duplicated names. The following list names are duplicated: "
+                                [
+                                    "This interface allows you to build a new Galaxy list of datasets. ",
+                                    "A list is a type of Galaxy dataset collection that is a permanent, ordered list of datasets that can be passed to tools ",
+                                    "and workflows in order to have analyses done on each member of the entire group. This interface allows ",
+                                    "you to create and re-order a list of datasets. The datasets in a Galaxy collection have an identifier that is preserved accross ",
+                                    "tool executions and serves as a form of sample tracking - setting the name in this form will pick the identifier for that element ",
+                                    "of the list but will not change the dataset's actual name in Galaxy.",
+                                ].join("")
                             )
                         }}
-                        <ol>
-                            <li v-for="name in duplicateNames" :key="name">{{ name }}</li>
-                        </ol>
-                        {{ localize("Please fix these duplicates and try again.") }}
-                    </BAlert>
-                </div>
-
-                <CollectionCreator
-                    :oncancel="oncancel"
-                    :hide-source-items="hideSourceItems"
-                    @onUpdateHideSourceItems="onUpdateHideSourceItems"
-                    @clicked-create="clickedCreate">
-                    <template v-slot:help-content>
-                        <p>
+                    </p>
+
+                    <ul>
+                        <li v-if="!fromSelection">
+                            Move datsets from the "Unselected" column to the "Selected" column below to compose the list
+                            in the intended order and with the intended datasets.
+                        </li>
+                        <li v-if="!fromSelection">
+                            The filter textbox can be used to rapidly find the datasets of interest by name.
+                        </li>
+                        <li>
+                            {{ localize("Change the identifier of elements in the list by clicking on") }}
+                            <i data-target=".collection-element .name">
+                                {{ localize("the existing name") }}
+                            </i>
+                            {{ localize(".") }}
+                        </li>
+
+                        <li>
+                            {{ localize("Discard elements from the final created list by clicking on the ") }}
+                            <i v-if="fromSelection" data-target=".collection-element .discard">
+                                {{ localize("Remove") }}
+                            </i>
+                            <i v-else data-target=".collection-element .discard">
+                                {{ localize("discard") }}
+                            </i>
+                            {{ localize("button.") }}
+                        </li>
+
+                        <li v-if="fromSelection">
                             {{
                                 localize(
-                                    [
-                                        "Collections of datasets are permanent, ordered lists of datasets that can be passed to tools ",
-                                        "and workflows in order to have analyses done on each member of the entire group. This interface allows ",
-                                        "you to create a collection and re-order the final collection.",
-                                    ].join("")
+                                    "Reorder the list by clicking and dragging elements. Select multiple elements by clicking on"
                                 )
                             }}
-                        </p>
-
-                        <ul>
-                            <li>
-                                {{ localize("Rename elements in the list by clicking on") }}
-                                <i data-target=".collection-element .name">
-                                    {{ localize("the existing name") }}
-                                </i>
-                                {{ localize(".") }}
-                            </li>
-
-                            <li>
-                                {{ localize("Discard elements from the final created list by clicking on the ") }}
-                                <i data-target=".collection-element .discard">
-                                    {{ localize("Discard") }}
-                                </i>
-                                {{ localize("button.") }}
-                            </li>
-
-                            <li>
-                                {{
-                                    localize(
-                                        "Reorder the list by clicking and dragging elements. Select multiple elements by clicking on"
-                                    )
-                                }}
-                                <i data-target=".collection-element">
-                                    {{ localize("them") }}
-                                </i>
-                                {{
-                                    localize(
-                                        "and you can then move those selected by dragging the entire group. Deselect them by clicking them again or by clicking the"
-                                    )
-                                }}
-                                <i data-target=".clear-selected">
-                                    {{ localize("Clear selected") }}
-                                </i>
-                                {{ localize("link.") }}
-                            </li>
-
-                            <li>
-                                {{ localize("Click ") }}
-                                <i data-target=".reset">
-                                    <FontAwesomeIcon :icon="faUndo" />
-                                </i>
-                                {{ localize("to begin again as if you had just opened the interface.") }}
-                            </li>
-
-                            <li>
-                                {{ localize("Click ") }}
-                                <i data-target=".sort-items">
-                                    <FontAwesomeIcon :icon="faSortAlphaDown" />
-                                </i>
-                                {{ localize("to sort datasets alphabetically.") }}
-                            </li>
-
-                            <li>
-                                {{ localize("Click the") }}
-                                <i data-target=".cancel-create">
-                                    {{ localize("Cancel") }}
-                                </i>
-                                {{ localize("button to exit the interface.") }}
-                            </li>
-                        </ul>
-
-                        <br />
-
-                        <p>
-                            {{ localize("Once your collection is complete, enter a ") }}
-                            <i data-target=".collection-name">
-                                {{ localize("name") }}
+                            <i data-target=".collection-element">
+                                {{ localize("them") }}
                             </i>
-                            {{ localize("and click") }}
-                            <i data-target=".create-collection">
-                                {{ localize("Create list") }}
+                            {{
+                                localize(
+                                    "and you can then move those selected by dragging the entire group. Deselect them by clicking them again or by clicking the"
+                                )
+                            }}
+                            <i data-target=".clear-selected">
+                                {{ localize("Clear selected") }}
                             </i>
-                            {{ localize(".") }}
-                        </p>
-                    </template>
+                            {{ localize("link.") }}
+                        </li>
 
-                    <template v-slot:middle-content>
-                        <div class="collection-elements-controls">
-                            <BButton class="reset" :title="localize('Undo all reordering and discards')" @click="reset">
+                        <li v-if="fromSelection">
+                            {{ localize("Click ") }}
+                            <i data-target=".reset">
                                 <FontAwesomeIcon :icon="faUndo" />
-                            </BButton>
+                            </i>
+                            {{ localize("to begin again as if you had just opened the interface.") }}
+                        </li>
 
-                            <BButton class="sort-items" :title="localize('Sort datasets by name')" @click="sortByName">
+                        <li v-if="fromSelection">
+                            {{ localize("Click ") }}
+                            <i data-target=".sort-items">
                                 <FontAwesomeIcon :icon="faSortAlphaDown" />
-                            </BButton>
-
-                            <a
-                                v-if="atLeastOneDatasetIsSelected"
-                                class="clear-selected"
-                                href="javascript:void(0);"
-                                role="button"
-                                :title="localize('De-select all selected datasets')"
-                                @click="clickClearAll">
-                                {{ localize("Clear selected") }}
+                            </i>
+                            {{ localize("to sort datasets alphabetically.") }}
+                        </li>
+
+                        <li>
+                            {{ localize("Click the") }}
+                            <i data-target=".cancel-create">
+                                {{ localize("Cancel") }}
+                            </i>
+                            {{ localize("button to exit the interface.") }}
+                        </li>
+                    </ul>
+
+                    <br />
+
+                    <p>
+                        {{ localize("Once your collection is complete, enter a ") }}
+                        <i data-target=".collection-name">
+                            {{ localize("name") }}
+                        </i>
+                        {{ localize("and click") }}
+                        <i data-target=".create-collection">
+                            {{ localize("Create list") }}
+                        </i>
+                        {{ localize(".") }}
+                    </p>
+                </template>
+
+                <template v-slot:middle-content>
+                    <BAlert v-if="listHasMixedExtensions" show variant="warning" dismissible>
+                        {{ localize("The selected datasets have mixed formats.") }}
+                        {{ localize("You can still create the list but generally") }}
+                        {{ localize("dataset lists should contain datasets of the same type.") }}
+                        <HelpText
+                            uri="galaxy.collections.collectionBuilder.whyHomogenousCollections"
+                            :text="localize('Why?')" />
+                    </BAlert>
+                    <div v-if="noInitialElements">
+                        <BAlert show variant="warning" dismissible>
+                            {{ localize("No datasets were selected") }}
+                            {{ localize("At least one element is needed for the collection. You may need to") }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ localize("cancel") }}
                             </a>
+                            {{ localize("and reselect new elements, or upload datasets.") }}
+                        </BAlert>
+                    </div>
+                    <div v-else-if="allElementsAreInvalid">
+                        <BAlert v-if="!fromSelection" show variant="warning">
+                            {{
+                                localize(
+                                    "No elements in your history are valid for this list. \
+                                    You may need to switch to a different history or upload valid datasets."
+                                )
+                            }}
+                            <div v-if="extensions?.length">
+                                {{ localize("The following format(s) are required for this list: ") }}
+                                <ul>
+                                    <li v-for="extension in extensions" :key="extension">
+                                        {{ extension }}
+                                    </li>
+                                </ul>
+                            </div>
+                        </BAlert>
+                        <BAlert v-else show variant="warning" dismissible>
+                            {{ localize("The following selections could not be included due to problems:") }}
+                            <ul>
+                                <li v-for="problem in returnInvalidElements" :key="problem">
+                                    {{ problem }}
+                                </li>
+                            </ul>
+                            {{ localize("At least one element is needed for the collection. You may need to") }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ localize("cancel") }}
+                            </a>
+                            {{ localize("and reselect new elements, or upload valid datasets.") }}
+                        </BAlert>
+                    </div>
+                    <div v-else-if="fromSelection">
+                        <div class="collection-elements-controls">
+                            <div>
+                                <BButton
+                                    class="reset"
+                                    :title="localize('Reset to original state')"
+                                    size="sm"
+                                    @click="reset">
+                                    <FontAwesomeIcon :icon="faUndo" fixed-width />
+                                    {{ localize("Reset") }}
+                                </BButton>
+                                <BButton
+                                    class="sort-items"
+                                    :title="localize('Sort datasets by name')"
+                                    size="sm"
+                                    @click="sortByName">
+                                    <FontAwesomeIcon :icon="faSortAlphaDown" />
+                                </BButton>
+                            </div>
+
+                            <div class="center-text">
+                                <u>{{ workingElements.length }}</u> {{ localize("elements in list") }}
+                            </div>
+
+                            <div>
+                                <span v-if="atLeastOneDatasetIsSelected"
+                                    >{{ localize("For selection") }} ({{ selectedDatasetElements.length }}):</span
+                                >
+                                <BButtonGroup class="" size="sm">
+                                    <BButton
+                                        v-if="atLeastOneDatasetIsSelected"
+                                        :title="localize('Remove selected datasets from the list')"
+                                        @click="clickRemoveSelected">
+                                        <FontAwesomeIcon :icon="faMinus" fixed-width />
+                                        {{ localize("Remove") }}
+                                    </BButton>
+                                    <BButton
+                                        v-if="
+                                            !atLeastOneDatasetIsSelected ||
+                                            selectedDatasetElements.length < workingElements.length
+                                        "
+                                        :title="localize('Select all datasets')"
+                                        size="sm"
+                                        @click="clickSelectAll">
+                                        <FontAwesomeIcon :icon="faSquare" fixed-width />
+                                        {{ localize("Select all") }}
+                                    </BButton>
+                                    <BButton
+                                        v-if="atLeastOneDatasetIsSelected"
+                                        class="clear-selected"
+                                        :title="localize('De-select all selected datasets')"
+                                        @click="clickClearAll">
+                                        <FontAwesomeIcon :icon="faTimes" fixed-width />
+                                        {{ localize("Clear") }}
+                                    </BButton>
+                                </BButtonGroup>
+                            </div>
+                        </div>
+
+                        <div v-if="noMoreValidDatasets">
+                            <BAlert show variant="warning">
+                                {{ localize("No elements left. Would you like to") }}
+                                <a class="reset-text" href="javascript:void(0)" role="button" @click="reset">
+                                    {{ localize("start over") }}
+                                </a>
+                                ?
+                            </BAlert>
                         </div>
 
                         <draggable
                             v-model="workingElements"
                             class="collection-elements scroll-container flex-row drop-zone"
-                            @start="drag = true"
-                            @end="drag = false">
-                            <div v-if="noMoreValidDatasets">
-                                <BAlert show variant="warning" dismissible>
-                                    {{ localize("No elements left. Would you like to") }}
-                                    <a class="reset-text" href="javascript:void(0)" role="button" @click="reset">
-                                        {{ localize("start over") }}
-                                    </a>
-                                    ?
-                                </BAlert>
-                            </div>
-
+                            chosen-class="bg-secondary">
                             <DatasetCollectionElementView
                                 v-for="element in workingElements"
-                                v-else
                                 :key="element.id"
                                 :class="{ selected: getSelectedDatasetElements.includes(element.id) }"
                                 :element="element"
+                                has-actions
+                                :selected="getSelectedDatasetElements.includes(element.id)"
                                 @element-is-selected="elementSelected"
                                 @element-is-discarded="elementDiscarded"
                                 @onRename="(name) => (element.name = name)" />
                         </draggable>
-                    </template>
-                </CollectionCreator>
-            </div>
+                    </div>
+
+                    <FormSelectMany
+                        v-else
+                        v-model="inListElements"
+                        maintain-selection-order
+                        :placeholder="localize('Filter datasets by name')"
+                        :options="workingElements.map((e) => ({ label: e.name || '', value: e }))">
+                        <template v-slot:label-area="{ value }">
+                            <DatasetCollectionElementView
+                                class="w-100"
+                                :element="value"
+                                :hide-extension="!showElementExtension(value)"
+                                @onRename="(name) => renameElement(value, name)" />
+                        </template>
+                    </FormSelectMany>
+                </template>
+            </CollectionCreator>
         </div>
     </div>
 </template>
 
 <style scoped lang="scss">
+@import "base.scss";
+@import "theme/blue.scss";
+
 .list-collection-creator {
     .footer {
         margin-top: 8px;
@@ -494,9 +715,15 @@ onMounted(() => {
 
     .collection-elements-controls {
         margin-bottom: 8px;
-
-        .clear-selected {
-            float: right !important;
+        display: flex;
+        justify-content: space-between;
+        align-items: center;
+        position: relative;
+
+        .center-text {
+            position: absolute;
+            transform: translateX(-50%);
+            left: 50%;
         }
     }
 
@@ -510,21 +737,28 @@ onMounted(() => {
     // TODO: taken from .dataset above - swap these out
     .collection-element {
         height: 32px;
-        margin: 2px 4px 0px 4px;
         opacity: 1;
-        border: 1px solid lightgrey;
-        border-radius: 3px;
         padding: 0 8px 0 8px;
         line-height: 28px;
         cursor: pointer;
         overflow: hidden;
+        border: 1px solid lightgrey;
+        border-radius: 3px;
 
-        &:last-of-type {
-            margin-bottom: 2px;
+        &.with-actions {
+            margin: 2px 4px 0px 4px;
+            &:hover {
+                border-color: black;
+            }
+        }
+        &:not(.with-actions) {
+            &:hover {
+                border: none;
+            }
         }
 
-        &:hover {
-            border-color: black;
+        &:last-of-type {
+            margin-bottom: 2px;
         }
 
         &.selected {
@@ -535,20 +769,6 @@ onMounted(() => {
                 color: white;
             }
         }
-
-        .name {
-            &:hover {
-                text-decoration: underline;
-            }
-        }
-
-        button {
-            margin-top: 3px;
-        }
-
-        .discard {
-            @extend .float-right !optional;
-        }
     }
 
     .empty-message {
diff --git a/client/src/components/Collections/ListCollectionCreatorModal.js b/client/src/components/Collections/ListCollectionCreatorModal.js
deleted file mode 100644
index 9993f240aa0a3bb3d7ccf45a2bd70822119d6006..0000000000000000000000000000000000000000
--- a/client/src/components/Collections/ListCollectionCreatorModal.js
+++ /dev/null
@@ -1,49 +0,0 @@
-import _l from "utils/localization";
-import Vue from "vue";
-
-import { collectionCreatorModalSetup } from "./common/modal";
-
-function listCollectionCreatorModal(elements, options) {
-    options = options || {};
-    options.title = _l("Create a collection from a list of datasets");
-    const { promise, showEl } = collectionCreatorModalSetup(options);
-    return import(/* webpackChunkName: "ListCollectionCreator" */ "./ListCollectionCreator.vue").then((module) => {
-        const listCollectionCreatorInstance = Vue.extend(module.default);
-        const vm = document.createElement("div");
-        showEl(vm);
-        new listCollectionCreatorInstance({
-            propsData: {
-                initialElements: elements,
-                creationFn: options.creationFn,
-                oncancel: options.oncancel,
-                oncreate: options.oncreate,
-                defaultHideSourceItems: options.defaultHideSourceItems,
-            },
-        }).$mount(vm);
-        return promise;
-    });
-}
-
-/** Use a modal to create a list collection, then add it to the given history contents.
- *  @returns {Promise} resolved when the collection is added to the history.
- */
-function createListCollection(contents, defaultHideSourceItems = true) {
-    const elements = contents.toJSON();
-    const promise = listCollectionCreatorModal(elements, {
-        defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function (elements, name, hideSourceItems) {
-            elements = elements.map((element) => ({
-                id: element.id,
-                name: element.name,
-                //TODO: this allows for list:list even if the filter above does not - reconcile
-                src: element.src || (element.history_content_type == "dataset" ? "hda" : "hdca"),
-            }));
-            return contents.createHDCA(elements, "list", name, hideSourceItems);
-        },
-    });
-    return promise;
-}
-export default {
-    listCollectionCreatorModal: listCollectionCreatorModal,
-    createListCollection: createListCollection,
-};
diff --git a/client/src/components/Collections/ListDatasetCollectionElementView.vue b/client/src/components/Collections/ListDatasetCollectionElementView.vue
index e7b41e4158de8d85e245691686b040a07ea618f1..f242499581a188ddc6874153c48a66ae5560cb4c 100644
--- a/client/src/components/Collections/ListDatasetCollectionElementView.vue
+++ b/client/src/components/Collections/ListDatasetCollectionElementView.vue
@@ -1,12 +1,19 @@
 <script setup lang="ts">
-import { onMounted, ref, watch } from "vue";
+import { faCheck, faMinus } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { ref, watch } from "vue";
 
+import type { HDASummary } from "@/api";
 import localize from "@/utils/localization";
 
 import ClickToEdit from "@/components/Collections/common/ClickToEdit.vue";
 
 interface Props {
-    element: any;
+    element: HDASummary;
+    selected?: boolean;
+    hasActions?: boolean;
+    notEditable?: boolean;
+    hideExtension?: boolean;
 }
 
 const props = defineProps<Props>();
@@ -17,7 +24,7 @@ const emit = defineEmits<{
     (event: "element-is-discarded", element: any): void;
 }>();
 
-const elementName = ref("");
+const elementName = ref(props.element.name || "...");
 
 watch(elementName, () => {
     emit("onRename", elementName.value);
@@ -26,28 +33,40 @@ watch(elementName, () => {
 function clickDiscard() {
     emit("element-is-discarded", props.element);
 }
-
-onMounted(() => {
-    elementName.value = props.element.name;
-});
 </script>
 
 <template>
-    <div class="collection-element" @click="emit('element-is-selected', element)">
-        <ClickToEdit v-model="elementName" :title="localize('Click to rename')" />
+    <div
+        class="collection-element d-flex justify-content-between"
+        :class="{ 'with-actions': hasActions }"
+        role="button"
+        tabindex="0"
+        @keyup.enter="emit('element-is-selected', element)"
+        @click="emit('element-is-selected', element)">
+        <span class="d-flex flex-gapx-1">
+            <span v-if="element.hid">{{ element.hid }}:</span>
+            <strong>
+                <ClickToEdit v-if="!notEditable" v-model="elementName" :title="localize('Click to rename')" />
+                <span v-else>{{ elementName }}</span>
+            </strong>
+            <i v-if="!hideExtension && element.extension"> ({{ element.extension }}) </i>
+        </span>
 
-        <button class="discard-btn btn-sm" :title="localize('Remove this dataset from the list')" @click="clickDiscard">
-            {{ localize("Discard") }}
-        </button>
+        <div v-if="hasActions" class="float-right">
+            <i v-if="!selected" class="mr-2">
+                <FontAwesomeIcon :icon="faCheck" class="text-success" /> Added to collection
+            </i>
+            <i v-else class="text-secondary">Selected</i>
+            <button class="btn-sm" :title="localize('Remove this dataset from the list')" @click="clickDiscard">
+                <FontAwesomeIcon :icon="faMinus" fixed-width />
+                {{ localize("Remove") }}
+            </button>
+        </div>
     </div>
 </template>
 
 <style scoped lang="scss">
 .collection-element {
     height: auto;
-
-    .discard-btn {
-        float: right;
-    }
 }
 </style>
diff --git a/client/src/components/Collections/PairCollectionCreator.vue b/client/src/components/Collections/PairCollectionCreator.vue
index 2520a3a022f8a99fa535590e0650baf0ee7dc07d..13e755dbd14f2655ff1f5bc3793e4852e1eaa7f2 100644
--- a/client/src/components/Collections/PairCollectionCreator.vue
+++ b/client/src/components/Collections/PairCollectionCreator.vue
@@ -1,32 +1,61 @@
 <script setup lang="ts">
-import { BAlert } from "bootstrap-vue";
-import { computed, onMounted, ref } from "vue";
-
-import type { HDCADetailed, HistoryItemSummary } from "@/api";
+import { faArrowsAltV } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BButton } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import type { HDASummary, HistoryItemSummary } from "@/api";
+import { useAnimationFrameResizeObserver } from "@/composables/sensors/animationFrameResizeObserver";
+import { useAnimationFrameScroll } from "@/composables/sensors/animationFrameScroll";
+import { Toast } from "@/composables/toast";
 import STATES from "@/mvc/dataset/states";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 import localize from "@/utils/localization";
 
+import type { DatasetPair } from "../History/adapters/buildCollectionModal";
+
+import DelayedInput from "../Common/DelayedInput.vue";
+import HelpText from "../Help/HelpText.vue";
+import DatasetCollectionElementView from "./ListDatasetCollectionElementView.vue";
 import CollectionCreator from "@/components/Collections/common/CollectionCreator.vue";
 
+const NOT_VALID_ELEMENT_MSG: string = localize("is not a valid element for this collection");
+
+interface SelectedDatasetPair {
+    forward: HDASummary | undefined;
+    reverse: HDASummary | undefined;
+}
+
 interface Props {
-    initialElements: Array<any>;
-    oncancel: () => void;
-    oncreate: () => void;
-    creationFn: (workingElements: HDCADetailed[], collectionName: string, hideSourceItems: boolean) => any;
+    historyId: string;
+    initialElements: HistoryItemSummary[];
     defaultHideSourceItems?: boolean;
+    fromSelection?: boolean;
+    extensions?: string[];
 }
 
 const props = defineProps<Props>();
 
 const emit = defineEmits<{
-    (event: "clicked-create", workingElements: HDCADetailed[], collectionName: string, hideSourceItems: boolean): void;
+    (event: "clicked-create", selectedPair: DatasetPair, collectionName: string, hideSourceItems: boolean): void;
+    (event: "on-cancel"): void;
 }>();
 
 const state = ref("build");
 const removeExtensions = ref(true);
 const initialSuggestedName = ref("");
 const invalidElements = ref<string[]>([]);
-const workingElements = ref<HDCADetailed[]>([]);
+const workingElements = ref<HDASummary[]>([]);
+const filterText = ref("");
+
+const filteredElements = computed(() => {
+    return workingElements.value.filter((element) => {
+        return `${element.hid}: ${element.name}`.toLowerCase().includes(filterText.value.toLowerCase());
+    });
+});
+
+/** If not `fromSelection`, the manually added elements that will become the pair */
+const inListElements = ref<SelectedDatasetPair>({ forward: undefined, reverse: undefined });
 
 const allElementsAreInvalid = computed(() => {
     return props.initialElements.length == invalidElements.value.length;
@@ -35,9 +64,61 @@ const noElementsSelected = computed(() => {
     return props.initialElements.length == 0;
 });
 const exactlyTwoValidElements = computed(() => {
-    return workingElements.value.length == 2;
+    return pairElements.value.forward && pairElements.value.reverse;
 });
 const hideSourceItems = ref(props.defaultHideSourceItems || false);
+const pairElements = computed<SelectedDatasetPair>(() => {
+    if (props.fromSelection) {
+        return {
+            forward: workingElements.value[0],
+            reverse: workingElements.value[1],
+        };
+    } else {
+        return inListElements.value;
+    }
+});
+const pairHasMixedExtensions = computed(() => {
+    return (
+        pairElements.value.forward?.extension &&
+        pairElements.value.reverse?.extension &&
+        pairElements.value.forward.extension !== pairElements.value.reverse.extension
+    );
+});
+
+// variables for datatype mapping and then filtering
+const datatypesMapperStore = useDatatypesMapperStore();
+const datatypesMapper = computed(() => datatypesMapperStore.datatypesMapper);
+
+/** Are we filtering by datatype? */
+const filterExtensions = computed(() => !!datatypesMapper.value && !!props.extensions?.length);
+
+// check if we have scrolled to the top or bottom of the scrollable div
+const scrollableDiv = ref<HTMLDivElement | null>(null);
+const { arrived } = useAnimationFrameScroll(scrollableDiv);
+const isScrollable = ref(false);
+useAnimationFrameResizeObserver(scrollableDiv, ({ clientSize, scrollSize }) => {
+    isScrollable.value = scrollSize.height >= clientSize.height + 1;
+});
+const scrolledTop = computed(() => !isScrollable.value || arrived.top);
+const scrolledBottom = computed(() => !isScrollable.value || arrived.bottom);
+
+watch(
+    () => props.initialElements,
+    () => {
+        // initialize; and then for any new/removed elements, sync working elements
+        _elementsSetUp();
+
+        // TODO: fix this, now either of those will almost always be empty
+        if (props.fromSelection && !initialSuggestedName.value) {
+            initialSuggestedName.value = _guessNameForPair(
+                workingElements.value[0] as HDASummary,
+                workingElements.value[1] as HDASummary,
+                removeExtensions.value
+            );
+        }
+    },
+    { immediate: true }
+);
 
 function _elementsSetUp() {
     /** a list of invalid elements and the reasons they aren't valid */
@@ -50,6 +131,38 @@ function _elementsSetUp() {
     // copy initial list, sort, add ids if needed
     workingElements.value = JSON.parse(JSON.stringify(props.initialElements.slice(0)));
 
+    // reverse the order of the elements to emulate what we have in the history panel
+    workingElements.value.reverse();
+
+    // for inListElements, reset their values (in order) to datasets from workingElements
+    const inListElementsPrev = inListElements.value;
+    inListElements.value = { forward: undefined, reverse: undefined };
+
+    for (const key of ["forward", "reverse"]) {
+        const prevElem = inListElementsPrev[key as keyof SelectedDatasetPair];
+        if (!prevElem) {
+            continue;
+        }
+        const element = workingElements.value.find(
+            (e) => e.id === inListElementsPrev[key as keyof SelectedDatasetPair]?.id
+        );
+        const problem = _isElementInvalid(prevElem);
+        if (element) {
+            inListElements.value[key as keyof SelectedDatasetPair] = element;
+        } else if (problem) {
+            const invalidMsg = `${prevElem.hid}: ${prevElem.name} ${problem} and ${NOT_VALID_ELEMENT_MSG}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Invalid element"));
+        } else {
+            const invalidMsg = `${prevElem.hid}: ${prevElem.name} ${localize("has been removed from the collection")}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Invalid element"));
+        }
+    }
+
+    // TODO: Next thing to add is: If the user adds an uploaded file, that is eventually nuked from workingElements
+    //       because it is invalid, Toast an error for that file by keeping track of uploaded ids in a separate list
+
     _ensureElementIds();
     _validateElements();
 }
@@ -86,7 +199,7 @@ function _isElementInvalid(element: HistoryItemSummary) {
         return localize("is a collection, this is not allowed");
     }
 
-    var validState = element.state === STATES.OK || STATES.NOT_READY_STATES.includes(element.state as string);
+    const validState = STATES.VALID_INPUT_STATES.includes(element.state as string);
 
     if (!validState) {
         return localize("has errored, is paused, or is not accessible");
@@ -96,23 +209,74 @@ function _isElementInvalid(element: HistoryItemSummary) {
         return localize("has been deleted or purged");
     }
 
+    // is the element's extension not a subtype of any of the required extensions?
+    if (
+        filterExtensions.value &&
+        element.extension &&
+        !datatypesMapper.value?.isSubTypeOfAny(element.extension, props.extensions!)
+    ) {
+        return localize(`has an invalid format: ${element.extension}`);
+    }
     return null;
 }
 
+function getPairElement(key: string) {
+    return pairElements.value[key as "forward" | "reverse"];
+}
+
+function removeElement(key: string) {
+    pairElements.value[key as "forward" | "reverse"] = undefined;
+}
+
+function selectElement(element: HDASummary) {
+    if (pairElements.value.forward?.id === element.id) {
+        pairElements.value.forward = undefined;
+    } else if (pairElements.value.reverse?.id === element.id) {
+        pairElements.value.reverse = undefined;
+    } else if (pairElements.value.forward === undefined) {
+        pairElements.value.forward = element;
+    } else if (pairElements.value.reverse === undefined) {
+        pairElements.value.reverse = element;
+    }
+}
+
 function swapButton() {
-    workingElements.value = [workingElements.value[1], workingElements.value[0]] as HDCADetailed[];
+    if (!exactlyTwoValidElements.value) {
+        return;
+    }
+    if (props.fromSelection) {
+        workingElements.value = [workingElements.value[1], workingElements.value[0]] as HDASummary[];
+    } else {
+        inListElements.value = {
+            forward: inListElements.value.reverse,
+            reverse: inListElements.value.forward,
+        };
+    }
+}
+
+function addUploadedFiles(files: HDASummary[]) {
+    // Any added files are added to workingElements in _elementsSetUp
+    // The user will have to manually select the files to add them to the pair
+
+    // Check for validity of uploads
+    files.forEach((file) => {
+        const problem = _isElementInvalid(file);
+        if (problem) {
+            const invalidMsg = `${file.hid}: ${file.name} ${problem} and ${NOT_VALID_ELEMENT_MSG}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Uploaded item invalid for pair"));
+        }
+    });
 }
 
 function clickedCreate(collectionName: string) {
-    if (state.value !== "error") {
-        emit("clicked-create", workingElements.value, collectionName, hideSourceItems.value);
-
-        return props
-            .creationFn(workingElements.value, collectionName, hideSourceItems.value)
-            .done(props.oncreate)
-            .fail(() => {
-                state.value = "error";
-            });
+    if (state.value !== "error" && exactlyTwoValidElements.value) {
+        const returnedPair = {
+            forward: pairElements.value.forward as HDASummary,
+            reverse: pairElements.value.reverse as HDASummary,
+            name: collectionName,
+        };
+        emit("clicked-create", returnedPair, collectionName, hideSourceItems.value);
     }
 }
 
@@ -120,13 +284,13 @@ function removeExtensionsToggle() {
     removeExtensions.value = !removeExtensions.value;
 
     initialSuggestedName.value = _guessNameForPair(
-        workingElements.value[0] as HDCADetailed,
-        workingElements.value[1] as HDCADetailed,
+        workingElements.value[0] as HDASummary,
+        workingElements.value[1] as HDASummary,
         removeExtensions.value
     );
 }
 
-function _guessNameForPair(fwd: HDCADetailed, rev: HDCADetailed, removeExtensions: boolean) {
+function _guessNameForPair(fwd: HDASummary, rev: HDASummary, removeExtensions: boolean) {
     removeExtensions = removeExtensions ? removeExtensions : removeExtensions;
 
     var fwdName = fwd.name ?? "";
@@ -199,16 +363,6 @@ function _naiveStartingAndEndingLCS(s1: string, s2: string) {
 
     return fwdLCS + revLCS;
 }
-
-onMounted(() => {
-    _elementsSetUp();
-
-    initialSuggestedName.value = _guessNameForPair(
-        workingElements.value[0] as HDCADetailed,
-        workingElements.value[1] as HDCADetailed,
-        removeExtensions.value
-    );
-});
 </script>
 
 <template>
@@ -219,23 +373,7 @@ onMounted(() => {
             </BAlert>
         </div>
         <div v-else>
-            <div v-if="noElementsSelected">
-                <BAlert show variant="warning" dismissible>
-                    {{ localize("No datasets were selected.") }}
-                    {{ localize("Exactly two elements needed for the collection. You may need to") }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ localize("cancel") }}
-                    </a>
-                    {{ localize("and reselect new elements.") }}
-                </BAlert>
-
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ localize("Cancel") }}
-                    </button>
-                </div>
-            </div>
-            <div v-else-if="allElementsAreInvalid">
+            <div v-if="fromSelection && invalidElements.length">
                 <BAlert show variant="warning" dismissible>
                     {{ localize("The following selections could not be included due to problems:") }}
                     <ul>
@@ -243,135 +381,204 @@ onMounted(() => {
                             {{ problem }}
                         </li>
                     </ul>
-                    {{ localize("Exactly two elements needed for the collection. You may need to") }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ localize("cancel") }}
-                    </a>
-                    {{ localize("and reselect new elements.") }}
                 </BAlert>
-
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ localize("Cancel") }}
-                    </button>
-                </div>
             </div>
-            <div v-else-if="!exactlyTwoValidElements">
-                <div v-if="invalidElements.length">
-                    <BAlert show variant="warning" dismissible>
-                        {{ localize("The following selections could not be included due to problems:") }}
-                        <ul>
-                            <li v-for="problem in invalidElements" :key="problem">
-                                {{ problem }}
-                            </li>
-                        </ul>
-                    </BAlert>
-                </div>
 
-                <BAlert show variant="warning" dismissible>
-                    {{ localize("Two (and only two) elements are needed for the pair. You may need to ") }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ localize("cancel") }}
-                    </a>
-                    {{ localize("and reselect new elements.") }}
-                </BAlert>
+            <CollectionCreator
+                :oncancel="() => emit('on-cancel')"
+                :history-id="props.historyId"
+                :hide-source-items="hideSourceItems"
+                :suggested-name="initialSuggestedName"
+                :extensions="props.extensions"
+                :extensions-toggle="removeExtensions"
+                collection-type="paired"
+                :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
+                @add-uploaded-files="addUploadedFiles"
+                @onUpdateHideSourceItems="onUpdateHideSourceItems"
+                @clicked-create="clickedCreate"
+                @remove-extensions-toggle="removeExtensionsToggle">
+                <template v-slot:help-content>
+                    <!-- TODO: Update help content for case where `fromSelection` is false -->
+                    <p>
+                        {{
+                            localize(
+                                [
+                                    "Pair collections are permanent collections containing two datasets: one forward and one reverse. ",
+                                    "Often these are forward and reverse reads. The pair collections can be passed to tools and workflows in ",
+                                    "order to have analyses done on both datasets. This interface allows you to create a pair, name it, and ",
+                                    "swap which is forward and which reverse.",
+                                ].join("")
+                            )
+                        }}
+                    </p>
 
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ localize("Cancel") }}
-                    </button>
-                </div>
-            </div>
-            <div v-else>
-                <div v-if="invalidElements.length">
-                    <BAlert show variant="warning" dismissible>
-                        {{ localize("The following selections could not be included due to problems:") }}
-                        <ul>
-                            <li v-for="problem in invalidElements" :key="problem">
-                                {{ problem }}
-                            </li>
-                        </ul>
-                    </BAlert>
-                </div>
-
-                <CollectionCreator
-                    :oncancel="oncancel"
-                    :hide-source-items="hideSourceItems"
-                    :suggested-name="initialSuggestedName"
-                    @onUpdateHideSourceItems="onUpdateHideSourceItems"
-                    @clicked-create="clickedCreate"
-                    @remove-extensions-toggle="removeExtensionsToggle">
-                    <template v-slot:help-content>
-                        <p>
+                    <ul>
+                        <li>
+                            {{ localize("Click the ") }}
+                            <i data-target=".swap">
+                                {{ localize("Swap") }}
+                            </i>
                             {{
                                 localize(
-                                    [
-                                        "Pair collections are permanent collections containing two datasets: one forward and one reverse. ",
-                                        "Often these are forward and reverse reads. The pair collections can be passed to tools and workflows in ",
-                                        "order to have analyses done on both datasets. This interface allows you to create a pair, name it, and ",
-                                        "swap which is forward and which reverse.",
-                                    ].join("")
+                                    "link to make your forward dataset the reverse and the reverse dataset forward"
                                 )
                             }}
-                        </p>
+                        </li>
 
-                        <ul>
-                            <li>
-                                {{ localize("Click the ") }}
-                                <i data-target=".swap">
-                                    {{ localize("Swap") }}
-                                </i>
-                                {{
-                                    localize(
-                                        "link to make your forward dataset the reverse and the reverse dataset forward"
-                                    )
-                                }}
-                            </li>
-
-                            <li>
-                                {{ localize("Click the ") }}
-                                <i data-target=".cancel-create">
-                                    {{ localize("Cancel") }}
-                                </i>
-                                {{ localize("button to exit the interface.") }}
-                            </li>
-                        </ul>
-
-                        <br />
-
-                        <p>
-                            {{ localize("Once your collection is complete, enter a ") }}
-                            <i data-target=".collection-name"> {{ localize("name") }}</i>
-                            {{ localize("and click ") }}
-                            <i data-target=".create-collection">
-                                {{ localize("Create list") }}
+                        <li>
+                            {{ localize("Click the ") }}
+                            <i data-target=".cancel-create">
+                                {{ localize("Cancel") }}
                             </i>
-                            {{ localize(".") }}
-                        </p>
-                    </template>
-
-                    <template v-slot:middle-content>
-                        <div class="collection-elements-controls">
-                            <a
-                                class="swap"
-                                href="javascript:void(0);"
-                                title="l('Swap forward and reverse datasets')"
-                                @click="swapButton">
-                                {{ localize("Swap") }}
+                            {{ localize("button to exit the interface.") }}
+                        </li>
+                    </ul>
+
+                    <br />
+
+                    <p>
+                        {{ localize("Once your collection is complete, enter a ") }}
+                        <i data-target=".collection-name"> {{ localize("name") }}</i>
+                        {{ localize("and click ") }}
+                        <i data-target=".create-collection">
+                            {{ localize("Create dataset pair") }}
+                        </i>
+                        {{ localize(".") }}
+                    </p>
+                </template>
+
+                <template v-slot:middle-content>
+                    <div v-if="noElementsSelected">
+                        <BAlert show variant="warning" dismissible>
+                            {{ localize("No datasets were selected.") }}
+                            {{ localize("Exactly two elements needed for the collection. You may need to") }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ localize("cancel") }}
+                            </a>
+                            {{ localize("and reselect new elements, or upload datasets.") }}
+                        </BAlert>
+                    </div>
+                    <div v-else-if="allElementsAreInvalid">
+                        <BAlert v-if="!fromSelection" show variant="warning">
+                            {{
+                                localize(
+                                    "No elements in your history are valid for this pair. \
+                                    You may need to switch to a different history or upload valid datasets."
+                                )
+                            }}
+                            <div v-if="extensions?.length">
+                                {{ localize("The following formats are required for this pair: ") }}
+                                <ul>
+                                    <li v-for="extension in extensions" :key="extension">
+                                        {{ extension }}
+                                    </li>
+                                </ul>
+                            </div>
+                        </BAlert>
+                        <BAlert v-else show variant="warning" dismissible>
+                            {{ localize("The following selections could not be included due to problems:") }}
+                            <ul>
+                                <li v-for="problem in invalidElements" :key="problem">
+                                    {{ problem }}
+                                </li>
+                            </ul>
+                            {{ localize("Exactly two elements needed for the collection. You may need to") }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ localize("cancel") }}
                             </a>
+                            {{ localize("and reselect new elements, or upload datasets.") }}
+                        </BAlert>
+                    </div>
+                    <div v-else>
+                        <div class="collection-elements-controls flex-gapx-1">
+                            <div>
+                                <BButton
+                                    class="swap"
+                                    size="sm"
+                                    :disabled="!exactlyTwoValidElements"
+                                    :title="localize('Swap forward and reverse datasets')"
+                                    @click="swapButton">
+                                    <FontAwesomeIcon :icon="faArrowsAltV" fixed-width />
+                                    {{ localize("Swap") }}
+                                </BButton>
+                            </div>
+                            <div class="flex-grow-1">
+                                <BAlert v-if="!exactlyTwoValidElements" show variant="warning">
+                                    {{ localize("Exactly two elements are needed for the pair.") }}
+                                    <span v-if="fromSelection">
+                                        <a
+                                            class="cancel-text"
+                                            href="javascript:void(0)"
+                                            role="button"
+                                            @click="emit('on-cancel')">
+                                            {{ localize("Cancel") }}
+                                        </a>
+                                        {{ localize("and reselect new elements.") }}
+                                    </span>
+                                </BAlert>
+                                <BAlert v-else-if="pairHasMixedExtensions" show variant="warning">
+                                    {{ localize("The selected datasets have mixed formats.") }}
+                                    {{ localize("You can still create the pair but generally") }}
+                                    {{ localize("dataset pairs should contain datasets of the same type.") }}
+                                    <HelpText
+                                        uri="galaxy.collections.collectionBuilder.whyHomogenousCollections"
+                                        :text="localize('Why?')" />
+                                </BAlert>
+                                <BAlert v-else show variant="success">
+                                    {{ localize("The Dataset Pair is ready to be created.") }}
+                                    {{ localize("Provide a name and click the button below to create the pair.") }}
+                                </BAlert>
+                            </div>
+                        </div>
+
+                        <div class="flex-row mb-3">
+                            <div v-for="dataset in ['forward', 'reverse']" :key="dataset">
+                                {{ localize(dataset) }}:
+                                <DatasetCollectionElementView
+                                    v-if="getPairElement(dataset)"
+                                    :key="getPairElement(dataset)?.id"
+                                    :element="getPairElement(dataset)"
+                                    has-actions
+                                    @element-is-discarded="removeElement(dataset)" />
+                                <div v-else class="collection-element alert-info">
+                                    <i>{{ localize("No dataset selected") }}</i>
+                                </div>
+                            </div>
                         </div>
 
-                        <div class="collection-elements scroll-container flex-row">
+                        <div v-if="!fromSelection">
+                            <DelayedInput v-model="filterText" placeholder="search datasets" :delay="800" />
+                            <strong>
+                                {{
+                                    localize("Manually select a forward and reverse dataset to create a dataset pair:")
+                                }}
+                            </strong>
                             <div
-                                v-for="(element, index) in workingElements"
-                                :key="element.id"
-                                class="collection-element">
-                                {{ index == 0 ? localize("forward") : localize("reverse") }}: {{ element.name }}
+                                v-if="filteredElements.length"
+                                class="scroll-list-container"
+                                :class="{ 'scrolled-top': scrolledTop, 'scrolled-bottom': scrolledBottom }">
+                                <div ref="scrollableDiv" class="collection-elements">
+                                    <DatasetCollectionElementView
+                                        v-for="element in filteredElements"
+                                        :key="element.id"
+                                        :class="{
+                                            selected: [pairElements.forward, pairElements.reverse].includes(element),
+                                        }"
+                                        :element="element"
+                                        not-editable
+                                        :selected="[pairElements.forward, pairElements.reverse].includes(element)"
+                                        @element-is-selected="selectElement"
+                                        @onRename="(name) => (element.name = name)" />
+                                </div>
                             </div>
+                            <BAlert v-else show variant="info">
+                                {{ localize(`No datasets found${filterText ? " matching '" + filterText + "'" : ""}`) }}
+                            </BAlert>
                         </div>
-                    </template>
-                </CollectionCreator>
-            </div>
+                    </div>
+                </template>
+            </CollectionCreator>
         </div>
     </div>
 </template>
@@ -382,16 +589,20 @@ onMounted(() => {
         margin-top: 8px;
     }
 
-    .main-help {
-        cursor: pointer;
-    }
-
     .collection-elements-controls {
-        margin-bottom: 8px;
+        display: flex;
+        justify-content: space-between;
+        align-items: center;
+
+        .alert {
+            padding: 0.25rem 0.5rem;
+            margin: 0;
+            text-align: center;
+        }
     }
 
     .collection-elements {
-        max-height: 400px;
+        max-height: 30vh;
         border: 0px solid lightgrey;
         overflow-y: auto;
         overflow-x: hidden;
@@ -433,6 +644,15 @@ onMounted(() => {
                 text-decoration: none;
             }
         }
+
+        &.selected {
+            border-color: black;
+            background: rgb(118, 119, 131);
+            color: white;
+            a {
+                color: white;
+            }
+        }
     }
 
     .empty-message {
diff --git a/client/src/components/Collections/PairCollectionCreatorModal.js b/client/src/components/Collections/PairCollectionCreatorModal.js
deleted file mode 100644
index 1cfa2a64dc7195282576ef7dcc8a3283e2aa0b58..0000000000000000000000000000000000000000
--- a/client/src/components/Collections/PairCollectionCreatorModal.js
+++ /dev/null
@@ -1,43 +0,0 @@
-import _l from "utils/localization";
-import Vue from "vue";
-
-import { collectionCreatorModalSetup } from "./common/modal";
-
-function pairCollectionCreatorModal(elements, options) {
-    options = options || {};
-    options.title = _l("Create a collection from a pair of datasets");
-    const { promise, showEl } = collectionCreatorModalSetup(options);
-    return import(/* webpackChunkName: "PairCollectionCreator" */ "./PairCollectionCreator.vue").then((module) => {
-        var pairCollectionCreatorInstance = Vue.extend(module.default);
-        var vm = document.createElement("div");
-        showEl(vm);
-        new pairCollectionCreatorInstance({
-            propsData: {
-                initialElements: elements,
-                creationFn: options.creationFn,
-                oncancel: options.oncancel,
-                oncreate: options.oncreate,
-                defaultHideSourceItems: options.defaultHideSourceItems,
-            },
-        }).$mount(vm);
-        return promise;
-    });
-}
-function createPairCollection(contents, defaultHideSourceItems = true) {
-    var elements = contents.toJSON();
-    var promise = pairCollectionCreatorModal(elements, {
-        defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function (elements, name, hideSourceItems) {
-            elements = [
-                { name: "forward", src: elements[0].src || "hda", id: elements[0].id },
-                { name: "reverse", src: elements[1].src || "hda", id: elements[1].id },
-            ];
-            return contents.createHDCA(elements, "paired", name, hideSourceItems);
-        },
-    });
-    return promise;
-}
-export default {
-    pairCollectionCreatorModal: pairCollectionCreatorModal,
-    createPairCollection: createPairCollection,
-};
diff --git a/client/src/components/Collections/PairedElementView.vue b/client/src/components/Collections/PairedElementView.vue
index 364832a22db231b9256a79a482db2fc488257359..42cd1d9e8af0415eed9532ee29a08e57128243f4 100644
--- a/client/src/components/Collections/PairedElementView.vue
+++ b/client/src/components/Collections/PairedElementView.vue
@@ -1,69 +1,58 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faUnlink } from "@fortawesome/free-solid-svg-icons";
+import { faArrowLeft, faArrowRight, faUnlink } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { onMounted, ref, watch } from "vue";
+import { BButton } from "bootstrap-vue";
+import { ref, watch } from "vue";
 
+import type { HDASummary } from "@/api";
 import localize from "@/utils/localization";
 
 import ClickToEdit from "@/components/Collections/common/ClickToEdit.vue";
 
-library.add(faUnlink);
-
 interface Props {
-    // TODO: Define the type of the pair prop
     pair: {
         name: string;
-        forward: { name: string };
-        reverse: { name: string };
+        forward: HDASummary;
+        reverse: HDASummary;
     };
-    unlinkFn: () => void;
 }
 
 const props = defineProps<Props>();
 
 const emit = defineEmits<{
     (event: "onPairRename", name: string): void;
+    (event: "onUnpair"): void;
 }>();
 
-const name = ref("");
-
-watch(
-    () => props.pair,
-    () => {
-        name.value = props.pair.name;
-    }
-);
-
-watch(name, () => {
-    emit("onPairRename", name.value);
-});
+const elementName = ref(props.pair.name);
 
-onMounted(() => {
-    name.value = props.pair.name;
+watch(elementName, () => {
+    emit("onPairRename", elementName.value);
 });
 </script>
 
 <template>
-    <div>
-        <li class="dataset paired">
+    <li class="d-flex align-items-center justify-content-between">
+        <div class="dataset paired w-100">
             <span class="forward-dataset-name flex-column">
                 {{ pair.forward.name }}
+                <FontAwesomeIcon :icon="faArrowRight" fixed-width />
             </span>
 
             <span class="pair-name-column flex-column">
                 <span class="pair-name">
-                    <ClickToEdit v-model="name" :title="localize('Click to rename')" />
+                    <ClickToEdit v-model="elementName" :title="localize('Click to rename')" />
                 </span>
             </span>
 
             <span class="reverse-dataset-name flex-column">
+                <FontAwesomeIcon :icon="faArrowLeft" fixed-width />
                 {{ pair.reverse.name }}
             </span>
-        </li>
+        </div>
 
-        <button class="unpair-btn" @click="unlinkFn">
+        <BButton class="unpair-btn" variant="link" @click="emit('onUnpair')">
             <FontAwesomeIcon :icon="faUnlink" :title="localize('Unpair')" />
-        </button>
-    </div>
+        </BButton>
+    </li>
 </template>
diff --git a/client/src/components/Collections/PairedListCollectionCreator.test.js b/client/src/components/Collections/PairedListCollectionCreator.test.js
index a798ba2f8f1746930cb14155d6c78bc207352c58..d62270b0433594b24f57ccab34b7d7ec6f8a83f4 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.test.js
+++ b/client/src/components/Collections/PairedListCollectionCreator.test.js
@@ -1,48 +1,69 @@
+import { createTestingPinia } from "@pinia/testing";
 import DATA from "@tests/test-data/paired-collection-creator.data.js";
 import { mount, shallowMount } from "@vue/test-utils";
 import PairedListCollectionCreator from "components/Collections/PairedListCollectionCreator";
+import flushPromises from "flush-promises";
+import Vue from "vue";
+
+import { useServerMock } from "@/api/client/__mocks__";
+
+// Mock the localize directive
+// (otherwise we get: [Vue warn]: Failed to resolve directive: localize)
+Vue.directive("localize", {
+    bind(el, binding) {
+        el.textContent = binding.value;
+    },
+});
+
+const { server, http } = useServerMock();
 
 describe("PairedListCollectionCreator", () => {
     let wrapper;
+    const pinia = createTestingPinia();
+
+    beforeEach(() => {
+        server.use(
+            http.get("/api/configuration", ({ response }) => {
+                return response(200).json({
+                    chunk_upload_size: 100,
+                    file_sources_configured: true,
+                });
+            })
+        );
+    });
+
+    it("performs an autopair on startup if we have a selection", async () => {
+        // Kind of deprecated because we are never using `props.fromSelection: true` anywhere
 
-    it("autopairs the dataset", async () => {
         wrapper = shallowMount(PairedListCollectionCreator, {
             propsData: {
+                historyId: "history_id",
                 initialElements: DATA._1,
-                creationFn: () => {
-                    return;
-                },
-                oncreate: () => {
-                    return;
-                },
-                oncancel: () => {
-                    return;
-                },
-                hideSourceItems: false,
+                fromSelection: true,
             },
+            pinia,
         });
-        await wrapper.vm.$nextTick();
+
+        await flushPromises();
         // Autopair is called on startup
-        expect(wrapper.findAll("li.dataset unpaired").length == 0).toBeTruthy();
+        const pairsCountDisplay = wrapper.find('[data-description="number of pairs"]');
+        expect(pairsCountDisplay.text()).toContain(`${DATA._1.length / 2} pairs`);
     });
 
-    it("selects the correct name for an auotpair", async () => {
+    it("selects the correct name for an autopair", async () => {
         wrapper = mount(PairedListCollectionCreator, {
             propsData: {
+                historyId: "history_id",
                 initialElements: DATA._2,
-                creationFn: () => {
-                    return;
-                },
-                oncreate: () => {
-                    return;
-                },
-                oncancel: () => {
-                    return;
-                },
-                hideSourceItems: false,
+            },
+            pinia,
+            stubs: {
+                FontAwesomeIcon: true,
+                BPopover: true,
             },
         });
-        await wrapper.vm.$nextTick();
+
+        await flushPromises();
         //change filter to .1.fastq/.2.fastq
         await wrapper.find("div.forward-unpaired-filter > div.input-group-append > button").trigger("click");
         await wrapper
@@ -56,7 +77,7 @@ describe("PairedListCollectionCreator", () => {
         const reverseFilter = wrapper.find("div.reverse-unpaired-filter > input").element.value;
         expect(reverseFilter).toBe(".2.fastq");
         // click Autopair
-        await wrapper.find("a.autopair-link").trigger("click");
+        await wrapper.find(".autopair-link").trigger("click");
         //assert pair-name longer name
         const pairname = wrapper.find("span.pair-name");
         expect(pairname.text()).toBe("DP134_1_FS_PSII_FSB_42C_A10");
@@ -65,20 +86,17 @@ describe("PairedListCollectionCreator", () => {
     it("removes the period from autopair name", async () => {
         wrapper = mount(PairedListCollectionCreator, {
             propsData: {
+                historyId: "history_id",
                 initialElements: DATA._3,
-                creationFn: () => {
-                    return;
-                },
-                oncreate: () => {
-                    return;
-                },
-                oncancel: () => {
-                    return;
-                },
-                hideSourceItems: false,
+            },
+            pinia,
+            stubs: {
+                FontAwesomeIcon: true,
+                BPopover: true,
             },
         });
-        await wrapper.vm.$nextTick();
+
+        await flushPromises();
         //change filter to .1.fastq/.2.fastq
         await wrapper.find("div.forward-unpaired-filter > div.input-group-append > button").trigger("click");
         await wrapper
@@ -92,7 +110,7 @@ describe("PairedListCollectionCreator", () => {
         const reverseFilter = wrapper.find("div.reverse-unpaired-filter > input").element.value;
         expect(reverseFilter).toBe(".2.fastq");
         // click Autopair
-        await wrapper.find("a.autopair-link").trigger("click");
+        await wrapper.find(".autopair-link").trigger("click");
         //assert pair-name longer name
         const pairname = wrapper.find("span.pair-name");
         expect(pairname.text()).toBe("UII_moo_1");
@@ -101,20 +119,17 @@ describe("PairedListCollectionCreator", () => {
     it("autopairs correctly when filters are typed in", async () => {
         wrapper = mount(PairedListCollectionCreator, {
             propsData: {
+                historyId: "history_id",
                 initialElements: DATA._4,
-                creationFn: () => {
-                    return;
-                },
-                oncreate: () => {
-                    return;
-                },
-                oncancel: () => {
-                    return;
-                },
-                hideSourceItems: false,
+            },
+            pinia,
+            stubs: {
+                FontAwesomeIcon: true,
+                BPopover: true,
             },
         });
-        await wrapper.vm.$nextTick();
+
+        await flushPromises();
         //change filter to _R1/_R2
         await wrapper.find("div.forward-unpaired-filter > input").setValue("_R1");
         await wrapper.find("div.reverse-unpaired-filter > input").setValue("_R2");
@@ -125,7 +140,7 @@ describe("PairedListCollectionCreator", () => {
         const reverseFilter = wrapper.find("div.reverse-unpaired-filter > input").element.value;
         expect(reverseFilter).toBe("_R2");
         // click Autopair
-        await wrapper.find("a.autopair-link").trigger("click");
+        await wrapper.find(".autopair-link").trigger("click");
         //assert all pairs matched
         expect(wrapper.findAll("li.dataset unpaired").length == 0).toBeTruthy();
     });
diff --git a/client/src/components/Collections/PairedListCollectionCreator.vue b/client/src/components/Collections/PairedListCollectionCreator.vue
index c699c0de70771d9c3227d5265c8c6cd5c6d5d7b7..6fd9f9be8259e283f6b5b38ef1d2dfa1e89d9a24 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.vue
+++ b/client/src/components/Collections/PairedListCollectionCreator.vue
@@ -1,1044 +1,1336 @@
+<script setup lang="ts">
+import {
+    faAngleDown,
+    faAngleUp,
+    faExclamationCircle,
+    faLink,
+    faTimes,
+    faUnlink,
+} from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BButton, BButtonGroup, BCard, BCardBody, BCardHeader } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+import draggable from "vuedraggable";
+
+import type { HDASummary, HistoryItemSummary } from "@/api";
+import { useConfirmDialog } from "@/composables/confirmDialog";
+import { Toast } from "@/composables/toast";
+import STATES from "@/mvc/dataset/states";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
+// import levenshteinDistance from '@/utils/levenshtein';
+import localize from "@/utils/localization";
+import { naturalSort } from "@/utils/naturalSort";
+
+import type { DatasetPair } from "../History/adapters/buildCollectionModal";
+
+import Heading from "../Common/Heading.vue";
+import PairedElementView from "./PairedElementView.vue";
+import UnpairedDatasetElementView from "./UnpairedDatasetElementView.vue";
+import CollectionCreator from "@/components/Collections/common/CollectionCreator.vue";
+
+const NOT_VALID_ELEMENT_MSG: string = localize("is not a valid element for this collection");
+const COMMON_FILTERS = {
+    illumina: ["_1", "_2"],
+    Rs: ["_R1", "_R2"],
+    dot12s: [".1.fastq", ".2.fastq"],
+};
+const DEFAULT_FILTER: keyof typeof COMMON_FILTERS = "illumina";
+const MATCH_PERCENTAGE = 0.99;
+
+// Titles and help text
+const CHOOSE_FILTER_TITLE = localize("Choose from common filters");
+const FILTER_TEXT_PLACEHOLDER = localize("Filter text");
+const FILTER_TEXT_TITLE = localize("Use this box to filter elements, using simple matching or regular expressions.");
+const ERROR_TEXT = localize("There was a problem creating the collection.");
+const INVALID_HEADER = localize("The following selections could not be included due to problems:");
+const ALL_INVALID_ELEMENTS_PART_ONE = localize("At least two elements are needed for the collection. You may need to");
+const CANCEL_TEXT = localize("Cancel");
+
+interface Props {
+    historyId: string;
+    initialElements: HistoryItemSummary[];
+    defaultHideSourceItems?: boolean;
+    fromSelection?: boolean;
+    extensions?: string[];
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "clicked-create", workingElements: DatasetPair[], collectionName: string, hideSourceItems: boolean): void;
+    (e: "on-cancel"): void;
+}>();
+
+// Titles and help text computed
+const noElementsHeader = props.fromSelection ? localize("No elements selected") : localize("No elements available");
+const allInvalidElementsPartTwo = props.fromSelection
+    ? localize("and reselect new elements.")
+    : localize("and change your current history or upload valid datasets for this collection.");
+
+// Flags
+const state = ref<"build" | "error" | "duplicates">("build");
+const hideSourceItems = ref(props.defaultHideSourceItems || false);
+const autoPairsPossible = ref(true);
+const twoPassAutoPairing = ref(true);
+const removeExtensions = ref(true);
+const firstAutoPairDone = ref(false);
+const showPairingSection = ref(true);
+
+// Elements
+const workingElements = ref<HDASummary[]>([]);
+const invalidElements = ref<string[]>([]);
+const generatedPairs = ref<DatasetPair[]>([]);
+const selectedForwardElement = ref<HDASummary | null>(null);
+const selectedReverseElement = ref<HDASummary | null>(null);
+const atLeastOnePair = ref(true);
+
+// Filters
+const forwardFilter = ref(COMMON_FILTERS[DEFAULT_FILTER][0] || "");
+const reverseFilter = ref(COMMON_FILTERS[DEFAULT_FILTER][1] || "");
+const hasFilter = computed(() => forwardFilter.value || reverseFilter.value);
+
+// Autopairing
+const strategy = ref(autoPairLCS);
+const duplicatePairNames = ref<string[]>([]);
+
+const canClearFilters = computed(() => {
+    return forwardFilter.value || reverseFilter.value;
+});
+
+const canAutoPair = computed(() => {
+    return forwardFilter.value && reverseFilter.value && pairableElements.value.length > 0;
+});
+
+const forwardElements = computed<HDASummary[]>(() => {
+    return filterElements(workingElements.value, forwardFilter.value);
+});
+const reverseElements = computed<HDASummary[]>(() => {
+    return filterElements(workingElements.value, reverseFilter.value);
+});
+const pairableElements = computed(() => {
+    const pairable: DatasetPair[] = [];
+    forwardElements.value.forEach((forwardElement, index) => {
+        const reverseElement = reverseElements.value[index];
+        if (!!reverseElement && !!forwardElement && forwardElement.id != reverseElement.id) {
+            pairable.push({
+                forward: forwardElement,
+                reverse: reverseElement,
+                name: _guessNameForPair(forwardElement, reverseElement),
+            });
+        }
+    });
+    return pairable;
+});
+const autoPairButton = computed(() => {
+    let variant;
+    let icon;
+    let text;
+    if (!canAutoPair.value) {
+        variant = "secondary";
+        icon = faLink;
+        text = localize("Specify simple filters to divide datasets into forward and reverse reads for pairing.");
+    } else if (!firstAutoPairDone.value && pairableElements.value.length > 0) {
+        variant = "primary";
+        icon = faExclamationCircle;
+        text = localize("Click to auto-pair datasets based on the current filters");
+    } else if (pairableElements.value.length > 0) {
+        variant = "secondary";
+        icon = faLink;
+        text = localize("Auto-pair possible based on current filters");
+    } else {
+        variant = "secondary";
+        icon = faLink;
+        text = localize("Click to attempt auto-pairing datasets");
+    }
+    return { variant, icon, text };
+});
+const numOfUnpairedForwardElements = computed(() => {
+    return forwardElements.value.length;
+});
+const numOfFilteredOutForwardElements = computed(() => {
+    return workingElements.value.length - numOfUnpairedForwardElements.value;
+});
+const numOfUnpairedReverseElements = computed(() => {
+    return reverseElements.value.length;
+});
+const numOfFilteredOutReverseElements = computed(() => {
+    return workingElements.value.length - numOfUnpairedReverseElements.value;
+});
+const numOfPairs = computed(() => {
+    return generatedPairs.value.length;
+});
+const returnInvalidElementsLength = computed(() => {
+    return invalidElements.value.length > 0;
+});
+const returnInvalidElements = computed(() => {
+    return invalidElements.value;
+});
+const allElementsAreInvalid = computed(() => {
+    return props.initialElements.length === invalidElements.value.length;
+});
+const noElementsSelected = computed(() => {
+    return props.initialElements.length === 0;
+});
+const tooFewElementsSelected = computed(() => {
+    return workingElements.value.length < 2 && generatedPairs.value.length === 0;
+});
+// TODO: Include in the template
+// const showDuplicateError = computed(() => {
+//     return duplicatePairNames.value.length > 0;
+// });
+
+const noUnpairedElementsDisplayed = computed(() => {
+    return numOfUnpairedForwardElements.value + numOfUnpairedReverseElements.value === 0;
+});
+
+// variables for datatype mapping and then filtering
+const datatypesMapperStore = useDatatypesMapperStore();
+const datatypesMapper = computed(() => datatypesMapperStore.datatypesMapper);
+
+/** Are we filtering by datatype? */
+const filterExtensions = computed(() => !!datatypesMapper.value && !!props.extensions?.length);
+
+function removeExtensionsToggle() {
+    removeExtensions.value = !removeExtensions.value;
+    generatedPairs.value.forEach((pair, index) => {
+        pair.name = _guessNameForPair(pair.forward, pair.reverse, removeExtensions.value);
+    });
+}
+
+watch(
+    () => props.initialElements,
+    () => {
+        // initialize; and then for any new/removed elements, sync working elements
+        _elementsSetUp();
+    },
+    { immediate: true }
+);
+
+/** Set up main data */
+function _elementsSetUp() {
+    // a list of invalid elements and the reasons they aren't valid
+    invalidElements.value = [];
+    //TODO: handle fundamental problem of syncing DOM, views, and list here
+    // data for list in progress
+    workingElements.value = [];
+    //TODO: this should maybe be in it's own method as it will get called everytime selected array has two elements and dumps again.
+    // selectedDatasetElems = [];
+    initialFiltersSet();
+    // copy initial list, sort, // TODO: add ids if needed
+    // copy initial list, sort, add ids if needed
+    workingElements.value = JSON.parse(JSON.stringify(props.initialElements.slice(0)));
+
+    // TODO: Here, we do what we do in other 2 creators; we check the already built pairs
+    //       and sync them with the workingElements, ensuring that there aren't any elements
+    //       in built pairs that no longer exist in workingElements
+
+    // _ensureElementIds();
+    _validateElements();
+    _sortInitialList();
+    // attempt to autopair
+    if (props.fromSelection) {
+        autoPair();
+    }
+}
+
+function initialFiltersSet() {
+    let illumina = 0;
+    let dot12s = 0;
+    let Rs = 0;
+    //should we limit the forEach? What if there are 1000s of elements?
+    props.initialElements.forEach((element) => {
+        if (element.name?.includes(".1.fastq") || element.name?.includes(".2.fastq")) {
+            dot12s++;
+        } else if (element.name?.includes("_R1") || element.name?.includes("_R2")) {
+            Rs++;
+        } else if (element.name?.includes("_1") || element.name?.includes("_2")) {
+            illumina++;
+        }
+    });
+    // if we cannot filter don't set an initial filter and hide all the data
+    if (illumina == 0 && dot12s == 0 && Rs == 0) {
+        forwardFilter.value = "";
+        reverseFilter.value = "";
+    } else if (illumina > dot12s && illumina > Rs) {
+        changeFilters("illumina");
+    } else if (dot12s > illumina && dot12s > Rs) {
+        changeFilters("dot12s");
+    } else if (Rs > illumina && Rs > dot12s) {
+        changeFilters("Rs");
+    } else {
+        changeFilters("illumina");
+    }
+}
+
+// TODO: Don't know if this is really necessary
+// function _ensureElementIds() {
+//     workingElements.value.forEach((element) => {
+//         if (!Object.prototype.hasOwnProperty.call(element, "id")) {
+//             console.warn("Element missing id", element);
+//         }
+//     });
+
+//     return workingElements.value;
+// }
+
+function _validateElements() {
+    workingElements.value = workingElements.value.filter((element) => {
+        var problem = _isElementInvalid(element);
+
+        if (problem) {
+            invalidElements.value.push(element.name + "  " + problem);
+        }
+
+        return !problem;
+    });
+    return workingElements.value;
+}
+
+function _isElementInvalid(element: HistoryItemSummary) {
+    if (element.history_content_type === "dataset_collection") {
+        return localize("is a collection, this is not allowed");
+    }
+    const validState = STATES.VALID_INPUT_STATES.includes(element.state as string);
+    if (!validState) {
+        return localize("has errored, is paused, or is not accessible");
+    }
+    if (element.deleted || element.purged) {
+        return localize("has been deleted or purged");
+    }
+
+    // is the element's extension not a subtype of any of the required extensions?
+    if (
+        filterExtensions.value &&
+        element.extension &&
+        !datatypesMapper.value?.isSubTypeOfAny(element.extension, props.extensions!)
+    ) {
+        return localize(`has an invalid format: ${element.extension}`);
+    }
+    return null;
+}
+
+function _sortInitialList() {
+    workingElements.value.sort((a, b) => naturalSort(a.name || "", b.name || ""));
+}
+
+function filterElements(elements: HDASummary[], filterText: string) {
+    return elements.filter((e) => filterElement(e, filterText));
+}
+
+function filterElement(element: HDASummary, filterText: string) {
+    return filterText == "" || new RegExp(filterText).test(element.name || "");
+}
+
+function forwardElementSelected(e: HDASummary) {
+    if (selectedForwardElement.value == null || selectedForwardElement.value.id != e.id) {
+        selectedForwardElement.value = e;
+    } else {
+        selectedForwardElement.value = null;
+    }
+    if (
+        selectedForwardElement.value &&
+        selectedReverseElement.value &&
+        selectedReverseElement.value != selectedForwardElement.value
+    ) {
+        _pair(selectedForwardElement.value, selectedReverseElement.value);
+    }
+}
+
+function reverseElementSelected(e: HDASummary) {
+    if (selectedReverseElement.value == null || selectedReverseElement.value.id != e.id) {
+        selectedReverseElement.value = e;
+    } else {
+        selectedReverseElement.value = null;
+    }
+    if (
+        selectedForwardElement.value &&
+        selectedReverseElement.value &&
+        selectedReverseElement.value != selectedForwardElement.value
+    ) {
+        _pair(selectedForwardElement.value, selectedReverseElement.value);
+    }
+}
+
+// ------------------------------------------------------- pairing / unpairing
+/**
+ * Create a pair from fwd and rev, removing them from unpaired,
+ * and placing the new pair in paired
+ */
+function _pair(fwd: HDASummary, rev: HDASummary, options: { name?: string } = {}) {
+    const pair = _createPair(fwd, rev, options.name);
+    generatedPairs.value.push(pair);
+    removePairFromUnpaired(fwd, rev);
+    // if (!options.silent) {
+    //     emit("pair:new", pair);
+    // }
+    return pair;
+}
+
+function removePairFromUnpaired(fwd: HDASummary, rev: HDASummary) {
+    workingElements.value.splice(workingElements.value.indexOf(rev), 1);
+    workingElements.value.splice(workingElements.value.indexOf(fwd), 1);
+    selectedForwardElement.value = null;
+    selectedReverseElement.value = null;
+}
+
+/**
+ * Create a pair Object from fwd and rev, adding the name attribute
+ * (will guess if not given)
+ */
+function _createPair(fwd: HDASummary, rev: HDASummary, name?: string) {
+    // ensure existance and don't pair something with itself
+    if (!(fwd && rev) || fwd === rev) {
+        throw new Error(`Bad pairing: ${[JSON.stringify(fwd), JSON.stringify(rev)]}`);
+    }
+    name = name || _guessNameForPair(fwd, rev);
+    return { forward: fwd, name: name, reverse: rev };
+}
+
+/** Try to find a good pair name for the given fwd and rev datasets */
+function _guessNameForPair(fwd: HDASummary, rev: HDASummary, willRemoveExtensions?: boolean) {
+    willRemoveExtensions = willRemoveExtensions ? willRemoveExtensions : removeExtensions.value;
+    let fwdName = fwd.name;
+    let revName = rev.name;
+    const fwdNameFilter = fwdName?.replace(new RegExp(forwardFilter.value || ""), "");
+    const revNameFilter = revName?.replace(new RegExp(reverseFilter.value || ""), "");
+    if (!fwdNameFilter || !revNameFilter || !fwdName || !revName) {
+        return `${fwdName} & ${revName}`;
+    }
+    let lcs = _naiveStartingAndEndingLCS(fwdNameFilter, revNameFilter);
+    // remove url prefix if files were uploaded by url
+    const lastSlashIndex = lcs.lastIndexOf("/");
+    if (lastSlashIndex > 0) {
+        const urlprefix = lcs.slice(0, lastSlashIndex + 1);
+        lcs = lcs.replace(urlprefix, "");
+    }
+
+    if (willRemoveExtensions) {
+        const lastDotIndex = lcs.lastIndexOf(".");
+        if (lastDotIndex > 0) {
+            const extension = lcs.slice(lastDotIndex, lcs.length);
+            lcs = lcs.replace(extension, "");
+            fwdName = fwdName.replace(extension, "");
+            revName = revName.replace(extension, "");
+        }
+    }
+    if (lcs.endsWith(".") || lcs.endsWith("_")) {
+        lcs = lcs.substring(0, lcs.length - 1);
+    }
+    return lcs || `${fwdName} & ${revName}`;
+}
+
+function clickAutopair() {
+    // Unselect any selected elements
+    selectedForwardElement.value = null;
+    selectedReverseElement.value = null;
+    autoPair();
+
+    workingElements.value = workingElements.value.filter((e) => {
+        return !generatedPairs.value.some((pair) => pair.forward.id === e.id || pair.reverse.id === e.id);
+    });
+}
+
+function clickUnpair(pair: DatasetPair) {
+    return _unpair(pair);
+}
+
+function clickClearFilters() {
+    forwardFilter.value = "";
+    reverseFilter.value = "";
+}
+
+function splitByFilter() {
+    const filters = [new RegExp(forwardFilter.value), new RegExp(reverseFilter.value)];
+    const split: [HDASummary[], HDASummary[]] = [[], []];
+    workingElements.value.forEach((e) => {
+        filters.forEach((filter, i) => {
+            if (e.name && filter.test(e.name)) {
+                split[i]?.push(e);
+            }
+        });
+    });
+    return split;
+}
+// ===========================================================================
+
+// -------------------------------------------------------------- auto pairing
+/** Autopair by exact match */
+function autoPairSimple(params: { listA: HDASummary[]; listB: HDASummary[] }) {
+    return autoPairFnBuilder({
+        match: (params) => {
+            params = params || {};
+            if (params.matchTo === params.possible) {
+                return {
+                    index: params.index,
+                    score: 1.0,
+                };
+            }
+            return params.bestMatch;
+        },
+        scoreThreshold: 0.6,
+    })(params);
+}
+
+// TODO: Currently unused?
+/** Autopair by levenstein distance */
+// function autoPairLevenshtein(params: { listA: HDASummary[]; listB: HDASummary[] }) {
+//     return autoPairFnBuilder({
+//         match: (params) => {
+//             params = params || {};
+//             const distance = levenshteinDistance(params.matchTo, params.possible);
+//             const score = 1.0 - distance / Math.max(params.matchTo.length, params.possible.length);
+//             if (score > params.bestMatch.score) {
+//                 return {
+//                     index: params.index,
+//                     score: score,
+//                 };
+//             }
+//             return params.bestMatch;
+//         },
+//         scoreThreshold: MATCH_PERCENTAGE,
+//     })(params);
+// }
+
+/** Autopair by longest common substrings scoring */
+function autoPairLCS(params: { listA: HDASummary[]; listB: HDASummary[] }) {
+    return autoPairFnBuilder({
+        match: (params) => {
+            params = params || {};
+            const match = _naiveStartingAndEndingLCS(params.matchTo, params.possible).length;
+            const score = match / Math.max(params.matchTo.length, params.possible.length);
+            if (score > params.bestMatch.score) {
+                return {
+                    index: params.index,
+                    score: score,
+                };
+            }
+            return params.bestMatch;
+        },
+        scoreThreshold: MATCH_PERCENTAGE,
+    })(params);
+}
+
+/**
+ * Two passes to automatically create pairs:
+ * use both simpleAutoPair, then the fn mentioned in strategy
+ */
+function autoPair(localStrategy?: (params: { listA: HDASummary[]; listB: HDASummary[] }) => DatasetPair[]) {
+    let split = splitByFilter();
+    let paired: DatasetPair[] = [];
+    if (twoPassAutoPairing.value) {
+        const simplePaired = autoPairSimple({
+            listA: split[0],
+            listB: split[1],
+        });
+        paired = simplePaired ? simplePaired : paired;
+        split = splitByFilter();
+    }
+
+    // then try the remainder with something less strict
+    localStrategy = localStrategy || strategy.value;
+    split = splitByFilter();
+    const pairedStrategy = localStrategy({
+        listA: split[0],
+        listB: split[1],
+    });
+    paired = pairedStrategy ? paired.concat(pairedStrategy) : paired;
+    autoPairsPossible.value = paired.length > 0;
+    firstAutoPairDone.value = true;
+    return paired;
+}
+
+/** Add a dataset to the unpaired list in it's proper order */
+function _addToUnpaired(dataset: HDASummary) {
+    /** Currently, unpaired is natural sorted by name, use binary search to find insertion point */
+    function binSearchSortedIndex(low: number, hi: number) {
+        if (low === hi) {
+            return low;
+        }
+
+        let mid = Math.floor((hi - low) / 2) + low;
+
+        const elementAtPoint = workingElements.value[mid];
+
+        const compared = naturalSort(dataset.name || "", elementAtPoint?.name || "");
+
+        if (compared < 0) {
+            return binSearchSortedIndex(low, mid);
+        } else if (compared > 0) {
+            return binSearchSortedIndex(mid + 1, hi);
+        } else if (!elementAtPoint) {
+            return mid;
+        }
+        // walk the equal to find the last // TODO: Investigate this, is this correct?
+        if (elementAtPoint?.name === dataset.name) {
+            mid++;
+        }
+        return mid;
+    }
+
+    workingElements.value.splice(binSearchSortedIndex(0, workingElements.value.length), 0, dataset);
+}
+
+/**
+ * Unpair a pair, removing it from paired, and adding the fwd,rev
+ * datasets back into unpaired
+ */
+function _unpair(pair: DatasetPair) {
+    if (!pair) {
+        throw new Error(`Bad pair: ${JSON.stringify(pair)}`);
+    }
+    generatedPairs.value.splice(generatedPairs.value.indexOf(pair), 1);
+    _addToUnpaired(pair.forward);
+    _addToUnpaired(pair.reverse);
+
+    return pair;
+}
+
+/** Unpair all paired datasets */
+function unpairAll() {
+    const pairs = [];
+    while (generatedPairs.value.length) {
+        if (generatedPairs.value[0]) {
+            pairs.push(_unpair(generatedPairs.value[0]));
+        }
+
+        // pairs.push(_unpair(this.generatedPairs[0], { silent: true }));
+    }
+}
+// ===========================================================================
+
+/** Returns an autopair function that uses the provided options.match function */
+function autoPairFnBuilder(options: {
+    match: (params: {
+        matchTo: string;
+        possible: string;
+        index: number;
+        bestMatch: { score: number; index: number };
+    }) => { score: number; index: number };
+    createPair?: (params: {
+        listA: HDASummary[];
+        indexA: number;
+        listB: HDASummary[];
+        indexB: number;
+    }) => DatasetPair | undefined;
+    preprocessMatch?: (params: {
+        matchTo: HDASummary;
+        possible: HDASummary;
+        index: number;
+        bestMatch: { score: number; index: number };
+    }) => { matchTo: string; possible: string; index: number; bestMatch: { score: number; index: number } };
+    scoreThreshold?: number;
+}) {
+    options = options || {};
+    options.createPair =
+        options.createPair ||
+        function _defaultCreatePair(params) {
+            params = params || {};
+            const a = params.listA.splice(params.indexA, 1)[0];
+            const b = params.listB.splice(params.indexB, 1)[0];
+            if (!a || !b) {
+                return undefined;
+            }
+            const aInBIndex = params.listB.indexOf(a);
+            const bInAIndex = params.listA.indexOf(b);
+            if (aInBIndex !== -1) {
+                params.listB.splice(aInBIndex, 1);
+            }
+            if (bInAIndex !== -1) {
+                params.listA.splice(bInAIndex, 1);
+            }
+            // return _pair(a, b, { silent: true });
+            return _pair(a, b);
+        };
+    // compile these here outside of the loop
+    let _regexps: RegExp[] = [];
+    function getRegExps() {
+        if (!_regexps.length) {
+            _regexps = [new RegExp(forwardFilter.value), new RegExp(reverseFilter.value)];
+        }
+        return _regexps;
+    }
+    // mangle params as needed
+    options.preprocessMatch =
+        options.preprocessMatch ||
+        function _defaultPreprocessMatch(params) {
+            const regexps = getRegExps();
+            return Object.assign(params, {
+                matchTo: params.matchTo.name?.replace(regexps[0] || "", ""),
+                possible: params.possible.name?.replace(regexps[1] || "", ""),
+                index: params.index,
+                bestMatch: params.bestMatch,
+            });
+        };
+
+    return function _strategy(params: { listA: HDASummary[]; listB: HDASummary[] }) {
+        params = params || {};
+        const listA = params.listA;
+        const listB = params.listB;
+        let indexA = 0;
+        let indexB;
+
+        let bestMatch = {
+            score: 0.0,
+            index: -1,
+        };
+
+        const paired = [];
+        while (indexA < listA.length) {
+            const matchTo = listA[indexA];
+            bestMatch.score = 0.0;
+
+            if (!matchTo) {
+                continue;
+            }
+            for (indexB = 0; indexB < listB.length; indexB++) {
+                const possible = listB[indexB] as HDASummary;
+                if (listA[indexA] !== listB[indexB]) {
+                    bestMatch = options.match(
+                        options.preprocessMatch!({
+                            matchTo: matchTo,
+                            possible: possible,
+                            index: indexB,
+                            bestMatch: bestMatch,
+                        })
+                    );
+                    if (bestMatch.score === 1.0) {
+                        break;
+                    }
+                }
+            }
+            const scoreThreshold = options.scoreThreshold ? options.scoreThreshold : MATCH_PERCENTAGE;
+            if (bestMatch.score >= scoreThreshold) {
+                const createdPair = options.createPair!({
+                    listA: listA,
+                    indexA: indexA,
+                    listB: listB,
+                    indexB: bestMatch.index,
+                });
+                if (createdPair) {
+                    paired.push(createdPair);
+                }
+            } else {
+                indexA += 1;
+            }
+            if (!listA.length || !listB.length) {
+                return paired;
+            }
+        }
+        return paired;
+    };
+}
+
+function changeFilters(filter: keyof typeof COMMON_FILTERS) {
+    forwardFilter.value = COMMON_FILTERS[filter][0] as string;
+    reverseFilter.value = COMMON_FILTERS[filter][1] as string;
+}
+
+function addUploadedFiles(files: HDASummary[]) {
+    // Any uploaded files are added to workingElements in _elementsSetUp
+    // The user will have to manually select the files to add them to the pair
+
+    // Check for validity of uploads
+    files.forEach((file) => {
+        const problem = _isElementInvalid(file);
+        if (problem) {
+            const invalidMsg = `${file.hid}: ${file.name} ${problem} and ${NOT_VALID_ELEMENT_MSG}`;
+            invalidElements.value.push(invalidMsg);
+            Toast.error(invalidMsg, localize("Uploaded item invalid for pair"));
+        }
+    });
+}
+
+const { confirm } = useConfirmDialog();
+
+async function clickedCreate(collectionName: string) {
+    checkForDuplicates();
+    atLeastOnePair.value = generatedPairs.value.length > 0;
+
+    let confirmed = false;
+    if (!atLeastOnePair.value) {
+        confirmed = await confirm("Are you sure you want to create a list with no pairs?", {
+            title: "Create an empty list of pairs",
+            okTitle: "Create",
+            okVariant: "primary",
+        });
+    }
+
+    if (state.value == "build" && (atLeastOnePair.value || confirmed)) {
+        emit("clicked-create", generatedPairs.value, collectionName, hideSourceItems.value);
+    }
+}
+
+function checkForDuplicates() {
+    const existingPairNames: Record<string, boolean> = {};
+    duplicatePairNames.value = [];
+    let valid = true;
+    generatedPairs.value.forEach((pair) => {
+        if (Object.prototype.hasOwnProperty.call(existingPairNames, pair.name)) {
+            valid = false;
+            duplicatePairNames.value.push(pair.name);
+        }
+        existingPairNames[pair.name] = true;
+    });
+    state.value = valid ? "build" : "duplicates";
+}
+
+// TODO: Where is this being used?
+// function stripExtension(name: string) {
+//     return name.includes(".") ? name.substring(0, name.lastIndexOf(".")) : name;
+// }
+
+/** Return the concat'd longest common prefix and suffix from two strings */
+function _naiveStartingAndEndingLCS(s1: string, s2: string) {
+    var fwdLCS = "";
+    var revLCS = "";
+    var i = 0;
+    var j = 0;
+    while (i < s1.length && i < s2.length) {
+        if (s1[i] !== s2[i]) {
+            break;
+        }
+        fwdLCS += s1[i];
+        i += 1;
+    }
+    if (i === s1.length) {
+        return s1;
+    }
+    if (i === s2.length) {
+        return s2;
+    }
+
+    i = s1.length - 1;
+    j = s2.length - 1;
+    while (i >= 0 && j >= 0) {
+        if (s1[i] !== s2[j]) {
+            break;
+        }
+        revLCS = [s1[i], revLCS].join("");
+        i -= 1;
+        j -= 1;
+    }
+    return fwdLCS + revLCS;
+}
+</script>
+
 <template>
     <div class="paired-list-collection-creator">
         <div v-if="state == 'error'">
-            <b-alert show variant="danger">
-                {{ errorText }}
-            </b-alert>
+            <BAlert show variant="danger">
+                {{ ERROR_TEXT }}
+            </BAlert>
         </div>
         <div v-else>
-            <div v-if="noElementsSelected">
-                <b-alert show variant="warning" dismissible>
-                    {{ noElementsHeader }}
-                    {{ allInvalidElementsPartOne }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ cancelText }}
-                    </a>
-                    {{ allInvalidElementsPartTwo }}
-                </b-alert>
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ l("Cancel") }}
-                    </button>
-                </div>
-            </div>
-            <div v-else-if="allElementsAreInvalid">
-                <b-alert show variant="warning" dismissible>
-                    {{ invalidHeader }}
+            <div v-if="fromSelection && returnInvalidElementsLength">
+                <BAlert show variant="warning" dismissible>
+                    {{ INVALID_HEADER }}
                     <ul>
                         <li v-for="problem in returnInvalidElements" :key="problem">
                             {{ problem }}
                         </li>
                     </ul>
-                    {{ allInvalidElementsPartOne }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ cancelText }}
-                    </a>
-                    {{ allInvalidElementsPartTwo }}
-                </b-alert>
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ l("Cancel") }}
-                    </button>
-                </div>
+                </BAlert>
+            </div>
+
+            <div v-if="!atLeastOnePair">
+                <BAlert show variant="warning" dismissible @dismissed="atLeastOnePair = true">
+                    {{ localize("At least one pair is needed for the list of pairs.") }}
+                    <span v-if="fromSelection">
+                        <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                            {{ localize("Cancel") }}
+                        </a>
+                        {{ localize("and reselect new elements.") }}
+                    </span>
+                </BAlert>
+            </div>
+
+            <div v-if="!autoPairsPossible">
+                <BAlert show variant="danger" dismissible @dismissed="autoPairsPossible = true">
+                    {{
+                        localize(
+                            "Could not automatically create any pairs from the given dataset names. You may want to choose or enter different filters and try auto-pairing again."
+                        )
+                    }}
+                    <span v-if="fromSelection">
+                        <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                            {{ CANCEL_TEXT }}
+                        </a>
+                        {{ allInvalidElementsPartTwo }}
+                    </span>
+                </BAlert>
             </div>
-            <div v-else-if="tooFewElementsSelected">
-                <div v-if="returnInvalidElementsLength">
-                    <b-alert show variant="warning" dismissible>
-                        {{ invalidHeader }}
-                        <ul>
-                            <li v-for="problem in returnInvalidElements" :key="problem">
-                                {{ problem }}
-                            </li>
-                        </ul>
-                    </b-alert>
-                </div>
-                <b-alert show variant="warning" dismissible>
-                    {{ allInvalidElementsPartOne }}
-                    <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                        {{ cancelText }}
-                    </a>
-                    {{ allInvalidElementsPartTwo }}
-                </b-alert>
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="oncancel">
-                        {{ l("Cancel") }}
-                    </button>
-                </div>
+
+            <div v-if="state == 'duplicates'">
+                <BAlert show variant="danger">
+                    {{
+                        localize("Collections cannot have duplicated names. The following list names are duplicated: ")
+                    }}
+                    <ul>
+                        <li v-for="name in duplicatePairNames" :key="name">{{ name }}</li>
+                    </ul>
+                    {{ localize("Please fix these duplicates and try again.") }}
+                </BAlert>
             </div>
-            <div v-else>
-                <div v-if="returnInvalidElementsLength">
-                    <b-alert show variant="warning" dismissible>
-                        {{ invalidHeader }}
-                        <ul>
-                            <li v-for="problem in returnInvalidElements" :key="problem">
-                                {{ problem }}
-                            </li>
-                        </ul>
-                    </b-alert>
-                </div>
-                <div v-if="!initialPairsPossible">
-                    <b-alert show variant="danger" dismissible>
+
+            <CollectionCreator
+                :oncancel="() => emit('on-cancel')"
+                :history-id="props.historyId"
+                :hide-source-items="hideSourceItems"
+                render-extensions-toggle
+                :extensions-toggle="removeExtensions"
+                :extensions="extensions"
+                collection-type="list:paired"
+                :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
+                @add-uploaded-files="addUploadedFiles"
+                @onUpdateHideSourceItems="hideSourceItems = $event"
+                @clicked-create="clickedCreate"
+                @remove-extensions-toggle="removeExtensionsToggle">
+                <template v-slot:help-content>
+                    <!-- TODO: Update help content for case where `fromSelection` is false -->
+                    <p>
                         {{
-                            l(
-                                "Could not automatically create any pairs from the given dataset names. You may want to choose or enter different filters and try auto-pairing again."
+                            localize(
+                                [
+                                    "This interface allows you to build a new Galaxy list of pairs. List of pairs are an ordered list of ",
+                                    "individual dataset paired together in their own paired collection (often forward and reverse reads). ",
+                                    "These lists can be passed to tools and workflows in order to have analyses done on each member of ",
+                                    "the entire group. This interface allows you to create such a list of paired datasets, choose which datasets are paired, ",
+                                    "and re-order the final collection.",
+                                ].join("")
                             )
                         }}
-                        <a class="cancel-text" href="javascript:void(0)" role="button" @click="oncancel">
-                            {{ cancelText }}
-                        </a>
-                        {{ allInvalidElementsPartTwo }}
-                    </b-alert>
-                </div>
-                <div v-if="state == 'duplicates'">
-                    <b-alert show variant="danger">
-                        {{ l("Collections cannot have duplicated names. The following list names are duplicated: ") }}
-                        <ul>
-                            <li v-for="name in duplicatePairNames" :key="name">{{ name }}</li>
-                        </ul>
-                        {{ l("Please fix these duplicates and try again.") }}
-                    </b-alert>
-                </div>
-                <collection-creator
-                    :oncancel="oncancel"
-                    :hide-source-items="hideSourceItems"
-                    :render-extensions-toggle="true"
-                    @onUpdateHideSourceItems="onUpdateHideSourceItems"
-                    @clicked-create="clickedCreate"
-                    @remove-extensions-toggle="removeExtensionsToggle">
-                    <template v-slot:help-content>
-                        <p>
+                    </p>
+                    <p>
+                        {{ localize("Unpaired datasets are shown in the") }}
+                        <i data-target=".unpaired-columns">
+                            {{ localize("unpaired section") }}
+                        </i>
+                        {{ "." }}
+                        {{ localize("Paired datasets are shown in the") }}
+                        <i data-target=".paired-columns">
+                            {{ localize("paired section") }}
+                        </i>
+                        {{ "." }}
+                    </p>
+                    <ul>
+                        {{
+                            localize("To pair datasets, you can:")
+                        }}
+                        <li>
+                            {{ localize("Click a dataset in the") }}
+                            <i data-target=".forward-column">
+                                {{ localize("forward column") }}
+                            </i>
+                            {{ localize("to select it then click a dataset in the") }}
+                            <i data-target=".reverse-column">
+                                {{ localize("reverse column") }}
+                            </i>
+                        </li>
+                        <li>
                             {{
-                                l(
-                                    [
-                                        "Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ",
-                                        "These collections can be passed to tools and workflows in order to have analyses done on each member of ",
-                                        "the entire group. This interface allows you to create a collection, choose which datasets are paired, ",
-                                        "and re-order the final collection.",
-                                    ].join("")
+                                localize(
+                                    "Click one of the Pair these datasets buttons in the middle column to pair the datasets in a particular row."
                                 )
                             }}
-                        </p>
-                        <p>
-                            {{ l("Unpaired datasets are shown in the") }}
-                            <i data-target=".unpaired-columns">
-                                {{ l("unpaired section") }}
+                        </li>
+                        <li>
+                            {{ localize("Click") }}
+                            <i data-target=".autopair-link">
+                                {{ localize("Auto-pair") }}
                             </i>
-                            {{ "." }}
-                            {{ l("Paired datasets are shown in the") }}
-                            <i data-target=".paired-columns">
-                                {{ l("paired section") }}
+                            {{ localize("to have your datasets automatically paired based on name.") }}
+                        </li>
+                    </ul>
+                    <ul>
+                        {{
+                            localize("You can filter what is shown in the unpaired sections by:")
+                        }}
+                        <li>
+                            {{ localize("Entering partial dataset names in either the ") }}
+                            <i data-target=".forward-unpaired-filter input">
+                                {{ localize("forward filter") }}
+                            </i>
+                            {{ localize("or ") }}
+                            <i data-target=".reverse-unpaired-filter input">
+                                {{ localize("reverse filter") }}
                             </i>
                             {{ "." }}
-                        </p>
-                        <ul>
-                            {{
-                                l("To pair datasets, you can:")
-                            }}
-                            <li>
-                                {{ l("Click a dataset in the") }}
-                                <i data-target=".forward-column">
-                                    {{ l("forward column") }}
-                                </i>
-                                {{ l("to select it then click a dataset in the") }}
-                                <i data-target=".reverse-column">
-                                    {{ l("reverse column") }}
-                                </i>
-                            </li>
-                            <li>
-                                {{
-                                    l(
-                                        "Click one of the Pair these datasets buttons in the middle column to pair the datasets in a particular row."
-                                    )
-                                }}
-                            </li>
-                            <li>
-                                {{ l("Click") }}
-                                <i data-target=".autopair-link">
-                                    {{ l("Auto-pair") }}
-                                </i>
-                                {{ l("to have your datasets automatically paired based on name.") }}
-                            </li>
-                        </ul>
-                        <ul>
+                        </li>
+                        <li>
                             {{
-                                l("You can filter what is shown in the unpaired sections by:")
+                                localize(
+                                    "Choosing from a list of preset filters by clicking the arrow beside the filter input."
+                                )
                             }}
-                            <li>
-                                {{ l("Entering partial dataset names in either the ") }}
-                                <i data-target=".forward-unpaired-filter input">
-                                    {{ l("forward filter") }}
-                                </i>
-                                {{ l("or ") }}
-                                <i data-target=".reverse-unpaired-filter input">
-                                    {{ l("reverse filter") }}
-                                </i>
-                                {{ "." }}
-                            </li>
-                            <li>
-                                {{
-                                    l(
-                                        "Choosing from a list of preset filters by clicking the arrow beside the filter input."
-                                    )
-                                }}
-                            </li>
-                            <li>
-                                {{ l("Entering regular expressions to match dataset names. See:") }}
-                                <a
-                                    href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions"
-                                    target="_blank">
-                                    {{ l("MDN's JavaScript Regular Expression Tutorial") }}</a
-                                >
-                                {{ l("Note: forward slashes (\\) are not needed.") }}
-                            </li>
-                            <li>
-                                {{ l("Clearing the filters by clicking the ") }}
-                                <i data-target=".clear-filters-link">
-                                    {{ l("Clear filters link") }}
-                                </i>
-                                {{ "." }}
-                            </li>
-                        </ul>
-                        <p>
-                            {{ l("To unpair individual dataset pairs, click the ") }}
-                            <i data-target=".unpair-btn">
-                                {{ l("unpair buttons (") }}
-                                <span class="fa fa-unlink"></span>
-                                {{ ")" }}
-                            </i>
-                            {{ l("Click the") }}
-                            <i data-target=".unpair-all-link">
-                                {{ l("Unpair all") }}
+                        </li>
+                        <li>
+                            {{ localize("Entering regular expressions to match dataset names. See:") }}
+                            <a
+                                href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions"
+                                target="_blank">
+                                {{ localize("MDN's JavaScript Regular Expression Tutorial") }}</a
+                            >
+                            {{ localize("Note: forward slashes (\\) are not needed.") }}
+                        </li>
+                        <li>
+                            {{ localize("Clearing the filters by clicking the ") }}
+                            <i data-target=".clear-filters-link">
+                                {{ localize("Clear filters link") }}
                             </i>
-                            {{ l("link to unpair all pairs.") }}
-                        </p>
-                        <p>
+                            {{ "." }}
+                        </li>
+                    </ul>
+                    <p>
+                        {{ localize("To unpair individual dataset pairs, click the ") }}
+                        <i data-target=".unpair-btn">
+                            {{ localize("unpair buttons (") }}
+                            <span class="fa fa-unlink"></span>
+                            {{ ")" }}
+                        </i>
+                        {{ localize("Click the") }}
+                        <i data-target=".unpair-all-link">
+                            {{ localize("Unpair all") }}
+                        </i>
+                        {{ localize("link to unpair all pairs.") }}
+                    </p>
+                    <p>
+                        {{
+                            localize(
+                                'You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the'
+                            )
+                        }}
+                        <i data-target=".remove-extensions-prompt">
+                            {{ localize("Remove file extensions from pair names?") }}
+                        </i>
+                        {{ localize("control.") }}
+                    </p>
+                    <p>
+                        {{ localize("Once your collection is complete, enter a") }}
+                        <i data-target=".collection-name">
+                            {{ localize("name") }}
+                        </i>
+                        {{ localize("and click ") }}
+                        <i data-target=".create-collection">
+                            {{ localize("Create list or pairs") }}
+                        </i>
+                        {{ localize(". (Note: you do not have to pair all unpaired datasets to finish.)") }}
+                    </p>
+                </template>
+                <template v-slot:middle-content>
+                    <div v-if="noElementsSelected">
+                        <BAlert show variant="warning" dismissible>
+                            {{ noElementsHeader }}
+                            {{ ALL_INVALID_ELEMENTS_PART_ONE }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ CANCEL_TEXT }}
+                            </a>
+                            {{ allInvalidElementsPartTwo }}
+                        </BAlert>
+                    </div>
+                    <div v-else-if="allElementsAreInvalid">
+                        <BAlert v-if="!fromSelection" show variant="warning">
                             {{
-                                l(
-                                    'You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the'
+                                localize(
+                                    "No elements in your history are valid for this collection. You may need to switch to a different history."
                                 )
                             }}
-                            <i data-target=".remove-extensions-prompt">
-                                {{ l("Remove file extensions from pair names?") }}
-                            </i>
-                            {{ l("control.") }}
-                        </p>
-                        <p>
-                            {{ l("Once your collection is complete, enter a") }}
-                            <i data-target=".collection-name">
-                                {{ l("name") }}
-                            </i>
-                            {{ l("and click ") }}
-                            <i data-target=".create-collection">
-                                {{ l("Create list") }}
-                            </i>
-                            {{ l(". (Note: you do not have to pair all unpaired datasets to finish.)") }}
-                        </p>
-                    </template>
-                    <template v-slot:middle-content>
-                        <div class="column-headers vertically-spaced flex-column-container">
-                            <div class="forward-column flex-column column">
-                                <div class="column-header">
-                                    <div class="column-title">
-                                        <span class="title">
-                                            {{ numOfUnpairedForwardElements }}
-                                            {{ l("unpaired forward") }}
-                                        </span>
-                                        <span class="title-info unpaired-info">
-                                            {{ numOfFilteredOutForwardElements }} {{ l("filtered out") }}
-                                        </span>
-                                    </div>
-                                    <div
-                                        class="unpaired-filter forward-unpaired-filter float-left search-input search-query input-group">
-                                        <input
-                                            v-model="forwardFilter"
-                                            type="text"
-                                            :placeholder="filterTextPlaceholder"
-                                            title="filterTextTitle" />
-                                        <div class="input-group-append" :title="chooseFilterTitle">
-                                            <button
-                                                class="btn btn-outline-secondary dropdown-toggle"
-                                                type="button"
-                                                data-toggle="dropdown"
-                                                aria-haspopup="true"
-                                                aria-expanded="false"></button>
-                                            <div class="dropdown-menu">
-                                                <a class="dropdown-item" @click="changeFilters('illumina')">_1</a>
-                                                <a class="dropdown-item" @click="changeFilters('Rs')">_R1</a>
-                                                <a class="dropdown-item" @click="changeFilters('dot12s')">.1.fastq</a>
+                            <span v-if="extensions?.length">
+                                {{ localize("The following format(s) are required for this collection: ") }}
+                                <ul>
+                                    <li v-for="extension in extensions" :key="extension">
+                                        {{ extension }}
+                                    </li>
+                                </ul>
+                            </span>
+                        </BAlert>
+                        <BAlert v-else show variant="warning" dismissible>
+                            {{ INVALID_HEADER }}
+                            <ul>
+                                <li v-for="problem in returnInvalidElements" :key="problem">
+                                    {{ problem }}
+                                </li>
+                            </ul>
+                            {{ ALL_INVALID_ELEMENTS_PART_ONE }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ CANCEL_TEXT }}
+                            </a>
+                            {{ allInvalidElementsPartTwo }}
+                        </BAlert>
+                    </div>
+                    <div v-else-if="tooFewElementsSelected">
+                        <div v-if="returnInvalidElementsLength">
+                            <BAlert show variant="warning" dismissible>
+                                {{ INVALID_HEADER }}
+                                <ul>
+                                    <li v-for="problem in returnInvalidElements" :key="problem">
+                                        {{ problem }}
+                                    </li>
+                                </ul>
+                            </BAlert>
+                        </div>
+                        <BAlert show variant="warning" dismissible>
+                            {{ ALL_INVALID_ELEMENTS_PART_ONE }}
+                            <a class="cancel-text" href="javascript:void(0)" role="button" @click="emit('on-cancel')">
+                                {{ CANCEL_TEXT }}
+                            </a>
+                            {{ allInvalidElementsPartTwo }}
+                        </BAlert>
+                    </div>
+                    <div v-else>
+                        <BCard no-body class="mb-2">
+                            <BCardHeader
+                                class="d-flex justify-content-between align-items-center unselectable"
+                                role="button"
+                                @click="showPairingSection = !showPairingSection">
+                                <Heading size="sm">Pairing</Heading>
+                                <i class="text-muted">
+                                    {{ localize("Click to hide/show datasets to pair") }}
+                                    <FontAwesomeIcon
+                                        :icon="showPairingSection ? faAngleUp : faAngleDown"
+                                        size="lg"
+                                        fixed-width />
+                                </i>
+                            </BCardHeader>
+                            <BCardBody v-show="showPairingSection" class="pairing-split-parent">
+                                <div class="column-headers vertically-spaced flex-column-container">
+                                    <div class="forward-column flex-column column">
+                                        <div class="column-header">
+                                            <div class="column-title">
+                                                <span class="title">
+                                                    {{ numOfUnpairedForwardElements }}
+                                                    {{ localize("unpaired forward") }}
+                                                </span>
+                                                <span class="title-info unpaired-info">
+                                                    {{ numOfFilteredOutForwardElements }} {{ localize("filtered out") }}
+                                                </span>
+                                            </div>
+                                            <div
+                                                class="unpaired-filter forward-unpaired-filter search-input search-query input-group">
+                                                <label for="forward-filter" class="sr-only">{{
+                                                    FILTER_TEXT_TITLE
+                                                }}</label>
+                                                <input
+                                                    id="foward-filter"
+                                                    v-model="forwardFilter"
+                                                    type="text"
+                                                    :placeholder="FILTER_TEXT_PLACEHOLDER"
+                                                    :title="FILTER_TEXT_TITLE" />
+                                                <div class="input-group-append" :title="CHOOSE_FILTER_TITLE">
+                                                    <button
+                                                        class="btn btn-outline-secondary dropdown-toggle"
+                                                        type="button"
+                                                        data-toggle="dropdown"
+                                                        aria-haspopup="true"
+                                                        aria-expanded="false"></button>
+                                                    <div class="dropdown-menu">
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('illumina')">
+                                                            _1
+                                                        </a>
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('Rs')">
+                                                            _R1
+                                                        </a>
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('dot12s')">
+                                                            .1.fastq
+                                                        </a>
+                                                    </div>
+                                                </div>
                                             </div>
                                         </div>
                                     </div>
-                                </div>
-                            </div>
-                            <div class="paired-column flex-column no-flex column">
-                                <div class="column-header">
-                                    <a
-                                        class="clear-filters-link"
-                                        href="javascript:void(0);"
-                                        role="button"
-                                        @click="clickClearFilters">
-                                        {{ l("Clear Filters") }}
-                                    </a>
-                                    <br />
-                                    <a
-                                        class="autopair-link"
-                                        href="javascript:void(0);"
-                                        role="button"
-                                        @click="clickAutopair">
-                                        {{ l("Auto-pair") }}
-                                    </a>
-                                </div>
-                            </div>
-                            <div class="reverse-column flex-column column">
-                                <div class="column-header">
-                                    <div class="column-title">
-                                        <span class="title">
-                                            {{ numOfUnpairedReverseElements }}
-                                            {{ l("unpaired reverse") }}
-                                        </span>
-                                        <span class="title-info unpaired-info">
-                                            {{ numOfFilteredOutReverseElements }} {{ l("filtered out") }}</span
-                                        >
+                                    <div class="paired-column flex-column no-flex column">
+                                        <BButtonGroup vertical>
+                                            <BButton
+                                                class="clear-filters-link"
+                                                :disabled="!canClearFilters"
+                                                size="sm"
+                                                :variant="hasFilter ? 'danger' : 'secondary'"
+                                                @click="clickClearFilters">
+                                                <FontAwesomeIcon :icon="faTimes" fixed-width />
+                                                {{ localize("Clear Filters") }}
+                                            </BButton>
+                                            <BButton
+                                                class="autopair-link"
+                                                :disabled="!canAutoPair"
+                                                size="sm"
+                                                :title="autoPairButton.text"
+                                                :variant="autoPairButton.variant"
+                                                @click="clickAutopair">
+                                                <FontAwesomeIcon :icon="autoPairButton.icon" fixed-width />
+                                                {{ localize("Auto-pair") }}
+                                            </BButton>
+                                        </BButtonGroup>
                                     </div>
-                                    <div
-                                        class="unpaired-filter reverse-unpaired-filter float-left search-input search-query input-group">
-                                        <input
-                                            v-model="reverseFilter"
-                                            type="text"
-                                            :placeholder="filterTextPlaceholder"
-                                            title="filterTextTitle" />
-                                        <div class="input-group-append" :title="chooseFilterTitle">
-                                            <button
-                                                class="btn btn-outline-secondary dropdown-toggle"
-                                                type="button"
-                                                data-toggle="dropdown"
-                                                aria-haspopup="true"
-                                                aria-expanded="false"></button>
-                                            <div class="dropdown-menu">
-                                                <a class="dropdown-item" @click="changeFilters('illumina')">_2</a>
-                                                <a class="dropdown-item" @click="changeFilters('Rs')">_R2</a>
-                                                <a class="dropdown-item" @click="changeFilters('dot12s')">.2.fastq</a>
+                                    <div class="reverse-column flex-column column">
+                                        <div class="column-header">
+                                            <div class="column-title">
+                                                <span class="title">
+                                                    {{ numOfUnpairedReverseElements }}
+                                                    {{ localize("unpaired reverse") }}
+                                                </span>
+                                                <span class="title-info unpaired-info">
+                                                    {{ numOfFilteredOutReverseElements }}
+                                                    {{ localize("filtered out") }}</span
+                                                >
+                                            </div>
+                                            <div
+                                                class="unpaired-filter reverse-unpaired-filter justify-content-end search-input search-query input-group">
+                                                <label for="reverse-filter" class="sr-only">{{
+                                                    FILTER_TEXT_TITLE
+                                                }}</label>
+                                                <input
+                                                    id="reverse-filter"
+                                                    v-model="reverseFilter"
+                                                    type="text"
+                                                    :placeholder="FILTER_TEXT_PLACEHOLDER"
+                                                    :title="FILTER_TEXT_TITLE" />
+                                                <div class="input-group-append" :title="CHOOSE_FILTER_TITLE">
+                                                    <button
+                                                        class="btn btn-outline-secondary dropdown-toggle"
+                                                        type="button"
+                                                        data-toggle="dropdown"
+                                                        aria-haspopup="true"
+                                                        aria-expanded="false"></button>
+                                                    <div class="dropdown-menu">
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('illumina')">
+                                                            _2
+                                                        </a>
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('Rs')">
+                                                            _R2
+                                                        </a>
+                                                        <a
+                                                            class="dropdown-item"
+                                                            href="javascript:void(0);"
+                                                            @click="changeFilters('dot12s')">
+                                                            .2.fastq
+                                                        </a>
+                                                    </div>
+                                                </div>
                                             </div>
                                         </div>
                                     </div>
                                 </div>
-                            </div>
-                        </div>
-                        <div class="pairing-split-parent">
-                            <div class="pairing-split-child">
-                                <div v-if="noUnpairedElementsDisplayed">
-                                    <b-alert show variant="warning">
-                                        {{ l("No datasets were found matching the current filters.") }}
-                                    </b-alert>
-                                </div>
-                                <div class="unpaired-columns flex-column-container scroll-container flex-row">
-                                    <div class="forward-column flex-column column truncate">
-                                        <ol class="column-datasets">
-                                            <UnpairedDatasetElementView
-                                                v-for="element in forwardElements"
-                                                :key="element.id"
-                                                :class="{
-                                                    selected:
-                                                        selectedForwardElement &&
-                                                        element.id == selectedForwardElement.id,
-                                                }"
-                                                :element="element"
-                                                @element-is-selected="forwardElementSelected" />
-                                        </ol>
+                                <div class="pairing-split-child">
+                                    <div v-if="noUnpairedElementsDisplayed">
+                                        <BAlert show variant="warning">
+                                            {{ localize("No datasets were found matching the current filters.") }}
+                                        </BAlert>
                                     </div>
-                                    <div class="paired-column flex-column no-flex column truncate">
-                                        <ol v-if="forwardFilter !== '' && reverseFilter !== ''" class="column-datasets">
-                                            <li
-                                                v-for="(pairableElement, index) in pairableElements"
-                                                :key="index"
-                                                class="dataset"
-                                                @click="_pair(pairableElement.forward, pairableElement.reverse)">
-                                                {{ l("Pair these datasets") }}
-                                            </li>
-                                        </ol>
-                                    </div>
-                                    <div class="reverse-column flex-column column truncate">
-                                        <ol class="column-datasets">
-                                            <UnpairedDatasetElementView
-                                                v-for="element in reverseElements"
-                                                :key="element.id"
-                                                :class="{
-                                                    selected:
-                                                        selectedReverseElement &&
-                                                        element.id == selectedReverseElement.id,
-                                                }"
-                                                :element="element"
-                                                @element-is-selected="reverseElementSelected" />
-                                        </ol>
+                                    <div class="unpaired-columns flex-column-container scroll-container flex-row">
+                                        <div class="forward-column flex-column column truncate">
+                                            <ol class="column-datasets">
+                                                <UnpairedDatasetElementView
+                                                    v-for="element in forwardElements"
+                                                    :key="element.id"
+                                                    :class="{
+                                                        selected:
+                                                            selectedForwardElement &&
+                                                            element.id === selectedForwardElement.id,
+                                                    }"
+                                                    :disabled="element.id === selectedReverseElement?.id"
+                                                    :element="element"
+                                                    @element-is-selected="forwardElementSelected" />
+                                            </ol>
+                                        </div>
+                                        <div class="paired-column flex-column no-flex column truncate">
+                                            <ol
+                                                v-if="forwardFilter !== '' && reverseFilter !== ''"
+                                                class="column-datasets">
+                                                <li
+                                                    v-for="(pairableElement, index) in pairableElements"
+                                                    :key="index"
+                                                    class="dataset"
+                                                    role="button"
+                                                    tabindex="0"
+                                                    @keyup.enter="
+                                                        _pair(pairableElement.forward, pairableElement.reverse)
+                                                    "
+                                                    @click="_pair(pairableElement.forward, pairableElement.reverse)">
+                                                    {{ localize("Pair these datasets") }}
+                                                </li>
+                                            </ol>
+                                        </div>
+                                        <div class="reverse-column flex-column column truncate">
+                                            <ol class="column-datasets">
+                                                <UnpairedDatasetElementView
+                                                    v-for="element in reverseElements"
+                                                    :key="element.id"
+                                                    :class="{
+                                                        selected:
+                                                            selectedReverseElement &&
+                                                            element.id == selectedReverseElement.id,
+                                                    }"
+                                                    :disabled="element.id === selectedForwardElement?.id"
+                                                    :element="element"
+                                                    @element-is-selected="reverseElementSelected" />
+                                            </ol>
+                                        </div>
                                     </div>
                                 </div>
-                            </div>
+                            </BCardBody>
+                        </BCard>
+                        <div>
                             <div class="pairing-split-child">
                                 <div class="column-header">
-                                    <div class="column-title paired-column-title">
-                                        <span class="title"> {{ numOfPairs }} {{ l(" pairs") }}</span>
+                                    <div class="column-title paired-column-title" data-description="number of pairs">
+                                        <span class="title"> {{ numOfPairs }} {{ localize("pairs") }}</span>
                                     </div>
-                                    <a
-                                        class="unpair-all-link"
-                                        href="javascript:void(0);"
-                                        role="button"
-                                        @click="unpairAll">
-                                        {{ l("Unpair all") }}
-                                    </a>
+                                    <BButton
+                                        v-if="generatedPairs.length > 0"
+                                        variant="link"
+                                        size="sm"
+                                        @click.stop="unpairAll">
+                                        <FontAwesomeIcon :icon="faUnlink" fixed-width />
+                                        {{ localize("Unpair all") }}
+                                    </BButton>
                                 </div>
                                 <div class="paired-columns flex-column-container scroll-container flex-row">
                                     <ol class="column-datasets">
-                                        <draggable v-model="pairedElements" @start="drag = true" @end="drag = false">
+                                        <draggable
+                                            v-model="generatedPairs"
+                                            handle=".dataset"
+                                            chosen-class="dragged-pair">
                                             <PairedElementView
-                                                v-for="pair in pairedElements"
-                                                :key="pair.id"
+                                                v-for="pair in generatedPairs"
+                                                :key="`${pair.forward.id}-${pair.reverse.id}`"
                                                 :pair="pair"
-                                                :unlink-fn="clickUnpair(pair)"
-                                                @onPairRename="(name) => (pair.name = name)" />
+                                                @onPairRename="(name) => (pair.name = name)"
+                                                @onUnpair="clickUnpair(pair)" />
                                         </draggable>
                                     </ol>
                                 </div>
                             </div>
                         </div>
-                    </template>
-                </collection-creator>
-            </div>
+                    </div>
+                </template>
+            </CollectionCreator>
         </div>
     </div>
 </template>
-<script>
-import BootstrapVue from "bootstrap-vue";
-import STATES from "mvc/dataset/states";
-import levenshteinDistance from "utils/levenshtein";
-import _l from "utils/localization";
-import naturalSort from "utils/natural-sort";
-import Vue from "vue";
-import draggable from "vuedraggable";
-
-import mixin from "./common/mixin";
-import PairedElementView from "./PairedElementView";
-import UnpairedDatasetElementView from "./UnpairedDatasetElementView";
-
-Vue.use(BootstrapVue);
-export default {
-    components: {
-        UnpairedDatasetElementView,
-        PairedElementView,
-        draggable,
-    },
-    mixins: [mixin],
-    data: function () {
-        return {
-            state: "build", //error, duplicates
-            dragToChangeTitle: _l("Drag to change"),
-            chooseFilterTitle: _l("Choose from common filters"),
-            filterTextPlaceholder: _l("Filter text"),
-            filterTextTitle: _l("Use this box to filter elements, using simple matching or regular expressions."),
-            pairedElements: [],
-            unpairedElements: [],
-            commonFilters: {
-                illumina: ["_1", "_2"],
-                Rs: ["_R1", "_R2"],
-                dot12s: [".1.fastq", ".2.fastq"],
-            },
-            DEFAULT_FILTERS: "illumina",
-            forwardFilter: "",
-            reverseFilter: "",
-            automaticallyPair: true,
-            initialPairsPossible: true,
-            matchPercentage: 0.99,
-            twoPassAutoPairing: true,
-            removeExtensions: true,
-            workingElements: [],
-
-            selectedForwardElement: null,
-            selectedReverseElement: null,
-            /** autopair by exact match */
-
-            autopairSimple: this.autoPairFnBuilder({
-                scoreThreshold: function () {
-                    return 0.6;
-                },
-                match: function _match(params) {
-                    params = params || {};
-                    if (params.matchTo === params.possible) {
-                        return {
-                            index: params.index,
-                            score: 1.0,
-                        };
-                    }
-                    return params.bestMatch;
-                },
-            }),
-            /** autopair by levenshtein edit distance scoring */
-            autopairLevenshtein: this.autoPairFnBuilder({
-                scoreThreshold: function () {
-                    return this.matchPercentage;
-                },
-                match: function _matches(params) {
-                    params = params || {};
-
-                    var distance = levenshteinDistance(params.matchTo, params.possible);
-
-                    var score = 1.0 - distance / Math.max(params.matchTo.length, params.possible.length);
-
-                    if (score > params.bestMatch.score) {
-                        return {
-                            index: params.index,
-                            score: score,
-                        };
-                    }
-                    return params.bestMatch;
-                },
-            }),
-            /** autopair by longest common substrings scoring */
-            autopairLCS: this.autoPairFnBuilder({
-                scoreThreshold: function () {
-                    return this.matchPercentage;
-                },
-                match: function _matches(params) {
-                    params = params || {};
-
-                    var match = this._naiveStartingAndEndingLCS(params.matchTo, params.possible).length;
-
-                    var score = match / Math.max(params.matchTo.length, params.possible.length);
-
-                    if (score > params.bestMatch.score) {
-                        return {
-                            index: params.index,
-                            score: score,
-                        };
-                    }
-                    return params.bestMatch;
-                },
-            }),
-            strategy: null,
-            errorText: _l("Galaxy could not be reached and may be updating.  Try again in a few minutes."),
-            invalidHeader: _l("The following selections could not be included due to problems:"),
-            allInvalidElementsPartOne: _l("At least two elements are needed for the collection. You may need to"),
-            noElementsHeader: _l("No datasets were selected"),
-            cancelText: _l("cancel"),
-            allInvalidElementsPartTwo: _l("and reselect new elements."),
-            duplicatePairNames: [],
-        };
-    },
-    computed: {
-        forwardElements: {
-            get() {
-                return this.filterElements(this.workingElements, this.forwardFilter);
-            },
-        },
-        reverseElements: {
-            get() {
-                return this.filterElements(this.workingElements, this.reverseFilter);
-            },
-        },
-        pairableElements: {
-            get() {
-                var pairable = [];
-                this.forwardElements.forEach((elem, index) => {
-                    if (this.reverseElements[index] && elem.id != this.reverseElements[index].id) {
-                        pairable.push({
-                            forward: this.forwardElements[index],
-                            reverse: this.reverseElements[index],
-                        });
-                    }
-                });
-                return pairable;
-            },
-        },
-        numOfUnpairedForwardElements: function () {
-            return this.forwardElements.length;
-        },
-        numOfFilteredOutForwardElements: function () {
-            return this.workingElements.length - this.numOfUnpairedForwardElements;
-        },
-        numOfUnpairedReverseElements: function () {
-            return this.reverseElements.length;
-        },
-        numOfFilteredOutReverseElements: function () {
-            return this.workingElements.length - this.numOfUnpairedReverseElements;
-        },
-        numOfPairs: function () {
-            return this.pairedElements.length;
-        },
-        returnInvalidElementsLength: function () {
-            return this.invalidElements.length > 0;
-        },
-        returnInvalidElements: function () {
-            return this.invalidElements;
-        },
-        allElementsAreInvalid: function () {
-            return this.initialElements.length == this.invalidElements.length;
-        },
-        noElementsSelected: function () {
-            return this.initialElements.length == 0;
-        },
-        tooFewElementsSelected: function () {
-            return this.workingElements.length < 2 && this.pairedElements.length == 0;
-        },
-        showDuplicateError() {
-            return this.duplicatePairNames.length > 0;
-        },
-        noUnpairedElementsDisplayed() {
-            return this.numOfUnpairedForwardElements + this.numOfUnpairedReverseElements == 0;
-        },
-        renderPairButton() {
-            return this;
-        },
-    },
-    created() {
-        this.strategy = this.autopairLCS;
-        //TODO convert to Fwd/Rev
-        // Setup inital filters and shallow copy the items
-        this.forwardFilter = this.commonFilters[this.DEFAULT_FILTERS][0];
-        this.reverseFilter = this.commonFilters[this.DEFAULT_FILTERS][1];
-        this._elementsSetUp();
-    },
-    methods: {
-        l(str) {
-            // _l conflicts private methods of Vue internals, expose as l instead
-            return _l(str);
-        },
-        removeExtensionsToggle: function () {
-            this.removeExtensions = !this.removeExtensions;
-            this.pairedElements.forEach((pair, index) => {
-                pair.name = this._guessNameForPair(pair.forward, pair.reverse, this.removeExtensions);
-            });
-        },
-        /** set up main data */
-        _elementsSetUp: function () {
-            /** a list of invalid elements and the reasons they aren't valid */
-            this.invalidElements = [];
-            //TODO: handle fundamental problem of syncing DOM, views, and list here
-            /** data for list in progress */
-            this.workingElements = [];
-            //TODO: this should maybe be in it's own method as it will get called everytime selected array has two elements and dumps again.
-            this.selectedDatasetElems = [];
-            this.initialFiltersSet();
-            // copy initial list, sort, add ids if needed
-            this.workingElements = JSON.parse(JSON.stringify(this.initialElements.slice(0)));
-            this._ensureElementIds();
-            this._validateElements();
-            this._sortInitialList();
-            //attempt to autopair
-            if (this.automaticallyPair == true) {
-                this.autoPair();
-                this.initialPairsPossible = this.pairedElements.length > 0;
-            }
-        },
-        initialFiltersSet: function () {
-            let illumina = 0;
-            let dot12s = 0;
-            let Rs = 0;
-            //should we limit the forEach? What if there are 1000s of elements?
-            this.initialElements.forEach((element) => {
-                if (element.name.includes(".1.fastq") || element.name.includes(".2.fastq")) {
-                    dot12s++;
-                } else if (element.name.includes("_R1") || element.name.includes("_R2")) {
-                    Rs++;
-                } else if (element.name.includes("_1") || element.name.includes("_2")) {
-                    illumina++;
-                }
-            });
-
-            if (illumina > dot12s && illumina > Rs) {
-                this.changeFilters("illumina");
-            } else if (dot12s > illumina && dot12s > Rs) {
-                this.changeFilters("dot12s");
-            } else if (Rs > illumina && Rs > dot12s) {
-                this.changeFilters("Rs");
-            } else {
-                this.changeFilters("illumina");
-            }
-        },
-        /** add ids to dataset objs in initial list if none */
-        _ensureElementIds: function () {
-            this.workingElements.forEach((element) => {
-                if (!Object.prototype.hasOwnProperty.call(element, "id")) {
-                    element.id = element._uid;
-                }
-            });
-            return this.workingElements;
-        },
-        // /** separate working list into valid and invalid elements for this collection */
-        _validateElements: function () {
-            this.workingElements = this.workingElements.filter((element) => {
-                var problem = this._isElementInvalid(element);
-                if (problem) {
-                    this.invalidElements.push(element.name + "  " + problem);
-                }
-                return !problem;
-            });
-            return this.workingElements;
-        },
-        /** describe what is wrong with a particular element if anything */
-        _isElementInvalid: function (element) {
-            if (element.history_content_type === "dataset_collection") {
-                return _l("is a collection, this is not allowed");
-            }
-            var validState = element.state === STATES.OK || STATES.NOT_READY_STATES.includes(element.state);
-            if (!validState) {
-                return _l("has errored, is paused, or is not accessible");
-            }
-            if (element.deleted || element.purged) {
-                return _l("has been deleted or purged");
-            }
-            return null;
-        },
-        /** sort initial list */
-        _sortInitialList: function () {
-            //console.debug( '-- _sortInitialList' );
-            this._sortDatasetList(this.workingElements);
-        },
-
-        /** sort a list of datasets */
-        _sortDatasetList: function (list) {
-            // currently only natural sort by name
-            list.sort((a, b) => naturalSort(a.name, b.name));
-            return list;
-        },
-        filterElements: function (elements, filterText) {
-            return elements.filter((e) => this.filterElement(e, filterText));
-        },
-        filterElement: function (element, filterText) {
-            return filterText == "" || new RegExp(filterText).test(element.name);
-        },
-        forwardElementSelected: function (e) {
-            if (this.selectedForwardElement == null || !this.selectedForwardElement.id == e.id) {
-                this.selectedForwardElement = e;
-            } else {
-                this.selectedForwardElement = null;
-            }
-            if (
-                this.selectedForwardElement &&
-                this.selectedReverseElement &&
-                this.selectedReverseElement != this.selectedForwardElement
-            ) {
-                this._pair(this.selectedForwardElement, this.selectedReverseElement);
-            }
-        },
-        reverseElementSelected: function (e) {
-            if (this.selectedReverseElement == null || !this.selectedReverseElement.id == e.id) {
-                this.selectedReverseElement = e;
-            } else {
-                this.selectedReverseElement = null;
-            }
-            if (
-                this.selectedForwardElement &&
-                this.selectedReverseElement &&
-                this.selectedReverseElement != this.selectedForwardElement
-            ) {
-                this._pair(this.selectedForwardElement, this.selectedReverseElement);
-            }
-        },
-
-        // ------------------------------------------------------------------------ pairing / unpairing
-        /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */
-        _pair: function (fwd, rev, options) {
-            options = options || {};
-            var pair = this._createPair(fwd, rev, options.name);
-            this.pairedElements.push(pair);
-            this.removePairFromUnpaired(fwd, rev);
-            if (!options.silent) {
-                this.$emit("pair:new", pair);
-            }
-            return pair;
-        },
-        removePairFromUnpaired: function (fwd, rev) {
-            this.workingElements.splice(this.workingElements.indexOf(rev), 1);
-            this.workingElements.splice(this.workingElements.indexOf(fwd), 1);
-            this.selectedForwardElement = null;
-            this.selectedReverseElement = null;
-        },
-        /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */
-        _createPair: function (fwd, rev, name) {
-            // ensure existance and don't pair something with itself
-            if (!(fwd && rev) || fwd === rev) {
-                throw new Error(`Bad pairing: ${[JSON.stringify(fwd), JSON.stringify(rev)]}`);
-            }
-            name = name || this._guessNameForPair(fwd, rev);
-            return { forward: fwd, name: name, reverse: rev };
-        },
-        /** try to find a good pair name for the given fwd and rev datasets */
-        _guessNameForPair: function (fwd, rev, removeExtensions) {
-            removeExtensions = removeExtensions ? removeExtensions : this.removeExtensions;
-            let fwdName = fwd.name;
-            let revName = rev.name;
-            const fwdNameFilter = fwdName.replace(new RegExp(this.forwardFilter), "");
-            const revNameFilter = revName.replace(new RegExp(this.reverseFilter), "");
-            let lcs = this._naiveStartingAndEndingLCS(fwdNameFilter, revNameFilter);
-            /** remove url prefix if files were uploaded by url */
-            const lastSlashIndex = lcs.lastIndexOf("/");
-            if (lastSlashIndex > 0) {
-                const urlprefix = lcs.slice(0, lastSlashIndex + 1);
-                lcs = lcs.replace(urlprefix, "");
-            }
-
-            if (removeExtensions) {
-                const lastDotIndex = lcs.lastIndexOf(".");
-                if (lastDotIndex > 0) {
-                    const extension = lcs.slice(lastDotIndex, lcs.length);
-                    lcs = lcs.replace(extension, "");
-                    fwdName = fwdName.replace(extension, "");
-                    revName = revName.replace(extension, "");
-                }
-            }
-            if (lcs.endsWith(".") || lcs.endsWith("_")) {
-                lcs = lcs.substring(0, lcs.length - 1);
-            }
-            return lcs || `${fwdName} & ${revName}`;
-        },
-        clickAutopair: function () {
-            // Unselect any selected elements
-            this.selectedForwardElement = null;
-            this.selectedReverseElement = null;
-            this.autoPair();
-            this.workingElements = this.workingElements.filter((e) => !this.pairedElements.includes(e));
-        },
-        clickUnpair: function (pair) {
-            return () => this._unpair(pair);
-        },
-        clickClearFilters: function () {
-            this.forwardFilter = "";
-            this.reverseFilter = "";
-        },
-        splitByFilter: function () {
-            var filters = [new RegExp(this.forwardFilter), new RegExp(this.reverseFilter)];
-            var split = [[], []];
-            this.workingElements.forEach((e) => {
-                filters.forEach((filter, i) => {
-                    if (filter.test(e.name)) {
-                        split[i].push(e);
-                    }
-                });
-            });
-            return split;
-        },
-        // ------------------------------------------------------------------------ auto pairing
-        /** two passes to automatically create pairs:
-         *  use both simpleAutoPair, then the fn mentioned in strategy
-         */
-        autoPair: function (strategy) {
-            var split = this.splitByFilter();
-            var paired = [];
-            if (this.twoPassAutopairing) {
-                var simplePaired = this.autopairSimple({
-                    listA: split[0],
-                    listB: split[1],
-                });
-                paired = simplePaired ? simplePaired : paired;
-                split = this.splitByFilter();
-            }
 
-            // uncomment to see printlns while running tests
-            //console.debug = function(){ console.log.apply( console, arguments ); };
-
-            // then try the remainder with something less strict
-            strategy = strategy || this.strategy;
-            split = this.splitByFilter();
-            var pairedStrategy = strategy.call(this, {
-                listA: split[0],
-                listB: split[1],
-            });
-            paired = pairedStrategy ? paired.concat(pairedStrategy) : paired;
-            return paired;
-        },
-        /** add a dataset to the unpaired list in it's proper order */
-        _addToUnpaired: function (dataset) {
-            // currently, unpaired is natural sorted by name, use binary search to find insertion point
-            var binSearchSortedIndex = (low, hi) => {
-                if (low === hi) {
-                    return low;
-                }
-
-                var mid = Math.floor((hi - low) / 2) + low;
-
-                var compared = naturalSort(dataset.name, this.workingElements[mid].name);
-
-                if (compared < 0) {
-                    return binSearchSortedIndex(low, mid);
-                } else if (compared > 0) {
-                    return binSearchSortedIndex(mid + 1, hi);
-                }
-                // walk the equal to find the last
-                while (this.workingElements[mid] && this.workingElements[mid].name === dataset.name) {
-                    mid++;
-                }
-                return mid;
-            };
-
-            this.workingElements.splice(binSearchSortedIndex(0, this.workingElements.length), 0, dataset);
-        },
-        /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */
-        _unpair: function (pair) {
-            if (!pair) {
-                throw new Error(`Bad pair: ${JSON.stringify(pair)}`);
-            }
-            this.pairedElements.splice(this.pairedElements.indexOf(pair), 1);
-            this._addToUnpaired(pair.forward);
-            this._addToUnpaired(pair.reverse);
-
-            return pair;
-        },
-        /** unpair all paired datasets */
-        unpairAll: function () {
-            var pairs = [];
-            while (this.pairedElements.length) {
-                pairs.push(this._unpair(this.pairedElements[0], { silent: true }));
-            }
-        },
-        // ============================================================================
-        /** returns an autopair function that uses the provided options.match function */
-        autoPairFnBuilder: function (options) {
-            options = options || {};
-            options.createPair =
-                options.createPair ||
-                function _defaultCreatePair(params) {
-                    params = params || {};
-                    var a = params.listA.splice(params.indexA, 1)[0];
-                    var b = params.listB.splice(params.indexB, 1)[0];
-                    var aInBIndex = params.listB.indexOf(a);
-                    var bInAIndex = params.listA.indexOf(b);
-                    if (aInBIndex !== -1) {
-                        params.listB.splice(aInBIndex, 1);
-                    }
-                    if (bInAIndex !== -1) {
-                        params.listA.splice(bInAIndex, 1);
-                    }
-                    return this._pair(a, b, { silent: true });
-                };
-            // compile these here outside of the loop
-            var _regexps = [];
-            function getRegExps() {
-                if (!_regexps.length) {
-                    _regexps = [new RegExp(this.forwardFilter), new RegExp(this.reverseFilter)];
-                }
-                return _regexps;
-            }
-            // mangle params as needed
-            options.preprocessMatch =
-                options.preprocessMatch ||
-                function _defaultPreprocessMatch(params) {
-                    var regexps = getRegExps.call(this);
-                    return Object.assign(params, {
-                        matchTo: params.matchTo.name.replace(regexps[0], ""),
-                        possible: params.possible.name.replace(regexps[1], ""),
-                    });
-                };
-
-            return function _strategy(params) {
-                // console.debug("autopair _strategy ---------------------------");
-                params = params || {};
-                var listA = params.listA;
-                var listB = params.listB;
-                var indexA = 0;
-                var indexB;
-
-                var bestMatch = {
-                    score: 0.0,
-                    index: null,
-                };
-
-                var paired = [];
-                //console.debug( 'params:', JSON.stringify( params, null, '  ' ) );
-                // console.debug("starting list lens:", listA.length, listB.length);
-                // console.debug("bestMatch (starting):", JSON.stringify(bestMatch, null, "  "));
-
-                while (indexA < listA.length) {
-                    var matchTo = listA[indexA];
-                    bestMatch.score = 0.0;
-
-                    for (indexB = 0; indexB < listB.length; indexB++) {
-                        var possible = listB[indexB];
-                        // console.debug(`${indexA}:${matchTo.name}`);
-                        // console.debug(`${indexB}:${possible.name}`);
-
-                        // no matching with self
-                        if (listA[indexA] !== listB[indexB]) {
-                            bestMatch = options.match.call(
-                                this,
-                                options.preprocessMatch.call(this, {
-                                    matchTo: matchTo,
-                                    possible: possible,
-                                    index: indexB,
-                                    bestMatch: bestMatch,
-                                })
-                            );
-                            // console.debug("bestMatch:", JSON.stringify(bestMatch, null, "  "));
-                            if (bestMatch.score === 1.0) {
-                                // console.debug("breaking early due to perfect match");
-                                break;
-                            }
-                        }
-                    }
-                    var scoreThreshold = options.scoreThreshold.call(this);
-                    // console.debug("scoreThreshold:", scoreThreshold);
-                    // console.debug("bestMatch.score:", bestMatch.score);
-
-                    if (bestMatch.score >= scoreThreshold) {
-                        //console.debug( 'autoPairFnBuilder.strategy', listA[ indexA ].name, listB[ bestMatch.index ].name );
-                        paired.push(
-                            options.createPair.call(this, {
-                                listA: listA,
-                                indexA: indexA,
-                                listB: listB,
-                                indexB: bestMatch.index,
-                            })
-                        );
-                        //console.debug( 'list lens now:', listA.length, listB.length );
-                    } else {
-                        indexA += 1;
-                    }
-                    if (!listA.length || !listB.length) {
-                        return paired;
-                    }
-                }
-                // console.debug("paired:", JSON.stringify(paired, null, "  "));
-                // console.debug("autopair _strategy ---------------------------");
-                return paired;
-            };
-        },
-        changeFilters: function (filter) {
-            this.forwardFilter = this.commonFilters[filter][0];
-            this.reverseFilter = this.commonFilters[filter][1];
-        },
-        clickedCreate: function (collectionName) {
-            this.checkForDuplicates();
-            if (this.state == "build") {
-                this.$emit("clicked-create", this.workingElements, this.collectionName, this.hideSourceItems);
-                return this.creationFn(this.pairedElements, collectionName, this.hideSourceItems)
-                    .done(this.oncreate)
-                    .fail(() => {
-                        this.state = "error";
-                    });
-            }
-        },
-        checkForDuplicates: function () {
-            var existingPairNames = {};
-            this.duplicatePairNames = [];
-            var valid = true;
-            this.pairedElements.forEach((pair) => {
-                if (Object.prototype.hasOwnProperty.call(existingPairNames, pair.name)) {
-                    valid = false;
-                    this.duplicatePairNames.push(pair.name);
-                }
-                existingPairNames[pair.name] = true;
-            });
-            this.state = valid ? "build" : "duplicates";
-        },
-        stripExtension(name) {
-            return name.includes(".") ? name.substring(0, name.lastIndexOf(".")) : name;
-        },
-    },
-};
-</script>
 <style lang="scss">
 $fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
 @import "~@fortawesome/fontawesome-free/scss/_variables";
 @import "~@fortawesome/fontawesome-free/scss/solid";
 @import "~@fortawesome/fontawesome-free/scss/fontawesome";
 @import "~@fortawesome/fontawesome-free/scss/brands";
+@import "~bootstrap/scss/_functions.scss";
+@import "theme/blue.scss";
 .paired-column {
     text-align: center;
     // mess with these two to make center more/scss priority
@@ -1060,6 +1352,13 @@ li.dataset.paired {
 .column-datasets {
     list-style: none;
     overflow: hidden;
+    .dragged-pair {
+        border-top: 2px solid black;
+    }
+    .unpair-btn {
+        border: none;
+        flex-shrink: 0;
+    }
     .dataset {
         height: 32px;
         margin-top: 2px;
@@ -1075,39 +1374,26 @@ li.dataset.paired {
             border-color: grey;
         }
         &.paired {
-            margin-left: 34px;
-            margin-right: 34px;
+            white-space: nowrap;
+            overflow: hidden;
             border: 2px solid grey;
-            background: #aff1af;
-            height: auto;
+            background: $state-success-bg;
+            text-align: center;
             span {
                 display: inline-block;
-                overflow: visible !important;
             }
             .forward-dataset-name {
                 text-align: right;
                 border-right: 1px solid grey;
                 padding-right: 8px;
-                &:after {
-                    @extend .fas;
-                    margin-left: 8px;
-                    content: fa-content($fa-var-arrow-right);
-                }
             }
             .pair-name-column {
+                padding: 0 8px;
                 text-align: center;
-                .pair-name:hover {
-                    text-decoration: underline;
-                }
             }
             .reverse-dataset-name {
                 border-left: 1px solid grey;
                 padding-left: 8px;
-                &:before {
-                    @extend .fas;
-                    margin-right: 8px;
-                    content: fa-content($fa-var-arrow-left);
-                }
             }
         }
         &:hover {
@@ -1143,14 +1429,41 @@ li.dataset.paired {
     }
     .reverse-column {
         .dataset.unpaired {
-            text-align: right;
             margin-left: 32px;
         }
     }
+    .dataset.unpaired {
+        white-space: nowrap;
+        overflow: hidden;
+        box-sizing: border-box;
+        position: relative;
+        .element-name {
+            display: inline-block;
+            position: relative;
+            min-width: 100%;
+        }
+        &:hover {
+            .element-name.moves {
+                animation: move-right 1s linear forwards;
+            }
+        }
+    }
+    @keyframes move-right {
+        10% {
+            transform: translate(0, 0);
+            left: 0%;
+        }
+        100% {
+            transform: translate(-100%, 0);
+            left: 100%;
+        }
+    }
 }
+
 .column-header {
     width: 100%;
     text-align: center;
+    justify-content: end;
     .column-title {
         display: inline;
     }
@@ -1168,21 +1481,6 @@ li.dataset.paired {
     .column-datasets {
         width: 100%;
     }
-    .unpair-btn {
-        float: right;
-        margin-top: -32px;
-        width: 31px;
-        height: 32px;
-        //z-index: 1;
-        border-color: transparent;
-        //border-color: #BFBFBF;
-        background: transparent;
-        font-size: 120%;
-        &:hover {
-            border-color: #bfbfbf;
-            background: #dedede;
-        }
-    }
     .empty-message {
         text-align: center;
     }
diff --git a/client/src/components/Collections/PairedListCollectionCreatorModal.js b/client/src/components/Collections/PairedListCollectionCreatorModal.js
deleted file mode 100644
index cab346fc7c637ebd245925b840952d0d3d7eb688..0000000000000000000000000000000000000000
--- a/client/src/components/Collections/PairedListCollectionCreatorModal.js
+++ /dev/null
@@ -1,60 +0,0 @@
-import _l from "utils/localization";
-import Vue from "vue";
-
-import { collectionCreatorModalSetup } from "./common/modal";
-
-import PairedListCollectionCreator from "./PairedListCollectionCreator.vue";
-
-function pairedListCollectionCreatorModal(elements, options) {
-    options = options || {};
-    options.title = _l("Create a collection of paired datasets");
-    const { promise, showEl } = collectionCreatorModalSetup(options);
-    var pairedListCollectionCreatorInstance = Vue.extend(PairedListCollectionCreator);
-    var vm = document.createElement("div");
-    showEl(vm);
-    new pairedListCollectionCreatorInstance({
-        propsData: {
-            initialElements: elements,
-            creationFn: options.creationFn,
-            oncancel: options.oncancel,
-            oncreate: options.oncreate,
-            defaultHideSourceItems: options.defaultHideSourceItems,
-        },
-    }).$mount(vm);
-    return promise;
-}
-
-/** Use a modal to create a list collection, then add it to the given history contents.
- *  @returns {Promise} resolved when the collection is added to the history.
- */
-function createPairedListCollection(contents, defaultHideSourceItems) {
-    const elements = contents.toJSON();
-    const promise = pairedListCollectionCreatorModal(elements, {
-        defaultHideSourceItems: defaultHideSourceItems,
-        creationFn: function (elements, name, hideSourceItems) {
-            elements = elements.map((pair) => ({
-                collection_type: "paired",
-                src: "new_collection",
-                name: pair.name,
-                element_identifiers: [
-                    {
-                        name: "forward",
-                        id: pair.forward.id,
-                        src: pair.forward.src || "hda",
-                    },
-                    {
-                        name: "reverse",
-                        id: pair.reverse.id,
-                        src: pair.reverse.src || "hda",
-                    },
-                ],
-            }));
-            return contents.createHDCA(elements, "list:paired", name, hideSourceItems);
-        },
-    });
-    return promise;
-}
-export default {
-    pairedListCollectionCreatorModal: pairedListCollectionCreatorModal,
-    createPairedListCollection: createPairedListCollection,
-};
diff --git a/client/src/components/Collections/UnpairedDatasetElementView.vue b/client/src/components/Collections/UnpairedDatasetElementView.vue
index 91494a082fea862a64dc7b1d89c62a144bcdc9d9..f9043ec513b0985c41d86ecd69f2f51b462e1010 100644
--- a/client/src/components/Collections/UnpairedDatasetElementView.vue
+++ b/client/src/components/Collections/UnpairedDatasetElementView.vue
@@ -1,21 +1,66 @@
 <script setup lang="ts">
+import { computed, ref } from "vue";
+
+import type { HDASummary } from "@/api";
+import { useAnimationFrameSize } from "@/composables/sensors/animationFrameSize";
+
 interface Props {
-    // TODO: Define the type of the element
-    element: any;
+    element: HDASummary;
+    disabled?: boolean;
+    showExtension?: boolean;
+    showHid?: boolean;
 }
 
-defineProps<Props>();
+const props = withDefaults(defineProps<Props>(), {
+    disabled: false,
+    showExtension: true,
+    showHid: true,
+});
 
 const emit = defineEmits<{
-    // TODO: Define the type of the element
-    (event: "element-is-selected", element: any): void;
+    (event: "element-is-selected", element: HDASummary): void;
 }>();
+
+const unpairedElement = ref<HTMLElement | null>(null);
+const elementName = ref<HTMLElement | null>(null);
+
+const { width: parentWidth } = useAnimationFrameSize(unpairedElement);
+
+const childWidth = computed(() => elementName.value?.clientWidth);
+const shouldMoveElement = computed(() => {
+    if (childWidth.value && parentWidth.value && childWidth.value <= parentWidth.value) {
+        return false;
+    } else {
+        return true;
+    }
+});
+
+function getExtension(): string {
+    return "extension" in props.element && props.element.extension ? props.element.extension : "";
+}
 </script>
 
 <template>
-    <li class="dataset unpaired" @click="emit('element-is-selected', element)">
-        <label>
-            {{ element.name }}
-        </label>
+    <li
+        ref="unpairedElement"
+        class="dataset unpaired"
+        :class="{ disabled: props.disabled }"
+        :aria-disabled="props.disabled"
+        role="button"
+        tabindex="0"
+        @keydown.enter="emit('element-is-selected', props.element)"
+        @click="emit('element-is-selected', props.element)">
+        <span ref="elementName" class="element-name" :class="{ moves: shouldMoveElement }">
+            <span v-if="props.element.hid && props.showHid">{{ props.element.hid }}:</span>
+            <strong>{{ props.element.name }}</strong>
+            <i v-if="props.element.extension && props.showExtension"> ({{ getExtension() }}) </i>
+        </span>
     </li>
 </template>
+
+<style scoped>
+.disabled {
+    pointer-events: none;
+    opacity: 0.5;
+}
+</style>
diff --git a/client/src/components/Collections/common/ClickToEdit.vue b/client/src/components/Collections/common/ClickToEdit.vue
index da60f01880d93f54d80f41321bcf92392de9032b..b77925d65a1d9d7589e9f5a3c032ef9a9d2a0ec8 100644
--- a/client/src/components/Collections/common/ClickToEdit.vue
+++ b/client/src/components/Collections/common/ClickToEdit.vue
@@ -1,5 +1,8 @@
 <script setup lang="ts">
-import { ref, watch } from "vue";
+import { faSave } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
 
 interface Props {
     value: string;
@@ -15,38 +18,52 @@ const emit = defineEmits<{
 const editable = ref(false);
 const localValue = ref(props.value);
 
-watch(
-    () => localValue.value,
-    (newLocalValue) => {
-        emit("input", newLocalValue);
-    }
-);
+const computedValue = computed(() => props.value);
 
 watch(
-    () => props.value,
-    (newValue) => {
-        localValue.value = newValue;
+    () => editable.value,
+    (value) => {
+        if (!value) {
+            emit("input", localValue.value);
+        }
     }
 );
 </script>
 
 <template>
-    <input
-        v-if="editable"
-        v-model="localValue"
-        class="click-to-edit-input"
-        contenteditable
-        @blur="editable = false"
-        @keyup.enter="editable = false" />
-
-    <label v-else @click="editable = true">
-        {{ localValue }}
+    <div v-if="editable">
+        <input
+            id="click-to-edit-input"
+            v-model="localValue"
+            tabindex="0"
+            contenteditable
+            @blur.prevent.stop="editable = false"
+            @keyup.prevent.stop.enter="editable = false"
+            @keyup.prevent.stop.escape="editable = false"
+            @click.prevent.stop />
+        <BButton class="p-0" style="border: none" variant="link" size="sm" @click.prevent.stop="editable = false">
+            <FontAwesomeIcon :icon="faSave" />
+        </BButton>
+    </div>
+
+    <label
+        v-else
+        role="button"
+        for="click-to-edit-input"
+        class="click-to-edit-label"
+        tabindex="0"
+        @keyup.enter="editable = true"
+        @click.stop="editable = true">
+        <span v-if="computedValue">{{ computedValue }}</span>
+        <i v-else>{{ title }}</i>
     </label>
 </template>
 
 <style scoped lang="scss">
-.click-to-edit-input {
-    width: 600px;
-    line-height: 1 !important;
+.click-to-edit-label {
+    cursor: text;
+    &:hover > * {
+        text-decoration: underline;
+    }
 }
 </style>
diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index 8ef14660d999b47537e4b64bedf23df3cb1880fb..eb446332bfc90f6b917e3dc5533efd5756dfefbe 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,47 +1,148 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faChevronDown, faChevronUp } from "@fortawesome/free-solid-svg-icons";
+import { faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BTab, BTabs } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
+import type { HDASummary } from "@/api";
+import type { CompositeFileInfo } from "@/api/datatypes";
+import { AUTO_EXTENSION, getUploadDatatypes } from "@/components/Upload/utils";
+import { useConfig } from "@/composables/config";
+import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 
-library.add(faChevronDown, faChevronUp);
+import CollectionCreatorFooterButtons from "./CollectionCreatorFooterButtons.vue";
+import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
+import CollectionCreatorNoItemsMessage from "./CollectionCreatorNoItemsMessage.vue";
+import CollectionCreatorShowExtensions from "./CollectionCreatorShowExtensions.vue";
+import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
+import CollectionNameInput from "./CollectionNameInput.vue";
+import DefaultBox from "@/components/Upload/DefaultBox.vue";
+
+const Tabs = {
+    create: 0,
+    upload: 1,
+};
+
+type ExtensionDetails = {
+    id: string;
+    text: string;
+    description: string | null;
+    description_url: string | null;
+    composite_files?: CompositeFileInfo[] | null;
+    upload_warning?: string | null;
+};
 
 interface Props {
     oncancel: () => void;
+    historyId: string;
     hideSourceItems: boolean;
     suggestedName?: string;
     renderExtensionsToggle?: boolean;
+    extensions?: string[];
+    extensionsToggle?: boolean;
+    noItems?: boolean;
+    collectionType?: string;
+    showUpload: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     suggestedName: "",
+    extensions: undefined,
+    extensionsToggle: false,
+    showUpload: true,
+    collectionType: undefined,
 });
 
 const emit = defineEmits<{
     (e: "remove-extensions-toggle"): void;
     (e: "clicked-create", value: string): void;
     (e: "onUpdateHideSourceItems", value: boolean): void;
+    (e: "on-update-datatype-toggle", value: "all" | "datatype" | "ext"): void;
+    (e: "add-uploaded-files", value: HDASummary[]): void;
 }>();
 
-const isExpanded = ref(false);
+const currentTab = ref(Tabs.create);
 const collectionName = ref(props.suggestedName);
 const localHideSourceItems = ref(props.hideSourceItems);
+const listExtensions = ref<ExtensionDetails[]>([]);
+const extensionsSet = ref(false);
 
 const validInput = computed(() => {
     return collectionName.value.length > 0;
 });
 
-function clickForHelp() {
-    isExpanded.value = !isExpanded.value;
-    return isExpanded.value;
+// If there are props.extensions, filter the list of extensions to only include those
+const validExtensions = computed(() => {
+    return listExtensions.value.filter((ext) => props.extensions?.includes(ext.id));
+});
+
+// Upload properties
+const { config, isConfigLoaded } = useConfig();
+
+const { currentUser } = storeToRefs(useUserStore());
+
+const configOptions = computed(() =>
+    isConfigLoaded.value
+        ? {
+              chunkUploadSize: config.value.chunk_upload_size,
+              fileSourcesConfigured: config.value.file_sources_configured,
+              ftpUploadSite: config.value.ftp_upload_site,
+              defaultDbKey: config.value.default_genome || "",
+              defaultExtension: config.value.default_extension || "",
+          }
+        : {}
+);
+
+const ftpUploadSite = computed(() =>
+    currentUser.value && "id" in currentUser.value ? configOptions.value.ftpUploadSite : null
+);
+
+const defaultExtension = computed(() => {
+    if (!configOptions.value || !extensionsSet.value) {
+        return "auto";
+    } else if (!props.extensions?.length) {
+        return configOptions.value.defaultExtension || "auto";
+    } else {
+        return props.extensions[0];
+    }
+});
+
+const shortWhatIsBeingCreated = computed<string>(() => {
+    // plain language for what is being created
+    if (props.collectionType === "list") {
+        return "list";
+    } else if (props.collectionType === "list:paired") {
+        return "list of pairs";
+    } else if (props.collectionType == "paired") {
+        return "dataset pair";
+    } else {
+        return "collection";
+    }
+});
+
+function addUploadedFiles(value: HDASummary[]) {
+    // TODO: We really need to wait for each of these items to get `state = 'ok'`
+    //       before we can add them to the collection.
+    emit("add-uploaded-files", value);
 }
 
 function cancelCreate() {
     props.oncancel();
 }
 
+function removeExtensionsToggle() {
+    emit("remove-extensions-toggle");
+}
+
+async function loadExtensions() {
+    listExtensions.value = await getUploadDatatypes(false, AUTO_EXTENSION);
+    extensionsSet.value = true;
+}
+
+loadExtensions();
+
 watch(
     () => localHideSourceItems.value,
     () => {
@@ -51,90 +152,112 @@ watch(
 </script>
 
 <template>
-    <div class="collection-creator">
-        <div class="header flex-row no-flex">
-            <div class="main-help well clear" :class="{ expanded: isExpanded }">
-                <a
-                    class="more-help"
-                    href="javascript:void(0);"
-                    role="button"
-                    :title="localize('Expand or Close Help')"
-                    @click="clickForHelp">
-                    <div v-if="!isExpanded">
-                        <FontAwesomeIcon :icon="faChevronDown" />
-                    </div>
-                    <div v-else>
-                        <FontAwesomeIcon :icon="faChevronUp" />
-                    </div>
-                </a>
-
-                <div class="help-content">
-                    <!-- each collection that extends this will add their own help content -->
+    <span>
+        <span v-if="!showUpload" class="collection-creator">
+            <div v-if="props.noItems">
+                <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
+            </div>
+            <div v-else>
+                <CollectionCreatorHelpHeader>
                     <slot name="help-content"></slot>
+                </CollectionCreatorHelpHeader>
 
-                    <a
-                        class="more-help"
-                        href="javascript:void(0);"
-                        role="button"
-                        :title="localize('Expand or Close Help')"
-                        @click="clickForHelp">
-                    </a>
-                </div>
-            </div>
-        </div>
-
-        <div class="middle flex-row flex-row-container">
-            <slot name="middle-content"></slot>
-        </div>
-
-        <div class="footer flex-row no-flex">
-            <div class="attributes clear">
-                <div class="clear">
-                    <label v-if="renderExtensionsToggle" class="setting-prompt float-right">
-                        {{ localize("Remove file extensions?") }}
-                        <input
-                            class="remove-extensions float-right"
-                            type="checkbox"
-                            checked
-                            @click="emit('remove-extensions-toggle')" />
-                    </label>
-
-                    <label class="setting-prompt float-right">
-                        {{ localize("Hide original elements?") }}
-                        <input v-model="localHideSourceItems" class="hide-originals float-right" type="checkbox" />
-                    </label>
+                <div class="middle flex-row flex-row-container">
+                    <slot name="middle-content"></slot>
                 </div>
 
-                <div class="clear">
-                    <input
-                        v-model="collectionName"
-                        class="collection-name form-control float-right"
-                        :placeholder="localize('Enter a name for your new collection')" />
+                <div class="footer flex-row">
+                    <div class="vertically-spaced">
+                        <CollectionCreatorShowExtensions :extensions="extensions" />
 
-                    <div class="collection-name-prompt float-right">
-                        {{ localize("Name:") }}
+                        <div class="d-flex align-items-center justify-content-between">
+                            <CollectionCreatorSourceOptions
+                                v-model="localHideSourceItems"
+                                :render-extensions-toggle="renderExtensionsToggle"
+                                :extensions-toggle="extensionsToggle"
+                                @remove-extensions-toggle="removeExtensionsToggle" />
+                            <CollectionNameInput
+                                v-model="collectionName"
+                                :short-what-is-being-created="shortWhatIsBeingCreated" />
+                        </div>
                     </div>
+
+                    <CollectionCreatorFooterButtons
+                        :short-what-is-being-created="shortWhatIsBeingCreated"
+                        :valid-input="validInput"
+                        @clicked-cancel="cancelCreate"
+                        @clicked-create="emit('clicked-create', collectionName)" />
                 </div>
             </div>
-
-            <div class="actions clear vertically-spaced">
-                <div class="float-left">
-                    <button class="cancel-create btn" tabindex="-1" @click="cancelCreate">
-                        {{ localize("Cancel") }}
-                    </button>
+        </span>
+        <BTabs v-else v-model="currentTab" fill justified>
+            <BTab class="collection-creator" :title="localize('Create Collection')">
+                <div v-if="props.noItems">
+                    <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
                 </div>
+                <div v-else>
+                    <CollectionCreatorHelpHeader>
+                        <slot name="help-content"></slot>
+                    </CollectionCreatorHelpHeader>
 
-                <div class="main-options float-right">
-                    <button
-                        class="create-collection btn btn-primary"
-                        :disabled="!validInput"
-                        @click="emit('clicked-create', collectionName)">
-                        {{ localize("Create collection") }}
-                    </button>
+                    <div class="middle flex-row flex-row-container">
+                        <slot name="middle-content"></slot>
+                    </div>
+
+                    <div class="footer flex-row">
+                        <div class="vertically-spaced">
+                            <CollectionCreatorShowExtensions :extensions="extensions" />
+
+                            <div class="d-flex align-items-center justify-content-between">
+                                <CollectionCreatorSourceOptions
+                                    v-model="localHideSourceItems"
+                                    :render-extensions-toggle="renderExtensionsToggle"
+                                    :extensions-toggle="extensionsToggle" />
+                                <CollectionNameInput
+                                    v-model="collectionName"
+                                    :short-what-is-being-created="shortWhatIsBeingCreated" />
+                            </div>
+                        </div>
+
+                        <CollectionCreatorFooterButtons
+                            :short-what-is-being-created="shortWhatIsBeingCreated"
+                            :valid-input="validInput"
+                            @clicked-cancel="cancelCreate"
+                            @clicked-create="emit('clicked-create', collectionName)" />
+                    </div>
                 </div>
-            </div>
-        </div>
-    </div>
+            </BTab>
+            <BTab>
+                <template v-slot:title>
+                    <FontAwesomeIcon :icon="faUpload" fixed-width />
+                    <span>{{ localize("Upload Files to Add to Collection") }}</span>
+                </template>
+                <DefaultBox
+                    v-if="configOptions && extensionsSet"
+                    :chunk-upload-size="configOptions.chunkUploadSize"
+                    :default-db-key="configOptions.defaultDbKey"
+                    :default-extension="defaultExtension"
+                    :effective-extensions="props.extensions?.length ? validExtensions : listExtensions"
+                    :file-sources-configured="configOptions.fileSourcesConfigured"
+                    :ftp-upload-site="ftpUploadSite"
+                    :has-callback="false"
+                    :history-id="historyId"
+                    :list-db-keys="[]"
+                    disable-footer
+                    emit-uploaded
+                    @uploaded="addUploadedFiles"
+                    @dismiss="currentTab = Tabs.create">
+                    <template v-slot:footer>
+                        <CollectionCreatorShowExtensions :extensions="extensions" upload />
+                    </template>
+                    <template v-slot:emit-btn-txt>
+                        <FontAwesomeIcon :icon="faPlus" fixed-width />
+                        {{ localize("Add Uploaded") }}
+                    </template>
+                </DefaultBox>
+            </BTab>
+        </BTabs>
+    </span>
 </template>
 
 <style lang="scss">
@@ -146,9 +269,6 @@ $fa-font-path: "../../../../node_modules/@fortawesome/fontawesome-free/webfonts/
 .collection-creator {
     height: 100%;
     overflow: hidden;
-    -webkit-user-select: none;
-    -moz-user-select: none;
-    -ms-user-select: none;
     // ------------------------------------------------------------------------ general
     ol,
     li {
@@ -367,38 +487,11 @@ $fa-font-path: "../../../../node_modules/@fortawesome/fontawesome-free/webfonts/
     }
     // ------------------------------------------------------------------------ footer
     .footer {
-        .attributes {
-            .setting-prompt {
-                //margin-right: 32px;
-                line-height: 32px;
-                padding-left: 10px;
-                .remove-extensions {
-                    display: inline-block;
-                    width: 24px;
-                    height: 24px;
-                }
-                .hide-originals {
-                    display: inline-block;
-                    width: 24px;
-                    height: 24px;
-                }
-            }
-            // actually appears/floats to the left of the input
-            .collection-name-prompt {
-                margin: 5px 4px 0 0;
-            }
-            .collection-name-prompt.validation-warning:before {
-                //TODO: localize (somehow)
-                content: "(required)";
-                margin-right: 4px;
-                color: red;
-            }
-            .collection-name {
-                width: 50%;
-                &.validation-warning {
-                    border-color: red;
-                }
-            }
+        .inputs-form-group > div {
+            width: 100%;
+            display: flex;
+            align-items: center;
+            column-gap: 0.25rem;
         }
         .actions {
             .other-options > * {
diff --git a/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
new file mode 100644
index 0000000000000000000000000000000000000000..3137ade35ad73999704757e28fa3baef011a5302
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
@@ -0,0 +1,27 @@
+<script setup lang="ts">
+import localize from "@/utils/localization";
+
+interface Props {
+    validInput: boolean;
+    shortWhatIsBeingCreated: string;
+}
+
+defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "clicked-create"): void;
+    (e: "clicked-cancel"): void;
+}>();
+</script>
+
+<template>
+    <div class="actions vertically-spaced d-flex justify-content-between">
+        <BButton tabindex="-1" @click="emit('clicked-cancel')">
+            {{ localize("Cancel") }}
+        </BButton>
+
+        <BButton class="create-collection" variant="primary" :disabled="!validInput" @click="emit('clicked-create')">
+            {{ localize("Create " + shortWhatIsBeingCreated) }}
+        </BButton>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
new file mode 100644
index 0000000000000000000000000000000000000000..2564230253d3c97276790628cf09d14bde36ba27
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
@@ -0,0 +1,50 @@
+<script setup lang="ts">
+import { faChevronDown, faChevronUp } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { ref } from "vue";
+
+import localize from "@/utils/localization";
+
+const isExpanded = ref(false);
+
+function clickForHelp() {
+    isExpanded.value = !isExpanded.value;
+    return isExpanded.value;
+}
+</script>
+
+<template>
+    <div class="header flex-row no-flex">
+        <div class="main-help well clear" :class="{ expanded: isExpanded }">
+            <a
+                class="more-help"
+                href="javascript:void(0);"
+                role="button"
+                :title="localize('Expand or Close Help')"
+                @click="clickForHelp">
+                <div v-if="!isExpanded">
+                    <FontAwesomeIcon :icon="faChevronDown" />
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </div>
+                <div v-else>
+                    <FontAwesomeIcon :icon="faChevronUp" />
+                    <span class="sr-only">{{ localize("Close Help") }}</span>
+                </div>
+            </a>
+
+            <div class="help-content">
+                <!-- each collection that extends this will add their own help content -->
+                <slot></slot>
+
+                <a
+                    class="more-help"
+                    href="javascript:void(0);"
+                    role="button"
+                    :title="localize('Expand or Close Help')"
+                    @click="clickForHelp">
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </a>
+            </div>
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
new file mode 100644
index 0000000000000000000000000000000000000000..e1fed5cae18ccde07dc979c2f241d92880eb8e3b
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
@@ -0,0 +1,18 @@
+<script setup lang="ts">
+import { BAlert, BLink } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+
+const emit = defineEmits<{
+    (e: "click-upload"): void;
+}>();
+</script>
+<template>
+    <BAlert variant="info" show>
+        {{ localize("No items available to create a collection.") }}
+        {{ localize("Exit and change your current history, or") }}
+        <BLink class="text-decoration-none" @click.stop.prevent="emit('click-upload')">
+            {{ localize("Upload some datasets.") }}
+        </BLink>
+    </BAlert>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
new file mode 100644
index 0000000000000000000000000000000000000000..c28346fc3ee5a135885ac61d71482c628800a80c
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
@@ -0,0 +1,39 @@
+<script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+import { orList } from "@/utils/strings";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    extensions?: string[];
+    upload?: boolean;
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <div class="d-flex align-items-center justify-content-between mt-2">
+        <BAlert
+            v-if="extensions?.length"
+            class="w-100 py-0 d-flex justify-content-between flex-gapx-1"
+            variant="secondary"
+            show>
+            <div>
+                <HelpText
+                    :uri="`galaxy.collections.collectionBuilder.${
+                        upload ? 'requiredUploadExtensions' : 'filteredExtensions'
+                    }`"
+                    :text="localize(`${upload ? 'Required' : 'Filtered'} format(s):`)" />
+                <strong>{{ orList(extensions) }}</strong>
+            </div>
+            <strong>
+                <i>
+                    <HelpText uri="galaxy.datasets.formatVsDatatypeVsExtension" :text="localize('format?')" />
+                </i>
+            </strong>
+        </BAlert>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
new file mode 100644
index 0000000000000000000000000000000000000000..c35c4bd7e779c5ed7f0b7e3d933e5fa3f442b7b5
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { BFormCheckbox, BFormGroup } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    value: boolean;
+    extensionsToggle?: boolean;
+    renderExtensionsToggle?: boolean;
+}
+
+const props = defineProps<Props>();
+
+const localHideSourceItems = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: boolean): void;
+    (e: "remove-extensions-toggle"): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        localHideSourceItems.value = newValue;
+    }
+);
+
+watch(localHideSourceItems, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup class="inputs-form-group">
+        <BFormCheckbox
+            v-if="renderExtensionsToggle"
+            name="remove-extensions"
+            switch
+            :checked="extensionsToggle"
+            @input="emit('remove-extensions-toggle')">
+            {{ localize("Remove file extensions?") }}
+        </BFormCheckbox>
+
+        <div data-description="hide original elements">
+            <BFormCheckbox v-model="localHideSourceItems" name="hide-originals" switch>
+                <HelpText
+                    uri="galaxy.collections.collectionBuilder.hideOriginalElements"
+                    :text="localize('Hide original elements')" />
+            </BFormCheckbox>
+        </div>
+    </BFormGroup>
+</template>
diff --git a/client/src/components/Collections/common/CollectionEditView.vue b/client/src/components/Collections/common/CollectionEditView.vue
index 5f231903a45164e940c3d127d0f8b879e83a1f73..eb3d55013f3de579df2db311fa1e6cc8d15926b1 100644
--- a/client/src/components/Collections/common/CollectionEditView.vue
+++ b/client/src/components/Collections/common/CollectionEditView.vue
@@ -7,7 +7,7 @@ import { BAlert, BButton, BSpinner, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
-import { copyCollection } from "@/api/datasetCollections";
+import { GalaxyApi } from "@/api";
 import { updateContentFields } from "@/components/History/model/queries";
 import { DatatypesProvider, DbKeyProvider, SuitableConvertersProvider } from "@/components/providers";
 import { useConfig } from "@/composables/config";
@@ -18,8 +18,6 @@ import localize from "@/utils/localization";
 import { prependPath } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import { HistoryContentBulkOperationPayload, updateHistoryItemsBulk } from "./services";
-
 import ChangeDatatypeTab from "@/components/Collections/common/ChangeDatatypeTab.vue";
 import DatabaseEditTab from "@/components/Collections/common/DatabaseEditTab.vue";
 import SuitableConvertersTab from "@/components/Collections/common/SuitableConvertersTab.vue";
@@ -55,9 +53,34 @@ const collectionChangeKey = ref(0);
 const attributesData = computed(() => {
     return collectionAttributesStore.getAttributes(props.collectionId);
 });
+
+const attributesLoadError = computed(() => {
+    const itemLoadError = collectionAttributesStore.getItemLoadError(props.collectionId);
+    if (itemLoadError) {
+        return errorMessageAsString(itemLoadError);
+    }
+    return undefined;
+});
+
 const collection = computed(() => {
     return collectionStore.getCollectionById(props.collectionId);
 });
+const collectionLoadError = computed(() => {
+    if (collection.value) {
+        const collectionElementLoadError = collectionStore.getLoadingCollectionElementsError(collection.value);
+        if (collectionElementLoadError) {
+            return errorMessageAsString(collectionElementLoadError);
+        }
+    }
+    return undefined;
+});
+watch([attributesLoadError, collectionLoadError], () => {
+    if (attributesLoadError.value) {
+        errorMessage.value = attributesLoadError.value;
+    } else if (collectionLoadError.value) {
+        errorMessage.value = collectionLoadError.value;
+    }
+});
 const databaseKeyFromElements = computed(() => {
     return attributesData.value?.dbkey;
 });
@@ -96,12 +119,14 @@ async function clickedSave(attribute: string, newValue: any) {
         return;
     }
 
-    const dbKey = newValue.id;
+    const dbKey = newValue.id as string;
 
-    try {
-        await copyCollection(props.collectionId, dbKey);
-    } catch (err) {
-        errorMessage.value = errorMessageAsString(err, "History import failed.");
+    const { error } = await GalaxyApi().POST("/api/dataset_collections/{id}/copy", {
+        params: { path: { id: props.collectionId } },
+        body: { dbkey: dbKey },
+    });
+    if (error) {
+        errorMessage.value = errorMessageAsString(error, `Changing ${attribute} failed.`);
     }
 }
 
@@ -119,36 +144,43 @@ async function clickedConvert(selectedConverter: any) {
         await axios.post(url, data).catch(handleError);
         successMessage.value = "Conversion started successfully.";
     } catch (err) {
-        errorMessage.value = errorMessageAsString(err, "History import failed.");
+        errorMessage.value = errorMessageAsString(err, "Conversion failed.");
     }
 }
 
 // TODO: Replace with actual datatype type
 async function clickedDatatypeChange(selectedDatatype: any) {
-    const data: HistoryContentBulkOperationPayload = {
-        items: [
-            {
-                history_content_type: "dataset_collection",
-                id: props.collectionId,
+    if (!currentHistoryId.value) {
+        errorMessage.value = "No current history selected.";
+        return;
+    }
+
+    const { error } = await GalaxyApi().PUT("/api/histories/{history_id}/contents/bulk", {
+        params: { path: { history_id: currentHistoryId.value } },
+        body: {
+            items: [
+                {
+                    history_content_type: "dataset_collection",
+                    id: props.collectionId,
+                },
+            ],
+            operation: "change_datatype",
+            params: {
+                type: "change_datatype",
+                datatype: selectedDatatype.id,
             },
-        ],
-        operation: "change_datatype",
-        params: {
-            type: "change_datatype",
-            datatype: selectedDatatype.id,
         },
-    };
+    });
 
-    try {
-        await updateHistoryItemsBulk(currentHistoryId.value ?? "", data);
-        successMessage.value = "Datatype changed successfully.";
-    } catch (err) {
-        errorMessage.value = errorMessageAsString(err, "History import failed.");
+    if (error) {
+        errorMessage.value = errorMessageAsString(error, "Datatype change failed.");
+        return;
     }
+    successMessage.value = "Datatype changed successfully.";
 }
 
 function handleError(err: any) {
-    errorMessage.value = errorMessageAsString(err, "History import failed.");
+    errorMessage.value = errorMessageAsString(err, "Datatype conversion failed.");
 
     if (err?.data?.stderr) {
         jobError.value = err.data;
@@ -191,14 +223,14 @@ async function saveAttrs() {
             {{ localize(infoMessage) }}
         </BAlert>
 
-        <BAlert v-if="jobError" show variant="danger" dismissible>
+        <BAlert v-if="errorMessage" show variant="danger">
             {{ localize(errorMessage) }}
         </BAlert>
 
         <BAlert v-if="successMessage" show variant="success" dismissible>
             {{ localize(successMessage) }}
         </BAlert>
-        <BTabs class="mt-3">
+        <BTabs v-if="!errorMessage" class="mt-3">
             <BTab title-link-class="collection-edit-attributes-nav" @click="updateInfoMessage('')">
                 <template v-slot:title>
                     <FontAwesomeIcon :icon="faBars" class="mr-1" />
diff --git a/client/src/components/Collections/common/CollectionNameInput.vue b/client/src/components/Collections/common/CollectionNameInput.vue
new file mode 100644
index 0000000000000000000000000000000000000000..7f299899efb92bb292f56ff3aeeddb553f0780be
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionNameInput.vue
@@ -0,0 +1,47 @@
+<script setup lang="ts">
+import { BFormGroup, BFormInput } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+interface Props {
+    value: string;
+    shortWhatIsBeingCreated: string;
+}
+
+const props = defineProps<Props>();
+
+const name = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: string): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        name.value = newValue;
+    }
+);
+
+watch(name, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup
+        class="flex-gapx-1 d-flex align-items-center w-50 inputs-form-group"
+        :label="localize('Name:')"
+        label-for="collection-name">
+        <BFormInput
+            id="collection-name"
+            v-model="name"
+            class="collection-name"
+            :placeholder="localize('Enter a name for your new ' + shortWhatIsBeingCreated)"
+            size="sm"
+            required
+            :state="!name ? false : null" />
+    </BFormGroup>
+</template>
diff --git a/client/src/components/Collections/common/modal.js b/client/src/components/Collections/common/modal.js
index a823d1c2765770da05f6a6254446261e884d4600..eaf90715aa3ec570a28997bc2c11390d6aff5dc6 100644
--- a/client/src/components/Collections/common/modal.js
+++ b/client/src/components/Collections/common/modal.js
@@ -17,8 +17,14 @@ export function collectionCreatorModalSetup(options, Galaxy = null) {
     });
     const showEl = function (el) {
         const close_event = options.closing_events === undefined || options.closing_events;
+        const title = options.title || _l("Create a collection");
+        const titleSuffix = options.historyName ? `From history: <b>${options.historyName}</b>` : "";
+        const titleHtml = `<div class='d-flex justify-content-between unselectable'>
+                <span>${title}</span>
+                <span>${titleSuffix}</span>
+            </div>`;
         modal.show({
-            title: options.title || _l("Create a collection"),
+            title: titleHtml,
             body: el,
             width: "85%",
             height: "100%",
diff --git a/client/src/components/Collections/common/modal.test.js b/client/src/components/Collections/common/modal.test.js
index e5a0f13849047ea932f1cce735a26c7a8b5a8031..97905524972becee83bb24a5b00b0e51161d6628 100644
--- a/client/src/components/Collections/common/modal.test.js
+++ b/client/src/components/Collections/common/modal.test.js
@@ -41,7 +41,7 @@ describe("modal.js", () => {
         it("should create showEl and resolve oncreate", async () => {
             expect(showOptions).toBe(null);
             showEl();
-            expect(showOptions.title).toEqual("Create a collection");
+            expect(showOptions.title).toContain("Create a collection");
 
             expect(hidden).toBeFalsy();
             options.oncreate(null, "testres");
diff --git a/client/src/components/Collections/common/services.ts b/client/src/components/Collections/common/services.ts
deleted file mode 100644
index fd6287c4114ecf47869481dce3d9f6b4e9151f93..0000000000000000000000000000000000000000
--- a/client/src/components/Collections/common/services.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import { updateHistoryItemsInBulk } from "@/api/histories";
-import { type components } from "@/api/schema";
-
-export type HistoryContentBulkOperationPayload = components["schemas"]["HistoryContentBulkOperationPayload"];
-
-export async function updateHistoryItemsBulk(historyId: string, changes: HistoryContentBulkOperationPayload) {
-    await updateHistoryItemsInBulk({ history_id: historyId, ...changes });
-}
diff --git a/client/src/components/Common/ButtonSpinner.vue b/client/src/components/Common/ButtonSpinner.vue
index e2b8def400c1fcb3bb49d5ece6853c584c15a03d..31fa475980afc6f4b914593ecab0bce5618fbff5 100644
--- a/client/src/components/Common/ButtonSpinner.vue
+++ b/client/src/components/Common/ButtonSpinner.vue
@@ -1,22 +1,27 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
+import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { faPlay, faSpinner } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 
-library.add(faPlay, faSpinner);
-
 interface Props {
-    title: string;
+    title?: string;
     wait?: boolean;
     tooltip?: string;
     disabled?: boolean;
+    size?: string;
+    variant?: string;
+    icon?: IconDefinition;
 }
 
 withDefaults(defineProps<Props>(), {
+    title: "",
     wait: false,
-    tooltip: undefined,
+    tooltip: "",
     disabled: false,
+    size: "md",
+    variant: "primary",
+    icon: undefined,
 });
 </script>
 
@@ -25,21 +30,27 @@ withDefaults(defineProps<Props>(), {
         v-if="wait"
         v-b-tooltip.hover.bottom
         disabled
+        :size="size"
         variant="info"
         title="Please Wait..."
         class="d-flex flex-nowrap align-items-center text-nowrap">
-        <FontAwesomeIcon :icon="faSpinner" class="mr-2" spin />
-        {{ title }}
+        <FontAwesomeIcon :icon="faSpinner" fixed-width spin />
+        <slot>
+            <span v-if="title">{{ title }}</span>
+        </slot>
     </BButton>
     <BButton
         v-else
         v-b-tooltip.hover.bottom
-        variant="primary"
+        :variant="variant"
         class="d-flex flex-nowrap align-items-center text-nowrap"
         :title="tooltip"
         :disabled="disabled"
+        :size="size"
         @click="$emit('onClick')">
-        <FontAwesomeIcon :icon="faPlay" class="mr-2" />
-        {{ title }}
+        <FontAwesomeIcon :icon="!icon ? faPlay : icon" fixed-width />
+        <slot>
+            <span v-if="title">{{ title }}</span>
+        </slot>
     </BButton>
 </template>
diff --git a/client/src/components/Common/DelayedInput.vue b/client/src/components/Common/DelayedInput.vue
index 490c33de45d1e7096a81822d5f983583166ba668..bbd9bc54664646408985472eceaf60dc6ffb2070 100644
--- a/client/src/components/Common/DelayedInput.vue
+++ b/client/src/components/Common/DelayedInput.vue
@@ -2,15 +2,16 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faAngleDoubleDown, faAngleDoubleUp, faSpinner, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { watchImmediate } from "@vueuse/core";
 import { BButton, BFormInput, BInputGroup, BInputGroupAppend } from "bootstrap-vue";
-import { onMounted, ref, watch } from "vue";
+import { ref, watch } from "vue";
 
 import localize from "@/utils/localization";
 
 library.add(faAngleDoubleDown, faAngleDoubleUp, faSpinner, faTimes);
 
 interface Props {
-    query?: string;
+    value?: string;
     delay?: number;
     loading?: boolean;
     placeholder?: string;
@@ -19,7 +20,7 @@ interface Props {
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    query: "",
+    value: "",
     delay: 1000,
     loading: false,
     placeholder: "Enter your search term here.",
@@ -28,13 +29,13 @@ const props = withDefaults(defineProps<Props>(), {
 });
 
 const emit = defineEmits<{
-    (e: "change", query: string): void;
+    (e: "input", value: string): void;
+    (e: "change", value: string): void;
     (e: "onToggle", showAdvanced: boolean): void;
 }>();
 
 const queryInput = ref<string>();
-const queryCurrent = ref<string>();
-const queryTimer = ref<any>(null);
+const queryTimer = ref<ReturnType<typeof setTimeout> | null>(null);
 const titleClear = ref("Clear Search (esc)");
 const titleAdvanced = ref("Toggle Advanced Search");
 const toolInput = ref<HTMLInputElement | null>(null);
@@ -57,16 +58,17 @@ function delayQuery(query: string) {
 }
 
 function setQuery(queryNew: string) {
-    clearTimer();
-
-    if (queryCurrent.value !== queryInput.value || queryCurrent.value !== queryNew) {
-        queryCurrent.value = queryInput.value = queryNew;
-        emit("change", queryCurrent.value);
-    }
+    emit("input", queryNew);
+    emit("change", queryNew);
 }
 
+watch(
+    () => queryInput.value,
+    () => delayQuery(queryInput.value ?? "")
+);
+
 function clearBox() {
-    setQuery("");
+    queryInput.value = "";
     toolInput.value?.focus();
 }
 
@@ -74,18 +76,12 @@ function onToggle() {
     emit("onToggle", !props.showAdvanced);
 }
 
-watch(
-    () => props.query,
+watchImmediate(
+    () => props.value,
     (newQuery) => {
-        setQuery(newQuery);
+        queryInput.value = newQuery;
     }
 );
-
-onMounted(() => {
-    if (props.query) {
-        setQuery(props.query);
-    }
-});
 </script>
 
 <template>
@@ -98,9 +94,7 @@ onMounted(() => {
             autocomplete="off"
             :placeholder="placeholder"
             data-description="filter text input"
-            @input="delayQuery"
-            @change="setQuery"
-            @keydown.esc="setQuery('')" />
+            @keydown.esc="clearBox" />
 
         <BInputGroupAppend>
             <BButton
diff --git a/client/src/components/Common/DraggableSeparator.vue b/client/src/components/Common/DraggableSeparator.vue
new file mode 100644
index 0000000000000000000000000000000000000000..f63aa8f397a9abfef00c05dcf88b0619513c1a76
--- /dev/null
+++ b/client/src/components/Common/DraggableSeparator.vue
@@ -0,0 +1,191 @@
+<script setup lang="ts">
+import { useDebounce, useDraggable, useElementBounding } from "@vueuse/core";
+import { computed, onMounted, ref, watch } from "vue";
+
+import { useEmit } from "@/composables/eventEmitter";
+import { useClamp } from "@/composables/math";
+import { useAnimationFrameThrottle } from "@/composables/throttle";
+
+const props = withDefaults(
+    defineProps<{
+        position: number;
+        min?: number;
+        max?: number;
+        showDelay?: number;
+        keyboardStepSize?: number;
+        side: "left" | "right";
+        inner?: boolean;
+    }>(),
+    {
+        showDelay: 100,
+        keyboardStepSize: 50,
+        min: 0,
+        max: Infinity,
+        inner: false,
+    }
+);
+
+const emit = defineEmits<{
+    (e: "positionChanged", position: number): void;
+    (e: "visibilityChanged", isVisible: boolean): void;
+    (e: "dragging", isDragging: boolean): void;
+}>();
+
+const { throttle } = useAnimationFrameThrottle();
+
+const draggable = ref<HTMLButtonElement | null>(null);
+const positionedParent = ref<HTMLElement | null>(null);
+
+onMounted(() => {
+    positionedParent.value = (draggable.value?.offsetParent as HTMLElement) ?? null;
+});
+
+const rootBoundingBox = useElementBounding(positionedParent);
+
+const { position: draggablePosition, isDragging } = useDraggable(draggable, {
+    preventDefault: true,
+    exact: true,
+    initialValue: { x: props.position, y: 0 },
+});
+
+useEmit(isDragging, emit, "dragging");
+
+const handlePosition = useClamp(
+    ref(props.position),
+    () => props.min,
+    () => props.max
+);
+
+useEmit(handlePosition, emit, "positionChanged");
+
+watch(
+    () => props.position,
+    () => (handlePosition.value = props.position)
+);
+
+const borderWidth = 6;
+
+function updatePosition() {
+    if (props.side === "left") {
+        handlePosition.value = draggablePosition.value.x - rootBoundingBox.left.value + borderWidth;
+    } else {
+        const clientWidth = document.body.clientWidth;
+        const rootRightDistance = document.body.clientWidth - rootBoundingBox.right.value;
+        handlePosition.value = clientWidth - draggablePosition.value.x - rootRightDistance - borderWidth;
+    }
+}
+
+watch(
+    () => draggablePosition.value,
+    () => throttle(updatePosition)
+);
+
+const hoverDraggable = ref(false);
+
+const hoverDraggableDebounced = useDebounce(
+    hoverDraggable,
+    computed(() => props.showDelay)
+);
+
+const showHover = computed(() => (hoverDraggable.value && hoverDraggableDebounced.value) || isDragging.value);
+
+useEmit(showHover, emit, "visibilityChanged");
+
+function onKeyLeft() {
+    handlePosition.value -= props.keyboardStepSize;
+}
+
+function onKeyRight() {
+    handlePosition.value += props.keyboardStepSize;
+}
+
+const style = computed(() => ({
+    "--position": handlePosition.value + "px",
+}));
+</script>
+
+<template>
+    <button
+        ref="draggable"
+        class="drag-handle"
+        :class="[`side-${props.side}`, { show: showHover, inner: props.inner }]"
+        :style="style"
+        @mouseenter="hoverDraggable = true"
+        @focusin="hoverDraggable = true"
+        @mouseout="hoverDraggable = false"
+        @focusout="hoverDraggable = false"
+        @keydown.left="onKeyLeft"
+        @keydown.right="onKeyRight">
+        <span class="sr-only"> Resizable drag handle </span>
+    </button>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+$border-width: 6px;
+
+.drag-handle {
+    --position: 0;
+
+    background-color: transparent;
+    border: none;
+    border-radius: 0;
+    position: absolute;
+    width: $border-width;
+    padding: 0;
+    height: 100%;
+    z-index: 10000;
+    top: 0;
+
+    --hover-expand: 4px;
+
+    &:hover {
+        cursor: ew-resize;
+        width: calc($border-width + var(--hover-expand));
+    }
+
+    &.side-left {
+        left: var(--position);
+
+        &.inner {
+            left: min(var(--position), calc(100% + 1px));
+        }
+
+        margin-left: -$border-width;
+    }
+
+    &.side-right {
+        right: var(--position);
+
+        &.inner {
+            right: min(var(--position), calc(100% + 1px));
+        }
+
+        margin-right: -$border-width;
+    }
+
+    &::after {
+        display: block;
+        content: "";
+        position: absolute;
+        top: 0;
+        width: $border-width;
+        height: 100%;
+        background-color: transparent;
+        transition: background-color 0.1s;
+    }
+
+    &.show::after {
+        background-color: $brand-info;
+    }
+
+    &.side-left.show::after {
+        left: 0;
+    }
+
+    &.side-right.show::after {
+        right: 0;
+    }
+}
+</style>
diff --git a/client/src/components/Common/ExportForm.vue b/client/src/components/Common/ExportForm.vue
index df58871a369bd74c3b0a3d3b24ebea4a168fba6a..18e0a7ff670209516a5b61cd34fb5539ef06f0f6 100644
--- a/client/src/components/Common/ExportForm.vue
+++ b/client/src/components/Common/ExportForm.vue
@@ -2,7 +2,7 @@
 import { BButton, BCol, BFormGroup, BFormInput, BRow } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { FilterFileSourcesOptions } from "@/api/remoteFiles";
+import { type FilterFileSourcesOptions } from "@/api/remoteFiles";
 import localize from "@/utils/localization";
 
 import FilesInput from "@/components/FilesDialog/FilesInput.vue";
diff --git a/client/src/components/Common/ExportRDMForm.test.ts b/client/src/components/Common/ExportRDMForm.test.ts
deleted file mode 100644
index 1f53d7cc1a99458e7d42e8f39974323908589588..0000000000000000000000000000000000000000
--- a/client/src/components/Common/ExportRDMForm.test.ts
+++ /dev/null
@@ -1,185 +0,0 @@
-import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
-import flushPromises from "flush-promises";
-
-import { type BrowsableFilesSourcePlugin, CreatedEntry } from "@/api/remoteFiles";
-import { mockFetcher } from "@/api/schema/__mocks__";
-
-import ExportRDMForm from "./ExportRDMForm.vue";
-import FilesInput from "@/components/FilesDialog/FilesInput.vue";
-
-jest.mock("@/api/schema");
-
-const localVue = getLocalVue(true);
-
-const CREATE_RECORD_BTN = "#create-record-button";
-const EXPORT_TO_NEW_RECORD_BTN = "#export-button-new-record";
-const EXPORT_TO_EXISTING_RECORD_BTN = "#export-button-existing-record";
-
-const FAKE_RDM_SOURCE_URI = "gxfiles://test-uri";
-const FAKE_RDM_EXISTING_RECORD_URI = "gxfiles://test-uri/test-record";
-const FAKE_RECORD_NAME = "test record name";
-const FAKE_ENTRY: CreatedEntry = {
-    uri: FAKE_RDM_SOURCE_URI,
-    name: FAKE_RECORD_NAME,
-    external_link: "http://example.com",
-};
-
-async function initWrapper(fileSource?: BrowsableFilesSourcePlugin) {
-    mockFetcher.path("/api/remote_files").method("post").mock({ data: FAKE_ENTRY });
-
-    const wrapper = mount(ExportRDMForm as object, {
-        propsData: {
-            fileSource,
-        },
-        localVue,
-    });
-    await flushPromises();
-    return wrapper;
-}
-
-describe("ExportRDMForm", () => {
-    let wrapper: Wrapper<Vue>;
-
-    beforeEach(async () => {
-        wrapper = await initWrapper();
-    });
-
-    describe("Export to new record", () => {
-        beforeEach(async () => {
-            await selectExportChoice("new");
-        });
-
-        it("enables the create new record button when the required fields are filled in", async () => {
-            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
-
-            await setRecordNameInput(FAKE_RECORD_NAME);
-            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
-
-            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
-        });
-
-        it("displays the export to this record button when the create new record button is clicked", async () => {
-            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeFalsy();
-
-            await setRecordNameInput(FAKE_RECORD_NAME);
-            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
-            await clickCreateNewRecordButton();
-
-            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeTruthy();
-        });
-
-        it("emits an export event when the export to new record button is clicked", async () => {
-            await setFileNameInput("test file name");
-            await setRecordNameInput(FAKE_RECORD_NAME);
-            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
-            await clickCreateNewRecordButton();
-
-            await wrapper.find(EXPORT_TO_NEW_RECORD_BTN).trigger("click");
-            expect(wrapper.emitted("export")).toBeTruthy();
-        });
-    });
-
-    describe("Export to existing record", () => {
-        beforeEach(async () => {
-            await selectExportChoice("existing");
-        });
-
-        it("enables the export to existing record button when the required fields are filled in", async () => {
-            expect(wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).attributes("disabled")).toBeTruthy();
-
-            await setFileNameInput("test file name");
-            await setRDMDirectoryInput(FAKE_RDM_EXISTING_RECORD_URI);
-
-            expect(wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).attributes("disabled")).toBeFalsy();
-        });
-
-        it("emits an export event when the export to existing record button is clicked", async () => {
-            await setFileNameInput("test file name");
-            await setRDMDirectoryInput(FAKE_RDM_EXISTING_RECORD_URI);
-            await wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).trigger("click");
-            expect(wrapper.emitted("export")).toBeTruthy();
-        });
-    });
-
-    describe("Pre-select specific File Source", () => {
-        beforeEach(async () => {
-            const specificFileSource: BrowsableFilesSourcePlugin = {
-                id: "test-file-source",
-                label: "Test File Source",
-                doc: "Test File Source Description",
-                uri_root: "gxfiles://test-file-source",
-                writable: true,
-                browsable: true,
-                type: "rdm",
-            };
-            wrapper = await initWrapper(specificFileSource);
-        });
-
-        it("enables the create new record button only by setting the record name", async () => {
-            await selectExportChoice("new", "test-file-source");
-            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
-
-            await setRecordNameInput(FAKE_RECORD_NAME);
-
-            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
-        });
-
-        it("displays the export to this record button when the create new record button is clicked", async () => {
-            await selectExportChoice("new", "test-file-source");
-            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeFalsy();
-
-            await setRecordNameInput(FAKE_RECORD_NAME);
-            await clickCreateNewRecordButton();
-
-            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeTruthy();
-        });
-
-        it("emits an export event when the export to new record button is clicked", async () => {
-            await selectExportChoice("new", "test-file-source");
-            await setFileNameInput("test file name");
-            await setRecordNameInput(FAKE_RECORD_NAME);
-            await clickCreateNewRecordButton();
-
-            await wrapper.find(EXPORT_TO_NEW_RECORD_BTN).trigger("click");
-            expect(wrapper.emitted("export")).toBeTruthy();
-        });
-    });
-
-    async function selectExportChoice(choice: string, fileSourceId?: string) {
-        const suffix = fileSourceId ? `${fileSourceId}` : "any";
-        const exportChoice = wrapper.find(`#radio-${choice}-${suffix}`);
-        await exportChoice.setChecked(true);
-    }
-
-    async function setRDMSourceInput(newValue: string) {
-        const component = wrapper.findComponent(FilesInput);
-        expect(component.attributes("placeholder")).toContain("source");
-        component.vm.$emit("input", newValue);
-        await flushPromises();
-    }
-
-    async function setRDMDirectoryInput(newValue: string) {
-        const component = wrapper.findComponent(FilesInput);
-        expect(component.attributes("placeholder")).toContain("directory");
-        component.vm.$emit("input", newValue);
-        await flushPromises();
-    }
-
-    async function setRecordNameInput(newValue: string) {
-        const recordNameInput = wrapper.find("#record-name-input");
-        await recordNameInput.setValue(newValue);
-    }
-
-    async function setFileNameInput(newValue: string) {
-        const recordNameInput = wrapper.find("#file-name-input");
-        await recordNameInput.setValue(newValue);
-    }
-
-    async function clickCreateNewRecordButton() {
-        const createRecordButton = wrapper.find(CREATE_RECORD_BTN);
-        expect(createRecordButton.attributes("disabled")).toBeFalsy();
-        await createRecordButton.trigger("click");
-        await flushPromises();
-    }
-});
diff --git a/client/src/components/Common/ExportRDMForm.vue b/client/src/components/Common/ExportRDMForm.vue
index f99510a59907e8984d198d46f7ede28354dd5d9f..aa8ea7ac01d4a170204d13e16c5f93f38fa24fba 100644
--- a/client/src/components/Common/ExportRDMForm.vue
+++ b/client/src/components/Common/ExportRDMForm.vue
@@ -1,23 +1,11 @@
 <script setup lang="ts">
-import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue";
+import { BButton, BFormGroup, BFormInput } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import {
-    BrowsableFilesSourcePlugin,
-    CreatedEntry,
-    createRemoteEntry,
-    FilterFileSourcesOptions,
-} from "@/api/remoteFiles";
-import { useToast } from "@/composables/toast";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 import localize from "@/utils/localization";
-import { errorMessageAsString } from "@/utils/simple-error";
 
-import { fileSourcePluginToItem } from "../FilesDialog/utilities";
-
-import ExternalLink from "@/components/ExternalLink.vue";
-import FilesInput from "@/components/FilesDialog/FilesInput.vue";
-
-const toast = useToast();
+import RDMDestinationSelector from "@/components/Common/RDMDestinationSelector.vue";
 
 interface Props {
     what?: string;
@@ -43,31 +31,17 @@ const emit = defineEmits<{
     (e: "export", recordUri: string, fileName: string, newRecordName?: string): void;
 }>();
 
-type ExportChoice = "existing" | "new";
-
-const includeOnlyRDMCompatible: FilterFileSourcesOptions = { include: ["rdm"] };
+const destinationSelector = ref<InstanceType<typeof RDMDestinationSelector>>();
 
 const recordUri = ref<string>("");
-const sourceUri = ref<string>(props.fileSource?.uri_root ?? "");
 const fileName = ref<string>(props.defaultFilename);
-const exportChoice = ref<ExportChoice>("new");
-const recordName = ref<string>(props.defaultRecordName);
-const newEntry = ref<CreatedEntry>();
-
-const canCreateRecord = computed(() => Boolean(sourceUri.value) && Boolean(recordName.value));
+const isNewRecord = ref(true);
 
 const canExport = computed(() => Boolean(recordUri.value) && Boolean(fileName.value));
 
-const repositoryRecordDescription = computed(() => localize(`Select a repository to export ${props.what} to.`));
-
 const nameDescription = computed(() => localize("Give the exported file a name."));
-const recordNameDescription = computed(() => localize("Give the new record a name or title."));
 
 const namePlaceholder = computed(() => localize("File name"));
-const recordNamePlaceholder = computed(() => localize("Record name"));
-
-const uniqueSourceId = computed(() => props.fileSource?.id ?? "any");
-const fileSourceAsItem = computed(() => (props.fileSource ? fileSourcePluginToItem(props.fileSource) : undefined));
 
 function doExport() {
     emit("export", recordUri.value, fileName.value);
@@ -77,20 +51,16 @@ function doExport() {
     }
 }
 
-async function doCreateRecord() {
-    try {
-        newEntry.value = await createRemoteEntry(sourceUri.value, recordName.value);
-        recordUri.value = newEntry.value.uri;
-    } catch (e) {
-        toast.error(errorMessageAsString(e));
-    }
-}
-
 function clearInputs() {
     recordUri.value = "";
-    sourceUri.value = props.fileSource?.uri_root ?? "";
     fileName.value = "";
-    newEntry.value = undefined;
+
+    //@ts-ignore incorrect property not found error
+    destinationSelector.value?.reset();
+}
+
+function onRecordSelected(selectedRecordUri: string) {
+    recordUri.value = selectedRecordUri;
 }
 </script>
 
@@ -100,106 +70,28 @@ function clearInputs() {
             <BFormInput id="file-name-input" v-model="fileName" :placeholder="namePlaceholder" required />
         </BFormGroup>
 
-        <p>
-            Your {{ what }} needs to be uploaded to an existing <i>draft</i> record. You will need to create a
-            <b>new record</b> or select an existing <b>draft record</b> and then export your {{ what }} to it.
-        </p>
-
-        <BFormRadioGroup v-model="exportChoice" class="export-radio-group">
-            <BFormRadio :id="`radio-new-${uniqueSourceId}`" v-localize name="exportChoice" value="new">
-                Export to new record
-            </BFormRadio>
-
-            <BFormRadio :id="`radio-existing-${uniqueSourceId}`" v-localize name="exportChoice" value="existing">
-                Export to existing draft record
-            </BFormRadio>
-        </BFormRadioGroup>
-
-        <div v-if="exportChoice === 'new'">
-            <div v-if="newEntry">
-                <BCard>
-                    <p>
-                        <b>{{ newEntry.name }}</b>
-                        <span v-localize> draft record has been created in the repository.</span>
-                    </p>
-
-                    <p v-if="newEntry.external_link">
-                        You can preview the record in the repository, further edit its metadata and decide when to
-                        publish it at
-                        <ExternalLink :href="newEntry.external_link">
-                            <b>{{ newEntry.external_link }}</b>
-                        </ExternalLink>
-                    </p>
-
-                    <p v-localize>Please use the button below to upload the exported {{ props.what }} to the record.</p>
-
-                    <BButton
-                        id="export-button-new-record"
-                        v-localize
-                        class="export-button"
-                        variant="primary"
-                        :disabled="!canExport"
-                        @click.prevent="doExport">
-                        Export to this record
-                    </BButton>
-                </BCard>
-            </div>
-            <div v-else>
-                <BFormGroup
-                    v-if="!props.fileSource"
-                    id="fieldset-record-new"
-                    label-for="source-selector"
-                    :description="repositoryRecordDescription"
-                    class="mt-3">
-                    <FilesInput
-                        id="source-selector"
-                        v-model="sourceUri"
-                        mode="source"
-                        :require-writable="true"
-                        :filter-options="includeOnlyRDMCompatible" />
-                </BFormGroup>
-
-                <BFormGroup
-                    id="fieldset-record-name"
-                    label-for="record-name"
-                    :description="recordNameDescription"
-                    class="mt-3">
-                    <BFormInput
-                        id="record-name-input"
-                        v-model="recordName"
-                        :placeholder="recordNamePlaceholder"
-                        required />
-                </BFormGroup>
-
-                <p v-localize>
-                    You need to create the new record in a repository before exporting the {{ props.what }} to it.
-                </p>
-
-                <BButton
-                    id="create-record-button"
-                    v-localize
-                    variant="primary"
-                    :disabled="!canCreateRecord"
-                    @click.prevent="doCreateRecord">
-                    Create new record
-                </BButton>
-            </div>
+        <RDMDestinationSelector
+            ref="destinationSelector"
+            :what="what"
+            :file-source="fileSource"
+            @onRecordSelected="onRecordSelected" />
+
+        <div v-if="isNewRecord">
+            <p v-localize class="mt-3">
+                Please use the button below to upload the exported {{ props.what }} to the record.
+            </p>
+
+            <BButton
+                id="export-button-new-record"
+                v-localize
+                class="export-button"
+                variant="primary"
+                :disabled="!canExport"
+                @click.prevent="doExport">
+                Export to this record
+            </BButton>
         </div>
         <div v-else>
-            <BFormGroup
-                id="fieldset-record-existing"
-                label-for="existing-record-selector"
-                :description="repositoryRecordDescription"
-                class="mt-3">
-                <FilesInput
-                    id="existing-record-selector"
-                    v-model="recordUri"
-                    mode="directory"
-                    :require-writable="true"
-                    :filter-options="fileSource ? undefined : includeOnlyRDMCompatible"
-                    :selected-item="fileSourceAsItem" />
-            </BFormGroup>
-
             <BButton
                 id="export-button-existing-record"
                 v-localize
diff --git a/client/src/components/Common/ExportRecordDOILink.vue b/client/src/components/Common/ExportRecordDOILink.vue
index 22683615482c291cb28e752bc0279e831477b6c9..4ea087d40b1215d42f0446baa979deb52d7c39f2 100644
--- a/client/src/components/Common/ExportRecordDOILink.vue
+++ b/client/src/components/Common/ExportRecordDOILink.vue
@@ -2,7 +2,7 @@
 import axios from "axios";
 import { ref, watch } from "vue";
 
-import { BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 import { useFileSources } from "@/composables/fileSources";
 
 import DOILink from "./DOILink.vue";
diff --git a/client/src/components/Common/ExportRecordDetails.vue b/client/src/components/Common/ExportRecordDetails.vue
index 6d4199f6e905af5c7d874ac343f61891d0b2445e..58ad35898ff27ec2d2c3de13cbed48bb3e513870 100644
--- a/client/src/components/Common/ExportRecordDetails.vue
+++ b/client/src/components/Common/ExportRecordDetails.vue
@@ -12,7 +12,7 @@ import { BAlert, BButton } from "bootstrap-vue";
 import { computed } from "vue";
 
 import type { ColorVariant } from ".";
-import { ExportRecord } from "./models/exportRecordModel";
+import { type ExportRecord } from "./models/exportRecordModel";
 
 import Heading from "@/components/Common/Heading.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
diff --git a/client/src/components/Common/FilterMenu.test.ts b/client/src/components/Common/FilterMenu.test.ts
index 8474981948dc59c77c5ab4a7bef114c984c61d6e..9ee23c61bc720be4071554405c57e4b8114b8c66 100644
--- a/client/src/components/Common/FilterMenu.test.ts
+++ b/client/src/components/Common/FilterMenu.test.ts
@@ -1,9 +1,9 @@
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 
 import { HistoryFilters } from "@/components/History/HistoryFilters";
-import { WorkflowFilters } from "@/components/Workflow/WorkflowFilters";
+import { getWorkflowFilters } from "@/components/Workflow/List/workflowFilters";
 import Filtering, { compare, contains, equals, toBool, toDate } from "@/utils/filtering";
 
 import FilterMenu from "./FilterMenu.vue";
@@ -198,48 +198,6 @@ describe("FilterMenu", () => {
         );
     });
 
-    it("test buttons that navigate menu and keyup.enter/esc events", async () => {
-        setUpWrapper("Test Items", "search test items", TestFilters);
-
-        expect(wrapper.find("[data-description='advanced filters']").exists()).toBe(false);
-        await wrapper.setProps({ showAdvanced: true });
-        expect(wrapper.find("[data-description='advanced filters']").exists()).toBe(true);
-
-        // only add name filter in the advanced menu
-        let filterName = wrapper.find("[placeholder='any name']");
-        if (filterName.vm && filterName.props().type == "text") {
-            await filterName.setValue("sample name");
-        }
-
-        // -------- Test keyup.enter key:  ---------
-        // toggles view out and performs a search
-        await filterName.trigger("keyup.enter");
-        await expectCorrectEmits("name:'sample name'", TestFilters, false);
-
-        // Test: clearing the filterText
-        const clearButton = wrapper.find("[data-description='reset query']");
-        await clearButton.trigger("click");
-        await expectCorrectEmits("", TestFilters, false);
-
-        // Test: toggling view back in
-        const toggleButton = wrapper.find("[data-description='toggle advanced search']");
-        await toggleButton.trigger("click");
-        await expectCorrectEmits("", TestFilters, true);
-
-        // -------- Test keyup.esc key:  ---------
-        // toggles view out only (doesn't cause a new search / doesn't emulate enter)
-
-        // find name field again (destroyed because of toggling out) and set value
-        filterName = wrapper.find("[placeholder='any name']");
-        if (filterName.vm && filterName.props().type == "text") {
-            filterName.setValue("newnamefilter");
-        }
-
-        // press esc key from name field (should not change emitted filterText unlike enter key)
-        await filterName.trigger("keyup.esc");
-        await expectCorrectEmits("", TestFilters, false);
-    });
-
     /**
      * Testing the default values of the filters defined in the HistoryFilters: Filtering
      * class, ensuring the default values are reflected in the radio-group buttons
@@ -303,7 +261,7 @@ describe("FilterMenu", () => {
      * class, ensuring the default values are reflected in the radio-group buttons
      */
     it("test compact menu with checkbox filters on WorkflowFilters", async () => {
-        const myWorkflowFilters = WorkflowFilters("my");
+        const myWorkflowFilters = getWorkflowFilters("my");
         setUpWrapper("Workflows", "search workflows", myWorkflowFilters);
         // a compact `FilterMenu` only needs to be opened once (doesn't toggle out automatically)
         await wrapper.setProps({ showAdvanced: true, view: "compact" });
diff --git a/client/src/components/Common/FilterMenu.vue b/client/src/components/Common/FilterMenu.vue
index 66a5e4c823f4fdd3a14565386e6a84ad80a824ca..6686a141471a1acadd2ec2c6d93664fa477708d7 100644
--- a/client/src/components/Common/FilterMenu.vue
+++ b/client/src/components/Common/FilterMenu.vue
@@ -207,7 +207,7 @@ function updateFilterText(newFilterText: string) {
             v-if="props.menuType !== 'standalone'"
             v-show="props.menuType == 'linked' || (props.menuType == 'separate' && !props.showAdvanced)"
             ref="delayedInputField"
-            :query="props.filterText"
+            :value="props.filterText"
             :delay="props.debounceDelay"
             :loading="props.loading"
             :show-advanced="props.showAdvanced"
diff --git a/client/src/components/Common/FilterMenuDropdown.vue b/client/src/components/Common/FilterMenuDropdown.vue
index b86b5ca5663e03d66db0b2a8b9965465b4d9b6b2..0fecfbbf6a81a89f9bc3e27a3b99cb30002b2af6 100644
--- a/client/src/components/Common/FilterMenuDropdown.vue
+++ b/client/src/components/Common/FilterMenuDropdown.vue
@@ -4,21 +4,17 @@ import { faQuestion } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton, BDropdown, BDropdownItem, BInputGroup, BInputGroupAppend, BModal } from "bootstrap-vue";
 import { capitalize } from "lodash";
-import { computed, onMounted, ref, type UnwrapRef, watch } from "vue";
+import { computed, onMounted, ref, watch } from "vue";
 
-import { QuotaUsage } from "@/components/User/DiskUsage/Quota/model";
+import { fetchCurrentUserQuotaUsages, type QuotaUsage } from "@/api/users";
 import { type FilterType, type ValidFilter } from "@/utils/filtering";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import { fetch } from "../User/DiskUsage/Quota/services";
-
 import QuotaUsageBar from "@/components/User/DiskUsage/Quota/QuotaUsageBar.vue";
 
 library.add(faQuestion);
 
-type QuotaUsageUnwrapped = UnwrapRef<QuotaUsage>;
-
-type FilterValue = QuotaUsageUnwrapped | string | boolean | undefined;
+type FilterValue = QuotaUsage | string | boolean | undefined;
 
 type DatalistItem = { value: string; text: string };
 
@@ -83,11 +79,11 @@ function onHelp(_: string, value: string) {
 }
 
 // Quota Source refs and operations
-const quotaUsages = ref<QuotaUsage[]>([] as QuotaUsage[]);
+const quotaUsages = ref<QuotaUsage[]>([]);
 const errorMessage = ref<string>();
 async function loadQuotaUsages() {
     try {
-        quotaUsages.value = await fetch();
+        quotaUsages.value = await fetchCurrentUserQuotaUsages();
 
         // if the propValue is a string, find the corresponding QuotaUsage object and update the localValue
         if (propValue.value && typeof propValue.value === "string") {
@@ -99,20 +95,23 @@ async function loadQuotaUsages() {
         errorMessage.value = errorMessageAsString(e);
     }
 }
+
 const hasMultipleQuotaSources = computed<boolean>(() => {
     return !!(quotaUsages.value && quotaUsages.value.length > 1);
 });
+
 onMounted(async () => {
     if (props.type === "QuotaSource") {
         await loadQuotaUsages();
     }
 });
-function isQuotaUsageVal(value: FilterValue): value is QuotaUsageUnwrapped {
+
+function isQuotaUsage(value: FilterValue): value is QuotaUsage {
     return !!(value && value instanceof Object && "rawSourceLabel" in value);
 }
 
 const dropDownText = computed<string>(() => {
-    if (props.type === "QuotaSource" && isQuotaUsageVal(localValue.value)) {
+    if (props.type === "QuotaSource" && isQuotaUsage(localValue.value)) {
         return localValue.value.sourceLabel;
     }
     if (localValue.value) {
@@ -127,7 +126,7 @@ const dropDownText = computed<string>(() => {
     return "(any)";
 });
 
-function setValue(val: string | QuotaUsage | undefined) {
+function setValue(val: FilterValue) {
     localValue.value = val;
 }
 </script>
@@ -168,7 +167,7 @@ function setValue(val: string | QuotaUsage | undefined) {
                 <span v-else-if="props.type === 'QuotaSource'">
                     <BDropdownItem
                         v-for="quotaUsage in quotaUsages"
-                        :key="quotaUsage.id"
+                        :key="quotaUsage.sourceLabel"
                         href="#"
                         @click="setValue(quotaUsage)">
                         {{ quotaUsage.sourceLabel }}
diff --git a/client/src/components/Common/FilterMenuMultiTags.vue b/client/src/components/Common/FilterMenuMultiTags.vue
index d9c157d51092276ec368a20cc783d3294464afcd..e4b81b3fe6a76aa11394ba38e8c6aeaf9f745865 100644
--- a/client/src/components/Common/FilterMenuMultiTags.vue
+++ b/client/src/components/Common/FilterMenuMultiTags.vue
@@ -2,7 +2,7 @@
 import { BInputGroup } from "bootstrap-vue";
 import { computed, ref, watch } from "vue";
 
-import { ValidFilter } from "@/utils/filtering";
+import { type ValidFilter } from "@/utils/filtering";
 
 import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
 
diff --git a/client/src/components/Common/FilterMenuObjectStore.vue b/client/src/components/Common/FilterMenuObjectStore.vue
index dd0dea4756ede77ee53d7f323c061aaabfabc621..ab4f24d8f0a7363daf5f902c7e1a58bfbcf3d82c 100644
--- a/client/src/components/Common/FilterMenuObjectStore.vue
+++ b/client/src/components/Common/FilterMenuObjectStore.vue
@@ -2,7 +2,7 @@
 import { computed, ref, watch } from "vue";
 
 import { useSelectableObjectStores } from "@/composables/useObjectStores";
-import { ValidFilter } from "@/utils/filtering";
+import { type ValidFilter } from "@/utils/filtering";
 
 import FilterObjectStoreLink from "./FilterObjectStoreLink.vue";
 
diff --git a/client/src/components/Common/FilterObjectStoreLink.vue b/client/src/components/Common/FilterObjectStoreLink.vue
index c68aeb6a8011a9a9f81e24f168827f1b2a552e69..5c83394b090259b1784d792d1641a212c0fd72a7 100644
--- a/client/src/components/Common/FilterObjectStoreLink.vue
+++ b/client/src/components/Common/FilterObjectStoreLink.vue
@@ -4,7 +4,7 @@ import { faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed, ref } from "vue";
 
-import { ConcreteObjectStoreModel } from "@/api";
+import { type ConcreteObjectStoreModel } from "@/api";
 import { useObjectStoreStore } from "@/stores/objectStoreStore";
 
 import ObjectStoreSelect from "./ObjectStoreSelect.vue";
diff --git a/client/src/components/Common/IdleLoad.vue b/client/src/components/Common/IdleLoad.vue
new file mode 100644
index 0000000000000000000000000000000000000000..8084bcf42c9fb248f562065e30792c356806d571
--- /dev/null
+++ b/client/src/components/Common/IdleLoad.vue
@@ -0,0 +1,38 @@
+<script setup lang="ts">
+// This component delays the rendering of slotted elements
+// in order to not slow down the rendering of parent components,
+// or the responsiveness of the UI
+
+import { BSpinner } from "bootstrap-vue";
+import { onMounted, ref } from "vue";
+
+const props = defineProps<{
+    spinner?: boolean;
+    center?: boolean;
+}>();
+
+const render = ref(false);
+const idleFallbackTime = 250;
+
+onMounted(() => {
+    if ("requestIdleCallback" in window) {
+        window.requestIdleCallback(() => (render.value = true));
+    } else {
+        setTimeout(() => (render.value = true), idleFallbackTime);
+    }
+});
+</script>
+
+<template>
+    <div class="idle-load" :class="{ center: props.center && !render }">
+        <slot v-if="render"></slot>
+        <BSpinner v-else-if="props.spinner"></BSpinner>
+    </div>
+</template>
+
+<style lang="scss" scoped>
+.idle-load.center {
+    display: grid;
+    place-items: center;
+}
+</style>
diff --git a/client/src/components/Common/ObjectStoreSelect.vue b/client/src/components/Common/ObjectStoreSelect.vue
index 3ded3de27b2e2231b70edc6c2f52daab475345c5..0382b9a27c8a60cacfa5261cf1b0ea17b20fb92e 100644
--- a/client/src/components/Common/ObjectStoreSelect.vue
+++ b/client/src/components/Common/ObjectStoreSelect.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { ConcreteObjectStoreModel } from "@/api";
+import { type ConcreteObjectStoreModel } from "@/api";
 
 import ObjectStoreSelectButton from "@/components/ObjectStore/ObjectStoreSelectButton.vue";
 import ObjectStoreSelectButtonDescribePopover from "@/components/ObjectStore/ObjectStoreSelectButtonDescribePopover.vue";
diff --git a/client/src/components/Common/PersistentTaskProgressMonitorAlert.test.ts b/client/src/components/Common/PersistentTaskProgressMonitorAlert.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..266d2128a1b74d4257a769632227046c3d348312
--- /dev/null
+++ b/client/src/components/Common/PersistentTaskProgressMonitorAlert.test.ts
@@ -0,0 +1,222 @@
+import { shallowMount } from "@vue/test-utils";
+import { type PropType, ref } from "vue";
+
+import { type TaskMonitor } from "@/composables/genericTaskMonitor";
+import {
+    type MonitoringData,
+    type MonitoringRequest,
+    usePersistentProgressTaskMonitor,
+} from "@/composables/persistentProgressMonitor";
+
+import PersistentTaskProgressMonitorAlert from "@/components/Common/PersistentTaskProgressMonitorAlert.vue";
+
+type ComponentUnderTestProps = Partial<PropType<typeof PersistentTaskProgressMonitorAlert>>;
+
+const selectors = {
+    ProgressAlert: ".progress-monitor-alert",
+} as const;
+
+const FAKE_MONITOR_REQUEST: MonitoringRequest = {
+    source: "test",
+    action: "testing",
+    taskType: "task",
+    object: { id: "1", type: "dataset" },
+    description: "Test description",
+};
+
+const FAKE_EXPIRATION_TIME = 1000;
+
+const FAKE_MONITOR: TaskMonitor = {
+    waitForTask: jest.fn(),
+    isRunning: ref(false),
+    isCompleted: ref(false),
+    hasFailed: ref(false),
+    requestHasFailed: ref(false),
+    taskStatus: ref(""),
+    expirationTime: FAKE_EXPIRATION_TIME,
+    isFinalState: jest.fn(),
+    loadStatus: jest.fn(),
+};
+
+const mountComponent = (
+    props: ComponentUnderTestProps = {
+        monitorRequest: FAKE_MONITOR_REQUEST,
+        useMonitor: FAKE_MONITOR,
+    }
+) => {
+    return shallowMount(PersistentTaskProgressMonitorAlert as object, {
+        propsData: {
+            ...props,
+        },
+    });
+};
+
+describe("PersistentTaskProgressMonitorAlert.vue", () => {
+    beforeEach(() => {
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, FAKE_MONITOR).reset();
+    });
+
+    it("does not render when no monitoring data is available", () => {
+        const wrapper = mountComponent();
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(false);
+    });
+
+    it("renders in progress when monitoring data is available and in progress", () => {
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            isRunning: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: "1",
+            taskType: "task",
+            request: FAKE_MONITOR_REQUEST,
+            startedAt: new Date(),
+        };
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: FAKE_MONITOR_REQUEST,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const inProgressAlert = wrapper.find('[variant="info"]');
+        expect(inProgressAlert.exists()).toBe(true);
+        expect(inProgressAlert.text()).toContain("Task is in progress");
+    });
+
+    it("renders completed when monitoring data is available and completed", () => {
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            isCompleted: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: "1",
+            taskType: "task",
+            request: FAKE_MONITOR_REQUEST,
+            startedAt: new Date(),
+        };
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: FAKE_MONITOR_REQUEST,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const completedAlert = wrapper.find('[variant="success"]');
+        expect(completedAlert.exists()).toBe(true);
+        expect(completedAlert.text()).toContain("Task completed");
+    });
+
+    it("renders failed when monitoring data is available and failed", () => {
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            hasFailed: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: "1",
+            taskType: "task",
+            request: FAKE_MONITOR_REQUEST,
+            startedAt: new Date(),
+        };
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: FAKE_MONITOR_REQUEST,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const failedAlert = wrapper.find('[variant="danger"]');
+        expect(failedAlert.exists()).toBe(true);
+        expect(failedAlert.text()).toContain("Task failed");
+    });
+
+    it("renders a link to download the task result when completed and task type is 'short_term_storage'", () => {
+        const taskId = "fake-task-id";
+        const monitoringRequest: MonitoringRequest = {
+            ...FAKE_MONITOR_REQUEST,
+            taskType: "short_term_storage",
+        };
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            isCompleted: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: taskId,
+            taskType: "short_term_storage",
+            request: monitoringRequest,
+            startedAt: new Date(),
+        };
+        usePersistentProgressTaskMonitor(monitoringRequest, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: monitoringRequest,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const completedAlert = wrapper.find('[variant="success"]');
+        expect(completedAlert.exists()).toBe(true);
+
+        const downloadLink = wrapper.find(".download-link");
+        expect(downloadLink.exists()).toBe(true);
+        expect(downloadLink.text()).toContain("Download here");
+        expect(downloadLink.attributes("href")).toBe(`/api/short_term_storage/${taskId}`);
+    });
+
+    it("does not render a link to download the task result when completed and task type is 'task'", () => {
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            isCompleted: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: "1",
+            taskType: "task",
+            request: FAKE_MONITOR_REQUEST,
+            startedAt: new Date(),
+        };
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: FAKE_MONITOR_REQUEST,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const completedAlert = wrapper.find('[variant="success"]');
+        expect(completedAlert.exists()).toBe(true);
+        expect(completedAlert.text()).not.toContain("Download here");
+    });
+
+    it("should render a warning alert when the task has expired even if the status is running", () => {
+        const useMonitor = {
+            ...FAKE_MONITOR,
+            isRunning: ref(true),
+        };
+        const existingMonitoringData: MonitoringData = {
+            taskId: "1",
+            taskType: "task",
+            request: FAKE_MONITOR_REQUEST,
+            startedAt: new Date(Date.now() - FAKE_EXPIRATION_TIME * 2), // Make sure the task has expired
+        };
+        usePersistentProgressTaskMonitor(FAKE_MONITOR_REQUEST, useMonitor, existingMonitoringData);
+
+        const wrapper = mountComponent({
+            monitorRequest: FAKE_MONITOR_REQUEST,
+            useMonitor,
+        });
+
+        expect(wrapper.find(selectors.ProgressAlert).exists()).toBe(true);
+
+        const warningAlert = wrapper.find('[variant="warning"]');
+        expect(warningAlert.exists()).toBe(true);
+        expect(warningAlert.text()).toContain("The testing task has expired and the result is no longer available");
+    });
+});
diff --git a/client/src/components/Common/PersistentTaskProgressMonitorAlert.vue b/client/src/components/Common/PersistentTaskProgressMonitorAlert.vue
new file mode 100644
index 0000000000000000000000000000000000000000..fc5e2594c39ce5dc72472e208707cd7b4004035c
--- /dev/null
+++ b/client/src/components/Common/PersistentTaskProgressMonitorAlert.vue
@@ -0,0 +1,153 @@
+<script setup lang="ts">
+import { faSpinner } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BLink } from "bootstrap-vue";
+import { computed, watch } from "vue";
+
+import { type TaskMonitor } from "@/composables/genericTaskMonitor";
+import { type MonitoringRequest, usePersistentProgressTaskMonitor } from "@/composables/persistentProgressMonitor";
+import { useShortTermStorage } from "@/composables/shortTermStorage";
+
+import FileSourceNameSpan from "@/components/FileSources/FileSourceNameSpan.vue";
+import UtcDate from "@/components/UtcDate.vue";
+
+interface Props {
+    monitorRequest: MonitoringRequest;
+    useMonitor: TaskMonitor;
+
+    /**
+     * The task ID to monitor. Can be a task ID or a short-term storage request ID.
+     * If provided, the component will start monitoring the task with the given ID.
+     */
+    taskId?: string;
+
+    /**
+     * If true, the download link will be automatically opened when the task is completed if the user
+     * remains on the page.
+     *
+     * Automatic download will only be possible if the task is completed and the task type is `short_term_storage`.
+     */
+    enableAutoDownload?: boolean;
+
+    inProgressMessage?: string;
+    completedMessage?: string;
+    failedMessage?: string;
+    requestFailedMessage?: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    taskId: undefined,
+    enableAutoDownload: false,
+    inProgressMessage: `Task is in progress. Please wait...`,
+    completedMessage: "Task completed successfully.",
+    failedMessage: "Task failed.",
+    requestFailedMessage: "Request failed.",
+});
+
+const emit = defineEmits<{
+    (e: "onDismiss"): void;
+}>();
+
+const { getDownloadObjectUrl } = useShortTermStorage();
+
+const {
+    hasMonitoringData,
+    isRunning,
+    isCompleted,
+    hasFailed,
+    requestHasFailed,
+    storedTaskId,
+    status,
+    hasExpired,
+    expirationDate,
+    monitoringData,
+    start,
+    reset,
+} = usePersistentProgressTaskMonitor(props.monitorRequest, props.useMonitor);
+
+const downloadUrl = computed(() => {
+    // We can only download the result if the task is completed and the task type is short_term_storage.
+    const requestId = props.taskId || storedTaskId;
+    if (requestId && props.monitorRequest.taskType === "short_term_storage") {
+        return getDownloadObjectUrl(requestId);
+    }
+    return undefined;
+});
+
+const remoteUri = computed(() => {
+    return monitoringData.value?.request.remoteUri;
+});
+
+if (hasMonitoringData.value) {
+    start();
+}
+
+watch(
+    () => props.taskId,
+    (newTaskId, oldTaskId) => {
+        if (newTaskId && newTaskId !== oldTaskId) {
+            start({
+                taskId: newTaskId,
+                taskType: props.monitorRequest.taskType,
+                request: props.monitorRequest,
+                startedAt: new Date(),
+            });
+        }
+    }
+);
+
+watch(
+    () => isCompleted.value,
+    (completed) => {
+        // We check for props.taskId to be defined to avoid auto-downloading when the task is completed and
+        // the component is first mounted like when refreshing the page.
+        if (completed && props.enableAutoDownload && downloadUrl.value && props.taskId) {
+            window.open(downloadUrl.value, "_blank");
+        }
+    }
+);
+
+function dismissAlert() {
+    reset();
+    emit("onDismiss");
+}
+</script>
+
+<template>
+    <div v-if="hasMonitoringData" class="progress-monitor-alert">
+        <BAlert v-if="hasExpired" variant="warning" show dismissible @dismissed="dismissAlert">
+            The {{ monitorRequest.action }} task has <b>expired</b> and the result is no longer available.
+        </BAlert>
+        <BAlert v-else-if="isRunning" variant="info" show>
+            <b>{{ inProgressMessage }}</b>
+            <FontAwesomeIcon :icon="faSpinner" class="mr-2" spin />
+        </BAlert>
+        <BAlert v-else-if="isCompleted" variant="success" show dismissible @dismissed="dismissAlert">
+            <span>{{ completedMessage }}</span>
+
+            <BLink v-if="downloadUrl" class="download-link" :href="downloadUrl">
+                <b>Download here</b>
+            </BLink>
+
+            <span v-if="remoteUri">
+                The result should be available at
+                <b><FileSourceNameSpan :uri="remoteUri" :show-full-uri="true" /></b>
+            </span>
+
+            <br />
+
+            <span v-if="expirationDate">
+                This result will <b>expire <UtcDate :date="expirationDate.toISOString()" mode="elapsed" /></b>
+            </span>
+        </BAlert>
+        <BAlert v-else-if="hasFailed" variant="danger" show dismissible @dismissed="dismissAlert">
+            <span>{{ failedMessage }}</span>
+            <span v-if="status">
+                Reason: <b>{{ status }}</b>
+            </span>
+        </BAlert>
+        <BAlert v-else-if="requestHasFailed" variant="danger" show dismissible @dismissed="dismissAlert">
+            <b>{{ requestFailedMessage }}</b>
+        </BAlert>
+    </div>
+</template>
diff --git a/client/src/components/History/Export/RDMCredentialsInfo.vue b/client/src/components/Common/RDMCredentialsInfo.vue
similarity index 94%
rename from client/src/components/History/Export/RDMCredentialsInfo.vue
rename to client/src/components/Common/RDMCredentialsInfo.vue
index 306944e64d8029823b2d049fadb17d93ea0e7ad9..1307d9cd65d7370a47e0f20dde6c06475efb0dff 100644
--- a/client/src/components/History/Export/RDMCredentialsInfo.vue
+++ b/client/src/components/Common/RDMCredentialsInfo.vue
@@ -4,12 +4,10 @@ import { RouterLink } from "vue-router";
 
 interface Props {
     selectedRepository?: string;
-    what?: string;
 }
 
 withDefaults(defineProps<Props>(), {
     selectedRepository: "the selected repository",
-    what: "file",
 });
 </script>
 
diff --git a/client/src/components/Common/RDMDestinationSelector.test.ts b/client/src/components/Common/RDMDestinationSelector.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..299e6a6498b055f25dfe833198e0b7d862f45f6c
--- /dev/null
+++ b/client/src/components/Common/RDMDestinationSelector.test.ts
@@ -0,0 +1,192 @@
+import { getLocalVue } from "@tests/jest/helpers";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+
+import { useServerMock } from "@/api/client/__mocks__";
+import { type BrowsableFilesSourcePlugin, type CreatedEntry } from "@/api/remoteFiles";
+
+import RDMDestinationSelector from "./RDMDestinationSelector.vue";
+import FilesInput from "@/components/FilesDialog/FilesInput.vue";
+
+const localVue = getLocalVue(true);
+
+const CREATE_RECORD_BTN = "#create-record-button";
+
+const FAKE_RDM_SOURCE_URI = "gxfiles://test-uri";
+const FAKE_RDM_EXISTING_RECORD_URI = "gxfiles://test-uri/test-record";
+const FAKE_RECORD_NAME = "test record name";
+const FAKE_ENTRY: CreatedEntry = {
+    uri: FAKE_RDM_SOURCE_URI,
+    name: FAKE_RECORD_NAME,
+    external_link: "http://example.com",
+};
+
+const { server, http } = useServerMock();
+
+async function initWrapper(fileSource?: BrowsableFilesSourcePlugin) {
+    server.use(
+        http.post("/api/remote_files", ({ response }) => {
+            return response(200).json(FAKE_ENTRY);
+        })
+    );
+
+    const wrapper = mount(RDMDestinationSelector as object, {
+        propsData: {
+            fileSource,
+        },
+        localVue,
+    });
+    await flushPromises();
+    return wrapper;
+}
+
+describe("RDMDestinationSelector", () => {
+    let wrapper: Wrapper<Vue>;
+
+    beforeEach(async () => {
+        wrapper = await initWrapper();
+    });
+
+    describe("Select new record", () => {
+        beforeEach(async () => {
+            await selectExportChoice("new");
+        });
+
+        it("enables the create new record button when the required fields are filled in", async () => {
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
+
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
+        });
+
+        it("emits onRecordSelected when the create new record button is clicked", async () => {
+            expect(wrapper.emitted("onRecordSelected")).toBeFalsy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
+            await clickCreateNewRecordButton();
+
+            const emitted = wrapper.emitted("onRecordSelected");
+
+            console.log("EMITTED", emitted);
+
+            expect(emitted).toBeTruthy();
+            expect(emitted?.at(0)[0]).toEqual(FAKE_ENTRY.uri);
+        });
+    });
+
+    describe("Select existing record", () => {
+        beforeEach(async () => {
+            await selectExportChoice("existing");
+        });
+
+        it("emits onRecordSelected event when the existing record is selected", async () => {
+            expect(wrapper.emitted("onRecordSelected")).toBeFalsy();
+
+            await setRDMDirectoryInput(FAKE_RDM_EXISTING_RECORD_URI);
+
+            const emitted = wrapper.emitted("onRecordSelected");
+            expect(emitted).toBeTruthy();
+            expect(emitted?.at(0)[0]).toEqual(FAKE_RDM_EXISTING_RECORD_URI);
+        });
+    });
+
+    describe("Pre-select specific File Source", () => {
+        const PRESELECTED_FILE_SOURCE_ID = "test-file-source";
+        const PRESELECTED_FILE_SOURCE_URI = "gxfiles://preselected-file-source";
+
+        beforeEach(async () => {
+            const specificFileSource: BrowsableFilesSourcePlugin = {
+                id: PRESELECTED_FILE_SOURCE_ID,
+                label: "Test File Source",
+                doc: "Test File Source Description",
+                uri_root: PRESELECTED_FILE_SOURCE_URI,
+                writable: true,
+                browsable: true,
+                type: "rdm",
+                supports: {
+                    pagination: false,
+                    search: false,
+                    sorting: false,
+                },
+            };
+            wrapper = await initWrapper(specificFileSource);
+        });
+
+        describe("Select new record", () => {
+            beforeEach(async () => {
+                await selectExportChoice("new", PRESELECTED_FILE_SOURCE_ID);
+            });
+
+            it("enables the create new record button only by setting the record name", async () => {
+                expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
+
+                await setRecordNameInput(FAKE_RECORD_NAME);
+
+                expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
+            });
+
+            it("emits onRecordSelected event when the create new record button is clicked", async () => {
+                expect(wrapper.emitted("onRecordSelected")).toBeFalsy();
+
+                await setRecordNameInput(FAKE_RECORD_NAME);
+                await clickCreateNewRecordButton();
+
+                const emitted = wrapper.emitted("onRecordSelected");
+                expect(emitted).toBeTruthy();
+                expect(emitted?.at(0)[0]).toEqual(FAKE_ENTRY.uri);
+            });
+        });
+
+        describe("Select existing record", () => {
+            beforeEach(async () => {
+                await selectExportChoice("existing", PRESELECTED_FILE_SOURCE_ID);
+            });
+
+            it("emits onRecordSelected event when the existing record is selected", async () => {
+                expect(wrapper.emitted("onRecordSelected")).toBeFalsy();
+
+                const fakeRecordUri = `${PRESELECTED_FILE_SOURCE_URI}/preselected-test-record`;
+                await setRDMDirectoryInput(fakeRecordUri);
+
+                const emitted = wrapper.emitted("onRecordSelected");
+                expect(emitted).toBeTruthy();
+                expect(emitted?.at(0)[0]).toEqual(fakeRecordUri);
+            });
+        });
+    });
+
+    async function selectExportChoice(choice: string, fileSourceId?: string) {
+        const suffix = fileSourceId ? `${fileSourceId}` : "any";
+        const exportChoice = wrapper.find(`#radio-${choice}-${suffix}`);
+        await exportChoice.setChecked(true);
+    }
+
+    async function setRDMSourceInput(newValue: string) {
+        const component = wrapper.findComponent(FilesInput);
+        expect(component.attributes("placeholder")).toContain("source");
+        component.vm.$emit("input", newValue);
+        await flushPromises();
+    }
+
+    async function setRDMDirectoryInput(newValue: string) {
+        const component = wrapper.findComponent(FilesInput);
+        expect(component.attributes("placeholder")).toContain("directory");
+        component.vm.$emit("input", newValue);
+        await flushPromises();
+    }
+
+    async function setRecordNameInput(newValue: string) {
+        const recordNameInput = wrapper.find("#record-name-input");
+        await recordNameInput.setValue(newValue);
+    }
+
+    async function clickCreateNewRecordButton() {
+        const createRecordButton = wrapper.find(CREATE_RECORD_BTN);
+        expect(createRecordButton.attributes("disabled")).toBeFalsy();
+        await createRecordButton.trigger("click");
+        await flushPromises();
+    }
+});
diff --git a/client/src/components/Common/RDMDestinationSelector.vue b/client/src/components/Common/RDMDestinationSelector.vue
new file mode 100644
index 0000000000000000000000000000000000000000..d2731528b763b2bdf4811f81bd9f499079fd2cf0
--- /dev/null
+++ b/client/src/components/Common/RDMDestinationSelector.vue
@@ -0,0 +1,201 @@
+<script setup lang="ts">
+import { BAlert, BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { type BrowsableFilesSourcePlugin, type CreatedEntry, type FilterFileSourcesOptions } from "@/api/remoteFiles";
+import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import { fileSourcePluginToItem } from "../FilesDialog/utilities";
+
+import ExternalLink from "@/components/ExternalLink.vue";
+import FilesInput from "@/components/FilesDialog/FilesInput.vue";
+
+type ExportChoice = "existing" | "new";
+
+interface Props {
+    what?: string;
+    /**
+     * If undefined, the user will need to select a repository to export to,
+     * otherwise this file source will be pre-selected.
+     */
+    fileSource?: BrowsableFilesSourcePlugin;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    what: "archive",
+    fileSource: undefined,
+});
+
+const emit = defineEmits<{
+    (e: "onRecordSelected", recordUri: string): void;
+}>();
+
+const includeOnlyRDMCompatible: FilterFileSourcesOptions = { include: ["rdm"] };
+
+const recordUri = ref<string>("");
+const sourceUri = ref<string>(props.fileSource?.uri_root ?? "");
+const exportChoice = ref<ExportChoice>("new");
+const recordName = ref<string>("");
+const newEntry = ref<CreatedEntry>();
+
+const canCreateRecord = computed(() => Boolean(sourceUri.value) && Boolean(recordName.value));
+
+const errorCreatingRecord = ref<string>();
+
+const repositoryRecordDescription = computed(() => localize(`Select a repository to export ${props.what} to.`));
+
+const recordNameDescription = computed(() => localize("Give the new record a name or title."));
+
+const recordNamePlaceholder = computed(() => localize("Record name"));
+
+const uniqueSourceId = computed(() => props.fileSource?.id ?? "any");
+const fileSourceAsItem = computed(() => (props.fileSource ? fileSourcePluginToItem(props.fileSource) : undefined));
+
+watch(
+    () => recordUri.value,
+    (value) => {
+        emit("onRecordSelected", value);
+    }
+);
+
+async function onCreateRecord() {
+    try {
+        await createRecord();
+    } catch (error) {
+        errorCreatingRecord.value = errorMessageAsString(error);
+    }
+}
+
+async function createRecord() {
+    const { data, error } = await GalaxyApi().POST("/api/remote_files", {
+        body: {
+            target: sourceUri.value,
+            name: recordName.value,
+        },
+    });
+
+    if (error) {
+        errorCreatingRecord.value = errorMessageAsString(error);
+        return;
+    }
+
+    newEntry.value = data;
+    recordUri.value = newEntry.value.uri;
+}
+
+function reset() {
+    recordUri.value = "";
+    recordName.value = "";
+    newEntry.value = undefined;
+    exportChoice.value = "new";
+}
+
+defineExpose({
+    reset,
+});
+</script>
+
+<template>
+    <div>
+        <p>
+            Your {{ what }} needs to be uploaded to an existing <i>draft</i> record. You will need to create a
+            <b>new record</b> or select an existing <b>draft record</b> and then export your {{ what }} to it.
+        </p>
+
+        <BFormRadioGroup v-model="exportChoice" class="export-radio-group">
+            <BFormRadio :id="`radio-new-${uniqueSourceId}`" v-localize name="exportChoice" value="new">
+                Export to new record
+            </BFormRadio>
+
+            <BFormRadio :id="`radio-existing-${uniqueSourceId}`" v-localize name="exportChoice" value="existing">
+                Export to existing draft record
+            </BFormRadio>
+        </BFormRadioGroup>
+
+        <div v-if="exportChoice === 'new'">
+            <div v-if="newEntry">
+                <BCard>
+                    <p>
+                        <b>{{ newEntry.name }}</b>
+                        <span v-localize> draft record has been created in the repository.</span>
+                    </p>
+
+                    <div v-if="newEntry.external_link">
+                        You can preview the record in the repository, further edit its metadata and decide when to
+                        publish it at
+                        <ExternalLink :href="newEntry.external_link">
+                            <b>{{ newEntry.external_link }}</b>
+                        </ExternalLink>
+                    </div>
+                </BCard>
+            </div>
+            <div v-else>
+                <BFormGroup
+                    v-if="!props.fileSource"
+                    id="fieldset-record-new"
+                    label-for="source-selector"
+                    :description="repositoryRecordDescription"
+                    class="mt-3">
+                    <FilesInput
+                        id="source-selector"
+                        v-model="sourceUri"
+                        mode="source"
+                        :require-writable="true"
+                        :filter-options="includeOnlyRDMCompatible" />
+                </BFormGroup>
+
+                <BFormGroup
+                    id="fieldset-record-name"
+                    label-for="record-name"
+                    :description="recordNameDescription"
+                    class="mt-3">
+                    <BFormInput
+                        id="record-name-input"
+                        v-model="recordName"
+                        :placeholder="recordNamePlaceholder"
+                        required />
+                </BFormGroup>
+
+                <p v-localize>
+                    You need to create the new record in a repository before exporting the {{ props.what }} to it.
+                </p>
+
+                <BAlert
+                    v-if="errorCreatingRecord"
+                    variant="danger"
+                    show
+                    dismissible
+                    @dismissed="errorCreatingRecord = undefined">
+                    An error occurred while creating the record:
+                    {{ errorCreatingRecord }}
+                </BAlert>
+
+                <BButton
+                    id="create-record-button"
+                    v-localize
+                    variant="primary"
+                    :disabled="!canCreateRecord"
+                    @click.prevent="onCreateRecord">
+                    Create new record
+                </BButton>
+            </div>
+        </div>
+        <div v-else>
+            <BFormGroup
+                id="fieldset-record-existing"
+                label-for="existing-record-selector"
+                :description="repositoryRecordDescription"
+                class="mt-3">
+                <FilesInput
+                    id="existing-record-selector"
+                    v-model="recordUri"
+                    mode="directory"
+                    :require-writable="true"
+                    :filter-options="fileSource ? undefined : includeOnlyRDMCompatible"
+                    :selected-item="fileSourceAsItem" />
+            </BFormGroup>
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Common/TextShort.vue b/client/src/components/Common/TextShort.vue
index 012c770c61370de5cd2ebffc67df4832a5ea4b27..e1f0842a508c3eb8f05d06d444fef6b76c9ac28f 100644
--- a/client/src/components/Common/TextShort.vue
+++ b/client/src/components/Common/TextShort.vue
@@ -10,7 +10,7 @@ const props = withDefaults(defineProps<Props>(), {
     maxLength: 24,
 });
 
-const text = computed(() => {
+const trimmedText = computed(() => {
     if (props.text.length > props.maxLength) {
         const partialText = props.text.slice(0, props.maxLength);
         return `${partialText}...`;
@@ -22,6 +22,6 @@ const text = computed(() => {
 
 <template>
     <span class="text-break text-center">
-        {{ text }}
+        {{ trimmedText }}
     </span>
 </template>
diff --git a/client/src/components/Common/TextSummary.vue b/client/src/components/Common/TextSummary.vue
index 19b7f40e98c7b72e7ffef45e9e3be62408df7a50..6ef4b607402d3c08cfc0dee4f7abf815a8117570 100644
--- a/client/src/components/Common/TextSummary.vue
+++ b/client/src/components/Common/TextSummary.vue
@@ -11,7 +11,8 @@ interface Props {
     maxLength?: number;
     /** The text to summarize */
     description: string;
-    /** If `true`, doesn't let unexpanded text go beyond height of one line */
+    /** If `true`, doesn't let unexpanded text go beyond height of one line
+     * and ignores `maxLength` */
     oneLineSummary?: boolean;
     /** If `true`, doesn't show expand/collapse buttons */
     noExpand?: boolean;
@@ -25,8 +26,17 @@ const props = withDefaults(defineProps<Props>(), {
 });
 
 const showDetails = ref(false);
+const refOneLineSummary = ref<HTMLElement | null>(null);
 
-const textTooLong = computed(() => props.description.length > props.maxLength);
+const textTooLong = computed(() => {
+    if (!props.oneLineSummary) {
+        return props.description.length > props.maxLength;
+    } else if (refOneLineSummary.value) {
+        return refOneLineSummary.value.scrollWidth > refOneLineSummary.value.clientWidth;
+    } else {
+        return false;
+    }
+});
 const text = computed(() =>
     textTooLong.value && !showDetails.value
         ? props.description.slice(0, Math.round(props.maxLength - props.maxLength / 2)) + "..."
@@ -35,8 +45,12 @@ const text = computed(() =>
 </script>
 
 <template>
-    <div>
-        <component :is="props.component" v-if="props.oneLineSummary" class="one-line-summary">
+    <div :class="{ 'd-flex': props.oneLineSummary && !noExpand }">
+        <component
+            :is="props.component"
+            v-if="props.oneLineSummary"
+            ref="refOneLineSummary"
+            :class="{ 'one-line-summary': !showDetails }">
             {{ props.description }}
         </component>
         <span v-else>{{ text }}</span>
diff --git a/client/src/components/Common/Wizard/GenericWizard.vue b/client/src/components/Common/Wizard/GenericWizard.vue
new file mode 100644
index 0000000000000000000000000000000000000000..3a2d165dd015be741cd67705a696436007f512b0
--- /dev/null
+++ b/client/src/components/Common/Wizard/GenericWizard.vue
@@ -0,0 +1,284 @@
+<script setup lang="ts">
+import { faCheck, faSpinner } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BCard, BCardBody, BCardTitle } from "bootstrap-vue";
+import { computed } from "vue";
+
+import type { WizardReturnType, WizardStep } from "./useWizard";
+
+interface Props {
+    /**
+     * The wizard stepper object.
+     *
+     * **Must be created using the `useWizard` composable.**
+     */
+    use?: WizardReturnType;
+
+    /**
+     * The title of the wizard.
+     *
+     * @default "Generic Wizard"
+     */
+    title?: string;
+
+    /**
+     * The label for the submit button.
+     *
+     * @default "Submit"
+     */
+    submitButtonLabel?: string;
+
+    /**
+     * Whether the wizard is busy.
+     *
+     * When the wizard is busy, the navigation buttons are disabled and
+     * a spinner is shown on the current step.
+     *
+     * @default false
+     */
+    isBusy?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    use: undefined,
+    title: "Generic Wizard",
+    submitButtonLabel: "Submit",
+    isBusy: false,
+});
+
+const emit = defineEmits(["submit"]);
+
+function goNext() {
+    if (props.use.current.value.isValid()) {
+        if (props.use.isLast.value) {
+            emit("submit");
+        }
+
+        let nextStepIndex = props.use.index.value + 1;
+        let nextStepName = props.use.stepNames.value.at(nextStepIndex);
+
+        while (nextStepName && props.use.steps.value[nextStepName]?.isSkippable()) {
+            nextStepIndex++;
+            nextStepName = props.use.stepNames.value.at(nextStepIndex);
+        }
+
+        if (nextStepName) {
+            props.use.goTo(nextStepName);
+        }
+    }
+}
+
+function goBack() {
+    let previousStepIndex = props.use.index.value - 1;
+    let previousStepName = props.use.stepNames.value.at(previousStepIndex);
+
+    while (previousStepName && props.use.steps.value[previousStepName]?.isSkippable()) {
+        previousStepIndex--;
+        previousStepName = props.use.stepNames.value.at(previousStepIndex);
+    }
+
+    if (previousStepName) {
+        props.use.goTo(previousStepName);
+    }
+}
+
+function determineDisplayStepIndex(index: number): number {
+    const steps = Array.from(Object.values(props.use.steps.value));
+    return steps.slice(0, index).filter((step) => !(step as WizardStep).isSkippable()).length + 1;
+}
+
+function allStepsBeforeAreValid(index: number): boolean {
+    const steps = Array.from(Object.values(props.use.steps.value));
+    return steps.slice(0, index).every((step) => (step as WizardStep).isValid() || (step as WizardStep).isSkippable());
+}
+
+function isStepDone(currentIndex: number): boolean {
+    return currentIndex < props.use.index.value;
+}
+
+/**
+ * This is a workaround to make the grid columns template dynamic based on the number of visible steps.
+ */
+const stepsGridColumnsTemplate = computed(() => {
+    const numVisibleSteps = Array.from(Object.values(props.use.steps.value)).filter(
+        (step) => !(step as WizardStep).isSkippable()
+    ).length;
+    return (
+        Array(numVisibleSteps - 1)
+            .fill("auto")
+            .join(" ") + " max-content"
+    );
+});
+</script>
+
+<template>
+    <BCard class="wizard-container">
+        <BCardTitle>
+            <h2>{{ title }}</h2>
+        </BCardTitle>
+        <BCardBody v-if="props.use?.steps?.value" class="wizard">
+            <BCard>
+                <BCardBody class="wizard-steps">
+                    <div
+                        v-for="(step, id, i) in props.use.steps.value"
+                        :key="id"
+                        class="wizard-step"
+                        :class="step.isSkippable() ? 'skipped ' : ''">
+                        <button
+                            class="step-number"
+                            :class="{ active: props.use.isCurrent(id), done: isStepDone(i) }"
+                            :disabled="(!allStepsBeforeAreValid(i) && props.use.isBefore(id)) || isBusy"
+                            @click="props.use.goTo(id)">
+                            <FontAwesomeIcon v-if="isStepDone(i)" :icon="faCheck" />
+                            <FontAwesomeIcon v-else-if="props.use.isLast && isBusy" :icon="faSpinner" spin />
+                            <span v-else>{{ determineDisplayStepIndex(i) }}</span>
+                        </button>
+                        <div class="step-label" v-text="step.label" />
+                        <div class="step-line" :class="{ fill: props.use.isAfter(id) }"></div>
+                    </div>
+                </BCardBody>
+            </BCard>
+
+            <div class="step-content">
+                <span class="h-md step-instructions" v-text="props.use.current.value.instructions" />
+
+                <div class="step-body">
+                    <slot>
+                        <p>
+                            Missing body for step <b>{{ props.use.current.value.label }}</b>
+                        </p>
+                    </slot>
+                </div>
+            </div>
+            <div class="wizard-actions">
+                <button v-if="!props.use.isFirst.value" class="go-back-btn" :disabled="isBusy" @click="goBack">
+                    Back
+                </button>
+
+                <button
+                    class="go-next-btn"
+                    :disabled="!props.use.current.value.isValid() || isBusy"
+                    :class="props.use.isLast.value ? 'btn-primary' : ''"
+                    @click="goNext">
+                    {{ props.use.isLast.value ? submitButtonLabel : "Next" }}
+                </button>
+            </div>
+        </BCardBody>
+    </BCard>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+.wizard {
+    padding: 0;
+
+    .wizard-steps {
+        padding: 0;
+        margin: 0;
+        display: grid;
+        grid-auto-flow: column;
+        grid-template-columns: v-bind(stepsGridColumnsTemplate);
+    }
+
+    .wizard-step {
+        padding: 0;
+        margin: 0;
+        display: grid;
+        grid-template-columns: 50px max-content auto;
+        grid-template-rows: auto;
+        grid-template-areas: "number label line";
+        justify-items: center;
+
+        .step-number {
+            border-radius: 50%;
+            width: 40px;
+            height: 40px;
+            background-color: $brand-secondary;
+            justify-content: center;
+            align-items: center;
+            font-size: 1rem;
+            grid-area: number;
+
+            &.active {
+                background-color: $brand-primary;
+                color: white;
+            }
+
+            &.done {
+                background-color: $brand-success;
+                color: white;
+            }
+        }
+
+        .step-label {
+            align-self: center;
+            grid-area: label;
+            text-align: center;
+            text-wrap: nowrap;
+        }
+
+        .step-line {
+            margin-left: 5px;
+            align-self: center;
+            grid-area: line;
+            width: 0;
+            height: 4px;
+            background-color: $brand-primary;
+
+            &.fill {
+                width: 100%;
+                transform-origin: left;
+                transition: width 0.2s;
+            }
+        }
+
+        &.skipped {
+            display: none;
+        }
+
+        &:last-child {
+            justify-self: end;
+        }
+    }
+
+    .step-content {
+        padding: 1rem 1rem 0rem 1rem;
+        display: flex;
+        flex-direction: column;
+        align-items: center;
+
+        .step-instructions {
+            margin-top: 0rem;
+            margin-bottom: 1rem;
+        }
+
+        .step-body {
+            display: flex;
+            flex-direction: column;
+            align-items: center;
+        }
+    }
+
+    .wizard-actions {
+        padding: 1rem 1rem 0rem 1rem;
+
+        .go-back-btn {
+            float: left;
+        }
+
+        .go-next-btn {
+            float: right;
+        }
+    }
+
+    .wizard-selection-card {
+        border-width: 3px;
+        text-align: center;
+
+        .card-header {
+            border-radius: 0;
+        }
+    }
+}
+</style>
diff --git a/client/src/components/Common/Wizard/useWizard.ts b/client/src/components/Common/Wizard/useWizard.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f863347fdad6f0062f795c8a18dde75ee2bb5add
--- /dev/null
+++ b/client/src/components/Common/Wizard/useWizard.ts
@@ -0,0 +1,42 @@
+import type { MaybeRef } from "@vueuse/core";
+import { useStepper } from "@vueuse/core";
+
+/**
+ * Represents a step in a wizard.
+ */
+export interface WizardStep {
+    /**
+     * The label of the step. It will be displayed in the wizard navigation.
+     */
+    label: MaybeRef<string>;
+
+    /**
+     * The instructions for the step. It will be displayed in the wizard content.
+     */
+    instructions: MaybeRef<string>;
+
+    /**
+     * Whether the step is valid and can be completed.
+     */
+    isValid: () => boolean;
+
+    /**
+     * Whether the step should be skipped.
+     * This is useful for optional or conditional steps.
+     */
+    isSkippable: () => boolean;
+}
+
+/**
+ * Composable for creating a wizard with multiple steps.
+ *
+ * This is a thin wrapper around `useStepper` that provides a more specific type.
+ * @param steps The steps of the wizard.
+ * @param initialStep The initial step to start the wizard on.
+ * @returns A stepper object for the wizard.
+ */
+export function useWizard<T extends Record<string, WizardStep>>(steps: MaybeRef<T>, initialStep?: keyof T) {
+    return useStepper(steps, initialStep);
+}
+
+export type WizardReturnType = ReturnType<typeof useWizard>;
diff --git a/client/src/components/Common/models/exportRecordModel.ts b/client/src/components/Common/models/exportRecordModel.ts
index 2b02536fbfeeaca2dcfb589844147ff991220efd..35ebd1abf4bc81c646c596f4cdf4a66e062bb351 100644
--- a/client/src/components/Common/models/exportRecordModel.ts
+++ b/client/src/components/Common/models/exportRecordModel.ts
@@ -1,12 +1,11 @@
 import { formatDistanceToNow, parseISO } from "date-fns";
 
-import type { components } from "@/api/schema";
-
-type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
-
-export type StoreExportPayload = components["schemas"]["StoreExportPayload"];
-export type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
-export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
+import {
+    type ExportObjectRequestMetadata,
+    type ModelStoreFormat,
+    type ObjectExportTaskResponse,
+    type StoreExportPayload,
+} from "@/api";
 
 export interface ExportParams {
     readonly modelStoreFormat: ModelStoreFormat;
@@ -41,8 +40,8 @@ export interface ExportRecord {
 }
 
 export class ExportParamsModel implements ExportParams {
-    private _params: StoreExportPayload;
-    constructor(data: StoreExportPayload = {}) {
+    private _params: Partial<StoreExportPayload>;
+    constructor(data: Partial<StoreExportPayload> = {}) {
         this._params = data;
     }
 
diff --git a/client/src/components/Common/models/testData/exportData.ts b/client/src/components/Common/models/testData/exportData.ts
index 665e51b70e9421b0210dc8a2671e6e21e8219858..3c7ac7db9eaadb873e3d1c265fcdef68b4afa6e4 100644
--- a/client/src/components/Common/models/testData/exportData.ts
+++ b/client/src/components/Common/models/testData/exportData.ts
@@ -1,10 +1,10 @@
-import type { components } from "@/api/schema";
+import {
+    type ExportObjectRequestMetadata,
+    type ExportObjectResultMetadata,
+    type ObjectExportTaskResponse,
+} from "@/api";
 import { ExportRecordModel } from "@/components/Common/models/exportRecordModel";
 
-type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
-type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
-type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];
-
 const PAST_EXPORT_DATE = new Date("11 November 2022 14:48 UTC").toISOString();
 const RECENT_EXPORT_DATE = new Date().toISOString();
 const STS_EXPORT_DURATION_IN_SECONDS = 86400;
diff --git a/client/src/components/ConfigTemplates/ActionSummary.vue b/client/src/components/ConfigTemplates/ActionSummary.vue
new file mode 100644
index 0000000000000000000000000000000000000000..6e4652a584fe4dd2f621f4730e2ee7a26064de08
--- /dev/null
+++ b/client/src/components/ConfigTemplates/ActionSummary.vue
@@ -0,0 +1,29 @@
+<script lang="ts" setup>
+import { BAlert, BButton } from "bootstrap-vue";
+import { ref } from "vue";
+
+import type { PluginStatus } from "@/api/configTemplates";
+
+import ConfigurationTestSummaryModal from "@/components/ConfigTemplates/ConfigurationTestSummaryModal.vue";
+
+interface Props {
+    error: String | null;
+    testResults?: PluginStatus;
+    errorDataDescription: string;
+}
+
+const showTestResults = ref(false);
+defineProps<Props>();
+</script>
+
+<template>
+    <div>
+        <ConfigurationTestSummaryModal v-model="showTestResults" :test-results="testResults" />
+        <BAlert v-if="error" variant="danger" class="configuration-instance-error" show>
+            <span :data-description="errorDataDescription">
+                {{ error }}
+            </span>
+            <BButton variant="link" @click="showTestResults = true">View configuration test status.</BButton>
+        </BAlert>
+    </div>
+</template>
diff --git a/client/src/components/ConfigTemplates/ConfigurationTestItem.vue b/client/src/components/ConfigTemplates/ConfigurationTestItem.vue
new file mode 100644
index 0000000000000000000000000000000000000000..91cea8421f0e0d99fba4faeecf2fbca6d0847ead
--- /dev/null
+++ b/client/src/components/ConfigTemplates/ConfigurationTestItem.vue
@@ -0,0 +1,26 @@
+<script lang="ts" setup>
+import { faCheckSquare, faSquare, faTimes } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BListGroupItem, BSpinner } from "bootstrap-vue";
+
+import type { PluginAspectStatus } from "@/api/configTemplates";
+
+interface Props {
+    status?: PluginAspectStatus;
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <BListGroupItem href="#" class="d-flex align-items-center">
+        <BSpinner v-if="status == undefined" class="mr-3" label="Testing...."></BSpinner>
+        <FontAwesomeIcon v-else-if="status?.state == 'ok'" class="mr-3 text-success" :icon="faCheckSquare" size="lg" />
+        <FontAwesomeIcon v-else-if="status?.state == 'not_ok'" class="mr-3 text-warning" :icon="faTimes" size="lg" />
+        <FontAwesomeIcon v-else-if="status?.state == 'unknown'" class="mr-3 text-info" :icon="faSquare" size="lg" />
+
+        <span v-if="status && status.message" class="mr-auto">
+            {{ status.message }}
+        </span>
+    </BListGroupItem>
+</template>
diff --git a/client/src/components/ConfigTemplates/ConfigurationTestSummary.vue b/client/src/components/ConfigTemplates/ConfigurationTestSummary.vue
new file mode 100644
index 0000000000000000000000000000000000000000..b781c6eae665a65491a94c65b759bfba69bd81e1
--- /dev/null
+++ b/client/src/components/ConfigTemplates/ConfigurationTestSummary.vue
@@ -0,0 +1,24 @@
+<script lang="ts" setup>
+import { BListGroup } from "bootstrap-vue";
+
+import type { PluginStatus } from "@/api/configTemplates";
+
+import ConfigurationTestItem from "./ConfigurationTestItem.vue";
+
+interface Props {
+    testResults?: PluginStatus;
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <BListGroup v-if="testResults">
+        <ConfigurationTestItem :status="testResults?.template_definition" />
+        <ConfigurationTestItem
+            v-if="testResults?.oauth2_access_token_generation != null"
+            :status="testResults?.oauth2_access_token_generation" />
+        <ConfigurationTestItem :status="testResults?.template_settings" />
+        <ConfigurationTestItem :status="testResults?.connection" />
+    </BListGroup>
+</template>
diff --git a/client/src/components/ConfigTemplates/ConfigurationTestSummaryModal.vue b/client/src/components/ConfigTemplates/ConfigurationTestSummaryModal.vue
new file mode 100644
index 0000000000000000000000000000000000000000..22fa8a8b47362ecd4c2758c1cc47e3da1283eda5
--- /dev/null
+++ b/client/src/components/ConfigTemplates/ConfigurationTestSummaryModal.vue
@@ -0,0 +1,39 @@
+<script lang="ts" setup>
+import { BAlert, BModal } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import type { PluginStatus } from "@/api/configTemplates";
+
+import ConfigurationTestSummary from "./ConfigurationTestSummary.vue";
+
+interface Props {
+    value: boolean;
+    testResults?: PluginStatus;
+    error?: string;
+}
+
+const props = defineProps<Props>();
+
+const show = ref(props.value);
+
+watch(props, () => {
+    show.value = props.value;
+});
+
+const emit = defineEmits<{
+    (e: "input", value: boolean): void;
+}>();
+
+watch(show, () => {
+    emit("input", show.value);
+});
+</script>
+
+<template>
+    <BModal v-model="show" title="Configuration Test Summary" hide-footer>
+        <BAlert v-if="error" variant="danger" show dismissible>
+            {{ error || "" }}
+        </BAlert>
+        <ConfigurationTestSummary :test-results="testResults" />
+    </BModal>
+</template>
diff --git a/client/src/components/ConfigTemplates/EditSecretsForm.vue b/client/src/components/ConfigTemplates/EditSecretsForm.vue
index 7d5cd1777d5b593ed0481916ec115023d9f0e44c..e32b45ddfee51e2f374ec1cf6ade2f9d2b862de1 100644
--- a/client/src/components/ConfigTemplates/EditSecretsForm.vue
+++ b/client/src/components/ConfigTemplates/EditSecretsForm.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { TemplateSummary } from "@/api/configTemplates";
+import { type TemplateSummary } from "@/api/configTemplates";
 
 import VaultSecret from "./VaultSecret.vue";
 import FormCard from "@/components/Form/FormCard.vue";
diff --git a/client/src/components/ConfigTemplates/ForceActionButton.vue b/client/src/components/ConfigTemplates/ForceActionButton.vue
new file mode 100644
index 0000000000000000000000000000000000000000..55d42274f3881b1d608dc47fa099a51acc314922
--- /dev/null
+++ b/client/src/components/ConfigTemplates/ForceActionButton.vue
@@ -0,0 +1,17 @@
+<script setup lang="ts">
+import { BButton } from "bootstrap-vue";
+
+interface Props {
+    action: string;
+}
+
+defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "click"): void;
+}>();
+</script>
+
+<template>
+    <BButton variant="link" @click="emit('click')">I know what I am doing, force {{ action.toLowerCase() }}.</BButton>
+</template>
diff --git a/client/src/components/ConfigTemplates/InstanceDropdown.test.ts b/client/src/components/ConfigTemplates/InstanceDropdown.test.ts
index e29d8d883113098ad8e20c1b650b05230ae78f56..abfca1e3070a1bb44ac81e2fdedcfc7c4e2aff73 100644
--- a/client/src/components/ConfigTemplates/InstanceDropdown.test.ts
+++ b/client/src/components/ConfigTemplates/InstanceDropdown.test.ts
@@ -19,7 +19,7 @@ describe("InstanceDropdown", () => {
         });
         const menu = wrapper.find(".dropdown-menu");
         const links = menu.findAll("button.dropdown-item");
-        expect(links.length).toBe(2);
+        expect(links.length).toBe(3);
     });
 
     it("should render a drop down with upgrade if upgrade available as an option", async () => {
@@ -35,6 +35,6 @@ describe("InstanceDropdown", () => {
         });
         const menu = wrapper.find(".dropdown-menu");
         const links = menu.findAll("button.dropdown-item");
-        expect(links.length).toBe(3);
+        expect(links.length).toBe(4);
     });
 });
diff --git a/client/src/components/ConfigTemplates/InstanceDropdown.vue b/client/src/components/ConfigTemplates/InstanceDropdown.vue
index 95bbbf863cb81119e24fbb65a460c730e89a1a8c..0f891a64033eb6aba86f11e9755fb7e8a8768236 100644
--- a/client/src/components/ConfigTemplates/InstanceDropdown.vue
+++ b/client/src/components/ConfigTemplates/InstanceDropdown.vue
@@ -1,6 +1,5 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faArrowUp, faCaretDown, faEdit, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { faArrowUp, faCaretDown, faEdit, faStethoscope, faTrash } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useRouter } from "vue-router/composables";
 
@@ -12,14 +11,13 @@ interface Props {
     isUpgradable: boolean;
 }
 
-library.add(faArrowUp, faCaretDown, faEdit, faTrash);
-
 const router = useRouter();
 
 defineProps<Props>();
 
 const emit = defineEmits<{
     (e: "remove"): void;
+    (e: "test"): void;
 }>();
 </script>
 
@@ -32,7 +30,7 @@ const emit = defineEmits<{
             aria-haspopup="true"
             aria-expanded="false"
             class="ui-link font-weight-bold text-nowrap">
-            <FontAwesomeIcon icon="caret-down" class="fa-lg" />
+            <FontAwesomeIcon :icon="faCaretDown" size="lg" />
             <span class="instance-dropdown-name font-weight-bold">{{ name }}</span>
         </button>
         <div class="dropdown-menu" :aria-labelledby="`${prefix}-instance-dropdown`">
@@ -50,11 +48,15 @@ const emit = defineEmits<{
                 :href="routeEdit"
                 @keypress="router.push(routeEdit)"
                 @click.prevent="router.push(routeEdit)">
-                <FontAwesomeIcon icon="edit" />
+                <FontAwesomeIcon :icon="faEdit" />
                 <span v-localize>Edit configuration</span>
             </button>
+            <button class="dropdown-item" @keypress="emit('test')" @click.prevent="emit('test')">
+                <FontAwesomeIcon :icon="faStethoscope" />
+                <span v-localize>Test instance</span>
+            </button>
             <button class="dropdown-item" @keypress="emit('remove')" @click.prevent="emit('remove')">
-                <FontAwesomeIcon icon="trash" />
+                <FontAwesomeIcon :icon="faTrash" />
                 <span v-localize>Remove instance</span>
             </button>
         </div>
diff --git a/client/src/components/ConfigTemplates/InstanceForm.test.ts b/client/src/components/ConfigTemplates/InstanceForm.test.ts
index 30189e068d548d094942c45e3922f955b15fa0b6..f11499ae445c6c9cee3bfe0e0a9dce1b3eaee833 100644
--- a/client/src/components/ConfigTemplates/InstanceForm.test.ts
+++ b/client/src/components/ConfigTemplates/InstanceForm.test.ts
@@ -1,7 +1,7 @@
 import { shallowMount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { FormEntry } from "./formUtil";
+import { type FormEntry } from "./formUtil";
 
 import InstanceForm from "./InstanceForm.vue";
 
diff --git a/client/src/components/ConfigTemplates/InstanceForm.vue b/client/src/components/ConfigTemplates/InstanceForm.vue
index 129870128228bf4dbea924d64f76d56b8705aa81..530cb0b95f756e1adedeaf4998a57bb62a385250 100644
--- a/client/src/components/ConfigTemplates/InstanceForm.vue
+++ b/client/src/components/ConfigTemplates/InstanceForm.vue
@@ -3,6 +3,7 @@ import { BButton } from "bootstrap-vue";
 
 import { type FormEntry } from "./formUtil";
 
+import ForceActionButton from "./ForceActionButton.vue";
 import FormCard from "@/components/Form/FormCard.vue";
 import FormDisplay from "@/components/Form/FormDisplay.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
@@ -12,14 +13,18 @@ interface Props {
     inputs?: Array<FormEntry>; // not fully reactive so make sure to not mutate this array
     submitTitle: string;
     loadingMessage: string;
+    busy: boolean;
+    showForceActionButton?: boolean;
 }
 
 withDefaults(defineProps<Props>(), {
     inputs: undefined,
+    showForceActionButton: false,
 });
 
 const emit = defineEmits<{
     (e: "onSubmit", formData: any): void;
+    (e: "onForceSubmit", formData: any): void;
 }>();
 
 let formData: any;
@@ -31,6 +36,10 @@ function onChange(incoming: any) {
 async function handleSubmit() {
     emit("onSubmit", formData);
 }
+
+async function handleForceSubmit() {
+    emit("onForceSubmit", formData);
+}
 </script>
 <template>
     <div>
@@ -42,9 +51,11 @@ async function handleSubmit() {
                 </template>
             </FormCard>
             <div class="mt-3">
-                <BButton id="submit" variant="primary" class="mr-1" @click="handleSubmit">
+                <BButton id="submit" variant="primary" class="mr-1" :disabled="busy" @click="handleSubmit">
                     {{ submitTitle }}
                 </BButton>
+                <ForceActionButton v-show="showForceActionButton" :action="submitTitle" @click="handleForceSubmit">
+                </ForceActionButton>
             </div>
         </div>
     </div>
diff --git a/client/src/components/ConfigTemplates/SelectTemplate.test.js b/client/src/components/ConfigTemplates/SelectTemplate.test.js
index ce631ceb54d0ad131ed717a02ee469f5d940d9b8..afa5ee5febc168e5cc48eb648511f7d560606f48 100644
--- a/client/src/components/ConfigTemplates/SelectTemplate.test.js
+++ b/client/src/components/ConfigTemplates/SelectTemplate.test.js
@@ -19,7 +19,6 @@ describe("SelectTemplate", () => {
             },
             localVue,
         });
-        console.log(wrapper.html());
         const helpText = wrapper.find(".file-source-template-select-help");
         expect(helpText.exists()).toBeTruthy();
         expect(helpText.text()).toBeLocalizationOf(help);
diff --git a/client/src/components/ConfigTemplates/formUtil.test.ts b/client/src/components/ConfigTemplates/formUtil.test.ts
index e95caf3d95f5c059e601e8294b3f413ff2a6c666..dd5b412d30ea975f6616f6a596714e7b7454bb2e 100644
--- a/client/src/components/ConfigTemplates/formUtil.test.ts
+++ b/client/src/components/ConfigTemplates/formUtil.test.ts
@@ -1,4 +1,4 @@
-import { TemplateVariable } from "@/api/configTemplates";
+import { type TemplateVariable } from "@/api/configTemplates";
 
 import { createTemplateForm, templateVariableFormEntry, upgradeForm } from "./formUtil";
 import {
diff --git a/client/src/components/ConfigTemplates/formUtil.ts b/client/src/components/ConfigTemplates/formUtil.ts
index e211cb3017294a4eabf09de9a0a50b5ad115dc18..b6908259dcf9aaba4103ddd3bca6549e47492b02 100644
--- a/client/src/components/ConfigTemplates/formUtil.ts
+++ b/client/src/components/ConfigTemplates/formUtil.ts
@@ -1,12 +1,13 @@
-import type {
-    Instance,
-    PluginStatus,
-    SecretData,
-    TemplateSecret,
-    TemplateSummary,
-    TemplateVariable,
-    VariableData,
-    VariableValueType,
+import {
+    type CreateInstancePayload,
+    type Instance,
+    type PluginStatus,
+    type SecretData,
+    type TemplateSecret,
+    type TemplateSummary,
+    type TemplateVariable,
+    type VariableData,
+    type VariableValueType,
 } from "@/api/configTemplates";
 import { markup } from "@/components/ObjectStore/configurationMarkdown";
 
@@ -39,7 +40,7 @@ export function metadataFormEntryDescription(what: string): FormEntry {
     };
 }
 
-export function templateVariableFormEntry(variable: TemplateVariable, variableValue: VariableValueType): FormEntry {
+export function templateVariableFormEntry(variable: TemplateVariable, variableValue?: VariableValueType): FormEntry {
     const common_fields = {
         name: variable.name,
         label: variable.label ?? variable.name,
@@ -139,7 +140,7 @@ export function createTemplateForm(template: TemplateSummary, what: string): For
     return form;
 }
 
-export function createFormDataToPayload(template: TemplateSummary, formData: any) {
+export function createFormDataToPayload(template: TemplateSummary, formData: any): CreateInstancePayload {
     const variables = template.variables ?? [];
     const secrets = template.secrets ?? [];
     const variableData: VariableData = {};
@@ -155,7 +156,7 @@ export function createFormDataToPayload(template: TemplateSummary, formData: any
     }
     const name: string = formData._meta_name;
     const description: string = formData._meta_description;
-    const payload = {
+    const payload: CreateInstancePayload = {
         name: name,
         description: description,
         secrets: secretData,
@@ -166,7 +167,7 @@ export function createFormDataToPayload(template: TemplateSummary, formData: any
     return payload;
 }
 
-export function formDataTypedGet(variableDefinition: TemplateVariable, formData: any): VariableValueType {
+export function formDataTypedGet(variableDefinition: TemplateVariable, formData: any): VariableValueType | undefined {
     // galaxy form library doesn't type values traditionally, so add a typed
     // access to the data if coming back as string. Though it does seem to be
     // typed properly - this might not be needed anymore?
diff --git a/client/src/components/ConfigTemplates/routing.ts b/client/src/components/ConfigTemplates/routing.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d8b63d60ca8dbd1c888bbd891a6766623937c0b2
--- /dev/null
+++ b/client/src/components/ConfigTemplates/routing.ts
@@ -0,0 +1,18 @@
+import { useRouter } from "vue-router/composables";
+
+export function buildInstanceRoutingComposable(index: string) {
+    return () => {
+        const router = useRouter();
+
+        async function goToIndex(query: Record<"message", string>) {
+            router.push({
+                path: index,
+                query: query,
+            });
+        }
+
+        return {
+            goToIndex,
+        };
+    };
+}
diff --git a/client/src/components/ConfigTemplates/test_fixtures.ts b/client/src/components/ConfigTemplates/test_fixtures.ts
index f29e8d5bd59878b166b128bea7d60ad5df933d08..8e5b967318c1d81d76e55507b79911bdff24fc2d 100644
--- a/client/src/components/ConfigTemplates/test_fixtures.ts
+++ b/client/src/components/ConfigTemplates/test_fixtures.ts
@@ -1,6 +1,7 @@
-import type { FileSourceTemplateSummary } from "@/api/fileSources";
-import type { UserConcreteObjectStore } from "@/components/ObjectStore/Instances/types";
-import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
+import { type PluginStatus } from "@/api/configTemplates";
+import { type FileSourceTemplateSummary } from "@/api/fileSources";
+import { type UserConcreteObjectStore } from "@/components/ObjectStore/Instances/types";
+import { type ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
 
 export const STANDARD_OBJECT_STORE_TEMPLATE: ObjectStoreTemplateSummary = {
     type: "aws_s3",
@@ -11,11 +12,13 @@ export const STANDARD_OBJECT_STORE_TEMPLATE: ObjectStoreTemplateSummary = {
             name: "oldvar",
             type: "string",
             help: "old var help",
+            default: "old default",
         },
         {
             name: "newvar",
             type: "string",
             help: "new var help",
+            default: "new default",
         },
     ],
     secrets: [
@@ -31,6 +34,7 @@ export const STANDARD_OBJECT_STORE_TEMPLATE: ObjectStoreTemplateSummary = {
     id: "moo",
     version: 2,
     badges: [],
+    hidden: false,
 };
 
 export const STANDARD_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
@@ -42,11 +46,13 @@ export const STANDARD_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
             name: "oldvar",
             type: "string",
             help: "old var help",
+            default: "old default",
         },
         {
             name: "newvar",
             type: "string",
             help: "new var help",
+            default: "new default",
         },
     ],
     secrets: [
@@ -61,6 +67,7 @@ export const STANDARD_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
     ],
     id: "moo",
     version: 2,
+    hidden: false,
 };
 
 export const GENERIC_FTP_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
@@ -69,12 +76,19 @@ export const GENERIC_FTP_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
     name: "Generic FTP Server",
     description: "Generic FTP configuration with all configuration options exposed.",
     variables: [
-        { name: "host", label: "FTP Host", type: "string", help: "Host of FTP Server to connect to." },
+        {
+            name: "host",
+            label: "FTP Host",
+            type: "string",
+            help: "Host of FTP Server to connect to.",
+            default: "ftp.example.com",
+        },
         {
             name: "user",
             label: "FTP User",
             type: "string",
             help: "Username to login to target FTP server with.",
+            default: "anonymous",
         },
         {
             name: "writable",
@@ -98,6 +112,8 @@ export const GENERIC_FTP_FILE_SOURCE_TEMPLATE: FileSourceTemplateSummary = {
             help: "Password to connect to FTP server with.",
         },
     ],
+    hidden: false,
+    version: 1,
 };
 
 export const OBJECT_STORE_INSTANCE: UserConcreteObjectStore = {
@@ -119,3 +135,18 @@ export const OBJECT_STORE_INSTANCE: UserConcreteObjectStore = {
     hidden: false,
     purged: false,
 };
+
+export const OK_PLUGIN_STATUS: PluginStatus = {
+    template_definition: {
+        state: "ok",
+        message: "ok",
+    },
+    template_settings: {
+        state: "ok",
+        message: "ok",
+    },
+    connection: {
+        state: "ok",
+        message: "ok",
+    },
+};
diff --git a/client/src/components/ConfigTemplates/useConfigurationTesting.ts b/client/src/components/ConfigTemplates/useConfigurationTesting.ts
new file mode 100644
index 0000000000000000000000000000000000000000..26ec1389cf8e6b7a11eab4b2bc4b4f7b0dd406a1
--- /dev/null
+++ b/client/src/components/ConfigTemplates/useConfigurationTesting.ts
@@ -0,0 +1,387 @@
+import { computed, type Ref, ref } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { type Instance, type PluginStatus, type TemplateSummary } from "@/api/configTemplates";
+import { type buildInstanceRoutingComposable } from "@/components/ConfigTemplates/routing";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import {
+    createFormDataToPayload,
+    createTemplateForm,
+    editFormDataToPayload,
+    editTemplateForm,
+    type FormEntry,
+    pluginStatusToErrorMessage,
+    upgradeForm,
+    upgradeFormDataToPayload,
+} from "./formUtil";
+
+import ActionSummary from "./ActionSummary.vue";
+import ConfigurationTestSummaryModal from "@/components/ConfigTemplates/ConfigurationTestSummaryModal.vue";
+import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+
+type InstanceRoutingComposableType = ReturnType<typeof buildInstanceRoutingComposable>;
+
+export function useConfigurationTesting() {
+    const testRunning = ref<boolean>(false);
+    const testResults = ref<PluginStatus | undefined>(undefined);
+
+    return {
+        testRunning,
+        testResults,
+    };
+}
+
+type CreateTestUrl = "/api/object_store_instances/test" | "/api/file_source_instances/test";
+type CreateUrl = "/api/object_store_instances" | "/api/file_source_instances";
+
+export function useConfigurationTemplateCreation<T extends TemplateSummary, R>(
+    what: string,
+    template: Ref<T>,
+    uuid: Ref<string | undefined>,
+    testUrl: CreateTestUrl,
+    createUrl: CreateUrl,
+    onCreate: (result: R) => unknown
+) {
+    const error = ref<string | null>(null);
+    const { testRunning, testResults } = useConfigurationTesting();
+
+    async function onSubmit(formData: any) {
+        const payload = createFormDataToPayload(template.value, formData);
+        if (uuid.value) {
+            payload.uuid = uuid.value;
+        }
+        let pluginStatus: PluginStatus;
+        try {
+            testRunning.value = true;
+            const { data, error: testRequestError } = await GalaxyApi().POST(testUrl, {
+                body: payload,
+            });
+            if (testRequestError) {
+                error.value = "Failed to verify configuration: " + errorMessageAsString(testRequestError);
+                return;
+            } else {
+                pluginStatus = data;
+                testResults.value = pluginStatus;
+            }
+        } catch (e) {
+            error.value = "Failed to verify configuration: " + errorMessageAsString(e);
+            return;
+        } finally {
+            testRunning.value = false;
+        }
+        if (pluginStatus) {
+            const testError = pluginStatusToErrorMessage(pluginStatus);
+            if (testError) {
+                error.value = testError;
+                return;
+            }
+        }
+        try {
+            const { data: userObject, error: createRequestError } = await GalaxyApi().POST(createUrl, {
+                body: payload,
+            });
+            if (createRequestError) {
+                error.value = errorMessageAsString(createRequestError);
+            } else {
+                onCreate(userObject as R);
+            }
+        } catch (e) {
+            error.value = errorMessageAsString(e);
+            return;
+        }
+    }
+
+    const inputs = computed<FormEntry[]>(() => {
+        return createTemplateForm(template.value, what);
+    });
+
+    const submitTitle = "Create";
+    const loadingMessage = `Loading ${what} template and instance information`;
+
+    return {
+        ActionSummary,
+        error,
+        inputs,
+        InstanceForm,
+        onSubmit,
+        submitTitle,
+        loadingMessage,
+        testRunning,
+        testResults,
+    };
+}
+
+type TestInstanceUrl = "/api/file_source_instances/{uuid}/test" | "/api/object_store_instances/{uuid}/test";
+
+export function useInstanceTesting<R extends Instance>(testUrl: TestInstanceUrl) {
+    const showTestResults = ref(false);
+    const testResults = ref<PluginStatus | undefined>(undefined);
+    const testingError = ref<string | undefined>(undefined);
+
+    async function test(instance: R) {
+        testResults.value = undefined;
+        testingError.value = undefined;
+        showTestResults.value = true;
+        try {
+            const { data, error } = await GalaxyApi().GET(testUrl, {
+                params: { path: { uuid: instance.uuid } },
+            });
+            const pluginStatus = data;
+            const testRequestError = error;
+            if (testRequestError) {
+                testingError.value = errorMessageAsString(testRequestError);
+            } else {
+                testResults.value = pluginStatus;
+            }
+        } catch (e) {
+            testingError.value = errorMessageAsString(e);
+        }
+    }
+
+    return {
+        ConfigurationTestSummaryModal,
+        showTestResults,
+        testResults,
+        testingError,
+        test,
+    };
+}
+
+type TestUpdateUrl = "/api/object_store_instances/{uuid}/test" | "/api/file_source_instances/{uuid}/test";
+type UpdateUrl = "/api/object_store_instances/{uuid}" | "/api/file_source_instances/{uuid}";
+
+export function useConfigurationTemplateEdit<T extends TemplateSummary, R extends Instance>(
+    what: string,
+    instance: Ref<R | null>,
+    template: Ref<T | null>,
+    testUpdateUrl: TestUpdateUrl,
+    updateUrl: UpdateUrl,
+    useRouting: InstanceRoutingComposableType
+) {
+    const { testRunning, testResults } = useConfigurationTesting();
+    const showForceActionButton = ref<boolean>(false);
+
+    const { goToIndex } = useRouting();
+
+    async function onUpdate(objectStore: R) {
+        const message = `Updated ${what} ${objectStore.name}`;
+        goToIndex({ message });
+    }
+
+    const inputs = computed<Array<FormEntry> | undefined>(() => {
+        const realizedInstance = instance.value;
+        const realizedTemplate = template.value;
+        if (!realizedInstance || !realizedTemplate) {
+            return undefined;
+        }
+        return editTemplateForm(realizedTemplate, what, realizedInstance);
+    });
+
+    const error = ref<string | null>(null);
+    const hasSecrets = computed(() => instance.value?.secrets && instance.value?.secrets.length > 0);
+    const submitTitle = "Update Settings";
+    const loadingMessage = `Loading ${what} template and instance information`;
+
+    async function onSubmit(formData: any) {
+        if (template.value && instance.value) {
+            const payload = editFormDataToPayload(template.value, formData);
+
+            let pluginStatus;
+            try {
+                testRunning.value = true;
+                showForceActionButton.value = false;
+                const { data: pluginStatus, error: testRequestError } = await GalaxyApi().POST(testUpdateUrl, {
+                    params: { path: { uuid: instance.value.uuid } },
+                    body: payload,
+                });
+                if (testRequestError) {
+                    error.value = errorMessageAsString(testRequestError);
+                    showForceActionButton.value = true;
+                }
+                testResults.value = pluginStatus;
+            } catch (e) {
+                error.value = errorMessageAsString(e);
+                showForceActionButton.value = true;
+                return;
+            } finally {
+                testRunning.value = false;
+            }
+            if (pluginStatus) {
+                const testError = pluginStatusToErrorMessage(pluginStatus);
+                if (testError) {
+                    error.value = testError;
+                    showForceActionButton.value = true;
+                    return;
+                }
+            }
+
+            try {
+                const { data, error: updateRequestError } = await GalaxyApi().PUT(updateUrl, {
+                    params: { path: { uuid: instance.value.uuid } },
+                    body: payload,
+                });
+                if (updateRequestError) {
+                    error.value = errorMessageAsString(updateRequestError);
+                } else {
+                    await onUpdate(data as R);
+                }
+            } catch (e) {
+                error.value = errorMessageAsString(e);
+                return;
+            }
+        }
+    }
+
+    async function onForceSubmit(formData: any) {
+        if (template.value && instance.value) {
+            const payload = editFormDataToPayload(template.value, formData);
+            try {
+                const { data, error: updateRequestError } = await GalaxyApi().PUT(updateUrl, {
+                    params: { path: { uuid: instance.value.uuid } },
+                    body: payload,
+                });
+                if (updateRequestError) {
+                    error.value = errorMessageAsString(updateRequestError);
+                } else {
+                    await onUpdate(data as R);
+                }
+            } catch (e) {
+                error.value = errorMessageAsString(e);
+                return;
+            }
+        }
+    }
+
+    return {
+        error,
+        ActionSummary,
+        inputs,
+        InstanceForm,
+        hasSecrets,
+        loadingMessage,
+        onForceSubmit,
+        onSubmit,
+        showForceActionButton,
+        submitTitle,
+        testResults,
+        testRunning,
+    };
+}
+
+export function useConfigurationTemplateUpgrade<T extends TemplateSummary, R extends Instance>(
+    what: string,
+    instance: Ref<R>,
+    template: Ref<T>,
+    testUpdateUrl: TestUpdateUrl,
+    updateUrl: UpdateUrl,
+    useRouting: InstanceRoutingComposableType
+) {
+    const { goToIndex } = useRouting();
+
+    async function onUpgrade(objectStore: R) {
+        const message = `Upgraded ${what} ${objectStore.name}`;
+        goToIndex({ message });
+    }
+
+    const error = ref<string | null>(null);
+    const { testRunning, testResults } = useConfigurationTesting();
+    const showForceActionButton = ref<boolean>(false);
+
+    const submitTitle = "Upgrade Configuration";
+    const loadingMessage = `Loading latest ${what} template and instance information`;
+
+    const inputs = computed<Array<FormEntry> | undefined>(() => {
+        const realizedInstance = instance.value;
+        const realizedLatestTemplate = template.value;
+        if (!realizedInstance || !realizedLatestTemplate) {
+            return undefined;
+        }
+        const form = upgradeForm(realizedLatestTemplate, realizedInstance);
+        return form;
+    });
+
+    async function onSubmit(formData: any) {
+        if (!instance.value || !template.value) {
+            return;
+        }
+
+        const payload = upgradeFormDataToPayload(template.value, formData);
+        let pluginStatus;
+        try {
+            testRunning.value = true;
+            showForceActionButton.value = false;
+            const { data: pluginStatus, error: testRequestError } = await GalaxyApi().POST(testUpdateUrl, {
+                params: { path: { uuid: instance.value.uuid } },
+                body: payload,
+            });
+            if (testRequestError) {
+                error.value = errorMessageAsString(testRequestError);
+                showForceActionButton.value = true;
+                return;
+            } else {
+                testResults.value = pluginStatus;
+            }
+        } catch (e) {
+            showForceActionButton.value = true;
+            error.value = errorMessageAsString(e);
+            return;
+        } finally {
+            testRunning.value = false;
+        }
+        if (pluginStatus) {
+            const testError = pluginStatusToErrorMessage(pluginStatus);
+            if (testError) {
+                error.value = testError;
+                showForceActionButton.value = true;
+                return;
+            }
+        }
+        try {
+            const { data, error: updateRequestError } = await GalaxyApi().PUT(updateUrl, {
+                params: { path: { uuid: instance.value.uuid } },
+                body: payload,
+            });
+            if (updateRequestError) {
+                error.value = errorMessageAsString(updateRequestError);
+            } else {
+                await onUpgrade(data as R);
+            }
+        } catch (e) {
+            error.value = errorMessageAsString(e);
+            return;
+        }
+    }
+
+    async function onForceSubmit(formData: any) {
+        const payload = upgradeFormDataToPayload(template.value, formData);
+        try {
+            const { data, error: updateRequestError } = await GalaxyApi().PUT(updateUrl, {
+                params: { path: { uuid: instance.value.uuid } },
+                body: payload,
+            });
+            if (updateRequestError) {
+                error.value = errorMessageAsString(updateRequestError);
+            } else {
+                await onUpgrade(data as R);
+            }
+        } catch (e) {
+            error.value = errorMessageAsString(e);
+            return;
+        }
+    }
+
+    return {
+        error,
+        ActionSummary,
+        inputs,
+        InstanceForm,
+        loadingMessage,
+        onForceSubmit,
+        onSubmit,
+        submitTitle,
+        showForceActionButton,
+        testResults,
+        testRunning,
+    };
+}
diff --git a/client/src/components/DataDialog/services.js b/client/src/components/DataDialog/services.js
index 7b3816e07dc2eee181b3a80b9a18a13b630b2d59..319213d59733c3f840b3a57ff8d374e7923c9755 100644
--- a/client/src/components/DataDialog/services.js
+++ b/client/src/components/DataDialog/services.js
@@ -48,6 +48,7 @@ export class Services {
     /** Populate record data from raw record source **/
     getRecord(record) {
         const host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
+        record.extension = record.extension ?? record.file_ext;
         record.details = record.extension || record.description;
         record.time = record.update_time || record.create_time;
         record.isLeaf = this.isDataset(record);
diff --git a/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue b/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
index 7ac0e57e36502544485af0e9c45451b37565cad0..5001d7f2b20ac45c0ef7f14292b0fbf2986692b0 100644
--- a/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
+++ b/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
@@ -2,7 +2,7 @@
 import { computed } from "vue";
 
 import type { DatasetExtraFiles } from "@/api/datasets";
-import { PathDestination, useDatasetPathDestination } from "@/composables/datasetPathDestination";
+import { type PathDestination, useDatasetPathDestination } from "@/composables/datasetPathDestination";
 
 interface Props {
     historyDatasetId: string;
diff --git a/client/src/components/Dataset/DatasetList.vue b/client/src/components/Dataset/DatasetList.vue
index cec54b0c7429bcb5f00e6c170c89c940e1fef2e7..524c33f414eaff4eb2a8af9acebdb6ce393e4e3c 100644
--- a/client/src/components/Dataset/DatasetList.vue
+++ b/client/src/components/Dataset/DatasetList.vue
@@ -3,10 +3,11 @@ import { BAlert, BTable } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, ref } from "vue";
 
-import { HDASummary } from "@/api";
-import { copyDataset, getDatasets } from "@/api/datasets";
+import { GalaxyApi, type HDASummary } from "@/api";
+import { copyDataset } from "@/api/datasets";
 import { updateTags } from "@/api/tags";
 import { useHistoryStore } from "@/stores/historyStore";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import DelayedInput from "@/components/Common/DelayedInput.vue";
 import DatasetName from "@/components/Dataset/DatasetName.vue";
@@ -68,18 +69,29 @@ async function load(concat = false) {
     loading.value = true;
 
     try {
-        const datasets = await getDatasets({
-            query: query.value,
-            sortBy: sortBy.value,
-            sortDesc: sortDesc.value,
-            offset: offset.value,
-            limit: limit.value,
+        const { data, error } = await GalaxyApi().GET("/api/datasets", {
+            params: {
+                query: {
+                    q: ["name-contains"],
+                    qv: [query.value],
+                    limit: limit.value,
+                    offset: offset.value,
+                    order: `${sortBy.value}${sortDesc.value ? "-dsc" : "-asc"}`,
+                    view: "summary",
+                },
+            },
         });
 
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const datasets = data as HDASummary[];
+
         if (concat) {
-            rows.value = rows.value.concat(datasets as HDASummary[]);
+            rows.value = rows.value.concat(datasets);
         } else {
-            rows.value = datasets as HDASummary[];
+            rows.value = datasets;
         }
     } catch (error: any) {
         onError(error);
@@ -92,7 +104,11 @@ async function onCopyDataset(item: HDASummary) {
     const dataset_id = item.id;
 
     try {
-        await copyDataset(dataset_id, currentHistoryId.value as string);
+        if (!currentHistoryId.value) {
+            throw new Error("No current history found.");
+        }
+
+        await copyDataset(dataset_id, currentHistoryId.value);
 
         historyStore.loadCurrentHistory();
     } catch (error: any) {
diff --git a/client/src/components/Dataset/DatasetName.vue b/client/src/components/Dataset/DatasetName.vue
index 71e629011e3a5b6929b3c740a483d4467e71a92a..2a1b176a48aedf58e671096fd13fb2f5bb432d5e 100644
--- a/client/src/components/Dataset/DatasetName.vue
+++ b/client/src/components/Dataset/DatasetName.vue
@@ -5,7 +5,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BLink } from "bootstrap-vue";
 import { computed } from "vue";
 
-import { HDASummary } from "@/api";
+import { type HDASummary } from "@/api";
 
 library.add(faCaretDown, faCopy, faEye, faTimesCircle, faPause);
 
diff --git a/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.js b/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.js
deleted file mode 100644
index 1a8a5a7cf7f190f8d3ce168e7a370e9526189f87..0000000000000000000000000000000000000000
--- a/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.js
+++ /dev/null
@@ -1,63 +0,0 @@
-import { shallowMount } from "@vue/test-utils";
-import flushPromises from "flush-promises";
-import { getLocalVue } from "tests/jest/helpers";
-
-import { mockFetcher } from "@/api/schema/__mocks__";
-
-import DatasetStorage from "./DatasetStorage";
-
-jest.mock("@/api/schema");
-
-const localVue = getLocalVue();
-
-const TEST_STORAGE_API_RESPONSE_WITHOUT_ID = {
-    object_store_id: null,
-    private: false,
-};
-const TEST_DATASET_ID = "1";
-const STORAGE_FETCH_URL = "/api/datasets/{dataset_id}/storage";
-const TEST_ERROR_MESSAGE = "Opps all errors.";
-
-describe("DatasetStorage.vue", () => {
-    let wrapper;
-
-    function mount() {
-        wrapper = shallowMount(DatasetStorage, {
-            propsData: { datasetId: TEST_DATASET_ID },
-            localVue,
-        });
-    }
-
-    async function mountWithResponse(response) {
-        mockFetcher.path(STORAGE_FETCH_URL).method("get").mock({ data: response });
-        mount();
-        await flushPromises();
-    }
-
-    it("test loading...", async () => {
-        mount();
-        await wrapper.vm.$nextTick();
-        expect(wrapper.findAll("loadingspan-stub").length).toBe(1);
-        expect(wrapper.findAll("describeobjectstore-stub").length).toBe(0);
-    });
-
-    it("test error rendering...", async () => {
-        mockFetcher
-            .path(STORAGE_FETCH_URL)
-            .method("get")
-            .mock(() => {
-                throw Error(TEST_ERROR_MESSAGE);
-            });
-        mount();
-        await flushPromises();
-        expect(wrapper.findAll(".error").length).toBe(1);
-        expect(wrapper.findAll(".error").at(0).text()).toBe(TEST_ERROR_MESSAGE);
-        expect(wrapper.findAll("loadingspan-stub").length).toBe(0);
-    });
-
-    it("test dataset storage with object store without id", async () => {
-        await mountWithResponse(TEST_STORAGE_API_RESPONSE_WITHOUT_ID);
-        expect(wrapper.findAll("loadingspan-stub").length).toBe(0);
-        expect(wrapper.findAll("describeobjectstore-stub").length).toBe(1);
-    });
-});
diff --git a/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.ts b/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a1b0b8e384dee82236fc9619b0da7aa0a9102d88
--- /dev/null
+++ b/client/src/components/Dataset/DatasetStorage/DatasetStorage.test.ts
@@ -0,0 +1,74 @@
+import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { type DatasetStorageDetails } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
+
+import DatasetStorage from "./DatasetStorage.vue";
+
+const localVue = getLocalVue();
+
+const TEST_STORAGE_API_RESPONSE_WITHOUT_ID: DatasetStorageDetails = {
+    object_store_id: null,
+    name: "Test name",
+    description: "Test description",
+    dataset_state: "ok",
+    quota: { enabled: false, source: null },
+    relocatable: false,
+    shareable: false,
+    badges: [],
+    hashes: [],
+    sources: [],
+    percent_used: 0,
+};
+const TEST_DATASET_ID = "1";
+const TEST_ERROR_MESSAGE = "Opps all errors.";
+
+const { server, http } = useServerMock();
+
+describe("DatasetStorage.vue", () => {
+    let wrapper: any;
+
+    function mount(options: { simulateError: boolean } = { simulateError: false }) {
+        server.use(
+            http.get("/api/datasets/{dataset_id}/storage", ({ response }) => {
+                if (options.simulateError) {
+                    return response("5XX").json({ err_msg: TEST_ERROR_MESSAGE, err_code: 500 }, { status: 500 });
+                }
+                return response(200).json(TEST_STORAGE_API_RESPONSE_WITHOUT_ID);
+            })
+        );
+
+        wrapper = shallowMount(DatasetStorage, {
+            propsData: { datasetId: TEST_DATASET_ID },
+            localVue,
+        });
+    }
+
+    it("test loading...", async () => {
+        mount();
+        // Do not await flushPromises here so the API call is not resolved
+        expect(wrapper.findAll("loadingspan-stub").length).toBe(1);
+        expect(wrapper.findAll("describeobjectstore-stub").length).toBe(0);
+
+        await flushPromises();
+        expect(wrapper.findAll("loadingspan-stub").length).toBe(0);
+        expect(wrapper.findAll("describeobjectstore-stub").length).toBe(1);
+    });
+
+    it("test error rendering...", async () => {
+        mount({ simulateError: true });
+        await flushPromises();
+        expect(wrapper.findAll(".error").length).toBe(1);
+        expect(wrapper.findAll(".error").at(0).text()).toBe(TEST_ERROR_MESSAGE);
+        expect(wrapper.findAll("loadingspan-stub").length).toBe(0);
+    });
+
+    it("test dataset storage with object store without id", async () => {
+        mount();
+        await flushPromises();
+        expect(wrapper.findAll("loadingspan-stub").length).toBe(0);
+        expect(wrapper.findAll("describeobjectstore-stub").length).toBe(1);
+    });
+});
diff --git a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
index b36bdfad2296b2ea92719bb256b121985d9636ff..da4756b225d1e9c409101d2154ad1d7e1cb20d13 100644
--- a/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
+++ b/client/src/components/Dataset/DatasetStorage/DatasetStorage.vue
@@ -1,9 +1,8 @@
 <script setup lang="ts">
 import { computed, ref, watch } from "vue";
 
-import { DatasetStorageDetails } from "@/api";
-import { fetchDatasetStorage } from "@/api/datasets";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { type DatasetStorageDetails, GalaxyApi } from "@/api";
+import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
 import RelocateLink from "./RelocateLink.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
@@ -47,8 +46,16 @@ async function fetch() {
     const datasetId = props.datasetId;
     const datasetType = props.datasetType;
     try {
-        const response = await fetchDatasetStorage({ dataset_id: datasetId, hda_ldda: datasetType });
-        storageInfo.value = response.data;
+        const { data, error } = await GalaxyApi().GET("/api/datasets/{dataset_id}/storage", {
+            params: {
+                path: { dataset_id: datasetId },
+                query: { hda_ldda: datasetType },
+            },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        storageInfo.value = data;
     } catch (error) {
         errorMessage.value = errorMessageAsString(error);
     }
diff --git a/client/src/components/Dataset/DatasetStorage/RelocateDialog.vue b/client/src/components/Dataset/DatasetStorage/RelocateDialog.vue
index 1caf060b53b16b758e728b246b6216076e165e8a..3cb59309f726608cf3bd2a96a85658b2529d5ade 100644
--- a/client/src/components/Dataset/DatasetStorage/RelocateDialog.vue
+++ b/client/src/components/Dataset/DatasetStorage/RelocateDialog.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { ConcreteObjectStoreModel } from "@/api";
+import { type ConcreteObjectStoreModel } from "@/api";
 
 import ObjectStoreSelectButton from "@/components/ObjectStore/ObjectStoreSelectButton.vue";
 import ObjectStoreSelectButtonDescribePopover from "@/components/ObjectStore/ObjectStoreSelectButtonDescribePopover.vue";
diff --git a/client/src/components/Dataset/DatasetStorage/RelocateLink.vue b/client/src/components/Dataset/DatasetStorage/RelocateLink.vue
index fb71dacc1b043f1da6e941ea1e10f70538ef3c5f..a097501d9f354e6f6f7da7bd1569e56ff848cace 100644
--- a/client/src/components/Dataset/DatasetStorage/RelocateLink.vue
+++ b/client/src/components/Dataset/DatasetStorage/RelocateLink.vue
@@ -3,7 +3,7 @@ import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
 
-import { ConcreteObjectStoreModel, DatasetStorageDetails } from "@/api";
+import { type ConcreteObjectStoreModel, type DatasetStorageDetails } from "@/api";
 import { updateObjectStore } from "@/api/objectStores";
 import { useObjectStoreStore } from "@/stores/objectStoreStore";
 
diff --git a/client/src/components/DatasetInformation/DatasetAttributes.vue b/client/src/components/DatasetInformation/DatasetAttributes.vue
index a9fa7db9acd0fdb7fbd50af3c9d7be3cc111d6a3..1444085890ff17c3d0d50ae3bfdf44b77d7cf47c 100644
--- a/client/src/components/DatasetInformation/DatasetAttributes.vue
+++ b/client/src/components/DatasetInformation/DatasetAttributes.vue
@@ -138,7 +138,8 @@ onMounted(async () => {
                     v-if="
                         (!datasetAttributes['conversion_disable'] || !datasetAttributes['datatype_disable']) &&
                         !datasetAttributes['metadata_disable']
-                    ">
+                    "
+                    title-link-class="dataset-edit-datatype-tab">
                     <template v-slot:title>
                         <FontAwesomeIcon :icon="faDatabase" class="mr-1" />
                         {{ localize("Datatypes") }}
@@ -168,7 +169,9 @@ onMounted(async () => {
                                     {{ localize("Save") }}
                                 </BButton>
 
-                                <BButton @click="submit('datatype', 'datatype_detect')">
+                                <BButton
+                                    id="dataset-attributes-autodetect-datatype"
+                                    @click="submit('datatype', 'datatype_detect')">
                                     <FontAwesomeIcon :icon="faRedo" class="mr-1" />
                                     {{ localize("Auto-detect") }}
                                 </BButton>
diff --git a/client/src/components/DatasetInformation/DatasetDetails.vue b/client/src/components/DatasetInformation/DatasetDetails.vue
index 7680606b31061be84c6ea92f24019e73dc66ba36..2df76e3206e7adaa4b4488525283a0ff1554b89c 100644
--- a/client/src/components/DatasetInformation/DatasetDetails.vue
+++ b/client/src/components/DatasetInformation/DatasetDetails.vue
@@ -1,14 +1,14 @@
 <script setup lang="ts">
-import { type AxiosError } from "axios";
 import { BAlert } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { onMounted, onUnmounted, ref } from "vue";
 
-import { type HDADetailed } from "@/api";
+import { GalaxyApi, type HDADetailed } from "@/api";
 import { fetchDatasetDetails } from "@/api/datasets";
-import { fetchJobDetails, JobDetails } from "@/api/jobs";
+import { type JobDetails } from "@/api/jobs";
 import { useConfig } from "@/composables/config";
 import { useUserStore } from "@/stores/userStore";
+import { errorMessageAsString } from "@/utils/simple-error";
 import { stateIsTerminal } from "@/utils/utils";
 
 import DatasetStorage from "@/components/Dataset/DatasetStorage/DatasetStorage.vue";
@@ -41,42 +41,43 @@ const datasetLoadingError = ref<string | null>(null);
 
 async function getDatasetDetails() {
     loading.value = true;
-
     try {
         const data = await fetchDatasetDetails({ id: props.datasetId });
-
         dataset.value = data;
     } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
-
-        datasetLoadingError.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
+        datasetLoadingError.value = errorMessageAsString(e) || "Unable to fetch available dataset details.";
     } finally {
         loading.value = false;
     }
 }
 
 async function loadJobDetails() {
-    try {
-        const { data } = await fetchJobDetails({ job_id: dataset.value?.creating_job as string, full: true });
-
-        if (stateIsTerminal(data)) {
-            clearTimeout(jobTimeOut.value);
-        } else {
-            jobTimeOut.value = setTimeout(loadJobDetails, 3000);
-        }
-
-        jobDetails.value = data;
-    } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
+    const { data, error } = await GalaxyApi().GET("/api/jobs/{job_id}", {
+        params: {
+            path: { job_id: dataset.value?.creating_job! },
+            query: { full: true },
+        },
+    });
+
+    if (error) {
+        jobLoadingError.value = errorMessageAsString(error);
+        return;
+    }
 
-        jobLoadingError.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
+    if (stateIsTerminal(data)) {
+        clearTimeout(jobTimeOut.value);
+    } else {
+        jobTimeOut.value = setTimeout(loadJobDetails, 3000);
     }
+
+    jobDetails.value = data;
 }
 
 onMounted(async () => {
     await getDatasetDetails();
 
-    if (dataset.value?.creating_job !== null) {
+    const creatingJobId = dataset.value?.creating_job;
+    if (creatingJobId) {
         await loadJobDetails();
     }
 });
diff --git a/client/src/components/DatasetInformation/DatasetError.test.ts b/client/src/components/DatasetInformation/DatasetError.test.ts
index c3213e8dc6fce6ad3ff4eace7fa4bd377e9e48ab..1c514acb3d14c44a513d2e9165ec05a00efb7a8d 100644
--- a/client/src/components/DatasetInformation/DatasetError.test.ts
+++ b/client/src/components/DatasetInformation/DatasetError.test.ts
@@ -1,9 +1,10 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
 import { useUserStore } from "@/stores/userStore";
 
 import DatasetError from "./DatasetError.vue";
@@ -12,41 +13,49 @@ const localVue = getLocalVue();
 
 const DATASET_ID = "dataset_id";
 
+const { server, http } = useServerMock();
+
 async function montDatasetError(has_duplicate_inputs = true, has_empty_inputs = true, user_email = "") {
     const pinia = createPinia();
 
-    mockFetcher
-        .path("/api/datasets/{dataset_id}")
-        .method("get")
-        .mock({
-            data: {
-                id: DATASET_ID,
-                creating_job: "creating_job",
-            },
-        });
-
-    mockFetcher
-        .path("/api/jobs/{job_id}")
-        .method("get")
-        .mock({
-            data: {
+    server.use(
+        http.get("/api/datasets/{dataset_id}", ({ response }) => {
+            // We need to use untyped here because this endpoint is not
+            // described in the OpenAPI spec due to its complexity for now.
+            return response.untyped(
+                HttpResponse.json({
+                    id: DATASET_ID,
+                    creating_job: "creating_job",
+                })
+            );
+        }),
+
+        http.get("/api/jobs/{job_id}", ({ response }) => {
+            return response(200).json({
                 tool_id: "tool_id",
                 tool_stderr: "tool_stderr",
                 job_stderr: "job_stderr",
                 job_messages: [{ desc: "message_1" }, { desc: "message_2" }],
-                user_email: user_email,
-            },
-        });
-
-    mockFetcher
-        .path("/api/jobs/{job_id}/common_problems")
-        .method("get")
-        .mock({
-            data: {
+                user_email,
+                create_time: "2021-01-01T00:00:00",
+                update_time: "2021-01-01T00:00:00",
+                id: "job_id",
+                model_class: "Job",
+                state: "ok",
+                inputs: {},
+                outputs: {},
+                params: {},
+                output_collections: {},
+            });
+        }),
+
+        http.get("/api/jobs/{job_id}/common_problems", ({ response }) => {
+            return response(200).json({
                 has_duplicate_inputs: has_duplicate_inputs,
                 has_empty_inputs: has_empty_inputs,
-            },
-        });
+            });
+        })
+    );
 
     const wrapper = mount(DatasetError as object, {
         propsData: {
@@ -57,13 +66,7 @@ async function montDatasetError(has_duplicate_inputs = true, has_empty_inputs =
     });
 
     const userStore = useUserStore();
-    userStore.currentUser = {
-        email: user_email || "email",
-        id: "user_id",
-        tags_used: [],
-        isAnonymous: false,
-        total_disk_usage: 0,
-    };
+    userStore.currentUser = getFakeRegisteredUser({ email: user_email });
 
     await flushPromises();
 
@@ -101,14 +104,13 @@ describe("DatasetError", () => {
     it("hides form fields and button on success", async () => {
         const wrapper = await montDatasetError();
 
-        mockFetcher
-            .path("/api/jobs/{job_id}/error")
-            .method("post")
-            .mock({
-                data: {
-                    messages: ["message", "success"],
-                },
-            });
+        server.use(
+            http.post("/api/jobs/{job_id}/error", ({ response }) => {
+                return response(200).json({
+                    messages: [["message"], ["success"]],
+                });
+            })
+        );
 
         const FormAndSubmitButton = "#dataset-error-form";
         expect(wrapper.find(FormAndSubmitButton).exists()).toBe(true);
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index 0c86dada34d9aa27d558a6c15772107a6da3359c..278a4b6de9462bfc25da859b90967b8c5f34b142 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -2,20 +2,22 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faBug } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { AxiosError } from "axios";
-import { BAlert, BButton } from "bootstrap-vue";
+import { BAlert, BButton, BCard } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, ref } from "vue";
 
-import { type HDADetailed } from "@/api";
+import { GalaxyApi, type HDADetailed } from "@/api";
 import { fetchDatasetDetails } from "@/api/datasets";
-import { fetchJobCommonProblems, fetchJobDetails, JobDetails, JobInputSummary, postJobErrorReport } from "@/api/jobs";
+import { type JobDetails, type JobInputSummary } from "@/api/jobs";
+import { useConfig } from "@/composables/config";
 import { useMarkdown } from "@/composables/markdown";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import DatasetErrorDetails from "@/components/DatasetInformation/DatasetErrorDetails.vue";
 import FormElement from "@/components/Form/FormElement.vue";
+import GalaxyWizard from "@/components/GalaxyWizard.vue";
 
 library.add(faBug);
 
@@ -26,9 +28,10 @@ interface Props {
 const props = defineProps<Props>();
 
 const userStore = useUserStore();
-const { currentUser } = storeToRefs(userStore);
+const { currentUser, isAnonymous } = storeToRefs(userStore);
 
 const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+const { config, isConfigLoaded } = useConfig();
 
 const message = ref("");
 const jobLoading = ref(true);
@@ -37,7 +40,7 @@ const datasetLoading = ref(false);
 const jobDetails = ref<JobDetails>();
 const jobProblems = ref<JobInputSummary>();
 const resultMessages = ref<string[][]>([]);
-const dataset = ref<HDADetailed | null>(null);
+const dataset = ref<HDADetailed>();
 
 const showForm = computed(() => {
     const noResult = !resultMessages.value.length;
@@ -46,74 +49,93 @@ const showForm = computed(() => {
     return noResult || hasError;
 });
 
+const showWizard = computed(() => isConfigLoaded && config.value?.llm_api_configured && !isAnonymous.value);
+
 async function getDatasetDetails() {
     datasetLoading.value = true;
-
     try {
         const data = await fetchDatasetDetails({ id: props.datasetId });
-
         dataset.value = data;
     } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
-
-        errorMessage.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
+        errorMessage.value = errorMessageAsString(e) || "Unable to fetch available dataset details.";
     } finally {
         datasetLoading.value = false;
     }
 }
 
-async function getJobDetails() {
+async function getJobDetails(jobId: string) {
     jobLoading.value = true;
-
     try {
-        const { data } = await fetchJobDetails({ job_id: dataset.value?.creating_job as string, full: true });
+        const { data, error } = await GalaxyApi().GET("/api/jobs/{job_id}", {
+            params: {
+                path: { job_id: jobId },
+                query: { full: true },
+            },
+        });
 
-        jobDetails.value = data;
-    } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
+        if (error) {
+            errorMessage.value = errorMessageAsString(error) || "Unable to fetch job details.";
+            return;
+        }
 
-        errorMessage.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
+        jobDetails.value = data;
     } finally {
         jobLoading.value = false;
     }
 }
 
-async function getJobProblems() {
-    try {
-        const { data } = await fetchJobCommonProblems({ job_id: dataset.value?.creating_job as string });
-
-        jobProblems.value = data;
-    } catch (e) {
-        const error = e as AxiosError<{ err_msg?: string }>;
-
-        errorMessage.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
+async function getJobProblems(jobId: string) {
+    const { data, error } = await GalaxyApi().GET("/api/jobs/{job_id}/common_problems", {
+        params: {
+            path: { job_id: jobId },
+        },
+    });
+    if (error) {
+        errorMessage.value = errorMessageAsString(error) || "Unable to fetch job problems.";
+        return;
     }
+    jobProblems.value = data;
 }
 
-async function submit(dataset: HDADetailed, userEmailJob?: string | null) {
-    const email = userEmailJob;
+async function submit(dataset?: HDADetailed, userEmailJob?: string | null) {
+    if (!dataset) {
+        errorMessage.value = "No dataset found.";
+        return;
+    }
 
-    try {
-        const { data } = await postJobErrorReport({
-            job_id: dataset.creating_job,
+    const { data, error } = await GalaxyApi().POST("/api/jobs/{job_id}/error", {
+        params: {
+            path: { job_id: dataset.creating_job },
+        },
+        body: {
             dataset_id: dataset.id,
             message: message.value,
-            email,
-        });
+            email: userEmailJob,
+        },
+    });
 
-        resultMessages.value = data.messages;
-    } catch (error: any) {
-        resultMessages.value = error;
+    if (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return;
     }
+
+    resultMessages.value = data.messages;
+}
+
+function onMissingJobId() {
+    errorMessage.value = "No job ID found for this dataset.";
 }
 
 onMounted(async () => {
     await getDatasetDetails();
 
-    if (dataset.value?.creating_job !== null) {
-        await getJobDetails();
-        await getJobProblems();
+    const creatingJobId = dataset.value?.creating_job;
+    if (!creatingJobId) {
+        onMissingJobId();
+        return;
     }
+    await getJobDetails(creatingJobId);
+    await getJobProblems(creatingJobId);
 });
 </script>
 
@@ -136,6 +158,22 @@ onMounted(async () => {
                 <b id="dataset-error-tool-id" class="text-break">{{ jobDetails.tool_id }}</b
                 >.
             </p>
+            <template v-if="showWizard">
+                <h4 class="mb-3 h-md">Possible Causes</h4>
+                <p>
+                    <span>
+                        We can use AI to analyze the issue and suggest possible fixes. Please note that the diagnosis
+                        may not always be accurate.
+                    </span>
+                </p>
+                <BCard class="mb-2">
+                    <GalaxyWizard
+                        view="error"
+                        :query="jobDetails.tool_stderr"
+                        context="tool_error"
+                        :job-id="jobDetails.id" />
+                </BCard>
+            </template>
 
             <DatasetErrorDetails
                 :tool-stderr="jobDetails.tool_stderr"
@@ -172,7 +210,6 @@ onMounted(async () => {
             </p>
 
             <h4 class="mb-3 h-md">Issue Report</h4>
-
             <BAlert v-for="(resultMessage, index) in resultMessages" :key="index" :variant="resultMessage[1]" show>
                 <span v-html="renderMarkdown(resultMessage[0])" />
             </BAlert>
@@ -192,7 +229,7 @@ onMounted(async () => {
                     id="dataset-error-submit"
                     variant="primary"
                     class="mt-3"
-                    @click="submit(dataset, jobDetails.user_email)">
+                    @click="submit(dataset, jobDetails?.user_email)">
                     <FontAwesomeIcon :icon="faBug" class="mr-1" />
                     Report
                 </BButton>
diff --git a/client/src/components/DatasetInformation/DatasetInformation.test.ts b/client/src/components/DatasetInformation/DatasetInformation.test.ts
index 1ef0379d7ae8d8adffb676957765d9d61e6d6a0e..74964e8034e759c28a6bc75089544f82f4e10246 100644
--- a/client/src/components/DatasetInformation/DatasetInformation.test.ts
+++ b/client/src/components/DatasetInformation/DatasetInformation.test.ts
@@ -1,5 +1,5 @@
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import { format, parseISO } from "date-fns";
diff --git a/client/src/components/DatasetInformation/DatasetInformation.vue b/client/src/components/DatasetInformation/DatasetInformation.vue
index b311f6eda8ee2e0b43ae0e277dbd461139064e69..14cbf06168206b10723463c847c558d9c32fc518 100644
--- a/client/src/components/DatasetInformation/DatasetInformation.vue
+++ b/client/src/components/DatasetInformation/DatasetInformation.vue
@@ -3,6 +3,7 @@ import { type HDADetailed } from "@/api";
 import { withPrefix } from "@/utils/redirect";
 import { bytesToString } from "@/utils/utils";
 
+import HelpText from "../Help/HelpText.vue";
 import DatasetHashes from "@/components/DatasetInformation/DatasetHashes.vue";
 import DatasetSources from "@/components/DatasetInformation/DatasetSources.vue";
 import DecodedId from "@/components/DecodedId.vue";
@@ -60,7 +61,9 @@ defineProps<Props>();
                 </tr>
 
                 <tr>
-                    <td>Format</td>
+                    <td>
+                        <HelpText uri="galaxy.datasets.formatVsDatatypeVsExtension" text="Format" />
+                    </td>
 
                     <td id="format">
                         {{ dataset.file_ext }}
diff --git a/client/src/components/Datatypes/factory.ts b/client/src/components/Datatypes/factory.ts
index 1c778eba03224ac70e650e1b640c706d6a546153..0102940fc8e45d93ac11a8f4a70bbafcd25c4f92 100644
--- a/client/src/components/Datatypes/factory.ts
+++ b/client/src/components/Datatypes/factory.ts
@@ -1,8 +1,14 @@
-import { fetchDatatypesAndMappings } from "@/api/datatypes";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import { DatatypesMapperModel } from "./model";
 
 export async function getDatatypesMapper(upload_only = true) {
-    const typesAndMapping = await fetchDatatypesAndMappings(upload_only);
-    return new DatatypesMapperModel(typesAndMapping);
+    const { data, error } = await GalaxyApi().GET("/api/datatypes/types_and_mapping", {
+        params: { query: { upload_only } },
+    });
+    if (error) {
+        rethrowSimple(error);
+    }
+    return new DatatypesMapperModel(data);
 }
diff --git a/client/src/components/Datatypes/index.test.js b/client/src/components/Datatypes/index.test.ts
similarity index 72%
rename from client/src/components/Datatypes/index.test.js
rename to client/src/components/Datatypes/index.test.ts
index 062bea3e2cbb3b48437ff1191a1f836af3f60415..560e4bad2b072fd08f8fe6ae3c61d70a3f352361 100644
--- a/client/src/components/Datatypes/index.test.js
+++ b/client/src/components/Datatypes/index.test.ts
@@ -1,14 +1,19 @@
-import { fetchDatatypesAndMappings } from "@/api/datatypes";
+import { useServerMock } from "@/api/client/__mocks__";
 
 import { getDatatypesMapper } from "./index";
 import { typesAndMappingResponse } from "./test_fixtures";
 
-jest.mock("@/api/datatypes");
+const { server, http } = useServerMock();
+
+server.use(
+    http.get("/api/datatypes/types_and_mapping", ({ response }) => {
+        return response(200).json(typesAndMappingResponse);
+    })
+);
 
 describe("Datatypes/index.js", () => {
     describe("getDatatypesMapper", () => {
         it("should fetch logic from API for comparing datatypes in a hierarchy", async () => {
-            fetchDatatypesAndMappings.mockResolvedValue(typesAndMappingResponse);
             await getDatatypesMapper().then((mapper) => {
                 expect(mapper.isSubType("txt", "data")).toBe(true);
                 expect(mapper.isSubType("txt", "txt")).toBe(true);
diff --git a/client/src/components/Datatypes/model.ts b/client/src/components/Datatypes/model.ts
index 797d0349e199d3f250c6b753905d5fe4da0a79d5..e0c2248031c4d6d49b29036d5257e1e3e7cd8dad 100644
--- a/client/src/components/Datatypes/model.ts
+++ b/client/src/components/Datatypes/model.ts
@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 export type DatatypesCombinedMap = components["schemas"]["DatatypesCombinedMap"];
 
@@ -39,4 +39,10 @@ export class DatatypesMapperModel {
     isSubTypeOfAny(child: string, parents: DatatypesCombinedMap["datatypes"]): boolean {
         return parents.some((parent) => this.isSubType(child, parent));
     }
+
+    /** For classes like `galaxy.datatypes.{parent}.{extension}`, get the extension's parent */
+    getParentDatatype(extension: string) {
+        const fullClassName = this.datatypesMapping.ext_to_class_name[extension];
+        return fullClassName?.split(".")[2];
+    }
 }
diff --git a/client/src/components/Datatypes/test_fixtures.ts b/client/src/components/Datatypes/test_fixtures.ts
index f8f1e9f2c5f74608aa7013047ba79b92e5c98317..803954b132dca95e0445ddadbad68e2840e342c7 100644
--- a/client/src/components/Datatypes/test_fixtures.ts
+++ b/client/src/components/Datatypes/test_fixtures.ts
@@ -2,8 +2,7 @@
 import DatatypesJson from "@tests/test-data/json/datatypes.json";
 import DatatypesMappingJson from "@tests/test-data/json/datatypes.mapping.json";
 
-import type { DatatypesCombinedMap } from "./model";
-import { DatatypesMapperModel } from "./model";
+import { type DatatypesCombinedMap, DatatypesMapperModel } from "./model";
 
 export const typesAndMappingResponse: DatatypesCombinedMap = {
     datatypes: DatatypesJson,
diff --git a/client/src/components/FileSources/FileSourceNameSpan.vue b/client/src/components/FileSources/FileSourceNameSpan.vue
new file mode 100644
index 0000000000000000000000000000000000000000..614eb03a5dfc57f950a6bb228a02396a6635831a
--- /dev/null
+++ b/client/src/components/FileSources/FileSourceNameSpan.vue
@@ -0,0 +1,26 @@
+<script setup lang="ts">
+import { computed } from "vue";
+
+import { useFileSources } from "@/composables/fileSources";
+
+interface Props {
+    uri: string;
+    showFullUri?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    showFullUri: false,
+});
+
+const { getFileSourceByUri } = useFileSources();
+
+const fileSource = computed(() => getFileSourceByUri(props.uri));
+
+const fileSourceName = computed(() => fileSource.value?.label ?? fileSource.value?.id);
+</script>
+
+<template>
+    <span>
+        {{ fileSourceName }} <span v-if="showFullUri">➡️ {{ props.uri }}</span>
+    </span>
+</template>
diff --git a/client/src/components/FileSources/FileSourceTypeSpan.vue b/client/src/components/FileSources/FileSourceTypeSpan.vue
index 95129c85a08563586f5cbd841d7181a79b23c370..890649e4cf86c0a8ad72f1e2b79dc54c9cbfebd8 100644
--- a/client/src/components/FileSources/FileSourceTypeSpan.vue
+++ b/client/src/components/FileSources/FileSourceTypeSpan.vue
@@ -1,13 +1,21 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import type { FileSourceTypes } from "@/api/fileSources";
+
 const MESSAGES = {
-    posix: "This is a simple path based storage location that assumes the all the relevant paths are already mounted on the Galaxy server and target worker nodes.",
-    s3fs: "This is an remote file source plugin based on the Amazon Simple Storage Service (S3) interface. The AWS interface has become an industry standard and many storage vendors support it and use it to expose 'object' based storage.",
+    posix: "This is a simple path based file source that assumes the all the relevant paths are already mounted on the Galaxy server and target worker nodes.",
+    s3fs: "This is a remote file source plugin based on the Amazon Simple Storage Service (S3) interface. The AWS interface has become an industry standard and many storage vendors support it and use it to expose 'object' based storage.",
+    azure: "This is a remote file source plugin based on the Azure service.",
+    onedata: "This is a remote file source plugin based on the Onedata service.",
+    ftp: "This is a remote file source plugin based on the FTP protocol.",
+    webdav: "This is a remote file source plugin based on the WebDAV protocol.",
+    dropbox: "This is a file source plugin that connects with the commercial Dropbox service.",
+    googledrive: "This is a file source plugin that connects with the commercial Google Drive service.",
 };
 
 interface Props {
-    type: "posix" | "s3fs";
+    type: FileSourceTypes;
 }
 
 const props = defineProps<Props>();
diff --git a/client/src/components/FileSources/Instances/CreateForm.vue b/client/src/components/FileSources/Instances/CreateForm.vue
index cb791c4ec4756784d019e85559483fb56e849b9f..0fb8eb4335838858f2d5ff33ff588c4c746070a5 100644
--- a/client/src/components/FileSources/Instances/CreateForm.vue
+++ b/client/src/components/FileSources/Instances/CreateForm.vue
@@ -1,63 +1,42 @@
 <script lang="ts" setup>
-import { BAlert } from "bootstrap-vue";
-import { computed, ref } from "vue";
+import { computed, toRef } from "vue";
 
 import type { FileSourceTemplateSummary, UserFileSourceModel } from "@/api/fileSources";
-import {
-    createFormDataToPayload,
-    createTemplateForm,
-    pluginStatusToErrorMessage,
-} from "@/components/ConfigTemplates/formUtil";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { useConfigurationTemplateCreation } from "@/components/ConfigTemplates/useConfigurationTesting";
 
-import { create, test } from "./services";
-
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+const createUrl = "/api/file_source_instances";
+const createTestUrl = "/api/file_source_instances/test";
 
 interface CreateFormProps {
     template: FileSourceTemplateSummary;
+    uuid?: string;
 }
-const error = ref<string | null>(null);
 const props = defineProps<CreateFormProps>();
-const title = "Create a new file source for your data";
-const submitTitle = "Submit";
-const loadingMessage = "Loading file source template and instance information";
-
-const inputs = computed(() => {
-    return createTemplateForm(props.template, "file source");
-});
-
-async function onSubmit(formData: any) {
-    const payload = createFormDataToPayload(props.template, formData);
-    const { data: pluginStatus } = await test(payload);
-    const testError = pluginStatusToErrorMessage(pluginStatus);
-    if (testError) {
-        error.value = testError;
-        return;
-    }
-    try {
-        const { data: fileSource } = await create(payload);
-        emit("created", fileSource);
-    } catch (e) {
-        error.value = errorMessageAsString(e);
-        return;
-    }
-}
+const title = computed(() => `Create a ${props.template.name} File Source`);
 
 const emit = defineEmits<{
     (e: "created", fileSource: UserFileSourceModel): void;
 }>();
+
+const { ActionSummary, error, inputs, InstanceForm, onSubmit, submitTitle, loadingMessage, testRunning, testResults } =
+    useConfigurationTemplateCreation(
+        "file source",
+        toRef(props, "template"),
+        toRef(props, "uuid"),
+        createTestUrl,
+        createUrl,
+        (fileSource: UserFileSourceModel) => emit("created", fileSource)
+    );
 </script>
 <template>
     <div id="create-file-source-landing">
-        <BAlert v-if="error" variant="danger" class="file-source-instance-creation-error" show>
-            {{ error }}
-        </BAlert>
+        <ActionSummary error-data-description="file-source-creation-error" :test-results="testResults" :error="error" />
         <InstanceForm
             :inputs="inputs"
             :title="title"
             :submit-title="submitTitle"
             :loading-message="loadingMessage"
+            :busy="testRunning"
             @onSubmit="onSubmit" />
     </div>
 </template>
diff --git a/client/src/components/FileSources/Instances/CreateInstance.vue b/client/src/components/FileSources/Instances/CreateInstance.vue
index 9b93e2d7c2693e763f2b86153985992a90b5fd2f..ed6def6c2f869cc5b5207130c48d3f17835ffe72 100644
--- a/client/src/components/FileSources/Instances/CreateInstance.vue
+++ b/client/src/components/FileSources/Instances/CreateInstance.vue
@@ -1,8 +1,11 @@
 <script setup lang="ts">
-import { computed } from "vue";
+import { BAlert } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
 
+import { GalaxyApi } from "@/api";
 import type { UserFileSourceModel } from "@/api/fileSources";
 import { useFileSourceTemplatesStore } from "@/stores/fileSourceTemplatesStore";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import { useInstanceRouting } from "./routing";
 
@@ -11,24 +14,80 @@ import LoadingSpan from "@/components/LoadingSpan.vue";
 
 interface Props {
     templateId: string;
+    uuid?: string;
 }
+
+const OAUTH2_TYPES = ["dropbox", "googledrive"];
+
 const fileSourceTemplatesStore = useFileSourceTemplatesStore();
 fileSourceTemplatesStore.fetchTemplates();
 
 const { goToIndex } = useInstanceRouting();
 
 const props = defineProps<Props>();
+
+const loading = ref(false);
+const errorMessage = ref("");
+
 const template = computed(() => fileSourceTemplatesStore.getLatestTemplate(props.templateId));
+const redirectMessage = computed(
+    () =>
+        `You will redirected to ${template.value?.name} to authorize Galaxy to access this resource remotely. Please wait`
+);
+const requiresOAuth2AuthorizeRedirect = computed(() => {
+    const templateValue = template.value;
+    return props.uuid == undefined && templateValue && OAUTH2_TYPES.indexOf(templateValue.type) >= 0;
+});
 
-async function onCreated(objectStore: UserFileSourceModel) {
+function onCreated(objectStore: UserFileSourceModel) {
     const message = `Created file source ${objectStore.name}`;
+
     goToIndex({ message });
 }
+
+watch(
+    requiresOAuth2AuthorizeRedirect,
+    async (requiresAuth) => {
+        const templateValue = template.value;
+
+        if (templateValue && requiresAuth) {
+            loading.value = true;
+
+            const { data, error: testRequestError } = await GalaxyApi().GET(
+                "/api/file_source_templates/{template_id}/{template_version}/oauth2",
+                {
+                    params: {
+                        path: {
+                            template_id: templateValue.id,
+                            template_version: templateValue.version || 0,
+                        },
+                    },
+                }
+            );
+
+            if (testRequestError) {
+                errorMessage.value = errorMessageAsString(testRequestError, "Error getting OAuth2 URL");
+
+                loading.value = false;
+            } else {
+                window.location.href = data.authorize_url;
+            }
+        }
+    },
+    { immediate: true }
+);
 </script>
 
 <template>
     <div>
-        <LoadingSpan v-if="!template" message="Loading file source templates" />
-        <CreateForm v-else :template="template" @created="onCreated"></CreateForm>
+        <BAlert v-if="loading" show variant="info">
+            <LoadingSpan v-if="!template" message="Loading file source templates" />
+            <LoadingSpan v-else-if="requiresOAuth2AuthorizeRedirect && !errorMessage" :message="redirectMessage" />
+        </BAlert>
+
+        <BAlert v-if="errorMessage" show variant="danger">
+            {{ errorMessage }}
+        </BAlert>
+        <CreateForm v-if="!loading && template" :uuid="uuid" :template="template" @created="onCreated" />
     </div>
 </template>
diff --git a/client/src/components/FileSources/Instances/EditInstance.vue b/client/src/components/FileSources/Instances/EditInstance.vue
index 40e62a309da16e8d08cf80b019e0d6b0e749e1a4..01469088fd16ded45410da91c92818b7c3e2f766 100644
--- a/client/src/components/FileSources/Instances/EditInstance.vue
+++ b/client/src/components/FileSources/Instances/EditInstance.vue
@@ -2,15 +2,15 @@
 import { BTab, BTabs } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import type { UserFileSourceModel } from "@/api/fileSources";
-import { editFormDataToPayload, editTemplateForm, type FormEntry } from "@/components/ConfigTemplates/formUtil";
+import { useConfigurationTemplateEdit } from "@/components/ConfigTemplates/useConfigurationTesting";
 
 import { useInstanceAndTemplate } from "./instance";
 import { useInstanceRouting } from "./routing";
-import { update } from "./services";
 
 import EditSecrets from "./EditSecrets.vue";
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+
+const editTestUrl = "/api/file_source_instances/{uuid}/test";
+const editUrl = "/api/file_source_instances/{uuid}";
 
 interface Props {
     instanceId: string;
@@ -19,45 +19,40 @@ interface Props {
 const props = defineProps<Props>();
 const { instance, template } = useInstanceAndTemplate(ref(props.instanceId));
 
-const inputs = computed<Array<FormEntry> | undefined>(() => {
-    template.value;
-    instance.value;
-    if (template.value && instance.value) {
-        return editTemplateForm(template.value, "storage location", instance.value);
-    }
-    return undefined;
-});
-
-const title = computed(() => `Edit File Source ${instance.value?.name} Settings`);
-const hasSecrets = computed(() => instance.value?.secrets && instance.value?.secrets.length > 0);
-const submitTitle = "Update Settings";
-const loadingMessage = "Loading file source template and instance information";
-
-async function onSubmit(formData: any) {
-    if (template.value) {
-        const payload = editFormDataToPayload(template.value, formData);
-        const args = { user_file_source_id: String(instance?.value?.uuid) };
-        const { data: fileSource } = await update({ ...args, ...payload });
-        await onUpdate(fileSource);
-    }
-}
-
-const { goToIndex } = useInstanceRouting();
+const title = computed(() => `Edit ${template.value?.name} settings for ${instance.value?.name}`);
+const errorDataDescription = "file-source-update-error";
 
-async function onUpdate(instance: UserFileSourceModel) {
-    const message = `Updated file source ${instance.name}`;
-    goToIndex({ message });
-}
+const {
+    error,
+    hasSecrets,
+    ActionSummary,
+    inputs,
+    InstanceForm,
+    loadingMessage,
+    onForceSubmit,
+    onSubmit,
+    testRunning,
+    testResults,
+    submitTitle,
+    showForceActionButton,
+} = useConfigurationTemplateEdit("file source", instance, template, editTestUrl, editUrl, useInstanceRouting);
 </script>
 <template>
     <div>
         <BTabs v-if="hasSecrets">
             <BTab title="Settings" active>
+                <ActionSummary
+                    :error-data-description="errorDataDescription"
+                    :test-results="testResults"
+                    :error="error" />
                 <InstanceForm
                     :inputs="inputs"
                     :title="title"
                     :submit-title="submitTitle"
                     :loading-message="loadingMessage"
+                    :busy="testRunning"
+                    :show-force-action-button="showForceActionButton"
+                    @onForceSubmit="onForceSubmit"
                     @onSubmit="onSubmit" />
             </BTab>
             <BTab title="Secrets">
@@ -66,12 +61,17 @@ async function onUpdate(instance: UserFileSourceModel) {
                 </div>
             </BTab>
         </BTabs>
-        <InstanceForm
-            v-else
-            :inputs="inputs"
-            :title="title"
-            :submit-title="submitTitle"
-            :loading-message="loadingMessage"
-            @onSubmit="onSubmit" />
+        <div v-else>
+            <ActionSummary :error-data-description="errorDataDescription" :test-results="testResults" :error="error" />
+            <InstanceForm
+                :inputs="inputs"
+                :title="title"
+                :submit-title="submitTitle"
+                :loading-message="loadingMessage"
+                :busy="testRunning"
+                :show-force-action-button="showForceActionButton"
+                @onForceSubmit="onForceSubmit"
+                @onSubmit="onSubmit" />
+        </div>
     </div>
 </template>
diff --git a/client/src/components/FileSources/Instances/EditSecrets.vue b/client/src/components/FileSources/Instances/EditSecrets.vue
index 200bcd85011c0d4a33562b2bad89f10e64a71267..1a3346f401ac838f54965e15baafb8d6fbd41088 100644
--- a/client/src/components/FileSources/Instances/EditSecrets.vue
+++ b/client/src/components/FileSources/Instances/EditSecrets.vue
@@ -1,9 +1,9 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import { GalaxyApi } from "@/api";
 import type { FileSourceTemplateSummary, UserFileSourceModel } from "@/api/fileSources";
-
-import { update } from "./services";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import EditSecretsForm from "@/components/ConfigTemplates/EditSecretsForm.vue";
 
@@ -15,12 +15,17 @@ const props = defineProps<Props>();
 const title = computed(() => `Update File Source ${props.fileSource?.name} Secrets`);
 
 async function onUpdate(secretName: string, secretValue: string) {
-    const payload = {
-        secret_name: secretName,
-        secret_value: secretValue,
-    };
-    const args = { user_file_source_id: String(props.fileSource.uuid) };
-    await update({ ...args, ...payload });
+    const { error } = await GalaxyApi().PUT("/api/file_source_instances/{uuid}", {
+        params: { path: { uuid: props.fileSource.uuid } },
+        body: {
+            secret_name: secretName,
+            secret_value: secretValue,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
 }
 </script>
 <template>
diff --git a/client/src/components/FileSources/Instances/InstanceDropdown.vue b/client/src/components/FileSources/Instances/InstanceDropdown.vue
index 9762fdc21dcc5508d7dde54c6c998f6861de43b2..0dd02f396aa45b38f343b7404017c6ed480af453 100644
--- a/client/src/components/FileSources/Instances/InstanceDropdown.vue
+++ b/client/src/components/FileSources/Instances/InstanceDropdown.vue
@@ -1,10 +1,10 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import { GalaxyApi } from "@/api";
 import type { UserFileSourceModel } from "@/api/fileSources";
 import { useFileSourceTemplatesStore } from "@/stores/fileSourceTemplatesStore";
-
-import { hide } from "./services";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import InstanceDropdown from "@/components/ConfigTemplates/InstanceDropdown.vue";
 
@@ -22,12 +22,23 @@ const isUpgradable = computed(() =>
 );
 
 async function onRemove() {
-    await hide(props.fileSource);
+    const { error } = await GalaxyApi().PUT("/api/file_source_instances/{uuid}", {
+        params: { path: { uuid: props.fileSource.uuid } },
+        body: {
+            hidden: true,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     emit("entryRemoved");
 }
 
 const emit = defineEmits<{
     (e: "entryRemoved"): void;
+    (e: "test"): void;
 }>();
 </script>
 
@@ -38,5 +49,6 @@ const emit = defineEmits<{
         :is-upgradable="isUpgradable"
         :route-upgrade="routeUpgrade"
         :route-edit="routeEdit"
+        @test="emit('test')"
         @remove="onRemove" />
 </template>
diff --git a/client/src/components/FileSources/Instances/ManageIndex.vue b/client/src/components/FileSources/Instances/ManageIndex.vue
index 784e0b84a685b0ea1381a41f5ab0a5193ef769a7..1ecc522d0acacc82957da9fc9c5eea599a7c9d08 100644
--- a/client/src/components/FileSources/Instances/ManageIndex.vue
+++ b/client/src/components/FileSources/Instances/ManageIndex.vue
@@ -3,6 +3,7 @@ import { BTable } from "bootstrap-vue";
 import { computed } from "vue";
 
 import { DESCRIPTION_FIELD, NAME_FIELD, TEMPLATE_FIELD, TYPE_FIELD } from "@/components/ConfigTemplates/fields";
+import { useInstanceTesting } from "@/components/ConfigTemplates/useConfigurationTesting";
 import { useFiltering } from "@/components/ConfigTemplates/useInstanceFiltering";
 import { useFileSourceInstancesStore } from "@/stores/fileSourceInstancesStore";
 
@@ -30,10 +31,16 @@ fileSourceInstancesStore.fetchInstances();
 function reload() {
     fileSourceInstancesStore.fetchInstances();
 }
+
+const testInstanceUrl = "/api/file_source_instances/{uuid}/test";
+
+const { ConfigurationTestSummaryModal, showTestResults, testResults, test, testingError } =
+    useInstanceTesting(testInstanceUrl);
 </script>
 
 <template>
     <div>
+        <ConfigurationTestSummaryModal v-model="showTestResults" :error="testingError" :test-results="testResults" />
         <ManageIndexHeader
             :message="message"
             create-button-id="file-source-create"
@@ -58,7 +65,7 @@ function reload() {
                 </b-alert>
             </template>
             <template v-slot:cell(name)="row">
-                <InstanceDropdown :file-source="row.item" @entryRemoved="reload" />
+                <InstanceDropdown :file-source="row.item" @entryRemoved="reload" @test="test(row.item)" />
             </template>
             <template v-slot:cell(type)="row">
                 <FileSourceTypeSpan :type="row.item.type" />
diff --git a/client/src/components/FileSources/Instances/UpgradeForm.vue b/client/src/components/FileSources/Instances/UpgradeForm.vue
index 9f0efa9a9a2831a5ad4a27d76e3ea6906aaca559..a33205c13f690c26305feeea03a4ec2ff79e2927 100644
--- a/client/src/components/FileSources/Instances/UpgradeForm.vue
+++ b/client/src/components/FileSources/Instances/UpgradeForm.vue
@@ -1,63 +1,55 @@
 <script setup lang="ts">
-import { BAlert } from "bootstrap-vue";
-import { computed, ref } from "vue";
+import { computed, toRef } from "vue";
 
-import type { FileSourceTemplateSummary, UserFileSourceModel } from "@/api/fileSources";
-import { type FormEntry, upgradeForm, upgradeFormDataToPayload } from "@/components/ConfigTemplates/formUtil";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { type FileSourceTemplateSummary, type UserFileSourceModel } from "@/api/fileSources";
+import { useConfigurationTemplateUpgrade } from "@/components/ConfigTemplates/useConfigurationTesting";
 
 import { useInstanceRouting } from "./routing";
-import { update } from "./services";
 
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+const editTestUrl = "/api/file_source_instances/{uuid}/test";
+const editUrl = "/api/file_source_instances/{uuid}";
 
 interface Props {
     instance: UserFileSourceModel;
     latestTemplate: FileSourceTemplateSummary;
 }
 
-const error = ref<string | null>(null);
 const props = defineProps<Props>();
 
-const inputs = computed<Array<FormEntry> | undefined>(() => {
-    const realizedInstance: UserFileSourceModel = props.instance;
-    const realizedLatestTemplate = props.latestTemplate;
-    const form = upgradeForm(realizedLatestTemplate, realizedInstance);
-    return form;
-});
 const title = computed(() => `Upgrade File Source ${props.instance.name}`);
-const submitTitle = "Update Settings";
-const loadingMessage = "Loading file source template and instance information";
 
-async function onSubmit(formData: any) {
-    const payload = upgradeFormDataToPayload(props.latestTemplate, formData);
-    const args = { user_file_source_id: String(props.instance.uuid) };
-    try {
-        const { data: fileSource } = await update({ ...args, ...payload });
-        await onUpgrade(fileSource);
-    } catch (e) {
-        error.value = errorMessageAsString(e);
-        return;
-    }
-}
-
-const { goToIndex } = useInstanceRouting();
-
-async function onUpgrade(fileSource: UserFileSourceModel) {
-    const message = `Upgraded file source ${fileSource.name}`;
-    goToIndex({ message });
-}
+const {
+    error,
+    ActionSummary,
+    inputs,
+    InstanceForm,
+    loadingMessage,
+    onForceSubmit,
+    onSubmit,
+    testRunning,
+    testResults,
+    showForceActionButton,
+    submitTitle,
+} = useConfigurationTemplateUpgrade(
+    "file source",
+    toRef(props, "instance"),
+    toRef(props, "latestTemplate"),
+    editTestUrl,
+    editUrl,
+    useInstanceRouting
+);
 </script>
 <template>
     <div>
-        <BAlert v-if="error" variant="danger" class="file-source-instance-upgrade-error" show>
-            {{ error }}
-        </BAlert>
+        <ActionSummary error-data-description="file-source-upgrade-error" :test-results="testResults" :error="error" />
         <InstanceForm
             :inputs="inputs"
             :title="title"
             :submit-title="submitTitle"
             :loading-message="loadingMessage"
+            :busy="testRunning"
+            :show-force-action-button="showForceActionButton"
+            @onForceSubmit="onForceSubmit"
             @onSubmit="onSubmit" />
     </div>
 </template>
diff --git a/client/src/components/FileSources/Instances/instance.ts b/client/src/components/FileSources/Instances/instance.ts
index 26755846ae53b036c516622dc4f6444d77ed5c6a..b5e6568539634cd8b1e4ec89aaf13cc4179f6781 100644
--- a/client/src/components/FileSources/Instances/instance.ts
+++ b/client/src/components/FileSources/Instances/instance.ts
@@ -1,6 +1,6 @@
 import { computed, type Ref } from "vue";
 
-import type { FileSourceTemplateSummary, UserFileSourceModel } from "@/api/fileSources";
+import { type FileSourceTemplateSummary, type UserFileSourceModel } from "@/api/fileSources";
 import { useFileSourceInstancesStore } from "@/stores/fileSourceInstancesStore";
 import { useFileSourceTemplatesStore } from "@/stores/fileSourceTemplatesStore";
 
diff --git a/client/src/components/FileSources/Instances/routing.ts b/client/src/components/FileSources/Instances/routing.ts
index 6d2ed12bae6e5abb519685c957e8324ad209f4a5..d2053263a750cf617e38bd4455f9729cb7ed8e81 100644
--- a/client/src/components/FileSources/Instances/routing.ts
+++ b/client/src/components/FileSources/Instances/routing.ts
@@ -1,16 +1,3 @@
-import { useRouter } from "vue-router/composables";
+import { buildInstanceRoutingComposable } from "@/components/ConfigTemplates/routing";
 
-export function useInstanceRouting() {
-    const router = useRouter();
-
-    async function goToIndex(query: Record<"message", string>) {
-        router.push({
-            path: "/file_source_instances/index",
-            query: query,
-        });
-    }
-
-    return {
-        goToIndex,
-    };
-}
+export const useInstanceRouting = buildInstanceRoutingComposable("/file_source_instances/index");
diff --git a/client/src/components/FileSources/Instances/services.ts b/client/src/components/FileSources/Instances/services.ts
index 357e792f9f221baa721d55feedd22cf645dc202f..01ab0d7441541380d5570e7e8aa435133265b2b4 100644
--- a/client/src/components/FileSources/Instances/services.ts
+++ b/client/src/components/FileSources/Instances/services.ts
@@ -1,13 +1,15 @@
+import { GalaxyApi } from "@/api";
 import type { UserFileSourceModel } from "@/api/fileSources";
-import { fetcher } from "@/api/schema/fetcher";
 
-export const create = fetcher.path("/api/file_source_instances").method("post").create();
-export const test = fetcher.path("/api/file_source_instances/test").method("post").create();
-export const update = fetcher.path("/api/file_source_instances/{user_file_source_id}").method("put").create();
+const updateUrl = "/api/file_source_instances/{uuid}";
 
 export async function hide(instance: UserFileSourceModel) {
     const payload = { hidden: true };
-    const args = { user_file_source_id: String(instance?.uuid) };
-    const { data: fileSource } = await update({ ...args, ...payload });
+    const { data: fileSource } = await GalaxyApi().PUT(updateUrl, {
+        params: {
+            path: { uuid: String(instance?.uuid) },
+        },
+        body: payload,
+    });
     return fileSource;
 }
diff --git a/client/src/components/FileSources/Templates/CreateUserFileSource.vue b/client/src/components/FileSources/Templates/CreateUserFileSource.vue
index 5cc4a9f8e3aa35d69a78a4f9172f9c514fc9cfa7..af85f683434e54c6b1595a7d939b3f22e4a31a62 100644
--- a/client/src/components/FileSources/Templates/CreateUserFileSource.vue
+++ b/client/src/components/FileSources/Templates/CreateUserFileSource.vue
@@ -1,5 +1,6 @@
 <script lang="ts" setup>
-import { computed } from "vue";
+import { BAlert } from "bootstrap-vue";
+import { computed, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { useFileSourceTemplatesStore } from "@/stores/fileSourceTemplatesStore";
@@ -17,14 +18,37 @@ const loading = computed(() => fileSourceTemplatesStore.loading);
 
 const router = useRouter();
 
-async function chooseTemplate(selectTemplateId: string) {
+const errorMessage = ref("");
+
+function chooseTemplate(selectTemplateId: string) {
     router.push({
         path: `/file_source_templates/${selectTemplateId}/new`,
     });
 }
+
+function handleOAuth2Redirect() {
+    if (router.currentRoute.query.error === "access_denied") {
+        errorMessage.value = "You must authorize Galaxy to access this resource. Please try again.";
+    } else if (router.currentRoute.query.error) {
+        const error = router.currentRoute.query.error;
+
+        if (Array.isArray(error)) {
+            errorMessage.value = error[0] || "There was an error creating the file source.";
+        } else {
+            errorMessage.value = error;
+        }
+    }
+}
+
+handleOAuth2Redirect();
 </script>
+
 <template>
     <CreateInstance :loading-message="loadingTemplatesInfoMessage" :loading="loading" prefix="file-source">
+        <BAlert v-if="errorMessage" variant="danger" show dismissible>
+            {{ errorMessage }}
+        </BAlert>
+
         <SelectTemplate :templates="templates" @onSubmit="chooseTemplate" />
     </CreateInstance>
 </template>
diff --git a/client/src/components/FilesDialog/FilesDialog.test.ts b/client/src/components/FilesDialog/FilesDialog.test.ts
index d826f977a5aa73704fb96cfdad70409f69b35c83..4c47f35fc39e2f61381972262a8ba85d43b34895 100644
--- a/client/src/components/FilesDialog/FilesDialog.test.ts
+++ b/client/src/components/FilesDialog/FilesDialog.test.ts
@@ -1,11 +1,10 @@
 import { createTestingPinia } from "@pinia/testing";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
-import type { SelectionItem } from "@/components/SelectionDialog/selectionTypes";
-import { SELECTION_STATES } from "@/components/SelectionDialog/selectionTypes";
+import { useServerMock } from "@/api/client/__mocks__";
+import { SELECTION_STATES, type SelectionItem, type SelectionState } from "@/components/SelectionDialog/selectionTypes";
 
 /**
  * The following imports mock a remote file resource directory structure,
@@ -27,6 +26,7 @@ import { SELECTION_STATES } from "@/components/SelectionDialog/selectionTypes";
  * |-- file1
  * |-- file2
  */
+import { type RemoteFilesList } from "./testingData";
 import {
     directory1RecursiveResponse,
     directory1Response,
@@ -34,7 +34,6 @@ import {
     directoryId,
     ftpId,
     pdbResponse,
-    RemoteFilesList,
     rootId,
     rootResponse,
     someErrorText,
@@ -47,7 +46,6 @@ import FilesDialog from "./FilesDialog.vue";
 import SelectionDialog from "@/components/SelectionDialog/SelectionDialog.vue";
 
 jest.mock("app");
-jest.mock("@/api/schema");
 
 jest.mock("@/composables/config", () => ({
     useConfig: jest.fn(() => ({
@@ -56,48 +54,56 @@ jest.mock("@/composables/config", () => ({
     })),
 }));
 
-interface RemoteFilesParams {
-    target: string;
-    recursive: boolean;
-    writeable?: boolean;
-}
+const { server, http } = useServerMock();
 
 interface RowElement extends SelectionItem, Element {
-    _rowVariant: string;
+    _rowVariant: SelectionState;
 }
 
-function paramsToKey(params: RemoteFilesParams) {
-    params.writeable = false;
-    return JSON.stringify(params);
+function paramsToKey(query: { target?: string | null; recursive?: string | null; writeable?: string | null }): string {
+    return `${query.target}?recursive=${query.recursive}&writeable=${query.writeable ?? "false"}`;
 }
 
 const mockedOkApiRoutesMap = new Map<string, RemoteFilesList>([
-    [paramsToKey({ target: "gxfiles://pdb-gzip", recursive: false }), pdbResponse],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: false }), directory1Response],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: true }), directory1RecursiveResponse],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory2", recursive: true }), directory2RecursiveResponse],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1/subdirectory1", recursive: false }), subsubdirectoryResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip", recursive: "false" }), pdbResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: "false" }), directory1Response],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: "true" }), directory1RecursiveResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory2", recursive: "true" }), directory2RecursiveResponse],
+    [
+        paramsToKey({ target: "gxfiles://pdb-gzip/directory1/subdirectory1", recursive: "false" }),
+        subsubdirectoryResponse,
+    ],
 ]);
 
 const mockedErrorApiRoutesMap = new Map<string, RemoteFilesList>([
-    [paramsToKey({ target: "gxfiles://empty-dir", recursive: false }), []],
+    [paramsToKey({ target: "gxfiles://empty-dir", recursive: "false" }), []],
 ]);
 
-function getMockedBrowseResponse(param: RemoteFilesParams) {
-    const responseKey = paramsToKey(param);
-    if (mockedErrorApiRoutesMap.has(responseKey)) {
-        throw Error(someErrorText);
-    }
-    const result = mockedOkApiRoutesMap.get(responseKey);
-    const headers = new Map([["total_matches", result?.length.toString() ?? "0"]]);
-    return { data: result, headers };
-}
-
 const initComponent = async (props: { multiple: boolean; mode?: string }) => {
     const localVue = getLocalVue();
 
-    mockFetcher.path("/api/remote_files/plugins").method("get").mock({ data: rootResponse });
-    mockFetcher.path("/api/remote_files").method("get").mock(getMockedBrowseResponse);
+    server.use(
+        http.get("/api/remote_files/plugins", ({ response }) => {
+            return response(200).json(rootResponse);
+        }),
+
+        http.get("/api/remote_files", ({ response, query }) => {
+            const responseKey = paramsToKey({
+                target: query.get("target"),
+                recursive: query.get("recursive"),
+                writeable: query.get("writeable"),
+            });
+            if (mockedErrorApiRoutesMap.has(responseKey)) {
+                return response("4XX").json({ err_msg: someErrorText, err_code: 400 }, { status: 400 });
+            }
+            const mockedResponse = mockedOkApiRoutesMap.get(responseKey);
+            const mockedTotalMatches = mockedResponse?.length.toString() ?? "0";
+            if (!mockedResponse) {
+                return response("5XX").json({ err_msg: "No mocked response found", err_code: 500 }, { status: 500 });
+            }
+            return response(200).json(mockedResponse, { headers: { total_matches: mockedTotalMatches } });
+        })
+    );
 
     const testingPinia = createTestingPinia({ stubActions: false });
     const wrapper = mount(FilesDialog, {
@@ -124,6 +130,14 @@ describe("FilesDialog, file mode", () => {
         expect(utils.getRenderedRows().length).toBe(pdbResponse.length);
     });
 
+    it("should list the user defined file sources first", async () => {
+        await utils.openRoot();
+        const rows = utils.getRenderedRows();
+        const firstItem = rows[0];
+        expect(firstItem).toBeDefined();
+        expect(firstItem!.url).toContain("gxuserfiles://");
+    });
+
     it("should allow selecting files and update OK button accordingly", async () => {
         await utils.openRootDirectory();
         const filesInResponse = pdbResponse.filter((item) => item.class === "File");
@@ -285,9 +299,13 @@ class Utils {
         this.wrapper = wrapper;
     }
 
-    async openRootDirectory() {
+    async openRoot() {
         expect(this.wrapper.findComponent(SelectionDialog).exists()).toBe(true);
         expect(this.getRenderedRows().length).toBe(rootResponse.length);
+    }
+
+    async openRootDirectory() {
+        await this.openRoot();
         await this.openDirectoryById(rootId);
     }
 
@@ -386,7 +404,7 @@ class Utils {
     }
 
     expectSelectAllIconStatusToBe(status: string) {
-        expect(this.getSelectionDialog().props("selectAllIcon")).toBe(status);
+        expect(this.getSelectionDialog().props("selectAllVariant")).toBe(status);
     }
 
     expectNoErrorMessage() {
diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue
index 5e6d2bde46e38d25d2400a10d8a57a35c4cb10d0..57e7ee89fbf3c5f5a7d072afe4c6caa2e2f7bf70 100644
--- a/client/src/components/FilesDialog/FilesDialog.vue
+++ b/client/src/components/FilesDialog/FilesDialog.vue
@@ -5,21 +5,23 @@ import Vue, { computed, onMounted, ref } from "vue";
 import {
     browseRemoteFiles,
     fetchFileSources,
-    FileSourceBrowsingMode,
-    FilterFileSourcesOptions,
-    RemoteEntry,
+    type FileSourceBrowsingMode,
+    type FilterFileSourcesOptions,
+    type RemoteEntry,
 } from "@/api/remoteFiles";
 import { UrlTracker } from "@/components/DataDialog/utilities";
 import { fileSourcePluginToItem, isSubPath } from "@/components/FilesDialog/utilities";
 import {
-    ItemsProvider,
-    ItemsProviderContext,
+    type ItemsProvider,
+    type ItemsProviderContext,
     SELECTION_STATES,
     type SelectionItem,
+    type SelectionState,
 } from "@/components/SelectionDialog/selectionTypes";
 import { useConfig } from "@/composables/config";
 import { useFileSources } from "@/composables/fileSources";
 import { errorMessageAsString } from "@/utils/simple-error";
+import { USER_FILE_PREFIX } from "@/utils/upload-payload";
 
 import { Model } from "./model";
 
@@ -42,6 +44,8 @@ interface FilesDialogProps {
     requireWritable?: boolean;
     /** Optional selected item to start browsing from */
     selectedItem?: SelectionItem;
+    /** Whether the dialog is visible at the start */
+    isOpen?: boolean;
 }
 
 const props = withDefaults(defineProps<FilesDialogProps>(), {
@@ -52,6 +56,7 @@ const props = withDefaults(defineProps<FilesDialogProps>(), {
     multiple: false,
     requireWritable: false,
     selectedItem: undefined,
+    isOpen: true,
 });
 
 const { config, isConfigLoaded } = useConfig();
@@ -64,7 +69,7 @@ const errorMessage = ref<string>();
 const filter = ref();
 const items = ref<SelectionItem[]>([]);
 const itemsProvider = ref<ItemsProvider>();
-const modalShow = ref(true);
+const modalShow = ref(props.isOpen);
 const optionsShow = ref(false);
 const undoShow = ref(false);
 const hasValue = ref(false);
@@ -73,7 +78,7 @@ const showDetails = ref(true);
 const isBusy = ref(false);
 const currentDirectory = ref<SelectionItem>();
 const showFTPHelper = ref(false);
-const selectAllIcon = ref(SELECTION_STATES.UNSELECTED);
+const selectAllIcon = ref<SelectionState>(SELECTION_STATES.UNSELECTED);
 const urlTracker = ref(new UrlTracker(""));
 const totalItems = ref(0);
 
@@ -248,7 +253,9 @@ function load(record?: SelectionItem) {
                 const convertedItems = results
                     .filter((item) => !props.requireWritable || item.writable)
                     .map(fileSourcePluginToItem);
-                items.value = convertedItems;
+
+                const sortedItems = convertedItems.sort(sortPrivateFileSourcesFirst);
+                items.value = sortedItems;
                 formatRows();
                 optionsShow.value = true;
                 showTime.value = false;
@@ -294,6 +301,20 @@ function load(record?: SelectionItem) {
     }
 }
 
+function isPrivateFileSource(item: SelectionItem): boolean {
+    return item.url.startsWith(USER_FILE_PREFIX);
+}
+
+function sortPrivateFileSourcesFirst(a: SelectionItem, b: SelectionItem): number {
+    if (isPrivateFileSource(a) && !isPrivateFileSource(b)) {
+        return -1;
+    }
+    if (!isPrivateFileSource(a) && isPrivateFileSource(b)) {
+        return 1;
+    }
+    return 0;
+}
+
 /**
  * Check if the current file source supports server-side pagination.
  * If it does, we will use the items provider to fetch items.
@@ -415,7 +436,7 @@ onMounted(() => {
         :modal-static="modalStatic"
         :multiple="multiple"
         :options-show="optionsShow"
-        :select-all-icon="selectAllIcon"
+        :select-all-variant="selectAllIcon"
         :show-select-icon="undoShow && multiple"
         :undo-show="undoShow"
         @onCancel="() => (modalShow = false)"
diff --git a/client/src/components/FilesDialog/FilesInput.vue b/client/src/components/FilesDialog/FilesInput.vue
index b1e7390a3483072c66ab0deb85eb6e8c4ad4397f..965eaab51f5a67f74ccaa1f8c06f7889cbd4a1f9 100644
--- a/client/src/components/FilesDialog/FilesInput.vue
+++ b/client/src/components/FilesDialog/FilesInput.vue
@@ -2,10 +2,10 @@
 import { BFormInput } from "bootstrap-vue";
 import { computed } from "vue";
 
-import { FileSourceBrowsingMode, FilterFileSourcesOptions } from "@/api/remoteFiles";
+import { type FileSourceBrowsingMode, type FilterFileSourcesOptions } from "@/api/remoteFiles";
 import { filesDialog } from "@/utils/data";
 
-import { SelectionItem } from "../SelectionDialog/selectionTypes";
+import { type SelectionItem } from "../SelectionDialog/selectionTypes";
 
 interface Props {
     value: string;
diff --git a/client/src/components/FilesDialog/testingData.ts b/client/src/components/FilesDialog/testingData.ts
index ab943342238ea07f4478200d3e31b4f4d195a6e2..f9c2c09e1af24b6baebce608cd8303e80ff2bdbd 100644
--- a/client/src/components/FilesDialog/testingData.ts
+++ b/client/src/components/FilesDialog/testingData.ts
@@ -1,4 +1,4 @@
-import { BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 
 export const ftpId = "_ftp";
 export const rootId = "pdb-gzip";
@@ -35,6 +35,11 @@ export const rootResponse: BrowsableFilesSourcePlugin[] = [
         doc: "Galaxy User's FTP Directory",
         writable: true,
         browsable: true,
+        supports: {
+            pagination: false,
+            search: false,
+            sorting: false,
+        },
     },
     {
         id: "pdb-gzip",
@@ -44,6 +49,11 @@ export const rootResponse: BrowsableFilesSourcePlugin[] = [
         doc: "Protein Data Bank (PDB)",
         writable: true,
         browsable: true,
+        supports: {
+            pagination: false,
+            search: false,
+            sorting: false,
+        },
     },
     {
         id: "empty-dir",
@@ -53,6 +63,25 @@ export const rootResponse: BrowsableFilesSourcePlugin[] = [
         doc: "Empty Directory",
         writable: true,
         browsable: true,
+        supports: {
+            pagination: false,
+            search: false,
+            sorting: false,
+        },
+    },
+    {
+        id: "c5504eb8-51cf-4b44-88f8-24347c031f52",
+        type: "ftp",
+        label: "My own FTP",
+        doc: "This FTP is accessible only by me",
+        browsable: true,
+        writable: true,
+        supports: {
+            pagination: true,
+            search: true,
+            sorting: false,
+        },
+        uri_root: "gxuserfiles://c5504eb8-51cf-4b44-88f8-24347c031f52",
     },
 ];
 
diff --git a/client/src/components/FilesDialog/utilities.ts b/client/src/components/FilesDialog/utilities.ts
index 68f1dfd76eacf13c471a34d6cd121e9e4a208072..f300d10349c641033a0275e9bb8a4d01169bc3e8 100644
--- a/client/src/components/FilesDialog/utilities.ts
+++ b/client/src/components/FilesDialog/utilities.ts
@@ -1,6 +1,6 @@
-import type { BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 
-import type { SelectionItem } from "../SelectionDialog/selectionTypes";
+import { type SelectionItem } from "../SelectionDialog/selectionTypes";
 
 export const isSubPath = (originPath: string, destinationPath: string) => {
     return subPathCondition(ensureTrailingSlash(originPath), ensureTrailingSlash(destinationPath));
diff --git a/client/src/components/Form/Elements/FormData/FormData.test.js b/client/src/components/Form/Elements/FormData/FormData.test.js
index ae5ed7f41cfc57c92afa3f32fb9d5f7a3476c1ee..71e2b6d49f9c7877a0ddbc15b6953469856236ce 100644
--- a/client/src/components/Form/Elements/FormData/FormData.test.js
+++ b/client/src/components/Form/Elements/FormData/FormData.test.js
@@ -1,3 +1,5 @@
+import "@/composables/__mocks__/filter";
+
 import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
 import { PiniaVuePlugin } from "pinia";
@@ -9,6 +11,8 @@ import { useEventStore } from "@/stores/eventStore";
 
 import MountTarget from "./FormData.vue";
 
+jest.mock("@/composables/filter");
+
 const localVue = getLocalVue();
 localVue.use(PiniaVuePlugin);
 
@@ -49,7 +53,7 @@ const defaultOptions = {
 };
 
 const SELECT_OPTIONS = ".multiselect__element";
-const SELECTED_VALUE = ".multiselect__option--selected span";
+const SELECTED_VALUE = ".multiselect__option--selected";
 
 describe("FormData", () => {
     it("regular data", async () => {
@@ -72,11 +76,11 @@ describe("FormData", () => {
         expect(options.at(0).classes()).toContain("active");
         expect(options.at(0).attributes("title")).toBe("Single dataset");
         expect(wrapper.emitted().input[0][0]).toEqual(value_0);
-        expect(wrapper.find(SELECTED_VALUE).text()).toEqual("dceName4 (as dataset)");
+        expect(wrapper.find(SELECTED_VALUE).text()).toContain("dceName4 (as dataset)");
         await wrapper.setProps({ value: value_0 });
         expect(wrapper.emitted().input.length).toEqual(1);
         await wrapper.setProps({ value: { values: [{ id: "hda2", src: "hda" }] } });
-        expect(wrapper.find(SELECTED_VALUE).text()).toEqual("2: hdaName2");
+        expect(wrapper.find(SELECTED_VALUE).text()).toContain("2: hdaName2");
         expect(wrapper.emitted().input.length).toEqual(1);
         const elements_0 = wrapper.findAll(SELECT_OPTIONS);
         expect(elements_0.length).toEqual(6);
@@ -84,7 +88,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input.length).toEqual(2);
         expect(wrapper.emitted().input[1][0]).toEqual(value_1);
         await wrapper.setProps({ value: value_1 });
-        expect(wrapper.find(SELECTED_VALUE).text()).toEqual("4: hdaName4");
+        expect(wrapper.find(SELECTED_VALUE).text()).toContain("4: hdaName4");
     });
 
     it("regular data no batch input", async () => {
@@ -138,8 +142,8 @@ describe("FormData", () => {
         expect(wrapper.emitted().input.length).toEqual(1);
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(2);
-        expect(selectedValues.at(0).text()).toBe("3: hdaName3");
-        expect(selectedValues.at(1).text()).toBe("2: hdaName2");
+        expect(selectedValues.at(0).text()).toContain("3: hdaName3");
+        expect(selectedValues.at(1).text()).toContain("2: hdaName2");
         const value_0 = {
             batch: false,
             product: false,
@@ -186,9 +190,9 @@ describe("FormData", () => {
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(3);
         // the values in the multiselect are sorted by hid DESC
-        expect(selectedValues.at(0).text()).toBe("3: hdaName3");
-        expect(selectedValues.at(1).text()).toBe("2: hdaName2");
-        expect(selectedValues.at(2).text()).toBe("1: hdaName1");
+        expect(selectedValues.at(0).text()).toContain("3: hdaName3");
+        expect(selectedValues.at(1).text()).toContain("2: hdaName2");
+        expect(selectedValues.at(2).text()).toContain("1: hdaName1");
         await selectedValues.at(0).trigger("click");
         const value_sorted = {
             batch: false,
@@ -236,11 +240,11 @@ describe("FormData", () => {
         expect(selectedValues.length).toBe(5);
         // when dces are mixed in their values are shown first and are
         // ordered by id descending
-        expect(selectedValues.at(0).text()).toBe("dceName4 (as dataset)");
-        expect(selectedValues.at(1).text()).toBe("dceName3 (as dataset)");
-        expect(selectedValues.at(2).text()).toBe("dceName2 (as dataset)");
-        expect(selectedValues.at(3).text()).toBe("2: hdaName2");
-        expect(selectedValues.at(4).text()).toBe("1: hdaName1");
+        expect(selectedValues.at(0).text()).toContain("dceName4 (as dataset)");
+        expect(selectedValues.at(1).text()).toContain("dceName3 (as dataset)");
+        expect(selectedValues.at(2).text()).toContain("dceName2 (as dataset)");
+        expect(selectedValues.at(3).text()).toContain("2: hdaName2");
+        expect(selectedValues.at(4).text()).toContain("1: hdaName1");
         await selectedValues.at(0).trigger("click");
         const value_sorted = {
             batch: false,
@@ -271,7 +275,7 @@ describe("FormData", () => {
         expect(wrapper.emitted().input.length).toEqual(1);
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(1);
-        expect(selectedValues.at(0).text()).toBe("dceName1 (as dataset)");
+        expect(selectedValues.at(0).text()).toContain("dceName1 (as dataset)");
     });
 
     it("dataset collection element as hdca without map_over_type", async () => {
@@ -284,7 +288,7 @@ describe("FormData", () => {
         await wrapper.vm.$nextTick();
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(1);
-        expect(selectedValues.at(0).text()).toBe("dceName2 (as dataset collection)");
+        expect(selectedValues.at(0).text()).toContain("dceName2 (as dataset collection)");
     });
 
     it("dataset collection element as hdca mapped to batch field", async () => {
@@ -301,7 +305,7 @@ describe("FormData", () => {
         await wrapper.vm.$nextTick();
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(1);
-        expect(selectedValues.at(0).text()).toBe("dceName3 (as dataset collection)");
+        expect(selectedValues.at(0).text()).toContain("dceName3 (as dataset collection)");
     });
 
     it("dataset collection element as hdca mapped to non-batch field", async () => {
@@ -319,7 +323,7 @@ describe("FormData", () => {
         await wrapper.vm.$nextTick();
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(1);
-        expect(selectedValues.at(0).text()).toBe("dceName3 (as dataset collection)");
+        expect(selectedValues.at(0).text()).toContain("dceName3 (as dataset collection)");
     });
 
     it("dataset collection mapped to non-batch field", async () => {
@@ -337,7 +341,7 @@ describe("FormData", () => {
         await wrapper.vm.$nextTick();
         const selectedValues = wrapper.findAll(SELECTED_VALUE);
         expect(selectedValues.length).toBe(1);
-        expect(selectedValues.at(0).text()).toBe("5: hdcaName5");
+        expect(selectedValues.at(0).text()).toContain("5: hdcaName5");
     });
 
     it("multiple dataset collection elements (as hdas)", async () => {
@@ -384,6 +388,54 @@ describe("FormData", () => {
         });
     });
 
+    it("rejects hda on collection input", async () => {
+        const wrapper = createTarget({
+            value: null,
+            options: defaultOptions,
+            type: "data_collection",
+        });
+        eventStore.setDragData({ id: "whatever", history_content_type: "dataset" });
+        dispatchEvent(wrapper, "dragenter");
+        dispatchEvent(wrapper, "drop");
+        expect(wrapper.emitted().alert[0][0]).toEqual("dataset is not a valid input for dataset collection parameter.");
+    });
+
+    it("rejects paired collection on list collection input", async () => {
+        const wrapper = createTarget({
+            value: null,
+            options: defaultOptions,
+            type: "data_collection",
+            collectionTypes: ["list"],
+        });
+        eventStore.setDragData({
+            id: "whatever",
+            history_content_type: "dataset_collection",
+            collection_type: "paired",
+        });
+        dispatchEvent(wrapper, "dragenter");
+        dispatchEvent(wrapper, "drop");
+        expect(wrapper.emitted().alert[0][0]).toEqual(
+            "paired dataset collection is not a valid input for list type dataset collection parameter."
+        );
+    });
+
+    it("accepts list:list collection on list collection input", async () => {
+        const wrapper = createTarget({
+            value: null,
+            options: defaultOptions,
+            type: "data_collection",
+            collectionTypes: ["list"],
+        });
+        eventStore.setDragData({
+            id: "whatever",
+            history_content_type: "dataset_collection",
+            collection_type: "list:list",
+        });
+        dispatchEvent(wrapper, "dragenter");
+        dispatchEvent(wrapper, "drop");
+        expect(wrapper.emitted().alert[0][0]).toEqual(undefined);
+    });
+
     it("linked and unlinked batch mode handling", async () => {
         const wrapper = createTarget({
             value: null,
@@ -475,22 +527,22 @@ describe("FormData", () => {
         });
         const select_0 = wrapper_0.findAll(SELECT_OPTIONS);
         expect(select_0.length).toBe(4);
-        expect(select_0.at(2).text()).toBe("2: hdaName2");
-        expect(select_0.at(3).text()).toBe("1: hdaName1");
+        expect(select_0.at(2).text()).toContain("2: hdaName2");
+        expect(select_0.at(3).text()).toContain("1: hdaName1");
         const wrapper_1 = createTarget({
             tag: "tag2",
             options: defaultOptions,
         });
         const select_1 = wrapper_1.findAll(SELECT_OPTIONS);
         expect(select_1.length).toBe(4);
-        expect(select_1.at(2).text()).toBe("3: hdaName3");
-        expect(select_1.at(3).text()).toBe("2: hdaName2");
+        expect(select_1.at(2).text()).toContain("3: hdaName3");
+        expect(select_1.at(3).text()).toContain("2: hdaName2");
         const wrapper_2 = createTarget({
             tag: "tag3",
             options: defaultOptions,
         });
         const select_2 = wrapper_2.findAll(SELECT_OPTIONS);
         expect(select_2.length).toBe(3);
-        expect(select_2.at(2).text()).toBe("3: hdaName3");
+        expect(select_2.at(2).text()).toContain("3: hdaName3");
     });
 });
diff --git a/client/src/components/Form/Elements/FormData/FormData.vue b/client/src/components/Form/Elements/FormData/FormData.vue
index aea6b25a7f4415cb8873bec027463ed36fb75f6b..7320e8986243aef05d4cf61045db6cbf756b3cf2 100644
--- a/client/src/components/Form/Elements/FormData/FormData.vue
+++ b/client/src/components/Form/Elements/FormData/FormData.vue
@@ -1,30 +1,57 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faCopy, faFile, faFolder } from "@fortawesome/free-regular-svg-icons";
-import { faCaretDown, faCaretUp, faExclamation, faLink, faUnlink } from "@fortawesome/free-solid-svg-icons";
+import {
+    faCaretDown,
+    faCaretUp,
+    faExclamation,
+    faLink,
+    faPlus,
+    faSpinner,
+    faUnlink,
+} from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton, BButtonGroup, BCollapse, BFormCheckbox, BTooltip } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
 import { computed, onMounted, type Ref, ref, watch } from "vue";
 
+import {
+    type DCESummary,
+    type HDAObject,
+    type HistoryItemSummary,
+    isDatasetElement,
+    isDCE,
+    isHDCA,
+    isHistoryItem,
+} from "@/api";
+import type { HistoryContentType } from "@/api/datasets";
 import { getGalaxyInstance } from "@/app";
 import { useDatatypesMapper } from "@/composables/datatypesMapper";
 import { useUid } from "@/composables/utils/uid";
 import { type EventData, useEventStore } from "@/stores/eventStore";
+import { useHistoryStore } from "@/stores/historyStore";
 import { orList } from "@/utils/strings";
 
 import type { DataOption } from "./types";
+import { containsDataOption } from "./types";
 import { BATCH, SOURCE, VARIANTS } from "./variants";
 
 import FormSelection from "../FormSelection.vue";
+import CollectionCreatorModal from "@/components/Collections/CollectionCreatorModal.vue";
 import FormSelect from "@/components/Form/Elements/FormSelect.vue";
+import HelpText from "@/components/Help/HelpText.vue";
 
-library.add(faCopy, faFile, faFolder, faCaretDown, faCaretUp, faExclamation, faLink, faUnlink);
+const COLLECTION_TYPE_TO_LABEL: Record<string, string> = {
+    list: "list",
+    "list:paired": "list of dataset pairs",
+    paired: "dataset pair",
+};
 
 type SelectOption = {
     label: string;
     value: DataOption | null;
 };
 
+type HistoryOrCollectionItem = HistoryItemSummary | DCESummary;
+
 const props = withDefaults(
     defineProps<{
         loading?: boolean;
@@ -35,7 +62,7 @@ const props = withDefaults(
             values: Array<DataOption>;
         };
         extensions?: Array<string>;
-        type?: string;
+        type?: "data" | "data_collection";
         collectionTypes?: Array<string>;
         flavor?: string;
         tag?: string;
@@ -71,9 +98,22 @@ const currentField = ref(0);
 const currentHighlighting: Ref<string | null> = ref(null);
 
 // Drag/Drop related values
-const dragData: Ref<EventData | null> = ref(null);
+const dragData: Ref<EventData[]> = ref([]);
 const dragTarget: Ref<EventTarget | null> = ref(null);
 
+// Collection creator modal settings
+const collectionModalShow = ref(false);
+const collectionModalType = ref<"list" | "list:paired" | "paired">("list");
+const { currentHistoryId } = storeToRefs(useHistoryStore());
+const restrictsExtensions = computed(() => {
+    const extensions = props.extensions;
+    if (!extensions || extensions.length == 0 || extensions.indexOf("data") >= 0) {
+        return false;
+    } else {
+        return true;
+    }
+});
+
 /** Store options which need to be preserved **/
 const keepOptions: Record<string, SelectOption> = {};
 
@@ -311,54 +351,58 @@ function getSourceType(val: DataOption) {
 }
 
 /** Add values from drag/drop or data dialog sources */
-function handleIncoming(incoming: Record<string, unknown>, partial = true) {
+function handleIncoming(incoming: Record<string, unknown> | Record<string, unknown>[], partial = true) {
     if (incoming) {
         const values = Array.isArray(incoming) ? incoming : [incoming];
-        const extensions = values.map((v) => v.extension || v.elements_datatypes).filter((v) => (v ? true : false));
+
+        // ensure all incoming values are isHistoryOrCollectionItem
+        if (!values.every(isHistoryOrCollectionItem)) {
+            return false;
+        }
+
+        const extensions = Array.from(
+            new Set(
+                values
+                    .map(getExtensionsForItem)
+                    .flat()
+                    .filter((v) => v !== null && v !== undefined)
+            )
+        ) as string[];
+
         if (!canAcceptDatatype(extensions)) {
             return false;
         }
+        if (
+            values.some((v) => {
+                const { historyContentType } = getSrcAndContentType(v);
+                const collectionType = "collection_type" in v && v.collection_type ? v.collection_type : undefined;
+                return !canAcceptSrc(historyContentType, collectionType);
+            })
+        ) {
+            return false;
+        }
         if (values.length > 0) {
             const incomingValues: Array<DataOption> = [];
-            values.forEach((v) => {
+            values.forEach((currVal) => {
                 // Map incoming objects to data option values
-                const newHid = v.hid;
-                const newId = v.id;
-                const newName = v.name ? v.name : newId;
-                const newSrc =
-                    v.src || (v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET);
-                const newValue: DataOption = {
-                    id: newId,
-                    src: newSrc,
-                    batch: false,
-                    map_over_type: undefined,
-                    hid: newHid,
-                    name: newName,
-                    keep: true,
-                    tags: [],
-                };
-                if (v.collection_type && props.collectionTypes?.length > 0) {
-                    if (!props.collectionTypes.includes(v.collection_type)) {
-                        const mapOverType = props.collectionTypes.find((collectionType) =>
-                            v.collection_type.endsWith(collectionType)
-                        );
-                        if (!mapOverType) {
-                            return false;
-                        }
-                        newValue["batch"] = true;
-                        newValue["map_over_type"] = mapOverType;
-                    }
+                const newValue = toDataOption(currVal);
+                if (!newValue) {
+                    return false;
                 }
                 // Verify that new value has corresponding option
-                const keepKey = `${newId}_${newSrc}`;
-                const existingOptions = props.options && props.options[newSrc];
-                const foundOption = existingOptions && existingOptions.find((option) => option.id === newId);
+                const keepKey = `${newValue.id}_${newValue.src}`;
+                const existingOptions = props.options && props.options[newValue.src];
+                const foundOption = existingOptions && existingOptions.find((option) => option.id === newValue.id);
                 if (!foundOption && !(keepKey in keepOptions)) {
-                    keepOptions[keepKey] = { label: `${newHid || "Selected"}: ${newName}`, value: newValue };
+                    keepOptions[keepKey] = {
+                        label: `${newValue.hid || "Selected"}: ${newValue.name}`,
+                        value: newValue,
+                    };
                 }
                 // Add new value to list
                 incomingValues.push(newValue);
             });
+            let hasDuplicates = false;
             if (incomingValues.length > 0 && incomingValues[0]) {
                 // Set new value
                 const config = currentVariant.value;
@@ -367,21 +411,68 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
                     if (config.multiple) {
                         const newValues = currentValue.value ? currentValue.value.slice() : [];
                         incomingValues.forEach((v) => {
-                            newValues.push(v);
+                            if (containsDataOption(newValues, v)) {
+                                hasDuplicates = true;
+                            } else {
+                                newValues.push(v);
+                            }
                         });
                         currentValue.value = newValues;
                     } else {
+                        if (containsDataOption(currentValue.value ?? [], firstValue)) {
+                            hasDuplicates = true;
+                        }
                         currentValue.value = [firstValue];
                     }
                 } else {
                     currentValue.value = incomingValues;
                 }
             }
+            if (hasDuplicates) {
+                return false;
+            }
         }
     }
     return true;
 }
 
+function toDataOption(item: HistoryOrCollectionItem): DataOption | null {
+    const { newSrc, datasetCollectionDataset } = getSrcAndContentType(item);
+    let v: HistoryOrCollectionItem | HDAObject;
+    if (datasetCollectionDataset) {
+        v = datasetCollectionDataset;
+    } else {
+        v = item;
+    }
+    const newHid = isHistoryItem(v) ? v.hid : undefined;
+    const newId = v.id;
+    const newName = isHistoryItem(v) && v.name ? v.name : newId;
+    const newValue: DataOption = {
+        id: newId,
+        src: newSrc,
+        batch: false,
+        map_over_type: undefined,
+        hid: newHid,
+        name: newName,
+        keep: true,
+        tags: [],
+    };
+    if (isHistoryItem(v) && isHDCA(v) && props.collectionTypes?.length > 0) {
+        const itemCollectionType = v.collection_type;
+        if (!props.collectionTypes.includes(itemCollectionType)) {
+            const mapOverType = props.collectionTypes.find((collectionType) =>
+                itemCollectionType.endsWith(collectionType)
+            );
+            if (!mapOverType) {
+                return null;
+            }
+            newValue["batch"] = true;
+            newValue["map_over_type"] = mapOverType;
+        }
+    }
+    return newValue;
+}
+
 /**
  * Open file dialog
  */
@@ -404,7 +495,10 @@ function onBrowse() {
 }
 
 function canAcceptDatatype(itemDatatypes: string | Array<string>) {
-    if (!(props.extensions?.length > 0)) {
+    // TODO: Shouldn't we enforce a datatype (at least "data") because of the case:
+    // What if the drop item is a `DCESummary`, then it has no extension (?) and we
+    // pass it as a valid item regardless of its elements' datatypes.
+    if (!(props.extensions?.length > 0) || props.extensions.includes("data")) {
         return true;
     }
     let datatypes: Array<string>;
@@ -422,19 +516,149 @@ function canAcceptDatatype(itemDatatypes: string | Array<string>) {
     return true;
 }
 
+/**
+ * Given an element, determine the source and content type.
+ * Also returns the collection element dataset object if it exists.
+ */
+function getSrcAndContentType(element: HistoryOrCollectionItem): {
+    historyContentType: HistoryContentType;
+    newSrc: string;
+    datasetCollectionDataset: HDAObject | undefined;
+} {
+    let historyContentType: HistoryContentType;
+    let newSrc: string;
+    let datasetCollectionDataset: HDAObject | undefined;
+    if (isDCE(element)) {
+        if (isDatasetElement(element)) {
+            historyContentType = "dataset";
+            newSrc = SOURCE.DATASET;
+            datasetCollectionDataset = element.object;
+        } else {
+            historyContentType = "dataset_collection";
+            newSrc = SOURCE.COLLECTION_ELEMENT;
+        }
+    } else {
+        historyContentType = element.history_content_type;
+        newSrc =
+            "src" in element && typeof element.src === "string"
+                ? element.src
+                : historyContentType === "dataset_collection"
+                ? SOURCE.COLLECTION
+                : SOURCE.DATASET;
+    }
+    return { historyContentType, newSrc, datasetCollectionDataset };
+}
+
+function canAcceptSrc(historyContentType: "dataset" | "dataset_collection", collectionType?: string) {
+    if (historyContentType === "dataset") {
+        // HDA can only be fed into data parameters, not collection parameters
+        if (props.type === "data") {
+            return true;
+        } else {
+            $emit("alert", "dataset is not a valid input for dataset collection parameter.");
+            return false;
+        }
+    } else if (historyContentType === "dataset_collection") {
+        if (props.type === "data") {
+            // collection can always be mapped over a data input ... in theory.
+            // One day we should also validate the map over model
+            return true;
+        }
+        if (!collectionType) {
+            // Should always be set if item is dataset collection
+            throw Error("Item is a dataset collection of unknown type.");
+        } else if (!props.collectionTypes) {
+            // if no collection_type is set all collections are valid
+            return true;
+        } else {
+            if (props.collectionTypes.includes(collectionType)) {
+                return true;
+            }
+            if (props.collectionTypes.some((element) => collectionType.endsWith(element))) {
+                return true;
+            } else {
+                $emit(
+                    "alert",
+                    `${collectionType} dataset collection is not a valid input for ${orList(
+                        props.collectionTypes
+                    )} type dataset collection parameter.`
+                );
+                return false;
+            }
+        }
+    } else {
+        throw Error("Unknown history content type.");
+    }
+}
+
+/** Allowed collection types for collection creation */
+const effectiveCollectionTypes = props.collectionTypes?.filter((collectionType) =>
+    ["list", "list:paired", "paired"].includes(collectionType)
+);
+
+function buildNewCollection(collectionType: string) {
+    if (!["list", "list:paired", "paired"].includes(collectionType)) {
+        throw Error(`Unknown collection type: ${collectionType}`);
+    }
+    collectionModalType.value = collectionType as "list" | "list:paired" | "paired";
+    collectionModalShow.value = true;
+}
+
+function createdCollection(collection: any) {
+    handleIncoming(collection);
+}
+
+/**
+ * Get the extension(s) for a given item
+ */
+function getExtensionsForItem(item: HistoryOrCollectionItem): string | string[] | null {
+    return "extension" in item ? item.extension : "elements_datatypes" in item ? item.elements_datatypes : null;
+}
+
+function isHistoryOrCollectionItem(item: EventData): item is HistoryOrCollectionItem {
+    return isHistoryItem(item) || isDCE(item);
+}
+
+function getNameForItem(item: HistoryOrCollectionItem): string {
+    if (isHistoryItem(item)) {
+        return item.name ?? `Item ${item.hid}`;
+    } else if (isDCE(item)) {
+        return item.element_identifier;
+    } else {
+        throw new Error("Unknown item type");
+    }
+}
+
 // Drag/Drop event handlers
 function onDragEnter(evt: MouseEvent) {
-    const eventData = eventStore.getDragData();
-    if (eventData) {
-        const extensions = (eventData.extension as string) || (eventData.elements_datatypes as Array<string>);
-        if (!canAcceptDatatype(extensions)) {
-            currentHighlighting.value = "warning";
-            $emit("alert", `${extensions} is not an acceptable format for this parameter.`);
-        } else {
-            currentHighlighting.value = "success";
+    const eventData = eventStore.getDragItems();
+    dragData.value = [];
+
+    for (const item of eventData) {
+        if (isHistoryOrCollectionItem(item)) {
+            const extensions = getExtensionsForItem(item);
+            const { historyContentType } = getSrcAndContentType(item);
+            const collectionType = "collection_type" in item && item.collection_type ? item.collection_type : undefined;
+            let highlightingState = "success";
+            if (extensions && !canAcceptDatatype(extensions)) {
+                highlightingState = "warning";
+                $emit("alert", `${extensions} is not an acceptable format for this parameter.`);
+            } else if (!canAcceptSrc(historyContentType, collectionType)) {
+                highlightingState = "warning";
+                $emit("alert", `${historyContentType} is not an acceptable input type for this parameter.`);
+            }
+            // Check if the item is already in the current value
+            const option = toDataOption(item);
+            const isAlreadyInValue = containsDataOption(currentValue.value ?? [], option);
+            if (isAlreadyInValue) {
+                highlightingState = "warning";
+                $emit("alert", `${getNameForItem(item)} is already selected.`);
+            }
+
+            currentHighlighting.value = highlightingState;
+            dragTarget.value = evt.target;
+            dragData.value.push(item);
         }
-        dragTarget.value = evt.target;
-        dragData.value = eventData;
     }
 }
 
@@ -446,20 +670,14 @@ function onDragLeave(evt: MouseEvent) {
 }
 
 function onDrop() {
-    if (dragData.value) {
-        let accept = false;
-        if (eventStore.multipleDragData) {
-            accept = handleIncoming(Object.values(dragData.value) as any, false);
-        } else {
-            accept = handleIncoming(dragData.value);
-        }
-        if (accept) {
+    if (dragData.value.length) {
+        if (handleIncoming(dragData.value, dragData.value.length === 1)) {
             currentHighlighting.value = "success";
         } else {
             currentHighlighting.value = "warning";
         }
         $emit("alert", undefined);
-        dragData.value = null;
+        dragData.value = [];
         clearHighlighting();
     }
 }
@@ -507,14 +725,26 @@ watch(
 const formatsVisible = ref(false);
 const formatsButtonId = useUid("form-data-formats-");
 
+function collectionTypeToText(collectionType: string): string {
+    if (collectionType == "list:paired") {
+        return "list of pairs";
+    } else {
+        return collectionType;
+    }
+}
+
 const warningListAmount = 4;
 const noOptionsWarningMessage = computed(() => {
-    if (!props.extensions || props.extensions.length === 0) {
-        return "No datasets available";
+    const itemType = props.type === "data" ? "datasets" : "dataset collections";
+    const collectionTypeLabel = props.collectionTypes?.length
+        ? `${orList(props.collectionTypes.map(collectionTypeToText))} `
+        : "";
+    if (!props.extensions || props.extensions.length === 0 || props.extensions.includes("data")) {
+        return `No ${collectionTypeLabel}${itemType} available`;
     } else if (props.extensions.length <= warningListAmount) {
-        return `No ${orList(props.extensions)} datasets available`;
+        return `No ${collectionTypeLabel}${itemType} with ${orList(props.extensions)} elements available`;
     } else {
-        return "No compatible datasets available";
+        return `No compatible ${collectionTypeLabel}${itemType} available`;
     }
 });
 </script>
@@ -540,15 +770,26 @@ const noOptionsWarningMessage = computed(() => {
                     <FontAwesomeIcon :icon="['far', v.icon]" />
                 </BButton>
                 <BButton v-if="canBrowse" v-b-tooltip.hover.bottom title="Browse or Upload Datasets" @click="onBrowse">
-                    <FontAwesomeIcon v-if="loading" icon="fa-spinner" spin />
+                    <FontAwesomeIcon v-if="loading" :icon="faSpinner" spin />
                     <span v-else class="font-weight-bold">...</span>
                 </BButton>
+                <BButtonGroup v-if="effectiveCollectionTypes?.length > 0" size="sm" buttons>
+                    <BButton
+                        v-for="collectionType in effectiveCollectionTypes"
+                        :key="collectionType"
+                        v-b-tooltip.hover.bottom
+                        :title="`Create a new ${COLLECTION_TYPE_TO_LABEL[collectionType]}`"
+                        :variant="formattedOptions.length === 0 ? 'warning' : 'secondary'"
+                        @click="buildNewCollection(collectionType)">
+                        <FontAwesomeIcon :icon="faPlus" fixed-width />
+                    </BButton>
+                </BButtonGroup>
             </BButtonGroup>
-            <div v-if="extensions && extensions.length > 0">
+            <div v-if="restrictsExtensions">
                 <BButton :id="formatsButtonId" class="ui-link" @click="formatsVisible = !formatsVisible">
                     accepted formats
-                    <FontAwesomeIcon v-if="formatsVisible" icon="fa-caret-up" />
-                    <FontAwesomeIcon v-else icon="fa-caret-down" />
+                    <FontAwesomeIcon v-if="formatsVisible" :icon="faCaretUp" />
+                    <FontAwesomeIcon v-else :icon="faCaretDown" />
                 </BButton>
                 <BCollapse v-model="formatsVisible">
                     <ul class="pl-3 m-0">
@@ -572,7 +813,7 @@ const noOptionsWarningMessage = computed(() => {
             :options="formattedOptions"
             :placeholder="`Select a ${placeholder}`">
             <template v-slot:no-options>
-                <BAlert variant="warning" show>
+                <BAlert class="w-100 align-items-center" variant="warning" show>
                     {{ noOptionsWarningMessage }}
                 </BAlert>
             </template>
@@ -584,6 +825,14 @@ const noOptionsWarningMessage = computed(() => {
             optional
             multiple />
 
+        <CollectionCreatorModal
+            v-if="currentHistoryId && effectiveCollectionTypes?.length > 0"
+            :history-id="currentHistoryId"
+            :collection-type="collectionModalType"
+            :extensions="props.extensions.filter((ext) => ext !== 'data')"
+            :show-modal.sync="collectionModalShow"
+            @created-collection="createdCollection" />
+
         <template v-if="currentVariant && currentVariant.batch !== BATCH.DISABLED">
             <BFormCheckbox
                 v-if="currentVariant.batch === BATCH.ENABLED"
@@ -591,19 +840,23 @@ const noOptionsWarningMessage = computed(() => {
                 class="checkbox no-highlight"
                 switch>
                 <span v-if="currentLinked">
-                    <FontAwesomeIcon icon="fa-link" />
+                    <FontAwesomeIcon :icon="faLink" />
                     <b v-localize class="mr-1">Linked:</b>
                     <span v-localize>Datasets will be run in matched order with other datasets.</span>
                 </span>
                 <span v-else>
-                    <FontAwesomeIcon icon="fa-unlink" />
+                    <FontAwesomeIcon :icon="faUnlink" />
                     <b v-localize class="mr-1">Unlinked:</b>
                     <span v-localize>Dataset will be run against *all* other datasets.</span>
                 </span>
             </BFormCheckbox>
             <div class="info text-info">
-                <FontAwesomeIcon icon="fa-exclamation" />
-                <span v-localize class="ml-1">
+                <FontAwesomeIcon :icon="faExclamation" />
+                <span v-if="props.type == 'data' && currentVariant.src == SOURCE.COLLECTION" class="ml-1">
+                    The supplied input will be <HelpText text="mapped over" uri="galaxy.collections.mapOver" /> this
+                    tool.
+                </span>
+                <span v-else v-localize class="ml-1">
                     This is a batch mode input field. Individual jobs will be triggered for each dataset.
                 </span>
             </div>
diff --git a/client/src/components/Form/Elements/FormData/FormDataUri.vue b/client/src/components/Form/Elements/FormData/FormDataUri.vue
new file mode 100644
index 0000000000000000000000000000000000000000..0c888fbc4fce1109cc4a2224897e2f7f7063d320
--- /dev/null
+++ b/client/src/components/Form/Elements/FormData/FormDataUri.vue
@@ -0,0 +1,66 @@
+<template>
+    <b-row align-v="center">
+        <b-col>
+            <b-form-input :id="id" v-model="displayValue" :class="['ui-input', cls]" :readonly="true" />
+        </b-col>
+    </b-row>
+</template>
+
+<script>
+export default {
+    props: {
+        value: {
+            type: Object,
+        },
+        id: {
+            type: String,
+            default: "",
+        },
+        multiple: {
+            type: Boolean,
+            default: false,
+        },
+        cls: {
+            // Refers to an optional custom css class name
+            type: String,
+            default: null,
+        },
+    },
+    computed: {
+        displayValue: {
+            get() {
+                return this.value.url;
+            },
+            set(newVal, oldValue) {
+                if (newVal !== this.value.url) {
+                    this.$emit("input", this.value);
+                }
+            },
+        },
+        currentValue: {
+            get() {
+                const v = this.value ?? "";
+                if (Array.isArray(v)) {
+                    if (v.length === 0) {
+                        return "";
+                    }
+                    return this.multiple
+                        ? this.value.reduce((str_value, v) => str_value + String(v) + "\n", "")
+                        : String(this.value[0]);
+                }
+                return String(v);
+            },
+            set(newVal, oldVal) {
+                if (newVal !== oldVal) {
+                    this.$emit("input", newVal);
+                }
+            },
+        },
+    },
+};
+</script>
+<style scoped>
+.ui-input-linked {
+    border-left-width: 0.5rem;
+}
+</style>
diff --git a/client/src/components/Form/Elements/FormData/types.ts b/client/src/components/Form/Elements/FormData/types.ts
index acdf8299eca6a6243fdc09cfe610d53e502c208b..4daa5467f33397c96382a48227925390bec29ba6 100644
--- a/client/src/components/Form/Elements/FormData/types.ts
+++ b/client/src/components/Form/Elements/FormData/types.ts
@@ -1,6 +1,6 @@
 export type DataOption = {
     id: string;
-    hid: number;
+    hid?: number;
     is_dataset?: boolean;
     keep: boolean;
     batch: boolean;
@@ -9,3 +9,15 @@ export type DataOption = {
     src: string;
     tags: Array<string>;
 };
+
+export function isDataOption(item: object): item is DataOption {
+    return !!item && "src" in item;
+}
+
+export function itemUniqueKey(item: DataOption): string {
+    return `${item.src}-${item.id}`;
+}
+
+export function containsDataOption(items: DataOption[], item: DataOption | null): boolean {
+    return item !== null && items.some((i) => itemUniqueKey(i) === itemUniqueKey(item));
+}
diff --git a/client/src/components/Form/Elements/FormDirectory.test.js b/client/src/components/Form/Elements/FormDirectory.test.js
index 589456f27836458664d90c79962721bf7d4899c4..12fea5a211d74d773d0c84a0814195aa5b3b8d41 100644
--- a/client/src/components/Form/Elements/FormDirectory.test.js
+++ b/client/src/components/Form/Elements/FormDirectory.test.js
@@ -1,17 +1,40 @@
 import { mount } from "@vue/test-utils";
-import FilesDialog from "components/FilesDialog/FilesDialog";
-import { rootResponse } from "components/FilesDialog/testingData";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
+import { rootResponse } from "@/components/FilesDialog/testingData";
 
-import FormDirectory from "./FormDirectory";
+import FormDirectory from "./FormDirectory.vue";
+import FilesDialog from "@/components/FilesDialog/FilesDialog.vue";
 
 const localVue = getLocalVue();
 jest.mock("app");
-jest.mock("@/api/schema");
+
+const { server, http } = useServerMock();
+
+async function init(wrapper, data) {
+    // the file dialog modal should exist
+    const filesDialogComponent = wrapper.findComponent(FilesDialog);
+    expect(filesDialogComponent.exists()).toBe(true);
+    filesDialogComponent.vm.callback({ url: data.url });
+    // HACK to avoid https://github.com/facebook/jest/issues/2549 (URL implementation is not the same as global node)
+    wrapper.vm.pathChunks = data.pathChunks;
+    await flushPromises();
+    await validateLatestEmittedPath(wrapper, data.url);
+}
+
+async function validateLatestEmittedPath(wrapper, expectedPath) {
+    const latestEmitIndex = wrapper.emitted()["input"].length - 1;
+    const latestPath = wrapper.emitted()["input"][latestEmitIndex][0];
+    expect(latestPath).toBe(expectedPath);
+
+    // also manually change prop value to be able to test the value being displayed
+    await wrapper.setProps({ value: latestPath });
+    const fullPathDisplayed = wrapper.find("[data-description='directory full path']");
+    expect(fullPathDisplayed.text()).toBe(`Directory Path: ${expectedPath}`);
+}
 
 describe("DirectoryPathEditableBreadcrumb", () => {
     let wrapper;
@@ -28,6 +51,11 @@ describe("DirectoryPathEditableBreadcrumb", () => {
     const validPath = "validpath";
     const invalidPath = "./];";
 
+    const testingDataWithSpecialChars = {
+        url: "gxfiles://directory/sub directory/with%20percent",
+        pathChunks: [{ pathChunk: "directory" }, { pathChunk: "sub%20directory" }, { pathChunk: "with%2520percent" }],
+    };
+
     const saveNewChunk = async (path) => {
         // enter a new path chunk
         const input = wrapper.find("#path-input-breadcrumb");
@@ -37,35 +65,32 @@ describe("DirectoryPathEditableBreadcrumb", () => {
         input.trigger("keyup.enter");
         return input;
     };
-    const init = async () => {
-        // the file dialog modal should exist
-        const filesDialogComponent = wrapper.findComponent(FilesDialog);
-        expect(filesDialogComponent.exists()).toBe(true);
-        filesDialogComponent.vm.callback({ url: testingData.url });
-        // HACK to avoid https://github.com/facebook/jest/issues/2549 (URL implementation is not the same as global node)
-        wrapper.vm.pathChunks = testingData.pathChunks;
-        await flushPromises();
-    };
 
     beforeEach(async () => {
         spyOnUrlSet = jest.spyOn(FormDirectory.methods, "setUrl");
         spyOnAddPath = jest.spyOn(FormDirectory.methods, "addPath");
         spyOnUpdateURL = jest.spyOn(FormDirectory.methods, "updateURL");
 
-        mockFetcher.path("/api/remote_files/plugins").method("get").mock({ data: rootResponse });
-        mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
+        server.use(
+            http.get("/api/remote_files/plugins", ({ response }) => {
+                return response(200).json(rootResponse);
+            }),
+
+            http.get("/api/configuration", ({ response }) => {
+                return response(200).json({});
+            })
+        );
 
         const pinia = createPinia();
 
         wrapper = mount(FormDirectory, {
             propsData: {
-                callback: () => {},
+                value: null,
             },
             localVue: localVue,
             pinia,
         });
         await flushPromises();
-        await init();
     });
     afterEach(async () => {
         if (wrapper) {
@@ -75,6 +100,7 @@ describe("DirectoryPathEditableBreadcrumb", () => {
     });
 
     it("should render Breadcrumb", async () => {
+        await init(wrapper, testingData);
         // after initial folder is chosen, setUrl() should be called and modal disappear
         expect(spyOnUrlSet).toHaveBeenCalled();
         expect(wrapper.findComponent(FilesDialog).exists()).toBe(false);
@@ -99,6 +125,7 @@ describe("DirectoryPathEditableBreadcrumb", () => {
     });
 
     it("should prevent invalid Paths", async () => {
+        await init(wrapper, testingData);
         // enter a new path chunk
         const input = await saveNewChunk(invalidPath);
         await flushPromises();
@@ -109,6 +136,7 @@ describe("DirectoryPathEditableBreadcrumb", () => {
     });
 
     it("should save and remove new Paths", async () => {
+        await init(wrapper, testingData);
         // enter a new path chunk
         const input = await saveNewChunk(validPath);
 
@@ -121,14 +149,20 @@ describe("DirectoryPathEditableBreadcrumb", () => {
         expect(wrapper.findAll("li.breadcrumb-item").length).toBe(testingData.expectedNumberOfPaths + 1);
         // find newly added chunk
         const addedChunk = wrapper.findAll("li.breadcrumb-item button").wrappers.find((e) => e.text() === validPath);
+
+        await validateLatestEmittedPath(wrapper, `${testingData.url}/${validPath}`);
+
         // remove chunk from the path
         await addedChunk.trigger("click");
         await flushPromises();
         // number of elements should be the same again
         expect(wrapper.findAll("li.breadcrumb-item").length).toBe(testingData.expectedNumberOfPaths);
+
+        await validateLatestEmittedPath(wrapper, testingData.url);
     });
 
     it("should update new path", async () => {
+        await init(wrapper, testingData);
         // enter a new path chunk
         expect(spyOnUpdateURL).toHaveBeenCalled();
         await saveNewChunk(validPath);
@@ -136,4 +170,10 @@ describe("DirectoryPathEditableBreadcrumb", () => {
 
         expect(spyOnUpdateURL).toHaveBeenCalled();
     });
+
+    it("should retain special characters in path", async () => {
+        // the init function itself validates that the emits and path display
+        // retain special characters in the url
+        await init(wrapper, testingDataWithSpecialChars);
+    });
 });
diff --git a/client/src/components/Form/Elements/FormDirectory.vue b/client/src/components/Form/Elements/FormDirectory.vue
index 75678d82b1adb80b5a32caee3bab3ab9e95cab50..4a5388d618b876589362891c26a6e3dd689ad2df 100644
--- a/client/src/components/Form/Elements/FormDirectory.vue
+++ b/client/src/components/Form/Elements/FormDirectory.vue
@@ -4,9 +4,14 @@
             <b-button id="select-btn" @click="reset">
                 <FontAwesomeIcon icon="folder-open" /> {{ selectText }}
             </b-button>
-            <FilesDialog :key="modalKey" mode="directory" :callback="setUrl" :require-writable="true" />
+            <FilesDialog
+                :key="modalKey"
+                mode="directory"
+                :callback="setUrl"
+                :require-writable="true"
+                :is-open="isModalShown" />
         </div>
-        <b-breadcrumb v-if="url">
+        <b-breadcrumb v-if="url" class="mb-0">
             <b-breadcrumb-item title="Select another folder" class="align-items-center" @click="reset">
                 <b-button class="pathname" variant="primary">
                     <FontAwesomeIcon icon="folder-open" /> {{ url.protocol }}</b-button
@@ -17,8 +22,8 @@
                 :key="index"
                 class="existent-url-path align-items-center">
                 <b-button class="regular-path-chunk" :disabled="!editable" variant="dark" @click="removePath(index)">
-                    {{ pathChunk }}</b-button
-                >
+                    {{ decodeURIComponent(pathChunk) }}
+                </b-button>
             </b-breadcrumb-item>
             <b-breadcrumb-item class="directory-input-field align-items-center">
                 <b-input
@@ -33,6 +38,11 @@
                     @keydown.8.capture="removeLastPath" />
             </b-breadcrumb-item>
         </b-breadcrumb>
+
+        <div v-if="value" class="px-2" data-description="directory full path">
+            <span v-localize>Directory Path:</span>
+            <code>{{ value }}</code>
+        </div>
     </div>
 </template>
 
@@ -41,8 +51,11 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faFolder, faFolderOpen } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { FilesDialog } from "components/FilesDialog";
+import { Toast } from "composables/toast";
 import _l from "utils/localization";
 
+import { errorMessageAsString } from "@/utils/simple-error";
+
 library.add(faFolder, faFolderOpen);
 
 const getDefaultValues = () => ({
@@ -57,6 +70,12 @@ export default {
         FontAwesomeIcon,
         FilesDialog,
     },
+    props: {
+        value: {
+            type: String,
+            default: null,
+        },
+    },
     data() {
         return { ...getDefaultValues(), modalKey: 0, selectText: _l("Select") };
     },
@@ -69,9 +88,13 @@ export default {
             return regex.test(this.currentDirectoryName);
         },
     },
+    mounted() {
+        this.updateURL(true);
+    },
     methods: {
         removePath(index) {
             this.pathChunks = this.pathChunks.slice(0, index);
+            this.updateURL();
         },
         reset() {
             const data = getDefaultValues();
@@ -83,6 +106,7 @@ export default {
         // https://michaelnthiessen.com/force-re-render/
         redrawModal() {
             this.modalKey += 1;
+            this.isModalShown = true;
         },
         removeLastPath(event) {
             // check whether the last item is editable
@@ -93,15 +117,19 @@ export default {
             }
         },
         setUrl({ url }) {
-            this.url = new URL(url);
-            // split path and keep only valid entries
-            this.pathChunks = this.url.href
-                .split(/[/\\]/)
-                .splice(2)
-                .map((x) => ({ pathChunk: x, editable: false }));
+            try {
+                this.url = new URL(encodeURI(url));
+                // split path and keep only valid entries
+                this.pathChunks = this.url.href
+                    .split(/[/\\]/)
+                    .splice(2)
+                    .map((x) => ({ pathChunk: x, editable: false }));
 
-            if (url) {
-                this.updateURL();
+                if (url) {
+                    this.updateURL();
+                }
+            } catch (error) {
+                Toast.error(errorMessageAsString(error), "Invalid directory path");
             }
         },
         addPath({ key }) {
@@ -116,7 +144,12 @@ export default {
             let url = undefined;
             if (!isReset) {
                 // create an string of path chunks separated by `/`
-                url = encodeURI(`${this.url.protocol}//${this.pathChunks.map(({ pathChunk }) => pathChunk).join("/")}`);
+                url = encodeURI(
+                    `${this.url.protocol}//${this.pathChunks
+                        .map(({ pathChunk }) => decodeURIComponent(pathChunk))
+                        .join("/")}`
+                );
+                url = decodeURI(url);
             }
             this.$emit("input", url);
         },
diff --git a/client/src/components/Form/Elements/FormDrilldown/FormDrilldown.vue b/client/src/components/Form/Elements/FormDrilldown/FormDrilldown.vue
index f023dcebc84d0d1303d3b692bdcb14e029f3cd86..6d12579650ddbccd9e92ccff012086132ba5177e 100644
--- a/client/src/components/Form/Elements/FormDrilldown/FormDrilldown.vue
+++ b/client/src/components/Form/Elements/FormDrilldown/FormDrilldown.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { BAlert, BFormCheckbox } from "bootstrap-vue";
 import { computed, type ComputedRef } from "vue";
 
 import { findDescendants, flattenValues, getAllValues, type Option, type Value } from "./utilities";
@@ -11,10 +12,12 @@ const props = withDefaults(
         value?: Value;
         options: Array<Option>;
         multiple: boolean;
+        showIcons?: boolean;
     }>(),
     {
         value: null,
         multiple: true,
+        showIcons: false,
     }
 );
 
@@ -91,20 +94,27 @@ function setElementValues(oldArray: string[], newArray: string[], value: string)
 </script>
 
 <template>
-    <div v-if="hasOptions">
-        <b-form-checkbox
-            v-if="multiple"
-            v-localize
-            :checked="selectAllChecked"
-            :indeterminate="selectAllIndeterminate"
-            class="d-inline select-all-checkbox"
-            @change="onSelectAll">
-            Select / Deselect All
-        </b-form-checkbox>
-        <FormDrilldownList
-            :multiple="multiple"
-            :current-value="currentValue"
-            :options="options"
-            :handle-click="handleClick" />
+    <div>
+        <div v-if="hasOptions">
+            <BFormCheckbox
+                v-if="multiple"
+                v-localize
+                :checked="selectAllChecked"
+                :indeterminate="selectAllIndeterminate"
+                class="d-inline select-all-checkbox"
+                @change="onSelectAll">
+                Select / Deselect All
+            </BFormCheckbox>
+
+            <FormDrilldownList
+                :show-icons="showIcons"
+                :multiple="multiple"
+                :current-value="currentValue"
+                :options="options"
+                :handle-click="handleClick" />
+        </div>
+        <div v-else>
+            <BAlert show variant="info" class="mt-2"> No options available. </BAlert>
+        </div>
     </div>
 </template>
diff --git a/client/src/components/Form/Elements/FormDrilldown/FormDrilldownList.vue b/client/src/components/Form/Elements/FormDrilldown/FormDrilldownList.vue
index 142538efed69f14d2817531bb83ff6a77b455f11..d49b7e3a46321071b1232cc5c6b1dd7b9dada48d 100644
--- a/client/src/components/Form/Elements/FormDrilldown/FormDrilldownList.vue
+++ b/client/src/components/Form/Elements/FormDrilldown/FormDrilldownList.vue
@@ -7,6 +7,7 @@ defineProps<{
     currentValue: string[];
     handleClick: Function;
     multiple: boolean;
+    showIcons?: boolean;
     options: Array<Option>;
 }>();
 </script>
@@ -15,6 +16,7 @@ defineProps<{
     <div class="ui-drilldown">
         <div v-for="option in options" :key="option.name" class="descendant-lines">
             <FormDrilldownOption
+                :show-icons="showIcons"
                 :current-value="currentValue"
                 :handle-click="handleClick"
                 :multiple="multiple"
diff --git a/client/src/components/Form/Elements/FormDrilldown/FormDrilldownOption.vue b/client/src/components/Form/Elements/FormDrilldown/FormDrilldownOption.vue
index f9bb1a0b8a45d466b02853770b4aa4224e1ef039..e403d43774c57bd9606ecf27c7dbd5b238047217 100644
--- a/client/src/components/Form/Elements/FormDrilldown/FormDrilldownOption.vue
+++ b/client/src/components/Form/Elements/FormDrilldown/FormDrilldownOption.vue
@@ -1,4 +1,7 @@
 <script setup lang="ts">
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { faCaretDown, faCaretRight, faFile, faFolder } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BFormCheckbox, BFormRadio } from "bootstrap-vue";
 import { computed, type ComputedRef, onMounted, ref } from "vue";
 
@@ -6,12 +9,20 @@ import { getAllValues, type Option } from "./utilities";
 
 import FormDrilldownList from "./FormDrilldownList.vue";
 
-const props = defineProps<{
+interface Props {
     currentValue: string[];
     option: Option;
     handleClick: Function;
     multiple: boolean;
-}>();
+    showIcons?: boolean;
+    leafIcon?: IconDefinition;
+    branchIcon?: IconDefinition;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    leafIcon: () => faFile,
+    branchIcon: () => faFolder,
+});
 
 const showChildren = ref(false);
 
@@ -43,6 +54,11 @@ function toggleInitialization(): void {
         }
     }
 }
+
+function getOptionIcon(option: Option) {
+    return option.leaf ? props.leafIcon : props.branchIcon;
+}
+
 onMounted(() => {
     toggleInitialization();
 });
@@ -51,22 +67,26 @@ onMounted(() => {
 <template>
     <div>
         <b-button v-if="hasOptions" variant="link" class="btn p-0" @click="toggleChildren">
-            <i v-if="showChildren" class="fa fa-caret-down align-checkbox" />
-            <i v-else class="fa fa-caret-right align-checkbox" />
+            <FontAwesomeIcon v-if="showChildren" :icon="faCaretDown" class="align-checkbox" />
+            <FontAwesomeIcon v-else :icon="faCaretRight" class="align-checkbox" />
         </b-button>
         <span v-if="!hasOptions" class="align-indent"></span>
         <component
             :is="isComponent"
+            :id="`drilldown-option-${option.name}`"
             class="drilldown-option d-inline"
             value="true"
+            :disabled="option.disabled"
             :checked="isChecked"
             @change="handleClick(option.value, $event)">
+            <FontAwesomeIcon v-if="props.showIcons" :icon="getOptionIcon(option)" />
             {{ option.name }}
         </component>
         <FormDrilldownList
             v-if="hasOptions"
             v-show="showChildren"
             class="indent"
+            :show-icons="props.showIcons"
             :current-value="currentValue"
             :multiple="multiple"
             :options="option.options"
diff --git a/client/src/components/Form/Elements/FormDrilldown/utilities.ts b/client/src/components/Form/Elements/FormDrilldown/utilities.ts
index 22db204189eed2003df5f19bcfeaaaa008fa3812..c634dcfc9bd3ae9e47d9c02f3699e07d98705b52 100644
--- a/client/src/components/Form/Elements/FormDrilldown/utilities.ts
+++ b/client/src/components/Form/Elements/FormDrilldown/utilities.ts
@@ -1,6 +1,9 @@
 export interface Option {
     name: string;
     value: string;
+    leaf?: boolean;
+    fullPath?: string;
+    disabled?: boolean;
     options: Array<Option>;
 }
 
diff --git a/client/src/components/Form/Elements/FormSelect.vue b/client/src/components/Form/Elements/FormSelect.vue
index 98ed4f551e81215ec9ef4ec1a8899fe40847690c..36018d37cb193f7f55dfd2809926e8c0cd41101c 100644
--- a/client/src/components/Form/Elements/FormSelect.vue
+++ b/client/src/components/Form/Elements/FormSelect.vue
@@ -2,21 +2,28 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { computed, type ComputedRef, onMounted, type PropType, watch } from "vue";
+import { computed, type ComputedRef, onMounted, type PropType, ref, watch } from "vue";
 import Multiselect from "vue-multiselect";
 
+import { useFilterObjectArray } from "@/composables/filter";
 import { useMultiselect } from "@/composables/useMultiselect";
 import { uid } from "@/utils/utils";
 
+import { type DataOption, isDataOption, itemUniqueKey } from "./FormData/types";
+
+import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
+
 library.add(faCheckSquare, faSquare);
 
 const { ariaExpanded, onOpen, onClose } = useMultiselect();
 
 type SelectValue = Record<string, unknown> | string | number | null;
+type ValueWithTags = SelectValue & { tags: string[] };
 
 interface SelectOption {
     label: string;
     value: SelectValue;
+    key?: string;
 }
 
 const props = defineProps({
@@ -51,28 +58,33 @@ const emit = defineEmits<{
     (e: "input", value: SelectValue | Array<SelectValue>): void;
 }>();
 
+const filter = ref("");
+const filteredOptions = useFilterObjectArray(() => props.options, filter, ["label", ["value", "tags"]]);
+
 /**
  * When there are more options than this, push selected options to the end
  */
 const optionReorderThreshold = 8;
 
 const reorderedOptions = computed(() => {
-    if (props.options.length <= optionReorderThreshold) {
-        return props.options;
+    let result;
+    if (!props.multiple || filteredOptions.value.length <= optionReorderThreshold) {
+        result = filteredOptions.value;
     } else {
         const selectedOptions: SelectOption[] = [];
         const unselectedOptions: SelectOption[] = [];
 
-        props.options.forEach((option) => {
-            if (selectedValues.value.includes(option.value)) {
+        filteredOptions.value.forEach((option) => {
+            if (isSelected(option.value)) {
                 selectedOptions.push(option);
             } else {
                 unselectedOptions.push(option);
             }
         });
 
-        return [...unselectedOptions, ...selectedOptions];
+        result = [...unselectedOptions, ...selectedOptions];
     }
+    return result.map(getSelectOption);
 });
 
 /**
@@ -107,11 +119,27 @@ const selectedLabel: ComputedRef<string> = computed(() => {
  */
 const selectedValues = computed(() => (Array.isArray(props.value) ? props.value : [props.value]));
 
+/**
+ * Tracks selected keys in case of form data options
+ */
+const selectedKeys = computed(() => {
+    return selectedValues.value
+        .map((v) => (isDataOptionObject(v) ? itemUniqueKey(v) : undefined))
+        .filter((v) => v !== undefined);
+});
+
+/**
+ * Whether current value(s) will be tracked by key or value
+ */
+const trackBy = computed(() => {
+    return selectedKeys.value.length > 0 ? "key" : "value";
+});
+
 /**
  * Tracks current value and emits changes
  */
 const currentValue = computed({
-    get: () => props.options.filter((option: SelectOption) => selectedValues.value.includes(option.value)),
+    get: () => props.options.filter((option: SelectOption) => isSelected(option.value)).map(getSelectOption),
     set: (val: Array<SelectOption> | SelectOption): void => {
         if (Array.isArray(val)) {
             if (val.length > 0) {
@@ -135,12 +163,24 @@ function setInitialValue(): void {
     }
 }
 
+function getSelectOption(option: SelectOption): SelectOption {
+    if (isDataOptionObject(option.value)) {
+        return {
+            ...option,
+            key: itemUniqueKey(option.value),
+        };
+    }
+    return option;
+}
+
 /**
  * Watches changes in select options and adjusts initial value if necessary
  */
 watch(
     () => props.options,
-    () => setInitialValue()
+    () => {
+        setInitialValue();
+    }
 );
 
 /**
@@ -149,6 +189,25 @@ watch(
 onMounted(() => {
     setInitialValue();
 });
+
+function isValueWithTags(item: SelectValue): item is ValueWithTags {
+    return item !== null && typeof item === "object" && (item as ValueWithTags).tags !== undefined;
+}
+
+function isDataOptionObject(item: SelectValue): item is DataOption {
+    return !!item && typeof item === "object" && isDataOption(item);
+}
+
+function onSearchChange(search: string): void {
+    filter.value = search;
+}
+
+function isSelected(item: SelectValue): boolean {
+    if (isDataOptionObject(item)) {
+        return selectedKeys.value.includes(itemUniqueKey(item));
+    }
+    return selectedValues.value.includes(item);
+}
 </script>
 
 <template>
@@ -168,13 +227,22 @@ onMounted(() => {
             :placeholder="placeholder"
             :selected-label="selectedLabel"
             :select-label="null"
-            track-by="value"
+            :track-by="trackBy"
+            :internal-search="false"
+            @search-change="onSearchChange"
             @open="onOpen"
             @close="onClose">
             <template v-slot:option="{ option }">
                 <div class="d-flex align-items-center justify-content-between">
-                    <span>{{ option.label }}</span>
-                    <FontAwesomeIcon v-if="selectedValues.includes(option.value)" :icon="faCheckSquare" />
+                    <div>
+                        <span>{{ option.label }}</span>
+                        <StatelessTags
+                            v-if="isValueWithTags(option.value)"
+                            class="tags mt-2"
+                            :value="option.value.tags"
+                            disabled />
+                    </div>
+                    <FontAwesomeIcon v-if="isSelected(option.value)" :icon="faCheckSquare" />
                     <FontAwesomeIcon v-else :icon="faSquare" />
                 </div>
             </template>
diff --git a/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.test.ts b/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.test.ts
index 12f36bdf55ef92a75df4afa7132053e9ece0c5b2..1f59b74a2b85cb552e6157ef2caa9e339b207c01 100644
--- a/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.test.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.test.ts
@@ -3,9 +3,9 @@ import "./worker/__mocks__/selectMany";
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
 import { mount } from "@vue/test-utils";
-import { PropType } from "vue";
+import { type PropType } from "vue";
 
-import type { SelectOption } from "./worker/selectMany";
+import { type SelectOption } from "./worker/selectMany";
 
 import FormSelectMany from "./FormSelectMany.vue";
 
diff --git a/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.vue b/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.vue
index 0c762ae90bd4acee77ee5beff2a7ffb0e632ccfd..4651b6b216d63e6e27327eb8c02fc31e1afecb32 100644
--- a/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.vue
+++ b/client/src/components/Form/Elements/FormSelectMany/FormSelectMany.vue
@@ -39,6 +39,10 @@ const props = defineProps({
         type: Array as PropType<SelectValue | SelectValue[]>,
         default: null,
     },
+    maintainSelectionOrder: {
+        type: Boolean,
+        default: false,
+    },
 });
 
 const emit = defineEmits<{
@@ -48,6 +52,7 @@ const emit = defineEmits<{
 const searchValue = ref("");
 const useRegex = ref(false);
 const caseSensitive = ref(false);
+const localSelectionOrder = computed(() => props.maintainSelectionOrder);
 
 const searchRegex = computed(() => {
     if (useRegex.value) {
@@ -94,6 +99,7 @@ const { unselectedOptionsFiltered, selectedOptionsFiltered, running, moreUnselec
     selectedDisplayCount,
     unselectedDisplayCount,
     caseSensitive,
+    maintainSelectionOrder: localSelectionOrder,
 });
 
 // debounced to it doesn't blink, and only appears when relevant
@@ -124,6 +130,29 @@ function focusOptionAtIndex(selected: "selected" | "unselected", index: number)
     }
 }
 
+/** convert array of select options to a map of select labels to select values */
+function optionsToLabelMap(options: SelectOption[]): Map<string, SelectValue> {
+    return new Map(options.map((o) => [o.label, o.value]));
+}
+
+function valuesToOptions(values: SelectValue[]): SelectOption[] {
+    function stringifyObject(value: SelectValue) {
+        return typeof value === "object" && value !== null ? JSON.stringify(value) : value;
+    }
+
+    const comparableValues = values.map(stringifyObject);
+    const valueSet = new Set(comparableValues);
+    const options: SelectOption[] = [];
+
+    props.options.forEach((option) => {
+        if (valueSet.has(stringifyObject(option.value))) {
+            options.push(option);
+        }
+    });
+
+    return options;
+}
+
 async function selectOption(event: MouseEvent, index: number): Promise<void> {
     if (event.shiftKey || event.ctrlKey) {
         handleHighlight(event, index, highlightUnselected);
@@ -168,10 +197,10 @@ async function deselectOption(event: MouseEvent, index: number) {
 function selectAll() {
     if (highlightUnselected.highlightedIndexes.length > 0) {
         const highlightedValues = highlightUnselected.highlightedOptions.map((o) => o.value);
-        const selectedSet = new Set([...selected.value, ...highlightedValues]);
-        selected.value = Array.from(selectedSet);
+        selected.value = [...selected.value, ...highlightedValues];
 
-        unselectedOptionsFiltered.value.filter((o) => highlightedValues.includes(o.value));
+        const highlightedMap = optionsToLabelMap(highlightUnselected.highlightedOptions);
+        unselectedOptionsFiltered.value.filter((o) => highlightedMap.has(o.label));
     } else if (searchValue.value === "") {
         selected.value = props.options.map((o) => o.value);
 
@@ -188,13 +217,13 @@ function selectAll() {
 
 function deselectAll() {
     if (highlightSelected.highlightedIndexes.length > 0) {
-        const selectedSet = new Set(selected.value);
-        const highlightedValues = highlightSelected.highlightedOptions.map((o) => o.value);
+        const selectedMap = optionsToLabelMap(valuesToOptions(selected.value));
+        const highlightedMap = optionsToLabelMap(highlightSelected.highlightedOptions);
 
-        highlightedValues.forEach((v) => selectedSet.delete(v));
-        selected.value = Array.from(selectedSet);
+        highlightedMap.forEach((_value, label) => selectedMap.delete(label));
+        selected.value = Array.from(selectedMap.values());
 
-        selectedOptionsFiltered.value.filter((o) => highlightedValues.includes(o.value));
+        selectedOptionsFiltered.value.filter((o) => highlightedMap.has(o.label));
     } else if (searchValue.value === "") {
         selected.value = [];
         selectedOptionsFiltered.value = [];
@@ -341,7 +370,9 @@ const selectedCount = computed(() => {
                     :class="{ highlighted: highlightUnselected.highlightedIndexes.includes(i) }"
                     @click="(e) => selectOption(e, i)"
                     @keydown="(e) => optionOnKey('unselected', e, i)">
-                    {{ option.label }}
+                    <slot name="label-area" v-bind="option">
+                        {{ option.label }}
+                    </slot>
                 </button>
 
                 <span v-if="moreUnselected" class="show-more-indicator">
@@ -373,7 +404,9 @@ const selectedCount = computed(() => {
                     :class="{ highlighted: highlightSelected.highlightedIndexes.includes(i) }"
                     @click="(e) => deselectOption(e, i)"
                     @keydown="(e) => optionOnKey('selected', e, i)">
-                    {{ option.label }}
+                    <slot name="label-area" v-bind="option">
+                        {{ option.label }}
+                    </slot>
                 </button>
 
                 <span v-if="moreSelected" class="show-more-indicator">
diff --git a/client/src/components/Form/Elements/FormSelectMany/useHighlight.ts b/client/src/components/Form/Elements/FormSelectMany/useHighlight.ts
index 8feb91eef7067dc98b5af249ebd7e5cbc7781915..c2c576e7601ded1fad1076c522c16942fbc82842 100644
--- a/client/src/components/Form/Elements/FormSelectMany/useHighlight.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/useHighlight.ts
@@ -2,7 +2,7 @@ import { type Ref, ref, watch } from "vue";
 
 import { assertDefined } from "@/utils/assertions";
 
-import type { SelectOption } from "./worker/selectMany";
+import { type SelectOption } from "./worker/selectMany";
 
 /**
  * Handles logic required for highlighting options
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/__mocks__/selectMany.ts b/client/src/components/Form/Elements/FormSelectMany/worker/__mocks__/selectMany.ts
index d040fb824da85de1a65901114d180bca21b8ed4f..a635e2bb63aa9edfa1653b502e0974494055d04c 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/__mocks__/selectMany.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/__mocks__/selectMany.ts
@@ -1,6 +1,6 @@
 import { reactive, ref, watch } from "vue";
 
-import type { SelectOption, useSelectMany as UseSelectMany } from "../selectMany";
+import { type SelectOption, type useSelectMany as UseSelectMany } from "../selectMany";
 import { main } from "../selectManyMain";
 
 jest.mock("@/components/Form/Elements/FormSelectMany/worker/selectMany", () => ({
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/filterOptions.ts b/client/src/components/Form/Elements/FormSelectMany/worker/filterOptions.ts
index 6c3c26f3a38c21c846707cba1ec66a99ca9c6150..add5e9bb244ddc87132d84b0130c550203130d3f 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/filterOptions.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/filterOptions.ts
@@ -1,4 +1,4 @@
-import { SelectOption } from "./selectMany";
+import { type SelectOption } from "./selectMany";
 
 export function filterOptions(options: SelectOption[], filter: string | RegExp, caseSensitive: boolean) {
     let filteredSelectOptions;
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.d.ts b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.d.ts
index 3f3ebf146dde1f5ac13a15776c56af7b240cf3e3..5aa5e4ee274fdef890a0bfb5041aa1fc6e200f9b 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.d.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.d.ts
@@ -1,4 +1,4 @@
-import type { Ref } from "vue";
+import { type Ref } from "vue";
 
 export type SelectValue = Record<string, unknown> | string | number | null;
 
@@ -14,6 +14,7 @@ export interface UseSelectManyOptions {
     unselectedDisplayCount: Ref<number>;
     selectedDisplayCount: Ref<number>;
     caseSensitive: Ref<boolean>;
+    maintainSelectionOrder: Ref<boolean>;
 }
 
 export interface UseSelectManyReturn {
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.js b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.js
index 485e55bd23fc876ae42d3d56f658463f7a8999f1..95c07be25d97d0f78b155f30fdf954e672718445 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.js
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.js
@@ -13,6 +13,7 @@ export function useSelectMany({
     unselectedDisplayCount,
     selectedDisplayCount,
     caseSensitive,
+    maintainSelectionOrder,
 }) {
     // only start a single worker
     if (!worker) {
@@ -64,6 +65,7 @@ export function useSelectMany({
             unselectedDisplayCount: unselectedDisplayCount.value,
             selectedDisplayCount: selectedDisplayCount.value,
             caseSensitive: caseSensitive.value,
+            maintainSelectionOrder: maintainSelectionOrder.value,
         });
     });
 
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.worker.js b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.worker.js
index 6eaed4c7638d3e0d3d9f8d807887c4527164dae6..05afb92301a1ac04e67c1f0a142199dde30f5719 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.worker.js
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/selectMany.worker.js
@@ -10,6 +10,7 @@ const createOptions = () => {
         unselectedDisplayCount: 1000,
         selectedDisplayCount: 1000,
         caseSensitive: false,
+        maintainSelectionOrder: false,
     };
 };
 
@@ -42,6 +43,7 @@ self.addEventListener("message", (e) => {
             options.unselectedDisplayCount = message.unselectedDisplayCount;
             options.selectedDisplayCount = message.selectedDisplayCount;
             options.caseSensitive = message.caseSensitive;
+            options.maintainSelectionOrder = message.maintainSelectionOrder;
             break;
 
         case "clear":
diff --git a/client/src/components/Form/Elements/FormSelectMany/worker/selectManyMain.ts b/client/src/components/Form/Elements/FormSelectMany/worker/selectManyMain.ts
index 0a35d9e042231a232b0e3f12345a32c9ce2f8d20..34c043022938c6f6a3692743255022f120bba31e 100644
--- a/client/src/components/Form/Elements/FormSelectMany/worker/selectManyMain.ts
+++ b/client/src/components/Form/Elements/FormSelectMany/worker/selectManyMain.ts
@@ -1,7 +1,7 @@
-import type { UnwrapNestedRefs } from "vue";
+import { type UnwrapNestedRefs } from "vue";
 
 import { filterOptions } from "./filterOptions";
-import type { SelectOption, SelectValue, UseSelectManyOptions, UseSelectManyReturn } from "./selectMany";
+import { type SelectOption, type SelectValue, type UseSelectManyOptions, type UseSelectManyReturn } from "./selectMany";
 
 export function main(options: UnwrapNestedRefs<UseSelectManyOptions>): UnwrapNestedRefs<UseSelectManyReturn> {
     const unselectedOptionsFiltered: SelectOption[] = [];
@@ -43,6 +43,19 @@ export function main(options: UnwrapNestedRefs<UseSelectManyOptions>): UnwrapNes
         }
     }
 
+    // In case maintainSelectionOrder is enabled, we need to maintain the order from selectedValues
+    if (options.maintainSelectionOrder) {
+        const selectedValuesArray = Array.from(selectedValues);
+        selectedOptionsFiltered.sort((a, b) => {
+            const aAsString = stringifyObject(a.value);
+            const bAsString = stringifyObject(b.value);
+
+            const aIndex = selectedValuesArray.findIndex((v) => v === aAsString);
+            const bIndex = selectedValuesArray.findIndex((v) => v === bAsString);
+            return aIndex - bIndex;
+        });
+    }
+
     return {
         unselectedOptionsFiltered,
         selectedOptionsFiltered,
diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index 5313cb646d03e969e1d04a292deb4db63f90fa97..a34c1ebefddff8e5bc38df855b739db7e606c582 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -15,6 +15,7 @@ import type { FormParameterAttributes, FormParameterTypes, FormParameterValue }
 import FormBoolean from "./Elements/FormBoolean.vue";
 import FormColor from "./Elements/FormColor.vue";
 import FormData from "./Elements/FormData/FormData.vue";
+import FormDataUri from "./Elements/FormData/FormDataUri.vue";
 import FormDataDialog from "./Elements/FormDataDialog.vue";
 import FormDirectory from "./Elements/FormDirectory.vue";
 import FormDrilldown from "./Elements/FormDrilldown/FormDrilldown.vue";
@@ -27,6 +28,7 @@ import FormSelection from "./Elements/FormSelection.vue";
 import FormTags from "./Elements/FormTags.vue";
 import FormText from "./Elements/FormText.vue";
 import FormUpload from "./Elements/FormUpload.vue";
+import FormElementHelpMarkdown from "./FormElementHelpMarkdown.vue";
 
 interface FormElementProps {
     id?: string;
@@ -35,6 +37,7 @@ interface FormElementProps {
     title?: string;
     refreshOnChange?: boolean;
     help?: string;
+    helpFormat?: string;
     error?: string;
     warning?: string;
     disabled?: boolean;
@@ -63,6 +66,7 @@ const props = withDefaults(defineProps<FormElementProps>(), {
     connectedDisableText: "Add connection to module.",
     connectedEnableIcon: "fa fa-times",
     connectedDisableIcon: "fa fa-arrows-alt-h",
+    helpFormat: "html",
     workflowBuildingMode: false,
 });
 
@@ -133,6 +137,14 @@ const elementId = computed(() => `form-element-${props.id}`);
 const hasAlert = computed(() => alerts.value.length > 0);
 const showPreview = computed(() => (collapsed.value && attrs.value["collapsible_preview"]) || props.disabled);
 const showField = computed(() => !collapsed.value && !props.disabled);
+const isUriDataField = computed(() => {
+    const dataField = props.type == "data";
+    if (dataField && props.value && "src" in props.value) {
+        const src = props.value.src;
+        return src == "url";
+    }
+    return false;
+});
 
 const previewText = computed(() => attrs.value["text_value"]);
 const helpText = computed(() => {
@@ -288,6 +300,7 @@ function onAlert(value: string | undefined) {
                 :options="attrs.options"
                 :optional="attrs.optional"
                 :multiple="attrs.multiple" />
+            <FormDataUri v-else-if="isUriDataField" :id="id" v-model="currentValue" :multiple="attrs.multiple" />
             <FormData
                 v-else-if="['data', 'data_collection'].includes(props.type)"
                 :id="id"
@@ -326,7 +339,13 @@ function onAlert(value: string | undefined) {
         </div>
 
         <div v-if="showPreview" class="ui-form-preview pt-1 pl-2 mt-1">{{ previewText }}</div>
-        <span v-if="Boolean(helpText)" class="ui-form-info form-text text-muted" v-html="helpText" />
+        <span
+            v-if="Boolean(helpText) && helpFormat != 'markdown'"
+            class="ui-form-info form-text text-muted"
+            v-html="helpText" />
+        <span v-else-if="Boolean(helpText)" class="ui-form-info form-text text-muted"
+            ><FormElementHelpMarkdown :content="helpText"
+        /></span>
     </div>
 </template>
 
diff --git a/client/src/components/Form/FormElementHelpMarkdown.vue b/client/src/components/Form/FormElementHelpMarkdown.vue
new file mode 100644
index 0000000000000000000000000000000000000000..e6271c9a2124218c73681afc553d117512729acb
--- /dev/null
+++ b/client/src/components/Form/FormElementHelpMarkdown.vue
@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { computed, onMounted, ref } from "vue";
+
+import { markup } from "@/components/ObjectStore/configurationMarkdown";
+import { getAppRoot } from "@/onload/loadConfig";
+
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
+const props = defineProps<{
+    content: string;
+}>();
+
+const markdownHtml = computed(() => markup(props.content ?? "", false));
+
+const helpHtml = ref<HTMLDivElement>();
+
+interface InternalTypeReference {
+    element: HTMLElement;
+    term: string;
+}
+
+const internalHelpReferences = ref<InternalTypeReference[]>([]);
+
+function setupPopovers() {
+    internalHelpReferences.value.length = 0;
+    if (helpHtml.value) {
+        const links = helpHtml.value.getElementsByTagName("a");
+        Array.from(links).forEach((link) => {
+            if (link.href.startsWith("gxhelp://")) {
+                const uri = link.href.substr("gxhelp://".length);
+                internalHelpReferences.value.push({ element: link, term: uri });
+                link.href = `${getAppRoot()}help/terms/${uri}`;
+                link.style.color = "inherit";
+                link.style.textDecorationLine = "underline";
+                link.style.textDecorationStyle = "dashed";
+            }
+        });
+    }
+}
+
+onMounted(setupPopovers);
+</script>
+
+<template>
+    <span>
+        <!-- Disable v-html warning because we allow markdown generated HTML
+            in various places in the Galaxy interface. Raw HTML is not allowed
+            here because admin = false in the call to markup.
+        -->
+        <!-- eslint-disable-next-line vue/no-v-html -->
+        <div ref="helpHtml" v-html="markdownHtml" />
+        <span v-for="(value, i) in internalHelpReferences" :key="i">
+            <HelpPopover :target="value.element" :term="value.term" />
+        </span>
+    </span>
+</template>
diff --git a/client/src/components/Form/FormInputs.vue b/client/src/components/Form/FormInputs.vue
index 1421a4b79ea31fe9f7cdd03bd1d29a6e9d5ce1fe..fafe1734b4787c8828e928dd9b976cd1cf5e1769 100644
--- a/client/src/components/Form/FormInputs.vue
+++ b/client/src/components/Form/FormInputs.vue
@@ -11,6 +11,7 @@
                         v-model="input.test_param.value"
                         :type="input.test_param.type"
                         :help="input.test_param.help"
+                        :help-format="input.test_param.help_format"
                         :refresh-on-change="false"
                         :disabled="sustainConditionals"
                         :attributes="input.test_param"
@@ -51,6 +52,7 @@
                 :error="input.error"
                 :warning="input.warning"
                 :help="input.help"
+                :help-format="input.help_format"
                 :refresh-on-change="input.refresh_on_change"
                 :attributes="input.attributes || input"
                 :collapsed-enable-text="collapsedEnableText"
diff --git a/client/src/components/GDateTime.vue b/client/src/components/GDateTime.vue
index 616bc8322684d20a6e27f0611f94684ae45f07f1..4b15864d63db0b353d9da26b6f117c11a9d3a29c 100644
--- a/client/src/components/GDateTime.vue
+++ b/client/src/components/GDateTime.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { BFormInput, BInputGroup } from "bootstrap-vue";
-import { Tuple } from "types/utilityTypes";
+import { type Tuple } from "types/utilityTypes";
 import { computed } from "vue";
 
 const props = defineProps<{
diff --git a/client/src/components/GalaxyWizard.vue b/client/src/components/GalaxyWizard.vue
new file mode 100644
index 0000000000000000000000000000000000000000..e648a3cda701e2c430bdb2032c2394b62162beb7
--- /dev/null
+++ b/client/src/components/GalaxyWizard.vue
@@ -0,0 +1,146 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faThumbsDown, faThumbsUp } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BButton, BSkeleton } from "bootstrap-vue";
+import { ref } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { useMarkdown } from "@/composables/markdown";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import LoadingSpan from "./LoadingSpan.vue";
+
+library.add(faThumbsUp, faThumbsDown);
+interface Props {
+    context?: string;
+    jobId: string;
+    query: string;
+    view?: "wizard" | "error";
+}
+const props = withDefaults(defineProps<Props>(), {
+    view: "error",
+    context: "username",
+});
+const query = ref(props.query);
+const queryResponse = ref("");
+const errorMessage = ref("");
+const busy = ref(false);
+const feedback = ref<null | "up" | "down">(null);
+const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true, removeNewlinesAfterList: true });
+/** On submit, query the server and put response in display box **/
+async function submitQuery() {
+    busy.value = true;
+    if (query.value === "") {
+        errorMessage.value = "There is no context to provide a response.";
+        busy.value = false;
+        return;
+    }
+    /**
+     * Note: We are using a POST request here, which at the backend checks if a response exists
+     * for the given job_id and returns it if it does. If it doesn't, it will create a new response.
+     * Curious whether this is better done by using a separate GET and then a POST?
+     * TODO: Remove this comment after discussion.
+     */
+    const { data, error } = await GalaxyApi().POST("/api/chat", {
+        params: {
+            query: { job_id: props.jobId },
+        },
+        body: {
+            query: query.value,
+            context: props.context,
+        },
+    });
+    if (error) {
+        errorMessage.value = errorMessageAsString(error, "Failed to get response from the server.");
+    } else {
+        queryResponse.value = data;
+    }
+    busy.value = false;
+}
+/** Send feedback to the server **/
+async function sendFeedback(value: "up" | "down") {
+    feedback.value = value;
+    // up is 1 and down is 0
+    const feedbackValue = value === "up" ? 1 : 0;
+    const { error } = await GalaxyApi().PUT("/api/chat/{job_id}/feedback", {
+        params: {
+            path: { job_id: props.jobId },
+            query: { feedback: feedbackValue },
+        },
+    });
+    if (error) {
+        errorMessage.value = errorMessageAsString(error, "Failed to send feedback to the server.");
+    }
+}
+</script>
+
+<template>
+    <div>
+        <!-- <Heading v-if="props.view == 'wizard'" inline h2>Ask the wizard</Heading>
+        <div :class="props.view == 'wizard' && 'mt-2'">
+            <b-input
+                v-if="props.query == ''"
+                id="wizardinput"
+                v-model="query"
+                style="width: 100%"
+                placeholder="What's the difference in fasta and fastq files?"
+                @keyup.enter="submitQuery" /> -->
+        <BAlert v-if="errorMessage" variant="danger" show>
+            {{ errorMessage }}
+        </BAlert>
+        <BButton v-else-if="!queryResponse" class="w-100" variant="info" :disabled="busy" @click="submitQuery">
+            <span v-if="!busy"> Let our Help Wizard Figure it out! </span>
+            <LoadingSpan v-else message="Thinking" />
+        </BButton>
+        <div :class="props.view == 'wizard' && 'mt-4'">
+            <div v-if="busy">
+                <BSkeleton animation="wave" width="85%" />
+                <BSkeleton animation="wave" width="55%" />
+                <BSkeleton animation="wave" width="70%" />
+            </div>
+            <!-- eslint-disable-next-line vue/no-v-html -->
+            <div v-else class="chatResponse" v-html="renderMarkdown(queryResponse)" />
+
+            <div v-if="queryResponse" class="feedback-buttons mt-2">
+                <hr class="w-100" />
+                <h4>Was this answer helpful?</h4>
+                <BButton
+                    variant="success"
+                    :disabled="feedback !== null"
+                    :class="{ submitted: feedback === 'up' }"
+                    @click="sendFeedback('up')">
+                    <FontAwesomeIcon :icon="faThumbsUp" fixed-width />
+                </BButton>
+                <BButton
+                    variant="danger"
+                    :disabled="feedback !== null"
+                    :class="{ submitted: feedback === 'down' }"
+                    @click="sendFeedback('down')">
+                    <FontAwesomeIcon :icon="faThumbsDown" fixed-width />
+                </BButton>
+                <i v-if="!feedback">This feedback helps us improve our responses.</i>
+                <i v-else>Thank you for your feedback!</i>
+            </div>
+        </div>
+    </div>
+</template>
+<style lang="scss" scoped>
+.chatResponse {
+    white-space: pre-wrap;
+}
+.submitted svg {
+    animation: swoosh-up 1s forwards;
+}
+@keyframes swoosh-up {
+    0% {
+        transform: translateY(0);
+    }
+    50% {
+        transform: translateY(-20px);
+    }
+    100% {
+        transform: translateY(0);
+    }
+}
+</style>
diff --git a/client/src/components/Grid/GridInvocation.vue b/client/src/components/Grid/GridInvocation.vue
index d8997096096f16684430710b6cd0c04c1f9c2cc5..65aed67b73f78c5799d141f028c992f25db3e369 100644
--- a/client/src/components/Grid/GridInvocation.vue
+++ b/client/src/components/Grid/GridInvocation.vue
@@ -2,7 +2,9 @@
 import { storeToRefs } from "pinia";
 import { computed } from "vue";
 
+import type { WorkflowInvocation } from "@/api/invocations";
 import invocationsGridConfig from "@/components/Grid/configs/invocations";
+import invocationsBatchConfig from "@/components/Grid/configs/invocationsBatch";
 import invocationsHistoryGridConfig from "@/components/Grid/configs/invocationsHistory";
 import invocationsWorkflowGridConfig from "@/components/Grid/configs/invocationsWorkflow";
 import { useUserStore } from "@/stores/userStore";
@@ -19,6 +21,7 @@ interface Props {
     headerMessage?: string;
     ownerGrid?: boolean;
     filteredFor?: { type: "History" | "StoredWorkflow"; id: string; name: string };
+    invocationsList?: WorkflowInvocation[];
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -26,12 +29,14 @@ const props = withDefaults(defineProps<Props>(), {
     headerMessage: "",
     ownerGrid: true,
     filteredFor: undefined,
+    invocationsList: undefined,
 });
 
 const { currentUser } = storeToRefs(useUserStore());
 
 const forStoredWorkflow = computed(() => props.filteredFor?.type === "StoredWorkflow");
 const forHistory = computed(() => props.filteredFor?.type === "History");
+const forBatch = computed(() => !!props.invocationsList?.length);
 
 const effectiveNoInvocationsMessage = computed(() => {
     let message = props.noInvocationsMessage;
@@ -51,6 +56,9 @@ const effectiveTitle = computed(() => {
 });
 
 const extraProps = computed(() => {
+    if (forBatch.value) {
+        return Object.fromEntries(props.invocationsList.map((invocation) => [invocation.id, invocation]));
+    }
     const params: {
         workflow_id?: string;
         history_id?: string;
@@ -72,7 +80,9 @@ const extraProps = computed(() => {
 });
 
 let gridConfig: GridConfig;
-if (forStoredWorkflow.value) {
+if (forBatch.value) {
+    gridConfig = invocationsBatchConfig;
+} else if (forStoredWorkflow.value) {
     gridConfig = invocationsWorkflowGridConfig;
 } else if (forHistory.value) {
     gridConfig = invocationsHistoryGridConfig;
@@ -97,9 +107,9 @@ function refreshTable() {
             :grid-message="props.headerMessage"
             :no-data-message="effectiveNoInvocationsMessage"
             :extra-props="extraProps"
-            :embedded="forStoredWorkflow || forHistory">
+            :embedded="forStoredWorkflow || forHistory || forBatch">
             <template v-slot:expanded="{ rowData }">
-                <span class="float-right position-absolute mr-4" style="right: 0" :data-invocation-id="rowData.id">
+                <span class="mb-2" :data-invocation-id="rowData.id">
                     <small>
                         <b>Last updated: <UtcDate :date="rowData.update_time" mode="elapsed" />; Invocation ID:</b>
                     </small>
diff --git a/client/src/components/Grid/GridList.vue b/client/src/components/Grid/GridList.vue
index 3490f2c1ab7b8cce3c2e1769596f9a27c3b56fab..fb62592c7ec8fe112a4c14eef1a8743ab331153a 100644
--- a/client/src/components/Grid/GridList.vue
+++ b/client/src/components/Grid/GridList.vue
@@ -7,7 +7,14 @@ import { BAlert, BButton, BCard, BFormCheckbox, BOverlay, BPagination } from "bo
 import { computed, nextTick, onMounted, onUnmounted, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { BatchOperation, FieldEntry, FieldHandler, GridConfig, Operation, RowData } from "./configs/types";
+import {
+    type BatchOperation,
+    type FieldEntry,
+    type FieldHandler,
+    type GridConfig,
+    type Operation,
+    type RowData,
+} from "./configs/types";
 
 import HelpText from "../Help/HelpText.vue";
 import SwitchToHistoryLink from "../History/SwitchToHistoryLink.vue";
diff --git a/client/src/components/Grid/configs/adminForms.ts b/client/src/components/Grid/configs/adminForms.ts
index a94e16fc308decb28f47c2037dc064e019dd6d1a..d4d8941c74941de9b76512268e533d0a3aea623d 100644
--- a/client/src/components/Grid/configs/adminForms.ts
+++ b/client/src/components/Grid/configs/adminForms.ts
@@ -2,13 +2,13 @@ import { faEdit, faPlus, faTrash, faTrashRestore } from "@fortawesome/free-solid
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { deleteForm, undeleteForm } from "@/api/forms";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -69,18 +69,19 @@ const fields: FieldArray = [
                 condition: (data: FormEntry) => !data.deleted,
                 handler: async (data: FormEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this form?"))) {
-                        try {
-                            await deleteForm({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/forms/{id}", {
+                            params: { path: { id: String(data.id) } },
+                        });
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to delete '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been deleted.`,
+                        };
                     }
                 },
             },
@@ -89,18 +90,19 @@ const fields: FieldArray = [
                 icon: faTrashRestore,
                 condition: (data: FormEntry) => !!data.deleted,
                 handler: async (data: FormEntry) => {
-                    try {
-                        await undeleteForm({ id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `'${data.name}' has been restored.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/forms/{id}/undelete", {
+                        params: { path: { id: String(data.id) } },
+                    });
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to restore '${data.name}': ${errorMessageAsString(e)}`,
+                            message: `Failed to restore '${data.name}': ${errorMessageAsString(error)}`,
                         };
                     }
+                    return {
+                        status: "success",
+                        message: `'${data.name}' has been restored.`,
+                    };
                 },
             },
         ],
@@ -145,7 +147,7 @@ const gridConfig: GridConfig = {
     getData: getData,
     plural: "Forms",
     sortBy: "name",
-    sortDesc: true,
+    sortDesc: false,
     sortKeys: ["name", "update_time"],
     title: "Forms",
 };
diff --git a/client/src/components/Grid/configs/adminGroups.ts b/client/src/components/Grid/configs/adminGroups.ts
index e4f143d997b05e353d84830323a59cd2af2fbe37..ffd2f6d0bee259da05383aa99dfa6c03e10aec99 100644
--- a/client/src/components/Grid/configs/adminGroups.ts
+++ b/client/src/components/Grid/configs/adminGroups.ts
@@ -2,13 +2,13 @@ import { faEdit, faKey, faPlus, faTrash, faTrashRestore } from "@fortawesome/fre
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { deleteGroup, purgeGroup, undeleteGroup } from "@/api/groups";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -77,18 +77,23 @@ const fields: FieldArray = [
                 condition: (data: GroupEntry) => !data.deleted,
                 handler: async (data: GroupEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this group?"))) {
-                        try {
-                            await deleteGroup({ group_id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/groups/{group_id}", {
+                            params: {
+                                path: { group_id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to delete '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been deleted.`,
+                        };
                     }
                 },
             },
@@ -98,18 +103,23 @@ const fields: FieldArray = [
                 condition: (data: GroupEntry) => !!data.deleted,
                 handler: async (data: GroupEntry) => {
                     if (confirm(_l("Are you sure that you want to purge this group?"))) {
-                        try {
-                            await purgeGroup({ group_id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been purged.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().POST("/api/groups/{group_id}/purge", {
+                            params: {
+                                path: { group_id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to purge '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to purge '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been purged.`,
+                        };
                     }
                 },
             },
@@ -118,18 +128,23 @@ const fields: FieldArray = [
                 icon: faTrashRestore,
                 condition: (data: GroupEntry) => !!data.deleted,
                 handler: async (data: GroupEntry) => {
-                    try {
-                        await undeleteGroup({ group_id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `'${data.name}' has been restored.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/groups/{group_id}/undelete", {
+                        params: {
+                            path: { group_id: String(data.id) },
+                        },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to restore '${data.name}': ${errorMessageAsString(e)}`,
+                            message: `Failed to restore '${data.name}': ${errorMessageAsString(error)}`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `'${data.name}' has been restored.`,
+                    };
                 },
             },
         ],
@@ -173,7 +188,7 @@ const gridConfig: GridConfig = {
     getData: getData,
     plural: "Groups",
     sortBy: "name",
-    sortDesc: true,
+    sortDesc: false,
     sortKeys: ["name", "update_time"],
     title: "Groups",
 };
diff --git a/client/src/components/Grid/configs/adminQuotas.ts b/client/src/components/Grid/configs/adminQuotas.ts
index 67f0d6162fac3f96faed610b0071e7c3995cd67f..79e67e83857916800268ed43d13d9b2c6bd05e9a 100644
--- a/client/src/components/Grid/configs/adminQuotas.ts
+++ b/client/src/components/Grid/configs/adminQuotas.ts
@@ -2,13 +2,13 @@ import { faCog, faDatabase, faEdit, faPlus, faTrash, faTrashRestore, faUsers } f
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { deleteQuota, purgeQuota, undeleteQuota } from "@/api/quotas";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -93,18 +93,23 @@ const fields: FieldArray = [
                 condition: (data: QuotaEntry) => !data.deleted,
                 handler: async (data: QuotaEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this quota?"))) {
-                        try {
-                            await deleteQuota({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/quotas/{id}", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to delete '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been deleted.`,
+                        };
                     }
                 },
             },
@@ -114,18 +119,23 @@ const fields: FieldArray = [
                 condition: (data: QuotaEntry) => !!data.deleted,
                 handler: async (data: QuotaEntry) => {
                     if (confirm(_l("Are you sure that you want to purge this quota?"))) {
-                        try {
-                            await purgeQuota({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been purged.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().POST("/api/quotas/{id}/purge", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to purge '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to purge '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been purged.`,
+                        };
                     }
                 },
             },
@@ -134,18 +144,23 @@ const fields: FieldArray = [
                 icon: faTrashRestore,
                 condition: (data: QuotaEntry) => !!data.deleted,
                 handler: async (data: QuotaEntry) => {
-                    try {
-                        await undeleteQuota({ id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `'${data.name}' has been restored.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/quotas/deleted/{id}/undelete", {
+                        params: {
+                            path: { id: String(data.id) },
+                        },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to restore '${data.name}': ${errorMessageAsString(e)}`,
+                            message: `Failed to restore '${data.name}': ${errorMessageAsString(error)}`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `'${data.name}' has been restored.`,
+                    };
                 },
             },
         ],
@@ -210,7 +225,7 @@ const gridConfig: GridConfig = {
     getData: getData,
     plural: "Quotas",
     sortBy: "name",
-    sortDesc: true,
+    sortDesc: false,
     sortKeys: ["name", "description", "update_time"],
     title: "Quotas",
 };
diff --git a/client/src/components/Grid/configs/adminRoles.ts b/client/src/components/Grid/configs/adminRoles.ts
index fe913e7fc41e832ab6eeec3e55988aa48f9ebe6c..92f6a4d6b02352629da18f6506a537ccebde6837 100644
--- a/client/src/components/Grid/configs/adminRoles.ts
+++ b/client/src/components/Grid/configs/adminRoles.ts
@@ -2,13 +2,13 @@ import { faEdit, faKey, faPlus, faTrash, faTrashRestore } from "@fortawesome/fre
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { deleteRole, purgeRole, undeleteRole } from "@/api/roles";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -77,18 +77,23 @@ const fields: FieldArray = [
                 condition: (data: RoleEntry) => !data.deleted,
                 handler: async (data: RoleEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this role?"))) {
-                        try {
-                            await deleteRole({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/roles/{id}", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to delete '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been deleted.`,
+                        };
                     }
                 },
             },
@@ -97,19 +102,24 @@ const fields: FieldArray = [
                 icon: faTrash,
                 condition: (data: RoleEntry) => !!data.deleted,
                 handler: async (data: RoleEntry) => {
-                    if (confirm(_l("Are you sure that you want to purge this role?"))) {
-                        try {
-                            await purgeRole({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.name}' has been purged.`,
-                            };
-                        } catch (e) {
+                    if (confirm(_l("Are you sure that you want to permanently delete this role?"))) {
+                        const { error } = await GalaxyApi().POST("/api/roles/{id}/purge", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to purge '${data.name}': ${errorMessageAsString(e)}`,
+                                message: `Failed to permanently delete '${data.name}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.name}' has been permanently deleted.`,
+                        };
                     }
                 },
             },
@@ -118,18 +128,23 @@ const fields: FieldArray = [
                 icon: faTrashRestore,
                 condition: (data: RoleEntry) => !!data.deleted,
                 handler: async (data: RoleEntry) => {
-                    try {
-                        await undeleteRole({ id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `'${data.name}' has been restored.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/roles/{id}/undelete", {
+                        params: {
+                            path: { id: String(data.id) },
+                        },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to restore '${data.name}': ${errorMessageAsString(e)}`,
+                            message: `Failed to restore '${data.name}': ${errorMessageAsString(error)}`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `'${data.name}' has been restored.`,
+                    };
                 },
             },
         ],
@@ -184,7 +199,7 @@ const gridConfig: GridConfig = {
     getData: getData,
     plural: "Roles",
     sortBy: "name",
-    sortDesc: true,
+    sortDesc: false,
     sortKeys: ["description", "name", "update_time"],
     title: "Roles",
 };
diff --git a/client/src/components/Grid/configs/adminUsers.test.js b/client/src/components/Grid/configs/adminUsers.test.js
index f10d62a77e2fd82e66b44600ed119e40dd0495dc..65d3b7f3a7751a9bacba00ea7b212786ae56154e 100644
--- a/client/src/components/Grid/configs/adminUsers.test.js
+++ b/client/src/components/Grid/configs/adminUsers.test.js
@@ -21,7 +21,7 @@ describe("AdminUsers", () => {
             "Key",
             "Impersonate",
             "Delete",
-            "Purge",
+            "Permanently Delete",
             "Restore",
         ];
         titles.forEach((title, index) => {
diff --git a/client/src/components/Grid/configs/adminUsers.ts b/client/src/components/Grid/configs/adminUsers.ts
index 50accb2571252548970e06fb219eda270c9e98c3..cdb21c29ba89c4567a202bc3666b021d20983a59 100644
--- a/client/src/components/Grid/configs/adminUsers.ts
+++ b/client/src/components/Grid/configs/adminUsers.ts
@@ -14,14 +14,14 @@ import {
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { createApiKey, deleteUser, recalculateDiskUsageByUserId, sendActivationEmail, undeleteUser } from "@/api/users";
-import type { GalaxyConfiguration } from "@/stores/configurationStore";
+import { GalaxyApi } from "@/api";
+import { type GalaxyConfiguration } from "@/stores/configurationStore";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -98,20 +98,23 @@ const fields: FieldArray = [
                 icon: faCalculator,
                 condition: (data: UserEntry) => !data.deleted,
                 handler: async (data: UserEntry) => {
-                    try {
-                        await recalculateDiskUsageByUserId({ user_id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `Disk usage of '${data.username}' has been recalculated.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().PUT("/api/users/{user_id}/recalculate_disk_usage", {
+                        params: { path: { user_id: String(data.id) } },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
                             message: `Failed to recalculate disk usage of '${data.username}': ${errorMessageAsString(
-                                e
+                                error
                             )}.`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `Disk usage of '${data.username}' has been recalculated.`,
+                    };
                 },
             },
             {
@@ -121,18 +124,22 @@ const fields: FieldArray = [
                     return config.value.user_activation_on && !data.deleted;
                 },
                 handler: async (data: UserEntry) => {
-                    try {
-                        await axios.put(withPrefix(`/api/users/${data.id}`), { active: true });
-                        return {
-                            status: "success",
-                            message: `'${data.username}' has been activated.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().PUT("/api/users/{user_id}", {
+                        params: { path: { user_id: String(data.id) } },
+                        body: { active: true },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to activate '${data.username}': ${errorMessageAsString(e)}.`,
+                            message: `Failed to activate '${data.username}': ${errorMessageAsString(error)}.`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `'${data.username}' has been activated.`,
+                    };
                 },
             },
             {
@@ -142,20 +149,23 @@ const fields: FieldArray = [
                     return config.value.user_activation_on && !data.deleted;
                 },
                 handler: async (data: UserEntry) => {
-                    try {
-                        await sendActivationEmail({ user_id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `Activation email has been sent to '${data.username}'.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/users/{user_id}/send_activation_email", {
+                        params: { path: { user_id: String(data.id) } },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
                             message: `Failed to send activation email to '${data.username}': ${errorMessageAsString(
-                                e
+                                error
                             )}.`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `Activation email has been sent to '${data.username}'.`,
+                    };
                 },
             },
             {
@@ -163,20 +173,23 @@ const fields: FieldArray = [
                 icon: faKey,
                 condition: (data: UserEntry) => !data.deleted,
                 handler: async (data: UserEntry) => {
-                    try {
-                        await createApiKey({ user_id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `New API Key for '${data.username}' has been generated.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/users/{user_id}/api_key", {
+                        params: { path: { user_id: String(data.id) } },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
                             message: `Failed to generate new API Key for '${data.username}': ${errorMessageAsString(
-                                e
+                                error
                             )}.`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `New API Key for '${data.username}' has been generated.`,
+                    };
                 },
             },
             {
@@ -197,41 +210,55 @@ const fields: FieldArray = [
                 },
                 handler: async (data: UserEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this user?"))) {
-                        try {
-                            await deleteUser({ user_id: String(data.id), purge: false });
-                            return {
-                                status: "success",
-                                message: `'${data.username}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/users/{user_id}", {
+                            params: {
+                                path: { user_id: String(data.id) },
+                                query: { purge: false },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.username}': ${errorMessageAsString(e)}`,
+                                message: `Failed to delete '${data.username}': ${errorMessageAsString(error)}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.username}' has been deleted.`,
+                        };
                     }
                 },
             },
             {
-                title: "Purge",
+                title: "Permanently Delete",
                 icon: faTrash,
                 condition: (data: UserEntry, config: GalaxyConfiguration) => {
                     return config.value.allow_user_deletion && data.deleted && !data.purged;
                 },
                 handler: async (data: UserEntry) => {
-                    if (confirm(_l("Are you sure that you want to purge this user?"))) {
-                        try {
-                            await deleteUser({ user_id: String(data.id), purge: true });
-                            return {
-                                status: "success",
-                                message: `'${data.username}' has been purged.`,
-                            };
-                        } catch (e) {
+                    if (confirm(_l("Are you sure that you want to permanently delete this user?"))) {
+                        const { error } = await GalaxyApi().DELETE("/api/users/{user_id}", {
+                            params: {
+                                path: { user_id: String(data.id) },
+                                query: { purge: true },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to purge '${data.username}': ${errorMessageAsString(e)}`,
+                                message: `Failed to permanently delete '${data.username}': ${errorMessageAsString(
+                                    error
+                                )}`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.username}' has been permanently deleted.`,
+                        };
                     }
                 },
             },
@@ -242,18 +269,21 @@ const fields: FieldArray = [
                     return config.value.allow_user_deletion && data.deleted && !data.purged;
                 },
                 handler: async (data: UserEntry) => {
-                    try {
-                        await undeleteUser({ user_id: String(data.id) });
-                        return {
-                            status: "success",
-                            message: `'${data.username}' has been restored.`,
-                        };
-                    } catch (e) {
+                    const { error } = await GalaxyApi().POST("/api/users/deleted/{user_id}/undelete", {
+                        params: { path: { user_id: String(data.id) } },
+                    });
+
+                    if (error) {
                         return {
                             status: "danger",
-                            message: `Failed to restore '${data.username}': ${errorMessageAsString(e)}`,
+                            message: `Failed to restore '${data.username}': ${errorMessageAsString(error)}`,
                         };
                     }
+
+                    return {
+                        status: "success",
+                        message: `'${data.username}' has been restored.`,
+                    };
                 },
             },
         ],
@@ -336,7 +366,7 @@ const gridConfig: GridConfig = {
     getData: getData,
     plural: "Users",
     sortBy: "email",
-    sortDesc: true,
+    sortDesc: false,
     sortKeys: ["active", "create_time", "disk_usage", "email", "external", "last_login", "username"],
     title: "Users",
 };
diff --git a/client/src/components/Grid/configs/histories.ts b/client/src/components/Grid/configs/histories.ts
index 70a865c21f1ed4f1cffe3a3b9f2665ea9e567011..cee19089ade96cc26f0df79e22d10c18f01ce7c0 100644
--- a/client/src/components/Grid/configs/histories.ts
+++ b/client/src/components/Grid/configs/histories.ts
@@ -1,4 +1,5 @@
 import {
+    faBurn,
     faExchangeAlt,
     faEye,
     faPlus,
@@ -10,14 +11,15 @@ import {
 } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { deleteHistories, deleteHistory, historiesFetcher, undeleteHistories, undeleteHistory } from "@/api/histories";
+import { GalaxyApi } from "@/api";
+import { type HistorySortByLiteral } from "@/api";
 import { updateTags } from "@/api/tags";
 import { useHistoryStore } from "@/stores/historyStore";
 import Filtering, { contains, equals, expandNameTag, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, BatchOperationArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type BatchOperationArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -25,25 +27,33 @@ const { emit } = useEventBus<string>("grid-router-push");
  * Local types
  */
 type HistoryEntry = Record<string, unknown>;
-type SortKeyLiteral = "create_time" | "name" | "update_time" | undefined;
 
 /**
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await historiesFetcher({
-        view: "summary",
-        keys: "create_time",
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_own: true,
-        show_published: false,
-        show_shared: false,
+    const { response, data, error } = await GalaxyApi().GET("/api/histories", {
+        params: {
+            query: {
+                view: "summary",
+                keys: "create_time",
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as HistorySortByLiteral,
+                sort_desc,
+                show_own: true,
+                show_published: false,
+                show_shared: false,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
@@ -70,7 +80,8 @@ const batch: BatchOperationArray = [
             if (confirm(_l(`Are you sure that you want to delete the selected histories?`))) {
                 try {
                     const historyIds = data.map((x) => String(x.id));
-                    await deleteHistories({ ids: historyIds });
+                    const historyStore = useHistoryStore();
+                    await historyStore.deleteHistories(historyIds);
                     return {
                         status: "success",
                         message: `Deleted ${data.length} histories.`,
@@ -92,7 +103,8 @@ const batch: BatchOperationArray = [
             if (confirm(_l(`Are you sure that you want to restore the selected histories?`))) {
                 try {
                     const historyIds = data.map((x) => String(x.id));
-                    await undeleteHistories({ ids: historyIds });
+                    const historyStore = useHistoryStore();
+                    await historyStore.restoreHistories(historyIds);
                     return {
                         status: "success",
                         message: `Restored ${data.length} histories.`,
@@ -108,21 +120,22 @@ const batch: BatchOperationArray = [
     },
     {
         title: "Purge",
-        icon: faTrash,
+        icon: faBurn,
         condition: (data: Array<HistoryEntry>) => !data.some((x) => x.purged),
         handler: async (data: Array<HistoryEntry>) => {
             if (confirm(_l(`Are you sure that you want to permanently delete the selected histories?`))) {
                 try {
                     const historyIds = data.map((x) => String(x.id));
-                    await deleteHistories({ ids: historyIds, purge: true });
+                    const historyStore = useHistoryStore();
+                    await historyStore.deleteHistories(historyIds, true);
                     return {
                         status: "success",
-                        message: `Purged ${data.length} histories.`,
+                        message: `Permanently deleted ${data.length} histories.`,
                     };
                 } catch (e) {
                     return {
                         status: "danger",
-                        message: `Failed to delete histories: ${errorMessageAsString(e)}`,
+                        message: `Failed to permanently delete histories: ${errorMessageAsString(e)}`,
                     };
                 }
             }
@@ -185,7 +198,8 @@ const fields: FieldArray = [
                 handler: async (data: HistoryEntry) => {
                     if (confirm(_l("Are you sure that you want to delete this history?"))) {
                         try {
-                            await deleteHistory({ history_id: String(data.id) });
+                            const historyStore = useHistoryStore();
+                            await historyStore.deleteHistory(String(data.id));
                             return {
                                 status: "success",
                                 message: `'${data.name}' has been deleted.`,
@@ -201,12 +215,13 @@ const fields: FieldArray = [
             },
             {
                 title: "Delete Permanently",
-                icon: faTrash,
+                icon: faBurn,
                 condition: (data: HistoryEntry) => !data.purged,
                 handler: async (data: HistoryEntry) => {
                     if (confirm(_l("Are you sure that you want to permanently delete this history?"))) {
                         try {
-                            await deleteHistory({ history_id: String(data.id), purge: true });
+                            const historyStore = useHistoryStore();
+                            await historyStore.deleteHistory(String(data.id), true);
                             return {
                                 status: "success",
                                 message: `'${data.name}' has been permanently deleted.`,
@@ -226,7 +241,8 @@ const fields: FieldArray = [
                 condition: (data: HistoryEntry) => !!data.deleted && !data.purged,
                 handler: async (data: HistoryEntry) => {
                     try {
-                        await undeleteHistory({ history_id: String(data.id) });
+                        const historyStore = useHistoryStore();
+                        await historyStore.restoreHistory(String(data.id));
                         return {
                             status: "success",
                             message: `'${data.name}' has been restored.`,
diff --git a/client/src/components/Grid/configs/historiesPublished.ts b/client/src/components/Grid/configs/historiesPublished.ts
index 5abfd9a388dd39983d2decb988f3dd5a635f1493..22ebfcd8f0c640356747651d646d6b435fa86795 100644
--- a/client/src/components/Grid/configs/historiesPublished.ts
+++ b/client/src/components/Grid/configs/historiesPublished.ts
@@ -1,11 +1,12 @@
 import { faEye } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { historiesFetcher } from "@/api/histories";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, expandNameTag, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { FieldArray, GridConfig } from "./types";
+import { type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -19,20 +20,29 @@ type SortKeyLiteral = "name" | "update_time" | undefined;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await historiesFetcher({
-        view: "summary",
-        keys: "username",
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_own: false,
-        show_published: true,
-        show_shared: false,
-        show_archived: true,
+    const { response, data, error } = await GalaxyApi().GET("/api/histories", {
+        params: {
+            query: {
+                view: "summary",
+                keys: "username",
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                show_own: false,
+                show_published: true,
+                show_shared: false,
+                show_archived: true,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/historiesShared.ts b/client/src/components/Grid/configs/historiesShared.ts
index d045f5279bc72035fe7e5eb344edf9acf3c8a77b..6baab4a2ece5cac9a104004569f2ea92e832c670 100644
--- a/client/src/components/Grid/configs/historiesShared.ts
+++ b/client/src/components/Grid/configs/historiesShared.ts
@@ -1,13 +1,14 @@
 import { faEye } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { historiesFetcher } from "@/api/histories";
+import { GalaxyApi } from "@/api";
+import { type HistorySortByLiteral } from "@/api";
 import { updateTags } from "@/api/tags";
 import Filtering, { contains, expandNameTag, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
 import { rethrowSimple } from "@/utils/simple-error";
 
-import type { FieldArray, GridConfig } from "./types";
+import { type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -15,26 +16,34 @@ const { emit } = useEventBus<string>("grid-router-push");
  * Local types
  */
 type HistoryEntry = Record<string, unknown>;
-type SortKeyLiteral = "create_time" | "name" | "update_time" | undefined;
 
 /**
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await historiesFetcher({
-        view: "summary",
-        keys: "username,create_time",
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_own: false,
-        show_published: false,
-        show_shared: true,
-        show_archived: true,
+    const { response, data, error } = await GalaxyApi().GET("/api/histories", {
+        params: {
+            query: {
+                view: "summary",
+                keys: "username,create_time",
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as HistorySortByLiteral,
+                sort_desc,
+                show_own: false,
+                show_published: false,
+                show_shared: true,
+                show_archived: true,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/invocations.ts b/client/src/components/Grid/configs/invocations.ts
index f81b1be2d8cea7467f414891ba8ac1cd0176be76..118037db8f62db41ddd08384c0f6f57974a21f0a 100644
--- a/client/src/components/Grid/configs/invocations.ts
+++ b/client/src/components/Grid/configs/invocations.ts
@@ -1,13 +1,15 @@
 import { faPlay, faPlus } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { invocationsFetcher, type WorkflowInvocation } from "@/api/invocations";
-import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
+import { type WorkflowInvocation } from "@/api/invocations";
+import { type StoredWorkflowDetailed } from "@/api/workflows";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
 import _l from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -42,8 +44,12 @@ export async function getData(
         params["user_id"] = extraProps["user_id"];
     }
 
-    const { data, headers } = await invocationsFetcher(params);
+    const { response, data, error } = await GalaxyApi().GET("/api/invocations", { params: { query: params } });
+    if (error) {
+        rethrowSimple(error);
+    }
     fetchHistoriesAndWorkflows(data);
+    const headers = response.headers;
     const totalMatches = parseInt(headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
diff --git a/client/src/components/Grid/configs/invocationsBatch.ts b/client/src/components/Grid/configs/invocationsBatch.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c84f0b39d27de41623ae879140a81552a060d042
--- /dev/null
+++ b/client/src/components/Grid/configs/invocationsBatch.ts
@@ -0,0 +1,80 @@
+import { faEye } from "@fortawesome/free-solid-svg-icons";
+
+import { type WorkflowInvocation } from "@/api/invocations";
+import { getAppRoot } from "@/onload";
+
+import { type FieldArray, type GridConfig } from "./types";
+
+/**
+ * Request and return invocations for the given workflow (and current user) from server
+ */
+async function getData(
+    offset: number,
+    limit: number,
+    search: string,
+    sort_by: string,
+    sort_desc: boolean,
+    extraProps?: Record<string, unknown>
+) {
+    // extra props will be Record<string, Invocation>; get array of invocations
+    const data = Object.values(extraProps ?? {}) as WorkflowInvocation[];
+    const totalMatches = data.length;
+    return [data, totalMatches];
+}
+
+/**
+ * Declare columns to be displayed
+ */
+const fields: FieldArray = [
+    {
+        key: "expand",
+        title: null,
+        type: "expand",
+    },
+    {
+        key: "view",
+        title: "View",
+        type: "button",
+        icon: faEye,
+        handler: (data) => {
+            const url = `${getAppRoot()}workflows/invocations/${(data as WorkflowInvocation).id}`;
+            window.open(url, "_blank");
+        },
+        converter: () => "",
+    },
+    {
+        key: "history_id",
+        title: "History",
+        type: "history",
+    },
+    {
+        key: "create_time",
+        title: "Invoked",
+        type: "date",
+    },
+    {
+        key: "state",
+        title: "State",
+        type: "helptext",
+        converter: (data) => {
+            const invocation = data as WorkflowInvocation;
+            return `galaxy.invocations.states.${invocation.state}`;
+        },
+    },
+];
+
+/**
+ * Grid configuration
+ */
+const gridConfig: GridConfig = {
+    id: "invocations-batch-grid",
+    fields: fields,
+    getData: getData,
+    plural: "Workflow Invocations",
+    sortBy: "create_time",
+    sortDesc: true,
+    sortKeys: [],
+    title: "Workflow Invocations in Batch",
+};
+
+export default gridConfig;
diff --git a/client/src/components/Grid/configs/invocationsHistory.ts b/client/src/components/Grid/configs/invocationsHistory.ts
index 0369b01193f48c2e74dbedbbff80e19f3d14331e..69c4281b9ced3cbf79fca160e13fbdc7b2d4e40c 100644
--- a/client/src/components/Grid/configs/invocationsHistory.ts
+++ b/client/src/components/Grid/configs/invocationsHistory.ts
@@ -1,13 +1,15 @@
 import { faArrowLeft, faPlay } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { invocationsFetcher, type WorkflowInvocation } from "@/api/invocations";
-import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
+import { type WorkflowInvocation } from "@/api/invocations";
+import { type StoredWorkflowDetailed } from "@/api/workflows";
 import { useUserStore } from "@/stores/userStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
 import _l from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -34,17 +36,25 @@ async function getData(
     }
     const historyId = extraProps["history_id"] as string;
 
-    const { data, headers } = await invocationsFetcher({
-        limit,
-        offset,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        user_id: userStore.currentUser.id,
-        include_nested_invocations: false,
-        history_id: historyId,
+    const { response, data, error } = await GalaxyApi().GET("/api/invocations", {
+        params: {
+            query: {
+                limit,
+                offset,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                user_id: userStore.currentUser.id,
+                include_nested_invocations: false,
+                history_id: historyId,
+            },
+        },
     });
+    if (error) {
+        rethrowSimple(error);
+    }
+
     fetchHistories(data);
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/invocationsWorkflow.ts b/client/src/components/Grid/configs/invocationsWorkflow.ts
index 3cad8d66cc0e68e7b0c69f05a249d7ec4be54012..c0c4049c7c297c5a42b5e3b9626e9698467dd645 100644
--- a/client/src/components/Grid/configs/invocationsWorkflow.ts
+++ b/client/src/components/Grid/configs/invocationsWorkflow.ts
@@ -1,14 +1,16 @@
 import { faArrowLeft, faEye, faPlay } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { invocationsFetcher, type WorkflowInvocation } from "@/api/invocations";
-import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
+import { type WorkflowInvocation } from "@/api/invocations";
+import { type StoredWorkflowDetailed } from "@/api/workflows";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
 import _l from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
@@ -35,16 +37,25 @@ async function getData(
     }
     const workflowId = extraProps["workflow_id"] as string;
 
-    const { data, headers } = await invocationsFetcher({
-        limit,
-        offset,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        user_id: userStore.currentUser.id,
-        workflow_id: workflowId,
+    const { response, data, error } = await GalaxyApi().GET("/api/invocations", {
+        params: {
+            query: {
+                limit,
+                offset,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                user_id: userStore.currentUser.id,
+                workflow_id: workflowId,
+            },
+        },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     fetchHistories(data);
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/pages.ts b/client/src/components/Grid/configs/pages.ts
index 4aa803d0d6c1b57fee4b5898158de53b9f1ac46a..4de599a2ddec4c9baeac08662143c6b2646e91f2 100644
--- a/client/src/components/Grid/configs/pages.ts
+++ b/client/src/components/Grid/configs/pages.ts
@@ -1,22 +1,15 @@
 import { faEdit, faEye, faPen, faPlus, faShareAlt, faTrash, faTrashRestore } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, equals, toBool, type ValidFilter } from "@/utils/filtering";
 import _l from "@/utils/localization";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
-/**
- * Api endpoint handlers
- */
-const getPages = fetcher.path("/api/pages").method("get").create();
-const deletePage = fetcher.path("/api/pages/{id}").method("delete").create();
-const undeletePage = fetcher.path("/api/pages/{id}/undelete").method("put").create();
-
 /**
  * Local types
  */
@@ -27,17 +20,26 @@ type PageEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await getPages({
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_published: false,
-        show_own: true,
-        show_shared: false,
+    const { response, data, error } = await GalaxyApi().GET("/api/pages", {
+        params: {
+            query: {
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                show_published: false,
+                show_own: true,
+                show_shared: false,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
@@ -101,18 +103,23 @@ const fields: FieldArray = [
                 condition: (data: PageEntry) => !data.deleted,
                 handler: async (data: PageEntry) => {
                     if (confirm(_l(`Are you sure that you want to delete the selected page?`))) {
-                        try {
-                            await deletePage({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.title}' has been deleted.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().DELETE("/api/pages/{id}", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to delete '${data.title}': ${errorMessageAsString(e)}.`,
+                                message: `Failed to delete '${data.title}': ${errorMessageAsString(error)}.`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.title}' has been deleted.`,
+                        };
                     }
                 },
             },
@@ -122,18 +129,23 @@ const fields: FieldArray = [
                 condition: (data: PageEntry) => !!data.deleted,
                 handler: async (data: PageEntry) => {
                     if (confirm(_l(`Are you sure that you want to restore the selected page?`))) {
-                        try {
-                            await undeletePage({ id: String(data.id) });
-                            return {
-                                status: "success",
-                                message: `'${data.title}' has been restored.`,
-                            };
-                        } catch (e) {
+                        const { error } = await GalaxyApi().PUT("/api/pages/{id}/undelete", {
+                            params: {
+                                path: { id: String(data.id) },
+                            },
+                        });
+
+                        if (error) {
                             return {
                                 status: "danger",
-                                message: `Failed to restore '${data.title}': ${errorMessageAsString(e)}.`,
+                                message: `Failed to restore '${data.title}': ${errorMessageAsString(error)}.`,
                             };
                         }
+
+                        return {
+                            status: "success",
+                            message: `'${data.title}' has been restored.`,
+                        };
                     }
                 },
             },
diff --git a/client/src/components/Grid/configs/pagesPublished.ts b/client/src/components/Grid/configs/pagesPublished.ts
index 615eb9c316961fb9fbaa155acd76c20295ef4484..b76c42d0cbdb9952dd195fbda37f4cb1afca3e04 100644
--- a/client/src/components/Grid/configs/pagesPublished.ts
+++ b/client/src/components/Grid/configs/pagesPublished.ts
@@ -1,18 +1,14 @@
 import { faEye, faPlus } from "@fortawesome/free-solid-svg-icons";
 import { useEventBus } from "@vueuse/core";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, type ValidFilter } from "@/utils/filtering";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
-/**
- * Api endpoint handlers
- */
-const getPages = fetcher.path("/api/pages").method("get").create();
-
 /**
  * Local types
  */
@@ -23,17 +19,26 @@ type PageEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await getPages({
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_own: false,
-        show_published: true,
-        show_shared: true,
+    const { response, data, error } = await GalaxyApi().GET("/api/pages", {
+        params: {
+            query: {
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                show_own: false,
+                show_published: true,
+                show_shared: true,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/types.ts b/client/src/components/Grid/configs/types.ts
index 01c60be4228ff291df9acb81478ab9830d2d7238..613d019294b936a397f0d81cfc737669621c3a34 100644
--- a/client/src/components/Grid/configs/types.ts
+++ b/client/src/components/Grid/configs/types.ts
@@ -1,7 +1,7 @@
-import { IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
 
-import type { GalaxyConfiguration } from "@/stores/configurationStore";
-import Filtering from "@/utils/filtering";
+import { type GalaxyConfiguration } from "@/stores/configurationStore";
+import type Filtering from "@/utils/filtering";
 
 export interface Action {
     title: string;
diff --git a/client/src/components/Grid/configs/visualizations.ts b/client/src/components/Grid/configs/visualizations.ts
index 08d657b89dbd1a483205069440d8c403076de96b..e688aae6e42a64d8e1a95c8e759fd9f386135319 100644
--- a/client/src/components/Grid/configs/visualizations.ts
+++ b/client/src/components/Grid/configs/visualizations.ts
@@ -2,21 +2,16 @@ import { faCopy, faEdit, faEye, faPlus, faShareAlt, faTrash, faTrashRestore } fr
 import { useEventBus } from "@vueuse/core";
 import axios from "axios";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import { updateTags } from "@/api/tags";
 import Filtering, { contains, equals, expandNameTag, toBool, type ValidFilter } from "@/utils/filtering";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
-import type { ActionArray, FieldArray, GridConfig } from "./types";
+import { type ActionArray, type FieldArray, type GridConfig } from "./types";
 
 const { emit } = useEventBus<string>("grid-router-push");
 
-/**
- * Api endpoint handlers
- */
-const getVisualizations = fetcher.path("/api/visualizations").method("get").create();
-
 /**
  * Local types
  */
@@ -27,17 +22,26 @@ type VisualizationEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await getVisualizations({
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_published: false,
-        show_own: true,
-        show_shared: false,
+    const { response, data, error } = await GalaxyApi().GET("/api/visualizations", {
+        params: {
+            query: {
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                show_published: false,
+                show_own: true,
+                show_shared: false,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Grid/configs/visualizationsPublished.ts b/client/src/components/Grid/configs/visualizationsPublished.ts
index b8888ffeb53502a32a0ccc871e51f7c6b7faad69..c4642247376d7da9bc3dd452539289192a240779 100644
--- a/client/src/components/Grid/configs/visualizationsPublished.ts
+++ b/client/src/components/Grid/configs/visualizationsPublished.ts
@@ -1,15 +1,11 @@
 import { faEye } from "@fortawesome/free-solid-svg-icons";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import Filtering, { contains, expandNameTag, type ValidFilter } from "@/utils/filtering";
 import { withPrefix } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import type { FieldArray, GridConfig } from "./types";
-
-/**
- * Api endpoint handlers
- */
-const getVisualizations = fetcher.path("/api/visualizations").method("get").create();
+import { type FieldArray, type GridConfig } from "./types";
 
 /**
  * Local types
@@ -21,17 +17,26 @@ type VisualizationEntry = Record<string, unknown>;
  * Request and return data from server
  */
 async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) {
-    const { data, headers } = await getVisualizations({
-        limit,
-        offset,
-        search,
-        sort_by: sort_by as SortKeyLiteral,
-        sort_desc,
-        show_own: false,
-        show_published: true,
-        show_shared: true,
+    const { response, data, error } = await GalaxyApi().GET("/api/visualizations", {
+        params: {
+            query: {
+                limit,
+                offset,
+                search,
+                sort_by: sort_by as SortKeyLiteral,
+                sort_desc,
+                show_own: false,
+                show_published: true,
+                show_shared: true,
+            },
+        },
     });
-    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("total_matches") ?? "0");
     return [data, totalMatches];
 }
 
diff --git a/client/src/components/Help/HelpPopover.vue b/client/src/components/Help/HelpPopover.vue
new file mode 100644
index 0000000000000000000000000000000000000000..200f76706a2b72df8fa5b2168d93dfa9be9fc0fc
--- /dev/null
+++ b/client/src/components/Help/HelpPopover.vue
@@ -0,0 +1,18 @@
+<script setup lang="ts">
+import { BPopover } from "bootstrap-vue";
+
+import HelpTerm from "./HelpTerm.vue";
+
+interface Props {
+    target: any;
+    term: string;
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <BPopover v-if="target" :target="target" triggers="hover" placement="bottom">
+        <HelpTerm :term="term" />
+    </BPopover>
+</template>
diff --git a/client/src/components/Help/HelpTerm.vue b/client/src/components/Help/HelpTerm.vue
new file mode 100644
index 0000000000000000000000000000000000000000..92db6966591d4413ec6945a672946b3214d8fa01
--- /dev/null
+++ b/client/src/components/Help/HelpTerm.vue
@@ -0,0 +1,31 @@
+<script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
+import { toRef } from "vue";
+
+import { useHelpForTerm } from "@/stores/helpTermsStore";
+
+import LoadingSpan from "@/components/LoadingSpan.vue";
+import ConfigurationMarkdown from "@/components/ObjectStore/ConfigurationMarkdown.vue";
+
+interface Props {
+    term: string;
+}
+
+const props = defineProps<Props>();
+
+const { loading, hasHelp, help } = useHelpForTerm(toRef(props, "term"));
+</script>
+
+<template>
+    <div>
+        <div v-if="loading">
+            <LoadingSpan message="Loading Galaxy help terms" />
+        </div>
+        <div v-else-if="hasHelp">
+            <ConfigurationMarkdown :markdown="help" :admin="true" />
+        </div>
+        <div v-else>
+            <BAlert variant="error"> Something went wrong, no Galaxy help found for term or URI {{ term }}. </BAlert>
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Help/HelpText.vue b/client/src/components/Help/HelpText.vue
index f3f1b4740af18e8a1bf0df2d4a3e82945e9ee5c0..bfd54ed79b61368b47f3b1a824e6b373926098bb 100644
--- a/client/src/components/Help/HelpText.vue
+++ b/client/src/components/Help/HelpText.vue
@@ -1,41 +1,27 @@
 <script setup lang="ts">
-import { computed } from "vue";
-
-import { hasHelp as hasHelpText, help as helpText } from "./terms";
-
-import ConfigurationMarkdown from "@/components/ObjectStore/ConfigurationMarkdown.vue";
+import HelpPopover from "./HelpPopover.vue";
 
 interface Props {
     uri: string;
     text: string;
+    forTitle?: boolean;
 }
 
-const props = defineProps<Props>();
-
-const hasHelp = computed<boolean>(() => {
-    return hasHelpText(props.uri);
-});
-
-const help = computed<string>(() => {
-    return helpText(props.uri) as string;
+withDefaults(defineProps<Props>(), {
+    forTitle: false,
 });
 </script>
 
 <template>
     <span>
-        <b-popover
-            v-if="hasHelp"
+        <HelpPopover
             :target="
                 () => {
                     return $refs.helpTarget;
                 }
             "
-            triggers="hover"
-            placement="bottom">
-            <ConfigurationMarkdown :markdown="help" :admin="true" />
-        </b-popover>
-        <span v-if="hasHelp" ref="helpTarget" class="help-text">{{ text }}</span>
-        <span v-else>{{ text }}</span>
+            :term="uri" />
+        <span ref="helpTarget" class="help-text" :class="{ 'title-help-text': forTitle }">{{ text }}</span>
     </span>
 </template>
 
@@ -45,4 +31,7 @@ const help = computed<string>(() => {
     text-decoration-line: underline;
     text-decoration-style: dashed;
 }
+.title-help-text {
+    text-decoration-thickness: 1px;
+}
 </style>
diff --git a/client/src/components/Help/terms.yml b/client/src/components/Help/terms.yml
index a6df4b852a638fb19eb38d4a2687ca710837c2c5..6ebb0f0f07be8017f803551be5d5fc662e7ed72e 100644
--- a/client/src/components/Help/terms.yml
+++ b/client/src/components/Help/terms.yml
@@ -27,9 +27,77 @@ unix:
     debug what is wrong with the execution of an application.
 
     More information on stack traces can be found on [Wikipedia](https://en.wikipedia.org/wiki/Stack_trace).
+programming:
+  python:
+    regex: |
+      Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in [this Python for Biologists tutorial](https://pythonforbiologists.com/tutorial/regex.html).
 
+      The website [regex101](https://regex101.com/) is a useful playground to explore regular expressions (be sure to enable "Python" as your flavor) and language models such as ChatGPT can help interactively build up and explain regular expressions from natural language prompts or examples.
 galaxy:
+  collections:
+    flatList: |
+      A flat list is just a simple dataset collection of type ``list`` that contains only datasets and not
+      other collections.
+    mapOver: |
+      When a tool consumes a dataset but is run with a collection, the collection *maps over* the collection.
+      This means instead of just running the tool once - the tool will be run once for each element of the
+      provided collection. Additionally, the outputs of the tool will be collected into a collection that
+      matches the structure of the provided collection. This matching structure means the output collections
+      will have the same element identifiers as the provided collection and they will appear in the same order.
+
+      It is easiest to visualize "mapping over" a collection is in the context of a tool that consumes a dataset
+      and produces a dataset, but the semantics apply rather naturally to tools that consume collections or
+      produce collections as well.
+      
+      For instance, consider a tool that consumes a ``paired`` collection and produces an output dataset.
+      If a list of paired collections (collection type ``list:paired``) is passed to the tool - it will
+      will produce a flat list (collection type ``list``) of output datasets with the same number of elements
+      in the same order as the provided list of ``paired`` collections.
+
+      In the case of outputs, consider a tool that takes in a dataset and produces a flat list. If this tool
+      is run over a flat list of datasets - that list will be "mapped over" and each element will produce a list.
+      These lists will be gathered together in a nested list structured (collection type ``list:list``) where
+      the outer element count and structure matches that of the input and the inner list for each of those
+      is just the outputs of the tool for the corresponding element of the input.
+    collectionBuilder:
+      hideOriginalElements: |
+        Toggling this on means that the original history items that will become a part of the collection
+        will be hidden from the history panel (they will still be searchable via the 'visible: false' filter).
+      filteredExtensions: |
+        The history is filtered for the formats that are required for this collection. You might see some
+        items with other formats since those can still be valid inputs via implicit conversion.
+      requiredUploadExtensions: |
+        The formats that are required for this collection. The files you upload will be assumed to have
+        these formats. In the case of more than one format, you can select a specific format for
+        each individual file above. If there is only one format, Galaxy will attempt to set that as the
+        format for each file.
+      whyHomogenousCollections: |
+        Dataset collections are designed to streamline the analysis of large numbers of datasets by grouping
+        them together into a single, manageable entity. Unlike generic folders on your computer, which can hold
+        any mix of file types, dataset collections are specifically intended to be homogenous. This homogeneity
+        is crucial for consistency in processing. Homogeneous datasets ensure that each dataset in the collection
+        can be processed uniformly with the same tools and workflows. This eliminates the need for individual
+        adjustments, which can be time-consuming and prone to error. Most tools and workflows in Galaxy are designed
+        to operate on collections of similar data types. Homogeneous collections allow these tools to operate
+        uniformly over the collection.
+
   jobs:
+    metrics:
+      cores: |
+        This is how many [cores](https://en.wikipedia.org/wiki/Central_processing_unit) (or distinct central processing units (CPUs)) are
+        allocated to run the job for the tool. This value is generally configured for the tool by the Galaxy administrator. This value
+        does not guarantee how many cores the job actually used - the job may have used more and less based on how Galaxy is configured
+        and how the tool is programmed.
+
+      walltime: |
+        This is estimate of the length of time the job ran created by recording the start and stop of the job in the job script
+        created for the tool execution and subtracting these values. 
+
+      allocated_core_time: |
+        This is the number of cores Galaxy believes is allocated for the job times the estimated walltime for the job. This can be thought
+        of as scaling the runtime/walltime metric by the number of cores allocated - when purchasing compute time per core hour or consuming
+        compute time from a compute center's allocation - this is likely to be a more interesting and useful number than the walltime.
+
     states:
       # upload, waiting, failed, paused, deleting, deleted, stop, stopped, skipped.
       ok: |
@@ -57,7 +125,7 @@ galaxy:
   invocations:
     states:
       scheduled: |
-        This state indicates the workflow invocation has had all of its job scheduled. This means all the
+        This state indicates the workflow invocation has had all of its jobs scheduled. This means all the
         datasets are likely created and Galaxy has created the stubs for the jobs in the workflow. *The jobs
         themselves might not have been queued or running.*
 
@@ -81,3 +149,26 @@ galaxy:
       failed: |
         This state indicates there was a problem scheduling the workflow invocation. No additional datasets
         or jobs will be created for this workflow invocation.
+  upload:
+    galaxyUploadUtil: |
+      A utility for uploading files to a Galaxy server from the command line. Use ``galaxy-upload`` to upload
+      file(s) to a Galaxy server, and ``galaxy-history-search``, a helper utility to find Galaxy histories
+      to pass to the ``galaxy-upload`` command.
+    ruleBased: |
+      Galaxy can bulk import lists & tables of URLs into datasets or collections using reproducible rules.
+  
+  datasets:
+    formatVsDatatypeVsExtension: |
+      In Galaxy, the terms "datatype," "format," and "extension" are used to describe the nature of a dataset,
+      each with specific meanings.
+      
+      The ``datatype`` defines how a dataset is interpreted, validated, and processed, such as "fastqsanger", "bam",
+      or "vcf". Each datatype corresponds to a Python class that specifies how Galaxy should handle the file.
+      
+      The ``format`` is the user-facing label for the dataset's datatype, appearing in the Galaxy user interface
+      to indicate the structure and content expectations of the dataset.
+      
+      The ``extension`` is a string associated with each datatype, stored in Galaxy’s database to identify the
+      dataset’s datatype. This extension can match a file’s actual disk suffix (e.g., ".vcf") but may also be more
+      specialized (e.g., "fastqsanger"). Understanding these distinctions ensures that datasets are processed
+      correctly within Galaxy, maintaining the integrity and reproducibility of analyses.
diff --git a/client/src/components/History/Archiving/ArchivedHistoryCard.vue b/client/src/components/History/Archiving/ArchivedHistoryCard.vue
index 15ca422fce17eacdc067684e549dba170112d173..3bd2a66dbca3ea9dffe584d0445197fa72ef1bf2 100644
--- a/client/src/components/History/Archiving/ArchivedHistoryCard.vue
+++ b/client/src/components/History/Archiving/ArchivedHistoryCard.vue
@@ -5,7 +5,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton, BButtonGroup } from "bootstrap-vue";
 import { computed } from "vue";
 
-import { ArchivedHistorySummary } from "@/api/histories.archived";
+import { type ArchivedHistorySummary } from "@/api/histories.archived";
 import localize from "@/utils/localization";
 
 import ExportRecordDOILink from "@/components/Common/ExportRecordDOILink.vue";
diff --git a/client/src/components/History/Archiving/HistoryArchive.vue b/client/src/components/History/Archiving/HistoryArchive.vue
index 24c3cd4ed417cf5e3d46a1092b86ab9fb27c95fe..7db329b99c4d6f849a6ea3be8e47e2556a2e31da 100644
--- a/client/src/components/History/Archiving/HistoryArchive.vue
+++ b/client/src/components/History/Archiving/HistoryArchive.vue
@@ -3,15 +3,13 @@ import { BAlert, BListGroup, BListGroupItem, BPagination } from "bootstrap-vue";
 import { computed, onMounted, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import {
-    ArchivedHistorySummary,
-    fetchArchivedHistories,
-    reimportArchivedHistoryFromExportRecord,
-} from "@/api/histories.archived";
+import { GalaxyApi } from "@/api";
+import { type ArchivedHistorySummary, fetchArchivedHistories } from "@/api/histories.archived";
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { useToast } from "@/composables/toast";
 import { useHistoryStore } from "@/stores/historyStore";
 import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import DelayedInput from "@/components/Common/DelayedInput.vue";
 import ArchivedHistoryCard from "@/components/History/Archiving/ArchivedHistoryCard.vue";
@@ -50,16 +48,24 @@ async function updateSearchQuery(query: string) {
 
 async function loadArchivedHistories() {
     isLoading.value = true;
-    const result = await fetchArchivedHistories({
-        query: searchText.value,
-        currentPage: currentPage.value,
-        pageSize: perPage.value,
-        sortBy: sortBy.value,
-        sortDesc: sortDesc.value,
-    });
-    totalRows.value = result.totalMatches;
-    archivedHistories.value = result.histories;
-    isLoading.value = false;
+    try {
+        const result = await fetchArchivedHistories({
+            query: searchText.value,
+            currentPage: currentPage.value,
+            pageSize: perPage.value,
+            sortBy: sortBy.value,
+            sortDesc: sortDesc.value,
+        });
+        totalRows.value = result.totalMatches;
+        archivedHistories.value = result.histories;
+    } catch (error) {
+        toast.error(
+            localize(`Failed to load archived histories with reason: ${errorMessageAsString(error)}`),
+            localize("Loading Failed")
+        );
+    } finally {
+        isLoading.value = false;
+    }
 }
 
 function onViewHistoryInCenterPanel(history: ArchivedHistorySummary) {
@@ -110,27 +116,42 @@ async function onImportCopy(history: ArchivedHistorySummary) {
         return;
     }
 
-    try {
-        await reimportArchivedHistoryFromExportRecord(history);
-        toast.success(
-            localize(
-                `The History '${history.name}' it's being imported. This process may take a while. Check your histories list after a few minutes.`
-            ),
-            localize("Importing History in background...")
+    if (!history.export_record_data) {
+        toast.error(
+            localize(`Failed to import history '${history.name}' because it does not have an export record.`),
+            localize("History Import Failed")
         );
-    } catch (error) {
+        return;
+    }
+
+    const { error } = await GalaxyApi().POST("/api/histories/from_store_async", {
+        body: {
+            model_store_format: history.export_record_data?.model_store_format,
+            store_content_uri: history.export_record_data?.target_uri,
+        },
+    });
+
+    if (error) {
         toast.error(
             localize(`Failed to import history '${history.name}' with reason: ${error}`),
             localize("History Import Failed")
         );
+        return;
     }
+
+    toast.success(
+        localize(
+            `The History '${history.name}' it's being imported. This process may take a while. Check your histories list after a few minutes.`
+        ),
+        localize("Importing History in background...")
+    );
 }
 </script>
 <template>
     <section id="archived-histories" class="d-flex flex-column">
         <div>
             <DelayedInput
-                :query="searchText"
+                :value="searchText"
                 class="m-1 mb-3"
                 placeholder="search by name"
                 @change="updateSearchQuery" />
diff --git a/client/src/components/History/Archiving/HistoryArchiveExportSelector.test.ts b/client/src/components/History/Archiving/HistoryArchiveExportSelector.test.ts
index 715482d64ef5b831129aee1f7970d8b24b81f3ae..0ad5de646db3c41ce5fb4cb25ee4c1f7b4c070b7 100644
--- a/client/src/components/History/Archiving/HistoryArchiveExportSelector.test.ts
+++ b/client/src/components/History/Archiving/HistoryArchiveExportSelector.test.ts
@@ -1,12 +1,10 @@
 import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import { BFormCheckbox } from "bootstrap-vue";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import type { HistorySummary } from "@/api";
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { type HistorySummary, type ObjectExportTaskResponse } from "@/api";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
 import {
     FAILED_FILE_SOURCE_STORE_RESPONSE,
     FILE_SOURCE_STORE_RESPONSE,
@@ -17,8 +15,6 @@ import {
 
 import HistoryArchiveExportSelector from "./HistoryArchiveExportSelector.vue";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue(true);
 
 const TEST_HISTORY_ID = "test-history-id";
@@ -28,8 +24,6 @@ const TEST_HISTORY = {
     archived: false,
 };
 
-const GET_EXPORTS_API_ENDPOINT = "/api/histories/{history_id}/exports";
-
 const EXPORT_RECORD_BTN = "#create-export-record-btn";
 const ARCHIVE_HISTORY_BTN = "#archive-history-btn";
 const CONFIRM_DELETE_CHECKBOX = "[type='checkbox']";
@@ -47,19 +41,26 @@ async function mountComponentWithHistory(history: HistorySummary) {
     return wrapper;
 }
 
-describe("HistoryArchiveExportSelector.vue", () => {
-    let axiosMock: MockAdapter;
-
-    beforeEach(async () => {
-        axiosMock = new MockAdapter(axios);
-    });
-
-    afterEach(() => {
-        axiosMock.restore();
-    });
+const { server, http } = useServerMock();
+
+function mockGetExportsApiResponse(taskExportResponse: ObjectExportTaskResponse[]) {
+    server.use(
+        http.get("/api/histories/{history_id}/exports", ({ response }) => {
+            // We need to use the untyped version of the response here because the typed version does not support the
+            // content-type "application/vnd.galaxy.task.export+json" that is returned by the server.
+            return response.untyped(
+                HttpResponse.json(taskExportResponse, {
+                    status: 200,
+                    headers: { "Content-Type": "application/vnd.galaxy.task.export+json" },
+                })
+            );
+        })
+    );
+}
 
+describe("HistoryArchiveExportSelector.vue", () => {
     it("should display a button to create an export record if there is no up to date export record", async () => {
-        mockFetcher.path(GET_EXPORTS_API_ENDPOINT).method("get").mock({ data: [] });
+        mockGetExportsApiResponse([]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -68,10 +69,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should display a button to create an export record if the most recent export record is not permanent", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [RECENT_STS_DOWNLOAD_RESPONSE] });
+        mockGetExportsApiResponse([RECENT_STS_DOWNLOAD_RESPONSE]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -80,10 +78,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should display a button to create an export record if there are permanent export records but none are up to date", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [FILE_SOURCE_STORE_RESPONSE, FAILED_FILE_SOURCE_STORE_RESPONSE] });
+        mockGetExportsApiResponse([FILE_SOURCE_STORE_RESPONSE, FAILED_FILE_SOURCE_STORE_RESPONSE]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -92,10 +87,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should not display a button to create an export record if there is an up to date export record", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [RECENT_FILE_SOURCE_STORE_RESPONSE] });
+        mockGetExportsApiResponse([RECENT_FILE_SOURCE_STORE_RESPONSE]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -104,10 +96,12 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should not display a button to create an export record if a record is being created", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [IN_PROGRESS_FILE_SOURCE_STORE_RESPONSE] });
+        mockGetExportsApiResponse([IN_PROGRESS_FILE_SOURCE_STORE_RESPONSE]);
+        server.use(
+            http.get("/api/tasks/{task_id}/state", ({ response }) => {
+                return response(200).json("PENDING");
+            })
+        );
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -116,7 +110,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should disable the Archive button if there is no up to date export record", async () => {
-        mockFetcher.path(GET_EXPORTS_API_ENDPOINT).method("get").mock({ data: [] });
+        mockGetExportsApiResponse([]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -125,10 +119,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should disable the Archive button if the confirm delete checkbox is not checked", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [RECENT_FILE_SOURCE_STORE_RESPONSE] });
+        mockGetExportsApiResponse([RECENT_FILE_SOURCE_STORE_RESPONSE]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
@@ -141,10 +132,7 @@ describe("HistoryArchiveExportSelector.vue", () => {
     });
 
     it("should enable the Archive button if there is an up to date export record and the confirm delete checkbox is checked", async () => {
-        mockFetcher
-            .path(GET_EXPORTS_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [RECENT_FILE_SOURCE_STORE_RESPONSE] });
+        mockGetExportsApiResponse([RECENT_FILE_SOURCE_STORE_RESPONSE]);
 
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
diff --git a/client/src/components/History/Archiving/HistoryArchiveWizard.test.ts b/client/src/components/History/Archiving/HistoryArchiveWizard.test.ts
index 83e5015db61b5a070598f57c39f008a6923e788f..2d1d05adc5274f0529e2f4c3e43e0c611b365154 100644
--- a/client/src/components/History/Archiving/HistoryArchiveWizard.test.ts
+++ b/client/src/components/History/Archiving/HistoryArchiveWizard.test.ts
@@ -4,14 +4,12 @@ import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import type { HistorySummary } from "@/api";
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { type HistorySummary } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
 import { useHistoryStore } from "@/stores/historyStore";
 
 import HistoryArchiveWizard from "./HistoryArchiveWizard.vue";
 
-jest.mock("@/api/schema");
-
 jest.mock("@/composables/config", () => ({
     useConfig: jest.fn(() => ({
         config: {
@@ -24,6 +22,8 @@ jest.mock("@/composables/config", () => ({
 
 const localVue = getLocalVue(true);
 
+const { server, http } = useServerMock();
+
 const TEST_HISTORY_ID = "test-history-id";
 const TEST_HISTORY = {
     id: TEST_HISTORY_ID,
@@ -36,8 +36,6 @@ const ARCHIVED_TEST_HISTORY = {
     archived: true,
 };
 
-const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
-
 async function mountComponentWithHistory(history?: HistorySummary) {
     const pinia = createTestingPinia({ stubActions: false });
     setActivePinia(pinia);
@@ -58,7 +56,11 @@ async function mountComponentWithHistory(history?: HistorySummary) {
 
 describe("HistoryArchiveWizard.vue", () => {
     beforeEach(async () => {
-        mockFetcher.path(REMOTE_FILES_API_ENDPOINT).method("get").mock({ data: [] });
+        server.use(
+            http.get("/api/remote_files/plugins", ({ response }) => {
+                return response(200).json([]);
+            })
+        );
     });
 
     it("should render the history name in the header", async () => {
@@ -76,11 +78,9 @@ describe("HistoryArchiveWizard.vue", () => {
     });
 
     it("should render both archival modes when writeable file sources and celery tasks are available", async () => {
-        mockFetcher
-            .path(REMOTE_FILES_API_ENDPOINT)
-            .method("get")
-            .mock({
-                data: [
+        server.use(
+            http.get("/api/remote_files/plugins", ({ response }) => {
+                return response(200).json([
                     {
                         id: "test-posix-source",
                         type: "posix",
@@ -88,11 +88,17 @@ describe("HistoryArchiveWizard.vue", () => {
                         label: "TestSource",
                         doc: "For testing",
                         writable: true,
-                        requires_roles: undefined,
-                        requires_groups: undefined,
+                        browsable: true,
+                        supports: {
+                            pagination: false,
+                            search: false,
+                            sorting: false,
+                        },
                     },
-                ],
-            });
+                ]);
+            })
+        );
+
         const wrapper = await mountComponentWithHistory(TEST_HISTORY as HistorySummary);
 
         const optionTabs = wrapper.findAll(".archival-option-tabs");
diff --git a/client/src/components/History/Content/Collection/CollectionProgress.vue b/client/src/components/History/Content/Collection/CollectionProgress.vue
index 37265ec91dd6a4868dbc93f9a4c791cd0d70d8a8..61a080d73d7a615f8f103b3ba5c355b9f98e73c1 100644
--- a/client/src/components/History/Content/Collection/CollectionProgress.vue
+++ b/client/src/components/History/Content/Collection/CollectionProgress.vue
@@ -2,7 +2,7 @@
 at components/JobStates/CollectionJobStates but it relies on the backbone data
 model, so probably has to go eventually.-->
 <script setup lang="ts">
-import { JobStateSummary } from "./JobStateSummary";
+import { type JobStateSummary } from "./JobStateSummary";
 
 interface Props {
     summary: JobStateSummary;
diff --git a/client/src/components/History/Content/ContentItem.test.js b/client/src/components/History/Content/ContentItem.test.js
index 269df341756c9f67eac52eeb2c2adbd7f449a454..d606d5ffc3eab65ef2aaf67a2859f77d672e1831 100644
--- a/client/src/components/History/Content/ContentItem.test.js
+++ b/client/src/components/History/Content/ContentItem.test.js
@@ -1,16 +1,18 @@
 import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
-import { updateContentFields } from "components/History/model/queries";
 import { PiniaVuePlugin } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 import VueRouter from "vue-router";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
+import { updateContentFields } from "@/components/History/model/queries";
 
-import ContentItem from "./ContentItem";
+import ContentItem from "./ContentItem.vue";
 
 jest.mock("components/History/model/queries");
 
+const { server, http } = useServerMock();
+
 const localVue = getLocalVue();
 localVue.use(VueRouter);
 localVue.use(PiniaVuePlugin);
@@ -36,7 +38,14 @@ describe("ContentItem", () => {
     let wrapper;
 
     beforeEach(() => {
-        mockFetcher.path("/api/datasets/{dataset_id}").method("get").mock({ data: item });
+        server.use(
+            http.get("/api/datasets/{dataset_id}", ({ response }) => {
+                // We need to use untyped here because this endpoint is not
+                // described in the OpenAPI spec due to its complexity for now.
+                return response.untyped(HttpResponse.json(item));
+            })
+        );
+
         wrapper = mount(ContentItem, {
             propsData: {
                 expandDataset: true,
diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index 071f1f4dd6536a0845ff5eae98fa926a7ba5d208..f167e7fa6e1b3a1e200bb024267d2bebb1eb11fd 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -1,7 +1,13 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
-import { faArrowCircleDown, faArrowCircleUp, faCheckCircle, faSpinner } from "@fortawesome/free-solid-svg-icons";
+import {
+    faArrowCircleDown,
+    faArrowCircleUp,
+    faCheckCircle,
+    faExchangeAlt,
+    faSpinner,
+} from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton, BCollapse } from "bootstrap-vue";
 import { computed, ref } from "vue";
@@ -14,14 +20,14 @@ import { useEventStore } from "@/stores/eventStore";
 import { clearDrag } from "@/utils/setDrag";
 
 import { JobStateSummary } from "./Collection/JobStateSummary";
-import { HIERARCHICAL_COLLECTION_JOB_STATES, type StateMap, STATES } from "./model/states";
+import { getContentItemState, type StateMap, STATES } from "./model/states";
 
 import CollectionDescription from "./Collection/CollectionDescription.vue";
 import ContentOptions from "./ContentOptions.vue";
 import DatasetDetails from "./Dataset/DatasetDetails.vue";
 import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
 
-library.add(faArrowCircleUp, faArrowCircleDown, faCheckCircle, faSpinner);
+library.add(faArrowCircleUp, faArrowCircleDown, faCheckCircle, faExchangeAlt, faSpinner);
 
 const router = useRouter();
 const route = useRoute();
@@ -41,6 +47,7 @@ interface Props {
     selectable?: boolean;
     filterable?: boolean;
     isPlaceholder?: boolean;
+    isSubItem?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -55,6 +62,7 @@ const props = withDefaults(defineProps<Props>(), {
     selectable: false,
     filterable: false,
     isPlaceholder: false,
+    isSubItem: false,
 });
 
 const emit = defineEmits<{
@@ -80,6 +88,7 @@ const entryPointStore = useEntryPointStore();
 const eventStore = useEventStore();
 
 const contentItem = ref<HTMLElement | null>(null);
+const subItemsVisible = ref(false);
 
 const jobState = computed(() => {
     return new JobStateSummary(props.item);
@@ -101,6 +110,15 @@ const contentCls = computed(() => {
         return `alert-${status}`;
     }
 });
+const computedClass = computed(() => {
+    return {
+        "content-item m-1 p-0 rounded btn-transparent-background": true,
+        [contentCls.value]: true,
+        "being-used": Object.values(itemUrls.value).includes(route.path),
+        "range-select-anchor": props.isRangeSelectAnchor,
+        "sub-item": props.isSubItem,
+    };
+});
 const contentState = computed(() => {
     return STATES[state.value] && STATES[state.value];
 });
@@ -117,28 +135,10 @@ const state = computed<keyof StateMap>(() => {
     if (props.isPlaceholder) {
         return "placeholder";
     }
-    if (props.item.accessible === false) {
-        return "inaccessible";
-    }
-    if (props.item.populated_state === "failed") {
-        return "failed_populated_state";
-    }
-    if (props.item.populated_state === "new") {
-        return "new_populated_state";
-    }
     if (props.isDataset && props.item.stopped) {
         return "stopped"
     }
-    if (props.item.job_state_summary) {
-        for (const jobState of HIERARCHICAL_COLLECTION_JOB_STATES) {
-            if (props.item.job_state_summary[jobState] > 0) {
-                return jobState;
-            }
-        }
-    } else if (props.item.state) {
-        return props.item.state;
-    }
-    return "ok";
+    return getContentItemState(props.item);
 });
 
 const dataState = computed(() => {
@@ -184,14 +184,6 @@ const itemUrls = computed<ItemUrls>(() => {
     };
 });
 
-const isBeingUsed = computed(() => {
-    return Object.values(itemUrls.value).includes(route.path) ? "being-used" : "";
-});
-
-const rangeSelectClass = computed(() => {
-    return props.isRangeSelectAnchor ? "range-select-anchor" : "";
-});
-
 /** Based on the user's keyboard platform, checks if it is the
  * typical key for selection (ctrl for windows/linux, cmd for mac)
  */
@@ -200,7 +192,8 @@ function isSelectKey(event: KeyboardEvent) {
 }
 
 function onKeyDown(event: KeyboardEvent) {
-    if (!(event.target as HTMLElement)?.classList?.contains("content-item")) {
+    const classList = (event.target as HTMLElement)?.classList;
+    if (!classList.contains("content-item") || classList.contains("sub-item")) {
         return;
     }
 
@@ -342,12 +335,12 @@ function unexpandedClick(event: Event) {
     <div
         :id="contentId"
         ref="contentItem"
-        :class="['content-item m-1 p-0 rounded btn-transparent-background', contentCls, isBeingUsed, rangeSelectClass]"
+        :class="computedClass"
         :data-hid="id"
         :data-state="dataState"
         tabindex="0"
         role="button"
-        :draggable="props.item.accessible === false ? false : true"
+        :draggable="props.item.accessible === false || props.isSubItem || subItemsVisible ? false : true"
         @dragstart="onDragStart"
         @dragend="onDragEnd"
         @keydown="onKeyDown">
@@ -397,26 +390,39 @@ function unexpandedClick(event: Event) {
                     <span class="id hid">{{ id }}:</span>
                     <span class="content-title name font-weight-bold">{{ name }}</span>
                 </span>
-                <span v-if="item.purged" class="align-self-start btn-group p-1">
+                <span v-if="item.purged" class="ml-auto align-self-start btn-group p-1">
                     <BBadge variant="secondary" title="This dataset has been permanently deleted">
                         <icon icon="burn" /> Purged
                     </BBadge>
                 </span>
-                <ContentOptions
-                    v-if="!isPlaceholder && !item.purged"
-                    :writable="writable"
-                    :is-dataset="isDataset"
-                    :is-deleted="item.deleted"
-                    :is-history-item="isHistoryItem"
-                    :is-visible="item.visible"
-                    :state="state"
-                    :item-urls="itemUrls"
-                    @delete="onDelete"
-                    @display="onDisplay"
-                    @showCollectionInfo="onShowCollectionInfo"
-                    @edit="onEdit"
-                    @undelete="onUndelete"
-                    @unhide="emit('unhide')" />
+                <span class="align-self-start btn-group">
+                    <BButton
+                        v-if="item.sub_items?.length && !isSubItem"
+                        title="Show converted items"
+                        tabindex="0"
+                        class="display-btn px-1 align-items-center"
+                        size="sm"
+                        variant="link"
+                        @click.prevent.stop="subItemsVisible = !subItemsVisible">
+                        <FontAwesomeIcon :icon="faExchangeAlt" />
+                        <span class="indicator">{{ item.sub_items?.length }}</span>
+                    </BButton>
+                    <ContentOptions
+                        v-if="!isPlaceholder && !item.purged"
+                        :writable="writable"
+                        :is-dataset="isDataset"
+                        :is-deleted="item.deleted"
+                        :is-history-item="isHistoryItem"
+                        :is-visible="item.visible"
+                        :state="state"
+                        :item-urls="itemUrls"
+                        @delete="onDelete"
+                        @display="onDisplay"
+                        @showCollectionInfo="onShowCollectionInfo"
+                        @edit="onEdit"
+                        @undelete="onUndelete"
+                        @unhide="emit('unhide')" />
+                </span>
             </div>
         </div>
         <!-- eslint-disable-next-line vuejs-accessibility/click-events-have-key-events, vuejs-accessibility/no-static-element-interactions -->
@@ -451,6 +457,7 @@ function unexpandedClick(event: Event) {
                 @edit="onEdit"
                 @toggleHighlights="toggleHighlights" />
         </BCollapse>
+        <slot name="sub_items" :sub-items-visible="subItemsVisible" />
     </div>
 </template>
 
@@ -465,6 +472,18 @@ function unexpandedClick(event: Event) {
         word-break: break-all;
     }
 
+    .indicator {
+        align-items: center;
+        border-radius: 50%;
+        color: $brand-primary;
+        display: flex;
+        justify-content: center;
+        height: 1.2rem;
+        position: absolute;
+        top: -0.3rem;
+        width: 1.2rem;
+    }
+
     // improve focus visibility
     &:deep(.btn:focus) {
         box-shadow: 0 0 0 0.2rem transparentize($brand-primary, 0.75);
diff --git a/client/src/components/History/Content/Dataset/DatasetActions.vue b/client/src/components/History/Content/Dataset/DatasetActions.vue
index af4235a593eb390bf53f35ce299e61c7650cec96..14169535a71ea02b7728714c7c6de4d44141a5ad 100644
--- a/client/src/components/History/Content/Dataset/DatasetActions.vue
+++ b/client/src/components/History/Content/Dataset/DatasetActions.vue
@@ -48,7 +48,7 @@ const showRerun = computed(() => {
 });
 const showVisualizations = computed(() => {
     // TODO: Check hasViz, if visualizations are activated in the config
-    return !props.item.purged && ["ok", "failed_metadata", "error"].includes(props.item.state);
+    return !props.item.purged && ["ok", "failed_metadata", "error", "deferred"].includes(props.item.state);
 });
 const reportErrorUrl = computed(() => {
     return prependPath(props.itemUrls.reportError!);
diff --git a/client/src/components/History/Content/Dataset/DatasetDownload.test.ts b/client/src/components/History/Content/Dataset/DatasetDownload.test.ts
index 2a1f1127e582ad6093bb66abc4bad4938d5d696f..f70377e6ad578e79a587009fceebd0fb3615ed5d 100644
--- a/client/src/components/History/Content/Dataset/DatasetDownload.test.ts
+++ b/client/src/components/History/Content/Dataset/DatasetDownload.test.ts
@@ -1,6 +1,6 @@
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
-import Vue from "vue";
+import { mount, type Wrapper } from "@vue/test-utils";
+import type Vue from "vue";
 
 import DatasetDownload from "./DatasetDownload.vue";
 
diff --git a/client/src/components/History/Content/GenericElement.vue b/client/src/components/History/Content/GenericElement.vue
index 8438d9db31225514e2bdfd20554948d9a90aef17..8643be275e0ebc96d030d32527aed659c53c8304 100644
--- a/client/src/components/History/Content/GenericElement.vue
+++ b/client/src/components/History/Content/GenericElement.vue
@@ -1,8 +1,7 @@
 <script setup lang="ts">
-import type { PropType } from "vue";
-import Vue, { ref } from "vue";
+import { type PropType, ref, set } from "vue";
 
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 import ContentItem from "./ContentItem.vue";
 
@@ -17,7 +16,7 @@ const expandCollections = ref({});
 const expandDatasets = ref({});
 
 function toggle(expansionMap: Record<string, boolean>, itemId: string) {
-    Vue.set(expansionMap, itemId, !expansionMap[itemId]);
+    set(expansionMap, itemId, !expansionMap[itemId]);
 }
 </script>
 
diff --git a/client/src/components/History/Content/model/stateTypes.d.ts b/client/src/components/History/Content/model/stateTypes.d.ts
index 368690474bd92dbb290c8ee336d6978bc999c90e..0562390f55575b8889e0b338698faab4c00075f1 100644
--- a/client/src/components/History/Content/model/stateTypes.d.ts
+++ b/client/src/components/History/Content/model/stateTypes.d.ts
@@ -1,4 +1,4 @@
-import { STATES } from "./states";
+import { type STATES } from "./states";
 
 export type State = {
     status: string;
diff --git a/client/src/components/History/Content/model/states.ts b/client/src/components/History/Content/model/states.ts
index 6dc021ef96a7a02867ae6a3b51220c7b6beb7728..2901ac635e2bcc1705a72eccbd484cda56985eed 100644
--- a/client/src/components/History/Content/model/states.ts
+++ b/client/src/components/History/Content/model/states.ts
@@ -1,4 +1,5 @@
-import type { components } from "@/api/schema";
+import { isHDCA } from "@/api";
+import { type components } from "@/api/schema";
 
 type DatasetState = components["schemas"]["DatasetState"];
 // The 'failed' state is for the collection job state summary, not a dataset state.
@@ -106,8 +107,8 @@ export const STATES: StateMap = {
     },
     /** the job has been manually stopped */
     stopped: {
-        text: "This job was stopped manually.",
         status: "stopped",
+        text: "This job was stopped manually.",
         icon: "stop-circle",
     },
     /** the dataset is not yet loaded in the UI. This state is only visual and transitional, it does not exist in the database. */
@@ -152,3 +153,26 @@ export const HIERARCHICAL_COLLECTION_JOB_STATES = [
     "queued",
     "new",
 ] as const;
+
+export function getContentItemState(item: any) {
+    if (isHDCA(item)) {
+        if (item.populated_state === "failed") {
+            return "failed_populated_state";
+        }
+        if (item.populated_state === "new") {
+            return "new_populated_state";
+        }
+        if (item.job_state_summary) {
+            for (const jobState of HIERARCHICAL_COLLECTION_JOB_STATES) {
+                if (item.job_state_summary[jobState] > 0) {
+                    return jobState;
+                }
+            }
+        }
+    } else if (item.accessible === false) {
+        return "inaccessible";
+    } else if (item.state) {
+        return item.state;
+    }
+    return "ok";
+}
diff --git a/client/src/components/History/CurrentCollection/CollectionOperations.vue b/client/src/components/History/CurrentCollection/CollectionOperations.vue
index c8c20b4bef5f63b58429991f126aecda2301e3dc..144c35e468e19ae203481a46640e9c92cd4a88b1 100644
--- a/client/src/components/History/CurrentCollection/CollectionOperations.vue
+++ b/client/src/components/History/CurrentCollection/CollectionOperations.vue
@@ -2,7 +2,7 @@
 import { computed } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { HDCADetailed } from "@/api";
+import { type HDCADetailed } from "@/api";
 import { getAppRoot } from "@/onload/loadConfig";
 
 const router = useRouter();
diff --git a/client/src/components/History/CurrentCollection/CollectionPanel.vue b/client/src/components/History/CurrentCollection/CollectionPanel.vue
index 825ba5a5baa5d94c3f5f93b2e7b3d7f8f21485db..70d13794a00228c48bfb8e4e02233dd8ebb56270 100644
--- a/client/src/components/History/CurrentCollection/CollectionPanel.vue
+++ b/client/src/components/History/CurrentCollection/CollectionPanel.vue
@@ -8,10 +8,13 @@ import { canMutateHistory, isCollectionElement, isHDCA } from "@/api";
 import ExpandedItems from "@/components/History/Content/ExpandedItems";
 import { updateContentFields } from "@/components/History/model/queries";
 import { useCollectionElementsStore } from "@/stores/collectionElementsStore";
+import { setItemDragstart } from "@/utils/setDrag";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import CollectionDetails from "./CollectionDetails.vue";
 import CollectionNavigation from "./CollectionNavigation.vue";
 import CollectionOperations from "./CollectionOperations.vue";
+import Alert from "@/components/Alert.vue";
 import ContentItem from "@/components/History/Content/ContentItem.vue";
 import ListingLayout from "@/components/History/Layout/ListingLayout.vue";
 
@@ -54,6 +57,7 @@ watch(
 
 const collectionElements = computed(() => collectionElementsStore.getCollectionElements(dsc.value) ?? []);
 const loading = computed(() => collectionElementsStore.isLoadingCollectionElements(dsc.value));
+const error = computed(() => collectionElementsStore.getLoadingCollectionElementsError(dsc.value));
 const jobState = computed(() => ("job_state_summary" in dsc.value ? dsc.value.job_state_summary : undefined));
 const populatedStateMsg = computed(() =>
     "populated_state_message" in dsc.value ? dsc.value.populated_state_message : undefined
@@ -68,12 +72,14 @@ const rootCollection = computed(() => {
 const isRoot = computed(() => dsc.value == rootCollection.value);
 const canEdit = computed(() => isRoot.value && canMutateHistory(props.history));
 
-function updateDsc(collection: any, fields: Object | undefined) {
-    updateContentFields(collection, fields).then((response) => {
-        Object.keys(response).forEach((key) => {
-            collection[key] = response[key];
-        });
-    });
+async function updateDsc(collection: CollectionEntry, fields: Object | undefined) {
+    if (!isHDCA(collection)) {
+        return;
+    }
+    const updatedCollection = await updateContentFields(collection, fields);
+    // Update only editable fields
+    collection.name = updatedCollection.name || collection.name;
+    collection.tags = updatedCollection.tags || collection.tags;
 }
 
 function getItemKey(item: DCESummary) {
@@ -118,7 +124,10 @@ watch(
 </script>
 
 <template>
-    <ExpandedItems v-slot="{ isExpanded, setExpanded }" :scope-key="dsc.id" :get-item-key="getItemKey">
+    <Alert v-if="error" variant="error">
+        {{ errorMessageAsString(error) }}
+    </Alert>
+    <ExpandedItems v-else v-slot="{ isExpanded, setExpanded }" :scope-key="dsc.id" :get-item-key="getItemKey">
         <section class="dataset-collection-panel w-100 d-flex flex-column">
             <section>
                 <CollectionNavigation
@@ -158,6 +167,7 @@ watch(
                                 :expand-dataset="isExpanded(item)"
                                 :is-dataset="item.element_type == 'hda'"
                                 :filterable="filterable"
+                                @drag-start="setItemDragstart(item, $event)"
                                 @update:expand-dataset="setExpanded(item, $event)"
                                 @view-collection="onViewDatasetCollectionElement(item)" />
                         </template>
diff --git a/client/src/components/History/CurrentHistory/HistoryCounter.vue b/client/src/components/History/CurrentHistory/HistoryCounter.vue
index bdadcafe08da7d7532e06b98ee330ec05fcb66dc..038924f0a920f7b9eddf047e335b8305d89e877c 100644
--- a/client/src/components/History/CurrentHistory/HistoryCounter.vue
+++ b/client/src/components/History/CurrentHistory/HistoryCounter.vue
@@ -57,6 +57,9 @@ const showPreferredObjectStoreModal = ref(false);
 const historyPreferredObjectStoreId = ref(props.history.preferred_object_store_id);
 
 const niceHistorySize = computed(() => prettyBytes(historySize.value));
+const canManageStorage = computed(
+    () => userOwnsHistory(currentUser.value, props.history) && !currentUser.value?.isAnonymous
+);
 
 const storageLocationTitle = computed(() => {
     if (isOnlyPreference.value) {
@@ -137,7 +140,7 @@ onMounted(() => {
             variant="link"
             size="sm"
             class="rounded-0 text-decoration-none history-storage-overview-button"
-            :disabled="!userOwnsHistory(currentUser, props.history)"
+            :disabled="!canManageStorage"
             data-description="storage dashboard button"
             @click="onDashboard">
             <FontAwesomeIcon :icon="faDatabase" />
diff --git a/client/src/components/History/CurrentHistory/HistoryDetails.vue b/client/src/components/History/CurrentHistory/HistoryDetails.vue
index 52619647dd25a43be93d49ffffbb942759aa769a..0fa1c0d90f7e881b5d8a8bee8e4c6ace545a2e9a 100644
--- a/client/src/components/History/CurrentHistory/HistoryDetails.vue
+++ b/client/src/components/History/CurrentHistory/HistoryDetails.vue
@@ -1,22 +1,22 @@
 <script setup lang="ts">
-import { BBadge } from "bootstrap-vue";
-
 import type { HistorySummary } from "@/api";
 import { useHistoryStore } from "@/stores/historyStore";
 
+import type { DetailsLayoutSummarized } from "../Layout/types";
+
+import HistoryIndicators from "../HistoryIndicators.vue";
 import TextSummary from "@/components/Common/TextSummary.vue";
 import DetailsLayout from "@/components/History/Layout/DetailsLayout.vue";
-import UtcDate from "@/components/UtcDate.vue";
 
 interface Props {
     history: HistorySummary;
     writeable: boolean;
-    summarized: boolean;
+    summarized?: DetailsLayoutSummarized;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     writeable: true,
-    summarized: false,
+    summarized: undefined,
 });
 
 const historyStore = useHistoryStore();
@@ -49,10 +49,7 @@ function onSave(newDetails: HistorySummary) {
                 no-expand />
         </template>
         <template v-if="summarized" v-slot:update-time>
-            <BBadge v-b-tooltip pill>
-                <span v-localize>last edited </span>
-                <UtcDate v-if="history.update_time" :date="history.update_time" mode="elapsed" />
-            </BBadge>
+            <HistoryIndicators :history="history" detailed-time />
         </template>
     </DetailsLayout>
 </template>
diff --git a/client/src/components/History/CurrentHistory/HistoryMessages.vue b/client/src/components/History/CurrentHistory/HistoryMessages.vue
index ab5b6c1180ccb07087af4acdb274b6f0d8ff8694..f3c87772568e3b7c61a8095a6101e0a55ffc7be0 100644
--- a/client/src/components/History/CurrentHistory/HistoryMessages.vue
+++ b/client/src/components/History/CurrentHistory/HistoryMessages.vue
@@ -5,14 +5,14 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { type GenericUser, type HistorySummary, userOwnsHistory } from "@/api";
+import { type AnyUser, type HistorySummary, userOwnsHistory } from "@/api";
 import localize from "@/utils/localization";
 
 library.add(faArchive, faBurn, faTrash);
 
 interface Props {
     history: HistorySummary;
-    currentUser: GenericUser | null;
+    currentUser: AnyUser;
 }
 
 const props = defineProps<Props>();
@@ -32,7 +32,7 @@ const currentUserOwnsHistory = computed(() => {
     <div v-if="hasMessages" class="mx-3 mt-2" data-description="history messages">
         <BAlert v-if="history.purged" :show="history.purged" variant="warning">
             <FontAwesomeIcon :icon="faBurn" fixed-width />
-            {{ localize("History has been purged") }}
+            {{ localize("History has been permanently deleted") }}
         </BAlert>
         <BAlert v-else-if="history.deleted" :show="history.deleted" variant="warning">
             <FontAwesomeIcon :icon="faTrash" fixed-width />
diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 1dd671f0e6a0aae3b4a4a0e4ae1f620019ff430e..ef9dc11ae0c9c3dd0078368539201d806e5367c4 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -3,6 +3,7 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import {
     faArchive,
     faBars,
+    faBurn,
     faColumns,
     faCopy,
     faExchangeAlt,
@@ -18,6 +19,7 @@ import {
     faUserLock,
 } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import axios from "axios";
 import {
     BButton,
     BButtonGroup,
@@ -34,9 +36,12 @@ import { computed, ref } from "vue";
 
 import { canMutateHistory, type HistorySummary } from "@/api";
 import { iframeRedirect } from "@/components/plugins/legacyNavigation";
+import { useToast } from "@/composables/toast";
+import { getAppRoot } from "@/onload/loadConfig";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import CopyModal from "@/components/History/Modals/CopyModal.vue";
 import SelectorModal from "@/components/History/Modals/SelectorModal.vue";
@@ -44,6 +49,7 @@ import SelectorModal from "@/components/History/Modals/SelectorModal.vue";
 library.add(
     faArchive,
     faBars,
+    faBurn,
     faColumns,
     faCopy,
     faExchangeAlt,
@@ -62,18 +68,25 @@ library.add(
 interface Props {
     histories: HistorySummary[];
     history: HistorySummary;
-    title?: string;
     historiesLoading?: boolean;
+    minimal?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    title: "Histories",
     historiesLoading: false,
+    minimal: false,
 });
 
+// modal refs
 const showSwitchModal = ref(false);
+const showDeleteModal = ref(false);
+const showPrivacyModal = ref(false);
+const showCopyModal = ref(false);
+
 const purgeHistory = ref(false);
 
+const toast = useToast();
+
 const userStore = useUserStore();
 const historyStore = useHistoryStore();
 
@@ -84,6 +97,10 @@ const canEditHistory = computed(() => {
     return canMutateHistory(props.history);
 });
 
+const isDeletedNotPurged = computed(() => {
+    return props.history.deleted && !props.history.purged;
+});
+
 const historyState = computed(() => {
     if (props.history.purged) {
         return "purged";
@@ -111,15 +128,28 @@ function userTitle(title: string) {
         return localize(title);
     }
 }
+
+async function resumePausedJobs() {
+    const url = `${getAppRoot()}history/resume_paused_jobs?current=True`;
+    try {
+        const response = await axios.get(url);
+        toast.success(response.data.message);
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
 </script>
 
 <template>
     <div>
-        <nav class="d-flex justify-content-between mx-3 my-2" aria-label="current history management">
-            <h2 class="m-1 h-sm">History</h2>
+        <nav
+            :class="{ 'd-flex justify-content-between mx-3 my-2': !props.minimal }"
+            aria-label="current history management">
+            <h2 v-if="!props.minimal" class="m-1 h-sm">History</h2>
 
             <BButtonGroup>
                 <BButton
+                    v-if="!props.minimal"
                     v-b-tooltip.top.hover.noninteractive
                     class="create-hist-btn"
                     data-description="create new history"
@@ -132,6 +162,7 @@ function userTitle(title: string) {
                 </BButton>
 
                 <BButton
+                    v-if="!props.minimal"
                     v-b-tooltip.top.hover.noninteractive
                     data-description="switch to another history"
                     size="sm"
@@ -146,10 +177,11 @@ function userTitle(title: string) {
                     v-b-tooltip.top.hover.noninteractive
                     no-caret
                     size="sm"
-                    variant="link"
+                    :variant="props.minimal ? 'outline-info' : 'link'"
                     toggle-class="text-decoration-none"
                     menu-class="history-options-button-menu"
                     title="History options"
+                    right
                     data-description="history options">
                     <template v-slot:button-content>
                         <FontAwesomeIcon fixed-width :icon="faBars" />
@@ -162,10 +194,12 @@ function userTitle(title: string) {
                             <span>Fetching histories from server</span>
                         </div>
 
-                        <span v-else>You have {{ totalHistoryCount }} histories.</span>
+                        <span v-else-if="!props.minimal">You have {{ totalHistoryCount }} histories.</span>
+                        <span v-else>Manage History</span>
                     </BDropdownText>
 
                     <BDropdownItem
+                        v-if="!props.minimal"
                         data-description="switch to multi history view"
                         :disabled="isAnonymous"
                         :title="userTitle('Open History Multiview')"
@@ -174,7 +208,7 @@ function userTitle(title: string) {
                         <span v-localize>Show Histories Side-by-Side</span>
                     </BDropdownItem>
 
-                    <BDropdownDivider />
+                    <BDropdownDivider v-if="!props.minimal" />
 
                     <BDropdownText v-if="!canEditHistory">
                         This history has been <span class="font-weight-bold">{{ historyState }}</span
@@ -187,7 +221,7 @@ function userTitle(title: string) {
                     <BDropdownItem
                         :disabled="!canEditHistory"
                         :title="localize('Resume all Paused Jobs in this History')"
-                        @click="iframeRedirect('/history/resume_paused_jobs?current=True')">
+                        @click="resumePausedJobs()">
                         <FontAwesomeIcon fixed-width :icon="faPlay" class="mr-1" />
                         <span v-localize>Resume Paused Jobs</span>
                     </BDropdownItem>
@@ -195,19 +229,20 @@ function userTitle(title: string) {
                     <BDropdownDivider />
 
                     <BDropdownItem
-                        v-b-modal:copy-current-history-modal
                         :disabled="isAnonymous"
-                        :title="userTitle('Copy History to a New History')">
+                        :title="userTitle('Copy History to a New History')"
+                        @click="showCopyModal = !showCopyModal">
                         <FontAwesomeIcon fixed-width :icon="faCopy" class="mr-1" />
                         <span v-localize>Copy this History</span>
                     </BDropdownItem>
 
                     <BDropdownItem
-                        v-b-modal:delete-history-modal
                         :disabled="!canEditHistory"
-                        :title="localize('Permanently Delete History')">
-                        <FontAwesomeIcon fixed-width :icon="faTrash" class="mr-1" />
-                        <span v-localize>Delete this History</span>
+                        :title="localize(isDeletedNotPurged ? 'Permanently Delete History' : 'Delete History')"
+                        @click="showDeleteModal = !showDeleteModal">
+                        <FontAwesomeIcon fixed-width :icon="isDeletedNotPurged ? faBurn : faTrash" class="mr-1" />
+                        <span v-if="isDeletedNotPurged" v-localize>Permanently Delete History</span>
+                        <span v-else v-localize>Delete this History</span>
                     </BDropdownItem>
 
                     <BDropdownItem
@@ -271,9 +306,9 @@ function userTitle(title: string) {
                     </BDropdownItem>
 
                     <BDropdownItem
-                        v-b-modal:history-privacy-modal
                         :disabled="isAnonymous || !canEditHistory"
-                        :title="userTitle('Make this History Private')">
+                        :title="userTitle('Make this History Private')"
+                        @click="showPrivacyModal = !showPrivacyModal">
                         <FontAwesomeIcon fixed-width :icon="faLock" class="mr-1" />
                         <span v-localize>Make Private</span>
                     </BDropdownItem>
@@ -282,6 +317,7 @@ function userTitle(title: string) {
         </nav>
 
         <SelectorModal
+            v-if="!props.minimal"
             v-show="showSwitchModal"
             id="selector-history-modal"
             :histories="histories"
@@ -289,13 +325,19 @@ function userTitle(title: string) {
             :show-modal.sync="showSwitchModal"
             @selectHistory="historyStore.setCurrentHistory($event.id)" />
 
-        <CopyModal id="copy-current-history-modal" :history="history" />
+        <CopyModal :history="history" :show-modal.sync="showCopyModal" />
 
         <BModal
-            id="history-privacy-modal"
+            v-model="showPrivacyModal"
             title="Make History Private"
             title-tag="h2"
             @ok="historyStore.secureHistory(history)">
+            <h4>
+                History:
+                <b>
+                    <i>{{ history.name }}</i>
+                </b>
+            </h4>
             <p v-localize>
                 This will make all the data in this history private (excluding library datasets), and will set
                 permissions such that all new data is created as private. Any datasets within that are currently shared
@@ -304,15 +346,15 @@ function userTitle(title: string) {
         </BModal>
 
         <BModal
-            id="delete-history-modal"
-            title="Delete History?"
+            v-model="showDeleteModal"
+            :title="isDeletedNotPurged ? 'Permanently Delete History?' : 'Delete History?'"
             title-tag="h2"
             @ok="onDelete"
-            @show="purgeHistory = false">
+            @show="purgeHistory = isDeletedNotPurged">
             <p v-localize>
                 Do you also want to permanently delete the history <i class="ml-1">{{ history.name }}</i>
             </p>
-            <BFormCheckbox id="purge-history" v-model="purgeHistory">
+            <BFormCheckbox id="purge-history" v-model="purgeHistory" :disabled="isDeletedNotPurged">
                 <span v-localize>Yes, permanently delete this history.</span>
             </BFormCheckbox>
         </BModal>
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/DefaultOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/DefaultOperations.vue
index 07bb357e4c3a44b6628aa39944e3a508982473fa..c7c4350e617fc9b7cbed1ea63b60b5ec9139417b 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/DefaultOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/DefaultOperations.vue
@@ -5,7 +5,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BDropdown, BDropdownItem, BDropdownText, BModal } from "bootstrap-vue";
 import { toRef } from "vue";
 
-import type { HistorySummary, HistorySummaryExtended } from "@/api";
+import { type HistorySummaryExtended } from "@/api";
 import {
     deleteAllHiddenContent,
     purgeAllDeletedContent,
@@ -42,7 +42,7 @@ function purgeAllDeleted() {
     runOperation(() => purgeAllDeletedContent(props.history));
 }
 
-async function runOperation(operation: () => Promise<HistorySummary>) {
+async function runOperation(operation: () => Promise<unknown>) {
     emit("update:operation-running", props.history.update_time);
     await operation();
     emit("update:operation-running", props.history.update_time);
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/HistoryOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/HistoryOperations.vue
index 4ae704e4b8fa2cc654bd7f025868fdd7ce63e2bc..a9e593631b7b45fab384ba68508e00b9016e7f86 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/HistoryOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/HistoryOperations.vue
@@ -12,6 +12,7 @@ library.add(faCheckSquare, faCompress);
 interface Props {
     history: HistorySummaryExtended;
     hasMatches: boolean;
+    editable: boolean;
     expandedCount: number;
     showSelection: boolean;
     isMultiViewItem: boolean;
@@ -32,7 +33,7 @@ function onUpdateOperationStatus(updateTime: number) {
 
 <template>
     <section>
-        <nav class="content-operations d-flex justify-content-between bg-secondary">
+        <nav v-if="editable" class="content-operations d-flex justify-content-between bg-secondary">
             <BButtonGroup>
                 <BButton
                     title="Select Items"
@@ -66,6 +67,17 @@ function onUpdateOperationStatus(updateTime: number) {
                 :history="history"
                 @update:operation-running="onUpdateOperationStatus" />
         </nav>
+        <nav v-else-if="isMultiViewItem" class="content-operations bg-secondary">
+            <BButton
+                title="Collapse Items"
+                class="rounded-0"
+                size="sm"
+                variant="link"
+                :disabled="!expandedCount"
+                @click="$emit('collapse-all')">
+                <FontAwesomeIcon :icon="faCompress" fixed-width />
+            </BButton>
+        </nav>
     </section>
 </template>
 
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
index cfb3c17149bb4846df234f4b8efa994648b7ca14..3f1d7c8a468f2bc7a21288983a78339c71611963 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionChangeWarning.vue
@@ -31,7 +31,7 @@ function onDoNotShowAgain() {
 watch(
     () => props.querySelectionBreak,
     () => {
-        dismissCountDown.value = showSelectionQueryBreakWarning ? dismissSecs.value : 0;
+        dismissCountDown.value = showSelectionQueryBreakWarning.value ? dismissSecs.value : 0;
     }
 );
 </script>
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.test.js b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.test.js
index 468321e1a7253cc061fd896f993e038edb6c7891..de5c632e5b2e6bed5362440c51d4a22226ebab00 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.test.js
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.test.js
@@ -1,26 +1,19 @@
 import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
 
 import SelectionOperations from "./SelectionOperations.vue";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue();
 
+const { server, http } = useServerMock();
+
 const FAKE_HISTORY_ID = "fake_history_id";
 const FAKE_HISTORY = { id: FAKE_HISTORY_ID, update_time: new Date() };
-const BULK_OPERATIONS_ENDPOINT = new RegExp(`/api/histories/${FAKE_HISTORY_ID}/contents/bulk`);
 const BULK_SUCCESS_RESPONSE = { success_count: 1, errors: [] };
-const BULK_ERROR_RESPONSE = {
-    success_count: 0,
-    errors: [{ error: "Error reason", item: { history_content_type: "dataset", id: "dataset_id" } }],
-};
 
 const NO_TASKS_CONFIG = {
     enable_celery_tasks: false,
@@ -39,7 +32,12 @@ const getDeletedSelection = () => new Map([["FAKE_ID", { deleted: true }]]);
 const getActiveSelection = () => new Map([["FAKE_ID", { deleted: false }]]);
 
 async function mountSelectionOperationsWrapper(config) {
-    mockFetcher.path("/api/configuration").method("get").mock({ data: config });
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json(config);
+        })
+    );
+
     const pinia = createPinia();
     const wrapper = shallowMount(SelectionOperations, {
         propsData: {
@@ -49,6 +47,7 @@ async function mountSelectionOperationsWrapper(config) {
             selectionSize: 1,
             isQuerySelection: false,
             totalItemsInQuery: 5,
+            isMultiViewItem: false,
         },
         localVue,
         pinia,
@@ -58,20 +57,14 @@ async function mountSelectionOperationsWrapper(config) {
 }
 
 describe("History Selection Operations", () => {
-    let axiosMock;
     let wrapper;
 
     describe("With Celery Enabled", () => {
         beforeEach(async () => {
-            axiosMock = new MockAdapter(axios);
             wrapper = await mountSelectionOperationsWrapper(TASKS_CONFIG);
             await flushPromises();
         });
 
-        afterEach(() => {
-            axiosMock.restore();
-        });
-
         describe("Dropdown Menu", () => {
             it("should not render if there is nothing selected", async () => {
                 await wrapper.setProps({ selectionSize: 0 });
@@ -218,23 +211,18 @@ describe("History Selection Operations", () => {
 
             it("should display collection building options only on active (non-deleted) items", async () => {
                 const buildListOption = '[data-description="build list"]';
-                const buildPairOption = '[data-description="build pair"]';
                 const buildListOfPairsOption = '[data-description="build list of pairs"]';
                 await wrapper.setProps({ filterText: "visible:true deleted:false" });
                 expect(wrapper.find(buildListOption).exists()).toBe(true);
-                expect(wrapper.find(buildPairOption).exists()).toBe(true);
                 expect(wrapper.find(buildListOfPairsOption).exists()).toBe(true);
                 await wrapper.setProps({ filterText: "deleted:true" });
                 expect(wrapper.find(buildListOption).exists()).toBe(false);
-                expect(wrapper.find(buildPairOption).exists()).toBe(false);
                 expect(wrapper.find(buildListOfPairsOption).exists()).toBe(false);
                 await wrapper.setProps({ filterText: "visible:any deleted:false" });
                 expect(wrapper.find(buildListOption).exists()).toBe(true);
-                expect(wrapper.find(buildPairOption).exists()).toBe(true);
                 expect(wrapper.find(buildListOfPairsOption).exists()).toBe(true);
                 await wrapper.setProps({ filterText: "deleted:any" });
                 expect(wrapper.find(buildListOption).exists()).toBe(false);
-                expect(wrapper.find(buildPairOption).exists()).toBe(false);
                 expect(wrapper.find(buildListOfPairsOption).exists()).toBe(false);
             });
 
@@ -249,7 +237,11 @@ describe("History Selection Operations", () => {
 
         describe("Operation Run", () => {
             it("should emit event to disable selection", async () => {
-                axiosMock.onPut(BULK_OPERATIONS_ENDPOINT).reply(200, BULK_SUCCESS_RESPONSE);
+                server.use(
+                    http.put("/api/histories/{history_id}/contents/bulk", ({ response }) => {
+                        return response(200).json(BULK_SUCCESS_RESPONSE);
+                    })
+                );
 
                 expect(wrapper.emitted()).not.toHaveProperty("update:show-selection");
                 wrapper.vm.hideSelected();
@@ -259,7 +251,11 @@ describe("History Selection Operations", () => {
             });
 
             it("should update operation-running state when running any operation that succeeds", async () => {
-                axiosMock.onPut(BULK_OPERATIONS_ENDPOINT).reply(200, BULK_SUCCESS_RESPONSE);
+                server.use(
+                    http.put("/api/histories/{history_id}/contents/bulk", ({ response }) => {
+                        return response(200).json(BULK_SUCCESS_RESPONSE);
+                    })
+                );
 
                 expect(wrapper.emitted()).not.toHaveProperty("update:operation-running");
                 wrapper.vm.hideSelected();
@@ -273,7 +269,11 @@ describe("History Selection Operations", () => {
             });
 
             it("should update operation-running state to null when the operation fails", async () => {
-                axiosMock.onPut(BULK_OPERATIONS_ENDPOINT).reply(400);
+                server.use(
+                    http.put("/api/histories/{history_id}/contents/bulk", ({ response }) => {
+                        return response("4XX").json({ err_msg: "Error", err_code: 400 }, { status: 400 });
+                    })
+                );
 
                 expect(wrapper.emitted()).not.toHaveProperty("update:operation-running");
                 wrapper.vm.hideSelected();
@@ -290,7 +290,11 @@ describe("History Selection Operations", () => {
             });
 
             it("should emit operation error event when the operation fails", async () => {
-                axiosMock.onPut(BULK_OPERATIONS_ENDPOINT).reply(400);
+                server.use(
+                    http.put("/api/histories/{history_id}/contents/bulk", ({ response }) => {
+                        return response("4XX").json({ err_msg: "Error", err_code: 400 }, { status: 400 });
+                    })
+                );
 
                 expect(wrapper.emitted()).not.toHaveProperty("operation-error");
                 wrapper.vm.hideSelected();
@@ -299,7 +303,15 @@ describe("History Selection Operations", () => {
             });
 
             it("should emit operation error event with the result when any item fail", async () => {
-                axiosMock.onPut(BULK_OPERATIONS_ENDPOINT).reply(200, BULK_ERROR_RESPONSE);
+                const BULK_ERROR_RESPONSE = {
+                    success_count: 0,
+                    errors: [{ error: "Error reason", item: { history_content_type: "dataset", id: "dataset_id" } }],
+                };
+                server.use(
+                    http.put("/api/histories/{history_id}/contents/bulk", ({ response }) => {
+                        return response(200).json(BULK_ERROR_RESPONSE);
+                    })
+                );
 
                 expect(wrapper.emitted()).not.toHaveProperty("operation-error");
                 wrapper.vm.hideSelected();
@@ -317,15 +329,10 @@ describe("History Selection Operations", () => {
 
     describe("With Celery Disabled", () => {
         beforeEach(async () => {
-            axiosMock = new MockAdapter(axios);
             wrapper = await mountSelectionOperationsWrapper(NO_TASKS_CONFIG);
             await flushPromises();
         });
 
-        afterEach(() => {
-            axiosMock.restore();
-        });
-
         describe("Dropdown Menu", () => {
             it("should hide `Change data type` option", async () => {
                 const option = '[data-description="change data type"]';
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
index 59076e8063af090ec896723a990d21747af49687..d36a3fb0d59da01251dd593673d53195cb56fa59 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
@@ -37,9 +37,6 @@
             <b-dropdown-item v-if="showBuildOptions" data-description="build list" @click="buildDatasetList">
                 <span v-localize>Build Dataset List</span>
             </b-dropdown-item>
-            <b-dropdown-item v-if="showBuildOptions" data-description="build pair" @click="buildDatasetPair">
-                <span v-localize>Build Dataset Pair</span>
-            </b-dropdown-item>
             <b-dropdown-item v-if="showBuildOptions" data-description="build list of pairs" @click="buildListOfPairs">
                 <span v-localize>Build List of Dataset Pairs</span>
             </b-dropdown-item>
@@ -102,7 +99,7 @@
                     collection-name="Database/Builds"
                     :loading="loadingDbKeys"
                     :items="dbkeys"
-                    :current-item-id="selectedDbKey"
+                    :current-item="selectedDbKey"
                     @update:selected-item="onSelectedDbKey" />
             </DbKeyProvider>
         </b-modal>
@@ -119,7 +116,7 @@
                     collection-name="Data Types"
                     :loading="loadingDatatypes"
                     :items="datatypes"
-                    :current-item-id="selectedDatatype"
+                    :current-item="selectedDatatype"
                     @update:selected-item="onSelectedDatatype" />
             </DatatypesProvider>
         </b-modal>
@@ -141,11 +138,20 @@
             <p v-localize>Remove the following tags from {{ numSelected }} items:</p>
             <StatelessTags v-model="selectedTags" class="tags" />
         </b-modal>
+        <CollectionCreatorModal
+            v-if="collectionModalType"
+            :history-id="history.id"
+            :collection-type="collectionModalType"
+            :filter-text="filterText"
+            :selected-items="collectionSelection"
+            :show-modal.sync="collectionModalShow"
+            hide-modal-on-create
+            default-hide-source-items
+            @created-collection="createdCollection" />
     </section>
 </template>
 
 <script>
-import { buildCollectionModal } from "components/History/adapters/buildCollectionModal";
 import { HistoryFilters } from "components/History/HistoryFilters";
 import {
     addTagsToSelectedContent,
@@ -158,15 +164,20 @@ import {
     undeleteSelectedContent,
     unhideSelectedContent,
 } from "components/History/model/crud";
-import { createDatasetCollection, getHistoryContent } from "components/History/model/queries";
 import { DatatypesProvider, DbKeyProvider } from "components/providers";
 import SingleItemSelector from "components/SingleItemSelector";
 import { StatelessTags } from "components/Tags";
 
+import { createDatasetCollection } from "@/components/History/model/queries";
 import { useConfig } from "@/composables/config";
 
+import { buildRuleCollectionModal } from "../../adapters/buildCollectionModal";
+
+import CollectionCreatorModal from "@/components/Collections/CollectionCreatorModal.vue";
+
 export default {
     components: {
+        CollectionCreatorModal,
         DbKeyProvider,
         DatatypesProvider,
         SingleItemSelector,
@@ -187,8 +198,11 @@ export default {
     },
     data: function () {
         return {
-            selectedDbKey: "?",
-            selectedDatatype: "auto",
+            collectionModalShow: false,
+            collectionModalType: null,
+            collectionSelection: undefined,
+            selectedDbKey: { id: "?", text: "unspecified (?)" },
+            selectedDatatype: { id: "auto", text: "Auto-detect" },
             selectedTags: [],
         };
     },
@@ -308,12 +322,12 @@ export default {
             this.runOnSelection(purgeSelectedContent);
         },
         changeDbkeyOfSelected() {
-            this.runOnSelection(changeDbkeyOfSelectedContent, { dbkey: this.selectedDbKey });
-            this.selectedDbKey = "?";
+            this.runOnSelection(changeDbkeyOfSelectedContent, { dbkey: this.selectedDbKey.id });
+            this.selectedDbKey = { id: "?" };
         },
         changeDatatypeOfSelected() {
-            this.runOnSelection(changeDatatypeOfSelectedContent, { datatype: this.selectedDatatype });
-            this.selectedDatatype = "auto";
+            this.runOnSelection(changeDatatypeOfSelectedContent, { datatype: this.selectedDatatype.id });
+            this.selectedDatatype = { id: "auto", text: "Auto-detect" };
         },
         addTagsToSelected() {
             this.runOnSelection(addTagsToSelectedContent, { tags: this.selectedTags });
@@ -355,38 +369,33 @@ export default {
             this.$emit("operation-error", { errorMessage, result });
         },
         onSelectedDbKey(dbkey) {
-            this.selectedDbKey = dbkey.id;
+            this.selectedDbKey = dbkey;
         },
         onSelectedDatatype(datatype) {
-            this.selectedDatatype = datatype.id;
+            this.selectedDatatype = datatype;
         },
 
         // collection creation, fires up a modal
-        async buildDatasetList() {
-            await this.buildNewCollection("list");
-        },
-        async buildDatasetListAll() {
-            let allContents = [];
-            const filters = HistoryFilters.getQueryDict(this.filterText);
-
-            allContents = await getHistoryContent(this.history.id, filters, "dataset");
-
-            this.buildNewCollection("list", allContents);
-        },
-        async buildDatasetPair() {
-            await this.buildNewCollection("paired");
-        },
-        async buildListOfPairs() {
-            await this.buildNewCollection("list:paired");
+        buildDatasetList() {
+            this.collectionModalType = "list";
+            this.collectionSelection = Array.from(this.contentSelection.values());
+            this.collectionModalShow = true;
+        },
+        buildDatasetListAll() {
+            this.collectionModalType = "list";
+            this.collectionSelection = undefined;
+            this.collectionModalShow = true;
+        },
+        buildListOfPairs() {
+            this.collectionModalType = "list:paired";
+            this.collectionSelection = Array.from(this.contentSelection.values());
+            this.collectionModalShow = true;
+        },
+        createdCollection(collection) {
+            this.$emit("reset-selection");
         },
         async buildCollectionFromRules() {
-            await this.buildNewCollection("rules");
-        },
-        async buildNewCollection(collectionType, contents) {
-            if (contents === undefined) {
-                contents = this.contentSelection;
-            }
-            const modalResult = await buildCollectionModal(collectionType, contents, this.history.id);
+            const modalResult = await buildRuleCollectionModal(this.contentSelection, this.history.id);
             await createDatasetCollection(this.history, modalResult);
 
             // have to hide the source items if that was requested
@@ -402,5 +411,6 @@ export default {
 <style>
 .modal-with-selector {
     overflow: initial;
+    min-height: 300px; /* To make room for the selector */
 }
 </style>
diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionStatus.test.ts b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionStatus.test.ts
index 91ec80f8055db90493133c05483e01fae14f4d8b..d127185d0ae178a3a1beef26a5141518f9f9ae70 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionStatus.test.ts
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionStatus.test.ts
@@ -1,4 +1,4 @@
-import { shallowMount, Wrapper } from "@vue/test-utils";
+import { shallowMount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index ca6738f303dd16f0983abf8881aa0f04e920433f..0833312230d6483b25f74cdae7f15592cb1ae10b 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -3,21 +3,20 @@ import { BAlert } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, type Ref, ref, set as VueSet, unref, watch } from "vue";
 
-import { type HistoryItemSummary, type HistorySummaryExtended, isHistoryItem, userOwnsHistory } from "@/api";
-import { copyDataset } from "@/api/datasets";
+import { type HistoryItemSummary, type HistorySummaryExtended, userOwnsHistory } from "@/api";
 import ExpandedItems from "@/components/History/Content/ExpandedItems";
 import SelectedItems from "@/components/History/Content/SelectedItems";
 import { HistoryFilters } from "@/components/History/HistoryFilters";
 import { deleteContent, updateContentFields } from "@/components/History/model/queries";
-import { Toast } from "@/composables/toast";
 import { useActiveElement } from "@/composables/useActiveElement";
 import { startWatchingHistory } from "@/store/historyStore/model/watchHistory";
-import { useEventStore } from "@/stores/eventStore";
 import { useHistoryItemsStore } from "@/stores/historyItemsStore";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 import { type Alias, getOperatorForAlias } from "@/utils/filtering";
-import { setDrag } from "@/utils/setDrag";
+import { setItemDragstart } from "@/utils/setDrag";
+
+import { useHistoryDragDrop } from "../../../composables/historyDragDrop";
 
 import HistoryCounter from "./HistoryCounter.vue";
 import HistoryDetails from "./HistoryDetails.vue";
@@ -70,11 +69,9 @@ const isLoading = ref(false);
 const offsetQueryParam = ref(0);
 const searchError = ref<BackendFilterError | undefined>(undefined);
 const showAdvanced = ref(false);
-const showDropZone = ref(false);
 const operationRunning = ref<string | null>(null);
 const operationError = ref(null);
 const querySelectionBreak = ref(false);
-const dragTarget = ref<EventTarget | null>(null);
 const contentItemRefs = computed(() => {
     return historyItems.value.reduce((acc: ContentItemRef, item) => {
         acc[itemUniqueKey(item)] = ref(null);
@@ -84,13 +81,16 @@ const contentItemRefs = computed(() => {
 const currItemFocused = useActiveElement();
 const lastItemId = ref<string | null>(null);
 
-const { currentFilterText, currentHistoryId } = storeToRefs(useHistoryStore());
+const { currentFilterText, currentHistoryId, pinnedHistories, storedHistories } = storeToRefs(useHistoryStore());
 const { lastCheckedTime, totalMatchesCount, isWatching } = storeToRefs(useHistoryItemsStore());
 
 const historyStore = useHistoryStore();
 const historyItemsStore = useHistoryItemsStore();
 const { currentUser } = storeToRefs(useUserStore());
 
+const historyIdComputed = computed(() => props.history.id);
+const { showDropZone, onDragEnter, onDragLeave, onDragOver, onDrop } = useHistoryDragDrop(historyIdComputed);
+
 const currentUserOwnsHistory = computed(() => {
     return userOwnsHistory(currentUser.value, props.history);
 });
@@ -143,6 +143,47 @@ const formattedSearchError = computed(() => {
     };
 });
 
+/** Returns a string that indicates whether all the pinned histories have annotations,
+ * tags, both, or none of them.
+ * This is used to format the `DetailsLayout` header uniformly for multi-view histories.
+ */
+const detailsSummarized = computed(() => {
+    if (!props.isMultiViewItem) {
+        return undefined;
+    }
+    if (pinnedHistories.value.length === 0) {
+        return "hidden";
+    }
+
+    let annotation = false;
+    let tags = false;
+    let loaded = true;
+
+    for (const h of pinnedHistories.value) {
+        const history = storedHistories.value[h.id];
+        if (!history) {
+            loaded = false;
+            break;
+        }
+        if (history.annotation) {
+            annotation = true;
+        }
+        if (history.tags.length > 0) {
+            tags = true;
+        }
+    }
+
+    if (!loaded || (annotation && tags)) {
+        return "both";
+    } else if (annotation) {
+        return "annotation";
+    } else if (tags) {
+        return "tags";
+    } else {
+        return "none";
+    }
+});
+
 const storeFilterText = computed(() => {
     if (props.history.id !== currentHistoryId.value) {
         return "";
@@ -219,19 +260,6 @@ watch(
     }
 );
 
-function dragSameHistory() {
-    return getDragData().sameHistory;
-}
-
-function getDragData() {
-    const eventStore = useEventStore();
-    const dragItems = eventStore.getDragItems();
-    // Filter out any non-history items
-    const historyItems = dragItems?.filter((item: any) => isHistoryItem(item)) as HistoryItemSummary[];
-    const historyId = historyItems?.[0]?.history_id;
-    return { data: historyItems, sameHistory: historyId === props.history.id, multiple: historyItems?.length > 1 };
-}
-
 function getHighlight(item: HistoryItemSummary) {
     if (unref(isLoading)) {
         return undefined;
@@ -345,70 +373,6 @@ function onOperationError(error: any) {
     operationError.value = error;
 }
 
-function onDragEnter(e: DragEvent) {
-    if (dragSameHistory()) {
-        return;
-    }
-    dragTarget.value = e.target;
-    showDropZone.value = true;
-}
-
-function onDragOver(e: DragEvent) {
-    if (dragSameHistory()) {
-        return;
-    }
-    e.preventDefault();
-}
-
-function onDragLeave(e: DragEvent) {
-    if (dragSameHistory()) {
-        return;
-    }
-    if (dragTarget.value === e.target) {
-        showDropZone.value = false;
-    }
-}
-
-async function onDrop() {
-    showDropZone.value = false;
-    const { data, sameHistory, multiple } = getDragData();
-    if (!data || sameHistory) {
-        return;
-    }
-
-    let datasetCount = 0;
-    let collectionCount = 0;
-    try {
-        // iterate over the data array and copy each item to the current history
-        for (const item of data) {
-            const dataSource = item.history_content_type === "dataset" ? "hda" : "hdca";
-            await copyDataset(item.id, props.history.id, item.history_content_type, dataSource);
-
-            if (item.history_content_type === "dataset") {
-                datasetCount++;
-                if (!multiple) {
-                    Toast.info("Dataset copied to history");
-                }
-            } else {
-                collectionCount++;
-                if (!multiple) {
-                    Toast.info("Collection copied to history");
-                }
-            }
-        }
-
-        if (multiple && datasetCount > 0) {
-            Toast.info(`${datasetCount} dataset${datasetCount > 1 ? "s" : ""} copied to new history`);
-        }
-        if (multiple && collectionCount > 0) {
-            Toast.info(`${collectionCount} collection${collectionCount > 1 ? "s" : ""} copied to new history`);
-        }
-        historyStore.loadHistoryById(props.history.id);
-    } catch (error) {
-        Toast.error(`${error}`);
-    }
-}
-
 function updateFilterValue(filterKey: string, newValue: any) {
     const currentFilterText = filterText.value;
     filterText.value = filterClass.setFilterValue(currentFilterText, filterKey, newValue);
@@ -451,24 +415,6 @@ function arrowNavigate(item: HistoryItemSummary, eventKey: string) {
     }
     return nextItem;
 }
-
-function setItemDragstart(
-    item: HistoryItemSummary,
-    itemIsSelected: boolean,
-    selectedItems: Map<string, HistoryItemSummary>,
-    selectionSize: number,
-    event: DragEvent
-) {
-    if (itemIsSelected && selectionSize > 1) {
-        const selectedItemsObj: any = {};
-        for (const [key, value] of selectedItems) {
-            selectedItemsObj[key] = value;
-        }
-        setDrag(event, selectedItemsObj, true);
-    } else {
-        setDrag(event, item as any);
-    }
-}
 </script>
 
 <template>
@@ -523,10 +469,10 @@ function setItemDragstart(
                     <HistoryDetails
                         :history="history"
                         :writeable="canEditHistory"
-                        :summarized="isMultiViewItem"
+                        :summarized="detailsSummarized"
                         @update:history="historyStore.updateHistory($event)" />
 
-                    <HistoryMessages :history="history" :current-user="currentUser" />
+                    <HistoryMessages v-if="!isMultiViewItem" :history="history" :current-user="currentUser" />
 
                     <HistoryCounter
                         :history="history"
@@ -539,8 +485,8 @@ function setItemDragstart(
                         @reloadContents="reloadContents" />
 
                     <HistoryOperations
-                        v-if="canEditHistory"
                         :history="history"
+                        :editable="canEditHistory"
                         :is-multi-view-item="isMultiViewItem"
                         :show-selection="showSelection"
                         :expanded-count="expandedCount"
@@ -629,10 +575,10 @@ function setItemDragstart(
                                     @drag-start="
                                         setItemDragstart(
                                             item,
+                                            $event,
                                             showSelection && isSelected(item),
-                                            selectedItems,
                                             selectionSize,
-                                            $event
+                                            selectedItems
                                         )
                                     "
                                     @hide-selection="setShowSelection(false)"
@@ -650,7 +596,22 @@ function setItemDragstart(
                                     @view-collection="$emit('view-collection', item, currentOffset)"
                                     @delete="onDelete"
                                     @undelete="onUndelete(item)"
-                                    @unhide="onUnhide(item)" />
+                                    @unhide="onUnhide(item)">
+                                    <template v-slot:sub_items="slotProps">
+                                        <div v-if="slotProps.subItemsVisible" class="pl-2 sub-items-content">
+                                            <ContentItem
+                                                v-for="subItem in item.sub_items"
+                                                :id="subItem.hid"
+                                                :key="subItem.id"
+                                                :item="subItem"
+                                                :name="subItem.name"
+                                                :expand-dataset="isExpanded(subItem)"
+                                                :is-dataset="isDataset(subItem)"
+                                                :is-sub-item="true"
+                                                @update:expand-dataset="setExpanded(subItem, $event)" />
+                                        </div>
+                                    </template>
+                                </ContentItem>
                             </template>
                         </ListingLayout>
                     </div>
@@ -659,3 +620,11 @@ function setItemDragstart(
         </SelectedItems>
     </ExpandedItems>
 </template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+.sub-items-content {
+    background: $body-bg;
+}
+</style>
diff --git a/client/src/components/History/CurrentHistory/SelectPreferredStore.test.ts b/client/src/components/History/CurrentHistory/SelectPreferredStore.test.ts
index 6bb0b9c67506d13228c9b83a52361e07693b0246..7638ef43b9187f76d9edb07dc299ab9110ec85aa 100644
--- a/client/src/components/History/CurrentHistory/SelectPreferredStore.test.ts
+++ b/client/src/components/History/CurrentHistory/SelectPreferredStore.test.ts
@@ -4,12 +4,15 @@ import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useServerMock } from "@/api/client/__mocks__";
 import { ROOT_COMPONENT } from "@/utils/navigation/schema";
 
 import { setupSelectableMock } from "../../ObjectStore/mockServices";
 
 import SelectPreferredStore from "./SelectPreferredStore.vue";
 
+const { server, http } = useServerMock();
+
 setupSelectableMock();
 
 const localVue = getLocalVue(true);
@@ -22,6 +25,11 @@ const TEST_HISTORY = {
 };
 
 async function mountComponent() {
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json({});
+        })
+    );
     const wrapper = mount(SelectPreferredStore as object, {
         propsData: { userPreferredObjectStoreId: null, history: TEST_HISTORY },
         localVue,
diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
index c2659cf1f32b2ac22509e9796d9223bf5509eddc..e4827c4e0fe76f0128e3f71d9676e2a7a9ea1f6a 100644
--- a/client/src/components/History/Export/HistoryExport.test.ts
+++ b/client/src/components/History/Export/HistoryExport.test.ts
@@ -1,15 +1,13 @@
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
 import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 
-import type { HistorySummary } from "@/api";
+import { type HistorySummary } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
 import { fetchHistoryExportRecords } from "@/api/histories.export";
-import type { FilesSourcePlugin } from "@/api/remoteFiles";
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { type FilesSourcePlugin } from "@/api/remoteFiles";
 import {
     EXPIRED_STS_DOWNLOAD_RECORD,
     FILE_SOURCE_STORE_RECORD,
@@ -20,7 +18,6 @@ import HistoryExport from "./HistoryExport.vue";
 
 const localVue = getLocalVue(true);
 
-jest.mock("@/api/schema");
 jest.mock("@/api/histories.export");
 const mockFetchExportRecords = fetchHistoryExportRecords as jest.MockedFunction<typeof fetchHistoryExportRecords>;
 mockFetchExportRecords.mockResolvedValue([]);
@@ -42,8 +39,6 @@ const FAKE_HISTORY: HistorySummary = {
     url: FAKE_HISTORY_URL,
 };
 
-const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
-
 const REMOTE_FILES_API_RESPONSE: FilesSourcePlugin[] = [
     {
         id: "test-posix-source",
@@ -54,6 +49,11 @@ const REMOTE_FILES_API_RESPONSE: FilesSourcePlugin[] = [
         browsable: true,
         requires_roles: undefined,
         requires_groups: undefined,
+        supports: {
+            pagination: false,
+            search: false,
+            sorting: false,
+        },
     },
 ];
 
@@ -70,13 +70,22 @@ async function mountHistoryExport() {
     return wrapper;
 }
 
-describe("HistoryExport.vue", () => {
-    let axiosMock: MockAdapter;
+const { server, http } = useServerMock();
 
+describe("HistoryExport.vue", () => {
     beforeEach(async () => {
-        mockFetcher.path(REMOTE_FILES_API_ENDPOINT).method("get").mock({ data: [] });
-        axiosMock = new MockAdapter(axios);
-        axiosMock.onGet(FAKE_HISTORY_URL).reply(200, FAKE_HISTORY);
+        server.use(
+            http.get("/api/histories/{history_id}", ({ response, params }) => {
+                const historyId = params.history_id;
+                if (historyId === FAKE_HISTORY_ID) {
+                    return response(200).json(FAKE_HISTORY);
+                }
+            }),
+
+            http.get("/api/remote_files/plugins", ({ response }) => {
+                return response(200).json([]);
+            })
+        );
     });
 
     it("should render the history name", async () => {
@@ -116,7 +125,10 @@ describe("HistoryExport.vue", () => {
     });
 
     it("should display file sources tab if there are available", async () => {
-        mockFetcher.path(REMOTE_FILES_API_ENDPOINT).method("get").mock({ data: REMOTE_FILES_API_RESPONSE });
+        server.use(
+            http.get("/api/remote_files/plugins", ({ response }) => response(200).json(REMOTE_FILES_API_RESPONSE))
+        );
+
         const wrapper = await mountHistoryExport();
 
         expect(wrapper.find("#direct-download-tab").exists()).toBe(true);
@@ -138,11 +150,14 @@ describe("HistoryExport.vue", () => {
             doc: "For testing",
             writable: true,
             browsable: true,
+            supports: {
+                pagination: false,
+                search: false,
+                sorting: false,
+            },
         };
-        mockFetcher
-            .path(REMOTE_FILES_API_ENDPOINT)
-            .method("get")
-            .mock({ data: [zenodoPlugin] });
+        server.use(http.get("/api/remote_files/plugins", ({ response }) => response(200).json([zenodoPlugin])));
+
         const wrapper = await mountHistoryExport();
 
         expect(wrapper.find("#zenodo-file-source-tab").exists()).toBe(true);
@@ -159,7 +174,18 @@ describe("HistoryExport.vue", () => {
     });
 
     it("should not render the UI and display a fatal error message if the history cannot be found or loaded", async () => {
-        axiosMock.onGet(FAKE_HISTORY_URL).reply(404);
+        server.use(
+            http.get("/api/histories/{history_id}", ({ response }) =>
+                response("4XX").json(
+                    {
+                        err_code: 404,
+                        err_msg: "History not found",
+                    },
+                    { status: 404 }
+                )
+            )
+        );
+
         const wrapper = await mountHistoryExport();
 
         expect(wrapper.find("#fatal-error-alert").exists()).toBe(true);
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index e47bd706388dada44a31a89bb31c6379c08a396d..701a9fc9d90332fe377d40fb133af5e6a0fdc8c5 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -12,7 +12,7 @@ import {
     reimportHistoryFromRecord,
 } from "@/api/histories.export";
 import type { ColorVariant } from "@/components/Common";
-import { areEqual, ExportParams, ExportRecord } from "@/components/Common/models/exportRecordModel";
+import { areEqual, type ExportParams, type ExportRecord } from "@/components/Common/models/exportRecordModel";
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { useFileSources } from "@/composables/fileSources";
 import { DEFAULT_EXPORT_PARAMS, useShortTermStorage } from "@/composables/shortTermStorage";
@@ -23,11 +23,11 @@ import { absPath } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import ExportOptions from "./ExportOptions.vue";
-import RDMCredentialsInfo from "./RDMCredentialsInfo.vue";
 import ExportToFileSourceForm from "@/components/Common/ExportForm.vue";
 import ExportToRDMRepositoryForm from "@/components/Common/ExportRDMForm.vue";
 import ExportRecordDetails from "@/components/Common/ExportRecordDetails.vue";
 import ExportRecordTable from "@/components/Common/ExportRecordTable.vue";
+import RDMCredentialsInfo from "@/components/Common/RDMCredentialsInfo.vue";
 import ExternalLink from "@/components/ExternalLink.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
diff --git a/client/src/components/History/HistoryIndicators.vue b/client/src/components/History/HistoryIndicators.vue
new file mode 100644
index 0000000000000000000000000000000000000000..d58df84906833046abf158fbb6d19e84e25bb701
--- /dev/null
+++ b/client/src/components/History/HistoryIndicators.vue
@@ -0,0 +1,45 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faArchive, faBurn, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+
+import { type HistorySummary, userOwnsHistory } from "@/api";
+import { useUserStore } from "@/stores/userStore";
+import localize from "@/utils/localization";
+
+import UtcDate from "../UtcDate.vue";
+
+library.add(faArchive, faBurn, faTrash);
+
+const userStore = useUserStore();
+const { currentUser } = storeToRefs(userStore);
+
+const props = defineProps<{
+    history: HistorySummary;
+    includeCount?: boolean;
+    detailedTime?: boolean;
+}>();
+</script>
+
+<template>
+    <div class="d-flex align-items-center flex-gapx-1">
+        <BBadge v-if="props.includeCount" pill :title="localize('Amount of items in history')">
+            {{ history.count }} {{ localize("items") }}
+        </BBadge>
+        <BBadge v-if="history.update_time" pill :title="localize('Last edited')">
+            <span v-if="props.detailedTime" v-localize>last edited </span>
+            <UtcDate :date="history.update_time" mode="elapsed" />
+        </BBadge>
+        <BBadge v-if="props.history.purged" pill class="alert-warning" title="Permanently deleted">
+            <FontAwesomeIcon :icon="faBurn" fixed-width />
+        </BBadge>
+        <BBadge v-else-if="history.deleted" pill class="alert-danger" title="Deleted">
+            <FontAwesomeIcon :icon="faTrash" fixed-width />
+        </BBadge>
+        <BBadge v-if="history.archived && userOwnsHistory(currentUser, props.history)" pill title="Archived">
+            <FontAwesomeIcon :icon="faArchive" fixed-width />
+        </BBadge>
+    </div>
+</template>
diff --git a/client/src/components/History/HistoryPublished.vue b/client/src/components/History/HistoryPublished.vue
index a9284130f1031c169d653790b304d78c4b3af411..6780ddbad41c710425f9ffaa5bc77260dc6973c7 100644
--- a/client/src/components/History/HistoryPublished.vue
+++ b/client/src/components/History/HistoryPublished.vue
@@ -1,7 +1,8 @@
 <script setup lang="ts">
 import { onMounted, ref } from "vue";
 
-import { historyFetcher } from "@/api/histories";
+import { GalaxyApi, type HistoryDetailed } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import PublishedItem from "@/components/Common/PublishedItem.vue";
 import HistoryView from "@/components/History/HistoryView.vue";
@@ -11,11 +12,22 @@ interface Props {
 }
 
 const props = defineProps<Props>();
-const history = ref({});
+const history = ref<HistoryDetailed>();
 
 onMounted(async () => {
-    const { data } = await historyFetcher({ history_id: props.id });
-    history.value = data;
+    const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+        params: {
+            path: { history_id: props.id },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+        return;
+    }
+
+    // The default view is the detailed view
+    history.value = data as HistoryDetailed;
 });
 </script>
 
diff --git a/client/src/components/History/HistoryScrollList.vue b/client/src/components/History/HistoryScrollList.vue
index dad3c94eb05a957cf70bfddc8e4597b489b421c1..56bb357735956da716963a53957080fd72909227 100644
--- a/client/src/components/History/HistoryScrollList.vue
+++ b/client/src/components/History/HistoryScrollList.vue
@@ -19,10 +19,10 @@ import localize from "@/utils/localization";
 import { HistoriesFilters } from "./HistoriesFilters";
 
 import TextSummary from "../Common/TextSummary.vue";
+import HistoryIndicators from "./HistoryIndicators.vue";
 import Heading from "@/components/Common/Heading.vue";
 import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
 import ScrollToTopButton from "@/components/ToolsList/ScrollToTopButton.vue";
-import UtcDate from "@/components/UtcDate.vue";
 
 type AdditionalOptions = "set-current" | "multi" | "center";
 type PinnedHistory = { id: string };
@@ -277,18 +277,7 @@ async function loadMore(noScroll = false) {
                                     </i>
                                 </div>
                                 <TextSummary v-else component="h4" :description="history.name" one-line-summary />
-                                <div class="d-flex align-items-center flex-gapx-1">
-                                    <BBadge pill :title="localize('Amount of items in history')">
-                                        {{ history.count }} {{ localize("items") }}
-                                    </BBadge>
-                                    <BBadge
-                                        v-if="history.update_time"
-                                        v-b-tooltip.noninteractive.hover
-                                        pill
-                                        :title="localize('Last edited')">
-                                        <UtcDate :date="history.update_time" mode="elapsed" />
-                                    </BBadge>
-                                </div>
+                                <HistoryIndicators :history="history" include-count />
                             </div>
 
                             <p v-if="!isMultiviewPanel && history.annotation" class="my-1">{{ history.annotation }}</p>
diff --git a/client/src/components/History/HistoryView.test.js b/client/src/components/History/HistoryView.test.js
index c37f4306b1248dc4a9b64babfbe8d810f71f6586..b00e2647f7a9eff8dda2d5f5bd01c62a4e65115b 100644
--- a/client/src/components/History/HistoryView.test.js
+++ b/client/src/components/History/HistoryView.test.js
@@ -1,19 +1,27 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
-import { getHistoryByIdFromServer, setCurrentHistoryOnServer } from "stores/services/history.services";
-import { useUserStore } from "stores/userStore";
 import { getLocalVue } from "tests/jest/helpers";
 
-import ContentItem from "./Content/ContentItem";
-import HistoryView from "./HistoryView";
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
+import { getHistoryByIdFromServer, setCurrentHistoryOnServer } from "@/stores/services/history.services";
+import { useUserStore } from "@/stores/userStore";
+
+import ContentItem from "./Content/ContentItem.vue";
+import HistoryView from "./HistoryView.vue";
 
 const localVue = getLocalVue();
 jest.mock("stores/services/history.services");
 
+const { server, http } = useServerMock();
+
+jest.mock("vue-router/composables", () => ({
+    useRoute: jest.fn(() => ({})),
+    useRouter: jest.fn(() => ({})),
+}));
+
 function create_history(historyId, userId, purged = false, archived = false) {
     const historyName = `${userId}'s History ${historyId}`;
     return {
@@ -60,10 +68,18 @@ async function createWrapper(localVue, currentUserId, history) {
     const pinia = createPinia();
     getHistoryByIdFromServer.mockResolvedValue(history);
     setCurrentHistoryOnServer.mockResolvedValue(history);
-    const axiosMock = new MockAdapter(axios);
-    const history_contents_url = `/api/histories/${history.id}/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true`;
     const history_contents_result = create_datasets(history.id, history.count);
-    axiosMock.onGet(history_contents_url).reply(200, history_contents_result);
+
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json({});
+        }),
+
+        http.get("/api/histories/{history_id}/contents", ({ response }) => {
+            return response(200).json(history_contents_result);
+        })
+    );
+
     const wrapper = mount(HistoryView, {
         propsData: { id: history.id },
         localVue,
@@ -76,10 +92,7 @@ async function createWrapper(localVue, currentUserId, history) {
         pinia,
     });
     const userStore = useUserStore();
-    const userData = {
-        id: currentUserId,
-    };
-    userStore.currentUser = { ...userStore.currentUser, ...userData };
+    userStore.currentUser = getFakeRegisteredUser({ id: currentUserId });
     await flushPromises();
     return wrapper;
 }
@@ -185,7 +198,9 @@ describe("History center panel View", () => {
         expect(storageDashboardButtonDisabled(wrapper)).toBeFalsy();
 
         // instead we have an alert
-        expect(wrapper.find("[data-description='history messages']").text()).toBe("History has been purged");
+        expect(wrapper.find("[data-description='history messages']").text()).toBe(
+            "History has been permanently deleted"
+        );
     });
 
     it("should not display archived message and should be importable when user is not owner and history is archived", async () => {
diff --git a/client/src/components/History/Index.vue b/client/src/components/History/Index.vue
index 5a192ef8bbb74fbc94ce2e9b3aa9252450e62a03..634d8f6c5a598804f337cf685f258211c15b988a 100644
--- a/client/src/components/History/Index.vue
+++ b/client/src/components/History/Index.vue
@@ -40,8 +40,7 @@ function onViewCollection(collection: CollectionEntry, currentOffset?: number) {
                 <HistoryNavigation
                     :history="currentHistory"
                     :histories="histories"
-                    :histories-loading="historiesLoading"
-                    title="Histories" />
+                    :histories-loading="historiesLoading" />
             </template>
         </HistoryPanel>
 
diff --git a/client/src/components/History/Layout/DetailsLayout.vue b/client/src/components/History/Layout/DetailsLayout.vue
index ef49938ca9f3b4c379d52fc153979eac178e8c2b..19611ba408b92464b9a8d0efe2a48873cfe1d8b0 100644
--- a/client/src/components/History/Layout/DetailsLayout.vue
+++ b/client/src/components/History/Layout/DetailsLayout.vue
@@ -9,6 +9,8 @@ import { computed, ref } from "vue";
 import { useUserStore } from "@/stores/userStore";
 import l from "@/utils/localization";
 
+import type { DetailsLayoutSummarized } from "./types";
+
 import TextSummary from "@/components/Common/TextSummary.vue";
 import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
 
@@ -20,7 +22,7 @@ interface Props {
     writeable?: boolean;
     annotation?: string;
     showAnnotation?: boolean;
-    summarized?: boolean;
+    summarized?: DetailsLayoutSummarized;
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -29,7 +31,7 @@ const props = withDefaults(defineProps<Props>(), {
     writeable: true,
     annotation: undefined,
     showAnnotation: true,
-    summarized: false,
+    summarized: undefined,
 });
 
 const emit = defineEmits(["save"]);
@@ -47,6 +49,20 @@ const localProps = ref<{ name: string; annotation: string | null; tags: string[]
     tags: [],
 });
 
+const detailsClass = computed(() => {
+    const classes: Record<string, boolean> = {
+        details: true,
+        "summarized-details": props.summarized && !editing.value,
+        "m-3": !props.summarized || editing.value,
+    };
+
+    if (props.summarized) {
+        classes[props.summarized] = true;
+    }
+
+    return classes;
+});
+
 const editButtonTitle = computed(() => {
     if (isAnonymous.value) {
         return l("Log in to Rename History");
@@ -90,10 +106,7 @@ function selectText() {
 </script>
 
 <template>
-    <section
-        class="details"
-        :class="summarized && !editing ? 'summarized-details' : 'm-3'"
-        data-description="edit details">
+    <section :class="detailsClass" data-description="edit details">
         <BButton
             :disabled="isAnonymous || !writeable"
             class="edit-button ml-1 float-right"
@@ -114,7 +127,9 @@ function selectText() {
                 v-short="annotation"
                 class="mt-2"
                 data-description="annotation value" />
-            <div v-else-if="summarized" style="min-height: 2rem">
+            <div
+                v-else-if="summarized"
+                :class="{ annotation: ['both', 'annotation'].includes(summarized), hidden: summarized === 'hidden' }">
                 <TextSummary
                     v-if="annotation"
                     :description="annotation"
@@ -124,8 +139,11 @@ function selectText() {
             </div>
             <StatelessTags
                 v-if="tags"
-                class="tags"
-                :class="!summarized && 'mt-2'"
+                :class="{
+                    'mt-2': !summarized,
+                    tags: ['both', 'tags'].includes(summarized),
+                    hidden: summarized === 'hidden',
+                }"
                 :value="tags"
                 disabled
                 :max-visible-tags="summarized ? 1 : 5" />
@@ -184,12 +202,20 @@ function selectText() {
 
 <style lang="scss" scoped>
 .summarized-details {
-    min-height: 8.5em;
-    margin: 1rem 1rem 0 1rem;
+    margin-left: 0.5rem;
     max-width: 15rem;
 
+    &.both {
+        min-height: 8.5em;
+    }
     .tags {
         min-height: 2rem;
     }
+    .annotation {
+        min-height: 2rem;
+    }
+    .hidden {
+        display: none;
+    }
 }
 </style>
diff --git a/client/src/components/History/Layout/types.ts b/client/src/components/History/Layout/types.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c637b520e8bea0dc13c21000f351619bef8f5092
--- /dev/null
+++ b/client/src/components/History/Layout/types.ts
@@ -0,0 +1 @@
+export type DetailsLayoutSummarized = "both" | "annotation" | "tags" | "none" | "hidden";
diff --git a/client/src/components/History/Modals/CopyModal.vue b/client/src/components/History/Modals/CopyModal.vue
index 7f0f6423b0f4110677da13a7f045592fcea52437..d31c41332672ecf9497b771f126a820923778a9f 100644
--- a/client/src/components/History/Modals/CopyModal.vue
+++ b/client/src/components/History/Modals/CopyModal.vue
@@ -20,9 +20,16 @@ import localize from "@/utils/localization";
 
 interface Props {
     history: HistorySummary;
+    showModal?: boolean;
 }
 
-const props = defineProps<Props>();
+const props = withDefaults(defineProps<Props>(), {
+    showModal: false,
+});
+
+const emit = defineEmits<{
+    (e: "update:show-modal", value: boolean): void;
+}>();
 
 const userStore = useUserStore();
 const historyStore = useHistoryStore();
@@ -32,6 +39,7 @@ const { currentUser, isAnonymous } = storeToRefs(userStore);
 const name = ref("");
 const copyAll = ref(false);
 const loading = ref(false);
+const localShowModal = ref(props.showModal);
 
 const title = computed(() => {
     return `Copying History: ${props.history.name}`;
@@ -55,6 +63,18 @@ const formValid = computed(() => {
     return newNameValid.value;
 });
 
+watch(
+    () => props.showModal,
+    (newVal) => {
+        localShowModal.value = newVal;
+    }
+);
+watch(
+    () => localShowModal.value,
+    (newVal) => {
+        emit("update:show-modal", newVal);
+    }
+);
 watch(
     () => props.history,
     (newHistory) => {
@@ -74,7 +94,7 @@ async function copy(close: () => void) {
 </script>
 
 <template>
-    <BModal v-bind="$attrs" :title="title" title-tag="h2" v-on="$listeners">
+    <BModal v-model="localShowModal" v-bind="$attrs" :title="title" title-tag="h2" v-on="$listeners">
         <transition name="fade">
             <BAlert v-localize :show="isAnonymous" variant="warning">
                 As an anonymous user, unless you log in or register, you will lose your current history after copying
diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index a78afe094f7b4efe7ca8c2868d8a4ce40e9b027a..c604d3fe2e9fc67ce93b19fb210ed466ca661dc0 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -1,27 +1,27 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import { BListGroupItem } from "bootstrap-vue";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
 
-import SelectorModal from "./SelectorModal";
+import SelectorModal from "./SelectorModal.vue";
 
 const localVue = getLocalVue();
 
 const CURRENT_HISTORY_ID = "COOL_ID";
 const getFakeHistorySummaries = (num, selectedIndex = 0) => {
     const result = Array.from({ length: num }, (_, index) => ({
-        id: `ID-${index}`,
+        id: index === selectedIndex ? CURRENT_HISTORY_ID : `ID-${index}`,
         name: `History-${index}`,
         tags: [],
         update_time: new Date().toISOString(),
     }));
-    result[selectedIndex].id = CURRENT_HISTORY_ID;
+
     return result;
 };
 const PROPS_FOR_MODAL = {
@@ -41,26 +41,28 @@ const CURRENT_USER = {
     email: "email",
     id: "user_id",
     tags_used: [],
-    isAnonymous: false,
     total_disk_usage: 0,
 };
 
+const { server, http } = useServerMock();
+
 describe("History SelectorModal.vue", () => {
     let wrapper;
-    let axiosMock;
     let historyStore;
     const allHistories = getFakeHistorySummaries(15);
 
-    function getUpdatedAxiosMock() {
-        const offset = historyStore.historiesOffset;
-        axiosMock
-            .onGet(`/api/histories?view=summary&order=update_time&offset=${offset}&limit=10`)
-            .reply(200, allHistories.slice(offset, offset + 10));
-
-        axiosMock.onGet(`/api/histories/count`).reply(200, 15);
-    }
-
     async function mountWith(props) {
+        server.use(
+            http.get("/api/histories", ({ response, query }) => {
+                const offset = Number(query.get("offset")) ?? 0;
+                const limit = Number(query.get("limit")) ?? 10;
+                return response(200).json(allHistories.slice(offset, offset + limit));
+            }),
+            http.get("/api/histories/count", ({ response }) => {
+                return response(200).json(allHistories.length);
+            })
+        );
+
         const pinia = createPinia();
         wrapper = mount(SelectorModal, {
             propsData: props,
@@ -72,11 +74,9 @@ describe("History SelectorModal.vue", () => {
         });
 
         const userStore = useUserStore();
-        userStore.setCurrentUser(CURRENT_USER);
+        userStore.setCurrentUser(getFakeRegisteredUser(CURRENT_USER));
 
         historyStore = useHistoryStore();
-        axiosMock = new MockAdapter(axios);
-        getUpdatedAxiosMock();
         await historyStore.loadHistories();
         await wrapper.setProps({
             histories: historyStore.histories,
@@ -91,7 +91,6 @@ describe("History SelectorModal.vue", () => {
 
         const currentHistoryRow = wrapper.find(`[data-pk="${CURRENT_HISTORY_ID}"]`);
         expect(currentHistoryRow.html()).toContain(CURRENT_HISTORY_INDICATION_TEXT);
-        axiosMock.restore();
     });
 
     it("paginates the histories", async () => {
@@ -101,7 +100,6 @@ describe("History SelectorModal.vue", () => {
         expect(displayedRows.length).toBe(10);
         expect(wrapper.find("[data-description='load more histories button']").exists()).toBe(true);
 
-        getUpdatedAxiosMock();
         await historyStore.loadHistories();
         await wrapper.setProps({
             histories: historyStore.histories,
@@ -110,7 +108,6 @@ describe("History SelectorModal.vue", () => {
         displayedRows = wrapper.findAllComponents(BListGroupItem).wrappers;
         expect(displayedRows.length).toBe(15);
         expect(wrapper.find("[data-description='load more histories button']").exists()).toBe(false);
-        axiosMock.restore();
     });
 
     it("emits selectHistory with the correct history ID when a row is clicked", async () => {
@@ -124,7 +121,6 @@ describe("History SelectorModal.vue", () => {
 
         expect(wrapper.emitted()["selectHistory"]).toBeDefined();
         expect(wrapper.emitted()["selectHistory"][0][0].id).toBe(targetHistoryId);
-        axiosMock.restore();
     });
 
     describe("Multi-selection Mode", () => {
@@ -149,7 +145,6 @@ describe("History SelectorModal.vue", () => {
             await button.trigger("click");
 
             expect(wrapper.emitted()["selectHistories"][0][0][0].id).toBe(targetHistoryId1);
-            axiosMock.restore();
         });
     });
 });
diff --git a/client/src/components/History/Multiple/MultipleView.test.js b/client/src/components/History/Multiple/MultipleView.test.js
index c8acf9c4fa4e5cd161edc90877a8c1079b91702a..cb7f8326416435b010973549334d7bc006c70771 100644
--- a/client/src/components/History/Multiple/MultipleView.test.js
+++ b/client/src/components/History/Multiple/MultipleView.test.js
@@ -1,18 +1,21 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
-import { useUserStore } from "stores/userStore";
 import { getLocalVue } from "tests/jest/helpers";
 
-import MultipleView from "./MultipleView";
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
+import MultipleView from "./MultipleView.vue";
 
 const USER_ID = "test-user-id";
 const FIRST_HISTORY_ID = "test-history-id-0";
 
-const getFakeHistorySummaries = (num, selectedIndex) => {
+const { server, http } = useServerMock();
+
+const getFakeHistorySummaries = (num) => {
     return Array.from({ length: num }, (_, index) => ({
         id: `test-history-id-${index}`,
         name: `History-${index}`,
@@ -20,24 +23,33 @@ const getFakeHistorySummaries = (num, selectedIndex) => {
         update_time: new Date().toISOString(),
     }));
 };
-const currentUser = { id: USER_ID };
 
 describe("MultipleView", () => {
-    let axiosMock;
-
-    beforeEach(() => {
-        axiosMock = new MockAdapter(axios);
-    });
-
-    afterEach(() => {
-        axiosMock.reset();
-    });
-
     async function setUpWrapper(count, currentHistoryId) {
-        const fakeSummaries = getFakeHistorySummaries(count, 0);
-        for (const summary of fakeSummaries) {
-            axiosMock.onGet(`api/histories/${summary.id}`).reply(200, summary);
-        }
+        const fakeSummaries = getFakeHistorySummaries(count);
+
+        server.use(
+            http.get("/api/configuration", ({ response }) => {
+                return response(200).json({});
+            }),
+
+            http.get("/api/histories/{history_id}", ({ response, params }) => {
+                const { history_id } = params;
+                const summary = fakeSummaries.find((s) => s.id === history_id);
+                if (!summary) {
+                    return response("4XX").json({ err_msg: "History not found", err_code: 404 }, { status: 404 });
+                }
+                return response(200).json(summary);
+            }),
+
+            http.get("/api/histories/{history_id}/contents", ({ response }) => {
+                return response(200).json({
+                    stats: { total_matches: 0 },
+                    contents: [],
+                });
+            })
+        );
+
         const wrapper = mount(MultipleView, {
             pinia: createPinia(),
             stubs: {
@@ -48,7 +60,7 @@ describe("MultipleView", () => {
         });
 
         const userStore = useUserStore();
-        userStore.currentUser = currentUser;
+        userStore.currentUser = getFakeRegisteredUser({ id: USER_ID });
 
         const historyStore = useHistoryStore();
         historyStore.setHistories(fakeSummaries);
@@ -66,8 +78,6 @@ describe("MultipleView", () => {
         // Set up UserHistories and wrapper
         const wrapper = await setUpWrapper(count, currentHistoryId);
 
-        console.log(wrapper.html());
-
         // Test: current (first) history should not be shown because only 4 latest are shown by default
         expect(wrapper.find("button[title='Current History']").exists()).toBeFalsy();
 
diff --git a/client/src/components/History/Multiple/MultipleViewItem.vue b/client/src/components/History/Multiple/MultipleViewItem.vue
index a61b7113edf031f380c077e766e44edc5fb3ed76..34e1959650d84212c1649d9c290b43cca10fd251 100644
--- a/client/src/components/History/Multiple/MultipleViewItem.vue
+++ b/client/src/components/History/Multiple/MultipleViewItem.vue
@@ -1,4 +1,7 @@
 <script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faTimes } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
@@ -6,10 +9,13 @@ import { computed, ref } from "vue";
 import { useExtendedHistory } from "@/composables/detailedHistory";
 import { useHistoryStore } from "@/stores/historyStore";
 
+import HistoryNavigation from "../CurrentHistory/HistoryNavigation.vue";
 import CollectionPanel from "@/components/History/CurrentCollection/CollectionPanel.vue";
 import HistoryPanel from "@/components/History/CurrentHistory/HistoryPanel.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
+library.add(faTimes);
+
 interface Props {
     source: {
         id: string;
@@ -20,7 +26,7 @@ interface Props {
 const props = defineProps<Props>();
 
 const historyStore = useHistoryStore();
-const { currentHistoryId, pinnedHistories } = storeToRefs(historyStore);
+const { currentHistoryId, histories, historiesLoading, pinnedHistories } = storeToRefs(historyStore);
 
 const { history } = useExtendedHistory(props.source.id);
 
@@ -42,7 +48,38 @@ function onViewCollection(collection: object) {
         </div>
     </div>
 
-    <div v-else id="list-item" class="d-flex flex-column align-items-center w-100">
+    <div v-else id="list-item" class="d-flex flex-column w-100">
+        <div class="d-flex justify-content-between align-items-center">
+            <div>
+                <BButton
+                    size="sm"
+                    class="my-1"
+                    :disabled="sameToCurrent"
+                    :variant="sameToCurrent ? 'disabled' : 'outline-info'"
+                    :title="sameToCurrent ? 'Current History' : 'Switch to this history'"
+                    @click="historyStore.setCurrentHistory(source.id)">
+                    {{ sameToCurrent ? "Current History" : "Switch to" }}
+                </BButton>
+                <BButton
+                    v-if="Object.keys(pinnedHistories).length > 0"
+                    size="sm"
+                    class="my-1"
+                    variant="outline-danger"
+                    title="Hide this history from the list"
+                    @click="historyStore.unpinHistories([source.id])">
+                    <FontAwesomeIcon :icon="faTimes" />
+                    Hide
+                </BButton>
+            </div>
+            <HistoryNavigation
+                :history="history"
+                :histories="histories"
+                :histories-loading="historiesLoading"
+                minimal />
+        </div>
+
+        <hr class="w-100 m-1" />
+
         <CollectionPanel
             v-if="selectedCollections.length && selectedCollections[0]?.history_id === source.id"
             :history="history"
@@ -57,28 +94,5 @@ function onViewCollection(collection: object) {
             :show-controls="false"
             is-multi-view-item
             @view-collection="onViewCollection" />
-
-        <hr class="w-100 m-2" />
-
-        <div class="flex-row flex-grow-0">
-            <BButton
-                size="sm"
-                class="my-1"
-                :disabled="sameToCurrent"
-                :variant="sameToCurrent ? 'disabled' : 'outline-info'"
-                :title="sameToCurrent ? 'Current History' : 'Switch to this history'"
-                @click="historyStore.setCurrentHistory(source.id)">
-                {{ sameToCurrent ? "Current History" : "Switch to" }}
-            </BButton>
-            <BButton
-                v-if="Object.keys(pinnedHistories).length > 0"
-                size="sm"
-                class="my-1"
-                variant="outline-danger"
-                title="Hide this history from the list"
-                @click="historyStore.unpinHistories([source.id])">
-                Hide
-            </BButton>
-        </div>
     </div>
 </template>
diff --git a/client/src/components/History/Multiple/MultipleViewList.vue b/client/src/components/History/Multiple/MultipleViewList.vue
index 36eaac0e68cbedd7daab43d89b418026381960a7..e84a89b0eadcb113894b59ee4d312e752f9e3bdd 100644
--- a/client/src/components/History/Multiple/MultipleViewList.vue
+++ b/client/src/components/History/Multiple/MultipleViewList.vue
@@ -6,16 +6,15 @@ import { computed, type Ref, ref } from "vue";
 //@ts-ignore missing typedefs
 import VirtualList from "vue-virtual-scroll-list";
 
-import { HistoryItemSummary, isHistoryItem } from "@/api";
-import { copyDataset } from "@/api/datasets";
 import { useAnimationFrameResizeObserver } from "@/composables/sensors/animationFrameResizeObserver";
 import { useAnimationFrameScroll } from "@/composables/sensors/animationFrameScroll";
 import { Toast } from "@/composables/toast";
-import { useEventStore } from "@/stores/eventStore";
 import { useHistoryStore } from "@/stores/historyStore";
 import localize from "@/utils/localization";
 import { errorMessageAsString } from "@/utils/simple-error";
 
+import { useHistoryDragDrop } from "../../../composables/historyDragDrop";
+
 import HistoryDropZone from "../CurrentHistory/HistoryDropZone.vue";
 import MultipleViewItem from "./MultipleViewItem.vue";
 
@@ -65,67 +64,7 @@ async function createAndPin() {
     }
 }
 
-const showDropZone = ref(false);
-const processingDrop = ref(false);
-async function onDrop(evt: any) {
-    const eventStore = useEventStore();
-    if (processingDrop.value) {
-        showDropZone.value = false;
-        return;
-    }
-    processingDrop.value = true;
-    showDropZone.value = false;
-    const dragItems = eventStore.getDragItems();
-    // Filter out any non-history items
-    const historyItems = dragItems?.filter((item: any) => isHistoryItem(item)) as HistoryItemSummary[];
-    const multiple = historyItems.length > 1;
-    const originalHistoryId = historyItems?.[0]?.history_id;
-
-    if (historyItems && originalHistoryId) {
-        await historyStore.createNewHistory();
-        const currentHistoryId = historyStore.currentHistoryId;
-
-        let datasetCount = 0;
-        let collectionCount = 0;
-        if (currentHistoryId) {
-            // iterate over the data array and copy each item to the new history
-            for (const item of historyItems) {
-                const dataSource = item.history_content_type === "dataset" ? "hda" : "hdca";
-                await copyDataset(item.id, currentHistoryId, item.history_content_type, dataSource)
-                    .then(() => {
-                        if (item.history_content_type === "dataset") {
-                            datasetCount++;
-                            if (!multiple) {
-                                Toast.info(localize("Dataset copied to new history"));
-                            }
-                        } else {
-                            collectionCount++;
-                            if (!multiple) {
-                                Toast.info(localize("Collection copied to new history"));
-                            }
-                        }
-                    })
-                    .catch((error) => {
-                        Toast.error(errorMessageAsString(error));
-                    });
-            }
-            if (multiple && datasetCount > 0) {
-                Toast.info(`${datasetCount} dataset${datasetCount > 1 ? "s" : ""} copied to new history`);
-            }
-            if (multiple && collectionCount > 0) {
-                Toast.info(`${collectionCount} collection${collectionCount > 1 ? "s" : ""} copied to new history`);
-            }
-
-            if (historyStore.pinnedHistories.length > 0) {
-                // pin the newly created history via the drop
-                historyStore.pinHistory(currentHistoryId);
-                // also pin the original history where the item came from
-                historyStore.pinHistory(originalHistoryId);
-            }
-        }
-        processingDrop.value = false;
-    }
-}
+const { showDropZone, onDragEnter, onDragLeave, onDragOver, onDrop } = useHistoryDragDrop(undefined, true, true);
 
 async function onKeyDown(evt: KeyboardEvent) {
     if (evt.key === "Enter" || evt.key === " ") {
@@ -159,9 +98,9 @@ async function onKeyDown(evt: KeyboardEvent) {
             <div
                 class="history-picker"
                 @drop.prevent="onDrop"
-                @dragenter.prevent="showDropZone = true"
-                @dragover.prevent
-                @dragleave.prevent="showDropZone = false">
+                @dragenter.prevent="onDragEnter"
+                @dragover="onDragOver"
+                @dragleave.prevent="onDragLeave">
                 <span v-if="!showDropZone" class="d-flex flex-column h-100">
                     <div
                         class="history-picker-box top-picker text-primary"
diff --git a/client/src/components/History/SwitchToHistoryLink.test.ts b/client/src/components/History/SwitchToHistoryLink.test.ts
index e45a043e5fa32f906ed182e97f3631683a0d0d5d..d5bf29c50b5e67be0e06a8afbbc932f2e3c5f1f6 100644
--- a/client/src/components/History/SwitchToHistoryLink.test.ts
+++ b/client/src/components/History/SwitchToHistoryLink.test.ts
@@ -1,27 +1,44 @@
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
-import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
+import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 
-import { type HistorySummary } from "@/api";
+import { type HistorySummaryExtended } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
+import { useUserStore } from "@/stores/userStore";
 
 import SwitchToHistoryLink from "./SwitchToHistoryLink.vue";
 
 const localVue = getLocalVue(true);
 
+const { server, http } = useServerMock();
+
 const selectors = {
     historyLink: ".history-link",
 } as const;
 
-function mountSwitchToHistoryLinkForHistory(history: HistorySummary) {
+// Mock the history store to always return the same current history id
+jest.mock("@/stores/historyStore", () => {
+    const originalModule = jest.requireActual("@/stores/historyStore");
+    return {
+        ...originalModule,
+        useHistoryStore: () => ({
+            ...originalModule.useHistoryStore(),
+            currentHistoryId: "current-history-id",
+        }),
+    };
+});
+
+function mountSwitchToHistoryLinkForHistory(history: HistorySummaryExtended) {
     const pinia = createTestingPinia();
 
-    const axiosMock = new MockAdapter(axios);
-    axiosMock.onGet(`/api/histories/${history.id}`).reply(200, history);
+    server.use(
+        http.get("/api/histories/{history_id}", ({ response }) => {
+            return response(200).json(history);
+        })
+    );
 
-    const wrapper = shallowMount(SwitchToHistoryLink as object, {
+    const wrapper = mount(SwitchToHistoryLink as object, {
         propsData: {
             historyId: history.id,
         },
@@ -31,10 +48,26 @@ function mountSwitchToHistoryLinkForHistory(history: HistorySummary) {
             FontAwesomeIcon: true,
         },
     });
+
+    const userStore = useUserStore();
+    userStore.currentUser = {
+        email: "email",
+        id: "user_id",
+        tags_used: [],
+        isAnonymous: false,
+        total_disk_usage: 0,
+        nice_total_disk_usage: "0 bytes",
+        purged: false,
+        deleted: false,
+        is_admin: false,
+        username: "user",
+        preferences: {},
+        quota: "abcdef",
+    };
     return wrapper;
 }
 
-async function expectOptionForHistory(option: string, history: HistorySummary) {
+async function expectOptionForHistory(option: string, history: HistorySummaryExtended) {
     const wrapper = mountSwitchToHistoryLinkForHistory(history);
 
     // Wait for the history to be loaded
@@ -52,7 +85,7 @@ describe("SwitchToHistoryLink", () => {
             deleted: false,
             archived: false,
             purged: false,
-        } as HistorySummary;
+        } as HistorySummaryExtended;
         const wrapper = mountSwitchToHistoryLinkForHistory(history);
 
         expect(wrapper.find(selectors.historyLink).exists()).toBe(false);
@@ -72,10 +105,23 @@ describe("SwitchToHistoryLink", () => {
             deleted: false,
             purged: false,
             archived: false,
-        } as HistorySummary;
+            user_id: "user_id",
+        } as HistorySummaryExtended;
         await expectOptionForHistory("Switch", history);
     });
 
+    it("should display the appropriate text when the history is the Current history", async () => {
+        const history = {
+            id: "current-history-id",
+            name: "History Current",
+            deleted: false,
+            purged: false,
+            archived: false,
+            user_id: "user_id",
+        } as HistorySummaryExtended;
+        await expectOptionForHistory("This is your current history", history);
+    });
+
     it("should display the View option when the history is purged", async () => {
         const history = {
             id: "purged-history-id",
@@ -83,7 +129,8 @@ describe("SwitchToHistoryLink", () => {
             deleted: false,
             purged: true,
             archived: false,
-        } as HistorySummary;
+            user_id: "user_id",
+        } as HistorySummaryExtended;
         await expectOptionForHistory("View", history);
     });
 
@@ -94,7 +141,23 @@ describe("SwitchToHistoryLink", () => {
             deleted: false,
             purged: false,
             archived: true,
-        } as HistorySummary;
+            user_id: "user_id",
+        } as HistorySummaryExtended;
         await expectOptionForHistory("View", history);
     });
+
+    it("should view in new tab when the history is accessible", async () => {
+        const history = {
+            id: "public-history-id",
+            name: "History Published",
+            deleted: false,
+            purged: false,
+            archived: false,
+            published: true,
+            user_id: "other_user_id",
+        } as HistorySummaryExtended;
+        await expectOptionForHistory("View", history);
+    });
+
+    // if the history is inaccessible, the HistorySummary would never be fetched in the first place
 });
diff --git a/client/src/components/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
index 4087ccecd27c8dcf69329fb9ae820c474c1e4d50..13916b4e9f3f455238b0cb40a8903f94a65bc049 100644
--- a/client/src/components/History/SwitchToHistoryLink.vue
+++ b/client/src/components/History/SwitchToHistoryLink.vue
@@ -6,8 +6,12 @@ import { BLink } from "bootstrap-vue";
 import { computed } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { HistorySummary } from "@/api";
+import { type HistorySummary, userOwnsHistory } from "@/api";
+import { Toast } from "@/composables/toast";
+import { useEventStore } from "@/stores/eventStore";
 import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
@@ -15,6 +19,7 @@ library.add(faArchive, faBurn);
 
 const router = useRouter();
 const historyStore = useHistoryStore();
+const userStore = useUserStore();
 
 interface Props {
     historyId: string;
@@ -25,7 +30,13 @@ const props = defineProps<Props>();
 
 const history = computed(() => historyStore.getHistoryById(props.historyId));
 
-const canSwitch = computed(() => !!history.value && !history.value.archived && !history.value.purged);
+const canSwitch = computed(
+    () =>
+        !!history.value &&
+        !history.value.archived &&
+        !history.value.purged &&
+        userOwnsHistory(userStore.currentUser, history.value)
+);
 
 const actionText = computed(() => {
     if (canSwitch.value) {
@@ -37,12 +48,29 @@ const actionText = computed(() => {
     return "View in new tab";
 });
 
-function onClick(history: HistorySummary) {
-    if (canSwitch.value) {
+const linkTitle = computed(() => {
+    if (historyStore.currentHistoryId === props.historyId) {
+        return "This is your current history";
+    } else {
+        return `<b>${actionText.value}</b><br>${history.value?.name}`;
+    }
+});
+
+async function onClick(event: MouseEvent, history: HistorySummary) {
+    const eventStore = useEventStore();
+    const ctrlKey = eventStore.isMac ? event.metaKey : event.ctrlKey;
+    if (!ctrlKey && historyStore.currentHistoryId === history.id) {
+        return;
+    }
+    if (!ctrlKey && canSwitch.value) {
         if (props.filters) {
             historyStore.applyFilters(history.id, props.filters);
         } else {
-            historyStore.setCurrentHistory(history.id);
+            try {
+                await historyStore.setCurrentHistory(history.id);
+            } catch (error) {
+                Toast.error(errorMessageAsString(error));
+            }
         }
         return;
     }
@@ -58,13 +86,14 @@ function viewHistoryInNewTab(history: HistorySummary) {
 <template>
     <div>
         <LoadingSpan v-if="!history" />
-        <div v-else class="history-link">
+        <div v-else class="history-link" data-description="switch to history link">
             <BLink
                 v-b-tooltip.hover.top.noninteractive.html
+                data-description="switch to history link"
                 class="truncate"
                 href="#"
-                :title="`<b>${actionText}</b><br>${history.name}`"
-                @click.stop="onClick(history)">
+                :title="linkTitle"
+                @click.stop="onClick($event, history)">
                 {{ history.name }}
             </BLink>
 
diff --git a/client/src/components/History/adapters/HistoryPanelProxy.js b/client/src/components/History/adapters/HistoryPanelProxy.js
index 28b95b38627f6cd6848b1dfb3a9ec29087aba86f..11972ef9fc2c6b693cb210fb08fd01830da748c3 100644
--- a/client/src/components/History/adapters/HistoryPanelProxy.js
+++ b/client/src/components/History/adapters/HistoryPanelProxy.js
@@ -8,7 +8,7 @@ import { startWatchingHistory } from "store/historyStore/model/watchHistory";
 import { useHistoryItemsStore } from "stores/historyItemsStore";
 import { useHistoryStore } from "stores/historyStore";
 
-import { buildCollectionModal } from "./buildCollectionModal";
+import { buildRuleCollectionModal } from "./buildCollectionModal";
 
 // extend existing current history panel
 export class HistoryPanelProxy {
@@ -45,7 +45,7 @@ export class HistoryPanelProxy {
         this.model.id = historyId;
         this.historyStore.setCurrentHistory(historyId);
     }
-    async buildCollection(collectionType, selection, historyId = null, fromRulesInput = false) {
+    async buildCollectionFromRules(selection, historyId = null, fromRulesInput = false) {
         let selectionContent = null;
         historyId = historyId || this.model.id;
         if (fromRulesInput) {
@@ -56,7 +56,7 @@ export class HistoryPanelProxy {
                 selectionContent.set(obj.id, obj);
             });
         }
-        const modalResult = await buildCollectionModal(collectionType, selectionContent, historyId, fromRulesInput);
+        const modalResult = await buildRuleCollectionModal(selectionContent, historyId, fromRulesInput);
         if (modalResult) {
             console.debug("Submitting collection build request.", modalResult);
             await createDatasetCollection({ id: historyId }, modalResult);
diff --git a/client/src/components/History/adapters/buildCollectionModal.js b/client/src/components/History/adapters/buildCollectionModal.ts
similarity index 51%
rename from client/src/components/History/adapters/buildCollectionModal.js
rename to client/src/components/History/adapters/buildCollectionModal.ts
index f5b5c030ea2719aabaea6311a9daf5afd01c1688..53a41b424914ee6f8687ee717c40477b4c096375 100644
--- a/client/src/components/History/adapters/buildCollectionModal.js
+++ b/client/src/components/History/adapters/buildCollectionModal.ts
@@ -1,4 +1,5 @@
 /**
+ * TODO: Update this description...
  * Temporary adapter to launch bootstrap modals from Vue components, for use with
  * the collection assembly modals. i.e. With selected..... create dataset collection,
  * create paired collection, etc.
@@ -8,44 +9,50 @@
  * deprecated jquery Deferred object.
  */
 
-import LIST_COLLECTION_CREATOR from "components/Collections/ListCollectionCreatorModal";
-import PAIR_COLLECTION_CREATOR from "components/Collections/PairCollectionCreatorModal";
-import LIST_OF_PAIRS_COLLECTION_CREATOR from "components/Collections/PairedListCollectionCreatorModal";
-import RULE_BASED_COLLECTION_CREATOR from "components/Collections/RuleBasedCollectionCreatorModal";
 import jQuery from "jquery";
 
+import type { HDASummary, HistoryItemSummary } from "@/api";
+import RULE_BASED_COLLECTION_CREATOR from "@/components/Collections/RuleBasedCollectionCreatorModal";
+
+export type CollectionType = "list" | "paired" | "list:paired" | "rules";
+export type DatasetPair = {
+    forward: HDASummary;
+    reverse: HDASummary;
+    name: string;
+};
+
 // stand-in for buildCollection from history-view-edit.js
-export async function buildCollectionModal(collectionType, selectedContent, historyId, fromRulesInput = false) {
+export async function buildRuleCollectionModal(
+    selectedContent: HistoryItemSummary[],
+    historyId: string,
+    fromRulesInput = false,
+    defaultHideSourceItems = true
+) {
     // select legacy function
-    let createFunc;
-    if (collectionType == "list") {
-        createFunc = LIST_COLLECTION_CREATOR.createListCollection;
-    } else if (collectionType == "paired") {
-        createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;
-    } else if (collectionType == "list:paired") {
-        createFunc = LIST_OF_PAIRS_COLLECTION_CREATOR.createPairedListCollection;
-    } else if (collectionType.startsWith("rules")) {
-        createFunc = RULE_BASED_COLLECTION_CREATOR.createCollectionViaRules;
-    } else {
-        throw new Error(`Unknown collectionType encountered ${collectionType}`);
-    }
+    const createFunc = RULE_BASED_COLLECTION_CREATOR.createCollectionViaRules;
     // pull up cached content by type_ids;
     if (fromRulesInput) {
         return await createFunc(selectedContent);
     } else {
-        const fakeBackboneContent = createBackboneContent(historyId, selectedContent);
+        const fakeBackboneContent = createBackboneContent(historyId, selectedContent, defaultHideSourceItems);
         return await createFunc(fakeBackboneContent);
     }
 }
 
-const createBackboneContent = (historyId, selection) => {
+const createBackboneContent = (historyId: string, selection: HistoryItemSummary[], defaultHideSourceItems: boolean) => {
     const selectionJson = Array.from(selection.values());
     return {
         historyId,
         toJSON: () => selectionJson,
         // result must be a $.Deferred object instead of a promise because
         // that's the kind of deprecated data format that backbone likes to use.
-        createHDCA(element_identifiers, collection_type, name, hide_source_items, options = {}) {
+        createHDCA(
+            element_identifiers: any,
+            collection_type: CollectionType,
+            name: string,
+            hide_source_items: boolean,
+            options = {}
+        ) {
             const def = jQuery.Deferred();
             return def.resolve(null, {
                 collection_type,
@@ -55,5 +62,6 @@ const createBackboneContent = (historyId, selection) => {
                 options,
             });
         },
+        defaultHideSourceItems,
     };
 };
diff --git a/client/src/components/History/model/queries.js b/client/src/components/History/model/queries.js
deleted file mode 100644
index 7604fec3883f63e90a49a1e351454eb008d1c93f..0000000000000000000000000000000000000000
--- a/client/src/components/History/model/queries.js
+++ /dev/null
@@ -1,134 +0,0 @@
-/**
- * Simple ajax queries that run against the api.
- *
- * A few history queries still hit routes that don't begin with /api. I have noted them
- * in the comments.
- */
-
-import axios from "axios";
-import { prependPath } from "utils/redirect";
-
-/**
- * Generic json getter
- * @param {*} response
- */
-
-const doResponse = (response) => {
-    if (response.status != 200) {
-        throw new Error(response);
-    }
-    return response.data;
-};
-
-/**
- * Legacy query string rendering. (generates q/qv syntax queries).
- * TODO: remove these converters when the api is modernized.
- */
-function buildQueryStringFrom(filters) {
-    const queryString = Object.entries(filters)
-        .map(([f, v]) => `q=${f}&qv=${v}`)
-        .join("&");
-    return queryString;
-}
-
-// #endregion
-
-/**
- * Content Queries
- */
-
-/**
- * Deletes item from history
- *
- * @param {Object} content Content object
- * @param {Boolean} purge Permanent delete
- * @param {Boolean} recursive Scorch the earth?
- */
-export async function deleteContent(content, deleteParams = {}) {
-    const defaults = { purge: false, recursive: false, stop_job: true };
-    const params = Object.assign({}, defaults, deleteParams);
-    const { history_id, history_content_type, id } = content;
-    const url = `api/histories/${history_id}/contents/${history_content_type}s/${id}`;
-    const response = await axios.delete(prependPath(url), { params });
-    return doResponse(response);
-}
-
-/**
-* Stops job and marks it as complete.
-*/
-export async function stopJob(job_id) {
-    const url = `api/jobs/${job_id}/finish`;
-    const response = await axios.put(prependPath(url));
-    return doResponse(response);
-}
-
-/**
- * Update specific fields on datasets or collections.
- * @param {Object} content content object
- * @param {Object} newFields key/value object of properties to update
- */
-export async function updateContentFields(content, newFields = {}) {
-    const { history_id, id, history_content_type: type } = content;
-    const url = `api/histories/${history_id}/contents/${type}s/${id}`;
-    const response = await axios.put(prependPath(url), newFields);
-    return doResponse(response);
-}
-
-/** Get all objects that match filters in a history
- *
- * @param {string} historyId
- * @param {Object} filters
- * @param {string} type
- *
- */
-export async function getHistoryContent(historyId, filters = {}, type = "dataset") {
-    const filterQuery = buildQueryStringFrom(filters);
-    const url = `api/histories/${historyId}/contents/${type}s?v=dev&${filterQuery}`;
-    const response = await axios.get(prependPath(url));
-    return doResponse(response);
-}
-
-/**
- * Performs an operation on a specific set of items or all the items
- * matching the filters.
- * If a specific set of items is provided, the filters are ignored, otherwise
- * the filters will determine which items are processed.
- *
- * @param {Object} history The history that contains the items
- * @param {String} operation The operation to perform on all items
- * @param {Object} filters The filter query parameters
- * @param {Object[]} items The set of items to process as `{ id, history_content_type }`
- * @param {Object} params Optional extra parameters passed to the operation
- */
-export async function bulkUpdate(history, operation, filters, items = [], params = null) {
-    const { id } = history;
-    const filterQuery = buildQueryStringFrom(filters);
-    const url = `api/histories/${id}/contents/bulk?${filterQuery}`;
-    const payload = {
-        operation,
-        items,
-        params,
-    };
-    const response = await axios.put(prependPath(url), payload);
-    return doResponse(response);
-}
-
-/**
- * Collections
- */
-
-export async function createDatasetCollection(history, inputs = {}) {
-    const defaults = {
-        collection_type: "list",
-        copy_elements: true,
-        name: "list",
-        element_identifiers: [],
-        hide_source_items: true,
-        type: "dataset_collection",
-    };
-
-    const payload = Object.assign({}, defaults, inputs);
-    const url = `api/histories/${history.id}/contents`;
-    const response = await axios.post(prependPath(url), payload);
-    return doResponse(response);
-}
diff --git a/client/src/components/History/model/queries.ts b/client/src/components/History/model/queries.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9112aee892fbae536dbbb61c172ce96b3932da83
--- /dev/null
+++ b/client/src/components/History/model/queries.ts
@@ -0,0 +1,118 @@
+import { type components, GalaxyApi, type HistoryItemSummary, type HistorySummary } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
+
+type BulkOperation = components["schemas"]["HistoryContentItemOperation"];
+type QueryFilters = Record<string, unknown>;
+
+export function filtersToQueryValues(filters: QueryFilters) {
+    const filterKeys = Object.keys(filters);
+    const filterValues = filterKeys.map((key) => `${filters[key]}`);
+    return { q: filterKeys, qv: filterValues };
+}
+
+/**
+ * Deletes item from history
+ */
+export async function deleteContent(
+    content: HistoryItemSummary,
+    deleteParams: Partial<{ purge: boolean; recursive: boolean }> = {}
+) {
+    const defaults = { purge: false, recursive: false, stop_job: true };
+    const params = Object.assign({}, defaults, deleteParams);
+    const { data, error } = await GalaxyApi().DELETE("/api/histories/{history_id}/contents/{type}s/{id}", {
+        params: {
+            path: { history_id: content.history_id, type: content.history_content_type, id: content.id },
+            query: params,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
+
+/**
+* Stops job and marks it as complete.
+*/
+export async function stopJob(jobId: string) {
+    const { data, error } = await GalaxyApi().PUT("/api/jobs/{job_id}/finish", {
+       params: { path: { job_id: jobId } },
+    });
+
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
+
+
+/**
+ * Update specific fields on datasets or collections.
+ */
+export async function updateContentFields(content: HistoryItemSummary, newFields = {}) {
+    const { data, error } = await GalaxyApi().PUT("/api/histories/{history_id}/contents/{type}s/{id}", {
+        params: {
+            path: { history_id: content.history_id, type: content.history_content_type, id: content.id },
+        },
+        body: newFields,
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
+
+/**
+ * Performs an operation on a specific set of items or all the items
+ * matching the filters.
+ * If a specific set of items is provided, the filters are ignored, otherwise
+ * the filters will determine which items are processed.
+ */
+export async function bulkUpdate(
+    history: HistorySummary,
+    operation: BulkOperation,
+    filters: QueryFilters,
+    items = [],
+    params = null
+) {
+    const { data, error } = await GalaxyApi().PUT("/api/histories/{history_id}/contents/bulk", {
+        params: {
+            path: { history_id: history.id },
+            query: filtersToQueryValues(filters),
+        },
+        body: {
+            operation,
+            items,
+            params,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
+
+export async function createDatasetCollection(history: HistorySummary, inputs = {}) {
+    const defaults = {
+        collection_type: "list",
+        copy_elements: true,
+        name: "list",
+        element_identifiers: [],
+        hide_source_items: true,
+    };
+    const payload = Object.assign({}, defaults, inputs);
+
+    const { data, error } = await GalaxyApi().POST("/api/histories/{history_id}/contents", {
+        params: { path: { history_id: history.id } },
+        body: { ...payload, instance_type: "history", type: "dataset_collection" },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
diff --git a/client/src/components/History/services.ts b/client/src/components/History/services.ts
index 572cb8768e8bc2f8640b55988b110d398e6fe548..9a8feafe027b3e7c82a4ff4e96d9b7e4a37fd7ff 100644
--- a/client/src/components/History/services.ts
+++ b/client/src/components/History/services.ts
@@ -1,37 +1,8 @@
 import axios from "axios";
 
-import { fetcher } from "@/api/schema";
 import { type Input, permissionInputParts } from "@/composables/datasetPermissions";
-import type Filtering from "@/utils/filtering";
 import { withPrefix } from "@/utils/redirect";
 
-const publishedHistoriesFetcher = fetcher.path("/api/histories/published").method("get").create();
-export async function getPublishedHistories(
-    limit: number,
-    offset: number | null,
-    sortBy: string,
-    sortDesc: boolean,
-    filterText: string,
-    filters: Filtering<unknown>
-) {
-    const view = "summary";
-    const keys = "username,username_and_slug";
-    const queryDict = filters.getQueryDict(filterText);
-    const order = sortBy ? `${sortBy}${sortDesc ? "-dsc" : "-asc"}` : undefined;
-
-    const { data } = await publishedHistoriesFetcher({
-        limit,
-        offset,
-        order,
-        view,
-        keys,
-        q: Object.keys(queryDict),
-        qv: Object.entries(queryDict).map(([__, v]) => v as string),
-    });
-
-    return data;
-}
-
 export function getPermissionsUrl(historyId: string) {
     return `/history/permissions?id=${historyId}`;
 }
diff --git a/client/src/components/HistoryExport/Index.test.js b/client/src/components/HistoryExport/Index.test.js
index 4c3fe309ed3e1a3e097a8f863b04313720d473b5..5c5c754a227ac134f1d0944ac3695a259a31e128 100644
--- a/client/src/components/HistoryExport/Index.test.js
+++ b/client/src/components/HistoryExport/Index.test.js
@@ -1,24 +1,20 @@
 import { createTestingPinia } from "@pinia/testing";
 import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useFileSources } from "@/composables/fileSources";
 
 import Index from "./Index.vue";
 
-jest.mock("@/api/schema");
+jest.mock("@/composables/fileSources");
 
 const localVue = getLocalVue();
 
-describe("Index.vue", () => {
-    beforeEach(() => {
-        mockFetcher
-            .path("/api/remote_files/plugins")
-            .method("get")
-            .mock({ data: [{ id: "foo", writable: false }] });
-    });
+useFileSources.mockReturnValue({ isLoading: false, hasWritable: true });
 
-    it("should render tabs", () => {
+describe("Index.vue", () => {
+    it("should render tabs", async () => {
         // just make sure the component renders to catch obvious big errors
         const pinia = createTestingPinia();
         const wrapper = shallowMount(Index, {
@@ -28,6 +24,8 @@ describe("Index.vue", () => {
             localVue,
             pinia,
         });
-        expect(wrapper.exists("b-tabs-stub")).toBeTruthy();
+        await flushPromises();
+        const tabs = wrapper.findComponent(".history-export-tabs");
+        expect(tabs.exists()).toBeTruthy();
     });
 });
diff --git a/client/src/components/HistoryExport/Index.vue b/client/src/components/HistoryExport/Index.vue
index 2b1552006b543c90ef0f7ec8593c4517faec7f21..b79a38e83c5fbe75b53bd5e93fb706297bb1bb5b 100644
--- a/client/src/components/HistoryExport/Index.vue
+++ b/client/src/components/HistoryExport/Index.vue
@@ -23,7 +23,7 @@ const props = defineProps<ExportHistoryProps>();
         </span>
         <span v-else-if="hasWritableFileSources">
             <BCard no-body>
-                <BTabs pills card vertical>
+                <BTabs pills card vertical class="history-export-tabs">
                     <BTab title="to a link" title-link-class="tab-export-to-link" active>
                         <b-card-text>
                             <ToLink :history-id="props.historyId" />
diff --git a/client/src/components/HistoryImport.test.js b/client/src/components/HistoryImport.test.js
index 588080aebb7d60521fe85c17d708052de32d197b..120a0c07306e4d6db9764b260ab569ff5be2616b 100644
--- a/client/src/components/HistoryImport.test.js
+++ b/client/src/components/HistoryImport.test.js
@@ -1,33 +1,45 @@
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
-import { waitOnJob } from "components/JobStates/wait";
 import flushPromises from "flush-promises";
 import { getLocalVue, wait } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
+import { waitOnJob } from "@/components/JobStates/wait";
 
 import HistoryImport from "./HistoryImport.vue";
 
 const localVue = getLocalVue();
 const TEST_JOB_ID = "job123789";
-const TEST_HISTORY_URI = "/api/histories";
 const TEST_SOURCE_URL = "http://galaxy.example/import";
-const TEST_PLUGINS_URL = "/api/remote_files/plugins";
 
-jest.mock("@/api/schema");
 jest.mock("components/JobStates/wait");
 
+const { server, http } = useServerMock();
+
 describe("HistoryImport.vue", () => {
-    let axiosMock;
     let wrapper;
 
     beforeEach(async () => {
-        axiosMock = new MockAdapter(axios);
-        mockFetcher
-            .path(TEST_PLUGINS_URL)
-            .method("get")
-            .mock({ data: [{ id: "foo", writable: false }] });
+        server.use(
+            http.get("/api/remote_files/plugins", ({ response }) => {
+                return response(200).json([
+                    {
+                        id: "_ftp",
+                        type: "gxftp",
+                        uri_root: "gxftp://",
+                        label: "FTP Directory",
+                        doc: "Galaxy User's FTP Directory",
+                        writable: false,
+                        browsable: true,
+                        supports: {
+                            pagination: false,
+                            search: false,
+                            sorting: false,
+                        },
+                    },
+                ]);
+            })
+        );
+
         wrapper = mount(HistoryImport, {
             propsData: {},
             localVue,
@@ -61,10 +73,14 @@ describe("HistoryImport.vue", () => {
             sourceURL: TEST_SOURCE_URL,
         });
         let formData;
-        axiosMock.onPost(TEST_HISTORY_URI).reply((request) => {
-            formData = request.data;
-            return [200, { job_id: TEST_JOB_ID }];
-        });
+
+        server.use(
+            http.post("/api/histories", async ({ response, request }) => {
+                formData = await request.formData();
+                return response(200).json({ job_id: TEST_JOB_ID });
+            })
+        );
+
         let then;
         waitOnJob.mockReturnValue(
             new Promise((then_) => {
@@ -99,8 +115,4 @@ describe("HistoryImport.vue", () => {
         const link = alert.find("a");
         expect(link.text()).toContain("GTN");
     });
-
-    afterEach(() => {
-        axiosMock.restore();
-    });
 });
diff --git a/client/src/components/HistoryImport.vue b/client/src/components/HistoryImport.vue
index 08b1eb44b21a387a16532595ec4eb1781bf5feb2..f024c0991485825a11d123a76584c66f7a30db5a 100644
--- a/client/src/components/HistoryImport.vue
+++ b/client/src/components/HistoryImport.vue
@@ -91,6 +91,7 @@ import { waitOnJob } from "components/JobStates/wait";
 import LoadingSpan from "components/LoadingSpan";
 import { getAppRoot } from "onload/loadConfig";
 import { errorMessageAsString } from "utils/simple-error";
+import { capitalizeFirstLetter } from "utils/strings";
 import Vue, { ref, watch } from "vue";
 
 import { fetchFileSources } from "@/api/remoteFiles";
@@ -165,7 +166,7 @@ export default {
             return this.invocationImport ? "invocation" : "history";
         },
         identifierTextCapitalized() {
-            return this.identifierText.charAt(0).toUpperCase() + this.identifierText.slice(1);
+            return capitalizeFirstLetter(this.identifierText);
         },
         identifierTextPlural() {
             return this.invocationImport ? "invocations" : "histories";
diff --git a/client/src/components/JobDestinationParams/JobDestinationParams.test.ts b/client/src/components/JobDestinationParams/JobDestinationParams.test.ts
index 5486f481f91d035a90aad83d56869b5383574c1d..b5f5fdc5d06a2a69ac274e4c5f21879c87d16d6e 100644
--- a/client/src/components/JobDestinationParams/JobDestinationParams.test.ts
+++ b/client/src/components/JobDestinationParams/JobDestinationParams.test.ts
@@ -1,9 +1,10 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { shallowMount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
 import { useUserStore } from "@/stores/userStore";
 
 import jobDestinationResponseData from "./testData/jobDestinationResponse.json";
@@ -12,14 +13,18 @@ import JobDestinationParams from "./JobDestinationParams.vue";
 
 const JOB_ID = "foo_job_id";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue();
 
 const jobDestinationResponse = jobDestinationResponseData as Record<string, string | null>;
 
+const { server, http } = useServerMock();
+
 async function mountJobDestinationParams() {
-    mockFetcher.path("/api/jobs/{job_id}/destination_params").method("get").mock({ data: jobDestinationResponse });
+    server.use(
+        http.get("/api/jobs/{job_id}/destination_params", ({ response }) => {
+            return response(200).json(jobDestinationResponse);
+        })
+    );
 
     const pinia = createPinia();
     const wrapper = shallowMount(JobDestinationParams as object, {
@@ -31,14 +36,7 @@ async function mountJobDestinationParams() {
     });
 
     const userStore = useUserStore();
-    userStore.currentUser = {
-        email: "admin@email",
-        id: "1",
-        tags_used: [],
-        isAnonymous: false,
-        total_disk_usage: 1048576,
-        is_admin: true,
-    };
+    userStore.currentUser = getFakeRegisteredUser({ is_admin: true });
 
     await flushPromises();
 
diff --git a/client/src/components/JobInformation/CodeRow.vue b/client/src/components/JobInformation/CodeRow.vue
index 0e5ec8e235979bf63165b9955a3066d250b2bf1f..f3a343a061408f15f99c6fff91ea5fc726e56123 100644
--- a/client/src/components/JobInformation/CodeRow.vue
+++ b/client/src/components/JobInformation/CodeRow.vue
@@ -13,9 +13,12 @@
                 <b-col cols="11">
                     <pre :class="codeClass">{{ codeItem }}</pre>
                 </b-col>
-                <b-col class="nopadding pointer"
+                <b-col
                     v-b-tooltip.hover
+                    class="nopadding pointer"
                     :title="`click to ${action}`"
+                    @mousedown="mouseIsDown = true"
+                    @mousemove="mouseIsDown ? (mouseMoved = true) : (mouseMoved = false)"
                     @mouseup="toggleExpanded()">
                     <FontAwesomeIcon :icon="iconClass" />
                 </b-col>
@@ -61,12 +64,12 @@ export default {
     updated() {
         try {
             var codeDiv = this.$el.querySelector(".code");
-            if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5)  {
-                    // scroll is at the bottom
-                    codeDiv.scrollTop = codeDiv.scrollHeight;
+            if (codeDiv.scrollTop + codeDiv.offsetHeight >= this.lastPos - 5) {
+                // scroll is at the bottom
+                codeDiv.scrollTop = codeDiv.scrollHeight;
             }
             this.lastPos = codeDiv.scrollHeight;
-        } catch(exception) {
+        } catch (exception) {
             console.debug("Code div is not present");
         }
     },
@@ -94,4 +97,8 @@ export default {
     padding: 0;
     margin: 0;
 }
+.code {
+    max-height: 50em;
+    overflow: auto;
+}
 </style>
diff --git a/client/src/components/JobInformation/JobDetails.vue b/client/src/components/JobInformation/JobDetails.vue
index a6fbc5dc619b37cc87306afd4a7cf4134c4cd96a..3a75449a67bf0db4838709783ed6b955f716e2cd 100644
--- a/client/src/components/JobInformation/JobDetails.vue
+++ b/client/src/components/JobInformation/JobDetails.vue
@@ -1,6 +1,7 @@
 <template>
     <b-card>
         <JobInformation :job_id="id" :include-times="true">
+            <!-- only needed for admin job component -->
             <tr v-if="hasTraceback">
                 <td>Traceback</td>
                 <td>
diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index ec6a612c9200bdf8e6e89f2085f02da87d58be50..5e7e2cf6d7f627b84b969b866f3660ae0458d8ad 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -1,12 +1,13 @@
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import JobInformation from "./JobInformation";
+import { useServerMock } from "@/api/client/__mocks__";
+
 import jobResponse from "./testData/jobInformationResponse.json";
 
+import JobInformation from "./JobInformation.vue";
+
 jest.mock("app");
 
 const JOB_ID = "test_id";
@@ -16,20 +17,30 @@ const STDOUT_TEXT = "stdout";
 
 const localVue = getLocalVue();
 
+const { server, http } = useServerMock();
+
 describe("JobInformation/JobInformation.vue", () => {
     let wrapper;
     let jobInfoTable;
-    let axiosMock;
 
     beforeEach(() => {
-        axiosMock = new MockAdapter(axios);
-        axiosMock.onGet(new RegExp(`api/configuration/decode/*`)).reply(200, { decoded_id: 123 });
-        axiosMock.onGet("/api/jobs/test_id?full=True").reply(200, jobResponse);
-        axiosMock.onGet("/api/invocations?job_id=test_id").reply(200, []);
-    });
-
-    afterEach(() => {
-        axiosMock.restore();
+        server.use(
+            http.get("/api/configuration/decode/{encoded_id}", ({ response }) => {
+                return response(200).json({ decoded_id: 123 });
+            }),
+            http.get("/api/jobs/{job_id}", ({ response }) => {
+                return response(200).json(jobResponse);
+            }),
+            http.get("/api/invocations", ({ response }) => {
+                return response(200).json([]);
+            }),
+            http.get("/api/jobs/{job_id}/console_output", ({ response }) => {
+                return response(200).json({
+                    stdout: "stdout",
+                    stderr: "stderr",
+                });
+            })
+        );
     });
 
     const verifyValues = (rendered_entries, infoTable, backendResponse) => {
@@ -65,8 +76,8 @@ describe("JobInformation/JobInformation.vue", () => {
         // table should exist
         expect(jobInfoTable).toBeTruthy();
         const rows = jobInfoTable.findAll("tr");
-        // should contain 9 rows
-        expect(rows.length).toBe(9);
+        // should contain 10 rows
+        expect(rows.length).toBe(10);
     });
 
     it("stdout and stderr should be rendered", async () => {
@@ -94,5 +105,6 @@ describe("JobInformation/JobInformation.vue", () => {
             { id: "encoded-copied-from-job-id", backend_key: "copied_from_job_id" },
         ];
         verifyValues(rendered_entries, jobInfoTable, jobResponse);
+        expect(wrapper.find('td[data-description="galaxy-job-state"]').exists()).toBe(true);
     });
 });
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index 0c68bc4d81903b49d4112569e7bade15dc1d6e4f..afe859e7a142bdcfb7e283ca1102738932f3065a 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -4,16 +4,18 @@ import HelpText from "components/Help/HelpText";
 import { JobConsoleOutputProvider, JobDetailsProvider } from "components/providers/JobProvider";
 import UtcDate from "components/UtcDate";
 import { NON_TERMINAL_STATES } from "components/WorkflowInvocationState/util";
-import { formatDuration, intervalToDuration } from "date-fns";
-import { computed, ref } from "vue";
+import { computed, ref, watch } from "vue";
 
-import { invocationForJob } from "@/api/invocations";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
+
+import { getJobDuration } from "./utilities";
 
 import DecodedId from "../DecodedId.vue";
 import CodeRow from "./CodeRow.vue";
 
 const job = ref(null);
-const invocationId = ref(null);
+const invocationId = ref(undefined);
 
 const props = defineProps({
     job_id: {
@@ -34,12 +36,18 @@ const stderr_text = ref("");
 const stdout_position = computed(() => stdout_text.value.length);
 const stderr_position = computed(() => stderr_text.value.length);
 
-const runTime = computed(() =>
-    formatDuration(intervalToDuration({ start: new Date(job.value.create_time), end: new Date(job.value.update_time) }))
-);
+const runTime = computed(() => getJobDuration(job.value));
+
+function jobStateIsTerminal(jobState) {
+    return jobState && !NON_TERMINAL_STATES.includes(jobState);
+}
 
-const jobIsTerminal = computed(() => job.value && !NON_TERMINAL_STATES.includes(job.value.state));
+function jobStateIsRunning(jobState) {
+    return jobState == "running";
+}
 
+const jobIsTerminal = computed(() => jobStateIsTerminal(job?.value?.state));
+const jobIsRunning = computed(() => jobStateIsRunning(job?.value?.state));
 const routeToInvocation = computed(() => `/workflows/invocations/${invocationId.value}`);
 
 const metadataDetail = ref({
@@ -49,10 +57,7 @@ const metadataDetail = ref({
 
 function updateJob(newJob) {
     job.value = newJob;
-    if (newJob) {
-        fetchInvocation(newJob.id);
-    }
-    if (jobIsTerminal.value) {
+    if (jobStateIsTerminal(newJob?.state)) {
         if (newJob.tool_stdout) {
             stdout_text.value = newJob.tool_stdout;
         }
@@ -85,20 +90,48 @@ function filterMetadata(jobMessages) {
     });
 }
 
-async function fetchInvocation(jobId) {
+async function fetchInvocationForJob(jobId) {
     if (jobId) {
-        const invocation = await invocationForJob({ jobId: jobId });
-        if (invocation) {
-            invocationId.value = invocation.id;
+        const { data: invocations, error } = await GalaxyApi().GET("/api/invocations", {
+            params: {
+                query: { job_id: jobId },
+            },
+        });
+
+        if (error) {
+            rethrowSimple(error);
         }
+
+        if (invocations.length) {
+            return invocations[0];
+        }
+
+        return null;
     }
 }
+
+// Fetches the invocation for the given job id to get the associated invocation id
+watch(
+    () => props.job_id,
+    async (newId, oldId) => {
+        if (newId && (invocationId.value === undefined || newId !== oldId)) {
+            const invocation = await fetchInvocationForJob(newId);
+            if (invocation) {
+                invocationId.value = invocation.id;
+            } else {
+                invocationId.value = null;
+            }
+        }
+    },
+    { immediate: true }
+);
 </script>
 
 <template>
     <div>
         <JobDetailsProvider auto-refresh :job-id="props.job_id" @update:result="updateJob" />
         <JobConsoleOutputProvider
+            v-if="jobIsRunning"
             auto-refresh
             :job-id="props.job_id"
             :stdout_position="stdout_position"
diff --git a/client/src/components/JobInformation/testData/jobInformationResponse.json b/client/src/components/JobInformation/testData/jobInformationResponse.json
index a53d9efa9108301ff75779009f26eb332d9d4744..4a74f832272d8dc63461f319a8fded9d1bff46db 100644
--- a/client/src/components/JobInformation/testData/jobInformationResponse.json
+++ b/client/src/components/JobInformation/testData/jobInformationResponse.json
@@ -7,5 +7,6 @@
     "command_line": "commandline",
     "job_messages": ["test-msg1", "test-msg2", "test-msg3", "test-msg4"],
     "id": "test_id",
-    "copied_from_job_id": "test_copied_from_job_id"
+    "copied_from_job_id": "test_copied_from_job_id",
+    "state": "running"
 }
diff --git a/client/src/components/JobInformation/utilities.ts b/client/src/components/JobInformation/utilities.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2dff242f94f300d265299fc6224e02c02a27bf46
--- /dev/null
+++ b/client/src/components/JobInformation/utilities.ts
@@ -0,0 +1,7 @@
+import { formatDuration, intervalToDuration } from "date-fns";
+
+import type { JobBaseModel } from "@/api/jobs";
+
+export function getJobDuration(job: JobBaseModel): string {
+    return formatDuration(intervalToDuration({ start: new Date(job.create_time), end: new Date(job.update_time) }));
+}
diff --git a/client/src/components/JobMetrics/JobMetrics.test.js b/client/src/components/JobMetrics/JobMetrics.test.js
index b8e934489e9db56b18acfbc4a506fd7a38c61a0d..529bf66a766353ddd079403d21ec70cc6298dbc4 100644
--- a/client/src/components/JobMetrics/JobMetrics.test.js
+++ b/client/src/components/JobMetrics/JobMetrics.test.js
@@ -6,6 +6,8 @@ import { getLocalVue } from "tests/jest/helpers";
 
 import JobMetrics from "./JobMetrics";
 
+const NO_METRICS_MESSAGE = "No metrics available for this job.";
+
 // Ignore all axios calls, data is mocked locally -- just say "OKAY!"
 jest.mock("axios", () => ({
     get: async () => {
@@ -26,7 +28,8 @@ describe("JobMetrics/JobMetrics.vue", () => {
         });
 
         await wrapper.vm.$nextTick();
-        expect(wrapper.find("div").exists()).toBe(false);
+        const alert = wrapper.find(".alert-info");
+        expect(alert.text()).toBe(NO_METRICS_MESSAGE);
     });
 
     it("should group plugins by type", async () => {
diff --git a/client/src/components/JobMetrics/JobMetrics.vue b/client/src/components/JobMetrics/JobMetrics.vue
index 469dc3062e731157e8a0ed014e6e8fb474137c2b..78dc294c002c0d3bb40348c05961a3024558340b 100644
--- a/client/src/components/JobMetrics/JobMetrics.vue
+++ b/client/src/components/JobMetrics/JobMetrics.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
 import { computed, ref, unref, watch } from "vue";
 
 import { useJobMetricsStore } from "@/stores/jobMetricsStore";
@@ -217,4 +218,5 @@ const estimatedServerInstance = computed(() => {
             :cores-allocated="coresAllocated"
             :memory-allocated-in-mebibyte="memoryAllocatedInMebibyte" />
     </div>
+    <BAlert v-else variant="info" show> No metrics available for this job. </BAlert>
 </template>
diff --git a/client/src/components/JobParameters/JobParameters.test.ts b/client/src/components/JobParameters/JobParameters.test.ts
index 5a1887356e1ae84cd73e42d141698fa3befc5fd8..72256723c4634d700bd02f02ff9f4bedabe6e9f9 100644
--- a/client/src/components/JobParameters/JobParameters.test.ts
+++ b/client/src/components/JobParameters/JobParameters.test.ts
@@ -1,4 +1,4 @@
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
diff --git a/client/src/components/JobParameters/JobParametersArrayValue.vue b/client/src/components/JobParameters/JobParametersArrayValue.vue
index 31be3694434ae301ea0ac232a6af1c3e3e5ea28b..014d0e6d12dec38c75174ae755521f97684a0bb2 100644
--- a/client/src/components/JobParameters/JobParametersArrayValue.vue
+++ b/client/src/components/JobParameters/JobParametersArrayValue.vue
@@ -1,8 +1,9 @@
 <template>
     <div>
         <div v-for="(elVal, pvIndex) in parameter_value" :key="pvIndex">
+            <span v-if="elVal === null">No input provided</span>
             <GenericHistoryItem
-                v-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
+                v-else-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
                 :item-id="elVal.id"
                 :item-src="elVal.src" />
             <span v-else> {{ elVal.hid }}: {{ elVal.name }} </span>
diff --git a/client/src/components/Landing/ToolLanding.vue b/client/src/components/Landing/ToolLanding.vue
new file mode 100644
index 0000000000000000000000000000000000000000..0d1b91c35ebba88ba765e097b5e0c25becd8a1c3
--- /dev/null
+++ b/client/src/components/Landing/ToolLanding.vue
@@ -0,0 +1,5 @@
+<script setup lang="ts"></script>
+
+<template>
+    <div>This a place holder for a feature that is not currently implemented.</div>
+</template>
diff --git a/client/src/components/Landing/WorkflowLanding.vue b/client/src/components/Landing/WorkflowLanding.vue
new file mode 100644
index 0000000000000000000000000000000000000000..5b4d1b90b4c7dcdcc067b0edaeed4993d9e46dca
--- /dev/null
+++ b/client/src/components/Landing/WorkflowLanding.vue
@@ -0,0 +1,52 @@
+<script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+
+import { useActivityStore } from "@/stores/activityStore";
+import { useWorkflowLandingStore } from "@/stores/workflowLandingStore";
+
+import LoadingSpan from "@/components/LoadingSpan.vue";
+import WorkflowRun from "@/components/Workflow/Run/WorkflowRun.vue";
+
+interface Props {
+    uuid: string;
+    secret?: string;
+    public?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    secret: undefined,
+    public: false,
+});
+
+const store = useWorkflowLandingStore();
+const { claimWorkflow } = store;
+const { claimState } = storeToRefs(store);
+
+const activityStore = useActivityStore("default");
+
+// Start claim immediately
+claimWorkflow(props.uuid, props.public, props.secret).then(() => {
+    activityStore.closeSideBar();
+});
+</script>
+
+<template>
+    <div>
+        <div v-if="claimState.errorMessage">
+            <BAlert variant="danger" show>
+                {{ claimState.errorMessage }}
+            </BAlert>
+        </div>
+        <div v-else-if="!claimState.workflowId">
+            <LoadingSpan message="Loading workflow parameters" />
+        </div>
+        <div v-else>
+            <WorkflowRun
+                :workflow-id="claimState.workflowId"
+                :prefer-simple-form="true"
+                :request-state="claimState.requestState"
+                :instance="claimState.instance" />
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Libraries/LibraryEditField.vue b/client/src/components/Libraries/LibraryEditField.vue
index f18a986d67337e35b4899c24fa5394b104a87219..40f88d4d0b0c9973fa5ba9b2bcfdceba1ad82501 100644
--- a/client/src/components/Libraries/LibraryEditField.vue
+++ b/client/src/components/Libraries/LibraryEditField.vue
@@ -6,7 +6,7 @@
                 <b-form-textarea class="form-control" :value="text" rows="3" no-resize @change="updateValue" />
             </div>
             <!-- shrink long text -->
-            <div v-else-if="text.length > maxDescriptionLength && !isExpanded">
+            <div v-else-if="text && text.length > maxDescriptionLength && !isExpanded">
                 <!-- eslint-disable vue/no-v-html -->
                 <span
                     class="shrinked-description"
@@ -20,10 +20,10 @@
             <!-- Regular -->
             <div v-else>
                 <!-- eslint-disable-next-line vue/no-v-html -->
-                <div v-html="linkify(sanitize(text))"></div>
+                <div v-html="linkify(sanitize(text ?? ''))"></div>
                 <!-- hide toggle expand if text is too short -->
                 <a
-                    v-if="text.length > maxDescriptionLength"
+                    v-if="text && text.length > maxDescriptionLength"
                     class="more-text-btn"
                     href="javascript:void(0)"
                     @click="toggleDescriptionExpand"
@@ -47,6 +47,7 @@ export default {
     props: {
         text: {
             type: String,
+            required: false,
         },
         changedValue: {
             type: String,
diff --git a/client/src/components/Libraries/LibraryFolder/LibraryFolder.vue b/client/src/components/Libraries/LibraryFolder/LibraryFolder.vue
index 6e2e6138ca00902f1d041f9cafe97b8ccc9ce5d7..0862a434916fc647aa2c3d57862fae5d20168cd1 100644
--- a/client/src/components/Libraries/LibraryFolder/LibraryFolder.vue
+++ b/client/src/components/Libraries/LibraryFolder/LibraryFolder.vue
@@ -1,9 +1,11 @@
 <template>
     <div>
         <FolderTopBar
+            :search-text="searchText"
+            :can-add-library-item="canAddLibraryItem"
             :folder-contents="folderContents"
             :include-deleted.sync="includeDeleted"
-            :folder_id="currentFolderId"
+            :folder-id="currentFolderId"
             :selected="selected"
             :metadata="folder_metadata"
             :unselected="unselected"
@@ -285,6 +287,7 @@ Vue.use(BootstrapVue);
 
 function initialFolderState() {
     return {
+        canAddLibraryItem: false,
         selected: [],
         unselected: [],
         expandedMessage: [],
@@ -381,12 +384,13 @@ export default {
                     this.sortBy,
                     this.sortDesc,
                     this.perPage,
-                    (this.currentPage - 1) * this.perPage,
+                    (this.currentPage ? this.currentPage - 1 : 0) * this.perPage,
                     this.searchText
                 )
                 .then((response) => {
                     this.folderContents = response.folder_contents;
                     this.folder_metadata = response.metadata;
+                    this.canAddLibraryItem = response.metadata.can_add_library_item;
                     this.total_rows = response.metadata.total_rows;
                     if (this.isAllSelectedMode) {
                         this.selected = [];
@@ -450,7 +454,12 @@ export default {
                 }
             });
 
-            return this.selected.length + unselectable === this.$refs.folder_content_table.computedItems.length;
+            const numComputedItems = this.$refs.folder_content_table.computedItems.length;
+            if (numComputedItems === 0 || numComputedItems === unselectable) {
+                return false;
+            }
+
+            return this.selected.length + unselectable === numComputedItems;
         },
         toggleSelect() {
             this.unselected = [];
diff --git a/client/src/components/Libraries/LibraryFolder/LibraryFolderDataset/LibraryDataset.vue b/client/src/components/Libraries/LibraryFolder/LibraryFolderDataset/LibraryDataset.vue
index fcf0365d0094505eee1177818a8764ca9c07939e..48133bf1e9d66710f2024d5dd61b1a5a8d153aec 100644
--- a/client/src/components/Libraries/LibraryFolder/LibraryFolderDataset/LibraryDataset.vue
+++ b/client/src/components/Libraries/LibraryFolder/LibraryFolderDataset/LibraryDataset.vue
@@ -38,7 +38,7 @@
                 </b-button>
             </span>
             <b-button
-                v-if="currentUser.is_admin"
+                v-if="currentUser?.is_admin"
                 title="Manage permissions"
                 class="mr-1 mb-2"
                 :to="{
@@ -83,7 +83,7 @@
                             collection-name="Data Types"
                             :loading="loadingDatatypes"
                             :items="datatypes"
-                            :current-item-id="dataset.file_ext"
+                            :current-item="datatypes?.find((datatype) => datatype.id === dataset.file_ext)"
                             @update:selected-item="onSelectedDatatype" />
                     </DatatypesProvider>
                     <DbKeyProvider
@@ -93,7 +93,7 @@
                             collection-name="Database/Builds"
                             :loading="loadingDbKeys"
                             :items="dbkeys"
-                            :current-item-id="dataset.genome_build"
+                            :current-item="dbkeys?.find((dbkey) => dbkey.id === dataset.genome_build)"
                             @update:selected-item="onSelectedDbKey" />
                     </DbKeyProvider>
                     <b-form-input
diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/DirectoryDatasetPicker.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/DirectoryDatasetPicker.vue
new file mode 100644
index 0000000000000000000000000000000000000000..80423a10e8597f3359c189ce6b9678bef32311e0
--- /dev/null
+++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/DirectoryDatasetPicker.vue
@@ -0,0 +1,366 @@
+<script setup lang="ts">
+import {
+    BAlert,
+    BButton,
+    BFormCheckbox,
+    BFormCheckboxGroup,
+    BFormGroup,
+    BFormTextarea,
+    BModal,
+    BTab,
+    BTabs,
+} from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { type Option } from "@/components/Form/Elements/FormDrilldown/utilities";
+import { type DetailedDatatypes, useDetailedDatatypes } from "@/composables/datatypes";
+import { Toast } from "@/composables/toast";
+import { useDbKeyStore } from "@/stores/dbKeyStore";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import FormDrilldown from "@/components/Form/Elements/FormDrilldown/FormDrilldown.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+import SingleItemSelector from "@/components/SingleItemSelector.vue";
+
+const autoExtension = {
+    id: "auto",
+    extension: "auto",
+    text: "Auto-detect",
+    description: `This system will try to detect the file type automatically.
+                     If your file is not detected properly as one of the known formats,
+                     it most likely means that it has some format problems (e.g., different
+                     number of columns on different rows). You can still coerce the system
+                     to set your data to the format you think it should be.
+                     You can also upload compressed files, which will automatically be decompressed`,
+    descriptionUrl: "",
+};
+
+type DbKey = { id: string; text: string };
+type DbKeyList = DbKey[];
+
+type RequestData = {
+    path: string;
+    source: string;
+    dbkey: string;
+    encoded_folder_id: string;
+    file_type?: string;
+    preserve_dirs?: boolean;
+    link_data: boolean;
+    space_to_tab: boolean;
+    to_posix_lines: boolean;
+    tag_using_filenames: boolean;
+};
+
+interface Props {
+    folderId: string;
+    target: "userdir" | "importdir" | "path";
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "reload"): void;
+    (e: "onClose"): void;
+    (e: "onSelect", items: RequestData[]): void;
+}>();
+
+const dbKeyStore = useDbKeyStore();
+const { datatypes, datatypesLoading } = useDetailedDatatypes();
+
+const activeTab = ref(0);
+const importing = ref(false);
+const paths = ref<string>("");
+const options = ref<Option[]>([]);
+const optionsLoading = ref(false);
+const selectedDbKey = ref<DbKey>();
+const dbKeyList = ref<DbKeyList>([]);
+const errorMessage = ref<string>("");
+const currentValue = ref<string[]>([]);
+const preserveOptions = ref<string[]>([]);
+const extensionsList = ref<DetailedDatatypes[]>([]);
+const selectedExtension = ref<DetailedDatatypes>(autoExtension);
+
+const pathMode = computed(() => {
+    return props.target === "path";
+});
+const filesMode = computed(() => {
+    return activeTab.value === 0;
+});
+const title = computed(() => {
+    return pathMode.value ? "Please enter paths to import" : "Please select folders or files";
+});
+const importDisable = computed(() => {
+    if (importing.value) {
+        return true;
+    }
+
+    if (pathMode.value) {
+        return paths.value?.length === 0;
+    }
+
+    return currentValue.value?.length === 0;
+});
+const okButtonText = computed(() => {
+    const length = currentValue.value?.length || 0;
+
+    return length === 0 ? "Import" : `Import ${length} dataset${length > 1 ? "s" : ""}`;
+});
+
+async function fetchOptions() {
+    optionsLoading.value = true;
+
+    const { data, error } = await GalaxyApi().GET("/api/remote_files", {
+        params: {
+            query: {
+                format: "jstree",
+                target: props.target,
+                disable: filesMode.value ? "folders" : "files",
+            },
+        },
+    });
+
+    options.value = mapDataToOptions(data);
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error, "Failed to load directories.");
+    }
+
+    optionsLoading.value = false;
+}
+
+function mapDataToOptions(data: any): Option[] {
+    return data?.map((item: any) => {
+        const option: Option = {
+            name: item.text,
+            fullPath: item.li_attr.full_path,
+            value: item.li_attr.id,
+            leaf: item.type === "file",
+            disabled: item.state.disabled,
+            options: item.children ? mapDataToOptions(item.children) : [],
+        };
+
+        return option;
+    });
+}
+
+function getFullPathById(id: string): string {
+    function traverse(nodes: Option[], targetId: string): string {
+        for (const node of nodes) {
+            if (node.value === targetId) {
+                return node.fullPath as string;
+            }
+            if (node.options?.length > 0) {
+                const result = traverse(node.options, targetId);
+
+                if (result) {
+                    return result;
+                }
+            }
+        }
+
+        return "";
+    }
+
+    return traverse(options.value, id);
+}
+
+async function fetchExtAndDbKey() {
+    extensionsList.value = datatypes.value;
+
+    extensionsList.value.sort((a, b) => (a.extension > b.extension ? 1 : a.extension < b.extension ? -1 : 0));
+
+    extensionsList.value = [autoExtension, ...extensionsList.value];
+
+    selectedExtension.value = autoExtension;
+
+    await dbKeyStore.fetchUploadDbKeys();
+
+    dbKeyList.value = dbKeyStore.uploadDbKeys as DbKeyList;
+
+    selectedDbKey.value = dbKeyStore.uploadDbKeys.find((item: DbKey) => item.id === "?");
+
+    dbKeyList.value.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
+}
+
+async function onImport() {
+    if (pathMode.value) {
+        const tmp: string[] = paths.value.split("\n");
+        const validPaths: string[] = [];
+
+        for (let i = tmp.length - 1; i >= 0; i--) {
+            var trimmed = tmp?.[i]?.trim();
+            if (trimmed && trimmed?.length !== 0) {
+                validPaths.push(trimmed);
+            }
+        }
+
+        if (validPaths.length === 0) {
+            Toast.error("Please provide a valid path");
+            return;
+        } else {
+            importFileOrFolder(validPaths, "admin_path");
+        }
+    } else {
+        const source = `${props.target}_${filesMode.value ? "file" : "folder"}`;
+        const validPaths: string[] = currentValue.value.map((item) => getFullPathById(item));
+
+        importFileOrFolder(validPaths, source);
+    }
+}
+
+async function importFileOrFolder(validPaths: string[], source: string) {
+    const items: RequestData[] = [];
+
+    for (const path of validPaths) {
+        const reqData: RequestData = {
+            path: path,
+            source: source,
+            dbkey: selectedDbKey.value?.id || "?",
+            encoded_folder_id: props.folderId,
+            link_data: preserveOptions.value.includes("link_files"),
+            space_to_tab: preserveOptions.value.includes("space_to_tab"),
+            to_posix_lines: preserveOptions.value.includes("to_posix_lines"),
+            tag_using_filenames: preserveOptions.value.includes("tags_from_filenames"),
+        };
+
+        if (!pathMode.value) {
+            reqData.file_type = selectedExtension.value.extension;
+        }
+
+        if (!filesMode.value) {
+            reqData.preserve_dirs = preserveOptions.value.includes("preserve_directory_structure");
+        }
+
+        items.push(reqData);
+    }
+
+    emit("onSelect", items);
+    emit("onClose");
+}
+
+watch(
+    activeTab,
+    () => {
+        if (!pathMode.value) {
+            fetchOptions();
+        }
+    },
+    { immediate: true }
+);
+
+function onSelectDbKey(item: DbKey) {
+    selectedDbKey.value = item;
+}
+
+function onSelectExtension(item: DetailedDatatypes) {
+    selectedExtension.value = item;
+}
+
+watch(
+    () => datatypesLoading.value,
+    () => {
+        if (!datatypesLoading.value) {
+            fetchExtAndDbKey();
+        }
+    }
+);
+</script>
+
+<template>
+    <BModal :title="title" visible scrollable content-class="directory-dataset-picker" @hide="emit('onClose')">
+        <BTabs v-if="!pathMode" v-model="activeTab" fill pills>
+            <BTab title="Choose Files" />
+
+            <BTab title="Choose Folders" />
+        </BTabs>
+
+        <BAlert v-if="filesMode" show class="mt-2">
+            All files you select will be imported into the current folder ignoring their folder structure.
+        </BAlert>
+        <BAlert v-else-if="!filesMode" show class="mt-2">
+            All files within the selected folders and their sub-folders will be imported into the current folder.
+        </BAlert>
+        <BAlert v-else-if="pathMode" show class="mt-2">
+            All files within the given folders and their sub-folders will be imported into the current folder.
+        </BAlert>
+
+        <BFormCheckboxGroup v-model="preserveOptions" switches class="directory-dataset-picker-options">
+            <BFormCheckbox value="link_files">Link files instead of copying </BFormCheckbox>
+            <BFormCheckbox value="to_posix_lines">Convert line endings to POSIX</BFormCheckbox>
+            <BFormCheckbox value="space_to_tab">Convert spaces to tabs</BFormCheckbox>
+            <BFormCheckbox value="tags_from_filenames">Tag datasets based on file names</BFormCheckbox>
+            <BFormCheckbox v-if="!filesMode || pathMode" value="preserve_directory_structure">
+                Preserve directory structure
+            </BFormCheckbox>
+        </BFormCheckboxGroup>
+
+        <hr />
+
+        You can set database/build and extension type for all imported datasets at once:
+        <BFormGroup label="Database/Build">
+            <SingleItemSelector
+                :current-item="selectedDbKey"
+                collection-name="DB Keys"
+                :items="dbKeyList"
+                @update:selected-item="onSelectDbKey" />
+        </BFormGroup>
+
+        <BFormGroup label="Extension">
+            <SingleItemSelector
+                :current-item="selectedExtension"
+                collection-name="Extensions"
+                :items="extensionsList"
+                track-by="extension"
+                label="extension"
+                @update:selected-item="onSelectExtension" />
+        </BFormGroup>
+
+        <hr />
+
+        <BFormTextarea
+            v-if="pathMode"
+            id="import_paths"
+            v-model="paths"
+            placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"
+            rows="5" />
+        <BAlert v-else-if="optionsLoading" variant="info" show>
+            <LoadingSpan message="Loading directories" />
+        </BAlert>
+        <BAlert v-else-if="errorMessage" variant="danger" show>
+            {{ errorMessage }}
+        </BAlert>
+        <FormDrilldown
+            v-else
+            :id="filesMode ? 'files' : 'folders'"
+            v-model="currentValue"
+            class="directory-dataset-picker-list"
+            show-icons
+            :options="options"
+            multiple />
+
+        <template v-slot:modal-footer>
+            <BButton size="sm" variant="secondary" :disabled="importing" @click="emit('onClose')">Close</BButton>
+            <BButton size="sm" variant="primary" :disabled="importDisable" @click="onImport">
+                {{ okButtonText }}
+            </BButton>
+        </template>
+    </BModal>
+</template>
+
+<style scoped lang="scss">
+.directory-dataset-picker {
+    display: grid;
+    grid-template-rows: max-content 1fr;
+
+    .directory-dataset-picker-options {
+        display: grid;
+        grid-template-columns: 1fr 1fr;
+    }
+
+    .directory-dataset-picker-list {
+        max-height: 100%;
+        overflow-y: auto;
+    }
+}
+</style>
diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue
index 41353ebb30d0d6a74a8053847c282604190b7c70..2e619d5d0a11b124898742b4e8d5f0336cb1fdd3 100644
--- a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue
+++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue
@@ -1,350 +1,451 @@
+<script setup lang="ts">
+import { faBook, faCaretDown, faDownload, faHome, faPlus, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import axios from "axios";
+import {
+    BAlert,
+    BButton,
+    BDropdown,
+    BDropdownDivider,
+    BDropdownGroup,
+    BDropdownItem,
+    BFormCheckbox,
+} from "bootstrap-vue";
+import { computed, reactive, ref } from "vue";
+
+import { GalaxyApi } from "@/api";
+import type { CollectionType } from "@/components/History/adapters/buildCollectionModal";
+import { Services } from "@/components/Libraries/LibraryFolder/services";
+import { deleteSelectedItems } from "@/components/Libraries/LibraryFolder/TopToolbar/delete-selected";
+import download from "@/components/Libraries/LibraryFolder/TopToolbar/download";
+import mod_import_collection from "@/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-collection";
+import mod_import_dataset from "@/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset";
+import { type SelectionItem } from "@/components/SelectionDialog/selectionTypes";
+import { useConfig } from "@/composables/config";
+import { Toast } from "@/composables/toast";
+import { getAppRoot } from "@/onload";
+import { useUserStore } from "@/stores/userStore";
+
+import CollectionCreatorModal from "@/components/Collections/CollectionCreatorModal.vue";
+import FolderDetails from "@/components/Libraries/LibraryFolder/FolderDetails/FolderDetails.vue";
+import LibraryBreadcrumb from "@/components/Libraries/LibraryFolder/LibraryBreadcrumb.vue";
+import SearchField from "@/components/Libraries/LibraryFolder/SearchField.vue";
+import DirectoryDatasetPicker from "@/components/Libraries/LibraryFolder/TopToolbar/DirectoryDatasetPicker.vue";
+import ProgressBar from "@/components/ProgressBar.vue";
+import HistoryDatasetPicker from "@/components/SelectionDialog/HistoryDatasetPicker.vue";
+
+type CollectionElement = {
+    deleted: boolean;
+    id: string;
+    name: string;
+    src: string;
+};
+
+interface Props {
+    metadata: any;
+    selected: any[];
+    folderId: string;
+    unselected: any[];
+    searchText: string;
+    folderContents: any[];
+    includeDeleted: boolean;
+    isAllSelectedMode: boolean;
+    canAddLibraryItem?: boolean;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "newFolder"): void;
+    (e: "refreshTable"): void;
+    (e: "fetchFolderContents"): void;
+    (e: "refreshTableContent"): void;
+    (e: "setBusy", value: boolean): void;
+    (e: "deleteFromTable", item: any): void;
+    (e: "updateSearch", value: string): void;
+    (e: "update:includeDeleted", value: boolean): void;
+}>();
+
+const { config, isConfigLoaded } = useConfig();
+
+const userStore = useUserStore();
+
+type ImportSource = "history" | "userdir" | "importdir" | "path" | undefined;
+const modalShow = ref<ImportSource>();
+const progress = ref(false);
+const progressNote = ref("");
+const progressStatus = reactive({
+    total: 0,
+    okCount: 0,
+    errorCount: 0,
+    runningCount: 0,
+});
+
+const services = new Services();
+
+const libraryImportDir = computed(() => isConfigLoaded && config.value?.library_import_dir);
+const allowLibraryPathPaste = computed(() => isConfigLoaded && config.value?.allow_library_path_paste);
+const userLibraryImportDirAvailable = computed(() => isConfigLoaded && config.value?.user_library_import_dir_available);
+const containsFileOrFolder = computed(() => {
+    return props.folderContents.find((el) => el.type === "folder" || el.type === "file");
+});
+const canDelete = computed(() => {
+    return !!props.metadata.can_modify_folder;
+});
+const datasetManipulation = computed(() => {
+    return !!(containsFileOrFolder.value && userStore.currentUser);
+});
+const totalRows = computed(() => {
+    return props.metadata?.total_rows ?? 0;
+});
+
+// Variables for Collection Creation
+const collectionModalType = ref<CollectionType | null>(null);
+const collectionModalShow = ref(false);
+const collectionSelection = ref<any[]>([]);
+const collectionHistoryId = ref<string | null>(null);
+
+function updateSearch(value: string) {
+    emit("updateSearch", value);
+}
+
+function newFolder() {
+    emit("newFolder");
+}
+
+async function getSelected() {
+    if (props.isAllSelectedMode) {
+        try {
+            emit("setBusy", true);
+
+            const selected = await services.getFilteredFolderContents(
+                props.folderId,
+                props.unselected,
+                props.searchText,
+                totalRows.value
+            );
+
+            emit("setBusy", false);
+
+            return selected;
+        } catch (err) {
+            console.error(err);
+        } finally {
+            emit("setBusy", false);
+        }
+
+        return [];
+    } else {
+        return props.selected;
+    }
+}
+
+async function deleteSelected() {
+    try {
+        const selected = await getSelected();
+
+        deleteSelectedItems(
+            selected,
+            (deletedItem: any) => emit("deleteFromTable", deletedItem),
+            () => emit("refreshTable"),
+            () => emit("refreshTableContent")
+        );
+    } catch (err) {
+        console.error(err);
+    }
+}
+
+async function findCheckedItems(idOnly = true) {
+    const folders: any[] = [];
+    const datasets: any[] = [];
+
+    try {
+        const selected = await getSelected();
+
+        selected.forEach((item: any) => {
+            const selectedItem = idOnly ? item.id : item;
+
+            item.type === "file" ? datasets.push(selectedItem) : folders.push(selectedItem);
+        });
+    } catch (err) {
+        console.error(err);
+    }
+
+    return { datasets, folders };
+}
+
+async function downloadData(format: string) {
+    try {
+        const { datasets, folders } = await findCheckedItems();
+
+        if (props.selected.length === 0) {
+            Toast.info("You must select at least one dataset to download");
+
+            return;
+        }
+
+        download(format, datasets, folders);
+    } catch (err) {
+        console.error(err);
+    }
+}
+
+async function importToHistoryModal(isCollection: boolean) {
+    try {
+        const { datasets, folders } = await findCheckedItems(!isCollection);
+
+        const checkedItems: any = props.selected;
+
+        checkedItems.dataset_ids = datasets;
+        checkedItems.folder_ids = folders;
+
+        if (isCollection) {
+            new mod_import_collection.ImportCollectionModal({
+                selected: checkedItems,
+                onCollectionImport: async (
+                    collectionType: string,
+                    selection: { models: CollectionElement[] },
+                    historyId: string
+                ) => {
+                    try {
+                        collectionHistoryId.value = historyId;
+                        collectionModalType.value = collectionType as CollectionType;
+                        collectionSelection.value = selection.models;
+                        collectionModalShow.value = true;
+                    } catch (err) {
+                        console.error(err);
+                    }
+                },
+            });
+        } else {
+            new mod_import_dataset.ImportDatasetModal({
+                selected: checkedItems,
+            });
+        }
+    } catch (err) {
+        console.error(err);
+    }
+}
+
+function onAddDatasets(source?: ImportSource) {
+    modalShow.value = source;
+}
+
+function resetProgress() {
+    progressStatus.total = 0;
+    progressStatus.okCount = 0;
+    progressStatus.errorCount = 0;
+    progressStatus.runningCount = 0;
+}
+
+async function addDatasets(
+    selectedDatasets: SelectionItem[] | Record<string, string | boolean>[],
+    datasetApiCall: Function
+) {
+    resetProgress();
+
+    progress.value = true;
+    progressStatus.total = selectedDatasets.length;
+    progressNote.value = "Adding datasets to the folder";
+
+    emit("setBusy", true);
+
+    for (const dataset of selectedDatasets) {
+        try {
+            progressStatus.runningCount++;
+
+            await datasetApiCall(dataset);
+
+            progressStatus.okCount++;
+        } catch (e) {
+            progressStatus.errorCount++;
+        } finally {
+            progressStatus.runningCount--;
+        }
+    }
+
+    if (progressStatus.errorCount > 0) {
+        progressNote.value = `Added ${progressStatus.okCount} dataset${
+            progressStatus.okCount > 1 ? "s" : ""
+        }, but failed to add ${progressStatus.errorCount} dataset${
+            progressStatus.errorCount > 1 ? "s" : ""
+        } to the folder`;
+    } else {
+        progressNote.value = `Added ${progressStatus.okCount} dataset${
+            progressStatus.okCount > 1 ? "s" : ""
+        } to the folder`;
+    }
+
+    emit("setBusy", false);
+    emit("fetchFolderContents");
+}
+
+function onAddDatasetsFromHistory(selectedDatasets: SelectionItem[]) {
+    const datasetApiCall = async (dataset: SelectionItem) => {
+        const { error } = await GalaxyApi().POST("/api/folders/{folder_id}/contents", {
+            params: {
+                path: { folder_id: props.folderId },
+            },
+            body: {
+                ldda_message: null,
+                from_hda_id: dataset.id,
+            },
+        });
+
+        if (error) {
+            throw new Error(error.err_msg);
+        }
+    };
+
+    addDatasets(selectedDatasets, datasetApiCall);
+}
+
+function onAddDatasetsDirectory(selectedDatasets: Record<string, string | boolean>[]) {
+    const datasetApiCall = async (dataset: Record<string, string | boolean>) => {
+        await axios.post(`${getAppRoot()}api/libraries/datasets`, dataset);
+    };
+
+    addDatasets(selectedDatasets, datasetApiCall);
+}
+</script>
+
 <template>
     <div>
         <div class="form-inline d-flex align-items-center mb-2">
-            <b-button
+            <BButton
                 class="mr-1 btn btn-secondary"
                 :to="{ path: `/libraries` }"
                 data-toggle="tooltip"
                 title="Go to libraries list">
-                <FontAwesomeIcon icon="home" />
-            </b-button>
+                <FontAwesomeIcon :icon="faHome" />
+            </BButton>
+
             <div>
                 <div class="form-inline">
                     <SearchField @updateSearch="updateSearch($event)"></SearchField>
-                    <button
-                        v-if="metadata.can_add_library_item"
+
+                    <BButton
+                        v-if="props.canAddLibraryItem"
                         title="Create new folder"
-                        class="btn btn-secondary toolbtn-create-folder add-library-items add-library-items-folder mr-1"
+                        class="add-library-items-folder mr-1"
                         type="button"
                         @click="newFolder">
-                        <FontAwesomeIcon icon="plus" />
+                        <FontAwesomeIcon :icon="faPlus" />
                         Folder
-                    </button>
-                    <div v-if="metadata.can_add_library_item">
-                        <div
-                            title="Add datasets to current folder"
-                            class="dropdown add-library-items add-library-items-datasets mr-1">
-                            <button type="button" class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
-                                <span class="fa fa-plus"></span> Datasets <span class="caret" />
-                            </button>
-                            <div class="dropdown-menu">
-                                <a class="dropdown-item cursor-pointer" @click="addDatasets('history')">
-                                    from History</a
-                                >
-                                <a
-                                    v-if="user_library_import_dir_available"
-                                    class="dropdown-item cursor-pointer"
-                                    @click="addDatasets('userdir')">
-                                    from User Directory
-                                </a>
-                                <div v-if="library_import_dir || allow_library_path_paste">
-                                    <h2 class="dropdown-header cursor-pointer h-text">Admins only</h2>
-                                    <a
-                                        v-if="library_import_dir"
-                                        class="dropdown-item cursor-pointer"
-                                        @click="addDatasets('importdir')">
-                                        from Import Directory
-                                    </a>
-                                    <a
-                                        v-if="allow_library_path_paste"
-                                        class="dropdown-item cursor-pointer"
-                                        @click="addDatasets('path')">
-                                        from Path
-                                    </a>
-                                </div>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="dropdown mr-1">
-                        <button
-                            type="button"
-                            class="primary-button dropdown-toggle add-to-history"
-                            data-toggle="dropdown">
-                            <FontAwesomeIcon icon="book" />
-                            Add to History <span class="caret"></span>
-                        </button>
-                        <div class="dropdown-menu" role="menu">
-                            <a
-                                href="javascript:void(0)"
-                                role="button"
-                                class="toolbtn-bulk-import add-to-history-datasets dropdown-item"
-                                @click="importToHistoryModal(false)">
-                                as Datasets
-                            </a>
-                            <a
-                                href="javascript:void(0)"
-                                role="button"
-                                class="toolbtn-collection-import add-to-history-collection dropdown-item"
-                                @click="importToHistoryModal(true)">
-                                as a Collection
-                            </a>
-                        </div>
-                    </div>
+                    </BButton>
+
+                    <BDropdown
+                        v-if="props.canAddLibraryItem"
+                        v-b-tooltip.top.noninteractive
+                        right
+                        no-caret
+                        class="add-library-items-datasets mr-1">
+                        <template v-slot:button-content>
+                            <FontAwesomeIcon :icon="faPlus" />
+                            Datasets
+                            <FontAwesomeIcon :icon="faCaretDown" />
+                        </template>
+
+                        <BDropdownItem @click="onAddDatasets('history')"> from History </BDropdownItem>
+
+                        <BDropdownItem v-if="userLibraryImportDirAvailable" @click="onAddDatasets('userdir')">
+                            from User Directory
+                        </BDropdownItem>
+
+                        <BDropdownDivider v-if="libraryImportDir || allowLibraryPathPaste" />
+
+                        <BDropdownGroup v-if="libraryImportDir || allowLibraryPathPaste" header="Admins Only">
+                            <BDropdownItem v-if="libraryImportDir" @click="onAddDatasets('importdir')">
+                                from Import Directory
+                            </BDropdownItem>
+
+                            <BDropdownItem v-if="allowLibraryPathPaste" @click="onAddDatasets('path')">
+                                from Path
+                            </BDropdownItem>
+                        </BDropdownGroup>
+                    </BDropdown>
+
+                    <BDropdown v-b-tooltip.top.noninteractive right no-caret class="add-to-history mr-1">
+                        <template v-slot:button-content>
+                            <FontAwesomeIcon :icon="faBook" />
+                            Add to History
+                            <FontAwesomeIcon :icon="faCaretDown" />
+                        </template>
+
+                        <BDropdownItem class="add-to-history-datasets" @click="importToHistoryModal(false)">
+                            as Datasets
+                        </BDropdownItem>
+
+                        <BDropdownItem class="add-to-history-collection" @click="importToHistoryModal(true)">
+                            as a Collection
+                        </BDropdownItem>
+                    </BDropdown>
+
                     <div
-                        v-if="dataset_manipulation"
+                        v-if="datasetManipulation"
                         title="Download items as archive"
                         class="dropdown dataset-manipulation mr-1">
-                        <button id="download--btn" type="button" class="primary-button" @click="downloadData('zip')">
-                            <FontAwesomeIcon icon="download" />
+                        <BButton id="download--btn" type="button" class="primary-button" @click="downloadData('zip')">
+                            <FontAwesomeIcon :icon="faDownload" />
                             Download
-                        </button>
+                        </BButton>
                     </div>
-                    <button
+
+                    <BButton
                         v-if="canDelete"
                         data-toggle="tooltip"
                         title="Mark items deleted"
                         class="primary-button toolbtn-bulk-delete logged-dataset-manipulation mr-1"
                         type="button"
                         @click="deleteSelected">
-                        <FontAwesomeIcon icon="trash" />
+                        <FontAwesomeIcon :icon="faTrash" />
                         Delete
-                    </button>
-                    <FolderDetails :id="folder_id" class="mr-1" :metadata="metadata" />
+                    </BButton>
+
+                    <FolderDetails :id="props.folderId" class="mr-1" :metadata="props.metadata" />
+
                     <div v-if="canDelete" class="form-check logged-dataset-manipulation mr-1">
-                        <b-form-checkbox :checked="includeDeleted" @change="$emit('update:includeDeleted', $event)">
+                        <BFormCheckbox :checked="props.includeDeleted" @change="$emit('update:includeDeleted', $event)">
                             include deleted
-                        </b-form-checkbox>
+                        </BFormCheckbox>
                     </div>
                 </div>
             </div>
         </div>
 
+        <BAlert v-model="progress" :dismissible="progressStatus.runningCount === 0" variant="info" class="mb-1">
+            <ProgressBar
+                :loading="progressStatus.runningCount > 0"
+                :note="progressNote"
+                :total="progressStatus.total"
+                :ok-count="progressStatus.okCount"
+                :error-count="progressStatus.errorCount"
+                :running-count="progressStatus.runningCount" />
+        </BAlert>
+
         <LibraryBreadcrumb
-            v-if="metadata && metadata.full_path"
-            :full_path="metadata.full_path"
-            :current-id="folder_id" />
+            v-if="props.metadata && props.metadata.full_path"
+            :full_path="props.metadata.full_path"
+            :current-id="props.folderId" />
+
+        <HistoryDatasetPicker
+            v-if="modalShow === 'history'"
+            :folder-id="props.folderId"
+            @onSelect="onAddDatasetsFromHistory"
+            @onClose="onAddDatasets" />
+        <DirectoryDatasetPicker
+            v-else-if="modalShow"
+            :target="modalShow"
+            :folder-id="props.folderId"
+            @onSelect="onAddDatasetsDirectory"
+            @onClose="onAddDatasets" />
+
+        <CollectionCreatorModal
+            v-if="collectionModalType && collectionHistoryId"
+            :history-id="collectionHistoryId"
+            :collection-type="collectionModalType"
+            :selected-items="collectionSelection"
+            :show-modal.sync="collectionModalShow"
+            default-hide-source-items />
     </div>
 </template>
-<script>
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { getGalaxyInstance } from "app";
-import BootstrapVue from "bootstrap-vue";
-import { initTopBarIcons } from "components/Libraries/icons";
-import FolderDetails from "components/Libraries/LibraryFolder/FolderDetails/FolderDetails";
-import LibraryBreadcrumb from "components/Libraries/LibraryFolder/LibraryBreadcrumb";
-import { Toast } from "composables/toast";
-import { getAppRoot } from "onload/loadConfig";
-import mod_utils from "utils/utils";
-import Vue from "vue";
-
-import SearchField from "../SearchField";
-import { Services } from "../services";
-import mod_add_datasets from "./add-datasets";
-import { deleteSelectedItems } from "./delete-selected";
-import download from "./download";
-import mod_import_collection from "./import-to-history/import-collection";
-import mod_import_dataset from "./import-to-history/import-dataset";
-
-initTopBarIcons();
-
-Vue.use(BootstrapVue);
-
-export default {
-    name: "FolderTopBar",
-    components: {
-        SearchField,
-        FontAwesomeIcon,
-        LibraryBreadcrumb,
-        FolderDetails,
-    },
-    props: {
-        folder_id: {
-            type: String,
-            required: true,
-        },
-        includeDeleted: {
-            type: Boolean,
-            required: true,
-        },
-        isAllSelectedMode: {
-            type: Boolean,
-            required: true,
-        },
-        selected: {
-            type: Array,
-            required: true,
-        },
-        unselected: {
-            type: Array,
-            required: true,
-        },
-        metadata: {
-            type: Object,
-            required: true,
-        },
-        folderContents: {
-            type: Array,
-            required: true,
-        },
-    },
-    data() {
-        return {
-            is_admin: false,
-            user_library_import_dir_available: false,
-            library_import_dir: false,
-            allow_library_path_paste: false,
-            list_genomes: [],
-            list_extensions: [],
-            // datatype placeholder for extension auto-detection
-            auto: {
-                id: "auto",
-                text: "Auto-detect",
-                description: `This system will try to detect the file type automatically.
-                     If your file is not detected properly as one of the known formats,
-                     it most likely means that it has some format problems (e.g., different
-                     number of columns on different rows). You can still coerce the system
-                     to set your data to the format you think it should be.
-                     You can also upload compressed files, which will automatically be decompressed`,
-            },
-        };
-    },
-    computed: {
-        contains_file_or_folder: function () {
-            return this.folderContents.find((el) => el.type === "folder" || el.type === "file");
-        },
-        canDelete: function () {
-            return !!(this.contains_file_or_folder && this.is_admin);
-        },
-        dataset_manipulation: function () {
-            const Galaxy = getGalaxyInstance();
-            // logic from legacy code
-            return !!(this.contains_file_or_folder && Galaxy.user);
-        },
-        totalRows: function () {
-            return this.metadata?.total_rows ?? 0;
-        },
-    },
-    created() {
-        const Galaxy = getGalaxyInstance();
-        this.services = new Services();
-        this.is_admin = Galaxy.user.attributes.is_admin;
-        this.user_library_import_dir_available = Galaxy.config.user_library_import_dir_available;
-        this.library_import_dir = Galaxy.config.library_import_dir;
-        this.allow_library_path_paste = Galaxy.config.allow_library_path_paste;
-
-        this.fetchExtAndGenomes();
-    },
-    methods: {
-        updateSearch: function (value) {
-            this.$emit("updateSearch", value);
-        },
-        deleteSelected: function () {
-            this.getSelected().then((selected) =>
-                deleteSelectedItems(
-                    selected,
-                    (deletedItem) => this.$emit("deleteFromTable", deletedItem),
-                    () => this.$emit("refreshTable"),
-                    () => this.$emit("refreshTableContent")
-                )
-            );
-        },
-        async getSelected() {
-            if (this.isAllSelectedMode) {
-                this.$emit("setBusy", true);
-                const selected = await this.services.getFilteredFolderContents(
-                    this.folder_id,
-                    this.unselected,
-                    this.$parent.searchText,
-                    this.totalRows
-                );
-                this.$emit("setBusy", false);
-                return selected;
-            } else {
-                return this.selected;
-            }
-        },
-        newFolder() {
-            this.$emit("newFolder");
-        },
-        downloadData(format) {
-            this.findCheckedItems().then(({ datasets, folders }) => {
-                if (this.selected.length === 0) {
-                    Toast.info("You must select at least one dataset to download");
-                    return;
-                }
-
-                download(format, datasets, folders);
-            });
-        },
-        addDatasets(source) {
-            new mod_add_datasets.AddDatasets({
-                source: source,
-                id: this.folder_id,
-                updateContent: this.updateContent,
-                list_genomes: this.list_genomes,
-                list_extensions: this.list_extensions,
-            });
-        },
-        // helper function to make legacy code compatible
-        findCheckedItems: async function (idOnly = true) {
-            const datasets = [];
-            const folders = [];
-            const selected = await this.getSelected();
-            selected.forEach((item) => {
-                const selected_item = idOnly ? item.id : item;
-                item.type === "file" ? datasets.push(selected_item) : folders.push(selected_item);
-            });
-            return { datasets: datasets, folders: folders };
-        },
-        importToHistoryModal: function (isCollection) {
-            this.findCheckedItems(!isCollection).then(({ datasets, folders }) => {
-                const checkedItems = this.selected;
-                checkedItems.dataset_ids = datasets;
-                checkedItems.folder_ids = folders;
-                if (isCollection) {
-                    new mod_import_collection.ImportCollectionModal({
-                        selected: checkedItems,
-                    });
-                } else {
-                    new mod_import_dataset.ImportDatasetModal({
-                        selected: checkedItems,
-                    });
-                }
-            });
-        },
-        /*
-            Slightly adopted Bootstrap code
-        */
-        /**
-         * Request all extensions and genomes from Galaxy
-         * and save them in sorted arrays.
-         */
-        fetchExtAndGenomes: function () {
-            mod_utils.get({
-                url: `${getAppRoot()}api/datatypes?extension_only=False`,
-                success: (datatypes) => {
-                    this.list_extensions = [];
-                    for (const key in datatypes) {
-                        this.list_extensions.push({
-                            id: datatypes[key].extension,
-                            text: datatypes[key].extension,
-                            description: datatypes[key].description,
-                            description_url: datatypes[key].description_url,
-                        });
-                    }
-                    this.list_extensions.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
-                    this.list_extensions.unshift(this.auto);
-                },
-                cache: true,
-            });
-            mod_utils.get({
-                url: `${getAppRoot()}api/genomes`,
-                success: (genomes) => {
-                    this.list_genomes = [];
-                    for (const key in genomes) {
-                        this.list_genomes.push({
-                            id: genomes[key][1],
-                            text: genomes[key][0],
-                        });
-                    }
-                    this.list_genomes.sort((a, b) => (a.id > b.id ? 1 : a.id < b.id ? -1 : 0));
-                },
-                cache: true,
-            });
-        },
-        updateContent: function () {
-            this.$emit("fetchFolderContents");
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/add-datasets.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/add-datasets.js
deleted file mode 100644
index 5733e40d4957c702c4b16c22eceaf4eac0f729ed..0000000000000000000000000000000000000000
--- a/client/src/components/Libraries/LibraryFolder/TopToolbar/add-datasets.js
+++ /dev/null
@@ -1,839 +0,0 @@
-import "libs/jquery/jstree";
-
-import { getGalaxyInstance } from "app";
-import Backbone from "backbone";
-import { Toast } from "composables/toast";
-import $ from "jquery";
-import { getAppRoot } from "onload/loadConfig";
-import _ from "underscore";
-import _l from "utils/localization";
-
-import { updateProgress } from "./delete-selected";
-import mod_library_model from "./library-model";
-import mod_select from "./ui-select";
-
-var AddDatasets = Backbone.View.extend({
-    options: null,
-
-    initialize: function (options) {
-        this.options = options;
-        this.options.chain_call_control = {
-            total_number: 0,
-            failed_number: 0,
-        };
-
-        this.list_extensions = options.list_extensions;
-        this.list_genomes = options.list_genomes;
-        this.showImportModal(options);
-    },
-
-    /*
-     Slightly adopted Backbone code
-     */
-    showImportModal: function (options) {
-        switch (options.source) {
-            case "history":
-                this.addFilesFromHistoryModal();
-                break;
-            case "importdir":
-                this.importFilesFromGalaxyFolderModal({
-                    source: "importdir",
-                });
-                break;
-            case "path":
-                this.importFilesFromPathModal();
-                break;
-            case "userdir":
-                this.importFilesFromGalaxyFolderModal({
-                    source: "userdir",
-                });
-                break;
-            default:
-                // Galaxy.libraries.library_router.back();
-                Toast.error("Invalid import source.");
-                break;
-        }
-    },
-    templateBrowserModal: function () {
-        return _.template(
-            `<div id="file_browser_modal">
-                    <div style="margin-bottom:1em;">
-                        <label title="Switch to selecting files" class="radio-inline import-type-switch">
-                            <input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked">
-                            Choose Files
-                        </label>
-                        <label title="Switch to selecting folders" class="radio-inline import-type-switch">
-                            <input type="radio" name="jstree-radio" value="jstree-disable-files">
-                            Choose Folders
-                        </label>
-                    </div>
-                    <div class="alert alert-info jstree-files-message">
-                        All files you select will be imported into the current folder ignoring their folder structure.
-                    </div>
-                    <div class="alert alert-info jstree-folders-message" style="display:none;">
-                        All files within the selected folders and their subfolders will be imported into the current folder.
-                    </div>
-                    <div style="margin-bottom:1em;">
-                        <label class="checkbox-inline jstree-preserve-structure" style="display:none;">
-                            <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">
-                                Preserve directory structure
-                            </label>
-                        <label class="checkbox-inline">
-                            <input class="link-checkbox" type="checkbox" value="link_files">
-                                Link files instead of copying
-                        </label>
-                        <label class="checkbox-inline">
-                            <input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">
-                                Convert line endings to POSIX
-                        </label>
-                        <label class="checkbox-inline">
-                            <input class="spacetab-checkbox" type="checkbox" value="space_to_tab">
-                                Convert spaces to tabs
-                        </label>
-                    </div>
-                    <button title="Select all files" type="button" class="button primary-button libimport-select-all">
-                        Select all
-                    </button>
-                    <button title="Select no files" type="button" class="button primary-button libimport-select-none">
-                        Unselect all
-                    </button>
-                    <hr /> <!-- append jstree object here -->
-                    <div id="jstree_browser">
-                    </div>
-                    <hr />
-                    <p>You can set extension type and genome for all imported datasets at once:</p>
-                    <div>
-                        Type: <span id="library_extension_select" class="library-extension-select" />
-                        Genome: <span id="library_genome_select" class="library-genome-select" />
-                    </div>
-                    <br />
-                    <div>
-                        <label class="checkbox-inline tag-files">
-                            Tag datasets based on file names
-                            <input class="tag-files" type="checkbox" value="tag_using_filenames">
-                        </label>
-                    </div>
-                </div>`
-        );
-    },
-    templateImportPathModal: function () {
-        return _.template(
-            `<div id="file_browser_modal">
-                <div class="alert alert-info jstree-folders-message">
-                    All files within the given folders and their subfolders will be imported into the current folder.
-                </div>
-                <div style="margin-bottom: 0.5em;">
-                    <label class="checkbox-inline">
-                        <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">
-                        Preserve directory structure
-                    </label>
-                    <label class="checkbox-inline">
-                        <input class="link-checkbox" type="checkbox" value="link_files">
-                        Link files instead of copying
-                    </label>
-                    <br>
-                    <label class="checkbox-inline">
-                        <input class="posix-checkbox" type="checkbox" value="to_posix_lines" checked="checked">
-                        Convert line endings to POSIX
-                    </label>
-                    <label class="checkbox-inline">
-                        <input class="spacetab-checkbox" type="checkbox" value="space_to_tab">
-                        Convert spaces to tabs
-                    </label>
-                </div>
-                <textarea id="import_paths" class="form-control" rows="5"
-                    placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline" autofocus>
-                </textarea>
-                <hr />
-                <p>You can set extension type and genome for all imported datasets at once:</p>
-                <div>
-                    Type: <span id="library_extension_select" class="library-extension-select"></span>
-                    Genome: <span id="library_genome_select" class="library-genome-select"></span>
-                </div>
-                <div>
-                    <label class="checkbox-inline tag-files">
-                        Tag datasets based on file names
-                        <input class="tag-files" type="checkbox" value="tag_using_filenames">
-                    </label>
-                </div>
-            </div>`
-        );
-    },
-    renderSelectBoxes: function () {
-        const Galaxy = getGalaxyInstance();
-        // This won't work properly unlesss we already have the data fetched.
-        // See this.fetchExtAndGenomes()
-        this.select_genome = new mod_select.View({
-            css: "library-genome-select",
-            data: this.list_genomes,
-            container: Galaxy.modal.$el.find("#library_genome_select"),
-            value: "?",
-        });
-        this.select_extension = new mod_select.View({
-            css: "library-extension-select",
-            data: this.list_extensions,
-            container: Galaxy.modal.$el.find("#library_extension_select"),
-            value: "auto",
-        });
-    },
-    addFilesFromHistoryModal: function () {
-        const Galaxy = getGalaxyInstance();
-        this.histories = new mod_library_model.GalaxyHistories();
-        this.histories
-            .fetch()
-            .done(() => {
-                this.modal = Galaxy.modal;
-                var template_modal = this.templateAddFilesFromHistory();
-                this.modal.show({
-                    closing_events: true,
-                    title: _l("Adding datasets from your history"),
-                    body: template_modal({
-                        histories: this.histories.models,
-                    }),
-                    buttons: {
-                        Add: () => {
-                            this.addAllDatasetsFromHistory();
-                        },
-                        Close: () => {
-                            Galaxy.modal.hide();
-                        },
-                    },
-                    closing_callback: () => {
-                        // TODO update table without fetching new content from the server
-                        // Galaxy.libraries.library_router.navigate(`folders/${this.id}`, { trigger: true });
-                    },
-                });
-                this.fetchAndDisplayHistoryContents(this.histories.models[0].id);
-                $("#dataset_add_bulk").change((event) => {
-                    this.fetchAndDisplayHistoryContents(event.target.value);
-                });
-            })
-            .fail((model, response) => {
-                if (typeof response.responseJSON !== "undefined") {
-                    Toast.error(response.responseJSON.err_msg);
-                } else {
-                    Toast.error("An error occurred.");
-                }
-            });
-    },
-    /**
-     * Create modal for importing from given directory
-     * on Galaxy. Bind jQuery events.
-     */
-    importFilesFromGalaxyFolderModal: function (options) {
-        var template_modal = this.templateBrowserModal();
-        const Galaxy = getGalaxyInstance();
-        this.modal = Galaxy.modal;
-        this.modal.show({
-            closing_events: true,
-            title: _l("Please select folders or files"),
-            body: template_modal({}),
-            buttons: {
-                Import: () => {
-                    this.importFromJstreePath(this, options);
-                },
-                Close: () => {
-                    Galaxy.modal.hide();
-                },
-            },
-            closing_callback: () => {
-                // TODO update table without fetching new content from the server
-                this.options.updateContent();
-                // Galaxy.libraries.library_router.navigate(`folders/${this.id}`, {
-                //     trigger: true,
-                // });
-            },
-        });
-
-        $(".libimport-select-all").bind("click", () => {
-            $("#jstree_browser").jstree("check_all");
-        });
-        $(".libimport-select-none").bind("click", () => {
-            $("#jstree_browser").jstree("uncheck_all");
-        });
-
-        this.renderSelectBoxes();
-        options.disabled_jstree_element = "folders";
-        this.renderJstree(options);
-
-        $("input[type=radio]").change((event) => {
-            if (event.target.value === "jstree-disable-folders") {
-                options.disabled_jstree_element = "folders";
-                this.renderJstree(options);
-                $(".jstree-folders-message").hide();
-                $(".jstree-preserve-structure").hide();
-                $(".jstree-files-message").show();
-            } else if (event.target.value === "jstree-disable-files") {
-                $(".jstree-files-message").hide();
-                $(".jstree-folders-message").show();
-                $(".jstree-preserve-structure").show();
-                options.disabled_jstree_element = "files";
-                this.renderJstree(options);
-            }
-        });
-    },
-    /**
-     * Take the selected items from the jstree, create a request queue
-     * and send them one by one to the server for importing into
-     * the current folder.
-     *
-     * jstree.js has to be loaded before
-     * @see renderJstree
-     */
-    importFromJstreePath: function (that, options) {
-        var all_nodes = $("#jstree_browser").jstree().get_selected(true);
-        // remove the disabled elements that could have been trigerred with the 'select all'
-        var selected_nodes = _.filter(all_nodes, (node) => node.state.disabled == false);
-        var preserve_dirs = this.modal.$el.find(".preserve-checkbox").is(":checked");
-        var link_data = this.modal.$el.find(".link-checkbox").is(":checked");
-        var space_to_tab = this.modal.$el.find(".spacetab-checkbox").is(":checked");
-        var to_posix_lines = this.modal.$el.find(".posix-checkbox").is(":checked");
-        var file_type = this.select_extension.value();
-        var dbkey = this.select_genome.value();
-        var tag_using_filenames = this.modal.$el.find(".tag-files").is(":checked");
-        var selection_type = selected_nodes[0].type;
-        var paths = [];
-        if (selected_nodes.length < 1) {
-            Toast.info("Please select some items first.");
-        } else {
-            this.modal.disableButton("Import");
-            for (let i = selected_nodes.length - 1; i >= 0; i--) {
-                if (selected_nodes[i].li_attr.full_path !== undefined) {
-                    // should be always String
-                    paths.push(`"${selected_nodes[i].li_attr.full_path}"`);
-                }
-            }
-            this.initChainCallControlAddingDatasets({
-                length: paths.length,
-            });
-            if (selection_type === "folder") {
-                const full_source = `${options.source}_folder`;
-                this.chainCallImportingFolders({
-                    paths: paths,
-                    preserve_dirs: preserve_dirs,
-                    link_data: link_data,
-                    space_to_tab: space_to_tab,
-                    to_posix_lines: to_posix_lines,
-                    source: full_source,
-                    file_type: file_type,
-                    dbkey: dbkey,
-                    tag_using_filenames: tag_using_filenames,
-                });
-            } else if (selection_type === "file") {
-                const full_source = `${options.source}_file`;
-                this.chainCallImportingUserdirFiles({
-                    paths: paths,
-                    file_type: file_type,
-                    dbkey: dbkey,
-                    link_data: link_data,
-                    space_to_tab: space_to_tab,
-                    to_posix_lines: to_posix_lines,
-                    source: full_source,
-                    tag_using_filenames: tag_using_filenames,
-                });
-            }
-        }
-    },
-    /**
-     * Take the array of paths and create a request for each of them
-     * calling them in chain. Update the progress bar in between each.
-     * @param  {array} paths                    paths relative to user folder on Galaxy
-     * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
-     */
-    chainCallImportingUserdirFiles: function (options) {
-        const Galaxy = getGalaxyInstance();
-        const popped_item = options.paths.pop();
-        if (typeof popped_item === "undefined") {
-            if (this.options.chain_call_control.failed_number === 0) {
-                Toast.success("Selected files imported into the current folder");
-                Galaxy.modal.hide();
-            } else {
-                Toast.error("An error occurred.");
-            }
-            return true;
-        }
-        const post_url = `${getAppRoot()}api/libraries/datasets`;
-        const post_data = {
-            encoded_folder_id: this.id,
-            source: options.source,
-            path: popped_item,
-            file_type: options.file_type,
-            link_data: options.link_data,
-            space_to_tab: options.space_to_tab,
-            to_posix_lines: options.to_posix_lines,
-            dbkey: options.dbkey,
-            tag_using_filenames: options.tag_using_filenames,
-        };
-        const promise = $.when($.post(post_url, post_data));
-        promise
-            .done((response) => {
-                updateProgress();
-                this.chainCallImportingUserdirFiles(options);
-            })
-            .fail(() => {
-                this.options.chain_call_control.failed_number += 1;
-                updateProgress();
-                this.chainCallImportingUserdirFiles(options);
-            });
-    },
-    /**
-     * Fetch the contents of user directory on Galaxy
-     * and render jstree component based on received
-     * data.
-     * @param  {[type]} options [description]
-     */
-    renderJstree: function (options) {
-        this.options = _.extend(this.options, options);
-        var target = options.source || "userdir";
-        var disabled_jstree_element = this.options.disabled_jstree_element;
-        this.jstree = new mod_library_model.Jstree();
-        this.jstree.url = `${this.jstree.urlRoot}?target=${target}&format=jstree&disable=${disabled_jstree_element}`;
-        this.jstree.fetch({
-            success: (model, response) => {
-                $("#jstree_browser").jstree("destroy");
-                $("#jstree_browser").jstree({
-                    core: {
-                        data: model,
-                    },
-                    plugins: ["types", "checkbox"],
-                    types: {
-                        folder: {
-                            icon: "jstree-folder",
-                        },
-                        file: {
-                            icon: "jstree-file",
-                        },
-                    },
-                    checkbox: {
-                        three_state: false,
-                    },
-                });
-            },
-            error: (model, response) => {
-                if (typeof response.responseJSON !== "undefined") {
-                    if (response.responseJSON.err_code === 404001) {
-                        Toast.warning(response.responseJSON.err_msg);
-                        getGalaxyInstance().modal.hide();
-                    } else {
-                        Toast.error(response.responseJSON.err_msg);
-                    }
-                } else {
-                    Toast.error("An error occurred.");
-                }
-            },
-        });
-    },
-    /**
-     * Create modal for importing from Galaxy path.
-     */
-    importFilesFromPathModal: function () {
-        const Galaxy = getGalaxyInstance();
-        this.modal = Galaxy.modal;
-        var template_modal = this.templateImportPathModal();
-        this.modal.show({
-            closing_events: true,
-            title: _l("Please enter paths to import"),
-            body: template_modal({}),
-            buttons: {
-                Import: () => {
-                    this.importFromPathsClicked(this);
-                },
-                Close: () => {
-                    Galaxy.modal.hide();
-                },
-            },
-            closing_callback: () => {
-                // TODO update table without fetching new content from the server
-                this.options.updateContent();
-
-                // Galaxy.libraries.library_router.navigate(`folders/${this.id}`, {
-                //     trigger: true,
-                // });
-            },
-        });
-        this.renderSelectBoxes();
-    },
-    /**
-     * Take the paths from the textarea, split it, create
-     * a request queue and call a function that starts sending
-     * one by one to be imported on the server.
-     */
-    importFromPathsClicked: function () {
-        var preserve_dirs = this.modal.$el.find(".preserve-checkbox").is(":checked");
-        var link_data = this.modal.$el.find(".link-checkbox").is(":checked");
-        var space_to_tab = this.modal.$el.find(".spacetab-checkbox").is(":checked");
-        var to_posix_lines = this.modal.$el.find(".posix-checkbox").is(":checked");
-        var tag_using_filenames = this.modal.$el.find(".tag-files").is(":checked");
-        var file_type = this.select_extension.value();
-        var dbkey = this.select_genome.value();
-        var paths = $("textarea#import_paths").val();
-        var valid_paths = [];
-        if (!paths) {
-            Toast.info("Please enter a path relative to Galaxy root.");
-        } else {
-            this.modal.disableButton("Import");
-            paths = paths.split("\n");
-            for (let i = paths.length - 1; i >= 0; i--) {
-                var trimmed = paths[i].trim();
-                if (trimmed.length !== 0) {
-                    valid_paths.push(trimmed);
-                }
-            }
-            this.initChainCallControlAddingDatasets({
-                length: valid_paths.length,
-            });
-            this.chainCallImportingFolders({
-                paths: valid_paths,
-                preserve_dirs: preserve_dirs,
-                link_data: link_data,
-                space_to_tab: space_to_tab,
-                to_posix_lines: to_posix_lines,
-                source: "admin_path",
-                file_type: file_type,
-                tag_using_filenames: tag_using_filenames,
-                dbkey: dbkey,
-            });
-        }
-    },
-    /**
-     * Take the array of paths and create a request for each of them
-     * calling them in series. Update the progress bar in between each.
-     * @param  {array} paths                    paths relative to Galaxy root folder
-     * @param  {boolean} preserve_dirs          indicates whether to preserve folder structure
-     * @param  {boolean} link_data              copy files to Galaxy or link instead
-     * @param  {boolean} to_posix_lines         convert line endings to POSIX standard
-     * @param  {boolean} space_to_tab           convert spaces to tabs
-     * @param  {str} source                     string representing what type of folder
-     *                                          is the source of import
-     * @param  {boolean} tag_using_filenames    add tags to datasets using names of files
-     */
-    chainCallImportingFolders: function (options) {
-        const Galaxy = getGalaxyInstance();
-        // TODO need to check which paths to call
-        const popped_item = options.paths.pop();
-        if (typeof popped_item == "undefined") {
-            if (this.options.chain_call_control.failed_number === 0) {
-                Toast.success("Selected folders and their contents imported into the current folder.");
-                Galaxy.modal.hide();
-            } else {
-                // TODO better error report
-                Toast.error("An error occurred.");
-            }
-            return true;
-        }
-        const post_url = `${getAppRoot()}api/libraries/datasets`;
-        const post_data = {
-            encoded_folder_id: this.id,
-            source: options.source,
-            path: popped_item,
-            preserve_dirs: options.preserve_dirs,
-            link_data: options.link_data,
-            to_posix_lines: options.to_posix_lines,
-            space_to_tab: options.space_to_tab,
-            file_type: options.file_type,
-            dbkey: options.dbkey,
-            tag_using_filenames: options.tag_using_filenames,
-        };
-        const promise = $.when($.post(post_url, post_data));
-        promise
-            .done((response) => {
-                updateProgress();
-                this.chainCallImportingFolders(options);
-            })
-            .fail(() => {
-                this.options.chain_call_control.failed_number += 1;
-                updateProgress();
-                this.chainCallImportingFolders(options);
-            });
-    },
-
-    fetchAndDisplayHistoryContents: function (history_id) {
-        var history_contents = new mod_library_model.HistoryContents({
-            id: history_id,
-        });
-        history_contents.fetch({
-            success: (history_contents) => {
-                var history_contents_template = this.templateHistoryContents();
-
-                if (history_contents.length > 0) {
-                    this.histories.get(history_id).set({ contents: history_contents });
-                    this.modal.$el.find(".library_selected_history_content").html(
-                        history_contents_template({
-                            history_contents: history_contents.models.reverse(),
-                        })
-                    );
-                    this.modal.$el.find(".history-import-select-all").bind("click", () => {
-                        $(".library_selected_history_content [type=checkbox]").prop("checked", true);
-                    });
-                    this.modal.$el.find(".history-import-unselect-all").bind("click", () => {
-                        $(".library_selected_history_content [type=checkbox]").prop("checked", false);
-                    });
-
-                    this.modal.$el.find(".history-import-toggle-all").bind("click", (e) => {
-                        this.selectAll(e);
-                    });
-
-                    this.modal.$el.find(".dataset_row").bind("click", (e) => {
-                        this.selectClickedRow(e);
-                    });
-                } else {
-                    this.modal.$el.find(".library_selected_history_content").html(`<p>Selected history is empty.</p>`);
-                }
-            },
-            error: (model, response) => {
-                if (typeof response.responseJSON !== "undefined") {
-                    Toast.error(response.responseJSON.err_msg);
-                } else {
-                    Toast.error("An error occurred.");
-                }
-            },
-        });
-    },
-    templateAddingDatasetsProgressBar: function () {
-        return _.template(
-            `<div class="import_text">
-                Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>
-            </div>
-            <div class="progress">
-                <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0"
-                    aria-valuemax="100" style="width: 00%;">
-                    <span class="completion_span">0% Complete</span>
-                </div>
-            </div>`
-        );
-    },
-    templateAddFilesFromHistory: function () {
-        return _.template(
-            `<div id="add_files_modal">
-                <div class="form-group">
-                    <label>1. Select history:</label>
-                    <select id="dataset_add_bulk" name="dataset_add_bulk" class="form-control">
-                        <% _.each(histories, function(history) { %> <!-- history select box -->
-                            <option value="<%= _.escape(history.get("id")) %>">
-                                <%= _.escape(history.get("name")) %>
-                            </option>
-                        <% }); %>
-                    </select>
-                </div>
-                <div class="library_selected_history_content">
-                </div>
-            </div>`
-        );
-    },
-    templateHistoryContents: function () {
-        return _.template(
-            `<div class="form-group">
-                <label>2. Choose the datasets to import:</label>
-                <div class="library_style_container" style="width: 100%;" id="dataset_list">
-                    <table class="grid table table-hover table-sm">
-                        <thead>
-                            <tr>
-                                <th style="width: 30px;" class="mid" title="Check to select all datasets">
-                                    <input class="history-import-toggle-all" style="margin: 0;" type="checkbox" />
-                                </th>
-                                <th style="width: 30px;"></th>
-                                <th>Name</th>
-                            </tr>
-                        </thead>
-                        <tbody>
-                            <% _.each(history_contents, function(history_item) { %>
-                                <% if (history_item.get("deleted") != true ) { %>
-                                    <% var item_name = history_item.get("name") %>
-                                    <% if (history_item.get("type") === "collection") { %>
-                                        <% var collection_type = history_item.get("collection_type") %>
-                                        <% if (collection_type === "list") { %>
-                                            <tr class="dataset_row" data-id="<%= _.escape(history_item.get("id")) %>"
-                                                data-name="<%= _.escape(history_item.get("type")) %>">
-                                                <td><input style="margin: 0;" type="checkbox"></td>
-                                                <td><%= _.escape(history_item.get("hid")) %></td>
-                                                <td>
-                                                    <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
-                                                    (Dataset Collection)
-                                                </td>
-                                            </tr>
-                                        <% } else { %>
-                                            <tr class="dataset_row" title="You can convert this collection into a collection of type list using the Collection Tools">
-                                                <td><input style="margin: 0;" type="checkbox" onclick="return false;" disabled="disabled" /></td>
-                                                <td><%= _.escape(history_item.get("hid")) %></td>
-                                                <td>
-                                                    <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
-                                                    (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)
-                                                </td>
-                                            </tr>
-                                        <% } %>
-                                    <% } else if (history_item.get("visible") === true && history_item.get("state") === "ok") { %>
-                                        <tr class="dataset_row" data-id="<%= _.escape(history_item.get("id")) %>"
-                                            data-name="<%= _.escape(history_item.get("type")) %>">
-                                            <td><input style="margin: 0;" type="checkbox"></td>
-                                            <td><%= _.escape(history_item.get("hid")) %></td>
-                                            <td>
-                                                <%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %>
-                                            </td>
-                                        </tr>
-                                    <% } %>
-                                <% } %>
-                            <% }); %>
-                        </tbody>
-                    </table>
-                </div>
-            </div>`
-        );
-    },
-    /**
-     * Check checkbox if user clicks on the whole row or
-     *  on the checkbox itself
-     */
-    selectClickedRow: function (event) {
-        var checkbox = "";
-        var $row;
-        var source;
-        $row = $(event.target).closest("tr");
-        if (event.target.localName === "input") {
-            checkbox = event.target;
-            source = "input";
-        } else if (event.target.localName === "td") {
-            checkbox = $row.find(":checkbox")[0];
-            source = "td";
-        }
-        if (checkbox.checked) {
-            if (source === "td") {
-                checkbox.checked = "";
-                this.makeWhiteRow($row);
-            } else if (source === "input") {
-                this.makeDarkRow($row);
-            }
-        } else {
-            if (source === "td") {
-                checkbox.checked = "selected";
-                this.makeDarkRow($row);
-            } else if (source === "input") {
-                this.makeWhiteRow($row);
-            }
-        }
-    },
-
-    /**
-     * User clicked the checkbox in the table heading
-     * @param  {context} event
-     */
-    selectAll: function (event) {
-        var selected = event.target.checked;
-        var self = this;
-        // Iterate each checkbox
-        $(":checkbox", "#dataset_list tbody").each(function () {
-            this.checked = selected;
-            var $row = $(this).closest("tr");
-            // Change color of selected/unselected
-            if (selected) {
-                self.makeDarkRow($row);
-            } else {
-                self.makeWhiteRow($row);
-            }
-        });
-    },
-
-    makeDarkRow: function ($row) {
-        $row.addClass("table-primary");
-    },
-
-    makeWhiteRow: function ($row) {
-        $row.removeClass("table-primary");
-    },
-    /**
-     * Import all selected datasets from history into the current folder.
-     */
-    addAllDatasetsFromHistory: function () {
-        var checked_hdas = this.modal.$el.find(".library_selected_history_content").find(":checked");
-        var history_item_ids = []; // can be hda or hdca
-        var history_item_types = [];
-        var items_to_add = [];
-        if (checked_hdas.length < 1) {
-            Toast.info("You must select some datasets first.");
-        } else {
-            this.modal.disableButton("Add");
-            checked_hdas.each(function () {
-                var hid = $(this).closest("tr").data("id");
-                if (hid) {
-                    var item_type = $(this).closest("tr").data("name");
-                    history_item_ids.push(hid);
-                    history_item_types.push(item_type);
-                }
-            });
-            for (let i = history_item_ids.length - 1; i >= 0; i--) {
-                var history_item_id = history_item_ids[i];
-                var folder_item = new mod_library_model.Item();
-                folder_item.url = `${getAppRoot()}api/folders/${this.options.id}/contents`;
-                if (history_item_types[i] === "collection") {
-                    folder_item.set({ from_hdca_id: history_item_id });
-                } else {
-                    folder_item.set({ from_hda_id: history_item_id });
-                }
-                items_to_add.push(folder_item);
-            }
-            this.initChainCallControlAddingDatasets({
-                length: items_to_add.length,
-            });
-            this.chainCallAddingHdas(items_to_add);
-        }
-    },
-    initChainCallControlAddingDatasets: function (options) {
-        var template;
-        template = this.templateAddingDatasetsProgressBar();
-        this.modal.$el.find(".modal-body").html(
-            template({
-                folder_name: this.options.folder_name,
-            })
-        );
-
-        // var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
-        // this.modal.$el.find( '.modal-body' ).html( progress_bar_tmpl( { folder_name : this.options.folder_name } ) );
-        this.progress = 0;
-        this.progressStep = 100 / options.length;
-        this.options.chain_call_control.total_number = options.length;
-        this.options.chain_call_control.failed_number = 0;
-    },
-
-    /**
-     * Take the array of hdas and create a request for each.
-     * Call them in chain and update progress bar in between each.
-     * @param  {array} hdas_set array of empty hda objects
-     */
-    chainCallAddingHdas: function (hdas_set) {
-        const Galaxy = getGalaxyInstance();
-        this.added_hdas = new mod_library_model.Folder();
-        var popped_item = hdas_set.pop();
-        if (typeof popped_item == "undefined") {
-            if (this.options.chain_call_control.failed_number === 0) {
-                Toast.success("Selected datasets from history added to the folder");
-            } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number) {
-                Toast.error("There was an error and no datasets were added to the folder.");
-            } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number) {
-                Toast.warning("Some of the datasets could not be added to the folder");
-            }
-            this.options.updateContent();
-            Galaxy.modal.hide();
-            return this.added_hdas;
-        }
-        var promise = $.when(
-            popped_item.save({
-                from_hda_id: popped_item.get("from_hda_id"),
-            })
-        );
-
-        promise
-            .done((model) => {
-                // TODO add to lib
-                // Galaxy.libraries.folderListView.collection.add(model);
-                updateProgress();
-                this.chainCallAddingHdas(hdas_set);
-            })
-            .fail(() => {
-                this.options.chain_call_control.failed_number += 1;
-                updateProgress();
-                this.chainCallAddingHdas(hdas_set);
-            });
-    },
-});
-export default {
-    AddDatasets: AddDatasets,
-};
diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-collection.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-collection.js
index 1642d31d89d369076e459cfe01d466f55e320565..78828e0bb73cf717b3b7a46d4ea39fc3c214ad59 100644
--- a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-collection.js
+++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-collection.js
@@ -54,6 +54,7 @@ var ImportCollectionModal = Backbone.View.extend({
                         buttons: {
                             Continue: () => {
                                 this.showCollectionBuilder(checked_items.dataset_ids);
+                                Galaxy.modal.hide();
                             },
                             Close: () => {
                                 Galaxy.modal.hide();
@@ -106,17 +107,19 @@ var ImportCollectionModal = Backbone.View.extend({
     },
     collectionImport: function (collectionElements, historyId) {
         const collectionType = this.modal.$el.find("#library-collection-type-select").val();
-        let selection = null;
+        let selection = {};
         if (collectionType == "rules") {
-            selection = collectionElements;
             selection.selectionType = "library_datasets";
-        } else {
-            selection = {
-                models: collectionElements,
-            };
         }
-        const Galaxy = getGalaxyInstance();
-        Galaxy.currHistoryPanel.buildCollection(collectionType, selection, historyId);
+        selection = {
+            models: collectionElements,
+        };
+        if (collectionType === "rules") {
+            const Galaxy = getGalaxyInstance();
+            Galaxy.currHistoryPanel.buildCollectionFromRules(selection, historyId);
+        } else if (this.options.onCollectionImport) {
+            this.options.onCollectionImport(collectionType, selection, historyId);
+        }
     },
     templateCollectionSelectModal: function () {
         return _.template(
diff --git a/client/src/components/Libraries/LibraryPermissions/LibraryPermissions.vue b/client/src/components/Libraries/LibraryPermissions/LibraryPermissions.vue
index e7ce705918c6306c20326e46a26cb82bd49e2be5..83238f78fd27a391a0c2b7c94be48b290fe7e8e5 100644
--- a/client/src/components/Libraries/LibraryPermissions/LibraryPermissions.vue
+++ b/client/src/components/Libraries/LibraryPermissions/LibraryPermissions.vue
@@ -31,6 +31,15 @@
             alert="User with  <strong>any</strong> of these roles can modify this library (name, synopsis, etc.)."
             title="Roles that can modify this library"
             @input="setUserPermissionsPreferences" />
+        <PermissionsInputField
+            v-if="manage_library_role_list"
+            :id="library_id"
+            :permission_type="manage_type"
+            :initial_value="manage_library_role_list"
+            :api-root-url="apiRootUrl"
+            alert="User with <strong>any</strong> of these roles can manage this library."
+            title="Roles that can manage this library"
+            @input="setUserPermissionsPreferences" />
         <button title="Save modifications" class="toolbtn_save_permissions" @click="postPermissions">
             <FontAwesomeIcon :icon="['far', 'save']" />
             Save
@@ -71,10 +80,12 @@ export default {
             library: undefined,
             add_library_item_role_list: undefined,
             modify_library_role_list: undefined,
+            manage_library_role_list: undefined,
             access_library_role_list: undefined,
             apiRootUrl: `${getAppRoot()}api/libraries`,
             add_type: "add_library_item_role_list",
             modify_type: "modify_library_role_list",
+            manage_type: "manage_library_role_list",
             access_type: "access_library_role_list",
         };
     },
@@ -85,6 +96,7 @@ export default {
             console.log("fetched_permissions", fetched_permissions);
             this.add_library_item_role_list = extractRoles(fetched_permissions.add_library_item_role_list);
             this.modify_library_role_list = extractRoles(fetched_permissions.modify_library_role_list);
+            this.manage_library_role_list = extractRoles(fetched_permissions.manage_library_role_list);
             this.access_library_role_list = extractRoles(fetched_permissions.access_library_role_list);
         });
         this.services.getLibrary(this.library_id).then((library) => {
@@ -103,6 +115,7 @@ export default {
                 [
                     { "add_ids[]": this.add_library_item_role_list },
                     { "modify_ids[]": this.modify_library_role_list },
+                    { "manage_ids[]": this.manage_library_role_list },
                     { "access_ids[]": this.access_library_role_list },
                 ],
                 (fetched_permissions) => {
diff --git a/client/src/components/Libraries/icons.js b/client/src/components/Libraries/icons.js
index 309572e919030a8d0abfebd6ddd86b39666512e7..7ae347b7dc5bcfd50b915c9eb77312e2e2e47228 100644
--- a/client/src/components/Libraries/icons.js
+++ b/client/src/components/Libraries/icons.js
@@ -3,14 +3,11 @@ import { faCheckSquare, faFile, faFolder, faSave, faSquare } from "@fortawesome/
 import {
     faAngleDoubleLeft,
     faBan,
-    faBook,
-    faDownload,
     faGlobe,
     faHome,
     faKey,
     faMinusSquare,
     faPencilAlt,
-    faPlus,
     faShieldAlt,
     faSpinner,
     faTimes,
@@ -38,7 +35,6 @@ const tableIcons = [
 ];
 
 const manageIcons = [faAngleDoubleLeft, faSave, faFile];
-const topBarIcons = [faHome, faPlus, faTrash, faDownload, faBook];
 const librariesIcons = [faGlobe, faPencilAlt, faSave, faTimes, faTrash, faUsers, faHome, faUnlock];
 
 export function initFolderTableIcons() {
@@ -51,6 +47,3 @@ export function initPermissionsIcons() {
 export function initLibrariesIcons() {
     librariesIcons.forEach((icon) => library.add(icon));
 }
-export function initTopBarIcons() {
-    topBarIcons.forEach((icon) => library.add(icon));
-}
diff --git a/client/src/components/License/LicenseSelector.vue b/client/src/components/License/LicenseSelector.vue
index e6208be03f15a4b00bd1f08d4c758dd1555c980d..a9f55d621e1c75acc27ef581e9f3451f80807558 100644
--- a/client/src/components/License/LicenseSelector.vue
+++ b/client/src/components/License/LicenseSelector.vue
@@ -1,130 +1,112 @@
+<script setup lang="ts">
+import { watchImmediate } from "@vueuse/core";
+import { BAlert } from "bootstrap-vue";
+import { computed, ref } from "vue";
+import Multiselect from "vue-multiselect";
+
+import { GalaxyApi } from "@/api";
+import { type components } from "@/api/schema";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import License from "@/components/License/License.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+const defaultLicense: LicenseType = {
+    licenseId: null,
+    name: "*Do not specify a license.*",
+};
+
+type LicenseMetadataModel = components["schemas"]["LicenseMetadataModel"];
+type LicenseType = {
+    licenseId: string | null;
+    name: string;
+};
+
+interface Props {
+    inputLicense: string;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "onLicense", license: string | null): void;
+}>();
+
+const licensesLoading = ref(false);
+const errorMessage = ref<string>("");
+const currentLicense = ref<LicenseType>();
+const licenses = ref<LicenseMetadataModel[] | undefined>([]);
+
+const licenseOptions = computed(() => {
+    const options: LicenseType[] = [];
+
+    options.push(defaultLicense);
+
+    for (const license of licenses.value || []) {
+        if (license.licenseId == currentLicense.value?.licenseId || license.recommended) {
+            options.push({
+                licenseId: license.licenseId,
+                name: license.name,
+            });
+        }
+    }
+
+    return options;
+});
+
+function onLicense(license: LicenseType) {
+    emit("onLicense", license.licenseId);
+}
+
+async function fetchLicenses() {
+    const { error, data } = await GalaxyApi().GET("/api/licenses");
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error) || "Unable to fetch licenses.";
+    }
+
+    licenses.value = data;
+
+    licensesLoading.value = false;
+}
+
+async function setCurrentLicense() {
+    if (!licenses.value?.length && !licensesLoading.value) {
+        licensesLoading.value = true;
+
+        await fetchLicenses();
+    }
+
+    const inputLicense = props.inputLicense;
+
+    currentLicense.value = (licenses.value || []).find((l) => l.licenseId == inputLicense) || defaultLicense;
+}
+
+watchImmediate(
+    () => props.inputLicense,
+    () => {
+        setCurrentLicense();
+    }
+);
+</script>
+
 <template>
-    <div v-if="editLicense">
-        <LoadingSpan v-if="licensesLoading" message="Loading licenses..." />
-        <b-form-select
+    <div>
+        <BAlert v-if="licensesLoading" variant="info" class="m-0" show>
+            <LoadingSpan message="Loading licenses" />
+        </BAlert>
+        <BAlert v-else-if="errorMessage" variant="danger" class="m-0" show>
+            {{ errorMessage }}
+        </BAlert>
+        <Multiselect
             v-else
-            v-model="license"
+            v-model="currentLicense"
             data-description="license select"
-            :options="licenseOptions"></b-form-select>
-        <License v-if="currentLicenseInfo" :license-id="license" :input-license-info="currentLicenseInfo">
-            <template v-slot:buttons>
-                <span v-b-tooltip.hover title="Save License"
-                    ><FontAwesomeIcon data-description="license save" icon="save" @click="onSave"
-                /></span>
-                <span v-b-tooltip.hover title="Cancel Edit"><FontAwesomeIcon icon="times" @click="disableEdit" /></span>
-            </template>
-        </License>
-        <div v-else>
-            <a href="#" @click.prevent="onSave">Save without license</a> or
-            <a href="#" @click.prevent="editLicense = false">cancel edit.</a>
-        </div>
-    </div>
-    <div v-else-if="license" data-description="license selector" :data-license="license">
-        <License :license-id="license">
-            <template v-slot:buttons>
-                <span v-b-tooltip.hover title="Edit License"
-                    ><FontAwesomeIcon icon="edit" data-description="edit license link" @click="editLicense = true"
-                /></span>
-            </template>
-        </License>
-    </div>
-    <div v-else data-description="license selector" data-license="null">
-        <i
-            ><a href="#" data-description="edit license link" @click.prevent="editLicense = true"
-                >Specify a license for this workflow.</a
-            ></i
-        >
+            track-by="licenseId"
+            :options="licenseOptions"
+            label="name"
+            placeholder="Select a license"
+            @select="onLicense" />
+        <License v-if="currentLicense?.licenseId" :license-id="currentLicense.licenseId" />
     </div>
 </template>
-
-<script>
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faEdit, faSave, faTimes } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import axios from "axios";
-import BootstrapVue from "bootstrap-vue";
-import LoadingSpan from "components/LoadingSpan";
-import { getAppRoot } from "onload/loadConfig";
-import Vue from "vue";
-
-import License from "./License";
-
-library.add(faSave);
-library.add(faTimes);
-library.add(faEdit);
-
-Vue.use(BootstrapVue);
-
-export default {
-    components: { License, LoadingSpan, FontAwesomeIcon },
-    props: {
-        inputLicense: {
-            type: String,
-        },
-    },
-    data() {
-        return {
-            license: this.inputLicense || null,
-            licensesLoading: false,
-            licenses: [],
-            editLicense: false,
-        };
-    },
-    computed: {
-        currentLicenseInfo() {
-            for (const license of this.licenses) {
-                if (license.licenseId == this.license) {
-                    return license;
-                }
-            }
-            return null;
-        },
-        licenseOptions() {
-            const options = [];
-            options.push({
-                value: null,
-                text: "*Do not specify a license.*",
-            });
-            for (const license of this.licenses) {
-                if (license.licenseId == this.license || license.recommended) {
-                    options.push({
-                        value: license.licenseId,
-                        text: license.name,
-                    });
-                }
-            }
-            return options;
-        },
-    },
-    watch: {
-        inputLicense() {
-            this.license = this.inputLicense;
-        },
-    },
-    mounted() {
-        const url = `${getAppRoot()}api/licenses`;
-        axios
-            .get(url)
-            .then((response) => response.data)
-            .then((data) => {
-                this.licenses = data;
-                this.licensesLoading = false;
-            })
-            .catch((e) => {
-                console.error(e);
-            });
-    },
-    methods: {
-        onSave() {
-            this.onLicense(this.license);
-            this.disableEdit();
-        },
-        disableEdit() {
-            this.editLicense = false;
-        },
-        onLicense(license) {
-            this.$emit("onLicense", license);
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Login/ChangePassword.test.ts b/client/src/components/Login/ChangePassword.test.ts
index cc8ad816ef18f28a8ec7ab52da51faad45f786ae..a3e91c404522d8e4320d2e665621d7d406c8aa9b 100644
--- a/client/src/components/Login/ChangePassword.test.ts
+++ b/client/src/components/Login/ChangePassword.test.ts
@@ -1,4 +1,4 @@
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import { getLocalVue } from "tests/jest/helpers";
diff --git a/client/src/components/Login/ChangePassword.vue b/client/src/components/Login/ChangePassword.vue
index 0c761c98ecd3288b45976bccdacc2bf4a8fa031c..8aa4f78650c72e9580014bb8c5e05c1fc1db2ea8 100644
--- a/client/src/components/Login/ChangePassword.vue
+++ b/client/src/components/Login/ChangePassword.vue
@@ -50,15 +50,15 @@ async function submit() {
 
         <BCard header="Change your password">
             <BFormGroup v-if="expiredUser" label="Current Password">
-                <BFormInput v-model="current" type="password" />
+                <BFormInput v-model="current" type="password" autocomplete="current-password" />
             </BFormGroup>
 
             <BFormGroup label="New Password">
-                <BFormInput v-model="password" type="password" />
+                <BFormInput v-model="password" type="password" autocomplete="new-password" />
             </BFormGroup>
 
             <BFormGroup label="Confirm password">
-                <BFormInput v-model="confirm" type="password" />
+                <BFormInput v-model="confirm" type="password" autocomplete="new-password" />
             </BFormGroup>
 
             <BButton type="submit">Save new password</BButton>
diff --git a/client/src/components/Login/LoginForm.vue b/client/src/components/Login/LoginForm.vue
index b0597f59a2ac61944dbd2b92a8b18563d68e706f..6b112d8a38d129ad7076dae6e09c868744f25462 100644
--- a/client/src/components/Login/LoginForm.vue
+++ b/client/src/components/Login/LoginForm.vue
@@ -196,7 +196,8 @@ function returnToLogin() {
                                             required
                                             :state="passwordState"
                                             name="password"
-                                            type="password" />
+                                            type="password"
+                                            autocomplete="current-password" />
 
                                         <BFormText v-if="showResetLink">
                                             <span v-localize>Forgot password?</span>
diff --git a/client/src/components/Login/RegisterForm.test.ts b/client/src/components/Login/RegisterForm.test.ts
index db5c2ee1083a9c7360d9043fcd526dbea528c722..9eae8bc69b8bf6967049bae5141d7a99b0f99a1d 100644
--- a/client/src/components/Login/RegisterForm.test.ts
+++ b/client/src/components/Login/RegisterForm.test.ts
@@ -1,5 +1,5 @@
 import { getLocalVue } from "@tests/jest/helpers";
-import { mount, Wrapper } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 
diff --git a/client/src/components/Login/RegisterForm.vue b/client/src/components/Login/RegisterForm.vue
index 25546ed46804924bda32a2449e9444098777fc5a..d2237174c1822bea74714698ea1f2653fbe7c211 100644
--- a/client/src/components/Login/RegisterForm.vue
+++ b/client/src/components/Login/RegisterForm.vue
@@ -79,7 +79,7 @@ async function submit() {
             Toast.info(response.data.message);
         }
 
-        window.location.href = props.redirect || withPrefix("/");
+        window.location.href = props.redirect ? withPrefix(props.redirect) : withPrefix("/");
     } catch (error: any) {
         disableCreate.value = false;
         messageText.value = errorMessageAsString(error, "Registration failed for an unknown reason.");
@@ -144,6 +144,7 @@ async function submit() {
                                         v-model="password"
                                         name="password"
                                         type="password"
+                                        autocomplete="new-password"
                                         required />
                                 </BFormGroup>
 
@@ -153,6 +154,7 @@ async function submit() {
                                         v-model="confirm"
                                         name="confirm"
                                         type="password"
+                                        autocomplete="new-password"
                                         required />
                                 </BFormGroup>
 
diff --git a/client/src/components/Markdown/Elements/HistoryDatasetDisplay.test.js b/client/src/components/Markdown/Elements/HistoryDatasetDisplay.test.js
index 0b4a58cfe7ece78e59ec2b390d6137207513fe3b..e80863bedf649885ed35a6f6dceb84198f9e4e58 100644
--- a/client/src/components/Markdown/Elements/HistoryDatasetDisplay.test.js
+++ b/client/src/components/Markdown/Elements/HistoryDatasetDisplay.test.js
@@ -1,15 +1,26 @@
+import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
-import { typesAndMappingResponse } from "components/Datatypes/test_fixtures";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
+
 import HistoryDatasetDisplay from "./HistoryDatasetDisplay.vue";
 
 const localVue = getLocalVue();
 
 const args = { history_dataset_id: "someId" };
-const api_paths_map = new Map([["/api/datatypes/types_and_mapping", typesAndMappingResponse]]);
+
+function setUpDatatypesStore() {
+    const pinia = createTestingPinia({ stubActions: false });
+
+    const datatypesStore = useDatatypesMapperStore();
+    datatypesStore.datatypesMapper = testDatatypesMapper;
+
+    return pinia;
+}
 
 describe("History Tabular Dataset Display", () => {
     let wrapper;
@@ -23,15 +34,14 @@ describe("History Tabular Dataset Display", () => {
 
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
-
-        for (const [path, response] of api_paths_map.entries()) {
-            axiosMock.onGet(path).reply(200, response);
-        }
-
         axiosMock.onGet(`/api/datasets/${args.history_dataset_id}`).reply(200, tabularMetaData);
         axiosMock.onGet(`/api/datasets/${args.history_dataset_id}/get_content_as_text`).reply(200, tabular);
 
-        wrapper = mount(HistoryDatasetDisplay, { localVue, propsData: { datasets: tabularDatasets, args } });
+        wrapper = mount(HistoryDatasetDisplay, {
+            localVue,
+            propsData: { datasets: tabularDatasets, args },
+            pinia: setUpDatatypesStore(),
+        });
     });
 
     afterEach(() => {
@@ -55,13 +65,13 @@ describe("History Text Dataset Display", () => {
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
 
-        for (const [path, response] of api_paths_map.entries()) {
-            axiosMock.onGet(path).reply(200, response);
-        }
-
         axiosMock.onGet(`/api/datasets/${args.history_dataset_id}/get_content_as_text`).reply(200, text);
 
-        wrapper = mount(HistoryDatasetDisplay, { localVue, propsData: { datasets: textDatasets, args } });
+        wrapper = mount(HistoryDatasetDisplay, {
+            localVue,
+            propsData: { datasets: textDatasets, args },
+            pinia: setUpDatatypesStore(),
+        });
     });
 
     afterEach(() => {
diff --git a/client/src/components/Markdown/Elements/HistoryDatasetDisplay.vue b/client/src/components/Markdown/Elements/HistoryDatasetDisplay.vue
index d44e22d74b4b9b52cb33a6ff1eabbd51f53cbca2..f16ca73a7deb541a84f4d029d68ca74a5b80592e 100644
--- a/client/src/components/Markdown/Elements/HistoryDatasetDisplay.vue
+++ b/client/src/components/Markdown/Elements/HistoryDatasetDisplay.vue
@@ -54,53 +54,66 @@
             </span>
         </b-card-header>
         <b-card-body>
-            <UrlDataProvider v-slot="{ result: itemContent, loading, error }" :url="itemUrl">
-                <UrlDataProvider v-slot="{ result: datatypesModel, loading: datatypesLoading }" :url="datatypesUrl">
-                    <LoadingSpan v-if="loading" message="Loading Dataset" />
-                    <LoadingSpan v-else-if="datatypesLoading" message="Loading Datatypes" />
-                    <div v-else-if="error">{{ error }}</div>
-                    <div v-else :class="contentClass">
-                        <b-embed
-                            v-if="isSubTypeOfAny(datasetType, ['pdf', 'html'], datatypesModel)"
-                            type="iframe"
-                            aspect="16by9"
-                            :src="displayUrl" />
-                        <HistoryDatasetAsImage
-                            v-else-if="isSubTypeOfAny(datasetType, ['galaxy.datatypes.images.Image'], datatypesModel)"
-                            :args="args" />
-                        <div v-else-if="itemContent.item_data">
-                            <div v-if="isSubTypeOfAny(datasetType, ['tabular'], datatypesModel)">
-                                <UrlDataProvider
-                                    v-slot="{ result: metaData, loading: metaLoading, error: metaError }"
-                                    :url="metaUrl">
-                                    <LoadingSpan v-if="metaLoading" message="Loading Metadata" />
-                                    <div v-else-if="metaError">{{ metaError }}</div>
+            <UrlDataProvider v-slot="{ result: itemContent, loading: datasetLoading, error }" :url="itemUrl">
+                <LoadingSpan v-if="datasetLoading" message="Loading Dataset" />
+                <LoadingSpan v-else-if="loading" message="Loading Datatypes" />
+                <div v-else-if="error">{{ error }}</div>
+                <div v-else-if="!datatypesMapper">Datatypes not loaded.</div>
+                <div v-else :class="contentClass">
+                    <b-embed
+                        v-if="datatypesMapper.isSubTypeOfAny(datasetType, ['pdf', 'html'])"
+                        type="iframe"
+                        aspect="16by9"
+                        :src="displayUrl" />
+                    <HistoryDatasetAsImage
+                        v-else-if="datatypesMapper.isSubTypeOfAny(datasetType, ['galaxy.datatypes.images.Image'])"
+                        :args="args" />
+                    <div v-else-if="itemContent.item_data">
+                        <div v-if="datatypesMapper.isSubTypeOfAny(datasetType, ['tabular'])">
+                            <UrlDataProvider
+                                v-slot="{ result: metaData, loading: metaLoading, error: metaError }"
+                                :url="metaUrl">
+                                <LoadingSpan v-if="metaLoading" message="Loading Metadata" />
+                                <div v-else-if="metaError">{{ metaError }}</div>
+                                <div v-else>
                                     <b-table
-                                        v-else
+                                        id="tabular-dataset-table"
+                                        sticky-header
+                                        thead-tr-class="sticky-top"
                                         striped
                                         hover
+                                        :per-page="perPage"
+                                        :current-page="currentPage"
                                         :fields="getFields(metaData)"
                                         :items="getItems(itemContent.item_data, metaData)" />
-                                </UrlDataProvider>
-                            </div>
-                            <pre v-else>
-                                <code class="word-wrap-normal">{{ itemContent.item_data }}</code>
-                            </pre>
+                                    <b-pagination
+                                        v-model="currentPage"
+                                        align="center"
+                                        :total-rows="getItems(itemContent.item_data, metaData).length"
+                                        :per-page="perPage"
+                                        aria-controls="tabular-dataset-table" />
+                                </div>
+                            </UrlDataProvider>
                         </div>
-                        <div v-else>No content found.</div>
-                        <b-link v-if="itemContent.truncated" :href="itemContent.item_url"> Show More... </b-link>
+                        <pre v-else>
+                            <code class="word-wrap-normal">{{ itemContent.item_data }}</code>
+                        </pre>
                     </div>
-                </UrlDataProvider>
+                    <div v-else>No content found.</div>
+                    <b-link v-if="itemContent.truncated" :href="itemContent.item_url"> Show More... </b-link>
+                </div>
             </UrlDataProvider>
         </b-card-body>
     </b-card>
 </template>
 
 <script>
-import { DatatypesMapperModel } from "components/Datatypes/model";
 import LoadingSpan from "components/LoadingSpan";
 import { UrlDataProvider } from "components/providers/UrlDataProvider";
 import { getAppRoot } from "onload/loadConfig";
+import { mapState } from "pinia";
+
+import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 
 import HistoryDatasetAsImage from "./HistoryDatasetAsImage.vue";
 
@@ -126,11 +139,17 @@ export default {
     },
     data() {
         return {
+            currentPage: 1,
             expanded: false,
+            perPage: 100,
         };
     },
     computed: {
+        ...mapState(useDatatypesMapperStore, ["createMapper", "datatypesMapper", "loading"]),
         contentClass() {
+            if (this.datatypesMapper?.isSubTypeOfAny(this.datasetType, ["tabular"])) {
+                return "";
+            }
             if (this.expanded) {
                 return "embedded-dataset-expanded";
             } else {
@@ -145,14 +164,11 @@ export default {
             const dataset = this.datasets[this.args.history_dataset_id];
             return dataset && dataset.name;
         },
-        datatypesUrl() {
-            return "/api/datatypes/types_and_mapping";
-        },
         downloadUrl() {
             return `${getAppRoot()}dataset/display?dataset_id=${this.args.history_dataset_id}`;
         },
         displayUrl() {
-            return `${getAppRoot()}datasets/${this.args.history_dataset_id}/display`;
+            return `${getAppRoot()}datasets/${this.args.history_dataset_id}/display/?preview=True`;
         },
         importUrl() {
             return `${getAppRoot()}dataset/imp?dataset_id=${this.args.history_dataset_id}`;
@@ -164,11 +180,10 @@ export default {
             return `/api/datasets/${this.args.history_dataset_id}`;
         },
     },
+    created() {
+        this.createMapper();
+    },
     methods: {
-        isSubTypeOfAny(child, parents, datatypesModel) {
-            const datatypesMapper = new DatatypesMapperModel(datatypesModel);
-            return datatypesMapper.isSubTypeOfAny(child, parents);
-        },
         getFields(metaData) {
             const fields = [];
             const columnNames = metaData.metadata_column_names || [];
diff --git a/client/src/components/Markdown/Elements/JobSelection.vue b/client/src/components/Markdown/Elements/JobSelection.vue
index 84ded526629aa906e60c8a55ea80641631421bc1..4d1d3b1ca38c26a55a506771b042f378d5069a03 100644
--- a/client/src/components/Markdown/Elements/JobSelection.vue
+++ b/client/src/components/Markdown/Elements/JobSelection.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { SelectOption } from "./handlesMappingJobs";
+import { type SelectOption } from "./handlesMappingJobs";
 
 interface JobSelectionProps {
     jobId?: string;
diff --git a/client/src/components/Markdown/Elements/handlesMappingJobs.ts b/client/src/components/Markdown/Elements/handlesMappingJobs.ts
index fa257872dd69b81a1b351da0900425e61999c53e..06c44a36653400b1858452b7b4302d6616affb89 100644
--- a/client/src/components/Markdown/Elements/handlesMappingJobs.ts
+++ b/client/src/components/Markdown/Elements/handlesMappingJobs.ts
@@ -1,9 +1,8 @@
 import { format, parseISO } from "date-fns";
-import { computed, Ref, ref, watch } from "vue";
+import { computed, type Ref, ref, watch } from "vue";
 
-import { fetcher } from "@/api/schema";
-
-const jobsFetcher = fetcher.path("/api/jobs").method("get").create();
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export interface SelectOption {
     value: string;
@@ -32,8 +31,18 @@ export function useMappingJobs(
         implicitCollectionJobsId,
         async () => {
             if (implicitCollectionJobsId.value) {
-                const response = await jobsFetcher({ implicit_collection_jobs_id: implicitCollectionJobsId.value });
-                const jobs: Job[] = response.data as unknown as Job[];
+                const { data: jobs, error } = await GalaxyApi().GET("/api/jobs", {
+                    params: {
+                        query: {
+                            implicit_collection_jobs_id: implicitCollectionJobsId.value,
+                        },
+                    },
+                });
+
+                if (error) {
+                    rethrowSimple(error);
+                }
+
                 selectJobOptions.value = jobs.map((value, index) => {
                     const isoCreateTime = parseISO(`${value.create_time}Z`);
                     const prettyTime = format(isoCreateTime, "eeee MMM do H:mm:ss yyyy zz");
diff --git a/client/src/components/Markdown/LabelSelector.vue b/client/src/components/Markdown/LabelSelector.vue
index 2527704f28c6f7e82de409e6986eb174effe2477..333bafc103ca4bbc61bb8cf906672c738b12d436 100644
--- a/client/src/components/Markdown/LabelSelector.vue
+++ b/client/src/components/Markdown/LabelSelector.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { WorkflowLabel } from "./labels";
+import { type WorkflowLabel } from "./labels";
 
 interface LabelSelectorProps {
     hasLabels: boolean;
diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 4d15b58b7e42dd47aefbc4a99435da29530839c3..895f0971430901ba224761e3d392d22803f11f30 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -130,7 +130,7 @@ export default {
             workflows: {},
             invocations: {},
             loading: true,
-            workflowID: "",
+            workflowID: undefined,
         };
     },
     computed: {
@@ -159,7 +159,7 @@ export default {
             return "unavailable";
         },
         workflowVersions() {
-            return this.getStoredWorkflowByInstanceId(this.workflowID);
+            return this.workflowID ? this.getStoredWorkflowByInstanceId(this.workflowID) : undefined;
         },
         version() {
             return this.markdownConfig.generate_version || "Unknown Galaxy Version";
@@ -172,7 +172,9 @@ export default {
     },
     created() {
         this.initConfig();
-        this.fetchWorkflowForInstanceId(this.workflowID);
+        if (this.workflowID) {
+            this.fetchWorkflowForInstanceId(this.workflowID);
+        }
     },
     methods: {
         ...mapActions(useWorkflowStore, ["getStoredWorkflowByInstanceId", "fetchWorkflowForInstanceId"]),
@@ -188,7 +190,7 @@ export default {
                 this.workflows = config.workflows || {};
                 this.invocations = config.invocations || {};
                 this.loading = false;
-                this.workflowID = Object.keys(this.markdownConfig.workflows)[0];
+                this.workflowID = Object.keys(this.markdownConfig?.workflows ?? {})[0];
             }
         },
         splitMarkdown(markdown) {
diff --git a/client/src/components/Markdown/MarkdownDialog.vue b/client/src/components/Markdown/MarkdownDialog.vue
index e610692f5a80c6a78880d075a498e833b56becf5..2d421ba8e64edf8e0e955d910432ae9bdb0fdec6 100644
--- a/client/src/components/Markdown/MarkdownDialog.vue
+++ b/client/src/components/Markdown/MarkdownDialog.vue
@@ -3,13 +3,11 @@ import BootstrapVue from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import Vue, { computed, ref } from "vue";
 
-import { publishedHistoriesFetcher } from "@/api/histories";
-import { invocationsFetcher } from "@/api/invocations";
-import { jobsFetcher } from "@/api/jobs";
-import { workflowsFetcher } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
 import { useHistoryStore } from "@/stores/historyStore";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import { WorkflowLabel, WorkflowLabels } from "./labels";
+import { type WorkflowLabel, type WorkflowLabels } from "./labels";
 
 import MarkdownSelector from "./MarkdownSelector.vue";
 import MarkdownVisualization from "./MarkdownVisualization.vue";
@@ -90,20 +88,36 @@ const selectedLabelTitle = computed(() => {
     return (config && config.labelTitle) || "Select Label";
 });
 
-function getInvocations() {
-    return invocationsFetcher({});
+async function getInvocations() {
+    const { data, error } = await GalaxyApi().GET("/api/invocations");
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
 }
 
-function getJobs() {
-    return jobsFetcher({});
+async function getJobs() {
+    const { data, error } = await GalaxyApi().GET("/api/jobs");
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
 }
 
-function getWorkflows() {
-    return workflowsFetcher({});
+async function getWorkflows() {
+    const { data, error } = await GalaxyApi().GET("/api/workflows");
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
 }
 
-function getHistories() {
-    return publishedHistoriesFetcher({});
+async function getHistories() {
+    const { data, error } = await GalaxyApi().GET("/api/histories/published");
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
 }
 
 function onData(response: string) {
diff --git a/client/src/components/Markdown/MarkdownEditor.vue b/client/src/components/Markdown/MarkdownEditor.vue
index 09ed3bd6e6bb47e416f9ea868ac365e93baeeeeb..0ace2e5a3b6d78dfaf120a6c9384d679a4e17cc2 100644
--- a/client/src/components/Markdown/MarkdownEditor.vue
+++ b/client/src/components/Markdown/MarkdownEditor.vue
@@ -1,7 +1,7 @@
 <template>
     <div id="columns" class="d-flex">
         <FlexPanel side="left">
-            <MarkdownToolBox :steps="steps" @onInsert="onInsert" />
+            <MarkdownToolBox :steps="steps" @insert="insertMarkdown" />
         </FlexPanel>
         <div id="center" class="overflow-auto w-100">
             <div class="markdown-editor h-100">
@@ -57,10 +57,10 @@ const FENCE = "```";
 
 export default {
     components: {
-        MarkdownToolBox,
         FlexPanel,
         FontAwesomeIcon,
         MarkdownHelpModal,
+        MarkdownToolBox,
     },
     props: {
         markdownText: {
@@ -97,7 +97,7 @@ export default {
         },
     },
     methods: {
-        onInsert(markdown) {
+        insertMarkdown(markdown) {
             markdown = markdown.replace(")(", ", ");
             markdown = `${FENCE}galaxy\n${markdown}\n${FENCE}\n`;
             const textArea = this.$refs["text-area"];
@@ -106,10 +106,10 @@ export default {
             let newContent = this.content.substr(0, cursorPosition);
             newContent += `\r\n${markdown.trim()}\r\n`;
             newContent += this.content.substr(cursorPosition);
-            this.$emit("onUpdate", newContent);
+            this.$emit("update", newContent);
         },
         onUpdate: _.debounce(function (e) {
-            this.$emit("onUpdate", this.content);
+            this.$emit("update", this.content);
         }, 300),
         onHelp() {
             this.$refs.help.showMarkdownHelp();
diff --git a/client/src/components/Markdown/MarkdownSelector.vue b/client/src/components/Markdown/MarkdownSelector.vue
index d6d16cefdfe87e24b5f56abcb36094781e67e2a9..ffa9b35e3b1cfd688ff68f4a30d55f156487c50d 100644
--- a/client/src/components/Markdown/MarkdownSelector.vue
+++ b/client/src/components/Markdown/MarkdownSelector.vue
@@ -2,7 +2,7 @@
 import { BModal } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { WorkflowLabel } from "./labels";
+import { type WorkflowLabel } from "./labels";
 
 import LabelSelector from "./LabelSelector.vue";
 
diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index fb2d9f0f91c84435e7aca953c211bb1a3bb12ac9..336c5951dce1cb4a5984dcd51639a797376764de 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -1,32 +1,21 @@
 <template>
-    <div class="unified-panel">
-        <div class="unified-panel-header" unselectable="on">
-            <div class="unified-panel-header-inner">
-                <div class="panel-header-text">Insert Objects</div>
-            </div>
-        </div>
-        <div class="unified-panel-body">
-            <div class="toolMenuContainer">
-                <b-alert v-if="error" variant="danger" class="my-2 mx-3 px-2 py-1" show>
-                    {{ error }}
-                </b-alert>
-                <ToolSection v-if="isWorkflow" :category="historyInEditorSection" :expanded="true" @onClick="onClick" />
-                <ToolSection v-else :category="historySection" :expanded="true" @onClick="onClick" />
-                <ToolSection :category="jobSection" :expanded="true" @onClick="onClick" />
-                <ToolSection
-                    v-if="isWorkflow"
-                    :category="workflowInEditorSection"
-                    :expanded="true"
-                    @onClick="onClick" />
-                <ToolSection v-else :category="workflowSection" :expanded="true" @onClick="onClick" />
-                <ToolSection :category="linksSection" :expanded="false" @onClick="onClick" />
-                <ToolSection :category="otherSection" :expanded="true" @onClick="onClick" />
-                <ToolSection
-                    v-if="hasVisualizations"
-                    :category="visualizationSection"
-                    :expanded="true"
-                    @onClick="onClick" />
-            </div>
+    <ActivityPanel title="Insert Markdown Objects">
+        <div class="toolMenuContainer">
+            <b-alert v-if="error" variant="danger" class="my-2 mx-3 px-2 py-1" show>
+                {{ error }}
+            </b-alert>
+            <ToolSection v-if="isWorkflow" :category="historyInEditorSection" :expanded="true" @onClick="onClick" />
+            <ToolSection v-else :category="historySection" :expanded="true" @onClick="onClick" />
+            <ToolSection :category="jobSection" :expanded="true" @onClick="onClick" />
+            <ToolSection v-if="isWorkflow" :category="workflowInEditorSection" :expanded="true" @onClick="onClick" />
+            <ToolSection v-else :category="workflowSection" :expanded="true" @onClick="onClick" />
+            <ToolSection :category="linksSection" :expanded="false" @onClick="onClick" />
+            <ToolSection :category="otherSection" :expanded="true" @onClick="onClick" />
+            <ToolSection
+                v-if="hasVisualizations"
+                :category="visualizationSection"
+                :expanded="true"
+                @onClick="onClick" />
         </div>
         <MarkdownDialog
             v-if="selectedShow"
@@ -37,7 +26,7 @@
             :use-labels="isWorkflow"
             @onInsert="onInsert"
             @onCancel="onCancel" />
-    </div>
+    </ActivityPanel>
 </template>
 
 <script>
@@ -51,6 +40,8 @@ import { directiveEntry } from "./directives.ts";
 import { fromSteps } from "./labels.ts";
 import MarkdownDialog from "./MarkdownDialog";
 
+import ActivityPanel from "@/components/Panels/ActivityPanel.vue";
+
 Vue.use(BootstrapVue);
 
 function historySharedElements(mode) {
@@ -95,6 +86,7 @@ export default {
     components: {
         MarkdownDialog,
         ToolSection,
+        ActivityPanel,
     },
     props: {
         steps: {
@@ -317,7 +309,7 @@ export default {
             }
         },
         onInsert(markdownBlock) {
-            this.$emit("onInsert", markdownBlock);
+            this.$emit("insert", markdownBlock);
             this.selectedShow = false;
         },
         onCancel() {
diff --git a/client/src/components/Markdown/MarkdownVisualization.test.js b/client/src/components/Markdown/MarkdownVisualization.test.js
index 55ab54943181918ba269f04a7946e94cdeaf3b1d..da48cf495b37e4eaf5d8f0ac80c73780106c5b13 100644
--- a/client/src/components/Markdown/MarkdownVisualization.test.js
+++ b/client/src/components/Markdown/MarkdownVisualization.test.js
@@ -9,7 +9,7 @@ describe("Markdown/MarkdownVisualization", () => {
                 argumentName: "name",
                 argumentPayload: {
                     settings: [{}, {}],
-                    groups: [{}],
+                    tracks: [{}],
                 },
                 history: "history_id",
                 labels: [],
diff --git a/client/src/components/Markdown/MarkdownVisualization.vue b/client/src/components/Markdown/MarkdownVisualization.vue
index 614cb1725fab75fb042d41f7231b92c5a81f14b7..02fd69bb643906b03fd0bb7961514af8ba890edd 100644
--- a/client/src/components/Markdown/MarkdownVisualization.vue
+++ b/client/src/components/Markdown/MarkdownVisualization.vue
@@ -73,14 +73,14 @@ export default {
             if (this.argumentPayload.settings && this.argumentPayload.settings.length > 0) {
                 settings = this.argumentPayload.settings.slice();
             }
-            if (this.argumentPayload.groups && this.argumentPayload.groups.length > 0) {
+            if (this.argumentPayload.tracks && this.argumentPayload.tracks.length > 0) {
                 settings = settings || [];
                 settings.push({
                     type: "repeat",
                     title: "Columns",
-                    name: "groups",
+                    name: "tracks",
                     min: 1,
-                    inputs: this.argumentPayload.groups.map((x) => {
+                    inputs: this.argumentPayload.tracks.map((x) => {
                         if (x.type == "data_column") {
                             x.is_workflow = true;
                         }
diff --git a/client/src/components/Masthead/Masthead.test.js b/client/src/components/Masthead/Masthead.test.js
index 58a7a88137fa9c0a1bfc0e82294766bb76deb8c0..b45b9f60bbf41b12d3534defbd74b70577a9d738 100644
--- a/client/src/components/Masthead/Masthead.test.js
+++ b/client/src/components/Masthead/Masthead.test.js
@@ -1,117 +1,77 @@
 import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
 import { WindowManager } from "layout/window-manager";
-import { PiniaVuePlugin, setActivePinia } from "pinia";
-import { useEntryPointStore } from "stores/entryPointStore";
+import { PiniaVuePlugin } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
+import { useUserStore } from "@/stores/userStore";
 
 import { loadWebhookMenuItems } from "./_webhooks";
-import { getActiveTab } from "./utilities";
 
-import { default as Masthead } from "./Masthead.vue";
+import Masthead from "./Masthead.vue";
 
 jest.mock("app");
 jest.mock("./_webhooks");
 jest.mock("vue-router/composables", () => ({
     useRoute: jest.fn(() => ({ name: "Home" })),
+    useRouter: jest.fn(),
 }));
-jest.mock("@/api/schema");
+
+const { server, http } = useServerMock();
+
+const currentUser = getFakeRegisteredUser();
 
 describe("Masthead.vue", () => {
     let wrapper;
     let localVue;
     let windowManager;
-    let tabs;
     let testPinia;
 
     function stubLoadWebhooks(items) {
         items.push({
             id: "extension",
             title: "Extension Point",
-            menu: false,
             url: "extension_url",
         });
     }
 
     loadWebhookMenuItems.mockImplementation(stubLoadWebhooks);
 
-    beforeEach(() => {
+    beforeEach(async () => {
         localVue = getLocalVue();
         localVue.use(PiniaVuePlugin);
         testPinia = createTestingPinia();
-        mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
-
-        tabs = [
-            // Main Analysis Tab..
-            {
-                id: "analysis",
-                title: "Analyze",
-                menu: false,
-                url: "root",
-            },
-            {
-                id: "shared",
-                title: "Shared Items",
-                menu: [{ title: "_menu_title", url: "_menu_url", target: "_menu_target" }],
-            },
-            // Hidden tab (pre-Vue framework supported this, not sure it is used
-            // anywhere?)
-            {
-                id: "hiddentab",
-                title: "Hidden Title",
-                menu: false,
-                hidden: true,
-            },
-        ];
 
-        const initialActiveTab = "shared";
+        server.use(
+            http.get("/api/configuration", ({ response }) => {
+                return response(200).json({});
+            })
+        );
+
         windowManager = new WindowManager({});
         const windowTab = windowManager.getTab();
+
+        const userStore = useUserStore();
+        userStore.currentUser = currentUser;
+
         wrapper = mount(Masthead, {
             propsData: {
-                tabs,
                 windowTab,
-                initialActiveTab,
             },
             localVue,
             pinia: testPinia,
         });
-    });
-
-    it("test basic active tab matching", () => {
-        expect(getActiveTab("root", tabs)).toBe("analysis");
-        expect(getActiveTab("_menu_url", tabs)).toBe("shared");
+        await flushPromises();
     });
 
     it("should render simple tab item links", () => {
-        expect(wrapper.findAll("li.nav-item").length).toBe(6);
+        expect(wrapper.findAll("li.nav-item").length).toBe(4);
         // Ensure specified link title respected.
-        expect(wrapper.find("#analysis a").text()).toBe("Analyze");
-        expect(wrapper.find("#analysis a").attributes("href")).toBe("root");
-    });
-
-    it("should render tab items with menus", () => {
-        // Ensure specified link title respected.
-        expect(wrapper.find("#shared a").text()).toBe("Shared Items");
-        expect(wrapper.find("#shared").classes("dropdown")).toBe(true);
-
-        expect(wrapper.findAll("#shared .dropdown-menu li").length).toBe(1);
-        expect(wrapper.find("#shared .dropdown-menu li a").attributes().href).toBe("_menu_url");
-        expect(wrapper.find("#shared .dropdown-menu li a").attributes().target).toBe("_menu_target");
-        expect(wrapper.find("#shared .dropdown-menu li a").text()).toBe("_menu_title");
-    });
-
-    it("should make hidden tabs hidden", () => {
-        expect(wrapper.find("#analysis").attributes().style).not.toEqual(expect.stringContaining("display: none"));
-        expect(wrapper.find("#hiddentab").attributes().style).toEqual(expect.stringContaining("display: none"));
-        expect(wrapper.get("#interactive").isVisible()).toBeFalsy();
-    });
-
-    it("should highlight the active tab", () => {
-        expect(wrapper.find("#analysis").classes("active")).toBe(false);
-        expect(wrapper.find("#shared").classes("active")).toBe(true);
+        expect(wrapper.find("#help").text()).toBe("Support, Contact, and Community");
+        expect(wrapper.find("#help a").attributes("href")).toBe("/about");
     });
 
     it("should display window manager button", async () => {
@@ -124,24 +84,4 @@ describe("Masthead.vue", () => {
     it("should load webhooks on creation", async () => {
         expect(wrapper.find("#extension a").text()).toBe("Extension Point");
     });
-
-    it("shows link to interactive tools if any is active", async () => {
-        setActivePinia(testPinia);
-        const entryPointStore = useEntryPointStore();
-        entryPointStore.entryPoints = [
-            {
-                model_class: "InteractiveToolEntryPoint",
-                id: "52e496b945151ee8",
-                job_id: "52e496b945151ee8",
-                name: "Jupyter Interactive Tool",
-                active: true,
-                created_time: "2020-02-24T15:59:18.122103",
-                modified_time: "2020-02-24T15:59:20.428594",
-                target: "http://52e496b945151ee8-be8a5bee5d5849a5b4e035b51305256e.interactivetoolentrypoint.interactivetool.localhost:8080/ipython/lab",
-            },
-        ];
-        // avoid race condition with store's reactivity
-        await new Promise((_) => setTimeout(_, 10));
-        expect(wrapper.get("#interactive").isVisible()).toBeTruthy();
-    });
 });
diff --git a/client/src/components/Masthead/Masthead.vue b/client/src/components/Masthead/Masthead.vue
index 0390029c3951cf81ccf2a8dfe036b4b2527da935..32a0814bb2d42a1ef7926a9b17d4514e0ae96cef 100644
--- a/client/src/components/Masthead/Masthead.vue
+++ b/client/src/components/Masthead/Masthead.vue
@@ -1,41 +1,29 @@
 <script setup>
 import { BNavbar, BNavbarBrand, BNavbarNav } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
-import { useEntryPointStore } from "stores/entryPointStore";
+import { userLogout } from "utils/logout";
 import { withPrefix } from "utils/redirect";
-import { onBeforeMount, onMounted, reactive, ref, watch } from "vue";
-import { useRoute } from "vue-router/composables";
+import { onMounted, ref } from "vue";
+import { useRouter } from "vue-router/composables";
 
 import { useConfig } from "@/composables/config";
 import { useUserStore } from "@/stores/userStore";
 
 import { loadWebhookMenuItems } from "./_webhooks";
+import MastheadDropdown from "./MastheadDropdown";
 import MastheadItem from "./MastheadItem";
 import QuotaMeter from "./QuotaMeter";
-import { getActiveTab } from "./utilities";
 
-import NotificationsBell from "@/components/Notifications/NotificationsBell.vue";
+const { isAnonymous, currentUser } = storeToRefs(useUserStore());
 
-const { isAnonymous } = storeToRefs(useUserStore());
-
-const route = useRoute();
+const router = useRouter();
 const { config, isConfigLoaded } = useConfig();
 
-const emit = defineEmits(["open-url"]);
-
 const props = defineProps({
-    tabs: {
-        type: Array,
-        default: () => [],
-    },
     brand: {
         type: String,
         default: null,
     },
-    initialActiveTab: {
-        type: String,
-        default: "analysis",
-    },
     logoUrl: {
         type: String,
         default: null,
@@ -54,49 +42,37 @@ const props = defineProps({
     },
 });
 
-const activeTab = ref(props.initialActiveTab);
 const extensionTabs = ref([]);
 const windowToggle = ref(false);
 
-let entryPointStore;
-const itsMenu = reactive({
-    id: "interactive",
-    url: "/interactivetool_entry_points/list",
-    tooltip: "See Running Interactive Tools",
-    icon: "fa-cogs",
-    hidden: true,
-});
+function openUrl(url, target = null) {
+    if (!target) {
+        router.push(url);
+    } else {
+        url = withPrefix(url);
+        if (target == "_blank") {
+            window.open(url);
+        } else {
+            window.location = url;
+        }
+    }
+}
 
-function setActiveTab() {
-    const currentRoute = route.path;
-    activeTab.value = getActiveTab(currentRoute, props.tabs) || activeTab.value;
+function extensionTabClick(tab) {
+    if (tab.url) {
+        openUrl(tab.url, tab.target);
+    } else if (typeof tab.onclick === "function") {
+        tab.onclick();
+    }
 }
 
 function onWindowToggle() {
     windowToggle.value = !windowToggle.value;
+    props.windowTab.onclick();
 }
-function updateVisibility(isActive) {
-    itsMenu.hidden = !isActive;
-}
-
-watch(
-    () => route.path,
-    () => {
-        setActiveTab();
-    }
-);
 
-/* lifecyle */
-onBeforeMount(() => {
-    entryPointStore = useEntryPointStore();
-    entryPointStore.startWatchingEntryPoints();
-    entryPointStore.$subscribe((mutation, state) => {
-        updateVisibility(state.entryPoints.length > 0);
-    });
-});
 onMounted(() => {
     loadWebhookMenuItems(extensionTabs.value);
-    setActiveTab();
 });
 </script>
 
@@ -104,47 +80,79 @@ onMounted(() => {
     <BNavbar id="masthead" type="dark" role="navigation" aria-label="Main" class="justify-content-between">
         <BNavbarNav>
             <BNavbarBrand
+                id="analysis"
                 v-b-tooltip.hover
-                class="ml-2 mr-2"
+                class="ml-2 mr-2 p-0"
                 title="Home"
                 aria-label="homepage"
                 :href="withPrefix(logoUrl)">
                 <img alt="logo" :src="withPrefix(logoSrc)" />
                 <img v-if="logoSrcSecondary" alt="logo" :src="withPrefix(logoSrcSecondary)" />
             </BNavbarBrand>
-            <span v-if="brand" class="navbar-text px-2">
+            <span v-if="brand" class="navbar-text py-0 px-2">
                 {{ brand }}
             </span>
         </BNavbarNav>
-        <BNavbarNav>
+        <BNavbarNav v-if="isConfigLoaded" class="mr-1">
             <MastheadItem
-                v-for="(tab, idx) in props.tabs"
-                v-show="tab.hidden !== true"
-                :key="`tab-${idx}`"
-                :tab="tab"
-                :active-tab="activeTab"
-                @open-url="emit('open-url', $event)" />
-            <MastheadItem
-                v-show="itsMenu.hidden !== true"
-                :key="`its-tab`"
-                :tab="itsMenu"
-                :active-tab="activeTab"
-                @open-url="emit('open-url', $event)" />
+                v-if="windowTab"
+                :id="windowTab.id"
+                :icon="windowTab.icon"
+                :toggle="windowToggle"
+                :tooltip="windowTab.tooltip"
+                @click="onWindowToggle" />
             <MastheadItem
                 v-for="(tab, idx) in extensionTabs"
                 v-show="tab.hidden !== true"
+                :id="tab.id"
                 :key="`extension-tab-${idx}`"
-                :tab="tab"
-                :active-tab="activeTab"
-                @open-url="emit('open-url', $event)" />
-            <MastheadItem v-if="windowTab" :tab="windowTab" :toggle="windowToggle" @click="onWindowToggle" />
-            <BNavItem
-                v-if="!isAnonymous && isConfigLoaded && config.enable_notification_system"
-                id="notifications-bell">
-                <NotificationsBell tooltip-placement="bottom" />
-            </BNavItem>
+                :title="tab.title"
+                :icon="tab.icon"
+                :url="tab.url"
+                :tooltip="tab.tooltip"
+                :target="tab.target"
+                @click="extensionTabClick(tab)" />
+            <MastheadItem
+                id="help"
+                icon="fa-question"
+                url="/about"
+                tooltip="Support, Contact, and Community"
+                @click="openUrl('/about')" />
+            <QuotaMeter />
+            <MastheadItem
+                v-if="isAnonymous && config.allow_user_creation"
+                id="user"
+                class="loggedout-only"
+                title="Login or Register"
+                @click="openUrl('/login/start')" />
+            <MastheadItem
+                v-if="isAnonymous && !config.allow_user_creation"
+                id="user"
+                class="loggedout-only"
+                title="Login"
+                @click="openUrl('/login/start')" />
+            <MastheadDropdown
+                v-if="currentUser && !isAnonymous && !config.single_user"
+                id="user"
+                class="loggedin-only"
+                icon="fa-user"
+                :title="currentUser.username"
+                tooltip="User Preferences"
+                :menu="[
+                    {
+                        title: 'Preferences',
+                        icon: 'fa-gear',
+                        handler: () => openUrl('/user'),
+                    },
+                    {
+                        title: 'Sign Out',
+                        icon: 'fa-sign-out-alt',
+                        handler: () => userLogout(),
+                    },
+                ]"
+                @click="userLogout" />
         </BNavbarNav>
-        <QuotaMeter />
+        <Icon v-else icon="spinner" class="fa-spin mr-2 text-light" />
     </BNavbar>
 </template>
 
@@ -180,15 +188,17 @@ onMounted(() => {
                 cursor: pointer;
                 text-decoration: none;
                 color: var(--masthead-text-color);
+                margin-right: 0.25rem;
+                margin-left: 0.25rem;
                 &:hover {
                     color: var(--masthead-text-hover);
                 }
                 &.nav-icon {
-                    font-size: 1.3em;
+                    font-size: 1.2em;
                     .nav-note {
                         position: absolute;
-                        left: 1.9rem;
-                        top: 1.9rem;
+                        left: 1.6rem;
+                        top: 1.6rem;
                         font-size: 0.6rem;
                         font-weight: bold;
                     }
@@ -201,11 +211,12 @@ onMounted(() => {
     }
     .navbar-brand {
         cursor: pointer;
+        line-height: $masthead-height;
         img {
             filter: $text-shadow;
             display: inline;
             border: none;
-            height: 2.3rem;
+            height: 2rem;
         }
     }
     .navbar-text {
@@ -213,7 +224,7 @@ onMounted(() => {
         font-weight: bold;
         font-family: Verdana, sans-serif;
         font-size: 1rem;
-        line-height: 2rem;
+        line-height: $masthead-height;
         color: var(--masthead-text-color);
     }
 }
diff --git a/client/src/components/Masthead/MastheadDropdown.vue b/client/src/components/Masthead/MastheadDropdown.vue
new file mode 100644
index 0000000000000000000000000000000000000000..02bd10771694ffd8cf7b9fc1b1315565497b5e5b
--- /dev/null
+++ b/client/src/components/Masthead/MastheadDropdown.vue
@@ -0,0 +1,48 @@
+<script setup>
+import { BDropdownItem, BNavItemDropdown, VBTooltipPlugin } from "bootstrap-vue";
+import Vue, { ref } from "vue";
+
+import TextShort from "@/components/Common/TextShort.vue";
+
+Vue.use(VBTooltipPlugin);
+
+const dropdown = ref(null);
+
+/* props */
+defineProps({
+    id: {
+        type: String,
+    },
+    icon: {
+        type: String,
+    },
+    target: {
+        type: String,
+    },
+    title: {
+        type: String,
+    },
+    tooltip: {
+        type: String,
+    },
+    menu: {
+        type: Array,
+    },
+});
+</script>
+
+<template>
+    <BNavItemDropdown :id="id" ref="dropdown" v-b-tooltip.noninteractive.hover.bottom :title="tooltip" right>
+        <template v-if="icon" v-slot:button-content>
+            <span class="sr-only">{{ tooltip || id }}</span>
+            <span class="fa fa-fw" :class="icon" />
+            <TextShort :text="title" />
+        </template>
+        <template>
+            <BDropdownItem v-for="(item, idx) in menu" :key="idx" role="menuitem" @click="item.handler">
+                <span class="fa fa-fw" :class="item.icon" />
+                <span>{{ item.title }}</span>
+            </BDropdownItem>
+        </template>
+    </BNavItemDropdown>
+</template>
diff --git a/client/src/components/Masthead/MastheadItem.test.js b/client/src/components/Masthead/MastheadItem.test.js
deleted file mode 100644
index 68e8780c00c0d8e924b0cb0fedd6ab7187fd043c..0000000000000000000000000000000000000000
--- a/client/src/components/Masthead/MastheadItem.test.js
+++ /dev/null
@@ -1,40 +0,0 @@
-import { mount } from "@vue/test-utils";
-import { getLocalVue } from "tests/jest/helpers";
-
-import MastheadItem from "./MastheadItem.vue";
-
-describe("MastheadItem.vue", () => {
-    let wrapper;
-    let localVue;
-
-    beforeEach(() => {
-        localVue = getLocalVue();
-    });
-
-    function m(active, menu) {
-        const tab = {
-            id: "mytab",
-            menu: menu,
-        };
-
-        return mount(MastheadItem, {
-            propsData: {
-                tab,
-                activeTab: active,
-            },
-            localVue,
-        });
-    }
-
-    it("should render active tab with menus", async () => {
-        wrapper = m("mytab", true);
-        expect(wrapper.classes("active")).toBe(true);
-        expect(wrapper.classes("b-nav-dropdown")).toBe(true);
-    });
-
-    it("should render inactive tabs without menus", async () => {
-        wrapper = m("othertab", false);
-        expect(wrapper.classes("active")).toBe(false);
-        expect(wrapper.classes("b-nav-dropdown")).toBe(false);
-    });
-});
diff --git a/client/src/components/Masthead/MastheadItem.vue b/client/src/components/Masthead/MastheadItem.vue
index 889526e01ffa45eadc704dd77ede1ee9e03cd124..f3c1ca5c3ab5b44d7965e52b6f0963412a6f7eac 100644
--- a/client/src/components/Masthead/MastheadItem.vue
+++ b/client/src/components/Masthead/MastheadItem.vue
@@ -1,125 +1,57 @@
 <script setup>
-import { BDropdownItem, BNavItem, BNavItemDropdown, VBPopoverPlugin, VBTooltipPlugin } from "bootstrap-vue";
+import { BNavItem, VBTooltipPlugin } from "bootstrap-vue";
 import { withPrefix } from "utils/redirect";
-import Vue, { computed, getCurrentInstance, ref } from "vue";
+import Vue from "vue";
 
-Vue.use(VBPopoverPlugin);
 Vue.use(VBTooltipPlugin);
 
-const instance = getCurrentInstance().proxy;
-const emit = defineEmits(["click", "open-url"]);
-const dropdown = ref(null);
-
 /* props */
-const props = defineProps({
-    tab: {
-        type: Object,
-        default: null,
+defineProps({
+    disabled: {
+        type: Boolean,
+    },
+    id: {
+        type: String,
+    },
+    icon: {
+        type: String,
+    },
+    target: {
+        type: String,
+    },
+    title: {
+        type: String,
+    },
+    tooltip: {
+        type: String,
     },
     toggle: {
         type: Boolean,
         default: false,
     },
-    activeTab: {
+    url: {
         type: String,
-        default: null,
     },
 });
-
-/* computed */
-const menu = computed(() => props.tab.menu);
-const popoverNote = computed(
-    () => `Please <a href="${withPrefix("/login")}">log in or register</a> to use this feature.`
-);
-const classes = computed(() => {
-    const isActiveTab = props.tab.id == props.activeTab;
-    return Object.fromEntries([
-        ["active", isActiveTab],
-        [props.tab.cls, !!props.tab.cls],
-    ]);
-});
-const linkClasses = computed(() => ({
-    "nav-icon": props.tab.icon,
-    toggle: props.toggle,
-}));
-const iconClasses = computed(() =>
-    Object.fromEntries([
-        ["fa fa-fw", true],
-        [props.tab.icon, !!props.tab.icon],
-    ])
-);
-
-/* methods */
-function open(tab, event) {
-    if (tab.onclick) {
-        event.preventDefault();
-        tab.onclick();
-        emit("click");
-    } else if (tab.disabled) {
-        event.preventDefault();
-        instance.$root.$emit("bv::hide::tooltip");
-        instance.$root.$emit("bv::show::popover", tab.id);
-        setTimeout(() => {
-            instance.$root.$emit("bv::hide::popover", tab.id);
-        }, 3000);
-    } else if (!tab.menu) {
-        event.preventDefault();
-        emit("open-url", { ...tab });
-    }
-}
 </script>
 
 <template>
     <BNavItem
-        v-if="!menu"
-        :id="tab.id"
-        v-b-tooltip.hover.bottom
-        v-b-popover.manual.bottom="{ id: tab.id, content: popoverNote, html: true }"
-        :class="classes"
-        :href="withPrefix(tab.url)"
-        :target="tab.target || '_parent'"
-        :link-classes="linkClasses"
-        :title="tab.tooltip"
-        @click="open(tab, $event)">
-        <template v-if="tab.icon">
+        :id="id"
+        v-b-tooltip.noninteractive.hover.bottom
+        :href="withPrefix(url)"
+        :target="target || '_parent'"
+        :link-classes="{ 'nav-icon': !!icon, toggle: toggle }"
+        :title="tooltip"
+        @click.prevent="$emit('click')">
+        <template v-if="icon">
             <!-- If this is an icon-based tab, inject tooltip directly for screen readers -->
-            <span class="sr-only">{{ tab.tooltip || tab.id }}</span>
-            <span :class="iconClasses" />
+            <span class="sr-only">{{ tooltip || id }}</span>
+            <span :class="`fa fa-fw ${icon}`" />
             <span v-if="toggle" class="nav-note fa fa-check" />
         </template>
         <template v-else>
-            {{ tab.title }}
+            {{ title }}
         </template>
     </BNavItem>
-    <BNavItemDropdown
-        v-else
-        :id="tab.id"
-        ref="dropdown"
-        v-b-tooltip.hover.bottom
-        v-b-popover.manual.bottom="{ id: tab.id, content: popoverNote, html: true }"
-        :class="classes"
-        :text="tab.title"
-        href="#"
-        :title="tab.tooltip"
-        @show="open(tab, $event)">
-        <template v-if="tab.icon" v-slot:button-content>
-            <span class="sr-only">{{ tab.tooltip || tab.id }}</span>
-            <span :class="iconClasses" />
-        </template>
-        <template v-for="(item, idx) in tab.menu">
-            <div v-if="item.divider" :key="`divider-${idx}`" class="dropdown-divider" />
-            <BDropdownItem
-                v-else-if="item.hidden !== true"
-                :key="`item-${idx}`"
-                :href="withPrefix(item.url)"
-                :target="item.target || '_parent'"
-                role="menuitem"
-                title=""
-                :active="item.disabled"
-                :disabled="item.disabled"
-                @click="open(item, $event)">
-                {{ item.title }}
-            </BDropdownItem>
-        </template>
-    </BNavItemDropdown>
 </template>
diff --git a/client/src/components/Masthead/QuotaMeter.test.ts b/client/src/components/Masthead/QuotaMeter.test.ts
index 583543cb38ad1d0afd321605f7c4fa8e4042000c..b405a5b36a12ffaee37706190bc466bb6d2a715e 100644
--- a/client/src/components/Masthead/QuotaMeter.test.ts
+++ b/client/src/components/Masthead/QuotaMeter.test.ts
@@ -1,23 +1,32 @@
 import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { type RegisteredUser } from "@/api";
 import { useUserStore } from "@/stores/userStore";
 
 import QuotaMeter from "./QuotaMeter.vue";
 
 jest.mock("@/api/schema");
 
+let configValues = { enable_quotas: true };
+
+jest.mock("@/composables/config", () => ({
+    useConfig: jest.fn(() => ({
+        config: { value: { ...configValues } },
+        isConfigLoaded: true,
+    })),
+}));
+
 const localVue = getLocalVue();
 
-async function createQuotaMeterWrapper(config: any, userData: any) {
-    mockFetcher.path("/api/configuration").method("get").mock({ data: config });
+async function createQuotaMeterWrapper(config: any, user: RegisteredUser) {
+    configValues = { ...config };
     const pinia = createTestingPinia();
     const userStore = useUserStore();
-    userStore.currentUser = { ...userStore.currentUser, ...userData };
-
+    userStore.currentUser = user;
     const wrapper = mount(QuotaMeter, {
         localVue,
         pinia,
@@ -26,80 +35,52 @@ async function createQuotaMeterWrapper(config: any, userData: any) {
     return wrapper;
 }
 
+const FAKE_USER = getFakeRegisteredUser({ quota: "100 MB", total_disk_usage: 5120, quota_percent: 50 });
+
 describe("QuotaMeter.vue", () => {
     it("shows a percentage usage", async () => {
-        const user = {
-            total_disk_usage: 5120,
-            quota_percent: 50,
-        };
-
         const config = { enable_quotas: true };
-        const wrapper = await createQuotaMeterWrapper(config, user);
-
-        expect(wrapper.find(".quota-progress > span").text()).toBe("Using 50%");
+        const wrapper = await createQuotaMeterWrapper(config, FAKE_USER);
+        expect(wrapper.find(".quota-progress > span").text()).toBe("Using 50% of 100 MB");
     });
 
     it("changes appearance depending on usage", async () => {
         const config = { enable_quotas: true };
-
         {
-            const user = { quota_percent: 30 };
+            const user = { ...FAKE_USER, quota_percent: 30 };
             const wrapper = await createQuotaMeterWrapper(config, user);
-
             expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-success");
         }
-
         {
-            const user = { quota_percent: 80 };
+            const user = { ...FAKE_USER, quota_percent: 80 };
             const wrapper = await createQuotaMeterWrapper(config, user);
-
             expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-warning");
         }
-
         {
-            const user = { quota_percent: 95 };
+            const user = { ...FAKE_USER, quota_percent: 95 };
             const wrapper = await createQuotaMeterWrapper(config, user);
-
             expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-danger");
         }
     });
 
-    it("prompts user to log in", async () => {
-        const config = { enable_quotas: true };
-        const wrapper = await createQuotaMeterWrapper(config, {});
-
-        expect(wrapper.find(".quota-meter > a").attributes("title")).toContain("Log in");
-    });
-
-    it("shows total usage in title", async () => {
-        const user = { total_disk_usage: 9216 };
+    it("displays tooltip", async () => {
         const config = { enable_quotas: true };
-        const wrapper = await createQuotaMeterWrapper(config, user);
-
-        expect(wrapper.find(".quota-progress").attributes("title")).toContain("9 KB");
+        const wrapper = await createQuotaMeterWrapper(config, FAKE_USER);
+        expect(wrapper.attributes("title")).toContain("Storage");
     });
 
     it("shows total usage when there is no quota", async () => {
         {
-            const user = { total_disk_usage: 7168 };
+            const user = { ...FAKE_USER, total_disk_usage: 7168 };
             const config = { enable_quotas: false };
             const wrapper = await createQuotaMeterWrapper(config, user);
-
-            expect(wrapper.find(".quota-text > a").text()).toBe("Using 7 KB");
-            expect(wrapper.find(".quota-text > a").attributes("title")).not.toContain("7 KB");
+            expect(wrapper.find("span").text()).toBe("Using 7 KB");
         }
-
         {
-            const user = {
-                total_disk_usage: 21504,
-                quota: "unlimited",
-            };
-
+            const user = { ...FAKE_USER, total_disk_usage: 21504, quota: "unlimited" };
             const config = { enable_quotas: true };
             const wrapper = await createQuotaMeterWrapper(config, user);
-
-            expect(wrapper.find(".quota-text > a").text()).toBe("Using 21 KB");
-            expect(wrapper.find(".quota-text > a").attributes("title")).not.toContain("21 KB");
+            expect(wrapper.find("span").text()).toBe("Using 21 KB");
         }
     });
 });
diff --git a/client/src/components/Masthead/QuotaMeter.vue b/client/src/components/Masthead/QuotaMeter.vue
index c2ddf28525c175549fd77290f8be476809b130b4..5d3dc01ae72b793f62b60a1785d05b31aeecf413 100644
--- a/client/src/components/Masthead/QuotaMeter.vue
+++ b/client/src/components/Masthead/QuotaMeter.vue
@@ -1,114 +1,78 @@
-<template>
-    <div>
-        <div v-if="!hasQuota" class="quota-text d-flex align-items-center">
-            <b-link
-                v-b-tooltip.hover.left
-                to="/storage"
-                :disabled="isAnonymous"
-                class="ml-auto"
-                :title="title"
-                data-description="storage dashboard link">
-                {{ usingString + " " + totalUsageString }}
-            </b-link>
-        </div>
-        <div v-else class="quota-meter d-flex align-items-center">
-            <b-link
-                v-b-tooltip.hover.left
-                class="quota-progress"
-                :disabled="isAnonymous"
-                to="/storage"
-                :title="title"
-                data-description="storage dashboard link">
-                <b-progress :max="100">
-                    <b-progress-bar aria-label="Quota usage" :value="usage" :variant="variant" />
-                </b-progress>
-                <span>{{ usingString + " " + usage.toFixed(0) }}%</span>
-            </b-link>
-        </div>
-    </div>
-</template>
+<script setup lang="ts">
+import { BLink, BProgress, BProgressBar } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed } from "vue";
 
-<script>
-import { mapState } from "pinia";
-import { bytesToString } from "utils/utils";
-
-import { useConfigStore } from "@/stores/configurationStore";
+import { isRegisteredUser } from "@/api";
+import { useConfig } from "@/composables/config";
 import { useUserStore } from "@/stores/userStore";
+import { bytesToString } from "@/utils/utils";
+
+const { config } = useConfig();
+const { currentUser, isAnonymous } = storeToRefs(useUserStore());
+
+const hasQuota = computed<boolean>(() => {
+    const quotasEnabled = config.value.enable_quotas ?? false;
+    const quotaLimited = (isRegisteredUser(currentUser.value) && currentUser.value.quota !== "unlimited") ?? false;
+    return quotasEnabled && quotaLimited;
+});
 
-export default {
-    name: "QuotaMeter",
-    data() {
-        return {
-            usingString: this.l("Using"),
-        };
-    },
-    computed: {
-        ...mapState(useConfigStore, ["config"]),
-        ...mapState(useUserStore, ["currentUser", "isAnonymous"]),
-        hasQuota() {
-            const quotasEnabled = this.config?.enable_quotas ?? false;
-            const quotaLimited = this.currentUser?.quota !== "unlimited" ?? false;
+const quotaLimit = computed(() => (isRegisteredUser(currentUser.value) && currentUser.value.quota) ?? null);
 
-            return quotasEnabled && quotaLimited;
-        },
-        usage() {
-            if (this.hasQuota) {
-                return this.currentUser?.quota_percent ?? 0;
-            } else {
-                return this.currentUser?.total_disk_usage ?? 0;
-            }
-        },
-        totalUsageString() {
-            const total = this.currentUser?.total_disk_usage ?? 0;
-            return bytesToString(total, true);
-        },
-        title() {
-            let details = "";
-            if (this.isAnonymous) {
-                details = this.l("Log in for details.");
-            } else {
-                details = this.l("Click for details.");
-            }
+const totalUsageString = computed(() => {
+    const total = currentUser.value?.total_disk_usage ?? 0;
+    return bytesToString(total, true);
+});
 
-            if (this.hasQuota) {
-                return this.usingString + " " + this.totalUsageString + ". " + details;
-            } else {
-                return details;
-            }
-        },
-        variant() {
-            if (!this.hasQuota || this.usage < 80) {
-                return "success";
-            } else if (this.usage < 95) {
-                return "warning";
-            } else {
-                return "danger";
-            }
-        },
-    },
-};
+const usage = computed(() => {
+    if (hasQuota.value) {
+        return currentUser.value?.quota_percent ?? 0;
+    }
+    return currentUser.value?.total_disk_usage ?? 0;
+});
+
+const quotaLink = computed(() => (isAnonymous.value ? "/login/start" : "/storage"));
+
+const quotaTitle = computed(() =>
+    isAnonymous.value ? "Login to Access Storage Details" : "Storage and Usage Details"
+);
+
+const variant = computed(() => {
+    if (!hasQuota.value || usage.value < 80) {
+        return "success";
+    } else if (usage.value < 95) {
+        return "warning";
+    }
+    return "danger";
+});
 </script>
 
+<template>
+    <div v-b-tooltip.hover.bottom class="quota-meter d-flex align-items-center" :title="quotaTitle">
+        <BLink class="quota-progress" :to="quotaLink" data-description="storage dashboard link">
+            <BProgress :max="100">
+                <BProgressBar aria-label="Quota usage" :value="usage" :variant="variant" />
+            </BProgress>
+            <span>
+                <span v-localize>Using</span>
+                <span v-if="hasQuota">
+                    <span>{{ usage.toFixed(0) }}%</span>
+                    <span v-if="quotaLimit !== null">of {{ quotaLimit }}</span>
+                </span>
+                <span v-else>{{ totalUsageString }}</span>
+            </span>
+        </BLink>
+    </div>
+</template>
+
 <style lang="scss" scoped>
-.quote-container {
+.quota-meter {
     position: relative;
     height: 100%;
+    margin-left: 0.5rem;
     margin-right: 0.5rem;
-}
-.quota-text {
-    @extend .quote-container;
-    background: var(--masthead-link-color);
-    padding-right: 0.5rem;
-    padding-left: 0.5rem;
-    a {
-        color: var(--masthead-text-color);
-        text-decoration: none;
-    }
-}
-.quota-meter {
-    @extend .quote-container;
     .quota-progress {
-        width: 100px;
+        width: 12rem;
         height: 1.4em;
         position: relative;
         & > * {
@@ -116,8 +80,6 @@ export default {
             width: 100%;
             height: 100%;
             text-align: center;
-        }
-        & > span {
             line-height: 1.4em;
             pointer-events: none;
         }
diff --git a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
index 624655b4e863a40f4272f031d79d4b01664885db..fb2b53f8aeb3877ef0787519a89e87321de30c27 100644
--- a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
+++ b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
@@ -31,7 +31,9 @@ function generateBroadcastNotification(overwrites: Partial<BroadcastNotification
         expiration_time: toApiDate(inTwoMonths),
         source: "testing",
         variant: "info",
+        category: "broadcast",
         content: {
+            category: "broadcast",
             subject: `Test subject ${overwrites.id ?? id}`,
             message: `Test message ${overwrites.id ?? id}`,
         },
diff --git a/client/src/components/Notifications/Categories/MessageNotification.vue b/client/src/components/Notifications/Categories/MessageNotification.vue
index b313b961454badccfe24e15e5e0ba1609d120737..ad1f533e32b021940f2f91f66e2fb182a230bf17 100644
--- a/client/src/components/Notifications/Categories/MessageNotification.vue
+++ b/client/src/components/Notifications/Categories/MessageNotification.vue
@@ -4,15 +4,13 @@ import { faInbox } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 
-import { type MessageNotification } from "@/api/notifications";
+import { type MessageNotification, type MessageNotificationCreateData } from "@/api/notifications";
 import { useMarkdown } from "@/composables/markdown";
 
 import NotificationActions from "@/components/Notifications/NotificationActions.vue";
 
 library.add(faInbox);
 
-type PartialNotification = Partial<MessageNotification> & { content: MessageNotification["content"] };
-
 type Options =
     | {
           previewMode?: false;
@@ -20,7 +18,7 @@ type Options =
       }
     | {
           previewMode: true;
-          notification: PartialNotification;
+          notification: MessageNotificationCreateData;
       };
 
 const props = defineProps<{
@@ -37,12 +35,16 @@ const notificationVariant = computed(() => {
             return props.options.notification.variant;
     }
 });
+
+const notificationSeen = computed(() => {
+    return "seen_time" in props.options.notification && !!props.options.notification.seen_time;
+});
 </script>
 
 <template>
     <div class="notification-container">
         <div class="notification-header">
-            <div :class="!props.options.notification.seen_time ? 'font-weight-bold' : ''" class="notification-title">
+            <div :class="!notificationSeen ? 'font-weight-bold' : ''" class="notification-title">
                 <FontAwesomeIcon :class="`text-${notificationVariant}`" :icon="faInbox" fixed-width size="sm" />
                 {{ props.options.notification?.content?.subject }}
             </div>
diff --git a/client/src/components/Notifications/Categories/SharedItemNotification.vue b/client/src/components/Notifications/Categories/SharedItemNotification.vue
index b141c87ed3086ce714358e361a08ff546af9ad45..dcd3de959765a8ee02adbab191604fd73cbdbb67 100644
--- a/client/src/components/Notifications/Categories/SharedItemNotification.vue
+++ b/client/src/components/Notifications/Categories/SharedItemNotification.vue
@@ -8,6 +8,7 @@ import { computed } from "vue";
 import type { SharedItemNotification } from "@/api/notifications";
 import { useNotificationsStore } from "@/stores/notificationsStore";
 import { absPath } from "@/utils/redirect";
+import { capitalizeFirstLetter } from "@/utils/strings";
 
 import NotificationActions from "@/components/Notifications/NotificationActions.vue";
 
@@ -21,10 +22,6 @@ const props = defineProps<Props>();
 
 const notificationsStore = useNotificationsStore();
 
-function capitalizeFirstLetter(string: string) {
-    return string.charAt(0).toUpperCase() + string.slice(1);
-}
-
 const content = computed(() => props.notification.content);
 
 const sharedItemType = computed(() => {
diff --git a/client/src/components/Notifications/NotificationActions.test.ts b/client/src/components/Notifications/NotificationActions.test.ts
index f098adff07cda37a2869630a317fea18c6a5fa6e..ad06cb27a24aab967da8bb45cce3711745e2b081 100644
--- a/client/src/components/Notifications/NotificationActions.test.ts
+++ b/client/src/components/Notifications/NotificationActions.test.ts
@@ -3,9 +3,9 @@ import { getLocalVue } from "@tests/jest/helpers";
 import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
-import Vue from "vue";
+import type Vue from "vue";
 
-import type { UserNotification } from "@/api/notifications";
+import { type UserNotification } from "@/api/notifications";
 import { generateMessageNotification, generateNewSharedItemNotification } from "@/components/Notifications/test-utils";
 import { useNotificationsStore } from "@/stores/notificationsStore";
 
diff --git a/client/src/components/Notifications/test-utils.ts b/client/src/components/Notifications/test-utils.ts
index c9ff19f586dde0038bf3a9149a41e4c29a4b64dd..c79dad3ca0ec5726e53ad1964dff0fb29958e29f 100644
--- a/client/src/components/Notifications/test-utils.ts
+++ b/client/src/components/Notifications/test-utils.ts
@@ -1,9 +1,9 @@
-import type {
-    MessageNotification,
-    NewSharedItemNotificationContentItemType,
-    NotificationVariants,
-    SharedItemNotification,
-    UserNotification,
+import {
+    type MessageNotification,
+    type NewSharedItemNotificationContentItemType,
+    type NotificationVariants,
+    type SharedItemNotification,
+    type UserNotification,
 } from "@/api/notifications";
 
 export function generateRandomItemType() {
diff --git a/client/src/components/ObjectStore/Instances/CreateForm.test.ts b/client/src/components/ObjectStore/Instances/CreateForm.test.ts
index 120fcde0696949f0fdb851088fa800cce201b788..1012bb09858c5bc45436183f61513abf1d8fe65a 100644
--- a/client/src/components/ObjectStore/Instances/CreateForm.test.ts
+++ b/client/src/components/ObjectStore/Instances/CreateForm.test.ts
@@ -2,15 +2,33 @@ import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { PluginStatus } from "@/api/configTemplates";
-import { mockFetcher } from "@/api/schema/__mocks__";
-import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
+import { useServerMock } from "@/api/client/__mocks__";
+import { OK_PLUGIN_STATUS } from "@/components/ConfigTemplates/test_fixtures";
+import { type ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
 
-import CreateForm from "./CreateForm.vue";
+import { type UserConcreteObjectStore } from "./types";
 
-jest.mock("@/api/schema");
+import CreateForm from "./CreateForm.vue";
 
-const FAKE_OBJECT_STORE = "A fake object store";
+const FAKE_OBJECT_STORE: UserConcreteObjectStore = {
+    name: "My New Name",
+    template_id: "moo",
+    template_version: 0,
+    active: true,
+    badges: [],
+    hidden: false,
+    private: false,
+    purged: false,
+    quota: {
+        enabled: false,
+    },
+    type: "aws_s3",
+    uuid: "test_UUID",
+    variables: {
+        myvar: "default",
+    },
+    secrets: ["mysecret"],
+};
 
 const localVue = getLocalVue(true);
 
@@ -23,6 +41,7 @@ const STANDARD_TEMPLATE: ObjectStoreTemplateSummary = {
             name: "myvar",
             type: "string",
             help: "*myvar help*",
+            default: "default",
         },
     ],
     secrets: [
@@ -34,6 +53,7 @@ const STANDARD_TEMPLATE: ObjectStoreTemplateSummary = {
     id: "moo",
     version: 0,
     badges: [],
+    hidden: false,
 };
 
 const SIMPLE_TEMPLATE: ObjectStoreTemplateSummary = {
@@ -45,6 +65,7 @@ const SIMPLE_TEMPLATE: ObjectStoreTemplateSummary = {
             name: "myvar",
             type: "string",
             help: "*myvar help*",
+            default: "default",
         },
     ],
     secrets: [
@@ -56,22 +77,10 @@ const SIMPLE_TEMPLATE: ObjectStoreTemplateSummary = {
     id: "moo",
     version: 0,
     badges: [],
+    hidden: false,
 };
 
-const FAKE_PLUGIN_STATUS: PluginStatus = {
-    template_definition: {
-        state: "ok",
-        message: "ok",
-    },
-    template_settings: {
-        state: "ok",
-        message: "ok",
-    },
-    connection: {
-        state: "ok",
-        message: "ok",
-    },
-};
+const { server, http } = useServerMock();
 
 describe("CreateForm", () => {
     it("should render a form with admin markdown converted to HTML in help", async () => {
@@ -99,17 +108,24 @@ describe("CreateForm", () => {
             },
             localVue,
         });
-        mockFetcher.path("/api/object_store_instances/test").method("post").mock({ data: FAKE_PLUGIN_STATUS });
-        mockFetcher.path("/api/object_store_instances").method("post").mock({ data: FAKE_OBJECT_STORE });
-        await flushPromises();
+
+        server.use(
+            http.post("/api/object_store_instances", ({ response }) => {
+                return response(200).json(FAKE_OBJECT_STORE);
+            }),
+            http.post("/api/object_store_instances/test", ({ response }) => {
+                return response(200).json(OK_PLUGIN_STATUS);
+            })
+        );
+
         const nameForElement = wrapper.find("#form-element-_meta_name");
-        nameForElement.find("input").setValue("My New Name");
+        await nameForElement.find("input").setValue("My New Name");
         const submitElement = wrapper.find("#submit");
-        submitElement.trigger("click");
+        await submitElement.trigger("click");
         await flushPromises();
         const emitted = wrapper.emitted("created") || [];
         expect(emitted).toHaveLength(1);
-        expect(emitted[0][0]).toBe(FAKE_OBJECT_STORE);
+        expect(emitted[0][0]).toMatchObject(FAKE_OBJECT_STORE);
     });
 
     it("should indicate an error on failure", async () => {
@@ -119,23 +135,26 @@ describe("CreateForm", () => {
             },
             localVue,
         });
-        mockFetcher.path("/api/object_store_instances/test").method("post").mock({ data: FAKE_PLUGIN_STATUS });
-        mockFetcher
-            .path("/api/object_store_instances")
-            .method("post")
-            .mock(() => {
-                throw Error("Error creating this");
-            });
+        server.use(
+            http.post("/api/object_store_instances", ({ response }) => {
+                return response("4XX").json({ err_msg: "Error creating this", err_code: 400 }, { status: 400 });
+            }),
+            http.post("/api/object_store_instances/test", ({ response }) => {
+                return response(200).json(OK_PLUGIN_STATUS);
+            })
+        );
+
         await flushPromises();
         const nameForElement = wrapper.find("#form-element-_meta_name");
         nameForElement.find("input").setValue("My New Name");
         const submitElement = wrapper.find("#submit");
-        expect(wrapper.find(".object-store-instance-creation-error").exists()).toBe(false);
+        expect(wrapper.find("[data-description='object-store-creation-error']").exists()).toBe(false);
         submitElement.trigger("click");
         await flushPromises();
         const emitted = wrapper.emitted("created") || [];
         expect(emitted).toHaveLength(0);
-        const errorEl = wrapper.find(".object-store-instance-creation-error");
+        const errorEl = wrapper.find("[data-description='object-store-creation-error']");
+        console.log(wrapper.html());
         expect(errorEl.exists()).toBe(true);
         expect(errorEl.html()).toContain("Error creating this");
     });
diff --git a/client/src/components/ObjectStore/Instances/CreateForm.vue b/client/src/components/ObjectStore/Instances/CreateForm.vue
index 6da11a92e3d95554059e3f86973fefbe12f69478..1c6b3cb5ad06912a4d301d8961104d26e313b02f 100644
--- a/client/src/components/ObjectStore/Instances/CreateForm.vue
+++ b/client/src/components/ObjectStore/Instances/CreateForm.vue
@@ -1,65 +1,46 @@
 <script lang="ts" setup>
-import { BAlert } from "bootstrap-vue";
-import { computed, ref } from "vue";
+import { toRef } from "vue";
 
-import {
-    createFormDataToPayload,
-    createTemplateForm,
-    type FormEntry,
-    pluginStatusToErrorMessage,
-} from "@/components/ConfigTemplates/formUtil";
+import { useConfigurationTemplateCreation } from "@/components/ConfigTemplates/useConfigurationTesting";
 import type { UserConcreteObjectStore } from "@/components/ObjectStore/Instances/types";
 import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
-import { errorMessageAsString } from "@/utils/simple-error";
 
-import { create, test } from "./services";
-
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+const createUrl = "/api/object_store_instances";
+const createTestUrl = "/api/object_store_instances/test";
 
 interface CreateFormProps {
     template: ObjectStoreTemplateSummary;
+    uuid?: string;
 }
-const error = ref<string | null>(null);
 const props = defineProps<CreateFormProps>();
 const title = "Create a new storage location for your data";
-const submitTitle = "Submit";
-const loadingMessage = "Loading storage location template and instance information";
-
-const inputs = computed<Array<FormEntry>>(() => {
-    return createTemplateForm(props.template, "storage location");
-});
-
-async function onSubmit(formData: any) {
-    const payload = createFormDataToPayload(props.template, formData);
-    const { data: pluginStatus } = await test(payload);
-    const testError = pluginStatusToErrorMessage(pluginStatus);
-    if (testError) {
-        error.value = testError;
-        return;
-    }
-    try {
-        const { data: objectStore } = await create(payload);
-        emit("created", objectStore);
-    } catch (e) {
-        error.value = errorMessageAsString(e);
-        return;
-    }
-}
 
 const emit = defineEmits<{
     (e: "created", objectStore: UserConcreteObjectStore): void;
 }>();
+
+const { ActionSummary, error, inputs, InstanceForm, onSubmit, submitTitle, loadingMessage, testRunning, testResults } =
+    useConfigurationTemplateCreation(
+        "storage location",
+        toRef(props, "template"),
+        toRef(props, "uuid"),
+        createTestUrl,
+        createUrl,
+        (instance: UserConcreteObjectStore) => emit("created", instance)
+    );
 </script>
 <template>
     <div id="create-object-store-landing">
-        <BAlert v-if="error" variant="danger" class="object-store-instance-creation-error" show>
-            {{ error }}
-        </BAlert>
+        <ActionSummary
+            error-data-description="object-store-creation-error"
+            :test-results="testResults"
+            :error="error" />
         <InstanceForm
             :inputs="inputs"
             :title="title"
             :submit-title="submitTitle"
             :loading-message="loadingMessage"
+            :busy="testRunning"
             @onSubmit="onSubmit" />
     </div>
 </template>
diff --git a/client/src/components/ObjectStore/Instances/EditInstance.vue b/client/src/components/ObjectStore/Instances/EditInstance.vue
index 0c6ea67cf4a63da967445c4fc21888ae59906eb8..57c4a211bf8ce073ac985179e487040456cb14e6 100644
--- a/client/src/components/ObjectStore/Instances/EditInstance.vue
+++ b/client/src/components/ObjectStore/Instances/EditInstance.vue
@@ -2,15 +2,15 @@
 import { BTab, BTabs } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { editFormDataToPayload, editTemplateForm, type FormEntry } from "@/components/ConfigTemplates/formUtil";
+import { useConfigurationTemplateEdit } from "@/components/ConfigTemplates/useConfigurationTesting";
 
 import { useInstanceAndTemplate } from "./instance";
 import { useInstanceRouting } from "./routing";
-import { update } from "./services";
-import type { UserConcreteObjectStore } from "./types";
 
 import EditSecrets from "./EditSecrets.vue";
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+
+const editTestUrl = "/api/object_store_instances/{uuid}/test";
+const editUrl = "/api/object_store_instances/{uuid}";
 
 interface Props {
     instanceId: string;
@@ -19,45 +19,40 @@ interface Props {
 const props = defineProps<Props>();
 const { instance, template } = useInstanceAndTemplate(ref(props.instanceId));
 
-const inputs = computed<Array<FormEntry> | undefined>(() => {
-    template.value;
-    instance.value;
-    if (template.value && instance.value) {
-        return editTemplateForm(template.value, "storage location", instance.value);
-    }
-    return undefined;
-});
-
 const title = computed(() => `Edit Storage Location ${instance.value?.name} Settings`);
-const hasSecrets = computed(() => instance.value?.secrets && instance.value?.secrets.length > 0);
-const submitTitle = "Update Settings";
-const loadingMessage = "Loading storage location template and instance information";
-
-async function onSubmit(formData: any) {
-    if (template.value) {
-        const payload = editFormDataToPayload(template.value, formData);
-        const args = { user_object_store_id: String(instance?.value?.uuid) };
-        const { data: objectStore } = await update({ ...args, ...payload });
-        await onUpdate(objectStore);
-    }
-}
-
-const { goToIndex } = useInstanceRouting();
+const errorDataDescription = "object-store-update-error";
 
-async function onUpdate(objectStore: UserConcreteObjectStore) {
-    const message = `Updated storage location ${objectStore.name}`;
-    goToIndex({ message });
-}
+const {
+    error,
+    hasSecrets,
+    ActionSummary,
+    inputs,
+    InstanceForm,
+    loadingMessage,
+    onForceSubmit,
+    onSubmit,
+    testRunning,
+    testResults,
+    showForceActionButton,
+    submitTitle,
+} = useConfigurationTemplateEdit("storage location", instance, template, editTestUrl, editUrl, useInstanceRouting);
 </script>
 <template>
     <div>
         <BTabs v-if="hasSecrets">
             <BTab title="Settings" active>
+                <ActionSummary
+                    :error-data-description="errorDataDescription"
+                    :test-results="testResults"
+                    :error="error" />
                 <InstanceForm
                     :inputs="inputs"
                     :title="title"
                     :submit-title="submitTitle"
                     :loading-message="loadingMessage"
+                    :busy="testRunning"
+                    :show-force-action-button="showForceActionButton"
+                    @onForceSubmit="onForceSubmit"
                     @onSubmit="onSubmit" />
             </BTab>
             <BTab title="Secrets">
@@ -66,12 +61,17 @@ async function onUpdate(objectStore: UserConcreteObjectStore) {
                 </div>
             </BTab>
         </BTabs>
-        <InstanceForm
-            v-else
-            :inputs="inputs"
-            :title="title"
-            :submit-title="submitTitle"
-            :loading-message="loadingMessage"
-            @onSubmit="onSubmit" />
+        <div v-else>
+            <ActionSummary :error-data-description="errorDataDescription" :test-results="testResults" :error="error" />
+            <InstanceForm
+                :inputs="inputs"
+                :title="title"
+                :submit-title="submitTitle"
+                :loading-message="loadingMessage"
+                :busy="testRunning"
+                :show-force-action-button="showForceActionButton"
+                @onForceSubmit="onForceSubmit"
+                @onSubmit="onSubmit" />
+        </div>
     </div>
 </template>
diff --git a/client/src/components/ObjectStore/Instances/EditSecrets.vue b/client/src/components/ObjectStore/Instances/EditSecrets.vue
index f300779adc110f295e6d570496b08f9231b7c68e..ab1644c62647e6b8708b1498217dcd6f4ecb3857 100644
--- a/client/src/components/ObjectStore/Instances/EditSecrets.vue
+++ b/client/src/components/ObjectStore/Instances/EditSecrets.vue
@@ -1,9 +1,10 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import { GalaxyApi } from "@/api";
 import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import { update } from "./services";
 import type { UserConcreteObjectStore } from "./types";
 
 import EditSecretsForm from "@/components/ConfigTemplates/EditSecretsForm.vue";
@@ -16,12 +17,17 @@ const props = defineProps<Props>();
 const title = computed(() => `Update Storage Location ${props.objectStore?.name} Secrets`);
 
 async function onUpdate(secretName: string, secretValue: string) {
-    const payload = {
-        secret_name: secretName,
-        secret_value: secretValue,
-    };
-    const args = { user_object_store_id: String(props.objectStore.uuid) };
-    await update({ ...args, ...payload });
+    const { error } = await GalaxyApi().PUT("/api/object_store_instances/{uuid}", {
+        params: { path: { uuid: props.objectStore.uuid } },
+        body: {
+            secret_name: secretName,
+            secret_value: secretValue,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
 }
 </script>
 <template>
diff --git a/client/src/components/ObjectStore/Instances/InstanceDropdown.vue b/client/src/components/ObjectStore/Instances/InstanceDropdown.vue
index f00bde90b603ed4aaecf3b0186eb7b4f3c62be42..e6f6cf06ace2d62e8230b97efd7c59f57a3d52a6 100644
--- a/client/src/components/ObjectStore/Instances/InstanceDropdown.vue
+++ b/client/src/components/ObjectStore/Instances/InstanceDropdown.vue
@@ -1,9 +1,10 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import { GalaxyApi } from "@/api";
 import { useObjectStoreTemplatesStore } from "@/stores/objectStoreTemplatesStore";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import { hide } from "./services";
 import type { UserConcreteObjectStore } from "./types";
 
 import InstanceDropdown from "@/components/ConfigTemplates/InstanceDropdown.vue";
@@ -22,12 +23,21 @@ const isUpgradable = computed(() =>
 );
 
 async function onRemove() {
-    await hide(props.objectStore);
+    const { error } = await GalaxyApi().PUT("/api/object_store_instances/{uuid}", {
+        params: { path: { uuid: props.objectStore.uuid } },
+        body: { hidden: true },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     emit("entryRemoved");
 }
 
 const emit = defineEmits<{
     (e: "entryRemoved"): void;
+    (e: "test"): void;
 }>();
 </script>
 
@@ -38,5 +48,6 @@ const emit = defineEmits<{
         :is-upgradable="isUpgradable"
         :route-upgrade="routeUpgrade"
         :route-edit="routeEdit"
+        @test="emit('test')"
         @remove="onRemove" />
 </template>
diff --git a/client/src/components/ObjectStore/Instances/ManageIndex.vue b/client/src/components/ObjectStore/Instances/ManageIndex.vue
index c30d1def521054c72b14ddecf00c9b8973d83901..b9a8d84f8fb3123eaced3136aa5c49fcd602a011 100644
--- a/client/src/components/ObjectStore/Instances/ManageIndex.vue
+++ b/client/src/components/ObjectStore/Instances/ManageIndex.vue
@@ -4,6 +4,7 @@ import { computed } from "vue";
 
 import type { UserConcreteObjectStore } from "@/api/objectStores";
 import { DESCRIPTION_FIELD, NAME_FIELD, TEMPLATE_FIELD, TYPE_FIELD } from "@/components/ConfigTemplates/fields";
+import { useInstanceTesting } from "@/components/ConfigTemplates/useConfigurationTesting";
 import { useFiltering } from "@/components/ConfigTemplates/useInstanceFiltering";
 import { useObjectStoreInstancesStore } from "@/stores/objectStoreInstancesStore";
 import _l from "@/utils/localization";
@@ -39,6 +40,11 @@ objectStoreInstancesStore.fetchInstances();
 function reload() {
     objectStoreInstancesStore.fetchInstances();
 }
+
+const testInstanceUrl = "/api/object_store_instances/{uuid}/test";
+
+const { ConfigurationTestSummaryModal, showTestResults, testResults, test, testingError } =
+    useInstanceTesting(testInstanceUrl);
 </script>
 
 <template>
@@ -48,6 +54,7 @@ function reload() {
             create-button-id="object-store-create"
             create-route="/object_store_instances/create">
         </ManageIndexHeader>
+        <ConfigurationTestSummaryModal v-model="showTestResults" :error="testingError" :test-results="testResults" />
         <BTable
             id="user-object-stores-index"
             no-sort-reset
@@ -68,7 +75,7 @@ function reload() {
                 <ObjectStoreBadges size="1x" :badges="row.item.badges" />
             </template>
             <template v-slot:cell(name)="row">
-                <InstanceDropdown :object-store="row.item" @entryRemoved="reload" />
+                <InstanceDropdown :object-store="row.item" @entryRemoved="reload" @test="test(row.item)" />
             </template>
             <template v-slot:cell(type)="row">
                 <ObjectStoreTypeSpan :type="row.item.type" />
diff --git a/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts b/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts
index 78a6588b118d4265167ec1c76a41eca61130de3b..eed6cf3bdf06d38b7e8c463dcf3dde4199c0cd09 100644
--- a/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts
+++ b/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts
@@ -2,14 +2,15 @@ import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue, injectTestRouter } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
-import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
+import { useServerMock } from "@/api/client/__mocks__";
+import { OK_PLUGIN_STATUS } from "@/components/ConfigTemplates/test_fixtures";
+import { type ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
 
-import type { UserConcreteObjectStore } from "./types";
+import { type UserConcreteObjectStore } from "./types";
 
 import UpgradeForm from "./UpgradeForm.vue";
 
-jest.mock("@/api/schema");
+const { server, http } = useServerMock();
 
 const localVue = getLocalVue(true);
 const router = injectTestRouter(localVue);
@@ -23,11 +24,13 @@ const STANDARD_TEMPLATE: ObjectStoreTemplateSummary = {
             name: "oldvar",
             type: "string",
             help: "old var help",
+            default: "old default",
         },
         {
             name: "newvar",
             type: "string",
             help: "new var help",
+            default: "",
         },
     ],
     secrets: [
@@ -43,6 +46,7 @@ const STANDARD_TEMPLATE: ObjectStoreTemplateSummary = {
     id: "moo",
     version: 2,
     badges: [],
+    hidden: false,
 };
 
 const INSTANCE: UserConcreteObjectStore = {
@@ -109,7 +113,15 @@ describe("UpgradeForm", () => {
             localVue,
             router,
         });
-        mockFetcher.path("/api/object_store_instances/{user_object_store_id}").method("put").mock({ data: INSTANCE });
+        server.use(
+            http.post("/api/object_store_instances/{uuid}/test", ({ response }) => {
+                return response(200).json(OK_PLUGIN_STATUS);
+            }),
+            http.put("/api/object_store_instances/{uuid}", ({ response }) => {
+                return response(200).json(INSTANCE);
+            })
+        );
+
         await flushPromises();
         const submitElement = wrapper.find("#submit");
         submitElement.trigger("click");
@@ -128,20 +140,22 @@ describe("UpgradeForm", () => {
             localVue,
             router,
         });
-        mockFetcher
-            .path("/api/object_store_instances/{user_object_store_id}")
-            .method("put")
-            .mock(() => {
-                throw Error("problem upgrading");
-            });
+        server.use(
+            http.post("/api/object_store_instances/{uuid}/test", ({ response }) => {
+                return response(200).json(OK_PLUGIN_STATUS);
+            }),
+            http.put("/api/object_store_instances/{uuid}", ({ response }) => {
+                return response("4XX").json({ err_msg: "problem upgrading", err_code: 400 }, { status: 400 });
+            })
+        );
         await flushPromises();
         const submitElement = wrapper.find("#submit");
-        expect(wrapper.find(".object-store-instance-upgrade-error").exists()).toBe(false);
+        expect(wrapper.find("[data-description='object-store-upgrade-error']").exists()).toBe(false);
         submitElement.trigger("click");
         await flushPromises();
         const emitted = wrapper.emitted("created") || [];
         expect(emitted).toHaveLength(0);
-        const errorEl = wrapper.find(".object-store-instance-upgrade-error");
+        const errorEl = wrapper.find("[data-description='object-store-upgrade-error']");
         expect(errorEl.exists()).toBe(true);
         expect(errorEl.html()).toContain("problem upgrading");
     });
diff --git a/client/src/components/ObjectStore/Instances/UpgradeForm.vue b/client/src/components/ObjectStore/Instances/UpgradeForm.vue
index 28aa658f31061146f59a6d338b345eb3024b206b..fd71339a6cdc3fcdb5b258763467a940ddd07011 100644
--- a/client/src/components/ObjectStore/Instances/UpgradeForm.vue
+++ b/client/src/components/ObjectStore/Instances/UpgradeForm.vue
@@ -1,64 +1,56 @@
 <script setup lang="ts">
-import { BAlert } from "bootstrap-vue";
-import { computed, ref } from "vue";
+import { computed, toRef } from "vue";
 
-import { type FormEntry, upgradeForm, upgradeFormDataToPayload } from "@/components/ConfigTemplates/formUtil";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { useConfigurationTemplateUpgrade } from "@/components/ConfigTemplates/useConfigurationTesting";
 
 import type { ObjectStoreTemplateSummary } from "../Templates/types";
 import { useInstanceRouting } from "./routing";
-import { update } from "./services";
-import type { UserConcreteObjectStore } from "./types";
+import { type UserConcreteObjectStore } from "./types";
 
-import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
+const editTestUrl = "/api/object_store_instances/{uuid}/test";
+const editUrl = "/api/object_store_instances/{uuid}";
 
 interface Props {
     instance: UserConcreteObjectStore;
     latestTemplate: ObjectStoreTemplateSummary;
 }
 
-const error = ref<string | null>(null);
 const props = defineProps<Props>();
 
-const inputs = computed<Array<FormEntry> | undefined>(() => {
-    const realizedInstance: UserConcreteObjectStore = props.instance;
-    const realizedLatestTemplate = props.latestTemplate;
-    const form = upgradeForm(realizedLatestTemplate, realizedInstance);
-    return form;
-});
 const title = computed(() => `Upgrade Object Store ${props.instance.name}`);
-const submitTitle = "Update Settings";
-const loadingMessage = "Loading storage location template and instance information";
 
-async function onSubmit(formData: any) {
-    const payload = upgradeFormDataToPayload(props.latestTemplate, formData);
-    const args = { user_object_store_id: String(props.instance.uuid) };
-    try {
-        const { data: objectStore } = await update({ ...args, ...payload });
-        await onUpgrade(objectStore);
-    } catch (e) {
-        error.value = errorMessageAsString(e);
-        return;
-    }
-}
-
-const { goToIndex } = useInstanceRouting();
-
-async function onUpgrade(objectStore: UserConcreteObjectStore) {
-    const message = `Upgraded storage location ${objectStore.name}`;
-    goToIndex({ message });
-}
+const {
+    error,
+    ActionSummary,
+    inputs,
+    InstanceForm,
+    loadingMessage,
+    showForceActionButton,
+    onForceSubmit,
+    onSubmit,
+    testRunning,
+    testResults,
+    submitTitle,
+} = useConfigurationTemplateUpgrade(
+    "storage location",
+    toRef(props, "instance"),
+    toRef(props, "latestTemplate"),
+    editTestUrl,
+    editUrl,
+    useInstanceRouting
+);
 </script>
 <template>
     <div>
-        <BAlert v-if="error" variant="danger" class="object-store-instance-upgrade-error" show>
-            {{ error }}
-        </BAlert>
+        <ActionSummary error-data-description="object-store-upgrade-error" :test-results="testResults" :error="error" />
         <InstanceForm
             :inputs="inputs"
             :title="title"
             :submit-title="submitTitle"
             :loading-message="loadingMessage"
+            :busy="testRunning"
+            :show-force-action-button="showForceActionButton"
+            @onForceSubmit="onForceSubmit"
             @onSubmit="onSubmit" />
     </div>
 </template>
diff --git a/client/src/components/ObjectStore/Instances/instance.ts b/client/src/components/ObjectStore/Instances/instance.ts
index 74d8383195622a35d7966a2f4879a1bb95aa77fd..c843bb05bee2b1be45442ac699312fe84ccc5a4a 100644
--- a/client/src/components/ObjectStore/Instances/instance.ts
+++ b/client/src/components/ObjectStore/Instances/instance.ts
@@ -1,10 +1,10 @@
 import { computed, type Ref } from "vue";
 
-import type { ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
+import { type ObjectStoreTemplateSummary } from "@/components/ObjectStore/Templates/types";
 import { useObjectStoreInstancesStore } from "@/stores/objectStoreInstancesStore";
 import { useObjectStoreTemplatesStore } from "@/stores/objectStoreTemplatesStore";
 
-import type { UserConcreteObjectStore } from "./types";
+import { type UserConcreteObjectStore } from "./types";
 
 export function useInstanceAndTemplate(instanceIdRef: Ref<string>) {
     const objectStoreTemplatesStore = useObjectStoreTemplatesStore();
diff --git a/client/src/components/ObjectStore/Instances/routing.ts b/client/src/components/ObjectStore/Instances/routing.ts
index 44aca677a052e1756bccbe15dca491f1b75112bd..2074914834236a8739bc85b25390f7bfed158346 100644
--- a/client/src/components/ObjectStore/Instances/routing.ts
+++ b/client/src/components/ObjectStore/Instances/routing.ts
@@ -1,16 +1,3 @@
-import { useRouter } from "vue-router/composables";
+import { buildInstanceRoutingComposable } from "@/components/ConfigTemplates/routing";
 
-export function useInstanceRouting() {
-    const router = useRouter();
-
-    async function goToIndex(query: Record<"message", string>) {
-        router.push({
-            path: "/object_store_instances/index",
-            query: query,
-        });
-    }
-
-    return {
-        goToIndex,
-    };
-}
+export const useInstanceRouting = buildInstanceRoutingComposable("/object_store_instances/index");
diff --git a/client/src/components/ObjectStore/Instances/services.ts b/client/src/components/ObjectStore/Instances/services.ts
index abb7bb6781c73bcbd8f8c0f5719ef795baab7194..fc82ca77f03d7763aea3ecdc467bf488a5677c5f 100644
--- a/client/src/components/ObjectStore/Instances/services.ts
+++ b/client/src/components/ObjectStore/Instances/services.ts
@@ -1,14 +1,16 @@
-import { fetcher } from "@/api/schema/fetcher";
+import { GalaxyApi } from "@/api";
 
 import type { UserConcreteObjectStore } from "./types";
 
-export const create = fetcher.path("/api/object_store_instances").method("post").create();
-export const test = fetcher.path("/api/object_store_instances/test").method("post").create();
-export const update = fetcher.path("/api/object_store_instances/{user_object_store_id}").method("put").create();
+const updateUrl = "/api/object_store_instances/{uuid}";
 
 export async function hide(instance: UserConcreteObjectStore) {
     const payload = { hidden: true };
-    const args = { user_object_store_id: String(instance?.uuid) };
-    const { data: objectStore } = await update({ ...args, ...payload });
+    const { data: objectStore } = await GalaxyApi().PUT(updateUrl, {
+        params: {
+            path: { uuid: String(instance?.uuid) },
+        },
+        body: payload,
+    });
     return objectStore;
 }
diff --git a/client/src/components/ObjectStore/Instances/types.ts b/client/src/components/ObjectStore/Instances/types.ts
index 0176eaec757a05c89ebd942d843396bab5aef241..0d533f0df32cf5cc00a4da058b667f4c9e9bd060 100644
--- a/client/src/components/ObjectStore/Instances/types.ts
+++ b/client/src/components/ObjectStore/Instances/types.ts
@@ -1,4 +1,3 @@
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema/schema";
 
 export type UserConcreteObjectStore = components["schemas"]["UserConcreteObjectStoreModel"];
-export type CreateInstancePayload = components["schemas"]["CreateInstancePayload"];
diff --git a/client/src/components/ObjectStore/ObjectStoreBadge.vue b/client/src/components/ObjectStore/ObjectStoreBadge.vue
index 76dae8bde07b58d38f481a18e552714483359f3a..3ee222093e0273f59e7b53b2a40ee8124ed4366b 100644
--- a/client/src/components/ObjectStore/ObjectStoreBadge.vue
+++ b/client/src/components/ObjectStore/ObjectStoreBadge.vue
@@ -4,7 +4,7 @@ import "./badgeIcons";
 import { FontAwesomeIcon, FontAwesomeLayers } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 import ConfigurationMarkdown from "./ConfigurationMarkdown.vue";
 
diff --git a/client/src/components/ObjectStore/ObjectStoreBadges.vue b/client/src/components/ObjectStore/ObjectStoreBadges.vue
index 042ce1bb469c41a15ea09365d34b71b8f73cec16..da0b439d6fe494604a26a07b67d854db861ea916 100644
--- a/client/src/components/ObjectStore/ObjectStoreBadges.vue
+++ b/client/src/components/ObjectStore/ObjectStoreBadges.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 import ObjectStoreBadge from "./ObjectStoreBadge.vue";
 
diff --git a/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue b/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
index 6e4113e820b8d390057f627d88d938486486dd10..84b946515ac4dd81ede9939dbc9385398916e5bf 100644
--- a/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
+++ b/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
-import { ObjectStoreTemplateType } from "@/api/objectStores";
+import { type ObjectStoreTemplateType } from "@/api/objectStores";
 
 const MESSAGES = {
     aws_s3: "This is a storage location based on the Amazon Simple Storage Service (S3). Data here is hosted by Amazon.",
@@ -11,6 +11,7 @@ const MESSAGES = {
     boto3: "This is a storage location based on the Amazon Simple Storage Service (S3) interface, but likely not stored by Amazon. The AWS interface has become an industry standard and many storage vendors support it and use it to expose object based storage.",
     generic_s3:
         "This is a storage location based on the Amazon Simple Storage Service (S3) interface, but likely not stored by Amazon. The AWS interface has become an industry standard and many storage vendors support it and use it to expose object based storage.",
+    onedata: "This is a storage location based on the Onedata system.",
 };
 
 interface Props {
diff --git a/client/src/components/ObjectStore/SelectObjectStore.vue b/client/src/components/ObjectStore/SelectObjectStore.vue
index 807806326bd8b07627aa107792d29bf65449175c..e1a21d18eb77619e7e78db583ab49cef403fef8f 100644
--- a/client/src/components/ObjectStore/SelectObjectStore.vue
+++ b/client/src/components/ObjectStore/SelectObjectStore.vue
@@ -2,7 +2,7 @@
 import { storeToRefs } from "pinia";
 import { computed, ref } from "vue";
 
-import { ConcreteObjectStoreModel } from "@/api";
+import { type ConcreteObjectStoreModel } from "@/api";
 import { useStorageLocationConfiguration } from "@/composables/storageLocation";
 import { useObjectStoreStore } from "@/stores/objectStoreStore";
 
diff --git a/client/src/components/ObjectStore/ShowSelectedObjectStore.test.js b/client/src/components/ObjectStore/ShowSelectedObjectStore.test.js
index 34135b89ab2a6cb8496e956d43414f1c5a2470c9..2ad292b5a3f1be0d7ea771c28c8b1afe0c6e3c9d 100644
--- a/client/src/components/ObjectStore/ShowSelectedObjectStore.test.js
+++ b/client/src/components/ObjectStore/ShowSelectedObjectStore.test.js
@@ -2,14 +2,13 @@ import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
-
-import ShowSelectedObjectStore from "./ShowSelectedObjectStore";
+import { useServerMock } from "@/api/client/__mocks__";
 
+import ShowSelectedObjectStore from "./ShowSelectedObjectStore.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 import DescribeObjectStore from "@/components/ObjectStore/DescribeObjectStore.vue";
 
-jest.mock("@/api/schema");
+const { server, http } = useServerMock();
 
 const localVue = getLocalVue(true);
 const TEST_OBJECT_ID = "os123";
@@ -19,19 +18,40 @@ const OBJECT_STORE_DATA = {
     description: null,
     object_store_id: TEST_OBJECT_ID,
     badges: [],
+    private: false,
+    quota: {
+        enabled: false,
+    },
 };
 
 const USER_OBJECT_STORE_DATA = {
     description: null,
     object_store_id: TEST_USER_OBJECT_STORE_ID,
     badges: [],
+    private: false,
+    quota: {
+        enabled: false,
+    },
+    active: true,
+    hidden: false,
+    purged: false,
+    secrets: [],
+    template_id: "disk",
+    template_version: 1,
+    type: "disk",
+    uuid: "34",
+    variables: {},
 };
 
 describe("ShowSelectedObjectStore", () => {
     let wrapper;
 
     it("should show a loading message and then a DescribeObjectStore component", async () => {
-        mockFetcher.path("/api/object_stores/{object_store_id}").method("get").mock({ data: OBJECT_STORE_DATA });
+        server.use(
+            http.get("/api/object_stores/{object_store_id}", ({ response }) => {
+                return response(200).json(OBJECT_STORE_DATA);
+            })
+        );
         wrapper = mount(ShowSelectedObjectStore, {
             propsData: { preferredObjectStoreId: TEST_OBJECT_ID, forWhat: "Data goes into..." },
             localVue,
@@ -46,11 +66,11 @@ describe("ShowSelectedObjectStore", () => {
     });
 
     it("should fetch from the user based object store APIs for dynamic ids that are uris", async () => {
-        mockFetcher
-            .path("/api/object_store_instances/{user_object_store_id}")
-            .method("get")
-            .mock({ data: USER_OBJECT_STORE_DATA });
-        // mockFetcher.path("/api/object_stores/{object_store_id}").method("get").mock({ data: OBJECT_STORE_DATA });
+        server.use(
+            http.get("/api/object_store_instances/{user_object_store_id}", ({ response }) => {
+                return response(200).json(USER_OBJECT_STORE_DATA);
+            })
+        );
 
         wrapper = mount(ShowSelectedObjectStore, {
             propsData: { preferredObjectStoreId: TEST_USER_OBJECT_STORE_ID, forWhat: "Data goes into..." },
diff --git a/client/src/components/ObjectStore/Templates/TemplateSummary.vue b/client/src/components/ObjectStore/Templates/TemplateSummary.vue
index ddb84e9527f95f705933d72e38821fc3569b3cbf..00c72d1fcd2008e007f4f753b38364bf9a37339e 100644
--- a/client/src/components/ObjectStore/Templates/TemplateSummary.vue
+++ b/client/src/components/ObjectStore/Templates/TemplateSummary.vue
@@ -1,9 +1,9 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema";
 
-import type { ObjectStoreTemplateSummary } from "./types";
+import { type ObjectStoreTemplateSummary } from "./types";
 
 import ConfigurationMarkdown from "@/components/ObjectStore/ConfigurationMarkdown.vue";
 import ObjectStoreBadges from "@/components/ObjectStore/ObjectStoreBadges.vue";
diff --git a/client/src/components/ObjectStore/Templates/types.ts b/client/src/components/ObjectStore/Templates/types.ts
index 186806b8e4880603c3ba33b76441083aea17ad46..c7608f21d0553db522ed8bc0ece23b35554d0d95 100644
--- a/client/src/components/ObjectStore/Templates/types.ts
+++ b/client/src/components/ObjectStore/Templates/types.ts
@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema/schema";
+import { type components } from "@/api/schema";
 
 export type ObjectStoreTemplateSummary = components["schemas"]["ObjectStoreTemplateSummary"];
 export type ObjectStoreTemplateSummaries = ObjectStoreTemplateSummary[];
diff --git a/client/src/components/ObjectStore/types.ts b/client/src/components/ObjectStore/types.ts
index de591e13ee39f4f96fa0a44faff4a025e4495f09..c35e1e4729f983108862e8e16458f4beee015cde 100644
--- a/client/src/components/ObjectStore/types.ts
+++ b/client/src/components/ObjectStore/types.ts
@@ -1,3 +1,3 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
 export type ConcreteObjectStoreModel = components["schemas"]["ConcreteObjectStoreModel"];
diff --git a/client/src/components/PageDisplay/PageDisplay.vue b/client/src/components/PageDisplay/PageDisplay.vue
index d3fb11855692d914bd5bcfc771cd5072eb519aeb..bfe855434724c01a715738569783f263d9e3bd98 100644
--- a/client/src/components/PageDisplay/PageDisplay.vue
+++ b/client/src/components/PageDisplay/PageDisplay.vue
@@ -56,7 +56,7 @@ export default {
     },
     computed: {
         userOwnsPage() {
-            return this.currentUser.username === this.page.username;
+            return this.currentUser?.username === this.page.username;
         },
         dataUrl() {
             return `/api/pages/${this.pageId}`;
diff --git a/client/src/components/PageEditor/ObjectPermissions.vue b/client/src/components/PageEditor/ObjectPermissions.vue
index 237afa739c1d8f6bd6cbc6c5c33fb090dd008c5b..00fd3028fedc7b57f6a0aca7f84b290fa984a1f4 100644
--- a/client/src/components/PageEditor/ObjectPermissions.vue
+++ b/client/src/components/PageEditor/ObjectPermissions.vue
@@ -1,12 +1,9 @@
 <script setup lang="ts">
 import axios from "axios";
-import Vue, { computed, Ref, ref, watch } from "vue";
+import Vue, { computed, type Ref, ref, watch } from "vue";
 
+import { GalaxyApi, type MessageException } from "@/api";
 import { fetchCollectionSummary } from "@/api/datasetCollections";
-import { enableLink, sharing } from "@/api/histories";
-import { fetchInvocationDetails } from "@/api/invocations";
-import { getJobDetails } from "@/api/jobs";
-import { enableLink as enableLinkWorkflow, sharing as sharingWorkflow } from "@/api/workflows";
 import { useToast } from "@/composables/toast";
 import { useDatasetStore } from "@/stores/datasetStore";
 import { useHistoryStore } from "@/stores/historyStore";
@@ -59,49 +56,62 @@ const workflowAccessible: AccessibleMapRef = ref({});
 const historyDatasetAccessible: AccessibleMapRef = ref({});
 
 function catchErrorToToast(title: string, prolog: string) {
-    function handleError(e: Error) {
+    function handleError(e: Error | MessageException) {
         toast.error(`${prolog} Reason: ${errorMessageAsString(e)}.`, title);
     }
     return handleError;
 }
 
 watch(referencedJobIds, async () => {
-    referencedJobIds.value.forEach((jobId) => {
+    referencedJobIds.value.forEach(async (jobId) => {
         if (jobId in jobsToHistories.value) {
             return;
         }
+
         const handleError = catchErrorToToast(
             "Failed to job information",
             "Some referenced objects may not be listed."
         );
-        getJobDetails({ job_id: jobId })
-            .then(({ data }) => {
-                if ("history_id" in data) {
-                    const historyId = data.history_id;
-                    Vue.set(jobsToHistories.value, jobId, historyId);
-                }
-            })
-            .catch(handleError);
+        const { data, error } = await GalaxyApi().GET("/api/jobs/{job_id}", {
+            params: { path: { job_id: jobId } },
+        });
+
+        if (error) {
+            handleError(error);
+            return;
+        }
+
+        if ("history_id" in data) {
+            const historyId = data.history_id;
+            Vue.set(jobsToHistories.value, jobId, historyId);
+        }
     });
 });
 
 watch(referencedInvocationIds, async () => {
-    referencedInvocationIds.value.forEach((invocationId) => {
+    referencedInvocationIds.value.forEach(async (invocationId) => {
         if (invocationId in invocationsToHistories.value) {
             return;
         }
+
         const handleError = catchErrorToToast(
             "Failed to fetch workflow information",
             "Some referenced objects may not be listed."
         );
-        fetchInvocationDetails({ id: invocationId })
-            .then(({ data }) => {
-                if ("history_id" in data) {
-                    const historyId = data.history_id;
-                    Vue.set(invocationsToHistories.value, invocationId, historyId);
-                }
-            })
-            .catch(handleError);
+
+        const { data, error } = await GalaxyApi().GET("/api/invocations/{invocation_id}", {
+            params: { path: { invocation_id: invocationId } },
+        });
+
+        if (error) {
+            handleError(error);
+            return;
+        }
+
+        if ("history_id" in data) {
+            const historyId = data.history_id;
+            Vue.set(invocationsToHistories.value, invocationId, historyId);
+        }
     });
 });
 
@@ -181,42 +191,50 @@ watch(
     { immediate: true }
 );
 
-watch(historyIds, () => {
+watch(historyIds, async () => {
     for (const historyId of historyIds.value) {
         loadHistoryById(historyId);
         if (historyId && !(historyId in historyAccessible.value)) {
             Vue.set(historyAccessible.value, historyId, null);
-            sharing({ history_id: historyId })
-                .then((response) => {
-                    const accessible = response.data.importable;
-                    Vue.set(historyAccessible.value, historyId, accessible);
-                })
-                .catch((e) => {
-                    const errorMessage = errorMessageAsString(e);
-                    const title = "Failed to fetch history metadata.";
-                    toast.error(errorMessage, title);
-                    Vue.set(historyAccessible.value, historyId, `${title} Reason: ${errorMessage}.`);
-                });
+
+            const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}/sharing", {
+                params: { path: { history_id: historyId } },
+            });
+
+            if (error) {
+                const errorMessage = errorMessageAsString(error);
+                const title = "Failed to fetch history metadata.";
+                toast.error(errorMessage, title);
+                Vue.set(historyAccessible.value, historyId, `${title} Reason: ${errorMessage}.`);
+                return;
+            }
+
+            const accessible = data.importable;
+            Vue.set(historyAccessible.value, historyId, accessible);
         }
     }
 });
 
-function initWorkflowData() {
+async function initWorkflowData() {
     for (const workflowId of referencedWorkflowIds.value) {
         fetchWorkflowForInstanceId(workflowId);
         if (workflowId && !(workflowId in workflowAccessible.value)) {
             Vue.set(workflowAccessible.value, workflowId, null);
-            sharingWorkflow({ workflow_id: workflowId })
-                .then((response) => {
-                    const accessible = response.data.importable;
-                    Vue.set(workflowAccessible.value, workflowId, accessible);
-                })
-                .catch((e) => {
-                    const errorMessage = errorMessageAsString(e);
-                    const title = "Failed to fetch workflow metadata.";
-                    toast.error(errorMessage, title);
-                    Vue.set(workflowAccessible.value, workflowId, `${title} Reason: ${errorMessage}.`);
-                });
+
+            const { data, error } = await GalaxyApi().GET("/api/workflows/{workflow_id}/sharing", {
+                params: { path: { workflow_id: workflowId } },
+            });
+
+            if (error) {
+                const errorMessage = errorMessageAsString(error);
+                const title = "Failed to fetch workflow metadata.";
+                toast.error(errorMessage, title);
+                Vue.set(workflowAccessible.value, workflowId, `${title} Reason: ${errorMessage}.`);
+                return;
+            }
+
+            const accessible = data.importable;
+            Vue.set(workflowAccessible.value, workflowId, accessible);
         }
     }
 }
@@ -256,41 +274,55 @@ const tableItems = computed<ItemInterface[]>(() => {
     return [...histories.value, ...workflows.value, ...datasets.value];
 });
 
-function makeAccessible(item: ItemInterface) {
-    let promise;
+async function makeAccessible(item: ItemInterface) {
+    let accessibleResult: Boolean | undefined = undefined;
+    let errorResult: MessageException | undefined = undefined;
     let accessibleMap: AccessibleMapRef;
     if (item.type == "history") {
-        promise = enableLink({ history_id: item.id });
+        const { data, error } = await GalaxyApi().PUT("/api/histories/{history_id}/enable_link_access", {
+            params: { path: { history_id: item.id } },
+        });
+
+        errorResult = error;
+        accessibleResult = data?.importable;
         accessibleMap = historyAccessible;
     } else if (item.type == "workflow") {
-        promise = enableLinkWorkflow({ workflow_id: item.id });
+        const { data, error } = await GalaxyApi().PUT("/api/workflows/{workflow_id}/enable_link_access", {
+            params: { path: { workflow_id: item.id } },
+        });
+
+        errorResult = error;
+        accessibleResult = data?.importable;
         accessibleMap = workflowAccessible;
     } else if (item.type == "historyDataset") {
-        const data = {
-            dataset_id: item.id,
-            action: "remove_restrictions",
-        };
-        promise = axios.put(withPrefix(`/api/datasets/${item.id}/permissions`), data);
+        const { data, error } = await GalaxyApi().PUT("/api/datasets/{dataset_id}/permissions", {
+            params: { path: { dataset_id: item.id } },
+            body: {
+                action: "remove_restrictions",
+            },
+        });
+
+        errorResult = error;
+        accessibleResult = data !== undefined;
         accessibleMap = historyDatasetAccessible;
-    }
-    if (!promise) {
+    } else {
         console.log("Serious client programming error - unknown object type encountered.");
         return;
     }
-    promise
-        .then(() => Vue.set(accessibleMap.value, item.id, true))
-        .catch((e) => {
-            const errorMessage = errorMessageAsString(e);
-            const title = "Failed update object accessibility.";
-            toast.error(errorMessage, title);
-            Vue.set(accessibleMap.value, item.id, `${title} Reason: ${errorMessage}.`);
-        });
+    if (errorResult) {
+        const errorMessage = errorMessageAsString(errorResult);
+        const title = "Failed update object accessibility.";
+        toast.error(errorMessage, title);
+        Vue.set(accessibleMap.value, item.id, `${title} Reason: ${errorMessage}.`);
+        return;
+    }
+    Vue.set(accessibleMap.value, item.id, accessibleResult);
 }
 </script>
 
 <template>
     <div>
-        <b-table :items="tableItems" :fields="tableFields">
+        <b-table :items="tableItems" show-empty :fields="tableFields">
             <template v-slot:empty>
                 <LoadingSpan v-if="loading" message="Loading objects" />
                 <b-alert v-else variant="info" show>
diff --git a/client/src/components/PageEditor/PageEditor.vue b/client/src/components/PageEditor/PageEditor.vue
index cb0b775f4345a798ae820a914d1fa4ef27484f8f..6be90d063c48ebb06b3452e183c44b12e084954a 100644
--- a/client/src/components/PageEditor/PageEditor.vue
+++ b/client/src/components/PageEditor/PageEditor.vue
@@ -1,12 +1,15 @@
 <template>
-    <LoadingSpan v-if="loading" message="Loading Page" class="m-3" />
-    <PageEditorMarkdown
-        v-else
-        :title="title"
-        :page-id="pageId"
-        :public-url="publicUrl"
-        :content="content"
-        :content-data="contentData" />
+    <div id="columns" class="d-flex">
+        <ActivityBar />
+        <LoadingSpan v-if="loading" message="Loading Page" class="m-3" />
+        <PageEditorMarkdown
+            v-else
+            :title="title"
+            :page-id="pageId"
+            :public-url="publicUrl"
+            :content="content"
+            :content-data="contentData" />
+    </div>
 </template>
 
 <script>
@@ -18,10 +21,13 @@ import { rethrowSimple } from "utils/simple-error";
 
 import PageEditorMarkdown from "./PageEditorMarkdown";
 
+import ActivityBar from "@/components/ActivityBar/ActivityBar.vue";
+
 export default {
     components: {
         PageEditorMarkdown,
         LoadingSpan,
+        ActivityBar,
     },
     props: {
         pageId: {
diff --git a/client/src/components/PageEditor/PageEditorMarkdown.vue b/client/src/components/PageEditor/PageEditorMarkdown.vue
index 6e1cb5bcc76a5565a5911de01e279af39fbca006..3d4834f4cd1e3788529a85b1c09a90fe1a3d91db 100644
--- a/client/src/components/PageEditor/PageEditorMarkdown.vue
+++ b/client/src/components/PageEditor/PageEditorMarkdown.vue
@@ -4,7 +4,7 @@
         :markdown-text="markdownText"
         :markdown-config="contentData"
         mode="page"
-        @onUpdate="onUpdate">
+        @update="onUpdate">
         <template v-slot:buttons>
             <ObjectPermissionsModal
                 id="object-permissions-modal"
diff --git a/client/src/components/PageEditor/object-permission-composables.ts b/client/src/components/PageEditor/object-permission-composables.ts
index 1902f24fd54d5299de17e18c3aad50f29ed54d88..c004165e1c2fc3eaa8885d91aa943ecd1d8f4129 100644
--- a/client/src/components/PageEditor/object-permission-composables.ts
+++ b/client/src/components/PageEditor/object-permission-composables.ts
@@ -1,4 +1,4 @@
-import { computed, Ref, ref } from "vue";
+import { computed, type Ref, ref } from "vue";
 
 import { referencedObjects } from "@/components/Markdown/parse";
 
diff --git a/client/src/components/Panels/ActivityPanel.vue b/client/src/components/Panels/ActivityPanel.vue
index df4d58a6de64b5d980ae6104b4c27bc652739e92..e0d3dd646ab844773e9dd9421553afa860baef47 100644
--- a/client/src/components/Panels/ActivityPanel.vue
+++ b/client/src/components/Panels/ActivityPanel.vue
@@ -1,7 +1,6 @@
 <script setup lang="ts">
-import { BButton } from "bootstrap-vue";
+import { BButton, BButtonGroup } from "bootstrap-vue";
 import { computed } from "vue";
-import { useRoute } from "vue-router/composables";
 
 interface Props {
     title: string;
@@ -14,16 +13,11 @@ interface Props {
 const props = withDefaults(defineProps<Props>(), {
     goToAllTitle: undefined,
     href: undefined,
-    goToOnHref: true,
 });
 
-const route = useRoute();
-
 const emit = defineEmits(["goToAll"]);
 
-const hasGoToAll = computed(
-    () => props.goToAllTitle && props.href && (props.goToOnHref || (!props.goToOnHref && route.path !== props.href))
-);
+const hasGoToAll = computed(() => props.goToAllTitle && props.href);
 </script>
 
 <template>
@@ -32,7 +26,9 @@ const hasGoToAll = computed(
             <nav unselectable="on" class="activity-panel-header-top">
                 <h2 id="activity-panel-heading" v-localize class="activity-panel-heading h-sm">{{ props.title }}</h2>
 
-                <slot name="header-buttons" />
+                <BButtonGroup>
+                    <slot name="header-buttons" />
+                </BButtonGroup>
             </nav>
 
             <slot name="header" class="activity-panel-header-description" />
@@ -83,18 +79,8 @@ const hasGoToAll = computed(
         display: flex;
         flex-direction: column;
         flex-grow: 1;
-        overflow-y: hidden;
-        button:first-child {
-            background: none;
-            border: none;
-            text-align: left;
-            transition: none;
-            width: 100%;
-            border-color: transparent;
-        }
-        button:first-child:hover {
-            background: $gray-200;
-        }
+        overflow-y: auto;
+        position: relative;
     }
 
     .activity-panel-footer {
diff --git a/client/src/components/Panels/Buttons/FavoritesButton.vue b/client/src/components/Panels/Buttons/FavoritesButton.vue
index c7d285bb4253e3022dd64f5885cc13f39f5bbe6d..37d932b6fedda0a132343a814da699752d63ebcf 100644
--- a/client/src/components/Panels/Buttons/FavoritesButton.vue
+++ b/client/src/components/Panels/Buttons/FavoritesButton.vue
@@ -3,6 +3,7 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faStar } from "@fortawesome/free-regular-svg-icons";
 import { faStar as faRegStar } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { watchImmediate } from "@vueuse/core";
 import { BButton } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
@@ -12,18 +13,33 @@ import { useUserStore } from "@/stores/userStore";
 library.add(faStar, faRegStar);
 
 interface Props {
-    query: string;
+    value?: boolean;
+    query?: string;
+    tooltip?: string;
 }
-const props = defineProps<Props>();
+
+const props = withDefaults(defineProps<Props>(), {
+    value: false,
+    query: undefined,
+    tooltip: "Show favorites",
+});
+
+const currentValue = computed(() => props.value ?? false);
+const toggle = ref(false);
+
+watchImmediate(
+    () => currentValue.value,
+    (val) => (toggle.value = val)
+);
 
 const emit = defineEmits<{
-    (e: "onFavorites", filter: string): void;
+    (e: "change", toggled: boolean): void;
+    (e: "input", toggled: boolean): void;
 }>();
 
 const { isAnonymous } = storeToRefs(useUserStore());
 
 const FAVORITES = ["#favorites", "#favs", "#favourites"];
-const toggle = ref(false);
 
 const tooltipText = computed(() => {
     if (isAnonymous.value) {
@@ -32,7 +48,7 @@ const tooltipText = computed(() => {
         if (toggle.value) {
             return "Clear";
         } else {
-            return "Show favorites";
+            return props.tooltip;
         }
     }
 });
@@ -40,17 +56,14 @@ const tooltipText = computed(() => {
 watch(
     () => props.query,
     () => {
-        toggle.value = FAVORITES.includes(props.query);
+        toggle.value = FAVORITES.includes(props.query ?? "");
     }
 );
 
-function onFavorites() {
+function toggleFavorites() {
     toggle.value = !toggle.value;
-    if (toggle.value) {
-        emit("onFavorites", "#favorites");
-    } else {
-        emit("onFavorites", "");
-    }
+    emit("input", toggle.value);
+    emit("change", toggle.value);
 }
 </script>
 
@@ -63,7 +76,7 @@ function onFavorites() {
         aria-label="Show favorite tools"
         :disabled="isAnonymous"
         :title="tooltipText"
-        @click="onFavorites">
+        @click="toggleFavorites">
         <FontAwesomeIcon :icon="toggle ? faRegStar : faStar" />
     </BButton>
 </template>
diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue
index 70b776fc7fc98c0015da3611e8eb11b463fcfe67..819c4af4aef62fe8b644256b481beb6deb6ce641 100644
--- a/client/src/components/Panels/Common/ToolSearch.vue
+++ b/client/src/components/Panels/Common/ToolSearch.vue
@@ -74,7 +74,9 @@ const localFilterText = computed({
         return props.query !== null ? props.query : "";
     },
     set: (newVal: any) => {
-        checkQuery(newVal);
+        if (newVal.trim() || props.query.trim()) {
+            checkQuery(newVal);
+        }
     },
 });
 
@@ -245,7 +247,7 @@ function onAdvancedSearch(filters: any) {
         <DelayedInput
             v-else
             class="mb-3"
-            :query="props.query"
+            :value="props.query"
             :delay="200"
             :loading="queryPending"
             :placeholder="placeholder"
diff --git a/client/src/components/Panels/FlexPanel.vue b/client/src/components/Panels/FlexPanel.vue
index 9d0031af395f49646e746081291e044d29935988..1dd518b66ed9cba9303b2f2f0479cee293ab38f7 100644
--- a/client/src/components/Panels/FlexPanel.vue
+++ b/client/src/components/Panels/FlexPanel.vue
@@ -2,14 +2,9 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faChevronLeft, faChevronRight } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { useDebounce, useDraggable } from "@vueuse/core";
 import { computed, ref, watch } from "vue";
 
-import { useTimeoutThrottle } from "@/composables/throttle";
-
-import { determineWidth } from "./utilities";
-
-const { throttle } = useTimeoutThrottle(10);
+import DraggableSeparator from "@/components/Common/DraggableSeparator.vue";
 
 library.add(faChevronLeft, faChevronRight);
 
@@ -28,26 +23,18 @@ const props = withDefaults(defineProps<Props>(), {
     defaultWidth: 300,
 });
 
-const draggable = ref<HTMLElement | null>(null);
-const root = ref<HTMLElement | null>(null);
-
 const panelWidth = ref(props.defaultWidth);
-const show = ref(true);
-
-const { position, isDragging } = useDraggable(draggable, {
-    preventDefault: true,
-    exact: true,
-});
 
-const hoverDraggable = ref(false);
-const hoverDraggableDebounced = useDebounce(hoverDraggable, 100);
-const showHover = computed(() => (hoverDraggable.value && hoverDraggableDebounced.value) || isDragging.value);
+const root = ref<HTMLElement | null>(null);
+const show = ref(true);
 
 const showToggle = ref(false);
 const hoverToggle = ref(false);
-const hoverDraggableOrToggle = computed(
-    () => (hoverDraggableDebounced.value || hoverToggle.value) && !isDragging.value
-);
+
+const isHoveringDragHandle = ref(false);
+const isDragging = ref(false);
+
+const hoverDraggableOrToggle = computed(() => (isHoveringDragHandle.value || hoverToggle.value) && !isDragging.value);
 
 const toggleLinger = 500;
 const toggleShowDelay = 600;
@@ -70,72 +57,6 @@ watch(
     }
 );
 
-/** Watch position changes and adjust width accordingly */
-watch(position, () => {
-    throttle(() => {
-        if (!root.value || !draggable.value) {
-            return;
-        }
-
-        const rectRoot = root.value.getBoundingClientRect();
-        const rectDraggable = draggable.value.getBoundingClientRect();
-        panelWidth.value = determineWidth(
-            rectRoot,
-            rectDraggable,
-            props.minWidth,
-            props.maxWidth,
-            props.side,
-            position.value.x
-        );
-    });
-});
-
-/** If the `maxWidth` changes, prevent the panel from exceeding it */
-watch(
-    () => props.maxWidth,
-    (newVal) => {
-        if (newVal && panelWidth.value > newVal) {
-            panelWidth.value = props.maxWidth;
-        }
-    },
-    { immediate: true }
-);
-
-/** If the `minWidth` changes, ensure the panel width is at least the `minWidth` */
-watch(
-    () => props.minWidth,
-    (newVal) => {
-        if (newVal && panelWidth.value < newVal) {
-            panelWidth.value = newVal;
-        }
-    },
-    { immediate: true }
-);
-
-function onKeyLeft() {
-    if (props.side === "left") {
-        decreaseWidth();
-    } else {
-        increaseWidth();
-    }
-}
-
-function onKeyRight() {
-    if (props.side === "left") {
-        increaseWidth();
-    } else {
-        decreaseWidth();
-    }
-}
-
-function increaseWidth(by = 50) {
-    panelWidth.value = Math.min(panelWidth.value + by, props.maxWidth);
-}
-
-function decreaseWidth(by = 50) {
-    panelWidth.value = Math.max(panelWidth.value - by, props.minWidth);
-}
-
 const sideClasses = computed(() => ({
     left: props.side === "left",
     right: props.side === "right",
@@ -148,19 +69,15 @@ const sideClasses = computed(() => ({
         :id="side"
         ref="root"
         class="flex-panel"
-        :class="{ ...sideClasses, 'show-hover': showHover }"
+        :class="{ ...sideClasses }"
         :style="`--width: ${panelWidth}px`">
-        <button
-            ref="draggable"
-            class="drag-handle"
-            @mouseenter="hoverDraggable = true"
-            @focusin="hoverDraggable = true"
-            @mouseout="hoverDraggable = false"
-            @focusout="hoverDraggable = false"
-            @keydown.left="onKeyLeft"
-            @keydown.right="onKeyRight">
-            <span class="sr-only"> Side panel drag handle </span>
-        </button>
+        <DraggableSeparator
+            :position="panelWidth"
+            :side="props.side"
+            :min="props.minWidth"
+            :max="props.maxWidth"
+            @positionChanged="(v) => (panelWidth = v)"
+            @visibilityChanged="(v) => (isHoveringDragHandle = v)"></DraggableSeparator>
 
         <button
             v-if="props.collapsible"
@@ -221,28 +138,12 @@ $border-width: 6px;
         background-color: $border-color;
     }
 
-    &.show-hover {
-        border-color: $brand-info;
-
-        &::after {
-            background-color: $brand-info;
-        }
-    }
-
     &.left {
         border-right-style: solid;
 
         &::after {
             right: -1px;
         }
-
-        .drag-handle {
-            right: -$border-width;
-
-            &:hover {
-                right: calc(-1 * $border-width - var(--hover-expand) / 2);
-            }
-        }
     }
 
     &.right {
@@ -251,32 +152,6 @@ $border-width: 6px;
         &::after {
             left: -1px;
         }
-
-        .drag-handle {
-            left: -$border-width;
-
-            &:hover {
-                left: calc(-1 * $border-width - var(--hover-expand) / 2);
-            }
-        }
-    }
-}
-
-.drag-handle {
-    background: none;
-    border: none;
-    border-radius: 0;
-    position: absolute;
-    width: $border-width;
-    padding: 0;
-    height: 100%;
-    z-index: 10000;
-
-    --hover-expand: 4px;
-
-    &:hover {
-        cursor: ew-resize;
-        width: calc($border-width + var(--hover-expand));
     }
 }
 
diff --git a/client/src/components/Panels/InputPanel.vue b/client/src/components/Panels/InputPanel.vue
new file mode 100644
index 0000000000000000000000000000000000000000..2150d969050a2c3ccf5afef1ae08b1319f846196
--- /dev/null
+++ b/client/src/components/Panels/InputPanel.vue
@@ -0,0 +1,83 @@
+<script setup lang="ts">
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+
+import type { WorkflowInput } from "../Workflow/Editor/modules/inputs";
+
+import ActivityPanel from "./ActivityPanel.vue";
+
+const props = defineProps<{
+    inputs: WorkflowInput[];
+}>();
+
+const emit = defineEmits<{
+    (e: "insertModule", id: string, name: string, state: WorkflowInput["stateOverwrites"]): void;
+}>();
+</script>
+
+<template>
+    <ActivityPanel title="Inputs">
+        <div class="input-list">
+            <button
+                v-for="(input, index) in props.inputs"
+                :key="index"
+                :data-id="input.id ?? input.moduleId"
+                class="workflow-input-button"
+                @click="emit('insertModule', input.moduleId, input.title, input.stateOverwrites)">
+                <FontAwesomeIcon class="input-icon" fixed-width :icon="input.icon" />
+                <span class="input-title"> {{ input.title }} </span>
+                <span class="input-description"> {{ input.description }} </span>
+            </button>
+        </div>
+    </ActivityPanel>
+</template>
+
+<style lang="scss" scoped>
+@import "theme/blue.scss";
+
+.input-list {
+    overflow-y: auto;
+    display: flex;
+    flex-direction: column;
+    gap: 0.5rem;
+}
+
+.workflow-input-button {
+    border-radius: 0.5rem;
+    border: 1px solid $gray-300;
+    background: transparent;
+
+    display: grid;
+    grid-template-columns: auto 1fr;
+    grid-template-areas:
+        "i t"
+        "d d";
+
+    text-align: left;
+    gap: 0.25rem;
+    align-items: center;
+
+    &:hover,
+    &:focus {
+        background-color: $gray-100;
+        border-color: $brand-primary;
+    }
+
+    &:active {
+        background-color: $gray-200;
+        border-color: $brand-primary;
+    }
+
+    .input-icon {
+        grid-area: i;
+    }
+
+    .input-title {
+        grid-area: t;
+        font-weight: bold;
+    }
+
+    .input-description {
+        grid-area: d;
+    }
+}
+</style>
diff --git a/client/src/components/Panels/InvocationsPanel.vue b/client/src/components/Panels/InvocationsPanel.vue
index cd329d1a2ae18104f9b3790b0bb62ebe80ea2be8..2d404dde6637cbf27fa4d507c9c5a8c427e597fd 100644
--- a/client/src/components/Panels/InvocationsPanel.vue
+++ b/client/src/components/Panels/InvocationsPanel.vue
@@ -1,22 +1,41 @@
 <script setup lang="ts">
 import { BAlert } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
+import { ref } from "vue";
 
+import { useActivityStore } from "@/stores/activityStore";
 import { useUserStore } from "@/stores/userStore";
 
 import InvocationScrollList from "../Workflow/Invocation/InvocationScrollList.vue";
 import ActivityPanel from "./ActivityPanel.vue";
 
-const { currentUser, toggledSideBar } = storeToRefs(useUserStore());
+const props = defineProps<{
+    activityBarId: string;
+}>();
+
+const { currentUser } = storeToRefs(useUserStore());
+const { toggledSideBar } = storeToRefs(useActivityStore(props.activityBarId));
+
+const shouldCollapse = ref(false);
+function collapseOnLeave() {
+    if (shouldCollapse.value) {
+        toggledSideBar.value = "";
+    }
+}
 </script>
 
 <template>
+    <!-- eslint-disable-next-line vuejs-accessibility/mouse-events-have-key-events -->
     <ActivityPanel
         title="Workflow Invocations"
         go-to-all-title="Open Invocations List"
         href="/workflows/invocations"
-        @goToAll="toggledSideBar = ''">
-        <InvocationScrollList v-if="currentUser && !currentUser?.isAnonymous" in-panel />
+        @goToAll="shouldCollapse = true"
+        @mouseleave.native="collapseOnLeave">
+        <InvocationScrollList
+            v-if="currentUser && !currentUser?.isAnonymous"
+            in-panel
+            @invocation-clicked="shouldCollapse = true" />
         <BAlert v-else variant="info" class="mt-3" show>Please log in to view your Workflow Invocations.</BAlert>
     </ActivityPanel>
 </template>
diff --git a/client/src/components/Panels/MultiviewPanel.vue b/client/src/components/Panels/MultiviewPanel.vue
index a71a31fda7465b48a90f973679d92831f6bfc01d..5f1c9dbe43cd27498d4bf0fdf25a809a63481b81 100644
--- a/client/src/components/Panels/MultiviewPanel.vue
+++ b/client/src/components/Panels/MultiviewPanel.vue
@@ -96,11 +96,7 @@ function userTitle(title: string) {
 </script>
 
 <template>
-    <ActivityPanel
-        title="Select Histories"
-        go-to-all-title="Open History Multiview"
-        href="/histories/view_multiple"
-        :go-to-on-href="false">
+    <ActivityPanel title="Select Histories">
         <template v-slot:header-buttons>
             <BButtonGroup>
                 <BButton
diff --git a/client/src/components/Panels/SettingsPanel.vue b/client/src/components/Panels/SettingsPanel.vue
index b488297217923608d64a543ec38208e5cd3b3787..7ffe6dbf5cd4e66f01af84d3f65653599874d236 100644
--- a/client/src/components/Panels/SettingsPanel.vue
+++ b/client/src/components/Panels/SettingsPanel.vue
@@ -1,10 +1,28 @@
 <script setup lang="ts">
+import { faUndo } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BModal } from "bootstrap-vue";
 import { ref } from "vue";
 
+import { useActivityStore } from "@/stores/activityStore";
+
 import ActivitySettings from "@/components/ActivityBar/ActivitySettings.vue";
 import DelayedInput from "@/components/Common/DelayedInput.vue";
 import ActivityPanel from "@/components/Panels/ActivityPanel.vue";
 
+const props = defineProps<{
+    activityBarId: string;
+    heading: string;
+    searchPlaceholder: string;
+}>();
+
+const emit = defineEmits<{
+    (e: "activityClicked", activityId: string): void;
+}>();
+
+const activityStore = useActivityStore(props.activityBarId);
+
+const confirmRestore = ref(false);
 const query = ref("");
 
 function onQuery(newQuery: string) {
@@ -13,11 +31,32 @@ function onQuery(newQuery: string) {
 </script>
 
 <template>
-    <ActivityPanel title="Settings" go-to-all-title="User Preferences" href="/user">
+    <ActivityPanel :title="props.heading">
         <template v-slot:header>
-            <h3>Customize Activity Bar</h3>
-            <DelayedInput :delay="100" placeholder="Search activities" @change="onQuery" />
+            <DelayedInput :delay="100" :placeholder="props.searchPlaceholder" @change="onQuery" />
+        </template>
+        <template v-slot:header-buttons>
+            <BButton
+                v-b-tooltip.bottom.hover
+                data-description="restore factory settings"
+                size="sm"
+                variant="link"
+                title="Restore default"
+                @click="confirmRestore = true">
+                <span v-localize>Reset</span>
+                <FontAwesomeIcon :icon="faUndo" fixed-width />
+            </BButton>
         </template>
-        <ActivitySettings :query="query" />
+        <ActivitySettings
+            :query="query"
+            :activity-bar-id="props.activityBarId"
+            @activityClicked="(...args) => emit('activityClicked', ...args)" />
+        <BModal
+            v-model="confirmRestore"
+            title="Restore Activity Bar Defaults"
+            title-tag="h2"
+            @ok="activityStore.restore()">
+            <p v-localize>Are you sure you want to reset the activity bar to its default settings?</p>
+        </BModal>
     </ActivityPanel>
 </template>
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index 61e202bce98577d6ef8da856604ba9f9bf9b6371..7bc8824680567d930bb40979eb1481af6a38c189 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -3,15 +3,12 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faEye, faEyeSlash } from "@fortawesome/free-regular-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { computed, ComputedRef, type PropType, type Ref, ref } from "vue";
+import { computed, type ComputedRef, type PropType, type Ref, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { getGalaxyInstance } from "@/app";
 import { useGlobalUploadModal } from "@/composables/globalUploadModal";
-import { getAppRoot } from "@/onload/loadConfig";
 import { type Tool, type ToolSection as ToolSectionType } from "@/stores/toolStore";
 import { useToolStore } from "@/stores/toolStore";
-import { Workflow, type Workflow as WorkflowType } from "@/stores/workflowStore";
 import localize from "@/utils/localization";
 
 import { filterTools, getValidPanelItems, getValidToolsInCurrentView, getValidToolsInEachSection } from "./utilities";
@@ -29,8 +26,6 @@ const emit = defineEmits<{
     (e: "update:panel-query", query: string): void;
     (e: "onInsertTool", toolId: string, toolName: string): void;
     (e: "onInsertModule", moduleName: string, moduleTitle: string | undefined): void;
-    (e: "onInsertWorkflow", workflowLatestId: string | undefined, workflowName: string): void;
-    (e: "onInsertWorkflowSteps", workflowId: string, workflowStepCount: number | undefined): void;
 }>();
 
 const props = defineProps({
@@ -38,7 +33,6 @@ const props = defineProps({
     panelView: { type: String, required: true },
     showAdvanced: { type: Boolean, default: false, required: true },
     panelQuery: { type: String, required: true },
-    editorWorkflows: { type: Array, default: null },
     dataManagers: { type: Array, default: null },
     moduleSections: { type: Array as PropType<Record<string, any>>, default: null },
 });
@@ -132,44 +126,6 @@ const localPanel: ComputedRef<Record<string, Tool | ToolSectionType> | null> = c
     }
 });
 
-const favWorkflows = computed(() => {
-    const Galaxy = getGalaxyInstance();
-    const storedWorkflowMenuEntries = Galaxy && Galaxy.config.stored_workflow_menu_entries;
-    if (storedWorkflowMenuEntries) {
-        const returnedWfs = [];
-        if (!props.workflow) {
-            returnedWfs.push({
-                title: localize("All workflows") as string,
-                href: `${getAppRoot()}workflows/list`,
-                id: "list",
-            });
-        }
-        const storedWfs = [
-            ...storedWorkflowMenuEntries.map((menuEntry: Workflow) => {
-                return {
-                    id: menuEntry.id,
-                    title: menuEntry.name,
-                    href: `${getAppRoot()}workflows/run?id=${menuEntry.id}`,
-                };
-            }),
-        ];
-        return returnedWfs.concat(storedWfs);
-    } else {
-        return [];
-    }
-});
-
-const workflowSection = computed(() => {
-    if (props.workflow && props.editorWorkflows.length > 0) {
-        return {
-            name: localize("Workflows"),
-            elems: props.workflow && props.editorWorkflows,
-        };
-    } else {
-        return null;
-    }
-});
-
 const buttonIcon = computed(() => (showSections.value ? faEyeSlash : faEye));
 const buttonText = computed(() => (showSections.value ? localize("Hide Sections") : localize("Show Sections")));
 
@@ -178,15 +134,6 @@ function onInsertModule(module: Record<string, any>, event: Event) {
     emit("onInsertModule", module.name, module.title);
 }
 
-function onInsertWorkflow(workflow: WorkflowType, event: Event) {
-    event.preventDefault();
-    emit("onInsertWorkflow", workflow.latest_id, workflow.name);
-}
-
-function onInsertWorkflowSteps(workflow: WorkflowType) {
-    emit("onInsertWorkflowSteps", workflow.id, workflow.step_count);
-}
-
 function onToolClick(tool: Tool, evt: Event) {
     if (!props.workflow) {
         if (tool.id === "upload1") {
@@ -309,29 +256,6 @@ function onToggle() {
                             @onFilter="onSectionFilter" />
                     </div>
                 </div>
-                <ToolSection
-                    v-if="props.workflow && workflowSection"
-                    :key="workflowSection.name"
-                    :category="workflowSection"
-                    section-name="workflows"
-                    :sort-items="false"
-                    operation-icon="fa fa-files-o"
-                    operation-title="Insert individual steps."
-                    :query-filter="queryFilter || undefined"
-                    :disable-filter="true"
-                    @onClick="onInsertWorkflow"
-                    @onOperation="onInsertWorkflowSteps" />
-                <div v-else-if="favWorkflows.length > 0">
-                    <ToolSection :category="{ text: 'Workflows' }" />
-                    <div id="internal-workflows" class="toolSectionBody">
-                        <div class="toolSectionBg" />
-                        <div v-for="wf in favWorkflows" :key="wf.id" class="toolTitle">
-                            <a class="title-link" href="javascript:void(0)" @click="router.push(wf.href)">{{
-                                wf.title
-                            }}</a>
-                        </div>
-                    </div>
-                </div>
             </div>
         </div>
     </div>
diff --git a/client/src/components/Panels/ToolPanel.test.js b/client/src/components/Panels/ToolPanel.test.js
deleted file mode 100644
index 7b5575f251c9361c86b1a15bc182bd0730b53a70..0000000000000000000000000000000000000000
--- a/client/src/components/Panels/ToolPanel.test.js
+++ /dev/null
@@ -1,100 +0,0 @@
-import "jest-location-mock";
-
-import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
-import toolsList from "components/ToolsView/testData/toolsList";
-import toolsListInPanel from "components/ToolsView/testData/toolsListInPanel";
-import flushPromises from "flush-promises";
-import { createPinia } from "pinia";
-import { getLocalVue } from "tests/jest/helpers";
-
-import { useConfig } from "@/composables/config";
-
-import viewsList from "./testData/viewsList";
-import ToolPanel from "./ToolPanel";
-import { types_to_icons } from "./utilities";
-
-const localVue = getLocalVue();
-
-const TEST_PANELS_URI = "/api/tool_panels";
-
-jest.mock("composables/config");
-useConfig.mockReturnValue({
-    config: {},
-    isConfigLoaded: true,
-});
-
-describe("ToolPanel", () => {
-    it("test navigation of tool panel views menu", async () => {
-        const axiosMock = new MockAdapter(axios);
-        axiosMock
-            .onGet(/\/api\/tool_panels\/.*/)
-            .reply(200, toolsListInPanel)
-            .onGet(`/api/tools?in_panel=False`)
-            .replyOnce(200, toolsList)
-            .onGet(TEST_PANELS_URI)
-            .reply(200, { default_panel_view: "default", views: viewsList });
-
-        const pinia = createPinia();
-        const wrapper = mount(ToolPanel, {
-            propsData: {
-                workflow: false,
-                editorWorkflows: null,
-                dataManagers: null,
-                moduleSections: null,
-            },
-            localVue,
-            stubs: {
-                icon: { template: "<div></div>" },
-                ToolBox: true,
-            },
-            pinia,
-        });
-
-        await flushPromises();
-
-        // there is a panel view selector initially collapsed
-        expect(wrapper.find(".panel-view-selector").exists()).toBe(true);
-        expect(wrapper.find(".dropdown-menu.show").exists()).toBe(false);
-
-        // Test: starts up with a default panel view, click to open menu
-        expect(wrapper.find("#toolbox-heading").text()).toBe("Tools");
-        await wrapper.find("#toolbox-heading").trigger("click");
-        await flushPromises();
-
-        const dropdownMenu = wrapper.find(".dropdown-menu.show");
-        expect(dropdownMenu.exists()).toBe(true);
-
-        // Test: check if the dropdown menu has all the panel views
-        const dropdownItems = dropdownMenu.findAll(".dropdown-item");
-        expect(dropdownItems.length).toEqual(Object.keys(viewsList).length);
-
-        // Test: click on each panel view, and check if the panel view is changed
-        for (const [key, value] of Object.entries(viewsList)) {
-            // find dropdown item
-            const currItem = dropdownMenu.find(`[data-panel-id='${key}']`);
-            if (key !== "default") {
-                // Test: check if the panel view has appropriate description
-                const description = currItem.attributes().title || null;
-                expect(description).toBe(value.description);
-
-                // set current panel view
-                await currItem.trigger("click");
-                await flushPromises();
-
-                // Test: check if the current panel view is selected now
-                expect(currItem.find(".fa-check").exists()).toBe(true);
-
-                // Test: check if the panel header now has an icon and a changed name
-                const panelViewIcon = wrapper.find("[data-description='panel view header icon']");
-                expect(panelViewIcon.classes()).toContain(`fa-${types_to_icons[value.view_type]}`);
-                expect(wrapper.find("#toolbox-heading").text()).toBe(value.name);
-            } else {
-                // Test: check if the default panel view is already selected, and no icon
-                expect(currItem.find(".fa-check").exists()).toBe(true);
-                expect(wrapper.find("[data-description='panel view header icon']").exists()).toBe(false);
-            }
-        }
-    });
-});
diff --git a/client/src/components/Panels/ToolPanel.test.ts b/client/src/components/Panels/ToolPanel.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d7775e48cc58bc5be5998e7cdc98242c063d857f
--- /dev/null
+++ b/client/src/components/Panels/ToolPanel.test.ts
@@ -0,0 +1,203 @@
+import "jest-location-mock";
+
+import { mount } from "@vue/test-utils";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
+import flushPromises from "flush-promises";
+import { createPinia } from "pinia";
+import { getLocalVue } from "tests/jest/helpers";
+import { ref } from "vue";
+
+import toolsList from "@/components/ToolsView/testData/toolsList.json";
+import toolsListInPanel from "@/components/ToolsView/testData/toolsListInPanel.json";
+import { useUserLocalStorage } from "@/composables/userLocalStorage";
+import { useToolStore } from "@/stores/toolStore";
+
+import viewsListJson from "./testData/viewsList.json";
+import { types_to_icons } from "./utilities";
+
+import ToolPanel from "./ToolPanel.vue";
+
+interface ToolPanelView {
+    id: string;
+    model_class: string;
+    name: string;
+    description: string | null;
+    view_type: string;
+    searchable: boolean;
+}
+
+const localVue = getLocalVue();
+
+const TEST_PANELS_URI = "/api/tool_panels";
+const DEFAULT_VIEW_ID = "default";
+const PANEL_VIEW_ERR_MSG = "Error loading panel view";
+
+jest.mock("@/composables/config", () => ({
+    useConfig: jest.fn(() => ({
+        config: {},
+        isConfigLoaded: true,
+    })),
+}));
+
+jest.mock("@/composables/userLocalStorage", () => ({
+    useUserLocalStorage: jest.fn(() => ref(DEFAULT_VIEW_ID)),
+}));
+
+describe("ToolPanel", () => {
+    const viewsList = viewsListJson as Record<string, ToolPanelView>;
+
+    /** Mocks and stores a non-default panel view as the current panel view */
+    function storeNonDefaultView() {
+        // find a view in object viewsList that is not DEFAULT_VIEW_ID
+        const viewKey = Object.keys(viewsList).find((id) => id !== DEFAULT_VIEW_ID);
+        if (!viewKey) {
+            throw new Error("No non-default view found in viewsList");
+        }
+        const view = viewsList[viewKey];
+        if (!view) {
+            throw new Error(`View with key ${viewKey} not found in viewsList`);
+        }
+        // ref and useUserLocalStorage are already imported at the top
+        (useUserLocalStorage as jest.Mock).mockImplementation(() => ref(viewKey));
+        return { viewKey, view };
+    }
+
+    /**
+     * Sets up wrapper for ToolPanel component
+     * @param {String} errorView If provided, we mock an error for this view
+     * @param {Boolean} failDefault If true and error view is provided, we
+     *                              mock an error for the default view as well
+     * @returns wrapper
+     */
+    async function createWrapper(errorView = "", failDefault = false) {
+        const axiosMock = new MockAdapter(axios);
+        axiosMock
+            .onGet(`/api/tools?in_panel=False`)
+            .replyOnce(200, toolsList)
+            .onGet(TEST_PANELS_URI)
+            .reply(200, { default_panel_view: DEFAULT_VIEW_ID, views: viewsList });
+
+        if (errorView) {
+            axiosMock.onGet(`/api/tool_panels/${errorView}`).reply(400, { err_msg: PANEL_VIEW_ERR_MSG });
+            if (errorView !== DEFAULT_VIEW_ID && !failDefault) {
+                axiosMock.onGet(`/api/tool_panels/${DEFAULT_VIEW_ID}`).reply(200, toolsListInPanel);
+            } else if (failDefault) {
+                axiosMock.onGet(`/api/tool_panels/${DEFAULT_VIEW_ID}`).reply(400, { err_msg: PANEL_VIEW_ERR_MSG });
+            }
+        } else {
+            // mock response for all panel views
+            axiosMock.onGet(/\/api\/tool_panels\/.*/).reply(200, toolsListInPanel);
+        }
+
+        // setting this because for the default view, we just show "Tools" as the name
+        // even though the backend returns "Full Tool Panel"
+        viewsList[DEFAULT_VIEW_ID]!.name = "Tools";
+
+        const pinia = createPinia();
+        const wrapper = mount(ToolPanel as object, {
+            propsData: {
+                workflow: false,
+                editorWorkflows: null,
+                dataManagers: null,
+                moduleSections: null,
+            },
+            localVue,
+            stubs: {
+                icon: { template: "<div></div>" },
+                ToolBox: true,
+            },
+            pinia,
+        });
+
+        await flushPromises();
+
+        return { wrapper };
+    }
+
+    it("test navigation of tool panel views menu", async () => {
+        const { wrapper } = await createWrapper();
+        // there is a panel view selector initially collapsed
+        expect(wrapper.find(".panel-view-selector").exists()).toBe(true);
+        expect(wrapper.find(".dropdown-menu.show").exists()).toBe(false);
+
+        // Test: starts up with a default panel view, click to open menu
+        expect(wrapper.find("#toolbox-heading").text()).toBe(viewsList[DEFAULT_VIEW_ID]!.name);
+        await wrapper.find("#toolbox-heading").trigger("click");
+        await flushPromises();
+
+        const dropdownMenu = wrapper.find(".dropdown-menu.show");
+        expect(dropdownMenu.exists()).toBe(true);
+
+        // Test: check if the dropdown menu has all the panel views
+        const dropdownItems = dropdownMenu.findAll(".dropdown-item");
+        expect(dropdownItems.length).toEqual(Object.keys(viewsList).length);
+
+        // Test: click on each panel view, and check if the panel view is changed
+        for (const [key, value] of Object.entries(viewsList)) {
+            // find dropdown item
+            const currItem = dropdownMenu.find(`[data-panel-id='${key}']`);
+            if (key !== DEFAULT_VIEW_ID) {
+                // Test: check if the panel view has appropriate description
+                const description = currItem.attributes().title || null;
+                expect(description).toBe(value.description);
+
+                // set current panel view
+                await currItem.trigger("click");
+                await flushPromises();
+
+                // Test: check if the current panel view is selected now
+                expect(currItem.find(".fa-check").exists()).toBe(true);
+
+                // Test: check if the panel header now has an icon and a changed name
+                const panelViewIcon = wrapper.find("[data-description='panel view header icon']");
+                expect(panelViewIcon.classes()).toContain(
+                    `fa-${types_to_icons[value.view_type as keyof typeof types_to_icons]}`
+                );
+                expect(wrapper.find("#toolbox-heading").text()).toBe(value!.name);
+            } else {
+                // Test: check if the default panel view is already selected, and no icon
+                expect(currItem.find(".fa-check").exists()).toBe(true);
+                expect(wrapper.find("[data-description='panel view header icon']").exists()).toBe(false);
+            }
+        }
+    });
+
+    it("initializes non default current panel view correctly", async () => {
+        const { viewKey, view } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper();
+
+        // starts up with a non default panel view
+        expect(wrapper.find("#toolbox-heading").text()).toBe(view!.name);
+        const toolStore = useToolStore();
+        expect(toolStore.currentPanelView).toBe(viewKey);
+    });
+
+    it("changes panel to default if current panel view throws error", async () => {
+        const { viewKey, view } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper(viewKey);
+
+        // does not initialize non default panel view, and changes to default
+        expect(wrapper.find("#toolbox-heading").text()).not.toBe(view!.name);
+        expect(wrapper.find("#toolbox-heading").text()).toBe(viewsList[DEFAULT_VIEW_ID]!.name);
+        const toolStore = useToolStore();
+        expect(toolStore.currentPanelView).toBe(DEFAULT_VIEW_ID);
+
+        // toolbox loaded
+        expect(wrapper.find('[data-description="panel toolbox"]').exists()).toBe(true);
+    });
+
+    it("simply shows error if even default panel view throws error", async () => {
+        const { viewKey } = storeNonDefaultView();
+
+        const { wrapper } = await createWrapper(viewKey, true);
+
+        // toolbox not loaded
+        expect(wrapper.find('[data-description="panel toolbox"]').exists()).toBe(false);
+
+        // error message shown
+        expect(wrapper.find('[data-description="tool panel error message"]').text()).toBe(PANEL_VIEW_ERR_MSG);
+    });
+});
diff --git a/client/src/components/Panels/ToolPanel.vue b/client/src/components/Panels/ToolPanel.vue
index a478b08f7c7a0a6bb8f4405a3c533f7b3d623f80..cf0fa3f4fcd5f8aa0ae84212948e24085956f083 100644
--- a/client/src/components/Panels/ToolPanel.vue
+++ b/client/src/components/Panels/ToolPanel.vue
@@ -1,12 +1,12 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCaretDown } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
-import { computed, onMounted, ref, watch } from "vue";
+import { computed, ref, watch } from "vue";
 
 import { useToolStore } from "@/stores/toolStore";
 import localize from "@/utils/localization";
+import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
 import { types_to_icons } from "./utilities";
 
@@ -16,11 +16,8 @@ import PanelViewMenu from "./Menus/PanelViewMenu.vue";
 import ToolBox from "./ToolBox.vue";
 import Heading from "@/components/Common/Heading.vue";
 
-library.add(faCaretDown);
-
 const props = defineProps({
     workflow: { type: Boolean, default: false },
-    editorWorkflows: { type: Array, default: null },
     dataManagers: { type: Array, default: null },
     moduleSections: { type: Array, default: null },
 });
@@ -40,17 +37,20 @@ const { currentPanelView, defaultPanelView, isPanelPopulated, loading, panel, pa
 const loadingView = ref<string | undefined>(undefined);
 const query = ref("");
 const showAdvanced = ref(false);
+const errorMessage = ref<string | undefined>(undefined);
 
-onMounted(async () => {
+initializeToolPanel();
+async function initializeToolPanel() {
     try {
         await toolStore.fetchPanelViews();
         await initializeTools();
     } catch (error) {
         console.error(error);
+        errorMessage.value = errorMessageAsString(error);
     } finally {
         arePanelsFetched.value = true;
     }
-});
+}
 
 watch(
     () => currentPanelView.value,
@@ -100,12 +100,29 @@ const viewIcon = computed(() => {
     }
 });
 
+const showFavorites = computed({
+    get() {
+        return query.value.includes("#favorites");
+    },
+    set(value) {
+        if (value) {
+            if (!query.value.includes("#favorites")) {
+                query.value = `#favorites ${query.value}`.trim();
+            }
+        } else {
+            query.value = query.value.replace("#favorites", "").trim();
+        }
+    },
+});
+
 async function initializeTools() {
     try {
         await toolStore.fetchTools();
         await toolStore.initCurrentPanelView(defaultPanelView.value);
     } catch (error: any) {
         console.error("ToolPanel - Intialize error:", error);
+        errorMessage.value = errorMessageAsString(error);
+        rethrowSimple(error);
     }
 }
 
@@ -130,10 +147,17 @@ function onInsertWorkflow(workflowId: string | undefined, workflowName: string)
 function onInsertWorkflowSteps(workflowId: string, workflowStepCount: number | undefined) {
     emit("onInsertWorkflowSteps", workflowId, workflowStepCount);
 }
+
+watch(
+    () => query.value,
+    (newQuery) => {
+        showFavorites.value = newQuery.includes("#favorites");
+    }
+);
 </script>
 
 <template>
-    <div v-if="arePanelsFetched" class="unified-panel" aria-labelledby="toolbox-heading">
+    <div v-if="arePanelsFetched" id="toolbox-panel" class="unified-panel" aria-labelledby="toolbox-heading">
         <div unselectable="on">
             <div class="unified-panel-header-inner mx-3 my-2 d-flex justify-content-between">
                 <PanelViewMenu
@@ -163,13 +187,13 @@ function onInsertWorkflowSteps(workflowId: string, workflowStepCount: number | u
                                 </Heading>
                             </div>
                             <div v-if="!showAdvanced" class="panel-header-buttons">
-                                <FontAwesomeIcon icon="caret-down" />
+                                <FontAwesomeIcon :icon="faCaretDown" />
                             </div>
                         </div>
                     </template>
                 </PanelViewMenu>
                 <div v-if="!showAdvanced" class="panel-header-buttons">
-                    <FavoritesButton :query="query" @onFavorites="(q) => (query = q)" />
+                    <FavoritesButton v-model="showFavorites" />
                 </div>
             </div>
         </div>
@@ -179,7 +203,6 @@ function onInsertWorkflowSteps(workflowId: string, workflowStepCount: number | u
             :panel-query.sync="query"
             :panel-view="currentPanelView"
             :show-advanced.sync="showAdvanced"
-            :editor-workflows="editorWorkflows"
             :data-managers="dataManagers"
             :module-sections="moduleSections"
             @updatePanelView="updatePanelView"
@@ -187,6 +210,11 @@ function onInsertWorkflowSteps(workflowId: string, workflowStepCount: number | u
             @onInsertModule="onInsertModule"
             @onInsertWorkflow="onInsertWorkflow"
             @onInsertWorkflowSteps="onInsertWorkflowSteps" />
+        <div v-else-if="errorMessage" data-description="tool panel error message">
+            <b-alert class="m-2" variant="danger" show>
+                {{ errorMessage }}
+            </b-alert>
+        </div>
         <div v-else>
             <b-badge class="alert-info w-100">
                 <LoadingSpan message="Loading Toolbox" />
diff --git a/client/src/components/Panels/VisualizationPanel.vue b/client/src/components/Panels/VisualizationPanel.vue
index d9fbf144aa2cfdf901900efeefd6ad41ea956435..70e2144c5fc1e15e00afa608543761fc5a0a1dff 100644
--- a/client/src/components/Panels/VisualizationPanel.vue
+++ b/client/src/components/Panels/VisualizationPanel.vue
@@ -104,11 +104,11 @@ onMounted(() => {
             <h3>Create Visualization</h3>
             <DelayedInput :delay="100" placeholder="Search visualizations" @change="query = $event" />
         </template>
-        <div class="overflow-y mt-2">
+        <div>
             <LoadingSpan v-if="isLoading" message="Loading visualizations" />
             <div v-else-if="filteredPlugins.length > 0">
                 <div v-for="plugin in filteredPlugins" :key="plugin.name">
-                    <button :data-plugin-name="plugin.name" @click="selectVisualization(plugin)">
+                    <button class="plugin-item" :data-plugin-name="plugin.name" @click="selectVisualization(plugin)">
                         <div class="d-flex">
                             <div class="plugin-thumbnail mr-2">
                                 <img v-if="plugin.logo" alt="visualization" :src="absPath(plugin.logo)" />
@@ -143,6 +143,20 @@ onMounted(() => {
 </template>
 
 <style lang="scss">
+@import "theme/blue.scss";
+
+.plugin-item {
+    background: none;
+    border: none;
+    text-align: left;
+    transition: none;
+    width: 100%;
+}
+
+.plugin-item:hover {
+    background: $gray-200;
+}
+
 .plugin-thumbnail {
     img {
         width: 2rem;
diff --git a/client/src/components/Panels/WorkflowPanel.vue b/client/src/components/Panels/WorkflowPanel.vue
new file mode 100644
index 0000000000000000000000000000000000000000..c596363d7fe3a1462ac0d47fa5158c04f8533b9b
--- /dev/null
+++ b/client/src/components/Panels/WorkflowPanel.vue
@@ -0,0 +1,216 @@
+<script setup lang="ts">
+import { faPlus } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { useMemoize, watchImmediate } from "@vueuse/core";
+import { BButton } from "bootstrap-vue";
+import { computed, ref, watch } from "vue";
+
+import { loadWorkflows, type Workflow } from "@/components/Workflow/workflows.services";
+import { useAnimationFrameScroll } from "@/composables/sensors/animationFrameScroll";
+import { useToast } from "@/composables/toast";
+
+import ActivityPanel from "./ActivityPanel.vue";
+import FavoritesButton from "./Buttons/FavoritesButton.vue";
+import DelayedInput from "@/components/Common/DelayedInput.vue";
+import ScrollToTopButton from "@/components/ToolsList/ScrollToTopButton.vue";
+import WorkflowCardList from "@/components/Workflow/List/WorkflowCardList.vue";
+
+const props = defineProps<{
+    currentWorkflowId: string;
+}>();
+
+const emit = defineEmits<{
+    (e: "insertWorkflow", id: string, name: string): void;
+    (e: "insertWorkflowSteps", id: string, stepCount: number): void;
+    (e: "createWorkflow"): void;
+}>();
+
+const scrollable = ref<HTMLDivElement | null>(null);
+const { arrived, scrollTop } = useAnimationFrameScroll(scrollable);
+
+const loading = ref(false);
+const totalWorkflowsCount = ref(Infinity);
+
+const allLoaded = computed(() => totalWorkflowsCount.value <= workflows.value.length);
+
+const filterText = ref("");
+
+const workflows = ref<Workflow[]>([]);
+
+const showFavorites = computed({
+    get() {
+        return filterText.value.includes("is:bookmarked");
+    },
+    set(value) {
+        if (value) {
+            if (!filterText.value.includes("is:bookmarked")) {
+                filterText.value = `is:bookmarked ${filterText.value}`.trim();
+            }
+        } else {
+            filterText.value = filterText.value.replace("is:bookmarked", "").trim();
+        }
+    },
+});
+
+const loadWorkflowsOptions = {
+    sortBy: "update_time",
+    sortDesc: true,
+    limit: 20,
+    showPublished: false,
+    skipStepCounts: false,
+} as const;
+
+const { error } = useToast();
+const getWorkflows = useMemoize(async (filterText: string, offset: number) => {
+    const { data, totalMatches } = await loadWorkflows({
+        ...loadWorkflowsOptions,
+        offset,
+        filterText,
+    });
+
+    return { data, totalMatches };
+});
+
+let fetchKey = "";
+let lastFetchKey = "";
+
+async function load() {
+    const isCurrentFetch = () => fetchKey.trim().toLowerCase() === lastFetchKey.trim().toLowerCase();
+
+    if (isCurrentFetch() && (loading.value || allLoaded.value)) {
+        return;
+    }
+
+    lastFetchKey = fetchKey;
+
+    loading.value = true;
+
+    try {
+        const { data, totalMatches } = await getWorkflows(filterText.value, workflows.value.length);
+
+        if (isCurrentFetch()) {
+            totalWorkflowsCount.value = totalMatches;
+
+            const workflowIds = new Set(workflows.value.map((w) => w.id));
+            const newWorkflows = data.filter((w) => !workflowIds.has(w.id));
+
+            workflows.value.push(...newWorkflows);
+        }
+    } catch (e) {
+        if (isCurrentFetch()) {
+            error(`Failed to load workflows: ${e}`);
+        }
+    } finally {
+        if (isCurrentFetch()) {
+            loading.value = false;
+        }
+    }
+}
+
+function resetWorkflows() {
+    workflows.value = [];
+    totalWorkflowsCount.value = Infinity;
+    loading.value = false;
+    fetchKey = "";
+}
+
+function refresh() {
+    resetWorkflows();
+    getWorkflows.clear();
+    load();
+}
+
+watchImmediate(
+    () => filterText.value,
+    (newFilterText) => {
+        showFavorites.value = newFilterText.includes("is:bookmarked");
+        resetWorkflows();
+        fetchKey = filterText.value;
+        load();
+    }
+);
+
+watch(
+    () => arrived.bottom,
+    () => {
+        if (arrived.bottom) {
+            load();
+        }
+    }
+);
+
+function scrollToTop() {
+    scrollable.value?.scrollTo({ top: 0, behavior: "smooth" });
+}
+
+function createNew(event: Event) {
+    event.preventDefault();
+    emit("createWorkflow");
+}
+</script>
+
+<template>
+    <ActivityPanel title="Workflows">
+        <template v-slot:header-buttons>
+            <BButton
+                v-b-tooltip.hover.top.noninteractive
+                size="sm"
+                variant="link"
+                class="create-button"
+                title="Create new workflow"
+                href="/workflows/edit"
+                @click="createNew">
+                <FontAwesomeIcon :icon="faPlus" />
+            </BButton>
+            <FavoritesButton v-model="showFavorites" tooltip="Show bookmarked" />
+        </template>
+
+        <DelayedInput
+            v-model="filterText"
+            placeholder="search workflows"
+            :delay="800"
+            :loading="loading"></DelayedInput>
+
+        <div ref="scrollable" class="workflow-scroll-list mt-2">
+            <WorkflowCardList
+                :hide-runs="true"
+                :workflows="workflows"
+                :filterable="false"
+                :current-workflow-id="props.currentWorkflowId"
+                editor-view
+                @insertWorkflow="(...args) => emit('insertWorkflow', ...args)"
+                @insertWorkflowSteps="(...args) => emit('insertWorkflowSteps', ...args)"
+                @refreshList="refresh" />
+
+            <div v-if="allLoaded || filterText !== ''" class="list-end">
+                <span v-if="workflows.length == 1"> - 1 workflow loaded - </span>
+                <span v-else-if="workflows.length > 1"> - All {{ workflows.length }} workflows loaded - </span>
+                <span v-else> - No workflows found - </span>
+            </div>
+            <div v-else-if="loading" class="list-end">- loading -</div>
+        </div>
+
+        <ScrollToTopButton :offset="scrollTop" @click="scrollToTop" />
+    </ActivityPanel>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+.workflow-scroll-list {
+    overflow-y: auto;
+    display: flex;
+    flex-direction: column;
+}
+
+.list-end {
+    align-self: center;
+    color: $text-light;
+    margin: 0.5rem;
+}
+
+.create-button:hover {
+    background-color: #c8cfd6;
+    border-color: #c1c9d0;
+}
+</style>
diff --git a/client/src/components/Panels/utilities.ts b/client/src/components/Panels/utilities.ts
index 95da1acbbf698a2ecce46e1b62f09c908306a110..38f7f4d335fe83bc43bd4787d076f2b1c6588fe8 100644
--- a/client/src/components/Panels/utilities.ts
+++ b/client/src/components/Panels/utilities.ts
@@ -4,17 +4,13 @@
  */
 import { orderBy } from "lodash";
 
-import {
-    type FilterSettings as ToolFilters,
-    type Tool,
-    type ToolSection,
-    type ToolSectionLabel,
-} from "@/stores/toolStore";
+import type { FilterSettings as ToolFilters, Tool, ToolSection, ToolSectionLabel } from "@/stores/toolStore";
 import levenshteinDistance from "@/utils/levenshtein";
 
 const FILTER_KEYS = {
     id: ["id", "tool_id"],
     panel_section_name: ["section", "panel_section_name"],
+    labels: ["label", "labels", "tag"],
 };
 const STRING_REPLACEMENTS: string[] = [" ", "-", "\\(", "\\)", "'", ":", `"`];
 const MINIMUM_DL_LENGTH = 5; // for Demerau-Levenshtein distance
@@ -286,7 +282,14 @@ export function searchToolsByKeys(
                 if (key === "combined") {
                     actualValue = `${tool.name.trim()} ${tool.description.trim()}`.toLowerCase();
                 } else {
-                    actualValue = (tool[key as keyof Tool] as string)?.trim().toLowerCase();
+                    const toolVal = tool[key as keyof Tool];
+                    if (typeof toolVal === "string") {
+                        actualValue = toolVal.trim().toLowerCase();
+                    } else if (Array.isArray(toolVal)) {
+                        actualValue = toolVal.join(" ").trim().toLowerCase();
+                    } else if (typeof toolVal === "number") {
+                        actualValue = toolVal.toString().trim().toLowerCase();
+                    }
                 }
 
                 // get all (space separated) words in actualValue for tool (for DL)
diff --git a/client/src/components/Popper/usePopper.ts b/client/src/components/Popper/usePopper.ts
index 8a2155e6a62ed2ce9fc8edd263b9c3fd877ec6e3..229b77e3d0694a263c204755b10201cbbf025082 100644
--- a/client/src/components/Popper/usePopper.ts
+++ b/client/src/components/Popper/usePopper.ts
@@ -1,6 +1,5 @@
 import { createPopper } from "@popperjs/core";
-import type { Ref } from "vue";
-import { onMounted, onUnmounted, onUpdated, ref, unref, watch } from "vue";
+import { onMounted, onUnmounted, onUpdated, type Ref, ref, unref, watch } from "vue";
 
 export type MaybeRef<T> = T | Ref<T>;
 
diff --git a/client/src/components/ProgressBar.vue b/client/src/components/ProgressBar.vue
index d980db5afac86f1dd348a53e4062280f5ac95325..eb10d0bbe240cc34414d57594b903629b2b2936d 100644
--- a/client/src/components/ProgressBar.vue
+++ b/client/src/components/ProgressBar.vue
@@ -1,58 +1,50 @@
+<script setup lang="ts">
+// Not really a very generic ProgressBar - consider renaming to StateProgressBar.
+
+import { BProgress, BProgressBar } from "bootstrap-vue";
+
+interface Props {
+    total?: number;
+    note: string;
+    loading?: boolean;
+    okCount?: number;
+    runningCount?: number;
+    newCount?: number;
+    errorCount?: number;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    total: 1,
+    note: undefined,
+    loading: false,
+    okCount: 0,
+    runningCount: 0,
+    newCount: 0,
+    errorCount: 0,
+});
+</script>
+
 <template>
-    <div class="my-1 progressContainer">
-        <small v-if="note" class="progressNote">
-            {{ note }}<span v-if="loading">.<span class="blinking">..</span></span>
+    <div class="my-1 progress-container">
+        <small v-if="props.note" class="progress-note">
+            {{ props.note }}<span v-if="props.loading">.<span class="blinking">..</span></span>
         </small>
-        <b-progress :max="total">
-            <b-progress-bar variant="success" :value="okCount" />
-            <b-progress-bar variant="danger" :value="errorCount" />
-            <b-progress-bar variant="warning" :value="runningCount" />
-            <b-progress-bar variant="warning" :value="newCount" />
-        </b-progress>
+        <BProgress :max="props.total">
+            <BProgressBar variant="success" :value="props.okCount" />
+            <BProgressBar variant="danger" :value="props.errorCount" />
+            <BProgressBar variant="warning" :value="props.runningCount" />
+            <BProgressBar variant="warning" :value="props.newCount" />
+        </BProgress>
     </div>
 </template>
-<script>
-// Not really a very generic ProgressBar - consider renaming to StateProgressBar.
-export default {
-    props: {
-        total: {
-            type: Number,
-            default: 1,
-        },
-        note: {
-            type: String,
-            default: null,
-        },
-        loading: {
-            type: Boolean,
-            default: false,
-        },
-        okCount: {
-            type: Number,
-            default: 0,
-        },
-        runningCount: {
-            type: Number,
-            default: 0,
-        },
-        newCount: {
-            type: Number,
-            default: 0,
-        },
-        errorCount: {
-            type: Number,
-            default: 0,
-        },
-    },
-};
-</script>
-<style lang="css" scoped>
-.progressNote {
+
+<style scoped>
+.progress-note {
     position: absolute;
     text-align: center;
     width: 100%;
 }
-.progressContainer {
+.progress-container {
     position: relative;
 }
 </style>
diff --git a/client/src/components/RuleBuilder/RegularExpressionInput.vue b/client/src/components/RuleBuilder/RegularExpressionInput.vue
index 3f7c089adf8071203717a9aa1d6ac4544cde4a4f..b3788e423abe65e3f0717debf76b98be3a0b86b7 100644
--- a/client/src/components/RuleBuilder/RegularExpressionInput.vue
+++ b/client/src/components/RuleBuilder/RegularExpressionInput.vue
@@ -1,7 +1,7 @@
 <template>
     <div>
-        <label v-b-tooltip.hover for="regular_expression" :title="title">{{ label }}</label>
-        <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
+        <label ref="helpTarget" v-b-tooltip.hover for="regular_expression">{{ label }}</label>
+        <HelpPopover :target="$refs.helpTarget" term="programming.python.regex" />
         <input
             v-b-tooltip.hover.left
             :title="title"
@@ -16,7 +16,10 @@
 <script>
 import _l from "utils/localization";
 
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
 export default {
+    components: { HelpPopover },
     props: {
         target: {
             required: true,
@@ -32,11 +35,6 @@ export default {
         popoverTitle() {
             return _l("Regular Expressions");
         },
-        popoverContent() {
-            return _l(
-                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/tutorial/regex.html">this Python for Biologists tutorial</a>.`
-            );
-        },
     },
 };
 </script>
diff --git a/client/src/components/SchemaOrg/CreatorEditor.vue b/client/src/components/SchemaOrg/CreatorEditor.vue
index 1310a1a2dfac70b564f7c3ba265cac4a15e9f9f0..7a5c6882fc95590b9d5661b01d27e7f5c697e8d9 100644
--- a/client/src/components/SchemaOrg/CreatorEditor.vue
+++ b/client/src/components/SchemaOrg/CreatorEditor.vue
@@ -10,12 +10,24 @@
             <div v-for="(creator, index) in creatorsCurrent" :key="index">
                 <CreatorViewer :creator="creator">
                     <template v-slot:buttons>
-                        <span v-b-tooltip.hover title="Edit Creator"
-                            ><FontAwesomeIcon icon="edit" @click="onEdit(index)"
-                        /></span>
-                        <span v-b-tooltip.hover title="Remove Creator">
-                            <FontAwesomeIcon icon="times" @click="onRemove(index)" />
-                        </span>
+                        <BButton
+                            v-b-tooltip.hover
+                            class="inline-icon-button"
+                            variant="link"
+                            size="sm"
+                            title="Edit Creator"
+                            @click="onEdit(index)">
+                            <FontAwesomeIcon icon="edit" />
+                        </BButton>
+                        <BButton
+                            v-b-tooltip.hover
+                            class="inline-icon-button"
+                            variant="link"
+                            size="sm"
+                            title="Remove Creator"
+                            @click="onRemove(index)">
+                            <FontAwesomeIcon icon="times" />
+                        </BButton>
                     </template>
                 </CreatorViewer>
             </div>
diff --git a/client/src/components/SelectionDialog/BasicSelectionDialog.vue b/client/src/components/SelectionDialog/BasicSelectionDialog.vue
index d80167ca3f7e26aeacdd38341657408a7c2e2a25..9697de20104b8200f78f8bd0713af0b1bec2296a 100644
--- a/client/src/components/SelectionDialog/BasicSelectionDialog.vue
+++ b/client/src/components/SelectionDialog/BasicSelectionDialog.vue
@@ -1,7 +1,6 @@
 <script setup lang="ts">
 import { computed, onMounted, type Ref, ref } from "vue";
 
-import { ApiResponse } from "@/api/schema";
 import { type SelectionItem } from "@/components/SelectionDialog/selectionTypes";
 import { errorMessageAsString } from "@/utils/simple-error";
 
@@ -9,7 +8,7 @@ import SelectionDialog from "@/components/SelectionDialog/SelectionDialog.vue";
 
 interface Props {
     detailsKey?: string;
-    getData: () => Promise<ApiResponse<Array<object>>>;
+    getData: () => Promise<object[]>;
     isEncoded?: boolean;
     labelKey?: string;
     leafIcon?: string;
@@ -51,8 +50,9 @@ const fields = computed(() => {
 async function load() {
     optionsShow.value = false;
     try {
-        const response = await props.getData();
-        const incoming = response.data;
+        // TODO: Consider supporting pagination here
+        // this could potentially load quite a lot of items
+        const incoming = await props.getData();
         items.value = incoming.map((item: any) => {
             const timeStamp = item[props.timeKey];
             showTime.value = !!timeStamp;
diff --git a/client/src/components/SelectionDialog/HistoryDatasetPicker.vue b/client/src/components/SelectionDialog/HistoryDatasetPicker.vue
new file mode 100644
index 0000000000000000000000000000000000000000..598146cb699e9bcaa2901b5ffc1c249599d5289f
--- /dev/null
+++ b/client/src/components/SelectionDialog/HistoryDatasetPicker.vue
@@ -0,0 +1,325 @@
+<script setup lang="ts">
+import { faHdd } from "@fortawesome/free-solid-svg-icons";
+import { computed, ref, set } from "vue";
+
+import { GalaxyApi, type HDASummary, type HistorySortByLiteral, type HistorySummary } from "@/api";
+import { HistoriesFilters } from "@/components/History/HistoriesFilters";
+import {
+    type ItemsProvider,
+    type ItemsProviderContext,
+    SELECTION_STATES,
+    type SelectionItem,
+} from "@/components/SelectionDialog/selectionTypes";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import SelectionDialog from "@/components/SelectionDialog/SelectionDialog.vue";
+
+interface HistoryRecord extends SelectionItem {
+    size: number;
+}
+
+interface Props {
+    folderId: string;
+    title?: string;
+    actionButtonText?: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    title: "Select datasets from your histories",
+    actionButtonText: "Select",
+});
+
+const emit = defineEmits<{
+    (e: "reload"): void;
+    (e: "onClose"): void;
+    (e: "onSelect", datasets: SelectionItem[]): void;
+}>();
+
+const selectionDialog = ref();
+
+const totalItems = ref(0);
+const loading = ref(false);
+const hasValue = ref(false);
+const modalShow = ref(true);
+const errorMessage = ref("");
+const submitting = ref(false);
+const allSelected = ref(false);
+const datasetsVisible = ref(false);
+
+const items = ref<SelectionItem[]>([]);
+const selected = ref<SelectionItem[]>([]);
+
+const itemsProvider = ref<ItemsProvider>(historiesProvider);
+
+const searchTitle = computed(() => {
+    if (datasetsVisible.value) {
+        return "datasets";
+    } else {
+        return "search histories";
+    }
+});
+const okButtonText = computed(() => {
+    if (selected.value.length === 0) {
+        return props.actionButtonText;
+    } else {
+        return `${props.actionButtonText} ${selected.value.length} dataset${selected.value.length > 1 ? "s" : ""}`;
+    }
+});
+const fields = computed(() => {
+    if (datasetsVisible.value) {
+        return [
+            { key: "label", label: "Name", sortable: true },
+            { key: "update_time", label: "Last Updated", sortable: true },
+        ];
+    } else {
+        return [
+            { key: "label", label: "History Name" },
+            { key: "size", label: "Datasets", sortable: false },
+            { key: "update_time", label: "Last Updated" },
+        ];
+    }
+});
+const selectAllIcon = computed(() => {
+    if (allSelected.value) {
+        return SELECTION_STATES.SELECTED;
+    } else if (selected.value.length > 0) {
+        return SELECTION_STATES.MIXED;
+    } else {
+        return SELECTION_STATES.UNSELECTED;
+    }
+});
+
+function historyEntryToRecord(entry: HistorySummary): HistoryRecord {
+    const result = {
+        id: entry.id,
+        label: entry.name,
+        details: entry.annotation || "",
+        isLeaf: false,
+        url: entry.url,
+        size: entry.count,
+        update_time: entry.update_time,
+    };
+
+    return result;
+}
+
+function datasetEntryToRecord(entry: HDASummary): SelectionItem {
+    const result = {
+        id: entry.id,
+        label: entry.name || "",
+        details: "",
+        isLeaf: true,
+        url: entry.url,
+        update_time: entry.update_time,
+    };
+
+    return result;
+}
+
+function formatRows() {
+    hasValue.value = selected.value.length > 0;
+
+    for (const item of items.value) {
+        if (item.isLeaf) {
+            const _rowVariant =
+                selected.value.findIndex((i) => i.id === item.id) !== -1
+                    ? SELECTION_STATES.SELECTED
+                    : SELECTION_STATES.UNSELECTED;
+
+            set(item, "_rowVariant", _rowVariant);
+        }
+    }
+
+    allSelected.value = checkIfAllSelected();
+}
+
+function checkIfAllSelected(): boolean {
+    return Boolean(
+        items.value.length &&
+            items.value.every((item) => {
+                return selected.value.findIndex((i) => i.id === item.id) !== -1;
+            })
+    );
+}
+
+async function historiesProvider(ctx: ItemsProviderContext, url?: string): Promise<SelectionItem[]> {
+    loading.value = true;
+
+    try {
+        const filter = ctx.filter;
+
+        if (filter) {
+            selectionDialog.value?.resetPagination();
+        }
+
+        const limit = ctx.perPage;
+        const offset = (ctx.currentPage - 1) * ctx.perPage;
+        const sortDesc = ctx.sortDesc;
+        const sortBy: HistorySortByLiteral =
+            ctx.sortBy === "label" ? "name" : (ctx.sortBy as HistorySortByLiteral) || "update_time";
+        const queryDict = HistoriesFilters.getQueryDict(ctx.filter);
+
+        const { response, data, error } = await GalaxyApi().GET("/api/histories", {
+            params: {
+                query: {
+                    search: filter,
+                    view: "summary",
+                    keys: "create_time",
+                    show_own: true,
+                    offset: offset,
+                    limit: limit,
+                    q: Object.keys(queryDict),
+                    qv: Object.values(queryDict),
+                    sort_by: sortBy,
+                    sort_desc: sortDesc,
+                },
+            },
+        });
+
+        if (error) {
+            errorMessage.value = errorMessageAsString(error);
+            return [];
+        }
+
+        totalItems.value = parseInt(response.headers.get("total_matches") ?? "0");
+
+        items.value = (data as HistorySummary[]).map(historyEntryToRecord);
+
+        formatRows();
+
+        return items.value;
+    } catch (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return [];
+    } finally {
+        loading.value = false;
+    }
+}
+
+async function datasetsProvider(ctx: ItemsProviderContext, selectedHistory: HistoryRecord) {
+    loading.value = true;
+
+    try {
+        const limit = ctx.perPage;
+        const offset = (ctx.currentPage - 1) * ctx.perPage;
+        const query = ctx.filter || "";
+        const querySortBy = ctx.sortBy === "time" ? "update_time" : "name";
+        const sortPrefix = ctx.sortDesc ? "-dsc" : "-asc";
+
+        const { response, data, error } = await GalaxyApi().GET("/api/datasets", {
+            params: {
+                query: {
+                    history_id: selectedHistory.id,
+                    q: ["name-contains"],
+                    qv: [query],
+                    order: `${querySortBy}${sortPrefix}`,
+                    offset: offset,
+                    limit: limit,
+                },
+            },
+        });
+
+        if (error) {
+            errorMessage.value = errorMessageAsString(error);
+            return [];
+        }
+
+        totalItems.value = parseInt(response.headers.get("total_matches") ?? "0");
+
+        items.value = (data as HDASummary[]).map(datasetEntryToRecord);
+
+        formatRows();
+
+        return items.value;
+    } catch (error) {
+        errorMessage.value = errorMessageAsString(error);
+
+        return [];
+    } finally {
+        loading.value = false;
+    }
+}
+
+function onHistoryClick(item: SelectionItem) {
+    if (!item.isLeaf) {
+        selectionDialog.value?.resetFilter();
+        selectionDialog.value?.resetPagination();
+        datasetsVisible.value = true;
+        itemsProvider.value = (ctx: ItemsProviderContext) => datasetsProvider(ctx, item as HistoryRecord);
+    }
+}
+
+async function onDatasetClick(item: SelectionItem) {
+    if (item.isLeaf) {
+        if (selected.value.findIndex((i) => i.id === item.id) !== -1) {
+            selected.value = selected.value.filter((i) => i.id !== item.id);
+        } else {
+            selected.value.push(item);
+        }
+
+        formatRows();
+    }
+}
+
+function selectAll() {
+    if (allSelected.value) {
+        selected.value = [];
+    } else {
+        for (const item of items.value) {
+            if (selected.value.findIndex((i) => i.id === item.id) === -1) {
+                selected.value.push(item);
+            }
+        }
+    }
+
+    formatRows();
+}
+
+async function onUndo() {
+    selectionDialog.value?.resetFilter();
+    selectionDialog.value?.resetPagination();
+    selected.value = [];
+    datasetsVisible.value = false;
+    itemsProvider.value = historiesProvider;
+}
+
+function onOk() {
+    emit("onSelect", selected.value);
+    emit("onClose");
+}
+
+function onCancel() {
+    modalShow.value = false;
+
+    emit("onClose");
+}
+</script>
+
+<template>
+    <SelectionDialog
+        ref="selectionDialog"
+        options-show
+        :disable-ok="!hasValue || submitting"
+        :fields="fields"
+        :ok-button-text="okButtonText"
+        :modal-show="modalShow"
+        :file-mode="false"
+        :multiple="true"
+        :select-all-variant="selectAllIcon"
+        :items="items"
+        :undo-show="datasetsVisible"
+        :total-items="totalItems"
+        :items-provider="itemsProvider"
+        :show-select-icon="datasetsVisible"
+        :folder-icon="faHdd"
+        :is-busy="loading"
+        :search-title="searchTitle"
+        :title="title"
+        :filter-class="datasetsVisible ? undefined : HistoriesFilters"
+        @onOk="onOk"
+        @onUndo="onUndo"
+        @onCancel="onCancel"
+        @onSelectAll="selectAll"
+        @onOpen="onHistoryClick"
+        @onClick="onDatasetClick" />
+</template>
diff --git a/client/src/components/SelectionDialog/SelectionDialog.vue b/client/src/components/SelectionDialog/SelectionDialog.vue
index ea501a7594112b018f260b33ca0cf69ea7c1eced..b05d8d1ee08c83b94d25a1090305ed88a8578ac7 100644
--- a/client/src/components/SelectionDialog/SelectionDialog.vue
+++ b/client/src/components/SelectionDialog/SelectionDialog.vue
@@ -1,15 +1,18 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
+import { type IconDefinition, library } from "@fortawesome/fontawesome-svg-core";
 import { faCheckSquare, faMinusSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
 import { faCaretLeft, faCheck, faFolder, faSpinner, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton, BLink, BModal, BPagination, BSpinner, BTable } from "bootstrap-vue";
 import { computed, ref, watch } from "vue";
 
-import { ItemsProvider, SELECTION_STATES } from "@/components/SelectionDialog/selectionTypes";
+import { type ItemsProvider, SELECTION_STATES, type SelectionState } from "@/components/SelectionDialog/selectionTypes";
+import type Filtering from "@/utils/filtering";
 
 import { type FieldEntry, type SelectionItem } from "./selectionTypes";
 
+import FilterMenu from "@/components/Common/FilterMenu.vue";
+import Heading from "@/components/Common/Heading.vue";
 import DataDialogSearch from "@/components/SelectionDialog/DataDialogSearch.vue";
 import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
 
@@ -30,14 +33,18 @@ interface Props {
     providerUrl?: string;
     totalItems?: number;
     leafIcon?: string;
+    folderIcon?: IconDefinition;
     modalShow?: boolean;
     modalStatic?: boolean;
     multiple?: boolean;
     optionsShow?: boolean;
     undoShow?: boolean;
-    selectAllIcon?: string;
+    selectAllVariant?: SelectionState;
     showSelectIcon?: boolean;
     title?: string;
+    searchTitle?: string;
+    okButtonText?: string;
+    filterClass?: Filtering<any>;
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -52,14 +59,18 @@ const props = withDefaults(defineProps<Props>(), {
     providerUrl: undefined,
     totalItems: 0,
     leafIcon: "fa fa-file-o",
+    folderIcon: () => faFolder,
     modalShow: true,
     modalStatic: false,
     multiple: false,
     optionsShow: false,
     undoShow: false,
-    selectAllIcon: SELECTION_STATES.UNSELECTED,
+    selectAllVariant: SELECTION_STATES.UNSELECTED,
     showSelectIcon: false,
     title: "",
+    searchTitle: undefined,
+    okButtonText: "Select",
+    filterClass: undefined,
 });
 
 const emit = defineEmits<{
@@ -74,6 +85,11 @@ const emit = defineEmits<{
 const filter = ref("");
 const currentPage = ref(1);
 const perPage = ref(25);
+const showAdvancedSearch = ref(false);
+
+const okButtonText = computed(() => {
+    return props.okButtonText ? props.okButtonText : props.fileMode ? "Select" : "Select this folder";
+});
 
 const fieldDetails = computed(() => {
     const fields = props.fields.slice().map((x) => {
@@ -101,9 +117,9 @@ function selectionIcon(variant: string) {
 }
 
 /** Resets pagination when a filter/search word is entered **/
-function filtered(items: Array<SelectionItem>) {
+function filtered(items: SelectionItem[]) {
     if (props.itemsProvider === undefined) {
-        currentPage.value = 1;
+        resetPagination();
     }
 }
 
@@ -123,6 +139,19 @@ function formatTime(value: string) {
     }
 }
 
+function resetFilter() {
+    filter.value = "";
+}
+
+function resetPagination() {
+    currentPage.value = 1;
+}
+
+defineExpose({
+    resetFilter,
+    resetPagination,
+});
+
 watch(
     () => props.items,
     () => {
@@ -135,7 +164,7 @@ watch(
     () => {
         // We need to reset the current page when drilling down sub-folders
         if (props.itemsProvider !== undefined) {
-            currentPage.value = 1;
+            resetPagination();
         }
     }
 );
@@ -145,11 +174,27 @@ watch(
     <BModal
         v-if="modalShow"
         modal-class="selection-dialog-modal"
+        header-class="flex-column"
         visible
         :static="modalStatic"
+        :title="title"
         @hide="emit('onCancel')">
         <template v-slot:modal-header>
-            <DataDialogSearch v-model="filter" :title="title" />
+            <slot name="header">
+                <Heading v-if="props.title" h2> {{ props.title }} </Heading>
+
+                <FilterMenu
+                    v-if="props.filterClass"
+                    :name="props.title"
+                    class="w-100"
+                    :placeholder="props.searchTitle || props.title"
+                    :filter-class="props.filterClass"
+                    :filter-text.sync="filter"
+                    :loading="props.isBusy"
+                    :show-advanced.sync="showAdvancedSearch" />
+
+                <DataDialogSearch v-else v-model="filter" :title="props.searchTitle || props.title" />
+            </slot>
         </template>
         <slot name="helper" />
         <BAlert v-if="errorMessage" variant="danger" show>
@@ -174,7 +219,7 @@ watch(
                         <FontAwesomeIcon
                             class="select-checkbox cursor-pointer"
                             title="Check to select all datasets"
-                            :icon="selectionIcon(selectAllIcon)"
+                            :icon="selectionIcon(selectAllVariant)"
                             @click="$emit('onSelectAll')" />
                     </template>
                     <template v-slot:cell(__select_icon__)="data">
@@ -191,7 +236,7 @@ watch(
                                     <span :title="`label-${data.item.url}`">{{ data.value ? data.value : "-" }}</span>
                                 </div>
                                 <div v-else @click.stop="emit('onOpen', data.item)">
-                                    <FontAwesomeIcon :icon="faFolder" />
+                                    <FontAwesomeIcon :icon="props.folderIcon" />
                                     <BLink :title="`label-${data.item.url}`">{{ data.value ? data.value : "-" }}</BLink>
                                 </div>
                             </span>
@@ -216,7 +261,7 @@ watch(
                     <BSpinner small type="grow" />
                     <BSpinner small type="grow" />
                 </div>
-                <div v-if="totalItems === 0">
+                <div v-else-if="totalItems === 0">
                     <div v-if="filter">
                         No search results found for: <b>{{ filter }}</b
                         >.
@@ -262,7 +307,7 @@ watch(
                         :disabled="disableOk"
                         @click="emit('onOk')">
                         <FontAwesomeIcon :icon="faCheck" />
-                        {{ fileMode ? "Ok" : "Select this folder" }}
+                        {{ okButtonText }}
                     </BButton>
                 </div>
             </div>
diff --git a/client/src/components/SelectionDialog/selectionTypes.ts b/client/src/components/SelectionDialog/selectionTypes.ts
index 894030920918df4a93c741c23eb64b083cf1c13a..aac6ebb4e0da53cc52698208de8953efd8c55b58 100644
--- a/client/src/components/SelectionDialog/selectionTypes.ts
+++ b/client/src/components/SelectionDialog/selectionTypes.ts
@@ -2,7 +2,9 @@ export const SELECTION_STATES = {
     SELECTED: "success",
     UNSELECTED: "default",
     MIXED: "secondary",
-};
+} as const;
+
+export type SelectionState = (typeof SELECTION_STATES)[keyof typeof SELECTION_STATES];
 
 export interface FieldEntry {
     key: string;
@@ -16,6 +18,7 @@ export interface SelectionItem {
     details: string;
     isLeaf: boolean;
     url: string;
+    _rowVariant?: SelectionState;
 }
 
 export interface ItemsProviderContext {
diff --git a/client/src/components/Sharing/SlugInput.vue b/client/src/components/Sharing/SlugInput.vue
index fc356dd4ad8f27348e4086fb5bb2b7fded07325d..8c9751ccca62fedd0ddf6f9daacc12203f1935dc 100644
--- a/client/src/components/Sharing/SlugInput.vue
+++ b/client/src/components/Sharing/SlugInput.vue
@@ -15,7 +15,7 @@ const initialSlug = props.slug;
 function onChange(value: string) {
     const slugFormatted = value
         .replace(/\s+/g, "-")
-        .replace(/[^a-zA-Z0-9-]/g, "")
+        .replace(/[/:?#]/g, "")
         .toLowerCase();
 
     emit("change", slugFormatted);
diff --git a/client/src/components/Sharing/UserSharing.vue b/client/src/components/Sharing/UserSharing.vue
index f85b5c22391393b969597b029d646b5dc392450a..270d80548a895a4bf95a0d84aac65ee8041b6dad 100644
--- a/client/src/components/Sharing/UserSharing.vue
+++ b/client/src/components/Sharing/UserSharing.vue
@@ -239,7 +239,7 @@ defineExpose({
                 class="mb-4">
                 <BFormSelect v-model="selectedSharingOption">
                     <BFormSelectOption value="make_public"> Make datasets public </BFormSelectOption>
-                    <BFormSelectOption value="make_accessible_and_shared">
+                    <BFormSelectOption value="make_accessible_to_shared">
                         Make datasets private to me and users this {{ modelClass }} is shared with
                     </BFormSelectOption>
                     <BFormSelectOption value="no_changes"> Share {{ modelClass }} anyways </BFormSelectOption>
diff --git a/client/src/components/SingleItemSelector.vue b/client/src/components/SingleItemSelector.vue
index 5148339547d9a7f7c5ebb0e67f82b07ce56264d1..0e78463372524ff96160e40915850760c5ec4f27 100644
--- a/client/src/components/SingleItemSelector.vue
+++ b/client/src/components/SingleItemSelector.vue
@@ -5,8 +5,8 @@
             v-if="items"
             v-model="selectedItem"
             :deselect-label="null"
-            track-by="id"
-            label="text"
+            :track-by="trackBy"
+            :label="label"
             :options="items"
             :searchable="true"
             :allow-empty="false"
@@ -54,9 +54,17 @@ export default {
             default: null,
         },
         /** The initially selected item. */
-        currentItemId: {
+        currentItem: {
+            type: Object,
+            default: null,
+        },
+        label: {
+            type: String,
+            default: "text",
+        },
+        trackBy: {
             type: String,
-            required: true,
+            default: "id",
         },
     },
     data() {
@@ -72,7 +80,7 @@ export default {
     },
     watch: {
         items: function () {
-            this.selectedItem = this.items.find((item) => item.id == this.currentItemId);
+            this.selectedItem = this.currentItem;
         },
     },
     methods: {
diff --git a/client/src/components/StsDownloadButton.test.js b/client/src/components/StsDownloadButton.test.js
index 4796e9e66b526a136561b377409622c4cc816ff3..e35f720a59b0289d3c40db815a05443c962724c6 100644
--- a/client/src/components/StsDownloadButton.test.js
+++ b/client/src/components/StsDownloadButton.test.js
@@ -7,11 +7,9 @@ import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
 
-import StsDownloadButton from "./StsDownloadButton";
-
-jest.mock("@/api/schema");
+import StsDownloadButton from "./StsDownloadButton.vue";
 
 const localVue = getLocalVue();
 const NO_TASKS_CONFIG = {
@@ -24,8 +22,15 @@ const FALLBACK_URL = "http://cow.com/direct_download";
 const DOWNLOAD_ENDPOINT = "http://cow.com/prepare_download";
 const STORAGE_REQUEST_ID = "moocow1235";
 
+const { server, http } = useServerMock();
+
 async function mountStsDownloadButtonWrapper(config) {
-    mockFetcher.path("/api/configuration").method("get").mock({ data: config });
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json(config);
+        })
+    );
+
     const pinia = createPinia();
     const wrapper = mount(StsDownloadButton, {
         propsData: {
@@ -57,7 +62,7 @@ describe("StsDownloadButton", () => {
         const wrapper = await mountStsDownloadButtonWrapper(NO_TASKS_CONFIG);
         wrapper.vm.onDownload(NO_TASKS_CONFIG);
         await flushPromises();
-        expect(window.open).toBeCalled();
+        expect(window.open).toHaveBeenCalled();
     });
 
     it("should poll until ready", async () => {
diff --git a/client/src/components/Tags/model.test.js b/client/src/components/Tags/model.test.js
index ce421e7c0c50f2db4e859d43bc401885c59f87ae..c70736920aeb343676311fc5bfaf76335379c0fb 100644
--- a/client/src/components/Tags/model.test.js
+++ b/client/src/components/Tags/model.test.js
@@ -64,13 +64,35 @@ describe("Tags/model.js", () => {
 
     describe("Tag matching regular expression tests", () => {
         it("Should allow valid tags", () => {
-            const validTags = ["tag1", "tag.subtag", "tag.subtag.subtag", "tag.subtag:value", "🌌", "name:🌌", "🌌.🌌"];
+            const validTags = [
+                "tag1",
+                "tag.subtag",
+                "tag.subtag.subtag",
+                "tag.subtag:value",
+                "🌌",
+                "name:🌌",
+                "🌌.🌌",
+                "name:value..separated",
+            ];
             for (const tag of validTags) {
                 expect(VALID_TAG_RE.test(tag)).toBeTruthy();
             }
         });
         it("Should not allow invalid tags", () => {
-            const invalidTags = ["", " ", ".", "..", "...", ":", ":value", "tag:", "tag.", ".tag"];
+            const invalidTags = [
+                "",
+                " ",
+                ".",
+                "..",
+                "...",
+                ":",
+                ":value",
+                "tag:",
+                "tag.",
+                ".tag",
+                "tag..subtag:value",
+                "tag:no spaces in value",
+            ];
             for (const tag of invalidTags) {
                 expect(VALID_TAG_RE.test(tag)).toBeFalsy();
             }
diff --git a/client/src/components/TagsMultiselect/StatelessTags.vue b/client/src/components/TagsMultiselect/StatelessTags.vue
index dfc30060dbb9802550f2d2a4fcee00d68fbeedf0..7f2256a4aaa3fa0d333012b9bff520524db46cef 100644
--- a/client/src/components/TagsMultiselect/StatelessTags.vue
+++ b/client/src/components/TagsMultiselect/StatelessTags.vue
@@ -7,6 +7,8 @@ import { useToast } from "@/composables/toast";
 import { useUid } from "@/composables/utils/uid";
 import { useUserTagsStore } from "@/stores/userTagsStore";
 
+import { VALID_TAG_RE } from "../Tags/model";
+
 import HeadlessMultiselect from "./HeadlessMultiselect.vue";
 import Tag from "./Tag.vue";
 
@@ -84,10 +86,8 @@ const slicedTags = computed(() => {
     }
 });
 
-const invalidTagRegex = /([.:\s][.:\s])|(^[.:])|([.:]$)|(^[\s]*$)/;
-
 function isValid(tag: string) {
-    return !tag.match(invalidTagRegex);
+    return tag.match(VALID_TAG_RE);
 }
 
 function onTagClicked(tag: string) {
diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index d28e4d46ad96ee486374c238a7fcfea1681ad25a..f76955803d2bf55890b0b94a2da6e0da1014f84f 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -118,7 +118,7 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable
 
 <template>
     <div class="position-relative">
-        <div class="underlay sticky-top" />
+        <div class="ui-form-header-underlay sticky-top" />
         <div class="tool-header sticky-top bg-secondary px-2 py-1 rounded">
             <div class="d-flex justify-content-between">
                 <div class="py-1 d-flex flex-wrap flex-gapx-1">
@@ -186,7 +186,7 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable
         <div>
             <div v-if="props.options.help" class="mt-2 mb-4">
                 <Heading h2 separator bold size="sm"> Help </Heading>
-                <ToolHelp :content="props.options.help" />
+                <ToolHelp :content="props.options.help" :format="props.options.help_format" />
             </div>
 
             <ToolTutorialRecommendations
@@ -209,19 +209,6 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable
 </template>
 
 <style lang="scss" scoped>
-@import "scss/theme/blue.scss";
-
-.underlay::after {
-    content: "";
-    display: block;
-    position: absolute;
-    top: -$margin-h;
-    left: -0.5rem;
-    right: -0.5rem;
-    height: 50px;
-    background: linear-gradient($white 75%, change-color($white, $alpha: 0));
-}
-
 .fa-wrench {
     cursor: unset;
 }
diff --git a/client/src/components/Tool/ToolForm.test.js b/client/src/components/Tool/ToolForm.test.js
index 7ceb7de148841e701d13b5b4af024f883f8b773f..ddb9f850d2bf3011278c5f9f9ea1e52170b973ca 100644
--- a/client/src/components/Tool/ToolForm.test.js
+++ b/client/src/components/Tool/ToolForm.test.js
@@ -1,18 +1,19 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
-import MockCurrentHistory from "components/providers/MockCurrentHistory";
+import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
-import { useUserStore } from "stores/userStore";
 import { getLocalVue } from "tests/jest/helpers";
-import Vue from "vue";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
+import MockCurrentHistory from "@/components/providers/MockCurrentHistory";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
 
-import ToolForm from "./ToolForm";
+import ToolForm from "./ToolForm.vue";
 
-jest.mock("@/api/schema");
+const { server, http } = useServerMock();
 
 const localVue = getLocalVue();
 const pinia = createPinia();
@@ -24,26 +25,28 @@ describe("ToolForm", () => {
     let historyStore;
 
     beforeEach(() => {
-        mockFetcher
-            .path("/api/configuration")
-            .method("get")
-            .mock({ data: { enable_tool_source_display: false, object_store_allows_id_selection: false } });
+        server.use(
+            http.get("/api/configuration", ({ response }) => {
+                return response.untyped(
+                    HttpResponse.json({
+                        enable_tool_source_display: false,
+                        object_store_allows_id_selection: false,
+                    })
+                );
+            })
+        );
 
         axiosMock = new MockAdapter(axios);
-
-        const toolData = {
+        axiosMock.onGet(`/api/tools/tool_id/build?tool_version=version`).reply(200, {
             id: "tool_id",
             name: "tool_name",
             version: "version",
             inputs: [],
             help: "help_text",
             creator: [{ class: "Person", givenName: "FakeName", familyName: "FakeSurname", email: "fakeEmail" }],
-        };
-        axiosMock.onGet(`/api/tools/tool_id/build?tool_version=version`).reply(200, toolData);
+        });
         axiosMock.onGet(`/api/webhooks`).reply(200, []);
-
-        const citations = [];
-        axiosMock.onGet(`/api/tools/tool_id/citations`).reply(200, citations);
+        axiosMock.onGet(`/api/tools/tool_id/citations`).reply(200, []);
 
         wrapper = mount(ToolForm, {
             propsData: {
@@ -58,7 +61,8 @@ describe("ToolForm", () => {
             pinia,
         });
         userStore = useUserStore();
-        userStore.currentUser = { id: "fakeUser" };
+        userStore.currentUser = getFakeRegisteredUser({ id: "fakeUser" });
+
         historyStore = useHistoryStore();
         historyStore.setHistories([{ id: "fakeHistory" }]);
         historyStore.setCurrentHistoryId("fakeHistory");
@@ -70,7 +74,7 @@ describe("ToolForm", () => {
     });
 
     it("shows props", async () => {
-        await Vue.nextTick();
+        await flushPromises();
         const button = wrapper.find(".btn-primary");
         expect(button.attributes("title")).toBe("Run tool: tool_name (version)");
         const dropdown = wrapper.findAll(".dropdown-item");
diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 33e430d1a1a89f0e9c40d099fa5a1ca83e305892..cf05496cfed9e1e3927da95833e1e3acd50b2876 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -14,7 +14,7 @@
             <b-alert v-if="errorMessage" show variant="danger">
                 {{ errorMessage }}
             </b-alert>
-            <b-alert show variant="warning">
+            <b-alert v-if="submissionRequestFailed" show variant="warning">
                 The server could not complete this request. Please verify your parameter settings, retry submission and
                 contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.
             </b-alert>
@@ -194,6 +194,7 @@ export default {
             entryPoints: [],
             jobDef: {},
             jobResponse: {},
+            submissionRequestFailed: false,
             validationInternal: null,
             validationScrollTo: null,
             currentVersion: this.version,
@@ -248,6 +249,9 @@ export default {
         canMutateHistory() {
             return this.currentHistory && canMutateHistory(this.currentHistory);
         },
+        runButtonTitle() {
+            return "Run Tool";
+        },
     },
     watch: {
         currentHistoryId() {
@@ -305,6 +309,7 @@ export default {
             console.debug("ToolForm - Requesting tool.", this.id);
             return getToolFormData(this.id, this.currentVersion, this.job_id, this.history_id)
                 .then((data) => {
+                    this.currentVersion = data.version;
                     this.formConfig = data;
                     this.remapAllowed = this.job_id && data.job_remap;
                     this.showForm = true;
@@ -361,6 +366,7 @@ export default {
             const prevRoute = this.$route.fullPath;
             submitJob(jobDef).then(
                 (jobResponse) => {
+                    this.submissionRequestFailed = false;
                     this.showExecuting = false;
                     let changeRoute = false;
                     refreshContentsWrapper();
@@ -369,7 +375,7 @@ export default {
                         this.entryPoints = jobResponse.jobs;
                     }
                     const nJobs = jobResponse && jobResponse.jobs ? jobResponse.jobs.length : 0;
-                    if (nJobs > 0) {
+                    if (nJobs > 0 && !jobResponse.errors?.length) {
                         this.showForm = false;
                         const toolName = this.toolName;
                         this.saveLatestResponse({
@@ -379,10 +385,23 @@ export default {
                         });
                         changeRoute = prevRoute === this.$route.fullPath;
                     } else {
+                        const defaultErrorTitle = "Job submission rejected.";
                         this.showError = true;
                         this.showForm = true;
-                        this.errorTitle = "Job submission rejected.";
-                        this.errorContent = jobResponse;
+                        if (jobResponse?.errors) {
+                            const nErrors = jobResponse.errors.length;
+                            if (nJobs > 0) {
+                                this.errorTitle = `Job submission for ${nErrors} out of ${
+                                    nJobs + nErrors
+                                } jobs failed.`;
+                            } else {
+                                this.errorTitle = defaultErrorTitle;
+                            }
+                            this.errorContent = jobResponse.errors;
+                        } else {
+                            this.errorTitle = defaultErrorTitle;
+                            this.errorContent = jobResponse;
+                        }
                     }
                     if (changeRoute) {
                         this.$router.push(`/jobs/submission/success`);
@@ -395,6 +414,7 @@ export default {
                 },
                 (e) => {
                     this.errorMessage = e?.response?.data?.err_msg;
+                    this.submissionRequestFailed = true;
                     this.showExecuting = false;
                     let genericError = true;
                     const errorData = e && e.response && e.response.data && e.response.data.err_data;
diff --git a/client/src/components/Tool/ToolHelp.vue b/client/src/components/Tool/ToolHelp.vue
index 88420b8b2ee6f7fca5e60bd1c2cd6b7e4d876c15..a246fcd60296ba50a075225e207a4c74ebca362a 100644
--- a/client/src/components/Tool/ToolHelp.vue
+++ b/client/src/components/Tool/ToolHelp.vue
@@ -1,42 +1,18 @@
-<script setup>
-import { useFormattedToolHelp } from "composables/formattedToolHelp";
-
-const props = defineProps({
-    content: {
-        type: String,
-        required: true,
-    },
-});
-
-const { formattedContent } = useFormattedToolHelp(props.content);
+<script setup lang="ts">
+import ToolHelpMarkdown from "./ToolHelpMarkdown.vue";
+import ToolHelpRst from "./ToolHelpRst.vue";
+
+defineProps<{
+    format: string;
+    content: string;
+}>();
 </script>
-
 <template>
-    <div class="form-help form-text" v-html="formattedContent" />
+    <span>
+        <ToolHelpMarkdown v-if="format == 'markdown'" :content="content" />
+        <ToolHelpRst v-else-if="format == 'restructuredtext'" :content="content" />
+        <div v-else class="form-help form-text">
+            {{ content }}
+        </div>
+    </span>
 </template>
-
-<style lang="scss" scoped>
-@import "scss/theme/blue.scss";
-
-.form-help {
-    &:deep(h3) {
-        font-size: $h4-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h4) {
-        font-size: $h5-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h5) {
-        font-size: $h6-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h6) {
-        font-size: $h6-font-size;
-        text-decoration: underline;
-    }
-}
-</style>
diff --git a/client/src/components/Tool/ToolHelpForum.vue b/client/src/components/Tool/ToolHelpForum.vue
index a3b14d538e23d54d797a43e684ec87b54a5ae3c6..8e389e4b0b78f773b4e0cba595211d2f72aa821a 100644
--- a/client/src/components/Tool/ToolHelpForum.vue
+++ b/client/src/components/Tool/ToolHelpForum.vue
@@ -3,7 +3,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton, BCard } from "bootstrap-vue";
 import { computed, onMounted, ref } from "vue";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import { useConfigStore } from "@/stores/configurationStore";
 import { getShortToolId } from "@/utils/tool";
 
@@ -19,8 +19,6 @@ const props = defineProps<{
 
 const toolHelpTag = "tool-help";
 
-const helpFetcher = fetcher.path("/api/help/forum/search").method("get").create();
-
 const topics = ref<HelpForumTopic[]>([]);
 const posts = ref<HelpForumPost[]>([]);
 const helpAvailable = computed(() => topics.value.length > 0);
@@ -31,12 +29,17 @@ const shortToolId = computed(() => getShortToolId(props.toolId));
 const query = computed(() => `tags:${shortToolId.value}+${toolHelpTag} status:solved`);
 
 onMounted(async () => {
-    const response = await helpFetcher({ query: query.value });
-
-    const data = response.data;
-
-    topics.value = (data.topics ?? []) as HelpForumTopic[];
-    posts.value = data.posts ?? [];
+    const { data, error } = await GalaxyApi().GET("/api/help/forum/search", {
+        params: {
+            query: { query: query.value },
+        },
+    });
+    if (error) {
+        console.error("Error fetching help forum data", error);
+    }
+
+    topics.value = data?.topics ?? [];
+    posts.value = data?.posts ?? [];
 });
 
 const displayCount = 5;
diff --git a/client/src/components/Tool/ToolHelpMarkdown.vue b/client/src/components/Tool/ToolHelpMarkdown.vue
new file mode 100644
index 0000000000000000000000000000000000000000..5fdda004e86b5549c24d265435a4cc1fabff9c78
--- /dev/null
+++ b/client/src/components/Tool/ToolHelpMarkdown.vue
@@ -0,0 +1,67 @@
+<script setup lang="ts">
+import { computed, onMounted, ref } from "vue";
+
+import { markup } from "@/components/ObjectStore/configurationMarkdown";
+import { useFormattedToolHelp } from "@/composables/formattedToolHelp";
+import { getAppRoot } from "@/onload/loadConfig";
+
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
+const props = defineProps<{
+    content: string;
+}>();
+
+const markdownHtml = computed(() => markup(props.content ?? "", false));
+// correct links and header information... this should work the same between rst and
+// markdown entirely I think.
+const { formattedContent } = useFormattedToolHelp(markdownHtml);
+
+const helpHtml = ref<HTMLDivElement>();
+
+interface InternalTypeReference {
+    element: HTMLElement;
+    term: string;
+}
+
+const internalHelpReferences = ref<InternalTypeReference[]>([]);
+
+function setupPopovers() {
+    internalHelpReferences.value.length = 0;
+    if (helpHtml.value) {
+        const links = helpHtml.value.getElementsByTagName("a");
+        Array.from(links).forEach((link) => {
+            if (link.href.startsWith("gxhelp://")) {
+                const uri = link.href.substr("gxhelp://".length);
+                internalHelpReferences.value.push({ element: link, term: uri });
+                link.href = `${getAppRoot()}help/terms/${uri}`;
+                link.style.color = "inherit";
+                link.style.textDecorationLine = "underline";
+                link.style.textDecorationStyle = "dashed";
+            }
+        });
+        const imgs = helpHtml.value.getElementsByTagName("img");
+        Array.from(imgs).forEach((img) => {
+            if (img.src.startsWith("gxstatic://")) {
+                const rest = img.src.substr("gxstatic://".length);
+                img.src = `${getAppRoot()}static/${rest}`;
+            }
+        });
+    }
+}
+
+onMounted(setupPopovers);
+</script>
+
+<template>
+    <span>
+        <!-- Disable v-html warning because we allow markdown generated HTML
+            in various places in the Galaxy interface. Raw HTML is not allowed
+            here because admin = false in the call to markup.
+        -->
+        <!-- eslint-disable-next-line vue/no-v-html -->
+        <div ref="helpHtml" v-html="formattedContent" />
+        <span v-for="(value, i) in internalHelpReferences" :key="i">
+            <HelpPopover :target="value.element" :term="value.term" />
+        </span>
+    </span>
+</template>
diff --git a/client/src/components/Tool/ToolHelp.test.js b/client/src/components/Tool/ToolHelpRst.test.js
similarity index 87%
rename from client/src/components/Tool/ToolHelp.test.js
rename to client/src/components/Tool/ToolHelpRst.test.js
index afbd19d4ba92fd5d3c2ae1f05fe756cd194b159d..40f8e95f2d1ed20fe89a0ef030b5ece92a6c3d49 100644
--- a/client/src/components/Tool/ToolHelp.test.js
+++ b/client/src/components/Tool/ToolHelpRst.test.js
@@ -1,7 +1,7 @@
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
-import ToolHelp from "./ToolHelp";
+import ToolHelpRst from "./ToolHelpRst";
 
 const localVue = getLocalVue();
 
@@ -25,9 +25,9 @@ const expectedHelpText = `
 <h6>h4 Heading</h6>
 <a target="_blank">empty link</a>`;
 
-describe("ToolHelp", () => {
+describe("ToolHelp RST", () => {
     it("modifies help text", () => {
-        const wrapper = mount(ToolHelp, {
+        const wrapper = mount(ToolHelpRst, {
             propsData: {
                 content: inputHelpText,
             },
diff --git a/client/src/components/Tool/ToolHelpRst.vue b/client/src/components/Tool/ToolHelpRst.vue
new file mode 100644
index 0000000000000000000000000000000000000000..88420b8b2ee6f7fca5e60bd1c2cd6b7e4d876c15
--- /dev/null
+++ b/client/src/components/Tool/ToolHelpRst.vue
@@ -0,0 +1,42 @@
+<script setup>
+import { useFormattedToolHelp } from "composables/formattedToolHelp";
+
+const props = defineProps({
+    content: {
+        type: String,
+        required: true,
+    },
+});
+
+const { formattedContent } = useFormattedToolHelp(props.content);
+</script>
+
+<template>
+    <div class="form-help form-text" v-html="formattedContent" />
+</template>
+
+<style lang="scss" scoped>
+@import "scss/theme/blue.scss";
+
+.form-help {
+    &:deep(h3) {
+        font-size: $h4-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h4) {
+        font-size: $h5-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h5) {
+        font-size: $h6-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h6) {
+        font-size: $h6-font-size;
+        text-decoration: underline;
+    }
+}
+</style>
diff --git a/client/src/components/Tool/ToolSelectPreferredObjectStore.test.js b/client/src/components/Tool/ToolSelectPreferredObjectStore.test.js
index e44f6fb0cfbd7487e865d1f5ecb7bac8c1362b9c..2bbad3ab37ca244cc89b3ecf5802748f8e003e99 100644
--- a/client/src/components/Tool/ToolSelectPreferredObjectStore.test.js
+++ b/client/src/components/Tool/ToolSelectPreferredObjectStore.test.js
@@ -2,6 +2,7 @@ import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useServerMock } from "@/api/client/__mocks__";
 import { setupSelectableMock } from "@/components/ObjectStore/mockServices";
 import { ROOT_COMPONENT } from "@/utils/navigation";
 
@@ -11,7 +12,15 @@ setupSelectableMock();
 
 const localVue = getLocalVue(true);
 
+const { server, http } = useServerMock();
+
 function mountComponent() {
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json({});
+        })
+    );
+
     const wrapper = mount(ToolSelectPreferredObjectStore, {
         propsData: { toolPreferredObjectStoreId: null },
         localVue,
@@ -24,6 +33,7 @@ const PREFERENCES = ROOT_COMPONENT.preferences;
 describe("ToolSelectPreferredObjectStore.vue", () => {
     it("updates object store to default on selection null", async () => {
         const wrapper = mountComponent();
+
         await flushPromises();
         const els = wrapper.findAll(PREFERENCES.object_store_selection.option_buttons.selector);
         expect(els.length).toBe(3);
diff --git a/client/src/components/Tool/helpForumUrls.ts b/client/src/components/Tool/helpForumUrls.ts
index 26f2febd91a2010b36cf2a995f03a514b52b52c9..f4472ca802d8f0de3bac463bc9ee3a4a9491929a 100644
--- a/client/src/components/Tool/helpForumUrls.ts
+++ b/client/src/components/Tool/helpForumUrls.ts
@@ -1,6 +1,6 @@
-import { computed, Ref } from "vue";
+import { computed, type Ref } from "vue";
 
-import { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { useConfigStore } from "@/stores/configurationStore";
 
 export type HelpForumTopic = components["schemas"]["HelpForumTopic"];
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.test.js b/client/src/components/Toolshed/RepositoryDetails/Index.test.js
deleted file mode 100644
index ba48a8ae6901e60da7e02bf4f55f4bb3acf81717..0000000000000000000000000000000000000000
--- a/client/src/components/Toolshed/RepositoryDetails/Index.test.js
+++ /dev/null
@@ -1,60 +0,0 @@
-import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
-import { getAppRoot } from "onload/loadConfig";
-import { createPinia } from "pinia";
-import { getLocalVue } from "tests/jest/helpers";
-
-import { mockFetcher } from "@/api/schema/__mocks__";
-
-import { Services } from "../services";
-import Index from "./Index";
-
-jest.mock("app");
-jest.mock("onload/loadConfig");
-getAppRoot.mockImplementation(() => "/");
-jest.mock("../services");
-jest.mock("@/api/schema");
-
-Services.mockImplementation(() => {
-    return {
-        async getRepository(toolshedUrl, repositoryId) {
-            expect(toolshedUrl).toBe("toolshedUrl");
-            expect(repositoryId).toBe("id");
-            return [];
-        },
-        async getInstalledRepositoriesByName(name, owner) {
-            expect(name).toBe("name");
-            expect(owner).toBe("owner");
-            return [];
-        },
-    };
-});
-
-describe("RepositoryDetails", () => {
-    it("test repository details index", async () => {
-        const axiosMock = new MockAdapter(axios);
-        axiosMock.onGet("api/tool_panels/default").reply(200, {});
-        mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
-        const localVue = getLocalVue();
-        const pinia = createPinia();
-        const wrapper = shallowMount(Index, {
-            propsData: {
-                repo: {
-                    id: "id",
-                    name: "name",
-                    owner: "owner",
-                    description: "description",
-                },
-                toolshedUrl: "toolshedUrl",
-            },
-            localVue,
-            pinia,
-        });
-        expect(wrapper.find(".loading-message").text()).toBe("Loading repository details...");
-        await localVue.nextTick();
-        expect(wrapper.findAll(".alert").length).toBe(0);
-        await localVue.nextTick();
-        expect(wrapper.findAll(".alert").length).toBe(0);
-    });
-});
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.test.ts b/client/src/components/Toolshed/RepositoryDetails/Index.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b2a8cc0b19a7a3e74c782f2d492a551c9150125e
--- /dev/null
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.test.ts
@@ -0,0 +1,51 @@
+import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { createPinia } from "pinia";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
+
+import Index from "./Index.vue";
+
+const { server, http } = useServerMock();
+
+describe("RepositoryDetails", () => {
+    it("test repository details index", async () => {
+        server.use(
+            http.get("/api/configuration", ({ response }) => {
+                return response(200).json({});
+            }),
+
+            http.untyped.get("/api/tool_panels/default", () => {
+                return HttpResponse.json({});
+            }),
+
+            http.untyped.get("api/tool_shed_repositories", () => {
+                return HttpResponse.json([]);
+            }),
+
+            http.untyped.get("api/tool_shed/request", () => {
+                return HttpResponse.json([]);
+            })
+        );
+
+        const localVue = getLocalVue();
+        const pinia = createPinia();
+        const wrapper = shallowMount(Index, {
+            propsData: {
+                repo: {
+                    id: "id",
+                    name: "name",
+                    owner: "owner",
+                    description: "description",
+                },
+                toolshedUrl: "toolshedUrl",
+            },
+            localVue,
+            pinia,
+        });
+        expect(wrapper.find(".loading-message").text()).toBe("Loading repository details...");
+        await flushPromises();
+        expect(wrapper.findAll(".alert").length).toBe(0);
+    });
+});
diff --git a/client/src/components/Toolshed/RepositoryDetails/Index.vue b/client/src/components/Toolshed/RepositoryDetails/Index.vue
index 7f99ae9d7ce1fc35f5518076e1bebbdb5c5943ba..371adad78789e77fcc78f99bb415ff88324aa068 100644
--- a/client/src/components/Toolshed/RepositoryDetails/Index.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/Index.vue
@@ -1,3 +1,221 @@
+<script setup>
+import { computed, onMounted, onUnmounted, ref } from "vue";
+
+import { useConfig } from "@/composables/config";
+import { useResourceWatcher } from "@/composables/resourceWatcher";
+import { useToolStore } from "@/stores/toolStore";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import { Services } from "../services";
+
+import InstallationActions from "./InstallationActions.vue";
+import InstallationSettings from "./InstallationSettings.vue";
+import RepositoryTools from "./RepositoryTools.vue";
+
+const props = defineProps({
+    repo: {
+        type: Object,
+        required: true,
+    },
+    toolshedUrl: {
+        type: String,
+        required: true,
+    },
+});
+
+const services = new Services();
+
+const { config } = useConfig(true);
+const { panel, fetchPanel } = useToolStore();
+
+const repositoryWatcher = useResourceWatcher(loadInstalledRepositories, {
+    shortPollingInterval: 2000,
+    enableBackgroundPolling: false,
+});
+
+const repoChecked = "fa fa-check text-success";
+const repoUnchecked = "fa fa-times text-danger";
+const repoFields = [
+    { key: "numeric_revision", label: "Revision" },
+    { key: "tools", label: "Tools and Versions" },
+    { key: "profile", label: "Requires" },
+    { key: "missing_test_components", label: "Tests" },
+    { key: "status" },
+    { key: "actions", label: "", class: "toolshed-repo-actions" },
+];
+
+const statusError = "Error";
+const statusInstalled = "Installed";
+const statusUninstalled = "Uninstalled";
+
+const revisionStateMap = new Map();
+const revisionWaitStateMap = new Map();
+
+const selectedChangeset = ref();
+const selectedRequiresPanel = ref(false);
+const repoTable = ref([]);
+const showSettings = ref(false);
+const error = ref();
+const loading = ref(true);
+
+const isActionBusy = computed(() => (item) => {
+    return revisionWaitStateMap.has(item.changeset_revision);
+});
+
+onMounted(() => {
+    load();
+    if (!panel["default"]) {
+        fetchPanel("default");
+    }
+    startWatchingRepository();
+});
+
+onUnmounted(() => {
+    stopWatchingRepository();
+});
+
+async function load() {
+    try {
+        const response = await services.getRepository(props.toolshedUrl, props.repo.id);
+        repoTable.value = response ?? [];
+        loadInstalledRepositories();
+    } catch (e) {
+        error.value = errorMessageAsString(e);
+        loading.value = false;
+    }
+}
+
+async function loadInstalledRepositories() {
+    try {
+        const revisions = await services.getInstalledRepositoriesByName(props.repo.name, props.repo.owner);
+
+        refreshRepositoryStatus(revisions);
+    } catch (e) {
+        error.value = errorMessageAsString(e);
+    } finally {
+        loading.value = false;
+    }
+}
+
+function refreshRepositoryStatus(updatedRevisions) {
+    repoTable.value.forEach((x) => {
+        const repoRevision = updatedRevisions[x.changeset_revision];
+        if (!repoRevision) {
+            return;
+        }
+        revisionStateMap.set(x.changeset_revision, repoRevision);
+        if (repoRevision.status !== x.status) {
+            x.status = repoRevision.status;
+            x.installed = repoRevision.installed;
+        }
+
+        if (hasReachedExpectedState(x.changeset_revision) || !isFinalState(repoRevision.status)) {
+            // We don't need to particularly watch this revision anymore
+            removeRevisionFromWatchList(x.changeset_revision);
+        }
+    });
+
+    repoTable.value = [...repoTable.value];
+}
+
+function isFinalState(status) {
+    return [statusError, statusInstalled, statusUninstalled].includes(status);
+}
+
+function removeRevisionFromWatchList(changesetRevision) {
+    if (revisionWaitStateMap.has(changesetRevision)) {
+        revisionWaitStateMap.delete(changesetRevision);
+    }
+}
+
+function hasReachedExpectedState(changesetRevision) {
+    const revisionState = revisionStateMap.get(changesetRevision);
+    if (!revisionState) {
+        return false;
+    }
+    const revisionWaitState = revisionWaitStateMap.get(changesetRevision);
+    if (!revisionWaitState) {
+        // No expected state set, consider it done
+        return true;
+    }
+    const hasReachedExpectedState = revisionWaitState.waitForStates.includes(revisionState.status);
+    return hasReachedExpectedState;
+}
+
+function onHide() {
+    showSettings.value = false;
+}
+
+function setupRepository(details) {
+    selectedChangeset.value = details.changeset_revision;
+    selectedRequiresPanel.value =
+        details.includes_tools_for_display_in_tool_panel || details.repository.type === "repository_suite_definition";
+    showSettings.value = true;
+}
+
+async function onInstallRepository(details) {
+    try {
+        waitForRevisionStatus({
+            changesetRevision: details.changeset_revision,
+            waitForStates: [statusInstalled, statusError],
+        });
+        await services.installRepository(details);
+        showSettings.value = false;
+    } catch (e) {
+        error.value = errorMessageAsString(e);
+    }
+}
+
+async function uninstallRepository(details) {
+    try {
+        waitForRevisionStatus({
+            changesetRevision: details.changeset_revision,
+            waitForStates: [statusUninstalled, statusError],
+        });
+        await services.uninstallRepository({
+            tool_shed_url: props.toolshedUrl,
+            name: props.repo.name,
+            owner: props.repo.owner,
+            changeset_revision: details.changeset_revision,
+        });
+    } catch (e) {
+        error.value = errorMessageAsString(e);
+    }
+}
+
+async function resetRepository(details) {
+    try {
+        waitForRevisionStatus({
+            changesetRevision: details.changeset_revision,
+            waitForStates: [statusUninstalled],
+        });
+        await services.uninstallRepository({
+            tool_shed_url: props.toolshedUrl,
+            name: props.repo.name,
+            owner: props.repo.owner,
+            changeset_revision: details.changeset_revision,
+        });
+    } catch (e) {
+        error.value = errorMessageAsString(e);
+    }
+}
+
+function waitForRevisionStatus({ changesetRevision, waitForStates }) {
+    revisionWaitStateMap.set(changesetRevision, { waitForStates });
+    repoTable.value = [...repoTable.value];
+}
+
+function startWatchingRepository() {
+    repositoryWatcher.startWatchingResource();
+}
+
+function stopWatchingRepository() {
+    repositoryWatcher.stopWatchingResource();
+    revisionStateMap.clear();
+    revisionWaitStateMap.clear();
+}
+</script>
+
 <template>
     <b-card>
         <div class="mb-1">{{ repo.long_description }}</div>
@@ -30,9 +248,7 @@
                         </template>
                         <template v-slot:cell(status)="row">
                             <span v-if="row.item.status">
-                                <span
-                                    v-if="!['Error', 'Installed', 'Uninstalled'].includes(row.item.status)"
-                                    class="fa fa-spinner fa-spin" />
+                                <span v-if="!isFinalState(row.item.status)" class="fa fa-spinner fa-spin" />
                                 {{ row.item.status }}
                             </span>
                             <span v-else> - </span>
@@ -40,12 +256,14 @@
                         <template v-slot:cell(actions)="row">
                             <InstallationActions
                                 :status="row.item.status"
+                                :is-busy="isActionBusy(row.item)"
                                 @onInstall="setupRepository(row.item)"
-                                @onUninstall="uninstallRepository(row.item)" />
+                                @onUninstall="uninstallRepository(row.item)"
+                                @onReset="resetRepository(row.item)" />
                         </template>
                     </b-table>
                     <InstallationSettings
-                        v-if="showSettings"
+                        v-if="showSettings && selectedChangeset"
                         :repo="repo"
                         :toolshed-url="toolshedUrl"
                         :changeset-revision="selectedChangeset"
@@ -53,167 +271,12 @@
                         :current-panel="panel['default']"
                         :tool-dynamic-configs="config.tool_dynamic_configs"
                         @hide="onHide"
-                        @ok="onOk" />
+                        @ok="onInstallRepository" />
                 </div>
             </div>
         </div>
     </b-card>
 </template>
-<script>
-import BootstrapVue from "bootstrap-vue";
-import { mapActions, mapState } from "pinia";
-import { useToolStore } from "stores/toolStore";
-import Vue from "vue";
-
-import { useConfig } from "@/composables/config";
-
-import { Services } from "../services";
-
-import InstallationActions from "./InstallationActions.vue";
-import InstallationSettings from "./InstallationSettings.vue";
-import RepositoryTools from "./RepositoryTools.vue";
-
-Vue.use(BootstrapVue);
-
-export default {
-    components: {
-        InstallationSettings,
-        InstallationActions,
-        RepositoryTools,
-    },
-    props: {
-        repo: {
-            type: Object,
-            required: true,
-        },
-        toolshedUrl: {
-            type: String,
-            required: true,
-        },
-    },
-    setup() {
-        const { config, isConfigLoaded } = useConfig(true);
-        return { config, isConfigLoaded };
-    },
-    data() {
-        return {
-            repoChecked: "fa fa-check text-success",
-            repoUnchecked: "fa fa-times text-danger",
-            selectedChangeset: null,
-            selectedRequiresPanel: false,
-            repoTable: [],
-            repoFields: [
-                { key: "numeric_revision", label: "Revision" },
-                { key: "tools", label: "Tools and Versions" },
-                { key: "profile", label: "Requires" },
-                { key: "missing_test_components", label: "Tests" },
-                { key: "status" },
-                { key: "actions", label: "", class: "toolshed-repo-actions" },
-            ],
-            showSettings: false,
-            error: null,
-            loading: true,
-            delay: 2000,
-        };
-    },
-    computed: {
-        ...mapState(useToolStore, ["panel"]),
-    },
-    created() {
-        this.services = new Services();
-        this.load();
-        if (!this.panel["default"]) {
-            this.fetchPanel("default");
-        }
-    },
-    destroyed() {
-        this.clearTimeout();
-    },
-    methods: {
-        ...mapActions(useToolStore, ["fetchPanel"]),
-        clearTimeout() {
-            if (this.timeout) {
-                clearTimeout(this.timeout);
-            }
-        },
-        setTimeout() {
-            this.clearTimeout();
-            this.timeout = setTimeout(() => {
-                this.loadInstalledRepositories();
-            }, this.delay);
-        },
-        load() {
-            this.services
-                .getRepository(this.toolshedUrl, this.repo.id)
-                .then((response) => {
-                    this.repoTable = response;
-                    this.loadInstalledRepositories();
-                })
-                .catch((error) => {
-                    this.error = error;
-                    this.loading = false;
-                });
-        },
-        loadInstalledRepositories() {
-            this.services
-                .getInstalledRepositoriesByName(this.repo.name, this.repo.owner)
-                .then((revisions) => {
-                    let changed = false;
-                    this.repoTable.forEach((x) => {
-                        const revision = revisions[x.changeset_revision];
-                        if (revision && revision.status !== x.status) {
-                            x.status = revision.status;
-                            x.installed = revision.installed;
-                            changed = true;
-                            return false;
-                        }
-                    });
-                    if (changed) {
-                        this.repoTable = [...this.repoTable];
-                    }
-                    this.setTimeout();
-                    this.loading = false;
-                })
-                .catch((error) => {
-                    this.error = error;
-                    this.loading = false;
-                });
-        },
-        onOk: function (details) {
-            this.services
-                .installRepository(details)
-                .then((response) => {
-                    this.showSettings = false;
-                })
-                .catch((error) => {
-                    console.log(error);
-                });
-        },
-        onHide: function () {
-            this.showSettings = false;
-        },
-        setupRepository: function (details) {
-            this.selectedChangeset = details.changeset_revision;
-            this.selectedRequiresPanel =
-                details.includes_tools_for_display_in_tool_panel ||
-                details.repository.type == "repository_suite_definition";
-            this.showSettings = true;
-        },
-        uninstallRepository: function (details) {
-            this.services
-                .uninstallRepository({
-                    tool_shed_url: this.toolshedUrl,
-                    name: this.repo.name,
-                    owner: this.repo.owner,
-                    changeset_revision: details.changeset_revision,
-                })
-                .catch((error) => {
-                    this.error = error;
-                });
-        },
-    },
-};
-</script>
 
 <style lang="scss">
 // make actions take up less space
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationActions.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationActions.vue
index 04228b87adf778adba7b21e7473a0a8dade90aab..e9d485301e488891e2273b5198b833d383578644 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationActions.vue
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationActions.vue
@@ -1,25 +1,33 @@
-<script setup>
+<script setup lang="ts">
 import { computed } from "vue";
 
-const props = defineProps({
-    status: String,
-});
+import localize from "@/utils/localization";
+
+interface Props {
+    status?: string;
+    isBusy?: boolean;
+}
+
+const props = defineProps<Props>();
 
 const installState = computed(() => !props.status || props.status === "Uninstalled");
 const uninstallState = computed(() => props.status === "Installed");
 
-const emit = defineEmits(["onInstall", "onUninstall"]);
+const emit = defineEmits(["onInstall", "onUninstall", "onReset"]);
 
-function onCancel() {
+function onReset() {
     if (window.confirm(`Do you want to reset this repository?`)) {
-        emit("onUninstall");
+        emit("onReset");
     }
 }
 </script>
 
 <template>
     <div>
-        <b-button v-if="installState" variant="primary" class="btn-sm" @click="() => emit('onInstall')">
+        <b-button v-if="isBusy" variant="secondary" class="btn-sm" disabled>
+            <b-spinner small></b-spinner>
+        </b-button>
+        <b-button v-else-if="installState" variant="primary" class="btn-sm" @click="() => emit('onInstall')">
             Install
         </b-button>
         <b-button v-else-if="uninstallState" variant="danger" class="btn-sm" @click="() => emit('onUninstall')">
@@ -29,8 +37,8 @@ function onCancel() {
             v-else
             variant="warning"
             class="btn-sm"
-            :title="l('Reset Broken or Stuck Installation')"
-            @click="onCancel">
+            :title="localize('Reset Broken or Stuck Installation')"
+            @click="onReset">
             Reset
         </b-button>
     </div>
diff --git a/client/src/components/Tour/TourList.vue b/client/src/components/Tour/TourList.vue
index 5f9f98f1a6c023bb11fec59707bc3a93b217807f..145a006ee48c48009304226305c348a2221b7b61 100644
--- a/client/src/components/Tour/TourList.vue
+++ b/client/src/components/Tour/TourList.vue
@@ -8,7 +8,7 @@
         <h2 class="h-sm">Tours</h2>
         <div v-if="error" class="alert alert-danger">{{ error }}</div>
         <div v-else>
-            <DelayedInput class="mb-3" :query="search" :placeholder="searchTours" :delay="0" @change="onSearch" />
+            <DelayedInput class="mb-3" :value="search" :placeholder="searchTours" :delay="0" @change="onSearch" />
             <div v-for="tour in tours" :key="tour.id">
                 <ul v-if="match(tour)" id="tourList" class="list-group">
                     <li class="list-group-item">
diff --git a/client/src/components/UndoRedo/UndoRedoStack.vue b/client/src/components/UndoRedo/UndoRedoStack.vue
new file mode 100644
index 0000000000000000000000000000000000000000..80de89bc6e94d62e119ec80a438d839433b80947
--- /dev/null
+++ b/client/src/components/UndoRedo/UndoRedoStack.vue
@@ -0,0 +1,180 @@
+<script setup lang="ts">
+import { ref, watch } from "vue";
+
+import { useUndoRedoStore } from "@/stores/undoRedoStore";
+
+import ActivityPanel from "../Panels/ActivityPanel.vue";
+
+const props = defineProps<{
+    storeId: string;
+}>();
+
+const currentStore = ref(useUndoRedoStore(props.storeId));
+
+watch(
+    () => props.storeId,
+    (id) => (currentStore.value = useUndoRedoStore(id))
+);
+
+function onInput(event: Event) {
+    const value = (event.target as HTMLInputElement).value;
+    const valueNumber = parseFloat(value);
+    const nonNanValue = isNaN(valueNumber) ? 0 : valueNumber;
+
+    currentStore.value.savedUndoActions = nonNanValue;
+    savedUndoActions.value = nonNanValue;
+}
+
+const savedUndoActions = ref(currentStore.value.savedUndoActions);
+
+function updateSavedUndoActions() {
+    savedUndoActions.value = currentStore.value.savedUndoActions;
+}
+</script>
+
+<template>
+    <ActivityPanel title="Latest Changes" class="undo-redo-stack">
+        <div class="scroll-list">
+            <button
+                v-for="action in currentStore.redoActionStack"
+                :key="action.id"
+                class="action future"
+                @click="currentStore.rollForwardTo(action)">
+                {{ action.name }}
+            </button>
+
+            <span class="state-indicator"> current state </span>
+
+            <button v-if="currentStore.pendingLazyAction" class="action lazy" @click="currentStore.undo">
+                {{ currentStore.pendingLazyAction.name }}
+            </button>
+
+            <button
+                v-for="action in [...currentStore.undoActionStack].reverse()"
+                :key="action.id"
+                class="action past"
+                @click="currentStore.rollBackTo(action)">
+                {{ action.name }}
+            </button>
+
+            <span v-if="currentStore.deletedActions.length !== 0" class="state-indicator"> latest saved state </span>
+
+            <span v-for="(action, i) in [...currentStore.deletedActions].reverse()" :key="i" class="action dead">
+                {{ action }}
+            </span>
+
+            <span class="state-indicator"> start of session </span>
+        </div>
+
+        <span class="info"> click an action to undo/redo multiple changes </span>
+
+        <label>
+            Max saved changes
+            <input
+                :value="savedUndoActions"
+                type="number"
+                step="1"
+                :min="currentStore.minUndoActions"
+                :max="currentStore.maxUndoActions"
+                @input="onInput"
+                @focusin="updateSavedUndoActions"
+                @focusout="updateSavedUndoActions"
+                @keyup.enter="updateSavedUndoActions" />
+        </label>
+    </ActivityPanel>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+.info {
+    line-height: 1;
+    margin-bottom: 0.5rem;
+    margin-top: 0.25rem;
+    color: $text-muted;
+    font-style: italic;
+}
+
+.undo-redo-stack {
+    width: 100%;
+
+    position: absolute;
+    top: 0;
+    left: 0;
+    bottom: 0;
+    right: 0;
+    overflow-y: hidden;
+
+    display: flex;
+    flex-direction: column;
+
+    .scroll-list {
+        display: flex;
+        flex-direction: column;
+        overflow-y: auto;
+        flex: 1;
+    }
+}
+
+.action {
+    text-align: left;
+    background-color: transparent;
+    border: none;
+    padding: 0.1rem;
+    padding-left: 0;
+    line-height: 1.2;
+
+    display: grid;
+    grid-template-columns: 8px auto;
+    align-items: center;
+    gap: 0.5rem;
+
+    &::before {
+        content: "";
+        display: block;
+        height: 2px;
+        background-color: $brand-secondary;
+    }
+
+    &:focus-visible {
+        background-color: $brand-secondary;
+    }
+
+    &.lazy {
+        color: $text-muted;
+    }
+
+    &.future {
+        color: $text-light;
+    }
+
+    &.past {
+        &::before {
+            background-color: $text-light;
+        }
+    }
+
+    &.dead {
+        color: $text-light;
+        &::before {
+            background-color: transparent;
+        }
+    }
+}
+
+.state-indicator {
+    display: grid;
+    grid-template-columns: 1rem auto 1fr;
+    gap: 0.5rem;
+    align-items: center;
+    color: $text-light;
+
+    &::before,
+    &::after {
+        content: "";
+        display: block;
+        height: 2px;
+        background-color: $brand-secondary;
+    }
+}
+</style>
diff --git a/client/src/components/Upload/DefaultBox.vue b/client/src/components/Upload/DefaultBox.vue
index 4afaa63ad7050644296db26f3a7cdf6024409a09..3023a3feeb98d78ffb7b7f898e1a83cfcf55021f 100644
--- a/client/src/components/Upload/DefaultBox.vue
+++ b/client/src/components/Upload/DefaultBox.vue
@@ -8,10 +8,10 @@ import Vue, { computed, ref } from "vue";
 
 import { UploadQueue } from "@/utils/upload-queue.js";
 
-import { collectionBuilder } from "./builders.js";
 import { defaultModel } from "./model.js";
 import { COLLECTION_TYPES, DEFAULT_FILE_NAME, hasBrowserSupport } from "./utils";
 
+import CollectionCreatorModal from "../Collections/CollectionCreatorModal.vue";
 import DefaultRow from "./DefaultRow.vue";
 import UploadBox from "./UploadBox.vue";
 import UploadSelect from "./UploadSelect.vue";
@@ -68,10 +68,20 @@ const props = defineProps({
         type: Boolean,
         default: false,
     },
+    disableFooter: {
+        type: Boolean,
+        default: false,
+    },
+    emitUploaded: {
+        type: Boolean,
+        default: false,
+    },
 });
 
-const emit = defineEmits(["dismiss", "progress"]);
+const emit = defineEmits(["dismiss", "progress", "uploaded"]);
 
+const collectionModalShow = ref(false);
+const collectionSelection = ref([]);
 const collectionType = ref("list");
 const counterAnnounce = ref(0);
 const counterError = ref(0);
@@ -147,8 +157,28 @@ function eventAnnounce(index, file) {
 }
 
 /** Populates collection builder with uploaded files */
-function eventBuild() {
-    collectionBuilder(historyId, collectionType.value, uploadValues.value);
+async function eventBuild(openModal = false) {
+    try {
+        collectionSelection.value = [];
+        uploadValues.value.forEach((model) => {
+            const outputs = model.outputs;
+            if (outputs) {
+                Object.entries(outputs).forEach((output) => {
+                    const outputDetails = output[1];
+                    collectionSelection.value.push(outputDetails);
+                });
+            } else {
+                console.debug("Warning, upload response does not contain outputs.", model);
+            }
+        });
+        if (openModal) {
+            collectionModalShow.value = true;
+        } else {
+            emit("uploaded", collectionSelection.value);
+        }
+    } catch (err) {
+        console.error(err);
+    }
     counterRunning.value = 0;
     eventReset();
     emit("dismiss");
@@ -369,8 +399,8 @@ defineExpose({
                     :file-name="uploadItem.fileName"
                     :file-size="uploadItem.fileSize"
                     :info="uploadItem.info"
-                    :list-extensions="isCollection ? null : listExtensions"
-                    :list-db-keys="isCollection ? null : listDbKeys"
+                    :list-extensions="!isCollection && listExtensions.length > 1 ? listExtensions : null"
+                    :list-db-keys="!isCollection && listDbKeys.length > 1 ? listDbKeys : null"
                     :percentage="uploadItem.percentage"
                     :space-to-tab="uploadItem.spaceToTab"
                     :status="uploadItem.status"
@@ -387,7 +417,7 @@ defineExpose({
             </div>
             <input ref="uploadFile" type="file" :multiple="multiple" @change="addFiles($event.target.files)" />
         </UploadBox>
-        <div class="upload-footer text-center">
+        <div v-if="!disableFooter" class="upload-footer text-center">
             <span v-if="isCollection" class="upload-footer-title">Collection:</span>
             <UploadSelect
                 v-if="isCollection"
@@ -416,6 +446,7 @@ defineExpose({
                 placeholder="Select Reference"
                 @input="updateDbKey" />
         </div>
+        <slot name="footer" />
         <div class="upload-buttons d-flex justify-content-end">
             <BButton id="btn-local" :disabled="!enableSources" @click="uploadFile.click()">
                 <FontAwesomeIcon icon="fa-laptop" />
@@ -443,9 +474,21 @@ defineExpose({
                 :disabled="!enableBuild"
                 title="Build"
                 :variant="enableBuild ? 'primary' : null"
-                @click="eventBuild">
+                @click="() => eventBuild(true)">
                 <span v-localize>Build</span>
             </BButton>
+            <BButton
+                v-if="emitUploaded"
+                id="btn-emit"
+                :disabled="!enableBuild"
+                title="Use Uploaded Files"
+                :variant="enableBuild ? 'primary' : null"
+                @click="() => eventBuild(false)">
+                <slot name="emit-btn-txt">
+                    <span v-localize>Use Uploaded</span>
+                </slot>
+                ({{ counterSuccess }})
+            </BButton>
             <BButton id="btn-stop" title="Pause" :disabled="!isRunning" @click="eventStop">
                 <span v-localize>Pause</span>
             </BButton>
@@ -457,5 +500,12 @@ defineExpose({
                 <span v-else v-localize>Close</span>
             </BButton>
         </div>
+        <CollectionCreatorModal
+            v-if="isCollection && historyId"
+            :history-id="historyId"
+            :collection-type="collectionType"
+            :selected-items="collectionSelection"
+            :show-modal.sync="collectionModalShow"
+            default-hide-source-items />
     </div>
 </template>
diff --git a/client/src/components/Upload/DefaultBoxORNL.vue b/client/src/components/Upload/DefaultBoxORNL.vue
index 11895d56e50b79bfbe3773e91fb2a08a99945261..b1442e0200c4e733f6f89a1841e85c2ecf2f6138 100644
--- a/client/src/components/Upload/DefaultBoxORNL.vue
+++ b/client/src/components/Upload/DefaultBoxORNL.vue
@@ -10,7 +10,6 @@ import { createDatasetCollection } from "components/History/model/queries";
 
 import { UploadQueue } from "@/utils/upload-queue.js";
 
-import { collectionBuilder } from "./builders.js";
 import { defaultModel } from "./model.js";
 import { COLLECTION_TYPES, DEFAULT_FILE_NAME, hasBrowserSupport } from "./utils";
 
@@ -60,7 +59,7 @@ const props = defineProps({
     },
     lazyLoad: {
         type: Number,
-        default: 50,
+        default: 150,
     },
     listDbKeys: {
         type: Array,
@@ -74,10 +73,18 @@ const props = defineProps({
         type: String,
         default: "",
         required: false,
-    }
+    },
+    disableFooter: {
+        type: Boolean,
+        default: false,
+    },
+    emitUploaded: {
+        type: Boolean,
+        default: false,
+    },
 });
 
-const emit = defineEmits(["dismiss", "progress", "updateCollectionName"]);
+const emit = defineEmits(["dismiss", "progress", "uploaded", "updateCollectionName"]);
 
 const collectionType = ref("list");
 const counterAnnounce = ref(0);
@@ -164,34 +171,38 @@ function eventAnnounce(index, file) {
 
 /** Populates collection builder with uploaded files */
 function eventBuild() {
-    const Galaxy = getGalaxyInstance();
-    const models = {};
-    uploadValues.value.forEach((model) => {
-        const outputs = model.outputs;
-        if (outputs) {
-            Object.entries(outputs).forEach((output) => {
-                const outputDetails = output[1];
-                models[outputDetails.id] = outputDetails;
-            });
-        } else {
-            console.debug("Warning, upload response does not contain outputs.", model);
-        }
-    });
-    var elements = Object.values(models);
-    elements = elements.map((element) => ({
-        id: element.id,
-        name: element.name,
-        //TODO: this allows for list:list even if the filter above does not - reconcile
-        src: element.src || (element.history_content_type == "dataset" ? "hda" : "hdca"),
-    }));
-    const queryBody = {
-        collection_type: "list",
-        name: collectionName.value,
-        hide_source_items: true,
-        element_identifiers: elements,
-        options: {}
-    };
-    createDatasetCollection({ id: Galaxy.currHistoryPanel.model.id }, queryBody);
+    try {
+        const Galaxy = getGalaxyInstance();
+        const models = {};
+        uploadValues.value.forEach((model) => {
+            const outputs = model.outputs;
+            if (outputs) {
+                Object.entries(outputs).forEach((output) => {
+                    const outputDetails = output[1];
+                    models[outputDetails.id] = outputDetails;
+                });
+            } else {
+                console.debug("Warning, upload response does not contain outputs.", model);
+            }
+        });
+        var elements = Object.values(models);
+        elements = elements.map((element) => ({
+            id: element.id,
+            name: element.name,
+            //TODO: this allows for list:list even if the filter above does not - reconcile
+            src: element.src || (element.history_content_type == "dataset" ? "hda" : "hdca"),
+        }));
+        const queryBody = {
+            collection_type: "list",
+            name: collectionName.value,
+            hide_source_items: true,
+            element_identifiers: elements,
+            options: {}
+        };
+        createDatasetCollection({ id: Galaxy.currHistoryPanel.model.id }, queryBody);
+    } catch (err) {
+        console.error(err)
+    }
     counterRunning.value = 0;
     eventReset();
     emit("dismiss");
@@ -435,8 +446,8 @@ defineExpose({
                     :file-name="uploadItem.fileName"
                     :file-size="uploadItem.fileSize"
                     :info="uploadItem.info"
-                    :list-extensions="isCollection ? null : listExtensions"
-                    :list-db-keys="isCollection ? null : listDbKeys"
+                    :list-extensions="!isCollection && listExtensions.length > 1 ? listExtensions : null"
+                    :list-db-keys="!isCollection && listDbKeys.length > 1 ? listDbKeys : null"
                     :percentage="uploadItem.percentage"
                     :space-to-tab="uploadItem.spaceToTab"
                     :status="uploadItem.status"
@@ -453,7 +464,7 @@ defineExpose({
             </div>
             <input ref="uploadFile" type="file" :multiple="multiple" @change="addFiles($event.target.files)" />
         </UploadBox>
-        <div class="upload-footer text-center">
+        <div v-if="!disableFooter" class="upload-footer text-center">
             <span v-if="isCollection" class="upload-footer-title">Collection:</span>
             <UploadSelect
                 v-if="isCollection"
@@ -482,6 +493,7 @@ defineExpose({
                 placeholder="Select Reference"
                 @input="updateDbKey" />
         </div>
+        <slot name="footer" />
         <div class="upload-buttons d-flex justify-content-end">
             <BButton id="btn-local" :disabled="!enableSources" @click="singleFileUpload()">
                 <FontAwesomeIcon icon="fa-laptop" />
diff --git a/client/src/components/Upload/RulesInput.vue b/client/src/components/Upload/RulesInput.vue
index 9cac3661a470b470bce03376484252e4fc74d71b..ed36d9636574deacd29dfb2bba94d67b3862e9fd 100644
--- a/client/src/components/Upload/RulesInput.vue
+++ b/client/src/components/Upload/RulesInput.vue
@@ -60,7 +60,7 @@ function eventBuild() {
     } else if (entry.selectionType == "remote_files") {
         entry.elements = uris.value;
     }
-    Galaxy.currHistoryPanel.buildCollection("rules", entry, null, true);
+    Galaxy.currHistoryPanel.buildCollectionFromRules(entry, null, true);
     emit("dismiss");
 }
 
diff --git a/client/src/components/Upload/UploadContainer.vue b/client/src/components/Upload/UploadContainer.vue
index 329e9b92315f8a63012f66fedebaf7bf242ac5e9..7b918c349545a7330595a61c9592f5412c3fb0fe 100644
--- a/client/src/components/Upload/UploadContainer.vue
+++ b/client/src/components/Upload/UploadContainer.vue
@@ -74,6 +74,7 @@ const props = defineProps({
     },
 });
 
+const collectionTabActive = ref(null);
 const extensionsSet = ref(false);
 const datatypesMapper = ref(null);
 const datatypesMapperReady = ref(false);
@@ -81,6 +82,7 @@ const dbKeysSet = ref(false);
 const listExtensions = ref([]);
 const listDbKeys = ref([]);
 const regular = ref(null);
+const regularTabActive = ref(null);
 
 const { percentage, status } = storeToRefs(useUploadStore());
 
@@ -112,12 +114,15 @@ const ready = computed(
 );
 const canUploadToHistory = computed(() => currentHistory.value && canMutateHistory(currentHistory.value));
 const showCollection = computed(() => !props.formats && props.multiple);
-const showComposite = computed(() => !props.formats || hasCompositeExtension);
-const showRegular = computed(() => !props.formats || hasRegularExtension);
+const showComposite = computed(() => !props.formats || hasCompositeExtension.value);
+const showRegular = computed(() => !props.formats || hasRegularExtension.value);
 const showRules = computed(() => !props.formats || props.multiple);
 
 function immediateUpload(files) {
-    regular.value?.addFiles(files, true);
+    if (showRegular.value) {
+        regularTabActive.value = true;
+        regular.value?.addFiles(files, true);
+    }
 }
 
 function toData(items, history_id, composite = false) {
@@ -172,21 +177,7 @@ defineExpose({
         </span>
     </BAlert>
     <BTabs v-else-if="ready">
-        <BTab v-if="showRegular" id="regular" title="Regular" button-id="tab-title-link-regular">
-            <DefaultBox
-                ref="regular"
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :list-db-keys="listDbKeys"
-                :multiple="multiple"
-                @progress="progress"
-                v-on="$listeners" />
+        <BTab v-if="showRegular" title="Regular" button-id="tab-title-link-regular" :active.sync="regularTabActive">
         </BTab>
         <BTab v-if="showComposite" id="composite" title="Composite" button-id="tab-title-link-composite">
             <CompositeBox
@@ -199,19 +190,11 @@ defineExpose({
                 :list-db-keys="listDbKeys"
                 v-on="$listeners" />
         </BTab>
-        <BTab v-if="showCollection" id="collection" title="Collection" button-id="tab-title-link-collection">
-            <DefaultBox
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :is-collection="true"
-                :list-db-keys="listDbKeys"
-                v-on="$listeners" />
+        <BTab
+            v-if="showCollection"
+            title="Collection"
+            button-id="tab-title-link-collection"
+            :active.sync="collectionTabActive">
         </BTab>
         <BTab v-if="showRules" id="rule-based" title="Rule-based" button-id="tab-title-link-rule-based">
             <RulesInput
@@ -221,6 +204,24 @@ defineExpose({
                 :history-id="currentHistoryId"
                 v-on="$listeners" />
         </BTab>
+        <DefaultBox
+            v-if="showRegular || showCollection"
+            v-show="regularTabActive || collectionTabActive"
+            :id="collectionTabActive ? 'collection' : 'regular'"
+            ref="regular"
+            :chunk-upload-size="chunkUploadSize"
+            :default-db-key="defaultDbKey"
+            :default-extension="defaultExtension"
+            :effective-extensions="effectiveExtensions"
+            :file-sources-configured="fileSourcesConfigured"
+            :ftp-upload-site="currentUserId && ftpUploadSite"
+            :has-callback="hasCallback"
+            :history-id="currentHistoryId"
+            :list-db-keys="listDbKeys"
+            :multiple="regularTabActive ? multiple : undefined"
+            :is-collection="collectionTabActive"
+            @progress="progress"
+            v-on="$listeners" />
     </BTabs>
     <div v-else>
         <LoadingSpan message="Loading required information from Galaxy server." />
diff --git a/client/src/components/Upload/UploadContainerORNL.vue b/client/src/components/Upload/UploadContainerORNL.vue
index 41ee19e641623e1d634674f759b9829146ff63e3..1ca7d51d3a864eb3e3b72113fa49e362f29d4f79 100644
--- a/client/src/components/Upload/UploadContainerORNL.vue
+++ b/client/src/components/Upload/UploadContainerORNL.vue
@@ -74,6 +74,7 @@ const props = defineProps({
     },
 });
 
+const collectionTabActive = ref(null);
 const extensionsSet = ref(false);
 const datatypesMapper = ref(null);
 const datatypesMapperReady = ref(false);
@@ -81,6 +82,7 @@ const dbKeysSet = ref(false);
 const listExtensions = ref([]);
 const listDbKeys = ref([]);
 const regular = ref(null);
+const regularTabActive = ref(null);
 
 const { percentage, status } = storeToRefs(useUploadStore());
 
@@ -119,7 +121,10 @@ const showRegular = computed(() => !props.formats || hasRegularExtension);
 const showRules = false;
 
 function immediateUpload(files) {
-    regular.value?.addFiles(files, true);
+    if (showRegular.value) {
+        regularTabActive.value = true;
+        regular.value?.addFiles(files, true);
+    }
 }
 
 function toData(items, history_id, composite = false) {
@@ -174,21 +179,7 @@ defineExpose({
         </span>
     </BAlert>
     <BTabs v-else-if="ready">
-        <BTab v-if="showRegular" id="regular" title="Regular" button-id="tab-title-link-regular">
-            <DefaultBoxORNL
-                ref="regular"
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :list-db-keys="listDbKeys"
-                :multiple="multiple"
-                @progress="progress"
-                v-on="$listeners" />
+        <BTab v-if="showRegular" title="Regular" button-id="tab-title-link-regular" :active.sync="regularTabActive">
         </BTab>
         <BTab v-if="showComposite" id="composite" title="Composite" button-id="tab-title-link-composite">
             <CompositeBox
@@ -201,19 +192,11 @@ defineExpose({
                 :list-db-keys="listDbKeys"
                 v-on="$listeners" />
         </BTab>
-        <BTab v-if="showCollection" id="collection" title="Collection" button-id="tab-title-link-collection">
-            <DefaultBoxORNL
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :is-collection="true"
-                :list-db-keys="listDbKeys"
-                v-on="$listeners" />
+        <BTab
+            v-if="showCollection"
+            title="Collection"
+            button-id="tab-title-link-collection"
+            :active.sync="collectionTabActive">
         </BTab>
         <BTab v-if="showRules" id="rule-based" title="Rule-based" button-id="tab-title-link-rule-based">
             <RulesInput
@@ -223,6 +206,24 @@ defineExpose({
                 :history-id="currentHistoryId"
                 v-on="$listeners" />
         </BTab>
+         <DefaultBoxORNL
+            v-if="showRegular || showCollection"
+            v-show="regularTabActive || collectionTabActive"
+            :id="collectionTabActive ? 'collection' : 'regular'"
+            ref="regular"
+            :chunk-upload-size="chunkUploadSize"
+            :default-db-key="defaultDbKey"
+            :default-extension="defaultExtension"
+            :effective-extensions="effectiveExtensions"
+            :file-sources-configured="fileSourcesConfigured"
+            :ftp-upload-site="currentUserId && ftpUploadSite"
+            :has-callback="hasCallback"
+            :history-id="currentHistoryId"
+            :list-db-keys="listDbKeys"
+            :multiple="regularTabActive ? multiple : undefined"
+            :is-collection="collectionTabActive"
+            @progress="progress"
+            v-on="$listeners" />
     </BTabs>
     <div v-else>
         <LoadingSpan message="Loading required information from Galaxy server." />
diff --git a/client/src/components/Upload/UploadModal.test.js b/client/src/components/Upload/UploadModal.test.js
index c565c4ae6c1f528e336f3047d4b2d5f2951be19e..b7e949336c2d7f65200bbd6e39ba2c92d79fdb94 100644
--- a/client/src/components/Upload/UploadModal.test.js
+++ b/client/src/components/Upload/UploadModal.test.js
@@ -1,18 +1,16 @@
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import { createPinia } from "pinia";
-import { useHistoryStore } from "stores/historyStore";
-import { useUserStore } from "stores/userStore";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
 
 import UploadContainerORNL from "./UploadContainerORNL.vue";
-import UploadModal from "./UploadModal.vue";
+//import UploadContainer from "./UploadContainer.vue";
 
-jest.mock("app");
-jest.mock("@/api/schema");
+import UploadModal from "./UploadModal.vue";
 
 jest.mock("@/composables/config", () => ({
     useConfig: jest.fn(() => ({
@@ -21,6 +19,8 @@ jest.mock("@/composables/config", () => ({
     })),
 }));
 
+const { server, http } = useServerMock();
+
 const fastaResponse = {
     description_url: "https://wiki.galaxyproject.org/Learn/Datatypes#Fasta",
     display_in_upload: true,
@@ -42,19 +42,23 @@ const propsData = {
 
 describe("UploadModal.vue", () => {
     let wrapper;
-    let axiosMock;
     let userStore;
     let historyStore;
 
     beforeEach(async () => {
-        mockFetcher
-            .path("/api/datatypes")
-            .method("get")
-            .mock({ data: [fastaResponse] });
-        mockFetcher.path("/api/genomes").method("get").mock({ data: genomesResponse });
+        server.use(
+            http.get("/api/datatypes", ({ response }) => {
+                return response(200).json([fastaResponse]);
+            }),
 
-        axiosMock = new MockAdapter(axios);
-        axiosMock.onGet(`/api/histories/count`).reply(200, 0);
+            http.get("/api/genomes", ({ response }) => {
+                return response(200).json(genomesResponse);
+            }),
+
+            http.get("/api/histories/count", ({ response }) => {
+                return response(200).json(0);
+            })
+        );
 
         const localVue = getLocalVue();
         const pinia = createPinia();
@@ -82,19 +86,16 @@ describe("UploadModal.vue", () => {
         await wrapper.vm.open();
     });
 
-    afterEach(() => {
-        axiosMock.restore();
-        axiosMock.reset();
-    });
-
     it("should load with correct defaults", async () => {
         const contentWrapper = wrapper.findComponent(UploadContainerORNL);
+//        const contentWrapper = wrapper.findComponent(UploadContainer);
         expect(contentWrapper.vm.auto.id).toBe("auto");
         expect(contentWrapper.vm.datatypesDisableAuto).toBe(false);
     });
 
     it("should fetch datatypes and parse them", async () => {
         const contentWrapper = wrapper.findComponent(UploadContainerORNL);
+//        const contentWrapper = wrapper.findComponent(UploadContainer);
         expect(contentWrapper.exists()).toBe(true);
         expect(contentWrapper.vm.listExtensions.length).toBe(2);
         expect(contentWrapper.vm.listExtensions[0].id).toBe("auto");
@@ -103,6 +104,7 @@ describe("UploadModal.vue", () => {
 
     it("should fetch genomes and parse them", async () => {
         const contentWrapper = wrapper.findComponent(UploadContainerORNL);
+//        const contentWrapper = wrapper.findComponent(UploadContainer);
         expect(contentWrapper.vm.listDbKeys.length).toBe(3);
     });
 });
diff --git a/client/src/components/Upload/UploadModal.vue b/client/src/components/Upload/UploadModal.vue
index 3d8e0447862b93bf28db41f5a7695f8540a301d1..74f044c56de6d048b0e9d612c9db82e27212d447 100644
--- a/client/src/components/Upload/UploadModal.vue
+++ b/client/src/components/Upload/UploadModal.vue
@@ -1,4 +1,5 @@
 <script setup>
+import { BCarousel, BCarouselSlide, BModal } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { ref, watch } from "vue";
 
@@ -8,9 +9,13 @@ import { useUserHistories } from "@/composables/userHistories";
 import { useUserStore } from "@/stores/userStore";
 import { wait } from "@/utils/utils";
 
+
 import UploadContainerORNL from "./UploadContainerORNL.vue";
+//import UploadContainer from "./UploadContainer.vue";
+import ExternalLink from "../ExternalLink.vue";
+import HelpText from "../Help/HelpText.vue";
 
-const { currentUser } = storeToRefs(useUserStore());
+const { currentUser, hasSeenUploadHelp } = storeToRefs(useUserStore());
 const { currentHistoryId, currentHistory } = useUserHistories(currentUser);
 
 const { config, isConfigLoaded } = useConfig();
@@ -62,7 +67,14 @@ async function open(overrideOptions) {
 
 watch(
     () => showModal.value,
-    (modalShown) => setIframeEvents(["galaxy_main"], modalShown)
+    (modalShown) => {
+        setIframeEvents(["galaxy_main"], modalShown);
+
+        // once the modal closes the first time a user sees help, we never show it again
+        if (!modalShown && !hasSeenUploadHelp.value) {
+            hasSeenUploadHelp.value = true;
+        }
+    }
 );
 
 defineExpose({
@@ -71,7 +83,7 @@ defineExpose({
 </script>
 
 <template>
-    <b-modal
+    <BModal
         v-model="showModal"
         :static="options.modalStatic"
         header-class="no-separator"
@@ -81,12 +93,41 @@ defineExpose({
         no-enforce-focus
         hide-footer>
         <template v-slot:modal-header>
-            <h2 class="title h-sm" tabindex="0">
-                {{ options.title }}
-                <span v-if="currentHistory">
-                    to <b>{{ currentHistory.name }}</b>
-                </span>
-            </h2>
+            <div class="d-flex justify-content-between w-100">
+                <h2 class="title h-sm" tabindex="0">
+                    {{ options.title }}
+                    <span v-if="currentHistory">
+                        to <b>{{ currentHistory.name }}</b>
+                    </span>
+                </h2>
+
+                <BCarousel v-if="!hasSeenUploadHelp" :interval="4000" no-touch>
+                    <BCarouselSlide>
+                        <template v-slot:img>
+                            <span class="text-nowrap float-right">
+                                <ExternalLink href="https://galaxy-upload.readthedocs.io/en/latest/">
+                                    Click here
+                                </ExternalLink>
+                                to check out the
+                                <HelpText uri="galaxy.upload.galaxyUploadUtil" text="galaxy-upload" />
+                                util!
+                            </span>
+                        </template>
+                    </BCarouselSlide>
+                    <BCarouselSlide>
+                        <template v-slot:img>
+                            <span class="text-nowrap float-right">
+                                More info on <HelpText uri="galaxy.upload.ruleBased" text="Rule-based" /> uploads
+                                <ExternalLink
+                                    href="https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-rules/tutorial.html">
+                                    here
+                                </ExternalLink>
+                                .
+                            </span>
+                        </template>
+                    </BCarouselSlide>
+                </BCarousel>
+            </div>
         </template>
         <UploadContainerORNL
             v-if="currentHistoryId"
@@ -95,7 +136,7 @@ defineExpose({
             :current-history-id="currentHistoryId"
             v-bind="options"
             @dismiss="dismiss" />
-    </b-modal>
+    </BModal>
 </template>
 
 <style>
diff --git a/client/src/components/Upload/builders.js b/client/src/components/Upload/builders.js
deleted file mode 100644
index 5253a8ba6b979328902f7674e1bd7264b942fe74..0000000000000000000000000000000000000000
--- a/client/src/components/Upload/builders.js
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Interface with rule builder
- */
-import { getGalaxyInstance } from "app";
-
-/** Populates collection builder with uploaded files */
-export function collectionBuilder(historyId, type, uploadValues) {
-    const Galaxy = getGalaxyInstance();
-    const models = {};
-    uploadValues.forEach((model) => {
-        const outputs = model.outputs;
-        if (outputs) {
-            Object.entries(outputs).forEach((output) => {
-                const outputDetails = output[1];
-                models[outputDetails.id] = outputDetails;
-            });
-        } else {
-            console.debug("Warning, upload response does not contain outputs.", model);
-        }
-    });
-    // Build selection object
-    const selection = {
-        models: Object.values(models),
-        historyId: historyId,
-    };
-    Galaxy.currHistoryPanel.buildCollection(type, selection);
-}
diff --git a/client/src/components/Upload/utils.js b/client/src/components/Upload/utils.js
index 637553275d22d0f16eac997087c61014a228ce81..7122711b811ef98d699983019d0f338a9788406e 100644
--- a/client/src/components/Upload/utils.js
+++ b/client/src/components/Upload/utils.js
@@ -3,9 +3,8 @@
  */
 import { errorMessageAsString, rethrowSimple } from "utils/simple-error";
 
-import { datatypesFetcher } from "@/api/datatypes";
-import { dbKeysFetcher } from "@/api/dbKeys";
-import { remoteFilesFetcher } from "@/api/remoteFiles";
+import { GalaxyApi } from "@/api";
+import { getDbKeys } from "@/api/dbKeys";
 
 export const AUTO_EXTENSION = {
     id: "auto",
@@ -51,7 +50,7 @@ async function loadDbKeys() {
     if (_cachedDbKeys) {
         return _cachedDbKeys;
     }
-    const { data: dbKeys } = await dbKeysFetcher();
+    const dbKeys = await getDbKeys();
     const dbKeyList = [];
     for (var key in dbKeys) {
         dbKeyList.push({
@@ -67,7 +66,9 @@ async function loadUploadDatatypes() {
     if (_cachedDatatypes) {
         return _cachedDatatypes;
     }
-    const { data: datatypes } = await datatypesFetcher({ extension_only: false });
+    const { data: datatypes } = await GalaxyApi().GET("/api/datatypes", {
+        params: { query: { extension_only: false } },
+    });
     const listExtensions = [];
     for (var key in datatypes) {
         listExtensions.push({
@@ -111,22 +112,28 @@ export async function getUploadDbKeys(defaultDbKey) {
     return dbKeyList;
 }
 
-export async function getRemoteEntries(success, error) {
-    try {
-        const { data } = await remoteFilesFetcher();
-        success(data);
-    } catch (e) {
-        error(errorMessageAsString(e));
+export async function getRemoteEntries(onSuccess, onError) {
+    const { data, error } = await GalaxyApi().GET("/api/remote_files");
+
+    if (error) {
+        onError(errorMessageAsString(error));
     }
+
+    onSuccess(data);
 }
 
 export async function getRemoteEntriesAt(target) {
-    try {
-        const { data: files } = await remoteFilesFetcher({ target });
-        return files;
-    } catch (e) {
-        rethrowSimple(e);
+    const { data: files, error } = await GalaxyApi().GET("/api/remote_files", {
+        params: {
+            query: { target },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
+
+    return files;
 }
 
 export function hasBrowserSupport() {
diff --git a/client/src/components/User/CloudAuth/CloudAuth.test.js b/client/src/components/User/CloudAuth/CloudAuth.test.js
deleted file mode 100644
index 705a304b5dde25474b7ab37f0cd3306f556bb32b..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/CloudAuth.test.js
+++ /dev/null
@@ -1,72 +0,0 @@
-import { shallowMount } from "@vue/test-utils";
-import flushPromises from "flush-promises";
-import { getLocalVue } from "tests/jest/helpers";
-
-import { default as CloudAuth } from "./CloudAuth";
-import CloudAuthItem from "./CloudAuthItem";
-
-jest.mock("./model/service", () => ({
-    listCredentials: async () => {
-        const listCredentials = require("./testdata/listCredentials.json");
-        const Credential = require("./model").Credential;
-        return listCredentials.map(Credential.create);
-    },
-}));
-
-const localVue = getLocalVue();
-
-describe("CloudAuth component", () => {
-    let wrapper;
-
-    beforeEach(async () => {
-        wrapper = shallowMount(CloudAuth, { localVue });
-        await flushPromises();
-    });
-
-    describe("initialization", () => {
-        it("should render the initial list", () => {
-            expect(wrapper).toBeTruthy();
-            expect(wrapper.findComponent(CloudAuthItem).exists()).toBeTruthy();
-            expect(wrapper.vm.items.length == 2).toBeTruthy();
-            expect(wrapper.vm.filteredItems.length == 2).toBeTruthy();
-        });
-    });
-
-    describe("text filter", () => {
-        it("should show filter result by text match", () => {
-            let results;
-
-            wrapper.vm.filter = "aws";
-            results = wrapper.vm.filteredItems;
-            expect(wrapper.findComponent(CloudAuthItem).exists()).toBeTruthy();
-            expect(results.length == 1).toBeTruthy();
-
-            wrapper.vm.filter = "azure";
-            results = wrapper.vm.filteredItems;
-            expect(results.length == 1).toBeTruthy();
-
-            wrapper.vm.filter = "";
-            results = wrapper.vm.filteredItems;
-            expect(results.length == 2).toBeTruthy();
-        });
-    });
-
-    describe("create button", () => {
-        it("clicking create button should add a blank key", () => {
-            let results = wrapper.vm.filteredItems;
-            expect(wrapper.findComponent(CloudAuthItem).exists()).toBeTruthy();
-            expect(results.length == 2).toBeTruthy();
-
-            const button = wrapper.find("button[name=createNewKey]");
-            expect(button).toBeTruthy();
-            button.trigger("click");
-
-            results = wrapper.vm.filteredItems;
-            expect(results.length == 3).toBeTruthy();
-
-            const blank = results.find((i) => i.id == null);
-            expect(blank).toBeTruthy();
-            expect(blank.id == null).toBeTruthy();
-        });
-    });
-});
diff --git a/client/src/components/User/CloudAuth/CloudAuth.vue b/client/src/components/User/CloudAuth/CloudAuth.vue
deleted file mode 100644
index 0a00e1d3c71a30f87e3d5f86a8c6e72a7281de79..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/CloudAuth.vue
+++ /dev/null
@@ -1,372 +0,0 @@
-<template>
-    <section class="cloud-auth">
-        <header>
-            <b-alert dismissible fade variant="warning" :show="errorMessage !== null" @dismissed="errorMessage = null">
-                {{ errorMessage }}
-            </b-alert>
-
-            <hgroup class="cloud-auth-title">
-                <h1 v-localize class="h-lg">Manage Cloud Authorization</h1>
-                <nav class="operations">
-                    <ul>
-                        <li class="cloudKeyHelp">
-                            <a
-                                v-b-tooltip.hover
-                                :class="{ active: showHelp }"
-                                aria-label="Instructions"
-                                title="Instructions"
-                                @click.prevent="showHelp = !showHelp">
-                                <span>Instructions</span>
-                            </a>
-                        </li>
-                        <li class="cloudKeyFilter">
-                            <a
-                                v-b-tooltip.hover
-                                :class="{ active: showFilter }"
-                                aria-label="Filter Results"
-                                title="Filter Results"
-                                @click.prevent="showFilter = !showFilter">
-                                <span>Filter</span>
-                            </a>
-                        </li>
-                        <li class="createCloudKey">
-                            <a
-                                v-b-tooltip.hover
-                                aria-label="Create New Key"
-                                title="Create New Key"
-                                @click.prevent="onCreate">
-                                <span>Create New Key</span>
-                            </a>
-                        </li>
-                    </ul>
-                </nav>
-            </hgroup>
-
-            <transition name="fade">
-                <hgroup v-if="showHelp">
-                    <p>See the online <a href="https://galaxyproject.org/authnz/">Documentation</a>.</p>
-                </hgroup>
-            </transition>
-
-            <transition name="fade">
-                <hgroup v-if="showFilter">
-                    <b-form-group :description="filterDescription">
-                        <b-form-input v-model="filter" type="text" placeholder="Filter" />
-                    </b-form-group>
-                </hgroup>
-            </transition>
-
-            <b-button-group class="mb-4">
-                <button name="createNewKey" @click="onCreate">Create New Authorization Key</button>
-            </b-button-group>
-        </header>
-
-        <div class="scroll-container">
-            <b-list-group>
-                <transition-group name="fade">
-                    <CloudAuthItem
-                        v-for="credential in filteredItems"
-                        :key="credential.counter"
-                        :credential="credential"
-                        class="mb-1"
-                        @delete="onDelete"
-                        @save="onSave"
-                        @expand="expand(credential, $event)" />
-                </transition-group>
-            </b-list-group>
-        </div>
-
-        <b-modal
-            id="deleteCredentialModal"
-            ref="deleteModal"
-            v-model="hasDoomed"
-            centered
-            title="Delete Key?"
-            size="sm"
-            @ok="deleteKey"
-            @cancel="doomedItem = null">
-        </b-modal>
-    </section>
-</template>
-
-<script>
-import BootstrapVue from "bootstrap-vue";
-import Vue from "vue";
-
-import CloudAuthItem from "./CloudAuthItem";
-import { Credential } from "./model";
-import svc from "./model/service";
-
-Vue.use(BootstrapVue);
-
-export default {
-    components: {
-        CloudAuthItem,
-    },
-    data() {
-        return {
-            items: [],
-            filter: "",
-            showHelp: true,
-            showFilter: false,
-            loading: false,
-            doomedItem: null,
-            errorMessage: null,
-        };
-    },
-    computed: {
-        filteredItems() {
-            return this.items.filter((o) => o.match(this.filter));
-        },
-        filterDescription() {
-            return `${this.filteredItems.length} matches out of ${this.items.length} items`;
-        },
-        deleteButtonVariant() {
-            return this.showDeleted ? "primary" : "secondary";
-        },
-        hasDoomed: {
-            get() {
-                return this.doomedItem !== null;
-            },
-            // This setter is here because vue-bootstrap modal
-            // tries to set this property for unfathomable reasons
-            set() {},
-        },
-    },
-    watch: {
-        showDeleted(deleted) {
-            this.loadCredentials({ deleted });
-        },
-    },
-    created() {
-        this.loadCredentials();
-    },
-    methods: {
-        loadCredentials(params = {}) {
-            this.loading = true;
-            svc.listCredentials(params)
-                .then((items) => (this.items = items))
-                .catch(this.setError("Unable to load cloud keys."))
-                .finally(() => (this.loading = false));
-        },
-        onCreate() {
-            const newItem = Credential.create({ expanded: true });
-            this.addItem(newItem);
-        },
-        onSave(item) {
-            if (!item.valid) {
-                return;
-            }
-            item.loading = true;
-            svc.saveCredential(item)
-                .then((result) => {
-                    item.id = result.id;
-                    item.updateState();
-                })
-                .catch(this.setError("Unable to save key."))
-                .finally(() => (item.loading = false));
-        },
-        onDelete(doomed) {
-            this.doomedItem = doomed;
-            if (doomed.id) {
-                this.$refs.deleteModal.show();
-            } else {
-                this.removeItem(doomed);
-                this.doomedItem = null;
-            }
-        },
-        deleteKey() {
-            // Called when the modal is closed with an "OK"
-            svc.deleteCredential(this.doomedItem)
-                .then(() => this.removeItem(this.doomedItem))
-                .catch(this.setError("Unable to delete cloud key."))
-                .finally(() => {
-                    this.doomedItem = null;
-                });
-        },
-        expand(credential, { expanded }) {
-            credential.expanded = expanded;
-            if (expanded) {
-                this.items.filter((i) => i !== credential).forEach((i) => (i.expanded = false));
-            }
-        },
-        addItem(item) {
-            this.items = [...this.items, item];
-        },
-        removeItem(item) {
-            this.items = this.items.filter((o) => o !== item);
-        },
-        setError(msg) {
-            return (err) => {
-                this.errorMessage = msg;
-                console.warn(err);
-            };
-        },
-    },
-};
-</script>
-
-<style lang="scss">
-@import "~bootstrap/scss/functions";
-@import "~bootstrap/scss/variables";
-@import "~bootstrap/scss/mixins";
-@import "~bootstrap/scss/utilities/spacing";
-
-@import "scss/theme/blue.scss";
-@import "scss/mixins";
-
-// TODO: build reusable icon menu? Maybe make into a component?
-// The existing one has lots of reusability problems
-
-.operations {
-    margin-bottom: 0;
-
-    ul {
-        @include list_reset();
-        display: flex;
-        li:not(:first-child) {
-            @extend .ml-2;
-        }
-    }
-}
-
-// General Layout
-
-.cloud-auth {
-    // header sticks, bottom part scrolls
-    @include scrollingListLayout("header", ".scroll-container");
-
-    // title left, icons right
-    .cloud-auth-title {
-        display: flex;
-        flex-direction: row;
-        justify-content: space-between;
-        align-items: center;
-
-        // top icon menu
-        .operations {
-            li {
-                a,
-                a::before {
-                    font-size: 1rem;
-                    color: $gray-400;
-                }
-                a.active::before,
-                a:hover::before {
-                    color: $brand-primary;
-                }
-            }
-
-            .cloudKeyHelp a {
-                @include fontawesome($fa-var-info-circle);
-            }
-            .cloudKeyFilter a {
-                @include fontawesome($fa-var-filter);
-            }
-            .createCloudKey a {
-                @include fontawesome($fa-var-plus);
-            }
-        }
-    }
-}
-
-// Single list item
-
-.cloud-auth-key {
-    header hgroup {
-        display: flex;
-        flex-direction: row;
-        justify-content: space-between;
-        align-items: center;
-        cursor: pointer;
-        user-select: none;
-
-        > * {
-            margin-bottom: 0;
-        }
-    }
-
-    form {
-        @extend .my-3;
-        @extend .pt-3;
-
-        // removes wierd double arrows on select
-        .custom-select {
-            background: none;
-        }
-
-        // Undo butchering from base.css so side-by-side labels work
-        .form-row {
-            display: flex;
-            input,
-            select {
-                max-width: none;
-            }
-            label {
-                font-weight: 400;
-            }
-        }
-
-        // button list at bottom of form
-        footer {
-            display: flex;
-            flex-direction: row;
-            justify-content: flex-end;
-            @extend .pt-3;
-
-            button:not(:first-child) {
-                @extend .ml-1;
-            }
-        }
-    }
-
-    // icon menu
-
-    .operations {
-        .save a {
-            @include fontawesome($fa-var-save);
-        }
-        .delete a {
-            @include fontawesome($fa-var-times);
-        }
-        .details a {
-            @include fontawesome($fa-var-window-minimize);
-            &:hover {
-                @include fontawesome($fa-var-window-maximize);
-            }
-        }
-    }
-
-    // reverse icons when key is expanded
-
-    &.expanded .details a {
-        @include fontawesome($fa-var-window-maximize);
-        &:hover {
-            @include fontawesome($fa-var-window-minimize);
-        }
-    }
-}
-
-// Transitions
-
-.fade-enter-active,
-.fade-leave-active {
-    transition: opacity 0.5s;
-}
-
-.fade-enter,
-.fade-leave-to {
-    opacity: 0;
-}
-
-// Delete modal
-
-#deleteCredentialModal {
-    .modal-body {
-        display: none;
-    }
-    .modal-dialog {
-        max-width: 300px;
-    }
-}
-</style>
diff --git a/client/src/components/User/CloudAuth/CloudAuthItem.vue b/client/src/components/User/CloudAuth/CloudAuthItem.vue
deleted file mode 100644
index 8c5526c3d0b3d164a272bf8e7fcfe78164c661c3..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/CloudAuthItem.vue
+++ /dev/null
@@ -1,93 +0,0 @@
-<template>
-    <b-list-group-item class="cloud-auth-key" :class="statusClasses" :variant="variant" :button="!expanded">
-        <header>
-            <hgroup>
-                <h2 class="h-sm" @click.prevent="expand()">{{ credential.title }}</h2>
-                <nav class="operations">
-                    <ul>
-                        <transition name="fade">
-                            <li v-if="expanded && credential.dirty" class="save">
-                                <a
-                                    v-b-tooltip.hover
-                                    aria-label="Save Key"
-                                    title="Save Key"
-                                    @click.prevent="$emit('save', credential)">
-                                    <span>Save Key</span>
-                                </a>
-                            </li>
-                        </transition>
-                        <li class="delete">
-                            <a
-                                v-b-tooltip.hover
-                                aria-label="Delete Key"
-                                title="Delete Key"
-                                @click.prevent="$emit('delete', credential)">
-                                <span>Delete Key</span>
-                            </a>
-                        </li>
-                        <li class="details">
-                            <a
-                                v-b-tooltip.hover
-                                aria-label="Show Details"
-                                title="Show Details"
-                                @click.prevent="expand()">
-                                <span>Details</span>
-                            </a>
-                        </li>
-                    </ul>
-                </nav>
-            </hgroup>
-        </header>
-        <!-- TODO: Restructure credential handling so we're not mutating the prop -->
-        <!-- eslint-disable vue/no-mutating-props-->
-        <CredentialForm
-            v-if="expanded"
-            v-model="credential"
-            class="border-top"
-            @click.self="expand()"
-            @save="$emit('save', credential)"
-            @delete="$emit('delete', credential)" />
-        <!-- eslint-enable vue/no-mutating-props-->
-    </b-list-group-item>
-</template>
-
-<script>
-import CredentialForm from "./CredentialForm";
-import { Credential } from "./model";
-
-export default {
-    components: {
-        CredentialForm,
-    },
-    props: {
-        credential: { type: Credential, required: true },
-    },
-    computed: {
-        statusClasses() {
-            const { expanded, valid, dirty, loading } = this.credential;
-            return { loading, expanded, valid, dirty, collapsed: !expanded };
-        },
-        variant() {
-            if (this.expanded) {
-                return "";
-            }
-            if (this.credential.dirty) {
-                return "warning";
-            }
-            if (!this.credential.valid) {
-                return "danger";
-            }
-            return "primary";
-        },
-        expanded() {
-            return this.credential.expanded;
-        },
-    },
-    methods: {
-        expand(forceState) {
-            const expanded = forceState !== undefined ? forceState : !this.expanded;
-            this.$emit("expand", { expanded });
-        },
-    },
-};
-</script>
diff --git a/client/src/components/User/CloudAuth/CredentialConfig.vue b/client/src/components/User/CloudAuth/CredentialConfig.vue
deleted file mode 100644
index f9faaeef7b3e18d5bea0d655c214fec34b304923..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/CredentialConfig.vue
+++ /dev/null
@@ -1,42 +0,0 @@
-<template>
-    <div>
-        <b-form-group
-            v-for="(field, fieldName) in fieldDefs"
-            :key="fieldName"
-            :label="field.label || fieldName"
-            :label-for="'config-' + fieldName"
-            label-cols-lg="3"
-            :state="config.fieldValid(fieldName)"
-            :invalid-feedback="config.errorMessage(fieldName)">
-            <MaskedInput
-                :id="'config-' + fieldName"
-                v-model="config[fieldName]"
-                :mask="field.mask"
-                :placeholder="field.placeholder"
-                :maxlength="field.maxlength || Math.Infinity"
-                :state="config.fieldValid(fieldName)"
-                trim />
-        </b-form-group>
-    </div>
-</template>
-
-<script>
-import MaskedInput from "components/MaskedInput";
-
-export default {
-    components: {
-        MaskedInput,
-    },
-    props: {
-        value: { type: Object, required: true },
-    },
-    computed: {
-        config() {
-            return this.value;
-        },
-        fieldDefs() {
-            return this.value.constructor.fields;
-        },
-    },
-};
-</script>
diff --git a/client/src/components/User/CloudAuth/CredentialForm.vue b/client/src/components/User/CloudAuth/CredentialForm.vue
deleted file mode 100644
index 4c44c6fe6926252b4e2908baa2c26d3e93e960ca..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/CredentialForm.vue
+++ /dev/null
@@ -1,101 +0,0 @@
-<template>
-    <b-form :validated="credential.isValid">
-        <!-- user label -->
-        <b-form-group label="Description" label-for="credentialDescription" label-cols-lg="3">
-            <b-form-input
-                id="credentialDescription"
-                v-model="credential.description"
-                :state="credential.fieldValid('description')"
-                placeholder="Description (optional)"
-                trim />
-        </b-form-group>
-
-        <!-- google-openidconnect -->
-        <b-form-group
-            v-if="identityProviders.length > 1"
-            label="Identity Provider"
-            label-for="identityProvider"
-            label-cols-lg="3">
-            <b-form-select
-                id="identityProvider"
-                v-model="credential.authn_id"
-                :state="credential.fieldValid('authn_id')"
-                :options="identityProviders" />
-        </b-form-group>
-
-        <!-- aws/azure, etc -->
-        <b-form-group label="Resource Provider" label-for="resourceProvider" label-cols-lg="3">
-            <b-form-select
-                id="resourceProvider"
-                v-model="credential.resourceProvider"
-                :state="credential.fieldValid('provider')"
-                :options="resourceProviderOptions" />
-        </b-form-group>
-
-        <CredentialConfig v-model="credential.config" />
-
-        <footer class="border-top">
-            <b-button variant="secondary" @click.prevent="$emit('delete', credential)"> Delete Key </b-button>
-            <b-button
-                aria-label="Save Key"
-                :variant="saveButtonVariant"
-                :disabled="saveButtonDisabled"
-                @click.prevent="$emit('save', credential)">
-                {{ saveButtonTitle }}
-            </b-button>
-        </footer>
-    </b-form>
-</template>
-
-<script>
-import CredentialConfig from "./CredentialConfig";
-import { Credential, ResourceProviders } from "./model";
-import { getIdentityProviders } from "./model/service";
-
-export default {
-    components: {
-        CredentialConfig,
-    },
-    props: {
-        value: { type: Credential, required: true },
-    },
-    data() {
-        return {
-            identityProviders: [],
-        };
-    },
-    computed: {
-        credential() {
-            return this.value;
-        },
-        // transformed for bootstrap component
-        resourceProviderOptions() {
-            return Array.from(ResourceProviders.entries()).map(([value, o]) => ({ value, text: o.label }));
-        },
-        config() {
-            return this.credential.config;
-        },
-        loading() {
-            return this.credential.loading;
-        },
-        saveButtonDisabled() {
-            return !(this.credential.valid && this.credential.dirty);
-        },
-        saveButtonVariant() {
-            return this.saveButtonDisabled ? "secondary" : "primary";
-        },
-        saveButtonTitle() {
-            return this.loading ? "Saving Key..." : "Save Key";
-        },
-    },
-    created() {
-        getIdentityProviders().then((result) => {
-            if (!this.credential.authn_id && result.length == 1) {
-                this.credential.authn_id = result[0].authn_id;
-                this.credential.updateState();
-            }
-            this.identityProviders = result;
-        });
-    },
-};
-</script>
diff --git a/client/src/components/User/CloudAuth/index.js b/client/src/components/User/CloudAuth/index.js
deleted file mode 100644
index 3e5bd9184df0e6118b2f97dffda21a85637d007d..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/index.js
+++ /dev/null
@@ -1 +0,0 @@
-export { default as CloudAuth } from "./CloudAuth.vue";
diff --git a/client/src/components/User/CloudAuth/model/AwsConfig.js b/client/src/components/User/CloudAuth/model/AwsConfig.js
deleted file mode 100644
index 9c4f27164d69b959561704bdb24c0af9c31fae69..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/AwsConfig.js
+++ /dev/null
@@ -1,28 +0,0 @@
-import { safeAssign } from "utils/safeAssign";
-
-import { BaseModel } from "./BaseModel";
-
-export class AwsConfig extends BaseModel {
-    constructor(props = {}) {
-        super();
-        this.role_arn = "";
-        safeAssign(this, props);
-        this.updateState();
-    }
-}
-
-AwsConfig.setValidator(function (model) {
-    const errors = {};
-    if (!model.role_arn.length) {
-        errors.role_arn = "Missing role_arn";
-    }
-    return errors;
-});
-
-AwsConfig.fields = {
-    role_arn: {
-        label: "Role ARN",
-        description: "The Amazon resource name (ARN) of the role to be assumed by Galaxy.",
-        placeholder: "arn:aws:iam::XXXXXXXXXXXX:role/XXXXXXXXXXX",
-    },
-};
diff --git a/client/src/components/User/CloudAuth/model/AwsConfig.test.js b/client/src/components/User/CloudAuth/model/AwsConfig.test.js
deleted file mode 100644
index 938fd1974e66d7950234e2b49b40fa1c53d42ff6..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/AwsConfig.test.js
+++ /dev/null
@@ -1,22 +0,0 @@
-import { AwsConfig } from "./AwsConfig";
-
-describe("AwsConfig", () => {
-    it("should instantiate", () => {
-        const instance = new AwsConfig();
-        expect(instance).toBeTruthy();
-        expect(!instance.dirty).toBeTruthy();
-        expect(!instance.valid).toBeTruthy();
-    });
-
-    it("should validate role_arn", () => {
-        const instance = new AwsConfig();
-        instance.role_arn = "abc";
-        expect(instance.fieldValid("role_arn")).toBeTruthy();
-    });
-
-    it("should invalidate role_arn", () => {
-        const instance = new AwsConfig();
-        instance.role_arn = "";
-        expect(!instance.fieldValid("role_arn")).toBeTruthy();
-    });
-});
diff --git a/client/src/components/User/CloudAuth/model/AzureConfig.js b/client/src/components/User/CloudAuth/model/AzureConfig.js
deleted file mode 100644
index 800dd7ea3344f105f9da0961d8c99c46fba5244d..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/AzureConfig.js
+++ /dev/null
@@ -1,62 +0,0 @@
-import { safeAssign } from "utils/safeAssign";
-
-import { BaseModel } from "./BaseModel";
-
-export class AzureConfig extends BaseModel {
-    constructor(props = {}) {
-        super();
-        this.tenant_id = "";
-        this.client_id = "";
-        this.client_secret = "";
-        safeAssign(this, props);
-        this.updateState();
-    }
-}
-
-AzureConfig.setValidator(function (model) {
-    const errors = {};
-
-    if (model.tenant_id.length < 36) {
-        errors.tenant_id = "Tenant ID too short";
-    }
-    if (!model.tenant_id) {
-        errors.tenant_id = "Missing Tenant ID";
-    }
-
-    if (model.client_id.length < 36) {
-        errors.client_id = "Client ID too short";
-    }
-    if (!model.client_id) {
-        errors.client_id = "Missing client ID";
-    }
-
-    if (!model.client_secret) {
-        errors.client_secret = "Missing secret";
-    }
-
-    return errors;
-});
-
-AzureConfig.fields = {
-    tenant_id: {
-        label: "Tenant ID",
-        mask: "********-****-****-****-************",
-        placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
-        maxlength: 36,
-        description: "Your Tenant ID (or Directory ID) on Azure.",
-    },
-    client_id: {
-        label: "Client ID",
-        mask: "********-****-****-****-************",
-        placeholder: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx",
-        maxlength: 36,
-        description: "The Client ID (or Application ID) you defined for Galaxy on your Azure directory.",
-    },
-    client_secret: {
-        label: "Client Secret",
-        mask: "",
-        placeholder: "Client Secret",
-        description:
-            "A secret string you obtained from Azure portal that Galaxy can use to prove its identity when requesting tokens to access your resources.",
-    },
-};
diff --git a/client/src/components/User/CloudAuth/model/AzureConfig.test.js b/client/src/components/User/CloudAuth/model/AzureConfig.test.js
deleted file mode 100644
index 35c4c96659371fe0a7aa148d011d8921cf61d74c..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/AzureConfig.test.js
+++ /dev/null
@@ -1,58 +0,0 @@
-import { AzureConfig } from "./AzureConfig";
-
-describe("AzureConfig", () => {
-    it("should instantiate", () => {
-        const instance = new AzureConfig();
-        expect(instance).toBeTruthy();
-        expect(!instance.dirty).toBeTruthy();
-        expect(!instance.valid).toBeTruthy();
-    });
-
-    describe("client_secret", () => {
-        it("should validate client_secret", () => {
-            const instance = new AzureConfig();
-            instance.client_secret = "abc";
-            expect(instance.fieldValid("client_secret")).toBeTruthy();
-        });
-
-        it("should invalidate client_secret", () => {
-            const instance = new AzureConfig();
-            instance.client_secret = "";
-            expect(!instance.fieldValid("client_secret")).toBeTruthy();
-        });
-    });
-
-    describe("tenant_id", () => {
-        it("should validate tenant_id", () => {
-            const validTenantId = "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx";
-            const instance = new AzureConfig();
-            instance.tenant_id = validTenantId;
-            expect(instance.fieldValid("tenant_id")).toBeTruthy();
-        });
-
-        it("should invalidate tenant_id", () => {
-            const instance = new AzureConfig();
-            instance.tenant_id = "";
-            expect(!instance.fieldValid("tenant_id")).toBeTruthy();
-            instance.tenant_id = "asdfa";
-            expect(!instance.fieldValid("tenant_id")).toBeTruthy();
-        });
-    });
-
-    describe("client_id", () => {
-        it("should validate client_id", () => {
-            const validClientId = "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx";
-            const instance = new AzureConfig();
-            instance.client_id = validClientId;
-            expect(instance.fieldValid("client_id")).toBeTruthy();
-        });
-
-        it("should invalidate client_id", () => {
-            const instance = new AzureConfig();
-            instance.client_id = "";
-            expect(!instance.fieldValid("client_id")).toBeTruthy();
-            instance.client_id = "asdf";
-            expect(!instance.fieldValid("client_id")).toBeTruthy();
-        });
-    });
-});
diff --git a/client/src/components/User/CloudAuth/model/BaseModel.js b/client/src/components/User/CloudAuth/model/BaseModel.js
deleted file mode 100644
index 5dede7517def4dbde918034fac4d8f0f6ab497b3..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/BaseModel.js
+++ /dev/null
@@ -1,102 +0,0 @@
-const lastState = new WeakMap();
-const validators = new WeakMap();
-const transients = new WeakMap();
-const counter = new WeakMap();
-
-// Helps with Vue for-loop keys
-let instanceCounter = 0;
-
-export class BaseModel {
-    constructor() {
-        counter.set(this, instanceCounter++);
-    }
-
-    /* object ID */
-
-    get counter() {
-        return counter.get(this);
-    }
-
-    /* Dirty state tracking */
-
-    get dirty() {
-        return lastState.get(this) != this.state;
-    }
-
-    get clean() {
-        return !this.dirty;
-    }
-
-    get state() {
-        // build state JSON ignoring transient fields
-        const tFields = this.transientFields;
-        return JSON.stringify(this, function (key) {
-            if (!tFields.has(key)) {
-                return this[key];
-            }
-            return undefined;
-        });
-    }
-
-    get lastState() {
-        return lastState.get(this);
-    }
-
-    get transientFields() {
-        const key = this.constructor;
-        if (!transients.has(key)) {
-            transients.set(key, new Set());
-        }
-        return transients.get(key);
-    }
-
-    updateState() {
-        lastState.set(this, this.state);
-    }
-
-    // Setting a property name as transient for a class means its
-    // state will be caclulated without regard to that propety
-    static setTransient(...fieldNames) {
-        const klass = this; // this will be a class
-        if (!transients.has(klass)) {
-            transients.set(klass, new Set());
-        }
-
-        const fields = transients.get(klass);
-        fieldNames.forEach((fieldName) => fields.add(fieldName));
-        transients.set(klass, fields);
-    }
-
-    /* Validation */
-
-    get valid() {
-        return Object.keys(this.validationErrors).length == 0;
-    }
-
-    get validationErrors() {
-        return this.constructor.validate(this);
-    }
-
-    errorMessage(field) {
-        if (field in this.validationErrors) {
-            return this.validationErrors[field];
-        }
-        return "errmessage";
-    }
-
-    fieldValid(fieldName) {
-        return !(fieldName in this.validationErrors);
-    }
-
-    static validate(model) {
-        if (validators.has(this)) {
-            const validator = validators.get(this);
-            return validator(model);
-        }
-        throw new Error("Missing validator");
-    }
-
-    static setValidator(validationFunction) {
-        validators.set(this, validationFunction);
-    }
-}
diff --git a/client/src/components/User/CloudAuth/model/Credential.js b/client/src/components/User/CloudAuth/model/Credential.js
deleted file mode 100644
index 6e5470d2bd0b4691c1e0be6a2d51a104880eee45..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/Credential.js
+++ /dev/null
@@ -1,105 +0,0 @@
-import { safeAssign } from "utils/safeAssign";
-
-import { BaseModel } from "./BaseModel";
-import { ResourceProviders } from "./ResourceProviders";
-
-export class Credential extends BaseModel {
-    constructor(props = {}) {
-        super();
-
-        this.id = null;
-        this.description = "";
-        this.authn_id = null; // identity provider
-        this.provider = null; // resource provider
-
-        // transient props, exclude from state
-        this.expanded = false;
-        this.loading = false;
-
-        // populate props
-        const options = Object.assign({}, Credential.defaults, props);
-        safeAssign(this, options);
-
-        // init nested config
-        this.config = new this.configClass(options.config);
-
-        // initialize state
-        this.updateState();
-    }
-
-    get title() {
-        return this.description.length ? this.description : this.provider;
-    }
-
-    get valid() {
-        return super.valid && this.config.valid;
-    }
-
-    // Alias for provider also changes config object when updated
-    // Set this when updating in the UI
-
-    get resourceProvider() {
-        return this.provider;
-    }
-
-    set resourceProvider(newProvider) {
-        this.provider = newProvider;
-        this.config = new this.configClass({});
-    }
-
-    // Polymorphic config class
-
-    get configClass() {
-        return ResourceProviders.get(this.provider).klass;
-    }
-
-    // Methods
-
-    match(searchText = "") {
-        // TODO: more robust object matching?
-        return searchText.length ? this.title.includes(searchText) : true;
-    }
-
-    // Statics
-
-    static get defaults() {
-        return {
-            authn_id: null,
-            provider: "aws",
-            expanded: false,
-        };
-    }
-
-    static create(props = {}) {
-        return new Credential(props);
-    }
-}
-
-/**
- * Transient fields do not factor into the state
- * for purposes of dirty tracking
- */
-Credential.setTransient("expanded", "loading");
-
-/**
- * A validator function's job is to return an object
- * where the keys are field names and the values are
- * error messages.
- */
-Credential.setValidator(function (model) {
-    const errors = {};
-
-    if (!model.provider) {
-        errors.provider = "Provider must be set";
-    }
-
-    if (!model.authn_id) {
-        errors.authn_id = "Please pick an identity provider";
-    }
-
-    if (!model.config.valid) {
-        errors.config = "Invalid config object";
-    }
-
-    return errors;
-});
diff --git a/client/src/components/User/CloudAuth/model/Credential.test.js b/client/src/components/User/CloudAuth/model/Credential.test.js
deleted file mode 100644
index 91978505d946c784c941efe2a4a57414f3fb2abf..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/Credential.test.js
+++ /dev/null
@@ -1,106 +0,0 @@
-import { Credential } from "./Credential";
-
-describe("Credential model", () => {
-    describe("basic model props", () => {
-        it("should exist", () => {
-            expect(Credential).toBeTruthy();
-        });
-
-        it("should build with defaults", () => {
-            const instance = new Credential();
-            expect(instance).toBeTruthy();
-        });
-
-        it("should build with props", () => {
-            const description = "i am the test description";
-            const props = { description };
-            const instance = new Credential(props);
-            expect(instance).toBeTruthy();
-            expect(instance.description == description).toBeTruthy();
-        });
-
-        it("default config object should be AWS", () => {
-            const instance = new Credential();
-            expect("role_arn" in instance.config).toBeTruthy();
-            expect(instance.config.constructor.name == "AwsConfig").toBeTruthy();
-        });
-
-        it("should load a different config object given the right provider", () => {
-            const provider = "azure";
-            const props = { provider };
-            const instance = new Credential(props);
-            expect(instance.provider == provider).toBeTruthy();
-            expect(instance.config.constructor.name == "AzureConfig").toBeTruthy();
-        });
-
-        it("should dynamically switch config objects as resourceProvider is changed", () => {
-            const instance = new Credential();
-            expect(instance.provider == "aws").toBeTruthy();
-            instance.resourceProvider = "azure";
-            expect(instance.config.constructor.name == "AzureConfig").toBeTruthy();
-            instance.resourceProvider = "aws";
-            expect(instance.config.constructor.name == "AwsConfig").toBeTruthy();
-        });
-    });
-
-    describe("dirty state", () => {
-        it("should flag as dirty when a prop is changed", () => {
-            const instance = new Credential();
-            instance.description = "foo";
-            expect(instance.dirty).toBeTruthy();
-        });
-
-        it("should flag as clean when a prop is restored", () => {
-            const instance = new Credential();
-            instance.description = "foo";
-            expect(instance.dirty).toBeTruthy();
-            instance.description = "";
-            expect(!instance.dirty).toBeTruthy();
-        });
-
-        it("should not flag as dirty when a transient prop is changed", () => {
-            const instance = new Credential();
-            instance.loading = true;
-            expect(!instance.dirty).toBeTruthy();
-        });
-    });
-
-    describe("validation", () => {
-        it("a new object should be invalid", () => {
-            const instance = new Credential();
-            expect(!instance.valid).toBeTruthy();
-        });
-
-        it("it should become valid when props are assigned", () => {
-            const instance = new Credential();
-            instance.authn_id = "floob";
-            instance.resourceProvider = "aws";
-            instance.config.role_arn = "abc";
-            expect(instance.valid).toBeTruthy();
-        });
-
-        it("it should be valid when initialized with correct props", () => {
-            const props = {
-                authn_id: "asdfasdf",
-                provider: "aws",
-                config: {
-                    role_arn: "floobar",
-                },
-            };
-            const instance = new Credential(props);
-            expect(instance.valid).toBeTruthy();
-        });
-
-        it("should be invalid when bad props assigned", () => {
-            const props = {
-                authn_id: "asdfasdf",
-                provider: "aws",
-                config: {
-                    role_arn: "",
-                },
-            };
-            const instance = new Credential(props);
-            expect(!instance.valid).toBeTruthy();
-        });
-    });
-});
diff --git a/client/src/components/User/CloudAuth/model/IdentityProvider.js b/client/src/components/User/CloudAuth/model/IdentityProvider.js
deleted file mode 100644
index 7c0974fc50b08066e0d579d41c6a8d78b5023e32..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/IdentityProvider.js
+++ /dev/null
@@ -1,29 +0,0 @@
-import { safeAssign } from "utils/safeAssign";
-
-export class IdentityProvider {
-    constructor(props = {}) {
-        this.id = "";
-        this.provider = "";
-        safeAssign(this, props);
-    }
-
-    // Aliases
-
-    get authn_id() {
-        return this.id;
-    }
-
-    get text() {
-        return this.provider;
-    }
-
-    get value() {
-        return this.id;
-    }
-
-    // Statics
-
-    static create(props = {}) {
-        return new IdentityProvider(props);
-    }
-}
diff --git a/client/src/components/User/CloudAuth/model/ResourceProviders.js b/client/src/components/User/CloudAuth/model/ResourceProviders.js
deleted file mode 100644
index cefcbb63faa6c023434c8d6e55617ba931a6e3ea..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/ResourceProviders.js
+++ /dev/null
@@ -1,14 +0,0 @@
-import { AwsConfig } from "./AwsConfig";
-import { AzureConfig } from "./AzureConfig";
-
-export const ResourceProviders = new Map();
-
-ResourceProviders.set("aws", {
-    klass: AwsConfig,
-    label: "Amazon Web Services (AWS)",
-});
-
-ResourceProviders.set("azure", {
-    klass: AzureConfig,
-    label: "Microsoft Azure",
-});
diff --git a/client/src/components/User/CloudAuth/model/index.js b/client/src/components/User/CloudAuth/model/index.js
deleted file mode 100644
index 24f019b67c531ae80b67deaea01298f0b3d1acd8..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/index.js
+++ /dev/null
@@ -1,3 +0,0 @@
-export { Credential } from "./Credential";
-export { IdentityProvider } from "./IdentityProvider";
-export { ResourceProviders } from "./ResourceProviders";
diff --git a/client/src/components/User/CloudAuth/model/service.js b/client/src/components/User/CloudAuth/model/service.js
deleted file mode 100644
index e5cdb03a66d949c31fce6c45b61daf3ec2417ca1..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/model/service.js
+++ /dev/null
@@ -1,81 +0,0 @@
-/**
- * Data retrieval/storage for the auth keys
- */
-
-import axios from "axios";
-import { getRootFromIndexLink } from "onload";
-
-import { Credential, IdentityProvider } from "./index";
-
-const getUrl = (path) => getRootFromIndexLink() + path;
-
-export async function listCredentials() {
-    const url = getUrl("api/cloud/authz");
-    const response = await axios.get(url);
-    if (response.status != 200) {
-        throw new Error("Unexpected response from listing.");
-    }
-    return response.data.map(Credential.create);
-}
-
-export async function getCredential(id) {
-    const url = getUrl("api/cloud/authz/${id}");
-    const response = await axios.get(url);
-    if (response.status != 200) {
-        throw new Error("Unexpected response loading key.");
-    }
-    return Credential.create(response.data);
-}
-
-export async function saveCredential(newItem) {
-    const model = Credential.create(newItem);
-    const response = await saveOrUpdate(model);
-    if (response.status != 200) {
-        throw new Error("Save failure.");
-    }
-    return Credential.create(response.data);
-}
-
-async function saveOrUpdate(model) {
-    return model.id
-        ? axios.put(getUrl(`api/cloud/authz/${model.id}`), model)
-        : axios.post(getUrl("api/cloud/authz"), model);
-}
-
-export async function deleteCredential(doomed) {
-    const model = Credential.create(doomed);
-    if (model.id) {
-        const url = getUrl(`api/cloud/authz/${doomed.id}`);
-        const response = await axios.delete(url);
-        if (response.status != 200) {
-            throw new Error("Delete failure.");
-        }
-    }
-    return model;
-}
-
-// Memoize results (basically never changes)
-
-let identityProviders;
-
-export async function getIdentityProviders() {
-    if (!identityProviders) {
-        const url = getUrl("authnz");
-        const response = await axios.get(url);
-        if (response.status != 200) {
-            throw new Error("Unable to load identity providers");
-        }
-        // This should be idempotent (and safe).
-        // eslint-disable-next-line require-atomic-updates
-        identityProviders = response.data.map(IdentityProvider.create);
-    }
-    return identityProviders;
-}
-
-export default {
-    listCredentials,
-    getCredential,
-    saveCredential,
-    deleteCredential,
-    getIdentityProviders,
-};
diff --git a/client/src/components/User/CloudAuth/testdata/listCredentials.json b/client/src/components/User/CloudAuth/testdata/listCredentials.json
deleted file mode 100644
index 82973dc3a7fca68e835b3c7862a2bc55d1934dbc..0000000000000000000000000000000000000000
--- a/client/src/components/User/CloudAuth/testdata/listCredentials.json
+++ /dev/null
@@ -1,32 +0,0 @@
-[
-    {
-        "authn_id": "f2db41e1fa331b3e",
-        "user_id": "f2db41e1fa331b3e",
-        "description": "aws description",
-        "last_update": "2019-04-04 09:13:16.135032",
-        "last_activity": "2019-04-04 09:13:16.135042",
-        "create_time": "2019-04-04 16:13:16.135755",
-        "provider": "aws",
-        "model_class": "CloudAuthz",
-        "config": {
-            "role_arn": "floobadooba"
-        },
-        "id": "a7db2fac67043c7e"
-    },
-    {
-        "authn_id": "f2db41e1fa331b3e",
-        "user_id": "f2db41e1fa331b3e",
-        "description": "azure description",
-        "last_update": "2019-04-03 20:21:51.350748",
-        "last_activity": "2019-04-03 20:21:51.350804",
-        "create_time": "2019-04-04 03:21:51.351508",
-        "provider": "azure",
-        "model_class": "CloudAuthz",
-        "config": {
-            "client_secret": "dannon likes Nickleback",
-            "client_id": "22222222-2222-2222-2222-222222222222",
-            "tenant_id": "11111111-1111-1111-1111-111111111111"
-        },
-        "id": "b472e2eb553fa0d1"
-    }
-]
\ No newline at end of file
diff --git a/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts b/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
index 06565d77b38505cefd757b0b5ed10807e2037912..3ed2d879e0689d7afdd46e0f220565890e7ddee7 100644
--- a/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
+++ b/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
@@ -1,38 +1,28 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { createPinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
-import { getCurrentUser } from "@/stores/users/queries";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
 import { useUserStore } from "@/stores/userStore";
 
-import { UserQuotaUsageData } from "./Quota/model";
+import { type UserQuotaUsageData } from "./Quota/model/QuotaUsage";
 
 import DiskUsageSummary from "./DiskUsageSummary.vue";
 
-jest.mock("@/api/schema");
-jest.mock("@/stores/users/queries");
-
 const localVue = getLocalVue();
 
+const { server, http } = useServerMock();
+
 const quotaUsageClassSelector = ".quota-usage";
 const basicDiskUsageSummaryId = "#basic-disk-usage-summary";
 
-const fakeUserWithQuota = {
-    id: "fakeUser",
-    email: "fakeUserEmail",
-    tags_used: [],
-    isAnonymous: false,
+const fakeUserWithQuota = getFakeRegisteredUser({
     total_disk_usage: 1048576,
     quota_bytes: 104857600,
     quota_percent: 1,
-    quota_source_label: "Default",
-};
-
-// TODO: Replace this with a mockFetcher when #16608 is merged
-const mockGetCurrentUser = getCurrentUser as jest.Mock;
-mockGetCurrentUser.mockImplementation(() => Promise.resolve(fakeUserWithQuota));
+});
 
 const fakeQuotaUsages: UserQuotaUsageData[] = [
     {
@@ -45,15 +35,17 @@ const fakeQuotaUsages: UserQuotaUsageData[] = [
 const FAKE_TASK_ID = "fakeTaskId";
 
 async function mountDiskUsageSummaryWrapper(enableQuotas: boolean) {
-    mockFetcher
-        .path("/api/configuration")
-        .method("get")
-        .mock({ data: { enable_quotas: enableQuotas } });
-    mockFetcher.path("/api/users/{user_id}/usage").method("get").mock({ data: fakeQuotaUsages });
-    mockFetcher
-        .path("/api/users/current/recalculate_disk_usage")
-        .method("put")
-        .mock({ status: 200, data: { id: FAKE_TASK_ID } });
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response.untyped(HttpResponse.json({ enable_quotas: enableQuotas }));
+        }),
+        http.get("/api/users/{user_id}", ({ response }) => {
+            return response(200).json(fakeUserWithQuota);
+        }),
+        http.get("/api/users/{user_id}/usage", ({ response }) => {
+            return response(200).json(fakeQuotaUsages);
+        })
+    );
 
     const pinia = createPinia();
     const wrapper = mount(DiskUsageSummary, {
@@ -67,6 +59,7 @@ async function mountDiskUsageSummaryWrapper(enableQuotas: boolean) {
 }
 
 describe("DiskUsageSummary.vue", () => {
+    jest.useFakeTimers();
     it("should display basic disk usage summary if quotas are NOT enabled", async () => {
         const enableQuotasInConfig = false;
         const wrapper = await mountDiskUsageSummaryWrapper(enableQuotasInConfig);
@@ -102,16 +95,33 @@ describe("DiskUsageSummary.vue", () => {
                 total_disk_usage: 2097152,
             },
         ];
-        mockFetcher.path("/api/users/{user_id}/usage").method("get").mock({ data: updatedFakeQuotaUsages });
-        mockFetcher.path("/api/tasks/{task_id}/state").method("get").mock({ data: "SUCCESS" });
+        server.use(
+            http.get("/api/users/{user_id}/usage", ({ response }) => {
+                return response(200).json(updatedFakeQuotaUsages);
+            }),
+            http.put("/api/users/current/recalculate_disk_usage", ({ response }) => {
+                return response(200).json({ id: FAKE_TASK_ID, ignored: false });
+            }),
+            http.get("/api/tasks/{task_id}/state", ({ response }) => {
+                return response(200).json("PENDING");
+            })
+        );
         const refreshButton = wrapper.find("#refresh-disk-usage");
         await refreshButton.trigger("click");
-        const refreshingAlert = wrapper.find(".refreshing-alert");
-        expect(refreshingAlert.exists()).toBe(true);
+        await flushPromises();
+        expect(wrapper.find(".refreshing-alert").exists()).toBe(true);
+
         // Make sure the refresh has finished before checking the quota usage
+        server.use(
+            http.get("/api/tasks/{task_id}/state", ({ response }) => {
+                return response(200).json("SUCCESS");
+            })
+        );
+        jest.runAllTimers();
         await flushPromises();
+
         // The refreshing alert should disappear and the quota usage should be updated
-        expect(refreshingAlert.exists()).toBe(false);
+        expect(wrapper.find(".refreshing-alert").exists()).toBe(false);
         expect(quotaUsage.text()).toContain("2 MB");
     });
 });
diff --git a/client/src/components/User/DiskUsage/DiskUsageSummary.vue b/client/src/components/User/DiskUsage/DiskUsageSummary.vue
index f17dc84d8688bdb45608228295455f3dd2db9f4d..1153c0bf50806c2da610f3684a93b9c8e1e77c39 100644
--- a/client/src/components/User/DiskUsage/DiskUsageSummary.vue
+++ b/client/src/components/User/DiskUsage/DiskUsageSummary.vue
@@ -2,16 +2,14 @@
 import { storeToRefs } from "pinia";
 import { computed, onMounted, ref, watch } from "vue";
 
-import { recalculateDiskUsage } from "@/api/users";
+import { type AsyncTaskResultSummary, GalaxyApi } from "@/api";
+import { fetchCurrentUserQuotaUsages, type QuotaUsage } from "@/api/users";
 import { useConfig } from "@/composables/config";
 import { useTaskMonitor } from "@/composables/taskMonitor";
 import { useUserStore } from "@/stores/userStore";
 import { errorMessageAsString } from "@/utils/simple-error";
 import { bytesToString } from "@/utils/utils";
 
-import { QuotaUsage } from "./Quota/model";
-import { fetch } from "./Quota/services";
-
 import QuotaUsageSummary from "@/components/User/DiskUsage/Quota/QuotaUsageSummary.vue";
 
 const { config, isConfigLoaded } = useConfig(true);
@@ -58,26 +56,30 @@ async function displayRecalculationForSeconds(seconds: number) {
 }
 
 async function onRefresh() {
-    try {
-        const response = await recalculateDiskUsage({});
-        if (response.status == 200) {
-            // Wait for the task to complete
-            waitForTask(response.data.id);
-        } else if (response.status == 204) {
-            // We cannot track any task, so just display the
-            // recalculation message for a reasonable amount of time
-            await displayRecalculationForSeconds(30);
-        }
-    } catch (e) {
-        errorMessage.value = errorMessageAsString(e);
+    const { response, data, error } = await GalaxyApi().PUT("/api/users/current/recalculate_disk_usage");
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return;
+    }
+
+    if (response.status == 200) {
+        // Wait for the task to complete
+        const asyncTaskResponse = data as AsyncTaskResultSummary;
+        waitForTask(asyncTaskResponse.id);
+    } else if (response.status == 204) {
+        // We cannot track any task, so just display the
+        // recalculation message for a reasonable amount of time
+        await displayRecalculationForSeconds(30);
     }
 }
 
 async function loadQuotaUsages() {
     try {
-        quotaUsages.value = await fetch();
-    } catch (e) {
-        errorMessage.value = errorMessageAsString(e);
+        const currentUserQuotaUsages = await fetchCurrentUserQuotaUsages();
+        quotaUsages.value = currentUserQuotaUsages;
+    } catch (error) {
+        errorMessage.value = errorMessageAsString(error);
     }
 }
 
diff --git a/client/src/components/User/DiskUsage/Management/Cleanup/categories.ts b/client/src/components/User/DiskUsage/Management/Cleanup/categories.ts
index c6a8b6bdb36f4189ddb6d4439f14bb6ba2478f4e..823b74707b4e46ded701bdb41f90869eabe67d48 100644
--- a/client/src/components/User/DiskUsage/Management/Cleanup/categories.ts
+++ b/client/src/components/User/DiskUsage/Management/Cleanup/categories.ts
@@ -12,7 +12,7 @@ import {
     fetchDiscardedHistories,
     fetchDiscardedHistoriesSummary,
 } from "../services";
-import type { CleanupCategory } from "./model";
+import { type CleanupCategory } from "./model";
 
 export function useCleanupCategories() {
     const cleanupCategories = ref<CleanupCategory[]>([
diff --git a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanableSummary.ts b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanableSummary.ts
index 92b5859afaa8e99ff37768891b9e8e07e94bff5e..42cb07b9c2215db31208482f5b4b5d9e0fc3cfd8 100644
--- a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanableSummary.ts
+++ b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanableSummary.ts
@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { bytesToString } from "@/utils/utils";
 
 type CleanableItemsSummaryResponse = components["schemas"]["CleanableItemsSummary"];
diff --git a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupCategory.ts b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupCategory.ts
index a7ed4d620591eba1a3e65bf2a4cae28654230081..62448cdcebc791d193c1e6e53dec4c945de934c3 100644
--- a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupCategory.ts
+++ b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupCategory.ts
@@ -1,4 +1,4 @@
-import type { CleanupOperation } from ".";
+import { type CleanupOperation } from ".";
 
 /**
  * Defines a new category to display in the Storage Management Dashboard to
diff --git a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupOperation.ts b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupOperation.ts
index 59b320b7ebe9bad2c52600538f2c07a61498dbfc..c3741862d39ee38c2b901ca6df6aa81b8e785b7e 100644
--- a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupOperation.ts
+++ b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupOperation.ts
@@ -1,7 +1,7 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 
-import type { CleanableSummary } from "./CleanableSummary";
-import type { CleanupResult } from "./CleanupResult";
+import { type CleanableSummary } from "./CleanableSummary";
+import { type CleanupResult } from "./CleanupResult";
 
 export type CleanableItem = components["schemas"]["StoredItem"];
 export type SortableKey = "name" | "size" | "update_time";
diff --git a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupResult.ts b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupResult.ts
index e777d865fc23e023ec4533adca8a1f448fa143d1..c1532b67969ae4fc7c2eb4527e239db7312cb75d 100644
--- a/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupResult.ts
+++ b/client/src/components/User/DiskUsage/Management/Cleanup/model/CleanupResult.ts
@@ -1,7 +1,7 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { bytesToString } from "@/utils/utils";
 
-import type { CleanableItem } from "./CleanupOperation";
+import { type CleanableItem } from "./CleanupOperation";
 
 export type StorageItemsCleanupResult = components["schemas"]["StorageItemsCleanupResult"];
 
diff --git a/client/src/components/User/DiskUsage/Management/services.ts b/client/src/components/User/DiskUsage/Management/services.ts
index 81cb5d343faef045dfd81c521559ee640f779787..228094da1a6e89236be9a7cb9d0647cf1f5548dd 100644
--- a/client/src/components/User/DiskUsage/Management/services.ts
+++ b/client/src/components/User/DiskUsage/Management/services.ts
@@ -1,107 +1,100 @@
-import { fetcher } from "@/api/schema";
-import { rethrowSimple } from "@/utils/simple-error";
+import { GalaxyApi } from "@/api";
+import { errorMessageAsString, rethrowSimple } from "@/utils/simple-error";
 
 import { type CleanableItem, CleanableSummary, CleanupResult, PaginationOptions } from "./Cleanup/model";
 
-const discardedDatasetsSummaryFetcher = fetcher.path("/api/storage/datasets/discarded/summary").method("get").create();
-
 export async function fetchDiscardedDatasetsSummary(): Promise<CleanableSummary> {
-    try {
-        const { data } = await discardedDatasetsSummaryFetcher({});
-        return new CleanableSummary(data);
-    } catch (e) {
-        rethrowSimple(e);
+    const { data, error } = await GalaxyApi().GET("/api/storage/datasets/discarded/summary");
+
+    if (error) {
+        rethrowSimple(error);
     }
-}
 
-const discardedDatasetsFetcher = fetcher.path("/api/storage/datasets/discarded").method("get").create();
+    return new CleanableSummary(data);
+}
 
 export async function fetchDiscardedDatasets(options?: PaginationOptions): Promise<CleanableItem[]> {
-    try {
-        options = options ?? new PaginationOptions();
-        const { data } = await discardedDatasetsFetcher({
-            offset: options.offset,
-            limit: options.limit,
-            order: options.order,
-        });
-        return data;
-    } catch (e) {
-        rethrowSimple(e);
+    options = options ?? new PaginationOptions();
+    const { data, error } = await GalaxyApi().GET("/api/storage/datasets/discarded", {
+        params: { query: options },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
-}
 
-const datasetsCleaner = fetcher.path("/api/storage/datasets").method("delete").create();
+    return data;
+}
 
 export async function cleanupDatasets(items: CleanableItem[]): Promise<CleanupResult> {
-    try {
-        const item_ids = items.map((item) => item.id);
-        const { data } = await datasetsCleaner({
-            item_ids,
-        });
-        return new CleanupResult(data, items);
-    } catch (error) {
-        return new CleanupResult(undefined, items, error as string);
+    const itemIds = items.map((item) => item.id);
+    const { data, error } = await GalaxyApi().DELETE("/api/storage/datasets", {
+        body: { item_ids: itemIds },
+    });
+
+    if (error) {
+        return new CleanupResult(undefined, items, errorMessageAsString(error));
     }
-}
 
-const discardedHistoriesSummaryFetcher = fetcher
-    .path("/api/storage/histories/discarded/summary")
-    .method("get")
-    .create();
+    return new CleanupResult(data, items);
+}
 
 export async function fetchDiscardedHistoriesSummary(): Promise<CleanableSummary> {
-    try {
-        const { data } = await discardedHistoriesSummaryFetcher({});
-        return new CleanableSummary(data);
-    } catch (e) {
-        rethrowSimple(e);
+    const { data, error } = await GalaxyApi().GET("/api/storage/histories/discarded/summary");
+
+    if (error) {
+        rethrowSimple(error);
     }
-}
 
-const discardedHistoriesFetcher = fetcher.path("/api/storage/histories/discarded").method("get").create();
+    return new CleanableSummary(data);
+}
 
 export async function fetchDiscardedHistories(options?: PaginationOptions): Promise<CleanableItem[]> {
-    try {
-        options = options ?? new PaginationOptions();
-        const { data } = await discardedHistoriesFetcher({
-            offset: options.offset,
-            limit: options.limit,
-            order: options.order,
-        });
-        return data;
-    } catch (e) {
-        rethrowSimple(e);
+    options = options ?? new PaginationOptions();
+
+    const { data, error } = await GalaxyApi().GET("/api/storage/histories/discarded", {
+        params: { query: options },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
+
+    return data;
 }
 
-const historiesCleaner = fetcher.path("/api/storage/histories").method("delete").create();
 export async function cleanupHistories(items: CleanableItem[]) {
-    try {
-        const item_ids = items.map((item) => item.id);
-        const { data } = await historiesCleaner({
-            item_ids,
-        });
-        return new CleanupResult(data, items);
-    } catch (error) {
-        return new CleanupResult(undefined, items, error as string);
+    const itemIds = items.map((item) => item.id);
+    const { data, error } = await GalaxyApi().DELETE("/api/storage/histories", {
+        body: { item_ids: itemIds },
+    });
+
+    if (error) {
+        return new CleanupResult(undefined, items, errorMessageAsString(error));
     }
-}
 
-const archivedHistoriesSummaryFetcher = fetcher.path("/api/storage/histories/archived/summary").method("get").create();
+    return new CleanupResult(data, items);
+}
 
 export async function fetchArchivedHistoriesSummary(): Promise<CleanableSummary> {
-    const { data } = await archivedHistoriesSummaryFetcher({});
+    const { data, error } = await GalaxyApi().GET("/api/storage/histories/archived/summary");
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     return new CleanableSummary(data);
 }
 
-const archivedHistoriesFetcher = fetcher.path("/api/storage/histories/archived").method("get").create();
-
 export async function fetchArchivedHistories(options?: PaginationOptions): Promise<CleanableItem[]> {
     options = options ?? new PaginationOptions();
-    const { data } = await archivedHistoriesFetcher({
-        offset: options.offset,
-        limit: options.limit,
-        order: options.order,
+    const { data, error } = await GalaxyApi().GET("/api/storage/histories/archived", {
+        params: { query: options },
     });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     return data;
 }
diff --git a/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.test.ts b/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.test.ts
index 289563e46d4204b4675c247005c1efc26cd181fc..5de1bb6d4342ca6e3b926083acb7376071e31003 100644
--- a/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.test.ts
+++ b/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.test.ts
@@ -1,20 +1,20 @@
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { QuotaUsage } from "./model";
+import { type QuotaUsage, toQuotaUsage } from "./model";
 
 import QuotaUsageBar from "./QuotaUsageBar.vue";
 
 const localVue = getLocalVue();
 
-const NON_DEFAULT_QUOTA_USAGE: QuotaUsage = new QuotaUsage({
+const NON_DEFAULT_QUOTA_USAGE: QuotaUsage = toQuotaUsage({
     quota_source_label: "The label",
     quota_bytes: 68468436,
     total_disk_usage: 4546654,
     quota_percent: 20,
 });
 
-const UNLIMITED_USAGE: QuotaUsage = new QuotaUsage({
+const UNLIMITED_USAGE: QuotaUsage = toQuotaUsage({
     quota_source_label: "Unlimited",
     quota_bytes: undefined,
     total_disk_usage: 4546654,
@@ -22,7 +22,7 @@ const UNLIMITED_USAGE: QuotaUsage = new QuotaUsage({
 });
 
 function mountQuotaUsageBarWith(quotaUsage: QuotaUsage) {
-    const wrapper = mount(QuotaUsageBar, { propsData: { quotaUsage }, localVue });
+    const wrapper = mount(QuotaUsageBar as object, { propsData: { quotaUsage }, localVue });
     return wrapper;
 }
 
diff --git a/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.vue b/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.vue
index 46ac1b46cc7f4cb587af7e0d23b20c1510ae3168..eb03f59664c1d9ab15a96394727e23358aed3b17 100644
--- a/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.vue
+++ b/client/src/components/User/DiskUsage/Quota/QuotaUsageBar.vue
@@ -3,7 +3,7 @@ import { computed, ref } from "vue";
 
 import localize from "@/utils/localization";
 
-import { DEFAULT_QUOTA_SOURCE_LABEL, QuotaUsage } from "./model/QuotaUsage";
+import { DEFAULT_QUOTA_SOURCE_LABEL, type QuotaUsage } from "./model/QuotaUsage";
 
 interface QuotaUsageBarProps {
     quotaUsage: QuotaUsage;
diff --git a/client/src/components/User/DiskUsage/Quota/QuotaUsageProvider.js b/client/src/components/User/DiskUsage/Quota/QuotaUsageProvider.js
index 5aa980b1c19ab264107d9c3d0eaad0e1c36ee16d..fe8bf99fab277708ee9b1cca28b6fda7bd3ccceb 100644
--- a/client/src/components/User/DiskUsage/Quota/QuotaUsageProvider.js
+++ b/client/src/components/User/DiskUsage/Quota/QuotaUsageProvider.js
@@ -1,26 +1,14 @@
-import axios from "axios";
 import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
-import { getAppRoot } from "onload/loadConfig";
-import { rethrowSimple } from "utils/simple-error";
 
-import { QuotaUsage } from "./model";
+import { fetchCurrentUserQuotaSourceUsage } from "@/api/users";
 
 /**
  * Fetches the disk usage corresponding to one quota source label -
  * or the default quota sources if the supplied label is null.
- * @returns {<QuotaUsage>}
  */
 async function fetchQuotaSourceUsage({ quotaSourceLabel = null }) {
-    if (quotaSourceLabel == null) {
-        quotaSourceLabel = "__null__";
-    }
-    const url = `${getAppRoot()}api/users/current/usage/${quotaSourceLabel}`;
-    try {
-        const { data } = await axios.get(url);
-        return new QuotaUsage(data);
-    } catch (e) {
-        rethrowSimple(e);
-    }
+    return fetchCurrentUserQuotaSourceUsage(quotaSourceLabel);
 }
 
+// TODO: replace provider pattern with composable
 export const QuotaSourceUsageProvider = SingleQueryProvider(fetchQuotaSourceUsage);
diff --git a/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.test.ts b/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.test.ts
index 0a79061792b60dd0578018725bf9a7a874226032..e0ccd5cfc18698df027f6ca80cb6d782a3e55ad0 100644
--- a/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.test.ts
+++ b/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.test.ts
@@ -1,7 +1,7 @@
 import { shallowMount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
-import { QuotaUsage } from "./model";
+import { type QuotaUsage, toQuotaUsage } from "./model";
 
 import QuotaUsageSummary from "./QuotaUsageSummary.vue";
 
@@ -11,17 +11,17 @@ const QUOTA_1_BYTES = 654846535;
 const QUOTA_2_BYTES = 68468436;
 
 const FAKE_QUOTA_USAGES_LIST: QuotaUsage[] = [
-    new QuotaUsage({
+    toQuotaUsage({
         quota_source_label: "source 1",
         quota_bytes: QUOTA_1_BYTES,
         total_disk_usage: QUOTA_1_BYTES,
     }),
-    new QuotaUsage({
+    toQuotaUsage({
         quota_source_label: "source 2",
         quota_bytes: QUOTA_2_BYTES,
         total_disk_usage: QUOTA_2_BYTES,
     }),
-    new QuotaUsage({
+    toQuotaUsage({
         quota_source_label: "Unlimited source",
         quota_bytes: undefined,
         total_disk_usage: 0,
@@ -29,7 +29,7 @@ const FAKE_QUOTA_USAGES_LIST: QuotaUsage[] = [
 ];
 
 function mountQuotaUsageSummaryWith(quotaUsages: QuotaUsage[]) {
-    const wrapper = shallowMount(QuotaUsageSummary, { propsData: { quotaUsages }, localVue });
+    const wrapper = shallowMount(QuotaUsageSummary as object, { propsData: { quotaUsages }, localVue });
     return wrapper;
 }
 
@@ -50,12 +50,12 @@ describe("QuotaUsageSummary.vue", () => {
 
     it("should display `unlimited` quota when all sources are unlimited", async () => {
         const FAKE_UNLIMITED_QUOTA_USAGES: QuotaUsage[] = [
-            new QuotaUsage({
+            toQuotaUsage({
                 quota_source_label: "Unlimited source 1",
                 quota_bytes: undefined,
                 total_disk_usage: QUOTA_1_BYTES,
             }),
-            new QuotaUsage({
+            toQuotaUsage({
                 quota_source_label: "Unlimited source 2",
                 quota_bytes: undefined,
                 total_disk_usage: QUOTA_2_BYTES,
diff --git a/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.vue b/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.vue
index 2a180cf0bf62697d7dc185eaff0a80258f51adba..eb57c797272c5abeedf87a0fc46b3ec803ac2457 100644
--- a/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.vue
+++ b/client/src/components/User/DiskUsage/Quota/QuotaUsageSummary.vue
@@ -3,7 +3,7 @@ import { computed } from "vue";
 
 import { bytesToString } from "@/utils/utils";
 
-import type { QuotaUsage } from "./model";
+import { type QuotaUsage } from "./model";
 
 import QuotaUsageBar from "./QuotaUsageBar.vue";
 
diff --git a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
index 006440faf1a2787b48ba6f11882f8232fa8edf3c..2b4cab27df7ef47ffe4b32397f2927dc53004201 100644
--- a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
+++ b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
@@ -1,4 +1,4 @@
-import { DEFAULT_QUOTA_SOURCE_LABEL, QuotaUsage, type UserQuotaUsageData } from "./QuotaUsage";
+import { DEFAULT_QUOTA_SOURCE_LABEL, toQuotaUsage, type UserQuotaUsageData } from "./QuotaUsage";
 
 const RAW_DEFAULT_QUOTA_USAGE: UserQuotaUsageData = {
     quota_source_label: undefined,
@@ -22,9 +22,9 @@ const RAW_UNLIMITED_SOURCE_QUOTA_USAGE: UserQuotaUsageData = {
 };
 
 describe("QuotaUsage", () => {
-    const defaultQuotaUsage = new QuotaUsage(RAW_DEFAULT_QUOTA_USAGE);
-    const limitedQuotaUsage = new QuotaUsage(RAW_LIMITED_SOURCE_QUOTA_USAGE);
-    const unlimitedQuotaUsage = new QuotaUsage(RAW_UNLIMITED_SOURCE_QUOTA_USAGE);
+    const defaultQuotaUsage = toQuotaUsage(RAW_DEFAULT_QUOTA_USAGE);
+    const limitedQuotaUsage = toQuotaUsage(RAW_LIMITED_SOURCE_QUOTA_USAGE);
+    const unlimitedQuotaUsage = toQuotaUsage(RAW_UNLIMITED_SOURCE_QUOTA_USAGE);
 
     test("default quota source label should have the default value", () => {
         expect(defaultQuotaUsage.sourceLabel).toBe(DEFAULT_QUOTA_SOURCE_LABEL);
diff --git a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
index 8e8a1c16d016d311adb97645ba37363b0ca2c075..bad31280ec3781da6e039a227d64b023b7d7b42b 100644
--- a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
+++ b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
@@ -1,4 +1,4 @@
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { bytesToString } from "@/utils/utils";
 
 export const DEFAULT_QUOTA_SOURCE_LABEL = "Default";
@@ -8,7 +8,55 @@ export type UserQuotaUsageData = components["schemas"]["UserQuotaUsage"];
 /**
  * Contains information about quota usage for a particular ObjectStore.
  */
-export class QuotaUsage {
+export interface QuotaUsage {
+    rawSourceLabel: string | null;
+
+    /**
+     * The name of the ObjectStore associated with the quota.
+     */
+    sourceLabel: string;
+
+    /**
+     * The maximum allowed disk usage in bytes.
+     */
+    quotaInBytes: number | undefined | null;
+
+    /**
+     * The total amount of bytes used in this ObjectStore.
+     */
+    totalDiskUsageInBytes: number;
+
+    /**
+     * The percentage of used quota.
+     */
+    quotaPercent: number | undefined | null;
+
+    /**
+     * The maximum allowed disk usage as human readable size.
+     */
+    niceQuota: string;
+
+    /**
+     * The total amount of disk used in this ObjectStore as human readable size.
+     */
+    niceTotalDiskUsage: string;
+
+    /**
+     * Whether this ObjectStore has unlimited quota
+     */
+    isUnlimited: boolean;
+}
+
+/**
+ * Converts a raw UserQuotaUsageData response to a QuotaUsage object.
+ * @param data The raw UserQuotaUsageData response.
+ * @returns The QuotaUsage object.
+ */
+export function toQuotaUsage(data: UserQuotaUsageData): QuotaUsage {
+    return new QuotaUsageModel(data);
+}
+
+class QuotaUsageModel implements QuotaUsage {
     private _data: UserQuotaUsageData;
 
     constructor(data: UserQuotaUsageData) {
@@ -19,37 +67,22 @@ export class QuotaUsage {
         return this._data.quota_source_label ?? null;
     }
 
-    /**
-     * The name of the ObjectStore associated with the quota.
-     */
     get sourceLabel(): string {
         return this.rawSourceLabel ?? DEFAULT_QUOTA_SOURCE_LABEL;
     }
 
-    /**
-     * The maximum allowed disk usage in bytes.
-     */
     get quotaInBytes(): number | undefined | null {
         return this._data.quota_bytes;
     }
 
-    /**
-     * The total amount of bytes used in this ObjectStore.
-     */
     get totalDiskUsageInBytes(): number {
         return this._data.total_disk_usage;
     }
 
-    /**
-     * The percentage of used quota.
-     */
     get quotaPercent(): number | undefined | null {
         return this._data.quota_percent;
     }
 
-    /**
-     * The maximum allowed disk usage as human readable size.
-     */
     get niceQuota(): string {
         if (this.isUnlimited) {
             return "unlimited";
@@ -60,16 +93,10 @@ export class QuotaUsage {
         return "unknown";
     }
 
-    /**
-     * The total amount of disk used in this ObjectStore as human readable size.
-     */
     get niceTotalDiskUsage(): string {
         return bytesToString(this.totalDiskUsageInBytes, true, undefined);
     }
 
-    /**
-     * Whether this ObjectStore has unlimited quota
-     */
     get isUnlimited(): boolean {
         return !this.quotaInBytes;
     }
diff --git a/client/src/components/User/DiskUsage/Quota/model/index.ts b/client/src/components/User/DiskUsage/Quota/model/index.ts
index c5818f3a191e80a73eceec9d3dcbfc549bb46e56..29238241745d0062166e5ce2d050c2fe8c7da7d9 100644
--- a/client/src/components/User/DiskUsage/Quota/model/index.ts
+++ b/client/src/components/User/DiskUsage/Quota/model/index.ts
@@ -1 +1 @@
-export { QuotaUsage, UserQuotaUsageData } from "./QuotaUsage";
+export { type QuotaUsage, toQuotaUsage } from "./QuotaUsage";
diff --git a/client/src/components/User/DiskUsage/Quota/services.ts b/client/src/components/User/DiskUsage/Quota/services.ts
deleted file mode 100644
index c9353d6170a62c955cad57fc17a2d1a0db007941..0000000000000000000000000000000000000000
--- a/client/src/components/User/DiskUsage/Quota/services.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import { fetchQuotaUsages } from "@/api/users";
-
-import { QuotaUsage, UserQuotaUsageData } from "./model/index";
-
-export async function fetch() {
-    const { data } = await fetchQuotaUsages({ user_id: "current" });
-    return data.map((u: UserQuotaUsageData) => new QuotaUsage(u));
-}
diff --git a/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.test.ts b/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.test.ts
index 0e86b15ba4b219e29afaff06e594e110e925276a..8dd4d51e99bd4156431cae9f72a276248d586ba0 100644
--- a/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.test.ts
+++ b/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.test.ts
@@ -1,6 +1,6 @@
 import { mount } from "@vue/test-utils";
 
-import type { DataValuePoint } from ".";
+import { type DataValuePoint } from ".";
 
 import BarChart from "./BarChart.vue";
 
diff --git a/client/src/components/User/DiskUsage/Visualizations/Charts/formatters.ts b/client/src/components/User/DiskUsage/Visualizations/Charts/formatters.ts
index 565922a65b0aa04d9070e3441aee154a9fbd8fe1..3d96ff7f56cdc1ceca6812e0a61b27c5ba452884 100644
--- a/client/src/components/User/DiskUsage/Visualizations/Charts/formatters.ts
+++ b/client/src/components/User/DiskUsage/Visualizations/Charts/formatters.ts
@@ -1,6 +1,6 @@
 import { bytesToString } from "@/utils/utils";
 
-import type { DataValuePoint } from ".";
+import { type DataValuePoint } from ".";
 
 export function bytesLabelFormatter(dataPoint?: DataValuePoint | null): string {
     return dataPoint ? `${dataPoint.label}: ${bytesToString(dataPoint.value)}` : "No data";
diff --git a/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue b/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
index 2f28f1fcba8bdcd110ef81bd62179c9e420c2018..55d7a7c70d7569201cb8c13c0228da4c1e6c6102 100644
--- a/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/ObjectStoreActions.vue
@@ -17,7 +17,7 @@ const props = defineProps<Props>();
 
 library.add(faChartBar);
 
-const label = computed(() => props.data.id);
+const label = computed(() => props.data.label);
 const viewDetailsIcon = computed(() => "chart-bar");
 
 const emit = defineEmits<{
diff --git a/client/src/components/User/DiskUsage/Visualizations/ObjectStoresStorageOverview.vue b/client/src/components/User/DiskUsage/Visualizations/ObjectStoresStorageOverview.vue
index aa6efe55a2fb4fc73dc01bdeff7f3e01df20151c..5fbf451e16123973c9e2d4b90ebbcc3cc83c23e1 100644
--- a/client/src/components/User/DiskUsage/Visualizations/ObjectStoresStorageOverview.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/ObjectStoresStorageOverview.vue
@@ -2,9 +2,10 @@
 import { ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { fetchObjectStoreUsages } from "@/api/users";
+import { GalaxyApi } from "@/api";
 import { useObjectStoreStore } from "@/stores/objectStoreStore";
 import localize from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import type { DataValuePoint } from "./Charts";
 import { byteFormattingForChart, useDataLoading } from "./util";
@@ -25,7 +26,15 @@ const { getObjectStoreNameById } = useObjectStoreStore();
 const { isLoading, loadDataOnMount } = useDataLoading();
 
 loadDataOnMount(async () => {
-    const { data } = await fetchObjectStoreUsages({ user_id: "current" });
+    const { data, error } = await GalaxyApi().GET("/api/users/{user_id}/objectstore_usage", {
+        params: { path: { user_id: "current" } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+        return;
+    }
+
     const objectStoresBySize = data.sort((a, b) => b.total_disk_usage - a.total_disk_usage);
     objectStoresBySizeData.value = objectStoresBySize.map((objectStore) => ({
         id: objectStore.object_store_id,
diff --git a/client/src/components/User/DiskUsage/Visualizations/service.ts b/client/src/components/User/DiskUsage/Visualizations/service.ts
index b6a64ee206160e544e5b469fb562ece8bb6b8b85..25a8856e654d64590ddbb6016ae7ec2389fea71e 100644
--- a/client/src/components/User/DiskUsage/Visualizations/service.ts
+++ b/client/src/components/User/DiskUsage/Visualizations/service.ts
@@ -1,5 +1,6 @@
-import { datasetsFetcher, purgeDataset, undeleteDataset } from "@/api/datasets";
-import { archivedHistoriesFetcher, deleteHistory, historiesFetcher, undeleteHistory } from "@/api/histories";
+import { GalaxyApi } from "@/api";
+import { purgeDataset, undeleteDataset } from "@/api/datasets";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export interface ItemSizeSummary {
     id: string;
@@ -16,19 +17,40 @@ interface PurgeableItemSizeSummary extends ItemSizeSummary {
 const itemSizeSummaryFields = "id,name,size,deleted,archived";
 
 export async function fetchAllHistoriesSizeSummary(): Promise<ItemSizeSummary[]> {
-    const nonPurgedHistoriesResponse = await historiesFetcher({
-        keys: itemSizeSummaryFields,
-        q: ["deleted", "purged"],
-        qv: ["None", "false"],
-    });
-    const nonPurgedArchivedHistories = await archivedHistoriesFetcher({
-        keys: itemSizeSummaryFields,
-        q: ["purged"],
-        qv: ["false"],
+    const { data: nonPurgedHistories, error: nonPurgedHistoriesError } = await GalaxyApi().GET("/api/histories", {
+        params: {
+            query: {
+                keys: itemSizeSummaryFields,
+                q: ["deleted", "purged"],
+                qv: ["None", "false"],
+            },
+        },
     });
+
+    if (nonPurgedHistoriesError) {
+        rethrowSimple(nonPurgedHistoriesError);
+    }
+
+    const { data: nonPurgedArchivedHistories, error: nonPurgedArchivedHistoriesError } = await GalaxyApi().GET(
+        "/api/histories/archived",
+        {
+            params: {
+                query: {
+                    keys: itemSizeSummaryFields,
+                    q: ["purged"],
+                    qv: ["false"],
+                },
+            },
+        }
+    );
+
+    if (nonPurgedArchivedHistoriesError) {
+        rethrowSimple(nonPurgedArchivedHistoriesError);
+    }
+
     const allHistoriesTakingStorageResponse = [
-        ...(nonPurgedHistoriesResponse.data as ItemSizeSummary[]),
-        ...(nonPurgedArchivedHistories.data as ItemSizeSummary[]),
+        ...(nonPurgedHistories as ItemSizeSummary[]),
+        ...(nonPurgedArchivedHistories as ItemSizeSummary[]),
     ];
     return allHistoriesTakingStorageResponse;
 }
@@ -46,36 +68,70 @@ export async function fetchHistoryContentsSizeSummary(
         qv.push(objectStoreId);
     }
 
-    const response = await datasetsFetcher({
-        history_id: historyId,
-        keys: itemSizeSummaryFields,
-        limit,
-        order: "size-dsc",
-        q: q,
-        qv: qv,
+    const { data, error } = await GalaxyApi().GET("/api/datasets", {
+        params: {
+            query: {
+                history_id: historyId,
+                keys: itemSizeSummaryFields,
+                limit,
+                order: "size-dsc",
+                q: q,
+                qv: qv,
+            },
+        },
     });
-    return response.data as unknown as ItemSizeSummary[];
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data as unknown as ItemSizeSummary[];
 }
 
 export async function fetchObjectStoreContentsSizeSummary(objectStoreId: string, limit = 5000) {
-    const response = await datasetsFetcher({
-        keys: itemSizeSummaryFields,
-        limit,
-        order: "size-dsc",
-        q: ["purged", "history_content_type", "object_store_id"],
-        qv: ["false", "dataset", objectStoreId],
+    const { data, error } = await GalaxyApi().GET("/api/datasets", {
+        params: {
+            query: {
+                keys: itemSizeSummaryFields,
+                limit,
+                order: "size-dsc",
+                q: ["purged", "history_content_type", "object_store_id"],
+                qv: ["false", "dataset", objectStoreId],
+            },
+        },
     });
-    return response.data as unknown as ItemSizeSummary[];
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data as unknown as ItemSizeSummary[];
 }
 
 export async function undeleteHistoryById(historyId: string): Promise<ItemSizeSummary> {
-    const response = await undeleteHistory({ history_id: historyId });
-    return response.data as unknown as ItemSizeSummary;
+    const { data, error } = await GalaxyApi().POST("/api/histories/deleted/{history_id}/undelete", {
+        params: {
+            path: { history_id: historyId },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    return data as ItemSizeSummary;
 }
 
 export async function purgeHistoryById(historyId: string): Promise<PurgeableItemSizeSummary> {
-    const response = await deleteHistory({ history_id: historyId, purge: true });
-    return response.data as unknown as PurgeableItemSizeSummary;
+    const { data, error } = await GalaxyApi().DELETE("/api/histories/{history_id}", {
+        params: {
+            path: { history_id: historyId },
+            query: { purge: true },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data as PurgeableItemSizeSummary;
 }
 
 export async function undeleteDatasetById(datasetId: string): Promise<ItemSizeSummary> {
diff --git a/client/src/components/User/DiskUsage/Visualizations/util.ts b/client/src/components/User/DiskUsage/Visualizations/util.ts
index 58581a001190a634ffe0b37d477cd0dd16601cba..11b60512e48690583d50252cf49a86812c3525ae 100644
--- a/client/src/components/User/DiskUsage/Visualizations/util.ts
+++ b/client/src/components/User/DiskUsage/Visualizations/util.ts
@@ -6,7 +6,7 @@ import { useConfirmDialog } from "@/composables/confirmDialog";
 import { useToast } from "@/composables/toast";
 import localize from "@/utils/localization";
 
-import type { DataValuePoint } from "./Charts";
+import { type DataValuePoint } from "./Charts";
 import { bytesLabelFormatter, bytesValueFormatter } from "./Charts/formatters";
 import { type ItemSizeSummary, purgeDatasetById, undeleteDatasetById } from "./service";
 
diff --git a/client/src/components/User/ExternalIdentities/ExternalIdentities.vue b/client/src/components/User/ExternalIdentities/ExternalIdentities.vue
index 6714b06b5da6f19ffff4c8cfe43cb0da51d60532..0165358c79e74396532ad778b047f88e30b7ab81 100644
--- a/client/src/components/User/ExternalIdentities/ExternalIdentities.vue
+++ b/client/src/components/User/ExternalIdentities/ExternalIdentities.vue
@@ -46,7 +46,8 @@
                 title="Disconnect External Identity"
                 class="d-block mt-3"
                 @click="onDisconnect(item)">
-                Disconnect {{ item.provider.charAt(0).toUpperCase() + item.provider.slice(1) }} - {{ item.email }}
+                Disconnect {{ capitalizeAsTitle(item.provider_label) }} -
+                {{ item.email }}
             </b-button>
 
             <b-modal
@@ -98,6 +99,8 @@ import { sanitize } from "dompurify";
 import { userLogout } from "utils/logout";
 import Vue from "vue";
 
+import { capitalizeFirstLetter } from "@/utils/strings";
+
 import svc from "./service";
 
 import ExternalLogin from "components/User/ExternalIdentities/ExternalLogin.vue";
@@ -156,6 +159,9 @@ export default {
         Toast.success(notificationMessage);
     },
     methods: {
+        capitalizeAsTitle(str) {
+            return capitalizeFirstLetter(str);
+        },
         loadIdentities() {
             this.loading = true;
             svc.getIdentityProviders()
diff --git a/client/src/components/User/ExternalIdentities/ExternalLogin.vue b/client/src/components/User/ExternalIdentities/ExternalLogin.vue
index 2d70b41416e0d4fbbf5c815faf8371cd377328a9..c89310471ec1ed194556842d2e8567e8a1e1d677 100644
--- a/client/src/components/User/ExternalIdentities/ExternalLogin.vue
+++ b/client/src/components/User/ExternalIdentities/ExternalLogin.vue
@@ -7,6 +7,7 @@ import Multiselect from "vue-multiselect";
 import { useConfig } from "@/composables/config";
 import { withPrefix } from "@/utils/redirect";
 import { errorMessageAsString } from "@/utils/simple-error";
+import { capitalizeFirstLetter } from "@/utils/strings";
 
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
@@ -16,7 +17,14 @@ interface Idp {
     OrganizationName: string;
     RandS: boolean;
 }
-type OIDCConfig = Record<string, { icon?: string }>;
+type OIDCConfig = Record<
+    string,
+    {
+        icon?: string;
+        label?: string;
+        custom_button_text?: string;
+    }
+>;
 
 interface Props {
     loginPage?: boolean;
@@ -77,7 +85,14 @@ async function submitOIDCLogin(idp: string) {
     loading.value = true;
 
     try {
-        const { data } = await axios.post(withPrefix(`/authnz/${idp}/login`));
+        const loginUrl = withPrefix(`/authnz/${idp}/login`);
+        const urlParams = new URLSearchParams(window.location.search);
+        const redirectParam = urlParams.get("redirect");
+
+        const formData = new FormData();
+        formData.append("next", redirectParam || "");
+
+        const { data } = await axios.post(loginUrl, formData, { withCredentials: true });
 
         if (data.redirect_uri) {
             window.location = data.redirect_uri;
@@ -246,6 +261,7 @@ function getIdpPreference() {
                     </small>
                 </p>
             </div>
+
             <span v-if="isConfigLoaded">
                 <div v-for="(iDPInfo, idp) in filteredOIDCIdps" :key="idp" class="m-1">
                     <span v-if="iDPInfo['icon']">
@@ -253,11 +269,22 @@ function getIdpPreference() {
                             <img :src="iDPInfo['icon']" height="45" :alt="idp" />
                         </BButton>
                     </span>
+                    <span v-else-if="iDPInfo['custom_button_text']">
+                        <BButton class="d-block mt-3" @click="submitOIDCLogin(idp)">
+                            <i :class="oIDCIdps[idp]" />
+                            Sign in with {{ iDPInfo["custom_button_text"] }}
+                        </BButton>
+                    </span>
                     <span v-else>
                         <BButton class="d-block mt-3" @click="submitOIDCLogin(idp)">
                             <i :class="oIDCIdps[idp]" />
                             Sign in with
-                            {{ iDPInfo['alias'] || idp.charAt(0).toUpperCase() + idp.slice(1) }}
+                            <span v-if="iDPInfo['label']">
+                                {{ iDPInfo["label"].charAt(0).toUpperCase() + iDPInfo["label"].slice(1) }}
+                            </span>
+                            <span v-else>
+                                {{ capitalizeFirstLetter(idp) }}
+                            </span>
                         </BButton>
                     </span>
                 </div>
diff --git a/client/src/components/User/Notifications/NotificationsCategorySettings.vue b/client/src/components/User/Notifications/NotificationsCategorySettings.vue
new file mode 100644
index 0000000000000000000000000000000000000000..cf46ab9c2a0f401dcad2d4081c5b28400062d34f
--- /dev/null
+++ b/client/src/components/User/Notifications/NotificationsCategorySettings.vue
@@ -0,0 +1,92 @@
+<script setup lang="ts">
+import { computed, ref, watch } from "vue";
+
+import {
+    type NotificationCategory,
+    type NotificationChannel,
+    type UserNotificationPreferences,
+} from "@/api/notifications";
+import { snakeCaseToTitleCase } from "@/utils/strings";
+
+import NotificationsChannelSettings from "./NotificationsChannelSettings.vue";
+
+const categoryDescriptionMap: Record<NotificationCategory, string> = {
+    message: `
+        You will receive these notifications only when your Galaxy administrators send you a message.
+        Please note that for certain critical or urgent messages, you will receive notifications even if you have disabled this channel.
+    `,
+    new_shared_item:
+        "You will receive these notifications when someone shares an item with you i.e. a history, workflow, visualization, etc.",
+};
+
+interface NotificationsCategorySettingsProps {
+    preferences: UserNotificationPreferences;
+    supportedChannels: NotificationChannel[];
+    category: NotificationCategory;
+}
+
+const props = defineProps<NotificationsCategorySettingsProps>();
+
+const emit = defineEmits<{
+    (event: "onCategoryEnabledChange", category: NotificationCategory, value: boolean): void;
+    (event: "onChannelChange", category: NotificationCategory, channel: NotificationChannel, value: boolean): void;
+}>();
+
+const isCategoryEnabled = ref(props.preferences[props.category]!.enabled);
+const checkBoxTitle = computed(() => (isCategoryEnabled.value ? "Disable notifications" : "Enable notifications"));
+const categoryDescription = computed(() => categoryDescriptionMap[props.category]);
+
+watch(
+    () => isCategoryEnabled.value,
+    (newValue) => {
+        emit("onCategoryEnabledChange", props.category, newValue);
+    }
+);
+
+function onChannelChange(category: NotificationCategory, channel: NotificationChannel, value: boolean) {
+    emit("onChannelChange", category, channel, value);
+}
+</script>
+
+<template>
+    <div>
+        <div class="category-header">
+            <BFormCheckbox v-model="isCategoryEnabled" v-b-tooltip.hover :title="checkBoxTitle" switch>
+                <span v-localize class="category-title">{{ snakeCaseToTitleCase(category) }}</span>
+            </BFormCheckbox>
+        </div>
+
+        <div v-if="categoryDescription" v-localize class="category-description">
+            {{ categoryDescription }}
+        </div>
+
+        <div v-for="channel in supportedChannels" :key="channel">
+            <NotificationsChannelSettings
+                :preferences="preferences"
+                :category="category"
+                :is-category-enabled="isCategoryEnabled"
+                :channel="channel"
+                @onChange="onChannelChange" />
+        </div>
+    </div>
+</template>
+
+<style scoped lang="scss">
+.category-header {
+    gap: 1rem;
+    display: flex;
+    align-items: center;
+    justify-content: space-between;
+    margin-bottom: 0.5rem;
+}
+
+.category-title {
+    font-weight: bold;
+}
+
+.category-description {
+    font-size: 0.8rem;
+    font-style: italic;
+    margin-bottom: 0.5rem;
+}
+</style>
diff --git a/client/src/components/User/Notifications/NotificationsChannelSettings.vue b/client/src/components/User/Notifications/NotificationsChannelSettings.vue
new file mode 100644
index 0000000000000000000000000000000000000000..6ff92890d6326c27059afdd1011614840280c80f
--- /dev/null
+++ b/client/src/components/User/Notifications/NotificationsChannelSettings.vue
@@ -0,0 +1,58 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faExclamationCircle } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { ref, watch } from "vue";
+
+import {
+    type NotificationCategory,
+    type NotificationChannel,
+    type UserNotificationPreferences,
+} from "@/api/notifications";
+import { snakeCaseToTitleCase } from "@/utils/strings";
+
+library.add(faExclamationCircle);
+
+interface NotificationsChannelSettingsProps {
+    preferences: UserNotificationPreferences;
+    category: NotificationCategory;
+    isCategoryEnabled: boolean;
+    channel: NotificationChannel;
+}
+
+const props = defineProps<NotificationsChannelSettingsProps>();
+
+const emit = defineEmits<{
+    (event: "onChange", category: NotificationCategory, channel: NotificationChannel, value: boolean): void;
+}>();
+
+const value = ref<boolean>(props.preferences[props.category]!.channels[props.channel]);
+
+watch(
+    () => value.value,
+    (newValue) => {
+        emit("onChange", props.category, props.channel, newValue);
+    }
+);
+</script>
+
+<template>
+    <div class="category-channel">
+        <BFormCheckbox v-model="value" v-localize :disabled="!isCategoryEnabled">
+            {{ snakeCaseToTitleCase(channel) }}
+        </BFormCheckbox>
+
+        <FontAwesomeIcon
+            v-if="channel === 'push'"
+            v-b-tooltip.hover="'Push notifications need to be enabled'"
+            class="mx-2"
+            :icon="faExclamationCircle" />
+    </div>
+</template>
+
+<style scoped lang="scss">
+.category-channel {
+    display: flex;
+    align-items: center;
+}
+</style>
diff --git a/client/src/components/User/Notifications/NotificationsPreferences.vue b/client/src/components/User/Notifications/NotificationsPreferences.vue
index 9e481ac90c3b9f6122e677f138d014338a5277db..46a29c9a19e5e3a597acb905afced54a8fb78f4d 100644
--- a/client/src/components/User/Notifications/NotificationsPreferences.vue
+++ b/client/src/components/User/Notifications/NotificationsPreferences.vue
@@ -1,15 +1,16 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faExclamationCircle } from "@fortawesome/free-solid-svg-icons";
+import { faCheckCircle, faExclamationCircle, faSave } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BFormCheckbox } from "bootstrap-vue";
+import { BAlert, BButton } from "bootstrap-vue";
 import { computed, ref, watch } from "vue";
 
+import { GalaxyApi } from "@/api";
 import {
-    getNotificationsPreferencesFromServer,
-    updateNotificationsPreferencesOnServer,
-    UserNotificationPreferencesExtended,
-} from "@/api/notifications.preferences";
+    type NotificationCategory,
+    type NotificationChannel,
+    type UserNotificationPreferences,
+} from "@/api/notifications";
 import { useConfig } from "@/composables/config";
 import { Toast } from "@/composables/toast";
 import {
@@ -17,12 +18,14 @@ import {
     pushNotificationsEnabled,
     togglePushNotifications,
 } from "@/composables/utils/pushNotifications";
+import { errorMessageAsString } from "@/utils/simple-error";
 
+import NotificationsCategorySettings from "./NotificationsCategorySettings.vue";
 import AsyncButton from "@/components/Common/AsyncButton.vue";
 import Heading from "@/components/Common/Heading.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
-library.add(faExclamationCircle);
+library.add(faCheckCircle, faExclamationCircle, faSave);
 
 interface NotificationsPreferencesProps {
     embedded?: boolean;
@@ -39,54 +42,48 @@ const { config } = useConfig(true);
 const loading = ref(false);
 const errorMessage = ref<string | null>(null);
 const pushNotificationsGranted = ref(pushNotificationsEnabled());
-const notificationsPreferences = ref<UserNotificationPreferencesExtended["preferences"]>({});
-const supportedChannels = ref<string[]>([]);
+const notificationsPreferences = ref<UserNotificationPreferences>({});
+const supportedChannels = ref<NotificationChannel[]>([]);
 
-const categories = computed(() => Object.keys(notificationsPreferences.value));
+const categories = computed<NotificationCategory[]>(
+    () => Object.keys(notificationsPreferences.value) as NotificationCategory[]
+);
 const showPreferences = computed(() => {
     return !loading.value && config.value.enable_notification_system && notificationsPreferences.value;
 });
 
-const categoryDescriptionMap: Record<string, string> = {
-    message: `
-        You will receive these notifications only when your Galaxy administrators send you a message.
-        Please note that for certain critical or urgent messages, you will receive notifications even if you have disabled this channel.
-    `,
-    new_shared_item:
-        "You will receive these notifications when someone shares an item with you i.e. a history, workflow, visualization, etc.",
-};
-
 async function getNotificationsPreferences() {
     loading.value = true;
-    await getNotificationsPreferencesFromServer()
-        .then((data) => {
-            supportedChannels.value = data.supportedChannels;
-            notificationsPreferences.value = data.preferences;
-        })
-        .catch((error: any) => {
-            errorMessage.value = error;
-        })
-        .finally(() => {
-            loading.value = false;
-        });
+    try {
+        const { response, data, error } = await GalaxyApi().GET("/api/notifications/preferences");
+
+        if (error) {
+            errorMessage.value = errorMessageAsString(error);
+            return;
+        }
+
+        const serverSupportedChannels = response.headers.get("supported-channels")?.split(",") ?? [];
+        supportedChannels.value = serverSupportedChannels as NotificationChannel[];
+        notificationsPreferences.value = data.preferences;
+    } finally {
+        loading.value = false;
+    }
 }
 
 async function updateNotificationsPreferences() {
-    await updateNotificationsPreferencesOnServer({ preferences: notificationsPreferences.value })
-        .then((data) => {
-            notificationsPreferences.value = data.preferences;
-            Toast.success("Notifications preferences updated");
-        })
-        .catch((error: any) => {
-            errorMessage.value = error;
-        });
-}
+    const { data, error } = await GalaxyApi().PUT("/api/notifications/preferences", {
+        body: {
+            preferences: notificationsPreferences.value,
+        },
+    });
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return;
+    }
 
-function capitalizeWords(str: string): string {
-    return str
-        .split("_")
-        .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
-        .join(" ");
+    notificationsPreferences.value = data.preferences;
+    Toast.success("Notifications preferences updated");
 }
 
 async function onTogglePushNotifications() {
@@ -102,6 +99,14 @@ watch(
     },
     { immediate: true }
 );
+
+function onCategoryEnabledChange(category: NotificationCategory, value: boolean) {
+    notificationsPreferences.value[category]!.enabled = value;
+}
+
+function onChannelChange(category: NotificationCategory, channel: NotificationChannel, value: boolean) {
+    notificationsPreferences.value[category]!.channels[channel] = value;
+}
 </script>
 
 <template>
@@ -134,38 +139,12 @@ watch(
 
         <div v-else-if="showPreferences" class="notifications-preferences-body">
             <div v-for="category in categories" :key="category" class="card-container">
-                <div class="category-header">
-                    <BFormCheckbox
-                        v-model="notificationsPreferences[category].enabled"
-                        v-b-tooltip.hover
-                        :title="
-                            notificationsPreferences[category].enabled
-                                ? 'Disable notifications'
-                                : 'Enable notifications'
-                        "
-                        switch>
-                        <span v-localize class="category-title">{{ capitalizeWords(category) }}</span>
-                    </BFormCheckbox>
-                </div>
-
-                <div v-if="categoryDescriptionMap[category]" v-localize class="category-description">
-                    {{ categoryDescriptionMap[category] }}
-                </div>
-
-                <div v-for="channel in supportedChannels" :key="channel" class="category-channel">
-                    <BFormCheckbox
-                        v-model="notificationsPreferences[category].channels[channel]"
-                        v-localize
-                        :disabled="!notificationsPreferences[category].enabled">
-                        {{ capitalizeWords(channel) }}
-                    </BFormCheckbox>
-
-                    <FontAwesomeIcon
-                        v-if="channel === 'push'"
-                        v-b-tooltip.hover="'Push notifications need to be enabled'"
-                        class="mx-2"
-                        icon="exclamation-circle" />
-                </div>
+                <NotificationsCategorySettings
+                    :preferences="notificationsPreferences"
+                    :supported-channels="supportedChannels"
+                    :category="category"
+                    @onCategoryEnabledChange="onCategoryEnabledChange"
+                    @onChannelChange="onChannelChange" />
             </div>
         </div>
 
@@ -187,18 +166,18 @@ watch(
             show
             variant="info"
             class="my-2">
-            <FontAwesomeIcon icon="check-circle" />
+            <FontAwesomeIcon :icon="faCheckCircle" />
             Push notifications are enabled. You can disable them by revoking the site notification privilege in your
             browser.
         </BAlert>
 
         <BAlert v-else-if="!loading" show variant="warning" class="my-2">
-            <FontAwesomeIcon icon="exclamation-circle" />
+            <FontAwesomeIcon :icon="faExclamationCircle" />
             Push notifications are not supported by this browser. You can still receive in-app notifications.
         </BAlert>
 
         <div v-if="!loading && config.enable_notification_system" class="d-flex justify-content-center">
-            <AsyncButton :action="updateNotificationsPreferences" icon="save" variant="primary" size="md">
+            <AsyncButton :action="updateNotificationsPreferences" :icon="faSave" variant="primary" size="md">
                 <span v-localize>Save</span>
             </AsyncButton>
         </div>
@@ -218,19 +197,6 @@ watch(
     .notifications-preferences-body {
         display: flex;
         justify-content: space-around;
-
-        .category-header {
-            gap: 1rem;
-            display: flex;
-            align-items: center;
-            justify-content: space-between;
-            margin-bottom: 0.5rem;
-        }
-
-        .category-channel {
-            display: flex;
-            align-items: center;
-        }
     }
 
     .push-notifications-notice {
@@ -239,16 +205,6 @@ watch(
     }
 }
 
-.category-title {
-    font-weight: bold;
-}
-
-.category-description {
-    font-size: 0.8rem;
-    font-style: italic;
-    margin-bottom: 0.5rem;
-}
-
 .card-container {
     margin: 0.5rem;
 }
diff --git a/client/src/components/User/Notifications/index.js b/client/src/components/User/Notifications/index.js
deleted file mode 100644
index 77471e2615069de506033a0b980e9e258b623407..0000000000000000000000000000000000000000
--- a/client/src/components/User/Notifications/index.js
+++ /dev/null
@@ -1 +0,0 @@
-export { default as NotificationsPreferences } from "./NotificationsPreferences.vue";
diff --git a/client/src/components/User/UserPreferences.vue b/client/src/components/User/UserPreferences.vue
index 695c5de0b58b82ac97f89c16df38d5631c813196..d452f8074f85cfd5d53fbf80dd276e00f632e9af 100644
--- a/client/src/components/User/UserPreferences.vue
+++ b/client/src/components/User/UserPreferences.vue
@@ -48,12 +48,6 @@
             title="Manage Notifications"
             description="Manage your notification settings."
             to="/user/notifications/preferences" />
-        <UserPreferencesElement
-            id="edit-preferences-cloud-auth"
-            icon="fa-cloud"
-            title="Manage Cloud Authorization"
-            description="Add or modify the configuration that grants Galaxy to access your cloud-based resources."
-            to="/user/cloud_auth" />
         <UserPreferencesElement
             v-if="isConfigLoaded && config.enable_oidc && !config.fixed_delegated_auth"
             id="manage-third-party-identities"
diff --git a/client/src/components/User/UserPreferencesModel.js b/client/src/components/User/UserPreferencesModel.js
index 5efff575efa7c881a60d12837cab145ff06ac7aa..a5a05dd3ad6d3e50a5bcdbbe10c8944beae8f465 100644
--- a/client/src/components/User/UserPreferencesModel.js
+++ b/client/src/components/User/UserPreferencesModel.js
@@ -9,13 +9,13 @@ export const getUserPreferencesModel = (user_id) => {
         information: {
             title: _l("Manage Information"),
             id: "edit-preferences-information",
-            description: config.enable_account_interface
-                ? _l("Edit your email, addresses and custom parameters or change your public name.")
-                : _l("Edit your custom parameters."),
+            description:
+                config.enable_account_interface && !config.use_remote_user
+                    ? _l("Edit your email, addresses and custom parameters or change your public name.")
+                    : _l("Edit your custom parameters."),
             url: `/api/users/${user_id}/information/inputs`,
             icon: "fa-user",
             redirect: "/user",
-            disabled: config.use_remote_user,
         },
         password: {
             title: _l("Change Password"),
diff --git a/client/src/components/User/UserPreferredObjectStore.test.js b/client/src/components/User/UserPreferredObjectStore.test.js
index a5c1ed74052f03f1b7ac381332581d105fd776e8..325617b84b4d7eab73fa956bdfd544b8111e929f 100644
--- a/client/src/components/User/UserPreferredObjectStore.test.js
+++ b/client/src/components/User/UserPreferredObjectStore.test.js
@@ -1,9 +1,9 @@
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useServerMock } from "@/api/client/__mocks__";
 import { ROOT_COMPONENT } from "@/utils/navigation";
 
 import { setupSelectableMock } from "../ObjectStore/mockServices";
@@ -14,9 +14,17 @@ setupSelectableMock();
 
 const localVue = getLocalVue(true);
 
+const { server, http } = useServerMock();
+
 const TEST_USER_ID = "myTestUserId";
 
 function mountComponent() {
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json({});
+        })
+    );
+
     const wrapper = mount(UserPreferredObjectStore, {
         propsData: { userId: TEST_USER_ID },
         localVue,
@@ -26,16 +34,6 @@ function mountComponent() {
 }
 
 describe("UserPreferredObjectStore.vue", () => {
-    let axiosMock;
-
-    beforeEach(async () => {
-        axiosMock = new MockAdapter(axios);
-    });
-
-    afterEach(async () => {
-        axiosMock.restore();
-    });
-
     it("contains a localized link", async () => {
         const wrapper = mountComponent();
         expect(wrapper.vm.$refs["modal"].isHidden).toBeTruthy();
@@ -56,7 +54,13 @@ describe("UserPreferredObjectStore.vue", () => {
             ROOT_COMPONENT.preferences.object_store_selection.option_button({ object_store_id: "__null__" }).selector
         );
         expect(galaxyDefaultOption.exists()).toBeTruthy();
-        axiosMock.onPut("/api/users/current", expect.objectContaining({ preferred_object_store_id: null })).reply(202);
+
+        server.use(
+            http.put("/api/users/{user_id}", ({ response }) => {
+                return response(200).json(getFakeRegisteredUser({ preferred_object_store_id: null }));
+            })
+        );
+
         await galaxyDefaultOption.trigger("click");
         await flushPromises();
         const errorEl = wrapper.find(".object-store-selection-error");
@@ -72,9 +76,13 @@ describe("UserPreferredObjectStore.vue", () => {
                 .selector
         );
         expect(objectStore2Option.exists()).toBeTruthy();
-        axiosMock
-            .onPut("/api/users/current", expect.objectContaining({ preferred_object_store_id: "object_store_2" }))
-            .reply(202);
+
+        server.use(
+            http.put("/api/users/{user_id}", ({ response }) => {
+                return response(200).json(getFakeRegisteredUser({ preferred_object_store_id: "object_store_2" }));
+            })
+        );
+
         await objectStore2Option.trigger("click");
         await flushPromises();
         const errorEl = wrapper.find(".object-store-selection-error");
@@ -89,9 +97,13 @@ describe("UserPreferredObjectStore.vue", () => {
             ROOT_COMPONENT.preferences.object_store_selection.option_button({ object_store_id: "__null__" }).selector
         );
         expect(galaxyDefaultOption.exists()).toBeTruthy();
-        axiosMock
-            .onPut("/api/users/current", expect.objectContaining({ preferred_object_store_id: null }))
-            .reply(400, { err_msg: "problem with selection.." });
+
+        server.use(
+            http.put("/api/users/{user_id}", ({ response }) => {
+                return response("4XX").json({ err_msg: "problem with selection.." }, { status: 400 });
+            })
+        );
+
         await galaxyDefaultOption.trigger("click");
         await flushPromises();
         const errorEl = await wrapper.find(".object-store-selection-error");
diff --git a/client/src/components/Visualizations/PluginList.vue b/client/src/components/Visualizations/PluginList.vue
index 987858f06fa5a6958f29bfed70eb32d886b6cc20..7245bb38eaf5504737f8efa701a8fad13035a832 100644
--- a/client/src/components/Visualizations/PluginList.vue
+++ b/client/src/components/Visualizations/PluginList.vue
@@ -4,7 +4,7 @@
         <template v-else>
             <DelayedInput
                 class="mb-3"
-                :query="search"
+                :value="search"
                 :placeholder="titleSearchVisualizations"
                 :delay="100"
                 @change="onSearch" />
diff --git a/client/src/components/Workflow/Editor/Actions/actions.test.ts b/client/src/components/Workflow/Editor/Actions/actions.test.ts
index aa8cf71c37ef6a1a751d4cea7466416ef7b8a2cb..08d373cbfe4984e1b78a826a014f52e2ba379ec6 100644
--- a/client/src/components/Workflow/Editor/Actions/actions.test.ts
+++ b/client/src/components/Workflow/Editor/Actions/actions.test.ts
@@ -1,6 +1,6 @@
 import { createPinia, setActivePinia } from "pinia";
 
-import { LazyUndoRedoAction, UndoRedoAction, useUndoRedoStore } from "@/stores/undoRedoStore";
+import { LazyUndoRedoAction, type UndoRedoAction, useUndoRedoStore } from "@/stores/undoRedoStore";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { useWorkflowCommentStore } from "@/stores/workflowEditorCommentStore";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
@@ -269,11 +269,8 @@ describe("Workflow Undo Redo Actions", () => {
 
         it("RemoveStepAction", () => {
             const step = addStep();
-            const showAttributesCallback = jest.fn();
-            const action = new RemoveStepAction(stepStore, stateStore, connectionStore, showAttributesCallback, step);
+            const action = new RemoveStepAction(stepStore, stateStore, connectionStore, step);
             testUndoRedo(action);
-
-            expect(showAttributesCallback).toBeCalledTimes(2);
         });
 
         it("CopyStepAction", () => {
diff --git a/client/src/components/Workflow/Editor/Actions/cloneStep.ts b/client/src/components/Workflow/Editor/Actions/cloneStep.ts
index 5a33d62ece846d87a75e9856a59b077e3068c7ce..161aca66b916743604c27d54514754226cedba76 100644
--- a/client/src/components/Workflow/Editor/Actions/cloneStep.ts
+++ b/client/src/components/Workflow/Editor/Actions/cloneStep.ts
@@ -1,4 +1,4 @@
-import type { Step, WorkflowStepStore } from "@/stores/workflowStepStore";
+import { type Step, type WorkflowStepStore } from "@/stores/workflowStepStore";
 
 /**
  * Copies a step and increments a trailing number in it's label,
diff --git a/client/src/components/Workflow/Editor/Actions/commentActions.ts b/client/src/components/Workflow/Editor/Actions/commentActions.ts
index 3b497886b323cf96b45d46fc91c188eccbad68b2..00b6192e4a31dbb867ce11937f96de158d39353e 100644
--- a/client/src/components/Workflow/Editor/Actions/commentActions.ts
+++ b/client/src/components/Workflow/Editor/Actions/commentActions.ts
@@ -4,8 +4,17 @@ import type {
     WorkflowComment,
     WorkflowCommentColor,
     WorkflowCommentStore,
+    WorkflowCommentType,
 } from "@/stores/workflowEditorCommentStore";
 
+function getCommentName(comment: { color: WorkflowCommentColor; type: WorkflowCommentType }) {
+    if (comment.color !== "none") {
+        return `${comment.color} ${comment.type} comment`;
+    } else {
+        return `${comment.type} comment`;
+    }
+}
+
 class CommentAction extends UndoRedoAction {
     protected store: WorkflowCommentStore;
     protected comment: WorkflowComment;
@@ -15,11 +24,15 @@ class CommentAction extends UndoRedoAction {
         this.store = store;
         this.comment = structuredClone(comment) as WorkflowComment;
     }
+
+    protected get commentName() {
+        return getCommentName(this.comment);
+    }
 }
 
 export class AddCommentAction extends CommentAction {
     get name() {
-        return `add ${this.comment.type} comment`;
+        return `add ${this.commentName}`;
     }
 
     undo() {
@@ -33,7 +46,7 @@ export class AddCommentAction extends CommentAction {
 
 export class DeleteCommentAction extends CommentAction {
     get name() {
-        return `delete ${this.comment.type} comment`;
+        return `delete ${this.commentName}`;
     }
 
     run() {
@@ -75,10 +88,11 @@ export class ChangeColorAction extends UndoRedoAction {
 }
 
 class LazyMutateCommentAction<K extends keyof WorkflowComment> extends LazyUndoRedoAction {
-    private commentId: number;
-    private startData: WorkflowComment[K];
-    private endData: WorkflowComment[K];
+    protected commentId: number;
+    protected startData: WorkflowComment[K];
+    protected endData: WorkflowComment[K];
     protected type;
+    protected color: WorkflowCommentColor;
     protected applyDataCallback: (commentId: number, data: WorkflowComment[K]) => void;
 
     constructor(
@@ -93,14 +107,19 @@ class LazyMutateCommentAction<K extends keyof WorkflowComment> extends LazyUndoR
         this.endData = structuredClone(data);
         this.applyDataCallback = applyDataCallback;
         this.type = comment.type;
+        this.color = comment.color;
     }
 
     queued() {
         this.applyDataCallback(this.commentId, this.endData);
     }
 
+    protected get commentName() {
+        return getCommentName({ type: this.type, color: this.color });
+    }
+
     get name() {
-        return `change ${this.type} comment`;
+        return `change ${this.commentName}`;
     }
 
     updateData(data: WorkflowComment[K]) {
@@ -122,6 +141,35 @@ export class LazyChangeDataAction extends LazyMutateCommentAction<"data"> {
         const callback = store.changeData;
         super(comment, "data", data, callback);
     }
+
+    get name() {
+        type TitleData = { title: string };
+        type TextData = { text: string };
+        type SizeData = { size: number };
+        type FormatData = { bold?: true; italic?: true };
+
+        if ((this.startData as TitleData).title !== (this.endData as TitleData).title) {
+            return `edit title of ${this.commentName}`;
+        }
+
+        if ((this.startData as TextData).text !== (this.endData as TextData).text) {
+            return `edit text of ${this.commentName}`;
+        }
+
+        if ((this.startData as SizeData).size !== (this.endData as SizeData).size) {
+            return `change text size of ${this.commentName}`;
+        }
+
+        if ((this.startData as FormatData).bold !== (this.endData as FormatData).bold) {
+            return `toggle bold of ${this.commentName}`;
+        }
+
+        if ((this.startData as FormatData).italic !== (this.endData as FormatData).italic) {
+            return `toggle italic of ${this.commentName}`;
+        }
+
+        return super.name;
+    }
 }
 
 export class LazyChangePositionAction extends LazyMutateCommentAction<"position"> {
@@ -131,7 +179,7 @@ export class LazyChangePositionAction extends LazyMutateCommentAction<"position"
     }
 
     get name() {
-        return `change ${this.type} comment position`;
+        return `move ${this.commentName}`;
     }
 }
 
@@ -142,7 +190,7 @@ export class LazyChangeSizeAction extends LazyMutateCommentAction<"size"> {
     }
 
     get name() {
-        return `resize ${this.type} comment`;
+        return `resize ${this.commentName}`;
     }
 }
 
diff --git a/client/src/components/Workflow/Editor/Actions/mockData.ts b/client/src/components/Workflow/Editor/Actions/mockData.ts
index ab285037c09cf63b59c06234aa8b090cc53262ee..414b56f716f90fd4380d3f283a59a2e589072a32 100644
--- a/client/src/components/Workflow/Editor/Actions/mockData.ts
+++ b/client/src/components/Workflow/Editor/Actions/mockData.ts
@@ -1,7 +1,7 @@
-import { FreehandWorkflowComment, WorkflowComment } from "@/stores/workflowEditorCommentStore";
-import type { Step } from "@/stores/workflowStepStore";
+import { type FreehandWorkflowComment, type WorkflowComment } from "@/stores/workflowEditorCommentStore";
+import { type Step } from "@/stores/workflowStepStore";
 
-import type { Workflow } from "../modules/model";
+import { type Workflow } from "../modules/model";
 
 export function mockToolStep(id: number): Step {
     return {
diff --git a/client/src/components/Workflow/Editor/Actions/stepActions.ts b/client/src/components/Workflow/Editor/Actions/stepActions.ts
index 9e29437040abdd41408c926877e418b31d158de7..c58573cc59e048eb23d901ba302d16f7e4229fdd 100644
--- a/client/src/components/Workflow/Editor/Actions/stepActions.ts
+++ b/client/src/components/Workflow/Editor/Actions/stepActions.ts
@@ -1,10 +1,11 @@
 import { replaceLabel } from "@/components/Markdown/parse";
 import { useToast } from "@/composables/toast";
 import { useRefreshFromStore } from "@/stores/refreshFromStore";
-import { LazyUndoRedoAction, UndoRedoAction, UndoRedoStore } from "@/stores/undoRedoStore";
-import { Connection, WorkflowConnectionStore } from "@/stores/workflowConnectionStore";
-import { WorkflowStateStore } from "@/stores/workflowEditorStateStore";
-import type { NewStep, Step, WorkflowStepStore } from "@/stores/workflowStepStore";
+import { LazyUndoRedoAction, UndoRedoAction, type UndoRedoStore } from "@/stores/undoRedoStore";
+import { type Connection, type WorkflowConnectionStore } from "@/stores/workflowConnectionStore";
+import { useWorkflowCommentStore } from "@/stores/workflowEditorCommentStore";
+import { type WorkflowStateStore } from "@/stores/workflowEditorStateStore";
+import { type NewStep, type Step, useWorkflowStepStore, type WorkflowStepStore } from "@/stores/workflowStepStore";
 import { assertDefined } from "@/utils/assertions";
 
 import { cloneStepWithUniqueLabel, getLabelSet } from "./cloneStep";
@@ -15,10 +16,11 @@ export class LazyMutateStepAction<K extends keyof Step> extends LazyUndoRedoActi
     toValue: Step[K];
     stepId;
     stepStore;
+    stepLabel;
     onUndoRedo?: () => void;
 
     get name() {
-        return this.internalName ?? "modify step";
+        return this.internalName ?? `modify step ${this.stepLabel}`;
     }
 
     set name(name: string | undefined) {
@@ -32,6 +34,13 @@ export class LazyMutateStepAction<K extends keyof Step> extends LazyUndoRedoActi
         this.key = key;
         this.fromValue = fromValue;
         this.toValue = toValue;
+
+        this.stepLabel = `${stepId + 1}`;
+        const step = this.stepStore.getStep(stepId);
+
+        if (step) {
+            this.stepLabel = `"${stepId + 1}: ${step.label ?? step.name}"`;
+        }
     }
 
     queued() {
@@ -160,10 +169,11 @@ export class UpdateStepAction extends UndoRedoAction {
     stepId;
     fromPartial;
     toPartial;
+    stepLabel;
     onUndoRedo?: () => void;
 
     get name() {
-        return this.internalName ?? "modify step";
+        return this.internalName ?? `modify step ${this.stepLabel}`;
     }
 
     set name(name: string | undefined) {
@@ -183,6 +193,13 @@ export class UpdateStepAction extends UndoRedoAction {
         this.stepId = stepId;
         this.fromPartial = fromPartial;
         this.toPartial = toPartial;
+
+        this.stepLabel = `${stepId + 1}`;
+        const step = this.stepStore.getStep(stepId);
+
+        if (step) {
+            this.stepLabel = `"${stepId + 1}: ${step.label ?? step.name}"`;
+        }
     }
 
     isEmpty() {
@@ -192,14 +209,12 @@ export class UpdateStepAction extends UndoRedoAction {
     run() {
         const step = this.stepStore.getStep(this.stepId);
         assertDefined(step);
-        this.stateStore.activeNodeId = this.stepId;
         this.stepStore.updateStep({ ...step, ...this.toPartial });
     }
 
     undo() {
         const step = this.stepStore.getStep(this.stepId);
         assertDefined(step);
-        this.stateStore.activeNodeId = this.stepId;
         this.stepStore.updateStep({ ...step, ...this.fromPartial });
         this.onUndoRedo?.();
     }
@@ -281,7 +296,6 @@ export class InsertStepAction extends UndoRedoAction {
     redo() {
         this.run();
         assertDefined(this.stepId);
-        this.stateStore.activeNodeId = this.stepId;
     }
 }
 
@@ -289,7 +303,6 @@ export class RemoveStepAction extends UndoRedoAction {
     stepStore;
     stateStore;
     connectionStore;
-    showAttributesCallback;
     step: Step;
     connections: Connection[];
 
@@ -297,32 +310,29 @@ export class RemoveStepAction extends UndoRedoAction {
         stepStore: WorkflowStepStore,
         stateStore: WorkflowStateStore,
         connectionStore: WorkflowConnectionStore,
-        showAttributesCallback: () => void,
         step: Step
     ) {
         super();
         this.stepStore = stepStore;
         this.stateStore = stateStore;
         this.connectionStore = connectionStore;
-        this.showAttributesCallback = showAttributesCallback;
         this.step = structuredClone(step);
         this.connections = structuredClone(this.connectionStore.getConnectionsForStep(this.step.id));
     }
 
     get name() {
-        return `remove ${this.step.label ?? this.step.name}`;
+        return `remove step "${this.step.id} ${this.step.label ?? this.step.name}"`;
     }
 
     run() {
         this.stepStore.removeStep(this.step.id);
-        this.showAttributesCallback();
+        this.stateStore.activeNodeId = null;
         this.stateStore.hasChanges = true;
     }
 
     undo() {
         this.stepStore.addStep(structuredClone(this.step), false, false);
         this.connections.forEach((connection) => this.connectionStore.addConnection(connection));
-        this.stateStore.activeNodeId = this.step.id;
         this.stateStore.hasChanges = true;
     }
 }
@@ -331,6 +341,7 @@ export class CopyStepAction extends UndoRedoAction {
     stepStore;
     stateStore;
     step: NewStep;
+    stepLabel;
     stepId?: number;
     onUndoRedo?: () => void;
 
@@ -340,18 +351,18 @@ export class CopyStepAction extends UndoRedoAction {
         this.stateStore = stateStore;
 
         const labelSet = getLabelSet(stepStore);
+        this.stepLabel = `${step.id + 1}: ${step.label ?? step.name}`;
         this.step = cloneStepWithUniqueLabel(step, labelSet);
         delete this.step.id;
     }
 
     get name() {
-        return `duplicate step ${this.step.label ?? this.step.name}`;
+        return `duplicate step "${this.stepLabel}"`;
     }
 
     run() {
         const newStep = this.stepStore.addStep(structuredClone(this.step));
         this.stepId = newStep.id;
-        this.stateStore.activeNodeId = this.stepId;
         this.stateStore.hasChanges = true;
     }
 
@@ -366,6 +377,7 @@ export class ToggleStepSelectedAction extends UndoRedoAction {
     stepStore;
     stepId;
     toggleTo: boolean;
+    stepLabel;
 
     constructor(stateStore: WorkflowStateStore, stepStore: WorkflowStepStore, stepId: number) {
         super();
@@ -374,11 +386,9 @@ export class ToggleStepSelectedAction extends UndoRedoAction {
         this.stepStore = stepStore;
         this.stepId = stepId;
         this.toggleTo = !this.stateStore.getStepMultiSelected(stepId);
-    }
 
-    get stepLabel() {
         const label = this.stepStore.getStep(this.stepId)?.label;
-        return label ?? `${this.stepId + 1}`;
+        this.stepLabel = label ?? `${this.stepId + 1}`;
     }
 
     get name() {
@@ -398,6 +408,112 @@ export class ToggleStepSelectedAction extends UndoRedoAction {
     }
 }
 
+interface Positions {
+    steps: { id: string; x: number; y: number }[];
+    comments: { id: string; x: number; y: number; w: number; h: number }[];
+}
+
+export class AutoLayoutAction extends UndoRedoAction {
+    stepStore;
+    commentStore;
+    positions: Positions;
+    oldPositions: Positions;
+    workflowId;
+    ran;
+
+    constructor(workflowId: string) {
+        super();
+
+        this.workflowId = workflowId;
+        this.stepStore = useWorkflowStepStore(workflowId);
+        this.commentStore = useWorkflowCommentStore(workflowId);
+
+        this.positions = {
+            steps: [],
+            comments: [],
+        };
+
+        this.oldPositions = {
+            steps: [],
+            comments: [],
+        };
+
+        this.ran = false;
+    }
+
+    get name() {
+        return "auto layout";
+    }
+
+    private mapPositionsToStore(positions: Positions) {
+        positions.steps.map((p) => {
+            const step = this.stepStore.steps[p.id];
+            if (step) {
+                this.stepStore.updateStep({
+                    ...step,
+                    position: {
+                        top: p.y,
+                        left: p.x,
+                    },
+                });
+            }
+        });
+
+        positions.comments.map((c) => {
+            const id = parseInt(c.id, 10);
+            const comment = this.commentStore.commentsRecord[id];
+            if (comment) {
+                this.commentStore.changePosition(id, [c.x, c.y]);
+                this.commentStore.changeSize(id, [c.w, c.h]);
+            }
+        });
+    }
+
+    async run() {
+        this.ran = true;
+
+        this.oldPositions.steps = Object.values(this.stepStore.steps).map((step) => ({
+            id: `${step.id}`,
+            x: step.position?.left ?? 0,
+            y: step.position?.top ?? 0,
+        }));
+
+        this.oldPositions.comments = this.commentStore.comments.map((comment) => ({
+            id: `${comment.id}`,
+            x: comment.position[0],
+            y: comment.position[1],
+            w: comment.size[0],
+            h: comment.size[1],
+        }));
+
+        const { autoLayout } = await import(
+            /* webpackChunkName: "workflowLayout" */ "@/components/Workflow/Editor/modules/layout"
+        );
+
+        this.commentStore.resolveCommentsInFrames();
+        this.commentStore.resolveStepsInFrames();
+
+        const newPositions = await autoLayout(this.workflowId, this.stepStore.steps, this.commentStore.comments);
+
+        assertDefined(newPositions);
+
+        this.positions = newPositions as Positions;
+
+        if (this.ran) {
+            this.mapPositionsToStore(this.positions);
+        }
+    }
+
+    undo() {
+        this.ran = false;
+        this.mapPositionsToStore(this.oldPositions);
+    }
+
+    redo() {
+        this.mapPositionsToStore(this.positions);
+    }
+}
+
 export function useStepActions(
     stepStore: WorkflowStepStore,
     undoRedoStore: UndoRedoStore,
@@ -445,6 +561,10 @@ export function useStepActions(
                 undoRedoStore.setLazyActionTimeout(timeout);
             }
 
+            if (name) {
+                actionForKey.name = name;
+            }
+
             return actionForKey;
         } else {
             const actionConstructor =
@@ -460,7 +580,6 @@ export function useStepActions(
             undoRedoStore.applyLazyAction(action, timeout);
 
             action.onUndoRedo = () => {
-                stateStore.activeNodeId = step.id;
                 stateStore.hasChanges = true;
             };
 
@@ -469,11 +588,21 @@ export function useStepActions(
     }
 
     function setPosition(step: Step, position: NonNullable<Step["position"]>) {
-        changeValueOrCreateAction({ step, key: "position", value: position, name: "change step position" });
+        changeValueOrCreateAction({
+            step,
+            key: "position",
+            value: position,
+            name: `move step "${step.id + 1}: ${step.label ?? step.name}"`,
+        });
     }
 
     function setAnnotation(step: Step, annotation: Step["annotation"]) {
-        changeValueOrCreateAction({ step, key: "annotation", value: annotation, name: "modify step annotation" });
+        changeValueOrCreateAction({
+            step,
+            key: "annotation",
+            value: annotation,
+            name: `edit annotation of step "${step.id + 1}: ${step.label ?? step.name}"`,
+        });
     }
 
     function setOutputLabel(
@@ -489,7 +618,7 @@ export function useStepActions(
             step,
             key: "workflow_outputs",
             value: workflowOutputs,
-            name: "modify step output label",
+            name: `edit output label of step "${step.id + 1}: ${step.label ?? step.name}"`,
             actionConstructor,
             keepActionAlive: true,
             timeout: 2000,
@@ -502,7 +631,7 @@ export function useStepActions(
             step,
             key: "label",
             value: label,
-            name: "modify step label",
+            name: `change label of step ${step.id + 1} to "${label}"`,
             actionConstructor,
             keepActionAlive: true,
             timeout: 2000,
@@ -516,7 +645,6 @@ export function useStepActions(
 
         if (!action.isEmpty()) {
             action.onUndoRedo = () => {
-                stateStore.activeNodeId = from.id;
                 stateStore.hasChanges = true;
                 refresh();
             };
@@ -524,8 +652,8 @@ export function useStepActions(
         }
     }
 
-    function removeStep(step: Step, showAttributesCallback: () => void) {
-        const action = new RemoveStepAction(stepStore, stateStore, connectionStore, showAttributesCallback, step);
+    function removeStep(step: Step) {
+        const action = new RemoveStepAction(stepStore, stateStore, connectionStore, step);
         undoRedoStore.applyAction(action);
     }
 
@@ -542,7 +670,6 @@ export function useStepActions(
 
         if (!action.isEmpty()) {
             action.onUndoRedo = () => {
-                stateStore.activeNodeId = id;
                 stateStore.hasChanges = true;
                 refresh();
             };
diff --git a/client/src/components/Workflow/Editor/Actions/workflowActions.ts b/client/src/components/Workflow/Editor/Actions/workflowActions.ts
index 44ba365e756a2cc1d9c3d2b3499bb353f0284c9b..4418e0a3c519fd9064424f59509834d6f7a94fe8 100644
--- a/client/src/components/Workflow/Editor/Actions/workflowActions.ts
+++ b/client/src/components/Workflow/Editor/Actions/workflowActions.ts
@@ -1,4 +1,4 @@
-import { LazyUndoRedoAction, UndoRedoAction, UndoRedoStore } from "@/stores/undoRedoStore";
+import { LazyUndoRedoAction, UndoRedoAction, type UndoRedoStore } from "@/stores/undoRedoStore";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import {
     useWorkflowCommentStore,
@@ -9,8 +9,8 @@ import { useWorkflowStateStore, type WorkflowStateStore } from "@/stores/workflo
 import { type Step, useWorkflowStepStore, type WorkflowStepStore } from "@/stores/workflowStepStore";
 import { ensureDefined } from "@/utils/assertions";
 
-import { defaultPosition } from "../composables/useDefaultStepPosition";
-import { fromSimple, Workflow } from "../modules/model";
+import { type defaultPosition } from "../composables/useDefaultStepPosition";
+import { fromSimple, type Workflow } from "../modules/model";
 import { cloneStepWithUniqueLabel, getLabelSet } from "./cloneStep";
 
 export class LazySetValueAction<T> extends LazyUndoRedoAction {
diff --git a/client/src/components/Workflow/Editor/Comments/WorkflowComment.test.ts b/client/src/components/Workflow/Editor/Comments/WorkflowComment.test.ts
index 30b57c4ff2a0f666c20cbeac1832435597592d0b..6673346c041e6e143ad95fa5a1a2cfdd7f194ad8 100644
--- a/client/src/components/Workflow/Editor/Comments/WorkflowComment.test.ts
+++ b/client/src/components/Workflow/Editor/Comments/WorkflowComment.test.ts
@@ -3,8 +3,8 @@ import { mount, shallowMount } from "@vue/test-utils";
 import { setActivePinia } from "pinia";
 import { nextTick } from "vue";
 
-import type { LazyUndoRedoAction, UndoRedoAction } from "@/stores/undoRedoStore";
-import type { TextWorkflowComment } from "@/stores/workflowEditorCommentStore";
+import { type LazyUndoRedoAction, type UndoRedoAction } from "@/stores/undoRedoStore";
+import { type TextWorkflowComment } from "@/stores/workflowEditorCommentStore";
 
 import MarkdownComment from "./MarkdownComment.vue";
 import TextComment from "./TextComment.vue";
diff --git a/client/src/components/Workflow/Editor/Draggable.vue b/client/src/components/Workflow/Editor/Draggable.vue
index cd3c6f52c9e4b22367ca6f5ba0c0b6461fde5349..c9b4b0a978d223b79939e71e9e233159a97c0bfd 100644
--- a/client/src/components/Workflow/Editor/Draggable.vue
+++ b/client/src/components/Workflow/Editor/Draggable.vue
@@ -1,8 +1,7 @@
 <script setup lang="ts">
 import type { ZoomTransform } from "d3-zoom";
 import { storeToRefs } from "pinia";
-import type { Ref } from "vue";
-import { computed, inject, PropType, reactive, ref } from "vue";
+import { computed, inject, type PropType, reactive, type Ref, ref } from "vue";
 
 import { useAnimationFrameSize } from "@/composables/sensors/animationFrameSize";
 import { useAnimationFrameThrottle } from "@/composables/throttle";
diff --git a/client/src/components/Workflow/Editor/Forms/FormDefault.test.js b/client/src/components/Workflow/Editor/Forms/FormDefault.test.js
index 2a09dc0d79634de59fefd530f87f2ca9d63f659c..7fb84f50763667f86a5a0e214d1fce4b4a0a95d0 100644
--- a/client/src/components/Workflow/Editor/Forms/FormDefault.test.js
+++ b/client/src/components/Workflow/Editor/Forms/FormDefault.test.js
@@ -24,6 +24,7 @@ describe("FormDefault", () => {
                     contentId: "id",
                     annotation: "annotation",
                     label: "label",
+                    name: "name",
                     type: "subworkflow",
                     configForm: {
                         inputs: [],
@@ -42,7 +43,7 @@ describe("FormDefault", () => {
 
     it("check initial value and value change", async () => {
         const title = wrapper.find(".portlet-title-text").text();
-        expect(title).toBe("label");
+        expect(title).toBe("name");
         const inputCount = wrapper.findAll("input").length;
         expect(inputCount).toBe(4);
         const outputLabelCount = wrapper.findAll("#__label__output-name").length;
diff --git a/client/src/components/Workflow/Editor/Forms/FormDefault.vue b/client/src/components/Workflow/Editor/Forms/FormDefault.vue
index 8ac56fd941daaf6113838af92bb1e0709df17413..3a0f82c0a9d6c3412f2e538757cd90dc414d89b7 100644
--- a/client/src/components/Workflow/Editor/Forms/FormDefault.vue
+++ b/client/src/components/Workflow/Editor/Forms/FormDefault.vue
@@ -97,9 +97,6 @@ const { stepId, contentId, annotation, label, name, type, configForm } = useStep
 const { stepStore } = useWorkflowStores();
 const uniqueErrorLabel = useUniqueLabelError(stepStore, label.value);
 const stepTitle = computed(() => {
-    if (label.value) {
-        return label.value;
-    }
     if (isSubworkflow.value) {
         return name.value;
     } else {
diff --git a/client/src/components/Workflow/Editor/Forms/FormTool.vue b/client/src/components/Workflow/Editor/Forms/FormTool.vue
index 67b5ae455c605c2c6fe2da02bc317fb9860be7f1..88f3eb406871d9c9d689020a302977761de107ea 100644
--- a/client/src/components/Workflow/Editor/Forms/FormTool.vue
+++ b/client/src/components/Workflow/Editor/Forms/FormTool.vue
@@ -141,6 +141,9 @@ export default {
             return !!this.configForm?.id;
         },
         inputs() {
+            // TODO: Refactor
+            // This code contains a computed side-effect and prop mutation.
+            // Both should be refactored
             const inputs = this.configForm.inputs;
             Utils.deepEach(inputs, (input) => {
                 if (input.type) {
@@ -150,10 +153,14 @@ export default {
                         input.info = `Data input '${input.name}' (${extensions})`;
                         input.value = { __class__: "RuntimeValue" };
                     } else {
-                        input.connectable = ["rules"].indexOf(input.type) == -1;
-                        input.collapsible_value = {
-                            __class__: "RuntimeValue",
-                        };
+                        const isRules = input.type === "rules";
+                        input.connectable = !isRules;
+                        input.collapsible_value = isRules
+                            ? undefined
+                            : {
+                                  __class__: "RuntimeValue",
+                              };
+
                         input.is_workflow =
                             (input.options && input.options.length === 0) ||
                             ["integer", "float"].indexOf(input.type) != -1;
diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue
index 5cbed1ed10ed61bafefe6e427065cfe88740c16d..cf098e8b0adb5ad20383c8280e5a7a4f0c0ed878 100644
--- a/client/src/components/Workflow/Editor/Index.vue
+++ b/client/src/components/Workflow/Editor/Index.vue
@@ -1,5 +1,5 @@
 <template>
-    <div v-if="isCanvas" id="columns" class="d-flex">
+    <div id="columns" class="d-flex">
         <StateUpgradeModal :state-messages="stateMessages" />
         <StateUpgradeModal
             :state-messages="insertedStateMessages"
@@ -27,160 +27,171 @@
                 <b-form-textarea v-model="saveAsAnnotation" />
             </b-form-group>
         </b-modal>
-        <FlexPanel side="left">
-            <ToolPanel
-                workflow
-                :module-sections="moduleSections"
-                :data-managers="dataManagers"
-                :editor-workflows="workflows"
-                @onInsertTool="onInsertTool"
-                @onInsertModule="onInsertModule"
-                @onInsertWorkflow="onInsertWorkflow"
-                @onInsertWorkflowSteps="onInsertWorkflowSteps" />
-        </FlexPanel>
-        <div id="center" class="workflow-center">
-            <div class="editor-top-bar" unselectable="on">
-                <span>
-                    <span class="sr-only">Workflow Editor</span>
-                    <span class="editor-title" :title="name"
-                        >{{ name }}
-                        <i v-if="hasChanges" class="text-muted"> (unsaved changes) </i>
-                    </span>
-                </span>
-
-                <b-button-group>
-                    <b-button
-                        :title="undoRedoStore.undoText + ' (Ctrl + Z)'"
-                        :variant="undoRedoStore.hasUndo ? 'secondary' : 'muted'"
-                        @click="undoRedoStore.undo()">
-                        <FontAwesomeIcon icon="fa-arrow-left" />
-                    </b-button>
+        <ActivityBar
+            ref="activityBar"
+            :default-activities="workflowEditorActivities"
+            :special-activities="specialWorkflowActivities"
+            activity-bar-id="workflow-editor"
+            :show-admin="false"
+            options-title="Options"
+            options-heading="Workflow Options"
+            options-tooltip="View additional workflow options"
+            options-search-placeholder="Search options"
+            initial-activity="workflow-editor-attributes"
+            :options-icon="faCog"
+            :hide-panel="reportActive"
+            @activityClicked="onActivityClicked">
+            <template v-slot:side-panel="{ isActiveSideBar }">
+                <ToolPanel
+                    v-if="isActiveSideBar('workflow-editor-tools')"
+                    workflow
+                    :module-sections="moduleSections"
+                    :data-managers="dataManagers"
+                    @onInsertTool="onInsertTool"
+                    @onInsertModule="onInsertModule"
+                    @onInsertWorkflow="onInsertWorkflow"
+                    @onInsertWorkflowSteps="onInsertWorkflowSteps" />
+                <InputPanel
+                    v-if="isActiveSideBar('workflow-editor-inputs')"
+                    :inputs="inputs"
+                    @insertModule="onInsertModule" />
+                <WorkflowLint
+                    v-else-if="isActiveSideBar('workflow-best-practices')"
+                    :untyped-parameters="parameters"
+                    :annotation="annotation"
+                    :creator="creator"
+                    :license="license"
+                    :steps="steps"
+                    :datatypes-mapper="datatypesMapper"
+                    @onAttributes="
+                        (e) => {
+                            showAttributes(e);
+                        }
+                    "
+                    @onHighlight="onHighlight"
+                    @onUnhighlight="onUnhighlight"
+                    @onRefactor="onAttemptRefactor"
+                    @onScrollTo="onScrollTo" />
+                <UndoRedoStack v-else-if="isActiveSideBar('workflow-undo-redo')" :store-id="id" />
+                <WorkflowPanel
+                    v-else-if="isActiveSideBar('workflow-editor-workflows')"
+                    :current-workflow-id="id"
+                    @insertWorkflow="onInsertWorkflow"
+                    @insertWorkflowSteps="onInsertWorkflowSteps"
+                    @createWorkflow="createNewWorkflow" />
+                <WorkflowAttributes
+                    v-else-if="isActiveSideBar('workflow-editor-attributes')"
+                    :id="id"
+                    :tags="tags"
+                    :highlight="highlightAttribute"
+                    :parameters="parameters"
+                    :annotation="annotation"
+                    :name="name"
+                    :version="version"
+                    :versions="versions"
+                    :license="license"
+                    :creator="creator"
+                    @version="onVersion"
+                    @tags="setTags"
+                    @license="onLicense"
+                    @creator="onCreator"
+                    @update:nameCurrent="setName"
+                    @update:annotationCurrent="setAnnotation" />
+            </template>
+        </ActivityBar>
+        <template v-if="reportActive">
+            <MarkdownEditor
+                ref="markdownEditor"
+                :markdown-text="report.markdown"
+                mode="report"
+                :title="'Workflow Report: ' + name"
+                :steps="steps"
+                @insert="insertMarkdown"
+                @update="onReportUpdate">
+                <template v-slot:buttons>
                     <b-button
-                        :title="undoRedoStore.redoText + ' (Ctrl + Shift + Z)'"
-                        :variant="undoRedoStore.hasRedo ? 'secondary' : 'muted'"
-                        @click="undoRedoStore.redo()">
-                        <FontAwesomeIcon icon="fa-arrow-right" />
+                        id="workflow-canvas-button"
+                        v-b-tooltip.hover.bottom
+                        title="Return to Workflow"
+                        variant="link"
+                        role="button"
+                        @click="showAttributes">
+                        <FontAwesomeIcon :icon="faTimes" />
                     </b-button>
-                </b-button-group>
-            </div>
-            <WorkflowGraph
-                v-if="!datatypesMapperLoading"
-                :steps="steps"
-                :datatypes-mapper="datatypesMapper"
-                :highlight-id="highlightId"
-                :scroll-to-id="scrollToId"
-                @scrollTo="scrollToId = null"
-                @transform="(value) => (transform = value)"
-                @graph-offset="(value) => (graphOffset = value)"
-                @onClone="onClone"
-                @onCreate="onInsertTool"
-                @onChange="onChange"
-                @onRemove="onRemove"
-                @onUpdateStepPosition="onUpdateStepPosition">
-            </WorkflowGraph>
-        </div>
-        <FlexPanel side="right">
-            <div class="unified-panel bg-white">
-                <div class="unified-panel-header" unselectable="on">
-                    <div class="unified-panel-header-inner">
-                        <WorkflowOptions
-                            :is-new-temp-workflow="isNewTempWorkflow"
-                            :has-changes="hasChanges"
-                            :has-invalid-connections="hasInvalidConnections"
-                            @onSave="onSave"
-                            @onCreate="onCreate"
-                            @onSaveAs="onSaveAs"
-                            @onRun="onRun"
-                            @onDownload="onDownload"
-                            @onReport="onReport"
-                            @onLayout="onLayout"
-                            @onEdit="onEdit"
-                            @onAttributes="showAttributes"
-                            @onLint="onLint"
-                            @onUpgrade="onUpgrade" />
-                    </div>
-                </div>
-                <div ref="rightPanelElement" class="unified-panel-body workflow-right p-2">
-                    <div v-if="!initialLoading">
-                        <FormTool
-                            v-if="hasActiveNodeTool"
-                            :key="activeStep.id"
-                            :step="activeStep"
-                            :datatypes="datatypes"
-                            @onChangePostJobActions="onChangePostJobActions"
-                            @onAnnotation="onAnnotation"
-                            @onLabel="onLabel"
-                            @onSetData="onSetData"
-                            @onUpdateStep="updateStep" />
-                        <FormDefault
-                            v-else-if="hasActiveNodeDefault"
-                            :step="activeStep"
-                            :datatypes="datatypes"
-                            @onAnnotation="onAnnotation"
-                            @onLabel="onLabel"
-                            @onEditSubworkflow="onEditSubworkflow"
-                            @onAttemptRefactor="onAttemptRefactor"
-                            @onSetData="onSetData"
-                            @onUpdateStep="updateStep" />
-                        <WorkflowAttributes
-                            v-else-if="attributesVisible"
-                            :id="id"
-                            :tags="tags"
-                            :parameters="parameters"
-                            :annotation="annotation"
-                            :name="name"
-                            :version="version"
-                            :versions="versions"
-                            :license="license"
-                            :creator="creator"
-                            @onVersion="onVersion"
-                            @onTags="setTags"
-                            @onLicense="onLicense"
-                            @onCreator="onCreator"
-                            @update:nameCurrent="setName"
-                            @update:annotationCurrent="setAnnotation" />
-                        <WorkflowLint
-                            v-else-if="showLint"
-                            :untyped-parameters="parameters"
-                            :annotation="annotation"
-                            :creator="creator"
-                            :license="license"
-                            :steps="steps"
-                            :datatypes-mapper="datatypesMapper"
-                            @onAttributes="showAttributes"
-                            @onHighlight="onHighlight"
-                            @onUnhighlight="onUnhighlight"
-                            @onRefactor="onAttemptRefactor"
-                            @onScrollTo="onScrollTo" />
-                    </div>
+                </template>
+            </MarkdownEditor>
+        </template>
+        <template v-else>
+            <div id="center" class="workflow-center">
+                <div class="editor-top-bar" unselectable="on">
+                    <span>
+                        <span class="sr-only">Workflow Editor</span>
+                        <span class="editor-title" :title="name"
+                            >{{ name }}
+                            <i v-if="hasChanges" class="text-muted"> (unsaved changes) </i>
+                        </span>
+                    </span>
+
+                    <b-button-group>
+                        <b-button
+                            :title="undoRedoStore.undoText + ' (Ctrl + Z)'"
+                            :variant="undoRedoStore.hasUndo ? 'secondary' : 'muted'"
+                            @click="undoRedoStore.undo()">
+                            <FontAwesomeIcon icon="fa-arrow-left" />
+                        </b-button>
+                        <b-button
+                            :title="undoRedoStore.redoText + ' (Ctrl + Shift + Z)'"
+                            :variant="undoRedoStore.hasRedo ? 'secondary' : 'muted'"
+                            @click="undoRedoStore.redo()">
+                            <FontAwesomeIcon icon="fa-arrow-right" />
+                        </b-button>
+                        <b-button
+                            id="workflow-save-button"
+                            class="py-1 px-2"
+                            variant="link"
+                            :disabled="!hasChanges"
+                            :title="saveWorkflowTitle"
+                            @click="saveOrCreate">
+                            <FontAwesomeIcon :icon="faSave" />
+                        </b-button>
+                    </b-button-group>
                 </div>
+                <WorkflowGraph
+                    v-if="!datatypesMapperLoading"
+                    :steps="steps"
+                    :datatypes-mapper="datatypesMapper"
+                    :highlight-id="highlightId"
+                    :scroll-to-id="scrollToId"
+                    :initial-position="{ x: 50, y: 50 }"
+                    @scrollTo="scrollToId = null"
+                    @transform="(value) => (transform = value)"
+                    @graph-offset="(value) => (graphOffset = value)"
+                    @onClone="onClone"
+                    @onCreate="onInsertTool"
+                    @onChange="onChange"
+                    @onRemove="onRemove"
+                    @onUpdateStepPosition="onUpdateStepPosition">
+                    <NodeInspector
+                        v-if="activeStep"
+                        :step="activeStep"
+                        :datatypes="datatypes"
+                        @postJobActionsChanged="onChangePostJobActions"
+                        @annotationChanged="onAnnotation"
+                        @labelChanged="onLabel"
+                        @dataChanged="onSetData"
+                        @stepUpdated="updateStep"
+                        @editSubworkflow="onEditSubworkflow"
+                        @attemptRefactor="onAttemptRefactor"
+                        @close="activeNodeId = null"></NodeInspector>
+                </WorkflowGraph>
             </div>
-        </FlexPanel>
-    </div>
-    <MarkdownEditor
-        v-else
-        :markdown-text="report.markdown"
-        mode="report"
-        :title="'Workflow Report: ' + name"
-        :steps="steps"
-        @onUpdate="onReportUpdate">
-        <template v-slot:buttons>
-            <b-button
-                id="workflow-canvas-button"
-                v-b-tooltip.hover.bottom
-                title="Return to Workflow"
-                variant="link"
-                role="button"
-                @click="onEdit">
-                <span class="fa fa-times" />
-            </b-button>
         </template>
-    </MarkdownEditor>
+    </div>
 </template>
 
 <script>
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faArrowLeft, faArrowRight } from "@fortawesome/free-solid-svg-icons";
+import { faArrowLeft, faArrowRight, faCog, faHistory, faSave, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useMagicKeys, whenever } from "@vueuse/core";
 import { logicAnd, logicNot, logicOr } from "@vueuse/math";
@@ -189,7 +200,7 @@ import { storeToRefs } from "pinia";
 import Vue, { computed, nextTick, onUnmounted, ref, unref, watch } from "vue";
 
 import { getUntypedWorkflowParameters } from "@/components/Workflow/Editor/modules/parameters";
-import { ConfirmDialog } from "@/composables/confirmDialog";
+import { ConfirmDialog, useConfirmDialog } from "@/composables/confirmDialog";
 import { useDatatypesMapper } from "@/composables/datatypesMapper";
 import { useUid } from "@/composables/utils/uid";
 import { provideScopedWorkflowStores } from "@/composables/workflowStores";
@@ -203,43 +214,47 @@ import { Services } from "../services";
 import { InsertStepAction, useStepActions } from "./Actions/stepActions";
 import { CopyIntoWorkflowAction, SetValueActionHandler } from "./Actions/workflowActions";
 import { defaultPosition } from "./composables/useDefaultStepPosition";
+import { useActivityLogic, useSpecialWorkflowActivities, workflowEditorActivities } from "./modules/activities";
+import { getWorkflowInputs } from "./modules/inputs";
 import { fromSimple } from "./modules/model";
 import { getModule, getVersions, loadWorkflow, saveWorkflow } from "./modules/services";
 import { getStateUpgradeMessages } from "./modules/utilities";
 import reportDefault from "./reportDefault";
 
-import WorkflowAttributes from "./Attributes.vue";
 import WorkflowLint from "./Lint.vue";
 import MessagesModal from "./MessagesModal.vue";
-import WorkflowOptions from "./Options.vue";
+import NodeInspector from "./NodeInspector.vue";
 import RefactorConfirmationModal from "./RefactorConfirmationModal.vue";
 import SaveChangesModal from "./SaveChangesModal.vue";
 import StateUpgradeModal from "./StateUpgradeModal.vue";
+import WorkflowAttributes from "./WorkflowAttributes.vue";
 import WorkflowGraph from "./WorkflowGraph.vue";
+import ActivityBar from "@/components/ActivityBar/ActivityBar.vue";
 import MarkdownEditor from "@/components/Markdown/MarkdownEditor.vue";
-import FlexPanel from "@/components/Panels/FlexPanel.vue";
+import InputPanel from "@/components/Panels/InputPanel.vue";
 import ToolPanel from "@/components/Panels/ToolPanel.vue";
-import FormDefault from "@/components/Workflow/Editor/Forms/FormDefault.vue";
-import FormTool from "@/components/Workflow/Editor/Forms/FormTool.vue";
+import WorkflowPanel from "@/components/Panels/WorkflowPanel.vue";
+import UndoRedoStack from "@/components/UndoRedo/UndoRedoStack.vue";
 
-library.add(faArrowLeft, faArrowRight);
+library.add(faArrowLeft, faArrowRight, faHistory);
 
 export default {
     components: {
+        ActivityBar,
         MarkdownEditor,
-        FlexPanel,
         SaveChangesModal,
         StateUpgradeModal,
         ToolPanel,
-        FormDefault,
-        FormTool,
-        WorkflowOptions,
         WorkflowAttributes,
         WorkflowLint,
         RefactorConfirmationModal,
         MessagesModal,
         WorkflowGraph,
         FontAwesomeIcon,
+        UndoRedoStack,
+        WorkflowPanel,
+        NodeInspector,
+        InputPanel,
     },
     props: {
         workflowId: {
@@ -262,10 +277,6 @@ export default {
             type: Array,
             required: true,
         },
-        workflows: {
-            type: Array,
-            required: true,
-        },
     },
     setup(props, { emit }) {
         const { datatypes, datatypesMapper, datatypesMapperLoading } = useDatatypesMapper();
@@ -284,7 +295,8 @@ export default {
         whenever(logicAnd(undoKeys, logicNot(redoKeys)), undo);
         whenever(redoKeys, redo);
 
-        const isCanvas = ref(true);
+        const activityBar = ref(null);
+        const reportActive = computed(() => activityBar.value?.isActiveSideBar("workflow-editor-report"));
 
         const parameters = ref(null);
 
@@ -292,12 +304,13 @@ export default {
             parameters.value = getUntypedWorkflowParameters(steps.value);
         }
 
-        const showInPanel = ref("attributes");
-
-        function showAttributes() {
+        function showAttributes(args) {
             ensureParametersSet();
             stateStore.activeNodeId = null;
-            showInPanel.value = "attributes";
+            activityBar.value?.setActiveSideBar("workflow-editor-attributes");
+            if (args?.highlight) {
+                this.highlightAttribute = args.highlight;
+            }
         }
 
         const name = ref("Unnamed Workflow");
@@ -436,13 +449,40 @@ export default {
 
         const stepActions = useStepActions(stepStore, undoRedoStore, stateStore, connectionStore);
 
+        const markdownEditor = ref(null);
+        function insertMarkdown(markdown) {
+            markdownEditor.value?.insertMarkdown(markdown);
+        }
+
+        const isNewTempWorkflow = computed(() => !props.workflowId);
+
+        const { specialWorkflowActivities } = useSpecialWorkflowActivities(
+            computed(() => ({
+                hasInvalidConnections: hasInvalidConnections.value,
+            }))
+        );
+
+        const saveWorkflowTitle = computed(() =>
+            hasInvalidConnections.value
+                ? "Workflow has invalid connections, review and remove invalid connections"
+                : "Save Workflow"
+        );
+
+        useActivityLogic(
+            computed(() => ({
+                activityBarId: "workflow-editor",
+                isNewTempWorkflow: isNewTempWorkflow.value,
+            }))
+        );
+
+        const { confirm } = useConfirmDialog();
+        const inputs = getWorkflowInputs();
+
         return {
             id,
             name,
-            isCanvas,
             parameters,
             ensureParametersSet,
-            showInPanel,
             showAttributes,
             setName,
             report,
@@ -473,6 +513,15 @@ export default {
             initialLoading,
             stepActions,
             undoRedoStore,
+            activityBar,
+            reportActive,
+            markdownEditor,
+            insertMarkdown,
+            specialWorkflowActivities,
+            isNewTempWorkflow,
+            saveWorkflowTitle,
+            confirm,
+            inputs,
         };
     },
     data() {
@@ -485,6 +534,7 @@ export default {
             refactorActions: [],
             scrollToId: null,
             highlightId: null,
+            highlightAttribute: null,
             messageTitle: null,
             messageBody: null,
             messageIsError: false,
@@ -497,27 +547,19 @@ export default {
             debounceTimer: null,
             showSaveChangesModal: false,
             navUrl: "",
+            workflowEditorActivities,
+            faTimes,
+            faCog,
+            faSave,
         };
     },
     computed: {
-        attributesVisible() {
-            return this.showInPanel == "attributes";
-        },
-        showLint() {
-            return this.showInPanel == "lint";
-        },
         activeNodeType() {
             return this.activeStep?.type;
         },
         hasActiveNodeDefault() {
             return this.activeStep && this.activeStep?.type != "tool";
         },
-        hasActiveNodeTool() {
-            return this.activeStep?.type == "tool";
-        },
-        isNewTempWorkflow() {
-            return !this.workflowId;
-        },
     },
     watch: {
         id(newId, oldId) {
@@ -616,7 +658,7 @@ export default {
             this.stepActions.updateStep(nodeId, partialStep);
         },
         onRemove(nodeId) {
-            this.stepActions.removeStep(this.steps[nodeId], this.showAttributes);
+            this.stepActions.removeStep(this.steps[nodeId]);
         },
         onEditSubworkflow(contentId) {
             const editUrl = `/workflows/edit?workflow_id=${contentId}`;
@@ -634,8 +676,8 @@ export default {
         onInsertTool(tool_id, tool_name) {
             this._insertStep(tool_id, tool_name, "tool");
         },
-        onInsertModule(module_id, module_name) {
-            this._insertStep(module_name, module_name, module_id);
+        async onInsertModule(module_id, module_name, state) {
+            this._insertStep(module_name, module_name, module_id, state);
         },
         onInsertWorkflow(workflow_id, workflow_name) {
             this._insertStep(workflow_id, workflow_name, "subworkflow");
@@ -657,10 +699,6 @@ export default {
             });
         },
         async onInsertWorkflowSteps(workflowId, stepCount) {
-            if (!this.isCanvas) {
-                this.isCanvas = true;
-                return;
-            }
             if (stepCount < 10) {
                 this.copyIntoWorkflow(workflowId);
             } else {
@@ -701,16 +739,64 @@ export default {
         onSaveAs() {
             this.showSaveAsModal = true;
         },
-        onLayout() {
-            return import(/* webpackChunkName: "workflowLayout" */ "./modules/layout.ts").then((layout) => {
-                layout.autoLayout(this.id, this.steps).then((newSteps) => {
-                    newSteps.map((step) => this.stepStore.updateStep(step));
-                });
-            });
+        async createNewWorkflow() {
+            await this.saveOrCreate();
+            this.$router.push("/workflows/edit");
+        },
+        async saveOrCreate() {
+            if (this.hasInvalidConnections) {
+                const confirmed = await this.confirm(
+                    `Workflow has invalid connections. You can save the workflow, but it may not run correctly.`,
+                    {
+                        id: "save-workflow-confirmation",
+                        okTitle: "Save Workflow",
+                    }
+                );
+
+                if (!confirmed) {
+                    return;
+                }
+            }
+
+            if (this.isNewTempWorkflow) {
+                await this.onCreate();
+            } else {
+                await this.onSave();
+            }
         },
-        onWorkflowTextEditor() {
-            this.stateStore.activeNodeId = null;
-            this.showInPanel = "attributes";
+        async onActivityClicked(activityId) {
+            if (activityId === "save-and-exit") {
+                await this.saveOrCreate();
+                this.$router.push("/workflows/list");
+            }
+
+            if (activityId === "exit") {
+                this.$router.push("/workflows/list");
+            }
+
+            if (activityId === "workflow-download") {
+                this.onDownload();
+            }
+
+            if (activityId === "workflow-upgrade") {
+                this.onUpgrade();
+            }
+
+            if (activityId === "workflow-run") {
+                this.onRun();
+            }
+
+            if (activityId === "save-workflow") {
+                await this.saveOrCreate();
+            }
+
+            if (activityId === "save-workflow-as") {
+                this.onSaveAs();
+            }
+
+            if (activityId === "workflow-create") {
+                this.createNewWorkflow();
+            }
         },
         onAnnotation(nodeId, newAnnotation) {
             this.stepActions.setAnnotation(this.steps[nodeId], newAnnotation);
@@ -733,6 +819,7 @@ export default {
                 const { id, name, number_of_steps } = await this.services.createWorkflow(this);
                 const message = `Created new workflow '${name}' with ${number_of_steps} steps.`;
                 this.hasChanges = false;
+                this.$emit("skipNextReload");
                 await this.routeToWorkflow(id);
                 Toast.success(message);
             } catch (e) {
@@ -784,20 +871,9 @@ export default {
         onUnhighlight(stepId) {
             this.highlightId = null;
         },
-        onLint() {
-            this.ensureParametersSet();
-            this.stateStore.activeNodeId = null;
-            this.showInPanel = "lint";
-        },
         onUpgrade() {
             this.onAttemptRefactor([{ action_type: "upgrade_all_steps" }]);
         },
-        onEdit() {
-            this.isCanvas = true;
-        },
-        onReport() {
-            this.isCanvas = false;
-        },
         onReportUpdate(markdown) {
             this.hasChanges = true;
             this.report.markdown = markdown;
@@ -859,12 +935,7 @@ export default {
                 this._loadCurrent(this.id, version);
             }
         },
-        _insertStep(contentId, name, type) {
-            if (!this.isCanvas) {
-                this.isCanvas = true;
-                return;
-            }
-
+        async _insertStep(contentId, name, type, state) {
             const action = new InsertStepAction(this.stepStore, this.stateStore, {
                 contentId,
                 name,
@@ -875,22 +946,24 @@ export default {
             this.undoRedoStore.applyAction(action);
             const stepData = action.getNewStepData();
 
-            getModule({ name, type, content_id: contentId }, stepData.id, this.stateStore.setLoadingState).then(
-                (response) => {
-                    const updatedStep = {
-                        ...stepData,
-                        tool_state: response.tool_state,
-                        inputs: response.inputs,
-                        outputs: response.outputs,
-                        config_form: response.config_form,
-                    };
+            const response = await getModule(
+                { name, type, content_id: contentId, tool_state: state },
+                stepData.id,
+                this.stateStore.setLoadingState
+            );
 
-                    this.stepStore.updateStep(updatedStep);
-                    action.updateStepData = updatedStep;
+            const updatedStep = {
+                ...stepData,
+                tool_state: response.tool_state,
+                inputs: response.inputs,
+                outputs: response.outputs,
+                config_form: response.config_form,
+            };
 
-                    this.stateStore.activeNodeId = stepData.id;
-                }
-            );
+            this.stepStore.updateStep(updatedStep);
+            action.updateStepData = updatedStep;
+
+            this.stateStore.activeNodeId = stepData.id;
         },
         async _loadEditorData(data) {
             if (data.name !== undefined) {
diff --git a/client/src/components/Workflow/Editor/Lint.test.js b/client/src/components/Workflow/Editor/Lint.test.js
index 6c8e516d428ffd7e3ac7692311871a8779cbab88..83b749fd4f5cb3ccf3462040889b23411c4ca8e7 100644
--- a/client/src/components/Workflow/Editor/Lint.test.js
+++ b/client/src/components/Workflow/Editor/Lint.test.js
@@ -111,28 +111,18 @@ describe("Lint", () => {
 
     it("test checked vs unchecked issues", async () => {
         const checked = wrapper.findAll("[data-icon='check']");
-        // Expecting 5 checks:
-        // 1. Workflow is annotated
-        // 2. Non-optional inputs (if available) are formal inputs
-        // 3. Inputs (if available) have labels and annotations
         expect(checked.length).toBe(2);
+
         const unchecked = wrapper.findAll("[data-icon='exclamation-triangle']");
-        // Expecting 3 warnings:
-        // 1. Workflow creator is not specified
-        // 2. Workflow license is not specified
-        // 3. Workflow has no labeled outputs
-        // 4. Untyped parameter found
-        // 5. Missing an annotation
-        // 6. Unlabeled output found
         expect(unchecked.length).toBe(5);
+
         const links = wrapper.findAll("a");
-        expect(links.length).toBe(6);
-        expect(links.at(0).text()).toContain("Try to automatically fix issues.");
-        expect(links.at(1).text()).toContain("Provide Creator Details.");
-        expect(links.at(2).text()).toContain("Specify a License.");
-        expect(links.at(3).text()).toContain("untyped_parameter");
-        expect(links.at(4).text()).toContain("data input: Missing an annotation");
-        expect(links.at(5).text()).toContain("step label: output");
+        expect(links.length).toBe(5);
+        expect(links.at(0).text()).toContain("Provide Creator Details.");
+        expect(links.at(1).text()).toContain("Specify a License.");
+        expect(links.at(2).text()).toContain("untyped_parameter");
+        expect(links.at(3).text()).toContain("data input: Missing an annotation");
+        expect(links.at(4).text()).toContain("step label: output");
     });
 
     it("should fire refactor event to extract untyped parameter and remove unlabeled workflows", async () => {
diff --git a/client/src/components/Workflow/Editor/Lint.vue b/client/src/components/Workflow/Editor/Lint.vue
index 86b80a1c392c4e1c2793019220f8e358b780a434..88d3781ccca4e46b501104a59bb50106e6de4454 100644
--- a/client/src/components/Workflow/Editor/Lint.vue
+++ b/client/src/components/Workflow/Editor/Lint.vue
@@ -1,77 +1,64 @@
 <template>
-    <b-card id="lint-panel" header-tag="header" body-class="p-0" class="right-content">
-        <template v-slot:header>
-            <div class="mb-1 font-weight-bold">
-                <FontAwesomeIcon icon="magic" class="mr-1" />
-                Best Practices Review
-            </div>
-            <div v-if="showRefactor">
-                <a class="refactor-button" href="#" @click="onRefactor"> Try to automatically fix issues. </a>
-            </div>
+    <ActivityPanel title="Best Practices Review">
+        <template v-if="showRefactor" v-slot:header>
+            <button class="refactor-button ui-link" @click="onRefactor">Try to automatically fix issues.</button>
         </template>
-        <b-card-body>
-            <LintSection
-                :okay="checkAnnotation"
-                success-message="This workflow is annotated. Ideally, this helps the executors of the workflow
+        <LintSection
+            :okay="checkAnnotation"
+            success-message="This workflow is annotated. Ideally, this helps the executors of the workflow
                     understand the purpose and usage of the workflow."
-                warning-message="This workflow is not annotated. Providing an annotation helps workflow executors
-                    understand the purpose and usage of the workflow."
-                attribute-link="Annotate your Workflow."
-                @onClick="onAttributes" />
-            <LintSection
-                :okay="checkCreator"
-                success-message="This workflow defines creator information."
-                warning-message="This workflow does not specify creator(s). This is important metadata for workflows
-                    that will be published and/or shared to help workflow executors know how to cite the
-                    workflow authors."
-                attribute-link="Provide Creator Details."
-                @onClick="onAttributes" />
-            <LintSection
-                :okay="checkLicense"
-                success-message="This workflow defines a license."
-                warning-message="This workflow does not specify a license. This is important metadata for workflows
-                    that will be published and/or shared to help workflow executors understand how it
-                    may be used."
-                attribute-link="Specify a License."
-                @onClick="onAttributes" />
-            <LintSection
-                success-message="Workflow parameters are using formal input parameters."
-                warning-message="This workflow uses legacy workflow parameters. They should be replaced with
+            :warning-message="bestPracticeWarningAnnotation"
+            attribute-link="Annotate your Workflow."
+            @onClick="onAttributes('annotation')" />
+        <LintSection
+            :okay="checkCreator"
+            success-message="This workflow defines creator information."
+            :warning-message="bestPracticeWarningCreator"
+            attribute-link="Provide Creator Details."
+            @onClick="onAttributes('creator')" />
+        <LintSection
+            :okay="checkLicense"
+            success-message="This workflow defines a license."
+            :warning-message="bestPracticeWarningLicense"
+            attribute-link="Specify a License."
+            @onClick="onAttributes('license')" />
+        <LintSection
+            success-message="Workflow parameters are using formal input parameters."
+            warning-message="This workflow uses legacy workflow parameters. They should be replaced with
                 formal workflow inputs. Formal input parameters make tracking workflow provenance, usage within subworkflows,
                 and executing the workflow via the API more robust:"
-                :warning-items="warningUntypedParameters"
-                @onMouseOver="onHighlight"
-                @onMouseLeave="onUnhighlight"
-                @onClick="onFixUntypedParameter" />
-            <LintSection
-                success-message="All non-optional inputs to workflow steps are connected to formal input parameters."
-                warning-message="Some non-optional inputs are not connected to formal workflow inputs. Formal input parameters
+            :warning-items="warningUntypedParameters"
+            @onMouseOver="onHighlight"
+            @onMouseLeave="onUnhighlight"
+            @onClick="onFixUntypedParameter" />
+        <LintSection
+            success-message="All non-optional inputs to workflow steps are connected to formal input parameters."
+            warning-message="Some non-optional inputs are not connected to formal workflow inputs. Formal input parameters
                 make tracking workflow provenance, usage within subworkflows, and executing the workflow via the API more robust:"
-                :warning-items="warningDisconnectedInputs"
-                @onMouseOver="onHighlight"
-                @onMouseLeave="onUnhighlight"
-                @onClick="onFixDisconnectedInput" />
-            <LintSection
-                success-message="All workflow inputs have labels and annotations."
-                warning-message="Some workflow inputs are missing labels and/or annotations:"
-                :warning-items="warningMissingMetadata"
-                @onMouseOver="onHighlight"
-                @onMouseLeave="onUnhighlight"
-                @onClick="onScrollTo" />
-            <LintSection
-                success-message="This workflow has outputs and they all have valid labels."
-                warning-message="The following workflow outputs have no labels, they should be assigned a useful label or
+            :warning-items="warningDisconnectedInputs"
+            @onMouseOver="onHighlight"
+            @onMouseLeave="onUnhighlight"
+            @onClick="onFixDisconnectedInput" />
+        <LintSection
+            success-message="All workflow inputs have labels and annotations."
+            warning-message="Some workflow inputs are missing labels and/or annotations:"
+            :warning-items="warningMissingMetadata"
+            @onMouseOver="onHighlight"
+            @onMouseLeave="onUnhighlight"
+            @onClick="openAndFocus" />
+        <LintSection
+            success-message="This workflow has outputs and they all have valid labels."
+            warning-message="The following workflow outputs have no labels, they should be assigned a useful label or
                     unchecked in the workflow editor to mark them as no longer being a workflow output:"
-                :warning-items="warningUnlabeledOutputs"
-                @onMouseOver="onHighlight"
-                @onMouseLeave="onUnhighlight"
-                @onClick="onFixUnlabeledOutputs" />
-            <div v-if="!hasActiveOutputs">
-                <FontAwesomeIcon icon="exclamation-triangle" class="text-warning" />
-                <span>This workflow has no labeled outputs, please select and label at least one output.</span>
-            </div>
-        </b-card-body>
-    </b-card>
+            :warning-items="warningUnlabeledOutputs"
+            @onMouseOver="onHighlight"
+            @onMouseLeave="onUnhighlight"
+            @onClick="onFixUnlabeledOutputs" />
+        <div v-if="!hasActiveOutputs">
+            <FontAwesomeIcon icon="exclamation-triangle" class="text-warning" />
+            <span>This workflow has no labeled outputs, please select and label at least one output.</span>
+        </div>
+    </ActivityPanel>
 </template>
 
 <script>
@@ -79,7 +66,6 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faExclamationTriangle, faMagic } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import BootstrapVue from "bootstrap-vue";
-import LintSection from "components/Workflow/Editor/LintSection";
 import { UntypedParameters } from "components/Workflow/Editor/modules/parameters";
 import { storeToRefs } from "pinia";
 import Vue from "vue";
@@ -88,6 +74,9 @@ import { DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useWorkflowStores } from "@/composables/workflowStores";
 
 import {
+    bestPracticeWarningAnnotation,
+    bestPracticeWarningCreator,
+    bestPracticeWarningLicense,
     fixAllIssues,
     fixDisconnectedInput,
     fixUnlabeledOutputs,
@@ -98,6 +87,9 @@ import {
     getUntypedParameters,
 } from "./modules/linting";
 
+import ActivityPanel from "@/components/Panels/ActivityPanel.vue";
+import LintSection from "@/components/Workflow/Editor/LintSection.vue";
+
 Vue.use(BootstrapVue);
 
 library.add(faExclamationTriangle);
@@ -107,6 +99,7 @@ export default {
     components: {
         FontAwesomeIcon,
         LintSection,
+        ActivityPanel,
     },
     props: {
         untypedParameters: {
@@ -136,9 +129,16 @@ export default {
     },
     setup() {
         const stores = useWorkflowStores();
-        const { connectionStore, stepStore } = stores;
+        const { connectionStore, stepStore, stateStore } = stores;
         const { hasActiveOutputs } = storeToRefs(stepStore);
-        return { stores, connectionStore, stepStore, hasActiveOutputs };
+        return { stores, connectionStore, stepStore, hasActiveOutputs, stateStore };
+    },
+    data() {
+        return {
+            bestPracticeWarningAnnotation: bestPracticeWarningAnnotation,
+            bestPracticeWarningCreator: bestPracticeWarningCreator,
+            bestPracticeWarningLicense: bestPracticeWarningLicense,
+        };
     },
     computed: {
         showRefactor() {
@@ -182,8 +182,9 @@ export default {
         },
     },
     methods: {
-        onAttributes() {
-            this.$emit("onAttributes");
+        onAttributes(highlight) {
+            const args = { highlight: highlight };
+            this.$emit("onAttributes", args);
         },
         onFixUntypedParameter(item) {
             if (
@@ -218,7 +219,8 @@ export default {
                 this.$emit("onScrollTo", item.stepId);
             }
         },
-        onScrollTo(item) {
+        openAndFocus(item) {
+            this.stateStore.activeNodeId = item.stepId;
             this.$emit("onScrollTo", item.stepId);
         },
         onHighlight(item) {
diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index 4af194ad89a6a25570d7ca062482149e4c7a56b1..1f4085242a70331c5856d3cd14cdaad492d054c8 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -18,7 +18,8 @@
         <div
             class="unselectable clearfix card-header py-1 px-2"
             :class="headerClass"
-            @click.exact="makeActive"
+            @pointerdown.exact="onPointerDown"
+            @pointerup.exact="onPointerUp"
             @click.shift.capture.prevent.stop="toggleSelected"
             @keyup.enter="makeActive">
             <b-button-group class="float-right">
@@ -91,7 +92,8 @@
             variant="danger"
             show
             class="node-error m-0 rounded-0 rounded-bottom"
-            @click.exact="makeActive"
+            @pointerdown.exact="onPointerDown"
+            @pointerup.exact="onPointerUp"
             @click.shift.capture.prevent.stop="toggleSelected">
             {{ errors }}
         </b-alert>
@@ -100,7 +102,8 @@
             v-else
             class="node-body position-relative card-body p-0 mx-2"
             :class="{ 'cursor-pointer': isInvocation }"
-            @click.exact="makeActive"
+            @pointerdown.exact="onPointerDown"
+            @pointerup.exact="onPointerUp"
             @click.shift.capture.prevent.stop="toggleSelected"
             @keyup.enter="makeActive">
             <NodeInput
@@ -160,7 +163,9 @@ import WorkflowIcons from "@/components/Workflow/icons";
 import type { GraphStep } from "@/composables/useInvocationGraph";
 import { useWorkflowStores } from "@/composables/workflowStores";
 import type { TerminalPosition, XYPosition } from "@/stores/workflowEditorStateStore";
+import { useWorkflowNodeInspectorStore } from "@/stores/workflowNodeInspectorStore";
 import type { Step } from "@/stores/workflowStepStore";
+import { composedPartialPath, isClickable } from "@/utils/dom";
 
 import { ToggleStepSelectedAction } from "./Actions/stepActions";
 import type { OutputTerminals } from "./modules/terminals";
@@ -224,12 +229,14 @@ const postJobActions = computed(() => props.step.post_job_actions || {});
 const workflowOutputs = computed(() => props.step.workflow_outputs || []);
 const { connectionStore, stateStore, stepStore, undoRedoStore } = useWorkflowStores();
 const isLoading = computed(() => Boolean(stateStore.getStepLoadingState(props.id)?.loading));
+
 useNodePosition(
     elHtml,
     props.id,
     stateStore,
     computed(() => props.scale)
 );
+
 const title = computed(() => props.step.label || props.step.name);
 const idString = computed(() => `wf-node-step-${props.id}`);
 const showRule = computed(() => props.step.inputs?.length > 0 && props.step.outputs?.length > 0);
@@ -247,10 +254,13 @@ const classes = computed(() => {
         "node-multi-selected": stateStore.getStepMultiSelected(props.id),
     };
 });
+
 const style = computed(() => {
     return { top: props.step.position!.top + "px", left: props.step.position!.left + "px" };
 });
+
 const errors = computed(() => props.step.errors || stateStore.getStepLoadingState(props.id)?.error);
+
 const headerClass = computed(() => {
     return {
         ...invocationStep.value.headerClass,
@@ -259,6 +269,7 @@ const headerClass = computed(() => {
         "cursor-move": !props.readonly && !props.isInvocation,
     };
 });
+
 const inputs = computed(() => {
     const connections = connectionStore.getConnectionsForStep(props.id);
     const extraStepInputs = stepStore.getStepExtraInputs(props.id);
@@ -275,6 +286,7 @@ const inputs = computed(() => {
     });
     return [...stepInputs, ...invalidInputTerminalSource];
 });
+
 const invalidOutputs = computed(() => {
     const connections = connectionStore.getConnectionsForStep(props.id);
     const invalidConnections = connections.filter(
@@ -287,6 +299,7 @@ const invalidOutputs = computed(() => {
         return { name, optional: false, datatypes: [], valid: false };
     });
 });
+
 const invocationStep = computed(() => props.step as GraphStep);
 const outputs = computed(() => {
     return [...props.step.outputs, ...invalidOutputs.value];
@@ -296,7 +309,56 @@ function onDragConnector(dragPosition: TerminalPosition, terminal: OutputTermina
     emit("onDragConnector", dragPosition, terminal);
 }
 
+const mouseMovementThreshold = 9;
+const singleClickTimeout = 800;
+const doubleClickTimeout = 500;
+
+let mouseDownTime = 0;
+let doubleClickTime = 0;
+
+let movementDistance = 0;
+let lastPosition: XYPosition | null = null;
+
+const inspectorStore = useWorkflowNodeInspectorStore();
+
+function onPointerDown() {
+    mouseDownTime = Date.now();
+}
+
+function onPointerUp(e: PointerEvent) {
+    const path = composedPartialPath(e);
+    const unclickable = path.every((target) => !isClickable(target as Element));
+
+    if (!unclickable) {
+        return;
+    }
+
+    const mouseUpTime = Date.now();
+    const clickTime = mouseUpTime - mouseDownTime;
+
+    if (clickTime <= singleClickTimeout && movementDistance <= mouseMovementThreshold) {
+        makeActive();
+    }
+
+    const timeBetweenClicks = mouseUpTime - doubleClickTime;
+
+    if (timeBetweenClicks < doubleClickTimeout) {
+        inspectorStore.setMaximized(props.step, true);
+    }
+
+    doubleClickTime = Date.now();
+    lastPosition = null;
+    movementDistance = 0;
+}
+
 function onMoveTo(position: XYPosition) {
+    if (lastPosition) {
+        movementDistance += Math.abs(position.x - lastPosition.x);
+        movementDistance += Math.abs(position.y - lastPosition.y);
+    }
+
+    lastPosition = position;
+
     emit("onUpdateStepPosition", props.id, {
         top: position.y + props.scroll.y.value / props.scale,
         left: position.x + props.scroll.x.value / props.scale,
@@ -337,6 +399,8 @@ function toggleSelected() {
 @import "theme/blue.scss";
 
 .workflow-node {
+    --dblclick: prevent;
+
     position: absolute;
     z-index: 100;
     width: $workflow-node-width;
diff --git a/client/src/components/Workflow/Editor/NodeInspector.vue b/client/src/components/Workflow/Editor/NodeInspector.vue
new file mode 100644
index 0000000000000000000000000000000000000000..af19ab5cd1bf918680094fe5f07c4ae0ba166148
--- /dev/null
+++ b/client/src/components/Workflow/Editor/NodeInspector.vue
@@ -0,0 +1,203 @@
+<script setup lang="ts">
+import { faCog, faTimes } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BButtonGroup, BDropdown, BDropdownForm, BDropdownItemButton, BFormCheckbox } from "bootstrap-vue";
+//@ts-ignore deprecated package without types (vue 2, remove this comment on vue 3 migration)
+import { ArrowLeftFromLine, ArrowRightToLine } from "lucide-vue";
+import { computed } from "vue";
+
+import { useWorkflowNodeInspectorStore } from "@/stores/workflowNodeInspectorStore";
+import type { Step } from "@/stores/workflowStepStore";
+
+import FormDefault from "./Forms/FormDefault.vue";
+import FormTool from "./Forms/FormTool.vue";
+import DraggableSeparator from "@/components/Common/DraggableSeparator.vue";
+import Heading from "@/components/Common/Heading.vue";
+import IdleLoad from "@/components/Common/IdleLoad.vue";
+
+const props = defineProps<{
+    step: Step;
+    datatypes: string[];
+}>();
+
+const emit = defineEmits<{
+    (e: "postJobActionsChanged", id: string, postJobActions: unknown): void;
+    (e: "annotationChanged", id: string, annotation: string): void;
+    (e: "labelChanged", id: string, label: string): void;
+    (e: "dataChanged", id: string, data: unknown): void;
+    (e: "stepUpdated", id: string, step: Step): void;
+    (e: "editSubworkflow", id: string): void;
+    (e: "attemptRefactor", ...args: any[]): void;
+    (e: "close"): void;
+}>();
+
+const inspectorStore = useWorkflowNodeInspectorStore();
+
+const maximized = computed(() => inspectorStore.maximized(props.step));
+const width = computed(() => inspectorStore.width(props.step));
+
+const cssVars = computed(() => ({
+    "--width": `${width.value}px`,
+}));
+
+const isTool = computed(() => props.step.type === "tool");
+
+const title = computed(() => `${props.step.id + 1}: ${props.step.label ?? props.step.name}`);
+
+function close() {
+    inspectorStore.generalMaximized = false;
+    emit("close");
+}
+</script>
+
+<template>
+    <section class="tool-inspector" :class="{ maximized }" :style="cssVars">
+        <DraggableSeparator
+            v-if="!maximized"
+            inner
+            :position="width"
+            side="right"
+            :min="100"
+            :max="1200"
+            @positionChanged="(v) => inspectorStore.setWidth(props.step, v)"></DraggableSeparator>
+
+        <div class="inspector-heading">
+            <Heading h2 inline size="sm"> {{ title }} </Heading>
+
+            <BButtonGroup>
+                <BButton
+                    v-if="!maximized"
+                    class="heading-button"
+                    variant="link"
+                    size="md"
+                    title="maximize"
+                    @click="inspectorStore.setMaximized(props.step, true)">
+                    <ArrowLeftFromLine absolute-stroke-width :size="17" />
+                </BButton>
+                <BButton
+                    v-else
+                    class="heading-button"
+                    variant="link"
+                    size="md"
+                    title="minimize"
+                    @click="inspectorStore.setMaximized(props.step, false)">
+                    <ArrowRightToLine absolute-stroke-width :size="17" />
+                </BButton>
+
+                <BDropdown class="dropdown" toggle-class="heading-button" variant="link" size="md" no-caret>
+                    <template v-slot:button-content>
+                        <FontAwesomeIcon :icon="faCog" fixed-width />
+                    </template>
+
+                    <BDropdownForm form-class="px-2" title="remember size for all steps using this tool">
+                        <BFormCheckbox
+                            :checked="inspectorStore.isStored(props.step)"
+                            @input="(v) => inspectorStore.setStored(props.step, v)">
+                            remember size
+                        </BFormCheckbox>
+                    </BDropdownForm>
+
+                    <BDropdownItemButton @click="inspectorStore.clearAllStored">
+                        reset all stored sizes
+                    </BDropdownItemButton>
+                </BDropdown>
+
+                <BButton class="heading-button" variant="link" size="md" title="close" @click="close">
+                    <FontAwesomeIcon :icon="faTimes" fixed-width />
+                </BButton>
+            </BButtonGroup>
+        </div>
+
+        <div class="inspector-content">
+            <IdleLoad :key="props.step.id" spinner center class="w-100 h-50">
+                <FormTool
+                    v-if="isTool"
+                    class="w-100"
+                    :step="props.step"
+                    :datatypes="props.datatypes"
+                    @onSetData="(id, d) => emit('dataChanged', id, d)"
+                    @onUpdateStep="(id, s) => emit('stepUpdated', id, s)"
+                    @onChangePostJobActions="(id, a) => emit('postJobActionsChanged', id, a)"
+                    @onAnnotation="(id, a) => emit('annotationChanged', id, a)"
+                    @onLabel="(id, l) => emit('labelChanged', id, l)"></FormTool>
+                <FormDefault
+                    v-else
+                    class="w-100"
+                    :step="props.step"
+                    :datatypes="datatypes"
+                    @onSetData="(id, d) => emit('dataChanged', id, d)"
+                    @onUpdateStep="(id, s) => emit('stepUpdated', id, s)"
+                    @onAnnotation="(id, a) => emit('annotationChanged', id, a)"
+                    @onLabel="(id, l) => emit('labelChanged', id, l)"
+                    @onEditSubworkflow="(id) => emit('editSubworkflow', id)"
+                    @onAttemptRefactor="(...args) => emit('attemptRefactor', ...args)" />
+            </IdleLoad>
+        </div>
+    </section>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+
+.tool-inspector {
+    --clearance: 8px;
+    --width: 300px;
+
+    position: absolute;
+    right: 0;
+    top: var(--clearance);
+    bottom: var(--clearance);
+    // add border width to node draggable separators width
+    width: calc(var(--width) + 1px);
+    max-width: calc(100% - var(--clearance));
+
+    overflow: hidden;
+
+    background-color: $white;
+
+    z-index: 50000;
+    border-color: $border-color;
+    border-width: 1px;
+    border-style: solid;
+    border-radius: 0.5rem 0 0 0.5rem;
+    display: flex;
+    flex-direction: column;
+
+    &.maximized {
+        border-radius: 0.5rem;
+        --clearance: 16px;
+        right: var(--clearance);
+        top: var(--clearance);
+        bottom: var(--clearance);
+        left: var(--clearance);
+        width: calc(100% - var(--clearance) * 2);
+    }
+
+    .inspector-heading {
+        padding: 0.25rem 0.5rem;
+        display: flex;
+        justify-content: space-between;
+
+        h2 {
+            word-break: break-word;
+        }
+
+        &:deep(.heading-button) {
+            padding: 0.4rem;
+            display: grid;
+            place-items: center;
+        }
+
+        .dropdown.show {
+            display: inline-flex;
+        }
+    }
+
+    .inspector-content {
+        overflow-y: auto;
+        overflow-x: hidden;
+        padding: 0.5rem 0.5rem;
+        padding-top: 0;
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/Editor/NodeInvocationText.vue b/client/src/components/Workflow/Editor/NodeInvocationText.vue
index acc3dd31f555ea30cf756e10eca668b6af2c109d..0b37b9be771c5efcdeaa937e1ae222ceb263973e 100644
--- a/client/src/components/Workflow/Editor/NodeInvocationText.vue
+++ b/client/src/components/Workflow/Editor/NodeInvocationText.vue
@@ -1,17 +1,13 @@
 <script setup lang="ts">
+import { faCheckSquare, faSquare } from "@fortawesome/free-regular-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 
 import { isWorkflowInput } from "@/components/Workflow/constants";
-import { type GraphStep, iconClasses } from "@/composables/useInvocationGraph";
+import { type GraphStep, iconClasses, statePlaceholders } from "@/composables/useInvocationGraph";
 
 const props = defineProps<{
     invocationStep: GraphStep;
 }>();
-
-const statePlaceholders: Record<string, string> = {
-    ok: "successful",
-    error: "failed",
-};
 </script>
 <template>
     <div class="p-1 unselectable">
@@ -29,11 +25,24 @@ const statePlaceholders: Record<string, string> = {
                 </span>
             </div>
         </div>
-        <div v-else-if="isWorkflowInput(props.invocationStep.type)">
-            <!-- TODO: Maybe put a ContentItem here? -->
-            This is an input
+        <div v-else-if="isWorkflowInput(props.invocationStep.type)" class="truncate w-100">
+            <span v-if="typeof props.invocationStep.nodeText === 'boolean'">
+                <FontAwesomeIcon :icon="props.invocationStep.nodeText ? faCheckSquare : faSquare" />
+                {{ props.invocationStep.nodeText }}
+            </span>
+            <!-- eslint-disable-next-line vue/no-v-html -->
+            <span v-else-if="props.invocationStep.nodeText !== undefined" v-html="props.invocationStep.nodeText" />
+            <span v-else>This is an input</span>
         </div>
         <div v-else-if="props.invocationStep.type === 'subworkflow'">This is a subworkflow.</div>
         <div v-else>This step has no jobs as of yet.</div>
     </div>
 </template>
+
+<style scoped>
+.truncate {
+    overflow: hidden;
+    white-space: nowrap;
+    text-overflow: ellipsis;
+}
+</style>
diff --git a/client/src/components/Workflow/Editor/NodeOutput.test.ts b/client/src/components/Workflow/Editor/NodeOutput.test.ts
index 9ee9a8d3361a0a1041737848e85b4fc232ceb096..414ebd7e42f3f3cb101180d05b1b5213429e43c7 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.test.ts
+++ b/client/src/components/Workflow/Editor/NodeOutput.test.ts
@@ -4,7 +4,7 @@ import { getLocalVue } from "tests/jest/helpers";
 import { nextTick, ref } from "vue";
 
 import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
-import { UndoRedoStore, useUndoRedoStore } from "@/stores/undoRedoStore";
+import { type UndoRedoStore, useUndoRedoStore } from "@/stores/undoRedoStore";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { type Step, type Steps, useWorkflowStepStore } from "@/stores/workflowStepStore";
 
diff --git a/client/src/components/Workflow/Editor/NodeOutput.vue b/client/src/components/Workflow/Editor/NodeOutput.vue
index d76c17e443455aab4aa6eeb85b5e3a40bd8c7b08..7c965e06c546451d3f8acb0d82fa541c6f9c550f 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.vue
+++ b/client/src/components/Workflow/Editor/NodeOutput.vue
@@ -11,7 +11,17 @@ import {
 } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import type { UseElementBoundingReturn, UseScrollReturn } from "@vueuse/core";
-import { computed, ComputedRef, nextTick, onBeforeUnmount, type Ref, ref, toRefs, type UnwrapRef, watch } from "vue";
+import {
+    computed,
+    type ComputedRef,
+    nextTick,
+    onBeforeUnmount,
+    type Ref,
+    ref,
+    toRefs,
+    type UnwrapRef,
+    watch,
+} from "vue";
 
 import type { DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useWorkflowStores } from "@/composables/workflowStores";
@@ -300,7 +310,7 @@ const outputDetails = computed(() => {
     const outputType =
         collectionType && collectionType.isCollection && collectionType.collectionType
             ? `output is ${collectionTypeToDescription(collectionType)}`
-            : `output is ${terminal.value.type || "dataset"}`;
+            : `output is  ${terminal.value.optional ? "optional " : ""}${terminal.value.type || "dataset"}`;
     if (isMultiple.value) {
         if (!collectionType) {
             collectionType = NULL_COLLECTION_TYPE_DESCRIPTION;
diff --git a/client/src/components/Workflow/Editor/Options.test.js b/client/src/components/Workflow/Editor/Options.test.js
deleted file mode 100644
index b51974a781b079a013b82e2beb7dd9c02af0473f..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Editor/Options.test.js
+++ /dev/null
@@ -1,32 +0,0 @@
-import { shallowMount } from "@vue/test-utils";
-import { getLocalVue } from "tests/jest/helpers";
-
-import Options from "./Options";
-
-const localVue = getLocalVue();
-
-describe("Options", () => {
-    it("render properly", async () => {
-        const wrapper = shallowMount(Options, {
-            propsData: { hasChanges: true },
-            localVue,
-        });
-        await wrapper.vm.$nextTick();
-        expect(wrapper.find(".editor-button-save").attributes("role")).toBe("button");
-        expect(wrapper.find(".editor-button-save").attributes("disabled")).toBeFalsy();
-        expect(wrapper.find(".editor-button-save-group").attributes("title")).toBe("Save Workflow");
-
-        // requires a non-shallow mount
-        // wrapper.find('.editor-button-attributes').trigger('click');
-        // expect(wrapper.emitted().onAttributes).toBeTruthy();
-    });
-
-    it("should disable save if no changes", async () => {
-        const wrapper = shallowMount(Options, {
-            propsData: { hasChanges: false },
-            localVue,
-        });
-        await wrapper.vm.$nextTick();
-        expect(wrapper.find(".editor-button-save").attributes("disabled")).toBe("true");
-    });
-});
diff --git a/client/src/components/Workflow/Editor/Options.vue b/client/src/components/Workflow/Editor/Options.vue
deleted file mode 100644
index 9d7e0035c4b25ffbea1bc7038d58d321d3710461..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Editor/Options.vue
+++ /dev/null
@@ -1,141 +0,0 @@
-<script setup lang="ts">
-import { BButton, BDropdown, BDropdownItem } from "bootstrap-vue";
-import { computed } from "vue";
-
-import { useConfirmDialog } from "@/composables/confirmDialog";
-
-const emit = defineEmits<{
-    (e: "onAttributes"): void;
-    (e: "onSave"): void;
-    (e: "onCreate"): void;
-    (e: "onReport"): void;
-    (e: "onSaveAs"): void;
-    (e: "onLayout"): void;
-    (e: "onLint"): void;
-    (e: "onUpgrade"): void;
-    (e: "onDownload"): void;
-    (e: "onRun"): void;
-}>();
-
-const props = defineProps<{
-    isNewTempWorkflow?: boolean;
-    hasChanges?: boolean;
-    hasInvalidConnections?: boolean;
-    requiredReindex?: boolean;
-}>();
-
-const { confirm } = useConfirmDialog();
-
-const saveHover = computed(() => {
-    if (props.isNewTempWorkflow) {
-        return "Save Workflow";
-    } else if (!props.hasChanges) {
-        return "Workflow has no changes";
-    } else if (props.hasInvalidConnections) {
-        return "Workflow has invalid connections, review and remove invalid connections";
-    } else {
-        return "Save Workflow";
-    }
-});
-
-function emitSaveOrCreate() {
-    if (props.isNewTempWorkflow) {
-        emit("onCreate");
-    } else {
-        emit("onSave");
-    }
-}
-
-async function onSave() {
-    if (props.hasInvalidConnections) {
-        console.log("getting confirmation");
-        const confirmed = await confirm(
-            `Workflow has invalid connections. You can save the workflow, but it may not run correctly.`,
-            {
-                id: "save-workflow-confirmation",
-                okTitle: "Save Workflow",
-            }
-        );
-        if (confirmed) {
-            emitSaveOrCreate();
-        }
-    } else {
-        emitSaveOrCreate();
-    }
-}
-</script>
-<template>
-    <div class="panel-header-buttons">
-        <BButton
-            id="workflow-home-button"
-            v-b-tooltip.hover.noninteractive
-            role="button"
-            title="Edit Attributes"
-            variant="link"
-            aria-label="Edit Attributes"
-            class="editor-button-attributes"
-            @click="$emit('onAttributes')">
-            <span class="fa fa-pencil-alt" />
-        </BButton>
-        <b-button-group v-b-tooltip.hover.noninteractive class="editor-button-save-group" :title="saveHover">
-            <BButton
-                id="workflow-save-button"
-                role="button"
-                :variant="isNewTempWorkflow ? 'primary' : 'link'"
-                aria-label="Save Workflow"
-                class="editor-button-save"
-                :disabled="!isNewTempWorkflow && !hasChanges"
-                @click="onSave">
-                <span class="fa fa-floppy-o" />
-            </BButton>
-        </b-button-group>
-        <BButton
-            id="workflow-report-button"
-            v-b-tooltip.hover.noninteractive
-            role="button"
-            title="Edit Report"
-            variant="link"
-            aria-label="Edit Report"
-            class="editor-button-report"
-            :disabled="isNewTempWorkflow"
-            @click="$emit('onReport')">
-            <span class="fa fa-edit" />
-        </BButton>
-        <BDropdown
-            id="workflow-options-button"
-            v-b-tooltip.hover.noninteractive
-            no-caret
-            right
-            role="button"
-            title="Workflow Options"
-            variant="link"
-            aria-label="Workflow Options"
-            class="editor-button-options"
-            :disabled="isNewTempWorkflow">
-            <template v-slot:button-content>
-                <span class="fa fa-cog" />
-            </template>
-            <BDropdownItem href="#" @click="$emit('onSaveAs')"><span class="fa fa-floppy-o" />Save As...</BDropdownItem>
-            <BDropdownItem href="#" @click="$emit('onLayout')"
-                ><span class="fa fa-align-left" />Auto Layout</BDropdownItem
-            >
-            <BDropdownItem href="#" @click="$emit('onLint')"><span class="fa fa-magic" />Best Practices</BDropdownItem>
-            <BDropdownItem href="#" @click="$emit('onUpgrade')"
-                ><span class="fa fa-recycle" />Upgrade Workflow</BDropdownItem
-            >
-            <BDropdownItem href="#" @click="$emit('onDownload')"><span class="fa fa-download" />Download</BDropdownItem>
-        </BDropdown>
-        <BButton
-            id="workflow-run-button"
-            v-b-tooltip.hover.noninteractive
-            role="button"
-            title="Run Workflow"
-            variant="link"
-            aria-label="Run Workflow"
-            class="editor-button-run"
-            :disabled="isNewTempWorkflow"
-            @click="$emit('onRun')">
-            <span class="fa fa-play" />
-        </BButton>
-    </div>
-</template>
diff --git a/client/src/components/Workflow/Editor/Tools/ToolBar.vue b/client/src/components/Workflow/Editor/Tools/ToolBar.vue
index c902f381bccf45b26c34873aeb29e792cc9b8beb..d68eaa62f0ce2351b828efcb4fe024a842e05024 100644
--- a/client/src/components/Workflow/Editor/Tools/ToolBar.vue
+++ b/client/src/components/Workflow/Editor/Tools/ToolBar.vue
@@ -17,7 +17,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useMagicKeys, whenever } from "@vueuse/core";
 import { BButton, BButtonGroup, BFormInput } from "bootstrap-vue";
 //@ts-ignore deprecated package without types (vue 2, remove this comment on vue 3 migration)
-import { BoxSelect } from "lucide-vue";
+import { BoxSelect, Workflow } from "lucide-vue";
 import { storeToRefs } from "pinia";
 import { computed, toRefs, watch } from "vue";
 
@@ -27,6 +27,7 @@ import { useWorkflowStores } from "@/composables/workflowStores";
 import { type CommentTool } from "@/stores/workflowEditorToolbarStore";
 import { match } from "@/utils/utils";
 
+import { AutoLayoutAction } from "../Actions/stepActions";
 import { useSelectionOperations } from "./useSelectionOperations";
 import { useToolLogic } from "./useToolLogic";
 
@@ -46,7 +47,7 @@ library.add(
     faTrash
 );
 
-const { toolbarStore, undoRedoStore, commentStore } = useWorkflowStores();
+const { toolbarStore, undoRedoStore, commentStore, workflowId } = useWorkflowStores();
 const { snapActive, currentTool } = toRefs(toolbarStore);
 
 const { commentOptions } = toolbarStore;
@@ -128,7 +129,7 @@ function onRemoveAllFreehand() {
 
 useToolLogic();
 
-const { ctrl_1, ctrl_2, ctrl_3, ctrl_4, ctrl_5, ctrl_6, ctrl_7, ctrl_8 } = useMagicKeys();
+const { ctrl_1, ctrl_2, ctrl_3, ctrl_4, ctrl_5, ctrl_6, ctrl_7, ctrl_8, ctrl_9 } = useMagicKeys();
 
 whenever(ctrl_1!, () => (toolbarStore.currentTool = "pointer"));
 whenever(ctrl_2!, () => (toolbarStore.snapActive = !toolbarStore.snapActive));
@@ -138,6 +139,7 @@ whenever(ctrl_5!, () => (toolbarStore.currentTool = "frameComment"));
 whenever(ctrl_6!, () => (toolbarStore.currentTool = "freehandComment"));
 whenever(ctrl_7!, () => (toolbarStore.currentTool = "freehandEraser"));
 whenever(ctrl_8!, () => (toolbarStore.currentTool = "boxSelect"));
+whenever(ctrl_9!, () => autoLayout());
 
 const toggleVisibilityButtonTitle = computed(() => {
     if (toolbarVisible.value) {
@@ -148,6 +150,10 @@ const toggleVisibilityButtonTitle = computed(() => {
 });
 
 const { anySelected, selectedCountText, deleteSelection, deselectAll, duplicateSelection } = useSelectionOperations();
+
+function autoLayout() {
+    undoRedoStore.applyAction(new AutoLayoutAction(workflowId));
+}
 </script>
 
 <template>
@@ -242,6 +248,17 @@ const { anySelected, selectedCountText, deleteSelection, deselectAll, duplicateS
                     @click="onClickBoxSelect">
                     <BoxSelect />
                 </BButton>
+
+                <BButton
+                    id="auto-layout-button"
+                    v-b-tooltip.hover.noninteractive.right
+                    title="Auto Layout (Ctrl + 9)"
+                    data-tool="auto_layout"
+                    class="button"
+                    variant="outline-primary"
+                    @click="autoLayout">
+                    <Workflow />
+                </BButton>
             </template>
 
             <BButton
@@ -255,6 +272,22 @@ const { anySelected, selectedCountText, deleteSelection, deselectAll, duplicateS
             </BButton>
         </div>
         <div v-if="toolbarVisible" class="options">
+            <div v-if="anySelected" class="selection-options">
+                <span>{{ selectedCountText }}</span>
+
+                <BButtonGroup>
+                    <BButton class="button" title="clear selection" @click="deselectAll">
+                        Clear <FontAwesomeIcon icon="fa-times" />
+                    </BButton>
+                    <BButton class="button" title="duplicate selected" @click="duplicateSelection">
+                        Duplicate <FontAwesomeIcon icon="fa-clone" />
+                    </BButton>
+                    <BButton class="button" title="delete selected" @click="deleteSelection">
+                        Delete <FontAwesomeIcon icon="fa-trash" />
+                    </BButton>
+                </BButtonGroup>
+            </div>
+
             <div
                 v-if="
                     toolbarStore.snapActive &&
@@ -381,22 +414,6 @@ const { anySelected, selectedCountText, deleteSelection, deselectAll, duplicateS
                 </BButtonGroup>
             </div>
         </div>
-
-        <div v-if="anySelected" class="selection-options">
-            <span>{{ selectedCountText }}</span>
-
-            <BButtonGroup>
-                <BButton class="button" title="clear selection" @click="deselectAll">
-                    Clear <FontAwesomeIcon icon="fa-times" />
-                </BButton>
-                <BButton class="button" title="duplicate selected" @click="duplicateSelection">
-                    Duplicate <FontAwesomeIcon icon="fa-clone" />
-                </BButton>
-                <BButton class="button" title="delete selected" @click="deleteSelection">
-                    Delete <FontAwesomeIcon icon="fa-trash" />
-                </BButton>
-            </BButtonGroup>
-        </div>
     </div>
 </template>
 
@@ -507,7 +524,7 @@ const { anySelected, selectedCountText, deleteSelection, deselectAll, duplicateS
         display: flex;
         padding: 0.25rem;
         gap: 0.25rem;
-        align-items: end;
+        align-items: start;
         flex-direction: column-reverse;
         align-self: flex-start;
 
diff --git a/client/src/components/Workflow/Editor/Tools/useToolLogic.ts b/client/src/components/Workflow/Editor/Tools/useToolLogic.ts
index 05b74a5405937d489c5210a8f7ee7a9dd073d33e..c9215b530d00e929eb1c0d9d50756432dd4678bd 100644
--- a/client/src/components/Workflow/Editor/Tools/useToolLogic.ts
+++ b/client/src/components/Workflow/Editor/Tools/useToolLogic.ts
@@ -2,7 +2,7 @@ import simplify from "simplify-js";
 import { ref, watch } from "vue";
 
 import { useWorkflowStores } from "@/composables/workflowStores";
-import type { BaseWorkflowComment } from "@/stores/workflowEditorCommentStore";
+import { type BaseWorkflowComment } from "@/stores/workflowEditorCommentStore";
 import { assertDefined } from "@/utils/assertions";
 import { match } from "@/utils/utils";
 
diff --git a/client/src/components/Workflow/Editor/Attributes.test.js b/client/src/components/Workflow/Editor/WorkflowAttributes.test.ts
similarity index 64%
rename from client/src/components/Workflow/Editor/Attributes.test.js
rename to client/src/components/Workflow/Editor/WorkflowAttributes.test.ts
index f195e4622725f8456e22ca22e1db2580dab87f09..8b9f0eb013b44ea6b7fafa6e9a5fec54fab7df46 100644
--- a/client/src/components/Workflow/Editor/Attributes.test.js
+++ b/client/src/components/Workflow/Editor/WorkflowAttributes.test.ts
@@ -1,12 +1,15 @@
-import { createLocalVue, mount } from "@vue/test-utils";
+import { getLocalVue } from "@tests/jest/helpers";
+import { mount } from "@vue/test-utils";
 import { isDate } from "date-fns";
-import { computed } from "vue";
+import flushPromises from "flush-promises";
+import { createPinia, setActivePinia } from "pinia";
 
 import { useUserTagsStore } from "@/stores/userTagsStore";
 
-import Attributes from "./Attributes";
 import { UntypedParameters } from "./modules/parameters";
 
+import WorkflowAttributes from "./WorkflowAttributes.vue";
+
 jest.mock("app");
 
 const TEST_ANNOTATION = "my cool annotation";
@@ -17,21 +20,19 @@ const TEST_VERSIONS = [
 ];
 const autocompleteTags = ["#named_uer_tag", "abc", "my_tag"];
 
-jest.mock("@/stores/userTagsStore");
-useUserTagsStore.mockReturnValue({
-    userTags: computed(() => autocompleteTags),
-    onNewTagSeen: jest.fn(),
-    onTagUsed: jest.fn(),
-    onMultipleNewTagsSeen: jest.fn(),
-});
-
-describe("Attributes", () => {
+describe("WorkflowAttributes", () => {
     it("test attributes", async () => {
-        const localVue = createLocalVue();
+        const pinia = createPinia();
+        const localVue = getLocalVue(true);
+
+        setActivePinia(pinia);
+
         const untypedParameters = new UntypedParameters();
+
         untypedParameters.getParameter("workflow_parameter_0");
         untypedParameters.getParameter("workflow_parameter_1");
-        const wrapper = mount(Attributes, {
+
+        const wrapper = mount(WorkflowAttributes as object, {
             propsData: {
                 id: "workflow_id",
                 name: TEST_NAME,
@@ -45,18 +46,30 @@ describe("Attributes", () => {
                 LicenseSelector: true,
             },
             localVue,
+            pinia,
         });
+
+        await flushPromises();
+
+        const userTagsStore = useUserTagsStore();
+        jest.spyOn(userTagsStore, "userTags", "get").mockReturnValue(autocompleteTags);
+        userTagsStore.onNewTagSeen = jest.fn();
+        userTagsStore.onTagUsed = jest.fn();
+        userTagsStore.onMultipleNewTagsSeen = jest.fn();
+
         expect(wrapper.find(`[itemprop='description']`).attributes("content")).toBe(TEST_ANNOTATION);
         expect(wrapper.find(`[itemprop='name']`).attributes("content")).toBe(TEST_NAME);
         expect(wrapper.find(`#workflow-version-area > select`).exists()).toBeTruthy();
 
         const name = wrapper.find("#workflow-name");
-        expect(name.element.value).toBe(TEST_NAME);
+        expect((name.element as HTMLInputElement).value).toBe(TEST_NAME);
         await wrapper.setProps({ name: "new_workflow_name" });
-        expect(name.element.value).toBe("new_workflow_name");
+        expect((name.element as HTMLInputElement).value).toBe("new_workflow_name");
+
+        const version = wrapper.findAll(`#workflow-version-area > select > option`);
 
-        const version = wrapper.findAllComponents(`#workflow-version-area > select > option`);
         expect(version).toHaveLength(TEST_VERSIONS.length);
+
         for (let i = 0; i < version.length; i++) {
             const versionLabel = version.at(i).text();
             const versionDate = versionLabel.substring(versionLabel.indexOf(":") + 1, versionLabel.indexOf(",")).trim();
@@ -67,6 +80,6 @@ describe("Attributes", () => {
         expect(parameters.length).toBe(2);
         expect(parameters.at(0).text()).toBe("1: workflow_parameter_0");
         expect(parameters.at(1).text()).toBe("2: workflow_parameter_1");
-        expect(wrapper.find("#workflow-annotation").element.value).toBe(TEST_ANNOTATION);
+        expect((wrapper.find("#workflow-annotation").element as HTMLInputElement).value).toBe(TEST_ANNOTATION);
     });
 });
diff --git a/client/src/components/Workflow/Editor/Attributes.vue b/client/src/components/Workflow/Editor/WorkflowAttributes.vue
similarity index 54%
rename from client/src/components/Workflow/Editor/Attributes.vue
rename to client/src/components/Workflow/Editor/WorkflowAttributes.vue
index c0d7311e06ee2dbaf903083e5610a6148c62c361..3f258d462062263c5c085d8b6ba25eb7539003a4 100644
--- a/client/src/components/Workflow/Editor/Attributes.vue
+++ b/client/src/components/Workflow/Editor/WorkflowAttributes.vue
@@ -1,5 +1,5 @@
 <template>
-    <div id="edit-attributes" class="right-content p-2" itemscope itemtype="http://schema.org/CreativeWork">
+    <ActivityPanel id="edit-attributes" title="Attributes" itemscope itemtype="http://schema.org/CreativeWork">
         <b-alert :variant="messageVariant" :show="!!message">
             {{ message }}
         </b-alert>
@@ -28,7 +28,10 @@
                 </b-list-group-item>
             </b-list-group>
         </div>
-        <div id="workflow-annotation-area" class="mt-2">
+        <div
+            id="workflow-annotation-area"
+            class="mt-2"
+            :class="{ 'bg-secondary': showAnnotationHightlight, 'highlight-attribute': showAnnotationHightlight }">
             <b>Annotation</b>
             <meta itemprop="description" :content="annotationCurrent" />
             <b-textarea
@@ -36,14 +39,50 @@
                 v-model="annotationCurrent"
                 @keyup="$emit('update:annotationCurrent', annotationCurrent)" />
             <div class="form-text text-muted">These notes will be visible when this workflow is viewed.</div>
+            <b-popover
+                custom-class="best-practice-popover"
+                target="workflow-annotation"
+                boundary="window"
+                placement="right"
+                :show.sync="showAnnotationHightlight"
+                triggers="manual"
+                title="Best Practice"
+                :content="bestPracticeWarningAnnotation">
+            </b-popover>
         </div>
-        <div id="workflow-license-area" class="mt-2">
+        <div
+            id="workflow-license-area"
+            class="mt-2"
+            :class="{ 'bg-secondary': showLicenseHightlight, 'highlight-attribute': showLicenseHightlight }">
             <b>License</b>
-            <LicenseSelector :input-license="license" @onLicense="onLicense" />
+            <LicenseSelector id="license-selector" :input-license="license" @onLicense="onLicense" />
+            <b-popover
+                custom-class="best-practice-popover"
+                target="license-selector"
+                boundary="window"
+                placement="right"
+                :show.sync="showLicenseHightlight"
+                triggers="manual"
+                title="Best Practice"
+                :content="bestPracticeWarningLicense">
+            </b-popover>
         </div>
-        <div id="workflow-creator-area" class="mt-2">
+        <div
+            id="workflow-creator-area"
+            class="mt-2"
+            :class="{ 'bg-secondary': showCreatorHightlight, 'highlight-attribute': showCreatorHightlight }">
             <b>Creator</b>
-            <CreatorEditor :creators="creatorAsList" @onCreators="onCreator" />
+            <CreatorEditor id="creator-editor" :creators="creatorAsList" @onCreators="onCreator" />
+            <b-popover
+                custom-class="best-practice-popover"
+                target="creator-editor"
+                boundary="window"
+                placement="right"
+                :show.sync="showCreatorHightlight"
+                triggers="manual"
+                title="Best Practice"
+                :content="bestPracticeWarningCreator">
+            </b-popover>
         </div>
         <div class="mt-2">
             <b>Tags</b>
@@ -52,28 +91,35 @@
                 Apply tags to make it easy to search for and find items with the same tag.
             </div>
         </div>
-    </div>
+    </ActivityPanel>
 </template>
 
 <script>
-import BootstrapVue from "bootstrap-vue";
-import LicenseSelector from "components/License/LicenseSelector";
-import CreatorEditor from "components/SchemaOrg/CreatorEditor";
-import StatelessTags from "components/TagsMultiselect/StatelessTags";
-import { Services } from "components/Workflow/services";
 import { format, parseISO } from "date-fns";
-import Vue from "vue";
 
+import { Services } from "@/components/Workflow/services";
+
+import {
+    bestPracticeWarningAnnotation,
+    bestPracticeWarningCreator,
+    bestPracticeWarningLicense,
+} from "./modules/linting";
 import { UntypedParameters } from "./modules/parameters";
 
-Vue.use(BootstrapVue);
+import LicenseSelector from "@/components/License/LicenseSelector.vue";
+import ActivityPanel from "@/components/Panels/ActivityPanel.vue";
+import CreatorEditor from "@/components/SchemaOrg/CreatorEditor.vue";
+import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
+
+const bestPracticeHighlightTime = 10000;
 
 export default {
-    name: "Attributes",
+    name: "WorkflowAttributes",
     components: {
         StatelessTags,
         LicenseSelector,
         CreatorEditor,
+        ActivityPanel,
     },
     props: {
         id: {
@@ -84,6 +130,10 @@ export default {
             type: String,
             default: null,
         },
+        highlight: {
+            type: String,
+            default: null,
+        },
         tags: {
             type: Array,
             required: true,
@@ -115,11 +165,17 @@ export default {
     },
     data() {
         return {
+            bestPracticeWarningAnnotation: bestPracticeWarningAnnotation,
+            bestPracticeWarningCreator: bestPracticeWarningCreator,
+            bestPracticeWarningLicense: bestPracticeWarningLicense,
             message: null,
             messageVariant: null,
             versionCurrent: this.version,
             annotationCurrent: this.annotation,
             nameCurrent: this.name,
+            showAnnotationHightlight: false,
+            showLicenseHightlight: false,
+            showCreatorHightlight: false,
         };
     },
     computed: {
@@ -179,6 +235,36 @@ export default {
         name() {
             this.nameCurrent = this.name;
         },
+        highlight: {
+            immediate: true,
+            handler(newHighlight, oldHighlight) {
+                if (newHighlight == oldHighlight) {
+                    return;
+                }
+                if (newHighlight == "annotation") {
+                    this.showAnnotationHightlight = true;
+                    this.showCreatorHightlight = false;
+                    this.showLicenseHightlight = false;
+                    setTimeout(() => {
+                        this.showAnnotationHightlight = false;
+                    }, bestPracticeHighlightTime);
+                } else if (newHighlight == "creator") {
+                    this.showAnnotationHightlight = false;
+                    this.showCreatorHightlight = true;
+                    this.showLicenseHightlight = false;
+                    setTimeout(() => {
+                        this.showCreatorHightlight = false;
+                    }, bestPracticeHighlightTime);
+                } else if (newHighlight == "license") {
+                    this.showAnnotationHightlight = false;
+                    this.showCreatorHightlight = false;
+                    this.showLicenseHightlight = true;
+                    setTimeout(() => {
+                        this.showLicenseHightlight = false;
+                    }, bestPracticeHighlightTime);
+                }
+            },
+        },
     },
     created() {
         this.services = new Services();
@@ -186,16 +272,16 @@ export default {
     methods: {
         onTags(tags) {
             this.onAttributes({ tags });
-            this.$emit("onTags", tags);
+            this.$emit("tags", tags);
         },
         onVersion() {
-            this.$emit("onVersion", this.versionCurrent);
+            this.$emit("version", this.versionCurrent);
         },
         onLicense(license) {
-            this.$emit("onLicense", license);
+            this.$emit("license", license);
         },
         onCreator(creator) {
-            this.$emit("onCreator", creator);
+            this.$emit("creator", creator);
         },
         onError(error) {
             this.message = error;
@@ -211,3 +297,14 @@ export default {
     },
 };
 </script>
+
+<style>
+.highlight-attribute {
+    border: 1px outset;
+    padding: 10px;
+}
+
+.best-practice-popover {
+    max-width: 250px !important;
+}
+</style>
diff --git a/client/src/components/Workflow/Editor/WorkflowGraph.vue b/client/src/components/Workflow/Editor/WorkflowGraph.vue
index 917e3cb55ad4d9386e155205fb5ef76f0519a925..b0a27f1b623593c55d3bca4c320f75559408f1f6 100644
--- a/client/src/components/Workflow/Editor/WorkflowGraph.vue
+++ b/client/src/components/Workflow/Editor/WorkflowGraph.vue
@@ -64,6 +64,7 @@
             :viewport-bounding-box="viewportBoundingBox"
             @panBy="panBy"
             @moveTo="moveTo" />
+        <slot></slot>
     </div>
 </template>
 <script setup lang="ts">
@@ -92,7 +93,7 @@ import WorkflowEdges from "@/components/Workflow/Editor/WorkflowEdges.vue";
 import WorkflowMinimap from "@/components/Workflow/Editor/WorkflowMinimap.vue";
 import ZoomControl from "@/components/Workflow/Editor/ZoomControl.vue";
 
-const emit = defineEmits(["transform", "graph-offset", "onRemove", "scrollTo"]);
+const emit = defineEmits(["transform", "graph-offset", "onRemove", "scrollTo", "stepClicked"]);
 const props = defineProps({
     steps: { type: Object as PropType<{ [index: string]: Step }>, required: true },
     datatypesMapper: { type: DatatypesMapperModel, required: true },
@@ -176,6 +177,7 @@ function onDragConnector(position: TerminalPosition, draggingTerminal: OutputTer
     isDragging.value = true;
 }
 function onActivate(nodeId: number | null) {
+    emit("stepClicked", nodeId);
     if (activeNodeId.value !== nodeId) {
         stateStore.activeNodeId = nodeId;
     }
diff --git a/client/src/components/Workflow/Editor/composables/d3Zoom.ts b/client/src/components/Workflow/Editor/composables/d3Zoom.ts
index d770c105913ebf6ed70be586ca7364f88500dfe5..d0f70851433446ff4dd690d8d41db0a7b4be2495 100644
--- a/client/src/components/Workflow/Editor/composables/d3Zoom.ts
+++ b/client/src/components/Workflow/Editor/composables/d3Zoom.ts
@@ -1,16 +1,28 @@
-import type { UseScrollReturn } from "@vueuse/core";
+import { type UseScrollReturn } from "@vueuse/core";
 import { select } from "d3-selection";
 import { type D3ZoomEvent, zoom, zoomIdentity } from "d3-zoom";
-import type { Ref } from "vue";
-import { ref, watch } from "vue";
+import { type Ref, ref, watch } from "vue";
 
-import type { XYPosition } from "@/stores/workflowEditorStateStore";
+import { type XYPosition } from "@/stores/workflowEditorStateStore";
 
 // if element is draggable it may implement its own drag handler,
 // but d3zoom would call preventDefault
-const filter = (event: any) => {
-    const preventZoom = event.target.classList.contains("prevent-zoom");
-    return !preventZoom;
+const filter = (event: D3ZoomEvent<HTMLElement, unknown>["sourceEvent"]) => {
+    const target = event.target as HTMLElement;
+
+    if (target.classList.contains("prevent-zoom")) {
+        return false;
+    }
+
+    if (event.type === "dblclick") {
+        const style = getComputedStyle(target);
+
+        if (style.getPropertyValue("--dblclick") === "prevent") {
+            return false;
+        }
+    }
+
+    return true;
 };
 
 export function useD3Zoom(
diff --git a/client/src/components/Workflow/Editor/composables/multiSelect.ts b/client/src/components/Workflow/Editor/composables/multiSelect.ts
index a0f199756a145996d4a2b0f61c3968b305b2a357..81a64152fea8a3917f657f2849655d3f1afd5a30 100644
--- a/client/src/components/Workflow/Editor/composables/multiSelect.ts
+++ b/client/src/components/Workflow/Editor/composables/multiSelect.ts
@@ -1,7 +1,7 @@
 import { computed, type Ref } from "vue";
 
 import { useWorkflowStores } from "@/composables/workflowStores";
-import type { Step } from "@/stores/workflowStepStore";
+import { type Step } from "@/stores/workflowStepStore";
 import { ensureDefined } from "@/utils/assertions";
 
 import { ClearSelectionAction } from "../Actions/workflowActions";
diff --git a/client/src/components/Workflow/Editor/composables/relativePosition.ts b/client/src/components/Workflow/Editor/composables/relativePosition.ts
index 938a4ad5cf4f4a9ca475d58beb4cdba3ae121b00..2c8215be53f29c45bed710fafbd6b77530807f87 100644
--- a/client/src/components/Workflow/Editor/composables/relativePosition.ts
+++ b/client/src/components/Workflow/Editor/composables/relativePosition.ts
@@ -1,4 +1,4 @@
-import type { ZoomTransform } from "d3-zoom";
+import { type ZoomTransform } from "d3-zoom";
 import { inject, onScopeDispose, type Ref, ref, watch } from "vue";
 
 /**
diff --git a/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts b/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
index e4a70fdbc776c080baea48e2d6c9a4af50dafc7a..18d3f2dff8a506dc63cf9e0aca67db4478852e14 100644
--- a/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
+++ b/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
@@ -1,6 +1,6 @@
-import type { UseElementBoundingReturn } from "@vueuse/core";
-import type { ZoomTransform } from "d3-zoom";
-import type { UnwrapRef } from "vue";
+import { type UseElementBoundingReturn } from "@vueuse/core";
+import { type ZoomTransform } from "d3-zoom";
+import { type UnwrapRef } from "vue";
 
 type ElementBounding = UnwrapRef<UseElementBoundingReturn>;
 
diff --git a/client/src/components/Workflow/Editor/composables/useNodePosition.ts b/client/src/components/Workflow/Editor/composables/useNodePosition.ts
index eba8b076bf0bae12548c0648b32ff4a37c0b6d46..45e9aebebee872cefe31f1ed583aeea0fe26e4c6 100644
--- a/client/src/components/Workflow/Editor/composables/useNodePosition.ts
+++ b/client/src/components/Workflow/Editor/composables/useNodePosition.ts
@@ -1,7 +1,7 @@
 import { useElementBounding } from "@vueuse/core";
 import { type ComputedRef, onUnmounted, type Ref, unref, watch } from "vue";
 
-import type { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
+import { type useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 
 export function useNodePosition(
     nodeRef: Ref<HTMLElement | null>,
diff --git a/client/src/components/Workflow/Editor/composables/useStepProps.ts b/client/src/components/Workflow/Editor/composables/useStepProps.ts
index 4c4ddb2aff5efe6420c7e4caa158b3da54b7d7ea..95e4787bdfd942298e5074cf493dbcf8e939f42d 100644
--- a/client/src/components/Workflow/Editor/composables/useStepProps.ts
+++ b/client/src/components/Workflow/Editor/composables/useStepProps.ts
@@ -1,7 +1,7 @@
 import { toRefs } from "@vueuse/core";
 import { computed, type Ref } from "vue";
 
-import type { Step } from "@/stores/workflowStepStore";
+import { type Step } from "@/stores/workflowStepStore";
 
 export function useStepProps(step: Ref<Step>) {
     const {
diff --git a/client/src/components/Workflow/Editor/composables/useTerminal.ts b/client/src/components/Workflow/Editor/composables/useTerminal.ts
index fbe92d11dda31850b710c4fe3795db4680853bd4..f8ec226de1876d9d216dd9933657412fef3965cd 100644
--- a/client/src/components/Workflow/Editor/composables/useTerminal.ts
+++ b/client/src/components/Workflow/Editor/composables/useTerminal.ts
@@ -1,9 +1,9 @@
 import { computed, type Ref, ref, watch } from "vue";
 
-import type { DatatypesMapperModel } from "@/components/Datatypes/model";
+import { type DatatypesMapperModel } from "@/components/Datatypes/model";
 import { terminalFactory } from "@/components/Workflow/Editor/modules/terminals";
 import { useWorkflowStores } from "@/composables/workflowStores";
-import type { Step, TerminalSource } from "@/stores/workflowStepStore";
+import { type Step, type TerminalSource } from "@/stores/workflowStepStore";
 
 export function useTerminal(
     stepId: Ref<Step["id"]>,
diff --git a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
index 331c1a70b7dc27ce4afe9af14e32f60bb3e7e2d7..d0b84db830ae2a6e1fd19d33f8233cbb70ae8ca6 100644
--- a/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
+++ b/client/src/components/Workflow/Editor/composables/useUniqueLabelError.ts
@@ -1,16 +1,14 @@
 import { ref } from "vue";
 
-import type { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import { type useWorkflowStepStore } from "@/stores/workflowStepStore";
 
 export function useUniqueLabelError(
     workflowStateStore: ReturnType<typeof useWorkflowStepStore>,
     label: string | null | undefined
 ) {
-    const error = ref("");
+    const error = ref<string | null>(null);
     if (label && workflowStateStore.workflowOutputs[label]) {
         error.value = `Duplicate label ${label}. Please fix this before saving the workflow.`;
-    } else {
-        error.value = "";
     }
     return error;
 }
diff --git a/client/src/components/Workflow/Editor/composables/viewportBoundingBox.ts b/client/src/components/Workflow/Editor/composables/viewportBoundingBox.ts
index 16c09f6cd1df4a81ba9ed4b462905bc6ff083650..79aa9f265210c08207b90d6646237345c1c8d68e 100644
--- a/client/src/components/Workflow/Editor/composables/viewportBoundingBox.ts
+++ b/client/src/components/Workflow/Editor/composables/viewportBoundingBox.ts
@@ -1,4 +1,4 @@
-import type { UseElementBoundingReturn } from "@vueuse/core";
+import { type UseElementBoundingReturn } from "@vueuse/core";
 import { type Ref, ref, unref, watch } from "vue";
 
 import { useAnimationFrameThrottle } from "@/composables/throttle";
diff --git a/client/src/components/Workflow/Editor/modules/activities.ts b/client/src/components/Workflow/Editor/modules/activities.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2d025509aa265a55ae24ec329f40032ec6344668
--- /dev/null
+++ b/client/src/components/Workflow/Editor/modules/activities.ts
@@ -0,0 +1,207 @@
+import { faSave as farSave } from "@fortawesome/free-regular-svg-icons";
+import {
+    faDownload,
+    faEdit,
+    faHistory,
+    faMagic,
+    faPencilAlt,
+    faPlay,
+    faPlus,
+    faRecycle,
+    faSave,
+    faSignOutAlt,
+    faSitemap,
+    faWrench,
+} from "@fortawesome/free-solid-svg-icons";
+import { watchImmediate } from "@vueuse/core";
+import { faDiagramNext } from "font-awesome-6";
+import { computed, type Ref } from "vue";
+
+import { type Activity, useActivityStore } from "@/stores/activityStore";
+
+export const workflowEditorActivities = [
+    {
+        title: "Attributes",
+        id: "workflow-editor-attributes",
+        tooltip: "Edit workflow attributes",
+        description: "View and edit the attributes of this workflow.",
+        panel: true,
+        icon: faPencilAlt,
+        visible: true,
+    },
+    {
+        title: "Inputs",
+        id: "workflow-editor-inputs",
+        tooltip: "Add input steps to your workflow",
+        description: "Add input steps to your workflow.",
+        icon: faDiagramNext,
+        panel: true,
+        visible: true,
+    },
+    {
+        title: "Tools",
+        id: "workflow-editor-tools",
+        description: "Displays the tool panel to search and place all available tools.",
+        icon: faWrench,
+        panel: true,
+        tooltip: "Search tools to use in your workflow",
+        visible: true,
+    },
+    {
+        title: "Workflows",
+        id: "workflow-editor-workflows",
+        description: "Browse other workflows and add them as sub-workflows.",
+        tooltip: "Search workflows to use in your workflow",
+        icon: faSitemap,
+        panel: true,
+        visible: true,
+        optional: true,
+    },
+    {
+        title: "Report",
+        id: "workflow-editor-report",
+        description: "Edit the report for this workflow.",
+        tooltip: "Edit workflow report",
+        icon: faEdit,
+        panel: true,
+        visible: true,
+        optional: true,
+    },
+    {
+        title: "Best Practices",
+        id: "workflow-best-practices",
+        description: "Show and test for the best practices in this workflow.",
+        tooltip: "Test workflow for best practices",
+        icon: faMagic,
+        panel: true,
+        visible: true,
+        optional: true,
+    },
+    {
+        title: "Changes",
+        id: "workflow-undo-redo",
+        description: "View, undo, and redo your latest changes.",
+        tooltip: "Show and manage latest changes",
+        icon: faHistory,
+        panel: true,
+        visible: true,
+        optional: true,
+    },
+    {
+        title: "Run",
+        id: "workflow-run",
+        description: "Run this workflow with specific parameters.",
+        tooltip: "Run workflow",
+        icon: faPlay,
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        description: "Save this workflow.",
+        icon: faSave,
+        id: "save-workflow",
+        title: "Save",
+        tooltip: "Save current changes",
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        description: "Save this workflow with a different name and annotation.",
+        icon: farSave,
+        id: "save-workflow-as",
+        title: "Save as",
+        tooltip: "Save a copy of this workflow",
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        title: "Upgrade",
+        id: "workflow-upgrade",
+        description: "Update all tools used in this workflow.",
+        tooltip: "Update all tools",
+        icon: faRecycle,
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        title: "Download",
+        id: "workflow-download",
+        description: "Download this workflow in '.ga' format.",
+        tooltip: "Download workflow",
+        icon: faDownload,
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        description: "Save this workflow and create a new workflow.",
+        icon: faPlus,
+        title: "Create new",
+        id: "workflow-create",
+        tooltip: "Save this workflow and create a new one",
+        visible: true,
+        click: true,
+        optional: true,
+    },
+    {
+        description: "Exit the workflow editor and return to the start screen.",
+        icon: faSignOutAlt,
+        id: "exit",
+        title: "Exit",
+        tooltip: "Exit workflow editor",
+        visible: false,
+        click: true,
+        optional: true,
+    },
+] as const satisfies Readonly<Activity[]>;
+
+interface ActivityLogicOptions {
+    activityBarId: string;
+    isNewTempWorkflow: boolean;
+}
+
+export function useActivityLogic(options: Ref<ActivityLogicOptions>) {
+    const store = useActivityStore(options.value.activityBarId);
+
+    watchImmediate(
+        () => options.value.isNewTempWorkflow,
+        (value) => {
+            store.setMeta("workflow-run", "disabled", value);
+        }
+    );
+}
+
+interface SpecialActivityOptions {
+    hasInvalidConnections: boolean;
+}
+
+export function useSpecialWorkflowActivities(options: Ref<SpecialActivityOptions>) {
+    const saveHover = computed(() => {
+        if (options.value.hasInvalidConnections) {
+            return "Workflow has invalid connections, review and remove invalid connections";
+        } else {
+            return "Save this workflow, then exit the workflow editor";
+        }
+    });
+
+    const specialWorkflowActivities = computed<Activity[]>(() => [
+        {
+            description: "",
+            icon: faSave,
+            id: "save-and-exit",
+            title: "Save + Exit",
+            tooltip: saveHover.value,
+            visible: false,
+            click: true,
+            mutable: false,
+        },
+    ]);
+
+    return {
+        specialWorkflowActivities,
+    };
+}
diff --git a/client/src/components/Workflow/Editor/modules/canvasDraw.ts b/client/src/components/Workflow/Editor/modules/canvasDraw.ts
index 9a3f26be6cf63618d840753c7c7a9ce556495d0c..8a2a7db27b4ef56374ef69458aaf37e9369ee1c0 100644
--- a/client/src/components/Workflow/Editor/modules/canvasDraw.ts
+++ b/client/src/components/Workflow/Editor/modules/canvasDraw.ts
@@ -1,14 +1,14 @@
 import { curveCatmullRom, line } from "d3";
 
 import * as commentColors from "@/components/Workflow/Editor/Comments/colors";
-import type {
-    FrameWorkflowComment,
-    FreehandWorkflowComment,
-    MarkdownWorkflowComment,
-    TextWorkflowComment,
+import {
+    type FrameWorkflowComment,
+    type FreehandWorkflowComment,
+    type MarkdownWorkflowComment,
+    type TextWorkflowComment,
 } from "@/stores/workflowEditorCommentStore";
-import type { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
-import type { Step } from "@/stores/workflowStepStore";
+import { type useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
+import { type Step } from "@/stores/workflowStepStore";
 
 export function drawBoxComments(
     ctx: CanvasRenderingContext2D,
diff --git a/client/src/components/Workflow/Editor/modules/geometry.ts b/client/src/components/Workflow/Editor/modules/geometry.ts
index eee7fc3d56beb8d34553151f699a3c17a49a92be..03bea2c0a3dc6aa60d05de087e5a89dfe7980fcb 100644
--- a/client/src/components/Workflow/Editor/modules/geometry.ts
+++ b/client/src/components/Workflow/Editor/modules/geometry.ts
@@ -108,6 +108,15 @@ export class AxisAlignedBoundingBox implements Rectangle {
             this.endY >= other.y + other.height
         );
     }
+
+    intersects(other: Rectangle) {
+        return (
+            this.x < other.x + other.width &&
+            this.endX > other.x &&
+            this.y < other.y + other.height &&
+            this.endY > other.y
+        );
+    }
 }
 
 /* Format
@@ -240,3 +249,16 @@ export function vecReduceFigures(a: Vector, significantFigures = 1): Vector {
 
     return [Math.round(a[0] * factor) / factor, Math.round(a[1] * factor) / factor];
 }
+
+export function rectCenterPoint(rect: Rectangle): Vector {
+    return [rect.x + rect.width / 2, rect.y + rect.height / 2];
+}
+
+export function rectDistance(a: Rectangle, b: Rectangle): number {
+    const vecA = rectCenterPoint(a);
+    const vecB = rectCenterPoint(b);
+    const dx = vecA[0] - vecB[0];
+    const dy = vecA[1] - vecB[1];
+
+    return Math.hypot(dx, dy);
+}
diff --git a/client/src/components/Workflow/Editor/modules/inputs.ts b/client/src/components/Workflow/Editor/modules/inputs.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c152058d43607753d83b198e826f3a47b3e142cd
--- /dev/null
+++ b/client/src/components/Workflow/Editor/modules/inputs.ts
@@ -0,0 +1,90 @@
+import { faFile, faFolder } from "@fortawesome/free-regular-svg-icons";
+import { faPencilAlt } from "@fortawesome/free-solid-svg-icons";
+import { type IconDefinition } from "font-awesome-6";
+
+export interface WorkflowInput {
+    id?: string; // unique ID. defaults to module ID
+    moduleId: string;
+    title: string;
+    description: string;
+    stateOverwrites?: {
+        parameter_type?: "text" | "integer" | "boolean" | "color" | "float" | "directory_uri";
+    };
+    icon: IconDefinition;
+}
+
+export function getWorkflowInputs(): WorkflowInput[] {
+    return [
+        {
+            moduleId: "data_input",
+            title: "Input Dataset",
+            description: "Single dataset input",
+            icon: faFile,
+        },
+        {
+            moduleId: "data_collection_input",
+            title: "Input Dataset Collection",
+            description: "Input for a collection of datasets",
+            icon: faFolder,
+        },
+        {
+            moduleId: "parameter_input",
+            title: "Text Input",
+            description: "Text parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "text",
+            },
+        },
+        {
+            id: "parameter_input_integer",
+            moduleId: "parameter_input",
+            title: "Integer Input",
+            description: "Whole number parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "integer",
+            },
+        },
+        {
+            id: "parameter_input_float",
+            moduleId: "parameter_input",
+            title: "Float Input",
+            description: "Imprecise decimal number parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "float",
+            },
+        },
+        {
+            id: "parameter_input_boolean",
+            moduleId: "parameter_input",
+            title: "Boolean Input",
+            description: "True / False parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "boolean",
+            },
+        },
+        {
+            id: "parameter_input_color",
+            moduleId: "parameter_input",
+            title: "Color Input",
+            description: "Color parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "color",
+            },
+        },
+        {
+            id: "parameter_input_directory_uri",
+            moduleId: "parameter_input",
+            title: "Directory Input",
+            description: "Directory parameter used for workflow logic",
+            icon: faPencilAlt,
+            stateOverwrites: {
+                parameter_type: "directory_uri",
+            },
+        },
+    ];
+}
diff --git a/client/src/components/Workflow/Editor/modules/layout.ts b/client/src/components/Workflow/Editor/modules/layout.ts
index 3a4882e6a53bd2598eedaed3317bc287d1fce66d..843867c7def12e6bf14d7c8530f106c85d0eaf85 100644
--- a/client/src/components/Workflow/Editor/modules/layout.ts
+++ b/client/src/components/Workflow/Editor/modules/layout.ts
@@ -1,88 +1,122 @@
-import ELK from "elkjs/lib/elk.bundled.js";
+import ELK, { type ElkExtendedEdge, type ElkNode } from "elkjs/lib/elk.bundled";
 
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import type { FreehandWorkflowComment, WorkflowComment } from "@/stores/workflowEditorCommentStore";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
-import type { Step } from "@/stores/workflowStepStore";
+import { type Step } from "@/stores/workflowStepStore";
 import { assertDefined } from "@/utils/assertions";
+import { match } from "@/utils/utils";
+
+import { AxisAlignedBoundingBox, type Rectangle, rectDistance } from "./geometry";
 
 const elk = new ELK();
 
-interface GraphChild {
-    id: string;
-    height: number;
-    width: number;
-    ports: {
-        id: string;
-        properties: {
-            "port.side": string;
-            "port.index": number;
-        };
-    }[];
+interface OptionObject {
+    [key: string]: OptionValue | OptionObject;
 }
+type OptionValue = number | string | boolean;
 
-interface GraphEdge {
-    id: string;
-    sources: string[];
-    targets: string[];
+export function elkOptionObject(object: OptionObject): string {
+    const entries = Object.entries(object);
+    const stringifiedEntries = entries.map(([key, value]) => {
+        const type = typeof value as "number" | "string" | "boolean" | "object";
+
+        const valueAsString = match(type, {
+            number: () => `${value}`,
+            string: () => `"${value}"`,
+            boolean: () => `${value}`,
+            object: () => elkOptionObject(value as OptionObject),
+        });
+
+        return `${key}=${valueAsString}`;
+    });
+
+    return `[${stringifiedEntries.join(", ")}]`;
 }
 
-interface NewGraph {
-    id: string;
-    layoutOptions: { [index: string]: string };
-    children: GraphChild[];
-    edges: GraphEdge[];
+export function elkSpacing(left = 0, top = 0, right = 0, bottom = 0) {
+    return elkOptionObject({
+        left,
+        top,
+        right,
+        bottom,
+    });
 }
 
-export async function autoLayout(id: string, steps: { [index: string]: Step }) {
+export async function autoLayout(id: string, steps: { [index: string]: Step }, comments: WorkflowComment[]) {
     const connectionStore = useConnectionStore(id);
     const stateStore = useWorkflowStateStore(id);
 
+    // making this follow the user set snapping distance get's messy fast, so it's hardcoded for simplicity
+    const snappingDistance = 10;
+    const horizontalDistance = Math.max(snappingDistance * 2, 100);
+    const verticalDistance = Math.max(snappingDistance, 50);
+
+    const roundUpToSnappingDistance = (value: number) => {
+        const floatErrorTolerance = 0.0001;
+        return Math.ceil(value / snappingDistance - floatErrorTolerance) * snappingDistance;
+    };
+
+    const childLayoutOptions = {
+        "elk.layered.spacing.nodeNodeBetweenLayers": `${horizontalDistance / 2}`,
+        "elk.portConstraints": "FIXED_POS",
+    };
+
     // Convert this to ELK compat.
-    const newGraph: NewGraph = {
+    const newGraph: ElkNode = {
         id: "",
         layoutOptions: {
+            "elk.padding": elkSpacing(0, 0),
+            "elk.hierarchyHandling": "INCLUDE_CHILDREN",
+            "elk.layered.spacing.baseValue": `${horizontalDistance}`,
             "elk.algorithm": "layered",
-            "crossingMinimization.semiInteractive": "true",
-            "nodePlacement.strategy": "NETWORK_SIMPLEX",
+            "elk.layered.nodePlacement.strategy": "NETWORK_SIMPLEX",
+            "elk.spacing.nodeNode": `${verticalDistance}`,
         },
         children: [],
         edges: [],
     };
 
-    newGraph.children = Object.entries(steps).map(([stepId, step]) => {
-        const inputs = Object.values(step.inputs).map((input) => {
-            return {
-                id: `${stepId}/in/${input.name}`,
-                properties: {
-                    "port.side": "WEST",
-                    "port.index": step.id,
-                },
-            };
-        });
+    const freehandComments: FreehandWorkflowComment[] = [];
+    const otherComments: WorkflowComment[] = [];
 
-        const outputs = Object.values(step.outputs).map((output) => {
-            return {
-                id: `${stepId}/out/${output.name}`,
-                properties: {
-                    "port.side": "EAST",
-                    "port.index": step.id,
-                },
-            };
-        });
+    comments.forEach((comment) => {
+        if (comment.type === "freehand") {
+            freehandComments.push(comment);
+        } else {
+            otherComments.push(comment);
+        }
+    });
 
+    const stepsWithRect = Object.entries(steps).map(([stepId, step]) => {
         const position = stateStore.stepPosition[step.id];
         assertDefined(position, `No StepPosition with step id ${step.id} found in workflowStateStore`);
 
         return {
             id: stepId,
-            height: position.height + 20,
-            width: position.width + 60,
-            ports: inputs.concat(outputs),
+            step,
+            rect: {
+                x: step.position?.left ?? 0,
+                y: step.position?.top ?? 0,
+                width: position.width,
+                height: position.height,
+            },
         };
     });
 
-    newGraph.edges = connectionStore.connections.map((connection) => {
-        const edge: GraphEdge = {
+    const collapsedFreehandComments = collapseFreehandComments(freehandComments);
+    populateClosestSteps(collapsedFreehandComments, stepsWithRect);
+
+    newGraph.children = graphToElkGraph(
+        steps,
+        otherComments,
+        stateStore,
+        roundUpToSnappingDistance,
+        childLayoutOptions
+    );
+
+    const dataEdges = connectionStore.connections.map((connection) => {
+        const edge: ElkExtendedEdge = {
             id: `e_${connection.input.stepId}_${connection.output.stepId}`,
             sources: [`${connection.output.stepId}/out/${connection.output.name}`],
             targets: [`${connection.input.stepId}/in/${connection.input.name}`],
@@ -90,15 +124,371 @@ export async function autoLayout(id: string, steps: { [index: string]: Step }) {
         return edge;
     });
 
+    const commentEdges = getCommentEdges(otherComments, stepsWithRect);
+
+    newGraph.edges = [...dataEdges, ...commentEdges];
+
+    const roundToSnappingDistance = (value: number) => Math.round(value / snappingDistance) * snappingDistance;
+
     try {
         const elkNode = await elk.layout(newGraph);
-        // Reapply positions to galaxy graph from our relayed out graph.
-        const newSteps = elkNode.children?.map((q) => {
-            const newStep = { ...steps[q.id], position: { top: q.y, left: q.x } };
-            return newStep;
-        });
-        return newSteps;
+        const positions = graphToPositions(elkNode.children, roundToSnappingDistance);
+
+        const freehandPositions = resolveDeltaPositions(collapsedFreehandComments, positions.steps);
+        positions.comments = positions.comments.concat(freehandPositions);
+
+        return positions;
     } catch (error) {
         console.error(error);
     }
 }
+
+interface HierarchicalComment {
+    comment: WorkflowComment;
+    root: boolean;
+    children: (HierarchicalComment | Step)[];
+}
+
+function graphToElkGraph(
+    steps: Record<number, Step>,
+    comments: WorkflowComment[],
+    stateStore: ReturnType<typeof useWorkflowStateStore>,
+    roundingFunction: (value: number) => number,
+    layoutOptions: Record<string, string>
+): ElkNode[] {
+    const flatHierarchicalComments: Map<number, HierarchicalComment> = new Map(
+        comments.map((comment) => [comment.id, { comment, root: true, children: [] }])
+    );
+
+    const rootSteps = new Map(Object.entries(steps));
+
+    flatHierarchicalComments.forEach((c) => {
+        if (c.comment.child_comments) {
+            c.comment.child_comments.forEach((id) => {
+                const childComment = flatHierarchicalComments.get(id);
+
+                if (childComment) {
+                    childComment.root = false;
+                    c.children.push(childComment);
+                }
+            });
+        }
+
+        if (c.comment.child_steps) {
+            c.comment.child_steps.forEach((id) => {
+                const idAsString = `${id}`;
+                const childStep = rootSteps.get(idAsString)!;
+                rootSteps.delete(idAsString);
+                c.children.push(childStep);
+            });
+        }
+    });
+
+    const rootHierarchicalComments: HierarchicalComment[] = [...flatHierarchicalComments.values()].filter(
+        (c) => c.root
+    );
+
+    const elkRootSteps = [...rootSteps.values()].map((step) => {
+        return stepToElkStep(step, stateStore, roundingFunction);
+    });
+
+    const elkRootComments = rootHierarchicalComments.map((c) =>
+        commentToElkStep(c, stateStore, roundingFunction, layoutOptions)
+    );
+
+    return [...elkRootSteps, ...elkRootComments];
+}
+
+function stepToElkStep(
+    step: Step,
+    stateStore: ReturnType<typeof useWorkflowStateStore>,
+    roundingFunction: (value: number) => number
+): ElkNode {
+    const inputs = Object.values(step.inputs).map((input, index) => {
+        return {
+            id: `${step.id}/in/${input.name}`,
+            properties: {
+                "port.side": "WEST",
+                "port.index": `${index}`,
+            },
+            x: 0,
+            y: index * 20,
+        };
+    });
+
+    const position = stateStore.stepPosition[step.id];
+    assertDefined(position, `No StepPosition with step id ${step.id} found in workflowStateStore`);
+
+    const outputs = Object.values(step.outputs).map((output, index) => {
+        return {
+            id: `${step.id}/out/${output.name}`,
+            properties: {
+                "port.side": "EAST",
+                "port.index": `${index}`,
+            },
+            x: position.width,
+            y: index * 20,
+        };
+    });
+
+    return {
+        id: `${step.id}`,
+        height: roundingFunction(position.height),
+        width: roundingFunction(position.width),
+        x: step.position?.left,
+        y: step.position?.top,
+        layoutOptions: {
+            "elk.portConstraints": "FIXED_POS",
+        },
+        ports: inputs.concat(outputs),
+    };
+}
+
+function commentToElkStep(
+    hierarchicalComment: HierarchicalComment,
+    stateStore: ReturnType<typeof useWorkflowStateStore>,
+    roundingFunction: (value: number) => number,
+    layoutOptions: Record<string, string>
+): ElkNode {
+    const base: ElkNode = {
+        id: `comment_${hierarchicalComment.comment.id}`,
+        x: hierarchicalComment.comment.position[0],
+        y: hierarchicalComment.comment.position[1],
+        width: hierarchicalComment.comment.size[0],
+        height: hierarchicalComment.comment.size[1],
+        layoutOptions: {
+            "elk.commentBox": hierarchicalComment.comment.type === "frame" ? "false" : "true",
+            ...layoutOptions,
+            "elk.padding": elkSpacing(20, 40, 20, 20),
+        },
+    };
+
+    const children: ElkNode[] = hierarchicalComment.children?.map((c) => {
+        if ("comment" in c) {
+            return commentToElkStep(c, stateStore, roundingFunction, layoutOptions);
+        } else {
+            return stepToElkStep(c, stateStore, roundingFunction);
+        }
+    });
+
+    return { ...base, children };
+}
+
+interface Positions {
+    steps: { id: string; x: number; y: number }[];
+    comments: { id: string; x: number; y: number; w: number; h: number }[];
+}
+
+function graphToPositions(
+    graph: ElkNode[] | undefined,
+    roundingFunction: (value: number) => number,
+    parentPosition?: { x: number; y: number }
+): Positions {
+    const positions: Positions = {
+        steps: [],
+        comments: [],
+    };
+
+    if (!graph) {
+        return positions;
+    }
+
+    const offset = parentPosition ?? { x: 0, y: 0 };
+
+    graph.forEach((node) => {
+        if (!node.id.startsWith("comment_")) {
+            positions.steps.push({
+                id: node.id,
+                x: roundingFunction(node.x ?? 0) + offset.x,
+                y: roundingFunction(node.y ?? 0) + offset.y,
+            });
+        } else {
+            const id = node.id.slice("comment_".length);
+
+            const position = {
+                x: roundingFunction(node.x ?? 0) + offset.x,
+                y: roundingFunction(node.y ?? 0) + offset.y,
+            };
+
+            positions.comments.push({
+                id,
+                ...position,
+                w: node.width ?? 0,
+                h: node.height ?? 0,
+            });
+
+            if (node.children) {
+                const childPositions = graphToPositions(node.children, roundingFunction, position);
+
+                positions.steps = positions.steps.concat(childPositions.steps);
+                positions.comments = positions.comments.concat(childPositions.comments);
+            }
+        }
+    });
+
+    return positions;
+}
+
+function getCommentEdges(comments: WorkflowComment[], stepsWithRect: StepWithRect[]): ElkExtendedEdge[] {
+    const edges: ElkExtendedEdge[] = [];
+
+    comments.forEach((comment) => {
+        if (comment.type === "freehand") {
+            return;
+        }
+
+        let closestDistance = Infinity;
+        let closestId: string | null = null;
+
+        const commentRect = {
+            x: comment.position[0],
+            y: comment.position[1],
+            width: comment.size[0],
+            height: comment.size[1],
+        };
+
+        stepsWithRect.forEach((step) => {
+            const distance = rectDistance(step.rect, commentRect);
+            if (distance < closestDistance) {
+                closestDistance = distance;
+                closestId = step.id;
+            }
+        });
+
+        if (closestId) {
+            const edge: ElkExtendedEdge = {
+                id: `comment_edge_${closestId}_${comment.id}`,
+                sources: [closestId],
+                targets: [`comment_${comment.id}`],
+            };
+
+            edges.push(edge);
+        }
+    });
+
+    return edges;
+}
+
+interface CollapsedFreehandComment {
+    aabb: AxisAlignedBoundingBox;
+    comments: FreehandWorkflowComment[];
+    closestStepId?: string;
+    positionFrom?: { x: number; y: number };
+}
+
+/** groups freehand comments into distinct sets with any amount of overlap */
+function collapseFreehandComments(comments: FreehandWorkflowComment[]): CollapsedFreehandComment[] {
+    const commentsAsCollapsed: CollapsedFreehandComment[] = comments.map((c) => {
+        const aabb = new AxisAlignedBoundingBox();
+        aabb.fitRectangle({
+            x: c.position[0],
+            y: c.position[1],
+            width: c.size[0],
+            height: c.size[1],
+        });
+
+        return {
+            aabb,
+            comments: [c],
+        };
+    });
+
+    const collapsedFreehandComments: Set<CollapsedFreehandComment> = new Set(commentsAsCollapsed);
+
+    const compareAgainstOtherCollapsed = (a: CollapsedFreehandComment) => {
+        const iterator = collapsedFreehandComments.values();
+
+        for (const other of iterator) {
+            if (a !== other && a.aabb.intersects(other.aabb)) {
+                mergeCollapsedComments(a, other);
+                break;
+            }
+        }
+    };
+
+    const mergeCollapsedComments = (a: CollapsedFreehandComment, b: CollapsedFreehandComment) => {
+        const aabb = new AxisAlignedBoundingBox();
+        aabb.fitRectangle(a.aabb);
+        aabb.fitRectangle(b.aabb);
+
+        collapsedFreehandComments.delete(a);
+        collapsedFreehandComments.delete(b);
+
+        const merged = {
+            aabb: aabb,
+            comments: [...a.comments, ...b.comments],
+        };
+
+        collapsedFreehandComments.add(merged);
+        compareAgainstOtherCollapsed(merged);
+    };
+
+    const iterator = collapsedFreehandComments.values();
+
+    for (const comment of iterator) {
+        compareAgainstOtherCollapsed(comment);
+    }
+
+    return [...collapsedFreehandComments.values()];
+}
+
+interface StepWithRect {
+    id: string;
+    step: Step;
+    rect: Rectangle;
+}
+
+/** find out which step is the closest to each comment, save it's id and position */
+function populateClosestSteps(collapsedFreehandComments: CollapsedFreehandComment[], stepsWithRect: StepWithRect[]) {
+    collapsedFreehandComments.forEach((comment) => {
+        let closestDistance = Infinity;
+
+        stepsWithRect.forEach((s) => {
+            const distance = rectDistance(comment.aabb, s.rect);
+            if (distance < closestDistance) {
+                closestDistance = distance;
+                comment.closestStepId = s.id;
+                comment.positionFrom = {
+                    x: s.rect.x,
+                    y: s.rect.y,
+                };
+            }
+        });
+    });
+}
+
+/** resolve by how much to move the freehand comments */
+function resolveDeltaPositions(
+    collapsedFreehandComments: CollapsedFreehandComment[],
+    stepPositions: Positions["steps"]
+): Positions["comments"] {
+    const positions: Positions["comments"] = [];
+    const stepPositionMap = new Map(stepPositions.map((p) => [p.id, p]));
+
+    collapsedFreehandComments.forEach((collapsed) => {
+        if (!collapsed.closestStepId) {
+            return;
+        }
+
+        const newPosition = stepPositionMap.get(collapsed.closestStepId);
+
+        if (newPosition) {
+            const delta = {
+                x: newPosition.x - (collapsed.positionFrom?.x ?? 0),
+                y: newPosition.y - (collapsed.positionFrom?.y ?? 0),
+            };
+
+            collapsed.comments.forEach((comment) => {
+                positions.push({
+                    id: `${comment.id}`,
+                    x: comment.position[0] + delta.x,
+                    y: comment.position[1] + delta.y,
+                    w: comment.size[0],
+                    h: comment.size[1],
+                });
+            });
+        }
+    });
+
+    return positions;
+}
diff --git a/client/src/components/Workflow/Editor/modules/linting.ts b/client/src/components/Workflow/Editor/modules/linting.ts
index b451229305c2db7d830b6561070f9b6018801852..75a7c142ab430f0591b5096e025c1020d07121de 100644
--- a/client/src/components/Workflow/Editor/modules/linting.ts
+++ b/client/src/components/Workflow/Editor/modules/linting.ts
@@ -1,7 +1,7 @@
-import type { DatatypesMapperModel } from "@/components/Datatypes/model";
-import type { UntypedParameters } from "@/components/Workflow/Editor/modules/parameters";
-import type { useWorkflowStores } from "@/composables/workflowStores";
-import type { Step, Steps } from "@/stores/workflowStepStore";
+import { type DatatypesMapperModel } from "@/components/Datatypes/model";
+import { type UntypedParameters } from "@/components/Workflow/Editor/modules/parameters";
+import { type useWorkflowStores } from "@/composables/workflowStores";
+import { type Step, type Steps } from "@/stores/workflowStepStore";
 import { assertDefined } from "@/utils/assertions";
 
 import { terminalFactory } from "./terminals";
@@ -15,6 +15,13 @@ interface LintState {
     autofix?: boolean;
 }
 
+export const bestPracticeWarningAnnotation =
+    "This workflow is not annotated. Providing an annotation helps workflow executors understand the purpose and usage of the workflow.";
+export const bestPracticeWarningCreator =
+    "This workflow does not specify creator(s). This is important metadata for workflows that will be published and/or shared to help workflow executors know how to cite the workflow authors.";
+export const bestPracticeWarningLicense =
+    "This workflow does not specify a license. This is important metadata for workflows that will be published and/or shared to help workflow executors understand how it may be used.";
+
 export function getDisconnectedInputs(
     steps: Steps = {},
     datatypesMapper: DatatypesMapperModel,
diff --git a/client/src/components/Workflow/Editor/modules/model.ts b/client/src/components/Workflow/Editor/modules/model.ts
index f4ad5da41dbac3cbc011aab03b44ca5c76c8a32b..0ea90f078a03103de3796bc833e75ae8aca901ee 100644
--- a/client/src/components/Workflow/Editor/modules/model.ts
+++ b/client/src/components/Workflow/Editor/modules/model.ts
@@ -2,7 +2,12 @@ import reportDefault from "@/components/Workflow/Editor/reportDefault";
 import { useWorkflowCommentStore, type WorkflowComment } from "@/stores/workflowEditorCommentStore";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import { useWorkflowEditorToolbarStore } from "@/stores/workflowEditorToolbarStore";
-import { type ConnectionOutputLink, type Steps, useWorkflowStepStore } from "@/stores/workflowStepStore";
+import {
+    type ConnectionOutputLink,
+    type StepInputConnection,
+    type Steps,
+    useWorkflowStepStore,
+} from "@/stores/workflowStepStore";
 
 export interface Workflow {
     name: string;
@@ -49,18 +54,32 @@ export async function fromSimple(
     // Galaxy assign new ones.
     if (options?.reassignIds ?? appendData) {
         const stepIdOffset = stepStore.getStepIndex + 1;
+        const stepArray = Object.values(data.steps);
 
-        Object.values(data.steps).forEach((step) => {
+        // Since we are resigning IDs based on index, ensure correct ordering
+        stepArray.sort((a, b) => a.id - b.id);
+
+        const stepIdMapOldToNew = new Map<number, number>();
+
+        stepArray.forEach((step, index) => {
+            const oldId = step.id;
+            step.id = index + stepIdOffset;
+            stepIdMapOldToNew.set(oldId, step.id);
+        });
+
+        stepArray.forEach((step) => {
             delete step.uuid;
             if (!step.position) {
                 // Should only happen for manually authored editor content,
                 // good enough for a first pass IMO.
                 step.position = { top: step.id * 100, left: step.id * 100 };
             }
-            step.id += stepIdOffset;
             step.position.left += defaultPosition.left;
             step.position.top += defaultPosition.top;
-            Object.values(step.input_connections).forEach((link) => {
+
+            const newInputConnections: StepInputConnection = {};
+
+            Object.entries(step.input_connections).forEach(([key, link]) => {
                 if (link === undefined) {
                     console.error("input connections invalid", step.input_connections);
                 } else {
@@ -70,11 +89,25 @@ export async function fromSimple(
                     } else {
                         linkArray = link;
                     }
-                    linkArray.forEach((link) => {
-                        link.id += stepIdOffset;
+
+                    const remappedLinkArray = linkArray.map((link) => {
+                        const newId = stepIdMapOldToNew.get(link.id);
+
+                        return {
+                            ...link,
+                            id: newId,
+                        };
                     });
+
+                    // id may be undefined, if the partial Workflow does not contain the step
+                    // in that case, remove the link
+                    const newLinkArray = remappedLinkArray.filter((link) => link.id) as ConnectionOutputLink[];
+
+                    newInputConnections[key] = newLinkArray;
                 }
             });
+
+            step.input_connections = newInputConnections;
         });
 
         data.comments.forEach((comment, index) => {
diff --git a/client/src/components/Workflow/Editor/modules/parameters.ts b/client/src/components/Workflow/Editor/modules/parameters.ts
index 40637c5805bbd5a60d9ee5649edb7728e5c25118..3bc624c38780224550b1d13e9648f5d762ca6367 100644
--- a/client/src/components/Workflow/Editor/modules/parameters.ts
+++ b/client/src/components/Workflow/Editor/modules/parameters.ts
@@ -1,4 +1,4 @@
-import type { PostJobAction, Step, Steps } from "@/stores/workflowStepStore";
+import { type PostJobAction, type Step, type Steps } from "@/stores/workflowStepStore";
 import Utils from "@/utils/utils";
 
 class UntypedParameterReference {
diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 844c9114bb1482a141c20c2b42d3ae2f43055c21..b90fb55cc1191efc951c21c00d06690bad9c19d0 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -6,7 +6,13 @@ import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { useWorkflowCommentStore } from "@/stores/workflowEditorCommentStore";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import { useWorkflowEditorToolbarStore } from "@/stores/workflowEditorToolbarStore";
-import { DataOutput, Step, Steps, type TerminalSource, useWorkflowStepStore } from "@/stores/workflowStepStore";
+import {
+    type DataOutput,
+    type Step,
+    type Steps,
+    type TerminalSource,
+    useWorkflowStepStore,
+} from "@/stores/workflowStepStore";
 
 import { advancedSteps, simpleSteps } from "../test_fixtures";
 import {
@@ -35,6 +41,7 @@ function useStores(id = "mock-workflow") {
     const undoRedoStore = useUndoRedoStore(id);
 
     return {
+        workflowId: id,
         connectionStore,
         stateStore,
         stepStore,
@@ -298,6 +305,16 @@ describe("canAccept", () => {
             "Cannot attach a text parameter to a integer input"
         );
     });
+    it("rejects optional integer to required parameter connection", () => {
+        const integerInputParam = terminals["multi data"]!["advanced|advanced_threshold"] as InputParameterTerminal;
+        const optionalIntegerOutputParam = terminals["optional integer parameter input"]![
+            "output"
+        ] as OutputParameterTerminal;
+        expect(integerInputParam.canAccept(optionalIntegerOutputParam).canAccept).toBe(false);
+        expect(integerInputParam.canAccept(optionalIntegerOutputParam).reason).toBe(
+            "Cannot attach an optional output to a required parameter"
+        );
+    });
     it("rejects data to parameter connection", () => {
         const dataOut = terminals["data input"]!["output"] as OutputTerminal;
         const integerInputParam = terminals["multi data"]!["advanced|advanced_threshold"] as InputParameterTerminal;
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 7ed030b537e2c2cac7ce6358eebf7d617fb0c3c2..49effcb402fefbac75c807440b0b5833b40309a8 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -1,16 +1,16 @@
 import EventEmitter from "events";
 
-import type { DatatypesMapperModel } from "@/components/Datatypes/model";
-import type { useWorkflowStores } from "@/composables/workflowStores";
+import { type DatatypesMapperModel } from "@/components/Datatypes/model";
+import { type useWorkflowStores } from "@/composables/workflowStores";
 import { type Connection, type ConnectionId, getConnectionId } from "@/stores/workflowConnectionStore";
-import type {
-    CollectionOutput,
-    DataCollectionStepInput,
-    DataOutput,
-    DataStepInput,
-    ParameterOutput,
-    ParameterStepInput,
-    TerminalSource,
+import {
+    type CollectionOutput,
+    type DataCollectionStepInput,
+    type DataOutput,
+    type DataStepInput,
+    type ParameterOutput,
+    type ParameterStepInput,
+    type TerminalSource,
 } from "@/stores/workflowStepStore";
 import { assertDefined } from "@/utils/assertions";
 
@@ -534,13 +534,33 @@ export class InputParameterTerminal extends BaseInputTerminal {
     }
 
     effectiveType(parameterType: string) {
-        return parameterType == "select" ? "text" : parameterType;
+        let newType: string;
+        switch (parameterType) {
+            case "select":
+                newType = "text";
+                break;
+            case "data_column":
+                newType = "integer";
+                break;
+            default:
+                newType = parameterType;
+        }
+        return newType;
     }
     attachable(other: BaseOutputTerminal) {
         const effectiveThisType = this.effectiveType(this.type);
         const otherType = ("type" in other && other.type) || "data";
         const effectiveOtherType = this.effectiveType(otherType);
+        if (!this.optional && other.optional) {
+            return new ConnectionAcceptable(false, `Cannot attach an optional output to a required parameter`);
+        }
         const canAccept = effectiveThisType === effectiveOtherType;
+        if (!this.multiple && other.multiple) {
+            return new ConnectionAcceptable(
+                false,
+                `This output parameter represents multiple values but input only accepts a single value`
+            );
+        }
         return new ConnectionAcceptable(
             canAccept,
             canAccept ? null : `Cannot attach a ${effectiveOtherType} parameter to a ${effectiveThisType} input`
@@ -801,12 +821,14 @@ export class OutputCollectionTerminal extends BaseOutputTerminal {
 
 interface OutputParameterTerminalArgs extends Omit<BaseOutputTerminalArgs, "datatypes"> {
     type: ParameterOutput["type"];
+    multiple: ParameterOutput["multiple"];
 }
 
 export class OutputParameterTerminal extends BaseOutputTerminal {
     constructor(attr: OutputParameterTerminalArgs) {
         super({ ...attr, datatypes: [] });
         this.type = attr.type;
+        this.multiple = attr.multiple;
     }
 }
 
@@ -977,6 +999,7 @@ export function terminalFactory<T extends TerminalSourceAndInvalid>(
         if (isOutputParameterArg(terminalSource)) {
             return new OutputParameterTerminal({
                 ...outputArgs,
+                multiple: terminalSource.multiple,
                 type: terminalSource.type,
             }) as TerminalOf<T>;
         } else if (isOutputCollectionArg(terminalSource)) {
diff --git a/client/src/components/Workflow/Editor/modules/zoomLevels.ts b/client/src/components/Workflow/Editor/modules/zoomLevels.ts
index 234c2456ee1b7846b426d666f2c6b3b2590e4f6b..ee151bb5f8eaa89e9d2050629300858b36988f16 100644
--- a/client/src/components/Workflow/Editor/modules/zoomLevels.ts
+++ b/client/src/components/Workflow/Editor/modules/zoomLevels.ts
@@ -1,4 +1,4 @@
-import type { Last } from "types/utilityTypes";
+import { type Last } from "types/utilityTypes";
 
 export const zoomLevels = [
     0.1, 0.2, 0.25, 0.33, 0.5, 0.67, 0.75, 0.8, 0.9, 1, 1.1, 1.25, 1.33, 1.5, 2, 2.5, 3, 4, 5,
diff --git a/client/src/components/Workflow/Editor/test-data/parameter_steps.json b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
index d3cff2cf8d981d7d08290340a25fa1fdba85bd9b..ef4db3bb7564272b3e6cb5006e04647be89edf07 100644
--- a/client/src/components/Workflow/Editor/test-data/parameter_steps.json
+++ b/client/src/components/Workflow/Editor/test-data/parameter_steps.json
@@ -19,7 +19,8 @@
         "extensions": [
           "input"
         ],
-        "optional": false
+        "optional": false,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -199,7 +200,7 @@
     "content_id": null,
     "name": "Input parameter",
     "tool_state": {
-      "parameter_definition": "{\"__current_case__\": 1, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"integer\"}",
+      "parameter_definition": "{\"__current_case__\": 1, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"integer\", \"multiple\": \"false\",}",
       "__page__": null,
       "__rerun_remap_job_id__": null
     },
@@ -211,7 +212,8 @@
         "label": "integer parameter input",
         "type": "integer",
         "optional": false,
-        "parameter": true
+        "parameter": true,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -427,7 +429,7 @@
     "content_id": null,
     "name": "Input parameter",
     "tool_state": {
-      "parameter_definition": "{\"__current_case__\": 0, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"text\", \"restrictions\": {\"__current_case__\": 0, \"how\": \"none\"}}",
+      "parameter_definition": "{\"__current_case__\": 0, \"optional\": {\"__current_case__\": 1, \"optional\": \"false\"}, \"parameter_type\": \"text\", \"multiple\": \"false\", \"restrictions\": {\"__current_case__\": 0, \"how\": \"none\"}}",
       "__page__": null,
       "__rerun_remap_job_id__": null
     },
@@ -439,7 +441,8 @@
         "label": "text parameter input",
         "type": "text",
         "optional": false,
-        "parameter": true
+        "parameter": true,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -746,7 +749,8 @@
           "txt"
         ],
         "type": "data",
-        "optional": false
+        "optional": false,
+        "multiple": false
       },
       {
         "name": "out2",
@@ -754,7 +758,8 @@
           "txt"
         ],
         "type": "data",
-        "optional": false
+        "optional": false,
+        "multiple": false
       }
     ],
     "annotation": "",
@@ -906,5 +911,71 @@
       "left": 12.8729248046875,
       "top": 501.7839660644531
     }
+  },
+  "19": {
+    "id": 19,
+    "type": "parameter_input",
+    "label": "optional text parameter input",
+    "content_id": null,
+    "name": "Input parameter",
+    "tool_state": {
+      "parameter_definition": "{\"__current_case__\": 0, \"optional\": {\"__current_case__\": 1, \"optional\": \"true\"}, \"parameter_type\": \"text\", \"restrictions\": {\"__current_case__\": 0, \"how\": \"none\"}}",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [],
+    "outputs": [
+      {
+        "name": "output",
+        "label": "optional text parameter input",
+        "type": "text",
+        "optional": true,
+        "parameter": true,
+        "multiple": false
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "uuid": "71c030ff-a29f-4e32-a735-37471e7a3f12",
+    "workflow_outputs": [],
+    "input_connections": {},
+    "position": {
+      "left": 95.0506591796875,
+      "top": 867.0427551269531
+    }
+  },
+  "20": {
+    "id": 20,
+    "type": "parameter_input",
+    "label": "optional integer parameter input",
+    "content_id": null,
+    "name": "Input parameter",
+    "tool_state": {
+      "parameter_definition": "{\"__current_case__\": 1, \"optional\": {\"__current_case__\": 1, \"optional\": \"true\"}, \"parameter_type\": \"integer\"}",
+      "__page__": null,
+      "__rerun_remap_job_id__": null
+    },
+    "errors": null,
+    "inputs": [],
+    "outputs": [
+      {
+        "name": "output",
+        "label": "integer parameter input",
+        "type": "integer",
+        "optional": true,
+        "parameter": true,
+        "multiple": false
+      }
+    ],
+    "annotation": "",
+    "post_job_actions": {},
+    "uuid": "634f06f1-b279-4160-9390-a004018e92ce",
+    "workflow_outputs": [],
+    "input_connections": {},
+    "position": {
+      "left": 148.72970581054688,
+      "top": 620.5069274902344
+    }
   }
 }
diff --git a/client/src/components/Workflow/Editor/test_fixtures.ts b/client/src/components/Workflow/Editor/test_fixtures.ts
index 7ac450e0dcc6203fb361865b1c8b86c489c57afe..c7ebe57a7f9c7846db846eb7a9d7970696b42998 100644
--- a/client/src/components/Workflow/Editor/test_fixtures.ts
+++ b/client/src/components/Workflow/Editor/test_fixtures.ts
@@ -1,7 +1,7 @@
-import type { UseElementBoundingReturn } from "@vueuse/core";
+import { type UseElementBoundingReturn } from "@vueuse/core";
 import { reactive, toRefs } from "vue";
 
-import type { Steps } from "@/stores/workflowStepStore";
+import { type Steps } from "@/stores/workflowStepStore";
 
 import * as _advancedSteps from "./test-data/parameter_steps.json";
 import * as _simpleSteps from "./test-data/simple_steps.json";
diff --git a/client/src/components/Workflow/Invocation/Export/ActionButton.vue b/client/src/components/Workflow/Invocation/Export/ActionButton.vue
index b622320680b9f9eac46297ddbbab998c338338ca..807063eaf0a3d787f40e3711eabe432da67ef0b1 100644
--- a/client/src/components/Workflow/Invocation/Export/ActionButton.vue
+++ b/client/src/components/Workflow/Invocation/Export/ActionButton.vue
@@ -1,14 +1,16 @@
-<script setup>
+<script setup lang="ts">
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { ref } from "vue";
 
-import { InvocationExportPluginAction } from "./model";
+import { type InvocationExportPluginAction } from "@/components/Workflow/Invocation/Export/Plugins";
 
-const modal = ref(null);
+const modal = ref();
 
-const props = defineProps({
-    action: { type: InvocationExportPluginAction, required: true },
-});
+interface Props {
+    action: InvocationExportPluginAction;
+}
+
+const props = defineProps<Props>();
 </script>
 
 <template>
diff --git a/client/src/components/Workflow/Invocation/Export/ExistingInvocationExportProgressCard.vue b/client/src/components/Workflow/Invocation/Export/ExistingInvocationExportProgressCard.vue
new file mode 100644
index 0000000000000000000000000000000000000000..0208010ac7ecc707b80aeeae981f9ecb94ef5832
--- /dev/null
+++ b/client/src/components/Workflow/Invocation/Export/ExistingInvocationExportProgressCard.vue
@@ -0,0 +1,105 @@
+<script setup lang="ts">
+import { BCard } from "bootstrap-vue";
+import { computed, ref } from "vue";
+
+import type { TaskMonitor } from "@/composables/genericTaskMonitor";
+import { getStoredProgressData, type MonitoringRequest } from "@/composables/persistentProgressMonitor";
+
+import PersistentTaskProgressMonitorAlert from "@/components/Common/PersistentTaskProgressMonitorAlert.vue";
+
+const monitoringSource = "wizard";
+
+interface Props {
+    invocationId: string;
+    useStsMonitor: TaskMonitor;
+    useRemoteMonitor: TaskMonitor;
+    exportToRemoteTaskId?: string;
+    exportToRemoteTargetUri?: string;
+    exportToStsRequestId?: string;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "onDismissSts"): void;
+    (e: "onDismissRemote"): void;
+}>();
+
+const hasExistingStsExportData = ref(false);
+const hasExistingRemoteExportData = ref(false);
+
+const exportToStsRequest = computed<MonitoringRequest>(() => ({
+    source: monitoringSource,
+    action: "export",
+    taskType: "short_term_storage",
+    object: {
+        id: props.invocationId,
+        type: "invocation",
+    },
+    description: `Exporting invocation ${props.invocationId} to Short Term Storage in preparation for download`,
+}));
+
+const exportToRemoteRequest = computed<MonitoringRequest>(() => ({
+    source: monitoringSource,
+    action: "export",
+    taskType: "task",
+    object: {
+        id: props.invocationId,
+        type: "invocation",
+    },
+    description: `Exporting invocation ${props.invocationId} to remote source`,
+    remoteUri: props.exportToRemoteTargetUri,
+}));
+
+function updateExistingExportProgress() {
+    const existingStsExportData = getStoredProgressData(exportToStsRequest.value);
+    hasExistingStsExportData.value = existingStsExportData !== null;
+
+    const existingRemoteExportData = getStoredProgressData(exportToRemoteRequest.value);
+    hasExistingRemoteExportData.value = existingRemoteExportData !== null;
+}
+
+function dismissStsExport() {
+    emit("onDismissSts");
+    hasExistingStsExportData.value = false;
+}
+
+function dismissRemoteExport() {
+    emit("onDismissRemote");
+    hasExistingRemoteExportData.value = false;
+}
+
+updateExistingExportProgress();
+
+defineExpose({
+    updateExistingExportProgress,
+});
+</script>
+
+<template>
+    <BCard v-show="hasExistingStsExportData || hasExistingRemoteExportData" class="mb-2">
+        <h2>Here is your latest export request:</h2>
+        <PersistentTaskProgressMonitorAlert
+            class="sts-export-monitor"
+            :monitor-request="exportToStsRequest"
+            :use-monitor="useStsMonitor"
+            :task-id="exportToStsRequestId"
+            :enable-auto-download="true"
+            in-progress-message="Preparing your export package. Please wait..."
+            completed-message="Your export is ready! It will start downloading shortly. If it does not start automatically..."
+            failed-message="Your export has failed."
+            request-failed-message="Failed to check export progress. Try again later."
+            @onDismiss="dismissStsExport" />
+
+        <PersistentTaskProgressMonitorAlert
+            class="task-export-monitor"
+            :monitor-request="exportToRemoteRequest"
+            :use-monitor="useRemoteMonitor"
+            :task-id="exportToRemoteTaskId"
+            in-progress-message="Exporting to remote source. It may take a while..."
+            completed-message="Export to remote source is complete!"
+            failed-message="Export to remote source has failed."
+            request-failed-message="Failed to check export progress. Try again later."
+            @onDismiss="dismissRemoteExport" />
+    </BCard>
+</template>
diff --git a/client/src/components/Workflow/Invocation/Export/ExportButton.vue b/client/src/components/Workflow/Invocation/Export/ExportButton.vue
new file mode 100644
index 0000000000000000000000000000000000000000..fbd5a9ee48dd631b294f12720b86c60dd6ae4dfd
--- /dev/null
+++ b/client/src/components/Workflow/Invocation/Export/ExportButton.vue
@@ -0,0 +1,32 @@
+<script setup lang="ts">
+import { type IconDefinition, library } from "@fortawesome/fontawesome-svg-core";
+import { faSpinner } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton } from "bootstrap-vue";
+import { computed } from "vue";
+
+library.add(faSpinner);
+
+interface Props {
+    title: string;
+    idleIcon: IconDefinition;
+    isBusy?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    isBusy: false,
+});
+
+const disabled = computed(() => props.isBusy);
+
+const emit = defineEmits(["onClick"]);
+</script>
+
+<template>
+    <span v-b-tooltip.hover.bottom :title="title">
+        <BButton :disabled="disabled" @click="() => emit('onClick')">
+            <FontAwesomeIcon v-if="isBusy" :icon="faSpinner" spin />
+            <FontAwesomeIcon v-else :icon="idleIcon" />
+        </BButton>
+    </span>
+</template>
diff --git a/client/src/components/Workflow/Invocation/Export/ExportToRemoteButton.vue b/client/src/components/Workflow/Invocation/Export/ExportToRemoteButton.vue
deleted file mode 100644
index ab91dac822959938d8dd7082eadb6b3f5bdc97ae..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/ExportToRemoteButton.vue
+++ /dev/null
@@ -1,46 +0,0 @@
-<script setup>
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faCheckCircle, faCloudUploadAlt, faExclamationCircle, faSpinner } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
-import { useTaskMonitor } from "composables/taskMonitor";
-import { watch } from "vue";
-
-library.add(faCloudUploadAlt, faSpinner, faCheckCircle, faExclamationCircle);
-
-const { isRunning, isCompleted, hasFailed, requestHasFailed, waitForTask } = useTaskMonitor();
-
-const props = defineProps({
-    title: { type: String, required: true },
-    taskId: { type: String, default: null },
-});
-
-const emit = defineEmits(["onClick", "onSuccess", "onFailure"]);
-
-watch(
-    () => props.taskId,
-    (newTaskId, oldTaskId) => {
-        if (newTaskId !== oldTaskId) {
-            waitForTask(newTaskId);
-        }
-    }
-);
-
-watch([isCompleted, hasFailed, requestHasFailed], ([newIsCompleted, newHasFailed, newRequestHasFailed]) => {
-    if (newIsCompleted) {
-        emit("onSuccess");
-    }
-    if (newHasFailed || newRequestHasFailed) {
-        emit("onFailure");
-    }
-});
-</script>
-
-<template>
-    <BButton v-b-tooltip.hover.bottom :title="props.title" @click="() => emit('onClick')">
-        <FontAwesomeIcon v-if="isRunning" icon="spinner" spin />
-        <FontAwesomeIcon v-else-if="hasFailed || requestHasFailed" icon="exclamation-circle" />
-        <FontAwesomeIcon v-else-if="isCompleted" icon="check-circle" />
-        <FontAwesomeIcon v-else icon="cloud-upload-alt" />
-    </BButton>
-</template>
diff --git a/client/src/components/Workflow/Invocation/Export/ExportToRemoteModal.vue b/client/src/components/Workflow/Invocation/Export/ExportToRemoteModal.vue
index a93a8c1a7baaf879042c4cbef4e950560328f7ea..290be9743b44b9dd636505ced8b27739afb83de3 100644
--- a/client/src/components/Workflow/Invocation/Export/ExportToRemoteModal.vue
+++ b/client/src/components/Workflow/Invocation/Export/ExportToRemoteModal.vue
@@ -1,32 +1,37 @@
-<script setup>
+<script setup lang="ts">
 import { BModal } from "bootstrap-vue";
-import ExportForm from "components/Common/ExportForm";
 import { computed, ref } from "vue";
 
-import { InvocationExportPlugin } from "./model";
+import { type InvocationExportPlugin } from "@/components/Workflow/Invocation/Export/Plugins";
 
-const modal = ref(null);
+import ExportForm from "@/components/Common/ExportForm.vue";
 
-const props = defineProps({
-    exportPlugin: { type: InvocationExportPlugin, required: true },
-    invocationId: { type: String, required: true },
-});
+const modal = ref<BModal>();
 
-const emit = defineEmits(["onExportToFileSource"]);
+interface Props {
+    exportPlugin: InvocationExportPlugin;
+    invocationId: string;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "onExportToFileSource", exportDirectory: string, fileName: string): void;
+}>();
 
 const title = computed(() => `Export ${props.exportPlugin.title} to remote file source`);
 
 /** Opens the modal dialog. */
 function showModal() {
-    modal.value.show();
+    modal.value?.show();
 }
 
 /** Closes the modal dialog. */
 function hideModal() {
-    modal.value.hide();
+    modal.value?.hide();
 }
 
-function doExport(exportDirectory, fileName) {
+function doExport(exportDirectory: string, fileName: string) {
     emit("onExportToFileSource", exportDirectory, fileName);
 }
 
diff --git a/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.test.js b/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.test.js
deleted file mode 100644
index bffb2b9129afa7d373340fcfd469b263c4896d04..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.test.js
+++ /dev/null
@@ -1,85 +0,0 @@
-import { shallowMount } from "@vue/test-utils";
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
-import flushPromises from "flush-promises";
-import { getLocalVue } from "tests/jest/helpers";
-
-import { InvocationExportPlugin, InvocationExportPluginAction } from "./model";
-
-import InvocationExportPluginCard from "./InvocationExportPluginCard.vue";
-
-const localVue = getLocalVue();
-
-const FAKE_INVOCATION_ID = "fake-invocation-id";
-const FAKE_EXPORT_PLUGIN = new InvocationExportPlugin({
-    title: "Plugin Title",
-    markdownDescription: `some **markdown** description`,
-    exportParams: {
-        modelStoreFormat: "tgz",
-        includeFiles: false,
-        includeDeleted: false,
-        includeHidden: false,
-    },
-    additionalActions: [
-        new InvocationExportPluginAction({
-            id: "fake-action-1",
-            title: "Fake export action 1",
-        }),
-        new InvocationExportPluginAction({
-            id: "fake-action-2",
-            title: "Fake export action 2",
-        }),
-    ],
-});
-
-describe("InvocationExportPluginCard", () => {
-    let wrapper;
-    let axiosMock;
-
-    beforeEach(async () => {
-        axiosMock = new MockAdapter(axios);
-        wrapper = shallowMount(InvocationExportPluginCard, {
-            propsData: { exportPlugin: FAKE_EXPORT_PLUGIN, invocationId: FAKE_INVOCATION_ID },
-            localVue,
-        });
-        await flushPromises();
-    });
-
-    afterEach(async () => {
-        axiosMock.reset();
-    });
-
-    it("should display the plugin's title", () => {
-        const title = wrapper.find(".export-plugin-title");
-        expect(title.exists()).toBeTruthy();
-        expect(title.text()).toBe("Plugin Title");
-    });
-
-    it("should render the plugin's description as markdown", () => {
-        const description = wrapper.find(".markdown-description");
-        expect(description.exists()).toBeTruthy();
-        expect(description.html()).toContain("<strong>markdown</strong>");
-    });
-
-    it("should have a direct download button", () => {
-        const downloadButton = wrapper.find(".download-button");
-        expect(downloadButton.exists()).toBeTruthy();
-    });
-
-    it("should have an export to remote file source button", () => {
-        const remoteExportButton = wrapper.find(".remote-export-button");
-        expect(remoteExportButton.exists()).toBeTruthy();
-    });
-
-    it("should generate the expected download URL for the invocation", () => {
-        const downloadButton = wrapper.find(".download-button");
-        expect(downloadButton.attributes("downloadendpoint")).toBe(
-            `/api/invocations/${FAKE_INVOCATION_ID}/prepare_store_download`
-        );
-    });
-
-    it("should display a button for each additional action", () => {
-        const actionButtons = wrapper.findAll(".action-button");
-        expect(actionButtons.length).toBe(FAKE_EXPORT_PLUGIN.additionalActions.length);
-    });
-});
diff --git a/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.vue b/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.vue
deleted file mode 100644
index 030bcdae97c25107d4ff8af8cbebc9ef54e7abee..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/InvocationExportPluginCard.vue
+++ /dev/null
@@ -1,107 +0,0 @@
-<script setup>
-import axios from "axios";
-import { BButtonGroup, BButtonToolbar, BCard, BCardTitle } from "bootstrap-vue";
-import { useMarkdown } from "composables/markdown";
-import { Toast } from "composables/toast";
-import { computed, provide, ref } from "vue";
-
-import { InvocationExportPlugin } from "./model";
-
-import ActionButton from "./ActionButton.vue";
-import StsDownloadButton from "components/StsDownloadButton.vue";
-import ExportToRemoteButton from "components/Workflow/Invocation/Export/ExportToRemoteButton.vue";
-import ExportToRemoteModal from "components/Workflow/Invocation/Export/ExportToRemoteModal.vue";
-
-const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
-
-const exportRemoteModal = ref(null);
-const exportToRemoteTaskId = ref(null);
-
-const props = defineProps({
-    exportPlugin: { type: InvocationExportPlugin, required: true },
-    invocationId: { type: String, required: true },
-});
-
-// Make `invocationId` available to child components via `inject`
-provide("invocationId", props.invocationId);
-
-const descriptionRendered = computed(() => renderMarkdown(props.exportPlugin.markdownDescription));
-const invocationDownloadUrl = computed(() => `/api/invocations/${props.invocationId}/prepare_store_download`);
-const downloadParams = computed(() => {
-    const exportParams = props.exportPlugin.exportParams;
-    return {
-        model_store_format: exportParams.modelStoreFormat,
-        include_files: exportParams.includeFiles,
-        include_deleted: exportParams.includeDeleted,
-        include_hidden: exportParams.includeHidden,
-    };
-});
-
-function openRemoteExportDialog() {
-    exportRemoteModal.value.showModal();
-}
-
-function exportToFileSource(exportDirectory, fileName) {
-    const exportFormat = props.exportPlugin.exportParams.modelStoreFormat;
-    const exportDirectoryUri = `${exportDirectory}/${fileName}.${exportFormat}`;
-    const writeStoreParams = {
-        target_uri: exportDirectoryUri,
-        ...downloadParams.value,
-    };
-    axios
-        .post(`/api/invocations/${props.invocationId}/write_store`, writeStoreParams)
-        .then((response) => {
-            exportToRemoteTaskId.value = response.data.id;
-        })
-        .catch((err) => {
-            Toast.error(`Failed to export to remote source. ${err}`);
-        });
-    exportRemoteModal.value.hideModal();
-}
-
-function onExportToFileSourceSuccess() {
-    Toast.success(`Invocation successfully exported to remote source`);
-}
-
-function onExportToFileSourceFailure() {
-    Toast.error(`Failed to export to remote source`);
-}
-</script>
-
-<template>
-    <div>
-        <BCard class="export-plugin-card mb-1">
-            <BCardTitle class="export-plugin-title align-items-center d-flex justify-content-between">
-                {{ exportPlugin.title }}
-                <BButtonToolbar aria-label="Export Options">
-                    <BButtonGroup>
-                        <StsDownloadButton
-                            :title="'Download Invocation as ' + exportPlugin.title"
-                            :download-endpoint="invocationDownloadUrl"
-                            :post-parameters="downloadParams"
-                            class="download-button" />
-                        <ExportToRemoteButton
-                            :title="'Export Invocation as ' + exportPlugin.title + ' and upload to remote source'"
-                            :task-id="exportToRemoteTaskId"
-                            class="remote-export-button"
-                            @onClick="openRemoteExportDialog"
-                            @onSuccess="onExportToFileSourceSuccess"
-                            @onFailure="onExportToFileSourceFailure" />
-                        <ActionButton
-                            v-for="action in exportPlugin.additionalActions"
-                            :key="action.id"
-                            :action="action"
-                            class="action-button" />
-                    </BButtonGroup>
-                </BButtonToolbar>
-            </BCardTitle>
-
-            <div class="markdown-description" v-html="descriptionRendered" />
-        </BCard>
-        <ExportToRemoteModal
-            ref="exportRemoteModal"
-            :invocation-id="props.invocationId"
-            :export-plugin="props.exportPlugin"
-            @onExportToFileSource="exportToFileSource" />
-    </div>
-</template>
diff --git a/client/src/components/Workflow/Invocation/Export/InvocationExportWizard.vue b/client/src/components/Workflow/Invocation/Export/InvocationExportWizard.vue
new file mode 100644
index 0000000000000000000000000000000000000000..23c6d1d0c8dd752816f4ec25e5d20b6eb0054cfb
--- /dev/null
+++ b/client/src/components/Workflow/Invocation/Export/InvocationExportWizard.vue
@@ -0,0 +1,485 @@
+<script setup lang="ts">
+import { BAlert, BCard, BCardGroup, BCardImg, BCardTitle, BFormCheckbox, BFormGroup, BFormInput } from "bootstrap-vue";
+import { computed, reactive, ref, watch } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { useWizard } from "@/components/Common/Wizard/useWizard";
+import {
+    AVAILABLE_INVOCATION_EXPORT_PLUGINS,
+    getInvocationExportPluginByType,
+    type InvocationExportPluginType,
+} from "@/components/Workflow/Invocation/Export/Plugins";
+import {
+    type BcoDatabaseExportData,
+    saveInvocationBCOToDatabase,
+} from "@/components/Workflow/Invocation/Export/Plugins/BioComputeObject/service";
+import { useFileSources } from "@/composables/fileSources";
+import { useMarkdown } from "@/composables/markdown";
+import { useShortTermStorageMonitor } from "@/composables/shortTermStorageMonitor";
+import { useTaskMonitor } from "@/composables/taskMonitor";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import RDMCredentialsInfo from "@/components/Common/RDMCredentialsInfo.vue";
+import RDMDestinationSelector from "@/components/Common/RDMDestinationSelector.vue";
+import GenericWizard from "@/components/Common/Wizard/GenericWizard.vue";
+import ExternalLink from "@/components/ExternalLink.vue";
+import FilesInput from "@/components/FilesDialog/FilesInput.vue";
+import FileSourceNameSpan from "@/components/FileSources/FileSourceNameSpan.vue";
+import ExistingInvocationExportProgressCard from "@/components/Workflow/Invocation/Export/ExistingInvocationExportProgressCard.vue";
+
+const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+
+const taskMonitor = useTaskMonitor();
+const stsMonitor = useShortTermStorageMonitor();
+
+const { hasWritable: hasWritableFileSources } = useFileSources({ exclude: ["rdm"] });
+const { hasWritable: hasWritableRDMFileSources } = useFileSources({ include: ["rdm"] });
+
+const resource = "workflow invocation";
+
+type InvocationExportDestination = "download" | "remote-source" | "rdm-repository" | "bco-database";
+
+interface ExportDestinationInfo {
+    destination: InvocationExportDestination;
+    label: string;
+    markdownDescription: string;
+}
+
+interface InvocationExportData {
+    exportPluginFormat: InvocationExportPluginType;
+    destination: InvocationExportDestination;
+    remoteUri: string;
+    outputFileName: string;
+    includeData: boolean;
+    bcoDatabase: BcoDatabaseExportData;
+}
+
+interface Props {
+    invocationId: string;
+}
+
+const props = defineProps<Props>();
+
+const exportToRemoteTaskId = ref();
+const exportToStsRequestId = ref();
+const errorMessage = ref<string>();
+
+const existingProgress = ref<InstanceType<typeof ExistingInvocationExportProgressCard>>();
+
+const exportData: InvocationExportData = reactive({
+    exportPluginFormat: "ro-crate",
+    destination: "download",
+    remoteUri: "",
+    outputFileName: "",
+    includeData: true,
+    bcoDatabase: {
+        serverBaseUrl: "https://biocomputeobject.org",
+        table: "GALXY",
+        ownerGroup: "",
+        authorization: "",
+    },
+});
+
+const exportButtonLabel = computed(() => {
+    switch (exportData.destination) {
+        case "download":
+            return "Generate Download Link";
+        case "remote-source":
+            return "Export to Remote Source";
+        case "rdm-repository":
+            return "Export to RDM Repository";
+        case "bco-database":
+            return "Export to BCODB";
+        default:
+            return "Export";
+    }
+});
+
+const needsFileName = computed(
+    () => exportData.destination === "remote-source" || exportData.destination === "rdm-repository"
+);
+
+const canIncludeData = computed(() => exportData.exportPluginFormat !== "bco");
+
+const exportDestinationSummary = computed(() => {
+    const exportDestination = exportDestinationTargets.value.find(
+        (target) => target.destination === exportData.destination
+    );
+    return exportDestination?.label ?? "Unknown Destination";
+});
+
+const exportDestinationTargets = computed(initializeExportDestinations);
+
+const exportPlugins = computed(() => Array.from(AVAILABLE_INVOCATION_EXPORT_PLUGINS.values()));
+
+const selectedExportPlugin = computed(() => getInvocationExportPluginByType(exportData.exportPluginFormat));
+
+const exportDestinationUri = computed(() => {
+    const uri = `${exportData.remoteUri}/${exportData.outputFileName}.${selectedExportPlugin.value.exportParams.modelStoreFormat}`;
+    return uri;
+});
+
+const exportPluginTitle = computed(() => {
+    const plugin = getInvocationExportPluginByType(exportData.exportPluginFormat);
+    return plugin ? plugin.title : "";
+});
+
+const isBusy = ref(false);
+
+const isWizardBusy = computed(() => stsMonitor.isRunning.value || taskMonitor.isRunning.value || isBusy.value);
+
+const wizard = useWizard({
+    "select-format": {
+        label: "Select output format",
+        instructions: computed(() => {
+            return `Select the format you would like to export the ${resource} to and click Next to continue.`;
+        }),
+        isValid: () => true,
+        isSkippable: () => false,
+    },
+    "select-destination": {
+        label: "Select destination",
+        instructions: computed(() => {
+            return `Select where you would like to export the ${resource} ${exportPluginTitle.value} to and click Next to continue.`;
+        }),
+        isValid: () => true,
+        isSkippable: () => false,
+    },
+    "setup-remote": {
+        label: "Select remote source",
+        instructions: "Select remote source directory",
+        isValid: () => Boolean(exportData.remoteUri),
+        isSkippable: () => exportData.destination !== "remote-source",
+    },
+    "setup-rdm": {
+        label: "Select RDM repository",
+        instructions: "Select RDM repository and provide a draft record to export to",
+        isValid: () => Boolean(exportData.remoteUri),
+        isSkippable: () => exportData.destination !== "rdm-repository",
+    },
+    "setup-bcodb": {
+        label: "Select BCODB Server",
+        instructions: "Provide BCODB server and authentication details",
+        isValid: () =>
+            Boolean(
+                exportData.bcoDatabase.serverBaseUrl &&
+                    exportData.bcoDatabase.authorization &&
+                    exportData.bcoDatabase.table &&
+                    exportData.bcoDatabase.ownerGroup
+            ),
+        isSkippable: () => exportData.destination !== "bco-database" || exportData.exportPluginFormat !== "bco",
+    },
+    "export-summary": {
+        label: "Export",
+        instructions: "Summary",
+        isValid: () =>
+            Boolean(exportData.outputFileName) ||
+            exportData.destination === "download" ||
+            exportData.destination === "bco-database",
+        isSkippable: () => false,
+    },
+});
+
+watch(
+    () => exportData.exportPluginFormat,
+    () => {
+        // Only allow BCO format to be exported to BCODB
+        if (exportData.destination === "bco-database" && exportData.exportPluginFormat !== "bco") {
+            exportData.destination = "download";
+        }
+    }
+);
+
+function onRecordSelected(recordUri: string) {
+    exportData.remoteUri = recordUri;
+}
+
+async function exportInvocation() {
+    switch (exportData.destination) {
+        case "download":
+            await exportToSts();
+            break;
+        case "remote-source":
+        case "rdm-repository":
+            await exportToFileSource();
+            break;
+        case "bco-database":
+            isBusy.value = true;
+            await saveInvocationBCOToDatabase(props.invocationId, exportData.bcoDatabase);
+            isBusy.value = false;
+            break;
+    }
+    //@ts-ignore incorrect property does not exist on type error
+    existingProgress.value?.updateExistingExportProgress();
+}
+
+async function exportToSts() {
+    const { data, error } = await GalaxyApi().POST("/api/invocations/{invocation_id}/prepare_store_download", {
+        params: { path: { invocation_id: props.invocationId } },
+        body: {
+            model_store_format: selectedExportPlugin.value.exportParams.modelStoreFormat,
+            include_deleted: selectedExportPlugin.value.exportParams.includeDeleted,
+            include_hidden: selectedExportPlugin.value.exportParams.includeHidden,
+            include_files: exportData.includeData,
+            bco_merge_history_metadata: false,
+        },
+    });
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return;
+    }
+
+    exportToStsRequestId.value = data.storage_request_id;
+}
+
+async function exportToFileSource() {
+    const { data, error } = await GalaxyApi().POST("/api/invocations/{invocation_id}/write_store", {
+        params: {
+            path: { invocation_id: props.invocationId },
+        },
+        body: {
+            target_uri: exportDestinationUri.value,
+            model_store_format: selectedExportPlugin.value.exportParams.modelStoreFormat,
+            include_deleted: selectedExportPlugin.value.exportParams.includeDeleted,
+            include_hidden: selectedExportPlugin.value.exportParams.includeHidden,
+            include_files: exportData.includeData,
+            bco_merge_history_metadata: false,
+        },
+    });
+
+    if (error) {
+        errorMessage.value = errorMessageAsString(error);
+        return;
+    }
+
+    exportToRemoteTaskId.value = data.id;
+}
+
+function initializeExportDestinations(): ExportDestinationInfo[] {
+    const destinations: ExportDestinationInfo[] = [
+        {
+            destination: "download",
+            label: "Temporary Direct Download",
+            markdownDescription: `Generate a link to the export file and download it directly to your computer.
+
+**Please note that the link will expire after 24 hours.**`,
+        },
+    ];
+
+    if (exportData.exportPluginFormat === "bco") {
+        destinations.push({
+            destination: "bco-database",
+            label: "BCO Database",
+            markdownDescription: `You can upload your ${resource} to a **BCODB** server here.
+
+Submission to the BCODB **requires that a user already has an authenticated account** at the server they wish to submit to.
+More information about how to set up an account and submit data to a BCODB server can be found [here](https://w3id.org/biocompute/tutorials/galaxy_quick_start).`,
+        });
+    }
+
+    if (hasWritableFileSources.value) {
+        destinations.push({
+            destination: "remote-source",
+            label: "Remote File Source",
+            markdownDescription: `If you need a **more permanent** way of storing your ${resource} you can export it directly to one of the available remote file sources here. You will be able to re-import it later as long as it remains available on the remote server.
+
+Examples of remote sources include Amazon S3, Azure Storage, Google Drive... and other public or personal file sources that you have setup access to.`,
+        });
+    }
+
+    if (hasWritableRDMFileSources.value) {
+        destinations.push({
+            destination: "rdm-repository",
+            label: "RDM Repository",
+            markdownDescription: `You can upload your ${resource} to one of the available **Research Data Management repositories** here.
+This will allow you to easily associate your ${resource} with your research project or publication.
+
+Examples of RDM repositories include [Zenodo](https://zenodo.org/), [Invenio RDM](https://inveniosoftware.org/products/rdm/) instances, and other public or personal repositories that you have setup access to.`,
+        });
+    }
+
+    return destinations;
+}
+</script>
+
+<template>
+    <div>
+        <ExistingInvocationExportProgressCard
+            ref="existingProgress"
+            :invocation-id="invocationId"
+            :export-to-remote-task-id="exportToRemoteTaskId"
+            :export-to-remote-target-uri="exportData.remoteUri"
+            :export-to-sts-request-id="exportToStsRequestId"
+            :use-sts-monitor="stsMonitor"
+            :use-remote-monitor="taskMonitor"
+            @onDismissSts="exportToStsRequestId = undefined"
+            @onDismissRemote="exportToRemoteTaskId = undefined" />
+        <GenericWizard
+            class="invocation-export-wizard"
+            title="Invocation Export Wizard"
+            :use="wizard"
+            :submit-button-label="exportButtonLabel"
+            :is-busy="isWizardBusy"
+            @submit="exportInvocation">
+            <div v-if="wizard.isCurrent('select-format')">
+                <BCardGroup deck>
+                    <BCard
+                        v-for="plugin in exportPlugins"
+                        :key="plugin.id"
+                        :data-invocation-export-type="plugin.id"
+                        class="wizard-selection-card"
+                        :border-variant="exportData.exportPluginFormat === plugin.id ? 'primary' : 'default'"
+                        @click="exportData.exportPluginFormat = plugin.id">
+                        <BCardTitle>
+                            <b>{{ plugin.title }}</b>
+                        </BCardTitle>
+                        <div v-if="plugin.img">
+                            <BCardImg :src="plugin.img" :alt="plugin.title" />
+                            <br />
+                            <ExternalLink v-if="plugin.url" :href="plugin.url">
+                                <b>Learn more</b>
+                            </ExternalLink>
+                        </div>
+                        <div v-else v-html="renderMarkdown(plugin.markdownDescription)" />
+                    </BCard>
+                </BCardGroup>
+            </div>
+
+            <div v-if="wizard.isCurrent('select-destination')">
+                <BCardGroup deck>
+                    <BCard
+                        v-for="target in exportDestinationTargets"
+                        :key="target.destination"
+                        :data-invocation-export-destination="target.destination"
+                        :border-variant="exportData.destination === target.destination ? 'primary' : 'default'"
+                        :header-bg-variant="exportData.destination === target.destination ? 'primary' : 'default'"
+                        :header-text-variant="exportData.destination === target.destination ? 'white' : 'default'"
+                        :header="target.label"
+                        class="wizard-selection-card"
+                        @click="exportData.destination = target.destination">
+                        <div v-html="renderMarkdown(target.markdownDescription)" />
+                    </BCard>
+                </BCardGroup>
+            </div>
+
+            <div v-if="wizard.isCurrent('setup-remote')">
+                <BFormGroup
+                    id="fieldset-directory"
+                    label-for="directory"
+                    :description="`Select a 'remote files' directory to export ${resource} to.`"
+                    class="mt-3">
+                    <FilesInput
+                        id="directory"
+                        v-model="exportData.remoteUri"
+                        mode="directory"
+                        :require-writable="true"
+                        :filter-options="{ exclude: ['rdm'] }" />
+                </BFormGroup>
+            </div>
+
+            <div v-if="wizard.isCurrent('setup-rdm')">
+                <RDMCredentialsInfo />
+
+                <RDMDestinationSelector :what="resource" @onRecordSelected="onRecordSelected" />
+            </div>
+
+            <div v-if="wizard.isCurrent('setup-bcodb')">
+                <p>
+                    To submit to a BCODB you need to already have an authenticated account. Instructions on submitting a
+                    BCO from Galaxy are available
+                    <ExternalLink href="https://w3id.org/biocompute/tutorials/galaxy_quick_start/" target="_blank">
+                        here
+                    </ExternalLink>
+                </p>
+                <BFormGroup label-for="bcodb-server" description="BCO DB URL (example: https://biocomputeobject.org)">
+                    <BFormInput
+                        id="bcodb-server"
+                        v-model="exportData.bcoDatabase.serverBaseUrl"
+                        type="text"
+                        placeholder="https://biocomputeobject.org"
+                        autocomplete="off"
+                        required />
+                </BFormGroup>
+
+                <BFormGroup label-for="bcodb-table" description="Prefix">
+                    <BFormInput
+                        id="bcodb-table"
+                        v-model="exportData.bcoDatabase.table"
+                        type="text"
+                        placeholder="GALXY"
+                        autocomplete="off"
+                        required />
+                </BFormGroup>
+
+                <BFormGroup label-for="bcodb-owner" description="User Name">
+                    <BFormInput
+                        id="bcodb-owner"
+                        v-model="exportData.bcoDatabase.ownerGroup"
+                        type="text"
+                        autocomplete="off"
+                        required />
+                </BFormGroup>
+
+                <BFormGroup label-for="bcodb-authorization" description="User API Key">
+                    <BFormInput
+                        id="bcodb-authorization"
+                        v-model="exportData.bcoDatabase.authorization"
+                        type="password"
+                        autocomplete="off"
+                        required />
+                </BFormGroup>
+            </div>
+
+            <div v-if="wizard.isCurrent('export-summary')">
+                <BFormGroup
+                    v-if="needsFileName"
+                    label-for="exported-file-name"
+                    :description="`Give the exported file a name.`"
+                    class="mt-3">
+                    <BFormInput
+                        id="exported-file-name"
+                        v-model="exportData.outputFileName"
+                        placeholder="enter file name"
+                        required />
+                </BFormGroup>
+
+                <BFormCheckbox v-if="canIncludeData" id="include-data" v-model="exportData.includeData" switch>
+                    Include data files in the export package.
+                </BFormCheckbox>
+
+                <br />
+
+                <div>
+                    Format <b>{{ exportPluginTitle }}</b>
+                </div>
+
+                <div>
+                    Destination
+                    <b>{{ exportDestinationSummary }}</b>
+                    <b v-if="exportData.destination !== 'download' && exportData.remoteUri">
+                        <FileSourceNameSpan :uri="exportData.remoteUri" class="text-primary" />
+                    </b>
+                    <b v-if="exportData.destination === 'bco-database'">
+                        <span class="text-primary">{{ exportData.bcoDatabase.table }}</span>
+                        <ExternalLink :href="exportData.bcoDatabase.serverBaseUrl">
+                            {{ exportData.bcoDatabase.serverBaseUrl }}
+                        </ExternalLink>
+                    </b>
+                </div>
+            </div>
+        </GenericWizard>
+        <BAlert v-if="errorMessage" show dismissible fade variant="danger" @dismissed="errorMessage = undefined">
+            {{ errorMessage }}
+        </BAlert>
+    </div>
+</template>
+
+<style scoped lang="scss">
+.card-img {
+    height: auto;
+    width: auto;
+    max-height: 100px;
+    max-inline-size: -webkit-fill-available;
+}
+</style>
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.js b/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.ts
similarity index 52%
rename from client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.js
rename to client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.ts
index db2bff4b076df1a2abd48c1e846c813b5b35cb9d..2454fa0b3c877ce1bb3242c4d4921368ef0c9293 100644
--- a/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.js
+++ b/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportPlugin.ts
@@ -1,14 +1,10 @@
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faDatabase } from "@fortawesome/free-solid-svg-icons";
+import { type InvocationExportPlugin } from "@/components/Workflow/Invocation/Export/Plugins";
 
-import { InvocationExportPlugin, InvocationExportPluginAction } from "../../model";
-
-import SendForm from "./SendForm.vue";
-
-library.add(faDatabase);
-
-export const BIO_COMPUTE_OBJ_EXPORT_PLUGIN = new InvocationExportPlugin({
+export const BIO_COMPUTE_OBJ_EXPORT_PLUGIN: InvocationExportPlugin = {
+    id: "bco",
     title: "BioCompute Object",
+    img: "https://www.biocomputeobject.org/static/media/logo.c8a91f1656efbad5d745.png",
+    url: "https://biocomputeobject.org/",
     markdownDescription: `
 A BioCompute Object (BCO) is the unofficial name for a JSON object that adheres to the [IEEE-2791-2020 standard](https://standards.ieee.org/ieee/2791/7337/).
 A BCO is designed to communicate High-throughput Sequencing (HTS) analysis results, data set creation, data curation, and bioinformatics verification protocols.
@@ -22,15 +18,4 @@ Instructions for [creating a BCO using Galaxy](https://w3id.org/biocompute/tutor
         includeDeleted: false,
         includeHidden: false,
     },
-    additionalActions: [
-        new InvocationExportPluginAction({
-            id: "send-to-bco-db",
-            title: "Send to BCODB",
-            icon: faDatabase,
-            run: (modal) => {
-                modal.showModal();
-            },
-            modal: SendForm,
-        }),
-    ],
-});
+};
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/SendForm.vue b/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/SendForm.vue
deleted file mode 100644
index ef219e57601ccc572d3fff7351d5b45d5a6950a3..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/SendForm.vue
+++ /dev/null
@@ -1,181 +0,0 @@
-<script setup>
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import axios from "axios";
-import { BModal } from "bootstrap-vue";
-import ExternalLink from "components/ExternalLink";
-import { Toast } from "composables/toast";
-import { withPrefix } from "utils/redirect";
-import { inject, reactive, ref } from "vue";
-
-import { wait } from "@/utils/utils";
-
-const sendBCOModal = ref(null);
-const generatingBCO = ref(false);
-
-const form = reactive({
-    fetch: "https://biocomputeobject.org",
-    authorization: "",
-    table: "BCO",
-    owner_group: "",
-});
-
-const invocationId = inject("invocationId");
-
-function showModal() {
-    resetForm();
-    sendBCOModal.value.show();
-}
-
-function hideModal() {
-    sendBCOModal.value.hide();
-}
-
-function resetForm() {
-    form.fetch = "";
-    form.authorization = "";
-    form.table = "GALXY";
-    form.owner_group = "";
-}
-
-function handleError(err) {
-    Toast.error(`Failed to send BCO. ${err}`);
-}
-
-async function generateBcoContent() {
-    try {
-        generatingBCO.value = true;
-        const data = {
-            model_store_format: "bco.json",
-            include_files: false,
-            include_deleted: false,
-            include_hidden: false,
-        };
-        const response = await axios.post(withPrefix(`/api/invocations/${invocationId}/prepare_store_download`), data);
-        const storage_request_id = response.data.storage_request_id;
-        const pollUrl = withPrefix(`/api/short_term_storage/${storage_request_id}/ready`);
-        const resultUrl = withPrefix(`/api/short_term_storage/${storage_request_id}`);
-        let pollingResponse = await axios.get(pollUrl);
-        let maxRetries = 120;
-        while (!pollingResponse.data && maxRetries) {
-            await wait(2000);
-            pollingResponse = await axios.get(pollUrl);
-            maxRetries -= 1;
-        }
-        if (!pollingResponse.data) {
-            throw Error("Timeout waiting for BioCompute Object export result!");
-        } else {
-            const resultResponse = await axios.get(resultUrl);
-            return resultResponse.data;
-        }
-    } catch (err) {
-        handleError(err);
-    } finally {
-        generatingBCO.value = false;
-    }
-}
-
-async function sendBco(bcoContent) {
-    const bcoData = {
-        POST_api_objects_draft_create: [
-            {
-                contents: bcoContent,
-                owner_group: form.owner_group,
-                schema: "IEEE",
-                prefix: form.table,
-            },
-        ],
-    };
-
-    const headers = {
-        Authorization: "Token " + form.authorization,
-        "Content-type": "application/json; charset=UTF-8",
-    };
-    try {
-        await axios.post(`${form.fetch}/api/objects/drafts/create/`, bcoData, { headers: headers });
-        Toast.success(`Invocation successfully sent to: ${form.fetch}`);
-    } catch (err) {
-        handleError(err);
-    }
-}
-
-async function submitForm() {
-    const bcoContent = await generateBcoContent();
-    hideModal();
-    await sendBco(bcoContent);
-    resetForm();
-}
-
-defineExpose({ showModal });
-</script>
-
-<template>
-    <BModal ref="sendBCOModal" title="Submit To BCODB" title-tag="h2" centered hide-footer>
-        <div>
-            <p>
-                To submit to a BCODB you need to already have an authenticated account. Instructions on submitting a BCO
-                from Galaxy are available
-                <ExternalLink href="https://w3id.org/biocompute/tutorials/galaxy_quick_start/" target="_blank"
-                    >here</ExternalLink
-                >.
-            </p>
-            <form @submit.prevent="submitForm">
-                <div class="form-group">
-                    <label for="fetch">
-                        <input
-                            id="fetch"
-                            v-model="form.fetch"
-                            type="text"
-                            class="form-control"
-                            placeholder="https://biocomputeobject.org"
-                            autocomplete="off"
-                            required />
-                        BCO DB URL (example: https://biocomputeobject.org)
-                    </label>
-                </div>
-                <div class="form-group">
-                    <label for="authorization">
-                        <input
-                            id="authorization"
-                            v-model="form.authorization"
-                            type="password"
-                            class="form-control"
-                            autocomplete="off"
-                            required />
-                        User API Key
-                    </label>
-                </div>
-                <div class="form-group">
-                    <label for="table">
-                        <input
-                            id="table"
-                            v-model="form.table"
-                            type="text"
-                            class="form-control"
-                            placeholder="GALXY"
-                            required />
-                        Prefix
-                    </label>
-                </div>
-                <div class="form-group">
-                    <label for="owner_group">
-                        <input
-                            id="owner_group"
-                            v-model="form.owner_group"
-                            type="text"
-                            class="form-control"
-                            autocomplete="off"
-                            required />
-                        User Name
-                    </label>
-                </div>
-                <div class="form-group">
-                    <div v-if="generatingBCO">
-                        <FontAwesomeIcon icon="spinner" spin />
-                        Generating BCO please wait...
-                    </div>
-                    <button v-else class="btn btn-primary">{{ "Submit" | localize }}</button>
-                </div>
-            </form>
-        </div>
-    </BModal>
-</template>
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/service.ts b/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/service.ts
new file mode 100644
index 0000000000000000000000000000000000000000..44e94d904e4e5c103eaa2142bf911ebe87e6fd44
--- /dev/null
+++ b/client/src/components/Workflow/Invocation/Export/Plugins/BioComputeObject/service.ts
@@ -0,0 +1,76 @@
+import axios from "axios";
+
+import { Toast } from "@/composables/toast";
+import { withPrefix } from "@/utils/redirect";
+import { errorMessageAsString } from "@/utils/simple-error";
+import { wait } from "@/utils/utils";
+
+/**
+ * Data needed to send a BioCompute Object to a BCODB server.
+ */
+export interface BcoDatabaseExportData {
+    serverBaseUrl: string;
+    authorization: string;
+    table: string;
+    ownerGroup: string;
+}
+
+/**
+ * Generate a BioCompute Object from an invocation and send it to a BCODB server.
+ * @param invocationId The ID of the invocation to export.
+ * @param inputData The data needed to send the BCO to the BCODB.
+ */
+export async function saveInvocationBCOToDatabase(invocationId: string, inputData: BcoDatabaseExportData) {
+    try {
+        const bcoContent = await generateBcoContent(invocationId);
+        await sendBco(bcoContent, inputData);
+        Toast.success(`Invocation successfully sent to: ${inputData.serverBaseUrl}`);
+    } catch (err) {
+        Toast.error(errorMessageAsString(err), "Error sending BioCompute Object to BCODB");
+    }
+}
+
+async function generateBcoContent(invocationId: string) {
+    const data = {
+        model_store_format: "bco.json",
+        include_files: false,
+        include_deleted: false,
+        include_hidden: false,
+    };
+    const response = await axios.post(withPrefix(`/api/invocations/${invocationId}/prepare_store_download`), data);
+    const storage_request_id = response.data.storage_request_id;
+    const pollUrl = withPrefix(`/api/short_term_storage/${storage_request_id}/ready`);
+    const resultUrl = withPrefix(`/api/short_term_storage/${storage_request_id}`);
+    let pollingResponse = await axios.get(pollUrl);
+    let maxRetries = 120;
+    while (!pollingResponse.data && maxRetries) {
+        await wait(2000);
+        pollingResponse = await axios.get(pollUrl);
+        maxRetries -= 1;
+    }
+    if (!pollingResponse.data) {
+        throw Error("Timeout waiting for BioCompute Object export result!");
+    } else {
+        const resultResponse = await axios.get(resultUrl);
+        return resultResponse.data;
+    }
+}
+
+async function sendBco(bcoContent: string, inputData: BcoDatabaseExportData) {
+    const bcoData = {
+        POST_api_objects_draft_create: [
+            {
+                contents: bcoContent,
+                owner_group: inputData.ownerGroup,
+                schema: "IEEE",
+                prefix: inputData.table,
+            },
+        ],
+    };
+
+    const headers = {
+        Authorization: "Token " + inputData.authorization,
+        "Content-type": "application/json; charset=UTF-8",
+    };
+    await axios.post(`${inputData.serverBaseUrl}/api/objects/drafts/create/`, bcoData, { headers: headers });
+}
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.js b/client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.ts
similarity index 55%
rename from client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.js
rename to client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.ts
index 648aa489b44d2792ce9dd4d3a57199782f67895c..3408343b683879527df6b959dcfee7458bd40c5f 100644
--- a/client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.js
+++ b/client/src/components/Workflow/Invocation/Export/Plugins/DefaultFileExportPlugin.ts
@@ -1,7 +1,8 @@
-import { InvocationExportPlugin } from "../model";
+import { type InvocationExportPlugin } from "@/components/Workflow/Invocation/Export/Plugins";
 
-export const DEFAULT_FILE_EXPORT_PLUGIN = new InvocationExportPlugin({
-    title: "File",
+export const DEFAULT_FILE_EXPORT_PLUGIN: InvocationExportPlugin = {
+    id: "default-file",
+    title: "Compressed File",
     markdownDescription: `Export the invocation to a compressed File containing the invocation data in Galaxy native format.`,
     exportParams: {
         modelStoreFormat: "tgz",
@@ -9,5 +10,4 @@ export const DEFAULT_FILE_EXPORT_PLUGIN = new InvocationExportPlugin({
         includeDeleted: false,
         includeHidden: false,
     },
-    additionalActions: [],
-});
+};
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.js b/client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.ts
similarity index 56%
rename from client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.js
rename to client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.ts
index ea8f932617551654e20139482f420258ba9e2f8b..7d261d114d8230c8a4cb717112a8b9a09632dc71 100644
--- a/client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.js
+++ b/client/src/components/Workflow/Invocation/Export/Plugins/ROCrateExportPlugin.ts
@@ -1,15 +1,18 @@
-import { InvocationExportPlugin } from "../model";
+import { type InvocationExportPlugin } from "@/components/Workflow/Invocation/Export/Plugins";
 
-export const RO_CRATE_EXPORT_PLUGIN = new InvocationExportPlugin({
-    title: "Research Object Crate (RO-Crate)",
+export const RO_CRATE_EXPORT_PLUGIN: InvocationExportPlugin = {
+    id: "ro-crate",
+    title: "Research Object Crate",
+    img: "https://www.researchobject.org/workflow-run-crate/img/ro-crate-workflow-run.svg",
+    url: "https://www.researchobject.org/workflow-run-crate/",
     markdownDescription: `
 RO-Crate is a community effort to establish a lightweight approach to packaging research data with their metadata. It is based on schema.org annotations in JSON-LD, and aims to make best-practice in formal metadata description accessible and practical for use in a wider variety of situations, from an individual researcher working with a folder of data, to large data-intensive computational research environments.
 
-Learn more about [RO Crate](https://www.researchobject.org/ro-crate/).`,
+Learn more about it [here](https://www.researchobject.org/workflow-run-crate/).`,
     exportParams: {
         modelStoreFormat: "rocrate.zip",
         includeFiles: true,
         includeDeleted: false,
         includeHidden: false,
     },
-});
+};
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/index.js b/client/src/components/Workflow/Invocation/Export/Plugins/index.js
deleted file mode 100644
index 80e08ee673c4a5b5d9945c39b7ce11334e1b5739..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/Plugins/index.js
+++ /dev/null
@@ -1,11 +0,0 @@
-import { BIO_COMPUTE_OBJ_EXPORT_PLUGIN } from "./BioComputeObject/BioComputeObjectExportPlugin";
-import { DEFAULT_FILE_EXPORT_PLUGIN } from "./DefaultFileExportPlugin";
-import { RO_CRATE_EXPORT_PLUGIN } from "./ROCrateExportPlugin";
-
-const AVAILABLE_INVOCATION_EXPORT_PLUGINS = [
-    RO_CRATE_EXPORT_PLUGIN,
-    BIO_COMPUTE_OBJ_EXPORT_PLUGIN,
-    DEFAULT_FILE_EXPORT_PLUGIN,
-];
-
-export { AVAILABLE_INVOCATION_EXPORT_PLUGINS };
diff --git a/client/src/components/Workflow/Invocation/Export/Plugins/index.ts b/client/src/components/Workflow/Invocation/Export/Plugins/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..429535076b5603580308de9160f53b755b4eead6
--- /dev/null
+++ b/client/src/components/Workflow/Invocation/Export/Plugins/index.ts
@@ -0,0 +1,59 @@
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
+
+import { type ExportParams } from "@/components/Common/models/exportRecordModel";
+
+import { BIO_COMPUTE_OBJ_EXPORT_PLUGIN } from "./BioComputeObject/BioComputeObjectExportPlugin";
+import { DEFAULT_FILE_EXPORT_PLUGIN } from "./DefaultFileExportPlugin";
+import { RO_CRATE_EXPORT_PLUGIN } from "./ROCrateExportPlugin";
+
+export type InvocationExportPluginType = "ro-crate" | "bco" | "default-file";
+
+export const AVAILABLE_INVOCATION_EXPORT_PLUGINS = new Map<InvocationExportPluginType, InvocationExportPlugin>([
+    ["ro-crate", RO_CRATE_EXPORT_PLUGIN],
+    ["bco", BIO_COMPUTE_OBJ_EXPORT_PLUGIN],
+    ["default-file", DEFAULT_FILE_EXPORT_PLUGIN],
+]);
+
+export function getInvocationExportPluginByType(pluginType: InvocationExportPluginType): InvocationExportPlugin {
+    const plugin = AVAILABLE_INVOCATION_EXPORT_PLUGINS.get(pluginType);
+    if (!plugin) {
+        throw new Error("Unregistered Invocation Export Plugin. Please register it first.");
+    }
+    return plugin;
+}
+
+/**
+ * Defines a UI plugin that can export a workflow invocation to a particular format.
+ */
+export interface InvocationExportPlugin {
+    /** The unique identifier for the plugin. */
+    id: InvocationExportPluginType;
+    /** The title of the plugin. */
+    title: string;
+    /** The image URL to display for the plugin. Usually a logo. */
+    img?: string;
+    /** The URL to link to additional information about the plugin. */
+    url?: string;
+    /** A markdown description of the plugin. */
+    markdownDescription: string;
+    /** The parameters to use when exporting the invocation. */
+    exportParams: ExportParams;
+}
+
+/**
+ * Defines an action that can be taken in addition to the main export action.
+ */
+export interface InvocationExportPluginAction {
+    /** The unique identifier for the action. */
+    id: string;
+    /** The title of the action. */
+    title: string;
+    /** The icon to display in the button for the action. */
+    icon?: IconDefinition | string;
+    /** The function to run when the action is triggered.
+     * @param modal - The modal dialog to show when the action is run.
+     */
+    run: (modal: any) => void;
+    /** The Vue component to render in a modal dialog when the action is run. */
+    modal?: any;
+}
diff --git a/client/src/components/Workflow/Invocation/Export/model.js b/client/src/components/Workflow/Invocation/Export/model.js
deleted file mode 100644
index a9197d94fb89d5431d0ae98954a109eb5f8c4d86..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/Invocation/Export/model.js
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
- * Defines a UI plugin that can export a workflow invocation to a particular format.
- */
-export class InvocationExportPlugin {
-    constructor(props = {}) {
-        /**
-         * The unique ID for this plugin.
-         * @type {string}
-         */
-        this.id = props.id ?? "undefined-plugin";
-
-        /**
-         * The display title for this plugin.
-         * @type {string}
-         */
-        this.title = props.title ?? "Unknown Plugin";
-
-        /**
-         * A detailed description of the format in Markdown.
-         * @type {string}
-         */
-        this.markdownDescription = props.markdownDescription ?? "No description provided";
-
-        /**
-         * An object with parameters for the Galaxy export store that handles the download format in the backend.
-         * Check lib/galaxy/model/store/__init__.py::get_export_store_factory for more info.
-         * @type {Object}
-         */
-        this.exportParams = props.exportParams ?? null;
-
-        /**
-         * A list of additional actions that this plugin can do with the exported invocation in addition
-         * to direct downloading the exported file or exporting it to a remote file source.
-         * @type {InvocationExportPluginAction[]}
-         */
-        this.additionalActions = props.additionalActions ?? [];
-    }
-}
-
-export class InvocationExportPluginAction {
-    constructor(props = {}) {
-        /**
-         * The unique ID for this action.
-         * @type {string}
-         */
-        this.id = props.id ?? "undefined-action";
-
-        /**
-         * The display title of the button for this action.
-         * @type {string}
-         */
-        this.title = props.title ?? "Untitled action";
-
-        /** An optional (fontawesome) icon definition for the action button. */
-        this.icon = props.icon ?? null;
-
-        /**
-         * The function that will run when the action button is pressed.
-         * @type {function}
-         */
-        this.run =
-            props.run ??
-            (() => {
-                alert("Undefined 'run' function in InvocationExportPluginAction");
-            });
-
-        /**
-         * The optional modal dialog (component) that can be displayed when running this action.
-         * @type {string}
-         */
-        this.modal = props.modal ?? null;
-    }
-}
diff --git a/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue b/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue
index f59331bcfeef901a0ec1fa84775874f4ddabe526..448cacdf3989319d3fdbcdf38d50232f420457dc 100644
--- a/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue
+++ b/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue
@@ -9,27 +9,21 @@ import {
     faTimes,
 } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { useElementBounding } from "@vueuse/core";
 import { BAlert, BButton, BCard, BCardBody, BCardHeader } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onUnmounted, ref, watch } from "vue";
 
 import type { WorkflowInvocationElementView } from "@/api/invocations";
-import { JobProvider } from "@/components/providers";
 import { useDatatypesMapper } from "@/composables/datatypesMapper";
 import { useInvocationGraph } from "@/composables/useInvocationGraph";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import type { Workflow } from "@/stores/workflowStore";
-import { withPrefix } from "@/utils/redirect";
 
-import WorkflowInvocationSteps from "./WorkflowInvocationSteps.vue";
 import Heading from "@/components/Common/Heading.vue";
-import ExternalLink from "@/components/ExternalLink.vue";
-import JobInformation from "@/components/JobInformation/JobInformation.vue";
-import JobParameters from "@/components/JobParameters/JobParameters.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
-import FlexPanel from "@/components/Panels/FlexPanel.vue";
 import WorkflowGraph from "@/components/Workflow/Editor/WorkflowGraph.vue";
+import WorkflowInvocationStep from "@/components/WorkflowInvocationState/WorkflowInvocationStep.vue";
+import WorkflowInvocationStepHeader from "@/components/WorkflowInvocationState/WorkflowInvocationStepHeader.vue";
 
 library.add(faArrowDown, faChevronDown, faChevronUp, faSignInAlt, faSitemap, faTimes);
 
@@ -40,8 +34,6 @@ interface Props {
     workflow: Workflow;
     /** Whether the invocation is terminal */
     isTerminal: boolean;
-    /** Whether the invocation is scheduled */
-    isScheduled: boolean;
     /** The zoom level for the graph */
     zoom?: number;
     /** Whether to show the minimap */
@@ -70,11 +62,9 @@ const loadingGraph = ref(true);
 const initialLoading = ref(true);
 const errored = ref(false);
 const errorMessage = ref("");
-const showingJobId = ref<string | undefined>(undefined);
 const pollTimeout = ref<any>(null);
-const hideGraph = ref(false);
-const jobCard = ref<BCard | null>(null);
-const loadedJobInfo = ref<HTMLDivElement | null>(null);
+const stepCard = ref<BCard | null>(null);
+const loadedJobInfo = ref<typeof WorkflowInvocationStep | null>(null);
 
 const invocationRef = computed(() => props.invocation);
 
@@ -109,50 +99,6 @@ watch(
     { immediate: true }
 );
 
-// on loading steps, toggle the first one with state === "error" or last one if none are errored
-watch(
-    () => initialLoading.value,
-    (newVal) => {
-        if (!newVal && steps.value) {
-            const errorStep = Object.values(steps.value).find((step) => step.state === "error");
-            if (errorStep) {
-                activeNodeId.value = errorStep.id;
-            } else if (props.isTerminal) {
-                activeNodeId.value = Object.values(steps.value)?.slice(-1)[0]?.id || null;
-            }
-        }
-    },
-    { immediate: true }
-);
-
-// when the graph is hidden/visible, reset the active node and showingJobId
-watch(
-    () => hideGraph.value,
-    () => {
-        showingJobId.value = undefined;
-        activeNodeId.value = null;
-    }
-);
-
-// scroll to the job card when it is loaded (only on invocation route)
-if (props.isFullPage) {
-    watch(
-        () => loadedJobInfo.value,
-        async (jobInfo) => {
-            if (jobInfo) {
-                scrollJobToView();
-            }
-        },
-        { immediate: true }
-    );
-}
-
-// properties for handling the flex-draggable steps panel
-const invocationContainer = ref<HTMLDivElement | null>(null);
-const { width: containerWidth } = useElementBounding(invocationContainer);
-const minWidth = computed(() => containerWidth.value * 0.3);
-const maxWidth = computed(() => 0.7 * containerWidth.value);
-
 onUnmounted(() => {
     clearTimeout(pollTimeout.value);
 });
@@ -196,16 +142,15 @@ async function pollInvocationGraph() {
     }
 }
 
-function scrollJobToView() {
-    const jobCardHeader = jobCard.value?.querySelector(".card-header");
-    jobCardHeader?.scrollIntoView({ behavior: "smooth", block: "start" });
+function scrollStepToView() {
+    const stepCardHeader = stepCard.value?.querySelector(".card-header");
+    stepCardHeader?.scrollIntoView({ behavior: "smooth", block: "start" });
 }
 
-function toggleActiveStep(stepId: number) {
-    if (activeNodeId.value === stepId) {
-        activeNodeId.value = null;
-    } else {
-        activeNodeId.value = stepId;
+/** On a repetition of the step clicked, scroll to the step */
+function stepClicked(nodeId: number | null) {
+    if (nodeId === activeNodeId.value) {
+        scrollStepToView();
     }
 }
 </script>
@@ -222,8 +167,8 @@ function toggleActiveStep(stepId: number) {
             <BAlert v-else show variant="danger"> Unknown Error </BAlert>
         </div>
         <div v-else-if="steps && datatypesMapper">
-            <div ref="invocationContainer" class="d-flex">
-                <div v-if="!hideGraph" class="position-relative w-100">
+            <div class="d-flex">
+                <div class="position-relative w-100">
                     <BCard no-body>
                         <WorkflowGraph
                             class="invocation-graph"
@@ -234,93 +179,49 @@ function toggleActiveStep(stepId: number) {
                             :show-minimap="props.showMinimap"
                             :show-zoom-controls="props.showZoomControls"
                             is-invocation
-                            readonly />
+                            readonly
+                            @stepClicked="stepClicked" />
                     </BCard>
-                    <BButton
-                        class="position-absolute text-decoration-none m-2"
-                        style="top: 0; right: 0"
-                        data-description="hide invocation graph"
-                        size="sm"
-                        @click="hideGraph = true">
-                        <FontAwesomeIcon :icon="faTimes" class="mr-1" />
-                        <span v-localize>Hide Graph</span>
-                    </BButton>
                 </div>
-                <BButton
-                    v-else
-                    v-b-tooltip.noninteractive.hover.right="'Show Graph'"
-                    size="sm"
-                    class="p-0"
-                    style="width: min-content"
-                    @click="hideGraph = false">
-                    <FontAwesomeIcon :icon="faSitemap" />
-                    <div v-localize>Show Graph</div>
-                </BButton>
-                <component
-                    :is="!hideGraph ? FlexPanel : 'div'"
-                    v-if="containerWidth"
-                    side="right"
-                    :collapsible="false"
-                    class="ml-2"
-                    :class="{ 'w-100': hideGraph }"
-                    :min-width="minWidth"
-                    :max-width="maxWidth"
-                    :default-width="containerWidth * 0.4">
-                    <WorkflowInvocationSteps
-                        class="graph-steps-aside"
-                        :class="{ 'steps-fixed-height': !hideGraph }"
-                        :steps="steps"
-                        :store-id="storeId"
-                        :invocation="invocationRef"
-                        :workflow="props.workflow"
-                        :is-full-page="props.isFullPage"
-                        :hide-graph="hideGraph"
-                        :showing-job-id="showingJobId || ''"
-                        :active-node-id="activeNodeId !== null ? activeNodeId : undefined"
-                        @update:showing-job-id="(jobId) => (showingJobId = jobId)"
-                        @focus-on-step="toggleActiveStep" />
-                </component>
             </div>
-            <BCard v-if="!hideGraph" ref="jobCard" class="mt-1" no-body>
-                <BCardHeader class="d-flex justify-content-between align-items-center">
-                    <Heading inline size="md">
-                        <span v-if="showingJobId">
-                            Showing Job Details for
-                            <ExternalLink :href="withPrefix(`/jobs/${showingJobId}/view`)">
-                                <code>{{ showingJobId }}</code>
-                            </ExternalLink>
-                        </span>
-                        <span v-else>No Job Selected</span>
+            <BCard ref="stepCard" class="mt-1" no-body>
+                <BCardHeader
+                    class="d-flex justify-content-between align-items-center"
+                    :class="activeNodeId !== null ? steps[activeNodeId]?.headerClass : ''">
+                    <Heading inline size="sm" class="w-100 mr-2">
+                        <WorkflowInvocationStepHeader
+                            v-if="activeNodeId !== null"
+                            class="w-100"
+                            :workflow-step="props.workflow.steps[activeNodeId]"
+                            :graph-step="steps[activeNodeId]"
+                            :invocation-step="props.invocation.steps[activeNodeId]" />
+                        <span v-else>No Step Selected</span>
                     </Heading>
-                    <div>
+                    <div class="d-flex flex-gapx-1">
                         <BButton
-                            v-if="showingJobId"
-                            v-b-tooltip.hover.noninteractive
-                            title="Scroll to Job"
-                            @click="scrollJobToView()">
+                            v-if="activeNodeId !== null"
+                            title="Scroll to Step"
+                            size="sm"
+                            @click="scrollStepToView()">
                             <FontAwesomeIcon :icon="faArrowDown" />
                         </BButton>
-                        <BButton
-                            v-if="showingJobId"
-                            v-b-tooltip.hover.noninteractive
-                            title="Hide Job"
-                            @click="showingJobId = undefined">
+                        <BButton v-if="activeNodeId !== null" title="Hide Step" size="sm" @click="activeNodeId = null">
                             <FontAwesomeIcon :icon="faTimes" />
                         </BButton>
                     </div>
                 </BCardHeader>
                 <BCardBody>
-                    <JobProvider v-if="showingJobId" :id="showingJobId" v-slot="{ item, loading }">
-                        <BAlert v-if="loading" show>
-                            <LoadingSpan message="Loading Job Information" />
-                        </BAlert>
-                        <div v-else ref="loadedJobInfo">
-                            <JobInformation v-if="item" :job_id="item.id" />
-                            <p></p>
-                            <JobParameters v-if="item" :job-id="item.id" :include-title="false" />
-                        </div>
-                    </JobProvider>
-                    <BAlert v-else show>Select a job from a step in the invocation to view its details here.</BAlert>
+                    <WorkflowInvocationStep
+                        v-if="activeNodeId !== null"
+                        ref="loadedJobInfo"
+                        :key="activeNodeId"
+                        :invocation="props.invocation"
+                        :workflow="props.workflow"
+                        :workflow-step="props.workflow.steps[activeNodeId]"
+                        in-graph-view
+                        :graph-step="steps[activeNodeId]"
+                        expanded />
+                    <BAlert v-else show>Click on a step in the invocation to view its details here.</BAlert>
                 </BCardBody>
             </BCard>
         </div>
diff --git a/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue b/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue
index 458d87aab8ad28e0f73acda83e931c945d08f03c..b481ece4beec9a587b5f7ee35279230949281597 100644
--- a/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue
+++ b/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue
@@ -2,84 +2,52 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faChevronDown, faChevronUp, faSignInAlt } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { computed, nextTick, ref, watch } from "vue";
+import { BAlert } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed, ref } from "vue";
 
 import type { WorkflowInvocationElementView } from "@/api/invocations";
 import { isWorkflowInput } from "@/components/Workflow/constants";
-import type { GraphStep } from "@/composables/useInvocationGraph";
-import type { Workflow } from "@/stores/workflowStore";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
+import { useInvocationStore } from "@/stores/invocationStore";
 
+import LoadingSpan from "@/components/LoadingSpan.vue";
 import WorkflowInvocationStep from "@/components/WorkflowInvocationState/WorkflowInvocationStep.vue";
 
 library.add(faChevronDown, faChevronUp, faSignInAlt);
 
-interface Props {
-    /** The steps for the invocation graph */
-    steps: { [index: string]: GraphStep };
+const props = defineProps<{
     /** The store id for the invocation graph */
     storeId: string;
     /** The invocation to display */
     invocation: WorkflowInvocationElementView;
-    /** The workflow which was run */
-    workflow: Workflow;
-    /** Whether the invocation graph is hidden */
-    hideGraph?: boolean;
-    /** The id for the currently shown job */
-    showingJobId: string;
     /** Whether the steps are being rendered on the dedicated invocation page/route */
     isFullPage?: boolean;
-    /** The active node on the graph */
-    activeNodeId?: number;
-}
-
-const emit = defineEmits<{
-    (e: "focus-on-step", stepId: number): void;
-    (e: "update:showing-job-id", value: string | undefined): void;
 }>();
 
-const props = withDefaults(defineProps<Props>(), {
-    hideGraph: true,
-    activeNodeId: undefined,
-});
+const invocationStore = useInvocationStore();
+const { graphStepsByStoreId } = storeToRefs(invocationStore);
+const graphSteps = computed(() => graphStepsByStoreId.value[props.storeId]);
 
 const stepsDiv = ref<HTMLDivElement>();
 
-const workflowInputSteps = Object.values(props.workflow.steps).filter((step) => isWorkflowInput(step.type));
+const { workflow, loading, error } = useWorkflowInstance(props.invocation.workflow_id);
+
+const workflowInputSteps = workflow.value
+    ? Object.values(workflow.value.steps).filter((step) => isWorkflowInput(step.type))
+    : [];
 const oneOrNoInput = computed(() => workflowInputSteps.length <= 1);
 const expandInvocationInputs = ref(oneOrNoInput.value);
-
-watch(
-    () => [props.activeNodeId, stepsDiv.value],
-    async ([nodeId, card]) => {
-        // if the active node id is an input step, expand the inputs section if not already expanded
-        if (!expandInvocationInputs.value) {
-            const isAnInput = workflowInputSteps.findIndex((step) => step.id === props.activeNodeId) !== -1;
-            expandInvocationInputs.value = isAnInput;
-        }
-
-        await nextTick();
-
-        // on full page view, scroll to the active step card in the steps section
-        if (props.isFullPage) {
-            if (nodeId !== undefined && card) {
-                // scroll to the active step card
-                const stepCard = stepsDiv.value?.querySelector(`[data-index="${props.activeNodeId}"]`);
-                stepCard?.scrollIntoView({ block: "nearest", inline: "start" });
-            }
-        }
-        // clear any job being shown
-        emit("update:showing-job-id", undefined);
-    },
-    { immediate: true }
-);
-
-function showJob(jobId: string | undefined) {
-    emit("update:showing-job-id", jobId);
-}
 </script>
 
 <template>
-    <div ref="stepsDiv" class="d-flex flex-column w-100">
+    <BAlert v-if="loading" variant="info" show>
+        <LoadingSpan message="Loading workflow" />
+    </BAlert>
+    <BAlert v-else-if="error" variant="danger" show>
+        {{ error }}
+    </BAlert>
+    <div v-else-if="graphSteps && workflow" ref="stepsDiv" class="d-flex flex-column w-100">
         <!-- Input Steps grouped in a separate portlet -->
         <div v-if="!oneOrNoInput" class="ui-portlet-section w-100">
             <div
@@ -97,20 +65,16 @@ function showJob(jobId: string | undefined) {
                 <FontAwesomeIcon class="float-right" :icon="expandInvocationInputs ? faChevronUp : faChevronDown" />
             </div>
         </div>
-        <div v-for="step in props.workflow.steps" :key="step.id">
+        <div v-for="step in workflow.steps" :key="step.id">
             <WorkflowInvocationStep
                 v-if="!isWorkflowInput(step.type) || (isWorkflowInput(step.type) && expandInvocationInputs)"
                 :class="{ 'mx-1': !oneOrNoInput && isWorkflowInput(step.type) }"
                 :data-index="step.id"
                 :invocation="props.invocation"
-                :workflow="props.workflow"
+                :workflow="workflow"
                 :workflow-step="step"
-                :in-graph-view="!props.hideGraph"
-                :graph-step="steps[step.id]"
-                :expanded="props.hideGraph ? undefined : props.activeNodeId === step.id"
-                :showing-job-id="props.showingJobId"
-                @show-job="showJob"
-                @update:expanded="emit('focus-on-step', step.id)" />
+                :graph-step="graphSteps[step.id]" />
         </div>
     </div>
+    <BAlert v-else variant="info" show> There are no steps to display. </BAlert>
 </template>
diff --git a/client/src/components/Workflow/Invocation/InvocationScrollList.vue b/client/src/components/Workflow/Invocation/InvocationScrollList.vue
index 0e78c686650f72c2592d00eee413920b1518ea82..2240a3d8c315747b0f8d9599d9bd5507ae1296ff 100644
--- a/client/src/components/Workflow/Invocation/InvocationScrollList.vue
+++ b/client/src/components/Workflow/Invocation/InvocationScrollList.vue
@@ -32,6 +32,8 @@ const props = withDefaults(defineProps<Props>(), {
     limit: 20,
 });
 
+const emit = defineEmits(["invocation-clicked"]);
+
 library.add(faEye, faArrowDown, faInfoCircle);
 
 const stateClasses: Record<string, string> = {
@@ -94,11 +96,10 @@ const route = useRoute();
 const router = useRouter();
 
 function cardClicked(invocation: WorkflowInvocation) {
-    let path = `/workflows/invocations/${invocation.id}`;
     if (props.inPanel) {
-        path += "?from_panel=true";
+        emit("invocation-clicked");
     }
-    router.push(path);
+    router.push(`/workflows/invocations/${invocation.id}`);
 }
 
 function scrollToTop() {
@@ -201,10 +202,14 @@ function workflowName(workflowId: string) {
                         @click="() => cardClicked(invocation)">
                         <div class="overflow-auto w-100">
                             <Heading bold size="text" icon="fa-sitemap">
-                                <span class="truncate-3-lines">{{ workflowName(invocation.workflow_id) }}</span>
+                                <span class="truncate-n-lines three-lines">
+                                    {{ workflowName(invocation.workflow_id) }}
+                                </span>
                             </Heading>
                             <Heading size="text" icon="fa-hdd">
-                                <small class="text-muted">{{ historyName(invocation.history_id) }}</small>
+                                <small class="text-muted truncate-n-lines two-lines">
+                                    {{ historyName(invocation.history_id) }}
+                                </small>
                             </Heading>
                             <div class="d-flex justify-content-between">
                                 <BBadge v-b-tooltip.noninteractive.hover pill>
@@ -254,12 +259,19 @@ function workflowName(workflowId: string) {
 </template>
 
 <style scoped lang="scss">
-@import "theme/blue.scss";
-
-.truncate-3-lines {
+.truncate-n-lines {
     display: -webkit-box;
-    -webkit-line-clamp: 3;
     -webkit-box-orient: vertical;
     overflow: hidden;
+    word-break: break-word;
+    overflow-wrap: break-word;
+    &.three-lines {
+        -webkit-line-clamp: 3;
+        line-clamp: 3;
+    }
+    &.two-lines {
+        -webkit-line-clamp: 2;
+        line-clamp: 2;
+    }
 }
 </style>
diff --git a/client/src/components/Workflow/List/WorkflowActions.vue b/client/src/components/Workflow/List/WorkflowActions.vue
new file mode 100644
index 0000000000000000000000000000000000000000..7202b22756d096c618b679d544e37dfd2682dd12
--- /dev/null
+++ b/client/src/components/Workflow/List/WorkflowActions.vue
@@ -0,0 +1,207 @@
+<script setup lang="ts">
+import { faStar as farStar } from "@fortawesome/free-regular-svg-icons";
+import {
+    faCaretDown,
+    faCopy,
+    faDownload,
+    faExternalLinkAlt,
+    faFileExport,
+    faLink,
+    faPlay,
+    faShareAlt,
+    faSpinner,
+    faStar,
+    faTrash,
+} from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BButtonGroup, BDropdown, BDropdownItem } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed } from "vue";
+
+import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { useUserStore } from "@/stores/userStore";
+
+import { useWorkflowActions } from "./useWorkflowActions";
+
+interface Props {
+    workflow: StoredWorkflowDetailed;
+    published?: boolean;
+    editor?: boolean;
+    current?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    published: false,
+    editor: false,
+    current: false,
+});
+
+const emit = defineEmits<{
+    (e: "refreshList", overlayLoading?: boolean): void;
+    (e: "dropdown", open: boolean): void;
+}>();
+
+const { bookmarkLoading, deleteWorkflow, toggleBookmark, copyPublicLink, copyWorkflow, downloadUrl } =
+    useWorkflowActions(
+        computed(() => props.workflow),
+        () => emit("refreshList", true)
+    );
+
+const userStore = useUserStore();
+const { isAnonymous } = storeToRefs(userStore);
+
+const shared = computed(() => {
+    return !userStore.matchesCurrentUsername(props.workflow.owner);
+});
+
+const sourceType = computed(() => {
+    if (props.workflow.source_metadata?.url) {
+        return "url";
+    } else if (props.workflow.source_metadata?.trs_server) {
+        return `trs_${props.workflow.source_metadata?.trs_server}`;
+    } else {
+        return "";
+    }
+});
+
+const runPath = computed(
+    () =>
+        `/workflows/run?id=${props.workflow.id}${
+            props.workflow.version !== undefined ? `&version=${props.workflow.version}` : ""
+        }`
+);
+</script>
+
+<template>
+    <div class="workflow-actions">
+        <BButtonGroup>
+            <BButton
+                v-if="!props.workflow.deleted && !props.workflow.show_in_tool_panel"
+                v-b-tooltip.hover.noninteractive
+                class="workflow-bookmark-button-add inline-icon-button"
+                variant="link"
+                title="Add to bookmarks"
+                tooltip="Add to bookmarks. This workflow will appear in the left tool panel."
+                size="sm"
+                @click="toggleBookmark(true)">
+                <FontAwesomeIcon v-if="!bookmarkLoading" :icon="farStar" fixed-width />
+                <FontAwesomeIcon v-else :icon="faSpinner" spin fixed-width />
+            </BButton>
+            <BButton
+                v-else-if="!props.workflow.deleted && props.workflow.show_in_tool_panel"
+                v-b-tooltip.hover.noninteractive
+                class="workflow-bookmark-button-remove inline-icon-button"
+                variant="link"
+                title="Remove bookmark"
+                size="sm"
+                @click="toggleBookmark(false)">
+                <FontAwesomeIcon v-if="!bookmarkLoading" :icon="faStar" fixed-width />
+                <FontAwesomeIcon v-else :icon="faSpinner" spin fixed-width />
+            </BButton>
+
+            <BDropdown
+                v-b-tooltip.top.noninteractive
+                :data-workflow-actions-dropdown="workflow.id"
+                right
+                no-caret
+                class="workflow-actions-dropdown"
+                title="Workflow actions"
+                toggle-class="inline-icon-button"
+                variant="link"
+                @show="() => emit('dropdown', true)"
+                @hide="() => emit('dropdown', false)">
+                <template v-slot:button-content>
+                    <FontAwesomeIcon :icon="faCaretDown" fixed-width />
+                </template>
+
+                <template v-if="props.editor">
+                    <BDropdownItem :to="runPath" title="Run workflow" size="sm" variant="link">
+                        <FontAwesomeIcon :icon="faPlay" fixed-width />
+                        Run
+                    </BDropdownItem>
+
+                    <BDropdownItem
+                        v-if="props.workflow.published"
+                        size="sm"
+                        title="Copy link to workflow"
+                        @click="copyPublicLink">
+                        <FontAwesomeIcon :icon="faLink" fixed-width />
+                        Link to Workflow
+                    </BDropdownItem>
+
+                    <BDropdownItem v-if="!isAnonymous && !shared" size="sm" title="Copy workflow" @click="copyWorkflow">
+                        <FontAwesomeIcon :icon="faCopy" fixed-width />
+                        Copy
+                    </BDropdownItem>
+
+                    <BDropdownItem
+                        size="sm"
+                        title="Download workflow in .ga format"
+                        target="_blank"
+                        :href="downloadUrl">
+                        <FontAwesomeIcon :icon="faDownload" fixed-width />
+                        Download
+                    </BDropdownItem>
+
+                    <BDropdownItem
+                        v-if="!isAnonymous && !shared"
+                        size="sm"
+                        title="Share"
+                        :to="`/workflows/sharing?id=${workflow.id}`">
+                        <FontAwesomeIcon :icon="faShareAlt" fixed-width />
+                        Share
+                    </BDropdownItem>
+                </template>
+
+                <BDropdownItem
+                    v-if="!isAnonymous && !shared && !props.workflow.deleted && !props.current"
+                    class="workflow-delete-button"
+                    title="Delete workflow"
+                    size="sm"
+                    @click="deleteWorkflow">
+                    <FontAwesomeIcon :icon="faTrash" fixed-width />
+                    Delete
+                </BDropdownItem>
+
+                <BDropdownItem
+                    v-if="sourceType.includes('trs')"
+                    class="source-trs-button"
+                    :title="`View on ${props.workflow.source_metadata?.trs_server}`"
+                    size="sm"
+                    :href="`https://dockstore.org/workflows${props.workflow?.source_metadata?.trs_tool_id?.slice(9)}`"
+                    target="_blank">
+                    <FontAwesomeIcon :icon="faExternalLinkAlt" fixed-width />
+                    View on Dockstore
+                </BDropdownItem>
+
+                <BDropdownItem
+                    v-if="sourceType == 'url'"
+                    class="workflow-view-external-link-button"
+                    title="View external link"
+                    size="sm"
+                    :href="props.workflow.source_metadata?.url"
+                    target="_blank">
+                    <FontAwesomeIcon :icon="faExternalLinkAlt" fixed-width />
+                    View external link
+                </BDropdownItem>
+
+                <BDropdownItem
+                    v-if="!props.workflow.deleted"
+                    class="workflow-export-button"
+                    title="Export"
+                    size="sm"
+                    :to="`/workflows/export?id=${props.workflow.id}`">
+                    <FontAwesomeIcon :icon="faFileExport" fixed-width />
+                    Export
+                </BDropdownItem>
+            </BDropdown>
+        </BButtonGroup>
+    </div>
+</template>
+
+<style scoped lang="scss">
+.workflow-actions {
+    display: flex;
+    align-items: center;
+}
+</style>
diff --git a/client/src/components/Workflow/List/WorkflowActionsExtend.vue b/client/src/components/Workflow/List/WorkflowActionsExtend.vue
new file mode 100644
index 0000000000000000000000000000000000000000..56082d79ac9cefcd5ed7701ed0c38476c85f628a
--- /dev/null
+++ b/client/src/components/Workflow/List/WorkflowActionsExtend.vue
@@ -0,0 +1,241 @@
+<script setup lang="ts">
+import {
+    faCopy,
+    faDownload,
+    faEdit,
+    faLink,
+    faPlusSquare,
+    faShareAlt,
+    faTrashRestore,
+    faUpload,
+} from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BButtonGroup } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed } from "vue";
+
+import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { undeleteWorkflow } from "@/components/Workflow/workflows.services";
+import { useConfirmDialog } from "@/composables/confirmDialog";
+import { Toast } from "@/composables/toast";
+import { useUserStore } from "@/stores/userStore";
+
+import { useWorkflowActions } from "./useWorkflowActions";
+
+import AsyncButton from "@/components/Common/AsyncButton.vue";
+import WorkflowRunButton from "@/components/Workflow/WorkflowRunButton.vue";
+
+interface Props {
+    workflow: StoredWorkflowDetailed;
+    published?: boolean;
+    editor?: boolean;
+    current?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    published: false,
+    editor: false,
+    current: false,
+});
+
+const emit = defineEmits<{
+    (e: "refreshList", overlayLoading?: boolean): void;
+    (e: "insert"): void;
+    (e: "insertSteps"): void;
+}>();
+
+const userStore = useUserStore();
+const { confirm } = useConfirmDialog();
+const { isAnonymous } = storeToRefs(useUserStore());
+
+const shared = computed(() => {
+    return !userStore.matchesCurrentUsername(props.workflow.owner);
+});
+
+async function onRestore() {
+    const confirmed = await confirm("Are you sure you want to restore this workflow?", "Restore workflow");
+
+    if (confirmed) {
+        await undeleteWorkflow(props.workflow.id);
+        emit("refreshList", true);
+        Toast.info("Workflow restored");
+    }
+}
+
+const editButtonTitle = computed(() => {
+    if (isAnonymous.value) {
+        return "Log in to edit Workflow";
+    } else {
+        if (props.workflow.deleted) {
+            return "You cannot edit a deleted workflow. Restore it first.";
+        } else {
+            return "Edit Workflow";
+        }
+    }
+});
+const importedButtonTitle = computed(() => {
+    if (isAnonymous.value) {
+        return "Log in to import workflow";
+    } else {
+        return "Import this workflow to edit";
+    }
+});
+const runButtonTitle = computed(() => {
+    if (isAnonymous.value) {
+        return "Log in to run workflow";
+    } else {
+        if (props.workflow.deleted) {
+            return "You cannot run a deleted workflow. Restore it first.";
+        } else {
+            return "Run workflow";
+        }
+    }
+});
+
+const { copyPublicLink, copyWorkflow, downloadUrl, importWorkflow } = useWorkflowActions(
+    computed(() => props.workflow),
+    () => emit("refreshList", true)
+);
+</script>
+
+<template>
+    <div class="workflow-card-actions flex-gapx-1">
+        <BButtonGroup>
+            <template v-if="!props.editor && !workflow.deleted">
+                <BButton
+                    v-if="workflow.published"
+                    id="workflow-copy-public-button"
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Copy link to workflow"
+                    variant="outline-primary"
+                    @click="copyPublicLink">
+                    <FontAwesomeIcon :icon="faLink" fixed-width />
+                    <span class="compact-view">Link to Workflow</span>
+                </BButton>
+
+                <BButton
+                    v-if="!isAnonymous && !shared"
+                    id="workflow-copy-button"
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Copy"
+                    variant="outline-primary"
+                    @click="copyWorkflow">
+                    <FontAwesomeIcon :icon="faCopy" fixed-width />
+                    <span class="compact-view">Copy</span>
+                </BButton>
+
+                <BButton
+                    id="workflow-download-button"
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Download workflow in .ga format"
+                    variant="outline-primary"
+                    :href="downloadUrl">
+                    <FontAwesomeIcon :icon="faDownload" fixed-width />
+                    <span class="compact-view">Download</span>
+                </BButton>
+
+                <BButton
+                    v-if="!isAnonymous && !shared"
+                    id="workflow-share-button"
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Share"
+                    variant="outline-primary"
+                    :to="`/workflows/sharing?id=${workflow.id}`">
+                    <FontAwesomeIcon :icon="faShareAlt" fixed-width />
+                    <span class="compact-view">Share</span>
+                </BButton>
+            </template>
+
+            <BButton
+                v-if="workflow.deleted"
+                id="restore-button"
+                v-b-tooltip.hover.noninteractive
+                size="sm"
+                title="Restore"
+                variant="outline-primary"
+                @click="onRestore">
+                <FontAwesomeIcon :icon="faTrashRestore" fixed-width />
+                <span class="compact-view">Restore</span>
+            </BButton>
+        </BButtonGroup>
+
+        <div>
+            <i v-if="props.current" class="mr-2"> current workflow </i>
+
+            <BButton
+                v-if="!isAnonymous && !shared && !props.current"
+                v-b-tooltip.hover.noninteractive
+                :disabled="workflow.deleted"
+                size="sm"
+                class="workflow-edit-button"
+                :title="editButtonTitle"
+                variant="outline-primary"
+                :to="`/workflows/edit?id=${workflow.id}`">
+                <FontAwesomeIcon :icon="faEdit" fixed-width />
+                Edit
+            </BButton>
+
+            <AsyncButton
+                v-else-if="!props.current"
+                v-b-tooltip.hover.noninteractive
+                size="sm"
+                :disabled="isAnonymous"
+                :title="importedButtonTitle"
+                :icon="faUpload"
+                variant="outline-primary"
+                :action="importWorkflow">
+                Import
+            </AsyncButton>
+
+            <WorkflowRunButton
+                v-if="!props.editor"
+                :id="workflow.id"
+                :disabled="isAnonymous || workflow.deleted"
+                :title="runButtonTitle" />
+
+            <BButtonGroup v-if="props.editor && !workflow.deleted">
+                <BButton
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Copy steps into workflow"
+                    variant="outline-primary"
+                    @click="emit('insertSteps')">
+                    <FontAwesomeIcon :icon="faCopy" fixed-width />
+                </BButton>
+
+                <BButton
+                    v-if="!props.current"
+                    v-b-tooltip.hover.noninteractive
+                    size="sm"
+                    title="Insert as sub-workflow"
+                    variant="primary"
+                    @click="emit('insert')">
+                    <FontAwesomeIcon :icon="faPlusSquare" fixed-width />
+                    <span> Insert </span>
+                </BButton>
+            </BButtonGroup>
+        </div>
+    </div>
+</template>
+
+<style scoped lang="scss">
+@import "_breakpoints.scss";
+
+.workflow-card-actions {
+    display: flex;
+    gap: 0.25rem;
+    margin-top: 0.25rem;
+    align-items: center;
+    justify-content: end;
+
+    @container (max-width: #{$breakpoint-md}) {
+        .compact-view {
+            display: none;
+        }
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/List/WorkflowCard.vue b/client/src/components/Workflow/List/WorkflowCard.vue
new file mode 100644
index 0000000000000000000000000000000000000000..953ac58ee5aa446d1e8280907858a8c30e0a71a4
--- /dev/null
+++ b/client/src/components/Workflow/List/WorkflowCard.vue
@@ -0,0 +1,269 @@
+<script setup lang="ts">
+import { faPen } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BButton, BLink } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed, ref } from "vue";
+
+import { updateWorkflow } from "@/components/Workflow/workflows.services";
+import { useUserStore } from "@/stores/userStore";
+
+import TextSummary from "@/components/Common/TextSummary.vue";
+import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
+import WorkflowActions from "@/components/Workflow/List/WorkflowActions.vue";
+import WorkflowActionsExtend from "@/components/Workflow/List/WorkflowActionsExtend.vue";
+import WorkflowIndicators from "@/components/Workflow/List/WorkflowIndicators.vue";
+import WorkflowInvocationsCount from "@/components/Workflow/WorkflowInvocationsCount.vue";
+
+interface Props {
+    workflow: any;
+    gridView?: boolean;
+    hideRuns?: boolean;
+    filterable?: boolean;
+    publishedView?: boolean;
+    editorView?: boolean;
+    current?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    gridView: false,
+    publishedView: false,
+    hideRuns: false,
+    filterable: true,
+    editorView: false,
+    current: false,
+});
+
+const emit = defineEmits<{
+    (e: "tagClick", tag: string): void;
+    (e: "refreshList", overlayLoading?: boolean, silent?: boolean): void;
+    (e: "updateFilter", key: string, value: any): void;
+    (e: "rename", id: string, name: string): void;
+    (e: "preview", id: string): void;
+    (e: "insert"): void;
+    (e: "insertSteps"): void;
+}>();
+
+const userStore = useUserStore();
+
+const { isAnonymous } = storeToRefs(userStore);
+
+const workflow = computed(() => props.workflow);
+
+const shared = computed(() => {
+    return !userStore.matchesCurrentUsername(workflow.value.owner);
+});
+
+const description = computed(() => {
+    if (workflow.value.annotations && workflow.value.annotations.length > 0) {
+        return workflow.value.annotations[0].trim();
+    } else {
+        return null;
+    }
+});
+
+async function onTagsUpdate(tags: string[]) {
+    workflow.value.tags = tags;
+    await updateWorkflow(workflow.value.id, { tags });
+    emit("refreshList", true, true);
+}
+
+async function onTagClick(tag: string) {
+    emit("tagClick", tag);
+}
+
+const dropdownOpen = ref(false);
+</script>
+
+<template>
+    <div
+        class="workflow-card"
+        :class="{ 'dropdown-open': dropdownOpen }"
+        :data-workflow-id="workflow.id"
+        :data-workflow-name="workflow.name">
+        <div
+            class="workflow-card-container"
+            :class="{
+                'workflow-shared': workflow.published,
+            }">
+            <div class="workflow-card-header">
+                <WorkflowIndicators
+                    class="workflow-card-indicators"
+                    :workflow="workflow"
+                    :published-view="publishedView"
+                    :filterable="props.filterable"
+                    @updateFilter="(k, v) => emit('updateFilter', k, v)" />
+
+                <div class="workflow-count-actions">
+                    <WorkflowInvocationsCount
+                        v-if="!props.hideRuns && !isAnonymous && !shared"
+                        class="invocations-count mx-1"
+                        :workflow="workflow" />
+
+                    <WorkflowActions
+                        :workflow="props.workflow"
+                        :published="props.publishedView"
+                        :editor="props.editorView"
+                        :current="props.current"
+                        @refreshList="emit('refreshList', true)"
+                        @dropdown="(open) => (dropdownOpen = open)" />
+                </div>
+
+                <span class="workflow-name font-weight-bold">
+                    <BLink
+                        v-b-tooltip.hover.noninteractive
+                        class="workflow-name-preview"
+                        title="Preview Workflow"
+                        @click.stop.prevent="emit('preview', props.workflow.id)">
+                        {{ workflow.name }}
+                    </BLink>
+                    <BButton
+                        v-if="!props.current && !shared && !workflow.deleted"
+                        v-b-tooltip.hover.noninteractive
+                        :data-workflow-rename="workflow.id"
+                        class="inline-icon-button workflow-rename"
+                        variant="link"
+                        size="sm"
+                        title="Rename"
+                        @click="emit('rename', props.workflow.id, props.workflow.name)">
+                        <FontAwesomeIcon :icon="faPen" fixed-width />
+                    </BButton>
+                </span>
+
+                <TextSummary
+                    v-if="description"
+                    class="workflow-summary my-1"
+                    :description="description"
+                    :max-length="gridView ? 100 : 250" />
+            </div>
+
+            <div class="workflow-card-footer">
+                <div class="workflow-card-tags">
+                    <StatelessTags
+                        clickable
+                        :value="workflow.tags"
+                        :disabled="props.current || isAnonymous || workflow.deleted || shared"
+                        :max-visible-tags="gridView ? 2 : 8"
+                        @input="onTagsUpdate($event)"
+                        @tag-click="onTagClick($event)" />
+                </div>
+
+                <WorkflowActionsExtend
+                    :workflow="workflow"
+                    :published="publishedView"
+                    :editor="editorView"
+                    :current="props.current"
+                    @refreshList="emit('refreshList', true)"
+                    @insert="(...args) => emit('insert', ...args)"
+                    @insertSteps="(...args) => emit('insertSteps', ...args)" />
+            </div>
+        </div>
+    </div>
+</template>
+
+<style scoped lang="scss">
+@import "theme/blue.scss";
+@import "_breakpoints.scss";
+
+.workflow-card {
+    container: workflow-card / inline-size;
+    padding: 0 0.25rem 0.5rem 0.25rem;
+
+    &.dropdown-open {
+        z-index: 10;
+    }
+
+    .workflow-rename {
+        opacity: 0;
+    }
+
+    &:hover,
+    &:focus-within {
+        .workflow-rename {
+            opacity: 1;
+        }
+    }
+
+    .workflow-card-container {
+        height: 100%;
+        display: flex;
+        gap: 0.5rem;
+        flex-direction: column;
+        justify-content: space-between;
+        border: 1px solid $brand-secondary;
+        border-radius: 0.5rem;
+        padding: 0.5rem;
+
+        &.workflow-shared {
+            border-left: 0.25rem solid $brand-primary;
+        }
+
+        .workflow-card-header {
+            display: grid;
+            position: relative;
+            align-items: start;
+            grid-template-areas:
+                "i b"
+                "n n"
+                "s s";
+
+            &:has(.invocations-count) {
+                @container workflow-card (max-width: #{$breakpoint-xs}) {
+                    grid-template-areas:
+                        "i b"
+                        "n b"
+                        "s s";
+                }
+            }
+
+            .workflow-card-indicators {
+                grid-area: i;
+            }
+
+            .workflow-count-actions {
+                grid-area: b;
+                display: flex;
+                align-items: center;
+                flex-direction: row;
+                justify-content: end;
+
+                @container workflow-card (max-width: #{$breakpoint-xs}) {
+                    align-items: end;
+                    flex-direction: column-reverse;
+                }
+            }
+
+            .workflow-name {
+                grid-area: n;
+                font-size: 1rem;
+                font-weight: bold;
+                word-break: break-all;
+            }
+
+            .workflow-summary {
+                grid-area: s;
+            }
+        }
+
+        .workflow-card-footer {
+            display: flex;
+            justify-content: space-between;
+            align-items: end;
+
+            .workflow-card-tags {
+                max-width: 60%;
+            }
+        }
+
+        @container workflow-card (max-width: #{$breakpoint-sm}) {
+            .workflow-card-footer {
+                display: inline-block;
+
+                .workflow-card-tags {
+                    max-width: 100%;
+                }
+            }
+        }
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/List/WorkflowCardList.vue b/client/src/components/Workflow/List/WorkflowCardList.vue
new file mode 100644
index 0000000000000000000000000000000000000000..a4ed88d3a193d5a8412d553ac588aed6b95a6c96
--- /dev/null
+++ b/client/src/components/Workflow/List/WorkflowCardList.vue
@@ -0,0 +1,145 @@
+<script setup lang="ts">
+import { BModal } from "bootstrap-vue";
+import { reactive, ref } from "vue";
+
+import type { Workflow } from "@/components/Workflow/workflows.services";
+
+import WorkflowCard from "./WorkflowCard.vue";
+import WorkflowRename from "./WorkflowRename.vue";
+import WorkflowPublished from "@/components/Workflow/Published/WorkflowPublished.vue";
+
+interface Props {
+    workflows: Workflow[];
+    gridView?: boolean;
+    hideRuns?: boolean;
+    filterable?: boolean;
+    publishedView?: boolean;
+    editorView?: boolean;
+    currentWorkflowId?: string;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "tagClick", tag: string): void;
+    (e: "refreshList", overlayLoading?: boolean, silent?: boolean): void;
+    (e: "updateFilter", key: string, value: any): void;
+    (e: "insertWorkflow", id: string, name: string): void;
+    (e: "insertWorkflowSteps", id: string, stepCount: number): void;
+}>();
+
+const modalOptions = reactive({
+    rename: {
+        id: "",
+        name: "",
+    },
+    preview: {
+        id: "",
+    },
+});
+
+const showRename = ref(false);
+
+function onRenameClose() {
+    showRename.value = false;
+    emit("refreshList", true);
+}
+
+function onRename(id: string, name: string) {
+    modalOptions.rename.id = id;
+    modalOptions.rename.name = name;
+    showRename.value = true;
+}
+
+const showPreview = ref(false);
+
+function onPreview(id: string) {
+    modalOptions.preview.id = id;
+    showPreview.value = true;
+}
+
+// TODO: clean-up types, as soon as better Workflow type is available
+function onInsert(workflow: Workflow) {
+    emit("insertWorkflow", workflow.latest_workflow_id as any, workflow.name as any);
+}
+
+function onInsertSteps(workflow: Workflow) {
+    emit("insertWorkflowSteps", workflow.id as any, workflow.number_of_steps as any);
+}
+</script>
+
+<template>
+    <div class="workflow-card-list" :class="{ grid: props.gridView }">
+        <WorkflowCard
+            v-for="workflow in props.workflows"
+            :key="workflow.id"
+            :workflow="workflow"
+            :grid-view="props.gridView"
+            :hide-runs="props.hideRuns"
+            :filterable="props.filterable"
+            :published-view="props.publishedView"
+            :editor-view="props.editorView"
+            :current="workflow.id === props.currentWorkflowId"
+            class="workflow-card"
+            @tagClick="(...args) => emit('tagClick', ...args)"
+            @refreshList="(...args) => emit('refreshList', ...args)"
+            @updateFilter="(...args) => emit('updateFilter', ...args)"
+            @rename="onRename"
+            @preview="onPreview"
+            @insert="onInsert(workflow)"
+            @insertSteps="onInsertSteps(workflow)">
+        </WorkflowCard>
+
+        <WorkflowRename
+            :id="modalOptions.rename.id"
+            :show="showRename"
+            :name="modalOptions.rename.name"
+            @close="onRenameClose" />
+
+        <BModal
+            v-model="showPreview"
+            ok-only
+            size="xl"
+            hide-header
+            dialog-class="workflow-card-preview-modal w-auto"
+            centered>
+            <WorkflowPublished v-if="showPreview" :id="modalOptions.preview.id" quick-view />
+        </BModal>
+    </div>
+</template>
+
+<style lang="scss">
+.workflow-card-preview-modal {
+    max-width: min(1400px, calc(100% - 200px));
+
+    .modal-content {
+        height: min(800px, calc(100vh - 80px));
+    }
+}
+</style>
+
+<style scoped lang="scss">
+@import "_breakpoints.scss";
+
+.workflow-card-list {
+    container: card-list / inline-size;
+    display: flex;
+    flex-wrap: wrap;
+
+    .workflow-card {
+        width: 100%;
+    }
+
+    &.grid .workflow-card {
+        width: calc(100% / 3);
+
+        @container card-list (max-width: #{$breakpoint-xl}) {
+            width: calc(100% / 2);
+        }
+
+        @container card-list (max-width: #{$breakpoint-sm}) {
+            width: 100%;
+        }
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/WorkflowIndicators.vue b/client/src/components/Workflow/List/WorkflowIndicators.vue
similarity index 67%
rename from client/src/components/Workflow/WorkflowIndicators.vue
rename to client/src/components/Workflow/List/WorkflowIndicators.vue
index 676e56932a03836df015391376dd7986cb4bd042..a0757714555fbfe3a62522906582bb9613f746e6 100644
--- a/client/src/components/Workflow/WorkflowIndicators.vue
+++ b/client/src/components/Workflow/List/WorkflowIndicators.vue
@@ -6,7 +6,7 @@ import { BBadge, BButton } from "bootstrap-vue";
 import { computed } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { Toast } from "@/composables/toast";
+import { useToast } from "@/composables/toast";
 import { useUserStore } from "@/stores/userStore";
 import { copy } from "@/utils/clipboard";
 
@@ -14,43 +14,54 @@ import UtcDate from "@/components/UtcDate.vue";
 
 library.add(faFileImport, faGlobe, faShieldAlt, faUsers, faUser);
 
+// TODO: replace me with a proper definition
+type Workflow = any;
+
 interface Props {
-    workflow: any;
+    workflow: Workflow;
     publishedView: boolean;
+    noEditTime?: boolean;
+    filterable?: boolean;
 }
 
 const props = defineProps<Props>();
 
 const emit = defineEmits<{
-    (e: "update-filter", key: string, value: any): void;
+    (e: "updateFilter", key: string, value: string | boolean): void;
 }>();
 
 const router = useRouter();
 const userStore = useUserStore();
 
 const publishedTitle = computed(() => {
-    if (userStore.currentUser?.username === props.workflow.owner) {
-        return "Published by you. Click to view all published workflows by you";
+    if (props.workflow.published && !props.publishedView) {
+        return "Published workflow" + (props.filterable ? ". Click to filter published workflows" : "");
+    } else if (userStore.matchesCurrentUsername(props.workflow.owner)) {
+        return "Published by you" + (props.filterable ? ". Click to view all published workflows by you" : "");
     } else {
-        return `Published by '${props.workflow.owner}'. Click to view all published workflows by '${props.workflow.owner}'`;
+        return (
+            `Published by '${props.workflow.owner}'` +
+            (props.filterable ? `. Click to view all published workflows by '${props.workflow.owner}'` : "")
+        );
     }
 });
+
 const shared = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username !== props.workflow.owner;
-    } else {
-        return false;
-    }
+    return !userStore.matchesCurrentUsername(props.workflow.owner);
 });
+
 const sourceType = computed(() => {
-    if (props.workflow.source_metadata?.url) {
+    const { url, trs_server, trs_tool_id } = props.workflow.source_metadata || {};
+    const trs = trs_server || trs_tool_id;
+    if (url) {
         return "url";
-    } else if (props.workflow.source_metadata?.trs_server) {
-        return `trs_${props.workflow.source_metadata?.trs_server}`;
+    } else if (trs) {
+        return `trs_${trs}`;
     } else {
         return "";
     }
 });
+
 const sourceTitle = computed(() => {
     if (sourceType.value.includes("trs")) {
         return `Imported from TRS ID (version: ${props.workflow.source_metadata.trs_version_id}). Click to copy ID`;
@@ -61,36 +72,46 @@ const sourceTitle = computed(() => {
     }
 });
 
+const { success } = useToast();
+
 function onCopyLink() {
     if (sourceType.value == "url") {
         copy(props.workflow.source_metadata.url);
-        Toast.success("URL copied");
+        success("URL copied");
     } else if (sourceType.value.includes("trs")) {
         copy(props.workflow.source_metadata.trs_tool_id);
-        Toast.success("TRS ID copied");
+        success("TRS ID copied");
     }
 }
 
 function onViewMySharedByUser() {
     router.push(`/workflows/list_shared_with_me?owner=${props.workflow.owner}`);
-    emit("update-filter", "user", `'${props.workflow.owner}'`);
+    emit("updateFilter", "user", `'${props.workflow.owner}'`);
 }
 
 function onViewUserPublished() {
     router.push(`/workflows/list_published?owner=${props.workflow.owner}`);
-    emit("update-filter", "user", `'${props.workflow.owner}'`);
+    emit("updateFilter", "user", `'${props.workflow.owner}'`);
+}
+
+function getStepText(steps: number) {
+    if (steps === 1) {
+        return "1 step";
+    } else {
+        return `${steps} steps`;
+    }
 }
 </script>
 
 <template>
-    <div>
+    <div class="workflow-indicators">
         <BButton
             v-if="workflow.published && !publishedView"
             v-b-tooltip.noninteractive.hover
             size="sm"
             class="workflow-published-icon inline-icon-button"
-            title="Published workflow. Click to filter published workflows"
-            @click="emit('update-filter', 'published', true)">
+            :title="publishedTitle"
+            @click="emit('updateFilter', 'published', true)">
             <FontAwesomeIcon :icon="faGlobe" fixed-width />
         </BButton>
         <FontAwesomeIcon
@@ -119,13 +140,17 @@ function onViewUserPublished() {
             <FontAwesomeIcon :icon="faFileImport" fixed-width @click="onCopyLink" />
         </BButton>
 
-        <span class="mr-1">
+        <span v-if="!noEditTime" class="mr-1">
             <small>
                 edited
                 <UtcDate :date="workflow.update_time" mode="elapsed" />
             </small>
         </span>
 
+        <BBadge v-if="workflow.number_of_steps" pill class="mr-1 step-count">
+            {{ getStepText(workflow.number_of_steps) }}
+        </BBadge>
+
         <BBadge
             v-if="shared && !publishedView"
             v-b-tooltip.noninteractive.hover
@@ -137,8 +162,9 @@ function onViewUserPublished() {
         </BBadge>
 
         <BBadge
-            v-if="publishedView"
+            v-if="publishedView && workflow.published"
             v-b-tooltip.noninteractive.hover
+            data-description="published owner badge"
             class="outline-badge cursor-pointer mx-1"
             :title="publishedTitle"
             @click="onViewUserPublished">
@@ -151,14 +177,14 @@ function onViewUserPublished() {
 <style scoped lang="scss">
 @import "theme/blue.scss";
 
-.workflow-badge {
-    background: $brand-secondary;
-    color: $brand-primary;
-    border: 1px solid $brand-primary;
+.workflow-indicators {
+    display: flex;
+    align-items: center;
+}
 
-    &:hover {
-        color: $brand-secondary;
-        background: $brand-primary;
-    }
+.step-count {
+    display: grid;
+    place-items: center;
+    height: 1rem;
 }
 </style>
diff --git a/client/src/components/Workflow/WorkflowList.test.ts b/client/src/components/Workflow/List/WorkflowList.test.ts
similarity index 70%
rename from client/src/components/Workflow/WorkflowList.test.ts
rename to client/src/components/Workflow/List/WorkflowList.test.ts
index 6d98ef33714dfa3a788329d675912408122f90f3..4d82fcf08c4f5e95b28b1838a2293739fcb9f3be 100644
--- a/client/src/components/Workflow/WorkflowList.test.ts
+++ b/client/src/components/Workflow/List/WorkflowList.test.ts
@@ -1,31 +1,29 @@
 import { createTestingPinia } from "@pinia/testing";
 import { getLocalVue } from "@tests/jest/helpers";
+import { getFakeRegisteredUser } from "@tests/test-data";
 import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
 import { useUserStore } from "@/stores/userStore";
 
-import { generateRandomWorkflowList } from "./testUtils";
+import { generateRandomWorkflowList } from "../testUtils";
 
 import WorkflowList from "./WorkflowList.vue";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue();
 
+const { server, http } = useServerMock();
+
 const FAKE_USER_ID = "fake_user_id";
 const FAKE_USERNAME = "fake_username";
 const FAKE_USER_EMAIL = "fake_user_email";
-const FAKE_USER = {
+const FAKE_USER = getFakeRegisteredUser({
     id: FAKE_USER_ID,
     email: FAKE_USER_EMAIL,
-    tags_used: [],
-    isAnonymous: false,
     username: FAKE_USERNAME,
-    total_disk_usage: 0,
-};
+});
 
 async function mountWorkflowList() {
     const pinia = createTestingPinia();
@@ -55,12 +53,20 @@ async function mountWorkflowList() {
 }
 
 describe("WorkflowList", () => {
-    afterEach(() => {
-        mockFetcher.clearMocks();
+    beforeEach(() => {
+        server.use(
+            http.get("/api/workflows/{workflow_id}/counts", ({ response }) => {
+                return response(200).json({});
+            })
+        );
     });
 
     it("render empty workflow list", async () => {
-        mockFetcher.path("/api/workflows").method("get").mock({ data: [] });
+        server.use(
+            http.get("/api/workflows", ({ response }) => {
+                return response(200).json([]);
+            })
+        );
 
         const wrapper = await mountWorkflowList();
 
@@ -71,7 +77,12 @@ describe("WorkflowList", () => {
     it("render workflow list", async () => {
         const FAKE_WORKFLOWS = generateRandomWorkflowList(FAKE_USERNAME, 10);
 
-        mockFetcher.path("/api/workflows").method("get").mock({ data: FAKE_WORKFLOWS });
+        server.use(
+            http.get("/api/workflows", ({ response }) => {
+                // TODO: We use untyped here because the response is not yet defined in the schema
+                return response.untyped(HttpResponse.json(FAKE_WORKFLOWS));
+            })
+        );
 
         const wrapper = await mountWorkflowList();
 
@@ -86,7 +97,12 @@ describe("WorkflowList", () => {
         const FAKE_WORKFLOWS = generateRandomWorkflowList(FAKE_USERNAME, 10);
         FAKE_WORKFLOWS.forEach((w) => (w.deleted = true));
 
-        mockFetcher.path("/api/workflows").method("get").mock({ data: FAKE_WORKFLOWS });
+        server.use(
+            http.get("/api/workflows", ({ response }) => {
+                // TODO: We use untyped here because the response is not yet defined in the schema
+                return response.untyped(HttpResponse.json(FAKE_WORKFLOWS));
+            })
+        );
 
         const wrapper = await mountWorkflowList();
 
diff --git a/client/src/components/Workflow/WorkflowList.vue b/client/src/components/Workflow/List/WorkflowList.vue
similarity index 83%
rename from client/src/components/Workflow/WorkflowList.vue
rename to client/src/components/Workflow/List/WorkflowList.vue
index 3cbda017cc013fd6f1b845fdde182a6fb41b400e..327c514bd495af437034b9a9a2592b619f0cd2ae 100644
--- a/client/src/components/Workflow/WorkflowList.vue
+++ b/client/src/components/Workflow/List/WorkflowList.vue
@@ -7,19 +7,19 @@ import { filter } from "underscore";
 import { computed, onMounted, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { loadWorkflows } from "@/components/Workflow/workflows.services";
+import { GalaxyApi } from "@/api";
+import { getWorkflowFilters, helpHtml } from "@/components/Workflow/List/workflowFilters";
 import { Toast } from "@/composables/toast";
 import { useUserStore } from "@/stores/userStore";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import { helpHtml, WorkflowFilters } from "./WorkflowFilters";
-
+import WorkflowCardList from "./WorkflowCardList.vue";
 import FilterMenu from "@/components/Common/FilterMenu.vue";
 import Heading from "@/components/Common/Heading.vue";
 import ListHeader from "@/components/Common/ListHeader.vue";
 import LoginRequired from "@/components/Common/LoginRequired.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
-import WorkflowCard from "@/components/Workflow/WorkflowCard.vue";
-import WorkflowListActions from "@/components/Workflow/WorkflowListActions.vue";
+import WorkflowListActions from "@/components/Workflow/List/WorkflowListActions.vue";
 
 library.add(faStar, faTrash);
 
@@ -44,7 +44,6 @@ const overlay = ref(false);
 const filterText = ref("");
 const totalWorkflows = ref(0);
 const showAdvanced = ref(false);
-const showBookmarked = ref(false);
 const listHeader = ref<any>(null);
 const workflowsLoaded = ref<WorkflowsList>([]);
 
@@ -65,6 +64,7 @@ const searchPlaceHolder = computed(() => {
 const published = computed(() => props.activeList === "published");
 const sharedWithMe = computed(() => props.activeList === "shared_with_me");
 const showDeleted = computed(() => filterText.value.includes("is:deleted"));
+const showBookmarked = computed(() => filterText.value.includes("is:bookmarked"));
 const currentPage = computed(() => Math.floor(offset.value / limit.value) + 1);
 const view = computed(() => (userStore.preferredListViewMode as ListView) || "grid");
 const sortDesc = computed(() => (listHeader.value && listHeader.value.sortDesc) ?? true);
@@ -77,7 +77,7 @@ const bookmarkButtonTitle = computed(() =>
 );
 
 // Filtering computed refs
-const workflowFilters = computed(() => WorkflowFilters(props.activeList));
+const workflowFilters = computed(() => getWorkflowFilters(props.activeList));
 const rawFilters = computed(() =>
     Object.fromEntries(workflowFilters.value.getFiltersForText(filterText.value, true, false))
 );
@@ -91,17 +91,12 @@ function updateFilterValue(filterKey: string, newValue: any) {
     filterText.value = workflowFilters.value.setFilterValue(currentFilterText, filterKey, newValue);
 }
 
-function toggleBookmarked(bookmarked?: boolean) {
-    showBookmarked.value = bookmarked ?? !showBookmarked.value;
-}
-
 function onToggleBookmarked() {
-    toggleBookmarked();
+    updateFilterValue("bookmarked", true);
 }
 
 function onToggleDeleted() {
     updateFilterValue("deleted", true);
-    toggleBookmarked(false);
 }
 
 async function load(overlayLoading = false, silent = false) {
@@ -131,31 +126,33 @@ async function load(overlayLoading = false, silent = false) {
     }
 
     try {
-        const { data, headers } = await loadWorkflows({
-            sortBy: sortBy.value,
-            sortDesc: sortDesc.value,
-            limit: limit.value,
-            offset: offset.value,
-            filterText: search?.trim(),
-            showPublished: published.value,
-            skipStepCounts: true,
+        const { response, data, error } = await GalaxyApi().GET("/api/workflows", {
+            params: {
+                query: {
+                    sort_by: sortBy.value,
+                    sort_desc: sortDesc.value,
+                    limit: limit.value,
+                    offset: offset.value,
+                    search: search?.trim(),
+                    show_published: published.value,
+                    skip_step_counts: true,
+                },
+            },
         });
 
-        let filteredWorkflows = showBookmarked.value
-            ? filter(data, (workflow: any) => workflow.show_in_tool_panel)
-            : data;
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        let filteredWorkflows = data;
 
         if (props.activeList === "my") {
-            filteredWorkflows = filter(filteredWorkflows, (w: any) => w.owner === userStore.currentUser?.username);
+            filteredWorkflows = filter(filteredWorkflows, (w: any) => userStore.matchesCurrentUsername(w.owner));
         }
 
         workflowsLoaded.value = filteredWorkflows;
 
-        if (showBookmarked.value) {
-            totalWorkflows.value = filteredWorkflows.length;
-        } else {
-            totalWorkflows.value = parseInt(headers.get("Total_matches") || "0", 10) || 0;
-        }
+        totalWorkflows.value = parseInt(response.headers.get("Total_matches") || "0", 10) || 0;
     } catch (e) {
         Toast.error(`Failed to load workflows: ${e}`);
     } finally {
@@ -181,7 +178,7 @@ function validatedFilterText() {
     return workflowFilters.value.getFilterText(validFilters.value, true);
 }
 
-watch([filterText, sortBy, sortDesc, showBookmarked], async () => {
+watch([filterText, sortBy, sortDesc], async () => {
     offset.value = 0;
     await load(true);
 });
@@ -261,7 +258,6 @@ onMounted(() => {
                             size="sm"
                             :title="bookmarkButtonTitle"
                             :pressed="showBookmarked"
-                            :disabled="showDeleted"
                             variant="outline-primary"
                             @click="onToggleBookmarked">
                             <FontAwesomeIcon :icon="faStar" fixed-width />
@@ -309,23 +305,14 @@ onMounted(() => {
             </BAlert>
         </span>
 
-        <BOverlay
-            v-else
-            id="workflow-cards"
-            :show="overlay"
-            rounded="sm"
-            class="cards-list mt-2"
-            :class="view === 'grid' ? 'd-flex flex-wrap' : ''">
-            <WorkflowCard
-                v-for="w in workflowsLoaded"
-                :key="w.id"
-                :workflow="w"
+        <BOverlay v-else id="workflow-cards" :show="overlay" rounded="sm" class="cards-list mt-2">
+            <WorkflowCardList
+                :workflows="workflowsLoaded"
                 :published-view="published"
                 :grid-view="view === 'grid'"
-                :class="view === 'grid' ? 'grid-view' : 'list-view'"
                 @refreshList="load"
                 @tagClick="(tag) => updateFilterValue('tag', `'${tag}'`)"
-                @update-filter="updateFilterValue" />
+                @updateFilter="updateFilterValue" />
 
             <BPagination
                 v-if="!loading && totalWorkflows > limit"
@@ -342,9 +329,6 @@ onMounted(() => {
 </template>
 
 <style lang="scss">
-@import "scss/mixins.scss";
-@import "breakpoints.scss";
-
 .workflows-list {
     overflow: auto;
     display: flex;
@@ -362,32 +346,13 @@ onMounted(() => {
     }
 
     .cards-list {
-        container: card-list / inline-size;
         scroll-behavior: smooth;
         min-height: 150px;
+        display: flex;
+        flex-direction: column;
 
         overflow-y: auto;
         overflow-x: hidden;
-
-        .list-view {
-            width: 100%;
-        }
-
-        .grid-view {
-            width: calc(100% / 3);
-        }
-
-        @container card-list (max-width: #{$breakpoint-xl}) {
-            .grid-view {
-                width: calc(100% / 2);
-            }
-        }
-
-        @container card-list (max-width: #{$breakpoint-sm}) {
-            .grid-view {
-                width: 100%;
-            }
-        }
     }
 }
 </style>
diff --git a/client/src/components/Workflow/WorkflowListActions.vue b/client/src/components/Workflow/List/WorkflowListActions.vue
similarity index 100%
rename from client/src/components/Workflow/WorkflowListActions.vue
rename to client/src/components/Workflow/List/WorkflowListActions.vue
diff --git a/client/src/components/Workflow/WorkflowRename.vue b/client/src/components/Workflow/List/WorkflowRename.vue
similarity index 100%
rename from client/src/components/Workflow/WorkflowRename.vue
rename to client/src/components/Workflow/List/WorkflowRename.vue
diff --git a/client/src/style/scss/breakpoints.scss b/client/src/components/Workflow/List/_breakpoints.scss
similarity index 83%
rename from client/src/style/scss/breakpoints.scss
rename to client/src/components/Workflow/List/_breakpoints.scss
index 641b39ff9d2b9da250271445c4fae75b39dbb1fe..d758c7980ec2b41e3fb18be0534b1907f6a96ba3 100644
--- a/client/src/style/scss/breakpoints.scss
+++ b/client/src/components/Workflow/List/_breakpoints.scss
@@ -1,3 +1,4 @@
+$breakpoint-xs: 300px;
 $breakpoint-sm: 576px;
 $breakpoint-md: 768px;
 $breakpoint-lg: 992px;
diff --git a/client/src/components/Workflow/List/useWorkflowActions.ts b/client/src/components/Workflow/List/useWorkflowActions.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d1900f86a5a613c709da197dffc3a0158ff2822a
--- /dev/null
+++ b/client/src/components/Workflow/List/useWorkflowActions.ts
@@ -0,0 +1,96 @@
+import { computed, type Ref, ref } from "vue";
+
+import type { StoredWorkflowDetailed } from "@/api/workflows";
+import {
+    copyWorkflow as copyWorkflowService,
+    deleteWorkflow as deleteWorkflowService,
+    updateWorkflow as updateWorkflowService,
+} from "@/components/Workflow/workflows.services";
+import { useConfirmDialog } from "@/composables/confirmDialog";
+import { useToast } from "@/composables/toast";
+import { copy } from "@/utils/clipboard";
+import { withPrefix } from "@/utils/redirect";
+import { getFullAppUrl } from "@/utils/utils";
+
+type Workflow = StoredWorkflowDetailed;
+
+export function useWorkflowActions(workflow: Ref<Workflow>, refreshCallback: () => void) {
+    const toast = useToast();
+
+    const bookmarkLoading = ref(false);
+
+    const toggleBookmark = async (checked: boolean) => {
+        try {
+            bookmarkLoading.value = true;
+
+            await updateWorkflowService(workflow.value.id, {
+                show_in_tool_panel: checked,
+            });
+
+            toast.info(`Workflow ${checked ? "added to" : "removed from"} bookmarks`);
+        } catch (error) {
+            toast.error("Failed to update workflow bookmark status");
+        } finally {
+            refreshCallback();
+            bookmarkLoading.value = false;
+        }
+    };
+
+    const { confirm } = useConfirmDialog();
+
+    const deleteWorkflow = async () => {
+        const confirmed = await confirm("Are you sure you want to delete this workflow?", {
+            title: "Delete workflow",
+            okTitle: "Delete",
+            okVariant: "danger",
+        });
+
+        if (confirmed) {
+            await deleteWorkflowService(workflow.value.id);
+            refreshCallback();
+            toast.info("Workflow deleted");
+        }
+    };
+
+    const relativeLink = computed(() => {
+        return `/published/workflow?id=${workflow.value.id}`;
+    });
+
+    const fullLink = computed(() => {
+        return getFullAppUrl(relativeLink.value.substring(1));
+    });
+
+    function copyPublicLink() {
+        copy(fullLink.value);
+        toast.success("Link to workflow copied");
+    }
+
+    async function copyWorkflow() {
+        const confirmed = await confirm("Are you sure you want to make a copy of this workflow?", "Copy workflow");
+
+        if (confirmed) {
+            await copyWorkflowService(workflow.value.id, workflow.value.owner);
+            refreshCallback();
+            toast.success("Workflow copied");
+        }
+    }
+
+    const downloadUrl = computed(() => {
+        return withPrefix(`/api/workflows/${workflow.value.id}/download?format=json-download`);
+    });
+
+    async function importWorkflow() {
+        await copyWorkflowService(workflow.value.id, workflow.value.owner);
+        toast.success("Workflow imported successfully");
+    }
+
+    return {
+        bookmarkLoading,
+        toggleBookmark,
+        deleteWorkflow,
+        copyPublicLink,
+        copyWorkflow,
+        importWorkflow,
+        downloadUrl,
+    };
+}
diff --git a/client/src/components/Workflow/WorkflowFilters.js b/client/src/components/Workflow/List/workflowFilters.ts
similarity index 94%
rename from client/src/components/Workflow/WorkflowFilters.js
rename to client/src/components/Workflow/List/workflowFilters.ts
index 1280b6e450a5332cf4754e938a09e54f1d1d572e..47f523b0a66ebed9cd7a729239d653c1eeb61556 100644
--- a/client/src/components/Workflow/WorkflowFilters.js
+++ b/client/src/components/Workflow/List/workflowFilters.ts
@@ -1,4 +1,4 @@
-import Filtering, { contains, equals, expandNameTag, toBool } from "utils/filtering";
+import Filtering, { contains, equals, expandNameTag, toBool } from "@/utils/filtering";
 
 export function helpHtml(activeList = "my") {
     let extra = "";
@@ -71,7 +71,7 @@ export function helpHtml(activeList = "my") {
     return conditionalHelpHtml;
 }
 
-export function WorkflowFilters(activeList = "my") {
+export function getWorkflowFilters(activeList = "my") {
     const commonFilters = {
         name: { placeholder: "name", type: String, handler: contains("name"), menuItem: true },
         n: { handler: contains("n"), menuItem: false },
@@ -82,7 +82,7 @@ export function WorkflowFilters(activeList = "my") {
             menuItem: true,
         },
         t: { type: "MultiTags", handler: contains("t", "t", expandNameTag), menuItem: false },
-    };
+    } as const;
 
     if (activeList === "my") {
         return new Filtering(
@@ -116,6 +116,13 @@ export function WorkflowFilters(activeList = "my") {
                     handler: equals("deleted", "deleted", toBool),
                     menuItem: true,
                 },
+                bookmarked: {
+                    placeholder: "Bookmarked",
+                    type: Boolean,
+                    boolType: "is",
+                    handler: equals("bookmarked", "bookmarked", toBool),
+                    menuItem: true,
+                },
             },
             undefined,
             false,
diff --git a/client/src/components/Workflow/Published/WorkflowInformation.vue b/client/src/components/Workflow/Published/WorkflowInformation.vue
index b9d9afb1acb5d7c99269ebabe114e47f873c86b1..dc41bdd27c85115d68c851e47f5e88faa69388cb 100644
--- a/client/src/components/Workflow/Published/WorkflowInformation.vue
+++ b/client/src/components/Workflow/Published/WorkflowInformation.vue
@@ -5,6 +5,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { computed } from "vue";
 import { RouterLink } from "vue-router";
 
+import { type WorkflowSummary } from "@/api/workflows";
 import { useUserStore } from "@/stores/userStore";
 import { getFullAppUrl } from "@/utils/utils";
 
@@ -16,19 +17,8 @@ import UtcDate from "@/components/UtcDate.vue";
 
 library.add(faBuilding, faUser);
 
-interface WorkflowInformation {
-    name: string;
-    [key: string]: unknown;
-    update_time: string;
-    license?: string;
-    tags?: string[];
-    creator?: {
-        [key: string]: unknown;
-    }[];
-}
-
 interface Props {
-    workflowInfo: WorkflowInformation;
+    workflowInfo: WorkflowSummary;
     embedded?: boolean;
 }
 
@@ -51,11 +41,7 @@ const fullLink = computed(() => {
 });
 
 const userOwned = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username === props.workflowInfo.owner;
-    } else {
-        return false;
-    }
+    return userStore.matchesCurrentUsername(props.workflowInfo.owner);
 });
 </script>
 
diff --git a/client/src/components/Workflow/Published/WorkflowPublished.vue b/client/src/components/Workflow/Published/WorkflowPublished.vue
index d2c14b7d18b3a3c31b7380d450489d6b18b7232e..524623314ab739262de8aae7198ee1499f06e98c 100644
--- a/client/src/components/Workflow/Published/WorkflowPublished.vue
+++ b/client/src/components/Workflow/Published/WorkflowPublished.vue
@@ -6,6 +6,7 @@ import { type AxiosError } from "axios";
 import { BAlert, BButton, BCard } from "bootstrap-vue";
 import { computed, onMounted, ref, watch } from "vue";
 
+import { type WorkflowSummary } from "@/api/workflows";
 import { fromSimple } from "@/components/Workflow/Editor/modules/model";
 import { getWorkflowFull, getWorkflowInfo } from "@/components/Workflow/workflows.services";
 import { useDatatypesMapper } from "@/composables/datatypesMapper";
@@ -22,14 +23,6 @@ import WorkflowInformation from "@/components/Workflow/Published/WorkflowInforma
 
 library.add(faBuilding, faDownload, faEdit, faPlay, faSpinner, faUser);
 
-type WorkflowInfo = {
-    name: string;
-    [key: string]: unknown;
-    license?: string;
-    tags?: string[];
-    update_time: string;
-};
-
 interface Props {
     id: string;
     zoom?: number;
@@ -65,7 +58,7 @@ const { stateStore } = provideScopedWorkflowStores(props.id);
 
 const loading = ref(true);
 const errorMessage = ref("");
-const workflowInfo = ref<WorkflowInfo>();
+const workflowInfo = ref<WorkflowSummary>();
 const workflow = ref<Workflow | null>(null);
 
 const hasError = computed(() => !!errorMessage.value);
@@ -80,13 +73,11 @@ const initialPosition = computed(() => ({
 }));
 
 const viewUrl = computed(() => withPrefix(`/published/workflow?id=${props.id}`));
+
 const sharedWorkflow = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username !== workflowInfo.value?.owner;
-    } else {
-        return false;
-    }
+    return !userStore.matchesCurrentUsername(workflowInfo.value?.owner);
 });
+
 const editButtonTitle = computed(() => {
     if (userStore.isAnonymous) {
         return "Log in to edit Workflow";
diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index 5f3a97e7dad07445311528066730905b2dfc219a..478652170197debb6ad9c246b88dafed7d0e9f80 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -1,12 +1,12 @@
 <script setup lang="ts">
 import { BAlert, BLink } from "bootstrap-vue";
-import { storeToRefs } from "pinia";
 import { computed, onMounted, ref, watch } from "vue";
 import { RouterLink } from "vue-router";
 import { useRouter } from "vue-router/composables";
 
 import { canMutateHistory } from "@/api";
-import { copyWorkflow } from "@/components/Workflow/workflows.services";
+import { copyWorkflow, getWorkflowInfo } from "@/components/Workflow/workflows.services";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
 import { useHistoryItemsStore } from "@/stores/historyItemsStore";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
@@ -22,7 +22,7 @@ import WorkflowRunSuccess from "@/components/Workflow/Run/WorkflowRunSuccess.vue
 
 const historyStore = useHistoryStore();
 const historyItemsStore = useHistoryItemsStore();
-const { currentUser } = storeToRefs(useUserStore());
+const userStore = useUserStore();
 const router = useRouter();
 
 interface Props {
@@ -31,6 +31,8 @@ interface Props {
     preferSimpleForm?: boolean;
     simpleFormTargetHistory?: string;
     simpleFormUseJobCache?: boolean;
+    requestState?: Record<string, never>;
+    instance?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
@@ -38,6 +40,8 @@ const props = withDefaults(defineProps<Props>(), {
     preferSimpleForm: false,
     simpleFormTargetHistory: "current",
     simpleFormUseJobCache: false,
+    requestState: undefined,
+    instance: false,
 });
 
 const loading = ref(true);
@@ -49,13 +53,14 @@ const submissionError = ref("");
 const workflowError = ref("");
 const workflowName = ref("");
 const workflowModel: any = ref(null);
+const owner = ref<string>();
 
 const currentHistoryId = computed(() => historyStore.currentHistoryId);
 const editorLink = computed(
     () => `/workflows/edit?id=${props.workflowId}${props.version ? `&version=${props.version}` : ""}`
 );
 const historyStatusKey = computed(() => `${currentHistoryId.value}_${lastUpdateTime.value}`);
-const isOwner = computed(() => currentUser.value?.username === workflowModel.value.runData.owner);
+const isOwner = computed(() => userStore.matchesCurrentUsername(owner.value));
 const lastUpdateTime = computed(() => historyItemsStore.lastUpdateTime);
 const canRunOnHistory = computed(() => {
     if (!currentHistoryId.value) {
@@ -65,6 +70,16 @@ const canRunOnHistory = computed(() => {
     return (history && canMutateHistory(history)) ?? false;
 });
 
+if (props.instance) {
+    const { workflow } = useWorkflowInstance(props.workflowId);
+    watch(workflow, () => {
+        if (workflow.value) {
+            workflowName.value = workflow.value?.name;
+            owner.value = workflow.value?.owner;
+        }
+    });
+}
+
 function handleInvocations(incomingInvocations: any) {
     invocations.value = incomingInvocations;
     // make sure any new histories are added to historyStore
@@ -79,7 +94,7 @@ function handleSubmissionError(error: string) {
 
 async function loadRun() {
     try {
-        const runData = await getRunData(props.workflowId, props.version || undefined);
+        const runData = await getRunData(props.workflowId, props.version || undefined, props.instance);
         const incomingModel = new WorkflowRunModel(runData);
 
         simpleForm.value = props.preferSimpleForm;
@@ -113,14 +128,31 @@ async function loadRun() {
         hasStepVersionChanges.value = incomingModel.hasStepVersionChanges;
         workflowName.value = incomingModel.name;
         workflowModel.value = incomingModel;
+        owner.value = incomingModel.runData.owner;
         loading.value = false;
     } catch (e) {
-        workflowError.value = errorMessageAsString(e);
+        const errMessage = errorMessageAsString(e);
+        if (errMessage === "Workflow step has upgrade messages") {
+            hasUpgradeMessages.value = true;
+            if (!props.instance) {
+                try {
+                    const storedWorkflow = await getWorkflowInfo(props.workflowId);
+                    owner.value = storedWorkflow.owner;
+                    workflowName.value = storedWorkflow.name;
+                } catch {
+                    // just show original error
+                    workflowError.value = errMessage;
+                }
+            }
+        } else {
+            workflowError.value = errMessage;
+        }
+        loading.value = false;
     }
 }
 
 async function onImport() {
-    const response = await copyWorkflow(props.workflowId, workflowModel.value.runData.owner, props.version);
+    const response = await copyWorkflow(props.workflowId, owner.value, props.version);
     router.push(`/workflows/edit?id=${response.id}`);
 }
 
@@ -192,15 +224,21 @@ defineExpose({
                     <span>before running this workflow.</span>
                 </BAlert>
                 <div v-else>
-                    <BAlert v-if="submissionError" class="mb-4" variant="danger" show>
+                    <BAlert
+                        v-if="submissionError"
+                        class="mb-4"
+                        variant="danger"
+                        data-description="workflow run error"
+                        show>
                         Workflow submission failed: {{ submissionError }}
                     </BAlert>
                     <WorkflowRunFormSimple
-                        v-else-if="fromVariant === 'simple'"
+                        v-if="fromVariant === 'simple'"
                         :model="workflowModel"
                         :target-history="simpleFormTargetHistory"
                         :use-job-cache="simpleFormUseJobCache"
                         :can-mutate-current-history="canRunOnHistory"
+                        :request-state="requestState"
                         @submissionSuccess="handleInvocations"
                         @submissionError="handleSubmissionError"
                         @showAdvanced="showAdvanced" />
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index e7e45723ff1694f9298255d0cec9ea8489464e16..eb87089b20ea56b97b1648fc5ea71af4afaaad38 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,56 +1,60 @@
 <template>
     <div>
-        <div v-if="isConfigLoaded" class="h4 clearfix mb-3">
+        <div class="ui-form-header-underlay sticky-top" />
+        <div v-if="isConfigLoaded" class="sticky-top">
             <BAlert v-if="!canRunOnHistory" variant="warning" show>
                 <span v-localize>
                     The workflow cannot run because the current history is immutable. Please select a different history
                     or send the results to a new one using the run settings ⚙️
                 </span>
             </BAlert>
-            <b>Workflow: {{ model.name }}</b> <i>(version: {{ model.runData.version + 1 }})</i>
-            <ButtonSpinner
-                id="run-workflow"
-                :wait="waitingForRequest"
-                :disabled="hasValidationErrors || !canRunOnHistory"
-                class="float-right"
-                title="Run Workflow"
-                @onClick="onExecute" />
-            <b-dropdown
-                v-if="showRuntimeSettings(currentUser)"
-                id="dropdown-form"
-                ref="dropdown"
-                class="workflow-run-settings float-right"
-                style="margin-right: 10px"
-                title="Workflow Run Settings"
-                no-caret>
-                <template v-slot:button-content>
-                    <span class="fa fa-cog" />
+            <WorkflowNavigationTitle
+                :workflow-id="model.runData.workflow_id"
+                :run-disabled="hasValidationErrors || !canRunOnHistory"
+                :run-waiting="waitingForRequest"
+                @on-execute="onExecute">
+                <template v-slot:workflow-title-actions>
+                    <b-dropdown
+                        v-if="showRuntimeSettings(currentUser)"
+                        id="dropdown-form"
+                        ref="dropdown"
+                        class="workflow-run-settings"
+                        title="Workflow Run Settings"
+                        size="sm"
+                        variant="link"
+                        no-caret>
+                        <template v-slot:button-content>
+                            <span class="fa fa-cog" />
+                        </template>
+                        <b-dropdown-form>
+                            <b-form-checkbox v-model="sendToNewHistory" class="workflow-run-settings-target">
+                                Send results to a new history
+                            </b-form-checkbox>
+                            <b-form-checkbox
+                                v-if="reuseAllowed(currentUser)"
+                                v-model="useCachedJobs"
+                                title="This may skip executing jobs that you have already run.">
+                                Attempt to re-use jobs with identical parameters?
+                            </b-form-checkbox>
+                            <b-form-checkbox
+                                v-if="isConfigLoaded && config.object_store_allows_id_selection"
+                                v-model="splitObjectStore">
+                                Send outputs and intermediate to different storage locations?
+                            </b-form-checkbox>
+                            <WorkflowStorageConfiguration
+                                v-if="isConfigLoaded && config.object_store_allows_id_selection"
+                                :split-object-store="splitObjectStore"
+                                :invocation-preferred-object-store-id="preferredObjectStoreId"
+                                :invocation-intermediate-preferred-object-store-id="preferredIntermediateObjectStoreId"
+                                @updated="onStorageUpdate">
+                            </WorkflowStorageConfiguration>
+                        </b-dropdown-form>
+                    </b-dropdown>
                 </template>
-                <b-dropdown-form>
-                    <b-form-checkbox v-model="sendToNewHistory" class="workflow-run-settings-target">
-                        Send results to a new history
-                    </b-form-checkbox>
-                    <b-form-checkbox
-                        v-if="reuseAllowed(currentUser)"
-                        v-model="useCachedJobs"
-                        title="This may skip executing jobs that you have already run.">
-                        Attempt to re-use jobs with identical parameters?
-                    </b-form-checkbox>
-                    <b-form-checkbox
-                        v-if="isConfigLoaded && config.object_store_allows_id_selection"
-                        v-model="splitObjectStore">
-                        Send outputs and intermediate to different storage locations?
-                    </b-form-checkbox>
-                    <WorkflowStorageConfiguration
-                        v-if="isConfigLoaded && config.object_store_allows_id_selection"
-                        :split-object-store="splitObjectStore"
-                        :invocation-preferred-object-store-id="preferredObjectStoreId"
-                        :invocation-intermediate-preferred-object-store-id="preferredIntermediateObjectStoreId"
-                        @updated="onStorageUpdate">
-                    </WorkflowStorageConfiguration>
-                </b-dropdown-form>
-            </b-dropdown>
+            </WorkflowNavigationTitle>
         </div>
+
+        <WorkflowAnnotation :workflow-id="model.runData.workflow_id" :history-id="model.historyId" show-details />
         <FormDisplay
             :inputs="formInputs"
             :allow-empty-value-on-required-input="true"
@@ -62,7 +66,6 @@
 </template>
 
 <script>
-import ButtonSpinner from "components/Common/ButtonSpinner";
 import FormDisplay from "components/Form/FormDisplay";
 import { allowCachedJobs } from "components/Tool/utilities";
 import { isWorkflowInput } from "components/Workflow/constants";
@@ -76,10 +79,14 @@ import { useUserStore } from "@/stores/userStore";
 import { invokeWorkflow } from "./services";
 import WorkflowStorageConfiguration from "./WorkflowStorageConfiguration";
 
+import WorkflowAnnotation from "../../Workflow/WorkflowAnnotation.vue";
+import WorkflowNavigationTitle from "../WorkflowNavigationTitle.vue";
+
 export default {
     components: {
-        ButtonSpinner,
         FormDisplay,
+        WorkflowAnnotation,
+        WorkflowNavigationTitle,
         WorkflowStorageConfiguration,
     },
     props: {
@@ -99,6 +106,10 @@ export default {
             type: Boolean,
             required: true,
         },
+        requestState: {
+            type: Object,
+            required: false,
+        },
     },
     setup() {
         const { config, isConfigLoaded } = useConfig(true);
@@ -135,6 +146,7 @@ export default {
                 if (isWorkflowInput(step.step_type)) {
                     const stepName = new String(step.step_index);
                     const stepLabel = step.step_label || new String(step.step_index + 1);
+                    const stepType = step.step_type;
                     const help = step.annotation;
                     const longFormInput = step.inputs[0];
                     const stepAsInput = Object.assign({}, longFormInput, {
@@ -142,10 +154,14 @@ export default {
                         help: help,
                         label: stepLabel,
                     });
+                    if (this.requestState && this.requestState[stepLabel]) {
+                        const value = this.requestState[stepLabel];
+                        stepAsInput.value = value;
+                    }
                     // disable collection mapping...
                     stepAsInput.flavor = "module";
                     inputs.push(stepAsInput);
-                    this.inputTypes[stepName] = step.step_type;
+                    this.inputTypes[stepName] = stepType;
                 }
             });
             return inputs;
diff --git a/client/src/components/Workflow/Run/WorkflowRunSuccess.vue b/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
index 4beabd2a4f04418cd400f8b277844864fedf65ec..f5d71a820167003e877903d961ad51ed1462853c 100644
--- a/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
@@ -1,102 +1,59 @@
+<script setup lang="ts">
+import { onMounted } from "vue";
+
+import type { WorkflowInvocation } from "@/api/invocations";
+import { useHistoryStore } from "@/stores/historyStore";
+import { refreshContentsWrapper } from "@/utils/data";
+import Webhooks from "@/utils/webhooks";
+
+import GridInvocation from "@/components/Grid/GridInvocation.vue";
+import WorkflowInvocationState from "@/components/WorkflowInvocationState/WorkflowInvocationState.vue";
+
+const props = defineProps<{
+    workflowName: string;
+    invocations: WorkflowInvocation[];
+}>();
+
+onMounted(() => {
+    new Webhooks.WebhookView({
+        type: "workflow",
+        toolId: null,
+        toolVersion: null,
+    });
+    refreshContentsWrapper();
+});
+
+const historyStore = useHistoryStore();
+
+const targetHistories = props.invocations.reduce((histories, invocation) => {
+    if (invocation.history_id && !histories.includes(invocation.history_id)) {
+        histories.push(invocation.history_id);
+    }
+    return histories;
+}, [] as string[]);
+const wasNewHistoryTarget =
+    props.invocations.length > 0 &&
+    !!props.invocations[0]?.history_id &&
+    historyStore.currentHistoryId !== props.invocations[0].history_id;
+</script>
+
 <template>
     <div>
-        <div class="donemessagelarge">
-            <p>
-                Successfully invoked workflow <b>{{ workflowName }}</b>
-                <em v-if="multipleInvocations"> - {{ timesExecuted }} times</em>.
-            </p>
-
-            <p v-if="multipleHistoryTargets">
+        <div v-if="props.invocations.length > 1" class="donemessagelarge">
+            Successfully invoked workflow <b>{{ props.workflowName }}</b>
+            <em> - {{ props.invocations.length }} times</em>.
+            <span v-if="targetHistories.length > 1">
                 This workflow will generate results in multiple histories. You can observe progress in the
                 <router-link to="/histories/view_multiple">history multi-view</router-link>.
-            </p>
-            <p v-else-if="wasNewHistoryTarget">
-                This workflow will generate results in a new history.
-                <a class="workflow-new-history-target-link" href="javascript:void(0)" @click="switchHistory"
-                    >Switch to that history now</a
-                >.
-            </p>
-            <p v-else>You can check the status of queued jobs and view the resulting data the History panel.</p>
-            <p>
-                View all of your workflow invocations in the
-                <router-link to="/workflows/invocations">Invocations List</router-link>.
-            </p>
+            </span>
         </div>
+        <GridInvocation v-if="props.invocations.length > 1" :invocations-list="props.invocations" />
         <WorkflowInvocationState
-            v-for="(invocation, index) in invocations"
-            :key="invocation.id"
-            :index="index"
-            :invocation-id="invocation.id"
-            full-page />
+            v-else-if="props.invocations.length === 1 && props.invocations[0]"
+            :invocation-id="props.invocations[0].id"
+            :new-history-target="wasNewHistoryTarget"
+            is-full-page
+            success />
         <div id="webhook-view"></div>
     </div>
 </template>
-
-<script>
-import WorkflowInvocationState from "components/WorkflowInvocationState/WorkflowInvocationState";
-import { getAppRoot } from "onload/loadConfig";
-import { mapActions, mapState } from "pinia";
-import { refreshContentsWrapper } from "utils/data";
-import Webhooks from "utils/webhooks";
-
-import { useHistoryStore } from "@/stores/historyStore";
-
-export default {
-    components: {
-        WorkflowInvocationState,
-    },
-    props: {
-        workflowName: {
-            type: String,
-            required: true,
-        },
-        invocations: {
-            type: Array,
-            required: true,
-        },
-    },
-    computed: {
-        ...mapState(useHistoryStore, ["currentHistoryId"]),
-        timesExecuted() {
-            return this.invocations.length;
-        },
-        multipleInvocations() {
-            return this.timesExecuted > 1;
-        },
-        multipleHistoryTargets() {
-            return this.targetHistories.length > 1;
-        },
-        targetHistories() {
-            return this.invocations.reduce((histories, invocation) => {
-                if (invocation.history_id && !histories.includes(invocation.history_id)) {
-                    histories.push(invocation.history_id);
-                }
-                return histories;
-            }, []);
-        },
-        multiHistoryView() {
-            return `${getAppRoot()}histories/view_multiple`;
-        },
-        wasNewHistoryTarget() {
-            if (this.invocations.length < 1) {
-                return false;
-            }
-            return this.invocations[0].history_id && this.currentHistoryId != this.invocations[0].history_id;
-        },
-    },
-    mounted() {
-        new Webhooks.WebhookView({
-            type: "workflow",
-            toolId: null,
-            toolVersion: null,
-        });
-        refreshContentsWrapper();
-    },
-    methods: {
-        ...mapActions(useHistoryStore, ["setCurrentHistory"]),
-        async switchHistory() {
-            await this.setCurrentHistory(this.invocations[0].history_id);
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Workflow/Run/WorkflowSelectPreferredObjectStore.test.js b/client/src/components/Workflow/Run/WorkflowSelectPreferredObjectStore.test.js
index e29b8c70eb1cb8066b722c70e2f5cc3567e93683..c83456a58c3d6959f8f6c14cef6f74c150cac1ee 100644
--- a/client/src/components/Workflow/Run/WorkflowSelectPreferredObjectStore.test.js
+++ b/client/src/components/Workflow/Run/WorkflowSelectPreferredObjectStore.test.js
@@ -2,6 +2,7 @@ import { mount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useServerMock } from "@/api/client/__mocks__";
 import { setupSelectableMock } from "@/components/ObjectStore/mockServices";
 import { ROOT_COMPONENT } from "@/utils/navigation";
 
@@ -11,7 +12,15 @@ setupSelectableMock();
 
 const localVue = getLocalVue(true);
 
+const { server, http } = useServerMock();
+
 function mountComponent() {
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json({});
+        })
+    );
+
     const wrapper = mount(WorkflowSelectPreferredObjectStore, {
         propsData: { invocationPreferredObjectStoreId: null },
         localVue,
@@ -27,6 +36,7 @@ describe("WorkflowSelectPreferredObjectStore.vue", () => {
         await flushPromises();
         const els = wrapper.findAll(PREFERENCES.object_store_selection.option_buttons.selector);
         expect(els.length).toBe(3);
+
         const galaxyDefaultOption = wrapper.find(
             PREFERENCES.object_store_selection.option_button({ object_store_id: "__null__" }).selector
         );
diff --git a/client/src/components/Workflow/Run/WorkflowStorageConfiguration.vue b/client/src/components/Workflow/Run/WorkflowStorageConfiguration.vue
index d67dc2b5a191200d17be347660f32c9bf0034655..893ecc310dcdff59426ce68e8baeeeb2b80c9360 100644
--- a/client/src/components/Workflow/Run/WorkflowStorageConfiguration.vue
+++ b/client/src/components/Workflow/Run/WorkflowStorageConfiguration.vue
@@ -91,7 +91,7 @@ export default {
             return `Invocation ${this.preferredOrEmptyString} Storage Location`;
         },
         intermediateModalTitle() {
-            return `Invocation {{ preferredOrEmptyString }} Storage Location (Intermediate Datasets)`;
+            return `Invocation ${this.preferredOrEmptyString} Storage Location (Intermediate Datasets)`;
         },
         suffixPrimary() {
             if (this.splitObjectStore) {
diff --git a/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue b/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue
index ba9bccf13a361fd587d573a9c5fe471a3e7cfbc3..b45d5eab24df8b65db8038c7fd41f452d61b3499 100644
--- a/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue
+++ b/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue
@@ -13,7 +13,7 @@
                 used.
             </div>
             <div v-localize>
-                Change {{ preferredOrEmptyString }} storage location by clicking on the storage button in the worklfow
+                Change {{ preferredOrEmptyString }} storage location by clicking on the storage button in the workflow
                 run header.
             </div>
         </div>
diff --git a/client/src/components/Workflow/Run/model.js b/client/src/components/Workflow/Run/model.js
index 29eeca92c369f4a53f97a39701028ff9bacce68b..1238146d7ba6934305f56b9ed25f48ffae6b3930 100644
--- a/client/src/components/Workflow/Run/model.js
+++ b/client/src/components/Workflow/Run/model.js
@@ -136,34 +136,30 @@ export class WorkflowRunModel {
         // or if an explicit reference is specified as data_ref and available
         _.each(this.steps, (step) => {
             if (step.step_type == "tool") {
-                var data_resolved = true;
+                let dataResolved = true;
                 visitInputs(step.inputs, (input, name, context) => {
-                    var is_runtime_value = input.value && input.value.__class__ == "RuntimeValue";
-                    var is_data_input = ["data", "data_collection"].indexOf(input.type) != -1;
-                    var data_ref = context[input.data_ref];
+                    const isRuntimeValue = input.value && input.value.__class__ == "RuntimeValue";
+                    const isDataInput = ["data", "data_collection"].indexOf(input.type) != -1;
+                    const dataRef = context[input.data_ref];
                     if (input.step_linked && !isDataStep(input.step_linked)) {
-                        data_resolved = false;
+                        dataResolved = false;
                     }
-                    if (input.options && ((input.options.length == 0 && !data_resolved) || input.wp_linked)) {
+                    if (input.options && ((input.options.length == 0 && !dataResolved) || input.wp_linked)) {
                         input.is_workflow = true;
                     }
-                    if (data_ref) {
+                    if (dataRef) {
                         input.is_workflow =
-                            (data_ref.step_linked && !isDataStep(data_ref.step_linked)) || input.wp_linked;
+                            (dataRef.step_linked && !isDataStep(dataRef.step_linked)) || input.wp_linked;
                     }
-                    if (
-                        !input.optional &&
-                        (is_data_input ||
-                            (input.value && input.value.__class__ == "RuntimeValue" && !input.step_linked))
-                    ) {
+                    if ((isDataInput && !input.optional) || (!isDataInput && isRuntimeValue && !input.step_linked)) {
                         step.expanded = true;
                         hasOpenToolSteps = true;
                     }
-                    if (is_runtime_value) {
+                    if (isRuntimeValue) {
                         input.value = null;
                     }
                     input.flavor = "workflow";
-                    if (!is_runtime_value && !is_data_input && input.type !== "hidden" && !input.wp_linked) {
+                    if (!isRuntimeValue && !isDataInput && input.type !== "hidden" && !input.wp_linked) {
                         if (input.optional || (!isEmpty(input.value) && input.value !== "")) {
                             input.collapsible_value = input.value;
                             input.collapsible_preview = true;
diff --git a/client/src/components/Workflow/Run/services.js b/client/src/components/Workflow/Run/services.js
index c6c841a09a790f63df59bdc0bcfe1df622e93f7b..107ce4a4b8b208e2f019b9a147b768b151afc2ef 100644
--- a/client/src/components/Workflow/Run/services.js
+++ b/client/src/components/Workflow/Run/services.js
@@ -12,8 +12,8 @@ import { rethrowSimple } from "utils/simple-error";
  * @param {String} workflowId - (Stored?) Workflow ID to fetch data for.
  * @param {String} version - Version of the workflow to fetch.
  */
-export async function getRunData(workflowId, version = null) {
-    let url = `${getAppRoot()}api/workflows/${workflowId}/download?style=run`;
+export async function getRunData(workflowId, version = null, instance = false) {
+    let url = `${getAppRoot()}api/workflows/${workflowId}/download?style=run&instance=${instance}`;
     if (version) {
         url += `&version=${version}`;
     }
diff --git a/client/src/components/Workflow/StoredWorkflowInvocations.vue b/client/src/components/Workflow/StoredWorkflowInvocations.vue
index 6d8bab09616c72c5d8c74805e10b29be227ce508..f76442af2be0365f2deb3b62bbdec3898262ad5a 100644
--- a/client/src/components/Workflow/StoredWorkflowInvocations.vue
+++ b/client/src/components/Workflow/StoredWorkflowInvocations.vue
@@ -2,7 +2,9 @@
 import { BAlert } from "bootstrap-vue";
 import { onMounted, ref } from "vue";
 
-import { type StoredWorkflowDetailed, workflowFetcher } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
+import { type StoredWorkflowDetailed } from "@/api/workflows";
+import { rethrowSimple } from "@/utils/simple-error";
 
 import GridInvocation from "../Grid/GridInvocation.vue";
 import LoadingSpan from "../LoadingSpan.vue";
@@ -13,14 +15,19 @@ interface Props {
 const props = defineProps<Props>();
 
 const loading = ref(true);
-const workflow = ref<StoredWorkflowDetailed | undefined>(undefined);
+const workflow = ref<StoredWorkflowDetailed>();
 
 onMounted(async () => {
     try {
-        const { data } = await workflowFetcher({ workflow_id: props.storedWorkflowId });
+        const { data, error } = await GalaxyApi().GET("/api/workflows/{workflow_id}", {
+            params: { path: { workflow_id: props.storedWorkflowId } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
         workflow.value = data;
-    } catch (error) {
-        console.error(error);
     } finally {
         loading.value = false;
     }
diff --git a/client/src/components/Workflow/WorkflowActions.vue b/client/src/components/Workflow/WorkflowActions.vue
deleted file mode 100644
index c7422119e868b1c384da1387dda38ee593b06fb7..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/WorkflowActions.vue
+++ /dev/null
@@ -1,276 +0,0 @@
-<script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faStar as farStar } from "@fortawesome/free-regular-svg-icons";
-import {
-    faCaretDown,
-    faExternalLinkAlt,
-    faEye,
-    faFileExport,
-    faStar,
-    faTrash,
-} from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
-import { storeToRefs } from "pinia";
-import { computed, type ComputedRef } from "vue";
-
-import { getGalaxyInstance } from "@/app";
-import { deleteWorkflow, updateWorkflow } from "@/components/Workflow/workflows.services";
-import { useConfirmDialog } from "@/composables/confirmDialog";
-import { Toast } from "@/composables/toast";
-import { useUserStore } from "@/stores/userStore";
-
-import type { ColorVariant } from "../Common";
-
-import AsyncButton from "@/components/Common/AsyncButton.vue";
-
-library.add(faCaretDown, faExternalLinkAlt, faEye, faFileExport, farStar, faStar, faTrash);
-
-interface Props {
-    workflow: any;
-    menu?: boolean;
-    published?: boolean;
-    buttonSize?: "sm" | "md" | "lg";
-}
-
-type BaseAction = {
-    condition?: boolean;
-    class?: string;
-    title: string;
-    tooltip?: string;
-    icon: any;
-    href?: string;
-    target?: "_blank";
-    size: "sm" | "md" | "lg";
-    component: "async" | "button";
-    variant: ColorVariant | "link";
-    onClick?: (e?: MouseEvent | KeyboardEvent) => void;
-};
-
-interface AAction extends BaseAction {
-    component: "async";
-    action: () => Promise<void>;
-}
-
-interface BAction extends BaseAction {
-    component: "button";
-    to?: string;
-}
-
-const props = withDefaults(defineProps<Props>(), {
-    buttonSize: "sm",
-});
-
-const emit = defineEmits<{
-    (e: "refreshList", a?: boolean): void;
-    (e: "toggleShowPreview", a?: boolean): void;
-}>();
-
-const userStore = useUserStore();
-const { isAnonymous } = storeToRefs(userStore);
-const { confirm } = useConfirmDialog();
-
-const shared = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username !== props.workflow.owner;
-    } else {
-        return false;
-    }
-});
-const sourceType = computed(() => {
-    if (props.workflow.source_metadata?.url) {
-        return "url";
-    } else if (props.workflow.source_metadata?.trs_server) {
-        return `trs_${props.workflow.source_metadata?.trs_server}`;
-    } else {
-        return "";
-    }
-});
-
-async function onToggleBookmark(checked: boolean) {
-    await updateWorkflow(props.workflow.id, {
-        show_in_tool_panel: checked,
-    });
-
-    emit("refreshList", true);
-
-    Toast.info(`Workflow ${checked ? "added to" : "removed from"} bookmarks`);
-
-    if (checked) {
-        getGalaxyInstance().config.stored_workflow_menu_entries.push({
-            id: props.workflow.id,
-            name: props.workflow.name,
-        });
-    } else {
-        const indexToRemove = getGalaxyInstance().config.stored_workflow_menu_entries.findIndex(
-            (w: any) => w.id === props.workflow.id
-        );
-        getGalaxyInstance().config.stored_workflow_menu_entries.splice(indexToRemove, 1);
-    }
-}
-
-async function onDelete() {
-    const confirmed = await confirm("Are you sure you want to delete this workflow?", {
-        title: "Delete workflow",
-        okTitle: "Delete",
-        okVariant: "danger",
-    });
-
-    if (confirmed) {
-        await deleteWorkflow(props.workflow.id);
-        emit("refreshList", true);
-        Toast.info("Workflow deleted");
-    }
-}
-
-const actions: ComputedRef<(AAction | BAction)[]> = computed(() => {
-    return [
-        {
-            condition: !props.workflow.deleted && !props.workflow.show_in_tool_panel,
-            class: "workflow-bookmark-button-add",
-            component: "async",
-            title: "Add bookmarks",
-            tooltip: "Add to bookmarks. This workflow will appear in the left tool panel.",
-            icon: farStar,
-            size: props.buttonSize,
-            variant: "link",
-            action: () => onToggleBookmark(true),
-        },
-        {
-            condition: !props.workflow.deleted && props.workflow.show_in_tool_panel,
-            class: "workflow-bookmark-button-remove",
-            component: "async",
-            title: "Remove bookmark",
-            tooltip: "Remove bookmark",
-            icon: faStar,
-            size: props.buttonSize,
-            variant: "link",
-            action: () => onToggleBookmark(false),
-        },
-        {
-            condition: true,
-            class: "workflow-view-button",
-            component: "button",
-            title: "View workflow",
-            tooltip: "View workflow",
-            icon: faEye,
-            size: props.buttonSize,
-            variant: "link",
-            onClick: () => emit("toggleShowPreview", true),
-        },
-    ];
-});
-
-const menuActions: ComputedRef<BAction[]> = computed(() => {
-    return [
-        {
-            condition: !isAnonymous.value && !shared.value && !props.workflow.deleted,
-            class: "workflow-delete-button",
-            component: "button",
-            title: "Delete workflow",
-            tooltip: "Delete workflow",
-            icon: faTrash,
-            size: props.buttonSize,
-            variant: "link",
-            onClick: () => onDelete(),
-        },
-        {
-            condition: sourceType.value.includes("trs"),
-            class: "source-trs-button",
-            component: "button",
-            title: `View on ${props.workflow.source_metadata?.trs_server}`,
-            href: `https://dockstore.org/workflows${props.workflow?.source_metadata?.trs_tool_id?.slice(9)}`,
-            target: "_blank",
-            icon: faExternalLinkAlt,
-            size: props.buttonSize,
-            variant: "link",
-        },
-        {
-            condition: sourceType.value == "url",
-            class: "workflow-view-external-link-button",
-            component: "button",
-            title: "View external link",
-            href: props.workflow.source_metadata?.url,
-            target: "_blank",
-            icon: faExternalLinkAlt,
-            size: props.buttonSize,
-            variant: "link",
-        },
-        {
-            condition: !props.workflow.deleted,
-            class: "workflow-export-button",
-            component: "button",
-            title: "Export",
-            icon: faFileExport,
-            size: props.buttonSize,
-            variant: "link",
-            to: `/workflows/export?id=${props.workflow.id}`,
-        },
-    ];
-});
-</script>
-
-<template>
-    <div class="workflow-actions">
-        <div v-for="action in actions" :key="action.class">
-            <AsyncButton
-                v-if="action.condition && action.component === 'async'"
-                v-b-tooltip.hover.noninteractive
-                :class="action.class"
-                class="inline-icon-button mr-1"
-                :variant="action.variant"
-                :size="action.size"
-                :title="action.tooltip"
-                :icon="action.icon"
-                :action="action.action" />
-
-            <BButton
-                v-else-if="action.condition && action.component === 'button'"
-                v-b-tooltip.hover.noninteractive
-                :class="action.class"
-                class="inline-icon-button mr-1"
-                :variant="action.variant"
-                :size="action.size"
-                :title="action.tooltip"
-                :href="action.href"
-                :to="action.to"
-                @click="action.onClick">
-                <FontAwesomeIcon :icon="action.icon" fixed-width />
-            </BButton>
-        </div>
-
-        <BDropdown
-            v-b-tooltip.top.noninteractive
-            :data-workflow-actions-dropdown="workflow.id"
-            right
-            no-caret
-            class="workflow-actions-dropdown"
-            toggle-class="inline-icon-button"
-            title="Workflow actions"
-            variant="link">
-            <template v-slot:button-content>
-                <FontAwesomeIcon :icon="faCaretDown" fixed-width />
-            </template>
-
-            <BDropdownItem
-                v-for="action in menuActions.filter((a) => a.condition).reverse()"
-                :key="action.class"
-                :class="action.class"
-                :href="action.href"
-                :title="action.title"
-                :target="action.target"
-                :to="action.to"
-                @click="action.onClick?.()">
-                <FontAwesomeIcon :icon="action.icon" fixed-width />
-                <span>{{ action.title }}</span>
-            </BDropdownItem>
-        </BDropdown>
-    </div>
-</template>
-
-<style scoped lang="scss">
-.workflow-actions {
-    display: flex;
-    align-items: center;
-}
-</style>
diff --git a/client/src/components/Workflow/WorkflowActionsExtend.vue b/client/src/components/Workflow/WorkflowActionsExtend.vue
deleted file mode 100644
index 98d0484e45cae78a0543a87f76fe04837373f257..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/WorkflowActionsExtend.vue
+++ /dev/null
@@ -1,164 +0,0 @@
-<script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faCopy, faDownload, faLink, faShareAlt, faTrashRestore } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
-import { storeToRefs } from "pinia";
-import { computed } from "vue";
-
-import { copyWorkflow, undeleteWorkflow } from "@/components/Workflow/workflows.services";
-import { useConfirmDialog } from "@/composables/confirmDialog";
-import { Toast } from "@/composables/toast";
-import { useUserStore } from "@/stores/userStore";
-import { copy } from "@/utils/clipboard";
-import { withPrefix } from "@/utils/redirect";
-import { getFullAppUrl } from "@/utils/utils";
-
-library.add(faCopy, faDownload, faLink, faShareAlt, faTrashRestore);
-
-interface Props {
-    workflow: any;
-    menu?: boolean;
-    published?: boolean;
-    buttonSize?: "sm" | "md" | "lg";
-}
-
-const props = withDefaults(defineProps<Props>(), {
-    buttonSize: "sm",
-});
-
-const emit = defineEmits<{
-    (e: "refreshList", overlayLoading?: boolean): void;
-}>();
-
-const userStore = useUserStore();
-const { confirm } = useConfirmDialog();
-const { isAnonymous } = storeToRefs(useUserStore());
-
-const downloadUrl = computed(() => {
-    return withPrefix(`/api/workflows/${props.workflow.id}/download?format=json-download`);
-});
-const shared = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username !== props.workflow.owner;
-    } else {
-        return false;
-    }
-});
-
-async function onCopy() {
-    const confirmed = await confirm("Are you sure you want to make a copy of this workflow?", "Copy workflow");
-
-    if (confirmed) {
-        await copyWorkflow(props.workflow.id, props.workflow.owner);
-        emit("refreshList", true);
-        Toast.success("Workflow copied");
-    }
-}
-
-async function onRestore() {
-    const confirmed = await confirm("Are you sure you want to restore this workflow?", "Restore workflow");
-
-    if (confirmed) {
-        await undeleteWorkflow(props.workflow.id);
-        emit("refreshList", true);
-        Toast.info("Workflow restored");
-    }
-}
-
-const relativeLink = computed(() => {
-    return `/published/workflow?id=${props.workflow.id}`;
-});
-
-const fullLink = computed(() => {
-    return getFullAppUrl(relativeLink.value.substring(1));
-});
-
-function onCopyPublicLink() {
-    copy(fullLink.value);
-    Toast.success("Link to workflow copied");
-}
-</script>
-
-<template>
-    <div class="workflow-actions-extend flex-gapx-1">
-        <BButtonGroup>
-            <BButton
-                v-if="workflow.published && !workflow.deleted"
-                id="workflow-copy-public-button"
-                v-b-tooltip.hover.noninteractive
-                :size="buttonSize"
-                title="Copy link to workflow"
-                variant="outline-primary"
-                @click="onCopyPublicLink">
-                <FontAwesomeIcon :icon="faLink" fixed-width />
-                <span class="compact-view">Link to Workflow</span>
-            </BButton>
-
-            <BButton
-                v-if="!isAnonymous && !shared && !workflow.deleted"
-                id="workflow-copy-button"
-                v-b-tooltip.hover.noninteractive
-                :size="buttonSize"
-                title="Copy"
-                variant="outline-primary"
-                @click="onCopy">
-                <FontAwesomeIcon :icon="faCopy" fixed-width />
-                <span class="compact-view">Copy</span>
-            </BButton>
-
-            <BButton
-                v-if="!workflow.deleted"
-                id="workflow-download-button"
-                v-b-tooltip.hover.noninteractive
-                :size="buttonSize"
-                title="Download workflow in .ga format"
-                variant="outline-primary"
-                :href="downloadUrl">
-                <FontAwesomeIcon :icon="faDownload" fixed-width />
-                <span class="compact-view">Download</span>
-            </BButton>
-
-            <BButton
-                v-if="!isAnonymous && !shared && !workflow.deleted"
-                id="workflow-share-button"
-                v-b-tooltip.hover.noninteractive
-                :size="buttonSize"
-                title="Share"
-                variant="outline-primary"
-                :to="`/workflows/sharing?id=${workflow.id}`">
-                <FontAwesomeIcon :icon="faShareAlt" fixed-width />
-                <span class="compact-view">Share</span>
-            </BButton>
-
-            <BButton
-                v-if="workflow.deleted"
-                id="restore-button"
-                v-b-tooltip.hover.noninteractive
-                :size="buttonSize"
-                title="Restore"
-                variant="outline-primary"
-                @click="onRestore">
-                <FontAwesomeIcon :icon="faTrashRestore" fixed-width />
-                <span class="compact-view">Restore</span>
-            </BButton>
-        </BButtonGroup>
-    </div>
-</template>
-
-<style scoped lang="scss">
-@import "breakpoints.scss";
-
-.workflow-actions-extend {
-    display: flex;
-    align-items: baseline;
-    flex-wrap: wrap;
-    justify-content: flex-end;
-
-    @container (max-width: #{$breakpoint-md}) {
-        .compact-view {
-            display: none;
-        }
-    }
-}
-</style>
diff --git a/client/src/components/Workflow/WorkflowAnnotation.test.ts b/client/src/components/Workflow/WorkflowAnnotation.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..597810fe7c2a62655191c5bbc4fed3e8e7dbb07f
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowAnnotation.test.ts
@@ -0,0 +1,170 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
+import { mount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
+import WorkflowAnnotation from "./WorkflowAnnotation.vue";
+
+// Constants
+const WORKFLOW_OWNER = "test-user";
+const OTHER_USER = "other-user";
+const WORKFLOW_UPDATE_TIME = "2023-01-01T00:00:00.000Z";
+const INVOCATION_TIME = "2024-01-01T00:00:00.000Z";
+const SAMPLE_WORKFLOW = {
+    id: "workflow-id",
+    name: "workflow-name",
+    owner: WORKFLOW_OWNER,
+    version: 1,
+    update_time: WORKFLOW_UPDATE_TIME,
+};
+const OTHER_USER_WORKFLOW_ID = "other-user-workflow-id";
+const SAMPLE_RUN_COUNT = 100;
+const TEST_HISTORY_ID = "test-history-id";
+const TEST_HISTORY = {
+    id: TEST_HISTORY_ID,
+    name: "fake-history-name",
+};
+
+const SELECTORS = {
+    RUN_COUNT: ".workflow-invocations-count",
+    INDICATORS_LINK: '[data-description="published owner badge"]',
+    SWITCH_TO_HISTORY_LINK: "[data-description='switch to history link']",
+    TIME_INFO: '[data-description="workflow annotation time info"]',
+    DATE: '[data-description="workflow annotation date"]',
+};
+
+// Mock the workflow store to return the sample workflow
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((id: string) => {
+                if (id === OTHER_USER_WORKFLOW_ID) {
+                    return { ...SAMPLE_WORKFLOW, id: OTHER_USER_WORKFLOW_ID, published: true };
+                }
+                return SAMPLE_WORKFLOW;
+            }),
+        }),
+    };
+});
+
+jest.mock("@/stores/historyStore"),
+    () => {
+        const originalModule = jest.requireActual("@/stores/historyStore");
+        return {
+            ...originalModule,
+            useHistoryStore: () => ({
+                ...originalModule.useHistoryStore(),
+                getHistoryById: jest.fn().mockImplementation(() => TEST_HISTORY),
+            }),
+        };
+    };
+
+const localVue = getLocalVue();
+const { server, http } = useServerMock();
+
+/**
+ * Mounts the WorkflowAnnotation component with props/stores adjusted given the parameters
+ * @param version The version of the component to mount (`run_form` or `invocation` view)
+ * @param ownsWorkflow Whether the user owns the workflow
+ * @returns The wrapper object
+ */
+async function mountWorkflowAnnotation(version: "run_form" | "invocation", ownsWorkflow = true) {
+    server.use(
+        http.get("/api/histories/{history_id}", ({ response }) => {
+            return response(200).json(TEST_HISTORY);
+        })
+    );
+    server.use(
+        http.get("/api/workflows/{workflow_id}/counts", ({ response }) => {
+            return response(200).json({ scheduled: SAMPLE_RUN_COUNT });
+        })
+    );
+
+    const wrapper = mount(WorkflowAnnotation as object, {
+        propsData: {
+            workflowId: ownsWorkflow ? SAMPLE_WORKFLOW.id : OTHER_USER_WORKFLOW_ID,
+            historyId: TEST_HISTORY_ID,
+            invocationUpdateTime: version === "invocation" ? INVOCATION_TIME : undefined,
+            showDetails: version === "run_form",
+        },
+        localVue,
+        pinia: createTestingPinia(),
+        stubs: {
+            FontAwesomeIcon: true,
+        },
+    });
+
+    const historyStore = useHistoryStore();
+    historyStore.setCurrentHistoryId(TEST_HISTORY_ID);
+
+    const userStore = useUserStore();
+    userStore.currentUser = getFakeRegisteredUser({
+        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
+    });
+
+    await flushPromises();
+
+    return { wrapper };
+}
+
+describe("WorkflowAnnotation renders", () => {
+    it("the run count and history, not indicators if owned not published", async () => {
+        async function checkHasRunCount(version: "run_form" | "invocation") {
+            const { wrapper } = await mountWorkflowAnnotation(version);
+
+            const runCount = wrapper.find(SELECTORS.RUN_COUNT);
+            expect(runCount.text()).toContain("workflow runs:");
+            expect(runCount.text()).toContain(SAMPLE_RUN_COUNT.toString());
+
+            if (version === "run_form") {
+                expect(wrapper.find(SELECTORS.SWITCH_TO_HISTORY_LINK).exists()).toBe(false);
+            } else {
+                expect(wrapper.find(SELECTORS.SWITCH_TO_HISTORY_LINK).text()).toBe(TEST_HISTORY.name);
+            }
+
+            // Since this is the user's own workflow, the indicators link
+            // (to view all published workflows by the owner) should not be present
+            expect(wrapper.find(SELECTORS.INDICATORS_LINK).exists()).toBe(false);
+        }
+        await checkHasRunCount("run_form");
+        await checkHasRunCount("invocation");
+    });
+
+    it("workflow indicators if the user does not own the workflow", async () => {
+        // we assume it is another user's published workflow in this case
+
+        async function checkHasIndicators(version: "run_form" | "invocation") {
+            const { wrapper } = await mountWorkflowAnnotation(version, false);
+
+            const indicatorsLink = wrapper.find(SELECTORS.INDICATORS_LINK);
+            expect(indicatorsLink.text()).toBe(WORKFLOW_OWNER);
+            expect(indicatorsLink.attributes("title")).toContain(`Published by '${WORKFLOW_OWNER}'`);
+        }
+        await checkHasIndicators("run_form");
+        await checkHasIndicators("invocation");
+    });
+
+    it("renders time since edit if run form view", async () => {
+        const { wrapper } = await mountWorkflowAnnotation("run_form");
+
+        const timeInfo = wrapper.find(SELECTORS.TIME_INFO);
+        expect(timeInfo.text()).toContain("edited");
+        expect(timeInfo.find(SELECTORS.DATE).attributes("title")).toBe(WORKFLOW_UPDATE_TIME);
+    });
+
+    it("renders time since invocation if invocation view", async () => {
+        const { wrapper } = await mountWorkflowAnnotation("invocation");
+
+        const timeInfo = wrapper.find(SELECTORS.TIME_INFO);
+        expect(timeInfo.text()).toContain("invoked");
+        expect(timeInfo.find(SELECTORS.DATE).attributes("title")).toBe(INVOCATION_TIME);
+    });
+});
diff --git a/client/src/components/Workflow/WorkflowAnnotation.vue b/client/src/components/Workflow/WorkflowAnnotation.vue
new file mode 100644
index 0000000000000000000000000000000000000000..0f77ff3a12b755cf7033de94cc7d4a691d3b0f91
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowAnnotation.vue
@@ -0,0 +1,100 @@
+<script setup lang="ts">
+import { faClock } from "@fortawesome/free-regular-svg-icons";
+import { faExclamation, faHdd } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed } from "vue";
+
+import { isRegisteredUser } from "@/api";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
+import TextSummary from "../Common/TextSummary.vue";
+import SwitchToHistoryLink from "../History/SwitchToHistoryLink.vue";
+import StatelessTags from "../TagsMultiselect/StatelessTags.vue";
+import UtcDate from "../UtcDate.vue";
+import WorkflowInvocationsCount from "../Workflow/WorkflowInvocationsCount.vue";
+import WorkflowIndicators from "@/components/Workflow/List/WorkflowIndicators.vue";
+
+interface Props {
+    workflowId: string;
+    invocationUpdateTime?: string;
+    historyId: string;
+    showDetails?: boolean;
+    newHistoryTarget?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    invocationUpdateTime: undefined,
+});
+
+const { workflow } = useWorkflowInstance(props.workflowId);
+
+const { currentUser } = storeToRefs(useUserStore());
+const owned = computed(() => {
+    if (isRegisteredUser(currentUser.value) && workflow.value) {
+        return currentUser.value.username === workflow.value.owner;
+    } else {
+        return false;
+    }
+});
+
+const description = computed(() => {
+    if (workflow.value?.annotation) {
+        return workflow.value.annotation?.trim();
+    } else {
+        return null;
+    }
+});
+
+const timeElapsed = computed(() => {
+    return props.invocationUpdateTime || workflow.value?.update_time;
+});
+
+const workflowTags = computed(() => {
+    return workflow.value?.tags || [];
+});
+</script>
+
+<template>
+    <div v-if="workflow" class="pb-2 pl-2">
+        <div class="d-flex justify-content-between align-items-center">
+            <div>
+                <i v-if="timeElapsed" data-description="workflow annotation time info">
+                    <FontAwesomeIcon :icon="faClock" class="mr-1" />
+                    <span v-localize>
+                        {{ props.invocationUpdateTime ? "invoked" : "edited" }}
+                    </span>
+                    <UtcDate :date="timeElapsed" mode="elapsed" data-description="workflow annotation date" />
+                </i>
+                <span v-if="invocationUpdateTime" class="d-flex flex-gapx-1 align-items-center">
+                    <FontAwesomeIcon :icon="faHdd" />History:
+                    <SwitchToHistoryLink :history-id="props.historyId" />
+                    <BBadge
+                        v-if="props.newHistoryTarget && useHistoryStore().currentHistoryId !== props.historyId"
+                        v-b-tooltip.hover.noninteractive
+                        data-description="new history badge"
+                        role="button"
+                        variant="info"
+                        title="Results generated in a new history. Click on history name to switch to that history.">
+                        <FontAwesomeIcon :icon="faExclamation" />
+                    </BBadge>
+                </span>
+            </div>
+            <slot name="middle-content" />
+            <div class="d-flex align-items-center">
+                <div class="d-flex flex-column align-items-end mr-2 flex-gapy-1">
+                    <WorkflowIndicators :workflow="workflow" published-view no-edit-time />
+                    <WorkflowInvocationsCount v-if="owned" class="mr-1" :workflow="workflow" />
+                </div>
+            </div>
+        </div>
+        <div v-if="props.showDetails">
+            <TextSummary v-if="description" class="my-1" :description="description" one-line-summary component="span" />
+            <StatelessTags v-if="workflowTags.length" :value="workflowTags" :disabled="true" />
+            <hr class="mb-0 mt-2" />
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Workflow/WorkflowCard.vue b/client/src/components/Workflow/WorkflowCard.vue
deleted file mode 100644
index f0df64bcebd826fbe941e6f89c40686b2fd1a60c..0000000000000000000000000000000000000000
--- a/client/src/components/Workflow/WorkflowCard.vue
+++ /dev/null
@@ -1,352 +0,0 @@
-<script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faEdit, faEye, faPen, faUpload } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BButton } from "bootstrap-vue";
-import { storeToRefs } from "pinia";
-import { computed, ref } from "vue";
-
-import { copyWorkflow, updateWorkflow } from "@/components/Workflow/workflows.services";
-import { Toast } from "@/composables/toast";
-import { useUserStore } from "@/stores/userStore";
-
-import AsyncButton from "@/components/Common/AsyncButton.vue";
-import TextSummary from "@/components/Common/TextSummary.vue";
-import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
-import WorkflowPublished from "@/components/Workflow/Published/WorkflowPublished.vue";
-import WorkflowActions from "@/components/Workflow/WorkflowActions.vue";
-import WorkflowActionsExtend from "@/components/Workflow/WorkflowActionsExtend.vue";
-import WorkflowIndicators from "@/components/Workflow/WorkflowIndicators.vue";
-import WorkflowInvocationsCount from "@/components/Workflow/WorkflowInvocationsCount.vue";
-import WorkflowRename from "@/components/Workflow/WorkflowRename.vue";
-import WorkflowRunButton from "@/components/Workflow/WorkflowRunButton.vue";
-
-library.add(faEdit, faEye, faPen, faUpload);
-
-interface Props {
-    workflow: any;
-    gridView?: boolean;
-    publishedView?: boolean;
-}
-
-const props = withDefaults(defineProps<Props>(), {
-    gridView: false,
-    publishedView: false,
-});
-
-const emit = defineEmits<{
-    (e: "tagClick", tag: string): void;
-    (e: "refreshList", overlayLoading?: boolean, b?: boolean): void;
-    (e: "update-filter", key: string, value: any): void;
-}>();
-
-const userStore = useUserStore();
-
-const { isAnonymous } = storeToRefs(userStore);
-
-const showRename = ref(false);
-const showPreview = ref(false);
-
-const workflow = computed(() => props.workflow);
-const shared = computed(() => {
-    if (userStore.currentUser) {
-        return userStore.currentUser.username !== workflow.value.owner;
-    } else {
-        return false;
-    }
-});
-const description = computed(() => {
-    if (workflow.value.annotations && workflow.value.annotations.length > 0) {
-        return workflow.value.annotations[0].trim();
-    } else {
-        return null;
-    }
-});
-const editButtonTitle = computed(() => {
-    if (isAnonymous.value) {
-        return "Log in to edit Workflow";
-    } else {
-        if (workflow.value.deleted) {
-            return "You cannot edit a deleted workflow. Restore it first.";
-        } else {
-            return "Edit Workflow";
-        }
-    }
-});
-const importedButtonTitle = computed(() => {
-    if (isAnonymous.value) {
-        return "Log in to import workflow";
-    } else {
-        return "Import this workflow to edit";
-    }
-});
-const runButtonTitle = computed(() => {
-    if (isAnonymous.value) {
-        return "Log in to run workflow";
-    } else {
-        if (workflow.value.deleted) {
-            return "You cannot run a deleted workflow. Restore it first.";
-        } else {
-            return "Run workflow";
-        }
-    }
-});
-
-async function onImport() {
-    await copyWorkflow(workflow.value.id, workflow.value.owner);
-    Toast.success("Workflow imported successfully");
-}
-
-function onRenameClose(e: any) {
-    showRename.value = false;
-    emit("refreshList", true);
-}
-
-function toggleShowPreview(val: boolean = false) {
-    showPreview.value = val;
-}
-
-async function onTagsUpdate(tags: string[]) {
-    workflow.value.tags = tags;
-    await updateWorkflow(workflow.value.id, { tags });
-    emit("refreshList", true, true);
-}
-
-async function onTagClick(tag: string) {
-    emit("tagClick", tag);
-}
-</script>
-
-<template>
-    <div class="workflow-card" :data-workflow-id="workflow.id">
-        <div
-            class="workflow-card-container"
-            :class="{
-                'workflow-shared': workflow.published,
-            }">
-            <div class="workflow-card-header">
-                <WorkflowIndicators
-                    :workflow="workflow"
-                    :published-view="publishedView"
-                    @update-filter="(k, v) => emit('update-filter', k, v)" />
-
-                <div class="workflow-count-actions">
-                    <WorkflowInvocationsCount v-if="!isAnonymous && !shared" class="mx-1" :workflow="workflow" />
-
-                    <WorkflowActions
-                        :workflow="workflow"
-                        :published="publishedView"
-                        @refreshList="emit('refreshList', true)"
-                        @toggleShowPreview="toggleShowPreview" />
-                </div>
-
-                <span class="workflow-name font-weight-bold">
-                    {{ workflow.name }}
-                    <BButton
-                        v-if="!shared && !workflow.deleted"
-                        v-b-tooltip.hover.noninteractive
-                        :data-workflow-rename="workflow.id"
-                        class="inline-icon-button workflow-rename"
-                        variant="link"
-                        size="sm"
-                        title="Rename"
-                        @click="showRename = !showRename">
-                        <FontAwesomeIcon :icon="faPen" fixed-width />
-                    </BButton>
-                </span>
-
-                <TextSummary
-                    v-if="description"
-                    class="my-1"
-                    :description="description"
-                    :max-length="gridView ? 100 : 250" />
-            </div>
-
-            <div class="workflow-card-footer">
-                <div class="workflow-card-tags">
-                    <StatelessTags
-                        clickable
-                        :value="workflow.tags"
-                        :disabled="isAnonymous || workflow.deleted || shared"
-                        :max-visible-tags="gridView ? 2 : 8"
-                        @input="onTagsUpdate($event)"
-                        @tag-click="onTagClick($event)" />
-                </div>
-
-                <div class="workflow-card-actions">
-                    <WorkflowActionsExtend
-                        :workflow="workflow"
-                        :published="publishedView"
-                        @refreshList="emit('refreshList', true)" />
-
-                    <div class="workflow-edit-run-buttons">
-                        <BButton
-                            v-if="!isAnonymous && !shared"
-                            v-b-tooltip.hover.noninteractive
-                            :disabled="workflow.deleted"
-                            size="sm"
-                            class="workflow-edit-button"
-                            :title="editButtonTitle"
-                            variant="outline-primary"
-                            :to="`/workflows/edit?id=${workflow.id}`">
-                            <FontAwesomeIcon :icon="faEdit" fixed-width />
-                            Edit
-                        </BButton>
-
-                        <AsyncButton
-                            v-else
-                            v-b-tooltip.hover.noninteractive
-                            size="sm"
-                            :disabled="isAnonymous"
-                            :title="importedButtonTitle"
-                            :icon="faUpload"
-                            variant="outline-primary"
-                            :action="onImport">
-                            Import
-                        </AsyncButton>
-
-                        <WorkflowRunButton
-                            :id="workflow.id"
-                            :disabled="isAnonymous || workflow.deleted"
-                            :title="runButtonTitle" />
-                    </div>
-                </div>
-            </div>
-
-            <WorkflowRename
-                v-if="!isAnonymous && !shared && !workflow.deleted"
-                :id="workflow.id"
-                :show="showRename"
-                :name="workflow.name"
-                @close="onRenameClose" />
-
-            <BModal
-                v-model="showPreview"
-                ok-only
-                size="xl"
-                hide-header
-                dialog-class="workflow-card-preview-modal w-auto"
-                centered>
-                <WorkflowPublished v-if="showPreview" :id="workflow.id" quick-view />
-            </BModal>
-        </div>
-    </div>
-</template>
-
-<style lang="scss">
-.workflow-card-preview-modal {
-    max-width: min(1400px, calc(100% - 200px));
-
-    .modal-content {
-        height: min(800px, calc(100vh - 80px));
-    }
-}
-</style>
-
-<style scoped lang="scss">
-@import "theme/blue.scss";
-@import "breakpoints.scss";
-
-.workflow-card {
-    container: workflow-card / inline-size;
-    padding: 0 0.25rem 0.5rem 0.25rem;
-
-    .workflow-rename {
-        opacity: 0;
-    }
-
-    &:hover,
-    &:focus-within {
-        .workflow-rename {
-            opacity: 1;
-        }
-    }
-
-    .workflow-card-container {
-        height: 100%;
-        display: flex;
-        gap: 0.5rem;
-        flex-direction: column;
-        justify-content: space-between;
-        border: 1px solid $brand-secondary;
-        border-radius: 0.5rem;
-        padding: 0.5rem;
-
-        &.workflow-shared {
-            border-left: 0.25rem solid $brand-primary;
-        }
-
-        .workflow-card-header {
-            display: grid;
-
-            .workflow-count-actions {
-                display: flex;
-                align-items: center;
-                flex-direction: row;
-                position: absolute;
-                right: 0.5rem;
-            }
-
-            .workflow-name {
-                font-size: 1rem;
-                font-weight: bold;
-                word-break: break-all;
-            }
-        }
-
-        .workflow-card-footer {
-            display: flex;
-            justify-content: space-between;
-            align-items: end;
-
-            .workflow-card-tags {
-                max-width: 60%;
-            }
-
-            .workflow-card-actions {
-                display: flex;
-                gap: 0.25rem;
-                margin-top: 0.25rem;
-                align-items: center;
-                justify-content: end;
-            }
-        }
-
-        @container workflow-card (max-width: #{$breakpoint-sm}) {
-            .workflow-card-footer {
-                display: inline-block;
-
-                .workflow-card-tags {
-                    max-width: 100%;
-                }
-            }
-        }
-
-        @container workflow-card (max-width: #{$breakpoint-sm}) {
-            .workflow-card-actions {
-                justify-content: space-between;
-            }
-        }
-
-        @container workflow-card (min-width: #{$breakpoint-sm}, max-width: #{$breakpoint-md}) {
-            .workflow-card-actions {
-                justify-content: end;
-            }
-        }
-    }
-
-    @container workflow-card (max-width: #{$breakpoint-md}) {
-        .workflow-count-actions {
-            align-items: baseline;
-            justify-content: end;
-        }
-    }
-
-    @container workflow-card (min-width: #{$breakpoint-md}) {
-        .workflow-count-actions {
-            align-items: end;
-            flex-direction: column-reverse;
-        }
-    }
-}
-</style>
diff --git a/client/src/components/Workflow/WorkflowInvocationsCount.vue b/client/src/components/Workflow/WorkflowInvocationsCount.vue
index 321e2568a4c8be587a1dff43baedf6cf071a8627..e9101f5def7a385747b5aa56c9e0afd4e6904d44 100644
--- a/client/src/components/Workflow/WorkflowInvocationsCount.vue
+++ b/client/src/components/Workflow/WorkflowInvocationsCount.vue
@@ -4,8 +4,9 @@ import { faList } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { onMounted, ref } from "vue";
 
-import { invocationCountsFetcher } from "@/api/workflows";
+import { GalaxyApi } from "@/api";
 import localize from "@/utils/localization";
+import { rethrowSimple } from "@/utils/simple-error";
 
 library.add(faList);
 
@@ -18,7 +19,14 @@ const props = defineProps<Props>();
 const count = ref<number | undefined>(undefined);
 
 async function initCounts() {
-    const { data } = await invocationCountsFetcher({ workflow_id: props.workflow.id });
+    const { data, error } = await GalaxyApi().GET("/api/workflows/{workflow_id}/counts", {
+        params: { path: { workflow_id: props.workflow.id } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
     let allCounts = 0;
     for (const stateCount of Object.values(data)) {
         if (stateCount) {
@@ -33,7 +41,7 @@ onMounted(initCounts);
 
 <template>
     <div class="workflow-invocations-count d-flex align-items-center flex-gapx-1">
-        <BBadge v-if="count != undefined && count === 0" pill class="list-view">
+        <BBadge v-if="count != undefined && count === 0" pill>
             <span>never run</span>
         </BBadge>
         <BBadge
@@ -41,7 +49,7 @@ onMounted(initCounts);
             v-b-tooltip.hover.noninteractive
             pill
             :title="localize('View workflow invocations')"
-            class="outline-badge cursor-pointer list-view"
+            class="outline-badge cursor-pointer"
             :to="`/workflows/${props.workflow.id}/invocations`">
             <FontAwesomeIcon :icon="faList" fixed-width />
 
diff --git a/client/src/components/Workflow/WorkflowNavigationTitle.test.ts b/client/src/components/Workflow/WorkflowNavigationTitle.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c1c8d7ac6ebc81c6546ade7941fc0adfb3ba3d5c
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowNavigationTitle.test.ts
@@ -0,0 +1,186 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
+import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import sampleInvocation from "@/components/Workflow/test/json/invocation.json";
+import { useUserStore } from "@/stores/userStore";
+
+import WorkflowNavigationTitle from "./WorkflowNavigationTitle.vue";
+
+// Constants
+const WORKFLOW_OWNER = "test-user";
+const OTHER_USER = "other-user";
+const UNIMPORTABLE_WORKFLOW_ID = "invalid-workflow-id";
+const UNIMPORTABLE_WORKFLOW_INSTANCE_ID = "invalid-instance-id";
+const SAMPLE_WORKFLOW = {
+    id: "workflow-id",
+    name: "workflow-name",
+    owner: WORKFLOW_OWNER,
+    version: 1,
+};
+const IMPORT_ERROR_MESSAGE = "Failed to import workflow";
+
+const SELECTORS = {
+    WORKFLOW_HEADING: "[data-description='workflow heading']",
+    ACTIONS_BUTTON_GROUP: "bbuttongroup-stub",
+    EDIT_WORKFLOW_BUTTON: `bbutton-stub[title='<b>Edit</b><br>${SAMPLE_WORKFLOW.name}']`,
+    IMPORT_WORKFLOW_BUTTON: "[data-description='import workflow button']",
+    EXECUTE_WORKFLOW_BUTTON: "[data-description='execute workflow button']",
+    ROUTE_TO_RUN_BUTTON: "[data-description='route to workflow run button']",
+    ALERT_MESSAGE: "balert-stub",
+};
+
+// Mock the copyWorkflow function for importing a workflow
+jest.mock("components/Workflow/workflows.services", () => ({
+    copyWorkflow: jest.fn().mockImplementation((workflowId: string) => {
+        if (workflowId === UNIMPORTABLE_WORKFLOW_ID) {
+            throw new Error(IMPORT_ERROR_MESSAGE);
+        }
+        return SAMPLE_WORKFLOW;
+    }),
+}));
+
+// Mock the workflow store to return the sample workflow
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((instanceId: string) => {
+                if (instanceId === UNIMPORTABLE_WORKFLOW_INSTANCE_ID) {
+                    return { ...SAMPLE_WORKFLOW, id: UNIMPORTABLE_WORKFLOW_ID };
+                }
+                return SAMPLE_WORKFLOW;
+            }),
+        }),
+    };
+});
+
+const localVue = getLocalVue();
+
+/**
+ * Mounts the WorkflowNavigationTitle component with props/stores adjusted given the parameters
+ * @param version The version of the component to mount (`run_form` or `invocation` view)
+ * @param ownsWorkflow Whether the user owns the workflow associated with the invocation
+ * @param unimportableWorkflow Whether the workflow import should fail
+ * @returns The wrapper object
+ */
+async function mountWorkflowNavigationTitle(
+    version: "run_form" | "invocation",
+    ownsWorkflow = true,
+    unimportableWorkflow = false
+) {
+    let workflowId: string;
+    let invocation;
+    if (version === "invocation") {
+        workflowId = !unimportableWorkflow ? sampleInvocation.workflow_id : UNIMPORTABLE_WORKFLOW_INSTANCE_ID;
+        invocation = {
+            ...sampleInvocation,
+            workflow_id: workflowId,
+        };
+    } else {
+        workflowId = !unimportableWorkflow ? SAMPLE_WORKFLOW.id : UNIMPORTABLE_WORKFLOW_INSTANCE_ID;
+        invocation = undefined;
+    }
+
+    const wrapper = shallowMount(WorkflowNavigationTitle as object, {
+        propsData: {
+            invocation,
+            workflowId,
+        },
+        localVue,
+        pinia: createTestingPinia(),
+    });
+
+    const userStore = useUserStore();
+    userStore.currentUser = getFakeRegisteredUser({
+        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
+    });
+
+    return { wrapper };
+}
+
+describe("WorkflowNavigationTitle renders", () => {
+    it("the workflow name in header and run button in actions; invocation version", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation");
+
+        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
+        expect(heading.text()).toContain(`Invoked Workflow: ${SAMPLE_WORKFLOW.name}`);
+        expect(heading.text()).toContain(`(Version: ${SAMPLE_WORKFLOW.version + 1})`);
+
+        const runButton = wrapper.find(SELECTORS.ROUTE_TO_RUN_BUTTON);
+        expect(runButton.attributes("title")).toContain("Rerun");
+        expect(runButton.attributes("title")).toContain(SAMPLE_WORKFLOW.name);
+    });
+
+    it("the workflow name in header and run button in actions; run form version", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("run_form");
+
+        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
+        expect(heading.text()).toContain(`Workflow: ${SAMPLE_WORKFLOW.name}`);
+        expect(heading.text()).toContain(`(Version: ${SAMPLE_WORKFLOW.version + 1})`);
+
+        const runButton = wrapper.find(SELECTORS.EXECUTE_WORKFLOW_BUTTON);
+        expect(runButton.attributes("title")).toContain("Run");
+    });
+
+    it("edit button if user owns the workflow", async () => {
+        async function findAndClickEditButton(version: "invocation" | "run_form") {
+            const { wrapper } = await mountWorkflowNavigationTitle(version);
+            const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+
+            const editButton = actionsGroup.find(SELECTORS.EDIT_WORKFLOW_BUTTON);
+            expect(editButton.attributes("to")).toBe(
+                `/workflows/edit?id=${SAMPLE_WORKFLOW.id}&version=${SAMPLE_WORKFLOW.version}`
+            );
+        }
+        await findAndClickEditButton("invocation");
+        await findAndClickEditButton("run_form");
+    });
+
+    it("import button instead if user does not own the workflow", async () => {
+        async function findImportButton(version: "invocation" | "run_form") {
+            const { wrapper } = await mountWorkflowNavigationTitle(version, false);
+            const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+            const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+            expect(importButton.exists()).toBe(true);
+        }
+        await findImportButton("invocation");
+        await findImportButton("run_form");
+    });
+});
+
+describe("Importing a workflow in WorkflowNavigationTitle", () => {
+    // We only need to test the `invocation` version because the button is the same in both versions
+
+    it("should show a confirmation dialog when the import is successful", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation", false);
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+
+        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
+        await importButton.props().action();
+        await flushPromises();
+
+        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
+        expect(alert.attributes("variant")).toBe("info");
+        expect(alert.text()).toContain(`Workflow ${SAMPLE_WORKFLOW.name} imported successfully`);
+    });
+
+    it("should show an error dialog when the import fails", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation", false, true);
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+
+        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
+        await importButton.props().action();
+        await flushPromises();
+
+        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
+        expect(alert.attributes("variant")).toBe("danger");
+        expect(alert.text()).toContain(IMPORT_ERROR_MESSAGE);
+    });
+});
diff --git a/client/src/components/Workflow/WorkflowNavigationTitle.vue b/client/src/components/Workflow/WorkflowNavigationTitle.vue
new file mode 100644
index 0000000000000000000000000000000000000000..5f467c90fe5307cb2b5210c5742b89d7ca071a20
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowNavigationTitle.vue
@@ -0,0 +1,188 @@
+<script setup lang="ts">
+import { faEdit, faSitemap, faUpload } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BButton, BButtonGroup } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed, ref } from "vue";
+import { RouterLink } from "vue-router";
+
+import { isRegisteredUser } from "@/api";
+import type { WorkflowInvocationElementView } from "@/api/invocations";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
+import { useUserStore } from "@/stores/userStore";
+import type { Workflow } from "@/stores/workflowStore";
+import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import { copyWorkflow } from "./workflows.services";
+
+import AsyncButton from "../Common/AsyncButton.vue";
+import ButtonSpinner from "../Common/ButtonSpinner.vue";
+import WorkflowRunButton from "./WorkflowRunButton.vue";
+
+interface Props {
+    invocation?: WorkflowInvocationElementView;
+    workflowId: string;
+    runDisabled?: boolean;
+    runWaiting?: boolean;
+    success?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    invocation: undefined,
+});
+
+const emit = defineEmits<{
+    (e: "on-execute"): void;
+}>();
+
+const { workflow, error } = useWorkflowInstance(props.workflowId);
+
+const { currentUser, isAnonymous } = storeToRefs(useUserStore());
+const owned = computed(() => {
+    if (isRegisteredUser(currentUser.value) && workflow.value) {
+        return currentUser.value.username === workflow.value.owner;
+    } else {
+        return false;
+    }
+});
+
+const importErrorMessage = ref<string | null>(null);
+const importedWorkflow = ref<Workflow | null>(null);
+const workflowImportedAttempted = ref(false);
+
+async function onImport() {
+    if (!workflow.value || !workflow.value.owner) {
+        return;
+    }
+    try {
+        const wf = await copyWorkflow(workflow.value.id, workflow.value.owner);
+        importedWorkflow.value = wf as unknown as Workflow;
+    } catch (error) {
+        importErrorMessage.value = errorMessageAsString(error, "Failed to import workflow");
+    } finally {
+        workflowImportedAttempted.value = true;
+    }
+}
+
+function getWorkflowName(): string {
+    return workflow.value?.name || "...";
+}
+
+const workflowImportTitle = computed(() => {
+    if (isAnonymous.value) {
+        return localize("Login to import this workflow");
+    } else if (workflowImportedAttempted.value) {
+        return localize("Workflow imported");
+    } else {
+        return localize("Import this workflow");
+    }
+});
+</script>
+
+<template>
+    <div>
+        <BAlert v-if="importErrorMessage" variant="danger" dismissible show @dismissed="importErrorMessage = null">
+            {{ importErrorMessage }}
+        </BAlert>
+        <BAlert v-else-if="importedWorkflow" variant="info" dismissible show @dismissed="importedWorkflow = null">
+            <span>
+                Workflow <b>{{ importedWorkflow.name }}</b> imported successfully.
+            </span>
+            <RouterLink to="/workflows/list">Click here</RouterLink> to view the imported workflow in the workflows
+            list.
+        </BAlert>
+
+        <BAlert v-if="error" variant="danger" show>{{ error }}</BAlert>
+
+        <div class="position-relative mb-2">
+            <div v-if="workflow" class="bg-secondary px-2 py-1 rounded">
+                <div class="d-flex align-items-center flex-gapx-1">
+                    <div class="flex-grow-1" data-description="workflow heading">
+                        <div>
+                            <FontAwesomeIcon :icon="faSitemap" fixed-width />
+                            <b> {{ props.invocation ? "Invoked " : "" }}Workflow: {{ getWorkflowName() }} </b>
+                            <span>(Version: {{ workflow.version + 1 }})</span>
+                        </div>
+                    </div>
+                    <BButtonGroup>
+                        <BButton
+                            v-if="owned && workflow"
+                            v-b-tooltip.hover.noninteractive.html
+                            size="sm"
+                            :title="
+                                !workflow.deleted
+                                    ? `<b>Edit</b><br>${getWorkflowName()}`
+                                    : 'This workflow has been deleted.'
+                            "
+                            variant="link"
+                            :disabled="workflow.deleted"
+                            :to="`/workflows/edit?id=${workflow.id}&version=${workflow.version}`">
+                            <FontAwesomeIcon :icon="faEdit" fixed-width />
+                        </BButton>
+                        <AsyncButton
+                            v-else
+                            v-b-tooltip.hover.noninteractive
+                            data-description="import workflow button"
+                            size="sm"
+                            :disabled="isAnonymous || workflowImportedAttempted"
+                            :title="workflowImportTitle"
+                            :icon="faUpload"
+                            variant="link"
+                            :action="onImport">
+                        </AsyncButton>
+
+                        <slot name="workflow-title-actions" />
+                    </BButtonGroup>
+                    <ButtonSpinner
+                        v-if="!props.invocation"
+                        id="run-workflow"
+                        data-description="execute workflow button"
+                        :wait="runWaiting"
+                        :disabled="runDisabled"
+                        size="sm"
+                        title="Run Workflow"
+                        @onClick="emit('on-execute')" />
+                    <WorkflowRunButton
+                        v-else
+                        :id="workflow.id"
+                        data-description="route to workflow run button"
+                        variant="link"
+                        :title="
+                            !workflow.deleted
+                                ? `<b>Rerun</b><br>${getWorkflowName()}`
+                                : 'This workflow has been deleted.'
+                        "
+                        :disabled="workflow.deleted"
+                        force
+                        full
+                        :version="workflow.version" />
+                </div>
+            </div>
+            <div v-if="props.success" class="donemessagelarge">
+                Successfully invoked workflow
+                <b>{{ getWorkflowName() }}</b>
+            </div>
+        </div>
+    </div>
+</template>
+
+<style scoped lang="scss">
+@keyframes fadeOut {
+    0% {
+        opacity: 1;
+    }
+    100% {
+        opacity: 0;
+        display: none;
+        pointer-events: none;
+    }
+}
+
+.donemessagelarge {
+    top: 0;
+    position: absolute;
+    width: 100%;
+    animation: fadeOut 3s forwards;
+}
+</style>
diff --git a/client/src/components/Workflow/WorkflowRunButton.test.ts b/client/src/components/Workflow/WorkflowRunButton.test.ts
index 11c02dc9554999dc00b758f10dbca4932b24cef2..431e8861a964b6a5ce20c0eb722463a688fea878 100644
--- a/client/src/components/Workflow/WorkflowRunButton.test.ts
+++ b/client/src/components/Workflow/WorkflowRunButton.test.ts
@@ -1,4 +1,5 @@
-import { mount } from "@vue/test-utils";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
 import { generateRandomString } from "./testUtils";
@@ -8,31 +9,72 @@ import WorkflowRunButton from "./WorkflowRunButton.vue";
 const localVue = getLocalVue();
 
 const WORKFLOW_ID = generateRandomString();
+const WORKFLOW_VERSION = 1;
 const WORKFLOW_RUN_BUTTON_SELECTOR = `[data-workflow-run="${WORKFLOW_ID}"]`;
 
-async function mountWorkflowRunButton(props?: { id: string; full?: boolean }) {
+function getPath() {
+    return `/workflows/run?id=${WORKFLOW_ID}&version=${WORKFLOW_VERSION}`;
+}
+
+async function mountWorkflowRunButton(
+    props?: { id: string; version: number; full?: boolean; force?: boolean },
+    currentPath?: string
+) {
+    const mockRouter = {
+        push: jest.fn(),
+        afterEach: jest.fn(),
+        currentRoute: {
+            fullPath: currentPath || getPath(),
+        },
+    };
+
     const wrapper = mount(WorkflowRunButton as object, {
         propsData: { ...props },
         localVue,
+        mocks: {
+            $router: mockRouter,
+        },
     });
 
-    return { wrapper };
+    return { wrapper, mockRouter };
+}
+
+async function clickButton(button: Wrapper<Vue>) {
+    // Remove the href and target attributes to prevent navigation error
+    // This is done because the `BButton` has a `:to` prop as well as an `@click` event
+    button.element.setAttribute("href", "javascript:void(0)");
+    button.element.setAttribute("target", "");
+
+    await button.trigger("click");
+    await flushPromises();
 }
 
 describe("WorkflowRunButton.vue", () => {
-    it("should render button with icon", async () => {
-        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID });
+    it("should render button with icon and route to it", async () => {
+        const { wrapper, mockRouter } = await mountWorkflowRunButton({ id: WORKFLOW_ID, version: WORKFLOW_VERSION });
+
+        const button = wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
+        expect(button.attributes("title")).toBe("Run workflow");
+        expect(button.text()).toBe("");
+        expect(button.attributes("href")).toBe(getPath());
 
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).exists()).toBeTruthy();
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).attributes("title")).toBe("Run workflow");
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).text()).toBe("");
+        await clickButton(button);
+
+        // Check that router.push was called with the correct arguments
+        expect(mockRouter.push).toHaveBeenCalledWith(getPath());
     });
 
-    it("should redirect to workflow run page", async () => {
-        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID });
+    it("should force route if on the same path", async () => {
+        const { wrapper, mockRouter } = await mountWorkflowRunButton(
+            { id: WORKFLOW_ID, version: WORKFLOW_VERSION, force: true },
+            getPath()
+        );
+
+        const button = wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
 
-        const runButton = await wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
+        await clickButton(button);
 
-        expect(runButton.attributes("href")).toBe(`/workflows/run?id=${WORKFLOW_ID}`);
+        // Check that router.push was called with the correct arguments
+        expect(mockRouter.push).toHaveBeenCalledWith(getPath(), { force: true });
     });
 });
diff --git a/client/src/components/Workflow/WorkflowRunButton.vue b/client/src/components/Workflow/WorkflowRunButton.vue
index 2b1957246caea85c6efc024995fe27ca2b5f222e..7a3f94b79486737cacba330486fa11f7dd39a852 100644
--- a/client/src/components/Workflow/WorkflowRunButton.vue
+++ b/client/src/components/Workflow/WorkflowRunButton.vue
@@ -1,11 +1,9 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
 import { faPlay } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { computed } from "vue";
-
-library.add(faPlay);
+import { useRoute, useRouter } from "vue-router/composables";
 
 interface Props {
     id: string;
@@ -13,13 +11,34 @@ interface Props {
     title?: string;
     disabled?: boolean;
     version?: number;
+    force?: boolean;
+    variant?: string;
 }
 
-const props = defineProps<Props>();
+const props = withDefaults(defineProps<Props>(), {
+    title: undefined,
+    version: undefined,
+    variant: "primary",
+});
+
+const route = useRoute();
+const router = useRouter();
 
 const runPath = computed(
     () => `/workflows/run?id=${props.id}${props.version !== undefined ? `&version=${props.version}` : ""}`
 );
+
+function routeToPath() {
+    if (props.force && route.fullPath === runPath.value) {
+        // vue-router 4 supports a native force push with clean URLs,
+        // but we're using a __vkey__ bit as a workaround
+        // Only conditionally force to keep urls clean most of the time.
+        // @ts-ignore - monkeypatched router, drop with migration.
+        router.push(runPath.value, { force: true });
+    } else {
+        router.push(runPath.value);
+    }
+}
 </script>
 
 <template>
@@ -28,10 +47,12 @@ const runPath = computed(
         v-b-tooltip.hover.top.html.noninteractive
         :title="title ?? 'Run workflow'"
         :data-workflow-run="id"
-        variant="primary"
+        :variant="variant"
         size="sm"
+        class="text-decoration-none"
         :disabled="disabled"
-        :to="runPath">
+        :to="runPath"
+        @click="routeToPath">
         <FontAwesomeIcon :icon="faPlay" fixed-width />
 
         <span v-if="full" v-localize>Run</span>
diff --git a/client/src/components/Workflow/redirectPath.ts b/client/src/components/Workflow/redirectPath.ts
index 1cc3db96a6e20738eafb84cbc53f8fc6d86680b6..fe2240e81f55d018bc192e6a65cfe0fdbe5c47b1 100644
--- a/client/src/components/Workflow/redirectPath.ts
+++ b/client/src/components/Workflow/redirectPath.ts
@@ -1,4 +1,4 @@
-import type { RawLocation } from "vue-router";
+import { type RawLocation } from "vue-router";
 
 import { Toast } from "@/composables/toast";
 
diff --git a/client/src/components/Workflow/workflows.services.ts b/client/src/components/Workflow/workflows.services.ts
index e0c9c7d328c98588ba8313f7dc809722f79554a6..4cfff88627d22fa31ed3c6f24eaea49e2d5f7ad8 100644
--- a/client/src/components/Workflow/workflows.services.ts
+++ b/client/src/components/Workflow/workflows.services.ts
@@ -1,12 +1,13 @@
 import axios from "axios";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 import { useUserStore } from "@/stores/userStore";
 import { withPrefix } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
 
-type SortBy = "create_time" | "update_time" | "name";
+export type Workflow = Record<string, never>;
 
-type Workflow = Record<string, never>;
+type SortBy = "create_time" | "update_time" | "name";
 
 interface LoadWorkflowsOptions {
     sortBy: SortBy;
@@ -18,7 +19,6 @@ interface LoadWorkflowsOptions {
     skipStepCounts: boolean;
 }
 
-const getWorkflows = fetcher.path("/api/workflows").method("get").create();
 export async function loadWorkflows({
     sortBy = "update_time",
     sortDesc = true,
@@ -27,17 +27,28 @@ export async function loadWorkflows({
     filterText = "",
     showPublished = false,
     skipStepCounts = true,
-}: LoadWorkflowsOptions): Promise<{ data: Workflow[]; headers: Headers }> {
-    const { data, headers } = await getWorkflows({
-        sort_by: sortBy,
-        sort_desc: sortDesc,
-        limit,
-        offset,
-        search: filterText,
-        show_published: showPublished,
-        skip_step_counts: skipStepCounts,
+}: LoadWorkflowsOptions): Promise<{ data: Workflow[]; totalMatches: number }> {
+    const { response, data, error } = await GalaxyApi().GET("/api/workflows", {
+        params: {
+            query: {
+                sort_by: sortBy,
+                sort_desc: sortDesc,
+                limit,
+                offset,
+                search: filterText,
+                show_published: showPublished,
+                skip_step_counts: skipStepCounts,
+            },
+        },
     });
-    return { data, headers };
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    const totalMatches = parseInt(response.headers.get("Total_matches") || "0", 10) || 0;
+
+    return { data, totalMatches };
 }
 
 export async function updateWorkflow(id: string, changes: object): Promise<Workflow> {
@@ -45,7 +56,7 @@ export async function updateWorkflow(id: string, changes: object): Promise<Workf
     return data;
 }
 
-export async function copyWorkflow(id: string, currentOwner: string, version?: string): Promise<Workflow> {
+export async function copyWorkflow(id: string, currentOwner?: string, version?: string): Promise<Workflow> {
     let path = `/api/workflows/${id}/download`;
     if (version) {
         path += `?version=${version}`;
@@ -53,9 +64,9 @@ export async function copyWorkflow(id: string, currentOwner: string, version?: s
     const { data: workflowData } = await axios.get(withPrefix(path));
 
     workflowData.name = `Copy of ${workflowData.name}`;
-    const currentUsername = useUserStore().currentUser?.username;
+    const userStore = useUserStore();
 
-    if (currentUsername !== currentOwner) {
+    if (!userStore.matchesCurrentUsername(currentOwner)) {
         workflowData.name += ` shared by user ${currentOwner}`;
     }
 
diff --git a/client/src/components/WorkflowInvocationState/InvocationMessage.vue b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
index 7c1561576f390581cb7099c20026c27ab2cfa325..3759dfe824631102d150fab393b4ca7b6282b2bc 100644
--- a/client/src/components/WorkflowInvocationState/InvocationMessage.vue
+++ b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
@@ -1,10 +1,9 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import type { InvocationMessage } from "@/api/invocations";
 import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
 
-import type { InvocationMessageResponseModel } from "./invocationMessageModel";
-
 import GenericHistoryItem from "@/components/History/Content/GenericItem.vue";
 import JobInformation from "@/components/JobInformation/JobInformation.vue";
 import WorkflowInvocationStep from "@/components/WorkflowInvocationState/WorkflowInvocationStep.vue";
@@ -21,6 +20,7 @@ type ReasonToLevel = {
     when_not_boolean: "error";
     unexpected_failure: "error";
     workflow_output_not_found: "warning";
+    workflow_parameter_invalid: "error";
 };
 
 const level: ReasonToLevel = {
@@ -35,6 +35,7 @@ const level: ReasonToLevel = {
     when_not_boolean: "error",
     unexpected_failure: "error",
     workflow_output_not_found: "warning",
+    workflow_parameter_invalid: "error",
 };
 
 const levelClasses = {
@@ -49,7 +50,7 @@ interface Invocation {
 }
 
 interface InvocationMessageProps {
-    invocationMessage: InvocationMessageResponseModel;
+    invocationMessage: InvocationMessage;
     invocation: Invocation;
 }
 
@@ -79,7 +80,7 @@ const workflowStep = computed(() => {
 const dependentWorkflowStep = computed(() => {
     if ("dependent_workflow_step_id" in props.invocationMessage && workflow.value) {
         const stepId = props.invocationMessage["dependent_workflow_step_id"];
-        if (stepId !== undefined) {
+        if (stepId !== undefined && stepId !== null) {
             return workflow.value.steps[stepId];
         }
     }
@@ -166,6 +167,10 @@ const infoString = computed(() => {
         return `Defined workflow output '${invocationMessage.output_name}' was not found in step ${
             invocationMessage.workflow_step_id + 1
         }.`;
+    } else if (reason === "workflow_parameter_invalid") {
+        return `Workflow parameter on step ${invocationMessage.workflow_step_id + 1} failed validation: ${
+            invocationMessage.details
+        }`;
     } else {
         return reason;
     }
diff --git a/client/src/components/WorkflowInvocationState/JobStep.test.js b/client/src/components/WorkflowInvocationState/JobStep.test.js
deleted file mode 100644
index b11420459940c7b8bca70bef8e159c7087bc67a3..0000000000000000000000000000000000000000
--- a/client/src/components/WorkflowInvocationState/JobStep.test.js
+++ /dev/null
@@ -1,79 +0,0 @@
-import { createLocalVue, mount } from "@vue/test-utils";
-import BootstrapVue from "bootstrap-vue";
-
-import JobStep from "./JobStep";
-import jobs from "./test/json/jobs.json";
-
-// create an extended `Vue` constructor
-const localVue = createLocalVue();
-
-// install plugins as normal
-localVue.use(BootstrapVue);
-
-describe("DatasetUIWrapper.vue with Dataset", () => {
-    let wrapper;
-    let propsData;
-
-    beforeEach(async () => {
-        propsData = {
-            jobs: jobs,
-        };
-        wrapper = mount(JobStep, {
-            localVue,
-            propsData,
-            stubs: {
-                JobProvider: { template: "<div class='expanded'>I am expanded</div>" },
-            },
-        });
-    });
-    test("it renders a table with 2 jobs", async () => {
-        expect(wrapper.find("tbody").findAll("tr").length).toBe(2);
-    });
-    test("it expands on row click", async () => {
-        // verify no item is expanded
-        expect(wrapper.vm.toggledItems["1"]).toBe(undefined);
-        expect(wrapper.find(".expanded").exists()).toBeFalsy();
-        // expand
-        await wrapper.find("tbody").find("tbody").find("tr").trigger("click");
-        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
-        expect(wrapper.find(".expanded").exists()).toBeTruthy();
-        await wrapper.find("tbody").find("tbody").find("tr").trigger("click");
-        // close again
-        expect(wrapper.vm.toggledItems["1"]).toBeFalsy();
-        expect(wrapper.find(".expanded").exists()).toBeFalsy();
-    });
-    test("it sustains expanded on prop update", async () => {
-        // verify no item is expanded
-        expect(wrapper.vm.toggledItems["1"]).toBe(undefined);
-        expect(wrapper.find(".expanded").exists()).toBeFalsy();
-        // expand
-        await wrapper.find("tbody").find("tbody").find("tr").trigger("click");
-        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
-        expect(wrapper.find(".expanded").exists()).toBeTruthy();
-        // 2 collapsed rows, plus 1 expanded row
-        expect(countVisibleRows(wrapper)).toBe(3);
-        // update data
-        const additionalJob = { ...jobs[0], id: 3 };
-        await wrapper.setProps({ jobs: [...jobs, additionalJob] });
-        // verify new data is displayed
-        expect(countVisibleRows(wrapper)).toBe(4);
-        // verify first row is still expanded
-        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
-        expect(wrapper.find(".expanded").exists()).toBeTruthy();
-    });
-});
-
-/** When expanding a row, a hidden `<tr>` may be added like:
- * ```
- * <tr aria-hidden="true" role="presentation" class="d-none"></tr>
- * ```
- * and this function will count rows other than these hidden ones.
- */
-function countVisibleRows(wrapper) {
-    const rows = wrapper.find("tbody").find("tbody").findAll("tr");
-    const visibleRows = rows.filter((row) => {
-        // only count rows that are not hidden
-        return !(row.attributes("aria-hidden") && row.attributes("aria-hidden") === "true");
-    });
-    return visibleRows.length;
-}
diff --git a/client/src/components/WorkflowInvocationState/JobStep.test.ts b/client/src/components/WorkflowInvocationState/JobStep.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..65ba2af0fcfddec895f724b24481bafc9d8f8355
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/JobStep.test.ts
@@ -0,0 +1,145 @@
+import { createTestingPinia } from "@pinia/testing";
+import { createLocalVue, mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
+import type { JobDisplayParametersSummary, ShowFullJobResponse } from "@/api/jobs";
+import paramResponse from "@/components/JobParameters/parameters-response.json";
+
+import jobs from "./test/json/jobs.json";
+
+import JobStep from "./JobStep.vue";
+
+const localVue = createLocalVue();
+
+const { server, http } = useServerMock();
+
+const SELECTORS = {
+    JOB_TABS_LIST: ".nav-pills",
+    JOB_TAB: ".nav-link",
+    JOB_CONTENT: "[data-description='workflow invocation job'] > .card-body",
+};
+
+describe("DatasetUIWrapper.vue with Dataset", () => {
+    let wrapper: Wrapper<Vue>;
+    let propsData;
+    let iteration: "base" | "state_change" = "base";
+    const pinia = createTestingPinia();
+
+    function getSummary(job_id: string) {
+        let summary = jobs.find((s) => s.id === job_id);
+        if (summary && iteration === "state_change" && job_id === "1") {
+            summary.state = "running";
+        }
+        if (job_id === "3") {
+            summary = { ...(jobs[0] as any), id: "3" };
+        }
+        return summary as ShowFullJobResponse;
+    }
+
+    beforeEach(async () => {
+        server.use(
+            http.get("/api/jobs/{job_id}", ({ response, params }) => {
+                const { job_id } = params;
+                const summary = getSummary(job_id);
+                if (!summary) {
+                    return response("4XX").json({ err_msg: "Job not found", err_code: 404 }, { status: 404 });
+                }
+                return response(200).json(summary);
+            })
+        );
+        server.use(
+            http.get("/api/invocations", ({ response }) => {
+                return response(200).json([]);
+            })
+        );
+        server.use(
+            http.get("/api/jobs/{job_id}/parameters_display", ({ response }) => {
+                return response(200).json(paramResponse as JobDisplayParametersSummary);
+            })
+        );
+        server.use(
+            http.get("/api/datasets/{dataset_id}", ({ response, params }) => {
+                const { dataset_id } = params;
+                // We need to use untyped here because this endpoint is not
+                // described in the OpenAPI spec due to its complexity for now.
+                return response.untyped(
+                    HttpResponse.json({
+                        id: dataset_id,
+                        creating_job: `job-${dataset_id}`,
+                    })
+                );
+            })
+        );
+
+        propsData = {
+            jobs: jobs,
+        };
+        wrapper = mount(JobStep as object, {
+            localVue,
+            propsData,
+            stubs: {
+                BPopover: true,
+                ContentItem: true,
+                FontAwesomeIcon: true,
+                JobInformation: true,
+                JobParameters: true,
+                BTooltip: true,
+                LoadingSpan: true,
+            },
+            pinia,
+        });
+        await flushPromises();
+    });
+    test("shows as many tabs as jobs and clicking tab changes shown job", async () => {
+        // it renders 2 jobs in 2 tabs with states
+        const ulTabs = wrapper.find(SELECTORS.JOB_TABS_LIST);
+        const liTabs = ulTabs.findAll(SELECTORS.JOB_TAB);
+        expect(liTabs.length).toBe(jobs.length);
+
+        const jobsContents = wrapper.findAll(SELECTORS.JOB_CONTENT);
+        expect(jobsContents.length).toBe(jobs.length);
+
+        liTabs.wrappers.forEach((liTab, i) => {
+            expect(jobs[i]).toBeTruthy();
+            expect(liTab.text()).toEqual(jobs[i]?.state);
+            // expect the first job to be shown and rest to be hidden
+            expect(liTab.attributes("aria-selected")).toEqual(i === 0 ? "true" : "false");
+            expect(jobsContents.at(i).attributes("style")).toEqual(i === 0 ? "" : "display: none;");
+        });
+
+        // click on the second tab
+        await liTabs.at(1).trigger("click");
+        await flushPromises();
+
+        // expect the second job to be shown and rest to be hidden
+        jobsContents.wrappers.forEach((jobContent, i) => {
+            expect(jobContent.attributes("style")).toEqual(i === 1 ? "" : "display: none;");
+            expect(liTabs.at(i).attributes("aria-selected")).toEqual(i === 1 ? "true" : "false");
+        });
+    });
+    test("it reacts to prop update", async () => {
+        // verify initial data is displayed for first tab
+        expect(wrapper.find(SELECTORS.JOB_TAB).text()).toBe("new");
+
+        // update first job to change state from 'new' to 'running'
+        iteration = "state_change";
+        // technically, we only need to trigger a prop update, the state
+        // change is handled by the mock server in `getSummary`
+        const updatedJob = { ...jobs[0], state: "running" };
+        await wrapper.setProps({ jobs: [updatedJob, ...jobs.slice(1)] });
+        await flushPromises();
+
+        // verify new data is displayed
+        expect(wrapper.find(SELECTORS.JOB_TAB).text()).toBe("running");
+
+        // update data
+        const additionalJob = { ...jobs[0], id: "3" };
+        await wrapper.setProps({ jobs: [...jobs, additionalJob] });
+        await flushPromises();
+        // verify new data is displayed
+        const ulTabs = wrapper.find(SELECTORS.JOB_TABS_LIST);
+        const liTabs = ulTabs.findAll(SELECTORS.JOB_TAB);
+        expect(liTabs.length).toBe(jobs.length + 1);
+    });
+});
diff --git a/client/src/components/WorkflowInvocationState/JobStep.vue b/client/src/components/WorkflowInvocationState/JobStep.vue
index 694d6304e2ab157d22ba46b558d5c3fdfc546470..89b7e97f102b17a2fd9190d7c95153a3f9e8eda2 100644
--- a/client/src/components/WorkflowInvocationState/JobStep.vue
+++ b/client/src/components/WorkflowInvocationState/JobStep.vue
@@ -1,144 +1,60 @@
-<template>
-    <b-card v-if="jobs">
-        <b-table
-            small
-            caption-top
-            :items="jobsProvider"
-            :fields="fields"
-            primary-key="id"
-            :tbody-tr-class="showingJobCls"
-            :striped="!invocationGraph"
-            @row-clicked="rowClicked">
-            <template v-slot:cell(showing_job)="data">
-                <span v-if="showingJobId === data.item.id || data.item._showDetails">
-                    <FontAwesomeIcon v-if="!invocationGraph" icon="caret-down" size="lg" />
-                    <span v-else>
-                        <FontAwesomeIcon class="text-primary" icon="fa-eye" />
-                    </span>
-                </span>
-                <span v-else>
-                    <FontAwesomeIcon v-if="!invocationGraph" icon="caret-right" size="lg" />
-                    <span v-else>
-                        <FontAwesomeIcon icon="fa-eye" />
-                    </span>
-                </span>
-            </template>
-            <template v-slot:row-details="row">
-                <JobProvider :id="row.item.id" v-slot="{ item, loading }">
-                    <div v-if="loading"><b-spinner label="Loading Job..."></b-spinner></div>
-                    <div v-else>
-                        <b-card>
-                            <JobInformation v-if="item" :job_id="item.id" />
-                            <p></p>
-                            <JobParameters v-if="item" :job-id="item.id" :include-title="false" />
-                        </b-card>
-                    </div>
-                </JobProvider>
-            </template>
-            <template v-slot:cell(create_time)="data">
-                <UtcDate :date="data.value" mode="elapsed" />
-            </template>
-            <template v-slot:cell(update_time)="data">
-                <UtcDate :date="data.value" mode="elapsed" />
-            </template>
-        </b-table>
-    </b-card>
-</template>
-<script>
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faCaretDown, faCaretRight } from "@fortawesome/free-solid-svg-icons";
+<script setup lang="ts">
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import BootstrapVue from "bootstrap-vue";
-import JobInformation from "components/JobInformation/JobInformation";
-import JobParameters from "components/JobParameters/JobParameters";
-import { JobProvider } from "components/providers";
-import UtcDate from "components/UtcDate";
-import Vue from "vue";
+import { BAlert, BTab, BTabs } from "bootstrap-vue";
+import { computed } from "vue";
 
-Vue.use(BootstrapVue);
-library.add(faCaretDown, faCaretRight);
+import { type JobBaseModel } from "@/api/jobs";
+import { getHeaderClass, iconClasses } from "@/composables/useInvocationGraph";
 
-export default {
-    components: {
-        FontAwesomeIcon,
-        UtcDate,
-        JobProvider,
-        JobParameters,
-        JobInformation,
-    },
-    props: {
-        jobs: { type: Array, required: true },
-        invocationGraph: { type: Boolean, default: false },
-        showingJobId: { type: String, default: null },
-    },
-    data() {
-        return {
-            fields: [
-                { key: "showing_job", label: "", sortable: false },
-                { key: "state", sortable: true },
-                { key: "update_time", label: "Updated", sortable: true },
-                { key: "create_time", label: "Created", sortable: true },
-            ],
-            toggledItems: {},
-        };
-    },
-    methods: {
-        jobsProvider(ctx, callback) {
-            // It may seem unnecessary to use a provider here, since the jobs prop
-            // is being updated externally. However we need to keep track of the
-            // _showDetails attribute which determines whether the row is shown as expanded
-            this.$watch(
-                "jobs",
-                function () {
-                    // update new jobs array with current state
-                    const toggledJobs = this.jobs.map((e) => {
-                        return { ...e, _showDetails: !!this.toggledItems[e.id] };
-                    });
-                    callback(toggledJobs);
-                },
-                { immediate: true }
-            );
-            return null;
-        },
-        toggleDetails(item) {
-            // toggle item
-            item._showDetails = !item._showDetails;
-            // update state
-            this.toggledItems[item.id] = item._showDetails;
-        },
-        rowClicked(item) {
-            if (this.invocationGraph) {
-                this.$emit("row-clicked", item.id);
-            } else {
-                this.toggleDetails(item);
-            }
-        },
-        showingJobCls(item, type) {
-            let cls = "job-tr-class cursor-pointer unselectable";
-            if (this.showingJobId === item.id) {
-                cls += " showing-job";
-            }
-            return cls;
-        },
-    },
-};
-</script>
+import JobDetailsDisplayed from "../JobInformation/JobDetails.vue";
+
+interface Props {
+    jobs: JobBaseModel[];
+}
 
-<style lang="scss">
-// NOTE: Couldn't use scoped style due to it not working for the BTable class rows
-@import "theme/blue.scss";
-@import "base.scss";
+const props = withDefaults(defineProps<Props>(), {
+    jobs: () => [],
+});
 
-// Table row class
-.job-tr-class {
-    &:hover {
-        background-color: $brand-secondary;
-    }
-    &.showing-job {
-        background-color: darken($brand-secondary, 10%);
-    }
-    &:not(.showing-job) {
-        border-top: 0.2rem solid $brand-secondary;
-    }
+const firstJob = computed(() => props.jobs[0]);
+const jobCount = computed(() => props.jobs.length);
+
+function getIcon(job: JobBaseModel) {
+    return iconClasses[job.state];
+}
+
+function getTabClass(job: JobBaseModel) {
+    return {
+        ...getHeaderClass(job.state),
+        "d-flex": true,
+        "text-center": true,
+    };
 }
-</style>
+</script>
+
+<template>
+    <BAlert v-if="!jobCount" variant="info" show> No jobs found for this step. </BAlert>
+    <div v-else-if="jobCount === 1 && firstJob">
+        <JobDetailsDisplayed :job-id="firstJob.id" />
+    </div>
+    <BTabs v-else lazy vertical pills card nav-class="p-0" active-tab-class="p-0">
+        <BTab
+            v-for="job in jobs"
+            :key="job.id"
+            data-description="workflow invocation job"
+            :title-item-class="getTabClass(job)"
+            title-link-class="w-100">
+            <template v-slot:title>
+                {{ job.state }}
+                <FontAwesomeIcon
+                    v-if="getIcon(job)"
+                    :class="getIcon(job)?.class"
+                    :icon="getIcon(job)?.icon"
+                    :spin="getIcon(job)?.spin" />
+            </template>
+            <div>
+                <JobDetailsDisplayed :job-id="job.id" />
+            </div>
+        </BTab>
+    </BTabs>
+</template>
diff --git a/client/src/components/WorkflowInvocationState/VegaWrapper.vue b/client/src/components/WorkflowInvocationState/VegaWrapper.vue
new file mode 100644
index 0000000000000000000000000000000000000000..8a46fec2fd0a35d70ebe5a2271552c26cc9294eb
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/VegaWrapper.vue
@@ -0,0 +1,54 @@
+<template>
+    <div ref="chartContainer" :style="style"></div>
+</template>
+
+<script setup lang="ts">
+import { useResizeObserver } from "@vueuse/core";
+import embed, { type VisualizationSpec } from "vega-embed";
+import { computed, onBeforeUnmount, onMounted, ref, watch } from "vue";
+
+export interface VisSpec {
+    spec: VisualizationSpec;
+    fillWidth?: boolean;
+}
+
+const props = withDefaults(defineProps<VisSpec>(), {
+    fillWidth: true,
+});
+
+const style = computed(() => {
+    if (props.fillWidth) {
+        return { width: "100%" };
+    }
+    return {};
+});
+
+const chartContainer = ref<HTMLDivElement | null>(null);
+let vegaView: any;
+
+async function embedChart() {
+    if (vegaView) {
+        vegaView.finalize();
+    }
+    if (chartContainer.value !== null) {
+        const result = await embed(chartContainer.value, props.spec, { renderer: "svg" });
+        vegaView = result.view;
+    }
+}
+
+onMounted(embedChart);
+
+watch(props, embedChart, { immediate: true, deep: true });
+useResizeObserver(chartContainer, () => {
+    if (vegaView) {
+        vegaView.resize();
+    }
+});
+
+// Cleanup the chart when the component is unmounted
+onBeforeUnmount(() => {
+    if (vegaView) {
+        vegaView.finalize();
+    }
+});
+</script>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationExportOptions.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationExportOptions.vue
index 935374a0bba4e02518724b388f06149cbc589a93..c15565b6fb5af2cc2708a5e0103a54b50edae754 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationExportOptions.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationExportOptions.vue
@@ -1,12 +1,9 @@
 <script setup>
 import { BCard } from "bootstrap-vue";
-import { AVAILABLE_INVOCATION_EXPORT_PLUGINS } from "components/Workflow/Invocation/Export/Plugins";
 import { useConfig } from "composables/config";
 
-import InvocationExportPluginCard from "components/Workflow/Invocation/Export/InvocationExportPluginCard.vue";
-import BioComputeObjectExportCard from "components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportCard.vue";
-
-const exportPlugins = AVAILABLE_INVOCATION_EXPORT_PLUGINS;
+import InvocationExportWizard from "@/components/Workflow/Invocation/Export/InvocationExportWizard.vue";
+import BioComputeObjectExportCard from "@/components/Workflow/Invocation/Export/Plugins/BioComputeObject/BioComputeObjectExportCard.vue";
 
 const { config } = useConfig(true);
 
@@ -20,9 +17,7 @@ defineProps({
 
 <template>
     <div v-if="config.enable_celery_tasks">
-        <div v-for="(plugin, index) in exportPlugins" :key="index" class="mb-2">
-            <InvocationExportPluginCard :export-plugin="plugin" :invocation-id="invocationId" />
-        </div>
+        <InvocationExportWizard :invocation-id="invocationId" />
     </div>
     <div v-else>
         <!--
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationMetrics.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationMetrics.vue
new file mode 100644
index 0000000000000000000000000000000000000000..da6962c36db81aa937f3f72b09e53d894c376730
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationMetrics.vue
@@ -0,0 +1,454 @@
+<script setup lang="ts">
+import { BAlert, BButtonGroup, BCol, BContainer, BRow } from "bootstrap-vue";
+import type { VisualizationSpec } from "vega-embed";
+import { computed, ref, watch } from "vue";
+import { type ComputedRef } from "vue";
+
+import { type components, GalaxyApi } from "@/api";
+import { getAppRoot } from "@/onload/loadConfig";
+import { errorMessageAsString } from "@/utils/simple-error";
+import { capitalizeFirstLetter } from "@/utils/strings";
+
+import LoadingSpan from "../LoadingSpan.vue";
+import HelpText from "@/components/Help/HelpText.vue";
+
+const VegaWrapper = () => import("./VegaWrapper.vue");
+
+interface Props {
+    invocationId: string;
+    notTerminal?: boolean;
+}
+const props = defineProps<Props>();
+
+const groupBy = ref<"tool_id" | "step_id">("tool_id");
+const timing = ref<"seconds" | "minutes" | "hours">("seconds");
+const jobMetrics = ref<components["schemas"]["WorkflowJobMetric"][]>();
+const fetchError = ref<string>();
+
+const attributeToLabel = {
+    tool_id: "Tool ID",
+    step_id: "Step",
+};
+
+async function fetchMetrics() {
+    const { data, error } = await GalaxyApi().GET("/api/invocations/{invocation_id}/metrics", {
+        params: {
+            path: {
+                invocation_id: props.invocationId,
+            },
+        },
+    });
+    if (error) {
+        fetchError.value = errorMessageAsString(error);
+    } else {
+        jobMetrics.value = data;
+    }
+}
+
+watch(
+    () => props.invocationId,
+    () => fetchMetrics(),
+    { immediate: true }
+);
+
+function itemToX(item: components["schemas"]["WorkflowJobMetric"]) {
+    if (groupBy.value === "tool_id") {
+        return item.tool_id;
+    } else if (groupBy.value === "step_id") {
+        return `${item.step_index + 1}: ${item.step_label || item.tool_id}`;
+    } else {
+        throw Error("Cannot happen");
+    }
+}
+
+interface boxplotData {
+    x_title: string;
+    y_title: string;
+    helpTerm?: string;
+    values?: { x: string; y: Number }[];
+}
+
+interface barChartData {
+    category_title: string;
+    y_title: string;
+    helpTerm?: string;
+    values?: { category: string; y: Number }[];
+}
+
+interface JobInfo {
+    toolId: string;
+    stepIndex: number;
+    stepLabel: string | null;
+}
+
+interface DerivedMetric {
+    name: string;
+    job_id: string;
+    raw_value: string;
+    tool_id: string;
+    step_index: number;
+    step_label: string | null;
+}
+
+type AnyMetric = components["schemas"]["WorkflowJobMetric"] & DerivedMetric;
+
+function computeAllocatedCoreTime(
+    jobMetrics: components["schemas"]["WorkflowJobMetric"][] | undefined
+): DerivedMetric[] {
+    const walltimePerJob: Record<string, number> = {};
+    const coresPerJob: Record<string, number> = {};
+    const jobInfo: Record<string, JobInfo> = {};
+    jobMetrics?.forEach((jobMetric) => {
+        if (jobMetric.name == "runtime_seconds") {
+            walltimePerJob[jobMetric.job_id] = parseFloat(jobMetric.raw_value);
+            jobInfo[jobMetric.job_id] = {
+                toolId: jobMetric.tool_id,
+                stepIndex: jobMetric.step_index,
+                stepLabel: jobMetric.step_label,
+            };
+        } else if (jobMetric.name == "galaxy_slots") {
+            coresPerJob[jobMetric.job_id] = parseFloat(jobMetric.raw_value);
+        }
+    });
+    const thisMetric: DerivedMetric[] = [];
+    Object.keys(walltimePerJob).map((jobId) => {
+        const walltime: number | undefined = walltimePerJob[jobId];
+        const cores: number | undefined = coresPerJob[jobId];
+        const thisJobInfo = jobInfo[jobId];
+        if (cores && thisJobInfo && walltime) {
+            const metric: DerivedMetric = {
+                name: "allocated_core_time",
+                job_id: jobId,
+                raw_value: (cores * walltime).toString(),
+                tool_id: thisJobInfo.toolId as string,
+                step_index: thisJobInfo.stepIndex,
+                step_label: thisJobInfo.stepLabel,
+            };
+            thisMetric.push(metric);
+        }
+    });
+    return thisMetric;
+}
+
+function metricToSpecData(
+    jobMetrics: AnyMetric[] | undefined,
+    metricName: string,
+    yTitle: string,
+    helpTerm?: string,
+    transform?: (param: number) => number
+): boxplotData {
+    const thisMetric = jobMetrics?.filter((jobMetric) => jobMetric.name == metricName);
+    const values = thisMetric?.map((item) => {
+        let y = parseFloat(item.raw_value);
+        if (transform !== undefined) {
+            y = transform(y);
+        }
+        return {
+            y,
+            x: itemToX(item),
+            job_id: item.job_id,
+            step_index: item.step_index,
+            tooltip: "click to view job",
+        };
+    });
+    return {
+        x_title: attributeToLabel[groupBy.value],
+        y_title: yTitle,
+        helpTerm,
+        values,
+    };
+}
+
+function metricToAggregateData(
+    jobMetrics: AnyMetric[] | undefined,
+    metricName: string,
+    yTitle: string,
+    helpTerm?: string,
+    transform?: (param: number) => number
+): barChartData {
+    const thisMetric = jobMetrics?.filter((jobMetric) => jobMetric.name == metricName);
+    const aggregateByX: Record<string, number> = {};
+    thisMetric?.forEach((item) => {
+        let y = parseFloat(item.raw_value);
+        if (transform !== undefined) {
+            y = transform(y);
+        }
+        const x = itemToX(item);
+        if (!(x in aggregateByX)) {
+            aggregateByX[x] = 0;
+        }
+        if (x in aggregateByX) {
+            aggregateByX[x] += y;
+        }
+    });
+    const values = Object.keys(aggregateByX).map((key) => {
+        const value = aggregateByX[key];
+        return {
+            category: key,
+            y: value || 0,
+        };
+    });
+    return {
+        category_title: attributeToLabel[groupBy.value],
+        y_title: yTitle,
+        helpTerm,
+        values,
+    };
+}
+
+function transformTime(time: number): number {
+    if (timing.value == "minutes") {
+        return time / 60;
+    } else if (timing.value == "hours") {
+        return time / 3600;
+    } else {
+        return time;
+    }
+}
+
+const allocatedCoreTime: ComputedRef<DerivedMetric[]> = computed(() => {
+    return computeAllocatedCoreTime(jobMetrics.value);
+});
+
+const wallclock: ComputedRef<boxplotData> = computed(() => {
+    const title = `Runtime (in ${timingInTitles.value})`;
+    return metricToSpecData(jobMetrics.value, "runtime_seconds", title, "galaxy.jobs.metrics.walltime", transformTime);
+});
+
+const wallclockAggregate: ComputedRef<barChartData> = computed(() => {
+    const title = `Runtime (in ${timingInTitles.value})`;
+    return metricToAggregateData(
+        jobMetrics.value,
+        "runtime_seconds",
+        title,
+        "galaxy.jobs.metrics.walltime",
+        transformTime
+    );
+});
+
+const allocatedCoreTimeSpec: ComputedRef<boxplotData> = computed(() => {
+    const title = `Allocated Core Time (in ${timingInTitles.value})`;
+    return metricToSpecData(
+        allocatedCoreTime.value as AnyMetric[],
+        "allocated_core_time",
+        title,
+        "galaxy.jobs.metrics.allocated_core_time",
+        transformTime
+    );
+});
+
+const allocatedCoreTimeAggregate: ComputedRef<barChartData> = computed(() => {
+    const title = `Allocated Core Time (in ${timingInTitles.value})`;
+    return metricToAggregateData(
+        allocatedCoreTime.value as AnyMetric[],
+        "allocated_core_time",
+        title,
+        "galaxy.jobs.metrics.allocated_core_time",
+        transformTime
+    );
+});
+
+const coresAllocated: ComputedRef<boxplotData> = computed(() => {
+    return metricToSpecData(jobMetrics.value, "galaxy_slots", "Cores Allocated", "galaxy.jobs.metrics.cores");
+});
+
+const memoryAllocated: ComputedRef<boxplotData> = computed(() => {
+    return metricToSpecData(jobMetrics.value, "galaxy_memory_mb", "Memory Allocated (in MB)");
+});
+
+const peakMemory: ComputedRef<boxplotData> = computed(() => {
+    return metricToSpecData(
+        jobMetrics.value,
+        "memory.peak",
+        "Max memory usage recorded (in MB)",
+        undefined,
+        (v) => v / 1024 ** 2
+    );
+});
+
+function itemToBarChartSpec(item: barChartData) {
+    const spec: VisualizationSpec = {
+        $schema: "https://vega.github.io/schema/vega-lite/v5.json",
+        description: "Aggregate data.",
+        data: {
+            values: item.values!,
+        },
+        mark: { type: "bar", tooltip: true },
+        encoding: {
+            order: { field: "y", type: "quantitative", sort: "descending" },
+            y: { field: "y", type: "quantitative", title: item.y_title },
+            color: {
+                field: "category",
+                type: "nominal",
+                sort: { field: "y", order: "descending" },
+                legend: {
+                    type: "symbol",
+                    title: item.category_title,
+                    labelExpr: "truncate(replace(datum.label, /(^\\d+: )?.*\\/repos\\/[^/]+\\/[^/]+\\//, '$1'), 32)",
+                },
+            },
+            tooltip: [
+                { field: "category", type: "nominal", title: item.category_title },
+                { field: "y", type: "quantitative", title: item.y_title },
+            ],
+        },
+        autosize: {
+            type: "fit",
+            resize: true,
+        },
+        width: 400,
+        height: 250,
+    };
+    return spec;
+}
+
+function itemToSpec(item: boxplotData) {
+    const spec: VisualizationSpec = {
+        $schema: "https://vega.github.io/schema/vega-lite/v5.json",
+        description: "A boxplot with jittered points.",
+        data: {
+            values: item.values!,
+        },
+        transform: [
+            {
+                calculate: "random() - 0.5",
+                as: "random_jitter",
+            },
+            {
+                calculate: "'" + getAppRoot() + "jobs/' + datum.job_id + '/view'",
+                as: "url",
+            },
+            {
+                calculate: "parseInt(datum.step_index)",
+                as: "x_numeric",
+            },
+        ],
+        encoding: {
+            y: {
+                field: "y",
+                type: "quantitative",
+                scale: { zero: false },
+                title: item.y_title,
+            },
+            x: {
+                field: "x",
+                type: "ordinal",
+                title: item.x_title,
+                axis: {
+                    labelAngle: -45,
+                    labelAlign: "right",
+                    // 35 seems to be the maximum amount of characters we can display
+                    labelExpr: "truncate(replace(datum.label, /(^\\d+: )?.*\\/repos\\/[^/]+\\/[^/]+\\//, '$1'), 35)",
+                },
+                sort: {
+                    field: "step_index",
+                },
+            },
+        },
+        layer: [
+            {
+                mark: { type: "boxplot", opacity: 0.5 },
+                width: "container",
+            },
+            {
+                mark: {
+                    type: "point",
+                    opacity: 0.7,
+                },
+                encoding: {
+                    xOffset: { field: "random_jitter", type: "quantitative", scale: { domain: [-2, 2] } },
+                    tooltip: { field: "tooltip", type: "nominal" },
+                    href: { field: "url", type: "nominal" },
+                    color: { field: "x", type: "nominal", legend: null },
+                },
+                width: "container",
+                height: 350,
+            },
+        ],
+    };
+    return spec;
+}
+
+const metrics = computed(() => {
+    const items = [
+        wallclock.value,
+        allocatedCoreTimeSpec.value,
+        coresAllocated.value,
+        memoryAllocated.value,
+        peakMemory.value,
+    ].filter((item) => item.values?.length);
+
+    return Object.fromEntries(items.map((item) => [item.y_title, { spec: itemToSpec(item), item: item }]));
+});
+
+const timingInTitles = computed(() => {
+    return capitalizeFirstLetter(timing.value);
+});
+
+const groupByInTitles = computed(() => {
+    return attributeToLabel[groupBy.value];
+});
+</script>
+
+<template>
+    <div>
+        <BAlert v-if="props.notTerminal" variant="warning" show>
+            <LoadingSpan message="Metrics will update and change as the workflow progresses." />
+        </BAlert>
+        <BContainer>
+            <BRow align-h="end" class="mb-2">
+                <BButtonGroup>
+                    <b-dropdown right :text="'Timing: ' + timingInTitles">
+                        <b-dropdown-item @click="timing = 'seconds'">
+                            {{ capitalizeFirstLetter("seconds") }}
+                        </b-dropdown-item>
+                        <b-dropdown-item @click="timing = 'minutes'">
+                            {{ capitalizeFirstLetter("minutes") }}
+                        </b-dropdown-item>
+                        <b-dropdown-item @click="timing = 'hours'">
+                            {{ capitalizeFirstLetter("hours") }}
+                        </b-dropdown-item>
+                    </b-dropdown>
+                    <b-dropdown right :text="'Group By: ' + groupByInTitles">
+                        <b-dropdown-item @click="groupBy = 'tool_id'">Tool</b-dropdown-item>
+                        <b-dropdown-item @click="groupBy = 'step_id'">Workflow Step</b-dropdown-item>
+                    </b-dropdown>
+                </BButtonGroup>
+            </BRow>
+            <BRow>
+                <BCol v-if="wallclockAggregate && wallclockAggregate.values" class="text-center">
+                    <h2 class="h-l truncate text-center">
+                        Aggregate
+                        <HelpText :for-title="true" uri="galaxy.jobs.metrics.walltime" text="Runtime Time" /> (in
+                        {{ timingInTitles }})
+                    </h2>
+                    <VegaWrapper :spec="itemToBarChartSpec(wallclockAggregate)" :fill-width="false" />
+                </BCol>
+                <BCol v-if="allocatedCoreTimeAggregate && allocatedCoreTimeAggregate.values" class="text-center">
+                    <h2 class="h-l truncate text-center">
+                        Aggregate
+                        <HelpText
+                            :for-title="true"
+                            uri="galaxy.jobs.metrics.allocated_core_time"
+                            text="Allocated Core Time" />
+                        (in {{ timingInTitles }})
+                    </h2>
+                    <VegaWrapper :spec="itemToBarChartSpec(allocatedCoreTimeAggregate)" :fill-width="false" />
+                </BCol>
+            </BRow>
+            <BRow v-for="({ spec, item }, key) in metrics" :key="key">
+                <BCol>
+                    <h2 class="h-l truncate text-center">
+                        <span v-if="item.helpTerm">
+                            <HelpText :for-title="true" :uri="item.helpTerm" :text="`${key}`" />
+                        </span>
+                        <span v-else>
+                            {{ key }}
+                        </span>
+                    </h2>
+                    <VegaWrapper :spec="spec" />
+                </BCol>
+            </BRow>
+        </BContainer>
+    </div>
+</template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.test.js b/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.test.js
index f4e069fb3cc739da0d562c1f05a521fc93d59632..8637fc6b8d5f211fd63be91186b39d5909645864 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.test.js
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.test.js
@@ -1,5 +1,6 @@
 import { createTestingPinia } from "@pinia/testing";
 import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
 import { getLocalVue } from "tests/jest/helpers";
 
 import invocationData from "../Workflow/test/json/invocation.json";
@@ -7,57 +8,75 @@ import WorkflowInvocationOverview from "./WorkflowInvocationOverview";
 
 const localVue = getLocalVue();
 
-describe("WorkflowInvocationOverview.vue with terminal invocation", () => {
-    let wrapper;
-    let propsData;
+// Constants
+const workflowData = {
+    id: "workflow-id",
+    name: "Test Workflow",
+    version: 0,
+};
+const selectors = {
+    bAlertStub: "balert-stub",
+};
+const alertMessages = {
+    unOwned: "Workflow is neither importable, nor owned by or shared with current user",
+    nonExistent: "No workflow found for this invocation.",
+};
 
-    beforeEach(async () => {
-        propsData = {
+// Mock the workflow store to return the expected workflow data given the stored workflow ID
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((workflowId) => {
+                if (["unowned-workflow", "nonexistant-workflow"].includes(workflowId)) {
+                    return undefined;
+                }
+                return workflowData;
+            }),
+            fetchWorkflowForInstanceId: jest.fn().mockImplementation((workflowId) => {
+                if (workflowId === "unowned-workflow") {
+                    throw new Error(alertMessages.unOwned);
+                }
+            }),
+        }),
+    };
+});
+
+describe("WorkflowInvocationOverview.vue for a valid/invalid workflow", () => {
+    async function loadWrapper(invocationData) {
+        const propsData = {
             invocation: invocationData,
             invocationAndJobTerminal: true,
             invocationSchedulingTerminal: true,
             jobStatesSummary: {},
         };
-        wrapper = shallowMount(WorkflowInvocationOverview, {
+        const wrapper = shallowMount(WorkflowInvocationOverview, {
             propsData,
             localVue,
             pinia: createTestingPinia(),
         });
-    });
-
-    it("displays pdf report links", async () => {
-        expect(wrapper.find(".invocation-pdf-link").exists()).toBeTruthy();
-    });
-
-    it("doesn't show cancel invocation button", async () => {
-        expect(wrapper.find(".cancel-workflow-scheduling").exists()).toBeFalsy();
-    });
-});
+        await flushPromises();
+        return wrapper;
+    }
 
-describe("WorkflowInvocationOverview.vue with invocation scheduling running", () => {
-    let wrapper;
-    let propsData;
-    let store;
-
-    beforeEach(async () => {
-        propsData = {
-            invocation: invocationData,
-            invocationAndJobTerminal: false,
-            invocationSchedulingTerminal: false,
-            jobStatesSummary: {},
-        };
-        wrapper = shallowMount(WorkflowInvocationOverview, {
-            store,
-            propsData,
-            localVue,
-        });
+    it("displays the workflow invocation graph for a valid workflow", async () => {
+        const wrapper = await loadWrapper(invocationData);
+        expect(wrapper.find("[data-description='workflow invocation graph']").exists()).toBeTruthy();
     });
 
-    it("does not display pdf report links", async () => {
-        expect(wrapper.find(".invocation-pdf-link").exists()).toBeFalsy();
+    it("displays an alert for an unowned workflow", async () => {
+        const wrapper = await loadWrapper({ ...invocationData, workflow_id: "unowned-workflow" });
+        expect(wrapper.find("[data-description='workflow invocation graph']").exists()).toBeFalsy();
+        const alert = wrapper.find(selectors.bAlertStub);
+        expect(alert.text()).toContain(alertMessages.unOwned);
     });
 
-    it("shows cancel invocation button", async () => {
-        expect(wrapper.find(".cancel-workflow-scheduling").exists()).toBeTruthy();
+    it("displays an alert for a nonexistant workflow", async () => {
+        const wrapper = await loadWrapper({ ...invocationData, workflow_id: "nonexistant-workflow" });
+        expect(wrapper.find("[data-description='workflow invocation graph']").exists()).toBeFalsy();
+        const alert = wrapper.find(selectors.bAlertStub);
+        expect(alert.text()).toContain(alertMessages.nonExistent);
     });
 });
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.vue
index ae69835b6479b31b719695d196dfae0ff0af8139..fb79d5bb3d9ede9df550c084c9490b537ecb0fc6 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationOverview.vue
@@ -1,248 +1,69 @@
 <script setup lang="ts">
-import { BAlert, BButton } from "bootstrap-vue";
+import { BAlert } from "bootstrap-vue";
 import { computed } from "vue";
 
-import { InvocationJobsSummary, InvocationStep, WorkflowInvocationElementView } from "@/api/invocations";
+import { type WorkflowInvocationElementView } from "@/api/invocations";
 import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
-import { getRootFromIndexLink } from "@/onload";
 import { withPrefix } from "@/utils/redirect";
 
-import {
-    errorCount as jobStatesSummaryErrorCount,
-    jobCount as jobStatesSummaryJobCount,
-    numTerminal,
-    okCount as jobStatesSummaryOkCount,
-    runningCount as jobStatesSummaryRunningCount,
-} from "./util";
-
 import ExternalLink from "../ExternalLink.vue";
 import HelpText from "../Help/HelpText.vue";
 import InvocationGraph from "../Workflow/Invocation/Graph/InvocationGraph.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
-import ProgressBar from "@/components/ProgressBar.vue";
 import InvocationMessage from "@/components/WorkflowInvocationState/InvocationMessage.vue";
 
-function getUrl(path: string): string {
-    return getRootFromIndexLink() + path;
-}
-
 interface Props {
-    invocation?: WorkflowInvocationElementView;
+    invocation: WorkflowInvocationElementView;
     invocationAndJobTerminal: boolean;
-    invocationSchedulingTerminal: boolean;
     isFullPage?: boolean;
-    jobStatesSummary: InvocationJobsSummary;
-    index?: number;
     isSubworkflow?: boolean;
 }
 
 const props = defineProps<Props>();
 
-const generatePdfTooltip = "Generate PDF report for this workflow invocation";
-
-const { workflow } = useWorkflowInstance(props.invocation?.workflow_id ?? "");
-
-const invocationId = computed<string | undefined>(() => props.invocation?.id);
-
-const indexStr = computed(() => {
-    if (props.index == undefined) {
-        return "";
-    } else {
-        return `${props.index + 1}`;
-    }
-});
-
-const invocationState = computed(() => {
-    return props.invocation?.state || "new";
-});
-
-const invocationStateSuccess = computed(() => {
-    return invocationState.value == "scheduled" && runningCount.value === 0 && props.invocationAndJobTerminal;
-});
-
-const disabledReportTooltip = computed(() => {
-    const state = invocationState.value;
-    const runCount = runningCount.value;
-    if (state != "scheduled") {
-        return `This workflow is not currently scheduled. The current state is ${state}. Once the workflow is fully scheduled and jobs have complete this option will become available.`;
-    } else if (runCount != 0) {
-        return `The workflow invocation still contains ${runCount} running job(s). Once these jobs have completed this option will become available.`;
-    } else {
-        return "Steps for this workflow are still running. A report will be available once complete.";
-    }
-});
-
-const stepCount = computed<number>(() => {
-    return props.invocation?.steps.length || 0;
-});
-
-type StepStateType = { [state: string]: number };
-
-const stepStates = computed<StepStateType>(() => {
-    const stepStates: StepStateType = {};
-    if (!props.invocation) {
-        return {};
-    }
-    const steps: InvocationStep[] = props.invocation?.steps || [];
-    for (const step of steps) {
-        if (!step) {
-            continue;
-        }
-        // the API defined state here allowing null and undefined is odd...
-        const stepState: string = step.state || "unknown";
-        if (!stepStates[stepState]) {
-            stepStates[stepState] = 1;
-        } else {
-            stepStates[stepState] += 1;
-        }
-    }
-    return stepStates;
-});
-
-const invocationPdfLink = computed<string | null>(() => {
-    const id = invocationId.value;
-    if (id) {
-        return getUrl(`api/invocations/${id}/report.pdf`);
-    } else {
-        return null;
-    }
-});
-
-const hasMessages = computed<boolean>(() => {
-    return props.invocation?.messages.length ? true : false;
-});
-
-const stepStatesStr = computed<string>(() => {
-    return `${stepStates.value?.scheduled || 0} of ${stepCount.value} steps successfully scheduled.`;
-});
+const { workflow, loading, error } = useWorkflowInstance(props.invocation.workflow_id);
 
-const okCount = computed<number>(() => {
-    return jobStatesSummaryOkCount(props.jobStatesSummary);
+const uniqueMessages = computed(() => {
+    const messages = props.invocation.messages || [];
+    const uniqueMessagesSet = new Set(messages.map((message) => JSON.stringify(message)));
+    return Array.from(uniqueMessagesSet).map((message) => JSON.parse(message)) as typeof messages;
 });
-
-const runningCount = computed<number>(() => {
-    return jobStatesSummaryRunningCount(props.jobStatesSummary);
-});
-
-const jobCount = computed<number>(() => {
-    return jobStatesSummaryJobCount(props.jobStatesSummary);
-});
-
-const errorCount = computed<number>(() => {
-    return jobStatesSummaryErrorCount(props.jobStatesSummary);
-});
-
-const newCount = computed<number>(() => {
-    return jobCount.value - okCount.value - runningCount.value - errorCount.value;
-});
-
-const jobStatesStr = computed(() => {
-    let jobStr = `${numTerminal(props.jobStatesSummary) || 0} of ${jobCount.value} jobs complete`;
-    if (!props.invocationSchedulingTerminal) {
-        jobStr += " (total number of jobs will change until all steps fully scheduled)";
-    }
-    return `${jobStr}.`;
-});
-
-const emit = defineEmits<{
-    (e: "invocation-cancelled"): void;
-}>();
-
-function onCancel() {
-    emit("invocation-cancelled");
-}
 </script>
 
 <template>
     <div class="mb-3 workflow-invocation-state-component">
-        <div v-if="!invocationAndJobTerminal">
-            <BAlert variant="info" show>
-                <LoadingSpan :message="`Waiting to complete invocation ${indexStr}`" />
-            </BAlert>
-            <BButton
-                v-b-tooltip.noninteractive.hover
-                class="cancel-workflow-scheduling"
-                title="Cancel scheduling of workflow invocation"
-                size="sm"
-                @click="onCancel">
-                <span class="fa fa-times mr-1" /> Cancel
-            </BButton>
-        </div>
-        <div class="d-flex align-items-center">
-            <div v-if="invocationAndJobTerminal" class="mr-1" :class="{ 'd-flex': !hasMessages }">
-                <BButton
-                    v-b-tooltip.hover
-                    :title="invocationStateSuccess ? generatePdfTooltip : disabledReportTooltip"
-                    :disabled="!invocationStateSuccess"
-                    size="sm"
-                    class="invocation-pdf-link text-nowrap w-100"
-                    :class="{ 'mt-1': hasMessages }"
-                    :href="invocationPdfLink"
-                    target="_blank">
-                    Generate PDF
-                </BButton>
-            </div>
-            <div class="w-100">
-                <ProgressBar
-                    v-if="!stepCount"
-                    note="Loading step state summary..."
-                    :loading="true"
-                    class="steps-progress" />
-                <template v-if="invocation && hasMessages">
-                    <InvocationMessage
-                        v-for="message in invocation.messages"
-                        :key="message.reason"
-                        class="steps-progress my-1"
-                        :invocation-message="message"
-                        :invocation="invocation">
-                    </InvocationMessage>
-                </template>
-                <ProgressBar
-                    v-else-if="invocationState == 'cancelled'"
-                    note="Invocation scheduling cancelled - expected jobs and outputs may not be generated."
-                    :error-count="1"
-                    class="steps-progress" />
-                <ProgressBar
-                    v-else-if="invocationState == 'failed'"
-                    note="Invocation scheduling failed - Galaxy administrator may have additional details in logs."
-                    :error-count="1"
-                    class="steps-progress" />
-                <ProgressBar
-                    v-else
-                    :note="stepStatesStr"
-                    :total="stepCount"
-                    :ok-count="stepStates.scheduled"
-                    :loading="!invocationSchedulingTerminal"
-                    class="steps-progress" />
-                <ProgressBar
-                    :note="jobStatesStr"
-                    :total="jobCount"
-                    :ok-count="okCount"
-                    :running-count="runningCount"
-                    :new-count="newCount"
-                    :error-count="errorCount"
-                    :loading="!invocationAndJobTerminal"
-                    class="jobs-progress" />
-            </div>
+        <BAlert v-if="isSubworkflow" variant="secondary" show>
+            This subworkflow is
+            <HelpText :uri="`galaxy.invocations.states.${invocation.state}`" :text="invocation.state" />.
+            <ExternalLink :href="withPrefix(`/workflows/invocations/${invocation.id}`)"> Click here </ExternalLink>
+            to view this subworkflow in graph view.
+        </BAlert>
+        <div v-if="uniqueMessages.length" class="d-flex align-items-center">
+            <InvocationMessage
+                v-for="message in uniqueMessages"
+                :key="message.reason"
+                class="steps-progress my-1 w-100"
+                :invocation-message="message"
+                :invocation="invocation">
+            </InvocationMessage>
         </div>
-        <!-- An invocation has been loaded, display the graph -->
-        <div v-if="invocation">
-            <div v-if="workflow && !isSubworkflow">
-                <InvocationGraph
-                    class="mt-1"
-                    :invocation="invocation"
-                    :workflow="workflow"
-                    :is-terminal="invocationAndJobTerminal"
-                    :is-scheduled="invocationSchedulingTerminal"
-                    :is-full-page="isFullPage"
-                    :show-minimap="isFullPage" />
-            </div>
-            <BAlert v-else-if="isSubworkflow" variant="secondary" show>
-                This subworkflow is
-                <HelpText :uri="`galaxy.invocations.states.${invocation.state}`" :text="invocation.state" />.
-                <ExternalLink :href="withPrefix(`/workflows/invocations/${invocation.id}`)"> Click here </ExternalLink>
-                to view this subworkflow in graph view.
-            </BAlert>
+        <!-- Once the workflow for the invocation has been loaded, display the graph -->
+        <BAlert v-if="loading" variant="info" show>
+            <LoadingSpan message="Loading workflow..." />
+        </BAlert>
+        <BAlert v-else-if="error" variant="danger" show>
+            {{ error }}
+        </BAlert>
+        <div v-else-if="workflow && !isSubworkflow">
+            <InvocationGraph
+                class="mt-1"
+                data-description="workflow invocation graph"
+                :invocation="invocation"
+                :workflow="workflow"
+                :is-terminal="invocationAndJobTerminal"
+                :is-full-page="isFullPage"
+                :show-minimap="isFullPage" />
         </div>
+        <BAlert v-else-if="!workflow" variant="info" show> No workflow found for this invocation. </BAlert>
     </div>
 </template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
index a57261db81100bf870dfea00ff504d0cf1ecff5c..16eeb0808b6b8176221a55870367b97a2c65ffb1 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.ts
@@ -1,5 +1,5 @@
 import { createTestingPinia } from "@pinia/testing";
-import { mount, shallowMount, Wrapper } from "@vue/test-utils";
+import { shallowMount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { PiniaVuePlugin, setActivePinia } from "pinia";
 import { getLocalVue } from "tests/jest/helpers";
@@ -13,6 +13,11 @@ localVue.use(PiniaVuePlugin);
 
 const selectors = {
     invocationSummary: ".invocation-overview",
+    bAlertStub: "balert-stub",
+    spanElement: "span",
+    invocationReportTab: '[titleitemclass="invocation-report-tab"]',
+    invocationExportTab: '[titleitemclass="invocation-export-tab"]',
+    fullPageHeading: "anonymous-stub[h1='true']",
 };
 
 /** Invocation data to be expected in the store */
@@ -51,7 +56,11 @@ const invocationJobsSummaryById = {
 // Mock the invocation store to return the expected invocation data given the invocation ID
 jest.mock("@/stores/invocationStore", () => {
     const originalModule = jest.requireActual("@/stores/invocationStore");
-    const mockFetchInvocationForId = jest.fn();
+    const mockFetchInvocationForId = jest.fn().mockImplementation((fetchParams) => {
+        if (fetchParams.id === "error-invocation") {
+            throw new Error("User does not own specified item.");
+        }
+    });
     const mockFetchInvocationJobsSummaryForId = jest.fn();
     return {
         ...originalModule,
@@ -71,32 +80,42 @@ jest.mock("@/stores/invocationStore", () => {
     };
 });
 
+// Mock the workflow store to return a workflow for `getStoredWorkflowByInstanceId`
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation(() => {
+                return {
+                    id: "workflow-id",
+                    name: "Test Workflow",
+                    version: 0,
+                };
+            }),
+        }),
+    };
+});
+
 /** Mount the WorkflowInvocationState component with the given invocation ID
  * @param invocationId The invocation ID to be passed as a prop
+ * @param shallow Whether to use shallowMount or mount
+ * @param fullPage Whether to render the header as well or just the invocation state tabs
  * @returns The mounted wrapper
  */
-async function mountWorkflowInvocationState(invocationId: string, shallow = true) {
+async function mountWorkflowInvocationState(invocationId: string, isFullPage = false) {
     const pinia = createTestingPinia();
     setActivePinia(pinia);
 
-    let wrapper;
-    if (shallow) {
-        wrapper = shallowMount(WorkflowInvocationState as object, {
-            propsData: {
-                invocationId,
-            },
-            pinia,
-            localVue,
-        });
-    } else {
-        wrapper = mount(WorkflowInvocationState as object, {
-            propsData: {
-                invocationId,
-            },
-            pinia,
-            localVue,
-        });
-    }
+    const wrapper = shallowMount(WorkflowInvocationState as object, {
+        propsData: {
+            invocationId,
+            isFullPage,
+        },
+        pinia,
+        localVue,
+    });
     await flushPromises();
     return wrapper;
 }
@@ -106,8 +125,8 @@ describe("WorkflowInvocationState check invocation and job terminal states", ()
         const wrapper = await mountWorkflowInvocationState(invocationData.id);
         expect(isInvocationAndJobTerminal(wrapper)).toBe(true);
 
-        // Neither the invocation nor the jobs summary should be fetched for terminal invocations
-        assertInvocationFetched(0);
+        // Invocation is fetched once and the jobs summary isn't fetched at all for terminal invocations
+        assertInvocationFetched(1);
         assertJobsSummaryFetched(0);
     });
 
@@ -115,17 +134,23 @@ describe("WorkflowInvocationState check invocation and job terminal states", ()
         const wrapper = await mountWorkflowInvocationState("not-fetched-invocation");
         expect(isInvocationAndJobTerminal(wrapper)).toBe(false);
 
-        // Both, the invocation and jobs summary should be fetched once if the invocation is not in the store
+        // Invocation is fetched once and the jobs summary is then never fetched if the invocation is not in the store
         assertInvocationFetched(1);
-        assertJobsSummaryFetched(1);
+        assertJobsSummaryFetched(0);
+
+        // expect there to be an alert for the missing invocation
+        const alert = wrapper.find(selectors.bAlertStub);
+        expect(alert.attributes("variant")).toBe("info");
+        const span = alert.find(selectors.spanElement);
+        expect(span.text()).toBe("Invocation not found.");
     });
 
     it("determines that invocation is not terminal with non-terminal state", async () => {
         const wrapper = await mountWorkflowInvocationState("non-terminal-id");
         expect(isInvocationAndJobTerminal(wrapper)).toBe(false);
 
-        // Only the invocation should be fetched for non-terminal invocations
-        assertInvocationFetched(1);
+        // Only the invocation is fetched for non-terminal invocations; once for the initial fetch and then for the polling
+        assertInvocationFetched(2);
         assertJobsSummaryFetched(0);
     });
 
@@ -133,22 +158,40 @@ describe("WorkflowInvocationState check invocation and job terminal states", ()
         const wrapper = await mountWorkflowInvocationState("non-terminal-jobs");
         expect(isInvocationAndJobTerminal(wrapper)).toBe(false);
 
-        // Only the jobs summary should be fetched, not the invocation since it is in scheduled/terminal state
-        assertInvocationFetched(0);
+        // Only the jobs summary should be polled, the invocation is initially fetched only since it is in scheduled/terminal state
+        assertInvocationFetched(1);
         assertJobsSummaryFetched(1);
     });
+
+    it("determines that errored invocation fetches are handled correctly", async () => {
+        const wrapper = await mountWorkflowInvocationState("error-invocation");
+        expect(isInvocationAndJobTerminal(wrapper)).toBe(false);
+
+        // Invocation is fetched once and the jobs summary isn't fetched at all for errored invocations
+        assertInvocationFetched(1);
+        assertJobsSummaryFetched(0);
+
+        // expect there to be an alert for the handled error
+        const alert = wrapper.find(selectors.bAlertStub);
+        expect(alert.attributes("variant")).toBe("danger");
+        expect(alert.text()).toBe("User does not own specified item.");
+    });
 });
 
-describe("WorkflowInvocationState check 'Report' tab disabled state", () => {
-    it("determines that 'Report' tab is disabled for non-terminal invocation", async () => {
-        const wrapper = await mountWorkflowInvocationState("non-terminal-id", false);
-        const reportTab = wrapper.find(".invocation-report-tab").find(".nav-link");
-        expect(reportTab.classes()).toContain("disabled");
+describe("WorkflowInvocationState check 'Report' and 'Export' tab disabled state and header", () => {
+    it("for non-terminal invocation", async () => {
+        const wrapper = await mountWorkflowInvocationState("non-terminal-id");
+        const reportTab = wrapper.find(selectors.invocationReportTab);
+        expect(reportTab.attributes("disabled")).toBe("true");
+        const exportTab = wrapper.find(selectors.invocationExportTab);
+        expect(exportTab.attributes("disabled")).toBe("true");
     });
-    it("determines that 'Report' tab is not disabled for terminal invocation", async () => {
-        const wrapper = await mountWorkflowInvocationState(invocationData.id, false);
-        const reportTab = wrapper.find(".invocation-report-tab").find(".nav-link");
-        expect(reportTab.classes()).not.toContain("disabled");
+    it("for terminal invocation", async () => {
+        const wrapper = await mountWorkflowInvocationState(invocationData.id);
+        const reportTab = wrapper.find(selectors.invocationReportTab);
+        expect(reportTab.attributes("disabled")).toBeUndefined();
+        const exportTab = wrapper.find(selectors.invocationExportTab);
+        expect(exportTab.attributes("disabled")).toBeUndefined();
     });
 });
 
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index c71970e3691ca63c6ee88f259064304b529a2725..741702b1cdc24798f27ad3ad91584d966b85da71 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -1,43 +1,44 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faArrowLeft, faClock, faEdit, faEye, faHdd, faPlay, faSitemap } from "@fortawesome/free-solid-svg-icons";
+import { faExclamation, faSquare, faTimes } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BButtonGroup, BTab, BTabs } from "bootstrap-vue";
-import { computed, onMounted, onUnmounted, ref, watch } from "vue";
+import { BAlert, BBadge, BButton, BTab, BTabs } from "bootstrap-vue";
+import { computed, onUnmounted, ref, watch } from "vue";
 
-import { type InvocationJobsSummary, type WorkflowInvocationElementView } from "@/api/invocations";
-import type { StoredWorkflowDetailed } from "@/api/workflows";
+import { type InvocationJobsSummary, type InvocationStep, type WorkflowInvocationElementView } from "@/api/invocations";
 import { useAnimationFrameResizeObserver } from "@/composables/sensors/animationFrameResizeObserver";
 import { useInvocationStore } from "@/stores/invocationStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
-import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
-import { cancelWorkflowScheduling } from "./services";
-import { isTerminal, jobCount, runningCount } from "./util";
+import {
+    errorCount as jobStatesSummaryErrorCount,
+    isTerminal,
+    jobCount as jobStatesSummaryJobCount,
+    numTerminal,
+    okCount as jobStatesSummaryOkCount,
+    runningCount as jobStatesSummaryRunningCount,
+} from "./util";
 
-import Heading from "../Common/Heading.vue";
-import SwitchToHistoryLink from "../History/SwitchToHistoryLink.vue";
-import UtcDate from "../UtcDate.vue";
+import ProgressBar from "../ProgressBar.vue";
+import WorkflowInvocationSteps from "../Workflow/Invocation/Graph/WorkflowInvocationSteps.vue";
 import InvocationReport from "../Workflow/InvocationReport.vue";
-import WorkflowInvocationsCount from "../Workflow/WorkflowInvocationsCount.vue";
-import WorkflowRunButton from "../Workflow/WorkflowRunButton.vue";
+import WorkflowAnnotation from "../Workflow/WorkflowAnnotation.vue";
+import WorkflowNavigationTitle from "../Workflow/WorkflowNavigationTitle.vue";
 import WorkflowInvocationExportOptions from "./WorkflowInvocationExportOptions.vue";
 import WorkflowInvocationInputOutputTabs from "./WorkflowInvocationInputOutputTabs.vue";
+import WorkflowInvocationMetrics from "./WorkflowInvocationMetrics.vue";
 import WorkflowInvocationOverview from "./WorkflowInvocationOverview.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
-library.add(faArrowLeft, faClock, faEdit, faEye, faHdd, faPlay, faSitemap);
-
 interface Props {
     invocationId: string;
-    index?: number;
     isSubworkflow?: boolean;
     isFullPage?: boolean;
-    fromPanel?: boolean;
+    success?: boolean;
+    newHistoryTarget?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    index: undefined,
     isSubworkflow: false,
 });
 
@@ -49,6 +50,9 @@ const invocationStore = useInvocationStore();
 
 const stepStatesInterval = ref<any>(undefined);
 const jobStatesInterval = ref<any>(undefined);
+const invocationLoaded = ref(false);
+const errorMessage = ref<string | null>(null);
+const cancellingInvocation = ref(false);
 
 // after the report tab is first activated, no longer lazy-render it from then on
 const reportActive = ref(false);
@@ -62,6 +66,26 @@ watch(
     }
 );
 
+const workflowStore = useWorkflowStore();
+const tabsDisabled = computed(
+    () =>
+        !invocationStateSuccess.value ||
+        !invocation.value ||
+        !workflowStore.getStoredWorkflowByInstanceId(invocation.value.workflow_id)
+);
+
+/** Tooltip message for the a tab when it is disabled */
+const disabledTabTooltip = computed(() => {
+    const state = invocationState.value;
+    if (state != "scheduled") {
+        return `This workflow is not currently scheduled. The current state is ${state}. Once the workflow is fully scheduled and jobs have complete any disabled tabs will become available.`;
+    } else if (runningCount.value != 0) {
+        return `The workflow invocation still contains ${runningCount.value} running job(s). Once these jobs have completed any disabled tabs will become available.`;
+    } else {
+        return "Steps for this workflow are still running. Any disabled tabs will be available once complete.";
+    }
+});
+
 const invocationTabs = ref<BTabs>();
 const scrollableDiv = computed(() => invocationTabs.value?.$el.querySelector(".tab-content") as HTMLElement);
 const isScrollable = ref(false);
@@ -69,8 +93,10 @@ useAnimationFrameResizeObserver(scrollableDiv, ({ clientSize, scrollSize }) => {
     isScrollable.value = scrollSize.height >= clientSize.height + 1;
 });
 
-const invocation = computed(
-    () => invocationStore.getInvocationById(props.invocationId) as WorkflowInvocationElementView
+const invocation = computed(() =>
+    invocationLoaded.value
+        ? (invocationStore.getInvocationById(props.invocationId) as WorkflowInvocationElementView)
+        : null
 );
 const invocationState = computed(() => invocation.value?.state || "new");
 const invocationAndJobTerminal = computed(() => invocationSchedulingTerminal.value && jobStatesTerminal.value);
@@ -82,7 +108,7 @@ const invocationSchedulingTerminal = computed(() => {
     );
 });
 const jobStatesTerminal = computed(() => {
-    if (invocationSchedulingTerminal.value && jobCount(jobStatesSummary.value as InvocationJobsSummary) === 0) {
+    if (invocationSchedulingTerminal.value && jobCount.value === 0) {
         // no jobs for this invocation (think subworkflow or just inputs)
         return true;
     }
@@ -93,30 +119,103 @@ const jobStatesSummary = computed(() => {
     return (!jobsSummary ? null : jobsSummary) as InvocationJobsSummary;
 });
 const invocationStateSuccess = computed(() => {
-    return (
-        invocationState.value == "scheduled" &&
-        runningCount(jobStatesSummary.value) === 0 &&
-        invocationAndJobTerminal.value
-    );
+    return invocationState.value == "scheduled" && runningCount.value === 0 && invocationAndJobTerminal.value;
 });
 
-const workflowStore = useWorkflowStore();
+type StepStateType = { [state: string]: number };
 
-const isDeletedWorkflow = computed(() => getWorkflow()?.deleted === true);
-const workflowVersion = computed(() => getWorkflow()?.version);
+const stepStates = computed<StepStateType>(() => {
+    const stepStates: StepStateType = {};
+    const steps: InvocationStep[] = invocation.value?.steps || [];
+    for (const step of steps) {
+        if (!step) {
+            continue;
+        }
+        // the API defined state here allowing null and undefined is odd...
+        const stepState: string = step.state || "unknown";
+        if (!stepStates[stepState]) {
+            stepStates[stepState] = 1;
+        } else {
+            stepStates[stepState] += 1;
+        }
+    }
+    return stepStates;
+});
+
+const stepCount = computed<number>(() => {
+    return invocation.value?.steps.length || 0;
+});
+
+const stepStatesStr = computed<string>(() => {
+    return `${stepStates.value?.scheduled || 0} of ${stepCount.value} steps successfully scheduled.`;
+});
 
-onMounted(() => {
-    pollStepStatesUntilTerminal();
-    pollJobStatesUntilTerminal();
+const okCount = computed<number>(() => {
+    return jobStatesSummaryOkCount(jobStatesSummary.value);
 });
 
+const errorCount = computed<number>(() => {
+    return jobStatesSummaryErrorCount(jobStatesSummary.value);
+});
+
+const runningCount = computed<number>(() => {
+    return jobStatesSummaryRunningCount(jobStatesSummary.value);
+});
+
+const jobCount = computed<number>(() => {
+    return jobStatesSummaryJobCount(jobStatesSummary.value);
+});
+
+const newCount = computed<number>(() => {
+    return jobCount.value - okCount.value - runningCount.value - errorCount.value;
+});
+
+const jobStatesStr = computed(() => {
+    let jobStr = `${numTerminal(jobStatesSummary.value) || 0} of ${jobCount.value} jobs complete`;
+    if (!invocationSchedulingTerminal.value) {
+        jobStr += " (total number of jobs will change until all steps fully scheduled)";
+    }
+    return `${jobStr}.`;
+});
+
+watch(
+    () => props.invocationId,
+    async (id) => {
+        invocationLoaded.value = false;
+        try {
+            await invocationStore.fetchInvocationForId({ id });
+            invocationLoaded.value = true;
+            // Only start polling if there is a valid invocation
+            if (invocation.value) {
+                await pollStepStatesUntilTerminal();
+                await pollJobStatesUntilTerminal();
+            }
+        } catch (e) {
+            errorMessage.value = errorMessageAsString(e);
+        }
+    },
+    { immediate: true }
+);
+
+const storeId = computed(() => (invocation.value ? `invocation-${invocation.value.id}` : undefined));
+
+watch(
+    () => invocationSchedulingTerminal.value,
+    async (newVal, oldVal) => {
+        if (oldVal && !newVal) {
+            // If the invocation was terminal and now is not, start polling again
+            await pollStepStatesUntilTerminal();
+        }
+    }
+);
+
 onUnmounted(() => {
     clearTimeout(stepStatesInterval.value);
     clearTimeout(jobStatesInterval.value);
 });
 
 async function pollStepStatesUntilTerminal() {
-    if (!invocation.value || !invocationSchedulingTerminal.value) {
+    if (!invocationSchedulingTerminal.value) {
         await invocationStore.fetchInvocationForId({ id: props.invocationId });
         stepStatesInterval.value = setTimeout(pollStepStatesUntilTerminal, 3000);
     }
@@ -130,99 +229,84 @@ async function pollJobStatesUntilTerminal() {
 function onError(e: any) {
     console.error(e);
 }
-function onCancel() {
-    emit("invocation-cancelled");
-}
-function cancelWorkflowSchedulingLocal() {
-    cancelWorkflowScheduling(props.invocationId).then(onCancel).catch(onError);
-}
-
-function getWorkflow() {
-    return invocation.value?.workflow_id
-        ? (workflowStore.getStoredWorkflowByInstanceId(
-              invocation.value?.workflow_id
-          ) as unknown as StoredWorkflowDetailed)
-        : undefined;
-}
-
-function getWorkflowId() {
-    return invocation.value?.workflow_id
-        ? workflowStore.getStoredWorkflowIdByInstanceId(invocation.value?.workflow_id)
-        : undefined;
-}
-
-function getWorkflowName() {
-    return workflowStore.getStoredWorkflowNameByInstanceId(invocation.value?.workflow_id);
+async function onCancel() {
+    try {
+        cancellingInvocation.value = true;
+        await invocationStore.cancelWorkflowScheduling(props.invocationId);
+    } catch (e) {
+        onError(e);
+    } finally {
+        emit("invocation-cancelled");
+        cancellingInvocation.value = false;
+    }
 }
 </script>
 
 <template>
-    <div v-if="invocation" class="d-flex flex-column w-100">
-        <div v-if="props.isFullPage" class="d-flex flex-gapx-1">
-            <Heading h1 separator inline truncate size="xl" class="flex-grow-1">
-                Invoked Workflow: "{{ getWorkflowName() }}"
-            </Heading>
-
-            <div v-if="!props.fromPanel">
+    <div v-if="invocation" class="d-flex flex-column w-100" data-description="workflow invocation state">
+        <WorkflowNavigationTitle
+            v-if="props.isFullPage"
+            :invocation="invocation"
+            :workflow-id="invocation.workflow_id"
+            :success="props.success">
+            <template v-slot:workflow-title-actions>
                 <BButton
-                    v-b-tooltip.hover.noninteractive
-                    :title="localize('Return to Invocations List')"
-                    class="text-nowrap"
+                    v-if="!invocationAndJobTerminal"
+                    v-b-tooltip.noninteractive.hover
+                    title="Cancel scheduling of workflow invocation"
+                    data-description="header cancel invocation button"
                     size="sm"
-                    variant="outline-primary"
-                    to="/workflows/invocations">
-                    <FontAwesomeIcon :icon="faArrowLeft" class="mr-1" />
-                    <span v-localize>Invocations List</span>
+                    class="text-decoration-none"
+                    variant="link"
+                    :disabled="cancellingInvocation || invocationState == 'cancelling'"
+                    @click="onCancel">
+                    <FontAwesomeIcon :icon="faSquare" fixed-width />
+                    Cancel
                 </BButton>
-            </div>
-        </div>
-        <div v-if="props.isFullPage" class="py-2 pl-3 d-flex justify-content-between align-items-center">
-            <div>
-                <i>
-                    <FontAwesomeIcon :icon="faClock" class="mr-1" />invoked
-                    <UtcDate :date="invocation.update_time" mode="elapsed" />
-                </i>
-                <span class="d-flex flex-gapx-1 align-items-center">
-                    <FontAwesomeIcon :icon="faHdd" />History:
-                    <SwitchToHistoryLink :history-id="invocation.history_id" />
-                </span>
-            </div>
-            <div v-if="getWorkflow()" class="d-flex flex-gapx-1 align-items-center">
-                <div class="d-flex flex-column align-items-end mr-2">
-                    <span v-if="workflowVersion !== undefined" class="mb-1">
-                        <FontAwesomeIcon :icon="faSitemap" />
-                        Workflow Version: {{ workflowVersion + 1 }}
-                    </span>
-                    <WorkflowInvocationsCount class="float-right" :workflow="getWorkflow()" />
+            </template>
+        </WorkflowNavigationTitle>
+        <WorkflowAnnotation
+            v-if="props.isFullPage"
+            :workflow-id="invocation.workflow_id"
+            :invocation-update-time="invocation.update_time"
+            :history-id="invocation.history_id"
+            :new-history-target="props.newHistoryTarget">
+            <template v-slot:middle-content>
+                <div class="progress-bars mx-1">
+                    <ProgressBar
+                        v-if="!stepCount"
+                        note="Loading step state summary..."
+                        :loading="true"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else-if="invocationState == 'cancelled'"
+                        note="Invocation scheduling cancelled - expected jobs and outputs may not be generated."
+                        :error-count="1"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else-if="invocationState == 'failed'"
+                        note="Invocation scheduling failed - Galaxy administrator may have additional details in logs."
+                        :error-count="1"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else
+                        :note="stepStatesStr"
+                        :total="stepCount"
+                        :ok-count="stepStates.scheduled"
+                        :loading="!invocationSchedulingTerminal"
+                        class="steps-progress" />
+                    <ProgressBar
+                        :note="jobStatesStr"
+                        :total="jobCount"
+                        :ok-count="okCount"
+                        :running-count="runningCount"
+                        :new-count="newCount"
+                        :error-count="errorCount"
+                        :loading="!invocationAndJobTerminal"
+                        class="jobs-progress" />
                 </div>
-                <BButtonGroup vertical>
-                    <BButton
-                        v-b-tooltip.hover.noninteractive.html
-                        :title="
-                            !isDeletedWorkflow
-                                ? `<b>Edit</b><br>${getWorkflowName()}`
-                                : 'This workflow has been deleted.'
-                        "
-                        size="sm"
-                        variant="secondary"
-                        :disabled="isDeletedWorkflow"
-                        :to="`/workflows/edit?id=${getWorkflowId()}&version=${workflowVersion}`">
-                        <FontAwesomeIcon :icon="faEdit" />
-                        <span v-localize>Edit</span>
-                    </BButton>
-                    <WorkflowRunButton
-                        :id="getWorkflowId() || ''"
-                        :title="
-                            !isDeletedWorkflow
-                                ? `<b>Rerun</b><br>${getWorkflowName()}`
-                                : 'This workflow has been deleted.'
-                        "
-                        :disabled="isDeletedWorkflow"
-                        full
-                        :version="workflowVersion" />
-                </BButtonGroup>
-            </div>
-        </div>
+            </template>
+        </WorkflowAnnotation>
         <BTabs
             ref="invocationTabs"
             class="mt-1 d-flex flex-column overflow-auto"
@@ -231,37 +315,96 @@ function getWorkflowName() {
                 <WorkflowInvocationOverview
                     class="invocation-overview"
                     :invocation="invocation"
-                    :index="index"
                     :is-full-page="props.isFullPage"
                     :invocation-and-job-terminal="invocationAndJobTerminal"
-                    :invocation-scheduling-terminal="invocationSchedulingTerminal"
-                    :job-states-summary="jobStatesSummary"
-                    :is-subworkflow="isSubworkflow"
-                    @invocation-cancelled="cancelWorkflowSchedulingLocal" />
+                    :is-subworkflow="isSubworkflow" />
+            </BTab>
+            <BTab v-if="!isSubworkflow" title="Steps" lazy>
+                <WorkflowInvocationSteps
+                    v-if="invocation && storeId"
+                    :invocation="invocation"
+                    :store-id="storeId"
+                    :is-full-page="props.isFullPage" />
             </BTab>
             <WorkflowInvocationInputOutputTabs :invocation="invocation" />
             <!-- <BTab title="Workflow Overview">
                 <p>TODO: Insert readonly version of workflow editor here</p>
             </BTab> -->
             <BTab
+                v-if="!props.isSubworkflow"
                 title="Report"
                 title-item-class="invocation-report-tab"
-                :disabled="!invocationStateSuccess"
+                :disabled="tabsDisabled"
                 :lazy="reportLazy"
                 :active.sync="reportActive">
                 <InvocationReport v-if="invocationStateSuccess" :invocation-id="invocation.id" />
             </BTab>
-            <BTab title="Export" lazy>
+            <BTab title="Export" title-item-class="invocation-export-tab" :disabled="tabsDisabled" lazy>
                 <div v-if="invocationAndJobTerminal">
                     <WorkflowInvocationExportOptions :invocation-id="invocation.id" />
                 </div>
-                <BAlert v-else variant="info" show>
-                    <LoadingSpan message="Waiting to complete invocation" />
-                </BAlert>
             </BTab>
+            <BTab title="Metrics" :lazy="true">
+                <WorkflowInvocationMetrics :invocation-id="invocation.id" :not-terminal="!invocationAndJobTerminal" />
+            </BTab>
+            <template v-slot:tabs-end>
+                <div class="ml-auto d-flex align-items-center">
+                    <BBadge
+                        v-if="tabsDisabled"
+                        v-b-tooltip.hover.noninteractive
+                        class="mr-1"
+                        :title="disabledTabTooltip"
+                        variant="primary">
+                        <FontAwesomeIcon :icon="faExclamation" />
+                    </BBadge>
+                    <BButton
+                        v-if="!props.isFullPage && !invocationAndJobTerminal"
+                        v-b-tooltip.noninteractive.hover
+                        class="my-1"
+                        title="Cancel scheduling of workflow invocation"
+                        data-description="cancel invocation button"
+                        size="sm"
+                        @click="onCancel">
+                        <FontAwesomeIcon :icon="faTimes" fixed-width />
+                        Cancel Workflow
+                    </BButton>
+                </div>
+            </template>
         </BTabs>
     </div>
-    <BAlert v-else variant="info" show>
+    <BAlert v-else-if="errorMessage" variant="danger" show>
+        {{ errorMessage }}
+    </BAlert>
+    <BAlert v-else-if="!invocationLoaded" variant="info" show>
         <LoadingSpan message="Loading invocation" />
     </BAlert>
+    <BAlert v-else variant="info" show>
+        <span v-localize>Invocation not found.</span>
+    </BAlert>
 </template>
+
+<style lang="scss">
+// To show the tooltip on the disabled report tab badge
+.invocation-report-tab,
+.invocation-export-tab {
+    .nav-link.disabled {
+        background-color: #e9edf0;
+    }
+}
+</style>
+
+<style scoped lang="scss">
+.progress-bars {
+    // progress bar shrinks to fit divs on either side
+    flex-grow: 1;
+    flex-shrink: 1;
+    max-width: 50%;
+
+    .steps-progress,
+    .jobs-progress {
+        // truncate text in progress bars
+        white-space: nowrap;
+        overflow: hidden;
+    }
+}
+</style>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
index 243c44d428d18f27062380abafe4c7eb8996129f..547da128116526b928f9c2840cb5ba01a82d070c 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
@@ -1,30 +1,20 @@
 <template>
     <div class="d-flex" :data-step="workflowStep.id">
-        <div class="ui-portlet-section" style="width: 100%">
+        <div :class="{ 'ui-portlet-section': !inGraphView }" style="width: 100%">
             <div
+                v-if="!inGraphView"
                 class="portlet-header portlet-operations cursor-pointer"
                 :class="graphStep?.headerClass"
                 role="button"
                 tabindex="0"
                 @keyup.enter="toggleStep"
                 @click="toggleStep">
-                <span :id="`step-icon-${workflowStep.id}`">
-                    <WorkflowStepIcon class="portlet-title-icon" :step-type="workflowStepType" />
-                </span>
-                <ToolLinkPopover :target="`step-icon-${workflowStep.id}`" v-bind="toolProps(workflowStep.id)" />
-                <span class="portlet-title-text">
-                    <u class="step-title">
-                        <WorkflowStepTitle v-bind="titleProps(workflowStep.id)" />
-                    </u>
-                </span>
-                <span class="float-right">
-                    <FontAwesomeIcon
-                        v-if="graphStep?.headerIcon"
-                        class="mr-1"
-                        :icon="graphStep.headerIcon"
-                        :spin="graphStep.headerIconSpin" />
-                    <FontAwesomeIcon :icon="computedExpanded ? 'fa-chevron-up' : 'fa-chevron-down'" />
-                </span>
+                <WorkflowInvocationStepHeader
+                    :workflow-step="workflowStep"
+                    :graph-step="graphStep"
+                    :invocation-step="step"
+                    can-expand
+                    :expanded="computedExpanded" />
             </div>
             <div v-if="computedExpanded" class="portlet-content">
                 <InvocationStepProvider
@@ -35,43 +25,33 @@
                     <div style="min-width: 1">
                         <LoadingSpan v-if="loading" :message="`Loading invocation step details`"> </LoadingSpan>
                         <div v-else>
-                            <details
-                                v-if="Object.values(stepDetails.outputs).length > 0"
-                                class="invocation-step-output-details"
-                                :open="!isDataStep && inGraphView">
-                                <summary><b>Output Datasets</b></summary>
+                            <div
+                                v-if="!isDataStep && Object.values(stepDetails.outputs).length > 0"
+                                class="invocation-step-output-details">
+                                <Heading size="md" separator>Output Datasets</Heading>
                                 <div v-for="(value, name) in stepDetails.outputs" :key="value.id">
                                     <b>{{ name }}</b>
                                     <GenericHistoryItem :item-id="value.id" :item-src="value.src" />
                                 </div>
-                            </details>
-                            <details
-                                v-if="Object.values(stepDetails.output_collections).length > 0"
-                                class="invocation-step-output-collection-details"
-                                :open="!isDataStep && inGraphView">
-                                <summary><b>Output Dataset Collections</b></summary>
+                            </div>
+                            <div
+                                v-if="!isDataStep && Object.values(stepDetails.output_collections).length > 0"
+                                class="invocation-step-output-collection-details">
+                                <Heading size="md" separator>Output Dataset Collections</Heading>
                                 <div v-for="(value, name) in stepDetails.output_collections" :key="value.id">
                                     <b>{{ name }}</b>
                                     <GenericHistoryItem :item-id="value.id" :item-src="value.src" />
                                 </div>
-                            </details>
+                            </div>
                             <div class="portlet-body" style="width: 100%; overflow-x: auto">
-                                <details
+                                <div
                                     v-if="workflowStepType == 'tool'"
                                     class="invocation-step-job-details"
                                     :open="inGraphView">
-                                    <summary>
-                                        <b>Jobs <i>(Click on any job to view its details)</i></b>
-                                    </summary>
-                                    <JobStep
-                                        v-if="stepDetails.jobs?.length"
-                                        :key="inGraphView"
-                                        :jobs="stepDetails.jobs"
-                                        :invocation-graph="inGraphView"
-                                        :showing-job-id="showingJobId"
-                                        @row-clicked="showJob" />
+                                    <Heading size="md" separator>{{ jobStepHeading(stepDetails) }}</Heading>
+                                    <JobStep v-if="stepDetails.jobs?.length" class="mt-1" :jobs="stepDetails.jobs" />
                                     <b-alert v-else v-localize variant="info" show>This step has no jobs</b-alert>
-                                </details>
+                                </div>
                                 <ParameterStep
                                     v-else-if="workflowStepType == 'parameter_input'"
                                     :parameters="[getParamInput(stepDetails)]" />
@@ -118,34 +98,29 @@
     </div>
 </template>
 <script>
-import { library } from "@fortawesome/fontawesome-svg-core";
-import { faChevronDown, faChevronUp } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import GenericHistoryItem from "components/History/Content/GenericItem";
 import LoadingSpan from "components/LoadingSpan";
 import { InvocationStepProvider } from "components/providers";
-import ToolLinkPopover from "components/Tool/ToolLinkPopover";
 import { mapActions, mapState } from "pinia";
 import { useToolStore } from "stores/toolStore";
 import { useWorkflowStore } from "stores/workflowStore";
 
-import JobStep from "./JobStep";
 import ParameterStep from "./ParameterStep";
-import WorkflowStepIcon from "./WorkflowStepIcon";
 import WorkflowStepTitle from "./WorkflowStepTitle";
 
-library.add(faChevronUp, faChevronDown);
+import Heading from "../Common/Heading.vue";
+import JobStep from "./JobStep.vue";
+import WorkflowInvocationStepHeader from "./WorkflowInvocationStepHeader.vue";
 
 export default {
     components: {
         LoadingSpan,
-        FontAwesomeIcon,
+        Heading,
         JobStep,
         ParameterStep,
         InvocationStepProvider,
         GenericHistoryItem,
-        ToolLinkPopover,
-        WorkflowStepIcon,
+        WorkflowInvocationStepHeader,
         WorkflowStepTitle,
         WorkflowInvocationState: () => import("components/WorkflowInvocationState/WorkflowInvocationState"),
     },
@@ -155,7 +130,6 @@ export default {
         workflow: Object,
         graphStep: { type: Object, default: undefined },
         expanded: { type: Boolean, default: undefined },
-        showingJobId: { type: String, default: null },
         inGraphView: { type: Boolean, default: false },
     },
     data() {
@@ -214,19 +188,18 @@ export default {
                 (param) => param.workflow_step_id === stepDetails.workflow_step_id
             );
         },
-        showJob(id) {
-            this.$emit("show-job", id);
+        jobStepHeading(stepDetails) {
+            if (stepDetails.jobs?.length > 1) {
+                return "Jobs (Click on any job to view its details)";
+            } else if (stepDetails.jobs?.length === 1) {
+                return "Job";
+            } else {
+                return "No jobs";
+            }
         },
         toggleStep() {
             this.computedExpanded = !this.computedExpanded;
         },
-        toolProps(stepIndex) {
-            const workflowStep = this.workflow.steps[stepIndex];
-            return {
-                toolId: workflowStep.tool_id,
-                toolVersion: workflowStep.tool_version,
-            };
-        },
         titleProps(stepIndex) {
             const invocationStep = this.invocation.steps[stepIndex];
             const workflowStep = this.workflow.steps[stepIndex];
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationStepHeader.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationStepHeader.vue
new file mode 100644
index 0000000000000000000000000000000000000000..ccd53e78592078ac40fae86af9021615275c0781
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationStepHeader.vue
@@ -0,0 +1,66 @@
+<script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faChevronDown, faChevronUp, faSignInAlt } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+
+import type { InvocationStep } from "@/api/invocations";
+import { isWorkflowInput } from "@/components/Workflow/constants";
+import { type GraphStep, statePlaceholders } from "@/composables/useInvocationGraph";
+import type { Step } from "@/stores/workflowStepStore";
+
+import ToolLinkPopover from "../Tool/ToolLinkPopover.vue";
+import WorkflowStepIcon from "./WorkflowStepIcon.vue";
+import WorkflowStepTitle from "./WorkflowStepTitle.vue";
+
+library.add(faChevronDown, faChevronUp, faSignInAlt);
+
+interface Props {
+    workflowStep: Step;
+    graphStep?: GraphStep;
+    invocationStep?: InvocationStep;
+    canExpand?: boolean;
+    expanded?: boolean;
+}
+
+const props = defineProps<Props>();
+</script>
+
+<template>
+    <div class="d-flex justify-content-between">
+        <div>
+            <span :id="`step-icon-${props.workflowStep.id}`">
+                <WorkflowStepIcon class="portlet-title-icon" :step-type="workflowStep.type" />
+            </span>
+            <ToolLinkPopover
+                :target="`step-icon-${props.workflowStep.id}`"
+                :tool-id="props.workflowStep.tool_id"
+                :tool-version="props.workflowStep.tool_version" />
+            <span class="portlet-title-text">
+                <u class="step-title">
+                    <WorkflowStepTitle
+                        :step-index="props.workflowStep.id"
+                        :step-label="props.invocationStep?.workflow_step_label"
+                        :step-type="props.workflowStep.type"
+                        :step-tool-id="props.workflowStep.tool_id"
+                        :step-subworkflow-id="props.workflowStep.workflow_id" />
+                </u>
+            </span>
+        </div>
+
+        <span v-if="props.graphStep">
+            <span v-if="isWorkflowInput(props.workflowStep.type)">
+                <i>workflow input</i>
+                <FontAwesomeIcon class="ml-1" :icon="faSignInAlt" />
+            </span>
+            <span v-else-if="props.graphStep.state">
+                <i>{{ statePlaceholders[props.graphStep.state] || props.graphStep.state }}</i>
+                <FontAwesomeIcon
+                    v-if="props.graphStep.headerIcon"
+                    class="ml-1"
+                    :icon="props.graphStep.headerIcon"
+                    :spin="props.graphStep.headerIconSpin" />
+            </span>
+            <FontAwesomeIcon v-if="props.canExpand" class="ml-1" :icon="props.expanded ? faChevronUp : faChevronDown" />
+        </span>
+    </div>
+</template>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowStepTitle.vue b/client/src/components/WorkflowInvocationState/WorkflowStepTitle.vue
index 1253d73e3e40904ae9713613000e0fe7d83b1b20..3735415dd58633e5246ad5f1bd116921f3e62a97 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowStepTitle.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowStepTitle.vue
@@ -1,8 +1,11 @@
 <script setup lang="ts">
-import { computed, watch } from "vue";
+import { faExclamationCircle } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { computed, ref, watch } from "vue";
 
 import { useToolStore } from "@/stores/toolStore";
 import { useWorkflowStore } from "@/stores/workflowStore";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 interface WorkflowInvocationStepTitleProps {
     stepIndex: number;
@@ -54,26 +57,36 @@ const title = computed(() => {
             return `Step ${oneBasedStepIndex}: Unknown step type '${workflowStepType}'`;
     }
 });
+const hoverError = ref("");
 
-function initStores() {
+async function initStores() {
     if (props.stepToolId && !toolStore.getToolForId(props.stepToolId)) {
         toolStore.fetchToolForId(props.stepToolId);
     }
 
     if (props.stepSubworkflowId) {
-        workflowStore.fetchWorkflowForInstanceId(props.stepSubworkflowId);
+        try {
+            await workflowStore.fetchWorkflowForInstanceId(props.stepSubworkflowId);
+        } catch (e) {
+            hoverError.value = errorMessageAsString(e, "Error fetching subworkflow");
+        }
     }
 }
 
 watch(
     props,
-    () => {
-        initStores();
+    async () => {
+        await initStores();
     },
     { immediate: true }
 );
 </script>
 
 <template>
-    <span>{{ title }}</span>
+    <span>
+        {{ title }}
+        <span v-b-tooltip.noninteractive.hover.v-danger :title="hoverError">
+            <FontAwesomeIcon v-if="hoverError" class="text-danger" :icon="faExclamationCircle" />
+        </span>
+    </span>
 </template>
diff --git a/client/src/components/WorkflowInvocationState/invocationMessageModel.ts b/client/src/components/WorkflowInvocationState/invocationMessageModel.ts
deleted file mode 100644
index 29ab6a9898478d87b5373f92f573b6d1ecda8ae4..0000000000000000000000000000000000000000
--- a/client/src/components/WorkflowInvocationState/invocationMessageModel.ts
+++ /dev/null
@@ -1,250 +0,0 @@
-/* tslint:disable */
-/* eslint-disable */
-/**
-/* This file was automatically generated from pydantic models by running pydantic2ts.
-/* Do not modify it by hand - just update the pydantic models and then re-run the script
-*/
-
-export type InvocationMessageResponseModel =
-    | GenericInvocationCancellationReviewFailedEncodedDatabaseIdField
-    | GenericInvocationCancellationHistoryDeletedEncodedDatabaseIdField
-    | GenericInvocationCancellationUserRequestEncodedDatabaseIdField
-    | GenericInvocationFailureDatasetFailedEncodedDatabaseIdField
-    | GenericInvocationFailureCollectionFailedEncodedDatabaseIdField
-    | GenericInvocationFailureJobFailedEncodedDatabaseIdField
-    | GenericInvocationFailureOutputNotFoundEncodedDatabaseIdField
-    | GenericInvocationFailureExpressionEvaluationFailedEncodedDatabaseIdField
-    | GenericInvocationFailureWhenNotBooleanEncodedDatabaseIdField
-    | GenericInvocationUnexpectedFailureEncodedDatabaseIdField
-    | GenericInvocationEvaluationWarningWorkflowOutputNotFoundEncodedDatabaseIdField;
-
-export interface GenericInvocationCancellationHistoryDeletedEncodedDatabaseIdField {
-    reason: "history_deleted";
-    /**
-     * History ID of history that was deleted.
-     */
-    history_id: string;
-}
-export interface GenericInvocationCancellationHistoryDeletedInt {
-    reason: "history_deleted";
-    /**
-     * History ID of history that was deleted.
-     */
-    history_id: number;
-}
-export interface GenericInvocationCancellationReviewFailedEncodedDatabaseIdField {
-    reason: "cancelled_on_review";
-    /**
-     * Workflow step id of paused step that did not pass review.
-     */
-    workflow_step_id: number;
-}
-export interface GenericInvocationCancellationReviewFailedInt {
-    reason: "cancelled_on_review";
-    /**
-     * Workflow step id of paused step that did not pass review.
-     */
-    workflow_step_id: number;
-}
-export interface GenericInvocationCancellationUserRequestEncodedDatabaseIdField {
-    reason: "user_request";
-}
-export interface GenericInvocationCancellationUserRequestInt {
-    reason: "user_request";
-}
-export interface GenericInvocationEvaluationWarningWorkflowOutputNotFoundEncodedDatabaseIdField {
-    reason: "workflow_output_not_found";
-    workflow_step_id: number;
-    /**
-     * Output that was designated as workflow output but that has not been found
-     */
-    output_name: string;
-}
-export interface GenericInvocationEvaluationWarningWorkflowOutputNotFoundInt {
-    reason: "workflow_output_not_found";
-    workflow_step_id: number;
-    /**
-     * Output that was designated as workflow output but that has not been found
-     */
-    output_name: string;
-}
-export interface GenericInvocationFailureCollectionFailedEncodedDatabaseIdField {
-    reason: "collection_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * HistoryDatasetCollectionAssociation ID that relates to failure.
-     */
-    hdca_id: string;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureCollectionFailedInt {
-    reason: "collection_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * HistoryDatasetCollectionAssociation ID that relates to failure.
-     */
-    hdca_id: number;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureDatasetFailedEncodedDatabaseIdField {
-    reason: "dataset_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * HistoryDatasetAssociation ID that relates to failure.
-     */
-    hda_id: string;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id?: number;
-}
-export interface GenericInvocationFailureDatasetFailedInt {
-    reason: "dataset_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * HistoryDatasetAssociation ID that relates to failure.
-     */
-    hda_id: number;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id?: number;
-}
-export interface GenericInvocationFailureExpressionEvaluationFailedEncodedDatabaseIdField {
-    reason: "expression_evaluation_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * May contain details to help troubleshoot this problem.
-     */
-    details?: string;
-}
-export interface GenericInvocationFailureExpressionEvaluationFailedInt {
-    reason: "expression_evaluation_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * May contain details to help troubleshoot this problem.
-     */
-    details?: string;
-}
-export interface GenericInvocationFailureJobFailedEncodedDatabaseIdField {
-    reason: "job_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * Job ID that relates to failure.
-     */
-    job_id: string;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureJobFailedInt {
-    reason: "job_failed";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * Job ID that relates to failure.
-     */
-    job_id: number;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureOutputNotFoundEncodedDatabaseIdField {
-    reason: "output_not_found";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    output_name: string;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureOutputNotFoundInt {
-    reason: "output_not_found";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    output_name: string;
-    /**
-     * Workflow step id of step that caused failure.
-     */
-    dependent_workflow_step_id: number;
-}
-export interface GenericInvocationFailureWhenNotBooleanEncodedDatabaseIdField {
-    reason: "when_not_boolean";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * Contains details to help troubleshoot this problem.
-     */
-    details: string;
-}
-export interface GenericInvocationFailureWhenNotBooleanInt {
-    reason: "when_not_boolean";
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id: number;
-    /**
-     * Contains details to help troubleshoot this problem.
-     */
-    details: string;
-}
-export interface GenericInvocationUnexpectedFailureEncodedDatabaseIdField {
-    reason: "unexpected_failure";
-    /**
-     * May contains details to help troubleshoot this problem.
-     */
-    details?: string;
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id?: number;
-}
-export interface GenericInvocationUnexpectedFailureInt {
-    reason: "unexpected_failure";
-    /**
-     * May contains details to help troubleshoot this problem.
-     */
-    details?: string;
-    /**
-     * Workflow step id of step that failed.
-     */
-    workflow_step_id?: number;
-}
diff --git a/client/src/components/WorkflowInvocationState/services.js b/client/src/components/WorkflowInvocationState/services.js
deleted file mode 100644
index 759354aa513d02860d9d50c39a146057993fed92..0000000000000000000000000000000000000000
--- a/client/src/components/WorkflowInvocationState/services.js
+++ /dev/null
@@ -1,14 +0,0 @@
-import axios from "axios";
-import { getRootFromIndexLink } from "onload";
-
-const getUrl = (path) => getRootFromIndexLink() + path;
-
-export function getInvocationJobsSummary(invocationId) {
-    const url = getUrl(`api/invocations/${invocationId}/jobs_summary`);
-    return axios.get(url);
-}
-
-export function cancelWorkflowScheduling(invocationId) {
-    const url = getUrl(`api/invocations/${invocationId}`);
-    return axios.delete(url);
-}
diff --git a/client/src/components/WorkflowInvocationState/test/json/jobs.json b/client/src/components/WorkflowInvocationState/test/json/jobs.json
index daacfc2e5b5b77d9c405cb78a594f84f7f7cd29c..35d0dde725d186e1f44068967e4b1a603540516d 100644
--- a/client/src/components/WorkflowInvocationState/test/json/jobs.json
+++ b/client/src/components/WorkflowInvocationState/test/json/jobs.json
@@ -13,7 +13,7 @@
     {
         "model_class": "Job",
         "id": "2",
-        "state": "new",
+        "state": "running",
         "exit_code": 0,
         "update_time": "2021-01-15T10:38:36.015269",
         "create_time": "2021-01-15T10:38:21.462106",
diff --git a/client/src/components/WorkflowInvocationState/util.ts b/client/src/components/WorkflowInvocationState/util.ts
index bbda2253e93353e108bf0af43edb436bac50231e..cbb466cc1ca3e30d391caabebd3777a3508fc1d2 100644
--- a/client/src/components/WorkflowInvocationState/util.ts
+++ b/client/src/components/WorkflowInvocationState/util.ts
@@ -1,4 +1,4 @@
-import { InvocationJobsSummary } from "@/api/invocations";
+import { type InvocationJobsSummary } from "@/api/invocations";
 
 export const NON_TERMINAL_STATES = ["new", "queued", "running", "waiting"];
 export const ERROR_STATES = ["error", "deleted"];
diff --git a/client/src/components/admin/JobLock.vue b/client/src/components/admin/JobLock.vue
index fb2ada5c53f47af5d473e60bfb65aa57f2654e17..e85c895f385c970c56aa72058b600abf987d3620 100644
--- a/client/src/components/admin/JobLock.vue
+++ b/client/src/components/admin/JobLock.vue
@@ -1,23 +1,28 @@
 <script setup lang="ts">
 import { onMounted, ref, watch } from "vue";
 
-import { jobLockStatus, jobLockUpdate } from "@/api/jobs";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 const jobLock = ref(false);
 const jobLockUpdating = ref(true);
 
-watch(jobLock, async (newVal) => {
+watch(jobLock, async (_newVal) => {
     jobLockUpdating.value = true;
-    const { data } = await jobLockUpdate({ active: jobLock.value });
+    const { data, error } = await GalaxyApi().PUT("/api/job_lock", { body: { active: jobLock.value } });
+    if (error) {
+        rethrowSimple(error);
+    }
     jobLock.value = data.active;
     jobLockUpdating.value = false;
 });
 
 onMounted(async () => {
-    // TODO: see if we can upstream an optional arg when no params are required?
-    // i.e. jobLockStatus() instead of jobLockStatus({})
-    const response = await jobLockStatus({});
-    jobLock.value = response.data.active;
+    const { data, error } = await GalaxyApi().GET("/api/job_lock");
+    if (error) {
+        rethrowSimple(error);
+    }
+    jobLock.value = data.active;
     jobLockUpdating.value = false;
 });
 </script>
diff --git a/client/src/components/admin/Notifications/BroadcastCard.vue b/client/src/components/admin/Notifications/BroadcastCard.vue
index 4e42947cc516e355f632f1ce4cb61de863d46cf9..153c6a3c8e8dc484afb42c83a0759e932845768f 100644
--- a/client/src/components/admin/Notifications/BroadcastCard.vue
+++ b/client/src/components/admin/Notifications/BroadcastCard.vue
@@ -14,7 +14,7 @@ import { computed } from "vue";
 
 import { useConfirmDialog } from "@/composables/confirmDialog";
 import { useMarkdown } from "@/composables/markdown";
-import { BroadcastNotification } from "@/stores/broadcastsStore";
+import { type BroadcastNotification } from "@/stores/broadcastsStore";
 
 import Heading from "@/components/Common/Heading.vue";
 import UtcDate from "@/components/UtcDate.vue";
diff --git a/client/src/components/admin/Notifications/BroadcastForm.test.ts b/client/src/components/admin/Notifications/BroadcastForm.test.ts
index 1f6d35f1e982661d97ab37af35dffd799dd361bc..0c486f8a1198e6317147b495cf2e7e3478d148c3 100644
--- a/client/src/components/admin/Notifications/BroadcastForm.test.ts
+++ b/client/src/components/admin/Notifications/BroadcastForm.test.ts
@@ -4,14 +4,12 @@ import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { HttpResponse, useServerMock } from "@/api/client/__mocks__";
 
 import { generateNewBroadcast, generateRandomString } from "./test.utils";
 
 import BroadcastForm from "./BroadcastForm.vue";
 
-jest.mock("@/api/schema");
-
 const SUBJECT_INPUT_SELECTOR = "#broadcast-subject";
 const MESSAGE_INPUT_SELECTOR = "#broadcast-message";
 const ACTION_LINK_SELECTOR = "#create-action-link";
@@ -47,6 +45,8 @@ async function mountBroadcastForm(props?: object) {
     return { wrapper, mockRouter };
 }
 
+const { server, http } = useServerMock();
+
 describe("BroadcastForm.vue", () => {
     function expectSubmitButton(wrapper: Wrapper<Vue>, enabled: boolean) {
         expect(wrapper.find(SUBMIT_BUTTON_SELECTOR).exists()).toBeTruthy();
@@ -57,7 +57,12 @@ describe("BroadcastForm.vue", () => {
     }
 
     async function createBroadcast(wrapper: Wrapper<Vue>, mockRouter: { push: jest.Mock }, actionsLink = false) {
-        mockFetcher.path("/api/notifications/broadcast").method("post").mock({ data: {} });
+        server.use(
+            http.post("/api/notifications/broadcast", ({ response }) => {
+                // We use untyped here because we don't care about the response
+                return response.untyped(HttpResponse.json({}, { status: 200 }));
+            })
+        );
 
         expectSubmitButton(wrapper, false);
 
@@ -67,7 +72,7 @@ describe("BroadcastForm.vue", () => {
         if (actionsLink) {
             await wrapper.find(ACTION_LINK_SELECTOR).trigger("click");
 
-            await wrapper.vm.$nextTick();
+            await flushPromises();
 
             await wrapper.find("#broadcast-action-link-name-0").setValue("Test link name");
             await wrapper.find("#broadcast-action-link-link-0").setValue("https://test.link");
@@ -77,7 +82,7 @@ describe("BroadcastForm.vue", () => {
 
         await wrapper.find(SUBMIT_BUTTON_SELECTOR).trigger("click");
 
-        await wrapper.vm.$nextTick();
+        await flushPromises();
 
         expect(mockRouter.push).toHaveBeenCalledTimes(1);
         expect(mockRouter.push).toHaveBeenCalledWith("/admin/notifications");
@@ -103,11 +108,15 @@ describe("BroadcastForm.vue", () => {
 
     it("should get broadcast data when id is defined", async () => {
         const FAKE_BROADCAST = generateNewBroadcast({ actionLink: true });
-        mockFetcher.path("/api/notifications/broadcast/{notification_id}").method("get").mock({ data: FAKE_BROADCAST });
+        server.use(
+            http.get("/api/notifications/broadcast/{notification_id}", ({ response }) => {
+                return response(200).json(FAKE_BROADCAST);
+            })
+        );
 
         const { wrapper } = await mountBroadcastForm({ id: FAKE_BROADCAST.id });
 
-        await wrapper.vm.$nextTick();
+        await flushPromises();
 
         expect((wrapper.find(SUBJECT_INPUT_SELECTOR).element as HTMLInputElement).value).toBe(
             FAKE_BROADCAST.content.subject
@@ -121,8 +130,15 @@ describe("BroadcastForm.vue", () => {
 
     it("should update broadcast when id is defined and all inputs are defined", async () => {
         const FAKE_BROADCAST = generateNewBroadcast({ actionLink: true });
-        mockFetcher.path("/api/notifications/broadcast/{notification_id}").method("get").mock({ data: FAKE_BROADCAST });
-        mockFetcher.path("/api/notifications/broadcast/{notification_id}").method("put").mock({ data: {} });
+        server.use(
+            http.get("/api/notifications/broadcast/{notification_id}", ({ response }) => {
+                return response(200).json(FAKE_BROADCAST);
+            }),
+
+            http.put("/api/notifications/broadcast/{notification_id}", ({ response }) => {
+                return response(204).empty();
+            })
+        );
 
         const { wrapper, mockRouter } = await mountBroadcastForm({ id: FAKE_BROADCAST.id });
 
@@ -133,7 +149,7 @@ describe("BroadcastForm.vue", () => {
 
         await wrapper.find(SUBMIT_BUTTON_SELECTOR).trigger("click");
 
-        await wrapper.vm.$nextTick();
+        await flushPromises();
 
         expect(mockRouter.push).toHaveBeenCalledTimes(1);
         expect(mockRouter.push).toHaveBeenCalledWith("/admin/notifications");
@@ -141,7 +157,11 @@ describe("BroadcastForm.vue", () => {
 
     it("should not show the published warning when editing a scheduled broadcast", async () => {
         const FAKE_BROADCAST = generateNewBroadcast({ published: false });
-        mockFetcher.path("/api/notifications/broadcast/{notification_id}").method("get").mock({ data: FAKE_BROADCAST });
+        server.use(
+            http.get("/api/notifications/broadcast/{notification_id}", ({ response }) => {
+                return response(200).json(FAKE_BROADCAST);
+            })
+        );
 
         const { wrapper } = await mountBroadcastForm({ id: FAKE_BROADCAST.id });
 
@@ -150,7 +170,11 @@ describe("BroadcastForm.vue", () => {
 
     it("should show the published published when editing a published broadcast", async () => {
         const FAKE_BROADCAST = generateNewBroadcast({ published: true });
-        mockFetcher.path("/api/notifications/broadcast/{notification_id}").method("get").mock({ data: FAKE_BROADCAST });
+        server.use(
+            http.get("/api/notifications/broadcast/{notification_id}", ({ response }) => {
+                return response(200).json(FAKE_BROADCAST);
+            })
+        );
 
         const { wrapper } = await mountBroadcastForm({ id: FAKE_BROADCAST.id });
 
diff --git a/client/src/components/admin/Notifications/BroadcastForm.vue b/client/src/components/admin/Notifications/BroadcastForm.vue
index ad9007e62c17b8863ec97e272bdc843188f0ac91..9c820da5eb4d6897c8e5f6c5680b77b3c0ecfb37 100644
--- a/client/src/components/admin/Notifications/BroadcastForm.vue
+++ b/client/src/components/admin/Notifications/BroadcastForm.vue
@@ -4,8 +4,8 @@ import { BAlert, BButton, BCol, BFormGroup, BFormInput, BRow } from "bootstrap-v
 import Vue, { computed, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { createBroadcast, fetchBroadcast, updateBroadcast } from "@/api/notifications.broadcast";
-import { type components } from "@/api/schema";
+import { type components, GalaxyApi } from "@/api";
+import { createBroadcast, updateBroadcast } from "@/api/notifications.broadcast";
 import { Toast } from "@/composables/toast";
 import { errorMessageAsString } from "@/utils/simple-error";
 
@@ -40,7 +40,9 @@ const loading = ref(false);
 const broadcastData = ref<BroadcastNotificationCreateRequest>({
     source: "admin",
     variant: "info",
+    category: "broadcast",
     content: {
+        category: "broadcast",
         subject: "",
         message: "",
     },
@@ -106,7 +108,19 @@ async function createOrUpdateBroadcast() {
 async function loadBroadcastData() {
     loading.value = true;
     try {
-        const loadedBroadcast = await fetchBroadcast(props.id);
+        const { data: loadedBroadcast, error } = await GalaxyApi().GET(
+            "/api/notifications/broadcast/{notification_id}",
+            {
+                params: {
+                    path: { notification_id: props.id },
+                },
+            }
+        );
+
+        if (error) {
+            Toast.error(errorMessageAsString(error));
+            return;
+        }
 
         broadcastData.value.publication_time = convertUTCtoLocal(loadedBroadcast.publication_time);
 
@@ -119,10 +133,9 @@ async function loadBroadcastData() {
         if (broadcastData.value.publication_time) {
             broadcastPublished.value = new Date(broadcastData.value.publication_time) < new Date();
         }
-    } catch (error: any) {
-        Toast.error(errorMessageAsString(error));
+    } finally {
+        loading.value = false;
     }
-    loading.value = false;
 }
 
 if (props.id) {
diff --git a/client/src/components/admin/Notifications/BroadcastsList.test.ts b/client/src/components/admin/Notifications/BroadcastsList.test.ts
index bde192f5ae5c408b2318a3f75554abca13648895..958fed2d22710a560f59831735812569fb662922 100644
--- a/client/src/components/admin/Notifications/BroadcastsList.test.ts
+++ b/client/src/components/admin/Notifications/BroadcastsList.test.ts
@@ -4,15 +4,13 @@ import { shallowMount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
-import { BroadcastNotification } from "@/stores/broadcastsStore";
+import { useServerMock } from "@/api/client/__mocks__";
+import { type BroadcastNotification } from "@/stores/broadcastsStore";
 
 import { generateNewBroadcast } from "./test.utils";
 
 import BroadcastsList from "./BroadcastsList.vue";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue(true);
 
 const selectors = {
@@ -23,14 +21,17 @@ const selectors = {
     broadcastItem: "[data-test-id='broadcast-item']",
 } as const;
 
+const { server, http } = useServerMock();
+
 async function mountBroadcastsList(broadcasts?: BroadcastNotification[]) {
     const pinia = createTestingPinia();
     setActivePinia(pinia);
 
-    mockFetcher
-        .path("/api/notifications/broadcast")
-        .method("get")
-        .mock({ data: broadcasts ?? [] });
+    server.use(
+        http.get("/api/notifications/broadcast", ({ response }) => {
+            return response(200).json(broadcasts ?? []);
+        })
+    );
 
     const wrapper = shallowMount(BroadcastsList as object, {
         localVue,
diff --git a/client/src/components/admin/Notifications/BroadcastsList.vue b/client/src/components/admin/Notifications/BroadcastsList.vue
index fe6c7f34e2482ddbdbb0979f0936f08ece2c3ed4..d7c2b4dfe3a37c0758aaa20a2ccb822349d94b1f 100644
--- a/client/src/components/admin/Notifications/BroadcastsList.vue
+++ b/client/src/components/admin/Notifications/BroadcastsList.vue
@@ -8,7 +8,7 @@ import { useRouter } from "vue-router/composables";
 
 import { fetchAllBroadcasts, updateBroadcast } from "@/api/notifications.broadcast";
 import { Toast } from "@/composables/toast";
-import { BroadcastNotification } from "@/stores/broadcastsStore";
+import { type BroadcastNotification } from "@/stores/broadcastsStore";
 
 import BroadcastCard from "./BroadcastCard.vue";
 import Heading from "@/components/Common/Heading.vue";
@@ -53,7 +53,7 @@ function onEdit(item: BroadcastNotification) {
 async function onForceExpire(item: BroadcastNotification) {
     await updateBroadcast(item.id, { expiration_time: new Date().toISOString().slice(0, 23) });
     await loadBroadcastsList(true);
-    Toast.info("Broadcast marked as expired and will be removed from the database in the next cleanup cycle.");
+    Toast.info("Broadcast marked as expired. It will be removed from the database in the next cleanup cycle.");
 }
 
 function onGoToLink(link: string) {
diff --git a/client/src/components/admin/Notifications/NotificationForm.test.ts b/client/src/components/admin/Notifications/NotificationForm.test.ts
index aebbcd4db0294c61eea6d8ea4c9ccdc272f77177..3f27b6d584e4d4c0ae2927554d68d20b14e6cadd 100644
--- a/client/src/components/admin/Notifications/NotificationForm.test.ts
+++ b/client/src/components/admin/Notifications/NotificationForm.test.ts
@@ -3,7 +3,7 @@ import { getLocalVue } from "@tests/jest/helpers";
 import { mount, type Wrapper } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
-import Vue from "vue";
+import type Vue from "vue";
 
 import NotificationForm from "./NotificationForm.vue";
 
diff --git a/client/src/components/admin/Notifications/NotificationForm.vue b/client/src/components/admin/Notifications/NotificationForm.vue
index efb72aa79754a8ca9693a2f59017ca389c346a30..37704c354c44c136b0c74575affcb2d3f801ee71 100644
--- a/client/src/components/admin/Notifications/NotificationForm.vue
+++ b/client/src/components/admin/Notifications/NotificationForm.vue
@@ -6,11 +6,8 @@ import { BAlert, BCard, BCol, BFormGroup, BRow } from "bootstrap-vue";
 import { computed, type Ref, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import { getAllGroups } from "@/api/groups";
-import { NotificationCreateRequest, sendNotification } from "@/api/notifications";
-import { getAllRoles } from "@/api/roles";
-import { type components } from "@/api/schema";
-import { getAllUsers } from "@/api/users";
+import { GalaxyApi } from "@/api";
+import { type MessageNotificationCreateRequest } from "@/api/notifications";
 import { Toast } from "@/composables/toast";
 import { errorMessageAsString } from "@/utils/simple-error";
 
@@ -24,16 +21,6 @@ import MessageNotification from "@/components/Notifications/Categories/MessageNo
 library.add(faInfoCircle);
 
 type SelectOption = [string, string];
-type NotificationCreateData = components["schemas"]["NotificationCreateData"];
-
-interface MessageNotificationCreateData extends NotificationCreateData {
-    category: "message";
-    content: components["schemas"]["MessageNotificationContent"];
-}
-
-interface MessageNotificationCreateRequest extends NotificationCreateRequest {
-    notification: MessageNotificationCreateData;
-}
 
 const router = useRouter();
 
@@ -96,12 +83,36 @@ async function loadData<T>(
     target: Ref<SelectOption[]>,
     formatter: (item: T) => SelectOption
 ) {
-    try {
-        const tmp = await getData();
-        target.value = tmp.map(formatter);
-    } catch (error: any) {
+    const tmp = await getData();
+    target.value = tmp.map(formatter);
+}
+
+async function getAllGroups() {
+    const { data, error } = await GalaxyApi().GET("/api/groups");
+    if (error) {
+        Toast.error(errorMessageAsString(error));
+        return [];
+    }
+    return data;
+}
+
+async function getAllRoles() {
+    const { data, error } = await GalaxyApi().GET("/api/roles");
+    if (error) {
+        Toast.error(errorMessageAsString(error));
+        return [];
+    }
+    return data;
+}
+
+// TODO: this can potentially be a very large list, consider adding filters
+async function getAllUsers() {
+    const { data, error } = await GalaxyApi().GET("/api/users");
+    if (error) {
         Toast.error(errorMessageAsString(error));
+        return [];
     }
+    return data;
 }
 
 loadData(getAllUsers, users, (user) => {
@@ -117,13 +128,17 @@ loadData(getAllGroups, groups, (group) => {
 });
 
 async function sendNewNotification() {
-    try {
-        await sendNotification(notificationData.value);
-        Toast.success("Notification sent");
-        router.push("/admin/notifications");
-    } catch (error: any) {
+    const { error } = await GalaxyApi().POST("/api/notifications", {
+        body: notificationData.value,
+    });
+
+    if (error) {
         Toast.error(errorMessageAsString(error));
+        return;
     }
+
+    Toast.success("Notification sent");
+    router.push("/admin/notifications");
 }
 </script>
 
diff --git a/client/src/components/admin/Notifications/NotificationsManagement.test.ts b/client/src/components/admin/Notifications/NotificationsManagement.test.ts
index 41474db5161859a22552e4902c0bb5f1011e8cb3..3192099371cb5723ff22e41229befcd60355b649 100644
--- a/client/src/components/admin/Notifications/NotificationsManagement.test.ts
+++ b/client/src/components/admin/Notifications/NotificationsManagement.test.ts
@@ -4,12 +4,10 @@ import { shallowMount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { setActivePinia } from "pinia";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
 
 import NotificationsManagement from "./NotificationsManagement.vue";
 
-jest.mock("@/api/schema");
-
 const localVue = getLocalVue(true);
 
 const selectors = {
@@ -17,11 +15,17 @@ const selectors = {
     createBroadcastButton: "#create-broadcast-button",
 } as const;
 
+const { server, http } = useServerMock();
+
 async function mountNotificationsManagement(config: any = {}) {
     const pinia = createTestingPinia();
     setActivePinia(pinia);
 
-    mockFetcher.path("/api/configuration").method("get").mock({ data: config });
+    server.use(
+        http.get("/api/configuration", ({ response }) => {
+            return response(200).json(config);
+        })
+    );
 
     const wrapper = shallowMount(NotificationsManagement as object, {
         localVue,
diff --git a/client/src/components/providers/JobProvider.js b/client/src/components/providers/JobProvider.js
index 3be3df9e97e0d718f53775d18bd002ffb87700b2..0cc077d83f10366df22b837c075439e8080da18b 100644
--- a/client/src/components/providers/JobProvider.js
+++ b/client/src/components/providers/JobProvider.js
@@ -26,7 +26,18 @@ async function jobConsoleOutput({
         `${getAppRoot()}api/jobs/${jobId}/console_output?stdout_position=${stdout_position}&stdout_length=${stdout_length}` +
         `&stderr_position=${stderr_position}&stderr_length=${stderr_length}`;
     try {
-        const { data } = await axios.get(url);
+        const { status, data } = await axios.get(url, {
+            validateStatus: function (status) {
+                return status == 200 || status == 403;
+            },
+        });
+        if (status == 403) {
+            if (data.err_code == 403004) {
+                console.log("This job destination does not support console output");
+                return { state: "ok" };
+            }
+            throw Error("Problem fetching state");
+        }
         return data;
     } catch (e) {
         rethrowSimple(e);
diff --git a/client/src/composables/__mocks__/filter.ts b/client/src/composables/__mocks__/filter.ts
new file mode 100644
index 0000000000000000000000000000000000000000..727c585991e2c4936f47b3b9f7fe64746a9ddb36
--- /dev/null
+++ b/client/src/composables/__mocks__/filter.ts
@@ -0,0 +1,13 @@
+import { toValue } from "@vueuse/core";
+import { computed, type Ref } from "vue";
+
+import type { useFilterObjectArray as UseFilterObjectArray } from "@/composables/filter";
+
+jest.mock("@/composables/filter", () => ({
+    useFilterObjectArray,
+}));
+
+export const useFilterObjectArray: typeof UseFilterObjectArray = (array): Ref<any[]> => {
+    console.debug("USING MOCKED useFilterObjectArray");
+    return computed(() => toValue(array));
+};
diff --git a/client/src/composables/datasetPermissions.ts b/client/src/composables/datasetPermissions.ts
index 5b5ae30576129b70a25f59657fd546bbda206cfe..738c5ac3452d0186a86d34ac7008f3cedc5d65a9 100644
--- a/client/src/composables/datasetPermissions.ts
+++ b/client/src/composables/datasetPermissions.ts
@@ -1,6 +1,5 @@
-import { AxiosResponse } from "axios";
-import type { Ref } from "vue";
-import { computed, ref } from "vue";
+import { type AxiosResponse } from "axios";
+import { computed, type Ref, ref } from "vue";
 
 import { useToast } from "@/composables/toast";
 import { errorMessageAsString } from "@/utils/simple-error";
diff --git a/client/src/composables/datatypes.ts b/client/src/composables/datatypes.ts
index a3c8bb9be04ff5724e04a64afd9eb783011ed824..49b775fae4dd28a7869a00ff2111bbdcda1f999a 100644
--- a/client/src/composables/datatypes.ts
+++ b/client/src/composables/datatypes.ts
@@ -1,7 +1,7 @@
-import type { Ref } from "vue";
-import { ref } from "vue";
+import { type Ref, ref } from "vue";
 
-import { datatypesFetcher, edamDataFetcher, edamFormatsFetcher } from "@/api/datatypes";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export interface DetailedDatatypes {
     extension: string;
@@ -25,21 +25,30 @@ export function useDetailedDatatypes() {
 
     async function getDatatypes() {
         try {
-            const datatypesPromise = datatypesFetcher({ extension_only: false });
-            const datatypeEDAMFormatsPromise = edamFormatsFetcher({});
-            const datatypeEDAMDataPromise = edamDataFetcher({});
+            const datatypesPromise = GalaxyApi().GET("/api/datatypes", {
+                params: { query: { extension_only: false } },
+            });
+            const datatypeEDAMFormatsPromise = GalaxyApi().GET("/api/datatypes/edam_formats/detailed");
+            const datatypeEDAMDataPromise = GalaxyApi().GET("/api/datatypes/edam_data/detailed");
+
+            const [
+                { data: baseData, error: baseError },
+                { data: datatypeEDAMFormats, error: edamFormatsError },
+                { data: datatypeEDAMData, error: edamDataError },
+            ] = await Promise.all([datatypesPromise, datatypeEDAMFormatsPromise, datatypeEDAMDataPromise]);
 
-            const [baseTypes, datatypeEDAMFormats, datatypeEDAMData] = await Promise.all([
-                datatypesPromise,
-                datatypeEDAMFormatsPromise,
-                datatypeEDAMDataPromise,
-            ]);
+            type BaseTypes = Exclude<typeof baseData, string[]>;
 
-            type BaseTypes = Exclude<typeof baseTypes.data, string[]>;
+            const error = baseError || edamFormatsError || edamDataError;
+            if (error) {
+                rethrowSimple(error);
+            }
 
-            datatypes.value = (baseTypes.data as BaseTypes).map((type) => {
-                const typeEDAMFormat = datatypeEDAMFormats.data[type.extension] ?? null;
-                const typeEDAMData = datatypeEDAMData.data[type.extension] ?? null;
+            const items = baseData as BaseTypes;
+            // We can safely use non-null assertions here because otherwise we would have thrown an error
+            datatypes.value = items!.map((type) => {
+                const typeEDAMFormat = datatypeEDAMFormats![type.extension] ?? null;
+                const typeEDAMData = datatypeEDAMData![type.extension] ?? null;
 
                 return {
                     extension: type.extension,
diff --git a/client/src/composables/datatypesMapper.ts b/client/src/composables/datatypesMapper.ts
index 28b2551b08c224561b67fa39f80bb507bdc7b016..0ad4e901bd4856cb6ddeea0261ff7ad7550cc7cb 100644
--- a/client/src/composables/datatypesMapper.ts
+++ b/client/src/composables/datatypesMapper.ts
@@ -1,7 +1,6 @@
-import type { Ref } from "vue";
-import { ref } from "vue";
+import { type Ref, ref } from "vue";
 
-import type { DatatypesMapperModel } from "@/components/Datatypes/model";
+import { type DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
 
 export function useDatatypesMapper() {
diff --git a/client/src/composables/eventEmitter.ts b/client/src/composables/eventEmitter.ts
new file mode 100644
index 0000000000000000000000000000000000000000..13f95a4992baceb82e1a3b1eb0ce416f72ec6d72
--- /dev/null
+++ b/client/src/composables/eventEmitter.ts
@@ -0,0 +1,20 @@
+import { type Ref, watch } from "vue";
+
+/**
+ * Emits an event whenever a value changes
+ * @param ref value to watch
+ * @param emit event emitter function
+ * @param name event to emit
+ */
+export function useEmit<Name extends string, T, F extends { (name: Name, arg: T): void }>(
+    ref: Ref<T>,
+    emit: F,
+    name: Name
+) {
+    watch(
+        () => ref.value,
+        () => {
+            emit(name, ref.value);
+        }
+    );
+}
diff --git a/client/src/composables/fileSources.test.ts b/client/src/composables/fileSources.test.ts
index e9a30d69d7bf01e6ea53a5540f17141e5e0e26d9..a7e8d947bce27f0f1e7360adcc3b988ac62f8a6e 100644
--- a/client/src/composables/fileSources.test.ts
+++ b/client/src/composables/fileSources.test.ts
@@ -3,12 +3,11 @@ import { shallowMount } from "@vue/test-utils";
 import flushPromises from "flush-promises";
 import { defineComponent } from "vue";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
+import { type BrowsableFilesSourcePlugin } from "@/api/remoteFiles";
 
 import { useFileSources } from "./fileSources";
 
-jest.mock("@/api/schema");
-
 const REMOTE_FILES_API_ROUTE = "/api/remote_files/plugins";
 
 const TestComponent = defineComponent({
@@ -33,9 +32,33 @@ function setupWrapper(): any {
     return shallowMount(TestComponent, { pinia });
 }
 
+function buildFakeFileSource(id: string, writable: boolean = true): BrowsableFilesSourcePlugin {
+    const type = `${id}Type`;
+    return {
+        id: id,
+        type,
+        uri_root: `${type}://`,
+        label: `${id} Label`,
+        doc: `${id} Doc`,
+        writable,
+        browsable: true,
+        supports: {
+            pagination: false,
+            search: false,
+            sorting: false,
+        },
+    };
+}
+
+const { server, http } = useServerMock();
+
 describe("useFileSources", () => {
     beforeEach(async () => {
-        mockFetcher.path(REMOTE_FILES_API_ROUTE).method("get").mock({ data: [] });
+        server.use(
+            http.get(REMOTE_FILES_API_ROUTE, ({ response }) => {
+                return response(200).json([]);
+            })
+        );
     });
 
     it("should be initially loading", async () => {
@@ -44,8 +67,12 @@ describe("useFileSources", () => {
     });
 
     it("should fetch file sources on mount", async () => {
-        const expectedFileSources = [{ id: "foo", writable: true }];
-        mockFetcher.path(REMOTE_FILES_API_ROUTE).method("get").mock({ data: expectedFileSources });
+        const expectedFileSources = [buildFakeFileSource("foo")];
+        server.use(
+            http.get(REMOTE_FILES_API_ROUTE, ({ response }) => {
+                return response(200).json(expectedFileSources);
+            })
+        );
 
         const wrapper = setupWrapper();
 
@@ -58,11 +85,12 @@ describe("useFileSources", () => {
     });
 
     it("should set hasWritable to false if no file sources are writable", async () => {
-        const expectedFileSources = [
-            { id: "foo", writable: false },
-            { id: "bar", writable: false },
-        ];
-        mockFetcher.path(REMOTE_FILES_API_ROUTE).method("get").mock({ data: expectedFileSources });
+        const expectedFileSources = [buildFakeFileSource("foo", false), buildFakeFileSource("bar", false)];
+        server.use(
+            http.get(REMOTE_FILES_API_ROUTE, ({ response }) => {
+                return response(200).json(expectedFileSources);
+            })
+        );
 
         const wrapper = setupWrapper();
 
@@ -72,11 +100,12 @@ describe("useFileSources", () => {
     });
 
     it("should set hasWritable to true if any file sources are writable", async () => {
-        const expectedFileSources = [
-            { id: "foo", writable: true },
-            { id: "bar", writable: false },
-        ];
-        mockFetcher.path(REMOTE_FILES_API_ROUTE).method("get").mock({ data: expectedFileSources });
+        const expectedFileSources = [buildFakeFileSource("foo", true), buildFakeFileSource("bar", false)];
+        server.use(
+            http.get(REMOTE_FILES_API_ROUTE, ({ response }) => {
+                return response(200).json(expectedFileSources);
+            })
+        );
 
         const wrapper = setupWrapper();
 
diff --git a/client/src/composables/fileSources.ts b/client/src/composables/fileSources.ts
index 674149d064aadc7910ee54ecf3c68fbc2f357494..7b880fd758c9fc8ba77feaeb34f80fcf78d559a3 100644
--- a/client/src/composables/fileSources.ts
+++ b/client/src/composables/fileSources.ts
@@ -1,6 +1,6 @@
 import { onMounted, readonly, ref } from "vue";
 
-import { BrowsableFilesSourcePlugin, FilterFileSourcesOptions } from "@/api/remoteFiles";
+import { type BrowsableFilesSourcePlugin, type FilterFileSourcesOptions } from "@/api/remoteFiles";
 import { useFileSourcesStore } from "@/stores/fileSourcesStore";
 
 /**
@@ -26,8 +26,20 @@ export function useFileSources(options: FilterFileSourcesOptions = {}) {
     }
 
     function getFileSourceByUri(uri: string) {
+        const sourceId = getFileSourceIdFromUri(uri);
+        let matchedFileSource = getFileSourceById(sourceId);
+        if (matchedFileSource) {
+            return matchedFileSource;
+        }
+
+        // Match by URI root if the source ID is not found.
+        matchedFileSource = fileSources.value.find((fs) => uri.startsWith(fs.uri_root));
+        return matchedFileSource;
+    }
+
+    function getFileSourceIdFromUri(uri: string) {
         const sourceId = uri.split("://")[1]?.split("/")[0] ?? "";
-        return getFileSourceById(sourceId);
+        return sourceId;
     }
 
     return {
diff --git a/client/src/composables/filter/filter.d.ts b/client/src/composables/filter/filter.d.ts
index 6efd44fb92d39fda93070264870a35ba6aff58b4..3b8fc75b3b240b5f23bde029d3db35f85b5b4a94 100644
--- a/client/src/composables/filter/filter.d.ts
+++ b/client/src/composables/filter/filter.d.ts
@@ -1,15 +1,15 @@
-import type { MaybeRefOrGetter } from "@vueuse/core";
-import type { Ref } from "vue";
+import { type MaybeRefOrGetter } from "@vueuse/core";
+import { type Ref } from "vue";
 
 /**
  * Reactively filter an array of objects, by comparing `filter` to all `fields`.
  * All parameters can optionally be refs.
  * @param array array of objects to filter
  * @param filter string to filter by
- * @param objectFields string array of fields to filter by on each object
+ * @param objectFields string array of fields to filter by on each object. To reach nested fields, use an array of strings (e.g. `["nested", "field"]`)
  */
 export declare function useFilterObjectArray<O extends object, K extends keyof O>(
     array: MaybeRefOrGetter<Array<O>>,
     filter: MaybeRefOrGetter<string>,
-    objectFields: MaybeRefOrGetter<Array<K>>
+    objectFields: MaybeRefOrGetter<Array<K | string[]>>
 ): Ref<O[]>;
diff --git a/client/src/composables/filter/filterFunction.ts b/client/src/composables/filter/filterFunction.ts
index be92ad46b162d6fca2e487f69b1659dc1d9a2e46..0599a72c892a98ee1a85d3eafaf819dcae7d90ad 100644
--- a/client/src/composables/filter/filterFunction.ts
+++ b/client/src/composables/filter/filterFunction.ts
@@ -1,19 +1,31 @@
-export function runFilter<O extends object, K extends keyof O>(f: string, arr: O[], fields: K[]) {
+export function runFilter<O extends object, K extends keyof O>(f: string, arr: O[], fields: (K | string[])[]) {
     if (f === "") {
         return arr;
     } else {
         return arr.filter((obj) => {
+            const lowerCaseFilter = f.toLocaleLowerCase();
             for (const field of fields) {
-                const val = obj[field];
+                let val: unknown;
+
+                if (typeof field === "string") {
+                    val = obj[field];
+                } else if (Array.isArray(field)) {
+                    val = field.reduce((acc: unknown, curr: string) => {
+                        if (acc && typeof acc === "object") {
+                            return (acc as Record<string, unknown>)[curr];
+                        }
+                        return undefined;
+                    }, obj);
+                }
 
                 if (typeof val === "string") {
-                    if (val.toLowerCase().includes(f.toLocaleLowerCase())) {
+                    if (val.toLowerCase().includes(lowerCaseFilter)) {
                         return true;
                     }
                 } else if (Array.isArray(val)) {
-                    if (val.includes(f)) {
-                        return true;
-                    }
+                    return val.find((v) => {
+                        return typeof v === "string" ? v.toLowerCase().includes(lowerCaseFilter) : false;
+                    });
                 }
             }
 
diff --git a/client/src/composables/genericTaskMonitor.ts b/client/src/composables/genericTaskMonitor.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e13876dda9b19fefa7c7cdd0237d2cf36e755852
--- /dev/null
+++ b/client/src/composables/genericTaskMonitor.ts
@@ -0,0 +1,175 @@
+import { computed, readonly, type Ref, ref } from "vue";
+
+import { errorMessageAsString } from "@/utils/simple-error";
+
+const DEFAULT_POLL_DELAY = 10000;
+
+/**
+ * Represents a task monitor that can be used to wait for a background task to complete or
+ * check its status.
+ */
+export interface TaskMonitor {
+    /**
+     * Waits for a particular task ID to be completed.
+     * While the task is pending, the state will be updated every `pollDelayInMs` by polling the server.
+     * @param taskId The task ID
+     * @param pollDelayInMs The time (milliseconds) between poll requests to update the task state.
+     */
+    waitForTask: (taskId: string, pollDelayInMs?: number) => Promise<void>;
+
+    /**
+     * Whether the task is currently running.
+     */
+    isRunning: Readonly<Ref<boolean>>;
+
+    /**
+     * Whether the task has been completed successfully.
+     */
+    isCompleted: Readonly<Ref<boolean>>;
+
+    /**
+     * Indicates the task has failed and will not yield results.
+     */
+    hasFailed: Readonly<Ref<boolean>>;
+
+    /**
+     * If true, the status of the task cannot be determined because of a request error.
+     */
+    requestHasFailed: Readonly<Ref<boolean>>;
+
+    /**
+     * The current status of the task.
+     * The meaning of the status string is up to the monitor implementation.
+     * In case of an error, this will be the error message.
+     */
+    taskStatus: Readonly<Ref<string | undefined>>;
+
+    /**
+     * Loads the status of the task from a stored value.
+     * @param storedStatus The status string to load.
+     */
+    loadStatus: (storedStatus: string) => void;
+
+    /**
+     * Determines if the status represents a final state.
+     * @param status The status string to check.
+     * @returns True if the status is a final state and is not expected to change.
+     */
+    isFinalState: (status?: string) => boolean;
+
+    /**
+     * If defined, the time (in milliseconds) after which the task should be considered expired.
+     * Requests to check the task status after this time should be avoided. As they are not guaranteed to return the correct status.
+     */
+    expirationTime?: number;
+}
+
+/**
+ * Composable for waiting (polling) on generic background tasks or processes.
+ */
+export function useGenericMonitor(options: {
+    /** Function to fetch the status of a task or process.
+     * The function should return a string representing the current status of the task.
+     * The meaning of the status string is determined by the `completedCondition` and `failedCondition` functions.
+     */
+    fetchStatus: (taskId: string) => Promise<string>;
+
+    /** Function to determine if the task has finished. */
+    completedCondition: (status?: string) => boolean;
+
+    /** Function to determine if the task has failed. */
+    failedCondition: (status?: string) => boolean;
+
+    /** Default delay between polling requests in milliseconds.
+     * By default, this is set to 10 seconds.
+     * The delay can be overridden when calling `waitForTask`.
+     */
+    defaultPollDelay?: number;
+
+    /** Optional expiration time for the task in milliseconds.
+     * After this time, the task should be considered expired.
+     * Requests to check the task status after this time should be avoided.
+     */
+    expirationTime?: number;
+}): TaskMonitor {
+    let timeout: NodeJS.Timeout | null = null;
+    let pollDelay = options.defaultPollDelay ?? DEFAULT_POLL_DELAY;
+
+    const isRunning = ref(false);
+    const taskStatus = ref<string>();
+    const requestId = ref<string>();
+    const requestHasFailed = ref(false);
+
+    const isCompleted = computed(() => options.completedCondition(taskStatus.value));
+    const hasFailed = computed(() => options.failedCondition(taskStatus.value));
+
+    function isFinalState(status?: string) {
+        return options.completedCondition(status) || options.failedCondition(status);
+    }
+
+    function loadStatus(storedStatus: string) {
+        taskStatus.value = storedStatus;
+    }
+
+    async function waitForTask(taskId: string, pollDelayInMs?: number) {
+        pollDelay = pollDelayInMs ?? pollDelay;
+        resetState();
+        requestId.value = taskId;
+        isRunning.value = true;
+        return fetchTaskStatus(taskId);
+    }
+
+    async function fetchTaskStatus(taskId: string) {
+        try {
+            const result = await options.fetchStatus(taskId);
+            taskStatus.value = result;
+            if (isCompleted.value || hasFailed.value) {
+                isRunning.value = false;
+            } else {
+                pollAfterDelay(taskId);
+            }
+        } catch (err) {
+            handleError(errorMessageAsString(err));
+        }
+    }
+
+    function pollAfterDelay(id: string) {
+        resetTimeout();
+        timeout = setTimeout(() => {
+            fetchTaskStatus(id);
+        }, pollDelay);
+    }
+
+    function handleError(err: string) {
+        taskStatus.value = err.toString();
+        requestHasFailed.value = true;
+        isRunning.value = false;
+        resetTimeout();
+    }
+
+    function resetTimeout() {
+        if (timeout) {
+            clearTimeout(timeout);
+            timeout = null;
+        }
+    }
+
+    function resetState() {
+        resetTimeout();
+        taskStatus.value = undefined;
+        requestHasFailed.value = false;
+        isRunning.value = false;
+    }
+
+    return {
+        waitForTask,
+        isFinalState,
+        loadStatus,
+        isRunning: readonly(isRunning),
+        isCompleted: readonly(isCompleted),
+        hasFailed: readonly(hasFailed),
+        requestHasFailed: readonly(requestHasFailed),
+        taskStatus: readonly(taskStatus),
+        expirationTime: options.expirationTime,
+    };
+}
diff --git a/client/src/composables/hashedUserId.ts b/client/src/composables/hashedUserId.ts
index c19786b6ea7adabf6632f658d77492f50492a994..a7f651a3c6289b1277b42c0ca7682e2b8c2cfe3b 100644
--- a/client/src/composables/hashedUserId.ts
+++ b/client/src/composables/hashedUserId.ts
@@ -1,10 +1,11 @@
-import { useLocalStorage } from "@vueuse/core";
 import { storeToRefs } from "pinia";
 import { computed, type Ref, ref, watch } from "vue";
 
-import type { GenericUser } from "@/api";
+import { type AnyUser } from "@/api";
 import { useUserStore } from "@/stores/userStore";
 
+import { usePersistentRef } from "./persistentRef";
+
 async function hash32(value: string): Promise<string> {
     const valueUtf8 = new TextEncoder().encode(value);
     const hashBuffer = await crypto.subtle.digest("SHA-256", valueUtf8);
@@ -32,8 +33,8 @@ let unhashedId: string | null = null;
 /**
  * One way hashed ID of the current User
  */
-export function useHashedUserId(user?: Ref<GenericUser | null>) {
-    let currentUser: Ref<GenericUser | null>;
+export function useHashedUserId(user?: Ref<AnyUser>) {
+    let currentUser: Ref<AnyUser>;
 
     if (user) {
         currentUser = user;
@@ -43,7 +44,7 @@ export function useHashedUserId(user?: Ref<GenericUser | null>) {
     }
 
     // salt the local store, to make a user untraceable by id across different clients
-    const localStorageSalt = useLocalStorage("local-storage-salt", createSalt());
+    const localStorageSalt = usePersistentRef("local-storage-salt", createSalt());
 
     watch(
         () => currentUser.value,
diff --git a/client/src/composables/historyDragDrop.ts b/client/src/composables/historyDragDrop.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5d0bfe89bdbd7ed106fc57ec95c3438ce0f58900
--- /dev/null
+++ b/client/src/composables/historyDragDrop.ts
@@ -0,0 +1,190 @@
+import { computed, type Ref, ref, unref } from "vue";
+
+import { type DCEDataset, type DCESummary, type HistoryItemSummary, isDatasetElement, isHistoryItem } from "@/api";
+import { copyDataset, type HistoryContentSource, type HistoryContentType } from "@/api/datasets";
+import { Toast } from "@/composables/toast";
+import { useEventStore } from "@/stores/eventStore";
+import { useHistoryStore } from "@/stores/historyStore";
+
+type DraggableHistoryItem = HistoryItemSummary | DCEDataset; // TODO: DCESummary instead of DCEDataset
+interface HistoryItemCopyData {
+    dataSource: HistoryContentSource;
+    type: HistoryContentType;
+    id: string;
+}
+
+export function useHistoryDragDrop(targetHistoryId?: Ref<string> | string, createNew = false, pinHistories = false) {
+    // convert destinationHistoryId to a ref if it's not already
+    const destinationHistoryId = computed(() => {
+        if (typeof targetHistoryId === "string") {
+            return targetHistoryId;
+        }
+        return unref(targetHistoryId);
+    });
+
+    const eventStore = useEventStore();
+    const historyStore = useHistoryStore();
+
+    const fromHistoryId = computed(() => {
+        const dragItems = getDragItems();
+        return dragItems[0]
+            ? isHistoryItem(dragItems[0])
+                ? dragItems[0].history_id
+                : dragItems[0].object?.history_id
+            : null;
+    });
+
+    const showDropZone = ref(false);
+    const dragTarget = ref<EventTarget | null>(null);
+    const processingDrop = ref(false);
+
+    const operationDisabled = computed(
+        () =>
+            !fromHistoryId.value ||
+            (destinationHistoryId.value && fromHistoryId.value === destinationHistoryId.value) ||
+            (!createNew && !destinationHistoryId.value) ||
+            !getDragItems().length ||
+            processingDrop.value
+    );
+
+    function getDragItems() {
+        const storeItems = eventStore.getDragItems();
+        // Filter out any non-history or `DatasetCollectionElement` items
+        return storeItems?.filter(
+            (item) => isHistoryItem(item) || isDatasetElement(item as DCESummary)
+        ) as DraggableHistoryItem[];
+    }
+
+    function onDragEnter(e: DragEvent) {
+        if (operationDisabled.value) {
+            return;
+        }
+        dragTarget.value = e.target;
+        showDropZone.value = true;
+    }
+
+    function onDragOver(e: DragEvent) {
+        if (operationDisabled.value) {
+            return;
+        }
+        e.preventDefault();
+    }
+
+    function onDragLeave(e: DragEvent) {
+        if (operationDisabled.value) {
+            return;
+        }
+        if (dragTarget.value === e.target) {
+            showDropZone.value = false;
+        }
+    }
+
+    async function onDrop() {
+        showDropZone.value = false;
+        if (operationDisabled.value) {
+            return;
+        }
+        processingDrop.value = true;
+
+        let datasetCount = 0;
+        let collectionCount = 0;
+
+        try {
+            const dragItems = getDragItems();
+            const multiple = dragItems.length > 1;
+            const originalHistoryId = fromHistoryId.value as string;
+
+            let historyId;
+            if (destinationHistoryId.value) {
+                historyId = destinationHistoryId.value;
+            } else if (createNew) {
+                await historyStore.createNewHistory();
+                historyId = historyStore.currentHistoryId;
+            } else {
+                historyId = null;
+            }
+            if (!historyId) {
+                throw new Error("Destination history not found or created");
+            }
+
+            const copyableItems: HistoryItemCopyData[] = [];
+            // iterate over the data array and get valid copyable items
+            for (const item of dragItems) {
+                let copyableItem: HistoryItemCopyData;
+                if (isHistoryItem(item)) {
+                    copyableItem = {
+                        dataSource: item.history_content_type === "dataset" ? "hda" : "hdca",
+                        type: item.history_content_type,
+                        id: item.id,
+                    };
+                }
+                // For DCEs, only `DCEDataset`s are droppable, `DCEDatasetCollection`s are not
+                else if (isDatasetElement(item) && item.object) {
+                    copyableItem = {
+                        dataSource: "hda",
+                        type: "dataset",
+                        id: item.object.id,
+                    };
+                } else {
+                    throw new Error(`Invalid item type${item.element_type ? `: ${item.element_type}` : ""}`);
+                }
+                copyableItems.push(copyableItem);
+            }
+
+            // iterate over the data array and copy each item to the current history
+            for (const item of copyableItems) {
+                const { dataSource, type, id } = item;
+                await copyDataset(id, historyId, type, dataSource);
+
+                if (dataSource === "hda") {
+                    datasetCount++;
+                    if (!multiple) {
+                        Toast.info(`Dataset copied to ${createNew ? "new" : ""} history`);
+                    }
+                } else {
+                    collectionCount++;
+                    if (!multiple) {
+                        Toast.info(`Collection copied to ${createNew ? "new" : ""} history`);
+                    }
+                }
+            }
+
+            if (multiple && datasetCount > 0) {
+                Toast.info(
+                    `${datasetCount} dataset${datasetCount > 1 ? "s" : ""} copied to ${createNew ? "new" : ""} history`
+                );
+            }
+            if (multiple && collectionCount > 0) {
+                Toast.info(
+                    `${collectionCount} collection${collectionCount > 1 ? "s" : ""} copied to ${
+                        createNew ? "new" : ""
+                    } history`
+                );
+            }
+
+            // if items were copied
+            if (datasetCount > 0 && collectionCount > 0) {
+                if (pinHistories && historyStore.pinnedHistories.length > 0) {
+                    // pin the target history
+                    historyStore.pinHistory(historyId);
+                    // also pin the original history where the item came from
+                    historyStore.pinHistory(originalHistoryId);
+                } else {
+                    historyStore.loadHistoryById(historyId);
+                }
+            }
+        } catch (error) {
+            Toast.error(`${error}`);
+        } finally {
+            processingDrop.value = false;
+        }
+    }
+
+    return {
+        showDropZone,
+        onDragEnter,
+        onDragOver,
+        onDragLeave,
+        onDrop,
+    };
+}
diff --git a/client/src/composables/keyedCache.test.ts b/client/src/composables/keyedCache.test.ts
index d792e7d0fd97a21d3b672a4ca5a025bb58043490..3617e66cbc694638990d3907b52499b13c88685a 100644
--- a/client/src/composables/keyedCache.test.ts
+++ b/client/src/composables/keyedCache.test.ts
@@ -21,9 +21,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
 
         const { storedItems, getItemById, isLoadingItem } = useKeyedCache<ItemData>(fetchItem);
 
@@ -43,7 +42,7 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
 
-        fetchItem.mockResolvedValue({ data: item });
+        fetchItem.mockResolvedValue(item);
 
         const { storedItems, getItemById, isLoadingItem } = useKeyedCache<ItemData>(fetchItem);
 
@@ -62,9 +61,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
         shouldFetch.mockReturnValue(() => true);
 
         const { storedItems, getItemById, isLoadingItem } = useKeyedCache<ItemData>(fetchItem, shouldFetch);
@@ -87,9 +85,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
 
         const { storedItems, getItemById, isLoadingItem } = useKeyedCache<ItemData>(fetchItem);
 
@@ -110,9 +107,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
         shouldFetch.mockReturnValue(() => true);
 
         const { storedItems, getItemById, isLoadingItem } = useKeyedCache<ItemData>(fetchItem, shouldFetch);
@@ -135,9 +131,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
 
         const fetchItemRef = ref(fetchItem);
 
@@ -158,9 +153,8 @@ describe("useKeyedCache", () => {
         const id = "1";
         const item = { id: id, name: "Item 1" };
         const fetchParams = { id: id };
-        const apiResponse = { data: item };
 
-        fetchItem.mockResolvedValue(apiResponse);
+        fetchItem.mockResolvedValue(item);
         shouldFetch.mockReturnValue(true);
 
         const shouldFetchComputed = computed(() => shouldFetch);
diff --git a/client/src/composables/keyedCache.ts b/client/src/composables/keyedCache.ts
index 7abd3f652c5df8f068682ef12ed6528850dcc3e0..1e3696bb77d76c7529492642bf58a910eb479e05 100644
--- a/client/src/composables/keyedCache.ts
+++ b/client/src/composables/keyedCache.ts
@@ -1,21 +1,19 @@
-import { MaybeRefOrGetter, toValue } from "@vueuse/core";
+import { type MaybeRefOrGetter, toValue } from "@vueuse/core";
 import { computed, del, type Ref, ref, set, unref } from "vue";
 
-import type { ApiResponse } from "@/api/schema";
-
 /**
  * Parameters for fetching an item from the server.
  *
  * Minimally, this should include an id for indexing the item.
  */
-interface FetchParams {
+export interface FetchParams {
     id: string;
 }
 
 /**
  * A function that fetches an item from the server.
  */
-type FetchHandler<T> = (params: FetchParams) => Promise<ApiResponse<T>>;
+type FetchHandler<T> = (params: FetchParams) => Promise<T>;
 
 /**
  * A function that returns true if the item should be fetched.
@@ -45,6 +43,7 @@ export function useKeyedCache<T>(
 ) {
     const storedItems = ref<{ [key: string]: T }>({});
     const loadingItem = ref<{ [key: string]: boolean }>({});
+    const loadingErrors = ref<{ [key: string]: Error }>({});
 
     const getItemById = computed(() => {
         return (id: string) => {
@@ -69,18 +68,27 @@ export function useKeyedCache<T>(
         };
     });
 
+    const getItemLoadError = computed(() => {
+        return (id: string) => {
+            return loadingErrors.value[id] ?? null;
+        };
+    });
+
     async function fetchItemById(params: FetchParams) {
         const itemId = params.id;
         const isAlreadyLoading = loadingItem.value[itemId] ?? false;
-        if (isAlreadyLoading) {
+        const failedLoading = loadingErrors.value[itemId];
+        if (isAlreadyLoading || failedLoading) {
             return;
         }
         set(loadingItem.value, itemId, true);
         try {
             const fetchItem = unref(fetchItemHandler);
-            const { data } = await fetchItem({ id: itemId });
-            set(storedItems.value, itemId, data);
-            return data;
+            const item = await fetchItem({ id: itemId });
+            set(storedItems.value, itemId, item);
+            return item;
+        } catch (error) {
+            set(loadingErrors.value, itemId, error);
         } finally {
             del(loadingItem.value, itemId);
         }
@@ -97,6 +105,10 @@ export function useKeyedCache<T>(
          * And reactively updated when the fetch completes.
          */
         getItemById,
+        /**
+         * A computed function holding errors
+         */
+        getItemLoadError,
         /**
          * A computed function that returns true if the item with the given id is currently being fetched.
          */
diff --git a/client/src/composables/markdown.ts b/client/src/composables/markdown.ts
index a6659f60d404408708308ee62c2b63cdfda1381a..43340deb55d91ede4456d8a6165b72be3f777941 100644
--- a/client/src/composables/markdown.ts
+++ b/client/src/composables/markdown.ts
@@ -69,9 +69,75 @@ function addRuleHeadingIncreaseLevel(engine: MarkdownIt, increaseBy: number) {
     };
 }
 
+/**
+ * Add a rule that removes newlines after list items.
+ */
+function addRuleRemoveNewlinesAfterList(engine: MarkdownIt) {
+    const defaultRenderListItemOpen =
+        engine.renderer.rules.list_item_open ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    const defaultRenderListItemClose =
+        engine.renderer.rules.list_item_close ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    const defaultRenderOrderedListOpen =
+        engine.renderer.rules.ordered_list_open ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    const defaultRenderOrderedListClose =
+        engine.renderer.rules.ordered_list_close ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    const defaultRenderBulletListOpen =
+        engine.renderer.rules.bullet_list_open ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    const defaultRenderBulletListClose =
+        engine.renderer.rules.bullet_list_close ||
+        function (tokens, idx, options, _env, self) {
+            return self.renderToken(tokens, idx, options);
+        };
+
+    engine.renderer.rules.list_item_open = function (tokens, idx, options, env, self) {
+        return defaultRenderListItemOpen(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+
+    engine.renderer.rules.list_item_close = function (tokens, idx, options, env, self) {
+        return defaultRenderListItemClose(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+
+    engine.renderer.rules.ordered_list_open = function (tokens, idx, options, env, self) {
+        return defaultRenderOrderedListOpen(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+
+    engine.renderer.rules.ordered_list_close = function (tokens, idx, options, env, self) {
+        return defaultRenderOrderedListClose(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+
+    engine.renderer.rules.bullet_list_open = function (tokens, idx, options, env, self) {
+        return defaultRenderBulletListOpen(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+
+    engine.renderer.rules.bullet_list_close = function (tokens, idx, options, env, self) {
+        return defaultRenderBulletListClose(tokens, idx, options, env, self).replace(/\n+$/, "");
+    };
+}
+
 interface UseMarkdownOptions {
     openLinksInNewPage?: boolean;
     increaseHeadingLevelBy?: number;
+    removeNewlinesAfterList?: boolean;
 }
 
 type RawMarkdown = string;
@@ -89,6 +155,10 @@ export function useMarkdown(options: UseMarkdownOptions = {}) {
         addRuleHeadingIncreaseLevel(mdEngine, options.increaseHeadingLevelBy);
     }
 
+    if (options.removeNewlinesAfterList) {
+        addRuleRemoveNewlinesAfterList(mdEngine);
+    }
+
     function renderMarkdown(markdown: RawMarkdown): HTMLString {
         return mdEngine.render(markdown);
     }
diff --git a/client/src/composables/math.ts b/client/src/composables/math.ts
new file mode 100644
index 0000000000000000000000000000000000000000..421a9ca24aa5465d5b6847f4042878905d55763a
--- /dev/null
+++ b/client/src/composables/math.ts
@@ -0,0 +1,49 @@
+/**
+ * There are similar functions to those in this module in vue-use, but they only work one-way.
+ * Unlike vue-use, these composables return refs which can be set.
+ */
+
+import { type MaybeRefOrGetter, toValue } from "@vueuse/core";
+import { computed, type Ref } from "vue";
+
+/**
+ * Wraps a number ref, restricting it's values to a given range
+ *
+ * @param ref ref containing a number to wrap
+ * @param min lowest possible value of range
+ * @param max highest possible value of range
+ * @returns clamped ref
+ */
+export function useClamp(ref: Ref<number>, min: MaybeRefOrGetter<number>, max: MaybeRefOrGetter<number>): Ref<number> {
+    const clamp = (value: number) => {
+        return Math.min(Math.max(value, toValue(min)), toValue(max));
+    };
+
+    const clampedRef = computed({
+        get: () => clamp(ref.value),
+        set: (value) => (ref.value = clamp(value)),
+    });
+
+    return clampedRef;
+}
+
+/**
+ * Wraps a number ref, restricting it's values to align to a given step size
+ *
+ * @param ref ref containing a number to wrap
+ * @param [stepSize = 1] size of steps to restrict value to. defaults to 1
+ * @returns wrapped red
+ */
+export function useStep(ref: Ref<number>, stepSize: MaybeRefOrGetter<number> = 1): Ref<number> {
+    const step = (value: number) => {
+        const stepSizeValue = toValue(stepSize);
+        return Math.round(value / stepSizeValue) * stepSizeValue;
+    };
+
+    const steppedRef = computed({
+        get: () => step(ref.value),
+        set: (value) => (ref.value = step(value)),
+    });
+
+    return steppedRef;
+}
diff --git a/client/src/composables/persistentProgressMonitor.test.ts b/client/src/composables/persistentProgressMonitor.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..88e21b79e7a0918129829f557bd92d9170b496f4
--- /dev/null
+++ b/client/src/composables/persistentProgressMonitor.test.ts
@@ -0,0 +1,98 @@
+import { ref } from "vue";
+
+import { type TaskMonitor } from "@/composables/genericTaskMonitor";
+import {
+    type MonitoringData,
+    type MonitoringRequest,
+    usePersistentProgressTaskMonitor,
+} from "@/composables/persistentProgressMonitor";
+
+// Mocks for dependencies
+jest.mock("@vueuse/core", () => ({
+    useLocalStorage: jest.fn().mockImplementation((key, initialValue) => ref(initialValue)),
+    StorageSerializers: {
+        object: {
+            read: (value: string) => JSON.parse(value),
+            write: (value: any) => JSON.stringify(value),
+        },
+    },
+}));
+
+function useMonitorMock(): TaskMonitor {
+    const isRunning = ref(false);
+    const taskStatus = ref();
+
+    return {
+        waitForTask: jest.fn().mockImplementation(() => {
+            isRunning.value = true;
+        }),
+        isRunning,
+        isCompleted: ref(false),
+        hasFailed: ref(false),
+        requestHasFailed: ref(false),
+        taskStatus,
+        expirationTime: 1000,
+        isFinalState: jest.fn(),
+        loadStatus(storedStatus) {
+            taskStatus.value = storedStatus;
+        },
+    };
+}
+const mockUseMonitor = useMonitorMock();
+
+const MOCK_REQUEST: MonitoringRequest = {
+    source: "testSource",
+    action: "export",
+    taskType: "task",
+    object: {
+        id: "1",
+        type: "dataset",
+    },
+    description: "Test description",
+};
+
+describe("usePersistentProgressTaskMonitor", () => {
+    it("should initialize with no monitoring data if none is provided or stored", () => {
+        const { hasMonitoringData } = usePersistentProgressTaskMonitor(MOCK_REQUEST, mockUseMonitor);
+        expect(hasMonitoringData.value).toBeFalsy();
+    });
+
+    it("should start monitoring with provided monitoring data", async () => {
+        const monitoringData: MonitoringData = {
+            taskId: "123",
+            taskType: "task",
+            request: MOCK_REQUEST,
+            startedAt: new Date(),
+        };
+
+        const { start, isRunning } = usePersistentProgressTaskMonitor(MOCK_REQUEST, mockUseMonitor, monitoringData);
+
+        await start();
+        expect(isRunning.value).toBeTruthy();
+    });
+
+    it("should throw an error if trying to start monitoring without monitoring data", async () => {
+        const { start } = usePersistentProgressTaskMonitor(MOCK_REQUEST, mockUseMonitor);
+        await expect(start()).rejects.toThrow(
+            "No monitoring data provided or stored. Cannot start monitoring progress."
+        );
+    });
+
+    it("should reset monitoring data", () => {
+        const monitoringData: MonitoringData = {
+            taskId: "123",
+            taskType: "task",
+            request: MOCK_REQUEST,
+            startedAt: new Date(),
+        };
+
+        const { reset, hasMonitoringData } = usePersistentProgressTaskMonitor(
+            MOCK_REQUEST,
+            mockUseMonitor,
+            monitoringData
+        );
+        expect(hasMonitoringData.value).toBeTruthy();
+        reset();
+        expect(hasMonitoringData.value).toBeFalsy();
+    });
+});
diff --git a/client/src/composables/persistentProgressMonitor.ts b/client/src/composables/persistentProgressMonitor.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a54773d718d2c26e8f43eb8919b6fe22f32d3f01
--- /dev/null
+++ b/client/src/composables/persistentProgressMonitor.ts
@@ -0,0 +1,303 @@
+import { StorageSerializers, useLocalStorage } from "@vueuse/core";
+import { computed, readonly, watch } from "vue";
+
+import { type TaskMonitor } from "./genericTaskMonitor";
+
+type TaskType = "task" | "short_term_storage";
+
+/**
+ * Represents an object that is being processed in the background.
+ * Used to provide more context to the user when displaying the progress.
+ */
+interface ProcessedObject {
+    /** The ID of the object. */
+    id: string;
+
+    /**
+     * The type of the object.
+     * For example, "history", "dataset", "workflow", "invocation", etc.
+     */
+    type: string;
+
+    /**
+     * The name of the object.
+     * If the name is not provided, the ID will be used instead.
+     */
+    name?: string;
+}
+
+/**
+ * Provides information about a long-running asynchronous process that persists across page navigation or refresh.
+ * This information can be used to display progress to the user.
+ */
+export interface MonitoringRequest {
+    /**
+     * The component that initiated the task.
+     * This can be used to provide more context to the user when displaying the progress.
+     */
+    source: string;
+
+    /**
+     * The action of the task.
+     * This can be used to provide more context to the user when displaying the progress.
+     * For example, "import", "export", "delete", etc.
+     */
+    action: string;
+
+    /**
+     * The type of the task to monitor.
+     * This can be either a task or a short-term storage request.
+     */
+    taskType: TaskType;
+
+    /**
+     * The object being processed by the task.
+     * This can be used to provide more context to the user when displaying the progress.
+     */
+    object: ProcessedObject;
+
+    /**
+     * A human-readable description of the task.
+     * This is optional and can be used to provide more context to the user
+     * when displaying the progress.
+     */
+    description?: string;
+
+    /**
+     * The remote URI associated with the task.
+     *
+     * This is optional and indicates the task is associated with a remote resource.
+     */
+    remoteUri?: string;
+}
+
+export interface MonitoringData {
+    /**
+     * The ID of the task or short-term storage request to monitor.
+     */
+    taskId: string;
+
+    /**
+     * The type of the task to monitor.
+     * This can be either a task or a short-term storage request.
+     */
+    taskType: TaskType;
+
+    /**
+     * The information about the task.
+     */
+    request: MonitoringRequest;
+
+    /**
+     * The time when the task was started.
+     */
+    startedAt: Date;
+
+    /**
+     * The status of the task when it was last checked.
+     * The meaning of the status string is up to the monitor implementation.
+     * In case of an error, this will be the error message.
+     */
+    taskStatus?: string;
+}
+
+/**
+ * This composable is used to store the information about a long-running asynchronous process
+ * that persists across page navigation or refresh.
+ *
+ * It supports both task and short-term storage monitoring. The actual monitoring is done by the provided `useMonitor` composable.
+ */
+export function usePersistentProgressTaskMonitor(
+    request: MonitoringRequest,
+    useMonitor: TaskMonitor,
+    monitoringData: MonitoringData | null = null
+) {
+    const {
+        waitForTask,
+        isFinalState,
+        loadStatus,
+        isRunning,
+        isCompleted,
+        hasFailed,
+        requestHasFailed,
+        taskStatus,
+        expirationTime,
+    } = useMonitor;
+
+    const localStorageKey = getPersistentKey(request);
+
+    const currentMonitoringData = useLocalStorage<MonitoringData | null>(localStorageKey, monitoringData, {
+        serializer: StorageSerializers.object,
+    });
+
+    const hasMonitoringData = computed(() => {
+        return Boolean(currentMonitoringData.value);
+    });
+
+    const canExpire = computed(() => {
+        return Boolean(expirationTime);
+    });
+
+    const hasExpired = computed(() => {
+        return isDataExpired(currentMonitoringData.value, expirationTime);
+    });
+
+    const expirationDate = computed(() => {
+        if (!currentMonitoringData.value || !expirationTime) {
+            return undefined;
+        }
+
+        const startedAt = new Date(currentMonitoringData.value.startedAt);
+        return new Date(startedAt.getTime() + expirationTime);
+    });
+
+    watch(
+        () => taskStatus.value,
+        (newStatus) => {
+            if (newStatus && currentMonitoringData.value) {
+                currentMonitoringData.value = {
+                    ...currentMonitoringData.value,
+                    taskStatus: newStatus,
+                };
+            }
+        },
+        { immediate: true }
+    );
+
+    async function start(monitoringData?: MonitoringData) {
+        if (monitoringData) {
+            currentMonitoringData.value = monitoringData;
+        }
+
+        if (!currentMonitoringData.value) {
+            throw new Error("No monitoring data provided or stored. Cannot start monitoring progress.");
+        }
+
+        if (isFinalState(currentMonitoringData.value.taskStatus)) {
+            // The task has already finished no need to start monitoring again.
+            // Instead, reload the stored status to update the UI.
+            return loadStatus(currentMonitoringData.value.taskStatus!);
+        }
+
+        if (hasExpired.value) {
+            // The monitoring data has expired. Requesting the status again will likely
+            // return incorrect results. Reset the monitoring data to start fresh.
+            return;
+        }
+
+        return waitForTask(currentMonitoringData.value.taskId);
+    }
+
+    function reset() {
+        currentMonitoringData.value = null;
+    }
+
+    return {
+        /**
+         * Start monitoring the background process.
+         * If no monitoring data is provided, it will use the stored one.
+         * @param monitoringData Optional monitoring data to override the stored one.
+         */
+        start,
+
+        /**
+         * Clears the monitoring data in the local storage.
+         */
+        reset,
+
+        /**
+         * The task is still running.
+         */
+        isRunning,
+
+        /**
+         * The task has been completed successfully.
+         */
+        isCompleted,
+
+        /**
+         * Indicates the task has failed and will not yield results.
+         */
+        hasFailed,
+
+        /**
+         * If true, the status of the task cannot be determined because of a request error.
+         */
+        requestHasFailed,
+
+        /**
+         * Indicates that there is monitoring data stored.
+         */
+        hasMonitoringData,
+
+        /**
+         * The task ID stored in the monitoring data or undefined if no monitoring data is available.
+         */
+        storedTaskId: currentMonitoringData.value?.taskId,
+
+        /**
+         * The current status of the task.
+         * The meaning of the status string is up to the monitor implementation.
+         * In case of an error, this will be the error message.
+         */
+        status: taskStatus,
+
+        /**
+         * True if the monitoring data can expire.
+         */
+        canExpire,
+
+        /**
+         * True if the monitoring data has expired.
+         * The monitoring data expires after the expiration time has passed since the task was started.
+         */
+        hasExpired,
+
+        /**
+         * The expiration date for the monitoring data.
+         * After this date, the monitoring data is considered expired and should not be used.
+         */
+        expirationDate,
+
+        /**
+         * The monitoring data stored in the local storage.
+         */
+        monitoringData: readonly(currentMonitoringData),
+    };
+}
+
+/**
+ * Retrieves task progress data from the local storage associated with the
+ * monitoring request information provided if it exists.
+ * @param request The monitoring request information.
+ * @returns The associated task progress data or null if there is no stored data.
+ */
+export function getStoredProgressData(request: MonitoringRequest): MonitoringData | null {
+    const localStorageKey = getPersistentKey(request);
+    const currentMonitoringData = useLocalStorage<MonitoringData | null>(localStorageKey, null, {
+        serializer: StorageSerializers.object,
+    });
+
+    return currentMonitoringData.value;
+}
+
+function getPersistentKey(request: MonitoringRequest) {
+    return `persistent-progress-${request.taskType}-${request.source}-${request.action}-${request.object.type}-${request.object.id}`;
+}
+
+/**
+ * Checks if the monitoring data has expired.
+ * @param monitoringData The monitoring data to check for expiration.
+ * @param expirationTime The expiration time in milliseconds.
+ * @returns True if the monitoring data has expired, false otherwise.
+ */
+export function isDataExpired(monitoringData: MonitoringData | null, expirationTime?: number): boolean {
+    if (!monitoringData || !expirationTime) {
+        return false;
+    }
+
+    const now = new Date();
+    const startedAt = new Date(monitoringData.startedAt);
+    const elapsedTimeInMs = now.getTime() - startedAt.getTime();
+    return elapsedTimeInMs > expirationTime;
+}
diff --git a/client/src/composables/persistentRef.ts b/client/src/composables/persistentRef.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3411f626037ef899cef75795f7c447c705baa461
--- /dev/null
+++ b/client/src/composables/persistentRef.ts
@@ -0,0 +1,67 @@
+/*
+   vueuse local storage has some strange, buggy side-effects,
+   so were re-implementing just the parts we need here
+*/
+
+import { type Ref, ref, watch } from "vue";
+
+import { match } from "@/utils/utils";
+
+function stringify(value: unknown): string {
+    if (typeof value !== "object") {
+        return `${value}`;
+    } else {
+        return JSON.stringify(value);
+    }
+}
+
+function parse<T>(value: string, type: "string" | "number" | "boolean" | "object"): T {
+    return match(type, {
+        string: () => value as T,
+        number: () => parseFloat(value) as T,
+        boolean: () => (value.toLowerCase().trim() === "true" ? true : false) as T,
+        object: () => JSON.parse(value),
+    });
+}
+
+export function syncRefToLocalStorage<T>(key: string, refToSync: Ref<T>) {
+    const stored = window.localStorage.getItem(key);
+
+    const sync = () => {
+        const stringified = stringify(refToSync.value);
+        window.localStorage.setItem(key, stringified);
+    };
+
+    if (stored !== null) {
+        try {
+            refToSync.value = parse(stored, typeof refToSync.value as "string" | "number" | "boolean" | "object");
+        } catch (e) {
+            console.error(`Failed to parse value "${stored}" from local storage key "${key}". Resetting key`);
+            sync();
+        }
+    } else {
+        sync();
+    }
+
+    watch(
+        () => refToSync.value,
+        () => {
+            sync();
+        },
+        { deep: true }
+    );
+}
+
+export function usePersistentRef(key: string, defaultValue: string): Ref<string>;
+export function usePersistentRef(key: string, defaultValue: number): Ref<number>;
+export function usePersistentRef<T>(key: string, defaultValue: T): Ref<T>;
+export function usePersistentRef<T extends string | number | boolean | object | null>(
+    key: string,
+    defaultValue: T
+): Ref<T> {
+    const storageSyncedRef = ref(defaultValue) as Ref<T>;
+
+    syncRefToLocalStorage(key, storageSyncedRef);
+
+    return storageSyncedRef;
+}
diff --git a/client/src/composables/resourceWatcher.ts b/client/src/composables/resourceWatcher.ts
index a5a36671421c1decb0f83f9e7744744d00ecb27f..62b2d2567ef4cdd148d3853265dac76c9cdc8a15 100644
--- a/client/src/composables/resourceWatcher.ts
+++ b/client/src/composables/resourceWatcher.ts
@@ -42,7 +42,7 @@ export function useResourceWatcher(watchHandler: WatchResourceHandler, options:
      * Starts watching the resource by polling the server continuously.
      */
     function startWatchingResource() {
-        stopWatchingResource();
+        stopWatcher();
         tryWatchResource();
     }
 
@@ -50,6 +50,10 @@ export function useResourceWatcher(watchHandler: WatchResourceHandler, options:
      * Stops continuously watching the resource.
      */
     function stopWatchingResource() {
+        stopWatcher();
+    }
+
+    function stopWatcher() {
         if (watchTimeout) {
             clearTimeout(watchTimeout);
             watchTimeout = null;
@@ -90,5 +94,6 @@ export function useResourceWatcher(watchHandler: WatchResourceHandler, options:
 
     return {
         startWatchingResource,
+        stopWatchingResource,
     };
 }
diff --git a/client/src/composables/route.ts b/client/src/composables/route.ts
index 89b1ee6a7dbf7976a23031566effdee380173e67..d783f14a36a1194de52c5f00d2564071da5cab05 100644
--- a/client/src/composables/route.ts
+++ b/client/src/composables/route.ts
@@ -1,4 +1,4 @@
-import { MaybeRefOrGetter, toValue } from "@vueuse/core";
+import { type MaybeRefOrGetter, toValue } from "@vueuse/core";
 import { computed } from "vue";
 import { useRoute } from "vue-router/composables";
 
diff --git a/client/src/composables/sensors/animationFrameResizeObserver.ts b/client/src/composables/sensors/animationFrameResizeObserver.ts
index 0b31ec6dabbb58ced243771122ec95bc7a36bd48..4c38ff3e410cc09f730570fde677591866897a6b 100644
--- a/client/src/composables/sensors/animationFrameResizeObserver.ts
+++ b/client/src/composables/sensors/animationFrameResizeObserver.ts
@@ -1,5 +1,4 @@
-import type { MaybeRefOrGetter } from "@vueuse/core";
-import { resolveUnref } from "@vueuse/core";
+import { type MaybeRefOrGetter, resolveUnref } from "@vueuse/core";
 
 import { useAnimationFrame } from "./animationFrame";
 
diff --git a/client/src/composables/sensors/animationFrameScroll.ts b/client/src/composables/sensors/animationFrameScroll.ts
index 97a1d0cf526dea35871e1377337d26abd240d14f..784171a6a1e56644b39162fce2091a2db2f40619 100644
--- a/client/src/composables/sensors/animationFrameScroll.ts
+++ b/client/src/composables/sensors/animationFrameScroll.ts
@@ -1,5 +1,4 @@
-import type { MaybeRefOrGetter } from "@vueuse/core";
-import { resolveUnref } from "@vueuse/core";
+import { type MaybeRefOrGetter, resolveUnref } from "@vueuse/core";
 import { reactive, ref } from "vue";
 
 import { useAnimationFrame } from "./animationFrame";
diff --git a/client/src/composables/shortTermStorage.ts b/client/src/composables/shortTermStorage.ts
index fb6cd45eccd6c62c70520859e7d09e0d893b111c..3237dc15e2fc4bc35a2f6c37a6035433b22d66ea 100644
--- a/client/src/composables/shortTermStorage.ts
+++ b/client/src/composables/shortTermStorage.ts
@@ -1,8 +1,12 @@
-import { readonly, ref } from "vue";
+import { readonly, ref, watch } from "vue";
 
-import { fetcher } from "@/api/schema";
-import { ExportParams, StoreExportPayload } from "@/components/Common/models/exportRecordModel";
+import { type StoreExportPayload } from "@/api";
+import { GalaxyApi } from "@/api";
+import { type ExportParams } from "@/components/Common/models/exportRecordModel";
 import { withPrefix } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
+
+import { useShortTermStorageMonitor } from "./shortTermStorageMonitor";
 
 export const DEFAULT_EXPORT_PARAMS: ExportParams = {
     modelStoreFormat: "rocrate.zip",
@@ -22,54 +26,57 @@ interface StorageRequestResponse {
 
 type StartPreparingDownloadCallback = (objectId: string, params: StoreExportPayload) => Promise<StorageRequestResponse>;
 
-const DEFAULT_POLL_DELAY = 1000;
+const DEFAULT_POLL_DELAY = 3000;
 const DEFAULT_OPTIONS: Options = { exportParams: DEFAULT_EXPORT_PARAMS, pollDelayInMs: DEFAULT_POLL_DELAY };
 
-const startPreparingHistoryDownload = fetcher
-    .path("/api/histories/{history_id}/prepare_store_download")
-    .method("post")
-    .create();
-const startPreparingInvocationDownload = fetcher
-    .path("/api/invocations/{invocation_id}/prepare_store_download")
-    .method("post")
-    .create();
-const getTempStorageRequestReady = fetcher
-    .path("/api/short_term_storage/{storage_request_id}/ready")
-    .method("get")
-    .create();
-
 /**
  * Composable to simplify and reuse the logic for downloading objects using Galaxy's Short Term Storage system.
  */
 export function useShortTermStorage() {
-    let timeout: NodeJS.Timeout | null = null;
-    let pollDelay = DEFAULT_POLL_DELAY;
+    const { waitForTask, isRunning } = useShortTermStorageMonitor();
 
     const isPreparing = ref(false);
 
+    watch(isRunning, (running) => {
+        if (!running) {
+            isPreparing.value = false;
+        }
+    });
+
     const forHistory: StartPreparingDownloadCallback = async (id: string, params: StoreExportPayload) => {
-        const { data } = await startPreparingHistoryDownload({ history_id: id, ...params });
+        const { data, error } = await GalaxyApi().POST("/api/histories/{history_id}/prepare_store_download", {
+            params: { path: { history_id: id } },
+            body: params,
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
         return data;
     };
 
     const forInvocation: StartPreparingDownloadCallback = async (id: string, params: StoreExportPayload) => {
-        const { data } = await startPreparingInvocationDownload({ invocation_id: id, ...params });
+        const { data, error } = await GalaxyApi().POST("/api/invocations/{invocation_id}/prepare_store_download", {
+            params: { path: { invocation_id: id } },
+            body: {
+                ...params,
+                bco_merge_history_metadata: false,
+            },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
         return data;
     };
 
     async function prepareHistoryDownload(historyId: string, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(forHistory, historyId, options, false);
-    }
-    async function downloadHistory(historyId: string, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(forHistory, historyId, options, true);
+        return prepareObjectDownload(forHistory, historyId, options);
     }
 
     async function prepareWorkflowInvocationDownload(invocationId: string, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(forInvocation, invocationId, options, false);
-    }
-
-    async function downloadWorkflowInvocation(invocationId: string, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(forInvocation, invocationId, options, true);
+        return prepareObjectDownload(forInvocation, invocationId, options);
     }
 
     function getDownloadObjectUrl(storageRequestId: string) {
@@ -85,13 +92,10 @@ export function useShortTermStorage() {
     async function prepareObjectDownload(
         startPreparingDownloadAsync: StartPreparingDownloadCallback,
         objectId: string,
-        options = DEFAULT_OPTIONS,
-        downloadWhenReady = true
+        options = DEFAULT_OPTIONS
     ) {
-        resetTimeout();
         isPreparing.value = true;
         const finalOptions = Object.assign(DEFAULT_OPTIONS, options);
-        pollDelay = finalOptions.pollDelayInMs;
         const exportParams: StoreExportPayload = {
             model_store_format: finalOptions.exportParams.modelStoreFormat,
             include_files: finalOptions.exportParams.includeFiles,
@@ -102,43 +106,9 @@ export function useShortTermStorage() {
         try {
             const response = await startPreparingDownloadAsync(objectId, exportParams);
             const storageRequestId = response.storage_request_id;
-            pollStorageRequestId(storageRequestId, downloadWhenReady);
+            waitForTask(storageRequestId, finalOptions.pollDelayInMs);
         } catch (err) {
-            stopPreparing();
-        }
-    }
-
-    async function pollStorageRequestId(storageRequestId: string, downloadWhenReady: boolean) {
-        try {
-            const { data: ready } = await getTempStorageRequestReady({ storage_request_id: storageRequestId });
-            if (ready) {
-                isPreparing.value = false;
-                if (downloadWhenReady) {
-                    downloadObjectByRequestId(storageRequestId);
-                }
-            } else {
-                pollAfterDelay(storageRequestId, downloadWhenReady);
-            }
-        } catch (err) {
-            stopPreparing();
-        }
-    }
-
-    function stopPreparing() {
-        isPreparing.value = false;
-    }
-
-    function pollAfterDelay(storageRequestId: string, downloadWhenReady: boolean) {
-        resetTimeout();
-        timeout = setTimeout(() => {
-            pollStorageRequestId(storageRequestId, downloadWhenReady);
-        }, pollDelay);
-    }
-
-    function resetTimeout() {
-        if (timeout) {
-            clearTimeout(timeout);
-            timeout = null;
+            isPreparing.value = false;
         }
     }
 
@@ -149,24 +119,12 @@ export function useShortTermStorage() {
          * @param {Object} options Options for the download preparation
          */
         prepareHistoryDownload,
-        /**
-         * Prepares a history download file in the short term storage and starts the download when ready.
-         * @param {String} historyId The ID of the history to be downloaded
-         * @param {Object} options Options for the download preparation
-         */
-        downloadHistory,
         /**
          * Starts preparing a workflow invocation download file in the short term storage.
          * @param {String} invocationId The ID of the workflow invocation to be prepared for download
          * @param {Object} options Options for the download preparation
          */
         prepareWorkflowInvocationDownload,
-        /**
-         * Starts preparing a workflow invocation download file in the short term storage and starts the download when ready.
-         * @param {String} invocationId The ID of the workflow invocation to be downloaded
-         * @param {Object} options Options for the download preparation
-         */
-        downloadWorkflowInvocation,
         /**
          * Starts a direct download of the object associated with the given `storageRequestId`.
          * For the download to succeed, the associated `storageRequestId` must be `ready` and not in failure state.
diff --git a/client/src/composables/shortTermStorageMonitor.test.ts b/client/src/composables/shortTermStorageMonitor.test.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2dc3974c06685c5bfa9e2d9f064906ba1e756199
--- /dev/null
+++ b/client/src/composables/shortTermStorageMonitor.test.ts
@@ -0,0 +1,105 @@
+import flushPromises from "flush-promises";
+
+import { useServerMock } from "@/api/client/__mocks__";
+import { useShortTermStorageMonitor } from "@/composables/shortTermStorageMonitor";
+
+const PENDING_TASK_ID = "pending-fake-task-id";
+const COMPLETED_TASK_ID = "completed-fake-task-id";
+const REQUEST_FAILED_TASK_ID = "request-failed-fake-task-id";
+
+const { server, http } = useServerMock();
+
+describe("useShortTermStorageMonitor", () => {
+    beforeEach(() => {
+        server.use(
+            http.get("/api/short_term_storage/{storage_request_id}/ready", ({ response, params }) => {
+                switch (params.storage_request_id) {
+                    case PENDING_TASK_ID:
+                        return response(200).json(false);
+
+                    case COMPLETED_TASK_ID:
+                        return response(200).json(true);
+
+                    case REQUEST_FAILED_TASK_ID:
+                        return response("5XX").json({ err_msg: "Request failed", err_code: 500 }, { status: 500 });
+
+                    default:
+                        return response("4XX").json({ err_msg: "Not found", err_code: 404 }, { status: 404 });
+                }
+            })
+        );
+    });
+
+    it("should indicate the task is running when it is still not ready", async () => {
+        const { waitForTask, isRunning, taskStatus } = useShortTermStorageMonitor();
+
+        expect(isRunning.value).toBe(false);
+        waitForTask(PENDING_TASK_ID);
+        await flushPromises();
+        expect(isRunning.value).toBe(true);
+        expect(taskStatus.value).toBe("PENDING");
+    });
+
+    it("should indicate the task is successfully completed when the state is ready", async () => {
+        const { waitForTask, isRunning, isCompleted, taskStatus } = useShortTermStorageMonitor();
+
+        expect(isCompleted.value).toBe(false);
+        waitForTask(COMPLETED_TASK_ID);
+        await flushPromises();
+        expect(isCompleted.value).toBe(true);
+        expect(isRunning.value).toBe(false);
+        expect(taskStatus.value).toBe("READY");
+    });
+
+    it("should indicate the task status request failed when the request failed", async () => {
+        const { waitForTask, requestHasFailed, isRunning, isCompleted, taskStatus } = useShortTermStorageMonitor();
+
+        expect(requestHasFailed.value).toBe(false);
+        waitForTask(REQUEST_FAILED_TASK_ID);
+        await flushPromises();
+        expect(requestHasFailed.value).toBe(true);
+        expect(isRunning.value).toBe(false);
+        expect(isCompleted.value).toBe(false);
+        expect(taskStatus.value).toBe("Request failed");
+    });
+
+    it("should load the status from the stored monitoring data", async () => {
+        const { loadStatus, isRunning, isCompleted, hasFailed, taskStatus } = useShortTermStorageMonitor();
+        const storedStatus = "READY";
+
+        loadStatus(storedStatus);
+
+        expect(taskStatus.value).toBe(storedStatus);
+        expect(isRunning.value).toBe(false);
+        expect(isCompleted.value).toBe(true);
+        expect(hasFailed.value).toBe(false);
+    });
+
+    describe("isFinalState", () => {
+        it("should indicate is final state when the task is completed", async () => {
+            const { waitForTask, isFinalState, isRunning, isCompleted, hasFailed, taskStatus } =
+                useShortTermStorageMonitor();
+
+            expect(isFinalState(taskStatus.value)).toBe(false);
+            waitForTask(COMPLETED_TASK_ID);
+            await flushPromises();
+            expect(isFinalState(taskStatus.value)).toBe(true);
+            expect(isRunning.value).toBe(false);
+            expect(isCompleted.value).toBe(true);
+            expect(hasFailed.value).toBe(false);
+        });
+
+        it("should indicate is final state when the task has failed", async () => {
+            const { waitForTask, isFinalState, isRunning, isCompleted, hasFailed, taskStatus } =
+                useShortTermStorageMonitor();
+
+            expect(isFinalState(taskStatus.value)).toBe(false);
+            waitForTask(REQUEST_FAILED_TASK_ID);
+            await flushPromises();
+            expect(isFinalState(taskStatus.value)).toBe(true);
+            expect(isRunning.value).toBe(false);
+            expect(isCompleted.value).toBe(false);
+            expect(hasFailed.value).toBe(true);
+        });
+    });
+});
diff --git a/client/src/composables/shortTermStorageMonitor.ts b/client/src/composables/shortTermStorageMonitor.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8fbbac62b3bc3475615c39fe06466409fe92c955
--- /dev/null
+++ b/client/src/composables/shortTermStorageMonitor.ts
@@ -0,0 +1,36 @@
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
+
+import { useGenericMonitor } from "./genericTaskMonitor";
+
+const DEFAULT_POLL_DELAY = 10000;
+const DEFAULT_EXPIRATION_TIME = 1000 * 60 * 60 * 24; // 24 hours
+
+const READY_STATE = "READY";
+const PENDING_STATE = "PENDING";
+const VALID_STATES = [READY_STATE, PENDING_STATE];
+
+/**
+ * Composable for waiting on Galaxy Short Term Storage requests.
+ */
+export function useShortTermStorageMonitor() {
+    const fetchStatus = async (taskId: string) => {
+        const { data, error } = await GalaxyApi().GET("/api/short_term_storage/{storage_request_id}/ready", {
+            params: { path: { storage_request_id: taskId } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        return data ? READY_STATE : PENDING_STATE;
+    };
+
+    return useGenericMonitor({
+        fetchStatus,
+        completedCondition: (status?: string) => status === READY_STATE,
+        failedCondition: (status?: string) => typeof status === "string" && !VALID_STATES.includes(status),
+        defaultPollDelay: DEFAULT_POLL_DELAY,
+        expirationTime: DEFAULT_EXPIRATION_TIME,
+    });
+}
diff --git a/client/src/composables/taskMonitor.test.ts b/client/src/composables/taskMonitor.test.ts
index 3a7db833b6c163a8890306b0981df12f8371246b..60702963e9838b31da29728270bcfed43d13fdc9 100644
--- a/client/src/composables/taskMonitor.test.ts
+++ b/client/src/composables/taskMonitor.test.ts
@@ -1,72 +1,118 @@
 import flushPromises from "flush-promises";
 
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { useServerMock } from "@/api/client/__mocks__";
 import { useTaskMonitor } from "@/composables/taskMonitor";
 
-jest.mock("@/api/schema");
-
 const PENDING_TASK_ID = "pending-fake-task-id";
 const COMPLETED_TASK_ID = "completed-fake-task-id";
 const FAILED_TASK_ID = "failed-fake-task-id";
 const REQUEST_FAILED_TASK_ID = "request-failed-fake-task-id";
 
-function getMockedTaskStatus({ task_id }: { task_id: string }) {
-    switch (task_id) {
-        case PENDING_TASK_ID:
-            return { data: "PENDING", status: 200 };
-
-        case COMPLETED_TASK_ID:
-            return { data: "SUCCESS", status: 200 };
-
-        case FAILED_TASK_ID:
-            return { data: "FAILURE", status: 200 };
-
-        case REQUEST_FAILED_TASK_ID:
-            throw new Error("Request failed");
-
-        default:
-            return { data: "UNKNOWN", status: 404 };
-    }
-}
-
-mockFetcher.path("/api/tasks/{task_id}/state").method("get").mock(getMockedTaskStatus);
+const { server, http } = useServerMock();
 
 describe("useTaskMonitor", () => {
+    beforeEach(() => {
+        server.use(
+            http.get("/api/tasks/{task_id}/state", ({ response, params }) => {
+                switch (params.task_id) {
+                    case PENDING_TASK_ID:
+                        return response(200).json("PENDING");
+
+                    case COMPLETED_TASK_ID:
+                        return response(200).json("SUCCESS");
+
+                    case FAILED_TASK_ID:
+                        return response(200).json("FAILURE");
+
+                    case REQUEST_FAILED_TASK_ID:
+                        return response("5XX").json({ err_msg: "Request failed", err_code: 500 }, { status: 500 });
+
+                    default:
+                        return response("4XX").json({ err_msg: "Not found", err_code: 404 }, { status: 404 });
+                }
+            })
+        );
+    });
+
     it("should indicate the task is running when it is still pending", async () => {
-        const { waitForTask, isRunning } = useTaskMonitor();
+        const { waitForTask, isRunning, taskStatus } = useTaskMonitor();
 
         expect(isRunning.value).toBe(false);
         waitForTask(PENDING_TASK_ID);
         await flushPromises();
         expect(isRunning.value).toBe(true);
+        expect(taskStatus.value).toBe("PENDING");
     });
 
     it("should indicate the task is successfully completed when the state is SUCCESS", async () => {
-        const { waitForTask, isRunning, isCompleted } = useTaskMonitor();
+        const { waitForTask, isRunning, isCompleted, taskStatus } = useTaskMonitor();
 
         expect(isCompleted.value).toBe(false);
         waitForTask(COMPLETED_TASK_ID);
         await flushPromises();
         expect(isCompleted.value).toBe(true);
         expect(isRunning.value).toBe(false);
+        expect(taskStatus.value).toBe("SUCCESS");
     });
 
     it("should indicate the task has failed when the state is FAILED", async () => {
-        const { waitForTask, isRunning, hasFailed } = useTaskMonitor();
+        const { waitForTask, isRunning, hasFailed, taskStatus } = useTaskMonitor();
 
         expect(hasFailed.value).toBe(false);
         waitForTask(FAILED_TASK_ID);
         await flushPromises();
         expect(hasFailed.value).toBe(true);
         expect(isRunning.value).toBe(false);
+        expect(taskStatus.value).toBe("FAILURE");
     });
 
     it("should indicate the task status request failed when the request failed", async () => {
-        const { waitForTask, requestHasFailed } = useTaskMonitor();
+        const { waitForTask, requestHasFailed, isRunning, isCompleted, taskStatus } = useTaskMonitor();
 
         expect(requestHasFailed.value).toBe(false);
         waitForTask(REQUEST_FAILED_TASK_ID);
         await flushPromises();
         expect(requestHasFailed.value).toBe(true);
+        expect(isRunning.value).toBe(false);
+        expect(isCompleted.value).toBe(false);
+        expect(taskStatus.value).toBe("Request failed");
+    });
+
+    it("should load the status from the stored monitoring data", async () => {
+        const { loadStatus, isRunning, isCompleted, hasFailed, taskStatus } = useTaskMonitor();
+        const storedStatus = "SUCCESS";
+
+        loadStatus(storedStatus);
+
+        expect(taskStatus.value).toBe(storedStatus);
+        expect(isRunning.value).toBe(false);
+        expect(isCompleted.value).toBe(true);
+        expect(hasFailed.value).toBe(false);
+    });
+
+    describe("isFinalState", () => {
+        it("should indicate is final state when the task is completed", async () => {
+            const { waitForTask, isFinalState, isRunning, isCompleted, hasFailed, taskStatus } = useTaskMonitor();
+
+            expect(isFinalState(taskStatus.value)).toBe(false);
+            waitForTask(COMPLETED_TASK_ID);
+            await flushPromises();
+            expect(isFinalState(taskStatus.value)).toBe(true);
+            expect(isRunning.value).toBe(false);
+            expect(isCompleted.value).toBe(true);
+            expect(hasFailed.value).toBe(false);
+        });
+
+        it("should indicate is final state when the task has failed", async () => {
+            const { waitForTask, isFinalState, isRunning, isCompleted, hasFailed, taskStatus } = useTaskMonitor();
+
+            expect(isFinalState(taskStatus.value)).toBe(false);
+            waitForTask(FAILED_TASK_ID);
+            await flushPromises();
+            expect(isFinalState(taskStatus.value)).toBe(true);
+            expect(isRunning.value).toBe(false);
+            expect(isCompleted.value).toBe(false);
+            expect(hasFailed.value).toBe(true);
+        });
     });
 });
diff --git a/client/src/composables/taskMonitor.ts b/client/src/composables/taskMonitor.ts
index 8f05470504a8fe60544753b406f06bca6db2f894..ee3c3f58e7042bbf3c90df677b2791cf408214e7 100644
--- a/client/src/composables/taskMonitor.ts
+++ b/client/src/composables/taskMonitor.ts
@@ -1,101 +1,33 @@
-import { computed, readonly, ref } from "vue";
+import { GalaxyApi } from "@/api";
+import { rethrowSimple } from "@/utils/simple-error";
 
-import { fetcher } from "@/api/schema";
-import { errorMessageAsString } from "@/utils/simple-error";
+import { useGenericMonitor } from "./genericTaskMonitor";
 
 const SUCCESS_STATE = "SUCCESS";
 const FAILURE_STATE = "FAILURE";
-const TASK_READY_STATES = [SUCCESS_STATE, FAILURE_STATE];
 const DEFAULT_POLL_DELAY = 10000;
-
-const getTaskStatus = fetcher.path("/api/tasks/{task_id}/state").method("get").create();
+const DEFAULT_EXPIRATION_TIME = 1000 * 60 * 60 * 24; // 24 hours
 
 /**
  * Composable for waiting on Galaxy background tasks.
  */
 export function useTaskMonitor() {
-    let timeout: NodeJS.Timeout | null = null;
-    let pollDelay = DEFAULT_POLL_DELAY;
-
-    const isRunning = ref(false);
-    const status = ref<string>();
-    const currentTaskId = ref<string>();
-    const requestHasFailed = ref(false);
-
-    const isCompleted = computed(() => status.value === SUCCESS_STATE);
-    const hasFailed = computed(() => status.value === FAILURE_STATE);
+    const fetchStatus = async (taskId: string) => {
+        const { data, error } = await GalaxyApi().GET("/api/tasks/{task_id}/state", {
+            params: { path: { task_id: taskId } },
+        });
 
-    async function waitForTask(taskId: string, pollDelayInMs = DEFAULT_POLL_DELAY) {
-        pollDelay = pollDelayInMs;
-        resetState();
-        currentTaskId.value = taskId;
-        isRunning.value = true;
-        return fetchTaskStatus(taskId);
-    }
-
-    async function fetchTaskStatus(taskId: string) {
-        try {
-            const { data } = await getTaskStatus({ task_id: taskId });
-            status.value = data;
-            const isReady = TASK_READY_STATES.includes(status.value);
-            if (isReady) {
-                isRunning.value = false;
-            } else {
-                pollAfterDelay(taskId);
-            }
-        } catch (err) {
-            handleError(errorMessageAsString(err));
+        if (error) {
+            rethrowSimple(error);
         }
-    }
-
-    function pollAfterDelay(taskId: string) {
-        resetTimeout();
-        timeout = setTimeout(() => {
-            fetchTaskStatus(taskId);
-        }, pollDelay);
-    }
-
-    function handleError(err: string) {
-        status.value = err;
-        requestHasFailed.value = true;
-        isRunning.value = false;
-        resetTimeout();
-    }
-
-    function resetTimeout() {
-        if (timeout) {
-            clearTimeout(timeout);
-        }
-    }
-
-    function resetState() {
-        resetTimeout();
-        status.value = undefined;
-    }
 
-    return {
-        /**
-         * Waits for a particular task ID to be completed.
-         * While the task is pending, the state will be updated every `pollDelayInMs` by polling the server.
-         * @param {string} taskId The task ID
-         * @param {Number} pollDelayInMs The time (milliseconds) between poll requests to update the task state.
-         */
-        waitForTask,
-        /**
-         * Whether the task is currently running.
-         */
-        isRunning: readonly(isRunning),
-        /**
-         * Whether the task has been completed successfully.
-         */
-        isCompleted: readonly(isCompleted),
-        /**
-         * Indicates the task has failed and will not yield results.
-         */
-        hasFailed: readonly(hasFailed),
-        /**
-         * If true, the status of the task cannot be determined because of a request error.
-         */
-        requestHasFailed: readonly(requestHasFailed),
+        return data;
     };
+    return useGenericMonitor({
+        fetchStatus,
+        completedCondition: (status?: string) => status === SUCCESS_STATE,
+        failedCondition: (status?: string) => status === FAILURE_STATE,
+        defaultPollDelay: DEFAULT_POLL_DELAY,
+        expirationTime: DEFAULT_EXPIRATION_TIME,
+    });
 }
diff --git a/client/src/composables/timeoutStoreDispose.ts b/client/src/composables/timeoutStoreDispose.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c9adcacdd577f37ac5a6c397a892cac780796447
--- /dev/null
+++ b/client/src/composables/timeoutStoreDispose.ts
@@ -0,0 +1,30 @@
+import type { Store } from "pinia";
+
+const referenceCountByStore = new WeakMap<Store, number>();
+
+/**
+ * Reference counts a store, and provides a function to safely dispose it after a timeout.
+ * @param store store to reference count and dispose
+ * @param timeout how long to wait before reference counting and attempting a dispose.
+ * @returns dispose function
+ */
+export function useTimeoutStoreDispose(store: Store, timeout = 1000) {
+    const currentReferenceCount = referenceCountByStore.get(store) ?? 0;
+    referenceCountByStore.set(store, currentReferenceCount + 1);
+
+    const disposeIfReferenceFree = () => {
+        const referenceCount = referenceCountByStore.get(store) ?? 0;
+
+        if (referenceCount <= 0) {
+            store.$dispose();
+        }
+    };
+
+    const dispose = () => {
+        const referenceCount = referenceCountByStore.get(store) ?? 1;
+        referenceCountByStore.set(store, referenceCount - 1);
+        setTimeout(disposeIfReferenceFree, timeout);
+    };
+
+    return dispose;
+}
diff --git a/client/src/composables/toast.ts b/client/src/composables/toast.ts
index 677a01135a73ccc5b029a7f8fad3224338262680..a19beeac1b71c54628ecd0389bae533aa6edb01b 100644
--- a/client/src/composables/toast.ts
+++ b/client/src/composables/toast.ts
@@ -1,5 +1,6 @@
 import type Vue from "vue";
-import { type Ref, ref } from "vue";
+import { type Ref } from "vue";
+import { ref } from "vue";
 
 import type ToastComponentFile from "@/components/Toast";
 
diff --git a/client/src/composables/useActiveElement.ts b/client/src/composables/useActiveElement.ts
index 6c2087a71afef7206681e52e64b2758e6bc90116..890d7131abd7967a82160574d4b2862081fd0b49 100644
--- a/client/src/composables/useActiveElement.ts
+++ b/client/src/composables/useActiveElement.ts
@@ -1,5 +1,5 @@
 // https://github.com/vueuse/vueuse/blob/main/packages/core/_configurable.ts
-import type { ConfigurableWindow, MaybeElementRef, UseFocusWithinReturn } from "@vueuse/core";
+import { type ConfigurableWindow, type MaybeElementRef, type UseFocusWithinReturn } from "@vueuse/core";
 import { unrefElement, useEventListener } from "@vueuse/core";
 import { computedWithControl, isClient } from "@vueuse/shared";
 import { computed } from "vue";
diff --git a/client/src/composables/useInvocationGraph.ts b/client/src/composables/useInvocationGraph.ts
index be5ea6e008dee56963dcafe479d70f9b76ea7f3b..211db6cd79793c31f1313a692647272a5285689b 100644
--- a/client/src/composables/useInvocationGraph.ts
+++ b/client/src/composables/useInvocationGraph.ts
@@ -8,19 +8,20 @@ import {
     faSpinner,
     faTrash,
 } from "@fortawesome/free-solid-svg-icons";
+import { storeToRefs } from "pinia";
 import { computed, type Ref, ref, set } from "vue";
 
-import {
-    type InvocationStep,
-    stepJobsSummaryFetcher,
-    type StepJobSummary,
-    type WorkflowInvocationElementView,
-} from "@/api/invocations";
+import { GalaxyApi } from "@/api";
+import { fetchCollectionDetails } from "@/api/datasetCollections";
+import { fetchDatasetDetails } from "@/api/datasets";
+import { type InvocationStep, type StepJobSummary, type WorkflowInvocationElementView } from "@/api/invocations";
+import { getContentItemState } from "@/components/History/Content/model/states";
 import { isWorkflowInput } from "@/components/Workflow/constants";
 import { fromSimple } from "@/components/Workflow/Editor/modules/model";
 import { getWorkflowFull } from "@/components/Workflow/workflows.services";
-import type { Step } from "@/stores/workflowStepStore";
-import type { Workflow } from "@/stores/workflowStore";
+import { useInvocationStore } from "@/stores/invocationStore";
+import { type Step } from "@/stores/workflowStepStore";
+import { type Workflow } from "@/stores/workflowStore";
 import { rethrowSimple } from "@/utils/simple-error";
 
 import { provideScopedWorkflowStores } from "./workflowStores";
@@ -43,6 +44,7 @@ export interface GraphStep extends Step {
     headerClass?: Record<string, boolean>;
     headerIcon?: IconDefinition;
     headerIconSpin?: boolean;
+    nodeText?: string | boolean;
 }
 interface InvocationGraph extends Workflow {
     steps: { [index: number]: GraphStep };
@@ -61,8 +63,13 @@ export const iconClasses: Record<string, { icon: IconDefinition; spin?: boolean;
     skipped: { icon: faForward, class: "text-warning" },
 };
 
+export const statePlaceholders: Record<string, string> = {
+    ok: "successful",
+    error: "failed",
+};
+
 /** Only one job needs to be in one of these states for the graph step to be in that state */
-const SINGLE_INSTANCE_STATES = ["error", "running", "paused"];
+const SINGLE_INSTANCE_STATES = ["error", "running", "paused", "deleting"];
 /** All jobs need to be in one of these states for the graph step to be in that state */
 const ALL_INSTANCES_STATES = ["deleted", "skipped", "new", "queued"];
 
@@ -82,6 +89,8 @@ export function useInvocationGraph(
     const storeId = computed(() => `invocation-${invocation.value.id}`);
 
     const lastStepsJobsSummary = ref<StepJobSummary[]>([]);
+    const invocationStore = useInvocationStore();
+    const { graphStepsByStoreId } = storeToRefs(invocationStore);
 
     /** The full invocation mapped onto the original workflow */
     const invocationGraph = ref<InvocationGraph | null>(null);
@@ -113,22 +122,24 @@ export function useInvocationGraph(
             }
 
             // get the job summary for each step in the invocation
-            const { data: stepsJobsSummary } = await stepJobsSummaryFetcher({ invocation_id: invocation.value.id });
-
-            // if the steps have not been populated or the job states have changed, update the steps
-            // TODO: What if the state of something not in the stepsJobsSummary has changed? (e.g.: subworkflows...)
-            if (
-                !stepsPopulated.value ||
-                JSON.stringify(stepsJobsSummary) !== JSON.stringify(lastStepsJobsSummary.value)
-            ) {
-                updateSteps(stepsJobsSummary);
-
-                // Load the invocation graph into the editor the first time
-                if (!stepsPopulated.value) {
-                    invocationGraph.value!.steps = { ...steps.value };
-                    await fromSimple(storeId.value, invocationGraph.value as any);
-                    stepsPopulated.value = true;
+            const { data: stepsJobsSummary, error } = await GalaxyApi().GET(
+                "/api/invocations/{invocation_id}/step_jobs_summary",
+                {
+                    params: { path: { invocation_id: invocation.value.id } },
                 }
+            );
+
+            if (error) {
+                rethrowSimple(error);
+            }
+
+            await updateSteps(stepsJobsSummary);
+
+            // Load the invocation graph into the editor the first time
+            if (!stepsPopulated.value) {
+                invocationGraph.value!.steps = { ...steps.value };
+                await fromSimple(storeId.value, invocationGraph.value as any);
+                stepsPopulated.value = true;
             }
         } catch (e) {
             rethrowSimple(e);
@@ -139,7 +150,7 @@ export function useInvocationGraph(
      * if they haven't been populated yet.
      * @param stepsJobsSummary - The job summary for each step in the invocation
      * */
-    function updateSteps(stepsJobsSummary: StepJobSummary[]) {
+    async function updateSteps(stepsJobsSummary: StepJobSummary[]) {
         /** Initialize with the original steps of the workflow, else update the existing graph steps */
         const fullSteps: Record<string, Step | GraphStep> = !stepsPopulated.value
             ? { ...loadedWorkflow.value.steps }
@@ -158,7 +169,13 @@ export function useInvocationGraph(
             /** The raw invocation step */
             const invocationStep = invocation.value.steps[i];
 
-            if (!isWorkflowInput(graphStepFromWfStep.type)) {
+            // TODO: What if the state of something not in the stepsJobsSummary has changed? (e.g.: subworkflows...)
+            /** if the steps have not been populated or the job states have changed, update the step */
+            const updateNonInputStep =
+                !stepsPopulated.value ||
+                JSON.stringify(stepsJobsSummary) !== JSON.stringify(lastStepsJobsSummary.value);
+
+            if (updateNonInputStep && !isWorkflowInput(graphStepFromWfStep.type)) {
                 let invocationStepSummary: StepJobSummary | undefined;
                 if (invocationStep) {
                     invocationStepSummary = stepsJobsSummary.find((stepJobSummary: StepJobSummary) => {
@@ -170,12 +187,18 @@ export function useInvocationGraph(
                     });
                 }
                 updateStep(graphStepFromWfStep, invocationStep, invocationStepSummary);
+            } else if (invocationStep && graphStepFromWfStep.nodeText === undefined) {
+                await initializeGraphInput(graphStepFromWfStep, invocationStep);
             }
 
             // add the graph step to the steps object if it doesn't exist yet
             if (!steps.value[i]) {
                 set(steps.value, i, graphStepFromWfStep);
             }
+
+            // update the invocation store's graph steps object
+            // TODO: Find a better way of doing this, instead of using two separate objects...?
+            set(graphStepsByStoreId.value, storeId.value, steps.value);
         }
 
         lastStepsJobsSummary.value = stepsJobsSummary;
@@ -257,19 +280,7 @@ export function useInvocationGraph(
         // if the state has changed, update the graph step
         if (graphStep.state !== newState) {
             graphStep.state = newState;
-
-            /** Setting the header class for the graph step */
-            graphStep.headerClass = {
-                "node-header-invocation": true,
-                [`header-${graphStep.state}`]: !!graphStep.state,
-            };
-            // TODO: maybe a different one for inputs? Currently they have no state either.
-
-            /** Setting the header icon for the graph step */
-            if (graphStep.state) {
-                graphStep.headerIcon = iconClasses[graphStep.state]?.icon;
-                graphStep.headerIconSpin = iconClasses[graphStep.state]?.spin;
-            }
+            setHeaderClass(graphStep);
         }
     }
 
@@ -282,6 +293,9 @@ export function useInvocationGraph(
     function getStepStateFromJobStates(jobStates: string[]): GraphStep["state"] | undefined {
         for (const state of SINGLE_INSTANCE_STATES) {
             if (jobStates.includes(state)) {
+                if (state === "deleting") {
+                    return "deleted";
+                }
                 return state as GraphStep["state"];
             }
         }
@@ -293,19 +307,47 @@ export function useInvocationGraph(
         return undefined;
     }
 
-    // TODO: Maybe we can use this to layout the graph after the steps are loaded (for neatness)?
-    // async function layoutGraph() {
-    //     const newSteps = await autoLayout(storeId.value, steps.value);
-    //     if (newSteps) {
-    //         newSteps?.map((step: any) => stepStore.updateStep(step));
-    //         // Object.assign(steps.value, {...steps.value, ...stepStore.steps});
-    //         Object.keys(steps.value).forEach((key) => {
-    //             steps.value[key] = { ...steps.value[key], ...(stepStore.steps[key] as GraphStep) };
-    //         });
-    //     }
-    //     invocationGraph.value!.steps = steps.value;
-    //     await fromSimple(storeId.value, invocationGraph.value as any);
-    // }
+    function setHeaderClass(graphStep: GraphStep) {
+        /** Setting the header class for the graph step */
+        graphStep.headerClass = getHeaderClass(graphStep.state as string);
+
+        /** Setting the header icon for the graph step */
+        if (graphStep.state) {
+            graphStep.headerIcon = iconClasses[graphStep.state]?.icon;
+            graphStep.headerIconSpin = iconClasses[graphStep.state]?.spin;
+        }
+    }
+
+    async function initializeGraphInput(graphStep: GraphStep, invocationStep: InvocationStep) {
+        const inputItem = invocation.value.inputs[graphStep.id];
+        const inputParam = getWorkflowInputParam(invocation.value, invocationStep);
+        if (inputItem && inputItem?.id !== undefined && inputItem?.id !== null) {
+            if (inputItem.src === "hda") {
+                const hda = await fetchDatasetDetails({ id: inputItem.id });
+                // TODO: There is a type mismatch for `hda.state` and `GraphStep["state"]`
+                set(graphStep, "state", getContentItemState(hda));
+                set(graphStep, "nodeText", `${hda.hid}: <b>${hda.name}</b>`);
+            } else {
+                const hdca = await fetchCollectionDetails({ id: inputItem.id });
+                // TODO: Same type mismatch as above
+                set(graphStep, "state", getContentItemState(hdca));
+                set(graphStep, "nodeText", `${hdca.hid}: <b>${hdca.name}</b>`);
+            }
+        } else if (inputParam) {
+            if (typeof inputParam.parameter_value === "boolean") {
+                set(graphStep, "nodeText", inputParam.parameter_value);
+            } else {
+                set(graphStep, "nodeText", `<b>${inputParam.parameter_value}</b>`);
+            }
+        }
+        setHeaderClass(graphStep);
+    }
+
+    function getWorkflowInputParam(invocation: WorkflowInvocationElementView, invocationStep: InvocationStep) {
+        return Object.values(invocation.input_step_parameters).find(
+            (param) => param.workflow_step_id === invocationStep.workflow_step_id
+        );
+    }
 
     return {
         /** An id used to scope the store to the invocation's id */
@@ -318,3 +360,10 @@ export function useInvocationGraph(
         loadInvocationGraph,
     };
 }
+
+export function getHeaderClass(state: string) {
+    return {
+        "node-header-invocation": true,
+        [`header-${state}`]: !!state,
+    };
+}
diff --git a/client/src/composables/useWorkflowInstance.ts b/client/src/composables/useWorkflowInstance.ts
index 426c9269bfbce2f14b9f21836f9d6e605fd122cc..53bb6d287dee97d3634e4e1b63d733c22f2a42c4 100644
--- a/client/src/composables/useWorkflowInstance.ts
+++ b/client/src/composables/useWorkflowInstance.ts
@@ -1,11 +1,13 @@
 import { computed, ref } from "vue";
 
 import { useWorkflowStore } from "@/stores/workflowStore";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 export function useWorkflowInstance(workflowId: string) {
     const workflowStore = useWorkflowStore();
     const workflow = computed(() => workflowStore.getStoredWorkflowByInstanceId(workflowId));
     const loading = ref(false);
+    const error = ref<string | null>(null);
 
     async function getWorkflowInstance() {
         if (!workflow.value) {
@@ -13,7 +15,7 @@ export function useWorkflowInstance(workflowId: string) {
             try {
                 await workflowStore.fetchWorkflowForInstanceId(workflowId);
             } catch (e) {
-                console.error("unable to fetch workflow \n", e);
+                error.value = errorMessageAsString(e);
             } finally {
                 loading.value = false;
             }
@@ -21,5 +23,5 @@ export function useWorkflowInstance(workflowId: string) {
     }
     getWorkflowInstance();
 
-    return { workflow, loading };
+    return { workflow, loading, error };
 }
diff --git a/client/src/composables/userLocalStorage.ts b/client/src/composables/userLocalStorage.ts
index 75375eb9d2145091ded87a2f45fad5e96add5a27..d81dfda55e0919188e53642609640b64555c8280 100644
--- a/client/src/composables/userLocalStorage.ts
+++ b/client/src/composables/userLocalStorage.ts
@@ -1,36 +1,31 @@
-import { useLocalStorage } from "@vueuse/core";
-import { computed, customRef, type Ref, ref } from "vue";
+import { watchImmediate } from "@vueuse/core";
+import { type Ref, ref } from "vue";
 
-import type { GenericUser } from "@/api";
+import { type AnyUser } from "@/api";
 
 import { useHashedUserId } from "./hashedUserId";
+import { syncRefToLocalStorage } from "./persistentRef";
 
 /**
  * Local storage composable specific to current user.
  * @param key
  * @param initialValue
  */
-export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<GenericUser | null>) {
+export function useUserLocalStorage<T>(key: string, initialValue: T, user?: Ref<AnyUser>) {
     const { hashedUserId } = useHashedUserId(user);
 
-    const storedRef = computed(() => {
-        if (hashedUserId.value) {
-            return useLocalStorage(`${key}-${hashedUserId.value}`, initialValue);
-        } else {
-            return ref(initialValue);
-        }
-    });
+    const refToSync = ref(initialValue);
+    let hasSynced = false;
 
-    const currentValue = customRef((track, trigger) => ({
-        get() {
-            track();
-            return storedRef.value.value;
-        },
-        set(newValue) {
-            storedRef.value.value = newValue;
-            trigger();
-        },
-    }));
+    watchImmediate(
+        () => hashedUserId.value,
+        () => {
+            if (hashedUserId.value && !hasSynced) {
+                syncRefToLocalStorage(`${key}-${hashedUserId.value}`, refToSync);
+                hasSynced = true;
+            }
+        }
+    );
 
-    return currentValue;
+    return refToSync;
 }
diff --git a/client/src/composables/workflowStores.ts b/client/src/composables/workflowStores.ts
index 79338bacfffb45901a00cb1a8ead9900f40ea37c..1d68e51625445b449347fb624119e6224f72eba6 100644
--- a/client/src/composables/workflowStores.ts
+++ b/client/src/composables/workflowStores.ts
@@ -7,6 +7,8 @@ import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import { useWorkflowEditorToolbarStore } from "@/stores/workflowEditorToolbarStore";
 import { useWorkflowStepStore } from "@/stores/workflowStepStore";
 
+import { useTimeoutStoreDispose } from "./timeoutStoreDispose";
+
 /**
  * Creates stores scoped to a specific workflowId, and manages their lifetime.
  * In child components, use `useWorkflowStores` instead.
@@ -30,13 +32,20 @@ export function provideScopedWorkflowStores(workflowId: Ref<string> | string) {
     const toolbarStore = useWorkflowEditorToolbarStore(workflowId.value);
     const undoRedoStore = useUndoRedoStore(workflowId.value);
 
+    const disposeConnectionStore = useTimeoutStoreDispose(connectionStore);
+    const disposeStateStore = useTimeoutStoreDispose(stateStore);
+    const disposeStepStore = useTimeoutStoreDispose(stepStore);
+    const disposeCommentStore = useTimeoutStoreDispose(commentStore);
+    const disposeToolbarStore = useTimeoutStoreDispose(toolbarStore);
+    const disposeUndoRedoStore = useTimeoutStoreDispose(undoRedoStore);
+
     onScopeDispose(() => {
-        connectionStore.$dispose();
-        stateStore.$dispose();
-        stepStore.$dispose();
-        commentStore.$dispose();
-        toolbarStore.$dispose();
-        undoRedoStore.$dispose();
+        disposeConnectionStore();
+        disposeStateStore();
+        disposeStepStore();
+        disposeCommentStore();
+        disposeToolbarStore();
+        disposeUndoRedoStore();
     });
 
     return {
@@ -76,6 +85,7 @@ export function useWorkflowStores(workflowId?: Ref<string> | string) {
     const undoRedoStore = useUndoRedoStore(id);
 
     return {
+        workflowId: id,
         connectionStore,
         stateStore,
         stepStore,
diff --git a/client/src/entry/analysis/App.vue b/client/src/entry/analysis/App.vue
index 658ff0e7eea81bc61391edd8e0cd5d8ba8da779c..00ba34659a8feda57ef1cf1ead0ddfea29b6fd32 100644
--- a/client/src/entry/analysis/App.vue
+++ b/client/src/entry/analysis/App.vue
@@ -10,9 +10,7 @@
                     :logo-url="config.logo_url"
                     :logo-src="theme?.['--masthead-logo-img'] ?? config.logo_src"
                     :logo-src-secondary="theme?.['--masthead-logo-img-secondary'] ?? config.logo_src_secondary"
-                    :tabs="tabs"
-                    :window-tab="windowTab"
-                    @open-url="openUrl" />
+                    :window-tab="windowTab" />
                 <Alert
                     v-if="config.message_box_visible && config.message_box_content"
                     id="messagebox"
@@ -55,17 +53,16 @@ import Toast from "components/Toast";
 import { setConfirmDialogComponentRef } from "composables/confirmDialog";
 import { setGlobalUploadModal } from "composables/globalUploadModal";
 import { setToastComponentRef } from "composables/toast";
-import { fetchMenu } from "entry/analysis/menu";
 import { WindowManager } from "layout/window-manager";
 import Modal from "mvc/ui/ui-modal";
 import { getAppRoot } from "onload";
 import { storeToRefs } from "pinia";
-import { withPrefix } from "utils/redirect";
 import { ref, watch } from "vue";
 import { useRoute } from "vue-router/composables";
 
 import short from "@/components/plugins/short";
 import { useRouteQueryBool } from "@/composables/route";
+import { useEntryPointStore } from "@/stores/entryPointStore";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useNotificationsStore } from "@/stores/notificationsStore";
 import { useUserStore } from "@/stores/userStore";
@@ -148,9 +145,6 @@ export default {
         };
     },
     computed: {
-        tabs() {
-            return fetchMenu(this.config);
-        },
         showMasthead() {
             const masthead = this.$route.query.hide_masthead;
             if (masthead !== undefined) {
@@ -192,6 +186,9 @@ export default {
             this.Galaxy.currHistoryPanel = new HistoryPanelProxy();
             this.Galaxy.modal = new Modal.View();
             this.Galaxy.frame = this.windowManager;
+            if (this.Galaxy.config.interactivetools_enable) {
+                this.startWatchingEntryPoints();
+            }
             if (this.Galaxy.config.enable_notification_system) {
                 this.startWatchingNotifications();
             }
@@ -209,22 +206,14 @@ export default {
         }
     },
     methods: {
+        startWatchingEntryPoints() {
+            const entryPointStore = useEntryPointStore();
+            entryPointStore.startWatchingEntryPoints();
+        },
         startWatchingNotifications() {
             const notificationsStore = useNotificationsStore();
             notificationsStore.startWatchingNotifications();
         },
-        openUrl(urlObj) {
-            if (!urlObj.target) {
-                this.$router.push(urlObj.url);
-            } else {
-                const url = withPrefix(urlObj.url);
-                if (urlObj.target == "_blank") {
-                    window.open(url);
-                } else {
-                    window.location = url;
-                }
-            }
-        },
     },
 };
 </script>
diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js
deleted file mode 100644
index 5c33d34b2dd6043b7c3c9a5b6eff41c68f465075..0000000000000000000000000000000000000000
--- a/client/src/entry/analysis/menu.js
+++ /dev/null
@@ -1,255 +0,0 @@
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
-import { userLogout } from "utils/logout";
-
-import { useUserStore } from "@/stores/userStore";
-
-export function fetchMenu(options = {}) {
-    const Galaxy = getGalaxyInstance();
-    const menu = [];
-    //
-    // Analyze data tab.
-    //
-    menu.push({
-        id: "analysis",
-        url: "/",
-        tooltip: _l("Tools and Current History"),
-        icon: "fa-home",
-        target: "_top",
-    });
-
-    //
-    // Workflow tab.
-    //
-    menu.push({
-        id: "workflow",
-        title: _l("Workflow"),
-        tooltip: _l("Chain tools into workflows"),
-        disabled: !Galaxy.user.id,
-        url: "/workflows/list",
-    });
-
-    //
-    // Visualization tab.
-    //
-    if (Galaxy.config.visualizations_visible) {
-        menu.push({
-            id: "visualization",
-            title: _l("Visualize"),
-            tooltip: _l("Visualize datasets"),
-            disabled: !Galaxy.user.id,
-            url: "/visualizations",
-        });
-    }
-
-    //
-    // 'Data' tab.
-    //
-    if (Galaxy.user.id) {
-        menu.push({
-            id: "resources",
-            title: _l("Data"),
-            url: "javascript:void(0)",
-            tooltip: _l("Access resources"),
-            menu: [
-                {
-                    title: _l("Data Libraries"),
-                    url: "/libraries",
-                },
-                {
-                    title: _l("Datasets"),
-                    url: "/datasets/list",
-                },
-                {
-                    title: _l("Histories"),
-                    url: "/histories/list",
-                },
-                {
-                    title: _l("Pages"),
-                    url: "/pages/list",
-                },
-                {
-                    title: _l("Visualizations"),
-                    url: "/visualizations/list",
-                },
-                {
-                    title: _l("Workflows"),
-                    url: "/workflows/list",
-                },
-                {
-                    title: _l("Workflow Invocations"),
-                    url: "/workflows/invocations",
-                },
-            ],
-        });
-    } else {
-        menu.push({
-            id: "resources",
-            title: _l("Data"),
-            url: "javascript:void(0)",
-            tooltip: _l("Access published resources"),
-            menu: [
-                {
-                    title: _l("Data Libraries"),
-                    url: "/libraries",
-                },
-                {
-                    title: _l("Histories"),
-                    url: "/histories/list_published",
-                },
-                {
-                    title: _l("Pages"),
-                    url: "/pages/list_published",
-                },
-                {
-                    title: _l("Visualizations"),
-                    url: "/visualizations/list_published",
-                },
-                {
-                    title: _l("Workflows"),
-                    url: "/workflows/list_published",
-                },
-            ],
-        });
-    }
-
-    //
-    // Admin.
-    //
-    if (Galaxy.user.get("is_admin")) {
-        menu.push({
-            id: "admin",
-            title: _l("Admin"),
-            url: "/admin",
-            tooltip: _l("Administer this Galaxy"),
-            cls: "admin-only",
-            onclick: () => {
-                const userStore = useUserStore();
-                userStore.toggleSideBar("admin");
-            },
-        });
-    }
-
-    //
-    // Help tab.
-    //
-    const helpTab = {
-        id: "help",
-        title: _l("Help"),
-        url: "javascript:void(0)",
-        tooltip: _l("Support, contact, and community"),
-        menu: [
-            {
-                title: _l("Galaxy Help"),
-                url: options.helpsite_url,
-                target: "_blank",
-                hidden: !options.helpsite_url,
-            },
-            {
-                title: _l("Support"),
-                url: options.support_url,
-                target: "_blank",
-                hidden: !options.support_url,
-            },
-            {
-                title: _l("Videos"),
-                url: options.screencasts_url,
-                target: "_blank",
-                hidden: !options.screencasts_url,
-            },
-            {
-                title: _l("Community Hub"),
-                url: options.wiki_url,
-                target: "_blank",
-                hidden: !options.wiki_url,
-            },
-            {
-                title: _l("How to Cite Galaxy"),
-                url: options.citation_url,
-                target: "_blank",
-            },
-            {
-                title: _l("Interactive Tours"),
-                url: "/tours",
-            },
-            {
-                title: _l("About"),
-                url: "/about",
-            },
-            {
-                title: _l("Terms and Conditions"),
-                url: options.terms_url,
-                target: "_blank",
-                hidden: !options.terms_url,
-            },
-        ],
-    };
-    menu.push(helpTab);
-
-    //
-    // User tab.
-    //
-    let userTab = {};
-    if (!Galaxy.user.id) {
-        if (options.allow_user_creation) {
-            userTab = {
-                id: "user",
-                title: _l("Log in or Register"),
-                cls: "loggedout-only",
-                url: "/login",
-                tooltip: _l("Log in or register a new account"),
-                target: "_top",
-            };
-        } else {
-            userTab = {
-                id: "user",
-                title: _l("Login"),
-                cls: "loggedout-only",
-                tooltip: _l("Login"),
-                url: "/login",
-                target: "_top",
-            };
-        }
-    } else {
-        userTab = {
-            id: "user",
-            title: _l("User"),
-            cls: "loggedin-only",
-            url: "javascript:void(0)",
-            tooltip: _l("Account and saved data"),
-            menu: [
-                {
-                    title: `${_l("Signed in as")} ${
-                        Galaxy.user.get("username") ? Galaxy.user.get("username") : Galaxy.user.get("email")
-                    }`,
-                    disabled: true,
-                },
-                { divider: true },
-            ],
-        };
-        if (Galaxy.config.interactivetools_enable) {
-            userTab.menu.push({
-                title: _l("Active Interactive Tools"),
-                url: "/interactivetool_entry_points/list",
-            });
-        }
-        if (Galaxy.config.enable_notification_system) {
-            userTab.menu.push({
-                title: _l("Notifications"),
-                url: "/user/notifications",
-            });
-        }
-        userTab.menu.push({ divider: true });
-        userTab.menu.push({
-            title: _l("Preferences"),
-            url: "/user",
-        });
-        userTab.menu.push({
-            title: _l("Sign Out"),
-            onclick: userLogout,
-            hidden: Galaxy.config.single_user || Galaxy.config.hide_sign_out,
-        });
-    }
-    menu.push(userTab);
-    return menu;
-}
diff --git a/client/src/entry/analysis/modules/CenterFrame.vue b/client/src/entry/analysis/modules/CenterFrame.vue
index 20e6a0cb080b47ffa824c284d5ba9ca995d11af3..7159891d88322de1d80d4070363957e41a00c2a7 100644
--- a/client/src/entry/analysis/modules/CenterFrame.vue
+++ b/client/src/entry/analysis/modules/CenterFrame.vue
@@ -1,46 +1,99 @@
-<template>
-    <iframe
-        :id="id"
-        :name="id"
-        :src="srcWithRoot"
-        class="center-frame"
-        frameborder="0"
-        title="galaxy frame"
-        width="100%"
-        height="100%"
-        @load="onLoad" />
-</template>
-<script>
-import { withPrefix } from "utils/redirect";
+<script setup lang="ts">
+import { storeToRefs } from "pinia";
+import { computed, ref, watch } from "vue";
 
-export default {
-    props: {
-        id: {
-            type: String,
-            default: "frame",
-        },
-        src: {
-            type: String,
-            default: "",
-        },
-    },
-    computed: {
-        srcWithRoot() {
-            return withPrefix(this.src);
-        },
-    },
-    methods: {
-        onLoad(ev) {
-            const iframe = ev.currentTarget;
-            const location = iframe.contentWindow && iframe.contentWindow.location;
+import { useUserStore } from "@/stores/userStore";
+import { withPrefix } from "@/utils/redirect";
+
+import Alert from "@/components/Alert.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+const emit = defineEmits(["load"]);
+const props = withDefaults(
+    defineProps<{
+        id?: string;
+        src?: string;
+        isPreview?: boolean;
+    }>(),
+    {
+        id: "frame",
+        src: "",
+        isPreview: false,
+    }
+);
+
+const { isAdmin } = storeToRefs(useUserStore());
+const srcWithRoot = computed(() => withPrefix(props.src));
+const sanitizedImport = ref(false);
+const sanitizedToolId = ref<String | false>(false);
+const isLoading = ref(true);
+watch(
+    () => srcWithRoot.value,
+    async () => {
+        sanitizedImport.value = false;
+        sanitizedToolId.value = false;
+        if (props.isPreview) {
             try {
-                if (location && location.host && location.pathname != "/") {
-                    this.$emit("load");
+                const response = await fetch(srcWithRoot.value, { method: "HEAD" });
+                const isImported = response.headers.get("x-sanitized-job-imported");
+                const toolId = response.headers.get("x-sanitized-tool-id");
+                if (isImported !== null) {
+                    sanitizedImport.value = true;
+                } else if (toolId !== null) {
+                    sanitizedToolId.value = toolId;
                 }
-            } catch (err) {
-                console.warn("CenterFrame - onLoad location access forbidden.", ev, location);
+            } catch (e) {
+                // I guess that's fine and the center panel will show something
+                console.error(e);
             }
-        },
+        }
     },
-};
+    { immediate: true }
+);
+
+const plainText = "Contents are shown as plain text.";
+const sanitizedMessage = computed(() => {
+    if (sanitizedImport.value) {
+        return `Dataset has been imported. ${plainText}`;
+    } else if (sanitizedToolId.value) {
+        return `Dataset created by a tool that is not known to create safe HTML. ${plainText}`;
+    }
+    return undefined;
+});
+
+function onLoad(ev: Event) {
+    isLoading.value = false;
+    const iframe = ev.currentTarget as HTMLIFrameElement;
+    const location = iframe?.contentWindow && iframe.contentWindow.location;
+    try {
+        if (location && location.host && location.pathname != "/") {
+            emit("load");
+        }
+    } catch (err) {
+        console.warn("CenterFrame - onLoad location access forbidden.", ev, location);
+    }
+}
 </script>
+<template>
+    <div class="h-100">
+        <Alert v-if="sanitizedMessage" :dismissible="true" variant="warning" data-description="sanitization warning">
+            {{ sanitizedMessage }}
+            <span v-if="isAdmin && sanitizedToolId">
+                <br />
+                <router-link data-description="allowlist link" to="/admin/sanitize_allow">Review Allowlist</router-link>
+                if outputs of {{ sanitizedToolId }} are trusted and should be shown as HTML.
+            </span>
+        </Alert>
+        <LoadingSpan v-if="isLoading">Loading ...</LoadingSpan>
+        <iframe
+            :id="id"
+            :name="id"
+            :src="srcWithRoot"
+            class="center-frame"
+            frameborder="0"
+            title="galaxy frame"
+            width="100%"
+            height="100%"
+            @load="onLoad" />
+    </div>
+</template>
diff --git a/client/src/entry/analysis/modules/WorkflowEditor.vue b/client/src/entry/analysis/modules/WorkflowEditor.vue
index fb8ed6eea9d57f2d8e387da60fda758b5e1b6e07..b05627cfbdb1071e700b1f0f308af24e8ae73e0b 100644
--- a/client/src/entry/analysis/modules/WorkflowEditor.vue
+++ b/client/src/entry/analysis/modules/WorkflowEditor.vue
@@ -7,8 +7,8 @@
         :initial-version="editorConfig.initialVersion"
         :module-sections="editorConfig.moduleSections"
         :workflow-tags="editorConfig.tags"
-        :workflows="editorConfig.workflows"
-        @update:confirmation="$emit('update:confirmation', $event)" />
+        @update:confirmation="$emit('update:confirmation', $event)"
+        @skipNextReload="() => (skipNextReload = true)" />
 </template>
 <script>
 import Editor from "components/Workflow/Editor/Index";
@@ -26,6 +26,7 @@ export default {
             version: null,
             editorConfig: null,
             editorReloadKey: 0,
+            skipNextReload: false,
         };
     },
     watch: {
@@ -40,14 +41,15 @@ export default {
         async getEditorConfig() {
             let reloadEditor = true;
 
-            // this will only be the case the first time the route updates from a new workflow
-            if (!this.storedWorkflowId && !this.workflowId) {
+            if (this.skipNextReload) {
                 reloadEditor = false;
+                this.skipNextReload = false;
             }
 
             this.storedWorkflowId = Query.get("id");
             this.workflowId = Query.get("workflow_id");
             this.version = Query.get("version");
+            this.previousHistoryLength = window.history.length;
 
             const params = {};
 
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 71b66c66ed9aa83116f8179e34910844e08a7060..34139e07accae0ebcf77f3b3e96a014096c44a5a 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -7,6 +7,8 @@ import DatasetAttributes from "components/DatasetInformation/DatasetAttributes";
 import DatasetDetails from "components/DatasetInformation/DatasetDetails";
 import DatasetError from "components/DatasetInformation/DatasetError";
 import FormGeneric from "components/Form/FormGeneric";
+import GalaxyWizard from "components/GalaxyWizard";
+import HelpTerm from "components/Help/HelpTerm";
 import HistoryExportTasks from "components/History/Export/HistoryExport";
 import HistoryPublished from "components/History/HistoryPublished";
 import HistoryView from "components/History/HistoryView";
@@ -16,6 +18,8 @@ import HistoryImport from "components/HistoryImport";
 import InteractiveTools from "components/InteractiveTools/InteractiveTools";
 import JobDetails from "components/JobInformation/JobDetails";
 import CarbonEmissionsCalculations from "components/JobMetrics/CarbonEmissions/CarbonEmissionsCalculations";
+import ToolLanding from "components/Landing/ToolLanding";
+import WorkflowLanding from "components/Landing/WorkflowLanding";
 import PageDisplay from "components/PageDisplay/PageDisplay";
 import PageEditor from "components/PageEditor/PageEditor";
 import ToolSuccess from "components/Tool/ToolSuccess";
@@ -24,10 +28,9 @@ import ToolsJson from "components/ToolsView/ToolsSchemaJson/ToolsJson";
 import TourList from "components/Tour/TourList";
 import TourRunner from "components/Tour/TourRunner";
 import { APIKey } from "components/User/APIKey";
-import { CloudAuth } from "components/User/CloudAuth";
 import CustomBuilds from "components/User/CustomBuilds";
 import { ExternalIdentities } from "components/User/ExternalIdentities";
-import { NotificationsPreferences } from "components/User/Notifications";
+import NotificationsPreferences from "components/User/Notifications/NotificationsPreferences";
 import UserPreferences from "components/User/UserPreferences";
 import UserPreferencesForm from "components/User/UserPreferencesForm";
 import VisualizationsList from "components/Visualizations/Index";
@@ -37,11 +40,11 @@ import HistoryInvocations from "components/Workflow/HistoryInvocations";
 import TrsImport from "components/Workflow/Import/TrsImport";
 import TrsSearch from "components/Workflow/Import/TrsSearch";
 import InvocationReport from "components/Workflow/InvocationReport";
+import WorkflowList from "components/Workflow/List/WorkflowList";
 import StoredWorkflowInvocations from "components/Workflow/StoredWorkflowInvocations";
 import WorkflowCreate from "components/Workflow/WorkflowCreate";
 import WorkflowExport from "components/Workflow/WorkflowExport";
 import WorkflowImport from "components/Workflow/WorkflowImport";
-import WorkflowList from "components/Workflow/WorkflowList";
 import Analysis from "entry/analysis/modules/Analysis";
 import CenterFrame from "entry/analysis/modules/CenterFrame";
 import Home from "entry/analysis/modules/Home";
@@ -59,6 +62,7 @@ import CreateFileSourceInstance from "@/components/FileSources/Instances/CreateI
 import GridHistory from "@/components/Grid/GridHistory";
 import GridPage from "@/components/Grid/GridPage";
 import CreateObjectStoreInstance from "@/components/ObjectStore/Instances/CreateInstance";
+import { requireAuth } from "@/router/guards";
 import { parseBool } from "@/utils/utils";
 
 import { patchRouterPush } from "./router-push";
@@ -89,10 +93,14 @@ Vue.use(VueRouter);
 patchRouterPush(VueRouter);
 
 // redirect anon users
-function redirectAnon() {
+function redirectAnon(redirect = "") {
     const Galaxy = getGalaxyInstance();
     if (!Galaxy.user || !Galaxy.user.id) {
-        return "/login/start";
+        if (redirect !== "") {
+            return redirect;
+        } else {
+            return "/login/start";
+        }
     }
 }
 
@@ -192,6 +200,11 @@ export function getRouter(Galaxy) {
                         path: "about",
                         component: AboutGalaxy,
                     },
+                    {
+                        path: "help/terms/:term",
+                        component: HelpTerm,
+                        props: true,
+                    },
                     {
                         path: "carbon_emissions_calculations",
                         component: CarbonEmissionsCalculations,
@@ -226,6 +239,7 @@ export function getRouter(Galaxy) {
                         component: CenterFrame,
                         props: (route) => ({
                             src: `/datasets/${route.params.datasetId}/display/?preview=True`,
+                            isPreview: true,
                         }),
                     },
                     {
@@ -314,7 +328,7 @@ export function getRouter(Galaxy) {
                         props: {
                             activeList: "my",
                         },
-                        redirect: redirectAnon(),
+                        redirect: redirectAnon("/histories/list_published"),
                     },
                     {
                         path: "histories/list_shared",
@@ -384,6 +398,11 @@ export function getRouter(Galaxy) {
                     {
                         path: "file_source_instances/create",
                         component: CreateUserFileSource,
+                        props: (route) => {
+                            return {
+                                error: route.params.error,
+                            };
+                        },
                     },
                     {
                         path: "file_source_instances/index",
@@ -405,7 +424,10 @@ export function getRouter(Galaxy) {
                     {
                         path: "file_source_templates/:templateId/new",
                         component: CreateFileSourceInstance,
-                        props: true,
+                        props: (route) => ({
+                            templateId: route.params.templateId,
+                            uuid: route.query.uuid,
+                        }),
                     },
                     {
                         path: "pages/create",
@@ -447,7 +469,7 @@ export function getRouter(Galaxy) {
                         props: {
                             activeList: "my",
                         },
-                        redirect: redirectAnon(),
+                        redirect: redirectAnon("/pages/list_published"),
                     },
                     {
                         path: "pages/list_published",
@@ -467,6 +489,10 @@ export function getRouter(Galaxy) {
                         path: "tours",
                         component: TourList,
                     },
+                    {
+                        path: "wizard",
+                        component: GalaxyWizard,
+                    },
                     {
                         path: "tours/:tourId",
                         component: TourRunner,
@@ -485,6 +511,21 @@ export function getRouter(Galaxy) {
                         path: "tools/json",
                         component: ToolsJson,
                     },
+                    {
+                        path: "tool_landings/:uuid",
+                        component: ToolLanding,
+                        props: true,
+                    },
+                    {
+                        path: "workflow_landings/:uuid",
+                        component: WorkflowLanding,
+                        props: (route) => ({
+                            uuid: route.params.uuid,
+                            public: route.query.public.toLowerCase() === "true",
+                            secret: route.query.client_secret,
+                        }),
+                        beforeEnter: requireAuth,
+                    },
                     {
                         path: "user",
                         component: UserPreferences,
@@ -499,11 +540,6 @@ export function getRouter(Galaxy) {
                         component: APIKey,
                         redirect: redirectAnon(),
                     },
-                    {
-                        path: "user/cloud_auth",
-                        component: CloudAuth,
-                        redirect: redirectAnon(),
-                    },
                     {
                         path: "user/external_ids",
                         component: ExternalIdentities,
@@ -628,13 +664,12 @@ export function getRouter(Galaxy) {
                         props: (route) => ({
                             invocationId: route.params.invocationId,
                             isFullPage: true,
-                            fromPanel: Boolean(route.query.from_panel),
                         }),
                     },
                     {
                         path: "workflows/list",
                         component: WorkflowList,
-                        redirect: redirectAnon(),
+                        redirect: redirectAnon("/workflows/list_published"),
                     },
                     {
                         path: "workflows/list_published",
diff --git a/client/src/mvc/dataset/states.ts b/client/src/mvc/dataset/states.ts
index dd5b37d7fb07e2ce463963c6c7efe47cbd0f033b..262b1e99fe6eb4fb0c212359a6e5f5937a11b652 100644
--- a/client/src/mvc/dataset/states.ts
+++ b/client/src/mvc/dataset/states.ts
@@ -2,7 +2,7 @@
 /** Map of possible HDA/collection/job states to their string equivalents.
  *      A port of galaxy.model.Dataset.states.
  */
-const STATES = {
+const RAW_STATES = {
     // NOT ready states
     /** is uploading and not ready */
     UPLOAD: "upload",
@@ -34,23 +34,31 @@ const STATES = {
     DEFERRED: "deferred",
     /** the tool producing this dataset failed */
     ERROR: "error",
-
-    READY_STATES: [] as string[],
-    NOT_READY_STATES: [] as string[],
 };
 
-STATES.READY_STATES = [
-    STATES.OK,
-    STATES.EMPTY,
-    STATES.PAUSED,
-    STATES.FAILED_METADATA,
-    STATES.NOT_VIEWABLE,
-    STATES.DEFERRED,
-    STATES.DISCARDED,
-    STATES.ERROR,
-];
-
-STATES.NOT_READY_STATES = [STATES.UPLOAD, STATES.QUEUED, STATES.RUNNING, STATES.SETTING_METADATA, STATES.NEW];
+const STATES = {
+    ...RAW_STATES,
+    READY_STATES: [
+        RAW_STATES.OK,
+        RAW_STATES.EMPTY,
+        RAW_STATES.PAUSED,
+        RAW_STATES.FAILED_METADATA,
+        RAW_STATES.NOT_VIEWABLE,
+        RAW_STATES.DEFERRED,
+        RAW_STATES.DISCARDED,
+        RAW_STATES.ERROR,
+    ],
+    NOT_READY_STATES: [
+        RAW_STATES.UPLOAD,
+        RAW_STATES.QUEUED,
+        RAW_STATES.RUNNING,
+        RAW_STATES.SETTING_METADATA,
+        RAW_STATES.NEW,
+    ],
+    VALID_INPUT_STATES: Object.values(RAW_STATES).filter(
+        (state) => ![RAW_STATES.ERROR, RAW_STATES.DISCARDED, RAW_STATES.FAILED_METADATA].includes(state)
+    ),
+};
 
 //==============================================================================
 export default STATES;
diff --git a/client/src/mvc/visualization/chart/components/model.js b/client/src/mvc/visualization/chart/components/model.js
index 458663122b1f89847df121cde01ba4b4db8efabb..814bbafe638610c8493dcc24a89cea629610e775 100644
--- a/client/src/mvc/visualization/chart/components/model.js
+++ b/client/src/mvc/visualization/chart/components/model.js
@@ -2,7 +2,7 @@ import Backbone from "backbone";
 import { Visualization } from "mvc/visualization/visualization-model";
 import Utils from "utils/utils";
 
-const MATCH_GROUP = /^groups_([0-9]+)\|([\w]+)/;
+const MATCH_GROUP = /^(groups|tracks)_([0-9]+)\|([\w]+)/;
 
 export default Backbone.Model.extend({
     defaults: {
diff --git a/client/src/mvc/visualization/chart/views/editor.js b/client/src/mvc/visualization/chart/views/editor.js
index 3c9c21bb3f3240ab7831218c2fc3c847767a63f0..3b0a3f026285496dc239aaa240b79cf041be0948 100644
--- a/client/src/mvc/visualization/chart/views/editor.js
+++ b/client/src/mvc/visualization/chart/views/editor.js
@@ -36,7 +36,7 @@ export default Backbone.View.extend({
                 )
                 .append(new Settings(this.app).$el),
         });
-        if (this.chart.plugin.groups) {
+        if (this.chart.plugin.tracks) {
             this.tabs.add({
                 id: "groups",
                 icon: "fa-database",
diff --git a/client/src/mvc/visualization/chart/views/groups.js b/client/src/mvc/visualization/chart/views/groups.js
index fa3f68f4f8be6e29ad78ddd913a76a1e793b3973..b262c9968fbebaaa44ffdec0b6c74ec56faf5d01 100644
--- a/client/src/mvc/visualization/chart/views/groups.js
+++ b/client/src/mvc/visualization/chart/views/groups.js
@@ -25,7 +25,7 @@ var GroupView = Backbone.View.extend({
     },
     render: function () {
         var self = this;
-        var inputs = Utils.clone(this.chart.plugin.groups) || [];
+        var inputs = Utils.clone(this.chart.plugin.tracks) || [];
         var dataset_id = this.chart.get("dataset_id");
         if (dataset_id) {
             this.chart.state("wait", "Loading metadata...");
@@ -127,7 +127,7 @@ export default Backbone.View.extend({
         });
     },
     render: function () {
-        if (_.size(this.chart.plugin.groups) > 0) {
+        if (_.size(this.chart.plugin.tracks) > 0) {
             this.repeat.$el.show();
         } else {
             this.repeat.$el.hide();
diff --git a/client/src/nls/es/locale.js b/client/src/nls/es/locale.js
index df68712e1d188e6e768d5b4a025662d6100f0cfa..fbfaf079c8918bc98f2f95b269deb12ee21a40f1 100644
--- a/client/src/nls/es/locale.js
+++ b/client/src/nls/es/locale.js
@@ -608,7 +608,7 @@ define({
         "Agregar o modificar la configuración que permite que Galaxy acceda a tus recursos en la nube",
 
     "Manage Toolbox Filters": "Manejar filtros de la caja de herramientas",
-    "Manage Custom Builds": "Administrar compilaciones personalizadas",
+    "Manage Custom Builds": "Administrar construcciones personalizadas",
 
     "Enable notifications": "Habilitar notificaciones",
     "Allow push and tab notifcations on job completion. To disable, revoke the site notification privilege in your browser.":
diff --git a/client/src/nls/ja/locale.js b/client/src/nls/ja/locale.js
index 02208bbf63f506f2068995ea6ba3297f0160e166..54205bf383aba5e2716a6f5c929515a0b04f5a9e 100644
--- a/client/src/nls/ja/locale.js
+++ b/client/src/nls/ja/locale.js
@@ -77,7 +77,7 @@ define({
     // ---- history-view
     "This history is empty": "ヒストリーは空です",
     "No matching datasets found": "一致するデータセットが見つかりませんでした",
-    //"An error occurred while getting updates from the server" :
+    "An error occurred while getting updates from the server": "サーバーから更新を取得中にエラーが起こりました",
     //false,
     //"Please contact a Galaxy administrator if the problem persists" :
     //false,
@@ -87,7 +87,8 @@ define({
     "Search datasets": "データセットを検索する",
     "You are currently viewing a deleted history!": "消去したヒストリーをみています。",
     "You are over your disk quota": "あなたはディスククォータを超えている",
-    //"Tool execution is on hold until your disk usage drops below your allocated quota" :
+    "Tool execution is on hold until your disk usage drops below your allocated quota":
+        "ディスク使用料があなたに割り当てられたクォータを下回るまでツールの実行は停止します",
     //false,
     All: "一式",
     None: "なし",
@@ -99,13 +100,13 @@ define({
     "Click to rename history": "ヒストリーの名前を変更するにはクリック",
     // multi operations
     "Operations on multiple datasets": "複数のデータセットに対する操作",
-    //"Hide datasets" :
+    "Hide datasets": "データセットを隠す",
     //false,
-    //"Unhide datasets" :
+    "Unhide datasets": "隠れたデータセットの回復",
     //false,
-    //"Delete datasets" :
+    "Delete datasets": "データセットの削除",
     //false,
-    //"Undelete datasets" :
+    "Undelete datasets": "削除されたデータセットの回復",
     //false,
     "Permanently delete datasets": "永久にデータセットを削除",
     "This will permanently remove the data in your datasets. Are you sure?":
@@ -113,7 +114,7 @@ define({
 
     // ---- history-view-annotated
     Dataset: "データセット",
-    //"Annotation" :
+    Annotation: "アノテーション",
     //false,
 
     // ---- history-view-edit-current
@@ -123,53 +124,56 @@ define({
     //TODO:
     //"You can <% loadYourOwn %> or <% externalSource %>" :
     //false,
-    //"load your own data" :
+    "load your own data": "自分のデータをロード",
     //false,
-    //"get data from an external source" :
+    "get data from an external source": "外部のソースからデータを取得",
     //false,
 
     // these aren't in zh/ginga.po and the template doesn't localize
-    //"Include Deleted Datasets" :
+    "Include Deleted Datasets": "削除されたデータセットを含める",
     //false,
-    //"Include Hidden Datasets" :
+    "Include Hidden Datasets": "隠れたデータセットを含める",
     //false,
 
     // ---------------------------------------------------------------------------- datasets
     // ---- hda-model
-    //"Unable to purge dataset" :
+    "Unable to purge dataset": "データセットを完全削除出来ません",
     //false,
 
     // ---- hda-base
     // display button
-    //"Cannot display datasets removed from disk" :
+    "Cannot display datasets removed from disk": "ディスクから消去されたデータは表示できません",
     //false,
-    //"This dataset must finish uploading before it can be viewed" :
+    "This dataset must finish uploading before it can be viewed":
+        "このデータセットは見る前にアップロードが完了する必要があります",
     //false,
-    //"This dataset is not yet viewable" :
+    "This dataset is not yet viewable": "このデータセットはまだ見ることができません",
     //false,
     "View data": "データを表示",
     // download button
     Download: "ダウンロード",
     "Download dataset": "データセットをダウンロード",
-    //"Additional files" :
+    "Additional files": "追加のファイル",
     //false,
     // info/show_params
     "View details": "細部を表示",
 
     // dataset states
     // state: new
-    //"This is a new dataset and not all of its data are available yet" :
+    "This is a new dataset and not all of its data are available yet":
+        "これは新しいデータセットですが、まだすべてのデータが利用可能にはなっていません",
     //false,
     // state: noPermission
-    //"You do not have permission to view this dataset" :
+    "You do not have permission to view this dataset": "このデータセットを見るための権限がありません",
     //false,
     // state: discarded
-    //"The job creating this dataset was cancelled before completion" :
+    "The job creating this dataset was cancelled before completion":
+        "このデータセットを作成するジョブは、完了する前にキャンセルされました",
     //false,
     // state: queued
     "This job is waiting to run": "ジョブは実行待ちです",
     // state: upload
-    //"This dataset is currently uploading" :
+    "This dataset is currently uploading": "このデータセットは現在アップロード中です",
     //false,
     // state: setting_metadata
     //"Metadata is being auto-detected" :
@@ -184,11 +188,12 @@ define({
     // state: empty
     "No data": "データ無し",
     // state: failed_metadata
-    //"An error occurred setting the metadata for this dataset" :
+    "An error occurred setting the metadata for this dataset":
+        "このデータセットのメタデータを設定する際にエラーがでました",
     //false,
 
     // ajax error prefix
-    //"There was an error getting the data for this dataset" :
+    "There was an error getting the data for this dataset": "このデータセットのデータを取得する際にエラーがでました",
     //false,
 
     // purged'd/del'd msg
@@ -201,17 +206,18 @@ define({
 
     // ---- hda-edit
     "Edit attributes": "変数を編集する",
-    //"Cannot edit attributes of datasets removed from disk" :
+    "Cannot edit attributes of datasets removed from disk": "ディスクから削除されたデータセットの属性は編集できない",
     //false,
     //"Undelete dataset to edit attributes" :
     //false,
-    //"This dataset must finish uploading before it can be edited" :
+    "This dataset must finish uploading before it can be edited":
+        "このデータセットは編集する前にアップロードが完了する必要がある",
     //false,
-    //"This dataset is not yet editable" :
+    "This dataset is not yet editable": "このデータセットは、まだ編集可能ではない",
     //false,
 
     Delete: "削除する",
-    //"Dataset is already deleted" :
+    "Dataset is already deleted": "データセットは、既に削除されている",
     //false,
 
     "View or report this error": "このエラーを届け出る",
@@ -233,9 +239,9 @@ define({
     //"set it manually or retry auto-detection" :
     //false,
 
-    //"Edit dataset tags" :
+    "Edit dataset tags": "データセットのタグを編集",
     //false,
-    //"Edit dataset annotation" :
+    "Edit dataset annotation": "データセットのアノテーションを編集",
     //false,
 
     // ---------------------------------------------------------------------------- admin
@@ -266,11 +272,11 @@ define({
     Data: "データ",
     "Form Definitions": "フォーム定義",
     // ---------------------------------------------------------------------------- misc. MVC
-    //"Tags" :
+    Tags: "タグ",
     //false,
-    //"Annotation" :
+    Annotation: "アノテーション",
     //false,
-    //"Edit annotation" :
+    "Edit annotation": "アノテーションを編集",
     //false,
     "Your workflows": "あなたのワークフロー",
 });
diff --git a/client/src/onload/console.js b/client/src/onload/console.js
index 3cc2afb908d9333c944596cce6a7271c4d9cc03a..de552ac937c02cc0608de7cd7d0c068480d67cf9 100644
--- a/client/src/onload/console.js
+++ b/client/src/onload/console.js
@@ -4,9 +4,10 @@
  * using the global functions
  * enableDebugging() and disableDebugging()
  */
-import { useLocalStorage } from "@vueuse/core";
 import { watch } from "vue";
 
+import { usePersistentRef } from "@/composables/persistentRef";
+
 export function overrideProductionConsole() {
     let defaultEnabled = true;
 
@@ -14,7 +15,7 @@ export function overrideProductionConsole() {
         defaultEnabled = false;
     }
 
-    const isEnabled = useLocalStorage("console-debugging-enabled", defaultEnabled);
+    const isEnabled = usePersistentRef("console-debugging-enabled", defaultEnabled);
 
     let storedConsole = null;
 
diff --git a/client/src/onload/getRootFromIndexLink.ts b/client/src/onload/getRootFromIndexLink.ts
index 7ca6c43c0b9d9f448d3db194cb71c71fe7ddbf21..9f40588879c01b04f3c0293708b44a7041aeb4a9 100644
--- a/client/src/onload/getRootFromIndexLink.ts
+++ b/client/src/onload/getRootFromIndexLink.ts
@@ -9,6 +9,9 @@ import { serverPath } from "@/utils/serverPath";
  * @returns {string}
  */
 export function getRootFromIndexLink(defaultRoot = "/"): string {
+    if (typeof document === "undefined") {
+        return defaultRoot;
+    }
     const links = document.getElementsByTagName("link");
     const indexLink = Array.from(links).find((link) => link.rel == "index");
     return indexLink && indexLink.href ? serverPath(indexLink.href) : defaultRoot;
diff --git a/client/src/router/guards.ts b/client/src/router/guards.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fa6b5ed18862dca193053fe498225bba84d77b65
--- /dev/null
+++ b/client/src/router/guards.ts
@@ -0,0 +1,19 @@
+import type { NavigationGuardNext, Route } from "vue-router";
+
+import { useUserStore } from "@/stores/userStore";
+
+export async function requireAuth(to: Route, from: Route, next: NavigationGuardNext) {
+    const userStore = useUserStore();
+    await userStore.loadUser(false);
+
+    if (userStore.isAnonymous) {
+        next({
+            path: "/login/start",
+            query: {
+                redirect: to.fullPath,
+            },
+        });
+        return;
+    }
+    next();
+}
diff --git a/client/src/store/historyStore/model/utilities.js b/client/src/store/historyStore/model/utilities.js
index 6a7ccb2d3f0cb749c83940217b126257ed2df98a..2fa81ffecca3f803811db75643537321904e59b3 100644
--- a/client/src/store/historyStore/model/utilities.js
+++ b/client/src/store/historyStore/model/utilities.js
@@ -12,11 +12,41 @@ export function mergeArray(id, payload, items, itemKey) {
             const localItem = itemArray[itemIndex];
             if (localItem.id == item.id) {
                 Object.keys(localItem).forEach((key) => {
-                    localItem[key] = item[key];
+                    // Maybe it's ok to overwrite the `sub_items` key here because that
+                    // array might contain items not returned for current filter?
+                    if (key !== "sub_items") {
+                        localItem[key] = item[key];
+                    }
                 });
             }
+            // the `item.id` is different with the same `hid`,
+            // so we add a key `sub_items` to this item and add any other related item(s) to it
+            else {
+                // But first, we check a few conditions and based on those, possibly replace the `localItem` with the new item
+                if (
+                    // 1: `localItem` is not in the `payload` (for filter)
+                    new Date(item.create_time) < new Date(localItem.create_time) ||
+                    // 2: `localItem` has fewer keys than the new item
+                    Object.keys(localItem).length < Object.keys(item).length
+                ) {
+                    set(itemArray, itemIndex, item);
+                    pushSubItem(item, localItem);
+                    localItem.sub_items = [];
+                } else {
+                    pushSubItem(localItem, item);
+                }
+            }
         } else {
             set(itemArray, itemIndex, item);
         }
     }
 }
+
+function pushSubItem(item, subItem) {
+    if (!item.sub_items) {
+        item["sub_items"] = [];
+    }
+    if (!item["sub_items"].find((i) => i.id === subItem.id)) {
+        item["sub_items"].push(subItem);
+    }
+}
diff --git a/client/src/stores/activitySetup.ts b/client/src/stores/activitySetup.ts
index 2e8bf5b1c26ec9560c46618e1383c3f18b99d547..af494b4b04092eae597adbcd826d43fffce9d4d2 100644
--- a/client/src/stores/activitySetup.ts
+++ b/client/src/stores/activitySetup.ts
@@ -1,17 +1,34 @@
 /**
  * List of built-in activities
  */
+import {
+    faChartBar,
+    faColumns,
+    faDatabase,
+    faFile,
+    faFileContract,
+    faFolder,
+    faHdd,
+    faLaptop,
+    faList,
+    faPlay,
+    faSitemap,
+    faUpload,
+    faWrench,
+} from "@fortawesome/free-solid-svg-icons";
+
 import { type Activity } from "@/stores/activityStore";
 import { type EventData } from "@/stores/eventStore";
 
-export const Activities = [
+export const defaultActivities = [
     {
         anonymous: false,
-        description: "Displays currently active interactive tools (ITs), if these are enabled by the administrator.",
-        icon: "fa-laptop",
+        description: "Displays currently running interactive tools (ITs), if these are enabled by the administrator.",
+        icon: faLaptop,
         id: "interactivetools",
         mutable: false,
         optional: false,
+        panel: false,
         title: "Interactive Tools",
         tooltip: "Show active interactive tools",
         to: "/interactivetool_entry_points/list",
@@ -20,10 +37,11 @@ export const Activities = [
     {
         anonymous: true,
         description: "Opens a data dialog, allowing uploads from URL, pasted content or disk.",
-        icon: "upload",
+        icon: faUpload,
         id: "upload",
         mutable: false,
         optional: false,
+        panel: false,
         title: "Upload",
         to: null,
         tooltip: "Download from URL or upload files from disk",
@@ -32,22 +50,24 @@ export const Activities = [
     {
         anonymous: true,
         description: "Displays the tool panel to search and access all available tools.",
-        icon: "wrench",
+        icon: faWrench,
         id: "tools",
         mutable: false,
         optional: false,
+        panel: true,
         title: "Tools",
         to: null,
         tooltip: "Search and run tools",
         visible: true,
     },
     {
-        anonymous: false,
+        anonymous: true,
         description: "Displays a panel to search and access workflows.",
-        icon: "sitemap",
+        icon: faSitemap,
         id: "workflows",
         mutable: false,
         optional: true,
+        panel: false,
         title: "Workflows",
         to: "/workflows/list",
         tooltip: "Search and run workflows",
@@ -56,34 +76,37 @@ export const Activities = [
     {
         anonymous: false,
         description: "Displays all workflow runs.",
-        icon: "fa-list",
+        icon: faList,
         id: "invocation",
         mutable: false,
         optional: true,
+        panel: true,
         title: "Workflow Invocations",
         tooltip: "Show all workflow runs",
         to: null,
         visible: true,
     },
     {
-        anonymous: false,
+        anonymous: true,
         description: "Displays the list of available visualizations.",
-        icon: "chart-bar",
+        icon: faChartBar,
         id: "visualizations",
         mutable: false,
         optional: true,
+        panel: true,
         title: "Visualization",
         to: null,
         tooltip: "Visualize datasets",
         visible: true,
     },
     {
-        anonymous: false,
+        anonymous: true,
         description: "Displays the list of all histories.",
-        icon: "fa-hdd",
+        icon: faHdd,
         id: "histories",
         mutable: false,
         optional: true,
+        panel: false,
         title: "Histories",
         tooltip: "Show all histories",
         to: "/histories/list",
@@ -92,10 +115,11 @@ export const Activities = [
     {
         anonymous: false,
         description: "Displays the history selector panel and opens History Multiview in the center panel.",
-        icon: "fa-columns",
+        icon: faColumns,
         id: "multiview",
         mutable: false,
         optional: true,
+        panel: true,
         title: "History Multiview",
         tooltip: "Select histories to show in History Multiview",
         to: "/histories/view_multiple",
@@ -104,38 +128,54 @@ export const Activities = [
     {
         anonymous: false,
         description: "Displays all of your datasets across all histories.",
-        icon: "fa-folder",
+        icon: faFolder,
         id: "datasets",
         mutable: false,
         optional: true,
+        panel: false,
         title: "Datasets",
         tooltip: "Show all datasets",
         to: "/datasets/list",
         visible: true,
     },
     {
-        anonymous: false,
-        description: "Display and create new Pages.",
-        icon: "fa-file-contract",
+        anonymous: true,
+        description: "Display and create new pages.",
+        icon: faFileContract,
         id: "pages",
         mutable: false,
         optional: true,
+        panel: false,
         title: "Pages",
         tooltip: "Show all pages",
         to: "/pages/list",
         visible: true,
     },
-];
+    {
+        anonymous: false,
+        description: "Display Data Libraries with datasets available to all users.",
+        icon: faDatabase,
+        id: "libraries",
+        mutable: false,
+        optional: true,
+        panel: false,
+        title: "Libraries",
+        tooltip: "Access data libraries",
+        to: "/libraries",
+        visible: true,
+    },
+] as const;
 
 export function convertDropData(data: EventData): Activity | null {
     if (data.history_content_type === "dataset") {
         return {
             anonymous: true,
             description: "Displays this dataset.",
-            icon: "fa-file",
+            icon: faFile,
             id: `dataset-${data.id}`,
             mutable: true,
             optional: true,
+            panel: false,
             title: data.name as string,
             tooltip: "View your dataset",
             to: `/datasets/${data.id}/preview`,
@@ -146,10 +186,11 @@ export function convertDropData(data: EventData): Activity | null {
         return {
             anonymous: false,
             description: data.description as string,
-            icon: "fa-play",
+            icon: faPlay,
             id: `workflow-${data.id}`,
             mutable: true,
             optional: true,
+            panel: false,
             title: data.name as string,
             tooltip: data.name as string,
             to: `/workflows/run?id=${data.id}`,
diff --git a/client/src/stores/activityStore.test.ts b/client/src/stores/activityStore.test.ts
index 95f71bba9cd2ee8c64d72727285c05893799e905..93eebee8e56bda77dbb76fe5c4747950f3644a16 100644
--- a/client/src/stores/activityStore.test.ts
+++ b/client/src/stores/activityStore.test.ts
@@ -1,17 +1,19 @@
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import { createPinia, setActivePinia } from "pinia";
 
 import { useActivityStore } from "@/stores/activityStore";
 
 // mock Galaxy object
 jest.mock("./activitySetup", () => ({
-    Activities: [
+    defaultActivities: [
         {
             anonymous: false,
             description: "a-description",
-            icon: "a-icon",
+            icon: "a-icon" as unknown as IconDefinition,
             id: "a-id",
             mutable: false,
             optional: false,
+            panel: true,
             title: "a-title",
             to: null,
             tooltip: "a-tooltip",
@@ -24,10 +26,11 @@ const newActivities = [
     {
         anonymous: false,
         description: "a-description-new",
-        icon: "a-icon-new",
+        icon: "a-icon-new" as unknown as IconDefinition,
         id: "a-id",
         mutable: false,
         optional: false,
+        panel: true,
         title: "a-title",
         to: "a-to-new",
         tooltip: "a-tooltip-new",
@@ -36,10 +39,11 @@ const newActivities = [
     {
         anonymous: false,
         description: "b-description-new",
-        icon: "b-icon-new",
+        icon: "b-icon-new" as unknown as IconDefinition,
         id: "b-id",
         mutable: true,
         optional: false,
+        panel: true,
         title: "b-title-new",
         to: "b-to-new",
         tooltip: "b-tooltip-new",
@@ -52,16 +56,16 @@ describe("Activity Store", () => {
         setActivePinia(createPinia());
     });
 
-    it("initialize store", () => {
-        const activityStore = useActivityStore();
+    it("initialize store", async () => {
+        const activityStore = useActivityStore("default");
         expect(activityStore.getAll().length).toBe(0);
-        activityStore.sync();
+        await activityStore.sync();
         expect(activityStore.getAll().length).toBe(1);
     });
 
-    it("add activity", () => {
-        const activityStore = useActivityStore();
-        activityStore.sync();
+    it("add activity", async () => {
+        const activityStore = useActivityStore("default");
+        await activityStore.sync();
         const initialActivities = activityStore.getAll();
         expect(initialActivities[0]?.visible).toBeTruthy();
         activityStore.setAll(newActivities);
@@ -69,7 +73,7 @@ describe("Activity Store", () => {
         const currentActivities = activityStore.getAll();
         expect(currentActivities[0]).toEqual(newActivities[0]);
         expect(currentActivities[1]).toEqual(newActivities[1]);
-        activityStore.sync();
+        await activityStore.sync();
         const syncActivities = activityStore.getAll();
         expect(syncActivities.length).toEqual(2);
         expect(syncActivities[0]?.description).toEqual("a-description");
@@ -77,19 +81,19 @@ describe("Activity Store", () => {
         expect(syncActivities[1]).toEqual(newActivities[1]);
     });
 
-    it("remove activity", () => {
-        const activityStore = useActivityStore();
-        activityStore.sync();
+    it("remove activity", async () => {
+        const activityStore = useActivityStore("default");
+        await activityStore.sync();
         const initialActivities = activityStore.getAll();
         expect(initialActivities.length).toEqual(1);
         activityStore.remove("a-id");
         expect(activityStore.getAll().length).toEqual(0);
-        activityStore.sync();
+        await activityStore.sync();
         expect(activityStore.getAll().length).toEqual(1);
         activityStore.setAll(newActivities);
         expect(activityStore.getAll().length).toEqual(2);
         activityStore.remove("b-id");
-        activityStore.sync();
+        await activityStore.sync();
         expect(activityStore.getAll().length).toEqual(1);
     });
 });
diff --git a/client/src/stores/activityStore.ts b/client/src/stores/activityStore.ts
index c7435f2ad10a8da67df205ca6e98586bd1946810..f7fad5271859f9b4964cd72fab8e5f51378e09f8 100644
--- a/client/src/stores/activityStore.ts
+++ b/client/src/stores/activityStore.ts
@@ -1,54 +1,111 @@
 /**
  * Stores the Activity Bar state
  */
+import { type IconDefinition } from "@fortawesome/fontawesome-svg-core";
+import { useDebounceFn, watchImmediate } from "@vueuse/core";
+import { computed, type Ref, ref, set } from "vue";
 
-import { defineStore } from "pinia";
-import { type Ref } from "vue";
-
+import { useHashedUserId } from "@/composables/hashedUserId";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
+import { ensureDefined } from "@/utils/assertions";
+
+import { defaultActivities } from "./activitySetup";
+import { defineScopedStore } from "./scopedStore";
 
-import { Activities } from "./activitySetup";
+export type ActivityVariant = "primary" | "danger" | "disabled";
 
 export interface Activity {
     // determine wether an anonymous user can access this activity
-    anonymous: boolean;
+    anonymous?: boolean;
     // description of the activity
     description: string;
     // unique identifier
     id: string;
     // icon to be displayed in activity bar
-    icon: string;
+    icon: IconDefinition;
     // indicate if this activity can be modified and/or deleted
-    mutable: boolean;
+    mutable?: boolean;
     // indicate wether this activity can be disabled by the user
-    optional: boolean;
+    optional?: boolean;
+    // specifiy wether this activity utilizes the side panel
+    panel?: boolean;
     // title to be displayed in the activity bar
     title: string;
     // route to be executed upon selecting the activity
-    to: string | null;
+    to?: string | null;
     // tooltip to be displayed when hovering above the icon
     tooltip: string;
     // indicate wether the activity should be visible by default
-    visible: boolean;
+    visible?: boolean;
+    // if activity should cause a click event
+    click?: true;
+    variant?: ActivityVariant;
+}
+
+export interface ActivityMeta {
+    disabled: boolean;
+}
+
+function defaultActivityMeta(): ActivityMeta {
+    return {
+        disabled: false,
+    };
 }
 
-export const useActivityStore = defineStore("activityStore", () => {
-    const activities: Ref<Array<Activity>> = useUserLocalStorage("activity-store-activities", []);
+export const useActivityStore = defineScopedStore("activityStore", (scope) => {
+    const activities: Ref<Array<Activity>> = useUserLocalStorage(`activity-store-activities-${scope}`, []);
+    const activityMeta: Ref<Record<string, ActivityMeta>> = ref({});
+
+    const { hashedUserId } = useHashedUserId();
+
+    const customDefaultActivities = ref<Activity[] | null>(null);
+    const currentDefaultActivities = computed(() => customDefaultActivities.value ?? defaultActivities);
+    const isSideBarOpen = computed(() => toggledSideBar.value !== "" && toggledSideBar.value !== "closed");
+
+    const toggledSideBar = useUserLocalStorage(`activity-store-current-side-bar-${scope}`, "tools");
+
+    function toggleSideBar(currentOpen = "") {
+        toggledSideBar.value = toggledSideBar.value === currentOpen ? "" : currentOpen;
+    }
+
+    function closeSideBar() {
+        toggledSideBar.value = "closed";
+    }
+
+    function overrideDefaultActivities(activities: Activity[]) {
+        customDefaultActivities.value = activities;
+        sync();
+    }
+
+    function resetDefaultActivities() {
+        customDefaultActivities.value = null;
+        sync();
+    }
+
+    /**
+     * Restores the default activity bar items
+     */
+    function restore() {
+        activities.value = currentDefaultActivities.value.slice();
+    }
 
     /**
      * The set of built-in activities is defined in activitySetup.js.
      * This helper function applies changes of the built-in activities,
      * to the user stored activities which are persisted in local cache.
      */
-    function sync() {
+    const sync = useDebounceFn(() => {
         // create a map of built-in activities
         const activitiesMap: Record<string, Activity> = {};
-        Activities.forEach((a) => {
+
+        currentDefaultActivities.value.forEach((a) => {
             activitiesMap[a.id] = a;
         });
+
         // create an updated array of activities
         const newActivities: Array<Activity> = [];
         const foundActivity = new Set();
+
         activities.value.forEach((a: Activity) => {
             if (a.mutable) {
                 // existing custom activity
@@ -57,6 +114,7 @@ export const useActivityStore = defineStore("activityStore", () => {
                 // update existing built-in activity attributes
                 // skip legacy built-in activities
                 const sourceActivity = activitiesMap[a.id];
+
                 if (sourceActivity) {
                     foundActivity.add(a.id);
                     newActivities.push({
@@ -66,17 +124,34 @@ export const useActivityStore = defineStore("activityStore", () => {
                 }
             }
         });
+
         // add new built-in activities
-        Activities.forEach((a) => {
+        currentDefaultActivities.value.forEach((a) => {
             if (!foundActivity.has(a.id)) {
                 newActivities.push({ ...a });
             }
         });
-        // update activities stored in local cache only if changes were applied
-        if (JSON.stringify(activities.value) !== JSON.stringify(newActivities)) {
-            activities.value = newActivities;
+
+        activities.value = newActivities;
+
+        // if toggled side-bar does not exist, choose the first option
+        if (isSideBarOpen.value) {
+            const allSideBars = activities.value.flatMap((activity) => {
+                if (activity.panel) {
+                    return [activity.id];
+                } else {
+                    return [];
+                }
+            });
+
+            const allSideBarsSet = new Set(allSideBars);
+            const firstSideBar = allSideBars[0];
+
+            if (firstSideBar && !allSideBarsSet.has(toggledSideBar.value)) {
+                toggledSideBar.value = firstSideBar;
+            }
         }
-    }
+    }, 10);
 
     function getAll() {
         return activities.value;
@@ -88,16 +163,58 @@ export const useActivityStore = defineStore("activityStore", () => {
 
     function remove(activityId: string) {
         const findIndex = activities.value.findIndex((a: Activity) => a.id === activityId);
+
         if (findIndex !== -1) {
             activities.value.splice(findIndex, 1);
         }
     }
 
+    const metaForId = computed(() => (activityId: string) => {
+        let meta = activityMeta.value[activityId];
+
+        if (!meta) {
+            set(activityMeta.value, activityId, defaultActivityMeta());
+            meta = ensureDefined(activityMeta.value[activityId]);
+        }
+
+        return meta;
+    });
+
+    function setMeta<K extends keyof ActivityMeta>(activityId: string, metaKey: K, value: ActivityMeta[K]) {
+        let meta = activityMeta.value[activityId];
+
+        if (!meta) {
+            set(activityMeta.value, activityId, defaultActivityMeta());
+            meta = ensureDefined(activityMeta.value[activityId]);
+        }
+
+        set(meta, metaKey, value);
+    }
+
+    watchImmediate(
+        () => hashedUserId.value,
+        () => {
+            sync();
+        }
+    );
+
     return {
+        toggledSideBar,
+        toggleSideBar,
+        closeSideBar,
+        isSideBarOpen,
         activities,
+        activityMeta,
+        metaForId,
+        setMeta,
         getAll,
         remove,
         setAll,
+        restore,
         sync,
+        customDefaultActivities,
+        currentDefaultActivities,
+        overrideDefaultActivities,
+        resetDefaultActivities,
     };
 });
diff --git a/client/src/stores/broadcastsStore.ts b/client/src/stores/broadcastsStore.ts
index adecba5739390b4f3715ed51ccbf015c7c1817ad..01eeaa353a269213801873f906b9d979ba6047da 100644
--- a/client/src/stores/broadcastsStore.ts
+++ b/client/src/stores/broadcastsStore.ts
@@ -2,7 +2,7 @@ import { defineStore } from "pinia";
 import { computed, ref, set } from "vue";
 
 import { fetchAllBroadcasts } from "@/api/notifications.broadcast";
-import type { components } from "@/api/schema";
+import { type components } from "@/api/schema";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { mergeObjectListsById } from "@/utils/utils";
 
diff --git a/client/src/stores/collectionAttributesStore.test.ts b/client/src/stores/collectionAttributesStore.test.ts
index 58e28d20851f05390b3b0ed7f4159a9a61747d6c..13f318e51934d5552a52ca8e662c7f490c4f570b 100644
--- a/client/src/stores/collectionAttributesStore.test.ts
+++ b/client/src/stores/collectionAttributesStore.test.ts
@@ -1,13 +1,11 @@
 import flushPromises from "flush-promises";
 import { createPinia, setActivePinia } from "pinia";
 
-import type { DatasetCollectionAttributes } from "@/api";
-import { mockFetcher } from "@/api/schema/__mocks__";
+import { type DatasetCollectionAttributes } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
 
 import { useCollectionAttributesStore } from "./collectionAttributesStore";
 
-jest.mock("@/api/schema");
-
 const FAKE_HDCA_ID = "123";
 
 const FAKE_ATTRIBUTES: DatasetCollectionAttributes = {
@@ -19,12 +17,19 @@ const FAKE_ATTRIBUTES: DatasetCollectionAttributes = {
     tags: ["tag1", "tag2"],
 };
 
-const fetchCollectionAttributes = jest.fn().mockResolvedValue({ data: FAKE_ATTRIBUTES });
+const fetchCollectionAttributesMock = jest.fn().mockReturnValue(FAKE_ATTRIBUTES);
+
+const { server, http } = useServerMock();
 
 describe("collectionAttributesStore", () => {
     beforeEach(() => {
         setActivePinia(createPinia());
-        mockFetcher.path("/api/dataset_collections/{id}/attributes").method("get").mock(fetchCollectionAttributes);
+
+        server.use(
+            http.get("/api/dataset_collections/{id}/attributes", ({ response }) => {
+                return response(200).json(fetchCollectionAttributesMock());
+            })
+        );
     });
 
     it("should fetch attributes and store them", async () => {
@@ -39,7 +44,7 @@ describe("collectionAttributesStore", () => {
         expect(store.isLoadingAttributes(FAKE_HDCA_ID)).toBeFalsy();
 
         expect(store.storedAttributes[FAKE_HDCA_ID]).toEqual(FAKE_ATTRIBUTES);
-        expect(fetchCollectionAttributes).toHaveBeenCalled();
+        expect(fetchCollectionAttributesMock).toHaveBeenCalled();
     });
 
     it("should not fetch attributes if already stored", async () => {
@@ -50,6 +55,6 @@ describe("collectionAttributesStore", () => {
         const result = store.getAttributes(FAKE_HDCA_ID);
 
         expect(result).toEqual(FAKE_ATTRIBUTES);
-        expect(fetchCollectionAttributes).not.toHaveBeenCalled();
+        expect(fetchCollectionAttributesMock).not.toHaveBeenCalled();
     });
 });
diff --git a/client/src/stores/collectionAttributesStore.ts b/client/src/stores/collectionAttributesStore.ts
index ba4c5ed78f531db88232a7993b5499df3447b5e9..5b1669b0a1c9c893a8645f0861f11616d4259895 100644
--- a/client/src/stores/collectionAttributesStore.ts
+++ b/client/src/stores/collectionAttributesStore.ts
@@ -1,17 +1,27 @@
 import { defineStore } from "pinia";
 
-import type { DatasetCollectionAttributes } from "@/api";
-import { fetchCollectionAttributes } from "@/api/datasetCollections";
-import { useKeyedCache } from "@/composables/keyedCache";
+import { type DatasetCollectionAttributes, GalaxyApi } from "@/api";
+import { type FetchParams, useKeyedCache } from "@/composables/keyedCache";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export const useCollectionAttributesStore = defineStore("collectionAttributesStore", () => {
-    const { storedItems, getItemById, isLoadingItem } = useKeyedCache<DatasetCollectionAttributes>((params) =>
-        fetchCollectionAttributes({ id: params.id, instance_type: "history" })
-    );
+    async function fetchAttributes(params: FetchParams): Promise<DatasetCollectionAttributes> {
+        const { data, error } = await GalaxyApi().GET("/api/dataset_collections/{id}/attributes", {
+            params: { path: params },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    const { storedItems, getItemById, isLoadingItem, getItemLoadError } =
+        useKeyedCache<DatasetCollectionAttributes>(fetchAttributes);
 
     return {
         storedAttributes: storedItems,
         getAttributes: getItemById,
         isLoadingAttributes: isLoadingItem,
+        getItemLoadError: getItemLoadError,
     };
 });
diff --git a/client/src/stores/collectionBuilderItemsStore.ts b/client/src/stores/collectionBuilderItemsStore.ts
new file mode 100644
index 0000000000000000000000000000000000000000..dc5705a7b4b77913feaece344a573c60c8652836
--- /dev/null
+++ b/client/src/stores/collectionBuilderItemsStore.ts
@@ -0,0 +1,78 @@
+import { defineStore } from "pinia";
+import { ref, set } from "vue";
+
+import { GalaxyApi, type HDASummary } from "@/api";
+import { HistoryFilters } from "@/components/History/HistoryFilters";
+import { filtersToQueryValues } from "@/components/History/model/queries";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+const DEFAULT_FILTERS = { visible: true, deleted: false };
+
+/**
+ * Fetches datasets for the Collection Builder modal. It caches the datasets for each filter text.
+ */
+export const useCollectionBuilderItemsStore = defineStore("collectionBuilderItemsStore", () => {
+    const cachedDatasetsForFilterText = ref<Record<string, HDASummary[]>>({});
+    const errorMessage = ref<string | null>(null);
+    const isFetching = ref<Record<string, boolean>>({});
+    const lastFetch = ref<{ id: string; time: string; text: string } | null>(null);
+
+    async function fetchDatasetsForFiltertext(historyId: string, historyUpdateTime?: string, filterText = "") {
+        if (isFetching.value[filterText]) {
+            return { data: [], error: null };
+        }
+
+        if (
+            lastFetch.value &&
+            lastFetch.value.id === historyId &&
+            lastFetch.value.time === historyUpdateTime &&
+            lastFetch.value.text === filterText
+        ) {
+            return {
+                data: cachedDatasetsForFilterText.value[filterText] || [],
+                error: errorMessage.value,
+            };
+        }
+
+        set(isFetching.value, filterText, true);
+
+        const filterQuery = getFilterQuery(filterText);
+
+        // Note: Had "/api/histories/{history_id}/contents/datasets" before but it was returning datasets and collections
+        const { data, error: apiError } = await GalaxyApi().GET("/api/histories/{history_id}/contents", {
+            params: {
+                path: { history_id: historyId },
+                query: { ...filterQuery, v: "dev" },
+            },
+        });
+        const returnedData = data as HDASummary[];
+
+        let error = null;
+        if (apiError) {
+            error = errorMessageAsString(apiError);
+            errorMessage.value = error;
+        } else {
+            set(cachedDatasetsForFilterText.value, filterText, returnedData);
+        }
+
+        set(isFetching.value, filterText, false);
+        lastFetch.value = { id: historyId, time: historyUpdateTime || "", text: filterText };
+
+        return { data: returnedData, error };
+    }
+
+    function getFilterQuery(filterText: string) {
+        let filters = filterText ? HistoryFilters.getQueryDict(filterText) : DEFAULT_FILTERS;
+        if (filters.history_content_type) {
+            delete filters.history_content_type;
+        }
+        filters = { ...filters, history_content_type: "dataset" };
+        return filtersToQueryValues(filters);
+    }
+
+    return {
+        cachedDatasetsForFilterText,
+        isFetching,
+        fetchDatasetsForFiltertext,
+    };
+});
diff --git a/client/src/stores/collectionElementsStore.test.ts b/client/src/stores/collectionElementsStore.test.ts
index 6af9a98f5d5747cbb9a28c5f6d46b50a46b4d85f..ef4a1b54426892454f9bde7fc1f5d8ed58b4a98f 100644
--- a/client/src/stores/collectionElementsStore.test.ts
+++ b/client/src/stores/collectionElementsStore.test.ts
@@ -1,19 +1,28 @@
 import flushPromises from "flush-promises";
 import { createPinia, setActivePinia } from "pinia";
 
-import type { DCESummary, HDCASummary } from "@/api";
-import { mockFetcher } from "@/api/schema/__mocks__";
-import { DCEEntry, useCollectionElementsStore } from "@/stores/collectionElementsStore";
+import { type DCESummary, type HDCASummary } from "@/api";
+import { useServerMock } from "@/api/client/__mocks__";
+import { type DCEEntry, useCollectionElementsStore } from "@/stores/collectionElementsStore";
 
-jest.mock("@/api/schema");
+const { server, http } = useServerMock();
 
+const fetchCollectionElementsSpy = jest.fn();
 describe("useCollectionElementsStore", () => {
     beforeEach(() => {
         setActivePinia(createPinia());
-        mockFetcher
-            .path("/api/dataset_collections/{hdca_id}/contents/{parent_id}")
-            .method("get")
-            .mock(fetchCollectionElements);
+        server.use(
+            http.get("/api/dataset_collections/{hdca_id}/contents/{parent_id}", ({ response, params, query }) => {
+                const elements: DCESummary[] = [];
+                const startIndex = Number(query.get("offset")) ?? 0;
+                const endIndex = startIndex + (Number(query.get("limit")) ?? 10);
+                for (let i = startIndex; i < endIndex; i++) {
+                    elements.push(mockElement(params.hdca_id, i));
+                }
+                fetchCollectionElementsSpy();
+                return response(200).json(elements);
+            })
+        );
     });
 
     it("should save collections", async () => {
@@ -42,12 +51,12 @@ describe("useCollectionElementsStore", () => {
         store.getCollectionElements(collection);
         expect(store.isLoadingCollectionElements(collection)).toEqual(false);
         await flushPromises();
-        expect(fetchCollectionElements).not.toHaveBeenCalled();
+        expect(fetchCollectionElementsSpy).not.toHaveBeenCalled();
 
         const limit = 5;
         store.fetchMissingElements(collection, 0, limit);
         await flushPromises();
-        expect(fetchCollectionElements).toHaveBeenCalled();
+        expect(fetchCollectionElementsSpy).toHaveBeenCalled();
 
         const collectionKey = store.getCollectionKey(collection);
         const elements = store.storedCollectionElements[collectionKey];
@@ -74,7 +83,7 @@ describe("useCollectionElementsStore", () => {
         // Getting the same collection elements range should not trigger a fetch
         store.fetchMissingElements(collection, offset, limit);
         expect(store.isLoadingCollectionElements(collection)).toEqual(false);
-        expect(fetchCollectionElements).not.toHaveBeenCalled();
+        expect(fetchCollectionElementsSpy).not.toHaveBeenCalled();
     });
 
     it("should fetch only missing elements if the requested range is not already stored", async () => {
@@ -87,7 +96,7 @@ describe("useCollectionElementsStore", () => {
         const initialElements = 3;
         store.fetchMissingElements(collection, 0, initialElements);
         await flushPromises();
-        expect(fetchCollectionElements).toHaveBeenCalled();
+        expect(fetchCollectionElementsSpy).toHaveBeenCalled();
         const collectionKey = store.getCollectionKey(collection);
         let elements = store.storedCollectionElements[collectionKey];
         // The first call will initialize the 10 placeholders and fetch the first 3 elements out of 10
@@ -100,7 +109,7 @@ describe("useCollectionElementsStore", () => {
         store.fetchMissingElements(collection, offset, limit);
         jest.runAllTimers();
         await flushPromises();
-        expect(fetchCollectionElements).toHaveBeenCalled();
+        expect(fetchCollectionElementsSpy).toHaveBeenCalled();
 
         elements = store.storedCollectionElements[collectionKey];
         expect(elements).toBeDefined();
@@ -115,6 +124,7 @@ function mockCollection(id: string, numElements = 10): HDCASummary {
     return {
         id: id,
         element_count: numElements,
+        elements_datatypes: ["txt"],
         collection_type: "list",
         populated_state: "ok",
         populated_state_message: "",
@@ -132,6 +142,7 @@ function mockCollection(id: string, numElements = 10): HDCASummary {
         update_time: "2021-05-25T14:00:00.000Z",
         type_id: "dataset_collection",
         url: "",
+        type: "collection",
     };
 }
 
@@ -156,27 +167,6 @@ function mockElement(collectionId: string, i: number): DCESummary {
     };
 }
 
-interface ApiRequest {
-    hdca_id: string;
-    parent_id: string;
-    offset: number;
-    limit: number;
-}
-
-const fetchCollectionElements = jest.fn(fakeCollectionElementsApiResponse);
-
-function fakeCollectionElementsApiResponse(params: ApiRequest) {
-    const elements: DCESummary[] = [];
-    const startIndex = params.offset ?? 0;
-    const endIndex = startIndex + (params.limit ?? 10);
-    for (let i = startIndex; i < endIndex; i++) {
-        elements.push(mockElement(params.hdca_id, i));
-    }
-    return {
-        data: elements,
-    };
-}
-
 /**
  * Filter out the placeholder elements from the given array.
  */
diff --git a/client/src/stores/collectionElementsStore.ts b/client/src/stores/collectionElementsStore.ts
index 9739c58baa3ae38dda490091295efb96515ea6b9..857055e6e95d87f2ea1d3df3ca1ec84b760acf94 100644
--- a/client/src/stores/collectionElementsStore.ts
+++ b/client/src/stores/collectionElementsStore.ts
@@ -1,8 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, del, ref, set } from "vue";
 
-import type { CollectionEntry, DCESummary, HDCASummary, HistoryContentItemBase } from "@/api";
-import { isHDCA } from "@/api";
+import { type CollectionEntry, type DCESummary, type HDCASummary, type HistoryContentItemBase, isHDCA } from "@/api";
 import { fetchCollectionDetails, fetchElementsFromCollection } from "@/api/datasetCollections";
 import { ensureDefined } from "@/utils/assertions";
 import { ActionSkippedError, LastQueue } from "@/utils/lastQueue";
@@ -37,6 +36,7 @@ const FETCH_LIMIT = 50;
 export const useCollectionElementsStore = defineStore("collectionElementsStore", () => {
     const storedCollections = ref<{ [key: string]: HDCASummary }>({});
     const loadingCollectionElements = ref<{ [key: string]: boolean }>({});
+    const loadingCollectionElementsErrors = ref<{ [key: string]: Error }>({});
     const storedCollectionElements = ref<{ [key: string]: DCEEntry[] }>({});
 
     /**
@@ -63,6 +63,12 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore",
         };
     });
 
+    const getLoadingCollectionElementsError = computed(() => {
+        return (collection: CollectionEntry) => {
+            return loadingCollectionElementsErrors.value[getCollectionKey(collection)] ?? false;
+        };
+    });
+
     type FetchParams = {
         storedElements: DCEEntry[];
         collection: CollectionEntry;
@@ -106,6 +112,8 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore",
             });
 
             return { fetchedElements, elementOffset: offset };
+        } catch (error) {
+            set(loadingCollectionElementsErrors.value, collectionKey, error);
         } finally {
             del(loadingCollectionElements.value, collectionKey);
         }
@@ -162,7 +170,7 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore",
     /** Returns collection from storedCollections, will load collection if not in store */
     const getCollectionById = computed(() => {
         return (collectionId: string) => {
-            if (!storedCollections.value[collectionId]) {
+            if (!storedCollections.value[collectionId] && !loadingCollectionElementsErrors.value[collectionId]) {
                 // TODO: Try to remove this as it can cause computed side effects (use keyedCache in this store instead?)
                 fetchCollection({ id: collectionId });
             }
@@ -176,6 +184,8 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore",
             const collection = await fetchCollectionDetails({ id: params.id });
             set(storedCollections.value, collection.id, collection);
             return collection;
+        } catch (error) {
+            set(loadingCollectionElementsErrors.value, params.id, error);
         } finally {
             del(loadingCollectionElements.value, params.id);
         }
@@ -203,6 +213,8 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore",
         storedCollectionElements,
         getCollectionElements,
         isLoadingCollectionElements,
+        getLoadingCollectionElementsError,
+        loadingCollectionElementsErrors,
         getCollectionById,
         fetchCollection,
         invalidateCollectionElements,
diff --git a/client/src/stores/configTemplatesUtil.ts b/client/src/stores/configTemplatesUtil.ts
index 2baeab3acb58f5b573058381f71c7bf0be768c10..c0e5e4f3bc8511090d6acc9e529201445ff6e52b 100644
--- a/client/src/stores/configTemplatesUtil.ts
+++ b/client/src/stores/configTemplatesUtil.ts
@@ -1,4 +1,4 @@
-import type { TemplateSummary } from "@/api/configTemplates";
+import { type TemplateSummary } from "@/api/configTemplates";
 
 export function findTemplate<T extends TemplateSummary>(
     templates: T[],
diff --git a/client/src/stores/configurationStore.ts b/client/src/stores/configurationStore.ts
index 1cd70b0d2c550843fc59113acbb84fffcf7d04ad..85eecffea2bfd845bbf7b72401f0bbbcec05d4c4 100644
--- a/client/src/stores/configurationStore.ts
+++ b/client/src/stores/configurationStore.ts
@@ -1,13 +1,11 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import { fetcher } from "@/api/schema";
+import { GalaxyApi } from "@/api";
 
 // Temporary set to any until schema model is defined
 export type GalaxyConfiguration = any;
 
-const fetchConfiguration = fetcher.path("/api/configuration").method("get").create();
-
 export const useConfigStore = defineStore("configurationStore", () => {
     const config = ref<GalaxyConfiguration>(null);
     const isLoading = ref(false);
@@ -17,11 +15,14 @@ export const useConfigStore = defineStore("configurationStore", () => {
         if (!isLoaded.value && !isLoading.value) {
             isLoading.value = true;
             try {
-                const { data } = await fetchConfiguration({});
+                const { data, error } = await GalaxyApi().GET("/api/configuration");
+
+                if (error) {
+                    console.error("Error loading Galaxy configuration", error);
+                }
+
                 config.value = data;
                 console.debug("Galaxy configuration loaded", config.value);
-            } catch (err) {
-                console.error("Error loading Galaxy configuration", err);
             } finally {
                 isLoading.value = false;
             }
diff --git a/client/src/stores/datasetExtraFilesStore.ts b/client/src/stores/datasetExtraFilesStore.ts
index 327f73c31eccdfde90e1c5589dd7aa7009b9ac99..8bd3f1f009828922140588609c2e10c0ac6ae25e 100644
--- a/client/src/stores/datasetExtraFilesStore.ts
+++ b/client/src/stores/datasetExtraFilesStore.ts
@@ -1,12 +1,23 @@
 import { defineStore } from "pinia";
 
-import { DatasetExtraFiles, fetchDatasetExtraFiles } from "@/api/datasets";
-import { useKeyedCache } from "@/composables/keyedCache";
+import { GalaxyApi } from "@/api";
+import { type DatasetExtraFiles } from "@/api/datasets";
+import { type FetchParams, useKeyedCache } from "@/composables/keyedCache";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export const useDatasetExtraFilesStore = defineStore("datasetExtraFilesStore", () => {
-    const { storedItems, getItemById, isLoadingItem, fetchItemById } = useKeyedCache<DatasetExtraFiles>((params) =>
-        fetchDatasetExtraFiles({ dataset_id: params.id })
-    );
+    async function fetchDatasetExtraFiles(params: FetchParams): Promise<DatasetExtraFiles> {
+        const { data, error } = await GalaxyApi().GET("/api/datasets/{dataset_id}/extra_files", {
+            params: { path: { dataset_id: params.id } },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    const { storedItems, getItemById, isLoadingItem, fetchItemById } =
+        useKeyedCache<DatasetExtraFiles>(fetchDatasetExtraFiles);
 
     return {
         storedDatasetExtraFiles: storedItems,
diff --git a/client/src/stores/datasetStore.ts b/client/src/stores/datasetStore.ts
index 02e493afd92f4b811cb849944c6241126b31687d..235b901f36cf2bd3628e72530547065018cc4b84 100644
--- a/client/src/stores/datasetStore.ts
+++ b/client/src/stores/datasetStore.ts
@@ -1,16 +1,10 @@
 import { defineStore } from "pinia";
 import { computed, set } from "vue";
 
-import { type DatasetEntry, type HDADetailed, type HistoryContentItemBase, isInaccessible } from "@/api";
-import { fetchDataset } from "@/api/datasets";
-import { ApiResponse } from "@/api/schema";
+import { type DatasetEntry, type HistoryContentItemBase, isInaccessible } from "@/api";
+import { fetchDatasetDetails } from "@/api/datasets";
 import { useKeyedCache } from "@/composables/keyedCache";
 
-async function fetchDatasetDetails(params: { id: string }): Promise<ApiResponse<HDADetailed>> {
-    const response = await fetchDataset({ dataset_id: params.id, view: "detailed" });
-    return response as unknown as ApiResponse<HDADetailed>;
-}
-
 export const useDatasetStore = defineStore("datasetStore", () => {
     const shouldFetch = computed(() => {
         return (dataset?: DatasetEntry) => {
diff --git a/client/src/stores/datatypesMapperStore.ts b/client/src/stores/datatypesMapperStore.ts
index 3731847ef573c1a783b2b6071bf2ce220de2ac66..5fef18a2f9691ac7e1bb5af2aa45a23427702ca7 100644
--- a/client/src/stores/datatypesMapperStore.ts
+++ b/client/src/stores/datatypesMapperStore.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia";
 
 import { getDatatypesMapper } from "@/components/Datatypes";
-import type { DatatypesMapperModel } from "@/components/Datatypes/model";
+import { type DatatypesMapperModel } from "@/components/Datatypes/model";
 import { rethrowSimple } from "@/utils/simple-error";
 
 interface State {
diff --git a/client/src/stores/fileSourceInstancesStore.ts b/client/src/stores/fileSourceInstancesStore.ts
index ec31d00e1e212d35b0af613185b2dcf2147f34e2..c62acc9f7da0fd7855b37d55b17503092e1b2a7f 100644
--- a/client/src/stores/fileSourceInstancesStore.ts
+++ b/client/src/stores/fileSourceInstancesStore.ts
@@ -1,11 +1,8 @@
 import { defineStore } from "pinia";
 
-import { fetcher } from "@/api/schema/fetcher";
-import type { components } from "@/api/schema/schema";
+import { type components, GalaxyApi } from "@/api";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-const getFileSourceInstances = fetcher.path("/api/file_source_instances").method("get").create();
-
 type UserFileSourceModel = components["schemas"]["UserFileSourceModel"];
 
 export const useFileSourceInstancesStore = defineStore("fileSourceInstances", {
@@ -35,12 +32,14 @@ export const useFileSourceInstancesStore = defineStore("fileSourceInstances", {
             this.error = errorMessageAsString(err);
         },
         async fetchInstances() {
-            try {
-                const { data: instances } = await getFileSourceInstances({});
-                this.handleInit(instances);
-            } catch (err) {
-                this.handleError(err);
+            const { data: instances, error } = await GalaxyApi().GET("/api/file_source_instances");
+
+            if (error) {
+                this.handleError(error);
+                return;
             }
+
+            this.handleInit(instances);
         },
         async ensureTemplates() {
             if (!this.fetched || this.error != null) {
diff --git a/client/src/stores/fileSourceTemplatesStore.ts b/client/src/stores/fileSourceTemplatesStore.ts
index 1efd7e67bfe041751e9b739c78c05b897d39abb7..f1e965db7ee31bdf7772e8e5411894b7ddcb70ee 100644
--- a/client/src/stores/fileSourceTemplatesStore.ts
+++ b/client/src/stores/fileSourceTemplatesStore.ts
@@ -1,13 +1,10 @@
 import { defineStore } from "pinia";
 
-import { fetcher } from "@/api/schema/fetcher";
-import type { components } from "@/api/schema/schema";
+import { type components, GalaxyApi } from "@/api";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { canUpgrade, findTemplate, getLatestVersion, getLatestVersionMap } from "./configTemplatesUtil";
 
-const getFileSourceTemplates = fetcher.path("/api/file_source_templates").method("get").create();
-
 type FileSourceTemplateSummary = components["schemas"]["FileSourceTemplateSummary"];
 type FileSourceTemplateSummaries = FileSourceTemplateSummary[];
 
@@ -54,12 +51,14 @@ export const useFileSourceTemplatesStore = defineStore("fileSourceTemplatesStore
             this.error = errorMessageAsString(err);
         },
         async fetchTemplates() {
-            try {
-                const { data: templates } = await getFileSourceTemplates({});
-                this.handleInit(templates);
-            } catch (err) {
-                this.handleError(err);
+            const { data: templates, error } = await GalaxyApi().GET("/api/file_source_templates");
+
+            if (error) {
+                this.handleError(error);
+                return;
             }
+
+            this.handleInit(templates);
         },
         async ensureTemplates() {
             if (!this.fetched || this.error != null) {
diff --git a/client/src/stores/helpTermsStore.ts b/client/src/stores/helpTermsStore.ts
new file mode 100644
index 0000000000000000000000000000000000000000..349ca4879802ad187a83ef9a979b0eaaeb54f551
--- /dev/null
+++ b/client/src/stores/helpTermsStore.ts
@@ -0,0 +1,129 @@
+import { defineStore } from "pinia";
+import { computed, type Ref, ref } from "vue";
+
+import { hasHelp as hasHelpTextFromYaml, help as helpTextFromYaml } from "@/components/Help/terms";
+
+import { useDatatypeStore } from "./datatypeStore";
+
+interface DatatypeDescription {
+    ext: string;
+    description: string | null;
+    descriptionUrl: string | null;
+}
+
+interface RawDatatypeDescription {
+    id: string;
+    text: string;
+    description: string | unknown | null;
+    description_url: string | unknown | null;
+    upload_warning: string | unknown | null;
+}
+
+export const useHelpTermsStore = defineStore("helpTermsStore", () => {
+    const initialized = ref(false);
+    const datatypeDescriptions = ref<DatatypeDescription[] | null>(null as DatatypeDescription[] | null);
+    const datatypeStore = useDatatypeStore();
+
+    function datatypeDescriptionForExtension(extension: string): DatatypeDescription | null {
+        if (!datatypeDescriptions.value) {
+            return null;
+        }
+        for (const description of datatypeDescriptions.value) {
+            if (description.ext == extension) {
+                return description;
+            }
+        }
+        return null;
+    }
+
+    function moreInformationFromUrlMarkdown(ext: string, url: string) {
+        return `More information on the datatype ${ext} can be found at [${url}](${url}).`;
+    }
+
+    function datatypeDescriptionToMarkdown(datatypeDescription: DatatypeDescription): string {
+        const ext = datatypeDescription.ext;
+        let description = datatypeDescription.description?.trimEnd();
+        const url = datatypeDescription.descriptionUrl;
+        if (!description && !url) {
+            return `${ext} is a registered Galaxy datatype.`;
+        } else if (!description) {
+            return moreInformationFromUrlMarkdown(ext, url as string);
+        } else if (!url) {
+            return description;
+        } else {
+            if (description.charAt(description.length - 1) != ".") {
+                description += ".";
+            }
+            return `${description}\n\n${moreInformationFromUrlMarkdown(ext, url)}`;
+        }
+    }
+
+    async function ensureInitialized() {
+        if (!initialized.value) {
+            await datatypeStore.fetchUploadDatatypes();
+            const rawDatatypes = datatypeStore.getUploadDatatypes as RawDatatypeDescription[];
+            datatypeDescriptions.value = rawDatatypes.map((datatype: RawDatatypeDescription) => {
+                return {
+                    ext: datatype.id,
+                    description: datatype.description || null,
+                    descriptionUrl: datatype.description_url || null,
+                } as DatatypeDescription;
+            });
+            initialized.value = true;
+        }
+    }
+
+    const loading = computed(() => {
+        return !initialized.value;
+    });
+
+    function hasHelpText(term: string): boolean {
+        if (term.startsWith("galaxy.datatypes.extensions.")) {
+            const extension = term.substring("galaxy.datatypes.extensions.".length);
+            return datatypeDescriptionForExtension(extension) != null;
+        } else {
+            return hasHelpTextFromYaml(term);
+        }
+    }
+
+    function helpText(term: string): string | null {
+        if (term.startsWith("galaxy.datatypes.extensions.")) {
+            const extension = term.substring("galaxy.datatypes.extensions.".length);
+            const description = datatypeDescriptionForExtension(extension);
+            if (!description) {
+                return null;
+            }
+            return datatypeDescriptionToMarkdown(description);
+        } else {
+            return helpTextFromYaml(term);
+        }
+    }
+
+    return {
+        ensureInitialized,
+        hasHelpText,
+        helpText,
+        loading,
+    };
+});
+
+export function useHelpForTerm(uri: Ref<string>) {
+    const termsStore = useHelpTermsStore();
+    termsStore.ensureInitialized();
+
+    const loading = computed(() => {
+        return termsStore.loading;
+    });
+    const hasHelp = computed(() => {
+        return termsStore.hasHelpText(uri.value);
+    });
+    const help = computed(() => {
+        return termsStore.helpText(uri.value);
+    });
+
+    return {
+        loading,
+        hasHelp,
+        help,
+    };
+}
diff --git a/client/src/stores/historyItemsStore.ts b/client/src/stores/historyItemsStore.ts
index 8b5dc1aca80724ab762a9564eeacc47ffccd3e4b..db3aad447320a49bf1cd05d1adde5dafeed2e584 100644
--- a/client/src/stores/historyItemsStore.ts
+++ b/client/src/stores/historyItemsStore.ts
@@ -8,19 +8,21 @@ import { reverse } from "lodash";
 import { defineStore } from "pinia";
 import { computed, ref, set } from "vue";
 
-import type { HistoryItemSummary } from "@/api";
+import { type HistoryItemSummary } from "@/api";
 import { HistoryFilters } from "@/components/History/HistoryFilters";
 import { mergeArray } from "@/store/historyStore/model/utilities";
 import { ActionSkippedError, LastQueue } from "@/utils/lastQueue";
 import { urlData } from "@/utils/url";
 
+type ExtendedHistoryItem = HistoryItemSummary & { sub_items?: HistoryItemSummary[] };
+
 const limit = 100;
 
 type ExpectedReturn = { stats: { total_matches: number }; contents: HistoryItemSummary[] };
 const queue = new LastQueue<typeof urlData>(1000, true);
 
 export const useHistoryItemsStore = defineStore("historyItemsStore", () => {
-    const items = ref<Record<string, HistoryItemSummary[]>>({});
+    const items = ref<Record<string, ExtendedHistoryItem[]>>({});
     const itemKey = ref("hid");
     const totalMatchesCount = ref<number | undefined>(undefined);
     const lastCheckedTime = ref(new Date());
@@ -35,12 +37,18 @@ export const useHistoryItemsStore = defineStore("historyItemsStore", () => {
                 (filter: [string, string]) => !filter[0].includes("related")
             );
             const relatedHid = HistoryFilters.getFilterValue(filterText, "related");
-            const filtered = itemArray.filter((item: HistoryItemSummary) => {
+            const filtered = itemArray.filter((item: ExtendedHistoryItem) => {
                 if (!item) {
                     return false;
                 }
                 if (!HistoryFilters.testFilters(filters, item)) {
-                    return false;
+                    // filters don't pass on the item, but they might pass on any of its sub_items
+                    if (
+                        !item.sub_items ||
+                        !item.sub_items.some((subItem) => HistoryFilters.testFilters(filters, subItem))
+                    ) {
+                        return false;
+                    }
                 }
                 const relationKey = `${historyId}-${relatedHid}-${item.hid}`;
                 if (relatedHid && !relatedItems.value[relationKey]) {
diff --git a/client/src/stores/historyStore.ts b/client/src/stores/historyStore.ts
index 38c430ead734e07723a7864b76cde12f9f5aa411..f9ba0c5c664dc86511bcc41533b04ca65a47bf8a 100644
--- a/client/src/stores/historyStore.ts
+++ b/client/src/stores/historyStore.ts
@@ -1,24 +1,22 @@
 import { defineStore } from "pinia";
 import { computed, del, ref, set } from "vue";
 
-import type {
-    AnyHistory,
-    HistoryContentsStats,
-    HistoryDevDetailed,
-    HistorySummary,
-    HistorySummaryExtended,
+import {
+    type AnyHistory,
+    GalaxyApi,
+    type HistoryContentsStats,
+    type HistoryDetailed,
+    type HistoryDevDetailed,
+    type HistorySummary,
+    type HistorySummaryExtended,
 } from "@/api";
-import { historyFetcher } from "@/api/histories";
-import { archiveHistory, unarchiveHistory } from "@/api/histories.archived";
+import { type ArchivedHistoryDetailed } from "@/api/histories.archived";
 import { HistoryFilters } from "@/components/History/HistoryFilters";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import {
-    cloneHistory,
     createAndSelectNewHistory,
-    deleteHistoryById,
     getCurrentHistoryFromServer,
     getHistoryByIdFromServer,
-    getHistoryCount,
     getHistoryList,
     secureHistoryOnServer,
     setCurrentHistoryOnServer,
@@ -98,9 +96,13 @@ export const useHistoryStore = defineStore("historyStore", () => {
     });
 
     async function setCurrentHistory(historyId: string) {
-        const currentHistory = (await setCurrentHistoryOnServer(historyId)) as HistoryDevDetailed;
-        selectHistory(currentHistory);
-        setFilterText(historyId, "");
+        try {
+            const currentHistory = (await setCurrentHistoryOnServer(historyId)) as HistoryDevDetailed;
+            selectHistory(currentHistory);
+            setFilterText(historyId, "");
+        } catch (error) {
+            rethrowSimple(error);
+        }
     }
 
     function setCurrentHistoryId(historyId: string) {
@@ -173,7 +175,21 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     async function copyHistory(history: HistorySummary, name: string, copyAll: boolean) {
-        const newHistory = (await cloneHistory(history, name, copyAll)) as HistorySummary;
+        const { data, error } = await GalaxyApi().POST("/api/histories", {
+            params: { query: { view: "detailed" } },
+            body: {
+                name,
+                all_datasets: copyAll,
+                history_id: history.id,
+                archive_type: undefined,
+            },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const newHistory = data as HistoryDetailed;
         await handleTotalCountChange(1);
         return setCurrentHistory(newHistory.id);
     }
@@ -190,19 +206,78 @@ export const useHistoryStore = defineStore("historyStore", () => {
         return filteredHistoryIds[0];
     }
 
-    async function deleteHistory(historyId: string, purge: boolean) {
-        const deletedHistory = (await deleteHistoryById(historyId, purge)) as HistorySummary;
-        const nextAvailableHistoryId = getNextAvailableHistoryId([deletedHistory.id]);
-        if (nextAvailableHistoryId) {
-            await setCurrentHistory(nextAvailableHistoryId);
-        } else {
-            await createNewHistory();
+    async function setNextAvailableHistoryId(excludedIds: string[]) {
+        if (currentHistoryId.value && excludedIds.includes(currentHistoryId.value)) {
+            const nextAvailableHistoryId = getNextAvailableHistoryId(excludedIds);
+            if (nextAvailableHistoryId) {
+                await setCurrentHistory(nextAvailableHistoryId);
+            } else {
+                await createNewHistory();
+            }
+        }
+    }
+
+    async function deleteHistory(historyId: string, purge = false) {
+        const { data, error } = await GalaxyApi().DELETE("/api/histories/{history_id}", {
+            params: { path: { history_id: historyId }, query: { purge } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
         }
+
+        const deletedHistory = data as AnyHistory;
+        await setNextAvailableHistoryId([deletedHistory.id]);
         del(storedHistories.value, deletedHistory.id);
-        unpinHistories([deletedHistory.id]);
         await handleTotalCountChange(1, true);
     }
 
+    async function deleteHistories(ids: string[], purge = false) {
+        const { data, error } = await GalaxyApi().PUT("/api/histories/batch/delete", {
+            body: { ids, purge },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const deletedHistories = data as AnyHistory[];
+        const historyIds = deletedHistories.map((history) => history.id);
+        await setNextAvailableHistoryId(historyIds);
+        deletedHistories.forEach((history) => {
+            del(storedHistories.value, history.id);
+        });
+        await handleTotalCountChange(deletedHistories.length, true);
+    }
+
+    async function restoreHistory(historyId: string) {
+        const { data, error } = await GalaxyApi().POST("/api/histories/deleted/{history_id}/undelete", {
+            params: { path: { history_id: historyId } },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const restoredHistory = data as AnyHistory;
+        await handleTotalCountChange(1);
+        setHistory(restoredHistory);
+    }
+
+    async function restoreHistories(ids: string[]) {
+        const { data, error } = await GalaxyApi().PUT("/api/histories/batch/undelete", {
+            body: { ids },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const restoredHistories = data as AnyHistory[];
+        await handleTotalCountChange(restoredHistories.length);
+        setHistories(restoredHistories);
+    }
+
     async function loadCurrentHistory(since?: string): Promise<HistoryDevDetailed | undefined> {
         try {
             const history = (await getCurrentHistoryFromServer(since)) as HistoryDevDetailed;
@@ -229,7 +304,13 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     async function loadTotalHistoryCount() {
-        totalHistoryCount.value = await getHistoryCount();
+        const { data, error } = await GalaxyApi().GET("/api/histories/count");
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        totalHistoryCount.value = data;
     }
 
     /** TODO:
@@ -288,11 +369,26 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     async function archiveHistoryById(historyId: string, archiveExportId?: string, purgeHistory = false) {
-        const history = await archiveHistory(historyId, archiveExportId, purgeHistory);
+        const { data, error } = await GalaxyApi().POST("/api/histories/{history_id}/archive", {
+            params: {
+                path: { history_id: historyId },
+            },
+            body: {
+                archive_export_id: archiveExportId,
+                purge_history: purgeHistory,
+            },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const history = data as ArchivedHistoryDetailed;
         setHistory(history);
         if (!history.archived) {
             return;
         }
+
         // If the current history is archived, we need to switch to another one as it is
         // no longer part of the active histories.
         const nextHistoryId = getNextAvailableHistoryId([historyId]);
@@ -304,7 +400,18 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     async function unarchiveHistoryById(historyId: string, force?: boolean) {
-        const history = await unarchiveHistory(historyId, force);
+        const { data, error } = await GalaxyApi().PUT("/api/histories/{history_id}/archive/restore", {
+            params: {
+                path: { history_id: historyId },
+                query: { force },
+            },
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const history = data as ArchivedHistoryDetailed;
         setHistory(history);
         return history;
     }
@@ -315,17 +422,20 @@ export const useHistoryStore = defineStore("historyStore", () => {
     }
 
     async function updateContentStats(historyId: string) {
-        try {
-            const { data } = await historyFetcher({
-                history_id: historyId,
-                keys: CONTENT_STATS_KEYS.join(","),
-            });
-            const contentStats = { id: historyId, ...data } as HistoryContentsStats;
-            setHistory(contentStats);
-            return contentStats;
-        } catch (error) {
+        const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+            params: {
+                path: { history_id: historyId },
+                query: { keys: CONTENT_STATS_KEYS.join(",") },
+            },
+        });
+
+        if (error) {
             rethrowSimple(error);
         }
+
+        const contentStats = { id: historyId, ...data } as HistoryContentsStats;
+        setHistory(contentStats);
+        return contentStats;
     }
 
     return {
@@ -334,6 +444,7 @@ export const useHistoryStore = defineStore("historyStore", () => {
         currentHistoryId,
         currentFilterText,
         pinnedHistories,
+        storedHistories,
         getHistoryById,
         getHistoryNameById,
         setCurrentHistory,
@@ -348,6 +459,10 @@ export const useHistoryStore = defineStore("historyStore", () => {
         copyHistory,
         createNewHistory,
         deleteHistory,
+        deleteHistories,
+        restoreHistory,
+        restoreHistories,
+        handleTotalCountChange,
         loadCurrentHistory,
         loadHistories,
         loadHistoryById,
diff --git a/client/src/stores/invocationStore.ts b/client/src/stores/invocationStore.ts
index ceac2109f4593b64c8b24d9954e5d0debae1432e..d212f8c6e6442e4d927a40fe94d1b2552b218185 100644
--- a/client/src/stores/invocationStore.ts
+++ b/client/src/stores/invocationStore.ts
@@ -1,24 +1,71 @@
 import { defineStore } from "pinia";
+import { ref } from "vue";
 
-import {
-    fetchInvocationDetails,
-    fetchInvocationJobsSummary,
-    fetchInvocationStep,
-    type WorkflowInvocation,
-    type WorkflowInvocationJobsSummary,
-    type WorkflowInvocationStep,
-} from "@/api/invocations";
-import { useKeyedCache } from "@/composables/keyedCache";
+import { GalaxyApi } from "@/api";
+import { type InvocationJobsSummary, type InvocationStep, type WorkflowInvocation } from "@/api/invocations";
+import { type FetchParams, useKeyedCache } from "@/composables/keyedCache";
+import type { GraphStep } from "@/composables/useInvocationGraph";
+import { rethrowSimple } from "@/utils/simple-error";
+
+type GraphSteps = { [index: string]: GraphStep };
 
 export const useInvocationStore = defineStore("invocationStore", () => {
-    const { getItemById: getInvocationById, fetchItemById: fetchInvocationForId } =
-        useKeyedCache<WorkflowInvocation>(fetchInvocationDetails);
+    const graphStepsByStoreId = ref<{ [index: string]: GraphSteps }>({});
+
+    async function fetchInvocationDetails(params: FetchParams): Promise<WorkflowInvocation> {
+        const { data, error } = await GalaxyApi().GET("/api/invocations/{invocation_id}", {
+            params: { path: { invocation_id: params.id } },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    async function fetchInvocationJobsSummary(params: FetchParams): Promise<InvocationJobsSummary> {
+        const { data, error } = await GalaxyApi().GET("/api/invocations/{invocation_id}/jobs_summary", {
+            params: { path: { invocation_id: params.id } },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    async function fetchInvocationStep(params: FetchParams): Promise<InvocationStep> {
+        const { data, error } = await GalaxyApi().GET("/api/invocations/steps/{step_id}", {
+            params: { path: { step_id: params.id } },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    async function cancelWorkflowScheduling(invocationId: string) {
+        const { data, error } = await GalaxyApi().DELETE("/api/invocations/{invocation_id}", {
+            params: {
+                path: { invocation_id: invocationId },
+            },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        storedInvocations.value[invocationId] = data;
+        return data;
+    }
+
+    const {
+        getItemById: getInvocationById,
+        fetchItemById: fetchInvocationForId,
+        storedItems: storedInvocations,
+    } = useKeyedCache<WorkflowInvocation>(fetchInvocationDetails);
 
     const { getItemById: getInvocationJobsSummaryById, fetchItemById: fetchInvocationJobsSummaryForId } =
-        useKeyedCache<WorkflowInvocationJobsSummary>(fetchInvocationJobsSummary);
+        useKeyedCache<InvocationJobsSummary>(fetchInvocationJobsSummary);
 
     const { getItemById: getInvocationStepById, fetchItemById: fetchInvocationStepById } =
-        useKeyedCache<WorkflowInvocationStep>(fetchInvocationStep);
+        useKeyedCache<InvocationStep>(fetchInvocationStep);
 
     return {
         getInvocationById,
@@ -27,5 +74,7 @@ export const useInvocationStore = defineStore("invocationStore", () => {
         fetchInvocationJobsSummaryForId,
         getInvocationStepById,
         fetchInvocationStepById,
+        cancelWorkflowScheduling,
+        graphStepsByStoreId,
     };
 });
diff --git a/client/src/stores/jobDestinationParametersStore.ts b/client/src/stores/jobDestinationParametersStore.ts
index eb4f48b214ea23a69f1ba35f2cea85f39d1b4bc2..3c6e0260f611c001e9da1088cd135edf4fd2873a 100644
--- a/client/src/stores/jobDestinationParametersStore.ts
+++ b/client/src/stores/jobDestinationParametersStore.ts
@@ -1,12 +1,24 @@
 import { defineStore } from "pinia";
 
-import { fetchJobDestinationParams, type JobDestinationParams } from "@/api/jobs";
-import { useKeyedCache } from "@/composables/keyedCache";
+import { GalaxyApi } from "@/api";
+import { type JobDestinationParams } from "@/api/jobs";
+import { type FetchParams, useKeyedCache } from "@/composables/keyedCache";
+import { rethrowSimple } from "@/utils/simple-error";
 
 export const useJobDestinationParametersStore = defineStore("jobDestinationParametersStore", () => {
-    const { storedItems, getItemById, isLoadingItem } = useKeyedCache<JobDestinationParams>((params) =>
-        fetchJobDestinationParams({ job_id: params.id })
-    );
+    async function fetchJobDestinationParams(params: FetchParams): Promise<JobDestinationParams> {
+        const { data, error } = await GalaxyApi().GET("/api/jobs/{job_id}/destination_params", {
+            params: {
+                path: { job_id: params.id },
+            },
+        });
+        if (error) {
+            rethrowSimple(error);
+        }
+        return data;
+    }
+
+    const { storedItems, getItemById, isLoadingItem } = useKeyedCache<JobDestinationParams>(fetchJobDestinationParams);
 
     return {
         storedJobDestinationParameters: storedItems,
diff --git a/client/src/stores/jobMetricsStore.ts b/client/src/stores/jobMetricsStore.ts
index e0979cba99d6ad91e56d11a06738d7ae67b60e5b..fe31aaed0dde7765cbb8192c4bfe648c1e5fa8bc 100644
--- a/client/src/stores/jobMetricsStore.ts
+++ b/client/src/stores/jobMetricsStore.ts
@@ -2,16 +2,9 @@ import axios from "axios";
 import { defineStore } from "pinia";
 import Vue, { computed, ref } from "vue";
 
+import type { JobMetric } from "@/api/jobs";
 import { prependPath } from "@/utils/redirect";
 
-interface JobMetric {
-    title: string;
-    value: string;
-    plugin: string;
-    name: string;
-    raw_value: string;
-}
-
 export const useJobMetricsStore = defineStore("jobMetricsStore", () => {
     const jobMetricsByHdaId = ref<Record<string, JobMetric[]>>({});
     const jobMetricsByLddaId = ref<Record<string, JobMetric[]>>({});
diff --git a/client/src/stores/notificationsStore.ts b/client/src/stores/notificationsStore.ts
index 0396d48b256f5e5b495fca5afc6ebf6094b470ee..0ba15fc88e7ab350268e923129f7c5aca7e2edc9 100644
--- a/client/src/stores/notificationsStore.ts
+++ b/client/src/stores/notificationsStore.ts
@@ -1,13 +1,14 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import type { NotificationChanges, UserNotification, UserNotificationsBatchUpdateRequest } from "@/api/notifications";
+import { GalaxyApi } from "@/api";
 import {
-    loadNotificationsFromServer,
-    loadNotificationsStatus,
-    updateBatchNotificationsOnServer,
+    type NotificationChanges,
+    type UserNotification,
+    type UserNotificationsBatchUpdateRequest,
 } from "@/api/notifications";
 import { useResourceWatcher } from "@/composables/resourceWatcher";
+import { rethrowSimple } from "@/utils/simple-error";
 import { mergeObjectListsById } from "@/utils/utils";
 
 import { useBroadcastsStore } from "./broadcastsStore";
@@ -31,8 +32,14 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
     const unreadNotifications = computed(() => notifications.value.filter((n) => !n.seen_time));
 
     async function loadNotifications() {
-        const data = await loadNotificationsFromServer();
-        notifications.value = mergeObjectListsById(data, [], "create_time", "desc");
+        const { data, error } = await GalaxyApi().GET("/api/notifications");
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
+        const useNotifications = data as UserNotification[]; // We are sure this cannot be a broadcast
+        notifications.value = mergeObjectListsById(useNotifications, [], "create_time", "desc");
     }
 
     async function getNotificationStatus() {
@@ -43,7 +50,18 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
                 await loadNotifications();
                 updateUnreadCount();
             } else {
-                const data = await loadNotificationsStatus(lastNotificationUpdate.value);
+                const { data, error } = await GalaxyApi().GET("/api/notifications/status", {
+                    params: {
+                        query: {
+                            since: lastNotificationUpdate.value.toISOString().replace("Z", ""),
+                        },
+                    },
+                });
+
+                if (error) {
+                    rethrowSimple(error);
+                }
+
                 totalUnreadCount.value = data.total_unread_count;
                 notifications.value = mergeObjectListsById(
                     notifications.value,
@@ -62,7 +80,14 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
     }
 
     async function updateBatchNotification(request: UserNotificationsBatchUpdateRequest) {
-        await updateBatchNotificationsOnServer(request);
+        const { error } = await GalaxyApi().PUT("/api/notifications", {
+            body: request,
+        });
+
+        if (error) {
+            rethrowSimple(error);
+        }
+
         if (request.changes.deleted) {
             notifications.value = notifications.value.filter((n) => !request.notification_ids.includes(n.id));
         }
diff --git a/client/src/stores/objectStoreInstancesStore.ts b/client/src/stores/objectStoreInstancesStore.ts
index e825c9c63e8611ae363cda21cb7ab21ffbd1c7b8..32bd76f13bbe87b64e806c2db7124fa52824a034 100644
--- a/client/src/stores/objectStoreInstancesStore.ts
+++ b/client/src/stores/objectStoreInstancesStore.ts
@@ -1,11 +1,8 @@
 import { defineStore } from "pinia";
 
-import { fetcher } from "@/api/schema/fetcher";
-import type { components } from "@/api/schema/schema";
+import { type components, GalaxyApi } from "@/api";
 import { errorMessageAsString } from "@/utils/simple-error";
 
-const getObjectStoreInstances = fetcher.path("/api/object_store_instances").method("get").create();
-
 type UserConcreteObjectStoreModel = components["schemas"]["UserConcreteObjectStoreModel"];
 
 export const useObjectStoreInstancesStore = defineStore("objectStoreInstances", {
@@ -35,12 +32,14 @@ export const useObjectStoreInstancesStore = defineStore("objectStoreInstances",
             this.error = errorMessageAsString(err);
         },
         async fetchInstances() {
-            try {
-                const { data: instances } = await getObjectStoreInstances({});
-                this.handleInit(instances);
-            } catch (err) {
-                this.handleError(err);
+            const { data: instances, error } = await GalaxyApi().GET("/api/object_store_instances");
+
+            if (error) {
+                this.handleError(error);
+                return;
             }
+
+            this.handleInit(instances);
         },
         async ensureTemplates() {
             if (!this.fetched || this.error != null) {
diff --git a/client/src/stores/objectStoreStore.ts b/client/src/stores/objectStoreStore.ts
index 09f9657667c9842be7434cec8128a72ffbfa3cba..cb58bf6cfeb59868976f6fef8235ca8b06a8f50a 100644
--- a/client/src/stores/objectStoreStore.ts
+++ b/client/src/stores/objectStoreStore.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import { ConcreteObjectStoreModel } from "@/api";
+import { type ConcreteObjectStoreModel } from "@/api";
 import { getSelectableObjectStores } from "@/api/objectStores";
 import { errorMessageAsString } from "@/utils/simple-error";
 
diff --git a/client/src/stores/objectStoreTemplatesStore.test.ts b/client/src/stores/objectStoreTemplatesStore.test.ts
index 214e83fd6b7b1444d3bda35ad1c7d22f570a6bc3..3fa941f4ad1723053ffa72d0b128518edee457c0 100644
--- a/client/src/stores/objectStoreTemplatesStore.test.ts
+++ b/client/src/stores/objectStoreTemplatesStore.test.ts
@@ -1,10 +1,11 @@
 import { type ObjectStoreTemplateType } from "@/api/objectStores";
+import { type ObjectStoreTemplateSummaries } from "@/api/objectStores.templates";
 import { useObjectStoreTemplatesStore } from "@/stores/objectStoreTemplatesStore";
 
 import { setupTestPinia } from "./testUtils";
 
 const s3 = "aws_s3" as ObjectStoreTemplateType;
-const TEMPLATES_BASIC = [
+const TEMPLATES_BASIC: ObjectStoreTemplateSummaries = [
     {
         type: s3,
         name: "moo",
@@ -14,10 +15,11 @@ const TEMPLATES_BASIC = [
         id: "moo",
         version: 0,
         badges: [],
+        hidden: false,
     },
 ];
 
-const TEMPLATES_EXPANDED = [
+const TEMPLATES_EXPANDED: ObjectStoreTemplateSummaries = [
     {
         type: s3,
         name: "Testing S3",
@@ -27,6 +29,7 @@ const TEMPLATES_EXPANDED = [
         id: "bucket_s3",
         version: 0,
         badges: [],
+        hidden: false,
     },
     {
         type: s3,
@@ -37,6 +40,7 @@ const TEMPLATES_EXPANDED = [
         id: "bucket_s3",
         version: 1,
         badges: [],
+        hidden: false,
     },
     {
         type: s3,
@@ -47,6 +51,7 @@ const TEMPLATES_EXPANDED = [
         id: "bucket_s3",
         version: 2,
         badges: [],
+        hidden: false,
     },
 ];
 
diff --git a/client/src/stores/objectStoreTemplatesStore.ts b/client/src/stores/objectStoreTemplatesStore.ts
index 4b9c852d494f47546b65dce7ba20020180612ad2..677ce9d1a0e077fa0be0515b038ec499d33901b9 100644
--- a/client/src/stores/objectStoreTemplatesStore.ts
+++ b/client/src/stores/objectStoreTemplatesStore.ts
@@ -1,16 +1,11 @@
 import { defineStore } from "pinia";
 
-import { fetcher } from "@/api/schema/fetcher";
-import type { components } from "@/api/schema/schema";
+import { GalaxyApi } from "@/api";
+import { type ObjectStoreTemplateSummaries, type ObjectStoreTemplateSummary } from "@/api/objectStores.templates";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { canUpgrade, findTemplate, getLatestVersion, getLatestVersionMap } from "./configTemplatesUtil";
 
-const getObjectStoreTemplates = fetcher.path("/api/object_store_templates").method("get").create();
-
-type ObjectStoreTemplateSummary = components["schemas"]["ObjectStoreTemplateSummary"];
-type ObjectStoreTemplateSummaries = ObjectStoreTemplateSummary[];
-
 export const useObjectStoreTemplatesStore = defineStore("objectStoreTemplatesStore", {
     state: () => ({
         templates: [] as ObjectStoreTemplateSummaries,
@@ -54,12 +49,14 @@ export const useObjectStoreTemplatesStore = defineStore("objectStoreTemplatesSto
             this.error = errorMessageAsString(err);
         },
         async fetchTemplates() {
-            try {
-                const { data: templates } = await getObjectStoreTemplates({});
-                this.handleInit(templates);
-            } catch (err) {
-                this.handleError(err);
+            const { data: templates, error } = await GalaxyApi().GET("/api/object_store_templates");
+
+            if (error) {
+                this.handleError(error);
+                return;
             }
+
+            this.handleInit(templates);
         },
         async ensureTemplates() {
             if (!this.fetched || this.error != null) {
diff --git a/client/src/stores/services/history.services.js b/client/src/stores/services/history.services.js
deleted file mode 100644
index 6f095015d0ae46ff83b14b9fe82dffb3b61341c9..0000000000000000000000000000000000000000
--- a/client/src/stores/services/history.services.js
+++ /dev/null
@@ -1,177 +0,0 @@
-import axios from "axios";
-import { prependPath } from "utils/redirect";
-
-/**
- * Generic json getter
- * @param {*} response
- * @return {Object} response.data or throws an error if response status is not 200
- */
-function doResponse(response) {
-    if (response.status !== 200) {
-        throw new Error(response);
-    }
-    return response.data;
-}
-
-/**
- * Some current endpoints don't accept JSON, so we need to
- * do some massaging to send in old form post data.
- * @param {Object} fields
- */
-function formData(fields = {}) {
-    return Object.keys(fields).reduce((result, fieldName) => {
-        result.set(fieldName, fields[fieldName]);
-        return result;
-    }, new FormData());
-}
-
-/**
- * Default history request parameters.
- */
-const stdHistoryParams = {
-    view: "summary",
-};
-
-/**
- * Extended history request parameters.
- * Retrieves additional details which are usually more "expensive".
- */
-const extendedHistoryParams = {
-    view: "summary",
-    keys: "size,contents_active,user_id",
-};
-
-/**
- * Create a new history, select it as the current history, and return it if successful.
- * @return {Object} the new history or throws an error if new history creation fails
- */
-export async function createAndSelectNewHistory() {
-    const url = "history/create_new_current";
-    const response = await axios.get(prependPath(url));
-    const newHistoryId = response?.data?.id || null;
-    if (!newHistoryId) {
-        throw new Error("failed to create and select new history");
-    }
-    return doResponse(response);
-}
-
-/**
- * Generates copy of history on server.
- * @param {Object} history Source history
- * @param {String} name New history name
- * @param {Boolean} copyAll Copy existing contents
- */
-export async function cloneHistory(history, name, copyAll) {
-    const url = "api/histories";
-    const payload = {
-        name,
-        current: true,
-        all_datasets: copyAll,
-        history_id: history.id,
-    };
-    const response = await axios.post(prependPath(url), payload, { params: stdHistoryParams });
-    return doResponse(response);
-}
-
-/**
- * Delete history on server and return the deleted history.
- * @param {String} id Encoded history id
- * @param {Boolean} [purge=false] Permanent delete
- */
-export async function deleteHistoryById(id, purge = false) {
-    const url = `api/histories/${id}` + (purge ? "?purge=True" : "");
-    const response = await axios.delete(prependPath(url), { params: stdHistoryParams });
-    return doResponse(response);
-}
-
-/**
- * Get current history from server and return it.
- * @param {String} since timestamp to get histories since
- * @return {Object} the current history
- */
-export async function getCurrentHistoryFromServer(since = undefined) {
-    const url = "history/current_history_json";
-    const response = await axios.get(prependPath(url), { params: { since: since } });
-    return doResponse(response);
-}
-
-/**
- * Set current history on server and return it.
- * @param {String} historyId Encoded history id
- * @return {Object} the current history
- */
-export async function setCurrentHistoryOnServer(historyId) {
-    const url = "history/set_as_current";
-    const response = await axios.get(prependPath(url), { params: { id: historyId } });
-    return doResponse(response);
-}
-
-/**
- * Get list of histories from server and return them.
- * @param {Number} offset to start from (default = 0)
- * @param {Number | null} limit of histories to load (default = null; in which case no limit)
- * @param {String} queryString to append to url in the form `q=filter&qv=val&q=...`
- * @return {Promise.<Array>} list of histories
- */
-export async function getHistoryList(offset = 0, limit = null, queryString = "") {
-    const params = `view=summary&order=update_time&offset=${offset}`;
-    let url = `api/histories?${params}`;
-    if (limit !== null) {
-        url += `&limit=${limit}`;
-    }
-    if (queryString !== "") {
-        url += `&${queryString}`;
-    }
-    const response = await axios.get(prependPath(url));
-    return doResponse(response);
-}
-
-/**
- * Get number of histories for current user from server and return them.
- * @return {Promise.<Number>} number of histories
- */
-export async function getHistoryCount() {
-    // This url is temp. for this PR, waiting on:
-    // https://github.com/galaxyproject/galaxy/pull/16075
-    const url = "api/histories/count";
-    const response = await axios.get(prependPath(url));
-    return doResponse(response);
-}
-
-/**
- * Load one history by id
- * @param {String} id
- */
-export async function getHistoryByIdFromServer(id) {
-    const path = `api/histories/${id}`;
-    const response = await axios.get(prependPath(path), { params: extendedHistoryParams });
-    return doResponse(response);
-}
-
-/**
- * Set permissions to private for indicated history
- * TODO: rewrite API endpoint for this
- * @param {Object} history the history to secure
- * @return {Object} the secured history
- */
-export async function secureHistoryOnServer(history) {
-    const { id } = history;
-    const url = "history/make_private";
-    const response = await axios.post(prependPath(url), formData({ history_id: id }));
-    if (response.status !== 200) {
-        throw new Error(response.statusText);
-    }
-    return await getHistoryByIdFromServer(id);
-}
-
-/**
- * Update specific fields in history
- * @param {Object} historyId the history id to update
- * @param {Object} payload fields to update
- * @return {Object} the updated history
- */
-export async function updateHistoryFields(historyId, payload) {
-    const url = `api/histories/${historyId}`;
-    const response = await axios.put(prependPath(url), payload, { params: extendedHistoryParams });
-    return doResponse(response);
-}
diff --git a/client/src/stores/services/history.services.ts b/client/src/stores/services/history.services.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cb880fa21cd650bdf7a6c9987f31c0c7853c28ba
--- /dev/null
+++ b/client/src/stores/services/history.services.ts
@@ -0,0 +1,155 @@
+import axios, { type AxiosResponse } from "axios";
+
+import type { AnyHistory, HistorySummaryExtended } from "@/api";
+import { GalaxyApi } from "@/api";
+import { prependPath } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
+
+/**
+ * Generic json getter
+ * @param response
+ * @return response.data or throws an error if response status is not 200
+ */
+function doResponse(response: AxiosResponse) {
+    if (response.status !== 200) {
+        throw new Error(response.statusText);
+    }
+    return response.data;
+}
+
+/**
+ * Some current endpoints don't accept JSON, so we need to
+ * do some massaging to send in old form post data.
+ */
+function formData(fields = {} as Record<string, any>) {
+    return Object.keys(fields).reduce((result, fieldName) => {
+        result.set(fieldName, fields[fieldName]);
+        return result;
+    }, new FormData());
+}
+
+/**
+ * Extended history request parameters.
+ * Retrieves additional details which are usually more "expensive".
+ */
+const extendedHistoryParams = {
+    view: "summary",
+    keys: "size,contents_active,user_id",
+};
+
+/**
+ * Create a new history, select it as the current history, and return it if successful.
+ * @return the new history or throws an error if new history creation fails
+ */
+export async function createAndSelectNewHistory() {
+    const url = "history/create_new_current";
+    const response = await axios.get(prependPath(url));
+    const newHistoryId = response?.data?.id || null;
+    if (!newHistoryId) {
+        throw new Error("failed to create and select new history");
+    }
+    return doResponse(response);
+}
+
+/**
+ * Get current history from server and return it.
+ * @param since timestamp to get histories since
+ * @return the current history
+ */
+export async function getCurrentHistoryFromServer(since: string | undefined = undefined) {
+    const url = "history/current_history_json";
+    const response = await axios.get(prependPath(url), { params: { since: since } });
+    return doResponse(response);
+}
+
+/**
+ * Set current history on server and return it.
+ * @param historyId Encoded history id
+ * @return the current history
+ */
+export async function setCurrentHistoryOnServer(historyId: string) {
+    const url = "history/set_as_current";
+    const response = await axios.get(prependPath(url), { params: { id: historyId } });
+    return doResponse(response);
+}
+
+/**
+ * Get list of histories from server and return them.
+ * @param offset to start from (default = 0)
+ * @param limit of histories to load (default = null; in which case no limit)
+ * @param queryString to append to url in the form `q=filter&qv=val&q=...`
+ * @return list of histories
+ */
+export async function getHistoryList(offset = 0, limit: number | null = null, queryString = "") {
+    // TODO: to convert this to openapi-fetch we need to fix the query string handling
+    // in the caller code to use the query object instead of a string
+
+    const params = `view=summary&order=update_time&offset=${offset}`;
+    let url = `api/histories?${params}`;
+    if (limit !== null) {
+        url += `&limit=${limit}`;
+    }
+    if (queryString !== "") {
+        url += `&${queryString}`;
+    }
+    const response = await axios.get(prependPath(url));
+    return doResponse(response);
+}
+
+/** Load one history by id */
+export async function getHistoryByIdFromServer(id: string) {
+    const { data, error } = await GalaxyApi().GET("/api/histories/{history_id}", {
+        params: {
+            path: { history_id: id },
+            query: extendedHistoryParams,
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    // We know that the data is a HistorySummaryExtended because we requested it
+    // with the extendedHistoryParams
+    return data as HistorySummaryExtended;
+}
+
+/**
+ * Set permissions to private for indicated history
+ * TODO: rewrite API endpoint for this
+ * @param history the history to secure
+ * @return the secured history
+ */
+export async function secureHistoryOnServer(history: AnyHistory) {
+    const { id } = history;
+    const url = "history/make_private";
+    const response = await axios.post(prependPath(url), formData({ history_id: id }));
+    if (response.status !== 200) {
+        throw new Error(response.statusText);
+    }
+    return await getHistoryByIdFromServer(id);
+}
+
+/**
+ * Update specific fields in history
+ * @param historyId the history id to update
+ * @param payload fields to update
+ * @return the updated history
+ */
+export async function updateHistoryFields(historyId: string, payload: Record<string, any>) {
+    const { data, error } = await GalaxyApi().PUT("/api/histories/{history_id}", {
+        params: {
+            path: { history_id: historyId },
+            query: extendedHistoryParams,
+        },
+        body: payload,
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+
+    // We know that the data is a HistorySummaryExtended because we requested it
+    // with the extendedHistoryParams
+    return data as HistorySummaryExtended;
+}
diff --git a/client/src/stores/toolStore.ts b/client/src/stores/toolStore.ts
index c653a0bdac6482bb06abe131e47fe550da5a5d69..a7214b1aabe13266dd28948347df87f0f18e572f 100644
--- a/client/src/stores/toolStore.ts
+++ b/client/src/stores/toolStore.ts
@@ -4,9 +4,9 @@
 
 import axios from "axios";
 import { defineStore } from "pinia";
-import Vue, { computed, Ref, ref, shallowRef } from "vue";
+import Vue, { computed, type Ref, ref, shallowRef } from "vue";
 
-import { createWhooshQuery, filterTools, types_to_icons } from "@/components/Panels/utilities";
+import { createWhooshQuery, filterTools, type types_to_icons } from "@/components/Panels/utilities";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { getAppRoot } from "@/onload/loadConfig";
 import { rethrowSimple } from "@/utils/simple-error";
@@ -158,6 +158,7 @@ export const useToolStore = defineStore("toolStore", () => {
     }
 
     async function fetchTools(filterSettings?: FilterSettings) {
+        // This is if we are performing a backend search
         if (filterSettings && Object.keys(filterSettings).length !== 0) {
             // Parsing filterSettings to Whoosh query
             const q = createWhooshQuery(filterSettings);
@@ -165,21 +166,25 @@ export const useToolStore = defineStore("toolStore", () => {
             if (toolResults.value[q]) {
                 return;
             }
-            const { data } = await axios.get(`${getAppRoot()}api/tools`, { params: { q } });
-            saveToolResults(q, data);
+            try {
+                const { data } = await axios.get(`${getAppRoot()}api/tools`, { params: { q } });
+                saveToolResults(q, data);
+            } catch (e) {
+                rethrowSimple(e);
+            }
         }
+
+        // This is if we are fetching all tools by ids
         if (!loading.value && !allToolsByIdFetched.value) {
             loading.value = true;
-            await axios
-                .get(`${getAppRoot()}api/tools?in_panel=False`)
-                .then(({ data }) => {
-                    saveAllTools(data as Tool[]);
-                    loading.value = false;
-                })
-                .catch((error) => {
-                    console.error(error);
-                    loading.value = false;
-                });
+            try {
+                const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=False`);
+                saveAllTools(data as Tool[]);
+            } catch (e) {
+                rethrowSimple(e);
+            } finally {
+                loading.value = false;
+            }
         }
     }
 
@@ -204,23 +209,24 @@ export const useToolStore = defineStore("toolStore", () => {
     async function initCurrentPanelView(siteDefaultPanelView: string) {
         if (!loading.value && !isPanelPopulated.value) {
             loading.value = true;
-            const panelView = currentPanelView.value || siteDefaultPanelView;
-            if (currentPanelView.value == "") {
-                currentPanelView.value = panelView;
+            currentPanelView.value = currentPanelView.value || siteDefaultPanelView;
+            try {
+                if (!currentPanelView.value) {
+                    throw new Error("No valid panel view found.");
+                }
+                const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${currentPanelView.value}`);
+                savePanelView(currentPanelView.value, data);
+                loading.value = false;
+            } catch (e) {
+                loading.value = false;
+
+                if (currentPanelView.value !== siteDefaultPanelView) {
+                    // If the stored panelView failed to load, try the default panel for this site.
+                    await setCurrentPanelView(siteDefaultPanelView);
+                } else {
+                    rethrowSimple(e);
+                }
             }
-            await axios
-                .get(`${getAppRoot()}api/tool_panels/${panelView}`)
-                .then(({ data }) => {
-                    loading.value = false;
-                    savePanelView(panelView, data);
-                })
-                .catch(async (error) => {
-                    loading.value = false;
-                    if (error.response && error.response.status == 400) {
-                        // Assume the stored panelView disappeared, revert to the panel default for this site.
-                        await setCurrentPanelView(siteDefaultPanelView);
-                    }
-                });
         }
     }
 
@@ -235,18 +241,21 @@ export const useToolStore = defineStore("toolStore", () => {
                 const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${panelView}`);
                 currentPanelView.value = panelView;
                 savePanelView(panelView, data);
-                loading.value = false;
             } catch (e) {
-                const error = e as { response: { data: { err_msg: string } } };
-                console.error("Could not change panel view", error.response.data.err_msg ?? error.response);
+                rethrowSimple(e);
+            } finally {
                 loading.value = false;
             }
         }
     }
 
     async function fetchPanel(panelView: string) {
-        const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${panelView}`);
-        savePanelView(panelView, data);
+        try {
+            const { data } = await axios.get(`${getAppRoot()}api/tool_panels/${panelView}`);
+            savePanelView(panelView, data);
+        } catch (e) {
+            rethrowSimple(e);
+        }
     }
 
     function saveToolForId(toolId: string, toolData: Tool) {
diff --git a/client/src/stores/undoRedoStore/index.ts b/client/src/stores/undoRedoStore/index.ts
index aee67a9e04b3cc88e8ba4557b990958b924df467..f83dd6f6d103c1b8118014b79369015343fbcab7 100644
--- a/client/src/stores/undoRedoStore/index.ts
+++ b/client/src/stores/undoRedoStore/index.ts
@@ -1,21 +1,43 @@
 import { computed, ref } from "vue";
 
+import { useClamp, useStep } from "@/composables/math";
+import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { defineScopedStore } from "@/stores/scopedStore";
 
-import { LazyUndoRedoAction, UndoRedoAction } from "./undoRedoAction";
+import { type LazyUndoRedoAction, UndoRedoAction } from "./undoRedoAction";
 
 export { LazyUndoRedoAction, UndoRedoAction } from "./undoRedoAction";
 
 export type UndoRedoStore = ReturnType<typeof useUndoRedoStore>;
 
+export class ActionOutOfBoundsError extends Error {
+    public action: UndoRedoAction;
+
+    constructor(action: UndoRedoAction, bounds: "undo" | "redo") {
+        super(`The action "${action.name}" is not in the ${bounds} stack`);
+        this.action = action;
+    }
+}
+
 export const useUndoRedoStore = defineScopedStore("undoRedoStore", () => {
     const undoActionStack = ref<UndoRedoAction[]>([]);
     const redoActionStack = ref<UndoRedoAction[]>([]);
-    const maxUndoActions = ref(100);
+
+    const minUndoActions = ref(10);
+    const maxUndoActions = ref(10000);
+
+    const savedUndoActionsValue = useUserLocalStorage(`undoRedoStore-savedUndoActions`, 100);
+    const savedUndoActions = useClamp(useStep(savedUndoActionsValue), minUndoActions, maxUndoActions);
+
+    /** names of actions which were deleted due to savedUndoActions being exceeded */
+    const deletedActions = ref<string[]>([]);
 
     function $reset() {
         undoActionStack.value.forEach((action) => action.destroy());
         undoActionStack.value = [];
+        deletedActions.value = [];
+        minUndoActions.value = 10;
+        maxUndoActions.value = 10000;
         clearRedoStack();
     }
 
@@ -44,8 +66,9 @@ export const useUndoRedoStore = defineScopedStore("undoRedoStore", () => {
         clearRedoStack();
         undoActionStack.value.push(action);
 
-        while (undoActionStack.value.length > maxUndoActions.value && undoActionStack.value.length > 0) {
+        while (undoActionStack.value.length > savedUndoActions.value && undoActionStack.value.length > 0) {
             const action = undoActionStack.value.shift();
+            deletedActions.value.push(action?.name ?? "unnamed action");
             action?.destroy();
         }
     }
@@ -141,10 +164,39 @@ export const useUndoRedoStore = defineScopedStore("undoRedoStore", () => {
         }
     });
 
+    function rollBackTo(action: UndoRedoAction) {
+        flushLazyAction();
+        const undoSet = new Set(undoActionStack.value);
+
+        if (!undoSet.has(action)) {
+            throw new ActionOutOfBoundsError(action, "undo");
+        }
+
+        while (nextRedoAction.value !== action) {
+            undo();
+        }
+    }
+
+    function rollForwardTo(action: UndoRedoAction) {
+        flushLazyAction();
+        const redoSet = new Set(redoActionStack.value);
+
+        if (!redoSet.has(action)) {
+            throw new ActionOutOfBoundsError(action, "redo");
+        }
+
+        while (nextUndoAction.value !== action) {
+            redo();
+        }
+    }
+
     return {
         undoActionStack,
         redoActionStack,
+        minUndoActions,
         maxUndoActions,
+        savedUndoActions,
+        deletedActions,
         undo,
         redo,
         applyAction,
@@ -162,6 +214,8 @@ export const useUndoRedoStore = defineScopedStore("undoRedoStore", () => {
         hasUndo,
         hasRedo,
         $reset,
+        rollBackTo,
+        rollForwardTo,
     };
 });
 
diff --git a/client/src/stores/undoRedoStore/undoRedoAction.ts b/client/src/stores/undoRedoStore/undoRedoAction.ts
index 63a54f5e4ff4775d053501639912137410d291c5..88a42a5a0971ac786f50f969b9d3185e67ef73b8 100644
--- a/client/src/stores/undoRedoStore/undoRedoAction.ts
+++ b/client/src/stores/undoRedoStore/undoRedoAction.ts
@@ -1,5 +1,12 @@
+let idCounter = 0;
+
 export class UndoRedoAction {
     protected internalName?: string;
+    public id: number;
+
+    constructor() {
+        this.id = idCounter++;
+    }
 
     get name(): string | undefined {
         return this.internalName;
diff --git a/client/src/stores/userStore.ts b/client/src/stores/userStore.ts
index 0eb44ca2ab2fca9d7d14d68ef6cc34452685cc55..ae7c0051c3dc4297516bed5ef822f7626ef5c28f 100644
--- a/client/src/stores/userStore.ts
+++ b/client/src/stores/userStore.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia";
 import { computed, ref } from "vue";
 
-import type { AnonymousUser, User } from "@/api";
+import { type AnyUser, isAdminUser, isAnonymousUser, isRegisteredUser, type RegisteredUser } from "@/api";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 import { useHistoryStore } from "@/stores/historyStore";
 import {
@@ -11,20 +11,24 @@ import {
     setCurrentThemeQuery,
 } from "@/stores/users/queries";
 
+interface FavoriteTools {
+    tools: string[];
+}
+
 interface Preferences {
-    theme: string;
-    favorites: { tools: string[] };
+    theme?: string;
+    favorites: FavoriteTools;
+    [key: string]: unknown;
 }
 
 type ListViewMode = "grid" | "list";
 
 export const useUserStore = defineStore("userStore", () => {
-    const currentUser = ref<User | AnonymousUser | null>(null);
+    const currentUser = ref<AnyUser>(null);
     const currentPreferences = ref<Preferences | null>(null);
 
-    // explicitly pass current User, because userStore might not exist yet
-    const toggledSideBar = useUserLocalStorage("user-store-toggled-side-bar", "tools", currentUser);
     const preferredListViewMode = useUserLocalStorage("user-store-preferred-list-view-mode", "grid", currentUser);
+    const hasSeenUploadHelp = useUserLocalStorage("user-store-seen-upload-help", false, currentUser);
 
     let loadPromise: Promise<void> | null = null;
 
@@ -35,11 +39,11 @@ export const useUserStore = defineStore("userStore", () => {
     }
 
     const isAdmin = computed(() => {
-        return currentUser.value?.is_admin ?? false;
+        return isAdminUser(currentUser.value);
     });
 
     const isAnonymous = computed(() => {
-        return !("email" in (currentUser.value || []));
+        return isAnonymousUser(currentUser.value);
     });
 
     const currentTheme = computed(() => {
@@ -54,33 +58,48 @@ export const useUserStore = defineStore("userStore", () => {
         }
     });
 
-    function setCurrentUser(user: User) {
+    const matchesCurrentUsername = computed(() => {
+        return (username?: string) => {
+            return isRegisteredUser(currentUser.value) && currentUser.value.username === username;
+        };
+    });
+
+    function setCurrentUser(user: RegisteredUser) {
         currentUser.value = user;
     }
 
     function loadUser(includeHistories = true) {
         if (!loadPromise) {
-            loadPromise = getCurrentUser()
-                .then(async (user) => {
-                    currentUser.value = { ...user, isAnonymous: !user.email };
-                    currentPreferences.value = user?.preferences ?? null;
-                    // TODO: This is a hack to get around the fact that the API returns a string
-                    if (currentPreferences.value?.favorites) {
-                        currentPreferences.value.favorites = JSON.parse(user?.preferences?.favorites ?? { tools: [] });
-                    }
-                    if (includeHistories) {
-                        const historyStore = useHistoryStore();
-                        // load first few histories for user to start pagination
-                        await historyStore.loadHistories();
+            loadPromise = new Promise<void>((resolve, reject) => {
+                (async () => {
+                    try {
+                        const user = await getCurrentUser();
+
+                        if (isRegisteredUser(user)) {
+                            currentUser.value = user;
+                            currentPreferences.value = processUserPreferences(user);
+                        } else if (isAnonymousUser(user)) {
+                            currentUser.value = user;
+                        } else if (user === null) {
+                            currentUser.value = null;
+                        }
+                        if (includeHistories) {
+                            const historyStore = useHistoryStore();
+                            await historyStore.loadHistories();
+                        }
+                        resolve(); // Resolve the promise after successful load
+                    } catch (e) {
+                        console.error("Failed to load user", e);
+                        reject(e); // Reject the promise on error
+                    } finally {
+                        //Don't clear the loadPromise, we still want multiple callers to await.
+                        //Instead we must clear it upon $reset
+                        // loadPromise = null;
                     }
-                })
-                .catch((e) => {
-                    console.error("Failed to load user", e);
-                })
-                .finally(() => {
-                    loadPromise = null;
-                });
+                })();
+            });
         }
+        return loadPromise; // Return the shared promise
     }
 
     async function setCurrentTheme(theme: string) {
@@ -110,7 +129,7 @@ export const useUserStore = defineStore("userStore", () => {
 
     function setFavoriteTools(tools: string[]) {
         if (currentPreferences.value) {
-            currentPreferences.value.favorites.tools = tools ?? { tools: [] };
+            currentPreferences.value.favorites.tools = tools;
         }
     }
 
@@ -118,8 +137,14 @@ export const useUserStore = defineStore("userStore", () => {
         preferredListViewMode.value = view;
     }
 
-    function toggleSideBar(currentOpen = "") {
-        toggledSideBar.value = toggledSideBar.value === currentOpen ? "" : currentOpen;
+    function processUserPreferences(user: RegisteredUser): Preferences {
+        // Favorites are returned as a JSON string by the API
+        const favorites =
+            typeof user.preferences.favorites === "string" ? JSON.parse(user.preferences.favorites) : { tools: [] };
+        return {
+            ...user.preferences,
+            favorites,
+        };
     }
 
     return {
@@ -129,15 +154,15 @@ export const useUserStore = defineStore("userStore", () => {
         isAnonymous,
         currentTheme,
         currentFavorites,
-        toggledSideBar,
         preferredListViewMode,
+        hasSeenUploadHelp,
         loadUser,
+        matchesCurrentUsername,
         setCurrentUser,
         setCurrentTheme,
         setPreferredListViewMode,
         addFavoriteTool,
         removeFavoriteTool,
-        toggleSideBar,
         $reset,
     };
 });
diff --git a/client/src/stores/users/queries.ts b/client/src/stores/users/queries.ts
index 693bb36b5790e9196f45cb6a5645603006d0613a..5cce609264005fdfe752e48b65880a11c5212452 100644
--- a/client/src/stores/users/queries.ts
+++ b/client/src/stores/users/queries.ts
@@ -1,43 +1,56 @@
-import axios from "axios";
-
-import { prependPath } from "@/utils/redirect";
+import { GalaxyApi } from "@/api";
 import { rethrowSimple } from "@/utils/simple-error";
 
 export async function getCurrentUser() {
-    const url = prependPath("/api/users/current");
-    const response = await axios.get(url);
-    if (response.status != 200) {
-        throw new Error("Failed to get current user");
+    const { data, error } = await GalaxyApi().GET("/api/users/{user_id}", {
+        params: { path: { user_id: "current" } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
-    return response.data;
+    return data;
 }
 
 export async function addFavoriteToolQuery(userId: string, toolId: string) {
-    const url = prependPath(`/api/users/${userId}/favorites/tools`);
-    try {
-        const { data } = await axios.put(url, { object_id: toolId });
-        return data["tools"];
-    } catch (e) {
-        rethrowSimple(e);
+    const { data, error } = await GalaxyApi().PUT("/api/users/{user_id}/favorites/{object_type}", {
+        params: { path: { user_id: userId, object_type: "tools" } },
+        body: { object_id: toolId },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
+
+    return data.tools;
 }
 
 export async function removeFavoriteToolQuery(userId: string, toolId: string) {
-    const url = prependPath(`/api/users/${userId}/favorites/tools/${encodeURIComponent(toolId)}`);
-    try {
-        const { data } = await axios.delete(url);
-        return data["tools"];
-    } catch (e) {
-        rethrowSimple(e);
+    const { data, error } = await GalaxyApi().DELETE("/api/users/{user_id}/favorites/{object_type}/{object_id}", {
+        params: {
+            path: {
+                user_id: userId,
+                object_type: "tools",
+                object_id: toolId,
+            },
+        },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
+
+    return data.tools;
 }
 
 export async function setCurrentThemeQuery(userId: string, theme: string) {
-    const url = prependPath(`/api/users/${userId}/theme/${theme}`);
-    try {
-        const { data } = await axios.put(url, { theme: theme });
-        return data;
-    } catch (e) {
-        rethrowSimple(e);
+    const { data, error } = await GalaxyApi().PUT("/api/users/{user_id}/theme/{theme}", {
+        params: { path: { user_id: userId, theme } },
+    });
+
+    if (error) {
+        rethrowSimple(error);
     }
+
+    return data;
 }
diff --git a/client/src/stores/workflowConnectionStore.test.ts b/client/src/stores/workflowConnectionStore.test.ts
index e1d14da9614806744127de85de91cffcf2d8d9e4..d2c40b72b4a2012de3af3b41702fceaca5c20dfd 100644
--- a/client/src/stores/workflowConnectionStore.test.ts
+++ b/client/src/stores/workflowConnectionStore.test.ts
@@ -1,9 +1,13 @@
 import { createPinia, setActivePinia } from "pinia";
 
-import type { Connection, InputTerminal, OutputTerminal } from "@/stores/workflowConnectionStore";
-import { getTerminalId, useConnectionStore } from "@/stores/workflowConnectionStore";
-import type { NewStep } from "@/stores/workflowStepStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import {
+    type Connection,
+    getTerminalId,
+    type InputTerminal,
+    type OutputTerminal,
+    useConnectionStore,
+} from "@/stores/workflowConnectionStore";
+import { type NewStep, useWorkflowStepStore } from "@/stores/workflowStepStore";
 
 const workflowStepZero: NewStep = {
     input_connections: {},
diff --git a/client/src/stores/workflowEditorCommentStore.test.ts b/client/src/stores/workflowEditorCommentStore.test.ts
index 6a0ba21b927e63082a72df2c867dc59dd7e84b60..e3e3d2e7d1c99399692d7ccd935645609a5f9280 100644
--- a/client/src/stores/workflowEditorCommentStore.test.ts
+++ b/client/src/stores/workflowEditorCommentStore.test.ts
@@ -1,9 +1,9 @@
 import { createPinia, setActivePinia } from "pinia";
 
 import {
-    FrameWorkflowComment,
+    type FrameWorkflowComment,
     type FreehandWorkflowComment,
-    MarkdownWorkflowComment,
+    type MarkdownWorkflowComment,
     type TextWorkflowComment,
     useWorkflowCommentStore,
 } from "./workflowEditorCommentStore";
diff --git a/client/src/stores/workflowEditorCommentStore.ts b/client/src/stores/workflowEditorCommentStore.ts
index 05b06cf934281df3490b2bd14931f4fd83b409af..d3a6c7e1993cdab36fd9a8c6678cfd3b09ddec1b 100644
--- a/client/src/stores/workflowEditorCommentStore.ts
+++ b/client/src/stores/workflowEditorCommentStore.ts
@@ -1,6 +1,6 @@
 import { computed, del, ref, set } from "vue";
 
-import type { Color } from "@/components/Workflow/Editor/Comments/colors";
+import { type Color } from "@/components/Workflow/Editor/Comments/colors";
 import {
     AxisAlignedBoundingBox,
     type Rectangle,
@@ -9,14 +9,14 @@ import {
     vecMin,
     vecReduceFigures,
     vecSubtract,
-    Vector,
+    type Vector,
 } from "@/components/Workflow/Editor/modules/geometry";
 import { assertDefined } from "@/utils/assertions";
 import { hasKeys, match } from "@/utils/utils";
 
 import { defineScopedStore } from "./scopedStore";
 import { useWorkflowStateStore } from "./workflowEditorStateStore";
-import { Step, useWorkflowStepStore } from "./workflowStepStore";
+import { type Step, useWorkflowStepStore } from "./workflowStepStore";
 
 export type WorkflowCommentColor = Color | "none";
 
@@ -69,6 +69,8 @@ export type WorkflowComment =
     | MarkdownWorkflowComment
     | FreehandWorkflowComment;
 
+export type WorkflowCommentType = WorkflowComment["type"];
+
 interface CommentsMetadata {
     justCreated?: boolean;
     multiSelected?: boolean;
diff --git a/client/src/stores/workflowEditorStateStore.ts b/client/src/stores/workflowEditorStateStore.ts
index dc9cbc0f4a4c1e7c0cc1023fad31cb3e712ebf83..d20aa429a66396598a1d0d88421477b636f15678 100644
--- a/client/src/stores/workflowEditorStateStore.ts
+++ b/client/src/stores/workflowEditorStateStore.ts
@@ -1,8 +1,7 @@
-import type { UseElementBoundingReturn } from "@vueuse/core";
-import type { UnwrapRef } from "vue";
-import { computed, reactive, ref, set } from "vue";
+import { type UseElementBoundingReturn } from "@vueuse/core";
+import { computed, reactive, ref, set, type UnwrapRef } from "vue";
 
-import type { OutputTerminals } from "@/components/Workflow/Editor/modules/terminals";
+import { type OutputTerminals } from "@/components/Workflow/Editor/modules/terminals";
 import reportDefault from "@/components/Workflow/Editor/reportDefault";
 
 import { defineScopedStore } from "./scopedStore";
diff --git a/client/src/stores/workflowEditorToolbarStore.ts b/client/src/stores/workflowEditorToolbarStore.ts
index cbb11b319c9e543f55e09bf5a0f7a0b7933d9ea2..3bb36ea75cda1438a9a8d5a7edcb17fd783a6f8b 100644
--- a/client/src/stores/workflowEditorToolbarStore.ts
+++ b/client/src/stores/workflowEditorToolbarStore.ts
@@ -1,11 +1,11 @@
 import { useMagicKeys } from "@vueuse/core";
 import { computed, onScopeDispose, reactive, ref, watch } from "vue";
 
-import { Rectangle } from "@/components/Workflow/Editor/modules/geometry";
+import { type Rectangle } from "@/components/Workflow/Editor/modules/geometry";
 import { useUserLocalStorage } from "@/composables/userLocalStorage";
 
 import { defineScopedStore } from "./scopedStore";
-import { WorkflowCommentColor } from "./workflowEditorCommentStore";
+import { type WorkflowCommentColor } from "./workflowEditorCommentStore";
 
 export type CommentTool = "textComment" | "markdownComment" | "frameComment" | "freehandComment" | "freehandEraser";
 export type EditorTool = "pointer" | "boxSelect" | CommentTool;
diff --git a/client/src/stores/workflowLandingStore.ts b/client/src/stores/workflowLandingStore.ts
new file mode 100644
index 0000000000000000000000000000000000000000..be2c023b3c10ce6d7d0143bee66344b93c96378c
--- /dev/null
+++ b/client/src/stores/workflowLandingStore.ts
@@ -0,0 +1,68 @@
+import { defineStore } from "pinia";
+import { ref } from "vue";
+
+import { GalaxyApi } from "@/api";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+interface ClaimState {
+    workflowId: string | null;
+    instance: boolean;
+    requestState: Record<string, never> | null;
+    errorMessage: string | null;
+}
+
+export const useWorkflowLandingStore = defineStore("workflowLanding", () => {
+    const claimState = ref<ClaimState>({
+        workflowId: null,
+        instance: false,
+        requestState: null,
+        errorMessage: null,
+    });
+
+    async function claimWorkflow(uuid: string, isPublic: boolean, secret?: string) {
+        let claim;
+        let claimError;
+
+        if (isPublic) {
+            const { data, error } = await GalaxyApi().GET("/api/workflow_landings/{uuid}", {
+                params: {
+                    path: { uuid },
+                },
+            });
+            claim = data;
+            claimError = error;
+        } else {
+            const { data, error } = await GalaxyApi().POST("/api/workflow_landings/{uuid}/claim", {
+                params: {
+                    path: { uuid },
+                },
+                body: {
+                    client_secret: secret,
+                },
+            });
+            claim = data;
+            claimError = error;
+        }
+
+        if (claim) {
+            claimState.value = {
+                workflowId: claim.workflow_id,
+                instance: claim.workflow_target_type === "workflow",
+                requestState: claim.request_state,
+                errorMessage: null,
+            };
+        } else {
+            claimState.value = {
+                workflowId: null,
+                instance: false,
+                requestState: null,
+                errorMessage: errorMessageAsString(claimError),
+            };
+        }
+    }
+
+    return {
+        claimState,
+        claimWorkflow,
+    };
+});
diff --git a/client/src/stores/workflowNodeInspectorStore.ts b/client/src/stores/workflowNodeInspectorStore.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e92683ac853de35b53a44eb9d2a6dd69358b0cad
--- /dev/null
+++ b/client/src/stores/workflowNodeInspectorStore.ts
@@ -0,0 +1,114 @@
+import { defineStore } from "pinia";
+import { computed, del, ref, set } from "vue";
+
+import { usePersistentRef } from "@/composables/persistentRef";
+import { ensureDefined } from "@/utils/assertions";
+import { getShortToolId } from "@/utils/tool";
+import { match } from "@/utils/utils";
+
+import type { Step } from "./workflowStepStore";
+
+interface StoredSize {
+    width: number;
+    maximized: boolean;
+}
+
+function getContentId(step: Step) {
+    return match(step.type, {
+        tool: () => `tool_${getShortToolId(ensureDefined(step.content_id))}`,
+        subworkflow: () => `subworkflow_${step.content_id}`,
+        data_collection_input: () => "input",
+        data_input: () => "input",
+        parameter_input: () => "input",
+        pause: () => "pause",
+    });
+}
+
+export const useWorkflowNodeInspectorStore = defineStore("workflowNodeInspectorStore", () => {
+    /** width of the node inspector if no other width is stored */
+    const generalWidth = usePersistentRef("workflowNodeInspectorGeneralWidth", 300);
+    /** maximized state of the node inspector if no other value is stored */
+    const generalMaximized = ref(false);
+    const storedSizes = usePersistentRef<Record<string, StoredSize>>("workflowNodeInspectorStoredSizes", {});
+
+    const isStored = computed(() => (step: Step) => {
+        const id = getContentId(step);
+        const storedIds = new Set(Object.keys(storedSizes.value));
+
+        return storedIds.has(id);
+    });
+
+    function setStored(step: Step, stored: boolean) {
+        const id = getContentId(step);
+        const storedValue = storedSizes.value[id];
+
+        if (stored) {
+            if (!storedValue) {
+                set(storedSizes.value, id, {
+                    width: generalWidth.value,
+                    maximized: generalMaximized.value,
+                });
+            }
+        } else {
+            if (storedValue) {
+                generalWidth.value = storedValue.width;
+                generalMaximized.value = storedValue.maximized;
+                del(storedSizes.value, id);
+            }
+        }
+    }
+
+    const width = computed(() => (step: Step) => {
+        const id = getContentId(step);
+        return storedSizes.value[id]?.width ?? generalWidth.value;
+    });
+
+    /**
+     * sets the inspectors width. If the width is stored,
+     * stores the new width, otherwise, updates the general width
+     */
+    function setWidth(step: Step, newWidth: number) {
+        const id = getContentId(step);
+
+        if (storedSizes.value[id]) {
+            storedSizes.value[id]!.width = newWidth;
+        } else {
+            generalWidth.value = newWidth;
+        }
+    }
+
+    const maximized = computed(() => (step: Step) => {
+        const id = getContentId(step);
+        return storedSizes.value[id]?.maximized ?? generalMaximized.value;
+    });
+
+    /**
+     * sets the inspectors maximized state. If the state is stored,
+     * stores the maximized state, otherwise, updates the general maximized state
+     */
+    function setMaximized(step: Step, newMaximized: boolean) {
+        const id = getContentId(step);
+
+        if (storedSizes.value[id]) {
+            storedSizes.value[id]!.maximized = newMaximized;
+        } else {
+            generalMaximized.value = newMaximized;
+        }
+    }
+
+    function clearAllStored() {
+        storedSizes.value = {};
+    }
+
+    return {
+        isStored,
+        setStored,
+        clearAllStored,
+        generalWidth,
+        generalMaximized,
+        width,
+        setWidth,
+        maximized,
+        setMaximized,
+    };
+});
diff --git a/client/src/stores/workflowStepStore.test.ts b/client/src/stores/workflowStepStore.test.ts
index 9d9258b965504fdcd2192f723c3e3a79bf405d0c..7b270eb4e05ac97d5124f724ad24eb2b60f632df 100644
--- a/client/src/stores/workflowStepStore.test.ts
+++ b/client/src/stores/workflowStepStore.test.ts
@@ -1,7 +1,6 @@
 import { createPinia, setActivePinia } from "pinia";
 
-import type { NewStep, StepInputConnection } from "@/stores/workflowStepStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import { type NewStep, type StepInputConnection, useWorkflowStepStore } from "@/stores/workflowStepStore";
 
 import { useConnectionStore } from "./workflowConnectionStore";
 
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index e619ef79e1fd348efea4c36d8ce8f216442dec25..dcb0547c9d7b0776bcfd953aa1c7163e47044b8d 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -1,6 +1,6 @@
 import { computed, del, ref, set } from "vue";
 
-import type { CollectionTypeDescriptor } from "@/components/Workflow/Editor/modules/collectionTypeDescription";
+import { type CollectionTypeDescriptor } from "@/components/Workflow/Editor/modules/collectionTypeDescription";
 import { type Connection, getConnectionId, useConnectionStore } from "@/stores/workflowConnectionStore";
 import { assertDefined } from "@/utils/assertions";
 
@@ -50,6 +50,7 @@ export declare const ParameterTypes: "text" | "integer" | "float" | "boolean" |
 export interface ParameterOutput extends Omit<DataOutput, "type" | "extensions"> {
     type: typeof ParameterTypes;
     parameter: true;
+    multiple: boolean;
 }
 
 interface BaseStepInput {
@@ -100,12 +101,14 @@ export interface NewStep {
     outputs: Array<OutputTerminalSource>;
     position?: StepPosition;
     post_job_actions?: PostJobActions;
+    tool_id?: string;
     tool_state: Record<string, unknown>;
     tool_version?: string;
     tooltip?: string | null;
     type: "tool" | "data_input" | "data_collection_input" | "subworkflow" | "parameter_input" | "pause";
     uuid?: string;
     when?: string | null;
+    workflow_id?: string;
     workflow_outputs?: WorkflowOutput[];
 }
 
diff --git a/client/src/stores/workflowStore.ts b/client/src/stores/workflowStore.ts
index b757fe868b20bc2f881e091580f9c5a5ac0043de..e68b62ab604ff512f136bb3d1dcb0b031bc710e3 100644
--- a/client/src/stores/workflowStore.ts
+++ b/client/src/stores/workflowStore.ts
@@ -2,8 +2,9 @@ import axios from "axios";
 import { defineStore } from "pinia";
 import { computed, ref, set } from "vue";
 
+// import type { StoredWorkflowDetailed } from "@/api/workflows"; // TODO: use this instead of locally defined type
 import { getAppRoot } from "@/onload/loadConfig";
-import type { Steps } from "@/stores/workflowStepStore";
+import { type Steps } from "@/stores/workflowStepStore";
 
 export interface Workflow {
     name: string;
@@ -12,6 +13,11 @@ export interface Workflow {
     step_count?: number;
     latest_id?: string;
     version: number;
+    deleted?: boolean;
+    owner?: string;
+    annotation?: string;
+    tags?: string[];
+    update_time?: string;
 }
 
 export const useWorkflowStore = defineStore("workflowStore", () => {
diff --git a/client/src/style/scss/base.scss b/client/src/style/scss/base.scss
index 3567d1e417e9d482836fab42671f6802b95891c5..4a20a6482f12a24173b57dfa793a4ca35851a7ef 100644
--- a/client/src/style/scss/base.scss
+++ b/client/src/style/scss/base.scss
@@ -31,7 +31,6 @@ $fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
 @import "library.scss";
 @import "trackster.scss";
 @import "toastr.scss";
-@import "jstree.scss";
 @import "tour.scss";
 @import "flex.scss";
 @import "charts.scss";
diff --git a/client/src/style/scss/jstree.scss b/client/src/style/scss/jstree.scss
deleted file mode 100644
index 1e49dcdc9689d926b80bd75b06accdcd330318fe..0000000000000000000000000000000000000000
--- a/client/src/style/scss/jstree.scss
+++ /dev/null
@@ -1,990 +0,0 @@
-/* jsTree default theme */
-.jstree-node,
-.jstree-children,
-.jstree-container-ul {
-    display: block;
-    margin: 0;
-    padding: 0;
-    list-style-type: none;
-    list-style-image: none;
-}
-.jstree-node {
-    white-space: nowrap;
-}
-.jstree-anchor {
-    display: inline-block;
-    color: black;
-    white-space: nowrap;
-    padding: 0 4px 0 1px;
-    margin: 0;
-    vertical-align: top;
-}
-.jstree-anchor:focus {
-    outline: 0;
-}
-.jstree-anchor,
-.jstree-anchor:link,
-.jstree-anchor:visited,
-.jstree-anchor:hover,
-.jstree-anchor:active {
-    text-decoration: none;
-    color: inherit;
-}
-.jstree-icon {
-    display: inline-block;
-    text-decoration: none;
-    margin: 0;
-    padding: 0;
-    vertical-align: top;
-    text-align: center;
-}
-.jstree-icon:empty {
-    display: inline-block;
-    text-decoration: none;
-    margin: 0;
-    padding: 0;
-    vertical-align: top;
-    text-align: center;
-}
-.jstree-ocl {
-    cursor: pointer;
-}
-.jstree-leaf > .jstree-ocl {
-    cursor: default;
-}
-.jstree .jstree-open > .jstree-children {
-    display: block;
-}
-.jstree .jstree-closed > .jstree-children,
-.jstree .jstree-leaf > .jstree-children {
-    display: none;
-}
-.jstree-anchor > .jstree-themeicon {
-    margin-right: 2px;
-}
-.jstree-no-icons .jstree-themeicon,
-.jstree-anchor > .jstree-themeicon-hidden {
-    display: none;
-}
-.jstree-rtl .jstree-anchor {
-    padding: 0 1px 0 4px;
-}
-.jstree-rtl .jstree-anchor > .jstree-themeicon {
-    margin-left: 2px;
-    margin-right: 0;
-}
-.jstree-rtl .jstree-node {
-    margin-left: 0;
-}
-.jstree-rtl .jstree-container-ul > .jstree-node {
-    margin-right: 0;
-}
-.jstree-wholerow-ul {
-    position: relative;
-    display: inline-block;
-    min-width: 100%;
-}
-.jstree-wholerow-ul .jstree-leaf > .jstree-ocl {
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-    background: url("../../assets/images/jstree/32px.png") -103px -71px no-repeat;
-}
-.jstree-default-small .jstree-folder {
-    background: url("../../assets/images/jstree/32px.png") -263px -7px no-repeat;
-}
-.jstree-default-small.jstree-rtl .jstree-node {
-    background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABIAAAACAQMAAABv1h6PAAAABlBMVEUAAAAdHRvEkCwcAAAAAXRSTlMAQObYZgAAAAxJREFUCNdjAAMHBgAAiABBI4gz9AAAAABJRU5ErkJggg==");
-}
-.jstree-default-small.jstree-rtl .jstree-last {
-    background: transparent;
-}
-.jstree-default-large .jstree-node {
-    min-height: 32px;
-    line-height: 32px;
-    margin-left: 32px;
-    min-width: 32px;
-}
-.jstree-default-large .jstree-anchor {
-    line-height: 32px;
-    height: 32px;
-}
-.jstree-default-large .jstree-icon {
-    width: 32px;
-    height: 32px;
-    line-height: 32px;
-}
-.jstree-default-large .jstree-icon:empty {
-    width: 32px;
-    height: 32px;
-    line-height: 32px;
-}
-.jstree-default-large.jstree-rtl .jstree-node {
-    margin-right: 32px;
-}
-.jstree-default-large .jstree-wholerow {
-    height: 32px;
-}
-.jstree-default-large .jstree-node,
-.jstree-default-large .jstree-icon {
-    background-image: url("../../assets/images/jstree/32px.png");
-}
-.jstree-default-large .jstree-node {
-    background-position: -288px 0px;
-    background-repeat: repeat-y;
-}
-.jstree-default-large .jstree-last {
-    background: transparent;
-}
-.jstree-default-large .jstree-open > .jstree-ocl {
-    background-position: -128px 0px;
-}
-.jstree-default-large .jstree-closed > .jstree-ocl {
-    background-position: -96px 0px;
-}
-.jstree-default-large .jstree-leaf > .jstree-ocl {
-    background-position: -64px 0px;
-}
-.jstree-default-large .jstree-themeicon {
-    background-position: -256px 0px;
-}
-.jstree-default-large > .jstree-no-dots .jstree-node,
-.jstree-default-large > .jstree-no-dots .jstree-leaf > .jstree-ocl {
-    background: transparent;
-}
-.jstree-default-large > .jstree-no-dots .jstree-open > .jstree-ocl {
-    background-position: -32px 0px;
-}
-.jstree-default-large > .jstree-no-dots .jstree-closed > .jstree-ocl {
-    background-position: 0px 0px;
-}
-.jstree-default-large .jstree-disabled {
-    background: transparent;
-}
-.jstree-default-large .jstree-disabled.jstree-hovered {
-    background: transparent;
-}
-.jstree-default-large .jstree-disabled.jstree-clicked {
-    background: #efefef;
-}
-.jstree-default-large .jstree-checkbox {
-    background-position: -160px 0px;
-}
-.jstree-default-large .jstree-checkbox:hover {
-    background-position: -160px -32px;
-}
-.jstree-default-large.jstree-checkbox-selection .jstree-clicked > .jstree-checkbox,
-.jstree-default-large .jstree-checked > .jstree-checkbox {
-    background-position: -224px 0px;
-}
-.jstree-default-large.jstree-checkbox-selection .jstree-clicked > .jstree-checkbox:hover,
-.jstree-default-large .jstree-checked > .jstree-checkbox:hover {
-    background-position: -224px -32px;
-}
-.jstree-default-large .jstree-anchor > .jstree-undetermined {
-    background-position: -192px 0px;
-}
-.jstree-default-large .jstree-anchor > .jstree-undetermined:hover {
-    background-position: -192px -32px;
-}
-.jstree-default-large > .jstree-striped {
-    background-size: auto 64px;
-}
-.jstree-default-large.jstree-rtl .jstree-node {
-    background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAACAQMAAAB49I5GAAAABlBMVEUAAAAdHRvEkCwcAAAAAXRSTlMAQObYZgAAAAxJREFUCNdjAAMOBgAAGAAJMwQHdQAAAABJRU5ErkJggg==");
-    background-position: 100% 1px;
-    background-repeat: repeat-y;
-}
-.jstree-default-large.jstree-rtl .jstree-last {
-    background: transparent;
-}
-.jstree-default-large.jstree-rtl .jstree-open > .jstree-ocl {
-    background-position: -128px -32px;
-}
-.jstree-default-large.jstree-rtl .jstree-closed > .jstree-ocl {
-    background-position: -96px -32px;
-}
-.jstree-default-large.jstree-rtl .jstree-leaf > .jstree-ocl {
-    background-position: -64px -32px;
-}
-.jstree-default-large.jstree-rtl > .jstree-no-dots .jstree-node,
-.jstree-default-large.jstree-rtl > .jstree-no-dots .jstree-leaf > .jstree-ocl {
-    background: transparent;
-}
-.jstree-default-large.jstree-rtl > .jstree-no-dots .jstree-open > .jstree-ocl {
-    background-position: -32px -32px;
-}
-.jstree-default-large.jstree-rtl > .jstree-no-dots .jstree-closed > .jstree-ocl {
-    background-position: 0px -32px;
-}
-.jstree-default-large .jstree-themeicon-custom {
-    background-color: transparent;
-    background-image: none;
-    background-position: 0 0;
-}
-.jstree-default-large > .jstree-container-ul .jstree-loading > .jstree-ocl {
-    background: url("../../assets/images/jstree/throbber.gif") center center no-repeat;
-}
-.jstree-default-large .jstree-file {
-    background: url("../../assets/images/jstree/32px.png") -96px -64px no-repeat;
-}
-.jstree-default-large .jstree-folder {
-    background: url("../../assets/images/jstree/32px.png") -256px 0px no-repeat;
-}
-.jstree-default-large.jstree-rtl .jstree-node {
-    background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAACAQMAAAAD0EyKAAAABlBMVEUAAAAdHRvEkCwcAAAAAXRSTlMAQObYZgAAAAxJREFUCNdjgIIGBgABCgCBvVLXcAAAAABJRU5ErkJggg==");
-}
-.jstree-default-large.jstree-rtl .jstree-last {
-    background: transparent;
-}
-@media (max-width: 768px) {
-    #jstree-dnd.jstree-dnd-responsive {
-        line-height: 40px;
-        font-weight: bold;
-        font-size: 1.1em;
-        text-shadow: 1px 1px white;
-    }
-    #jstree-dnd.jstree-dnd-responsive > i {
-        background: transparent;
-        width: 40px;
-        height: 40px;
-    }
-    #jstree-dnd.jstree-dnd-responsive > .jstree-ok {
-        background-image: url("../../assets/images/jstree/40px.png");
-        background-position: 0 -200px;
-        background-size: 120px 240px;
-    }
-    #jstree-dnd.jstree-dnd-responsive > .jstree-er {
-        background-image: url("../../assets/images/jstree/40px.png");
-        background-position: -40px -200px;
-        background-size: 120px 240px;
-    }
-    #jstree-marker.jstree-dnd-responsive {
-        border-left-width: 10px;
-        border-top-width: 10px;
-        border-bottom-width: 10px;
-        margin-top: -10px;
-    }
-}
-@media (max-width: 768px) {
-    .jstree-default-responsive {
-        /*
-		.jstree-open > .jstree-ocl,
-		.jstree-closed > .jstree-ocl { border-radius:20px; background-color:white; }
-		*/
-    }
-    .jstree-default-responsive .jstree-icon {
-        background-image: url("../../assets/images/jstree/40px.png");
-    }
-    .jstree-default-responsive .jstree-node,
-    .jstree-default-responsive .jstree-leaf > .jstree-ocl {
-        background: transparent;
-    }
-    .jstree-default-responsive .jstree-node {
-        min-height: 40px;
-        line-height: 40px;
-        margin-left: 40px;
-        min-width: 40px;
-        white-space: nowrap;
-    }
-    .jstree-default-responsive .jstree-anchor {
-        line-height: 40px;
-        height: 40px;
-    }
-    .jstree-default-responsive .jstree-icon,
-    .jstree-default-responsive .jstree-icon:empty {
-        width: 40px;
-        height: 40px;
-        line-height: 40px;
-    }
-    .jstree-default-responsive > .jstree-container-ul > .jstree-node {
-        margin-left: 0;
-    }
-    .jstree-default-responsive.jstree-rtl .jstree-node {
-        margin-left: 0;
-        margin-right: 40px;
-    }
-    .jstree-default-responsive.jstree-rtl .jstree-container-ul > .jstree-node {
-        margin-right: 0;
-    }
-    .jstree-default-responsive .jstree-ocl,
-    .jstree-default-responsive .jstree-themeicon,
-    .jstree-default-responsive .jstree-checkbox {
-        background-size: 120px 240px;
-    }
-    .jstree-default-responsive .jstree-leaf > .jstree-ocl {
-        background: transparent;
-    }
-    .jstree-default-responsive .jstree-open > .jstree-ocl {
-        background-position: 0 0px !important;
-    }
-    .jstree-default-responsive .jstree-closed > .jstree-ocl {
-        background-position: 0 -40px !important;
-    }
-    .jstree-default-responsive.jstree-rtl .jstree-closed > .jstree-ocl {
-        background-position: -40px 0px !important;
-    }
-    .jstree-default-responsive .jstree-themeicon {
-        background-position: -40px -40px;
-    }
-    .jstree-default-responsive .jstree-checkbox,
-    .jstree-default-responsive .jstree-checkbox:hover {
-        background-position: -40px -80px;
-    }
-    .jstree-default-responsive.jstree-checkbox-selection .jstree-clicked > .jstree-checkbox,
-    .jstree-default-responsive.jstree-checkbox-selection .jstree-clicked > .jstree-checkbox:hover,
-    .jstree-default-responsive .jstree-checked > .jstree-checkbox,
-    .jstree-default-responsive .jstree-checked > .jstree-checkbox:hover {
-        background-position: 0 -80px;
-    }
-    .jstree-default-responsive .jstree-anchor > .jstree-undetermined,
-    .jstree-default-responsive .jstree-anchor > .jstree-undetermined:hover {
-        background-position: 0 -120px;
-    }
-    .jstree-default-responsive .jstree-anchor {
-        font-weight: bold;
-        font-size: 1.1em;
-        text-shadow: 1px 1px white;
-    }
-    .jstree-default-responsive > .jstree-striped {
-        background: transparent;
-    }
-    .jstree-default-responsive .jstree-wholerow {
-        border-top: 1px solid rgba(255, 255, 255, 0.7);
-        border-bottom: 1px solid rgba(64, 64, 64, 0.2);
-        background: #ebebeb;
-        height: 40px;
-    }
-    .jstree-default-responsive .jstree-wholerow-hovered {
-        background: #e7f4f9;
-    }
-    .jstree-default-responsive .jstree-wholerow-clicked {
-        background: #beebff;
-    }
-    .jstree-default-responsive .jstree-children .jstree-last > .jstree-wholerow {
-        box-shadow: inset 0 -6px 3px -5px #666666;
-    }
-    .jstree-default-responsive .jstree-children .jstree-open > .jstree-wholerow {
-        box-shadow: inset 0 6px 3px -5px #666666;
-        border-top: 0;
-    }
-    .jstree-default-responsive .jstree-children .jstree-open + .jstree-open {
-        box-shadow: none;
-    }
-    .jstree-default-responsive .jstree-node,
-    .jstree-default-responsive .jstree-icon,
-    .jstree-default-responsive .jstree-node > .jstree-ocl,
-    .jstree-default-responsive .jstree-themeicon,
-    .jstree-default-responsive .jstree-checkbox {
-        background-image: url("../../assets/images/jstree/40px.png");
-        background-size: 120px 240px;
-    }
-    .jstree-default-responsive .jstree-node {
-        background-position: -80px 0;
-        background-repeat: repeat-y;
-    }
-    .jstree-default-responsive .jstree-last {
-        background: transparent;
-    }
-    .jstree-default-responsive .jstree-leaf > .jstree-ocl {
-        background-position: -40px -120px;
-    }
-    .jstree-default-responsive .jstree-last > .jstree-ocl {
-        background-position: -40px -160px;
-    }
-    .jstree-default-responsive .jstree-themeicon-custom {
-        background-color: transparent;
-        background-image: none;
-        background-position: 0 0;
-    }
-    .jstree-default-responsive .jstree-file {
-        background: url("../../assets/images/jstree/40px.png") 0 -160px no-repeat;
-        background-size: 120px 240px;
-    }
-    .jstree-default-responsive .jstree-folder {
-        background: url("../../assets/images/jstree/40px.png") -40px -40px no-repeat;
-        background-size: 120px 240px;
-    }
-}
-.jstree-default > .jstree-container-ul > .jstree-node {
-    margin-left: 0;
-    margin-right: 0;
-}
diff --git a/client/src/style/scss/multiselect.scss b/client/src/style/scss/multiselect.scss
index 05b4b3961220c22b9d99a5afe83b5d40da1bb74c..ec2f6484d32ec6028b838a79da20e33a1c8fca76 100644
--- a/client/src/style/scss/multiselect.scss
+++ b/client/src/style/scss/multiselect.scss
@@ -47,7 +47,7 @@
         }
 
         &.multiselect__option--highlight {
-            background: $brand-danger;
+            background: darken($brand-secondary, 40%);
 
             &::after {
                 background: unset;
@@ -95,3 +95,7 @@
         }
     }
 }
+
+.multiselect--active {
+    z-index: 1500; // Should be on top of everything
+}
diff --git a/client/src/style/scss/theme/blue.scss b/client/src/style/scss/theme/blue.scss
index 0e43739c0e5b01aec5424b9326e5052a788807c0..48007ae469d012a16cad4d212f8b36b9bdf69f64 100644
--- a/client/src/style/scss/theme/blue.scss
+++ b/client/src/style/scss/theme/blue.scss
@@ -110,7 +110,7 @@ $input-color-placeholder: $text-muted;
 $body-bg: $white;
 
 // Masthead
-$masthead-height: 3rem;
+$masthead-height: 2.5rem;
 
 // Side panels
 $panel-bg-color: $brand-light;
diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index d29d057590502cd46d4fbf679dc139e6d3d530b3..468e35e00a4a96c836b62aed9101e23305c8c077 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -71,6 +71,9 @@ $ui-margin-horizontal-large: $margin-v * 2;
 .ui-modal {
     display: none;
     overflow: auto;
+    .title {
+        width: 100%;
+    }
     .modal-header.no-separator {
         border: none !important;
         padding-bottom: 0px !important;
@@ -192,6 +195,17 @@ $ui-margin-horizontal-large: $margin-v * 2;
     }
 }
 
+.ui-form-header-underlay::after {
+    content: "";
+    display: block;
+    position: absolute;
+    top: -$margin-h;
+    left: -0.5rem;
+    right: -0.5rem;
+    height: 50px;
+    background: linear-gradient($white 75%, change-color($white, $alpha: 0));
+}
+
 // popovers
 .popover {
     max-width: 70%;
@@ -224,7 +238,7 @@ $ui-margin-horizontal-large: $margin-v * 2;
 
 .ui-textarea {
     @extend .ui-input;
-    height: 100px !important;
+    min-height: 100px;
 }
 
 .ui-switch {
diff --git a/client/src/style/scss/windows.scss b/client/src/style/scss/windows.scss
index 521f15683d1f6ce614a59c1303d809daf6b73f69..1427bb2b1c2d9f5657a52f8c7d209e098dc07031 100644
--- a/client/src/style/scss/windows.scss
+++ b/client/src/style/scss/windows.scss
@@ -1,6 +1,15 @@
 .winbox {
     border-radius: $border-radius-base;
-    margin-top: 3rem;
+    margin-left: 1px;
+    margin-top: calc($masthead-height + 1px);
+}
+
+.winbox.max {
+    border-radius: 0;
+    margin: 0;
+    .wb-header {
+        border-radius: 0;
+    }
 }
 
 .winbox.min {
@@ -8,8 +17,9 @@
 }
 
 .wb-header {
-    border-radius: $border-radius-base;
     background: $brand-info;
+    border-top-left-radius: $border-radius-base;
+    border-top-right-radius: $border-radius-base;
 }
 
 .wb-icon * {
diff --git a/client/src/utils/dom.ts b/client/src/utils/dom.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7fd2ec12dd68248fa9cf1bb246cebe0e4e2bd341
--- /dev/null
+++ b/client/src/utils/dom.ts
@@ -0,0 +1,33 @@
+/**
+ * composed array of all Event Targets between the original and current target
+ *
+ * @param e Event to return partial composed path of
+ */
+export function composedPartialPath(e: Event): EventTarget[] {
+    const current = e.currentTarget;
+    const composed = e.composedPath();
+
+    const currentIndex = composed.findIndex((target) => target === current);
+
+    if (currentIndex === -1) {
+        throw new Error("current target is not part of composed path");
+    }
+
+    const partial = composed.slice(0, currentIndex);
+
+    return partial;
+}
+
+/**
+ * checks if an element has a valid mouse interaction
+ */
+export function isClickable(element: Element): boolean {
+    const clickable =
+        element instanceof HTMLButtonElement ||
+        element instanceof HTMLInputElement ||
+        element instanceof HTMLAnchorElement ||
+        element instanceof HTMLSelectElement ||
+        element instanceof HTMLLabelElement;
+
+    return clickable;
+}
diff --git a/client/src/utils/filterConversion.test.js b/client/src/utils/filterConversion.test.js
index cf3230e4d13d27780e23801284989f6571b0368f..84affdcae555314798a718414232b4525d5cb843 100644
--- a/client/src/utils/filterConversion.test.js
+++ b/client/src/utils/filterConversion.test.js
@@ -1,9 +1,9 @@
-import { HistoryFilters } from "components/History/HistoryFilters";
-import { WorkflowFilters } from "components/Workflow/WorkflowFilters";
+import { HistoryFilters } from "@/components/History/HistoryFilters";
+import { getWorkflowFilters } from "@/components/Workflow/List/workflowFilters";
 
 describe("test filtering helpers to convert filters to filter text", () => {
-    const MyWorkflowFilters = WorkflowFilters("my");
-    const PublishedWorkflowFilters = WorkflowFilters("published");
+    const MyWorkflowFilters = getWorkflowFilters("my");
+    const PublishedWorkflowFilters = getWorkflowFilters("published");
     it("conversion from filters to new filter text", async () => {
         const normalized = HistoryFilters.defaultFilters;
         expect(Object.keys(normalized).length).toBe(2);
@@ -66,7 +66,7 @@ describe("test filtering helpers to convert filters to filter text", () => {
 });
 
 describe("test filtering helpers to convert filter text to filters", () => {
-    const PublishedWorkflowFilters = WorkflowFilters("published");
+    const PublishedWorkflowFilters = getWorkflowFilters("published");
     function getFilters(filteringClass, filterText) {
         return filteringClass.getValidFilters(Object.fromEntries(filteringClass.getFiltersForText(filterText)))
             .validFilters;
diff --git a/client/src/utils/filtering.ts b/client/src/utils/filtering.ts
index 480eec597b9de0abdfebf5b56dd925fb33868af1..4b25ad56bec464cbb7cbbe7db3a82befcc662eef 100644
--- a/client/src/utils/filtering.ts
+++ b/client/src/utils/filtering.ts
@@ -10,7 +10,7 @@
  */
 
 import { isEqual, omit } from "lodash";
-import type { DefineComponent } from "vue";
+import { type DefineComponent } from "vue";
 
 export type Converter<T> = (value: T) => T;
 type Handler<T> = (v: T, q: T) => boolean;
@@ -525,13 +525,16 @@ export default class Filtering<T> {
             if (this.validFilters[key]?.type === "MultiTags" && Array.isArray(value)) {
                 const validValues = value
                     .map((v) => this.getConvertedValue(key, v, backendFormatted))
-                    .filter((v) => v !== undefined);
+                    .filter((v) => v !== undefined) as T[];
+
                 if (validValues.length > 0) {
                     validFilters[key] = validValues as T;
                 }
+
                 const invalidValues = value.filter(
-                    (v) => !validValues.includes(this.getConvertedValue(key, v, backendFormatted))
+                    (v) => !validValues.includes(this.getConvertedValue(key, v, backendFormatted) as T)
                 );
+
                 if (invalidValues.length > 0) {
                     invalidFilters[key] = invalidValues as T;
                 }
diff --git a/client/src/utils/natural-sort.js b/client/src/utils/natural-sort.js
deleted file mode 100644
index c620f169163fc1a1c3c52e48190ba3fa7e2c4bc2..0000000000000000000000000000000000000000
--- a/client/src/utils/natural-sort.js
+++ /dev/null
@@ -1,38 +0,0 @@
-// Alphanumeric/natural sort fn
-function naturalSort(a, b) {
-    // setup temp-scope variables for comparison evauluation
-    var re = /(-?[0-9.]+)/g;
-
-    var x = a.toString().toLowerCase() || "";
-    var y = b.toString().toLowerCase() || "";
-    var nC = String.fromCharCode(0);
-    var xN = x.replace(re, `${nC}$1${nC}`).split(nC);
-    var yN = y.replace(re, `${nC}$1${nC}`).split(nC);
-    var xD = new Date(x).getTime();
-    var yD = xD ? new Date(y).getTime() : null;
-    // natural sorting of dates
-    if (yD) {
-        if (xD < yD) {
-            return -1;
-        } else if (xD > yD) {
-            return 1;
-        }
-    }
-
-    // natural sorting through split numeric strings and default strings
-    var oFxNcL;
-
-    var oFyNcL;
-    for (var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++) {
-        oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];
-        oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];
-        if (oFxNcL < oFyNcL) {
-            return -1;
-        } else if (oFxNcL > oFyNcL) {
-            return 1;
-        }
-    }
-    return 0;
-}
-
-export default naturalSort;
diff --git a/client/src/utils/naturalSort.ts b/client/src/utils/naturalSort.ts
new file mode 100644
index 0000000000000000000000000000000000000000..91a047b90dd04d4877c04fa446d97f58aa591041
--- /dev/null
+++ b/client/src/utils/naturalSort.ts
@@ -0,0 +1,45 @@
+// Alphanumeric/natural sort fn
+export function naturalSort(a = "", b = ""): number {
+    // setup temp-scope variables for comparison evauluation
+    const re = /(-?[0-9.]+)/g;
+
+    const x = a.toString().toLowerCase() || "";
+    const y = b.toString().toLowerCase() || "";
+    const nC = String.fromCharCode(0);
+    const xN = x.replace(re, `${nC}$1${nC}`).split(nC);
+    const yN = y.replace(re, `${nC}$1${nC}`).split(nC);
+    const xD = new Date(x).getTime();
+    const yD = xD ? new Date(y).getTime() : null;
+    // natural sorting of dates
+    if (yD) {
+        if (xD < yD) {
+            return -1;
+        } else if (xD > yD) {
+            return 1;
+        }
+    }
+
+    // natural sorting through split numeric strings and default strings
+    let oFxNcL;
+
+    let oFyNcL;
+    for (let cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++) {
+        oFxNcL = parseFloat(xN[cLoc] || "") || xN[cLoc];
+        oFyNcL = parseFloat(yN[cLoc] || "") || yN[cLoc];
+
+        // Check if either part is undefined
+        if (oFxNcL === undefined) {
+            return -1;
+        }
+        if (oFyNcL === undefined) {
+            return 1;
+        }
+
+        if (oFxNcL < oFyNcL) {
+            return -1;
+        } else if (oFxNcL > oFyNcL) {
+            return 1;
+        }
+    }
+    return 0;
+}
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 7ff2b7b344e73fa8a2754c59ce9536351b5bfb49..2333fd58f1091d30adb6baf1fcb9dfadfa904bae 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -9,14 +9,18 @@
 _:  # global stuff
 
   selectors:
+    center_panel: '#center'
     editable_text: '.editable-text'
     tooltip_balloon: '.tooltip'
     tooltip_inner: .tooltip-inner
+    left_panel: '#left'
     left_panel_drag: '.flex-panel.left .drag-handle'
     left_panel_collapse: '.collapse-button.left'
     right_panel_drag: '.flex-panel.right .drag-handle'
     right_panel_collapse: '.collapse-button.right'
     by_attribute: '${scope} [${name}="${value}"]'
+    active_nav_item: '.nav-item-active'
+    toolbox_panel: '#toolbox-panel'
 
     confirm_button:
       type: xpath
@@ -38,46 +42,28 @@ masthead:
   selectors:
     _: '#masthead'
 
-    # bootstrap-vue a tag doesn't work as link target, need to hit span inside
-    user: '#user.loggedin-only > a.nav-link.dropdown-toggle > span'
-    register_or_login: '#user.loggedout-only > .nav-link'
-
-    user_menu: '#user .dropdown-menu a'
-    workflow: '#workflow .nav-link'
-
-    username:
-      type: xpath
-      selector: '//a[contains(text(), "Signed in as")]'
-
+    help: '#help'
+    home: '#analysis'
+    login: '#user'
+    logout: '.dropdown-menu > li > a > .fa-sign-out-alt'
     logged_in_only: '.loggedin-only'
     logged_out_only: '.loggedout-only'
+    preferences: '.dropdown-menu > li > a > .fa-gear'
+    register_or_login: '#user.loggedout-only > .nav-link'
     storage_dashboard_link:
       selector: 'storage dashboard link'
       type: data-description
-
-  labels:
-    # top-level menus
-    admin: 'Admin'
-    analyze: 'Analyze Data'
-    data: 'Data'
-    help: 'Help'
-    user: 'User'
-    visualization: 'Visualization'
-    workflow: 'Workflow'
-
-    # user menu
-    logout: 'Sign Out'
-    preferences: 'Preferences'
-
-    # data menu
-    libraries: 'Data Libraries'
-    histories: 'Histories'
-    invocations: 'Workflow Invocations'
-    pages: 'Pages'
-    workflows: 'Workflows'
+    user: '#user.loggedin-only > a.nav-link > .fa'
+    username:
+      type: xpath
+      selector: '//a[contains(text(), "Signed in as")]'
+    window_manager: '#enable-window-manager'
+    workflow: '#workflow .nav-link'
 
 preferences:
   selectors:
+    activity: "#activity-settings"
+    activity_expand: ".activity-panel-footer"
     sign_out: "#edit-preferences-sign-out"
     change_password: "#edit-preferences-password"
     manage_information: '#edit-preferences-information'
@@ -108,10 +94,10 @@ object_store_instances:
       create_button: '#object-store-create'
       _: '#user-object-stores-index'
 
-  create: 
+  create:
     selectors:
       select: '.object-store-template-select-button[data-template-id="${template_id}"]'
-      _: '#create-object-store-landing'      
+      _: '#create-object-store-landing'
       submit: '#submit'
 
 file_source_instances:
@@ -120,10 +106,10 @@ file_source_instances:
       create_button: '#file-source-create'
       _: '#user-file-sources-index'
 
-  create: 
+  create:
     selectors:
       select: '.file-source-template-select-button[data-template-id="${template_id}"]'
-      _: '#create-file-source-landing'      
+      _: '#create-file-source-landing'
       submit: '#submit'
 
 toolbox_filters:
@@ -365,7 +351,10 @@ edit_dataset_attributes:
     name_input: '[aria-labelledby="dataset-attributes-heading"] input#name'
     info_input: '[aria-labelledby="dataset-attributes-heading"] textarea#info'
     annotation_input: '[aria-labelledby="dataset-attributes-heading"] textarea#annotation'
+    datatypes_tab: '.dataset-edit-datatype-tab'
+    datatype_dropdown: ' #datatype .multiselect'
     save_button: '#dataset-attributes-default-save'
+    auto_detect_datatype_button: '#dataset-attributes-autodetect-datatype'
     alert: '.dataset-attributes-alert'
 
   dbkey_dropdown_results:
@@ -390,10 +379,12 @@ edit_collection_attributes:
 
 tool_panel:
   selectors:
+    tool_box: '[data-description="panel toolbox"]'
     tool_link: 'a[href$$="tool_runner?tool_id=${tool_id}"]'
     outer_tool_link: '.toolTitle a[href$$="tool_runner?tool_id=${tool_id}"]'
     data_source_tool_link: 'a[href$$="tool_runner/data_source_redirect?tool_id=${tool_id}"]'
     search: '.search-query'
+    toolbox: '[data-description="panel toolbox"]'
     workflow_names: '#internal-workflows .toolTitle'
     views_button: '.tool-panel-dropdown'
     views_menu_item: '[data-panel-id="${panel_id}"]'
@@ -450,13 +441,14 @@ history_copy_elements:
 
 collection_builders:
   selectors:
-    clear_filters: "a.clear-filters-link"
+    clear_filters: "button.clear-filters-link"
     forward_datasets: ".forward-column .column-datasets"
     reverse_datasets: ".reverse-column .column-datasets"
     name: "input.collection-name"
 
 histories:
   selectors:
+    activity: '#activity-histories'
     advanced_search_toggle: '#histories-grid [data-description="toggle advanced search"]'
     advanced_search_name_input: '#histories-advanced-filter-name'
     advanced_search_tag_area: '#histories-advanced-filter-tag .stateless-tags button'
@@ -532,6 +524,7 @@ history_import:
 
 pages:
   selectors:
+    activity: "#activity-pages"
     create: '#page-create'
     submit: '#submit'
     create_title_input: '#form-element-title input'
@@ -578,6 +571,7 @@ tool_form:
     parameter_div: 'div.ui-form-element[id="form-element-${parameter}"]'
     parameter_error: 'div.ui-form-element[id="form-element-${parameter}"] .ui-form-error-text'
     parameter_checkbox: 'div.ui-form-element[id="form-element-${parameter}"] .ui-switch'
+    parameter_select: 'div.ui-form-element[id="form-element-${parameter}"] .multiselect'
     parameter_input: 'div.ui-form-element[id="form-element-${parameter}"] .ui-input'
     parameter_textarea: 'div.ui-form-element[id="form-element-${parameter}"] textarea'
     parameter_data_input_single: 'div.ui-form-element[id="form-element-${parameter}"] button[title="Single dataset"]'
@@ -594,12 +588,14 @@ tool_form:
     drilldown_select_all: 'div.ui-form-element[id="form-element-${parameter}"] div.select-all-checkbox'
     drilldown_option: '.drilldown-option'
     drilldown_expand: '.fa-caret-down'
+    tool_version_button: ".tool-versions"
 
   labels:
     generate_tour: 'Generate Tour'
 
 workflows:
   selectors:
+    activity: '#activity-workflows'
     shared_with_me_tab: '#shared-with-me'
     published_tab: '#published a'
     new_button: '#workflow-create'
@@ -615,6 +611,7 @@ workflows:
     workflows_list_empty: '#workflow-list-empty'
     workflow_not_found_message: '#no-workflow-found'
     workflow_card: '.workflow-card'
+    workflow_card_button: '.workflow-card[data-workflow-name="${name}"] button[title="${title}"]'
     workflow_cards: '#workflow-cards'
     external_link: '.workflow-external-link'
     trs_icon: '.workflow-trs-icon'
@@ -626,7 +623,7 @@ workflows:
     rename_input: '#workflow-name-input'
     workflow_drop_down: '[data-workflow-actions-dropdown]'
     delete_button: '.workflow-delete-button'
-    view_button: '.workflow-view-button'
+    view_button: '.workflow-name-preview'
     workflow_preview_container: '.workflow-card-preview-modal .workflow-published .published-workflow'
     workflow_preview_information: '.workflow-information'
     view_external_link: ".workflow-view-external-link-button"
@@ -650,6 +647,7 @@ workflows:
 visualization:
   selectors:
     _: '#center div.plugin-list'
+    activity: '#activity-visualizations'
     plugin_item: '[data-plugin-name*="${id}"]'
 
 trs_search:
@@ -682,6 +680,7 @@ trs_import:
 workflow_run:
   selectors:
     warning: '[data-description="workflow run warning"]'
+    run_error: '[data-description="workflow run error"]'
     input_div: "[step-label='${label}']"
     input_data_div: "[step-label='${label}'] .multiselect"
     # TODO: put step labels in the DOM ideally
@@ -691,7 +690,8 @@ workflow_run:
     validation_error: ".validation-error"
     expand_form_link: '.workflow-expand-form-link'
     expanded_form: '.workflow-expanded-form'
-    new_history_target_link: '.workflow-new-history-target-link'
+    new_history_badge: '[data-description="new history badge"]'
+    history_target_link: '[data-description="switch to history link"]'
     runtime_setting_button: '.workflow-run-settings'
     runtime_setting_target: '.workflow-run-settings-target'
     simplified_input:
@@ -707,6 +707,7 @@ workflow_editor:
   node:
     selectors:
       _: "[node-label='${label}']"
+      by_id: "#wf-node-step-${id}"
       title: '${_} .node-title'
       destroy: '${_} .node-destroy'
       clone: '${_} .node-clone'
@@ -738,6 +739,7 @@ workflow_editor:
       clear_selection: "[title='clear selection']"
       duplicate_selection: "[title='duplicate selected']"
       delete_selection: "[title='delete selected']"
+      auto_layout: "#auto-layout-button"
   comment:
     selectors:
       _: ".workflow-editor-comment"
@@ -750,19 +752,21 @@ workflow_editor:
       freehand_comment: ".freehand-workflow-comment"
       freehand_path: ".freehand-workflow-comment path"
       delete: "button[title='Delete comment']"
+  inputs:
+    selectors:
+      activity_button: "#activity-workflow-editor-inputs"
+      activity_panel: ".activity-panel[data-description='Inputs']"
+      input: ".workflow-input-button[data-id='${id}']"
   selectors:
+    node_inspector: '.tool-inspector'
+    node_inspector_close: ".tool-inspector [title='close']"
     canvas_body: '#workflow-canvas'
     edit_annotation: '#workflow-annotation'
     edit_name: '#workflow-name'
-    license_selector:
-      selector: 'license selector'
-      type: data-description
-    edit_license_link:
-      selector: 'edit license link'
-      type: data-description
-    license_select:
-      selector: 'license select'
-      type: data-description
+    license_selector: '[data-description="license select"]'
+    license_current_value: '[data-description="license select"] .multiselect__single'
+    license_selector_input: '[data-description="license select"] input.multiselect__input'
+    license_selector_option: '[data-description="license select"] .multiselect__element'
     license_save:
       selector: 'license save'
       type: data-description
@@ -815,10 +819,7 @@ workflow_editor:
       type: xpath
       selector: >
         //div[@data-label='Change datatype']//div[contains(@class, 'multiselect')]
-    select_datatype_text_search:
-      type: xpath
-      selector: >
-        //input[@class="multiselect__input"]
+    select_datatype_text_search: "div[data-label='Change datatype'] .multiselect__input"
     select_datatype:
       type: xpath
       selector: >
@@ -842,10 +843,12 @@ workflow_editor:
     tool_version_button: ".tool-versions"
     connector_for: "#connection-${sink_id}-${source_id}"
     connector_invalid_for: "#connection-${sink_id}-${source_id} .connection.invalid"
-    save_button: '.editor-button-save'
+    save_button: '#workflow-save-button'
     save_workflow_confirmation_button: '#save-workflow-confirmation .btn-primary'
     state_modal_body: '.state-upgrade-modal'
     modal_button_continue: '.modal-footer .btn'
+    workflow_activity: '#activity-workflow-editor-workflows'
+    save_as_activity: "#activity-save-workflow-as"
 
 workflow_show:
   selectors:
@@ -855,8 +858,12 @@ workflow_show:
 
 invocations:
   selectors:
+    activity: "#activity-invocation"
+    activity_expand: ".activity-panel-footer"
     invocations_table: '#invocations-grid .grid-table'
     invocations_table_rows: '#invocations-grid .grid-table [data-description="grid item"]'
+    invocations_panel_list: '[data-description="Workflow Invocations"] .scroll-list'
+    invocations_panel_list_items: '[data-description="Workflow Invocations"] .scroll-list button.panel-item'
     pager: '[data-description="grid pager"]'
     pager_page: '[data-description="grid pager"] .gx-grid-pager-page [aria-posinset=${page}]'
     pager_page_next: '[data-description="grid pager"] .gx-grid-pager-next button'
@@ -864,11 +871,9 @@ invocations:
     pager_page_first: '[data-description="grid pager"] .gx-grid-pager-first button'
     pager_page_previous: '[data-description="grid pager"] .gx-grid-pager-prev button'
     pager_page_active: '[data-description="grid pager"] .gx-grid-pager-page.active button'
-    state_details: '.workflow-invocation-state-component'
-    toggle_invocation_details: '[data-description="toggle row details"]'
-    progress_steps_note: '.workflow-invocation-state-component .steps-progress .progressNote'
-    progress_jobs_note: '.workflow-invocation-state-component .jobs-progress .progressNote'
-    hide_invocation_graph: '.workflow-invocation-state-component [data-description="hide invocation graph"]'
+    state_details: '[data-description="workflow invocation state"]'
+    progress_steps_note: '[data-description="workflow invocation state"] .steps-progress .progress-note'
+    progress_jobs_note: '[data-description="workflow invocation state"] .jobs-progress .progress-note'
     invocation_tab:
       type: xpath
       selector: '//a[text()="${label}"]'
@@ -880,16 +885,20 @@ invocations:
     step_title: '[data-step="${order_index}"] .step-title'
     step_details: '[data-step="${order_index}"] .portlet-operations'
     step_output_collection: '[data-step="${order_index}"] .invocation-step-output-collection-details'
-    step_output_collection_toggle: '[data-step="${order_index}"] .invocation-step-output-collection-details .name'
+    step_output_collection_toggle: '[data-step="${order_index}"] .invocation-step-output-collection-details .content-title'
     step_output_collection_element_identifier:
       type: xpath
       selector: '//span[contains(@class, "content-title name")][text()="${element_identifier}"]'
     step_output_collection_element_datatype: '[data-step="${order_index}"] .invocation-step-output-collection-details .not-loading .datatype .value'
     step_job_details: '[data-step="${order_index}"] .invocation-step-job-details'
-    step_job_table: '[data-step="${order_index}"] .invocation-step-job-details table'
-    step_job_table_rows: '[data-step="${order_index}"] .invocation-step-job-details table tbody tr'
-    step_job_information: '[data-step="${order_index}"] .invocation-step-job-details table tbody .b-table-details .info_data_table'
-    step_job_information_tool_id: '[data-step="${order_index}"] .invocation-step-job-details table tbody .b-table-details .info_data_table #galaxy-tool-id'
+    step_job_information: '[data-step="${order_index}"] .invocation-step-job-details .info_data_table'
+    step_job_information_tool_id: '[data-step="${order_index}"] .invocation-step-job-details .info_data_table #galaxy-tool-id'
+    export_tab: '.invocation-export-tab'
+    export_output_format: '[data-invocation-export-type="${type}"] .card-body'
+    export_destination: '[data-invocation-export-destination="${destination}"] .card-body'
+    wizard_next_button: '.wizard-actions .go-next-btn'
+    wizard_export_button: '.wizard-actions .go-next-btn.btn-primary'
+    export_download_link: '.download-link'
 
 tour:
   popover:
@@ -900,6 +909,18 @@ tour:
       next: '${_} .tour-next'
       end: '${_} .tour-end'
 
+tools:
+  selectors:
+    activity: '#activity-tools'
+    tools_activity_workflow_editor: '#activity-workflow-editor-tools'
+    workflows_activity: '#activity-workflow-editor-workflows'
+    body: '#center #tool-card-body'
+    execute: '#execute'
+    help: 'div.form-help'
+    search: '#toolbox-panel .search-query'
+    clear_search: '#toolbox-panel .search-clear'
+    title: '.toolSectionTitle'
+
 admin:
   allowlist:
     selectors:
@@ -1008,6 +1029,7 @@ libraries:
 
   selectors:
     _: '#libraries_list'
+    activity: '#activity-libraries'
     create_new_library_btn: '#create-new-lib'
     permission_library_btn: '.permission_library_btn'
     toolbtn_save_permissions: '.toolbtn_save_permissions'
@@ -1031,17 +1053,30 @@ libraries:
       add_to_history_collection: '.add-to-history-collection'
       # TODO: Most of these aren't very good selectors but the same DOM elements
       # are reused without adding specific classes, IDs, or roles to anything.
-      import_modal: '.modal'
-      import_datasets_ok_button: '.modal-footer .buttons #button-0'
-      import_datasets_cancel_button: '.modal-footer .buttons #button-1'
+      import_modal: '.directory-dataset-picker'
+      import_datasets_from_history_modal: '.selection-dialog-modal'
+      import_datasets_from_history_modal_history_search: '.selection-dialog-modal .search-query'
+      import_datasets_from_history_modal_dataset_search: '.selection-dialog-modal input[placeholder="search datasets"]'
+      import_datasets_from_history_modal_list_is_ready: '.selection-dialog-modal .selection-dialog-table[aria-busy="false"]'
+      import_datasets_from_history_modal_select_list_items: '.selection-dialog-modal table tbody tr'
+      import_datasets_from_history_modal_select_list_item_by_index: '.selection-dialog-modal table tbody tr[aria-rowindex="${row_index}"] td[aria-colindex="1"]'
+      import_datasets_from_history_modal_ok: '.selection-dialog-modal [data-description="selection dialog ok"]'
+      import_datasets_from_history_modal_cancel: '.selection-dialog-modal [data-description="selection dialog cancel"]'
+      add_to_history_as_collection:
+        type: xpath
+        selector: '//button[contains(text(), "Continue")]'
+      import_datasets_ok_button:
+        type: xpath
+        selector: '//button[contains(text(), "Import")]'
+      import_datasets_cancel_button:
+        type: xpath
+        selector: '//button[contains(text(), "Close")]'
       export_to_history_options: '#library-collection-type-select'
       export_to_history_paired_option: 'option[value="${collection_option}"]'
       export_to_history_collection_name: '.collection-name'
       export_to_history_new_history: 'input[name=history_name]'
-      clear_filters: '.clear-filters-link'
+      clear_filters: "button.clear-filters-link"
       import_progress_bar: '.progress-bar-import'
-      import_history_content: '.library_selected_history_content'
-      import_history_contents_items: '.library_selected_history_content tbody > tr'
       import_from_path_textarea: '#import_paths'
       select_all: '#select-all-checkboxes'
       select_one: '.lib-folder-checkbox'
@@ -1059,8 +1094,10 @@ libraries:
       download_button: '#download-btn'
       delete_btn: '.toolbtn-bulk-delete'
       toast_msg: '.b-toast'
-      toast_warning: '.b-toast-warning'
-      select_import_dir_item: 'li[full_path="${name}"] .jstree-anchor'
+      alert_not_exists_user_import_dir:
+        type: xpath
+        selector: //div[contains(@class, "alert-danger") and contains(normalize-space(text()), "Your user import directory does not exist")]
+      select_import_dir_item: '[for="drilldown-option-${name}"]'
       import_dir_btn:
         type: xpath
         selector: '//button[contains(text(), "Import")]'
@@ -1070,7 +1107,6 @@ libraries:
       private_dataset_icon: '.fa-key'
       open_location_details_btn: '.details-btn'
       location_details_ok_btn: '#details-modal .btn-primary'
-      add_history_items: '#dataset_add_bulk'
 
     labels:
       from_history: 'from History'
@@ -1127,7 +1163,8 @@ upload:
     setting_space_to_tab: '.upload-space-to-tab'
     source_button: '#upload-row-${n} .upload-source'
     start: '#activity-upload'
-    start_button: '#btn-start'
+    start_button: '#regular #btn-start'
+    local_button: '#btn-local'
 
 new_user_welcome:
   selectors:
diff --git a/client/src/utils/navigation/schema.ts b/client/src/utils/navigation/schema.ts
index ac4a2a8f60aed0100bcfa71d08a8655d12fd3c34..12dc5489e6fb886de51ec06d485296ca927d2d44 100644
--- a/client/src/utils/navigation/schema.ts
+++ b/client/src/utils/navigation/schema.ts
@@ -1,5 +1,4 @@
-import type { Component, SelectorTemplate } from "./index";
-import { ROOT_COMPONENT as raw_root_component } from "./index";
+import { type Component, ROOT_COMPONENT as raw_root_component, type SelectorTemplate } from "./index";
 
 interface Root_messages extends Component {
     all: SelectorTemplate;
@@ -419,7 +418,8 @@ interface Rootworkflow_run extends Component {
     validation_error: SelectorTemplate;
     expand_form_link: SelectorTemplate;
     expanded_form: SelectorTemplate;
-    new_history_target_link: SelectorTemplate;
+    new_history_badge: SelectorTemplate;
+    history_target_link: SelectorTemplate;
     runtime_setting_button: SelectorTemplate;
     runtime_setting_target: SelectorTemplate;
     input_select_field: SelectorTemplate;
@@ -480,6 +480,8 @@ interface Rootworkflow_show extends Component {
 interface Rootinvocations extends Component {
     invocations_table: SelectorTemplate;
     invocations_table_rows: SelectorTemplate;
+    invocations_panel_list: SelectorTemplate;
+    invocations_panel_list_items: SelectorTemplate;
     pager: SelectorTemplate;
     pager_page: SelectorTemplate;
     pager_page_next: SelectorTemplate;
@@ -488,10 +490,8 @@ interface Rootinvocations extends Component {
     pager_page_previous: SelectorTemplate;
     pager_page_active: SelectorTemplate;
     state_details: SelectorTemplate;
-    toggle_invocation_details: SelectorTemplate;
     progress_steps_note: SelectorTemplate;
     progress_jobs_note: SelectorTemplate;
-    hide_invocation_graph: SelectorTemplate;
     invocation_tab: SelectorTemplate;
     invocation_details_tab: SelectorTemplate;
     input_details_title: SelectorTemplate;
@@ -503,8 +503,6 @@ interface Rootinvocations extends Component {
     step_output_collection_element_identifier: SelectorTemplate;
     step_output_collection_element_datatype: SelectorTemplate;
     step_job_details: SelectorTemplate;
-    step_job_table: SelectorTemplate;
-    step_job_table_rows: SelectorTemplate;
     step_job_information: SelectorTemplate;
     step_job_information_tool_id: SelectorTemplate;
 }
diff --git a/client/src/utils/redirect.test.ts b/client/src/utils/redirect.test.ts
index 4be3d59d79142c4aa76d9239456f0f004796d7f6..a3887f510a3748f52654b29a5820412be2048b60 100644
--- a/client/src/utils/redirect.test.ts
+++ b/client/src/utils/redirect.test.ts
@@ -10,6 +10,10 @@ test("route prefix changes", async () => {
     expect(withPrefix("http://")).toEqual("http://");
     expect(withPrefix("/")).toEqual("/prefix/");
     expect(withPrefix("/home")).toEqual("/prefix/home");
+    // keep protocols in query parameters intact
+    expect(withPrefix("/authz/cilogon/login?idphint=https://test.com")).toEqual(
+        "/prefix/authz/cilogon/login?idphint=https://test.com"
+    );
     // ensure that it can only be called once
     expect(withPrefix(withPrefix("/home"))).toEqual("/prefix/prefix/home");
     // This doesn't do what it looks like it should do?
diff --git a/client/src/utils/redirect.ts b/client/src/utils/redirect.ts
index 3b074309300716c30347e908850f6dcd8db4bd1c..756613723bf0b52017ee65651310263b18564c2d 100644
--- a/client/src/utils/redirect.ts
+++ b/client/src/utils/redirect.ts
@@ -10,7 +10,7 @@ export function reloadPage() {
     window.location.reload();
 }
 
-const slashCleanup = /(\/)+/g;
+const slashCleanup = /(?<!:)(\/)+/g;
 /**
  * Prepends the configured app root to given url
  * @param path
diff --git a/client/src/utils/setDrag.ts b/client/src/utils/setDrag.ts
index baa079764f3642b1cfa67e0300a2a6400c1d7307..f6d1023c9241e4a3042ef19a2e9ef01cfcab04ef 100644
--- a/client/src/utils/setDrag.ts
+++ b/client/src/utils/setDrag.ts
@@ -1,8 +1,11 @@
 /**
  * Helper to configure datatransfer for drag & drop operations
  */
+import { type DCESummary, isDCE } from "@/api";
 import { type EventData, useEventStore } from "@/stores/eventStore";
 
+type NamedDCESummary = DCESummary & { name: string };
+
 export function setDrag(evt: DragEvent, data?: EventData, multiple = false) {
     const eventStore = useEventStore();
     if (data) {
@@ -25,3 +28,29 @@ export function clearDrag() {
     const eventStore = useEventStore();
     eventStore.clearDragData();
 }
+
+export function setItemDragstart<T>(
+    item: T,
+    event: DragEvent,
+    itemIsSelected = false,
+    selectionSize = 0,
+    selectedItems?: Map<string, T>
+) {
+    if (selectedItems && itemIsSelected && selectionSize > 1) {
+        const selectedItemsObj: Record<string, T> = {};
+        for (const [key, value] of selectedItems) {
+            setCollectionElementName(value as any);
+            selectedItemsObj[key] = value;
+        }
+        setDrag(event, selectedItemsObj, true);
+    } else {
+        setCollectionElementName(item as any);
+        setDrag(event, item as any);
+    }
+}
+
+function setCollectionElementName<T extends NamedDCESummary>(obj: T) {
+    if (isDCE(obj as object)) {
+        obj["name"] = obj.element_identifier;
+    }
+}
diff --git a/client/src/utils/simple-error.ts b/client/src/utils/simple-error.ts
index 05680d279ab93ba64f61c1c246e0e8ea86c77346..daecb876b50e2379f26eca0e06a9d509460f974d 100644
--- a/client/src/utils/simple-error.ts
+++ b/client/src/utils/simple-error.ts
@@ -6,6 +6,8 @@ export function errorMessageAsString(e: any, defaultMessage = "Request failed.")
         message = e.response.data.err_msg;
     } else if (e && e.data && e.data.err_msg) {
         message = e.data.err_msg;
+    } else if (e && e.err_msg) {
+        message = e.err_msg;
     } else if (e && e.response) {
         message = `${e.response.statusText} (${e.response.status})`;
     } else if (e instanceof Error) {
diff --git a/client/src/utils/strings.ts b/client/src/utils/strings.ts
index 503169c6f9af56869a14116e026e4ae09592cbae..083e10029962dbcaa2d1a89384e7702acd2ae230 100644
--- a/client/src/utils/strings.ts
+++ b/client/src/utils/strings.ts
@@ -28,3 +28,24 @@ export function orList(items: string[]): string {
         .reverse()
         .join("");
 }
+
+/**
+ * Capitalize the first letter of each word of a string in snake_case format
+ *
+ * @param str String to capitalize in snake_case format (e.g. "this_is_a_string")
+ * @returns Capitalized string in title case (e.g. "This Is A String")
+ */
+export function snakeCaseToTitleCase(str: string): string {
+    return str
+        .split("_")
+        .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
+        .join(" ");
+}
+
+/**
+ * Capitalize the first letter of a string
+ */
+export function capitalizeFirstLetter(str: string): string {
+    str = str.trim();
+    return str.charAt(0).toUpperCase() + str.slice(1);
+}
diff --git a/client/src/utils/upload-payload.js b/client/src/utils/upload-payload.js
index 2fbca26c06daeadfd1fee091b61635d1b2c25903..d78735b1c819ff1bde2f4d8aa7d4bc81899b7eff 100644
--- a/client/src/utils/upload-payload.js
+++ b/client/src/utils/upload-payload.js
@@ -1,4 +1,5 @@
 export const DEFAULT_FILE_NAME = "New File";
+export const USER_FILE_PREFIX = "gxuserfiles://";
 export const URI_PREFIXES = [
     "http://",
     "https://",
@@ -7,7 +8,7 @@ export const URI_PREFIXES = [
     "gxfiles://",
     "gximport://",
     "gxuserimport://",
-    "gxuserfiles://",
+    USER_FILE_PREFIX,
     "gxftp://",
     "drs://",
     "invenio://",
diff --git a/client/src/viz/trackster.js b/client/src/viz/trackster.js
index d3c3162479a4fea38adfabe1e870ed364b582609..aef56dc7c27b0c2393a547d391cf7538250d50d0 100644
--- a/client/src/viz/trackster.js
+++ b/client/src/viz/trackster.js
@@ -74,23 +74,30 @@ export class TracksterUI extends Backbone.Model {
             },
             bookmarks: bookmarks,
         };
-
-        // Make call to save visualization.
-        return $.ajax({
-            url: `${getAppRoot()}visualization/save`,
-            type: "POST",
+        const request = {
             dataType: "json",
-            data: {
+            contentType: "application/json; charset=utf-8",
+            data: JSON.stringify({
                 id: this.view.vis_id,
                 title: this.view.config.get_value("name"),
                 dbkey: this.view.dbkey,
                 type: "trackster",
-                vis_json: JSON.stringify(viz_config),
-            },
-        })
+                config: viz_config,
+            }),
+        };
+        if (!this.view.vis_id) {
+            request.url = `${getAppRoot()}api/visualizations`;
+            request.type = "POST";
+        } else {
+            request.url = `${getAppRoot()}api/visualizations/${this.view.vis_id}`;
+            request.type = "PUT";
+        }
+
+        // Make call to save visualization.
+        return $.ajax(request)
             .success((vis_info) => {
                 Galaxy.modal.hide();
-                this.view.vis_id = vis_info.vis_id;
+                this.view.vis_id = vis_info.id;
                 this.view.has_changes = false;
 
                 // Needed to set URL when first saving a visualization.
diff --git a/client/tests/jest/jest-environment.js b/client/tests/jest/jest-environment.js
index 4664dbc122be30661199e38dcfa480e4d116190b..0db72743393b9ffe00c4d03c7226e8d5d5b4d57a 100644
--- a/client/tests/jest/jest-environment.js
+++ b/client/tests/jest/jest-environment.js
@@ -1,6 +1,6 @@
 import "jsdom-worker";
 
-import JSDOMEnvironment from "jest-environment-jsdom";
+import JSDOMEnvironment from "jest-fixed-jsdom";
 
 class MockObserver {
     constructor(...args) {}
diff --git a/client/tests/jest/jest.config.js b/client/tests/jest/jest.config.js
index 58f9c852e11adb56f3fef6ab086b6297e955e0a2..aa7a796cf58459e23d77808e863ec530a997bf68 100644
--- a/client/tests/jest/jest.config.js
+++ b/client/tests/jest/jest.config.js
@@ -12,9 +12,28 @@ const modulesToTransform = [
     "winbox",
     "pretty-bytes",
     "@fortawesome",
-    "openapi-typescript-fetch",
 ].join("|");
 
+// Override verbatimModuleSyntax to false to allow jest to transform the module syntax like it wants.
+// This is necessary to allow jest to transform the module syntax to commonjs, which is necessary for
+// jest to work properly.  I think.
+
+const configOverride = {
+    "^.+.tsx?$": [
+        "ts-jest",
+        {
+            tsconfig: {
+                verbatimModuleSyntax: false,
+            },
+        },
+    ],
+};
+
+const mergedTSJTransform = {
+    ...tsjPreset.transform,
+    ...configOverride,
+};
+
 module.exports = {
     preset: "ts-jest",
     clearMocks: true,
@@ -42,13 +61,16 @@ module.exports = {
     roots: ["<rootDir>/src/", "<rootDir>/tests/jest/standalone/"],
     setupFilesAfterEnv: ["<rootDir>/tests/jest/jest.setup.js"],
     testEnvironment: "<rootDir>/tests/jest/jest-environment.js",
+    testEnvironmentOptions: {
+        customExportConditions: ["msw"],
+    },
     testPathIgnorePatterns: ["/node_modules/", "/dist/"],
     transform: {
         "^.+\\.js$": "babel-jest",
         "^.*\\.(vue)$": "@vue/vue2-jest",
         "^.+\\.ya?ml$": "<rootDir>/tests/jest/yaml-jest.js",
         "^.+\\.txt$": "<rootDir>/tests/jest/jest-raw-loader.js",
-        ...tsjPreset.transform,
+        ...mergedTSJTransform,
     },
     transformIgnorePatterns: [`/node_modules/(?!${modulesToTransform})`],
 };
diff --git a/client/tests/jest/jest.setup.js b/client/tests/jest/jest.setup.js
index 2bf7b9188cf2b3ed3ce52116adb54d5465c5379d..505e186fd5170b412fd4fa1bf77b2f23a2de4360 100644
--- a/client/tests/jest/jest.setup.js
+++ b/client/tests/jest/jest.setup.js
@@ -1,5 +1,6 @@
 import "@testing-library/jest-dom";
 import "@testing-library/jest-dom/jest-globals";
+import "fake-indexeddb/auto";
 
 import Vue from "vue";
 
@@ -9,7 +10,6 @@ Vue.config.devtools = false;
 
 /* still don't understand what was invoking the following, but nothing should,
 and this makes the tag tests work correctly */
-global.XMLHttpRequest = undefined;
 global.setImmediate = global.setTimeout;
 
 // Always mock the following imports
diff --git a/client/tests/test-data/index.ts b/client/tests/test-data/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b4fa53c750deb79931ddbcd4848e1c99811e1843
--- /dev/null
+++ b/client/tests/test-data/index.ts
@@ -0,0 +1,19 @@
+import { type RegisteredUser } from "@/api";
+
+export function getFakeRegisteredUser(data: Partial<RegisteredUser> = {}): RegisteredUser {
+    return {
+        id: "fake_user_id",
+        email: "fake_user_email",
+        tags_used: [],
+        isAnonymous: false,
+        username: "fake_username",
+        total_disk_usage: 0,
+        nice_total_disk_usage: "0.0 bytes",
+        deleted: false,
+        purged: false,
+        is_admin: false,
+        preferences: {},
+        quota: "default",
+        ...data,
+    };
+}
diff --git a/client/tests/test-data/paired-collection-creator.data.js b/client/tests/test-data/paired-collection-creator.data.js
index 1e2638c8a754c495a707a526696e544dea1113a1..2f8a1bc10f8734d8c938e3e8e1c291adc63a40b8 100644
--- a/client/tests/test-data/paired-collection-creator.data.js
+++ b/client/tests/test-data/paired-collection-creator.data.js
@@ -2,39 +2,39 @@ import STATES from "mvc/dataset/states";
 // ============================================================================
 // plain 3 step job chain
 var datasets1 = [
-    { name: "SET1-01_1.fastq", state: STATES.OK },
-    { name: "SET1-01_2.fastq", state: STATES.OK },
-    { name: "SET1-02_1.fastq", state: STATES.OK },
-    { name: "SET1-02_2.fastq", state: STATES.OK },
-    { name: "SET1-03_1.fastq", state: STATES.OK },
-    { name: "SET1-03_2.fastq", state: STATES.OK },
-    { name: "SET1-04_1.fastq", state: STATES.OK },
-    { name: "SET1-04_2.fastq", state: STATES.OK },
-    { name: "SET1-05_1.fastq", state: STATES.OK },
-    { name: "SET1-05_2.fastq", state: STATES.OK },
-    { name: "SET1-06_1.fastq", state: STATES.OK },
-    { name: "SET1-06_2.fastq", state: STATES.OK },
-    { name: "SET1-07_1.fastq", state: STATES.OK },
-    { name: "SET1-07_2.fastq", state: STATES.OK },
+    { name: "SET1-01_1.fastq", state: STATES.OK, id: "011" },
+    { name: "SET1-01_2.fastq", state: STATES.OK, id: "012" },
+    { name: "SET1-02_1.fastq", state: STATES.OK, id: "021" },
+    { name: "SET1-02_2.fastq", state: STATES.OK, id: "022" },
+    { name: "SET1-03_1.fastq", state: STATES.OK, id: "031" },
+    { name: "SET1-03_2.fastq", state: STATES.OK, id: "032" },
+    { name: "SET1-04_1.fastq", state: STATES.OK, id: "041" },
+    { name: "SET1-04_2.fastq", state: STATES.OK, id: "042" },
+    { name: "SET1-05_1.fastq", state: STATES.OK, id: "051" },
+    { name: "SET1-05_2.fastq", state: STATES.OK, id: "052" },
+    { name: "SET1-06_1.fastq", state: STATES.OK, id: "061" },
+    { name: "SET1-06_2.fastq", state: STATES.OK, id: "062" },
+    { name: "SET1-07_1.fastq", state: STATES.OK, id: "071" },
+    { name: "SET1-07_2.fastq", state: STATES.OK, id: "072" },
 ];
 
 var datasets2 = [
-    { name: "DP134_1_FS_PSII_FSB_42C_A10.1.fastq", state: STATES.OK },
-    { name: "DP134_1_FS_PSII_FSB_42C_A10.2.fastq", state: STATES.OK },
+    { name: "DP134_1_FS_PSII_FSB_42C_A10.1.fastq", state: STATES.OK, id: "101" },
+    { name: "DP134_1_FS_PSII_FSB_42C_A10.2.fastq", state: STATES.OK, id: "102" },
 ];
 
 var datasets3 = [
-    { name: "UII_moo_1.1.fastq", state: STATES.OK },
-    { name: "UII_moo_1.2.fastq", state: STATES.OK },
+    { name: "UII_moo_1.1.fastq", state: STATES.OK, id: "11" },
+    { name: "UII_moo_1.2.fastq", state: STATES.OK, id: "12" },
 ];
 
 var datasets4 = [
-    { name: "SET1-01_R1.fastq", state: STATES.OK },
-    { name: "SET1-01_R2.fastq", state: STATES.OK },
-    { name: "SET1-02_R1.fastq", state: STATES.OK },
-    { name: "SET1-02_R2.fastq", state: STATES.OK },
-    { name: "SET1-03_R1.fastq", state: STATES.OK },
-    { name: "SET1-03_R2.fastq", state: STATES.OK },
+    { name: "SET1-01_R1.fastq", state: STATES.OK, id: "111" },
+    { name: "SET1-01_R2.fastq", state: STATES.OK, id: "112" },
+    { name: "SET1-02_R1.fastq", state: STATES.OK, id: "211" },
+    { name: "SET1-02_R2.fastq", state: STATES.OK, id: "212" },
+    { name: "SET1-03_R1.fastq", state: STATES.OK, id: "311" },
+    { name: "SET1-03_R2.fastq", state: STATES.OK, id: "312" },
 ];
 
 var datasets1CreateRequestJSON = {
diff --git a/client/tsconfig.json b/client/tsconfig.json
index a1d577d10852503c732f2c3a73dbb70ac2d560f2..86381a0cbe583a9f29849bc2e47f725faf81e593 100644
--- a/client/tsconfig.json
+++ b/client/tsconfig.json
@@ -1,16 +1,10 @@
 {
     "extends": "@vue/tsconfig/tsconfig.json",
     "compilerOptions": {
-        "target": "es2016",
+        "target": "es2020",
         "module": "es2020",
 
-        // @vue/tsconfig now sets this by default, but this doesn't play well
-        // with the ts-jest presets.
-        // It doesn't seem to have any immediate impact, and may not be worth
-        // fighting with as we want to swap to vitest anyway
-        // TODO: revisit and drop this override
-        // See https://www.typescriptlang.org/tsconfig#verbatimModuleSyntax for context
-        "verbatimModuleSyntax": false,
+        "verbatimModuleSyntax": true,
 
         "baseUrl": ".",
         "paths": {
diff --git a/client/webpack.config.js b/client/webpack.config.js
index 6ca6b748151d59b23082075235eaf38fcd362c81..43699d475e3a681dce99ecaf53774a2dbca13723 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -25,6 +25,9 @@ const modulesExcludedFromLibs = [
     "elkjs",
     "@citation-js",
     "citeproc",
+    "vega",
+    "vega-embed",
+    "vega-lite",
 ].join("|");
 
 const buildDate = new Date();
diff --git a/client/yarn.lock b/client/yarn.lock
index 64aea473dbb412659c42d2244d8199fd5b00e702..cd6c4bf5f55a506c2997cf701dfc388cb7de30c0 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -7,10 +7,10 @@
   resolved "https://registry.yarnpkg.com/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz#bd9154aec9983f77b3a034ecaa015c2e4201f6cf"
   integrity sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==
 
-"@adobe/css-tools@^4.3.1":
-  version "4.3.2"
-  resolved "https://registry.yarnpkg.com/@adobe/css-tools/-/css-tools-4.3.2.tgz#a6abc715fb6884851fca9dad37fc34739a04fd11"
-  integrity sha512-DA5a1C0gD/pLOvhv33YMrbf2FK3oUzwNl9oOJqE4XVjuEtt6XIakRcsd7eLiOSPkp1kTRQGICTA8cKra/vFbjw==
+"@adobe/css-tools@^4.4.0":
+  version "4.4.0"
+  resolved "https://registry.yarnpkg.com/@adobe/css-tools/-/css-tools-4.4.0.tgz#728c484f4e10df03d5a3acd0d8adcbbebff8ad63"
+  integrity sha512-Ff9+ksdQQB3rMncgqDK78uLznstjyfIf2Arnh22pW8kBpLs6rpKDwgnZT46hin5Hl1WzazzK64DOrhSwYpS7bQ==
 
 "@ampproject/remapping@^2.1.0":
   version "2.2.0"
@@ -1340,6 +1340,28 @@
   resolved "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz"
   integrity sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==
 
+"@bundled-es-modules/cookie@^2.0.0":
+  version "2.0.0"
+  resolved "https://registry.yarnpkg.com/@bundled-es-modules/cookie/-/cookie-2.0.0.tgz#c3b82703969a61cf6a46e959a012b2c257f6b164"
+  integrity sha512-Or6YHg/kamKHpxULAdSqhGqnWFneIXu1NKvvfBBzKGwpVsYuFIQ5aBPHDnnoR3ghW1nvSkALd+EF9iMtY7Vjxw==
+  dependencies:
+    cookie "^0.5.0"
+
+"@bundled-es-modules/statuses@^1.0.1":
+  version "1.0.1"
+  resolved "https://registry.yarnpkg.com/@bundled-es-modules/statuses/-/statuses-1.0.1.tgz#761d10f44e51a94902c4da48675b71a76cc98872"
+  integrity sha512-yn7BklA5acgcBr+7w064fGV+SGIFySjCKpqjcWgBAIfrAkY+4GQTJJHQMeT3V/sgz23VTEVV8TtOmkvJAhFVfg==
+  dependencies:
+    statuses "^2.0.1"
+
+"@bundled-es-modules/tough-cookie@^0.1.6":
+  version "0.1.6"
+  resolved "https://registry.yarnpkg.com/@bundled-es-modules/tough-cookie/-/tough-cookie-0.1.6.tgz#fa9cd3cedfeecd6783e8b0d378b4a99e52bde5d3"
+  integrity sha512-dvMHbL464C0zI+Yqxbz6kZ5TOEp7GLW+pry/RWndAR8MJQAXZ2rPmIs8tziTZjeIyhSNZgZbCePtfSbdWqStJw==
+  dependencies:
+    "@types/tough-cookie" "^4.0.5"
+    tough-cookie "^4.1.4"
+
 "@cerner/duplicate-package-checker-webpack-plugin@^2.3.0":
   version "2.3.0"
   resolved "https://registry.npmjs.org/@cerner/duplicate-package-checker-webpack-plugin/-/duplicate-package-checker-webpack-plugin-2.3.0.tgz"
@@ -1424,11 +1446,6 @@
   resolved "https://registry.yarnpkg.com/@eslint/js/-/js-8.52.0.tgz#78fe5f117840f69dc4a353adf9b9cd926353378c"
   integrity sha512-mjZVbpaeMZludF2fsWLD0Z9gCref1Tk4i9+wddjRvpUNqqcndPkBD09N/Mapey0b3jaXbLm2kICwFv2E64QinA==
 
-"@fastify/busboy@^2.0.0":
-  version "2.0.0"
-  resolved "https://registry.yarnpkg.com/@fastify/busboy/-/busboy-2.0.0.tgz#f22824caff3ae506b18207bad4126dbc6ccdb6b8"
-  integrity sha512-JUFJad5lv7jxj926GPgymrWQxxjPYuJNiNjNMzqT+HiuP6Vl3dk5xzG+8sTX96np0ZAluvaMzPsjhHZ5rNuNQQ==
-
 "@fontsource/atkinson-hyperlegible@^5.0.17":
   version "5.0.17"
   resolved "https://registry.yarnpkg.com/@fontsource/atkinson-hyperlegible/-/atkinson-hyperlegible-5.0.17.tgz#d1a43a7403644f6ad31a54e8e1ae779693fbcd9d"
@@ -1439,6 +1456,11 @@
   resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-6.2.1.tgz#411e02a820744d3f7e0d8d9df9d82b471beaa073"
   integrity sha512-Sz07mnQrTekFWLz5BMjOzHl/+NooTdW8F8kDQxjWwbpOJcnoSg4vUDng8d/WR1wOxM0O+CY9Zw0nR054riNYtQ==
 
+"@fortawesome/fontawesome-common-types@6.7.1":
+  version "6.7.1"
+  resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-6.7.1.tgz#6201640f39fdcf8e41cd9d1a92b2da3a96817fa4"
+  integrity sha512-gbDz3TwRrIPT3i0cDfujhshnXO9z03IT1UKRIVi/VEjpNHtSBIP2o5XSm+e816FzzCFEzAxPw09Z13n20PaQJQ==
+
 "@fortawesome/fontawesome-common-types@^0.2.36":
   version "0.2.36"
   resolved "https://registry.npmjs.org/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-0.2.36.tgz"
@@ -1511,6 +1533,45 @@
   resolved "https://registry.yarnpkg.com/@humanwhocodes/object-schema/-/object-schema-2.0.1.tgz#e5211452df060fa8522b55c7b3c0c4d1981cb044"
   integrity sha512-dvuCeX5fC9dXgJn9t+X5atfmgQAzUOWqS1254Gh0m6i8wKd10ebXkfNKiRK+1GWi/yTvvLDHpoxLr0xxxeslWw==
 
+"@inquirer/confirm@^3.0.0":
+  version "3.1.19"
+  resolved "https://registry.yarnpkg.com/@inquirer/confirm/-/confirm-3.1.19.tgz#29dbe7017905b94bcbb430448d399947796b111b"
+  integrity sha512-dcLbnxmhx3a72c4fM6CwhydG8rS8TZCXtCYU7kUraA+qU2Ue8gNCiYOxnlhb0H0wbTKL23lUo68fX0iMP8t2Dw==
+  dependencies:
+    "@inquirer/core" "^9.0.7"
+    "@inquirer/type" "^1.5.1"
+
+"@inquirer/core@^9.0.7":
+  version "9.0.7"
+  resolved "https://registry.yarnpkg.com/@inquirer/core/-/core-9.0.7.tgz#ec529c2e8b531d574155f12615fbff42bb615da4"
+  integrity sha512-wyqnTmlnd9p7cX6tfMlth+/Nx7vV2t/FvtO9VMSi2XjBkNy0MkPr19RSOyP3qrywdlJT+BQbEnXLPqq0wFMw3A==
+  dependencies:
+    "@inquirer/figures" "^1.0.5"
+    "@inquirer/type" "^1.5.1"
+    "@types/mute-stream" "^0.0.4"
+    "@types/node" "^22.0.0"
+    "@types/wrap-ansi" "^3.0.0"
+    ansi-escapes "^4.3.2"
+    cli-spinners "^2.9.2"
+    cli-width "^4.1.0"
+    mute-stream "^1.0.0"
+    signal-exit "^4.1.0"
+    strip-ansi "^6.0.1"
+    wrap-ansi "^6.2.0"
+    yoctocolors-cjs "^2.1.2"
+
+"@inquirer/figures@^1.0.5":
+  version "1.0.5"
+  resolved "https://registry.yarnpkg.com/@inquirer/figures/-/figures-1.0.5.tgz#57f9a996d64d3e3345d2a3ca04d36912e94f8790"
+  integrity sha512-79hP/VWdZ2UVc9bFGJnoQ/lQMpL74mGgzSYX1xUqCVk7/v73vJCMw1VuyWN1jGkZ9B3z7THAbySqGbCNefcjfA==
+
+"@inquirer/type@^1.5.1":
+  version "1.5.1"
+  resolved "https://registry.yarnpkg.com/@inquirer/type/-/type-1.5.1.tgz#cdd36732e38ea5d2b1a4336aada65ebe7d2765e0"
+  integrity sha512-m3YgGQlKNS0BM+8AFiJkCsTqHEFCWn6s/Rqye3mYwvqY6LdfUv12eSwbsgNzrYyrLXiy7IrrjDLPysaSBwEfhw==
+  dependencies:
+    mute-stream "^1.0.0"
+
 "@isaacs/cliui@^8.0.2":
   version "8.0.2"
   resolved "https://registry.yarnpkg.com/@isaacs/cliui/-/cliui-8.0.2.tgz#b37667b7bc181c168782259bab42474fbf52b550"
@@ -1794,14 +1855,6 @@
   resolved "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz"
   integrity sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==
 
-"@jridgewell/source-map@^0.3.2":
-  version "0.3.2"
-  resolved "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.2.tgz"
-  integrity sha512-m7O9o2uR8k2ObDysZYzdfhb08VuEml5oWGiosa1VdaPZ/A6QyPkAJuwN0Q1lhULOf6B7MtQmHENS743hWtCrgw==
-  dependencies:
-    "@jridgewell/gen-mapping" "^0.3.0"
-    "@jridgewell/trace-mapping" "^0.3.9"
-
 "@jridgewell/source-map@^0.3.3":
   version "0.3.5"
   resolved "https://registry.yarnpkg.com/@jridgewell/source-map/-/source-map-0.3.5.tgz#a3bb4d5c6825aab0d281268f47f6ad5853431e91"
@@ -1836,13 +1889,13 @@
     "@jridgewell/resolve-uri" "^3.1.0"
     "@jridgewell/sourcemap-codec" "^1.4.14"
 
-"@jridgewell/trace-mapping@^0.3.7":
-  version "0.3.14"
-  resolved "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.14.tgz"
-  integrity sha512-bJWEfQ9lPTvm3SneWwRFVLzrh6nhjwqw7TUFFBEMzwvg7t7PCDenf2lDwqo4NQXzdpgBXyFgDWnQA+2vkruksQ==
+"@jridgewell/trace-mapping@^0.3.20":
+  version "0.3.25"
+  resolved "https://registry.yarnpkg.com/@jridgewell/trace-mapping/-/trace-mapping-0.3.25.tgz#15f190e98895f3fc23276ee14bc76b675c2e50f0"
+  integrity sha512-vNk6aEwybGtawWmy/PzwnGDOjCkLWSD2wqvjGGAgOAwCGWySYXfYoxt00IJkTF+8Lb57DwOb3Aa0o9CApepiYQ==
   dependencies:
-    "@jridgewell/resolve-uri" "^3.0.3"
-    "@jridgewell/sourcemap-codec" "^1.4.10"
+    "@jridgewell/resolve-uri" "^3.1.0"
+    "@jridgewell/sourcemap-codec" "^1.4.14"
 
 "@jridgewell/trace-mapping@^0.3.9":
   version "0.3.15"
@@ -1867,6 +1920,18 @@
   resolved "https://registry.yarnpkg.com/@mdn/browser-compat-data/-/browser-compat-data-5.3.23.tgz#b662225a8b72482d940143a824b824677666bdae"
   integrity sha512-UnUu2mvVam9CtEMR2+k7eEsbtrYAecmd3SWRrXGDJrAIddnE6Ln+SmihqNMwHRa64VfNkVFSV/mVphvlwky/Bw==
 
+"@mswjs/interceptors@^0.29.0":
+  version "0.29.1"
+  resolved "https://registry.yarnpkg.com/@mswjs/interceptors/-/interceptors-0.29.1.tgz#e77fc58b5188569041d0440b25c9e9ebb1ccd60a"
+  integrity sha512-3rDakgJZ77+RiQUuSK69t1F0m8BQKA8Vh5DCS5V0DWvNY67zob2JhhQrhCO0AKLGINTRSFd1tBaHcJTkhefoSw==
+  dependencies:
+    "@open-draft/deferred-promise" "^2.2.0"
+    "@open-draft/logger" "^0.3.0"
+    "@open-draft/until" "^2.0.0"
+    is-node-process "^1.2.0"
+    outvariant "^1.2.1"
+    strict-event-emitter "^0.5.1"
+
 "@nodelib/fs.scandir@2.1.5":
   version "2.1.5"
   resolved "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz"
@@ -1897,6 +1962,24 @@
     consola "^2.15.0"
     node-fetch "^2.6.7"
 
+"@open-draft/deferred-promise@^2.2.0":
+  version "2.2.0"
+  resolved "https://registry.yarnpkg.com/@open-draft/deferred-promise/-/deferred-promise-2.2.0.tgz#4a822d10f6f0e316be4d67b4d4f8c9a124b073bd"
+  integrity sha512-CecwLWx3rhxVQF6V4bAgPS5t+So2sTbPgAzafKkVizyi7tlwpcFpdFqq+wqF2OwNBmqFuu6tOyouTuxgpMfzmA==
+
+"@open-draft/logger@^0.3.0":
+  version "0.3.0"
+  resolved "https://registry.yarnpkg.com/@open-draft/logger/-/logger-0.3.0.tgz#2b3ab1242b360aa0adb28b85f5d7da1c133a0954"
+  integrity sha512-X2g45fzhxH238HKO4xbSr7+wBS8Fvw6ixhTDuvLd5mqh6bJJCFAPwU9mPDxbcrRtfxv4u5IHCEH77BmxvXmmxQ==
+  dependencies:
+    is-node-process "^1.2.0"
+    outvariant "^1.4.0"
+
+"@open-draft/until@^2.0.0", "@open-draft/until@^2.1.0":
+  version "2.1.0"
+  resolved "https://registry.yarnpkg.com/@open-draft/until/-/until-2.1.0.tgz#0acf32f470af2ceaf47f095cdecd40d68666efda"
+  integrity sha512-U69T3ItWHvLwGg5eJ0n3I62nWuE6ilHlmz7zM0npLBRvPRd7e6NYmg54vvRtP5mZG7kZqZCFVdsTWo7BPtBujg==
+
 "@pinia/testing@0.1.3":
   version "0.1.3"
   resolved "https://registry.yarnpkg.com/@pinia/testing/-/testing-0.1.3.tgz#ee46a5a51d437f845ddc9c7b048c98b6a435e68b"
@@ -1914,6 +1997,38 @@
   resolved "https://registry.yarnpkg.com/@popperjs/core/-/core-2.11.8.tgz#6b79032e760a0899cd4204710beede972a3a185f"
   integrity sha512-P1st0aksCrn9sGZhp8GMYwBnQsbvAWsZAX44oXNNvLHGqAOcoVxmjZiohstwQ7SqKnbR47akdNi+uleWD8+g6A==
 
+"@redocly/ajv@^8.11.0":
+  version "8.11.0"
+  resolved "https://registry.yarnpkg.com/@redocly/ajv/-/ajv-8.11.0.tgz#2fad322888dc0113af026e08fceb3e71aae495ae"
+  integrity sha512-9GWx27t7xWhDIR02PA18nzBdLcKQRgc46xNQvjFkrYk4UOmvKhJ/dawwiX0cCOeetN5LcaaiqQbVOWYK62SGHw==
+  dependencies:
+    fast-deep-equal "^3.1.1"
+    json-schema-traverse "^1.0.0"
+    require-from-string "^2.0.2"
+    uri-js "^4.2.2"
+
+"@redocly/config@^0.6.2":
+  version "0.6.3"
+  resolved "https://registry.yarnpkg.com/@redocly/config/-/config-0.6.3.tgz#0dab6278721abd5aae6b375deee97665005b0472"
+  integrity sha512-hGWJgCsXRw0Ow4rplqRlUQifZvoSwZipkYnt11e3SeH1Eb23VUIDBcRuaQOUqy1wn0eevXkU2GzzQ8fbKdQ7Mg==
+
+"@redocly/openapi-core@^1.16.0":
+  version "1.17.1"
+  resolved "https://registry.yarnpkg.com/@redocly/openapi-core/-/openapi-core-1.17.1.tgz#d18c5223e5b578d64d789c4101b96cbb589162dc"
+  integrity sha512-PQxDLLNk5cBatJBBxvfk49HFw/nVozw1XZ6Dw/GX0Tviq+WxeEjEuLAKfnLVvb5L0wgs4TNmVG4Y+JyofSPu1A==
+  dependencies:
+    "@redocly/ajv" "^8.11.0"
+    "@redocly/config" "^0.6.2"
+    colorette "^1.2.0"
+    https-proxy-agent "^7.0.4"
+    js-levenshtein "^1.1.6"
+    js-yaml "^4.1.0"
+    lodash.isequal "^4.5.0"
+    minimatch "^5.0.1"
+    node-fetch "^2.6.1"
+    pluralize "^8.0.0"
+    yaml-ast-parser "0.0.43"
+
 "@sentry-internal/feedback@7.114.0":
   version "7.114.0"
   resolved "https://registry.yarnpkg.com/@sentry-internal/feedback/-/feedback-7.114.0.tgz#8a1c3d8bbd014c1823d30b9b1128eb244d357c3e"
@@ -2083,18 +2198,18 @@
   dependencies:
     "@sinonjs/commons" "^3.0.0"
 
-"@testing-library/jest-dom@^6.1.4":
-  version "6.1.4"
-  resolved "https://registry.yarnpkg.com/@testing-library/jest-dom/-/jest-dom-6.1.4.tgz#cf0835c33bc5ef00befb9e672b1e3e6a710e30e3"
-  integrity sha512-wpoYrCYwSZ5/AxcrjLxJmCU6I5QAJXslEeSiMQqaWmP2Kzpd1LvF/qxmAIW2qposULGWq2gw30GgVNFLSc2Jnw==
+"@testing-library/jest-dom@^6.4.8":
+  version "6.4.8"
+  resolved "https://registry.yarnpkg.com/@testing-library/jest-dom/-/jest-dom-6.4.8.tgz#9c435742b20c6183d4e7034f2b329d562c079daa"
+  integrity sha512-JD0G+Zc38f5MBHA4NgxQMR5XtO5Jx9g86jqturNTt2WUfRmLDIY7iKkWHDCCTiDuFMre6nxAD5wHw9W5kI4rGw==
   dependencies:
-    "@adobe/css-tools" "^4.3.1"
+    "@adobe/css-tools" "^4.4.0"
     "@babel/runtime" "^7.9.2"
     aria-query "^5.0.0"
     chalk "^3.0.0"
     css.escape "^1.5.1"
-    dom-accessibility-api "^0.5.6"
-    lodash "^4.17.15"
+    dom-accessibility-api "^0.6.3"
+    lodash "^4.17.21"
     redent "^3.0.0"
 
 "@tootallnate/once@2":
@@ -2175,6 +2290,11 @@
   dependencies:
     "@types/node" "*"
 
+"@types/cookie@^0.6.0":
+  version "0.6.0"
+  resolved "https://registry.yarnpkg.com/@types/cookie/-/cookie-0.6.0.tgz#eac397f28bf1d6ae0ae081363eca2f425bedf0d5"
+  integrity sha512-4Kh9a6B2bQciAhf7FSuMRRkUWecJgJu9nPnx3yzpsfXX/c50REIqpHY4C82bXP90qrLtXtkDxTZosYO3UpOwlA==
+
 "@types/d3-array@*":
   version "3.0.4"
   resolved "https://registry.yarnpkg.com/@types/d3-array/-/d3-array-3.0.4.tgz#44eebe40be57476cad6a0cd6a85b0f57d54185a2"
@@ -2392,36 +2512,15 @@
   dependencies:
     "@types/trusted-types" "*"
 
-"@types/eslint-scope@^3.7.3":
-  version "3.7.4"
-  resolved "https://registry.npmjs.org/@types/eslint-scope/-/eslint-scope-3.7.4.tgz"
-  integrity sha512-9K4zoImiZc3HlIp6AVUDE4CWYx22a+lhSZMYNpbjW04+YF0KWj4pJXnEMjdnFTiQibFFmElcsasJXDbdI/EPhA==
-  dependencies:
-    "@types/eslint" "*"
-    "@types/estree" "*"
-
-"@types/eslint@*":
-  version "8.4.5"
-  resolved "https://registry.npmjs.org/@types/eslint/-/eslint-8.4.5.tgz"
-  integrity sha512-dhsC09y1gpJWnK+Ff4SGvCuSnk9DaU0BJZSzOwa6GVSg65XtTugLBITDAAzRU5duGBoXBHpdR/9jHGxJjNflJQ==
-  dependencies:
-    "@types/estree" "*"
-    "@types/json-schema" "*"
-
-"@types/estree@*":
-  version "1.0.0"
-  resolved "https://registry.npmjs.org/@types/estree/-/estree-1.0.0.tgz"
-  integrity sha512-WulqXMDUTYAXCjZnk6JtIHPigp55cVtDgDrO2gHRwhyJto21+1zbVCtOYB2L1F9w4qCQ0rOGWBnBe0FNTiEJIQ==
-
-"@types/estree@^0.0.51":
-  version "0.0.51"
-  resolved "https://registry.npmjs.org/@types/estree/-/estree-0.0.51.tgz"
-  integrity sha512-CuPgU6f3eT/XgKKPqKd/gLZV1Xmvf1a2R5POBOGQa6uv82xpls89HU5zKeVoyR8XzHd1RGNOlQlvUe3CFkjWNQ==
-
 "@types/estree@^1.0.0":
-  version "1.0.2"
-  resolved "https://registry.yarnpkg.com/@types/estree/-/estree-1.0.2.tgz#ff02bc3dc8317cd668dfec247b750ba1f1d62453"
-  integrity sha512-VeiPZ9MMwXjO32/Xu7+OwflfmeoRwkE/qzndw42gGtgJwZopBnzy2gD//NN1+go1mADzkDcqf/KnFRSjTJ8xJA==
+  version "1.0.6"
+  resolved "https://registry.yarnpkg.com/@types/estree/-/estree-1.0.6.tgz#628effeeae2064a1b4e79f78e81d87b7e5fc7b50"
+  integrity sha512-AYnb1nQyY49te+VRAVgmzfcgjYS91mY5P0TKUDCLEM+gNnA+3T6rWITXRLYCpahpqSQbN5cE+gHpnPyXjHWxcw==
+
+"@types/estree@^1.0.5":
+  version "1.0.5"
+  resolved "https://registry.yarnpkg.com/@types/estree/-/estree-1.0.5.tgz#a6ce3e556e00fd9895dd872dd172ad0d4bd687f4"
+  integrity sha512-/kYRxGDLWzHOB7q+wtSUQlFrtcdUccpfy+X+9iMBpHK8QLLhx2wIPYuS5DYtR9Wa/YlZAbIovy7qVdB1Aq6Lyw==
 
 "@types/express-serve-static-core@*", "@types/express-serve-static-core@^4.17.18":
   version "4.17.30"
@@ -2447,6 +2546,11 @@
   resolved "https://registry.yarnpkg.com/@types/geojson/-/geojson-7946.0.10.tgz#6dfbf5ea17142f7f9a043809f1cd4c448cb68249"
   integrity sha512-Nmh0K3iWQJzniTuPRcJn5hxXkfB1T1pgB89SBig5PlJQU5yocazeu4jATJlaA0GYFKWMqDdvYemoSnF2pXgLVA==
 
+"@types/geojson@7946.0.4":
+  version "7946.0.4"
+  resolved "https://registry.yarnpkg.com/@types/geojson/-/geojson-7946.0.4.tgz#4e049756383c3f055dd8f3d24e63fb543e98eb07"
+  integrity sha512-MHmwBtCb7OCv1DSivz2UNJXPGU/1btAWRKlqJ2saEhVJkpkvqHMMaOpKg0v4sAbDWSQekHGvPVMM8nQ+Jen03Q==
+
 "@types/graceful-fs@^4.1.3":
   version "4.1.5"
   resolved "https://registry.npmjs.org/@types/graceful-fs/-/graceful-fs-4.1.5.tgz"
@@ -2480,10 +2584,10 @@
   dependencies:
     "@types/istanbul-lib-report" "*"
 
-"@types/jest@^29.5.6":
-  version "29.5.6"
-  resolved "https://registry.yarnpkg.com/@types/jest/-/jest-29.5.6.tgz#f4cf7ef1b5b0bfc1aa744e41b24d9cc52533130b"
-  integrity sha512-/t9NnzkOpXb4Nfvg17ieHE6EeSjDS2SGSpNYfoLbUAeL/EOueU/RSdOWFpfQTXBEM7BguYW1XQ0EbM+6RlIh6w==
+"@types/jest@^29.5.12":
+  version "29.5.12"
+  resolved "https://registry.yarnpkg.com/@types/jest/-/jest-29.5.12.tgz#7f7dc6eb4cf246d2474ed78744b05d06ce025544"
+  integrity sha512-eDC8bTvT/QhYdxJAulQikueigY5AsdBRH2yDKW3yveW7svY3+DzN84/2NUgkw10RTiJbWqZrTtoGVdYlvFJdLw==
   dependencies:
     expect "^29.0.0"
     pretty-format "^29.0.0"
@@ -2504,16 +2608,16 @@
     "@types/tough-cookie" "*"
     parse5 "^7.0.0"
 
-"@types/json-schema@*", "@types/json-schema@^7.0.8", "@types/json-schema@^7.0.9":
-  version "7.0.11"
-  resolved "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.11.tgz"
-  integrity sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==
-
 "@types/json-schema@^7.0.12":
   version "7.0.13"
   resolved "https://registry.yarnpkg.com/@types/json-schema/-/json-schema-7.0.13.tgz#02c24f4363176d2d18fc8b70b9f3c54aba178a85"
   integrity sha512-RbSSoHliUbnXj3ny0CNFOoxrIDV6SUGyStHsvDqosw6CkdPV8TtWGlfecuK4ToyMEAql6pzNxgCFKanovUzlgQ==
 
+"@types/json-schema@^7.0.8", "@types/json-schema@^7.0.9":
+  version "7.0.11"
+  resolved "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.11.tgz"
+  integrity sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==
+
 "@types/json5@^0.0.29":
   version "0.0.29"
   resolved "https://registry.yarnpkg.com/@types/json5/-/json5-0.0.29.tgz#ee28707ae94e11d2b827bcbe5270bcea7f3e71ee"
@@ -2559,11 +2663,25 @@
   resolved "https://registry.npmjs.org/@types/mime/-/mime-3.0.1.tgz"
   integrity sha512-Y4XFY5VJAuw0FgAqPNd6NNoV44jbq9Bz2L7Rh/J6jLTiHBSBJa9fxqQIvkIld4GsoDOcCbvzOUAbLPsSKKg+uA==
 
+"@types/mute-stream@^0.0.4":
+  version "0.0.4"
+  resolved "https://registry.yarnpkg.com/@types/mute-stream/-/mute-stream-0.0.4.tgz#77208e56a08767af6c5e1237be8888e2f255c478"
+  integrity sha512-CPM9nzrCPPJHQNA9keH9CVkVI+WR5kMa+7XEs5jcGQ0VoAGnLv242w8lIVgwAEfmE4oufJRaTc9PNLQl0ioAow==
+  dependencies:
+    "@types/node" "*"
+
 "@types/node@*":
   version "18.6.5"
   resolved "https://registry.npmjs.org/@types/node/-/node-18.6.5.tgz"
   integrity sha512-Xjt5ZGUa5WusGZJ4WJPbOT8QOqp6nDynVFRKcUt32bOgvXEoc6o085WNkYTMO7ifAj2isEfQQ2cseE+wT6jsRw==
 
+"@types/node@^22.0.0":
+  version "22.0.0"
+  resolved "https://registry.yarnpkg.com/@types/node/-/node-22.0.0.tgz#04862a2a71e62264426083abe1e27e87cac05a30"
+  integrity sha512-VT7KSYudcPOzP5Q0wfbowyNLaVR8QWUdw+088uFWwfvpY6uCWaXpqV6ieLAu9WBcnTa7H4Z5RLK8I5t2FuOcqw==
+  dependencies:
+    undici-types "~6.11.1"
+
 "@types/qs@*":
   version "6.9.7"
   resolved "https://registry.npmjs.org/@types/qs/-/qs-6.9.7.tgz"
@@ -2626,6 +2744,11 @@
   resolved "https://registry.npmjs.org/@types/stacktrace-js/-/stacktrace-js-0.0.33.tgz"
   integrity sha512-aqJ6QM9QThNL4dHBhwl1f9B0oDqiREkYLn9RldghUKsGeFWWGlCsqsRWxbh+hDvvmptMFqc4aIfFIGz9BBu8Qg==
 
+"@types/statuses@^2.0.4":
+  version "2.0.5"
+  resolved "https://registry.yarnpkg.com/@types/statuses/-/statuses-2.0.5.tgz#f61ab46d5352fd73c863a1ea4e1cef3b0b51ae63"
+  integrity sha512-jmIUGWrAiwu3dZpxntxieC+1n/5c3mjrImkmOSQ2NC5uP6cYO4aAZDdSmRcI5C1oiTmqlZGHC+/NmJrKogbP5A==
+
 "@types/strip-bom@^3.0.0":
   version "3.0.0"
   resolved "https://registry.yarnpkg.com/@types/strip-bom/-/strip-bom-3.0.0.tgz#14a8ec3956c2e81edb7520790aecf21c290aebd2"
@@ -2641,6 +2764,11 @@
   resolved "https://registry.yarnpkg.com/@types/tough-cookie/-/tough-cookie-4.0.2.tgz#6286b4c7228d58ab7866d19716f3696e03a09397"
   integrity sha512-Q5vtl1W5ue16D+nIaW8JWebSSraJVlK+EthKn7e7UcD4KWsaSJ8BqGPXNaPghgtcn/fhvrN17Tv8ksUsQpiplw==
 
+"@types/tough-cookie@^4.0.5":
+  version "4.0.5"
+  resolved "https://registry.yarnpkg.com/@types/tough-cookie/-/tough-cookie-4.0.5.tgz#cb6e2a691b70cb177c6e3ae9c1d2e8b2ea8cd304"
+  integrity sha512-/Ad8+nIOV7Rl++6f1BdKxFSMgmoqEoYbHRpPcx3JEfv8VRsQe9Z4mCXeJBzxs7mbHY/XOZZuXlRNfhpVPbs6ZA==
+
 "@types/trusted-types@*":
   version "2.0.5"
   resolved "https://registry.yarnpkg.com/@types/trusted-types/-/trusted-types-2.0.5.tgz#5cac7e7df3275bb95f79594f192d97da3b4fd5fe"
@@ -2656,6 +2784,11 @@
   resolved "https://registry.yarnpkg.com/@types/web-bluetooth/-/web-bluetooth-0.0.18.tgz#74bd1c8fd3a2058cb6fc76b188fcded50a83d866"
   integrity sha512-v/ZHEj9xh82usl8LMR3GarzFY1IrbXJw5L4QfQhokjRV91q+SelFqxQWSep1ucXEZ22+dSTwLFkXeur25sPIbw==
 
+"@types/wrap-ansi@^3.0.0":
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/@types/wrap-ansi/-/wrap-ansi-3.0.0.tgz#18b97a972f94f60a679fd5c796d96421b9abb9fd"
+  integrity sha512-ltIpx+kM7g/MLRZfkbL7EsCEjfzCcScLpkg37eXEtx5kmrAKBkTJwd1GIAjDSL8wTpM6Hzn5YO4pSb91BEwu1g==
+
 "@types/ws@^8.5.5":
   version "8.5.7"
   resolved "https://registry.yarnpkg.com/@types/ws/-/ws-8.5.7.tgz#1ca585074fe5d2c81dec7a3d451f244a2a6d83cb"
@@ -2858,60 +2991,28 @@
   dependencies:
     vue-demi ">=0.14.7"
 
-"@webassemblyjs/ast@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.11.1.tgz"
-  integrity sha512-ukBh14qFLjxTQNTXocdyksN5QdM28S1CxHt2rdskFyL+xFV7VremuBLVbmCePj+URalXBENx/9Lm7lnhihtCSw==
-  dependencies:
-    "@webassemblyjs/helper-numbers" "1.11.1"
-    "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
-
-"@webassemblyjs/ast@1.11.6", "@webassemblyjs/ast@^1.11.5":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/ast/-/ast-1.11.6.tgz#db046555d3c413f8966ca50a95176a0e2c642e24"
-  integrity sha512-IN1xI7PwOvLPgjcf180gC1bqn3q/QaOCwYUahIOhbYUu8KA/3tw2RT/T0Gidi1l7Hhj5D/INhJxiICObqpMu4Q==
+"@webassemblyjs/ast@1.12.1", "@webassemblyjs/ast@^1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/ast/-/ast-1.12.1.tgz#bb16a0e8b1914f979f45864c23819cc3e3f0d4bb"
+  integrity sha512-EKfMUOPRRUTy5UII4qJDGPpqfwjOmZ5jeGFwid9mnoqIFK+e0vqoi1qH56JpmZSzEL53jKnNzScdmftJyG5xWg==
   dependencies:
     "@webassemblyjs/helper-numbers" "1.11.6"
     "@webassemblyjs/helper-wasm-bytecode" "1.11.6"
 
-"@webassemblyjs/floating-point-hex-parser@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/floating-point-hex-parser/-/floating-point-hex-parser-1.11.1.tgz"
-  integrity sha512-iGRfyc5Bq+NnNuX8b5hwBrRjzf0ocrJPI6GWFodBFzmFnyvrQ83SHKhmilCU/8Jv67i4GJZBMhEzltxzcNagtQ==
-
 "@webassemblyjs/floating-point-hex-parser@1.11.6":
   version "1.11.6"
   resolved "https://registry.yarnpkg.com/@webassemblyjs/floating-point-hex-parser/-/floating-point-hex-parser-1.11.6.tgz#dacbcb95aff135c8260f77fa3b4c5fea600a6431"
   integrity sha512-ejAj9hfRJ2XMsNHk/v6Fu2dGS+i4UaXBXGemOfQ/JfQ6mdQg/WXtwleQRLLS4OvfDhv8rYnVwH27YJLMyYsxhw==
 
-"@webassemblyjs/helper-api-error@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/helper-api-error/-/helper-api-error-1.11.1.tgz"
-  integrity sha512-RlhS8CBCXfRUR/cwo2ho9bkheSXG0+NwooXcc3PAILALf2QLdFyj7KGsKRbVc95hZnhnERon4kW/D3SZpp6Tcg==
-
 "@webassemblyjs/helper-api-error@1.11.6":
   version "1.11.6"
   resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-api-error/-/helper-api-error-1.11.6.tgz#6132f68c4acd59dcd141c44b18cbebbd9f2fa768"
   integrity sha512-o0YkoP4pVu4rN8aTJgAyj9hC2Sv5UlkzCHhxqWj8butaLvnpdc2jOwh4ewE6CX0txSfLn/UYaV/pheS2Txg//Q==
 
-"@webassemblyjs/helper-buffer@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/helper-buffer/-/helper-buffer-1.11.1.tgz"
-  integrity sha512-gwikF65aDNeeXa8JxXa2BAk+REjSyhrNC9ZwdT0f8jc4dQQeDQ7G4m0f2QCLPJiMTTO6wfDmRmj/pW0PsUvIcA==
-
-"@webassemblyjs/helper-buffer@1.11.6":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-buffer/-/helper-buffer-1.11.6.tgz#b66d73c43e296fd5e88006f18524feb0f2c7c093"
-  integrity sha512-z3nFzdcp1mb8nEOFFk8DrYLpHvhKC3grJD2ardfKOzmbmJvEf/tPIqCY+sNcwZIY8ZD7IkB2l7/pqhUhqm7hLA==
-
-"@webassemblyjs/helper-numbers@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/helper-numbers/-/helper-numbers-1.11.1.tgz"
-  integrity sha512-vDkbxiB8zfnPdNK9Rajcey5C0w+QJugEglN0of+kmO8l7lDb77AnlKYQF7aarZuCrv+l0UvqL+68gSDr3k9LPQ==
-  dependencies:
-    "@webassemblyjs/floating-point-hex-parser" "1.11.1"
-    "@webassemblyjs/helper-api-error" "1.11.1"
-    "@xtuc/long" "4.2.2"
+"@webassemblyjs/helper-buffer@1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-buffer/-/helper-buffer-1.12.1.tgz#6df20d272ea5439bf20ab3492b7fb70e9bfcb3f6"
+  integrity sha512-nzJwQw99DNDKr9BVCOZcLuJJUlqkJh+kVzVl6Fmq/tI5ZtEyWT1KZMyOXltXLZJmDtvLCDgwsyrkohEtopTXCw==
 
 "@webassemblyjs/helper-numbers@1.11.6":
   version "1.11.6"
@@ -2922,42 +3023,20 @@
     "@webassemblyjs/helper-api-error" "1.11.6"
     "@xtuc/long" "4.2.2"
 
-"@webassemblyjs/helper-wasm-bytecode@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/helper-wasm-bytecode/-/helper-wasm-bytecode-1.11.1.tgz"
-  integrity sha512-PvpoOGiJwXeTrSf/qfudJhwlvDQxFgelbMqtq52WWiXC6Xgg1IREdngmPN3bs4RoO83PnL/nFrxucXj1+BX62Q==
-
 "@webassemblyjs/helper-wasm-bytecode@1.11.6":
   version "1.11.6"
   resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-wasm-bytecode/-/helper-wasm-bytecode-1.11.6.tgz#bb2ebdb3b83aa26d9baad4c46d4315283acd51e9"
   integrity sha512-sFFHKwcmBprO9e7Icf0+gddyWYDViL8bpPjJJl0WHxCdETktXdmtWLGVzoHbqUcY4Be1LkNfwTmXOJUFZYSJdA==
 
-"@webassemblyjs/helper-wasm-section@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/helper-wasm-section/-/helper-wasm-section-1.11.1.tgz"
-  integrity sha512-10P9No29rYX1j7F3EVPX3JvGPQPae+AomuSTPiF9eBQeChHI6iqjMIwR9JmOJXwpnn/oVGDk7I5IlskuMwU/pg==
+"@webassemblyjs/helper-wasm-section@1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-wasm-section/-/helper-wasm-section-1.12.1.tgz#3da623233ae1a60409b509a52ade9bc22a37f7bf"
+  integrity sha512-Jif4vfB6FJlUlSbgEMHUyk1j234GTNG9dBJ4XJdOySoj518Xj0oGsNi59cUQF4RRMS9ouBUxDDdyBVfPTypa5g==
   dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/helper-buffer" "1.11.1"
-    "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
-    "@webassemblyjs/wasm-gen" "1.11.1"
-
-"@webassemblyjs/helper-wasm-section@1.11.6":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/helper-wasm-section/-/helper-wasm-section-1.11.6.tgz#ff97f3863c55ee7f580fd5c41a381e9def4aa577"
-  integrity sha512-LPpZbSOwTpEC2cgn4hTydySy1Ke+XEu+ETXuoyvuyezHO3Kjdu90KK95Sh9xTbmjrCsUwvWwCOQQNta37VrS9g==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.6"
-    "@webassemblyjs/helper-buffer" "1.11.6"
+    "@webassemblyjs/ast" "1.12.1"
+    "@webassemblyjs/helper-buffer" "1.12.1"
     "@webassemblyjs/helper-wasm-bytecode" "1.11.6"
-    "@webassemblyjs/wasm-gen" "1.11.6"
-
-"@webassemblyjs/ieee754@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/ieee754/-/ieee754-1.11.1.tgz"
-  integrity sha512-hJ87QIPtAMKbFq6CGTkZYJivEwZDbQUgYd3qKSadTNOhVY7p+gfP6Sr0lLRVTaG1JjFj+r3YchoqRYxNH3M0GQ==
-  dependencies:
-    "@xtuc/ieee754" "^1.2.0"
+    "@webassemblyjs/wasm-gen" "1.12.1"
 
 "@webassemblyjs/ieee754@1.11.6":
   version "1.11.6"
@@ -2966,13 +3045,6 @@
   dependencies:
     "@xtuc/ieee754" "^1.2.0"
 
-"@webassemblyjs/leb128@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/leb128/-/leb128-1.11.1.tgz"
-  integrity sha512-BJ2P0hNZ0u+Th1YZXJpzW6miwqQUGcIHT1G/sf72gLVD9DZ5AdYTqPNbHZh6K1M5VmKvFXwGSWZADz+qBWxeRw==
-  dependencies:
-    "@xtuc/long" "4.2.2"
-
 "@webassemblyjs/leb128@1.11.6":
   version "1.11.6"
   resolved "https://registry.yarnpkg.com/@webassemblyjs/leb128/-/leb128-1.11.6.tgz#70e60e5e82f9ac81118bc25381a0b283893240d7"
@@ -2980,124 +3052,64 @@
   dependencies:
     "@xtuc/long" "4.2.2"
 
-"@webassemblyjs/utf8@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/utf8/-/utf8-1.11.1.tgz"
-  integrity sha512-9kqcxAEdMhiwQkHpkNiorZzqpGrodQQ2IGrHHxCy+Ozng0ofyMA0lTqiLkVs1uzTRejX+/O0EOT7KxqVPuXosQ==
-
 "@webassemblyjs/utf8@1.11.6":
   version "1.11.6"
   resolved "https://registry.yarnpkg.com/@webassemblyjs/utf8/-/utf8-1.11.6.tgz#90f8bc34c561595fe156603be7253cdbcd0fab5a"
   integrity sha512-vtXf2wTQ3+up9Zsg8sa2yWiQpzSsMyXj0qViVP6xKGCUT8p8YJ6HqI7l5eCnWx1T/FYdsv07HQs2wTFbbof/RA==
 
-"@webassemblyjs/wasm-edit@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/wasm-edit/-/wasm-edit-1.11.1.tgz"
-  integrity sha512-g+RsupUC1aTHfR8CDgnsVRVZFJqdkFHpsHMfJuWQzWU3tvnLC07UqHICfP+4XyL2tnr1amvl1Sdp06TnYCmVkA==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/helper-buffer" "1.11.1"
-    "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
-    "@webassemblyjs/helper-wasm-section" "1.11.1"
-    "@webassemblyjs/wasm-gen" "1.11.1"
-    "@webassemblyjs/wasm-opt" "1.11.1"
-    "@webassemblyjs/wasm-parser" "1.11.1"
-    "@webassemblyjs/wast-printer" "1.11.1"
-
-"@webassemblyjs/wasm-edit@^1.11.5":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-edit/-/wasm-edit-1.11.6.tgz#c72fa8220524c9b416249f3d94c2958dfe70ceab"
-  integrity sha512-Ybn2I6fnfIGuCR+Faaz7YcvtBKxvoLV3Lebn1tM4o/IAJzmi9AWYIPWpyBfU8cC+JxAO57bk4+zdsTjJR+VTOw==
+"@webassemblyjs/wasm-edit@^1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-edit/-/wasm-edit-1.12.1.tgz#9f9f3ff52a14c980939be0ef9d5df9ebc678ae3b"
+  integrity sha512-1DuwbVvADvS5mGnXbE+c9NfA8QRcZ6iKquqjjmR10k6o+zzsRVesil54DKexiowcFCPdr/Q0qaMgB01+SQ1u6g==
   dependencies:
-    "@webassemblyjs/ast" "1.11.6"
-    "@webassemblyjs/helper-buffer" "1.11.6"
+    "@webassemblyjs/ast" "1.12.1"
+    "@webassemblyjs/helper-buffer" "1.12.1"
     "@webassemblyjs/helper-wasm-bytecode" "1.11.6"
-    "@webassemblyjs/helper-wasm-section" "1.11.6"
-    "@webassemblyjs/wasm-gen" "1.11.6"
-    "@webassemblyjs/wasm-opt" "1.11.6"
-    "@webassemblyjs/wasm-parser" "1.11.6"
-    "@webassemblyjs/wast-printer" "1.11.6"
-
-"@webassemblyjs/wasm-gen@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/wasm-gen/-/wasm-gen-1.11.1.tgz"
-  integrity sha512-F7QqKXwwNlMmsulj6+O7r4mmtAlCWfO/0HdgOxSklZfQcDu0TpLiD1mRt/zF25Bk59FIjEuGAIyn5ei4yMfLhA==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
-    "@webassemblyjs/ieee754" "1.11.1"
-    "@webassemblyjs/leb128" "1.11.1"
-    "@webassemblyjs/utf8" "1.11.1"
-
-"@webassemblyjs/wasm-gen@1.11.6":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-gen/-/wasm-gen-1.11.6.tgz#fb5283e0e8b4551cc4e9c3c0d7184a65faf7c268"
-  integrity sha512-3XOqkZP/y6B4F0PBAXvI1/bky7GryoogUtfwExeP/v7Nzwo1QLcq5oQmpKlftZLbT+ERUOAZVQjuNVak6UXjPA==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.6"
+    "@webassemblyjs/helper-wasm-section" "1.12.1"
+    "@webassemblyjs/wasm-gen" "1.12.1"
+    "@webassemblyjs/wasm-opt" "1.12.1"
+    "@webassemblyjs/wasm-parser" "1.12.1"
+    "@webassemblyjs/wast-printer" "1.12.1"
+
+"@webassemblyjs/wasm-gen@1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-gen/-/wasm-gen-1.12.1.tgz#a6520601da1b5700448273666a71ad0a45d78547"
+  integrity sha512-TDq4Ojh9fcohAw6OIMXqiIcTq5KUXTGRkVxbSo1hQnSy6lAM5GSdfwWeSxpAo0YzgsgF182E/U0mDNhuA0tW7w==
+  dependencies:
+    "@webassemblyjs/ast" "1.12.1"
     "@webassemblyjs/helper-wasm-bytecode" "1.11.6"
     "@webassemblyjs/ieee754" "1.11.6"
     "@webassemblyjs/leb128" "1.11.6"
     "@webassemblyjs/utf8" "1.11.6"
 
-"@webassemblyjs/wasm-opt@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/wasm-opt/-/wasm-opt-1.11.1.tgz"
-  integrity sha512-VqnkNqnZlU5EB64pp1l7hdm3hmQw7Vgqa0KF/KCNO9sIpI6Fk6brDEiX+iCOYrvMuBWDws0NkTOxYEb85XQHHw==
+"@webassemblyjs/wasm-opt@1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-opt/-/wasm-opt-1.12.1.tgz#9e6e81475dfcfb62dab574ac2dda38226c232bc5"
+  integrity sha512-Jg99j/2gG2iaz3hijw857AVYekZe2SAskcqlWIZXjji5WStnOpVoat3gQfT/Q5tb2djnCjBtMocY/Su1GfxPBg==
   dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/helper-buffer" "1.11.1"
-    "@webassemblyjs/wasm-gen" "1.11.1"
-    "@webassemblyjs/wasm-parser" "1.11.1"
+    "@webassemblyjs/ast" "1.12.1"
+    "@webassemblyjs/helper-buffer" "1.12.1"
+    "@webassemblyjs/wasm-gen" "1.12.1"
+    "@webassemblyjs/wasm-parser" "1.12.1"
 
-"@webassemblyjs/wasm-opt@1.11.6":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-opt/-/wasm-opt-1.11.6.tgz#d9a22d651248422ca498b09aa3232a81041487c2"
-  integrity sha512-cOrKuLRE7PCe6AsOVl7WasYf3wbSo4CeOk6PkrjS7g57MFfVUF9u6ysQBBODX0LdgSvQqRiGz3CXvIDKcPNy4g==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.6"
-    "@webassemblyjs/helper-buffer" "1.11.6"
-    "@webassemblyjs/wasm-gen" "1.11.6"
-    "@webassemblyjs/wasm-parser" "1.11.6"
-
-"@webassemblyjs/wasm-parser@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/wasm-parser/-/wasm-parser-1.11.1.tgz"
-  integrity sha512-rrBujw+dJu32gYB7/Lup6UhdkPx9S9SnobZzRVL7VcBH9Bt9bCBLEuX/YXOOtBsOZ4NQrRykKhffRWHvigQvOA==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/helper-api-error" "1.11.1"
-    "@webassemblyjs/helper-wasm-bytecode" "1.11.1"
-    "@webassemblyjs/ieee754" "1.11.1"
-    "@webassemblyjs/leb128" "1.11.1"
-    "@webassemblyjs/utf8" "1.11.1"
-
-"@webassemblyjs/wasm-parser@1.11.6", "@webassemblyjs/wasm-parser@^1.11.5":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-parser/-/wasm-parser-1.11.6.tgz#bb85378c527df824004812bbdb784eea539174a1"
-  integrity sha512-6ZwPeGzMJM3Dqp3hCsLgESxBGtT/OeCvCZ4TA1JUPYgmhAx38tTPR9JaKy0S5H3evQpO/h2uWs2j6Yc/fjkpTQ==
+"@webassemblyjs/wasm-parser@1.12.1", "@webassemblyjs/wasm-parser@^1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/wasm-parser/-/wasm-parser-1.12.1.tgz#c47acb90e6f083391e3fa61d113650eea1e95937"
+  integrity sha512-xikIi7c2FHXysxXe3COrVUPSheuBtpcfhbpFj4gmu7KRLYOzANztwUU0IbsqvMqzuNK2+glRGWCEqZo1WCLyAQ==
   dependencies:
-    "@webassemblyjs/ast" "1.11.6"
+    "@webassemblyjs/ast" "1.12.1"
     "@webassemblyjs/helper-api-error" "1.11.6"
     "@webassemblyjs/helper-wasm-bytecode" "1.11.6"
     "@webassemblyjs/ieee754" "1.11.6"
     "@webassemblyjs/leb128" "1.11.6"
     "@webassemblyjs/utf8" "1.11.6"
 
-"@webassemblyjs/wast-printer@1.11.1":
-  version "1.11.1"
-  resolved "https://registry.npmjs.org/@webassemblyjs/wast-printer/-/wast-printer-1.11.1.tgz"
-  integrity sha512-IQboUWM4eKzWW+N/jij2sRatKMh99QEelo3Eb2q0qXkvPRISAj8Qxtmw5itwqK+TTkBuUIE45AxYPToqPtL5gg==
+"@webassemblyjs/wast-printer@1.12.1":
+  version "1.12.1"
+  resolved "https://registry.yarnpkg.com/@webassemblyjs/wast-printer/-/wast-printer-1.12.1.tgz#bcecf661d7d1abdaf989d8341a4833e33e2b31ac"
+  integrity sha512-+X4WAlOisVWQMikjbcvY2e0rwPsKQ9F688lksZhBcPycBBuii3O7m8FACbDMWDojpAqvjIncrG8J0XHKyQfVeA==
   dependencies:
-    "@webassemblyjs/ast" "1.11.1"
-    "@xtuc/long" "4.2.2"
-
-"@webassemblyjs/wast-printer@1.11.6":
-  version "1.11.6"
-  resolved "https://registry.yarnpkg.com/@webassemblyjs/wast-printer/-/wast-printer-1.11.6.tgz#a7bf8dd7e362aeb1668ff43f35cb849f188eff20"
-  integrity sha512-JM7AhRcE+yW2GWYaKeHL5vt4xqee5N2WcezptmgyhNS+ScggqcT1OtXykhAb13Sn5Yas0j2uv9tHgrjwvzAP4A==
-  dependencies:
-    "@webassemblyjs/ast" "1.11.6"
+    "@webassemblyjs/ast" "1.12.1"
     "@xtuc/long" "4.2.2"
 
 "@webpack-cli/configtest@^2.1.1":
@@ -3151,15 +3163,10 @@ acorn-globals@^7.0.0:
     acorn "^8.1.0"
     acorn-walk "^8.0.2"
 
-acorn-import-assertions@^1.7.6:
-  version "1.8.0"
-  resolved "https://registry.npmjs.org/acorn-import-assertions/-/acorn-import-assertions-1.8.0.tgz"
-  integrity sha512-m7VZ3jwz4eK6A4Vtt8Ew1/mNbP24u0FhdyfA7fSvnJR6LMdfOYnmuIrrJAgrYfYJ10F/otaHTtrtrtmHdMNzEw==
-
-acorn-import-assertions@^1.9.0:
-  version "1.9.0"
-  resolved "https://registry.yarnpkg.com/acorn-import-assertions/-/acorn-import-assertions-1.9.0.tgz#507276249d684797c84e0734ef84860334cfb1ac"
-  integrity sha512-cmMwop9x+8KFhxvKrKfPYmN6/pKTYYHBqLa0DfvVZcKMJWNyWLnaqND7dx/qn66R7ewM1UX5XMaDVP5wlVTaVA==
+acorn-import-attributes@^1.9.5:
+  version "1.9.5"
+  resolved "https://registry.yarnpkg.com/acorn-import-attributes/-/acorn-import-attributes-1.9.5.tgz#7eb1557b1ba05ef18b5ed0ec67591bfab04688ef"
+  integrity sha512-n02Vykv5uA3eHGM/Z2dQrcD56kL8TyDb2p1+0P83PClMnC/nc+anbQRhIOWnSq4Ke/KvDPrY3C9hDtC/A3eHnQ==
 
 acorn-jsx@^5.3.2:
   version "5.3.2"
@@ -3171,17 +3178,7 @@ acorn-walk@^8.0.2:
   resolved "https://registry.yarnpkg.com/acorn-walk/-/acorn-walk-8.2.0.tgz#741210f2e2426454508853a2f44d0ab83b7f69c1"
   integrity sha512-k+iyHEuPgSw6SbuDpGQM+06HQUa04DZ3o+F6CSzXMvvI5KMvnaEqXe+YVe555R9nn6GPt404fos4wcgpw12SDA==
 
-acorn@^8.1.0, acorn@^8.8.1:
-  version "8.8.1"
-  resolved "https://registry.yarnpkg.com/acorn/-/acorn-8.8.1.tgz#0a3f9cbecc4ec3bea6f0a80b66ae8dd2da250b73"
-  integrity sha512-7zFpHzhnqYKrkYdUjF1HI1bzd0VygEGX8lFk4k5zVMqHEoES+P+7TKI+EvLO9WVMJ8eekdO0aDEK044xTXwPPA==
-
-acorn@^8.5.0, acorn@^8.7.1, acorn@^8.8.0:
-  version "8.8.0"
-  resolved "https://registry.npmjs.org/acorn/-/acorn-8.8.0.tgz"
-  integrity sha512-QOxyigPVrpZ2GXT+PFyZTl6TtOFc5egxHIP9IlQ+RbupQuX4RkT/Bee4/kQuC02Xkzg84JcT7oLYtDIQxp+v7w==
-
-acorn@^8.8.2, acorn@^8.9.0:
+acorn@^8.1.0, acorn@^8.7.1, acorn@^8.8.0, acorn@^8.8.1, acorn@^8.8.2, acorn@^8.9.0:
   version "8.10.0"
   resolved "https://registry.yarnpkg.com/acorn/-/acorn-8.10.0.tgz#8be5b3907a67221a81ab23c7889c4c5526b62ec5"
   integrity sha512-F0SAmZ8iUtS//m8DmCTA0jlh6TDKkHQyK6xc6V4KDTyZKA9dnvX9/3sRTVQrWm79glUAZbnmmNcdYwUIHWVybw==
@@ -3193,6 +3190,13 @@ agent-base@6:
   dependencies:
     debug "4"
 
+agent-base@^7.0.2:
+  version "7.1.1"
+  resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-7.1.1.tgz#bdbded7dfb096b751a2a087eeeb9664725b2e317"
+  integrity sha512-H0TSyFNDMomMNJQBn8wFV5YC/2eJ+VXECwOadZJT554xP6cODZHPX3H9QMQECxvrgiSOP1pHjy1sMWQVYJOUOA==
+  dependencies:
+    debug "^4.3.4"
+
 aggregate-error@^3.0.0:
   version "3.1.0"
   resolved "https://registry.npmjs.org/aggregate-error/-/aggregate-error-3.1.0.tgz"
@@ -3221,7 +3225,7 @@ ajv-keywords@^3.5.2:
   resolved "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-3.5.2.tgz"
   integrity sha512-5p6WTN0DdTGVQk6VjcEju19IgaHudalcfabD7yhDGeA6bcQnmL+CpveLJq/3hvfwd1aof6L386Ougkx6RfyMIQ==
 
-ajv-keywords@^5.0.0, ajv-keywords@^5.1.0:
+ajv-keywords@^5.1.0:
   version "5.1.0"
   resolved "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-5.1.0.tgz"
   integrity sha512-YCS/JNFAUyr5vAuhk1DWm1CBxRHW9LbJ2ozWeemrIqpbsqKjHVxYPyi5GC0rjZIT5JxJ3virVTS8wk4i/Z+krw==
@@ -3238,7 +3242,7 @@ ajv@^6.12.4, ajv@^6.12.5:
     json-schema-traverse "^0.4.1"
     uri-js "^4.2.2"
 
-ajv@^8.0.0, ajv@^8.8.0:
+ajv@^8.0.0:
   version "8.11.0"
   resolved "https://registry.npmjs.org/ajv/-/ajv-8.11.0.tgz"
   integrity sha512-wGgprdCvMalC0BztXvitD2hC04YffAvtsUn93JbGXYLAtCUO4xd17mCCZQxUOItiBwZvJScWo8NIvQMQ71rdpg==
@@ -3278,7 +3282,7 @@ ansi-colors@^4.1.3:
   resolved "https://registry.yarnpkg.com/ansi-colors/-/ansi-colors-4.1.3.tgz#37611340eb2243e70cc604cad35d63270d48781b"
   integrity sha512-/6w/C21Pm1A7aZitlI5Ni/2J6FFQN8i1Cvz3kHABAAbw93v/NlvKdVOqz7CCWz/3iv/JplRSEEZ83XION15ovw==
 
-ansi-escapes@^4.2.1:
+ansi-escapes@^4.2.1, ansi-escapes@^4.3.2:
   version "4.3.2"
   resolved "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-4.3.2.tgz"
   integrity sha512-gKXj5ALrKWQLsYG9jlTRmR/xKluxHV+Z9QEwNIgCfM1/uwPMCuzVVnh5mwTd+OuBZcwSIMbqssNWRm1lE51QaQ==
@@ -3584,6 +3588,11 @@ async-settle@^1.0.0:
   dependencies:
     async-done "^1.2.2"
 
+async@^3.2.3:
+  version "3.2.5"
+  resolved "https://registry.yarnpkg.com/async/-/async-3.2.5.tgz#ebd52a8fdaf7a2289a24df399f8d8485c8a46b66"
+  integrity sha512-baNZyqaaLhyLVKm/DlvdW051MSgO6b8eVfIezl9E5PqWxFgzLm/wQntEW4zOytVburDEr0JlALEpdOFwvErLsg==
+
 asynckit@^0.4.0:
   version "0.4.0"
   resolved "https://registry.npmjs.org/asynckit/-/asynckit-0.4.0.tgz"
@@ -3620,11 +3629,11 @@ axios-mock-adapter@^1.22.0:
     is-buffer "^2.0.5"
 
 axios@^1.6.2:
-  version "1.6.2"
-  resolved "https://registry.yarnpkg.com/axios/-/axios-1.6.2.tgz#de67d42c755b571d3e698df1b6504cde9b0ee9f2"
-  integrity sha512-7i24Ri4pmDRfJTR7LDBhsOTtcm+9kjX5WiY1X3wIisx6G9So3pfMkEiU7emUBe46oceVImccTEM3k6C5dbVW8A==
+  version "1.7.4"
+  resolved "https://registry.yarnpkg.com/axios/-/axios-1.7.4.tgz#4c8ded1b43683c8dd362973c393f3ede24052aa2"
+  integrity sha512-DukmaFRnY6AzAALSH4J2M3k6PkaC+MfaAGdEERRWcC9q3/TWQwLpHR8ZRLKTdQ3aBDL64EdluRDjJqKw+BPZEw==
   dependencies:
-    follow-redirects "^1.15.0"
+    follow-redirects "^1.15.6"
     form-data "^4.0.0"
     proxy-from-env "^1.1.0"
 
@@ -3819,10 +3828,10 @@ bluebird@^3.1.1:
   resolved "https://registry.npmjs.org/bluebird/-/bluebird-3.7.2.tgz"
   integrity sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg==
 
-body-parser@1.20.2:
-  version "1.20.2"
-  resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.2.tgz#6feb0e21c4724d06de7ff38da36dad4f57a747fd"
-  integrity sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==
+body-parser@1.20.3:
+  version "1.20.3"
+  resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.3.tgz#1953431221c6fb5cd63c4b36d53fab0928e548c6"
+  integrity sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==
   dependencies:
     bytes "3.1.2"
     content-type "~1.0.5"
@@ -3832,7 +3841,7 @@ body-parser@1.20.2:
     http-errors "2.0.0"
     iconv-lite "0.4.24"
     on-finished "2.4.1"
-    qs "6.11.0"
+    qs "6.13.0"
     raw-body "2.5.2"
     type-is "~1.6.18"
     unpipe "1.0.0"
@@ -3906,17 +3915,7 @@ braces@^3.0.2, braces@~3.0.2:
   dependencies:
     fill-range "^7.0.1"
 
-browserslist@^4.0.0, browserslist@^4.14.5, browserslist@^4.20.2:
-  version "4.21.3"
-  resolved "https://registry.npmjs.org/browserslist/-/browserslist-4.21.3.tgz"
-  integrity sha512-898rgRXLAyRkM1GryrrBHGkqA5hlpkV5MhtZwg9QXeiyLUYs2k00Un05aX5l2/yJIOObYKOpS2JNo8nJDE7fWQ==
-  dependencies:
-    caniuse-lite "^1.0.30001370"
-    electron-to-chromium "^1.4.202"
-    node-releases "^2.0.6"
-    update-browserslist-db "^1.0.5"
-
-browserslist@^4.21.10, browserslist@^4.21.4, browserslist@^4.21.9, browserslist@^4.22.1:
+browserslist@^4.0.0, browserslist@^4.20.2, browserslist@^4.21.10, browserslist@^4.21.4, browserslist@^4.21.9, browserslist@^4.22.1:
   version "4.22.1"
   resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.22.1.tgz#ba91958d1a59b87dab6fed8dfbcb3da5e2e9c619"
   integrity sha512-FEVc202+2iuClEhZhrWy6ZiAcRLvNMyYcxZ8raemul1DYVOVdFsbqckWLdsixQZCpJlwe77Z3UTalE7jsjnKfQ==
@@ -4009,6 +4008,17 @@ call-bind@^1.0.0, call-bind@^1.0.2:
     function-bind "^1.1.1"
     get-intrinsic "^1.0.2"
 
+call-bind@^1.0.7:
+  version "1.0.7"
+  resolved "https://registry.yarnpkg.com/call-bind/-/call-bind-1.0.7.tgz#06016599c40c56498c18769d2730be242b6fa3b9"
+  integrity sha512-GHTSNSYICQ7scH7sZ+M2rFopRoLh8t2bLSW6BbgrtLsahOIB5iyAVJf9GjWK3cYTDaMj4XdBpM1cA6pIS0Kv2w==
+  dependencies:
+    es-define-property "^1.0.0"
+    es-errors "^1.3.0"
+    function-bind "^1.1.2"
+    get-intrinsic "^1.2.4"
+    set-function-length "^1.2.1"
+
 callsites@^3.0.0:
   version "3.1.0"
   resolved "https://registry.npmjs.org/callsites/-/callsites-3.1.0.tgz"
@@ -4039,7 +4049,7 @@ caniuse-api@^3.0.0:
     lodash.memoize "^4.1.2"
     lodash.uniq "^4.5.0"
 
-caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001370, caniuse-lite@^1.0.30001524, caniuse-lite@^1.0.30001538, caniuse-lite@^1.0.30001541:
+caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001524, caniuse-lite@^1.0.30001538, caniuse-lite@^1.0.30001541:
   version "1.0.30001551"
   resolved "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001551.tgz"
   integrity sha512-vtBAez47BoGMMzlbYhfXrMV1kvRF2WP/lqiMuDu1Sb4EE4LKEgjopFDSRtZfdVnslNRpOqV/woE+Xgrwj6VQlg==
@@ -4080,7 +4090,7 @@ chalk@^3.0.0:
     ansi-styles "^4.1.0"
     supports-color "^7.1.0"
 
-chalk@^4.0.0, chalk@^4.1.0, chalk@~4.1.0:
+chalk@^4.0.0, chalk@^4.0.2, chalk@^4.1.0, chalk@^4.1.2, chalk@~4.1.0:
   version "4.1.2"
   resolved "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz"
   integrity sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA==
@@ -4155,6 +4165,16 @@ clean-stack@^4.0.0:
   dependencies:
     escape-string-regexp "5.0.0"
 
+cli-spinners@^2.9.2:
+  version "2.9.2"
+  resolved "https://registry.yarnpkg.com/cli-spinners/-/cli-spinners-2.9.2.tgz#1773a8f4b9c4d6ac31563df53b3fc1d79462fe41"
+  integrity sha512-ywqV+5MmyL4E7ybXgKys4DugZbX0FC6LnwrhjuykIjnK9k8OQacQ7axGKnjDXWNhns0xot3bZI5h55H8yo9cJg==
+
+cli-width@^4.1.0:
+  version "4.1.0"
+  resolved "https://registry.yarnpkg.com/cli-width/-/cli-width-4.1.0.tgz#42daac41d3c254ef38ad8ac037672130173691c5"
+  integrity sha512-ouuZd4/dm2Sw5Gmqy6bGyNNNe1qt9RpmxveLSO7KcgsTnU7RXfsw+/bukWGo1abgBiMAic068rclZsO4IWmmxQ==
+
 cliui@^3.2.0:
   version "3.2.0"
   resolved "https://registry.npmjs.org/cliui/-/cliui-3.2.0.tgz"
@@ -4284,6 +4304,11 @@ colord@^2.9.1:
   resolved "https://registry.npmjs.org/colord/-/colord-2.9.3.tgz"
   integrity sha512-jeC1axXpnb0/2nn/Y1LPuLdgXBLH7aDcHu4KEKfqw3CUhX7ZpfBSlPKyqXE6btIgEzfWtrX3/tyBCaCvXvMkOw==
 
+colorette@^1.2.0:
+  version "1.4.0"
+  resolved "https://registry.yarnpkg.com/colorette/-/colorette-1.4.0.tgz#5190fbb87276259a86ad700bff2c6d6faa3fca40"
+  integrity sha512-Y2oEozpomLn7Q3HFP7dpww7AtMJplbM9lGZP6RDfHqmbeRjiwRg4n6VM6j4KLmRke85uWEI7JqF17f3pqdRA0g==
+
 colorette@^2.0.10, colorette@^2.0.14:
   version "2.0.19"
   resolved "https://registry.npmjs.org/colorette/-/colorette-2.0.19.tgz"
@@ -4304,6 +4329,11 @@ combined-stream@^1.0.8:
   dependencies:
     delayed-stream "~1.0.0"
 
+commander@2, commander@^2.19.0, commander@^2.20.0:
+  version "2.20.3"
+  resolved "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz"
+  integrity sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==
+
 commander@7, commander@^7.2.0:
   version "7.2.0"
   resolved "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz"
@@ -4314,11 +4344,6 @@ commander@^10.0.1:
   resolved "https://registry.yarnpkg.com/commander/-/commander-10.0.1.tgz#881ee46b4f77d1c1dccc5823433aa39b022cbe06"
   integrity sha512-y4Mg2tXshplEbSGzx7amzPwKKOCGuoSRP/CjEdwwk0FOGlUbq6lKuoyDZTNZkmxHdJtp54hdfY/JUrdL7Xfdug==
 
-commander@^2.19.0, commander@^2.20.0:
-  version "2.20.3"
-  resolved "https://registry.npmjs.org/commander/-/commander-2.20.3.tgz"
-  integrity sha512-GpVkmM8vF2vQUkj2LvZmD35JxeJOLCwJ9cUkugyk2nuhbv3+mJvpLYYt+0+USMxE+oj+ey/lJEnhZw75x/OMcQ==
-
 component-emitter@^1.2.1:
   version "1.3.0"
   resolved "https://registry.npmjs.org/component-emitter/-/component-emitter-1.3.0.tgz"
@@ -4432,6 +4457,11 @@ cookie@0.6.0:
   resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.6.0.tgz#2798b04b071b0ecbff0dbb62a505a8efa4e19051"
   integrity sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw==
 
+cookie@^0.5.0:
+  version "0.5.0"
+  resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.5.0.tgz#d1f5d71adec6558c58f389987c366aa47e994f8b"
+  integrity sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw==
+
 copy-descriptor@^0.1.0:
   version "0.1.1"
   resolved "https://registry.npmjs.org/copy-descriptor/-/copy-descriptor-0.1.1.tgz"
@@ -4532,9 +4562,9 @@ create-jest@^29.7.0:
     prompts "^2.0.1"
 
 cross-spawn@^7.0.0, cross-spawn@^7.0.2, cross-spawn@^7.0.3:
-  version "7.0.3"
-  resolved "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz"
-  integrity sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==
+  version "7.0.5"
+  resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.5.tgz#910aac880ff5243da96b728bc6521a5f6c2f2f82"
+  integrity sha512-ZVJrKKYunU38/76t0RMOulHOnUcbU9GbpWKAOZ0mhjr7CX6FVrH+4FrAapSOekrgFQ3f/8gwMEuIft0aKq6Hug==
   dependencies:
     path-key "^3.1.0"
     shebang-command "^2.0.0"
@@ -4707,6 +4737,13 @@ custom-error-instance@2.1.1:
   resolved "https://registry.npmjs.org/custom-error-instance/-/custom-error-instance-2.1.1.tgz"
   integrity sha512-p6JFxJc3M4OTD2li2qaHkDCw9SfMw82Ldr6OC9Je1aXiGfhx2W8p3GaoeaGrPJTUN9NirTM/KTxHWMUdR1rsUg==
 
+"d3-array@1 - 3", d3-array@3.2.4, d3-array@^3.2.2:
+  version "3.2.4"
+  resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-3.2.4.tgz#15fec33b237f97ac5d7c986dc77da273a8ed0bb5"
+  integrity sha512-tdQAmyA18i4J7wprpYq8ClcxZy3SC31QMeByyCFyRt7BVHdREQZ5lpzoe5mFEYZUWe+oq8HBvk9JjpibyEV4Jg==
+  dependencies:
+    internmap "1 - 2"
+
 "d3-array@2 - 3", "d3-array@2.10.0 - 3", "d3-array@2.5.0 - 3", d3-array@3, d3-array@^3.2.0:
   version "3.2.1"
   resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-3.2.1.tgz#39331ea706f5709417d31bbb6ec152e0328b39b3"
@@ -4737,7 +4774,7 @@ d3-chord@3:
   dependencies:
     d3-path "1 - 3"
 
-"d3-color@1 - 3", d3-color@3:
+"d3-color@1 - 3", d3-color@3, d3-color@^3.1.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-3.1.0.tgz#395b2833dfac71507f12ac2f7af23bf819de24e2"
   integrity sha512-zg/chbXyeBtMQ1LbD/WSoW2DpC3I0mpmPdW+ynRTj/x2DAWYrIY7qeZIHidozwV24m4iavr15lNwIwLxRmOxhA==
@@ -4756,6 +4793,13 @@ d3-delaunay@6:
   dependencies:
     delaunator "5"
 
+d3-delaunay@^6.0.2:
+  version "6.0.4"
+  resolved "https://registry.yarnpkg.com/d3-delaunay/-/d3-delaunay-6.0.4.tgz#98169038733a0a5babbeda55054f795bb9e4a58b"
+  integrity sha512-mdjtIZ1XLAM8bm/hx3WwjfHt6Sggek7qH043O8KEjDXN40xi3vx/6pYSVTwLjEgiXQTbvaouWKynLBiUZ6SK6A==
+  dependencies:
+    delaunator "5"
+
 "d3-dispatch@1 - 3", d3-dispatch@3:
   version "3.0.1"
   resolved "https://registry.yarnpkg.com/d3-dispatch/-/d3-dispatch-3.0.1.tgz#5fc75284e9c2375c36c839411a0cf550cbfc4d5e"
@@ -4769,7 +4813,7 @@ d3-delaunay@6:
     d3-dispatch "1 - 3"
     d3-selection "3"
 
-"d3-dsv@1 - 3", d3-dsv@3:
+"d3-dsv@1 - 3", d3-dsv@3, d3-dsv@^3.0.1:
   version "3.0.1"
   resolved "https://registry.yarnpkg.com/d3-dsv/-/d3-dsv-3.0.1.tgz#c63af978f4d6a0d084a52a673922be2160789b73"
   integrity sha512-UG6OvdI5afDIFP9w4G0mNq50dSOsXHJaRE8arAS5o9ApWnIElp8GZw1Dun8vP8OyHOZ/QJUKUJwxiiCCnUwm+Q==
@@ -4790,7 +4834,7 @@ d3-fetch@3:
   dependencies:
     d3-dsv "1 - 3"
 
-d3-force@3:
+d3-force@3, d3-force@^3.0.0:
   version "3.0.0"
   resolved "https://registry.yarnpkg.com/d3-force/-/d3-force-3.0.0.tgz#3e2ba1a61e70888fe3d9194e30d6d14eece155c4"
   integrity sha512-zxV/SsA+U4yte8051P4ECydjD/S+qeYtnaIyAs9tgHCqfguma/aAQDjo85A9Z6EKhBirHRJHXIgJUlffT4wdLg==
@@ -4799,11 +4843,27 @@ d3-force@3:
     d3-quadtree "1 - 3"
     d3-timer "1 - 3"
 
-"d3-format@1 - 3", d3-format@3:
+"d3-format@1 - 3", d3-format@3, d3-format@^3.1.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-3.1.0.tgz#9260e23a28ea5cb109e93b21a06e24e2ebd55641"
   integrity sha512-YyUI6AEuY/Wpt8KWLgZHsIU86atmikuoOmCfommt0LYHiQSPjvX2AcFc38PX0CBpr2RCyZhjex+NS/LPOv6YqA==
 
+d3-geo-projection@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/d3-geo-projection/-/d3-geo-projection-4.0.0.tgz#dc229e5ead78d31869a4e87cf1f45bd2716c48ca"
+  integrity sha512-p0bK60CEzph1iqmnxut7d/1kyTmm3UWtPlwdkM31AU+LW+BXazd5zJdoCn7VFxNCHXRngPHRnsNn5uGjLRGndg==
+  dependencies:
+    commander "7"
+    d3-array "1 - 3"
+    d3-geo "1.12.0 - 3"
+
+"d3-geo@1.12.0 - 3", d3-geo@^3.1.0:
+  version "3.1.1"
+  resolved "https://registry.yarnpkg.com/d3-geo/-/d3-geo-3.1.1.tgz#6027cf51246f9b2ebd64f99e01dc7c3364033a4d"
+  integrity sha512-637ln3gXKXOwhalDzinUgY83KzNWZRKbYubaG+fGVuc/dxO64RRljtCTnf5ecMyE1RIdtqpkVcq0IbtU2S8j2Q==
+  dependencies:
+    d3-array "2.5.0 - 3"
+
 d3-geo@3:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/d3-geo/-/d3-geo-3.1.0.tgz#74fd54e1f4cebd5185ac2039217a98d39b0a4c0e"
@@ -4811,12 +4871,12 @@ d3-geo@3:
   dependencies:
     d3-array "2.5.0 - 3"
 
-d3-hierarchy@3:
+d3-hierarchy@3, d3-hierarchy@^3.1.2:
   version "3.1.2"
   resolved "https://registry.yarnpkg.com/d3-hierarchy/-/d3-hierarchy-3.1.2.tgz#b01cd42c1eed3d46db77a5966cf726f8c09160c6"
   integrity sha512-FX/9frcub54beBdugHjDCdikxThEqjnR93Qt7PvQTOHxyiNCAlvMrHhclk3cD5VeAaq9fxmfRp+CnWw9rEMBuA==
 
-"d3-interpolate@1 - 3", "d3-interpolate@1.2.0 - 3", d3-interpolate@3:
+"d3-interpolate@1 - 3", "d3-interpolate@1.2.0 - 3", d3-interpolate@3, d3-interpolate@^3.0.1:
   version "3.0.1"
   resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-3.0.1.tgz#3c47aa5b32c5b3dfb56ef3fd4342078a632b400d"
   integrity sha512-3bYs1rOD33uo8aqJfKP3JWPAibgw8Zm2+L9vBKEHJ2Rg+viTR7o5Mmv5mZcieN+FRYaAOWX5SJATX6k1PWz72g==
@@ -4851,7 +4911,15 @@ d3-scale-chromatic@3:
     d3-color "1 - 3"
     d3-interpolate "1 - 3"
 
-d3-scale@4:
+d3-scale-chromatic@^3.1.0:
+  version "3.1.0"
+  resolved "https://registry.yarnpkg.com/d3-scale-chromatic/-/d3-scale-chromatic-3.1.0.tgz#34c39da298b23c20e02f1a4b239bd0f22e7f1314"
+  integrity sha512-A3s5PWiZ9YCXFye1o246KoscMWqf8BsD9eRiJ3He7C9OBaxKhAd5TFCdEx/7VbKtxxTsu//1mMJFrEt572cEyQ==
+  dependencies:
+    d3-color "1 - 3"
+    d3-interpolate "1 - 3"
+
+d3-scale@4, d3-scale@^4.0.2:
   version "4.0.2"
   resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-4.0.2.tgz#82b38e8e8ff7080764f8dcec77bd4be393689396"
   integrity sha512-GZW464g1SH7ag3Y7hXjf8RoUuAFIqklOAq3MRl4OaWabTFJY9PN/E1YklhXLh+OQ3fM9yS2nOkCoS+WLZ6kvxQ==
@@ -4867,28 +4935,28 @@ d3-scale@4:
   resolved "https://registry.yarnpkg.com/d3-selection/-/d3-selection-3.0.0.tgz#c25338207efa72cc5b9bd1458a1a41901f1e1b31"
   integrity sha512-fmTRWbNMmsmWq6xJV8D19U/gw/bwrHfNXxrIN+HfZgnzqTHp9jOmKMhsTUjXOJnZOdZY9Q28y4yebKzqDKlxlQ==
 
-d3-shape@3:
+d3-shape@3, d3-shape@^3.2.0:
   version "3.2.0"
   resolved "https://registry.yarnpkg.com/d3-shape/-/d3-shape-3.2.0.tgz#a1a839cbd9ba45f28674c69d7f855bcf91dfc6a5"
   integrity sha512-SaLBuwGm3MOViRq2ABk3eLoxwZELpH6zhl3FbAoJ7Vm1gofKx6El1Ib5z23NUEhF9AsGl7y+dzLe5Cw2AArGTA==
   dependencies:
     d3-path "^3.1.0"
 
-"d3-time-format@2 - 4", d3-time-format@4:
+"d3-time-format@2 - 4", d3-time-format@4, d3-time-format@^4.1.0:
   version "4.1.0"
   resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-4.1.0.tgz#7ab5257a5041d11ecb4fe70a5c7d16a195bb408a"
   integrity sha512-dJxPBlzC7NugB2PDLwo9Q8JiTR3M3e4/XANkreKSUxF8vvXKqm1Yfq4Q5dl8budlunRVlUUaDUgFt7eA8D6NLg==
   dependencies:
     d3-time "1 - 3"
 
-"d3-time@1 - 3", "d3-time@2.1.1 - 3", d3-time@3:
+"d3-time@1 - 3", "d3-time@2.1.1 - 3", d3-time@3, d3-time@^3.1.0:
   version "3.1.0"
   resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-3.1.0.tgz#9310db56e992e3c0175e1ef385e545e48a9bb5c7"
   integrity sha512-VqKjzBLejbSMT4IgbmVgDjpkYrNWUYJnbCGo874u7MMKIWsILRX+OpX/gTk8MqjpT1A/c6HY2dCA77ZN0lkQ2Q==
   dependencies:
     d3-array "2 - 3"
 
-"d3-timer@1 - 3", d3-timer@3:
+"d3-timer@1 - 3", d3-timer@3, d3-timer@^3.0.1:
   version "3.0.1"
   resolved "https://registry.yarnpkg.com/d3-timer/-/d3-timer-3.0.1.tgz#6284d2a2708285b1abb7e201eda4380af35e63b0"
   integrity sha512-ndfJ/JxxMd3nw31uyKoY2naivF+r29V+Lc0svZxe1JvvIRmi8hUsrMvdOwgS1o6uBHmiz91geQ0ylPP0aj1VUA==
@@ -5069,6 +5137,15 @@ define-data-property@^1.0.1:
     gopd "^1.0.1"
     has-property-descriptors "^1.0.0"
 
+define-data-property@^1.1.4:
+  version "1.1.4"
+  resolved "https://registry.yarnpkg.com/define-data-property/-/define-data-property-1.1.4.tgz#894dc141bb7d3060ae4366f6a0107e68fbe48c5e"
+  integrity sha512-rBMvIzlpA8v6E+SJZoo++HAYqsLrkg7MSfIinMPFhmkorw7X+dOXVJQs+QT69zGkzMyfDnIMN2Wid1+NbL3T+A==
+  dependencies:
+    es-define-property "^1.0.0"
+    es-errors "^1.3.0"
+    gopd "^1.0.1"
+
 define-lazy-prop@^2.0.0:
   version "2.0.0"
   resolved "https://registry.npmjs.org/define-lazy-prop/-/define-lazy-prop-2.0.0.tgz"
@@ -5211,10 +5288,10 @@ doctrine@^3.0.0:
   dependencies:
     esutils "^2.0.2"
 
-dom-accessibility-api@^0.5.6:
-  version "0.5.14"
-  resolved "https://registry.npmjs.org/dom-accessibility-api/-/dom-accessibility-api-0.5.14.tgz"
-  integrity sha512-NMt+m9zFMPZe0JcY9gN224Qvk6qLIdqex29clBvc/y75ZBX9YA9wNK3frsYvu2DI1xcCIwxwnX+TlsJ2DSOADg==
+dom-accessibility-api@^0.6.3:
+  version "0.6.3"
+  resolved "https://registry.yarnpkg.com/dom-accessibility-api/-/dom-accessibility-api-0.6.3.tgz#993e925cc1d73f2c662e7d75dd5a5445259a8fd8"
+  integrity sha512-7ZgogeTnjuHbo+ct10G9Ffp0mif17idi0IyWNVA/wcwcm7NPOD/WEHVP3n7n3MhXqxoIYm8d6MuZohYWIZ4T3w==
 
 dom-event-types@^1.0.0:
   version "1.1.0"
@@ -5255,14 +5332,14 @@ domhandler@^5.0.2, domhandler@^5.0.3:
     domelementtype "^2.3.0"
 
 dompurify@^2.2.0:
-  version "2.3.10"
-  resolved "https://registry.npmjs.org/dompurify/-/dompurify-2.3.10.tgz"
-  integrity sha512-o7Fg/AgC7p/XpKjf/+RC3Ok6k4St5F7Q6q6+Nnm3p2zGWioAY6dh0CbbuwOhH2UcSzKsdniE/YnE2/92JcsA+g==
+  version "2.5.6"
+  resolved "https://registry.yarnpkg.com/dompurify/-/dompurify-2.5.6.tgz#8402b501611eaa7fb3786072297fcbe2787f8592"
+  integrity sha512-zUTaUBO8pY4+iJMPE1B9XlO2tXVYIcEA4SNGtvDELzTSCQO7RzH+j7S180BmhmJId78lqGU2z19vgVx2Sxs/PQ==
 
 dompurify@^3.0.6:
-  version "3.0.6"
-  resolved "https://registry.yarnpkg.com/dompurify/-/dompurify-3.0.6.tgz#925ebd576d54a9531b5d76f0a5bef32548351dae"
-  integrity sha512-ilkD8YEnnGh1zJ240uJsW7AzE+2qpbOUYjacomn3AvJ6J4JhKGSZ2nh4wUIXPZrEPppaCLx5jFe8T89Rk8tQ7w==
+  version "3.1.6"
+  resolved "https://registry.yarnpkg.com/dompurify/-/dompurify-3.1.6.tgz#43c714a94c6a7b8801850f82e756685300a027e2"
+  integrity sha512-cTOAhc36AalkjtBpfG6O8JimdTMWNXjiePT2xQH/ppBGi/4uIpmj8eKyIkMJErXWARyINV/sB38yf8JCLF5pbQ==
 
 domutils@^3.0.1:
   version "3.1.0"
@@ -5303,6 +5380,14 @@ eastasianwidth@^0.2.0:
   resolved "https://registry.yarnpkg.com/eastasianwidth/-/eastasianwidth-0.2.0.tgz#696ce2ec0aa0e6ea93a397ffcf24aa7840c827cb"
   integrity sha512-I88TYZWc9XiYHRQ4/3c5rjjfgkjhLyW2luGIheGERbNQ6OY7yTybanSpDXZa8y7VUP9YmDcYa+eyq4ca7iLqWA==
 
+echarts@^5.5.1:
+  version "5.5.1"
+  resolved "https://registry.yarnpkg.com/echarts/-/echarts-5.5.1.tgz#8dc9c68d0c548934bedcb5f633db07ed1dd2101c"
+  integrity sha512-Fce8upazaAXUVUVsjgV6mBnGuqgO+JNDlcgF79Dksy4+wgGpQB2lmYoO4TSweFg/mZITdpGHomw/cNBJZj1icA==
+  dependencies:
+    tslib "2.3.0"
+    zrender "5.6.0"
+
 editorconfig@^0.15.3:
   version "0.15.3"
   resolved "https://registry.npmjs.org/editorconfig/-/editorconfig-0.15.3.tgz"
@@ -5318,10 +5403,12 @@ ee-first@1.1.1:
   resolved "https://registry.npmjs.org/ee-first/-/ee-first-1.1.1.tgz"
   integrity sha512-WMwm9LhRUo+WUaRN+vRuETqG89IgZphVSNkdFgeb6sS/E4OrDIN7t48CAewSHXc6C8lefD8KKfr5vY61brQlow==
 
-electron-to-chromium@^1.4.202:
-  version "1.4.213"
-  resolved "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.4.213.tgz"
-  integrity sha512-+3DbGHGOCHTVB/Ms63bGqbyC1b8y7Fk86+7ltssB8NQrZtSCvZG6eooSl9U2Q0yw++fL2DpHKOdTU0NVEkFObg==
+ejs@^3.1.10:
+  version "3.1.10"
+  resolved "https://registry.yarnpkg.com/ejs/-/ejs-3.1.10.tgz#69ab8358b14e896f80cc39e62087b88500c3ac3b"
+  integrity sha512-UeJmFfOrAQS8OJWPZ4qtgHyWExa088/MtK5UEyoJGFH67cDEXkZSviOiKRCZ4Xij0zxI3JECgYs3oKx+AizQBA==
+  dependencies:
+    jake "^10.8.5"
 
 electron-to-chromium@^1.4.535:
   version "1.4.554"
@@ -5363,6 +5450,11 @@ encodeurl@~1.0.2:
   resolved "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz"
   integrity sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==
 
+encodeurl@~2.0.0:
+  version "2.0.0"
+  resolved "https://registry.yarnpkg.com/encodeurl/-/encodeurl-2.0.0.tgz#7b8ea898077d7e409d3ac45474ea38eaf0857a58"
+  integrity sha512-Q0n9HRi4m6JuGIV1eFlmvJB7ZEVxu93IrMyiMsGC0lrMJMWzRgx6WGquyfQgZVb31vhGgXnfmPNNXmxnOkRBrg==
+
 end-of-stream@^1.0.0, end-of-stream@^1.1.0:
   version "1.4.4"
   resolved "https://registry.npmjs.org/end-of-stream/-/end-of-stream-1.4.4.tgz"
@@ -5370,26 +5462,10 @@ end-of-stream@^1.0.0, end-of-stream@^1.1.0:
   dependencies:
     once "^1.4.0"
 
-enhanced-resolve@^5.0.0, enhanced-resolve@^5.10.0:
-  version "5.10.0"
-  resolved "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.10.0.tgz"
-  integrity sha512-T0yTFjdpldGY8PmuXXR0PyQ1ufZpEGiHVrp7zHKB7jdR4qlmZHhONVM5AQOAWXuF/w3dnHbEQVrNptJgt7F+cQ==
-  dependencies:
-    graceful-fs "^4.2.4"
-    tapable "^2.2.0"
-
-enhanced-resolve@^5.15.0:
-  version "5.15.0"
-  resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.15.0.tgz#1af946c7d93603eb88e9896cee4904dc012e9c35"
-  integrity sha512-LXYT42KJ7lpIKECr2mAXIaMldcNCh/7E0KBKOu4KSfkHmP+mZmSs+8V5gBAqisWBy0OO4W5Oyys0GO1Y8KtdKg==
-  dependencies:
-    graceful-fs "^4.2.4"
-    tapable "^2.2.0"
-
-enhanced-resolve@^5.7.0:
-  version "5.12.0"
-  resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.12.0.tgz#300e1c90228f5b570c4d35babf263f6da7155634"
-  integrity sha512-QHTXI/sZQmko1cbDoNAa3mJ5qhWUUNAq3vR0/YiD379fWQrcfuoX1+HW2S0MTt7XmoPLapdaDKUtelUSPic7hQ==
+enhanced-resolve@^5.0.0, enhanced-resolve@^5.17.1, enhanced-resolve@^5.7.0:
+  version "5.17.1"
+  resolved "https://registry.yarnpkg.com/enhanced-resolve/-/enhanced-resolve-5.17.1.tgz#67bfbbcc2f81d511be77d686a90267ef7f898a15"
+  integrity sha512-LMHl3dXhTcfv8gM4kEzIUeTQ+7fpdA0l2tUf34BddXPkz2A5xJ5L/Pchd5BL6rdccM9QGvu0sWZzK1Z1t4wwyg==
   dependencies:
     graceful-fs "^4.2.4"
     tapable "^2.2.0"
@@ -5513,10 +5589,17 @@ es-abstract@^1.22.1:
     unbox-primitive "^1.0.2"
     which-typed-array "^1.1.11"
 
-es-module-lexer@^0.9.0:
-  version "0.9.3"
-  resolved "https://registry.npmjs.org/es-module-lexer/-/es-module-lexer-0.9.3.tgz"
-  integrity sha512-1HQ2M2sPtxwnvOvT1ZClHyQDiggdNjURWpY2we6aMKCQiUVxTmVs2UYPLIrD84sS+kMdUwfBSylbJPwNnBrnHQ==
+es-define-property@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/es-define-property/-/es-define-property-1.0.0.tgz#c7faefbdff8b2696cf5f46921edfb77cc4ba3845"
+  integrity sha512-jxayLKShrEqqzJ0eumQbVhTYQM27CfT1T35+gCgDFoL82JLsXqTJ76zv6A0YLOgEnLUMvLzsDsGIrl8NFpT2gQ==
+  dependencies:
+    get-intrinsic "^1.2.4"
+
+es-errors@^1.3.0:
+  version "1.3.0"
+  resolved "https://registry.yarnpkg.com/es-errors/-/es-errors-1.3.0.tgz#05f75a25dab98e4fb1dcd5e1472c0546d5057c8f"
+  integrity sha512-Zf5H2Kxt2xjTvbJvP2ZWLEICxA6j+hAmMzIlypy4xcBg1vKVnx89Wy0GbS+kf5cwCVFFzdCFh2XSCFNULS6csw==
 
 es-module-lexer@^1.2.1:
   version "1.3.1"
@@ -5714,15 +5797,7 @@ eslint-scope@5.1.1:
     esrecurse "^4.3.0"
     estraverse "^4.1.1"
 
-eslint-scope@^7.1.1:
-  version "7.1.1"
-  resolved "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.1.1.tgz"
-  integrity sha512-QKQM/UXpIiHcLqJ5AOyIW7XZmzjkzQXYE54n1++wb0u9V/abW3l9uQnxX8Z5Xd18xyKIMTUAyQ0k1e8pz6LUrw==
-  dependencies:
-    esrecurse "^4.3.0"
-    estraverse "^5.2.0"
-
-eslint-scope@^7.2.2:
+eslint-scope@^7.1.1, eslint-scope@^7.2.2:
   version "7.2.2"
   resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-7.2.2.tgz#deb4f92563390f32006894af62a22dba1c46423f"
   integrity sha512-dOt21O7lTMhDM+X9mB4GX+DZrZtCUJPL/wlcTqxyrx5IvO0IYtILdtrQGQp+8n5S0gwSVmOf9NQrjMOgfQZlIg==
@@ -5938,36 +6013,36 @@ expose-loader@^4.1.0:
   integrity sha512-oLAesnzerwDGGADzBMnu0LPqqnlVz6e2V9lTa+/4X6VeW9W93x/nJpw05WBrcIdbqXm/EdnEQpiVDFFiQXuNfg==
 
 express@^4.17.3:
-  version "4.19.2"
-  resolved "https://registry.yarnpkg.com/express/-/express-4.19.2.tgz#e25437827a3aa7f2a827bc8171bbbb664a356465"
-  integrity sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==
+  version "4.21.0"
+  resolved "https://registry.yarnpkg.com/express/-/express-4.21.0.tgz#d57cb706d49623d4ac27833f1cbc466b668eb915"
+  integrity sha512-VqcNGcj/Id5ZT1LZ/cfihi3ttTn+NJmkli2eZADigjq29qTlWi/hAQ43t/VLPq8+UX06FCEx3ByOYet6ZFblng==
   dependencies:
     accepts "~1.3.8"
     array-flatten "1.1.1"
-    body-parser "1.20.2"
+    body-parser "1.20.3"
     content-disposition "0.5.4"
     content-type "~1.0.4"
     cookie "0.6.0"
     cookie-signature "1.0.6"
     debug "2.6.9"
     depd "2.0.0"
-    encodeurl "~1.0.2"
+    encodeurl "~2.0.0"
     escape-html "~1.0.3"
     etag "~1.8.1"
-    finalhandler "1.2.0"
+    finalhandler "1.3.1"
     fresh "0.5.2"
     http-errors "2.0.0"
-    merge-descriptors "1.0.1"
+    merge-descriptors "1.0.3"
     methods "~1.1.2"
     on-finished "2.4.1"
     parseurl "~1.3.3"
-    path-to-regexp "0.1.7"
+    path-to-regexp "0.1.10"
     proxy-addr "~2.0.7"
-    qs "6.11.0"
+    qs "6.13.0"
     range-parser "~1.2.1"
     safe-buffer "5.2.1"
-    send "0.18.0"
-    serve-static "1.15.0"
+    send "0.19.0"
+    serve-static "1.16.2"
     setprototypeof "1.2.0"
     statuses "2.0.1"
     type-is "~1.6.18"
@@ -6015,6 +6090,11 @@ extglob@^2.0.4:
     snapdragon "^0.8.1"
     to-regex "^3.0.1"
 
+fake-indexeddb@^6.0.0:
+  version "6.0.0"
+  resolved "https://registry.yarnpkg.com/fake-indexeddb/-/fake-indexeddb-6.0.0.tgz#3173d5ad141436dace95f8de6e9ecdc3d9787d5d"
+  integrity sha512-YEboHE5VfopUclOck7LncgIqskAqnv4q0EWbYCaxKKjAvO93c+TJIaBuGy8CBFdbg9nKdpN3AuPRwVBJ4k7NrQ==
+
 fancy-log@^1.3.2:
   version "1.3.3"
   resolved "https://registry.npmjs.org/fancy-log/-/fancy-log-1.3.3.tgz"
@@ -6030,17 +6110,6 @@ fast-deep-equal@^3.1.1, fast-deep-equal@^3.1.3:
   resolved "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz"
   integrity sha512-f3qQ9oQy9j2AhBe/H9VC91wLmKBCCU/gDOnKNAYG5hswO7BLKj09Hc5HYNz9cGI++xlpDCIgDaitVs03ATR84Q==
 
-fast-glob@^3.2.12:
-  version "3.2.12"
-  resolved "https://registry.yarnpkg.com/fast-glob/-/fast-glob-3.2.12.tgz#7f39ec99c2e6ab030337142da9e0c18f37afae80"
-  integrity sha512-DVj4CQIYYow0BlaelwK1pHl5n5cRSJfM60UA0zK891sVInoPri2Ekj7+e1CT3/3qxXenpI+nBBmQAcJPJgaj4w==
-  dependencies:
-    "@nodelib/fs.stat" "^2.0.2"
-    "@nodelib/fs.walk" "^1.2.3"
-    glob-parent "^5.1.2"
-    merge2 "^1.3.0"
-    micromatch "^4.0.4"
-
 fast-glob@^3.2.9:
   version "3.2.11"
   resolved "https://registry.npmjs.org/fast-glob/-/fast-glob-3.2.11.tgz"
@@ -6063,6 +6132,11 @@ fast-glob@^3.3.0:
     merge2 "^1.3.0"
     micromatch "^4.0.4"
 
+fast-json-patch@^3.1.1:
+  version "3.1.1"
+  resolved "https://registry.yarnpkg.com/fast-json-patch/-/fast-json-patch-3.1.1.tgz#85064ea1b1ebf97a3f7ad01e23f9337e72c66947"
+  integrity sha512-vf6IHUX2SBcA+5/+4883dsIjpBTqmfBjmYiWK1savxQmFk4JfBMLa7ynTYOs1Rolp/T1betJxHiGD3g1Mn8lUQ==
+
 fast-json-stable-stringify@2.x, fast-json-stable-stringify@^2.0.0, fast-json-stable-stringify@^2.1.0:
   version "2.1.0"
   resolved "https://registry.npmjs.org/fast-json-stable-stringify/-/fast-json-stable-stringify-2.1.0.tgz"
@@ -6128,6 +6202,13 @@ file-saver@^2.0.5:
   resolved "https://registry.npmjs.org/file-saver/-/file-saver-2.0.5.tgz"
   integrity sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA==
 
+filelist@^1.0.4:
+  version "1.0.4"
+  resolved "https://registry.yarnpkg.com/filelist/-/filelist-1.0.4.tgz#f78978a1e944775ff9e62e744424f215e58352b5"
+  integrity sha512-w1cEuf3S+DrLCQL7ET6kz+gmlJdbq9J7yXCSjK/OZCPA+qEN1WyF4ZAf0YYJa4/shHJra2t/d/r8SV4Ji+x+8Q==
+  dependencies:
+    minimatch "^5.0.1"
+
 fill-range@^4.0.0:
   version "4.0.0"
   resolved "https://registry.npmjs.org/fill-range/-/fill-range-4.0.0.tgz"
@@ -6145,13 +6226,13 @@ fill-range@^7.0.1:
   dependencies:
     to-regex-range "^5.0.1"
 
-finalhandler@1.2.0:
-  version "1.2.0"
-  resolved "https://registry.npmjs.org/finalhandler/-/finalhandler-1.2.0.tgz"
-  integrity sha512-5uXcUVftlQMFnWC9qu/svkWv3GTd2PfUhK/3PLkYNAe7FbqJMt3515HaxE6eRL74GdsriiwujiawdaB1BpEISg==
+finalhandler@1.3.1:
+  version "1.3.1"
+  resolved "https://registry.yarnpkg.com/finalhandler/-/finalhandler-1.3.1.tgz#0c575f1d1d324ddd1da35ad7ece3df7d19088019"
+  integrity sha512-6BN9trH7bp3qvnrRyzsBz+g3lZxTNZTbVO2EV1CS0WIcDbawYVdYvGflME/9QP0h0pYlCDBCTjYa9nZzMDpyxQ==
   dependencies:
     debug "2.6.9"
-    encodeurl "~1.0.2"
+    encodeurl "~2.0.0"
     escape-html "~1.0.3"
     on-finished "2.4.1"
     parseurl "~1.3.3"
@@ -6254,11 +6335,18 @@ flush-write-stream@^1.0.2:
     inherits "^2.0.3"
     readable-stream "^2.3.6"
 
-follow-redirects@^1.0.0, follow-redirects@^1.15.0:
+follow-redirects@^1.0.0, follow-redirects@^1.15.6:
   version "1.15.6"
   resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.15.6.tgz#7f815c0cda4249c74ff09e95ef97c23b5fd0399b"
   integrity sha512-wWN62YITEaOpSK584EZXJafH1AGpO8RVgElfkuXbTOrPX4fIfOyEpW/CsiNd8JdYrAoOvafRTOEnvsO++qCqFA==
 
+"font-awesome-6@npm:@fortawesome/free-solid-svg-icons@6":
+  version "6.7.1"
+  resolved "https://registry.yarnpkg.com/@fortawesome/free-solid-svg-icons/-/free-solid-svg-icons-6.7.1.tgz#c1f9a6c25562a12c283e87e284f9d82a5b0dbcc0"
+  integrity sha512-BTKc0b0mgjWZ2UDKVgmwaE0qt0cZs6ITcDgjrti5f/ki7aF5zs+N91V6hitGo3TItCFtnKg6cUVGdTmBFICFRg==
+  dependencies:
+    "@fortawesome/fontawesome-common-types" "6.7.1"
+
 for-each@^0.3.3:
   version "0.3.3"
   resolved "https://registry.yarnpkg.com/for-each/-/for-each-0.3.3.tgz#69b447e88a0a5d32c3e7084f3f1710034b21376e"
@@ -6317,6 +6405,15 @@ fresh@0.5.2:
   resolved "https://registry.npmjs.org/fresh/-/fresh-0.5.2.tgz"
   integrity sha512-zJ2mQYM18rEFOudeV4GShTGIQ7RbzA7ozbU9I/XBpm7kqgMywgmylMwXHxZJmkVoYkna9d2pVXVXPdYTP9ej8Q==
 
+fs-extra@^11.2.0:
+  version "11.2.0"
+  resolved "https://registry.yarnpkg.com/fs-extra/-/fs-extra-11.2.0.tgz#e70e17dfad64232287d01929399e0ea7c86b0e5b"
+  integrity sha512-PmDi3uwK5nFuXh7XDTlVnS17xJS7vW36is2+w3xcv8SVxiB4NyATf4ctkVY5bkSjX0Y4nbvZCq1/EjtEyr9ktw==
+  dependencies:
+    graceful-fs "^4.2.0"
+    jsonfile "^6.0.1"
+    universalify "^2.0.0"
+
 fs-mkdirp-stream@^1.0.0:
   version "1.0.0"
   resolved "https://registry.npmjs.org/fs-mkdirp-stream/-/fs-mkdirp-stream-1.0.0.tgz"
@@ -6340,7 +6437,7 @@ fsevents@^2.3.2, fsevents@~2.3.2:
   resolved "https://registry.npmjs.org/fsevents/-/fsevents-2.3.2.tgz"
   integrity sha512-xiqMQR4xAeHTuB9uWm+fFRcIOgKBMiOBP+eXiyT7jsgVCq1bkVygt00oASowB7EdtpOHaaPgKt812P9ab+DDKA==
 
-function-bind@^1.1.1:
+function-bind@^1.1.1, function-bind@^1.1.2:
   version "1.1.2"
   resolved "https://registry.yarnpkg.com/function-bind/-/function-bind-1.1.2.tgz#2c02d864d97f3ea6c8830c464cbd11ab6eab7a1c"
   integrity sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA==
@@ -6394,6 +6491,17 @@ get-intrinsic@^1.1.3:
     has "^1.0.3"
     has-symbols "^1.0.3"
 
+get-intrinsic@^1.2.4:
+  version "1.2.4"
+  resolved "https://registry.yarnpkg.com/get-intrinsic/-/get-intrinsic-1.2.4.tgz#e385f5a4b5227d449c3eabbad05494ef0abbeadd"
+  integrity sha512-5uYhsJH8VJBTv7oslg4BznJYhDoRI6waYCxMmCdnTrcCrHA/fCFKoTFz2JKKE0HdDFUF7/oQuhzumXJK7paBRQ==
+  dependencies:
+    es-errors "^1.3.0"
+    function-bind "^1.1.2"
+    has-proto "^1.0.1"
+    has-symbols "^1.0.3"
+    hasown "^2.0.0"
+
 get-package-type@^0.1.0:
   version "0.1.0"
   resolved "https://registry.npmjs.org/get-package-type/-/get-package-type-0.1.0.tgz"
@@ -6588,7 +6696,7 @@ graceful-fs@^4.0.0, graceful-fs@^4.1.11, graceful-fs@^4.1.2, graceful-fs@^4.1.6,
   resolved "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.10.tgz"
   integrity sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA==
 
-graceful-fs@^4.2.10:
+graceful-fs@^4.2.0, graceful-fs@^4.2.10, graceful-fs@^4.2.11:
   version "4.2.11"
   resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.11.tgz#4183e4e8bf08bb6e05bbb2f7d2e0c8f712ca40e3"
   integrity sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==
@@ -6598,6 +6706,11 @@ graphemer@^1.4.0:
   resolved "https://registry.yarnpkg.com/graphemer/-/graphemer-1.4.0.tgz#fb2f1d55e0e3a1849aeffc90c4fa0dd53a0e66c6"
   integrity sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==
 
+graphql@^16.8.1:
+  version "16.9.0"
+  resolved "https://registry.yarnpkg.com/graphql/-/graphql-16.9.0.tgz#1c310e63f16a49ce1fbb230bd0a000e99f6f115f"
+  integrity sha512-GGTKBX4SD7Wdb8mqeDLni2oaRGYQWjWHGKPQ24ZMnUtKfcsVoiv4uX8+LJr1K6U5VW2Lu1BwJnj7uiori0YtRw==
+
 gulp-cli@^2.2.0:
   version "2.3.0"
   resolved "https://registry.npmjs.org/gulp-cli/-/gulp-cli-2.3.0.tgz"
@@ -6675,6 +6788,13 @@ has-property-descriptors@^1.0.0:
   dependencies:
     get-intrinsic "^1.1.1"
 
+has-property-descriptors@^1.0.2:
+  version "1.0.2"
+  resolved "https://registry.yarnpkg.com/has-property-descriptors/-/has-property-descriptors-1.0.2.tgz#963ed7d071dc7bf5f084c5bfbe0d1b6222586854"
+  integrity sha512-55JNKuIW+vq4Ke1BjOTjM2YctQIvCT7GFzHwmfZPGo5wnrgkid0YQtnAleFSqumZm4az3n2BS+erby5ipJdgrg==
+  dependencies:
+    es-define-property "^1.0.0"
+
 has-proto@^1.0.1:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/has-proto/-/has-proto-1.0.1.tgz#1885c1305538958aff469fef37937c22795408e0"
@@ -6733,11 +6853,23 @@ hash-sum@^1.0.2:
   resolved "https://registry.npmjs.org/hash-sum/-/hash-sum-1.0.2.tgz"
   integrity sha512-fUs4B4L+mlt8/XAtSOGMUO1TXmAelItBPtJG7CyHJfYTdDjwisntGO2JQz7oUsatOY9o68+57eziUVNw/mRHmA==
 
+hasown@^2.0.0:
+  version "2.0.2"
+  resolved "https://registry.yarnpkg.com/hasown/-/hasown-2.0.2.tgz#003eaf91be7adc372e84ec59dc37252cedb80003"
+  integrity sha512-0hJU9SCPvmMzIBdZFqNPXWa6dqh7WdH0cII9y+CyS8rG3nL48Bclra9HmKhVVUHyPWNH5Y7xDwAB7bfgSjkUMQ==
+  dependencies:
+    function-bind "^1.1.2"
+
 he@^1.2.0:
   version "1.2.0"
   resolved "https://registry.npmjs.org/he/-/he-1.2.0.tgz"
   integrity sha512-F/1DnUGPopORZi0ni+CvrCgHQ5FyEAHRLSApuYWMmrbSwoN2Mn/7k+Gl38gJnR7yyDZk6WLXwiGod1JOWNDKGw==
 
+headers-polyfill@^4.0.2:
+  version "4.0.3"
+  resolved "https://registry.yarnpkg.com/headers-polyfill/-/headers-polyfill-4.0.3.tgz#922a0155de30ecc1f785bcf04be77844ca95ad07"
+  integrity sha512-IScLbePpkvO846sIwOtOTDjutRMWdXdJmXdMvk6gCBHxFO8d+QKOQedyZSxFTTFYRSmlgSTDtXqqq4pcenBXLQ==
+
 homedir-polyfill@^1.0.1:
   version "1.0.3"
   resolved "https://registry.npmjs.org/homedir-polyfill/-/homedir-polyfill-1.0.3.tgz"
@@ -6831,9 +6963,9 @@ http-proxy-agent@^5.0.0:
     debug "4"
 
 http-proxy-middleware@^2.0.3:
-  version "2.0.6"
-  resolved "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.6.tgz"
-  integrity sha512-ya/UeJ6HVBYxrgYotAZo1KvPWlgB48kUJLDePFeneHsVujFaW5WNj2NgWCAE//B1Dl02BIfYlpNgBy8Kf8Rjmw==
+  version "2.0.7"
+  resolved "https://registry.yarnpkg.com/http-proxy-middleware/-/http-proxy-middleware-2.0.7.tgz#915f236d92ae98ef48278a95dedf17e991936ec6"
+  integrity sha512-fgVY8AV7qU7z/MmXJ/rxwbrtQH4jBQ9m7kp3llF0liB7glmFeVZFBepQb32T3y8n8k2+AEYuMPCpinYW+/CuRA==
   dependencies:
     "@types/http-proxy" "^1.17.8"
     http-proxy "^1.18.1"
@@ -6858,6 +6990,14 @@ https-proxy-agent@^5.0.1:
     agent-base "6"
     debug "4"
 
+https-proxy-agent@^7.0.4:
+  version "7.0.5"
+  resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-7.0.5.tgz#9e8b5013873299e11fab6fd548405da2d6c602b2"
+  integrity sha512-1e4Wqeblerz+tMKPIq2EMGiiWW1dIjZOksyHWSUm1rmuvw/how9hBHZ38lAGj5ID4Ik6EdkOw7NmWPy6LAwalw==
+  dependencies:
+    agent-base "^7.0.2"
+    debug "4"
+
 human-signals@^2.1.0:
   version "2.1.0"
   resolved "https://registry.npmjs.org/human-signals/-/human-signals-2.1.0.tgz"
@@ -6958,6 +7098,11 @@ indent-string@^5.0.0:
   resolved "https://registry.yarnpkg.com/indent-string/-/indent-string-5.0.0.tgz#4fd2980fccaf8622d14c64d694f4cf33c81951a5"
   integrity sha512-m6FAo/spmsW2Ab2fU35JTYwtOKa2yAwXSwgjSv1TJzh4Mh7mC3lzAOVLBprb72XsTrgkEIsl7YrFNAiDiRhIGg==
 
+index-to-position@^0.1.2:
+  version "0.1.2"
+  resolved "https://registry.yarnpkg.com/index-to-position/-/index-to-position-0.1.2.tgz#e11bfe995ca4d8eddb1ec43274488f3c201a7f09"
+  integrity sha512-MWDKS3AS1bGCHLBA2VLImJz42f7bJh8wQsTGCzI3j519/CASStoDONUBVz2I/VID0MpiX3SGSnbOD2xUalbE5g==
+
 inflight@^1.0.4:
   version "1.0.6"
   resolved "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz"
@@ -7239,6 +7384,11 @@ is-negative-zero@^2.0.2:
   resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150"
   integrity sha512-dqJvarLawXsFbNDeJW7zAz8ItJ9cd28YufuuFzh0G8pNHjJMnY08Dv7sYX2uF5UpQOwieAeOExEYAWWfu7ZZUA==
 
+is-node-process@^1.2.0:
+  version "1.2.0"
+  resolved "https://registry.yarnpkg.com/is-node-process/-/is-node-process-1.2.0.tgz#ea02a1b90ddb3934a19aea414e88edef7e11d134"
+  integrity sha512-Vg4o6/fqPxIjtxgUH5QLJhwZ7gW5diGCVlXpuUfELC62CuxM1iHcRe51f2W1FDy04Ai4KJkagKjx3XaqyfRKXw==
+
 is-number-object@^1.0.4:
   version "1.0.7"
   resolved "https://registry.yarnpkg.com/is-number-object/-/is-number-object-1.0.7.tgz#59d50ada4c45251784e9904f5246c742f07a42fc"
@@ -7484,6 +7634,16 @@ jackspeak@^2.3.5:
   optionalDependencies:
     "@pkgjs/parseargs" "^0.11.0"
 
+jake@^10.8.5:
+  version "10.9.2"
+  resolved "https://registry.yarnpkg.com/jake/-/jake-10.9.2.tgz#6ae487e6a69afec3a5e167628996b59f35ae2b7f"
+  integrity sha512-2P4SQ0HrLQ+fw6llpLnOaGAvN2Zu6778SJMrCUwns4fOoG9ayrTiZk3VV8sCPkVZF8ab0zksVpS8FDY5pRCNBA==
+  dependencies:
+    async "^3.2.3"
+    chalk "^4.0.2"
+    filelist "^1.0.4"
+    minimatch "^3.1.2"
+
 javascript-stringify@^2.0.1:
   version "2.1.0"
   resolved "https://registry.npmjs.org/javascript-stringify/-/javascript-stringify-2.1.0.tgz"
@@ -7623,6 +7783,11 @@ jest-environment-node@^29.7.0:
     jest-mock "^29.7.0"
     jest-util "^29.7.0"
 
+jest-fixed-jsdom@^0.0.2:
+  version "0.0.2"
+  resolved "https://registry.yarnpkg.com/jest-fixed-jsdom/-/jest-fixed-jsdom-0.0.2.tgz#2a15d2db64cf9276afd162c451ae727b89a8811e"
+  integrity sha512-rQ7tcI7Sz3XGxEzk7Ic/4n3y83O0cGnSK3lFU3lqHhYaxp/00yoolBBOTnY6bLKkI1XzO4EMgyHYZ1IBRpEesw==
+
 jest-get-type@^29.6.3:
   version "29.6.3"
   resolved "https://registry.yarnpkg.com/jest-get-type/-/jest-get-type-29.6.3.tgz#36f499fdcea197c1045a127319c0481723908fd1"
@@ -7937,6 +8102,11 @@ js-beautify@^1.6.12:
     glob "^8.0.3"
     nopt "^6.0.0"
 
+js-levenshtein@^1.1.6:
+  version "1.1.6"
+  resolved "https://registry.yarnpkg.com/js-levenshtein/-/js-levenshtein-1.1.6.tgz#c6cee58eb3550372df8deb85fad5ce66ce01d59d"
+  integrity sha512-X2BB11YZtrRqY4EnQcLX5Rh373zbK4alC1FW7D7MBhL2gtcC17cTnr6DmfHZeS0s2rTHjUTMMHfG7gO8SSdw+g==
+
 js-tokens@^4.0.0:
   version "4.0.0"
   resolved "https://registry.npmjs.org/js-tokens/-/js-tokens-4.0.0.tgz"
@@ -8032,6 +8202,11 @@ json-stable-stringify-without-jsonify@^1.0.1:
   resolved "https://registry.npmjs.org/json-stable-stringify-without-jsonify/-/json-stable-stringify-without-jsonify-1.0.1.tgz"
   integrity sha512-Bdboy+l7tA3OGW6FjyFHWkP5LuByj1Tk33Ljyq0axyzdk9//JSi2u3fP1QSmd1KNwq6VOKYGlAu87CisVir6Pw==
 
+json-stringify-pretty-compact@^3.0.0, json-stringify-pretty-compact@~3.0.0:
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/json-stringify-pretty-compact/-/json-stringify-pretty-compact-3.0.0.tgz#f71ef9d82ef16483a407869556588e91b681d9ab"
+  integrity sha512-Rc2suX5meI0S3bfdZuA7JMFBGkJ875ApfVyq2WHELjBiiG22My/l7/8zPpH/CfFVQHuVLd8NLR0nv6vi0BYYKA==
+
 json5@^1.0.1:
   version "1.0.1"
   resolved "https://registry.npmjs.org/json5/-/json5-1.0.1.tgz"
@@ -8056,6 +8231,15 @@ json5@^2.2.2, json5@^2.2.3:
   resolved "https://registry.yarnpkg.com/json5/-/json5-2.2.3.tgz#78cd6f1a19bdc12b73db5ad0c61efd66c1e29283"
   integrity sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==
 
+jsonfile@^6.0.1:
+  version "6.1.0"
+  resolved "https://registry.yarnpkg.com/jsonfile/-/jsonfile-6.1.0.tgz#bc55b2634793c679ec6403094eb13698a6ec0aae"
+  integrity sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==
+  dependencies:
+    universalify "^2.0.0"
+  optionalDependencies:
+    graceful-fs "^4.1.6"
+
 jspdf@^2.5.1:
   version "2.5.1"
   resolved "https://registry.npmjs.org/jspdf/-/jspdf-2.5.1.tgz"
@@ -8489,10 +8673,10 @@ meow@^12.0.1:
   resolved "https://registry.yarnpkg.com/meow/-/meow-12.1.1.tgz#e558dddbab12477b69b2e9a2728c327f191bace6"
   integrity sha512-BhXM0Au22RwUneMPwSCnyhTOizdWoIEPU9sp0Aqa1PnDMR5Wv2FGXYDjuzJEIX+Eo2Rb8xuYe5jrnm5QowQFkw==
 
-merge-descriptors@1.0.1:
-  version "1.0.1"
-  resolved "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.1.tgz"
-  integrity sha512-cCi6g3/Zr1iqQi6ySbseM1Xvooa98N0w31jzUYrXPX2xqObmFGHJ0tQ5u74H3mVh7wLouTseZyYIq39g8cNp1w==
+merge-descriptors@1.0.3:
+  version "1.0.3"
+  resolved "https://registry.yarnpkg.com/merge-descriptors/-/merge-descriptors-1.0.3.tgz#d80319a65f3c7935351e5cfdac8f9318504dbed5"
+  integrity sha512-gaNvAS7TZ897/rVaZ0nMtAyxNyi/pdbjbAwUpFQpN70GqnVfOiXpeUUMKRBmzXaSQ8DdTX4/0ms62r2K+hE6mQ==
 
 merge-source-map@^1.1.0:
   version "1.1.0"
@@ -8656,6 +8840,29 @@ ms@2.1.3, ms@^2.1.1:
   resolved "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz"
   integrity sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==
 
+msw@^2.3.4:
+  version "2.3.4"
+  resolved "https://registry.yarnpkg.com/msw/-/msw-2.3.4.tgz#3caac6c8e1ceb8040f512c32f9b8a6e850739c03"
+  integrity sha512-sHMlwrajgmZSA2l1o7qRSe+azm/I+x9lvVVcOxAzi4vCtH8uVPJk1K5BQYDkzGl+tt0RvM9huEXXdeGrgcc79g==
+  dependencies:
+    "@bundled-es-modules/cookie" "^2.0.0"
+    "@bundled-es-modules/statuses" "^1.0.1"
+    "@bundled-es-modules/tough-cookie" "^0.1.6"
+    "@inquirer/confirm" "^3.0.0"
+    "@mswjs/interceptors" "^0.29.0"
+    "@open-draft/until" "^2.1.0"
+    "@types/cookie" "^0.6.0"
+    "@types/statuses" "^2.0.4"
+    chalk "^4.1.2"
+    graphql "^16.8.1"
+    headers-polyfill "^4.0.2"
+    is-node-process "^1.2.0"
+    outvariant "^1.4.2"
+    path-to-regexp "^6.2.0"
+    strict-event-emitter "^0.5.1"
+    type-fest "^4.9.0"
+    yargs "^17.7.2"
+
 multicast-dns@^7.2.5:
   version "7.2.5"
   resolved "https://registry.npmjs.org/multicast-dns/-/multicast-dns-7.2.5.tgz"
@@ -8669,6 +8876,11 @@ mute-stdout@^1.0.0:
   resolved "https://registry.npmjs.org/mute-stdout/-/mute-stdout-1.0.1.tgz"
   integrity sha512-kDcwXR4PS7caBpuRYYBUz9iVixUk3anO3f5OYFiIPwK/20vCzKCHyKoulbiDY1S53zD2bxUpxN/IJ+TnXjfvxg==
 
+mute-stream@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-1.0.0.tgz#e31bd9fe62f0aed23520aa4324ea6671531e013e"
+  integrity sha512-avsJQhyd+680gKXyG/sQc0nXaC6rBkPOfyHYcFb9+hdkqQkR9bdnkJ0AMZhke0oesPqIO+mFFJ+IdBc7mst4IA==
+
 nanoid@^3.3.4:
   version "3.3.4"
   resolved "https://registry.npmjs.org/nanoid/-/nanoid-3.3.4.tgz"
@@ -8743,11 +8955,6 @@ node-releases@^2.0.13:
   resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-2.0.13.tgz#d5ed1627c23e3461e819b02e57b75e4899b1c81d"
   integrity sha512-uYr7J37ae/ORWdZeQ1xxMJe3NtdmqMC/JZK+geofDrkLUApKRHPd18/TxtBOJ4A0/+uUIliorNrfYV6s1b02eQ==
 
-node-releases@^2.0.6:
-  version "2.0.6"
-  resolved "https://registry.npmjs.org/node-releases/-/node-releases-2.0.6.tgz"
-  integrity sha512-PiVXnNuFm5+iYkLBNeq5211hvO38y63T0i2KKh2KnUs3RpzJ+JtODFjkD8yjLwnDkTYF1eKXheUwdssR+NRZdg==
-
 nopt@^6.0.0:
   version "6.0.0"
   resolved "https://registry.npmjs.org/nopt/-/nopt-6.0.0.tgz"
@@ -8839,6 +9046,11 @@ object-inspect@^1.12.3:
   resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.12.3.tgz#ba62dffd67ee256c8c086dfae69e016cd1f198b9"
   integrity sha512-geUvdk7c+eizMNUDkRpW1wJwgfOiOeHbxBR/hLXK1aT6zmVSO0jsQcs7fj6MGw89jC/cjGfLcNOrtMYtGqm81g==
 
+object-inspect@^1.13.1:
+  version "1.13.2"
+  resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.13.2.tgz#dea0088467fb991e67af4058147a24824a3043ff"
+  integrity sha512-IRZSRuzJiynemAXPYtPe5BoI/RESNYR7TYm50MC5Mqbd3Jmw5y790sErYw3V6SryFJD64b74qQQs9wn5Bg/k3g==
+
 object-inspect@^1.9.0:
   version "1.13.0"
   resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.13.0.tgz#42695d3879e1cd5bda6df5062164d80c996e23e2"
@@ -8985,21 +9197,39 @@ open@^8.0.9:
     is-docker "^2.1.1"
     is-wsl "^2.2.0"
 
-openapi-typescript-fetch@^1.1.3:
-  version "1.1.3"
-  resolved "https://registry.yarnpkg.com/openapi-typescript-fetch/-/openapi-typescript-fetch-1.1.3.tgz#354e6803b7885c7142ae11adc1b758afafd8aa2e"
-  integrity sha512-smLZPck4OkKMNExcw8jMgrMOGgVGx2N/s6DbKL2ftNl77g5HfoGpZGFy79RBzU/EkaO0OZpwBnslfdBfh7ZcWg==
+openapi-fetch@^0.10.6:
+  version "0.10.6"
+  resolved "https://registry.yarnpkg.com/openapi-fetch/-/openapi-fetch-0.10.6.tgz#255017e3e609c5e7be16bc1ed7a973977c085cdc"
+  integrity sha512-6xXfvIEL/POtLGOaFPsp3O+pDe+J3DZYxbD9BrsQHXOTeNK8z/gsWHT6adUy1KcpQOhmkerMzlQrJM6DbN55dQ==
+  dependencies:
+    openapi-typescript-helpers "^0.0.11"
 
-openapi-typescript@^6.1.0:
-  version "6.1.0"
-  resolved "https://registry.yarnpkg.com/openapi-typescript/-/openapi-typescript-6.1.0.tgz#404d94ea8598f757c526f9a414e66ba96c050dad"
-  integrity sha512-4G0hQu9zXHESZe4fZouucmA+6J5oKSBNYzG0gPbV9V4aKBNIwfUY86ur/cxyTMzuN9vQuAiMe//q4ZMXgMvGtQ==
+openapi-msw@^0.7.0:
+  version "0.7.0"
+  resolved "https://registry.yarnpkg.com/openapi-msw/-/openapi-msw-0.7.0.tgz#031ceeb4075b309b4476de32d71a24a4edaf4a45"
+  integrity sha512-K35jmP8dgu/EXvTg6vyg2HvJt4n4WfIiehgrzOyTyIV7cYs/nYQ3XSt8GklEGYND0JZcOpC0kEj4H28/FKy+Cg==
+  dependencies:
+    openapi-typescript-helpers "0.0.8"
+
+openapi-typescript-helpers@0.0.8:
+  version "0.0.8"
+  resolved "https://registry.yarnpkg.com/openapi-typescript-helpers/-/openapi-typescript-helpers-0.0.8.tgz#460f395362cc16e4a5de56264b7b1c5a03746e35"
+  integrity sha512-1eNjQtbfNi5Z/kFhagDIaIRj6qqDzhjNJKz8cmMW0CVdGwT6e1GLbAfgI0d28VTJa1A8jz82jm/4dG8qNoNS8g==
+
+openapi-typescript-helpers@^0.0.11:
+  version "0.0.11"
+  resolved "https://registry.yarnpkg.com/openapi-typescript-helpers/-/openapi-typescript-helpers-0.0.11.tgz#d05e88216b8f3771d5df41c863ebc5c9d10e2954"
+  integrity sha512-xofUHlVFq+BMquf3nh9I8N2guHckW6mrDO/F3kaFgrL7MGbjldDnQ9TIT+rkH/+H0LiuO+RuZLnNmsJwsjwUKg==
+
+openapi-typescript@^7.3.0:
+  version "7.3.0"
+  resolved "https://registry.yarnpkg.com/openapi-typescript/-/openapi-typescript-7.3.0.tgz#046845f7ae3225410c54f280469cfe5a0f2e0020"
+  integrity sha512-EkljRjYWOPwGXiK++uI9MkGv2Y7uhbkZbi9V1z3r3EpmWVO6aFTHXSLNvxIWo6UT6LCTYgEYkUB3BWQjwwXthg==
   dependencies:
+    "@redocly/openapi-core" "^1.16.0"
     ansi-colors "^4.1.3"
-    fast-glob "^3.2.12"
-    js-yaml "^4.1.0"
-    supports-color "^9.2.3"
-    undici "^5.12.0"
+    parse-json "^8.1.0"
+    supports-color "^9.4.0"
     yargs-parser "^21.1.1"
 
 optionator@^0.8.1:
@@ -9040,6 +9270,11 @@ os-locale@^1.4.0:
   dependencies:
     lcid "^1.0.0"
 
+outvariant@^1.2.1, outvariant@^1.4.0, outvariant@^1.4.2:
+  version "1.4.3"
+  resolved "https://registry.yarnpkg.com/outvariant/-/outvariant-1.4.3.tgz#221c1bfc093e8fec7075497e7799fdbf43d14873"
+  integrity sha512-+Sl2UErvtsoajRDKCE5/dBz4DIvHXQQnAxtQTF04OJxY0+DyZXSo5P5Bb7XYWOh81syohlYL24hbDwxedPUJCA==
+
 p-event@^5.0.1:
   version "5.0.1"
   resolved "https://registry.yarnpkg.com/p-event/-/p-event-5.0.1.tgz#614624ec02ae7f4f13d09a721c90586184af5b0c"
@@ -9152,6 +9387,15 @@ parse-json@^5.2.0:
     json-parse-even-better-errors "^2.3.0"
     lines-and-columns "^1.1.6"
 
+parse-json@^8.1.0:
+  version "8.1.0"
+  resolved "https://registry.yarnpkg.com/parse-json/-/parse-json-8.1.0.tgz#91cdc7728004e955af9cb734de5684733b24a717"
+  integrity sha512-rum1bPifK5SSar35Z6EKZuYPJx85pkNaFrxBK3mwdfSJ1/WKbYrjoW/zTPSjRRamfmVX1ACBIdFAO0VRErW/EA==
+  dependencies:
+    "@babel/code-frame" "^7.22.13"
+    index-to-position "^0.1.2"
+    type-fest "^4.7.1"
+
 parse-node-version@^1.0.0:
   version "1.0.1"
   resolved "https://registry.npmjs.org/parse-node-version/-/parse-node-version-1.0.1.tgz"
@@ -9231,10 +9475,15 @@ path-scurry@^1.10.1:
     lru-cache "^9.1.1 || ^10.0.0"
     minipass "^5.0.0 || ^6.0.2 || ^7.0.0"
 
-path-to-regexp@0.1.7:
-  version "0.1.7"
-  resolved "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.7.tgz"
-  integrity sha512-5DFkuoqlv1uYQKxy8omFBeJPQcdoE07Kv2sferDCrAq1ohOU+MSDswDIbnx3YAM60qIOnYa53wBhXW0EbMonrQ==
+path-to-regexp@0.1.10:
+  version "0.1.10"
+  resolved "https://registry.yarnpkg.com/path-to-regexp/-/path-to-regexp-0.1.10.tgz#67e9108c5c0551b9e5326064387de4763c4d5f8b"
+  integrity sha512-7lf7qcQidTku0Gu3YDPc8DJ1q7OOucfa/BSsIwjuh56VU7katFvuM8hULfkwB3Fns/rsVF7PwPKVw1sl5KQS9w==
+
+path-to-regexp@^6.2.0:
+  version "6.2.2"
+  resolved "https://registry.yarnpkg.com/path-to-regexp/-/path-to-regexp-6.2.2.tgz#324377a83e5049cbecadc5554d6a63a9a4866b36"
+  integrity sha512-GQX3SSMokngb36+whdpRXE+3f9V8UzyAorlYvOGx87ufGHehNTn5lCxrKtLyZ4Yl/wEKnNnr98ZzOwwDZV5ogw==
 
 path-type@^1.0.0:
   version "1.1.0"
@@ -9314,6 +9563,11 @@ pkg-dir@^4.2.0:
   dependencies:
     find-up "^4.0.0"
 
+pluralize@^8.0.0:
+  version "8.0.0"
+  resolved "https://registry.yarnpkg.com/pluralize/-/pluralize-8.0.0.tgz#1a6fa16a38d12a1901e0320fa017051c539ce3b1"
+  integrity sha512-Nc3IT5yHzflTfbjgqWcCPpo7DaKy4FnpB0l/zCAW0Tc7jxAiuqSxHasntB3D7887LSrA93kDJ9IXovxJYxyLCA==
+
 popper.js@^1.16.1:
   version "1.16.1"
   resolved "https://registry.npmjs.org/popper.js/-/popper.js-1.16.1.tgz"
@@ -9749,12 +10003,12 @@ pyre-to-regexp@^0.0.6:
   resolved "https://registry.yarnpkg.com/pyre-to-regexp/-/pyre-to-regexp-0.0.6.tgz#2950f234f5b17bd780e93a591bb09cd74846736e"
   integrity sha512-keIgqWbZjteRBT4wLtFSlJl+LoKxxWLhdve/tBduOr+jlpXlx027c/7K3ytT91hzhC+//5citGmEB2chVNQpuw==
 
-qs@6.11.0:
-  version "6.11.0"
-  resolved "https://registry.yarnpkg.com/qs/-/qs-6.11.0.tgz#fd0d963446f7a65e1367e01abd85429453f0c37a"
-  integrity sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q==
+qs@6.13.0:
+  version "6.13.0"
+  resolved "https://registry.yarnpkg.com/qs/-/qs-6.13.0.tgz#6ca3bd58439f7e245655798997787b0d88a51906"
+  integrity sha512-+38qI9SOr8tfZ4QmJNplMUxqjbe7LKvvZgWdExBOmd+egZTtjLB67Gu0HRX3u/XOq7UU2Nx6nsjvS16Z9uwfpg==
   dependencies:
-    side-channel "^1.0.4"
+    side-channel "^1.0.6"
 
 querystring-es3@^0.2.1:
   version "0.2.1"
@@ -10043,10 +10297,10 @@ require-main-filename@^1.0.1:
   resolved "https://registry.npmjs.org/require-main-filename/-/require-main-filename-1.0.1.tgz"
   integrity sha512-IqSUtOVP4ksd1C/ej5zeEh/BIP2ajqpn8c5x+q99gvcIG/Qf0cud5raVnE/Dwd0ua9TXYDoDc0RE5hBSdz22Ug==
 
-requirejs@2.3.6:
-  version "2.3.6"
-  resolved "https://registry.npmjs.org/requirejs/-/requirejs-2.3.6.tgz"
-  integrity sha512-ipEzlWQe6RK3jkzikgCupiTbTvm4S0/CAU5GlgptkN5SO6F3u0UD0K18wy6ErDqiCyP4J4YYe1HuAShvsxePLg==
+requirejs@2.3.7:
+  version "2.3.7"
+  resolved "https://registry.yarnpkg.com/requirejs/-/requirejs-2.3.7.tgz#0b22032e51a967900e0ae9f32762c23a87036bd0"
+  integrity sha512-DouTG8T1WanGok6Qjg2SXuCMzszOo0eHeH9hDZ5Y4x8Je+9JB38HdTLT4/VA8OaUhBa0JPVHJ0pyBkM1z+pDsw==
 
 requires-port@^1.0.0:
   version "1.0.0"
@@ -10278,6 +10532,11 @@ sass@^1.69.4:
     immutable "^4.0.0"
     source-map-js ">=0.6.2 <2.0.0"
 
+sax@>=0.6.0:
+  version "1.4.1"
+  resolved "https://registry.yarnpkg.com/sax/-/sax-1.4.1.tgz#44cc8988377f126304d3b3fc1010c733b929ef0f"
+  integrity sha512-+aWOz7yVScEGoKNd4PA10LZ8sk0A/z5+nXQG5giUO5rprX9jgYsTdov9qCchZiPIZezbZH+jRut8nPodFAX4Jg==
+
 sax@^1.2.4:
   version "1.2.4"
   resolved "https://registry.yarnpkg.com/sax/-/sax-1.2.4.tgz#2816234e2378bddc4e5354fab5caa895df7100d9"
@@ -10290,16 +10549,7 @@ saxes@^6.0.0:
   dependencies:
     xmlchars "^2.2.0"
 
-schema-utils@^3.0.0, schema-utils@^3.1.0, schema-utils@^3.1.1:
-  version "3.1.1"
-  resolved "https://registry.npmjs.org/schema-utils/-/schema-utils-3.1.1.tgz"
-  integrity sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==
-  dependencies:
-    "@types/json-schema" "^7.0.8"
-    ajv "^6.12.5"
-    ajv-keywords "^3.5.2"
-
-schema-utils@^3.2.0:
+schema-utils@^3.0.0, schema-utils@^3.1.1, schema-utils@^3.2.0:
   version "3.3.0"
   resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-3.3.0.tgz#f50a88877c3c01652a15b622ae9e9795df7a60fe"
   integrity sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==
@@ -10308,17 +10558,7 @@ schema-utils@^3.2.0:
     ajv "^6.12.5"
     ajv-keywords "^3.5.2"
 
-schema-utils@^4.0.0:
-  version "4.0.0"
-  resolved "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.0.tgz"
-  integrity sha512-1edyXKgh6XnJsJSQ8mKWXnN/BVaIbFMLpouRUrXgVq7WYne5kw3MW7UPhO44uRXQSIpTSXoJbmrR2X0w9kUTyg==
-  dependencies:
-    "@types/json-schema" "^7.0.9"
-    ajv "^8.8.0"
-    ajv-formats "^2.1.1"
-    ajv-keywords "^5.0.0"
-
-schema-utils@^4.0.1:
+schema-utils@^4.0.0, schema-utils@^4.0.1:
   version "4.2.0"
   resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-4.2.0.tgz#70d7c93e153a273a805801882ebd3bff20d89c8b"
   integrity sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==
@@ -10364,10 +10604,15 @@ semver@^7.3.4, semver@^7.3.6, semver@^7.3.8, semver@^7.5.3, semver@^7.5.4:
   dependencies:
     lru-cache "^6.0.0"
 
-send@0.18.0:
-  version "0.18.0"
-  resolved "https://registry.npmjs.org/send/-/send-0.18.0.tgz"
-  integrity sha512-qqWzuOjSFOuqPjFe4NOsMLafToQQwBSOEpS+FwEt3A2V3vKubTquT3vmLTQpFgMXp8AlFWFuP1qKaJZOtPpVXg==
+semver@^7.6.2:
+  version "7.6.3"
+  resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.3.tgz#980f7b5550bc175fb4dc09403085627f9eb33143"
+  integrity sha512-oVekP1cKtI+CTDvHWYFUcMtsK/00wmAEfyqKfNdARm8u1wNVhSgaX7A8d4UuIlUI5e84iEwOhs7ZPYRmzU9U6A==
+
+send@0.19.0:
+  version "0.19.0"
+  resolved "https://registry.yarnpkg.com/send/-/send-0.19.0.tgz#bbc5a388c8ea6c048967049dbeac0e4a3f09d7f8"
+  integrity sha512-dW41u5VfLXu8SJh5bwRmyYUbAoSB3c9uQh6L8h/KtsFREPWpbX1lrljJo186Jc4nmci/sGUZ9a0a0J2zgfq2hw==
   dependencies:
     debug "2.6.9"
     depd "2.0.0"
@@ -10383,13 +10628,6 @@ send@0.18.0:
     range-parser "~1.2.1"
     statuses "2.0.1"
 
-serialize-javascript@^6.0.0:
-  version "6.0.0"
-  resolved "https://registry.npmjs.org/serialize-javascript/-/serialize-javascript-6.0.0.tgz"
-  integrity sha512-Qr3TosvguFt8ePWqsvRfrKyQXIiW+nGbYpy8XK24NQHE83caxWt+mIymTT19DGFbNWNLfEwsrkSmN64lVWB9ag==
-  dependencies:
-    randombytes "^2.1.0"
-
 serialize-javascript@^6.0.1:
   version "6.0.1"
   resolved "https://registry.yarnpkg.com/serialize-javascript/-/serialize-javascript-6.0.1.tgz#b206efb27c3da0b0ab6b52f48d170b7996458e5c"
@@ -10410,21 +10648,33 @@ serve-index@^1.9.1:
     mime-types "~2.1.17"
     parseurl "~1.3.2"
 
-serve-static@1.15.0:
-  version "1.15.0"
-  resolved "https://registry.npmjs.org/serve-static/-/serve-static-1.15.0.tgz"
-  integrity sha512-XGuRDNjXUijsUL0vl6nSD7cwURuzEgglbOaFuZM9g3kwDXOWVTck0jLzjPzGD+TazWbboZYu52/9/XPdUgne9g==
+serve-static@1.16.2:
+  version "1.16.2"
+  resolved "https://registry.yarnpkg.com/serve-static/-/serve-static-1.16.2.tgz#b6a5343da47f6bdd2673848bf45754941e803296"
+  integrity sha512-VqpjJZKadQB/PEbEwvFdO43Ax5dFBZ2UECszz8bQ7pi7wt//PWe1P6MN7eCnjsatYtBT6EuiClbjSWP2WrIoTw==
   dependencies:
-    encodeurl "~1.0.2"
+    encodeurl "~2.0.0"
     escape-html "~1.0.3"
     parseurl "~1.3.3"
-    send "0.18.0"
+    send "0.19.0"
 
 set-blocking@^2.0.0:
   version "2.0.0"
   resolved "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz"
   integrity sha512-KiKBS8AnWGEyLzofFfmvKwpdPzqiy16LvQfK3yv/fVH7Bj13/wl3JSR1J+rfgRE9q7xUJK4qvgS8raSOeLUehw==
 
+set-function-length@^1.2.1:
+  version "1.2.2"
+  resolved "https://registry.yarnpkg.com/set-function-length/-/set-function-length-1.2.2.tgz#aac72314198eaed975cf77b2c3b6b880695e5449"
+  integrity sha512-pgRc4hJ4/sNjWCSS9AmnS40x3bNMDTknHgL5UaMBTMyJnU90EgWh1Rz+MC9eFu4BuN/UwZjKQuY/1v3rM7HMfg==
+  dependencies:
+    define-data-property "^1.1.4"
+    es-errors "^1.3.0"
+    function-bind "^1.1.2"
+    get-intrinsic "^1.2.4"
+    gopd "^1.0.1"
+    has-property-descriptors "^1.0.2"
+
 set-function-name@^2.0.0:
   version "2.0.1"
   resolved "https://registry.yarnpkg.com/set-function-name/-/set-function-name-2.0.1.tgz#12ce38b7954310b9f61faa12701620a0c882793a"
@@ -10492,6 +10742,16 @@ side-channel@^1.0.4:
     get-intrinsic "^1.0.2"
     object-inspect "^1.9.0"
 
+side-channel@^1.0.6:
+  version "1.0.6"
+  resolved "https://registry.yarnpkg.com/side-channel/-/side-channel-1.0.6.tgz#abd25fb7cd24baf45466406b1096b7831c9215f2"
+  integrity sha512-fDW/EZ6Q9RiO8eFG8Hj+7u/oW+XrPTIChwCOM2+th2A6OblDtYYIpve9m+KvI9Z4C9qSEXlaGR6bTEYHReuglA==
+  dependencies:
+    call-bind "^1.0.7"
+    es-errors "^1.3.0"
+    get-intrinsic "^1.2.4"
+    object-inspect "^1.13.1"
+
 sigmund@^1.0.1:
   version "1.0.1"
   resolved "https://registry.npmjs.org/sigmund/-/sigmund-1.0.1.tgz"
@@ -10502,7 +10762,7 @@ signal-exit@^3.0.2, signal-exit@^3.0.3, signal-exit@^3.0.7:
   resolved "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz"
   integrity sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==
 
-signal-exit@^4.0.1:
+signal-exit@^4.0.1, signal-exit@^4.1.0:
   version "4.1.0"
   resolved "https://registry.yarnpkg.com/signal-exit/-/signal-exit-4.1.0.tgz#952188c1cbd546070e2dd20d0f41c0ae0530cb04"
   integrity sha512-bzyZ1e88w9O1iNJbKnOlvYTrWPDl46O1bG0D3XInv+9tkPrxrN8jUUTiFlDkkmKWgn1M6CfIA13SuGqOa9Korw==
@@ -10737,7 +10997,7 @@ static-extend@^0.1.1:
     define-property "^0.2.5"
     object-copy "^0.1.0"
 
-statuses@2.0.1:
+statuses@2.0.1, statuses@^2.0.1:
   version "2.0.1"
   resolved "https://registry.npmjs.org/statuses/-/statuses-2.0.1.tgz"
   integrity sha512-RwNA9Z/7PrK06rYLIzFMlaF+l73iwpzsqRIFgbMLbTcLD6cOao82TaWefPXQvB2fOC4AjuYSEndS7N/mTCbkdQ==
@@ -10770,6 +11030,11 @@ stream-shift@^1.0.0:
   resolved "https://registry.npmjs.org/stream-shift/-/stream-shift-1.0.1.tgz"
   integrity sha512-AiisoFqQ0vbGcZgQPY1cdP2I76glaVA/RauYR4G4thNFgkTqr90yXTo4LYX60Jl+sIlPNHHdGSwo01AvbKUSVQ==
 
+strict-event-emitter@^0.5.1:
+  version "0.5.1"
+  resolved "https://registry.yarnpkg.com/strict-event-emitter/-/strict-event-emitter-0.5.1.tgz#1602ece81c51574ca39c6815e09f1a3e8550bd93"
+  integrity sha512-vMgjE/GGEPEFnhFub6pa4FmJBRBVOLpIII2hvCZ8Kzb7K0hlHo7mQv6xYrBvCL2LtAIBwFUK8wvuJgTVSQ5MFQ==
+
 string-length@^4.0.1:
   version "4.0.2"
   resolved "https://registry.npmjs.org/string-length/-/string-length-4.0.2.tgz"
@@ -10988,10 +11253,10 @@ supports-color@^8.0.0:
   dependencies:
     has-flag "^4.0.0"
 
-supports-color@^9.2.3:
-  version "9.3.0"
-  resolved "https://registry.yarnpkg.com/supports-color/-/supports-color-9.3.0.tgz#cce566c5ad562eece4dfe5a4502a58efc54986a9"
-  integrity sha512-hJ6RYjNbcBFkpHi+ykjar+7GgHs+65Kxyw940nBLOSjaWZ13acq4A5f+gWiV5w+xfsg5MbnjDxTigLcUuljerw==
+supports-color@^9.4.0:
+  version "9.4.0"
+  resolved "https://registry.yarnpkg.com/supports-color/-/supports-color-9.4.0.tgz#17bfcf686288f531db3dea3215510621ccb55954"
+  integrity sha512-VL+lNrEoIXww1coLPOmiEmK/0sGigko5COxI09KzHc2VJXJsQ37UaQ+8quuxjDeA7+KnLGTWRyOXSLLR2Wb4jw==
 
 supports-preserve-symlinks-flag@^1.0.0:
   version "1.0.0"
@@ -11041,48 +11306,27 @@ tapable@^2.1.1, tapable@^2.2.0:
   resolved "https://registry.npmjs.org/tapable/-/tapable-2.2.1.tgz"
   integrity sha512-GNzQvQTOIP6RyTfE2Qxb8ZVlNmw0n88vp1szwWRimP02mnTsx3Wtn5qRdqY9w2XduFNUgvOwhNnQsjwCp+kqaQ==
 
-terser-webpack-plugin@^5.1.3:
-  version "5.3.3"
-  resolved "https://registry.npmjs.org/terser-webpack-plugin/-/terser-webpack-plugin-5.3.3.tgz"
-  integrity sha512-Fx60G5HNYknNTNQnzQ1VePRuu89ZVYWfjRAeT5rITuCY/1b08s49e5kSQwHDirKZWuoKOBRFS98EUUoZ9kLEwQ==
+terser-webpack-plugin@^5.3.10:
+  version "5.3.10"
+  resolved "https://registry.yarnpkg.com/terser-webpack-plugin/-/terser-webpack-plugin-5.3.10.tgz#904f4c9193c6fd2a03f693a2150c62a92f40d199"
+  integrity sha512-BKFPWlPDndPs+NGGCr1U59t0XScL5317Y0UReNrHaw9/FwhPENlq6bfgs+4yPfyP51vqC1bQ4rp1EfXW5ZSH9w==
   dependencies:
-    "@jridgewell/trace-mapping" "^0.3.7"
-    jest-worker "^27.4.5"
-    schema-utils "^3.1.1"
-    serialize-javascript "^6.0.0"
-    terser "^5.7.2"
-
-terser-webpack-plugin@^5.3.7:
-  version "5.3.9"
-  resolved "https://registry.yarnpkg.com/terser-webpack-plugin/-/terser-webpack-plugin-5.3.9.tgz#832536999c51b46d468067f9e37662a3b96adfe1"
-  integrity sha512-ZuXsqE07EcggTWQjXUj+Aot/OMcD0bMKGgF63f7UxYcu5/AJF53aIpK1YoP5xR9l6s/Hy2b+t1AM0bLNPRuhwA==
-  dependencies:
-    "@jridgewell/trace-mapping" "^0.3.17"
+    "@jridgewell/trace-mapping" "^0.3.20"
     jest-worker "^27.4.5"
     schema-utils "^3.1.1"
     serialize-javascript "^6.0.1"
-    terser "^5.16.8"
+    terser "^5.26.0"
 
-terser@^5.16.8:
-  version "5.22.0"
-  resolved "https://registry.yarnpkg.com/terser/-/terser-5.22.0.tgz#4f18103f84c5c9437aafb7a14918273310a8a49d"
-  integrity sha512-hHZVLgRA2z4NWcN6aS5rQDc+7Dcy58HOf2zbYwmFcQ+ua3h6eEFf5lIDKTzbWwlazPyOZsFQO8V80/IjVNExEw==
+terser@^5.26.0:
+  version "5.31.6"
+  resolved "https://registry.yarnpkg.com/terser/-/terser-5.31.6.tgz#c63858a0f0703988d0266a82fcbf2d7ba76422b1"
+  integrity sha512-PQ4DAriWzKj+qgehQ7LK5bQqCFNMmlhjR2PFFLuqGCpuCAauxemVBWwWOxo3UIwWQx8+Pr61Df++r76wDmkQBg==
   dependencies:
     "@jridgewell/source-map" "^0.3.3"
     acorn "^8.8.2"
     commander "^2.20.0"
     source-map-support "~0.5.20"
 
-terser@^5.7.2:
-  version "5.14.2"
-  resolved "https://registry.npmjs.org/terser/-/terser-5.14.2.tgz"
-  integrity sha512-oL0rGeM/WFQCUd0y2QrWxYnq7tfSuKBiqTjRPWrRgB46WD/kiwHwF8T23z78H6Q6kGCuuHcPB+KULHRdxvVGQA==
-  dependencies:
-    "@jridgewell/source-map" "^0.3.2"
-    acorn "^8.5.0"
-    commander "^2.20.0"
-    source-map-support "~0.5.20"
-
 test-exclude@^6.0.0:
   version "6.0.0"
   resolved "https://registry.npmjs.org/test-exclude/-/test-exclude-6.0.0.tgz"
@@ -11206,6 +11450,13 @@ toidentifier@1.0.1:
   resolved "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.1.tgz"
   integrity sha512-o5sSPKEkg/DIQNmH43V0/uerLrpzVedkUh8tGNvaeXpfpuwjKenlSox/2O/BTlZUtEe+JG7s5YhEz608PlAHRA==
 
+topojson-client@^3.1.0:
+  version "3.1.0"
+  resolved "https://registry.yarnpkg.com/topojson-client/-/topojson-client-3.1.0.tgz#22e8b1ed08a2b922feeb4af6f53b6ef09a467b99"
+  integrity sha512-605uxS6bcYxGXw9qi62XyrV6Q3xwbndjachmNxu8HWTtVPxZfEJN9fd/SZS1Q54Sn2y0TMyMxFj/cJINqGHrKw==
+  dependencies:
+    commander "2"
+
 tough-cookie@^4.1.2:
   version "4.1.3"
   resolved "https://registry.yarnpkg.com/tough-cookie/-/tough-cookie-4.1.3.tgz#97b9adb0728b42280aa3d814b6b999b2ff0318bf"
@@ -11216,6 +11467,16 @@ tough-cookie@^4.1.2:
     universalify "^0.2.0"
     url-parse "^1.5.3"
 
+tough-cookie@^4.1.4:
+  version "4.1.4"
+  resolved "https://registry.yarnpkg.com/tough-cookie/-/tough-cookie-4.1.4.tgz#945f1461b45b5a8c76821c33ea49c3ac192c1b36"
+  integrity sha512-Loo5UUvLD9ScZ6jh8beX1T6sO1w2/MpCRpEP7V280GKMVUQ0Jzar2U3UJPsrdbziLEMMhu3Ujnq//rhiFuIeag==
+  dependencies:
+    psl "^1.1.33"
+    punycode "^2.1.1"
+    universalify "^0.2.0"
+    url-parse "^1.5.3"
+
 tr46@^3.0.0:
   version "3.0.0"
   resolved "https://registry.yarnpkg.com/tr46/-/tr46-3.0.0.tgz#555c4e297a950617e8eeddef633c87d4d9d6cbf9"
@@ -11233,12 +11494,13 @@ ts-api-utils@^1.0.1:
   resolved "https://registry.yarnpkg.com/ts-api-utils/-/ts-api-utils-1.0.3.tgz#f12c1c781d04427313dbac808f453f050e54a331"
   integrity sha512-wNMeqtMz5NtwpT/UZGY5alT+VoKdSsOOP/kqHFcUW1P/VRhH2wJ48+DN2WwUliNbQ976ETwDL0Ifd2VVvgonvg==
 
-ts-jest@^29.1.1:
-  version "29.1.1"
-  resolved "https://registry.yarnpkg.com/ts-jest/-/ts-jest-29.1.1.tgz#f58fe62c63caf7bfcc5cc6472082f79180f0815b"
-  integrity sha512-D6xjnnbP17cC85nliwGiL+tpoKN0StpgE0TeOjXQTU6MVCfsB4v7aW05CgQ/1OywGb0x/oy9hHFnN+sczTiRaA==
+ts-jest@^29.2.3:
+  version "29.2.3"
+  resolved "https://registry.yarnpkg.com/ts-jest/-/ts-jest-29.2.3.tgz#3d226ac36b8b820151a38f164414f9f6b412131f"
+  integrity sha512-yCcfVdiBFngVz9/keHin9EnsrQtQtEu3nRykNy9RVp+FiPFFbPJ3Sg6Qg4+TkmH0vMP5qsTKgXSsk80HRwvdgQ==
   dependencies:
     bs-logger "0.x"
+    ejs "^3.1.10"
     fast-json-stable-stringify "2.x"
     jest-util "^29.0.0"
     json5 "^2.2.3"
@@ -11296,6 +11558,11 @@ tsconfig@^7.0.0:
     strip-bom "^3.0.0"
     strip-json-comments "^2.0.0"
 
+tslib@2.3.0:
+  version "2.3.0"
+  resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.3.0.tgz#803b8cdab3e12ba581a4ca41c8839bbb0dacb09e"
+  integrity sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==
+
 tslib@^1.9.0:
   version "1.14.1"
   resolved "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz"
@@ -11316,6 +11583,16 @@ tslib@^2.4.0:
   resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.6.2.tgz#703ac29425e7b37cd6fd456e92404d46d1f3e4ae"
   integrity sha512-AEYxH93jGFPn/a2iVAwW87VuUIkR1FVUKB77NwMF7nBTDkDrrT/Hpt/IrCJ0QXhW27jTBDcf5ZY7w6RiqTMw2Q==
 
+tslib@^2.6.3:
+  version "2.8.0"
+  resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.8.0.tgz#d124c86c3c05a40a91e6fdea4021bd31d377971b"
+  integrity sha512-jWVzBLplnCmoaTr13V9dYbiQ99wvZRd0vNWaDRg+aVYRcjDF3nDksxFDE/+fkXnKhpnUUkmx5pK/v8mCtLVqZA==
+
+tslib@~2.6.3:
+  version "2.6.3"
+  resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.6.3.tgz#0438f810ad7a9edcde7a241c3d80db693c8cbfe0"
+  integrity sha512-xNvxJEOUiWPGhUuUdQgAJPKOOJfGnIyKySOc09XkKsgdUV/3E2zvwZYdejjmRgPCgcym1juLH3226yA7sEFJKQ==
+
 tus-js-client@^3.1.1:
   version "3.1.1"
   resolved "https://registry.yarnpkg.com/tus-js-client/-/tus-js-client-3.1.1.tgz#87cb72e528d274d0a8ff62e9c18165f1e901ce9e"
@@ -11358,6 +11635,16 @@ type-fest@^0.21.3:
   resolved "https://registry.npmjs.org/type-fest/-/type-fest-0.21.3.tgz"
   integrity sha512-t0rzBq87m3fVcduHDUFhKmyyX+9eo6WQjZvf51Ea/M0Q7+T374Jp1aUiyUl0GKxp8M/OETVHSDvmkyPgvX+X2w==
 
+type-fest@^4.7.1:
+  version "4.21.0"
+  resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-4.21.0.tgz#2eec399d9bda4ac686286314d07c6675fef3fdd8"
+  integrity sha512-ADn2w7hVPcK6w1I0uWnM//y1rLXZhzB9mr0a3OirzclKF1Wp6VzevUmzz/NRAWunOT6E8HrnpGY7xOfc6K57fA==
+
+type-fest@^4.9.0:
+  version "4.23.0"
+  resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-4.23.0.tgz#8196561a6b835175473be744f3e41e2dece1496b"
+  integrity sha512-ZiBujro2ohr5+Z/hZWHESLz3g08BBdrdLMieYFULJO+tWc437sn8kQsWLJoZErY8alNhxre9K4p3GURAG11n+w==
+
 type-is@~1.6.18:
   version "1.6.18"
   resolved "https://registry.npmjs.org/type-is/-/type-is-1.6.18.tgz"
@@ -11476,12 +11763,10 @@ undertaker@^1.2.1:
     object.reduce "^1.0.0"
     undertaker-registry "^1.0.0"
 
-undici@^5.12.0:
-  version "5.28.4"
-  resolved "https://registry.yarnpkg.com/undici/-/undici-5.28.4.tgz#6b280408edb6a1a604a9b20340f45b422e373068"
-  integrity sha512-72RFADWFqKmUb2hmmvNODKL3p9hcB6Gt2DOQMis1SEBaV6a4MH8soBvzg+95CYhCKPFedut2JY9bMfrDl9D23g==
-  dependencies:
-    "@fastify/busboy" "^2.0.0"
+undici-types@~6.11.1:
+  version "6.11.1"
+  resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-6.11.1.tgz#432ea6e8efd54a48569705a699e62d8f4981b197"
+  integrity sha512-mIDEX2ek50x0OlRgxryxsenE5XaQD4on5U2inY7RApK3SOJpofyw7uW2AyfMKkhAxXIceo2DeWGVGwyvng1GNQ==
 
 unicode-canonical-property-names-ecmascript@^2.0.0:
   version "2.0.0"
@@ -11534,6 +11819,11 @@ universalify@^0.2.0:
   resolved "https://registry.yarnpkg.com/universalify/-/universalify-0.2.0.tgz#6451760566fa857534745ab1dde952d1b1761be0"
   integrity sha512-CJ1QgKmNg3CwvAv/kOFmtnEN05f0D/cn9QntgNOQlQF9dgvVTHj3t+8JPdjqawCHk7V/KA+fbUqzZ9XWhcqPUg==
 
+universalify@^2.0.0:
+  version "2.0.1"
+  resolved "https://registry.yarnpkg.com/universalify/-/universalify-2.0.1.tgz#168efc2180964e6386d061e094df61afe239b18d"
+  integrity sha512-gptHNQghINnc/vTGIk0SOFGFNXw7JVrlRUtConJRlvaw6DuX0wO5Jeko9sWrMBhh+PsYAZ7oXAiOnf/UKogyiw==
+
 unpipe@1.0.0, unpipe@~1.0.0:
   version "1.0.0"
   resolved "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz"
@@ -11555,14 +11845,6 @@ update-browserslist-db@^1.0.13:
     escalade "^3.1.1"
     picocolors "^1.0.0"
 
-update-browserslist-db@^1.0.5:
-  version "1.0.5"
-  resolved "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.5.tgz"
-  integrity sha512-dteFFpCyvuDdr9S/ff1ISkKt/9YZxKjI9WlRR99c180GaztJtRa/fn18FdxGVKVsnPY7/a/FDN68mcvUmP4U7Q==
-  dependencies:
-    escalade "^3.1.1"
-    picocolors "^1.0.0"
-
 uri-js@^4.2.2:
   version "4.4.1"
   resolved "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz"
@@ -11660,6 +11942,371 @@ vary@~1.1.2:
   resolved "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz"
   integrity sha512-BNGbWLfd0eUPabhkXUVm0j8uuvREyTh5ovRa/dyow/BqAbZJyC+5fU+IzQOzmAKzYqYRAISoRhdQr3eIZ/PXqg==
 
+vega-canvas@^1.2.7:
+  version "1.2.7"
+  resolved "https://registry.yarnpkg.com/vega-canvas/-/vega-canvas-1.2.7.tgz#cf62169518f5dcd91d24ad352998c2248f8974fb"
+  integrity sha512-OkJ9CACVcN9R5Pi9uF6MZBF06pO6qFpDYHWSKBJsdHP5o724KrsgR6UvbnXFH82FdsiTOff/HqjuaG8C7FL+9Q==
+
+vega-crossfilter@~4.1.2:
+  version "4.1.2"
+  resolved "https://registry.yarnpkg.com/vega-crossfilter/-/vega-crossfilter-4.1.2.tgz#810281c279b3592310f12814bc61206dd42ca61d"
+  integrity sha512-J7KVEXkpfRJBfRvwLxn5vNCzQCNkrnzmDvkvwhuiwT4gPm5sk7MK5TuUP8GCl/iKYw+kWeVXEtrVHwWtug+bcQ==
+  dependencies:
+    d3-array "^3.2.2"
+    vega-dataflow "^5.7.6"
+    vega-util "^1.17.2"
+
+vega-dataflow@^5.7.6, vega-dataflow@~5.7.6:
+  version "5.7.6"
+  resolved "https://registry.yarnpkg.com/vega-dataflow/-/vega-dataflow-5.7.6.tgz#21dfad9120cb18d9aeaed578658670839d1adc95"
+  integrity sha512-9Md8+5iUC1MVKPKDyZ7pCEHk6I9am+DgaMzZqo/27O/KI4f23/WQXPyuI8jbNmc/mkm340P0TKREmzL5M7+2Dg==
+  dependencies:
+    vega-format "^1.1.2"
+    vega-loader "^4.5.2"
+    vega-util "^1.17.2"
+
+vega-embed@^6.26.0:
+  version "6.26.0"
+  resolved "https://registry.yarnpkg.com/vega-embed/-/vega-embed-6.26.0.tgz#25ca51783b2819adf6e6330ae6dd5771e8da8653"
+  integrity sha512-AZCTdKHDAuhp6TFZRQOOs332tStCwZr/5e4uZMNEuJL69A57cT66NNZJdNiCP6u66REzIToYtMJhMTL9wl5B3A==
+  dependencies:
+    fast-json-patch "^3.1.1"
+    json-stringify-pretty-compact "^3.0.0"
+    semver "^7.6.2"
+    tslib "^2.6.3"
+    vega-interpreter "^1.0.5"
+    vega-schema-url-parser "^2.2.0"
+    vega-themes "^2.15.0"
+    vega-tooltip "^0.34.0"
+
+vega-encode@~4.10.1:
+  version "4.10.1"
+  resolved "https://registry.yarnpkg.com/vega-encode/-/vega-encode-4.10.1.tgz#1656e20396db99c414f495704ef3d9cff99631df"
+  integrity sha512-d25nVKZDrg109rC65M8uxE+7iUrTxktaqgK4fU3XZBgpWlh1K4UbU5nDag7kiHVVN4tKqwgd+synEotra9TiVQ==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-interpolate "^3.0.1"
+    vega-dataflow "^5.7.6"
+    vega-scale "^7.4.1"
+    vega-util "^1.17.2"
+
+vega-event-selector@^3.0.1, vega-event-selector@~3.0.1:
+  version "3.0.1"
+  resolved "https://registry.yarnpkg.com/vega-event-selector/-/vega-event-selector-3.0.1.tgz#b99e92147b338158f8079d81b28b2e7199c2e259"
+  integrity sha512-K5zd7s5tjr1LiOOkjGpcVls8GsH/f2CWCrWcpKy74gTCp+llCdwz0Enqo013ZlGaRNjfgD/o1caJRt3GSaec4A==
+
+vega-expression@^5.0.1, vega-expression@^5.1.1, vega-expression@~5.1.1:
+  version "5.1.1"
+  resolved "https://registry.yarnpkg.com/vega-expression/-/vega-expression-5.1.1.tgz#9b2d287a1f34d990577c9798ae68ec88453815ef"
+  integrity sha512-zv9L1Hm0KHE9M7mldHyz8sXbGu3KmC0Cdk7qfHkcTNS75Jpsem6jkbu6ZAwx5cNUeW91AxUQOu77r4mygq2wUQ==
+  dependencies:
+    "@types/estree" "^1.0.0"
+    vega-util "^1.17.2"
+
+vega-force@~4.2.1:
+  version "4.2.1"
+  resolved "https://registry.yarnpkg.com/vega-force/-/vega-force-4.2.1.tgz#bdce6ec8572867b4ff2fb7e09d2894798c5358ec"
+  integrity sha512-2BcuuqFr77vcCyKfcpedNFeYMxi+XEFCrlgLWNx7YV0PI8pdP5y/yPkzyuE9Tb894+KkRAvfQHZRAshcnFNcMw==
+  dependencies:
+    d3-force "^3.0.0"
+    vega-dataflow "^5.7.6"
+    vega-util "^1.17.2"
+
+vega-format@^1.1.2, vega-format@~1.1.2:
+  version "1.1.2"
+  resolved "https://registry.yarnpkg.com/vega-format/-/vega-format-1.1.2.tgz#d344ba8a2680144e92127459c149a4181e9e7f84"
+  integrity sha512-0kUfAj0dg0U6GcEY0Kp6LiSTCZ8l8jl1qVdQyToMyKmtZg/q56qsiJQZy3WWRr1MtWkTIZL71xSJXgjwjeUaAw==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-format "^3.1.0"
+    d3-time-format "^4.1.0"
+    vega-time "^2.1.2"
+    vega-util "^1.17.2"
+
+vega-functions@^5.15.0, vega-functions@~5.15.0:
+  version "5.15.0"
+  resolved "https://registry.yarnpkg.com/vega-functions/-/vega-functions-5.15.0.tgz#a7905e1dd6457efe265dbf954cbc0a5721c484b0"
+  integrity sha512-pCqmm5efd+3M65jrJGxEy3UGuRksmK6DnWijoSNocnxdCBxez+yqUUVX9o2pN8VxMe3648vZnR9/Vk5CXqRvIQ==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-color "^3.1.0"
+    d3-geo "^3.1.0"
+    vega-dataflow "^5.7.6"
+    vega-expression "^5.1.1"
+    vega-scale "^7.4.1"
+    vega-scenegraph "^4.13.0"
+    vega-selections "^5.4.2"
+    vega-statistics "^1.9.0"
+    vega-time "^2.1.2"
+    vega-util "^1.17.2"
+
+vega-geo@~4.4.2:
+  version "4.4.2"
+  resolved "https://registry.yarnpkg.com/vega-geo/-/vega-geo-4.4.2.tgz#da4a08ee39c9488bfc4fe6493779f584dd8bb412"
+  integrity sha512-unuV/UxUHf6UJu6GYxMZonC3SZlMfFXYLOkgEsRSvmsMPt3+CVv8FmG88dXNRUJUrdROrJepgecqx0jOwMSnGA==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-color "^3.1.0"
+    d3-geo "^3.1.0"
+    vega-canvas "^1.2.7"
+    vega-dataflow "^5.7.6"
+    vega-projection "^1.6.1"
+    vega-statistics "^1.9.0"
+    vega-util "^1.17.2"
+
+vega-hierarchy@~4.1.2:
+  version "4.1.2"
+  resolved "https://registry.yarnpkg.com/vega-hierarchy/-/vega-hierarchy-4.1.2.tgz#e42938c42527b392b110b1e3bf89eaa456dba1b8"
+  integrity sha512-m+xDtT5092YPSnV0rdTLW+AWmoCb+A54JQ66MUJwiDBpKxvfKnTiQeuiWDU2YudjUoXZN9EBOcI6QHF8H2Lu2A==
+  dependencies:
+    d3-hierarchy "^3.1.2"
+    vega-dataflow "^5.7.6"
+    vega-util "^1.17.2"
+
+vega-interpreter@^1.0.5:
+  version "1.0.5"
+  resolved "https://registry.yarnpkg.com/vega-interpreter/-/vega-interpreter-1.0.5.tgz#19e1d1b5f84a4ea9cb25c4e90a05ce16cd058484"
+  integrity sha512-po6oTOmeQqr1tzTCdD15tYxAQLeUnOVirAysgVEemzl+vfmvcEP7jQmlc51jz0jMA+WsbmE6oJywisQPu/H0Bg==
+
+vega-label@~1.3.0:
+  version "1.3.0"
+  resolved "https://registry.yarnpkg.com/vega-label/-/vega-label-1.3.0.tgz#21b3e5ef40e63f51ac987a449d183068c4961503"
+  integrity sha512-EfSFSCWAwVPsklM5g0gUEuohALgryuGC/SKMmsOH7dYT/bywmLBZhLVbrE+IHJAUauoGrMhYw1mqnXL/0giJBg==
+  dependencies:
+    vega-canvas "^1.2.7"
+    vega-dataflow "^5.7.6"
+    vega-scenegraph "^4.13.0"
+    vega-util "^1.17.2"
+
+vega-lite@^5.21.0:
+  version "5.21.0"
+  resolved "https://registry.yarnpkg.com/vega-lite/-/vega-lite-5.21.0.tgz#21ce8b905a02ba364b7b1d7ef471497ba3e12e93"
+  integrity sha512-hNxM9nuMqpI1vkUOhEx6ewEf23WWLmJxSFJ4TA86AW43ixJyqcLV+iSCO0NipuVTE0rlDcc2e8joSewWyOlEwA==
+  dependencies:
+    json-stringify-pretty-compact "~3.0.0"
+    tslib "~2.6.3"
+    vega-event-selector "~3.0.1"
+    vega-expression "~5.1.1"
+    vega-util "~1.17.2"
+    yargs "~17.7.2"
+
+vega-loader@^4.5.2, vega-loader@~4.5.2:
+  version "4.5.2"
+  resolved "https://registry.yarnpkg.com/vega-loader/-/vega-loader-4.5.2.tgz#7212f093c397b153f69f7e6cfef47817c17c5c01"
+  integrity sha512-ktIdGz3DRIS3XfTP9lJ6oMT5cKwC86nQkjUbXZbOtwXQFVNE2xVWBuH13GP6FKUZxg5hJCMtb5v/e/fwTvhKsQ==
+  dependencies:
+    d3-dsv "^3.0.1"
+    node-fetch "^2.6.7"
+    topojson-client "^3.1.0"
+    vega-format "^1.1.2"
+    vega-util "^1.17.2"
+
+vega-parser@~6.4.0:
+  version "6.4.0"
+  resolved "https://registry.yarnpkg.com/vega-parser/-/vega-parser-6.4.0.tgz#6a12f07f0f9178492a17842efe7e1f51a2d36bed"
+  integrity sha512-/hFIJs0yITxfvLIfhhcpUrcbKvu4UZYoMGmly5PSsbgo60oAsVQW8ZbX2Ji3iNFqZJh1ifoX/P0j+9wep1OISw==
+  dependencies:
+    vega-dataflow "^5.7.6"
+    vega-event-selector "^3.0.1"
+    vega-functions "^5.15.0"
+    vega-scale "^7.4.1"
+    vega-util "^1.17.2"
+
+vega-projection@^1.6.1, vega-projection@~1.6.1:
+  version "1.6.1"
+  resolved "https://registry.yarnpkg.com/vega-projection/-/vega-projection-1.6.1.tgz#da687abc60f4a93bb888385beb23e0a1000f8b57"
+  integrity sha512-sqfnAAHumU7MWU1tQN3b6HNgKGF3legek0uLHhjLKcDJQxEc7kwcD18txFz2ffQks6d5j+AUhBiq4GARWf0DEQ==
+  dependencies:
+    d3-geo "^3.1.0"
+    d3-geo-projection "^4.0.0"
+    vega-scale "^7.4.1"
+
+vega-regression@~1.3.0:
+  version "1.3.0"
+  resolved "https://registry.yarnpkg.com/vega-regression/-/vega-regression-1.3.0.tgz#3e68e234fa9460041fac082c6a3469c896d436a8"
+  integrity sha512-gxOQfmV7Ft/MYKpXDEo09WZyBuKOBqxqDRWay9KtfGq/E0Y4vbTPsWLv2cB1ToPJdKE6XSN6Re9tCIw5M/yMUg==
+  dependencies:
+    d3-array "^3.2.2"
+    vega-dataflow "^5.7.6"
+    vega-statistics "^1.9.0"
+    vega-util "^1.17.2"
+
+vega-runtime@^6.2.0, vega-runtime@~6.2.0:
+  version "6.2.0"
+  resolved "https://registry.yarnpkg.com/vega-runtime/-/vega-runtime-6.2.0.tgz#10f435089fff11d8e1b49cb0cbab8041731e6f06"
+  integrity sha512-30UXbujWjKNd5aeP+oeHuwFmzuyVYlBj4aDy9+AjfWLECu8wJt4K01vwegcaGPdCWcPLVIv4Oa9Lob4mcXn5KQ==
+  dependencies:
+    vega-dataflow "^5.7.6"
+    vega-util "^1.17.2"
+
+vega-scale@^7.4.1, vega-scale@~7.4.1:
+  version "7.4.1"
+  resolved "https://registry.yarnpkg.com/vega-scale/-/vega-scale-7.4.1.tgz#2dcd3e39ebb00269b03a8be86e44c7b48c67442a"
+  integrity sha512-dArA28DbV/M92O2QvswnzCmQ4bq9WwLKUoyhqFYWCltmDwkmvX7yhqiFLFMWPItIm7mi4Qyoygby6r4DKd1X2A==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-interpolate "^3.0.1"
+    d3-scale "^4.0.2"
+    d3-scale-chromatic "^3.1.0"
+    vega-time "^2.1.2"
+    vega-util "^1.17.2"
+
+vega-scenegraph@^4.13.0, vega-scenegraph@~4.13.0:
+  version "4.13.0"
+  resolved "https://registry.yarnpkg.com/vega-scenegraph/-/vega-scenegraph-4.13.0.tgz#c4fa5c82773f6244a9ca8b01a44e380adf03fabd"
+  integrity sha512-nfl45XtuqB5CxyIZJ+bbJ+dofzosPCRlmF+eUQo+0J23NkNXsTzur+1krJDSdhcw0SOYs4sbYRoMz1cpuOM4+Q==
+  dependencies:
+    d3-path "^3.1.0"
+    d3-shape "^3.2.0"
+    vega-canvas "^1.2.7"
+    vega-loader "^4.5.2"
+    vega-scale "^7.4.1"
+    vega-util "^1.17.2"
+
+vega-schema-url-parser@^2.2.0:
+  version "2.2.0"
+  resolved "https://registry.yarnpkg.com/vega-schema-url-parser/-/vega-schema-url-parser-2.2.0.tgz#a0d1e02915adfbfcb1fd517c8c2ebe2419985c1e"
+  integrity sha512-yAtdBnfYOhECv9YC70H2gEiqfIbVkq09aaE4y/9V/ovEFmH9gPKaEgzIZqgT7PSPQjKhsNkb6jk6XvSoboxOBw==
+
+vega-selections@^5.4.2:
+  version "5.4.2"
+  resolved "https://registry.yarnpkg.com/vega-selections/-/vega-selections-5.4.2.tgz#cb4f41f5d4c0ee924ebf131b8dbd43e7885bcad4"
+  integrity sha512-99FUhYmg0jOJr2/K4TcEURmJRkuibrCDc8KBUX7qcQEITzrZ5R6a4QE+sarCvbb3hi8aA9GV2oyST6MQeA9mgQ==
+  dependencies:
+    d3-array "3.2.4"
+    vega-expression "^5.0.1"
+    vega-util "^1.17.1"
+
+vega-statistics@^1.9.0, vega-statistics@~1.9.0:
+  version "1.9.0"
+  resolved "https://registry.yarnpkg.com/vega-statistics/-/vega-statistics-1.9.0.tgz#7d6139cea496b22d60decfa6abd73346f70206f9"
+  integrity sha512-GAqS7mkatpXcMCQKWtFu1eMUKLUymjInU0O8kXshWaQrVWjPIO2lllZ1VNhdgE0qGj4oOIRRS11kzuijLshGXQ==
+  dependencies:
+    d3-array "^3.2.2"
+
+vega-themes@^2.15.0:
+  version "2.15.0"
+  resolved "https://registry.yarnpkg.com/vega-themes/-/vega-themes-2.15.0.tgz#cf7592efb45406957e9beb67d7033ee5f7b7a511"
+  integrity sha512-DicRAKG9z+23A+rH/3w3QjJvKnlGhSbbUXGjBvYGseZ1lvj9KQ0BXZ2NS/+MKns59LNpFNHGi9us/wMlci4TOA==
+
+vega-time@^2.1.2, vega-time@~2.1.2:
+  version "2.1.2"
+  resolved "https://registry.yarnpkg.com/vega-time/-/vega-time-2.1.2.tgz#0c414e74780613d6d3234fb97f19b50c0ebd9f49"
+  integrity sha512-6rXc6JdDt8MnCRy6UzUCsa6EeFycPDmvioMddLfKw38OYCV8pRQC5nw44gyddOwXgUTJLiCtn/sp53P0iA542A==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-time "^3.1.0"
+    vega-util "^1.17.2"
+
+vega-tooltip@^0.34.0:
+  version "0.34.0"
+  resolved "https://registry.yarnpkg.com/vega-tooltip/-/vega-tooltip-0.34.0.tgz#e0aa4d9c9bcf155e257650ba7e670fad7b1ff5ab"
+  integrity sha512-TtxwkcLZ5aWQTvKGlfWDou8tISGuxmqAW1AgGZjrDpf75qsXvgtbPdRAAls2LZMqDxpr5T1kMEZs9XbSpiI8yw==
+  dependencies:
+    vega-util "^1.17.2"
+
+vega-transforms@~4.12.0:
+  version "4.12.0"
+  resolved "https://registry.yarnpkg.com/vega-transforms/-/vega-transforms-4.12.0.tgz#6a69e0b67934b0c0a40a6f607fdb543bf749955e"
+  integrity sha512-bh/2Qbj85O70mjfLRgPKAsABArgSUP0k+GjmaY54zukIRxoGxKju+85nigeX/aR/INpEqNWif+5lL+NvmyWA5w==
+  dependencies:
+    d3-array "^3.2.2"
+    vega-dataflow "^5.7.6"
+    vega-statistics "^1.9.0"
+    vega-time "^2.1.2"
+    vega-util "^1.17.2"
+
+vega-typings@~1.3.1:
+  version "1.3.1"
+  resolved "https://registry.yarnpkg.com/vega-typings/-/vega-typings-1.3.1.tgz#025a6031505794b44d9b6e2c49d4551b8918d4ae"
+  integrity sha512-j9Sdgmvowz09jkMgTFGVfiv7ycuRP/TQkdHRPXIYwt3RDgPQn7inyFcJ8C8ABFt4MiMWdjOwbneF6KWW8TRXIw==
+  dependencies:
+    "@types/geojson" "7946.0.4"
+    vega-event-selector "^3.0.1"
+    vega-expression "^5.1.1"
+    vega-util "^1.17.2"
+
+vega-util@^1.17.1, vega-util@^1.17.2, vega-util@~1.17.2:
+  version "1.17.2"
+  resolved "https://registry.yarnpkg.com/vega-util/-/vega-util-1.17.2.tgz#f69aa09fd5d6110c19c4a0f0af9e35945b99987d"
+  integrity sha512-omNmGiZBdjm/jnHjZlywyYqafscDdHaELHx1q96n5UOz/FlO9JO99P4B3jZg391EFG8dqhWjQilSf2JH6F1mIw==
+
+vega-view-transforms@~4.6.0:
+  version "4.6.0"
+  resolved "https://registry.yarnpkg.com/vega-view-transforms/-/vega-view-transforms-4.6.0.tgz#829d56ca3c8116b0dded4ec0502f4ac70253de9a"
+  integrity sha512-z3z66aJTA3ZRo4oBY4iBXnn+A4KqBGZT/UrlKDbm+7Ec+Ip+hK2tF8Kmhp/WNcMsDZoUWFqLJgR2VgOgvJk9RA==
+  dependencies:
+    vega-dataflow "^5.7.6"
+    vega-scenegraph "^4.13.0"
+    vega-util "^1.17.2"
+
+vega-view@~5.13.0:
+  version "5.13.0"
+  resolved "https://registry.yarnpkg.com/vega-view/-/vega-view-5.13.0.tgz#8ea96da9fcdf42fe7c0e95fe6258933477524745"
+  integrity sha512-ZPAAQ3iYz6YrQjJoDT+0bcxJkXt9PKF5v4OO7Omw8PFhkIv++jFXeKlQTW1bBtyQ92dkdGGHv5lYY67Djqjf3A==
+  dependencies:
+    d3-array "^3.2.2"
+    d3-timer "^3.0.1"
+    vega-dataflow "^5.7.6"
+    vega-format "^1.1.2"
+    vega-functions "^5.15.0"
+    vega-runtime "^6.2.0"
+    vega-scenegraph "^4.13.0"
+    vega-util "^1.17.2"
+
+vega-voronoi@~4.2.3:
+  version "4.2.3"
+  resolved "https://registry.yarnpkg.com/vega-voronoi/-/vega-voronoi-4.2.3.tgz#54c4bb96b9b94c3fa0160bee24695dcb9d583fe1"
+  integrity sha512-aYYYM+3UGqwsOx+TkVtF1IZfguy0H7AN79dR8H0nONRIc+vhk/lbnlkgwY2nSzEu0EZ4b5wZxeGoDBEVmdDEcg==
+  dependencies:
+    d3-delaunay "^6.0.2"
+    vega-dataflow "^5.7.6"
+    vega-util "^1.17.2"
+
+vega-wordcloud@~4.1.5:
+  version "4.1.5"
+  resolved "https://registry.yarnpkg.com/vega-wordcloud/-/vega-wordcloud-4.1.5.tgz#789c9e67225c77f3f35a6fc052beec1c2bdc8b5e"
+  integrity sha512-p+qXU3cb9VeWzJ/HEdax0TX2mqDJcSbrCIfo2d/EalOXGkvfSLKobsmMQ8DxPbtVp0uhnpvfCGDyMJw+AzcI2A==
+  dependencies:
+    vega-canvas "^1.2.7"
+    vega-dataflow "^5.7.6"
+    vega-scale "^7.4.1"
+    vega-statistics "^1.9.0"
+    vega-util "^1.17.2"
+
+vega@^5.30.0:
+  version "5.30.0"
+  resolved "https://registry.yarnpkg.com/vega/-/vega-5.30.0.tgz#d12350c829878b481453ab28ce10855a954df06d"
+  integrity sha512-ZGoC8LdfEUV0LlXIuz7hup9jxuQYhSaWek2M7r9dEHAPbPrzSQvKXZ0BbsJbrarM100TGRpTVN/l1AFxCwDkWw==
+  dependencies:
+    vega-crossfilter "~4.1.2"
+    vega-dataflow "~5.7.6"
+    vega-encode "~4.10.1"
+    vega-event-selector "~3.0.1"
+    vega-expression "~5.1.1"
+    vega-force "~4.2.1"
+    vega-format "~1.1.2"
+    vega-functions "~5.15.0"
+    vega-geo "~4.4.2"
+    vega-hierarchy "~4.1.2"
+    vega-label "~1.3.0"
+    vega-loader "~4.5.2"
+    vega-parser "~6.4.0"
+    vega-projection "~1.6.1"
+    vega-regression "~1.3.0"
+    vega-runtime "~6.2.0"
+    vega-scale "~7.4.1"
+    vega-scenegraph "~4.13.0"
+    vega-statistics "~1.9.0"
+    vega-time "~2.1.2"
+    vega-transforms "~4.12.0"
+    vega-typings "~1.3.1"
+    vega-util "~1.17.2"
+    vega-view "~5.13.0"
+    vega-view-transforms "~4.6.0"
+    vega-voronoi "~4.2.3"
+    vega-wordcloud "~4.1.5"
+
 vinyl-fs@^3.0.0:
   version "3.0.3"
   resolved "https://registry.npmjs.org/vinyl-fs/-/vinyl-fs-3.0.3.tgz"
@@ -11718,6 +12365,18 @@ vue-demi@>=0.14.7:
   resolved "https://registry.yarnpkg.com/vue-demi/-/vue-demi-0.14.7.tgz#8317536b3ef74c5b09f268f7782e70194567d8f2"
   integrity sha512-EOG8KXDQNwkJILkx/gPcoL/7vH+hORoBaKgGe+6W7VFMvCYJfmF2dGbvgDroVnI8LU7/kTu8mbjRZGBU1z9NTA==
 
+vue-demi@^0.13.11:
+  version "0.13.11"
+  resolved "https://registry.yarnpkg.com/vue-demi/-/vue-demi-0.13.11.tgz#7d90369bdae8974d87b1973564ad390182410d99"
+  integrity sha512-IR8HoEEGM65YY3ZJYAjMlKygDQn25D5ajNFNoKh9RSDMQtlzCxtfQjdQgv9jjK+m3377SsJXY8ysq8kLCZL25A==
+
+vue-echarts@^7.0.3:
+  version "7.0.3"
+  resolved "https://registry.yarnpkg.com/vue-echarts/-/vue-echarts-7.0.3.tgz#bf79f7ee0144bbdc6aee5610e8443fed91f6abbe"
+  integrity sha512-/jSxNwOsw5+dYAUcwSfkLwKPuzTQ0Cepz1LxCOpj2QcHrrmUa/Ql0eQqMmc1rTPQVrh2JQ29n2dhq75ZcHvRDw==
+  dependencies:
+    vue-demi "^0.13.11"
+
 vue-eslint-parser@^9.0.1:
   version "9.0.3"
   resolved "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-9.0.3.tgz"
@@ -11857,10 +12516,10 @@ walker@^1.0.8:
   dependencies:
     makeerror "1.0.12"
 
-watchpack@^2.4.0:
-  version "2.4.0"
-  resolved "https://registry.npmjs.org/watchpack/-/watchpack-2.4.0.tgz"
-  integrity sha512-Lcvm7MGST/4fup+ifyKi2hjyIAwcdI4HRgtvTpIUxBRhB+RFtUh8XtDOxUfctVCnhVi+QQj49i91OyvzkJl6cg==
+watchpack@^2.4.1:
+  version "2.4.2"
+  resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.4.2.tgz#2feeaed67412e7c33184e5a79ca738fbd38564da"
+  integrity sha512-TnbFSbcOCcDgjZ4piURLCbJ3nJhznVh9kw6F6iokjiFPl8ONxe9A6nMDVXDiNbrSfLILs6vB07F7wLBrwPYzJw==
   dependencies:
     glob-to-regexp "^0.4.1"
     graceful-fs "^4.1.2"
@@ -11970,64 +12629,33 @@ webpack-sources@^3.2.3:
   resolved "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz"
   integrity sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==
 
-"webpack@>=4.0.0 <6.0.0":
-  version "5.74.0"
-  resolved "https://registry.npmjs.org/webpack/-/webpack-5.74.0.tgz"
-  integrity sha512-A2InDwnhhGN4LYctJj6M1JEaGL7Luj6LOmyBHjcI8529cm5p6VXiTIW2sn6ffvEAKmveLzvu4jrihwXtPojlAA==
+"webpack@>=4.0.0 <6.0.0", webpack@^5.89.0:
+  version "5.94.0"
+  resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.94.0.tgz#77a6089c716e7ab90c1c67574a28da518a20970f"
+  integrity sha512-KcsGn50VT+06JH/iunZJedYGUJS5FGjow8wb9c0v5n1Om8O1g4L6LjtfxwlXIATopoQu+vOXXa7gYisWxCoPyg==
   dependencies:
-    "@types/eslint-scope" "^3.7.3"
-    "@types/estree" "^0.0.51"
-    "@webassemblyjs/ast" "1.11.1"
-    "@webassemblyjs/wasm-edit" "1.11.1"
-    "@webassemblyjs/wasm-parser" "1.11.1"
+    "@types/estree" "^1.0.5"
+    "@webassemblyjs/ast" "^1.12.1"
+    "@webassemblyjs/wasm-edit" "^1.12.1"
+    "@webassemblyjs/wasm-parser" "^1.12.1"
     acorn "^8.7.1"
-    acorn-import-assertions "^1.7.6"
-    browserslist "^4.14.5"
-    chrome-trace-event "^1.0.2"
-    enhanced-resolve "^5.10.0"
-    es-module-lexer "^0.9.0"
-    eslint-scope "5.1.1"
-    events "^3.2.0"
-    glob-to-regexp "^0.4.1"
-    graceful-fs "^4.2.9"
-    json-parse-even-better-errors "^2.3.1"
-    loader-runner "^4.2.0"
-    mime-types "^2.1.27"
-    neo-async "^2.6.2"
-    schema-utils "^3.1.0"
-    tapable "^2.1.1"
-    terser-webpack-plugin "^5.1.3"
-    watchpack "^2.4.0"
-    webpack-sources "^3.2.3"
-
-webpack@^5.89.0:
-  version "5.89.0"
-  resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.89.0.tgz#56b8bf9a34356e93a6625770006490bf3a7f32dc"
-  integrity sha512-qyfIC10pOr70V+jkmud8tMfajraGCZMBWJtrmuBymQKCrLTRejBI8STDp1MCyZu/QTdZSeacCQYpYNQVOzX5kw==
-  dependencies:
-    "@types/eslint-scope" "^3.7.3"
-    "@types/estree" "^1.0.0"
-    "@webassemblyjs/ast" "^1.11.5"
-    "@webassemblyjs/wasm-edit" "^1.11.5"
-    "@webassemblyjs/wasm-parser" "^1.11.5"
-    acorn "^8.7.1"
-    acorn-import-assertions "^1.9.0"
-    browserslist "^4.14.5"
+    acorn-import-attributes "^1.9.5"
+    browserslist "^4.21.10"
     chrome-trace-event "^1.0.2"
-    enhanced-resolve "^5.15.0"
+    enhanced-resolve "^5.17.1"
     es-module-lexer "^1.2.1"
     eslint-scope "5.1.1"
     events "^3.2.0"
     glob-to-regexp "^0.4.1"
-    graceful-fs "^4.2.9"
+    graceful-fs "^4.2.11"
     json-parse-even-better-errors "^2.3.1"
     loader-runner "^4.2.0"
     mime-types "^2.1.27"
     neo-async "^2.6.2"
     schema-utils "^3.2.0"
     tapable "^2.1.1"
-    terser-webpack-plugin "^5.3.7"
-    watchpack "^2.4.0"
+    terser-webpack-plugin "^5.3.10"
+    watchpack "^2.4.1"
     webpack-sources "^3.2.3"
 
 websocket-driver@>=0.5.1, websocket-driver@^0.7.4:
@@ -12157,6 +12785,15 @@ wrap-ansi@^2.0.0:
     string-width "^1.0.1"
     strip-ansi "^3.0.1"
 
+wrap-ansi@^6.2.0:
+  version "6.2.0"
+  resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-6.2.0.tgz#e9393ba07102e6c91a3b221478f0257cd2856e53"
+  integrity sha512-r6lPcBGxZXlIcymEu7InxDMhdW0KDxpLgoFLcguasxCaJ/SOIZwINatK9KY/tf+ZrlywOKU0UDj3ATXUBfxJXA==
+  dependencies:
+    ansi-styles "^4.0.0"
+    string-width "^4.1.0"
+    strip-ansi "^6.0.0"
+
 wrap-ansi@^7.0.0:
   version "7.0.0"
   resolved "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz"
@@ -12188,15 +12825,10 @@ write-file-atomic@^4.0.2:
     imurmurhash "^0.1.4"
     signal-exit "^3.0.7"
 
-ws@^8.11.0:
-  version "8.11.0"
-  resolved "https://registry.yarnpkg.com/ws/-/ws-8.11.0.tgz#6a0d36b8edfd9f96d8b25683db2f8d7de6e8e143"
-  integrity sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg==
-
-ws@^8.13.0:
-  version "8.13.0"
-  resolved "https://registry.yarnpkg.com/ws/-/ws-8.13.0.tgz#9a9fb92f93cf41512a0735c8f4dd09b8a1211cd0"
-  integrity sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA==
+ws@^8.11.0, ws@^8.13.0:
+  version "8.17.1"
+  resolved "https://registry.yarnpkg.com/ws/-/ws-8.17.1.tgz#9293da530bb548febc95371d90f9c878727d919b"
+  integrity sha512-6XQFvXTkbfUOZOKKILFG1PDK2NDQs4azKQl26T0YS5CxqWLgXajbPZ+h4gZekJyRqFU8pvnbAbbs/3TgRPy+GQ==
 
 xml-beautifier@^0.5.0:
   version "0.5.0"
@@ -12217,6 +12849,19 @@ xml-name-validator@^4.0.0:
   resolved "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz"
   integrity sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==
 
+xml2js@^0.6.2:
+  version "0.6.2"
+  resolved "https://registry.yarnpkg.com/xml2js/-/xml2js-0.6.2.tgz#dd0b630083aa09c161e25a4d0901e2b2a929b499"
+  integrity sha512-T4rieHaC1EXcES0Kxxj4JWgaUQHDk+qwHcYOCFHfiwKz7tOVPLq7Hjq9dM1WCMhylqMEfP7hMcOIChvotiZegA==
+  dependencies:
+    sax ">=0.6.0"
+    xmlbuilder "~11.0.0"
+
+xmlbuilder@~11.0.0:
+  version "11.0.1"
+  resolved "https://registry.yarnpkg.com/xmlbuilder/-/xmlbuilder-11.0.1.tgz#be9bae1c8a046e76b31127726347d0ad7002beb3"
+  integrity sha512-fDlsI/kFEx7gLvbecc0/ohLG50fugQp8ryHzMTuW9vSa1GJ0XYWKnhsUx7oie3G98+r56aTQIUB4kht42R3JvA==
+
 xmlchars@^2.2.0:
   version "2.2.0"
   resolved "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz"
@@ -12252,6 +12897,11 @@ yallist@^4.0.0:
   resolved "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz"
   integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==
 
+yaml-ast-parser@0.0.43:
+  version "0.0.43"
+  resolved "https://registry.yarnpkg.com/yaml-ast-parser/-/yaml-ast-parser-0.0.43.tgz#e8a23e6fb4c38076ab92995c5dca33f3d3d7c9bb"
+  integrity sha512-2PTINUwsRqSd+s8XxKaJWQlUuEMHJQyEuh2edBbW8KNJz0SJPwUSD2zRWqezFEdN7IzAgeuYHFUCF7o8zRdZ0A==
+
 yaml-jest@^1.2.0:
   version "1.2.0"
   resolved "https://registry.yarnpkg.com/yaml-jest/-/yaml-jest-1.2.0.tgz#5e863a8c3ce5aa7b9f63e12f8bffd6e2e47b4bf7"
@@ -12299,6 +12949,19 @@ yargs@^17.3.1:
     y18n "^5.0.5"
     yargs-parser "^21.1.1"
 
+yargs@^17.7.2, yargs@~17.7.2:
+  version "17.7.2"
+  resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269"
+  integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==
+  dependencies:
+    cliui "^8.0.1"
+    escalade "^3.1.1"
+    get-caller-file "^2.0.5"
+    require-directory "^2.1.1"
+    string-width "^4.2.3"
+    y18n "^5.0.5"
+    yargs-parser "^21.1.1"
+
 yargs@^7.1.0:
   version "7.1.2"
   resolved "https://registry.npmjs.org/yargs/-/yargs-7.1.2.tgz"
@@ -12322,3 +12985,15 @@ yocto-queue@^0.1.0:
   version "0.1.0"
   resolved "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz"
   integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==
+
+yoctocolors-cjs@^2.1.2:
+  version "2.1.2"
+  resolved "https://registry.yarnpkg.com/yoctocolors-cjs/-/yoctocolors-cjs-2.1.2.tgz#f4b905a840a37506813a7acaa28febe97767a242"
+  integrity sha512-cYVsTjKl8b+FrnidjibDWskAv7UKOfcwaVZdp/it9n1s9fU3IkgDbhdIRKCW4JDsAlECJY0ytoVPT3sK6kideA==
+
+zrender@5.6.0:
+  version "5.6.0"
+  resolved "https://registry.yarnpkg.com/zrender/-/zrender-5.6.0.tgz#01325b0bb38332dd5e87a8dbee7336cafc0f4a5b"
+  integrity sha512-uzgraf4njmmHAbEUxMJ8Oxg+P3fT04O+9p7gY+wJRVxo8Ge+KmYv0WJev945EH4wFuc4OY2NLXz46FZrWS9xJg==
+  dependencies:
+    tslib "2.3.0"
diff --git a/config/job_conf.yml.interactivetools.podman b/config/job_conf.yml.interactivetools.podman
index b377c45f2c2174b3a1f8eea9dd41759dd69378d1..d634b2e7f83e9e6da5ff10f2fea329e1fed60b00 100644
--- a/config/job_conf.yml.interactivetools.podman
+++ b/config/job_conf.yml.interactivetools.podman
@@ -24,9 +24,9 @@ execution:
       docker_set_user:
 
       # For containers running as root (on the inside)
-      docker_run_extra_arguments: --security-opt label=disable
+      docker_run_extra_arguments: --security-opt label=disable --network slirp4netns:allow_host_loopback=true
       # Should work for containers with non-root user (on the inside)
-      #docker_run_extra_arguments:  --userns=keep-id --security-opt label=disable
+      #docker_run_extra_arguments:  --userns=keep-id --security-opt label=disable --network slirp4netns:allow_host_loopback=true
 
       # Change to home directory of the galaxy user, not the directory of the galaxy installation
       docker_cmd: HOME="/home/galaxy"; podman
diff --git a/config/plugins/tours/core.galaxy_ui.yaml b/config/plugins/tours/core.galaxy_ui.yaml
index 8cdbed21d4a1224e99f1bbdedd94942e13f22290..eb950864e7a75e6adbff66c53f16b887c9dd6b36 100644
--- a/config/plugins/tours/core.galaxy_ui.yaml
+++ b/config/plugins/tours/core.galaxy_ui.yaml
@@ -22,16 +22,16 @@ steps:
       postclick: true
 
     - title: "Upload your data"
-      element: "#btn-local"
+      component: upload.local_button
       intro: "You can upload data from your computer."
 
     - title: "Upload your data"
-      element: "#btn-new"
+      component: upload.create_button
       intro: "Copy and paste data directly into Galaxy or include URLs that lead to your data"
       preclick: true
 
     - title: "Insert URLs"
-      element: ".upload-text-content"
+      component: upload.paste_content(n=0)
       intro: "URLs separated by a line break are automatically downloaded by Galaxy."
       textinsert: |
         https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/augustus/test-data/human_augustus.fa
@@ -49,15 +49,15 @@ steps:
       postclick: true
 
     - title: "Tools"
-      element: "#left"
+      component: _.left_panel
       intro: "This is your ToolBox. All tools available in your Galaxy instance you can find here."
 
     - title: "Tool categories"
-      element: '.toolSectionTitle'
+      component: tools.title
       intro: "Tools are grouped into categories to make them easier to find."
 
     - title: "Tool search bar"
-      element: '.search-query'
+      component: tools.search
       intro: "You can search for tools by keywords."
       textinsert: 'filter'
 
@@ -67,26 +67,26 @@ steps:
       postclick: true
 
     - title: "Filter Tool"
-      element: '#center'
+      component: _.center_panel
       intro: "Your tool is loaded into the main Galaxy page and ready for use."
 
     - title: "Tool parameters"
-      element: '#center #tool-card-body'
+      component: tools.body
       intro: "Here you can choose your tool parameters. Select your input dataset from your history and specify parameters for your analysis."
 
     - title: "Tool help"
-      element: 'div.form-help'
+      component: tools.help
       intro: "Every Galaxy tool has a help section with detailed information about the tool and its parameters.
               Have a look and study your tool in depth by reading it."
 
     - title: "Run your tool"
-      element: '#execute'
+      component: tools.execute
       intro: "Click on 'Execute' to run your tool and send it to the compute cluster.
               Don't be afraid to test different settings in parallel. Galaxy can handle multiple runs of the same tool."
       postclick: true
 
     - title: "History"
-      element: "#current-history-panel"
+      component: history_panel
       intro: "This is your Galaxy history! All analysis steps with results of the tools and their parameters will be recorded here and can be redone at any time.<br>
               A running tool is shown in yellow and if your calculation is done, it turns green. If your dataset is
               grey this means you are queued and need to wait until your tool can be started. If your dataset turns into red, an error has occurred. Please report the bug to the Galaxy team with the bug report button."
@@ -117,37 +117,30 @@ steps:
       element: "#current-history-panel div.content-item .rerun-btn"
       intro: "By clicking the reload button, you can re-run your tool again (e.g. with different parameters or on another dataset)."
 
-    - title: "Top panel"
-      element: "#masthead"
-      intro: "The top panel will give you access to a lot of useful things."
-
     - title: "Analyze data"
+      component: masthead.home
       element: "#analysis"
       intro: "This is the current view. Start your <b>Analysis</b> from here."
 
     - title: "Workflow"
-      element: "#workflow"
+      component: workflows.activity
       intro: "Create, manage, import, export and share your <b>Workflows</b>."
-
-    - title: "Data"
-      element: "#resources"
-      intro: "Get access to all <b>Workflows</b>, <b>Histories</b>, <b>Pages</b> and <b>Visualizations</b>."
-
+    
     - title: "Visualization"
-      element: "#visualization"
+      component: visualization.activity
       intro: "Galaxy offers a lot of visualizations to review your data!"
 
     - title: "Help"
-      element: "#help"
+      component: masthead.help
       intro: "Here you get more help from the Galaxy <b>Community</b> with Videos, a QA board and more tours."
 
-    - title: "User Preferences"
-      element: "#user"
-      intro: "Login and start your analysis!"
-
     - title: "Window Manager"
-      element: "#enable-window-manager"
+      component: masthead.window_manager
       intro: "Window Manager offers you multiple visualizations next to each other. Have a look at our Window Manager tour to learn more about it."
 
+    - title: "Login"
+      component: masthead.login
+      intro: "Login and start your analysis!"
+
     - title: "Enjoy Galaxy"
       intro: "Thanks for taking this tour! Happy research with Galaxy!"
diff --git a/config/plugins/tours/core.history.yaml b/config/plugins/tours/core.history.yaml
index d0c1ecce2f54edf8638c3cf57da9896eb7000ed3..5f8401e0c2a0da77a3dd0d4d51bea4270c86b810 100644
--- a/config/plugins/tours/core.history.yaml
+++ b/config/plugins/tours/core.history.yaml
@@ -28,11 +28,11 @@ steps:
         https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/statistics/test-data/anderson.tabular
 
     - title: "Start the upload"
-      element: "#btn-start"
+      element: "#regular #btn-start"
       intro: "Upload the data into your Galaxy <b>History</b>."
       postclick:
-        - "#btn-start"
-        - "#btn-close"
+        - "#regular #btn-start"
+        - "#regular #btn-close"
 
     - title: "History"
       element: "#current-history-panel"
diff --git a/config/plugins/visualizations/annotate_image/config/annotate_image.xml b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
index 0e6781078cf0eb0459506d98c2fbd88de1482066..b5bcfe76a7abd5f199679ad971c221b752a65f70 100644
--- a/config/plugins/visualizations/annotate_image/config/annotate_image.xml
+++ b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
@@ -13,5 +13,5 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="jquery.contextMenu.css"/>
+    <entry_point entry_point_type="script" src="script.js" css="jquery.contextMenu.css"/>
 </visualization>
diff --git a/config/plugins/visualizations/annotate_image/package.json b/config/plugins/visualizations/annotate_image/package.json
index f546269cf52a9a4ccc762068f276f0f98c9dd67c..ae7cd6a66da903f1d1c1dd902e0b707e847ec87b 100644
--- a/config/plugins/visualizations/annotate_image/package.json
+++ b/config/plugins/visualizations/annotate_image/package.json
@@ -19,7 +19,7 @@
     },
     "scripts": {
         "build": "yarn build-css && yarn build-js",
-        "build-css": "cp 'node_modules/jquery-contextmenu/dist/jquery.contextMenu.css' 'static/'",
+        "build-css": "cp -f 'node_modules/jquery-contextmenu/dist/jquery.contextMenu.css' 'static/'",
         "build-js": "parcel build src/script.js --dist-dir static"
     }
 }
diff --git a/config/plugins/visualizations/annotate_image/src/script.js b/config/plugins/visualizations/annotate_image/src/script.js
index 443c1932b6cf5f6fc9448c3a5a5fc48e62d91554..b90b3cb1901d625559853e14b91a21f4c9820d02 100644
--- a/config/plugins/visualizations/annotate_image/src/script.js
+++ b/config/plugins/visualizations/annotate_image/src/script.js
@@ -5,12 +5,6 @@ import _ from "underscore";
 // Use lighter weight 'core' version of paper since we don't need paperscript
 import paper from "../node_modules/paper/dist/paper-core.js";
 
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
 const CommandManager = (function () {
     function CommandManager() {}
 
@@ -60,10 +54,7 @@ const generateUUID = function () {
     return uuid;
 };
 
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (opt) {
-    const chart = opt.chart;
-    const dataset = opt.dataset;
+function render(downloadUrl) {
     const defaults = { color: "red", width: 4, opacity: 0.5 };
     $.fn.createCanvas = function (options) {
         let settings = $.extend({}, defaults, options || {});
@@ -441,17 +432,13 @@ window.bundleEntries.load = function (opt) {
         });
     };
 
-    const downloadUrl = prefixedDownloadUrl(opt.root, dataset.download_url);
-
     fetch(downloadUrl)
         .then((response) => {
             if (!response.ok) {
                 throw new Error("Failed to access dataset.");
             }
-            return response.text();
-        })
-        .then((content) => {
-            const $chartViewer = $("#" + opt.target);
+
+            const $chartViewer = $("#app");
             $chartViewer.html("<img id='image-annotate' src='" + downloadUrl + "' />");
             $chartViewer.css("overflow", "auto");
             $chartViewer.css("position", "relative");
@@ -470,12 +457,16 @@ window.bundleEntries.load = function (opt) {
                     img_height: height,
                 });
             });
-
-            chart.state("ok", "Chart drawn.");
-            opt.process.resolve();
         })
         .catch((error) => {
-            chart.state("failed", error.message);
-            opt.process.resolve();
+            console.error(error.message);
         });
 };
+
+const { root, visualization_config } = JSON.parse(document.getElementById("app").dataset.incoming);
+
+const datasetId = visualization_config.dataset_id;
+
+const downloadUrl = window.location.origin + root + "api/datasets/" + datasetId + "/display";
+
+render(downloadUrl);
diff --git a/config/plugins/visualizations/common/templates/script_entry_point.mako b/config/plugins/visualizations/common/templates/script_entry_point.mako
index dfdf4137666b22d8e7b9703d9e609d44ad128e31..80ad349089301c93af013dd148025c8d18b45324 100644
--- a/config/plugins/visualizations/common/templates/script_entry_point.mako
+++ b/config/plugins/visualizations/common/templates/script_entry_point.mako
@@ -1,10 +1,36 @@
 # -*- coding: utf-8 -*-
 <%inherit file="visualization_base.mako"/>
 
-## No stylesheets
-<%def name="stylesheets()"></%def>
-## No javascript libraries
-<%def name="late_javascripts()">
-    <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_attributes.items() ]) %>
-    <script type="text/javascript" ${tag_attrs}></script>
+## Add stylesheet
+<%def name="stylesheets()">
+    <% script_css = script_attributes.get("css") %>
+    %if script_css is not None:
+        <% script_css = script_css if h.is_url(script_css) else f"{static_url}{script_css}" %>
+        <link rel="stylesheet" href="${script_css}">
+    %endif
+</%def>
+
+## Create a container, attach data and import script file
+<%def name="get_body()">
+    ## Collect incoming data
+    <%
+        from markupsafe import escape
+        data_incoming = {
+            "root": h.url_for("/"),
+            "visualization_id": visualization_id,
+            "visualization_name": visualization_name,
+            "visualization_plugin": visualization_plugin,
+            "visualization_title": escape(title),
+            "visualization_config": config }
+    %>
+
+    ## Create a container with default identifier `app`
+    <% container = script_attributes.get("container") or "app" %>
+    <div id="${container}" data-incoming='${h.dumps(data_incoming)}'></div>
+
+    ## Add script tag
+    <% script_src = script_attributes.get("src") %>
+    <% script_src = script_src if h.is_url(script_src) else f"{static_url}{script_src}" %>
+    <% script_type = script_attributes.get("type") or "module" %>
+    <script type="${script_type}" src="${script_src}"></script>
 </%def>
diff --git a/config/plugins/visualizations/cytoscape/config/cytoscape.xml b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
index b73ec2e8728b993b71d6a45c748e093d119079e9..79de685142faf9aa9861e7a46e9b9cd5a74a3b2c 100644
--- a/config/plugins/visualizations/cytoscape/config/cytoscape.xml
+++ b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
@@ -13,7 +13,10 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js"/>
+    <requirements>
+        <requirement type="npm" version="0.0.3" package="@galaxyproject/cytoscape"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
         <input>
             <label>Curve style</label>
@@ -69,10 +72,6 @@
                     <label>Grid</label>
                     <value>grid</value>
                 </data>
-                <data>
-                    <label>Null</label>
-                    <value>null</value>
-                </data>
                 <data>
                     <label>Preset</label>
                     <value>preset</value>
@@ -87,18 +86,7 @@
             <label>Directed/Undirected</label>
             <name>directed</name>
             <help>Select a kind of edge.</help>
-            <type>select</type>
-            <display>radio</display>
-            <data>
-                <data>
-                    <label>Directed</label>
-                    <value>triangle</value>
-                </data>
-                <data>
-                    <label>Undirected</label>
-                    <value></value>
-                </data>
-            </data>
+            <type>boolean</type>
         </input>
         <input>
             <label>Graph algorithms</label>
@@ -115,10 +103,6 @@
                     <label>Depth First Search</label>
                     <value>dfs</value>
                 </data>
-                <data>
-                    <label>Depth First Search</label>
-                    <value>dfs</value>
-                </data>
                 <data>
                     <label>Minimum Spanning Tree (Kruskal)</label>
                     <value>kruskal</value>
diff --git a/config/plugins/visualizations/cytoscape/package.json b/config/plugins/visualizations/cytoscape/package.json
deleted file mode 100644
index 09a404bb79180ff5039c106190df2ff31541acca..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/cytoscape/package.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.1.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "cytoscape": "^3.2.8",
-        "jquery": "^3.1.1"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "^2.12.0"
-    }
-}
diff --git a/config/plugins/visualizations/cytoscape/src/script.js b/config/plugins/visualizations/cytoscape/src/script.js
deleted file mode 100644
index a2d0fdd2d0100546ff17a85fa617b2b32e775a04..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/cytoscape/src/script.js
+++ /dev/null
@@ -1,279 +0,0 @@
-import Cytoscape from 'cytoscape';
-
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
-// Public method. Return graph data as JSON
-var parse_sif = function( text ) {
-    // Private variables and methods
-    var nodes = {}, links = {}, content = [];
-
-    // Add a node
-    var _getNode = function( id ) {
-        if(!nodes[id]) {
-            nodes[id] = {id: id};
-        }
-        return nodes[id];
-    };
-
-    // Parse each line of the SIF file
-    var _parse = function( line, i ) {
-        var source, interaction, j, length;
-        line = ( line.split('\t').length > 1 ) ? line.split('\t') : line.split(' ');
-        source = _getNode( line[0] );
-        interaction = ( line[1] ? line[1] : "" );
-        if( line.length && line.length > 0 && line[0] !== "" ) {
-            if( interaction !== "" ) {
-                // Get all the target nodes for a source
-                for ( j = 2, length = line.length; j < length; j++ ) {
-                    if( line[j] !== "" ) {
-                        // Create an object for each target for the source
-                        var target = _getNode( line[j] ),
-                        relation_object = {target: target.id,
-                            source: source.id,
-                            id: source.id + target.id,
-                            relation: interaction.replace(/[''""]+/g, '') }; // Replace quotes in relation
-                        if( source < target ) {
-                            links[ source.id + target.id + interaction ] = relation_object;
-                        } else {
-                            links[ target.id + source.id + interaction ] = relation_object;
-                        }
-                    }
-                }
-            }
-            // Handle the case of single node i.e. no relation with any other node
-            // and only the source exists
-            else {
-                links[ source.id ] = { target: "", source: source.id, id: source.id, relation: "" };
-            }
-        }
-    };
-
-    // Convert to array from objects
-    var _toArr = function( obj ) {
-        var arr = [];
-        for (var key in obj) {
-            arr.push( obj[key] );
-        }
-        return arr;
-    };
-
-    // Make content from list of nodes and links
-    var _toDataArr = function( nodes, links ) {
-        var content = [], node_length, links_length;
-        // Make a list of all nodes
-        for(var i = 0, node_length = nodes.length; i < node_length; i++) {
-            content.push( { 'data': nodes[i] } );
-        }
-        // Make a list of all relationships among nodes
-        for(var i = 0, links_length = links.length; i < links_length; i++) {
-            content.push( { 'data': links[i] } );
-        }
-        return content;
-    };
-
-    var lines = text.split('\n'), i, length, nodesarr, linksarr;
-    for ( i = 0, length = lines.length; i < length; i++ ) {
-        if( lines[i] !== "" ) {
-            _parse( lines[i], i );
-        }
-    }
-    nodesarr = _toArr( nodes );
-    linksarr = _toArr( links );
-    return { content: _toDataArr( nodesarr, linksarr ) };
-};
-
-function run_search_algorithm( cytoscape, root_id, type, self ) {
-    var algorithm = "", i = 0;
-    var selectNextElement = function() {
-        if( i < algorithm.path.length ) {
-            // Add css class for the selected edge(s)
-            algorithm.path[i].addClass( 'searchpath' );
-            i++;
-            // Animate the edges and nodes coloring
-            // of the path with a delay of 500ms
-            setTimeout( selectNextElement, 500 );
-        }
-    };
-    switch( type ) {
-        // Breadth First Search
-        case "bfs":
-            algorithm = cytoscape.elements().bfs( '#' + root_id, function() { }, true );
-            selectNextElement();
-            break;
-        // Depth First Search
-        case "dfs":
-            algorithm = cytoscape.elements().dfs( '#' + root_id, function() { }, true );
-            selectNextElement();
-            break;
-        // A* search
-        case "astar":
-            // Choose root and destination for performing A*
-            if( !self.astar_root ) {
-                self.astar_root = root_id;
-            }
-            else {
-                self.astar_destination = root_id;
-            }
-            if( self.astar_root && self.astar_destination ) {
-                algorithm = cytoscape.elements().aStar({ root: "#" + self.astar_root, goal: "#" + self.astar_destination },function() {}, true);
-                selectNextElement();
-            }
-         default:
-            return;
-    }
-};
-
-function run_traversal_type( cytoscape, root_id, type ) {
-    var node_collection;
-    switch( type ) {
-        // Recursively get edges (and their sources) coming into the nodes in a collection
-        case "predecessors":
-             node_collection = cytoscape.$( '#' + root_id ).predecessors();
-             break;
-        // Recursively get edges (and their targets) coming out of the nodes in a collection
-        case "successors":
-             node_collection = cytoscape.$( '#' + root_id ).successors();
-             break;
-        // Get edges (and their targets) coming out of the nodes in a collection.
-        case "outgoers":
-             node_collection = cytoscape.$( '#' + root_id ).outgoers();
-             break;
-        // Get edges (and their sources) coming into the nodes in a collection.
-        case "incomers":
-             node_collection = cytoscape.$( '#' + root_id ).incomers();
-             break;
-        // From the set of calling nodes, get the nodes which are roots
-        case "roots":
-             node_collection = cytoscape.$( '#' + root_id ).roots();
-             break;
-        // From the set of calling nodes, get the nodes which are leaves
-        case "leaves":
-             node_collection = cytoscape.$( '#' + root_id ).leaves();
-             break;
-        default:
-             return;
-    }
-    // Add CSS class for selected nodes and edges
-    node_collection.edges().addClass( 'searchpath' );
-    node_collection.nodes().addClass( 'searchpath' );
-};
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    var self = this,
-    chart    = options.chart,
-    dataset  = options.dataset,
-    settings = options.chart.settings,
-    data_content = null,
-    cytoscape = null,
-    sif_file_ext = "sif",
-    highlighted_color = settings.get( 'color_picker_highlighted' );
-    $.ajax({
-        url     : prefixedDownloadUrl(options.root, dataset.download_url),
-        success : function( content ) {
-            // Select data for the graph
-            if( dataset.file_ext === sif_file_ext ) {
-                data_content = parse_sif( content ).content;
-            }
-            else {
-                data_content = content.elements ? content.elements : content;
-            }
-            try {
-                cytoscape = Cytoscape({
-                    container: document.getElementById( options.target ),
-                    layout: {
-                        name: settings.get( 'layout_name' ),
-                        idealEdgeLength: 100,
-                        nodeOverlap: 20
-                    },
-                    minZoom: 0.1,
-                    maxZoom: 20,
-                    style: [{
-                        selector: 'node',
-                        style: {
-                            'background-color': settings.get( 'color_picker_nodes' ),
-                            'opacity': 1,
-                            'content': 'data(id)',
-                            'text-valign': 'center',
-                        }
-                    },
-                    {
-                        selector: 'core',
-                        style: {
-                                'selection-box-color':'#AAD8FF',
-                                'selection-box-border-color':'#8BB0D0',
-                                'selection-box-opacity':'0.5'
-                        }
-                    },
-                    {
-                        selector: 'edge',
-                        style: {
-                            'curve-style': settings.get( 'curve_style' ),
-                            'haystack-radius': 0,
-                            'width': 3,
-                            'opacity': 1,
-                            'line-color': settings.get( 'color_picker_edges' ),
-                            'target-arrow-shape': settings.get( 'directed' ),
-                            "overlay-padding":"3px"
-                        }
-                    },
-                    {
-                        selector:'node:selected',
-                        style: {
-                            "border-width": "6px",
-                            "border-color": "#AAD8FF",
-                            "border-opacity": "0.5",
-                            "background-color": "#77828C",
-                            "text-outline-color": "#77828C"
-                        }
-                    },
-                    {
-                        selector: '.searchpath',
-                        style: {
-                            'background-color': highlighted_color,
-                            'line-color': highlighted_color,
-                            'target-arrow-color': highlighted_color,
-                            'transition-property': 'background-color, line-color, target-arrow-color',
-                            'transition-duration': '0.5s'
-                    }
-                    }],
-                    elements: data_content // Set the JSON data for viewing
-                });
-                // Highlight the minimum spanning tree found using Kruskal algorithm
-                if( settings.get( 'search_algorithm' ) === "kruskal" ) {
-                    var kruskal = cytoscape.elements().kruskal();
-                    kruskal.edges().addClass( 'searchpath' );
-                }
-                // Register tap (clicking a node) event on graph nodes
-                // On tapping any node, BFS or DFS start from that node
-                cytoscape.$( 'node' ).on('tap', function( e ) {
-                    var ele = e.cyTarget,
-                        search_algorithm = settings.get( 'search_algorithm' ),
-                        traversal_type = settings.get( 'graph_traversal' );
-                    // If search algorithm and traversal both are chosen,
-                    // search algorithm will take preference
-                    if( settings.get( 'search_algorithm' ) !== "" ) {
-                        run_search_algorithm( cytoscape, ele.id(), search_algorithm, self );
-                    }
-                    else if( settings.get( 'graph_traversal' ) !== "" ) {
-                        run_traversal_type( cytoscape, ele.id(), traversal_type );
-                    }
-                });
-                chart.state( 'ok', 'Chart drawn.' );
-                // Re-renders the graph view when window is resized
-                $( window ).resize( function() { cytoscape.layout(); } );
-            } catch( err ) {
-                chart.state( 'failed', err );
-            }
-            options.process.resolve();
-        },
-        error: function() {
-            chart.state( 'failed', 'Failed to access dataset.' );
-            options.process.resolve();
-        }
-    });
-};
diff --git a/config/plugins/visualizations/cytoscape/static/logo.png b/config/plugins/visualizations/cytoscape/static/logo.png
index ce891f674bb8dafb23cc9a12596ea127670cf2ee..4c49f1d32aa8a144c666f31f5c63d3df9586ea86 100644
Binary files a/config/plugins/visualizations/cytoscape/static/logo.png and b/config/plugins/visualizations/cytoscape/static/logo.png differ
diff --git a/config/plugins/visualizations/editor/templates/editor.mako b/config/plugins/visualizations/editor/templates/editor.mako
index 385edbba62057d94aa0056006d5203429f5acdd3..1046842c3417c915d65663a04fb58a2a69dad2b1 100755
--- a/config/plugins/visualizations/editor/templates/editor.mako
+++ b/config/plugins/visualizations/editor/templates/editor.mako
@@ -62,11 +62,11 @@
 
     const ajax_url = "${h.url_for( controller='/datasets', action='index')}/" + hda_id + "/display";
     const data = httpGet(ajax_url);
-    document.getElementById("editor").innerHTML = data;
     var editor = ace.edit("editor", {
         mode: "ace/mode/powershell",
         theme: "ace/theme/textmate"
     });
+    editor.setValue(data, -1);
 </script>
 </body>
 </html>
diff --git a/config/plugins/visualizations/example/config/example.xml b/config/plugins/visualizations/example/config/example.xml
index cc2dd898fb7949bd5c3292d596391a4142c40528..7ebf2f643a12e90254a22614ac5ba78505db6c30 100644
--- a/config/plugins/visualizations/example/config/example.xml
+++ b/config/plugins/visualizations/example/config/example.xml
@@ -1,45 +1,33 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="Example" embeddable="false">
-    <description>This is a developer example which demonstrates how to implement and configure a basic d3-based plugin for charts.</description>
+<visualization name="Minimal Example" embeddable="false">
+    <description>Welcome to the Minimal JS-Based Example Plugin.</description>
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
             <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
-            <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.CSV</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js"/>
+    <entry_point entry_point_type="script" src="script.js" />
     <settings>
         <input>
-            <name>data_dialog</name>
-            <label>Some data selector</label>
-            <type>data_dialog</type>
-            <multiple>false</multiple>
+            <name>setting_input</name>
+            <help>setting help</help>
+            <type>setting_type</type>
         </input>
     </settings>
-    <groups>
+    <tracks>
         <input>
-            <name>x</name>
-            <label>Bubble x-position</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
+            <name>track_input</name>
+            <help>track help</help>
+            <type>track_type</type>
         </input>
-        <input>
-            <name>y</name>
-            <label>Bubbles y-position</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
-        </input>
-        <input>
-            <name>z</name>
-            <label>Bubble size</label>
-            <type>data_column</type>
-            <is_numeric>true</is_numeric>
-        </input>
-    </groups>
-</visualization>
\ No newline at end of file
+    </tracks>
+    <specs>
+        <spec_name>spec_value</spec_name>
+    </specs>
+</visualization>
diff --git a/config/plugins/visualizations/example/package.json b/config/plugins/visualizations/example/package.json
deleted file mode 100644
index 199cab67b0830246568b8f8d698fa710246caba3..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/example/package.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.2.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "@galaxyproject/charts": "^0.1.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "d3": "^4.12.2",
-        "jquery": "^3.1.1",
-        "underscore": "^1.8.3"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "2.11.0"
-    }
-}
diff --git a/config/plugins/visualizations/example/src/script.js b/config/plugins/visualizations/example/src/script.js
deleted file mode 100644
index 4fda38c2380df09d2a790466023210000823ccfc..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/example/src/script.js
+++ /dev/null
@@ -1,54 +0,0 @@
-import * as d3 from "d3";
-import * as _ from "underscore";
-import { request as requestDatasets } from "@galaxyproject/charts/lib/utilities/datasets";
-
-_.extend(window.bundleEntries || {}, {
-    load: function(options) {
-        var chart = options.chart;
-        var root = options.root;
-        requestDatasets({
-            root: root,
-            dataset_id: chart.get("dataset_id"),
-            dataset_groups: chart.groups,
-            success: function(groups) {
-                var colors = d3.scaleOrdinal(d3.schemeCategory20);
-                var error = null;
-                _.each(groups, function(group, group_index) {
-                    try {
-                        $("#" + options.target).append("<svg id='myexample'/>");
-                        var svg = d3.select("#myexample");
-                        var height = parseInt(svg.style("height"));
-                        var width = parseInt(svg.style("width"));
-                        var maxValue = d3.max(group.values, function(d) {
-                            return Math.max(d.x, d.y);
-                        });
-                        svg
-                            .selectAll("bubbles")
-                            .data(group.values)
-                            .enter()
-                            .append("circle")
-                            .attr("r", function(d) {
-                                return Math.abs(d.z) * 20 / maxValue;
-                            })
-                            .attr("cy", function(d, i) {
-                                return height * d.y / maxValue;
-                            })
-                            .attr("cx", function(d) {
-                                return width * d.x / maxValue;
-                            })
-                            .style("stroke", colors(group_index))
-                            .style("fill", "white");
-                    } catch (err) {
-                        error = err;
-                    }
-                });
-                if (error) {
-                    chart.state("failed", error);
-                } else {
-                    chart.state("ok", "Workshop chart has been drawn.");
-                }
-                options.process.resolve();
-            }
-        });
-    }
-});
diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
new file mode 100644
index 0000000000000000000000000000000000000000..262765a0150223cf099997da1925fec64dec90d9
--- /dev/null
+++ b/config/plugins/visualizations/example/static/script.js
@@ -0,0 +1,33 @@
+const { root, visualization_config, visualization_plugin } = JSON.parse(document.getElementById("app").dataset.incoming);
+
+const div = Object.assign(document.createElement("div"), {
+    style: "border: 2px solid #25537b; border-radius: 1rem; padding: 1rem"
+});
+
+const img = Object.assign(document.createElement("img"), {
+    src: root + visualization_plugin.logo,
+    style: "height: 3rem"
+});
+div.appendChild(img);
+
+Object.entries(visualization_plugin).forEach(([key, value]) => {
+    const row = document.createElement("div");
+    const spanKey = Object.assign(document.createElement("span"), {
+        innerText: `${key}: `,
+        style: "font-weight: bold"
+    });
+    const spanValue = Object.assign(document.createElement("span"), {
+        innerText: JSON.stringify(value)
+    });
+    row.appendChild(spanKey);
+    row.appendChild(spanValue);
+    div.appendChild(row);
+});
+
+const dataset = Object.assign(document.createElement("div"), {
+    innerText: `You have selected dataset: ${visualization_config.dataset_id}.`,
+    style: "font-weight: bold; padding-top: 1rem;"
+});
+div.appendChild(dataset);
+
+document.body.appendChild(div);
diff --git a/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml b/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4d67c16da013df531eb6641cb5989af38fe88c21
--- /dev/null
+++ b/config/plugins/visualizations/fits_graph_viewer/config/fits_graph_viewer.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="FITS Graph viewer" embeddable="false">
+    <description>Basic plugin for fits file table visualization</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">binary.FITS</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="script" src="fits_graph_viewer.js"/>
+</visualization>
diff --git a/config/plugins/visualizations/fits_graph_viewer/package.json b/config/plugins/visualizations/fits_graph_viewer/package.json
new file mode 100644
index 0000000000000000000000000000000000000000..94523876cb519eb26f313c7ebffa58ad16a93299
--- /dev/null
+++ b/config/plugins/visualizations/fits_graph_viewer/package.json
@@ -0,0 +1,21 @@
+{
+    "name": "fits-graph-visualization",
+    "version": "1.0.0",
+    "keywords": [
+        "galaxy",
+        "visualization"
+    ],
+    "main": "index.js",
+    "license": "AFL-3.0",
+    "dependencies": {
+        "astrovisjs": "0.9.92",
+        "webpack": "^5.94.0"
+    },
+    "devDependencies": {
+        "webpack-cli": "^5.1.4"
+    },
+    "scripts": {
+        "build": "npx webpack build --config webpack.prod.js --output-path=./static"
+    }
+}
+
diff --git a/config/plugins/visualizations/fits_graph_viewer/src/index.js b/config/plugins/visualizations/fits_graph_viewer/src/index.js
new file mode 100644
index 0000000000000000000000000000000000000000..87bf33349263383565d9b27462dc7b1743622d14
--- /dev/null
+++ b/config/plugins/visualizations/fits_graph_viewer/src/index.js
@@ -0,0 +1,13 @@
+import {init} from 'astrovisjs/dist/astrovis/astrovis';
+
+document.addEventListener('DOMContentLoaded', () => {
+
+    const {root, visualization_config} = JSON.parse(
+        document.getElementById("app")
+            .getAttribute("data-incoming") || "{}");
+
+    const dataset_id = visualization_config.dataset_id;
+    const file_url = root + "datasets/" + dataset_id + "/display"
+
+    init('app', file_url);
+});
\ No newline at end of file
diff --git a/config/plugins/visualizations/fits_graph_viewer/static/fits_graph_viewer.js b/config/plugins/visualizations/fits_graph_viewer/static/fits_graph_viewer.js
new file mode 100644
index 0000000000000000000000000000000000000000..551b2600a23172e4f5c800e28368e116fbe60710
--- /dev/null
+++ b/config/plugins/visualizations/fits_graph_viewer/static/fits_graph_viewer.js
@@ -0,0 +1 @@
+(()=>{var __webpack_modules__={449:function(module){var e;e=()=>(()=>{var __webpack_modules__={8157:function(t,e){!function(t){"use strict";function e(t,e){return null==t||null==e?NaN:t<e?-1:t>e?1:t>=e?0:NaN}function n(t,e){return null==t||null==e?NaN:e<t?-1:e>t?1:e>=t?0:NaN}function r(t){let r,o,a;function s(t,e,n=0,i=t.length){if(n<i){if(0!==r(e,e))return i;do{const r=n+i>>>1;o(t[r],e)<0?n=r+1:i=r}while(n<i)}return n}return 2!==t.length?(r=e,o=(n,r)=>e(t(n),r),a=(e,n)=>t(e)-n):(r=t===e||t===n?t:i,o=t,a=t),{left:s,center:function(t,e,n=0,r=t.length){const i=s(t,e,n,r-1);return i>n&&a(t[i-1],e)>-a(t[i],e)?i-1:i},right:function(t,e,n=0,i=t.length){if(n<i){if(0!==r(e,e))return i;do{const r=n+i>>>1;o(t[r],e)<=0?n=r+1:i=r}while(n<i)}return n}}}function i(){return 0}function o(t){return null===t?NaN:+t}const a=r(e),s=a.right,l=a.left,c=r(o).center;var u=s;const d=p(T),h=p((function(t){const 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r{constructor(t,e){this.glyph=e,this.nvertices=0,this.size_changed=!1,this.data_changed=!1,this.visuals_changed=!1,this.regl_wrapper=t}set_data_changed(){const{data_size:t}=this.glyph;t!=this.nvertices&&(this.nvertices=t,this.size_changed=!0),this.data_changed=!0}set_visuals_changed(){this.visuals_changed=!0}render(t,e,n){if(0==e.length)return!0;const{width:r,height:i}=this.glyph.renderer.plot_view.canvas_view.webgl.canvas,o={pixel_ratio:this.glyph.renderer.plot_view.canvas_view.pixel_ratio,width:r,height:i};return this.draw(e,n,o),!0}}r.__name__="BaseGLGlyph"},7649:(t,e,n)=>{"use strict";n.d(e,{V:()=>l});var r=n(8192),i=n(9863),o=n(3202),a=n(7555),s=n(3764);class l extends r.z{constructor(t,e){super(t,e),this.glyph=e,this._antialias=1.5,this._miter_limit=5}_draw_impl(t,e,n){this.visuals_changed&&(this._set_visuals(),this.visuals_changed=!1),n.data_changed&&(n._set_data(),n.data_changed=!1);const 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e=isFinite(t[2*i+2])&&isFinite(t[2*i+3]);n[i]=r&&e?1:0,r=e}if(this._is_closed?(n[0]=n[e-1],n[e]=n[1]):(n[0]=0,n[e]=0),this._show.update(),this._is_dashed()){const r=e-1;null==this._length_so_far&&(this._length_so_far=new i.iz(this.regl_wrapper));const o=this._length_so_far.get_sized_array(r);let a=0;for(let e=0;e<r;e++)o[e]=a,1==n[e+1]&&(a+=Math.sqrt((t[2*e+4]-t[2*e+2])**2+(t[2*e+5]-t[2*e+3])**2));this._length_so_far.update()}}_set_visuals(){const t=this._get_visuals().line,e=(0,a.qG)(t.line_color.value,t.line_alpha.value);this._color=e.map((t=>t/255)),this._linewidth=t.line_width.value,this._linewidth<1&&(this._color[3]*=this._linewidth,this._linewidth=1),this._line_dash=(0,s.b_)(t.line_dash.value),this._is_dashed()&&([this._dash_tex_info,this._dash_tex,this._dash_scale]=this.regl_wrapper.get_dash(this._line_dash),this._dash_offset=t.line_dash_offset.value)}}l.__name__="BaseLineGL"},9329:(t,e,n)=>{"use strict";n.d(e,{x:()=>a});var r=n(8192),i=n(9863),o=n(3202);class a extends r.z{constructor(t,e){super(t,e),this.glyph=e,this._antialias=1.5,this._show_all=!1}_draw_one_marker_type(t,e,n){const r={scissor:this.regl_wrapper.scissor,viewport:this.regl_wrapper.viewport,canvas_size:[e.width,e.height],pixel_ratio:e.pixel_ratio,center:n._centers,width:n._widths,height:n._heights,angle:n._angles,size_hint:(0,o.uw)(t),nmarkers:n.nvertices,antialias:this._antialias,linewidth:this._linewidths,line_color:this._line_rgba,fill_color:this._fill_rgba,line_cap:this._line_caps,line_join:this._line_joins,show:this._show};if(this._have_hatch){const e={...r,hatch_pattern:this._hatch_patterns,hatch_scale:this._hatch_scales,hatch_weight:this._hatch_weights,hatch_color:this._hatch_rgba};this.regl_wrapper.marker_hatch(t)(e)}else this.regl_wrapper.marker_no_hatch(t)(r)}_set_visuals(){const t=this._get_visuals(),e=t.fill,n=t.line;if(null==this._linewidths&&(this._linewidths=new i.iz(this.regl_wrapper),this._line_caps=new i.Lv(this.regl_wrapper),this._line_joins=new i.Lv(this.regl_wrapper),this._line_rgba=new i.S7(this.regl_wrapper),this._fill_rgba=new i.S7(this.regl_wrapper)),this._linewidths.set_from_prop(n.line_width),this._line_caps.set_from_line_cap(n.line_cap),this._line_joins.set_from_line_join(n.line_join),this._line_rgba.set_from_color(n.line_color,n.line_alpha),this._fill_rgba.set_from_color(e.fill_color,e.fill_alpha),this._have_hatch=t.hatch.doit,this._have_hatch){const e=t.hatch;null==this._hatch_patterns&&(this._hatch_patterns=new i.Lv(this.regl_wrapper),this._hatch_scales=new i.iz(this.regl_wrapper),this._hatch_weights=new i.iz(this.regl_wrapper),this._hatch_rgba=new i.S7(this.regl_wrapper)),this._hatch_patterns.set_from_hatch_pattern(e.hatch_pattern),this._hatch_scales.set_from_prop(e.hatch_scale),this._hatch_weights.set_from_prop(e.hatch_weight),this._hatch_rgba.set_from_color(e.hatch_color,e.hatch_alpha)}}}a.__name__="BaseMarkerGL",a.missing_point=-1e4},9863:(t,e,n)=>{"use strict";n.d(e,{Lv:()=>s,S7:()=>l,iz:()=>a});var r=n(3202),i=n(7555);class o{constructor(t){this.regl_wrapper=t,this.is_scalar=!0}get_sized_array(t){return null!=this.array&&this.array.length==t||(this.array=this.new_array(t)),this.array}is_normalized(){return!1}get length(){return null!=this.array?this.array.length:0}set_from_array(t){const e=t.length,n=this.get_sized_array(e);for(let r=0;r<e;r++)n[r]=t[r];this.update()}set_from_prop(t,e=4){const n=t.is_Scalar()?e:t.length,r=this.get_sized_array(n);for(let e=0;e<n;e++)r[e]=t.get(e);this.update(t.is_Scalar())}set_from_scalar(t,e=4){this.get_sized_array(e).fill(t),this.update(!0)}to_attribute_config(t=0){return{buffer:this.buffer,divisor:this.is_scalar?0:1,normalized:this.is_normalized(),offset:t}}update(t=!1){null==this.buffer?this.buffer=this.regl_wrapper.buffer({usage:"dynamic",data:this.array}):this.buffer({data:this.array}),this.is_scalar=t}}o.__name__="WrappedBuffer";class a extends o{new_array(t){return new Float32Array(t)}}a.__name__="Float32Buffer";class s extends o{new_array(t){return new Uint8Array(t)}set_from_color(t,e,n=4){const r=t.is_Scalar()&&e.is_Scalar(),o=r?n:t.length,a=this.get_sized_array(4*o);for(let n=0;n<o;n++){const[r,o,s,l]=(0,i.qG)(t.get(n),e.get(n));a[4*n]=r,a[4*n+1]=o,a[4*n+2]=s,a[4*n+3]=l}this.update(r)}set_from_hatch_pattern(t,e=4){const n=t.is_Scalar()?e:t.length,i=this.get_sized_array(n);for(let e=0;e<n;e++)i[e]=(0,r.j2)(t.get(e));this.update(t.is_Scalar())}set_from_line_cap(t,e=4){const n=t.is_Scalar()?e:t.length,i=this.get_sized_array(n);for(let e=0;e<n;e++)i[e]=r.iD[t.get(e)];this.update(t.is_Scalar())}set_from_line_join(t,e=4){const n=t.is_Scalar()?e:t.length,i=this.get_sized_array(n);for(let e=0;e<n;e++)i[e]=r.sN[t.get(e)];this.update(t.is_Scalar())}}s.__name__="Uint8Buffer";class l extends s{is_normalized(){return!0}}l.__name__="NormalizedUint8Buffer"},1457:(t,e,n)=>{"use strict";n.d(e,{CircleGL:()=>o});var r=n(9863),i=n(194);class o extends i.k{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph,"circle")}_get_visuals(){return this.glyph.visuals}_set_data(){const t=this.nvertices;null==this._centers&&(this._centers=new r.iz(this.regl_wrapper),this._widths=new r.iz(this.regl_wrapper),this._heights=this._widths,this._angles=new r.iz(this.regl_wrapper));const e=this._centers.get_sized_array(2*t),n=this._widths.get_sized_array(t);for(let r=0;r<t;r++)isFinite(this.glyph.sx[r])&&isFinite(this.glyph.sy[r])?(e[2*r]=this.glyph.sx[r],e[2*r+1]=this.glyph.sy[r]):(e[2*r]=i.k.missing_point,e[2*r+1]=i.k.missing_point),n[r]=2*this.glyph.sradius[r];this._centers.update(),this._widths.update(),this._angles.set_from_prop(this.glyph.angle)}}o.__name__="CircleGL"},2619:(t,e,n)=>{"use strict";n.d(e,{HexTileGL:()=>o});var r=n(9863),i=n(194);class o extends i.k{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph,"hex")}_get_visuals(){return this.glyph.visuals}_set_data(){const t=this.nvertices;null==this._centers&&(this._centers=new r.iz(this.regl_wrapper),this._widths=new r.iz(this.regl_wrapper),this._heights=new r.iz(this.regl_wrapper),this._angles=new r.iz(this.regl_wrapper));const e=this._centers.get_sized_array(2*t);for(let n=0;n<t;n++)isFinite(this.glyph.sx[n])&&isFinite(this.glyph.sy[n])?(e[2*n]=this.glyph.sx[n],e[2*n+1]=this.glyph.sy[n]):(e[2*n]=i.k.missing_point,e[2*n+1]=i.k.missing_point);this._centers.update(),"pointytop"==this.glyph.model.orientation?(this._angles.set_from_scalar(.5*Math.PI),this._widths.set_from_scalar(2*this.glyph.svy[0]),this._heights.set_from_scalar(4*this.glyph.svx[4]/Math.sqrt(3))):(this._angles.set_from_scalar(0),this._widths.set_from_scalar(2*this.glyph.svx[0]),this._heights.set_from_scalar(4*this.glyph.svy[4]/Math.sqrt(3)))}}o.__name__="HexTileGL"},4237:(t,e,n)=>{"use strict";n.r(e),n.d(e,{BaseLineGL:()=>m.V,BaseMarkerGL:()=>g.x,CircleGL:()=>_.CircleGL,HexTileGL:()=>b.HexTileGL,LRTBGL:()=>y.LRTBGL,LineGL:()=>v.LineGL,MultiMarkerGL:()=>x.MultiMarkerGL,RectGL:()=>w.RectGL,SingleMarkerGL:()=>L.k,StepGL:()=>A.StepGL,get_regl:()=>Q});var r=n(364),i=n.n(r);function o(t,e){let n,r;t>e?(n=t,r=e):(n=e,r=t);let i=n%r;for(;0!=i;)n=r,r=i,i=n%r;return r}function a(t){let e=t[0];for(let n=1;n<t.length;n++)e=o(e,t[n]);return e}var s=n(4042),l=n(4218);class c{constructor(t){this._regl=t,this._map=new Map}_create_texture(t){const e=t.length;let n=0;const r=[];let i=0,o=0;for(let a=0;a<e;a++)n+=t[a],r.push(t[a]+t[(a+1)%e]),a%2==0?o=Math.max(o,t[a]):i=Math.min(i,-t[a]);i*=.5,o*=.5;const s=a(r),l=[0];for(let n=0;n<e;n++)l.push(l[n]+t[n]);const c=2*n/s,u=!((d=c)&d-1||!d);var d;const h=u?c:128,p=.5*s*c/h;let f;u?(f=.5*t[0],p<f&&(f-=Math.floor(f/p)*p)):f=0;const Q=f-.5*p,T=new Uint8Array(h);let m=0;for(let e=0;e<h;e++){const n=f+e*p;n>l[m+1]&&m++;const r=t[m],a=l[m]+.5*r;let s=.5*r-Math.abs(n-a);m%2==1&&(s=-s),T[e]=Math.round(255*(s-i)/(o-i))}return[[n,Q,i,o],this._regl.texture({shape:[h,1,1],data:T,wrapS:"repeat",format:"alpha",type:"uint8",mag:"linear",min:"linear"})]}_get_key(t){return t.join(",")}_get_or_create(t){const e=this._get_key(t);let n=this._map.get(e);if(null==n){const r=a(t);if(r>1){t=(0,l.Tj)(t,(t=>t/r)),n=this._get_or_create(t);const[i,o,a]=n;n=[i,o,r],this._map.set(e,n)}else{const[i,o]=this._create_texture(t);n=[i,o,r],this._map.set(e,n)}}return n}get(t){return t.length%2==1&&(t=(0,s.xW)([t,t])),this._get_or_create(t)}}c.__name__="DashCache";const u="\nprecision mediump float;\n\nconst int butt_cap   = 0;\nconst int round_cap  = 1;\nconst int square_cap = 2;\n\nconst int miter_join = 0;\nconst int round_join = 1;\nconst int bevel_join = 2;\n\nattribute vec2 a_position;\nattribute vec2 a_point_prev;\nattribute vec2 a_point_start;\nattribute vec2 a_point_end;\nattribute vec2 a_point_next;\nattribute float a_show_prev;\nattribute float a_show_curr;\nattribute float a_show_next;\n#ifdef DASHED\nattribute float a_length_so_far;\n#endif\n\nuniform float u_pixel_ratio;\nuniform vec2 u_canvas_size;\nuniform float u_linewidth;\nuniform float u_antialias;\nuniform float u_line_join;\nuniform float u_line_cap;\nuniform float u_miter_limit;\n\nvarying float v_segment_length;\nvarying vec2 v_coords;\nvarying float v_flags;  // Booleans for start/end caps and miters too long.\nvarying float v_cos_theta_turn_right_start;  // Sign gives turn_right, abs gives\nvarying float v_cos_theta_turn_right_end;    //   cos(theta).\n#ifdef DASHED\nvarying float v_length_so_far;\n#endif\n\nfloat cross_z(in vec2 v0, in vec2 v1)\n{\n    return v0.x*v1.y - v0.y*v1.x;\n}\n\nvec2 right_vector(in vec2 v)\n{\n    return vec2(v.y, -v.x);\n}\n\nvec2 line_intersection(in vec2 point0, in vec2 dir0,\n                       in vec2 point1, in vec2 dir1)\n{\n    // Line-line intersection: point0 + lambda0 dir0 = point1 + lambda1 dir1.\n    // Not checking if lines are parallel!\n    float lambda0 = cross_z(point1 - point0, dir1) / cross_z(dir0, dir1);\n    return point0 + lambda0*dir0;\n}\n\nfloat sign_no_zero(in float x)\n{\n    return x >= 0.0 ? 1.0 : -1.0;\n}\n\nvoid main()\n{\n    if (a_show_curr < 0.5) {\n        // Line segment has non-finite value at one or both ends, do not render.\n        gl_Position = vec4(-2.0, -2.0, 0.0, 1.0);\n        return;\n    }\n\n    const float min_miter_factor_round_join_mesh = sqrt(2.0);\n\n    int join_type = int(u_line_join + 0.5);\n    int cap_type = int(u_line_cap + 0.5);\n    float halfwidth = 0.5*(u_linewidth + u_antialias);\n    vec2 segment_along = normalize(a_point_end - a_point_start); // unit vector.\n    v_segment_length = length(a_point_end - a_point_start);\n    vec2 segment_right = right_vector(segment_along);  // unit vector.\n    vec2 xy;\n\n    bool miter_too_large_start = false;\n    bool miter_too_large_end = false;\n\n    v_coords.y = a_position.y*halfwidth;  // Overwritten later for end points.\n\n    bool has_start_cap = a_show_prev < 0.5;\n    bool has_end_cap = a_show_next < 0.5;\n\n    vec2 point_normal_start;\n    float cos_theta_start;\n    float turn_right_start;\n    if (has_start_cap)\n        point_normal_start = segment_right;\n    else {\n        vec2 prev_right = right_vector(normalize(a_point_start - a_point_prev));\n        point_normal_start = normalize(segment_right + prev_right);\n        cos_theta_start = dot(segment_right, point_normal_start);  // Always +ve\n        turn_right_start = sign_no_zero(dot(segment_right, a_point_prev - a_point_start));\n    }\n\n    vec2 point_normal_end;\n    float cos_theta_end;\n    float turn_right_end;\n    if (has_end_cap)\n        point_normal_end = segment_right;\n    else {\n        vec2 next_right = right_vector(normalize(a_point_next - a_point_end));\n        point_normal_end = normalize(segment_right + next_right);\n        cos_theta_end = dot(segment_right, point_normal_end);  // Always +ve\n        turn_right_end = sign_no_zero(dot(segment_right, a_point_next - a_point_end));\n    }\n\n    float miter_factor_start = 1.0 / dot(segment_right, point_normal_start);\n    float miter_factor_end = 1.0 / dot(segment_right, point_normal_end);\n    if (join_type == miter_join) {\n        // If miter too large, use bevel join instead.\n        miter_too_large_start = (miter_factor_start > u_miter_limit);\n        miter_too_large_end = (miter_factor_end > u_miter_limit);\n    }\n\n    float sign_at_start = -sign(a_position.x);  // +ve at segment start, -ve end.\n    vec2 point = sign_at_start > 0.0 ? a_point_start : a_point_end;\n    vec2 adjacent_point =\n        sign_at_start > 0.0 ? (has_start_cap ? a_point_start : a_point_prev)\n                            : (has_end_cap ? a_point_end : a_point_next);\n\n    if ( (has_start_cap && sign_at_start > 0.0) ||\n         (has_end_cap && sign_at_start < 0.0) ) {\n        // Cap.\n        xy = point - segment_right*(halfwidth*a_position.y);\n        if (cap_type == butt_cap)\n            xy -= sign_at_start*0.5*u_antialias*segment_along;\n        else\n            xy -= sign_at_start*halfwidth*segment_along;\n    }\n    else { // Join.\n        // +ve if turning to right, -ve if to left.\n        float turn_sign = sign_at_start > 0.0 ? turn_right_start : turn_right_end;\n\n        vec2 adjacent_right = sign_at_start*normalize(right_vector(point - adjacent_point));\n        vec2 point_right = normalize(segment_right + adjacent_right);\n        float miter_factor = sign_at_start > 0.0 ? miter_factor_start : miter_factor_end;\n        bool miter_too_large = sign_at_start > 0.0 ? miter_too_large_start : miter_too_large_end;\n\n        if (abs(a_position.x) > 1.5) {\n            // Outer point, meets prev/next segment.\n            float factor;  // multiplied by halfwidth...\n\n            if (join_type == bevel_join || (join_type == miter_join && miter_too_large))\n                factor = 1.0 / miter_factor;  // cos_theta.\n            else if (join_type == round_join &&\n                     miter_factor > min_miter_factor_round_join_mesh)\n                factor = 1.0;\n            else  // miter, or round (small angle only).\n                factor = miter_factor;\n\n            xy = point - point_right*(halfwidth*turn_sign*factor);\n            v_coords.y = turn_sign*halfwidth*factor / miter_factor;\n        }\n        else if (turn_sign*a_position.y < 0.0) {\n            // Inner point, meets prev/next segment.\n            float len = halfwidth*miter_factor;\n            float segment_len = v_segment_length;\n            float adjacent_len = distance(point, adjacent_point);\n\n            if (len <= min(segment_len, adjacent_len))\n                // Normal behaviour.\n                xy = point - point_right*(len*a_position.y);\n            else\n                // For short wide line segments the inner point using the above\n                // calculation can be outside of the line.  Here clipping it.\n                xy = point + segment_right*(halfwidth*turn_sign);\n        }\n        else {\n            // Point along outside edge.\n            xy = point - segment_right*(halfwidth*a_position.y);\n            if (join_type == round_join &&\n                miter_factor > min_miter_factor_round_join_mesh) {\n                xy = line_intersection(xy, segment_along,\n                                       point - turn_sign*point_right*halfwidth,\n                                       right_vector(point_right));\n            }\n        }\n    }\n\n    vec2 pos = xy + 0.5;  // Bokeh's offset.\n    pos /= u_canvas_size / u_pixel_ratio;  // in 0..1\n    gl_Position = vec4(2.0*pos.x - 1.0, 1.0 - 2.0*pos.y, 0.0, 1.0);\n\n    v_coords.x = dot(xy - a_point_start, segment_along);\n    v_flags = float(int(has_start_cap) +\n                    2*int(has_end_cap) +\n                    4*int(miter_too_large_start) +\n                    8*int(miter_too_large_end));\n    v_cos_theta_turn_right_start = cos_theta_start*turn_right_start;\n    v_cos_theta_turn_right_end = cos_theta_end*turn_right_end;\n\n#ifdef DASHED\n    v_length_so_far = a_length_so_far;\n#endif\n}\n",d="\nprecision mediump float;\n\nconst int butt_cap   = 0;\nconst int round_cap  = 1;\nconst int square_cap = 2;\n\nconst int miter_join = 0;\nconst int round_join = 1;\nconst int bevel_join = 2;\n\nuniform float u_linewidth;\nuniform float u_antialias;\nuniform float u_line_join;\nuniform float u_line_cap;\nuniform vec4 u_line_color;\n#ifdef DASHED\nuniform sampler2D u_dash_tex;\nuniform vec4 u_dash_tex_info;\nuniform float u_dash_scale;\nuniform float u_dash_offset;\n#endif\n\nvarying float v_segment_length;\nvarying vec2 v_coords;\nvarying float v_flags;\nvarying float v_cos_theta_turn_right_start;\nvarying float v_cos_theta_turn_right_end;\n#ifdef DASHED\nvarying float v_length_so_far;\n#endif\n\nfloat cross_z(in vec2 v0, in vec2 v1)\n{\n    return v0.x*v1.y - v0.y*v1.x;\n}\n\nfloat point_line_side(in vec2 point, in vec2 start, in vec2 end)\n{\n    // +ve if point to right of line.\n    // Alternatively could do dot product with right_vector.\n    return cross_z(point - start, end - start);\n}\n\nfloat point_line_distance(in vec2 point, in vec2 start, in vec2 end)\n{\n    return point_line_side(point, start, end) / distance(start, end);\n}\n\nvec2 right_vector(in vec2 v)\n{\n    return vec2(v.y, -v.x);\n}\n\nfloat bevel_join_distance(in float sign_start, in float halfwidth)\n{\n    float cos_theta_turn_right = sign_start > 0.0 ? v_cos_theta_turn_right_start\n                                                  : v_cos_theta_turn_right_end;\n    float cos_theta = abs(cos_theta_turn_right);\n    float turn_right = sign(cos_theta_turn_right);\n    float distance_along = sign_start > 0.0 ? 0.0 : v_segment_length;\n\n    // In v_coords reference frame (x is along segment, y across).\n    vec2 line_start = vec2(distance_along, halfwidth*turn_right);\n    float sin_alpha = cos_theta;\n    float cos_alpha = sqrt(1.0 - sin_alpha*sin_alpha);\n    vec2 line_along = vec2(-sign_start*turn_right*sin_alpha, -cos_alpha);\n\n    return halfwidth + sign_start*point_line_distance(\n        v_coords, line_start, line_start+line_along);\n}\n\nfloat cap(in int cap_type, in float x, in float y)\n{\n    // x is distance along segment in direction away from end of segment,\n    // y is distance across segment.\n    if (cap_type == butt_cap)\n        return max(0.5*u_linewidth - x, abs(y));\n    else if (cap_type == square_cap)\n        return max(-x, abs(y));\n    else  // cap_type == round_cap\n        return distance(vec2(min(x, 0.0), y), vec2(0.0, 0.0));\n}\n\nfloat distance_to_alpha(in float dist)\n{\n    return 1.0 - smoothstep(0.5*(u_linewidth - u_antialias),\n                            0.5*(u_linewidth + u_antialias), dist);\n}\n\n#ifdef DASHED\nfloat dash_distance(in float x)\n{\n    // x is in direction of v_coords.x, i.e. along segment.\n    float tex_length = u_dash_tex_info.x;\n    float tex_offset = u_dash_tex_info.y;\n    float tex_dist_min = u_dash_tex_info.z;\n    float tex_dist_max = u_dash_tex_info.w;\n\n    // Apply offset.\n    x += v_length_so_far - u_dash_scale*tex_offset + u_dash_offset;\n\n    // Interpolate within texture to obtain distance to dash.\n    float dist = texture2D(u_dash_tex,\n                           vec2(x / (tex_length*u_dash_scale), 0.0)).a;\n\n    // Scale distance within min and max limits.\n    dist = tex_dist_min + dist*(tex_dist_max - tex_dist_min);\n\n    return u_dash_scale*dist;\n}\n\nfloat clip_dash_distance(in float x, in float offset, in float sign_along)\n{\n    // Return clipped dash distance, sign_along is +1.0 if looking forward\n    // into next segment and -1.0 if looking backward into previous segment.\n    float half_antialias = 0.5*u_antialias;\n\n    if (sign_along*x > half_antialias) {\n        // Outside antialias region, use usual dash distance.\n        return dash_distance(offset + x);\n    }\n    else {\n        // Inside antialias region.\n        // Dash distance at edge of antialias region clipped to half_antialias.\n        float edge_dist = min(dash_distance(offset + sign_along*half_antialias), half_antialias);\n\n        // Physical distance from dash distance at edge of antialias region.\n        return edge_dist + sign_along*x - half_antialias;\n    }\n}\n\nmat2 rotation_matrix(in float sign_start)\n{\n    // Rotation matrix for v_coords from this segment to prev or next segment.\n    float cos_theta_turn_right = sign_start > 0.0 ? v_cos_theta_turn_right_start\n                                                  : v_cos_theta_turn_right_end;\n    float cos_theta = abs(cos_theta_turn_right);\n    float turn_right = sign(cos_theta_turn_right);\n\n    float sin_theta = sqrt(1.0 - cos_theta*cos_theta)*sign_start*turn_right;\n    float cos_2theta = 2.0*cos_theta*cos_theta - 1.0;\n    float sin_2theta = 2.0*sin_theta*cos_theta;\n    return mat2(cos_2theta, -sin_2theta, sin_2theta, cos_2theta);\n}\n#endif\n\nvoid main()\n{\n    int join_type = int(u_line_join + 0.5);\n    int cap_type = int(u_line_cap + 0.5);\n    float halfwidth = 0.5*(u_linewidth + u_antialias);\n    float half_antialias = 0.5*u_antialias;\n\n    // Extract flags.\n    int flags = int(v_flags + 0.5);\n    bool miter_too_large_end = (flags / 8 > 0);\n    flags -= 8*int(miter_too_large_end);\n    bool miter_too_large_start = (flags / 4 > 0);\n    flags -= 4*int(miter_too_large_start);\n    bool has_end_cap = (flags / 2 > 0);\n    flags -= 2*int(has_end_cap);\n    bool has_start_cap = flags > 0;\n\n    float dist = v_coords.y;  // For straight segment, and miter join.\n\n    // Along-segment coords with respect to end of segment, +ve inside segment\n    // so equivalent to v_coords.x at start of segment.\n    float end_coords_x = v_segment_length - v_coords.x;\n\n    if (v_coords.x <= half_antialias) {\n        // At start of segment, either cap or join.\n        if (has_start_cap)\n            dist = cap(cap_type, v_coords.x, v_coords.y);\n        else if (join_type == round_join)\n            dist = distance(v_coords, vec2(0.0, 0.0));\n        else if (join_type == bevel_join ||\n                 (join_type == miter_join && miter_too_large_start))\n            dist = max(abs(dist), bevel_join_distance(1.0, halfwidth));\n        // else a miter join which uses the default dist calculation.\n    }\n    else if (end_coords_x <= half_antialias) {\n        // At end of segment, either cap or join.\n        if (has_end_cap)\n            dist = cap(cap_type, end_coords_x, v_coords.y);\n        else if (join_type == round_join)\n            dist = distance(v_coords, vec2(v_segment_length, 0));\n        else if ((join_type == bevel_join ||\n                 (join_type == miter_join && miter_too_large_end)))\n            dist = max(abs(dist), bevel_join_distance(-1.0, halfwidth));\n        // else a miter join which uses the default dist calculation.\n    }\n\n    float alpha = distance_to_alpha(abs(dist));\n\n#ifdef DASHED\n    if (u_dash_tex_info.x >= 0.0) {\n        // Dashes in straight segments (outside of joins) are easily calculated.\n        dist = dash_distance(v_coords.x);\n\n        if (!has_start_cap && cap_type == butt_cap) {\n            if (v_coords.x < half_antialias) {\n                // Outer of start join rendered solid color or not at all\n                // depending on whether corner point is in dash or gap, with\n                // antialiased ends.\n                if (dash_distance(0.0) > 0.0) {\n                    // Corner is solid color.\n                    dist = max(dist, min(half_antialias, -v_coords.x));\n                    // Avoid visible antialiasing band between corner and dash.\n                    dist = max(dist, dash_distance(half_antialias));\n                }\n                else {\n                    // Use large negative value so corner not colored.\n                    dist = -halfwidth;\n\n                    if (v_coords.x > -half_antialias) {\n                        // Consider antialias region of dash after start region.\n                        float edge_dist = min(dash_distance(half_antialias), half_antialias);\n                        dist = max(dist, edge_dist + v_coords.x - half_antialias);\n                    }\n                }\n            }\n\n            vec2 prev_coords = rotation_matrix(1.0)*v_coords;\n\n            if (abs(prev_coords.y) < halfwidth && prev_coords.x < half_antialias) {\n                // Extend dashes across from end of previous segment, with antialiased end.\n                float new_dist = clip_dash_distance(prev_coords.x, 0.0, -1.0);\n                new_dist = min(new_dist, 0.5*u_linewidth - abs(prev_coords.y));\n                dist = max(dist, new_dist);\n            }\n        }\n\n        if (!has_end_cap && cap_type == butt_cap) {\n            if (end_coords_x < half_antialias) {\n                // Similar for end join.\n                if (dash_distance(v_segment_length) > 0.0) {\n                    // Corner is solid color.\n                    dist = max(dist, min(half_antialias, -end_coords_x));\n                    // Avoid visible antialiasing band between corner and dash.\n                    dist = max(dist, dash_distance(v_segment_length - half_antialias));\n                }\n                else {\n                    // Use large negative value so corner not colored.\n                    dist = -halfwidth;\n\n                    if (end_coords_x > -half_antialias) {\n                        // Consider antialias region of dash before end region.\n                        float edge_dist = min(dash_distance(v_segment_length - half_antialias),\n                                              half_antialias);\n                        dist = max(dist, edge_dist + end_coords_x - half_antialias);\n                    }\n                }\n            }\n\n            vec2 next_coords = rotation_matrix(-1.0)*(v_coords - vec2(v_segment_length, 0.0));\n\n            if (abs(next_coords.y) < halfwidth && next_coords.x > -half_antialias) {\n                // Extend dashes across from next segment, with antialiased end.\n                float new_dist = clip_dash_distance(next_coords.x, v_segment_length, 1.0);\n                new_dist = min(new_dist, 0.5*u_linewidth - abs(next_coords.y));\n                dist = max(dist, new_dist);\n            }\n        }\n\n        dist = cap(cap_type, dist, v_coords.y);\n\n        float dash_alpha = distance_to_alpha(dist);\n        alpha = min(alpha, dash_alpha);\n    }\n#endif\n\n    alpha = u_line_color.a*alpha;\n    gl_FragColor = vec4(u_line_color.rgb*alpha, alpha);  // Premultiplied alpha.\n}\n",h="\nprecision mediump float;\n\nattribute vec2 a_position;\nattribute vec2 a_center;\nattribute float a_width;\nattribute float a_height;\nattribute float a_angle; // In radians\nattribute float a_linewidth;\nattribute vec4 a_line_color;\nattribute vec4 a_fill_color;\nattribute float a_line_cap;\nattribute float a_line_join;\nattribute float a_show;\n#ifdef HATCH\nattribute float a_hatch_pattern;\nattribute float a_hatch_scale;\nattribute float a_hatch_weight;\nattribute vec4 a_hatch_color;\n#endif\n\nuniform float u_pixel_ratio;\nuniform vec2 u_canvas_size;\nuniform float u_antialias;\nuniform float u_size_hint;\n\nvarying float v_linewidth;\nvarying vec2 v_size; // 2D size for rects compared to 1D for markers.\nvarying vec4 v_line_color;\nvarying vec4 v_fill_color;\nvarying float v_line_cap;\nvarying float v_line_join;\nvarying vec2 v_coords;\n#ifdef HATCH\nvarying float v_hatch_pattern;\nvarying float v_hatch_scale;\nvarying float v_hatch_weight;\nvarying vec4 v_hatch_color;\nvarying vec2 v_hatch_coords;\n#endif\n\nvoid main()\n{\n  if (a_show < 0.5 || a_width <= 0.0 || a_height <= 0.0) {\n    // Do not show this rect.\n    gl_Position = vec4(-2.0, -2.0, 0.0, 1.0);\n    return;\n  }\n\n  v_size = vec2(a_width, a_height);\n  v_linewidth = a_linewidth;\n  v_line_color = a_line_color;\n  v_fill_color = a_fill_color;\n  v_line_cap = a_line_cap;\n  v_line_join = a_line_join;\n\n  if (v_linewidth < 1.0) {\n    // Linewidth less than 1 is implemented as 1 but with reduced alpha.\n    v_line_color.a *= v_linewidth;\n    v_linewidth = 1.0;\n  }\n\n#ifdef HATCH\n  v_hatch_pattern = a_hatch_pattern;\n  v_hatch_scale = a_hatch_scale;\n  v_hatch_weight = a_hatch_weight;\n  v_hatch_color = a_hatch_color;\n#endif\n\n  vec2 enclosing_size;\n  // Need extra size of (v_linewidth+u_antialias) if edge of marker parallel to\n  // edge of bounding box.  If symmetric spike towards edge then multiply by\n  // 1/cos(theta) where theta is angle between spike and bbox edges.\n  int size_hint = int(u_size_hint + 0.5);\n  if (size_hint == 1)  // Dash\n    enclosing_size = vec2(v_size.x + v_linewidth + u_antialias,\n                          v_linewidth + u_antialias);\n  else if (size_hint == 2)  // Dot\n    enclosing_size = 0.25*v_size + u_antialias;\n  else if (size_hint == 3)  // Diamond\n    enclosing_size = vec2(v_size.x*(2.0/3.0) + (v_linewidth + u_antialias)*1.20185,\n                          v_size.y + (v_linewidth + u_antialias)*1.80278);\n  else if (size_hint == 4)  // Hex\n    enclosing_size = v_size + (v_linewidth + u_antialias)*vec2(2.0/sqrt(3.0), 1.0);\n  else if (size_hint == 5)  // Square pin\n    enclosing_size = v_size + (v_linewidth + u_antialias)*3.1;\n  else if (size_hint == 6)  // Triangle\n    enclosing_size = vec2(v_size.x + (v_linewidth + u_antialias)*sqrt(3.0),\n                          v_size.y*(2.0/sqrt(3.0)) + (v_linewidth + u_antialias)*2.0);\n  else if (size_hint == 7)  // Triangle pin\n    enclosing_size = v_size + (v_linewidth + u_antialias)*vec2(4.8, 6.0);\n  else if (size_hint == 8)  // Star\n    enclosing_size = vec2(v_size.x*0.95106 + (v_linewidth + u_antialias)*3.0,\n                          v_size.y + (v_linewidth + u_antialias)*3.2);\n  else\n    enclosing_size = v_size + v_linewidth + u_antialias;\n\n  // Coordinates in rotated frame with respect to center of marker, used for\n  // distance functions in fragment shader.\n  v_coords = a_position*enclosing_size;\n\n  float c = cos(-a_angle);\n  float s = sin(-a_angle);\n  mat2 rotation = mat2(c, -s, s, c);\n\n  vec2 pos = a_center + rotation*v_coords;\n#ifdef HATCH\n  // Coordinates for hatching in unrotated frame of reference.\n  v_hatch_coords = pos - 0.5;\n#endif\n  pos += 0.5; // Make up for Bokeh's offset.\n  pos /= u_canvas_size / u_pixel_ratio; // 0 to 1.\n  gl_Position = vec4(2.0*pos.x - 1.0, 1.0 - 2.0*pos.y, 0.0, 1.0);\n}\n",p="\nprecision mediump float;\n\nconst float SQRT2 = sqrt(2.0);\nconst float SQRT3 = sqrt(3.0);\nconst float PI = 3.14159265358979323846;\n\nconst int butt_cap = 0;\nconst int round_cap = 1;\nconst int square_cap = 2;\n\nconst int miter_join = 0;\nconst int round_join = 1;\nconst int bevel_join = 2;\n\n#ifdef HATCH\nconst int hatch_dot = 1;\nconst int hatch_ring = 2;\nconst int hatch_horizontal_line = 3;\nconst int hatch_vertical_line = 4;\nconst int hatch_cross = 5;\nconst int hatch_horizontal_dash = 6;\nconst int hatch_vertical_dash = 7;\nconst int hatch_spiral = 8;\nconst int hatch_right_diagonal_line = 9;\nconst int hatch_left_diagonal_line = 10;\nconst int hatch_diagonal_cross = 11;\nconst int hatch_right_diagonal_dash = 12;\nconst int hatch_left_diagonal_dash = 13;\nconst int hatch_horizontal_wave = 14;\nconst int hatch_vertical_wave = 15;\nconst int hatch_criss_cross = 16;\n#endif\n\nuniform float u_antialias;\n\nvarying float v_linewidth;\nvarying vec2 v_size;\nvarying vec4 v_line_color;\nvarying vec4 v_fill_color;\nvarying float v_line_cap;\nvarying float v_line_join;\nvarying vec2 v_coords;\n#ifdef HATCH\nvarying float v_hatch_pattern;\nvarying float v_hatch_scale;\nvarying float v_hatch_weight;\nvarying vec4 v_hatch_color;\nvarying vec2 v_hatch_coords;\n#endif\n\n// Lines within the marker (dot, cross, x and y) are added at the end as they are\n// on top of the fill rather than astride it.\n#if defined(USE_CIRCLE_DOT) || defined(USE_DIAMOND_DOT) || defined(USE_DOT) ||     defined(USE_HEX_DOT) || defined(USE_SQUARE_DOT) || defined(USE_STAR_DOT) ||     defined(USE_TRIANGLE_DOT)\n  #define APPEND_DOT\n#endif\n\n#if defined(USE_CIRCLE_CROSS) || defined(USE_SQUARE_CROSS)\n  #define APPEND_CROSS\n#endif\n\n#ifdef USE_DIAMOND_CROSS\n  #define APPEND_CROSS_2\n#endif\n\n#ifdef USE_CIRCLE_X\n  #define APPEND_X\n  #define APPEND_X_LEN (0.5*v_size.x)\n#endif\n\n#ifdef USE_SQUARE_X\n  #define APPEND_X\n  #define APPEND_X_LEN (v_size.x/SQRT2)\n#endif\n\n#ifdef USE_CIRCLE_Y\n  #define APPEND_Y\n#endif\n\n#if defined(USE_ASTERISK) || defined(USE_CROSS) || defined(USE_DASH) ||     defined(USE_DOT) || defined(USE_X) || defined(USE_Y)\n  // No fill.\n  #define LINE_ONLY\n#endif\n\n#if defined(LINE_ONLY) || defined(APPEND_CROSS) || defined(APPEND_CROSS_2) ||     defined(APPEND_X) || defined(APPEND_Y)\nfloat end_cap_distance(in vec2 p, in vec2 end_point, in vec2 unit_direction, in int line_cap)\n{\n  vec2 offset = p - end_point;\n  if (line_cap == butt_cap)\n    return dot(offset, unit_direction) + 0.5*v_linewidth;\n  else if (line_cap == square_cap)\n    return dot(offset, unit_direction);\n  else if (line_cap == round_cap && dot(offset, unit_direction) > 0.0)\n    return length(offset);\n  else\n    // Default is outside of line and should be -0.5*(v_linewidth+u_antialias) or less,\n    // so here avoid the multiplication.\n    return -v_linewidth-u_antialias;\n}\n#endif\n\n#if !(defined(LINE_ONLY) || defined(USE_SQUARE_PIN) || defined(USE_TRIANGLE_PIN))\n// For line join at a vec2 corner where 2 line segments meet, consider bevel points which are the 2\n// points obtained by moving half a linewidth away from the corner point in the directions normal to\n// the line segments.  The line through these points is the bevel line, characterised by a vec2\n// unit_normal and offset distance from the corner point.  Edge of bevel join straddles this line,\n// round join occurs outside of this line centred on the corner point.  In general\n//   offset = (linewidth/2)*sin(alpha/2)\n// where alpha is the angle between the 2 line segments at the corner.\nfloat line_join_distance_no_miter(\n  in vec2 p, in vec2 corner, in vec2 unit_normal, in float offset, in int line_join)\n{\n  // Simplified version of line_join_distance ignoring miter which most markers do implicitly\n  // as they are composed of straight line segments.\n  float dist_outside = dot((p - corner), unit_normal) - offset;\n\n  if (line_join == bevel_join && dist_outside > -0.5*u_antialias)\n    return dist_outside + 0.5*v_linewidth;\n  else if (dist_outside > 0.0)  // round_join\n    return distance(p, corner);\n  else\n    // Default is outside of line and should be -0.5*(v_linewidth+u_antialias) or less,\n    // so here avoid the multiplication.\n    return -v_linewidth-u_antialias;\n}\n#endif\n\n#if defined(USE_SQUARE_PIN) || defined(USE_TRIANGLE_PIN)\n// Line join distance including miter but only one-sided check as assuming use of symmetry in\n// calling function.\nfloat line_join_distance_incl_miter(\n  in vec2 p, in vec2 corner, in vec2 unit_normal, in float offset, in int line_join,\n  vec2 miter_unit_normal)\n{\n  float dist_outside = dot((p - corner), unit_normal) - offset;\n\n  if (line_join == miter_join && dist_outside > 0.0)\n    return dot((p - corner), miter_unit_normal);\n  else if (line_join == bevel_join && dist_outside > -0.5*u_antialias)\n    return dist_outside + 0.5*v_linewidth;\n  else if (dist_outside > 0.0)  // round_join\n    return distance(p, corner);\n  else\n    return -v_linewidth-u_antialias;\n}\n#endif\n\n#if defined(APPEND_CROSS) || defined(APPEND_X) || defined(USE_ASTERISK) ||     defined(USE_CROSS) || defined(USE_X)\nfloat one_cross(in vec2 p, in int line_cap, in float len)\n{\n  p = abs(p);\n  p = (p.y > p.x) ? p.yx : p.xy;\n  float dist = p.y;\n  float end_dist = end_cap_distance(p, vec2(len, 0.0), vec2(1.0, 0.0), line_cap);\n  return max(dist, end_dist);\n}\n#endif\n\n#ifdef APPEND_CROSS_2\nfloat one_cross_2(in vec2 p, in int line_cap, in vec2 lengths)\n{\n  // Cross with different length in x and y directions.\n  p = abs(p);\n  bool switch_xy = (p.y > p.x);\n  p = switch_xy ? p.yx : p.xy;\n  float len = switch_xy ? lengths.y : lengths.x;\n  float dist = p.y;\n  float end_dist = end_cap_distance(p, vec2(len, 0.0), vec2(1.0, 0.0), line_cap);\n  return max(dist, end_dist);\n}\n#endif\n\n#if defined(APPEND_Y) || defined(USE_Y)\nfloat one_y(in vec2 p, in int line_cap, in float len)\n{\n  p = vec2(abs(p.x), -p.y);\n\n  // End point of line to right is (1/2, 1/3)*len*SQRT3.\n  // Unit vector along line is (1/2, 1/3)*k where k = 6/SQRT13.\n  const float k = 6.0/sqrt(13.0);\n  vec2 unit_along = vec2(0.5*k, k/3.0);\n  vec2 end_point = vec2(0.5*len*SQRT3, len*SQRT3/3.0);\n  float dist = max(abs(dot(p, vec2(-unit_along.y, unit_along.x))),\n                   end_cap_distance(p, end_point, unit_along, line_cap));\n\n  if (p.y < 0.0) {\n    // Vertical line.\n    float vert_dist = max(p.x,\n                          end_cap_distance(p, vec2(0.0, -len), vec2(0.0, -1.0), line_cap));\n    dist = min(dist, vert_dist);\n  }\n  return dist;\n}\n#endif\n\n// One marker_distance function per marker type.\n// Distance is zero on edge of marker, +ve outside and -ve inside.\n\n#ifdef USE_ASTERISK\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  vec2 p_diag = vec2((p.x + p.y)/SQRT2, (p.x - p.y)/SQRT2);\n  float len = 0.5*v_size.x;\n  return min(one_cross(p, line_cap, len),  // cross\n             one_cross(p_diag, line_cap, len));  // x\n}\n#endif\n\n#if defined(USE_CIRCLE) || defined(USE_CIRCLE_CROSS) || defined(USE_CIRCLE_DOT) ||     defined(USE_CIRCLE_X) || defined(USE_CIRCLE_Y)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  return length(p) - 0.5*v_size.x;\n}\n#endif\n\n#ifdef USE_CROSS\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  return one_cross(p, line_cap, 0.5*v_size.x);\n}\n#endif\n\n#ifdef USE_DASH\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  p = abs(p);\n  float dist = p.y;\n  float end_dist = end_cap_distance(p, vec2(0.5*v_size.x, 0.0), vec2(1.0, 0.0), line_cap);\n  return max(dist, end_dist);\n}\n#endif\n\n#if defined(USE_DIAMOND) || defined(USE_DIAMOND_CROSS) || defined(USE_DIAMOND_DOT)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  // Only need to consider +ve quadrant, the 2 end points are (2r/3, 0) and (0, r)\n  // where r = radius = v_size.x/2.\n  // Line has outward-facing unit normal vec2(1, 2/3)/k where k = SQRT13/3\n  // hence vec2(3, 2)/SQRT13, and distance from origin of 2r/(3k) = 2r/SQRT13.\n  p = abs(p);\n  float r = 0.5*v_size.x;\n  const float SQRT13 = sqrt(13.0);\n  float dist = dot(p, vec2(3.0, 2.0))/SQRT13 - 2.0*r/SQRT13;\n\n  if (line_join != miter_join) {\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(0.0, r), vec2(0.0, 1.0), v_linewidth/SQRT13, line_join));\n\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(r*2.0/3.0, 0.0), vec2(1.0, 0.0), v_linewidth*(1.5/SQRT13), line_join));\n  }\n\n  return dist;\n}\n#endif\n\n#ifdef USE_DOT\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Dot is always appended.\n  return v_linewidth+u_antialias;\n}\n#endif\n\n#if defined(USE_HEX) || defined(USE_HEX_DOT)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // A regular hexagon has v_size.x == v.size_y = r where r is the length of\n  // each of the 3 sides of the 6 equilateral triangles that comprise the hex.\n  // Only consider +ve quadrant, the 3 corners are at (0, h), (rx/2, h), (rx, 0)\n  // where rx = 0.5*v_size.x, ry = 0.5*v_size.y and h = ry*SQRT3/2.\n  // Sloping line has outward normal vec2(h, rx/2).  Length of this is\n  // len = sqrt(h**2 + rx**2/4) to give unit normal (h, rx/2)/len and distance\n  // from origin of this line is rx*h/len.\n  p = abs(p);\n  float rx = v_size.x/2.0;\n  float h = v_size.y*(SQRT3/4.0);\n  float len_normal = sqrt(h*h + 0.25*rx*rx);\n  vec2 unit_normal = vec2(h, 0.5*rx) / len_normal;\n  float dist = max(dot(p, unit_normal) - rx*h/len_normal,  // Distance from sloping line.\n                   p.y - h);  // Distance from horizontal line.\n\n  if (line_join != miter_join) {\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(rx, 0.0), vec2(1.0, 0.0), 0.5*v_linewidth*unit_normal.x, line_join));\n\n    unit_normal = normalize(unit_normal + vec2(0.0, 1.0));  // At (rx/2, h) corner.\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(0.5*rx, h), unit_normal, 0.5*v_linewidth*unit_normal.y, line_join));\n  }\n  return dist;\n}\n#endif\n\n#ifdef USE_PLUS\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  // Only need to consider one octant, the +ve quadrant with x >= y.\n  p = abs(p);\n  p = (p.y > p.x) ? p.yx : p.xy;\n\n  // 3 corners are (r, 0), (r, 3r/8) and (3r/8, 3r/8).\n  float r = 0.5*v_size.x;\n  p = p - vec2(r, 0.375*r);  // Distance with respect to outside corner\n  float dist = max(p.x, p.y);\n\n  if (line_join != miter_join) {\n    // Outside corner\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(0.0, 0.0), vec2(1.0/SQRT2, 1.0/SQRT2), v_linewidth/(2.0*SQRT2), line_join));\n\n    // Inside corner\n    dist = min(dist, -line_join_distance_no_miter(\n      p, vec2(-5.0*r/8.0, 0.0), vec2(-1.0/SQRT2, -1.0/SQRT2), v_linewidth/(2.0*SQRT2), line_join));\n  }\n\n  return dist;\n}\n#endif\n\n#if defined(USE_SQUARE) || defined(USE_SQUARE_CROSS) || defined(USE_SQUARE_DOT) ||     defined(USE_SQUARE_X)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  vec2 p2 = abs(p) - v_size/2.0;  // Offset from corner\n  float dist = max(p2.x, p2.y);\n\n  if (line_join != miter_join)\n    dist = max(dist, line_join_distance_no_miter(\n      p2, vec2(0.0, 0.0), vec2(1.0/SQRT2, 1.0/SQRT2), v_linewidth/(2.0*SQRT2), line_join));\n\n  return dist;\n}\n#endif\n\n#ifdef USE_SQUARE_PIN\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  p = abs(p);\n  p = (p.y > p.x) ? p.yx : p.xy;\n  // p is in octant between y=0 and y=x.\n  // Quadratic bezier curve passes through (r, r), (11r/16, 0) and (r, -r).\n  // Circular arc that passes through the same points has center at\n  // x = r + 231r/160 = 2.44275r and y = 0 and hence radius is\n  // x - 11r/16 = 1.75626 precisely.\n  float r = 0.5*v_size.x;\n  float center_x = r*2.44375;\n  float radius = r*1.75626;\n  float dist = radius - distance(p, vec2(center_x, 0.0));\n\n  // Magic number is 0.5*sin(atan(8/5) - pi/4)\n  dist = max(dist, line_join_distance_incl_miter(\n    p, vec2(r, r), vec2(1.0/SQRT2, 1.0/SQRT2), v_linewidth*0.1124297533493792, line_join,\n    vec2(8.0/sqrt(89.0), -5.0/sqrt(89.0))));\n\n  return dist;\n}\n#endif\n\n#if defined(USE_STAR) || defined(USE_STAR_DOT)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  const float SQRT5 = sqrt(5.0);\n  const float COS72 = 0.25*(SQRT5 - 1.0);\n  const float SIN72 = sqrt((5.0+SQRT5) / 8.0);\n\n  float angle = atan(p.x, p.y);  // In range -pi to +pi clockwise from +y direction.\n  angle = mod(angle, 0.4*PI) - 0.2*PI;  // In range -pi/5 to +pi/5 clockwise from +y direction.\n  p = length(p)*vec2(cos(angle), abs(sin(angle)));  // (x,y) in pi/10 (36 degree) sector.\n\n  // 2 corners are at (r, 0) and (r-a*SIN72, a*COS72) where a = r sqrt(5-2*sqrt(5)).\n  // Line has outward-facing unit normal vec2(COS72, SIN72) and distance from\n  // origin of dot(vec2(r, 0), vec2(COS72, SIN72)) = r*COS72\n  float r = 0.5*v_size.x;\n  float a = r*sqrt(5.0 - 2.0*SQRT5);\n  float dist = dot(p, vec2(COS72, SIN72)) - r*COS72;\n\n  if (line_join != miter_join) {\n    // Outside corner\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(r, 0.0), vec2(1.0, 0.0), v_linewidth*(0.5*COS72), line_join));\n\n    // Inside corner\n    const float COS36 = sqrt(0.5 + COS72/2.0);\n    const float SIN36 = sqrt(0.5 - COS72/2.0);\n    dist = min(dist, -line_join_distance_no_miter(\n      p, vec2(r-a*SIN72, a*COS72), vec2(-COS36, -SIN36), v_linewidth*(0.5*COS36), line_join));\n  }\n\n  return dist;\n}\n#endif\n\n#if defined(USE_TRIANGLE) || defined(USE_TRIANGLE_DOT) || defined(USE_INVERTED_TRIANGLE)\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  // For normal triangle 3 corners are at (-r, a), (r, a), (0, a-h)=(0, -2h/3)\n  // given r = radius = v_size.x/2, h = SQRT3*r, a = h/3.\n  // Sloping line has outward-facing unit normal vec2(h, -r)/2r = vec2(SQRT3, -1)/2\n  // and distance from origin of a.  Horizontal line has outward-facing unit normal\n  // vec2(0, 1) and distance from origin of a.\n  float r = 0.5*v_size.x;\n  float a = r*SQRT3/3.0;\n\n  // Only need to consider +ve x.\n#ifdef USE_INVERTED_TRIANGLE\n  p = vec2(abs(p.x), -p.y);\n#else\n  p = vec2(abs(p.x), p.y);\n#endif\n\n  float dist = max(0.5*dot(p, vec2(SQRT3, -1.0)) - a,  // Distance from sloping line.\n                   p.y - a);  // Distance from horizontal line.\n\n  if (line_join != miter_join) {\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(0.0, -(2.0/SQRT3)*r), vec2(0.0, -1.0), v_linewidth*0.25, line_join));\n\n    dist = max(dist, line_join_distance_no_miter(\n      p, vec2(r, a), vec2(SQRT3/2.0, 0.5), v_linewidth*0.25, line_join));\n  }\n\n  return dist;\n}\n#endif\n\n#ifdef USE_TRIANGLE_PIN\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  float angle = atan(p.x, -p.y);  // In range -pi to +pi.\n  angle = mod(angle, PI*2.0/3.0) - PI/3.0;  // In range -pi/3 to pi/3.\n  p = length(p)*vec2(cos(angle), abs(sin(angle)));  // (x,y) in range 0 to pi/3.\n  // Quadratic bezier curve passes through (a, r), ((a+b)/2, 0) and (a, -r) where\n  // a = r/SQRT3, b = 3a/8 = r SQRT3/8.  Circular arc that passes through the same points has\n  // center at (a+x, 0) and radius x+c where c = (a-b)/2 and x = (r**2 - c**2) / (2c).\n  // Ignore r factor until the end so can use const.\n  const float a = 1.0/SQRT3;\n  const float b = SQRT3/8.0;\n  const float c = (a-b)/2.0;\n  const float x = (1.0 - c*c) / (2.0*c);\n  const float center_x = x + a;\n  const float radius = x + c;\n  float r = 0.5*v_size.x;\n  float dist = r*radius - distance(p, vec2(r*center_x, 0.0));\n\n  // Magic number is 0.5*sin(atan(8*sqrt(3)/5) - pi/3)\n  dist = max(dist, line_join_distance_incl_miter(\n    p, vec2(a*r, r), vec2(0.5, 0.5*SQRT3), v_linewidth*0.0881844526878324, line_join,\n    vec2(8.0*SQRT3, -5.0)/sqrt(217.0)));\n\n  return dist;\n}\n#endif\n\n#ifdef USE_X\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  p = vec2((p.x + p.y)/SQRT2, (p.x - p.y)/SQRT2);\n  return one_cross(p, line_cap, 0.5*v_size.x);\n}\n#endif\n\n#ifdef USE_Y\nfloat marker_distance(in vec2 p, in int line_cap, in int line_join)\n{\n  // Assuming v_size.x == v.size_y\n  return one_y(p, line_cap, 0.5*v_size.x);\n}\n#endif\n\n// Convert distance from edge of marker to fraction in range 0 to 1, depending\n// on antialiasing width.\nfloat distance_to_fraction(in float dist)\n{\n  return 1.0 - smoothstep(-0.5*u_antialias, 0.5*u_antialias, dist);\n}\n\n// Return fraction from 0 (no fill color) to 1 (full fill color).\nfloat fill_fraction(in float dist)\n{\n  return distance_to_fraction(dist);\n}\n\n// Return fraction in range 0 (no line color) to 1 (full line color).\nfloat line_fraction(in float dist)\n{\n  return distance_to_fraction(abs(dist) - 0.5*v_linewidth);\n}\n\n// Return fraction (in range 0 to 1) of a color, with premultiplied alpha.\nvec4 fractional_color(in vec4 color, in float fraction)\n{\n  color.a *= fraction;\n  color.rgb *= color.a;\n  return color;\n}\n\n// Blend colors that have premultiplied alpha.\nvec4 blend_colors(in vec4 src, in vec4 dest)\n{\n  return (1.0 - src.a)*dest + src;\n}\n\n#ifdef APPEND_DOT\nfloat dot_fraction(in vec2 p)\n{\n  // Assuming v_size.x == v_size.y\n  float radius = 0.125*v_size.x;\n  float dot_distance = max(length(p) - radius, -0.5*u_antialias);\n  return fill_fraction(dot_distance);\n}\n#endif\n\n#ifdef HATCH\n// Wrap coordinate(s) by removing integer part to give distance from center of\n// repeat, in the range -0.5 to +0.5.\nfloat wrap(in float x)\n{\n  return fract(x) - 0.5;\n}\n\nvec2 wrap(in vec2 xy)\n{\n  return fract(xy) - 0.5;\n}\n\n// Return fraction from 0 (no hatch color) to 1 (full hatch color).\nfloat hatch_fraction(in vec2 coords, in int hatch_pattern)\n{\n  float scale = v_hatch_scale; // Hatch repeat distance.\n\n  // Coordinates and linewidth/halfwidth are scaled to hatch repeat distance.\n  coords = coords / scale;\n  float halfwidth = 0.5*v_hatch_weight / scale; // Half the hatch linewidth.\n\n  // Default is to return fraction of zero, i.e. no pattern.\n  float dist = u_antialias;\n\n  if (hatch_pattern == hatch_dot) {\n    const float dot_radius = 0.25;\n    dist = length(wrap(coords)) - dot_radius;\n  }\n  else if (hatch_pattern == hatch_ring) {\n    const float ring_radius = 0.25;\n    dist = abs(length(wrap(coords)) - ring_radius) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_horizontal_line) {\n    dist = abs(wrap(coords.y)) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_vertical_line) {\n    dist = abs(wrap(coords.x)) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_cross) {\n    dist = min(abs(wrap(coords.x)), abs(wrap(coords.y))) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_horizontal_dash) {\n    // Dashes have square caps.\n    const float halflength = 0.25;\n    dist = max(abs(wrap(coords.y)),\n               abs(wrap(coords.x) + 0.25) - halflength) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_vertical_dash) {\n    const float halflength = 0.25;\n    dist = max(abs(wrap(coords.x)),\n               abs(wrap(coords.y) + 0.25) - halflength) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_spiral) {\n    vec2 wrap2 = wrap(coords);\n    float angle = wrap(atan(wrap2.y, wrap2.x) / (2.0*PI));\n    // Canvas spiral radius increases by scale*pi/15 each rotation.\n    const float dr = PI/15.0;\n    float radius = length(wrap2);\n    // At any angle, spiral lines are equally spaced dr apart.\n    // Find distance to nearest of these lines.\n    float frac = fract((radius - dr*angle) / dr); // 0 to 1.\n    dist = dr*(abs(frac - 0.5));\n    dist = min(dist, radius) - halfwidth; // Consider center point also.\n  }\n  else if (hatch_pattern == hatch_right_diagonal_line) {\n    dist = abs(wrap(2.0*coords.x + coords.y))/sqrt(5.0) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_left_diagonal_line) {\n    dist = abs(wrap(2.0*coords.x - coords.y))/sqrt(5.0) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_diagonal_cross) {\n    coords = vec2(coords.x + coords.y + 0.5, coords.x - coords.y + 0.5);\n    dist = min(abs(wrap(coords.x)), abs(wrap(coords.y))) / SQRT2 - halfwidth;\n  }\n  else if (hatch_pattern == hatch_right_diagonal_dash) {\n    float across = coords.x + coords.y + 0.5;\n    dist = abs(wrap(across)) / SQRT2; // Distance to nearest solid line.\n\n    across = floor(across); // Offset for dash.\n    float along = wrap(0.5*(coords.x - coords.y + across));\n    const float halflength = 0.25;\n    along = abs(along) - halflength; // Distance along line.\n\n    dist = max(dist, along) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_left_diagonal_dash) {\n    float across = coords.x - coords.y + 0.5;\n    dist = abs(wrap(across)) / SQRT2; // Distance to nearest solid line.\n\n    across = floor(across); // Offset for dash.\n    float along = wrap(0.5*(coords.x + coords.y + across));\n    const float halflength = 0.25;\n    along = abs(along) - halflength; // Distance along line.\n\n    dist = max(dist, along) - halfwidth;\n  }\n  else if (hatch_pattern == hatch_horizontal_wave) {\n    float wrapx = wrap(coords.x);\n    float wrapy = wrap(coords.y - 0.25 + abs(wrapx));\n    dist = abs(wrapy) / SQRT2 - halfwidth;\n  }\n  else if (hatch_pattern == hatch_vertical_wave) {\n    float wrapy = wrap(coords.y);\n    float wrapx = wrap(coords.x - 0.25 + abs(wrapy));\n    dist = abs(wrapx) / SQRT2 - halfwidth;\n  }\n  else if (hatch_pattern == hatch_criss_cross) {\n    float plus = min(abs(wrap(coords.x)), abs(wrap(coords.y)));\n\n    coords = vec2(coords.x + coords.y + 0.5, coords.x - coords.y + 0.5);\n    float X = min(abs(wrap(coords.x)), abs(wrap(coords.y))) / SQRT2;\n\n    dist = min(plus, X) - halfwidth;\n  }\n\n  return distance_to_fraction(dist*scale);\n}\n#endif\n\nvoid main()\n{\n  int line_cap = int(v_line_cap + 0.5);\n  int line_join = int(v_line_join + 0.5);\n#ifdef HATCH\n  int hatch_pattern = int(v_hatch_pattern + 0.5);\n#endif\n\n  float dist = marker_distance(v_coords, line_cap, line_join);\n\n#ifdef LINE_ONLY\n  vec4 color = vec4(0.0, 0.0, 0.0, 0.0);\n#else\n  float fill_frac = fill_fraction(dist);\n  vec4 color = fractional_color(v_fill_color, fill_frac);\n#endif\n\n#if defined(HATCH) && !defined(LINE_ONLY)\n  if (hatch_pattern > 0 && fill_frac > 0.0) {\n    float hatch_frac = hatch_fraction(v_hatch_coords, hatch_pattern);\n    vec4 hatch_color = fractional_color(v_hatch_color, hatch_frac*fill_frac);\n    color = blend_colors(hatch_color, color);\n  }\n#endif\n\n  float line_frac = line_fraction(dist);\n\n#ifdef APPEND_DOT\n  line_frac = max(line_frac, dot_fraction(v_coords));\n#endif\n#ifdef APPEND_CROSS\n  line_frac = max(line_frac, line_fraction(one_cross(v_coords, line_cap, 0.5*v_size.x)));\n#endif\n#ifdef APPEND_CROSS_2\n  vec2 lengths = vec2(v_size.x/3.0, v_size.x/2.0);\n  line_frac = max(line_frac, line_fraction(one_cross_2(v_coords, line_cap, lengths)));\n#endif\n#ifdef APPEND_X\n  vec2 p = vec2((v_coords.x + v_coords.y)/SQRT2, (v_coords.x - v_coords.y)/SQRT2);\n  line_frac = max(line_frac, line_fraction(one_cross(p, line_cap, APPEND_X_LEN)));\n#endif\n#ifdef APPEND_Y\n  line_frac = max(line_frac, line_fraction(one_y(v_coords, line_cap, 0.5*v_size.x)));\n#endif\n\n  if (line_frac > 0.0) {\n    vec4 line_color = fractional_color(v_line_color, line_frac);\n    color = blend_colors(line_color, color);\n  }\n\n  gl_FragColor = color;\n}\n";let f=null;function Q(t){return null==f&&(f=new T(t)),f}class T{constructor(t){try{this._regl=i()({gl:t,extensions:["ANGLE_instanced_arrays","EXT_blend_minmax"]}),this._regl_available=!0,this._line_geometry=this._regl.buffer({usage:"static",type:"float",data:[[-2,0],[-1,-1],[1,-1],[2,0],[1,1],[-1,1]]}),this._line_triangles=this._regl.elements({usage:"static",primitive:"triangles",data:[[0,1,5],[1,2,5],[5,2,4],[2,3,4]]})}catch(t){this._regl_available=!1}}buffer(t){return this._regl.buffer(t)}clear(t,e){this._viewport={x:0,y:0,width:t,height:e},this._regl.clear({color:[0,0,0,0]})}get has_webgl(){return this._regl_available}get scissor(){return this._scissor}set_scissor(t,e,n,r){this._scissor={x:t,y:e,width:n,height:r}}get viewport(){return this._viewport}dashed_line(){return null==this._dashed_line&&(this._dashed_line=function(t,e,n){const r={vert:`#define DASHED\n\n${u}`,frag:`#define DASHED\n\n${d}`,attributes:{a_position:{buffer:e,divisor:0},a_point_prev:(t,e)=>e.points.to_attribute_config(),a_point_start:(t,e)=>e.points.to_attribute_config(2*Float32Array.BYTES_PER_ELEMENT),a_point_end:(t,e)=>e.points.to_attribute_config(4*Float32Array.BYTES_PER_ELEMENT),a_point_next:(t,e)=>e.points.to_attribute_config(6*Float32Array.BYTES_PER_ELEMENT),a_show_prev:(t,e)=>e.show.to_attribute_config(),a_show_curr:(t,e)=>e.show.to_attribute_config(Uint8Array.BYTES_PER_ELEMENT),a_show_next:(t,e)=>e.show.to_attribute_config(2*Uint8Array.BYTES_PER_ELEMENT),a_length_so_far:(t,e)=>e.length_so_far.to_attribute_config()},uniforms:{u_canvas_size:t.prop("canvas_size"),u_pixel_ratio:t.prop("pixel_ratio"),u_antialias:t.prop("antialias"),u_line_color:t.prop("line_color"),u_linewidth:t.prop("linewidth"),u_miter_limit:t.prop("miter_limit"),u_line_join:t.prop("line_join"),u_line_cap:t.prop("line_cap"),u_dash_tex:t.prop("dash_tex"),u_dash_tex_info:t.prop("dash_tex_info"),u_dash_scale:t.prop("dash_scale"),u_dash_offset:t.prop("dash_offset")},elements:n,instances:t.prop("nsegments"),blend:{enable:!0,equation:"max",func:{srcRGB:1,srcAlpha:1,dstRGB:1,dstAlpha:1}},depth:{enable:!1},scissor:{enable:!0,box:t.prop("scissor")},viewport:t.prop("viewport")};return t(r)}(this._regl,this._line_geometry,this._line_triangles)),this._dashed_line}get_dash(t){return null==this._dash_cache&&(this._dash_cache=new c(this._regl)),this._dash_cache.get(t)}marker_no_hatch(t){null==this._marker_no_hatch_map&&(this._marker_no_hatch_map=new Map);let e=this._marker_no_hatch_map.get(t);return null==e&&(e=function(t,e){const n={vert:h,frag:`#define USE_${e.toUpperCase()}\n${p}`,attributes:{a_position:{buffer:t.buffer([[-.5,-.5],[-.5,.5],[.5,.5],[.5,-.5]]),divisor:0},a_center:(t,e)=>e.center.to_attribute_config(),a_width:(t,e)=>e.width.to_attribute_config(),a_height:(t,e)=>e.height.to_attribute_config(),a_angle:(t,e)=>e.angle.to_attribute_config(),a_linewidth:(t,e)=>e.linewidth.to_attribute_config(),a_line_color:(t,e)=>e.line_color.to_attribute_config(),a_fill_color:(t,e)=>e.fill_color.to_attribute_config(),a_line_cap:(t,e)=>e.line_cap.to_attribute_config(),a_line_join:(t,e)=>e.line_join.to_attribute_config(),a_show:(t,e)=>e.show.to_attribute_config()},uniforms:{u_canvas_size:t.prop("canvas_size"),u_pixel_ratio:t.prop("pixel_ratio"),u_antialias:t.prop("antialias"),u_size_hint:t.prop("size_hint")},count:4,primitive:"triangle fan",instances:t.prop("nmarkers"),blend:{enable:!0,func:{srcRGB:"one",srcAlpha:"one",dstRGB:"one minus src alpha",dstAlpha:"one minus src alpha"}},depth:{enable:!1},scissor:{enable:!0,box:t.prop("scissor")},viewport:t.prop("viewport")};return t(n)}(this._regl,t),this._marker_no_hatch_map.set(t,e)),e}marker_hatch(t){null==this._marker_hatch_map&&(this._marker_hatch_map=new Map);let e=this._marker_hatch_map.get(t);return null==e&&(e=function(t,e){const n={vert:`#define HATCH\n${h}`,frag:`#define USE_${e.toUpperCase()}\n#define HATCH\n${p}`,attributes:{a_position:{buffer:t.buffer([[-.5,-.5],[-.5,.5],[.5,.5],[.5,-.5]]),divisor:0},a_center:(t,e)=>e.center.to_attribute_config(),a_width:(t,e)=>e.width.to_attribute_config(),a_height:(t,e)=>e.height.to_attribute_config(),a_angle:(t,e)=>e.angle.to_attribute_config(),a_linewidth:(t,e)=>e.linewidth.to_attribute_config(),a_line_color:(t,e)=>e.line_color.to_attribute_config(),a_fill_color:(t,e)=>e.fill_color.to_attribute_config(),a_line_cap:(t,e)=>e.line_cap.to_attribute_config(),a_line_join:(t,e)=>e.line_join.to_attribute_config(),a_show:(t,e)=>e.show.to_attribute_config(),a_hatch_pattern:(t,e)=>e.hatch_pattern.to_attribute_config(),a_hatch_scale:(t,e)=>e.hatch_scale.to_attribute_config(),a_hatch_weight:(t,e)=>e.hatch_weight.to_attribute_config(),a_hatch_color:(t,e)=>e.hatch_color.to_attribute_config()},uniforms:{u_canvas_size:t.prop("canvas_size"),u_pixel_ratio:t.prop("pixel_ratio"),u_antialias:t.prop("antialias"),u_size_hint:t.prop("size_hint")},count:4,primitive:"triangle fan",instances:t.prop("nmarkers"),blend:{enable:!0,func:{srcRGB:"one",srcAlpha:"one",dstRGB:"one minus src alpha",dstAlpha:"one minus src alpha"}},depth:{enable:!1},scissor:{enable:!0,box:t.prop("scissor")},viewport:t.prop("viewport")};return t(n)}(this._regl,t),this._marker_hatch_map.set(t,e)),e}solid_line(){return null==this._solid_line&&(this._solid_line=function(t,e,n){const r={vert:u,frag:d,attributes:{a_position:{buffer:e,divisor:0},a_point_prev:(t,e)=>e.points.to_attribute_config(),a_point_start:(t,e)=>e.points.to_attribute_config(2*Float32Array.BYTES_PER_ELEMENT),a_point_end:(t,e)=>e.points.to_attribute_config(4*Float32Array.BYTES_PER_ELEMENT),a_point_next:(t,e)=>e.points.to_attribute_config(6*Float32Array.BYTES_PER_ELEMENT),a_show_prev:(t,e)=>e.show.to_attribute_config(),a_show_curr:(t,e)=>e.show.to_attribute_config(Uint8Array.BYTES_PER_ELEMENT),a_show_next:(t,e)=>e.show.to_attribute_config(2*Uint8Array.BYTES_PER_ELEMENT)},uniforms:{u_canvas_size:t.prop("canvas_size"),u_pixel_ratio:t.prop("pixel_ratio"),u_antialias:t.prop("antialias"),u_line_color:t.prop("line_color"),u_linewidth:t.prop("linewidth"),u_miter_limit:t.prop("miter_limit"),u_line_join:t.prop("line_join"),u_line_cap:t.prop("line_cap")},elements:n,instances:t.prop("nsegments"),blend:{enable:!0,equation:"max",func:{srcRGB:1,srcAlpha:1,dstRGB:1,dstAlpha:1}},depth:{enable:!1},scissor:{enable:!0,box:t.prop("scissor")},viewport:t.prop("viewport")};return t(r)}(this._regl,this._line_geometry,this._line_triangles)),this._solid_line}}T.__name__="ReglWrapper";var m=n(7649),g=n(9329),_=n(1457),b=n(2619),v=n(3461),y=n(1897),x=n(9485),w=n(3571),L=n(194),A=n(2019)},3461:(t,e,n)=>{"use strict";n.d(e,{LineGL:()=>o});var r=n(7649),i=n(9863);class o extends r.V{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph)}_get_show_buffer(t,e){const n=e._show;let r=n;if(t.length!=n.length-1){const e=this.glyph.parent.nonselection_glyph==this.glyph,o=n.length,a=n.get_sized_array(o);null==this._show&&(this._show=new i.Lv(this.regl_wrapper));const s=this._show.get_sized_array(o);s.fill(0);let l=t[0];e&&l>0&&(s[l]=a[l]);for(let n=1;n<t.length;n++){const r=t[n];r==l+1?s[r]=a[r]:e&&(s[l+1]=a[l+1],s[r]=a[r]),l=r}e&&l!=o-2&&(s[l+1]=a[l+1]),this._show.update(),r=this._show}return r}_get_visuals(){return this.glyph.visuals}_set_data_points(){const t=this.glyph.sx,e=this.glyph.sy,n=t.length;this._is_closed=n>2&&t[0]==t[n-1]&&e[0]==e[n-1]&&isFinite(t[0])&&isFinite(e[0]),null==this._points&&(this._points=new i.iz(this.regl_wrapper));const r=this._points.get_sized_array(2*(n+2));for(let i=1;i<n+1;i++)r[2*i]=t[i-1],r[2*i+1]=e[i-1];return this._is_closed?(r[0]=r[2*n-2],r[1]=r[2*n-1],r[2*n+2]=r[4],r[2*n+3]=r[5]):(r[0]=0,r[1]=0,r[2*n+2]=0,r[2*n+3]=0),this._points.update(),r}}o.__name__="LineGL"},1897:(t,e,n)=>{"use strict";n.d(e,{LRTBGL:()=>o});var r=n(9863),i=n(194);class o extends i.k{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph,"square")}_get_visuals(){return this.glyph.visuals}_set_data(){const t=this.nvertices;null==this._centers&&(this._centers=new r.iz(this.regl_wrapper),this._widths=new r.iz(this.regl_wrapper),this._heights=new r.iz(this.regl_wrapper),this._angles=new r.iz(this.regl_wrapper),this._angles.set_from_scalar(0));const e=this._centers.get_sized_array(2*t),n=this._heights.get_sized_array(t),o=this._widths.get_sized_array(t);for(let r=0;r<t;r++){const t=this.glyph.sleft[r],a=this.glyph.sright[r],s=this.glyph.stop[r],l=this.glyph.sbottom[r];isFinite(t)&&isFinite(a)&&isFinite(s)&&isFinite(l)?(e[2*r]=(t+a)/2,e[2*r+1]=(s+l)/2,n[r]=Math.abs(s-l),o[r]=Math.abs(a-t)):(e[2*r]=i.k.missing_point,e[2*r+1]=i.k.missing_point,n[r]=i.k.missing_point,o[r]=i.k.missing_point)}this._centers.update(),this._heights.update(),this._widths.update()}}o.__name__="LRTBGL"},9485:(t,e,n)=>{"use strict";n.d(e,{MultiMarkerGL:()=>o});var r=n(9329),i=n(9863);class o extends r.x{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){const r=e.glglyph;r.data_changed&&(r._set_data(),r.data_changed=!1),this.visuals_changed&&(this._set_visuals(),this.visuals_changed=!1);const o=r.nvertices;null==this._show&&(this._show=new i.Lv(this.regl_wrapper));const a=r._unique_marker_types.length;for(const e of r._unique_marker_types){if(null==e)continue;let i=o;const s=this._show.length,l=this._show.get_sized_array(o);if(a>1||t.length<o){this._show_all=!1,l.fill(0),i=0;for(const n of t)1!=a&&r._marker_types.get(n)!=e||(l[n]=255,i++)}else this._show_all&&s==o||(this._show_all=!0,l.fill(255));this._show.update(),0!=i&&this._draw_one_marker_type(e,n,r)}}_get_visuals(){return this.glyph.visuals}_set_data(){const t=this.nvertices;null==this._centers&&(this._centers=new i.iz(this.regl_wrapper),this._widths=new i.iz(this.regl_wrapper),this._heights=this._widths,this._angles=new i.iz(this.regl_wrapper));const e=this._centers.get_sized_array(2*t);for(let n=0;n<t;n++)isFinite(this.glyph.sx[n])&&isFinite(this.glyph.sy[n])?(e[2*n]=this.glyph.sx[n],e[2*n+1]=this.glyph.sy[n]):(e[2*n]=r.x.missing_point,e[2*n+1]=r.x.missing_point);this._centers.update(),this._widths.set_from_prop(this.glyph.size),this._angles.set_from_prop(this.glyph.angle),this._marker_types=this.glyph.marker,this._unique_marker_types=[...new Set(this._marker_types)]}}o.__name__="MultiMarkerGL"},3571:(t,e,n)=>{"use strict";n.d(e,{RectGL:()=>o});var r=n(9863),i=n(194);class o extends i.k{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph,"square")}_get_visuals(){return this.glyph.visuals}_set_data(){const t=this.nvertices;null==this._centers&&(this._centers=new r.iz(this.regl_wrapper),this._widths=new r.iz(this.regl_wrapper),this._heights=new r.iz(this.regl_wrapper),this._angles=new r.iz(this.regl_wrapper));const e=this._centers.get_sized_array(2*t);for(let n=0;n<t;n++)isFinite(this.glyph.sx[n])&&isFinite(this.glyph.sy[n])?(e[2*n]=this.glyph.sx[n],e[2*n+1]=this.glyph.sy[n]):(e[2*n]=i.k.missing_point,e[2*n+1]=i.k.missing_point);this._centers.update(),this._widths.set_from_array(this.glyph.sw),this._heights.set_from_array(this.glyph.sh),this._angles.set_from_prop(this.glyph.angle)}}o.__name__="RectGL"},194:(t,e,n)=>{"use strict";n.d(e,{k:()=>o});var r=n(9329),i=n(9863);class o extends r.x{constructor(t,e){super(t,e),this.glyph=e}_draw_impl(t,e,n,r){n.data_changed&&(n._set_data(),n.data_changed=!1),this.visuals_changed&&(this._set_visuals(),this.visuals_changed=!1);const o=n.nvertices;null==this._show&&(this._show=new i.Lv(this.regl_wrapper));const a=this._show.length,s=this._show.get_sized_array(o);if(t.length<o){this._show_all=!1;for(let t=0;t<o;t++)s[t]=0;for(let e=0;e<t.length;e++)s[t[e]]=255}else if(!this._show_all||a!=o){this._show_all=!0;for(let t=0;t<o;t++)s[t]=255}this._show.update(),this._draw_one_marker_type(r,e,n)}}o.__name__="SingleMarkerGL"},2019:(t,e,n)=>{"use strict";n.d(e,{StepGL:()=>a});var r=n(7649),i=n(9863),o=n(6785);class a extends r.V{constructor(t,e){super(t,e),this.glyph=e}draw(t,e,n){this._draw_impl(t,n,e.glglyph)}_get_show_buffer(t,e){return e._show}_get_visuals(){return this.glyph.visuals}_set_data_points(){const t=this.glyph.sx,e=this.glyph.sy,n=this.glyph.model.mode;let r=t.length;this._is_closed=r>2&&t[0]==t[r-1]&&e[0]==e[r-1]&&isFinite(t[0])&&isFinite(e[0]);const a="center"==n?2*r:2*r-1;null==this._points&&(this._points=new i.iz(this.regl_wrapper));const s=this._points.get_sized_array(2*(a+2));let l=isFinite(t[0]+e[0]),c=2;"center"==n&&(s[c++]=l?t[0]:NaN,s[c++]=e[0]);for(let i=0;i<r-1;i++){const 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t=r.data(this,o.datakey);t.active=[],t.anyactive=0,t.winner=0})),e.droppable=n,i.drag.hijack(t,"dropinit",e);break;case"mousemove":case"touchmove":o.event=t,o.timer||o.tolerate(e);break;case"mouseup":case"touchend":o.timer=clearTimeout(o.timer),e.propagates&&(i.drag.hijack(t,"drop",e),i.drag.hijack(t,"dropend",e))}},locate:function(t,e){var n=r.data(t,o.datakey),i=r(t),a=i.length&&!i.is(document)?i.offset():{},s=i.outerHeight(),l=i.outerWidth(),c={elem:t,width:l,height:s,top:a.top,left:a.left,right:a.left+l,bottom:a.top+s};return n&&(n.location=c,n.index=e,n.elem=t),c},contains:function(t,e){return(e[0]||e.left)>=t.left&&(e[0]||e.right)<=t.right&&(e[1]||e.top)>=t.top&&(e[1]||e.bottom)<=t.bottom},modes:{intersect:function(t,e,n){return this.contains(n,[t.pageX,t.pageY])?1e9:this.modes.overlap.apply(this,arguments)},overlap:function(t,e,n){return Math.max(0,Math.min(n.bottom,e.bottom)-Math.max(n.top,e.top))*Math.max(0,Math.min(n.right,e.right)-Math.max(n.left,e.left))},fit:function(t,e,n){return this.contains(n,e)?1:0},middle:function(t,e,n){return this.contains(n,[e.left+.5*e.width,e.top+.5*e.height])?1:0}},sort:function(t,e){return e.winner-t.winner||t.index-e.index},tolerate:function(t){var e,n,a,s,l,c,u,d,h=0,p=t.interactions.length,f=[o.event.pageX,o.event.pageY],Q=o.tolerance||o.modes[o.mode];do{if(d=t.interactions[h]){if(!d)return;d.drop=[],l=[],c=d.droppable.length,Q&&(a=o.locate(d.proxy)),e=0;do{if(u=d.droppable[e]){if(!(n=(s=r.data(u,o.datakey)).location))continue;s.winner=Q?Q.call(o,o.event,a,n):o.contains(n,f)?1:0,l.push(s)}}while(++e<c);l.sort(o.sort),e=0;do{(s=l[e])&&(s.winner&&d.drop.length<o.multi?(s.active[h]||s.anyactive||(!1!==i.drag.hijack(o.event,"dropstart",t,h,s.elem)[0]?(s.active[h]=1,s.anyactive+=1):s.winner=0),s.winner&&d.drop.push(s.elem)):s.active[h]&&1==s.anyactive&&(i.drag.hijack(o.event,"dropend",t,h,s.elem),s.active[h]=0,s.anyactive-=1))}while(++e<c)}}while(++h<p);o.last&&f[0]==o.last.pageX&&f[1]==o.last.pageY?delete o.timer:o.timer=setTimeout((function(){o.tolerate(t)}),o.delay),o.last=o.event}};i.dropinit=i.dropstart=i.dropend=o},5967:(t,e,n)=>{var r=n(7771),i=n(1614),o=i.keyCode;t.exports={CellExternalCopyManager:function(t){var e,n,a=this,s=t||{},l=s.copiedCellStyleLayerKey||"copy-manager",c=s.copiedCellStyle||"copied",u=0,d=s.bodyElement||document.body,h=s.onCopyInit||null,p=s.onCopySuccess||null;function f(t){if(s.headerColumnValueExtractor){var e=s.headerColumnValueExtractor(t);if(e)return e}return t.name}function Q(t,n,i){if(s.dataItemColumnValueExtractor){var o=s.dataItemColumnValueExtractor(t,n);if(o)return o}var a="";if(n.editor){var l={container:r("<p>"),column:n,position:{top:0,left:0},grid:e,event:i},c=new n.editor(l);c.loadValue(t),a=c.serializeValue(),c.destroy()}else a=t[n.field];return a}function T(t,n,i){if(n.denyPaste)return null;if(s.dataItemColumnValueSetter)return s.dataItemColumnValueSetter(t,n,i);if(n.editor){var o={container:r("body"),column:n,position:{top:0,left:0},grid:e},a=new n.editor(o);a.loadValue(t),a.applyValue(t,i),a.destroy()}else t[n.field]=i}function m(t){var e=document.createElement("textarea");return e.style.position="absolute",e.style.left="-1000px",e.style.top=document.body.scrollTop+"px",e.value=t,d.appendChild(e),e.select(),e}function g(t,r){var i;if(!e.getEditorLock().isActive()||e.getOptions().autoEdit){if(t.which==o.ESC&&n&&(t.preventDefault(),b(),a.onCopyCancelled.notify({ranges:n}),n=null),(t.which===o.C||t.which===o.INSERT)&&(t.ctrlKey||t.metaKey)&&!t.shiftKey&&(h&&h.call(),0!==(i=e.getSelectionModel().getSelectedRanges()).length)){n=i,_(i),a.onCopyCells.notify({ranges:i});for(var l=e.getColumns(),c="",u=0;u<i.length;u++){for(var g=i[u],v=[],y=g.fromRow;y<g.toRow+1;y++){var x=[],w=e.getDataItem(y);if(0===v.length&&s.includeHeaderWhenCopying){for(var L=[],A=g.fromCell;A<g.toCell+1;A++)l[A].name.length>0&&L.push(f(l[A]));v.push(L.join("\t"))}for(A=g.fromCell;A<g.toCell+1;A++)x.push(Q(w,l[A],t));v.push(x.join("\t"))}c+=v.join("\r\n")+"\r\n"}if(window.clipboardData)return window.clipboardData.setData("Text",c),!0;var H,k=document.activeElement;return(M=m(c)).focus(),setTimeout((function(){d.removeChild(M),k?k.focus():console.log("Not element to restore focus to after copy?")}),100),p&&(H=1===i.length?i[0].toRow+1-i[0].fromRow:i.length,p.call(this,H)),!1}if(!s.readOnlyMode&&(t.which===o.V&&(t.ctrlKey||t.metaKey)&&!t.shiftKey||t.which===o.INSERT&&t.shiftKey&&!t.ctrlKey)){var M=m("");return setTimeout((function(){!function(t,e){var n=t.getColumns(),r=e.value.split(/[\n\f\r]/);""===r[r.length-1]&&r.pop();var i=[],o=0;d.removeChild(e);for(var l=0;l<r.length;l++)""!==r[l]?i[o++]=r[l].split("\t"):i[o++]=[""];var c=t.getActiveCell(),u=t.getSelectionModel().getSelectedRanges(),h=u&&u.length?u[0]:null,p=null,f=null;if(h)p=h.fromRow,f=h.fromCell;else{if(!c)return;p=c.row,f=c.cell}var Q=!1,m=i.length,g=i.length?i[0].length:0;1==i.length&&1==i[0].length&&h&&(Q=!0,m=h.toRow-h.fromRow+1,g=h.toCell-h.fromCell+1);var b=t.getData().length-p,v=0;if(b<m&&s.newRowCreator){var y=t.getData();for(v=1;v<=m-b;v++)y.push({});t.setData(y),t.render()}var x=p+m>t.getDataLength();if(s.newRowCreator&&x){var w=p+m-t.getDataLength();s.newRowCreator(w)}var L={isClipboardCommand:!0,clippedRange:i,oldValues:[],cellExternalCopyManager:a,_options:s,setDataItemValueForColumn:T,markCopySelection:_,oneCellToMultiple:Q,activeRow:p,activeCell:f,destH:m,destW:g,maxDestY:t.getDataLength(),maxDestX:t.getColumns().length,h:0,w:0,execute:function(){this.h=0;for(var e=0;e<this.destH;e++){this.oldValues[e]=[],this.w=0,this.h++;for(var r=0;r<this.destW;r++){this.w++;var o=p+e,a=f+r;if(o<this.maxDestY&&a<this.maxDestX){t.getCellNode(o,a);var s=t.getDataItem(o);this.oldValues[e][r]=s[n[a].field],Q?this.setDataItemValueForColumn(s,n[a],i[0][0]):this.setDataItemValueForColumn(s,n[a],i[e]?i[e][r]:""),t.updateCell(o,a),t.onCellChange.notify({row:o,cell:a,item:s,grid:t})}}}var l={fromCell:f,fromRow:p,toCell:f+this.w-1,toRow:p+this.h-1};this.markCopySelection([l]),t.getSelectionModel().setSelectedRanges([l]),this.cellExternalCopyManager.onPasteCells.notify({ranges:[l]})},undo:function(){for(var e=0;e<this.destH;e++)for(var r=0;r<this.destW;r++){var i=p+e,o=f+r;if(i<this.maxDestY&&o<this.maxDestX){t.getCellNode(i,o);var a=t.getDataItem(i);Q?this.setDataItemValueForColumn(a,n[o],this.oldValues[0][0]):this.setDataItemValueForColumn(a,n[o],this.oldValues[e][r]),t.updateCell(i,o),t.onCellChange.notify({row:i,cell:o,item:a,grid:t})}}var s={fromCell:f,fromRow:p,toCell:f+this.w-1,toRow:p+this.h-1};if(this.markCopySelection([s]),t.getSelectionModel().setSelectedRanges([s]),this.cellExternalCopyManager.onPasteCells.notify({ranges:[s]}),v>1){for(var l=t.getData();v>1;v--)l.splice(l.length-1,1);t.setData(l),t.render()}}};s.clipboardCommandHandler?s.clipboardCommandHandler(L):L.execute()}(e,M)}),100),!1}}}function _(t){b();for(var n=e.getColumns(),r={},i=0;i<t.length;i++)for(var o=t[i].fromRow;o<=t[i].toRow;o++){r[o]={};for(var s=t[i].fromCell;s<=t[i].toCell&&s<n.length;s++)r[o][n[s].id]=c}e.setCellCssStyles(l,r),clearTimeout(u),u=setTimeout((function(){a.clearCopySelection()}),2e3)}function b(){e.removeCellCssStyles(l)}r.extend(this,{init:function(t){(e=t).onKeyDown.subscribe(g);var n=t.getSelectionModel();if(!n)throw new Error("Selection model is mandatory for this plugin. Please set a selection model on the grid before adding this plugin: grid.setSelectionModel(new Slick.CellSelectionModel())");n.onSelectedRangesChanged.subscribe((function(t,n){e.focus()}))},destroy:function(){e.onKeyDown.unsubscribe(g)},pluginName:"CellExternalCopyManager",clearCopySelection:b,handleKeyDown:g,onCopyCells:new i.Event,onCopyCancelled:new i.Event,onPasteCells:new i.Event,setIncludeHeaderWhenCopying:function(t){s.includeHeaderWhenCopying=t}})}}},4295:(t,e,n)=>{var r=n(7771),i=n(1614);t.exports={CheckboxSelectColumn:function(t){var e,n=null,o=g(),a=new i.EventHandler,s={},l=!1,c=r.extend(!0,{},{columnId:"_checkbox_selector",cssClass:null,hideSelectAllCheckbox:!1,toolTip:"Select/Deselect All",width:30,hideInColumnTitleRow:!1,hideInFilterHeaderRow:!0},t);function u(){e.updateColumnHeader(c.columnId,"","")}function d(){r("#filter-checkbox-selectall-container").hide()}function h(t,i){var a,u,d,h=e.getSelectedRows(),p={},f=0;if("function"==typeof n)for(d=0;d<e.getDataLength();d++)b(u,e.getDataItem(d),e)||f++;var Q=[];for(u=0;u<h.length;u++)a=h[u],b(u,e.getDataItem(a),e)?(p[a]=!0,p[a]!==s[a]&&(e.invalidateRow(a),delete s[a])):Q.push(a);for(u in s)e.invalidateRow(u);if(s=p,e.render(),l=h.length&&h.length+f>=e.getDataLength(),c.hideInColumnTitleRow||c.hideSelectAllCheckbox||v(l),c.hideInFilterHeaderRow||r("#header-filter-selector"+o).prop("checked",l),Q.length>0){for(u=0;u<Q.length;u++){var T=h.indexOf(Q[u]);h.splice(T,1)}e.setSelectedRows(h)}}function p(t,n){32==t.which&&e.getColumns()[n.cell].id===c.columnId&&(e.getEditorLock().isActive()&&!e.getEditorLock().commitCurrentEdit()||Q(n.row),t.preventDefault(),t.stopImmediatePropagation())}function f(t,n){if(e.getColumns()[n.cell].id===c.columnId&&r(t.target).is(":checkbox")){if(e.getEditorLock().isActive()&&!e.getEditorLock().commitCurrentEdit())return t.preventDefault(),void t.stopImmediatePropagation();Q(n.row),t.stopPropagation(),t.stopImmediatePropagation()}}function Q(t){var n=e.getDataItem(t);b(t,n,e)&&(s[t]?e.setSelectedRows(r.grep(e.getSelectedRows(),(function(e){return e!=t}))):e.setSelectedRows(e.getSelectedRows().concat(t)),e.setActiveCell(t,function(){if(null===m){m=0;for(var t=e.getColumns(),n=0;n<t.length;n++)t[n].id==c.columnId&&(m=n)}return m}()))}function T(t,n){if(n.column.id==c.columnId&&r(t.target).is(":checkbox")){if(e.getEditorLock().isActive()&&!e.getEditorLock().commitCurrentEdit())return t.preventDefault(),void t.stopImmediatePropagation();if(r(t.target).is(":checked")){for(var i=[],o=0;o<e.getDataLength();o++){var a=e.getDataItem(o);a.__group||a.__groupTotals||!b(o,a,e)||i.push(o)}e.setSelectedRows(i)}else e.setSelectedRows([]);t.stopPropagation(),t.stopImmediatePropagation()}}"function"==typeof c.selectableOverride&&y(c.selectableOverride);var m=null;function g(){return Math.round(1e7*Math.random())}function _(t,e,n,r,i,o){var a=g()+t;return i&&b(t,i,o)?s[t]?"<input id='selector"+a+"' type='checkbox' checked='checked'><label for='selector"+a+"'></label>":"<input id='selector"+a+"' type='checkbox'><label for='selector"+a+"'></label>":null}function b(t,e,r){return"function"!=typeof n||n(t,e,r)}function v(t){t?e.updateColumnHeader(c.columnId,"<input id='header-selector"+o+"' type='checkbox' checked='checked'><label for='header-selector"+o+"'></label>",c.toolTip):e.updateColumnHeader(c.columnId,"<input id='header-selector"+o+"' type='checkbox'><label for='header-selector"+o+"'></label>",c.toolTip)}function y(t){n=t}r.extend(this,{init:function(t){e=t,a.subscribe(e.onSelectedRowsChanged,h).subscribe(e.onClick,f).subscribe(e.onKeyDown,p),c.hideInFilterHeaderRow||function(t){a.subscribe(t.onHeaderRowCellRendered,(function(t,e){"sel"===e.column.field&&(r(e.node).empty(),r("<span id='filter-checkbox-selectall-container'><input id='header-filter-selector"+o+"' type='checkbox'><label for='header-filter-selector"+o+"'></label></span>").appendTo(e.node).on("click",(function(t){T(t,e)})))}))}(t),c.hideInColumnTitleRow||a.subscribe(e.onHeaderClick,T)},destroy:function(){a.unsubscribeAll()},pluginName:"CheckboxSelectColumn",deSelectRows:function(t){var n,i=t.length,o=[];for(n=0;n<i;n++)s[t[n]]&&(o[o.length]=t[n]);e.setSelectedRows(r.grep(e.getSelectedRows(),(function(t){return o.indexOf(t)<0})))},selectRows:function(t){var n,r=t.length,i=[];for(n=0;n<r;n++)s[t[n]]||(i[i.length]=t[n]);e.setSelectedRows(e.getSelectedRows().concat(i))},getColumnDefinition:function(){return{id:c.columnId,name:c.hideSelectAllCheckbox||c.hideInColumnTitleRow?"":"<input id='header-selector"+o+"' type='checkbox'><label for='header-selector"+o+"'></label>",toolTip:c.hideSelectAllCheckbox||c.hideInColumnTitleRow?"":c.toolTip,field:"sel",width:c.width,resizable:!1,sortable:!1,cssClass:c.cssClass,hideSelectAllCheckbox:c.hideSelectAllCheckbox,formatter:_}},getOptions:function(){return c},selectableOverride:y,setOptions:function(t){if((c=r.extend(!0,{},c,t)).hideSelectAllCheckbox)u(),d();else if(c.hideInColumnTitleRow?u():(v(l),a.subscribe(e.onHeaderClick,T)),c.hideInFilterHeaderRow)d();else{var n=r("#filter-checkbox-selectall-container");n.show(),n.find('input[type="checkbox"]').prop("checked",l)}}})}}},1449:(t,e,n)=>{var r=n(7771),i=n(1614);t.exports={RowSelectionModel:function(t){var e,n,o,a=[],s=this,l=new i.EventHandler,c={selectActiveRow:!0};function u(t){return function(){n||(n=!0,t.apply(this,arguments),n=!1)}}function d(t){for(var e=[],n=0;n<t.length;n++)for(var r=t[n].fromRow;r<=t[n].toRow;r++)e.push(r);return e}function h(t){for(var n=[],r=e.getColumns().length-1,o=0;o<t.length;o++)n.push(new i.Range(t[o],0,t[o],r));return n}function p(){return d(a)}function f(t){(a&&0!==a.length||t&&0!==t.length)&&(a=t,s.onSelectedRangesChanged.notify(a))}function Q(t,n){o.selectActiveRow&&null!=n.row&&f([new i.Range(n.row,0,n.row,e.getColumns().length-1)])}function T(t){var n=e.getActiveCell();if(e.getOptions().multiSelect&&n&&t.shiftKey&&!t.ctrlKey&&!t.altKey&&!t.metaKey&&(t.which==i.keyCode.UP||t.which==i.keyCode.DOWN)){var r=p();r.sort((function(t,e){return t-e})),r.length||(r=[n.row]);var o,a=r[0],s=r[r.length-1];(o=t.which==i.keyCode.DOWN?n.row<s||a==s?++s:++a:n.row<s?--s:--a)>=0&&o<e.getDataLength()&&(e.scrollRowIntoView(o),f(h(function(t,e){var n,r=[];for(n=t;n<=e;n++)r.push(n);for(n=e;n<t;n++)r.push(n);return r}(a,s)))),t.preventDefault(),t.stopPropagation()}}function m(t){var n=e.getCellFromEvent(t);if(!n||!e.canCellBeActive(n.row,n.cell))return!1;if(!e.getOptions().multiSelect||!t.ctrlKey&&!t.shiftKey&&!t.metaKey)return!1;var i=d(a),o=r.inArray(n.row,i);if(-1===o&&(t.ctrlKey||t.metaKey))i.push(n.row),e.setActiveCell(n.row,n.cell);else if(-1!==o&&(t.ctrlKey||t.metaKey))i=r.grep(i,(function(t,e){return t!==n.row})),e.setActiveCell(n.row,n.cell);else if(i.length&&t.shiftKey){var s=i.pop(),l=Math.min(n.row,s),c=Math.max(n.row,s);i=[];for(var u=l;u<=c;u++)u!==s&&i.push(u);i.push(s),e.setActiveCell(n.row,n.cell)}return f(h(i)),t.stopImmediatePropagation(),!0}r.extend(this,{getSelectedRows:p,setSelectedRows:function(t){f(h(t))},getSelectedRanges:function(){return a},setSelectedRanges:f,init:function(n){o=r.extend(!0,{},c,t),e=n,l.subscribe(e.onActiveCellChanged,u(Q)),l.subscribe(e.onKeyDown,u(T)),l.subscribe(e.onClick,u(m))},destroy:function(){l.unsubscribeAll()},pluginName:"RowSelectionModel",onSelectedRangesChanged:new i.Event})}}},1614:(t,e,n)=>{var r=n(7771);function i(){var t=!1,e=!1;this.stopPropagation=function(){t=!0},this.isPropagationStopped=function(){return t},this.stopImmediatePropagation=function(){e=!0},this.isImmediatePropagationStopped=function(){return e}}function o(){this.__nonDataRow=!0}function a(){this.__group=!0,this.level=0,this.count=0,this.value=null,this.title=null,this.collapsed=!1,this.selectChecked=!1,this.totals=null,this.rows=[],this.groups=null,this.groupingKey=null}function s(){this.__groupTotals=!0,this.group=null,this.initialized=!1}function l(){var t=null;this.isActive=function(e){return e?t===e:null!==t},this.activate=function(e){if(e!==t){if(null!==t)throw new Error("SlickGrid.EditorLock.activate: an editController is still active, can't activate another editController");if(!e.commitCurrentEdit)throw new Error("SlickGrid.EditorLock.activate: editController must implement .commitCurrentEdit()");if(!e.cancelCurrentEdit)throw new Error("SlickGrid.EditorLock.activate: editController must implement .cancelCurrentEdit()");t=e}},this.deactivate=function(e){if(t){if(t!==e)throw new Error("SlickGrid.EditorLock.deactivate: specified editController is not the currently active 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t.push({event:e,handler:n}),e.subscribe(n),this},this.unsubscribe=function(e,n){for(var r=t.length;r--;)if(t[r].event===e&&t[r].handler===n)return t.splice(r,1),void e.unsubscribe(n);return this},this.unsubscribeAll=function(){for(var e=t.length;e--;)t[e].event.unsubscribe(t[e].handler);return t=[],this}},Range:function(t,e,n,r){void 0===n&&void 0===r&&(n=t,r=e),this.fromRow=Math.min(t,n),this.fromCell=Math.min(e,r),this.toRow=Math.max(t,n),this.toCell=Math.max(e,r),this.isSingleRow=function(){return this.fromRow==this.toRow},this.isSingleCell=function(){return this.fromRow==this.toRow&&this.fromCell==this.toCell},this.contains=function(t,e){return t>=this.fromRow&&t<=this.toRow&&e>=this.fromCell&&e<=this.toCell},this.toString=function(){return this.isSingleCell()?"("+this.fromRow+":"+this.fromCell+")":"("+this.fromRow+":"+this.fromCell+" - "+this.toRow+":"+this.toCell+")"}},Map:c,NonDataRow:o,Group:a,GroupTotals:s,EditorLock:l,GlobalEditorLock:new l,TreeColumns:function(t){var 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n=t.column.validator(e.val(),t);if(!n.valid)return n}return{valid:!0,msg:null}},this.init()}}}},4686:(t,e,n)=>{n(1614),t.exports={Formatters:{PercentComplete:function(t,e,n,r,i){return null==n||""===n?"-":n<50?"<span style='color:red;font-weight:bold;'>"+n+"%</span>":"<span style='color:green'>"+n+"%</span>"},PercentCompleteBar:function(t,e,n,r,i){return null==n||""===n?"":"<span class='percent-complete-bar' style='background:"+(n<30?"red":n<70?"silver":"green")+";width:"+n+"%'></span>"},YesNo:function(t,e,n,r,i){return n?"Yes":"No"},Checkmark:function(t,e,n,r,i){return n?"<img src='../images/tick.png'>":""},Checkbox:function(t,e,n,r,i){return'<img class="slick-edit-preclick" src="../images/'+(n?"CheckboxY":"CheckboxN")+'.png">'}}}},8517:(module,__unused_webpack_exports,__nested_webpack_require_491187__)=>{const jQuery=__nested_webpack_require_491187__(7771),$=jQuery;var Slick=__nested_webpack_require_491187__(1614),scrollbarDimensions,maxSupportedCssHeight;function 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init(){if(($container=container instanceof $?container:$(container)).length<1)throw new Error("SlickGrid requires a valid container, "+container+" does not exist in the DOM.");if(maxSupportedCssHeight=maxSupportedCssHeight||getMaxSupportedCssHeight(),options=$.extend({},defaults,options),validateAndEnforceOptions(),columnDefaults.width=options.defaultColumnWidth,options.suppressCssChangesOnHiddenInit||cacheCssForHiddenInit(),treeColumns=new Slick.TreeColumns(columns),columns=treeColumns.extractColumns(),updateColumnProps(),options.enableColumnReorder&&!$.fn.sortable)throw new Error("SlickGrid's 'enableColumnReorder = true' option requires jquery-ui.sortable module to be loaded");if(editController={commitCurrentEdit,cancelCurrentEdit},$container.empty().css("overflow","hidden").css("outline",0).addClass(uid).addClass("ui-widget"),/relative|absolute|fixed/.test($container.css("position"))||$container.css("position","relative"),$focusSink=$("<div tabIndex='0' hideFocus style='position:fixed;width:0;height:0;top:0;left:0;outline:0;'></div>").appendTo($container),$paneHeaderL=$("<div class='slick-pane slick-pane-header slick-pane-left' tabIndex='0' />").appendTo($container),$paneHeaderR=$("<div class='slick-pane slick-pane-header slick-pane-right' tabIndex='0' />").appendTo($container),$paneTopL=$("<div class='slick-pane slick-pane-top slick-pane-left' tabIndex='0' />").appendTo($container),$paneTopR=$("<div class='slick-pane slick-pane-top slick-pane-right' tabIndex='0' />").appendTo($container),$paneBottomL=$("<div class='slick-pane slick-pane-bottom slick-pane-left' tabIndex='0' />").appendTo($container),$paneBottomR=$("<div class='slick-pane slick-pane-bottom slick-pane-right' tabIndex='0' />").appendTo($container),options.createPreHeaderPanel&&($preHeaderPanelScroller=$("<div class='slick-preheader-panel ui-state-default' style='overflow:hidden;position:relative;' />").appendTo($paneHeaderL),$preHeaderPanel=$("<div />").appendTo($preHeaderPanelScroller),$preHeaderPanelSpacer=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").appendTo($preHeaderPanelScroller),$preHeaderPanelScrollerR=$("<div class='slick-preheader-panel ui-state-default' style='overflow:hidden;position:relative;' />").appendTo($paneHeaderR),$preHeaderPanelR=$("<div />").appendTo($preHeaderPanelScrollerR),$preHeaderPanelSpacerR=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").appendTo($preHeaderPanelScrollerR),options.showPreHeaderPanel||($preHeaderPanelScroller.hide(),$preHeaderPanelScrollerR.hide())),$headerScrollerL=$("<div class='slick-header ui-state-default slick-header-left' />").appendTo($paneHeaderL),$headerScrollerR=$("<div class='slick-header ui-state-default slick-header-right' />").appendTo($paneHeaderR),$headerScroller=$().add($headerScrollerL).add($headerScrollerR),treeColumns.hasDepth()){$groupHeadersL=[],$groupHeadersR=[];for(var t=0;t<treeColumns.getDepth()-1;t++)$groupHeadersL[t]=$("<div class='slick-group-header-columns slick-group-header-columns-left' style='left:-1000px' />").appendTo($headerScrollerL),$groupHeadersR[t]=$("<div class='slick-group-header-columns slick-group-header-columns-right' style='left:-1000px' />").appendTo($headerScrollerR);$groupHeaders=$().add($groupHeadersL).add($groupHeadersR)}$headerL=$("<div class='slick-header-columns slick-header-columns-left' style='left:-1000px' />").appendTo($headerScrollerL),$headerR=$("<div class='slick-header-columns slick-header-columns-right' style='left:-1000px' />").appendTo($headerScrollerR),$headers=$().add($headerL).add($headerR),$headerRowScrollerL=$("<div class='slick-headerrow ui-state-default' />").appendTo($paneTopL),$headerRowScrollerR=$("<div class='slick-headerrow ui-state-default' />").appendTo($paneTopR),$headerRowScroller=$().add($headerRowScrollerL).add($headerRowScrollerR),$headerRowSpacerL=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").appendTo($headerRowScrollerL),$headerRowSpacerR=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").appendTo($headerRowScrollerR),$headerRowL=$("<div class='slick-headerrow-columns slick-headerrow-columns-left' />").appendTo($headerRowScrollerL),$headerRowR=$("<div class='slick-headerrow-columns slick-headerrow-columns-right' />").appendTo($headerRowScrollerR),$headerRow=$().add($headerRowL).add($headerRowR),$topPanelScrollerL=$("<div class='slick-top-panel-scroller ui-state-default' />").appendTo($paneTopL),$topPanelScrollerR=$("<div class='slick-top-panel-scroller ui-state-default' />").appendTo($paneTopR),$topPanelScroller=$().add($topPanelScrollerL).add($topPanelScrollerR),$topPanelL=$("<div class='slick-top-panel' style='width:10000px' />").appendTo($topPanelScrollerL),$topPanelR=$("<div class='slick-top-panel' style='width:10000px' />").appendTo($topPanelScrollerR),$topPanel=$().add($topPanelL).add($topPanelR),options.showColumnHeader||$headerScroller.hide(),options.showTopPanel||$topPanelScroller.hide(),options.showHeaderRow||$headerRowScroller.hide(),$viewportTopL=$("<div class='slick-viewport slick-viewport-top slick-viewport-left' tabIndex='0' hideFocus />").appendTo($paneTopL),$viewportTopR=$("<div class='slick-viewport slick-viewport-top slick-viewport-right' tabIndex='0' hideFocus />").appendTo($paneTopR),$viewportBottomL=$("<div class='slick-viewport slick-viewport-bottom slick-viewport-left' tabIndex='0' hideFocus />").appendTo($paneBottomL),$viewportBottomR=$("<div class='slick-viewport slick-viewport-bottom slick-viewport-right' tabIndex='0' hideFocus />").appendTo($paneBottomR),$viewport=$().add($viewportTopL).add($viewportTopR).add($viewportBottomL).add($viewportBottomR),$activeViewportNode=$viewportTopL,$canvasTopL=$("<div class='grid-canvas grid-canvas-top grid-canvas-left' tabIndex='0' hideFocus />").appendTo($viewportTopL),$canvasTopR=$("<div class='grid-canvas grid-canvas-top grid-canvas-right' tabIndex='0' hideFocus />").appendTo($viewportTopR),$canvasBottomL=$("<div class='grid-canvas grid-canvas-bottom grid-canvas-left' tabIndex='0' hideFocus />").appendTo($viewportBottomL),$canvasBottomR=$("<div class='grid-canvas grid-canvas-bottom grid-canvas-right' tabIndex='0' hideFocus />").appendTo($viewportBottomR),options.viewportClass&&$viewport.toggleClass(options.viewportClass,!0),$canvas=$().add($canvasTopL).add($canvasTopR).add($canvasBottomL).add($canvasBottomR),scrollbarDimensions=scrollbarDimensions||measureScrollbar(),$activeCanvasNode=$canvasTopL,$preHeaderPanelSpacer&&$preHeaderPanelSpacer.css("width",getCanvasWidth()+scrollbarDimensions.width+"px"),$headers.width(getHeadersWidth()),$headerRowSpacerL.css("width",getCanvasWidth()+scrollbarDimensions.width+"px"),$headerRowSpacerR.css("width",getCanvasWidth()+scrollbarDimensions.width+"px"),options.createFooterRow&&($footerRowScrollerR=$("<div class='slick-footerrow ui-state-default' />").appendTo($paneTopR),$footerRowScrollerL=$("<div class='slick-footerrow ui-state-default' />").appendTo($paneTopL),$footerRowScroller=$().add($footerRowScrollerL).add($footerRowScrollerR),$footerRowSpacerL=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").css("width",getCanvasWidth()+scrollbarDimensions.width+"px").appendTo($footerRowScrollerL),$footerRowSpacerR=$("<div style='display:block;height:1px;position:absolute;top:0;left:0;'></div>").css("width",getCanvasWidth()+scrollbarDimensions.width+"px").appendTo($footerRowScrollerR),$footerRowL=$("<div class='slick-footerrow-columns slick-footerrow-columns-left' />").appendTo($footerRowScrollerL),$footerRowR=$("<div class='slick-footerrow-columns slick-footerrow-columns-right' />").appendTo($footerRowScrollerR),$footerRow=$().add($footerRowL).add($footerRowR),options.showFooterRow||$footerRowScroller.hide()),$focusSink2=$focusSink.clone().appendTo($container),options.explicitInitialization||finishInitialization()}function finishInitialization(){initialized||(initialized=!0,getViewportWidth(),getViewportHeight(),measureCellPaddingAndBorder(),disableSelection($headers),options.enableTextSelectionOnCells||$viewport.on("selectstart.ui",(function(t){return $(t.target).is("input,textarea")})),setFrozenOptions(),setPaneVisibility(),setScroller(),setOverflow(),updateColumnCaches(),createColumnHeaders(),createColumnGroupHeaders(),createColumnFooter(),setupColumnSort(),createCssRules(),resizeCanvas(),bindAncestorScrollEvents(),$container.on("resize.slickgrid",resizeCanvas),$viewport.on("scroll",handleScroll),jQuery.fn.mousewheel&&options.enableMouseWheelScrollHandler&&$viewport.on("mousewheel",handleMouseWheel),$headerScroller.on("contextmenu",handleHeaderContextMenu).on("click",handleHeaderClick).on("mouseenter",".slick-header-column",handleHeaderMouseEnter).on("mouseleave",".slick-header-column",handleHeaderMouseLeave),$headerRowScroller.on("scroll",handleHeaderRowScroll),options.createFooterRow&&($footerRow.on("contextmenu",handleFooterContextMenu).on("click",handleFooterClick),$footerRowScroller.on("scroll",handleFooterRowScroll)),options.createPreHeaderPanel&&$preHeaderPanelScroller.on("scroll",handlePreHeaderPanelScroll),$focusSink.add($focusSink2).on("keydown",handleKeyDown),$canvas.on("keydown",handleKeyDown).on("click",handleClick).on("dblclick",handleDblClick).on("contextmenu",handleContextMenu).on("draginit",handleDragInit).on("dragstart",{distance:3},handleDragStart).on("drag",handleDrag).on("dragend",handleDragEnd).on("mouseenter",".slick-cell",handleMouseEnter).on("mouseleave",".slick-cell",handleMouseLeave),options.suppressCssChangesOnHiddenInit||restoreCssFromHiddenInit())}function cacheCssForHiddenInit(){($hiddenParents=$container.parents().addBack().not(":visible")).each((function(){var t={};for(var e in cssShow)t[e]=this.style[e],this.style[e]=cssShow[e];oldProps.push(t)}))}function restoreCssFromHiddenInit(){$hiddenParents.each((function(t){var e=oldProps[t];for(var n in cssShow)this.style[n]=e[n]}))}function hasFrozenColumns(){return options.frozenColumn>-1}function registerPlugin(t){plugins.unshift(t),t.init(self)}function unregisterPlugin(t){for(var e=plugins.length;e>=0;e--)if(plugins[e]===t){plugins[e].destroy&&plugins[e].destroy(),plugins.splice(e,1);break}}function getPluginByName(t){for(var e=plugins.length-1;e>=0;e--)if(plugins[e].pluginName===t)return plugins[e]}function setSelectionModel(t){selectionModel&&(selectionModel.onSelectedRangesChanged.unsubscribe(handleSelectedRangesChanged),selectionModel.destroy&&selectionModel.destroy()),(selectionModel=t)&&(selectionModel.init(self),selectionModel.onSelectedRangesChanged.subscribe(handleSelectedRangesChanged))}function getSelectionModel(){return selectionModel}function getCanvasNode(t,e){return _getContainerElement(getCanvases(),t,e)}function getActiveCanvasNode(t){return setActiveCanvasNode(t),$activeCanvasNode[0]}function getCanvases(){return $canvas}function setActiveCanvasNode(t){t&&($activeCanvasNode=$(t.target).closest(".grid-canvas"))}function getViewportNode(t,e){return _getContainerElement(getViewports(),t,e)}function getViewports(){return $viewport}function getActiveViewportNode(t){return setActiveViewportNode(t),$activeViewportNode[0]}function setActiveViewportNode(t){t&&($activeViewportNode=$(t.target).closest(".slick-viewport"))}function _getContainerElement(t,e,n){if(t){e||(e=0),n||(n=0);var r="number"==typeof e?e:getColumnIndex(e);return t[(hasFrozenRows&&n>=actualFrozenRow+(options.frozenBottom?0:1)?2:0)+(hasFrozenColumns()&&r>options.frozenColumn?1:0)]}}function measureScrollbar(){var t=$('<div class="'+$viewport.className+'" style="position:absolute; top:-10000px; left:-10000px; overflow:auto; width:100px; height:100px;"></div>').appendTo("body"),e=$('<div style="width:200px; height:200px; overflow:auto;"></div>').appendTo(t),n={width:t[0].offsetWidth-t[0].clientWidth,height:t[0].offsetHeight-t[0].clientHeight};return e.remove(),t.remove(),n}function getHeadersWidth(){headersWidth=headersWidthL=headersWidthR=0;for(var t=!options.autoHeight,e=0,n=columns.length;e<n;e++){var r=columns[e].width;options.frozenColumn>-1&&e>options.frozenColumn?headersWidthR+=r:headersWidthL+=r}return t&&(options.frozenColumn>-1&&e>options.frozenColumn?headersWidthR+=scrollbarDimensions.width:headersWidthL+=scrollbarDimensions.width),hasFrozenColumns()?(headersWidthL+=1e3,headersWidthR=Math.max(headersWidthR,viewportW)+headersWidthL,headersWidthR+=scrollbarDimensions.width):(headersWidthL+=scrollbarDimensions.width,headersWidthL=Math.max(headersWidthL,viewportW)+1e3),headersWidth=headersWidthL+headersWidthR,Math.max(headersWidth,viewportW)+1e3}function getHeadersWidthL(){return headersWidthL=0,columns.forEach((function(t,e){options.frozenColumn>-1&&e>options.frozenColumn||(headersWidthL+=t.width)})),hasFrozenColumns()?headersWidthL+=1e3:(headersWidthL+=scrollbarDimensions.width,headersWidthL=Math.max(headersWidthL,viewportW)+1e3),headersWidthL}function getHeadersWidthR(){return headersWidthR=0,columns.forEach((function(t,e){options.frozenColumn>-1&&e>options.frozenColumn&&(headersWidthR+=t.width)})),hasFrozenColumns()&&(headersWidthR=Math.max(headersWidthR,viewportW)+getHeadersWidthL(),headersWidthR+=scrollbarDimensions.width),headersWidthR}function getCanvasWidth(){var t=viewportHasVScroll?viewportW-scrollbarDimensions.width:viewportW,e=columns.length;for(canvasWidthL=canvasWidthR=0;e--;)hasFrozenColumns()&&e>options.frozenColumn?canvasWidthR+=columns[e].width:canvasWidthL+=columns[e].width;var n=canvasWidthL+canvasWidthR;return options.fullWidthRows?Math.max(n,t):n}function updateCanvasWidth(t){var e,n=canvasWidth,r=canvasWidthL,i=canvasWidthR;((e=(canvasWidth=getCanvasWidth())!==n||canvasWidthL!==r||canvasWidthR!==i)||hasFrozenColumns()||hasFrozenRows)&&($canvasTopL.width(canvasWidthL),getHeadersWidth(),$headerL.width(headersWidthL),$headerR.width(headersWidthR),hasFrozenColumns()?($canvasTopR.width(canvasWidthR),$paneHeaderL.width(canvasWidthL),$paneHeaderR.css("left",canvasWidthL),$paneHeaderR.css("width",viewportW-canvasWidthL),$paneTopL.width(canvasWidthL),$paneTopR.css("left",canvasWidthL),$paneTopR.css("width",viewportW-canvasWidthL),$headerRowScrollerL.width(canvasWidthL),$headerRowScrollerR.width(viewportW-canvasWidthL),$headerRowL.width(canvasWidthL),$headerRowR.width(canvasWidthR),options.createFooterRow&&($footerRowScrollerL.width(canvasWidthL),$footerRowScrollerR.width(viewportW-canvasWidthL),$footerRowL.width(canvasWidthL),$footerRowR.width(canvasWidthR)),options.createPreHeaderPanel&&$preHeaderPanel.width(canvasWidth),$viewportTopL.width(canvasWidthL),$viewportTopR.width(viewportW-canvasWidthL),hasFrozenRows&&($paneBottomL.width(canvasWidthL),$paneBottomR.css("left",canvasWidthL),$viewportBottomL.width(canvasWidthL),$viewportBottomR.width(viewportW-canvasWidthL),$canvasBottomL.width(canvasWidthL),$canvasBottomR.width(canvasWidthR))):($paneHeaderL.width("100%"),$paneTopL.width("100%"),$headerRowScrollerL.width("100%"),$headerRowL.width(canvasWidth),options.createFooterRow&&($footerRowScrollerL.width("100%"),$footerRowL.width(canvasWidth)),options.createPreHeaderPanel&&($preHeaderPanel.width("100%"),$preHeaderPanel.width(canvasWidth)),$viewportTopL.width("100%"),hasFrozenRows&&($viewportBottomL.width("100%"),$canvasBottomL.width(canvasWidthL))),viewportHasHScroll=canvasWidth>=viewportW-scrollbarDimensions.width),$headerRowSpacerL.width(canvasWidth+(viewportHasVScroll?scrollbarDimensions.width:0)),$headerRowSpacerR.width(canvasWidth+(viewportHasVScroll?scrollbarDimensions.width:0)),options.createFooterRow&&($footerRowSpacerL.width(canvasWidth+(viewportHasVScroll?scrollbarDimensions.width:0)),$footerRowSpacerR.width(canvasWidth+(viewportHasVScroll?scrollbarDimensions.width:0))),(e||t)&&applyColumnWidths()}function disableSelection(t){t&&t.jquery&&t.attr("unselectable","on").css("MozUserSelect","none").on("selectstart.ui",(function(){return!1}))}function getMaxSupportedCssHeight(){for(var t=1e6,e=navigator.userAgent.toLowerCase().match(/firefox/)?6e6:1e9,n=$("<div style='display:none' />").appendTo(document.body);;){var r=2*t;if(n.css("height",r),r>e||n.height()!==r)break;t=r}return n.remove(),t}function getUID(){return uid}function getHeaderColumnWidthDiff(){return headerColumnWidthDiff}function getScrollbarDimensions(){return scrollbarDimensions}function bindAncestorScrollEvents(){for(var t=hasFrozenRows&&!options.frozenBottom?$canvasBottomL[0]:$canvasTopL[0];(t=t.parentNode)!=document.body&&null!=t;)if(t==$viewportTopL[0]||t.scrollWidth!=t.clientWidth||t.scrollHeight!=t.clientHeight){var e=$(t);$boundAncestors=$boundAncestors?$boundAncestors.add(e):e,e.on("scroll."+uid,handleActiveCellPositionChange)}}function unbindAncestorScrollEvents(){$boundAncestors&&($boundAncestors.off("scroll."+uid),$boundAncestors=null)}function updateColumnHeader(t,e,n){if(initialized){var r=getColumnIndex(t);if(null!=r){var i=columns[r],o=$headers.children().eq(r);o&&(void 0!==e&&(columns[r].name=e),void 0!==n&&(columns[r].toolTip=n),trigger(self.onBeforeHeaderCellDestroy,{node:o[0],column:i,grid:self}),o.attr("title",n||"").children().eq(0).html(e),trigger(self.onHeaderCellRendered,{node:o[0],column:i,grid:self}))}}}function getHeader(t){if(!t)return hasFrozenColumns()?$headers:$headerL;var e=getColumnIndex(t.id);return hasFrozenColumns()?e<=options.frozenColumn?$headerL:$headerR:$headerL}function getHeaderColumn(t){var e="number"==typeof t?t:getColumnIndex(t),n=hasFrozenColumns()?e<=options.frozenColumn?$headerL:$headerR:$headerL,r=hasFrozenColumns()?e<=options.frozenColumn?e:e-options.frozenColumn-1:e,i=n.children().eq(r);return i&&i[0]}function getHeaderRow(){return hasFrozenColumns()?$headerRow:$headerRow[0]}function getFooterRow(){return hasFrozenColumns()?$footerRow:$footerRow[0]}function getPreHeaderPanel(){return $preHeaderPanel[0]}function getPreHeaderPanelRight(){return $preHeaderPanelR[0]}function getHeaderRowColumn(t){var e,n="number"==typeof t?t:getColumnIndex(t);hasFrozenColumns()?n<=options.frozenColumn?e=$headerRowL:(e=$headerRowR,n-=options.frozenColumn+1):e=$headerRowL;var r=e.children().eq(n);return r&&r[0]}function getFooterRowColumn(t){var e,n="number"==typeof t?t:getColumnIndex(t);hasFrozenColumns()?n<=options.frozenColumn?e=$footerRowL:(e=$footerRowR,n-=options.frozenColumn+1):e=$footerRowL;var r=e&&e.children().eq(n);return r&&r[0]}function createColumnFooter(){if(options.createFooterRow){$footerRow.find(".slick-footerrow-column").each((function(){var t=$(this).data("column");t&&trigger(self.onBeforeFooterRowCellDestroy,{node:this,column:t,grid:self})})),$footerRowL.empty(),$footerRowR.empty();for(var t=0;t<columns.length;t++){var e=columns[t],n=$("<div class='ui-state-default slick-footerrow-column l"+t+" r"+t+"'></div>").data("column",e).addClass(hasFrozenColumns()&&t<=options.frozenColumn?"frozen":"").appendTo(hasFrozenColumns()&&t>options.frozenColumn?$footerRowR:$footerRowL);trigger(self.onFooterRowCellRendered,{node:n[0],column:e,grid:self})}}}function createColumnGroupHeaders(){var t=0,e=!1;if(treeColumns.hasDepth()){for(var n=0;n<$groupHeadersL.length;n++){$groupHeadersL[n].empty(),$groupHeadersR[n].empty();var r=treeColumns.getColumnsInDepth(n);for(var i in r){var o=r[i];t+=o.extractColumns().length,hasFrozenColumns()&&0===n&&t-1===options.frozenColumn&&(e=!0),$("<div class='ui-state-default slick-group-header-column' />").html("<span class='slick-column-name'>"+o.name+"</span>").attr("id",""+uid+o.id).attr("title",o.toolTip||"").data("column",o).addClass(o.headerCssClass||"").addClass(hasFrozenColumns()&&t-1>options.frozenColumn?"frozen":"").appendTo(hasFrozenColumns()&&t-1>options.frozenColumn?$groupHeadersR[n]:$groupHeadersL[n])}if(hasFrozenColumns()&&0===n&&!e){$groupHeadersL[n].empty(),$groupHeadersR[n].empty(),alert("All columns of group should to be grouped!");break}}applyColumnGroupHeaderWidths()}}function createColumnHeaders(){function t(){$(this).addClass("ui-state-hover")}function e(){$(this).removeClass("ui-state-hover")}$headers.find(".slick-header-column").each((function(){var t=$(this).data("column");t&&trigger(self.onBeforeHeaderCellDestroy,{node:this,column:t,grid:self})})),$headerL.empty(),$headerR.empty(),getHeadersWidth(),$headerL.width(headersWidthL),$headerR.width(headersWidthR),$headerRow.find(".slick-headerrow-column").each((function(){var t=$(this).data("column");t&&trigger(self.onBeforeHeaderRowCellDestroy,{node:this,column:t,grid:self})})),$headerRowL.empty(),$headerRowR.empty(),options.createFooterRow&&($footerRowL.find(".slick-footerrow-column").each((function(){var t=$(this).data("column");t&&trigger(self.onBeforeFooterRowCellDestroy,{node:this,column:t,grid:self})})),$footerRowL.empty(),hasFrozenColumns()&&($footerRowR.find(".slick-footerrow-column").each((function(){var t=$(this).data("column");t&&trigger(self.onBeforeFooterRowCellDestroy,{node:this,column:t,grid:self})})),$footerRowR.empty()));for(var n=0;n<columns.length;n++){var r=columns[n],i=hasFrozenColumns()?n<=options.frozenColumn?$headerL:$headerR:$headerL,o=hasFrozenColumns()?n<=options.frozenColumn?$headerRowL:$headerRowR:$headerRowL,a=$("<div class='ui-state-default slick-header-column' />").html("<span class='slick-column-name'>"+r.name+"</span>").width(r.width-headerColumnWidthDiff).attr("id",""+uid+r.id).attr("title",r.toolTip||"").data("column",r).addClass(r.headerCssClass||"").addClass(hasFrozenColumns()&&n<=options.frozenColumn?"frozen":"").appendTo(i);if((options.enableColumnReorder||r.sortable)&&a.on("mouseenter",t).on("mouseleave",e),r.hasOwnProperty("headerCellAttrs")&&r.headerCellAttrs instanceof Object)for(var s in r.headerCellAttrs)r.headerCellAttrs.hasOwnProperty(s)&&a.attr(s,r.headerCellAttrs[s]);if(r.sortable&&(a.addClass("slick-header-sortable"),a.append("<span class='slick-sort-indicator"+(options.numberedMultiColumnSort&&!options.sortColNumberInSeparateSpan?" slick-sort-indicator-numbered":"")+"' />"),options.numberedMultiColumnSort&&options.sortColNumberInSeparateSpan&&a.append("<span class='slick-sort-indicator-numbered' />")),trigger(self.onHeaderCellRendered,{node:a[0],column:r,grid:self}),options.showHeaderRow){var l=$("<div class='ui-state-default slick-headerrow-column l"+n+" r"+n+"'></div>").data("column",r).addClass(hasFrozenColumns()&&n<=options.frozenColumn?"frozen":"").appendTo(o);trigger(self.onHeaderRowCellRendered,{node:l[0],column:r,grid:self})}if(options.createFooterRow&&options.showFooterRow){var c=$("<div class='ui-state-default slick-footerrow-column l"+n+" r"+n+"'></div>").data("column",r).appendTo($footerRow);trigger(self.onFooterRowCellRendered,{node:c[0],column:r,grid:self})}}setSortColumns(sortColumns),setupColumnResize(),options.enableColumnReorder&&("function"==typeof options.enableColumnReorder?options.enableColumnReorder(self,$headers,headerColumnWidthDiff,setColumns,setupColumnResize,columns,getColumnIndex,uid,trigger):setupColumnReorder())}function setupColumnSort(){$headers.click((function(t){if(!columnResizeDragging&&(t.metaKey=t.metaKey||t.ctrlKey,!$(t.target).hasClass("slick-resizable-handle"))){var e=$(t.target).closest(".slick-header-column");if(e.length){var n=e.data("column");if(n.sortable){if(!getEditorLock().commitCurrentEdit())return;for(var r=$.extend(!0,[],sortColumns),i=null,o=0;o<sortColumns.length;o++)if(sortColumns[o].columnId==n.id){(i=sortColumns[o]).sortAsc=!i.sortAsc;break}var a,s=!!i;options.tristateMultiColumnSort?(i||(i={columnId:n.id,sortAsc:n.defaultSortAsc}),s&&i.sortAsc&&(sortColumns.splice(o,1),i=null),options.multiColumnSort||(sortColumns=[]),!i||s&&options.multiColumnSort||sortColumns.push(i)):t.metaKey&&options.multiColumnSort?i&&sortColumns.splice(o,1):((t.shiftKey||t.metaKey)&&options.multiColumnSort||(sortColumns=[]),i?0===sortColumns.length&&sortColumns.push(i):(i={columnId:n.id,sortAsc:n.defaultSortAsc},sortColumns.push(i))),a=options.multiColumnSort?{multiColumnSort:!0,previousSortColumns:r,sortCols:$.map(sortColumns,(function(t){return{columnId:columns[getColumnIndex(t.columnId)].id,sortCol:columns[getColumnIndex(t.columnId)],sortAsc:t.sortAsc}}))}:{multiColumnSort:!1,previousSortColumns:r,columnId:sortColumns.length>0?n.id:null,sortCol:sortColumns.length>0?n:null,sortAsc:!(sortColumns.length>0)||sortColumns[0].sortAsc},!1!==trigger(self.onBeforeSort,a,t)&&(setSortColumns(sortColumns),trigger(self.onSort,a,t))}}}}))}function currentPositionInHeader(t){var e=0;return $headers.find(".slick-header-column").each((function(n){if(this.id==t)return e=n,!1})),e}function limitPositionInGroup(t){var e,n=0,r=0;return treeColumns.getColumnsInDepth($groupHeadersL.length-1).some((function(i){return n=r,r+=i.columns.length,i.columns.some((function(n){return n.id===t&&(e=i),e})),e})),r--,{start:n,end:r,group:e}}function remove(t,e){var n=t.lastIndexOf(e);n>-1&&(t.splice(n,1),remove(t,e))}function columnPositionValidInGroup(t){var e=currentPositionInHeader(t[0].id),n=limitPositionInGroup(t.data("column").id),r=n.start<=e&&e<=n.end;return{limit:n,valid:r,message:r?"":'Column "'.concat(t.text(),'" can be reordered only within the "',n.group.name,'" group!')}}function setupColumnReorder(){$headers.filter(":ui-sortable").sortable("destroy");var t,e=null;function n(){$viewportScrollContainerX[0].scrollLeft=$viewportScrollContainerX[0].scrollLeft+10}function r(){$viewportScrollContainerX[0].scrollLeft=$viewportScrollContainerX[0].scrollLeft-10}$headers.sortable({containment:"parent",distance:3,axis:"x",cursor:"default",tolerance:"intersection",helper:"clone",placeholder:"slick-sortable-placeholder ui-state-default slick-header-column",start:function(e,n){n.placeholder.width(n.helper.outerWidth()-headerColumnWidthDiff),t=!hasFrozenColumns()||n.placeholder.offset().left+n.placeholder.width()>$viewportScrollContainerX.offset().left,$(n.helper).addClass("slick-header-column-active")},beforeStop:function(t,e){$(e.helper).removeClass("slick-header-column-active")},sort:function(i,o){t&&i.originalEvent.pageX>$container[0].clientWidth?e||(e=setInterval(n,100)):t&&i.originalEvent.pageX<$viewportScrollContainerX.offset().left?e||(e=setInterval(r,100)):(clearInterval(e),e=null)},stop:function(t,n){var r=!1;clearInterval(e),e=null;var i=null;if(treeColumns.hasDepth()){var o=columnPositionValidInGroup(n.item);i=o.limit,(r=!o.valid)&&alert(o.message)}if(!r&&getEditorLock().commitCurrentEdit()){var a=$headerL.sortable("toArray");a=a.concat($headerR.sortable("toArray"));for(var s=[],l=0;l<a.length;l++)s.push(columns[getColumnIndex(a[l].replace(uid,""))]);setColumns(s),trigger(self.onColumnsReordered,{impactedColumns:getImpactedColumns(i)}),t.stopPropagation(),setupColumnResize()}else $(this).sortable("cancel")}})}function getImpactedColumns(t){var e=[];if(t)for(var n=t.start;n<=t.end;n++)e.push(columns[n]);else e=columns;return e}function setupColumnResize(){var t,e,n,r,i,o,a,s,l,c=0;(i=$headers.children()).find(".slick-resizable-handle").remove(),i.each((function(t,e){t>=columns.length||columns[t].resizable&&(void 0===s&&(s=t),l=t)})),void 0!==s&&i.each((function(u,d){u>=columns.length||u<s||options.forceFitColumns&&u>=l||($(d),$("<div class='slick-resizable-handle' />").appendTo(d).on("dragstart",(function(e,s){if(!getEditorLock().commitCurrentEdit())return!1;r=e.pageX,c=0,$(this).parent().addClass("slick-header-column-active");var l=null,d=null;if(i.each((function(t,e){t>=columns.length||(columns[t].previousWidth=$(e).outerWidth())})),options.forceFitColumns)for(l=0,d=0,t=u+1;t<columns.length;t++)(n=columns[t]).resizable&&(null!==d&&(n.maxWidth?d+=n.maxWidth-n.previousWidth:d=null),l+=n.previousWidth-Math.max(n.minWidth||0,absoluteColumnMinWidth));var h=0,p=0;for(t=0;t<=u;t++)(n=columns[t]).resizable&&(null!==p&&(n.maxWidth?p+=n.maxWidth-n.previousWidth:p=null),h+=n.previousWidth-Math.max(n.minWidth||0,absoluteColumnMinWidth));null===l&&(l=1e5),null===h&&(h=1e5),null===d&&(d=1e5),null===p&&(p=1e5),a=r+Math.min(l,p),o=r-Math.min(h,d)})).on("drag",(function(i,s){columnResizeDragging=!0;var l,d,h=Math.min(a,Math.max(o,i.pageX))-r,p=0,f=viewportHasVScroll?viewportW-scrollbarDimensions.width:viewportW;if(h<0){for(d=h,t=u;t>=0;t--)(n=columns[t]).resizable&&(l=Math.max(n.minWidth||0,absoluteColumnMinWidth),d&&n.previousWidth+d<l?(d+=n.previousWidth-l,n.width=l):(n.width=n.previousWidth+d,d=0));for(e=0;e<=u;e++)n=columns[e],hasFrozenColumns()&&e>options.frozenColumn?n.width:p+=n.width;if(options.forceFitColumns)for(d=-h,t=u+1;t<columns.length;t++)(n=columns[t]).resizable&&(d&&n.maxWidth&&n.maxWidth-n.previousWidth<d?(d-=n.maxWidth-n.previousWidth,n.width=n.maxWidth):(n.width=n.previousWidth+d,d=0),hasFrozenColumns()&&t>options.frozenColumn?n.width:p+=n.width);else for(t=u+1;t<columns.length;t++)n=columns[t],hasFrozenColumns()&&t>options.frozenColumn?n.width:p+=n.width;if(options.forceFitColumns)for(d=-h,t=u+1;t<columns.length;t++)(n=columns[t]).resizable&&(d&&n.maxWidth&&n.maxWidth-n.previousWidth<d?(d-=n.maxWidth-n.previousWidth,n.width=n.maxWidth):(n.width=n.previousWidth+d,d=0))}else{for(d=h,p=0,t=u;t>=0;t--)if((n=columns[t]).resizable)if(d&&n.maxWidth&&n.maxWidth-n.previousWidth<d)d-=n.maxWidth-n.previousWidth,n.width=n.maxWidth;else{var Q=n.previousWidth+d,T=canvasWidthL+d;hasFrozenColumns()&&t<=options.frozenColumn?(Q>c&&T<f-options.frozenRightViewportMinWidth&&(c=Q),n.width=T+options.frozenRightViewportMinWidth>f?c:Q):n.width=Q,d=0}for(e=0;e<=u;e++)n=columns[e],hasFrozenColumns()&&e>options.frozenColumn?n.width:p+=n.width;if(options.forceFitColumns)for(d=-h,t=u+1;t<columns.length;t++)(n=columns[t]).resizable&&(l=Math.max(n.minWidth||0,absoluteColumnMinWidth),d&&n.previousWidth+d<l?(d+=n.previousWidth-l,n.width=l):(n.width=n.previousWidth+d,d=0),hasFrozenColumns()&&t>options.frozenColumn?n.width:p+=n.width);else for(t=u+1;t<columns.length;t++)n=columns[t],hasFrozenColumns()&&t>options.frozenColumn?n.width:p+=n.width}hasFrozenColumns()&&p!=canvasWidthL&&($headerL.width(p+1e3),$paneHeaderR.css("left",p)),applyColumnHeaderWidths(),applyColumnGroupHeaderWidths(),options.syncColumnCellResize&&applyColumnWidths(),trigger(self.onColumnsDrag,{triggeredByColumn:$(this).parent().attr("id").replace(uid,""),resizeHandle:$(this)})})).on("dragend",(function(e,r){$(this).parent().removeClass("slick-header-column-active");var o,a=$(this).parent().attr("id").replace(uid,"");for(!0===trigger(self.onBeforeColumnsResize,{triggeredByColumn:a})&&(applyColumnHeaderWidths(),applyColumnGroupHeaderWidths()),t=0;t<columns.length;t++)n=columns[t],o=$(i[t]).outerWidth(),n.previousWidth!==o&&n.rerenderOnResize&&invalidateAllRows();updateCanvasWidth(!0),render(),trigger(self.onColumnsResized,{triggeredByColumn:a}),setTimeout((function(){columnResizeDragging=!1}),300)})).on("dblclick",(function(){var t=$(this).parent().attr("id").replace(uid,"");trigger(self.onColumnsResizeDblClick,{triggeredByColumn:t})})))}))}function getVBoxDelta(t){var e=0;return t&&"function"==typeof t.css&&$.each(["borderTopWidth","borderBottomWidth","paddingTop","paddingBottom"],(function(n,r){e+=parseFloat(t.css(r))||0})),e}function setFrozenOptions(){if(options.frozenColumn=options.frozenColumn>=0&&options.frozenColumn<columns.length?parseInt(options.frozenColumn):-1,options.frozenRow>-1){hasFrozenRows=!0,frozenRowsHeight=options.frozenRow*options.rowHeight;var t=getDataLength();actualFrozenRow=options.frozenBottom?t-options.frozenRow:options.frozenRow}else hasFrozenRows=!1}function setPaneVisibility(){hasFrozenColumns()?($paneHeaderR.show(),$paneTopR.show(),hasFrozenRows?($paneBottomL.show(),$paneBottomR.show()):($paneBottomR.hide(),$paneBottomL.hide())):($paneHeaderR.hide(),$paneTopR.hide(),$paneBottomR.hide(),hasFrozenRows?$paneBottomL.show():($paneBottomR.hide(),$paneBottomL.hide()))}function setOverflow(){$viewportTopL.css({"overflow-x":hasFrozenColumns()?hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"hidden":"scroll":hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"hidden":"auto","overflow-y":!hasFrozenColumns()&&options.alwaysShowVerticalScroll?"scroll":hasFrozenColumns()?"hidden":hasFrozenRows?"scroll":"auto"}),$viewportTopR.css({"overflow-x":hasFrozenColumns()?hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"hidden":"scroll":hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"hidden":"auto","overflow-y":options.alwaysShowVerticalScroll?"scroll":(hasFrozenColumns(),hasFrozenRows?"scroll":"auto")}),$viewportBottomL.css({"overflow-x":hasFrozenColumns()?hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"scroll":"auto":(hasFrozenRows&&options.alwaysAllowHorizontalScroll,"auto"),"overflow-y":!hasFrozenColumns()&&options.alwaysShowVerticalScroll?"scroll":hasFrozenColumns()?"hidden":hasFrozenRows?"scroll":"auto"}),$viewportBottomR.css({"overflow-x":hasFrozenColumns()?hasFrozenRows&&!options.alwaysAllowHorizontalScroll?"scroll":"auto":(hasFrozenRows&&options.alwaysAllowHorizontalScroll,"auto"),"overflow-y":options.alwaysShowVerticalScroll?"scroll":(hasFrozenColumns(),"auto")}),options.viewportClass&&($viewportTopL.toggleClass(options.viewportClass,!0),$viewportTopR.toggleClass(options.viewportClass,!0),$viewportBottomL.toggleClass(options.viewportClass,!0),$viewportBottomR.toggleClass(options.viewportClass,!0))}function setScroller(){hasFrozenColumns()?($headerScrollContainer=$headerScrollerR,$headerRowScrollContainer=$headerRowScrollerR,$footerRowScrollContainer=$footerRowScrollerR,hasFrozenRows?options.frozenBottom?($viewportScrollContainerX=$viewportBottomR,$viewportScrollContainerY=$viewportTopR):$viewportScrollContainerX=$viewportScrollContainerY=$viewportBottomR:$viewportScrollContainerX=$viewportScrollContainerY=$viewportTopR):($headerScrollContainer=$headerScrollerL,$headerRowScrollContainer=$headerRowScrollerL,$footerRowScrollContainer=$footerRowScrollerL,hasFrozenRows?options.frozenBottom?($viewportScrollContainerX=$viewportBottomL,$viewportScrollContainerY=$viewportTopL):$viewportScrollContainerX=$viewportScrollContainerY=$viewportBottomL:$viewportScrollContainerX=$viewportScrollContainerY=$viewportTopL)}function measureCellPaddingAndBorder(){var t,e=["borderLeftWidth","borderRightWidth","paddingLeft","paddingRight"],n=["borderTopWidth","borderBottomWidth","paddingTop","paddingBottom"],r=$.fn.jquery.split(".");jQueryNewWidthBehaviour=1==r[0]&&r[1]>=8||r[0]>=2,t=$("<div class='ui-state-default slick-header-column' style='visibility:hidden'>-</div>").appendTo($headers),headerColumnWidthDiff=headerColumnHeightDiff=0,"border-box"!=t.css("box-sizing")&&"border-box"!=t.css("-moz-box-sizing")&&"border-box"!=t.css("-webkit-box-sizing")&&($.each(e,(function(e,n){headerColumnWidthDiff+=parseFloat(t.css(n))||0})),$.each(n,(function(e,n){headerColumnHeightDiff+=parseFloat(t.css(n))||0}))),t.remove();var i=$("<div class='slick-row' />").appendTo($canvas);t=$("<div class='slick-cell' id='' style='visibility:hidden'>-</div>").appendTo(i),cellWidthDiff=cellHeightDiff=0,"border-box"!=t.css("box-sizing")&&"border-box"!=t.css("-moz-box-sizing")&&"border-box"!=t.css("-webkit-box-sizing")&&($.each(e,(function(e,n){cellWidthDiff+=parseFloat(t.css(n))||0})),$.each(n,(function(e,n){cellHeightDiff+=parseFloat(t.css(n))||0}))),i.remove(),absoluteColumnMinWidth=Math.max(headerColumnWidthDiff,cellWidthDiff)}function createCssRules(){$style=$("<style type='text/css' rel='stylesheet' />"),$container[0].parentNode instanceof ShadowRoot?$container[0].parentNode.insertBefore($style[0],$container[0]):$style.appendTo($("head"));for(var t=options.rowHeight-cellHeightDiff,e=["."+uid+" .slick-group-header-column { left: 1000px; }","."+uid+" .slick-header-column { left: 1000px; }","."+uid+" .slick-top-panel { height:"+options.topPanelHeight+"px; }","."+uid+" .slick-preheader-panel { height:"+options.preHeaderPanelHeight+"px; }","."+uid+" .slick-headerrow-columns { height:"+options.headerRowHeight+"px; }","."+uid+" .slick-footerrow-columns { height:"+options.footerRowHeight+"px; }","."+uid+" .slick-cell { height:"+t+"px; }","."+uid+" .slick-row { height:"+options.rowHeight+"px; }"],n=0;n<columns.length;n++)e.push("."+uid+" .l"+n+" { }"),e.push("."+uid+" .r"+n+" { }");$style[0].styleSheet?$style[0].styleSheet.cssText=e.join(" "):$style[0].appendChild(document.createTextNode(e.join(" ")))}function getColumnCssRules(t){var e;if(!stylesheet){var n;for(n=$container[0].parentNode instanceof ShadowRoot?$container[0].parentNode.styleSheets:document.styleSheets,e=0;e<n.length;e++)if((n[e].ownerNode||n[e].owningElement)==$style[0]){stylesheet=n[e];break}if(!stylesheet)throw new Error("SlickGrid Cannot find stylesheet.");columnCssRulesL=[],columnCssRulesR=[];var r,i,o=stylesheet.cssRules||stylesheet.rules;for(e=0;e<o.length;e++){var a=o[e].selectorText;(r=/\.l\d+/.exec(a))?(i=parseInt(r[0].substr(2,r[0].length-2),10),columnCssRulesL[i]=o[e]):(r=/\.r\d+/.exec(a))&&(i=parseInt(r[0].substr(2,r[0].length-2),10),columnCssRulesR[i]=o[e])}}return{left:columnCssRulesL[t],right:columnCssRulesR[t]}}function removeCssRules(){$style.remove(),stylesheet=null}function destroy(t){getEditorLock().cancelCurrentEdit(),trigger(self.onBeforeDestroy,{});for(var e=plugins.length;e--;)unregisterPlugin(plugins[e]);options.enableColumnReorder&&$headers.filter(":ui-sortable").sortable("destroy"),unbindAncestorScrollEvents(),$container.off(".slickgrid"),removeCssRules(),$canvas.off(),$viewport.off(),$headerScroller.off(),$headerRowScroller.off(),$footerRow&&$footerRow.off(),$footerRowScroller&&$footerRowScroller.off(),$preHeaderPanelScroller&&$preHeaderPanelScroller.off(),$focusSink.off(),$(".slick-resizable-handle").off(),$(".slick-header-column").off(),$container.empty().removeClass(uid),t&&destroyAllElements()}function destroyAllElements(){$activeCanvasNode=null,$activeViewportNode=null,$boundAncestors=null,$canvas=null,$canvasTopL=null,$canvasTopR=null,$canvasBottomL=null,$canvasBottomR=null,$container=null,$focusSink=null,$focusSink2=null,$groupHeaders=null,$groupHeadersL=null,$groupHeadersR=null,$headerL=null,$headerR=null,$headers=null,$headerRow=null,$headerRowL=null,$headerRowR=null,$headerRowSpacerL=null,$headerRowSpacerR=null,$headerRowScrollContainer=null,$headerRowScroller=null,$headerRowScrollerL=null,$headerRowScrollerR=null,$headerScrollContainer=null,$headerScroller=null,$headerScrollerL=null,$headerScrollerR=null,$hiddenParents=null,$footerRow=null,$footerRowL=null,$footerRowR=null,$footerRowSpacerL=null,$footerRowSpacerR=null,$footerRowScroller=null,$footerRowScrollerL=null,$footerRowScrollerR=null,$footerRowScrollContainer=null,$preHeaderPanel=null,$preHeaderPanelR=null,$preHeaderPanelScroller=null,$preHeaderPanelScrollerR=null,$preHeaderPanelSpacer=null,$preHeaderPanelSpacerR=null,$topPanel=null,$topPanelScroller=null,$style=null,$topPanelScrollerL=null,$topPanelScrollerR=null,$topPanelL=null,$topPanelR=null,$paneHeaderL=null,$paneHeaderR=null,$paneTopL=null,$paneTopR=null,$paneBottomL=null,$paneBottomR=null,$viewport=null,$viewportTopL=null,$viewportTopR=null,$viewportBottomL=null,$viewportBottomR=null,$viewportScrollContainerX=null,$viewportScrollContainerY=null}var canvas=null,canvas_context=null;function autosizeColumn(t,e){var n=t;if("number"==typeof t)n=columns[t];else if("string"==typeof t)for(var r=0;r<columns.length;r++)columns[r].Id===t&&(n=columns[r]);getColAutosizeWidth(n,$(getCanvasNode(0,0)),e)}function autosizeColumns(t,e){if((t=t||options.autosizeColsMode)!==Slick.GridAutosizeColsMode.LegacyForceFit&&t!==Slick.GridAutosizeColsMode.LegacyOff){if(t!==Slick.GridAutosizeColsMode.None){(canvas=document.createElement("canvas"))&&canvas.getContext&&(canvas_context=canvas.getContext("2d"));var n,r,i,o,a=$(getCanvasNode(0,0)),s=viewportHasVScroll?viewportW-scrollbarDimensions.width:viewportW,l=0,c=0,u=0,d=0,h=0;for(n=0;n<columns.length;n++)getColAutosizeWidth(r=columns[n],a,e),h+=r.autoSize.autosizeMode===Slick.ColAutosizeMode.Locked?r.width:0,d+=r.autoSize.autosizeMode===Slick.ColAutosizeMode.Locked?r.width:r.minWidth,l+=r.autoSize.widthPx,c+=r.autoSize.sizeToRemaining?0:r.autoSize.widthPx,u+=r.autoSize.sizeToRemaining&&r.minWidth||0;var p=l-c;if(t===Slick.GridAutosizeColsMode.FitViewportToCols){var f=l+scrollbarDimensions.width;t=Slick.GridAutosizeColsMode.IgnoreViewport,options.viewportMaxWidthPx&&f>options.viewportMaxWidthPx?(f=options.viewportMaxWidthPx,t=Slick.GridAutosizeColsMode.FitColsToViewport):options.viewportMinWidthPx&&f<options.viewportMinWidthPx&&(f=options.viewportMinWidthPx,t=Slick.GridAutosizeColsMode.FitColsToViewport),$container.width(f)}if(t===Slick.GridAutosizeColsMode.FitColsToViewport)if(p>0&&c<s-u)for(n=0;n<columns.length;n++){var Q=s-c;i=(r=columns[n]).autoSize.sizeToRemaining?Q*r.autoSize.widthPx/p:r.autoSize.widthPx,r.rerenderOnResize&&r.width!=i&&(o=!0),r.width=i}else if(options.viewportSwitchToScrollModeWidthPercent&&c+u>s*options.viewportSwitchToScrollModeWidthPercent/100||d>s)t=Slick.GridAutosizeColsMode.IgnoreViewport;else{var T=c-h,m=s-h-u;for(n=0;n<columns.length;n++)i=(r=columns[n]).width,r.autoSize.autosizeMode!==Slick.ColAutosizeMode.Locked&&(r.autoSize.sizeToRemaining?i=r.minWidth:((i=m/T*r.autoSize.widthPx)<r.minWidth&&(i=r.minWidth),T-=r.autoSize.widthPx,m-=i)),r.rerenderOnResize&&r.width!=i&&(o=!0),r.width=i}if(t===Slick.GridAutosizeColsMode.IgnoreViewport)for(n=0;n<columns.length;n++)i=columns[n].autoSize.widthPx,columns[n].rerenderOnResize&&columns[n].width!=i&&(o=!0),columns[n].width=i;reRenderColumns(o)}}else legacyAutosizeColumns()}function LogColWidths(){for(var t="Col Widths:",e=0;e<columns.length;e++)t+=" "+columns[e].width;console.log(t)}function getColAutosizeWidth(t,e,n){var r=t.autoSize;if(r.widthPx=t.width,r.autosizeMode!==Slick.ColAutosizeMode.Locked&&r.autosizeMode!==Slick.ColAutosizeMode.Guide){var i=getDataLength();if(r.autosizeMode===Slick.ColAutosizeMode.ContentIntelligent){var o,a=r.colDataTypeOf;if(i>0){var s=getDataItem(0);s&&"object"==(a=typeof(o=s[t.field]))&&(o instanceof Date&&(a="date"),"undefined"!=typeof moment&&o instanceof moment&&(a="moment"))}"boolean"===a&&(r.colValueArray=[!0,!1]),"number"===a&&(r.valueFilterMode=Slick.ValueFilterMode.GetGreatestAndSub,r.rowSelectionMode=Slick.RowSelectionMode.AllRows),"string"===a&&(r.valueFilterMode=Slick.ValueFilterMode.GetLongestText,r.rowSelectionMode=Slick.RowSelectionMode.AllRows,r.allowAddlPercent=5),"date"===a&&(r.colValueArray=[new Date(2009,8,30,12,20,20)]),"moment"===a&&"undefined"!=typeof moment&&(r.colValueArray=[moment([2009,8,30,12,20,20])])}var l=getColContentSize(t,e,n);l=l*(r.allowAddlPercent?1+r.allowAddlPercent/100:1)+options.autosizeColPaddingPx,t.minWidth&&l<t.minWidth&&(l=t.minWidth),t.maxWidth&&l>t.maxWidth&&(l=t.maxWidth),r.widthPx=l}}function getColContentSize(t,e,n){var r,i=t.autoSize,o=1,a=0,s=0;if(i.ignoreHeaderText||(s=getColHeaderWidth(t)),i.colValueArray)return a=getColWidth(t,e,i.colValueArray),Math.max(s,a);var l=getData();l.getItems&&(l=l.getItems());var c=(n?i.rowSelectionModeOnInit:void 0)||i.rowSelectionMode;if(c===Slick.RowSelectionMode.FirstRow&&(l=l.slice(0,1)),c===Slick.RowSelectionMode.LastRow&&(l=l.slice(l.length-1,l.length)),c===Slick.RowSelectionMode.FirstNRows&&(l=l.slice(0,i.rowSelectionCount)),i.valueFilterMode===Slick.ValueFilterMode.DeDuplicate){var u={};for(d=0,r=l.length;d<r;d++)u[l[d][t.field]]=!0;if(Object.keys)l=Object.keys(u);else for(var d in l=[],u)l.push(d)}if(i.valueFilterMode===Slick.ValueFilterMode.GetGreatestAndSub){var h,p=0;for(d=0,r=l.length;d<r;d++)Q=l[d][t.field],Math.abs(Q)>p&&(h=Q,p=Math.abs(Q));h=""+h,l=[h=+(h=Array(h.length+1).join("9"))]}if(i.valueFilterMode===Slick.ValueFilterMode.GetLongestTextAndSub){var f=0;for(d=0,r=l.length;d<r;d++)((Q=l[d][t.field])||"").length>f&&(f=Q.length);Q=Array(f+1).join("m"),o=options.autosizeTextAvgToMWidthRatio,l=[Q]}if(i.valueFilterMode===Slick.ValueFilterMode.GetLongestText){f=0;var Q,T=0;if(row.length){for(d=0,r=l.length;d<r;d++)((Q=l[d][t.field])||"").length>f&&(f=Q.length,T=d);Q=l[T][t.field]}l=[Q]}return a=getColWidth(t,e,l)*o,Math.max(s,a)}function getColWidth(t,e,n){var r=getColumnIndex(t.id),i=$('<div class="slick-row ui-widget-content"></div>'),o=$('<div class="slick-cell"></div>');o.css({position:"absolute",visibility:"hidden","text-overflow":"initial","white-space":"nowrap"}),i.append(o),e.append(i);var a,s,l,c,u=0;return canvas_context&&t.autoSize.widthEvalMode===Slick.WidthEvalMode.CanvasTextSize?(canvas_context.font=o.css("font-size")+" "+o.css("font-family"),$(n).each((function(e,n){c=Array.isArray(n)?n[t.field]:n,(a=(s=""+c)?canvas_context.measureText(s).width:0)>u&&(u=a,l=s)})),o.html(l),a=o.outerWidth(),i.remove(),o=null,a):($(n).each((function(e,n){c=Array.isArray(n)?n[t.field]:n,applyFormatResultToCellNode(t.formatterOverride?t.formatterOverride(e,r,c,t,n,self):t.formatter?t.formatter(e,r,c,t,n,self):""+c,o[0]),(a=o.outerWidth())>u&&(u=a)})),i.remove(),o=null,u)}function getColHeaderWidth(t){var e=0,n=getUID()+t.id,r=document.getElementById(n),i=n+"_";if(r){var o=r.cloneNode(!0);o.id=i,o.style.cssText="position: absolute; visibility: hidden;right: auto;text-overflow: initial;white-space: nowrap;",r.parentNode.insertBefore(o,r),e=o.offsetWidth,o.parentNode.removeChild(o)}else{var a=getHeader(t);e=(r=$("<div class='ui-state-default slick-header-column' />").html("<span class='slick-column-name'>"+t.name+"</span>").attr("id",i).css({position:"absolute",visibility:"hidden",right:"auto","text-overflow:":"initial","white-space":"nowrap"}).addClass(t.headerCssClass||"").appendTo(a))[0].offsetWidth,a[0].removeChild(r[0])}return e}function legacyAutosizeColumns(){var t,e,n,r=[],i=0,o=0,a=viewportHasVScroll?viewportW-scrollbarDimensions.width:viewportW;for(t=0;t<columns.length;t++)e=columns[t],r.push(e.width),o+=e.width,e.resizable&&(i+=e.width-Math.max(e.minWidth,absoluteColumnMinWidth));for(n=o;o>a&&i;){var s=(o-a)/i;for(t=0;t<columns.length&&o>a;t++){e=columns[t];var l=r[t];if(!(!e.resizable||l<=e.minWidth||l<=absoluteColumnMinWidth)){var c=Math.max(e.minWidth,absoluteColumnMinWidth),u=Math.floor(s*(l-c))||1;o-=u=Math.min(u,l-c),i-=u,r[t]-=u}}if(n<=o)break;n=o}for(n=o;o<a;){var d=a/o;for(t=0;t<columns.length&&o<a;t++){e=columns[t];var h,p=r[t];o+=h=!e.resizable||e.maxWidth<=p?0:Math.min(Math.floor(d*p)-p,e.maxWidth-p||1e6)||1,r[t]+=o<=a?h:0}if(n>=o)break;n=o}var f=!1;for(t=0;t<columns.length;t++)columns[t].rerenderOnResize&&columns[t].width!=r[t]&&(f=!0),columns[t].width=r[t];reRenderColumns(f)}function reRenderColumns(t){applyColumnHeaderWidths(),applyColumnGroupHeaderWidths(),updateCanvasWidth(!0),trigger(self.onAutosizeColumns,{columns}),t&&(invalidateAllRows(),render())}function trigger(t,e,n){return n=n||new Slick.EventData,(e=e||{}).grid=self,t.notify(e,n,self)}function getEditorLock(){return options.editorLock}function getEditController(){return editController}function getColumnIndex(t){return columnsById[t]}function applyColumnGroupHeaderWidths(){if(treeColumns.hasDepth())for(var t=$groupHeadersL.length-1;t>=0;t--)treeColumns.getColumnsInDepth(t),$().add($groupHeadersL[t]).add($groupHeadersR[t]).each((function(t){var e=$(this),n=0;e.width(0===t?getHeadersWidthL():getHeadersWidthR()),e.children().each((function(){var t=$(this),r=$(this).data("column");r.width=0,r.columns.forEach((function(){var t=e.next().children(":eq("+n+++")");r.width+=t.outerWidth()})),t.width(r.width-headerColumnWidthDiff)}))}))}function applyColumnHeaderWidths(){if(initialized){for(var t,e=0,n=$headers.children(),r=columns.length;e<r;e++)t=$(n[e]),jQueryNewWidthBehaviour?t.outerWidth()!==columns[e].width&&t.outerWidth(columns[e].width):t.width()!==columns[e].width-headerColumnWidthDiff&&t.width(columns[e].width-headerColumnWidthDiff);updateColumnCaches()}}function applyColumnWidths(){for(var t,e,n=0,r=0;r<columns.length;r++)t=columns[r].width,(e=getColumnCssRules(r)).left.style.left=n+"px",e.right.style.right=(-1!=options.frozenColumn&&r>options.frozenColumn?canvasWidthR:canvasWidthL)-n-t+"px",options.frozenColumn==r?n=0:n+=columns[r].width}function setSortColumn(t,e){setSortColumns([{columnId:t,sortAsc:e}])}function setSortColumns(t){sortColumns=t;var e=options.numberedMultiColumnSort&&sortColumns.length>1,n=$headers.children();n.removeClass("slick-header-column-sorted").find(".slick-sort-indicator").removeClass("slick-sort-indicator-asc slick-sort-indicator-desc"),n.find(".slick-sort-indicator-numbered").text(""),$.each(sortColumns,(function(t,r){null==r.sortAsc&&(r.sortAsc=!0);var i=getColumnIndex(r.columnId);null!=i&&(n.eq(i).addClass("slick-header-column-sorted").find(".slick-sort-indicator").addClass(r.sortAsc?"slick-sort-indicator-asc":"slick-sort-indicator-desc"),e&&n.eq(i).find(".slick-sort-indicator-numbered").text(t+1))}))}function getSortColumns(){return sortColumns}function handleSelectedRangesChanged(t,e){var n=selectedRows.slice(0);selectedRows=[];for(var r={},i=0;i<e.length;i++)for(var o=e[i].fromRow;o<=e[i].toRow;o++){r[o]||(selectedRows.push(o),r[o]={});for(var a=e[i].fromCell;a<=e[i].toCell;a++)canCellBeSelected(o,a)&&(r[o][columns[a].id]=options.selectedCellCssClass)}setCellCssStyles(options.selectedCellCssClass,r),simpleArrayEquals(n,selectedRows)||trigger(self.onSelectedRowsChanged,{rows:getSelectedRows(),previousSelectedRows:n},t)}function simpleArrayEquals(t,e){if(!Array.isArray(t)||!Array.isArray(e))return!0;const n=new Set(t),r=new Set(e);if(n.size!=r.size)return!1;for(const t of n)if(!r.has(t))return!1;return!0}function getColumns(){return columns}function updateColumnCaches(){columnPosLeft=[],columnPosRight=[];for(var t=0,e=0,n=columns.length;e<n;e++)columnPosLeft[e]=t,columnPosRight[e]=t+columns[e].width,options.frozenColumn==e?t=0:t+=columns[e].width}function updateColumnProps(){columnsById={};for(var t=0;t<columns.length;t++){columns[t].width&&(columns[t].widthRequest=columns[t].width);var e=columns[t]=$.extend({},columnDefaults,columns[t]);e.autoSize=$.extend({},columnAutosizeDefaults,e.autoSize),columnsById[e.id]=t,e.minWidth&&e.width<e.minWidth&&(e.width=e.minWidth),e.maxWidth&&e.width>e.maxWidth&&(e.width=e.maxWidth),e.resizable}}function setColumns(t){trigger(self.onBeforeSetColumns,{previousColumns:columns,newColumns:t,grid:self});var e=new Slick.TreeColumns(t);columns=e.hasDepth()?(treeColumns=e).extractColumns():t,updateColumnProps(),updateColumnCaches(),initialized&&(setPaneVisibility(),setOverflow(),invalidateAllRows(),createColumnHeaders(),createColumnGroupHeaders(),createColumnFooter(),removeCssRules(),createCssRules(),resizeCanvas(),updateCanvasWidth(),applyColumnHeaderWidths(),applyColumnWidths(),handleScroll())}function getOptions(){return options}function setOptions(t,e,n,r){if(getEditorLock().commitCurrentEdit()){makeActiveCellNormal(),void 0!==t.showColumnHeader&&setColumnHeaderVisibility(t.showColumnHeader),options.enableAddRow!==t.enableAddRow&&invalidateRow(getDataLength());var i=$.extend(!0,{},options);if(options=$.extend(options,t),trigger(self.onSetOptions,{optionsBefore:i,optionsAfter:options}),validateAndEnforceOptions(),$viewport.css("overflow-y",options.autoHeight?"hidden":"auto"),e||render(),setFrozenOptions(),setScroller(),r||setOverflow(),n||setColumns(treeColumns.extractColumns()),options.enableMouseWheelScrollHandler&&$viewport&&jQuery.fn.mousewheel){var o=$._data($viewport[0],"events");o&&o.mousewheel||$viewport.on("mousewheel",handleMouseWheel)}else!1===options.enableMouseWheelScrollHandler&&$viewport.off("mousewheel")}}function validateAndEnforceOptions(){options.autoHeight&&(options.leaveSpaceForNewRows=!1),options.forceFitColumns&&(options.autosizeColsMode=Slick.GridAutosizeColsMode.LegacyForceFit,console.log("forceFitColumns option is deprecated - use autosizeColsMode"))}function setData(t,e){data=t,invalidateAllRows(),updateRowCount(),e&&scrollTo(0)}function getData(){return data}function getDataLength(){return data.getLength?data.getLength():data&&data.length||0}function getDataLengthIncludingAddNew(){return getDataLength()+(!options.enableAddRow||pagingActive&&!pagingIsLastPage?0:1)}function getDataItem(t){return data.getItem?data.getItem(t):data[t]}function getTopPanel(){return $topPanel[0]}function setTopPanelVisibility(t,e){var n=!1!==e;options.showTopPanel!=t&&(options.showTopPanel=t,t?n?$topPanelScroller.slideDown("fast",resizeCanvas):($topPanelScroller.show(),resizeCanvas()):n?$topPanelScroller.slideUp("fast",resizeCanvas):($topPanelScroller.hide(),resizeCanvas()))}function setHeaderRowVisibility(t,e){var n=!1!==e;options.showHeaderRow!=t&&(options.showHeaderRow=t,t?n?$headerRowScroller.slideDown("fast",resizeCanvas):($headerRowScroller.show(),resizeCanvas()):n?$headerRowScroller.slideUp("fast",resizeCanvas):($headerRowScroller.hide(),resizeCanvas()))}function setColumnHeaderVisibility(t,e){options.showColumnHeader!=t&&(options.showColumnHeader=t,t?e?$headerScroller.slideDown("fast",resizeCanvas):($headerScroller.show(),resizeCanvas()):e?$headerScroller.slideUp("fast",resizeCanvas):($headerScroller.hide(),resizeCanvas()))}function setFooterRowVisibility(t,e){var n=!1!==e;options.showFooterRow!=t&&(options.showFooterRow=t,t?n?$footerRowScroller.slideDown("fast",resizeCanvas):($footerRowScroller.show(),resizeCanvas()):n?$footerRowScroller.slideUp("fast",resizeCanvas):($footerRowScroller.hide(),resizeCanvas()))}function setPreHeaderPanelVisibility(t,e){var n=!1!==e;options.showPreHeaderPanel!=t&&(options.showPreHeaderPanel=t,t?n?($preHeaderPanelScroller.slideDown("fast",resizeCanvas),$preHeaderPanelScrollerR.slideDown("fast",resizeCanvas)):($preHeaderPanelScroller.show(),$preHeaderPanelScrollerR.show(),resizeCanvas()):n?($preHeaderPanelScroller.slideUp("fast",resizeCanvas),$preHeaderPanelScrollerR.slideUp("fast",resizeCanvas)):($preHeaderPanelScroller.hide(),$preHeaderPanelScrollerR.hide(),resizeCanvas()))}function getContainerNode(){return $container.get(0)}function getRowTop(t){return options.rowHeight*t-offset}function getRowFromPosition(t){return Math.floor((t+offset)/options.rowHeight)}function scrollTo(t){t=Math.max(t,0),t=Math.min(t,th-$viewportScrollContainerY.height()+(viewportHasHScroll||hasFrozenColumns()?scrollbarDimensions.height:0));var e=offset;page=Math.min(n-1,Math.floor(t/ph));var r=t-(offset=Math.round(page*cj));offset!=e&&(cleanupRows(getVisibleRange(r)),updateRowPositions()),prevScrollTop!=r&&(vScrollDir=prevScrollTop+e<r+offset?1:-1,lastRenderedScrollTop=scrollTop=prevScrollTop=r,hasFrozenColumns()&&($viewportTopL[0].scrollTop=r),hasFrozenRows&&($viewportBottomL[0].scrollTop=$viewportBottomR[0].scrollTop=r),$viewportScrollContainerY[0].scrollTop=r,trigger(self.onViewportChanged,{}))}function defaultFormatter(t,e,n,r,i,o){return null==n?"":(n+"").replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/>/g,"&gt;")}function getFormatter(t,e){var n=data.getItemMetadata&&data.getItemMetadata(t),r=n&&n.columns&&(n.columns[e.id]||n.columns[getColumnIndex(e.id)]);return r&&r.formatter||n&&n.formatter||e.formatter||options.formatterFactory&&options.formatterFactory.getFormatter(e)||options.defaultFormatter}function getEditor(t,e){var n=columns[e],r=data.getItemMetadata&&data.getItemMetadata(t),i=r&&r.columns;return i&&i[n.id]&&void 0!==i[n.id].editor?i[n.id].editor:i&&i[e]&&void 0!==i[e].editor?i[e].editor:n.editor||options.editorFactory&&options.editorFactory.getEditor(n)}function getDataItemValueForColumn(t,e){return options.dataItemColumnValueExtractor?options.dataItemColumnValueExtractor(t,e):t[e.field]}function appendRowHtml(t,e,n,r,i){var o=getDataItem(n),a=n<i&&!o,s="slick-row"+(hasFrozenRows&&n<=options.frozenRow?" frozen":"")+(a?" loading":"")+(n===activeRow&&options.showCellSelection?" active":"")+(n%2==1?" odd":" even");o||(s+=" "+options.addNewRowCssClass);var l=data.getItemMetadata&&data.getItemMetadata(n);l&&l.cssClasses&&(s+=" "+l.cssClasses);var c,u,d=getFrozenRowOffset(n),h="<div class='ui-widget-content "+s+"' style='top:"+(getRowTop(n)-d)+"px'>";t.push(h),hasFrozenColumns()&&e.push(h);for(var p=0,f=columns.length;p<f;p++){if(u=columns[p],c=1,l&&l.columns){var Q=l.columns[u.id]||l.columns[p];"*"===(c=Q&&Q.colspan||1)&&(c=f-p)}if(columnPosRight[Math.min(f-1,p+c-1)]>r.leftPx){if(!u.alwaysRenderColumn&&columnPosLeft[p]>r.rightPx)break;hasFrozenColumns()&&p>options.frozenColumn?appendCellHtml(e,n,p,c,o):appendCellHtml(t,n,p,c,o)}else(u.alwaysRenderColumn||hasFrozenColumns()&&p<=options.frozenColumn)&&appendCellHtml(t,n,p,c,o);c>1&&(p+=c-1)}t.push("</div>"),hasFrozenColumns()&&e.push("</div>")}function appendCellHtml(t,e,n,r,i){var o=columns[n],a="slick-cell l"+n+" r"+Math.min(columns.length-1,n+r-1)+(o.cssClass?" "+o.cssClass:"");for(var s in hasFrozenColumns()&&n<=options.frozenColumn&&(a+=" frozen"),e===activeRow&&n===activeCell&&options.showCellSelection&&(a+=" active"),cellCssClasses)cellCssClasses[s][e]&&cellCssClasses[s][e][o.id]&&(a+=" "+cellCssClasses[s][e][o.id]);var l=null,c="";i&&(l=getDataItemValueForColumn(i,o),null==(c=getFormatter(e,o)(e,n,l,o,i,self))&&(c=""));var u=trigger(self.onBeforeAppendCell,{row:e,cell:n,value:l,dataContext:i})||"";u+=c&&c.addClasses?(u?" ":"")+c.addClasses:"";var d=c&&c.toolTip?"title='"+c.toolTip+"'":"",h="";if(o.hasOwnProperty("cellAttrs")&&o.cellAttrs instanceof Object)for(var s in o.cellAttrs)o.cellAttrs.hasOwnProperty(s)&&(h+=" "+s+'="'+o.cellAttrs[s]+'" ');t.push("<div class='"+a+(u?" "+u:"")+"' "+d+h+">"),i&&t.push("[object Object]"!==Object.prototype.toString.call(c)?c:c.text),t.push("</div>"),rowsCache[e].cellRenderQueue.push(n),rowsCache[e].cellColSpans[n]=r}function cleanupRows(t){for(var e in rowsCache){var n=!0;hasFrozenRows&&(options.frozenBottom&&e>=actualFrozenRow||!options.frozenBottom&&e<=actualFrozenRow)&&(n=!1),(e=parseInt(e,10))!==activeRow&&(e<t.top||e>t.bottom)&&n&&removeRowFromCache(e)}options.enableAsyncPostRenderCleanup&&startPostProcessingCleanup()}function invalidate(){updateRowCount(),invalidateAllRows(),render()}function invalidateAllRows(){for(var t in currentEditor&&makeActiveCellNormal(),rowsCache)removeRowFromCache(t);options.enableAsyncPostRenderCleanup&&startPostProcessingCleanup()}function queuePostProcessedRowForCleanup(t,e,n){for(var r in postProcessgroupId++,e)e.hasOwnProperty(r)&&postProcessedCleanupQueue.push({actionType:"C",groupId:postProcessgroupId,node:t.cellNodesByColumnIdx[0|r],columnIdx:0|r,rowIdx:n});postProcessedCleanupQueue.push({actionType:"R",groupId:postProcessgroupId,node:t.rowNode}),t.rowNode.detach()}function queuePostProcessedCellForCleanup(t,e,n){postProcessedCleanupQueue.push({actionType:"C",groupId:postProcessgroupId,node:t,columnIdx:e,rowIdx:n}),$(t).detach()}function removeRowFromCache(t){var e=rowsCache[t];e&&(options.enableAsyncPostRenderCleanup&&postProcessedRows[t]?queuePostProcessedRowForCleanup(e,postProcessedRows[t],t):e.rowNode.each((function(){this.parentElement.removeChild(this)})),delete rowsCache[t],delete postProcessedRows[t],renderedRows--,counter_rows_removed++)}function invalidateRows(t){var e,n;if(t&&t.length){for(vScrollDir=0,n=t.length,e=0;e<n;e++)currentEditor&&activeRow===t[e]&&makeActiveCellNormal(),rowsCache[t[e]]&&removeRowFromCache(t[e]);options.enableAsyncPostRenderCleanup&&startPostProcessingCleanup()}}function invalidateRow(t){(t||0===t)&&invalidateRows([t])}function applyFormatResultToCellNode(t,e,n){null==t&&(t=""),"[object Object]"===Object.prototype.toString.call(t)?(e.innerHTML=t.text,t.removeClasses&&!n&&$(e).removeClass(t.removeClasses),t.addClasses&&$(e).addClass(t.addClasses),t.toolTip&&$(e).attr("title",t.toolTip)):e.innerHTML=t}function updateCell(t,e){var n=getCellNode(t,e);if(n){var r=columns[e],i=getDataItem(t);currentEditor&&activeRow===t&&activeCell===e?currentEditor.loadValue(i):(applyFormatResultToCellNode(i?getFormatter(t,r)(t,e,getDataItemValueForColumn(i,r),r,i,self):"",n),invalidatePostProcessingResults(t))}}function updateRow(t){var e=rowsCache[t];if(e){ensureCellNodesInRowsCache(t);var n=getDataItem(t);for(var r in e.cellNodesByColumnIdx)if(e.cellNodesByColumnIdx.hasOwnProperty(r)){var i=columns[r|=0],o=e.cellNodesByColumnIdx[r][0];t===activeRow&&r===activeCell&&currentEditor?currentEditor.loadValue(n):n?applyFormatResultToCellNode(getFormatter(t,i)(t,r,getDataItemValueForColumn(n,i),i,n,self),o):o.innerHTML=""}invalidatePostProcessingResults(t)}}function getViewportHeight(){if(options.autoHeight&&-1==options.frozenColumn||(topPanelH=options.showTopPanel?options.topPanelHeight+getVBoxDelta($topPanelScroller):0,headerRowH=options.showHeaderRow?options.headerRowHeight+getVBoxDelta($headerRowScroller):0,footerRowH=options.showFooterRow?options.footerRowHeight+getVBoxDelta($footerRowScroller):0),options.autoHeight){var t=$paneHeaderL.outerHeight();t+=options.showHeaderRow?options.headerRowHeight+getVBoxDelta($headerRowScroller):0,t+=options.showFooterRow?options.footerRowHeight+getVBoxDelta($footerRowScroller):0,t+=getCanvasWidth()>viewportW?scrollbarDimensions.height:0,viewportH=options.rowHeight*getDataLengthIncludingAddNew()+(-1==options.frozenColumn?t:0)}else{var e=options.showColumnHeader?parseFloat($.css($headerScroller[0],"height"))+getVBoxDelta($headerScroller):0,n=options.createPreHeaderPanel&&options.showPreHeaderPanel?options.preHeaderPanelHeight+getVBoxDelta($preHeaderPanelScroller):0;viewportH=parseFloat($.css($container[0],"height",!0))-parseFloat($.css($container[0],"paddingTop",!0))-parseFloat($.css($container[0],"paddingBottom",!0))-e-topPanelH-headerRowH-footerRowH-n}return numVisibleRows=Math.ceil(viewportH/options.rowHeight),viewportH}function getViewportWidth(){viewportW=parseFloat($container.width())}function resizeCanvas(){if(initialized){paneTopH=0,paneBottomH=0,viewportTopH=0,viewportBottomH=0,getViewportWidth(),getViewportHeight(),hasFrozenRows?options.frozenBottom?(paneTopH=viewportH-frozenRowsHeight-scrollbarDimensions.height,paneBottomH=frozenRowsHeight+scrollbarDimensions.height):(paneTopH=frozenRowsHeight,paneBottomH=viewportH-frozenRowsHeight):paneTopH=viewportH,paneTopH+=topPanelH+headerRowH+footerRowH,hasFrozenColumns()&&options.autoHeight&&(paneTopH+=scrollbarDimensions.height),viewportTopH=paneTopH-topPanelH-headerRowH-footerRowH,options.autoHeight&&(hasFrozenColumns()&&$container.height(paneTopH+parseFloat($.css($headerScrollerL[0],"height"))),$paneTopL.css("position","relative")),$paneTopL.css({top:$paneHeaderL.height()||(options.showHeaderRow?options.headerRowHeight:0)+(options.showPreHeaderPanel?options.preHeaderPanelHeight:0),height:paneTopH});var t=$paneTopL.position().top+paneTopH;options.autoHeight||$viewportTopL.height(viewportTopH),hasFrozenColumns()?($paneTopR.css({top:$paneHeaderL.height(),height:paneTopH}),$viewportTopR.height(viewportTopH),hasFrozenRows&&($paneBottomL.css({top:t,height:paneBottomH}),$paneBottomR.css({top:t,height:paneBottomH}),$viewportBottomR.height(paneBottomH))):hasFrozenRows&&($paneBottomL.css({width:"100%",height:paneBottomH}),$paneBottomL.css("top",t)),hasFrozenRows?($viewportBottomL.height(paneBottomH),options.frozenBottom?($canvasBottomL.height(frozenRowsHeight),hasFrozenColumns()&&$canvasBottomR.height(frozenRowsHeight)):($canvasTopL.height(frozenRowsHeight),hasFrozenColumns()&&$canvasTopR.height(frozenRowsHeight))):$viewportTopR.height(viewportTopH),scrollbarDimensions&&scrollbarDimensions.width||(scrollbarDimensions=measureScrollbar()),options.autosizeColsMode===Slick.GridAutosizeColsMode.LegacyForceFit&&autosizeColumns(),updateRowCount(),handleScroll(),lastRenderedScrollLeft=-1,render()}}function updatePagingStatusFromView(t){pagingActive=0!==t.pageSize,pagingIsLastPage=t.pageNum==t.totalPages-1}function updateRowCount(){if(initialized){var t,e=getDataLength(),r=getDataLengthIncludingAddNew(),i=hasFrozenRows&&!options.frozenBottom?$canvasBottomL.height():$canvasTopL.height();t=hasFrozenRows?getDataLength()-options.frozenRow:r+(options.leaveSpaceForNewRows?numVisibleRows-1:0);var o=$viewportScrollContainerY.height(),a=viewportHasVScroll;viewportHasVScroll=options.alwaysShowVerticalScroll||!options.autoHeight&&t*options.rowHeight>o,makeActiveCellNormal();var s=e-1;for(var l in rowsCache)l>s&&removeRowFromCache(l);options.enableAsyncPostRenderCleanup&&startPostProcessingCleanup(),activeCellNode&&activeRow>s&&resetActiveCell(),i=h,options.autoHeight?h=options.rowHeight*t:(th=Math.max(options.rowHeight*t,o-scrollbarDimensions.height))<maxSupportedCssHeight?(h=ph=th,n=1,cj=0):(ph=(h=maxSupportedCssHeight)/100,n=Math.floor(th/ph),cj=(th-h)/(n-1)),h!==i&&(hasFrozenRows&&!options.frozenBottom?($canvasBottomL.css("height",h),hasFrozenColumns()&&$canvasBottomR.css("height",h)):($canvasTopL.css("height",h),$canvasTopR.css("height",h)),scrollTop=$viewportScrollContainerY[0].scrollTop);var c=scrollTop+offset<=th-o;0==th||0==scrollTop?page=offset=0:scrollTo(c?scrollTop+offset:th-o),h!=i&&options.autoHeight&&resizeCanvas(),options.autosizeColsMode===Slick.GridAutosizeColsMode.LegacyForceFit&&a!=viewportHasVScroll&&autosizeColumns(),updateCanvasWidth(!1)}}function getVisibleRange(t,e){return null==t&&(t=scrollTop),null==e&&(e=scrollLeft),{top:getRowFromPosition(t),bottom:getRowFromPosition(t+viewportH)+1,leftPx:e,rightPx:e+viewportW}}function getRenderedRange(t,e){var n=getVisibleRange(t,e),r=Math.round(viewportH/options.rowHeight),i=options.minRowBuffer;return-1==vScrollDir?(n.top-=r,n.bottom+=i):1==vScrollDir?(n.top-=i,n.bottom+=r):(n.top-=i,n.bottom+=i),n.top=Math.max(0,n.top),n.bottom=Math.min(getDataLengthIncludingAddNew()-1,n.bottom),n.leftPx-=viewportW,n.rightPx+=viewportW,n.leftPx=Math.max(0,n.leftPx),n.rightPx=Math.min(canvasWidth,n.rightPx),n}function ensureCellNodesInRowsCache(t){var e=rowsCache[t];if(e&&e.cellRenderQueue.length)for(var n=e.rowNode.children().last();e.cellRenderQueue.length;){var r=e.cellRenderQueue.pop();e.cellNodesByColumnIdx[r]=n,0===(n=n.prev()).length&&(n=$(e.rowNode[0]).children().last())}}function cleanUpCells(t,e){if(!hasFrozenRows||!(options.frozenBottom&&e>actualFrozenRow||e<=actualFrozenRow)){var n,r,i=rowsCache[e],o=[];for(var a in i.cellNodesByColumnIdx)if(i.cellNodesByColumnIdx.hasOwnProperty(a)&&!((a|=0)<=options.frozenColumn||Array.isArray(columns)&&columns[a]&&columns[a].alwaysRenderColumn)){var s=i.cellColSpans[a];(columnPosLeft[a]>t.rightPx||columnPosRight[Math.min(columns.length-1,a+s-1)]<t.leftPx)&&(e==activeRow&&a==activeCell||o.push(a))}for(;null!=(n=o.pop());)r=i.cellNodesByColumnIdx[n][0],options.enableAsyncPostRenderCleanup&&postProcessedRows[e]&&postProcessedRows[e][n]?queuePostProcessedCellForCleanup(r,n,e):r.parentElement.removeChild(r),delete i.cellColSpans[n],delete i.cellNodesByColumnIdx[n],postProcessedRows[e]&&delete postProcessedRows[e][n]}}function cleanUpAndRenderCells(t){for(var e,n,r,i=[],o=[],a=t.top,s=t.bottom;a<=s;a++)if(e=rowsCache[a]){ensureCellNodesInRowsCache(a),cleanUpCells(t,a),n=0;var l=data.getItemMetadata&&data.getItemMetadata(a);l=l&&l.columns;for(var c=getDataItem(a),u=0,d=columns.length;u<d&&!(columnPosLeft[u]>t.rightPx);u++)if(null==(r=e.cellColSpans[u])){if(r=1,l){var h=l[columns[u].id]||l[u];"*"===(r=h&&h.colspan||1)&&(r=d-u)}columnPosRight[Math.min(d-1,u+r-1)]>t.leftPx&&(appendCellHtml(i,a,u,r,c),n++),u+=r>1?r-1:0}else u+=r>1?r-1:0;n&&o.push(a)}if(i.length){var p,f,Q=document.createElement("div");for(Q.innerHTML=i.join("");null!=(p=o.pop());){var T;for(e=rowsCache[p];null!=(T=e.cellRenderQueue.pop());)f=Q.lastChild,hasFrozenColumns()&&T>options.frozenColumn?e.rowNode[1].appendChild(f):e.rowNode[0].appendChild(f),e.cellNodesByColumnIdx[T]=$(f)}}}function renderRows(t){for(var e=[],n=[],r=[],i=!1,o=getDataLength(),a=t.top,s=t.bottom;a<=s;a++)rowsCache[a]||hasFrozenRows&&options.frozenBottom&&a==getDataLength()||(renderedRows++,r.push(a),rowsCache[a]={rowNode:null,cellColSpans:[],cellNodesByColumnIdx:[],cellRenderQueue:[]},appendRowHtml(e,n,a,t,o),activeCellNode&&activeRow===a&&(i=!0),counter_rows_rendered++);if(r.length){var l=document.createElement("div"),c=document.createElement("div");for(l.innerHTML=e.join(""),c.innerHTML=n.join(""),a=0,s=r.length;a<s;a++)hasFrozenRows&&r[a]>=actualFrozenRow?hasFrozenColumns()?(rowsCache[r[a]].rowNode=$().add($(l.firstChild)).add($(c.firstChild)),$canvasBottomL[0].append(l.firstChild),$canvasBottomR[0].append(c.firstChild)):(rowsCache[r[a]].rowNode=$().add($(l.firstChild)),$canvasBottomL[0].append($(l.firstChild))):hasFrozenColumns()?(rowsCache[r[a]].rowNode=$().add($(l.firstChild)).add($(c.firstChild)),$canvasTopL[0].append(l.firstChild),$canvasTopR[0].append(c.firstChild)):(rowsCache[r[a]].rowNode=$().add($(l.firstChild)),$canvasTopL[0].append(l.firstChild));i&&(activeCellNode=getCellNode(activeRow,activeCell))}}function startPostProcessing(){options.enableAsyncPostRender&&(clearTimeout(h_postrender),h_postrender=setTimeout(asyncPostProcessRows,options.asyncPostRenderDelay))}function startPostProcessingCleanup(){options.enableAsyncPostRenderCleanup&&(clearTimeout(h_postrenderCleanup),h_postrenderCleanup=setTimeout(asyncPostProcessCleanupRows,options.asyncPostRenderCleanupDelay))}function invalidatePostProcessingResults(t){for(var e in postProcessedRows[t])postProcessedRows[t].hasOwnProperty(e)&&(postProcessedRows[t][e]="C");postProcessFromRow=Math.min(postProcessFromRow,t),postProcessToRow=Math.max(postProcessToRow,t),startPostProcessing()}function updateRowPositions(){for(var t in rowsCache){var e=t?parseInt(t):0;rowsCache[e].rowNode[0].style.top=getRowTop(e)+"px"}}function render(){if(initialized){scrollThrottle.dequeue();var t=getVisibleRange(),e=getRenderedRange();if(cleanupRows(e),lastRenderedScrollLeft!=scrollLeft){if(hasFrozenRows){var n=$.extend(!0,{},e);options.frozenBottom?(n.top=actualFrozenRow,n.bottom=getDataLength()):(n.top=0,n.bottom=options.frozenRow),cleanUpAndRenderCells(n)}cleanUpAndRenderCells(e)}renderRows(e),hasFrozenRows&&(options.frozenBottom?renderRows({top:actualFrozenRow,bottom:getDataLength()-1,leftPx:e.leftPx,rightPx:e.rightPx}):renderRows({top:0,bottom:options.frozenRow-1,leftPx:e.leftPx,rightPx:e.rightPx})),postProcessFromRow=t.top,postProcessToRow=Math.min(getDataLengthIncludingAddNew()-1,t.bottom),startPostProcessing(),lastRenderedScrollTop=scrollTop,lastRenderedScrollLeft=scrollLeft,h_render=null,trigger(self.onRendered,{startRow:t.top,endRow:t.bottom,grid:self})}}function handleHeaderScroll(){handleElementScroll($headerScrollContainer[0])}function handleHeaderRowScroll(){var t=$headerRowScrollContainer[0].scrollLeft;t!=$viewportScrollContainerX[0].scrollLeft&&($viewportScrollContainerX[0].scrollLeft=t)}function handleFooterRowScroll(){var t=$footerRowScrollContainer[0].scrollLeft;t!=$viewportScrollContainerX[0].scrollLeft&&($viewportScrollContainerX[0].scrollLeft=t)}function handlePreHeaderPanelScroll(){handleElementScroll($preHeaderPanelScroller[0])}function handleElementScroll(t){var e=t.scrollLeft;e!=$viewportScrollContainerX[0].scrollLeft&&($viewportScrollContainerX[0].scrollLeft=e)}function handleScroll(){return scrollTop=$viewportScrollContainerY[0].scrollTop,scrollLeft=$viewportScrollContainerX[0].scrollLeft,_handleScroll(!1)}function _handleScroll(t){var e=$viewportScrollContainerY[0].scrollHeight-$viewportScrollContainerY[0].clientHeight,r=$viewportScrollContainerY[0].scrollWidth-$viewportScrollContainerY[0].clientWidth;e=Math.max(0,e),r=Math.max(0,r),scrollTop>e&&(scrollTop=e),scrollLeft>r&&(scrollLeft=r);var i=Math.abs(scrollTop-prevScrollTop),o=Math.abs(scrollLeft-prevScrollLeft);if(o&&(prevScrollLeft=scrollLeft,$viewportScrollContainerX[0].scrollLeft=scrollLeft,$headerScrollContainer[0].scrollLeft=scrollLeft,$topPanelScroller[0].scrollLeft=scrollLeft,$headerRowScrollContainer[0].scrollLeft=scrollLeft,options.createFooterRow&&($footerRowScrollContainer[0].scrollLeft=scrollLeft),options.createPreHeaderPanel&&(hasFrozenColumns()?$preHeaderPanelScrollerR[0].scrollLeft=scrollLeft:$preHeaderPanelScroller[0].scrollLeft=scrollLeft),hasFrozenColumns()?hasFrozenRows&&($viewportTopR[0].scrollLeft=scrollLeft):hasFrozenRows&&($viewportTopL[0].scrollLeft=scrollLeft)),i)if(vScrollDir=prevScrollTop<scrollTop?1:-1,prevScrollTop=scrollTop,t&&($viewportScrollContainerY[0].scrollTop=scrollTop),hasFrozenColumns()&&(hasFrozenRows&&!options.frozenBottom?$viewportBottomL[0].scrollTop=scrollTop:$viewportTopL[0].scrollTop=scrollTop),i<viewportH)scrollTo(scrollTop+offset);else{var a=offset;page=h==viewportH?0:Math.min(n-1,Math.floor(scrollTop*((th-viewportH)/(h-viewportH))*(1/ph))),a!=(offset=Math.round(page*cj))&&invalidateAllRows()}if(o||i){var s=Math.abs(lastRenderedScrollLeft-scrollLeft),l=Math.abs(lastRenderedScrollTop-scrollTop);(s>20||l>20)&&(options.forceSyncScrolling||l<viewportH&&s<viewportW?render():scrollThrottle.enqueue(),trigger(self.onViewportChanged,{}))}return trigger(self.onScroll,{scrollLeft,scrollTop}),!(!o&&!i)}function ActionThrottle(t,e){var n=!1,r=!1;function i(){r=!1}function o(){n=!0,setTimeout(a,e),t()}function a(){r?(i(),o()):n=!1}return{enqueue:function(){n?r=!0:o()},dequeue:i}}function asyncPostProcessRows(){for(var t=getDataLength();postProcessFromRow<=postProcessToRow;){var e=vScrollDir>=0?postProcessFromRow++:postProcessToRow--,n=rowsCache[e];if(n&&!(e>=t)){for(var r in postProcessedRows[e]||(postProcessedRows[e]={}),ensureCellNodesInRowsCache(e),n.cellNodesByColumnIdx)if(n.cellNodesByColumnIdx.hasOwnProperty(r)){var i=columns[r|=0],o=postProcessedRows[e][r];if(i.asyncPostRender&&"R"!==o){var a=n.cellNodesByColumnIdx[r];a&&i.asyncPostRender(a,e,getDataItem(e),i,"C"===o),postProcessedRows[e][r]="R"}}return void(h_postrender=setTimeout(asyncPostProcessRows,options.asyncPostRenderDelay))}}}function asyncPostProcessCleanupRows(){if(postProcessedCleanupQueue.length>0){for(var t=postProcessedCleanupQueue[0].groupId;postProcessedCleanupQueue.length>0&&postProcessedCleanupQueue[0].groupId==t;){var e=postProcessedCleanupQueue.shift();if("R"==e.actionType&&$(e.node).remove(),"C"==e.actionType){var n=columns[e.columnIdx];n.asyncPostRenderCleanup&&e.node&&n.asyncPostRenderCleanup(e.node,e.rowIdx,n)}}h_postrenderCleanup=setTimeout(asyncPostProcessCleanupRows,options.asyncPostRenderCleanupDelay)}}function updateCellCssStylesOnRenderedRows(t,e){var n,r,i,o;for(var a in rowsCache){if(o=e&&e[a],i=t&&t[a],o)for(r in o)i&&o[r]==i[r]||(n=getCellNode(a,getColumnIndex(r)))&&$(n).removeClass(o[r]);if(i)for(r in i)o&&o[r]==i[r]||(n=getCellNode(a,getColumnIndex(r)))&&$(n).addClass(i[r])}}function addCellCssStyles(t,e){if(cellCssClasses[t])throw new Error("SlickGrid addCellCssStyles: cell CSS hash with key '"+t+"' already exists.");cellCssClasses[t]=e,updateCellCssStylesOnRenderedRows(e,null),trigger(self.onCellCssStylesChanged,{key:t,hash:e,grid:self})}function removeCellCssStyles(t){cellCssClasses[t]&&(updateCellCssStylesOnRenderedRows(null,cellCssClasses[t]),delete cellCssClasses[t],trigger(self.onCellCssStylesChanged,{key:t,hash:null,grid:self}))}function setCellCssStyles(t,e){var n=cellCssClasses[t];cellCssClasses[t]=e,updateCellCssStylesOnRenderedRows(e,n),trigger(self.onCellCssStylesChanged,{key:t,hash:e,grid:self})}function getCellCssStyles(t){return cellCssClasses[t]}function flashCell(t,e,n){n=n||100,rowsCache[t]&&function t(e,r){r&&setTimeout((function(){e.queue((function(){e.toggleClass(options.cellFlashingCssClass).dequeue(),t(e,r-1)}))}),n)}($(getCellNode(t,e)),4)}function handleMouseWheel(t,e,n,r){scrollTop=Math.max(0,$viewportScrollContainerY[0].scrollTop-r*options.rowHeight),scrollLeft=$viewportScrollContainerX[0].scrollLeft+10*n,_handleScroll(!0)&&t.preventDefault()}function handleDragInit(t,e){var n=getCellFromEvent(t);if(!n||!cellExists(n.row,n.cell))return!1;var r=trigger(self.onDragInit,e,t);return!!t.isImmediatePropagationStopped()&&r}function handleDragStart(t,e){var n=getCellFromEvent(t);if(!n||!cellExists(n.row,n.cell))return!1;var r=trigger(self.onDragStart,e,t);return!!t.isImmediatePropagationStopped()&&r}function handleDrag(t,e){return trigger(self.onDrag,e,t)}function handleDragEnd(t,e){trigger(self.onDragEnd,e,t)}function handleKeyDown(t){trigger(self.onKeyDown,{row:activeRow,cell:activeCell},t);var e=t.isImmediatePropagationStopped(),n=Slick.keyCode;if(!e&&!t.shiftKey&&!t.altKey){if(options.editable&&currentEditor&&currentEditor.keyCaptureList&&currentEditor.keyCaptureList.indexOf(t.which)>-1)return;t.which==n.HOME?e=t.ctrlKey?navigateTop():navigateRowStart():t.which==n.END&&(e=t.ctrlKey?navigateBottom():navigateRowEnd())}if(!e)if(t.shiftKey||t.altKey||t.ctrlKey)t.which!=n.TAB||!t.shiftKey||t.ctrlKey||t.altKey||(e=navigatePrev());else{if(options.editable&&currentEditor&&currentEditor.keyCaptureList&&currentEditor.keyCaptureList.indexOf(t.which)>-1)return;if(t.which==n.ESCAPE){if(!getEditorLock().isActive())return;cancelEditAndSetFocus()}else t.which==n.PAGE_DOWN?(navigatePageDown(),e=!0):t.which==n.PAGE_UP?(navigatePageUp(),e=!0):t.which==n.LEFT?e=navigateLeft():t.which==n.RIGHT?e=navigateRight():t.which==n.UP?e=navigateUp():t.which==n.DOWN?e=navigateDown():t.which==n.TAB?e=navigateNext():t.which==n.ENTER&&(options.editable&&(currentEditor?activeRow===getDataLength()?navigateDown():commitEditAndSetFocus():getEditorLock().commitCurrentEdit()&&makeActiveCellEditable(void 0,void 0,t)),e=!0)}if(e){t.stopPropagation(),t.preventDefault();try{t.originalEvent.keyCode=0}catch(t){}}}function handleClick(t){if(!currentEditor&&(t.target!=document.activeElement||$(t.target).hasClass("slick-cell"))){var e=getTextSelection();setFocus(),setTextSelection(e)}var n=getCellFromEvent(t);if(n&&(null===currentEditor||activeRow!=n.row||activeCell!=n.cell)&&(trigger(self.onClick,{row:n.row,cell:n.cell},t),!t.isImmediatePropagationStopped()&&canCellBeActive(n.row,n.cell)&&(!getEditorLock().isActive()||getEditorLock().commitCurrentEdit()))){scrollRowIntoView(n.row,!1);var r=t.target&&t.target.className===Slick.preClickClassName,i=columns[n.cell],o=!!(options.editable&&i&&i.editor&&options.suppressActiveCellChangeOnEdit);setActiveCellInternal(getCellNode(n.row,n.cell),null,r,o,t)}}function handleContextMenu(t){var e=$(t.target).closest(".slick-cell",$canvas);0!==e.length&&(activeCellNode===e[0]&&null!==currentEditor||trigger(self.onContextMenu,{},t))}function handleDblClick(t){var e=getCellFromEvent(t);!e||null!==currentEditor&&activeRow==e.row&&activeCell==e.cell||(trigger(self.onDblClick,{row:e.row,cell:e.cell},t),t.isImmediatePropagationStopped()||options.editable&&gotoCell(e.row,e.cell,!0,t))}function handleHeaderMouseEnter(t){trigger(self.onHeaderMouseEnter,{column:$(this).data("column"),grid:self},t)}function handleHeaderMouseLeave(t){trigger(self.onHeaderMouseLeave,{column:$(this).data("column"),grid:self},t)}function handleHeaderContextMenu(t){var e=$(t.target).closest(".slick-header-column",".slick-header-columns"),n=e&&e.data("column");trigger(self.onHeaderContextMenu,{column:n},t)}function handleHeaderClick(t){if(!columnResizeDragging){var e=$(t.target).closest(".slick-header-column",".slick-header-columns"),n=e&&e.data("column");n&&trigger(self.onHeaderClick,{column:n},t)}}function handleFooterContextMenu(t){var e=$(t.target).closest(".slick-footerrow-column",".slick-footerrow-columns"),n=e&&e.data("column");trigger(self.onFooterContextMenu,{column:n},t)}function handleFooterClick(t){var e=$(t.target).closest(".slick-footerrow-column",".slick-footerrow-columns"),n=e&&e.data("column");trigger(self.onFooterClick,{column:n},t)}function handleMouseEnter(t){trigger(self.onMouseEnter,{},t)}function handleMouseLeave(t){trigger(self.onMouseLeave,{},t)}function cellExists(t,e){return!(t<0||t>=getDataLength()||e<0||e>=columns.length)}function getCellFromPoint(t,e){for(var n=getRowFromPosition(e),r=0,i=0,o=0;o<columns.length&&i<t;o++)i+=columns[o].width,r++;return r<0&&(r=0),{row:n,cell:r-1}}function getCellFromNode(t){var e=/l\d+/.exec(t.className);if(!e)throw new Error("SlickGrid getCellFromNode: cannot get cell - "+t.className);return parseInt(e[0].substr(1,e[0].length-1),10)}function getRowFromNode(t){for(var e in rowsCache)for(var n in rowsCache[e].rowNode)if(rowsCache[e].rowNode[n]===t)return e?parseInt(e):0;return null}function getFrozenRowOffset(t){return hasFrozenRows?options.frozenBottom?t>=actualFrozenRow?h<viewportTopH?actualFrozenRow*options.rowHeight:h:0:t>=actualFrozenRow?frozenRowsHeight:0:0}function getCellFromEvent(t){var e,n,r=$(t.target).closest(".slick-cell",$canvas);if(!r.length)return null;if(e=getRowFromNode(r[0].parentNode),hasFrozenRows){var i=r.parents(".grid-canvas").offset(),o=0;r.parents(".grid-canvas-bottom").length&&(o=options.frozenBottom?$canvasTopL.height():frozenRowsHeight),e=getCellFromPoint(t.clientX-i.left,t.clientY-i.top+o+$(document).scrollTop()).row}return n=getCellFromNode(r[0]),null==e||null==n?null:{row:e,cell:n}}function getCellNodeBox(t,e){if(!cellExists(t,e))return null;for(var n=getFrozenRowOffset(t),r=getRowTop(t)-n,i=r+options.rowHeight-1,o=0,a=0;a<e;a++)o+=columns[a].width,options.frozenColumn==a&&(o=0);return{top:r,left:o,bottom:i,right:o+columns[e].width}}function resetActiveCell(){setActiveCellInternal(null,!1)}function setFocus(){-1==tabbingDirection?$focusSink[0].focus():$focusSink2[0].focus()}function scrollCellIntoView(t,e,n){if(scrollRowIntoView(t,n),!(e<=options.frozenColumn)){var r=getColspan(t,e);internalScrollColumnIntoView(columnPosLeft[e],columnPosRight[e+(r>1?r-1:0)])}}function internalScrollColumnIntoView(t,e){var n=scrollLeft+$viewportScrollContainerX.width();t<scrollLeft?($viewportScrollContainerX.scrollLeft(t),handleScroll(),render()):e>n&&($viewportScrollContainerX.scrollLeft(Math.min(t,e-$viewportScrollContainerX[0].clientWidth)),handleScroll(),render())}function scrollColumnIntoView(t){internalScrollColumnIntoView(columnPosLeft[t],columnPosRight[t])}function setActiveCellInternal(t,e,n,r,i){if(null!==activeCellNode&&(makeActiveCellNormal(),$(activeCellNode).removeClass("active"),rowsCache[activeRow]&&rowsCache[activeRow].rowNode.removeClass("active")),null!=(activeCellNode=t)){var o=$(activeCellNode),a=o.offset(),s=Math.floor(o.parents(".grid-canvas").offset().top),l=o.parents(".grid-canvas-bottom").length;hasFrozenRows&&l&&(s-=options.frozenBottom?$canvasTopL.height():frozenRowsHeight);var c=getCellFromPoint(a.left,Math.ceil(a.top)-s);activeRow=c.row,activeCell=activePosX=activeCell=activePosX=getCellFromNode(activeCellNode),null==e&&(e=activeRow==getDataLength()||options.autoEdit),options.showCellSelection&&(o.addClass("active"),rowsCache[activeRow]&&rowsCache[activeRow].rowNode.addClass("active")),options.editable&&e&&isCellPotentiallyEditable(activeRow,activeCell)&&(clearTimeout(h_editorLoader),options.asyncEditorLoading?h_editorLoader=setTimeout((function(){makeActiveCellEditable(void 0,n,i)}),options.asyncEditorLoadDelay):makeActiveCellEditable(void 0,n,i))}else activeRow=activeCell=null;r||trigger(self.onActiveCellChanged,getActiveCell())}function clearTextSelection(){if(document.selection&&document.selection.empty)try{document.selection.empty()}catch(t){}else if(window.getSelection){var t=window.getSelection();t&&t.removeAllRanges&&t.removeAllRanges()}}function isCellPotentiallyEditable(t,e){var n=getDataLength();return!(t<n&&!getDataItem(t)||columns[e].cannotTriggerInsert&&t>=n||!getEditor(t,e))}function makeActiveCellNormal(){if(currentEditor){if(trigger(self.onBeforeCellEditorDestroy,{editor:currentEditor}),currentEditor.destroy(),currentEditor=null,activeCellNode){var t=getDataItem(activeRow);if($(activeCellNode).removeClass("editable invalid"),t){var e=columns[activeCell];applyFormatResultToCellNode(getFormatter(activeRow,e)(activeRow,activeCell,getDataItemValueForColumn(t,e),e,t,self),activeCellNode),invalidatePostProcessingResults(activeRow)}}navigator.userAgent.toLowerCase().match(/msie/)&&clearTextSelection(),getEditorLock().deactivate(editController)}}function makeActiveCellEditable(t,e,n){if(activeCellNode){if(!options.editable)throw new Error("SlickGrid makeActiveCellEditable : should never get called when options.editable is false");if(clearTimeout(h_editorLoader),isCellPotentiallyEditable(activeRow,activeCell)){var r=columns[activeCell],i=getDataItem(activeRow);if(!1!==trigger(self.onBeforeEditCell,{row:activeRow,cell:activeCell,item:i,column:r,target:"grid"})){getEditorLock().activate(editController),$(activeCellNode).addClass("editable");var o=t||getEditor(activeRow,activeCell);t||o.suppressClearOnEdit||(activeCellNode.innerHTML="");var a=data.getItemMetadata&&data.getItemMetadata(activeRow),s=(a=a&&a.columns)&&(a[r.id]||a[activeCell]);currentEditor=new o({grid:self,gridPosition:absBox($container[0]),position:absBox(activeCellNode),container:activeCellNode,column:r,columnMetaData:s,item:i||{},event:n,commitChanges:commitEditAndSetFocus,cancelChanges:cancelEditAndSetFocus}),i&&(currentEditor.loadValue(i),e&&currentEditor.preClick&&currentEditor.preClick()),serializedEditorValue=currentEditor.serializeValue(),currentEditor.position&&handleActiveCellPositionChange()}else setFocus()}}}function commitEditAndSetFocus(){getEditorLock().commitCurrentEdit()&&(setFocus(),options.autoEdit&&navigateDown())}function cancelEditAndSetFocus(){getEditorLock().cancelCurrentEdit()&&setFocus()}function absBox(t){var e={top:t.offsetTop,left:t.offsetLeft,bottom:0,right:0,width:$(t).outerWidth(),height:$(t).outerHeight(),visible:!0};e.bottom=e.top+e.height,e.right=e.left+e.width;for(var n=t.offsetParent;(t=t.parentNode)!=document.body&&null!=t;)e.visible&&t.scrollHeight!=t.offsetHeight&&"visible"!=$(t).css("overflowY")&&(e.visible=e.bottom>t.scrollTop&&e.top<t.scrollTop+t.clientHeight),e.visible&&t.scrollWidth!=t.offsetWidth&&"visible"!=$(t).css("overflowX")&&(e.visible=e.right>t.scrollLeft&&e.left<t.scrollLeft+t.clientWidth),e.left-=t.scrollLeft,e.top-=t.scrollTop,t===n&&(e.left+=t.offsetLeft,e.top+=t.offsetTop,n=t.offsetParent),e.bottom=e.top+e.height,e.right=e.left+e.width;return e}function getActiveCellPosition(){return absBox(activeCellNode)}function getGridPosition(){return absBox($container[0])}function handleActiveCellPositionChange(){if(activeCellNode&&(trigger(self.onActiveCellPositionChanged,{}),currentEditor)){var t=getActiveCellPosition();currentEditor.show&&currentEditor.hide&&(t.visible?currentEditor.show():currentEditor.hide()),currentEditor.position&&currentEditor.position(t)}}function getCellEditor(){return currentEditor}function getActiveCell(){return activeCellNode?{row:activeRow,cell:activeCell}:null}function getActiveCellNode(){return activeCellNode}function getTextSelection(){var t=null;if(window.getSelection){var e=window.getSelection();e.rangeCount>0&&(t=e.getRangeAt(0))}return t}function setTextSelection(t){if(window.getSelection&&t){var e=window.getSelection();e.removeAllRanges(),e.addRange(t)}}function scrollRowIntoView(t,e){if(!hasFrozenRows||!options.frozenBottom&&t>actualFrozenRow-1||options.frozenBottom&&t<actualFrozenRow-1){var n=$viewportScrollContainerY.height(),r=hasFrozenRows&&!options.frozenBottom?t-options.frozenRow:t,i=r*options.rowHeight,o=(r+1)*options.rowHeight-n+(viewportHasHScroll?scrollbarDimensions.height:0);(r+1)*options.rowHeight>scrollTop+n+offset?(scrollTo(e?i:o),render()):r*options.rowHeight<scrollTop+offset&&(scrollTo(e?o:i),render())}}function scrollRowToTop(t){scrollTo(t*options.rowHeight),render()}function scrollPage(t){var e=t*numVisibleRows;if(scrollTo((getRowFromPosition(scrollTop+options.rowHeight-1)+e)*options.rowHeight),render(),options.enableCellNavigation&&null!=activeRow){var n=activeRow+e,r=getDataLengthIncludingAddNew();n>=r&&(n=r-1),n<0&&(n=0);for(var i=0,o=null,a=activePosX;i<=activePosX;)canCellBeActive(n,i)&&(o=i),i+=getColspan(n,i);null!==o?(setActiveCellInternal(getCellNode(n,o)),activePosX=a):resetActiveCell()}}function navigatePageDown(){scrollPage(1)}function navigatePageUp(){scrollPage(-1)}function navigateTop(){navigateToRow(0)}function navigateBottom(){navigateToRow(getDataLength()-1)}function navigateToRow(t){var e=getDataLength();if(!e)return!0;if(t<0?t=0:t>=e&&(t=e-1),scrollCellIntoView(t,0,!0),options.enableCellNavigation&&null!=activeRow){for(var n=0,r=null,i=activePosX;n<=activePosX;)canCellBeActive(t,n)&&(r=n),n+=getColspan(t,n);null!==r?(setActiveCellInternal(getCellNode(t,r)),activePosX=i):resetActiveCell()}return!0}function getColspan(t,e){var n=data.getItemMetadata&&data.getItemMetadata(t);if(!n||!n.columns)return 1;var r=n.columns[columns[e].id]||n.columns[e],i=r&&r.colspan;return"*"===i?columns.length-e:i||1}function findFirstFocusableCell(t){for(var e=0;e<columns.length;){if(canCellBeActive(t,e))return e;e+=getColspan(t,e)}return null}function findLastFocusableCell(t){for(var e=0,n=null;e<columns.length;)canCellBeActive(t,e)&&(n=e),e+=getColspan(t,e);return n}function gotoRight(t,e,n){if(e>=columns.length)return null;do{e+=getColspan(t,e)}while(e<columns.length&&!canCellBeActive(t,e));return e<columns.length?{row:t,cell:e,posX:e}:null}function gotoLeft(t,e,n){if(e<=0)return null;var r=findFirstFocusableCell(t);if(null===r||r>=e)return null;for(var i,o={row:t,cell:r,posX:r};;){if(!(i=gotoRight(o.row,o.cell,o.posX)))return null;if(i.cell>=e)return o;o=i}}function gotoDown(t,e,n){for(var r,i=getDataLengthIncludingAddNew();;){if(++t>=i)return null;for(r=e=0;e<=n;)r=e,e+=getColspan(t,e);if(canCellBeActive(t,r))return{row:t,cell:r,posX:n}}}function gotoUp(t,e,n){for(var r;;){if(--t<0)return null;for(r=e=0;e<=n;)r=e,e+=getColspan(t,e);if(canCellBeActive(t,r))return{row:t,cell:r,posX:n}}}function gotoNext(t,e,n){if(null==t&&null==e&&canCellBeActive(t=e=n=0,e))return{row:t,cell:e,posX:e};var r=gotoRight(t,e,n);if(r)return r;var i=null,o=getDataLengthIncludingAddNew();for(t===o-1&&t--;++t<o;)if(null!==(i=findFirstFocusableCell(t)))return{row:t,cell:i,posX:i};return null}function gotoPrev(t,e,n){if(null==t&&null==e&&canCellBeActive(t=getDataLengthIncludingAddNew()-1,e=n=columns.length-1))return{row:t,cell:e,posX:e};for(var r,i;!r&&!(r=gotoLeft(t,e,n));){if(--t<0)return null;e=0,null!==(i=findLastFocusableCell(t))&&(r={row:t,cell:i,posX:i})}return r}function gotoRowStart(t,e,n){var r=findFirstFocusableCell(t);return null===r?null:{row:t,cell:r,posX:r}}function gotoRowEnd(t,e,n){var r=findLastFocusableCell(t);return null===r?null:{row:t,cell:r,posX:r}}function navigateRight(){return navigate("right")}function navigateLeft(){return navigate("left")}function navigateDown(){return navigate("down")}function navigateUp(){return navigate("up")}function navigateNext(){return navigate("next")}function navigatePrev(){return navigate("prev")}function navigateRowStart(){return navigate("home")}function navigateRowEnd(){return navigate("end")}function navigate(t){if(!options.enableCellNavigation)return!1;if(!activeCellNode&&"prev"!=t&&"next"!=t)return!1;if(!getEditorLock().commitCurrentEdit())return!0;setFocus(),tabbingDirection={up:-1,down:1,left:-1,right:1,prev:-1,next:1,home:-1,end:1}[t];var e=(0,{up:gotoUp,down:gotoDown,left:gotoLeft,right:gotoRight,prev:gotoPrev,next:gotoNext,home:gotoRowStart,end:gotoRowEnd}[t])(activeRow,activeCell,activePosX);if(e){if(hasFrozenRows&&options.frozenBottom&e.row==getDataLength())return;var n=e.row==getDataLength();return(!options.frozenBottom&&e.row>=actualFrozenRow||options.frozenBottom&&e.row<actualFrozenRow)&&scrollCellIntoView(e.row,e.cell,!n&&options.emulatePagingWhenScrolling),setActiveCellInternal(getCellNode(e.row,e.cell)),activePosX=e.posX,!0}return setActiveCellInternal(getCellNode(activeRow,activeCell)),!1}function getCellNode(t,e){if(rowsCache[t]){ensureCellNodesInRowsCache(t);try{return rowsCache[t].cellNodesByColumnIdx.length>e?rowsCache[t].cellNodesByColumnIdx[e][0]:null}catch(n){return rowsCache[t].cellNodesByColumnIdx[e]}}return null}function setActiveCell(t,e,n,r,i){initialized&&(t>getDataLength()||t<0||e>=columns.length||e<0||options.enableCellNavigation&&(scrollCellIntoView(t,e,!1),setActiveCellInternal(getCellNode(t,e),n,r,i)))}function setActiveRow(t,e,n){initialized&&(t>getDataLength()||t<0||e>=columns.length||e<0||(activeRow=t,n||scrollCellIntoView(t,e||0,!1)))}function canCellBeActive(t,e){if(!options.enableCellNavigation||t>=getDataLengthIncludingAddNew()||t<0||e>=columns.length||e<0)return!1;var n=data.getItemMetadata&&data.getItemMetadata(t);if(n&&void 0!==n.focusable)return!!n.focusable;var r=n&&n.columns;return r&&r[columns[e].id]&&void 0!==r[columns[e].id].focusable?!!r[columns[e].id].focusable:r&&r[e]&&void 0!==r[e].focusable?!!r[e].focusable:!!columns[e].focusable}function canCellBeSelected(t,e){if(t>=getDataLength()||t<0||e>=columns.length||e<0)return!1;var n=data.getItemMetadata&&data.getItemMetadata(t);if(n&&void 0!==n.selectable)return!!n.selectable;var r=n&&n.columns&&(n.columns[columns[e].id]||n.columns[e]);return r&&void 0!==r.selectable?!!r.selectable:!!columns[e].selectable}function gotoCell(t,e,n,r){if(initialized&&canCellBeActive(t,e)&&getEditorLock().commitCurrentEdit()){scrollCellIntoView(t,e,!1);var i=getCellNode(t,e),o=columns[e],a=!!(options.editable&&o&&o.editor&&options.suppressActiveCellChangeOnEdit);setActiveCellInternal(i,n||t===getDataLength()||options.autoEdit,null,a,r),currentEditor||setFocus()}}function commitCurrentEdit(){var t=getDataItem(activeRow),e=columns[activeCell];if(currentEditor){if(currentEditor.isValueChanged()){var n=currentEditor.validate();if(n.valid){if(activeRow<getDataLength()){var r={row:activeRow,cell:activeCell,editor:currentEditor,serializedValue:currentEditor.serializeValue(),prevSerializedValue:serializedEditorValue,execute:function(){this.editor.applyValue(t,this.serializedValue),updateRow(this.row),trigger(self.onCellChange,{command:"execute",row:this.row,cell:this.cell,item:t,column:e})},undo:function(){this.editor.applyValue(t,this.prevSerializedValue),updateRow(this.row),trigger(self.onCellChange,{command:"undo",row:this.row,cell:this.cell,item:t,column:e})}};options.editCommandHandler?(makeActiveCellNormal(),options.editCommandHandler(t,e,r)):(r.execute(),makeActiveCellNormal())}else{var i={};currentEditor.applyValue(i,currentEditor.serializeValue()),makeActiveCellNormal(),trigger(self.onAddNewRow,{item:i,column:e})}return!getEditorLock().isActive()}return $(activeCellNode).removeClass("invalid"),$(activeCellNode).width(),$(activeCellNode).addClass("invalid"),trigger(self.onValidationError,{editor:currentEditor,cellNode:activeCellNode,validationResults:n,row:activeRow,cell:activeCell,column:e}),currentEditor.focus(),!1}makeActiveCellNormal()}return!0}function cancelCurrentEdit(){return makeActiveCellNormal(),!0}function rowsToRanges(t){for(var e=[],n=columns.length-1,r=0;r<t.length;r++)e.push(new Slick.Range(t[r],0,t[r],n));return e}function getSelectedRows(){if(!selectionModel)throw new Error("SlickGrid Selection model is not set");return selectedRows.slice(0)}function setSelectedRows(t){if(!selectionModel)throw new Error("SlickGrid Selection model is not set");self&&self.getEditorLock&&!self.getEditorLock().isActive()&&selectionModel.setSelectedRanges(rowsToRanges(t))}this.debug=function(){var t="";t+="\ncounter_rows_rendered:  "+counter_rows_rendered,t+="\ncounter_rows_removed:  "+counter_rows_removed,t+="\nrenderedRows:  "+renderedRows,t+="\nnumVisibleRows:  "+numVisibleRows,t+="\nmaxSupportedCssHeight:  "+maxSupportedCssHeight,t+="\nn(umber of pages):  "+n,t+="\n(current) page:  "+page,t+="\npage height (ph):  "+ph,t+="\nvScrollDir:  "+vScrollDir,alert(t)},this.eval=function(expr){return eval(expr)},$.extend(this,{slickGridVersion:"2.4.41",onScroll:new Slick.Event,onBeforeSort:new Slick.Event,onSort:new Slick.Event,onHeaderMouseEnter:new Slick.Event,onHeaderMouseLeave:new Slick.Event,onHeaderContextMenu:new Slick.Event,onHeaderClick:new Slick.Event,onHeaderCellRendered:new Slick.Event,onBeforeHeaderCellDestroy:new Slick.Event,onHeaderRowCellRendered:new Slick.Event,onFooterRowCellRendered:new Slick.Event,onFooterContextMenu:new Slick.Event,onFooterClick:new Slick.Event,onBeforeHeaderRowCellDestroy:new Slick.Event,onBeforeFooterRowCellDestroy:new Slick.Event,onMouseEnter:new Slick.Event,onMouseLeave:new Slick.Event,onClick:new Slick.Event,onDblClick:new Slick.Event,onContextMenu:new Slick.Event,onKeyDown:new Slick.Event,onAddNewRow:new Slick.Event,onBeforeAppendCell:new Slick.Event,onValidationError:new Slick.Event,onViewportChanged:new Slick.Event,onColumnsReordered:new Slick.Event,onColumnsDrag:new Slick.Event,onColumnsResized:new Slick.Event,onColumnsResizeDblClick:new Slick.Event,onBeforeColumnsResize:new Slick.Event,onCellChange:new Slick.Event,onCompositeEditorChange:new Slick.Event,onBeforeEditCell:new Slick.Event,onBeforeCellEditorDestroy:new Slick.Event,onBeforeDestroy:new Slick.Event,onActiveCellChanged:new Slick.Event,onActiveCellPositionChanged:new Slick.Event,onDragInit:new Slick.Event,onDragStart:new Slick.Event,onDrag:new Slick.Event,onDragEnd:new Slick.Event,onSelectedRowsChanged:new Slick.Event,onCellCssStylesChanged:new Slick.Event,onAutosizeColumns:new Slick.Event,onBeforeSetColumns:new Slick.Event,onRendered:new Slick.Event,onSetOptions:new Slick.Event,registerPlugin,unregisterPlugin,getPluginByName,getColumns,setColumns,getColumnIndex,updateColumnHeader,setSortColumn,setSortColumns,getSortColumns,autosizeColumns,autosizeColumn,getOptions,setOptions,getData,getDataLength,getDataItem,setData,getSelectionModel,setSelectionModel,getSelectedRows,setSelectedRows,getContainerNode,updatePagingStatusFromView,applyFormatResultToCellNode,render,reRenderColumns,invalidate,invalidateRow,invalidateRows,invalidateAllRows,updateCell,updateRow,getViewport:getVisibleRange,getRenderedRange,resizeCanvas,updateRowCount,scrollRowIntoView,scrollRowToTop,scrollCellIntoView,scrollColumnIntoView,getCanvasNode,getUID,getHeaderColumnWidthDiff,getScrollbarDimensions,getHeadersWidth,getCanvasWidth,getCanvases,getActiveCanvasNode,setActiveCanvasNode,getViewportNode,getViewports,getActiveViewportNode,setActiveViewportNode,focus:setFocus,scrollTo,cacheCssForHiddenInit,restoreCssFromHiddenInit,getCellFromPoint,getCellFromEvent,getActiveCell,setActiveCell,setActiveRow,getActiveCellNode,getActiveCellPosition,resetActiveCell,editActiveCell:makeActiveCellEditable,getCellEditor,getCellNode,getCellNodeBox,canCellBeSelected,canCellBeActive,navigatePrev,navigateNext,navigateUp,navigateDown,navigateLeft,navigateRight,navigatePageUp,navigatePageDown,navigateTop,navigateBottom,navigateRowStart,navigateRowEnd,gotoCell,getTopPanel,setTopPanelVisibility,getPreHeaderPanel,getPreHeaderPanelLeft:getPreHeaderPanel,getPreHeaderPanelRight,setPreHeaderPanelVisibility,getHeader,getHeaderColumn,setHeaderRowVisibility,getHeaderRow,getHeaderRowColumn,setFooterRowVisibility,getFooterRow,getFooterRowColumn,getGridPosition,flashCell,addCellCssStyles,setCellCssStyles,removeCellCssStyles,getCellCssStyles,getFrozenRowOffset,setColumnHeaderVisibility,init:finishInitialization,destroy,getEditorLock,getEditController}),init()}module.exports={Grid:SlickGrid}},317:(t,e,n)=>{var r=n(7771),i=n(1614);t.exports={GroupItemMetadataProvider:function(t){var e,n={checkboxSelect:!1,checkboxSelectCssClass:"slick-group-select-checkbox",checkboxSelectPlugin:null,groupCssClass:"slick-group",groupTitleCssClass:"slick-group-title",totalsCssClass:"slick-group-totals",groupFocusable:!0,totalsFocusable:!1,toggleCssClass:"slick-group-toggle",toggleExpandedCssClass:"expanded",toggleCollapsedCssClass:"collapsed",enableExpandCollapse:!0,groupFormatter:function(t,e,n,r,i,a){if(!o.enableExpandCollapse)return i.title;var s=15*i.level+"px";return(o.checkboxSelect?'<span class="'+o.checkboxSelectCssClass+" "+(i.selectChecked?"checked":"unchecked")+'"></span>':"")+"<span class='"+o.toggleCssClass+" "+(i.collapsed?o.toggleCollapsedCssClass:o.toggleExpandedCssClass)+"' style='margin-left:"+s+"'></span><span class='"+o.groupTitleCssClass+"' level='"+i.level+"'>"+i.title+"</span>"},totalsFormatter:function(t,e,n,r,i,o){return r.groupTotalsFormatter&&r.groupTotalsFormatter(i,r,o)||""},includeHeaderTotals:!1},o=r.extend(!0,{},n,t);function a(t,n){var a=r(t.target),s=this.getDataItem(n.row);if(s&&s instanceof i.Group&&a.hasClass(o.toggleCssClass)){var l=e.getRenderedRange();this.getData().setRefreshHints({ignoreDiffsBefore:l.top,ignoreDiffsAfter:l.bottom+1}),s.collapsed?this.getData().expandGroup(s.groupingKey):this.getData().collapseGroup(s.groupingKey),t.stopImmediatePropagation(),t.preventDefault()}if(s&&s instanceof i.Group&&a.hasClass(o.checkboxSelectCssClass)){s.selectChecked=!s.selectChecked,a.removeClass(s.selectChecked?"unchecked":"checked"),a.addClass(s.selectChecked?"checked":"unchecked");var c=e.getData().mapItemsToRows(s.rows);(s.selectChecked?o.checkboxSelectPlugin.selectRows:o.checkboxSelectPlugin.deSelectRows)(c)}}function s(t,n){if(o.enableExpandCollapse&&t.which==i.keyCode.SPACE){var r=this.getActiveCell();if(r){var a=this.getDataItem(r.row);if(a&&a instanceof i.Group){var 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i(t){n.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!n.has(t)){var r=e.get(t);r&&i(r)}})),r.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){n.has(t.name)||i(t)})),r}var pn={placement:"bottom",modifiers:[],strategy:"absolute"};function fn(){for(var t=arguments.length,e=new Array(t),n=0;n<t;n++)e[n]=arguments[n];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function Qn(t){void 0===t&&(t={});var e=t,n=e.defaultModifiers,r=void 0===n?[]:n,i=e.defaultOptions,o=void 0===i?pn:i;return function(t,e,n){void 0===n&&(n=o);var i,a,s={placement:"bottom",orderedModifiers:[],options:Object.assign({},pn,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,u={state:s,setOptions:function(n){var i="function"==typeof 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t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(R.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...T(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const n=B.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter((t=>s(t)));n.length&&g(n,e,t===wn,!n.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=$n.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(2===t.button||"keyup"===t.type&&"Tab"!==t.key)return;const e=B.find(On);for(const n of e){const e=$n.getInstance(n);if(!e||!1===e._config.autoClose)continue;const r=t.composedPath(),i=r.includes(e._menu);if(r.includes(e._element)||"inside"===e._config.autoClose&&!i||"outside"===e._config.autoClose&&i)continue;if(e._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;const o={relatedTarget:e._element};"click"===t.type&&(o.clickEvent=t),e._completeHide(o)}}static dataApiKeydownHandler(t){const e=/input|textarea/i.test(t.target.tagName),n="Escape"===t.key,r=[xn,wn].includes(t.key);if(!r&&!n)return;if(e&&!n)return;t.preventDefault();const i=this.matches(Vn)?this:B.prev(this,Vn)[0]||B.next(this,Vn)[0]||B.findOne(Vn,t.delegateTarget.parentNode),o=$n.getOrCreateInstance(i);if(r)return t.stopPropagation(),o.show(),void 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e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(qn),this._emulateAnimation((()=>{T(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(qn),this._emulateAnimation((()=>{this.dispose(),T(t)}))):T(t)}dispose(){this._isAppended&&(O.off(this._element,Un),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=a(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),O.on(t,Un,(()=>{T(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){m(t,this._getElement(),this._config.isAnimated)}}const Kn=".bs.focustrap",Yn=`focusin${Kn}`,Jn=`keydown.tab${Kn}`,tr="backward",er={autofocus:!0,trapElement:null},nr={autofocus:"boolean",trapElement:"element"};class rr extends I{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return er}static get DefaultType(){return nr}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),O.off(document,Kn),O.on(document,Yn,(t=>this._handleFocusin(t))),O.on(document,Jn,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,O.off(document,Kn))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const n=B.focusableChildren(e);0===n.length?e.focus():this._lastTabNavDirection===tr?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tr:"forward")}}const ir=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",or=".sticky-top",ar="padding-right",sr="margin-right";class lr{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,ar,(e=>e+t)),this._setElementAttributes(ir,ar,(e=>e+t)),this._setElementAttributes(or,sr,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,ar),this._resetElementAttributes(ir,ar),this._resetElementAttributes(or,sr)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,n){const r=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+r)return;this._saveInitialAttribute(t,e);const i=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${n(Number.parseFloat(i))}px`)}))}_saveInitialAttribute(t,e){const n=t.style.getPropertyValue(e);n&&R.setDataAttribute(t,e,n)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const n=R.getDataAttribute(t,e);null!==n?(R.removeDataAttribute(t,e),t.style.setProperty(e,n)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const n of B.find(t,this._element))e(n)}}const cr=".bs.modal",ur=`hide${cr}`,dr=`hidePrevented${cr}`,hr=`hidden${cr}`,pr=`show${cr}`,fr=`shown${cr}`,Qr=`resize${cr}`,Tr=`click.dismiss${cr}`,mr=`mousedown.dismiss${cr}`,gr=`keydown.dismiss${cr}`,_r=`click${cr}.data-api`,br="modal-open",vr="show",yr="modal-static",xr={backdrop:!0,focus:!0,keyboard:!0},wr={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class Lr extends j{constructor(t,e){super(t,e),this._dialog=B.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new lr,this._addEventListeners()}static get Default(){return xr}static get DefaultType(){return wr}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||O.trigger(this._element,pr,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(br),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(O.trigger(this._element,ur).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(vr),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){O.off(window,cr),O.off(this._dialog,cr),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Xn({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new rr({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=B.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(vr),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,O.trigger(this._element,fr,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){O.on(this._element,gr,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),O.on(window,Qr,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),O.on(this._element,mr,(t=>{O.one(this._element,Tr,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(br),this._resetAdjustments(),this._scrollBar.reset(),O.trigger(this._element,hr)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(O.trigger(this._element,dr).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(yr)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(yr),this._queueCallback((()=>{this._element.classList.remove(yr),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),n=e>0;if(n&&!t){const t=f()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!n&&t){const t=f()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const n=Lr.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===n[t])throw new TypeError(`No method named "${t}"`);n[t](e)}}))}}O.on(document,_r,'[data-bs-toggle="modal"]',(function(t){const e=B.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),O.one(e,pr,(t=>{t.defaultPrevented||O.one(e,hr,(()=>{s(this)&&this.focus()}))}));const n=B.findOne(".modal.show");n&&Lr.getInstance(n).hide(),Lr.getOrCreateInstance(e).toggle(this)})),F(Lr),Q(Lr);const Ar=".bs.offcanvas",Hr=".data-api",kr=`load${Ar}${Hr}`,Mr="show",Cr="showing",Sr="hiding",Er=".offcanvas.show",Vr=`show${Ar}`,Or=`shown${Ar}`,Pr=`hide${Ar}`,Dr=`hidePrevented${Ar}`,Nr=`hidden${Ar}`,Rr=`resize${Ar}`,Ir=`click${Ar}${Hr}`,jr=`keydown.dismiss${Ar}`,zr={backdrop:!0,keyboard:!0,scroll:!1},Br={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class Fr extends j{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zr}static get DefaultType(){return Br}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||O.trigger(this._element,Vr,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new lr).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Cr),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Mr),this._element.classList.remove(Cr),O.trigger(this._element,Or,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(O.trigger(this._element,Pr).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add(Sr),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Mr,Sr),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new lr).reset(),O.trigger(this._element,Nr)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Xn({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():O.trigger(this._element,Dr)}:null})}_initializeFocusTrap(){return new rr({trapElement:this._element})}_addEventListeners(){O.on(this._element,jr,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():O.trigger(this._element,Dr))}))}static jQueryInterface(t){return this.each((function(){const e=Fr.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}O.on(document,Ir,'[data-bs-toggle="offcanvas"]',(function(t){const e=B.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;O.one(e,Nr,(()=>{s(this)&&this.focus()}));const n=B.findOne(Er);n&&n!==e&&Fr.getInstance(n).hide(),Fr.getOrCreateInstance(e).toggle(this)})),O.on(window,kr,(()=>{for(const t of B.find(Er))Fr.getOrCreateInstance(t).show()})),O.on(window,Rr,(()=>{for(const t of B.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&Fr.getOrCreateInstance(t).hide()})),F(Fr),Q(Fr);const $r={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],dd:[],div:[],dl:[],dt:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Gr=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),qr=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Ur=(t,e)=>{const n=t.nodeName.toLowerCase();return e.includes(n)?!Gr.has(n)||Boolean(qr.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(n)))},Wr={allowList:$r,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"<div></div>"},Zr={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Xr={entry:"(string|element|function|null)",selector:"(string|element)"};class Kr extends I{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Wr}static get DefaultType(){return Zr}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,n]of Object.entries(this._config.content))this._setContent(t,n,e);const e=t.children[0],n=this._resolvePossibleFunction(this._config.extraClass);return n&&e.classList.add(...n.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,n]of Object.entries(t))super._typeCheckConfig({selector:e,entry:n},Xr)}_setContent(t,e,n){const r=B.findOne(n,t);r&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(a(e),r):this._config.html?r.innerHTML=this._maybeSanitize(e):r.textContent=e:r.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,n){if(!t.length)return t;if(n&&"function"==typeof n)return n(t);const r=(new window.DOMParser).parseFromString(t,"text/html"),i=[].concat(...r.body.querySelectorAll("*"));for(const t of i){const n=t.nodeName.toLowerCase();if(!Object.keys(e).includes(n)){t.remove();continue}const r=[].concat(...t.attributes),i=[].concat(e["*"]||[],e[n]||[]);for(const e of r)Ur(e,i)||t.removeAttribute(e.nodeName)}return r.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return T(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Yr=new Set(["sanitize","allowList","sanitizeFn"]),Jr="fade",ti="show",ei=".modal",ni="hide.bs.modal",ri="hover",ii="focus",oi={AUTO:"auto",TOP:"top",RIGHT:f()?"left":"right",BOTTOM:"bottom",LEFT:f()?"right":"left"},ai={allowList:$r,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',title:"",trigger:"hover focus"},si={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class li extends j{constructor(t,e){if(void 0===_n)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return ai}static get DefaultType(){return si}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),O.off(this._element.closest(ei),ni,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=O.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const n=this._getTipElement();this._element.setAttribute("aria-describedby",n.getAttribute("id"));const{container:r}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(r.append(n),O.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(n),n.classList.add(ti),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))O.on(t,"mouseover",u);this._queueCallback((()=>{O.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!O.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(ti),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))O.off(t,"mouseover",u);this._activeTrigger.click=!1,this._activeTrigger[ii]=!1,this._activeTrigger[ri]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),O.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(Jr,ti),e.classList.add(`bs-${this.constructor.NAME}-auto`);const n=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",n),this._isAnimated()&&e.classList.add(Jr),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Kr({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(Jr)}_isShown(){return this.tip&&this.tip.classList.contains(ti)}_createPopper(t){const e=T(this._config.placement,[this,t,this._element]),n=oi[e.toUpperCase()];return gn(this._element,t,this._getPopperConfig(n))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return T(t,[this._element])}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,...T(this._config.popperConfig,[e])}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)O.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else if("manual"!==e){const t=e===ri?this.constructor.eventName("mouseenter"):this.constructor.eventName("focusin"),n=e===ri?this.constructor.eventName("mouseleave"):this.constructor.eventName("focusout");O.on(this._element,t,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusin"===t.type?ii:ri]=!0,e._enter()})),O.on(this._element,n,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusout"===t.type?ii:ri]=e._element.contains(t.relatedTarget),e._leave()}))}this._hideModalHandler=()=>{this._element&&this.hide()},O.on(this._element.closest(ei),ni,this._hideModalHandler)}_fixTitle(){const t=this._element.getAttribute("title");t&&(this._element.getAttribute("aria-label")||this._element.textContent.trim()||this._element.setAttribute("aria-label",t),this._element.setAttribute("data-bs-original-title",t),this._element.removeAttribute("title"))}_enter(){this._isShown()||this._isHovered?this._isHovered=!0:(this._isHovered=!0,this._setTimeout((()=>{this._isHovered&&this.show()}),this._config.delay.show))}_leave(){this._isWithActiveTrigger()||(this._isHovered=!1,this._setTimeout((()=>{this._isHovered||this.hide()}),this._config.delay.hide))}_setTimeout(t,e){clearTimeout(this._timeout),this._timeout=setTimeout(t,e)}_isWithActiveTrigger(){return Object.values(this._activeTrigger).includes(!0)}_getConfig(t){const e=R.getDataAttributes(this._element);for(const t of Object.keys(e))Yr.has(t)&&delete e[t];return t={...e,..."object"==typeof t&&t?t:{}},t=this._mergeConfigObj(t),t=this._configAfterMerge(t),this._typeCheckConfig(t),t}_configAfterMerge(t){return t.container=!1===t.container?document.body:a(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),t}_getDelegateConfig(){const t={};for(const[e,n]of Object.entries(this._config))this.constructor.Default[e]!==n&&(t[e]=n);return t.selector=!1,t.trigger="manual",t}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null),this.tip&&(this.tip.remove(),this.tip=null)}static jQueryInterface(t){return this.each((function(){const e=li.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}Q(li);const ci={...li.Default,content:"",offset:[0,8],placement:"right",template:'<div class="popover" role="tooltip"><div class="popover-arrow"></div><h3 class="popover-header"></h3><div class="popover-body"></div></div>',trigger:"click"},ui={...li.DefaultType,content:"(null|string|element|function)"};class di extends li{static get Default(){return ci}static get DefaultType(){return ui}static get NAME(){return"popover"}_isWithContent(){return this._getTitle()||this._getContent()}_getContentForTemplate(){return{".popover-header":this._getTitle(),".popover-body":this._getContent()}}_getContent(){return this._resolvePossibleFunction(this._config.content)}static jQueryInterface(t){return this.each((function(){const e=di.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}Q(di);const hi=".bs.scrollspy",pi=`activate${hi}`,fi=`click${hi}`,Qi=`load${hi}.data-api`,Ti="active",mi="[href]",gi=".nav-link",_i=`${gi}, .nav-item > ${gi}, .list-group-item`,bi={offset:null,rootMargin:"0px 0px -25%",smoothScroll:!1,target:null,threshold:[.1,.5,1]},vi={offset:"(number|null)",rootMargin:"string",smoothScroll:"boolean",target:"element",threshold:"array"};class yi extends j{constructor(t,e){super(t,e),this._targetLinks=new Map,this._observableSections=new Map,this._rootElement="visible"===getComputedStyle(this._element).overflowY?null:this._element,this._activeTarget=null,this._observer=null,this._previousScrollData={visibleEntryTop:0,parentScrollTop:0},this.refresh()}static get Default(){return bi}static get DefaultType(){return vi}static get NAME(){return"scrollspy"}refresh(){this._initializeTargetsAndObservables(),this._maybeEnableSmoothScroll(),this._observer?this._observer.disconnect():this._observer=this._getNewObserver();for(const t of this._observableSections.values())this._observer.observe(t)}dispose(){this._observer.disconnect(),super.dispose()}_configAfterMerge(t){return t.target=a(t.target)||document.body,t.rootMargin=t.offset?`${t.offset}px 0px 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t){if(!o.isIntersecting){this._activeTarget=null,this._clearActiveClass(e(o));continue}const t=o.target.offsetTop>=this._previousScrollData.visibleEntryTop;if(i&&t){if(n(o),!r)return}else i||t||n(o)}}_initializeTargetsAndObservables(){this._targetLinks=new Map,this._observableSections=new Map;const t=B.find(mi,this._config.target);for(const e of t){if(!e.hash||l(e))continue;const t=B.findOne(decodeURI(e.hash),this._element);s(t)&&(this._targetLinks.set(decodeURI(e.hash),e),this._observableSections.set(e.hash,t))}}_process(t){this._activeTarget!==t&&(this._clearActiveClass(this._config.target),this._activeTarget=t,t.classList.add(Ti),this._activateParents(t),O.trigger(this._element,pi,{relatedTarget:t}))}_activateParents(t){if(t.classList.contains("dropdown-item"))B.findOne(".dropdown-toggle",t.closest(".dropdown")).classList.add(Ti);else for(const e of B.parents(t,".nav, .list-group"))for(const t of B.prev(e,_i))t.classList.add(Ti)}_clearActiveClass(t){t.classList.remove(Ti);const 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e=B.getElementFromSelector(t);e&&(this._setAttributeIfNotExists(e,"role","tabpanel"),t.id&&this._setAttributeIfNotExists(e,"aria-labelledby",`${t.id}`))}_toggleDropDown(t,e){const n=this._getOuterElement(t);if(!n.classList.contains("dropdown"))return;const r=(t,r)=>{const i=B.findOne(t,n);i&&i.classList.toggle(r,e)};r(ji,Ni),r(".dropdown-menu",Ii),n.setAttribute("aria-expanded",e)}_setAttributeIfNotExists(t,e,n){t.hasAttribute(e)||t.setAttribute(e,n)}_elemIsActive(t){return t.classList.contains(Ni)}_getInnerElement(t){return t.matches(Fi)?t:B.findOne(Fi,t)}_getOuterElement(t){return t.closest(".nav-item, .list-group-item")||t}static jQueryInterface(t){return this.each((function(){const e=Gi.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named 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.offcanvas{position:static;z-index:auto;flex-grow:1;width:auto!important;height:auto!important;visibility:visible!important;background-color:transparent!important;border:0!important;transform:none!important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;flex-grow:0;padding:0;overflow-y:visible}}@media (min-width:1400px){.navbar-expand-xxl{flex-wrap:nowrap;justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex!important;flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl 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.offcanvas{position:static;z-index:auto;flex-grow:1;width:auto!important;height:auto!important;visibility:visible!important;background-color:transparent!important;border:0!important;transform:none!important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme=dark]{--bs-navbar-color:rgba(255, 255, 255, 0.55);--bs-navbar-hover-color:rgba(255, 255, 255, 0.75);--bs-navbar-disabled-color:rgba(255, 255, 255, 0.25);--bs-navbar-active-color:#fff;--bs-navbar-brand-color:#fff;--bs-navbar-brand-hover-color:#fff;--bs-navbar-toggler-border-color:rgba(255, 255, 255, 0.1);--bs-navbar-toggler-icon-bg:url(${z})}[data-bs-theme=dark] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg:url(${z})}.card{--bs-card-spacer-y:1rem;--bs-card-spacer-x:1rem;--bs-card-title-spacer-y:0.5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width:var(--bs-border-width);--bs-card-border-color:var(--bs-border-color-translucent);--bs-card-border-radius:var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius:calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y:0.5rem;--bs-card-cap-padding-x:1rem;--bs-card-cap-bg:rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg:var(--bs-body-bg);--bs-card-img-overlay-padding:1rem;--bs-card-group-margin:0.75rem;position:relative;display:flex;flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid 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var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion:reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type>.accordion-header .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type>.accordion-header .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type>.accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush>.accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush>.accordion-item:first-child{border-top:0}.accordion-flush>.accordion-item:last-child{border-bottom:0}.accordion-flush>.accordion-item>.accordion-header .accordion-button,.accordion-flush>.accordion-item>.accordion-header .accordion-button.collapsed{border-radius:0}.accordion-flush>.accordion-item>.accordion-collapse{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon:url(${$});--bs-accordion-btn-active-icon:url(${$})}.breadcrumb{--bs-breadcrumb-padding-x:0;--bs-breadcrumb-padding-y:0;--bs-breadcrumb-margin-bottom:1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color:var(--bs-secondary-color);--bs-breadcrumb-item-padding-x:0.5rem;--bs-breadcrumb-item-active-color:var(--bs-secondary-color);display:flex;flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/")}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x:0.75rem;--bs-pagination-padding-y:0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color:var(--bs-link-color);--bs-pagination-bg:var(--bs-body-bg);--bs-pagination-border-width:var(--bs-border-width);--bs-pagination-border-color:var(--bs-border-color);--bs-pagination-border-radius:var(--bs-border-radius);--bs-pagination-hover-color:var(--bs-link-hover-color);--bs-pagination-hover-bg:var(--bs-tertiary-bg);--bs-pagination-hover-border-color:var(--bs-border-color);--bs-pagination-focus-color:var(--bs-link-hover-color);--bs-pagination-focus-bg:var(--bs-secondary-bg);--bs-pagination-focus-box-shadow:0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-pagination-active-color:#fff;--bs-pagination-active-bg:#0d6efd;--bs-pagination-active-border-color:#0d6efd;--bs-pagination-disabled-color:var(--bs-secondary-color);--bs-pagination-disabled-bg:var(--bs-secondary-bg);--bs-pagination-disabled-border-color:var(--bs-border-color);display:flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media (prefers-reduced-motion:reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.active>.page-link,.page-link.active{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.disabled>.page-link,.page-link.disabled{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x:1.5rem;--bs-pagination-padding-y:0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius:var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x:0.5rem;--bs-pagination-padding-y:0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius:var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x:0.65em;--bs-badge-padding-y:0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight:700;--bs-badge-color:#fff;--bs-badge-border-radius:var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg:transparent;--bs-alert-padding-x:1rem;--bs-alert-padding-y:1rem;--bs-alert-margin-bottom:1rem;--bs-alert-color:inherit;--bs-alert-border-color:transparent;--bs-alert-border:var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius:var(--bs-border-radius);--bs-alert-link-color:inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-primary{--bs-alert-color:var(--bs-primary-text-emphasis);--bs-alert-bg:var(--bs-primary-bg-subtle);--bs-alert-border-color:var(--bs-primary-border-subtle);--bs-alert-link-color:var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color:var(--bs-secondary-text-emphasis);--bs-alert-bg:var(--bs-secondary-bg-subtle);--bs-alert-border-color:var(--bs-secondary-border-subtle);--bs-alert-link-color:var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color:var(--bs-success-text-emphasis);--bs-alert-bg:var(--bs-success-bg-subtle);--bs-alert-border-color:var(--bs-success-border-subtle);--bs-alert-link-color:var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color:var(--bs-info-text-emphasis);--bs-alert-bg:var(--bs-info-bg-subtle);--bs-alert-border-color:var(--bs-info-border-subtle);--bs-alert-link-color:var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color:var(--bs-warning-text-emphasis);--bs-alert-bg:var(--bs-warning-bg-subtle);--bs-alert-border-color:var(--bs-warning-border-subtle);--bs-alert-link-color:var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color:var(--bs-danger-text-emphasis);--bs-alert-bg:var(--bs-danger-bg-subtle);--bs-alert-border-color:var(--bs-danger-border-subtle);--bs-alert-link-color:var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color:var(--bs-light-text-emphasis);--bs-alert-bg:var(--bs-light-bg-subtle);--bs-alert-border-color:var(--bs-light-border-subtle);--bs-alert-link-color:var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color:var(--bs-dark-text-emphasis);--bs-alert-bg:var(--bs-dark-bg-subtle);--bs-alert-border-color:var(--bs-dark-border-subtle);--bs-alert-link-color:var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height:1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg:var(--bs-secondary-bg);--bs-progress-border-radius:var(--bs-border-radius);--bs-progress-box-shadow:var(--bs-box-shadow-inset);--bs-progress-bar-color:#fff;--bs-progress-bar-bg:#0d6efd;--bs-progress-bar-transition:width 0.6s ease;display:flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;flex-direction:column;justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion:reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg,rgba(255,255,255,.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,.15) 50%,rgba(255,255,255,.15) 75%,transparent 75%,transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion:reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color:var(--bs-body-color);--bs-list-group-bg:var(--bs-body-bg);--bs-list-group-border-color:var(--bs-border-color);--bs-list-group-border-width:var(--bs-border-width);--bs-list-group-border-radius:var(--bs-border-radius);--bs-list-group-item-padding-x:1rem;--bs-list-group-item-padding-y:0.5rem;--bs-list-group-action-color:var(--bs-secondary-color);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-tertiary-bg);--bs-list-group-action-active-color:var(--bs-body-color);--bs-list-group-action-active-bg:var(--bs-secondary-bg);--bs-list-group-disabled-color:var(--bs-secondary-color);--bs-list-group-disabled-bg:var(--bs-body-bg);--bs-list-group-active-color:#fff;--bs-list-group-active-bg:#0d6efd;--bs-list-group-active-border-color:#0d6efd;display:flex;flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:focus,.list-group-item-action:hover{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width:576px){.list-group-horizontal-sm{flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:768px){.list-group-horizontal-md{flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:992px){.list-group-horizontal-lg{flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:1200px){.list-group-horizontal-xl{flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width:1400px){.list-group-horizontal-xxl{flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-primary{--bs-list-group-color:var(--bs-primary-text-emphasis);--bs-list-group-bg:var(--bs-primary-bg-subtle);--bs-list-group-border-color:var(--bs-primary-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-primary-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-primary-border-subtle);--bs-list-group-active-color:var(--bs-primary-bg-subtle);--bs-list-group-active-bg:var(--bs-primary-text-emphasis);--bs-list-group-active-border-color:var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color:var(--bs-secondary-text-emphasis);--bs-list-group-bg:var(--bs-secondary-bg-subtle);--bs-list-group-border-color:var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-secondary-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-secondary-border-subtle);--bs-list-group-active-color:var(--bs-secondary-bg-subtle);--bs-list-group-active-bg:var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color:var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color:var(--bs-success-text-emphasis);--bs-list-group-bg:var(--bs-success-bg-subtle);--bs-list-group-border-color:var(--bs-success-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-success-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-success-border-subtle);--bs-list-group-active-color:var(--bs-success-bg-subtle);--bs-list-group-active-bg:var(--bs-success-text-emphasis);--bs-list-group-active-border-color:var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color:var(--bs-info-text-emphasis);--bs-list-group-bg:var(--bs-info-bg-subtle);--bs-list-group-border-color:var(--bs-info-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-info-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-info-border-subtle);--bs-list-group-active-color:var(--bs-info-bg-subtle);--bs-list-group-active-bg:var(--bs-info-text-emphasis);--bs-list-group-active-border-color:var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color:var(--bs-warning-text-emphasis);--bs-list-group-bg:var(--bs-warning-bg-subtle);--bs-list-group-border-color:var(--bs-warning-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-warning-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-warning-border-subtle);--bs-list-group-active-color:var(--bs-warning-bg-subtle);--bs-list-group-active-bg:var(--bs-warning-text-emphasis);--bs-list-group-active-border-color:var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color:var(--bs-danger-text-emphasis);--bs-list-group-bg:var(--bs-danger-bg-subtle);--bs-list-group-border-color:var(--bs-danger-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-danger-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-danger-border-subtle);--bs-list-group-active-color:var(--bs-danger-bg-subtle);--bs-list-group-active-bg:var(--bs-danger-text-emphasis);--bs-list-group-active-border-color:var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color:var(--bs-light-text-emphasis);--bs-list-group-bg:var(--bs-light-bg-subtle);--bs-list-group-border-color:var(--bs-light-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-light-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-light-border-subtle);--bs-list-group-active-color:var(--bs-light-bg-subtle);--bs-list-group-active-bg:var(--bs-light-text-emphasis);--bs-list-group-active-border-color:var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color:var(--bs-dark-text-emphasis);--bs-list-group-bg:var(--bs-dark-bg-subtle);--bs-list-group-border-color:var(--bs-dark-border-subtle);--bs-list-group-action-hover-color:var(--bs-emphasis-color);--bs-list-group-action-hover-bg:var(--bs-dark-border-subtle);--bs-list-group-action-active-color:var(--bs-emphasis-color);--bs-list-group-action-active-bg:var(--bs-dark-border-subtle);--bs-list-group-active-color:var(--bs-dark-bg-subtle);--bs-list-group-active-bg:var(--bs-dark-text-emphasis);--bs-list-group-active-border-color:var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color:#000;--bs-btn-close-bg:url(${G});--bs-btn-close-opacity:0.5;--bs-btn-close-hover-opacity:0.75;--bs-btn-close-focus-shadow:0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-btn-close-focus-opacity:1;--bs-btn-close-disabled-opacity:0.25;--bs-btn-close-white-filter:invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close.disabled,.btn-close:disabled{pointer-events:none;-webkit-user-select:none;-moz-user-select:none;user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex:1090;--bs-toast-padding-x:0.75rem;--bs-toast-padding-y:0.5rem;--bs-toast-spacing:1.5rem;--bs-toast-max-width:350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg:rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width:var(--bs-border-width);--bs-toast-border-color:var(--bs-border-color-translucent);--bs-toast-border-radius:var(--bs-border-radius);--bs-toast-box-shadow:var(--bs-box-shadow);--bs-toast-header-color:var(--bs-secondary-color);--bs-toast-header-bg:rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color:var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex:1090;position:absolute;z-index:var(--bs-toast-zindex);width:-webkit-max-content;width:-moz-max-content;width:max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex:1055;--bs-modal-width:500px;--bs-modal-padding:1rem;--bs-modal-margin:0.5rem;--bs-modal-color: ;--bs-modal-bg:var(--bs-body-bg);--bs-modal-border-color:var(--bs-border-color-translucent);--bs-modal-border-width:var(--bs-border-width);--bs-modal-border-radius:var(--bs-border-radius-lg);--bs-modal-box-shadow:var(--bs-box-shadow-sm);--bs-modal-inner-border-radius:calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x:1rem;--bs-modal-header-padding-y:1rem;--bs-modal-header-padding:1rem 1rem;--bs-modal-header-border-color:var(--bs-border-color);--bs-modal-header-border-width:var(--bs-border-width);--bs-modal-title-line-height:1.5;--bs-modal-footer-gap:0.5rem;--bs-modal-footer-bg: 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e=this.table.length-1,n=-1;c.default.getAttribute(c.default.getChildren(this.table[0])[0],"columnalign")||c.default.setAttribute(c.default.getChildren(this.table[0])[0],"columnalign",d.TexConstant.Align.LEFT),c.default.getAttribute(c.default.getChildren(this.table[e])[0],"columnalign")||c.default.setAttribute(c.default.getChildren(this.table[e])[0],"columnalign",d.TexConstant.Align.RIGHT);var r=this.factory.configuration.tags.getTag();if(r){n=this.arraydef.side===d.TexConstant.Align.LEFT?0:this.table.length-1;var i=this.table[n],o=this.create("node","mlabeledtr",[r].concat(c.default.getChildren(i)));c.default.copyAttributes(i,o),this.table[n]=o}}this.factory.configuration.tags.end()},e}(s.ArrayItem);e.MultlineItem=h;var p=function(t){function e(e,n,r,i,o){var a=t.call(this,e)||this;return a.name=n,a.numbered=r,a.padded=i,a.center=o,a.factory.configuration.tags.start(n,r,r),a}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"flalign"},enumerable:!1,configurable:!0}),e.prototype.EndEntry=function(){t.prototype.EndEntry.call(this);var e=this.getProperty("xalignat");if(e&&this.row.length>e)throw new u.default("XalignOverflow","Extra %1 in row of %2","&",this.name)},e.prototype.EndRow=function(){for(var e,n=this.row,r=this.getProperty("xalignat");n.length<r;)n.push(this.create("node","mtd"));for(this.row=[],this.padded&&this.row.push(this.create("node","mtd"));e=n.shift();)this.row.push(e),(e=n.shift())&&this.row.push(e),(n.length||this.padded)&&this.row.push(this.create("node","mtd"));this.row.length>this.maxrow&&(this.maxrow=this.row.length),t.prototype.EndRow.call(this);var i=this.table[this.table.length-1];if(this.getProperty("zeroWidthLabel")&&i.isKind("mlabeledtr")){var a=c.default.getChildren(i)[0],s=this.factory.configuration.options.tagSide,l=o({width:0},"right"===s?{lspace:"-1width"}:{}),u=this.create("node","mpadded",c.default.getChildren(a),l);a.setChildren([u])}},e.prototype.EndTable=function(){t.prototype.EndTable.call(this),this.center&&this.maxrow<=2&&(delete this.arraydef.width,delete this.global.indentalign)},e}(s.EqnArrayItem);e.FlalignItem=p},7403:function(t,e,n){"use strict";var r=this&&this.__createBinding||(Object.create?function(t,e,n,r){void 0===r&&(r=n);var i=Object.getOwnPropertyDescriptor(e,n);i&&!("get"in i?!e.__esModule:i.writable||i.configurable)||(i={enumerable:!0,get:function(){return e[n]}}),Object.defineProperty(t,r,i)}:function(t,e,n,r){void 0===r&&(r=n),t[r]=e[n]}),i=this&&this.__setModuleDefault||(Object.create?function(t,e){Object.defineProperty(t,"default",{enumerable:!0,value:e})}:function(t,e){t.default=e}),o=this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)"default"!==n&&Object.prototype.hasOwnProperty.call(t,n)&&r(e,t,n);return i(e,t),e},a=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var s=n(8840),l=o(n(209)),c=n(469),u=a(n(2960)),d=a(n(6980)),h=n(747),p=n(6810);new l.CharacterMap("AMSmath-mathchar0mo",u.default.mathchar0mo,{iiiint:["⨌",{texClass:h.TEXCLASS.OP}]}),new l.RegExpMap("AMSmath-operatorLetter",s.AmsMethods.operatorLetter,/[-*]/i),new l.CommandMap("AMSmath-macros",{mathring:["Accent","02DA"],nobreakspace:"Tilde",negmedspace:["Spacer",p.MATHSPACE.negativemediummathspace],negthickspace:["Spacer",p.MATHSPACE.negativethickmathspace],idotsint:["MultiIntegral","\\int\\cdots\\int"],dddot:["Accent","20DB"],ddddot:["Accent","20DC"],sideset:"SideSet",boxed:["Macro","\\fbox{$\\displaystyle{#1}$}",1],tag:"HandleTag",notag:"HandleNoTag",eqref:["HandleRef",!0],substack:["Macro","\\begin{subarray}{c}#1\\end{subarray}",1],injlim:["NamedOp","inj&thinsp;lim"],projlim:["NamedOp","proj&thinsp;lim"],varliminf:["Macro","\\mathop{\\underline{\\mmlToken{mi}{lim}}}"],varlimsup:["Macro","\\mathop{\\overline{\\mmlToken{mi}{lim}}}"],varinjlim:["Macro","\\mathop{\\underrightarrow{\\mmlToken{mi}{lim}}}"],varprojlim:["Macro","\\mathop{\\underleftarrow{\\mmlToken{mi}{lim}}}"],DeclareMathOperator:"HandleDeclareOp",operatorname:"HandleOperatorName",genfrac:"Genfrac",frac:["Genfrac","","","",""],tfrac:["Genfrac","","","","1"],dfrac:["Genfrac","","","","0"],binom:["Genfrac","(",")","0",""],tbinom:["Genfrac","(",")","0","1"],dbinom:["Genfrac","(",")","0","0"],cfrac:"CFrac",shoveleft:["HandleShove",c.TexConstant.Align.LEFT],shoveright:["HandleShove",c.TexConstant.Align.RIGHT],xrightarrow:["xArrow",8594,5,10],xleftarrow:["xArrow",8592,10,5]},s.AmsMethods),new l.EnvironmentMap("AMSmath-environment",u.default.environment,{"equation*":["Equation",null,!1],"eqnarray*":["EqnArray",null,!1,!0,"rcl",d.default.cols(0,p.MATHSPACE.thickmathspace),".5em"],align:["EqnArray",null,!0,!0,"rl",d.default.cols(0,2)],"align*":["EqnArray",null,!1,!0,"rl",d.default.cols(0,2)],multline:["Multline",null,!0],"multline*":["Multline",null,!1],split:["EqnArray",null,!1,!1,"rl",d.default.cols(0)],gather:["EqnArray",null,!0,!0,"c"],"gather*":["EqnArray",null,!1,!0,"c"],alignat:["AlignAt",null,!0,!0],"alignat*":["AlignAt",null,!1,!0],alignedat:["AlignAt",null,!1,!1],aligned:["AmsEqnArray",null,null,null,"rl",d.default.cols(0,2),".5em","D"],gathered:["AmsEqnArray",null,null,null,"c",null,".5em","D"],xalignat:["XalignAt",null,!0,!0],"xalignat*":["XalignAt",null,!1,!0],xxalignat:["XalignAt",null,!1,!1],flalign:["FlalignArray",null,!0,!1,!0,"rlc","auto auto fit"],"flalign*":["FlalignArray",null,!1,!1,!0,"rlc","auto auto 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l.CharacterMap("AMSsymbols-mathchar0mi",u.default.mathchar0mi,{digamma:"ϝ",varkappa:"ϰ",varGamma:["Γ",{mathvariant:c.TexConstant.Variant.ITALIC}],varDelta:["Δ",{mathvariant:c.TexConstant.Variant.ITALIC}],varTheta:["Θ",{mathvariant:c.TexConstant.Variant.ITALIC}],varLambda:["Λ",{mathvariant:c.TexConstant.Variant.ITALIC}],varXi:["Ξ",{mathvariant:c.TexConstant.Variant.ITALIC}],varPi:["Π",{mathvariant:c.TexConstant.Variant.ITALIC}],varSigma:["Σ",{mathvariant:c.TexConstant.Variant.ITALIC}],varUpsilon:["Υ",{mathvariant:c.TexConstant.Variant.ITALIC}],varPhi:["Φ",{mathvariant:c.TexConstant.Variant.ITALIC}],varPsi:["Ψ",{mathvariant:c.TexConstant.Variant.ITALIC}],varOmega:["Ω",{mathvariant:c.TexConstant.Variant.ITALIC}],beth:"ℶ",gimel:"ℷ",daleth:"ℸ",backprime:["‵",{variantForm:!0}],hslash:"ℏ",varnothing:["∅",{variantForm:!0}],blacktriangle:"▴",triangledown:["▽",{variantForm:!0}],blacktriangledown:"▾",square:"◻",Box:"◻",blacksquare:"◼",lozenge:"◊",Diamond:"◊",blacklozenge:"⧫",circledS:["Ⓢ",{mathvariant:c.TexConstant.Variant.NORMAL}],bigstar:"★",sphericalangle:"∢",measuredangle:"∡",nexists:"∄",complement:"∁",mho:"℧",eth:["ð",{mathvariant:c.TexConstant.Variant.NORMAL}],Finv:"Ⅎ",diagup:"╱",Game:"⅁",diagdown:"╲",Bbbk:["k",{mathvariant:c.TexConstant.Variant.DOUBLESTRUCK}],yen:"¥",circledR:"®",checkmark:"✓",maltese:"✠"}),new l.CharacterMap("AMSsymbols-mathchar0mo",u.default.mathchar0mo,{dotplus:"∔",ltimes:"⋉",smallsetminus:["∖",{variantForm:!0}],rtimes:"⋊",Cap:"⋒",doublecap:"⋒",leftthreetimes:"⋋",Cup:"⋓",doublecup:"⋓",rightthreetimes:"⋌",barwedge:"⊼",curlywedge:"⋏",veebar:"⊻",curlyvee:"⋎",doublebarwedge:"⩞",boxminus:"⊟",circleddash:"⊝",boxtimes:"⊠",circledast:"⊛",boxdot:"⊡",circledcirc:"⊚",boxplus:"⊞",centerdot:["⋅",{variantForm:!0}],divideontimes:"⋇",intercal:"⊺",leqq:"≦",geqq:"≧",leqslant:"⩽",geqslant:"⩾",eqslantless:"⪕",eqslantgtr:"⪖",lesssim:"≲",gtrsim:"≳",lessapprox:"⪅",gtrapprox:"⪆",approxeq:"≊",lessdot:"⋖",gtrdot:"⋗",lll:"⋘",llless:"⋘",ggg:"⋙",gggtr:"⋙",lessgtr:"≶",gtrless:"≷",lesseqgtr:"⋚",gtreqless:"⋛",lesseqqgtr:"⪋",gtreqqless:"⪌",doteqdot:"≑",Doteq:"≑",eqcirc:"≖",risingdotseq:"≓",circeq:"≗",fallingdotseq:"≒",triangleq:"≜",backsim:"∽",thicksim:["∼",{variantForm:!0}],backsimeq:"⋍",thickapprox:["≈",{variantForm:!0}],subseteqq:"⫅",supseteqq:"⫆",Subset:"⋐",Supset:"⋑",sqsubset:"⊏",sqsupset:"⊐",preccurlyeq:"≼",succcurlyeq:"≽",curlyeqprec:"⋞",curlyeqsucc:"⋟",precsim:"≾",succsim:"≿",precapprox:"⪷",succapprox:"⪸",vartriangleleft:"⊲",lhd:"⊲",vartriangleright:"⊳",rhd:"⊳",trianglelefteq:"⊴",unlhd:"⊴",trianglerighteq:"⊵",unrhd:"⊵",vDash:["⊨",{variantForm:!0}],Vdash:"⊩",Vvdash:"⊪",smallsmile:["⌣",{variantForm:!0}],shortmid:["∣",{variantForm:!0}],smallfrown:["⌢",{variantForm:!0}],shortparallel:["∥",{variantForm:!0}],bumpeq:"≏",between:"≬",Bumpeq:"≎",pitchfork:"⋔",varpropto:["∝",{variantForm:!0}],backepsilon:"∍",blacktriangleleft:"◂",blacktriangleright:"▸",therefore:"∴",because:"∵",eqsim:"≂",vartriangle:["△",{variantForm:!0}],Join:"⋈",nless:"≮",ngtr:"≯",nleq:"≰",ngeq:"≱",nleqslant:["⪇",{variantForm:!0}],ngeqslant:["⪈",{variantForm:!0}],nleqq:["≰",{variantForm:!0}],ngeqq:["≱",{variantForm:!0}],lneq:"⪇",gneq:"⪈",lneqq:"≨",gneqq:"≩",lvertneqq:["≨",{variantForm:!0}],gvertneqq:["≩",{variantForm:!0}],lnsim:"⋦",gnsim:"⋧",lnapprox:"⪉",gnapprox:"⪊",nprec:"⊀",nsucc:"⊁",npreceq:["⋠",{variantForm:!0}],nsucceq:["⋡",{variantForm:!0}],precneqq:"⪵",succneqq:"⪶",precnsim:"⋨",succnsim:"⋩",precnapprox:"⪹",succnapprox:"⪺",nsim:"≁",ncong:"≇",nshortmid:["∤",{variantForm:!0}],nshortparallel:["∦",{variantForm:!0}],nmid:"∤",nparallel:"∦",nvdash:"⊬",nvDash:"⊭",nVdash:"⊮",nVDash:"⊯",ntriangleleft:"⋪",ntriangleright:"⋫",ntrianglelefteq:"⋬",ntrianglerighteq:"⋭",nsubseteq:"⊈",nsupseteq:"⊉",nsubseteqq:["⊈",{variantForm:!0}],nsupseteqq:["⊉",{variantForm:!0}],subsetneq:"⊊",supsetneq:"⊋",varsubsetneq:["⊊",{variantForm:!0}],varsupsetneq:["⊋",{variantForm:!0}],subsetneqq:"⫋",supsetneqq:"⫌",varsubsetneqq:["⫋",{variantForm:!0}],varsupsetneqq:["⫌",{variantForm:!0}],leftleftarrows:"⇇",rightrightarrows:"⇉",leftrightarrows:"⇆",rightleftarrows:"⇄",Lleftarrow:"⇚",Rrightarrow:"⇛",twoheadleftarrow:"↞",twoheadrightarrow:"↠",leftarrowtail:"↢",rightarrowtail:"↣",looparrowleft:"↫",looparrowright:"↬",leftrightharpoons:"⇋",rightleftharpoons:["⇌",{variantForm:!0}],curvearrowleft:"↶",curvearrowright:"↷",circlearrowleft:"↺",circlearrowright:"↻",Lsh:"↰",Rsh:"↱",upuparrows:"⇈",downdownarrows:"⇊",upharpoonleft:"↿",upharpoonright:"↾",downharpoonleft:"⇃",restriction:"↾",multimap:"⊸",downharpoonright:"⇂",leftrightsquigarrow:"↭",rightsquigarrow:"⇝",leadsto:"⇝",dashrightarrow:"⇢",dashleftarrow:"⇠",nleftarrow:"↚",nrightarrow:"↛",nLeftarrow:"⇍",nRightarrow:"⇏",nleftrightarrow:"↮",nLeftrightarrow:"⇎"}),new l.DelimiterMap("AMSsymbols-delimiter",u.default.delimiter,{"\\ulcorner":"⌜","\\urcorner":"⌝","\\llcorner":"⌞","\\lrcorner":"⌟"}),new l.CommandMap("AMSsymbols-macros",{implies:["Macro","\\;\\Longrightarrow\\;"],impliedby:["Macro","\\;\\Longleftarrow\\;"]},s.AmsMethods)},8840:function(t,e,n){"use strict";var r=this&&this.__assign||function(){return r=Object.assign||function(t){for(var e,n=1,r=arguments.length;n<r;n++)for(var i in e=arguments[n])Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t},r.apply(this,arguments)},i=this&&this.__read||function(t,e){var n="function"==typeof Symbol&&t[Symbol.iterator];if(!n)return t;var r,i,o=n.call(t),a=[];try{for(;(void 0===e||e-- >0)&&!(r=o.next()).done;)a.push(r.value)}catch(t){i={error:t}}finally{try{r&&!r.done&&(n=o.return)&&n.call(o)}finally{if(i)throw i.error}}return a},o=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.NEW_OPS=e.AmsMethods=void 0;var a=o(n(6980)),s=o(n(2960)),l=o(n(2691)),c=n(469),u=o(n(5845)),d=o(n(8770)),h=n(7151),p=o(n(8364)),f=n(747);function Q(t){if(!t||t.isInferred&&0===t.childNodes.length)return[null,null];if(t.isKind("msubsup")&&T(t))return[t,null];var e=l.default.getChildAt(t,0);return t.isInferred&&e&&T(e)?(t.childNodes.splice(0,1),[e,t]):[null,t]}function T(t){var e=t.childNodes[0];return e&&e.isKind("mi")&&""===e.getText()}e.AmsMethods={},e.AmsMethods.AmsEqnArray=function(t,e,n,r,i,o,s){var l=t.GetBrackets("\\begin{"+e.getName()+"}"),c=p.default.EqnArray(t,e,n,r,i,o,s);return a.default.setArrayAlign(c,l)},e.AmsMethods.AlignAt=function(t,n,r,i){var o,s,l=n.getName(),c="",u=[];if(i||(s=t.GetBrackets("\\begin{"+l+"}")),(o=t.GetArgument("\\begin{"+l+"}")).match(/[^0-9]/))throw new d.default("PositiveIntegerArg","Argument to %1 must me a positive integer","\\begin{"+l+"}");for(var h=parseInt(o,10);h>0;)c+="rl",u.push("0em 0em"),h--;var p=u.join(" ");if(i)return e.AmsMethods.EqnArray(t,n,r,i,c,p);var f=e.AmsMethods.EqnArray(t,n,r,i,c,p);return a.default.setArrayAlign(f,s)},e.AmsMethods.Multline=function(t,e,n){t.Push(e),a.default.checkEqnEnv(t);var r=t.itemFactory.create("multline",n,t.stack);return r.arraydef={displaystyle:!0,rowspacing:".5em",columnspacing:"100%",width:t.options.ams.multlineWidth,side:t.options.tagSide,minlabelspacing:t.options.tagIndent,framespacing:t.options.ams.multlineIndent+" 0",frame:"","data-width-includes-label":!0},r},e.AmsMethods.XalignAt=function(t,n,r,i){var o=t.GetArgument("\\begin{"+n.getName()+"}");if(o.match(/[^0-9]/))throw new d.default("PositiveIntegerArg","Argument to %1 must me a positive integer","\\begin{"+n.getName()+"}");var a=i?"crl":"rlc",s=i?"fit auto auto":"auto auto fit",l=e.AmsMethods.FlalignArray(t,n,r,i,!1,a,s,!0);return l.setProperty("xalignat",2*parseInt(o)),l},e.AmsMethods.FlalignArray=function(t,e,n,r,i,o,s,l){void 0===l&&(l=!1),t.Push(e),a.default.checkEqnEnv(t),o=o.split("").join(" ").replace(/r/g,"right").replace(/l/g,"left").replace(/c/g,"center");var c=t.itemFactory.create("flalign",e.getName(),n,r,i,t.stack);return c.arraydef={width:"100%",displaystyle:!0,columnalign:o,columnspacing:"0em",columnwidth:s,rowspacing:"3pt",side:t.options.tagSide,minlabelspacing:l?"0":t.options.tagIndent,"data-width-includes-label":!0},c.setProperty("zeroWidthLabel",l),c},e.NEW_OPS="ams-declare-ops",e.AmsMethods.HandleDeclareOp=function(t,n){var r=t.GetStar()?"*":"",i=a.default.trimSpaces(t.GetArgument(n));"\\"===i.charAt(0)&&(i=i.substr(1));var o=t.GetArgument(n);t.configuration.handlers.retrieve(e.NEW_OPS).add(i,new h.Macro(i,e.AmsMethods.Macro,["\\operatorname".concat(r,"{").concat(o,"}")]))},e.AmsMethods.HandleOperatorName=function(t,e){var n=t.GetStar(),i=a.default.trimSpaces(t.GetArgument(e)),o=new u.default(i,r(r({},t.stack.env),{font:c.TexConstant.Variant.NORMAL,multiLetterIdentifiers:/^[-*a-z]+/i,operatorLetters:!0}),t.configuration).mml();if(o.isKind("mi")||(o=t.create("node","TeXAtom",[o])),l.default.setProperties(o,{movesupsub:n,movablelimits:!0,texClass:f.TEXCLASS.OP}),!n){var s=t.GetNext(),d=t.i;"\\"===s&&++t.i&&"limits"!==t.GetCS()&&(t.i=d)}t.Push(o)},e.AmsMethods.SideSet=function(t,e){var 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i=t.call(this,e)||this;return i.setProperty("delim",n),r&&i.setProperty("color",r),i}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"middle"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isClose",{get:function(){return!0},enumerable:!1,configurable:!0}),e}(f.BaseItem);e.Middle=x;var w=function(t){function e(e,n,r){var i=t.call(this,e)||this;return i.setProperty("delim",n),r&&i.setProperty("color",r),i}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"right"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isClose",{get:function(){return!0},enumerable:!1,configurable:!0}),e}(f.BaseItem);e.RightItem=w;var L=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"begin"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isOpen",{get:function(){return!0},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){if(e.isKind("end")){if(e.getName()!==this.getName())throw new d.default("EnvBadEnd","\\begin{%1} ended with \\end{%2}",this.getName(),e.getName());return this.getProperty("end")?f.BaseItem.fail:[[this.factory.create("mml",this.toMml())],!0]}if(e.isKind("stop"))throw new d.default("EnvMissingEnd","Missing \\end{%1}",this.getName());return t.prototype.checkItem.call(this,e)},e}(f.BaseItem);e.BeginItem=L;var A=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"end"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isClose",{get:function(){return!0},enumerable:!1,configurable:!0}),e}(f.BaseItem);e.EndItem=A;var H=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"style"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){if(!e.isClose)return t.prototype.checkItem.call(this,e);var n=this.create("node","mstyle",this.nodes,this.getProperty("styles"));return[[this.factory.create("mml",n),e],!0]},e}(f.BaseItem);e.StyleItem=H;var k=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"position"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){if(e.isClose)throw new d.default("MissingBoxFor","Missing box for %1",this.getName());if(e.isFinal){var n=e.toMml();switch(this.getProperty("move")){case"vertical":return n=this.create("node","mpadded",[n],{height:this.getProperty("dh"),depth:this.getProperty("dd"),voffset:this.getProperty("dh")}),[[this.factory.create("mml",n)],!0];case"horizontal":return[[this.factory.create("mml",this.getProperty("left")),e,this.factory.create("mml",this.getProperty("right"))],!0]}}return t.prototype.checkItem.call(this,e)},e}(f.BaseItem);e.PositionItem=k;var M=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"cell"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isClose",{get:function(){return!0},enumerable:!1,configurable:!0}),e}(f.BaseItem);e.CellItem=M;var C=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"isFinal",{get:function(){return!0},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"kind",{get:function(){return"mml"},enumerable:!1,configurable:!0}),e}(f.BaseItem);e.MmlItem=C;var S=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"fn"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){var n=this.First;if(n){if(e.isOpen)return f.BaseItem.success;if(!e.isKind("fn")){var r=e.First;if(!e.isKind("mml")||!r)return[[n,e],!0];if(p.default.isType(r,"mstyle")&&r.childNodes.length&&p.default.isType(r.childNodes[0].childNodes[0],"mspace")||p.default.isType(r,"mspace"))return[[n,e],!0];p.default.isEmbellished(r)&&(r=p.default.getCoreMO(r));var i=p.default.getForm(r);if(null!=i&&[0,0,1,1,0,1,1,0,0,0][i[2]])return[[n,e],!0]}return[[n,this.create("token","mo",{texClass:u.TEXCLASS.NONE},c.entities.ApplyFunction),e],!0]}return t.prototype.checkItem.apply(this,arguments)},e}(f.BaseItem);e.FnItem=S;var E=function(t){function e(){var e=null!==t&&t.apply(this,arguments)||this;return e.remap=l.MapHandler.getMap("not_remap"),e}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"not"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(t){var e,n,r;if(t.isKind("open")||t.isKind("left"))return f.BaseItem.success;if(t.isKind("mml")&&(p.default.isType(t.First,"mo")||p.default.isType(t.First,"mi")||p.default.isType(t.First,"mtext"))&&(e=t.First,1===(n=p.default.getText(e)).length&&!p.default.getProperty(e,"movesupsub")&&1===p.default.getChildren(e).length))return this.remap.contains(n)?(r=this.create("text",this.remap.lookup(n).char),p.default.setChild(e,0,r)):(r=this.create("text","̸"),p.default.appendChildren(e,[r])),[[t],!0];r=this.create("text","⧸");var i=this.create("node","mtext",[],{},r),o=this.create("node","mpadded",[i],{width:0});return[[e=this.create("node","TeXAtom",[o],{texClass:u.TEXCLASS.REL}),t],!0]},e}(f.BaseItem);e.NotItem=E;var V=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"nonscript"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(t){if(t.isKind("mml")&&1===t.Size()){var e=t.First;if(e.isKind("mstyle")&&e.notParent&&(e=p.default.getChildren(p.default.getChildren(e)[0])[0]),e.isKind("mspace")){if(e!==t.First){var n=this.create("node","mrow",[t.Pop()]);t.Push(n)}this.factory.configuration.addNode("nonscript",t.First)}}return[[t],!0]},e}(f.BaseItem);e.NonscriptItem=V;var O=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"dots"},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(t){if(t.isKind("open")||t.isKind("left"))return f.BaseItem.success;var e=this.getProperty("ldots"),n=t.First;if(t.isKind("mml")&&p.default.isEmbellished(n)){var r=p.default.getTexClass(p.default.getCoreMO(n));r!==u.TEXCLASS.BIN&&r!==u.TEXCLASS.REL||(e=this.getProperty("cdots"))}return[[e,t],!0]},e}(f.BaseItem);e.DotsItem=O;var P=function(t){function e(){var e=null!==t&&t.apply(this,arguments)||this;return e.table=[],e.row=[],e.frame=[],e.hfill=[],e.arraydef={},e.dashed=!1,e}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"array"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isOpen",{get:function(){return!0},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"copyEnv",{get:function(){return!1},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){if(e.isClose&&!e.isKind("over")){if(e.getProperty("isEntry"))return this.EndEntry(),this.clearEnv(),f.BaseItem.fail;if(e.getProperty("isCR"))return this.EndEntry(),this.EndRow(),this.clearEnv(),f.BaseItem.fail;this.EndTable(),this.clearEnv();var n=this.factory.create("mml",this.createMml());if(this.getProperty("requireClose")){if(e.isKind("close"))return[[n],!0];throw new d.default("MissingCloseBrace","Missing close brace")}return[[n,e],!0]}return t.prototype.checkItem.call(this,e)},e.prototype.createMml=function(){var t=this.arraydef.scriptlevel;delete this.arraydef.scriptlevel;var e=this.create("node","mtable",this.table,this.arraydef);return t&&e.setProperty("scriptlevel",t),4===this.frame.length?p.default.setAttribute(e,"frame",this.dashed?"dashed":"solid"):this.frame.length&&(this.arraydef.rowlines&&(this.arraydef.rowlines=this.arraydef.rowlines.replace(/none( none)+$/,"none")),p.default.setAttribute(e,"frame",""),e=this.create("node","menclose",[e],{notation:this.frame.join(" ")}),"none"===(this.arraydef.columnlines||"none")&&"none"===(this.arraydef.rowlines||"none")||p.default.setAttribute(e,"data-padding",0)),(this.getProperty("open")||this.getProperty("close"))&&(e=h.default.fenced(this.factory.configuration,this.getProperty("open"),e,this.getProperty("close"))),e},e.prototype.EndEntry=function(){var t=this.create("node","mtd",this.nodes);this.hfill.length&&(0===this.hfill[0]&&p.default.setAttribute(t,"columnalign","right"),this.hfill[this.hfill.length-1]===this.Size()&&p.default.setAttribute(t,"columnalign",p.default.getAttribute(t,"columnalign")?"center":"left")),this.row.push(t),this.Clear(),this.hfill=[]},e.prototype.EndRow=function(){var t;this.getProperty("isNumbered")&&3===this.row.length?(this.row.unshift(this.row.pop()),t=this.create("node","mlabeledtr",this.row)):t=this.create("node","mtr",this.row),this.table.push(t),this.row=[]},e.prototype.EndTable=function(){(this.Size()||this.row.length)&&(this.EndEntry(),this.EndRow()),this.checkLines()},e.prototype.checkLines=function(){if(this.arraydef.rowlines){var t=this.arraydef.rowlines.split(/ /);t.length===this.table.length?(this.frame.push("bottom"),t.pop(),this.arraydef.rowlines=t.join(" ")):t.length<this.table.length-1&&(this.arraydef.rowlines+=" none")}if(this.getProperty("rowspacing")){for(var e=this.arraydef.rowspacing.split(/ /);e.length<this.table.length;)e.push(this.getProperty("rowspacing")+"em");this.arraydef.rowspacing=e.join(" ")}},e.prototype.addRowSpacing=function(t){if(this.arraydef.rowspacing){var e=this.arraydef.rowspacing.split(/ /);if(!this.getProperty("rowspacing")){var n=h.default.dimen2em(e[0]);this.setProperty("rowspacing",n)}for(var r=this.getProperty("rowspacing");e.length<this.table.length;)e.push(h.default.Em(r));e[this.table.length-1]=h.default.Em(Math.max(0,r+h.default.dimen2em(t))),this.arraydef.rowspacing=e.join(" ")}},e}(f.BaseItem);e.ArrayItem=P;var D=function(t){function e(e){for(var n=[],r=1;r<arguments.length;r++)n[r-1]=arguments[r];var i=t.call(this,e)||this;return i.maxrow=0,i.factory.configuration.tags.start(n[0],n[2],n[1]),i}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"eqnarray"},enumerable:!1,configurable:!0}),e.prototype.EndEntry=function(){this.row.length&&h.default.fixInitialMO(this.factory.configuration,this.nodes);var t=this.create("node","mtd",this.nodes);this.row.push(t),this.Clear()},e.prototype.EndRow=function(){this.row.length>this.maxrow&&(this.maxrow=this.row.length);var t="mtr",e=this.factory.configuration.tags.getTag();e&&(this.row=[e].concat(this.row),t="mlabeledtr"),this.factory.configuration.tags.clearTag();var n=this.create("node",t,this.row);this.table.push(n),this.row=[]},e.prototype.EndTable=function(){t.prototype.EndTable.call(this),this.factory.configuration.tags.end(),this.extendArray("columnalign",this.maxrow),this.extendArray("columnwidth",this.maxrow),this.extendArray("columnspacing",this.maxrow-1)},e.prototype.extendArray=function(t,e){if(this.arraydef[t]){var n=this.arraydef[t].split(/ /),r=a([],o(n),!1);if(r.length>1){for(;r.length<e;)r.push.apply(r,a([],o(n),!1));this.arraydef[t]=r.slice(0,e).join(" ")}}},e}(P);e.EqnArrayItem=D;var N=function(t){function e(e){for(var n=[],r=1;r<arguments.length;r++)n[r-1]=arguments[r];var i=t.call(this,e)||this;return i.factory.configuration.tags.start("equation",!0,n[0]),i}return i(e,t),Object.defineProperty(e.prototype,"kind",{get:function(){return"equation"},enumerable:!1,configurable:!0}),Object.defineProperty(e.prototype,"isOpen",{get:function(){return!0},enumerable:!1,configurable:!0}),e.prototype.checkItem=function(e){if(e.isKind("end")){var n=this.toMml(),r=this.factory.configuration.tags.getTag();return this.factory.configuration.tags.end(),[[r?this.factory.configuration.tags.enTag(n,r):n,e],!0]}if(e.isKind("stop"))throw new d.default("EnvMissingEnd","Missing \\end{%1}",this.getName());return t.prototype.checkItem.call(this,e)},e}(f.BaseItem);e.EquationItem=N},9447:function(t,e,n){"use strict";var r=this&&this.__createBinding||(Object.create?function(t,e,n,r){void 0===r&&(r=n);var i=Object.getOwnPropertyDescriptor(e,n);i&&!("get"in i?!e.__esModule:i.writable||i.configurable)||(i={enumerable:!0,get:function(){return e[n]}}),Object.defineProperty(t,r,i)}:function(t,e,n,r){void 0===r&&(r=n),t[r]=e[n]}),i=this&&this.__setModuleDefault||(Object.create?function(t,e){Object.defineProperty(t,"default",{enumerable:!0,value:e})}:function(t,e){t.default=e}),o=this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)"default"!==n&&Object.prototype.hasOwnProperty.call(t,n)&&r(e,t,n);return i(e,t),e},a=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});var s=o(n(209)),l=n(469),c=a(n(8364)),u=a(n(2960)),d=a(n(6980)),h=n(747),p=n(6810);new s.RegExpMap("letter",u.default.variable,/[a-z]/i),new s.RegExpMap("digit",u.default.digit,/[0-9.,]/),new s.RegExpMap("command",u.default.controlSequence,/^\\/),new s.MacroMap("special",{"{":"Open","}":"Close","~":"Tilde","^":"Superscript",_:"Subscript"," ":"Space","\t":"Space","\r":"Space","\n":"Space","'":"Prime","%":"Comment","&":"Entry","#":"Hash"," ":"Space","’":"Prime"},c.default),new s.CharacterMap("mathchar0mi",u.default.mathchar0mi,{alpha:"α",beta:"β",gamma:"γ",delta:"δ",epsilon:"ϵ",zeta:"ζ",eta:"η",theta:"θ",iota:"ι",kappa:"κ",lambda:"λ",mu:"μ",nu:"ν",xi:"ξ",omicron:"ο",pi:"π",rho:"ρ",sigma:"σ",tau:"τ",upsilon:"υ",phi:"ϕ",chi:"χ",psi:"ψ",omega:"ω",varepsilon:"ε",vartheta:"ϑ",varpi:"ϖ",varrho:"ϱ",varsigma:"ς",varphi:"φ",S:["§",{mathvariant:l.TexConstant.Variant.NORMAL}],aleph:["ℵ",{mathvariant:l.TexConstant.Variant.NORMAL}],hbar:["ℏ",{variantForm:!0}],imath:"ı",jmath:"ȷ",ell:"ℓ",wp:["℘",{mathvariant:l.TexConstant.Variant.NORMAL}],Re:["ℜ",{mathvariant:l.TexConstant.Variant.NORMAL}],Im:["ℑ",{mathvariant:l.TexConstant.Variant.NORMAL}],partial:["∂",{mathvariant:l.TexConstant.Variant.ITALIC}],infty:["∞",{mathvariant:l.TexConstant.Variant.NORMAL}],prime:["′",{variantForm:!0}],emptyset:["∅",{mathvariant:l.TexConstant.Variant.NORMAL}],nabla:["∇",{mathvariant:l.TexConstant.Variant.NORMAL}],top:["⊤",{mathvariant:l.TexConstant.Variant.NORMAL}],bot:["⊥",{mathvariant:l.TexConstant.Variant.NORMAL}],angle:["∠",{mathvariant:l.TexConstant.Variant.NORMAL}],triangle:["△",{mathvariant:l.TexConstant.Variant.NORMAL}],backslash:["∖",{mathvariant:l.TexConstant.Variant.NORMAL}],forall:["∀",{mathvariant:l.TexConstant.Variant.NORMAL}],exists:["∃",{mathvariant:l.TexConstant.Variant.NORMAL}],neg:["¬",{mathvariant:l.TexConstant.Variant.NORMAL}],lnot:["¬",{mathvariant:l.TexConstant.Variant.NORMAL}],flat:["♭",{mathvariant:l.TexConstant.Variant.NORMAL}],natural:["♮",{mathvariant:l.TexConstant.Variant.NORMAL}],sharp:["♯",{mathvariant:l.TexConstant.Variant.NORMAL}],clubsuit:["♣",{mathvariant:l.TexConstant.Variant.NORMAL}],diamondsuit:["♢",{mathvariant:l.TexConstant.Variant.NORMAL}],heartsuit:["♡",{mathvariant:l.TexConstant.Variant.NORMAL}],spadesuit:["♠",{mathvariant:l.TexConstant.Variant.NORMAL}]}),new 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i=t.itemFactory.create("over").setProperty("name",t.currentCS);n||r?(i.setProperty("open",n),i.setProperty("close",r)):e.match(/withdelims$/)&&(i.setProperty("open",t.GetDelimiter(e)),i.setProperty("close",t.GetDelimiter(e))),e.match(/^\\above/)?i.setProperty("thickness",t.GetDimen(e)):(e.match(/^\\atop/)||n||r)&&i.setProperty("thickness",0),t.Push(i)},b.Frac=function(t,e){var n=t.ParseArg(e),r=t.ParseArg(e),i=t.create("node","mfrac",[n,r]);t.Push(i)},b.Sqrt=function(t,e){var n=t.GetBrackets(e),r=t.GetArgument(e);"\\frac"===r&&(r+="{"+t.GetArgument(r)+"}{"+t.GetArgument(r)+"}");var i=new h.default(r,t.stack.env,t.configuration).mml();i=n?t.create("node","mroot",[i,x(t,n)]):t.create("node","msqrt",[i]),t.Push(i)},b.Root=function(t,e){var n=t.GetUpTo(e,"\\of"),r=t.ParseArg(e),i=t.create("node","mroot",[r,x(t,n)]);t.Push(i)},b.MoveRoot=function(t,e,n){if(!t.stack.env.inRoot)throw new d.default("MisplacedMoveRoot","%1 can appear only within a root",t.currentCS);if(t.stack.global[n])throw new d.default("MultipleMoveRoot","Multiple use of %1",t.currentCS);var r=t.GetArgument(e);if(!r.match(/-?[0-9]+/))throw new d.default("IntegerArg","The argument to %1 must be an integer",t.currentCS);"-"!==(r=parseInt(r,10)/15+"em").substr(0,1)&&(r="+"+r),t.stack.global[n]=r},b.Accent=function(t,e,n,i){var o=t.ParseArg(e),a=r(r({},f.default.getFontDef(t)),{accent:!0,mathaccent:!0}),s=u.default.createEntity(n),l=t.create("token","mo",a,s);u.default.setAttribute(l,"stretchy",!!i);var c=u.default.isEmbellished(o)?u.default.getCoreMO(o):o;(u.default.isType(c,"mo")||u.default.getProperty(c,"movablelimits"))&&u.default.setProperties(c,{movablelimits:!1});var d=t.create("node","munderover");u.default.setChild(d,0,o),u.default.setChild(d,1,null),u.default.setChild(d,2,l);var h=t.create("node","TeXAtom",[d]);t.Push(h)},b.UnderOver=function(t,e,n,r){var i=u.default.createEntity(n),o=t.create("token","mo",{stretchy:!0,accent:!0},i),a="o"===e.charAt(1)?"over":"under",s=t.ParseArg(e);t.Push(f.default.underOver(t,s,o,a,r))},b.Overset=function(t,e){var n=t.ParseArg(e),r=t.ParseArg(e);f.default.checkMovableLimits(r),n.isKind("mo")&&u.default.setAttribute(n,"accent",!1);var i=t.create("node","mover",[r,n]);t.Push(i)},b.Underset=function(t,e){var n=t.ParseArg(e),r=t.ParseArg(e);f.default.checkMovableLimits(r),n.isKind("mo")&&u.default.setAttribute(n,"accent",!1);var i=t.create("node","munder",[r,n],{accentunder:!1});t.Push(i)},b.Overunderset=function(t,e){var n=t.ParseArg(e),r=t.ParseArg(e),i=t.ParseArg(e);f.default.checkMovableLimits(i),n.isKind("mo")&&u.default.setAttribute(n,"accent",!1),r.isKind("mo")&&u.default.setAttribute(r,"accent",!1);var o=t.create("node","munderover",[i,r,n],{accent:!1,accentunder:!1});t.Push(o)},b.TeXAtom=function(t,e,n){var r,i,o,a={texClass:n};if(n===Q.TEXCLASS.OP){a.movesupsub=a.movablelimits=!0;var 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n=f.default.trimSpaces(t.GetBrackets(e,"")),r=t.create("node","mpadded",[t.ParseArg(e)]);switch(n){case"b":u.default.setAttribute(r,"depth",0);break;case"t":u.default.setAttribute(r,"height",0);break;default:u.default.setAttribute(r,"height",0),u.default.setAttribute(r,"depth",0)}var i=t.create("node","TeXAtom",[r]);t.Push(i)},b.Lap=function(t,e){var n=t.create("node","mpadded",[t.ParseArg(e)],{width:0});"\\llap"===e&&u.default.setAttribute(n,"lspace","-1width");var r=t.create("node","TeXAtom",[n]);t.Push(r)},b.RaiseLower=function(t,e){var n=t.GetDimen(e),r=t.itemFactory.create("position").setProperties({name:t.currentCS,move:"vertical"});"-"===n.charAt(0)&&(n=n.slice(1),e="raise"===e.substr(1)?"\\lower":"\\raise"),"\\lower"===e?(r.setProperty("dh","-"+n),r.setProperty("dd","+"+n)):(r.setProperty("dh","+"+n),r.setProperty("dd","-"+n)),t.Push(r)},b.MoveLeftRight=function(t,e){var n=t.GetDimen(e),r="-"===n.charAt(0)?n.slice(1):"-"+n;if("\\moveleft"===e){var 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i=String(r*=v).replace(/(\.\d\d\d).+/,"$1")+"em",o=t.GetDelimiter(e,!0),a=t.create("token","mo",{minsize:i,maxsize:i,fence:!0,stretchy:!0,symmetric:!0},o),s=t.create("node","TeXAtom",[a],{texClass:n});t.Push(s)},b.BuildRel=function(t,e){var n=t.ParseUpTo(e,"\\over"),r=t.ParseArg(e),i=t.create("node","munderover");u.default.setChild(i,0,r),u.default.setChild(i,1,null),u.default.setChild(i,2,n);var o=t.create("node","TeXAtom",[i],{texClass:Q.TEXCLASS.REL});t.Push(o)},b.HBox=function(t,e,n,r){t.PushAll(f.default.internalMath(t,t.GetArgument(e),n,r))},b.FBox=function(t,e){var n=f.default.internalMath(t,t.GetArgument(e)),r=t.create("node","menclose",n,{notation:"box"});t.Push(r)},b.FrameBox=function(t,e){var n=t.GetBrackets(e),r=t.GetBrackets(e)||"c",i=f.default.internalMath(t,t.GetArgument(e));n&&(i=[t.create("node","mpadded",i,{width:n,"data-align":(0,_.lookup)(r,{l:"left",r:"right"},"center")})]);var 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o>3&&a&&Object.defineProperty(e,n,a),a};function st(t){return e=>{e.prototype.event_name=t}}class lt{[H.lK](t){const{event_name:e,event_values:n}=this;return{type:"event",name:e,values:t.encode(n)}}[A.aI](t,e){return this.event_name==t.event_name&&e.eq(this.event_values,t.event_values)}}lt.__name__="BokehEvent";class ct extends lt{constructor(){super(...arguments),this.origin=null}get event_values(){return{model:this.origin}}}ct.__name__="ModelEvent";let ut=class extends lt{get event_values(){return{}}};ut.__name__="DocumentReady",ut=at([st("document_ready")],ut);let dt=class extends ct{};dt.__name__="ButtonClick",dt=at([st("button_click")],dt);let ht=class extends ct{constructor(t){super(),this.item=t}get event_values(){const{item:t}=this;return{...super.event_values,item:t}}};ht.__name__="MenuItemClick",ht=at([st("menu_item_click")],ht);class pt extends ct{}pt.__name__="UIEvent";let ft=class extends pt{};ft.__name__="LODStart",ft=at([st("lodstart")],ft);let Qt=class extends pt{};Qt.__name__="LODEnd",Qt=at([st("lodend")],Qt);let Tt=class extends pt{constructor(t,e,n,r){super(),this.x0=t,this.x1=e,this.y0=n,this.y1=r}get event_values(){const{x0:t,x1:e,y0:n,y1:r}=this;return{...super.event_values,x0:t,x1:e,y0:n,y1:r}}};Tt.__name__="RangesUpdate",Tt=at([st("rangesupdate")],Tt);let mt=class extends pt{constructor(t,e){super(),this.geometry=t,this.final=e}get event_values(){const{geometry:t,final:e}=this;return{...super.event_values,geometry:t,final:e}}};mt.__name__="SelectionGeometry",mt=at([st("selectiongeometry")],mt);let gt=class extends pt{};gt.__name__="Reset",gt=at([st("reset")],gt);class _t extends pt{constructor(t,e,n,r){super(),this.sx=t,this.sy=e,this.x=n,this.y=r}get event_values(){const{sx:t,sy:e,x:n,y:r}=this;return{...super.event_values,sx:t,sy:e,x:n,y:r}}}_t.__name__="PointEvent";let bt=class extends _t{constructor(t,e,n,r,i,o){super(t,e,n,r),this.delta_x=i,this.delta_y=o}get event_values(){const{delta_x:t,delta_y:e}=this;return{...super.event_values,delta_x:t,delta_y:e}}};bt.__name__="Pan",bt=at([st("pan")],bt);let vt=class extends _t{constructor(t,e,n,r,i){super(t,e,n,r),this.scale=i}get event_values(){const{scale:t}=this;return{...super.event_values,scale:t}}};vt.__name__="Pinch",vt=at([st("pinch")],vt);let yt=class extends _t{constructor(t,e,n,r,i){super(t,e,n,r),this.rotation=i}get event_values(){const{rotation:t}=this;return{...super.event_values,rotation:t}}};yt.__name__="Rotate",yt=at([st("rotate")],yt);let xt=class extends _t{constructor(t,e,n,r,i){super(t,e,n,r),this.delta=i}get event_values(){const{delta:t}=this;return{...super.event_values,delta:t}}};xt.__name__="MouseWheel",xt=at([st("wheel")],xt);let wt=class extends _t{};wt.__name__="MouseMove",wt=at([st("mousemove")],wt);let Lt=class extends _t{};Lt.__name__="MouseEnter",Lt=at([st("mouseenter")],Lt);let At=class extends _t{};At.__name__="MouseLeave",At=at([st("mouseleave")],At);let Ht=class extends _t{};Ht.__name__="Tap",Ht=at([st("tap")],Ht);let kt=class extends _t{};kt.__name__="DoubleTap",kt=at([st("doubletap")],kt);let Mt=class extends _t{};Mt.__name__="Press",Mt=at([st("press")],Mt);let Ct=class extends _t{};Ct.__name__="PressUp",Ct=at([st("pressup")],Ct);let St=class extends _t{};St.__name__="PanStart",St=at([st("panstart")],St);let Et=class extends _t{};Et.__name__="PanEnd",Et=at([st("panend")],Et);let Vt=class extends _t{};Vt.__name__="PinchStart",Vt=at([st("pinchstart")],Vt);let Ot=class extends _t{};Ot.__name__="PinchEnd",Ot=at([st("pinchend")],Ot);let Pt=class extends _t{};Pt.__name__="RotateStart",Pt=at([st("rotatestart")],Pt);let Dt=class extends _t{};Dt.__name__="RotateEnd",Dt=at([st("rotateend")],Dt);var Nt=n(2652),Rt=n(4042),It=n(7708),jt=n(7337);class zt{constructor({start:t,stop:e,step:n}={}){this.start=t??null,this.stop=e??null,this.step=n??null}[H.lK](t){return{type:"slice",start:t.encode(this.start),stop:t.encode(this.stop),step:t.encode(this.step)}}}zt.__name__="Slice";const Bt=new Map;class Ft extends Error{}Ft.__name__="DeserializationError";class $t{constructor(t,e=new Map,n){this.resolver=t,this.references=e,this.finalize=n,this._decoding=!1,this._buffers=new Map,this._finalizable=new Set}static register(t,e){if(Bt.has(t))throw new Error(`'${t}' already registered for decoding`);Bt.set(t,e)}decode(t,e){if(null!=e)for(const[t,n]of e)this._buffers.set(t,n);if(this._decoding)return this._decode(t);let n;this._decoding=!0;const r=(()=>{try{return this._decode(t)}finally{n=new Set(this._finalizable),this._decoding=!1,this._buffers.clear(),this._finalizable.clear()}})();for(const t of n)this.finalize?.(t),t.finalize();for(const t of n)t.connect_signals();return r}_decode(t){if((0,f.cy)(t))return this._decode_plain_array(t);if(!(0,f.Qd)(t))return t;if(!(0,f.Kg)(t.type))return(0,f.Kg)(t.id)?this._decode_ref(t):this._decode_plain_object(t);{const e=Bt.get(t.type);if(null!=e)return e(t,this);switch(t.type){case"ref":return this._decode_ref(t);case"symbol":return this._decode_symbol(t);case"number":return this._decode_number(t);case"array":return this._decode_array(t);case"set":return this._decode_set(t);case"map":return this._decode_map(t);case"bytes":return this._decode_bytes(t);case"slice":return this._decode_slice(t);case"value":return this._decode_value(t);case"field":return this._decode_field(t);case"expr":return this._decode_expr(t);case"typed_array":return this._decode_typed_array(t);case"ndarray":return this._decode_ndarray(t);case"object":return(0,f.Kg)(t.id)?this._decode_object_ref(t):this._decode_object(t);default:this.error(`unable to decode an object of type '${t.type}'`)}}}_decode_symbol(t){this.error(`can't resolve named symbol '${t.name}'`)}_decode_number(t){if("value"in t){const{value:e}=t;if((0,f.Kg)(e))switch(e){case"nan":return NaN;case"+inf":return 1/0;case"-inf":return-1/0}else if((0,f.Et)(e))return e}this.error(`invalid number representation '${t}'`)}_decode_plain_array(t){return(0,Rt.Tj)(t,(t=>this._decode(t)))}_decode_plain_object(t){const e={};for(const[n,r]of(0,Q.jO)(t))e[n]=this._decode(r);return e}_decode_array(t){const e=[];for(const n of t.entries??[])e.push(this._decode(n));return e}_decode_set(t){const e=new Set;for(const n of t.entries??[])e.add(this._decode(n));return e}_decode_map(t){const e=(0,Rt.Tj)(t.entries??[],(([t,e])=>[this._decode(t),this._decode(e)]));if((0,Rt.Si)(e,(([t])=>(0,f.Kg)(t)))){const t={};for(const[n,r]of e)t[n]=r;return t}return new Map(e)}_decode_bytes(t){const{data:e}=t;if(!function(t){return(0,f.Qd)(t)&&"id"in t&&!("type"in t)}(e))return(0,f.Kg)(e)?(0,jt.Bw)(e):e.buffer;{const t=this._buffers.get(e.id);if(null!=t)return t;this.error(`buffer for id=${e.id} not found`)}}_decode_slice(t){const e=this._decode(t.start),n=this._decode(t.stop),r=this._decode(t.step);return new zt({start:e,stop:n,step:r})}_decode_value(t){return{value:this._decode(t.value),transform:null!=t.transform?this._decode(t.transform):void 0,units:null!=t.units?this._decode(t.units):void 0}}_decode_field(t){return{field:this._decode(t.field),transform:null!=t.transform?this._decode(t.transform):void 0,units:null!=t.units?this._decode(t.units):void 0}}_decode_expr(t){return{expr:this._decode(t.expr),transform:null!=t.transform?this._decode(t.transform):void 0,units:null!=t.units?this._decode(t.units):void 0}}_decode_typed_array(t){const{array:e,order:n,dtype:r}=t,i=this._decode(e);switch(n!=It.Yj&&(0,jt.wg)(i,r),r){case"uint8":return new Uint8Array(i);case"int8":return new Int8Array(i);case"uint16":return new Uint16Array(i);case"int16":return new Int16Array(i);case"uint32":return new Uint32Array(i);case"int32":return new Int32Array(i);case"float32":return new Float32Array(i);case"float64":return new Float64Array(i);default:this.error(`unsupported dtype '${r}'`)}}_decode_ndarray(t){const{array:e,order:n,dtype:r,shape:i}=t,o=this._decode(e);return o instanceof ArrayBuffer&&n!=It.Yj&&(0,jt.wg)(o,r),(0,Nt.iI)(o,{dtype:r,shape:i})}_decode_object(t){const{type:e,attributes:n}=t,r=this._resolve_type(e);return null!=n?new r(this._decode(n)):new r}_decode_ref(t){const e=this.references.get(t.id);if(null!=e)return e;this.error(`reference ${t.id} isn't known`)}_decode_object_ref(t){this.references.has(t.id)&&this.error(`reference already known '${t.id}'`);const{id:e,name:n,attributes:r}=t,i=new(this._resolve_type(n))({id:e});this.references.set(e,i);const o=this._decode(r??{});return i.initialize_props(new Q.Bi(o)),this._finalizable.add(i),i}error(t){throw new Ft(t)}_resolve_type(t){const e=this.resolver.get(t);if(null!=e)return e;this.error(`could not resolve type '${t}', which could be due to a widget or a custom model not being registered before first usage`)}}var Gt;$t.__name__="Deserializer";class qt extends tt{constructor(t){super(t)}get is_syncable(){return this.syncable}[A.aI](t,e){return(!!e.structural||e.eq(this.id,t.id))&&super[A.aI](t,e)}initialize(){super.initialize(),this._js_callbacks=new Map}connect_signals(){super.connect_signals(),this._update_property_callbacks(),this.connect(this.properties.js_property_callbacks.change,(()=>this._update_property_callbacks())),this.connect(this.properties.js_event_callbacks.change,(()=>this._update_event_callbacks())),this.connect(this.properties.subscribed_events.change,(()=>this._update_event_callbacks()))}_process_event(t){for(const e of(0,Q.jd)(this.js_event_callbacks).get(t.event_name)??[])e.execute(t);null!=this.document&&this.subscribed_events.has(t.event_name)&&this.document.event_manager.send_event(t)}trigger_event(t){null!=this.document&&(t.origin=this,this.document.event_manager.trigger(t))}_update_event_callbacks(){null!=this.document?this.document.event_manager.subscribed_models.add(this):ot.vF.warn("WARNING: Document not defined for updating event callbacks")}_update_property_callbacks(){const t=t=>{const[e,n=null]=t.split(":");return null!=n?this.properties[n][e]:this[e]};for(const[e,n]of this._js_callbacks){const r=t(e);for(const t of n)this.disconnect(r,t)}this._js_callbacks.clear();for(const[e,n]of(0,Q.jd)(this.js_property_callbacks)){const r=n.map((t=>()=>t.execute(this)));this._js_callbacks.set(e,r);const i=t(e);for(const t of r)this.connect(i,t)}}_doc_attached(){(0,Q.jd)(this.js_event_callbacks).is_empty&&0==this.subscribed_events.size||this._update_event_callbacks()}_doc_detached(){this.document.event_manager.subscribed_models.delete(this)}select(t){if((0,f.Kg)(t))return[...this.references()].filter((e=>e instanceof qt&&e.name===t));if((0,f.Qd)(t)&&"type"in t)return[...this.references()].filter((e=>e.type==t.type));if(t.prototype instanceof tt)return[...this.references()].filter((e=>e instanceof t));throw new Error(`invalid selector ${t}`)}select_one(t){const e=this.select(t);switch(e.length){case 0:return null;case 1:return e[0];default:throw new Error(`found more than one object matching given selector ${t}`)}}on_event(t,e){const n=(0,f.Kg)(t)?t:t.prototype.event_name;this.js_event_callbacks[n]=[...(0,Q.jd)(this.js_event_callbacks).get(n)??[],(0,f.Tn)(e)?{execute:e}:e]}}Gt=qt,qt.__name__="Model",Gt.define((({Any:t,Unknown:e,Boolean:n,String:r,Array:i,Set:o,Dict:a,Nullable:s})=>({tags:[i(e),[]],name:[s(r),null],js_property_callbacks:[a(i(t)),{}],js_event_callbacks:[a(i(t)),{}],subscribed_events:[o(r),new globalThis.Set],syncable:[n,!0]}))),$t.register("model",(function(t,e){var n;function r(t){if((0,f.Kg)(t))switch(t){case"Any":return g.Any;case"Unknown":return g.Unknown;case"Boolean":return g.Boolean;case"Number":return g.Number;case"Int":return g.Int;case"Bytes":return g.Bytes;case"String":return g.String;case"Null":return g.Null}else switch(t[0]){case"Regex":{const[,e,n]=t;return g.Regex(new RegExp(e,n))}case"Nullable":{const[,e]=t;return g.Nullable(r(e))}case"Or":{const[,e,...n]=t;return g.Or(r(e),...n.map(r))}case"Tuple":{const[,e,...n]=t;return g.Tuple(r(e),...n.map(r))}case"Array":{const[,e]=t;return g.Array(r(e))}case"Struct":{const[,...e]=t,n=e.map((([t,e])=>[t,r(e)]));return g.Struct((0,Q.Wh)(n))}case"Dict":{const[,e]=t;return g.Dict(r(e))}case"Map":{const[,e,n]=t;return g.Map(r(e),r(n))}case"Enum":{const[,...e]=t;return g.Enum(...e)}case"Ref":{const[,n]=t,r=e.resolver.get(n.id);if(null!=r)return g.Ref(r);throw new Error(`${n.id} wasn't defined before referencing it`)}case"AnyRef":return g.AnyRef()}}const i=(()=>{const n=t.extends?.id??"Model";if("Model"==n)return qt;const r=e.resolver.get(n);if(null!=r)return r;throw new Error(`base model ${n} of ${t.name} is not defined`)})(),o=((n=class extends i{}).__qualified__=t.name,n);function a(t){return void 0===t?t:e.decode(t)}for(const e of t.properties??[]){const t=r(e.kind);o.define({[e.name]:[t,a(e.default)]})}for(const e of t.overrides??[])o.override({[e.name]:a(e.default)});return e.resolver.register(o),o}));class Ut{constructor(t){this.document=t,this.subscribed_models=new Set}send_event(t){const e=new S(this.document,"bokeh_event",t);this.document._trigger_on_change(e)}trigger(t){for(const e of this.subscribed_models)null!=t.origin&&t.origin!=e||e._process_event(t)}}Ut.__name__="EventManager";const Wt=[];class Zt{constructor(t){Wt.push(this),this._init_timestamp=Date.now(),this._resolver=t?.resolver??new et(nt),this._title="Bokeh Application",this._roots=[],this._all_models=new Map,this._new_models=new Set,this._all_models_freeze_count=0,this._callbacks=new Map,this._message_callbacks=new Map,this.event_manager=new Ut(this),this.idle=new T.n2(this,"idle"),this._idle_roots=new WeakSet,this._interactive_timestamp=null,this._interactive_plot=null}[A.aI](t,e){return this==t}get is_idle(){for(const t of this._roots)if(!this._idle_roots.has(t))return!1;return!0}notify_idle(t){this._idle_roots.add(t),this.is_idle&&(ot.vF.info(`document idle at ${Date.now()-this._init_timestamp} ms`),this.event_manager.send_event(new ut),this.idle.emit())}clear(){this._push_all_models_freeze();try{for(;this._roots.length>0;)this.remove_root(this._roots[0])}finally{this._pop_all_models_freeze()}}interactive_start(t,e=null){null==this._interactive_plot&&(this._interactive_plot=t,this._interactive_plot.trigger_event(new ft)),this._interactive_finalize=e,this._interactive_timestamp=Date.now()}interactive_stop(){null!=this._interactive_plot&&(this._interactive_plot.trigger_event(new Qt),null!=this._interactive_finalize&&this._interactive_finalize()),this._interactive_plot=null,this._interactive_timestamp=null,this._interactive_finalize=null}interactive_duration(){return null==this._interactive_timestamp?-1:Date.now()-this._interactive_timestamp}destructively_move(t){if(t===this)throw new Error("Attempted to overwrite a document with itself");t.clear();const e=(0,Rt.C)(this._roots);this.clear();for(const t of e)if(null!=t.document)throw new Error(`Somehow we didn't detach ${t}`);if(0!=this._all_models.size)throw new Error(`this._all_models still had stuff in it: ${this._all_models}`);for(const n of e)t.add_root(n);t.set_title(this._title)}_push_all_models_freeze(){this._all_models_freeze_count+=1}_pop_all_models_freeze(){this._all_models_freeze_count-=1,0===this._all_models_freeze_count&&this._recompute_all_models()}_invalidate_all_models(){ot.vF.debug("invalidating document models"),0===this._all_models_freeze_count&&this._recompute_all_models()}_recompute_all_models(){let t=new Set;for(const e of this._roots)t=W(t,e.references());const e=new Set(this._all_models.values()),n=Z(e,t),r=Z(t,e),i=new Map;for(const e of t)i.set(e.id,e);for(const t of n)t.detach_document();for(const t of r)t.attach_document(this),this._new_models.add(t);this._all_models=i}roots(){return this._roots}_add_root(t){if((0,Rt.mK)(this._roots,t))return!1;this._push_all_models_freeze();try{this._roots.push(t)}finally{this._pop_all_models_freeze()}return!0}_remove_root(t){const e=this._roots.indexOf(t);if(e<0)return!1;this._push_all_models_freeze();try{this._roots.splice(e,1)}finally{this._pop_all_models_freeze()}return!0}_set_title(t){const e=t!=this._title;return e&&(this._title=t),e}add_root(t){this._add_root(t)&&this._trigger_on_change(new N(this,t))}remove_root(t){this._remove_root(t)&&this._trigger_on_change(new R(this,t))}set_title(t){this._set_title(t)&&this._trigger_on_change(new D(this,t))}title(){return this._title}get_model_by_id(t){return this._all_models.get(t)??null}get_model_by_name(t){const e=[];for(const n of this._all_models.values())n instanceof qt&&n.name==t&&e.push(n);switch(e.length){case 0:return null;case 1:return e[0];default:throw new Error(`Multiple models are named '${t}'`)}}on_message(t,e){const n=this._message_callbacks.get(t);null==n?this._message_callbacks.set(t,new Set([e])):n.add(e)}remove_on_message(t,e){this._message_callbacks.get(t)?.delete(e)}_trigger_on_message(t,e){const n=this._message_callbacks.get(t);if(null!=n)for(const t of n)t(e)}on_change(t,e=!1){this._callbacks.has(t)||this._callbacks.set(t,e)}remove_on_change(t){this._callbacks.delete(t)}_trigger_on_change(t){for(const[e,n]of this._callbacks)if(!n&&t instanceof M)for(const n of t.events)e(n);else e(t)}to_json_string(t=!0){return JSON.stringify(this.to_json(t))}to_json(t=!0){const e=new H.hE({include_defaults:t}).encode(this._roots);return{version:it,title:this._title,roots:e}}static from_json_string(t,e){const n=JSON.parse(t);return Zt.from_json(n,e)}static _handle_version(t){if(null!=t.version){const e=t.version,n=-1!==e.indexOf("+")||-1!==e.indexOf("-"),r=`Library versions: JS (${it}) / Python (${e})`;n||function(t){return t.replace(/-(dev|rc)\./,".$1")}(it)==e?ot.vF.debug(r):(ot.vF.warn("JS/Python version mismatch"),ot.vF.warn(r))}else ot.vF.warn("'version' field is missing")}static from_json(t,e){ot.vF.debug("Creating Document from JSON"),Zt._handle_version(t);const n=new et(nt);null!=t.defs&&new $t(n).decode(t.defs);const r=new Zt({resolver:n});r._push_all_models_freeze();const i=t=>e?.push(t);r.on_change(i,!0);const o=new $t(n,r._all_models,(t=>t.attach_document(r))).decode(t.roots);r.remove_on_change(i);for(const t of o)r.add_root(t);return null!=t.title&&r.set_title(t.title),r._pop_all_models_freeze(),r}replace_with_json(t){Zt.from_json(t).destructively_move(this)}create_json_patch(t){for(const e of t)if(e.document!=this)throw new Error("Cannot create a patch using events from a different document");const e=new Map;for(const t of this._all_models.values())this._new_models.has(t)||e.set(t,t.ref());const n={events:new H.hE({references:e,binary:!0}).encode(t)};return this._new_models.clear(),n}apply_json_patch(t,e=new Map){this._push_all_models_freeze();const n=new $t(this._resolver,this._all_models,(t=>t.attach_document(this))).decode(t.events,e);for(const t of n)switch(t.kind){case"MessageSent":{const{msg_type:e,msg_data:n}=t;this._trigger_on_message(e,n);break}case"ModelChanged":{const{model:e,attr:n,new:r}=t;e.setv({[n]:r},{sync:!1});break}case"ColumnDataChanged":{const{model:e,attr:n,cols:r,data:i}=t;if(null!=r){const t=e.property(n).get_value();for(const e in t)e in i||(i[e]=t[e])}e.setv({data:i},{sync:!1,check_eq:!1});break}case"ColumnsStreamed":{const{model:e,attr:n,data:r,rollover:i}=t,o=e.property(n);e.stream_to(o,r,i,{sync:!1});break}case"ColumnsPatched":{const{model:e,attr:n,patches:r}=t,i=e.property(n);e.patch_to(i,r,{sync:!1});break}case"RootAdded":this._add_root(t.model);break;case"RootRemoved":this._remove_root(t.model);break;case"TitleChanged":this._set_title(t.title);break;default:throw new Error(`unknown patch event type '${t.kind}'`)}this._pop_all_models_freeze()}}Zt.__name__="Document";var Xt=n(767);class Kt{constructor(t){this.removed=new T.n2(this,"removed"),this._ready=Promise.resolve(void 0),this._slots=new WeakMap,this._removed=!1,this._idle_notified=!1;const{model:e,parent:n,owner:r}=t;this.model=e,this.parent=n,null==n?(this.root=this,this.owner=r??new Yt([this])):(this.root=n.root,this.owner=this.root.owner)}get ready(){return this._ready}*children(){}connect(t,e){let n=this._slots.get(e);return null==n&&(n=(t,n)=>{const r=Promise.resolve(e.call(this,t,n));this._ready=this._ready.then((()=>r)),this.root!=this&&(this.root._ready=this.root._ready.then((()=>this._ready)))},this._slots.set(e,n)),t.connect(n,this)}disconnect(t,e){return t.disconnect(e,this)}initialize(){this._has_finished=!1}async lazy_initialize(){}remove(){this.disconnect_signals(),this.removed.emit(),this._removed=!0}toString(){return`${this.model.type}View(${this.model.id})`}serializable_state(){return{type:this.model.type}}get is_root(){return null==this.parent}has_finished(){return this._has_finished}get is_idle(){return this.has_finished()}connect_signals(){}disconnect_signals(){T.HN.disconnect_receiver(this)}on_change(t,e){for(const n of(0,f.cy)(t)?t:[t])this.connect(n.change,e)}cursor(t,e){return null}notify_finished(){this.is_root?!this._idle_notified&&this.has_finished()&&null!=this.model.document&&(this._idle_notified=!0,this.model.document.notify_idle(this.model)):this.root.notify_finished()}}Kt.__name__="View";class Yt{constructor(t=[]){this.roots=new Set(t)}get(t){for(const e of this.roots)if(e.model==t)return e;return null}add(t){this.roots.add(t)}delete(t){this.roots.delete(t)}*[Symbol.iterator](){yield*this.roots}*query(t){function*e(n){if(t(n))yield n;else for(const t of n.children())yield*e(t)}for(const t of this.roots)yield*e(t)}*find(t){yield*this.query((e=>e.model==t))}get_one(t){const e=this.find_one(t);if(null!=e)return e;throw new Error(`cannot find a view for ${t}`)}find_one(t){for(const e of this.find(t))return e;return null}find_all(t){return[...this.find(t)]}}Yt.__name__="ViewManager";var Jt=n(4631);const{min:te,max:ee}=Math;function ne(t,e){return{x0:te(t.x0,e.x0),x1:ee(t.x1,e.x1),y0:te(t.y0,e.y0),y1:ee(t.y1,e.y1)}}class re{constructor(t,e=!1){if(null==t)this.x0=0,this.y0=0,this.x1=0,this.y1=0;else if("x0"in t){const{x0:e,y0:n,x1:r,y1:i}=t;if(!(e<=r&&n<=i))throw new Error(`invalid bbox {x0: ${e}, y0: ${n}, x1: ${r}, y1: ${i}}`);this.x0=e,this.y0=n,this.x1=r,this.y1=i}else if("x"in t){const{x:e,y:n,width:r,height:i}=t;if(!(r>=0&&i>=0))throw new Error(`invalid bbox {x: ${e}, y: ${n}, width: ${r}, height: ${i}}`);this.x0=e,this.y0=n,this.x1=e+r,this.y1=n+i}else{let n,r,i,o;if("width"in t)if("left"in t)n=t.left,r=n+t.width;else if("right"in t)r=t.right,n=r-t.width;else{const e=t.width/2;n=t.hcenter-e,r=t.hcenter+e}else n=t.left,r=t.right;if("height"in t)if("top"in t)i=t.top,o=i+t.height;else if("bottom"in t)o=t.bottom,i=o-t.height;else{const e=t.height/2;i=t.vcenter-e,o=t.vcenter+e}else i=t.top,o=t.bottom;if(n>r||i>o){if(!e)throw new Error(`invalid bbox {left: ${n}, top: ${i}, right: ${r}, bottom: ${o}}`);n>r&&(n=r),i>o&&(i=o)}this.x0=n,this.y0=i,this.x1=r,this.y1=o}}static from_lrtb({left:t,right:e,top:n,bottom:r}){return new re({x0:Math.min(t,e),y0:Math.min(n,r),x1:Math.max(t,e),y1:Math.max(n,r)})}clone(){return new re(this)}equals(t){return this.x0==t.x0&&this.y0==t.y0&&this.x1==t.x1&&this.y1==t.y1}[A.aI](t,e){return e.eq(this.x0,t.x0)&&e.eq(this.y0,t.y0)&&e.eq(this.x1,t.x1)&&e.eq(this.y1,t.y1)}toString(){return`BBox({left: ${this.left}, top: ${this.top}, width: ${this.width}, height: ${this.height}})`}get is_empty(){const{x0:t,x1:e,y0:n,y1:r}=this;return 0==t&&0==e&&0==n&&0==r}get left(){return this.x0}get top(){return this.y0}get right(){return this.x1}get bottom(){return this.y1}get p0(){return[this.x0,this.y0]}get p1(){return[this.x1,this.y1]}get x(){return this.x0}get y(){return this.y0}get width(){return this.x1-this.x0}get height(){return this.y1-this.y0}get size(){return{width:this.width,height:this.height}}get rect(){const{x0:t,y0:e,x1:n,y1:r}=this;return{p0:{x:t,y:e},p1:{x:n,y:e},p2:{x:n,y:r},p3:{x:t,y:r}}}get box(){const{x:t,y:e,width:n,height:r}=this;return{x:t,y:e,width:n,height:r}}get lrtb(){const{left:t,right:e,top:n,bottom:r}=this;return{left:t,right:e,top:n,bottom:r}}get h_range(){return{start:this.x0,end:this.x1}}get v_range(){return{start:this.y0,end:this.y1}}get ranges(){return[this.h_range,this.v_range]}get aspect(){return this.width/this.height}get hcenter(){return(this.left+this.right)/2}get vcenter(){return(this.top+this.bottom)/2}get area(){return this.width*this.height}relative(){const{width:t,height:e}=this;return new re({x:0,y:0,width:t,height:e})}translate(t,e){const{x:n,y:r,width:i,height:o}=this;return new re({x:t+n,y:e+r,width:i,height:o})}relativize(t,e){return[t-this.x,e-this.y]}contains(t,e){return this.x0<=t&&t<=this.x1&&this.y0<=e&&e<=this.y1}clip(t,e){return t<this.x0?t=this.x0:t>this.x1&&(t=this.x1),e<this.y0?e=this.y0:e>this.y1&&(e=this.y1),[t,e]}grow_by(t){return new re({left:this.left-t,right:this.right+t,top:this.top-t,bottom:this.bottom+t})}shrink_by(t){return new re({left:this.left+t,right:this.right-t,top:this.top+t,bottom:this.bottom-t},!0)}union(t){return new re({x0:te(this.x0,t.x0),y0:te(this.y0,t.y0),x1:ee(this.x1,t.x1),y1:ee(this.y1,t.y1)})}intersection(t){return this.intersects(t)?new re({x0:ee(this.x0,t.x0),y0:ee(this.y0,t.y0),x1:te(this.x1,t.x1),y1:te(this.y1,t.y1)}):null}intersects(t){return!(t.x1<this.x0||t.x0>this.x1||t.y1<this.y0||t.y0>this.y1)}get xview(){return{compute:t=>this.left+t,v_compute:t=>{const e=new Jt.mR(t.length),n=this.left;for(let r=0;r<t.length;r++)e[r]=n+t[r];return e},invert:t=>t-this.left,v_invert:t=>{const e=new Jt.mR(t.length),n=this.left;for(let r=0;r<t.length;r++)e[r]=t[r]-n;return e}}}get yview(){return{compute:t=>this.bottom-t,v_compute:t=>{const e=new Jt.mR(t.length),n=this.bottom;for(let r=0;r<t.length;r++)e[r]=n-t[r];return e},invert:t=>this.bottom-t,v_invert:t=>{const e=new Jt.mR(t.length),n=this.bottom;for(let r=0;r<t.length;r++)e[r]=n-t[r];return e}}}}re.__name__="BBox";const ie=t=>(e={},...n)=>{const r=document.createElement(t);(0,f.Qd)(e)||(n=[e,...n],e={});for(let[t,n]of(0,Q.jO)(e))if(null!=n&&(!(0,f.Lm)(n)||n))if("class"===t&&((0,f.Kg)(n)&&(n=n.split(/\s+/)),(0,f.cy)(n)))for(const t of n)null!=t&&r.classList.add(t);else if("style"===t&&(0,f.Qd)(n))for(const[t,e]of(0,Q.jO)(n))r.style[t]=e;else if("data"===t&&(0,f.Qd)(n))for(const[t,e]of(0,Q.jO)(n))r.dataset[t]=e;else r.setAttribute(t,n);function i(t){if((0,f.Kg)(t))r.appendChild(document.createTextNode(t));else if(t instanceof Node)r.appendChild(t);else if(t instanceof NodeList||t instanceof HTMLCollection)for(const e of t)r.appendChild(e);else if(null!=t&&!1!==t)throw new Error(`expected a DOM element, string, false or null, got ${JSON.stringify(t)}`)}for(const t of n)if((0,f.cy)(t))for(const e of t)i(e);else i(t);return r},oe=ie("div"),ae=ie("span"),se=ie("canvas"),le=ie("link"),ce=ie("style"),ue=ie("a"),de=ie("p"),he=ie("i"),pe=ie("pre"),fe=ie("button"),Qe=ie("label"),Te=ie("legend"),me=ie("fieldset"),ge=ie("input"),_e=ie("select"),be=ie("option"),ve=ie("optgroup"),ye=ie("textarea");function xe(t){return document.createTextNode(t)}function we(t,...e){for(const n of e)t.appendChild(n)}function Le(t){const e=t.parentNode;null!=e&&e.removeChild(t)}function Ae(t,e=!1){let n;for(;n=t.firstChild;)t.removeChild(n);if(e&&t instanceof Element)for(const e of t.attributes)t.removeAttributeNode(e)}function He(t,e=!0){t.style.display=e?"":"none"}function ke(t){t.style.display="none"}function Me(t){t.style.visibility=""}function Ce(t){t.style.visibility="hidden"}function Se(t){const{x:e,y:n,width:r,height:i}=t.getBoundingClientRect();return new re({x:e,y:n,width:r,height:i})}class Ee{constructor(t){this.class_list=t}get values(){const t=[];for(let e=0;e<this.class_list.length;e++){const n=this.class_list.item(e);null!=n&&t.push(n)}return t}has(t){return this.class_list.contains(t)}add(...t){for(const e of t)this.class_list.add(e);return this}remove(...t){for(const e of t)(0,f.cy)(e)?e.forEach((t=>this.class_list.remove(t))):this.class_list.remove(e);return this}clear(){for(const t of this.values)this.class_list.remove(t);return this}toggle(t,e){return(null!=e?e:!this.has(t))?this.add(t):this.remove(t),this}}function Ve(t,e,n){null==n&&(n=!t.hasAttribute(e)),n?t.setAttribute(e,"true"):t.removeAttribute(e)}var Oe;Ee.__name__="ClassList",function(t){t[t.None=0]="None",t[t.Primary=1]="Primary",t[t.Secondary=2]="Secondary",t[t.Auxiliary=4]="Auxiliary",t[t.Left=1]="Left",t[t.Right=2]="Right",t[t.Middle=4]="Middle"}(Oe||(Oe={}));class Pe{constructor(t){this.el=ce({type:"text/css"},t)}clear(){this.replace("")}*_to_rules(t){for(const[e,n]of(0,Q.jO)(t))if(null!=n){const t=e.replace(/_/g,"-");yield`${t}: ${n};`}}_to_css(t,e){return null==e?t:`${t}{${[...this._to_rules(e)].join("")}}`}replace(t,e){this.el.textContent=this._to_css(t,e)}prepend(t,e){const n=this.el.textContent??"";this.el.textContent=`${this._to_css(t,e)}\n${n}`}append(t,e){const n=this.el.textContent??"";this.el.textContent=`${n}\n${this._to_css(t,e)}`}remove(){Le(this.el)}}Pe.__name__="StyleSheet";class De extends Pe{initialize(){this.el.isConnected||document.head.appendChild(this.el)}}De.__name__="GlobalStyleSheet";class Ne{constructor(t){this.el=le({rel:"stylesheet",href:t})}replace(t){this.el.href=t}remove(){Le(this.el)}}function Re(t){return`${t}px`}Ne.__name__="ImportedStyleSheet",class extends Pe{initialize(){this.el.isConnected||document.head.appendChild(this.el)}}.__name__="GlobalImportedStyleSheet",ShadowRoot.prototype;const Ie=":host{--base-font:var(--bokeh-base-font, Helvetica, Arial, sans-serif);--mono-font:var(--bokeh-mono-font, monospace);--font-size:12px;--line-height:calc(20 / 14);--line-height-computed:calc(var(--font-size) * var(--line-height));--border-radius:4px;--padding-vertical:6px;--padding-horizontal:12px;}:host{box-sizing:border-box;font-family:var(--base-font);font-size:13px;line-height:var(--line-height);}*,*:before,*:after{box-sizing:inherit;font-family:inherit;}pre{font-family:var(--mono-font);margin:0;}";class je extends Kt{get children_el(){return this.shadow_el??this.el}initialize(){super.initialize(),this.el=this._createElement()}remove(){Le(this.el),super.remove()}css_classes(){return[]}styles(){return[]}render_to(t){t.appendChild(this.el),this.render()}finish(){this._has_finished=!0,this.notify_finished()}_createElement(){return function(t,e,...n){return ie(t)(e,...n)}(this.constructor.tag_name,{class:this.css_classes()})}}je.__name__="DOMView",je.tag_name="div";class ze extends je{initialize(){super.initialize(),this.class_list=new Ee(this.el.classList)}}ze.__name__="DOMElementView";class Be extends ze{initialize(){super.initialize(),this.shadow_el=this.el.attachShadow({mode:"open"})}styles(){return[...super.styles(),Ie]}empty(){Ae(this.shadow_el),this.class_list.clear()}render(){this.empty(),this._apply_stylesheets(this.styles()),this._apply_classes(this.css_classes())}_apply_stylesheets(t){for(const e of t){const t=(0,f.Kg)(e)?new Pe(e):e;this.shadow_el.appendChild(t.el)}}_apply_classes(t){this.class_list.add(...t)}}async function Fe(t,e,n){(0,_.vA)(null!=t,"model doesn't implement a view");const r=new t({...n,model:e});return r.initialize(),await r.lazy_initialize(),r}async function $e(t,e={parent:null},n=t=>t.default_view){const r=await Fe(n(t),t,e);return r.connect_signals(),r}async function Ge(t,e,n={parent:null},r=t=>t.default_view){const i=(0,Rt.iv)([...t.keys()],e),o=[];for(const e of i){const n=t.get(e);null!=n&&(t.delete(e),o.push(n),n.remove())}const a=[],s=e.filter((e=>!t.has(e)));for(const e of s){const i=await Fe(r(e),e,n);t.set(e,i),a.push(i)}for(const t of a)t.connect_signals();return{created:a,removed:o}}function qe(t){for(const[e,n]of t)n.remove(),t.delete(e)}Be.__name__="DOMComponentView";const Ue={};class We{constructor(t,e,n){this.header=t,this.metadata=e,this.content=n,this._buffers=new Map}get buffers(){return this._buffers}static assemble(t,e,n){const r=JSON.parse(t),i=JSON.parse(e),o=JSON.parse(n);return new We(r,i,o)}assemble_buffer(t,e){const n=this.header.num_buffers??0;if(n<=this._buffers.size)throw new Error(`too many buffers received, expecting ${n}`);const{id:r}=JSON.parse(t);this._buffers.set(r,e)}static create(t,e,n){const r=We.create_header(t);return new We(r,e,n)}static create_header(t){return{msgid:y(),msgtype:t}}complete(){const{num_buffers:t}=this.header;return null==t||this._buffers.size==t}send(t){(0,_.vA)(null==this.header.num_buffers);const e=[],n=JSON.stringify(this.content,((t,n)=>{if(n instanceof H.hp){const t={id:`${e.length}`};return e.push([t,n.buffer]),t}return n})),r=e.length;r>0&&(this.header.num_buffers=r);const i=JSON.stringify(this.header),o=JSON.stringify(this.metadata);t.send(i),t.send(o),t.send(n);for(const[n,r]of e)t.send(JSON.stringify(n)),t.send(r)}msgid(){return this.header.msgid}msgtype(){return this.header.msgtype}reqid(){return this.header.reqid}problem(){return"msgid"in this.header?"msgtype"in this.header?null:"No msgtype in header":"No msgid in header"}}We.__name__="Message",new Map;var Ze=n(3764),Xe=n(2114),Ke=n(1050),Ye=n(7555);class Je extends Xe.E{get doit(){const t=this.fill_color.get_value(),e=this.fill_alpha.get_value();return!(null==t||0==e)}apply(t,e){const{doit:n}=this;return n&&(this.set_value(t),t.fill(e)),n}values(){return{color:this.fill_color.get_value(),alpha:this.fill_alpha.get_value()}}set_value(t){const e=this.fill_color.get_value(),n=this.fill_alpha.get_value();t.fillStyle=(0,Ye.do)(e,n)}}Je.__name__="Fill";class tn extends Xe.o{get doit(){const t=this.fill_color.value,e=this.fill_alpha.value;return!(0==t||0==e)}apply(t,e){const{doit:n}=this;return n&&(this.set_value(t),t.fill(e)),n}values(){return{color:this.fill_color.value,alpha:this.fill_alpha.value}}set_value(t){const e=this.fill_color.value,n=this.fill_alpha.value;t.fillStyle=(0,Ye.do)(e,n)}}tn.__name__="FillScalar";class en extends Xe.o{get doit(){const{fill_color:t}=this;if(t.is_Scalar()&&0==t.value)return!1;const{fill_alpha:e}=this;return!e.is_Scalar()||0!=e.value}v_doit(t){return 0!=this.fill_color.get(t)&&0!=this.fill_alpha.get(t)}apply(t,e,n){const r=this.v_doit(e);return r&&(this.set_vectorize(t,e),t.fill(n)),r}values(t){return{color:this.fill_color.get(t),alpha:this.fill_alpha.get(t)}}set_vectorize(t,e){const n=this.fill_color.get(e),r=this.fill_alpha.get(e);t.fillStyle=(0,Ye.do)(n,r)}}en.__name__="FillVector",Je.prototype.type="fill",Je.prototype.attrs=Object.keys(Ke.SQ),tn.prototype.type="fill",tn.prototype.attrs=Object.keys(Ke.GA),en.prototype.type="fill",en.prototype.attrs=Object.keys(Ke.H_);const nn=new Map;function rn(t,e){const n=nn.get(t);if(null==n){const n=new WeakSet([e]);nn.set(t,n)}else{if(n.has(e))return;n.add(e)}const{fonts:r}=document;r.check(t)||r.load(t).then((()=>e.request_render()))}class on extends Xe.E{get doit(){const t=this.text_color.get_value(),e=this.text_alpha.get_value();return!(null==t||0==e)}update(){this.doit&&rn(this.font_value(),this.obj)}values(){return{color:this.text_color.get_value(),outline_color:this.text_outline_color.get_value(),alpha:this.text_alpha.get_value(),font:this.text_font.get_value(),font_size:this.text_font_size.get_value(),font_style:this.text_font_style.get_value(),align:this.text_align.get_value(),baseline:this.text_baseline.get_value(),line_height:this.text_line_height.get_value()}}set_value(t){const e=this.text_color.get_value(),n=this.text_outline_color.get_value(),r=this.text_alpha.get_value();t.fillStyle=(0,Ye.do)(e,r),t.strokeStyle=(0,Ye.do)(n,r),t.font=this.font_value(),t.textAlign=this.text_align.get_value(),t.textBaseline=this.text_baseline.get_value()}font_value(){return`${this.text_font_style.get_value()} ${this.text_font_size.get_value()} ${this.text_font.get_value()}`}}on.__name__="Text";class an extends Xe.o{get doit(){const t=this.text_color.value,e=this.text_alpha.value;return!(0==t||0==e)}update(){this.doit&&rn(this.font_value(),this.obj)}values(){return{color:this.text_color.value,outline_color:this.text_outline_color.value,alpha:this.text_alpha.value,font:this.text_font.value,font_size:this.text_font_size.value,font_style:this.text_font_style.value,align:this.text_align.value,baseline:this.text_baseline.value,line_height:this.text_line_height.value}}set_value(t){const e=this.text_color.value,n=this.text_alpha.value,r=this.text_outline_color.value,i=this.font_value(),o=this.text_align.value,a=this.text_baseline.value;t.fillStyle=(0,Ye.do)(e,n),t.strokeStyle=(0,Ye.do)(r,n),t.font=i,t.textAlign=o,t.textBaseline=a}font_value(){return`${this.text_font_style.value} ${this.text_font_size.value} ${this.text_font.value}`}}an.__name__="TextScalar";class sn extends Xe.o{_assert_font(t){rn(this.font_value(t),this.obj)}values(t){return this._assert_font(t),{color:this.text_color.get(t),outline_color:this.text_outline_color.get(t),alpha:this.text_alpha.get(t),font:this.text_font.get(t),font_size:this.text_font_size.get(t),font_style:this.text_font_style.get(t),align:this.text_align.get(t),baseline:this.text_baseline.get(t),line_height:this.text_line_height.get(t)}}get doit(){const{text_color:t}=this;if(t.is_Scalar()&&0==t.value)return!1;const{text_alpha:e}=this;return!e.is_Scalar()||0!=e.value}v_doit(t){return 0!=this.text_color.get(t)&&0!=this.text_alpha.get(t)}apply(t,e){const n=this.v_doit(e);return n&&this.set_vectorize(t,e),n}set_vectorize(t,e){this._assert_font(e);const n=this.text_color.get(e),r=this.text_outline_color.get(e),i=this.text_alpha.get(e),o=this.font_value(e),a=this.text_align.get(e),s=this.text_baseline.get(e);t.fillStyle=(0,Ye.do)(n,i),t.strokeStyle=(0,Ye.do)(r,i),t.font=o,t.textAlign=a,t.textBaseline=s}font_value(t){return`${this.text_font_style.get(t)} ${this.text_font_size.get(t)} ${this.text_font.get(t)}`}}sn.__name__="TextVector",on.prototype.type="text",on.prototype.attrs=Object.keys(Ke.EY),an.prototype.type="text",an.prototype.attrs=Object.keys(Ke.uv),sn.prototype.type="text",sn.prototype.attrs=Object.keys(Ke.Dt);var ln=n(8865);class cn extends Xe.E{constructor(){super(...arguments),this._update_iteration=0}update(){if(this._update_iteration++,this._hatch_image=null,!this.doit)return;const t=this.hatch_color.get_value(),e=this.hatch_alpha.get_value(),n=this.hatch_scale.get_value(),r=this.hatch_pattern.get_value(),i=this.hatch_weight.get_value(),o=t=>{this._hatch_image=t},a=this.hatch_extra.get_value()[r];if(null!=a){const r=a.get_pattern(t,e,n,i);if(r instanceof Promise){const{_update_iteration:t}=this;r.then((e=>{this._update_iteration==t&&(o(e),this.obj.request_render())}))}else o(r)}else{const a=this.obj.canvas.create_layer(),s=(0,ln.C)(a,r,t,e,n,i);o(s)}}get doit(){const t=this.hatch_color.get_value(),e=this.hatch_alpha.get_value(),n=this.hatch_pattern.get_value();return!(null==t||0==e||" "==n||"blank"==n||null==n)}apply(t,e){const{doit:n}=this;return n&&(this.set_value(t),t.layer.undo_transform((()=>t.fill(e)))),n}set_value(t){const e=this.pattern(t);t.fillStyle=e??"transparent"}pattern(t){const e=this._hatch_image;return null==e?null:t.createPattern(e,this.repetition())}repetition(){const t=this.hatch_pattern.get_value(),e=this.hatch_extra.get_value()[t];if(null==e)return"repeat";switch(e.repetition){case"repeat":return"repeat";case"repeat_x":return"repeat-x";case"repeat_y":return"repeat-y";case"no_repeat":return"no-repeat"}}}cn.__name__="Hatch";class un extends Xe.o{constructor(){super(...arguments),this._static_doit=!1,this._update_iteration=0}_compute_static_doit(){const t=this.hatch_color.value,e=this.hatch_alpha.value,n=this.hatch_pattern.value;return!(null==t||0==e||" "==n||"blank"==n||null==n)}update(){this._update_iteration++;const t=this.hatch_color.length;if(this._hatch_image=new m.J3(null,t),this._static_doit=this._compute_static_doit(),!this._static_doit)return;const e=this.hatch_color.value,n=this.hatch_alpha.value,r=this.hatch_scale.value,i=this.hatch_pattern.value,o=this.hatch_weight.value,a=e=>{this._hatch_image=new m.J3(e,t)},s=this.hatch_extra.value[i];if(null!=s){const t=s.get_pattern(e,n,r,o);if(t instanceof Promise){const{_update_iteration:e}=this;t.then((t=>{this._update_iteration==e&&(a(t),this.obj.request_render())}))}else a(t)}else{const t=this.obj.canvas.create_layer(),s=(0,ln.C)(t,i,e,n,r,o);a(s)}}get doit(){return this._static_doit}apply(t,e){const{doit:n}=this;return n&&(this.set_value(t),t.layer.undo_transform((()=>t.fill(e)))),n}set_value(t){t.fillStyle=this.pattern(t)??"transparent"}pattern(t){const e=this._hatch_image.value;return null==e?null:t.createPattern(e,this.repetition())}repetition(){const t=this.hatch_pattern.value,e=this.hatch_extra.value[t];if(null==e)return"repeat";switch(e.repetition){case"repeat":return"repeat";case"repeat_x":return"repeat-x";case"repeat_y":return"repeat-y";case"no_repeat":return"no-repeat"}}}un.__name__="HatchScalar";class dn extends Xe.o{constructor(){super(...arguments),this._static_doit=!1,this._update_iteration=0}_compute_static_doit(){const{hatch_color:t}=this;if(t.is_Scalar()&&0==t.value)return!1;const{hatch_alpha:e}=this;if(e.is_Scalar()&&0==e.value)return!1;const{hatch_pattern:n}=this;if(n.is_Scalar()){const t=n.value;if(" "==t||"blank"==t||null==t)return!1}return!0}update(){this._update_iteration++;const t=this.hatch_color.length;if(this._hatch_image=new m.J3(null,t),this._static_doit=this._compute_static_doit(),!this._static_doit)return;const e=(t,e,n,r,i,o)=>{const a=this.hatch_extra.value[t];if(null!=a){const t=a.get_pattern(e,n,r,i);if(t instanceof Promise){const{_update_iteration:e}=this;t.then((t=>{this._update_iteration==e&&(o(t),this.obj.request_render())}))}else o(t)}else{const a=this.obj.canvas.create_layer(),s=(0,ln.C)(a,t,e,n,r,i);o(s)}};if(this.hatch_color.is_Scalar()&&this.hatch_alpha.is_Scalar()&&this.hatch_scale.is_Scalar()&&this.hatch_pattern.is_Scalar()&&this.hatch_weight.is_Scalar()){const n=this.hatch_color.value,r=this.hatch_alpha.value,i=this.hatch_scale.value;e(this.hatch_pattern.value,n,r,i,this.hatch_weight.value,(e=>{this._hatch_image=new m.J3(e,t)}))}else{const n=new Array(t);n.fill(null),this._hatch_image=new m.aG(n);for(let r=0;r<t;r++){const t=this.hatch_color.get(r),i=this.hatch_alpha.get(r),o=this.hatch_scale.get(r);e(this.hatch_pattern.get(r),t,i,o,this.hatch_weight.get(r),(t=>{n[r]=t}))}}}get doit(){return this._static_doit}v_doit(t){if(!this.doit)return!1;if(0==this.hatch_color.get(t))return!1;if(0==this.hatch_alpha.get(t))return!1;const e=this.hatch_pattern.get(t);return" "!=e&&"blank"!=e&&null!=e}apply(t,e,n){const r=this.v_doit(e);return r&&(this.set_vectorize(t,e),t.layer.undo_transform((()=>t.fill(n)))),r}set_vectorize(t,e){t.fillStyle=this.pattern(t,e)??"transparent"}pattern(t,e){const n=this._hatch_image.get(e);return null==n?null:t.createPattern(n,this.repetition(e))}repetition(t){const e=this.hatch_pattern.get(t),n=this.hatch_extra.value[e];if(null==n)return"repeat";switch(n.repetition){case"repeat":return"repeat";case"repeat_x":return"repeat-x";case"repeat_y":return"repeat-y";case"no_repeat":return"no-repeat"}}}dn.__name__="HatchVector",cn.prototype.type="hatch",cn.prototype.attrs=Object.keys(Ke.LD),un.prototype.type="hatch",un.prototype.attrs=Object.keys(Ke.JG),dn.prototype.type="hatch",dn.prototype.attrs=Object.keys(Ke.y7);class hn extends Xe.E{get doit(){return!(0==this.global_alpha.get_value())}apply(t){const{doit:e}=this;return e&&this.set_value(t),e}values(){return{global_alpha:this.global_alpha.get_value()}}set_value(t){const e=this.global_alpha.get_value();t.globalAlpha=e}}hn.__name__="Image";class pn extends Xe.o{get doit(){return!(0==this.global_alpha.value)}apply(t){const{doit:e}=this;return e&&this.set_value(t),e}values(){return{global_alpha:this.global_alpha.value}}set_value(t){const e=this.global_alpha.value;t.globalAlpha=e}}pn.__name__="ImageScalar";class fn extends Xe.o{get doit(){const{global_alpha:t}=this;return!t.is_Scalar()||0!=t.value}v_doit(t){return 0!=this.global_alpha.get(t)}apply(t,e){const n=this.v_doit(e);return n&&this.set_vectorize(t,e),n}values(t){return{alpha:this.global_alpha.get(t)}}set_vectorize(t,e){const n=this.global_alpha.get(e);t.globalAlpha=n}}fn.__name__="ImageVector",hn.prototype.type="image",hn.prototype.attrs=Object.keys(Ke._V),pn.prototype.type="image",pn.prototype.attrs=Object.keys(Ke.SJ),fn.prototype.type="image",fn.prototype.attrs=Object.keys(Ke.Hl);class Qn{constructor(t){this._visuals=[];for(const[e,n]of t.model._mixins){const r=(()=>{switch(n){case Ke.N1:return new Ze.N1(t,e);case Ke.Rb:return new Ze.Rb(t,e);case Ke.UT:return new Ze.UT(t,e);case Ke.SQ:return new Je(t,e);case Ke.GA:return new tn(t,e);case Ke.H_:return new en(t,e);case Ke.EY:return new on(t,e);case Ke.uv:return new an(t,e);case Ke.Dt:return new sn(t,e);case Ke.LD:return new cn(t,e);case Ke.JG:return new un(t,e);case Ke.y7:return new dn(t,e);case Ke._V:return new hn(t,e);case Ke.SJ:return new pn(t,e);case Ke.Hl:return new fn(t,e);default:throw new Error("unknown visual")}})();r instanceof Xe.E&&r.update(),this._visuals.push(r),Object.defineProperty(this,e+r.type,{get:()=>r,configurable:!1,enumerable:!0})}}*[Symbol.iterator](){yield*this._visuals}}Qn.__name__="Visuals";var Tn,mn,gn,_n=n(9668),bn=n(4218);class vn extends qt{constructor(t){super(t)}}vn.__name__="Transform";class yn extends qt{constructor(t){super(t),this.have_updated_interactively=!1}get is_reversed(){return this.start>this.end}get is_valid(){return isFinite(this.min)&&isFinite(this.max)}get span(){return Math.abs(this.end-this.start)}}Tn=yn,yn.__name__="Range",Tn.define((({Number:t,Tuple:e,Or:n,Auto:r,Nullable:i})=>({bounds:[i(n(e(i(t),i(t)),r)),null],min_interval:[i(t),null],max_interval:[i(t),null]})));class xn extends yn{constructor(t){super(t)}_set_auto_bounds(){if("auto"==this.bounds){const t=Math.min(this._reset_start,this._reset_end),e=Math.max(this._reset_start,this._reset_end);this.setv({bounds:[t,e]},{silent:!0})}}initialize(){super.initialize(),this._set_auto_bounds()}get min(){return Math.min(this.start,this.end)}get max(){return Math.max(this.start,this.end)}reset(){this._set_auto_bounds();const{_reset_start:t,_reset_end:e}=this;this.start!=t||this.end!=e?this.setv({start:t,end:e}):this.change.emit()}map(t){return new xn({start:t(this.start),end:t(this.end)})}widen(t){let{start:e,end:n}=this;return this.is_reversed?(e+=t,n-=t):(e-=t,n+=t),new xn({start:e,end:n})}}mn=xn,xn.__name__="Range1d",mn.define((({Number:t,Nullable:e})=>({start:[t,0],end:[t,1],reset_start:[e(t),null,{on_update(t,e){e._reset_start=t??e.start}}],reset_end:[e(t),null,{on_update(t,e){e._reset_end=t??e.end}}]})));class wn extends vn{constructor(t){super(t)}compute(t){return this.s_compute(t)}v_compute(t){const e=new Jt.mR(t.length),{s_compute:n}=this;for(let r=0;r<t.length;r++)e[r]=n(t[r]);return e}invert(t){return this.s_invert(t)}v_invert(t){const e=new Float64Array(t.length),{s_invert:n}=this;for(let r=0;r<t.length;r++)e[r]=n(t[r]);return e}r_compute(t,e){const{s_compute:n}=this;return this.target_range.is_reversed?[n(e),n(t)]:[n(t),n(e)]}r_invert(t,e){const{s_invert:n}=this;return this.target_range.is_reversed?[n(e),n(t)]:[n(t),n(e)]}}gn=wn,wn.__name__="Scale",gn.internal((({Ref:t})=>({source_range:[t(yn)],target_range:[t(xn)]})));class Ln extends wn{constructor(t){super(t)}}Ln.__name__="ContinuousScale";class An extends Ln{constructor(t){super(t)}get s_compute(){const[t,e]=this._linear_compute_state();return n=>t*n+e}get s_invert(){const[t,e]=this._linear_compute_state();return n=>(n-e)/t}_linear_compute_state(){const t=this.source_range.start,e=this.source_range.end,n=this.target_range.start,r=(this.target_range.end-n)/(e-t);return[r,-r*t+n]}}An.__name__="LinearScale";class Hn extends Ln{constructor(t){super(t)}get s_compute(){const[t,e,n,r]=this._compute_state();return i=>{if(0==n)return 0;{const o=(Math.log(i)-r)/n;return isFinite(o)?o*t+e:NaN}}}get s_invert(){const[t,e,n,r]=this._compute_state();return i=>{const o=(i-e)/t;return Math.exp(n*o+r)}}_get_safe_factor(t,e){let n=t<0?0:t,r=e<0?0:e;if(n==r)if(0==n)[n,r]=[1,10];else{const t=Math.log10(n);n=10**Math.floor(t),r=Math.ceil(t)!=Math.floor(t)?10**Math.ceil(t):10**(Math.ceil(t)+1)}return[n,r]}_compute_state(){const t=this.source_range.start,e=this.source_range.end,n=this.target_range.start,r=this.target_range.end-n,[i,o]=this._get_safe_factor(t,e);let a,s;return 0==i?(a=Math.log(o),s=0):(a=Math.log(o/i),s=Math.log(i)),[r,n,a,s]}}Hn.__name__="LogScale";const{_linear_compute_state:kn}=An.prototype;class Mn extends wn{constructor(t){super(t)}get s_compute(){const[t,e]=kn.call(this),n=this.source_range;return r=>t*n.synthetic(r)+e}get s_invert(){const[t,e]=kn.call(this);return n=>(n-e)/t}}var Cn;Mn.__name__="CategoricalScale";class Sn extends yn{constructor(t){super(t)}}Cn=Sn,Sn.__name__="DataRange",Cn.define((({Array:t,AnyRef:e,Or:n,Auto:r})=>({renderers:[n(t(e()),r),[]]})));var En,Vn,On=n(2153);function Pn(t,e){return"auto"==t?e:t??[]}class Dn extends Sn{constructor(t){super(t),this.plots=new Set,this.have_updated_interactively=!1}initialize(){super.initialize(),this._initial_start=isNaN(this.start)?null:this.start,this._initial_end=isNaN(this.end)?null:this.end,this._initial_range_padding=this.range_padding,this._initial_range_padding_units=this.range_padding_units,this._initial_follow=this.follow,this._initial_follow_interval=this.follow_interval,this._initial_default_span=this.default_span,this._plot_bounds=new Map}get min(){return Math.min(this.start,this.end)}get max(){return Math.max(this.start,this.end)}computed_renderers(){const{renderers:t}=this,e=(0,On.Jx)(this.plots,(t=>t.data_renderers));return Pn(0==t.length?"auto":t,[...e])}_compute_plot_bounds(t,e){let n={x0:1/0,y0:1/0,x1:-1/0,y1:-1/0};for(const r of t){const t=e.get(r);null==t||!r.visible&&this.only_visible||(n=ne(n,t))}return n}adjust_bounds_for_aspect(t,e){const n={x0:1/0,y0:1/0,x1:-1/0,y1:-1/0};let r=t.x1-t.x0;r<=0&&(r=1);let i=t.y1-t.y0;i<=0&&(i=1);const o=.5*(t.x1+t.x0),a=.5*(t.y1+t.y0);return r<e*i?r=e*i:i=r/e,n.x1=o+.5*r,n.x0=o-.5*r,n.y1=a+.5*i,n.y0=a-.5*i,n}_compute_min_max(t,e){let n,r,i={x0:1/0,y0:1/0,x1:-1/0,y1:-1/0};for(const[e,n]of t)e.visible&&(i=ne(i,n));return[n,r]=0==e?[i.x0,i.x1]:[i.y0,i.y1],[n,r]}_compute_range(t,e){const n=this.range_padding;let r,i;if(null!=this._initial_start&&(t=this._initial_start),null!=this._initial_end&&(e=this._initial_end),"log"==this.scale_hint){let o,a;if((isNaN(t)||!isFinite(t)||t<=0)&&(t=isNaN(e)||!isFinite(e)||e<=0?.1:e/100,ot.vF.warn(`could not determine minimum data value for log axis, DataRange1d using value ${t}`)),(isNaN(e)||!isFinite(e)||e<=0)&&(e=isNaN(t)||!isFinite(t)||t<=0?10:100*t,ot.vF.warn(`could not determine maximum data value for log axis, DataRange1d using value ${e}`)),e==t)a=this.default_span+.001,o=Math.log10(t);else{let r,i;"percent"==this.range_padding_units?(r=Math.log10(t),i=Math.log10(e),a=(i-r)*(1+n)):(r=Math.log10(t-n),i=Math.log10(e+n),a=i-r),o=(r+i)/2}r=10**(o-a/2),i=10**(o+a/2)}else{let o;o=e==t?this.default_span:"percent"==this.range_padding_units?(e-t)*(1+n):e-t+2*n;const a=(e+t)/2;r=a-o/2,i=a+o/2}let o=1;this.flipped&&([r,i]=[i,r],o=-1);const a=this.follow_interval;return null!=a&&Math.abs(r-i)>a&&("start"==this.follow?i=r+o*a:"end"==this.follow&&(r=i-o*a)),[r,i]}update(t,e,n,r){if(this.have_updated_interactively)return;const i=this.computed_renderers();let o=this._compute_plot_bounds(i,t);null!=r&&(o=this.adjust_bounds_for_aspect(o,r)),this._plot_bounds.set(n,o);const[a,s]=this._compute_min_max(this._plot_bounds.entries(),e);let[l,c]=this._compute_range(a,s);null!=this._initial_start&&("log"==this.scale_hint?this._initial_start>0&&(l=this._initial_start):l=this._initial_start),null!=this._initial_end&&("log"==this.scale_hint?this._initial_end>0&&(c=this._initial_end):c=this._initial_end);let u=!1;"auto"==this.bounds&&(this.setv({bounds:[l,c]},{silent:!0}),u=!0);const[d,h]=[this.start,this.end];if(l!=d||c!=h){const t={};l!=d&&(t.start=l),c!=h&&(t.end=c),this.setv(t),u=!1}u&&this.change.emit()}reset(){this.have_updated_interactively=!1,this.setv({range_padding:this._initial_range_padding,range_padding_units:this._initial_range_padding_units,follow:this._initial_follow,follow_interval:this._initial_follow_interval,default_span:this._initial_default_span},{silent:!0}),this.change.emit()}}En=Dn,Dn.__name__="DataRange1d",En.define((({Boolean:t,Number:e,Nullable:n})=>({start:[e,NaN],end:[e,NaN],range_padding:[e,.1],range_padding_units:[_n.VI,"percent"],flipped:[t,!1],follow:[n(_n.qw),null],follow_interval:[n(e),null],default_span:[e,2],only_visible:[t,!1]}))),En.internal((({Enum:t})=>({scale_hint:[t("log","auto"),"auto"]}))),(0,g.Or)(g.String,(0,g.Tuple)(g.String,g.String),(0,g.Tuple)(g.String,g.String,g.String));const Nn=(0,g.Or)((0,g.Array)(g.String),(0,g.Array)((0,g.Tuple)(g.String,g.String)),(0,g.Array)((0,g.Tuple)(g.String,g.String,g.String)));function Rn(t,e,n=0){const r=new Map;for(let i=0;i<t.length;i++){const o=t[i];if(r.has(o))throw new Error(`duplicate factor or subfactor: ${o}`);r.set(o,{value:.5+i*(1+e)+n})}return[r,(t.length-1)*e]}function In(t,e,n,r=0){const i=new Map,o=new Map;for(const[e,n]of t){const t=o.get(e)??[];o.set(e,[...t,n])}let a=r,s=0;for(const[t,r]of o){const o=r.length,[l,c]=Rn(r,n,a);s+=c;const u=(0,Rt.cz)(r.map((t=>l.get(t).value)));i.set(t,{value:u/o,mapping:l}),a+=o+e+c}return[i,(o.size-1)*e+s]}class jn extends yn{constructor(t){super(t)}get min(){return this.start}get max(){return this.end}initialize(){super.initialize(),this._init(!0)}connect_signals(){super.connect_signals(),this.connect(this.properties.factors.change,(()=>this.reset())),this.connect(this.properties.factor_padding.change,(()=>this.reset())),this.connect(this.properties.group_padding.change,(()=>this.reset())),this.connect(this.properties.subgroup_padding.change,(()=>this.reset())),this.connect(this.properties.range_padding.change,(()=>this.reset())),this.connect(this.properties.range_padding_units.change,(()=>this.reset()))}reset(){this._init(!1),this.change.emit()}_lookup(t){switch(t.length){case 1:{const[e]=t,n=this._mapping.get(e);return null!=n?n.value:NaN}case 2:{const[e,n]=t,r=this._mapping.get(e);if(null!=r){const t=r.mapping.get(n);if(null!=t)return t.value}return NaN}case 3:{const[e,n,r]=t,i=this._mapping.get(e);if(null!=i){const t=i.mapping.get(n);if(null!=t){const e=t.mapping.get(r);if(null!=e)return e.value}}return NaN}default:(0,_.HB)()}}synthetic(t){if((0,f.Et)(t))return t;if((0,f.Kg)(t))return this._lookup([t]);let e=0;const n=t[t.length-1];return(0,f.Et)(n)&&(e=n,t=t.slice(0,-1)),this._lookup(t)+e}v_synthetic(t){const e=t.length,n=new Jt.mR(e);for(let r=0;r<e;r++)n[r]=this.synthetic(t[r]);return n}_init(t){const{levels:e,mapping:n,tops:r,mids:i,inside_padding:o}=(()=>{if((0,Rt.Si)(this.factors,f.Kg)){const t=this.factors,[e,n]=Rn(t,this.factor_padding);return{levels:1,mapping:e,tops:null,mids:null,inside_padding:n}}if((0,Rt.Si)(this.factors,(t=>(0,f.cy)(t)&&2==t.length&&(0,f.Kg)(t[0])&&(0,f.Kg)(t[1])))){const t=this.factors,[e,n]=In(t,this.group_padding,this.factor_padding),r=[...e.keys()];return{levels:2,mapping:e,tops:r,mids:null,inside_padding:n}}if((0,Rt.Si)(this.factors,(t=>(0,f.cy)(t)&&3==t.length&&(0,f.Kg)(t[0])&&(0,f.Kg)(t[1])&&(0,f.Kg)(t[2])))){const t=this.factors,[e,n]=function(t,e,n,r,i=0){const o=new Map,a=new Map;for(const[e,n,r]of t){const t=a.get(e)??[];a.set(e,[...t,[n,r]])}let s=i,l=0;for(const[t,i]of a){const a=i.length,[c,u]=In(i,n,r,s);l+=u;const d=(0,Rt.cz)(i.map((([t])=>c.get(t).value)));o.set(t,{value:d/a,mapping:c}),s+=a+e+u}return[o,(a.size-1)*e+l]}(t,this.group_padding,this.subgroup_padding,this.factor_padding),r=[...e.keys()],i=[];for(const[t,n]of e)for(const e of n.mapping.keys())i.push([t,e]);return{levels:3,mapping:e,tops:r,mids:i,inside_padding:n}}(0,_.HB)()})();this._mapping=n,this.tops=r,this.mids=i;let a=0,s=this.factors.length+o;if("percent"==this.range_padding_units){const t=(s-a)*this.range_padding/2;a-=t,s+=t}else a-=this.range_padding,s+=this.range_padding;this.setv({start:a,end:s,levels:e},{silent:t}),"auto"==this.bounds&&this.setv({bounds:[a,s]},{silent:!0})}}var zn,Bn,Fn,$n,Gn,qn,Un,Wn,Zn;Vn=jn,jn.__name__="FactorRange",Vn.define((({Number:t})=>({factors:[Nn,[]],factor_padding:[t,0],subgroup_padding:[t,.8],group_padding:[t,1.4],range_padding:[t,0],range_padding_units:[_n.VI,"percent"],start:[t,NaN],end:[t,NaN]}))),Vn.internal((({Number:t,String:e,Array:n,Tuple:r,Nullable:i})=>({levels:[t],mids:[i(n(r(e,e))),null],tops:[i(n(e)),null]})));class Xn{constructor(t,e){this.x_scale=t,this.y_scale=e,this.x_source=this.x_scale.source_range,this.y_source=this.y_scale.source_range,this.ranges=[this.x_source,this.y_source],this.scales=[this.x_scale,this.y_scale]}map_to_screen(t,e){return[this.x_scale.v_compute(t),this.y_scale.v_compute(e)]}map_from_screen(t,e){return[this.x_scale.v_invert(t),this.y_scale.v_invert(e)]}}Xn.__name__="CoordinateTransform";class Kn extends qt{constructor(t){super(t)}get x_ranges(){return new Map([["default",this.x_source]])}get y_ranges(){return new Map([["default",this.y_source]])}_get_scale(t,e,n){if(t instanceof jn!=e instanceof Mn)throw new Error(`Range ${t.type} is incompatible is Scale ${e.type}`);e instanceof Hn&&t instanceof Dn&&(t.scale_hint="log");const r=e.clone();return r.setv({source_range:t,target_range:n}),r}get_transform(t){const{x_source:e,x_scale:n,x_target:r}=this,i=this._get_scale(e,n,r),{y_source:o,y_scale:a,y_target:s}=this,l=this._get_scale(o,a,s),c=new Yn({source_scale:i,source_range:i.source_range,target_scale:t.x_scale,target_range:t.x_target}),u=new Yn({source_scale:l,source_range:l.source_range,target_scale:t.y_scale,target_range:t.y_target});return new Xn(c,u)}}zn=Kn,Kn.__name__="CoordinateMapping",zn.define((({Ref:t})=>({x_source:[t(yn),()=>new Dn],y_source:[t(yn),()=>new Dn],x_scale:[t(wn),()=>new An],y_scale:[t(wn),()=>new An],x_target:[t(yn)],y_target:[t(yn)]})));class Yn extends wn{constructor(t){super(t)}get s_compute(){const t=this.source_scale.s_compute,e=this.target_scale.s_compute;return n=>e(t(n))}get s_invert(){const t=this.source_scale.s_invert,e=this.target_scale.s_invert;return n=>t(e(n))}compute(t){return this.s_compute(t)}v_compute(t){const{s_compute:e}=this;return(0,bn.Tj)(t,e)}invert(t){return this.s_invert(t)}v_invert(t){const{s_invert:e}=this;return(0,bn.Tj)(t,e)}}Bn=Yn,Yn.__name__="CompositeScale",Bn.internal((({Ref:t})=>({source_scale:[t(wn)],target_scale:[t(wn)]})));class Jn extends qt{constructor(t){super(t)}}Fn=Jn,Jn.__name__="RendererGroup",Fn.define((({Boolean:t})=>({visible:[t,!0]})));class tr extends Kt{get coordinates(){const{_coordinates:t}=this;return null!=t?t:this._coordinates=this._initialize_coordinates()}initialize(){super.initialize(),this.visuals=new Qn(this),this.needs_webgl_blit=!1}connect_signals(){super.connect_signals();const{group:t}=this.model;null!=t&&this.on_change(t.properties.visible,(()=>{this.model.visible=t.visible}));const{x_range_name:e,y_range_name:n}=this.model.properties;this.on_change([e,n],(()=>delete this._coordinates)),this.connect(this.plot_view.frame.change,(()=>delete this._coordinates))}_initialize_coordinates(){const{coordinates:t}=this.model,{frame:e}=this.plot_view;if(null!=t)return t.get_transform(e);{const{x_range_name:t,y_range_name:n}=this.model,r=e.x_scales.get(t),i=e.y_scales.get(n);return new Xn(r,i)}}get plot_view(){return this.parent}get plot_model(){return this.parent.model}get layer(){const{overlays:t,primary:e}=this.canvas;return"overlay"==this.model.level?t:e}get canvas(){return this.plot_view.canvas_view}request_render(){this.request_paint()}request_paint(){this.plot_view.request_paint(this)}request_layout(){this.plot_view.request_layout()}notify_finished(){this.plot_view.notify_finished()}notify_finished_after_paint(){this.plot_view.notify_finished_after_paint()}get needs_clip(){return!1}get has_webgl(){return!1}get displayed(){return this.model.visible}render(){this.displayed&&this._render(),this._has_finished=!0}renderer_view(t){}}tr.__name__="RendererView";class er extends qt{constructor(t){super(t)}}$n=er,er.__name__="Renderer",$n.define((({Boolean:t,String:e,Ref:n,Nullable:r})=>({group:[r(n(Jn)),null],level:[_n.Bw,"image"],visible:[t,!0],x_range_name:[e,"default"],y_range_name:[e,"default"],coordinates:[r(n(Kn)),null]})));class nr extends tr{get_size(){if(this.displayed){const{width:t,height:e}=this._get_size();return{width:Math.round(t),height:Math.round(e)}}return{width:0,height:0}}_get_size(){throw new Error("not implemented")}connect_signals(){super.connect_signals();const t=this.model.properties;this.on_change(t.visible,(()=>{null!=this.layout&&(this.layout.visible=this.model.visible,this.plot_view.request_layout())}))}get needs_clip(){return null==this.layout}serializable_state(){const t=super.serializable_state();return null==this.layout?t:{...t,bbox:this.layout.bbox.box}}}nr.__name__="AnnotationView";class rr extends er{constructor(t){super(t)}}Gn=rr,rr.__name__="Annotation",Gn.override({level:"annotation"});class ir extends qt{constructor(t){super(t)}get_view(){return this.view}get selected_glyph(){return this.selected_glyphs.length>0?this.selected_glyphs[0]:null}add_to_selected_glyphs(t){this.selected_glyphs.push(t)}update(t,e=!0,n="replace"){switch(n){case"replace":this.indices=t.indices,this.line_indices=t.line_indices,this.multiline_indices=t.multiline_indices,this.image_indices=t.image_indices,this.view=t.view,this.selected_glyphs=t.selected_glyphs;break;case"append":this.update_through_union(t);break;case"intersect":this.update_through_intersection(t);break;case"subtract":this.update_through_subtraction(t)}}clear(){this.indices=[],this.line_indices=[],this.multiline_indices={},this.image_indices=[],this.view=null,this.selected_glyphs=[]}map(t){return new ir({...this.attributes,indices:this.indices.map(t),multiline_indices:(0,Q.Wh)((0,Q.jO)(this.multiline_indices).map((([e,n])=>[t(Number(e)),n]))),image_indices:this.image_indices.map((e=>({...e,index:t(e.index)})))})}is_empty(){return 0==this.indices.length&&0==this.line_indices.length&&0==this.image_indices.length}update_through_union(t){this.indices=(0,Rt.KC)(this.indices,t.indices),this.selected_glyphs=(0,Rt.KC)(t.selected_glyphs,this.selected_glyphs),this.line_indices=(0,Rt.KC)(t.line_indices,this.line_indices),this.view=t.view,this.multiline_indices=(0,Q.h1)(t.multiline_indices,this.multiline_indices)}update_through_intersection(t){this.indices=(0,Rt.E$)(this.indices,t.indices),this.selected_glyphs=(0,Rt.KC)(t.selected_glyphs,this.selected_glyphs),this.line_indices=(0,Rt.KC)(t.line_indices,this.line_indices),this.view=t.view,this.multiline_indices=(0,Q.h1)(t.multiline_indices,this.multiline_indices)}update_through_subtraction(t){this.indices=(0,Rt.iv)(this.indices,t.indices),this.selected_glyphs=(0,Rt.KC)(t.selected_glyphs,this.selected_glyphs),this.line_indices=(0,Rt.KC)(t.line_indices,this.line_indices),this.view=t.view,this.multiline_indices=(0,Q.h1)(t.multiline_indices,this.multiline_indices)}}function or(t){return"GlyphRenderer"==t.model.type}function ar(t){return"GraphRenderer"==t.model.type}qn=ir,ir.__name__="Selection",qn.define((({Int:t,Array:e,Dict:n,Struct:r})=>({indices:[e(t),[]],line_indices:[e(t),[]],multiline_indices:[n(e(t)),{}],image_indices:[e(r({index:t,i:t,j:t,flat_index:t})),[]]}))),qn.internal((({Array:t,AnyRef:e,Nullable:n})=>({selected_glyphs:[t(e()),[]],view:[n(e()),null]})));class sr{constructor(t){this.source=t,this.inspectors=new Map}select(t,e,n,r="replace"){const i=[],o=[];for(const e of t)or(e)?i.push(e):ar(e)&&o.push(e);let a=!1;for(const t of o){const i=t.model.selection_policy.hit_test(e,t);a=a||t.model.selection_policy.do_selection(i,t.model,n,r)}if(i.length>0){const t=this.source.selection_policy.hit_test(e,i);a=a||this.source.selection_policy.do_selection(t,this.source,n,r)}return a}inspect(t,e){let n=!1;if(or(t)){const r=t.hit_test(e);if(null!=r){n=!r.is_empty();const i=this.get_or_create_inspector(t.model);i.update(r,!0,"replace"),this.source.setv({inspected:i},{silent:!0}),this.source.inspect.emit([t.model,{geometry:e}])}}else if(ar(t)){const r=t.model.inspection_policy.hit_test(e,t);n=t.model.inspection_policy.do_inspection(r,e,t,!1,"replace")}return n}clear(t){this.source.selected.clear(),null!=t&&this.get_or_create_inspector(t.model).clear()}get_or_create_inspector(t){let e=this.inspectors.get(t);return null==e&&(e=new ir,this.inspectors.set(t,e)),e}}sr.__name__="SelectionManager";class lr extends qt{do_selection(t,e,n,r){return null!=t&&(e.selected.update(t,n,r),e._select.emit(),!e.selected.is_empty())}}lr.__name__="SelectionPolicy";class cr extends lr{hit_test(t,e){const n=[];for(const r of e){const e=r.hit_test(t);null!=e&&n.push(e)}if(n.length>0){const t=n[0];for(const e of n)t.update_through_intersection(e);return t}return null}}cr.__name__="IntersectRenderers";class ur extends lr{hit_test(t,e){const n=[];for(const r of e){const e=r.hit_test(t);null!=e&&n.push(e)}if(n.length>0){const t=n[0];for(const e of n)t.update_through_union(e);return t}return null}}ur.__name__="UnionRenderers";class dr extends qt{constructor(t){super(t)}}Un=dr,dr.__name__="DataSource",Un.define((({Ref:t})=>({selected:[t(ir),()=>new ir]})));class hr extends dr{constructor(t){super(t),this.selection_manager=new sr(this)}get_array(t){let e=this.data[t];return null==e?this.data[t]=e=[]:(0,f.cy)(e)||(this.data[t]=e=Array.from(e)),e}initialize(){super.initialize(),this._select=new T.n2(this,"select"),this.inspect=new T.HN(this,"inspect")}get_column(t){return t in this.data?this.data[t]:null}columns(){return(0,Q.HP)(this.data)}get_length(t=!0){const e=(0,Rt.sb)((0,Q.zu)(this.data).map((t=>(0,Nt.jV)(t)?t.shape[0]:t.length)));switch(e.length){case 0:return null;case 1:return e[0];default:{const n="data source has columns of inconsistent lengths";if(t)return ot.vF.warn(n),e.sort()[0];throw new Error(n)}}}get length(){return this.get_length()??0}clear(){const t={};for(const e of this.columns())t[e]=new this.data[e].constructor(0);this.data=t}}Wn=hr,hr.__name__="ColumnarDataSource",Wn.define((({Ref:t})=>({selection_policy:[t(lr),()=>new ur]}))),Wn.internal((({AnyRef:t})=>({inspected:[t(),()=>new ir]})));class pr extends hr{constructor(t){super(t)}stream(t,e,{sync:n}={}){this.stream_to(this.properties.data,t,e,{sync:n})}patch(t,{sync:e}={}){this.patch_to(this.properties.data,t,{sync:e})}}Zn=pr,pr.__name__="ColumnDataSource",Zn.define((({Any:t,Dict:e,Arrayable:n})=>({data:[e(n(t)),{}]})));var fr=6378137,Qr=.0066943799901413165,Tr=484813681109536e-20,mr=Math.PI/2,gr=.017453292519943295,_r=57.29577951308232,br=Math.PI/4,vr=2*Math.PI,yr={greenwich:0,lisbon:-9.131906111111,paris:2.337229166667,bogota:-74.080916666667,madrid:-3.687938888889,rome:12.452333333333,bern:7.439583333333,jakarta:106.807719444444,ferro:-17.666666666667,brussels:4.367975,stockholm:18.058277777778,athens:23.7163375,oslo:10.722916666667};const xr={ft:{to_meter:.3048},"us-ft":{to_meter:1200/3937}};var wr=/[\s_\-\/\(\)]/g;function Lr(t,e){if(t[e])return t[e];for(var n,r=Object.keys(t),i=e.toLowerCase().replace(wr,""),o=-1;++o<r.length;)if((n=r[o]).toLowerCase().replace(wr,"")===i)return t[n]}function Ar(t){var e,n,r,i={},o=t.split("+").map((function(t){return t.trim()})).filter((function(t){return t})).reduce((function(t,e){var n=e.split("=");return n.push(!0),t[n[0].toLowerCase()]=n[1],t}),{}),a={proj:"projName",datum:"datumCode",rf:function(t){i.rf=parseFloat(t)},lat_0:function(t){i.lat0=t*gr},lat_1:function(t){i.lat1=t*gr},lat_2:function(t){i.lat2=t*gr},lat_ts:function(t){i.lat_ts=t*gr},lon_0:function(t){i.long0=t*gr},lon_1:function(t){i.long1=t*gr},lon_2:function(t){i.long2=t*gr},alpha:function(t){i.alpha=parseFloat(t)*gr},gamma:function(t){i.rectified_grid_angle=parseFloat(t)},lonc:function(t){i.longc=t*gr},x_0:function(t){i.x0=parseFloat(t)},y_0:function(t){i.y0=parseFloat(t)},k_0:function(t){i.k0=parseFloat(t)},k:function(t){i.k0=parseFloat(t)},a:function(t){i.a=parseFloat(t)},b:function(t){i.b=parseFloat(t)},r:function(t){i.a=i.b=parseFloat(t)},r_a:function(){i.R_A=!0},zone:function(t){i.zone=parseInt(t,10)},south:function(){i.utmSouth=!0},towgs84:function(t){i.datum_params=t.split(",").map((function(t){return parseFloat(t)}))},to_meter:function(t){i.to_meter=parseFloat(t)},units:function(t){i.units=t;var e=Lr(xr,t);e&&(i.to_meter=e.to_meter)},from_greenwich:function(t){i.from_greenwich=t*gr},pm:function(t){var e=Lr(yr,t);i.from_greenwich=(e||parseFloat(t))*gr},nadgrids:function(t){"@null"===t?i.datumCode="none":i.nadgrids=t},axis:function(t){var e="ewnsud";3===t.length&&-1!==e.indexOf(t.substr(0,1))&&-1!==e.indexOf(t.substr(1,1))&&-1!==e.indexOf(t.substr(2,1))&&(i.axis=t)},approx:function(){i.approx=!0}};for(e in o)n=o[e],e in a?"function"==typeof(r=a[e])?r(n):i[r]=n:i[e]=n;return"string"==typeof i.datumCode&&"WGS84"!==i.datumCode&&(i.datumCode=i.datumCode.toLowerCase()),i}var Hr=/\s/,kr=/[A-Za-z]/,Mr=/[A-Za-z84_]/,Cr=/[,\]]/,Sr=/[\d\.E\-\+]/;function Er(t){if("string"!=typeof t)throw new Error("not a string");this.text=t.trim(),this.level=0,this.place=0,this.root=null,this.stack=[],this.currentObject=null,this.state=1}function Vr(t,e,n){Array.isArray(e)&&(n.unshift(e),e=null);var r=e?{}:t,i=n.reduce((function(t,e){return Or(e,t),t}),r);e&&(t[e]=i)}function Or(t,e){if(Array.isArray(t)){var n=t.shift();if("PARAMETER"===n&&(n=t.shift()),1===t.length)return Array.isArray(t[0])?(e[n]={},void Or(t[0],e[n])):void(e[n]=t[0]);if(t.length)if("TOWGS84"!==n){if("AXIS"===n)return n in e||(e[n]=[]),void e[n].push(t);var r;switch(Array.isArray(n)||(e[n]={}),n){case"UNIT":case"PRIMEM":case"VERT_DATUM":return e[n]={name:t[0].toLowerCase(),convert:t[1]},void(3===t.length&&Or(t[2],e[n]));case"SPHEROID":case"ELLIPSOID":return e[n]={name:t[0],a:t[1],rf:t[2]},void(4===t.length&&Or(t[3],e[n]));case"PROJECTEDCRS":case"PROJCRS":case"GEOGCS":case"GEOCCS":case"PROJCS":case"LOCAL_CS":case"GEODCRS":case"GEODETICCRS":case"GEODETICDATUM":case"EDATUM":case"ENGINEERINGDATUM":case"VERT_CS":case"VERTCRS":case"VERTICALCRS":case"COMPD_CS":case"COMPOUNDCRS":case"ENGINEERINGCRS":case"ENGCRS":case"FITTED_CS":case"LOCAL_DATUM":case"DATUM":return t[0]=["name",t[0]],void Vr(e,n,t);default:for(r=-1;++r<t.length;)if(!Array.isArray(t[r]))return Or(t,e[n]);return Vr(e,n,t)}}else e[n]=t;else e[n]=!0}else e[t]=!0}function Pr(t){return.017453292519943295*t}function Dr(t){var e=new Er(t).output(),n=e.shift(),r=e.shift();e.unshift(["name",r]),e.unshift(["type",n]);var i={};return Or(e,i),function(t){if("GEOGCS"===t.type?t.projName="longlat":"LOCAL_CS"===t.type?(t.projName="identity",t.local=!0):"object"==typeof t.PROJECTION?t.projName=Object.keys(t.PROJECTION)[0]:t.projName=t.PROJECTION,t.AXIS){for(var e="",n=0,r=t.AXIS.length;n<r;++n){var i=[t.AXIS[n][0].toLowerCase(),t.AXIS[n][1].toLowerCase()];-1!==i[0].indexOf("north")||("y"===i[0]||"lat"===i[0])&&"north"===i[1]?e+="n":-1!==i[0].indexOf("south")||("y"===i[0]||"lat"===i[0])&&"south"===i[1]?e+="s":-1!==i[0].indexOf("east")||("x"===i[0]||"lon"===i[0])&&"east"===i[1]?e+="e":-1===i[0].indexOf("west")&&("x"!==i[0]&&"lon"!==i[0]||"west"!==i[1])||(e+="w")}2===e.length&&(e+="u"),3===e.length&&(t.axis=e)}t.UNIT&&(t.units=t.UNIT.name.toLowerCase(),"metre"===t.units&&(t.units="meter"),t.UNIT.convert&&("GEOGCS"===t.type?t.DATUM&&t.DATUM.SPHEROID&&(t.to_meter=t.UNIT.convert*t.DATUM.SPHEROID.a):t.to_meter=t.UNIT.convert));var o=t.GEOGCS;function a(e){return e*(t.to_meter||1)}"GEOGCS"===t.type&&(o=t),o&&(o.DATUM?t.datumCode=o.DATUM.name.toLowerCase():t.datumCode=o.name.toLowerCase(),"d_"===t.datumCode.slice(0,2)&&(t.datumCode=t.datumCode.slice(2)),"new_zealand_geodetic_datum_1949"!==t.datumCode&&"new_zealand_1949"!==t.datumCode||(t.datumCode="nzgd49"),"wgs_1984"!==t.datumCode&&"world_geodetic_system_1984"!==t.datumCode||("Mercator_Auxiliary_Sphere"===t.PROJECTION&&(t.sphere=!0),t.datumCode="wgs84"),"_ferro"===t.datumCode.slice(-6)&&(t.datumCode=t.datumCode.slice(0,-6)),"_jakarta"===t.datumCode.slice(-8)&&(t.datumCode=t.datumCode.slice(0,-8)),~t.datumCode.indexOf("belge")&&(t.datumCode="rnb72"),o.DATUM&&o.DATUM.SPHEROID&&(t.ellps=o.DATUM.SPHEROID.name.replace("_19","").replace(/[Cc]larke\_18/,"clrk"),"international"===t.ellps.toLowerCase().slice(0,13)&&(t.ellps="intl"),t.a=o.DATUM.SPHEROID.a,t.rf=parseFloat(o.DATUM.SPHEROID.rf,10)),o.DATUM&&o.DATUM.TOWGS84&&(t.datum_params=o.DATUM.TOWGS84),~t.datumCode.indexOf("osgb_1936")&&(t.datumCode="osgb36"),~t.datumCode.indexOf("osni_1952")&&(t.datumCode="osni52"),(~t.datumCode.indexOf("tm65")||~t.datumCode.indexOf("geodetic_datum_of_1965"))&&(t.datumCode="ire65"),"ch1903+"===t.datumCode&&(t.datumCode="ch1903"),~t.datumCode.indexOf("israel")&&(t.datumCode="isr93")),t.b&&!isFinite(t.b)&&(t.b=t.a),[["standard_parallel_1","Standard_Parallel_1"],["standard_parallel_1","Latitude 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r={x:-n.x,y:n.y},i={x:Number.NaN,y:Number.NaN},o=[];t:for(var a=0;a<t.grids.length;a++){var s=t.grids[a];if(o.push(s.name),s.isNull){i=r;break}if(s.mandatory,null!==s.grid)for(var l=s.grid.subgrids,c=0,u=l.length;c<u;c++){var d=l[c],h=(Math.abs(d.del[1])+Math.abs(d.del[0]))/1e4,p=d.ll[0]-h,f=d.ll[1]-h,Q=d.ll[0]+(d.lim[0]-1)*d.del[0]+h,T=d.ll[1]+(d.lim[1]-1)*d.del[1]+h;if(!(f>r.y||p>r.x||T<r.y||Q<r.x||(i=oi(r,e,d),isNaN(i.x))))break t}else if(s.mandatory)return console.log("Unable to find mandatory grid '"+s.name+"'"),-1}return isNaN(i.x)?(console.log("Failed to find a grid shift table for location '"+-r.x*_r+" "+r.y*_r+" tried: '"+o+"'"),-1):(n.x=-i.x,n.y=i.y,0)}function oi(t,e,n){var r={x:Number.NaN,y:Number.NaN};if(isNaN(t.x))return r;var i={x:t.x,y:t.y};i.x-=n.ll[0],i.y-=n.ll[1],i.x=Br(i.x-Math.PI)+Math.PI;var o=ai(i,n);if(e){if(isNaN(o.x))return r;o.x=i.x-o.x,o.y=i.y-o.y;var a,s,l=9;do{if(s=ai(o,n),isNaN(s.x)){console.log("Inverse grid shift iteration failed, presumably at grid 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0!==n.z)switch(0===o?(r=a,i=-1!=="ew".indexOf(t.axis[o])?"x":"y"):1===o?(r=s,i=-1!=="ns".indexOf(t.axis[o])?"y":"x"):(r=l,i="z"),t.axis[o]){case"e":case"n":c[i]=r;break;case"w":case"s":c[i]=-r;break;case"u":void 0!==n[i]&&(c.z=r);break;case"d":void 0!==n[i]&&(c.z=-r);break;default:return null}return c}function li(t){if("function"==typeof Number.isFinite){if(Number.isFinite(t))return;throw new TypeError("coordinates must be finite numbers")}if("number"!=typeof t||t!=t||!isFinite(t))throw new TypeError("coordinates must be finite numbers")}function ci(t,e,n,r){var i,o,a;Array.isArray(n)?(a={x:(o=n)[0],y:o[1]},o.length>2&&(a.z=o[2]),o.length>3&&(a.m=o[3]),n=a):n={x:n.x,y:n.y,z:n.z,m:n.m};var s=void 0!==n.z;if(function(t){li(t.x),li(t.y)}(n),t.datum&&e.datum&&function(t,e){return(1===t.datum.datum_type||2===t.datum.datum_type||3===t.datum.datum_type)&&"WGS84"!==e.datumCode||(1===e.datum.datum_type||2===e.datum.datum_type||3===e.datum.datum_type)&&"WGS84"!==t.datumCode}(t,e)&&(n=ci(t,i=new 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3===e.datum_type&&(o=fr,a=6356752.314,s=Qr),i!==s||r!==o||ri(t.datum_type)||ri(e.datum_type)?(n=function(t,e,n){var r,i,o,a,s=t.x,l=t.y,c=t.z?t.z:0;if(l<-mr&&l>-1.001*mr)l=-mr;else if(l>mr&&l<1.001*mr)l=mr;else{if(l<-mr)return{x:-1/0,y:-1/0,z:t.z};if(l>mr)return{x:1/0,y:1/0,z:t.z}}return s>Math.PI&&(s-=2*Math.PI),i=Math.sin(l),a=Math.cos(l),o=i*i,{x:((r=n/Math.sqrt(1-e*o))+c)*a*Math.cos(s),y:(r+c)*a*Math.sin(s),z:(r*(1-e)+c)*i}}(n,i,r),ri(t.datum_type)&&(n=function(t,e,n){if(1===e)return{x:t.x+n[0],y:t.y+n[1],z:t.z+n[2]};if(2===e){var r=n[0],i=n[1],o=n[2],a=n[3],s=n[4],l=n[5],c=n[6];return{x:c*(t.x-l*t.y+s*t.z)+r,y:c*(l*t.x+t.y-a*t.z)+i,z:c*(-s*t.x+a*t.y+t.z)+o}}}(n,t.datum_type,t.datum_params)),ri(e.datum_type)&&(n=function(t,e,n){if(1===e)return{x:t.x-n[0],y:t.y-n[1],z:t.z-n[2]};if(2===e){var r=n[0],i=n[1],o=n[2],a=n[3],s=n[4],l=n[5],c=n[6],u=(t.x-r)/c,d=(t.y-i)/c,h=(t.z-o)/c;return{x:u+l*d-s*h,y:-l*u+d+a*h,z:s*u-a*d+h}}}(n,e.datum_type,e.datum_params)),n=function(t,e,n,r){var i,o,a,s,l,c,u,d,h,p,f,Q,T,m,g,_=t.x,b=t.y,v=t.z?t.z:0;if(i=Math.sqrt(_*_+b*b),o=Math.sqrt(_*_+b*b+v*v),i/n<1e-12){if(m=0,o/n<1e-12)return g=-r,{x:t.x,y:t.y,z:t.z}}else m=Math.atan2(b,_);a=v/o,d=(s=i/o)*(1-e)*(l=1/Math.sqrt(1-e*(2-e)*s*s)),h=a*l,T=0;do{T++,c=e*(u=n/Math.sqrt(1-e*h*h))/(u+(g=i*d+v*h-u*(1-e*h*h))),Q=(f=a*(l=1/Math.sqrt(1-c*(2-c)*s*s)))*d-(p=s*(1-c)*l)*h,d=p,h=f}while(Q*Q>1e-24&&T<30);return{x:m,y:Math.atan(f/Math.abs(p)),z:g}}(n,s,o,a),3!==e.datum_type||0===ii(e,!0,n)?n:void 0):n}(t.datum,e.datum,n))return e.from_greenwich&&(n={x:n.x-e.from_greenwich,y:n.y,z:n.z||0}),"longlat"===e.projName?n={x:n.x*_r,y:n.y*_r,z:n.z||0}:(n=e.forward(n),e.to_meter&&(n={x:n.x/e.to_meter,y:n.y/e.to_meter,z:n.z||0})),r&&"enu"!==e.axis?si(e,!0,n):(n&&!s&&delete n.z,n)}var ui=ni("WGS84");function di(t,e,n,r){var i,o,a;return Array.isArray(n)?(i=ci(t,e,n,r)||{x:NaN,y:NaN},n.length>2?void 0!==t.name&&"geocent"===t.name||void 0!==e.name&&"geocent"===e.name?"number"==typeof i.z?[i.x,i.y,i.z].concat(n.slice(3)):[i.x,i.y,n[2]].concat(n.slice(3)):[i.x,i.y].concat(n.slice(2)):[i.x,i.y]):(o=ci(t,e,n,r),2===(a=Object.keys(n)).length||a.forEach((function(r){if(void 0!==t.name&&"geocent"===t.name||void 0!==e.name&&"geocent"===e.name){if("x"===r||"y"===r||"z"===r)return}else if("x"===r||"y"===r)return;o[r]=n[r]})),o)}function hi(t){return t instanceof ni?t:t.oProj?t.oProj:ni(t)}const pi=new ni("GOOGLE"),fi=function(t,e,n){t=hi(t);var r,i=!1;return void 0===e?(e=t,t=ui,i=!0):(void 0!==e.x||Array.isArray(e))&&(n=e,e=t,t=ui,i=!0),e=hi(e),n?di(t,e,n):(r={forward:function(n,r){return di(t,e,n,r)},inverse:function(n,r){return di(e,t,n,r)}},i&&(r.oProj=e),r)}(new ni("WGS84"),pi),Qi=(t,e)=>isFinite(t)&&isFinite(e)?fi.forward([t,e]):[NaN,NaN],Ti=(t,e)=>isFinite(t)&&isFinite(e)?fi.inverse([t,e]):[NaN,NaN],mi={lon:[-20026376.39,20026376.39],lat:[-20048966.1,20048966.1]},gi={lon:[-180,180],lat:[-85.06,85.06]},{min:_i,max:bi}=Math;function vi(t,e){const[n,r]=gi[e];return n<t&&t<r}var yi,xi,wi,Li,Ai,Hi,ki,Mi;!function(t){function e(t,e,n,r){const i=_i(t.length,e.length);n=n??t,r=r??e;for(let o=0;o<i;o++){const i=t[o],a=e[o],[s,l]=Qi(i,a);n[o]=s,r[o]=l}}t.project_xy=e,t.project_xsys=function(t,n,r,i){const o=_i(t.length,n.length);r=r??t,i=i??n;for(let a=0;a<o;a++)e(t[a],n[a],r[a],i[a])}}(yi||(yi={}));class Ci extends nr{constructor(){super(...arguments),this._initial_set_data=!1}connect_signals(){super.connect_signals();const t=()=>{this.set_data(this.model.source),this._rerender()};this.connect(this.model.change,t),this.connect(this.model.source.streaming,t),this.connect(this.model.source.patching,t),this.connect(this.model.source.change,t)}_rerender(){this.request_render()}set_data(t){const e=this;for(const n of this.model)if(n instanceof m.Pz||n instanceof m._n)if(n instanceof m.PR){const r=n.array(t);e[`_${n.attr}`]=r}else{const r=n.uniform(t);e[`${n.attr}`]=r}this.plot_model.use_map&&(null!=e._x&&yi.project_xy(e._x,e._y),null!=e._xs&&yi.project_xsys(e._xs,e._ys));for(const t of this.visuals)t.update()}_render(){this._initial_set_data||(this.set_data(this.model.source),this._initial_set_data=!0),this.map_data(),this.paint(this.layer.ctx)}}Ci.__name__="DataAnnotationView";class Si extends rr{constructor(t){super(t)}}xi=Si,Si.__name__="DataAnnotation",xi.define((({Ref:t})=>({source:[t(hr),()=>new pr]})));class Ei extends Kt{initialize(){super.initialize(),this.visuals=new Qn(this)}request_render(){this.parent.request_render()}get canvas(){return this.parent.canvas}set_data(t,e){const n=this;for(const r of this.model){if(!(r instanceof m.Pz||r instanceof m._n))continue;const i=r.uniform(t).select(e);n[`${r.attr}`]=i}}}Ei.__name__="MarkingView";class Vi extends qt{constructor(t){super(t)}}wi=Vi,Vi.__name__="Marking",wi.define((({})=>({})));class Oi extends Ei{}Oi.__name__="ArrowHeadView";class Pi extends Vi{constructor(t){super(t)}}Li=Pi,Pi.__name__="ArrowHead",Li.define((()=>({size:[m.fY,25]})));class Di extends Oi{clip(t,e){this.visuals.line.set_vectorize(t,e);const n=this.size.get(e);t.moveTo(.5*n,n),t.lineTo(.5*n,-2),t.lineTo(-.5*n,-2),t.lineTo(-.5*n,n),t.lineTo(0,0),t.lineTo(.5*n,n)}render(t,e){const n=this.size.get(e);t.beginPath(),t.moveTo(.5*n,n),t.lineTo(0,0),t.lineTo(-.5*n,n),this.visuals.line.apply(t,e)}}Di.__name__="OpenHeadView";class Ni extends Pi{constructor(t){super(t)}}Ai=Ni,Ni.__name__="OpenHead",Ai.prototype.default_view=Di,Ai.mixins(Ke.UT);class Ri extends Oi{clip(t,e){this.visuals.line.set_vectorize(t,e);const n=this.size.get(e);t.moveTo(.5*n,n),t.lineTo(.5*n,-2),t.lineTo(-.5*n,-2),t.lineTo(-.5*n,n),t.lineTo(.5*n,n)}render(t,e){const n=this.size.get(e);t.beginPath(),t.moveTo(.5*n,n),t.lineTo(0,0),t.lineTo(-.5*n,n),t.closePath(),this.visuals.fill.apply(t,e),this.visuals.line.apply(t,e)}}Ri.__name__="NormalHeadView";class Ii extends Pi{constructor(t){super(t)}}Hi=Ii,Ii.__name__="NormalHead",Hi.prototype.default_view=Ri,Hi.mixins([Ke.UT,Ke.H_]),Hi.override({fill_color:"black"});class ji extends Oi{clip(t,e){this.visuals.line.set_vectorize(t,e);const n=this.size.get(e);t.moveTo(.5*n,n),t.lineTo(.5*n,-2),t.lineTo(-.5*n,-2),t.lineTo(-.5*n,n),t.lineTo(0,.5*n),t.lineTo(.5*n,n)}render(t,e){const n=this.size.get(e);t.beginPath(),t.moveTo(.5*n,n),t.lineTo(0,0),t.lineTo(-.5*n,n),t.lineTo(0,.5*n),t.closePath(),this.visuals.fill.apply(t,e),this.visuals.line.apply(t,e)}}ji.__name__="VeeHeadView";class zi extends Pi{constructor(t){super(t)}}ki=zi,zi.__name__="VeeHead",ki.prototype.default_view=ji,ki.mixins([Ke.UT,Ke.H_]),ki.override({fill_color:"black"});class Bi extends Oi{render(t,e){const n=this.size.get(e);t.beginPath(),t.moveTo(.5*n,0),t.lineTo(-.5*n,0),this.visuals.line.apply(t,e)}clip(t,e){}}Bi.__name__="TeeHeadView";class Fi extends Pi{constructor(t){super(t)}}Mi=Fi,Fi.__name__="TeeHead",Mi.prototype.default_view=Bi,Mi.mixins(Ke.UT);var $i,Gi=n(9669);class qi extends Ci{*children(){yield*super.children();const{start:t,end:e}=this;null!=t&&(yield t),null!=e&&(yield e)}async lazy_initialize(){await super.lazy_initialize();const{start:t,end:e}=this.model;null!=t&&(this.start=await $e(t,{parent:this})),null!=e&&(this.end=await $e(e,{parent:this}))}set_data(t){super.set_data(t);const e=Jt.et.all_set(this._x_start.length);this.start?.set_data(t,e),this.end?.set_data(t,e)}remove(){this.start?.remove(),this.end?.remove(),super.remove()}map_data(){const{frame:t}=this.plot_view,[e,n]=(()=>{switch(this.model.start_units){case"canvas":return[new Jt.mR(this._x_start),new Jt.mR(this._y_start)];case"screen":return[t.bbox.xview.v_compute(this._x_start),t.bbox.yview.v_compute(this._y_start)];case"data":return[this.coordinates.x_scale.v_compute(this._x_start),this.coordinates.y_scale.v_compute(this._y_start)]}})(),[r,i]=(()=>{switch(this.model.end_units){case"canvas":return[new Jt.mR(this._x_end),new Jt.mR(this._y_end)];case"screen":return[t.bbox.xview.v_compute(this._x_end),t.bbox.yview.v_compute(this._y_end)];case"data":return[this.coordinates.x_scale.v_compute(this._x_end),this.coordinates.y_scale.v_compute(this._y_end)]}})();this._sx_start=e,this._sy_start=n,this._sx_end=r,this._sy_end=i;const o=e.length,a=this._angles=new Jt.mR(o);for(let t=0;t<o;t++)a[t]=Math.PI/2+(0,Gi.FP)([e[t],n[t]],[r[t],i[t]])}paint(t){const{start:e,end:n}=this,{_sx_start:r,_sy_start:i,_sx_end:o,_sy_end:a,_angles:s}=this,{x:l,y:c,width:u,height:d}=this.plot_view.frame.bbox;for(let h=0,p=r.length;h<p;h++)null!=n&&(t.save(),t.translate(o[h],a[h]),t.rotate(s[h]),n.render(t,h),t.restore()),null!=e&&(t.save(),t.translate(r[h],i[h]),t.rotate(s[h]+Math.PI),e.render(t,h),t.restore()),this.visuals.line.doit&&(t.save(),null==e&&null==n||(t.beginPath(),t.rect(l,c,u,d),null!=n&&(t.save(),t.translate(o[h],a[h]),t.rotate(s[h]),n.clip(t,h),t.restore()),null!=e&&(t.save(),t.translate(r[h],i[h]),t.rotate(s[h]+Math.PI),e.clip(t,h),t.restore()),t.closePath(),t.clip()),t.beginPath(),t.moveTo(r[h],i[h]),t.lineTo(o[h],a[h]),this.visuals.line.apply(t,h),t.restore())}}qi.__name__="ArrowView";class Ui extends Si{constructor(t){super(t)}}$i=Ui,Ui.__name__="Arrow",$i.prototype.default_view=qi,$i.mixins(Ke.UT),$i.define((({Ref:t,Nullable:e})=>({x_start:[m.up,{field:"x_start"}],y_start:[m.fZ,{field:"y_start"}],start_units:[_n.yx,"data"],start:[e(t(Pi)),null],x_end:[m.up,{field:"x_end"}],y_end:[m.fZ,{field:"y_end"}],end_units:[_n.yx,"data"],end:[e(t(Pi)),()=>new Ni]})));const{min:Wi,max:Zi}=Math;class Xi{constructor(t={}){this.width=null!=t.width?t.width:0,this.height=null!=t.height?t.height:0}bounded_to({width:t,height:e}){return new Xi({width:this.width==1/0&&null!=t?t:this.width,height:this.height==1/0&&null!=e?e:this.height})}expanded_to({width:t,height:e}){return new Xi({width:t!=1/0?Zi(this.width,t):this.width,height:e!=1/0?Zi(this.height,e):this.height})}expand_to({width:t,height:e}){this.width=Zi(this.width,t),this.height=Zi(this.height,e)}narrowed_to({width:t,height:e}){return new Xi({width:Wi(this.width,t),height:Wi(this.height,e)})}narrow_to({width:t,height:e}){this.width=Wi(this.width,t),this.height=Wi(this.height,e)}grow_by({left:t,right:e,top:n,bottom:r}){const i=this.width+t+e,o=this.height+n+r;return new Xi({width:i,height:o})}shrink_by({left:t,right:e,top:n,bottom:r}){const i=Zi(this.width-t-e,0),o=Zi(this.height-n-r,0);return new Xi({width:i,height:o})}map(t,e){return new Xi({width:t(this.width),height:(null!=e?e:t)(this.height)})}}Xi.__name__="Sizeable";const Ki=(0,g.Enum)("fixed","fit","min","max"),{min:Yi,max:Ji,round:to}=Math;class eo{constructor(){this.absolute=!1,this._bbox=new re,this._inner_bbox=new re,this._dirty=!1,this._handlers=[]}*[Symbol.iterator](){}get bbox(){return this._bbox}get inner_bbox(){return this._inner_bbox}get sizing(){return this._sizing}get visible(){return this._sizing.visible}set visible(t){this._sizing.visible!=t&&(this._sizing.visible=t,this._dirty=!0)}set_sizing(t={}){const e=t.width_policy??"fit",n=t.width,r=t.min_width,i=t.max_width,o=t.height_policy??"fit",a=t.height,s=t.min_height,l=t.max_height,c=t.aspect,u=t.margin??{top:0,right:0,bottom:0,left:0},d=t.visible??!0,h=t.halign??"start",p=t.valign??"start";this._sizing={width_policy:e,min_width:r,width:n,max_width:i,height_policy:o,min_height:s,height:a,max_height:l,aspect:c,margin:u,visible:d,halign:h,valign:p,size:{width:n,height:a}},this._init()}_init(){}_set_geometry(t,e){this._bbox=t,this._inner_bbox=e}set_geometry(t,e){const{fixup_geometry:n}=this;null!=n&&([t,e]=n(t,e)),this._set_geometry(t,e??t);for(const t of this._handlers)t(this._bbox,this._inner_bbox)}on_resize(t){this._handlers.push(t)}is_width_expanding(){return"max"==this.sizing.width_policy}is_height_expanding(){return"max"==this.sizing.height_policy}apply_aspect(t,{width:e,height:n}){const{aspect:r}=this.sizing;if(null!=r){const{width_policy:i,height_policy:o}=this.sizing,a=(t,e)=>{const n={max:4,fit:3,min:2,fixed:1};return n[t]>n[e]};if("fixed"!=i&&"fixed"!=o)if(i==o){const i=e,o=to(e/r),a=to(n*r),s=n;Math.abs(t.width-i)+Math.abs(t.height-o)<=Math.abs(t.width-a)+Math.abs(t.height-s)?(e=i,n=o):(e=a,n=s)}else a(i,o)?n=to(e/r):e=to(n*r);else"fixed"==i?n=to(e/r):"fixed"==o&&(e=to(n*r))}return{width:e,height:n}}measure(t){if(!this.sizing.visible)return{width:0,height:0};const e=t=>"fixed"==this.sizing.width_policy&&null!=this.sizing.width?this.sizing.width:t,n=t=>"fixed"==this.sizing.height_policy&&null!=this.sizing.height?this.sizing.height:t,r=new Xi(t).shrink_by(this.sizing.margin).map(e,n),i=this._measure(r),o=this.clip_size(i,r),a=e(o.width),s=n(o.height),l=this.apply_aspect(r,{width:a,height:s});return{...i,...l}}compute(t={}){const e=this.measure({width:null!=t.width&&this.is_width_expanding()?t.width:1/0,height:null!=t.height&&this.is_height_expanding()?t.height:1/0}),{width:n,height:r}=e,i=new re({left:0,top:0,width:n,height:r});let o;if(null!=e.inner){const{left:t,top:i,right:a,bottom:s}=e.inner;o=new re({left:t,top:i,right:n-a,bottom:r-s})}this.set_geometry(i,o)}get xview(){return this.bbox.xview}get yview(){return this.bbox.yview}clip_size(t,e){function n(t,e,n,r){return null==n?n=0:(0,f.Et)(n)||(n=Math.round(n.percent*e)),null==r?r=1/0:(0,f.Et)(r)||(r=Math.round(r.percent*e)),Ji(n,Yi(t,r))}return{width:n(t.width,e.width,this.sizing.min_width,this.sizing.max_width),height:n(t.height,e.height,this.sizing.min_height,this.sizing.max_height)}}has_size_changed(){const{_dirty:t}=this;return this._dirty=!1,t}}eo.__name__="Layoutable";class no extends eo{_measure(t){const e=this._content_size(),n=t.bounded_to(this.sizing.size).bounded_to(e);return{width:(()=>{switch(this.sizing.width_policy){case"fixed":return null!=this.sizing.width?this.sizing.width:e.width;case"min":return e.width;case"fit":return n.width;case"max":return Math.max(e.width,n.width)}})(),height:(()=>{switch(this.sizing.height_policy){case"fixed":return null!=this.sizing.height?this.sizing.height:e.height;case"min":return e.height;case"fit":return n.height;case"max":return Math.max(e.height,n.height)}})()}}}no.__name__="ContentLayoutable";const ro=Math.PI/2,io={above:{parallel:0,normal:-ro,horizontal:0,vertical:-ro},below:{parallel:0,normal:ro,horizontal:0,vertical:ro},left:{parallel:-ro,normal:0,horizontal:0,vertical:-ro},right:{parallel:ro,normal:0,horizontal:0,vertical:ro}},oo={above:{parallel:"bottom",normal:"center",horizontal:"bottom",vertical:"center"},below:{parallel:"top",normal:"center",horizontal:"top",vertical:"center"},left:{parallel:"bottom",normal:"center",horizontal:"center",vertical:"bottom"},right:{parallel:"bottom",normal:"center",horizontal:"center",vertical:"bottom"}},ao={above:{parallel:"center",normal:"left",horizontal:"center",vertical:"left"},below:{parallel:"center",normal:"left",horizontal:"center",vertical:"left"},left:{parallel:"center",normal:"right",horizontal:"right",vertical:"center"},right:{parallel:"center",normal:"left",horizontal:"left",vertical:"center"}},so={above:"right",below:"left",left:"right",right:"left"},lo={above:"left",below:"right",left:"right",right:"left"};class co{constructor(t){this.side=t}get dimension(){return"above"==this.side||"below"==this.side?0:1}get normals(){switch(this.side){case"above":return[0,-1];case"below":return[0,1];case"left":return[-1,0];case"right":return[1,0]}}get orientation(){return this.is_horizontal?"horizontal":"vertical"}get is_horizontal(){return 0==this.dimension}get is_vertical(){return 1==this.dimension}get_label_text_heuristics(t){const{side:e}=this;return(0,f.Kg)(t)?{vertical_align:oo[e][t],align:ao[e][t]}:{vertical_align:"center",align:(t<0?so:lo)[e]}}get_label_angle_heuristic(t){return(0,f.Kg)(t)?io[this.side][t]:-t}}co.__name__="Panel";class uo extends no{constructor(t,e,n=!1){super(),this.panel=t,this.get_size=e,this.rotate=n,this.panel.is_horizontal?this.set_sizing({width_policy:"max",height_policy:"fixed"}):this.set_sizing({width_policy:"fixed",height_policy:"max"})}_content_size(){const{width:t,height:e}=this.get_size();return!this.rotate||this.panel.is_horizontal?new Xi({width:t,height:e}):new Xi({width:e,height:t})}has_size_changed(){const{width:t,height:e}=this._content_size();return this.panel.is_horizontal?this.bbox.height!=e:this.bbox.width!=t}}var ho;uo.__name__="SideLayout";class po extends Kt{}po.__name__="BaseTextView";class fo extends qt{constructor(t){super(t)}}ho=fo,fo.__name__="BaseText",ho.define((({String:t})=>({text:[t]})));class Qo{constructor(t,e={}){this.image=new Image,this._finished=!1;const{attempts:n=1,timeout:r=1}=e;this.promise=new Promise(((i,o)=>{this.image.crossOrigin="anonymous";let a=0;this.image.onerror=()=>{if(++a==n){const r=`unable to load ${t} image after ${n} attempts`;if(ot.vF.warn(r),null==this.image.crossOrigin)return void(null!=e.failed&&e.failed());ot.vF.warn(`attempting to load ${t} without a cross origin policy`),this.image.crossOrigin=null,a=0}setTimeout((()=>this.image.src=t),r)},this.image.onload=()=>{this._finished=!0,null!=e.loaded&&e.loaded(this.image),i(this.image)},this.image.src=t}))}get finished(){return this._finished}}Qo.__name__="ImageLoader";const To=(()=>{try{return"undefined"!=typeof OffscreenCanvas&&null!=new OffscreenCanvas(0,0).getContext("2d")}catch{return!1}})()?(t,e)=>new OffscreenCanvas(t,e):(t,e)=>{const n=document.createElement("canvas");return n.width=t,n.height=e,n},mo=(()=>{const t=To(0,0).getContext("2d");return e=>{t.font=e;const n=t.measureText("M"),r=t.measureText("x"),i=t.measureText("ÅŚg|"),o=i.fontBoundingBoxAscent,a=i.fontBoundingBoxDescent;if((0,f.Z3)(o)&&(0,f.Z3)(a))return{height:o+a,ascent:o,descent:a,cap_height:n.actualBoundingBoxAscent,x_height:r.actualBoundingBoxAscent};const s=i.actualBoundingBoxAscent,l=i.actualBoundingBoxDescent;if((0,f.Z3)(s)&&(0,f.Z3)(l))return{height:s+l,ascent:s,descent:l,cap_height:n.actualBoundingBoxAscent,x_height:r.actualBoundingBoxAscent};(0,_.HB)()}})(),go=(()=>{const t=document.createElement("canvas"),e=t.getContext("2d");let n=-1,r=-1;return(i,o=1)=>{e.font=i;const{width:a}=e.measureText("M"),s=a*o,l=Math.ceil(s),c=Math.ceil(2*s),u=Math.ceil(1.5*s);n<l&&(n=l,t.width=l),r<c&&(r=c,t.height=c),e.save(),e.scale(o,o),e.fillStyle="#f00",e.fillRect(0,0,l,c);const d=t=>{let e=0;for(let n=0;n<=u;n++)for(let r=0;r<l;r++,e+=4)if(255!=t[e])return u-n;return 0};e.font=i,e.fillStyle="#000";for(const t of"xa")e.fillText(t,0,u/o);const{data:h}=e.getImageData(0,0,l,c),p=d(h)/o;for(const t of"ASQ")e.fillText(t,0,u/o);const{data:f}=e.getImageData(0,0,l,c),Q=d(f)/o;for(const t of"ÅŚgy")e.fillText(t,0,u/o);const{data:T}=e.getImageData(0,0,l,c),m=d(T)/o,g=(t=>{let e=t.length-4;for(let n=c;n>=u;n--)for(let r=0;r<l;r++,e-=4)if(255!=t[e])return n-u;return 0})(T)/o;return e.restore(),{height:m+g,ascent:m,cap_height:Q,x_height:p,descent:g}}})(),_o=(()=>{try{return mo("normal 10px sans-serif"),mo}catch{return go}})(),bo=new Map;function vo(t){let e=bo.get(t);if(null==e){const n=document.fonts.check(t);e={font:_o(t)},n&&bo.set(t,e)}return e.font}function yo(t){const e=t.match(/^\s*(\d+(\.\d+)?)(\w+)\s*$/);if(null!=e){const[,t,,n]=e,r=Number(t);if(isFinite(r))return{value:r,unit:n}}return null}const{sin:xo,cos:wo}=Math;class Lo{constructor(t=1,e=0,n=0,r=1,i=0,o=0){this.a=t,this.b=e,this.c=n,this.d=r,this.e=i,this.f=o}toString(){const{a:t,b:e,c:n,d:r,e:i,f:o}=this;return`matrix(${t}, ${e}, ${n}, ${r}, ${i}, ${o})`}static from_DOMMatrix(t){const{a:e,b:n,c:r,d:i,e:o,f:a}=t;return new Lo(e,n,r,i,o,a)}to_DOMMatrix(){const{a:t,b:e,c:n,d:r,e:i,f:o}=this;return new DOMMatrix([t,e,n,r,i,o])}clone(){const{a:t,b:e,c:n,d:r,e:i,f:o}=this;return new Lo(t,e,n,r,i,o)}get is_identity(){const{a:t,b:e,c:n,d:r,e:i,f:o}=this;return 1==t&&0==e&&0==n&&1==r&&0==i&&0==o}apply_point(t){const[e,n]=this.apply(t.x,t.y);return{x:e,y:n}}apply_rect(t){return{p0:this.apply_point(t.p0),p1:this.apply_point(t.p1),p2:this.apply_point(t.p2),p3:this.apply_point(t.p3)}}apply(t,e){const{a:n,b:r,c:i,d:o,e:a,f:s}=this;return[n*t+i*e+a,r*t+o*e+s]}iv_apply(t,e){const{a:n,b:r,c:i,d:o,e:a,f:s}=this,l=t.length;for(let c=0;c<l;c++){const l=t[c],u=e[c];t[c]=n*l+i*u+a,e[c]=r*l+o*u+s}}transform(t,e,n,r,i,o){const{a,b:s,c:l,d:c,e:u,f:d}=this;return this.a=a*t+l*e,this.c=a*n+l*r,this.e=a*i+l*o+u,this.b=s*t+c*e,this.d=s*n+c*r,this.f=s*i+c*o+d,this}translate(t,e){return this.transform(1,0,0,1,t,e)}scale(t,e){return this.transform(t,0,0,e,0,0)}skew(t,e){return this.transform(1,e,t,1,0,0)}rotate(t){const e=xo(t),n=wo(t);return this.transform(n,e,-e,n,0,0)}rotate_ccw(t){return this.rotate(-t)}translate_x(t){return this.translate(t,0)}translate_y(t){return this.translate(0,t)}flip(){return this.scale(-1,-1)}flip_x(){return this.scale(1,-1)}flip_y(){return this.scale(-1,1)}}Lo.__name__="AffineTransform";const Ao=(()=>{const t=document.createElement("canvas").getContext("2d");let e="";return(n,r)=>(r!=e&&(e=r,t.font=r),t.measureText(n).width)})();class Ho{constructor(){this._position={sx:0,sy:0},this.font_size_scale=1,this.align="left",this._base_font_size=13,this._x_anchor="left",this._y_anchor="center"}set base_font_size(t){null!=t&&(this._base_font_size=t)}get base_font_size(){return this._base_font_size}set position(t){this._position=t}get position(){return this._position}infer_text_height(){return"ascent_descent"}bbox(){const{p0:t,p1:e,p2:n,p3:r}=this.rect(),i=Math.min(t.x,e.x,n.x,r.x),o=Math.min(t.y,e.y,n.y,r.y),a=Math.max(t.x,e.x,n.x,r.x),s=Math.max(t.y,e.y,n.y,r.y);return new re({left:i,right:a,top:o,bottom:s})}size(){const{width:t,height:e}=this._size(),{angle:n}=this;if(null==n||0==n)return{width:t,height:e};{const r=Math.cos(Math.abs(n)),i=Math.sin(Math.abs(n));return{width:Math.abs(t*r+e*i),height:Math.abs(t*i+e*r)}}}rect(){const t=this._rect(),{angle:e}=this;if(null==e||0==e)return t;{const{sx:n,sy:r}=this.position,i=new Lo;return i.translate(n,r),i.rotate(e),i.translate(-n,-r),i.apply_rect(t)}}paint_rect(t){const{p0:e,p1:n,p2:r,p3:i}=this.rect();t.save(),t.strokeStyle="red",t.lineWidth=1,t.beginPath();const{round:o}=Math;t.moveTo(o(e.x),o(e.y)),t.lineTo(o(n.x),o(n.y)),t.lineTo(o(r.x),o(r.y)),t.lineTo(o(i.x),o(i.y)),t.closePath(),t.stroke(),t.restore()}paint_bbox(t){const{x:e,y:n,width:r,height:i}=this.bbox();t.save(),t.strokeStyle="blue",t.lineWidth=1,t.beginPath();const{round:o}=Math;t.moveTo(o(e),o(n)),t.lineTo(o(e),o(n+i)),t.lineTo(o(e+r),o(n+i)),t.lineTo(o(e+r),o(n)),t.closePath(),t.stroke(),t.restore()}}Ho.__name__="GraphicsBox";class ko extends Ho{constructor({text:t}){super(),this._visual_align="left",this.text=t}set visuals(t){const e=t.color,n=t.alpha,r=t.outline_color,i=t.font_style;let o=t.font_size;const a=t.font,{font_size_scale:s,base_font_size:l}=this,c=yo(o);if(null!=c){let{value:t,unit:e}=c;t*=s,"em"==e&&l&&(t*=l,e="px"),o=`${t}${e}`}const u=`${i} ${o} ${a}`;this.font=u,this.color=(0,Ye.do)(e,n),this.outline_color=(0,Ye.do)(r,n),this.line_height=t.line_height;const d=t.align;this._visual_align=d,this._x_anchor=d;const h=t.baseline;this._y_anchor=(()=>{switch(h){case"top":return"top";case"middle":return"center";case"bottom":return"bottom";default:return"baseline"}})()}infer_text_height(){if(this.text.includes("\n"))return"ascent_descent";{function t(t){for(const e of new Set(t))if(!("0"<=e&&e<="9"))switch(e){case",":case".":case"+":case"-":case"−":case"e":continue;default:return!1}return!0}return t(this.text)?"cap":"ascent_descent"}}_text_line(t){const e=this.text_height_metric??this.infer_text_height(),n=(()=>{switch(e){case"x":case"x_descent":return t.x_height;case"cap":case"cap_descent":return t.cap_height;case"ascent":case"ascent_descent":return t.ascent}})(),r=(()=>{switch(e){case"x":case"cap":case"ascent":return 0;case"x_descent":case"cap_descent":case"ascent_descent":return t.descent}})();return{height:n+r,ascent:n,descent:r}}get nlines(){return this.text.split("\n").length}_size(){const{font:t}=this,e=vo(t),n=(this.line_height-1)*e.height,r=""==this.text,i=this.text.split("\n"),o=i.length,a=i.map((e=>Ao(e,t))),s=this._text_line(e).height*o,l="%"==this.width?.unit?this.width.value:1,c="%"==this.height?.unit?this.height.value:1;return{width:(0,Rt.T9)(a)*l,height:r?0:(s+n*(o-1))*c,metrics:e}}_computed_position(t,e,n){const{width:r,height:i}=t,{sx:o,sy:a,x_anchor:s=this._x_anchor,y_anchor:l=this._y_anchor}=this.position;return{x:o-(()=>{if((0,f.Et)(s))return s*r;switch(s){case"left":return 0;case"center":return.5*r;case"right":return r}})(),y:a-(()=>{if((0,f.Et)(l))return l*i;switch(l){case"top":return 0;case"center":return.5*i;case"bottom":return i;case"baseline":if(1!=n)return.5*i;switch(this.text_height_metric??this.infer_text_height()){case"x":case"x_descent":return e.x_height;case"cap":case"cap_descent":return e.cap_height;case"ascent":case"ascent_descent":return e.ascent}}})()}}_rect(){const{width:t,height:e,metrics:n}=this._size(),r=this.text.split("\n").length,{x:i,y:o}=this._computed_position({width:t,height:e},n,r);return new re({x:i,y:o,width:t,height:e}).rect}paint(t){const{font:e}=this,n=vo(e),r=(this.line_height-1)*n.height,i=this.text.split("\n"),o=i.length,a=i.map((t=>Ao(t,e))),s=this._text_line(n),l=s.height*o,c="%"==this.width?.unit?this.width.value:1,u="%"==this.height?.unit?this.height.value:1,d=(0,Rt.T9)(a)*c,h=(l+r*(o-1))*u;t.save(),t.fillStyle=this.color,t.strokeStyle=this.outline_color,t.font=this.font,t.textAlign="left",t.textBaseline="alphabetic";const{sx:p,sy:f}=this.position,{align:Q}=this,{angle:T}=this;null!=T&&0!=T&&(t.translate(p,f),t.rotate(T),t.translate(-p,-f));let{x:m,y:g}=this._computed_position({width:d,height:h},n,o);if("justify"==Q)for(let n=0;n<o;n++){let o=m;const a=i[n].split(" "),l=a.length,c=a.map((t=>Ao(t,e))),u=(d-(0,Rt.cz)(c))/(l-1);for(let e=0;e<l;e++)t.fillText(a[e],o,g),t.strokeText(a[e],o,g),o+=c[e]+u;g+=s.height+r}else for(let e=0;e<o;e++){const n=m+(()=>{switch("auto"==Q?this._visual_align:Q){case"left":return 0;case"center":return.5*(d-a[e]);case"right":return d-a[e]}})(),o=i[e],l=g+s.ascent;t.fillText(o,n,l),t.strokeText(o,n,l),g+=s.height+r}t.restore()}}ko.__name__="TextBox";class Mo extends Ho{constructor(t,e){super(),this.base=t,this.expo=e}get children(){return[this.base,this.expo]}set base_font_size(t){super.base_font_size=t,this.base.base_font_size=t,this.expo.base_font_size=t}set position(t){this._position=t;const e=this.base.size(),n=this.expo.size(),r=this._shift_scale()*e.height,i=Math.max(e.height,r+n.height);this.base.position={sx:0,x_anchor:"left",sy:i,y_anchor:"bottom"},this.expo.position={sx:e.width,x_anchor:"left",sy:r,y_anchor:"bottom"}}get position(){return this._position}set visuals(t){this.expo.font_size_scale=.7,this.base.visuals=t,this.expo.visuals=t}_shift_scale(){if(this.base instanceof ko&&1==this.base.nlines){const{x_height:t,cap_height:e}=vo(this.base.font);return t/e}return 2/3}infer_text_height(){return this.base.infer_text_height()}_rect(){const t=this.base.bbox(),e=this.expo.bbox(),n=t.union(e),{x:r,y:i}=this._computed_position();return n.translate(r,i).rect}_size(){const t=this.base.size(),e=this.expo.size();return{width:t.width+e.width,height:Math.max(t.height,this._shift_scale()*t.height+e.height)}}paint(t){t.save();const{angle:e}=this;if(null!=e&&0!=e){const{sx:n,sy:r}=this.position;t.translate(n,r),t.rotate(e),t.translate(-n,-r)}const{x:n,y:r}=this._computed_position();t.translate(n,r),this.base.paint(t),this.expo.paint(t),t.restore()}paint_bbox(t){super.paint_bbox(t);const{x:e,y:n}=this._computed_position();t.save(),t.translate(e,n);for(const e of this.children)e.paint_bbox(t);t.restore()}_computed_position(){const{width:t,height:e}=this._size(),{sx:n,sy:r,x_anchor:i=this._x_anchor,y_anchor:o=this._y_anchor}=this.position;return{x:n-(()=>{if((0,f.Et)(i))return i*t;switch(i){case"left":return 0;case"center":return.5*t;case"right":return t}})(),y:r-(()=>{if((0,f.Et)(o))return o*e;switch(o){case"top":return 0;case"center":case"baseline":return.5*e;case"bottom":return e}})()}}}Mo.__name__="BaseExpo";class Co{constructor(t){this.items=t}set base_font_size(t){for(const e of this.items)e.base_font_size=t}get length(){return this.items.length}set visuals(t){for(const e of this.items)e.visuals=t;const e={x:0,cap:1,ascent:2,x_descent:3,cap_descent:4,ascent_descent:5},n=(0,Rt.Pe)(this.items.map((t=>t.infer_text_height())),(t=>e[t]));for(const t of this.items)t.text_height_metric=n}set angle(t){for(const e of this.items)e.angle=t}max_size(){let t=0,e=0;for(const n of this.items){const r=n.size();t=Math.max(t,r.width),e=Math.max(e,r.height)}return{width:t,height:e}}}async function So(t){try{return await t}catch(t){if((e=t)instanceof Error&&"code"in e&&"MODULE_NOT_FOUND"===t.code)return null;throw t}var e}Co.__name__="GraphicsBoxes";class Eo{constructor(){this.ready=new T.n2(this,"ready"),this.status="not_started"}}Eo.__name__="MathJaxProvider",class extends Eo{get MathJax(){return null}async fetch(){this.status="failed"}}.__name__="NoProvider",class extends Eo{get MathJax(){return"undefined"!=typeof MathJax?MathJax:null}async fetch(){const t=document.createElement("script");t.src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js",t.onload=()=>{this.status="loaded",this.ready.emit()},t.onerror=()=>{this.status="failed"},this.status="loading",document.head.appendChild(t)}}.__name__="CDNProvider";class Vo extends Eo{get MathJax(){return this._mathjax}async fetch(){this.status="loading";try{const t=await So(Promise.resolve().then(n.bind(n,9469)));this._mathjax=t,this.status="loaded",this.ready.emit()}catch(t){this.status="failed"}}}Vo.__name__="BundleProvider";const Oo=new Vo;var Po,Do,No,Ro;class Io extends po{constructor(){super(...arguments),this._position={sx:0,sy:0},this.align="left",this._x_anchor="left",this._y_anchor="center",this._base_font_size=13,this.font_size_scale=1,this.svg_image=null}graphics(){return this}infer_text_height(){return"ascent_descent"}set base_font_size(t){null!=t&&(this._base_font_size=t)}get base_font_size(){return this._base_font_size}_rect(){const{width:t,height:e}=this._size(),{x:n,y:r}=this._computed_position();return new re({x:n,y:r,width:t,height:e}).rect}set position(t){this._position=t}get position(){return this._position}get text(){return this.model.text}get provider(){return Oo}async lazy_initialize(){await super.lazy_initialize(),"not_started"==this.provider.status&&await this.provider.fetch()}connect_signals(){super.connect_signals(),this.on_change(this.model.properties.text,(()=>this.load_image()))}set visuals(t){const e=t.color,n=t.alpha,r=t.font_style;let i=t.font_size;const o=t.font,{font_size_scale:a,_base_font_size:s}=this,l=yo(i);if(null!=l){let{value:t,unit:e}=l;t*=a,"em"==e&&s&&(t*=s,e="px"),i=`${t}${e}`}const c=`${r} ${i} ${o}`;this.font=c,this.color=(0,Ye.do)(e,n);const u=t.align;this._x_anchor=u;const d=t.baseline;this._y_anchor=(()=>{switch(d){case"top":return"top";case"middle":return"center";case"bottom":return"bottom";default:return"baseline"}})()}_computed_position(){const{width:t,height:e}=this._size(),{sx:n,sy:r,x_anchor:i=this._x_anchor,y_anchor:o=this._y_anchor}=this.position,a=vo(this.font);return{x:n-(()=>{if((0,f.Et)(i))return i*t;switch(i){case"left":return 0;case"center":return.5*t;case"right":return t}})(),y:r-(()=>{if((0,f.Et)(o))return o*e;switch(o){case"top":return a.height>e?e-(-this.valign-a.descent)-a.height:0;case"center":case"baseline":return.5*e;case"bottom":return a.height>e?e+a.descent+this.valign:e}})()}}size(){const{width:t,height:e}=this._size(),{angle:n}=this;if(null==n||0==n)return{width:t,height:e};{const r=Math.cos(Math.abs(n)),i=Math.sin(Math.abs(n));return{width:Math.abs(t*r+e*i),height:Math.abs(t*i+e*r)}}}get_image_dimensions(){const t=vo(this.font),e=this.svg_element.getAttribute("style")?.split(";");if(e){const n=new Map;e.forEach((t=>{const[e,r]=t.split(":");e&&n.set(e.trim(),r.trim())}));const r=function(t){const e=t.match(/^\s*(-?\d+(\.\d+)?)(\w+)\s*$/);if(null!=e){const[,t,,n]=e,r=Number(t);if(isFinite(r))return{value:r,unit:n}}return null}(n.get("vertical-align"));"ex"==r?.unit?this.valign=r.value*t.x_height:"px"==r?.unit&&(this.valign=r.value)}const n=(()=>{const t=this.svg_element.getAttribute("width"),e=this.svg_element.getAttribute("height");return{width:null!=t&&t.endsWith("ex")?parseFloat(t):1,height:null!=e&&e.endsWith("ex")?parseFloat(e):1}})();return{width:t.x_height*n.width,height:t.x_height*n.height}}get truncated_text(){return this.model.text.length>6?`${this.model.text.substring(0,6)}...`:this.model.text}_size(){if(!this.svg_image)return"failed"==this.provider.status||"not_started"==this.provider.status?{width:Ao(this.truncated_text,this.font),height:vo(this.font).height}:{width:this._base_font_size,height:this._base_font_size};const t=vo(this.font);let{width:e,height:n}=this.get_image_dimensions();return n=Math.max(n,t.height),{width:e*("%"==this.width?.unit?this.width.value:1),height:n*("%"==this.height?.unit?this.height.value:1)}}bbox(){const{p0:t,p1:e,p2:n,p3:r}=this.rect(),i=Math.min(t.x,e.x,n.x,r.x),o=Math.min(t.y,e.y,n.y,r.y),a=Math.max(t.x,e.x,n.x,r.x),s=Math.max(t.y,e.y,n.y,r.y);return new re({left:i,right:a,top:o,bottom:s})}rect(){const t=this._rect(),{angle:e}=this;if(null==e||0==e)return t;{const{sx:n,sy:r}=this.position,i=new Lo;return i.translate(n,r),i.rotate(e),i.translate(-n,-r),i.apply_rect(t)}}paint_rect(t){const{p0:e,p1:n,p2:r,p3:i}=this.rect();t.save(),t.strokeStyle="red",t.lineWidth=1,t.beginPath();const{round:o}=Math;t.moveTo(o(e.x),o(e.y)),t.lineTo(o(n.x),o(n.y)),t.lineTo(o(r.x),o(r.y)),t.lineTo(o(i.x),o(i.y)),t.closePath(),t.stroke(),t.restore()}paint_bbox(t){const{x:e,y:n,width:r,height:i}=this.bbox();t.save(),t.strokeStyle="blue",t.lineWidth=1,t.beginPath();const{round:o}=Math;t.moveTo(o(e),o(n)),t.lineTo(o(e),o(n+i)),t.lineTo(o(e+r),o(n+i)),t.lineTo(o(e+r),o(n)),t.closePath(),t.stroke(),t.restore()}async load_image(){if(null==this.provider.MathJax)return null;const t=this._process_text();if(null==t)return this._has_finished=!0,null;const e=t.children[0];this.svg_element=e,e.setAttribute("font",this.font),e.setAttribute("stroke",this.color);const n=e.outerHTML,r=`data:image/svg+xml;utf-8,${encodeURIComponent(n)}`;return this.svg_image=await async function(t){return new Qo(t,void 0).promise}(r),this.parent.request_layout(),this.svg_image}paint(t){this.svg_image||("not_started"!=this.provider.status&&"loading"!=this.provider.status||this.provider.ready.connect((()=>this.load_image())),"loaded"==this.provider.status&&this.load_image()),t.save();const{sx:e,sy:n}=this.position,{angle:r}=this;null!=r&&0!=r&&(t.translate(e,n),t.rotate(r),t.translate(-e,-n));const{x:i,y:o}=this._computed_position();if(this.svg_image){const{width:e,height:n}=this.get_image_dimensions();t.drawImage(this.svg_image,i,o,e,n)}else"failed"!=this.provider.status&&"not_started"!=this.provider.status||(t.fillStyle=this.color,t.font=this.font,t.textAlign="left",t.textBaseline="alphabetic",t.fillText(this.truncated_text,i,o+vo(this.font).ascent));t.restore(),this._has_finished||"failed"!=this.provider.status&&!this.svg_image||(this._has_finished=!0,this.parent.notify_finished_after_paint())}}Io.__name__="MathTextView";class jo extends fo{constructor(t){super(t)}}jo.__name__="MathText";class zo extends Io{get styled_text(){return this.text}_process_text(){}_size(){return{width:Ao(this.text,this.font),height:vo(this.font).height}}paint(t){t.save();const{sx:e,sy:n}=this.position,{angle:r}=this;null!=r&&0!=r&&(t.translate(e,n),t.rotate(r),t.translate(-e,-n));const{x:i,y:o}=this._computed_position();t.fillStyle=this.color,t.font=this.font,t.textAlign="left",t.textBaseline="alphabetic",t.fillText(this.text,i,o+vo(this.font).ascent),t.restore(),this._has_finished=!0,this.parent.notify_finished_after_paint()}}zo.__name__="AsciiView";class Bo extends jo{constructor(t){super(t)}}Po=Bo,Bo.__name__="Ascii",Po.prototype.default_view=zo;class Fo extends Io{get styled_text(){let t=this.text.trim(),e=t.match(/<math(.*?[^?])?>/s);return e?(t=L(t,t.indexOf(e[0])+e[0].length,`<mstyle displaystyle="true" mathcolor="${(0,Ye.Kr)(this.color)}" ${this.font.includes("bold")?'mathvariant="bold"':""}>`),e=t.match(/<\/[^>]*?math.*?>/s),e?L(t,t.indexOf(e[0]),"</mstyle>"):this.text.trim()):this.text.trim()}_process_text(){const t=vo(this.font);return this.provider.MathJax?.mathml2svg(this.styled_text,{em:this.base_font_size,ex:t.x_height})}}Fo.__name__="MathMLView";class $o extends jo{constructor(t){super(t)}}Do=$o,$o.__name__="MathML",Do.prototype.default_view=Fo;class Go extends Io{get styled_text(){const[t,e,n]=(0,Ye.qG)(this.color);return`\\color[RGB]{${t}, ${e}, ${n}} ${this.font.includes("bold")?`\\pmb{${this.text}}`:this.text}`}_process_text(){const t=vo(this.font);return this.provider.MathJax?.tex2svg(this.styled_text,{display:!this.model.inline,em:this.base_font_size,ex:t.x_height},this.model.macros)}}Go.__name__="TeXView";class qo extends jo{constructor(t){super(t)}}No=qo,qo.__name__="TeX",No.prototype.default_view=Go,No.define((({Boolean:t,Number:e,String:n,Dict:r,Tuple:i,Or:o})=>({macros:[r(o(n,i(n,e))),{}],inline:[t,!1]})));class Uo extends po{initialize(){super.initialize(),this._has_finished=!0}graphics(){return new ko({text:this.model.text})}}Uo.__name__="PlainTextView";class Wo extends fo{constructor(t){super(t)}}Ro=Wo,Wo.__name__="PlainText",Ro.prototype.default_view=Uo;const Zo=[{start:"$$",end:"$$",inline:!1},{start:"\\[",end:"\\]",inline:!1},{start:"\\(",end:"\\)",inline:!0}];function Xo(t){for(const e of Zo){const n=t.indexOf(e.start),r=n+e.start.length;if(0==n){const n=t.indexOf(e.end,r),i=n;if(n==t.length-e.end.length)return new qo({text:t.slice(r,i),inline:e.inline});break}}return new Wo({text:t})}var Ko,Yo,Jo,ta,ea,na;class ra extends nr{*children(){yield*super.children(),yield this._text_view}async lazy_initialize(){await super.lazy_initialize(),await this._init_text()}async _init_text(){const{text:t}=this.model,e=(0,f.Kg)(t)?Xo(t):t;this._text_view=await $e(e,{parent:this})}update_layout(){const{panel:t}=this;this.layout=null!=t?new uo(t,(()=>this.get_size()),!0):void 0}connect_signals(){super.connect_signals();const{text:t}=this.model.properties;this.on_change(t,(async()=>{this._text_view.remove(),await this._init_text()})),this.connect(this.model.change,(()=>this.request_render()))}remove(){this._text_view.remove(),super.remove()}has_finished(){return!!super.has_finished()&&!!this._text_view.has_finished()}get displayed(){return super.displayed&&""!=this._text_view.model.text&&this.visuals.text.doit}_paint(t,e,n){const r=this._text_view.graphics();r.angle=n,r.position=e,r.align="auto",r.visuals=this.visuals.text.values();const{background_fill:i,border_line:o}=this.visuals;if(i.doit||o.doit){const{p0:e,p1:n,p2:i,p3:o}=r.rect();t.beginPath(),t.moveTo(e.x,e.y),t.lineTo(n.x,n.y),t.lineTo(i.x,i.y),t.lineTo(o.x,o.y),t.closePath(),this.visuals.background_fill.apply(t),this.visuals.border_line.apply(t)}this.visuals.text.doit&&r.paint(t)}}ra.__name__="TextAnnotationView";class ia extends rr{constructor(t){super(t)}}Ko=ia,ia.__name__="TextAnnotation",Ko.mixins([Ke.EY,["border_",Ke.N1],["background_",Ke.SQ]]),Ko.define((({String:t,Or:e,Ref:n})=>({text:[e(t,n(fo)),""]}))),Ko.override({background_fill_color:null,border_line_color:null});class oa extends ra{_get_position(){const t=this.model.offset,e=this.model.standoff/2,{align:n,vertical_align:r}=this.model;let i,o;const{bbox:a}=this.layout;switch(this.panel.side){case"above":case"below":switch(r){case"top":o=a.top+e;break;case"middle":o=a.vcenter;break;case"bottom":o=a.bottom-e}switch(n){case"left":i=a.left+t;break;case"center":i=a.hcenter;break;case"right":i=a.right-t}break;case"left":switch(r){case"top":i=a.left+e;break;case"middle":i=a.hcenter;break;case"bottom":i=a.right-e}switch(n){case"left":o=a.bottom-t;break;case"center":o=a.vcenter;break;case"right":o=a.top+t}break;case"right":switch(r){case"top":i=a.right-e;break;case"middle":i=a.hcenter;break;case"bottom":i=a.left+e}switch(n){case"left":o=a.top+t;break;case"center":o=a.vcenter;break;case"right":o=a.bottom-t}}return{sx:i,sy:o,x_anchor:n,y_anchor:"middle"==r?"center":r}}_render(){const t=this._get_position(),e=this.panel.get_label_angle_heuristic("parallel");this._paint(this.layer.ctx,t,e)}_get_size(){if(!this.displayed)return{width:0,height:0};const t=this._text_view.graphics();t.visuals=this.visuals.text.values();const{width:e,height:n}=t._size();return{width:e,height:0==n?0:2+n+this.model.standoff}}}oa.__name__="TitleView";class aa extends ia{constructor(t){super(t)}}Yo=aa,aa.__name__="Title",Yo.prototype.default_view=oa,Yo.define((({Number:t})=>({vertical_align:[_n.G4,"bottom"],align:[_n.nO,"left"],offset:[t,0],standoff:[t,10]}))),Yo.override({text_font_size:"13px",text_font_style:"bold",text_line_height:1});class sa{constructor(t,e,n,r,i={},o={},a={},s={}){this.in_x_scale=t,this.in_y_scale=e,this.x_range=n,this.y_range=r,this.extra_x_ranges=i,this.extra_y_ranges=o,this.extra_x_scales=a,this.extra_y_scales=s,this._bbox=new re,this.change=new T.n2(this,"change"),(0,_.vA)(t.properties.source_range.is_unset&&t.properties.target_range.is_unset),(0,_.vA)(e.properties.source_range.is_unset&&e.properties.target_range.is_unset),this._configure_scales()}get bbox(){return this._bbox}_get_ranges(t,e){return new Map((0,Q.jO)({...e,default:t}))}_get_scales(t,e,n,r){const i=new Map((0,Q.jO)({...e,default:t})),o=new Map;for(const[e,a]of n){if(a instanceof jn!=t instanceof Mn)throw new Error(`Range ${a.type} is incompatible is Scale ${t.type}`);t instanceof Hn&&a instanceof Dn&&(a.scale_hint="log");const n=(i.get(e)??t).clone();n.setv({source_range:a,target_range:r}),o.set(e,n)}return o}_configure_frame_ranges(){const{bbox:t}=this;this._x_target=new xn({start:t.left,end:t.right}),this._y_target=new xn({start:t.bottom,end:t.top})}_configure_scales(){this._configure_frame_ranges(),this._x_ranges=this._get_ranges(this.x_range,this.extra_x_ranges),this._y_ranges=this._get_ranges(this.y_range,this.extra_y_ranges),this._x_scales=this._get_scales(this.in_x_scale,this.extra_x_scales,this._x_ranges,this._x_target),this._y_scales=this._get_scales(this.in_y_scale,this.extra_y_scales,this._y_ranges,this._y_target)}configure_scales(){this._configure_scales(),this.change.emit()}_update_scales(){this._configure_frame_ranges();for(const[,t]of this._x_scales)t.target_range=this._x_target;for(const[,t]of this._y_scales)t.target_range=this._y_target}set_geometry(t){this._bbox=t,this._update_scales()}get x_target(){return this._x_target}get y_target(){return this._y_target}get x_ranges(){return this._x_ranges}get y_ranges(){return this._y_ranges}get ranges(){return new Set([...this.x_ranges.values(),...this.y_ranges.values()])}get x_scales(){return this._x_scales}get y_scales(){return this._y_scales}get scales(){return new Set([...this.x_scales.values(),...this.y_scales.values()])}get x_scale(){return this._x_scales.get("default")}get y_scale(){return this._y_scales.get("default")}}sa.__name__="CartesianFrame";class la extends tr{}la.__name__="GuideRendererView";class ca extends er{constructor(t){super(t)}}Jo=ca,ca.__name__="GuideRenderer",Jo.override({level:"guide"});class ua extends qt{constructor(t){super(t)}}ua.__name__="Ticker";class da extends qt{constructor(t){super(t)}format_graphics(t,e){return this.doFormat(t,e).map((t=>new ko({text:t})))}compute(t,e){return this.doFormat([t],e??{loc:0})[0]}v_compute(t,e){return this.doFormat(t,e??{loc:0})}}da.__name__="TickFormatter";class ha extends qt{constructor(t){super(t)}}ha.__name__="LabelingPolicy";class pa extends ha{constructor(t){super(t)}filter(t,e,n){return t}}pa.__name__="AllLabels";class fa extends ha{constructor(t){super(t)}filter(t,e,n){const{min_distance:r}=this;let i=null;for(const e of t)null!=i&&n(i,e)<r?t.unset(e):i=e;return t}}ta=fa,fa.__name__="NoOverlap",ta.define((({Number:t})=>({min_distance:[t,5]})));class Qa extends ha{constructor(t){super(t)}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}get func(){const t=x(this.code);return new Jt.qJ("indices","bboxes","distance",...this.names,t)}filter(t,e,n){const r=Object.create(null),i=this.func.call(r,t,e,n,...this.values);let o=i.next();if(o.done&&void 0!==o.value){const{value:e}=o;return e instanceof Jt.et?e:void 0===e?t:(0,f.xZ)(e)?Jt.et.from_indices(t.size,e):Jt.et.all_unset(t.size)}{const e=[];do{e.push(o.value),o=i.next()}while(!o.done);return Jt.et.from_indices(t.size,e)}}}ea=Qa,Qa.__name__="CustomLabelingPolicy",ea.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));const{abs:Ta}=Math;class ma extends la{constructor(){super(...arguments),this._axis_label_view=null,this._major_label_views=new Map}*children(){yield*super.children(),null!=this._axis_label_view&&(yield this._axis_label_view),yield*this._major_label_views.values()}async lazy_initialize(){await super.lazy_initialize(),await this._init_axis_label(),await this._init_major_labels()}async _init_axis_label(){const{axis_label:t}=this.model;if(null!=t){const e=(0,f.Kg)(t)?Xo(t):t;this._axis_label_view=await $e(e,{parent:this})}else this._axis_label_view=null}async _init_major_labels(){for(const[t,e]of this.model.major_label_overrides){const n=(0,f.Kg)(e)?Xo(e):e;this._major_label_views.set(t,await $e(n,{parent:this}))}}update_layout(){this.layout=new uo(this.panel,(()=>this.get_size()),!0),this.layout.on_resize((()=>this._coordinates=void 0))}get_size(){const{visible:t,fixed_location:e}=this.model;if(t&&null==e&&this.is_renderable){const{extents:t}=this;return{width:0,height:Math.round(t.tick+t.tick_label+t.axis_label)}}return{width:0,height:0}}get is_renderable(){const[t,e]=this.ranges;return t.is_valid&&e.is_valid&&t.span>0&&e.span>0}_render(){if(!this.is_renderable)return;const{tick_coords:t,extents:e}=this,n=this.layer.ctx;n.save(),this._draw_rule(n,e),this._draw_major_ticks(n,e,t),this._draw_minor_ticks(n,e,t),this._draw_major_labels(n,e,t),this._draw_axis_label(n,e,t),this._paint?.(n,e,t),n.restore()}connect_signals(){super.connect_signals();const{axis_label:t,major_label_overrides:e}=this.model.properties;this.on_change(t,(async()=>{this._axis_label_view?.remove(),await this._init_axis_label()})),this.on_change(e,(async()=>{for(const t of this._major_label_views.values())t.remove();await this._init_major_labels()})),this.connect(this.model.change,(()=>this.plot_view.request_layout()))}get needs_clip(){return null!=this.model.fixed_location}_draw_rule(t,e){if(!this.visuals.axis_line.doit)return;const[n,r]=this.rule_coords,[i,o]=this.coordinates.map_to_screen(n,r),[a,s]=this.normals,[l,c]=this.offsets;this.visuals.axis_line.set_value(t),t.beginPath();for(let e=0;e<i.length;e++){const n=Math.round(i[e]+a*l),r=Math.round(o[e]+s*c);t.lineTo(n,r)}t.stroke()}_draw_major_ticks(t,e,n){const r=this.model.major_tick_in,i=this.model.major_tick_out,o=this.visuals.major_tick_line;this._draw_ticks(t,n.major,r,i,o)}_draw_minor_ticks(t,e,n){const r=this.model.minor_tick_in,i=this.model.minor_tick_out,o=this.visuals.minor_tick_line;this._draw_ticks(t,n.minor,r,i,o)}_draw_major_labels(t,e,n){const r=n.major,i=this.compute_labels(r[this.dimension]),o=this.model.major_label_orientation,a=e.tick+this.model.major_label_standoff,s=this.visuals.major_label_text;this._draw_oriented_labels(t,i,r,o,this.panel.side,a,s)}_axis_label_extent(){if(null==this._axis_label_view)return 0;const t=this._axis_label_view.graphics();t.visuals=this.visuals.axis_label_text.values(),t.angle=this.panel.get_label_angle_heuristic("parallel"),(0,f.Et)(this.plot_view.base_font_size)&&(t.base_font_size=this.plot_view.base_font_size);const e=t.size(),n=0==this.dimension?e.height:e.width,r=this.model.axis_label_standoff;return n>0?r+n+3:0}_draw_axis_label(t,e,n){if(null==this._axis_label_view||null!=this.model.fixed_location)return;const[r,i]=(()=>{const{bbox:t}=this.layout;switch(this.panel.side){case"above":return[t.hcenter,t.bottom];case"below":return[t.hcenter,t.top];case"left":return[t.right,t.vcenter];case"right":return[t.left,t.vcenter]}})(),[o,a]=this.normals,s=e.tick+e.tick_label+this.model.axis_label_standoff,{vertical_align:l,align:c}=this.panel.get_label_text_heuristics("parallel"),u={sx:r+o*s,sy:i+a*s,x_anchor:c,y_anchor:l},d=this._axis_label_view.graphics();d.visuals=this.visuals.axis_label_text.values(),d.angle=this.panel.get_label_angle_heuristic("parallel"),null!=this.plot_view.base_font_size&&(d.base_font_size=this.plot_view.base_font_size),d.position=u,d.align=c,d.paint(t)}_draw_ticks(t,e,n,r,i){if(!i.doit)return;const[o,a]=e,[s,l]=this.coordinates.map_to_screen(o,a),[c,u]=this.normals,[d,h]=this.offsets,[p,f]=[c*(d-n),u*(h-n)],[Q,T]=[c*(d+r),u*(h+r)];i.set_value(t),t.beginPath();for(let e=0;e<s.length;e++){const n=Math.round(s[e]+Q),r=Math.round(l[e]+T),i=Math.round(s[e]+p),o=Math.round(l[e]+f);t.moveTo(n,r),t.lineTo(i,o)}t.stroke()}_draw_oriented_labels(t,e,n,r,i,o,a){if(!a.doit||0==e.length)return;const[s,l]=n,[c,u]=this.coordinates.map_to_screen(s,l),[d,h]=this.offsets,[p,f]=this.normals,Q=p*(d+o),T=f*(h+o),{vertical_align:m,align:g}=this.panel.get_label_text_heuristics(r),_=this.panel.get_label_angle_heuristic(r);e.visuals=a.values(),e.angle=_,e.base_font_size=this.plot_view.base_font_size;for(let t=0;t<e.length;t++){const n=e.items[t];n.position={sx:c[t]+Q,sy:u[t]+T,x_anchor:g,y_anchor:m},n instanceof ko&&(n.align=g)}const b=e.length,v=Jt.et.all_set(b),{items:y}=e,x=y.map((t=>t.bbox())),w=(()=>{const[t]=this.ranges;return t.is_reversed?0==this.dimension?(t,e)=>x[t].left-x[e].right:(t,e)=>x[e].top-x[t].bottom:0==this.dimension?(t,e)=>x[e].left-x[t].right:(t,e)=>x[t].top-x[e].bottom})(),{major_label_policy:L}=this.model,A=L.filter(v,x,w),H=[...A.ones()];if(0!=H.length){const t=this.parent.canvas_view.bbox,e=e=>{const n=x[e];if(n.left<0){const t=-n.left,{position:r}=y[e];y[e].position={...r,sx:r.sx+t}}else if(n.right>t.width){const r=n.right-t.width,{position:i}=y[e];y[e].position={...i,sx:i.sx-r}}},n=e=>{const n=x[e];if(n.top<0){const t=-n.top,{position:r}=y[e];y[e].position={...r,sy:r.sy+t}}else if(n.bottom>t.height){const r=n.bottom-t.height,{position:i}=y[e];y[e].position={...i,sy:i.sy-r}}},r=H[0],i=H[H.length-1];0==this.dimension?(e(r),e(i)):(n(r),n(i))}for(const e of A)y[e].paint(t)}_tick_extent(){return this.model.major_tick_out}_tick_label_extents(){const t=this.tick_coords.major,e=this.compute_labels(t[this.dimension]),n=this.model.major_label_orientation,r=this.model.major_label_standoff,i=this.visuals.major_label_text;return[this._oriented_labels_extent(e,n,r,i)]}get extents(){const t=this._tick_label_extents();return{tick:this._tick_extent(),tick_labels:t,tick_label:(0,Rt.cz)(t),axis_label:this._axis_label_extent()}}_oriented_labels_extent(t,e,n,r){if(0==t.length||!r.doit)return 0;const i=this.panel.get_label_angle_heuristic(e);t.visuals=r.values(),t.angle=i,t.base_font_size=this.plot_view.base_font_size;const o=t.max_size(),a=0==this.dimension?o.height:o.width;return a>0?n+a+3:0}get normals(){return this.panel.normals}get dimension(){return this.panel.dimension}compute_labels(t){const e=this.model.formatter.format_graphics(t,this),{_major_label_views:n}=this,r=new Set;for(let i=0;i<t.length;i++){const o=n.get(t[i]);null!=o&&(r.add(o),e[i]=o.graphics())}for(const t of this._major_label_views.values())r.has(t)||(t._has_finished=!0);return new Co(e)}get offsets(){if(null!=this.model.fixed_location)return[0,0];const{frame:t}=this.plot_view;let[e,n]=[0,0];switch(this.panel.side){case"below":n=Ta(this.layout.bbox.top-t.bbox.bottom);break;case"above":n=Ta(this.layout.bbox.bottom-t.bbox.top);break;case"right":e=Ta(this.layout.bbox.left-t.bbox.right);break;case"left":e=Ta(this.layout.bbox.right-t.bbox.left)}return[e,n]}get ranges(){const t=this.dimension,e=1-t,{ranges:n}=this.coordinates;return[n[t],n[e]]}get computed_bounds(){const[t]=this.ranges,e=this.model.bounds,n=[t.min,t.max];if("auto"==e)return[t.min,t.max];{let t,r;const[i,o]=e,[a,s]=n,{min:l,max:c}=Math;return Ta(i-o)>Ta(a-s)?(t=c(l(i,o),a),r=l(c(i,o),s)):(t=l(i,o),r=c(i,o)),[t,r]}}get rule_coords(){const t=this.dimension,e=1-t,[n]=this.ranges,[r,i]=this.computed_bounds,o=[new Array(2),new Array(2)];return o[t][0]=Math.max(r,n.min),o[t][1]=Math.min(i,n.max),o[t][0]>o[t][1]&&(o[t][0]=o[t][1]=NaN),o[e][0]=this.loc,o[e][1]=this.loc,o}get tick_coords(){const t=this.dimension,e=1-t,[n]=this.ranges,[r,i]=this.computed_bounds,o=this.model.ticker.get_ticks(r,i,n,this.loc),a=o.major,s=o.minor,l=[[],[]],c=[[],[]],[u,d]=[n.min,n.max];for(let n=0;n<a.length;n++)a[n]<u||a[n]>d||(l[t].push(a[n]),l[e].push(this.loc));for(let n=0;n<s.length;n++)s[n]<u||s[n]>d||(c[t].push(s[n]),c[e].push(this.loc));return{major:l,minor:c}}get loc(){const{fixed_location:t}=this.model;if(null!=t){if((0,f.Et)(t))return t;const[,e]=this.ranges;if(e instanceof jn)return e.synthetic(t);(0,_.HB)()}const[,e]=this.ranges;switch(this.panel.side){case"left":case"below":return e.start;case"right":case"above":return e.end}}serializable_state(){return{...super.serializable_state(),bbox:this.layout.bbox.box}}remove(){this._axis_label_view?.remove();for(const t of this._major_label_views.values())t.remove();super.remove()}has_finished(){if(!super.has_finished())return!1;if(null!=this._axis_label_view&&!this._axis_label_view.has_finished())return!1;for(const t of this._major_label_views.values())if(!t.has_finished())return!1;return!0}}ma.__name__="AxisView";class ga extends ca{constructor(t){super(t)}}na=ga,ga.__name__="Axis",na.prototype.default_view=ma,na.mixins([["axis_",Ke.N1],["major_tick_",Ke.N1],["minor_tick_",Ke.N1],["major_label_",Ke.EY],["axis_label_",Ke.EY]]),na.define((({Any:t,Int:e,Number:n,String:r,Ref:i,Map:o,Tuple:a,Or:s,Nullable:l,Auto:c})=>({bounds:[s(a(n,n),c),"auto"],ticker:[i(ua)],formatter:[i(da)],axis_label:[l(s(r,i(fo))),null],axis_label_standoff:[e,5],major_label_standoff:[e,5],major_label_orientation:[s(_n.K0,n),"horizontal"],major_label_overrides:[o(s(r,n),s(r,i(fo))),new globalThis.Map,{convert:t=>(0,f.Qd)(t)?new Q.Bi(t):t}],major_label_policy:[i(ha),()=>new pa],major_tick_in:[n,2],major_tick_out:[n,6],minor_tick_in:[n,0],minor_tick_out:[n,4],fixed_location:[l(s(n,t)),null]}))),na.override({axis_line_color:"black",major_tick_line_color:"black",minor_tick_line_color:"black",major_label_text_font_size:"11px",major_label_text_align:"center",major_label_text_baseline:"alphabetic",axis_label_text_font_size:"13px",axis_label_text_font_style:"italic"});class _a extends ua{constructor(t){super(t)}get_ticks(t,e,n,r){return{major:this._collect(n.factors,n,t,e),minor:[],tops:this._collect(n.tops??[],n,t,e),mids:this._collect(n.mids??[],n,t,e)}}_collect(t,e,n,r){const i=[];for(const o of t){const t=e.synthetic(o);t>n&&t<r&&i.push(o)}return i}}_a.__name__="CategoricalTicker";class ba extends da{constructor(t){super(t)}doFormat(t,e){return(0,Rt.C)(t)}}var va;ba.__name__="CategoricalTickFormatter";class ya extends ma{_paint(t,e,n){this._draw_group_separators(t,e,n)}_draw_group_separators(t,e,n){const[r]=this.ranges,[i,o]=this.computed_bounds;if(!r.tops||r.tops.length<2||!this.visuals.separator_line.doit)return;const a=this.dimension,s=1-a,l=[[],[]];let c=0;for(let t=0;t<r.tops.length-1;t++){let e,n;for(let i=c;i<r.factors.length;i++)if(r.factors[i][0]==r.tops[t+1]){[e,n]=[r.factors[i-1],r.factors[i]],c=i;break}const u=(r.synthetic(e)+r.synthetic(n))/2;u>i&&u<o&&(l[a].push(u),l[s].push(this.loc))}const u=this.extents.tick_label;this._draw_ticks(t,l,-3,u-6,this.visuals.separator_line)}_draw_major_labels(t,e,n){const r=this._get_factor_info();let i=e.tick+this.model.major_label_standoff;for(let n=0;n<r.length;n++){const[o,a,s,l]=r[n];this._draw_oriented_labels(t,o,a,s,this.panel.side,i,l),i+=e.tick_labels[n]}}_tick_label_extents(){const t=this._get_factor_info(),e=[];for(const[n,,r,i]of t){const t=this._oriented_labels_extent(n,r,this.model.major_label_standoff,i);e.push(t)}return e}_get_factor_info(){const[t]=this.ranges,[e,n]=this.computed_bounds,r=this.loc,i=this.model.ticker.get_ticks(e,n,t,r),o=this.tick_coords,a=[],s=t=>new Co(t.map((t=>(0,f.Kg)(t)?new ko({text:t}):t))),l=t=>s(this.model.formatter.doFormat(t,this));if(1==t.levels){const t=l(i.major);a.push([t,o.major,this.model.major_label_orientation,this.visuals.major_label_text])}else if(2==t.levels){const t=l(i.major.map((t=>t[1])));a.push([t,o.major,this.model.major_label_orientation,this.visuals.major_label_text]),a.push([s(i.tops),o.tops,this.model.group_label_orientation,this.visuals.group_text])}else if(3==t.levels){const t=l(i.major.map((t=>t[2]))),e=i.mids.map((t=>t[1]));a.push([t,o.major,this.model.major_label_orientation,this.visuals.major_label_text]),a.push([s(e),o.mids,this.model.subgroup_label_orientation,this.visuals.subgroup_text]),a.push([s(i.tops),o.tops,this.model.group_label_orientation,this.visuals.group_text])}return a}get tick_coords(){const t=this.dimension,e=1-t,[n]=this.ranges,[r,i]=this.computed_bounds,o=this.model.ticker.get_ticks(r,i,n,this.loc),a={major:[[],[]],mids:[[],[]],tops:[[],[]],minor:[[],[]]};return a.major[t]=o.major,a.major[e]=o.major.map((()=>this.loc)),3==n.levels&&(a.mids[t]=o.mids,a.mids[e]=o.mids.map((()=>this.loc))),n.levels>1&&(a.tops[t]=o.tops,a.tops[e]=o.tops.map((()=>this.loc))),a}}ya.__name__="CategoricalAxisView";class xa extends ga{constructor(t){super(t)}}va=xa,xa.__name__="CategoricalAxis",va.prototype.default_view=ya,va.mixins([["separator_",Ke.N1],["group_",Ke.EY],["subgroup_",Ke.EY]]),va.define((({Number:t,Or:e})=>({group_label_orientation:[e(_n.K0,t),"parallel"],subgroup_label_orientation:[e(_n.K0,t),"parallel"]}))),va.override({ticker:()=>new _a,formatter:()=>new ba,separator_line_color:"lightgrey",separator_line_width:2,group_text_font_style:"bold",group_text_font_size:"11px",group_text_color:"grey",subgroup_text_font_style:"bold",subgroup_text_font_size:"11px"});class wa extends 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$a=["microseconds","milliseconds","seconds","minsec","minutes","hourmin","hours","days","months","years"],Ga=new Map;for(const t of $a)Ga.set(t,0);function qa(t,e){const n=Ea("$1%06d",function(t){return Math.round(t/1e3%1*1e6)}(t));return-1==(e=e.replace(/((^|[^%])(%%)*)%f/,n)).indexOf("%")?e:Ma()(t,e)}Ga.set("seconds",5),Ga.set("minsec",4),Ga.set("minutes",4),Ga.set("hourmin",3),Ga.set("hours",3);class Ua extends da{constructor(t){super(t)}doFormat(t,e,n){if(0==t.length)return[];const r=Math.abs(t[t.length-1]-t[0])/1e3,i=r/(t.length-1),o=(0,f.cA)(n)?function(t,e){const n=1.1*t*1e3,r=1e3*e;return n<1?"microseconds":n<1e3?"milliseconds":n<6e4?r>=6e4?"minsec":"seconds":n<Da?r>=Da?"hourmin":"minutes":n<Na?"hours":n<Ra?"days":n<Ia?"months":"years"}(i,r):n,a=[];for(const[e,n]of(0,On.HL)(t)){const r=this._compute_label(e,o),i=this._add_context(e,r,n,t.length,o);a.push(i)}return a}_compute_label(t,e){const n=qa(t,this[e]),r=function(t){return Ma()(t,"%Y %m %d %H %M 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Wa,Za,Xa,Ka,Ya,Ja,ts,es,ns,rs,is,os;Fa=Ua,Ua.__name__="DatetimeTickFormatter",Fa.define((({Boolean:t,Nullable:e,Or:n,Ref:r,String:i})=>({microseconds:[i,"%fus"],milliseconds:[i,"%3Nms"],seconds:[i,"%Ss"],minsec:[i,":%M:%S"],minutes:[i,":%M"],hourmin:[i,"%H:%M"],hours:[i,"%Hh"],days:[i,"%m/%d"],months:[i,"%m/%Y"],years:[i,"%Y"],strip_leading_zeros:[t,!0],context:[e(n(i,r(Ua))),null],context_which:[_n.$N,"start"],context_location:[_n.aZ,"below"]})));class as extends ua{constructor(t){super(t)}get_ticks(t,e,n,r){return this.get_ticks_no_defaults(t,e,r,this.desired_num_ticks)}get_ticks_no_defaults(t,e,n,r){const i=this.get_interval(t,e,r),o=Math.floor(t/i),a=Math.ceil(e/i);let s;s=isFinite(o)&&isFinite(a)?(0,Rt.y1)(o,a+1):[];const l=s.map((t=>t*i)).filter((n=>t<=n&&n<=e)),c=this.num_minor_ticks,u=[];if(c>0&&l.length>0){const n=i/c,r=(0,Rt.y1)(0,c).map((t=>t*n));for(const n of r.slice(1)){const r=l[0]-n;t<=r&&r<=e&&u.push(r)}for(const n of l)for(const i of r){const r=n+i;t<=r&&r<=e&&u.push(r)}}return{major:l,minor:u}}get_ideal_interval(t,e,n){return(e-t)/n}}Wa=as,as.__name__="ContinuousTicker",Wa.define((({Int:t})=>({num_minor_ticks:[t,5],desired_num_ticks:[t,6]})));class ss extends as{constructor(t){super(t)}get_min_interval(){return this.min_interval}get_max_interval(){return this.max_interval??1/0}initialize(){super.initialize();const t=(0,Rt.lo)(this.mantissas,-1)/this.base,e=(0,Rt.lo)(this.mantissas,0)*this.base;this.extended_mantissas=[t,...this.mantissas,e],this.base_factor=0===this.get_min_interval()?1:this.get_min_interval()}get_interval(t,e,n){const r=e-t,i=this.get_ideal_interval(t,e,n),o=Math.floor((0,Gi.Rm)(i/this.base_factor,this.base)),a=this.base**o*this.base_factor,s=this.extended_mantissas,l=s.map((t=>Math.abs(n-r/(t*a)))),c=s[(0,Rt.PN)(l)]*a;return(0,Gi.qE)(c,this.get_min_interval(),this.get_max_interval())}}Za=ss,ss.__name__="AdaptiveTicker",Za.define((({Number:t,Array:e,Nullable:n})=>({base:[t,10],mantissas:[e(t),[1,2,5]],min_interval:[t,0],max_interval:[n(t),null]})));class ls extends as{constructor(t){super(t)}get min_intervals(){return this.tickers.map((t=>t.get_min_interval()))}get max_intervals(){return this.tickers.map((t=>t.get_max_interval()))}get_min_interval(){return this.min_intervals[0]}get_max_interval(){return this.max_intervals[0]}get_best_ticker(t,e,n){const r=e-t,i=this.get_ideal_interval(t,e,n),o=[(0,Rt.P8)(this.min_intervals,i)-1,(0,Rt.P8)(this.max_intervals,i)],a=[this.min_intervals[o[0]],this.max_intervals[o[1]]].map((t=>Math.abs(n-r/t)));let s;if((0,Rt.Jb)(a.filter((t=>!isNaN(t)))))s=this.tickers[0];else{const t=o[(0,Rt.PN)(a)];s=this.tickers[t]}return s}get_interval(t,e,n){return this.get_best_ticker(t,e,n).get_interval(t,e,n)}get_ticks_no_defaults(t,e,n,r){return this.get_best_ticker(t,e,r).get_ticks_no_defaults(t,e,n,r)}}Xa=ls,ls.__name__="CompositeTicker",Xa.define((({Array:t,Ref:e})=>({tickers:[t(e(as)),[]]})));class cs extends as{constructor(t){super(t)}get_interval(t,e,n){return this.interval}get_min_interval(){return this.interval}get_max_interval(){return this.interval}}Ka=cs,cs.__name__="SingleIntervalTicker",Ka.define((({Number:t})=>({interval:[t]})));class us extends cs{constructor(t){super(t)}initialize(){super.initialize();const t=this.days;t.length>1?this.interval=(t[1]-t[0])*Na:this.interval=26784e5}get_ticks_no_defaults(t,e,n,r){const i=function(t,e){const n=za(new Date(t)),r=za(new Date(e));r.setUTCMonth(r.getUTCMonth()+1);const i=[],o=n;for(;i.push(ja(o)),o.setUTCMonth(o.getUTCMonth()+1),!(o>r););return i}(t,e),o=this.days,a=this.interval,s=(0,Rt.xW)(i.map((t=>((t,e)=>{const n=t.getUTCMonth(),r=[];for(const i of o){const o=ja(t);o.setUTCDate(i),new Date(o.getTime()+e/2).getUTCMonth()==n&&r.push(o)}return r})(t,a))));return{major:s.map((t=>t.getTime())).filter((n=>t<=n&&n<=e)),minor:[]}}}Ya=us,us.__name__="DaysTicker",Ya.define((({Int:t,Array:e})=>({days:[e(t),[]]}))),Ya.override({num_minor_ticks:0});class ds extends cs{constructor(t){super(t)}initialize(){super.initialize();const t=this.months;t.length>1?this.interval=(t[1]-t[0])*Ra:this.interval=31104e6}get_ticks_no_defaults(t,e,n,r){const i=function(t,e){const n=Ba(new Date(t)),r=Ba(new Date(e));r.setUTCFullYear(r.getUTCFullYear()+1);const i=[],o=n;for(;i.push(ja(o)),o.setUTCFullYear(o.getUTCFullYear()+1),!(o>r););return i}(t,e),o=this.months;return{major:(0,Rt.xW)(i.map((t=>o.map((e=>{const n=ja(t);return n.setUTCMonth(e),n}))))).map((t=>t.getTime())).filter((n=>t<=n&&n<=e)),minor:[]}}}Ja=ds,ds.__name__="MonthsTicker",Ja.define((({Int:t,Array:e})=>({months:[e(t),[]]})));class hs extends ss{constructor(t){super(t)}}hs.__name__="BasicTicker";class ps extends cs{constructor(t){super(t)}initialize(){super.initialize(),this.interval=Ia,this.basic_ticker=new hs({num_minor_ticks:0})}get_ticks_no_defaults(t,e,n,r){const i=Ba(new Date(t)).getUTCFullYear(),o=Ba(new Date(e)).getUTCFullYear();return{major:this.basic_ticker.get_ticks_no_defaults(i,o,n,r).major.map((t=>Date.UTC(t,0,1))).filter((n=>t<=n&&n<=e)),minor:[]}}}ps.__name__="YearsTicker";class fs extends ls{constructor(t){super(t)}}ts=fs,fs.__name__="DatetimeTicker",ts.override({num_minor_ticks:0,tickers:()=>[new ss({mantissas:[1,2,5],base:10,min_interval:0,max_interval:500,num_minor_ticks:0}),new ss({mantissas:[1,2,5,10,15,20,30],base:60,min_interval:1e3,max_interval:18e5,num_minor_ticks:0}),new ss({mantissas:[1,2,4,6,8,12],base:24,min_interval:Da,max_interval:432e5,num_minor_ticks:0}),new us({days:(0,Rt.y1)(1,32)}),new us({days:(0,Rt.y1)(1,31,3)}),new us({days:[1,8,15,22]}),new us({days:[1,15]}),new ds({months:(0,Rt.y1)(0,12,1)}),new ds({months:(0,Rt.y1)(0,12,2)}),new ds({months:(0,Rt.y1)(0,12,4)}),new ds({months:(0,Rt.y1)(0,12,6)}),new ps({})]});class Qs extends wa{}Qs.__name__="DatetimeAxisView";class Ts extends La{constructor(t){super(t)}}function ms(t){let e="";for(const n of t)e+="-"==n?"−":n;return e}es=Ts,Ts.__name__="DatetimeAxis",es.prototype.default_view=Qs,es.override({ticker:()=>new fs,formatter:()=>new Ua});class gs extends da{constructor(t){super(t),this.last_precision=3}get scientific_limit_low(){return 10**this.power_limit_low}get scientific_limit_high(){return 10**this.power_limit_high}_need_sci(t){if(!this.use_scientific)return!1;const{scientific_limit_high:e}=this,{scientific_limit_low:n}=this,r=t.length<2?0:Math.abs(t[1]-t[0])/1e4;for(const i of t){const t=Math.abs(i);if(!(t<=r)&&(t>=e||t<=n))return!0}return!1}_format_with_precision(t,e,n){return e?t.map((t=>ms(t.toExponential(n)))):t.map((t=>ms(w(t,n))))}_auto_precision(t,e){const n=new Array(t.length),r=this.last_precision<=15;t:for(let i=this.last_precision;r?i<=15:i>=1;r?i++:i--){if(e){n[0]=t[0].toExponential(i);for(let e=1;e<t.length;e++)if(n[e]==n[e-1])continue t;this.last_precision=i;break}n[0]=w(t[0],i);for(let e=1;e<t.length;e++)if(n[e]=w(t[e],i),n[e]==n[e-1])continue t;this.last_precision=i;break}return this.last_precision}doFormat(t,e){if(0==t.length)return[];const n=this._need_sci(t),r="auto"==this.precision?this._auto_precision(t,n):this.precision;return this._format_with_precision(t,n,r)}}ns=gs,gs.__name__="BasicTickFormatter",ns.define((({Boolean:t,Int:e,Auto:n,Or:r})=>({precision:[r(e,n),"auto"],use_scientific:[t,!0],power_limit_high:[e,5],power_limit_low:[e,-3]})));class _s extends wa{}_s.__name__="LinearAxisView";class bs extends La{constructor(t){super(t)}}rs=bs,bs.__name__="LinearAxis",rs.prototype.default_view=_s,rs.override({ticker:()=>new hs,formatter:()=>new gs});class vs extends ss{constructor(t){super(t)}get_ticks_no_defaults(t,e,n,r){const i=this.num_minor_ticks,o=[],a=this.base,s=Math.log(t)/Math.log(a),l=Math.log(e)/Math.log(a),c=l-s;let u;if(isFinite(c)&&0!=c)if(c<2){const n=this.get_interval(t,e,r),a=Math.floor(t/n),s=Math.ceil(e/n);if(u=(0,Rt.y1)(a,s+1).filter((t=>0!=t)).map((t=>t*n)).filter((n=>t<=n&&n<=e)),i>0&&u.length>0){const t=n/i,e=(0,Rt.y1)(0,i).map((e=>e*t));for(const t of e.slice(1))o.push(u[0]-t);for(const t of u)for(const n of e)o.push(t+n)}}else{const t=Math.ceil(.999999*s),e=Math.floor(1.000001*l),n=Math.ceil((e-t)/9);if(u=(0,Rt.y1)(t-1,e+1,n).map((t=>a**t)),i>0&&u.length>0){const t=a**n/i,e=(0,Rt.y1)(1,i+1).map((e=>e*t));for(const t of e)o.push(u[0]/t);o.push(u[0]);for(const t of u)for(const n of e)o.push(t*n)}}else u=[];return{major:u.filter((n=>t<=n&&n<=e)),minor:o.filter((n=>t<=n&&n<=e))}}}is=vs,vs.__name__="LogTicker",is.override({mantissas:[1,5]});const{abs:ys,log:xs,round:ws}=Math;class Ls extends da{constructor(t){super(t)}initialize(){super.initialize(),this.basic_formatter=new gs}format_graphics(t,e){if(0==t.length)return[];const n=this.ticker?.base??10,r=this._exponents(t,n);return null==r?this.basic_formatter.format_graphics(t,e):r.map((t=>{if(ys(t)<this.min_exponent){const e=new ko({text:ms(`${n**t}`)}),r=new ko({text:""});return new Mo(e,r)}{const e=new ko({text:ms(`${n}`)}),r=new ko({text:ms(`${t}`)});return new Mo(e,r)}}))}_exponents(t,e){let n=null;const r=[];for(const i of t){const t=ws(xs(i)/xs(e));if(n==t)return null;n=t,r.push(t)}return r}doFormat(t,e){if(0==t.length)return[];const n=this.ticker?.base??10,r=this._exponents(t,n);return null==r?this.basic_formatter.doFormat(t,e):r.map((t=>ys(t)<this.min_exponent?ms(`${n**t}`):ms(`${n}^${t}`)))}}var As,Hs,ks,Ms,Cs,Ss,Es,Vs;os=Ls,Ls.__name__="LogTickFormatter",os.define((({Int:t,Ref:e,Nullable:n})=>({ticker:[n(e(vs)),null],min_exponent:[t,0]})));class Os extends wa{}Os.__name__="LogAxisView";class Ps extends La{constructor(t){super(t)}}As=Ps,Ps.__name__="LogAxis",As.prototype.default_view=Os,As.override({ticker:()=>new vs,formatter:()=>new Ls});class Ds extends gs{constructor(t){super(t)}doFormat(t,e){if(null==this.dimension)throw new Error("MercatorTickFormatter.dimension not configured");if(0==t.length)return[];const n=t.length,r=new Array(n);if("lon"==this.dimension)for(let i=0;i<n;i++){const[n]=Ti(t[i],e.loc);r[i]=n}else for(let i=0;i<n;i++){const[,n]=Ti(e.loc,t[i]);r[i]=n}return super.doFormat(r,e)}}Hs=Ds,Ds.__name__="MercatorTickFormatter",Hs.define((({Nullable:t})=>({dimension:[t(_n.B7),null]})));class Ns extends hs{constructor(t){super(t)}get_ticks_no_defaults(t,e,n,r){if(null==this.dimension)throw new Error(`${this}.dimension wasn't configured`);return[t,e]=function(t,e,n){const[r,i]=mi[n];return[bi(t,r),_i(e,i)]}(t,e,this.dimension),"lon"==this.dimension?this._get_ticks_lon(t,e,n,r):this._get_ticks_lat(t,e,n,r)}_get_ticks_lon(t,e,n,r){const[i]=Ti(t,n),[o,a]=Ti(e,n),s=super.get_ticks_no_defaults(i,o,n,r),l=[];for(const t of s.major)if(vi(t,"lon")){const[e]=Qi(t,a);l.push(e)}const c=[];for(const t of s.minor)if(vi(t,"lon")){const[e]=Qi(t,a);c.push(e)}return{major:l,minor:c}}_get_ticks_lat(t,e,n,r){const[,i]=Ti(n,t),[o,a]=Ti(n,e),s=super.get_ticks_no_defaults(i,a,n,r),l=[];for(const t of s.major)if(vi(t,"lat")){const[,e]=Qi(o,t);l.push(e)}const c=[];for(const t of s.minor)if(vi(t,"lat")){const[,e]=Qi(o,t);c.push(e)}return{major:l,minor:c}}}ks=Ns,Ns.__name__="MercatorTicker",ks.define((({Nullable:t})=>({dimension:[t(_n.B7),null]})));class Rs extends ma{}Rs.__name__="MercatorAxisView";class Is extends bs{constructor(t){super(t)}}Ms=Is,Is.__name__="MercatorAxis",Ms.prototype.default_view=Rs,Ms.override({ticker:()=>new Ns({dimension:"lat"}),formatter:()=>new Ds({dimension:"lat"})});class js extends as{constructor(t){super(t)}get_ticks_no_defaults(t,e,n,r){return{major:[...this.ticks],minor:[...this.minor_ticks]}}get_interval(t,e,n){return 0}get_min_interval(){return 0}get_max_interval(){return 0}}Cs=js,js.__name__="FixedTicker",Cs.define((({Number:t,Arrayable:e})=>({ticks:[e(t),[]],minor_ticks:[e(t),[]]})));class zs extends vn{constructor(t){super(t)}compute(t){throw new Error("mapping single values is not supported")}}function Bs(t){return(0,Ye.Wh)((0,Ye.qG)(t))}zs.__name__="Mapper";class Fs extends zs{constructor(t){super(t)}initialize(){super.initialize(),this.metrics_change=new T.n2(this,"metrics_change")}v_compute(t){const e=new Array(t.length);return this._v_compute(t,e,this.palette,this._colors((t=>t))),e}get rgba_mapper(){const t=this,e=function(t){const e=new Uint32Array(t.length);for(let n=0,r=t.length;n<r;n++)e[n]=Bs(t[n]);return e}(this.palette),n=this._colors(Bs);return{v_compute(r){const i=new Jt.x8(r.length);return t._v_compute(r,i,e,n),new Uint8ClampedArray((0,It.vv)(i).buffer)}}}_colors(t){return{nan_color:t(this.nan_color)}}}Ss=Fs,Fs.__name__="ColorMapper",Ss.define((({Color:t,Array:e})=>({palette:[e(t)],nan_color:[t,"gray"]})));class $s extends tr{get xscale(){return this.coordinates.x_scale}get yscale(){return this.coordinates.y_scale}}$s.__name__="DataRendererView";class Gs extends er{constructor(t){super(t)}get selection_manager(){return this.get_selection_manager()}}Es=Gs,Gs.__name__="DataRenderer",Es.override({level:"glyph"});class qs{constructor(t,e){this.offsets=t,this.array=e}[(Vs=Symbol.toStringTag,A.aI)](t,e){return e.arrays(this.offsets,t.offsets)&&e.arrays(this.array,t.array)}get length(){return this.offsets.length}clone(){return new qs(this.offsets.slice(),this.array.slice())}static from(t,e){const n=t.length;let r=0;const i=(()=>{const e=new Uint32Array(n);for(let i=0;i<n;i++){const n=t[i].length;e[i]=r,r+=n}return r<256?new Uint8Array(e):r<65536?new Uint16Array(e):e})(),o=new e(r);for(let e=0;e<n;e++)o.set(t[e],i[e]);return new qs(i,o)}*[Symbol.iterator](){const{offsets:t,length:e}=this;for(let n=0;n<e;n++)yield this.array.subarray(t[n],t[n+1])}_check_bounds(t){(0,_.vA)(0<=t&&t<this.length,`Out of bounds: 0 <= ${t} < ${this.length}`)}get(t){this._check_bounds(t);const{offsets:e}=this;return this.array.subarray(e[t],e[t+1])}set(t,e){this._check_bounds(t),this.array.set(e,this.offsets[t])}}qs.__name__="RaggedArray",qs[Vs]="RaggedArray";class Us{constructor(){this.ids=[],this.values=[],this.length=0}clear(){this.length=0}push(t,e){let n=this.length++;for(;n>0;){const t=n-1>>1,r=this.values[t];if(e>=r)break;this.ids[n]=this.ids[t],this.values[n]=r,n=t}this.ids[n]=t,this.values[n]=e}pop(){if(0===this.length)return;const t=this.ids[0];if(this.length--,this.length>0){const t=this.ids[0]=this.ids[this.length],e=this.values[0]=this.values[this.length],n=this.length>>1;let r=0;for(;r<n;){let t=1+(r<<1);const n=t+1;let i=this.ids[t],o=this.values[t];const a=this.values[n];if(n<this.length&&a<o&&(t=n,i=this.ids[n],o=a),o>=e)break;this.ids[r]=i,this.values[r]=o,r=t}this.ids[r]=t,this.values[r]=e}return t}peek(){if(0!==this.length)return this.ids[0]}peekValue(){if(0!==this.length)return this.values[0]}shrink(){this.ids.length=this.values.length=this.length}}const Ws=[Int8Array,Uint8Array,Uint8ClampedArray,Int16Array,Uint16Array,Int32Array,Uint32Array,Float32Array,Float64Array];class Zs{static from(t,e=0){if(e%8!=0)throw new Error("byteOffset must be 8-byte aligned.");if(!t||void 0===t.byteLength||t.buffer)throw new Error("Data must be an instance of ArrayBuffer or SharedArrayBuffer.");const[n,r]=new Uint8Array(t,e+0,2);if(251!==n)throw new Error("Data does not appear to be in a Flatbush format.");const i=r>>4;if(3!==i)throw new Error(`Got v${i} data when expected v3.`);const o=Ws[15&r];if(!o)throw new Error("Unrecognized array type.");const[a]=new Uint16Array(t,e+2,1),[s]=new Uint32Array(t,e+4,1);return new Zs(s,a,o,void 0,t,e)}constructor(t,e=16,n=Float64Array,r=ArrayBuffer,i,o=0){if(void 0===t)throw new Error("Missing required argument: numItems.");if(isNaN(t)||t<=0)throw new Error(`Unexpected numItems value: ${t}.`);this.numItems=+t,this.nodeSize=Math.min(Math.max(+e,2),65535),this.byteOffset=o;let a=t,s=a;this._levelBounds=[4*a];do{a=Math.ceil(a/this.nodeSize),s+=a,this._levelBounds.push(4*s)}while(1!==a);this.ArrayType=n,this.IndexArrayType=s<16384?Uint16Array:Uint32Array;const l=Ws.indexOf(this.ArrayType),c=4*s*this.ArrayType.BYTES_PER_ELEMENT;if(l<0)throw new Error(`Unexpected typed array class: ${n}.`);i&&void 0!==i.byteLength&&!i.buffer?(this.data=i,this._boxes=new this.ArrayType(this.data,o+8,4*s),this._indices=new this.IndexArrayType(this.data,o+8+c,s),this._pos=4*s,this.minX=this._boxes[this._pos-4],this.minY=this._boxes[this._pos-3],this.maxX=this._boxes[this._pos-2],this.maxY=this._boxes[this._pos-1]):(this.data=new r(8+c+s*this.IndexArrayType.BYTES_PER_ELEMENT),this._boxes=new this.ArrayType(this.data,8,4*s),this._indices=new this.IndexArrayType(this.data,8+c,s),this._pos=0,this.minX=1/0,this.minY=1/0,this.maxX=-1/0,this.maxY=-1/0,new Uint8Array(this.data,0,2).set([251,48+l]),new Uint16Array(this.data,2,1)[0]=e,new Uint32Array(this.data,4,1)[0]=t),this._queue=new Us}add(t,e,n=t,r=e){const i=this._pos>>2,o=this._boxes;return this._indices[i]=i,o[this._pos++]=t,o[this._pos++]=e,o[this._pos++]=n,o[this._pos++]=r,t<this.minX&&(this.minX=t),e<this.minY&&(this.minY=e),n>this.maxX&&(this.maxX=n),r>this.maxY&&(this.maxY=r),i}finish(){if(this._pos>>2!==this.numItems)throw new Error(`Added ${this._pos>>2} items when expected ${this.numItems}.`);const t=this._boxes;if(this.numItems<=this.nodeSize)return t[this._pos++]=this.minX,t[this._pos++]=this.minY,t[this._pos++]=this.maxX,void(t[this._pos++]=this.maxY);const e=this.maxX-this.minX||1,n=this.maxY-this.minY||1,r=new Uint32Array(this.numItems);for(let i=0,o=0;i<this.numItems;i++){const a=t[o++],s=t[o++],l=t[o++],c=t[o++],u=Math.floor(65535*((a+l)/2-this.minX)/e),d=Math.floor(65535*((s+c)/2-this.minY)/n);r[i]=tl(u,d)}Ys(r,t,this._indices,0,this.numItems-1,this.nodeSize);for(let e=0,n=0;e<this._levelBounds.length-1;e++){const r=this._levelBounds[e];for(;n<r;){const e=n;let i=t[n++],o=t[n++],a=t[n++],s=t[n++];for(let e=1;e<this.nodeSize&&n<r;e++)i=Math.min(i,t[n++]),o=Math.min(o,t[n++]),a=Math.max(a,t[n++]),s=Math.max(s,t[n++]);this._indices[this._pos>>2]=e,t[this._pos++]=i,t[this._pos++]=o,t[this._pos++]=a,t[this._pos++]=s}}}search(t,e,n,r,i){if(this._pos!==this._boxes.length)throw new Error("Data not yet indexed - call index.finish().");let o=this._boxes.length-4;const a=[],s=[];for(;void 0!==o;){const l=Math.min(o+4*this.nodeSize,Ks(o,this._levelBounds));for(let c=o;c<l;c+=4){if(n<this._boxes[c])continue;if(r<this._boxes[c+1])continue;if(t>this._boxes[c+2])continue;if(e>this._boxes[c+3])continue;const l=0|this._indices[c>>2];o>=4*this.numItems?a.push(l):(void 0===i||i(l))&&s.push(l)}o=a.pop()}return s}neighbors(t,e,n=1/0,r=1/0,i){if(this._pos!==this._boxes.length)throw new Error("Data not yet indexed - call index.finish().");let o=this._boxes.length-4;const a=this._queue,s=[],l=r*r;t:for(;void 0!==o;){const r=Math.min(o+4*this.nodeSize,Ks(o,this._levelBounds));for(let n=o;n<r;n+=4){const r=0|this._indices[n>>2],s=Xs(t,this._boxes[n],this._boxes[n+2]),c=Xs(e,this._boxes[n+1],this._boxes[n+3]),u=s*s+c*c;u>l||(o>=4*this.numItems?a.push(r<<1,u):(void 0===i||i(r))&&a.push(1+(r<<1),u))}for(;a.length&&1&a.peek();){if(a.peekValue()>l)break t;if(s.push(a.pop()>>1),s.length===n)break t}o=a.length?a.pop()>>1:void 0}return a.clear(),s}}function Xs(t,e,n){return t<e?e-t:t<=n?0:t-n}function Ks(t,e){let n=0,r=e.length-1;for(;n<r;){const i=n+r>>1;e[i]>t?r=i:n=i+1}return e[n]}function Ys(t,e,n,r,i,o){if(Math.floor(r/o)>=Math.floor(i/o))return;const a=t[r+i>>1];let s=r-1,l=i+1;for(;;){do{s++}while(t[s]<a);do{l--}while(t[l]>a);if(s>=l)break;Js(t,e,n,s,l)}Ys(t,e,n,r,l,o),Ys(t,e,n,l+1,i,o)}function Js(t,e,n,r,i){const o=t[r];t[r]=t[i],t[i]=o;const a=4*r,s=4*i,l=e[a],c=e[a+1],u=e[a+2],d=e[a+3];e[a]=e[s],e[a+1]=e[s+1],e[a+2]=e[s+2],e[a+3]=e[s+3],e[s]=l,e[s+1]=c,e[s+2]=u,e[s+3]=d;const h=n[r];n[r]=n[i],n[i]=h}function tl(t,e){let n=t^e,r=65535^n,i=65535^(t|e),o=t&(65535^e),a=n|r>>1,s=n>>1^n,l=i>>1^r&o>>1^i,c=n&i>>1^o>>1^o;n=a,r=s,i=l,o=c,a=n&n>>2^r&r>>2,s=n&r>>2^r&(n^r)>>2,l^=n&i>>2^r&o>>2,c^=r&i>>2^(n^r)&o>>2,n=a,r=s,i=l,o=c,a=n&n>>4^r&r>>4,s=n&r>>4^r&(n^r)>>4,l^=n&i>>4^r&o>>4,c^=r&i>>4^(n^r)&o>>4,n=a,r=s,i=l,o=c,l^=n&i>>8^r&o>>8,c^=r&i>>8^(n^r)&o>>8,n=l^l>>1,r=c^c>>1;let u=t^e,d=r|65535^(u|n);return u=16711935&(u|u<<8),u=252645135&(u|u<<4),u=858993459&(u|u<<2),u=1431655765&(u|u<<1),d=16711935&(d|d<<8),d=252645135&(d|d<<4),d=858993459&(d|d<<2),d=1431655765&(d|d<<1),(d<<1|u)>>>0}function el(t,e){let n=0,r=e.length-1;for(;n<r;){const i=n+r>>1;e[i]>t?r=i:n=i+1}return e[n]}class nl extends Zs{get boxes(){return this._boxes}search_indices(t,e,n,r){if(this._pos!==this._boxes.length)throw new Error("Data not yet indexed - call index.finish().");let i=this._boxes.length-4;const o=[],a=new Jt.et(this.numItems);for(;void 0!==i;){const s=Math.min(i+4*this.nodeSize,el(i,this._levelBounds));for(let l=i;l<s;l+=4){const s=0|this._indices[l>>2],c=this._boxes[l+0],u=this._boxes[l+1],d=this._boxes[l+2],h=this._boxes[l+3];n<c||r<u||t>d||e>h||(i<4*this.numItems?a.set(s):o.push(s))}i=o.pop()}return a}}nl.__name__="_FlatBush";class rl{constructor(t){this.index=null,t>0&&(this.index=new nl(t))}add_rect(t,e,n,r){isFinite(t+e+n+r)?this.index?.add(t,e,n,r):this.add_empty()}add_point(t,e){isFinite(t+e)?this.index?.add(t,e,t,e):this.add_empty()}add_empty(){this.index?.add(1/0,1/0,-1/0,-1/0)}finish(){this.index?.finish()}_normalize(t){let{x0:e,y0:n,x1:r,y1:i}=t;return e>r&&([e,r]=[r,e]),n>i&&([n,i]=[i,n]),{x0:e,y0:n,x1:r,y1:i}}get bbox(){if(null==this.index)return{x0:1/0,y0:1/0,x1:-1/0,y1:-1/0};{const{minX:t,minY:e,maxX:n,maxY:r}=this.index;return{x0:t,y0:e,x1:n,y1:r}}}indices(t){if(null==this.index)return new Jt.et(0);{const{x0:e,y0:n,x1:r,y1:i}=this._normalize(t);return this.index.search_indices(e,n,r,i)}}bounds(t){const e={x0:1/0,y0:1/0,x1:-1/0,y1:-1/0};if(null==this.index)return e;const{boxes:n}=this.index;for(const r of this.indices(t)){const i=n[4*r+0],o=n[4*r+1],a=n[4*r+2],s=n[4*r+3];i>=t.x0&&i<e.x0&&(e.x0=i),a<=t.x1&&a>e.x1&&(e.x1=a),o>=t.y0&&o<e.y0&&(e.y0=o),s<=t.y1&&s>e.y1&&(e.y1=s)}return e}}var il,ol;rl.__name__="SpatialIndex";class al extends Kt{*children(){yield*super.children(),yield this.marking}async lazy_initialize(){await super.lazy_initialize(),this.marking=await $e(this.model.marking,{parent:this.parent})}}al.__name__="DecorationView";class sl extends qt{constructor(t){super(t)}}il=sl,sl.__name__="Decoration",il.prototype.default_view=al,il.define((({Enum:t,Ref:e})=>({marking:[e(Vi)],node:[t("start","middle","end")]})));const{abs:ll,ceil:cl}=Math;class ul extends Kt{constructor(){super(...arguments),this._index=null,this._data_size=null,this._nohit_warned=new Set,this.decorations=new Map}get renderer(){return this.parent}get has_webgl(){return null!=this.glglyph}get index(){const{_index:t}=this;if(null!=t)return t;throw new Error(`${this}.index_data() wasn't called`)}get data_size(){const{_data_size:t}=this;if(null!=t)return t;throw new Error(`${this}.set_data() wasn't called`)}initialize(){super.initialize(),this.visuals=new Qn(this)}*children(){yield*super.children(),yield*this.decorations.values()}async lazy_initialize(){await super.lazy_initialize(),await Ge(this.decorations,this.model.decorations,{parent:this.parent})}request_render(){this.parent.request_render()}get canvas(){return this.renderer.parent.canvas_view}render(t,e,n){null!=this.glglyph&&(this.renderer.needs_webgl_blit=this.glglyph.render(t,e,this.base??this),this.renderer.needs_webgl_blit)||this._render(t,e,n??this.base)}has_finished(){return!0}notify_finished(){this.renderer.notify_finished()}_bounds(t){return t}bounds(){return this._bounds(this.index.bbox)}log_bounds(){const{x0:t,x1:e}=this.index.bounds({x0:Number.MIN_VALUE,y0:-1/0,x1:1/0,y1:1/0}),{y0:n,y1:r}=this.index.bounds({x0:-1/0,y0:Number.MIN_VALUE,x1:1/0,y1:1/0});return this._bounds({x0:t,y0:n,x1:e,y1:r})}get_anchor_point(t,e,[n,r]){switch(t){case"center":case"center_center":{const[t,i]=this.scenterxy(e,n,r);return{x:t,y:i}}default:return null}}sdist(t,e,n,r="edge",i=!1){const o=e.length,a=new Jt.mR(o),s=t.s_compute;if("center"==r)for(let t=0;t<o;t++){const r=e[t],i=n.get(t)/2,o=s(r-i),l=s(r+i);a[t]=ll(l-o)}else for(let t=0;t<o;t++){const r=e[t],i=s(r),o=s(r+n.get(t));a[t]=ll(o-i)}return i&&(0,bn.io)(a,(t=>cl(t))),a}draw_legend_for_index(t,e,n){}hit_test(t){switch(t.type){case"point":if(null!=this._hit_point)return this._hit_point(t);break;case"span":if(null!=this._hit_span)return this._hit_span(t);break;case"rect":if(null!=this._hit_rect)return this._hit_rect(t);break;case"poly":if(null!=this._hit_poly)return this._hit_poly(t)}return this._nohit_warned.has(t.type)||(ot.vF.debug(`'${t.type}' selection not available for ${this.model.type}`),this._nohit_warned.add(t.type)),null}_hit_rect_against_index(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,[o,a]=this.renderer.coordinates.x_scale.r_invert(e,n),[s,l]=this.renderer.coordinates.y_scale.r_invert(r,i),c=[...this.index.indices({x0:o,x1:a,y0:s,y1:l})];return new ir({indices:c})}_project_data(){}*_iter_visuals(){for(const t of this.visuals)for(const e of t)(e instanceof m.Pz||e instanceof m._n)&&(yield e)}set_base(t){t!=this&&t instanceof this.constructor&&(this.base=t)}_configure(t,e){Object.defineProperty(this,(0,f.Kg)(t)?t:t.attr,{configurable:!0,enumerable:!0,...e})}set_visuals(t,e){for(const n of this._iter_visuals()){const{base:r}=this;if(null!=r){const t=r.model.properties[n.attr];if(null!=t&&(0,A.g4)(n.get_value(),t.get_value())){this._configure(n,{get:()=>r[`${n.attr}`]});continue}}const i=n.uniform(t).select(e);this._configure(n,{value:i})}for(const t of this.visuals)t.update();this.glglyph?.set_visuals_changed()}set_data(t,e,n){const{x_source:r,y_source:i}=this.renderer.coordinates,o=new Set(this._iter_visuals());this._data_size=e.count;for(const n of this.model)if((n instanceof m.Pz||n instanceof m._n)&&!o.has(n))if(n instanceof m.PR){const o=n.array(t);let a=e.select(o);const s="x"==n.dimension?r:i;if(s instanceof jn)if(n instanceof m.Ok)a=s.v_synthetic(a);else if(n instanceof m.B2)for(let t=0;t<a.length;t++)a[t]=s.v_synthetic(a[t]);let l;l=n instanceof m.B2?qs.from(a,Float64Array):a,this._configure(`_${n.attr}`,{value:l})}else{const r=n.uniform(t).select(e);if(this._configure(n,{value:r}),n instanceof m.x0){const t=r.is_Scalar()?r.value:(0,bn.T9)(r.array);this._configure(`max_${n.attr}`,{value:t})}}this.renderer.plot_view.model.use_map&&this._project_data(),this._set_data(n??null);for(const n of this.decorations.values())n.marking.set_data(t,e);this.glglyph?.set_data_changed(),this.index_data()}_set_data(t){}get _index_size(){return this.data_size}index_data(){const t=new rl(this._index_size);this._index_data(t),t.finish(),this._index=t}mask_data(){return null==this._mask_data?Jt.et.all_set(this.data_size):this._mask_data()}map_data(){const t=this,{x_scale:e,y_scale:n}=this.renderer.coordinates;for(const r of this.model)if(r instanceof m.PR){const i="x"==r.dimension?e:n;let o=t[`_${r.attr}`];if(o instanceof qs){const t=i.v_compute(o.array);o=new qs(o.offsets,t)}else o=i.v_compute(o);this[`s${r.attr}`]=o}this._map_data(),this.glglyph?.set_data_changed()}_map_data(){}}ul.__name__="GlyphView";class dl extends qt{constructor(t){super(t)}}var hl,pl,fl,Ql,Tl,ml,gl,_l,bl;ol=dl,dl.__name__="Glyph",ol.define((({Array:t,Ref:e})=>({decorations:[t(e(sl)),[]]})));class vl extends ul{_project_data(){yi.project_xy(this._x,this._y)}_index_data(t){const{_x:e,_y:n,data_size:r}=this;for(let i=0;i<r;i++){const r=e[i],o=n[i];t.add_point(r,o)}}scenterxy(t){return[this.sx[t],this.sy[t]]}}vl.__name__="XYGlyphView";class yl extends dl{constructor(t){super(t)}}function xl(t,e,n,r){let i=!1,o=n[n.length-1],a=r[r.length-1];for(let s=0;s<n.length;s++){const l=n[s],c=r[s];a<e!=c<e&&o+(e-a)/(c-a)*(l-o)<t&&(i=!i),o=l,a=c}return i}function wl(t,e,n,r,i,o,a){return((Math.cos(n)/i)**2+(Math.sin(n)/r)**2)*(t-o)**2+2*Math.cos(n)*Math.sin(n)*((1/i)**2-(1/r)**2)*(t-o)*(e-a)+((Math.cos(n)/r)**2+(Math.sin(n)/i)**2)*(e-a)**2<=1}function Ll(t,e){return(t.x-e.x)**2+(t.y-e.y)**2}function Al(t,e,n){const r=Ll(e,n);if(0==r)return Ll(t,e);const i=((t.x-e.x)*(n.x-e.x)+(t.y-e.y)*(n.y-e.y))/r;return Ll(t,i<0?e:i>1?n:{x:e.x+i*(n.x-e.x),y:e.y+i*(n.y-e.y)})}function Hl(t,e,n){return Math.sqrt(Al(t,e,n))}function kl(t,e,{x0:n,x1:r,y0:i,y1:o}){e.save(),e.beginPath(),e.moveTo(n,(i+o)/2),e.lineTo(r,(i+o)/2),t.line.apply(e),e.restore()}function Ml(t,e,{x0:n,x1:r,y0:i,y1:o},a){e.save(),e.beginPath(),e.moveTo(n,(i+o)/2),e.lineTo(r,(i+o)/2),t.line.apply(e,a),e.restore()}function Cl(t,e,{x0:n,x1:r,y0:i,y1:o}){const a=.1*Math.abs(r-n),s=.1*Math.abs(o-i),l=n+a,c=r-a,u=i+s,d=o-s;e.beginPath(),e.rect(l,u,c-l,d-u),t.fill.apply(e),t.hatch?.apply(e),t.line?.apply(e)}function Sl(t,e,{x0:n,x1:r,y0:i,y1:o},a){const s=.1*Math.abs(r-n),l=.1*Math.abs(o-i),c=n+s,u=r-s,d=i+l,h=o-l;e.beginPath(),e.rect(c,d,u-c,h-d),t.fill.apply(e,a),t.hatch?.apply(e,a),t.line?.apply(e,a)}function El(t,e,n,r,i,o){const{sx:a,sy:s}=e;let l,c,u,d;"point"==e.type?([u,d]=t.yscale.r_invert(s-1,s+1),[l,c]=t.xscale.r_invert(a-1,a+1)):"v"==e.direction?([u,d]=t.yscale.r_invert(s,s),[l,c]=[Math.min(n-1,i-1),Math.max(n+1,i+1)]):([l,c]=t.xscale.r_invert(a,a),[u,d]=[Math.min(r-1,o-1),Math.max(r+1,o+1)]);const{x:h,y:p}=function(t,e,n,r,i,o,a,s){const l=(s-o)*(n-t)-(a-i)*(r-e);if(0==l)return{hit:!1,x:null,y:null};{let c=e-o,u=t-i;const d=(n-t)*c-(r-e)*u;return c=((a-i)*c-(s-o)*u)/l,u=d/l,{hit:c>0&&c<1&&u>0&&u<1,x:t+c*(n-t),y:e+c*(r-e)}}}(l,u,c,d,n,r,i,o);return[h,p]}hl=yl,yl.__name__="XYGlyph",hl.define((({})=>({x:[m.up,{field:"x"}],y:[m.fZ,{field:"y"}]})));class Vl extends vl{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{LineGL:e}=await Promise.resolve().then(n.bind(n,3461));this.glglyph=new e(t.regl_wrapper,this)}}_render(t,e,n){const{sx:r,sy:i}=n??this,o=this.parent.nonselection_glyph==this;let a=null;const s=t=>null!=a&&t-a!=1;let l=!0;t.beginPath();for(const n of e){const e=r[n],c=i[n];o&&!l&&null!=a&&n-a>1&&isFinite(r[a+1]+i[a+1])&&t.lineTo(r[a+1],i[a+1]),isFinite(e+c)?(l||s(n)?(o&&n>0&&isFinite(r[n-1]+i[n-1])?(t.moveTo(r[n-1],i[n-1]),t.lineTo(e,c)):t.moveTo(e,c),l=!1):t.lineTo(e,c),a=n):l=!0}if(o&&!l&&null!=a){const e=r.length;a<e-1&&isFinite(r[a+1]+i[a+1])&&t.lineTo(r[a+1],i[a+1])}this.visuals.line.set_value(t),t.stroke()}_hit_point(t){const e=new ir,n={x:t.sx,y:t.sy};let r=9999;const i=Math.max(2,this.line_width.value/2);for(let t=0,o=this.sx.length-1;t<o;t++){const o=Hl(n,{x:this.sx[t],y:this.sy[t]},{x:this.sx[t+1],y:this.sy[t+1]});o<i&&o<r&&(r=o,e.add_to_selected_glyphs(this.model),e.view=this,e.line_indices=[t])}return e}_hit_span(t){const{sx:e,sy:n}=t,r=new ir;let i,o;"v"==t.direction?(i=this.renderer.yscale.invert(n),o=this._y):(i=this.renderer.xscale.invert(e),o=this._x);for(let t=0,e=o.length-1;t<e;t++)(o[t]<=i&&i<=o[t+1]||o[t+1]<=i&&i<=o[t])&&(r.add_to_selected_glyphs(this.model),r.view=this,r.line_indices.push(t));return r}get_interpolation_hit(t,e){const[n,r,i,o]=[this._x[t],this._y[t],this._x[t+1],this._y[t+1]];return El(this.renderer,e,n,r,i,o)}draw_legend_for_index(t,e,n){kl(this.visuals,t,e)}}Vl.__name__="LineView";class Ol extends yl{constructor(t){super(t)}}pl=Ol,Ol.__name__="Line",pl.prototype.default_view=Vl,pl.mixins(Ke.Rb);class Pl extends vl{_render(t,e,n){const{sx:r,sy:i}=n??this;let o=!0;t.beginPath();for(const n of e){const e=r[n],a=i[n];isFinite(e+a)?o?(t.moveTo(e,a),o=!1):t.lineTo(e,a):(t.closePath(),o=!0)}t.closePath(),this.visuals.fill.apply(t),this.visuals.hatch.apply(t),this.visuals.line.apply(t)}draw_legend_for_index(t,e,n){Cl(this.visuals,t,e)}_hit_point(t){const e=new ir;return xl(t.sx,t.sy,this.sx,this.sy)&&(e.add_to_selected_glyphs(this.model),e.view=this),e}}Pl.__name__="PatchView";class Dl extends yl{constructor(t){super(t)}}fl=Dl,Dl.__name__="Patch",fl.prototype.default_view=Pl,fl.mixins([Ke.Rb,Ke.GA,Ke.JG]);class Nl extends ul{draw_legend_for_index(t,e,n){Cl(this.visuals,t,e)}}Nl.__name__="AreaView";class Rl extends dl{constructor(t){super(t)}}Ql=Rl,Rl.__name__="Area",Ql.mixins([Ke.GA,Ke.JG]);class Il extends Nl{_index_data(t){const{min:e,max:n}=Math,{data_size:r}=this;for(let i=0;i<r;i++){const r=this._x1[i],o=this._x2[i],a=this._y[i];t.add_rect(e(r,o),a,n(r,o),a)}}_render(t,e,n){const{sx1:r,sx2:i,sy:o}=n??this;t.beginPath();for(let e=0,n=r.length;e<n;e++)t.lineTo(r[e],o[e]);for(let e=i.length-1;e>=0;e--)t.lineTo(i[e],o[e]);t.closePath(),this.visuals.fill.apply(t),this.visuals.hatch.apply(t)}_hit_point(t){const e=this.sy.length,n=new ir;for(let r=0,i=e-1;r<i;r++){const e=[this.sx1[r],this.sx1[r+1],this.sx2[r+1],this.sx2[r]],i=[this.sy[r],this.sy[r+1],this.sy[r+1],this.sy[r]];if(xl(t.sx,t.sy,e,i)){n.add_to_selected_glyphs(this.model),n.view=this,n.line_indices=[r];break}}return n}scenterxy(t){return[(this.sx1[t]+this.sx2[t])/2,this.sy[t]]}_map_data(){this.sx1=this.renderer.xscale.v_compute(this._x1),this.sx2=this.renderer.xscale.v_compute(this._x2),this.sy=this.renderer.yscale.v_compute(this._y)}}Il.__name__="HAreaView";class jl extends Rl{constructor(t){super(t)}}Tl=jl,jl.__name__="HArea",Tl.prototype.default_view=Il,Tl.define((({})=>({x1:[m.up,{field:"x1"}],x2:[m.up,{field:"x2"}],y:[m.fZ,{field:"y"}]})));class zl extends Nl{_index_data(t){const{min:e,max:n}=Math,{data_size:r}=this;for(let i=0;i<r;i++){const r=this._x[i],o=this._y1[i],a=this._y2[i];t.add_rect(r,e(o,a),r,n(o,a))}}_render(t,e,n){const{sx:r,sy1:i,sy2:o}=n??this;t.beginPath();for(let e=0,n=i.length;e<n;e++)t.lineTo(r[e],i[e]);for(let e=o.length-1;e>=0;e--)t.lineTo(r[e],o[e]);t.closePath(),this.visuals.fill.apply(t),this.visuals.hatch.apply(t)}scenterxy(t){return[this.sx[t],(this.sy1[t]+this.sy2[t])/2]}_hit_point(t){const e=this.sx.length,n=new ir;for(let r=0,i=e-1;r<i;r++){const e=[this.sx[r],this.sx[r+1],this.sx[r+1],this.sx[r]],i=[this.sy1[r],this.sy1[r+1],this.sy2[r+1],this.sy2[r]];if(xl(t.sx,t.sy,e,i)){n.add_to_selected_glyphs(this.model),n.view=this,n.line_indices=[r];break}}return n}_map_data(){this.sx=this.renderer.xscale.v_compute(this._x),this.sy1=this.renderer.yscale.v_compute(this._y1),this.sy2=this.renderer.yscale.v_compute(this._y2)}}zl.__name__="VAreaView";class Bl extends Rl{constructor(t){super(t)}}ml=Bl,Bl.__name__="VArea",ml.prototype.default_view=zl,ml.define((({})=>({x:[m.up,{field:"x"}],y1:[m.fZ,{field:"y1"}],y2:[m.fZ,{field:"y2"}]})));class Fl extends qt{constructor(t){super(t)}}Fl.__name__="Filter";class $l extends Fl{constructor(t){super(t)}compute_indices(t){const e=t.get_length()??1;return Jt.et.all_set(e)}}$l.__name__="AllIndices";class Gl extends Fl{constructor(t){super(t)}compute_indices(t){const{operands:e}=this;if(0==e.length){const e=t.get_length()??1;return Jt.et.all_set(e)}{const[n,...r]=e.map((e=>e.compute_indices(t)));for(const t of r)n.intersect(t);return n}}}gl=Gl,Gl.__name__="IntersectionFilter",gl.define((({Array:t,Ref:e})=>({operands:[t(e(Fl))]})));class ql extends Kt{initialize(){super.initialize(),this.compute_indices()}connect_signals(){super.connect_signals();const{filter:t}=this.model.properties;this.on_change(t,(()=>this.compute_indices()));const e=()=>{const t=()=>this.compute_indices(),e=this.parent.data_source.get_value();this.connect(e.change,t),this.connect(e.streaming,t),this.connect(e.patching,t)};e();const{data_source:n}=this.parent;this.on_change(n,(()=>{e()}))}compute_indices(){const t=this.parent.data_source.get_value(),e=t.get_length()??1,n=Jt.et.all_set(e),r=this.model.filter.compute_indices(t);n.intersect(r),this.model.indices=n,this.model._indices_map_to_subset()}}ql.__name__="CDSViewView";class Ul extends qt{constructor(t){super(t)}_indices_map_to_subset(){this._indices=[...this.indices],this.indices_map={};for(let t=0;t<this._indices.length;t++)this.indices_map[this._indices[t]]=t}convert_selection_from_subset(t){return t.map((t=>this._indices[t]))}convert_selection_to_subset(t){return t.map((t=>this.indices_map[t]))}convert_indices_from_subset(t){return t.map((t=>this._indices[t]))}get filters(){const{filter:t}=this;return t instanceof Gl?t.operands:t instanceof $l?[]:[t]}set filters(t){0==t.length?this.filter=new $l:1==t.length?this.filter=t[0]:this.filter=new Gl({operands:t})}}_l=Ul,Ul.__name__="CDSView",_l.prototype.default_view=ql,_l.define((({Ref:t})=>({filter:[t(Fl),()=>new $l]}))),_l.internal((({Int:t,Dict:e,Ref:n,Nullable:r})=>({indices:[n(Jt.et)],indices_map:[e(t),{}],masked:[r(n(Jt.et)),null]})));const Wl={fill:{},line:{}},Zl={fill:{fill_alpha:.3,fill_color:"grey"},line:{line_alpha:.3,line_color:"grey"}},Xl={fill:{fill_alpha:.2},line:{}},Kl={fill:{fill_alpha:.2},line:{}};class Yl extends $s{get glyph_view(){return this.glyph}*children(){yield*super.children(),yield this.cds_view,yield this.glyph,yield this.selection_glyph,yield this.nonselection_glyph,null!=this.hover_glyph&&(yield this.hover_glyph),yield this.muted_glyph,yield this.decimated_glyph}get data_source(){return this.model.properties.data_source}async lazy_initialize(){await super.lazy_initialize(),this.cds_view=await $e(this.model.view,{parent:this});const t=this.model.glyph;this.glyph=await this.build_glyph_view(t);const e="fill"in this.glyph.visuals,n="line"in this.glyph.visuals,r={...t.attributes};function i(i,o){return o instanceof dl?o:function(i){const o=(0,Q.o8)(r);return e&&(0,Q.X$)(o,i.fill),n&&(0,Q.X$)(o,i.line),new t.constructor(o)}("auto"==o?i:{fill:{},line:{}})}delete r.id;let{selection_glyph:o,nonselection_glyph:a,hover_glyph:s,muted_glyph:l}=this.model;o=i(Wl,o),this.selection_glyph=await this.build_glyph_view(o),a=i(Xl,a),this.nonselection_glyph=await this.build_glyph_view(a),null!=s&&(this.hover_glyph=await this.build_glyph_view(s)),l=i(Kl,l),this.muted_glyph=await this.build_glyph_view(l);const c=i(Zl,"auto");this.decimated_glyph=await this.build_glyph_view(c),this.selection_glyph.set_base(this.glyph),this.nonselection_glyph.set_base(this.glyph),this.hover_glyph?.set_base(this.glyph),this.muted_glyph.set_base(this.glyph),this.decimated_glyph.set_base(this.glyph),this.set_data()}async build_glyph_view(t){return $e(t,{parent:this})}remove(){this.cds_view.remove(),this.glyph.remove(),this.selection_glyph.remove(),this.nonselection_glyph.remove(),this.hover_glyph?.remove(),this.muted_glyph.remove(),this.decimated_glyph.remove(),super.remove()}connect_signals(){super.connect_signals();const t=()=>this.request_render(),e=()=>this.update_data();this.connect(this.model.change,t),this.connect(this.glyph.model.change,e),this.connect(this.selection_glyph.model.change,e),this.connect(this.nonselection_glyph.model.change,e),null!=this.hover_glyph&&this.connect(this.hover_glyph.model.change,e),this.connect(this.muted_glyph.model.change,e),this.connect(this.decimated_glyph.model.change,e),this.connect(this.model.data_source.change,e),this.connect(this.model.data_source.streaming,e),this.connect(this.model.data_source.patching,(t=>this.update_data(t))),this.connect(this.model.data_source.selected.change,t),this.connect(this.model.data_source._select,t),null!=this.hover_glyph&&this.connect(this.model.data_source.inspect,(()=>{const{inspected:e}=this.model.data_source,n={indices:e.indices,line_indices:e.line_indices,multiline_indices:e.multiline_indices,image_indices:e.image_indices,selected_glyphs:e.selected_glyphs};(0,A.g4)(this._previous_inspected,n)||(this._previous_inspected=n,t())})),this.connect(this.model.properties.view.change,(async()=>{this.cds_view.remove(),this.cds_view=await $e(this.model.view,{parent:this}),e()})),this.connect(this.model.view.properties.indices.change,e),this.connect(this.model.view.properties.masked.change,(()=>this.set_visuals())),this.connect(this.model.properties.visible.change,(()=>this.plot_view.invalidate_dataranges=!0));const{x_ranges:n,y_ranges:r}=this.plot_view.frame;for(const[,t]of n)t instanceof jn&&this.connect(t.change,e);for(const[,t]of r)t instanceof jn&&this.connect(t.change,e);const{transformchange:i,exprchange:o}=this.model.glyph;this.connect(i,e),this.connect(o,e)}_update_masked_indices(){const t=this.glyph.mask_data();return this.model.view.masked=t,t}update_data(t){this.set_data(t),this.request_render()}set_data(t){const e=this.model.data_source;this.all_indices=this.model.view.indices;const{all_indices:n}=this;this.glyph.set_data(e,n,t),this.set_visuals(),this._update_masked_indices();const{lod_factor:r}=this.plot_model,i=this.all_indices.count;this.decimated=new Jt.et(i);for(let t=0;t<i;t+=r)this.decimated.set(t);this.plot_view.invalidate_dataranges=!0}set_visuals(){const t=this.model.data_source,{all_indices:e}=this;this.glyph.set_visuals(t,e),this.decimated_glyph.set_visuals(t,e),this.selection_glyph.set_visuals(t,e),this.nonselection_glyph.set_visuals(t,e),this.hover_glyph?.set_visuals(t,e),this.muted_glyph.set_visuals(t,e)}get has_webgl(){return this.glyph.has_webgl}_render(){const t=this.has_webgl;this.glyph.map_data();const e=[...this.all_indices];let n=[...this._update_masked_indices()];const{ctx:r}=this.layer;r.save();const{selected:i}=this.model.data_source;let o;o=i.is_empty()?[]:this.glyph instanceof Vl&&i.selected_glyph===this.glyph.model?this.model.view.convert_indices_from_subset(n):i.indices;const{inspected:a}=this.model.data_source;this._previous_inspected={indices:a.indices,line_indices:a.line_indices,multiline_indices:a.multiline_indices,image_indices:a.image_indices,selected_glyphs:a.selected_glyphs};const s=new Set((()=>a.is_empty()?[]:a.selected_glyph?this.model.view.convert_indices_from_subset(n):a.indices.length>0?a.indices:Object.keys(a.multiline_indices).map((t=>parseInt(t))))()),l=(0,bn.pb)(n,(t=>s.has(e[t]))),{lod_threshold:c}=this.plot_model;let u,d,h;if(null!=this.model.document&&this.model.document.interactive_duration()>0&&!t&&null!=c&&e.length>c?(n=[...this.decimated],u=this.decimated_glyph,d=this.decimated_glyph,h=this.selection_glyph):(u=this.model.muted?this.muted_glyph:this.glyph,d=this.nonselection_glyph,h=this.selection_glyph),null!=this.hover_glyph&&l.length){const t=new Set(n);for(const e of l)t.delete(e);n=[...t]}if(o.length){const t=new Set(o),i=new Array,a=new Array;if(this.glyph instanceof Vl)for(const n of e)t.has(n)?i.push(n):a.push(n);else for(const r of n)t.has(e[r])?i.push(r):a.push(r);d.render(r,a),h.render(r,i),null!=this.hover_glyph&&(this.glyph instanceof Vl?this.hover_glyph.render(r,this.model.view.convert_indices_from_subset(l)):this.hover_glyph.render(r,l))}else if(this.glyph instanceof Vl)null!=this.hover_glyph&&l.length?this.hover_glyph.render(r,this.model.view.convert_indices_from_subset(l)):u.render(r,e);else if(this.glyph instanceof Pl||this.glyph instanceof Il||this.glyph instanceof zl)if(0==a.selected_glyphs.length||null==this.hover_glyph)u.render(r,e);else for(const t of a.selected_glyphs)t==this.glyph.model&&this.hover_glyph.render(r,e);else u.render(r,n),null!=this.hover_glyph&&l.length&&this.hover_glyph.render(r,l);r.restore()}get_reference_point(t,e){if(null!=t){const n=this.model.data_source.get_column(t);if(null!=n)for(const[t,r]of(0,Q.jO)(this.model.view.indices_map))if(n[parseInt(t)]==e)return r}return 0}draw_legend(t,e,n,r,i,o,a,s){0!=this.glyph.data_size&&(null==s&&(s=this.get_reference_point(o,a)),this.glyph.draw_legend_for_index(t,{x0:e,x1:n,y0:r,y1:i},s))}hit_test(t){if(!this.model.visible)return null;const e=this.glyph.hit_test(t);return null==e?null:this.model.view.convert_selection_from_subset(e)}}Yl.__name__="GlyphRendererView";class Jl extends Gs{constructor(t){super(t)}get_selection_manager(){return this.data_source.selection_manager}add_decoration(t,e){const n=new sl({marking:t,node:e}),r=[this.glyph,this.selection_glyph,this.nonselection_glyph,this.hover_glyph,this.muted_glyph];for(const t of r)t instanceof dl&&(t.decorations=[...t.decorations,n]);return n}}var tc,ec,nc,rc,ic,oc;bl=Jl,Jl.__name__="GlyphRenderer",bl.prototype.default_view=Yl,bl.define((({Boolean:t,Auto:e,Or:n,Ref:r,Null:i,Nullable:o})=>({data_source:[r(hr)],view:[r(Ul),()=>new Ul],glyph:[r(dl)],hover_glyph:[o(r(dl)),null],nonselection_glyph:[n(r(dl),e,i),"auto"],selection_glyph:[n(r(dl),e,i),"auto"],muted_glyph:[n(r(dl),e,i),"auto"],muted:[t,!1]})));class ac extends Fs{constructor(t){super(t),this._scan_data=null}connect_signals(){super.connect_signals();const t=()=>{for(const[t]of this.domain)this.connect(t.view.change,(()=>this.update_data())),this.connect(t.data_source.selected.change,(()=>this.update_data()))},{high:e,low:n,high_color:r,low_color:i,palette:o,nan_color:a}=this.properties;this.on_change([e,n,r,i,o,a],(()=>this.update_data())),this.connect(this.properties.domain.change,(()=>t())),t()}update_data(){const{domain:t,palette:e}=this,n=[...this._collect(t)];this._scan_data=this.scan(n,e.length),this.metrics_change.emit(),this.change.emit()}get metrics(){return null==this._scan_data&&this.update_data(),this._scan_data}*_collect(t){for(const[e,n]of t)for(const t of(0,f.cy)(n)?n:[n]){if(e.view.properties.indices.is_unset)continue;const n=e.data_source.get_column(t);if(null==n)continue;let r=e.view.indices.select(n);const i=e.view.masked,o=e.data_source.selected.indices;let a;if(null!=i&&o.length>0?a=(0,Rt.E$)([...i],o):null!=i?a=[...i]:o.length>0&&(a=o),null!=a&&(r=(0,Rt.Tj)(a,(t=>r[t]))),r.length>0&&!(0,f.Et)(r[0]))for(const t of r)yield*t;else yield*r}}_v_compute(t,e,n,r){const{nan_color:i}=r;let{low_color:o,high_color:a}=r;null==o&&(o=n[0]),null==a&&(a=n[n.length-1]);const{domain:s}=this,l=(0,Rt.Jb)(s)?t:[...this._collect(s)];this._scan_data=this.scan(l,n.length),this.metrics_change.emit();for(let r=0,s=t.length;r<s;r++){const s=t[r];isNaN(s)?e[r]=i:e[r]=this.cmap(s,n,o,a)}}_colors(t){return{...super._colors(t),low_color:null!=this.low_color?t(this.low_color):void 0,high_color:null!=this.high_color?t(this.high_color):void 0}}cmap(t,e,n,r){const i=this.value_to_index(t,e.length);return i<0?n:i>=e.length?r:e[i]}}tc=ac,ac.__name__="ContinuousColorMapper",tc.define((({Number:t,String:e,Ref:n,Color:r,Or:i,Tuple:o,Array:a,Nullable:s})=>({high:[s(t),null],low:[s(t),null],high_color:[s(r),null],low_color:[s(r),null],domain:[a(o(n(Jl),i(e,a(e)))),[]]})));class sc extends ac{constructor(t){super(t)}index_to_value(t){return this._scan_data.binning[t]}value_to_index(t,e){const n=this._scan_data;return t<n.binning[0]?-1:t>n.binning[n.binning.length-1]?e:(0,bn.d7)(t,n.binning)}}sc.__name__="ScanningColorMapper";class lc extends ua{constructor(t){super(t)}get_ticks(t,e,n,r){const{binning:i}=this.mapper.metrics,o=Math.max(0,(0,bn.d7)(t,i)),a=Math.min((0,bn.d7)(e,i)+1,i.length-1),s=[];for(let t=o;t<=a;t++)s.push(i[t]);const{num_major_ticks:l}=this,c=[],u="auto"==l?s.length:l,d=Math.max(1,Math.floor(s.length/u));for(let t=0;t<s.length;t+=d)c.push(s[t]);return{major:c,minor:[]}}}ec=lc,lc.__name__="BinnedTicker",ec.define((({Number:t,Ref:e,Or:n,Auto:r})=>({mapper:[e(sc)],num_major_ticks:[n(t,r),8]})));class cc extends da{constructor(t){super(t)}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}_make_func(){const t=x(this.code);return new Function("tick","index","ticks",...this.names,t)}doFormat(t,e){const n=this._make_func().bind({});return t.map(((t,e,r)=>`${n(t,e,r,...this.values)}`))}}nc=cc,cc.__name__="CustomJSTickFormatter",nc.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));class uc extends da{constructor(t){super(t)}get _rounding_fn(){switch(this.rounding){case"round":case"nearest":return Math.round;case"floor":case"rounddown":return Math.floor;case"ceil":case"roundup":return Math.ceil}}doFormat(t,e){const{format:n,language:r,_rounding_fn:i}=this;return t.map((t=>Aa.format(t,n,r,i)))}}rc=uc,uc.__name__="NumeralTickFormatter",rc.define((({String:t})=>({format:[t,"0,0"],language:[t,"en"],rounding:[_n.PN,"round"]})));class dc extends da{constructor(t){super(t)}doFormat(t,e){return t.map((t=>Ea(this.format,t)))}}ic=dc,dc.__name__="PrintfTickFormatter",ic.define((({String:t})=>({format:[t,"%s"]})));class hc extends wn{constructor(t){super(t)}initialize(){super.initialize();const{source_range:t,target_range:e}=this.properties;t.is_unset||e.is_unset||(this.linear_scale=new An({source_range:t.get_value(),target_range:e.get_value()}))}connect_signals(){super.connect_signals();const{source_range:t,target_range:e}=this.properties;this.on_change([t,e],(()=>{this.linear_scale=new An({source_range:this.source_range,target_range:this.target_range})}))}get s_compute(){throw new Error("not implemented")}get s_invert(){throw new Error("not implemented")}compute(t){return t}v_compute(t){const{binning:e}=this,{start:n,end:r}=this.source_range,i=n,o=r,a=e.length,s=(r-n)/(a-1),l=new Float64Array(a);for(let t=0;t<a;t++)l[t]=n+t*s;const c=(0,bn.Tj)(t,(t=>{if(t<i)return i;if(t>o)return o;const n=(0,bn.d7)(t,e);if(-1==n)return i;if(n>=a-1)return o;const r=e[n],s=(t-r)/(e[n+1]-r),c=l[n];return c+s*(l[n+1]-c)}));return this.linear_scale.v_compute(c)}invert(t){return t}v_invert(t){return new Float64Array(t)}}oc=hc,hc.__name__="LinearInterpolationScale",oc.internal((({Number:t,Arrayable:e,Ref:n})=>({binning:[e(t)],linear_scale:[n(An)]})));class pc extends eo{constructor(){super(...arguments),this.children=[]}*[Symbol.iterator](){yield*this.children}}pc.__name__="Stack";class fc extends pc{_measure(t){let e=0,n=0;for(const t of this.children){const r=t.measure({width:0,height:0});e+=r.width,n=Math.max(n,r.height)}return{width:e,height:n}}_set_geometry(t,e){if(super._set_geometry(t,e),t.is_empty)for(const t of this.children)t.set_geometry(new re);else{const e=this.absolute?t.top:0;let n=this.absolute?t.left:0;const{height:r}=t;for(const t of this.children){const{width:i}=t.measure({width:0,height:0});t.set_geometry(new re({left:n,width:i,top:e,height:r})),n+=i}}}}fc.__name__="HStack";class Qc extends pc{_measure(t){let e=0,n=0;for(const t of this.children){const r=t.measure({width:0,height:0});e=Math.max(e,r.width),n+=r.height}return{width:e,height:n}}_set_geometry(t,e){if(super._set_geometry(t,e),t.is_empty)for(const t of this.children)t.set_geometry(new re);else{const e=this.absolute?t.left:0;let n=this.absolute?t.top:0;const{width:r}=t;for(const t of this.children){const{height:i}=t.measure({width:0,height:0});t.set_geometry(new re({top:n,height:i,left:e,width:r})),n+=i}}}}Qc.__name__="VStack";class Tc extends eo{constructor(){super(...arguments),this.children=[]}*[Symbol.iterator](){yield*this.children}_measure(t){const{width_policy:e,height_policy:n}=this.sizing,{min:r,max:i}=Math;let o=0,a=0;for(const e of this.children){const{width:n,height:r}=e.measure(t);o=i(o,n),a=i(a,r)}return{width:(()=>{const{width:n}=this.sizing;if(t.width==1/0)return"fixed"==e?n??o:o;switch(e){case"fixed":return n??o;case"min":return o;case"fit":return null!=n?r(t.width,n):t.width;case"max":return null!=n?i(t.width,n):t.width}})(),height:(()=>{const{height:e}=this.sizing;if(t.height==1/0)return"fixed"==n?e??a:a;switch(n){case"fixed":return e??a;case"min":return a;case"fit":return null!=e?r(t.height,e):t.height;case"max":return null!=e?i(t.height,e):t.height}})()}}_set_geometry(t,e){if(super._set_geometry(t,e),t.is_empty)for(const t of this.children)t.set_geometry(new re);else{const e=this.absolute?t:t.relative(),{left:n,right:r,top:i,bottom:o}=e,a=Math.round(e.vcenter),s=Math.round(e.hcenter);for(const e of this.children){const{margin:l,halign:c="start",valign:u="start"}=e.sizing,{width:d,height:h,inner:p}=e.measure(t),f=(()=>{switch(`${u}_${c}`){case"start_start":return new re({left:n+l.left,top:i+l.top,width:d,height:h});case"start_center":return new re({hcenter:s,top:i+l.top,width:d,height:h});case"start_end":return new re({right:r-l.right,top:i+l.top,width:d,height:h});case"center_start":return new re({left:n+l.left,vcenter:a,width:d,height:h});case"center_center":return new re({hcenter:s,vcenter:a,width:d,height:h});case"center_end":return new re({right:r-l.right,vcenter:a,width:d,height:h});case"end_start":return new re({left:n+l.left,bottom:o-l.bottom,width:d,height:h});case"end_center":return new re({hcenter:s,bottom:o-l.bottom,width:d,height:h});case"end_end":return new re({right:r-l.right,bottom:o-l.bottom,width:d,height:h})}})(),Q=null==p?f:new re({left:f.left+p.left,top:f.top+p.top,right:f.right-p.right,bottom:f.bottom-p.bottom});e.set_geometry(f,Q)}}}}Tc.__name__="NodeLayout";const{max:mc,round:gc}=Math;class _c{constructor(t){this.def=t,this._map=new Map}get(t){let e=this._map.get(t);return void 0===e&&(e=this.def(),this._map.set(t,e)),e}apply(t,e){const n=this.get(t);this._map.set(t,e(n))}}_c.__name__="DefaultMap";class bc{constructor(){this._items=[],this._nrows=0,this._ncols=0}get size(){return this._items.length}get nrows(){return this._nrows}get ncols(){return this._ncols}add(t,e){const{r1:n,c1:r}=t;this._nrows=mc(this._nrows,n+1),this._ncols=mc(this._ncols,r+1),this._items.push({span:t,data:e})}at(t,e){return this._items.filter((({span:n})=>n.r0<=t&&t<=n.r1&&n.c0<=e&&e<=n.c1)).map((({data:t})=>t))}row(t){return this._items.filter((({span:e})=>e.r0<=t&&t<=e.r1)).map((({data:t})=>t))}col(t){return this._items.filter((({span:e})=>e.c0<=t&&t<=e.c1)).map((({data:t})=>t))}*[Symbol.iterator](){yield*this._items}foreach(t){for(const{span:e,data:n}of this._items)t(e,n)}map(t){const e=new bc;for(const{span:n,data:r}of this._items)e.add(n,t(n,r));return e}}bc.__name__="Container";class vc extends eo{constructor(t=[]){super(),this.items=t,this.rows="auto",this.cols="auto",this.spacing=0}*[Symbol.iterator](){for(const{layout:t}of this.items)yield t}is_width_expanding(){if(super.is_width_expanding())return!0;if("fixed"==this.sizing.width_policy)return!1;const{cols:t}=this._state;return(0,Rt.zN)(t,(t=>"max"==t.policy))}is_height_expanding(){if(super.is_height_expanding())return!0;if("fixed"==this.sizing.height_policy)return!1;const{rows:t}=this._state;return(0,Rt.zN)(t,(t=>"max"==t.policy))}_init(){super._init();const t=new bc;for(const{layout:e,row:n,col:r,row_span:i=1,col_span:o=1}of this.items)if(e.sizing.visible){const a=n,s=r,l=n+i-1,c=r+o-1;t.add({r0:a,c0:s,r1:l,c1:c},e)}const{nrows:e,ncols:n}=t,r=new Array(e);for(let n=0;n<e;n++){const e=(()=>{const t=(0,f.Qd)(this.rows)?this.rows[n]??this.rows["*"]:this.rows;return null==t?{policy:"auto"}:(0,f.Et)(t)?{policy:"fixed",height:t}:(0,f.Kg)(t)?{policy:t}:t})(),i=e.align??"auto";"fixed"==e.policy?r[n]={policy:"fixed",height:e.height,align:i}:"min"==e.policy?r[n]={policy:"min",align:i}:"fit"==e.policy||"max"==e.policy?r[n]={policy:e.policy,flex:e.flex??1,align:i}:(0,Rt.zN)(t.row(n),(t=>t.is_height_expanding()))?r[n]={policy:"max",flex:1,align:i}:r[n]={policy:"min",align:i}}const i=new Array(n);for(let e=0;e<n;e++){const n=(()=>{const t=(0,f.Qd)(this.cols)?this.cols[e]??this.cols["*"]:this.cols;return null==t?{policy:"auto"}:(0,f.Et)(t)?{policy:"fixed",width:t}:(0,f.Kg)(t)?{policy:t}:t})(),r=n.align??"auto";"fixed"==n.policy?i[e]={policy:"fixed",width:n.width,align:r}:"min"==n.policy?i[e]={policy:"min",align:r}:"fit"==n.policy||"max"==n.policy?i[e]={policy:n.policy,flex:n.flex??1,align:r}:(0,Rt.zN)(t.col(e),(t=>t.is_width_expanding()))?i[e]={policy:"max",flex:1,align:r}:i[e]={policy:"min",align:r}}const[o,a]=(0,f.Et)(this.spacing)?[this.spacing,this.spacing]:this.spacing;this._state={items:t,nrows:e,ncols:n,rows:r,cols:i,rspacing:o,cspacing:a}}_measure_totals(t,e){const{nrows:n,ncols:r,rspacing:i,cspacing:o}=this._state;return{height:(0,Rt.cz)(t)+(n-1)*i,width:(0,Rt.cz)(e)+(r-1)*o}}_measure_cells(t){const{items:e,nrows:n,ncols:r,rows:i,cols:o,rspacing:a,cspacing:s}=this._state,l=new Array(n);for(let t=0;t<n;t++){const e=i[t];l[t]="fixed"==e.policy?e.height:0}const c=new Array(r);for(let t=0;t<r;t++){const e=o[t];c[t]="fixed"==e.policy?e.width:0}const u=new bc;return e.foreach(((e,n)=>{const{r0:r,c0:d,r1:h,c1:p}=e,f=(h-r)*a,Q=(p-d)*s;let T=0;for(let e=r;e<=h;e++)T+=t(e,d).height;T+=f;let m=0;for(let e=d;e<=p;e++)m+=t(r,e).width;m+=Q;const g=n.measure({width:m,height:T});u.add(e,{layout:n,size_hint:g});const _=new Xi(g).grow_by(n.sizing.margin);_.height-=f,_.width-=Q;const b=[];for(let t=r;t<=h;t++){const e=i[t];"fixed"==e.policy?_.height-=e.height:b.push(t)}if(_.height>0){const t=gc(_.height/b.length);for(const e of b)l[e]=mc(l[e],t)}const v=[];for(let t=d;t<=p;t++){const e=o[t];"fixed"==e.policy?_.width-=e.width:v.push(t)}if(_.width>0){const t=gc(_.width/v.length);for(const e of v)c[e]=mc(c[e],t)}})),{size:this._measure_totals(l,c),row_heights:l,col_widths:c,size_hints:u}}_measure_grid(t){const{nrows:e,ncols:n,rows:r,cols:i,rspacing:o,cspacing:a}=this._state,s=this._measure_cells(((t,e)=>{const n=r[t],o=i[e];return{width:"fixed"==o.policy?o.width:1/0,height:"fixed"==n.policy?n.height:1/0}}));let l;l="fixed"==this.sizing.height_policy&&null!=this.sizing.height?this.sizing.height:t.height!=1/0&&this.is_height_expanding()?t.height:s.size.height;let c,u=0;for(let t=0;t<e;t++){const e=r[t];"fit"==e.policy||"max"==e.policy?u+=e.flex:l-=s.row_heights[t]}if(l-=(e-1)*o,0!=u&&l>0)for(let t=0;t<e;t++){const e=r[t];if("fit"==e.policy||"max"==e.policy){const n=gc(l*(e.flex/u));l-=n,s.row_heights[t]=n,u-=e.flex}}else if(l<0){let t=0;for(let n=0;n<e;n++)"fixed"!=r[n].policy&&t++;let n=-l;for(let i=0;i<e;i++)if("fixed"!=r[i].policy){const e=s.row_heights[i],r=gc(n/t);s.row_heights[i]=mc(e-r,0),n-=r>e?e:r,t--}}c="fixed"==this.sizing.width_policy&&null!=this.sizing.width?this.sizing.width:t.width!=1/0&&this.is_width_expanding()?t.width:s.size.width;let d=0;for(let t=0;t<n;t++){const e=i[t];"fit"==e.policy||"max"==e.policy?d+=e.flex:c-=s.col_widths[t]}if(c-=(n-1)*a,0!=d&&c>0)for(let t=0;t<n;t++){const e=i[t];if("fit"==e.policy||"max"==e.policy){const n=gc(c*(e.flex/d));c-=n,s.col_widths[t]=n,d-=e.flex}}else if(c<0){let t=0;for(let e=0;e<n;e++)"fixed"!=i[e].policy&&t++;let e=-c;for(let r=0;r<n;r++)if("fixed"!=i[r].policy){const n=s.col_widths[r],i=gc(e/t);s.col_widths[r]=mc(n-i,0),e-=i>n?n:i,t--}}const{row_heights:h,col_widths:p,size_hints:f}=this._measure_cells(((t,e)=>({width:s.col_widths[e],height:s.row_heights[t]})));return{size:this._measure_totals(h,p),row_heights:h,col_widths:p,size_hints:f}}_measure(t){const{size:e}=this._measure_grid(t);return e}_set_geometry(t,e){super._set_geometry(t,e);const{nrows:n,ncols:r,rspacing:i,cspacing:o}=this._state,{row_heights:a,col_widths:s,size_hints:l}=this._measure_grid(t),c=this._state.rows.map(((t,e)=>({...t,top:0,height:a[e],get bottom(){return this.top+this.height}}))),u=this._state.cols.map(((t,e)=>({...t,left:0,width:s[e],get right(){return this.left+this.width}}))),d=l.map(((t,e)=>({...e,outer:new re,inner:new re})));for(let e=0,r=this.absolute?t.top:0;e<n;e++){const t=c[e];t.top=r,r+=t.height+i}for(let e=0,n=this.absolute?t.left:0;e<r;e++){const t=u[e];t.left=n,n+=t.width+o}d.foreach((({r0:t,c0:e,r1:n,c1:r},a)=>{const{layout:s,size_hint:l}=a,{sizing:d}=s,{width:h,height:p}=l,f=function(t,e){let n=(e-t)*o;for(let r=t;r<=e;r++)n+=u[r].width;return n}(e,r),Q=function(t,e){let n=(e-t)*i;for(let r=t;r<=e;r++)n+=c[r].height;return n}(t,n),T=e==r&&"auto"!=u[e].align?u[e].align:d.halign,m=t==n&&"auto"!=c[t].align?c[t].align:d.valign;let g=u[e].left;"start"==T?g+=d.margin.left:"center"==T?g+=gc((f-h)/2):"end"==T&&(g+=f-d.margin.right-h);let _=c[t].top;"start"==m?_+=d.margin.top:"center"==m?_+=gc((Q-p)/2):"end"==m&&(_+=Q-d.margin.bottom-p),a.outer=new re({left:g,top:_,width:h,height:p})}));const h=c.map((()=>({start:new _c((()=>0)),end:new _c((()=>0))}))),p=u.map((()=>({start:new _c((()=>0)),end:new _c((()=>0))})));d.foreach((({r0:t,c0:e,r1:n,c1:r},{size_hint:i,outer:o})=>{const{inner:a}=i;null!=a&&(h[t].start.apply(o.top,(t=>mc(t,a.top))),h[n].end.apply(c[n].bottom-o.bottom,(t=>mc(t,a.bottom))),p[e].start.apply(o.left,(t=>mc(t,a.left))),p[r].end.apply(u[r].right-o.right,(t=>mc(t,a.right))))})),d.foreach((({r0:t,c0:e,r1:n,c1:r},i)=>{const{size_hint:o,outer:a}=i,s=t=>{const e=this.absolute?a:a.relative(),n=e.left+t.left,r=e.top+t.top,i=e.right-t.right,o=e.bottom-t.bottom;return new re({left:n,top:r,right:i,bottom:o})};if(null!=o.inner){let l=s(o.inner);const d=h[t].start.get(a.top),f=h[n].end.get(c[n].bottom-a.bottom),Q=p[e].start.get(a.left),T=p[r].end.get(u[r].right-a.right);try{l=s({top:d,bottom:f,left:Q,right:T})}catch{}i.inner=l}else i.inner=a})),d.foreach(((t,{layout:e,outer:n,inner:r})=>{e.set_geometry(n,r)}))}}vc.__name__="Grid";class yc extends vc{constructor(t){super(),this.items=t.map(((t,e)=>({layout:t,row:0,col:e}))),this.rows="fit"}}yc.__name__="Row";class xc extends vc{constructor(t){super(),this.items=t.map(((t,e)=>({layout:t,row:e,col:0}))),this.cols="fit"}}xc.__name__="Column";class wc extends eo{constructor(){super(...arguments),this.aligns={left:!0,right:!0,top:!0,bottom:!0},this.min_border={left:0,top:0,right:0,bottom:0},this.padding={left:0,top:0,right:0,bottom:0},this.center_border_width=0}*[Symbol.iterator](){yield this.top_panel,yield this.bottom_panel,yield this.left_panel,yield this.right_panel,yield this.center_panel}_measure(t){t=new Xi({width:"fixed"==this.sizing.width_policy||t.width==1/0?this.sizing.width:t.width,height:"fixed"==this.sizing.height_policy||t.height==1/0?this.sizing.height:t.height});const e=this.left_panel.measure({width:0,height:t.height}),n=Math.max(e.width,this.min_border.left)+this.padding.left,r=this.right_panel.measure({width:0,height:t.height}),i=Math.max(r.width,this.min_border.right)+this.padding.right,o=this.top_panel.measure({width:t.width,height:0}),a=Math.max(o.height,this.min_border.top)+this.padding.top,s=this.bottom_panel.measure({width:t.width,height:0}),l=Math.max(s.height,this.min_border.bottom)+this.padding.bottom,c=new Xi(t).shrink_by({left:n,right:i,top:a,bottom:l}),u=this.center_panel.measure(c);return{width:n+u.width+i,height:a+u.height+l,inner:{left:n,right:i,top:a,bottom:l},align:(()=>{const{width_policy:t,height_policy:e}=this.center_panel.sizing;return{...this.aligns,fixed_width:"fixed"==t,fixed_height:"fixed"==e}})()}}_set_geometry(t,e){if(super._set_geometry(t,e),this.sizing.visible){this.center_panel.set_geometry(e);const n=this.left_panel.measure({width:0,height:t.height}),r=this.right_panel.measure({width:0,height:t.height}),i=this.top_panel.measure({width:t.width,height:0}),o=this.bottom_panel.measure({width:t.width,height:0}),{left:a,top:s,right:l,bottom:c}=e;this.top_panel.set_geometry(new re({left:a,right:l,bottom:s,height:i.height})),this.bottom_panel.set_geometry(new re({left:a,right:l,top:c,height:o.height})),this.left_panel.set_geometry(new re({top:s,bottom:c,right:a,width:n.width})),this.right_panel.set_geometry(new re({top:s,bottom:c,left:l,width:r.width}));const u=e.shrink_by(this.center_border_width);if(null!=this.inner_top_panel){const{left:t,right:e,top:n,width:r}=u,i=this.inner_top_panel.measure({width:r,height:0});this.inner_top_panel.set_geometry(new re({left:t,right:e,top:n,height:i.height}))}if(null!=this.inner_bottom_panel){const{left:t,right:e,bottom:n,width:r}=u,i=this.inner_bottom_panel.measure({width:r,height:0});this.inner_bottom_panel.set_geometry(new re({left:t,right:e,bottom:n,height:i.height}))}if(null!=this.inner_left_panel){const{top:t,bottom:e,left:n,height:r}=u,i=this.inner_left_panel.measure({width:0,height:r});this.inner_left_panel.set_geometry(new re({top:t,bottom:e,left:n,width:i.width}))}if(null!=this.inner_right_panel){const{top:t,bottom:e,right:n,height:r}=u,i=this.inner_right_panel.measure({width:0,height:r});this.inner_right_panel.set_geometry(new re({top:t,bottom:e,right:n,width:i.width}))}}else this.center_panel.set_geometry(new re),this.top_panel.set_geometry(new re),this.bottom_panel.set_geometry(new re),this.left_panel.set_geometry(new re),this.right_panel.set_geometry(new re),this.inner_top_panel?.set_geometry(new re),this.inner_bottom_panel?.set_geometry(new re),this.inner_left_panel?.set_geometry(new re),this.inner_right_panel?.set_geometry(new re)}}var Lc,Ac,Hc,kc,Mc,Cc,Sc,Ec,Vc,Oc,Pc,Dc,Nc,Rc,Ic,jc,zc,Bc;wc.__name__="BorderLayout";class Fc extends nr{get orientation(){return this._orientation}*children(){yield*super.children(),yield this._axis_view,yield this._title_view}initialize(){super.initialize();const{ticker:t,formatter:e}=this.model;this._ticker="auto"!=t?t:this._create_ticker(),this._formatter="auto"!=e?e:this._create_formatter(),this._major_range=this._create_major_range(),this._major_scale=this._create_major_scale(),this._minor_range=new xn({start:0,end:1}),this._minor_scale=new An,this._frame=new sa(this._major_scale,this._minor_scale,this._major_range,this._minor_range),this._axis=this._create_axis(),this._apply_axis_properties(),this._title=new aa,this._apply_title_properties()}async lazy_initialize(){await super.lazy_initialize();const t=this,e={get parent(){return t.parent},get root(){return t.root},get frame(){return t._frame},get canvas_view(){return t.parent.canvas_view},request_layout(){t.parent.request_layout()},request_paint(){t.parent.request_paint(t)},request_render(){t.request_paint()}};this._axis_view=await $e(this._axis,{parent:e}),this._title_view=await $e(this._title,{parent:e})}remove(){this._title_view.remove(),this._axis_view.remove(),super.remove()}_apply_axis_properties(){const t={ticker:this._ticker,formatter:this._formatter,major_label_standoff:this.model.label_standoff,axis_line_color:null,major_tick_in:this.model.major_tick_in,major_tick_out:this.model.major_tick_out,minor_tick_in:this.model.minor_tick_in,minor_tick_out:this.model.minor_tick_out,major_label_overrides:this.model.major_label_overrides,major_label_policy:this.model.major_label_policy,...Ke.tI(this.model,"major_label_",Ke.EY,!0),...Ke.tI(this.model,"major_tick_",Ke.N1,!0),...Ke.tI(this.model,"minor_tick_",Ke.N1,!0)};this._axis.setv(t)}_apply_title_properties(){const t={text:this.model.title??"",standoff:this.model.title_standoff,...Ke.tI(this.model,"title_",Ke.EY,!1)};this._title.setv(t)}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>{this._apply_title_properties(),this._apply_axis_properties()})),this.connect(this._ticker.change,(()=>this.request_render())),this.connect(this._formatter.change,(()=>this.request_render()))}_update_frame(){const[t,e,n,r]=(()=>"horizontal"==this.orientation?[this._major_scale,this._minor_scale,this._major_range,this._minor_range]:[this._minor_scale,this._major_scale,this._minor_range,this._major_range])();this._frame.in_x_scale=t,this._frame.in_y_scale=e,this._frame.x_range=n,this._frame.y_range=r,this._frame.configure_scales()}update_layout(){const{location:t,width:e,height:n,padding:r,margin:i}=this.model,[o,a]=(()=>{if(!(0,f.Kg)(t))return["end","start"];switch(t){case"top_left":return["start","start"];case"top":case"top_center":return["start","center"];case"top_right":return["start","end"];case"bottom_left":return["end","start"];case"bottom":case"bottom_center":return["end","center"];case"bottom_right":return["end","end"];case"left":case"center_left":return["center","start"];case"center":case"center_center":return["center","center"];case"right":case"center_right":return["center","end"]}})(),s=this._orientation=(()=>{const{orientation:t}=this.model;return"auto"==t?null!=this.panel?this.panel.is_horizontal?"horizontal":"vertical":"start"==a||"end"==a||"center"==o?"vertical":"horizontal":t})();this._update_frame();const l=new Tc,c=new Qc,u=new Qc,d=new fc,h=new fc;l.absolute=!0,c.absolute=!0,u.absolute=!0,d.absolute=!0,h.absolute=!0,l.on_resize((t=>this._frame.set_geometry(t)));const p=new wc;this._inner_layout=p,p.absolute=!0,p.center_panel=l,p.top_panel=c,p.bottom_panel=u,p.left_panel=d,p.right_panel=h;const Q={left:r,right:r,top:r,bottom:r},T=(()=>{if(null==this.panel){if((0,f.Kg)(t))return{left:i,right:i,top:i,bottom:i};{const[e,n]=t;return{left:e,right:i,top:i,bottom:n}}}if(!(0,f.Kg)(t)){const[e,n]=t;return p.fixup_geometry=(t,r)=>{const i=t,o=this.layout.bbox,{width:a,height:s}=t;if(t=new re({left:o.left+e,bottom:o.bottom-n,width:a,height:s}),null!=r){const e=t.left-i.left,n=t.top-i.top,{left:o,top:a,width:s,height:l}=r;r=new re({left:o+e,top:a+n,width:s,height:l})}return[t,r]},{left:e,right:0,top:0,bottom:n}}p.fixup_geometry=(t,e)=>{const n=t;if("horizontal"==s){const{top:e,width:n,height:r}=t;if("end"==a){const{right:i}=this.layout.bbox;t=new re({right:i,top:e,width:n,height:r})}else if("center"==a){const{hcenter:i}=this.layout.bbox;t=new re({hcenter:Math.round(i),top:e,width:n,height:r})}}else{const{left:e,width:n,height:r}=t;if("end"==o){const{bottom:i}=this.layout.bbox;t=new re({left:e,bottom:i,width:n,height:r})}else if("center"==o){const{vcenter:i}=this.layout.bbox;t=new re({left:e,vcenter:Math.round(i),width:n,height:r})}}if(null!=e){const r=t.left-n.left,i=t.top-n.top,{left:o,top:a,width:s,height:l}=e;e=new re({left:o+r,top:a+i,width:s,height:l})}return[t,e]}})();let m,g,_,b;if(p.padding=Q,null!=this.panel)m="max",g=void 0,_=void 0,b=void 0;else if("auto"==("horizontal"==s?e:n)){m="fixed";const t=this._get_major_size_factor();null!=t&&(g=25*t),_={percent:.3},b={percent:.8}}else m="fit",g=void 0;if("horizontal"==s){const t="auto"==e?void 0:e,r="auto"==n?25:n;p.set_sizing({width_policy:m,height_policy:"min",width:g,min_width:_,max_width:b,halign:a,valign:o,margin:T}),p.center_panel.set_sizing({width_policy:"auto"==e?"fit":"fixed",height_policy:"fixed",width:t,height:r})}else{const t="auto"==e?25:e,r="auto"==n?void 0:n;p.set_sizing({width_policy:"min",height_policy:m,height:g,min_height:_,max_height:b,halign:a,valign:o,margin:T}),p.center_panel.set_sizing({width_policy:"fixed",height_policy:"auto"==n?"fit":"fixed",width:t,height:r})}c.set_sizing({width_policy:"fit",height_policy:"min"}),u.set_sizing({width_policy:"fit",height_policy:"min"}),d.set_sizing({width_policy:"min",height_policy:"fit"}),h.set_sizing({width_policy:"min",height_policy:"fit"});const{_title_view:v}=this;"horizontal"==s?(v.panel=new co("above"),v.update_layout(),c.children.push(v.layout)):(v.panel=new co("left"),v.update_layout(),d.children.push(v.layout));const{panel:y}=this,x=null!=y&&s==y.orientation?y.side:"horizontal"==s?"below":"right",w=(()=>{switch(x){case"above":return c;case"below":return u;case"left":return d;case"right":return h}})(),{_axis_view:L}=this;if(L.panel=new co(x),L.update_layout(),w.children.push(L.layout),null!=this.panel){const t=new vc([{layout:p,row:0,col:0}]);t.absolute=!0,"horizontal"==s?t.set_sizing({width_policy:"max",height_policy:"min"}):t.set_sizing({width_policy:"min",height_policy:"max"}),this.layout=t}else this.layout=this._inner_layout;const{visible:A}=this.model;this.layout.sizing.visible=A}_create_axis(){return new bs}_create_formatter(){return new gs}_create_major_range(){return new xn({start:0,end:1})}_create_major_scale(){return new An}_create_ticker(){return new hs}_get_major_size_factor(){return null}_render(){const{ctx:t}=this.layer;t.save(),this._paint_bbox(t,this._inner_layout.bbox),this._paint_colors(t,this._inner_layout.center_panel.bbox),this._title_view.render(),this._axis_view.render(),t.restore()}_paint_bbox(t,e){const{x:n,y:r}=e;let{width:i,height:o}=e;n+i>=this.parent.canvas_view.bbox.width&&(i-=1),r+o>=this.parent.canvas_view.bbox.height&&(o-=1),t.save(),this.visuals.background_fill.doit&&(this.visuals.background_fill.set_value(t),t.fillRect(n,r,i,o)),this.visuals.border_line.doit&&(this.visuals.border_line.set_value(t),t.strokeRect(n,r,i,o)),t.restore()}serializable_state(){const{children:t=[],...e}=super.serializable_state();return t.push(this._title_view.serializable_state()),t.push(this._axis_view.serializable_state()),{...e,children:t}}}Fc.__name__="BaseColorBarView";class $c extends rr{constructor(t){super(t)}}Lc=$c,$c.__name__="BaseColorBar",Lc.mixins([["major_label_",Ke.EY],["title_",Ke.EY],["major_tick_",Ke.N1],["minor_tick_",Ke.N1],["border_",Ke.N1],["bar_",Ke.N1],["background_",Ke.SQ]]),Lc.define((({Alpha:t,Number:e,String:n,Tuple:r,Map:i,Or:o,Ref:a,Auto:s,Nullable:l})=>({location:[o(_n.Mz,r(e,e)),"top_right"],orientation:[o(_n.t4,s),"auto"],title:[l(n),null],title_standoff:[e,2],width:[o(e,s),"auto"],height:[o(e,s),"auto"],scale_alpha:[t,1],ticker:[o(a(ua),s),"auto"],formatter:[o(a(da),s),"auto"],major_label_overrides:[i(o(n,e),o(n,a(fo))),new globalThis.Map,{convert:t=>(0,f.Qd)(t)?new Q.Bi(t):t}],major_label_policy:[a(ha),()=>new fa],label_standoff:[e,5],margin:[e,30],padding:[e,10],major_tick_in:[e,5],major_tick_out:[e,0],minor_tick_in:[e,0],minor_tick_out:[e,0]}))),Lc.override({background_fill_color:"#ffffff",background_fill_alpha:.95,bar_line_color:null,border_line_color:null,major_label_text_font_size:"11px",major_tick_line_color:"#ffffff",minor_tick_line_color:null,title_text_font_size:"13px",title_text_font_style:"italic"});class Gc extends Ci{map_data(){const{frame:t}=this.plot_view,e=this.model.dimension,n=this.coordinates.x_scale,r=this.coordinates.y_scale,i="height"==e?r:n,o="height"==e?n:r,a="height"==e?t.bbox.yview:t.bbox.xview,s="height"==e?t.bbox.xview:t.bbox.yview,l=(()=>{switch(this.model.properties.lower.units){case"canvas":return new Jt.mR(this._lower);case"screen":return a.v_compute(this._lower);case"data":return i.v_compute(this._lower)}})(),c=(()=>{switch(this.model.properties.upper.units){case"canvas":return new Jt.mR(this._upper);case"screen":return a.v_compute(this._upper);case"data":return i.v_compute(this._upper)}})(),u=(()=>{switch(this.model.properties.base.units){case"canvas":return new Jt.mR(this._base);case"screen":return s.v_compute(this._base);case"data":return o.v_compute(this._base)}})(),[d,h]="height"==e?[1,0]:[0,1],p=[l,u],f=[c,u];this._lower_sx=p[d],this._lower_sy=p[h],this._upper_sx=f[d],this._upper_sy=f[h]}}Gc.__name__="UpperLowerView";class qc extends m.Ok{constructor(){super(...arguments),this._value=m.wC}get dimension(){return"width"==this.obj.dimension?"x":"y"}get units(){return this._value===m.wC?"data":this._value.units??"data"}}qc.__name__="XOrYCoordinateSpec";class Uc extends Si{constructor(t){super(t)}}Ac=Uc,Uc.__name__="UpperLower",Ac.define((()=>({dimension:[_n.fg,"height"],lower:[qc,{field:"lower"}],upper:[qc,{field:"upper"}],base:[qc,{field:"base"}]})));class Wc extends Gc{paint(t){t.beginPath(),t.moveTo(this._lower_sx[0],this._lower_sy[0]);for(let e=0,n=this._lower_sx.length;e<n;e++)t.lineTo(this._lower_sx[e],this._lower_sy[e]);for(let e=this._upper_sx.length-1;e>=0;e--)t.lineTo(this._upper_sx[e],this._upper_sy[e]);t.closePath(),this.visuals.fill.apply(t),t.beginPath(),t.moveTo(this._lower_sx[0],this._lower_sy[0]);for(let e=0,n=this._lower_sx.length;e<n;e++)t.lineTo(this._lower_sx[e],this._lower_sy[e]);this.visuals.line.apply(t),t.beginPath(),t.moveTo(this._upper_sx[0],this._upper_sy[0]);for(let e=0,n=this._upper_sx.length;e<n;e++)t.lineTo(this._upper_sx[e],this._upper_sy[e]);this.visuals.line.apply(t)}}Wc.__name__="BandView";class Zc extends Uc{constructor(t){super(t)}}Hc=Zc,Zc.__name__="Band",Hc.prototype.default_view=Wc,Hc.mixins([Ke.N1,Ke.SQ]),Hc.override({fill_color:"#fff9ba",fill_alpha:.4,line_color:"#cccccc",line_alpha:.3});class Xc extends nr{constructor(){super(...arguments),this.bbox=new re}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render()))}_render(){const{left:t,right:e,top:n,bottom:r}=this.model,{frame:i}=this.plot_view,o=this.coordinates.x_scale,a=this.coordinates.y_scale,s=(t,e,n,r,i)=>{if(null==t)return i;switch(e){case"canvas":return t;case"screen":return r.compute(t);case"data":return n.compute(t)}};this.bbox=re.from_lrtb({left:s(t,this.model.left_units,o,i.bbox.xview,i.bbox.left),right:s(e,this.model.right_units,o,i.bbox.xview,i.bbox.right),top:s(n,this.model.top_units,a,i.bbox.yview,i.bbox.top),bottom:s(r,this.model.bottom_units,a,i.bbox.yview,i.bbox.bottom)}),this._paint_box()}_paint_box(){const{ctx:t}=this.layer;t.save();const{left:e,top:n,width:r,height:i}=this.bbox;t.beginPath(),t.rect(e,n,r,i),this.visuals.fill.apply(t),this.visuals.hatch.apply(t),this.visuals.line.apply(t),t.restore()}interactive_bbox(){const t=this.model.line_width+2.5;return this.bbox.grow_by(t)}interactive_hit(t,e){return null!=this.model.in_cursor&&this.interactive_bbox().contains(t,e)}cursor(t,e){const{left:n,right:r,bottom:i,top:o}=this.bbox;return Math.abs(t-n)<3||Math.abs(t-r)<3?this.model.ew_cursor:Math.abs(e-i)<3||Math.abs(e-o)<3?this.model.ns_cursor:this.bbox.contains(t,e)?this.model.in_cursor:null}}Xc.__name__="BoxAnnotationView";class Kc extends rr{constructor(t){super(t)}update({left:t,right:e,top:n,bottom:r}){this.setv({left:t,right:e,top:n,bottom:r,visible:!0})}clear(){this.visible=!1}}function Yc(t,e){if(t.length!=e.length)return!1;for(let n=0,r=t.length;n<r;n++)if(t[n]!==e[n])return!1;return!0}function Jc(t,e,n,r,i,o,a){const s=t.length;for(let l=0;l<s;l++){let s,c,u=t[l];(0,f.Kg)(u)?s=(0,bn.lc)(e,u):(u=u.slice(i,o??void 0),s=1==u.length?(0,bn.lc)(e,u[0]):(0,bn.TJ)(e,(t=>Yc(t,u)))),c=s<0||s>=n.length?a:n[s],r[l]=c}}kc=Kc,Kc.__name__="BoxAnnotation",kc.prototype.default_view=Xc,kc.mixins([Ke.N1,Ke.SQ,Ke.LD]),kc.define((({Number:t,Nullable:e})=>({top:[e(t),null],bottom:[e(t),null],left:[e(t),null],right:[e(t),null],top_units:[_n.yx,"data"],bottom_units:[_n.yx,"data"],left_units:[_n.yx,"data"],right_units:[_n.yx,"data"]}))),kc.internal((({String:t,Nullable:e})=>({ew_cursor:[e(t),null],ns_cursor:[e(t),null],in_cursor:[e(t),null]}))),kc.override({fill_color:"#fff9ba",fill_alpha:.4,line_color:"#cccccc",line_alpha:.3});class tu extends Fs{constructor(t){super(t)}_v_compute(t,e,n,{nan_color:r}){Jc(t,this.factors,n,e,this.start,this.end,r)}}Mc=tu,tu.__name__="CategoricalColorMapper",Mc.define((({Number:t,Nullable:e})=>({factors:[Nn],start:[t,0],end:[e(t),null]})));class eu extends zs{constructor(t){super(t)}v_compute(t){const e=new Array(t.length);return Jc(t,this.factors,this.markers,e,this.start,this.end,this.default_value),e}}Cc=eu,eu.__name__="CategoricalMarkerMapper",Cc.define((({Number:t,Array:e,Nullable:n})=>({factors:[Nn],markers:[e(_n.TG)],start:[t,0],end:[n(t),null],default_value:[_n.TG,"circle"]})));class nu extends zs{constructor(t){super(t)}v_compute(t){const e=new Array(t.length);return Jc(t,this.factors,this.patterns,e,this.start,this.end,this.default_value),e}}Sc=nu,nu.__name__="CategoricalPatternMapper",Sc.define((({Number:t,Array:e,Nullable:n})=>({factors:[Nn],patterns:[e(_n.N8)],start:[t,0],end:[n(t),null],default_value:[_n.N8," "]})));class ru extends ac{constructor(t){super(t)}scan(t,e){const n=null!=this.low?this.low:(0,bn.jk)(t),r=null!=this.high?this.high:(0,bn.T9)(t);return{max:r,min:n,norm_factor:1/(r-n),normed_interval:1/e}}index_to_value(t){const e=this._scan_data;return e.min+e.normed_interval*t/e.norm_factor}value_to_index(t,e){const n=this._scan_data;if(t==n.max)return e-1;const r=(t-n.min)*n.norm_factor,i=Math.floor(r/n.normed_interval);return(0,Gi.qE)(i,-1,e)}}ru.__name__="LinearColorMapper";class iu extends ac{constructor(t){super(t)}scan(t,e){const n=null!=this.low?this.low:(0,bn.jk)(t),r=null!=this.high?this.high:(0,bn.T9)(t);return{max:r,min:n,scale:e/Math.log(r/n)}}index_to_value(t){const e=this._scan_data;return e.min*Math.exp(t/e.scale)}value_to_index(t,e){const n=this._scan_data;if(t==n.max)return e-1;if(t>n.max)return e;if(t<n.min)return-1;const r=Math.log(t/n.min),i=Math.floor(r*n.scale);return(0,Gi.qE)(i,-1,e)}}iu.__name__="LogColorMapper";class ou extends sc{constructor(t){super(t)}scan(t,e){const n=null!=this.low?this.low:(0,bn.jk)(t),r=null!=this.high?this.high:(0,bn.T9)(t),i=this.bins,o=(0,Rt.mT)(n,r,i+1),a=(0,bn.R1)(t,o);let s=0;for(let t=0;t<i;t++)0!=a[t]&&s++;const l=new Array(s+1),c=new Array(s+1);for(let t=0,e=1;t<i;t++)0!=a[t]&&(l[e]=a[t],c[e]=(o[t]+o[t+1])/2,e++);l[0]=0,c[0]=2*c[1]-c[s];const u=(0,Rt.rC)(l),d=u[1],h=u[s]-d;for(let t=1;t<=s;t++)u[t]=(u[t]-d)/h;u[0]=-1;let{rescale_discrete_levels:p}=this,f=0;if(p){const t=-.5/98,e=t*s+(1.5-2*t);e>1?f=1-e:p=!1}const Q=(0,Rt.mT)(f,1,e+1),T=(0,bn.GW)(Q,u,c);let m=!1;if(p){const t=(0,bn.P8)(T,n);n<T[t]&&t>0&&(T[t-1]=n),m=!0}else T[0]=n;return T[T.length-1]=r,{min:n,max:r,binning:T,force_low_cutoff:m}}}Ec=ou,ou.__name__="EqHistColorMapper",Ec.define((({Boolean:t,Int:e})=>({bins:[e,65536],rescale_discrete_levels:[t,!1]})));class au extends Fc{connect_signals(){super.connect_signals(),this.connect(this.model.properties.color_mapper.change,(async()=>{this._title_view.remove(),this._axis_view.remove(),this.initialize(),await this.lazy_initialize(),this.plot_view.invalidate_layout()})),this.connect(this.model.color_mapper.metrics_change,(()=>this._metrics_changed())),this.connect(this.model.properties.display_low.change,(()=>this._metrics_changed())),this.connect(this.model.properties.display_high.change,(()=>this._metrics_changed()))}update_layout(){super.update_layout(),this._set_canvas_image()}_create_axis(){const{color_mapper:t}=this.model;return t instanceof tu?new xa:t instanceof iu?new Ps:new bs}_create_formatter(){const{color_mapper:t}=this.model;return this._ticker instanceof vs?new Ls:t instanceof tu?new ba:new gs}_create_major_range(){const{color_mapper:t}=this.model;if(t instanceof tu)return new jn({factors:t.factors});if(t instanceof ac){const{min:e,max:n}=this._continuous_metrics(t);return new xn({start:e,end:n})}(0,_.HB)()}_create_major_scale(){const{color_mapper:t}=this.model;return t instanceof ru?new An:t instanceof iu?new Hn:t instanceof sc?new hc({binning:this._scanning_binning(t)}):t instanceof tu?new Mn:void(0,_.HB)()}_create_ticker(){const{color_mapper:t}=this.model;return t instanceof iu?new vs:t instanceof sc?new lc({mapper:t}):t instanceof tu?new _a:new hs}_continuous_metrics(t){const{display_low:e,display_high:n}=this.model;let{min:r,max:i}=t.metrics;if(null!=n&&null!=e&&n<e)return this._index_low=0,this._index_high=-1,{min:NaN,max:NaN};if(this._index_high=null,null!=n){const e=t.palette.length,r=t.value_to_index(n,e);r<e-1&&(this._index_high=r,i=t.index_to_value(r+1))}if(this._index_low=null,null!=e){const n=t.value_to_index(e,t.palette.length);n>0&&(this._index_low=n,r=t.index_to_value(n))}return{min:r,max:i}}_get_major_size_factor(){return this.model.color_mapper.palette.length}_metrics_changed(){const t=this._major_range,e=this._major_scale,{color_mapper:n}=this.model;if(n instanceof sc&&e instanceof hc){const t=this._scanning_binning(n);e.binning=t;const r="vertical"==this.orientation,i=r?this._frame.y_scale:this._frame.x_scale;if(i instanceof hc){i.binning=t;const e=r?this._frame.y_range:this._frame.x_range;e instanceof xn&&(e.start=t[0],e.end=t[t.length-1])}}else if(n instanceof ac&&t instanceof xn){const{min:e,max:r}=this._continuous_metrics(n);t.setv({start:e,end:r})}this._set_canvas_image(),this.plot_view.request_layout()}_paint_colors(t,e){const{x:n,y:r,width:i,height:o}=e;t.save(),t.globalAlpha=this.model.scale_alpha,null!=this._image&&(t.setImageSmoothingEnabled(!1),t.drawImage(this._image,n,r,i,o)),this.visuals.bar_line.doit&&(this.visuals.bar_line.set_value(t),t.strokeRect(n,r,i,o)),t.restore()}_scanning_binning(t){let{binning:e,force_low_cutoff:n}=t.metrics;const{display_high:r}=this.model;let{display_low:i}=this.model;if(n&&(null==i||t.metrics.min>i)&&(i=t.metrics.min),null!=r&&null!=i&&r<i)return this._index_low=0,this._index_high=-1,[NaN];if(this._index_high=null,null!=r){const n=t.value_to_index(r,e.length);n<e.length-1&&(this._index_high=n)}if(this._index_low=null,null!=i){const n=t.value_to_index(i,e.length);n>0&&(this._index_low=n)}if(null!=this._index_low||null!=this._index_high){const t=null!=this._index_low?this._index_low:0,n=(null!=this._index_high?this._index_high+1:e.length-1)-t+1;if(n>0){const r=new Array(n);for(let i=0;i<n;i++)r[i]=e[i+t];e=r}else e=[NaN]}return e}_set_canvas_image(){const{orientation:t}=this;let{palette:e}=this.model.color_mapper;if(null==this._index_high&&null==this._index_low||(e=e.slice(null!=this._index_low?this._index_low:0,null!=this._index_high?this._index_high+1:e.length)),e.length<1)return void(this._image=null);"vertical"==t&&(e=(0,Rt.TY)(e));const[n,r]="vertical"==t?[1,e.length]:[e.length,1],i=this._image=document.createElement("canvas");i.width=n,i.height=r;const o=i.getContext("2d"),a=o.getImageData(0,0,n,r),s=new ru({palette:e}).rgba_mapper.v_compute((0,Rt.y1)(0,e.length));a.data.set(s),o.putImageData(a,0,0)}}au.__name__="ColorBarView";class su extends $c{constructor(t){super(t)}}Vc=su,su.__name__="ColorBar",Vc.prototype.default_view=au,Vc.define((({Nullable:t,Number:e,Ref:n})=>({color_mapper:[n(Fs)],display_low:[t(e),null],display_high:[t(e),null]})));class lu extends Fc{*children(){yield*super.children(),yield this._fill_view,yield this._line_view}async lazy_initialize(){await super.lazy_initialize();const{fill_renderer:t,line_renderer:e}=this.model;this._fill_view=await $e(t,{parent:this.parent}),this._line_view=await $e(e,{parent:this.parent})}remove(){this._fill_view.remove(),this._line_view.remove(),super.remove()}_create_major_range(){const t=this.model.levels;return t.length>0?new xn({start:t[0],end:t[t.length-1]}):new xn({start:0,end:1})}_paint_colors(t,e){const n="vertical"==this.orientation,r=this.model.levels,i=this._major_scale;i.source_range=this._major_range,i.target_range=new xn(n?{start:e.bottom,end:e.top}:{start:e.left,end:e.right});const o=i.v_compute(r),a=this._fill_view.glyph,s=a.data_size;if(s>0){(0,_.vA)(r.length==s+1,"Inconsistent number of filled contour levels"),t.save();for(let r=0;r<s;r++)t.beginPath(),n?t.rect(e.left,o[r],e.width,o[r+1]-o[r]):t.rect(o[r],e.top,o[r+1]-o[r],e.height),a.visuals.fill.apply(t,r),a.visuals.hatch.apply(t,r);t.restore()}const l=this._line_view.glyph,c=l.data_size;if(c>0){(0,_.vA)(r.length==c,"Inconsistent number of line contour levels"),t.save();for(let r=0;r<c;r++)t.beginPath(),n?(t.moveTo(e.left,o[r]),t.lineTo(e.right,o[r])):(t.moveTo(o[r],e.bottom),t.lineTo(o[r],e.top)),l.visuals.line.set_vectorize(t,r),t.stroke();t.restore()}}}lu.__name__="ContourColorBarView";class cu extends $c{constructor(t){super(t)}}Oc=cu,cu.__name__="ContourColorBar",Oc.prototype.default_view=lu,Oc.define((({Array:t,Number:e,Ref:n})=>({fill_renderer:[n(Jl)],line_renderer:[n(Jl)],levels:[t(e),[]]})));class uu extends ra{update_layout(){const{panel:t}=this;this.layout=null!=t?new uo(t,(()=>this.get_size()),!1):void 0}_get_size(){if(!this.displayed)return{width:0,height:0};const t=this._text_view.graphics(),{angle:e,angle_units:n}=this.model;t.angle=(0,Gi.rk)(e,n),t.visuals=this.visuals.text.values();const{width:r,height:i}=t.size();return{width:r,height:i}}_render(){const{angle:t,angle_units:e}=this.model,n=(0,Gi.rk)(t,e),r=null!=this.layout?this.layout:this.plot_view.frame,i=this.coordinates.x_scale,o=this.coordinates.y_scale;let a=(()=>{switch(this.model.x_units){case"canvas":return this.model.x;case"screen":return r.bbox.xview.compute(this.model.x);case"data":return i.compute(this.model.x)}})(),s=(()=>{switch(this.model.y_units){case"canvas":return this.model.y;case"screen":return r.bbox.yview.compute(this.model.y);case"data":return o.compute(this.model.y)}})();a+=this.model.x_offset,s-=this.model.y_offset,this._paint(this.layer.ctx,{sx:a,sy:s},n)}}uu.__name__="LabelView";class du extends ia{constructor(t){super(t)}}Pc=du,du.__name__="Label",Pc.prototype.default_view=uu,Pc.define((({Number:t,Angle:e})=>({x:[t],x_units:[_n.yx,"data"],y:[t],y_units:[_n.yx,"data"],angle:[e,0],angle_units:[_n.xb,"rad"],x_offset:[t,0],y_offset:[t,0]})));class hu extends Ci{map_data(){const{x_scale:t,y_scale:e}=this.coordinates,n=null!=this.layout?this.layout:this.plot_view.frame;this.sx=(()=>{switch(this.model.x_units){case"canvas":return new Jt.mR(this._x);case"screen":return n.bbox.xview.v_compute(this._x);case"data":return t.v_compute(this._x)}})(),this.sy=(()=>{switch(this.model.y_units){case"canvas":return new Jt.mR(this._y);case"screen":return n.bbox.yview.v_compute(this._y);case"data":return e.v_compute(this._y)}})()}paint(){const{ctx:t}=this.layer;for(let e=0,n=this.text.length;e<n;e++){const n=this.x_offset.get(e),r=this.y_offset.get(e),i=this.sx[e]+n,o=this.sy[e]-r,a=this.angle.get(e),s=this.text.get(e);isFinite(i+o+a)&&null!=s&&this._paint(t,e,`${s}`,i,o,a)}}_paint(t,e,n,r,i,o){const a=new ko({text:n});a.angle=o,a.position={sx:r,sy:i},a.visuals=this.visuals.text.values(e);const{background_fill:s,border_line:l}=this.visuals;if(s.doit||l.doit){const{p0:n,p1:r,p2:i,p3:o}=a.rect();t.beginPath(),t.moveTo(n.x,n.y),t.lineTo(r.x,r.y),t.lineTo(i.x,i.y),t.lineTo(o.x,o.y),t.closePath(),this.visuals.background_fill.apply(t,e),this.visuals.border_line.apply(t,e)}this.visuals.text.doit&&a.paint(t)}}hu.__name__="LabelSetView";class pu extends Si{constructor(t){super(t)}}Dc=pu,pu.__name__="LabelSet",Dc.prototype.default_view=hu,Dc.mixins([Ke.Dt,["border_",Ke.UT],["background_",Ke.H_]]),Dc.define((()=>({x:[m.up,{field:"x"}],y:[m.fZ,{field:"y"}],x_units:[_n.yx,"data"],y_units:[_n.yx,"data"],text:[m.C1,{field:"text"}],angle:[m.XS,0],x_offset:[m.fY,{value:0}],y_offset:[m.fY,{value:0}]}))),Dc.override({background_fill_color:null,border_line_color:null});class fu extends qt{constructor(t){super(t)}_check_data_sources_on_renderers(){if(null!=this.get_field_from_label_prop()){if(this.renderers.length<1)return!1;const t=this.renderers[0].data_source;for(const e of this.renderers)if(e.data_source!=t)return!1}return!0}_check_field_label_on_data_source(){const t=this.get_field_from_label_prop();if(null!=t){if(this.renderers.length<1)return!1;const e=this.renderers[0].data_source;if(!(0,Rt.mK)(e.columns(),t))return!1}return!0}initialize(){super.initialize(),this.legend=null,this.connect(this.change,(()=>this.legend?.item_change.emit())),this._check_data_sources_on_renderers()||ot.vF.error("Non matching data sources on legend item renderers"),this._check_field_label_on_data_source()||ot.vF.error(`Bad column name on label: ${this.label}`)}get_field_from_label_prop(){const{label:t}=this;return(0,U.dt)(t)?t.field:null}get_labels_list_from_label_prop(){if(!this.visible)return[];if((0,U.ml)(this.label)){const{value:t}=this.label;return null!=t?[t]:[]}const t=this.get_field_from_label_prop();if(null!=t){let e;if(0==this.renderers.length)return["No source found"];if(e=this.renderers[0].data_source,e instanceof hr){const n=e.get_column(t);return null!=n?(0,Rt.sb)(Array.from(n)):["Invalid field"]}}return[]}}Nc=fu,fu.__name__="LegendItem",Nc.define((({Boolean:t,Int:e,Array:n,Ref:r,Nullable:i})=>({label:[m.C1,null],renderers:[n(r(Jl)),[]],index:[i(e),null],visible:[t,!0]})));class Qu extends nr{update_layout(){const{panel:t}=this;this.layout=null!=t?new uo(t,(()=>this.get_size())):void 0}cursor(t,e){return"none"==this.model.click_policy?null:"pointer"}get legend_padding(){return null!=this.model.border_line_color?this.model.padding:0}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render())),this.connect(this.model.item_change,(()=>this.request_render()))}compute_legend_bbox(){const{glyph_height:t,glyph_width:e}=this.model,{label_height:n,label_width:r}=this.model,i=[];for(const t of this.model.items){const e=t.get_field_from_label_prop(),n=t.get_labels_list_from_label_prop();for(const r of n){const n=new ko({text:`${r}`});n.visuals=this.visuals.label_text.values(),i.push({item:t,field:e,label:r,text_box:n,bbox:n.bbox()})}}this.text_widths=new Map;for(const t of i)this.text_widths.set(t.label,(0,Rt.T9)([t.bbox.width,r]));this.max_label_height=(0,Rt.T9)([n,t,...i.map((t=>t.bbox.height))]);const o=(0,Rt.T9)([0,...this.text_widths.values()]),{title:a}=this.model;if(null==a||0==a.length)this.title_width=0,this.title_height=0;else{const t=new ko({text:a});t.visuals=this.visuals.title_text.values();const{width:e,height:n}=t.bbox();this.title_width=e,this.title_height=n+this.model.title_standoff}const s=this.model.margin,{legend_padding:l}=this,c=this.model.spacing,{label_standoff:u}=this.model;let d,h;if("vertical"==this.model.orientation)d=i.length*this.max_label_height+Math.max(i.length-1,0)*c+2*l+this.title_height,h=(0,Rt.T9)([o+e+u+2*l,this.title_width+2*l]);else{let t=2*l+Math.max(i.length-1,0)*c;for(const[,n]of this.text_widths)t+=(0,Rt.T9)([n,r])+e+u;h=(0,Rt.T9)([this.title_width+2*l,t]),d=this.max_label_height+this.title_height+2*l}const p=null!=this.layout?this.layout:this.plot_view.frame,[Q,T]=p.bbox.ranges,{location:m}=this.model;let g,_;if((0,f.Kg)(m))switch(m){case"top_left":g=Q.start+s,_=T.start+s;break;case"top":case"top_center":g=(Q.end+Q.start)/2-h/2,_=T.start+s;break;case"top_right":g=Q.end-s-h,_=T.start+s;break;case"bottom_right":g=Q.end-s-h,_=T.end-s-d;break;case"bottom":case"bottom_center":g=(Q.end+Q.start)/2-h/2,_=T.end-s-d;break;case"bottom_left":g=Q.start+s,_=T.end-s-d;break;case"left":case"center_left":g=Q.start+s,_=(T.end+T.start)/2-d/2;break;case"center":case"center_center":g=(Q.end+Q.start)/2-h/2,_=(T.end+T.start)/2-d/2;break;case"right":case"center_right":g=Q.end-s-h,_=(T.end+T.start)/2-d/2}else{const[t,e]=m;g=p.bbox.xview.compute(t),_=p.bbox.yview.compute(e)-d}return new re({left:g,top:_,width:h,height:d})}interactive_bbox(){return this.compute_legend_bbox()}interactive_hit(t,e){return this.interactive_bbox().contains(t,e)}on_hit(t,e){let n;const{glyph_width:r}=this.model,{legend_padding:i}=this,o=this.model.spacing,{label_standoff:a}=this.model;let s=n=i;const l=this.compute_legend_bbox(),c="vertical"==this.model.orientation;for(const u of this.model.items){const d=u.get_labels_list_from_label_prop();for(const h of d){const d=l.x+s,p=l.y+n+this.title_height;let f,Q;if([f,Q]=c?[l.width-2*i,this.max_label_height]:[this.text_widths.get(h)+r+a,this.max_label_height],new re({left:d,top:p,width:f,height:Q}).contains(t,e)){switch(this.model.click_policy){case"hide":for(const t of u.renderers)t.visible=!t.visible;break;case"mute":for(const t of u.renderers)t.muted=!t.muted}return!0}c?n+=this.max_label_height+o:s+=this.text_widths.get(h)+r+a+o}}return!1}_render(){if(0==this.model.items.length)return;if(!(0,Rt.zN)(this.model.items,(t=>t.visible)))return;for(const t of this.model.items)t.legend=this.model;const{ctx:t}=this.layer,e=this.compute_legend_bbox();t.save(),this._draw_legend_box(t,e),this._draw_legend_items(t,e),this._draw_title(t,e),t.restore()}_draw_legend_box(t,e){t.beginPath(),t.rect(e.x,e.y,e.width,e.height),this.visuals.background_fill.apply(t),this.visuals.border_line.apply(t)}_draw_legend_items(t,e){const{glyph_width:n,glyph_height:r}=this.model,{legend_padding:i}=this,o=this.model.spacing,{label_standoff:a}=this.model;let s=i,l=i;const c="vertical"==this.model.orientation;for(const u of this.model.items){if(!u.visible)continue;const d=u.get_labels_list_from_label_prop(),h=u.get_field_from_label_prop();if(0==d.length)continue;const p=(()=>{switch(this.model.click_policy){case"none":return!0;case"hide":return(0,Rt.Si)(u.renderers,(t=>t.visible));case"mute":return(0,Rt.Si)(u.renderers,(t=>!t.muted))}})();for(const f of d){const d=e.x+s,Q=e.y+l+this.title_height,T=d+n,m=Q+r;c?l+=this.max_label_height+o:s+=this.text_widths.get(f)+n+a+o,this.visuals.label_text.set_value(t),t.fillText(f,T+a,Q+this.max_label_height/2);for(const e of u.renderers){const n=this.plot_view.renderer_view(e);n?.draw_legend(t,d,T,Q,m,h,f,u.index)}if(!p){let r,o;[r,o]=c?[e.width-2*i,this.max_label_height]:[this.text_widths.get(f)+n+a,this.max_label_height],t.beginPath(),t.rect(d,Q,r,o),this.visuals.inactive_fill.set_value(t),t.fill()}}}}_draw_title(t,e){const{title:n}=this.model;null!=n&&0!=n.length&&this.visuals.title_text.doit&&(t.save(),t.translate(e.x0,e.y0+this.title_height),this.visuals.title_text.set_value(t),t.fillText(n,this.legend_padding,this.legend_padding-this.model.title_standoff),t.restore())}_get_size(){const{width:t,height:e}=this.compute_legend_bbox();return{width:t+2*this.model.margin,height:e+2*this.model.margin}}}Qu.__name__="LegendView";class Tu extends rr{constructor(t){super(t)}initialize(){super.initialize(),this.item_change=new T.n2(this,"item_change")}get_legend_names(){const t=[];for(const e of this.items){const n=e.get_labels_list_from_label_prop();t.push(...n)}return t}}Rc=Tu,Tu.__name__="Legend",Rc.prototype.default_view=Qu,Rc.mixins([["label_",Ke.EY],["title_",Ke.EY],["inactive_",Ke.SQ],["border_",Ke.N1],["background_",Ke.SQ]]),Rc.define((({Number:t,String:e,Array:n,Tuple:r,Or:i,Ref:o,Nullable:a})=>({orientation:[_n.t4,"vertical"],location:[i(_n.Lo,r(t,t)),"top_right"],title:[a(e),null],title_standoff:[t,5],label_standoff:[t,5],glyph_height:[t,20],glyph_width:[t,20],label_height:[t,20],label_width:[t,20],margin:[t,10],padding:[t,10],spacing:[t,3],items:[n(o(fu)),[]],click_policy:[_n.gI,"none"]}))),Rc.override({border_line_color:"#e5e5e5",border_line_alpha:.5,border_line_width:1,background_fill_color:"#ffffff",background_fill_alpha:.95,inactive_fill_color:"white",inactive_fill_alpha:.7,label_text_font_size:"13px",label_text_baseline:"middle",title_text_font_size:"13px",title_text_font_style:"italic"});class mu extends nr{connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render()))}_render(){const{xs:t,ys:e}=this.model;if(t.length!=e.length)return;const n=t.length;if(n<3)return;const{frame:r}=this.plot_view,{ctx:i}=this.layer,o=this.coordinates.x_scale,a=this.coordinates.y_scale;function s(t,e,n,r){switch(e){case"canvas":return t;case"screen":return r.v_compute(t);case"data":return n.v_compute(t)}}const l=s(t,this.model.xs_units,o,r.bbox.xview),c=s(e,this.model.ys_units,a,r.bbox.yview);i.beginPath();for(let t=0;t<n;t++)i.lineTo(l[t],c[t]);i.closePath(),this.visuals.fill.apply(i),this.visuals.hatch.apply(i),this.visuals.line.apply(i)}}mu.__name__="PolyAnnotationView";class gu extends rr{constructor(t){super(t)}update({xs:t,ys:e}){this.setv({xs:(0,Rt.C)(t),ys:(0,Rt.C)(e),visible:!0})}clear(){this.setv({xs:[],ys:[],visible:!1})}}Ic=gu,gu.__name__="PolyAnnotation",Ic.prototype.default_view=mu,Ic.mixins([Ke.N1,Ke.SQ,Ke.LD]),Ic.define((({Number:t,Array:e})=>({xs:[e(t),[]],ys:[e(t),[]],xs_units:[_n.yx,"data"],ys_units:[_n.yx,"data"]}))),Ic.override({fill_color:"#fff9ba",fill_alpha:.4,line_color:"#cccccc",line_alpha:.3});class _u extends nr{connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render()))}_render(){const{gradient:t,y_intercept:e}=this.model;if(null==t||null==e)return;const{frame:n}=this.plot_view,r=this.coordinates.x_scale,i=this.coordinates.y_scale;let o,a,s,l;if(0==t)o=i.compute(e),a=o,s=n.bbox.left,l=s+n.bbox.width;else{o=n.bbox.top,a=o+n.bbox.height;const c=(i.invert(o)-e)/t,u=(i.invert(a)-e)/t;s=r.compute(c),l=r.compute(u)}const{ctx:c}=this.layer;c.save(),c.beginPath(),this.visuals.line.set_value(c),c.moveTo(s,o),c.lineTo(l,a),c.stroke(),c.restore()}}_u.__name__="SlopeView";class bu extends rr{constructor(t){super(t)}}jc=bu,bu.__name__="Slope",jc.prototype.default_view=_u,jc.mixins(Ke.N1),jc.define((({Number:t,Nullable:e})=>({gradient:[e(t),null],y_intercept:[e(t),null]}))),jc.override({line_color:"black"});class vu extends nr{connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.plot_view.request_paint(this)))}_render(){const{location:t}=this.model;if(null==t)return;const{frame:e}=this.plot_view,n=this.coordinates.x_scale,r=this.coordinates.y_scale,i=(e,n)=>{switch(this.model.location_units){case"canvas":return t;case"screen":return n.compute(t);case"data":return e.compute(t)}};let o,a,s,l;"width"==this.model.dimension?(s=i(r,e.bbox.yview),a=e.bbox.left,l=e.bbox.width,o=this.model.line_width):(s=e.bbox.top,a=i(n,e.bbox.xview),l=this.model.line_width,o=e.bbox.height);const{ctx:c}=this.layer;c.save(),c.beginPath(),this.visuals.line.set_value(c),c.moveTo(a,s),"width"==this.model.dimension?c.lineTo(a+l,s):c.lineTo(a,s+o),c.stroke(),c.restore()}}vu.__name__="SpanView";class yu extends rr{constructor(t){super(t)}}zc=yu,yu.__name__="Span",zc.prototype.default_view=vu,zc.mixins(Ke.N1),zc.define((({Number:t,Nullable:e})=>({location:[e(t),null],location_units:[_n.yx,"data"],dimension:[_n.fg,"width"]}))),zc.override({line_color:"black"});class xu extends 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t=this.__createElement("g");t.setAttribute("clip-path",this._clip_path),t.appendChild(e),u.appendChild(t)}else u.appendChild(e)}}createPattern(t,e){const n=this.__document.createElementNS("http://www.w3.org/2000/svg","pattern"),r=this._random_string();if(n.setAttribute("id",r),n.setAttribute("width",`${this._to_number(t.width)}`),n.setAttribute("height",`${this._to_number(t.height)}`),n.setAttribute("patternUnits","userSpaceOnUse"),t instanceof HTMLCanvasElement||t instanceof HTMLImageElement||t instanceof SVGImageElement){const e=this.__document.createElementNS("http://www.w3.org/2000/svg","image"),r=t instanceof HTMLCanvasElement?t.toDataURL():t.getAttribute("src");e.setAttribute("href",r),n.appendChild(e),this.__defs.appendChild(n)}else if(t instanceof Bu){for(const e of[...t.__root.childNodes])e instanceof SVGDefsElement||n.appendChild(e.cloneNode(!0));this.__defs.appendChild(n)}else{if(!(t instanceof SVGSVGElement))throw new Error("unsupported");for(const e of[...t.childNodes])e instanceof SVGDefsElement||n.appendChild(e.cloneNode(!0));this.__defs.appendChild(n)}return new zu(n,this)}getLineDash(){const{lineDash:t}=this;return(0,f.Kg)(t)?t.split(",").map((t=>parseInt(t))):null==t?[]:t}setLineDash(t){t.length>0?this.lineDash=t.join(","):this.lineDash=null}_to_number(t){return(0,f.Et)(t)?t:t.baseVal.value}getTransform(){return this._transform.to_DOMMatrix()}setTransform(...t){let e;e=(0,f.Et)(t[0])?new DOMMatrix(t):t[0]instanceof DOMMatrix?t[0]:new DOMMatrix(Object.values(!t[0])),this._transform=Lo.from_DOMMatrix(e)}resetTransform(){this._transform=new Lo}isPointInPath(...t){throw new Error("not implemented")}isPointInStroke(...t){throw new Error("not implemented")}createImageData(...t){throw new Error("not implemented")}getImageData(t,e,n,r){throw new Error("not implemented")}putImageData(...t){throw new Error("not implemented")}drawFocusIfNeeded(...t){throw new Error("not implemented")}scrollPathIntoView(...t){throw new Error("not implemented")}}Bu.__name__="SVGRenderingContext2D",Bu.__random=Pu;class Fu{constructor(t,e){switch(this.backend=t,this.hidpi=e,this.pixel_ratio=1,this.bbox=new re,t){case"webgl":case"canvas":{this._el=this._canvas=se({class:"bk-layer"});const t=this.canvas.getContext("2d");if(null==t)throw new Error("unable to obtain 2D rendering context");this._ctx=t,e&&(this.pixel_ratio=devicePixelRatio);break}case"svg":{const t=new Bu;this._ctx=t,this._canvas=t.get_svg(),this._el=oe({class:"bk-layer"}),this._el.attachShadow({mode:"open"}).appendChild(this._canvas);break}}var n;this._ctx.layer=this,function(t){void 0===t.lineDash&&Object.defineProperty(t,"lineDash",{get:()=>t.getLineDash(),set:e=>t.setLineDash(e)})}(n=this._ctx),function(t){t.setImageSmoothingEnabled=e=>{t.imageSmoothingEnabled=e,t.mozImageSmoothingEnabled=e,t.oImageSmoothingEnabled=e,t.webkitImageSmoothingEnabled=e,t.msImageSmoothingEnabled=e},t.getImageSmoothingEnabled=()=>{const e=t.imageSmoothingEnabled;return null==e||e}}(n),function(t){t.ellipse||(t.ellipse=function(e,n,r,i,o,a,s,l=!1){const c=.551784;t.translate(e,n),t.rotate(o);let u=r,d=i;l&&(u=-r,d=-i),t.moveTo(-u,0),t.bezierCurveTo(-u,d*c,-u*c,d,0,d),t.bezierCurveTo(u*c,d,u,d*c,u,0),t.bezierCurveTo(u,-d*c,u*c,-d,0,-d),t.bezierCurveTo(-u*c,-d,-u,-d*c,-u,0),t.rotate(-o),t.translate(-e,-n)})}(n)}get canvas(){return this._canvas}get ctx(){return this._ctx}get el(){return this._el}resize(t,e){if(this.bbox.width==t&&this.bbox.height==e)return;this.bbox=new re({left:0,top:0,width:t,height:e});const{target:n}=this;n.width=t*this.pixel_ratio,n.height=e*this.pixel_ratio}get target(){return this._ctx instanceof Bu?this._ctx:this.canvas}undo_transform(t){const{ctx:e}=this,n=e.getTransform();e.setTransform(this._base_transform);try{t(e)}finally{e.setTransform(n)}}prepare(){const{ctx:t,hidpi:e,pixel_ratio:n}=this;t.save(),e&&(t.scale(n,n),t.translate(.5,.5)),this._base_transform=t.getTransform(),this.clear()}clear(){const{x:t,y:e,width:n,height:r}=this.bbox;this.ctx.clearRect(t,e,n,r)}finish(){this.ctx.restore()}to_blob(){const{_canvas:t}=this;if(t instanceof HTMLCanvasElement)return new Promise(((e,n)=>{t.toBlob((t=>null!=t?e(t):n()),"image/png")}));{const t=this._ctx.get_serialized_svg(!0),e=new Blob([t],{type:"image/svg+xml"});return Promise.resolve(e)}}}var $u;Fu.__name__="CanvasLayer";const{round:Gu}=Math;function*qu(t){if(t instanceof xu){const e=new Set((0,Q.HP)(qt.prototype._props));for(const n of t)e.has(n.attr)||(yield[n.attr,n.get_value()])}else yield*(0,Q.jO)(t)}class Uu extends Be{constructor(){super(...arguments),this._display=new Pe,this.style=new Pe,this._is_displayed=!1}get stylesheets(){return[...this._stylesheets()]}*_stylesheets(){yield this.style,yield this._display}get classes(){return[...this.css_classes(),...this._classes()]}*_classes(){yield`bk-${this.model.type}`}styles(){return[...super.styles(),":host{position:relative;}"]}update_style(){this.style.clear()}box_sizing(){return{width_policy:"auto",height_policy:"auto",width:null,height:null,aspect_ratio:null}}get bbox(){return null==this._bbox&&this._update_bbox(),this._bbox}update_bbox(){this._update_bbox()}_update_bbox(){const t=null!=this.el.offsetParent,e=t?(()=>{const t=this.el.getBoundingClientRect(),{left:e,top:n}=(()=>{if(null!=this.parent){const e=this.parent.el.getBoundingClientRect();return{left:t.left-e.left,top:t.top-e.top}}return{left:0,top:0}})();return new re({left:Gu(e),top:Gu(n),width:Gu(t.width),height:Gu(t.height)})})():new re;this._bbox=e,this._is_displayed=t}initialize(){super.initialize(),this._resize_observer=new ResizeObserver((t=>this.after_resize())),this._resize_observer.observe(this.el,{box:"border-box"})}connect_signals(){super.connect_signals();const{visible:t,styles:e}=this.model.properties;this.on_change(t,(()=>this._apply_visible())),this.on_change(e,(()=>this._apply_styles()))}remove(){this._resize_observer.disconnect(),super.remove()}_after_resize(){}after_resize(){this.update_bbox(),this._after_resize(),this.finish()}render_to(t){super.render_to(t),this.after_render()}render(){this.empty(),this._apply_stylesheets(this.styles()),this._apply_stylesheets(this.stylesheets),this._apply_stylesheets(this.model.stylesheets),this._apply_styles(),this._apply_classes(this.classes),this._apply_classes(this.model.classes),this._apply_visible()}after_render(){this.update_style(),this.update_bbox(),this.is_displayed||this.finish()}get is_displayed(){return this._is_displayed}_apply_styles(){const{styles:t}=this.model,e=(t,e)=>{const n=t in this.el.style;return n&&(0,f.Kg)(e)&&(this.el.style[t]=e),n};for(const[n,r]of qu(t)){const t=n.replace(/_/g,"-");e(t,r)||e(`-webkit-${t}`,r)||e(`-moz-${t}`,r)||ot.vF.trace(`unknown CSS property '${t}'`)}}_apply_stylesheets(t){super._apply_stylesheets(t.map((t=>{if((0,f.Qd)(t)){const e=[];for(const[n,r]of(0,Q.jO)(t)){e.push(`${n} {`);for(const[t,n]of qu(r)){const r=t.replace(/_/g,"-");(0,f.Kg)(n)&&0!=n.length&&e.push(`  ${r}: ${n};`)}e.push("}")}return e.join("\n")}return t})))}_apply_visible(){this.model.visible?this._display.clear():this._display.replace(":host { display: none !important; }")}export(t="auto",e=!0){const n=new Fu("auto"==t||"png"==t?"canvas":"svg",e),{width:r,height:i}=this.bbox;return n.resize(r,i),n}serializable_state(){return{...super.serializable_state(),bbox:this.bbox.box}}}Uu.__name__="UIElementView";class Wu extends qt{constructor(t){super(t)}}var Zu,Xu;$u=Wu,Wu.__name__="UIElement",$u.define((({Boolean:t,Array:e,Dict:n,String:r,Ref:i,Or:o,Nullable:a})=>{const s=o(n(a(r)),i(xu));return{visible:[t,!0],classes:[e(r),[]],styles:[s,{}],stylesheets:[e(o(r,n(s))),[]]}}));class Ku extends Kt{connect_signals(){super.connect_signals(),this.connect(this.model.properties.active.change,(()=>{this.model.active?this.activate():this.deactivate()}))}get overlays(){return[]}activate(){}deactivate(){}}Ku.__name__="ToolView";class Yu extends qt{constructor(t){super(t)}get event_role(){const{event_type:t}=this;return(0,f.Kg)(t)?t:"multi"}get event_types(){const{event_type:t}=this;return null==t?[]:(0,f.Kg)(t)?[t]:t}get tooltip(){return this.description??this.tool_name}get computed_icon(){const{icon:t,tool_icon:e}=this;return t??(null!=e?`.${e}`:void 0)}get menu(){return null}_get_dim_limits([t,e],[n,r],i,o){const a=i.bbox.h_range;let s;"width"==o||"both"==o?(s=[(0,Rt.jk)([t,n]),(0,Rt.T9)([t,n])],s=[(0,Rt.T9)([s[0],a.start]),(0,Rt.jk)([s[1],a.end])]):s=[a.start,a.end];const l=i.bbox.v_range;let c;return"height"==o||"both"==o?(c=[(0,Rt.jk)([e,r]),(0,Rt.T9)([e,r])],c=[(0,Rt.T9)([c[0],l.start]),(0,Rt.jk)([c[1],l.end])]):c=[l.start,l.end],[s,c]}_get_dim_tooltip(t){const{description:e,tool_name:n}=this;return null!=e?e:"both"==t?n:"auto"==t?`${n} (either x, y or both dimensions)`:`${n} (${"width"==t?"x":"y"}-axis)`}static register_alias(t,e){this.prototype._known_aliases.set(t,e)}static from_string(t){const e=this.prototype._known_aliases.get(t);if(null!=e)return e();{const e=[...this.prototype._known_aliases.keys()];throw new Error(`unexpected tool name '${t}', possible tools are ${e.join(", ")}`)}}}Zu=Yu,Yu.__name__="Tool",Zu.prototype._known_aliases=new Map,Zu.define((({String:t,Regex:e,Nullable:n,Or:r})=>({icon:[n(r(_n.si,e(/^--/),e(/^\./),e(/^data:image/))),null],description:[n(t),null]}))),Zu.internal((({Boolean:t})=>({active:[t,!1],disabled:[t,!1]})));class Ju extends qt{constructor(t){super(t)}get underlying(){return this.tools[0]}tool_button(){const t=this.tools[0].tool_button();return t.tool=this,t}get event_type(){return this.tools[0].event_type}get event_role(){return this.tools[0].event_role}get event_types(){return this.tools[0].event_types}get default_order(){return this.tools[0].default_order}get tooltip(){return this.tools[0].tooltip}get tool_name(){return this.tools[0].tool_name}get computed_icon(){return this.tools[0].computed_icon}get toggleable(){const t=this.tools[0];return"toggleable"in t&&t.toggleable}initialize(){super.initialize(),this.do=new T.n2(this,"do")}connect_signals(){super.connect_signals(),this.connect(this.do,(()=>this.doit())),this.connect(this.properties.active.change,(()=>this.set_active()));for(const t of this.tools)this.connect(t.properties.active.change,(()=>{this.active=t.active}))}doit(){for(const t of this.tools)t.do.emit()}set_active(){for(const t of this.tools)t.active=this.active}get menu(){const{menu:t}=this.tools[0];if(null==t)return null;const e=[];for(const[n,r]of(0,On.HL)(t))if(null==n)e.push(null);else{const t=()=>{for(const t of this.tools)t.menu?.[r]?.handler?.()};e.push({...n,handler:t})}return e}}Xu=Ju,Ju.__name__="ToolProxy",Xu.define((({Boolean:t,Array:e,Ref:n})=>({tools:[e(n(Yu)),[]],active:[t,t=>(0,On.zN)(t.tools,(t=>t.active))],disabled:[t,!1]})));const td="bk-menu-icon",ed="bk-horizontal",nd="bk-vertical",rd="bk-divider",id="bk-active",od=".bk-menu-icon{width:28px;height:28px;mask-size:60% 60%;mask-position:center center;mask-repeat:no-repeat;-webkit-mask-size:60% 60%;-webkit-mask-position:center center;-webkit-mask-repeat:no-repeat;background-size:60%;background-color:transparent;background-repeat:no-repeat;background-position:center center;}:host{position:absolute;display:inline-flex;flex-wrap:nowrap;user-select:none;-webkit-user-select:none;width:auto;height:auto;z-index:100;cursor:pointer;font-size:var(--font-size);background-color:#fff;border:1px solid #ccc;border-radius:var(--border-radius);box-shadow:0 6px 12px rgba(0, 0, 0, 0.175);}:host(.bk-horizontal){flex-direction:row;}:host(.bk-vertical){flex-direction:column;}.bk-divider{cursor:default;overflow:hidden;background-color:#e5e5e5;}:host(.bk-horizontal) > .bk-divider{width:1px;margin:5px 0;}:host(.bk-vertical) > .bk-divider{height:1px;margin:0 5px;}:host > :not(.bk-divider){border:1px solid transparent;--active-tool-highlight:#26aae1;}:host > :not(.bk-divider).bk-active{border-color:var(--active-tool-highlight);}:host > :not(.bk-divider):hover{background-color:#f9f9f9;}:host > :not(.bk-divider):focus,:host > :not(.bk-divider):focus-visible{outline:1px dotted var(--active-tool-highlight);outline-offset:-1px;}:host > :not(.bk-divider)::-moz-focus-inner{border:0;}:host(.bk-horizontal) > :not(.bk-divider):first-child{border-top-left-radius:var(--border-radius);border-bottom-left-radius:var(--border-radius);}:host(.bk-horizontal) > :not(.bk-divider):last-child{border-top-right-radius:var(--border-radius);border-bottom-right-radius:var(--border-radius);}:host(.bk-vertical) > :not(.bk-divider):first-child{border-top-left-radius:var(--border-radius);border-top-right-radius:var(--border-radius);}:host(.bk-vertical) > :not(.bk-divider):last-child{border-bottom-left-radius:var(--border-radius);border-bottom-right-radius:var(--border-radius);}",ad="bk-tool-icon-box-zoom",sd="bk-tool-icon-x-box-zoom",ld="bk-tool-icon-y-box-zoom",cd="bk-tool-icon-auto-box-zoom",ud="bk-tool-icon-pan",dd="bk-tool-icon-x-pan",hd="bk-tool-icon-y-pan",pd=':host{--bokeh-icon-color:#a1a6a9;--bokeh-icon-color-disabled:#d4d9db;}.bk-tool-icon-copy{background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-copy);-webkit-mask-image:var(--bokeh-icon-copy);}.bk-tool-icon-replace-mode{background-image:var(--bokeh-icon-replace-mode, url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAABmJLR0QA/wD/AP+gvaeTAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH5AUFFxokK3gniQAAAHpJREFUWMNjXLhsJcNAAiaGAQajDhhwB7DgEP+PxmeksvjgDwFcLmYkUh2hkBj8IcBIZXsYh1w2/I8v3sgAOM0bLYhGc8GgrwuICgldfQO88pcvXvg/aOuCUQeM5oLRuoCFCJcTbOMh5XOiW0JDNhdQS3y0IBp1ABwAAF8KGrhC1Eg6AAAAAElFTkSuQmCC"));}.bk-tool-icon-append-mode{background-image:var(--bokeh-icon-append-mode, url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAABmJLR0QA/wD/AP+gvaeTAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH5AUFFxkZWD04WwAAAB1pVFh0Q29tbWVudAAAAAAAQ3JlYXRlZCB3aXRoIEdJTVBkLmUHAAAAoUlEQVRYw+1WQQ6AIAwrhO8Y/bIXEz9jIMSDr8ETCUEPQzA4pMeFLKNbu4l5WR0CDOMEALBGIzMuQIBEZQjPgP9JLjwTfBjY9sO9lZsFA9IafZng3BlIyVefgd8XQFZBAWe8jfNxwsDhir6rzoCiPiy1K+J8/FRQemv2XfAdFcQ9znU4Viqg9ta1qYJ+D1BnAIBrkgGVOrXNqUA9rbyZm/AEzFh4jEeY/soAAAAASUVORK5CYII="));}.bk-tool-icon-intersect-mode{background-image:var(--bokeh-icon-intersect-mode, 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fd{constructor(t,e){this.items=t,this.el=oe(),this._open=!1,this._item_click=t=>{t.handler?.(),this.hide()},this._on_mousedown=t=>{t.composedPath().includes(this.el)||this.prevent_hide?.(t)||this.hide()},this._on_keydown=t=>{"Escape"==t.key&&this.hide()},this._on_blur=()=>{this.hide()},this.target=e.target,this.orientation=e.orientation??"vertical",this.reversed=e.reversed??!1,this.prevent_hide=e.prevent_hide,this.extra_styles=e.extra_styles??[],this.shadow_el=this.el.attachShadow({mode:"open"}),this.class_list=new Ee(this.el.classList)}get is_open(){return this._open}get can_open(){return 0!=this.items.length}remove(){this._unlisten(),Le(this.el)}_listen(){document.addEventListener("mousedown",this._on_mousedown),document.addEventListener("keydown",this._on_keydown),window.addEventListener("blur",this._on_blur)}_unlisten(){document.removeEventListener("mousedown",this._on_mousedown),document.removeEventListener("keydown",this._on_keydown),window.removeEventListener("blur",this._on_blur)}_position(t){const e=(()=>{if("left_of"in t){const{left:e,top:n}=t.left_of.getBoundingClientRect();return{right:e,top:n}}if("right_of"in t){const{top:e,right:n}=t.right_of.getBoundingClientRect();return{left:n,top:e}}if("below"in t){const{left:e,bottom:n}=t.below.getBoundingClientRect();return{left:e,top:n}}if("above"in t){const{left:e,top:n}=t.above.getBoundingClientRect();return{left:e,bottom:n}}return t})(),n=this.el.offsetParent??document.body,r=(()=>{const t=n.getBoundingClientRect(),e=getComputedStyle(n);return{left:t.left-parseFloat(e.marginLeft),right:t.right+parseFloat(e.marginRight),top:t.top-parseFloat(e.marginTop),bottom:t.bottom+parseFloat(e.marginBottom)}})(),{style:i}=this.el;i.left=null!=e.left?e.left-r.left+"px":"auto",i.top=null!=e.top?e.top-r.top+"px":"auto",i.right=null!=e.right?r.right-e.right+"px":"auto",i.bottom=null!=e.bottom?r.bottom-e.bottom+"px":"auto"}styles(){return[Ie,od,pd,...this.extra_styles]}empty(){Ae(this.shadow_el),this.class_list.clear()}render(){this.empty();for(const t of this.styles()){const e=(0,f.Kg)(t)?new Pe(t):t;this.shadow_el.appendChild(e.el)}this.class_list.add(r[this.orientation]);const t=this.reversed?(0,Rt.TY)(this.items):this.items;for(const e of t){let t;if(null==e)t=oe({class:rd});else{if(null!=e.if&&!e.if())continue;if(null!=e.content)t=e.content;else{const n=null!=e.icon?oe({class:[td,e.icon]}):null,r=[e.active?.()?id:null,e.class];t=oe({class:r,title:e.tooltip,tabIndex:0},n,e.label,e.content),t.addEventListener("click",(()=>{this._item_click(e)})),t.addEventListener("keydown",(t=>{"Enter"==t.key&&this._item_click(e)}))}}this.shadow_el.appendChild(t)}}show(t){if(0!=this.items.length&&!this._open){if(this.render(),0==this.shadow_el.children.length)return;(this.target.shadowRoot??this.target).appendChild(this.el),this._position(t??{left:0,top:0}),this._listen(),this._open=!0}}hide(){this._open&&(this._open=!1,this._unlisten(),Le(this.el))}toggle(t){this._open?this.hide():this.show(t)}}fd.__name__="ContextMenu";const Qd="bk-tool-icon",Td="bk-disabled",md="bk-tool-chevron",gd="bk-above",_d="bk-below",bd="bk-left",vd="bk-right",yd="bk-active",xd=":host{--button-width:30px;--button-height:30px;--button-color:lightgray;--button-border:2px;--active-tool-highlight:#26aae1;--active-tool-border:var(--button-border) solid transparent;}:host{position:relative;width:var(--button-width);height:var(--button-height);cursor:pointer;user-select:none;-webkit-user-select:none;}.bk-tool-icon{position:relative;top:calc(var(--button-border)/2);width:calc(var(--button-width) - var(--button-border));height:calc(var(--button-height) - var(--button-border));mask-size:60% 60%;mask-position:center center;mask-repeat:no-repeat;-webkit-mask-size:60% 60%;-webkit-mask-position:center center;-webkit-mask-repeat:no-repeat;background-size:60% 60%;background-origin:border-box;background-position:center center;background-repeat:no-repeat;}:host(.bk-disabled) .bk-tool-icon{background-color:var(--bokeh-icon-color-disabled);cursor:not-allowed;}.bk-tool-chevron{position:absolute;visibility:hidden;width:8px;height:8px;mask-size:100% 100%;mask-position:center center;mask-repeat:no-repeat;-webkit-mask-size:100% 100%;-webkit-mask-position:center center;-webkit-mask-repeat:no-repeat;}:host(:hover) .bk-tool-chevron{visibility:visible;}:host(.bk-above) .bk-tool-chevron{right:0;bottom:0;background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-chevron-down);-webkit-mask-image:var(--bokeh-icon-chevron-down);}:host(.bk-below) .bk-tool-chevron{right:0;top:0;background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-chevron-up);-webkit-mask-image:var(--bokeh-icon-chevron-up);}:host(.bk-left) .bk-tool-chevron{right:0;bottom:0;background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-chevron-right);-webkit-mask-image:var(--bokeh-icon-chevron-right);}:host(.bk-right) .bk-tool-chevron{left:0;bottom:0;background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-chevron-left);-webkit-mask-image:var(--bokeh-icon-chevron-left);}:host(:hover){background-color:rgba(192, 192, 192, 0.15);}:host(:focus),:host(:focus-visible){outline:1px dotted var(--active-tool-highlight);outline-offset:-1px;}:host::-moz-focus-inner{border:0;}:host(.bk-above){border-bottom:var(--active-tool-border);}:host(.bk-above.bk-active){border-bottom-color:var(--active-tool-highlight);}:host(.bk-below){border-top:var(--active-tool-border);}:host(.bk-below.bk-active){border-top-color:var(--active-tool-highlight);}:host(.bk-right){border-left:var(--active-tool-border);}:host(.bk-right.bk-active){border-left-color:var(--active-tool-highlight);}:host(.bk-left){border-right:var(--active-tool-border);}:host(.bk-left.bk-active){border-right-color:var(--active-tool-highlight);}";var wd,Ld,Ad,Hd,kd;class Md extends Uu{initialize(){super.initialize();const{location:t}=this.parent.model,e="left"==t||"above"==t,n=this.parent.model.horizontal?"vertical":"horizontal",r=this.model.tool.menu??[];this._menu=new fd(e?(0,Rt.TY)(r):r,{target:this.root.el,orientation:n,prevent_hide:t=>t.composedPath().includes(this.el)});let i=null;this.el.addEventListener("pointerdown",(t=>{t.buttons==Oe.Left&&(i=t.timeStamp)})),this.el.addEventListener("pointerup",(t=>{if(null!=i){if(t.timeStamp-i>=250)this._pressed();else{if(this._menu.is_open)return void this._menu.hide();t.composedPath().includes(this.el)&&this._clicked()}i=null}})),this.el.addEventListener("keydown",(t=>{"Enter"==t.key&&this._clicked()}))}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.render())),this.connect(this.model.tool.change,(()=>this.render()))}remove(){this._menu.remove(),super.remove()}styles(){return[...super.styles(),xd,pd]}render(){super.render(),this.class_list.add(i[this.parent.model.location]),this.model.tool.disabled&&this.class_list.add(Td);const t=oe({class:Qd});this.shadow_el.appendChild(t);const e=this.model.icon??this.model.tool.computed_icon;if(null!=e)if(e.startsWith("data:image")){const n=`url("${encodeURI(e)}")`;t.style.backgroundImage=n}else if(e.startsWith("--"))t.style.backgroundImage=`var(${e})`;else if(e.startsWith(".")){const n=e.substring(1);t.classList.add(n)}else if(_n.si.valid(e)){const n=`bk-tool-icon-${e.replace(/_/g,"-")}`;t.classList.add(n)}if(null!=this.model.tool.menu){const t=oe({class:md});this.shadow_el.appendChild(t)}const n=this.model.tooltip??this.model.tool.tooltip;this.el.title=n,this.el.tabIndex=0}_pressed(){const t=(()=>{switch(this.parent.model.location){case"right":return{left_of:this.el};case"left":return{right_of:this.el};case"above":return{below:this.el};case"below":return{above:this.el}}})();this._menu.toggle(t)}}Md.__name__="ToolButtonView";class Cd extends Wu{constructor(t){super(t)}}wd=Cd,Cd.__name__="ToolButton",wd.define((({String:t,Regex:e,Ref:n,Nullable:r,Or:i})=>({tool:[i(n(Yu),n(Ju))],icon:[r(i(_n.si,e(/^--/),e(/^\./),e(/^data:image/))),null],tooltip:[r(t),null]})));class Sd extends Md{_toggle_active(){this.class_list.toggle(yd,this.model.tool.active)}connect_signals(){super.connect_signals();const{active:t}=this.model.tool.properties;this.on_change(t,(()=>{this._toggle_active()}))}render(){super.render(),this._toggle_active()}_clicked(){const{active:t}=this.model.tool;this.model.tool.active=!t}}Sd.__name__="OnOffButtonView";class Ed extends Cd{constructor(t){super(t)}}Ld=Ed,Ed.__name__="OnOffButton",Ld.prototype.default_view=Sd;class Vd extends Ku{get plot_view(){return this.parent}}Vd.__name__="GestureToolView";class Od extends Yu{constructor(t){super(t)}tool_button(){return new Ed({tool:this})}}Od.__name__="GestureTool";class Pd extends Ku{get plot_view(){return this.parent}}Pd.__name__="InspectToolView";class Dd extends Yu{constructor(t){super(t),this.event_type="move"}tool_button(){return new Ed({tool:this})}}Ad=Dd,Dd.__name__="InspectTool",Ad.define((({Boolean:t})=>({toggleable:[t,!0]}))),Ad.override({active:!0});class Nd extends Md{_clicked(){this.model.tool.do.emit(void 0)}}Nd.__name__="ClickButtonView";class Rd extends Cd{constructor(t){super(t)}}Hd=Rd,Rd.__name__="ClickButton",Hd.prototype.default_view=Nd;class Id extends Ku{connect_signals(){super.connect_signals(),this.connect(this.model.do,(t=>this.doit(t)))}}Id.__name__="ActionToolView";class jd extends Yu{constructor(t){super(t),this.do=new T.HN(this,"do")}tool_button(){return new Rd({tool:this})}}jd.__name__="ActionTool";class zd extends Id{doit(){window.open(this.model.redirect)}}zd.__name__="HelpToolView";class Bd extends jd{constructor(t){super(t),this.tool_name="Help",this.tool_icon="bk-tool-icon-help"}}kd=Bd,Bd.__name__="HelpTool",kd.prototype.default_view=zd,kd.define((({String:t})=>({redirect:[t,"https://docs.bokeh.org/en/latest/docs/user_guide/tools.html"]}))),kd.override({description:"Click the question mark to learn more about Bokeh plot tools."}),kd.register_alias("help",(()=>new Bd));const Fd="bk-inner",$d="bk-hidden",Gd="bk-logo",qd="bk-above",Ud="bk-below",Wd="bk-left",Zd="bk-right",Xd="bk-divider",Kd="bk-tool-overflow",Yd="bk-horizontal",Jd="bk-vertical",th=':host{--button-width:30px;--button-height:30px;--button-color:lightgray;}:host{display:flex;flex-wrap:nowrap;align-items:center;user-select:none;-webkit-user-select:none;}:host(.bk-inner){background-color:white;opacity:0.8;}:host(.bk-hidden){visibility:hidden;opacity:0;transition:visibility 0.3s linear, opacity 0.3s linear;}.bk-logo{flex-shrink:0;}:host(.bk-above),:host(.bk-below){flex-direction:row;justify-content:flex-end;}:host(.bk-above) .bk-logo,:host(.bk-below) .bk-logo{order:1;margin-left:5px;margin-right:0px;}:host(.bk-left),:host(.bk-right){flex-direction:column;justify-content:flex-start;}:host(.bk-left) .bk-logo,:host(.bk-right) .bk-logo{order:0;margin-bottom:5px;margin-top:0px;}.bk-divider{content:" ";display:inline-block;background-color:var(--button-color);}:host(.bk-above) .bk-divider,:host(.bk-below) .bk-divider{height:10px;width:1px;}:host(.bk-left) .bk-divider,:host(.bk-right) .bk-divider{height:1px;width:10px;}.bk-tool-overflow{color:gray;display:flex;align-items:center;}.bk-tool-overflow:hover{background-color:rgba(192, 192, 192, 0.15);}.bk-tool-overflow:focus,.bk-tool-overflow:focus-visible{outline:1px dotted var(--active-tool-highlight);outline-offset:-1px;}.bk-tool-overflow::-moz-focus-inner{border:0;}:host(.bk-above) .bk-tool-overflow,:host(.bk-below) .bk-tool-overflow,:host(.bk-horizontal) .bk-tool-overflow{width:calc(var(--button-width)/2);height:var(--button-height);flex-direction:row;}:host(.bk-left) .bk-tool-overflow,:host(.bk-right) .bk-tool-overflow,:host(.bk-vertical) .bk-tool-overflow{width:var(--button-width);height:calc(var(--button-height)/2);flex-direction:column;}';var eh;class nh extends Uu{constructor(){super(...arguments),this._tool_button_views=new Map,this._visible=null}get overflow_el(){return this._overflow_el}get visible(){return!!this.model.visible&&(!this.model.autohide||(this._visible??!1))}*children(){yield*super.children(),yield*this._tool_button_views.values()}has_finished(){if(!super.has_finished())return!1;for(const t of this._tool_button_views.values())if(!t.has_finished())return!1;return!0}initialize(){super.initialize();const{location:t}=this.model,e="left"==t||"above"==t,n=this.model.horizontal?"vertical":"horizontal";this._overflow_menu=new fd([],{target:this.root.el,orientation:n,reversed:e,prevent_hide:t=>t.composedPath().includes(this._overflow_el)})}async lazy_initialize(){await super.lazy_initialize(),await this._build_tool_button_views()}connect_signals(){super.connect_signals();const{buttons:t,tools:e}=this.model.properties;this.on_change([t,e],(async()=>{await this._build_tool_button_views(),this.render()})),this.connect(this.model.properties.autohide.change,(()=>{this._on_visible_change()}))}styles(){return[...super.styles(),th,".bk-logo{margin:5px;position:relative;display:block;background-repeat:no-repeat;}.bk-logo.bk-grey{filter:url(\"data:image/svg+xml;utf8,<svg xmlns='http://www.w3.org/2000/svg'><filter id='grayscale'><feColorMatrix type='matrix' values='0.3333 0.3333 0.3333 0 0 0.3333 0.3333 0.3333 0 0 0.3333 0.3333 0.3333 0 0 0 0 0 1 0'/></filter></svg>#grayscale\");-webkit-filter:grayscale(100%);}.bk-logo-small{width:20px;height:20px;background-image:url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABQAAAAUCAYAAACNiR0NAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAALEgAACxIB0t1+/AAAABx0RVh0U29mdHdhcmUAQWRvYmUgRmlyZXdvcmtzIENTNui8sowAAAOkSURBVDiNjZRtaJVlGMd/1/08zzln5zjP1LWcU9N0NkN8m2CYjpgQYQXqSs0I84OLIC0hkEKoPtiH3gmKoiJDU7QpLgoLjLIQCpEsNJ1vqUOdO7ppbuec5+V+rj4ctwzd8IIbbi6u+8f1539dt3A78eXC7QizUF7gyV1fD1Yqg4JWz84yffhm0qkFqBogB9rM8tZdtwVsPUhWhGcFJngGeWrPzHm5oaMmkfEg1usvLFyc8jLRqDOMru7AyC8saQr7GG7f5fvDeH7Ej8CM66nIF+8yngt6HWaKh7k49Soy9nXurCi1o3qUbS3zWfrYeQDTB/Qj6kX6Ybhw4B+bOYoLKCC9H3Nu/leUTZ1JdRWkkn2ldcCamzrcf47KKXdAJllSlxAOkRgyHsGC/zRday5Qld9DyoM4/q/rUoy/CXh3jzOu3bHUVZeU+DEn8FInkPBFlu3+nW3Nw0mk6vCDiWg8CeJaxEwuHS3+z5RgY+YBR6V1Z1nxSOfoaPa4LASWxxdNp+VWTk7+4vzaou8v8PN+xo+KY2xsw6une2frhw05CTYOmQvsEhjhWjn0bmXPjpE1+kplmmkP3suftwTubK9Vq22qKmrBhpY4jvd5afdRA3wGjFAgcnTK2s4hY0/GPNIb0nErGMCRxWOOX64Z8RAC4oCXdklmEvcL8o0BfkNK4lUg9HTl+oPlQxdNo3Mg4Nv175e/1LDGzZen30MEjRUtmXSfiTVu1kK8W4txyV6BMKlbgk3lMwYCiusNy9fVfvvwMxv8Ynl6vxoByANLTWplvuj/nF9m2+PDtt1eiHPBr1oIfhCChQMBw6Aw0UulqTKZdfVvfG7VcfIqLG9bcldL/+pdWTLxLUy8Qq38heUIjh4XlzZxzQm19lLFlr8vdQ97rjZVOLf8nclzckbcD4wxXMidpX30sFd37Fv/GtwwhzhxGVAprjbg0gCAEeIgwCZyTV2Z1REEW8O4py0wsjeloKoMr6iCY6dP92H6Vw/oTyICIthibxjm/DfN9lVz8IqtqKYLUXfoKVMVQVVJOElGjrnnUt9T9wbgp8AyYKaGlqingHZU/uG2NTZSVqwHQTWkx9hxjkpWDaCg6Ckj5qebgBVbT3V3NNXMSiWSDdGV3hrtzla7J+duwPOToIg42ChPQOQjspnSlp1V+Gjdged7+8UN5CRAV7a5EdFNwCjEaBR27b3W890TE7g24NAP/mMDXRWrGoFPQI9ls/MWO2dWFAar/xcOIImbbpA3zgAAAABJRU5ErkJggg==);}",pd]}remove(){qe(this._tool_button_views),super.remove()}async _build_tool_button_views(){this._tool_buttons=(()=>{const{buttons:t}=this.model;return"auto"==t?[...(0,Q.zu)(this.model.gestures).map((t=>t.tools)),this.model.actions,this.model.inspectors.filter((t=>t.toggleable))].map((t=>t.map((t=>t.tool_button())))):(0,Rt.lD)(t,null)})(),await Ge(this._tool_button_views,this._tool_buttons.flat(),{parent:this})}set_visibility(t){t!=this._visible&&(this._visible=t,this._on_visible_change())}_on_visible_change(){this.el.classList.toggle($d,!this.visible)}_after_resize(){super._after_resize(),this.render()}render(){super.render(),this.el.classList.add(o[this.model.location]),this.el.classList.toggle(Fd,this.model.inner),this._on_visible_change();const{horizontal:t}=this.model;this._overflow_el=oe({class:Kd,tabIndex:0},t?"⋮":"⋯");const e=()=>{const t=(()=>{switch(this.model.location){case"right":return{left_of:this._overflow_el};case"left":return{right_of:this._overflow_el};case"above":return{below:this._overflow_el};case"below":return{above:this._overflow_el}}})();this._overflow_menu.toggle(t)};this._overflow_el.addEventListener("click",(()=>{e()})),this._overflow_el.addEventListener("keydown",(t=>{"Enter"==t.key&&e()}));let n=0;if(null!=this.model.logo){const e="grey"===this.model.logo?"bk-grey":null,r=ue({href:"https://bokeh.org/",target:"_blank",class:["bk-logo","bk-logo-small",e]});this.shadow_el.appendChild(r);const{width:i,height:o}=r.getBoundingClientRect();n+=t?i:o}for(const[,t]of this._tool_button_views)t.render(),t.after_render();const r=this._tool_buttons.map((t=>t.map((t=>this._tool_button_views.get(t).el)))).filter((t=>0!=t.length)),i=()=>oe({class:Xd}),{bbox:a}=this,s=t?Zd:qd;let l=!1;for(const e of(0,On.fj)(r,i))if(l)this._overflow_menu.items.push({content:e,class:s});else{this.shadow_el.appendChild(e);const{width:r,height:i}=e.getBoundingClientRect();n+=t?r:i,l=t?n>a.width-15:n>a.height-15,l&&(this.shadow_el.removeChild(e),this.shadow_el.appendChild(this._overflow_el),(0,Rt.IU)(this._overflow_menu.items),this._overflow_menu.items.push({content:e,class:s}))}}}nh.__name__="ToolbarView";const rh=Yu,ih=Yu,oh=Yu,ah=Yu;function sh(){return{pan:{tools:[],active:null},scroll:{tools:[],active:null},pinch:{tools:[],active:null},tap:{tools:[],active:null},doubletap:{tools:[],active:null},press:{tools:[],active:null},pressup:{tools:[],active:null},rotate:{tools:[],active:null},move:{tools:[],active:null},multi:{tools:[],active:null}}}class lh extends Wu{constructor(t){super(t)}get horizontal(){return"above"==this.location||"below"==this.location}get vertical(){return"left"==this.location||"right"==this.location}connect_signals(){super.connect_signals();const{tools:t,active_drag:e,active_inspect:n,active_scroll:r,active_tap:i,active_multi:o}=this.properties;this.on_change([t,e,n,r,i,o],(()=>{this._init_tools(),this._activate_tools()}))}initialize(){super.initialize(),this._init_tools(),this._activate_tools()}_init_tools(){function t(t,e){return(t instanceof Ju?t.underlying:t)instanceof e}const e=this.tools.filter((e=>t(e,Dd)));this.inspectors=e;const n=this.tools.filter((e=>t(e,Bd)));this.help=n;const r=this.tools.filter((e=>t(e,jd)));this.actions=r;const i={pan:{tools:[],active:null},scroll:{tools:[],active:null},pinch:{tools:[],active:null},tap:{tools:[],active:null},doubletap:{tools:[],active:null},press:{tools:[],active:null},pressup:{tools:[],active:null},rotate:{tools:[],active:null},move:{tools:[],active:null},multi:{tools:[],active:null}};for(const e of this.tools)t(e,Od)&&i[e.event_role].tools.push(e);for(const t of(0,Q.OA)(i)){const e=this.gestures[t];e.tools=(0,Rt.D6)(i[t].tools,(t=>t.default_order)),e.active&&(0,Rt.Si)(e.tools,(t=>t.id!=e.active?.id))&&(e.active=null)}}_activate_tools(){if("auto"==this.active_inspect);else if(null==this.active_inspect)for(const t of this.inspectors)t.active=!1;else if((0,f.cy)(this.active_inspect)){const t=(0,Rt.E$)(this.active_inspect,this.inspectors);t.length!=this.active_inspect.length&&(this.active_inspect=t);for(const t of this.inspectors)(0,Rt.mK)(this.active_inspect,t)||(t.active=!1)}else{let t=!1;for(const e of this.inspectors)e!=this.active_inspect?e.active=!1:t=!0;t||(this.active_inspect=null)}const t=t=>{t.active?this._active_change(t):t.active=!0};for(const t of(0,Q.zu)(this.gestures))for(const e of t.tools)this.connect(e.properties.active.change,(()=>this._active_change(e)));function e(t){switch(t){case"tap":return"active_tap";case"pan":return"active_drag";case"pinch":case"scroll":return"active_scroll";case"multi":return"active_multi"}return null}function n(t){return"tap"==t||"pan"==t}for(const[r,i]of(0,Q.jO)(this.gestures)){const o=r,a=e(o);if(a){const e=this[a];if("auto"==e)0!=i.tools.length&&n(o)&&t(i.tools[0]);else if(null!=e)(0,Rt.mK)(this.tools,e)?t(e):this[a]=null;else{this.gestures[o].active=null;for(const t of this.gestures[o].tools)t.active=!1}}}}_active_change(t){const{event_types:e}=t;for(const n of e)if(t.active){const e=this.gestures[n].active;null!=e&&t!=e&&(ot.vF.debug(`Toolbar: deactivating tool: ${e} for event type '${n}'`),e.active=!1),this.gestures[n].active=t,ot.vF.debug(`Toolbar: activating tool: ${t} for event type '${n}'`)}else this.gestures[n].active=null}}var ch,uh,dh,hh,ph,fh,Qh,Th;eh=lh,lh.__name__="Toolbar",eh.prototype.default_view=nh,eh.define((({Boolean:t,Array:e,Or:n,Ref:r,Nullable:i,Auto:o})=>({tools:[e(n(r(Yu),r(Ju))),[]],logo:[i(_n.gu),"normal"],autohide:[t,!1],active_drag:[i(n(r(rh),o)),"auto"],active_inspect:[i(n(r(ih),e(r(ih)),o)),"auto"],active_scroll:[i(n(r(oh),o)),"auto"],active_tap:[i(n(r(ah),o)),"auto"],active_multi:[i(n(r(Od),o)),"auto"]}))),eh.internal((({Array:t,Boolean:e,Ref:n,Or:r,Struct:i,Nullable:o,Null:a,Auto:s})=>{const l=i({tools:t(n(Od)),active:o(n(Od))}),c=i({pan:l,scroll:l,pinch:l,tap:l,doubletap:l,press:l,pressup:l,rotate:l,move:l,multi:l});return{buttons:[r(t(r(n(Cd),a)),s),"auto"],location:[_n.aZ,"right"],inner:[e,!1],gestures:[c,sh],actions:[t(r(n(jd),n(Ju))),[]],inspectors:[t(r(n(Dd),n(Ju))),[]],help:[t(r(n(Bd),n(Ju))),[]]}}));class mh extends nr{constructor(){super(...arguments),this._invalidate_toolbar=!0,this._previous_bbox=new re}update_layout(){this.layout=new uo(this.panel,(()=>this.get_size()),!0)}has_finished(){return super.has_finished()&&this.toolbar_view.has_finished()}*children(){yield*super.children(),yield this.toolbar_view}initialize(){super.initialize(),this.el=oe(),this.plot_view.canvas_view.add_event(this.el)}async lazy_initialize(){await super.lazy_initialize(),this.toolbar_view=await $e(this.model.toolbar,{parent:this.canvas})}connect_signals(){super.connect_signals(),this.plot_view.mouseenter.connect((()=>{this.toolbar_view.set_visibility(!0)})),this.plot_view.mouseleave.connect((()=>{this.toolbar_view.set_visibility(!1)}))}remove(){this.toolbar_view.remove(),Le(this.el),super.remove()}render(){this.model.visible||ke(this.el),super.render()}_render(){const{style:t}=this.toolbar_view.el;this.toolbar_view.model.horizontal?(t.width="100%",t.height="unset"):(t.width="unset",t.height="100%");const{bbox:e}=this.layout;this._previous_bbox.equals(e)||(function(t,e){const{style:n}=t;n.left=`${e.x}px`,n.top=`${e.y}px`,n.width=`${e.width}px`,n.height=`${e.height}px`,n.margin=""}(this.el,e),this._previous_bbox=e,this._invalidate_toolbar=!0),this._invalidate_toolbar&&(this.el.style.position="absolute",Ae(this.el),this.el.appendChild(this.toolbar_view.el),this.toolbar_view.render(),this.toolbar_view.after_render(),this._invalidate_toolbar=!1),He(this.el)}_get_size(){const{tools:t,logo:e}=this.model.toolbar;return{width:30*t.length+(null!=e?25:0)+15,height:30}}}mh.__name__="ToolbarPanelView";class gh extends rr{constructor(t){super(t)}}ch=gh,gh.__name__="ToolbarPanel",ch.prototype.default_view=mh,ch.define((({Ref:t})=>({toolbar:[t(lh)]})));class _h extends Gc{*children(){yield*super.children();const{lower_head:t,upper_head:e}=this;null!=t&&(yield t),null!=e&&(yield e)}async lazy_initialize(){await super.lazy_initialize();const{lower_head:t,upper_head:e}=this.model;null!=t&&(this.lower_head=await $e(t,{parent:this})),null!=e&&(this.upper_head=await $e(e,{parent:this}))}set_data(t){super.set_data(t);const e=Jt.et.all_set(this._lower.length);this.lower_head?.set_data(t,e),this.upper_head?.set_data(t,e)}paint(t){if(this.visuals.line.doit)for(let e=0,n=this._lower_sx.length;e<n;e++)t.beginPath(),t.moveTo(this._lower_sx[e],this._lower_sy[e]),t.lineTo(this._upper_sx[e],this._upper_sy[e]),this.visuals.line.apply(t,e);const e="height"==this.model.dimension?0:Math.PI/2;if(null!=this.lower_head)for(let n=0,r=this._lower_sx.length;n<r;n++)t.save(),t.translate(this._lower_sx[n],this._lower_sy[n]),t.rotate(e+Math.PI),this.lower_head.render(t,n),t.restore();if(null!=this.upper_head)for(let n=0,r=this._upper_sx.length;n<r;n++)t.save(),t.translate(this._upper_sx[n],this._upper_sy[n]),t.rotate(e),this.upper_head.render(t,n),t.restore()}}_h.__name__="WhiskerView";class bh extends Uc{constructor(t){super(t)}}uh=bh,bh.__name__="Whisker",uh.prototype.default_view=_h,uh.mixins(Ke.UT),uh.define((({Ref:t,Nullable:e})=>({lower_head:[e(t(Pi)),()=>new Fi({size:10})],upper_head:[e(t(Pi)),()=>new Fi({size:10})]}))),uh.override({level:"underlay"});class vh extends nr{update_layout(){const{panel:t}=this;this.layout=null!=t?new uo(t,(()=>this.get_size()),!0):void 0}initialize(){super.initialize(),this.el=oe(),this.plot_view.canvas_view.add_overlay(this.el)}remove(){Le(this.el),super.remove()}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.render()))}render(){this.model.visible||ke(this.el),super.render()}_paint(t,e,n,r,i){const{el:o}=this;ke(o),o.textContent=e,this.visuals.text.set_value(t),o.style.position="absolute",o.style.left=`${n}px`,o.style.top=`${r}px`,o.style.color=t.fillStyle,o.style.webkitTextStroke=`1px ${t.strokeStyle}`,o.style.font=t.font,o.style.lineHeight="normal",o.style.whiteSpace="pre";const[a,s]=(()=>{switch(this.visuals.text.text_align.get_value()){case"left":return["left","0%"];case"center":return["center","-50%"];case"right":return["right","-100%"]}})(),[l,c]=(()=>{switch(this.visuals.text.text_baseline.get_value()){case"top":return["top","0%"];case"middle":default:return["center","-50%"];case"bottom":return["bottom","-100%"]}})();let u=`translate(${s}, ${c})`;i&&(u+=`rotate(${i}rad)`),o.style.transformOrigin=`${a} ${l}`,o.style.transform=u,this.layout,this.visuals.background_fill.doit&&(this.visuals.background_fill.set_value(t),o.style.backgroundColor=t.fillStyle),this.visuals.border_line.doit&&(this.visuals.border_line.set_value(t),o.style.borderStyle=t.lineDash.length<2?"solid":"dashed",o.style.borderWidth=`${t.lineWidth}px`,o.style.borderColor=t.strokeStyle),He(o)}}vh.__name__="TextAnnotationView";class yh extends rr{constructor(t){super(t)}}yh.__name__="TextAnnotation";class xh extends vh{update_layout(){const{panel:t}=this;this.layout=null!=t?new uo(t,(()=>this.get_size()),!1):void 0}_get_size(){const{text:t}=this.model,e=new ko({text:t}),{angle:n,angle_units:r}=this.model;e.angle=(0,Gi.rk)(n,r),e.visuals=this.visuals.text.values();const{width:i,height:o}=e.size();return{width:i,height:o}}_render(){const{angle:t,angle_units:e}=this.model,n=(0,Gi.rk)(t,e),r=null!=this.layout?this.layout:this.plot_view.frame,i=this.coordinates.x_scale,o=this.coordinates.y_scale;let a=(()=>{switch(this.model.x_units){case"canvas":return this.model.x;case"screen":return r.bbox.xview.compute(this.model.x);case"data":return i.compute(this.model.x)}})(),s=(()=>{switch(this.model.y_units){case"canvas":return this.model.y;case"screen":return r.bbox.yview.compute(this.model.y);case"data":return o.compute(this.model.y)}})();a+=this.model.x_offset,s-=this.model.y_offset,this._paint(this.layer.ctx,this.model.text,a,s,n)}}xh.__name__="HTMLLabelView";class wh extends yh{constructor(t){super(t)}}dh=wh,wh.__name__="HTMLLabel",dh.prototype.default_view=xh,dh.mixins([Ke.EY,["border_",Ke.N1],["background_",Ke.SQ]]),dh.define((({Number:t,String:e,Angle:n})=>({x:[t],x_units:[_n.yx,"data"],y:[t],y_units:[_n.yx,"data"],text:[e,""],angle:[n,0],angle_units:[_n.xb,"rad"],x_offset:[t,0],y_offset:[t,0]}))),dh.override({background_fill_color:null,border_line_color:null});class Lh extends Ci{constructor(){super(...arguments),this.els=[]}set_data(t){super.set_data(t),this.els.forEach((t=>Le(t))),this.els=[];for(const t of this.text){const t=oe({style:{display:"none"}});this.plot_view.canvas_view.add_overlay(t),this.els.push(t)}}remove(){this.els.forEach((t=>Le(t))),this.els=[],super.remove()}_rerender(){this.render()}map_data(){const{x_scale:t,y_scale:e}=this.coordinates,n=null!=this.layout?this.layout:this.plot_view.frame;this.sx=(()=>{switch(this.model.x_units){case"canvas":return new Jt.mR(this._x);case"screen":return n.bbox.xview.v_compute(this._x);case"data":return t.v_compute(this._x)}})(),this.sy=(()=>{switch(this.model.y_units){case"canvas":return new Jt.mR(this._y);case"screen":return n.bbox.yview.v_compute(this._y);case"data":return e.v_compute(this._y)}})()}paint(){const{ctx:t}=this.layer;for(let e=0,n=this.text.length;e<n;e++){const n=this.x_offset.get(e),r=this.y_offset.get(e),i=this.sx[e]+n,o=this.sy[e]-r,a=this.angle.get(e),s=this.text.get(e);isFinite(i+o+a)&&null!=s&&this._paint(t,e,s,i,o,a)}}_paint(t,e,n,r,i,o){(0,_.vA)(e in this.els);const a=this.els[e];a.textContent=n,this.visuals.text.set_vectorize(t,e),a.style.position="absolute",a.style.left=`${r}px`,a.style.top=`${i}px`,a.style.color=t.fillStyle,a.style.webkitTextStroke=`1px ${t.strokeStyle}`,a.style.font=t.font,a.style.lineHeight="normal",a.style.whiteSpace="pre";const[s,l]=(()=>{switch(this.visuals.text.text_align.get(e)){case"left":return["left","0%"];case"center":return["center","-50%"];case"right":return["right","-100%"]}})(),[c,u]=(()=>{switch(this.visuals.text.text_baseline.get(e)){case"top":return["top","0%"];case"middle":default:return["center","-50%"];case"bottom":return["bottom","-100%"]}})();let d=`translate(${l}, ${u})`;o&&(d+=`rotate(${o}rad)`),a.style.transformOrigin=`${s} ${c}`,a.style.transform=d,this.layout,this.visuals.background_fill.doit&&(this.visuals.background_fill.set_vectorize(t,e),a.style.backgroundColor=t.fillStyle),this.visuals.border_line.doit&&(this.visuals.border_line.set_vectorize(t,e),a.style.borderStyle=t.lineDash.length<2?"solid":"dashed",a.style.borderWidth=`${t.lineWidth}px`,a.style.borderColor=t.strokeStyle),He(a)}}Lh.__name__="HTMLLabelSetView";class Ah extends Si{constructor(t){super(t)}}hh=Ah,Ah.__name__="HTMLLabelSet",hh.prototype.default_view=Lh,hh.mixins([Ke.Dt,["border_",Ke.UT],["background_",Ke.H_]]),hh.define((()=>({x:[m.up,{field:"x"}],y:[m.fZ,{field:"y"}],x_units:[_n.yx,"data"],y_units:[_n.yx,"data"],text:[m.C1,{field:"text"}],angle:[m.XS,0],x_offset:[m.fY,{value:0}],y_offset:[m.fY,{value:0}]}))),hh.override({background_fill_color:null,border_line_color:null});class Hh extends vh{_get_location(){const t=this.model.offset,e=this.model.standoff/2;let n,r;const{bbox:i}=this.layout;switch(this.panel.side){case"above":case"below":switch(this.model.vertical_align){case"top":r=i.top+e;break;case"middle":r=i.vcenter;break;case"bottom":r=i.bottom-e}switch(this.model.align){case"left":n=i.left+t;break;case"center":n=i.hcenter;break;case"right":n=i.right-t}break;case"left":switch(this.model.vertical_align){case"top":n=i.left+e;break;case"middle":n=i.hcenter;break;case"bottom":n=i.right-e}switch(this.model.align){case"left":r=i.bottom-t;break;case"center":r=i.vcenter;break;case"right":r=i.top+t}break;case"right":switch(this.model.vertical_align){case"top":n=i.right-e;break;case"middle":n=i.hcenter;break;case"bottom":n=i.left+e}switch(this.model.align){case"left":r=i.top+t;break;case"center":r=i.vcenter;break;case"right":r=i.bottom-t}}return[n,r]}_render(){const{text:t}=this.model;if(0==t.length)return;this.model.text_baseline=this.model.vertical_align,this.model.text_align=this.model.align;const[e,n]=this._get_location(),r=this.panel.get_label_angle_heuristic("parallel");this._paint(this.layer.ctx,t,e,n,r)}_get_size(){const{text:t}=this.model,e=new ko({text:t});e.visuals=this.visuals.text.values();const{width:n,height:r}=e.size();return{width:n,height:0==r?0:2+r+this.model.standoff}}}Hh.__name__="HTMLTitleView";class kh extends yh{constructor(t){super(t)}}ph=kh,kh.__name__="HTMLTitle",ph.prototype.default_view=Hh,ph.mixins([Ke.EY,["border_",Ke.N1],["background_",Ke.SQ]]),ph.define((({Number:t,String:e})=>({text:[e,""],vertical_align:[_n.G4,"bottom"],align:[_n.nO,"left"],offset:[t,0],standoff:[t,10]}))),ph.prototype._props.text_align.options.internal=!0,ph.prototype._props.text_baseline.options.internal=!0,ph.override({text_font_size:"13px",text_font_style:"bold",text_line_height:1,background_fill_color:null,border_line_color:null});class Mh extends qt{constructor(t){super(t)}}Mh.__name__="Callback";class Ch extends Mh{constructor(t){super(t)}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}get func(){const t=x(this.code);return new Function(...this.names,"cb_obj","cb_data",t)}execute(t,e={}){return this.func.apply(t,this.values.concat(t,e))}}fh=Ch,Ch.__name__="CustomJS",fh.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));class Sh extends Mh{constructor(t){super(t)}navigate(t){this.same_tab?window.location.href=t:window.open(t)}execute(t,{source:e}){const n=t=>{const n=Pa(this.url,e,t,void 0,void 0,encodeURI);if(!(0,f.Kg)(n))throw new Error("HTML output is not supported in this context");this.navigate(n)},{selected:r}=e;for(const t of r.indices)n(t);for(const t of r.line_indices)n(t)}}Qh=Sh,Sh.__name__="OpenURL",Qh.define((({Boolean:t,String:e})=>({url:[e,"http://"],same_tab:[t,!1]})));class Eh extends Mh{constructor(t){super(t)}execute(){const{obj:t,attr:e,value:n}=this;e in t.properties?t.setv({[e]:n}):ot.vF.error(`${t.type}.${e} is not a property`)}}Th=Eh,Eh.__name__="SetValue",Th.define((({String:t,Unknown:e,Ref:n})=>({obj:[n(tt)],attr:[t],value:[e]})));var Vh,Oh=n(7168),Ph=n.n(Oh);function Dh(t){const e=getComputedStyle(t).fontSize,n=parseInt(e,10);return isNaN(n)?null:n}function Nh(t){let e=-t.deltaY;if(t.target instanceof HTMLElement)switch(t.deltaMode){case t.DOM_DELTA_LINE:e*=Dh((n=t.target).offsetParent??document.body)??Dh(n)??16;break;case t.DOM_DELTA_PAGE:e*=function(t){return t.clientHeight}(t.target)}var n;return e}class Rh{constructor(t){this.canvas_view=t,this.pan_start=new T.HN(this,"pan:start"),this.pan=new T.HN(this,"pan"),this.pan_end=new T.HN(this,"pan:end"),this.pinch_start=new T.HN(this,"pinch:start"),this.pinch=new T.HN(this,"pinch"),this.pinch_end=new T.HN(this,"pinch:end"),this.rotate_start=new T.HN(this,"rotate:start"),this.rotate=new T.HN(this,"rotate"),this.rotate_end=new T.HN(this,"rotate:end"),this.tap=new T.HN(this,"tap"),this.doubletap=new T.HN(this,"doubletap"),this.press=new T.HN(this,"press"),this.pressup=new T.HN(this,"pressup"),this.move_enter=new T.HN(this,"move:enter"),this.move=new T.HN(this,"move"),this.move_exit=new T.HN(this,"move:exit"),this.scroll=new T.HN(this,"scroll"),this.keydown=new T.HN(this,"keydown"),this.keyup=new T.HN(this,"keyup"),this.hammer=new(Ph())(this.hit_area,{cssProps:{},touchAction:"auto",inputClass:It.SU?Ph().TouchMouseInput:Ph().PointerEventInput}),this._prev_move=null,this._curr_pan=null,this._curr_pinch=null,this._curr_rotate=null,this._configure_hammerjs(),this.hit_area.addEventListener("mousemove",(t=>this._mouse_move(t))),this.hit_area.addEventListener("mouseenter",(t=>this._mouse_enter(t))),this.hit_area.addEventListener("mouseleave",(t=>this._mouse_exit(t))),this.hit_area.addEventListener("contextmenu",(t=>this._context_menu(t))),this.hit_area.addEventListener("wheel",(t=>this._mouse_wheel(t))),document.addEventListener("keydown",this),document.addEventListener("keyup",this)}get hit_area(){return this.canvas_view.events_el}destroy(){this.hammer.destroy(),document.removeEventListener("keydown",this),document.removeEventListener("keyup",this)}handleEvent(t){"keydown"==t.type?this._key_down(t):"keyup"==t.type&&this._key_up(t)}_configure_hammerjs(){this.hammer.get("doubletap").recognizeWith("tap"),this.hammer.get("tap").requireFailure("doubletap"),this.hammer.get("doubletap").dropRequireFailure("tap"),this.hammer.on("doubletap",(t=>this._doubletap(t))),this.hammer.on("tap",(t=>this._tap(t))),this.hammer.on("press",(t=>this._press(t))),this.hammer.on("pressup",(t=>this._pressup(t))),this.hammer.get("pan").set({direction:Ph().DIRECTION_ALL}),this.hammer.on("panstart",(t=>this._pan_start(t))),this.hammer.on("pan",(t=>this._pan(t))),this.hammer.on("panend",(t=>this._pan_end(t))),this.hammer.get("pinch").set({enable:!0}),this.hammer.on("pinchstart",(t=>this._pinch_start(t))),this.hammer.on("pinch",(t=>this._pinch(t))),this.hammer.on("pinchend",(t=>this._pinch_end(t))),this.hammer.get("rotate").set({enable:!0}),this.hammer.on("rotatestart",(t=>this._rotate_start(t))),this.hammer.on("rotate",(t=>this._rotate(t))),this.hammer.on("rotateend",(t=>this._rotate_end(t)))}register_tool(t){let e=!0;for(const n of t.model.event_types)this._register_tool(t,n,e),e=!1}_register_tool(t,e,n=!0){const r=t,{id:i}=r.model,o=t=>e=>{e.id==i&&t(e.e)},a=t=>e=>{t(e.e)};switch(e){case"pan":null!=r._pan_start&&r.connect(this.pan_start,o(r._pan_start.bind(r))),null!=r._pan&&r.connect(this.pan,o(r._pan.bind(r))),null!=r._pan_end&&r.connect(this.pan_end,o(r._pan_end.bind(r)));break;case"pinch":null!=r._pinch_start&&r.connect(this.pinch_start,o(r._pinch_start.bind(r))),null!=r._pinch&&r.connect(this.pinch,o(r._pinch.bind(r))),null!=r._pinch_end&&r.connect(this.pinch_end,o(r._pinch_end.bind(r)));break;case"rotate":null!=r._rotate_start&&r.connect(this.rotate_start,o(r._rotate_start.bind(r))),null!=r._rotate&&r.connect(this.rotate,o(r._rotate.bind(r))),null!=r._rotate_end&&r.connect(this.rotate_end,o(r._rotate_end.bind(r)));break;case"move":null!=r._move_enter&&r.connect(this.move_enter,o(r._move_enter.bind(r))),null!=r._move&&r.connect(this.move,o(r._move.bind(r))),null!=r._move_exit&&r.connect(this.move_exit,o(r._move_exit.bind(r)));break;case"tap":null!=r._tap&&r.connect(this.tap,o(r._tap.bind(r)));case"doubletap":null!=r._doubletap&&r.connect(this.doubletap,o(r._doubletap.bind(r)));break;case"press":null!=r._press&&r.connect(this.press,o(r._press.bind(r)));break;case"pressup":null!=r._pressup&&r.connect(this.pressup,o(r._pressup.bind(r)));break;case"scroll":null!=r._scroll&&r.connect(this.scroll,o(r._scroll.bind(r)))}n&&(null!=r._keydown&&r.connect(this.keydown,a(r._keydown.bind(r))),null!=r._keyup&&r.connect(this.keyup,a(r._keyup.bind(r))),It.SU&&null!=r._scroll&&"pinch"==e&&(ot.vF.debug("Registering scroll on touch screen"),r.connect(this.scroll,o(r._scroll.bind(r)))))}_hit_test_renderers(t,e,n){const r=t.get_renderer_views();for(const t of(0,Rt.TY)(r))if(t.interactive_hit?.(e,n))return t;return null}set_cursor(t="default"){this.hit_area.style.cursor=t}_hit_test_frame(t,e,n){return t.frame.bbox.contains(e,n)}_hit_test_plot(t,e){for(const n of this.canvas_view.plot_views)if(n.bbox.relative().contains(t,e))return n;return null}_trigger(t,e,n){if(!this.hit_area.isConnected)return;const{sx:r,sy:i}=e,o=this._hit_test_plot(r,i),a=t=>{const[n,o]=[r,i];return{...e,sx:n,sy:o}};if("panstart"==e.type||"pan"==e.type||"panend"==e.type){let r;if("panstart"==e.type&&null!=o?(this._curr_pan={plot_view:o},r=o):"pan"==e.type&&null!=this._curr_pan?r=this._curr_pan.plot_view:"panend"==e.type&&null!=this._curr_pan?(r=this._curr_pan.plot_view,this._curr_pan=null):r=null,null!=r){const e=a();this.__trigger(r,t,e,n)}}else if("pinchstart"==e.type||"pinch"==e.type||"pinchend"==e.type){let r;if("pinchstart"==e.type&&null!=o?(this._curr_pinch={plot_view:o},r=o):"pinch"==e.type&&null!=this._curr_pinch?r=this._curr_pinch.plot_view:"pinchend"==e.type&&null!=this._curr_pinch?(r=this._curr_pinch.plot_view,this._curr_pinch=null):r=null,null!=r){const e=a();this.__trigger(r,t,e,n)}}else if("rotatestart"==e.type||"rotate"==e.type||"rotateend"==e.type){let r;if("rotatestart"==e.type&&null!=o?(this._curr_rotate={plot_view:o},r=o):"rotate"==e.type&&null!=this._curr_rotate?r=this._curr_rotate.plot_view:"rotateend"==e.type&&null!=this._curr_rotate?(r=this._curr_rotate.plot_view,this._curr_rotate=null):r=null,null!=r){const e=a();this.__trigger(r,t,e,n)}}else if("mouseenter"==e.type||"mousemove"==e.type||"mouseleave"==e.type){const s=this._prev_move?.plot_view;if(null!=s&&("mouseleave"==e.type||s!=o)){const{sx:t,sy:e}=a();this.__trigger(s,this.move_exit,{type:"mouseleave",sx:t,sy:e,shift_key:!1,ctrl_key:!1},n)}if(null!=o&&("mouseenter"==e.type||s!=o)){const{sx:t,sy:e}=a();this.__trigger(o,this.move_enter,{type:"mouseenter",sx:t,sy:e,shift_key:!1,ctrl_key:!1},n)}if(null!=o&&"mousemove"==e.type){const e=a();this.__trigger(o,t,e,n)}this._prev_move={sx:r,sy:i,plot_view:o}}else if(null!=o){const e=a();this.__trigger(o,t,e,n)}}__trigger(t,e,n,r){const i=t.model.toolbar.gestures,o=e.name.split(":")[0],a=this._hit_test_renderers(t,n.sx,n.sy);switch(o){case"move":{const r=i.move.active;null!=r&&this.trigger(e,n,r.id);const o=t.model.toolbar.inspectors.filter((t=>t.active));let s="default";null!=a?(s=a.cursor(n.sx,n.sy)??s,(0,Rt.Jb)(o)||(e=this.move_exit)):this._hit_test_frame(t,n.sx,n.sy)&&((0,Rt.Jb)(o)||(s="crosshair")),this.set_cursor(s),o.map((t=>this.trigger(e,n,t.id)));break}case"tap":{const o=r.path??r.composedPath();if(0!=o.length&&o[0]!=this.hit_area)return;if(a?.on_hit?.(n.sx,n.sy),this._hit_test_frame(t,n.sx,n.sy)){const t=i.tap.active;null!=t&&this.trigger(e,n,t.id)}break}case"doubletap":if(this._hit_test_frame(t,n.sx,n.sy)){const t=i.doubletap.active??i.tap.active;null!=t&&this.trigger(e,n,t.id)}break;case"scroll":{const t=i[It.SU?"pinch":"scroll"].active;null!=t&&(r.preventDefault(),r.stopPropagation(),this.trigger(e,n,t.id));break}case"pan":{const t=i.pan.active;null!=t&&(r.preventDefault(),this.trigger(e,n,t.id));break}default:{const t=i[o].active;null!=t&&this.trigger(e,n,t.id)}}this._trigger_bokeh_event(t,n)}trigger(t,e,n=null){t.emit({id:n,e})}_trigger_bokeh_event(t,e){const n=(()=>{const{sx:n,sy:r}=e,i=t.frame.x_scale.invert(n),o=t.frame.y_scale.invert(r);switch(e.type){case"wheel":return new xt(n,r,i,o,e.delta);case"mousemove":return new wt(n,r,i,o);case"mouseenter":return new Lt(n,r,i,o);case"mouseleave":return new At(n,r,i,o);case"tap":return new Ht(n,r,i,o);case"doubletap":return new kt(n,r,i,o);case"press":return new Mt(n,r,i,o);case"pressup":return new Ct(n,r,i,o);case"pan":return new bt(n,r,i,o,e.dx,e.dy);case"panstart":return new St(n,r,i,o);case"panend":return new Et(n,r,i,o);case"pinch":return new vt(n,r,i,o,e.scale);case"pinchstart":return new Vt(n,r,i,o);case"pinchend":return new Ot(n,r,i,o);case"rotate":return new yt(n,r,i,o,e.rotation);case"rotatestart":return new Pt(n,r,i,o);case"rotateend":return new Dt(n,r,i,o);default:return}})();null!=n&&t.model.trigger_event(n)}_get_sxy(t){const{pageX:e,pageY:n}=function(t){return"undefined"!=typeof TouchEvent&&t instanceof TouchEvent}(t)?(0!=t.touches.length?t.touches:t.changedTouches)[0]:t,{left:r,top:i}=function(t){const{top:e,left:n,width:r,height:i}=t.getBoundingClientRect();return new re({left:n+scrollX-document.documentElement.clientLeft,top:e+scrollY-document.documentElement.clientTop,width:r,height:i})}(this.hit_area);return{sx:e-r,sy:n-i}}_pan_event(t){return{type:t.type,...this._get_sxy(t.srcEvent),dx:t.deltaX,dy:t.deltaY,shift_key:t.srcEvent.shiftKey,ctrl_key:t.srcEvent.ctrlKey}}_pinch_event(t){return{type:t.type,...this._get_sxy(t.srcEvent),scale:t.scale,shift_key:t.srcEvent.shiftKey,ctrl_key:t.srcEvent.ctrlKey}}_rotate_event(t){return{type:t.type,...this._get_sxy(t.srcEvent),rotation:t.rotation,shift_key:t.srcEvent.shiftKey,ctrl_key:t.srcEvent.ctrlKey}}_tap_event(t){return{type:t.type,...this._get_sxy(t.srcEvent),shift_key:t.srcEvent.shiftKey,ctrl_key:t.srcEvent.ctrlKey}}_move_event(t){return{type:t.type,...this._get_sxy(t),shift_key:t.shiftKey,ctrl_key:t.ctrlKey}}_scroll_event(t){return{type:t.type,...this._get_sxy(t),delta:Nh(t),shift_key:t.shiftKey,ctrl_key:t.ctrlKey}}_key_event(t){return{type:t.type,key:t.key}}_pan_start(t){const e=this._pan_event(t);e.sx-=t.deltaX,e.sy-=t.deltaY,this._trigger(this.pan_start,e,t.srcEvent)}_pan(t){this._trigger(this.pan,this._pan_event(t),t.srcEvent)}_pan_end(t){this._trigger(this.pan_end,this._pan_event(t),t.srcEvent)}_pinch_start(t){this._trigger(this.pinch_start,this._pinch_event(t),t.srcEvent)}_pinch(t){this._trigger(this.pinch,this._pinch_event(t),t.srcEvent)}_pinch_end(t){this._trigger(this.pinch_end,this._pinch_event(t),t.srcEvent)}_rotate_start(t){this._trigger(this.rotate_start,this._rotate_event(t),t.srcEvent)}_rotate(t){this._trigger(this.rotate,this._rotate_event(t),t.srcEvent)}_rotate_end(t){this._trigger(this.rotate_end,this._rotate_event(t),t.srcEvent)}_tap(t){this._trigger(this.tap,this._tap_event(t),t.srcEvent)}_doubletap(t){this._trigger(this.doubletap,this._tap_event(t),t.srcEvent)}_press(t){this._trigger(this.press,this._tap_event(t),t.srcEvent)}_pressup(t){this._trigger(this.pressup,this._tap_event(t),t.srcEvent)}_mouse_enter(t){this._trigger(this.move_enter,this._move_event(t),t)}_mouse_move(t){this._trigger(this.move,this._move_event(t),t)}_mouse_exit(t){this._trigger(this.move_exit,this._move_event(t),t)}_mouse_wheel(t){this._trigger(this.scroll,this._scroll_event(t),t)}_context_menu(t){}_key_down(t){this.trigger(this.keydown,this._key_event(t))}_key_up(t){this.trigger(this.keyup,this._key_event(t))}}Rh.__name__="UIEventBus";const Ih=(()=>{let t;return async()=>void 0!==t?t:t=await async function(){const t=document.createElement("canvas"),e=t.getContext("webgl",{premultipliedAlpha:!0});if(null!=e){const r=await So(Promise.resolve().then(n.bind(n,4237)));if(null!=r){const n=r.get_regl(e);if(n.has_webgl)return{canvas:t,regl_wrapper:n};ot.vF.trace("WebGL is supported, but not the required extensions")}else ot.vF.trace("WebGL is supported, but bokehjs(.min).js bundle is not available")}else ot.vF.trace("WebGL is not supported");return null}()})();class jh extends Uu{constructor(){super(...arguments),this.webgl=null,this._size=new Pe,this.plot_views=[]}initialize(){super.initialize(),this.underlays_el=oe({class:"bk-layer"}),this.primary=this.create_layer(),this.overlays=this.create_layer(),this.overlays_el=oe({class:"bk-layer"}),this.events_el=oe({class:["bk-layer","bk-events"]}),this.ui_event_bus=new Rh(this)}async lazy_initialize(){if(await super.lazy_initialize(),"webgl"==this.model.output_backend&&(this.webgl=await Ih(),b.W.force_webgl&&null==this.webgl))throw new Error("webgl is not available")}remove(){this.ui_event_bus.destroy(),super.remove()}styles(){return[...super.styles(),".bk-layer{position:absolute;top:0;left:0;width:100%;height:100%;}.bk-layer.bk-events{user-select:none;-webkit-user-select:none;touch-action:auto;-webkit-user-drag:none;-webkit-tap-highlight-color:rgba(0, 0, 0, 0);}",this._size]}render(){super.render();const t=[this.underlays_el,this.primary.el,this.overlays.el,this.overlays_el,this.events_el];we(this.shadow_el,...t)}add_underlay(t){this.underlays_el.appendChild(t)}add_overlay(t){this.overlays_el.appendChild(t)}add_event(t){this.events_el.appendChild(t)}get pixel_ratio(){return this.primary.pixel_ratio}_update_bbox(){super._update_bbox();const{width:t,height:e}=this.bbox;this._size.replace(`\n    .bk-layer {\n      width: ${t}px;\n      height: ${e}px;\n    }\n    `)}_after_resize(){if(0!=this.plot_views.length)return;super._after_resize();const{width:t,height:e}=this.bbox;this.primary.resize(t,e),this.overlays.resize(t,e)}resize(){this._update_bbox();const{width:t,height:e}=this.bbox;this.primary.resize(t,e),this.overlays.resize(t,e)}prepare_webgl(t){const{webgl:e}=this;if(null!=e){const{width:n,height:r}=this.bbox;e.canvas.width=this.pixel_ratio*n,e.canvas.height=this.pixel_ratio*r;const[i,o,a,s]=t,{xview:l,yview:c}=this.bbox,u=l.compute(i),d=c.compute(o+s),h=this.pixel_ratio;e.regl_wrapper.set_scissor(h*u,h*d,h*a,h*s),this._clear_webgl()}}blit_webgl(t){const{webgl:e}=this;if(null!=e){if(ot.vF.debug("Blitting WebGL canvas"),t.restore(),t.drawImage(e.canvas,0,0),t.save(),this.model.hidpi){const e=this.pixel_ratio;t.scale(e,e),t.translate(.5,.5)}this._clear_webgl()}}_clear_webgl(){const{webgl:t}=this;if(null!=t){const{regl_wrapper:e,canvas:n}=t;e.clear(n.width,n.height)}}compose(){const t=this.create_layer(),{width:e,height:n}=this.bbox;return t.resize(e,n),t.ctx.drawImage(this.primary.canvas,0,0),t.ctx.drawImage(this.overlays.canvas,0,0),t}create_layer(){const{output_backend:t,hidpi:e}=this.model;return new Fu(t,e)}to_blob(){return this.compose().to_blob()}}jh.__name__="CanvasView";class zh extends Wu{constructor(t){super(t)}}Vh=zh,zh.__name__="Canvas",Vh.prototype.default_view=jh,Vh.define((({Boolean:t})=>({hidpi:[t,!0],output_backend:[_n.wf,"canvas"]})));class Bh extends qt{constructor(t){super(t)}initialize(){super.initialize(),this._result=new Map}v_compute(t){let e=this._result.get(t);return(void 0===e||t.changed_for(this))&&(e=this._v_compute(t),this._result.set(t,e)),e}}Bh.__name__="Expression";class Fh extends qt{constructor(t){super(t)}initialize(){super.initialize(),this._result=new Map}compute(t){let e=this._result.get(t);return(void 0===e||t.changed_for(this))&&(e=this._compute(t),this._result.set(t,e)),e}}var $h,Gh,qh,Uh,Wh,Zh,Xh,Kh,Yh,Jh,tp,ep,np,rp,ip,op,ap,sp,lp,cp,up,dp,hp,pp,fp,Qp,Tp,mp,gp,_p,bp,vp,yp,xp,wp,Lp,Ap,Hp;Fh.__name__="ScalarExpression";class kp extends Bh{constructor(t){super(t)}connect_signals(){super.connect_signals();for(const t of(0,Q.zu)(this.args))t instanceof tt&&t.change.connect((()=>{this._result.clear(),this.change.emit()}))}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}get func(){const t=x(this.code);return new Jt.qJ(...this.names,t)}_v_compute(t){const e=this.func.apply(t,this.values);let n=e.next();if(n.done&&void 0!==n.value){const{value:e}=n;return(0,f.cy)(e)||(0,f.iu)(e)?e:(0,f.xZ)(e)?[...e]:(0,Rt.ux)(e,t.length)}{const t=[];do{t.push(n.value),n=e.next()}while(!n.done);return t}}}$h=kp,kp.__name__="CustomJSExpr",$h.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));class Mp extends Bh{constructor(t){super(t)}_v_compute(t){const e=t.get_length()??0,n=new Float64Array(e);for(const r of this.fields){const i=(0,Q.jd)(t.data).get(r);if(null!=i){const t=Math.min(e,i.length);for(let e=0;e<t;e++)n[e]+=i[e]}}return n}}Gh=Mp,Mp.__name__="Stack",Gh.define((({String:t,Array:e})=>({fields:[e(t),[]]})));class Cp extends Bh{constructor(t){super(t)}_v_compute(t){const e=new Float64Array(t.get_length()??0),n=t.data[this.field],r=this.include_zero?1:0;e[0]=this.include_zero?0:n[0];for(let t=1;t<e.length;t++)e[t]=e[t-1]+n[t-r];return e}}qh=Cp,Cp.__name__="CumSum",qh.define((({Boolean:t,String:e})=>({field:[e],include_zero:[t,!1]})));class Sp extends Fh{constructor(t){super(t)}_compute(t){const e=(0,Q.jd)(t.data).get(this.field)??[];return Math.min(this.initial,(0,Rt.jk)(e))}}Uh=Sp,Sp.__name__="Minimum",Uh.define((({Number:t,String:e})=>({field:[e],initial:[t,1/0]})));class Ep extends Fh{constructor(t){super(t)}_compute(t){const e=(0,Q.jd)(t.data).get(this.field)??[];return Math.max(this.initial,(0,Rt.T9)(e))}}Wh=Ep,Ep.__name__="Maximum",Wh.define((({Number:t,String:e})=>({field:[e],initial:[t,-1/0]})));class Vp extends Bh{constructor(t){super(t)}get x(){return new Pp({transform:this})}get y(){return new Dp({transform:this})}}Vp.__name__="CoordinateTransform";class Op extends Bh{constructor(t){super(t)}}Zh=Op,Op.__name__="XYComponent",Zh.define((({Ref:t})=>({transform:[t(Vp)]})));class Pp extends Op{constructor(t){super(t)}_v_compute(t){return this.transform.v_compute(t).x}}Pp.__name__="XComponent";class Dp extends Op{constructor(t){super(t)}_v_compute(t){return this.transform.v_compute(t).y}}Dp.__name__="YComponent";class Np extends Vp{constructor(t){super(t)}_v_compute(t){const e=this.properties.radius.uniform(t),n=this.properties.angle.uniform(t),r="anticlock"==this.direction?-1:1,i=Math.min(e.length,n.length),o=new Float64Array(i),a=new Float64Array(i);for(let t=0;t<i;t++){const i=e.get(t),s=n.get(t)*r;o[t]=i*Math.cos(s),a[t]=i*Math.sin(s)}return{x:o,y:a}}}Xh=Np,Np.__name__="PolarTransform",Xh.define((({})=>({radius:[m.x0,{field:"radius"}],angle:[m.XS,{field:"angle"}],direction:[_n.OP,"anticlock"]})));class Rp extends Fl{constructor(t){super(t)}compute_indices(t){const e=t.get_length()??1,{booleans:n}=this;return null==n?Jt.et.all_set(e):Jt.et.from_booleans(e,n)}}Kh=Rp,Rp.__name__="BooleanFilter",Kh.define((({Boolean:t,Array:e,Nullable:n})=>({booleans:[n(e(t)),null]})));class Ip extends Fl{constructor(t){super(t)}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}get func(){const t=x(this.code);return new Function(...this.names,"source",t)}compute_indices(t){const e=t.get_length()??1,n=this.func(...this.values,t);if(null==n)return Jt.et.all_set(e);if((0,f.lF)(n,f.Fq))return Jt.et.from_indices(e,n);if((0,f.lF)(n,f.Lm))return Jt.et.from_booleans(e,n);throw new Error(`expect an array of integers or booleans, or null, got ${n}`)}}Yh=Ip,Ip.__name__="CustomJSFilter",Yh.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));class jp extends Fl{constructor(t){super(t)}compute_indices(t){const e=t.get_column(this.column_name),n=t.get_length()??1;if(null==e)return ot.vF.warn(`${this}: groupby column '${this.column_name}' not found in the data source`),Jt.et.all_set(n);{const t=new Jt.et(n,0);for(let n=0;n<t.size;n++)e[n]===this.group&&t.set(n);return t}}}Jh=jp,jp.__name__="GroupFilter",Jh.define((({String:t})=>({column_name:[t],group:[t]})));class zp extends Fl{constructor(t){super(t)}compute_indices(t){const e=t.get_length()??1,{indices:n}=this;return null==n?Jt.et.all_set(e):Jt.et.from_indices(e,n)}}tp=zp,zp.__name__="IndexFilter",tp.define((({Int:t,Array:e,Nullable:n})=>({indices:[n(e(t)),null]})));class Bp extends Fl{constructor(t){super(t)}compute_indices(t){const e=this.operand.compute_indices(t);return e.invert(),e}}ep=Bp,Bp.__name__="InversionFilter",ep.define((({Ref:t})=>({operand:[t(Fl)]})));class Fp extends Fl{constructor(t){super(t)}compute_indices(t){const{operands:e}=this;if(0==e.length){const e=t.get_length()??1;return Jt.et.all_set(e)}{const[n,...r]=e.map((e=>e.compute_indices(t)));for(const t of r)n.add(t);return n}}}np=Fp,Fp.__name__="UnionFilter",np.define((({Array:t,Ref:e})=>({operands:[t(e(Fl))]})));class $p extends Fl{constructor(t){super(t)}compute_indices(t){const{operands:e}=this;if(0==e.length){const e=t.get_length()??1;return Jt.et.all_set(e)}{const[n,...r]=e.map((e=>e.compute_indices(t)));for(const t of r)n.subtract(t);return n}}}rp=$p,$p.__name__="DifferenceFilter",rp.define((({Array:t,Ref:e})=>({operands:[t(e(Fl))]})));class Gp extends Fl{constructor(t){super(t)}compute_indices(t){const{operands:e}=this;if(0==e.length){const e=t.get_length()??1;return Jt.et.all_set(e)}{const[n,...r]=e.map((e=>e.compute_indices(t)));for(const t of r)n.symmetric_subtract(t);return n}}}ip=Gp,Gp.__name__="SymmetricDifferenceFilter",ip.define((({Array:t,Ref:e})=>({operands:[t(e(Fl))]})));class qp extends vl{_map_data(){"data"==this.model.properties.inner_radius.units?this.sinner_radius=this.sdist(this.renderer.xscale,this._x,this.inner_radius):this.sinner_radius=(0,Jt.nl)(this.inner_radius),"data"==this.model.properties.outer_radius.units?this.souter_radius=this.sdist(this.renderer.xscale,this._x,this.outer_radius):this.souter_radius=(0,Jt.nl)(this.outer_radius),this.max_souter_radius=(0,bn.T9)(this.souter_radius)}_render(t,e,n){const{sx:r,sy:i,start_angle:o,end_angle:a,sinner_radius:s,souter_radius:l}=n??this,c="anticlock"==this.model.direction;for(const n of e){const e=r[n],u=i[n],d=s[n],h=l[n],p=o.get(n),f=a.get(n);if(!isFinite(e+u+d+h+p+f))continue;const Q=f-p;t.translate(e,u),t.rotate(p),t.beginPath(),t.moveTo(h,0),t.arc(0,0,h,0,Q,c),t.rotate(Q),t.lineTo(d,0),t.arc(0,0,d,0,-Q,!c),t.closePath(),t.rotate(-Q-p),t.translate(-e,-u),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n)}}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=e-this.max_souter_radius,a=e+this.max_souter_radius,[s,l]=this.renderer.xscale.r_invert(o,a),c=n-this.max_souter_radius,u=n+this.max_souter_radius,[d,h]=this.renderer.yscale.r_invert(c,u),p=[];for(const t of this.index.indices({x0:s,x1:l,y0:d,y1:h})){const e=this.souter_radius[t]**2,n=this.sinner_radius[t]**2,[o,a]=this.renderer.xscale.r_compute(r,this._x[t]),[s,l]=this.renderer.yscale.r_compute(i,this._y[t]),c=(o-a)**2+(s-l)**2;c<=e&&c>=n&&p.push(t)}const f="anticlock"==this.model.direction,Q=[];for(const t of p){const r=Math.atan2(n-this.sy[t],e-this.sx[t]);(Math.abs(this.start_angle.get(t)-this.end_angle.get(t))>=2*Math.PI||(0,Gi.Hc)(-r,-this.start_angle.get(t),-this.end_angle.get(t),f))&&Q.push(t)}return new ir({indices:Q})}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}scenterxy(t){const e=(this.sinner_radius[t]+this.souter_radius[t])/2,n=(this.start_angle.get(t)+this.end_angle.get(t))/2;return[this.sx[t]+e*Math.cos(n),this.sy[t]+e*Math.sin(n)]}}qp.__name__="AnnularWedgeView";class Up extends yl{constructor(t){super(t)}}op=Up,Up.__name__="AnnularWedge",op.prototype.default_view=qp,op.mixins([Ke.UT,Ke.H_,Ke.y7]),op.define((({})=>({direction:[_n.OP,"anticlock"],inner_radius:[m.x0,{field:"inner_radius"}],outer_radius:[m.x0,{field:"outer_radius"}],start_angle:[m.XS,{field:"start_angle"}],end_angle:[m.XS,{field:"end_angle"}]})));class Wp extends vl{_map_data(){"data"==this.model.properties.inner_radius.units?this.sinner_radius=this.sdist(this.renderer.xscale,this._x,this.inner_radius):this.sinner_radius=(0,Jt.nl)(this.inner_radius),"data"==this.model.properties.outer_radius.units?this.souter_radius=this.sdist(this.renderer.xscale,this._x,this.outer_radius):this.souter_radius=(0,Jt.nl)(this.outer_radius)}_render(t,e,n){const{sx:r,sy:i,sinner_radius:o,souter_radius:a}=n??this;for(const n of e){const e=r[n],s=i[n],l=o[n],c=a[n];isFinite(e+s+l+c)&&(t.beginPath(),t.arc(e,s,l,0,2*Math.PI,!0),t.moveTo(e+c,s),t.arc(e,s,c,2*Math.PI,0,!1),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n);let o,a,s,l;if("data"==this.model.properties.outer_radius.units)o=r-this.max_outer_radius,s=r+this.max_outer_radius,a=i-this.max_outer_radius,l=i+this.max_outer_radius;else{const t=e-this.max_outer_radius,r=e+this.max_outer_radius;[o,s]=this.renderer.xscale.r_invert(t,r);const i=n-this.max_outer_radius,c=n+this.max_outer_radius;[a,l]=this.renderer.yscale.r_invert(i,c)}const c=[];for(const t of this.index.indices({x0:o,x1:s,y0:a,y1:l})){const e=this.souter_radius[t]**2,n=this.sinner_radius[t]**2,[o,a]=this.renderer.xscale.r_compute(r,this._x[t]),[s,l]=this.renderer.yscale.r_compute(i,this._y[t]),u=(o-a)**2+(s-l)**2;u<=e&&u>=n&&c.push(t)}return new ir({indices:c})}draw_legend_for_index(t,{x0:e,y0:n,x1:r,y1:i},o){const a=o+1,s=new Array(a);s[o]=(e+r)/2;const l=new Array(a);l[o]=(n+i)/2;const c=.5*Math.min(Math.abs(r-e),Math.abs(i-n)),u=new Array(a);u[o]=.4*c;const d=new Array(a);d[o]=.8*c,this._render(t,[o],{sx:s,sy:l,sinner_radius:u,souter_radius:d})}}Wp.__name__="AnnulusView";class Zp extends yl{constructor(t){super(t)}}ap=Zp,Zp.__name__="Annulus",ap.prototype.default_view=Wp,ap.mixins([Ke.UT,Ke.H_,Ke.y7]),ap.define((({})=>({inner_radius:[m.x0,{field:"inner_radius"}],outer_radius:[m.x0,{field:"outer_radius"}]})));class Xp extends vl{_map_data(){"data"==this.model.properties.radius.units?this.sradius=this.sdist(this.renderer.xscale,this._x,this.radius):this.sradius=(0,Jt.nl)(this.radius)}_render(t,e,n){if(!this.visuals.line.doit)return;const{sx:r,sy:i,sradius:o,start_angle:a,end_angle:s}=n??this,l="anticlock"==this.model.direction;for(const n of e){const e=r[n],c=i[n],u=o[n],d=a.get(n),h=s.get(n);isFinite(e+c+u+d+h)&&(this._render_decorations(t,n,e,c,u,d,h,l),t.beginPath(),t.arc(e,c,u,d,h,l),this.visuals.line.apply(t,n))}}_render_decorations(t,e,n,r,i,o,a,s){const{sin:l,cos:c,PI:u}=Math;for(const s of this.decorations.values()){if(t.save(),"start"==s.model.node){const e=i*c(o)+n,a=i*l(o)+r;t.translate(e,a),t.rotate(o+u)}else if("end"==s.model.node){const e=i*Math.cos(a)+n,o=i*Math.sin(a)+r;t.translate(e,o),t.rotate(a)}s.marking.render(t,e),t.restore()}}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}}Xp.__name__="ArcView";class Kp extends yl{constructor(t){super(t)}}function Yp(t,e,n,r,i,o,a,s){const l=[],c=[[],[]];for(let c=0;c<=2;c++){let u,d,h;if(0===c?(d=6*t-12*n+6*i,u=-3*t+9*n-9*i+3*a,h=3*n-3*t):(d=6*e-12*r+6*o,u=-3*e+9*r-9*o+3*s,h=3*r-3*e),Math.abs(u)<1e-12){if(Math.abs(d)<1e-12)continue;const t=-h/d;0<t&&t<1&&l.push(t);continue}const p=d*d-4*h*u,f=Math.sqrt(p);if(p<0)continue;const Q=(-d+f)/(2*u);0<Q&&Q<1&&l.push(Q);const T=(-d-f)/(2*u);0<T&&T<1&&l.push(T)}let u=l.length;const d=u;for(;u--;){const d=l[u],h=1-d,p=h*h*h*t+3*h*h*d*n+3*h*d*d*i+d*d*d*a;c[0][u]=p;const f=h*h*h*e+3*h*h*d*r+3*h*d*d*o+d*d*d*s;c[1][u]=f}return c[0][d]=t,c[1][d]=e,c[0][d+1]=a,c[1][d+1]=s,[Math.min(...c[0]),Math.max(...c[1]),Math.max(...c[0]),Math.min(...c[1])]}sp=Kp,Kp.__name__="Arc",sp.prototype.default_view=Xp,sp.mixins(Ke.UT),sp.define((({})=>({direction:[_n.OP,"anticlock"],radius:[m.x0,{field:"radius"}],start_angle:[m.XS,{field:"start_angle"}],end_angle:[m.XS,{field:"end_angle"}]})));class Jp extends ul{_project_data(){yi.project_xy(this._x0,this._y0),yi.project_xy(this._x1,this._y1)}_index_data(t){const{data_size:e,_x0:n,_y0:r,_x1:i,_y1:o,_cx0:a,_cy0:s,_cx1:l,_cy1:c}=this;for(let u=0;u<e;u++){const e=n[u],d=r[u],h=i[u],p=o[u],f=a[u],Q=s[u],T=l[u],m=c[u];if(isFinite(e+h+d+p+f+Q+T+m)){const[n,r,i,o]=Yp(e,d,h,p,f,Q,T,m);t.add_rect(n,r,i,o)}else t.add_empty()}}_render(t,e,n){if(!this.visuals.line.doit)return;const{sx0:r,sy0:i,sx1:o,sy1:a,scx0:s,scy0:l,scx1:c,scy1:u}=n??this;for(const n of e){const e=r[n],d=i[n],h=o[n],p=a[n],f=s[n],Q=l[n],T=c[n],m=u[n];isFinite(e+d+h+p+f+Q+T+m)&&(t.beginPath(),t.moveTo(e,d),t.bezierCurveTo(f,Q,T,m,h,p),this.visuals.line.apply(t,n))}}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}scenterxy(){throw new Error(`${this}.scenterxy() is not implemented`)}}Jp.__name__="BezierView";class tf extends dl{constructor(t){super(t)}}lp=tf,tf.__name__="Bezier",lp.prototype.default_view=Jp,lp.define((({})=>({x0:[m.up,{field:"x0"}],y0:[m.fZ,{field:"y0"}],x1:[m.up,{field:"x1"}],y1:[m.fZ,{field:"y1"}],cx0:[m.up,{field:"cx0"}],cy0:[m.fZ,{field:"cy0"}],cx1:[m.up,{field:"cx1"}],cy1:[m.fZ,{field:"cy1"}]}))),lp.mixins(Ke.UT);class ef extends ul{get_anchor_point(t,e,n){const r=Math.min(this.sleft[e],this.sright[e]),i=Math.max(this.sright[e],this.sleft[e]),o=Math.min(this.stop[e],this.sbottom[e]),a=Math.max(this.sbottom[e],this.stop[e]);switch(t){case"top_left":return{x:r,y:o};case"top":case"top_center":return{x:(r+i)/2,y:o};case"top_right":return{x:i,y:o};case"bottom_left":return{x:r,y:a};case"bottom":case"bottom_center":return{x:(r+i)/2,y:a};case"bottom_right":return{x:i,y:a};case"left":case"center_left":return{x:r,y:(o+a)/2};case"center":case"center_center":return{x:(r+i)/2,y:(o+a)/2};case"right":case"center_right":return{x:i,y:(o+a)/2}}}_index_data(t){const{min:e,max:n}=Math,{data_size:r}=this;for(let i=0;i<r;i++){const[r,o,a,s]=this._lrtb(i);t.add_rect(e(r,o),e(a,s),n(o,r),n(a,s))}}_render(t,e,n){const{sleft:r,sright:i,stop:o,sbottom:a}=n??this;for(const n of e){const e=r[n],s=o[n],l=i[n],c=a[n];isFinite(e+s+l+c)&&(t.beginPath(),t.rect(e,s,l-e,c-s),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_clamp_viewport(){const t=this.renderer.plot_view.frame.bbox.h_range,e=this.renderer.plot_view.frame.bbox.v_range,n=this.stop.length;for(let r=0;r<n;r++)this.stop[r]=Math.max(this.stop[r],e.start),this.sbottom[r]=Math.min(this.sbottom[r],e.end),this.sleft[r]=Math.max(this.sleft[r],t.start),this.sright[r]=Math.min(this.sright[r],t.end)}_hit_rect(t){return this._hit_rect_against_index(t)}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=[...this.index.indices({x0:r,y0:i,x1:r,y1:i})];return new ir({indices:o})}_hit_span(t){const{sx:e,sy:n}=t;let r;if("v"==t.direction){const t=this.renderer.yscale.invert(n),e=this.renderer.plot_view.frame.bbox.h_range,[i,o]=this.renderer.xscale.r_invert(e.start,e.end);r=[...this.index.indices({x0:i,y0:t,x1:o,y1:t})]}else{const t=this.renderer.xscale.invert(e),n=this.renderer.plot_view.frame.bbox.v_range,[i,o]=this.renderer.yscale.r_invert(n.start,n.end);r=[...this.index.indices({x0:t,y0:i,x1:t,y1:o})]}return new ir({indices:r})}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}}ef.__name__="LRTBView";class nf extends dl{constructor(t){super(t)}}cp=nf,nf.__name__="LRTB",cp.mixins([Ke.UT,Ke.H_,Ke.y7]);class rf extends ef{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{LRTBGL:e}=await Promise.resolve().then(n.bind(n,1897));this.glglyph=new e(t.regl_wrapper,this)}}scenterxy(t){return[this.sleft[t]/2+this.sright[t]/2,this.stop[t]/2+this.sbottom[t]/2]}_lrtb(t){const e=this._x[t],n=this._y[t],r=this.width.get(t),i=this.height.get(t);return[Math.min(e,e+r),Math.max(e,e+r),Math.max(n,n+i),Math.min(n,n+i)]}_map_data(){const t=this.renderer.xscale.v_compute(this._x),e=this.renderer.yscale.v_compute(this._y),n=this.sdist(this.renderer.xscale,this._x,this.width,"edge"),r=this.sdist(this.renderer.yscale,this._y,this.height,"edge"),i=t.length;this.stop=new Jt.mR(i),this.sbottom=new Jt.mR(i),this.sleft=new Jt.mR(i),this.sright=new Jt.mR(i);for(let o=0;o<i;o++)this.stop[o]=e[o]-r[o],this.sbottom[o]=e[o],this.sleft[o]=t[o],this.sright[o]=t[o]+n[o];this._clamp_viewport()}}rf.__name__="BlockView";class of extends nf{constructor(t){super(t)}}up=of,of.__name__="Block",up.prototype.default_view=rf,up.define((({})=>({x:[m.up,{field:"x"}],y:[m.fZ,{field:"y"}],width:[m.fY,{value:1}],height:[m.fY,{value:1}]})));class af extends vl{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{CircleGL:e}=await Promise.resolve().then(n.bind(n,1457));this.glglyph=new e(t.regl_wrapper,this)}}get use_radius(){return!(this.radius.is_Scalar()&&isNaN(this.radius.value))}_set_data(t){super._set_data(t);const e=(()=>{if(this.use_radius)return 2*this.max_radius;{const{size:t}=this;return t.is_Scalar()?t.value:(0,bn.T9)(t.array)}})();this._configure("max_size",{value:e})}_index_data(t){if(this.use_radius){const{_x:e,_y:n,radius:r,data_size:i}=this;for(let o=0;o<i;o++){const i=e[o],a=n[o],s=r.get(o);t.add_rect(i-s,a-s,i+s,a+s)}}else super._index_data(t)}_map_data(){if(this.use_radius)if("data"==this.model.properties.radius.units)switch(this.model.radius_dimension){case"x":this.sradius=this.sdist(this.renderer.xscale,this._x,this.radius);break;case"y":this.sradius=this.sdist(this.renderer.yscale,this._y,this.radius);break;case"max":{const t=this.sdist(this.renderer.xscale,this._x,this.radius),e=this.sdist(this.renderer.yscale,this._y,this.radius);this.sradius=(0,bn.Tj)(t,((t,n)=>Math.max(t,e[n])));break}case"min":{const t=this.sdist(this.renderer.xscale,this._x,this.radius),e=this.sdist(this.renderer.yscale,this._y,this.radius);this.sradius=(0,bn.Tj)(t,((t,n)=>Math.min(t,e[n])));break}}else this.sradius=(0,Jt.nl)(this.radius);else{const t=Jt.mR.from(this.size);this.sradius=(0,bn.Tj)(t,(t=>t/2))}}_mask_data(){const{frame:t}=this.renderer.plot_view,e=t.x_target,n=t.y_target;let r,i;return this.use_radius&&"data"==this.model.properties.radius.units?(r=e.map((t=>this.renderer.xscale.invert(t))).widen(this.max_radius),i=n.map((t=>this.renderer.yscale.invert(t))).widen(this.max_radius)):(r=e.widen(this.max_size).map((t=>this.renderer.xscale.invert(t))),i=n.widen(this.max_size).map((t=>this.renderer.yscale.invert(t)))),this.index.indices({x0:r.start,x1:r.end,y0:i.start,y1:i.end})}_render(t,e,n){const{sx:r,sy:i,sradius:o}=n??this;for(const n of e){const e=r[n],a=i[n],s=o[n];isFinite(e+a+s)&&(t.beginPath(),t.arc(e,a,s,0,2*Math.PI,!1),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),{hit_dilation:o}=this.model;let a,s,l,c;if(this.use_radius&&"data"==this.model.properties.radius.units)a=r-this.max_radius*o,s=r+this.max_radius*o,l=i-this.max_radius*o,c=i+this.max_radius*o;else{const t=e-this.max_size*o,r=e+this.max_size*o;[a,s]=this.renderer.xscale.r_invert(t,r);const i=n-this.max_size*o,u=n+this.max_size*o;[l,c]=this.renderer.yscale.r_invert(i,u)}const u=this.index.indices({x0:a,x1:s,y0:l,y1:c}),d=[];if(this.use_radius&&"data"==this.model.properties.radius.units)for(const t of u){const e=(this.sradius[t]*o)**2,[n,a]=this.renderer.xscale.r_compute(r,this._x[t]),[s,l]=this.renderer.yscale.r_compute(i,this._y[t]);(n-a)**2+(s-l)**2<=e&&d.push(t)}else for(const t of u){const r=(this.sradius[t]*o)**2;(this.sx[t]-e)**2+(this.sy[t]-n)**2<=r&&d.push(t)}return new ir({indices:d})}_hit_span(t){const{sx:e,sy:n}=t,r=this.bounds();let i,o,a,s;if("h"==t.direction){let t,n;if(a=r.y0,s=r.y1,this.use_radius&&"data"==this.model.properties.radius.units)t=e-this.max_radius,n=e+this.max_radius,[i,o]=this.renderer.xscale.r_invert(t,n);else{const r=this.max_size/2;t=e-r,n=e+r,[i,o]=this.renderer.xscale.r_invert(t,n)}}else{let t,e;if(i=r.x0,o=r.x1,this.use_radius&&"data"==this.model.properties.radius.units)t=n-this.max_radius,e=n+this.max_radius,[a,s]=this.renderer.yscale.r_invert(t,e);else{const r=this.max_size/2;t=n-r,e=n+r,[a,s]=this.renderer.yscale.r_invert(t,e)}}const l=[...this.index.indices({x0:i,x1:o,y0:a,y1:s})];return new ir({indices:l})}_hit_rect(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,[o,a]=this.renderer.xscale.r_invert(e,n),[s,l]=this.renderer.yscale.r_invert(r,i),c=[...this.index.indices({x0:o,x1:a,y0:s,y1:l})];return new ir({indices:c})}_hit_poly(t){const{sx:e,sy:n}=t,r=(0,Rt.y1)(0,this.sx.length),i=[];for(let t=0,o=r.length;t<o;t++){const o=r[t];xl(this.sx[t],this.sy[t],e,n)&&i.push(o)}return new ir({indices:i})}draw_legend_for_index(t,{x0:e,y0:n,x1:r,y1:i},o){const a=o+1,s=new Array(a);s[o]=(e+r)/2;const l=new Array(a);l[o]=(n+i)/2;const c=new Array(a);c[o]=.2*Math.min(Math.abs(r-e),Math.abs(i-n)),this._render(t,[o],{sx:s,sy:l,sradius:c})}}af.__name__="CircleView";class sf extends yl{constructor(t){super(t)}}dp=sf,sf.__name__="Circle",dp.prototype.default_view=af,dp.mixins([Ke.UT,Ke.H_,Ke.y7]),dp.define((({Number:t})=>({angle:[m.XS,0],size:[m.$A,{value:4}],radius:[m.qm,null],radius_dimension:[_n.bf,"x"],hit_dilation:[t,1]})));class lf extends vl{get max_w2(){return"data"==this.model.properties.width.units?this.max_width/2:0}get max_h2(){return"data"==this.model.properties.height.units?this.max_height/2:0}_bounds({x0:t,x1:e,y0:n,y1:r}){const{max_w2:i,max_h2:o}=this;return{x0:t-i,x1:e+i,y0:n-o,y1:r+o}}}lf.__name__="CenterRotatableView";class cf extends yl{constructor(t){super(t)}}hp=cf,cf.__name__="CenterRotatable",hp.mixins([Ke.UT,Ke.H_,Ke.y7]),hp.define((({})=>({angle:[m.XS,0],width:[m.x0,{field:"width"}],height:[m.x0,{field:"height"}]})));class uf extends lf{_map_data(){"data"==this.model.properties.width.units?this.sw=this.sdist(this.renderer.xscale,this._x,this.width,"center"):this.sw=(0,Jt.nl)(this.width),"data"==this.model.properties.height.units?this.sh=this.sdist(this.renderer.yscale,this._y,this.height,"center"):this.sh=(0,Jt.nl)(this.height)}_render(t,e,n){const{sx:r,sy:i,sw:o,sh:a,angle:s}=n??this;for(const n of e){const e=r[n],l=i[n],c=o[n],u=a[n],d=s.get(n);isFinite(e+l+c+u+d)&&(t.beginPath(),t.ellipse(e,l,c/2,u/2,d,0,2*Math.PI),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_hit_point(t){let e,n,r,i,o,a,s,l,c;const{sx:u,sy:d}=t,h=this.renderer.xscale.invert(u),p=this.renderer.yscale.invert(d);"data"==this.model.properties.width.units?(e=h-this.max_width,n=h+this.max_width):(a=u-this.max_width,s=u+this.max_width,[e,n]=this.renderer.xscale.r_invert(a,s)),"data"==this.model.properties.height.units?(r=p-this.max_height,i=p+this.max_height):(l=d-this.max_height,c=d+this.max_height,[r,i]=this.renderer.yscale.r_invert(l,c));const f=this.index.indices({x0:e,x1:n,y0:r,y1:i}),Q=[];for(const t of f)o=wl(u,d,this.angle.get(t),this.sh[t]/2,this.sw[t]/2,this.sx[t],this.sy[t]),o&&Q.push(t);return new ir({indices:Q})}draw_legend_for_index(t,{x0:e,y0:n,x1:r,y1:i},o){const a=o+1,s=new Array(a);s[o]=(e+r)/2;const l=new Array(a);l[o]=(n+i)/2;const c=this.sw[o]/this.sh[o],u=.8*Math.min(Math.abs(r-e),Math.abs(i-n)),d=new Array(a),h=new Array(a);c>1?(d[o]=u,h[o]=u/c):(d[o]=u*c,h[o]=u);const p=new m.J3(0,a);this._render(t,[o],{sx:s,sy:l,sw:d,sh:h,angle:p})}}uf.__name__="EllipseView";class df extends cf{constructor(t){super(t)}}pp=df,df.__name__="Ellipse",pp.prototype.default_view=uf;class hf extends ef{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{LRTBGL:e}=await Promise.resolve().then(n.bind(n,1897));this.glglyph=new e(t.regl_wrapper,this)}}scenterxy(t){return[(this.sleft[t]+this.sright[t])/2,this.sy[t]]}_lrtb(t){const e=this._left[t],n=this._right[t],r=this._y[t],i=this.height.get(t)/2;return[Math.min(e,n),Math.max(e,n),r+i,r-i]}_map_data(){this.sy=this.renderer.yscale.v_compute(this._y),this.sh=this.sdist(this.renderer.yscale,this._y,this.height,"center"),this.sleft=this.renderer.xscale.v_compute(this._left),this.sright=this.renderer.xscale.v_compute(this._right);const t=this.sy.length;this.stop=new Jt.mR(t),this.sbottom=new Jt.mR(t);for(let e=0;e<t;e++)this.stop[e]=this.sy[e]-this.sh[e]/2,this.sbottom[e]=this.sy[e]+this.sh[e]/2;this._clamp_viewport()}}hf.__name__="HBarView";class pf extends nf{constructor(t){super(t)}}fp=pf,pf.__name__="HBar",fp.prototype.default_view=hf,fp.define((({})=>({left:[m.up,{value:0}],y:[m.fZ,{field:"y"}],height:[m.fY,{value:1}],right:[m.up,{field:"right"}]})));class ff extends ul{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{HexTileGL:e}=await Promise.resolve().then(n.bind(n,2619));this.glglyph=new e(t.regl_wrapper,this)}}scenterxy(t){return[this.sx[t],this.sy[t]]}_set_data(){const{orientation:t,size:e,aspect_scale:n}=this.model,{q:r,r:i}=this,o=this.q.length;this._x=new Float64Array(o),this._y=new Float64Array(o);const{_x:a,_y:s}=this,l=Math.sqrt(3);if("pointytop"==t)for(let t=0;t<o;t++){const o=r.get(t),c=i.get(t)/2;a[t]=e*l*(o+c)/n,s[t]=-3*e*c}else for(let t=0;t<o;t++){const o=r.get(t)/2,c=i.get(t);a[t]=3*e*o,s[t]=-e*l*(c+o)*n}}_project_data(){yi.project_xy(this._x,this._y)}_index_data(t){let e=this.model.size,n=Math.sqrt(3)*e/2;"flattop"==this.model.orientation?([n,e]=[e,n],e*=this.model.aspect_scale):n/=this.model.aspect_scale;const{data_size:r}=this;for(let i=0;i<r;i++){const r=this._x[i],o=this._y[i];t.add_rect(r-n,o-e,r+n,o+e)}}map_data(){[this.sx,this.sy]=this.renderer.coordinates.map_to_screen(this._x,this._y),[this.svx,this.svy]=this._get_unscaled_vertices(),this.glglyph?.set_data_changed()}_get_unscaled_vertices(){const t=this.model.size,e=this.model.aspect_scale;if("pointytop"==this.model.orientation){const n=this.renderer.yscale,r=this.renderer.xscale,i=Math.abs(n.compute(0)-n.compute(t)),o=Math.sqrt(3)/2*Math.abs(r.compute(0)-r.compute(t))/e,a=i/2;return[[0,-o,-o,0,o,o],[i,a,-a,-i,-a,a]]}{const n=this.renderer.xscale,r=this.renderer.yscale,i=Math.abs(n.compute(0)-n.compute(t)),o=Math.sqrt(3)/2*Math.abs(r.compute(0)-r.compute(t))*e,a=i/2;return[[i,a,-a,-i,-a,a],[0,-o,-o,0,o,o]]}}_render(t,e,n){const{sx:r,sy:i,svx:o,svy:a,scale:s}=n??this;for(const n of e){const e=r[n],l=i[n],c=s.get(n);if(isFinite(e+l+c)){t.translate(e,l),t.beginPath();for(let e=0;e<6;e++)t.lineTo(o[e]*c,a[e]*c);t.closePath(),t.translate(-e,-l),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n)}}}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=this.index.indices({x0:r,y0:i,x1:r,y1:i}),a=[];for(const t of o)xl(e-this.sx[t],n-this.sy[t],this.svx,this.svy)&&a.push(t);return new ir({indices:a})}_hit_span(t){const{sx:e,sy:n}=t;let r;if("v"==t.direction){const t=this.renderer.yscale.invert(n),e=this.renderer.plot_view.frame.bbox.h_range,[i,o]=this.renderer.xscale.r_invert(e.start,e.end);r=[...this.index.indices({x0:i,y0:t,x1:o,y1:t})]}else{const t=this.renderer.xscale.invert(e),n=this.renderer.plot_view.frame.bbox.v_range,[i,o]=this.renderer.yscale.r_invert(n.start,n.end);r=[...this.index.indices({x0:t,y0:i,x1:t,y1:o})]}return new ir({indices:r})}_hit_rect(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,[o,a]=this.renderer.xscale.r_invert(e,n),[s,l]=this.renderer.yscale.r_invert(r,i),c=[...this.index.indices({x0:o,x1:a,y0:s,y1:l})];return new ir({indices:c})}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}}ff.__name__="HexTileView";class Qf extends dl{constructor(t){super(t)}}Qp=Qf,Qf.__name__="HexTile",Qp.prototype.default_view=ff,Qp.mixins([Ke.UT,Ke.H_,Ke.y7]),Qp.define((({Number:t})=>({r:[m.fY,{field:"r"}],q:[m.fY,{field:"q"}],scale:[m.fY,1],size:[t,1],aspect_scale:[t,1],orientation:[_n.g3,"pointytop"]}))),Qp.override({line_color:null});class Tf extends vl{connect_signals(){super.connect_signals(),this.connect(this.model.properties.global_alpha.change,(()=>this.renderer.request_render()))}get xy_scale(){switch(this.model.origin){case"bottom_left":return[1,-1];case"top_left":return[1,1];case"bottom_right":return[-1,-1];case"top_right":return[-1,1]}}get xy_offset(){switch(this.model.origin){case"bottom_left":return[0,1];case"top_left":return[0,0];case"bottom_right":return[1,1];case"top_right":return[1,0]}}get xy_anchor(){const{anchor:t}=this.model;if(!(0,f.Kg)(t))return[(()=>{const[e]=t;switch(e){case"start":case"left":return 0;case"center":return.5;case"end":case"right":return 1;default:return e}})(),(()=>{const[,e]=t;switch(e){case"start":case"top":return 0;case"center":return.5;case"end":case"bottom":return 1;default:return e}})()];switch(t){case"top_left":return[0,0];case"top":case"top_center":return[.5,0];case"top_right":return[1,0];case"right":case"center_right":return[1,.5];case"bottom_right":return[1,1];case"bottom":case"bottom_center":return[.5,1];case"bottom_left":return[0,1];case"left":case"center_left":return[0,.5];case"center":case"center_center":return[.5,.5]}}get xy_sign(){const t=this.renderer.xscale.source_range,e=this.renderer.yscale.source_range;return[t.is_reversed?-1:1,e.is_reversed?-1:1]}_render(t,e,n){const{image_data:r,sx:i,sy:o,sw:a,sh:s}=n??this,l=t.getImageSmoothingEnabled();t.setImageSmoothingEnabled(!1);const[c,u]=this.xy_sign,[d,h]=this.xy_scale,[p,f]=this.xy_offset,[Q,T]=this.xy_anchor;if(this.visuals.image.doit)for(const n of e){const e=r[n],l=i[n],m=o[n],g=a[n],_=s[n];if(null==e||!isFinite(l+m+g+_))continue;const b=c*Q*g,v=u*T*_;t.save(),t.translate(l-b,m-v),t.scale(c*d,u*h),this.visuals.image.set_vectorize(t,n),t.drawImage(e,-p*g,-f*_,g,_),t.restore()}t.setImageSmoothingEnabled(l)}_set_data(t){this._set_width_heigh_data();for(let e=0,n=this.image.length;e<n;e++){if(null!=t&&t.indexOf(e)<0)continue;const n=this.image.get(e);(0,_.vA)(2==n.dimension,"expected a 2D array"),this._height[e]=n.shape[0],this._width[e]=n.shape[1];const r=this._flat_img_to_buf8(n);this._set_image_data_from_buffer(e,r)}}_index_data(t){const{data_size:e}=this;for(let n=0;n<e;n++){const[e,r,i,o]=this._lrtb(n);t.add_rect(e,o,r,i)}}_lrtb(t){const e=this.dw.get(t),n=this.dh.get(t),r=this._x[t],i=this._y[t],[o,a]=this.xy_sign,[s,l]=this.xy_anchor,[c,u]=[r-o*s*e,r+o*(1-s)*e],[d,h]=[i+a*l*n,i-a*(1-l)*n],[p,f]=c<u?[c,u]:[u,c],[Q,T]=d<h?[d,h]:[h,d];return[p,f,T,Q]}_set_width_heigh_data(){null!=this.image_data&&this.image_data.length==this.image.length||(this.image_data=new Array(this.image.length)),null!=this._width&&this._width.length==this.image.length||(this._width=new Uint32Array(this.image.length)),null!=this._height&&this._height.length==this.image.length||(this._height=new Uint32Array(this.image.length))}_get_or_create_canvas(t){const e=this.image_data[t];if(null!=e&&e.width==this._width[t]&&e.height==this._height[t])return e;{const e=document.createElement("canvas");return e.width=this._width[t],e.height=this._height[t],e}}_set_image_data_from_buffer(t,e){const n=this._get_or_create_canvas(t),r=n.getContext("2d"),i=r.getImageData(0,0,this._width[t],this._height[t]);i.data.set(e),r.putImageData(i,0,0),this.image_data[t]=n}_map_data(){"data"==this.model.properties.dw.units?this.sw=this.sdist(this.renderer.xscale,this._x,this.dw,"edge",this.model.dilate):this.sw=(0,Jt.nl)(this.dw),"data"==this.model.properties.dh.units?this.sh=this.sdist(this.renderer.yscale,this._y,this.dh,"edge",this.model.dilate):this.sh=(0,Jt.nl)(this.dh)}_image_index(t,e,n){const[r,i,o,a]=this._lrtb(t),s=this._width[t],l=this._height[t],c=(i-r)/s,u=(o-a)/l;let d=Math.floor((e-r)/c),h=Math.floor((n-a)/u);return this.renderer.xscale.source_range.is_reversed&&(d=s-d-1),this.renderer.yscale.source_range.is_reversed&&(h=l-h-1),{index:t,i:d,j:h,flat_index:h*s+d}}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=this.index.indices({x0:r,x1:r,y0:i,y1:i}),a=new ir,s=[];for(const t of o)e!=1/0&&n!=1/0&&(s.push(t),a.image_indices.push(this._image_index(t,r,i)));return a.indices=s,a}}Tf.__name__="ImageBaseView";class mf extends yl{constructor(t){super(t)}}Tp=mf,mf.__name__="ImageBase",Tp.mixins(Ke.Hl),Tp.define((({Boolean:t,Number:e,Or:n,Tuple:r})=>({image:[m.xP,{field:"image"}],dw:[m.x0,{field:"dw"}],dh:[m.x0,{field:"dh"}],dilate:[t,!1],origin:[_n.Wo,"bottom_left"],anchor:[n(_n.Mz,r(n(_n.W3,_n.oX,e),n(_n.W3,_n.gy,e))),"bottom_left"]})));class gf extends Tf{connect_signals(){super.connect_signals(),this.connect(this.model.color_mapper.change,(()=>this._update_image()))}_update_image(){null!=this.image_data&&(this._set_data(null),this.renderer.request_render())}_flat_img_to_buf8(t){return this.model.color_mapper.rgba_mapper.v_compute(t)}}gf.__name__="ImageView";class _f extends mf{constructor(t){super(t)}}mp=_f,_f.__name__="Image",mp.prototype.default_view=gf,mp.define((({Ref:t})=>({color_mapper:[t(Fs),()=>new ru({palette:["#000000","#252525","#525252","#737373","#969696","#bdbdbd","#d9d9d9","#f0f0f0","#ffffff"]})]})));class bf extends Tf{_flat_img_to_buf8(t){let e;return e=(0,f.cy)(t)?new Uint32Array(t):t,new Uint8ClampedArray(e.buffer)}}bf.__name__="ImageRGBAView";class vf extends mf{constructor(t){super(t)}}gp=vf,vf.__name__="ImageRGBA",gp.prototype.default_view=bf;class yf extends vl{constructor(){super(...arguments),this._images_rendered=!1,this._set_data_iteration=0}connect_signals(){super.connect_signals(),this.connect(this.model.properties.global_alpha.change,(()=>this.renderer.request_render()))}_index_data(t){const{data_size:e}=this;for(let n=0;n<e;n++)t.add_empty()}_set_data(){this._set_data_iteration++;const t=this.url.length;this.image=new Array(t),this.rendered=new Jt.et(t);const{retry_attempts:e,retry_timeout:n}=this.model,{_set_data_iteration:r}=this;for(let i=0;i<t;i++){const t=this.url.get(i);if(!t)continue;const o=new Qo(t,{loaded:()=>{this._set_data_iteration!=r||this.rendered.get(i)||this.renderer.request_render()},failed:()=>{this._set_data_iteration==r&&(this.image[i]=void 0)},attempts:e+1,timeout:n});this.image[i]=o.image}const i="data"==this.model.properties.w.units,o="data"==this.model.properties.h.units,a=this._x.length,s=new Jt.mR(i?2*a:a),l=new Jt.mR(o?2*a:a),{anchor:c}=this.model;function u(t,e){switch(c){case"top_left":case"bottom_left":case"left":case"center_left":return[t,t+e];case"top":case"top_center":case"bottom":case"bottom_center":case"center":case"center_center":return[t-e/2,t+e/2];case"top_right":case"bottom_right":case"right":case"center_right":return[t-e,t]}}function d(t,e){switch(c){case"top_left":case"top":case"top_center":case"top_right":return[t,t-e];case"bottom_left":case"bottom":case"bottom_center":case"bottom_right":return[t+e,t];case"left":case"center_left":case"center":case"center_center":case"right":case"center_right":return[t+e/2,t-e/2]}}if(i)for(let t=0;t<a;t++)[s[t],s[a+t]]=u(this._x[t],this.w.get(t));else s.set(this._x,0);if(o)for(let t=0;t<a;t++)[l[t],l[a+t]]=d(this._y[t],this.h.get(t));else l.set(this._y,0);const[h,p]=(0,bn.LK)(s),[f,Q]=(0,bn.LK)(l);this._bounds_rect={x0:h,x1:p,y0:f,y1:Q}}has_finished(){return super.has_finished()&&this._images_rendered}_map_data(){"data"==this.model.properties.w.units?this.sw=this.sdist(this.renderer.xscale,this._x,this.w,"edge",this.model.dilate):this.sw=(0,Jt.nl)(this.w),"data"==this.model.properties.h.units?this.sh=this.sdist(this.renderer.yscale,this._y,this.h,"edge",this.model.dilate):this.sh=(0,Jt.nl)(this.h)}_render(t,e,n){const{image:r,sx:i,sy:o,sw:a,sh:s,angle:l,global_alpha:c}=n??this,{frame:u}=this.renderer.plot_view,{left:d,top:h,width:p,height:f}=u.bbox;t.beginPath(),t.rect(d+1,h+1,p-2,f-2),t.clip();let Q=!0;for(const n of e){const e=r[n];isFinite(i[n]+o[n]+l.get(n)+c.get(n))&&null!=e&&(e.complete?0==e.naturalWidth&&0==e.naturalHeight||this._render_image(t,n,e,i,o,a,s,l,c):Q=!1)}Q&&!this._images_rendered&&(this._images_rendered=!0,this.notify_finished())}_final_sx_sy(t,e,n,r,i){switch(t){case"top_left":return[e,n];case"top":case"top_center":return[e-r/2,n];case"top_right":return[e-r,n];case"right":case"center_right":return[e-r,n-i/2];case"bottom_right":return[e-r,n-i];case"bottom":case"bottom_center":return[e-r/2,n-i];case"bottom_left":return[e,n-i];case"left":case"center_left":return[e,n-i/2];case"center":case"center_center":return[e-r/2,n-i/2]}}_render_image(t,e,n,r,i,o,a,s,l){isFinite(o[e])||(o[e]=n.width),isFinite(a[e])||(a[e]=n.height);const c=o[e],u=a[e],{anchor:d}=this.model,[h,p]=this._final_sx_sy(d,r[e],i[e],c,u),f=s.get(e),Q=l.get(e);t.save(),t.globalAlpha=Q;const T=c/2,m=u/2;f?(t.translate(h,p),t.translate(T,m),t.rotate(f),t.translate(-T,-m),t.drawImage(n,0,0,c,u),t.translate(T,m),t.rotate(-f),t.translate(-T,-m),t.translate(-h,-p)):t.drawImage(n,h,p,c,u),t.restore(),this.rendered.set(e)}bounds(){return this._bounds_rect}}yf.__name__="ImageURLView";class xf extends yl{constructor(t){super(t)}}_p=xf,xf.__name__="ImageURL",_p.prototype.default_view=yf,_p.define((({Boolean:t,Int:e})=>({url:[m.zG,{field:"url"}],anchor:[_n.Mz,"top_left"],global_alpha:[m.fY,{value:1}],angle:[m.XS,0],w:[m.qm,null],h:[m.qm,null],dilate:[t,!1],retry_attempts:[e,0],retry_timeout:[e,0]})));class wf extends ul{_project_data(){yi.project_xy(this._xs.array,this._ys.array)}_index_data(t){const{data_size:e}=this;for(let n=0;n<e;n++){const e=this._xs.get(n),r=this._ys.get(n),[i,o,a,s]=(0,bn.RN)(e,r);t.add_rect(i,a,o,s)}}_render(t,e,n){const{sxs:r,sys:i}=n??this;for(const n of e){const e=r.get(n),o=i.get(n),a=Math.min(e.length,o.length);let s=!0;t.beginPath();for(let n=0;n<a;n++){const r=e[n],i=o[n];isFinite(r+i)?s?(t.moveTo(r,i),s=!1):t.lineTo(r,i):s=!0}this.visuals.line.set_vectorize(t,n),t.stroke()}}_hit_point(t){const e={x:t.sx,y:t.sy};let n=9999;const r=new Map;for(let t=0,i=this.sxs.length;t<i;t++){const i=Math.max(2,this.line_width.get(t)/2),o=this.sxs.get(t),a=this.sys.get(t);let s=null;for(let t=0,r=o.length-1;t<r;t++){const r=Hl(e,{x:o[t],y:a[t]},{x:o[t+1],y:a[t+1]});r<i&&r<n&&(n=r,s=[t])}null!=s&&r.set(t,s)}return new ir({indices:[...r.keys()],multiline_indices:(0,Q.Wh)(r)})}_hit_span(t){const{sx:e,sy:n}=t;let r,i;"v"==t.direction?(r=this.renderer.yscale.invert(n),i=this._ys):(r=this.renderer.xscale.invert(e),i=this._xs);const o=new Map;for(let t=0,e=i.length;t<e;t++){const e=i.get(t),n=[];for(let t=0,i=e.length-1;t<i;t++)e[t]<=r&&r<=e[t+1]&&n.push(t);n.length>0&&o.set(t,n)}return new ir({indices:[...o.keys()],multiline_indices:(0,Q.Wh)(o)})}get_interpolation_hit(t,e,n){const r=this._xs.get(t),i=this._ys.get(t),o=r[e],a=i[e],s=r[e+1],l=i[e+1];return El(this.renderer,n,o,a,s,l)}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}scenterxy(){throw new Error(`${this}.scenterxy() is not implemented`)}}wf.__name__="MultiLineView";class Lf extends dl{constructor(t){super(t)}}bp=Lf,Lf.__name__="MultiLine",bp.prototype.default_view=wf,bp.define((({})=>({xs:[m.vs,{field:"xs"}],ys:[m.m3,{field:"ys"}]}))),bp.mixins(Ke.UT);class Af extends ul{_project_data(){}_index_data(t){const{min:e,max:n}=Math,{data_size:r}=this;for(let i=0;i<r;i++){const r=this._xs[i],o=this._ys[i];if(0==r.length||0==o.length){t.add_empty();continue}let a=1/0,s=-1/0,l=1/0,c=-1/0;for(let t=0,i=r.length;t<i;t++){const i=r[t][0],u=o[t][0];if(0!=i.length&&0!=u.length){const[t,r]=(0,bn.LK)(i),[o,d]=(0,bn.LK)(u);a=e(a,t),s=n(s,r),l=e(l,o),c=n(c,d)}}t.add_rect(a,l,s,c)}this._hole_index=this._index_hole_data()}_index_hole_data(){const{min:t,max:e}=Math,{data_size:n}=this,r=new rl(n);for(let i=0;i<n;i++){const n=this._xs[i],o=this._ys[i];if(0==n.length||0==o.length){r.add_empty();continue}let a=1/0,s=-1/0,l=1/0,c=-1/0;for(let r=0,i=n.length;r<i;r++){const i=n[r],u=o[r];if(i.length>1&&u.length>1)for(let n=1,r=i.length;n<r;n++){const[r,o]=(0,bn.LK)(i[n]),[d,h]=(0,bn.LK)(u[n]);a=t(a,r),s=e(s,o),l=t(l,d),c=e(c,h)}}r.add_rect(a,l,s,c)}return r.finish(),r}_mask_data(){const{x_range:t,y_range:e}=this.renderer.plot_view.frame;return this.index.indices({x0:t.min,x1:t.max,y0:e.min,y1:e.max})}_render(t,e,n){if(!this.visuals.fill.doit&&!this.visuals.line.doit)return;const{sxs:r,sys:i}=n??this;for(const n of e){t.beginPath();const e=r[n],o=i[n],a=Math.min(e.length,o.length);for(let n=0;n<a;n++){const r=e[n],i=o[n],a=Math.min(r.length,i.length);for(let e=0;e<a;e++){const n=r[e],o=i[e],a=Math.min(n.length,o.length);for(let e=0;e<a;e++){const r=n[e],i=o[e];0==e?t.moveTo(r,i):t.lineTo(r,i)}t.closePath()}}this.visuals.fill.apply(t,n,"evenodd"),this.visuals.hatch.apply(t,n,"evenodd"),this.visuals.line.apply(t,n)}}_hit_rect(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,o=[e,n,n,e],a=[r,r,i,i],[s,l]=this.renderer.xscale.r_invert(e,n),[c,u]=this.renderer.yscale.r_invert(r,i),d=this.index.indices({x0:s,x1:l,y0:c,y1:u}),h=[];for(const t of d){const e=this.sxs[t],n=this.sys[t];let r=!0;for(let t=0,i=e.length;t<i;t++){for(let i=0,s=e[t][0].length;i<s;i++)if(!xl(e[t][0][i],n[t][0][i],o,a)){r=!1;break}if(!r)break}r&&h.push(t)}return new ir({indices:h})}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=this.index.indices({x0:r,y0:i,x1:r,y1:i}),a=this._hole_index.indices({x0:r,y0:i,x1:r,y1:i}),s=[];for(const t of o){const r=this.sxs[t],i=this.sys[t];for(let o=0,l=r.length;o<l;o++){const l=r[o].length;if(xl(e,n,r[o][0],i[o][0]))if(1==l)s.push(t);else if(a.get(t)){if(l>1){let a=!1;for(let t=1;t<l;t++)if(xl(e,n,r[o][t],i[o][t])){a=!0;break}a||s.push(t)}}else s.push(t)}}return new ir({indices:s})}_get_snap_coord(t){return(0,bn.cz)(t)/t.length}scenterxy(t,e,n){if(1==this.sxs[t].length)return[this._get_snap_coord(this.sxs[t][0][0]),this._get_snap_coord(this.sys[t][0][0])];{const r=this.sxs[t],i=this.sys[t];for(let t=0,o=r.length;t<o;t++)if(xl(e,n,r[t][0],i[t][0]))return[this._get_snap_coord(r[t][0]),this._get_snap_coord(i[t][0])]}(0,_.HB)()}map_data(){const t=this._xs.length;this.sxs=new Array(t),this.sys=new Array(t);for(let e=0;e<t;e++){const t=this._xs[e].length;this.sxs[e]=new Array(t),this.sys[e]=new Array(t);for(let n=0;n<t;n++){const t=this._xs[e][n].length;this.sxs[e][n]=new Array(t),this.sys[e][n]=new Array(t);for(let r=0;r<t;r++){const[t,i]=this.renderer.coordinates.map_to_screen(this._xs[e][n][r],this._ys[e][n][r]);this.sxs[e][n][r]=t,this.sys[e][n][r]=i}}}}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}}Af.__name__="MultiPolygonsView";class Hf extends dl{constructor(t){super(t)}}vp=Hf,Hf.__name__="MultiPolygons",vp.prototype.default_view=Af,vp.define((({})=>({xs:[m.dq,{field:"xs"}],ys:[m.wN,{field:"ys"}]}))),vp.mixins([Ke.UT,Ke.H_,Ke.y7]);class kf extends ul{_project_data(){yi.project_xy(this._xs.array,this._ys.array)}_index_data(t){const{data_size:e}=this;for(let n=0;n<e;n++){const e=this._xs.get(n),r=this._ys.get(n),[i,o,a,s]=(0,bn.RN)(e,r);t.add_rect(i,a,o,s)}}_mask_data(){const{x_range:t,y_range:e}=this.renderer.plot_view.frame;return this.index.indices({x0:t.min,x1:t.max,y0:e.min,y1:e.max})}_render(t,e,n){const{sxs:r,sys:i}=n??this;for(const n of e){const e=r.get(n),o=i.get(n);let a=!0;t.beginPath();const s=Math.min(e.length,o.length);for(let n=0;n<s;n++){const r=e[n],i=o[n];isFinite(r+i)?a?(t.moveTo(r,i),a=!1):t.lineTo(r,i):(t.closePath(),a=!0)}t.closePath(),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n)}}_hit_rect(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,o=[e,n,n,e],a=[r,r,i,i],[s,l]=this.renderer.xscale.r_invert(e,n),[c,u]=this.renderer.yscale.r_invert(r,i),d=this.index.indices({x0:s,x1:l,y0:c,y1:u}),h=[];for(const t of d){const e=this.sxs.get(t),n=this.sys.get(t);let r=!0;for(let t=0,i=e.length;t<i;t++)if(!xl(e[t],n[t],o,a)){r=!1;break}r&&h.push(t)}return new ir({indices:h})}_hit_point(t){const{sx:e,sy:n}=t,r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=this.index.indices({x0:r,y0:i,x1:r,y1:i}),a=[];for(const t of o){const r=this.sxs.get(t),i=this.sys.get(t),o=r.length;for(let s=0,l=0;;l++){if(isNaN(r[l])||l==o){if(xl(e,n,r.subarray(s,l),i.subarray(s,l))){a.push(t);break}s=l+1}if(l==o)break}}return new ir({indices:a})}_get_snap_coord(t){return(0,bn.cz)(t)/t.length}scenterxy(t,e,n){const r=this.sxs.get(t),i=this.sys.get(t),o=r.length;let a=!1;for(let t=0,s=0;;s++){const l=isNaN(r[s]);if(a=a||l,s==o&&!a)return[this._get_snap_coord(r),this._get_snap_coord(i)];if(l||s==o){const o=r.subarray(t,s),a=i.subarray(t,s);if(xl(e,n,o,a))return[this._get_snap_coord(o),this._get_snap_coord(a)];t=s+1}if(s==o)break}(0,_.HB)()}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}}kf.__name__="PatchesView";class Mf extends dl{constructor(t){super(t)}}yp=Mf,Mf.__name__="Patches",yp.prototype.default_view=kf,yp.define((({})=>({xs:[m.vs,{field:"xs"}],ys:[m.m3,{field:"ys"}]}))),yp.mixins([Ke.UT,Ke.H_,Ke.y7]);class Cf extends ef{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{LRTBGL:e}=await Promise.resolve().then(n.bind(n,1897));this.glglyph=new e(t.regl_wrapper,this)}}scenterxy(t){return[this.sleft[t]/2+this.sright[t]/2,this.stop[t]/2+this.sbottom[t]/2]}_lrtb(t){return[this._left[t],this._right[t],this._top[t],this._bottom[t]]}}Cf.__name__="QuadView";class Sf extends nf{constructor(t){super(t)}}function Ef(t,e,n){if(e==(t+n)/2)return[t,n];{const r=(t-e)/(t-2*e+n),i=t*(1-r)**2+2*e*(1-r)*r+n*r**2;return[Math.min(t,n,i),Math.max(t,n,i)]}}xp=Sf,Sf.__name__="Quad",xp.prototype.default_view=Cf,xp.define((({})=>({right:[m.up,{field:"right"}],bottom:[m.fZ,{field:"bottom"}],left:[m.up,{field:"left"}],top:[m.fZ,{field:"top"}]})));class Vf extends ul{_project_data(){yi.project_xy(this._x0,this._y0),yi.project_xy(this._x1,this._y1)}_index_data(t){const{_x0:e,_x1:n,_y0:r,_y1:i,_cx:o,_cy:a,data_size:s}=this;for(let l=0;l<s;l++){const s=e[l],c=n[l],u=r[l],d=i[l],h=o[l],p=a[l];if(isFinite(s+c+u+d+h+p)){const[e,n]=Ef(s,h,c),[r,i]=Ef(u,p,d);t.add_rect(e,r,n,i)}else t.add_empty()}}_render(t,e,n){if(!this.visuals.line.doit)return;const{sx0:r,sy0:i,sx1:o,sy1:a,scx:s,scy:l}=n??this;for(const n of e){const e=r[n],c=i[n],u=o[n],d=a[n],h=s[n],p=l[n];isFinite(e+c+u+d+h+p)&&(t.beginPath(),t.moveTo(e,c),t.quadraticCurveTo(h,p,u,d),this.visuals.line.apply(t,n))}}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}scenterxy(){throw new Error(`${this}.scenterxy() is not implemented`)}}Vf.__name__="QuadraticView";class Of extends dl{constructor(t){super(t)}}wp=Of,Of.__name__="Quadratic",wp.prototype.default_view=Vf,wp.define((({})=>({x0:[m.up,{field:"x0"}],y0:[m.fZ,{field:"y0"}],x1:[m.up,{field:"x1"}],y1:[m.fZ,{field:"y1"}],cx:[m.up,{field:"cx"}],cy:[m.fZ,{field:"cy"}]}))),wp.mixins(Ke.UT);class Pf extends vl{_map_data(){"data"==this.model.properties.length.units?this.slength=this.sdist(this.renderer.xscale,this._x,this.length):this.slength=(0,Jt.nl)(this.length);const{width:t,height:e}=this.renderer.plot_view.frame.bbox,n=2*(t+e),{slength:r}=this;for(let t=0,e=r.length;t<e;t++)0==r[t]&&(r[t]=n)}_render(t,e,n){if(!this.visuals.line.doit)return;const{sx:r,sy:i,slength:o,angle:a}=n??this;for(const n of e){const e=r[n],s=i[n],l=a.get(n),c=o[n];isFinite(e+s+l+c)&&(t.translate(e,s),t.rotate(l),t.beginPath(),t.moveTo(0,0),t.lineTo(c,0),this.visuals.line.apply(t,n),t.rotate(-l),t.translate(-e,-s))}}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}}Pf.__name__="RayView";class Df extends yl{constructor(t){super(t)}}Lp=Df,Df.__name__="Ray",Lp.prototype.default_view=Pf,Lp.mixins(Ke.UT),Lp.define((({})=>({length:[m.x0,0],angle:[m.XS,0]})));class Nf extends lf{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{RectGL:e}=await Promise.resolve().then(n.bind(n,3571));this.glglyph=new e(t.regl_wrapper,this)}}_map_data(){if("data"==this.model.properties.width.units)[this.sw,this.sx0]=this._map_dist_corner_for_data_side_length(this._x,this.width,this.renderer.xscale);else{this.sw=(0,Jt.nl)(this.width);const t=this.sx.length;this.sx0=new Jt.mR(t);for(let e=0;e<t;e++)this.sx0[e]=this.sx[e]-this.sw[e]/2}if("data"==this.model.properties.height.units)[this.sh,this.sy1]=this._map_dist_corner_for_data_side_length(this._y,this.height,this.renderer.yscale);else{this.sh=(0,Jt.nl)(this.height);const t=this.sy.length;this.sy1=new Jt.mR(t);for(let e=0;e<t;e++)this.sy1[e]=this.sy[e]-this.sh[e]/2}const t=this.sw.length;this.ssemi_diag=new Jt.mR(t);for(let e=0;e<t;e++)this.ssemi_diag[e]=Math.sqrt(this.sw[e]/2*this.sw[e]/2+this.sh[e]/2*this.sh[e]/2)}_render(t,e,n){const{sx:r,sy:i,sx0:o,sy1:a,sw:s,sh:l,angle:c}=n??this;for(const n of e){const e=r[n],u=i[n],d=o[n],h=a[n],p=s[n],f=l[n],Q=c.get(n);isFinite(e+u+d+h+p+f+Q)&&0!=p&&0!=f&&(t.beginPath(),Q?(t.translate(e,u),t.rotate(Q),t.rect(-p/2,-f/2,p,f),t.rotate(-Q),t.translate(-e,-u)):t.rect(d,h,p,f),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_hit_rect(t){return this._hit_rect_against_index(t)}_hit_point(t){let{sx:e,sy:n}=t;const r=this.renderer.xscale.invert(e),i=this.renderer.yscale.invert(n),o=this.sx0.length,a=new Jt.mR(o);for(let t=0;t<o;t++)a[t]=this.sx0[t]+this.sw[t]/2;const s=new Jt.mR(o);for(let t=0;t<o;t++)s[t]=this.sy1[t]+this.sh[t]/2;const l=(0,bn.T9)(this._ddist(0,a,this.ssemi_diag)),c=(0,bn.T9)(this._ddist(1,s,this.ssemi_diag)),u=r-l,d=r+l,h=i-c,p=i+c;let f,Q;const T=[];for(const t of this.index.indices({x0:u,x1:d,y0:h,y1:p})){const r=this.angle.get(t);if(r){const i=Math.sin(-r),o=Math.cos(-r),a=o*(e-this.sx[t])-i*(n-this.sy[t])+this.sx[t],s=i*(e-this.sx[t])+o*(n-this.sy[t])+this.sy[t];e=a,n=s,f=Math.abs(this.sx[t]-e)<=this.sw[t]/2,Q=Math.abs(this.sy[t]-n)<=this.sh[t]/2}else{const r=e-this.sx0[t],i=n-this.sy1[t];f=0<=r&&r<=this.sw[t],Q=0<=i&&i<=this.sh[t]}f&&Q&&T.push(t)}return new ir({indices:T})}_map_dist_corner_for_data_side_length(t,e,n){const r=t.length,i=new Float64Array(r),o=new Float64Array(r);for(let n=0;n<r;n++){const r=t[n],a=e.get(n)/2;i[n]=r-a,o[n]=r+a}const a=n.v_compute(i),s=n.v_compute(o),l=this.sdist(n,i,e,"edge",this.model.dilate);let c=a;for(let t=0;t<r;t++){const e=a[t],n=s[t];if(!isNaN(e+n)&&e!=n){c=e<n?a:s;break}}return[l,c]}_ddist(t,e,n){const r=(0,Jt.Q9)(e,n),i=0==t?this.renderer.xscale:this.renderer.yscale,o=e,a=o.length,s=new r(a);for(let t=0;t<a;t++)s[t]=o[t]+n[t];const l=i.v_invert(o),c=i.v_invert(s),u=l.length,d=new r(u);for(let t=0;t<u;t++)d[t]=Math.abs(c[t]-l[t]);return d}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}}Nf.__name__="RectView";class Rf extends cf{constructor(t){super(t)}}Ap=Rf,Rf.__name__="Rect",Ap.prototype.default_view=Nf,Ap.define((({Boolean:t})=>({dilate:[t,!1]})));class If extends vl{_render(t,e,n){const{sx:r,sy:i,size:o,angle:a}=n??this;for(const n of e){const e=r[n],s=i[n],l=o.get(n),c=a.get(n);if(!isFinite(e+s+l+c))continue;const u=l/2;t.beginPath(),t.translate(e,s),c&&t.rotate(c),this._render_one(t,n,u,this.visuals),c&&t.rotate(-c),t.translate(-e,-s)}}_mask_data(){const{x_target:t,y_target:e}=this.renderer.plot_view.frame,n=t.widen(this.max_size).map((t=>this.renderer.xscale.invert(t))),r=e.widen(this.max_size).map((t=>this.renderer.yscale.invert(t)));return this.index.indices({x0:n.start,x1:n.end,y0:r.start,y1:r.end})}_hit_point(t){const{sx:e,sy:n}=t,{max_size:r}=this,{hit_dilation:i}=this.model,o=e-r*i,a=e+r*i,[s,l]=this.renderer.xscale.r_invert(o,a),c=n-r*i,u=n+r*i,[d,h]=this.renderer.yscale.r_invert(c,u),p=this.index.indices({x0:s,x1:l,y0:d,y1:h}),f=[];for(const t of p){const r=this.size.get(t)/2*i;Math.abs(this.sx[t]-e)<=r&&Math.abs(this.sy[t]-n)<=r&&f.push(t)}return new ir({indices:f})}_hit_span(t){const{sx:e,sy:n}=t,r=this.bounds(),i=this.max_size/2;let o,a,s,l;if("h"==t.direction){s=r.y0,l=r.y1;const t=e-i,n=e+i;[o,a]=this.renderer.xscale.r_invert(t,n)}else{o=r.x0,a=r.x1;const t=n-i,e=n+i;[s,l]=this.renderer.yscale.r_invert(t,e)}const c=[...this.index.indices({x0:o,x1:a,y0:s,y1:l})];return new ir({indices:c})}_hit_rect(t){const{sx0:e,sx1:n,sy0:r,sy1:i}=t,[o,a]=this.renderer.xscale.r_invert(e,n),[s,l]=this.renderer.yscale.r_invert(r,i),c=[...this.index.indices({x0:o,x1:a,y0:s,y1:l})];return new ir({indices:c})}_hit_poly(t){const{sx:e,sy:n}=t,r=(0,Rt.y1)(0,this.sx.length),i=[];for(let t=0,o=r.length;t<o;t++){const o=r[t];xl(this.sx[t],this.sy[t],e,n)&&i.push(o)}return new ir({indices:i})}_get_legend_args({x0:t,x1:e,y0:n,y1:r},i){const o=i+1,a=new Array(o),s=new Array(o);a[i]=(t+e)/2,s[i]=(n+r)/2;const l=.4*Math.min(Math.abs(e-t),Math.abs(r-n));return{sx:a,sy:s,size:new m.J3(l,o),angle:new m.J3(0,o)}}draw_legend_for_index(t,{x0:e,x1:n,y0:r,y1:i},o){const a=this._get_legend_args({x0:e,x1:n,y0:r,y1:i},o);this._render(t,[o],a)}}If.__name__="MarkerView";class jf extends yl{constructor(t){super(t)}}Hp=jf,jf.__name__="Marker",Hp.mixins([Ke.UT,Ke.H_,Ke.y7]),Hp.define((({Number:t})=>({size:[m.$A,{value:4}],angle:[m.XS,0],hit_dilation:[t,1]})));const zf=Math.sqrt(3),Bf=Math.sqrt(5),Ff=(Bf+1)/4,$f=Math.sqrt((5-Bf)/8),Gf=(Bf-1)/4,qf=Math.sqrt((5+Bf)/8);function Uf(t,e){t.rotate(Math.PI/4),Zf(t,e),t.rotate(-Math.PI/4)}function Wf(t,e){const n=e*zf,r=n/3;t.moveTo(-n/2,-r),t.lineTo(0,0),t.lineTo(n/2,-r),t.lineTo(0,0),t.lineTo(0,e)}function Zf(t,e){t.moveTo(0,e),t.lineTo(0,-e),t.moveTo(-e,0),t.lineTo(e,0)}function Xf(t,e){t.moveTo(0,e),t.lineTo(e/1.5,0),t.lineTo(0,-e),t.lineTo(-e/1.5,0),t.closePath()}function Kf(t,e){const n=e*zf,r=n/3;t.moveTo(-e,r),t.lineTo(e,r),t.lineTo(0,r-n),t.closePath()}function Yf(t,e,n,r){t.arc(0,0,n,0,2*Math.PI,!1),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}function Jf(t,e,n,r){Xf(t,n),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}function tQ(t,e,n,r){!function(t,e){t.beginPath(),t.arc(0,0,e/4,0,2*Math.PI,!1),t.closePath()}(t,n),r.line.set_vectorize(t,e),t.fillStyle=t.strokeStyle,t.fill()}function eQ(t,e,n,r){!function(t,e){const n=e/2,r=zf*n;t.moveTo(e,0),t.lineTo(n,-r),t.lineTo(-n,-r),t.lineTo(-e,0),t.lineTo(-n,r),t.lineTo(n,r),t.closePath()}(t,n),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}function nQ(t,e,n,r){const i=2*n;t.rect(-n,-n,i,i),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}function rQ(t,e,n,r){!function(t,e){const n=Math.sqrt(5-2*Bf)*e;t.moveTo(0,-e),t.lineTo(n*Gf,n*qf-e),t.lineTo(n*(1+Gf),n*qf-e),t.lineTo(n*(1+Gf-Ff),n*(qf+$f)-e),t.lineTo(n*(1+2*Gf-Ff),n*(2*qf+$f)-e),t.lineTo(0,2*n*qf-e),t.lineTo(-n*(1+2*Gf-Ff),n*(2*qf+$f)-e),t.lineTo(-n*(1+Gf-Ff),n*(qf+$f)-e),t.lineTo(-n*(1+Gf),n*qf-e),t.lineTo(-n*Gf,n*qf-e),t.closePath()}(t,n),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}function iQ(t,e,n,r){Kf(t,n),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)}const oQ={asterisk:function(t,e,n,r){Zf(t,n),Uf(t,n),r.line.apply(t,e)},circle:Yf,circle_cross:function(t,e,n,r){t.arc(0,0,n,0,2*Math.PI,!1),r.fill.apply(t,e),r.hatch.apply(t,e),Zf(t,n),r.line.apply(t,e)},circle_dot:function(t,e,n,r){Yf(t,e,n,r),tQ(t,e,n,r)},circle_y:function(t,e,n,r){t.arc(0,0,n,0,2*Math.PI,!1),r.fill.apply(t,e),r.hatch.apply(t,e),Wf(t,n),r.line.apply(t,e)},circle_x:function(t,e,n,r){t.arc(0,0,n,0,2*Math.PI,!1),r.fill.apply(t,e),r.hatch.apply(t,e),Uf(t,n),r.line.apply(t,e)},cross:function(t,e,n,r){Zf(t,n),r.line.apply(t,e)},diamond:Jf,diamond_dot:function(t,e,n,r){Jf(t,e,n,r),tQ(t,e,n,r)},diamond_cross:function(t,e,n,r){Xf(t,n),r.fill.apply(t,e),r.hatch.apply(t,e),t.moveTo(0,n),t.lineTo(0,-n),t.moveTo(-n/1.5,0),t.lineTo(n/1.5,0),r.line.apply(t,e)},dot:tQ,hex:eQ,hex_dot:function(t,e,n,r){eQ(t,e,n,r),tQ(t,e,n,r)},inverted_triangle:function(t,e,n,r){t.rotate(Math.PI),Kf(t,n),t.rotate(-Math.PI),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)},plus:function(t,e,n,r){const i=3*n/8,o=[i,i,n,n,i,i,-i,-i,-n,-n,-i,-i],a=[n,i,i,-i,-i,-n,-n,-i,-i,i,i,n];t.beginPath();for(let e=0;e<12;e++)t.lineTo(o[e],a[e]);t.closePath(),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)},square:nQ,square_cross:function(t,e,n,r){const i=2*n;t.rect(-n,-n,i,i),r.fill.apply(t,e),r.hatch.apply(t,e),Zf(t,n),r.line.apply(t,e)},square_dot:function(t,e,n,r){nQ(t,e,n,r),tQ(t,e,n,r)},square_pin:function(t,e,n,r){const i=3*n/8;t.moveTo(-n,-n),t.quadraticCurveTo(0,-i,n,-n),t.quadraticCurveTo(i,0,n,n),t.quadraticCurveTo(0,i,-n,n),t.quadraticCurveTo(-i,0,-n,-n),t.closePath(),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)},square_x:function(t,e,n,r){const i=2*n;t.rect(-n,-n,i,i),r.fill.apply(t,e),r.hatch.apply(t,e),t.moveTo(-n,n),t.lineTo(n,-n),t.moveTo(-n,-n),t.lineTo(n,n),r.line.apply(t,e)},star:rQ,star_dot:function(t,e,n,r){rQ(t,e,n,r),tQ(t,e,n,r)},triangle:iQ,triangle_dot:function(t,e,n,r){iQ(t,e,n,r),tQ(t,e,n,r)},triangle_pin:function(t,e,n,r){const i=n*zf,o=i/3,a=3*o/8;t.moveTo(-n,o),t.quadraticCurveTo(0,a,n,o),t.quadraticCurveTo(zf*a/2,a/2,0,o-i),t.quadraticCurveTo(-zf*a/2,a/2,-n,o),t.closePath(),r.fill.apply(t,e),r.hatch.apply(t,e),r.line.apply(t,e)},dash:function(t,e,n,r){!function(t,e){t.moveTo(-e,0),t.lineTo(e,0)}(t,n),r.line.apply(t,e)},x:function(t,e,n,r){Uf(t,n),r.line.apply(t,e)},y:function(t,e,n,r){Wf(t,n),r.line.apply(t,e)}};var aQ,sQ,lQ,cQ,uQ,dQ,hQ,pQ,fQ,QQ,TQ,mQ;class gQ extends If{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{MultiMarkerGL:e}=await Promise.resolve().then(n.bind(n,9485));this.glglyph=new e(t.regl_wrapper,this)}}_render(t,e,n){const{sx:r,sy:i,size:o,angle:a,marker:s}=n??this;for(const n of e){const e=r[n],l=i[n],c=o.get(n),u=a.get(n),d=s.get(n);if(!isFinite(e+l+c+u)||null==d)continue;const h=c/2;t.beginPath(),t.translate(e,l),u&&t.rotate(u),oQ[d](t,n,h,this.visuals),u&&t.rotate(-u),t.translate(-e,-l)}}draw_legend_for_index(t,{x0:e,x1:n,y0:r,y1:i},o){const a=o+1,s=this.marker.get(o),l={...this._get_legend_args({x0:e,x1:n,y0:r,y1:i},o),marker:new m.J3(s,a)};this._render(t,[o],l)}}gQ.__name__="ScatterView";class _Q extends jf{constructor(t){super(t)}}aQ=_Q,_Q.__name__="Scatter",aQ.prototype.default_view=gQ,aQ.define((()=>({marker:[m.Qj,{value:"circle"}]})));class bQ extends ul{_project_data(){yi.project_xy(this._x0,this._y0),yi.project_xy(this._x1,this._y1)}_index_data(t){const{min:e,max:n}=Math,{_x0:r,_x1:i,_y0:o,_y1:a,data_size:s}=this;for(let l=0;l<s;l++){const s=r[l],c=i[l],u=o[l],d=a[l];t.add_rect(e(s,c),e(u,d),n(s,c),n(u,d))}}_render(t,e,n){if(!this.visuals.line.doit)return;const{sx0:r,sy0:i,sx1:o,sy1:a}=n??this;for(const n of e){const e=r[n],s=i[n],l=o[n],c=a[n];isFinite(e+s+l+c)&&(this._render_decorations(t,n,e,s,l,c),t.beginPath(),t.moveTo(e,s),t.lineTo(l,c),this.visuals.line.apply(t,n))}}_render_decorations(t,e,n,r,i,o){const{PI:a}=Math,s=(0,Gi.FP)([n,r],[i,o])+a/2;for(const l of this.decorations.values())t.save(),"start"==l.model.node?(t.translate(n,r),t.rotate(s+a)):"end"==l.model.node&&(t.translate(i,o),t.rotate(s)),l.marking.render(t,e),t.restore()}_hit_point(t){const{sx:e,sy:n}=t,r={x:e,y:n},[i,o]=this.renderer.xscale.r_invert(e-2,e+2),[a,s]=this.renderer.yscale.r_invert(n-2,n+2),l=this.index.indices({x0:i,y0:a,x1:o,y1:s}),c=[];for(const t of l){const e=Math.max(2,this.line_width.get(t)/2)**2;Al(r,{x:this.sx0[t],y:this.sy0[t]},{x:this.sx1[t],y:this.sy1[t]})<e&&c.push(t)}return new ir({indices:c})}_hit_span(t){const[e,n]=this.renderer.plot_view.frame.bbox.ranges,{sx:r,sy:i}=t;let o,a,s;"v"==t.direction?(s=this.renderer.yscale.invert(i),[o,a]=[this._y0,this._y1]):(s=this.renderer.xscale.invert(r),[o,a]=[this._x0,this._x1]);const l=[],[c,u]=this.renderer.xscale.r_invert(e.start,e.end),[d,h]=this.renderer.yscale.r_invert(n.start,n.end),p=this.index.indices({x0:c,y0:d,x1:u,y1:h});for(const e of p){(o[e]<=s&&s<=a[e]||a[e]<=s&&s<=o[e])&&l.push(e);const n=1.5+this.line_width.get(e)/2;o[e]==a[e]&&("h"==t.direction?Math.abs(this.sx0[e]-r)<=n&&l.push(e):Math.abs(this.sy0[e]-i)<=n&&l.push(e))}return new ir({indices:l})}scenterxy(t){return[this.sx0[t]/2+this.sx1[t]/2,this.sy0[t]/2+this.sy1[t]/2]}draw_legend_for_index(t,e,n){Ml(this.visuals,t,e,n)}}bQ.__name__="SegmentView";class vQ extends dl{constructor(t){super(t)}}sQ=vQ,vQ.__name__="Segment",sQ.prototype.default_view=bQ,sQ.define((({})=>({x0:[m.up,{field:"x0"}],y0:[m.fZ,{field:"y0"}],x1:[m.up,{field:"x1"}],y1:[m.fZ,{field:"y1"}]}))),sQ.mixins(Ke.UT);class yQ extends vl{_set_data(){const{tension:t,closed:e}=this.model;[this._xt,this._yt]=function(t,e,n=10,r=.5,i=!1){(0,_.vA)(t.length==e.length);const o=t.length,a=i?o+1:o,s=(0,Jt.Q9)(t,e),l=new s(a+2),c=new s(a+2);l.set(t,1),c.set(e,1),i?(l[0]=t[o-1],c[0]=e[o-1],l[a]=t[0],c[a]=e[0],l[a+1]=t[1],c[a+1]=e[1]):(l[0]=t[0],c[0]=e[0],l[a+1]=t[o-1],c[a+1]=e[o-1]);const u=new s(4*(n+1));for(let t=0,e=0;t<=n;t++){const r=t/n,i=r**2,o=r*i;u[e++]=2*o-3*i+1,u[e++]=-2*o+3*i,u[e++]=o-2*i+r,u[e++]=o-i}const d=new s((a-1)*(n+1)),h=new s((a-1)*(n+1));for(let t=1,e=0;t<a;t++){const i=(l[t+1]-l[t-1])*r,o=(c[t+1]-c[t-1])*r,a=(l[t+2]-l[t])*r,s=(c[t+2]-c[t])*r;for(let r=0;r<=4*n;e++){const n=u[r++],p=u[r++],f=u[r++],Q=u[r++];d[e]=n*l[t]+p*l[t+1]+f*i+Q*a,h[e]=n*c[t]+p*c[t+1]+f*o+Q*s}}return[d,h]}(this._x,this._y,20,t,e)}_map_data(){const{x_scale:t,y_scale:e}=this.renderer.coordinates;this.sxt=t.v_compute(this._xt),this.syt=e.v_compute(this._yt)}_render(t,e,n){const{sxt:r,syt:i}=n??this;let o=!0;t.beginPath();const a=r.length;for(let e=0;e<a;e++){const n=r[e],a=i[e];isFinite(n+a)?o?(t.moveTo(n,a),o=!1):t.lineTo(n,a):o=!0}this.visuals.line.set_value(t),t.stroke()}}yQ.__name__="SplineView";class xQ extends yl{constructor(t){super(t)}}lQ=xQ,xQ.__name__="Spline",lQ.prototype.default_view=yQ,lQ.mixins(Ke.Rb),lQ.define((({Boolean:t,Number:e})=>({tension:[e,.5],closed:[t,!1]})));class wQ extends vl{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{StepGL:e}=await Promise.resolve().then(n.bind(n,2019));this.glglyph=new e(t.regl_wrapper,this)}}_render(t,e,n){const r=e.length;if(r<2)return;const{sx:i,sy:o}=n??this,a=this.model.mode;this.visuals.line.set_value(t);let s=!1,l=!1;const c=e[0];let u=isFinite(i[c]+o[c]);"center"==a&&(s=this._render_xy(t,s,u?i[c]:NaN,o[c]));for(const n of e){const e=isFinite(i[n+1]+o[n+1]);switch(a){case"before":s=this._render_xy(t,s,u?i[n]:NaN,o[n]),n<i.length-1&&(s=this._render_xy(t,s,u&&e?i[n]:NaN,o[n+1]));break;case"after":s=this._render_xy(t,s,u?i[n]:NaN,o[n]),n<i.length-1&&(s=this._render_xy(t,s,u&&e?i[n+1]:NaN,o[n]));break;case"center":if(u&&e){const e=(i[n]+i[n+1])/2;s=this._render_xy(t,s,e,o[n]),s=this._render_xy(t,s,e,o[n+1])}else l&&(s=this._render_xy(t,s,u?i[n]:NaN,o[n])),s=this._render_xy(t,s,e?i[n+1]:NaN,o[n+1]);break;default:(0,_.HB)()}l=u,u=e}if(s){const n=e[r-1];this._render_xy(t,s,u?i[n]:NaN,o[n])&&t.stroke()}}_render_xy(t,e,n,r){return isFinite(n+r)?e?t.lineTo(n,r):(t.beginPath(),t.moveTo(n,r),e=!0):e&&(t.stroke(),e=!1),e}draw_legend_for_index(t,e,n){kl(this.visuals,t,e)}}wQ.__name__="StepView";class LQ extends yl{constructor(t){super(t)}}cQ=LQ,LQ.__name__="Step",cQ.prototype.default_view=wQ,cQ.mixins(Ke.Rb),cQ.define((()=>({mode:[_n.CY,"before"]})));class AQ extends vl{_set_data(t){super._set_data(t),this.labels=Array.from(this.text,(t=>null!=t?new ko({text:`${t}`}):null))}_render(t,e,n){const{sx:r,sy:i,x_offset:o,y_offset:a,angle:s,labels:l}=n??this;for(const n of e){const e=r[n],c=i[n],u=o.get(n),d=a.get(n),h=s.get(n),p=l[n];isFinite(e+c+u+d+h)&&null!=p&&this.visuals.text.v_doit(n)&&(p.visuals=this.visuals.text.values(n),p.position={sx:e+u,sy:c+d},p.angle=h,p.align="auto",p.paint(t))}}_hit_point(t){const{sx:e,sy:n}=t,r=[];let i=0;for(const t of this.labels){if(null!=t){const{p0:o,p1:a,p2:s,p3:l}=t.rect();xl(e,n,[o.x,a.x,s.x,l.x],[o.y,a.y,s.y,l.y])&&r.push(i)}i+=1}return new ir({indices:r})}scenterxy(t){const e=this.labels[t];(0,_.vA)(null!=e);const{p0:n,p1:r,p2:i,p3:o}=e.rect();return[(n.x+r.x+i.x+o.x)/4,(n.y+r.y+i.y+o.y)/4]}}AQ.__name__="TextView";class HQ extends yl{constructor(t){super(t)}}uQ=HQ,HQ.__name__="Text",uQ.prototype.default_view=AQ,uQ.mixins(Ke.Dt),uQ.define((({})=>({text:[m.C1,{field:"text"}],angle:[m.XS,0],x_offset:[m.fY,0],y_offset:[m.fY,0]})));class kQ extends ef{async lazy_initialize(){await super.lazy_initialize();const{webgl:t}=this.renderer.plot_view.canvas_view;if(null!=t&&t.regl_wrapper.has_webgl){const{LRTBGL:e}=await Promise.resolve().then(n.bind(n,1897));this.glglyph=new e(t.regl_wrapper,this)}}scenterxy(t){return[this.sx[t],(this.stop[t]+this.sbottom[t])/2]}_lrtb(t){const e=this.width.get(t)/2,n=this._x[t],r=this._top[t],i=this._bottom[t];return[n-e,n+e,Math.max(r,i),Math.min(r,i)]}_map_data(){this.sx=this.renderer.xscale.v_compute(this._x),this.sw=this.sdist(this.renderer.xscale,this._x,this.width,"center"),this.stop=this.renderer.yscale.v_compute(this._top),this.sbottom=this.renderer.yscale.v_compute(this._bottom);const t=this.sx.length;this.sleft=new Jt.mR(t),this.sright=new Jt.mR(t);for(let e=0;e<t;e++)this.sleft[e]=this.sx[e]-this.sw[e]/2,this.sright[e]=this.sx[e]+this.sw[e]/2;this._clamp_viewport()}}kQ.__name__="VBarView";class MQ extends nf{constructor(t){super(t)}}dQ=MQ,MQ.__name__="VBar",dQ.prototype.default_view=kQ,dQ.define((({})=>({x:[m.up,{field:"x"}],bottom:[m.fZ,{value:0}],width:[m.fY,{value:1}],top:[m.fZ,{field:"top"}]})));class CQ extends vl{_map_data(){"data"==this.model.properties.radius.units?this.sradius=this.sdist(this.renderer.xscale,this._x,this.radius):this.sradius=(0,Jt.nl)(this.radius),this.max_sradius=(0,bn.T9)(this.sradius)}_render(t,e,n){const{sx:r,sy:i,sradius:o,start_angle:a,end_angle:s}=n??this,l="anticlock"==this.model.direction;for(const n of e){const e=r[n],c=i[n],u=o[n],d=a.get(n),h=s.get(n);isFinite(e+c+u+d+h)&&(t.beginPath(),t.arc(e,c,u,d,h,l),t.lineTo(e,c),t.closePath(),this.visuals.fill.apply(t,n),this.visuals.hatch.apply(t,n),this.visuals.line.apply(t,n))}}_hit_point(t){let e,n,r,i,o;const{sx:a,sy:s}=t,l=this.renderer.xscale.invert(a),c=this.renderer.yscale.invert(s);n=a-this.max_sradius,r=a+this.max_sradius;const[u,d]=this.renderer.xscale.r_invert(n,r);i=s-this.max_sradius,o=s+this.max_sradius;const[h,p]=this.renderer.yscale.r_invert(i,o),f=[];for(const t of this.index.indices({x0:u,x1:d,y0:h,y1:p})){const a=this.sradius[t]**2;[n,r]=this.renderer.xscale.r_compute(l,this._x[t]),[i,o]=this.renderer.yscale.r_compute(c,this._y[t]),e=(n-r)**2+(i-o)**2,e<=a&&f.push(t)}const Q="anticlock"==this.model.direction,T=[];for(const t of f){const e=Math.atan2(s-this.sy[t],a-this.sx[t]);(Math.abs(this.start_angle.get(t)-this.end_angle.get(t))>=2*Math.PI||(0,Gi.Hc)(-e,-this.start_angle.get(t),-this.end_angle.get(t),Q))&&T.push(t)}return new ir({indices:T})}draw_legend_for_index(t,e,n){Sl(this.visuals,t,e,n)}scenterxy(t){const e=this.sradius[t]/2,n=(this.start_angle.get(t)+this.end_angle.get(t))/2;return[this.sx[t]+e*Math.cos(n),this.sy[t]+e*Math.sin(n)]}}CQ.__name__="WedgeView";class SQ extends yl{constructor(t){super(t)}}hQ=SQ,SQ.__name__="Wedge",hQ.prototype.default_view=CQ,hQ.mixins([Ke.UT,Ke.H_,Ke.y7]),hQ.define((({})=>({direction:[_n.OP,"anticlock"],radius:[m.x0,{field:"radius"}],start_angle:[m.XS,{field:"start_angle"}],end_angle:[m.XS,{field:"end_angle"}]})));class EQ extends qt{constructor(t){super(t)}_hit_test(t,e,n){if(!e.model.visible)return null;const r=n.glyph.hit_test(t);return null==r?null:n.model.view.convert_selection_from_subset(r)}}EQ.__name__="GraphHitTestPolicy";class VQ extends EQ{constructor(t){super(t)}hit_test(t,e){return this._hit_test(t,e,e.edge_view)}do_selection(t,e,n,r){if(null==t)return!1;const i=e.edge_renderer.data_source.selected;return i.update(t,n,r),e.edge_renderer.data_source._select.emit(),!i.is_empty()}do_inspection(t,e,n,r,i){if(null==t)return!1;const{edge_renderer:o}=n.model,a=o.get_selection_manager().get_or_create_inspector(n.edge_view.model);return a.update(t,r,i),n.edge_view.model.data_source.setv({inspected:a},{silent:!0}),n.edge_view.model.data_source.inspect.emit([n.edge_view.model,{geometry:e}]),!a.is_empty()}}VQ.__name__="EdgesOnly";class OQ extends EQ{constructor(t){super(t)}hit_test(t,e){return this._hit_test(t,e,e.node_view)}do_selection(t,e,n,r){if(null==t)return!1;const i=e.node_renderer.data_source.selected;return i.update(t,n,r),e.node_renderer.data_source._select.emit(),!i.is_empty()}do_inspection(t,e,n,r,i){if(null==t)return!1;const{node_renderer:o}=n.model,a=o.get_selection_manager().get_or_create_inspector(n.node_view.model);return a.update(t,r,i),n.node_view.model.data_source.setv({inspected:a},{silent:!0}),n.node_view.model.data_source.inspect.emit([n.node_view.model,{geometry:e}]),!a.is_empty()}}OQ.__name__="NodesOnly";class PQ extends EQ{constructor(t){super(t)}hit_test(t,e){return this._hit_test(t,e,e.node_view)}get_linked_edges(t,e,n){let r=[];"selection"==n?r=t.selected.indices.map((e=>t.data.index[e])):"inspection"==n&&(r=t.inspected.indices.map((e=>t.data.index[e])));const i=[];for(let t=0;t<e.data.start.length;t++)((0,Rt.gR)(r,e.data.start[t])||(0,Rt.gR)(r,e.data.end[t]))&&i.push(t);const o=new ir;for(const t of i)o.multiline_indices[t]=[0];return o.indices=i,o}do_selection(t,e,n,r){if(null==t)return!1;const i=e.node_renderer.data_source.selected;i.update(t,n,r);const o=e.edge_renderer.data_source.selected,a=this.get_linked_edges(e.node_renderer.data_source,e.edge_renderer.data_source,"selection");return o.update(a,n,r),e.node_renderer.data_source._select.emit(),!i.is_empty()}do_inspection(t,e,n,r,i){if(null==t)return!1;const o=n.node_view.model.data_source.selection_manager.get_or_create_inspector(n.node_view.model);o.update(t,r,i),n.node_view.model.data_source.setv({inspected:o},{silent:!0});const a=n.edge_view.model.data_source.selection_manager.get_or_create_inspector(n.edge_view.model),s=this.get_linked_edges(n.node_view.model.data_source,n.edge_view.model.data_source,"inspection");return a.update(s,r,i),n.edge_view.model.data_source.setv({inspected:a},{silent:!0}),n.node_view.model.data_source.inspect.emit([n.node_view.model,{geometry:e}]),!o.is_empty()}}PQ.__name__="NodesAndLinkedEdges";class DQ extends EQ{constructor(t){super(t)}hit_test(t,e){return this._hit_test(t,e,e.edge_view)}get_linked_nodes(t,e,n){let r=[];"selection"==n?r=e.selected.indices:"inspection"==n&&(r=e.inspected.indices);const i=[];for(const t of r)i.push(e.data.start[t]),i.push(e.data.end[t]);const o=(0,Rt.sb)(i).map((e=>(0,bn.qh)(t.data.index,e)));return new ir({indices:o})}do_selection(t,e,n,r){if(null==t)return!1;const i=e.edge_renderer.data_source.selected;i.update(t,n,r);const o=e.node_renderer.data_source.selected,a=this.get_linked_nodes(e.node_renderer.data_source,e.edge_renderer.data_source,"selection");return o.update(a,n,r),e.edge_renderer.data_source._select.emit(),!i.is_empty()}do_inspection(t,e,n,r,i){if(null==t)return!1;const o=n.edge_view.model.data_source.selection_manager.get_or_create_inspector(n.edge_view.model);o.update(t,r,i),n.edge_view.model.data_source.setv({inspected:o},{silent:!0});const a=n.node_view.model.data_source.selection_manager.get_or_create_inspector(n.node_view.model),s=this.get_linked_nodes(n.node_view.model.data_source,n.edge_view.model.data_source,"inspection");return a.update(s,r,i),n.node_view.model.data_source.setv({inspected:a},{silent:!0}),n.edge_view.model.data_source.inspect.emit([n.edge_view.model,{geometry:e}]),!o.is_empty()}}DQ.__name__="EdgesAndLinkedNodes";class NQ extends EQ{constructor(t){super(t)}hit_test(t,e){return this._hit_test(t,e,e.node_view)}get_adjacent_nodes(t,e,n){let r=[];"selection"==n?r=t.selected.indices.map((e=>t.data.index[e])):"inspection"==n&&(r=t.inspected.indices.map((e=>t.data.index[e])));const i=[],o=[];for(let t=0;t<e.data.start.length;t++)(0,Rt.gR)(r,e.data.start[t])&&(i.push(e.data.end[t]),o.push(e.data.start[t])),(0,Rt.gR)(r,e.data.end[t])&&(i.push(e.data.start[t]),o.push(e.data.end[t]));for(let t=0;t<o.length;t++)i.push(o[t]);const a=(0,Rt.sb)(i).map((e=>(0,bn.qh)(t.data.index,e)));return new ir({indices:a})}do_selection(t,e,n,r){if(null==t)return!1;const i=e.node_renderer.data_source.selected;i.update(t,n,r);const o=this.get_adjacent_nodes(e.node_renderer.data_source,e.edge_renderer.data_source,"selection");return o.is_empty()||i.update(o,n,r),e.node_renderer.data_source._select.emit(),!i.is_empty()}do_inspection(t,e,n,r,i){if(null==t)return!1;const o=n.node_view.model.data_source.selection_manager.get_or_create_inspector(n.node_view.model);o.update(t,r,i),n.node_view.model.data_source.setv({inspected:o},{silent:!0});const a=this.get_adjacent_nodes(n.node_view.model.data_source,n.edge_view.model.data_source,"inspection");return a.is_empty()||(o.update(a,r,i),n.node_view.model.data_source.setv({inspected:o},{silent:!0})),n.node_view.model.data_source.inspect.emit([n.node_view.model,{geometry:e}]),!o.is_empty()}}NQ.__name__="NodesAndAdjacentNodes";class RQ extends qt{constructor(t){super(t)}get node_coordinates(){return new jQ({layout:this})}get edge_coordinates(){return new zQ({layout:this})}}RQ.__name__="LayoutProvider";class IQ extends Vp{constructor(t){super(t)}}pQ=IQ,IQ.__name__="GraphCoordinates",pQ.define((({Ref:t})=>({layout:[t(RQ)]})));class jQ extends IQ{constructor(t){super(t)}_v_compute(t){const[e,n]=this.layout.get_node_coordinates(t);return{x:e,y:n}}}jQ.__name__="NodeCoordinates";class zQ extends IQ{constructor(t){super(t)}_v_compute(t){const[e,n]=this.layout.get_edge_coordinates(t);return{x:e,y:n}}}zQ.__name__="EdgeCoordinates";class BQ extends RQ{constructor(t){super(t)}get_node_coordinates(t){const e=new Q.Bi(t.data).get("index")??[],n=e.length,r=new Float64Array(n),i=new Float64Array(n),{graph_layout:o}=this;for(let t=0;t<n;t++){const n=e[t],[a,s]=o.get(n)??[NaN,NaN];r[t]=a,i[t]=s}return[r,i]}get_edge_coordinates(t){const e=new Q.Bi(t.data),n=e.get("start")??[],r=e.get("end")??[],i=Math.min(n.length,r.length),o=[],a=[],s=e.get("xs"),l=e.get("ys"),c=null!=s&&null!=l,{graph_layout:u}=this;for(let t=0;t<i;t++){const e=u.has(n[t])&&u.has(r[t]);if(c&&e)o.push(s[t]),a.push(l[t]);else{const e=u.get(n[t])??[NaN,NaN],i=u.get(r[t])??[NaN,NaN];o.push([e[0],i[0]]),a.push([e[1],i[1]])}}return[o,a]}}fQ=BQ,BQ.__name__="StaticLayoutProvider",fQ.define((({Number:t,Int:e,Arrayable:n,Map:r})=>({graph_layout:[r(e,n(t)),new globalThis.Map]})));class FQ extends la{_render(){const t=this.layer.ctx;t.save(),this._draw_regions(t),this._draw_minor_grids(t),this._draw_grids(t),t.restore()}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render()))}_draw_regions(t){if(!this.visuals.band_fill.doit&&!this.visuals.band_hatch.doit)return;const[e,n]=this.grid_coords("major",!1);for(let r=0;r<e.length-1;r++){if(r%2!=1)continue;const[i,o]=this.coordinates.map_to_screen(e[r],n[r]),[a,s]=this.coordinates.map_to_screen(e[r+1],n[r+1]);t.beginPath(),t.rect(i[0],o[0],a[1]-i[0],s[1]-o[0]),this.visuals.band_fill.apply(t),this.visuals.band_hatch.apply(t)}}_draw_grids(t){if(!this.visuals.grid_line.doit)return;const[e,n]=this.grid_coords("major");this._draw_grid_helper(t,this.visuals.grid_line,e,n)}_draw_minor_grids(t){if(!this.visuals.minor_grid_line.doit)return;const[e,n]=this.grid_coords("minor");this._draw_grid_helper(t,this.visuals.minor_grid_line,e,n)}_draw_grid_helper(t,e,n,r){e.set_value(t),t.beginPath();for(let e=0;e<n.length;e++){const[i,o]=this.coordinates.map_to_screen(n[e],r[e]);t.moveTo(Math.round(i[0]),Math.round(o[0]));for(let e=1;e<i.length;e++)t.lineTo(Math.round(i[e]),Math.round(o[e]))}t.stroke()}ranges(){const t=this.model.dimension,e=1-t,{ranges:n}=this.coordinates;return[n[t],n[e]]}computed_bounds(){const[t]=this.ranges(),e=this.model.bounds,n=[t.min,t.max];let r,i;if((0,f.cy)(e))r=Math.min(e[0],e[1]),i=Math.max(e[0],e[1]),r<n[0]&&(r=n[0]),i>n[1]&&(i=n[1]);else{[r,i]=n;for(const t of this.plot_view.axis_views)t.dimension==this.model.dimension&&t.model.x_range_name==this.model.x_range_name&&t.model.y_range_name==this.model.y_range_name&&([r,i]=t.computed_bounds)}return[r,i]}grid_coords(t,e=!0){const n=this.model.dimension,r=1-n,[i,o]=this.ranges(),[a,s]=(()=>{const[t,e]=this.computed_bounds();return[Math.min(t,e),Math.max(t,e)]})(),l=[[],[]],c=this.model.get_ticker();if(null==c)return l;const u=c.get_ticks(a,s,i,o.min)[t],d=i.min,h=i.max,[p,f]=(()=>{const{cross_bounds:t}=this.model;return"auto"==t?[o.min,o.max]:t})();e||(u[0]!=d&&u.splice(0,0,d),u[u.length-1]!=h&&u.push(h));for(let t=0;t<u.length;t++){if((u[t]==d||u[t]==h)&&e)continue;const i=[],o=[],a=2;for(let e=0;e<a;e++){const n=p+(f-p)/(a-1)*e;i.push(u[t]),o.push(n)}l[n].push(i),l[r].push(o)}return l}}FQ.__name__="GridView";class $Q extends ca{constructor(t){super(t)}get_ticker(){return null!=this.ticker?this.ticker:null!=this.axis?this.axis.ticker:null}}QQ=$Q,$Q.__name__="Grid",QQ.prototype.default_view=FQ,QQ.mixins([["grid_",Ke.N1],["minor_grid_",Ke.N1],["band_",Ke.SQ],["band_",Ke.LD]]),QQ.define((({Number:t,Auto:e,Enum:n,Ref:r,Tuple:i,Or:o,Nullable:a})=>({bounds:[o(i(t,t),e),"auto"],cross_bounds:[o(i(t,t),e),"auto"],dimension:[n(0,1),0],axis:[a(r(ga)),null],ticker:[a(r(ua)),null]}))),QQ.override({level:"underlay",band_fill_color:null,band_fill_alpha:0,grid_line_color:"#e5e5e5",minor_grid_line_color:null});class GQ extends Uu{styles(){return[...super.styles(),od,pd]}}GQ.__name__="MenuItemView";class qQ extends Wu{constructor(t){super(t)}}qQ.__name__="MenuItem",class extends Uu{constructor(){super(...arguments),this.items=new Map}styles(){return[...super.styles(),od]}*children(){yield*super.children(),yield*this.items.values()}async lazy_initialize(){await super.lazy_initialize(),await Ge(this.items,this.model.items)}remove(){qe(this.items),super.remove()}render(){super.render(),this.el.classList.add(r[this.model.orientation]);const t=(()=>{const{items:t,reversed:e}=this.model,n=e?(0,On.BE)(t):t;return(0,On.Tj)(n,(t=>this.items.get(t)))})();for(const e of t)e.render(),this.shadow_el.appendChild(e.el)}}.__name__="MenuView";class UQ extends Wu{constructor(t){super(t)}}TQ=UQ,UQ.__name__="Menu",TQ.define((({Boolean:t,Array:e,Ref:n})=>({items:[e(n(qQ)),[]],reversed:[t,!1],orientation:[_n.t4,"vertical"]})));class WQ extends Uu{constructor(){super(...arguments),this._child_views=new Map,this.mouseenter=new T.HN(this,"mouseenter"),this.mouseleave=new T.HN(this,"mouseleave"),this.disabled=new T.HN(this,"disabled"),this._resized=!1,this._auto_width="fit-content",this._auto_height="fit-content"}get is_layout_root(){return this.is_root||!(this.parent instanceof WQ)}_after_resize(){this._resized=!0,super._after_resize(),this.compute_layout()}async lazy_initialize(){await super.lazy_initialize(),await this.build_child_views()}remove(){for(const t of this.child_views)t.remove();this._child_views.clear(),super.remove()}connect_signals(){super.connect_signals(),this.el.addEventListener("mouseenter",(t=>{this.mouseenter.emit(t)})),this.el.addEventListener("mouseleave",(t=>{this.mouseleave.emit(t)})),this.el.addEventListener("contextmenu",(t=>{null!=this.model.context_menu&&(console.log("context menu"),t.preventDefault())})),this.parent instanceof WQ&&this.connect(this.parent.disabled,(t=>{this.disabled.emit(t||this.model.disabled)}));const t=this.model.properties;this.on_change(t.disabled,(()=>{this.disabled.emit(this.model.disabled)})),this.on_change([t.width,t.height,t.min_width,t.min_height,t.max_width,t.max_height,t.margin,t.width_policy,t.height_policy,t.flow_mode,t.sizing_mode,t.aspect_ratio,t.visible],(()=>this.invalidate_layout())),this.on_change([t.css_classes,t.stylesheets],(()=>this.invalidate_render()))}css_classes(){return[...super.css_classes(),...this.model.css_classes]}*children(){yield*super.children(),yield*this.child_views}get child_views(){return this.child_models.map((t=>this._child_views.get(t)))}get layoutable_views(){return this.child_views.filter((t=>t instanceof WQ))}async build_child_views(){const{created:t,removed:e}=await Ge(this._child_views,this.child_models,{parent:this});for(const t of e)this._resize_observer.unobserve(t.el);for(const e of t)this._resize_observer.observe(e.el,{box:"border-box"});return t}render(){super.render(),this.class_list.add(...this.css_classes());for(const t of this.child_views)this.shadow_el.appendChild(t.el),t.render(),t.after_render()}_update_children(){}async update_children(){const t=new Set(await this.build_child_views());if(0!=t.size){for(const t of this.child_views)Le(t.el);for(const e of this.child_views)this.shadow_el.append(e.el),t.has(e)&&(e.render(),e.after_render())}this._update_children(),this.invalidate_layout()}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"flow"}}_update_layout(){function t(t,e,n){switch(t){case"auto":return null!=e?Re(e):n;case"fixed":return null!=e?Re(e):"fit-content";case"fit":return"fit-content";case"min":return"min-content";case"max":return"100%"}}function e(t){return(0,f.Et)(t)?Re(t):`${t.percent}%`}const n={},r=this._intrinsic_display();n.display=function(t){const{inner:e,outer:n}=t;switch(`${e} ${n}`){case"block flow":return"block";case"inline flow":return"inline";case"block flow-root":return"flow-root";case"inline flow-root":return"inline-block";case"block flex":return"flex";case"inline flex":return"inline-flex";case"block grid":return"grid";case"inline grid":return"inline-grid";case"block table":return"table";case"inline table":return"inline-table";default:(0,_.HB)()}}(r);const i=this.box_sizing(),{width_policy:o,height_policy:a,width:s,height:l,aspect_ratio:c}=i,u=(()=>{if("auto"==c){if(null!=s&&null!=l)return s/l}else if((0,f.Et)(c))return c;return null})();"auto"==c?n.aspect_ratio=null!=s&&null!=l?`${s} / ${l}`:"auto":(0,f.Et)(c)&&(n.aspect_ratio=`${c}`);const[d,h]=(()=>{const e=t(o,s,this._auto_width),n=t(a,l,this._auto_height);if(null!=c){if(o!=a)return"fixed"==o?[e,"auto"]:"fixed"==a?["auto",n]:"max"==o?[e,"auto"]:"max"==a?["auto",n]:["auto","auto"];if("fixed"!=o&&"fixed"!=a&&null!=u)return u>=1?[e,"auto"]:["auto",n]}return[e,n]})();n.width=d,n.height=h;const{min_width:p,max_width:Q}=this.model,{min_height:T,max_height:m}=this.model;n.min_width=null==p?"0px":e(p),n.min_height=null==T?"0px":e(T),this.is_layout_root?(null!=Q&&(n.max_width=e(Q)),null!=m&&(n.max_height=e(m))):(null!=Q?n.max_width=`min(${e(Q)}, 100%)`:"fixed"!=o&&(n.max_width="100%"),null!=m?n.max_height=`min(${e(m)}, 100%)`:"fixed"!=a&&(n.max_height="100%"));const{margin:g}=this.model;if(null!=g)if((0,f.Et)(g))n.margin=Re(g);else if(2==g.length){const[t,e]=g;n.margin=`${Re(t)} ${Re(e)}`}else{const[t,e,r,i]=g;n.margin=`${Re(t)} ${Re(e)} ${Re(r)} ${Re(i)}`}const{resizable:b}=this.model;if(!1!==b){const t=(()=>{switch(b){case"width":return"horizontal";case"height":return"vertical";case!0:case"both":return"both"}})();n.resize=t,n.overflow="auto"}this.style.append(":host",n)}update_layout(){this.update_style();for(const t of this.layoutable_views)t.update_layout();this._update_layout()}get is_managed(){return this.parent instanceof WQ}_measure_layout(){}measure_layout(){for(const t of this.layoutable_views)t.measure_layout();this._measure_layout()}compute_layout(){this.parent instanceof WQ?this.parent.compute_layout():(this.measure_layout(),this.update_bbox(),this._compute_layout(),this.after_layout())}_compute_layout(){if(null!=this.layout){this.layout.compute(this.bbox.size);for(const t of this.layoutable_views)null==t.layout?t._compute_layout():t._propagate_layout()}else for(const t of this.layoutable_views)t._compute_layout()}_propagate_layout(){for(const t of this.layoutable_views)null==t.layout&&t._compute_layout()}update_bbox(){for(const t of this.child_views)t.update_bbox();super.update_bbox(),null!=this.layout&&(this.layout.visible=this.is_displayed)}_after_layout(){}after_layout(){for(const t of this.layoutable_views)t.after_layout();this._after_layout()}render_to(t){t.appendChild(this.el),this.build(),this.notify_finished()}after_render(){this.is_managed||this.invalidate_layout(),this._has_finished||(this.is_displayed?(0,Xt.v6)().then((()=>{this._resized||this.finish()})):this.finish())}build(){if(!this.is_layout_root)throw new Error(`${this.toString()} is not a root layout`);return this.render(),this.after_render(),this}async rebuild(){await this.build_child_views(),this.invalidate_render()}invalidate_layout(){this.parent instanceof WQ?this.parent.invalidate_layout():(this.update_layout(),this.compute_layout())}invalidate_render(){this.render(),this.invalidate_layout()}has_finished(){if(!super.has_finished())return!1;for(const t of this.child_views)if(!t.has_finished())return!1;return!0}box_sizing(){let{width_policy:t,height_policy:e,aspect_ratio:n}=this.model;const{sizing_mode:r}=this.model;if(null!=r)if("inherit"==r){if(this.parent instanceof WQ){const r=this.parent.box_sizing();t=r.width_policy,e=r.height_policy,null==n&&(n=r.aspect_ratio)}}else if("fixed"==r)t=e="fixed";else if("stretch_both"==r)t=e="max";else if("stretch_width"==r)t="max";else if("stretch_height"==r)e="max";else switch(null==n&&(n="auto"),r){case"scale_width":t="max",e="min";break;case"scale_height":t="min",e="max";break;case"scale_both":t="max",e="max"}const[i,o]=(()=>{const{align:t}=this.model;return"auto"==t?[void 0,void 0]:(0,f.cy)(t)?t:[t,t]})(),{width:a,height:s}=this.model;return{width_policy:t,height_policy:e,width:a,height:s,aspect_ratio:n,halign:i,valign:o}}export(t="auto",e=!0){const n=(()=>{switch(t){case"auto":case"png":return"canvas";case"svg":return"svg"}})(),r=new Fu(n,e),{x:i,y:o,width:a,height:s}=this.bbox;r.resize(a,s);const l=getComputedStyle(this.el).backgroundColor;r.ctx.fillStyle=l,r.ctx.fillRect(i,o,a,s);for(const n of this.child_views){const i=n.export(t,e),{x:o,y:a}=n.bbox;r.ctx.drawImage(i.canvas,o,a)}return r}serializable_state(){return{...super.serializable_state(),children:this.child_views.map((t=>t.serializable_state()))}}}WQ.__name__="LayoutDOMView";class ZQ extends Wu{constructor(t){super(t)}}mQ=ZQ,ZQ.__name__="LayoutDOM",mQ.define((t=>{const{Boolean:e,Number:n,String:r,Auto:i,Array:o,Tuple:a,Or:s,Null:l,Nullable:c,Ref:u}=t,d=a(n,n),h=a(n,n,n,n);return{width:[c(n),null],height:[c(n),null],min_width:[c(n),null],min_height:[c(n),null],max_width:[c(n),null],max_height:[c(n),null],margin:[c(s(n,d,h)),null],width_policy:[s(Ki,i),"auto"],height_policy:[s(Ki,i),"auto"],aspect_ratio:[s(n,i,l),null],flow_mode:[_n.ar,"block"],sizing_mode:[c(_n.MZ),null],disabled:[e,!1],align:[s(_n.W3,a(_n.W3,_n.W3),i),"auto"],css_classes:[o(r),[]],context_menu:[c(u(UQ)),null],resizable:[s(e,_n.Et),!1]}}));const{max:XQ}=Math;class KQ extends eo{constructor(t){super(),this.children=t}_measure(t){return{width:0,height:0}}compute(t={}){const{width:e,height:n}=t;(0,_.vA)(null!=e&&null!=n);const r={width:e,height:n},i=new re({left:0,top:0,width:e,height:n});let o;if(null!=r.inner){const{left:t,top:i,right:a,bottom:s}=r.inner;o=new re({left:t,top:i,right:e-a,bottom:n-s})}this.set_geometry(i,o)}_set_geometry(t,e){super._set_geometry(t,e);const n=this.children.map(((t,e)=>{const{layout:n,bbox:r}=e;(0,_.vA)(null!=n);const i=n.measure(r);return{child:e,layout:n,bbox:r,size_hint:i}})),r=Array(n.nrows).fill(null).map((()=>({top:0,bottom:0}))),i=Array(n.ncols).fill(null).map((()=>({left:0,right:0})));n.foreach((({r0:t,c0:e,r1:n,c1:o},{size_hint:a})=>{const{inner:s}=a;null!=s&&(i[e].left=XQ(i[e].left,s.left),i[o].right=XQ(i[o].right,s.right),r[t].top=XQ(r[t].top,s.top),r[n].bottom=XQ(r[n].bottom,s.bottom))})),n.foreach((({r0:t,c0:e,r1:n,c1:o},{layout:a,size_hint:s,bbox:l})=>{const c=l,u=null==s.inner?void 0:(()=>{const{inner:a,align:l}=s,u=l?.left??!0,d=l?.right??!0,h=l?.top??!0,p=l?.bottom??!0,f=l?.fixed_width??!1,Q=l?.fixed_height??!1,{left:T,right:m}=(()=>{if(f){const t=c.width-a.right-a.left;if(u){const n=i[e].left;return{left:n,right:c.width-(n+t)}}if(d){const e=i[o].right;return{left:c.width-(e+t),right:e}}return{left:a.left,right:a.right}}return{left:u?i[e].left:a.left,right:d?i[o].right:a.right}})(),{top:g,bottom:_}=(()=>{if(Q){const e=c.height-a.bottom-a.top;if(h){const n=r[t].top;return{top:n,bottom:c.height-(n+e)}}if(p){const t=r[n].bottom;return{top:c.height-(t+e),bottom:t}}return{top:a.top,bottom:a.bottom}}return{top:h?r[t].top:a.top,bottom:p?r[n].bottom:a.bottom}})(),{width:b,height:v}=c;return re.from_lrtb({left:T,top:g,right:b-m,bottom:v-_})})();a.set_geometry(c,u)}))}}var YQ,JQ,tT;KQ.__name__="GridAlignmentLayout";class eT extends WQ{connect_signals(){super.connect_signals();const{children:t}=this.model.properties;this.on_change(t,(()=>this.update_children()))}get child_models(){return this.model.children}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"flex"}}_update_layout(){super._update_layout(),this.style.append(":host",{flex_direction:this._direction,gap:Re(this.model.spacing)});const t=new bc;let e=0,n=0;for(const r of this.child_views){if(!(r instanceof WQ))continue;const i=r.box_sizing(),o=(()=>{const t="row"==this._direction?i.width_policy:i.height_policy,e="row"==this._direction?i.width:i.height,n=null!=e?Re(e):"auto";switch(t){case"auto":case"fixed":return`0 0 ${n}`;case"fit":return"1 1 auto";case"min":return"0 1 auto";case"max":return"1 0 0px"}})(),a=(()=>{switch("row"==this._direction?i.height_policy:i.width_policy){case"auto":case"fixed":case"fit":case"min":return"row"==this._direction?i.valign:i.halign;case"max":return"stretch"}})();r.style.append(":host",{flex:o,align_self:a}),"row"==this._direction?"max"==i.height_policy&&r.style.append(":host",{height:"auto"}):"max"==i.width_policy&&r.style.append(":host",{width:"auto"}),null!=r.layout&&(t.add({r0:e,c0:n,r1:e+1,c1:n+1},r),"row"==this._direction?n+=1:e+=1)}0!=t.size?(this.layout=new KQ(t),this.layout.set_sizing()):delete this.layout}}eT.__name__="FlexBoxView";class nT extends ZQ{constructor(t){super(t)}}YQ=nT,nT.__name__="FlexBox",YQ.define((({Number:t,Array:e,Ref:n})=>({children:[e(n(Wu)),[]],spacing:[t,0]})));class rT extends eT{constructor(){super(...arguments),this._direction="column"}}rT.__name__="ColumnView";class iT extends nT{constructor(t){super(t)}}JQ=iT,iT.__name__="Column",JQ.prototype.default_view=rT;const{max:oT}=Math,aT=(0,g.Enum)("start","center","end","auto"),sT=g.String,lT=g.Struct({size:g.Opt(sT),align:g.Opt(aT)}),cT=g.Or(sT,lT),uT=g.Or(cT,g.Array(cT),g.Map(g.Int,cT));class dT extends WQ{connect_signals(){super.connect_signals();const{spacing:t}=this.model.properties;this.on_change(t,(()=>this.invalidate_layout()))}get child_models(){return this._children.map((([t])=>t))}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"grid"}}_update_layout(){super._update_layout();const t={},[e,n]=(()=>{const{spacing:t}=this.model;return(0,f.Et)(t)?[t,t]:t})();t.row_gap=Re(e),t.column_gap=Re(n);let r=0,i=0;const o=new bc;for(const[[,t,e,n=1,a=1],s]of(0,On.HL)(this._children)){const l=this.child_views[s];r=oT(r,t+n),i=oT(i,e+a);const c={};if(c.grid_row_start=`${t+1}`,c.grid_row_end=`span ${n}`,c.grid_column_start=`${e+1}`,c.grid_column_end=`span ${a}`,l.style.append(":host",c),l instanceof WQ&&null!=l.layout){const r=t,i=e,s=t+n-1,c=e+a-1;o.add({r0:r,c0:i,r1:s,c1:c},l)}}const{_rows:a,_cols:s}=this;function l(t,e){if(t instanceof Map)for(const[n,r]of t.entries())(0,f.Kg)(r)?e[n].size=r:e[n]=r;else if((0,f.cy)(t))for(const[n,r]of(0,On.HL)(t))(0,f.Kg)(n)?e[r].size=n:e[r]=n;else if(null!=t)for(const n of e)(0,f.Kg)(t)?n.size=t:(n.size=t.size,n.align=t.align)}a instanceof Map?r=oT(r,...a.keys()):(0,f.cy)(a)&&(r=oT(r,a.length)),s instanceof Map?i=oT(i,...s.keys()):(0,f.cy)(s)&&(i=oT(i,s.length));const c=Array(r).fill(null).map((()=>({}))),u=Array(i).fill(null).map((()=>({})));l(a,c),l(s,u);for(const[[,t,e],n]of(0,On.HL)(this._children)){const r=this.child_views[n],{halign:i,valign:o}=r.box_sizing();r.style.append(":host",{justify_self:i??u[e].align,align_self:o??c[t].align})}t.grid_template_rows=c.map((({size:t})=>t??"1fr")).join(" "),t.grid_template_columns=u.map((({size:t})=>t??"1fr")).join(" "),this.style.append(":host",t),0!=o.size?(this.layout=new KQ(o),this.layout.set_sizing()):delete this.layout}}dT.__name__="CSSGridBoxView";class hT extends ZQ{constructor(t){super(t)}}var pT,fT,QT,TT,mT,gT,_T;tT=hT,hT.__name__="CSSGridBox",tT.define((({Number:t,Tuple:e,Or:n})=>({spacing:[n(t,e(t,t)),0]})));class bT extends dT{connect_signals(){super.connect_signals();const{children:t,rows:e,cols:n}=this.model.properties;this.on_change(t,(()=>this.update_children())),this.on_change([e,n],(()=>this.invalidate_layout()))}get _children(){return this.model.children}get _rows(){return this.model.rows}get _cols(){return this.model.cols}}bT.__name__="GridBoxView";class vT extends hT{constructor(t){super(t)}}pT=vT,vT.__name__="GridBox",pT.prototype.default_view=bT,pT.define((({Int:t,Tuple:e,Array:n,Ref:r,Opt:i,Nullable:o})=>({children:[n(e(r(Wu),t,t,i(t),i(t))),[]],rows:[o(uT),null],cols:[o(uT),null]})));class yT extends WQ{styles(){return[...super.styles(),"legend{display:flex;gap:0.5em;padding:0 calc(var(--padding-horizontal) / 2);}fieldset{border:1px solid #ccc;}"]}connect_signals(){super.connect_signals();const{child:t}=this.model.properties;this.on_change(t,(()=>this.update_children()));const{checkable:e,disabled:n}=this.model.properties;this.on_change(e,(()=>{He(this.checkbox_el,this.model.checkable)})),this.on_change(n,(()=>{this.checkbox_el.checked=!this.model.disabled}))}get child_models(){return[this.model.child]}render(){super.render();const{checkable:t,disabled:e,title:n}=this.model;this.checkbox_el=ge({type:"checkbox",checked:!e}),this.checkbox_el.addEventListener("change",(()=>{this.model.disabled=!this.checkbox_el.checked})),He(this.checkbox_el,t);const r=Te({},this.checkbox_el,n),i=this.child_views.map((t=>t.el));this.fieldset_el=me({},r,...i),this.shadow_el.appendChild(this.fieldset_el)}_update_children(){const t=this.child_views.map((t=>t.el));this.fieldset_el.append(...t)}}yT.__name__="GroupBoxView";class xT extends ZQ{constructor(t){super(t)}}fT=xT,xT.__name__="GroupBox",fT.prototype.default_view=yT,fT.define((({Boolean:t,String:e,Nullable:n,Ref:r})=>({title:[n(e),null],child:[r(Wu)],checkable:[t,!1]})));class wT extends dT{connect_signals(){super.connect_signals();const{children:t,cols:e}=this.model.properties;this.on_change(t,(()=>this.update_children())),this.on_change(e,(()=>this.invalidate_layout()))}get _children(){return this.model.children.map((({child:t,col:e,span:n},r)=>[t,0,e??r,1,n??1]))}get _rows(){return null}get _cols(){return this.model.cols}}wT.__name__="HBoxView";class LT extends hT{constructor(t){super(t)}}QT=LT,LT.__name__="HBox",QT.prototype.default_view=wT,QT.define((({Int:t,Struct:e,Array:n,Ref:r,Opt:i,Nullable:o})=>({children:[n(e({child:r(Wu),col:i(t),span:i(t)})),[]],cols:[o(uT),null]})));class AT extends eT{constructor(){super(...arguments),this._direction="row"}}AT.__name__="RowView";class HT extends nT{constructor(t){super(t)}}TT=HT,HT.__name__="Row",TT.prototype.default_view=AT;class kT extends WQ{styles(){return[...super.styles()]}connect_signals(){super.connect_signals();const{child:t,horizontal_scrollbar:e,vertical_scrollbar:n}=this.model.properties;this.on_change(t,(()=>this.update_children())),this.on_change([e,n],(()=>this.invalidate_layout()))}get child_models(){return[this.model.child]}_update_layout(){function t(t){switch(t){case"auto":return"auto";case"visible":return"scroll";case"hidden":return"hidden"}}super._update_layout();const{horizontal_scrollbar:e,vertical_scrollbar:n}=this.model;this.style.append(":host",{overflow_x:t(e),overflow_y:t(n)})}}kT.__name__="ScrollBoxView";class MT extends ZQ{constructor(t){super(t)}}mT=MT,MT.__name__="ScrollBox",mT.prototype.default_view=kT,mT.define((({Ref:t})=>({child:[t(Wu)],horizontal_scrollbar:[_n.RL,"auto"],vertical_scrollbar:[_n.RL,"auto"]})));class CT extends WQ{constructor(){super(...arguments),this._auto_width="auto",this._auto_height="auto"}get child_models(){return[]}}CT.__name__="SpacerView";class ST extends ZQ{constructor(t){super(t)}}gT=ST,ST.__name__="Spacer",gT.prototype.default_view=CT;class ET extends qt{constructor(t){super(t)}}_T=ET,ET.__name__="TabPanel",_T.define((({Boolean:t,String:e,Ref:n})=>({title:[e,""],child:[n(Wu)],closable:[t,!1],disabled:[t,!1]})));const VT="bk-above",OT="bk-below",PT="bk-left",DT="bk-right",NT="bk-header",RT="bk-tab",IT="bk-active",jT="bk-close",zT="bk-disabled",BT=':host{display:grid;}:host(.bk-above){grid-template:"header" max-content "stack" 1fr / 1fr;}:host(.bk-below){grid-template:"stack" 1fr "header" max-content / 1fr;}:host(.bk-left){grid-template:"header stack" 1fr / max-content 1fr;}:host(.bk-right){grid-template:"stack header" 1fr / 1fr max-content;}.bk-header{grid-area:"header";display:flex;flex-wrap:nowrap;align-items:stretch;user-select:none;-webkit-user-select:none;}:host(.bk-above) .bk-header,:host(.bk-below) .bk-header{flex-direction:row;}:host(.bk-left) .bk-header,:host(.bk-right) .bk-header{flex-direction:column;}:host(.bk-above) .bk-header{border-bottom:1px solid #e6e6e6;}:host(.bk-right) .bk-header{border-left:1px solid #e6e6e6;}:host(.bk-below) .bk-header{border-top:1px solid #e6e6e6;}:host(.bk-left) .bk-header{border-right:1px solid #e6e6e6;}.bk-tab{padding:4px 8px;border:solid transparent;outline:0;outline-offset:-5px;white-space:nowrap;cursor:pointer;text-align:center;}.bk-tab:hover{background-color:#f2f2f2;}.bk-tab:focus,.bk-tab:active{outline:1px dotted #ccc;}.bk-tab.bk-active{color:#4d4d4d;background-color:white;border-color:#e6e6e6;}.bk-tab .bk-close{margin-left:10px;}.bk-tab.bk-disabled{cursor:not-allowed;pointer-events:none;opacity:0.65;}:host(.bk-above) .bk-tab{border-width:3px 1px 0px 1px;border-radius:var(--border-radius) var(--border-radius) 0 0;}:host(.bk-right) .bk-tab{border-width:1px 3px 1px 0px;border-radius:0 var(--border-radius) var(--border-radius) 0;}:host(.bk-below) .bk-tab{border-width:0px 1px 3px 1px;border-radius:0 0 var(--border-radius) var(--border-radius);}:host(.bk-left) .bk-tab{border-width:1px 0px 1px 3px;border-radius:var(--border-radius) 0 0 var(--border-radius);}.bk-close{display:inline-block;vertical-align:middle;width:14px;height:14px;cursor:pointer;background-color:gray;mask-image:var(--bokeh-icon-x);mask-size:contain;mask-repeat:no-repeat;-webkit-mask-image:var(--bokeh-icon-x);-webkit-mask-size:contain;-webkit-mask-repeat:no-repeat;}.bk-close:hover{background-color:red;}';var FT,$T,GT,qT,UT,WT,ZT,XT,KT,YT,JT,tm,em;class nm extends WQ{connect_signals(){super.connect_signals();const{tabs:t,active:e}=this.model.properties;this.on_change(t,(()=>{this._update_headers(),this.update_children()})),this.on_change(e,(()=>{this.update_active()}))}styles(){return[...super.styles(),BT,pd]}get child_models(){return this.model.tabs.map((t=>t.child))}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"grid"}}_update_layout(){super._update_layout();const t=this.model.tabs_location;this.class_list.remove([..._n.aZ].map((t=>a[t]))),this.class_list.add(a[t]);const e=new bc;for(const t of this.child_views)t.style.append(":host",{grid_area:"stack"}),t instanceof WQ&&null!=t.layout&&e.add({r0:0,c0:0,r1:1,c1:1},t);0!=e.size?(this.layout=new KQ(e),this.layout.set_sizing()):delete this.layout}_after_layout(){super._after_layout();const{child_views:t}=this;for(const e of t)Ce(e.el);const{active:e}=this.model;e in t&&Me(t[e].el)}render(){super.render(),this.header_el=oe({class:NT}),this.shadow_el.append(this.header_el),this._update_headers()}_update_headers(){const{active:t}=this.model,e=this.model.tabs.map(((e,n)=>{const r=oe({class:[RT,n==t?IT:null],tabIndex:0},e.title);if(r.addEventListener("click",(t=>{this.model.disabled||t.target==t.currentTarget&&this.change_active(n)})),e.closable){const t=oe({class:jT});t.addEventListener("click",(t=>{if(t.target==t.currentTarget){this.model.tabs=(0,Rt.bS)(this.model.tabs,n);const t=this.model.tabs.length;this.model.active>t-1&&(this.model.active=t-1)}})),r.appendChild(t)}return(this.model.disabled||e.disabled)&&r.classList.add(zT),r}));this.header_els=e,Ae(this.header_el),this.header_el.append(...e)}change_active(t){t!=this.model.active&&(this.model.active=t)}update_active(){const t=this.model.active,{header_els:e}=this;for(const t of e)t.classList.remove(IT);t in e&&e[t].classList.add(IT);const{child_views:n}=this;for(const t of n)Ce(t.el);t in n&&Me(n[t].el)}}nm.__name__="TabsView";class rm extends ZQ{constructor(t){super(t)}}FT=rm,rm.__name__="Tabs",FT.prototype.default_view=nm,FT.define((({Int:t,Array:e,Ref:n})=>({tabs:[e(n(ET)),[]],tabs_location:[_n.aZ,"above"],active:[t,0]})));class im extends dT{connect_signals(){super.connect_signals();const{children:t,rows:e}=this.model.properties;this.on_change(t,(()=>this.update_children())),this.on_change(e,(()=>this.invalidate_layout()))}get _children(){return this.model.children.map((({child:t,row:e,span:n},r)=>[t,e??r,0,n??1,1]))}get _rows(){return this.model.rows}get _cols(){return null}}im.__name__="VBoxView";class om extends hT{constructor(t){super(t)}}$T=om,om.__name__="VBox",$T.prototype.default_view=im,$T.define((({Int:t,Struct:e,Array:n,Ref:r,Opt:i,Nullable:o})=>({children:[n(e({child:r(Wu),row:i(t),span:i(t)})),[]],rows:[o(uT),null]})));class am extends Be{}am.__name__="IconView";class sm extends qt{constructor(t){super(t)}}GT=sm,sm.__name__="Icon",GT.define((({Number:t,Or:e,CSSLength:n})=>({size:[e(t,n),"1em"]})));class lm extends GQ{_click(){}render(){super.render();const{label:t,description:e}=this.model;this.el.tabIndex=0,this.el.title=e??"",this.el.appendChild(ae(t)),this.el.addEventListener("click",(()=>{this._click()})),this.el.addEventListener("keydown",(t=>{"Enter"==t.key&&this._click()}))}}lm.__name__="ActionView";class cm extends qQ{constructor(t){super(t)}}qT=cm,cm.__name__="Action",qT.prototype.default_view=lm,qT.define((({String:t,Nullable:e,Ref:n})=>({icon:[e(n(sm)),null],label:[t],description:[e(t),null],menu:[e(n(UQ)),null]})));class um extends lm{}um.__name__="CheckActionView";class dm extends cm{constructor(t){super(t)}}UT=dm,dm.__name__="CheckAction",UT.prototype.default_view=um,UT.define((({Boolean:t})=>({checked:[t,!1]})));class hm extends GQ{render(){super.render()}}hm.__name__="SectionView";class pm extends qQ{constructor(t){super(t)}}WT=pm,pm.__name__="Section",WT.prototype.default_view=hm,WT.define((({Array:t,Ref:e})=>({items:[t(e(qQ)),[]]})));class fm extends GQ{render(){super.render(),this.el.classList.add(rd)}}fm.__name__="DividerView";class Qm extends qQ{constructor(t){super(t)}}ZT=Qm,Qm.__name__="Divider",ZT.prototype.default_view=fm;class Tm extends vn{constructor(t){super(t)}get names(){return(0,Q.HP)(this.args)}get values(){return(0,Q.zu)(this.args)}_make_transform(t,e){return new Function(...this.names,t,x(e))}get scalar_transform(){return this._make_transform("x",this.func)}get vector_transform(){return this._make_transform("xs",this.v_func)}compute(t){return this.scalar_transform(...this.values,t)}v_compute(t){return this.vector_transform(...this.values,t)}}XT=Tm,Tm.__name__="CustomJSTransform",XT.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],func:[e,""],v_func:[e,""]})));class mm extends vn{constructor(t){super(t)}v_compute(t){let e;this.range instanceof jn?e=this.range.v_synthetic(t):(0,f.b)(t,f.Et)?e=t:(0,_.HB)();const n=new((0,Jt.Q9)(e))(e.length);for(let t=0;t<e.length;t++){const r=e[t];n[t]=this._compute(r)}return n}compute(t){return this.range instanceof jn?this._compute(this.range.synthetic(t)):(0,f.Et)(t)?this._compute(t):void(0,_.HB)()}}KT=mm,mm.__name__="RangeTransform",KT.define((({Ref:t,Nullable:e})=>({range:[e(t(yn)),null]})));class gm extends mm{constructor(t){super(t)}_compute(t){return t+this.value}}YT=gm,gm.__name__="Dodge",YT.define((({Number:t})=>({value:[t,0]})));class _m extends vn{constructor(t){super(t),this._sorted_dirty=!0}connect_signals(){super.connect_signals(),this.connect(this.change,(()=>this._sorted_dirty=!0))}v_compute(t){const e=new((0,Jt.Q9)(t))(t.length);for(let n=0;n<t.length;n++){const r=t[n];e[n]=this.compute(r)}return e}sort(t=!1){if(!this._sorted_dirty)return;let e,n;if((0,f.Kg)(this.x)&&(0,f.Kg)(this.y)&&null!=this.data){const t=this.data.columns();if(!(0,Rt.mK)(t,this.x))throw new Error("The x parameter does not correspond to a valid column name defined in the data parameter");if(!(0,Rt.mK)(t,this.y))throw new Error("The y parameter does not correspond to a valid column name defined in the data parameter");e=this.data.get_column(this.x),n=this.data.get_column(this.y)}else{if(!(0,f.cy)(this.x)||!(0,f.cy)(this.y))throw new Error("parameters 'x' and 'y' must be both either string fields or arrays");e=this.x,n=this.y}if(e.length!==n.length)throw new Error("The length for x and y do not match");if(e.length<2)throw new Error("x and y must have at least two elements to support interpolation");const r=e.length,i=new Uint32Array(r);for(let t=0;t<r;t++)i[t]=t;const o=t?-1:1;i.sort(((t,n)=>o*(e[t]-e[n]))),this._x_sorted=new((0,Jt.Q9)(e))(r),this._y_sorted=new((0,Jt.Q9)(n))(r);for(let t=0;t<r;t++)this._x_sorted[t]=e[i[t]],this._y_sorted[t]=n[i[t]];this._sorted_dirty=!1}}JT=_m,_m.__name__="Interpolator",JT.define((({Boolean:t,Number:e,String:n,Ref:r,Array:i,Or:o,Nullable:a})=>({x:[o(n,i(e))],y:[o(n,i(e))],data:[a(r(hr)),null],clip:[t,!0]})));class bm extends qt{constructor(t){super(t)}}bm.__name__="RandomGenerator";class vm extends mm{constructor(t){super(t),this._previous_offsets=null}initialize(){super.initialize(),this._generator=this.random_generator?.generator()??new Eu}v_compute(t){const e=(()=>this.range instanceof jn?this.range.v_synthetic(t):t)(),n=(()=>{const t=e.length;return this._previous_offsets?.length!=t&&(this._previous_offsets=this._v_compute(t)),this._previous_offsets})();return(0,bn.Tj)(n,((t,n)=>t+e[n]))}_compute(){const{mean:t,width:e}=this;switch(this.distribution){case"uniform":return this._generator.uniform(t,e);case"normal":return this._generator.normal(t,e)}}_v_compute(t){const{mean:e,width:n}=this;switch(this.distribution){case"uniform":return this._generator.uniforms(e,n,t);case"normal":return this._generator.normals(e,n,t)}}}tm=vm,vm.__name__="Jitter",tm.define((({Number:t})=>({mean:[t,0],width:[t,1],distribution:[_n.zm,"uniform"]}))),tm.internal((({Nullable:t,Ref:e})=>({random_generator:[t(e(bm)),null]})));class ym extends _m{constructor(t){super(t)}compute(t){if(this.sort(!1),this.clip){if(t<this._x_sorted[0]||t>this._x_sorted[this._x_sorted.length-1])return NaN}else{if(t<this._x_sorted[0])return this._y_sorted[0];if(t>this._x_sorted[this._x_sorted.length-1])return this._y_sorted[this._y_sorted.length-1]}if(t==this._x_sorted[0])return this._y_sorted[0];const e=(0,Rt.e)(this._x_sorted,(e=>e<t)),n=this._x_sorted[e],r=this._x_sorted[e+1],i=this._y_sorted[e],o=this._y_sorted[e+1];return i+(t-n)/(r-n)*(o-i)}}ym.__name__="LinearInterpolator";class xm extends _m{constructor(t){super(t)}compute(t){if(this.sort(!1),this.clip){if(t<this._x_sorted[0]||t>this._x_sorted[this._x_sorted.length-1])return NaN}else{if(t<this._x_sorted[0])return this._y_sorted[0];if(t>this._x_sorted[this._x_sorted.length-1])return this._y_sorted[this._y_sorted.length-1]}let e;switch(this.mode){case"after":e=(0,Rt.e)(this._x_sorted,(e=>t>=e));break;case"before":e=(0,Rt.TJ)(this._x_sorted,(e=>t<=e));break;case"center":{const n=(0,Rt.Tj)(this._x_sorted,(e=>Math.abs(e-t))),r=(0,Rt.jk)(n);e=(0,Rt.TJ)(n,(t=>r===t));break}default:throw new Error(`unknown mode: ${this.mode}`)}return-1!=e?this._y_sorted[e]:NaN}}em=xm,xm.__name__="StepInterpolator",em.define((()=>({mode:[_n.CY,"after"]})));class wm{constructor(t){this.parent=t,this.invalidate_dataranges=!0}get frame(){return this.parent.frame}update(t,e={}){const{x_ranges:n,y_ranges:r}=this.frame;if(null==t){for(const[,t]of n)t.reset();for(const[,t]of r)t.reset();this.update_dataranges()}else{const i=[];for(const[e,r]of n)i.push([r,t.xrs.get(e)]);for(const[e,n]of r)i.push([n,t.yrs.get(e)]);e.scrolling&&this._update_ranges_together(i),this._update_ranges_individually(i,e)}}reset(){this.update(null)}_update_dataranges(t){const e=new Map,n=new Map;let r=!1;for(const[,e]of t.x_ranges)e instanceof Dn&&"log"==e.scale_hint&&(r=!0);for(const[,e]of t.y_ranges)e instanceof Dn&&"log"==e.scale_hint&&(r=!0);for(const t of this.parent.model.data_renderers){const i=this.parent.renderer_view(t);if(null==i)continue;const o=i.glyph_view.bounds();if(e.set(t,o),r){const e=i.glyph_view.log_bounds();n.set(t,e)}}let i=!1,o=!1;const a=t.x_target.span,s=t.y_target.span;let l;!1!==this.parent.model.match_aspect&&0!=a&&0!=s&&(l=1/this.parent.model.aspect_scale*(a/s));for(const[,r]of t.x_ranges){if(r instanceof Dn){const t="log"==r.scale_hint?n:e;r.update(t,0,this.parent.model,l),r.follow&&(i=!0)}null!=r.bounds&&(o=!0)}for(const[,r]of t.y_ranges){if(r instanceof Dn){const t="log"==r.scale_hint?n:e;r.update(t,1,this.parent.model,l),r.follow&&(i=!0)}null!=r.bounds&&(o=!0)}if(i&&o){ot.vF.warn("Follow enabled so bounds are unset.");for(const[,e]of t.x_ranges)e.bounds=null;for(const[,e]of t.y_ranges)e.bounds=null}}update_dataranges(){this._update_dataranges(this.frame);for(const t of this.parent.model.renderers){const{coordinates:e}=t;null!=e&&this._update_dataranges(e)}null!=this.compute_initial()&&(this.invalidate_dataranges=!1)}compute_initial(){let t=!0;const{x_ranges:e,y_ranges:n}=this.frame,r=new Map,i=new Map;for(const[n,i]of e){const{start:e,end:o}=i;if(isNaN(e+o)){t=!1;break}r.set(n,{start:e,end:o})}if(t)for(const[e,r]of n){const{start:n,end:o}=r;if(isNaN(n+o)){t=!1;break}i.set(e,{start:n,end:o})}return t?{xrs:r,yrs:i}:(ot.vF.warn("could not set initial ranges"),null)}_update_ranges_together(t){let e=1;for(const[n,r]of t)e=Math.min(e,this._get_weight_to_constrain_interval(n,r));if(e<1)for(const[n,r]of t)r.start=e*r.start+(1-e)*n.start,r.end=e*r.end+(1-e)*n.end}_update_ranges_individually(t,e={}){const n=e.panning??!1,r=e.scrolling??!1,i=e.maintain_focus??!1;let o=!1;for(const[e,i]of t){if(!r){const t=this._get_weight_to_constrain_interval(e,i);t<1&&(i.start=t*i.start+(1-t)*e.start,i.end=t*i.end+(1-t)*e.end)}if(null!=e.bounds&&"auto"!=e.bounds){const[t,a]=e.bounds,s=Math.abs(i.end-i.start);e.is_reversed?(null!=t&&t>i.end&&(o=!0,i.end=t,(n||r)&&(i.start=t+s)),null!=a&&a<i.start&&(o=!0,i.start=a,(n||r)&&(i.end=a-s))):(null!=t&&t>i.start&&(o=!0,i.start=t,(n||r)&&(i.end=t+s)),null!=a&&a<i.end&&(o=!0,i.end=a,(n||r)&&(i.start=a-s)))}}if(!(r&&o&&i))for(const[e,n]of t)e.have_updated_interactively=!0,e.start==n.start&&e.end==n.end||e.setv(n)}_get_weight_to_constrain_interval(t,e){const{min_interval:n}=t;let{max_interval:r}=t;if(null!=t.bounds&&"auto"!=t.bounds){const[e,n]=t.bounds;if(null!=e&&null!=n){const t=Math.abs(n-e);r=null!=r?Math.min(r,t):t}}let i=1;if(null!=n||null!=r){const o=Math.abs(t.end-t.start),a=Math.abs(e.end-e.start);null!=n&&n>0&&a<n&&(i=(o-n)/(o-a)),null!=r&&r>0&&a>r&&(i=(r-o)/(a-o)),i=Math.max(0,Math.min(1,i))}return i}}wm.__name__="RangeManager";class Lm{constructor(t,e){this.parent=t,this.initial_state=e,this.changed=new T.n2(this.parent,"state_changed"),this.history=[],this.index=-1}_do_state_change(t){const e=t in this.history?this.history[t].state:this.initial_state;return null!=e.range&&this.parent.update_range(e.range),null!=e.selection&&this.parent.update_selection(e.selection),e}peek(){return this.can_undo?this.history[this.index]:null}push(t,e){const{history:n,index:r}=this,i=r in n?n[r].state:{},o={...this.initial_state,...i,...e};this.history=this.history.slice(0,this.index+1),this.history.push({type:t,state:o}),this.index=this.history.length-1,this.changed.emit()}clear(){this.history=[],this.index=-1,this.changed.emit()}undo(){if(this.can_undo){this.index-=1;const t=this._do_state_change(this.index);return this.changed.emit(),t}return null}redo(){if(this.can_redo){this.index+=1;const t=this._do_state_change(this.index);return this.changed.emit(),t}return null}get can_undo(){return this.index>=0}get can_redo(){return this.index<this.history.length-1}}Lm.__name__="StateManager";const{max:Am}=Math;class Hm extends WQ{constructor(){super(...arguments),this._computed_style=new Pe,this._outer_bbox=new re,this._inner_bbox=new re,this._needs_paint=!0,this._invalidated_painters=new Set,this._invalidate_all=!0,this.renderer_views=new Map,this.tool_views=new Map,this._needs_notify=!1}get canvas(){return this.canvas_view}styles(){return[...super.styles(),':host{display:grid;grid-template-areas:".    above  .    " "left center right" ".    below  .    ";grid-template-rows:0px 1fr 0px;grid-template-columns:0px 1fr 0px;}.bk-Canvas{grid-row-start:1;grid-row-end:span 3;grid-column-start:1;grid-column-end:span 3;}',this._computed_style]}get toolbar_panel(){return null!=this._toolbar?this.renderer_view(this._toolbar):void 0}get state(){return this._state_manager}set invalidate_dataranges(t){this._range_manager.invalidate_dataranges=t}renderer_view(t){const e=this.renderer_views.get(t);if(null==e)for(const[,e]of this.renderer_views){const n=e.renderer_view(t);if(null!=n)return n}return e}get base_font_size(){const t=yo(getComputedStyle(this.el).fontSize);if(null!=t){const{value:e,unit:n}=t;if("px"==n)return e}return null}*children(){yield*super.children(),yield*this.renderer_views.values(),yield*this.tool_views.values(),yield this.canvas}get is_paused(){return null!=this._is_paused&&0!==this._is_paused}get child_models(){return[]}pause(){null==this._is_paused?this._is_paused=1:this._is_paused+=1}unpause(t=!1){if(null==this._is_paused)throw new Error("wasn't paused");this._is_paused=Math.max(this._is_paused-1,0),0!=this._is_paused||t||this.request_paint("everything")}notify_finished_after_paint(){this._needs_notify=!0}request_render(){this.request_paint("everything")}request_paint(t){this.invalidate_painters(t),this.schedule_paint()}invalidate_painters(t){if("everything"==t)this._invalidate_all=!0;else if((0,f.cy)(t))for(const e of t)this._invalidated_painters.add(e);else this._invalidated_painters.add(t)}schedule_paint(){if(!this.is_paused){const t=this.throttled_paint();this._ready=this._ready.then((()=>t))}}request_layout(){this.request_paint("everything")}reset(){"standard"==this.model.reset_policy&&(this.state.clear(),this.reset_range(),this.reset_selection()),this.model.trigger_event(new gt)}remove(){for(const t of this.frame.ranges.values())t instanceof Dn&&t.plots.delete(this.model);qe(this.renderer_views),qe(this.tool_views),this.canvas_view.remove(),super.remove()}render(){super.render(),this.shadow_el.appendChild(this.canvas_view.el),this.canvas_view.render()}initialize(){this.pause(),super.initialize(),this.lod_started=!1,this.visuals=new Qn(this),this._initial_state={selection:new Map},this.frame=new sa(this.model.x_scale,this.model.y_scale,this.model.x_range,this.model.y_range,this.model.extra_x_ranges,this.model.extra_y_ranges,this.model.extra_x_scales,this.model.extra_y_scales);for(const t of this.frame.ranges.values())t instanceof Dn&&t.plots.add(this.model);this._range_manager=new wm(this),this._state_manager=new Lm(this,this._initial_state),this.throttled_paint=function(t,e){let n,r=null,i=null,o=0,a=!1;const s=function(){return new Promise(((s,l)=>{n=s;const c=function(){o=Date.now(),r=null,i=null,a=!1;try{t(),s()}catch(t){l(t)}},u=Date.now(),d=e-(u-o);d<=0&&!a?(null!=r&&clearTimeout(r),a=!0,i=requestAnimationFrame(c)):null!=r||a?s():r=setTimeout((()=>i=requestAnimationFrame(c)),d)}))};return s.stop=function(){null!=r&&clearTimeout(r),null!=i&&cancelAnimationFrame(i),n()},s}((()=>{this._removed||this.repaint()}),1e3/60);const{title_location:t,title:e}=this.model;null!=t&&null!=e&&(this._title=e instanceof aa?e:new aa({text:e}));const{toolbar_location:n,toolbar_inner:r,toolbar:i}=this.model;null!=n&&(this._toolbar=new gh({toolbar:i}),i.location=n,i.inner=r)}async lazy_initialize(){await super.lazy_initialize();const{hidpi:t,output_backend:e}=this.model,n=new zh({hidpi:t,output_backend:e});this.canvas_view=await $e(n,{parent:this}),this.canvas_view.plot_views=[this],await this.build_tool_views(),await this.build_renderer_views(),this._range_manager.update_dataranges()}box_sizing(){const{width_policy:t,height_policy:e,...n}=super.box_sizing(),{frame_width:r,frame_height:i}=this.model;return{...n,width_policy:null!=r&&"auto"==t?"fit":t,height_policy:null!=i&&"auto"==e?"fit":e}}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"grid"}}_update_layout(){super._update_layout(),this._invalidate_all=!0,this._needs_paint=!0;const t=new wc,{frame_align:e}=this.model;if(t.aligns=(()=>{if((0,f.Lm)(e))return{left:e,right:e,top:e,bottom:e};{const{left:t=!0,right:n=!0,top:r=!0,bottom:i=!0}=e;return{left:t,right:n,top:r,bottom:i}}})(),t.set_sizing({width_policy:"max",height_policy:"max"}),this.visuals.outline_line.doit){const e=this.visuals.outline_line.line_width.get_value();t.center_border_width=e}const n=(0,Rt.C)(this.model.above),r=(0,Rt.C)(this.model.below),i=(0,Rt.C)(this.model.left),o=(0,Rt.C)(this.model.right),a=[],s=[],l=[],c=[],u=(t,e=!1)=>{switch(t){case"above":return e?a:n;case"below":return e?s:r;case"left":return e?l:i;case"right":return e?c:o}},{title_location:d}=this.model;if(null!=d&&null!=this._title&&u(d).push(this._title),null!=this._toolbar){const{location:t}=this._toolbar.toolbar;if(this.model.toolbar_inner)u(t,!0).push(this._toolbar);else{const e=u(t);let n=!0;if(this.model.toolbar_sticky)for(let r=0;r<e.length;r++){const i=e[r];if(i instanceof aa){e[r]="above"==t||"below"==t?[i,this._toolbar]:[this._toolbar,i],n=!1;break}}n&&e.push(this._toolbar)}}const h=(t,e)=>{const n=this.renderer_view(e);return n.panel=new co(t),n.update_layout?.(),n.layout},p=(t,e)=>{const n="above"==t||"below"==t,r=[];for(const i of e)if((0,f.cy)(i)){const e=i.map((e=>{const r=h(t,e);if(e instanceof gh){const t=n?"width_policy":"height_policy";r.set_sizing({...r.sizing,[t]:"min"})}return r}));let o;n?(o=new yc(e),o.set_sizing({width_policy:"max",height_policy:"min"})):(o=new xc(e),o.set_sizing({width_policy:"min",height_policy:"max"})),o.absolute=!0,r.push(o)}else r.push(h(t,i));return r},Q=this.model.min_border??0;t.min_border={left:this.model.min_border_left??Q,top:this.model.min_border_top??Q,right:this.model.min_border_right??Q,bottom:this.model.min_border_bottom??Q};const T=new Tc,m=new Qc,g=new Qc,_=new fc,b=new fc,v=new Qc,y=new Qc,x=new fc,w=new fc;T.absolute=!0,m.absolute=!0,g.absolute=!0,_.absolute=!0,b.absolute=!0,v.absolute=!0,y.absolute=!0,x.absolute=!0,w.absolute=!0,T.children=this.model.center.filter((t=>t instanceof rr)).map((t=>{const e=this.renderer_view(t);return e.update_layout?.(),e.layout})).filter((t=>null!=t));const{frame_width:L,frame_height:A}=this.model;T.set_sizing({...null!=L?{width_policy:"fixed",width:L}:{width_policy:"fit"},...null!=A?{height_policy:"fixed",height:A}:{height_policy:"fit"}}),T.on_resize((t=>this.frame.set_geometry(t))),m.children=(0,Rt.TY)(p("above",n)),g.children=p("below",r),_.children=(0,Rt.TY)(p("left",i)),b.children=p("right",o),v.children=p("above",a),y.children=p("below",s),x.children=p("left",l),w.children=p("right",c),m.set_sizing({width_policy:"fit",height_policy:"min"}),g.set_sizing({width_policy:"fit",height_policy:"min"}),_.set_sizing({width_policy:"min",height_policy:"fit"}),b.set_sizing({width_policy:"min",height_policy:"fit"}),v.set_sizing({width_policy:"fit",height_policy:"min"}),y.set_sizing({width_policy:"fit",height_policy:"min"}),x.set_sizing({width_policy:"min",height_policy:"fit"}),w.set_sizing({width_policy:"min",height_policy:"fit"}),t.center_panel=T,t.top_panel=m,t.bottom_panel=g,t.left_panel=_,t.right_panel=b,0!=v.children.length&&(t.inner_top_panel=v),0!=y.children.length&&(t.inner_bottom_panel=y),0!=x.children.length&&(t.inner_left_panel=x),0!=w.children.length&&(t.inner_right_panel=w),this.layout=t}_measure_layout(){const{frame_width:t,frame_height:e}=this.model,n=null==t?"1fr":Re(t),r=null==e?"1fr":Re(e),{layout:i}=this,o=i.top_panel.measure({width:1/0,height:1/0}),a=i.bottom_panel.measure({width:1/0,height:1/0}),s=i.left_panel.measure({width:1/0,height:1/0}),l=i.right_panel.measure({width:1/0,height:1/0}),c=Am(o.height,i.min_border.top),u=Am(a.height,i.min_border.bottom),d=Am(s.width,i.min_border.left),h=Am(l.width,i.min_border.right);this._computed_style.replace(`\n      :host {\n        grid-template-rows: ${c}px ${r} ${u}px;\n        grid-template-columns: ${d}px ${n} ${h}px;\n      }\n    `)}get axis_views(){const t=[];for(const[,e]of this.renderer_views)e instanceof ma&&t.push(e);return t}update_range(t,e){this.pause(),this._range_manager.update(t,e),this.unpause()}reset_range(){this.update_range(null),this.trigger_ranges_update_event()}trigger_ranges_update_event(){const{x_range:t,y_range:e}=this.model;this.model.trigger_event(new Tt(t.start,t.end,e.start,e.end))}get_selection(){const t=new Map;for(const e of this.model.data_renderers){const{selected:n}=e.selection_manager.source;t.set(e,n)}return t}update_selection(t){for(const e of this.model.data_renderers){const n=e.selection_manager.source;if(null!=t){const r=t.get(e);null!=r&&n.selected.update(r,!0)}else n.selection_manager.clear()}}reset_selection(){this.update_selection(null)}_invalidate_layout_if_needed(){(()=>{for(const t of this.model.side_panels){const e=this.renderer_views.get(t);if(e.layout?.has_size_changed())return this.invalidate_painters(e),!0}return!1})()&&this.compute_layout()}get_renderer_views(){return this.computed_renderers.map((t=>this.renderer_views.get(t)))}*_compute_renderers(){const{above:t,below:e,left:n,right:r,center:i,renderers:o}=this.model;yield*o,yield*t,yield*e,yield*n,yield*r,yield*i,null!=this._title&&(yield this._title),null!=this._toolbar&&(yield this._toolbar);for(const[,t]of this.tool_views)yield*t.overlays}async build_renderer_views(){this.computed_renderers=[...this._compute_renderers()],await Ge(this.renderer_views,this.computed_renderers,{parent:this})}async build_tool_views(){const t=(0,On.Jx)(this.model.toolbar.tools,(t=>t instanceof Ju?t.tools:[t])),{created:e}=await Ge(this.tool_views,[...t],{parent:this});e.map((t=>this.canvas_view.ui_event_bus.register_tool(t)))}connect_signals(){super.connect_signals();const{extra_x_ranges:t,extra_y_ranges:e,extra_x_scales:n,extra_y_scales:r}=this.model.properties;this.on_change([t,e,n,r],(()=>{this.frame.x_range=this.model.x_range,this.frame.y_range=this.model.y_range,this.frame.in_x_scale=this.model.x_scale,this.frame.in_y_scale=this.model.y_scale,this.frame.extra_x_ranges=this.model.extra_x_ranges,this.frame.extra_y_ranges=this.model.extra_y_ranges,this.frame.extra_x_scales=this.model.extra_x_scales,this.frame.extra_y_scales=this.model.extra_y_scales,this.frame.configure_scales()}));const{above:i,below:o,left:a,right:s,center:l,renderers:c}=this.model.properties,u=[i,o,a,s,l];this.on_change(c,(async()=>{await this.build_renderer_views()})),this.on_change(u,(async()=>{await this.build_renderer_views(),this.invalidate_layout()})),this.connect(this.model.toolbar.properties.tools.change,(async()=>{await this.build_tool_views(),await this.build_renderer_views()}));const{x_ranges:d,y_ranges:h}=this.frame;for(const[,t]of d)this.connect(t.change,(()=>{this.request_paint("everything")}));for(const[,t]of h)this.connect(t.change,(()=>{this.request_paint("everything")}));this.connect(this.model.change,(()=>this.request_paint("everything"))),this.connect(this.model.reset,(()=>this.reset()));const{toolbar_location:p}=this.model.properties;this.on_change(p,(async()=>{const{toolbar_location:t}=this.model;if(null!=this._toolbar)null!=t?this._toolbar.toolbar.location=t:(this._toolbar=void 0,await this.build_renderer_views());else if(null!=t){const{toolbar:e,toolbar_inner:n}=this.model;this._toolbar=new gh({toolbar:e}),e.location=t,e.inner=n,await this.build_renderer_views()}this.invalidate_layout()}));const{hold_render:f}=this.model.properties;this.on_change(f,(()=>this._hold_render_changed()))}has_finished(){if(!super.has_finished())return!1;if(this.model.visible)for(const[,t]of this.renderer_views)if(!t.has_finished())return!1;return!0}_after_layout(){super._after_layout(),this.unpause(!0);const t=this.layout.left_panel.bbox,e=this.layout.right_panel.bbox,n=this.layout.center_panel.bbox,r=this.layout.top_panel.bbox,i=this.layout.bottom_panel.bbox,{bbox:o}=this,a=r.bottom,s=o.height-i.top,l=t.right,c=o.width-e.left;this.canvas.style.replace(`\n      .bk-layer.bk-events {\n        display: grid;\n        grid-template-areas:\n          ".    above  .    "\n          "left center right"\n          ".    below  .    ";\n        grid-template-rows: ${Re(a)} ${Re(n.height)} ${Re(s)};\n        grid-template-columns: ${Re(l)} ${Re(n.width)} ${Re(c)};\n      }\n    `);for(const[,t]of this.renderer_views)t instanceof nr&&t.after_layout?.();this.model.setv({inner_width:Math.round(this.frame.bbox.width),inner_height:Math.round(this.frame.bbox.height),outer_width:Math.round(this.bbox.width),outer_height:Math.round(this.bbox.height)},{no_change:!0}),this.model.match_aspect&&(this.pause(),this._range_manager.update_dataranges(),this.unpause(!0)),this._outer_bbox.equals(this.bbox)||(this.canvas_view.resize(),this._outer_bbox=this.bbox,this._invalidate_all=!0,this._needs_paint=!0);const{inner_bbox:u}=this.layout;this._inner_bbox.equals(u)||(this._inner_bbox=u,this._needs_paint=!0),this._needs_paint&&this.paint()}repaint(){this._invalidate_layout_if_needed(),this.paint()}paint(){this.is_paused||(this.model.visible&&(ot.vF.trace(`${this.toString()}.paint()`),this._actual_paint()),this._needs_notify&&(this._needs_notify=!1,this.notify_finished()))}_actual_paint(){const{document:t}=this.model;if(null!=t){const e=t.interactive_duration();e>=0&&e<this.model.lod_interval?setTimeout((()=>{t.interactive_duration()>this.model.lod_timeout&&t.interactive_stop(),this.request_paint("everything")}),this.model.lod_timeout):t.interactive_stop()}this._range_manager.invalidate_dataranges&&(this._range_manager.update_dataranges(),this._invalidate_layout_if_needed());let e=!1,n=!1;if(this._invalidate_all)e=!0,n=!0;else for(const t of this._invalidated_painters){const{level:r}=t.model;if("overlay"!=r?e=!0:n=!0,e&&n)break}this._invalidated_painters.clear(),this._invalidate_all=!1;const r=[this.frame.bbox.left,this.frame.bbox.top,this.frame.bbox.width,this.frame.bbox.height],{primary:i,overlays:o}=this.canvas_view;e&&(i.prepare(),this.canvas_view.prepare_webgl(r),this._paint_empty(i.ctx,r),this._paint_outline(i.ctx,r),this._paint_levels(i.ctx,"image",r,!0),this._paint_levels(i.ctx,"underlay",r,!0),this._paint_levels(i.ctx,"glyph",r,!0),this._paint_levels(i.ctx,"guide",r,!1),this._paint_levels(i.ctx,"annotation",r,!1),i.finish()),(n||b.W.wireframe)&&(o.prepare(),this._paint_levels(o.ctx,"overlay",r,!1),b.W.wireframe&&this._paint_layout(o.ctx,this.layout),o.finish()),null==this._initial_state.range&&(this._initial_state.range=this._range_manager.compute_initial()??void 0),this._needs_paint=!1}_paint_levels(t,e,n,r){for(const i of this.computed_renderers){if(i.level!=e)continue;const o=this.renderer_views.get(i);t.save(),(r||o.needs_clip)&&(t.beginPath(),t.rect(...n),t.clip()),o.render(),t.restore(),o.has_webgl&&o.needs_webgl_blit&&this.canvas_view.blit_webgl(t)}}_paint_layout(t,e){const{x:n,y:r,width:i,height:o}=e.bbox;t.strokeStyle="blue",t.strokeRect(n,r,i,o);for(const i of e)t.save(),e.absolute||t.translate(n,r),this._paint_layout(t,i),t.restore()}_paint_empty(t,e){const[n,r,i,o]=[0,0,this.bbox.width,this.bbox.height],[a,s,l,c]=e;this.visuals.border_fill.doit&&(this.visuals.border_fill.set_value(t),t.fillRect(n,r,i,o),t.clearRect(a,s,l,c)),this.visuals.background_fill.doit&&(this.visuals.background_fill.set_value(t),t.fillRect(a,s,l,c))}_paint_outline(t,e){if(this.visuals.outline_line.doit){t.save(),this.visuals.outline_line.set_value(t);let[n,r,i,o]=e;n+i==this.bbox.width&&(i-=1),r+o==this.bbox.height&&(o-=1),t.strokeRect(n,r,i,o),t.restore()}}export(t="auto",e=!0){const n=(()=>{switch(t){case"auto":return this.canvas_view.model.output_backend;case"png":return"canvas";case"svg":return"svg"}})(),r=new Fu(n,e),{width:i,height:o}=this.bbox;if(r.resize(i,o),0!=i&&0!=o){const{canvas:t}=this.canvas_view.compose();r.ctx.drawImage(t,0,0)}return r}serializable_state(){const{children:t,...e}=super.serializable_state(),n=this.get_renderer_views().map((t=>t.serializable_state())).filter((t=>null!=t.bbox));return{...e,children:[...t??[],{type:"CartesianFrame",bbox:this.frame.bbox.box},...n]}}_hold_render_changed(){this.model.hold_render?this.pause():this.unpause()}}var km;Hm.__name__="PlotView";class Mm extends ZQ{constructor(t){super(t),this.use_map=!1,this.reset=new T.n2(this,"reset")}add_layout(t,e="center"){const n=this.properties[e].get_value();this.setv({[e]:[...n,t]})}remove_layout(t){const e=e=>{(0,Rt.pD)(e,(e=>e==t))};e(this.left),e(this.right),e(this.above),e(this.below),e(this.center)}get data_renderers(){return this.renderers.filter((t=>t instanceof Gs))}add_renderers(...t){this.renderers=[...this.renderers,...t]}add_glyph(t,e=new pr,n={}){const r=new Jl({...n,data_source:e,glyph:t});return this.add_renderers(r),r}add_tools(...t){const e=t.map((t=>t instanceof Yu?t:Yu.from_string(t)));this.toolbar.tools=[...this.toolbar.tools,...e]}remove_tools(...t){this.toolbar.tools=[...Z(new Set(this.toolbar.tools),new Set(t))]}get panels(){return[...this.side_panels,...this.center]}get side_panels(){const{above:t,below:e,left:n,right:r}=this;return(0,Rt.xW)([t,e,n,r])}}km=Mm,Mm.__name__="Plot",km.prototype.default_view=Hm,km.mixins([["outline_",Ke.N1],["background_",Ke.SQ],["border_",Ke.SQ]]),km.define((({Boolean:t,Number:e,String:n,Array:r,Dict:i,Or:o,Ref:a,Null:s,Nullable:l,Struct:c,Opt:u})=>({toolbar:[a(lh),()=>new lh],toolbar_location:[l(_n.aZ),"right"],toolbar_sticky:[t,!0],toolbar_inner:[t,!1],frame_width:[l(e),null],frame_height:[l(e),null],frame_align:[o(t,c({left:u(t),right:u(t),top:u(t),bottom:u(t)})),!0],title:[o(a(aa),n,s),"",{convert:t=>(0,f.Kg)(t)?new aa({text:t}):t}],title_location:[l(_n.aZ),"above"],above:[r(o(a(rr),a(ga))),[]],below:[r(o(a(rr),a(ga))),[]],left:[r(o(a(rr),a(ga))),[]],right:[r(o(a(rr),a(ga))),[]],center:[r(o(a(rr),a($Q))),[]],renderers:[r(a(er)),[]],x_range:[a(yn),()=>new Dn],y_range:[a(yn),()=>new Dn],x_scale:[a(wn),()=>new An],y_scale:[a(wn),()=>new An],extra_x_ranges:[i(a(yn)),{}],extra_y_ranges:[i(a(yn)),{}],extra_x_scales:[i(a(wn)),{}],extra_y_scales:[i(a(wn)),{}],lod_factor:[e,10],lod_interval:[e,300],lod_threshold:[l(e),2e3],lod_timeout:[e,500],hidpi:[t,!0],output_backend:[_n.wf,"canvas"],min_border:[l(e),5],min_border_top:[l(e),null],min_border_left:[l(e),null],min_border_bottom:[l(e),null],min_border_right:[l(e),null],inner_width:[e,0],inner_height:[e,0],outer_width:[e,0],outer_height:[e,0],match_aspect:[t,!1],aspect_scale:[e,1],reset_policy:[_n.Cl,"standard"],hold_render:[t,!1]}))),km.override({width:600,height:600,outline_line_color:"#e5e5e5",border_fill_color:"#ffffff",background_fill_color:"#ffffff"});const Cm=new T.n2({},"gmaps_ready");class Sm extends Hm{initialize(){super.initialize(),this._tiles_loaded=!1,this.zoom_count=0;const{zoom:t,lat:e,lng:n}=this.model.map_options;this.initial_zoom=t,this.initial_lat=e,this.initial_lng=n;const r=new TextDecoder("utf-8");if(this._api_key=r.decode(this.model.api_key),!this._api_key){const t="https://developers.google.com/maps/documentation/javascript/get-api-key";ot.vF.error(`api_key is required. See ${t} for more information on how to obtain your own.`)}}async lazy_initialize(){if(await super.lazy_initialize(),this.map_el=oe({style:{position:"absolute"}}),this.canvas_view.add_underlay(this.map_el),"undefined"==typeof google||void 0===google.maps){if(void 0===window._bokeh_gmaps_callback){const{api_version:t}=this.model;!function(t,e){window._bokeh_gmaps_callback=()=>Cm.emit();const n=encodeURIComponent,r=document.createElement("script");r.type="text/javascript",r.src=`https://maps.googleapis.com/maps/api/js?v=${n(e)}&key=${n(t)}&callback=_bokeh_gmaps_callback`,document.body.appendChild(r)}(this._api_key,t)}Cm.connect((()=>{this._build_map(),this.request_paint("everything")}))}else this._build_map()}remove(){Le(this.map_el),super.remove()}update_range(t,e){if(null==t)this.map.setCenter({lat:this.initial_lat,lng:this.initial_lng}),this.map.setOptions({zoom:this.initial_zoom}),super.update_range(null,e);else if(null!=t.sdx||null!=t.sdy)this.map.panBy(t.sdx??0,t.sdy??0),super.update_range(t,e);else if(null!=t.factor){if(10!==this.zoom_count)return void(this.zoom_count+=1);this.zoom_count=0,this.pause(),super.update_range(t,e);const n=t.factor<0?-1:1,r=this.map.getZoom();if(null!=r){const t=r+n;if(t>=2){this.map.setZoom(t);const[e,n]=this._get_projected_bounds();n-e<0&&this.map.setZoom(r)}}this.unpause()}this._set_bokeh_ranges()}_build_map(){const{maps:t}=google;this.map_types={satellite:t.MapTypeId.SATELLITE,terrain:t.MapTypeId.TERRAIN,roadmap:t.MapTypeId.ROADMAP,hybrid:t.MapTypeId.HYBRID};const e=this.model.map_options,n={center:new t.LatLng(e.lat,e.lng),zoom:e.zoom,disableDefaultUI:!0,mapTypeId:this.map_types[e.map_type],scaleControl:e.scale_control,tilt:e.tilt};null!=e.styles&&(n.styles=JSON.parse(e.styles)),this.map=new t.Map(this.map_el,n),t.event.addListener(this.map,"idle",(()=>this._set_bokeh_ranges())),t.event.addListener(this.map,"bounds_changed",(()=>this._set_bokeh_ranges())),t.event.addListenerOnce(this.map,"tilesloaded",(()=>this._render_finished())),this.connect(this.model.properties.map_options.change,(()=>this._update_options())),this.connect(this.model.map_options.properties.styles.change,(()=>this._update_styles())),this.connect(this.model.map_options.properties.lat.change,(()=>this._update_center("lat"))),this.connect(this.model.map_options.properties.lng.change,(()=>this._update_center("lng"))),this.connect(this.model.map_options.properties.zoom.change,(()=>this._update_zoom())),this.connect(this.model.map_options.properties.map_type.change,(()=>this._update_map_type())),this.connect(this.model.map_options.properties.scale_control.change,(()=>this._update_scale_control())),this.connect(this.model.map_options.properties.tilt.change,(()=>this._update_tilt()))}_render_finished(){this._tiles_loaded=!0,this.notify_finished()}has_finished(){return super.has_finished()&&!0===this._tiles_loaded}_get_latlon_bounds(){const t=this.map.getBounds(),e=t.getNorthEast(),n=t.getSouthWest();return[n.lng(),e.lng(),n.lat(),e.lat()]}_get_projected_bounds(){const[t,e,n,r]=this._get_latlon_bounds(),[i,o]=Qi(t,n),[a,s]=Qi(e,r);return[i,a,o,s]}_set_bokeh_ranges(){const[t,e,n,r]=this._get_projected_bounds();this.frame.x_range.setv({start:t,end:e}),this.frame.y_range.setv({start:n,end:r})}_update_center(t){const e=this.map.getCenter()?.toJSON();null!=e&&(e[t]=this.model.map_options[t],this.map.setCenter(e),this._set_bokeh_ranges())}_update_map_type(){this.map.setOptions({mapTypeId:this.map_types[this.model.map_options.map_type]})}_update_scale_control(){this.map.setOptions({scaleControl:this.model.map_options.scale_control})}_update_tilt(){this.map.setOptions({tilt:this.model.map_options.tilt})}_update_options(){this._update_styles(),this._update_center("lat"),this._update_center("lng"),this._update_zoom(),this._update_map_type()}_update_styles(){const{styles:t}=this.model.map_options;this.map.setOptions({styles:null!=t?JSON.parse(t):null})}_update_zoom(){this.map.setOptions({zoom:this.model.map_options.zoom}),this._set_bokeh_ranges()}_after_layout(){super._after_layout();const{left:t,top:e,width:n,height:r}=this.frame.bbox;this.map_el.style.top=`${e}px`,this.map_el.style.left=`${t}px`,this.map_el.style.width=`${n}px`,this.map_el.style.height=`${r}px`}}var Em,Vm,Om,Pm,Dm,Nm,Rm,Im,jm,zm,Bm,Fm,$m;Sm.__name__="GMapPlotView";class Gm extends qt{constructor(t){super(t)}}Em=Gm,Gm.__name__="MapOptions",Em.define((({Int:t,Number:e})=>({lat:[e],lng:[e],zoom:[t,12]})));class qm extends Gm{constructor(t){super(t)}}Vm=qm,qm.__name__="GMapOptions",Vm.define((({Boolean:t,Int:e,String:n,Nullable:r})=>({map_type:[_n.Nw,"roadmap"],scale_control:[t,!1],styles:[r(n),null],tilt:[e,45]})));class Um extends Mm{constructor(t){super(t),this.use_map=!0}}Om=Um,Um.__name__="GMapPlot",Om.prototype.default_view=Sm,Om.define((({String:t,Bytes:e,Ref:n})=>({map_options:[n(qm)],api_key:[e],api_version:[t,"weekly"]}))),Om.override({x_range:()=>new xn,y_range:()=>new xn,background_fill_alpha:0});class Wm extends Sm{serializable_state(){return{...super.serializable_state(),type:"GMapPlot"}}}Wm.__name__="GMapView";class Zm extends Um{constructor(t){super(t)}}Pm=Zm,Zm.__name__="GMap",Pm.prototype.default_view=Wm;class Xm extends WQ{constructor(){super(...arguments),this._tool_views=new Map}get toolbar_view(){return this.child_views.find((t=>t.model==this.model.toolbar))}get grid_box_view(){return this.child_views.find((t=>t.model==this._grid_box))}_update_location(){const t=this.model.toolbar_location;null==t?this.model.toolbar.visible=!1:this.model.toolbar.setv({visible:!0,location:t})}initialize(){super.initialize(),this._update_location();const{children:t,rows:e,cols:n,spacing:r}=this.model;this._grid_box=new vT({children:t,rows:e,cols:n,spacing:r})}async lazy_initialize(){await super.lazy_initialize(),await this.build_tool_views()}connect_signals(){super.connect_signals();const{toolbar:t,toolbar_location:e,children:n,rows:r,cols:i,spacing:o}=this.model.properties;this.on_change(e,(()=>{this._update_location(),this.rebuild()})),this.on_change([t,n,r,i,o],(()=>{this.rebuild()})),this.on_change(this.model.toolbar.properties.tools,(async()=>{await this.build_tool_views()})),this.mouseenter.connect((()=>{this.toolbar_view.set_visibility(!0)})),this.mouseleave.connect((()=>{this.toolbar_view.set_visibility(!1)}))}remove(){qe(this._tool_views),super.remove()}async build_tool_views(){const t=this.model.toolbar.tools.filter((t=>t instanceof jd));await Ge(this._tool_views,t,{parent:this})}*children(){yield*super.children(),yield*this._tool_views.values()}get child_models(){return[this.model.toolbar,this._grid_box]}_intrinsic_display(){return{inner:this.model.flow_mode,outer:"flex"}}_update_layout(){super._update_layout();const{location:t}=this.model.toolbar,e=(()=>{switch(t){case"above":return"column";case"below":return"column-reverse";case"left":return"row";case"right":return"row-reverse"}})();this.style.append(":host",{flex_direction:e})}export(t="auto",e=!0){const n=(()=>{switch(t){case"auto":case"png":return"canvas";case"svg":return"svg"}})(),r=new Fu(n,e),{x:i,y:o,width:a,height:s}=this.grid_box_view.bbox.relative();r.resize(a,s),r.ctx.save();const l=getComputedStyle(this.el).backgroundColor;r.ctx.fillStyle=l,r.ctx.fillRect(i,o,a,s);for(const n of this.child_views){const i=n.export(t,e),{x:o,y:a}=n.bbox;r.ctx.drawImage(i.canvas,o,a)}return r.ctx.restore(),r}}Xm.__name__="GridPlotView";class Km extends ZQ{constructor(t){super(t)}}Dm=Km,Km.__name__="GridPlot",Dm.prototype.default_view=Xm,Dm.define((({Int:t,Number:e,Tuple:n,Array:r,Ref:i,Or:o,Opt:a,Nullable:s})=>({toolbar:[i(lh),()=>new lh],toolbar_location:[s(_n.aZ),"above"],children:[r(n(i(ZQ),t,t,a(t),a(t))),[]],rows:[s(uT),"max-content"],cols:[s(uT),"max-content"],spacing:[o(e,n(e,e)),0]})));class Ym extends Hm{serializable_state(){return{...super.serializable_state(),type:"Plot"}}}Ym.__name__="FigureView";class Jm extends Mm{constructor(t){super(t)}}Nm=Jm,Jm.__name__="Figure",Nm.prototype.default_view=Ym;class tg extends bm{constructor(t){super(t)}generator(){return new Vu(this.seed??Date.now())}}Rm=tg,tg.__name__="ParkMillerLCG",Rm.define((({Int:t,Nullable:e})=>({seed:[e(t),null]})));class eg extends $s{*children(){yield*super.children(),yield this.fill_view,yield this.line_view}get glyph_view(){return this.fill_view.glyph.data_size>0?this.fill_view.glyph:this.line_view.glyph}async lazy_initialize(){await super.lazy_initialize();const{parent:t}=this,{fill_renderer:e,line_renderer:n}=this.model;this.fill_view=await $e(e,{parent:t}),this.line_view=await $e(n,{parent:t})}remove(){this.fill_view.remove(),this.line_view.remove(),super.remove()}_render(){this.fill_view.render(),this.line_view.render()}renderer_view(t){if(t instanceof Jl){if(t==this.fill_view.model)return this.fill_view;if(t==this.line_view.model)return this.line_view}return super.renderer_view(t)}}eg.__name__="ContourRendererView";class ng extends Gs{constructor(t){super(t)}get_selection_manager(){return this.fill_renderer.data_source.selection_manager}}Im=ng,ng.__name__="ContourRenderer",Im.prototype.default_view=eg,Im.define((({Array:t,Number:e,Ref:n})=>({fill_renderer:[n(Jl)],line_renderer:[n(Jl)],levels:[t(e),[]]})));class rg extends $s{get glyph_view(){return this.node_view.glyph}*children(){yield*super.children(),yield this.edge_view,yield this.node_view}async lazy_initialize(){await super.lazy_initialize(),this.apply_coordinates();const{parent:t}=this,{edge_renderer:e,node_renderer:n}=this.model;this.edge_view=await $e(e,{parent:t}),this.node_view=await $e(n,{parent:t})}connect_signals(){super.connect_signals(),this.connect(this.model.layout_provider.change,(()=>{this.apply_coordinates(),this.edge_view.set_data(),this.node_view.set_data(),this.request_render()}))}apply_coordinates(){const{edge_renderer:t,node_renderer:e}=this.model;if(!(t.glyph instanceof Lf||t.glyph instanceof Mf))throw new Error(`${this}.edge_renderer.glyph must be a MultiLine glyph`);if(!(e.glyph instanceof yl))throw new Error(`${this}.node_renderer.glyph must be a XYGlyph glyph`);const n=this.model.layout_provider.edge_coordinates,r=this.model.layout_provider.node_coordinates;t.glyph.properties.xs.internal=!0,t.glyph.properties.ys.internal=!0,e.glyph.properties.x.internal=!0,e.glyph.properties.y.internal=!0,t.glyph.xs={expr:n.x},t.glyph.ys={expr:n.y},e.glyph.x={expr:r.x},e.glyph.y={expr:r.y}}remove(){this.edge_view.remove(),this.node_view.remove(),super.remove()}_render(){this.edge_view.render(),this.node_view.render()}renderer_view(t){if(t instanceof Jl){if(t==this.edge_view.model)return this.edge_view;if(t==this.node_view.model)return this.node_view}return super.renderer_view(t)}}rg.__name__="GraphRendererView";class ig extends Gs{constructor(t){super(t)}get_selection_manager(){return this.node_renderer.data_source.selection_manager}}jm=ig,ig.__name__="GraphRenderer",jm.prototype.default_view=rg,jm.define((({Ref:t})=>({layout_provider:[t(RQ)],node_renderer:[t(Jl)],edge_renderer:[t(Jl)],selection_policy:[t(EQ),()=>new OQ],inspection_policy:[t(EQ),()=>new OQ]})));class og extends qt{constructor(t){super(t)}}zm=og,og.__name__="Selector",zm.define((({String:t})=>({query:[t]})));class ag extends og{constructor(t){super(t)}find_one(t){return t.querySelector(`#${this.query}`)}}ag.__name__="ByID";class sg extends og{constructor(t){super(t)}find_one(t){return t.querySelector(`.${this.query}`)}}sg.__name__="ByClass";class lg extends og{constructor(t){super(t)}find_one(t){return t.querySelector(this.query)}}lg.__name__="ByCSS";class cg extends og{constructor(t){super(t)}find_one(t){return document.evaluate(this.query,t).iterateNext()}}cg.__name__="ByXPath";class ug extends pr{constructor(t){super(t)}get_column(t){return t in this.data?this.data[t]:[]}get_length(){return super.get_length()??0}initialize(){super.initialize(),this.setup()}load_data(t,e,n){const{adapter:r}=this;let i;switch(i=null!=r?r.execute(this,{response:t}):t,e){case"replace":this.data=i;break;case"append":{const t=this.data;for(const e of this.columns()){const r=Array.from(t[e]),o=Array.from(i[e]),a=r.concat(o);i[e]=null!=n?a.slice(-n):a}this.data=i;break}}}}Bm=ug,ug.__name__="WebDataSource",Bm.define((({Any:t,Int:e,String:n,Nullable:r})=>({max_size:[r(e),null],mode:[_n.nu,"replace"],adapter:[r(t),null],data_url:[n]})));class dg extends ug{constructor(t){super(t),this.initialized=!1}setup(){this.initialized||(this.initialized=!0,new EventSource(this.data_url).onmessage=t=>{this.load_data(JSON.parse(t.data),this.mode,this.max_size??void 0)})}}dg.__name__="ServerSentDataSource";class hg extends ug{constructor(t){super(t),this.interval=null,this.initialized=!1}destroy(){null!=this.interval&&clearInterval(this.interval),super.destroy()}setup(){if(!this.initialized&&(this.initialized=!0,this.get_data(this.mode),null!=this.polling_interval)){const t=()=>this.get_data(this.mode,this.max_size,this.if_modified);this.interval=setInterval(t,this.polling_interval)}}get_data(t,e=null,n=!1){const r=this.prepare_request();r.addEventListener("load",(()=>this.do_load(r,t,e??void 0))),r.addEventListener("error",(()=>this.do_error(r))),r.send()}prepare_request(){const t=new XMLHttpRequest;t.open(this.method,this.data_url,!0),t.withCredentials=!1,t.setRequestHeader("Content-Type",this.content_type);const e=this.http_headers;for(const[n,r]of(0,Q.jO)(e))t.setRequestHeader(n,r);return t}do_load(t,e,n){if(200===t.status){const r=JSON.parse(t.responseText);this.load_data(r,e,n)}}do_error(t){ot.vF.error(`Failed to fetch JSON from ${this.data_url} with code ${t.status}`)}}function pg(t){return null!=t?t:NaN}Fm=hg,hg.__name__="AjaxDataSource",Fm.define((({Boolean:t,Int:e,String:n,Dict:r,Nullable:i})=>({polling_interval:[i(e),null],content_type:[n,"application/json"],http_headers:[r(n),{}],method:[_n.aG,"POST"],if_modified:[t,!1]})));const{hasOwnProperty:fg}=Object.prototype;class Qg extends hr{constructor(t){super(t)}initialize(){super.initialize(),this._update_data()}connect_signals(){super.connect_signals(),this.connect(this.properties.geojson.change,(()=>this._update_data()))}_update_data(){this.data=this.geojson_to_column_data()}_get_new_list_array(t){return(0,Rt.y1)(0,t).map((t=>[]))}_get_new_nan_array(t){return(0,Rt.y1)(0,t).map((t=>NaN))}_add_properties(t,e,n,r){const i=t.properties??{};for(const[t,o]of(0,Q.jO)(i))fg.call(e,t)||(e[t]=this._get_new_nan_array(r)),e[t][n]=pg(o)}_add_geometry(t,e,n){function r(t,e){return t.concat([[NaN,NaN,NaN]]).concat(e)}switch(t.type){case"Point":{const[r,i,o]=t.coordinates;e.x[n]=r,e.y[n]=i,e.z[n]=pg(o);break}case"LineString":{const{coordinates:r}=t;for(let t=0;t<r.length;t++){const[i,o,a]=r[t];e.xs[n][t]=i,e.ys[n][t]=o,e.zs[n][t]=pg(a)}break}case"Polygon":{t.coordinates.length>1&&ot.vF.warn("Bokeh does not support Polygons with holes in, only exterior ring used.");const r=t.coordinates[0];for(let t=0;t<r.length;t++){const[i,o,a]=r[t];e.xs[n][t]=i,e.ys[n][t]=o,e.zs[n][t]=pg(a)}break}case"MultiPoint":ot.vF.warn("MultiPoint not supported in Bokeh");break;case"MultiLineString":{const i=t.coordinates.reduce(r);for(let t=0;t<i.length;t++){const[r,o,a]=i[t];e.xs[n][t]=r,e.ys[n][t]=o,e.zs[n][t]=pg(a)}break}case"MultiPolygon":{const i=[];for(const e of t.coordinates)e.length>1&&ot.vF.warn("Bokeh does not support Polygons with holes in, only exterior ring used."),i.push(e[0]);const o=i.reduce(r);for(let t=0;t<o.length;t++){const[r,i,a]=o[t];e.xs[n][t]=r,e.ys[n][t]=i,e.zs[n][t]=pg(a)}break}default:throw new Error(`Invalid GeoJSON geometry type: ${t.type}`)}}geojson_to_column_data(){const t=JSON.parse(this.geojson);let e;switch(t.type){case"GeometryCollection":if((0,f.cA)(t.geometries))throw new Error("No geometries found in GeometryCollection");if(0===t.geometries.length)throw new Error("geojson.geometries must have one or more items");e=t.geometries;break;case"FeatureCollection":if((0,f.cA)(t.features))throw new Error("No features found in FeaturesCollection");if(0==t.features.length)throw new Error("geojson.features must have one or more items");e=t.features;break;default:throw new Error("Bokeh only supports type GeometryCollection and FeatureCollection at top level")}let n=0;for(const t of e){const e="Feature"===t.type?t.geometry:t;"GeometryCollection"==e.type?n+=e.geometries.length:n+=1}const r={x:this._get_new_nan_array(n),y:this._get_new_nan_array(n),z:this._get_new_nan_array(n),xs:this._get_new_list_array(n),ys:this._get_new_list_array(n),zs:this._get_new_list_array(n)};let i=0;for(const t of e){const e="Feature"==t.type?t.geometry:t;if("GeometryCollection"==e.type)for(const o of e.geometries)this._add_geometry(o,r,i),"Feature"===t.type&&this._add_properties(t,r,i,n),i+=1;else this._add_geometry(e,r,i),"Feature"===t.type&&this._add_properties(t,r,i,n),i+=1}return r}}var Tg,mg,gg,_g,bg,vg,yg,xg,wg,Lg,Ag,Hg,kg;$m=Qg,Qg.__name__="GeoJSONDataSource",$m.define((({String:t})=>({geojson:[t]}))),$m.internal((({Any:t,Dict:e,Arrayable:n})=>({data:[e(n(t)),{}]})));class Mg extends qt{constructor(t){super(t)}initialize(){super.initialize(),this.tiles=new Map,this._normalize_case()}connect_signals(){super.connect_signals(),this.connect(this.change,(()=>this._clear_cache()))}string_lookup_replace(t,e){let n=t;for(const[t,r]of(0,Q.jO)(e))n=n.replace(`{${t}}`,r);return n}_normalize_case(){const t=this.url.replace("{x}","{X}").replace("{y}","{Y}").replace("{z}","{Z}").replace("{q}","{Q}").replace("{xmin}","{XMIN}").replace("{ymin}","{YMIN}").replace("{xmax}","{XMAX}").replace("{ymax}","{YMAX}");this.url=t}_clear_cache(){this.tiles=new Map}tile_xyz_to_key(t,e,n){return`${t}:${e}:${n}`}key_to_tile_xyz(t){const[e,n,r]=t.split(":").map((t=>parseInt(t)));return[e,n,r]}sort_tiles_from_center(t,e){const[n,r,i,o]=e,a=(i-n)/2+n,s=(o-r)/2+r;t.sort((function(t,e){return Math.sqrt((a-t[0])**2+(s-t[1])**2)-Math.sqrt((a-e[0])**2+(s-e[1])**2)}))}get_image_url(t,e,n){return this.string_lookup_replace(this.url,this.extra_url_vars).replace("{X}",t.toString()).replace("{Y}",e.toString()).replace("{Z}",n.toString())}}function Cg(t,e){return Ti(t,e)}Tg=Mg,Mg.__name__="TileSource",Tg.define((({Number:t,String:e,Dict:n,Nullable:r})=>({url:[e,""],tile_size:[t,256],max_zoom:[t,30],min_zoom:[t,0],extra_url_vars:[n(e),{}],attribution:[e,""],x_origin_offset:[t],y_origin_offset:[t],initial_resolution:[r(t),null]})));class Sg extends Mg{constructor(t){super(t)}initialize(){super.initialize(),this._resolutions=(0,Rt.y1)(this.min_zoom,this.max_zoom+1).map((t=>this.get_resolution(t)))}_computed_initial_resolution(){return null!=this.initial_resolution?this.initial_resolution:2*Math.PI*6378137/this.tile_size}is_valid_tile(t,e,n){return!(!this.wrap_around&&(t<0||t>=2**n)||e<0||e>=2**n)}parent_by_tile_xyz(t,e,n){const r=this.tile_xyz_to_quadkey(t,e,n),i=r.substring(0,r.length-1);return this.quadkey_to_tile_xyz(i)}get_resolution(t){return this._computed_initial_resolution()/2**t}get_resolution_by_extent(t,e,n){return[(t[2]-t[0])/n,(t[3]-t[1])/e]}get_level_by_extent(t,e,n){const r=(t[2]-t[0])/n,i=(t[3]-t[1])/e,o=Math.max(r,i);let a=0;for(const t of this._resolutions){if(o>t){if(0==a)return 0;if(a>0)return a-1}a+=1}return a-1}get_closest_level_by_extent(t,e,n){const r=(t[2]-t[0])/n,i=(t[3]-t[1])/e,o=Math.max(r,i),a=this._resolutions.reduce((function(t,e){return Math.abs(e-o)<Math.abs(t-o)?e:t}));return this._resolutions.indexOf(a)}snap_to_zoom_level(t,e,n,r){const[i,o,a,s]=t,l=this._resolutions[r];let c=n*l,u=e*l;if(!this.snap_to_zoom){const t=(a-i)/c,e=(s-o)/u;t>e?(c=a-i,u*=t):(c*=e,u=s-o)}const d=(c-(a-i))/2,h=(u-(s-o))/2;return[i-d,o-h,a+d,s+h]}tms_to_wmts(t,e,n){return[t,2**n-1-e,n]}wmts_to_tms(t,e,n){return[t,2**n-1-e,n]}pixels_to_meters(t,e,n){const r=this.get_resolution(n);return[t*r-this.x_origin_offset,e*r-this.y_origin_offset]}meters_to_pixels(t,e,n){const r=this.get_resolution(n);return[(t+this.x_origin_offset)/r,(e+this.y_origin_offset)/r]}pixels_to_tile(t,e){let n=Math.ceil(t/this.tile_size);return n=0===n?n:n-1,[n,Math.max(Math.ceil(e/this.tile_size)-1,0)]}pixels_to_raster(t,e,n){return[t,(this.tile_size<<n)-e]}meters_to_tile(t,e,n){const[r,i]=this.meters_to_pixels(t,e,n);return this.pixels_to_tile(r,i)}get_tile_meter_bounds(t,e,n){const[r,i]=this.pixels_to_meters(t*this.tile_size,e*this.tile_size,n),[o,a]=this.pixels_to_meters((t+1)*this.tile_size,(e+1)*this.tile_size,n);return[r,i,o,a]}get_tile_geographic_bounds(t,e,n){const r=this.get_tile_meter_bounds(t,e,n),[i,o,a,s]=function(t){const[e,n,r,i]=t,[o,a]=Cg(e,n),[s,l]=Cg(r,i);return[o,a,s,l]}(r);return[i,o,a,s]}get_tiles_by_extent(t,e,n=1){const[r,i,o,a]=t;let[s,l]=this.meters_to_tile(r,i,e),[c,u]=this.meters_to_tile(o,a,e);s-=n,l-=n,c+=n,u+=n;const d=[];for(let t=u;t>=l;t--)for(let n=s;n<=c;n++)this.is_valid_tile(n,t,e)&&d.push([n,t,e,this.get_tile_meter_bounds(n,t,e)]);return this.sort_tiles_from_center(d,[s,l,c,u]),d}quadkey_to_tile_xyz(t){let e=0,n=0;const r=t.length;for(let i=r;i>0;i--){const o=1<<i-1;switch(t.charAt(r-i)){case"0":continue;case"1":e|=o;break;case"2":n|=o;break;case"3":e|=o,n|=o;break;default:throw new TypeError(`Invalid Quadkey: ${t}`)}}return[e,n,r]}tile_xyz_to_quadkey(t,e,n){let r="";for(let i=n;i>0;i--){const n=1<<i-1;let o=0;t&n&&(o+=1),e&n&&(o+=2),r+=o.toString()}return r}children_by_tile_xyz(t,e,n){const r=this.tile_xyz_to_quadkey(t,e,n),i=[];for(let t=0;t<=3;t++){const[e,n,o]=this.quadkey_to_tile_xyz(r+t.toString()),a=this.get_tile_meter_bounds(e,n,o);i.push([e,n,o,a])}return i}get_closest_parent_by_tile_xyz(t,e,n){const r=this.calculate_world_x_by_tile_xyz(t,e,n);[t,e,n]=this.normalize_xyz(t,e,n);let i=this.tile_xyz_to_quadkey(t,e,n);for(;i.length>0;)if(i=i.substring(0,i.length-1),[t,e,n]=this.quadkey_to_tile_xyz(i),[t,e,n]=this.denormalize_xyz(t,e,n,r),this.tiles.has(this.tile_xyz_to_key(t,e,n)))return[t,e,n];return[0,0,0]}normalize_xyz(t,e,n){if(this.wrap_around){const r=2**n;return[(t%r+r)%r,e,n]}return[t,e,n]}denormalize_xyz(t,e,n,r){return[t+r*2**n,e,n]}denormalize_meters(t,e,n,r){return[t+2*r*Math.PI*6378137,e]}calculate_world_x_by_tile_xyz(t,e,n){return Math.floor(t/2**n)}}mg=Sg,Sg.__name__="MercatorTileSource",mg.define((({Boolean:t})=>({snap_to_zoom:[t,!1],wrap_around:[t,!0]}))),mg.override({x_origin_offset:20037508.34,y_origin_offset:20037508.34,initial_resolution:156543.03392804097});class Eg extends Sg{constructor(t){super(t)}get_image_url(t,e,n){const r=this.string_lookup_replace(this.url,this.extra_url_vars);let i,o,a,s;return this.use_latlon?[o,s,i,a]=this.get_tile_geographic_bounds(t,e,n):[o,s,i,a]=this.get_tile_meter_bounds(t,e,n),r.replace("{XMIN}",o.toString()).replace("{YMIN}",s.toString()).replace("{XMAX}",i.toString()).replace("{YMAX}",a.toString())}}gg=Eg,Eg.__name__="BBoxTileSource",gg.define((({Boolean:t})=>({use_latlon:[t,!1]})));class Vg extends Sg{constructor(t){super(t)}get_image_url(t,e,n){const r=this.string_lookup_replace(this.url,this.extra_url_vars),[i,o,a]=this.tms_to_wmts(t,e,n),s=this.tile_xyz_to_quadkey(i,o,a);return r.replace("{Q}",s)}}Vg.__name__="QUADKEYTileSource";class Og extends Sg{constructor(t){super(t)}get_image_url(t,e,n){const r=this.string_lookup_replace(this.url,this.extra_url_vars),[i,o,a]=this.tms_to_wmts(t,e,n);return r.replace("{X}",i.toString()).replace("{Y}",o.toString()).replace("{Z}",a.toString())}}Og.__name__="WMTSTileSource";class Pg extends tr{initialize(){this._tiles=[],super.initialize()}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.request_render())),this.connect(this.model.tile_source.change,(()=>this.request_render()))}remove(){null!=this.attribution_el&&Le(this.attribution_el),super.remove()}get_extent(){return[this.x_range.start,this.y_range.start,this.x_range.end,this.y_range.end]}get map_plot(){return this.plot_model}get map_canvas(){return this.layer.ctx}get map_frame(){return this.plot_view.frame}get x_range(){return this.map_plot.x_range}get y_range(){return this.map_plot.y_range}_set_data(){this.extent=this.get_extent(),this._last_height=void 0,this._last_width=void 0}_update_attribution(){null!=this.attribution_el&&Le(this.attribution_el);const{attribution:t}=this.model.tile_source;if((0,f.Kg)(t)&&t.length>0){const{layout:e,frame:n}=this.plot_view,r=e.bbox.width-n.bbox.right,i=e.bbox.height-n.bbox.bottom,o=n.bbox.width;this.attribution_el=oe({style:{right:`${r}px`,bottom:`${i}px`,"max-width":`${o}px`}});const a=oe();a.innerHTML=t;const s=this.attribution_el.attachShadow({mode:"open"}),l=new Pe(":host{position:absolute;padding:2px;background-color:rgba(255, 255, 255, 0.5);font-size:9px;line-height:1.05;white-space:nowrap;overflow:hidden;text-overflow:ellipsis;}a{color:black;}");s.appendChild(l.el),s.appendChild(a),this.attribution_el.title=a.textContent.replace(/\s*\n\s*/g," "),this.plot_view.canvas_view.add_event(this.attribution_el)}}_map_data(){this.initial_extent=this.get_extent();const t=this.model.tile_source.get_level_by_extent(this.initial_extent,this.map_frame.bbox.height,this.map_frame.bbox.width),e=this.model.tile_source.snap_to_zoom_level(this.initial_extent,this.map_frame.bbox.height,this.map_frame.bbox.width,t);this.x_range.start=e[0],this.y_range.start=e[1],this.x_range.end=e[2],this.y_range.end=e[3],this.x_range instanceof xn&&(this.x_range.reset_start=e[0],this.x_range.reset_end=e[2]),this.y_range instanceof xn&&(this.y_range.reset_start=e[1],this.y_range.reset_end=e[3]),this._update_attribution()}_create_tile(t,e,n,r,i=!1){const o=this.model.tile_source.tile_xyz_to_quadkey(t,e,n),a=this.model.tile_source.tile_xyz_to_key(t,e,n);if(this.model.tile_source.tiles.has(a))return;const[s,l,c]=this.model.tile_source.normalize_xyz(t,e,n),u=this.model.tile_source.get_image_url(s,l,c),d={img:void 0,tile_coords:[t,e,n],normalized_coords:[s,l,c],quadkey:o,cache_key:a,bounds:r,loaded:!1,finished:!1,x_coord:r[0],y_coord:r[3]};this.model.tile_source.tiles.set(a,d),this._tiles.push(d),new Qo(u,{loaded:t=>{Object.assign(d,{img:t,loaded:!0}),i?(d.finished=!0,this.notify_finished()):this.request_render()},failed(){d.finished=!0}})}_enforce_aspect_ratio(){if(this._last_height!==this.map_frame.bbox.height||this._last_width!==this.map_frame.bbox.width){const t=this.get_extent(),e=this.model.tile_source.get_level_by_extent(t,this.map_frame.bbox.height,this.map_frame.bbox.width),n=this.model.tile_source.snap_to_zoom_level(t,this.map_frame.bbox.height,this.map_frame.bbox.width,e);this.x_range.setv({start:n[0],end:n[2]}),this.y_range.setv({start:n[1],end:n[3]}),this.extent=n,this._last_height=this.map_frame.bbox.height,this._last_width=this.map_frame.bbox.width}}has_finished(){if(!super.has_finished())return!1;if(0==this._tiles.length)return!1;for(const t of this._tiles)if(!t.finished)return!1;return!0}_render(){null==this.map_initialized&&(this._set_data(),this._map_data(),this.map_initialized=!0),this._enforce_aspect_ratio(),this._update(),null!=this.prefetch_timer&&clearTimeout(this.prefetch_timer),this.prefetch_timer=setTimeout(this._prefetch_tiles.bind(this),500),this.has_finished()&&this.notify_finished()}_draw_tile(t){const e=this.model.tile_source.tiles.get(t);if(null!=e&&e.loaded){const[[t],[n]]=this.coordinates.map_to_screen([e.bounds[0]],[e.bounds[3]]),[[r],[i]]=this.coordinates.map_to_screen([e.bounds[2]],[e.bounds[1]]),o=r-t,a=i-n,s=t,l=n,c=this.map_canvas.getImageSmoothingEnabled();this.map_canvas.setImageSmoothingEnabled(this.model.smoothing),this.map_canvas.drawImage(e.img,s,l,o,a),this.map_canvas.setImageSmoothingEnabled(c),e.finished=!0}}_set_rect(){const t=this.plot_model.outline_line_width,e=this.map_frame.bbox.left+t/2,n=this.map_frame.bbox.top+t/2,r=this.map_frame.bbox.width-t,i=this.map_frame.bbox.height-t;this.map_canvas.rect(e,n,r,i),this.map_canvas.clip()}_render_tiles(t){this.map_canvas.save(),this._set_rect(),this.map_canvas.globalAlpha=this.model.alpha;for(const e of t)this._draw_tile(e);this.map_canvas.restore()}_prefetch_tiles(){const{tile_source:t}=this.model,e=this.get_extent(),n=this.map_frame.bbox.height,r=this.map_frame.bbox.width,i=this.model.tile_source.get_level_by_extent(e,n,r),o=this.model.tile_source.get_tiles_by_extent(e,i);for(let e=0,n=Math.min(10,o.length);e<n;e++){const[n,r,i]=o[e],a=this.model.tile_source.children_by_tile_xyz(n,r,i);for(const e of a){const[n,r,i,o]=e;t.tiles.has(t.tile_xyz_to_key(n,r,i))||this._create_tile(n,r,i,o,!0)}}}_fetch_tiles(t){for(const e of t){const[t,n,r,i]=e;this._create_tile(t,n,r,i)}}_update(){const{tile_source:t}=this.model,{min_zoom:e}=t,{max_zoom:n}=t;let r=this.get_extent();const i=this.extent[2]-this.extent[0]<r[2]-r[0],o=this.map_frame.bbox.height,a=this.map_frame.bbox.width;let s=t.get_level_by_extent(r,o,a),l=!1;s<e?(r=this.extent,s=e,l=!0):s>n&&(r=this.extent,s=n,l=!0),l&&(this.x_range.setv({start:r[0],end:r[2]}),this.y_range.setv({start:r[1],end:r[3]})),this.extent=r;const c=t.get_tiles_by_extent(r,s),u=[],d=[],h=[],p=[];for(const e of c){const[n,r,o]=e,a=t.tile_xyz_to_key(n,r,o),s=t.tiles.get(a);if(null!=s&&s.loaded)d.push(a);else if(this.model.render_parents){const[e,a,s]=t.get_closest_parent_by_tile_xyz(n,r,o),l=t.tile_xyz_to_key(e,a,s),c=t.tiles.get(l);if(null!=c&&c.loaded&&!(0,Rt.mK)(h,l)&&h.push(l),i){const e=t.children_by_tile_xyz(n,r,o);for(const[n,r,i]of e){const e=t.tile_xyz_to_key(n,r,i);t.tiles.has(e)&&p.push(e)}}}null==s&&u.push(e)}this._render_tiles(h),this._render_tiles(p),this._render_tiles(d),null!=this.render_timer&&clearTimeout(this.render_timer),this.render_timer=setTimeout((()=>this._fetch_tiles(u)),65)}}Pg.__name__="TileRendererView";class Dg extends er{constructor(t){super(t)}}_g=Dg,Dg.__name__="TileRenderer",_g.prototype.default_view=Pg,_g.define((({Boolean:t,Number:e,Ref:n})=>({alpha:[e,1],smoothing:[t,!0],tile_source:[n(Mg),()=>new Og],render_parents:[t,!0]}))),_g.override({level:"image"});class Ng extends Sg{constructor(t){super(t)}get_image_url(t,e,n){return this.string_lookup_replace(this.url,this.extra_url_vars).replace("{X}",t.toString()).replace("{Y}",e.toString()).replace("{Z}",n.toString())}}Ng.__name__="TMSTileSource";class Rg extends qt{constructor(t){super(t)}}bg=Rg,Rg.__name__="Texture",bg.define((()=>({repetition:[_n.tB,"repeat"]})));class Ig extends Rg{constructor(t){super(t)}get func(){const t=x(this.code);return new Function("ctx","color","scale","weight",t)}get_pattern(t,e,n){const r=document.createElement("canvas");r.width=e,r.height=e;const i=r.getContext("2d");return this.func.call(this,i,t,e,n),r}}vg=Ig,Ig.__name__="CanvasTexture",vg.define((({String:t})=>({code:[t]})));class jg extends Rg{constructor(t){super(t)}initialize(){super.initialize(),this._loader=new Qo(this.url)}get_pattern(t,e,n){const{_loader:r}=this;return this._loader.finished?r.image:r.promise}}yg=jg,jg.__name__="ImageURLTexture",yg.define((({String:t})=>({url:[t]})));class zg extends am{constructor(){super(...arguments),this._style=new Pe}styles(){return[...super.styles(),pd,this._style]}render(){super.render();const t=`var(--bokeh-icon-${this.model.icon_name})`,e=(0,Ye.do)(this.model.color),n=(()=>{const{size:t}=this.model;return(0,f.Et)(t)?`${t}px`:t})();this._style.replace(`\n      :host {\n        display: inline-block;\n        vertical-align: middle;\n        width: ${n};\n        height: ${n};\n        background-color: ${e};\n        mask-image: ${t};\n        mask-size: contain;\n        mask-repeat: no-repeat;\n        -webkit-mask-image: ${t};\n        -webkit-mask-size: contain;\n        -webkit-mask-repeat: no-repeat;\n      }\n    `)}}zg.__name__="BuiltinIconView";class Bg extends sm{constructor(t){super(t)}}xg=Bg,Bg.__name__="BuiltinIcon",xg.prototype.default_view=zg,xg.define((({String:t,Color:e})=>({icon_name:[t],color:[e,"gray"]})));class Fg extends am{constructor(){super(...arguments),this._style=new Pe}styles(){return[...super.styles(),this._style]}render(){super.render();const t=(()=>{const{size:t}=this.model;return(0,f.Et)(t)?`${t}px`:t})();this._style.replace(`\n      :host {\n        display: inline-block;\n        vertical-align: middle;\n      }\n      :host svg {\n        width: ${t};\n        height: ${t};\n      }\n    `);const e=(new DOMParser).parseFromString(this.model.svg,"image/svg+xml");this.shadow_el.append(e.documentElement)}}Fg.__name__="SVGIconView";class $g extends sm{constructor(t){super(t)}}wg=$g,$g.__name__="SVGIcon",wg.prototype.default_view=Fg,wg.define((({String:t})=>({svg:[t]})));class Gg extends am{constructor(){super(...arguments),this._tabler=new Ne(`${Gg._url}/tabler-icons.min.css`),this._style=new Pe}styles(){return[...super.styles(),this._tabler,this._style]}initialize(){super.initialize(),Gg._fonts.initialize()}render(){super.render();const t=(()=>{const{size:t}=this.model;return(0,f.Et)(t)?`${t}px`:t})();this._style.replace(`\n      :host {\n        display: inline-block;\n        vertical-align: middle;\n        font-size: ${t};\n      }\n    `);const e=ae({class:["ti",`ti-${this.model.icon_name}`]});this.shadow_el.appendChild(e)}}Lg=Gg,Gg.__name__="TablerIconView",Gg._url="https://unpkg.com/@tabler/icons@latest/iconfont",Gg._fonts=new De(`    /*!\n    * Tabler Icons 1.68.0 by tabler - https://tabler.io\n    * License - https://github.com/tabler/tabler-icons/blob/master/LICENSE\n    */\n  @font-face {\n    font-family: "tabler-icons";\n    font-style: normal;\n    font-weight: 400;\n    src: url("${Lg._url}/fonts/tabler-icons.eot");\n    src: url("${Lg._url}/fonts/tabler-icons.eot?#iefix") format("embedded-opentype"),\n         url("${Lg._url}/fonts/tabler-icons.woff2") format("woff2"),\n         url("${Lg._url}/fonts/tabler-icons.woff") format("woff"),\n         url("${Lg._url}/fonts/tabler-icons.ttf") format("truetype"),\n         url("${Lg._url}/fonts/tabler-icons.svg#tabler-icons") format("svg");\n  }\n\n  @media screen and (-webkit-min-device-pixel-ratio: 0) {\n    @font-face {\n      font-family: "tabler-icons";\n      src: url("${Lg._url}/fonts/tabler-icons.svg#tabler-icons") format("svg");\n    }\n  }\n`);class qg extends sm{constructor(t){super(t)}}Ag=qg,qg.__name__="TablerIcon",Ag.prototype.default_view=Gg,Ag.define((({String:t})=>({icon_name:[t]})));class Ug extends je{}Ug.__name__="DOMNodeView";class Wg extends qt{constructor(t){super(t)}}Wg.__name__="DOMNode",Wg.__module__="bokeh.models.dom";class Zg extends Ug{render(){this.el.textContent=this.model.content}_createElement(){return document.createTextNode("")}}Zg.__name__="TextView";class Xg extends Wg{constructor(t){super(t)}}Hg=Xg,Xg.__name__="Text",Hg.prototype.default_view=Zg,Hg.define((({String:t})=>({content:[t,""]})));const Kg=Wu;class Yg extends Uu{*children(){yield*super.children(),yield this._content}styles(){return[...super.styles(),":host{--bokeh-bg-color:white;--bokeh-border-color:#e5e5e5;--bokeh-shadow-color:#e5e5e5;}:host{position:fixed;z-index:1000;left:0;right:0;top:0;bottom:0;margin-left:auto;margin-right:auto;margin-top:auto;margin-bottom:auto;width:80vw;height:60vh;overflow:hidden;display:flex;flex-direction:column;flex-wrap:nowrap;background-color:var(--bokeh-bg-color);border:1px solid var(--bokeh-border-color);box-shadow:5px 5px 10px var(--bokeh-shadow-color);}.bk-title{position:relative;flex:1;min-height:0;}.bk-content{position:relative;flex:1;min-height:100%;display:flex;}.bk-buttons{position:relative;flex:1;min-height:0;}.bk-close{position:absolute;top:0;right:0;width:18px;height:18px;cursor:pointer;background-color:gray;mask-image:var(--bokeh-icon-x);mask-size:contain;mask-repeat:no-repeat;-webkit-mask-image:var(--bokeh-icon-x);-webkit-mask-size:contain;-webkit-mask-repeat:no-repeat;}.bk-close:hover{background-color:red;}",pd]}async lazy_initialize(){await super.lazy_initialize();const t=(()=>{const{content:t}=this.model;return(0,f.Kg)(t)?new Xg({content:t}):t})();this._content=await $e(t,{parent:this})}connect_signals(){super.connect_signals();const{visible:t}=this.model.properties;this.on_change(t,(()=>this.render()))}remove(){this._content.remove(),super.remove()}render(){if(super.render(),!this.model.visible)return void this.el.remove();document.body.appendChild(this.el),this._content.render();const t=oe({class:"bk-title"}),e=oe({class:"bk-content"},this._content.el),n=oe({class:"bk-buttons"});if(this.shadow_el.appendChild(t),this.shadow_el.appendChild(e),this.shadow_el.appendChild(n),this.model.closable){const t=oe({class:"bk-close"});t.addEventListener("click",(()=>this.model.visible=!1)),this.shadow_el.appendChild(t)}}}Yg.__name__="DialogView";class Jg extends Wu{constructor(t){super(t)}}kg=Jg,Jg.__name__="Dialog",kg.prototype.default_view=Yg,kg.define((({Boolean:t,String:e,Array:n,Ref:r,Or:i,Nullable:o})=>({title:[o(i(e,r(Wg))),null],content:[i(e,r(Wg),r(Wu))],buttons:[n(r(Kg)),[]],modal:[t,!1],closable:[t,!0],draggable:[t,!0]})));var t_,e_,n_,r_=n(3542);class i_{constructor(t,e,n){this.click=t,this.max_items=e,this.max_depth=n,this.visited=new WeakSet,this.depth=0}to_html(t){if((0,f.Gv)(t)){if(this.visited.has(t))return ae("<circular>");this.visited.add(t)}return null==t?this.null():(0,f.Lm)(t)?this.boolean(t):(0,f.Et)(t)?this.number(t):(0,f.Kg)(t)?this.string(t):(0,f.Bm)(t)?this.symbol(t):t instanceof qt?this.model(t):t instanceof m.mA?this.property(t):(0,f.Qd)(t)?this.object(t):(0,f.cy)(t)?this.array(t):(0,f.xZ)(t)?this.iterable(t):ae(z(t))}null(){return ae({class:"null"},"null")}token(t){return ae({class:"token"},t)}boolean(t){return ae({class:"boolean"},`${t}`)}number(t){return ae({class:"number"},`${t}`)}string(t){const e=t.includes("'"),n=t.includes('"'),r=e&&n?`\`${t.replace(/`/g,"\\`")}\``:n?`'${t}'`:`"${t}"`;return ae({class:"string"},r)}symbol(t){return ae({class:"symbol"},t.toString())}array(t){const e=this.token,n=[];let r=0;for(const e of t)if(n.push(this.to_html(e)),r++>this.max_items){n.push(ae("…"));break}return ae({class:"array"},e("["),...(0,On.CC)(n,(()=>e(", "))),e("]"))}iterable(t){const e=this.token,n=Object(t)[Symbol.toStringTag]??"Object",r=this.array([...t]);return ae({class:"iterable"},`${n}`,e("("),r,e(")"))}object(t){const e=this.token,n=[];let r=0;for(const[i,o]of(0,Q.jO)(t))if(n.push(ae(`${i}`,e(": "),this.to_html(o))),r++>this.max_items){n.push(ae("…"));break}return ae({class:"object"},e("{"),...(0,On.CC)(n,(()=>e(", "))),e("}"))}model(t){const e=this.token,n=ae({class:"model"},t.constructor.__qualified__,e("("),this.to_html(t.id),e(")"));return n.addEventListener("click",(()=>this.click(t))),n}property(t){const e=this.model(t.obj),n=ae({class:"attr"},t.attr);return ae(e,this.token("."),n)}}i_.__name__="HTMLPrinter";class o_ extends Uu{constructor(){super(...arguments),this.prev_listener=null,this.watched_props=new Set}styles(){return[...super.styles(),'.null{color:#7724c1;}.token{color:#881280;}.boolean{color:#007500;}.number{color:#1a1aa6;}.string{color:#994500;}.symbol{color:#c80000;}.model{cursor:pointer;}.attr{color:#c80000;}:root{--common-padding:3px;--common-outline:#1a73e8 solid 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Map}*children(){yield*super.children(),yield*this._refs.values()}async lazy_initialize(){await super.lazy_initialize(),await Ge(this._refs,this.model.refs)}remove(){qe(this._refs),super.remove()}render(){Ae(this.el),this.el.style.display="contents";const t=new DOMParser,e=(()=>{const{html:e}=this.model;if((0,f.Kg)(e)){const n=t.parseFromString(e,"text/html"),r=n.createNodeIterator(n,NodeFilter.SHOW_ELEMENT,(t=>"ref"==t.nodeName.toLowerCase()?NodeFilter.FILTER_ACCEPT:NodeFilter.FILTER_REJECT));let i;for(;i=r.nextNode();){(0,_.vA)(i instanceof Element);const t=i.getAttribute("id");if(null!=t)for(const[e,n]of this._refs)if(e.id==t){n.render(),i.replaceWith(n.el);break}}return[...n.body.childNodes]}return[]})();for(const t of e)this.el.appendChild(t)}}c_.__name__="HTMLView";class u_ extends Wg{constructor(t){super(t)}}n_=u_,u_.__name__="HTML",n_.prototype.default_view=c_,n_.define((({String:t,Array:e,Or:n,Ref:r})=>({html:[n(t,e(n(t,r(Wg),r(Wu))))],refs:[e(n(r(Wg),r(Wu))),[]]})));const 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";display:block;top:calc(-1*var(--tooltip-arrow-height));border-bottom-width:var(--tooltip-arrow-height);border-bottom-color:var(--tooltip-arrow-color);}:host(.bk-below) .bk-tooltip-content::after{position:absolute;margin:0 0 0 calc(-1*var(--tooltip-arrow-half-width));left:50%;width:0;height:0;border-style:solid;border-width:0 var(--tooltip-arrow-half-width) 0 var(--tooltip-arrow-half-width);border-color:transparent;content:" ";display:block;bottom:calc(-1*var(--tooltip-arrow-height));border-top-width:var(--tooltip-arrow-height);border-top-color:var(--tooltip-arrow-color);}.bk-tooltip-row-label{text-align:right;color:#26aae1;}.bk-tooltip-row-value{color:none;}.bk-tooltip-color-block{width:12px;height:12px;margin-left:5px;margin-right:5px;outline:#dddddd solid 1px;display:inline-block;}.bk-close{position:absolute;top:2px;right:2px;width:12px;height:12px;cursor:pointer;background-color:gray;mask-image:var(--bokeh-icon-x);mask-size:contain;mask-repeat:no-repeat;-webkit-mask-image:var(--bokeh-icon-x);-webkit-mask-size:contain;-webkit-mask-repeat:no-repeat;}.bk-close:hover{background-color:red;}',pd]}get content(){const{content:t}=this.model;return(0,f.Kg)(t)?document.createTextNode(t):t instanceof u_?((0,_.vA)(null!=this._html),this._html.el):t}render(){if(super.render(),this._html?.render(),this.content_el=oe({class:"bk-tooltip-content"},this.content),this.shadow_el.appendChild(this.content_el),this.model.closable){const t=oe({class:"bk-close"});t.addEventListener("click",(()=>{this.model.visible=!1})),this.shadow_el.appendChild(t)}this.el.classList.toggle("bk-tooltip-arrow",this.model.show_arrow),this.el.classList.toggle("bk-non-interactive",!this.model.interactive),this._reposition()}_anchor_to_align(t){switch(t){case"top_left":return["top","left"];case"top":case"top_center":return["top","center"];case"top_right":return["top","right"];case"left":case"center_left":return["center","left"];case"center":case"center_center":return["center","center"];case"right":case"center_right":return["center","right"];case"bottom_left":return["bottom","left"];case"bottom":case"bottom_center":return["bottom","center"];case"bottom_right":return["bottom","right"]}}_reposition(){const{position:t,visible:e}=this.model;if(null==t||!e)return void this.el.remove();(this.target.shadowRoot??this.target).appendChild(this.el);const n=Se(this.target).relative(),[r,i]=(()=>{if((0,f.Kg)(t)){const[e,r]=this._anchor_to_align(t);return[(()=>{switch(r){case"left":return n.left;case"center":return n.hcenter;case"right":return n.right}})(),(()=>{switch(e){case"top":return n.top;case"center":return n.vcenter;case"bottom":return n.bottom}})()]}return t})(),o=(()=>{const e=(()=>{const{attachment:e}=this.model;if("auto"==e){if((0,f.Kg)(t)){const[e,n]=this._anchor_to_align(t);if("center"!=n)return"left"==n?"left":"right";if("center"!=e)return"top"==e?"above":"below"}return"horizontal"}return e})();switch(e){case"horizontal":return r<n.hcenter?"right":"left";case"vertical":return i<n.vcenter?"below":"above";default:return e}})();let a;this.el.classList.remove(h_),this.el.classList.remove(d_),this.el.classList.remove(p_),this.el.classList.remove(f_);let s=null,l=null;const{width:c,height:u}=Se(this.el);switch(o){case"right":this.el.classList.add(d_),s=r+(c-this.el.clientWidth)+10,a=i-u/2;break;case"left":this.el.classList.add(h_),l=n.width-r+10,a=i-u/2;break;case"below":this.el.classList.add(p_),a=i+(u-this.el.clientHeight)+10,s=Math.round(r-c/2);break;case"above":this.el.classList.add(f_),a=i-u-10,s=Math.round(r-c/2)}this.el.style.top=`${a}px`,this.el.style.left=null!=s?`${s}px`:"",this.el.style.right=null!=l?`${l}px`:""}}I_.__name__="TooltipView";class j_ extends Wu{constructor(t){super(t)}clear(){this.position=null}}T_=j_,j_.__name__="Tooltip",T_.prototype.default_view=I_,T_.define((({Boolean:t,Number:e,String:n,Tuple:r,Or:i,Ref:o,Nullable:a,Auto:s})=>({target:[i(o(Wu),o(og),o(Node),s),"auto"],position:[a(i(_n.Mz,r(e,e))),null],content:[i(n,o(u_),o(Node))],attachment:[i(_n.l6,s),"auto"],show_arrow:[t,!0],closable:[t,!1],interactive:[t,!0]}))),T_.override({visible:!1});class z_ extends Id{async copy(){const t=await this.parent.export().to_blob(),e=new ClipboardItem({[t.type]:t});await navigator.clipboard.write([e])}doit(){this.copy()}}z_.__name__="CopyToolView";class B_ extends jd{constructor(t){super(t),this.tool_name="Copy",this.tool_icon="bk-tool-icon-copy"}}m_=B_,B_.__name__="CopyTool",m_.prototype.default_view=z_,m_.register_alias("copy",(()=>new B_));class F_ extends Id{doit(){this.model.callback?.execute(this.model)}}F_.__name__="CustomActionView";class $_ extends jd{constructor(t){super(t),this.tool_name="Custom Action",this.tool_icon="bk-tool-icon-unknown"}}g_=$_,$_.__name__="CustomAction",g_.prototype.default_view=F_,g_.define((({Any:t,Nullable:e})=>({callback:[e(t),null]}))),g_.override({description:"Perform a Custom Action"});class G_ extends Id{doit(){null!=document.fullscreenElement?document.exitFullscreen():(async()=>{await this.parent.el.requestFullscreen()})()}}G_.__name__="FullscreenToolView";class q_ extends jd{constructor(t){super(t),this.tool_name="Fullscreen",this.tool_icon="bk-tool-icon-fullscreen"}}__=q_,q_.__name__="FullscreenTool",__.prototype.default_view=G_,__.register_alias("fullscreen",(()=>new q_));class U_ extends Id{*children(){yield*super.children(),yield this._dialog}async lazy_initialize(){await super.lazy_initialize();const t=new Jg({content:new a_({target:this.parent.model}),closable:!0,visible:!1});this._dialog=await $e(t,{parent:this.parent})}doit(){this._dialog.model.visible=!0}}U_.__name__="ExamineToolView";class W_ extends jd{constructor(t){super(t),this.tool_name="Examine",this.tool_icon="bk-tool-icon-settings"}}b_=W_,W_.__name__="ExamineTool",b_.prototype.default_view=U_,b_.register_alias("examine",(()=>new W_));class Z_ extends Id{get plot_view(){return this.parent}}Z_.__name__="PlotActionToolView";class X_ extends jd{constructor(t){super(t)}}X_.__name__="PlotActionTool";class K_ extends Z_{connect_signals(){super.connect_signals(),this.connect(this.plot_view.state.changed,(()=>this.model.disabled=!this.plot_view.state.can_redo))}doit(){const t=this.plot_view.state.redo();null!=t?.range&&this.plot_view.trigger_ranges_update_event()}}K_.__name__="RedoToolView";class Y_ extends X_{constructor(t){super(t),this.tool_name="Redo",this.tool_icon="bk-tool-icon-redo"}}v_=Y_,Y_.__name__="RedoTool",v_.prototype.default_view=K_,v_.override({disabled:!0}),v_.register_alias("redo",(()=>new Y_));class J_ extends Z_{doit(){this.plot_view.reset()}}J_.__name__="ResetToolView";class tb extends X_{constructor(t){super(t),this.tool_name="Reset",this.tool_icon="bk-tool-icon-reset"}}y_=tb,tb.__name__="ResetTool",y_.prototype.default_view=J_,y_.register_alias("reset",(()=>new tb));class eb extends Id{async copy(){const t=await this.parent.export().to_blob(),e=new ClipboardItem({[t.type]:t});await navigator.clipboard.write([e])}async save(t){const e=await this.parent.export().to_blob(),n=document.createElement("a");n.href=URL.createObjectURL(e),n.download=t,n.target="_blank",n.dispatchEvent(new MouseEvent("click"))}doit(t="save"){switch(t){case"save":{const t=this.model.filename??prompt("Enter filename","bokeh_plot");null!=t&&this.save(t);break}case"copy":this.copy()}}}eb.__name__="SaveToolView";class nb extends jd{constructor(t){super(t),this.tool_name="Save",this.tool_icon="bk-tool-icon-save"}get menu(){return[{icon:"bk-tool-icon-copy",tooltip:"Copy image to clipboard",if:()=>"undefined"!=typeof ClipboardItem,handler:()=>{this.do.emit("copy")}}]}}x_=nb,nb.__name__="SaveTool",x_.prototype.default_view=eb,x_.define((({String:t,Nullable:e})=>({filename:[e(t),null]}))),x_.register_alias("save",(()=>new nb));class rb extends Z_{connect_signals(){super.connect_signals(),this.connect(this.plot_view.state.changed,(()=>this.model.disabled=!this.plot_view.state.can_undo))}doit(){const t=this.plot_view.state.undo();null!=t?.range&&this.plot_view.trigger_ranges_update_event()}}rb.__name__="UndoToolView";class ib extends X_{constructor(t){super(t),this.tool_name="Undo",this.tool_icon="bk-tool-icon-undo"}}function ob(t,e,n){const[r,i]=[t.start,t.end],o=null!=n?n:(i+r)/2;return[r-(r-o)*e,i-(i-o)*e]}function ab(t,[e,n]){const r=new Map;for(const[i,o]of t){const[t,a]=o.r_invert(e,n);r.set(i,{start:t,end:a})}return r}function sb(t,e,n=!0,r=!0,i){const o=n?e:0,[a,s]=ob(t.bbox.h_range,o,null!=i?i.x:void 0),l=ab(t.x_scales,[a,s]),c=r?e:0,[u,d]=ob(t.bbox.v_range,c,null!=i?i.y:void 0);return{xrs:l,yrs:ab(t.y_scales,[u,d]),factor:e}}w_=ib,ib.__name__="UndoTool",w_.prototype.default_view=rb,w_.override({disabled:!0}),w_.register_alias("undo",(()=>new ib));class lb extends Z_{doit(){const t=this.plot_view.frame,e=this.model.dimensions,n="width"==e||"both"==e,r="height"==e||"both"==e,i=sb(t,this.model.get_factor(),n,r);this.plot_view.state.push("zoom_out",{range:i}),this.plot_view.update_range(i,{scrolling:!0,maintain_focus:this.model.maintain_focus}),this.model.document?.interactive_start(this.plot_view.model),this.plot_view.trigger_ranges_update_event()}}lb.__name__="ZoomBaseToolView";class cb extends X_{constructor(t){super(t)}get tooltip(){return this._get_dim_tooltip(this.dimensions)}}L_=cb,cb.__name__="ZoomBaseTool",L_.define((({Percent:t})=>({factor:[t,.1],dimensions:[_n.Et,"both"]})));class ub extends lb{}ub.__name__="ZoomInToolView";class db extends cb{constructor(t){super(t),this.maintain_focus=!0,this.tool_name="Zoom In",this.tool_icon="bk-tool-icon-zoom-in"}get_factor(){return this.factor}}A_=db,db.__name__="ZoomInTool",A_.prototype.default_view=ub,A_.register_alias("zoom_in",(()=>new db({dimensions:"both"}))),A_.register_alias("xzoom_in",(()=>new db({dimensions:"width"}))),A_.register_alias("yzoom_in",(()=>new db({dimensions:"height"})));class hb extends lb{}hb.__name__="ZoomOutToolView";class pb extends cb{constructor(t){super(t),this.tool_name="Zoom Out",this.tool_icon="bk-tool-icon-zoom-out"}get_factor(){return-this.factor/(1-this.factor)}}H_=pb,pb.__name__="ZoomOutTool",H_.prototype.default_view=hb,H_.define((({Boolean:t})=>({maintain_focus:[t,!0]}))),H_.register_alias("zoom_out",(()=>new pb({dimensions:"both"}))),H_.register_alias("xzoom_out",(()=>new pb({dimensions:"width"}))),H_.register_alias("yzoom_out",(()=>new pb({dimensions:"height"})));class fb extends Vd{constructor(){super(...arguments),this._mouse_in_frame=!0}_select_mode(t){const{shift_key:e,ctrl_key:n}=t;return e||n?e&&!n?"append":!e&&n?"intersect":e&&n?"subtract":void(0,_.HB)():"replace"}_move_enter(t){this._mouse_in_frame=!0}_move_exit(t){this._mouse_in_frame=!1}_map_drag(t,e,n){if(!this.plot_view.frame.bbox.contains(t,e))return null;const r=this.plot_view.renderer_view(n);return null==r?null:[r.coordinates.x_scale.invert(t),r.coordinates.y_scale.invert(e)]}_delete_selected(t){const e=t.data_source,n=e.selected.indices;n.sort();for(const t of e.columns()){const r=e.get_array(t);for(let t=0;t<n.length;t++){const e=n[t];r.splice(e-t,1)}}this._emit_cds_changes(e)}_pop_glyphs(t,e){const n=t.columns();if(e&&n.length)for(const r of n){let n=t.get_array(r);const i=n.length-e+1;i<1||((0,f.cy)(n)||(n=Array.from(n),t.data[r]=n),n.splice(0,i))}}_emit_cds_changes(t,e=!0,n=!0,r=!0){if(n&&t.selection_manager.clear(),e&&t.change.emit(),r){const{data:e}=t;t.setv({data:e},{check_eq:!1})}}_drag_points(t,e,n="both"){if(null==this._basepoint)return;const[r,i]=this._basepoint;for(const o of e){const e=this._map_drag(r,i,o),a=this._map_drag(t.sx,t.sy,o);if(null==a||null==e)continue;const[s,l]=a,[c,u]=e,[d,h]=[s-c,l-u],p=o.glyph,f=o.data_source,[Q,T]=[p.x.field,p.y.field];for(const t of f.selected.indices)!Q||"width"!=n&&"both"!=n||(f.data[Q][t]+=d),!T||"height"!=n&&"both"!=n||(f.data[T][t]+=h);f.change.emit()}this._basepoint=[t.sx,t.sy]}_pad_empty_columns(t,e){for(const n of t.columns())(0,Rt.mK)(e,n)||t.get_array(n).push(this.model.empty_value)}_select_event(t,e,n){const r=this.plot_view.frame,{sx:i,sy:o}=t;if(!r.bbox.contains(i,o))return[];const a={type:"point",sx:i,sy:o},s=[];for(const t of n){const n=t.get_selection_manager(),r=t.data_source,i=this.plot_view.renderer_view(t);null!=i&&(n.select([i],a,!0,e)&&s.push(t),r.properties.selected.change.emit())}return s}}fb.__name__="EditToolView";class Qb extends Od{constructor(t){super(t)}}k_=Qb,Qb.__name__="EditTool",k_.define((({Unknown:t,Array:e,Ref:n})=>({empty_value:[t],renderers:[e(n(Jl)),[]]})));class Tb extends fb{_tap(t){null==this._draw_basepoint&&null==this._basepoint&&this._select_event(t,this._select_mode(t),this.model.renderers)}_keyup(t){if(this.model.active&&this._mouse_in_frame)for(const e of this.model.renderers)"Backspace"==t.key?this._delete_selected(e):"Escape"==t.key&&e.data_source.selection_manager.clear()}_set_extent([t,e],[n,r],i,o=!1){const a=this.model.renderers[0],s=this.plot_view.renderer_view(a);if(null==s)return;const l=a.glyph,c=a.data_source,[u,d]=s.coordinates.x_scale.r_invert(t,e),[h,p]=s.coordinates.y_scale.r_invert(n,r),[f,Q]=[(u+d)/2,(h+p)/2],[T,m]=[d-u,p-h],[g,_]=[l.x.field,l.y.field],[b,v]=[l.width.field,l.height.field];if(i)this._pop_glyphs(c,this.model.num_objects),g&&c.get_array(g).push(f),_&&c.get_array(_).push(Q),b&&c.get_array(b).push(T),v&&c.get_array(v).push(m),this._pad_empty_columns(c,[g,_,b,v]);else{const t=c.data[g].length-1;g&&(c.data[g][t]=f),_&&(c.data[_][t]=Q),b&&(c.data[b][t]=T),v&&(c.data[v][t]=m)}this._emit_cds_changes(c,!0,!1,o)}_update_box(t,e=!1,n=!1){if(null==this._draw_basepoint)return;const r=[t.sx,t.sy],i=this.plot_view.frame,o=this.model.dimensions,[a,s]=this.model._get_dim_limits(this._draw_basepoint,r,i,o);this._set_extent(a,s,e,n)}_doubletap(t){this.model.active&&(null!=this._draw_basepoint?(this._update_box(t,!1,!0),this._draw_basepoint=null):(this._draw_basepoint=[t.sx,t.sy],this._select_event(t,"append",this.model.renderers),this._update_box(t,!0,!1)))}_move(t){this._update_box(t,!1,!1)}_pan_start(t){if(t.shift_key){if(null!=this._draw_basepoint)return;this._draw_basepoint=[t.sx,t.sy],this._update_box(t,!0,!1)}else{if(null!=this._basepoint)return;this._select_event(t,"append",this.model.renderers),this._basepoint=[t.sx,t.sy]}}_pan(t,e=!1,n=!1){if(t.shift_key){if(null==this._draw_basepoint)return;this._update_box(t,e,n)}else{if(null==this._basepoint)return;this._drag_points(t,this.model.renderers)}}_pan_end(t){if(this._pan(t,!1,!0),t.shift_key)this._draw_basepoint=null;else{this._basepoint=null;for(const t of this.model.renderers)this._emit_cds_changes(t.data_source,!1,!0,!0)}}}Tb.__name__="BoxEditToolView";class mb extends Qb{constructor(t){super(t),this.tool_name="Box Edit Tool",this.tool_icon="bk-tool-icon-box-edit",this.event_type=["tap","pan","move"],this.default_order=1}}M_=mb,mb.__name__="BoxEditTool",M_.prototype.default_view=Tb,M_.define((({Int:t})=>({dimensions:[_n.Et,"both"],num_objects:[t,0]})));class gb extends fb{_draw(t,e,n=!1){if(!this.model.active)return;const r=this.model.renderers[0],i=this._map_drag(t.sx,t.sy,r);if(null==i)return;const[o,a]=i,s=r.data_source,l=r.glyph,[c,u]=[l.xs.field,l.ys.field];if("new"==e)this._pop_glyphs(s,this.model.num_objects),c&&s.get_array(c).push([o]),u&&s.get_array(u).push([a]),this._pad_empty_columns(s,[c,u]);else if("add"==e){if(c){const t=s.data[c].length-1;let e=s.get_array(c)[t];(0,f.cy)(e)||(e=Array.from(e),s.data[c][t]=e),e.push(o)}if(u){const t=s.data[u].length-1;let e=s.get_array(u)[t];(0,f.cy)(e)||(e=Array.from(e),s.data[u][t]=e),e.push(a)}}this._emit_cds_changes(s,!0,!0,n)}_pan_start(t){this._draw(t,"new")}_pan(t){this._draw(t,"add")}_pan_end(t){this._draw(t,"add",!0)}_tap(t){this._select_event(t,this._select_mode(t),this.model.renderers)}_keyup(t){if(this.model.active&&this._mouse_in_frame)for(const e of this.model.renderers)"Escape"==t.key?e.data_source.selection_manager.clear():"Backspace"==t.key&&this._delete_selected(e)}}gb.__name__="FreehandDrawToolView";class _b extends Qb{constructor(t){super(t),this.tool_name="Freehand Draw Tool",this.tool_icon="bk-tool-icon-freehand-draw",this.event_type=["pan","tap"],this.default_order=3}}C_=_b,_b.__name__="FreehandDrawTool",C_.prototype.default_view=gb,C_.define((({Int:t})=>({num_objects:[t,0]}))),C_.register_alias("freehand_draw",(()=>new _b));class bb extends fb{_set_intersection(t,e){const n=this.model.intersection_renderer.glyph,r=this.model.intersection_renderer.data_source,[i,o]=[n.x.field,n.y.field];i&&((0,f.cy)(t)?r.data[i]=t:n.x={value:t}),o&&((0,f.cy)(e)?r.data[o]=e:n.y={value:e}),this._emit_cds_changes(r,!0,!0,!1)}_hide_intersections(){this._set_intersection([],[])}}bb.__name__="LineToolView";class vb extends Qb{constructor(t){super(t)}}S_=vb,vb.__name__="LineTool",S_.define((({AnyRef:t})=>({intersection_renderer:[t()]})));class yb extends bb{constructor(){super(...arguments),this._drawing=!1}_doubletap(t){if(!this.model.active)return;const e=this.model.renderers;for(const n of e)1==this._select_event(t,"replace",[n]).length&&(this._selected_renderer=n);this._show_intersections(),this._update_line_cds()}_show_intersections(){if(!this.model.active)return;if(null==this._selected_renderer)return;if(!this.model.renderers.length)return this._set_intersection([],[]),this._selected_renderer=null,void(this._drawing=!1);const t=this._selected_renderer.data_source,e=this._selected_renderer.glyph,[n,r]=[e.x.field,e.y.field],i=t.get_array(n),o=t.get_array(r);this._set_intersection(i,o)}_tap(t){const e=this.model.intersection_renderer;if(null==this._map_drag(t.sx,t.sy,e))return;if(this._drawing&&this._selected_renderer){const n=this._select_mode(t);if(0==this._select_event(t,n,[e]).length)return}const n=this._select_mode(t);this._select_event(t,n,[e]),this._select_event(t,n,this.model.renderers)}_update_line_cds(){if(null==this._selected_renderer)return;const t=this.model.intersection_renderer.glyph,e=this.model.intersection_renderer.data_source,[n,r]=[t.x.field,t.y.field];if(n&&r){const t=e.data[n],i=e.data[r];this._selected_renderer.data_source.data[n]=t,this._selected_renderer.data_source.data[r]=i}this._emit_cds_changes(this._selected_renderer.data_source,!0,!0,!1)}_pan_start(t){this._select_event(t,"append",[this.model.intersection_renderer]),this._basepoint=[t.sx,t.sy]}_pan(t){null!=this._basepoint&&(this._drag_points(t,[this.model.intersection_renderer],this.model.dimensions),this._selected_renderer&&this._selected_renderer.data_source.change.emit())}_pan_end(t){null!=this._basepoint&&(this._drag_points(t,[this.model.intersection_renderer]),this._emit_cds_changes(this.model.intersection_renderer.data_source,!1,!0,!0),this._selected_renderer&&this._emit_cds_changes(this._selected_renderer.data_source),this._basepoint=null)}activate(){this._drawing=!0}deactivate(){this._selected_renderer&&(this._drawing&&(this._drawing=!1),this._hide_intersections())}}yb.__name__="LineEditToolView";class xb extends vb{constructor(t){super(t),this.tool_name="Line Edit Tool",this.tool_icon="bk-tool-icon-line-edit",this.event_type=["tap","pan","move"],this.default_order=4}get tooltip(){return this._get_dim_tooltip(this.dimensions)}}E_=xb,xb.__name__="LineEditTool",E_.prototype.default_view=yb,E_.define((()=>({dimensions:[_n.Et,"both"]})));class wb extends fb{_tap(t){if(this._select_event(t,this._select_mode(t),this.model.renderers).length||!this.model.add)return;const e=this.model.renderers[0],n=this._map_drag(t.sx,t.sy,e);if(null==n)return;const r=e.glyph,i=e.data_source,[o,a]=[r.x.field,r.y.field],[s,l]=n;this._pop_glyphs(i,this.model.num_objects),o&&i.get_array(o).push(s),a&&i.get_array(a).push(l),this._pad_empty_columns(i,[o,a]);const{data:c}=i;i.setv({data:c},{check_eq:!1})}_keyup(t){if(this.model.active&&this._mouse_in_frame)for(const e of this.model.renderers)"Backspace"==t.key?this._delete_selected(e):"Escape"==t.key&&e.data_source.selection_manager.clear()}_pan_start(t){this.model.drag&&(this._select_event(t,"append",this.model.renderers),this._basepoint=[t.sx,t.sy])}_pan(t){this.model.drag&&null!=this._basepoint&&this._drag_points(t,this.model.renderers)}_pan_end(t){if(this.model.drag){this._pan(t);for(const t of this.model.renderers)this._emit_cds_changes(t.data_source,!1,!0,!0);this._basepoint=null}}}wb.__name__="PointDrawToolView";class Lb extends Qb{constructor(t){super(t),this.tool_name="Point Draw Tool",this.tool_icon="bk-tool-icon-point-draw",this.event_type=["tap","pan","move"],this.default_order=2}}V_=Lb,Lb.__name__="PointDrawTool",V_.prototype.default_view=wb,V_.define((({Boolean:t,Int:e})=>({add:[t,!0],drag:[t,!0],num_objects:[e,0]})));class Ab extends fb{_set_vertices(t,e){const{vertex_renderer:n}=this.model;(0,_.vA)(null!=n);const r=n.glyph,i=n.data_source,[o,a]=[r.x.field,r.y.field];o&&((0,f.cy)(t)?i.data[o]=t:r.x={value:t}),a&&((0,f.cy)(e)?i.data[a]=e:r.y={value:e}),this._emit_cds_changes(i,!0,!0,!1)}_hide_vertices(){this._set_vertices([],[])}_snap_to_vertex(t,e,n){if(this.model.vertex_renderer){const r=this._select_event(t,"replace",[this.model.vertex_renderer]),i=this.model.vertex_renderer.data_source,o=this.model.vertex_renderer.glyph,[a,s]=[o.x.field,o.y.field];if(r.length){const t=i.selected.indices[0];a&&(e=i.data[a][t]),s&&(n=i.data[s][t]),i.selection_manager.clear()}}return[e,n]}}Ab.__name__="PolyToolView";class Hb extends Qb{constructor(t){super(t)}}O_=Hb,Hb.__name__="PolyTool",O_.define((({AnyRef:t,Nullable:e})=>({vertex_renderer:[e(t()),null]})));class kb extends Ab{constructor(){super(...arguments),this._drawing=!1,this._initialized=!1}_tap(t){this._drawing?this._draw(t,"add",!0):this._select_event(t,this._select_mode(t),this.model.renderers)}_draw(t,e,n=!1){const r=this.model.renderers[0],i=this._map_drag(t.sx,t.sy,r);if(this._initialized||this.activate(),null==i)return;const[o,a]=this._snap_to_vertex(t,...i),s=r.data_source,l=r.glyph,[c,u]=[l.xs.field,l.ys.field];if("new"==e)this._pop_glyphs(s,this.model.num_objects),c&&s.get_array(c).push([o,o]),u&&s.get_array(u).push([a,a]),this._pad_empty_columns(s,[c,u]);else if("edit"==e){if(c){const t=s.data[c][s.data[c].length-1];t[t.length-1]=o}if(u){const t=s.data[u][s.data[u].length-1];t[t.length-1]=a}}else if("add"==e){if(c){const t=s.data[c].length-1;let e=s.get_array(c)[t];const n=e[e.length-1];e[e.length-1]=o,(0,f.cy)(e)||(e=Array.from(e),s.data[c][t]=e),e.push(n)}if(u){const t=s.data[u].length-1;let e=s.get_array(u)[t];const n=e[e.length-1];e[e.length-1]=a,(0,f.cy)(e)||(e=Array.from(e),s.data[u][t]=e),e.push(n)}}this._emit_cds_changes(s,!0,!1,n)}_show_vertices(){if(!this.model.active)return;const t=[],e=[];for(let n=0;n<this.model.renderers.length;n++){const r=this.model.renderers[n],i=r.data_source,o=r.glyph,[a,s]=[o.xs.field,o.ys.field];if(a)for(const e of i.get_array(a))t.push(...e);if(s)for(const t of i.get_array(s))e.push(...t);this._drawing&&n==this.model.renderers.length-1&&(t.splice(t.length-1,1),e.splice(e.length-1,1))}this._set_vertices(t,e)}_doubletap(t){this.model.active&&(this._drawing?(this._drawing=!1,this._draw(t,"edit",!0)):(this._drawing=!0,this._draw(t,"new",!0)))}_move(t){this._drawing&&this._draw(t,"edit")}_remove(){const t=this.model.renderers[0],e=t.data_source,n=t.glyph,[r,i]=[n.xs.field,n.ys.field];if(r){const t=e.data[r].length-1,n=e.get_array(r)[t];n.splice(n.length-1,1)}if(i){const t=e.data[i].length-1,n=e.get_array(i)[t];n.splice(n.length-1,1)}this._emit_cds_changes(e)}_keyup(t){if(this.model.active&&this._mouse_in_frame)for(const e of this.model.renderers)"Backspace"==t.key?this._delete_selected(e):"Escape"==t.key&&(this._drawing&&(this._remove(),this._drawing=!1),e.data_source.selection_manager.clear())}_pan_start(t){this.model.drag&&(this._select_event(t,"append",this.model.renderers),this._basepoint=[t.sx,t.sy])}_pan(t){if(null==this._basepoint||!this.model.drag)return;const[e,n]=this._basepoint;for(const r of this.model.renderers){const i=this._map_drag(e,n,r),o=this._map_drag(t.sx,t.sy,r);if(null==o||null==i)continue;const a=r.data_source,s=r.glyph,[l,c]=[s.xs.field,s.ys.field];if(!l&&!c)continue;const[u,d]=o,[h,p]=i,[f,Q]=[u-h,d-p];for(const t of a.selected.indices){let e,n,r;l&&(n=a.data[l][t]),c?(r=a.data[c][t],e=r.length):e=n.length;for(let t=0;t<e;t++)n&&(n[t]+=f),r&&(r[t]+=Q)}a.change.emit()}this._basepoint=[t.sx,t.sy]}_pan_end(t){if(this.model.drag){this._pan(t);for(const t of this.model.renderers)this._emit_cds_changes(t.data_source);this._basepoint=null}}activate(){if(null!=this.model.vertex_renderer&&this.model.active){if(this._show_vertices(),!this._initialized)for(const t of this.model.renderers){const e=t.data_source;e.connect(e.properties.data.change,(()=>this._show_vertices()))}this._initialized=!0}}deactivate(){this._drawing&&(this._remove(),this._drawing=!1),this.model.vertex_renderer&&this._hide_vertices()}}kb.__name__="PolyDrawToolView";class Mb extends Hb{constructor(t){super(t),this.tool_name="Polygon Draw Tool",this.tool_icon="bk-tool-icon-poly-draw",this.event_type=["pan","tap","move"],this.default_order=3}}P_=Mb,Mb.__name__="PolyDrawTool",P_.prototype.default_view=kb,P_.define((({Boolean:t,Int:e})=>({drag:[t,!0],num_objects:[e,0]})));class Cb extends Ab{constructor(){super(...arguments),this._drawing=!1,this._cur_index=null}_doubletap(t){if(null==this.model.vertex_renderer||!this.model.active)return;const e=this._map_drag(t.sx,t.sy,this.model.vertex_renderer);if(null==e)return;const[n,r]=e,i=this._select_event(t,"replace",[this.model.vertex_renderer]),o=this.model.vertex_renderer.data_source,a=this.model.vertex_renderer.glyph,[s,l]=[a.x.field,a.y.field];if(i.length&&null!=this._selected_renderer){const t=o.selected.indices[0];this._drawing?(this._drawing=!1,o.selection_manager.clear()):(o.selected.indices=[t+1],s&&o.get_array(s).splice(t+1,0,n),l&&o.get_array(l).splice(t+1,0,r),this._drawing=!0),o.change.emit(),this._emit_cds_changes(this._selected_renderer.data_source)}else this._show_vertices(t)}_show_vertices(t){if(!this.model.active)return;if(0==this.model.renderers.length)return;const e=this.model.renderers[0],n=()=>this._update_vertices(e),r=e.data_source,i=this._select_event(t,"replace",this.model.renderers);if(!i.length)return this._set_vertices([],[]),this._selected_renderer=null,this._drawing=!1,this._cur_index=null,void r.disconnect(r.properties.data.change,n);r.connect(r.properties.data.change,n),this._cur_index=i[0].data_source.selected.indices[0],this._update_vertices(i[0])}_update_vertices(t){const e=t.glyph,n=t.data_source,r=this._cur_index,[i,o]=[e.xs.field,e.ys.field];if(this._drawing)return;if(null==r&&(i||o))return;let a,s;i&&null!=r?(a=n.data[i][r],(0,f.cy)(a)||(n.data[i][r]=a=Array.from(a))):a=e.xs.value,o&&null!=r?(s=n.data[o][r],(0,f.cy)(s)||(n.data[o][r]=s=Array.from(s))):s=e.ys.value,this._selected_renderer=t,this._set_vertices(a,s)}_move(t){if(this._drawing&&null!=this._selected_renderer){const e=this.model.vertex_renderer;if(null==e)return;const n=e.data_source,r=e.glyph,i=this._map_drag(t.sx,t.sy,e);if(null==i)return;let[o,a]=i;const s=n.selected.indices;[o,a]=this._snap_to_vertex(t,o,a),n.selected.indices=s;const[l,c]=[r.x.field,r.y.field],u=s[0];l&&(n.data[l][u]=o),c&&(n.data[c][u]=a),n.change.emit(),this._selected_renderer.data_source.change.emit()}}_tap(t){const e=this.model.vertex_renderer;if(null==e)return;const n=this._map_drag(t.sx,t.sy,e);if(null==n)return;if(this._drawing&&this._selected_renderer){let[r,i]=n;const o=e.data_source,a=e.glyph,[s,l]=[a.x.field,a.y.field],c=o.selected.indices;[r,i]=this._snap_to_vertex(t,r,i);const u=c[0];if(o.selected.indices=[u+1],s){const t=o.get_array(s),e=t[u];t[u]=r,t.splice(u+1,0,e)}if(l){const t=o.get_array(l),e=t[u];t[u]=i,t.splice(u+1,0,e)}return o.change.emit(),void this._emit_cds_changes(this._selected_renderer.data_source,!0,!1,!0)}const r=this._select_mode(t);this._select_event(t,r,[e]),this._select_event(t,r,this.model.renderers)}_remove_vertex(){if(!this._drawing||!this._selected_renderer)return;const t=this.model.vertex_renderer;if(null==t)return;const e=t.data_source,n=t.glyph,r=e.selected.indices[0],[i,o]=[n.x.field,n.y.field];i&&e.get_array(i).splice(r,1),o&&e.get_array(o).splice(r,1),e.change.emit(),this._emit_cds_changes(this._selected_renderer.data_source)}_pan_start(t){null!=this.model.vertex_renderer&&(this._select_event(t,"append",[this.model.vertex_renderer]),this._basepoint=[t.sx,t.sy])}_pan(t){null!=this._basepoint&&null!=this.model.vertex_renderer&&(this._drag_points(t,[this.model.vertex_renderer]),this._selected_renderer&&this._selected_renderer.data_source.change.emit())}_pan_end(t){null!=this._basepoint&&null!=this.model.vertex_renderer&&(this._drag_points(t,[this.model.vertex_renderer]),this._emit_cds_changes(this.model.vertex_renderer.data_source,!1,!0,!0),this._selected_renderer&&this._emit_cds_changes(this._selected_renderer.data_source),this._basepoint=null)}_keyup(t){if(!this.model.active||!this._mouse_in_frame)return;let e;if(this._selected_renderer){const{vertex_renderer:t}=this.model;e=null!=t?[t]:[]}else e=this.model.renderers;for(const n of e)"Backspace"==t.key?(this._delete_selected(n),this._selected_renderer&&this._emit_cds_changes(this._selected_renderer.data_source)):"Escape"==t.key&&(this._drawing?(this._remove_vertex(),this._drawing=!1):this._selected_renderer&&this._hide_vertices(),n.data_source.selection_manager.clear())}deactivate(){this._selected_renderer&&(this._drawing&&(this._remove_vertex(),this._drawing=!1),this._hide_vertices())}}Cb.__name__="PolyEditToolView";class Sb extends Hb{constructor(t){super(t),this.tool_name="Poly Edit Tool",this.tool_icon="bk-tool-icon-poly-edit",this.event_type=["tap","pan","move"],this.default_order=4}}D_=Sb,Sb.__name__="PolyEditTool",D_.prototype.default_view=Cb;class Eb extends Vd{connect_signals(){super.connect_signals(),this.model.clear.connect((()=>this._clear()))}get computed_renderers(){const{renderers:t}=this.model;return Pn(t,this.plot_view.model.data_renderers)}_computed_renderers_by_data_source(){const t=new Map;for(const e of this.computed_renderers){let n;if(e instanceof Jl)n=e.data_source;else{if(!(e instanceof ig))continue;n=e.node_renderer.data_source}const r=t.get(n)??[];t.set(n,[...r,e])}return t}_select_mode(t){const{shift_key:e,ctrl_key:n}=t;return e||n?e&&!n?"append":!e&&n?"intersect":e&&n?"subtract":void(0,_.HB)():this.model.mode}_keyup(t){"Escape"==t.key&&this._clear()}_clear(){for(const t of this.computed_renderers)t.get_selection_manager().clear();const t=this.computed_renderers.map((t=>this.plot_view.renderer_view(t)));this.plot_view.request_paint(t)}_select(t,e,n){const r=this._computed_renderers_by_data_source();for(const[,i]of r){const r=i[0].get_selection_manager(),o=[];for(const t of i){const e=this.plot_view.renderer_view(t);null!=e&&o.push(e)}r.select(o,t,e,n)}null!=this.model.callback&&this._emit_callback(t),this._emit_selection_event(t,e)}_emit_selection_event(t,e=!0){const{x_scale:n,y_scale:r}=this.plot_view.frame;let i;switch(t.type){case"point":{const{sx:e,sy:o}=t,a=n.invert(e),s=r.invert(o);i={...t,x:a,y:s};break}case"span":{const{sx:e,sy:o}=t,a=n.invert(e),s=r.invert(o);i={...t,x:a,y:s};break}case"rect":{const{sx0:e,sx1:o,sy0:a,sy1:s}=t,[l,c]=n.r_invert(e,o),[u,d]=r.r_invert(a,s);i={...t,x0:l,y0:u,x1:c,y1:d};break}case"poly":{const{sx:e,sy:o}=t,a=n.v_invert(e),s=r.v_invert(o);i={...t,x:a,y:s};break}}this.plot_view.model.trigger_event(new mt(i,e))}}Eb.__name__="SelectToolView";class Vb extends Od{constructor(t){super(t)}initialize(){super.initialize(),this.clear=new T.n2(this,"clear")}get menu(){return[{icon:"bk-tool-icon-replace-mode",tooltip:"Replace the current selection",active:()=>"replace"==this.mode,handler:()=>{this.mode="replace",this.active=!0}},{icon:"bk-tool-icon-append-mode",tooltip:"Append to the current selection (Shift)",active:()=>"append"==this.mode,handler:()=>{this.mode="append",this.active=!0}},{icon:"bk-tool-icon-intersect-mode",tooltip:"Intersect with the current selection (Ctrl)",active:()=>"intersect"==this.mode,handler:()=>{this.mode="intersect",this.active=!0}},{icon:"bk-tool-icon-subtract-mode",tooltip:"Subtract from the current selection (Shift+Ctrl)",active:()=>"subtract"==this.mode,handler:()=>{this.mode="subtract",this.active=!0}},null,{icon:"bk-tool-icon-clear-selection",tooltip:"Clear the current selection (Esc)",handler:()=>{this.clear.emit()}}]}}N_=Vb,Vb.__name__="SelectTool",N_.define((({Array:t,Ref:e,Or:n,Auto:r})=>({renderers:[n(t(e(Gs)),r),"auto"],mode:[_n.Qc,"replace"]})));class Ob extends Eb{get overlays(){return[...super.overlays,this.model.overlay]}_compute_limits(t){const e=this.plot_view.frame,n=this.model.dimensions;let r=this._base_point;if("center"==this.model.origin){const[e,n]=r,[i,o]=t;r=[e-(i-e),n-(o-n)]}return this.model._get_dim_limits(r,t,e,n)}_pan_start(t){const{sx:e,sy:n}=t;this.plot_view.frame.bbox.contains(e,n)&&(this._base_point=[e,n])}_pan(t){if(null==this._base_point)return;const{sx:e,sy:n}=t,[r,i]=this._compute_limits([e,n]),[[o,a],[s,l]]=[r,i];this.model.overlay.update({left:o,right:a,top:s,bottom:l}),this.model.select_every_mousemove&&this._do_select(r,i,!1,this._select_mode(t))}_pan_end(t){if(null==this._base_point)return;const{sx:e,sy:n}=t,[r,i]=this._compute_limits([e,n]);this._do_select(r,i,!0,this._select_mode(t)),this.model.overlay.clear(),this._base_point=null,this.plot_view.state.push("box_select",{selection:this.plot_view.get_selection()})}_do_select([t,e],[n,r],i,o="replace"){const a={type:"rect",sx0:t,sx1:e,sy0:n,sy1:r};this._select(a,i,o)}}Ob.__name__="BoxSelectToolView";const Pb=()=>new Kc({level:"overlay",visible:!1,top_units:"canvas",left_units:"canvas",bottom_units:"canvas",right_units:"canvas",fill_color:"lightgrey",fill_alpha:.5,line_color:"black",line_alpha:1,line_width:2,line_dash:[4,4]});class Db extends Vb{constructor(t){super(t),this.tool_name="Box Select",this.event_type="pan",this.default_order=30}get computed_icon(){const t=super.computed_icon;if(null!=t)return t;switch(this.dimensions){case"both":return".bk-tool-icon-box-select";case"width":return".bk-tool-icon-x-box-select";case"height":return".bk-tool-icon-y-box-select"}}get tooltip(){return this._get_dim_tooltip(this.dimensions)}}var Nb;R_=Db,Db.__name__="BoxSelectTool",R_.prototype.default_view=Ob,R_.define((({Boolean:t,Ref:e})=>({dimensions:[_n.Et,"both"],select_every_mousemove:[t,!1],overlay:[e(Kc),Pb],origin:[_n._0,"corner"]}))),R_.register_alias("box_select",(()=>new Db)),R_.register_alias("xbox_select",(()=>new Db({dimensions:"width"}))),R_.register_alias("ybox_select",(()=>new Db({dimensions:"height"})));class Rb extends Vd{constructor(){super(...arguments),this._base_point=null}get overlays(){return[...super.overlays,this.model.overlay]}_match_aspect([t,e],[n,r],i){const o=i.bbox.aspect,a=i.bbox.h_range.end,s=i.bbox.h_range.start,l=i.bbox.v_range.end,c=i.bbox.v_range.start;let u=Math.abs(t-n),d=Math.abs(e-r);const h=0==d?0:u/d,[p]=h>=o?[1,h/o]:[o/h,1];let f,Q,T,m;return t<=n?(f=t,Q=t+u*p,Q>a&&(Q=a)):(Q=t,f=t-u*p,f<s&&(f=s)),u=Math.abs(Q-f),e<=r?(m=e,T=e+u/o,T>l&&(T=l)):(T=e,m=e-u/o,m<c&&(m=c)),d=Math.abs(T-m),t<=n?Q=t+o*d:f=t-o*d,[[f,Q],[m,T]]}_compute_limits(t,e){const{frame:n}=this.plot_view;if("center"==this.model.origin){const[n,r]=t,[i,o]=e;t=[n-(i-n),r-(o-r)]}const r=(()=>{const{dimensions:n}=this.model;if("auto"==n){const[n,r]=t,[i,o]=e,a=Math.abs(n-i),s=Math.abs(r-o),l=5;return a<l&&s>l?"height":a>l&&s<l?"width":"both"}return n})();return this.model.match_aspect&&"both"==r?this._match_aspect(t,e,n):this.model._get_dim_limits(t,e,n,r)}_pan_start(t){const{sx:e,sy:n}=t;this.plot_view.frame.bbox.contains(e,n)&&(this._base_point=[e,n])}_pan(t){if(null==this._base_point)return;const[[e,n],[r,i]]=this._compute_limits(this._base_point,[t.sx,t.sy]);this.model.overlay.update({left:e,right:n,top:r,bottom:i})}_pan_end(t){if(null==this._base_point)return;const[e,n]=this._compute_limits(this._base_point,[t.sx,t.sy]);this._update(e,n),this._stop()}_stop(){this.model.overlay.clear(),this._base_point=null}_keydown(t){"Escape"==t.key&&this._stop()}_doubletap(t){const{state:e}=this.plot_view;"box_zoom"==e.peek()?.type&&e.undo()}_update([t,e],[n,r]){if(Math.abs(e-t)<=5||Math.abs(r-n)<=5)return;const{x_scales:i,y_scales:o}=this.plot_view.frame,a=new Map;for(const[n,r]of i){const[i,o]=r.r_invert(t,e);a.set(n,{start:i,end:o})}const s=new Map;for(const[t,e]of o){const[i,o]=e.r_invert(n,r);s.set(t,{start:i,end:o})}const l={xrs:a,yrs:s};this.plot_view.state.push("box_zoom",{range:l}),this.plot_view.update_range(l),this.plot_view.trigger_ranges_update_event()}}Rb.__name__="BoxZoomToolView";const Ib=()=>new Kc({level:"overlay",visible:!1,top_units:"canvas",left_units:"canvas",bottom_units:"canvas",right_units:"canvas",fill_color:"lightgrey",fill_alpha:.5,line_color:"black",line_alpha:1,line_width:2,line_dash:[4,4]});class jb extends Od{constructor(t){super(t),this.tool_name="Box Zoom",this.event_type=["pan","doubletap"],this.default_order=20}get event_role(){return"pan"}get computed_icon(){const t=super.computed_icon;if(null!=t)return t;switch(this.dimensions){case"both":return`.${ad}`;case"width":return`.${sd}`;case"height":return`.${ld}`;case"auto":return`.${cd}`}}get tooltip(){return this._get_dim_tooltip(this.dimensions)}get menu(){return[{icon:ad,tooltip:"Box zoom in both dimensions",active:()=>"both"==this.dimensions,handler:()=>{this.dimensions="both",this.active=!0}},{icon:sd,tooltip:"Box zoom in x-dimension",active:()=>"width"==this.dimensions,handler:()=>{this.dimensions="width",this.active=!0}},{icon:ld,tooltip:"Box zoom in y-dimension",active:()=>"height"==this.dimensions,handler:()=>{this.dimensions="height",this.active=!0}},{icon:cd,tooltip:"Automatic mode (box zoom in x, y or both dimensions, depending on the mouse gesture)",active:()=>"auto"==this.dimensions,handler:()=>{this.dimensions="auto",this.active=!0}}]}}var zb;Nb=jb,jb.__name__="BoxZoomTool",Nb.prototype.default_view=Rb,Nb.define((({Boolean:t,Ref:e,Or:n,Auto:r})=>({dimensions:[n(_n.Et,r),"both"],overlay:[e(Kc),Ib],match_aspect:[t,!1],origin:[_n._0,"corner"]}))),Nb.register_alias("box_zoom",(()=>new jb({dimensions:"both"}))),Nb.register_alias("xbox_zoom",(()=>new jb({dimensions:"width"}))),Nb.register_alias("ybox_zoom",(()=>new jb({dimensions:"height"}))),Nb.register_alias("auto_box_zoom",(()=>new jb({dimensions:"auto"})));class Bb extends Eb{constructor(){super(...arguments),this.sxs=[],this.sys=[]}get overlays(){return[...super.overlays,this.model.overlay]}connect_signals(){super.connect_signals(),this.connect(this.model.properties.active.change,(()=>this._active_change()))}_active_change(){this.model.active||this._clear_data()}_keyup(t){"Enter"==t.key&&this._clear_data()}_doubletap(t){this._do_select(this.sxs,this.sys,!0,this._select_mode(t)),this.plot_view.state.push("poly_select",{selection:this.plot_view.get_selection()}),this._clear_data()}_clear_data(){this.sxs=[],this.sys=[],this.model.overlay.clear()}_tap(t){const{sx:e,sy:n}=t;this.plot_view.frame.bbox.contains(e,n)&&(this.sxs.push(e),this.sys.push(n),this.model.overlay.update({xs:this.sxs,ys:this.sys}))}_do_select(t,e,n,r){const i={type:"poly",sx:t,sy:e};this._select(i,n,r)}}Bb.__name__="PolySelectToolView";const Fb=()=>new gu({level:"overlay",visible:!1,xs_units:"canvas",ys_units:"canvas",fill_color:"lightgrey",fill_alpha:.5,line_color:"black",line_alpha:1,line_width:2,line_dash:[4,4]});class $b extends Vb{constructor(t){super(t),this.tool_name="Poly Select",this.tool_icon="bk-tool-icon-polygon-select",this.event_type="tap",this.default_order=11}}var Gb,qb,Ub;zb=$b,$b.__name__="PolySelectTool",zb.prototype.default_view=Bb,zb.define((({Ref:t})=>({overlay:[t(gu),Fb]}))),zb.register_alias("poly_select",(()=>new $b));class Wb extends Eb{constructor(){super(...arguments),this.sxs=[],this.sys=[]}get overlays(){return[...super.overlays,this.model.overlay]}connect_signals(){super.connect_signals(),this.connect(this.model.properties.active.change,(()=>this._active_change()))}_active_change(){this.model.active||this._clear_overlay()}_keyup(t){("Enter"==t.key||"Escape"==t.key&&this.model.persistent)&&this._clear_overlay()}_pan_start(t){this.sxs=[],this.sys=[];const{sx:e,sy:n}=t;this._append_overlay(e,n)}_pan(t){const[e,n]=this.plot_view.frame.bbox.clip(t.sx,t.sy);this._append_overlay(e,n),this.model.select_every_mousemove&&this._do_select(this.sxs,this.sys,!1,this._select_mode(t))}_pan_end(t){const{sxs:e,sys:n}=this;this.model.persistent||this._clear_overlay(),this._do_select(e,n,!0,this._select_mode(t)),this.plot_view.state.push("lasso_select",{selection:this.plot_view.get_selection()})}_append_overlay(t,e){this.sxs.push(t),this.sys.push(e),this.model.overlay.update({xs:this.sxs,ys:this.sys})}_clear_overlay(){this.sxs=[],this.sys=[],this.model.overlay.clear()}_do_select(t,e,n,r){const i={type:"poly",sx:t,sy:e};this._select(i,n,r)}}Wb.__name__="LassoSelectToolView";class Zb extends Vb{constructor(t){super(t),this.tool_name="Lasso Select",this.tool_icon="bk-tool-icon-lasso-select",this.event_type="pan",this.default_order=12}}function Xb(t,e,n){const r=new Map;for(const[i,o]of t){const[t,a]=o.r_invert(e,n);r.set(i,{start:t,end:a})}return r}Gb=Zb,Zb.__name__="LassoSelectTool",Gb.prototype.default_view=Wb,Gb.define((({Boolean:t,Ref:e})=>({select_every_mousemove:[t,!0],overlay:[e(gu),Fb]}))),Gb.internal((({Boolean:t})=>({persistent:[t,!1]}))),Gb.register_alias("lasso_select",(()=>new Zb));class Kb extends Vd{_pan_start(t){this.last_dx=0,this.last_dy=0;const{sx:e,sy:n}=t,r=this.plot_view.frame.bbox;if(!r.contains(e,n)){const t=r.h_range,i=r.v_range;(e<t.start||e>t.end)&&(this.v_axis_only=!0),(n<i.start||n>i.end)&&(this.h_axis_only=!0)}this.model.document?.interactive_start(this.plot_view.model)}_pan(t){this._update(t.dx,t.dy),this.model.document?.interactive_start(this.plot_view.model)}_pan_end(t){this.h_axis_only=!1,this.v_axis_only=!1,null!=this.pan_info&&this.plot_view.state.push("pan",{range:this.pan_info}),this.plot_view.trigger_ranges_update_event()}_update(t,e){const n=this.plot_view.frame,r=t-this.last_dx,i=e-this.last_dy,o=n.bbox.h_range,a=o.start-r,s=o.end-r,l=n.bbox.v_range,c=l.start-i,u=l.end-i,d=this.model.dimensions;let h,p,f,Q,T,m;"width"!=d&&"both"!=d||this.v_axis_only?(h=o.start,p=o.end,f=0):(h=a,p=s,f=-r),"height"!=d&&"both"!=d||this.h_axis_only?(Q=l.start,T=l.end,m=0):(Q=c,T=u,m=-i),this.last_dx=t,this.last_dy=e;const{x_scales:g,y_scales:_}=n,b=Xb(g,h,p),v=Xb(_,Q,T);this.pan_info={xrs:b,yrs:v,sdx:f,sdy:m},this.plot_view.update_range(this.pan_info,{panning:!0})}}Kb.__name__="PanToolView";class Yb extends Od{constructor(t){super(t),this.tool_name="Pan",this.event_type="pan",this.default_order=10}get tooltip(){return this._get_dim_tooltip(this.dimensions)}get computed_icon(){const t=super.computed_icon;if(null!=t)return t;switch(this.dimensions){case"both":return`.${ud}`;case"width":return`.${dd}`;case"height":return`.${hd}`}}get menu(){return[{icon:ud,tooltip:"Pan in both dimensions",active:()=>"both"==this.dimensions,handler:()=>{this.dimensions="both",this.active=!0}},{icon:dd,tooltip:"Pan in x-dimension",active:()=>"width"==this.dimensions,handler:()=>{this.dimensions="width",this.active=!0}},{icon:hd,tooltip:"Pan in y-dimension",active:()=>"height"==this.dimensions,handler:()=>{this.dimensions="height",this.active=!0}}]}}function Jb(t){switch(t){case 1:return 2;case 2:return 1;case 4:return 5;case 5:return 4;default:return t}}function tv(t,e,n,r){if(null==e)return!1;const i=n.compute(e);return Math.abs(t-i)<r}function ev(t,e,n,r,i){let o=!0;if(null!=i.left&&null!=i.right){const e=n.invert(t);(e<i.left||e>i.right)&&(o=!1)}if(null!=i.bottom&&null!=i.top){const t=r.invert(e);(t<i.bottom||t>i.top)&&(o=!1)}return o}function nv(t,e,n){let r=0;return t>=n.start&&t<=n.end&&(r+=1),e>=n.start&&e<=n.end&&(r+=1),r}function rv(t,e,n,r){const i=e.compute(t),o=e.invert(i+n);return o>=r.start&&o<=r.end?o:t}function iv(t,e,n){return t>e.start?(e.end=t,n):(e.end=e.start,e.start=t,Jb(n))}function ov(t,e,n){return t<e.end?(e.start=t,n):(e.start=e.end,e.end=t,Jb(n))}function av(t,e,n,r){const[i,o]=e.r_compute(t.start,t.end),[a,s]=e.r_invert(i+n,o+n),l=nv(t.start,t.end,r);nv(a,s,r)>=l&&(t.start=a,t.end=s)}qb=Yb,Yb.__name__="PanTool",qb.prototype.default_view=Kb,qb.define((()=>({dimensions:[_n.Et,"both"]}))),qb.register_alias("pan",(()=>new Yb({dimensions:"both"}))),qb.register_alias("xpan",(()=>new Yb({dimensions:"width"}))),qb.register_alias("ypan",(()=>new Yb({dimensions:"height"})));class sv extends Vd{get overlays(){return[...super.overlays,this.model.overlay]}initialize(){super.initialize(),this.side=0,this.model.update_overlay_from_ranges()}connect_signals(){super.connect_signals(),null!=this.model.x_range&&this.connect(this.model.x_range.change,(()=>this.model.update_overlay_from_ranges())),null!=this.model.y_range&&this.connect(this.model.y_range.change,(()=>this.model.update_overlay_from_ranges()))}_pan_start(t){this.last_dx=0,this.last_dy=0;const e=this.model.x_range,n=this.model.y_range,{frame:r}=this.plot_view,i=r.x_scale,o=r.y_scale,a=this.model.overlay,{left:s,right:l,top:c,bottom:u}=a,d=this.model.overlay.line_width+2.5;null!=e&&this.model.x_interaction&&(tv(t.sx,s,i,d)?this.side=1:tv(t.sx,l,i,d)?this.side=2:ev(t.sx,t.sy,i,o,a)&&(this.side=3)),null!=n&&this.model.y_interaction&&(0==this.side&&tv(t.sy,u,o,d)&&(this.side=4),0==this.side&&tv(t.sy,c,o,d)?this.side=5:ev(t.sx,t.sy,i,o,this.model.overlay)&&(3==this.side?this.side=7:this.side=6))}_pan(t){const e=this.plot_view.frame,n=t.dx-this.last_dx,r=t.dy-this.last_dy,i=this.model.x_range,o=this.model.y_range,a=e.x_scale,s=e.y_scale;if(null!=i)if(3==this.side||7==this.side)av(i,a,n,e.x_range);else if(1==this.side){const t=rv(i.start,a,n,e.x_range);this.side=ov(t,i,this.side)}else if(2==this.side){const t=rv(i.end,a,n,e.x_range);this.side=iv(t,i,this.side)}if(null!=o)if(6==this.side||7==this.side)av(o,s,r,e.y_range);else if(4==this.side){const t=rv(o.start,s,r,e.y_range);this.side=ov(t,o,this.side)}else if(5==this.side){const t=rv(o.end,s,r,e.y_range);this.side=iv(t,o,this.side)}this.last_dx=t.dx,this.last_dy=t.dy}_pan_end(t){this.side=0,this.plot_view.trigger_ranges_update_event()}}sv.__name__="RangeToolView";const lv=()=>new Kc({level:"overlay",fill_color:"lightgrey",fill_alpha:.5,line_color:"black",line_alpha:1,line_width:.5,line_dash:[2,2]});class cv extends Od{constructor(t){super(t),this.tool_name="Range Tool",this.tool_icon="bk-tool-icon-range",this.event_type="pan",this.default_order=1}initialize(){super.initialize(),this.overlay.in_cursor="grab",this.overlay.ew_cursor=null!=this.x_range&&this.x_interaction?"ew-resize":null,this.overlay.ns_cursor=null!=this.y_range&&this.y_interaction?"ns-resize":null}update_overlay_from_ranges(){null==this.x_range&&null==this.y_range&&(this.overlay.left=null,this.overlay.right=null,this.overlay.bottom=null,this.overlay.top=null,ot.vF.warn("RangeTool not configured with any Ranges.")),null==this.x_range?(this.overlay.left=null,this.overlay.right=null):(this.overlay.left=this.x_range.start,this.overlay.right=this.x_range.end),null==this.y_range?(this.overlay.bottom=null,this.overlay.top=null):(this.overlay.bottom=this.y_range.start,this.overlay.top=this.y_range.end)}}var uv,dv,hv,pv,fv,Qv,Tv,mv,gv,_v,bv,vv,yv,xv,wv,Lv,Av,Hv,kv;Ub=cv,cv.__name__="RangeTool",Ub.prototype.default_view=sv,Ub.define((({Boolean:t,Ref:e,Nullable:n})=>({x_range:[n(e(xn)),null],x_interaction:[t,!0],y_range:[n(e(xn)),null],y_interaction:[t,!0],overlay:[e(Kc),lv]})));class Mv extends Eb{_tap(t){"tap"==this.model.gesture&&this._handle_tap(t)}_doubletap(t){"doubletap"==this.model.gesture&&this._handle_tap(t)}_handle_tap(t){const{sx:e,sy:n}=t,r={type:"point",sx:e,sy:n};this._select(r,!0,this._select_mode(t))}_select(t,e,n){const{callback:r}=this.model;if("select"==this.model.behavior){const i=this._computed_renderers_by_data_source();for(const[,o]of i){const i=o[0].get_selection_manager(),a=o.map((t=>this.plot_view.renderer_view(t))).filter((t=>null!=t));if(i.select(a,t,e,n)&&null!=r){const e=a[0].coordinates.x_scale.invert(t.sx),n=a[0].coordinates.y_scale.invert(t.sy),o={geometries:{...t,x:e,y:n},source:i.source};r.execute(this.model,o)}}this._emit_selection_event(t),this.plot_view.state.push("tap",{selection:this.plot_view.get_selection()})}else for(const e of this.computed_renderers){const n=this.plot_view.renderer_view(e);if(null==n)continue;const i=e.get_selection_manager();if(i.inspect(n,t)&&null!=r){const e=n.coordinates.x_scale.invert(t.sx),o=n.coordinates.y_scale.invert(t.sy),a={geometries:{...t,x:e,y:o},source:i.source};r.execute(this.model,a)}}}}Mv.__name__="TapToolView";class Cv extends Vb{constructor(t){super(t),this.tool_name="Tap",this.tool_icon="bk-tool-icon-tap-select",this.event_type="tap",this.default_order=10}}uv=Cv,Cv.__name__="TapTool",uv.prototype.default_view=Mv,uv.define((({Any:t,Enum:e,Nullable:n})=>({behavior:[_n.qQ,"select"],gesture:[e("tap","doubletap"),"tap"],callback:[n(t),null]}))),uv.register_alias("click",(()=>new Cv({behavior:"inspect"}))),uv.register_alias("tap",(()=>new Cv)),uv.register_alias("doubletap",(()=>new Cv({gesture:"doubletap"})));class Sv extends Vd{_scroll(t){let e=this.model.speed*t.delta;e>.9?e=.9:e<-.9&&(e=-.9),this._update_ranges(e)}_update_ranges(t){const{frame:e}=this.plot_view,n=e.bbox.h_range,r=e.bbox.v_range,[i,o]=[n.start,n.end],[a,s]=[r.start,r.end];let l,c,u,d;switch(this.model.dimension){case"height":{const e=Math.abs(s-a);l=i,c=o,u=a-e*t,d=s-e*t;break}case"width":{const e=Math.abs(o-i);l=i-e*t,c=o-e*t,u=a,d=s;break}}const{x_scales:h,y_scales:p}=e,f={xrs:Xb(h,l,c),yrs:Xb(p,u,d),factor:t};this.plot_view.state.push("wheel_pan",{range:f}),this.plot_view.update_range(f,{scrolling:!0}),this.model.document?.interactive_start(this.plot_view.model,(()=>this.plot_view.trigger_ranges_update_event()))}}Sv.__name__="WheelPanToolView";class Ev extends Od{constructor(t){super(t),this.tool_name="Wheel Pan",this.tool_icon="bk-tool-icon-wheel-pan",this.event_type="scroll",this.default_order=12}get tooltip(){return this._get_dim_tooltip(this.dimension)}}dv=Ev,Ev.__name__="WheelPanTool",dv.prototype.default_view=Sv,dv.define((()=>({dimension:[_n.fg,"width"]}))),dv.internal((({Number:t})=>({speed:[t,.001]}))),dv.register_alias("xwheel_pan",(()=>new Ev({dimension:"width"}))),dv.register_alias("ywheel_pan",(()=>new Ev({dimension:"height"})));class Vv extends Vd{_pinch(t){const{sx:e,sy:n,scale:r,ctrl_key:i,shift_key:o}=t;let a;a=r>=1?20*(r-1):-20/r,this._scroll({type:"wheel",sx:e,sy:n,delta:a,ctrl_key:i,shift_key:o})}_scroll(t){const{frame:e}=this.plot_view,n=e.bbox.h_range,r=e.bbox.v_range,{sx:i,sy:o}=t,a=this.model.dimensions,s=("width"==a||"both"==a)&&n.start<i&&i<n.end,l=("height"==a||"both"==a)&&r.start<o&&o<r.end;if(!(s&&l||this.model.zoom_on_axis))return;const c=sb(e,this.model.speed*t.delta,s,l,{x:i,y:o});this.plot_view.state.push("wheel_zoom",{range:c});const{maintain_focus:u}=this.model;this.plot_view.update_range(c,{scrolling:!0,maintain_focus:u}),this.model.document?.interactive_start(this.plot_view.model,(()=>this.plot_view.trigger_ranges_update_event()))}}Vv.__name__="WheelZoomToolView";class Ov extends Od{constructor(t){super(t),this.tool_name="Wheel Zoom",this.tool_icon="bk-tool-icon-wheel-zoom",this.event_type=It.SU?"pinch":"scroll",this.default_order=10}get tooltip(){return this._get_dim_tooltip(this.dimensions)}}hv=Ov,Ov.__name__="WheelZoomTool",hv.prototype.default_view=Vv,hv.define((({Boolean:t,Number:e})=>({dimensions:[_n.Et,"both"],maintain_focus:[t,!0],zoom_on_axis:[t,!0],speed:[e,1/600]}))),hv.register_alias("wheel_zoom",(()=>new Ov({dimensions:"both"}))),hv.register_alias("xwheel_zoom",(()=>new Ov({dimensions:"width"}))),hv.register_alias("ywheel_zoom",(()=>new Ov({dimensions:"height"})));class Pv extends Pd{get overlays(){return[...super.overlays,...this._spans]}initialize(){super.initialize(),this._update_overlays()}connect_signals(){super.connect_signals();const{overlay:t,dimensions:e,line_color:n,line_width:r,line_alpha:i}=this.model.properties;this.on_change([t,e,n,r,i],(()=>{this._update_overlays()}))}_update_overlays(){const{overlay:t}=this.model;if("auto"==t){const{dimensions:e,line_color:n,line_alpha:r,line_width:i}=this.model;function o(t){return new yu({dimension:t,location_units:"canvas",level:"overlay",line_color:n,line_width:i,line_alpha:r})}switch(e){case"width":this._spans=[o("width")];break;case"height":this._spans=[o("height")];break;case"both":this._spans=[o("width"),o("height")]}}else(0,f.cy)(t)?this._spans=[...t]:this._spans=[t]}_move(t){if(!this.model.active)return;const{sx:e,sy:n}=t;this.plot_view.frame.bbox.contains(e,n)?this._update_spans(e,n):this._update_spans(NaN,NaN)}_move_exit(t){this._update_spans(NaN,NaN)}_update_spans(t,e){const{frame:n}=this.plot_view;function r(t,e,r){const{dimension:i}=t;switch(t.location_units){case"canvas":return"width"==i?r:e;case"screen":{const{xview:t,yview:o}=n.bbox;return"width"==i?o.invert(r):t.invert(e)}case"data":{const{x_scale:t,y_scale:o}=n;return"width"==i?o.invert(r):t.invert(e)}}}for(const n of this._spans)n.location=r(n,t,e)}}Pv.__name__="CrosshairToolView";class Dv extends Dd{constructor(t){super(t),this.tool_name="Crosshair",this.tool_icon="bk-tool-icon-crosshair"}get tooltip(){return this._get_dim_tooltip(this.dimensions)}}pv=Dv,Dv.__name__="CrosshairTool",pv.prototype.default_view=Pv,pv.define((({Alpha:t,Number:e,Color:n,Auto:r,Tuple:i,Ref:o,Or:a})=>({overlay:[a(r,o(yu),i(o(yu),o(yu))),"auto"],dimensions:[_n.Et,"both"],line_color:[n,"black"],line_width:[e,1],line_alpha:[t,1]}))),pv.register_alias("crosshair",(()=>new Dv));class Nv extends qt{constructor(t){super(t)}get values(){return(0,Q.zu)(this.args)}_make_code(t,e,n,r){return new Function(...(0,Q.HP)(this.args),t,e,n,x(r))}format(t,e,n){return this._make_code("value","format","special_vars",this.code)(...this.values,t,e,n)}}fv=Nv,Nv.__name__="CustomJSHover",fv.define((({Unknown:t,String:e,Dict:n})=>({args:[n(t),{}],code:[e,""]})));class Rv extends Ug{constructor(){super(...arguments),this.child_views=new Map}*children(){yield*super.children(),yield*this.child_views.values()}async lazy_initialize(){await super.lazy_initialize();const t=this.model.children.filter((t=>!(0,f.Kg)(t)));await Ge(this.child_views,t,{parent:this})}remove(){qe(this.child_views),super.remove()}render(){const{style:t}=this.model;if(null!=t)if(t instanceof xu)for(const e of t){const t=e.get_value();if((0,f.Kg)(t)){const n=e.attr.replace(/_/g,"-");this.el.style.hasOwnProperty(n)&&this.el.style.setProperty(n,t)}}else for(const[e,n]of(0,Q.jO)(t)){const t=e.replace(/_/g,"-");this.el.style.hasOwnProperty(t)&&this.el.style.setProperty(t,n)}for(const t of this.model.children)if((0,f.Kg)(t)){const e=document.createTextNode(t);this.el.appendChild(e)}else this.child_views.get(t).render_to(this.el);this.finish()}}Rv.__name__="DOMElementView";class Iv extends Wg{constructor(t){super(t)}}Qv=Iv,Iv.__name__="DOMElement",Qv.define((({String:t,Array:e,Dict:n,Or:r,Nullable:i,Ref:o})=>({style:[i(r(o(xu),n(t))),null],children:[e(r(t,o(Wg),o(Wu))),[]]})));class jv extends Kt{}jv.__name__="ActionView";class zv extends qt{constructor(t){super(t)}}zv.__name__="Action",zv.__module__="bokeh.models.dom";class Bv extends Ug{render(){}}Bv.__name__="PlaceholderView",Bv.tag_name="span";class Fv extends Wg{constructor(t){super(t)}}Fv.__name__="Placeholder";class $v extends Rv{constructor(){super(...arguments),this.action_views=new Map}*children(){yield*super.children(),yield*this.action_views.values()}async lazy_initialize(){await super.lazy_initialize(),await Ge(this.action_views,this.model.actions,{parent:this})}remove(){qe(this.action_views),super.remove()}update(t,e,n={}){!function r(i){for(const o of i.child_views.values())o instanceof Bv?o.update(t,e,n):o instanceof Rv&&r(o)}(this);for(const r of this.action_views.values())r.update(t,e,n)}}$v.__name__="TemplateView",$v.tag_name="div";class Gv extends Iv{}function qv(t,e,n,r){const i={x:n[t],y:r[t]},o={x:n[t+1],y:r[t+1]},{sx:a,sy:s}=e,[l,c]=function(){if("span"==e.type)return"h"==e.direction?[Math.abs(i.x-a),Math.abs(o.x-a)]:[Math.abs(i.y-s),Math.abs(o.y-s)];const t={x:a,y:s};return[Ll(i,t),Ll(o,t)]}();return l<c?[[i.x,i.y],t]:[[o.x,o.y],t+1]}function Uv(t,e,n){return[[t[n],e[n]],n]}Tv=Gv,Gv.__name__="Template",Tv.prototype.default_view=$v,Tv.define((({Array:t,Ref:e})=>({actions:[t(e(zv)),[]]})));class Wv extends Pd{constructor(){super(...arguments),this.ttmodels=new Map,this._ttviews=new Map}*children(){yield*super.children(),yield*this._ttviews.values(),null!=this._template_view&&(yield this._template_view)}async lazy_initialize(){await super.lazy_initialize(),await this._update_ttmodels();const{tooltips:t}=this.model;t instanceof Gv&&(this._template_view=await $e(t,{parent:this.plot_view.canvas}),this._template_view.render())}remove(){this._template_view?.remove(),qe(this._ttviews),super.remove()}connect_signals(){super.connect_signals();const t=this.plot_view.model.properties.renderers,{renderers:e,tooltips:n}=this.model.properties;this.on_change(n,(()=>delete this._template_el)),this.on_change([t,e,n],(async()=>await this._update_ttmodels()))}async _update_ttmodels(){const{ttmodels:t}=this;t.clear();const{tooltips:e}=this.model;if(null==e)return;const{computed_renderers:n}=this;for(const e of n){const n=new j_({content:document.createElement("div"),attachment:this.model.attachment,show_arrow:this.model.show_arrow,interactive:!1,visible:!0,position:null,target:this.parent.canvas.overlays_el});e instanceof Jl?t.set(e,n):e instanceof ig&&(t.set(e.node_renderer,n),t.set(e.edge_renderer,n))}await Ge(this._ttviews,[...t.values()],{parent:this.plot_view});const r=[...function*(){for(const t of n)t instanceof Jl?yield t:t instanceof ig&&(yield t.node_renderer,yield t.edge_renderer)}()],i=this._slots.get(this.update);if(null!=i){const t=new Set(r.map((t=>t.data_source)));T.HN.disconnect_receiver(this,i,t)}for(const t of r)this.connect(t.data_source.inspect,this.update)}get computed_renderers(){const{renderers:t}=this.model;return Pn(t,this.plot_view.model.data_renderers)}_clear(){this._inspect(1/0,1/0);for(const[,t]of this.ttmodels)t.clear()}_move(t){if(!this.model.active)return;const{sx:e,sy:n}=t;this.plot_view.frame.bbox.contains(e,n)?this._inspect(e,n):this._clear()}_move_exit(){this._clear()}_inspect(t,e){let n;n="mouse"==this.model.mode?{type:"point",sx:t,sy:e}:{type:"span",direction:"vline"==this.model.mode?"h":"v",sx:t,sy:e};for(const t of this.computed_renderers){const e=t.get_selection_manager(),r=this.plot_view.renderer_view(t);null!=r&&e.inspect(r,n)}this._emit_callback(n)}_update(t,e,n){const r=t.get_selection_manager(),i=r.inspectors.get(t),o=t.view.convert_selection_to_subset(i);if(i.is_empty()&&null==i.view)return void n.clear();const a=r.source,s=this.plot_view.renderer_view(t);if(null==s)return;const{sx:l,sy:c}=e,u=s.coordinates.x_scale,d=s.coordinates.y_scale,h=u.invert(l),p=d.invert(c),{glyph:f}=s,T=[];if(f instanceof Pl){const[e,n]=[l,c],[r,i]=[h,p],o={index:null,glyph_view:f,x:h,y:p,sx:l,sy:c,snap_x:r,snap_y:i,snap_sx:e,snap_sy:n,name:t.name},s=this._render_tooltips(a,o);T.push([e,n,s])}else if(f instanceof zl||f instanceof Il)for(const e of o.line_indices){const[n,r]=[h,p],[i,s]=[l,c],u={index:e,glyph_view:f,x:h,y:p,sx:l,sy:c,snap_x:n,snap_y:r,snap_sx:i,snap_sy:s,name:t.name,indices:o.line_indices},d=this._render_tooltips(a,u);T.push([i,s,d])}else if(f instanceof Vl){const{line_policy:n}=this.model;for(const r of o.line_indices){const[[i,Q],[m,g],_]=(()=>{const[t,i]=[f._x,f._y];switch(n){case"interp":{const[t,n]=f.get_interpolation_hit(r,e);return[[t,n],[u.compute(t),d.compute(n)],r]}case"prev":{const[e,n]=Uv(f.sx,f.sy,r);return[[t[r+1],i[r+1]],e,n]}case"next":{const[e,n]=Uv(f.sx,f.sy,r+1);return[[t[r+1],i[r+1]],e,n]}case"nearest":{const[n,o]=qv(r,e,f.sx,f.sy);return[[t[o],i[o]],n,o]}case"none":{const t=s.coordinates.x_scale,e=s.coordinates.y_scale;return[[t.invert(l),e.invert(c)],[l,c],r]}}})(),b={index:_,glyph_view:f,x:h,y:p,sx:l,sy:c,snap_x:i,snap_y:Q,snap_sx:m,snap_sy:g,name:t.name,indices:o.line_indices},v=this._render_tooltips(a,b);T.push([m,g,v])}}else if(f instanceof Tf)for(const e of i.image_indices){const[n,r]=[l,c],[i,o]=[h,p],s={index:e.index,glyph_view:f,x:h,y:p,sx:l,sy:c,snap_x:i,snap_y:o,snap_sx:n,snap_sy:r,name:t.name,image_index:e},u=this._render_tooltips(a,s);T.push([n,r,u])}else for(const n of o.indices)if(f instanceof wf&&!(0,Q.Jb)(o.multiline_indices)){const{line_policy:r}=this.model;for(const i of 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Hy([Ay(Mm,{background_fill_color:"#2C001e",border_fill_color:"#15191c",outline_line_color:"#e0e0e0",outline_line_alpha:.25}),Ay($Q,{grid_line_color:"#e0e0e0",grid_line_alpha:.25}),Ay(ga,{major_tick_line_alpha:0,major_tick_line_color:"#e0e0e0",minor_tick_line_alpha:0,minor_tick_line_color:"#e0e0e0",axis_line_alpha:0,axis_line_color:"#e0e0e0",major_label_text_color:"#e0e0e0",major_label_text_font:"Helvetica",major_label_text_font_size:"1.025em",axis_label_standoff:10,axis_label_text_color:"#e0e0e0",axis_label_text_font:"Helvetica",axis_label_text_font_size:"1.25em",axis_label_text_font_style:"normal"}),Ay(Tu,{spacing:8,glyph_width:15,label_standoff:8,label_text_color:"#e0e0e0",label_text_font:"Helvetica",label_text_font_size:"1.025em",border_line_alpha:0,background_fill_alpha:.25,background_fill_color:"#2C001e"}),Ay($c,{title_text_color:"#e0e0e0",title_text_font:"Helvetica",title_text_font_size:"1.025em",title_text_font_style:"normal",major_label_text_color:"#e0e0e0",major_label_text_font:"Helvetica",major_label_text_font_size:"1.025em",background_fill_color:"#15191c",major_tick_line_alpha:0,bar_line_alpha:0}),Ay(aa,{text_color:"#e0e0e0",text_font:"Helvetica",text_font_size:"1.15em"})]),Symbol("Compound"),Symbol("Literal"),Symbol("Identifier"),Symbol("MemberExpression"),Symbol("IndexExpression"),Symbol("CallExpression"),Symbol("UnaryExpression"),Symbol("BinaryExpression"),Symbol("SequenceExpression"),Symbol("ArrayExpression"),Symbol("Failure"),new Set(["$","_"]),ky({"-":1,"!":1,"~":1,"+":1}),ky({"||":1,"&&":2,"|":3,"^":4,"&":5,"==":6,"!=":6,"<":7,">":7,"<=":7,">=":7,"<<":8,">>":8,"+":9,"-":9,"*":10,"/":10,"%":10,"**":11});class My extends Error{}My.__name__="ParseError";class Cy extends WQ{update_style(){super.update_style(),this.style.append(":host",{margin:"5px"})}get child_models(){return[]}get provider(){return Oo}async lazy_initialize(){await super.lazy_initialize(),"not_started"==this.provider.status&&await this.provider.fetch()}_after_layout(){super._after_layout(),"loading"==this.provider.status&&(this._has_finished=!1)}process_tex(t){if(!this.provider.MathJax)return t;const e=this.provider.MathJax.find_tex(t),n=[];let r=0;for(const i of e)n.push(t.slice(r,i.start.n)),n.push(this.provider.MathJax.tex2svg(i.math,{display:i.display}).outerHTML),r=i.end.n;return r<t.length&&n.push(t.slice(r)),n.join("")}contains_tex_string(t){return!!this.provider.MathJax&&this.provider.MathJax.find_tex(t).length>0}}Cy.__name__="WidgetView";class Sy extends ZQ{constructor(t){super(t)}}Sy.__name__="Widget";class Ey extends Cy{connect_signals(){super.connect_signals(),this.connect(this.disabled,(t=>{for(const e of this.controls())Ve(e,"disabled",t)}))}}Ey.__name__="ControlView";class Vy extends Sy{constructor(t){super(t)}}Vy.__name__="Control";const Oy="bk-btn",Py="bk-active",Dy="bk-btn-default",Ny="bk-btn-primary",Ry="bk-btn-success",Iy="bk-btn-warning",jy="bk-btn-danger",zy="bk-btn-light",By="bk-btn-group",Fy="bk-vertical",$y="bk-horizontal",Gy="bk-dropdown-toggle",qy=".bk-btn,::file-selector-button{height:100%;display:inline-block;text-align:center;vertical-align:middle;white-space:nowrap;cursor:pointer;padding:var(--padding-vertical) var(--padding-horizontal);font-size:var(--font-size);border:1px solid transparent;border-radius:var(--border-radius);outline:0;outline-offset:-5px;user-select:none;-webkit-user-select:none;}.bk-btn:hover,::file-selector-button:hover,.bk-btn:focus,::file-selector-button:focus{text-decoration:none;}.bk-btn:active,::file-selector-button:active,.bk-active.bk-btn,.bk-active::file-selector-button{background-image:none;box-shadow:inset 0 3px 5px rgba(0, 0, 0, 0.125);}.bk-btn[disabled]{cursor:not-allowed;pointer-events:none;opacity:0.65;box-shadow:none;}::file-selector-button{color:#333;background-color:#fff;border-color:#ccc;}::file-selector-button:hover{background-color:#f5f5f5;border-color:#b8b8b8;}.bk-active::file-selector-button{background-color:#ebebeb;border-color:#adadad;}::file-selector-button[disabled],::file-selector-button[disabled]:hover,::file-selector-button[disabled]:focus,::file-selector-button[disabled]:active,.bk-active::file-selector-button[disabled]{background-color:#e6e6e6;border-color:#ccc;}::file-selector-button:focus,::file-selector-button:active{outline:1px dotted #ccc;}.bk-btn-default{color:#333;background-color:#fff;border-color:#ccc;}.bk-btn-default:hover{background-color:#f5f5f5;border-color:#b8b8b8;}.bk-active.bk-btn-default{background-color:#ebebeb;border-color:#adadad;}.bk-btn-default[disabled],.bk-btn-default[disabled]:hover,.bk-btn-default[disabled]:focus,.bk-btn-default[disabled]:active,.bk-active.bk-btn-default[disabled]{background-color:#e6e6e6;border-color:#ccc;}.bk-btn-default:focus,.bk-btn-default:active{outline:1px dotted #ccc;}.bk-btn-primary{color:#fff;background-color:#428bca;border-color:#357ebd;}.bk-btn-primary:hover{background-color:#3681c1;border-color:#2c699e;}.bk-active.bk-btn-primary{background-color:#3276b1;border-color:#285e8e;}.bk-btn-primary[disabled],.bk-btn-primary[disabled]:hover,.bk-btn-primary[disabled]:focus,.bk-btn-primary[disabled]:active,.bk-active.bk-btn-primary[disabled]{background-color:#506f89;border-color:#357ebd;}.bk-btn-primary:focus,.bk-btn-primary:active{outline:1px dotted #ccc;}.bk-btn-success{color:#fff;background-color:#5cb85c;border-color:#4cae4c;}.bk-btn-success:hover{background-color:#4eb24e;border-color:#409240;}.bk-active.bk-btn-success{background-color:#47a447;border-color:#398439;}.bk-btn-success[disabled],.bk-btn-success[disabled]:hover,.bk-btn-success[disabled]:focus,.bk-btn-success[disabled]:active,.bk-active.bk-btn-success[disabled]{background-color:#667b66;border-color:#4cae4c;}.bk-btn-success:focus,.bk-btn-success:active{outline:1px dotted #ccc;}.bk-btn-warning{color:#fff;background-color:#f0ad4e;border-color:#eea236;}.bk-btn-warning:hover{background-color:#eea43b;border-color:#e89014;}.bk-active.bk-btn-warning{background-color:#ed9c28;border-color:#d58512;}.bk-btn-warning[disabled],.bk-btn-warning[disabled]:hover,.bk-btn-warning[disabled]:focus,.bk-btn-warning[disabled]:active,.bk-active.bk-btn-warning[disabled]{background-color:#c89143;border-color:#eea236;}.bk-btn-warning:focus,.bk-btn-warning:active{outline:1px dotted #ccc;}.bk-btn-danger{color:#fff;background-color:#d9534f;border-color:#d43f3a;}.bk-btn-danger:hover{background-color:#d5433e;border-color:#bd2d29;}.bk-active.bk-btn-danger{background-color:#d2322d;border-color:#ac2925;}.bk-btn-danger[disabled],.bk-btn-danger[disabled]:hover,.bk-btn-danger[disabled]:focus,.bk-btn-danger[disabled]:active,.bk-active.bk-btn-danger[disabled]{background-color:#a55350;border-color:#d43f3a;}.bk-btn-danger:focus,.bk-btn-danger:active{outline:1px dotted #ccc;}.bk-btn-light{color:#333;background-color:#fff;border-color:#ccc;border-color:transparent;}.bk-btn-light:hover{background-color:#f5f5f5;border-color:#b8b8b8;}.bk-active.bk-btn-light{background-color:#ebebeb;border-color:#adadad;}.bk-btn-light[disabled],.bk-btn-light[disabled]:hover,.bk-btn-light[disabled]:focus,.bk-btn-light[disabled]:active,.bk-active.bk-btn-light[disabled]{background-color:#e6e6e6;border-color:#ccc;}.bk-btn-light:focus,.bk-btn-light:active{outline:1px dotted #ccc;}.bk-btn-group{height:100%;display:flex;flex-wrap:nowrap;align-items:center;}.bk-btn-group:not(.bk-vertical),.bk-btn-group.bk-horizontal{flex-direction:row;}.bk-btn-group.bk-vertical{flex-direction:column;}.bk-btn-group > .bk-btn{flex-grow:1;}.bk-btn-group:not(.bk-vertical) > .bk-btn + .bk-btn{margin-left:-1px;}.bk-btn-group.bk-vertical > .bk-btn + .bk-btn{margin-top:-1px;}.bk-btn-group:not(.bk-vertical) > .bk-btn:first-child:not(:last-child){border-bottom-right-radius:0;border-top-right-radius:0;}.bk-btn-group.bk-vertical > .bk-btn:first-child:not(:last-child){border-bottom-left-radius:0;border-bottom-right-radius:0;}.bk-btn-group:not(.bk-vertical) > .bk-btn:not(:first-child):last-child{border-bottom-left-radius:0;border-top-left-radius:0;}.bk-btn-group.bk-vertical > .bk-btn:not(:first-child):last-child{border-top-left-radius:0;border-top-right-radius:0;}.bk-btn-group > .bk-btn:not(:first-child):not(:last-child){border-radius:0;}.bk-btn-group.bk-vertical > 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e)t.insertBefore(r,n)}(this.button_el,this.icon_view.el,t),this.icon_view.render()}this.group_el=oe({class:By},this.button_el),this.shadow_el.appendChild(this.group_el)}click(){}}Wy.__name__="AbstractButtonView";class Zy extends Vy{constructor(t){super(t)}}Uy=Zy,Zy.__name__="AbstractButton",Uy.define((({String:t,Ref:e,Nullable:n})=>({label:[t,"Button"],icon:[n(e(sm)),null],button_type:[_n.VQ,"default"]})));const Xy="bk-input",Ky="bk-input-group",Yy="bk-inline",Jy=':host{--input-min-height:calc(var(--line-height-computed) + 2*var(--padding-vertical) + 2px);}.bk-input{display:inline-block;width:100%;flex-grow:1;min-height:var(--input-min-height);padding:0 var(--padding-horizontal);background-color:#fff;border:1px solid #ccc;border-radius:var(--border-radius);}.bk-input:focus{border-color:#66afe9;outline:0;box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 8px rgba(102, 175, 233, 0.6);}.bk-input::placeholder,.bk-input:-ms-input-placeholder,.bk-input::-moz-placeholder,.bk-input::-webkit-input-placeholder{color:#999;opacity:1;}.bk-input[disabled]{cursor:not-allowed;background-color:#eee;opacity:1;}.bk-input-container{width:100%;height:100%;display:flex;flex-direction:row;flex-wrap:nowrap;}.bk-input-container .bk-input-prefix,.bk-input-container .bk-input-suffix{display:flex;align-items:center;flex:0 1 0;border:1px solid #ccc;border-radius:var(--border-radius);padding:0 var(--padding-horizontal);background-color:#e6e6e6;}.bk-input-container .bk-input-prefix{border-right:none;border-top-right-radius:0;border-bottom-right-radius:0;}.bk-input-container .bk-input-suffix{border-left:none;border-top-left-radius:0;border-bottom-left-radius:0;}.bk-input-container .bk-input{flex:1 0 0;}.bk-input-container .bk-input:not(:first-child){border-top-left-radius:0;border-bottom-left-radius:0;}.bk-input-container .bk-input:not(:last-child){border-top-right-radius:0;border-bottom-right-radius:0;}input[type=file].bk-input{padding-left:0;}input[type=file]::file-selector-button{box-sizing:inherit;font-family:inherit;font-size:inherit;line-height:inherit;}select:not([multiple]).bk-input,select:not([size]).bk-input{height:auto;appearance:none;-webkit-appearance:none;background-image:url(\'data:image/svg+xml;utf8,<svg version="1.1" viewBox="0 0 25 20" xmlns="http://www.w3.org/2000/svg"><path d="M 0,0 25,0 12.5,20 Z" fill="black" /></svg>\');background-position:right 0.5em center;background-size:8px 6px;background-repeat:no-repeat;padding-right:calc(var(--padding-horizontal) + 8px);}option{padding:0;}select[multiple].bk-input,select[size].bk-input,textarea.bk-input{height:auto;}.bk-input-group{width:100%;height:100%;display:inline-flex;flex-wrap:nowrap;align-items:start;flex-direction:column;white-space:nowrap;}.bk-input-group.bk-inline{flex-direction:row;}.bk-input-group.bk-inline > *:not(:first-child){margin-left:5px;}.bk-input-group > .bk-spin-wrapper{display:inherit;width:inherit;height:inherit;position:relative;overflow:hidden;padding:0;vertical-align:middle;}.bk-input-group > .bk-spin-wrapper input{padding-right:20px;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn{position:absolute;display:block;height:50%;min-height:0;min-width:0;width:30px;padding:0;margin:0;right:0;border:none;background:none;cursor:pointer;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn:before{content:"";display:inline-block;transform:translateY(-50%);border-left:5px solid transparent;border-right:5px solid transparent;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-up{top:0;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-up:before{border-bottom:5px solid black;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-up:disabled:before{border-bottom-color:grey;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-down{bottom:0;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-down:before{border-top:5px solid black;}.bk-input-group > .bk-spin-wrapper > .bk-spin-btn.bk-spin-btn-down:disabled:before{border-top-color:grey;}.bk-description{position:relative;display:inline-block;margin-left:0.25em;vertical-align:middle;margin-top:-2px;cursor:pointer;}.bk-description > .bk-icon{opacity:0.5;width:18px;height:18px;background-color:gray;mask-image:var(--bokeh-icon-help);mask-size:contain;mask-repeat:no-repeat;-webkit-mask-image:var(--bokeh-icon-help);-webkit-mask-size:contain;-webkit-mask-repeat:no-repeat;}label:hover > .bk-description > .bk-icon,.bk-icon.bk-opaque{opacity:1;}';var tx,ex,nx;class rx extends Ey{constructor(){super(...arguments),this.description=null,this.desc_el=null}*controls(){yield this.input_el}*children(){yield*super.children(),null!=this.description&&(yield this.description)}async lazy_initialize(){await super.lazy_initialize();const{description:t}=this.model;t instanceof j_&&(this.description=await $e(t,{parent:this}))}remove(){this.description?.remove(),super.remove()}connect_signals(){super.connect_signals(),this.connect(this.model.properties.title.change,(()=>{this.label_el.textContent=this.model.title}))}styles(){return[...super.styles(),Jy,pd]}render(){super.render();const{title:t,description:e}=this.model;if(null==e)this.desc_el=null;else{const t=oe({class:"bk-icon"});if(this.desc_el=oe({class:"bk-description"},t),(0,f.Kg)(e))this.desc_el.title=e;else{const{description:e}=this;(0,_.vA)(null!=e);const{desc_el:n}=this;e.model.target=n;let r=!1;const i=n=>{e.model.setv({visible:n,closable:r}),t.classList.toggle("bk-opaque",n&&r)};this.on_change(e.model.properties.visible,(()=>{const{visible:t}=e.model;t||(r=!1),i(t)})),n.addEventListener("mouseenter",(()=>{i(!0)})),n.addEventListener("mouseleave",(()=>{r||i(!1)})),document.addEventListener("mousedown",(t=>{const o=t.composedPath();o.includes(e.el)||(o.includes(n)?(r=!r,i(r)):(r=!1,i(!1)))})),window.addEventListener("blur",(()=>{r=!1,i(!1)}))}}this.label_el=Qe({style:{display:0==t.length?"none":""}},t,this.desc_el),this.group_el=oe({class:Ky},this.label_el),this.shadow_el.appendChild(this.group_el)}change_input(){}}rx.__name__="InputWidgetView";class ix extends Vy{constructor(t){super(t)}}tx=ix,ix.__name__="InputWidget",tx.define((({String:t,Nullable:e,Or:n,Ref:r})=>({title:[t,""],description:[e(n(t,r(j_))),null]})));class ox extends rx{connect_signals(){super.connect_signals(),this.connect(this.model.properties.name.change,(()=>this.input_el.name=this.model.name??"")),this.connect(this.model.properties.value.change,(()=>this.input_el.value=this.model.value)),this.connect(this.model.properties.value_input.change,(()=>this.input_el.value=this.model.value_input)),this.connect(this.model.properties.disabled.change,(()=>this.input_el.disabled=this.model.disabled)),this.connect(this.model.properties.placeholder.change,(()=>this.input_el.placeholder=this.model.placeholder)),this.connect(this.model.properties.max_length.change,(()=>{const{max_length:t}=this.model;null!=t?this.input_el.maxLength=t:this.input_el.removeAttribute("maxLength")}))}render(){super.render();const t=this._render_input();this.group_el.appendChild(t);const{input_el:e}=this;e.name=this.model.name??"",e.value=this.model.value,e.disabled=this.model.disabled,e.placeholder=this.model.placeholder,null!=this.model.max_length&&(e.maxLength=this.model.max_length),e.addEventListener("change",(()=>this.change_input())),e.addEventListener("input",(()=>this.change_input_value()))}change_input(){this.model.value=this.input_el.value,super.change_input()}change_input_value(){this.model.value_input=this.input_el.value,super.change_input()}}ox.__name__="TextLikeInputView";class ax extends ix{constructor(t){super(t)}}ex=ax,ax.__name__="TextLikeInput",ex.define((({Int:t,String:e,Nullable:n})=>({value:[e,""],value_input:[e,""],placeholder:[e,""],max_length:[n(t),null]})));class sx extends ox{connect_signals(){super.connect_signals();const{prefix:t,suffix:e}=this.model.properties;this.on_change([t,e],(()=>this.render()))}_render_input(){this.input_el=ge({type:"text",class:Xy});const{prefix:t,suffix:e}=this.model,n=null!=t?oe({class:"bk-input-prefix"},t):null,r=null!=e?oe({class:"bk-input-suffix"},e):null;return oe({class:"bk-input-container"},n,this.input_el,r)}}sx.__name__="TextInputView";class lx extends ax{constructor(t){super(t)}}nx=lx,lx.__name__="TextInput",nx.prototype.default_view=sx,nx.define((({String:t,Nullable:e})=>({prefix:[e(t),null],suffix:[e(t),null]})));const cx="bk-menu",ux="bk-below",dx="bk-active",hx=":host{position:relative;}.bk-menu{position:absolute;left:0;width:100%;z-index:100;cursor:pointer;font-size:var(--font-size);background-color:#fff;border:1px solid #ccc;border-radius:var(--border-radius);box-shadow:0 6px 12px rgba(0, 0, 0, 0.175);}.bk-menu.bk-above{bottom:100%;}.bk-menu.bk-below{top:100%;}.bk-menu > .bk-divider{height:1px;margin:calc(var(--line-height-computed)/2 - 1px) 0;overflow:hidden;background-color:#e5e5e5;}.bk-menu > :not(.bk-divider){padding:var(--padding-vertical) var(--padding-horizontal);}.bk-menu > :not(.bk-divider):hover,.bk-menu > :not(.bk-divider).bk-active{background-color:#e6e6e6;}";var px,fx,Qx,Tx,mx;class gx extends sx{constructor(){super(...arguments),this._open=!1,this._last_value="",this._hover_index=0}styles(){return[...super.styles(),hx]}render(){super.render(),this.input_el.addEventListener("keydown",(t=>this._keydown(t))),this.input_el.addEventListener("keyup",(t=>this._keyup(t))),this.input_el.addEventListener("focusin",(()=>this._toggle_menu())),this.menu=oe({class:[cx,ux]}),this.menu.addEventListener("click",(t=>this._menu_click(t))),this.menu.addEventListener("mouseover",(t=>this._menu_hover(t))),this.shadow_el.appendChild(this.menu),ke(this.menu)}change_input(){this._open&&this.menu.children.length>0?(this.model.value=this.menu.children[this._hover_index].textContent,this.input_el.focus(),this._hide_menu()):this.model.restrict||super.change_input()}_update_completions(t){Ae(this.menu);const{max_completions:e}=this.model,n=null!=e?(0,On.s)(t,e):t;for(const t of n){const e=oe(t);this.menu.append(e)}this.menu.firstElementChild?.classList.add(dx)}_toggle_menu(){const{value:t}=this.input_el;if(t.length<this.model.min_characters)return void this._hide_menu();const e=(()=>{const{case_sensitive:t}=this.model;return t?t=>t:t=>t.toLowerCase()})(),n=[];for(const r of this.model.completions)e(r).startsWith(e(t))&&n.push(r);this._update_completions(n),0==n.length?this._hide_menu():this._show_menu()}_show_menu(){if(!this._open){this._open=!0,this._hover_index=0,this._last_value=this.model.value,He(this.menu);const t=e=>{e.composedPath().includes(this.el)||(document.removeEventListener("click",t),this._hide_menu())};document.addEventListener("click",t)}}_hide_menu(){this._open&&(this._open=!1,ke(this.menu))}_menu_click(t){t.target!=t.currentTarget&&t.target instanceof Element&&(this.model.value=t.target.textContent,this.input_el.focus(),this._hide_menu())}_menu_hover(t){if(t.target!=t.currentTarget&&t.target instanceof Element)for(let e=0;e<this.menu.children.length;e++)if(this.menu.children[e].textContent==t.target.textContent){this._bump_hover(e);break}}_bump_hover(t){const e=this.menu.children.length;this._open&&e>0&&(this.menu.children[this._hover_index].classList.remove(dx),this._hover_index=(0,Gi.qE)(t,0,e-1),this.menu.children[this._hover_index].classList.add(dx))}_keydown(t){}_keyup(t){switch(t.key){case"Enter":this.change_input();break;case"Escape":this._hide_menu();break;case"ArrowUp":this._bump_hover(this._hover_index-1);break;case"ArrowDown":this._bump_hover(this._hover_index+1);break;default:this._toggle_menu()}}}gx.__name__="AutocompleteInputView";class _x extends lx{constructor(t){super(t)}}px=_x,_x.__name__="AutocompleteInput",px.prototype.default_view=gx,px.define((({Boolean:t,Int:e,String:n,Array:r,NonNegative:i,Positive:o,Nullable:a})=>({completions:[r(n),[]],min_characters:[i(e),2],max_completions:[a(o(e)),null],case_sensitive:[t,!0],restrict:[t,!0]})));class bx extends Wy{click(){this.model.trigger_event(new dt),super.click()}}bx.__name__="ButtonView";class vx extends Zy{constructor(t){super(t)}on_click(t){this.on_event(dt,t)}}fx=vx,vx.__name__="Button",fx.prototype.default_view=bx,fx.override({label:"Button"});class yx extends Ey{}yx.__name__="OrientedControlView";class xx extends Vy{constructor(t){super(t)}}Qx=xx,xx.__name__="OrientedControl",Qx.define((()=>({orientation:[_n.t4,"horizontal"]})));class wx extends yx{*controls(){yield*this._buttons}connect_signals(){super.connect_signals();const t=this.model.properties;this.on_change(t.button_type,(()=>this.render())),this.on_change(t.labels,(()=>this.render())),this.on_change(t.active,(()=>this._update_active()))}styles(){return[...super.styles(),qy]}render(){super.render(),this._buttons=this.model.labels.map(((t,e)=>{const n=fe({class:[Oy,u[`btn_${this.model.button_type}`]],disabled:this.model.disabled},t);return n.addEventListener("click",(()=>{this.change_active(e),this.model.trigger_event(new dt)})),n})),this._update_active();const t="horizontal"==this.model.orientation?$y:Fy,e=oe({class:[By,t]},this._buttons);this.shadow_el.appendChild(e)}}wx.__name__="ToggleButtonGroupView";class Lx extends xx{constructor(t){super(t)}}Tx=Lx,Lx.__name__="ToggleButtonGroup",Tx.define((({String:t,Array:e})=>({labels:[e(t),[]],button_type:[_n.VQ,"default"]})));class Ax extends wx{get active(){return new Set(this.model.active)}change_active(t){const{active:e}=this;e.has(t)?e.delete(t):e.add(t),this.model.active=[...e].sort()}_update_active(){const{active:t}=this;this._buttons.forEach(((e,n)=>{e.classList.toggle(Py,t.has(n))}))}}Ax.__name__="CheckboxButtonGroupView";class Hx extends Lx{constructor(t){super(t)}}mx=Hx,Hx.__name__="CheckboxButtonGroup",mx.prototype.default_view=Ax,mx.define((({Int:t,Array:e})=>({active:[e(t),[]]})));const kx='input[type="checkbox"],input[type="radio"]{margin:0;}input[type="checkbox"] + *,input[type="radio"] + *{position:relative;top:-2px;margin-left:3px;}';var Mx,Cx,Sx,Ex,Vx;class Ox extends Ey{*controls(){yield*this._inputs}connect_signals(){super.connect_signals();const{labels:t,inline:e}=this.model.properties;this.on_change([t,e],(()=>this.render()))}styles(){return[...super.styles(),Jy,kx]}}Ox.__name__="ToggleInputGroupView";class Px extends Vy{constructor(t){super(t)}}Mx=Px,Px.__name__="ToggleInputGroup",Mx.define((({Boolean:t,String:e,Array:n})=>({labels:[n(e),[]],inline:[t,!1]})));class Dx extends Ox{get active(){return new Set(this.model.active)}connect_signals(){super.connect_signals();const{active:t}=this.model.properties;this.on_change(t,(()=>{const{active:t}=this;for(const[e,n]of(0,On.HL)(this._inputs))e.checked=t.has(n)}))}render(){super.render();const t=oe({class:[Ky,this.model.inline?Yy:null]});this.shadow_el.appendChild(t);const{active:e,labels:n}=this.model;this._inputs=[];for(let r=0;r<n.length;r++){const i=ge({type:"checkbox",value:`${r}`});i.addEventListener("change",(()=>this.change_active(r))),this._inputs.push(i),this.model.disabled&&(i.disabled=!0),(0,Rt.mK)(e,r)&&(i.checked=!0);const o=Qe(i,ae(n[r]));t.appendChild(o)}}change_active(t){const{active:e}=this;e.has(t)?e.delete(t):e.add(t),this.model.active=[...e].sort()}}Dx.__name__="CheckboxGroupView";class Nx extends Px{constructor(t){super(t)}}Cx=Nx,Nx.__name__="CheckboxGroup",Cx.prototype.default_view=Dx,Cx.define((({Int:t,Array:e})=>({active:[e(t),[]]})));class Rx extends Cy{connect_signals(){super.connect_signals();const{active:t,disabled:e}=this.model.properties;this.on_change(t,(()=>this._update_active())),this.on_change(e,(()=>this._update_disabled()))}_toggle_active(){this.model.disabled||(this.model.active=!this.model.active)}}Rx.__name__="ToggleInputView";class Ix extends Sy{constructor(t){super(t)}}Sx=Ix,Ix.__name__="ToggleInput",Sx.define((({Boolean:t})=>({active:[t,!1]})));class jx extends Rx{styles(){return[...super.styles(),kx]}connect_signals(){super.connect_signals();const{label:t}=this.model.properties;this.on_change(t,(()=>this._update_label()))}render(){super.render(),this.checkbox_el=ge({type:"checkbox"}),this.label_el=ae(this.model.label),this.checkbox_el.addEventListener("change",(()=>this._toggle_active())),this._update_active(),this._update_disabled(),this.shadow_el.append(this.checkbox_el,this.label_el)}_update_active(){this.checkbox_el.checked=this.model.active}_update_disabled(){this.checkbox_el.toggleAttribute("disabled",this.model.disabled)}_update_label(){this.label_el.textContent=this.model.label}}jx.__name__="CheckboxView";class zx extends Ix{constructor(t){super(t)}}Ex=zx,zx.__name__="Checkbox",Ex.prototype.default_view=jx,Ex.define((({String:t})=>({label:[t,""]})));class Bx extends rx{connect_signals(){super.connect_signals(),this.connect(this.model.properties.name.change,(()=>this.input_el.name=this.model.name??"")),this.connect(this.model.properties.color.change,(()=>this.input_el.value=(0,Ye.Kr)(this.model.color))),this.connect(this.model.properties.disabled.change,(()=>this.input_el.disabled=this.model.disabled))}render(){super.render(),this.input_el=ge({type:"color",class:Xy,name:this.model.name,value:this.model.color,disabled:this.model.disabled}),this.input_el.addEventListener("change",(()=>this.change_input())),this.group_el.appendChild(this.input_el)}change_input(){this.model.color=this.input_el.value,super.change_input()}}Bx.__name__="ColorPickerView";class Fx extends ix{constructor(t){super(t)}}Vx=Fx,Fx.__name__="ColorPicker",Vx.prototype.default_view=Bx,Vx.define((({Color:t})=>({color:[t,"#000000"]})));var 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0===e&&(e=2),("000"+t).slice(-1*e)},Zx=function(t){return!0===t?1:0};function Xx(t,e){var n;return function(){var r=this,i=arguments;clearTimeout(n),n=setTimeout((function(){return t.apply(r,i)}),e)}}var Kx=function(t){return t instanceof Array?t:[t]};function Yx(t,e,n){if(!0===n)return t.classList.add(e);t.classList.remove(e)}function Jx(t,e,n){var r=window.document.createElement(t);return e=e||"",n=n||"",r.className=e,void 0!==n&&(r.textContent=n),r}function tw(t){for(;t.firstChild;)t.removeChild(t.firstChild)}function ew(t,e){return e(t)?t:t.parentNode?ew(t.parentNode,e):void 0}function nw(t,e){var n=Jx("div","numInputWrapper"),r=Jx("input","numInput "+t),i=Jx("span","arrowUp"),o=Jx("span","arrowDown");if(-1===navigator.userAgent.indexOf("MSIE 9.0")?r.type="number":(r.type="text",r.pattern="\\d*"),void 0!==e)for(var a in e)r.setAttribute(a,e[a]);return n.appendChild(r),n.appendChild(i),n.appendChild(o),n}function rw(t){try{return"function"==typeof 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a.dateObj=e,a.$i=i,a.setAttribute("aria-label",n.formatDate(e,n.config.ariaDateFormat)),-1===t.indexOf("hidden")&&0===dw(e,n.now)&&(n.todayDateElem=a,a.classList.add("today"),a.setAttribute("aria-current","date")),o?(a.tabIndex=-1,X(e)&&(a.classList.add("selected"),n.selectedDateElem=a,"range"===n.config.mode&&(Yx(a,"startRange",n.selectedDates[0]&&0===dw(e,n.selectedDates[0],!0)),Yx(a,"endRange",n.selectedDates[1]&&0===dw(e,n.selectedDates[1],!0)),"nextMonthDay"===t&&a.classList.add("inRange")))):a.classList.add("flatpickr-disabled"),"range"===n.config.mode&&function(t){return!("range"!==n.config.mode||n.selectedDates.length<2)&&dw(t,n.selectedDates[0])>=0&&dw(t,n.selectedDates[1])<=0}(e)&&!X(e)&&a.classList.add("inRange"),n.weekNumbers&&1===n.config.showMonths&&"prevMonthDay"!==t&&i%7==6&&n.weekNumbers.insertAdjacentHTML("beforeend","<span class='flatpickr-day'>"+n.config.getWeek(e)+"</span>"),W("onDayCreate",a),a}function m(t){t.focus(),"range"===n.config.mode&&P(t)}function g(t){for(var e=t>0?0:n.config.showMonths-1,r=t>0?n.config.showMonths:-1,i=e;i!=r;i+=t)for(var o=n.daysContainer.children[i],a=t>0?0:o.children.length-1,s=t>0?o.children.length:-1,l=a;l!=s;l+=t){var c=o.children[l];if(-1===c.className.indexOf("hidden")&&S(c.dateObj))return c}}function _(t,e){var i=r(),o=E(i||document.body),a=void 0!==t?t:o?i:void 0!==n.selectedDateElem&&E(n.selectedDateElem)?n.selectedDateElem:void 0!==n.todayDateElem&&E(n.todayDateElem)?n.todayDateElem:g(e>0?1:-1);void 0===a?n._input.focus():o?function(t,e){for(var r=-1===t.className.indexOf("Month")?t.dateObj.getMonth():n.currentMonth,i=e>0?n.config.showMonths:-1,o=e>0?1:-1,a=r-n.currentMonth;a!=i;a+=o)for(var s=n.daysContainer.children[a],l=r-n.currentMonth===a?t.$i+e:e<0?s.children.length-1:0,c=s.children.length,u=l;u>=0&&u<c&&u!=(e>0?c:-1);u+=o){var d=s.children[u];if(-1===d.className.indexOf("hidden")&&S(d.dateObj)&&Math.abs(t.$i-u)>=Math.abs(e))return m(d)}n.changeMonth(o),_(g(o),0)}(a,e):m(a)}function b(t,e){for(var r=(new Date(t,e,1).getDay()-n.l10n.firstDayOfWeek+7)%7,i=n.utils.getDaysInMonth((e-1+12)%12,t),o=n.utils.getDaysInMonth(e,t),a=window.document.createDocumentFragment(),s=n.config.showMonths>1,l=s?"prevMonthDay hidden":"prevMonthDay",c=s?"nextMonthDay hidden":"nextMonthDay",u=i+1-r,d=0;u<=i;u++,d++)a.appendChild(T("flatpickr-day "+l,new Date(t,e-1,u),0,d));for(u=1;u<=o;u++,d++)a.appendChild(T("flatpickr-day",new Date(t,e,u),0,d));for(var h=o+1;h<=42-r&&(1===n.config.showMonths||d%7!=0);h++,d++)a.appendChild(T("flatpickr-day "+c,new Date(t,e+1,h%o),0,d));var p=Jx("div","dayContainer");return p.appendChild(a),p}function v(){if(void 0!==n.daysContainer){tw(n.daysContainer),n.weekNumbers&&tw(n.weekNumbers);for(var t=document.createDocumentFragment(),e=0;e<n.config.showMonths;e++){var r=new 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t,e=Jx("div","flatpickr-month"),r=window.document.createDocumentFragment();n.config.showMonths>1||"static"===n.config.monthSelectorType?t=Jx("span","cur-month"):(n.monthsDropdownContainer=Jx("select","flatpickr-monthDropdown-months"),n.monthsDropdownContainer.setAttribute("aria-label",n.l10n.monthAriaLabel),d(n.monthsDropdownContainer,"change",(function(t){var e=rw(t),r=parseInt(e.value,10);n.changeMonth(r-n.currentMonth),W("onMonthChange")})),y(),t=n.monthsDropdownContainer);var i=nw("cur-year",{tabindex:"-1"}),o=i.getElementsByTagName("input")[0];o.setAttribute("aria-label",n.l10n.yearAriaLabel),n.config.minDate&&o.setAttribute("min",n.config.minDate.getFullYear().toString()),n.config.maxDate&&(o.setAttribute("max",n.config.maxDate.getFullYear().toString()),o.disabled=!!n.config.minDate&&n.config.minDate.getFullYear()===n.config.maxDate.getFullYear());var a=Jx("div","flatpickr-current-month");return a.appendChild(t),a.appendChild(i),r.appendChild(a),e.appendChild(r),{container:e,yearElement:o,monthElement:t}}function w(){tw(n.monthNav),n.monthNav.appendChild(n.prevMonthNav),n.config.showMonths&&(n.yearElements=[],n.monthElements=[]);for(var t=n.config.showMonths;t--;){var e=x();n.yearElements.push(e.yearElement),n.monthElements.push(e.monthElement),n.monthNav.appendChild(e.container)}n.monthNav.appendChild(n.nextMonthNav)}function L(){n.weekdayContainer?tw(n.weekdayContainer):n.weekdayContainer=Jx("div","flatpickr-weekdays");for(var t=n.config.showMonths;t--;){var e=Jx("div","flatpickr-weekdaycontainer");n.weekdayContainer.appendChild(e)}return A(),n.weekdayContainer}function A(){if(n.weekdayContainer){var t=n.l10n.firstDayOfWeek,e=Qw(n.l10n.weekdays.shorthand);t>0&&t<e.length&&(e=Qw(e.splice(t,e.length),e.splice(0,t)));for(var r=n.config.showMonths;r--;)n.weekdayContainer.children[r].innerHTML="\n      <span class='flatpickr-weekday'>\n        "+e.join("</span><span 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0!==n.input.value&&a(),n.close(),n.config&&"range"===n.config.mode&&1===n.selectedDates.length&&n.clear(!1))}}function C(t){if(!(!t||n.config.minDate&&t<n.config.minDate.getFullYear()||n.config.maxDate&&t>n.config.maxDate.getFullYear())){var e=t,r=n.currentYear!==e;n.currentYear=e||n.currentYear,n.config.maxDate&&n.currentYear===n.config.maxDate.getFullYear()?n.currentMonth=Math.min(n.config.maxDate.getMonth(),n.currentMonth):n.config.minDate&&n.currentYear===n.config.minDate.getFullYear()&&(n.currentMonth=Math.max(n.config.minDate.getMonth(),n.currentMonth)),r&&(n.redraw(),W("onYearChange"),y())}}function S(t,e){var r;void 0===e&&(e=!0);var i=n.parseDate(t,void 0,e);if(n.config.minDate&&i&&dw(i,n.config.minDate,void 0!==e?e:!n.minDateHasTime)<0||n.config.maxDate&&i&&dw(i,n.config.maxDate,void 0!==e?e:!n.maxDateHasTime)>0)return!1;if(!n.config.enable&&0===n.config.disable.length)return!0;if(void 0===i)return!1;for(var o=!!n.config.enable,a=null!==(r=n.config.enable)&&void 0!==r?r:n.config.disable,s=0,l=void 0;s<a.length;s++){if("function"==typeof(l=a[s])&&l(i))return o;if(l instanceof Date&&void 0!==i&&l.getTime()===i.getTime())return o;if("string"==typeof l){var c=n.parseDate(l,void 0,!0);return c&&c.getTime()===i.getTime()?o:!o}if("object"==typeof l&&void 0!==i&&l.from&&l.to&&i.getTime()>=l.from.getTime()&&i.getTime()<=l.to.getTime())return o}return!o}function E(t){return void 0!==n.daysContainer&&-1===t.className.indexOf("hidden")&&-1===t.className.indexOf("flatpickr-disabled")&&n.daysContainer.contains(t)}function V(t){var e=t.target===n._input,r=n._input.value.trimEnd()!==Y();!e||!r||t.relatedTarget&&k(t.relatedTarget)||n.setDate(n._input.value,!0,t.target===n.altInput?n.config.altFormat:n.config.dateFormat)}function O(e){var i=rw(e),o=n.config.wrap?t.contains(i):i===n._input,l=n.config.allowInput,c=n.isOpen&&(!l||!o),u=n.config.inline&&o&&!l;if(13===e.keyCode&&o){if(l)return n.setDate(n._input.value,!0,i===n.altInput?n.config.altFormat:n.config.dateFormat),n.close(),i.blur();n.open()}else if(k(i)||c||u){var d=!!n.timeContainer&&n.timeContainer.contains(i);switch(e.keyCode){case 13:d?(e.preventDefault(),a(),B()):F(e);break;case 27:e.preventDefault(),B();break;case 8:case 46:o&&!n.config.allowInput&&(e.preventDefault(),n.clear());break;case 37:case 39:if(d||o)n.hourElement&&n.hourElement.focus();else{e.preventDefault();var h=r();if(void 0!==n.daysContainer&&(!1===l||h&&E(h))){var p=39===e.keyCode?1:-1;e.ctrlKey?(e.stopPropagation(),H(p),_(g(1),0)):_(void 0,p)}}break;case 38:case 40:e.preventDefault();var f=40===e.keyCode?1:-1;n.daysContainer&&void 0!==i.$i||i===n.input||i===n.altInput?e.ctrlKey?(e.stopPropagation(),C(n.currentYear-f),_(g(1),0)):d||_(void 0,7*f):i===n.currentYearElement?C(n.currentYear-f):n.config.enableTime&&(!d&&n.hourElement&&n.hourElement.focus(),a(e),n._debouncedChange());break;case 9:if(d){var 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r=n.config["_"+t+"Date"]=n.parseDate(e,n.config.dateFormat),i=n.config["_"+("min"===t?"max":"min")+"Date"];void 0!==r&&(n["min"===t?"minDateHasTime":"maxDateHasTime"]=r.getHours()>0||r.getMinutes()>0||r.getSeconds()>0),n.selectedDates&&(n.selectedDates=n.selectedDates.filter((function(t){return S(t)})),n.selectedDates.length||"min"!==t||l(r),J()),n.daysContainer&&(z(),void 0!==r?n.currentYearElement[t]=r.getFullYear().toString():n.currentYearElement.removeAttribute(t),n.currentYearElement.disabled=!!i&&void 0!==r&&i.getFullYear()===r.getFullYear())}}function R(){return n.config.wrap?t.querySelector("[data-input]"):t}function I(){"object"!=typeof n.config.locale&&void 0===gw.l10ns[n.config.locale]&&n.config.errorHandler(new Error("flatpickr: invalid locale "+n.config.locale)),n.l10n=fw(fw({},gw.l10ns.default),"object"==typeof n.config.locale?n.config.locale:"default"!==n.config.locale?gw.l10ns[n.config.locale]:void 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t=document.createElement("style");return document.head.appendChild(t),t.sheet}()}();if(void 0===g)return;var _=window.document.body.offsetWidth,b=Math.max(0,_/2-i/2),v=g.cssRules.length,y="{left:"+l.left+"px;right:auto;}";Yx(n.calendarContainer,"rightMost",!1),Yx(n.calendarContainer,"centerMost",!0),g.insertRule(".flatpickr-calendar.centerMost:before,.flatpickr-calendar.centerMost:after"+y,v),n.calendarContainer.style.left=b+"px",n.calendarContainer.style.right="auto"}else n.calendarContainer.style.left="auto",n.calendarContainer.style.right=Q+"px";else n.calendarContainer.style.left=h+"px",n.calendarContainer.style.right="auto"}}}else n.config.position(n,t)}function z(){n.config.noCalendar||n.isMobile||(y(),K(),v())}function B(){n._input.focus(),-1!==window.navigator.userAgent.indexOf("MSIE")||void 0!==navigator.msMaxTouchPoints?setTimeout(n.close,0):n.close()}function F(t){t.preventDefault(),t.stopPropagation();var e=ew(rw(t),(function(t){return 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n.altInput),n.input&&(n.input.type=n.input._type,n.input.classList.remove("flatpickr-input"),n.input.removeAttribute("readonly")),["_showTimeInput","latestSelectedDateObj","_hideNextMonthArrow","_hidePrevMonthArrow","__hideNextMonthArrow","__hidePrevMonthArrow","isMobile","isOpen","selectedDateElem","minDateHasTime","maxDateHasTime","days","daysContainer","_input","_positionElement","innerContainer","rContainer","monthNav","todayDateElem","calendarContainer","weekdayContainer","prevMonthNav","nextMonthNav","monthsDropdownContainer","currentMonthElement","currentYearElement","navigationCurrentMonth","selectedDateElem","config"].forEach((function(t){try{delete n[t]}catch(t){}}))},n.isEnabled=S,n.jumpToDate=p,n.updateValue=J,n.open=function(t,e){if(void 0===e&&(e=n._positionElement),!0===n.isMobile){if(t){t.preventDefault();var r=rw(t);r&&r.blur()}return void 0!==n.mobileInput&&(n.mobileInput.focus(),n.mobileInput.click()),void W("onOpen")}if(!n._input.disabled&&!n.config.inline){var i=n.isOpen;n.isOpen=!0,i||(n.calendarContainer.classList.add("open"),n._input.classList.add("active"),W("onOpen"),j(e)),!0===n.config.enableTime&&!0===n.config.noCalendar&&(!1!==n.config.allowInput||void 0!==t&&n.timeContainer.contains(t.relatedTarget)||setTimeout((function(){return n.hourElement.select()}),50))}},n.redraw=z,n.set=function(t,e){if(null!==t&&"object"==typeof t)for(var r in Object.assign(n.config,t),t)void 0!==$[r]&&$[r].forEach((function(t){return t()}));else n.config[t]=e,void 0!==$[t]?$[t].forEach((function(t){return t()})):$x.indexOf(t)>-1&&(n.config[t]=Kx(e));n.redraw(),J(!0)},n.setDate=function(t,e,r){if(void 0===e&&(e=!1),void 0===r&&(r=n.config.dateFormat),0!==t&&!t||t instanceof Array&&0===t.length)return n.clear(e);G(t,r),n.latestSelectedDateObj=n.selectedDates[n.selectedDates.length-1],n.redraw(),p(void 0,e),l(),0===n.selectedDates.length&&n.clear(!1),J(e),e&&W("onChange")},n.toggle=function(t){if(!0===n.isOpen)return n.close();n.open(t)};var $={locale:[I,A],showMonths:[w,o,L],minDate:[p],maxDate:[p],positionElement:[U],clickOpens:[function(){!0===n.config.clickOpens?(d(n._input,"focus",n.open),d(n._input,"click",n.open)):(n._input.removeEventListener("focus",n.open),n._input.removeEventListener("click",n.open))}]};function G(t,e){var r=[];if(t instanceof Array)r=t.map((function(t){return n.parseDate(t,e)}));else if(t instanceof Date||"number"==typeof t)r=[n.parseDate(t,e)];else if("string"==typeof t)switch(n.config.mode){case"single":case"time":r=[n.parseDate(t,e)];break;case"multiple":r=t.split(n.config.conjunction).map((function(t){return n.parseDate(t,e)}));break;case"range":r=t.split(n.l10n.rangeSeparator).map((function(t){return n.parseDate(t,e)}))}else n.config.errorHandler(new Error("Invalid date supplied: "+JSON.stringify(t)));n.selectedDates=n.config.allowInvalidPreload?r:r.filter((function(t){return t instanceof Date&&S(t,!1)})),"range"===n.config.mode&&n.selectedDates.sort((function(t,e){return t.getTime()-e.getTime()}))}function q(t){return t.slice().map((function(t){return"string"==typeof t||"number"==typeof t||t instanceof Date?n.parseDate(t,void 0,!0):t&&"object"==typeof t&&t.from&&t.to?{from:n.parseDate(t.from,void 0),to:n.parseDate(t.to,void 0)}:t})).filter((function(t){return t}))}function U(){n._positionElement=n.config.positionElement||n._input}function W(t,e){if(void 0!==n.config){var r=n.config[t];if(void 0!==r&&r.length>0)for(var i=0;r[i]&&i<r.length;i++)r[i](n.selectedDates,n.input.value,n,e);"onChange"===t&&(n.input.dispatchEvent(Z("change")),n.input.dispatchEvent(Z("input")))}}function Z(t){var e=document.createEvent("Event");return e.initEvent(t,!0,!0),e}function X(t){for(var e=0;e<n.selectedDates.length;e++){var r=n.selectedDates[e];if(r instanceof Date&&0===dw(r,t))return""+e}return!1}function K(){n.config.noCalendar||n.isMobile||!n.monthNav||(n.yearElements.forEach((function(t,e){var r=new 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r=["wrap","weekNumbers","allowInput","allowInvalidPreload","clickOpens","time_24hr","enableTime","noCalendar","altInput","shorthandCurrentMonth","inline","static","enableSeconds","disableMobile"],o=fw(fw({},JSON.parse(JSON.stringify(t.dataset||{}))),e),a={};n.config.parseDate=o.parseDate,n.config.formatDate=o.formatDate,Object.defineProperty(n.config,"enable",{get:function(){return n.config._enable},set:function(t){n.config._enable=q(t)}}),Object.defineProperty(n.config,"disable",{get:function(){return n.config._disable},set:function(t){n.config._disable=q(t)}});var s="time"===o.mode;if(!o.dateFormat&&(o.enableTime||s)){var l=gw.defaultConfig.dateFormat||Gx.dateFormat;a.dateFormat=o.noCalendar||s?"H:i"+(o.enableSeconds?":S":""):l+" H:i"+(o.enableSeconds?":S":"")}if(o.altInput&&(o.enableTime||s)&&!o.altFormat){var c=gw.defaultConfig.altFormat||Gx.altFormat;a.altFormat=o.noCalendar||s?"h:i"+(o.enableSeconds?":S K":" K"):c+" h:i"+(o.enableSeconds?":S":"")+" 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0!==n.config[t]})).forEach((function(t){n.config[t]=Kx(n.config[t]||[]).map(i)})),n.isMobile=!n.config.disableMobile&&!n.config.inline&&"single"===n.config.mode&&!n.config.disable.length&&!n.config.enable&&!n.config.weekNumbers&&/Android|webOS|iPhone|iPad|iPod|BlackBerry|IEMobile|Opera Mini/i.test(navigator.userAgent),d=0;d<n.config.plugins.length;d++){var h=n.config.plugins[d](n)||{};for(var p in h)$x.indexOf(p)>-1?n.config[p]=Kx(h[p]).map(i).concat(n.config[p]):void 0===o[p]&&(n.config[p]=h[p])}o.altInputClass||(n.config.altInputClass=R().className+" 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t=n.config.defaultDate||("INPUT"!==n.input.nodeName&&"TEXTAREA"!==n.input.nodeName||!n.input.placeholder||n.input.value!==n.input.placeholder?n.input.value:null);t&&G(t,n.config.dateFormat),n._initialDate=n.selectedDates.length>0?n.selectedDates[0]:n.config.minDate&&n.config.minDate.getTime()>n.now.getTime()?n.config.minDate:n.config.maxDate&&n.config.maxDate.getTime()<n.now.getTime()?n.config.maxDate:n.now,n.currentYear=n._initialDate.getFullYear(),n.currentMonth=n._initialDate.getMonth(),n.selectedDates.length>0&&(n.latestSelectedDateObj=n.selectedDates[0]),void 0!==n.config.minTime&&(n.config.minTime=n.parseDate(n.config.minTime,"H:i")),void 0!==n.config.maxTime&&(n.config.maxTime=n.parseDate(n.config.maxTime,"H:i")),n.minDateHasTime=!!n.config.minDate&&(n.config.minDate.getHours()>0||n.config.minDate.getMinutes()>0||n.config.minDate.getSeconds()>0),n.maxDateHasTime=!!n.config.maxDate&&(n.config.maxDate.getHours()>0||n.config.maxDate.getMinutes()>0||n.config.maxDate.getSeconds()>0)}(),n.utils={getDaysInMonth:function(t,e){return void 0===t&&(t=n.currentMonth),void 0===e&&(e=n.currentYear),1===t&&(e%4==0&&e%100!=0||e%400==0)?29:n.l10n.daysInMonth[t]}},n.isMobile||function(){var t=window.document.createDocumentFragment();if(n.calendarContainer=Jx("div","flatpickr-calendar"),n.calendarContainer.tabIndex=-1,!n.config.noCalendar){if(t.appendChild((n.monthNav=Jx("div","flatpickr-months"),n.yearElements=[],n.monthElements=[],n.prevMonthNav=Jx("span","flatpickr-prev-month"),n.prevMonthNav.innerHTML=n.config.prevArrow,n.nextMonthNav=Jx("span","flatpickr-next-month"),n.nextMonthNav.innerHTML=n.config.nextArrow,w(),Object.defineProperty(n,"_hidePrevMonthArrow",{get:function(){return n.__hidePrevMonthArrow},set:function(t){n.__hidePrevMonthArrow!==t&&(Yx(n.prevMonthNav,"flatpickr-disabled",t),n.__hidePrevMonthArrow=t)}}),Object.defineProperty(n,"_hideNextMonthArrow",{get:function(){return n.__hideNextMonthArrow},set:function(t){n.__hideNextMonthArrow!==t&&(Yx(n.nextMonthNav,"flatpickr-disabled",t),n.__hideNextMonthArrow=t)}}),n.currentYearElement=n.yearElements[0],K(),n.monthNav)),n.innerContainer=Jx("div","flatpickr-innerContainer"),n.config.weekNumbers){var e=function(){n.calendarContainer.classList.add("hasWeeks");var t=Jx("div","flatpickr-weekwrapper");t.appendChild(Jx("span","flatpickr-weekday",n.l10n.weekAbbreviation));var e=Jx("div","flatpickr-weeks");return t.appendChild(e),{weekWrapper:t,weekNumbers:e}}(),r=e.weekWrapper,i=e.weekNumbers;n.innerContainer.appendChild(r),n.weekNumbers=i,n.weekWrapper=r}n.rContainer=Jx("div","flatpickr-rContainer"),n.rContainer.appendChild(L()),n.daysContainer||(n.daysContainer=Jx("div","flatpickr-days"),n.daysContainer.tabIndex=-1),v(),n.rContainer.appendChild(n.daysContainer),n.innerContainer.appendChild(n.rContainer),t.appendChild(n.innerContainer)}n.config.enableTime&&t.appendChild(function(){n.calendarContainer.classList.add("hasTime"),n.config.noCalendar&&n.calendarContainer.classList.add("noCalendar");var t=pw(n.config);n.timeContainer=Jx("div","flatpickr-time"),n.timeContainer.tabIndex=-1;var e=Jx("span","flatpickr-time-separator",":"),r=nw("flatpickr-hour",{"aria-label":n.l10n.hourAriaLabel});n.hourElement=r.getElementsByTagName("input")[0];var i=nw("flatpickr-minute",{"aria-label":n.l10n.minuteAriaLabel});if(n.minuteElement=i.getElementsByTagName("input")[0],n.hourElement.tabIndex=n.minuteElement.tabIndex=-1,n.hourElement.value=Wx(n.latestSelectedDateObj?n.latestSelectedDateObj.getHours():n.config.time_24hr?t.hours:function(t){switch(t%24){case 0:case 12:return 12;default:return t%12}}(t.hours)),n.minuteElement.value=Wx(n.latestSelectedDateObj?n.latestSelectedDateObj.getMinutes():t.minutes),n.hourElement.setAttribute("step",n.config.hourIncrement.toString()),n.minuteElement.setAttribute("step",n.config.minuteIncrement.toString()),n.hourElement.setAttribute("min",n.config.time_24hr?"0":"1"),n.hourElement.setAttribute("max",n.config.time_24hr?"23":"12"),n.hourElement.setAttribute("maxlength","2"),n.minuteElement.setAttribute("min","0"),n.minuteElement.setAttribute("max","59"),n.minuteElement.setAttribute("maxlength","2"),n.timeContainer.appendChild(r),n.timeContainer.appendChild(e),n.timeContainer.appendChild(i),n.config.time_24hr&&n.timeContainer.classList.add("time24hr"),n.config.enableSeconds){n.timeContainer.classList.add("hasSeconds");var o=nw("flatpickr-second");n.secondElement=o.getElementsByTagName("input")[0],n.secondElement.value=Wx(n.latestSelectedDateObj?n.latestSelectedDateObj.getSeconds():t.seconds),n.secondElement.setAttribute("step",n.minuteElement.getAttribute("step")),n.secondElement.setAttribute("min","0"),n.secondElement.setAttribute("max","59"),n.secondElement.setAttribute("maxlength","2"),n.timeContainer.appendChild(Jx("span","flatpickr-time-separator",":")),n.timeContainer.appendChild(o)}return n.config.time_24hr||(n.amPM=Jx("span","flatpickr-am-pm",n.l10n.amPM[Zx((n.latestSelectedDateObj?n.hourElement.value:n.config.defaultHour)>11)]),n.amPM.title=n.l10n.toggleTitle,n.amPM.tabIndex=-1,n.timeContainer.appendChild(n.amPM)),n.timeContainer}()),Yx(n.calendarContainer,"rangeMode","range"===n.config.mode),Yx(n.calendarContainer,"animate",!0===n.config.animate),Yx(n.calendarContainer,"multiMonth",n.config.showMonths>1),n.calendarContainer.appendChild(t);var o=void 0!==n.config.appendTo&&void 0!==n.config.appendTo.nodeType;if((n.config.inline||n.config.static)&&(n.calendarContainer.classList.add(n.config.inline?"inline":"static"),n.config.inline&&(!o&&n.element.parentNode?n.element.parentNode.insertBefore(n.calendarContainer,n._input.nextSibling):void 0!==n.config.appendTo&&n.config.appendTo.appendChild(n.calendarContainer)),n.config.static)){var a=Jx("div","flatpickr-wrapper");n.element.parentNode&&n.element.parentNode.insertBefore(a,n.element),a.appendChild(n.element),n.altInput&&a.appendChild(n.altInput),a.appendChild(n.calendarContainer)}n.config.static||n.config.inline||(void 0!==n.config.appendTo?n.config.appendTo:window.document.body).appendChild(n.calendarContainer)}(),function(){if(n.config.wrap&&["open","close","toggle","clear"].forEach((function(t){Array.prototype.forEach.call(n.element.querySelectorAll("[data-"+t+"]"),(function(e){return d(e,"click",n[t])}))})),n.isMobile)!function(){var t=n.config.enableTime?n.config.noCalendar?"time":"datetime-local":"date";n.mobileInput=Jx("input",n.input.className+" flatpickr-mobile"),n.mobileInput.tabIndex=1,n.mobileInput.type=t,n.mobileInput.disabled=n.input.disabled,n.mobileInput.required=n.input.required,n.mobileInput.placeholder=n.input.placeholder,n.mobileFormatStr="datetime-local"===t?"Y-m-d\\TH:i:S":"date"===t?"Y-m-d":"H:i:S",n.selectedDates.length>0&&(n.mobileInput.defaultValue=n.mobileInput.value=n.formatDate(n.selectedDates[0],n.mobileFormatStr)),n.config.minDate&&(n.mobileInput.min=n.formatDate(n.config.minDate,"Y-m-d")),n.config.maxDate&&(n.mobileInput.max=n.formatDate(n.config.maxDate,"Y-m-d")),n.input.getAttribute("step")&&(n.mobileInput.step=String(n.input.getAttribute("step"))),n.input.type="hidden",void 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0);}}span.flatpickr-day.selected{font-weight:bold;}']}render(){if(null!=this._picker)return;super.render(),this.input_el=ge({type:"text",class:Xy,disabled:this.model.disabled}),this.group_el.appendChild(this.input_el);const t={appendTo:this.group_el,positionElement:this.input_el,defaultDate:this.model.value,inline:this.model.inline,position:this._position.bind(this),onChange:(t,e,n)=>this._on_change(t,e,n)},{min_date:e,max_date:n,disabled_dates:r,enabled_dates:i}=this.model;null!=e&&(t.minDate=e),null!=n&&(t.maxDate=n),null!=r&&(t.disable=xw(r)),null!=i&&(t.enable=xw(i)),this._picker=_w(this.input_el,t)}_on_change(t,e,n){this.model.value=e,this.change_input()}_position(t,e){const n=e??t._positionElement,r=[...t.calendarContainer.children].reduce(((t,e)=>t+Se(e).height),0),i=t.calendarContainer.offsetWidth,o=this.model.position.split(" "),a=o[0],s=o.length>1?o[1]:null,l=n.offsetTop,c=n.offsetTop+n.offsetHeight,u=n.offsetLeft,d=n.offsetLeft+n.offsetWidth,h=n.offsetWidth,p=window.innerHeight-c,f="above"===a||"below"!==a&&p<r&&l>r,Q=t.config.appendTo?l+(f?-r-2:n.offsetHeight+2):window.scrollY+l+(f?-r-2:n.offsetHeight+2);if(t.calendarContainer.classList.toggle("arrowTop",!f),t.calendarContainer.classList.toggle("arrowBottom",f),t.config.inline)return;let T=window.scrollX+u,m=!1,g=!1;"center"===s?(T-=(i-h)/2,m=!0):"right"===s&&(T-=i-h,g=!0),t.calendarContainer.classList.toggle("arrowLeft",!m&&!g),t.calendarContainer.classList.toggle("arrowCenter",m),t.calendarContainer.classList.toggle("arrowRight",g);const _=window.document.body.offsetWidth-(window.scrollX+d),b=T+i>window.document.body.offsetWidth,v=_+i>window.document.body.offsetWidth;if(t.calendarContainer.classList.toggle("rightMost",b),!t.config.static)if(t.calendarContainer.style.top=`${Q}px`,b)if(v){const e=this.shadow_el.styleSheets[0],n=window.document.body.offsetWidth,r=Math.max(0,n/2-i/2),o=".flatpickr-calendar.centerMost:before",a=".flatpickr-calendar.centerMost:after",s=e.cssRules.length,l=`{left:${u}px;right:auto;}`;t.calendarContainer.classList.toggle("rightMost",!1),t.calendarContainer.classList.toggle("centerMost",!0),e.insertRule(`${o},${a}${l}`,s),t.calendarContainer.style.left=`${r}px`,t.calendarContainer.style.right="auto"}else t.calendarContainer.style.left="auto",t.calendarContainer.style.right=`${_}px`;else t.calendarContainer.style.left=`${T}px`,t.calendarContainer.style.right="auto"}}ww.__name__="DatePickerView";class Lw extends ix{constructor(t){super(t)}}function Aw(t){return"object"==typeof t&&"function"==typeof t.to}function Hw(t){t.parentElement.removeChild(t)}function kw(t){return null!=t}function Mw(t){t.preventDefault()}function Cw(t){return"number"==typeof t&&!isNaN(t)&&isFinite(t)}function Sw(t,e,n){n>0&&(Pw(t,e),setTimeout((function(){Dw(t,e)}),n))}function Ew(t){return Math.max(Math.min(t,100),0)}function Vw(t){return Array.isArray(t)?t:[t]}function Ow(t){var e=(t=String(t)).split(".");return e.length>1?e[1].length:0}function Pw(t,e){t.classList&&!/\s/.test(e)?t.classList.add(e):t.className+=" "+e}function Dw(t,e){t.classList&&!/\s/.test(e)?t.classList.remove(e):t.className=t.className.replace(new RegExp("(^|\\b)"+e.split(" ").join("|")+"(\\b|$)","gi")," ")}function Nw(t){var e=void 0!==window.pageXOffset,n="CSS1Compat"===(t.compatMode||"");return{x:e?window.pageXOffset:n?t.documentElement.scrollLeft:t.body.scrollLeft,y:e?window.pageYOffset:n?t.documentElement.scrollTop:t.body.scrollTop}}function Rw(t,e){return 100/(e-t)}function Iw(t,e,n){return 100*e/(t[n+1]-t[n])}function jw(t,e){for(var n=1;t>=e[n];)n+=1;return n}bw=Lw,Lw.__name__="DatePicker",bw.prototype.default_view=ww,bw.define((({Boolean:t,String:e,Array:n,Tuple:r,Or:i,Nullable:o})=>{const a=n(i(e,r(e,e)));return{value:[e],min_date:[o(e),null],max_date:[o(e),null],disabled_dates:[o(a),null],enabled_dates:[o(a),null],position:[_n.C8,"auto"],inline:[t,!1]}})),function(t){t.Range="range",t.Steps="steps",t.Positions="positions",t.Count="count",t.Values="values"}(vw||(vw={})),function(t){t[t.None=-1]="None",t[t.NoValue=0]="NoValue",t[t.LargeValue=1]="LargeValue",t[t.SmallValue=2]="SmallValue"}(yw||(yw={}));var zw=function(){function t(t,e,n){var r;this.xPct=[],this.xVal=[],this.xSteps=[],this.xNumSteps=[],this.xHighestCompleteStep=[],this.xSteps=[n||!1],this.xNumSteps=[!1],this.snap=e;var i=[];for(Object.keys(t).forEach((function(e){i.push([Vw(t[e]),e])})),i.sort((function(t,e){return t[0][0]-e[0][0]})),r=0;r<i.length;r++)this.handleEntryPoint(i[r][1],i[r][0]);for(this.xNumSteps=this.xSteps.slice(0),r=0;r<this.xNumSteps.length;r++)this.handleStepPoint(r,this.xNumSteps[r])}return t.prototype.getDistance=function(t){for(var e=[],n=0;n<this.xNumSteps.length-1;n++)e[n]=Iw(this.xVal,t,n);return e},t.prototype.getAbsoluteDistance=function(t,e,n){var r,i=0;if(t<this.xPct[this.xPct.length-1])for(;t>this.xPct[i+1];)i++;else t===this.xPct[this.xPct.length-1]&&(i=this.xPct.length-2);n||t!==this.xPct[i+1]||i++,null===e&&(e=[]);var o=1,a=e[i],s=0,l=0,c=0,u=0;for(r=n?(t-this.xPct[i])/(this.xPct[i+1]-this.xPct[i]):(this.xPct[i+1]-t)/(this.xPct[i+1]-this.xPct[i]);a>0;)s=this.xPct[i+1+u]-this.xPct[i+u],e[i+u]*o+100-100*r>100?(l=s*r,o=(a-100*r)/e[i+u],r=1):(l=e[i+u]*s/100*o,o=0),n?(c-=l,this.xPct.length+u>=1&&u--):(c+=l,this.xPct.length-u>=1&&u++),a=e[i+u]*o;return t+c},t.prototype.toStepping=function(t){return function(t,e,n){if(n>=t.slice(-1)[0])return 100;var r=jw(n,t),i=t[r-1],o=t[r],a=e[r-1],s=e[r];return a+function(t,e){return Iw(t,t[0]<0?e+Math.abs(t[0]):e-t[0],0)}([i,o],n)/Rw(a,s)}(this.xVal,this.xPct,t)},t.prototype.fromStepping=function(t){return function(t,e,n){if(n>=100)return t.slice(-1)[0];var r=jw(n,e),i=t[r-1],o=t[r],a=e[r-1];return function(t,e){return e*(t[1]-t[0])/100+t[0]}([i,o],(n-a)*Rw(a,e[r]))}(this.xVal,this.xPct,t)},t.prototype.getStep=function(t){return function(t,e,n,r){if(100===r)return r;var i=jw(r,t),o=t[i-1],a=t[i];return n?r-o>(a-o)/2?a:o:e[i-1]?t[i-1]+function(t,e){return Math.round(t/e)*e}(r-t[i-1],e[i-1]):r}(this.xPct,this.xSteps,this.snap,t)},t.prototype.getDefaultStep=function(t,e,n){var r=jw(t,this.xPct);return(100===t||e&&t===this.xPct[r-1])&&(r=Math.max(r-1,1)),(this.xVal[r]-this.xVal[r-1])/n},t.prototype.getNearbySteps=function(t){var e=jw(t,this.xPct);return{stepBefore:{startValue:this.xVal[e-2],step:this.xNumSteps[e-2],highestStep:this.xHighestCompleteStep[e-2]},thisStep:{startValue:this.xVal[e-1],step:this.xNumSteps[e-1],highestStep:this.xHighestCompleteStep[e-1]},stepAfter:{startValue:this.xVal[e],step:this.xNumSteps[e],highestStep:this.xHighestCompleteStep[e]}}},t.prototype.countStepDecimals=function(){var t=this.xNumSteps.map(Ow);return Math.max.apply(null,t)},t.prototype.hasNoSize=function(){return this.xVal[0]===this.xVal[this.xVal.length-1]},t.prototype.convert=function(t){return this.getStep(this.toStepping(t))},t.prototype.handleEntryPoint=function(t,e){var n;if(!Cw(n="min"===t?0:"max"===t?100:parseFloat(t))||!Cw(e[0]))throw new Error("noUiSlider: 'range' value isn't numeric.");this.xPct.push(n),this.xVal.push(e[0]);var r=Number(e[1]);n?this.xSteps.push(!isNaN(r)&&r):isNaN(r)||(this.xSteps[0]=r),this.xHighestCompleteStep.push(0)},t.prototype.handleStepPoint=function(t,e){if(e)if(this.xVal[t]!==this.xVal[t+1]){this.xSteps[t]=Iw([this.xVal[t],this.xVal[t+1]],e,0)/Rw(this.xPct[t],this.xPct[t+1]);var n=(this.xVal[t+1]-this.xVal[t])/this.xNumSteps[t],r=Math.ceil(Number(n.toFixed(3))-1),i=this.xVal[t]+this.xNumSteps[t]*r;this.xHighestCompleteStep[t]=i}else this.xSteps[t]=this.xHighestCompleteStep[t]=this.xVal[t]},t}(),Bw={to:function(t){return void 0===t?"":t.toFixed(2)},from:Number},Fw={target:"target",base:"base",origin:"origin",handle:"handle",handleLower:"handle-lower",handleUpper:"handle-upper",touchArea:"touch-area",horizontal:"horizontal",vertical:"vertical",background:"background",connect:"connect",connects:"connects",ltr:"ltr",rtl:"rtl",textDirectionLtr:"txt-dir-ltr",textDirectionRtl:"txt-dir-rtl",draggable:"draggable",drag:"state-drag",tap:"state-tap",active:"active",tooltip:"tooltip",pips:"pips",pipsHorizontal:"pips-horizontal",pipsVertical:"pips-vertical",marker:"marker",markerHorizontal:"marker-horizontal",markerVertical:"marker-vertical",markerNormal:"marker-normal",markerLarge:"marker-large",markerSub:"marker-sub",value:"value",valueHorizontal:"value-horizontal",valueVertical:"value-vertical",valueNormal:"value-normal",valueLarge:"value-large",valueSub:"value-sub"},$w=".__tooltips",Gw=".__aria";function qw(t,e){if(!Cw(e))throw new Error("noUiSlider: 'step' is not numeric.");t.singleStep=e}function Uw(t,e){if(!Cw(e))throw new Error("noUiSlider: 'keyboardPageMultiplier' is not numeric.");t.keyboardPageMultiplier=e}function Ww(t,e){if(!Cw(e))throw new Error("noUiSlider: 'keyboardMultiplier' is not numeric.");t.keyboardMultiplier=e}function Zw(t,e){if(!Cw(e))throw new Error("noUiSlider: 'keyboardDefaultStep' is not numeric.");t.keyboardDefaultStep=e}function Xw(t,e){if("object"!=typeof e||Array.isArray(e))throw new Error("noUiSlider: 'range' is not an object.");if(void 0===e.min||void 0===e.max)throw new Error("noUiSlider: Missing 'min' or 'max' in 'range'.");t.spectrum=new zw(e,t.snap||!1,t.singleStep)}function Kw(t,e){if(e=Vw(e),!Array.isArray(e)||!e.length)throw new Error("noUiSlider: 'start' option is incorrect.");t.handles=e.length,t.start=e}function Yw(t,e){if("boolean"!=typeof e)throw new Error("noUiSlider: 'snap' option must be a boolean.");t.snap=e}function Jw(t,e){if("boolean"!=typeof e)throw new Error("noUiSlider: 'animate' option must be a boolean.");t.animate=e}function tL(t,e){if("number"!=typeof e)throw new Error("noUiSlider: 'animationDuration' option must be a number.");t.animationDuration=e}function eL(t,e){var n,r=[!1];if("lower"===e?e=[!0,!1]:"upper"===e&&(e=[!1,!0]),!0===e||!1===e){for(n=1;n<t.handles;n++)r.push(e);r.push(!1)}else{if(!Array.isArray(e)||!e.length||e.length!==t.handles+1)throw new Error("noUiSlider: 'connect' option doesn't match handle count.");r=e}t.connect=r}function nL(t,e){switch(e){case"horizontal":t.ort=0;break;case"vertical":t.ort=1;break;default:throw new Error("noUiSlider: 'orientation' option is invalid.")}}function rL(t,e){if(!Cw(e))throw new Error("noUiSlider: 'margin' option must be numeric.");0!==e&&(t.margin=t.spectrum.getDistance(e))}function iL(t,e){if(!Cw(e))throw new Error("noUiSlider: 'limit' option must be numeric.");if(t.limit=t.spectrum.getDistance(e),!t.limit||t.handles<2)throw new Error("noUiSlider: 'limit' option is only supported on linear sliders with 2 or more handles.")}function oL(t,e){var n;if(!Cw(e)&&!Array.isArray(e))throw new Error("noUiSlider: 'padding' option must be numeric or array of exactly 2 numbers.");if(Array.isArray(e)&&2!==e.length&&!Cw(e[0])&&!Cw(e[1]))throw new Error("noUiSlider: 'padding' option must be numeric or array of exactly 2 numbers.");if(0!==e){for(Array.isArray(e)||(e=[e,e]),t.padding=[t.spectrum.getDistance(e[0]),t.spectrum.getDistance(e[1])],n=0;n<t.spectrum.xNumSteps.length-1;n++)if(t.padding[0][n]<0||t.padding[1][n]<0)throw new Error("noUiSlider: 'padding' option must be a positive number(s).");var r=e[0]+e[1],i=t.spectrum.xVal[0];if(r/(t.spectrum.xVal[t.spectrum.xVal.length-1]-i)>1)throw new Error("noUiSlider: 'padding' option must not exceed 100% of the range.")}}function aL(t,e){switch(e){case"ltr":t.dir=0;break;case"rtl":t.dir=1;break;default:throw new Error("noUiSlider: 'direction' option was not recognized.")}}function sL(t,e){if("string"!=typeof e)throw new Error("noUiSlider: 'behaviour' must be a string containing options.");var n=e.indexOf("tap")>=0,r=e.indexOf("drag")>=0,i=e.indexOf("fixed")>=0,o=e.indexOf("snap")>=0,a=e.indexOf("hover")>=0,s=e.indexOf("unconstrained")>=0,l=e.indexOf("invert-connects")>=0,c=e.indexOf("drag-all")>=0,u=e.indexOf("smooth-steps")>=0;if(i){if(2!==t.handles)throw new Error("noUiSlider: 'fixed' behaviour must be used with 2 handles");rL(t,t.start[1]-t.start[0])}if(l&&2!==t.handles)throw new Error("noUiSlider: 'invert-connects' behaviour must be used with 2 handles");if(s&&(t.margin||t.limit))throw new Error("noUiSlider: 'unconstrained' behaviour cannot be used with margin or limit");t.events={tap:n||o,drag:r,dragAll:c,smoothSteps:u,fixed:i,snap:o,hover:a,unconstrained:s,invertConnects:l}}function lL(t,e){if(!1!==e)if(!0===e||Aw(e)){t.tooltips=[];for(var n=0;n<t.handles;n++)t.tooltips.push(e)}else{if((e=Vw(e)).length!==t.handles)throw new Error("noUiSlider: must pass a formatter for all handles.");e.forEach((function(t){if("boolean"!=typeof t&&!Aw(t))throw new Error("noUiSlider: 'tooltips' must be passed a formatter or 'false'.")})),t.tooltips=e}}function cL(t,e){if(e.length!==t.handles)throw new Error("noUiSlider: must pass a attributes for all handles.");t.handleAttributes=e}function uL(t,e){if(!Aw(e))throw new Error("noUiSlider: 'ariaFormat' requires 'to' method.");t.ariaFormat=e}function dL(t,e){if(!function(t){return Aw(t)&&"function"==typeof t.from}(e))throw new Error("noUiSlider: 'format' requires 'to' and 'from' methods.");t.format=e}function hL(t,e){if("boolean"!=typeof e)throw new Error("noUiSlider: 'keyboardSupport' option must be a boolean.");t.keyboardSupport=e}function pL(t,e){t.documentElement=e}function fL(t,e){if("string"!=typeof e&&!1!==e)throw new Error("noUiSlider: 'cssPrefix' must be a string or `false`.");t.cssPrefix=e}function QL(t,e){if("object"!=typeof e)throw new Error("noUiSlider: 'cssClasses' must be an object.");"string"==typeof t.cssPrefix?(t.cssClasses={},Object.keys(e).forEach((function(n){t.cssClasses[n]=t.cssPrefix+e[n]}))):t.cssClasses=e}function TL(t){var e={margin:null,limit:null,padding:null,animate:!0,animationDuration:300,ariaFormat:Bw,format:Bw},n={step:{r:!1,t:qw},keyboardPageMultiplier:{r:!1,t:Uw},keyboardMultiplier:{r:!1,t:Ww},keyboardDefaultStep:{r:!1,t:Zw},start:{r:!0,t:Kw},connect:{r:!0,t:eL},direction:{r:!0,t:aL},snap:{r:!1,t:Yw},animate:{r:!1,t:Jw},animationDuration:{r:!1,t:tL},range:{r:!0,t:Xw},orientation:{r:!1,t:nL},margin:{r:!1,t:rL},limit:{r:!1,t:iL},padding:{r:!1,t:oL},behaviour:{r:!0,t:sL},ariaFormat:{r:!1,t:uL},format:{r:!1,t:dL},tooltips:{r:!1,t:lL},keyboardSupport:{r:!0,t:hL},documentElement:{r:!1,t:pL},cssPrefix:{r:!0,t:fL},cssClasses:{r:!0,t:QL},handleAttributes:{r:!1,t:cL}},r={connect:!1,direction:"ltr",behaviour:"tap",orientation:"horizontal",keyboardSupport:!0,cssPrefix:"noUi-",cssClasses:Fw,keyboardPageMultiplier:5,keyboardMultiplier:1,keyboardDefaultStep:10};t.format&&!t.ariaFormat&&(t.ariaFormat=t.format),Object.keys(n).forEach((function(i){if(kw(t[i])||void 0!==r[i])n[i].t(e,kw(t[i])?t[i]:r[i]);else if(n[i].r)throw new Error("noUiSlider: '"+i+"' is required.")})),e.pips=t.pips;var i=document.createElement("div"),o=void 0!==i.style.msTransform,a=void 0!==i.style.transform;return e.transformRule=a?"transform":o?"msTransform":"webkitTransform",e.style=[["left","top"],["right","bottom"]][e.dir][e.ort],e}var mL,gL,_L,bL,vL,yL,xL,wL,LL,AL,HL,kL;class ML extends yx{constructor(){super(...arguments),this._auto_width="auto",this._auto_height="auto"}*controls(){yield this.slider_el}get _steps(){return this._noUiSlider.steps}connect_signals(){super.connect_signals();const{direction:t,orientation:e,tooltips:n}=this.model.properties;this.on_change([t,e,n],(()=>this.render()));const{start:r,end:i,value:o,step:a,title:s}=this.model.properties;this.on_change([r,i,o,a],(()=>{const{start:t,end:e,value:n,step:r}=this._calc_to();this._noUiSlider.updateOptions({range:{min:t,max:e},start:n,step:r},!0)}));const{bar_color:l}=this.model.properties;this.on_change(l,(()=>{this._set_bar_color()}));const{show_value:c}=this.model.properties;this.on_change([o,s,c],(()=>this._update_title()))}styles(){return[...super.styles(),'.noUi-target,.noUi-target *{-webkit-touch-callout:none;-webkit-tap-highlight-color:rgba(0, 0, 0, 0);-webkit-user-select:none;-ms-touch-action:none;touch-action:none;-ms-user-select:none;-moz-user-select:none;user-select:none;-moz-box-sizing:border-box;box-sizing:border-box;}.noUi-target{position:relative;}.noUi-base,.noUi-connects{width:100%;height:100%;position:relative;z-index:1;}.noUi-connects{overflow:hidden;z-index:0;}.noUi-connect,.noUi-origin{will-change:transform;position:absolute;z-index:1;top:0;right:0;height:100%;width:100%;-ms-transform-origin:0 0;-webkit-transform-origin:0 0;-webkit-transform-style:preserve-3d;transform-origin:0 0;transform-style:flat;}.noUi-txt-dir-rtl.noUi-horizontal .noUi-origin{left:0;right:auto;}.noUi-vertical .noUi-origin{top:-100%;width:0;}.noUi-horizontal .noUi-origin{height:0;}.noUi-handle{-webkit-backface-visibility:hidden;backface-visibility:hidden;position:absolute;}.noUi-touch-area{height:100%;width:100%;}.noUi-state-tap .noUi-connect,.noUi-state-tap .noUi-origin{-webkit-transition:transform 0.3s;transition:transform 0.3s;}.noUi-state-drag *{cursor:inherit !important;}.noUi-horizontal{height:18px;}.noUi-horizontal .noUi-handle{width:34px;height:28px;right:-17px;top:-6px;}.noUi-vertical{width:18px;}.noUi-vertical .noUi-handle{width:28px;height:34px;right:-6px;bottom:-17px;}.noUi-txt-dir-rtl.noUi-horizontal .noUi-handle{left:-17px;right:auto;}.noUi-target{background:#FAFAFA;border-radius:4px;border:1px solid #D3D3D3;box-shadow:inset 0 1px 1px #F0F0F0, 0 3px 6px -5px #BBB;}.noUi-connects{border-radius:3px;}.noUi-connect{background:#3FB8AF;}.noUi-draggable{cursor:ew-resize;}.noUi-vertical .noUi-draggable{cursor:ns-resize;}.noUi-handle{border:1px solid #D9D9D9;border-radius:3px;background:#FFF;cursor:default;box-shadow:inset 0 0 1px #FFF, inset 0 1px 7px #EBEBEB, 0 3px 6px -3px #BBB;}.noUi-active{box-shadow:inset 0 0 1px #FFF, inset 0 1px 7px #DDD, 0 3px 6px -3px #BBB;}.noUi-handle:before,.noUi-handle:after{content:"";display:block;position:absolute;height:14px;width:1px;background:#E8E7E6;left:14px;top:6px;}.noUi-handle:after{left:17px;}.noUi-vertical .noUi-handle:before,.noUi-vertical .noUi-handle:after{width:14px;height:1px;left:6px;top:14px;}.noUi-vertical .noUi-handle:after{top:17px;}[disabled] .noUi-connect{background:#B8B8B8;}[disabled].noUi-target,[disabled].noUi-handle,[disabled] .noUi-handle{cursor:not-allowed;}.noUi-pips,.noUi-pips *{-moz-box-sizing:border-box;box-sizing:border-box;}.noUi-pips{position:absolute;color:#999;}.noUi-value{position:absolute;white-space:nowrap;text-align:center;}.noUi-value-sub{color:#ccc;font-size:10px;}.noUi-marker{position:absolute;background:#CCC;}.noUi-marker-sub{background:#AAA;}.noUi-marker-large{background:#AAA;}.noUi-pips-horizontal{padding:10px 0;height:80px;top:100%;left:0;width:100%;}.noUi-value-horizontal{-webkit-transform:translate(-50%, 50%);transform:translate(-50%, 50%);}.noUi-rtl .noUi-value-horizontal{-webkit-transform:translate(50%, 50%);transform:translate(50%, 50%);}.noUi-marker-horizontal.noUi-marker{margin-left:-1px;width:2px;height:5px;}.noUi-marker-horizontal.noUi-marker-sub{height:10px;}.noUi-marker-horizontal.noUi-marker-large{height:15px;}.noUi-pips-vertical{padding:0 10px;height:100%;top:0;left:100%;}.noUi-value-vertical{-webkit-transform:translate(0, -50%);transform:translate(0, -50%);padding-left:25px;}.noUi-rtl .noUi-value-vertical{-webkit-transform:translate(0, 50%);transform:translate(0, 50%);}.noUi-marker-vertical.noUi-marker{width:5px;height:2px;margin-top:-1px;}.noUi-marker-vertical.noUi-marker-sub{width:10px;}.noUi-marker-vertical.noUi-marker-large{width:15px;}.noUi-tooltip{display:block;position:absolute;border:1px solid #D9D9D9;border-radius:3px;background:#fff;color:#000;padding:5px;text-align:center;white-space:nowrap;}.noUi-horizontal .noUi-tooltip{-webkit-transform:translate(-50%, 0);transform:translate(-50%, 0);left:50%;bottom:120%;}.noUi-vertical .noUi-tooltip{-webkit-transform:translate(0, -50%);transform:translate(0, -50%);top:50%;right:120%;}.noUi-horizontal .noUi-origin > .noUi-tooltip{-webkit-transform:translate(50%, 0);transform:translate(50%, 0);left:auto;bottom:10px;}.noUi-vertical .noUi-origin > .noUi-tooltip{-webkit-transform:translate(0, -18px);transform:translate(0, -18px);top:auto;right:28px;}.noUi-handle{cursor:grab;cursor:-webkit-grab;}.noUi-handle.noUi-active{cursor:grabbing;cursor:-webkit-grabbing;}.noUi-handle:after,.noUi-handle:before{display:none;}.noUi-tooltip{display:none;white-space:nowrap;}.noUi-handle:hover .noUi-tooltip{display:block;}:host{--slider-size:10px;--handle-width:14px;--handle-height:18px;--handle-right:calc(-1*var(--handle-width)/2);--handle-top:calc(-1*(var(--handle-height) - var(--slider-size))/2 - 1px);--slider-margin:calc((var(--handle-height) - var(--slider-size))/2 + 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this._noUiSlider.updateOptions({range:{min:t,max:e},start:n,step:r},!0);this._set_bar_color(),this.model.disabled?this.slider_el.setAttribute("disabled","true"):this.slider_el.removeAttribute("disabled"),this.title_el=oe({class:"bk-slider-title"}),this._update_title(),this.group_el=oe({class:Ky},this.title_el,this.slider_el),this.shadow_el.appendChild(this.group_el),this._has_finished=!0}_slide(t){this.model.value=this._calc_from(t)}_change(t){const e=this._calc_from(t);this.model.setv({value:e,value_throttled:e})}}ML.__name__="AbstractBaseSliderView";class CL extends ML{_calc_to(){return{start:this.model.start,end:this.model.end,value:[this.model.value],step:this.model.step}}_calc_from([t]){return Number.isInteger(this.model.start)&&Number.isInteger(this.model.end)&&Number.isInteger(this.model.step)?Math.round(t):t}}CL.__name__="AbstractSliderView";class SL extends ML{_calc_to(){return{start:this.model.start,end:this.model.end,value:this.model.value,step:this.model.step}}_calc_from(t){return t}}SL.__name__="AbstractRangeSliderView";class EL extends xx{constructor(t){super(t),this.connected=!1}pretty(t){return this._formatter(t,this.format)}}mL=EL,EL.__name__="AbstractSlider",mL.define((({Any:t,Boolean:e,Number:n,String:r,Color:i,Or:o,Enum:a,Ref:s,Nullable:l})=>({title:[l(r),""],show_value:[e,!0],start:[t],end:[t],value:[t],value_throttled:[t],step:[n,1],format:[o(r,s(da))],direction:[a("ltr","rtl"),"ltr"],tooltips:[e,!0],bar_color:[i,"#e6e6e6"]}))),mL.override({width:300});class VL extends SL{_calc_to(){const{start:t,end:e,value:n,step:r}=this.model;return{start:t,end:e,value:n,step:864e5*r}}}VL.__name__="DateRangeSliderView";class OL extends EL{constructor(t){super(t),this.behaviour="drag",this.connected=[!1,!0,!1]}_formatter(t,e){return(0,f.Kg)(e)?Ma()(t,e):e.compute(t)}}gL=OL,OL.__name__="DateRangeSlider",gL.prototype.default_view=VL,gL.override({format:"%d %b %Y"});class PL extends CL{_calc_to(){const{start:t,end:e,value:n,step:r}=this.model;return{start:t,end:e,value:[n],step:864e5*r}}}PL.__name__="DateSliderView";class DL extends EL{constructor(t){super(t),this.behaviour="tap",this.connected=[!0,!1]}_formatter(t,e){return(0,f.Kg)(e)?Ma()(t,e):e.compute(t)}}_L=DL,DL.__name__="DateSlider",_L.prototype.default_view=PL,_L.override({format:"%d %b %Y"});class NL extends SL{}NL.__name__="DatetimeRangeSliderView";class RL extends EL{constructor(t){super(t),this.behaviour="drag",this.connected=[!1,!0,!1]}_formatter(t,e){return(0,f.Kg)(e)?Ma()(t,e):e.compute(t)}}bL=RL,RL.__name__="DatetimeRangeSlider",bL.prototype.default_view=NL,bL.override({format:"%d %b %Y %H:%M:%S",step:36e5});class IL extends Cy{constructor(){super(...arguments),this._auto_width="fit-content",this._auto_height="auto"}async lazy_initialize(){await super.lazy_initialize(),"not_started"!=this.provider.status&&"loading"!=this.provider.status||this.provider.ready.connect((()=>{this.contains_tex_string(this.model.text)&&this.rerender()}))}has_math_disabled(){return this.model.disable_math||!this.contains_tex_string(this.model.text)}rerender(){this.render()}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>{this.rerender()}))}styles(){return[...super.styles(),'.bk-clearfix:before,.bk-clearfix:after{content:"";display:table;}.bk-clearfix:after{clear:both;}',"p { margin: 0; }"]}render(){super.render(),this.markup_el=oe({class:"bk-clearfix",style:{display:"inline-block"}}),this.shadow_el.appendChild(this.markup_el),"failed"!=this.provider.status&&"loaded"!=this.provider.status||(this._has_finished=!0)}}IL.__name__="MarkupView";class jL extends Sy{constructor(t){super(t)}}vL=jL,jL.__name__="Markup",vL.define((({Boolean:t,String:e})=>({text:[e,""],disable_math:[t,!1]})));class zL extends IL{render(){super.render(),this.model.render_as_text?this.markup_el.textContent=this.model.text:this.markup_el.innerHTML=this.has_math_disabled()?this.model.text:this.process_tex(this.model.text)}}zL.__name__="DivView";class BL extends jL{constructor(t){super(t)}}yL=BL,BL.__name__="Div",yL.prototype.default_view=zL,yL.define((({Boolean:t})=>({render_as_text:[t,!1]})));class FL extends Wy{constructor(){super(...arguments),this._open=!1}styles(){return[...super.styles(),hx,":host{--caret-width:4px;}.bk-caret{display:inline-block;vertical-align:middle;width:0;height:0;margin:0 5px;}.bk-caret.bk-down{border-top:var(--caret-width) solid;}.bk-caret.bk-up{border-bottom:var(--caret-width) solid;}.bk-caret.bk-down,.bk-caret.bk-up{border-right:var(--caret-width) solid transparent;border-left:var(--caret-width) solid transparent;}.bk-caret.bk-left{border-right:var(--caret-width) solid;}.bk-caret.bk-right{border-left:var(--caret-width) solid;}.bk-caret.bk-left,.bk-caret.bk-right{border-top:var(--caret-width) solid transparent;border-bottom:var(--caret-width) solid transparent;}"]}render(){super.render();const t=oe({class:["bk-caret","bk-down"]});if(this.model.is_split){const e=this._render_button(t);e.classList.add(Gy),e.addEventListener("click",(()=>this._toggle_menu())),this.group_el.appendChild(e)}else this.button_el.appendChild(t);const e=this.model.menu.map(((t,e)=>{if(null==t)return oe({class:"bk-divider"});{const n=(0,f.Kg)(t)?t:t[0],r=oe(n);return r.addEventListener("click",(()=>this._item_click(e))),r}}));this.menu=oe({class:[cx,ux]},e),this.shadow_el.appendChild(this.menu),ke(this.menu)}_show_menu(){if(!this._open){this._open=!0,He(this.menu);const t=e=>{e.composedPath().includes(this.el)||(document.removeEventListener("click",t),this._hide_menu())};document.addEventListener("click",t)}}_hide_menu(){this._open&&(this._open=!1,ke(this.menu))}_toggle_menu(){this._open?this._hide_menu():this._show_menu()}click(){this.model.is_split?(this._hide_menu(),this.model.trigger_event(new dt),super.click()):this._toggle_menu()}_item_click(t){this._hide_menu();const e=this.model.menu[t];if(null!=e){const n=(0,f.Kg)(e)?e:e[1];(0,f.Kg)(n)?this.model.trigger_event(new ht(n)):n.execute(this.model,{index:t})}}}FL.__name__="DropdownView";class $L extends Zy{constructor(t){super(t)}get is_split(){return this.split}}xL=$L,$L.__name__="Dropdown",xL.prototype.default_view=FL,xL.define((({Null:t,Boolean:e,String:n,Array:r,Tuple:i,Or:o})=>({split:[e,!1],menu:[r(o(n,i(n,o(n)),t)),[]]}))),xL.override({label:"Dropdown"});class GL extends rx{styles(){return[...super.styles(),qy]}render(){super.render();const{multiple:t,disabled:e}=this.model,n=(()=>{const{accept:t}=this.model;return(0,f.Kg)(t)?t:t.join(",")})();this.input_el=ge({type:"file",class:Xy,multiple:t,accept:n,disabled:e}),this.group_el.appendChild(this.input_el),this.input_el.addEventListener("change",(()=>{const{files:t}=this.input_el;null!=t&&this.load_files(t)}))}async load_files(t){const e=[],n=[],r=[];for(const i of t){const t=await this._read_file(i),[,o="",,a=""]=t.split(/[:;,]/,4);e.push(a),n.push(i.name),r.push(o)}const[i,o,a]=(()=>this.model.multiple?[e,n,r]:0!=t.length?[e[0],n[0],r[0]]:["","",""])();this.model.setv({value:i,filename:o,mime_type:a})}_read_file(t){return new Promise(((e,n)=>{const r=new FileReader;r.onload=()=>{const{result:i}=r;null!=i?e(i):n(r.error??new Error(`unable to read '${t.name}'`))},r.readAsDataURL(t)}))}}GL.__name__="FileInputView";class qL extends ix{constructor(t){super(t)}}wL=qL,qL.__name__="FileInput",wL.prototype.default_view=GL,wL.define((({Boolean:t,String:e,Array:n,Or:r})=>({value:[r(e,n(e)),""],mime_type:[r(e,n(e)),""],filename:[r(e,n(e)),""],accept:[r(e,n(e)),""],multiple:[t,!1]})));class UL extends Wy{*children(){yield*super.children(),yield this.tooltip}async lazy_initialize(){await super.lazy_initialize();const{tooltip:t}=this.model;this.tooltip=await $e(t,{parent:this})}remove(){this.tooltip.remove(),super.remove()}render(){super.render();let t=!1;const e=e=>{this.tooltip.model.setv({visible:e,closable:t})};this.on_change(this.tooltip.model.properties.visible,(()=>{const{visible:n}=this.tooltip.model;n||(t=!1),e(n)})),this.el.addEventListener("mouseenter",(()=>{e(!0)})),this.el.addEventListener("mouseleave",(()=>{t||e(!1)})),document.addEventListener("mousedown",(n=>{const r=n.composedPath();r.includes(this.tooltip.el)||(r.includes(this.el)?(t=!t,e(t)):(t=!1,e(!1)))})),window.addEventListener("blur",(()=>{t=!1,e(!1)}))}}UL.__name__="HelpButtonView";class WL extends Zy{constructor(t){super(t)}}LL=WL,WL.__name__="HelpButton",LL.prototype.default_view=UL,LL.define((({Ref:t})=>({tooltip:[t(j_)]}))),LL.override({label:"",icon:new Bg({icon_name:"help",size:18}),button_type:"default"});class ZL extends rx{connect_signals(){super.connect_signals(),this.connect(this.model.properties.value.change,(()=>this.render_selection())),this.connect(this.model.properties.options.change,(()=>this.render())),this.connect(this.model.properties.name.change,(()=>this.render())),this.connect(this.model.properties.title.change,(()=>this.render())),this.connect(this.model.properties.size.change,(()=>this.render())),this.connect(this.model.properties.disabled.change,(()=>this.render()))}render(){super.render();const t=this.model.options.map((t=>{let e,n;return(0,f.Kg)(t)?e=n=t:[e,n]=t,be({value:e},n)}));this.input_el=_e({multiple:!0,class:Xy,name:this.model.name,disabled:this.model.disabled},t),this.input_el.addEventListener("change",(()=>this.change_input())),this.group_el.appendChild(this.input_el),this.render_selection()}render_selection(){const t=new Set(this.model.value);for(const e of this.shadow_el.querySelectorAll("option"))e.selected=t.has(e.value);this.input_el.size=this.model.size}change_input(){const t=null!=this.shadow_el.querySelector("select:focus"),e=[];for(const t of this.shadow_el.querySelectorAll("option"))t.selected&&e.push(t.value);this.model.value=e,super.change_input(),t&&this.input_el.focus()}}ZL.__name__="MultiSelectView";class XL extends ix{constructor(t){super(t)}}AL=XL,XL.__name__="MultiSelect",AL.prototype.default_view=ZL,AL.define((({Int:t,String:e,Array:n,Tuple:r,Or:i})=>({value:[n(e),[]],options:[n(i(e,r(e,e))),[]],size:[t,4]})));class KL extends IL{render(){super.render();const t=de({style:{margin:0}});this.has_math_disabled()?t.textContent=this.model.text:t.innerHTML=this.process_tex(this.model.text),this.markup_el.appendChild(t)}}KL.__name__="ParagraphView";class YL extends jL{constructor(t){super(t)}}HL=YL,YL.__name__="Paragraph",HL.prototype.default_view=KL;class JL extends sx{styles(){return[...super.styles(),":host{--toggle-size:14px;--toggle-padding:4px;--toggle-width:calc(var(--toggle-size) + 2*var(--toggle-padding));}.bk-input{padding-right:max(var(--padding-horizontal), var(--toggle-width));}.bk-toggle{position:absolute;right:0;top:0;width:var(--toggle-width);height:100%;padding:0 var(--toggle-padding);background-color:var(--bokeh-icon-color);mask-image:var(--bokeh-icon-see-off);-webkit-mask-image:var(--bokeh-icon-see-off);mask-size:var(--toggle-size) var(--toggle-size);-webkit-mask-size:var(--toggle-size) var(--toggle-size);mask-position:center center;-webkit-mask-position:center center;mask-repeat:no-repeat;-webkit-mask-repeat:no-repeat;cursor:pointer;}.bk-toggle.bk-visible{mask-image:var(--bokeh-icon-see-on);-webkit-mask-image:var(--bokeh-icon-see-on);}",pd]}render(){super.render(),this.input_el.type="password",this.toggle_el=oe({class:"bk-toggle"}),this.toggle_el.addEventListener("click",(()=>{const{input_el:t,toggle_el:e}=this,n="text"==t.type;e.classList.toggle("bk-visible",!n),t.type=n?"password":"text"})),this.shadow_el.append(this.toggle_el)}}JL.__name__="PasswordInputView";class tA extends lx{constructor(t){super(t)}}kL=tA,tA.__name__="PasswordInput",kL.prototype.default_view=JL;var eA=function(t,e){return eA=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n])},eA(t,e)};function nA(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");function n(){this.constructor=t}eA(t,e),t.prototype=null===e?Object.create(e):(n.prototype=e.prototype,new n)}var rA=function(){return rA=Object.assign||function(t){for(var e,n=1,r=arguments.length;n<r;n++)for(var i in e=arguments[n])Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t},rA.apply(this,arguments)};function iA(t,e,n){if(n||2===arguments.length)for(var r,i=0,o=e.length;i<o;i++)!r&&i in e||(r||(r=Array.prototype.slice.call(e,0,i)),r[i]=e[i]);return t.concat(r||Array.prototype.slice.call(e))}"function"==typeof SuppressedError&&SuppressedError;var oA,aA="ADD_CHOICE",sA="REMOVE_CHOICE",lA="FILTER_CHOICES",cA="ACTIVATE_CHOICES",uA="CLEAR_CHOICES",dA="ADD_GROUP",hA="ADD_ITEM",pA="REMOVE_ITEM",fA="HIGHLIGHT_ITEM",QA="search",TA="removeItem",mA="highlightItem",gA=["fuseOptions","classNames"],_A="select-one",bA="select-multiple",vA=function(t){return{type:sA,choice:t}},yA=function(t){return{type:pA,item:t}},xA=function(t,e){return{type:fA,item:t,highlighted:e}},wA=function(t){return Array.from({length:t},(function(){return Math.floor(36*Math.random()+0).toString(36)})).join("")},LA=function(t){if("string"!=typeof t){if(null==t)return"";if("object"==typeof t){if("raw"in t)return LA(t.raw);if("trusted"in t)return t.trusted}return t}return t.replace(/&/g,"&amp;").replace(/>/g,"&gt;").replace(/</g,"&lt;").replace(/'/g,"&#039;").replace(/"/g,"&quot;")},AA=(oA=document.createElement("div"),function(t){oA.innerHTML=t.trim();for(var e=oA.children[0];oA.firstChild;)oA.removeChild(oA.firstChild);return e}),HA=function(t,e){return"function"==typeof t?t(LA(e),e):t},kA=function(t){return"function"==typeof t?t():t},MA=function(t){if("string"==typeof t)return t;if("object"==typeof t){if("trusted"in t)return t.trusted;if("raw"in t)return t.raw}return""},CA=function(t,e){return t?function(t){if("string"==typeof t)return t;if("object"==typeof t){if("escaped"in t)return t.escaped;if("trusted"in t)return t.trusted}return""}(e):LA(e)},SA=function(t,e,n){t.innerHTML=CA(e,n)},EA=function(t,e){return t.rank-e.rank},VA=function(t){return Array.isArray(t)?t:[t]},OA=function(t){return t&&Array.isArray(t)?t.map((function(t){return".".concat(t)})).join(""):".".concat(t)},PA=function(t,e){var n;(n=t.classList).add.apply(n,VA(e))},DA=function(t,e){var n;(n=t.classList).remove.apply(n,VA(e))},NA=function(t){if(void 0!==t)try{return JSON.parse(t)}catch(e){return t}return{}},RA=function(){function t(t){var e=t.element,n=t.type,r=t.classNames;this.element=e,this.classNames=r,this.type=n,this.isActive=!1}return t.prototype.show=function(){return PA(this.element,this.classNames.activeState),this.element.setAttribute("aria-expanded","true"),this.isActive=!0,this},t.prototype.hide=function(){return DA(this.element,this.classNames.activeState),this.element.setAttribute("aria-expanded","false"),this.isActive=!1,this},t}(),IA=function(){function t(t){var e=t.element,n=t.type,r=t.classNames,i=t.position;this.element=e,this.classNames=r,this.type=n,this.position=i,this.isOpen=!1,this.isFlipped=!1,this.isDisabled=!1,this.isLoading=!1}return t.prototype.shouldFlip=function(t,e){var n=!1;return"auto"===this.position?n=this.element.getBoundingClientRect().top-e>=0&&!window.matchMedia("(min-height: ".concat(t+1,"px)")).matches:"top"===this.position&&(n=!0),n},t.prototype.setActiveDescendant=function(t){this.element.setAttribute("aria-activedescendant",t)},t.prototype.removeActiveDescendant=function(){this.element.removeAttribute("aria-activedescendant")},t.prototype.open=function(t,e){PA(this.element,this.classNames.openState),this.element.setAttribute("aria-expanded","true"),this.isOpen=!0,this.shouldFlip(t,e)&&(PA(this.element,this.classNames.flippedState),this.isFlipped=!0)},t.prototype.close=function(){DA(this.element,this.classNames.openState),this.element.setAttribute("aria-expanded","false"),this.removeActiveDescendant(),this.isOpen=!1,this.isFlipped&&(DA(this.element,this.classNames.flippedState),this.isFlipped=!1)},t.prototype.addFocusState=function(){PA(this.element,this.classNames.focusState)},t.prototype.removeFocusState=function(){DA(this.element,this.classNames.focusState)},t.prototype.enable=function(){DA(this.element,this.classNames.disabledState),this.element.removeAttribute("aria-disabled"),this.type===_A&&this.element.setAttribute("tabindex","0"),this.isDisabled=!1},t.prototype.disable=function(){PA(this.element,this.classNames.disabledState),this.element.setAttribute("aria-disabled","true"),this.type===_A&&this.element.setAttribute("tabindex","-1"),this.isDisabled=!0},t.prototype.wrap=function(t){var e=this.element,n=t.parentNode;n&&(t.nextSibling?n.insertBefore(e,t.nextSibling):n.appendChild(e)),e.appendChild(t)},t.prototype.unwrap=function(t){var e=this.element,n=e.parentNode;n&&(n.insertBefore(t,e),n.removeChild(e))},t.prototype.addLoadingState=function(){PA(this.element,this.classNames.loadingState),this.element.setAttribute("aria-busy","true"),this.isLoading=!0},t.prototype.removeLoadingState=function(){DA(this.element,this.classNames.loadingState),this.element.removeAttribute("aria-busy"),this.isLoading=!1},t}(),jA=function(){function t(t){var e=t.element,n=t.type,r=t.classNames,i=t.preventPaste;this.element=e,this.type=n,this.classNames=r,this.preventPaste=i,this.isFocussed=this.element.isEqualNode(document.activeElement),this.isDisabled=e.disabled,this._onPaste=this._onPaste.bind(this),this._onInput=this._onInput.bind(this),this._onFocus=this._onFocus.bind(this),this._onBlur=this._onBlur.bind(this)}return Object.defineProperty(t.prototype,"placeholder",{set:function(t){this.element.placeholder=t},enumerable:!1,configurable:!0}),Object.defineProperty(t.prototype,"value",{get:function(){return this.element.value},set:function(t){this.element.value=t},enumerable:!1,configurable:!0}),t.prototype.addEventListeners=function(){var t=this.element;t.addEventListener("paste",this._onPaste),t.addEventListener("input",this._onInput,{passive:!0}),t.addEventListener("focus",this._onFocus,{passive:!0}),t.addEventListener("blur",this._onBlur,{passive:!0})},t.prototype.removeEventListeners=function(){var t=this.element;t.removeEventListener("input",this._onInput),t.removeEventListener("paste",this._onPaste),t.removeEventListener("focus",this._onFocus),t.removeEventListener("blur",this._onBlur)},t.prototype.enable=function(){this.element.removeAttribute("disabled"),this.isDisabled=!1},t.prototype.disable=function(){this.element.setAttribute("disabled",""),this.isDisabled=!0},t.prototype.focus=function(){this.isFocussed||this.element.focus()},t.prototype.blur=function(){this.isFocussed&&this.element.blur()},t.prototype.clear=function(t){return void 0===t&&(t=!0),this.element.value="",t&&this.setWidth(),this},t.prototype.setWidth=function(){var t=this.element;t.style.minWidth="".concat(t.placeholder.length+1,"ch"),t.style.width="".concat(t.value.length+1,"ch")},t.prototype.setActiveDescendant=function(t){this.element.setAttribute("aria-activedescendant",t)},t.prototype.removeActiveDescendant=function(){this.element.removeAttribute("aria-activedescendant")},t.prototype._onInput=function(){this.type!==_A&&this.setWidth()},t.prototype._onPaste=function(t){this.preventPaste&&t.preventDefault()},t.prototype._onFocus=function(){this.isFocussed=!0},t.prototype._onBlur=function(){this.isFocussed=!1},t}(),zA=function(){function t(t){var e=t.element;this.element=e,this.scrollPos=this.element.scrollTop,this.height=this.element.offsetHeight}return t.prototype.prepend=function(t){var e=this.element.firstElementChild;e?this.element.insertBefore(t,e):this.element.append(t)},t.prototype.scrollToTop=function(){this.element.scrollTop=0},t.prototype.scrollToChildElement=function(t,e){var n=this;if(t){var 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singleRegex(){return/^(.*)$/}search(t){return this._bitapSearch.searchIn(t)}}class MH extends AH{constructor(t){super(t)}static get type(){return"include"}static get multiRegex(){return/^'"(.*)"$/}static get singleRegex(){return/^'(.*)$/}search(t){let e,n=0;const r=[],i=this.pattern.length;for(;(e=t.indexOf(this.pattern,n))>-1;)n=e+i,r.push([e,n-1]);const o=!!r.length;return{isMatch:o,score:o?0:1,indices:r}}}const CH=[class extends AH{constructor(t){super(t)}static get type(){return"exact"}static get multiRegex(){return/^="(.*)"$/}static get singleRegex(){return/^=(.*)$/}search(t){const e=t===this.pattern;return{isMatch:e,score:e?0:1,indices:[0,this.pattern.length-1]}}},MH,class extends AH{constructor(t){super(t)}static get type(){return"prefix-exact"}static get multiRegex(){return/^\^"(.*)"$/}static get singleRegex(){return/^\^(.*)$/}search(t){const e=t.startsWith(this.pattern);return{isMatch:e,score:e?0:1,indices:[0,this.pattern.length-1]}}},class extends 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o.setKeys(r),o.setIndexRecords(i),o},FH.config=gH,FH.parseQuery=jH,function(...t){OH.push(...t)}(class{constructor(t,{isCaseSensitive:e=gH.isCaseSensitive,includeMatches:n=gH.includeMatches,minMatchCharLength:r=gH.minMatchCharLength,ignoreLocation:i=gH.ignoreLocation,findAllMatches:o=gH.findAllMatches,location:a=gH.location,threshold:s=gH.threshold,distance:l=gH.distance}={}){this.query=null,this.options={isCaseSensitive:e,includeMatches:n,minMatchCharLength:r,findAllMatches:o,ignoreLocation:i,location:a,threshold:s,distance:l},this.pattern=e?t:t.toLowerCase(),this.query=function(t,e={}){return t.split("|").map((t=>{let n=t.trim().split(EH).filter((t=>t&&!!t.trim())),r=[];for(let t=0,i=n.length;t<i;t+=1){const i=n[t];let o=!1,a=-1;for(;!o&&++a<SH;){const t=CH[a];let n=t.isMultiMatch(i);n&&(r.push(new t(n,e)),o=!0)}if(!o)for(a=-1;++a<SH;){const t=CH[a];let n=t.isSingleMatch(i);if(n){r.push(new t(n,e));break}}}return r}))}(this.pattern,this.options)}static condition(t,e){return e.useExtendedSearch}searchIn(t){const e=this.query;if(!e)return{isMatch:!1,score:1};const{includeMatches:n,isCaseSensitive:r}=this.options;t=r?t:t.toLowerCase();let i=0,o=[],a=0;for(let r=0,s=e.length;r<s;r+=1){const s=e[r];o.length=0,i=0;for(let e=0,r=s.length;e<r;e+=1){const r=s[e],{isMatch:l,indices:c,score:u}=r.search(t);if(!l){a=0,i=0,o.length=0;break}if(i+=1,a+=u,n){const t=r.constructor.type;VH.has(t)?o=[...o,...c]:o.push(c)}}if(i){let t={isMatch:!0,score:a/i};return n&&(t.indices=o),t}}return{isMatch:!1,score:1}}});var $H,GH,qH=function(){function t(t){this._haystack=[],this._fuseOptions=rA(rA({},t.fuseOptions),{keys:iA([],t.searchFields,!0),includeMatches:!0})}return t.prototype.index=function(t){this._haystack=t,this._fuse&&this._fuse.setCollection(t)},t.prototype.reset=function(){this._haystack=[],this._fuse=void 0},t.prototype.isEmptyIndex=function(){return!this._haystack.length},t.prototype.search=function(t){return this._fuse||(this._fuse=new 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n=t.classNames.list,r=document.createElement("div");return PA(r,n),e||r.setAttribute("aria-multiselectable","true"),r.setAttribute("role","listbox"),r},choiceGroup:function(t,e){var n=t.allowHTML,r=t.classNames,i=r.group,o=r.groupHeading,a=r.itemDisabled,s=e.id,l=e.label,c=e.disabled,u=MA(l),d=document.createElement("div");PA(d,i),c&&PA(d,a),d.setAttribute("role","group"),d.dataset.group="",d.dataset.id=s,d.dataset.value=u,c&&d.setAttribute("aria-disabled","true");var h=document.createElement("div");return PA(h,o),SA(h,n,l||""),d.appendChild(h),d},choice:function(t,e,n,r){var i=t.allowHTML,o=t.classNames,a=o.item,s=o.itemChoice,l=o.itemSelectable,c=o.selectedState,u=o.itemDisabled,d=o.description,h=o.placeholder,p=e.label,f=MA(e.value),Q=document.createElement("div");Q.id=e.elementId,PA(Q,a),PA(Q,s),r&&"string"==typeof p&&(p=CA(i,p),p={trusted:p+=" (".concat(r,")")});var T=Q;if(e.labelClass){var m=document.createElement("span");SA(m,i,p),PA(m,e.labelClass),T=m,Q.appendChild(m)}else 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0,this._hasNonChoicePlaceholder=!1,this._lastAddedChoiceId=0,this._lastAddedGroupId=0;var i=t.defaults;this.config=rA(rA(rA({},i.allOptions),i.options),n),gA.forEach((function(t){r.config[t]=rA(rA(rA({},i.allOptions[t]),i.options[t]),n[t])}));var o=this.config;o.silent||this._validateConfig();var a=o.shadowRoot||document.documentElement;this._docRoot=a;var s="string"==typeof e?a.querySelector(e):e;if(!s||"object"!=typeof s||"INPUT"!==s.tagName&&!UA(s)){if(!s&&"string"==typeof e)throw TypeError("Selector ".concat(e," failed to find an element"));throw TypeError("Expected one of the following types text|select-one|select-multiple")}var l=s.type,c="text"===l;(c||1!==o.maxItemCount)&&(o.singleModeForMultiSelect=!1),o.singleModeForMultiSelect&&(l=bA);var u=l===_A,d=l===bA,h=u||d;if(this._elementType=l,this._isTextElement=c,this._isSelectOneElement=u,this._isSelectMultipleElement=d,this._isSelectElement=u||d,this._canAddUserChoices=c&&o.addItems||h&&o.addChoices,"boolean"!=typeof o.renderSelectedChoices&&(o.renderSelectedChoices="always"===o.renderSelectedChoices||u),"auto"===o.closeDropdownOnSelect?o.closeDropdownOnSelect=c||u||o.singleModeForMultiSelect:o.closeDropdownOnSelect=$A(o.closeDropdownOnSelect),o.placeholder&&(o.placeholderValue?this._hasNonChoicePlaceholder=!0:s.dataset.placeholder&&(this._hasNonChoicePlaceholder=!0,o.placeholderValue=s.dataset.placeholder)),n.addItemFilter&&"function"!=typeof n.addItemFilter){var p=n.addItemFilter instanceof RegExp?n.addItemFilter:new RegExp(n.addItemFilter);o.addItemFilter=p.test.bind(p)}if(this._isTextElement)this.passedElement=new FA({element:s,classNames:o.classNames});else{var f=s;this.passedElement=new WA({element:f,classNames:o.classNames,template:function(t){return r._templates.option(t)},extractPlaceholder:o.placeholder&&!this._hasNonChoicePlaceholder})}if(this.initialised=!1,this._store=new YA(o),this._currentValue="",o.searchEnabled=!c&&o.searchEnabled||d,this._canSearch=o.searchEnabled,this._isScrollingOnIe=!1,this._highlightPosition=0,this._wasTap=!0,this._placeholderValue=this._generatePlaceholderValue(),this._baseId=function(t){var e=t.id||t.name&&"".concat(t.name,"-").concat(wA(2))||wA(4);return e=e.replace(/(:|\.|\[|\]|,)/g,""),"".concat("choices-","-").concat(e)}(s),this._direction=s.dir,!this._direction){var Q=window.getComputedStyle(s).direction;Q!==window.getComputedStyle(document.documentElement).direction&&(this._direction=Q)}if(this._idNames={itemChoice:"item-choice"},this._templates=i.templates,this._render=this._render.bind(this),this._onFocus=this._onFocus.bind(this),this._onBlur=this._onBlur.bind(this),this._onKeyUp=this._onKeyUp.bind(this),this._onKeyDown=this._onKeyDown.bind(this),this._onInput=this._onInput.bind(this),this._onClick=this._onClick.bind(this),this._onTouchMove=this._onTouchMove.bind(this),this._onTouchEnd=this._onTouchEnd.bind(this),this._onMouseDown=this._onMouseDown.bind(this),this._onMouseOver=this._onMouseOver.bind(this),this._onFormReset=this._onFormReset.bind(this),this._onSelectKey=this._onSelectKey.bind(this),this._onEnterKey=this._onEnterKey.bind(this),this._onEscapeKey=this._onEscapeKey.bind(this),this._onDirectionKey=this._onDirectionKey.bind(this),this._onDeleteKey=this._onDeleteKey.bind(this),this.passedElement.isActive)return o.silent||console.warn("Trying to initialise Choices on element already initialised",{element:e}),this.initialised=!0,void(this.initialisedOK=!1);this.init(),this._initialItems=this._store.items.map((function(t){return t.value}))}return Object.defineProperty(t,"defaults",{get:function(){return Object.preventExtensions({get options(){return KH},get allOptions(){return ZA},get templates(){return ZH}})},enumerable:!1,configurable:!0}),t.prototype.init=function(){if(!this.initialised&&void 0===this.initialisedOK){var t;this._searcher=(t=this.config,new qH(t)),this._loadChoices(),this._createTemplates(),this._createElements(),this._createStructure(),this._isTextElement&&!this.config.addItems||this.passedElement.element.hasAttribute("disabled")||this.passedElement.element.closest("fieldset:disabled")?this.disable():(this.enable(),this._addEventListeners()),this._initStore(),this.initialised=!0,this.initialisedOK=!0;var e=this.config.callbackOnInit;"function"==typeof e&&e.call(this)}},t.prototype.destroy=function(){this.initialised&&(this._removeEventListeners(),this.passedElement.reveal(),this.containerOuter.unwrap(this.passedElement.element),this._store._listeners=[],this.clearStore(!1),this._stopSearch(),this._templates=t.defaults.templates,this.initialised=!1,this.initialisedOK=void 0)},t.prototype.enable=function(){return this.passedElement.isDisabled&&this.passedElement.enable(),this.containerOuter.isDisabled&&(this._addEventListeners(),this.input.enable(),this.containerOuter.enable()),this},t.prototype.disable=function(){return this.passedElement.isDisabled||this.passedElement.disable(),this.containerOuter.isDisabled||(this._removeEventListeners(),this.input.disable(),this.containerOuter.disable()),this},t.prototype.highlightItem=function(t,e){if(void 0===e&&(e=!0),!t||!t.id)return this;var n=this._store.items.find((function(e){return e.id===t.id}));return!n||n.highlighted||(this._store.dispatch(xA(n,!0)),e&&this.passedElement.triggerEvent(mA,this._getChoiceForOutput(n))),this},t.prototype.unhighlightItem=function(t,e){if(void 0===e&&(e=!0),!t||!t.id)return this;var n=this._store.items.find((function(e){return e.id===t.id}));return n&&n.highlighted?(this._store.dispatch(xA(n,!1)),e&&this.passedElement.triggerEvent("unhighlightItem",this._getChoiceForOutput(n)),this):this},t.prototype.highlightAll=function(){var t=this;return this._store.withTxn((function(){t._store.items.forEach((function(e){e.highlighted||(t._store.dispatch(xA(e,!0)),t.passedElement.triggerEvent(mA,t._getChoiceForOutput(e)))}))})),this},t.prototype.unhighlightAll=function(){var t=this;return this._store.withTxn((function(){t._store.items.forEach((function(e){e.highlighted&&(t._store.dispatch(xA(e,!1)),t.passedElement.triggerEvent(mA,t._getChoiceForOutput(e)))}))})),this},t.prototype.removeActiveItemsByValue=function(t){var e=this;return this._store.withTxn((function(){e._store.items.filter((function(e){return e.value===t})).forEach((function(t){return e._removeItem(t)}))})),this},t.prototype.removeActiveItems=function(t){var e=this;return this._store.withTxn((function(){e._store.items.filter((function(e){return e.id!==t})).forEach((function(t){return e._removeItem(t)}))})),this},t.prototype.removeHighlightedItems=function(t){var e=this;return void 0===t&&(t=!1),this._store.withTxn((function(){e._store.highlightedActiveItems.forEach((function(n){e._removeItem(n),t&&e._triggerChange(n.value)}))})),this},t.prototype.showDropdown=function(t){var e=this;return this.dropdown.isActive||requestAnimationFrame((function(){e.dropdown.show();var n=e.dropdown.element.getBoundingClientRect();e.containerOuter.open(n.bottom,n.height),!t&&e._canSearch&&e.input.focus(),e.passedElement.triggerEvent("showDropdown")})),this},t.prototype.hideDropdown=function(t){var e=this;return this.dropdown.isActive?(requestAnimationFrame((function(){e.dropdown.hide(),e.containerOuter.close(),!t&&e._canSearch&&(e.input.removeActiveDescendant(),e.input.blur()),e.passedElement.triggerEvent("hideDropdown")})),this):this},t.prototype.getValue=function(t){var e=this,n=this._store.items.map((function(n){return t?n.value:e._getChoiceForOutput(n)}));return this._isSelectOneElement||this.config.singleModeForMultiSelect?n[0]:n},t.prototype.setValue=function(t){var e=this;return this.initialisedOK?(this._store.withTxn((function(){t.forEach((function(t){t&&e._addChoice(qA(t,!1))}))})),this._searcher.reset(),this):(this._warnChoicesInitFailed("setValue"),this)},t.prototype.setChoiceByValue=function(t){var e=this;return this.initialisedOK?(this._isTextElement||(this._store.withTxn((function(){(Array.isArray(t)?t:[t]).forEach((function(t){return e._findAndSelectChoiceByValue(t)})),e.unhighlightAll()})),this._searcher.reset()),this):(this._warnChoicesInitFailed("setChoiceByValue"),this)},t.prototype.setChoices=function(t,e,n,r,i){var o=this;if(void 0===t&&(t=[]),void 0===e&&(e="value"),void 0===n&&(n="label"),void 0===r&&(r=!1),void 0===i&&(i=!0),!this.initialisedOK)return this._warnChoicesInitFailed("setChoices"),this;if(!this._isSelectElement)throw new TypeError("setChoices can't be used with INPUT based Choices");if("string"!=typeof e||!e)throw new TypeError("value parameter must be a name of 'value' field in passed objects");if(r&&this.clearChoices(),"function"==typeof t){var a=t(this);if("function"==typeof Promise&&a instanceof Promise)return new Promise((function(t){return requestAnimationFrame(t)})).then((function(){return o._handleLoadingState(!0)})).then((function(){return a})).then((function(t){return o.setChoices(t,e,n,r)})).catch((function(t){o.config.silent||console.error(t)})).then((function(){return o._handleLoadingState(!1)})).then((function(){return o}));if(!Array.isArray(a))throw new TypeError(".setChoices first argument function must return either array of choices or Promise, got: ".concat(typeof a));return this.setChoices(a,e,n,!1)}if(!Array.isArray(t))throw new TypeError(".setChoices must be called either with array of choices with a function resulting into Promise of array of choices");return this.containerOuter.removeLoadingState(),this._store.withTxn((function(){i&&(o._isSearching=!1);var r="value"===e,a="label"===n;t.forEach((function(t){if("choices"in t){var i=t;a||(i=rA(rA({},i),{label:i[n]})),o._addGroup(qA(i,!0))}else{var s=t;a&&r||(s=rA(rA({},s),{value:s[e],label:s[n]})),o._addChoice(qA(s,!1))}})),o.unhighlightAll()})),this._searcher.reset(),this},t.prototype.refresh=function(t,e,n){var r=this;return void 0===t&&(t=!1),void 0===e&&(e=!1),void 0===n&&(n=!1),this._isSelectElement?(this._store.withTxn((function(){var i=r.passedElement.optionsAsChoices(),o={};n||r._store.items.forEach((function(t){t.id&&t.active&&t.selected&&!t.disabled&&(o[t.value]=!0)})),r.clearStore(!1);var a=function(t){n?r._store.dispatch(yA(t)):o[t.value]&&(t.selected=!0)};i.forEach((function(t){"choices"in t?t.choices.forEach(a):a(t)})),r._addPredefinedChoices(i,e,t),r._isSearching&&r._searchChoices(r.input.value)})),this):(this.config.silent||console.warn("refresh method can only be used on choices backed by a <select> element"),this)},t.prototype.removeChoice=function(t){var e=this._store.choices.find((function(e){return e.value===t}));return e?(this._clearNotice(),this._store.dispatch(vA(e)),this._searcher.reset(),e.selected&&this.passedElement.triggerEvent(TA,this._getChoiceForOutput(e)),this):this},t.prototype.clearChoices=function(){var t=this;return this._store.withTxn((function(){t._store.choices.forEach((function(e){e.selected||t._store.dispatch(vA(e))}))})),this._searcher.reset(),this},t.prototype.clearStore=function(t){return void 0===t&&(t=!0),this._stopSearch(),t&&this.passedElement.element.replaceChildren(""),this.itemList.element.replaceChildren(""),this.choiceList.element.replaceChildren(""),this._store.reset(),this._lastAddedChoiceId=0,this._lastAddedGroupId=0,this._searcher.reset(),this},t.prototype.clearInput=function(){var t=!this._isSelectOneElement;return this.input.clear(t),this._stopSearch(),this},t.prototype._validateConfig=function(){var t=this.config,e=function(t,e){var n=Object.keys(t).sort(),r=Object.keys(e).sort();return n.filter((function(t){return r.indexOf(t)<0}))}(t,ZA);e.length&&console.warn("Unknown config option(s) passed",e.join(", ")),t.allowHTML&&t.allowHtmlUserInput&&(t.addItems&&console.warn("Warning: allowHTML/allowHtmlUserInput/addItems all being true is strongly not recommended and may lead to XSS attacks"),t.addChoices&&console.warn("Warning: allowHTML/allowHtmlUserInput/addChoices all being true is strongly not recommended and may lead to XSS attacks"))},t.prototype._render=function(t){void 0===t&&(t={choices:!0,groups:!0,items:!0}),this._store.inTxn()||(this._isSelectElement&&(t.choices||t.groups)&&this._renderChoices(),t.items&&this._renderItems())},t.prototype._renderChoices=function(){var t=this;if(this._canAddItems()){var e=this.config,n=this._isSearching,r=this._store,i=r.activeGroups,o=r.activeChoices,a=0;if(n&&e.searchResultLimit>0?a=e.searchResultLimit:e.renderChoiceLimit>0&&(a=e.renderChoiceLimit),this._isSelectElement){var s=o.filter((function(t){return!t.element}));s.length&&this.passedElement.addOptions(s)}var l=document.createDocumentFragment(),c=function(t){return t.filter((function(t){return!t.placeholder&&(n?!!t.rank:e.renderSelectedChoices||!t.selected)}))},u=!1,d=function(r,i,o){n?r.sort(EA):e.shouldSort&&r.sort(e.sorter);var s=r.length;s=!i&&a&&s>a?a:s,s--,r.every((function(r,i){var a=r.choiceEl||t._templates.choice(e,r,e.itemSelectText,o);return r.choiceEl=a,l.appendChild(a),r.disabled||!n&&r.selected||(u=!0),i<s}))};o.length&&(e.resetScrollPosition&&requestAnimationFrame((function(){return t.choiceList.scrollToTop()})),this._hasNonChoicePlaceholder||n||!this._isSelectOneElement||d(o.filter((function(t){return t.placeholder&&!t.group})),!1,void 0),i.length&&!n?(e.shouldSort&&i.sort(e.sorter),d(o.filter((function(t){return!t.placeholder&&!t.group})),!1,void 0),i.forEach((function(r){var i=c(r.choices);if(i.length){if(r.label){var o=r.groupEl||t._templates.choiceGroup(t.config,r);r.groupEl=o,o.remove(),l.appendChild(o)}d(i,!0,e.appendGroupInSearch&&n?r.label:void 0)}}))):d(c(o),!1,void 0)),u||(this._notice||(this._notice={text:kA(n?e.noResultsText:e.noChoicesText),type:n?tH:JA}),l.replaceChildren("")),this._renderNotice(l),this.choiceList.element.replaceChildren(l),u&&this._highlightChoice()}},t.prototype._renderItems=function(){var t=this,e=this._store.items||[],n=this.itemList.element,r=this.config,i=document.createDocumentFragment(),o=function(t){return n.querySelector('[data-item][data-id="'.concat(t.id,'"]'))},a=function(e){var n=e.itemEl;n&&n.parentElement||(n=o(e)||t._templates.item(r,e,r.removeItemButton),e.itemEl=n,i.appendChild(n))};e.forEach(a);var s=!!i.childNodes.length;if(this._isSelectOneElement&&this._hasNonChoicePlaceholder){var l=n.children.length;if(s||l>1){var c=n.querySelector(OA(r.classNames.placeholder));c&&c.remove()}else l||(s=!0,a(qA({selected:!0,value:"",label:r.placeholderValue||"",placeholder:!0},!1)))}s&&(n.append(i),r.shouldSortItems&&!this._isSelectOneElement&&(e.sort(r.sorter),e.forEach((function(t){var e=o(t);e&&(e.remove(),i.append(e))})),n.append(i))),this._isTextElement&&(this.passedElement.value=e.map((function(t){return t.value})).join(r.delimiter))},t.prototype._displayNotice=function(t,e,n){void 0===n&&(n=!0);var r=this._notice;r&&(r.type===e&&r.text===t||r.type===eH&&(e===tH||e===JA))?n&&this.showDropdown(!0):(this._clearNotice(),this._notice=t?{text:t,type:e}:void 0,this._renderNotice(),n&&t&&this.showDropdown(!0))},t.prototype._clearNotice=function(){if(this._notice){var t=this.choiceList.element.querySelector(OA(this.config.classNames.notice));t&&t.remove(),this._notice=void 0}},t.prototype._renderNotice=function(t){var e=this._notice;if(e){var n=this._templates.notice(this.config,e.text,e.type);t?t.append(n):this.choiceList.prepend(n)}},t.prototype._getChoiceForOutput=function(t,e){return{id:t.id,highlighted:t.highlighted,labelClass:t.labelClass,labelDescription:t.labelDescription,customProperties:t.customProperties,disabled:t.disabled,active:t.active,label:t.label,placeholder:t.placeholder,value:t.value,groupValue:t.group?t.group.label:void 0,element:t.element,keyCode:e}},t.prototype._triggerChange=function(t){null!=t&&this.passedElement.triggerEvent("change",{value:t})},t.prototype._handleButtonAction=function(t){var e=this,n=this._store.items;if(n.length&&this.config.removeItems&&this.config.removeItemButton){var r=t&&YH(t.parentElement),i=r&&n.find((function(t){return t.id===r}));i&&this._store.withTxn((function(){if(e._removeItem(i),e._triggerChange(i.value),e._isSelectOneElement&&!e._hasNonChoicePlaceholder){var t=e._store.choices.reverse().find((function(t){return!t.disabled&&t.placeholder}));t&&(e._addItem(t),e.unhighlightAll(),t.value&&e._triggerChange(t.value))}}))}},t.prototype._handleItemAction=function(t,e){var n=this;void 0===e&&(e=!1);var r=this._store.items;if(r.length&&this.config.removeItems&&!this._isSelectOneElement){var i=YH(t);i&&(r.forEach((function(t){t.id!==i||t.highlighted?!e&&t.highlighted&&n.unhighlightItem(t):n.highlightItem(t)})),this.input.focus())}},t.prototype._handleChoiceAction=function(t){var e=this,n=YH(t),r=n&&this._store.getChoiceById(n);if(!r||r.disabled)return!1;var i=this.dropdown.isActive;if(!r.selected){if(!this._canAddItems())return!0;this._store.withTxn((function(){e._addItem(r,!0,!0),e.clearInput(),e.unhighlightAll()})),this._triggerChange(r.value)}return i&&this.config.closeDropdownOnSelect&&(this.hideDropdown(!0),this.containerOuter.element.focus()),!0},t.prototype._handleBackspace=function(t){var e=this.config;if(e.removeItems&&t.length){var n=t[t.length-1],r=t.some((function(t){return t.highlighted}));e.editItems&&!r&&n?(this.input.value=n.value,this.input.setWidth(),this._removeItem(n),this._triggerChange(n.value)):(r||this.highlightItem(n,!1),this.removeHighlightedItems(!0))}},t.prototype._loadChoices=function(){var t,e=this.config;if(this._isTextElement){if(this._presetChoices=e.items.map((function(t){return qA(t,!1)})),this.passedElement.value){var n=this.passedElement.value.split(e.delimiter).map((function(t){return qA(t,!1)}));this._presetChoices=this._presetChoices.concat(n)}this._presetChoices.forEach((function(t){t.selected=!0}))}else if(this._isSelectElement){this._presetChoices=e.choices.map((function(t){return qA(t,!0)}));var r=this.passedElement.optionsAsChoices();r&&(t=this._presetChoices).push.apply(t,r)}},t.prototype._handleLoadingState=function(t){void 0===t&&(t=!0);var e=this.itemList.element;t?(this.disable(),this.containerOuter.addLoadingState(),this._isSelectOneElement?e.replaceChildren(this._templates.placeholder(this.config,this.config.loadingText)):this.input.placeholder=this.config.loadingText):(this.enable(),this.containerOuter.removeLoadingState(),this._isSelectOneElement?(e.replaceChildren(""),this._render()):this.input.placeholder=this._placeholderValue||"")},t.prototype._handleSearch=function(t){if(this.input.isFocussed)if(null!=t&&t.length>=this.config.searchFloor){var e=this.config.searchChoices?this._searchChoices(t):0;null!==e&&this.passedElement.triggerEvent(QA,{value:t,resultCount:e})}else this._store.choices.some((function(t){return!t.active}))&&this._stopSearch()},t.prototype._canAddItems=function(){var t=this.config,e=t.maxItemCount,n=t.maxItemText;return!(!t.singleModeForMultiSelect&&e>0&&e<=this._store.items.length&&(this.choiceList.element.replaceChildren(""),this._displayNotice("function"==typeof n?n(e):n,eH),1))},t.prototype._canCreateItem=function(t){var e=this.config,n=!0,r="";if(n&&"function"==typeof e.addItemFilter&&!e.addItemFilter(t)&&(n=!1,r=HA(e.customAddItemText,t)),n){var i=this._store.choices.find((function(n){return e.valueComparer(n.value,t)}));if(this._isSelectElement){if(i)return this._displayNotice("",eH),!1}else this._isTextElement&&!e.duplicateItemsAllowed&&i&&(n=!1,r=HA(e.uniqueItemText,t))}return n&&(r=HA(e.addItemText,t)),r&&this._displayNotice(r,eH),n},t.prototype._searchChoices=function(t){var e=t.trim().replace(/\s{2,}/," ");if(!e.length||e===this._currentValue)return null;var n=this._searcher;n.isEmptyIndex()&&n.index(this._store.searchableChoices);var r=n.search(e);this._currentValue=e,this._highlightPosition=0,this._isSearching=!0;var i=this._notice;return(i&&i.type)!==eH&&(r.length?this._clearNotice():this._displayNotice(kA(this.config.noResultsText),tH)),this._store.dispatch(function(t){return{type:lA,results:t}}(r)),r.length},t.prototype._stopSearch=function(){this._isSearching&&(this._currentValue="",this._isSearching=!1,this._clearNotice(),this._store.dispatch({type:cA,active:!0}),this.passedElement.triggerEvent(QA,{value:"",resultCount:0}))},t.prototype._addEventListeners=function(){var t=this._docRoot,e=this.containerOuter.element,n=this.input.element;t.addEventListener("touchend",this._onTouchEnd,!0),e.addEventListener("keydown",this._onKeyDown,!0),e.addEventListener("mousedown",this._onMouseDown,!0),t.addEventListener("click",this._onClick,{passive:!0}),t.addEventListener("touchmove",this._onTouchMove,{passive:!0}),this.dropdown.element.addEventListener("mouseover",this._onMouseOver,{passive:!0}),this._isSelectOneElement&&(e.addEventListener("focus",this._onFocus,{passive:!0}),e.addEventListener("blur",this._onBlur,{passive:!0})),n.addEventListener("keyup",this._onKeyUp,{passive:!0}),n.addEventListener("input",this._onInput,{passive:!0}),n.addEventListener("focus",this._onFocus,{passive:!0}),n.addEventListener("blur",this._onBlur,{passive:!0}),n.form&&n.form.addEventListener("reset",this._onFormReset,{passive:!0}),this.input.addEventListeners()},t.prototype._removeEventListeners=function(){var t=this._docRoot,e=this.containerOuter.element,n=this.input.element;t.removeEventListener("touchend",this._onTouchEnd,!0),e.removeEventListener("keydown",this._onKeyDown,!0),e.removeEventListener("mousedown",this._onMouseDown,!0),t.removeEventListener("click",this._onClick),t.removeEventListener("touchmove",this._onTouchMove),this.dropdown.element.removeEventListener("mouseover",this._onMouseOver),this._isSelectOneElement&&(e.removeEventListener("focus",this._onFocus),e.removeEventListener("blur",this._onBlur)),n.removeEventListener("keyup",this._onKeyUp),n.removeEventListener("input",this._onInput),n.removeEventListener("focus",this._onFocus),n.removeEventListener("blur",this._onBlur),n.form&&n.form.removeEventListener("reset",this._onFormReset),this.input.removeEventListeners()},t.prototype._onKeyDown=function(t){var e=t.keyCode,n=this.dropdown.isActive,r=1===t.key.length||2===t.key.length&&t.key.charCodeAt(0)>=55296||"Unidentified"===t.key;switch(this._isTextElement||n||(this.showDropdown(),!this.input.isFocussed&&r&&(this.input.value+=t.key," "===t.key&&t.preventDefault())),e){case 65:return this._onSelectKey(t,this.itemList.element.hasChildNodes());case 13:return this._onEnterKey(t,n);case 27:return this._onEscapeKey(t,n);case 38:case 33:case 40:case 34:return this._onDirectionKey(t,n);case 8:case 46:return this._onDeleteKey(t,this._store.items,this.input.isFocussed)}},t.prototype._onKeyUp=function(){this._canSearch=this.config.searchEnabled},t.prototype._onInput=function(){var t=this.input.value;t?this._canAddItems()&&(this._canSearch&&this._handleSearch(t),this._canAddUserChoices&&(this._canCreateItem(t),this._isSelectElement&&(this._highlightPosition=0,this._highlightChoice()))):this._isTextElement?this.hideDropdown(!0):this._stopSearch()},t.prototype._onSelectKey=function(t,e){(t.ctrlKey||t.metaKey)&&e&&(this._canSearch=!1,this.config.removeItems&&!this.input.value&&this.input.element===document.activeElement&&this.highlightAll())},t.prototype._onEnterKey=function(t,e){var n=this,r=this.input.value,i=t.target;if(t.preventDefault(),i&&i.hasAttribute("data-button"))this._handleButtonAction(i);else if(e){var o=this.dropdown.element.querySelector(OA(this.config.classNames.highlightedState));if(!o||!this._handleChoiceAction(o))if(i&&r){if(this._canAddItems()){var a=!1;this._store.withTxn((function(){if(!(a=n._findAndSelectChoiceByValue(r,!0))){if(!n._canAddUserChoices)return;if(!n._canCreateItem(r))return;var t=LA(r),e=n.config.allowHtmlUserInput||t===r?r:{escaped:t,raw:r};n._addChoice(qA({value:e,label:e,selected:!0},!1),!0,!0),a=!0}n.clearInput(),n.unhighlightAll()})),a&&(this._triggerChange(r),this.config.closeDropdownOnSelect&&this.hideDropdown(!0))}}else this.hideDropdown(!0)}else(this._isSelectElement||this._notice)&&this.showDropdown()},t.prototype._onEscapeKey=function(t,e){e&&(t.stopPropagation(),this.hideDropdown(!0),this.containerOuter.element.focus())},t.prototype._onDirectionKey=function(t,e){var n,r,i,o=t.keyCode;if(e||this._isSelectOneElement){this.showDropdown(),this._canSearch=!1;var a=40===o||34===o?1:-1,s=void 0;if(t.metaKey||34===o||33===o)s=a>0?this.dropdown.element.querySelector("".concat(JH,":last-of-type")):this.dropdown.element.querySelector(JH);else{var l=this.dropdown.element.querySelector(OA(this.config.classNames.highlightedState));s=l?function(t,e,n){void 0===n&&(n=1);for(var r="".concat(n>0?"next":"previous","ElementSibling"),i=t[r];i;){if(i.matches(e))return i;i=i[r]}return null}(l,JH,a):this.dropdown.element.querySelector(JH)}s&&(n=s,r=this.choiceList.element,void 0===(i=a)&&(i=1),(i>0?r.scrollTop+r.offsetHeight>=n.offsetTop+n.offsetHeight:n.offsetTop>=r.scrollTop)||this.choiceList.scrollToChildElement(s,a),this._highlightChoice(s)),t.preventDefault()}},t.prototype._onDeleteKey=function(t,e,n){this._isSelectOneElement||t.target.value||!n||(this._handleBackspace(e),t.preventDefault())},t.prototype._onTouchMove=function(){this._wasTap&&(this._wasTap=!1)},t.prototype._onTouchEnd=function(t){var e=(t||t.touches[0]).target;this._wasTap&&this.containerOuter.element.contains(e)&&((e===this.containerOuter.element||e===this.containerInner.element)&&(this._isTextElement?this.input.focus():this._isSelectMultipleElement&&this.showDropdown()),t.stopPropagation()),this._wasTap=!0},t.prototype._onMouseDown=function(t){var e=t.target;if(e instanceof HTMLElement){if(XH&&this.choiceList.element.contains(e)){var n=this.choiceList.element.firstElementChild;this._isScrollingOnIe="ltr"===this._direction?t.offsetX>=n.offsetWidth:t.offsetX<n.offsetLeft}if(e!==this.input.element){var r=e.closest("[data-button],[data-item],[data-choice]");r instanceof HTMLElement&&("button"in r.dataset?this._handleButtonAction(r):"item"in r.dataset?this._handleItemAction(r,t.shiftKey):"choice"in r.dataset&&this._handleChoiceAction(r)),t.preventDefault()}}},t.prototype._onMouseOver=function(t){var e=t.target;e instanceof HTMLElement&&"choice"in e.dataset&&this._highlightChoice(e)},t.prototype._onClick=function(t){var e=t.target,n=this.containerOuter;n.element.contains(e)?this.dropdown.isActive||n.isDisabled?this._isSelectOneElement&&e!==this.input.element&&!this.dropdown.element.contains(e)&&this.hideDropdown():this._isTextElement?document.activeElement!==this.input.element&&this.input.focus():(this.showDropdown(),n.element.focus()):(n.removeFocusState(),this.hideDropdown(!0),this.unhighlightAll())},t.prototype._onFocus=function(t){var e=t.target,n=this.containerOuter;if(e&&n.element.contains(e)){var r=e===this.input.element;this._isTextElement?r&&n.addFocusState():this._isSelectMultipleElement?r&&(this.showDropdown(!0),n.addFocusState()):(n.addFocusState(),r&&this.showDropdown(!0))}},t.prototype._onBlur=function(t){var e=t.target,n=this.containerOuter;if(e&&n.element.contains(e)&&!this._isScrollingOnIe){var r=e===this.input.element;this._isTextElement||this._isSelectMultipleElement?r&&(n.removeFocusState(),this.hideDropdown(!0),this.unhighlightAll()):(n.removeFocusState(),(r||e===n.element&&!this._canSearch)&&this.hideDropdown(!0))}else this._isScrollingOnIe=!1,this.input.element.focus()},t.prototype._onFormReset=function(){var t=this;this._store.withTxn((function(){t.clearInput(),t.hideDropdown(),t.refresh(!1,!1,!0),t._initialItems.length&&t.setChoiceByValue(t._initialItems)}))},t.prototype._highlightChoice=function(t){void 0===t&&(t=null);var e=Array.from(this.dropdown.element.querySelectorAll(JH));if(e.length){var n=t,r=this.config.classNames.highlightedState;Array.from(this.dropdown.element.querySelectorAll(OA(r))).forEach((function(t){DA(t,r),t.setAttribute("aria-selected","false")})),n?this._highlightPosition=e.indexOf(n):(n=e.length>this._highlightPosition?e[this._highlightPosition]:e[e.length-1])||(n=e[0]),PA(n,r),n.setAttribute("aria-selected","true"),this.passedElement.triggerEvent("highlightChoice",{el:n}),this.dropdown.isActive&&(this.input.setActiveDescendant(n.id),this.containerOuter.setActiveDescendant(n.id))}},t.prototype._addItem=function(t,e,n){if(void 0===e&&(e=!0),void 0===n&&(n=!1),!t.id)throw new TypeError("item.id must be set before _addItem is called for a choice/item");(this.config.singleModeForMultiSelect||this._isSelectOneElement)&&this.removeActiveItems(t.id),this._store.dispatch(function(t){return{type:hA,item:t}}(t)),e&&(this.passedElement.triggerEvent("addItem",this._getChoiceForOutput(t)),n&&this.passedElement.triggerEvent("choice",this._getChoiceForOutput(t)))},t.prototype._removeItem=function(t){t.id&&(this._store.dispatch(yA(t)),this.passedElement.triggerEvent(TA,this._getChoiceForOutput(t)))},t.prototype._addChoice=function(t,e,n){if(void 0===e&&(e=!0),void 0===n&&(n=!1),t.id)throw new TypeError("Can not re-add a choice which has already been added");var r=this.config;if(!this._isSelectElement&&r.duplicateItemsAllowed||!this._store.choices.find((function(e){return r.valueComparer(e.value,t.value)}))){this._lastAddedChoiceId++,t.id=this._lastAddedChoiceId,t.elementId="".concat(this._baseId,"-").concat(this._idNames.itemChoice,"-").concat(t.id);var i=r.prependValue,o=r.appendValue;i&&(t.value=i+t.value),o&&(t.value+=o.toString()),(i||o)&&t.element&&(t.element.value=t.value),this._clearNotice(),this._store.dispatch(function(t){return{type:aA,choice:t}}(t)),t.selected&&this._addItem(t,e,n)}},t.prototype._addGroup=function(t,e){var n=this;if(void 0===e&&(e=!0),t.id)throw new TypeError("Can not re-add a group which has already been added");this._store.dispatch(function(t){return{type:dA,group:t}}(t)),t.choices&&(this._lastAddedGroupId++,t.id=this._lastAddedGroupId,t.choices.forEach((function(r){r.group=t,t.disabled&&(r.disabled=!0),n._addChoice(r,e)})))},t.prototype._createTemplates=function(){var t=this,e=this.config.callbackOnCreateTemplates,n={};"function"==typeof e&&(n=e.call(this,AA,CA,VA));var r={};Object.keys(this._templates).forEach((function(e){r[e]=e in n?n[e].bind(t):t._templates[e].bind(t)})),this._templates=r},t.prototype._createElements=function(){var t=this._templates,e=this.config,n=this._isSelectOneElement,r=e.position,i=e.classNames,o=this._elementType;this.containerOuter=new IA({element:t.containerOuter(e,this._direction,this._isSelectElement,n,e.searchEnabled,o,e.labelId),classNames:i,type:o,position:r}),this.containerInner=new IA({element:t.containerInner(e),classNames:i,type:o,position:r}),this.input=new jA({element:t.input(e,this._placeholderValue),classNames:i,type:o,preventPaste:!e.paste}),this.choiceList=new zA({element:t.choiceList(e,n)}),this.itemList=new zA({element:t.itemList(e,n)}),this.dropdown=new RA({element:t.dropdown(e),classNames:i,type:o})},t.prototype._createStructure=function(){var t=this,e=t.containerInner,n=t.containerOuter,r=t.passedElement,i=this.dropdown.element;r.conceal(),e.wrap(r.element),n.wrap(e.element),this._isSelectOneElement?this.input.placeholder=this.config.searchPlaceholderValue||"":(this._placeholderValue&&(this.input.placeholder=this._placeholderValue),this.input.setWidth()),n.element.appendChild(e.element),n.element.appendChild(i),e.element.appendChild(this.itemList.element),i.appendChild(this.choiceList.element),this._isSelectOneElement?this.config.searchEnabled&&i.insertBefore(this.input.element,i.firstChild):e.element.appendChild(this.input.element),this._highlightPosition=0,this._isSearching=!1},t.prototype._initStore=function(){var t=this;this._store.subscribe(this._render).withTxn((function(){t._addPredefinedChoices(t._presetChoices,t._isSelectOneElement&&!t._hasNonChoicePlaceholder,!1)})),(!this._store.choices.length||this._isSelectOneElement&&this._hasNonChoicePlaceholder)&&this._render()},t.prototype._addPredefinedChoices=function(t,e,n){var r=this;void 0===e&&(e=!1),void 0===n&&(n=!0),e&&-1===t.findIndex((function(t){return t.selected}))&&t.some((function(t){return!t.disabled&&!("choices"in t)&&(t.selected=!0,!0)})),t.forEach((function(t){"choices"in t?r._isSelectElement&&r._addGroup(t,n):r._addChoice(t,n)}))},t.prototype._findAndSelectChoiceByValue=function(t,e){var n=this;void 0===e&&(e=!1);var r=this._store.choices.find((function(e){return n.config.valueComparer(e.value,t)}));return!(!r||r.disabled||r.selected||(this._addItem(r,!0,e),0))},t.prototype._generatePlaceholderValue=function(){var t=this.config;if(!t.placeholder)return null;if(this._hasNonChoicePlaceholder)return t.placeholderValue;if(this._isSelectElement){var e=this.passedElement.placeholderOption;return e?e.text:null}return null},t.prototype._warnChoicesInitFailed=function(t){if(!this.config.silent){if(!this.initialised)throw new TypeError("".concat(t," called on a non-initialised instance of Choices"));if(!this.initialisedOK)throw new TypeError("".concat(t," called for an element which has multiple instances of Choices initialised on it"))}},t.version="11.0.2",t}();function ek(t){return Object.defineProperty(t,"target",{get:()=>t.composedPath()[0]??null,configurable:!0}),t}class nk extends tk{_onFocus(t){super._onFocus(ek(t))}_onBlur(t){super._onBlur(ek(t))}_onKeyUp(t){super._onKeyUp(ek(t))}_onKeyDown(t){super._onKeyDown(ek(t))}_onClick(t){super._onClick(ek(t))}_onTouchEnd(t){super._onTouchEnd(ek(t))}_onMouseDown(t){super._onMouseDown(ek(t))}_onMouseOver(t){super._onMouseOver(ek(t))}}nk.__name__="OurChoices";class rk extends rx{connect_signals(){super.connect_signals(),this.connect(this.model.properties.disabled.change,(()=>this.set_disabled()));const{value:t,max_items:e,option_limit:n,search_option_limit:r,delete_button:i,placeholder:o,options:a,name:s,title:l}=this.model.properties;this.on_change([t,e,n,r,i,o,a,s,l],(()=>this.render()))}styles(){return[...super.styles(),'.choices{position:relative;overflow:hidden;margin-bottom:24px;font-size:16px;}.choices:focus{outline:none;}.choices:last-child{margin-bottom:0;}.choices.is-open{overflow:visible;}.choices.is-disabled .choices__inner,.choices.is-disabled .choices__input{background-color:#eaeaea;cursor:not-allowed;-webkit-user-select:none;user-select:none;}.choices.is-disabled .choices__item{cursor:not-allowed;}.choices [hidden]{display:none !important;}.choices[data-type*=select-one]{cursor:pointer;}.choices[data-type*=select-one] .choices__inner{padding-bottom:7.5px;}.choices[data-type*=select-one] .choices__input{display:block;width:100%;padding:10px;border-bottom:1px solid #ddd;background-color:#fff;margin:0;}.choices[data-type*=select-one] .choices__button{background-image:url("data:image/svg+xml;base64,PHN2ZyB3aWR0aD0iMjEiIGhlaWdodD0iMjEiIHZpZXdCb3g9IjAgMCAyMSAyMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj48ZyBmaWxsPSIjMDAwIiBmaWxsLXJ1bGU9ImV2ZW5vZGQiPjxwYXRoIGQ9Ik0yLjU5Mi4wNDRsMTguMzY0IDE4LjM2NC0yLjU0OCAyLjU0OEwuMDQ0IDIuNTkyeiIvPjxwYXRoIGQ9Ik0wIDE4LjM2NEwxOC4zNjQgMGwyLjU0OCAyLjU0OEwyLjU0OCAyMC45MTJ6Ii8+PC9nPjwvc3ZnPg==");padding:0;background-size:8px;position:absolute;top:50%;right:0;margin-top:-10px;margin-right:25px;height:20px;width:20px;border-radius:10em;opacity:0.25;}.choices[data-type*=select-one] .choices__button:hover,.choices[data-type*=select-one] .choices__button:focus{opacity:1;}.choices[data-type*=select-one] .choices__button:focus{box-shadow:0 0 0 2px #00bcd4;}.choices[data-type*=select-one] .choices__item[data-value=""] .choices__button{display:none;}.choices[data-type*=select-one]::after{content:"";height:0;width:0;border-style:solid;border-color:#333 transparent transparent transparent;border-width:5px;position:absolute;right:11.5px;top:50%;margin-top:-2.5px;pointer-events:none;}.choices[data-type*=select-one].is-open::after{border-color:transparent transparent #333 transparent;margin-top:-7.5px;}.choices[data-type*=select-one][dir=rtl]::after{left:11.5px;right:auto;}.choices[data-type*=select-one][dir=rtl] .choices__button{right:auto;left:0;margin-left:25px;margin-right:0;}.choices[data-type*=select-multiple] .choices__inner,.choices[data-type*=text] .choices__inner{cursor:text;}.choices[data-type*=select-multiple] .choices__button,.choices[data-type*=text] .choices__button{position:relative;display:inline-block;margin-top:0;margin-right:-4px;margin-bottom:0;margin-left:8px;padding-left:16px;border-left:1px solid #008fa1;background-image:url("data:image/svg+xml;base64,PHN2ZyB3aWR0aD0iMjEiIGhlaWdodD0iMjEiIHZpZXdCb3g9IjAgMCAyMSAyMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj48ZyBmaWxsPSIjRkZGIiBmaWxsLXJ1bGU9ImV2ZW5vZGQiPjxwYXRoIGQ9Ik0yLjU5Mi4wNDRsMTguMzY0IDE4LjM2NC0yLjU0OCAyLjU0OEwuMDQ0IDIuNTkyeiIvPjxwYXRoIGQ9Ik0wIDE4LjM2NEwxOC4zNjQgMGwyLjU0OCAyLjU0OEwyLjU0OCAyMC45MTJ6Ii8+PC9nPjwvc3ZnPg==");background-size:8px;width:8px;line-height:1;opacity:0.75;border-radius:0;}.choices[data-type*=select-multiple] .choices__button:hover,.choices[data-type*=select-multiple] .choices__button:focus,.choices[data-type*=text] .choices__button:hover,.choices[data-type*=text] .choices__button:focus{opacity:1;}.choices__inner{display:inline-block;vertical-align:top;width:100%;background-color:#f9f9f9;padding:7.5px 7.5px 3.75px;border:1px solid #ddd;border-radius:2.5px;font-size:14px;min-height:44px;overflow:hidden;}.is-focused .choices__inner,.is-open .choices__inner{border-color:#b7b7b7;}.is-open .choices__inner{border-radius:2.5px 2.5px 0 0;}.is-flipped.is-open .choices__inner{border-radius:0 0 2.5px 2.5px;}.choices__list{margin:0;padding-left:0;list-style:none;}.choices__list--single{display:inline-block;padding:4px 16px 4px 4px;width:100%;}[dir=rtl] .choices__list--single{padding-right:4px;padding-left:16px;}.choices__list--single .choices__item{width:100%;}.choices__list--multiple{display:inline;}.choices__list--multiple .choices__item{display:inline-block;vertical-align:middle;border-radius:20px;padding:4px 10px;font-size:12px;font-weight:500;margin-right:3.75px;margin-bottom:3.75px;background-color:#00bcd4;border:1px solid #00a5bb;color:#fff;word-break:break-all;box-sizing:border-box;}.choices__list--multiple .choices__item[data-deletable]{padding-right:5px;}[dir=rtl] .choices__list--multiple .choices__item{margin-right:0;margin-left:3.75px;}.choices__list--multiple .choices__item.is-highlighted{background-color:#00a5bb;border:1px solid #008fa1;}.is-disabled .choices__list--multiple .choices__item{background-color:#aaaaaa;border:1px solid #919191;}.choices__list--dropdown,.choices__list[aria-expanded]{visibility:hidden;z-index:1;position:absolute;width:100%;background-color:#fff;border:1px solid #ddd;top:100%;margin-top:-1px;border-bottom-left-radius:2.5px;border-bottom-right-radius:2.5px;overflow:hidden;word-break:break-all;will-change:visibility;}.is-active.choices__list--dropdown,.is-active.choices__list[aria-expanded]{visibility:visible;}.is-open .choices__list--dropdown,.is-open .choices__list[aria-expanded]{border-color:#b7b7b7;}.is-flipped .choices__list--dropdown,.is-flipped .choices__list[aria-expanded]{top:auto;bottom:100%;margin-top:0;margin-bottom:-1px;border-radius:0.25rem 0.25rem 0 0;}.choices__list--dropdown .choices__list,.choices__list[aria-expanded] .choices__list{position:relative;max-height:300px;overflow:auto;-webkit-overflow-scrolling:touch;will-change:scroll-position;}.choices__list--dropdown .choices__item,.choices__list[aria-expanded] .choices__item{position:relative;padding:10px;font-size:14px;}[dir=rtl] .choices__list--dropdown .choices__item,[dir=rtl] .choices__list[aria-expanded] .choices__item{text-align:right;}@media (min-width: 640px){.choices__list--dropdown .choices__item--selectable,.choices__list[aria-expanded] .choices__item--selectable{padding-right:100px;}.choices__list--dropdown .choices__item--selectable::after,.choices__list[aria-expanded] .choices__item--selectable::after{content:attr(data-select-text);font-size:12px;opacity:0;position:absolute;right:10px;top:50%;transform:translateY(-50%);}[dir=rtl] .choices__list--dropdown .choices__item--selectable,[dir=rtl] .choices__list[aria-expanded] .choices__item--selectable{text-align:right;padding-left:100px;padding-right:10px;}[dir=rtl] .choices__list--dropdown .choices__item--selectable::after,[dir=rtl] .choices__list[aria-expanded] .choices__item--selectable::after{right:auto;left:10px;}}.choices__list--dropdown .choices__item--selectable.is-highlighted,.choices__list[aria-expanded] .choices__item--selectable.is-highlighted{background-color:#f2f2f2;}.choices__list--dropdown .choices__item--selectable.is-highlighted::after,.choices__list[aria-expanded] .choices__item--selectable.is-highlighted::after{opacity:0.5;}.choices__item{cursor:default;}.choices__item--selectable{cursor:pointer;}.choices__item--disabled{cursor:not-allowed;-webkit-user-select:none;user-select:none;opacity:0.5;}.choices__heading{font-weight:600;font-size:12px;padding:10px;border-bottom:1px solid #f7f7f7;color:gray;}.choices__button{text-indent:-9999px;-webkit-appearance:none;appearance:none;border:0;background-color:transparent;background-repeat:no-repeat;background-position:center;cursor:pointer;}.choices__button:focus{outline:none;}.choices__input{display:inline-block;vertical-align:baseline;background-color:#f9f9f9;font-size:14px;margin-bottom:5px;border:0;border-radius:0;max-width:100%;padding:4px 0 4px 2px;}.choices__input:focus{outline:0;}.choices__input::-webkit-search-decoration,.choices__input::-webkit-search-cancel-button,.choices__input::-webkit-search-results-button,.choices__input::-webkit-search-results-decoration{display:none;}.choices__input::-ms-clear,.choices__input::-ms-reveal{display:none;width:0;height:0;}[dir=rtl] .choices__input{padding-right:2px;padding-left:0;}.choices__placeholder{opacity:0.5;}.choices{width:100%;}.choices{box-sizing:border-box;}.choices *,.choices *:before,.choices *:after{box-sizing:inherit;}input[type="search"]{margin:0;}.choices__inner .choices__item.light{background-color:rgba(0, 126, 255, 0.08);border-radius:5px;border:1px solid rgba(0, 126, 255, 0.24);color:#007eff;}.choices__inner .choices__item.solid{background-color:#1f77b4;border:none;border-radius:5px;color:white;}.choices__inner .choices__item.solid .is-highlighted{background-color:#1f77b4;border:none;}.choices__input{background-color:transparent;}.choices__inner{background:transparent;border:1px solid darkgray;border-radius:5px;min-height:0;padding:calc(var(--padding-vertical) / 2) var(--padding-horizontal);}.choices__list{white-space:initial;}.choices__list--dropdown,.choices__list[aria-expanded]{z-index:100;}.choices__list--dropdown .choices__item--selectable,.choices__list[aria-expanded] .choices__item--selectable{padding-right:0;}.choices[data-type*=select-multiple] .choices__button.light{background-image:url(data:image/svg+xml;base64,PHN2ZyB3aWR0aD0iMjEiIGhlaWdodD0iMjEiIHZpZXdCb3g9IjAgMCAyMSAyMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj48ZyBmaWxsPSIjMDA3ZWZmIiBmaWxsLXJ1bGU9ImV2ZW5vZGQiPjxwYXRoIGQ9Ik0yLjU5Mi4wNDRsMTguMzY0IDE4LjM2NC0yLjU0OCAyLjU0OEwuMDQ0IDIuNTkyeiIvPjxwYXRoIGQ9Ik0wIDE4LjM2NEwxOC4zNjQgMGwyLjU0OCAyLjU0OEwyLjU0OCAyMC45MTJ6Ii8+PC9nPjwvc3ZnPg==);}.choices[data-type*=select-multiple] .choices__button.solid{background-image:url(data:image/svg+xml;base64,PHN2ZyB3aWR0aD0iMjEiIGhlaWdodD0iMjEiIHZpZXdCb3g9IjAgMCAyMSAyMSIgeG1sbnM9Imh0dHA6Ly93d3cudzMub3JnLzIwMDAvc3ZnIj48ZyBmaWxsPSIjZmZmZmZmIiBmaWxsLXJ1bGU9ImV2ZW5vZGQiPjxwYXRoIGQ9Ik0yLjU5Mi4wNDRsMTguMzY0IDE4LjM2NC0yLjU0OCAyLjU0OEwuMDQ0IDIuNTkyeiIvPjxwYXRoIGQ9Ik0wIDE4LjM2NEwxOC4zNjQgMGwyLjU0OCAyLjU0OEwyLjU0OCAyMC45MTJ6Ii8+PC9nPjwvc3ZnPg==);border-left:1px solid white;opacity:1;}']}render(){super.render(),this.input_el=_e({multiple:!0,class:Xy,name:this.model.name,disabled:this.model.disabled}),this.group_el.appendChild(this.input_el);const t=new Set(this.model.value),e=this.model.options.map((e=>{let n,r;return(0,f.Kg)(e)?n=r=e:[n,r]=e,{value:n,label:r,selected:t.has(n)}})),n=this.model.solid?"solid":"light",r=`choices__item ${n}`,i=`choices__button ${n}`,o={choices:e,itemSelectText:"",duplicateItemsAllowed:!1,shouldSort:!1,removeItemButton:this.model.delete_button,classNames:{item:r,button:i},placeholderValue:this.model.placeholder??void 0,maxItemCount:this.model.max_items??void 0,renderChoiceLimit:this.model.option_limit??void 0,searchResultLimit:this.model.search_option_limit??void 0};this.choice_el=new nk(this.input_el,o),this.input_el.addEventListener("change",(()=>this.change_input()))}set_disabled(){this.model.disabled?this.choice_el.disable():this.choice_el.enable()}change_input(){const t=null!=this.shadow_el.querySelector("select:focus"),e=[];for(const t of this.shadow_el.querySelectorAll("option"))t.selected&&e.push(t.value);this.model.value=e,super.change_input(),t&&this.input_el.focus()}}rk.__name__="MultiChoiceView";class ik extends ix{constructor(t){super(t)}}$H=ik,ik.__name__="MultiChoice",$H.prototype.default_view=rk,$H.define((({Boolean:t,Int:e,String:n,Array:r,Tuple:i,Or:o,Nullable:a})=>({value:[r(n),[]],options:[r(o(n,i(n,n))),[]],max_items:[a(e),null],delete_button:[t,!0],placeholder:[a(n),null],option_limit:[a(e),null],search_option_limit:[a(e),null],solid:[t,!0]})));const ok=/^[-+]?\d*$/,ak=/^[-+]?\d*\.?\d*(?:(?:\d|\d.)[eE][-+]?)*\d*$/;class sk extends rx{connect_signals(){super.connect_signals(),this.connect(this.model.properties.name.change,(()=>this.input_el.name=this.model.name??"")),this.connect(this.model.properties.value.change,(()=>{this.input_el.value=this.format_value,this.old_value=this.input_el.value})),this.connect(this.model.properties.low.change,(()=>{const{value:t,low:e,high:n}=this.model;null!=e&&null!=n&&(0,_.vA)(e<=n,"Invalid bounds, low must be inferior to high"),null!=t&&null!=e&&t<e&&(this.model.value=e)})),this.connect(this.model.properties.high.change,(()=>{const{value:t,low:e,high:n}=this.model;null!=e&&null!=n&&(0,_.vA)(n>=e,"Invalid bounds, high must be superior to low"),null!=t&&null!=n&&t>n&&(this.model.value=n)})),this.connect(this.model.properties.high.change,(()=>this.input_el.placeholder=this.model.placeholder)),this.connect(this.model.properties.disabled.change,(()=>this.input_el.disabled=this.model.disabled)),this.connect(this.model.properties.placeholder.change,(()=>this.input_el.placeholder=this.model.placeholder))}get format_value(){return null!=this.model.value?this.model.pretty(this.model.value):""}_set_input_filter(t){this.input_el.addEventListener("input",(()=>{const{selectionStart:e,selectionEnd:n}=this.input_el;if(t(this.input_el.value))this.old_value=this.input_el.value;else{const t=this.old_value.length-this.input_el.value.length;this.input_el.value=this.old_value,null!=e&&null!=n&&this.input_el.setSelectionRange(e-1,n+t)}}))}render(){super.render(),this.input_el=ge({type:"text",class:Xy,name:this.model.name,value:this.format_value,disabled:this.model.disabled,placeholder:this.model.placeholder}),this.old_value=this.format_value,this.set_input_filter(),this.input_el.addEventListener("change",(()=>this.change_input())),this.input_el.addEventListener("focusout",(()=>this.input_el.value=this.format_value)),this.group_el.appendChild(this.input_el)}set_input_filter(){const t="int"==this.model.mode?ok:ak;this._set_input_filter((e=>t.test(e)))}bound_value(t){let e=t;const{low:n,high:r}=this.model;return e=null!=n?Math.max(n,e):e,e=null!=r?Math.min(r,e):e,e}get value(){let t=""!=this.input_el.value?Number(this.input_el.value):null;return null!=t&&(t=this.bound_value(t)),t}change_input(){null==this.value?this.model.value=null:Number.isNaN(this.value)||(this.model.value=this.value)}}sk.__name__="NumericInputView";class lk extends ix{constructor(t){super(t)}_formatter(t,e){return(0,f.Kg)(e)?Aa.format(t,e):e.doFormat([t],{loc:0})[0]}pretty(t){return null!=this.format?this._formatter(t,this.format):`${t}`}}var ck,uk,dk,hk,pk,fk,Qk;GH=lk,lk.__name__="NumericInput",GH.prototype.default_view=sk,GH.define((({Number:t,String:e,Enum:n,Ref:r,Or:i,Nullable:o})=>({value:[o(t),null],placeholder:[e,""],mode:[n("int","float"),"int"],format:[o(i(e,r(da))),null],low:[o(t),null],high:[o(t),null]})));class Tk extends IL{render(){super.render();const t=pe({style:{overflow:"auto"}},this.model.text);this.markup_el.appendChild(t)}}Tk.__name__="PreTextView";class mk extends jL{constructor(t){super(t)}}ck=mk,mk.__name__="PreText",ck.prototype.default_view=Tk;class gk extends wx{change_active(t){this.model.active!==t&&(this.model.active=t)}_update_active(){const{active:t}=this.model;this._buttons.forEach(((e,n)=>{e.classList.toggle(Py,t===n)}))}}gk.__name__="RadioButtonGroupView";class _k extends Lx{constructor(t){super(t)}}uk=_k,_k.__name__="RadioButtonGroup",uk.prototype.default_view=gk,uk.define((({Int:t,Nullable:e})=>({active:[e(t),null]})));class bk extends Ox{connect_signals(){super.connect_signals();const{active:t}=this.model.properties;this.on_change(t,(()=>{const{active:t}=this.model;for(const[e,n]of(0,On.HL)(this._inputs))e.checked=t==n}))}render(){super.render();const t=oe({class:[Ky,this.model.inline?Yy:null]});this.shadow_el.appendChild(t);const e=y(),{active:n,labels:r}=this.model;this._inputs=[];for(let i=0;i<r.length;i++){const o=ge({type:"radio",name:e,value:`${i}`});o.addEventListener("change",(()=>this.change_active(i))),this._inputs.push(o),this.model.disabled&&(o.disabled=!0),i==n&&(o.checked=!0);const a=Qe(o,ae(r[i]));t.appendChild(a)}}change_active(t){this.model.active=t}}bk.__name__="RadioGroupView";class vk extends Px{constructor(t){super(t)}}dk=vk,vk.__name__="RadioGroup",dk.prototype.default_view=bk,dk.define((({Int:t,Nullable:e})=>({active:[e(t),null]})));class yk extends SL{}yk.__name__="RangeSliderView";class xk extends EL{constructor(t){super(t),this.behaviour="drag",this.connected=[!1,!0,!1]}_formatter(t,e){return(0,f.Kg)(e)?Aa.format(t,e):e.compute(t)}}hk=xk,xk.__name__="RangeSlider",hk.prototype.default_view=yk,hk.override({format:"0[.]00"});class wk extends rx{constructor(){super(...arguments),this._known_values=new Set}connect_signals(){super.connect_signals();const{value:t,options:e}=this.model.properties;this.on_change(t,(()=>{this._update_value()})),this.on_change(e,(()=>{Ae(this.input_el),we(this.input_el,...this.options_el()),this._update_value()}))}options_el(){const{_known_values:t}=this;function e(e){return e.map((e=>{let n,r;return(0,f.Kg)(e)?n=r=e:[n,r]=e,t.add(n),be({value:n},r)}))}t.clear();const{options:n}=this.model;return(0,f.cy)(n)?e(n):(0,Q.jO)(n).map((([t,n])=>ve({label:t},e(n))))}render(){super.render(),this.input_el=_e({class:Xy,name:this.model.name,disabled:this.model.disabled},this.options_el()),this._update_value(),this.input_el.addEventListener("change",(()=>this.change_input())),this.group_el.appendChild(this.input_el)}change_input(){const t=this.input_el.value;this.model.value=t,super.change_input()}_update_value(){const{value:t}=this.model;this._known_values.has(t)?this.input_el.value=t:this.input_el.removeAttribute("value")}}wk.__name__="SelectView";class Lk extends ix{constructor(t){super(t)}}pk=Lk,Lk.__name__="Select",pk.prototype.default_view=wk,pk.define((({String:t,Array:e,Tuple:n,Dict:r,Or:i})=>{const o=e(i(t,n(t,t)));return{value:[t,""],options:[i(o,r(o)),[]]}}));class Ak extends CL{}Ak.__name__="SliderView";class Hk extends EL{constructor(t){super(t),this.behaviour="tap",this.connected=[!0,!1]}_formatter(t,e){return(0,f.Kg)(e)?Aa.format(t,e):e.compute(t)}}fk=Hk,Hk.__name__="Slider",fk.prototype.default_view=Ak,fk.override({format:"0[.]00"});const{min:kk,max:Mk,floor:Ck,abs:Sk}=Math;function Ek(t){return Ck(t)!==t?t.toFixed(16).replace(/0+$/,"").split(".")[1].length:0}class Vk extends sk{*buttons(){yield this.btn_up_el,yield this.btn_down_el}initialize(){super.initialize(),this._handles={interval:void 0,timeout:void 0},this._interval=200}connect_signals(){super.connect_signals();const t=this.model.properties;this.on_change(t.disabled,(()=>{for(const t of this.buttons())Ve(t,"disabled",this.model.disabled)}))}render(){super.render(),this.wrapper_el=oe({class:"bk-spin-wrapper"}),this.group_el.replaceChild(this.wrapper_el,this.input_el),this.btn_up_el=fe({class:"bk-spin-btn bk-spin-btn-up"}),this.btn_down_el=fe({class:"bk-spin-btn bk-spin-btn-down"}),this.wrapper_el.appendChild(this.input_el),this.wrapper_el.appendChild(this.btn_up_el),this.wrapper_el.appendChild(this.btn_down_el);for(const t of this.buttons())Ve(t,"disabled",this.model.disabled),t.addEventListener("mousedown",(t=>this._btn_mouse_down(t))),t.addEventListener("mouseup",(()=>this._btn_mouse_up())),t.addEventListener("mouseleave",(()=>this._btn_mouse_leave()));this.input_el.addEventListener("keydown",(t=>{this._input_key_down(t)})),this.input_el.addEventListener("keyup",(()=>{this.model.value_throttled=this.model.value})),this.input_el.addEventListener("wheel",(t=>{this._input_mouse_wheel(t)})),this.input_el.addEventListener("wheel",function(t,e,n=!1){let r;return function(...i){const o=this,a=n&&void 0===r;void 0!==r&&clearTimeout(r),r=setTimeout((function(){r=void 0,n||t.apply(o,i)}),e),a&&t.apply(o,i)}}((()=>{this.model.value_throttled=this.model.value}),this.model.wheel_wait,!1))}get precision(){const{low:t,high:e,step:n}=this.model,r=Ek;return Mk(r(Sk(t??0)),r(Sk(e??0)),r(Sk(n)))}remove(){this._stop_incrementation(),super.remove()}_start_incrementation(t){clearInterval(this._handles.interval),this._counter=0;const{step:e}=this.model,n=t=>{if(this._counter+=1,this._counter%5==0){const e=Math.floor(this._counter/5);e<10?(clearInterval(this._handles.interval),this._handles.interval=setInterval((()=>n(t)),this._interval/(e+1))):e>=10&&e<=13&&(clearInterval(this._handles.interval),this._handles.interval=setInterval((()=>n(2*t)),this._interval/10))}this.increment(t)};this._handles.interval=setInterval((()=>n(t*e)),this._interval)}_stop_incrementation(){clearTimeout(this._handles.timeout),this._handles.timeout=void 0,clearInterval(this._handles.interval),this._handles.interval=void 0,this.model.value_throttled=this.model.value}_btn_mouse_down(t){t.preventDefault();const e=t.currentTarget===this.btn_up_el?1:-1;this.increment(e*this.model.step),this.input_el.focus(),this._handles.timeout=setTimeout((()=>this._start_incrementation(e)),this._interval)}_btn_mouse_up(){this._stop_incrementation()}_btn_mouse_leave(){this._stop_incrementation()}_input_mouse_wheel(t){if(document.activeElement===this.input_el){t.preventDefault();const e=t.deltaY>0?-1:1;this.increment(e*this.model.step)}}_input_key_down(t){switch(t.key){case"ArrowUp":return t.preventDefault(),this.increment(this.model.step);case"ArrowDown":return t.preventDefault(),this.increment(-this.model.step);case"PageUp":return t.preventDefault(),this.increment(this.model.page_step_multiplier*this.model.step);case"PageDown":return t.preventDefault(),this.increment(-this.model.page_step_multiplier*this.model.step)}}adjust_to_precision(t){return this.bound_value(Number(t.toFixed(this.precision)))}increment(t){const{low:e,high:n}=this.model;null==this.model.value?t>0?this.model.value=null!=e?e:null!=n?kk(0,n):0:t<0&&(this.model.value=null!=n?n:null!=e?Mk(e,0):0):this.model.value=this.adjust_to_precision(this.model.value+t)}change_input(){super.change_input(),this.model.value_throttled=this.model.value}}Vk.__name__="SpinnerView";class Ok extends lk{constructor(t){super(t)}}var Pk,Dk,Nk;Qk=Ok,Ok.__name__="Spinner",Qk.prototype.default_view=Vk,Qk.define((({Number:t,Nullable:e})=>({value_throttled:[e(t),null],step:[t,1],page_step_multiplier:[t,10],wheel_wait:[t,100]}))),Qk.override({mode:"float"});class Rk extends Rx{styles(){return[...super.styles(),":host{cursor:pointer;}:host(.disabled){cursor:default;}:host{--switch-size:16px;--bar-height:10px;}.body{width:100%;height:var(--switch-size);}.bar{position:relative;top:calc(50% - var(--bar-height)/2);height:var(--bar-height);border-radius:calc(var(--bar-height)/2);background-color:#e5e5e5;transition-property:background-color;}.knob{position:absolute;top:0;left:0;width:var(--switch-size);height:var(--switch-size);border-radius:8px;background-color:#adadad;transition-property:left, background-color;}:host(.active) .bar{background-color:#c2d5f7;}:host(.active) .knob{left:calc(100% - var(--switch-size));background-color:#3b80f0;}"]}connect_signals(){super.connect_signals(),this.el.addEventListener("keydown",(t=>{switch(t.key){case"Enter":case" ":t.preventDefault(),this._toggle_active()}})),this.el.addEventListener("click",(()=>this._toggle_active()))}render(){super.render(),this.bar_el=oe({class:"bar"}),this.knob_el=oe({class:"knob",tabIndex:0});const t=oe({class:"body"},this.bar_el,this.knob_el);this._update_active(),this._update_disabled(),this.shadow_el.appendChild(t)}_update_active(){this.el.classList.toggle("active",this.model.active)}_update_disabled(){this.el.classList.toggle("disabled",this.model.disabled)}}Rk.__name__="SwitchView";class Ik extends Ix{constructor(t){super(t)}}Pk=Ik,Ik.__name__="Switch",Pk.prototype.default_view=Rk,Pk.override({width:32});class jk extends ox{connect_signals(){super.connect_signals(),this.connect(this.model.properties.rows.change,(()=>this.input_el.rows=this.model.rows)),this.connect(this.model.properties.cols.change,(()=>this.input_el.cols=this.model.cols))}_render_input(){return this.input_el=ye({class:Xy})}render(){super.render(),this.input_el.cols=this.model.cols,this.input_el.rows=this.model.rows}}jk.__name__="TextAreaInputView";class zk extends ax{constructor(t){super(t)}}Dk=zk,zk.__name__="TextAreaInput",Dk.prototype.default_view=jk,Dk.define((({Int:t})=>({cols:[t,20],rows:[t,2]}))),Dk.override({max_length:500});class Bk extends Wy{connect_signals(){super.connect_signals(),this.connect(this.model.properties.active.change,(()=>this._update_active()))}render(){super.render(),this._update_active()}click(){this.model.active=!this.model.active,this.model.trigger_event(new dt),super.click()}_update_active(){this.button_el.classList.toggle(Py,this.model.active)}}Bk.__name__="ToggleView";class Fk extends Zy{constructor(t){super(t)}}Nk=Fk,Fk.__name__="Toggle",Nk.prototype.default_view=Bk,Nk.define((({Boolean:t})=>({active:[t,!1]}))),Nk.override({label:"Toggle"}),rt(d);const $k="__bkdt_internal_index__";var Gk,qk,Uk,Wk,Zk,Xk,Kk,Yk,Jk;class tM extends Be{constructor(t){const{model:e,parent:n}=t.column;super({model:e,parent:n,...t}),this.args=t,this.initialize(),this.render()}get emptyValue(){return null}initialize(){super.initialize(),this.inputEl=this._createInput(),this.defaultValue=null}async lazy_initialize(){throw new Error("unsupported")}css_classes(){return super.css_classes().concat("bk-cell-editor")}render(){this.args.container.append(this.el),this.shadow_el.appendChild(this.inputEl),this.renderEditor(),this.disableNavigation()}renderEditor(){}disableNavigation(){this.inputEl.addEventListener("keydown",(t=>{switch(t.key){case"ArrowLeft":case"ArrowRight":case"ArrowUp":case"ArrowDown":case"PageUp":case"PageDown":t.stopImmediatePropagation()}}))}destroy(){this.remove()}focus(){this.inputEl.focus()}show(){}hide(){}position(){}getValue(){return this.inputEl.value}setValue(t){this.inputEl.value=t}serializeValue(){return this.getValue()}isValueChanged(){return!(""==this.getValue()&&null==this.defaultValue)&&this.getValue()!==this.defaultValue}applyValue(t,e){const n=this.args.grid.getData(),r=n.index.indexOf(t[$k]);n.setField(r,this.args.column.field,e)}loadValue(t){const e=t[this.args.column.field];this.defaultValue=null!=e?e:this.emptyValue,this.setValue(this.defaultValue)}validateValue(t){if(this.args.column.validator){const e=this.args.column.validator(t);if(!e.valid)return e}return{valid:!0,msg:null}}validate(){return this.validateValue(this.getValue())}}tM.__name__="CellEditorView";class eM extends qt{}eM.__name__="CellEditor";class nM extends tM{get emptyValue(){return""}_createInput(){return ge({type:"text"})}renderEditor(){this.inputEl.focus(),this.inputEl.select()}loadValue(t){super.loadValue(t),this.inputEl.defaultValue=this.defaultValue,this.inputEl.select()}}nM.__name__="StringEditorView";class rM extends eM{}Gk=rM,rM.__name__="StringEditor",Gk.prototype.default_view=nM,Gk.define((({String:t,Array:e})=>({completions:[e(t),[]]})));class iM extends tM{_createInput(){return ye()}renderEditor(){this.inputEl.focus(),this.inputEl.select()}}iM.__name__="TextEditorView";class oM extends eM{}qk=oM,oM.__name__="TextEditor",qk.prototype.default_view=iM;class aM extends tM{_createInput(){return _e()}renderEditor(){for(const t of this.model.options)this.inputEl.appendChild(be({value:t},t));this.focus()}}aM.__name__="SelectEditorView";class sM extends eM{}Uk=sM,sM.__name__="SelectEditor",Uk.prototype.default_view=aM,Uk.define((({String:t,Array:e})=>({options:[e(t),[]]})));class lM extends tM{_createInput(){return ge({type:"text"})}}lM.__name__="PercentEditorView";class cM extends eM{}Wk=cM,cM.__name__="PercentEditor",Wk.prototype.default_view=lM;class uM extends tM{_createInput(){return ge({type:"checkbox"})}renderEditor(){this.focus()}loadValue(t){this.defaultValue=!!t[this.args.column.field],this.inputEl.checked=this.defaultValue}serializeValue(){return this.inputEl.checked}}uM.__name__="CheckboxEditorView";class dM extends eM{}Zk=dM,dM.__name__="CheckboxEditor",Zk.prototype.default_view=uM;class hM extends tM{_createInput(){return ge({type:"text"})}renderEditor(){this.inputEl.focus(),this.inputEl.select()}remove(){super.remove()}serializeValue(){const t=parseInt(this.getValue(),10);return isNaN(t)?0:t}loadValue(t){super.loadValue(t),this.inputEl.defaultValue=this.defaultValue,this.inputEl.select()}validateValue(t){return(0,f.Kg)(t)&&(t=Number(t)),(0,f.Fq)(t)?super.validateValue(t):{valid:!1,msg:"Please enter a valid integer"}}}hM.__name__="IntEditorView";class pM extends eM{}Xk=pM,pM.__name__="IntEditor",Xk.prototype.default_view=hM,Xk.define((({Int:t})=>({step:[t,1]})));class fM extends tM{_createInput(){return ge({type:"text"})}renderEditor(){this.inputEl.focus(),this.inputEl.select()}remove(){super.remove()}serializeValue(){const t=parseFloat(this.getValue());return isNaN(t)?0:t}loadValue(t){super.loadValue(t),this.inputEl.defaultValue=this.defaultValue,this.inputEl.select()}validateValue(t){return isNaN(t)?{valid:!1,msg:"Please enter a valid number"}:super.validateValue(t)}}fM.__name__="NumberEditorView";class QM extends eM{}Kk=QM,QM.__name__="NumberEditor",Kk.prototype.default_view=fM,Kk.define((({Number:t})=>({step:[t,.01]})));class TM extends tM{_createInput(){return ge({type:"text"})}}TM.__name__="TimeEditorView";class mM extends eM{}Yk=mM,mM.__name__="TimeEditor",Yk.prototype.default_view=TM;class gM extends tM{_createInput(){return ge({type:"text"})}get emptyValue(){return new Date}renderEditor(){this.inputEl.focus(),this.inputEl.select()}destroy(){super.destroy()}show(){super.show()}hide(){super.hide()}position(){return super.position()}getValue(){}setValue(t){}}gM.__name__="DateEditorView";class _M extends eM{}Jk=_M,_M.__name__="DateEditor",Jk.prototype.default_view=gM;var bM,vM,yM,xM,wM,LM,AM=n(347);class HM extends qt{constructor(t){super(t)}doFormat(t,e,n,r,i){return null==n?"":`${n}`.replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/>/g,"&gt;")}}HM.__name__="CellFormatter";class kM extends HM{constructor(t){super(t)}doFormat(t,e,n,r,i){const{font_style:o,text_align:a,text_color:s}=this,l=oe(null==n?"":`${n}`);switch(o){case"bold":l.style.fontWeight="bold";break;case"italic":l.style.fontStyle="italic"}return l.style.textAlign=a,null!=s&&(l.style.color=(0,Ye.do)(s)),l.outerHTML}}bM=kM,kM.__name__="StringFormatter",bM.define((({Color:t,Nullable:e,String:n})=>({font_style:[_n.zz,"normal"],text_align:[_n.nO,"left"],text_color:[e(t),null],nan_format:[n,"-"]})));class MM extends kM{constructor(t){super(t)}get scientific_limit_low(){return 10**this.power_limit_low}get scientific_limit_high(){return 10**this.power_limit_high}doFormat(t,e,n,r,i){const o=Math.abs(n)<=this.scientific_limit_low||Math.abs(n)>=this.scientific_limit_high;let a=this.precision;return a<1&&(a=1),n=null==n||isNaN(n)?this.nan_format:0==n?w(n,1):o?n.toExponential(a):w(n,a),super.doFormat(t,e,n,r,i)}}vM=MM,MM.__name__="ScientificFormatter",vM.define((({Number:t})=>({precision:[t,10],power_limit_high:[t,5],power_limit_low:[t,-3]})));class CM extends kM{constructor(t){super(t)}doFormat(t,e,n,r,i){const{format:o,language:a,nan_format:s}=this,l=(()=>{switch(this.rounding){case"round":case"nearest":return Math.round;case"floor":case"rounddown":return Math.floor;case"ceil":case"roundup":return Math.ceil}})();return n=null==n||isNaN(n)?s:Aa.format(n,o,a,l),super.doFormat(t,e,n,r,i)}}yM=CM,CM.__name__="NumberFormatter",yM.define((({String:t})=>({format:[t,"0,0"],language:[t,"en"],rounding:[_n.PN,"round"]})));class SM extends HM{constructor(t){super(t)}doFormat(t,e,n,r,i){return n?he({class:this.icon}).outerHTML:""}}xM=SM,SM.__name__="BooleanFormatter",xM.define((({String:t})=>({icon:[t,"check"]})));class EM extends kM{constructor(t){super(t)}getFormat(){switch(this.format){case"ATOM":case"W3C":case"RFC-3339":case"ISO-8601":return"%Y-%m-%d";case"COOKIE":return"%a, %d %b %Y";case"RFC-850":return"%A, %d-%b-%y";case"RFC-1123":case"RFC-2822":return"%a, %e %b %Y";case"RSS":case"RFC-822":case"RFC-1036":return"%a, %e %b %y";case"TIMESTAMP":return;default:return this.format}}doFormat(t,e,n,r,i){const{nan_format:o}=this;let a;return a=null==(n=(0,f.Kg)(n)?parseInt(n,10):n)||isNaN(n)||-9223372036854776===n?o:Ma()(n,this.getFormat()),super.doFormat(t,e,a,r,i)}}wM=EM,EM.__name__="DateFormatter",wM.define((({String:t})=>({format:[t,"ISO-8601"]})));class VM extends HM{constructor(t){super(t)}doFormat(t,e,n,r,i){const{template:o}=this;return null==n?"":AM._.template(o)({...i,value:n})}}LM=VM,VM.__name__="HTMLTemplateFormatter",LM.define((({String:t})=>({template:[t,"<%= value %>"]})));var OM,PM,DM,NM=n(1449),RM=n(4295),IM=n(5967),jM=n(5915);class zM extends Sy{constructor(t){super(t)}}OM=zM,zM.__name__="TableWidget",OM.define((({Ref:t})=>({source:[t(pr),()=>new pr],view:[t(Ul),()=>new Ul]})));class BM extends qt{constructor(t){super(t)}toColumn(){return{id:y(),field:this.field,name:this.title??this.field,width:this.width,formatter:this.formatter.doFormat.bind(this.formatter),model:this.editor,editor:this.editor.default_view,sortable:this.sortable,defaultSortAsc:"ascending"==this.default_sort}}}PM=BM,BM.__name__="TableColumn",PM.define((({Boolean:t,Number:e,String:n,Nullable:r,Ref:i})=>({field:[n],title:[r(n),null],width:[e,300],formatter:[i(HM),()=>new kM],editor:[i(eM),()=>new rM],sortable:[t,!0],default_sort:[_n.FU,"ascending"],visible:[t,!0]})));const FM={fit_columns:"FCV",fit_viewport:"FVC",force_fit:"LFF",none:"NOA"};let $M=!1;class GM{constructor(t,e){this.init(t,e)}init(t,e){if($k in t.data)throw new Error(`special name ${$k} cannot be used as a data table column`);this.source=t,this.view=e,this.index=[...this.view.indices]}getLength(){return this.index.length}getItem(t){const e={};for(const n of(0,Q.HP)(this.source.data))e[n]=this.source.data[n][this.index[t]];return e[$k]=this.index[t],e}getField(t,e){return e==$k?this.index[t]:this.source.data[e][this.index[t]]}setField(t,e,n){const r=this.index[t];this.source.patch({[e]:[[r,n]]})}getRecords(){return(0,Rt.y1)(0,this.getLength()).map((t=>this.getItem(t)))}getItems(){return this.getRecords()}slice(t,e,n=1){return e=e??this.getLength(),(0,Rt.y1)(t,e,n).map((t=>this.getItem(t)))}sort(t){let e=t.map((t=>[t.sortCol.field,t.sortAsc?1:-1]));0==e.length&&(e=[[$k,1]]);const n=this.getRecords(),r=this.index.slice();this.index.sort(((t,i)=>{for(const[o,a]of e){const e=n[r.indexOf(t)][o],s=n[r.indexOf(i)][o];if(e!==s)return(0,f.Et)(e)&&(0,f.Et)(s)?a*(e-s||+isNaN(e)-+isNaN(s)):`${e}`>`${s}`?a:-a}return 0}))}}GM.__name__="TableDataProvider";class qM extends Cy{constructor(){super(...arguments),this._in_selection_update=!1,this._width=null}get data_source(){return this.model.properties.source}*children(){yield*super.children(),yield this.cds_view}async lazy_initialize(){await super.lazy_initialize(),this.cds_view=await $e(this.model.view,{parent:this})}remove(){this.cds_view.remove(),this.grid.destroy(),super.remove()}connect_signals(){super.connect_signals(),this.connect(this.model.change,(()=>this.render())),this.connect(this.model.source.streaming,(()=>this.updateGrid())),this.connect(this.model.source.patching,(()=>this.updateGrid())),this.connect(this.model.source.change,(()=>this.updateGrid())),this.connect(this.model.source.properties.data.change,(()=>this.updateGrid())),this.connect(this.model.source.selected.change,(()=>this.updateSelection())),this.connect(this.model.source.selected.properties.indices.change,(()=>this.updateSelection()));for(const t of this.model.columns)this.connect(t.change,(()=>{this.invalidate_layout(),this.render()}))}styles(){return[...super.styles(),'.slick-header.ui-state-default,.slick-headerrow.ui-state-default,.slick-footerrow.ui-state-default,.slick-top-panel-scroller.ui-state-default,.slick-group-header.ui-state-default{width:100%;overflow:auto;position:relative;border-left:0px !important;}.slick-header.ui-state-default{overflow:inherit;}.slick-header::-webkit-scrollbar,.slick-headerrow::-webkit-scrollbar,.slick-footerrow::-webkit-scrollbar{display:none;}.slick-header-columns,.slick-headerrow-columns,.slick-footerrow-columns,.slick-group-header-columns{position:relative;white-space:nowrap;cursor:default;overflow:hidden;}.slick-header-column.ui-state-default,.slick-group-header-column.ui-state-default{position:relative;display:inline-block;box-sizing:content-box !important;overflow:hidden;-o-text-overflow:ellipsis;text-overflow:ellipsis;height:16px;line-height:16px;margin:0;padding:4px;border-right:1px 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silver;border-left:0px;border-top:0px;border-bottom:0px;float:left;line-height:20px;vertical-align:middle;}.slick-headerrow-column.ui-state-default,.slick-footerrow-column.ui-state-default{padding:4px;}.slick-header-column-sorted{font-style:italic;}.slick-sort-indicator{display:inline-block;width:8px;height:5px;margin-left:4px;margin-top:6px;float:left;}.slick-sort-indicator-numbered{display:inline-block;width:8px;height:5px;margin-left:4px;margin-top:0;line-height:20px;float:left;font-family:Arial;font-style:normal;font-weight:bold;color:#6190CD;}.slick-sort-indicator-desc{background:url(images/sort-desc.gif);}.slick-sort-indicator-asc{background:url(images/sort-asc.gif);}.slick-resizable-handle{position:absolute;font-size:0.1px;display:block;cursor:col-resize;width:9px;right:-5px;top:0;height:100%;z-index:1;}.slick-sortable-placeholder{background:silver;}.grid-canvas{position:relative;outline:0;}.slick-row.ui-widget-content,.slick-row.ui-state-active{position:absolute;border:0px;width:100%;}.slick-cell,.slick-headerrow-column,.slick-footerrow-column{position:absolute;border:1px 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black;}.slick-pane{position:absolute;outline:0;overflow:hidden;width:100%;}.slick-pane-header{display:block;}.slick-header{overflow:hidden;position:relative;}.slick-headerrow{overflow:hidden;position:relative;}.slick-top-panel-scroller{overflow:hidden;position:relative;}.slick-top-panel{width:10000px;}.slick-viewport{position:relative;outline:0;width:100%;}.slick-header-columns{background:url(\'images/header-columns-bg.gif\') repeat-x center bottom;border-bottom:1px solid silver;}.slick-header-column{background:url(\'images/header-columns-bg.gif\') repeat-x center bottom;border-right:1px solid silver;}.slick-header-column:hover,.slick-header-column-active{background:white url(\'images/header-columns-over-bg.gif\') repeat-x center 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input[type="checkbox"]{margin-left:4px;margin-right:4px;}.bk-cell-special-defaults{border-right-color:silver;border-right-style:solid;background:#f5f5f5;}.bk-cell-select{border-right-color:silver;border-right-style:solid;background:#f5f5f5;}.slick-cell.bk-cell-index{border-right-color:silver;border-right-style:solid;background:#f5f5f5;text-align:right;background:#f0f0f0;color:#909090;}.bk-header-index .slick-column-name{float:right;}.slick-row.selected .bk-cell-index{background-color:transparent;}.slick-row.odd{background:#f0f0f0;}.slick-cell{padding-left:4px;padding-right:4px;border-right-color:transparent;border:0.25px solid transparent;}.slick-cell .bk{line-height:inherit;}.slick-cell.active{border-style:dashed;}.slick-cell.selected{background-color:#F0F8FF;}.slick-cell.editable{padding-left:0;padding-right:0;}.bk-cell-editor{display:contents;}.bk-cell-editor input,.bk-cell-editor select{width:100%;height:100%;border:0;margin:0;padding:0;outline:0;background:transparent;vertical-align:baseline;}.bk-cell-editor input{padding-left:4px;padding-right:4px;}.bk-cell-editor-completion{font-size:var(--data-table-font-size);}']}_after_resize(){super._after_resize(),this.grid.resizeCanvas(),this.updateLayout(!0,!1)}box_sizing(){const t=super.box_sizing();return"fit_viewport"===this.model.autosize_mode&&null!=this._width&&(t.width=this._width),t}updateLayout(t,e){const n=this.autosize;n===FM.fit_columns||n===FM.force_fit?(t||this.grid.resizeCanvas(),this.grid.autosizeColumns()):t&&e&&n===FM.fit_viewport&&this.invalidate_layout()}updateGrid(){if(this.cds_view.compute_indices(),this.data.init(this.model.source,this.model.view),this.model.sortable){const t=this.grid.getColumns(),e=this.grid.getSortColumns().map((e=>({sortCol:{field:t[this.grid.getColumnIndex(e.columnId)].field},sortAsc:e.sortAsc})));this.data.sort(e)}this.grid.invalidate(),this.updateLayout(!0,!0)}updateSelection(){if(!1===this.model.selectable||this._in_selection_update)return;const{selected:t}=this.model.source,e=t.indices.map((t=>this.data.index.indexOf(t))).sort();this._in_selection_update=!0;try{this.grid.setSelectedRows(e)}finally{this._in_selection_update=!1}const n=this.grid.getViewport(),r=this.model.get_scroll_index(n,e);null!=r&&this.grid.scrollRowToTop(r)}newIndexColumn(){return{id:y(),name:this.model.index_header,field:$k,width:this.model.index_width,behavior:"select",cannotTriggerInsert:!0,resizable:!1,selectable:!1,sortable:!0,cssClass:"bk-cell-index",headerCssClass:"bk-header-index"}}get autosize(){let t;return t=!0===this.model.fit_columns?FM.force_fit:!1===this.model.fit_columns?FM.none:FM[this.model.autosize_mode],t}render(){super.render(),this.wrapper_el=oe({class:"bk-data-table"}),this.shadow_el.appendChild(this.wrapper_el),this._render()}_render(){const t=this.model.columns.filter((t=>t.visible)).map((t=>({...t.toColumn(),parent:this})));let e=null;if("checkbox"==this.model.selectable&&(e=new RM.CheckboxSelectColumn({cssClass:"bk-cell-select"}),t.unshift(e.getColumnDefinition())),null!=this.model.index_position){const e=this.model.index_position,n=this.newIndexColumn();-1==e?t.push(n):e<-1?t.splice(e+1,0,n):t.splice(e,0,n)}let{reorderable:n}=this.model;!n||"undefined"!=typeof $&&void 0!==$.fn&&"sortable"in $.fn||($M||(ot.vF.warn("jquery-ui is required to enable DataTable.reorderable"),$M=!0),n=!1);let r=-1,i=!1;const{frozen_rows:o,frozen_columns:a}=this.model,s=null==a?-1:a-1;null!=o&&(i=o<0,r=Math.abs(o));const l={enableCellNavigation:!1!==this.model.selectable,enableColumnReorder:n,autosizeColsMode:this.autosize,multiColumnSort:this.model.sortable,editable:this.model.editable,autoEdit:this.model.auto_edit,autoHeight:!1,rowHeight:this.model.row_height,frozenColumn:s,frozenRow:r,frozenBottom:i},c=(0,f.Z3)(this.grid);if(this.data=new GM(this.model.source,this.model.view),this.grid=new jM.Grid(this.wrapper_el,this.data,t,l),this.autosize==FM.fit_viewport){this.grid.autosizeColumns();let e=0;for(const n of t)e+=n.width??0;this._width=Math.ceil(e)}if(this.grid.onSort.subscribe(((t,e)=>{if(!this.model.sortable)return;const n=e.sortCols;null!=n&&(this.data.sort(n),this.grid.invalidate(),this.updateSelection(),this.grid.render(),this.model.header_row||this._hide_header(),this.model.update_sort_columns(n))})),!1!==this.model.selectable){this.grid.setSelectionModel(new NM.RowSelectionModel({selectActiveRow:null==e})),null!=e&&this.grid.registerPlugin(e);const t={dataItemColumnValueExtractor(t,e){let n=t[e.field];return(0,f.Kg)(n)&&(n=n.replace(/\n/g,"\\n")),n},includeHeaderWhenCopying:!1};this.grid.registerPlugin(new IM.CellExternalCopyManager(t)),this.grid.onSelectedRowsChanged.subscribe(((t,e)=>{this._in_selection_update||(this.model.source.selected.indices=e.rows.map((t=>this.data.index[t])))})),this.updateSelection(),this.model.header_row||this._hide_header()}c&&this.updateLayout(c,!1)}_hide_header(){for(const t of this.shadow_el.querySelectorAll(".slick-header-columns"))t.style.height="0px";this.grid.resizeCanvas()}}qM.__name__="DataTableView";class UM extends zM{constructor(t){super(t),this._sort_columns=[]}get sort_columns(){return this._sort_columns}update_sort_columns(t){this._sort_columns=t.map((({sortCol:t,sortAsc:e})=>({field:t.field,sortAsc:e})))}get_scroll_index(t,e){return this.scroll_to_selection&&0!=e.length?(0,Rt.zN)(e,(e=>t.top<=e&&e<=t.bottom))?null:Math.max(0,Math.min(...e)-1):null}}var WM;DM=UM,UM.__name__="DataTable",DM.prototype.default_view=qM,DM.define((({Array:t,Boolean:e,Int:n,Ref:r,String:i,Enum:o,Or:a,Nullable:s})=>({autosize_mode:[o("fit_columns","fit_viewport","none","force_fit"),"force_fit"],auto_edit:[e,!1],columns:[t(r(BM)),[]],fit_columns:[s(e),null],frozen_columns:[s(n),null],frozen_rows:[s(n),null],sortable:[e,!0],reorderable:[e,!0],editable:[e,!1],selectable:[a(e,o("checkbox")),!0],index_position:[s(n),0],index_header:[i,"#"],index_width:[n,40],scroll_to_selection:[e,!0],header_row:[e,!0],row_height:[n,25]}))),DM.override({width:600,height:400});const{Avg:ZM,Min:XM,Max:KM,Sum:YM}=jM.Data.Aggregators;class JM extends qt{constructor(t){super(t)}}WM=JM,JM.__name__="RowAggregator",WM.define((({String:t})=>({field_:[t,""]})));const tC=new ZM;class eC extends JM{constructor(){super(...arguments),this.key="avg",this.init=tC.init,this.accumulate=tC.accumulate,this.storeResult=tC.storeResult}}eC.__name__="AvgAggregator";const nC=new XM;class rC extends JM{constructor(){super(...arguments),this.key="min",this.init=nC.init,this.accumulate=nC.accumulate,this.storeResult=nC.storeResult}}rC.__name__="MinAggregator";const iC=new KM;class oC extends JM{constructor(){super(...arguments),this.key="max",this.init=iC.init,this.accumulate=iC.accumulate,this.storeResult=iC.storeResult}}oC.__name__="MaxAggregator";const aC=new YM;class sC extends JM{constructor(){super(...arguments),this.key="sum",this.init=aC.init,this.accumulate=aC.accumulate,this.storeResult=aC.storeResult}}var lC,cC;function uC(t,e,n,r,i){const{collapsed:o,level:a,title:s}=i,l=ae({class:"slick-group-toggle "+(o?"collapsed":"expanded"),style:{"margin-left":15*a+"px"}}),c=ae({class:"slick-group-title",level:a},s);return`${l.outerHTML}${c.outerHTML}`}function dC(t,e){const n=this.getDataItem(e.row);n instanceof jM.Group&&t.target.classList.contains("slick-group-toggle")&&(n.collapsed?this.getData().expandGroup(n.groupingKey):this.getData().collapseGroup(n.groupingKey),t.stopImmediatePropagation(),t.preventDefault(),this.invalidate(),this.render())}sC.__name__="SumAggregator";class hC extends qt{constructor(t){super(t)}get comparer(){return(t,e)=>t.value===e.value?0:t.value>e.value?1:-1}}lC=hC,hC.__name__="GroupingInfo",lC.define((({Boolean:t,String:e,Array:n,Ref:r})=>({getter:[e,""],aggregators:[n(r(JM)),[]],collapsed:[t,!1]})));class pC extends GM{constructor(t,e,n,r){super(t,e),this.columns=n,this.groupingInfos=[],this.groupingDelimiter=":|:",this.target=r}setGrouping(t){this.groupingInfos=t,this.toggledGroupsByLevel=t.map((()=>({}))),this.refresh()}extractGroups(t,e){const n=[],r=new Map,i=e?e.level+1:0,{comparer:o,getter:a}=this.groupingInfos[i];return t.forEach((t=>{const o=this.source.data[a][t];let s=r.get(o);if(!s){const t=e?`${e.groupingKey}${this.groupingDelimiter}${o}`:`${o}`;s=Object.assign(new jM.Group,{value:o,level:i,groupingKey:t}),n.push(s),r.set(o,s)}s.rows.push(t)})),i<this.groupingInfos.length-1&&n.forEach((t=>{t.groups=this.extractGroups(t.rows,t)})),n.sort(o),n}calculateTotals(t,e){const n={avg:{},max:{},min:{},sum:{}},{source:{data:r}}=this,i=Object.keys(r),o=t.rows.map((t=>i.reduce(((e,n)=>({...e,[n]:r[n][t]})),{})));return e.forEach((t=>{t.init(),o.forEach((e=>t.accumulate(e))),t.storeResult(n)})),n}addTotals(t,e=0){const{aggregators:n,collapsed:r}=this.groupingInfos[e],i=this.toggledGroupsByLevel[e];t.forEach((t=>{(0,f.bl)(t.groups)||this.addTotals(t.groups,e+1),n.length&&t.rows.length&&(t.totals=this.calculateTotals(t,n)),t.collapsed=r!==i[t.groupingKey],t.title=t.value?`${t.value}`:""}))}flattenedGroupedRows(t,e=0){const n=[];return t.forEach((t=>{if(n.push(t),!t.collapsed){const r=(0,f.bl)(t.groups)?t.rows:this.flattenedGroupedRows(t.groups,e+1);n.push(...r)}})),n}refresh(){const t=this.extractGroups([...this.view.indices]),e=this.source.data[this.columns[0].field];t.length&&(this.addTotals(t),this.rows=this.flattenedGroupedRows(t),this.target.data={row_indices:this.rows.map((t=>t instanceof jM.Group?t.rows:t)),labels:this.rows.map((t=>t instanceof jM.Group?t.title:e[t]))})}getLength(){return this.rows.length}getItem(t){const e=this.rows[t],{source:{data:n}}=this;return e instanceof jM.Group?e:Object.keys(n).reduce(((t,r)=>({...t,[r]:n[r][e]})),{[$k]:e})}getItemMetadata(t){const e=this.rows[t],n=this.columns.slice(1),r=e instanceof jM.Group?this.groupingInfos[e.level].aggregators:[];return e instanceof jM.Group?{selectable:!1,focusable:!1,cssClasses:"slick-group",columns:[{formatter:uC},...n.map((function(t){const{field:e,formatter:n}=t,i=r.find((({field_:t})=>t===e));if(i){const{key:t}=i;return{formatter:(r,i,o,a,s)=>n?n(r,i,s.totals[t][e],a,s):""}}return{}}))]}:{}}collapseGroup(t){const e=t.split(this.groupingDelimiter).length-1;this.toggledGroupsByLevel[e][t]=!this.groupingInfos[e].collapsed,this.refresh()}expandGroup(t){const e=t.split(this.groupingDelimiter).length-1;this.toggledGroupsByLevel[e][t]=this.groupingInfos[e].collapsed,this.refresh()}}pC.__name__="DataCubeProvider";class fC extends qM{_render(){const t={enableCellNavigation:!1!==this.model.selectable,enableColumnReorder:!1,autosizeColsMode:this.autosize,multiColumnSort:!1,editable:this.model.editable,autoEdit:this.model.auto_edit,rowHeight:this.model.row_height},e=this.model.columns.map((t=>t.toColumn()));var n,r;e[0].formatter=(n=e[0].formatter,r=this.model.grouping.length,(t,e,i,o,a)=>{const s=ae({class:"slick-group-toggle",style:{"margin-left":15*(r??0)+"px"}}),l=n?n(t,e,i,o,a):`${i}`;return`${s.outerHTML}${l&&l.replace(/^<div/,"<span").replace(/div>$/,"span>")}`}),delete e[0].editor,this.data=new pC(this.model.source,this.model.view,e,this.model.target),this.data.setGrouping(this.model.grouping),this.el.style.width=`${this.model.width}px`,this.grid=new jM.Grid(this.wrapper_el,this.data,e,t),this.grid.onClick.subscribe(dC)}}fC.__name__="DataCubeView";class QC extends UM{constructor(t){super(t)}}cC=QC,QC.__name__="DataCube",cC.prototype.default_view=fC,cC.define((({Array:t,Ref:e})=>({grouping:[t(e(hC)),[]],target:[e(pr)]}))),rt(h),n(9469);class TC{container_id=null;container=null;static plt=c;static scale_functions={linear:An,log:Hn};source=null;y_error_bar;x_error_bar;columns;data_table;static supported_tool_array=["pan","box_zoom","wheel_zoom","hover","crosshair","reset","save","lasso_select","poly_select","tap","examine,","undo","redo"];static default_tool_array=["pan","box_zoom","wheel_zoom","hover","crosshair","reset","save"];static default_tool_string="pan,box_zoom,wheel_zoom,hover,crosshair,reset,save";tool_array=[];tool_string="";has_data_table=!1;constructor(t="#visualization-container"){this.container_id=t}setup(){this._setContainer()}_setContainer(){this.container=document.getElementById(this.container_id)}initializeSettings(t,e,n,r,i=null,o=null){if(this.setupSource(t),i)this.setupPlot(r,t.y_low,t.y_up);else if(o){let e=[],n=[],i=[],a=[];null!==o.x?(null!==o.x.lower_bound?e.push(o.x.lower_bound):e=t.x,null!==o.x.upper_bound?n.push(o.x.upper_bound):n=t.x):(e=t.x,n=t.x),null!==o.y?(null!==o.y.lower_bound?i.push(o.y.lower_bound):i=t.y,null!==o.y.upper_bound?a.push(o.y.upper_bound):a=t.y):(i=t.y,a=t.y),this.setupPlot(r,i,a,e,n)}else this.setupPlot(r,t.y,t.y);this.setupData(),this.setupScales(n),this.setupLabels(e),i&&this.setupErrorBars()}initializeGraph(){this.has_data_table?TC.plt.show(new iT({children:[p,data_table]}),"#graph-container"):TC.plt.show(this.plot,this.container_id)}setupPlot(t,e,n,r=null,i=null){this.plot=TC.plt.figure({title:t,tools:TC.default_tool_string,width:800,height:600})}setupSource(t){this.source=new pr({data:t})}setupData(){this.plot.circle({field:"x"},{field:"y"},4,{source:this.source,fill_color:"navy",line_color:null})}setupErrorBars(){this.y_error_bar=new bh({dimension:"height",source:this.source,base:{field:"x"},lower:{field:"y_low"},upper:{field:"y_up"},line_color:"navy",lower_head:null,upper_head:null}),this.x_error_bar=new bh({dimension:"width",source:this.source,base:{field:"y"},lower:{field:"x_low"},upper:{field:"x_up"},line_color:"navy",lower_head:null,upper_head:null}),this.plot.add_layout(this.y_error_bar),this.plot.add_layout(this.x_error_bar)}setupScales(t){t&&(this.plot.x_scale=new TC.scale_functions[t.x],this.plot.y_scale=new TC.scale_functions[t.y])}setupLabels(t){this.plot.xaxis.axis_label=t.x,this.plot.yaxis.axis_label=t.y}setupColumns(t,e){this.columns=[new BM({field:"x",title:t.x}),new BM({field:"y",title:t.y})]}setupDataTable(){this.data_table=new UM({source:this.source,columns:this.columns,width:800})}createToolArray(t){this.tool_array=t}addToolToToolArray(t){!this.tool_array.includes(t)&&TC.supported_tool_array.includes(t)&&this.tool_array.push(t)}removeToolFromToolArray(t){this.tool_array=this.tool_array.filter((e=>e!==t))}setToolStringFromToolArray(){this.tool_string=this.tool_array.join(",")}}},7508:(t,e,n)=>{"use strict";function r(t,e){let n,r;if(void 0===e)for(const e of t)null!=e&&(void 0===n?e>=e&&(n=r=e):(n>e&&(n=e),r<e&&(r=e)));else{let i=-1;for(let o of t)null!=(o=e(o,++i,t))&&(void 0===n?o>=o&&(n=r=o):(n>o&&(n=o),r<o&&(r=o)))}return[n,r]}function i(t){return t}n.d(e,{g:()=>ii});var o=1e-6;function a(t){return"translate("+t+",0)"}function s(t){return"translate(0,"+t+")"}function 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default_axis_tick_format=".2f";constructor(t="visualization-container",e=null){this.container_id=t,this.dataset=e,this._updateChart=this._updateChart.bind(this),this.initialized=!1}setup(){this._setContainer()}_setContainer(){try{this.container=document.getElementById(this.container_id)}catch(t){console.log(t)}}initializeSettings(t,e,n=ii.default_scales,r=null,i=!1,o=null){let a=!1;try{if(this.dataset=t,this.x_axis_data_col=e.x,this.y_axis_data_col=e.y,this.x_scale_type=n.x,this.y_scale_type=n.y,r?(this.has_error_bars=!0,this.error_bars=r,this.x_axis_data_col_error_bar=e.x.value,this.y_axis_data_col_error_bar=e.y.value):this.has_error_bars=!1,o){this.has_multiple_plots=!0,this.additional_plots=[];let t=[];o.forEach((function(e){t.push(e)})),this.additional_plots=t}this.has_line=i,a=!0}catch(t){console.log("Error during graph settings process")}return a}initializeGraph(){try{this._setSVGContainer(),this._setXScale(),this._setYScale(),this._setXAxis(),this._setXAxisLabel(),this._setYAxis(),this._setYAxisLabel(),this._setDataPlot(),this._setZoomBehavior(),this.has_error_bars&&this._setErrorBars(this.error_bars),this.has_line&&this._setAxisLine(),this.has_multiple_plots&&this._setAdditionalPlots(),this.initialized=!0}catch(t){console.log("Error during graph initialization"),this.initialized=!1}return this.initialized}_setSVGContainer(){let t=this._getFullWidth(),e=this._getFullHeight();this.svg=wr(this.container).append("svg").attr("width",t).attr("height",e).append("g").attr("transform","translate("+this.margin.left+","+this.margin.top+")")}_setXScale(){this.x_scale=ii.scale_functions[this.x_scale_type]().domain(r(this.dataset,(t=>t[this.x_axis_data_col]))).range([0,this.width])}_setYScale(){this.y_scale=ii.scale_functions[this.y_scale_type]().domain(r(this.dataset,(t=>t[this.y_axis_data_col]))).range([this.height,0])}_setXAxis(t=ii.default_axis_tick_format){this.x_axis=this.svg.append("g").attr("id","x").attr("transform","translate(0,"+this.height+")").call(h(this.x_scale).tickFormat(Rn(t))).call((t=>t.selectAll(".tick line").clone().attr("class","tick-line").attr("y2",-this.height).attr("stroke-opacity",.2)))}_setYAxis(t=ii.default_axis_tick_format){this.y_axis=this.svg.append("g").attr("id","y").call(p(this.y_scale).tickFormat(Rn(t))).call((t=>t.selectAll(".tick 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e(t[r])})).attr("r",4).style("fill","transparent").style("stroke","black").style("opacity",1)}_setAdditionalPlots(){let t;for(let e=0;this.additional_plots.length,e++;)t=this.additional_plots[e]}_setErrorBars(t){if(this.error_bars=t,t.y){let e=Dr().x((t=>this.x_scale(t[this.x_axis_data_col]))).y((t=>this.y_scale(t.bound)));t.y.forEach((t=>{wr("#data-plot").append("path").attr("class","error-bar-x").attr("fill","none").attr("stroke","steelblue").attr("stroke-width",1.5).attr("d",e(t))}))}if(t.x){let e=Dr().x((t=>this.x_scale(t.bound))).y((t=>this.y_scale(t[this.y_axis_data_col])));t.x.forEach((t=>{wr("#data-plot").append("path").attr("class","error-bar-x").attr("fill","none").attr("stroke","steelblue").attr("stroke-width",1.5).attr("d",e(t))}))}}_setAxisLine(){let 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arguments.length?(l[0]=+t[0],l[1]=+t[1],Q):[l[0],l[1]]},Q.translateExtent=function(t){return arguments.length?(c[0][0]=+t[0][0],c[1][0]=+t[1][0],c[0][1]=+t[0][1],c[1][1]=+t[1][1],Q):[[c[0][0],c[0][1]],[c[1][0],c[1][1]]]},Q.constrain=function(t){return arguments.length?(o=t,Q):o},Q.duration=function(t){return arguments.length?(u=+t,Q):u},Q.interpolate=function(t){return arguments.length?(d=t,Q):d},Q.on=function(){var t=h.on.apply(h,arguments);return t===h?Q:t},Q.clickDistance=function(t){return arguments.length?(p=(t=+t)*t,Q):Math.sqrt(p)},Q.tapDistance=function(t){return arguments.length?(f=+t,Q):f},Q}().scaleExtent([.5,20]).extent([[0,0],[this.width,this.height]]).on("zoom",this._updateChart),this.zoom_rect=this.svg.append("rect").attr("width",this.width).attr("height",this.height).style("fill","none").style("pointer-events","all").attr("transform","translate("+this.margin.left+","+this.margin.top+")").call(this.zoom)}_updateChart(t){let e=t.transform.rescaleX(this.x_scale),n=t.transform.rescaleY(this.y_scale);this.x_axis.call(h(e).tickFormat(Rn(ii.default_axis_tick_format))),this.y_axis.call(p(n).tickFormat(Rn(ii.default_axis_tick_format))),this.svg.selectAll(".tick-line").remove(),this.svg.selectAll("#y-label").remove(),this.svg.selectAll("#x-label").remove(),this.svg.selectAll(".error-bar-x").remove(),this.x_axis.selectAll(".tick line").clone().attr("class","tick-line").attr("y2",-this.height).attr("stroke-opacity",.2),this.y_axis.selectAll(".tick line").clone().attr("class","tick-line").attr("x2",this.width).attr("stroke-opacity",.2),this._setXAxisLabel(),this._setYAxisLabel();let r=this.x_axis_data_col,i=this.y_axis_data_col;if(this.svg.selectAll("circle").data(this.dataset).transition().duration(150).attr("cx",(function(t){return e(t[r])})).attr("cy",(function(t){return n(t[i])})),this.has_line&&(this.svg.selectAll("path").remove(),this._setAxisLine()),this.has_error_bars){if(this.error_bars.y){let t=Dr().x((t=>e(t[this.x_axis_data_col]))).y((t=>n(t.bound)));this.error_bars.y.forEach((e=>{wr("#data-plot").append("path").attr("class","error-bar-x").attr("fill","none").attr("stroke","steelblue").attr("stroke-width",1.5).attr("d",t(e))}))}if(this.error_bars.x){let t=Dr().x((t=>e(t.bound))).y((t=>n(t[this.y_axis_data_col])));this.error_bars.x.forEach((e=>{wr("#data-plot").append("path").attr("class","error-bar-x").attr("fill","none").attr("stroke","steelblue").attr("stroke-width",1.5).attr("d",t(e))}))}}}_getFullWidth(){return this.width+this.margin.left+this.margin.right}_getFullHeight(){return this.height+this.margin.top+this.margin.bottom}}},2976:(t,e,n)=>{"use strict";n.d(e,{d:()=>s});var r=n(8533),i=n(8845),o=n(1539),a=(n(8326),n(9319));class s{static container_id="visualization-container";static library="bokeh";static title={"light-curve":"Light curve",spectrum:"spectrum"};static 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__nested_webpack_require_4077833__.d(e,{a:e}),e},__nested_webpack_require_4077833__.d=(t,e)=>{for(var n in e)__nested_webpack_require_4077833__.o(e,n)&&!__nested_webpack_require_4077833__.o(t,n)&&Object.defineProperty(t,n,{enumerable:!0,get:e[n]})},__nested_webpack_require_4077833__.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),__nested_webpack_require_4077833__.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},__nested_webpack_require_4077833__.b=document.baseURI||self.location.href,__nested_webpack_require_4077833__.nc=void 0;var __nested_webpack_exports__={};return(()=>{"use strict";__nested_webpack_require_4077833__.r(__nested_webpack_exports__),__nested_webpack_require_4077833__.d(__nested_webpack_exports__,{init:()=>$});var t=__nested_webpack_require_4077833__(7333),e=__nested_webpack_require_4077833__(2976),n=__nested_webpack_require_4077833__(6518),r=__nested_webpack_require_4077833__(8326),i=__nested_webpack_require_4077833__(1539),o=__nested_webpack_require_4077833__(3152),a=__nested_webpack_require_4077833__(1142),s=__nested_webpack_require_4077833__(5764);class l extends HTMLElement{container_id="fits-settings-container";select_hdu_id="select-hdu-file";table_header_id="table-header-data";table_data_id="table-data";file=null;is_current=!1;add_to_plot_btn_id="add-to-plot";remove_from_plot_btn_id="remove-from-plot";save_btn_id="save-file-settings";product_type_select_id="product-type-select";arf_file_select_id="arf-file-select";rmf_file_select_id="rmf-file-select";container='<div id="fits-settings-container" class="full-width-column" style="grid-column: 1 / span 2;"><div class="card"><div class="card-body"></div></div></div>';select_hdu_file='<select id="select-hdu-file" class="form-select"></select>';inner_container='<div class="inner-row"></div>';header_column='<div class="left-column"><div class="card-header">Header</div><div class="card-body"><div id="header-hdu-file"></div></div>';table_header='<table id="table-header-data" class="table table-striped">    <thead>    <tr>        <th scope="col">#</th>        <th scope="col">Name</th>        <th scope="col">Value</th>        <th scope="col">Comment</th>    </tr>    </thead>    <tbody class="table-group-divider">    </tbody></table>';data_column='<div class="right-column"><div class="card-header">Data</div><div class="card-body">   <div id="data-hdu-file">   </div></div>';table_data='<table id="table-data" class="table table-striped">    <thead>       <tr>       </tr>    </thead>    <tbody class="table-group-divider">    </tbody></table>';btn_save_settings='<button class="btn btn-success" id="save-file-settings">Save changes</button>';btn_add_to_plot='<button class="btn btn-primary" id="add-to-plot">Add to plot</button>;';btn_remove_from_plot='<button class="btn btn-danger" id="remove-from-plot">Remove from plot</button>';constructor(t=null,e=null){super(),this.file=t,this.is_current=e,this.innerHTML='<div class="full-width-column" style="grid-column: 1 / span 2;">\n                            <div class="card">\n                                <div class="card-header">File settings</div>\n                                <div class="card-body">\n <label for="product-type-select">Product type :</label> <select id="product-type-select" class="form-select"><option selected="selected" value="none">None</option><option value="lightcurve">Light Curve</option><option value="spectrum">Spectrum</option></select>  <label for="product-type-select" class="spectrum-settings">ARF file : </label> <select id="arf-file-select" class="form-select spectrum-settings"></select> <label for="product-type-select" class="spectrum-settings">RMF file :</label> <select id="rmf-file-select" class="form-select spectrum-settings"></select> <label for="select-hdu-file">HDU :</label>                                    <select id="select-hdu-file" class="form-select">\n\n                                    </select>\n\n                                    <div class="inner-row">\n                                        <div class="left-column">\n                                            <div class="card">\n                                                <div class="card-header">Header</div>\n                                                <div class="card-body">\n                                                    <div id="header-hdu-file" class="file-data-container">\n                                                        <table id="table-header-data" class="table table-striped">\n                                                            <thead>\n                                                            <tr>\n                                                                <th scope="col">#</th>\n                                                                <th scope="col">Name</th>\n                                                                <th scope="col">Value</th>\n                                                                <th scope="col">Comment</th>\n                                                            </tr>\n                                                            </thead>\n                                                            <tbody class="table-group-divider">\n\n                                                            </tbody>\n                                                        </table>\n                                                    </div>\n                                                </div>\n                                            </div>\n                                        </div>\n                                        <div class="right-column">\n                                            <div class="card">\n                                                <div class="card-header">Data</div>\n                                                <div class="card-body">\n                                                    <div id="data-hdu-file" class="file-data-container">\n<table id="table-data" class="table table-striped">    <thead>       <tr>       </tr>    </thead>    <tbody class="table-group-divider">    </tbody></table>                                                    </div>\n                                                </div>\n                                            </div>\n                                        </div>\n                                    </div>\n\n                                    <button class="btn btn-success" id="save-file-settings">Save changes</button>\n                                    <button class="btn btn-primary" id="add-to-plot">Add to plot</button>\n                                    <button class="btn btn-danger" id="remove-from-plot">Remove from plot</button>\n                                </div>\n                            </div>\n                        </div>'}setupComponent(){this.setHDUSelect(),this.setupActionButtons(),this.setProductSettings();let t=document.getElementById(this.select_hdu_id).value;this.setTables(t),this.setupInnerElementListeners()}setHDUSelect(){let t=document.getElementById(this.select_hdu_id);t.innerHTML="";let e=r.H.getFITSReaderWrapper();e.setFile(this.file.file);let n=e.getHDUs(),i=[];n.forEach((t=>{let e=document.createElement("option");e.value=t.index,e.text=t.name+" "+t.extname,i.push(e)})),i.forEach((e=>{t.add(e)}))}setupInnerElementListeners(){this.setHDUSelectListener(),this.setSaveButtonListener(),this.setProductTypeSelectListener(),this.setARFFileSelectListener(),this.setRMFFileSelectListener()}setupActionButtons(){let t=document.getElementById(this.add_to_plot_btn_id),e=document.getElementById(this.remove_from_plot_btn_id);this.is_current?(t.style.display="none",e.style.display="initial"):(t.style.display="initial",e.style.display="none"),t.addEventListener("click",(t=>{o.W.addToCurrentFiles(this.file),this.is_current=!0;let e=new a.o;try{e.dispatchToSubscribers()}catch(t){console.log("No subsribers for event : "+a.o.name)}})),e.addEventListener("click",(t=>{o.W.removeFromCurrentFiles(this.file.id),this.is_current=!1;let e=new a.o;try{e.dispatchToSubscribers()}catch(t){console.log("No subscribers for specified event : "+a.o.name)}}))}setProductSettings(){let t=null,e=null,n=null;this.file.product_type&&(t=this.file.product_type),this.file.rmf_id&&(e=this.file.rmf_id),this.file.arf_id&&(n=this.file.arf_id),this.setProductTypeSelect(t),this.setRMFFileSelect(e),this.setARFFileSelect(n)}setTables(t){this.resetTables();let e=document.getElementById(this.table_header_id),n=document.getElementById(this.table_data_id),i=r.H.getFITSReaderWrapper();i.setFile(this.file.file);let o=i.getHeaderCardsValueFromHDU(t),a=e.querySelector("tbody");o.forEach((t=>{let e=a.insertRow(),n=e.insertCell(0),r=e.insertCell(1),i=e.insertCell(2),o=e.insertCell(3);n.textContent=t.index,r.textContent=t.card_name,i.textContent=t.value,o.textContent=t.comment}));try{let e=i.getColumnsNameFromHDU(t),r=i.getColumnsJSONDataFromHDU(t),o=n.tHead.insertRow();a=n.querySelector("tbody"),e.forEach((t=>{let e=document.createElement("th");e.textContent=t,o.appendChild(e)})),r.forEach((t=>{const e=a.insertRow();for(let n in t)Object.hasOwnProperty.call(t,n)&&(e.insertCell().textContent=t[n])}))}catch(t){console.log("HDU not tabular")}}resetTables(){let t=document.getElementById(this.table_header_id),e=document.getElementById(this.table_data_id),n=t.querySelector("tbody");n.innerHTML="",n=e.querySelector("tbody");let r=e.querySelector("thead");n.innerHTML="",r.innerHTML="<tr></tr>"}setHDUSelectListener(){document.getElementById(this.select_hdu_id).addEventListener("change",(t=>{this.setTables(t.target.value)}))}setSaveButtonListener(){document.getElementById(this.save_btn_id).addEventListener("click",(t=>{if("spectrum"===document.getElementById(this.product_type_select_id).value){let t=document.getElementById(this.rmf_file_select_id),e=document.getElementById(this.arf_file_select_id),n=t.value,r=e.value;o.W.setFileMetadata(this.file.id,[{rmf_file:n},{arf_file:r},{product_type:"spectrum"}]),alert("File parameters have been set")}}))}setProductTypeSelect(t=null){let e=document.getElementById(this.product_type_select_id);t?(e.value=t,"spectrum"===e.value?this.setProductSettingsVisibility("spectrum"):"lightcurve"===e.value?this.setProductSettingsVisibility("lightcurve"):this.setProductSettingsVisibility()):e.value="none"}setProductTypeSelectListener(){let t=document.getElementById(this.product_type_select_id);t.addEventListener("change",(e=>{"spectrum"===t.value?this.setProductSettingsVisibility("spectrum"):"lightcurve"===t.value?this.setProductSettingsVisibility("lightcurve"):this.setProductSettingsVisibility()}))}setRMFFileSelect(t=null){let e=document.getElementById(this.rmf_file_select_id);this.getFilesOptionsList().forEach((t=>{e.appendChild(t)})),e.value=t||"none"}setRMFFileSelectListener(){document.getElementById(this.rmf_file_select_id).addEventListener("change",(t=>{}))}setARFFileSelect(t=null){let e=document.getElementById(this.arf_file_select_id);this.getFilesOptionsList().forEach((t=>{e.appendChild(t)})),e.value=t||"none"}setARFFileSelectListener(){document.getElementById(this.arf_file_select_id).addEventListener("change",(t=>{}))}setProductSettingsVisibility(t=null){let e=document.getElementById(this.rmf_file_select_id),n=document.getElementById(this.arf_file_select_id);e.style.display="none",n.style.display="none";let r=document.getElementsByClassName("spectrum-settings");for(let t=0;t<r.length;t++)r[t].style.display="none";if(t&&"spectrum"===t){e.style.display="block",n.style.display="block";for(let t=0;t<r.length;t++)r[t].style.display="block"}}resetContainerForCurrentFile(){this.setupComponent()}getFilesOptionsList(){let t=[],e=o.W.getAllFiles(),n=document.createElement("option");return n.setAttribute("selected","selected"),n.value="none",n.text="None",t.push(n),e.forEach((e=>{n=document.createElement("option"),n.value=e.id,n.text=e.file_name,t.push(n)})),t}}class c extends HTMLElement{container_id;container;content='<div id="visualization-container"></div>';constructor(t="visualization-container"){super(),this.innerHTML=this.content,this.container_id=t}setup(){this._setContainer()}_setContainer(){this.container=document.getElementById(this.container_id)}resetContainer(){this.container.innerHTML=""}}class u extends HTMLElement{file=null;is_current=null;constructor(t,e){super(),this.file=t,this.is_current=e}}class d{static defaultOptions={bubbles:!0,composed:!0};static name="arithmetic-column-change";static main_root_id="jsvis-main";static main_root_element=null;event=null;constructor(t={},e={}){this.detail={...t},this.options={...d.defaultOptions,...e},this.event=new CustomEvent(d.name,{detail:this.detail,...this.options})}dispatchToTarget(t){t.dispatchEvent(this.event)}dispatchToMainRoot(){null===d.main_root_element&&(d.main_root_element=document.getElementById(d.main_root_id)),document.dispatchEvent(this.event)}dispatchToSubscribers(){let t=s.D.getRegistryContainer().getEventSubscribersRegistry().getSubscribersForEvent(d.name),e=null;t.forEach((t=>{e=document.getElementById(t),e.dispatchEvent(this.event)}))}}class h{static columns=[];static column_counter=0;constructor(){}static getAvailableColumnsList(){return h.columns=h.columns.filter((t=>void 0!==t)),h.columns}static addToAvailableColumns(t){let e={...t,id:h.column_counter};return h.columns.push(e),h.column_counter++,e}static removeFromAvailableColumns(t){h.columns=h.columns.filter((e=>e.id!==parseInt(t))),h.sendRegistryChangeEvent()}static getColumnById(t){let e=null;return e=h.columns.filter((e=>e.id===parseInt(t))),e}static sendRegistryChangeEvent(){(new d).dispatchToSubscribers()}}class p extends HTMLElement{static column_display_id="column-display-list";static column_create_button_id="column-edit-button";static column_main_input_id="column-main-input";static column_list_id="column-input-list";static input_expression="input-expression";static button_commands=["C","<--","--\x3e","V"];column_display="<ul id='column-display-list'></ul>";column_create_button="<button id='column-edit-button' class='btn btn-primary'>Create column</button>";column_main_input="<div id='column-main-input'><div id='input-display'><input id='input-expression' type='text'></div><div id='input-container' 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id='column-input-list'></ul></div></div></div>";display_formula="";inner_formula="";constructor(){super(),this.innerHTML=this.column_display+this.column_main_input+this.column_create_button}setup(){this._setupEventHandlers(),this._setupListeners()}_setupListeners(){this._setupInnerElementsListeners(),this._setupExternalListeners()}_setupEventHandlers(){this.handleFileChangeEvent=this.handleFileChangeEvent.bind(this)}_setupExternalListeners(){this.addEventListener("file-registry-change",this.handleFileChangeEvent)}_setupInnerElementsListeners(){this._setCreateButtonListener(),this._setKeyboardListener(),this._setColumnListListener()}_setCreateButtonListener(){document.getElementById(p.column_create_button_id).addEventListener("click",(t=>{document.getElementById(p.column_main_input_id).classList.toggle("visible")}))}_setColumnListListener(){document.getElementById(p.column_display_id).addEventListener("click",(t=>{if("BUTTON"===t.target.tagName){let e=t.target.parentElement,n=e.getAttribute("data-id");h.removeFromAvailableColumns(n),e.remove()}}))}handleFileChangeEvent(t){let e=o.W.getCurrentFilesList(),n=[];this._resetColumnInput(),e.forEach((t=>{if("fits"===t.type){let e=r.H.getFITSReaderWrapper();e.setFile(t.file),e.getAllColumns().forEach((e=>{let r={...e,file_id:t.id};n.push(r)}))}}));let i=n.reduce(((t,e)=>(t[e.file_id]||(t[e.file_id]=[]),t[e.file_id].push(e),t)),{}),a=[];for(let t in i)if(i.hasOwnProperty(t)){let e=o.W.getFileById(t),n=(e.file_name,r.H.getFITSReaderWrapper());n.setFile(e.file),a.push(this.createColumnsList(i[t],n))}this.setColumnInput(a),this._setColumnInputListener()}executeCommand(t){let e=document.getElementById(p.input_expression);switch(t){case"C":e.value="";break;case"V":let t={expression:e.value};t=h.addToAvailableColumns(t),this.addColumnToDisplay(e.value,t),(new d).dispatchToSubscribers()}}createColumnsList(t,e){let n=[];return t.forEach((t=>{let r=document.createElement("li"),i=e.getHeaderCardValueByNameFromHDU(t.hdu_index,"XTENSION")+"-"+e.getHeaderCardValueByNameFromHDU(t.hdu_index,"EXTNAME")+" "+t.name;t.is_from_header&&(i+="(HEADER)"),t.is_processed?(r.innerHTML=i,r.setAttribute("dataset-id",`${t.from_file}.${t.hdu_index}$${t.name}`)):(r.innerHTML=i,r.setAttribute("data-id",`${t.file_id}.${t.hdu_index}$${t.name}`)),n.push(r)})),n}setColumnInput(t){let e=document.getElementById(p.column_list_id);t.forEach((t=>{t.forEach((t=>{e.appendChild(t)}))}))}_setKeyboardListener(){let t=document.querySelectorAll("div.button-grid button"),e=document.getElementById(p.input_expression);t.forEach((t=>{t.addEventListener("click",(n=>{let r=t.textContent;p.button_commands.includes(r)?this.executeCommand(r):e.value+=r}))}))}_resetColumnInput(){document.getElementById(p.column_list_id).innerHTML=""}_setColumnInputListener(){let t=document.querySelectorAll("ul#column-input-list li"),e=document.getElementById(p.input_expression);t.forEach((function(t){t.addEventListener("click",(n=>{let r=t.getAttribute("data-id");e.value+=r}))}))}addColumnToDisplay(t,e){let n=document.getElementById(p.column_display_id),r=document.createElement("li");r.innerHTML=t+' <button class="btn btn-danger">X</button>',r.setAttribute("data-column",t),r.setAttribute("data-id",e.id),n.appendChild(r)}}class f{static default_settings={library:"",data_type:"",axis:{},scales:{},error_bars:{}};settings={};settings_library=null;settings_data_type=null;settings_hdus=null;settings_axis=null;settings_columns=null;settings_scales=null;settings_error_bars=null;constructor(t=null){this.settings=t?JSON.parse(JSON.stringify(t)):JSON.parse(JSON.stringify(f.default_settings))}setLibrarySettings(t){this.settings_library=t}getLibrarySettings(){return this.settings_library?this.settings_library:null}setDataTypeSettings(t){this.settings_data_type=t}getDataTypeSettings(){return this.settings_data_type?this.settings_data_type:null}getLightCurveSettings(){}getSpectrumSettings(){}setHDUsSettings(t){this.settings_hdus=t}getHDUsSettings(){return null!==this.settings_hdus?this.settings_hdus:null}setAxisSettings(t){this.settings_axis=t}getAxisSettings(){return this.settings_axis?this.settings_axis:null}setColumnsSettings(t){this.settings_columns=t}getColumnsSettings(){return this.settings_columns?this.settings_columns:null}setScalesSettings(t){this.settings_scales=t}getScalesSettings(){return this.settings_scales?this.settings_scales:null}setErrorBarsSettings(t){this.settings_error_bars=t}getErrorBarsSettings(){return this.settings_error_bars?this.settings_error_bars:null}setRangesSettings(t){this.settings_ranges=t}getRangesSettings(){return this.settings_ranges}getAdditionalDatasetsSettings(){}reset(){this.settings_library=null,this.settings_data_type=null,this.settings_hdus=null,this.settings_axis=null,this.settings_scales=null,this.settings_error_bars=null}}var Q=__nested_webpack_require_4077833__(9319);class T{constructor(){}getVisualizationSettingsObject(){return new f}getSettingsConfigurationObject(){return new Q.M}static getSettingsContainer(){return new T}}class m extends Error{constructor(t){super(t),this.name="NoEventToDispatch"}}class g{static defaultOptions={bubbles:!0,composed:!1,cancelable:!0};static name="settings-changed";event=null;constructor(t,e={},n={}){this.detail={...e,settings_object:t},this.options={...g.defaultOptions,...n},this.event=new CustomEvent(g.name,{detail:this.detail,...this.options})}dispatch(){if(null===this.event)throw new m("No event to dispatch");document.dispatchEvent(this.event)}}class _{static defaultOptions={bubbles:!0,composed:!1,cancelable:!0};static name="visualization-generation";event=null;constructor(t,e={},n={}){this.detail={...e,settings_object:t},this.options={..._.defaultOptions,...n},this.event=new CustomEvent(_.name,{detail:this.detail,...this.options})}dispatch(){if(null===this.event)throw 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          </div>\n                            </div>\n                            <div id="d3-settings" class="card">\n                                <div class="card-body">\n                                    <h6 class="card-title">D3 Settings</h6>\n                                </div>\n                            </div>\n                            \x3c!-- DATA TYPE SETTINGS --\x3e\n                            <div id="data-type-settings" class="card">\n                                <div class="card-body">\n                                    <h6 class="card-title">Data type selection</h6>\n                                    <select id="select-data-type" class="form-select">\n                                        <option selected>Generic</option>\n                                        <option value="light-curve">Light Curve</option>\n                                        <option value="spectrum">Spectrum</option>\n                                    </select>\n                                </div>\n                            </div>\n                            \x3c!-- DATA TYPE SPECIFIC SETTINGS --\x3e\n                            <div id="light-curve-settings" class="card">\n                                <div class="card-body">\n                                    <h6 class="card-title">Light Curve Settings</h6>\n                                </div>\n                            </div>\n                            <div id="spectrum-settings" class="card">\n                                <div class="card-body">\n                                    <h6 class="card-title">Spectrum Settings</h6>\n                                </div>\n                            </div>\n                            \x3c!-- HDUS SETTINGS --\x3e\n                            <div id="hdus-settings" class="card">\n                                <div id="card-body-hdus" class="card-body">\n                                    <h6 class="card-title">HDU Selection</h6>\n                                    <select id="select-hdus" class="form-select">\n                                        <option selected>HDUs</option>\n                                    </select>\n                                </div>\n                            </div>\n                            \x3c!-- COLUMN SETTINGS --\x3e\n                            <div id="columns-settings" class="card">\n                                <div id="card-body-columns" class="card-body column-creation-container">\n                                    <h6 class="card-title">Column Creation</h6>\n                                    <arithmetic-column-component id="arithmetic-column-component"></arithmetic-column-component>                                </div>\n                            </div>\n                            \x3c!-- AXIS SETTINGS --\x3e\n                            <div id="axis-settings" class="card">\n                                <div id="card-body-axis" class="card-body">\n                                    <h6 class="card-title">Axis Settings</h6>\n\n                                    <select id="select-axis-x" class="form-select select-axis">\n                                        <option selected>X axis</option>\n                                    </select>\n                                    <select id="select-axis-x-scale" class="form-select select-axis-scale static-select">\n                                        <option value="linear" selected>Linear</option>\n                                        <option value="log" selected>Log</option>\n                                    </select>\n\n                                    <label for="has-x-range-checkbox">Add X Range:</label>\n                                    <input type="checkbox" id="has-x-range-checkbox" class="form-checkbox" name="add-x-range">\n                                    <div id="x-range-fields" class="axis-range-div" style="">\n                                        <label for="x-lower-bound">X Lower Bound:</label>\n                                        <input type="number" id="x-lower-bound" class="form-input" name="x-lower-bound">\n                                        <label for="x-higher-bound">X Upper Bound:</label>\n                                        <input type="number" id="x-higher-bound" class="form-input" name="x-higher-bound">\n                                    </div>\n\n                                    <select id="select-axis-y" class="form-select select-axis">\n                                        <option selected>Y axis</option>\n                                    </select>\n                                    <select id="select-axis-y-scale" class="form-select select-axis-scale static-select">\n                                        <option value="linear" selected>Linear</option>\n                                        <option value="log" selected>Log</option>\n                                    </select>\n\n                                    <label for="has-y-range-checkbox">Add Y Range:</label>\n                                    <input type="checkbox" id="has-y-range-checkbox" class="form-checkbox" name="add-y-range">\n                                    <div id="y-range-fields" class="axis-range-div" style="">\n                                        <label for="y-lower-bound">Y Lower Bound:</label>\n                                        <input type="number" id="y-lower-bound" class="form-input" name="y-lower-bound">\n                                        <label for="y-higher-bound">Y Upper Bound:</label>\n                                        <input type="number" id="y-higher-bound" class="form-input" name="y-higher-bound">\n                                    </div>\n\n                                </div>\n                            </div>\n                            \x3c!-- ERROR BARS SETTINGS --\x3e\n                            <div id="error-bars-settings" class="card">\n                                <div id="card-body-error-bars" class="card-body">\n                                    <h6 class="card-title">Error Bars</h6>\n                                    <label for="has-error-bars-checkbox">Add Error Bars: </label>\n                                    <input type="checkbox" id="has-error-bars-checkbox" class="form-checkbox" name="has-error-bars-checkbox">\n                                    <select id="select-axis-x-error-bar" class="form-select select-axis-error-bars">\n                                        <option value="none" selected>X axis error bars</option>\n                                    </select>\n                                    <select id="select-axis-y-error-bar" class="form-select select-axis-error-bars">\n                                        <option value="none" selected>Y axis error bars</option>\n                                    </select>\n                                </div>\n                            </div>\n                            \x3c!-- BINNING SETTINGS --\x3e\n                            <div id="binning-settings" class="card">\n                                <div class="card-body">\n                                    <h6 class="card-title">Binning Settings</h6>\n                                </div>\n                            </div>\n                            \x3c!-- ADDITIONAL DATASET SETTINGS --\x3e\n                            <div id="additional-dataset-settings" class="card">\n                                <div id="card-body-dataset" class="card-body">\n                                    <h6 class="card-title">Dataset Selection</h6>\n                                </div>\n                            </div>\n\n                            <button id="button-generate" class="btn btn-primary">Generate</button>\n                        </div>\n                    </div>';arithmetic_column_component_id="arithmetic-column-component";arithmetic_column_component=null;constructor(){super(),this.arithmetic_column_component=y.getArithmeticColumnComponent(),this.innerHTML=this.content,this.container_id=v.container_id,this.settings_object=T.getSettingsContainer().getVisualizationSettingsObject()}setup(){this._setContainer(),this.arithmetic_column_component=document.getElementById(this.arithmetic_column_component_id),this.arithmetic_column_component.setup(),this._setupListeners(),this._setupEventHandlers()}_setupListeners(){this._setupExternalListeners(),this._setupInnerListeners(),this._setupInnerElementsListeners()}_setupEventHandlers(){this.handleFITSLoadedEvent=this.handleFITSLoadedEvent.bind(this),this.handleConfigurationEvent=this.handleConfigurationEvent.bind(this),this.handleLibraryChangeEvent=this.handleLibraryChangeEvent.bind(this),this.handleDataTypeChangeEvent=this.handleDataTypeChangeEvent.bind(this),this.handleHDUsChangeEvent=this.handleHDUsChangeEvent.bind(this),this.handleGenerateEvent=this.handleGenerateEvent.bind(this),this.handleFileChangeEvent=this.handleFileChangeEvent.bind(this),this.handleArithmeticColumnChangeEvent=this.handleArithmeticColumnChangeEvent.bind(this)}_injectArithmeticColumnComponent(){document.querySelector(".column-creation-container").appendChild(this.arithmetic_column_component)}_setupExternalListeners(){this.addEventListener("fits-loaded",this.handleFITSLoadedEvent),this.addEventListener("configuration",this.handleConfigurationEvent),this.addEventListener("file-registry-change",this.handleFileChangeEvent)}_setupInnerListeners(){this.addEventListener("select-library-change",this.handleLibraryChangeEvent),this.addEventListener("select-data-type-change",this.handleDataTypeChangeEvent),this.addEventListener("select-hdus-change",this.handleHDUsChangeEvent),this.addEventListener("button-generate-click",this.handleGenerateEvent),this.addEventListener("arithmetic-column-change",this.handleArithmeticColumnChangeEvent)}_setupInnerElementsListeners(){this._setSelectLibraryListener(),this._setSelectDataTypeListener(),this._setSelectHDUsListener(),this._setSelectAxisListener(),this._setGenerateButtonListener(),this._setCalculationRadioListeners()}setupListeners(){this._setupExternalListeners(),this._setupInnerListeners(),this._setupInnerElementsListeners()}handleFITSLoadedEvent(t){this.fits_reader_wrapper=t.detail.fits_reader_wrapper;let e=this.fits_reader_wrapper.getHDUs();if(this._setSelectHDUs(e),this.fits_reader_wrapper.isHDUTabular(e[0].index)){let t=this.fits_reader_wrapper.getColumnsNameFromHDU(e[0].index);this._setSelectAxis(t),this._setSelectErrorBars(t)}else this._resetSelectAxis(),this._resetSelectErrorBars()}handleConfigurationEvent(t){let e=t.detail.configuration_object;this.updateSettings(e)}handleLibraryChangeEvent(t){t.stopPropagation(),this.updateSettingsObject(),new g(this.settings_object).dispatch()}handleDataTypeChangeEvent(t){t.stopPropagation();let e=t.detail.data_type;if(v.supported_data_types.includes(e))switch(this.updateSettingsObject(),e){case"light-curve":document.getElementById(v.light_curve_settings_id).style.display="block",document.getElementById(v.spectrum_settings_id).style.display="none";break;case"spectrum":document.getElementById(v.spectrum_settings_id).style.display="block",document.getElementById(v.light_curve_settings_id).style.display="none";break;default:document.getElementById(v.spectrum_settings_id).style.display="none",document.getElementById(v.light_curve_settings_id).style.display="none"}}handleHDUsChangeEvent(t){t.stopPropagation();let e=t.detail.hdu_index;if(this.fits_reader_wrapper.isHDUTabular(e)){let t=this.fits_reader_wrapper.getColumnsNameFromHDU(e);this._setSelectAxis(t),this._setSelectErrorBars(t)}else this._resetSelectAxis(),this._resetSelectErrorBars()}handleGenerateEvent(t){t.stopPropagation(),this.settings_object.reset(),this.updateSettingsObject(),new _(this.settings_object).dispatch()}handleFileChangeEvent(t){let e=o.W.getCurrentFilesList(),n=[];e.forEach((t=>{if("fits"===t.type){let e=r.H.getFITSReaderWrapper();"spectrum"!==t.product_type?e.setFile(t.file):"spectrum"===t.product_type&&e.setFileFromFileObject(t),e.getAllColumns().forEach((e=>{let r={...e,file_id:t.id};n.push(r)}))}else t.type}));let i=n.reduce(((t,e)=>(t[e.file_id]||(t[e.file_id]=[]),t[e.file_id].push(e),t)),{}),a=[];for(let t in i)if(i.hasOwnProperty(t)){let e=o.W.getFileById(t),n=e.file_name,s=r.H.getFITSReaderWrapper();s.setFile(e.file),a.push(this._createFileColumnsOptionsGroup(i[t],n,"opt-group",s))}this._setSelectGroupAxis(a),a.unshift(this._createGenericColumnOptionsGroup()),this._setSelectGroupErrorBars(a)}handleArithmeticColumnChangeEvent(t){let e=this._createColumnsOptGroups(),n=this._createGenericColumnOptionsGroup();this._setSelectGroupAxis(e),e[0]=n,this._setSelectGroupErrorBars(e)}_setContainer(){this.container=document.getElementById(this.container_id)}_resetContainer(){this.container.innerHTML=""}_setSelectHDUs(t){this._resetSelectHDUs();let e=document.getElementById(v.select_hdus_id);this._createHDUsOptions(t).forEach((function(t){e.add(t)}))}_resetSelectHDUs(){document.getElementById(v.select_hdus_id).innerHTML=""}_createHDUsOptions(t){let e,n=[];return t.forEach((function(t,r){e=document.createElement("option"),0===r&&e.setAttribute("selected","true"),e.value=t.index,e.text=t.name,n.push(e)})),n}_createFileColumnsOptionsGroup(t,e,n,r){let i=document.createElement("optgroup");return i.label=e,i.className+=n,t.forEach((t=>{let e=document.createElement("option"),n=r.getHeaderCardValueByNameFromHDU(t.hdu_index,"XTENSION")+"-"+r.getHeaderCardValueByNameFromHDU(t.hdu_index,"EXTNAME")+" "+t.name;t.is_from_header&&(n+="(HEADER)"),t.is_processed?(e.text=n,e.value=`${t.from_file}.${t.hdu_index}$${t.name}`):(e.text=n,e.value=`${t.file_id}.${t.hdu_index}$${t.name}`),i.appendChild(e)})),i}_createGenericColumnOptionsGroup(t=!1){let e=document.createElement("optgroup");e.label="Generic columns",e.className+="generic";let n=document.createElement("option");n.text="None",n.value="none",t||e.appendChild(n);let r=h.getAvailableColumnsList();return r.length>0&&r.forEach((t=>{n=document.createElement("option"),n.text=t.expression,n.value=t.expression,n.setAttribute("data-column-type","processed"),e.appendChild(n)})),e}_setSelectAxis(t){this._resetSelectAxis();let e=[document.getElementById(v.select_axis_x_id),document.getElementById(v.select_axis_y_id)];this._createColumnsOptions(t).forEach((function(t){e.forEach((function(e){let n=t.cloneNode(!0);e.add(n)}))}))}_setSelectGroupAxis(t){this._resetSelectAxis();let e=[document.getElementById(v.select_axis_x_id),document.getElementById(v.select_axis_y_id)];t.forEach((t=>{e.forEach((e=>{let n=t.cloneNode(!0);e.add(n)}))}))}_resetSelectAxis(){let t=document.getElementById(v.select_axis_x_id),e=document.getElementById(v.select_axis_y_id);t.innerHTML="",e.innerHTML=""}_setSelectErrorBars(t){this._resetSelectErrorBars();let e=[document.getElementById(v.select_error_bar_x_id),document.getElementById(v.select_error_bar_y_id)];this._createColumnsOptions(t).forEach((function(t){e.forEach((function(e){let n=t.cloneNode(!0);e.add(n)}))}))}_setSelectGroupErrorBars(t){this._resetSelectErrorBars();let e=[document.getElementById(v.select_error_bar_x_id),document.getElementById(v.select_error_bar_y_id)];t.forEach((t=>{e.forEach((e=>{let n=t.cloneNode(!0);e.add(n)}))}))}_resetSelectErrorBars(){let t=document.getElementById(v.select_error_bar_x_id),e=document.getElementById(v.select_error_bar_y_id);t.innerHTML="",e.innerHTML=""}_createColumnsOptions(t){let e,n=[];return t.forEach((function(t){e=document.createElement("option"),e.value=t,e.text=t,n.push(e)})),n}_createColumnsOptGroups(){let t=o.W.getCurrentFilesList(),e=[];t.forEach((t=>{if("fits"===t.type){let n=r.H.getFITSReaderWrapper();"spectrum"!==t.product_type?n.setFile(t.file):"spectrum"===t.product_type&&n.setFileFromFileObject(t),n.getAllColumns().forEach((n=>{let r={...n,file_id:t.id};e.push(r)}))}else t.type}));let n=e.reduce(((t,e)=>(t[e.file_id]||(t[e.file_id]=[]),t[e.file_id].push(e),t)),{}),i=[];for(let t in n)if(n.hasOwnProperty(t)){let e=o.W.getFileById(t),a=e.file_name,s=r.H.getFITSReaderWrapper();s.setFile(e.file),i.push(this._createFileColumnsOptionsGroup(n[t],a,"opt-group",s))}return i.unshift(this._createGenericColumnOptionsGroup(!0)),i}_setSelectLibraryListener(){let t=document.getElementById(v.select_library_id);t.addEventListener("change",(e=>{e.preventDefault();const n=new CustomEvent("select-library-change",{bubbles:!1,compose:!1,cancelable:!0,detail:{library:t.value}});this.dispatchEvent(n)}))}_setSelectDataTypeListener(){let t=document.getElementById(v.select_data_type_id);t.addEventListener("change",(e=>{e.preventDefault();const n=new CustomEvent("select-data-type-change",{bubbles:!1,compose:!1,cancelable:!0,detail:{data_type:t.value}});this.dispatchEvent(n)}))}_setSelectHDUsListener(){let t=document.getElementById(v.select_hdus_id);t.addEventListener("change",(e=>{e.preventDefault();const n=new CustomEvent("select-hdus-change",{bubbles:!1,compose:!1,cancelable:!0,detail:{hdu_index:t.value}});this.dispatchEvent(n)}))}_setSelectAxisListener(){let t=document.getElementById(v.select_axis_x_id),e=document.getElementById(v.select_axis_y_id),n=document.getElementById(v.select_error_bar_x_id),i=document.getElementById(v.select_error_bar_y_id);t.addEventListener("change",(t=>{let e=t.target.value;if("light-curve"===document.getElementById(v.select_data_type_id).value){let t=b.A.getColumnSettings(e),i=o.W.getFileById(t.file_id),a=r.H.getFITSReaderWrapper();a.setFile(i.file);let s=a.getAllColumns();"RATE"===t.column_name.toUpperCase()&&s.some((e=>"ERROR"===e.name.toUpperCase()&&parseInt(e.hdu_index)===parseInt(t.hdu_index)))&&Array.from(n.options).forEach((e=>{let r=b.A.getColumnSettings(e.value);r.file_id===t.file_id&&r.hdu_index===t.hdu_index&&"ERROR"===r.column_name.toUpperCase()&&(n.value=e.value)})),"TIME"===t.column_name.toUpperCase()&&s.some((e=>"TIMEDEL"===e.name.toUpperCase()&&parseInt(e.hdu_index)===parseInt(t.hdu_index)))&&Array.from(n.options).forEach((e=>{let r=b.A.getColumnSettings(e.value);r.file_id===t.file_id&&r.hdu_index===t.hdu_index&&"TIMEDEL"===r.column_name.toUpperCase()&&(n.value=e.value)}))}})),e.addEventListener("change",(t=>{let e=t.target.value;if("light-curve"===document.getElementById(v.select_data_type_id).value){let t=b.A.getColumnSettings(e),n=o.W.getFileById(t.file_id),a=r.H.getFITSReaderWrapper();a.setFile(n.file);let s=a.getAllColumns();"RATE"===t.column_name.toUpperCase()&&s.some((e=>"ERROR"===e.name.toUpperCase()&&parseInt(e.hdu_index)===parseInt(t.hdu_index)))&&Array.from(i.options).forEach((e=>{let n=b.A.getColumnSettings(e.value);n.file_id===t.file_id&&n.hdu_index===t.hdu_index&&"ERROR"===n.column_name.toUpperCase()&&(i.value=e.value)})),"TIME"===t.column_name.toUpperCase()&&s.some((e=>"TIMEDEL"===e.name.toUpperCase()&&parseInt(e.hdu_index)===parseInt(t.hdu_index)))&&Array.from(i.options).forEach((e=>{let n=b.A.getColumnSettings(e.value);n.file_id===t.file_id&&n.hdu_index===t.hdu_index&&"TIMEDEL"===n.column_name.toUpperCase()&&(i.value=e.value)}))}}))}_setCalculationRadioListeners(){document.querySelectorAll("."+v.calculation_radio_class).forEach((t=>{t.addEventListener("change",(t=>{}))}))}_setGenerateButtonListener(){document.getElementById("button-generate").addEventListener("click",(t=>{t.preventDefault();const e=new CustomEvent("button-generate-click",{bubbles:!1,compose:!1,cancelable:!0,detail:{}});this.dispatchEvent(e)}))}updateSettings(t){for(let[e,n]of Object.entries(t)){let t=document.getElementById(e);t&&(!0===n.display?t.style.display="block":t.style.display="none")}}updateSettingsObject(){let t=this._extractFormValues(),e={};e.library=t["select-library"].value,this.settings_object.setLibrarySettings(e);let n={};n.hdu_index=t["select-hdus"].value,this.settings_object.setHDUsSettings(n);let r={};if(r.type=t["select-data-type"].value,this.settings_object.setDataTypeSettings(r),t["select-axis-x"]&&t["select-axis-y"]){let e={},n={x:{},y:{}},r={};n.x.column_type="standard",n.y.column_type="standard","processed"===t["select-axis-x"].column_type&&(n.x.column_type="processed"),"processed"===t["select-axis-y"].column_type&&(n.y.column_type="processed"),e.x=t["select-axis-x"].value,e.y=t["select-axis-y"].value,r.x=t["select-axis-x-scale"].value,r.y=t["select-axis-y-scale"].value,this.settings_object.setAxisSettings(e),this.settings_object.setColumnsSettings(n),this.settings_object.setScalesSettings(r)}if(t["has-error-bars-checkbox"]&&!0===t["has-error-bars-checkbox"].checked){let e={},n=this.settings_object.getColumnsSettings();if(void 0!==t["select-axis-x-error-bar"]){let r;e.x=t["select-axis-x-error-bar"].value;let i={};null!=t["select-axis-x-error-bar"].column_type&&(r="processed"===t["select-axis-x-error-bar"].column_type?"processed":"standard"),i.column_type=r,n.x_error=i}else delete e.x;if(void 0!==t["select-axis-y-error-bar"]){let r;e.y=t["select-axis-y-error-bar"].value;let i={};null!=t["select-axis-y-error-bar"].column_type&&(r="processed"===t["select-axis-y-error-bar"].column_type?"processed":"standard"),i.column_type=r,n.y_error=i}else delete e.y;this.settings_object.setErrorBarsSettings(e),this.settings_object.setColumnsSettings(n)}if(!0===t["has-x-range-checkbox"].checked||!0===t["has-y-range-checkbox"].checked){let e={x:{},y:{}};!0===t["has-x-range-checkbox"].checked?(e.x.lower_bound=t["x-lower-bound"].value,e.x.upper_bound=t["x-higher-bound"].value):e.x=null,!0===t["has-y-range-checkbox"].checked?(e.y.lower_bound=t["y-lower-bound"].value,e.y.upper_bound=t["y-higher-bound"].value):e.y=null,this.settings_object.setRangesSettings(e)}else this.settings_object.setRangesSettings(null)}_extractFormValues(){let t={};return this.container.querySelectorAll(".form-select").forEach((e=>{let n=e.id,r=e.className.split(" "),i=e.value,o="standard";o=e.options[e.selectedIndex].dataset.columnType,"none"!==window.getComputedStyle(e,null).getPropertyValue("display")&&"none"!==i&&(t[n]={classes:r,value:i,column_type:o})})),this.container.querySelectorAll(".form-checkbox").forEach((e=>{let n=e.id,r=e.className.split(" "),i=e.checked;t[n]={classes:r,checked:i}})),this.container.querySelectorAll(".form-input").forEach((e=>{let n=e.id,r=e.className.split(" "),i=e.value;t[n]={classes:r,value:i}})),t}}class y{static main_container_id="js-vis-main";static standard_container_class="container";static double_container_class="container-graph-settings";static file_component_column_id="column-file";static visualization_component_column_id="column-graph";static settings_component_column_id="settings-column";constructor(){}static getMainContainer(){let t=document.createElement("div");return t.setAttribute("id",y.main_container_id),t}static getStandardContainer(){let t=document.createElement("div");return t.classList.add(y.standard_container_class),t}static getDoubleColumnContainer(){let t=document.createElement("div");return t.classList.add(y.standard_container_class),t.classList.add(y.double_container_class),t}static getFileComponentColumn(){let t=document.createElement("div");return t.setAttribute("id",y.file_component_column_id),t}static getFileComponentStructure(){let t=[],e=y.getStandardContainer(),n=y.getFileComponentColumn();return t.push(e),t.push(n),t}static getVisualizationComponentColumn(){let t=document.createElement("div");return t.setAttribute("id",y.visualization_component_column_id),t}static getVisualizationComponentStructure(){let t=[],e=y.getVisualizationComponentColumn();return t.push(e),t}static getSettingsComponentColumn(){let t=document.createElement("div");return t.setAttribute("id",y.settings_component_column_id),t}static getSettingsComponentStructure(){let t=[],e=y.getSettingsComponentColumn();return t.push(e),t}static getFileComponent(t=null){const e=new x(t);return e.setAttribute("id","file-component"),e}static getCSVSettingsComponent(t,e){return new u(t,e)}static getFITSSettingsComponent(t,e){return new l(t,e)}static getVisualizationComponent(){return new c}static getSettingsComponent(){const t=new v;return t.setAttribute("id","settings-component"),t}static getArithmeticColumnComponent(){return new p}}class x extends HTMLElement{static component_id="file-component";static select_file="select-file";static input_file_url="file-input-url";static input_file_local="file-input-local";static input_file_type="select-file-type";static load_button="load-file";static available_files_list_id="available-files-list";static current_files_list_id="current-files-list";static file_settings_container_id="file-settings-container";static save_button_id="save-file-settings";static add_button_id="add-to-plot";static remove_button_id="remove-from-plot";static content='<div id="file-component-container" class="grid-container">\n                        <div class="full-width-column" style="grid-column: 1 / span 2;">\n                            <div class="card">\n                                <div class="card-header">Download</div>\n                                <div class="card-body">\n                                    <input type="file" id="file-input-local">\n                                    <select id="select-file-type">\n                                        <option value="fits">FITS</option>\n                                    </select>\n                                </div>\n                            </div>\n                        </div>\n                        <div class="left-column">\n                            <div id="available-files-card" class="card">\n                                <div class="card-header">Available files</div>\n                                <div class="card-body">\n                                    <div id="available-files-list" class="list-group">\n\n                                    </div>\n                                </div>\n                            </div>\n                        </div>\n                        <div class="right-column">\n                            <div id="current-files-card" class="card">\n                                <div class="card-header">Current files</div>\n                                <div class="card-body">\n                                    <div id="current-files-list" class="list-group">\n                                    </div>\n                                </div>\n                            </div>\n                        </div>\n                        <div id="file-settings-container" class="full-width-column">\n\n                        </div>\n                    </div>';container_id;container;fits_reader_wrapper=null;fits_component=null;csv_component=null;constructor(t="file-component-container"){super(),this.innerHTML=x.content,this.container_id=t}setup(){this._setContainer(),this._setupEventHandlers(),this._setupListeners()}_setupListeners(){this._setupExternalListeners(),this._setupInnerListeners(),this._setupInnerElementsListeners()}_setupEventHandlers(){this.handleFITSLoadedEvent=this.handleFITSLoadedEvent.bind(this),this.handleSelectChangeEvent=this.handleSelectChangeEvent.bind(this),this.handleLoadFileEvent=this.handleLoadFileEvent.bind(this),this.handleFileLoadedEvent=this.handleFileLoadedEvent.bind(this),this.handleFileRegistryChangeEvent=this.handleFileRegistryChangeEvent.bind(this)}_injectInnerComponents(){document.getElementById("file-settings-container").appendChild(this.fits_component)}_setupExternalListeners(){this.addEventListener("fits-loaded",this.handleFITSLoadedEvent),this.addEventListener("file-loaded",this.handleFileLoadedEvent),this.addEventListener("file-registry-change",this.handleFileRegistryChangeEvent)}_setupInnerListeners(){this.addEventListener("select-change",this.handleSelectChangeEvent),this.addEventListener("load-file",this.handleLoadFileEvent)}_setupInnerElementsListeners(){this._setLoadLocalFileButtonListener(),this._setFilesListsListeners()}_setLoadLocalFileButtonListener(){let t=document.getElementById(x.input_file_local),e=document.getElementById(x.input_file_type).value;t.addEventListener("change",(function(t){let n=t.target.files[0];"fits"===e?n.arrayBuffer().then((t=>{r.H.getFITSReaderWrapper().initializeFromBuffer(t,n.name)})).catch((t=>{console.error("Error reading file as ArrayBuffer:",t)})):"csv"===e&&((new FileReader).onload=function(t){t.target.result})}))}_setFilesListsListeners(){let t=document.getElementById(x.available_files_list_id),e=document.getElementById(x.current_files_list_id),n=t.querySelectorAll("button"),r=e.querySelectorAll("button"),i=Array.from(n).concat(Array.from(r));i.forEach((t=>{t.addEventListener("click",(()=>{t.classList.toggle("active");let e=t.getAttribute("aria-current");if(e&&"true"===e)t.removeAttribute("aria-current"),this.clearFileSettingsPanel();else{t.setAttribute("aria-current","true");let e=o.W.getFileById(t.getAttribute("data-id"));this.setFileSettingsPanel(e)}Array.from(i).filter((e=>e!==t)).forEach((t=>{t.classList.remove("active"),t.removeAttribute("aria-current")}))}))}))}_setFileSettingsButtonsListeners(){let t=document.getElementById(x.save_button_id),e=document.getElementById(x.add_button_id);t.addEventListener("click",(t=>{})),e.addEventListener("click",(t=>{let e=t.target.getAttribute("data-id"),n=o.W.getFileById(e);o.W.addToCurrentFiles(n),this.updateCurrentFilesList(),this.updateAvailableFilesList(),(new a.o).dispatchToSubscribers()}))}handleFITSLoadedEvent(t){this.fits_reader_wrapper=t.detail.fits_reader_wrapper;let e=this.fits_reader_wrapper.getFilePath();this._addFileToSelect(e)}handleFileLoadedEvent(t){o.W.addToAvailableFiles(t.detail),this.updateAvailableFilesList(),this.updateCurrentFilesList(),this._setFilesListsListeners(),document.querySelector("fits-component")&&(this.clearFileSettingsPanel(),document.getElementById(x.component_id).scrollIntoView({behavior:"smooth"}))}handleFileRegistryChangeEvent(t){this.updateAvailableFilesList(),this.updateCurrentFilesList(),this._setFilesListsListeners(),this.clearFileSettingsPanel(),document.getElementById(x.component_id).scrollIntoView({behavior:"smooth"})}handleLoadFileEvent(t){}updateFilesLists(){this.updateAvailableFilesList(),this.updateCurrentFilesList()}updateAvailableFilesList(){let t=document.getElementById(x.available_files_list_id);t.innerHTML="",this._createFileSelection("available").forEach((e=>{t.appendChild(e)}))}updateCurrentFilesList(){let t=document.getElementById(x.current_files_list_id);t.innerHTML="",this._createFileSelection("current").forEach((e=>{t.appendChild(e)}))}clearFileSettingsPanel(){document.getElementById(x.file_settings_container_id).innerHTML=""}setFileSettingsPanel(t){if(this.clearFileSettingsPanel(),"fits"===t.type){let e=o.W.isFileCurrent(t.id),n=new l(t,e);document.getElementById(x.file_settings_container_id).appendChild(n),n.setupComponent()}}_addFileToSelect(t){let e=this._createSelectOption(t);document.getElementById(x.select_file).add(e)}_createFileSelection(t="available"){let e;e="available"===t?o.W.getAvailableFilesList():o.W.getCurrentFilesList();let n,r=[];return e.forEach((t=>{let e=t.id+"."+t.file_name;n=document.createElement("button"),n.setAttribute("type","button"),n.setAttribute("class","available-file-selection list-group-item list-group-item-action"),n.setAttribute("data-id",t.id),n.textContent=e,r.push(n)})),r}_createSelectOption(t){let e=document.createElement("option");return e.value=t,e.text=t,e}handleSelectChangeEvent(t){t.stopPropagation()}_setContainer(){this.container=document.getElementById(this.container_id)}resetContainer(){this.container.innerHTML=""}}var w=__nested_webpack_require_4077833__(7508),L=__nested_webpack_require_4077833__(2890),A=__nested_webpack_require_4077833__(310),H=__nested_webpack_require_4077833__.n(A),k=__nested_webpack_require_4077833__(7825),M=__nested_webpack_require_4077833__.n(k),C=__nested_webpack_require_4077833__(7659),S=__nested_webpack_require_4077833__.n(C),E=__nested_webpack_require_4077833__(5056),V=__nested_webpack_require_4077833__.n(E),O=__nested_webpack_require_4077833__(540),P=__nested_webpack_require_4077833__.n(O),D=__nested_webpack_require_4077833__(1113),N=__nested_webpack_require_4077833__.n(D),R=__nested_webpack_require_4077833__(1261),I={};I.styleTagTransform=N(),I.setAttributes=V(),I.insert=S().bind(null,"head"),I.domAPI=M(),I.insertStyleElement=P(),H()(R.A,I),R.A&&R.A.locals&&R.A.locals,__nested_webpack_require_4077833__(8736);var j=__nested_webpack_require_4077833__(3552),z={};z.styleTagTransform=N(),z.setAttributes=V(),z.insert=S().bind(null,"head"),z.domAPI=M(),z.insertStyleElement=P(),H()(j.A,z),j.A&&j.A.locals&&j.A.locals;let B=new e.d,F=new n.L;function $(e,n=null){let o=document.getElementById(e),a=function(){let t={};return t.file_component=y.getFileComponent(),t.visualization_component=y.getVisualizationComponent(),t.settings_components=y.getSettingsComponent(),t}(),s=y.getMainContainer(),l=y.getFileComponentStructure(),c=y.getVisualizationComponentStructure(),u=y.getSettingsComponentStructure(),d=y.getDoubleColumnContainer();o.appendChild(s),s.appendChild(l[0]),l[0].appendChild(l[1]),l[1].appendChild(a.file_component),a.file_component.setup(),s.appendChild(d),d.appendChild(c[0]),c[0].appendChild(a.visualization_component),a.visualization_component.setup(),d.appendChild(u[0]),u[0].appendChild(a.settings_components),a.settings_components.setup(),F.setup(),i.C.getD3Visualization().setup(),B.setup(),i.C.getBokehVisualization().setup(),n&&function(e){var n;e&&(n=new t.v(e),r.H.setFITSReaderWrapper(n))}(n)}r.H.setBokehWrapper(B),r.H.setD3Wrapper(F),i.C.setBokehVisualization(new L.Y),i.C.setD3Visualization(new w.g),s.D.setFileRegistry(new o.W),s.D.setCustomColumnRegistry(new h),customElements.define("file-component",x),customElements.define("settings-component",v),customElements.define("visualization-component",c),customElements.define("fits-component",l),customElements.define("csv-component",u),customElements.define("arithmetic-column-component",p)})(),__nested_webpack_exports__})(),module.exports=e()}},__webpack_module_cache__={};function __webpack_require__(t){var e=__webpack_module_cache__[t];if(void 0!==e)return e.exports;var n=__webpack_module_cache__[t]={exports:{}};return __webpack_modules__[t].call(n.exports,n,n.exports,__webpack_require__),n.exports}__webpack_require__.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return __webpack_require__.d(e,{a:e}),e},__webpack_require__.d=(t,e)=>{for(var n in e)__webpack_require__.o(e,n)&&!__webpack_require__.o(t,n)&&Object.defineProperty(t,n,{enumerable:!0,get:e[n]})},__webpack_require__.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),(()=>{"use strict";var t=__webpack_require__(449);document.addEventListener("DOMContentLoaded",(()=>{const{root:e,visualization_config:n}=JSON.parse(document.getElementById("app").getAttribute("data-incoming")||"{}"),r=e+"datasets/"+n.dataset_id+"/display";(0,t.init)("app",r)}))})()})();
\ No newline at end of file
diff --git a/config/plugins/visualizations/fits_graph_viewer/static/logo.png b/config/plugins/visualizations/fits_graph_viewer/static/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..b5e53554f7a3c24245042685839a984c2b4ab906
Binary files /dev/null and b/config/plugins/visualizations/fits_graph_viewer/static/logo.png differ
diff --git a/config/plugins/visualizations/fits_graph_viewer/webpack.prod.js b/config/plugins/visualizations/fits_graph_viewer/webpack.prod.js
new file mode 100644
index 0000000000000000000000000000000000000000..1826c341552c19de4fef51999e3af5699d902fd2
--- /dev/null
+++ b/config/plugins/visualizations/fits_graph_viewer/webpack.prod.js
@@ -0,0 +1,9 @@
+const path = require('path');
+
+module.exports = {
+    mode: 'production',
+    entry: './src/index.js',
+    output: {
+        filename: 'fits_graph_viewer.js'
+    },
+};
\ No newline at end of file
diff --git a/config/plugins/visualizations/msa/config/msa.xml b/config/plugins/visualizations/msa/config/msa.xml
index 566a036ebe9bb2ff61e4c46d60531c3350e98148..2fd3761c48474d3b5b5db652c7671d5825d0b02b 100644
--- a/config/plugins/visualizations/msa/config/msa.xml
+++ b/config/plugins/visualizations/msa/config/msa.xml
@@ -11,6 +11,9 @@
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
+    <requirements>
+        <requirement type="npm" version="0.2.1" package="@galaxyproject/msa"/>
+    </requirements>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
diff --git a/config/plugins/visualizations/msa/package.json b/config/plugins/visualizations/msa/package.json
index 1a011c6ef6b1cd9c4f1c4f18f74dc4adf906eb1f..6d96f0a712b187644d2dccbcc257d1b5eaabbc44 100644
--- a/config/plugins/visualizations/msa/package.json
+++ b/config/plugins/visualizations/msa/package.json
@@ -1,19 +1,20 @@
 {
-    "name": "visualization",
-    "version": "0.1.0",
+    "name": "@galaxyproject/msa",
+    "version": "0.2.1",
     "keywords": [
         "galaxy",
         "visualization"
     ],
     "license": "AFL-3.0",
-    "dependencies": {
-        "babel-plugin-transform-export-extensions": "^6.22.0",
-        "babel-preset-env": "^1.6.1"
-    },
+    "files": [
+        "static"
+    ],
     "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
+        "build": "parcel build src/script.js --dist-dir static --no-source-maps"
     },
     "devDependencies": {
+        "babel-plugin-transform-export-extensions": "^6.22.0",
+        "babel-preset-env": "^1.6.1",
         "parcel": "^2.12.0"
     }
 }
diff --git a/config/plugins/visualizations/ngl/config/ngl.xml b/config/plugins/visualizations/ngl/config/ngl.xml
index 0a38c8b71872a0b77d8a769ded1a7c7e00138906..18607ed2c427d5773fd5ac17386a06bff4f7aa10 100644
--- a/config/plugins/visualizations/ngl/config/ngl.xml
+++ b/config/plugins/visualizations/ngl/config/ngl.xml
@@ -12,7 +12,10 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="dist/ngl.js"/>
+    <requirements>
+        <requirement type="npm" version="0.0.11" package="@galaxyproject/ngl"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
         <input>
             <label>Quality</label>
diff --git a/config/plugins/visualizations/ngl/package.json b/config/plugins/visualizations/ngl/package.json
deleted file mode 100644
index 724d0011652e23400fea729ef76629bd4bfa891e..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/ngl/package.json
+++ /dev/null
@@ -1,23 +0,0 @@
-{
-    "name": "ngl_load",
-    "version": "0.1.0",
-    "description": "NGL visualization plugin.",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "jquery": "^3.1.1",
-        "ngl": "^0.10.4"
-    },
-    "scripts": {
-        "build": "parcel build src/ngl.js --dist-dir static/dist"
-    },
-    "devDependencies": {
-        "parcel": "^2.12.0"
-    }
-}
diff --git a/config/plugins/visualizations/ngl/src/ngl.js b/config/plugins/visualizations/ngl/src/ngl.js
deleted file mode 100644
index 5d9ee9cfd6f5fb9627dcf9ce8a5e75f01901b77f..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/ngl/src/ngl.js
+++ /dev/null
@@ -1,48 +0,0 @@
-import * as ngl from "./viewer";
-
-/** Get boolean as string */
-function asBoolean(value) {
-    return String(value).toLowerCase() == "true";
-}
-
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    const dataset = options.dataset;
-    const settings = options.chart.settings;
-    const stage = new ngl.Stage(options.target, { backgroundColor: settings.get("backcolor") });
-    const representationParameters = {
-        radius: settings.get("radius"),
-        assembly: settings.get("assembly"),
-        color: settings.get("colorscheme"),
-        opacity: settings.get("opacity"),
-    };
-    const stageParameters = { ext: dataset.extension, defaultRepresentation: true };
-
-    try {
-        stage
-            .loadFile(prefixedDownloadUrl(options.root, dataset.download_url), stageParameters)
-            .then(function (component) {
-                component.addRepresentation(settings.get("mode"), representationParameters);
-                options.chart.state("ok", "Chart drawn.");
-                options.process.resolve();
-            });
-    } catch (e) {
-        options.chart.state("failed", "Could not load PDB file.");
-        options.process.resolve();
-    }
-    stage.setQuality(settings.get("quality"));
-    const spin = String(settings.get("spin")).toLowerCase() == "true";
-    if (spin) {
-        stage.setSpin([0, 1, 0], 0.01);
-    }
-    // Re-renders the molecule view when window is resized
-    window.onresize = function () {
-        stage.handleResize();
-    };
-};
diff --git a/config/plugins/visualizations/ngl/src/viewer.js b/config/plugins/visualizations/ngl/src/viewer.js
deleted file mode 100644
index e4f8d646be1297aa40393e4ef61b919316293c4e..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/ngl/src/viewer.js
+++ /dev/null
@@ -1,30 +0,0 @@
-!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?e(exports):"function"==typeof define&&define.amd?define(["exports"],e):e(t.NGL=t.NGL||{})}(this,function(t){"use strict";function e(){}function i(t,e){return function(){t.apply(e,arguments)}}function n(t){if("object"!=typeof this)throw new TypeError("Promises must be constructed via new");if("function"!=typeof t)throw new TypeError("not a function");this._state=0,this._handled=!1,this._value=void 0,this._deferreds=[],u(t,this)}function r(t,e){for(;3===t._state;)t=t._value;return 0===t._state?void t._deferreds.push(e):(t._handled=!0,void mh(function(){var i=1===t._state?e.onFulfilled:e.onRejected;if(null===i)return void(1===t._state?o:a)(e.promise,t._value);var n;try{n=i(t._value)}catch(t){return void a(e.promise,t)}o(e.promise,n)}))}function o(t,e){try{if(e===t)throw new TypeError("A promise cannot be resolved with itself.");if(e&&("object"==typeof e||"function"==typeof e)){var r=e.then;if(e instanceof n)return t._state=3,t._value=e,void s(t);if("function"==typeof r)return void u(i(r,e),t)}t._state=1,t._value=e,s(t)}catch(e){a(t,e)}}function a(t,e){t._state=2,t._value=e,s(t)}function s(t){2===t._state&&0===t._deferreds.length&&mh(function(){t._handled||gh(t._value)});for(var e=0,i=t._deferreds.length;e<i;e++)r(t,t._deferreds[e]);t._deferreds=null}function c(t,e,i){this.onFulfilled="function"==typeof t?t:null,this.onRejected="function"==typeof e?e:null,this.promise=i}function u(t,e){var i=!1;try{t(function(t){i||(i=!0,o(e,t))},function(t){i||(i=!0,a(e,t))})}catch(t){if(i)return;i=!0,a(e,t)}}function h(t){if("undefined"!=typeof window){var e=new RegExp(t+"=([^&#=]*)"),i=e.exec(window.location.search);return i?decodeURIComponent(i[1]):void 0}}function l(t){return!!t&&("string"!=typeof t||/^1|true|t|yes|y$/i.test(t))}function d(t,e){return void 0!==t?t:e}function f(){var t=window.location.protocol;return null===t.match(/http(s)?:/gi)?"http:":t}function p(){if("undefined"==typeof window)return!1;var t=window.navigator.userAgent;return/Opera|OPR/.test(t)?"Opera":/Chrome/i.test(t)?"Chrome":/Firefox/i.test(t)?"Firefox":/Mobile(\/.*)? 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Float32Array(c*u*3),p=new Float32Array(c*u*2),m=0,g=0,v=0;v<u;v++)for(var y=v*l-o,b=0;b<c;b++){var x=b*h-r;d[m]=x,d[m+1]=-y,f[m+2]=1,p[g]=b/a,p[g+1]=1-v/s,m+=3,g+=2}m=0;for(var w=new(d.length/3>65535?Uint32Array:Uint16Array)(a*s*6),v=0;v<s;v++)for(var b=0;b<a;b++){var _=b+c*v,S=b+c*(v+1),A=b+1+c*(v+1),M=b+1+c*v;w[m]=_,w[m+1]=S,w[m+2]=M,w[m+3]=S,w[m+4]=A,w[m+5]=M,m+=6}this.setIndex(new Kt(w,1)),this.addAttribute("position",new Kt(d,3)),this.addAttribute("normal",new Kt(f,3)),this.addAttribute("uv",new Kt(p,2))}function Pe(){re.call(this),this.type="Camera",this.matrixWorldInverse=new O,this.projectionMatrix=new O}function Ce(t,e,i,n){Pe.call(this),this.type="PerspectiveCamera",this.fov=void 0!==t?t:50,this.zoom=1,this.near=void 0!==i?i:.1,this.far=void 0!==n?n:2e3,this.focus=10,this.aspect=void 0!==e?e:1,this.view=null,this.filmGauge=35,this.filmOffset=0,this.updateProjectionMatrix()}function Te(t,e,i,n,r,o){Pe.call(this),this.type="OrthographicCamera",this.zoom=1,this.view=null,this.left=t,this.right=e,this.top=i,this.bottom=n,this.near=void 0!==r?r:.1,this.far=void 0!==o?o:2e3,this.updateProjectionMatrix()}function Ee(t){function e(){return null===rt?vt:1}function i(t,e,i,n){W===!0&&(t*=n,e*=n,i*=n),Gt.clearColor(t,e,i,n)}function n(){Gt.init(),Gt.scissor(ut.copy(yt).multiplyScalar(vt)),Gt.viewport(lt.copy(At).multiplyScalar(vt)),i(ft.r,ft.g,ft.b,pt)}function r(){nt=null,ct=null,st="",at=-1,Gt.reset()}function o(t){t.preventDefault(),r(),n(),Ht.clear()}function a(t){var e=t.target;e.removeEventListener("dispose",a),s(e)}function s(t){c(t),Ht.delete(t)}function c(t){var e=Ht.get(t).program;t.program=void 0,void 0!==e&&qt.releaseProgram(e)}function u(t,e,i,n){var r;if(i&&i.isInstancedBufferGeometry&&(r=$t.get("ANGLE_instanced_arrays"),null===r))return void console.error("THREE.WebGLRenderer.setupVertexAttributes: using THREE.InstancedBufferGeometry but hardware does not 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t.object.renderOrder!==e.object.renderOrder?t.object.renderOrder-e.object.renderOrder:t.material.program&&e.material.program&&t.material.program!==e.material.program?t.material.program.id-e.material.program.id:t.material.id!==e.material.id?t.material.id-e.material.id:t.z!==e.z?t.z-e.z:t.id-e.id}function d(t,e){return t.object.renderOrder!==e.object.renderOrder?t.object.renderOrder-e.object.renderOrder:t.z!==e.z?e.z-t.z:t.id-e.id}function f(t,e,i,n,r){var o,a;i.transparent?(o=K,a=++Q):(o=Y,a=++Z);var s=o[a];void 0!==s?(s.id=t.id,s.object=t,s.geometry=e,s.material=i,s.z=kt.z,s.group=r):(s={id:t.id,object:t,geometry:e,material:i,z:kt.z,group:r},o.push(s))}function p(t){var e=t.geometry;return null===e.boundingSphere&&e.computeBoundingSphere(),Rt.copy(e.boundingSphere).applyMatrix4(t.matrixWorld),g(Rt)}function m(t){return Rt.center.set(0,0,0),Rt.radius=.7071067811865476,Rt.applyMatrix4(t.matrixWorld),g(Rt)}function g(t){if(!Mt.intersectsSphere(t))return!1;var e=Tt.numPlanes;if(0===e)return!0;var i=it.clippingPlanes,n=t.center,r=-t.radius,o=0;do if(i[o].distanceToPoint(n)<r)return!1;while(++o!==e);return!0}function v(t,e){if(t.visible!==!1){var i=0!==(t.layers.mask&e.layers.mask);if(i)if(t.isLight)q.push(t);else if(t.isSprite)t.frustumCulled!==!1&&m(t)!==!0||tt.push(t);else if(t.isLensFlare)et.push(t);else if(t.isImmediateRenderObject)it.sortObjects===!0&&(kt.setFromMatrixPosition(t.matrixWorld),kt.applyProjection(Nt)),f(t,null,t.material,kt.z,null);else if((t.isMesh||t.isLine||t.isPoints)&&(t.isSkinnedMesh&&t.skeleton.update(),t.frustumCulled===!1||p(t)===!0)){var n=t.material;if(n.visible===!0){it.sortObjects===!0&&(kt.setFromMatrixPosition(t.matrixWorld),kt.applyProjection(Nt));var r=Xt.update(t);if(n.isMultiMaterial)for(var o=r.groups,a=n.materials,s=0,c=o.length;s<c;s++){var u=o[s],h=a[u.materialIndex];h.visible===!0&&f(t,r,h,kt.z,u)}else f(t,r,n,kt.z,null)}}for(var l=t.children,s=0,c=l.length;s<c;s++)v(l[s],e)}}function y(t,e,i,n){for(var r=0,o=t.length;r<o;r++){var a=t[r],s=a.object,c=a.geometry,u=void 0===n?a.material:n,h=a.group;if(s.modelViewMatrix.multiplyMatrices(e.matrixWorldInverse,s.matrixWorld),s.normalMatrix.getNormalMatrix(s.modelViewMatrix),s.isImmediateRenderObject){x(u);var l=w(e,i,u,s);st="",s.render(function(t){it.renderBufferImmediate(t,l,u)})}else it.renderBufferDirect(e,i,c,u,s,h)}}function b(t,e,i){var n=Ht.get(t),r=qt.getParameters(t,zt,e,Tt.numPlanes,i),o=qt.getProgramCode(t,r),s=n.program,u=!0;if(void 0===s)t.addEventListener("dispose",a);else if(s.code!==o)c(t);else{if(void 0!==r.shaderID)return;u=!1}if(u){if(r.shaderID){var h=Bp[r.shaderID];n.__webglShader={name:t.type,uniforms:Fd.clone(h.uniforms),vertexShader:h.vertexShader,fragmentShader:h.fragmentShader}}else n.__webglShader={name:t.type,uniforms:t.uniforms,vertexShader:t.vertexShader,fragmentShader:t.fragmentShader};t.__webglShader=n.__webglShader,s=qt.acquireProgram(t,r,o),n.program=s,t.program=s}var l=s.getAttributes();if(t.morphTargets){t.numSupportedMorphTargets=0;for(var d=0;d<it.maxMorphTargets;d++)l["morphTarget"+d]>=0&&t.numSupportedMorphTargets++}if(t.morphNormals){t.numSupportedMorphNormals=0;for(var d=0;d<it.maxMorphNormals;d++)l["morphNormal"+d]>=0&&t.numSupportedMorphNormals++}var f=n.__webglShader.uniforms;!t.isShaderMaterial&&!t.isRawShaderMaterial|t.clipping===!0&&(n.numClippingPlanes=Tt.numPlanes,f.clippingPlanes=Tt.uniform),n.fog=e,n.lightsHash=zt.hash,t.lights&&(f.ambientLightColor.value=zt.ambient,f.directionalLights.value=zt.directional,f.spotLights.value=zt.spot,f.pointLights.value=zt.point,f.hemisphereLights.value=zt.hemi,f.directionalShadowMap.value=zt.directionalShadowMap,f.directionalShadowMatrix.value=zt.directionalShadowMatrix,f.spotShadowMap.value=zt.spotShadowMap,f.spotShadowMatrix.value=zt.spotShadowMatrix,f.pointShadowMap.value=zt.pointShadowMap,f.pointShadowMatrix.value=zt.pointShadowMatrix);var p=n.program.getUniforms(),m=bt.seqWithValue(p.seq,f);n.uniformsList=m,n.dynamicUniforms=bt.splitDynamic(m,f)}function x(t){t.side===Ch?Gt.disable(Ut.CULL_FACE):Gt.enable(Ut.CULL_FACE),Gt.setFlipSided(t.side===Ph),t.transparent===!0?Gt.setBlending(t.blending,t.blendEquation,t.blendSrc,t.blendDst,t.blendEquationAlpha,t.blendSrcAlpha,t.blendDstAlpha,t.premultipliedAlpha):Gt.setBlending(Oh),Gt.setDepthFunc(t.depthFunc),Gt.setDepthTest(t.depthTest),Gt.setDepthWrite(t.depthWrite),Gt.setColorWrite(t.colorWrite),Gt.setPolygonOffset(t.polygonOffset,t.polygonOffsetFactor,t.polygonOffsetUnits)}function w(t,e,i,n){dt=0;var r=Ht.get(i);if(Et&&(Lt||t!==ct)){var o=t===ct&&i.id===at;Tt.setState(i.clippingPlanes,i.clipShadows,t,r,o)}i.needsUpdate===!1&&(void 0===r.program?i.needsUpdate=!0:i.fog&&r.fog!==e?i.needsUpdate=!0:i.lights&&r.lightsHash!==zt.hash?i.needsUpdate=!0:void 0!==r.numClippingPlanes&&r.numClippingPlanes!==Tt.numPlanes&&(i.needsUpdate=!0)),i.needsUpdate&&(b(i,e,n),i.needsUpdate=!1);var a=!1,s=!1,c=!1,u=r.program,h=u.getUniforms(),l=r.__webglShader.uniforms;if(u.id!==nt&&(Ut.useProgram(u.program),nt=u.id,a=!0,s=!0,c=!0),i.id!==at&&(at=i.id,s=!0),a||t!==ct){if(h.set(Ut,t,"projectionMatrix"),Vt.logarithmicDepthBuffer&&h.setValue(Ut,"logDepthBufFC",2/(Math.log(t.far+1)/Math.LN2)),t!==ct&&(ct=t,s=!0,c=!0),i.isShaderMaterial||i.isMeshPhongMaterial||i.isMeshStandardMaterial||i.envMap){var d=h.map.cameraPosition;void 0!==d&&d.setValue(Ut,kt.setFromMatrixPosition(t.matrixWorld))}(i.isMeshPhongMaterial||i.isMeshLambertMaterial||i.isMeshBasicMaterial||i.isMeshStandardMaterial||i.isShaderMaterial||i.skinning)&&h.setValue(Ut,"viewMatrix",t.matrixWorldInverse),h.set(Ut,it,"toneMappingExposure"),h.set(Ut,it,"toneMappingWhitePoint")}if(i.skinning){h.setOptional(Ut,n,"bindMatrix"),h.setOptional(Ut,n,"bindMatrixInverse");var f=n.skeleton;f&&(Vt.floatVertexTextures&&f.useVertexTexture?(h.set(Ut,f,"boneTexture"),h.set(Ut,f,"boneTextureWidth"),h.set(Ut,f,"boneTextureHeight")):h.setOptional(Ut,f,"boneMatrices"))}s&&(i.lights&&L(l,c),e&&i.fog&&P(l,e),(i.isMeshBasicMaterial||i.isMeshLambertMaterial||i.isMeshPhongMaterial||i.isMeshStandardMaterial||i.isMeshDepthMaterial)&&_(l,i),i.isLineBasicMaterial?S(l,i):i.isLineDashedMaterial?(S(l,i),A(l,i)):i.isPointsMaterial?M(l,i):i.isMeshLambertMaterial?C(l,i):i.isMeshPhongMaterial?T(l,i):i.isMeshPhysicalMaterial?I(l,i):i.isMeshStandardMaterial?E(l,i):i.isMeshDepthMaterial?i.displacementMap&&(l.displacementMap.value=i.displacementMap,l.displacementScale.value=i.displacementScale,l.displacementBias.value=i.displacementBias):i.isMeshNormalMaterial&&(l.opacity.value=i.opacity),bt.upload(Ut,r.uniformsList,l,it)),h.set(Ut,n,"modelViewMatrix"),h.set(Ut,n,"normalMatrix"),h.setValue(Ut,"modelMatrix",n.matrixWorld);var p=r.dynamicUniforms;return null!==p&&(bt.evalDynamic(p,l,n,t),bt.upload(Ut,p,l,it)),u}function _(t,e){t.opacity.value=e.opacity,t.diffuse.value=e.color,e.emissive&&t.emissive.value.copy(e.emissive).multiplyScalar(e.emissiveIntensity),t.map.value=e.map,t.specularMap.value=e.specularMap,t.alphaMap.value=e.alphaMap,e.aoMap&&(t.aoMap.value=e.aoMap,t.aoMapIntensity.value=e.aoMapIntensity);var i;if(e.map?i=e.map:e.specularMap?i=e.specularMap:e.displacementMap?i=e.displacementMap:e.normalMap?i=e.normalMap:e.bumpMap?i=e.bumpMap:e.roughnessMap?i=e.roughnessMap:e.metalnessMap?i=e.metalnessMap:e.alphaMap?i=e.alphaMap:e.emissiveMap&&(i=e.emissiveMap),void 0!==i){i.isWebGLRenderTarget&&(i=i.texture);var n=i.offset,r=i.repeat;t.offsetRepeat.value.set(n.x,n.y,r.x,r.y)}t.envMap.value=e.envMap,t.flipEnvMap.value=e.envMap&&e.envMap.isCubeTexture?-1:1,t.reflectivity.value=e.reflectivity,t.refractionRatio.value=e.refractionRatio}function S(t,e){t.diffuse.value=e.color,t.opacity.value=e.opacity}function A(t,e){t.dashSize.value=e.dashSize,t.totalSize.value=e.dashSize+e.gapSize,t.scale.value=e.scale}function M(t,e){if(t.diffuse.value=e.color,t.opacity.value=e.opacity,t.size.value=e.size*vt,t.scale.value=.5*U.clientHeight,t.map.value=e.map,null!==e.map){var i=e.map.offset,n=e.map.repeat;t.offsetRepeat.value.set(i.x,i.y,n.x,n.y)}}function P(t,e){t.fogColor.value=e.color,e.isFog?(t.fogNear.value=e.near,t.fogFar.value=e.far):e.isFogExp2&&(t.fogDensity.value=e.density)}function C(t,e){e.lightMap&&(t.lightMap.value=e.lightMap,t.lightMapIntensity.value=e.lightMapIntensity),e.emissiveMap&&(t.emissiveMap.value=e.emissiveMap)}function T(t,e){t.specular.value=e.specular,t.shininess.value=Math.max(e.shininess,1e-4),e.lightMap&&(t.lightMap.value=e.lightMap,t.lightMapIntensity.value=e.lightMapIntensity),e.emissiveMap&&(t.emissiveMap.value=e.emissiveMap),e.bumpMap&&(t.bumpMap.value=e.bumpMap,t.bumpScale.value=e.bumpScale),e.normalMap&&(t.normalMap.value=e.normalMap,t.normalScale.value.copy(e.normalScale)),e.displacementMap&&(t.displacementMap.value=e.displacementMap,t.displacementScale.value=e.displacementScale,t.displacementBias.value=e.displacementBias)}function E(t,e){t.roughness.value=e.roughness,t.metalness.value=e.metalness,e.roughnessMap&&(t.roughnessMap.value=e.roughnessMap),e.metalnessMap&&(t.metalnessMap.value=e.metalnessMap),e.lightMap&&(t.lightMap.value=e.lightMap,t.lightMapIntensity.value=e.lightMapIntensity),e.emissiveMap&&(t.emissiveMap.value=e.emissiveMap),e.bumpMap&&(t.bumpMap.value=e.bumpMap,t.bumpScale.value=e.bumpScale),e.normalMap&&(t.normalMap.value=e.normalMap,t.normalScale.value.copy(e.normalScale)),e.displacementMap&&(t.displacementMap.value=e.displacementMap,t.displacementScale.value=e.displacementScale,t.displacementBias.value=e.displacementBias),e.envMap&&(t.envMapIntensity.value=e.envMapIntensity)}function I(t,e){t.clearCoat.value=e.clearCoat,t.clearCoatRoughness.value=e.clearCoatRoughness,E(t,e)}function L(t,e){t.ambientLightColor.needsUpdate=e,t.directionalLights.needsUpdate=e,t.pointLights.needsUpdate=e,t.spotLights.needsUpdate=e,t.hemisphereLights.needsUpdate=e}function R(t){for(var e=0,i=0,n=t.length;i<n;i++){var r=t[i];r.castShadow&&(zt.shadows[e++]=r)}zt.shadows.length=e}function D(t,e){var i,n,r,o,a,s,c,u=0,h=0,l=0,d=e.matrixWorldInverse,f=0,p=0,m=0,g=0;for(i=0,n=t.length;i<n;i++)if(r=t[i],o=r.color,a=r.intensity,s=r.distance,c=r.shadow&&r.shadow.map?r.shadow.map.texture:null,r.isAmbientLight)u+=o.r*a,h+=o.g*a,l+=o.b*a;else if(r.isDirectionalLight){var v=Yt.get(r);v.color.copy(r.color).multiplyScalar(r.intensity),v.direction.setFromMatrixPosition(r.matrixWorld),kt.setFromMatrixPosition(r.target.matrixWorld),v.direction.sub(kt),v.direction.transformDirection(d),v.shadow=r.castShadow,r.castShadow&&(v.shadowBias=r.shadow.bias,v.shadowRadius=r.shadow.radius,v.shadowMapSize=r.shadow.mapSize),zt.directionalShadowMap[f]=c,zt.directionalShadowMatrix[f]=r.shadow.matrix,zt.directional[f++]=v}else if(r.isSpotLight){var v=Yt.get(r);v.position.setFromMatrixPosition(r.matrixWorld),v.position.applyMatrix4(d),v.color.copy(o).multiplyScalar(a),v.distance=s,v.direction.setFromMatrixPosition(r.matrixWorld),kt.setFromMatrixPosition(r.target.matrixWorld),v.direction.sub(kt),v.direction.transformDirection(d),v.coneCos=Math.cos(r.angle),v.penumbraCos=Math.cos(r.angle*(1-r.penumbra)),v.decay=0===r.distance?0:r.decay,v.shadow=r.castShadow,r.castShadow&&(v.shadowBias=r.shadow.bias,v.shadowRadius=r.shadow.radius,v.shadowMapSize=r.shadow.mapSize),zt.spotShadowMap[m]=c,zt.spotShadowMatrix[m]=r.shadow.matrix,zt.spot[m++]=v}else if(r.isPointLight){var v=Yt.get(r);v.position.setFromMatrixPosition(r.matrixWorld),v.position.applyMatrix4(d),v.color.copy(r.color).multiplyScalar(r.intensity),v.distance=r.distance,v.decay=0===r.distance?0:r.decay,v.shadow=r.castShadow,r.castShadow&&(v.shadowBias=r.shadow.bias,v.shadowRadius=r.shadow.radius,v.shadowMapSize=r.shadow.mapSize),zt.pointShadowMap[p]=c,void 0===zt.pointShadowMatrix[p]&&(zt.pointShadowMatrix[p]=new O),kt.setFromMatrixPosition(r.matrixWorld).negate(),zt.pointShadowMatrix[p].identity().setPosition(kt),zt.point[p++]=v}else if(r.isHemisphereLight){var v=Yt.get(r);v.direction.setFromMatrixPosition(r.matrixWorld),v.direction.transformDirection(d),v.direction.normalize(),v.skyColor.copy(r.color).multiplyScalar(a),v.groundColor.copy(r.groundColor).multiplyScalar(a),zt.hemi[g++]=v}zt.ambient[0]=u,zt.ambient[1]=h,zt.ambient[2]=l,zt.directional.length=f,zt.spot.length=m,zt.point.length=p,zt.hemi.length=g,zt.hash=f+","+p+","+m+","+g+","+zt.shadows.length}function F(){var t=dt;return t>=Vt.maxTextures&&console.warn("WebGLRenderer: trying to use "+t+" texture units while this GPU supports only "+Vt.maxTextures),dt+=1,t}function B(t){var e;if(t===Ml)return Ut.REPEAT;if(t===Pl)return Ut.CLAMP_TO_EDGE;if(t===Cl)return Ut.MIRRORED_REPEAT;if(t===Tl)return Ut.NEAREST;if(t===El)return Ut.NEAREST_MIPMAP_NEAREST;if(t===Il)return Ut.NEAREST_MIPMAP_LINEAR;if(t===Ll)return Ut.LINEAR;if(t===Rl)return Ut.LINEAR_MIPMAP_NEAREST;if(t===Ol)return Ut.LINEAR_MIPMAP_LINEAR;if(t===Dl)return Ut.UNSIGNED_BYTE;if(t===$l)return Ut.UNSIGNED_SHORT_4_4_4_4;if(t===Vl)return Ut.UNSIGNED_SHORT_5_5_5_1;if(t===Gl)return Ut.UNSIGNED_SHORT_5_6_5;if(t===Nl)return Ut.BYTE;if(t===kl)return Ut.SHORT;if(t===Fl)return Ut.UNSIGNED_SHORT;if(t===zl)return Ut.INT;if(t===Bl)return Ut.UNSIGNED_INT;if(t===Ul)return Ut.FLOAT;if(e=$t.get("OES_texture_half_float"),null!==e&&t===jl)return e.HALF_FLOAT_OES;if(t===Wl)return Ut.ALPHA;if(t===Xl)return Ut.RGB;if(t===ql)return Ut.RGBA;if(t===Yl)return Ut.LUMINANCE;if(t===Zl)return Ut.LUMINANCE_ALPHA;if(t===Kl)return Ut.DEPTH_COMPONENT;if(t===Ql)return Ut.DEPTH_STENCIL;if(t===Bh)return Ut.FUNC_ADD;if(t===Uh)return Ut.FUNC_SUBTRACT;if(t===jh)return Ut.FUNC_REVERSE_SUBTRACT;if(t===Gh)return Ut.ZERO;if(t===Hh)return Ut.ONE;if(t===Wh)return Ut.SRC_COLOR;if(t===Xh)return Ut.ONE_MINUS_SRC_COLOR;if(t===qh)return Ut.SRC_ALPHA;if(t===Yh)return Ut.ONE_MINUS_SRC_ALPHA;if(t===Zh)return Ut.DST_ALPHA;if(t===Kh)return Ut.ONE_MINUS_DST_ALPHA;if(t===Qh)return Ut.DST_COLOR;if(t===Jh)return Ut.ONE_MINUS_DST_COLOR;if(t===tl)return Ut.SRC_ALPHA_SATURATE;if(e=$t.get("WEBGL_compressed_texture_s3tc"),null!==e){if(t===Jl)return e.COMPRESSED_RGB_S3TC_DXT1_EXT;if(t===td)return e.COMPRESSED_RGBA_S3TC_DXT1_EXT;if(t===ed)return e.COMPRESSED_RGBA_S3TC_DXT3_EXT;if(t===id)return e.COMPRESSED_RGBA_S3TC_DXT5_EXT}if(e=$t.get("WEBGL_compressed_texture_pvrtc"),null!==e){if(t===nd)return e.COMPRESSED_RGB_PVRTC_4BPPV1_IMG;if(t===rd)return e.COMPRESSED_RGB_PVRTC_2BPPV1_IMG;if(t===od)return e.COMPRESSED_RGBA_PVRTC_4BPPV1_IMG;if(t===ad)return e.COMPRESSED_RGBA_PVRTC_2BPPV1_IMG}if(e=$t.get("WEBGL_compressed_texture_etc1"),null!==e&&t===sd)return e.COMPRESSED_RGB_ETC1_WEBGL;if(e=$t.get("EXT_blend_minmax"),null!==e){if(t===$h)return e.MIN_EXT;if(t===Vh)return e.MAX_EXT}return e=$t.get("WEBGL_depth_texture"),null!==e&&t===Hl?e.UNSIGNED_INT_24_8_WEBGL:0}console.log("THREE.WebGLRenderer",yh),t=t||{};var U=void 0!==t.canvas?t.canvas:document.createElementNS("http://www.w3.org/1999/xhtml","canvas"),j=void 0!==t.context?t.context:null,$=void 0!==t.alpha&&t.alpha,V=void 0===t.depth||t.depth,G=void 0===t.stencil||t.stencil,H=void 0!==t.antialias&&t.antialias,W=void 0===t.premultipliedAlpha||t.premultipliedAlpha,X=void 0!==t.preserveDrawingBuffer&&t.preserveDrawingBuffer,q=[],Y=[],Z=-1,K=[],Q=-1,J=new Float32Array(8),tt=[],et=[];this.domElement=U,this.context=null,this.autoClear=!0,this.autoClearColor=!0,this.autoClearDepth=!0,this.autoClearStencil=!0,this.sortObjects=!0,this.clippingPlanes=[],this.localClippingEnabled=!1,this.gammaFactor=2,this.gammaInput=!1,this.gammaOutput=!1,this.physicallyCorrectLights=!1,this.toneMapping=fl,this.toneMappingExposure=1,this.toneMappingWhitePoint=1,this.maxMorphTargets=8,this.maxMorphNormals=4;var it=this,nt=null,rt=null,ot=null,at=-1,st="",ct=null,ut=new wt,ht=null,lt=new wt,dt=0,ft=new Ct(0),pt=0,mt=U.width,gt=U.height,vt=1,yt=new wt(0,0,mt,gt),St=!1,At=new wt(0,0,mt,gt),Mt=new Ot,Tt=new ge,Et=!1,Lt=!1,Rt=new It,Nt=new O,kt=new N,zt={hash:"",ambient:[0,0,0],directional:[],directionalShadowMap:[],directionalShadowMatrix:[],spot:[],spotShadowMap:[],spotShadowMatrix:[],point:[],pointShadowMap:[],pointShadowMatrix:[],hemi:[],shadows:[]},Bt={calls:0,vertices:0,faces:0,points:0};this.info={render:Bt,memory:{geometries:0,textures:0},programs:null};var Ut;try{var jt={alpha:$,depth:V,stencil:G,antialias:H,premultipliedAlpha:W,preserveDrawingBuffer:X};if(Ut=j||U.getContext("webgl",jt)||U.getContext("experimental-webgl",jt),null===Ut)throw null!==U.getContext("webgl")?"Error creating WebGL context with your selected attributes.":"Error creating WebGL context.";void 0===Ut.getShaderPrecisionFormat&&(Ut.getShaderPrecisionFormat=function(){return{rangeMin:1,rangeMax:1,precision:1}}),U.addEventListener("webglcontextlost",o,!1)}catch(t){console.error("THREE.WebGLRenderer: "+t)}var $t=new pe(Ut);$t.get("WEBGL_depth_texture"),$t.get("OES_texture_float"),$t.get("OES_texture_float_linear"),$t.get("OES_texture_half_float"),$t.get("OES_texture_half_float_linear"),$t.get("OES_standard_derivatives"),$t.get("ANGLE_instanced_arrays"),$t.get("OES_element_index_uint")&&(ue.MaxIndex=4294967296);var Vt=new fe(Ut,$t,t),Gt=new _t(Ut,$t,B),Ht=new Ft,Wt=new xt(Ut,$t,Gt,Ht,Vt,B,this.info),Xt=new le(Ut,Ht,this.info),qt=new Zt(this,Vt),Yt=new de;this.info.programs=qt.programs;var Kt=new ve(Ut,$t,Bt),Qt=new me(Ut,$t,Bt),Jt=new Te(-1,1,1,-1,0,1),te=new Ce,ee=new Ae(new Me(2,2),new Se({depthTest:!1,depthWrite:!1,fog:!1})),ie=Bp.cube,ne=new Ae(new be(5,5,5),new Pt({uniforms:ie.uniforms,vertexShader:ie.vertexShader,fragmentShader:ie.fragmentShader,side:Ph,depthTest:!1,depthWrite:!1,fog:!1}));n(),this.context=Ut,this.capabilities=Vt,this.extensions=$t,this.properties=Ht,this.state=Gt;var re=new Dt(this,zt,Xt,Vt);this.shadowMap=re;var oe=new k(this,tt),ae=new z(this,et);this.getContext=function(){return Ut},this.getContextAttributes=function(){return Ut.getContextAttributes()},this.forceContextLoss=function(){$t.get("WEBGL_lose_context").loseContext()},this.getMaxAnisotropy=function(){return Vt.getMaxAnisotropy()},this.getPrecision=function(){return Vt.precision},this.getPixelRatio=function(){return vt},this.setPixelRatio=function(t){void 0!==t&&(vt=t,this.setSize(At.z,At.w,!1))},this.getSize=function(){return{width:mt,height:gt}},this.setSize=function(t,e,i){mt=t,gt=e,U.width=t*vt,U.height=e*vt,i!==!1&&(U.style.width=t+"px",U.style.height=e+"px"),this.setViewport(0,0,t,e)},this.setViewport=function(t,e,i,n){Gt.viewport(At.set(t,e,i,n))},this.setScissor=function(t,e,i,n){Gt.scissor(yt.set(t,e,i,n))},this.setScissorTest=function(t){Gt.setScissorTest(St=t)},this.getClearColor=function(){return ft},this.setClearColor=function(t,e){ft.set(t),pt=void 0!==e?e:1,i(ft.r,ft.g,ft.b,pt)},this.getClearAlpha=function(){return pt},this.setClearAlpha=function(t){pt=t,i(ft.r,ft.g,ft.b,pt)},this.clear=function(t,e,i){var n=0;(void 0===t||t)&&(n|=Ut.COLOR_BUFFER_BIT),(void 0===e||e)&&(n|=Ut.DEPTH_BUFFER_BIT),(void 0===i||i)&&(n|=Ut.STENCIL_BUFFER_BIT),Ut.clear(n)},this.clearColor=function(){this.clear(!0,!1,!1)},this.clearDepth=function(){this.clear(!1,!0,!1)},this.clearStencil=function(){this.clear(!1,!1,!0)},this.clearTarget=function(t,e,i,n){this.setRenderTarget(t),this.clear(e,i,n)},this.resetGLState=r,this.dispose=function(){K=[],Q=-1,Y=[],Z=-1,U.removeEventListener("webglcontextlost",o,!1)},this.renderBufferImmediate=function(t,e,i){Gt.initAttributes();var n=Ht.get(t);t.hasPositions&&!n.position&&(n.position=Ut.createBuffer()),t.hasNormals&&!n.normal&&(n.normal=Ut.createBuffer()),t.hasUvs&&!n.uv&&(n.uv=Ut.createBuffer()),t.hasColors&&!n.color&&(n.color=Ut.createBuffer());var r=e.getAttributes();if(t.hasPositions&&(Ut.bindBuffer(Ut.ARRAY_BUFFER,n.position),Ut.bufferData(Ut.ARRAY_BUFFER,t.positionArray,Ut.DYNAMIC_DRAW),Gt.enableAttribute(r.position),Ut.vertexAttribPointer(r.position,3,Ut.FLOAT,!1,0,0)),t.hasNormals){if(Ut.bindBuffer(Ut.ARRAY_BUFFER,n.normal),!i.isMeshPhongMaterial&&!i.isMeshStandardMaterial&&i.shading===Th)for(var o=0,a=3*t.count;o<a;o+=9){var s=t.normalArray,c=(s[o+0]+s[o+3]+s[o+6])/3,u=(s[o+1]+s[o+4]+s[o+7])/3,h=(s[o+2]+s[o+5]+s[o+8])/3;s[o+0]=c,s[o+1]=u,
-s[o+2]=h,s[o+3]=c,s[o+4]=u,s[o+5]=h,s[o+6]=c,s[o+7]=u,s[o+8]=h}Ut.bufferData(Ut.ARRAY_BUFFER,t.normalArray,Ut.DYNAMIC_DRAW),Gt.enableAttribute(r.normal),Ut.vertexAttribPointer(r.normal,3,Ut.FLOAT,!1,0,0)}t.hasUvs&&i.map&&(Ut.bindBuffer(Ut.ARRAY_BUFFER,n.uv),Ut.bufferData(Ut.ARRAY_BUFFER,t.uvArray,Ut.DYNAMIC_DRAW),Gt.enableAttribute(r.uv),Ut.vertexAttribPointer(r.uv,2,Ut.FLOAT,!1,0,0)),t.hasColors&&i.vertexColors!==Ih&&(Ut.bindBuffer(Ut.ARRAY_BUFFER,n.color),Ut.bufferData(Ut.ARRAY_BUFFER,t.colorArray,Ut.DYNAMIC_DRAW),Gt.enableAttribute(r.color),Ut.vertexAttribPointer(r.color,3,Ut.FLOAT,!1,0,0)),Gt.disableUnusedAttributes(),Ut.drawArrays(Ut.TRIANGLES,0,t.count),t.count=0},this.renderBufferDirect=function(t,i,n,r,o,a){x(r);var s=w(t,i,r,o),c=!1,l=n.id+"_"+s.id+"_"+r.wireframe;l!==st&&(st=l,c=!0);var d=o.morphTargetInfluences;if(void 0!==d){for(var f=[],p=0,m=d.length;p<m;p++){var g=d[p];f.push([g,p])}f.sort(h),f.length>8&&(f.length=8);for(var v=n.morphAttributes,p=0,m=f.length;p<m;p++){var g=f[p];if(J[p]=g[0],0!==g[0]){var y=g[1];r.morphTargets===!0&&v.position&&n.addAttribute("morphTarget"+p,v.position[y]),r.morphNormals===!0&&v.normal&&n.addAttribute("morphNormal"+p,v.normal[y])}else r.morphTargets===!0&&n.removeAttribute("morphTarget"+p),r.morphNormals===!0&&n.removeAttribute("morphNormal"+p)}s.getUniforms().setValue(Ut,"morphTargetInfluences",J),c=!0}var y=n.index,b=n.attributes.position;r.wireframe===!0&&(y=Xt.getWireframeAttribute(n));var _;null!==y?(_=Qt,_.setIndex(y)):_=Kt,c&&(u(r,s,n),null!==y&&Ut.bindBuffer(Ut.ELEMENT_ARRAY_BUFFER,Xt.getAttributeBuffer(y)));var S=0,A=1/0;null!==y?A=y.count:void 0!==b&&(A=b.count);var M=n.drawRange.start,P=n.drawRange.count,C=null!==a?a.start:0,T=null!==a?a.count:1/0,E=Math.max(S,M,C),I=Math.min(S+A,M+P,C+T)-1,L=Math.max(0,I-E+1);if(o.isMesh)if(r.wireframe===!0)Gt.setLineWidth(r.wireframeLinewidth*e()),_.setMode(Ut.LINES);else switch(o.drawMode){case vd:_.setMode(Ut.TRIANGLES);break;case yd:_.setMode(Ut.TRIANGLE_STRIP);break;case bd:_.setMode(Ut.TRIANGLE_FAN)}else if(o.isLine){var R=r.linewidth;void 0===R&&(R=1),Gt.setLineWidth(R*e()),o.isLineSegments?_.setMode(Ut.LINES):_.setMode(Ut.LINE_STRIP)}else o.isPoints&&_.setMode(Ut.POINTS);n&&n.isInstancedBufferGeometry?n.maxInstancedCount>0&&_.renderInstances(n,E,L):_.render(E,L)},this.render=function(t,e,n,r){if((e&&e.isCamera)===!1)return void console.error("THREE.WebGLRenderer.render: camera is not an instance of THREE.Camera.");var o=t.fog;st="",at=-1,ct=null,t.autoUpdate===!0&&t.updateMatrixWorld(),null===e.parent&&e.updateMatrixWorld(),e.matrixWorldInverse.getInverse(e.matrixWorld),Nt.multiplyMatrices(e.projectionMatrix,e.matrixWorldInverse),Mt.setFromMatrix(Nt),q.length=0,Z=-1,Q=-1,tt.length=0,et.length=0,Lt=this.localClippingEnabled,Et=Tt.init(this.clippingPlanes,Lt,e),v(t,e),Y.length=Z+1,K.length=Q+1,it.sortObjects===!0&&(Y.sort(l),K.sort(d)),Et&&Tt.beginShadows(),R(q),re.render(t,e),D(q,e),Et&&Tt.endShadows(),Bt.calls=0,Bt.vertices=0,Bt.faces=0,Bt.points=0,void 0===n&&(n=null),this.setRenderTarget(n);var a=t.background;if(null===a?i(ft.r,ft.g,ft.b,pt):a&&a.isColor&&(i(a.r,a.g,a.b,1),r=!0),(this.autoClear||r)&&this.clear(this.autoClearColor,this.autoClearDepth,this.autoClearStencil),a&&a.isCubeTexture?(te.projectionMatrix.copy(e.projectionMatrix),te.matrixWorld.extractRotation(e.matrixWorld),te.matrixWorldInverse.getInverse(te.matrixWorld),ne.material.uniforms.tCube.value=a,ne.modelViewMatrix.multiplyMatrices(te.matrixWorldInverse,ne.matrixWorld),Xt.update(ne),it.renderBufferDirect(te,null,ne.geometry,ne.material,ne,null)):a&&a.isTexture&&(ee.material.map=a,Xt.update(ee),it.renderBufferDirect(Jt,null,ee.geometry,ee.material,ee,null)),t.overrideMaterial){var s=t.overrideMaterial;y(Y,e,o,s),y(K,e,o,s)}else Gt.setBlending(Oh),y(Y,e,o),y(K,e,o);oe.render(t,e),ae.render(t,e,lt),n&&Wt.updateRenderTargetMipmap(n),Gt.setDepthTest(!0),Gt.setDepthWrite(!0),Gt.setColorWrite(!0)},this.setFaceCulling=function(t,e){Gt.setCullFace(t),Gt.setFlipSided(e===_h)},this.allocTextureUnit=F,this.setTexture2D=function(){var t=!1;return function(e,i){e&&e.isWebGLRenderTarget&&(t||(console.warn("THREE.WebGLRenderer.setTexture2D: don't use render targets as textures. Use their .texture property instead."),t=!0),e=e.texture),Wt.setTexture2D(e,i)}}(),this.setTexture=function(){var t=!1;return function(e,i){t||(console.warn("THREE.WebGLRenderer: .setTexture is deprecated, use setTexture2D instead."),t=!0),Wt.setTexture2D(e,i)}}(),this.setTextureCube=function(){var t=!1;return function(e,i){e&&e.isWebGLRenderTargetCube&&(t||(console.warn("THREE.WebGLRenderer.setTextureCube: don't use cube render targets as textures. Use their .texture property instead."),t=!0),e=e.texture),e&&e.isCubeTexture||Array.isArray(e.image)&&6===e.image.length?Wt.setTextureCube(e,i):Wt.setTextureCubeDynamic(e,i)}}(),this.getCurrentRenderTarget=function(){return rt},this.setRenderTarget=function(t){rt=t,t&&void 0===Ht.get(t).__webglFramebuffer&&Wt.setupRenderTarget(t);var e,i=t&&t.isWebGLRenderTargetCube;if(t){var n=Ht.get(t);e=i?n.__webglFramebuffer[t.activeCubeFace]:n.__webglFramebuffer,ut.copy(t.scissor),ht=t.scissorTest,lt.copy(t.viewport)}else e=null,ut.copy(yt).multiplyScalar(vt),ht=St,lt.copy(At).multiplyScalar(vt);if(ot!==e&&(Ut.bindFramebuffer(Ut.FRAMEBUFFER,e),ot=e),Gt.scissor(ut),Gt.setScissorTest(ht),Gt.viewport(lt),i){var r=Ht.get(t.texture);Ut.framebufferTexture2D(Ut.FRAMEBUFFER,Ut.COLOR_ATTACHMENT0,Ut.TEXTURE_CUBE_MAP_POSITIVE_X+t.activeCubeFace,r.__webglTexture,t.activeMipMapLevel)}},this.readRenderTargetPixels=function(t,e,i,n,r,o){if((t&&t.isWebGLRenderTarget)===!1)return void console.error("THREE.WebGLRenderer.readRenderTargetPixels: renderTarget is not THREE.WebGLRenderTarget.");var a=Ht.get(t).__webglFramebuffer;if(a){var s=!1;a!==ot&&(Ut.bindFramebuffer(Ut.FRAMEBUFFER,a),s=!0);try{var c=t.texture,u=c.format,h=c.type;if(u!==ql&&B(u)!==Ut.getParameter(Ut.IMPLEMENTATION_COLOR_READ_FORMAT))return void console.error("THREE.WebGLRenderer.readRenderTargetPixels: renderTarget is not in RGBA or implementation defined format.");if(!(h===Dl||B(h)===Ut.getParameter(Ut.IMPLEMENTATION_COLOR_READ_TYPE)||h===Ul&&($t.get("OES_texture_float")||$t.get("WEBGL_color_buffer_float"))||h===jl&&$t.get("EXT_color_buffer_half_float")))return void console.error("THREE.WebGLRenderer.readRenderTargetPixels: renderTarget is not in UnsignedByteType or implementation defined type.");Ut.checkFramebufferStatus(Ut.FRAMEBUFFER)===Ut.FRAMEBUFFER_COMPLETE?e>=0&&e<=t.width-n&&i>=0&&i<=t.height-r&&Ut.readPixels(e,i,n,r,B(u),B(h),o):console.error("THREE.WebGLRenderer.readRenderTargetPixels: readPixels from renderTarget failed. 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Ve(e,c),this.add(this.cone),this.update()}function un(t,e,i,n,r,o,a){ue.call(this),this.type="SphereBufferGeometry",this.parameters={radius:t,widthSegments:e,heightSegments:i,phiStart:n,phiLength:r,thetaStart:o,thetaLength:a},t=t||50,e=Math.max(3,Math.floor(e)||8),i=Math.max(2,Math.floor(i)||6),n=void 0!==n?n:0,r=void 0!==r?r:2*Math.PI,o=void 0!==o?o:0,a=void 0!==a?a:Math.PI;for(var s=o+a,c=(e+1)*(i+1),u=new Kt(new Float32Array(3*c),3),h=new Kt(new Float32Array(3*c),3),l=new Kt(new Float32Array(2*c),2),d=0,f=[],p=new N,m=0;m<=i;m++){for(var g=[],v=m/i,y=0;y<=e;y++){var b=y/e,x=-t*Math.cos(n+b*r)*Math.sin(o+v*a),w=t*Math.cos(o+v*a),_=t*Math.sin(n+b*r)*Math.sin(o+v*a);p.set(x,w,_).normalize(),u.setXYZ(d,x,w,_),h.setXYZ(d,p.x,p.y,p.z),l.setXY(d,b,1-v),g.push(d),d++}f.push(g)}for(var S=[],m=0;m<i;m++)for(var y=0;y<e;y++){var A=f[m][y+1],M=f[m][y],P=f[m+1][y],C=f[m+1][y+1];(0!==m||o>0)&&S.push(A,M,C),(m!==i-1||s<Math.PI)&&S.push(M,P,C)}this.setIndex(new(u.count>65535?Jt:Qt)(S,1)),this.addAttribute("position",u),this.addAttribute("normal",h),this.addAttribute("uv",l),this.boundingSphere=new It(new N,t)}function hn(t,e,i,n,r,o,a){ae.call(this),this.type="SphereGeometry",this.parameters={radius:t,widthSegments:e,heightSegments:i,phiStart:n,phiLength:r,thetaStart:o,thetaLength:a},this.fromBufferGeometry(new un(t,e,i,n,r,o,a))}function ln(t,e){re.call(this),this.light=t,this.light.updateMatrixWorld(),this.matrix=t.matrixWorld,this.matrixAutoUpdate=!1,this.colors=[new Ct,new Ct];var i=new hn(e,4,2);i.rotateX(-Math.PI/2);for(var n=0,r=8;n<r;n++)i.faces[n].color=this.colors[n<4?0:1];var o=new Se({vertexColors:Lh,wireframe:!0});this.lightSphere=new Ae(i,o),this.add(this.lightSphere),this.update()}function dn(t,e,i,n){this.object=t,this.size=void 0!==e?e:1;var r=void 0!==i?i:16776960,o=void 0!==n?n:1,a=0,s=this.object.geometry;s&&s.isGeometry?a=s.faces.length:console.warn("THREE.FaceNormalsHelper: only THREE.Geometry is supported. Use THREE.VertexNormalsHelper, instead.");var c=new ue,u=new te(2*a*3,3);c.addAttribute("position",u),Ve.call(this,c,new je({color:r,linewidth:o})),this.matrixAutoUpdate=!1,this.update()}function fn(t,e){function i(t,e){return t-e}ue.call(this),e=void 0!==e?e:1;var n,r=Math.cos(Ed.DEG2RAD*e),o=[0,0],a={},s=["a","b","c"];t&&t.isBufferGeometry?(n=new ae,n.fromBufferGeometry(t)):n=t.clone(),n.mergeVertices(),n.computeFaceNormals();for(var c=n.vertices,u=n.faces,h=0,l=u.length;h<l;h++)for(var d=u[h],f=0;f<3;f++){o[0]=d[s[f]],o[1]=d[s[(f+1)%3]],o.sort(i);var p=o.toString();void 0===a[p]?a[p]={vert1:o[0],vert2:o[1],face1:h,face2:void 0}:a[p].face2=h}var m=[];for(var p in a){var g=a[p];if(void 0===g.face2||u[g.face1].normal.dot(u[g.face2].normal)<=r){var v=c[g.vert1];m.push(v.x),m.push(v.y),m.push(v.z),v=c[g.vert2],m.push(v.x),m.push(v.y),m.push(v.z)}}this.addAttribute("position",new Kt(new Float32Array(m),3))}function pn(t,e){re.call(this),this.light=t,this.light.updateMatrixWorld(),this.matrix=t.matrixWorld,this.matrixAutoUpdate=!1,void 0===e&&(e=1);var i=new ue;i.addAttribute("position",new te([-e,e,0,e,e,0,e,-e,0,-e,-e,0,-e,e,0],3));var n=new je({fog:!1});this.add(new $e(i,n)),i=new ue,i.addAttribute("position",new te([0,0,0,0,0,1],3)),this.add(new $e(i,n)),this.update()}function mn(t){function e(t,e,n){i(t,n),i(e,n)}function i(t,e){n.vertices.push(new N),n.colors.push(new Ct(e)),void 0===o[t]&&(o[t]=[]),o[t].push(n.vertices.length-1)}var n=new ae,r=new 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Float32Array(3*p),3),b=new Kt(new Float32Array(2*p),2),x=0,w=0,_=[],S=i/2,A=0;h(),o===!1&&(t>0&&l(!0),e>0&&l(!1)),this.setIndex(g),this.addAttribute("position",v),this.addAttribute("normal",y),this.addAttribute("uv",b)}function bn(t,e,i,n,r,o){re.call(this),void 0===n&&(n=16776960),void 0===i&&(i=1),void 0===r&&(r=.2*i),void 0===o&&(o=.2*r),this.position.copy(e),this.line=new $e(Kp,new je({color:n})),this.line.matrixAutoUpdate=!1,this.add(this.line),this.cone=new Ae(Qp,new Se({color:n})),this.cone.matrixAutoUpdate=!1,this.add(this.cone),this.setDirection(t),this.setLength(i,r,o)}function xn(t,e,i,n){function r(t){var e=t.normalize().clone();e.index=h.vertices.push(e)-1;var i=s(t)/2/Math.PI+.5,n=c(t)/Math.PI+.5;return e.uv=new I(i,1-n),e}function o(t,e,i){var n=new ee(t.index,e.index,i.index,[t.clone(),e.clone(),i.clone()]);h.faces.push(n),b.copy(t).add(e).add(i).divideScalar(3);var r=s(b);h.faceVertexUvs[0].push([u(t.uv,t,r),u(e.uv,e,r),u(i.uv,i,r)])}function a(t,e){for(var i=Math.pow(2,e),n=r(h.vertices[t.a]),a=r(h.vertices[t.b]),s=r(h.vertices[t.c]),c=[],u=0;u<=i;u++){c[u]=[];for(var l=r(n.clone().lerp(s,u/i)),d=r(a.clone().lerp(s,u/i)),f=i-u,p=0;p<=f;p++)0===p&&u===i?c[u][p]=l:c[u][p]=r(l.clone().lerp(d,p/f))}for(var u=0;u<i;u++)for(var p=0;p<2*(i-u)-1;p++){var m=Math.floor(p/2);p%2===0?o(c[u][m+1],c[u+1][m],c[u][m]):o(c[u][m+1],c[u+1][m+1],c[u+1][m])}}function s(t){return Math.atan2(t.z,-t.x)}function c(t){return Math.atan2(-t.y,Math.sqrt(t.x*t.x+t.z*t.z))}function u(t,e,i){return i<0&&1===t.x&&(t=new I(t.x-1,t.y)),0===e.x&&0===e.z&&(t=new I(i/2/Math.PI+.5,t.y)),t.clone()}ae.call(this),this.type="PolyhedronGeometry",this.parameters={vertices:t,indices:e,radius:i,detail:n},i=i||1,n=n||0;for(var h=this,l=0,d=t.length;l<d;l+=3)r(new N(t[l],t[l+1],t[l+2]));for(var f=this.vertices,p=[],l=0,m=0,d=e.length;l<d;l+=3,m++){var g=f[e[l]],v=f[e[l+1]],y=f[e[l+2]];p[m]=new ee(g.index,v.index,y.index,[g.clone(),v.clone(),y.clone()])}for(var b=new N,l=0,d=p.length;l<d;l++)a(p[l],n);for(var l=0,d=this.faceVertexUvs[0].length;l<d;l++){var x=this.faceVertexUvs[0][l],w=x[0].x,_=x[1].x,S=x[2].x,A=Math.max(w,_,S),M=Math.min(w,_,S);A>.9&&M<.1&&(w<.2&&(x[0].x+=1),_<.2&&(x[1].x+=1),S<.2&&(x[2].x+=1))}for(var l=0,d=this.vertices.length;l<d;l++)this.vertices[l].multiplyScalar(i);this.mergeVertices(),this.computeFaceNormals(),this.boundingSphere=new It(new N,i)}function wn(t,e){var i=(1+Math.sqrt(5))/2,n=[-1,i,0,1,i,0,-1,-i,0,1,-i,0,0,-1,i,0,1,i,0,-1,-i,0,1,-i,i,0,-1,i,0,1,-i,0,-1,-i,0,1],r=[0,11,5,0,5,1,0,1,7,0,7,10,0,10,11,1,5,9,5,11,4,11,10,2,10,7,6,7,1,8,3,9,4,3,4,2,3,2,6,3,6,8,3,8,9,4,9,5,2,4,11,6,2,10,8,6,7,9,8,1];xn.call(this,n,r,t,e),this.type="IcosahedronGeometry",this.parameters={radius:t,detail:e}}function _n(t,e,i,n,r,o){function a(t,e,i,n,r){var o=Math.cos(t),a=Math.sin(t),s=i/e*t,c=Math.cos(s);r.x=n*(2+c)*.5*o,r.y=n*(2+c)*a*.5,r.z=n*Math.sin(s)*.5}ue.call(this),this.type="TorusKnotBufferGeometry",this.parameters={radius:t,tube:e,tubularSegments:i,radialSegments:n,p:r,q:o},t=t||100,e=e||40,i=Math.floor(i)||64,n=Math.floor(n)||8,r=r||2,o=o||3;var s,c,u=(n+1)*(i+1),h=n*i*2*3,l=new Kt(new(h>65535?Uint32Array:Uint16Array)(h),1),d=new Kt(new Float32Array(3*u),3),f=new Kt(new Float32Array(3*u),3),p=new Kt(new Float32Array(2*u),2),m=0,g=0,v=new N,y=new N,b=new I,x=new N,w=new N,_=new N,S=new N,A=new N;for(s=0;s<=i;++s){var M=s/i*r*Math.PI*2;for(a(M,r,o,t,x),a(M+.01,r,o,t,w),S.subVectors(w,x),A.addVectors(w,x),_.crossVectors(S,A),A.crossVectors(_,S),_.normalize(),A.normalize(),c=0;c<=n;++c){var P=c/n*Math.PI*2,C=-e*Math.cos(P),T=e*Math.sin(P);v.x=x.x+(C*A.x+T*_.x),v.y=x.y+(C*A.y+T*_.y),v.z=x.z+(C*A.z+T*_.z),d.setXYZ(m,v.x,v.y,v.z),y.subVectors(v,x).normalize(),f.setXYZ(m,y.x,y.y,y.z),
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n="ABCDEFGHIJKLMNOPQRSTUVWXYZ",r=n.length,o=e.modelStore,a=e.chainStore,s=e.residueStore,c=function(t,e,i,n){for(var r=a.count,c=0;c<n;++c)s.chainIndex[i+c]=r;a.growIfFull(),a.modelIndex[r]=t,a.setChainname(r,e),a.setChainid(r,e),a.residueOffset[r]=i,a.residueCount[r]=n,a.count+=1,o.chainCount[t]+=1},u=function(t){for(var e=t,i=0,o=n[e%r];e>=r;)e=Math.floor(e/r),o+=n[e%r],i+=1;return i>=5&&Pv.warn("chainname overflow"),o},h=e.getAtomProxy(),l=e.getAtomProxy(),d=0,f=0,p=0,m=0,g=[];1===s.count?g.push({mIndex:0,chainname:"A",rStart:0,rCount:1}):e.eachResidueN(2,function(t,e){var i=!1,n=t.backboneType,r=e.backboneType,o=fm;m=t.index,t.modelIndex!==e.modelIndex?i=!0:t.moleculeType!==e.moleculeType?i=!0:n!==o&&n===r&&(h.index=t.backboneEndAtomIndex,l.index=e.backboneStartAtomIndex,h.connectedTo(l)||(i=!0)),i||e.index!==s.count-1||(i=!0,m=e.index),i&&(g.push({mIndex:f,chainname:u(d),rStart:p,rCount:m-p+1}),d+=1,t.modelIndex!==e.modelIndex&&(d=0,f+=1),e.index===s.count-1&&m!==e.index&&g.push({mIndex:f,chainname:u(d),rStart:s.count-1,rCount:1}),p=e.index,m=e.index)}),a.count=0,g.forEach(function(t){c(t.mIndex,t.chainname,t.rStart,t.rCount)});var v=0;e.eachModel(function(t){o.chainOffset[t.index]=v,o.chainCount[t.index]-=1,v+=o.chainCount[t.index]})}t.Debug&&Pv.timeEnd("calculateChainnames")}function Zo(e){t.Debug&&Pv.time("calculateBonds"),Jo(e),ta(e),t.Debug&&Pv.timeEnd("calculateBonds")}function Ko(e){var i=e.structure,n=i.getAtomProxy(),r=i.getAtomProxy(),o=e.atomCount,a=e.atomOffset,s=a+o,c=s-1;if(o>500)return void(t.Debug&&Pv.warn("more than 500 atoms, skip residue for auto-bonding",e.qualifiedName()));var u,h,l=[],d=[],f=[];if(o>50){var p=new Vo(e,!0),m=e.isCg()?1.2:2.3;for(u=a;u<c;++u){n.index=u;var g=n.covalent+m+.3,v=p.nearest(n,1/0,g*g),y=v.length;for(h=0;h<y;++h)r.index=v[h].index,n.index<r.index&&n.connectedTo(r)&&(l.push(n.index-a),d.push(r.index-a),f.push(1))}}else for(u=a;u<c;++u)for(n.index=u,h=u+1;h<=c;++h)r.index=h,n.connectedTo(r)&&(l.push(u-a),d.push(h-a),f.push(1));return{atomIndices1:l,atomIndices2:d,bondOrders:f}}function Qo(e){t.Debug&&Pv.time("calculateAtomBondMap");var i=[];return e.eachBond(function(t){var e=t.atomIndex1,n=t.atomIndex2;void 0===i[e]&&(i[e]=[]),i[e][n]=t.index}),t.Debug&&Pv.timeEnd("calculateAtomBondMap"),i}function Jo(e,i){t.Debug&&Pv.time("calculateBondsWithin");var n=e.bondStore,r=e.rungBondStore,o=e.getAtomSet(!1),a=e.getAtomProxy(),s=e.getAtomProxy(),c=e.getBondProxy(),u=Qo(e);e.eachResidue(function(t){if(!i){var e=t.atomCount,h=t.atomOffset;if(e>500)return void Pv.warn("more than 500 atoms, skip residue for auto-bonding",t.qualifiedName());for(var l=t.getBonds(),d=l.atomIndices1,f=l.atomIndices2,p=l.bondOrders,m=d.length,g=0;g<m;++g){var v=d[g]+h,y=f[g]+h,b=u[v];if(void 0!==b&&void 0!==(b=b[y])){c.index=b;var x=t.residueType.getBondIndex(v,y);p[x]=c.bondOrder}else a.index=v,s.index=y,n.addBond(a,s,p[g])}}var w=t.residueType.traceAtomIndex,_=t.residueType.rungEndAtomIndex;w!==-1&&_!==-1&&(a.index=t.traceAtomIndex,s.index=t.rungEndAtomIndex,r.addBond(a,s),o.add_unsafe(a.index),o.add_unsafe(s.index))}),e.atomSetDict.rung=o,t.Debug&&Pv.timeEnd("calculateBondsWithin")}function ta(e,i){function n(t,e){var n=t.backboneType,u=e.backboneType;n!==fm&&n===u&&(s.index=t.backboneEndAtomIndex,c.index=e.backboneStartAtomIndex,s.connectedTo(c)&&(i||r.addBond(s,c,1),s.index=t.traceAtomIndex,c.index=e.traceAtomIndex,o.addBond(s,c),a.add_unsafe(s.index),a.add_unsafe(c.index)))}t.Debug&&Pv.time("calculateBondsBetween");var r=e.bondStore,o=e.backboneBondStore,a=e.getAtomSet(!1),s=e.getAtomProxy(),c=e.getAtomProxy();0===o.count&&o.resize(e.residueStore.count),e.eachResidueN(2,n);var u=e.getResidueProxy(),h=e.getResidueProxy();e.eachChain(function(t){0!==t.residueCount&&(u.index=t.residueOffset,h.index=t.residueOffset+t.residueCount-1,n(h,u))}),e.atomSetDict.backbone=a,t.Debug&&Pv.timeEnd("calculateBondsBetween")}function ea(e){function i(t){var e=[];return Object.keys(o).forEach(function(i){var u=o[i].clone();s.copy(r).applyMatrix4(u),c.setFromMatrixPosition(u),c.sub(a),s.x>1&&(c.x-=1),s.x<0&&(c.x+=1),s.y>1&&(c.y-=1),s.y<0&&(c.y+=1),s.z>1&&(c.z-=1),s.z<0&&(c.z+=1),t&&c.add(t),u.setPosition(c),u.multiplyMatrices(n.fracToCart,u),u.multiply(n.cartToFrac),e.push(u)}),e}if(e.unitcell){t.Debug&&Pv.time("buildUnitcellAssembly");var n=e.unitcell,r=e.center.clone().applyMatrix4(n.cartToFrac),o=Go(n.spacegroup),a=new N,s=new N,c=new N;r.x>1&&(a.x-=1),r.x<0&&(a.x+=1),r.y>1&&(a.y-=1),r.y<0&&(a.y+=1),r.z>1&&(a.z-=1),r.z<0&&(a.z+=1);var u,h=new Wo("UNITCELL"),l=i();if(e.biomolDict.NCS){u=[new O].concat(e.biomolDict.NCS.partList[0].matrixList);var d=[];l.forEach(function(t){u.forEach(function(e){d.push(t.clone().multiply(e))})}),h.addPart(d)}else h.addPart(l);var f=new N,p=new Wo("SUPERCELL"),m=Array.prototype.concat.call(i(),i(f.set(1,1,1)),i(f.set(-1,-1,-1)),i(f.set(1,0,0)),i(f.set(1,1,0)),i(f.set(1,0,1)),i(f.set(0,1,0)),i(f.set(0,1,1)),i(f.set(0,0,1)),i(f.set(-1,0,0)),i(f.set(-1,-1,0)),i(f.set(-1,0,-1)),i(f.set(0,-1,0)),i(f.set(0,-1,-1)),i(f.set(0,0,-1)),i(f.set(1,-1,-1)),i(f.set(1,1,-1)),i(f.set(1,-1,1)),i(f.set(-1,1,1)),i(f.set(-1,-1,1)),i(f.set(-1,1,-1)),i(f.set(0,1,-1)),i(f.set(0,-1,1)),i(f.set(1,0,-1)),i(f.set(-1,0,1)),i(f.set(1,-1,0)),i(f.set(-1,1,0)));if(e.biomolDict.NCS){var g=[];m.forEach(function(t){u.forEach(function(e){g.push(t.clone().multiply(e))})}),p.addPart(g)}else p.addPart(m);e.biomolDict.UNITCELL=h,e.biomolDict.SUPERCELL=p,t.Debug&&Pv.timeEnd("buildUnitcellAssembly")}}function ia(t){var e=t.bondHash,i=e.countArray,n=e.offsetArray,r=e.indexArray,o=t.getBondProxy();t.eachResidue(function(t){var e=t.residueType;if(void 0===e.bonds){var a=t.atomOffset,s=[],c=[],u=[],h={};t.eachAtom(function(t){for(var e=t.index,l=n[e],d=i[e],f=0,p=d;f<p;++f){o.index=r[l+f];var m=o.atomIndex1,g=o.atomIndex2;if(m>g){var v=g;g=m,m=v}var y=m+"|"+g;void 0===h[y]&&(h[y]=!0,s.push(m-a),c.push(g-a),u.push(o.bondOrder))}}),e.bonds={atomIndices1:s,atomIndices2:c,bondOrders:u}}})}function na(t,e,i){this.structure=t,i=i||iy(e),this.atomname=e,this.element=i,this.vdw=Cm[i],this.covalent=Em[i]}function ra(t){function e(t,e){return t+"|"+e}function i(i,n){n=n||iy(i);var a=e(i,n),s=r[a];if(void 0===s){var c=new na(t,i,n);s=o.length,r[a]=s,o.push(c)}return s}function n(t){return o[t]}var r={},o=[];this.add=i,this.get=n,this.list=o,this.dict=r,this.toJSON=function(){var t={metadata:{version:.1,type:"AtomMap",generator:"AtomMapExporter"},idDict:r,typeList:o.map(function(t){return t.toJSON()})};return t},this.fromJSON=function(e){r=e.idDict,o=e.typeList.map(function(e){return new na(t,e.atomname,e.element)}),this.list=o,this.dict=r}}function oa(t,e,i,n,r,o){this.structure=t,this.resname=e,this.atomTypeIdList=i,this.hetero=n?1:0,this.chemCompType=r,this.bonds=o,this.rings=void 0,this.atomCount=i.length,this.moleculeType=this.getMoleculeType(),this.backboneType=this.getBackboneType(0),this.backboneEndType=this.getBackboneType(-1),this.backboneStartType=this.getBackboneType(1),this.backboneIndexList=this.getBackboneIndexList();var a=Vm[this.backboneType],s=Vm[this.backboneStartType],c=Vm[this.backboneEndType],u=this.getAtomIndexByName(a.trace);this.traceAtomIndex=void 0!==u?u:-1;var h=this.getAtomIndexByName(a.direction1);this.direction1AtomIndex=void 0!==h?h:-1;var l=this.getAtomIndexByName(a.direction2);this.direction2AtomIndex=void 0!==l?l:-1;var d=this.getAtomIndexByName(s.backboneStart);this.backboneStartAtomIndex=void 0!==d?d:-1;var f=this.getAtomIndexByName(c.backboneEnd);this.backboneEndAtomIndex=void 0!==f?f:-1;var p;p=Fm.includes(e)?this.getAtomIndexByName("N1"):this.getAtomIndexByName("N3"),this.rungEndAtomIndex=void 0!==p?p:-1,this.bondReferenceAtomIndices=[]}function aa(t){function e(t,e,i,n){return t+"|"+e.join(",")+"|"+(i?1:0)+"|"+(n?n:"")}function i(i,n,a,s,c){i=i.toUpperCase();var u=e(i,n,a,s),h=r[u];if(void 0===h){var l=new oa(t,i,n,a,s,c);h=o.length,r[u]=h,o.push(l)}return h}function n(t){return o[t]}var r={},o=[];this.add=i,this.get=n,this.list=o,this.dict=r}function sa(t,e){this.structure=t,this.bondStore=t.bondStore,this.index=e,this._v12=new N,this._v13=new N,this._ap1=this.structure.getAtomProxy(),this._ap2=this.structure.getAtomProxy(),this._ap3=this.structure.getAtomProxy()}function ca(t,e){this.structure=t,this.chainStore=t.chainStore,this.residueStore=t.residueStore,this.atomStore=t.atomStore,this.residueMap=t.residueMap,this.atomMap=t.atomMap,this.bondHash=t.bondHash,this.index=e}function ua(t,e){this.structure=t,this.chainStore=t.chainStore,this.residueStore=t.residueStore,this.atomStore=t.atomStore,this.residueMap=t.residueMap,this.atomMap=t.atomMap,this.index=e}function ha(t,e,i){this.structure=t,this.chainStore=t.chainStore,this.residueStore=t.residueStore,this.atomStore=t.atomStore,this.residueIndexStart=e,this.residueIndexEnd=i,this.residueCount=i-e+1;var n=this.structure.getResidueProxy(this.residueIndexStart),r=this.structure.getResidueProxy(this.residueIndexEnd);this.isPrevConnected=void 0!==n.getPreviousConnectedResidue();var o=r.getNextConnectedResidue();this.isNextConnected=void 0!==o,this.isNextNextConnected=this.isNextConnected&&void 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r,o,a=n||{},s=this.geo,c=t.length/3;s.vertices&&s.faces?(this.geoPosition=Na(s),this.geoNormal=Fa(s),this.geoIndex=ka(s),r=s.vertices.length,o=s.faces.length):(this.geoPosition=s.attributes.position.array,this.geoNormal=s.attributes.normal.array,this.geoIndex=s.index.array,r=this.geoPosition.length/3,o=this.geoIndex.length/3),this.size=c*r,this.positionCount=c,this.geoPositionCount=r,this.geoFacesCount=o,this.transformedGeoPosition=new Float32Array(3*r),this.transformedGeoNormal=new Float32Array(3*r),this.meshPosition=new Float32Array(3*this.size),this.meshNormal=new Float32Array(3*this.size),this.meshColor=new Float32Array(3*this.size),this.meshPickingColor=new Float32Array(3*this.size);var u=this.meshPosition.length/3>65535?Uint32Array:Uint16Array;this.meshIndex=new u(c*o*3),this.makeIndex(),Da.call(this,this.meshPosition,this.meshColor,this.meshIndex,this.meshNormal,this.meshPickingColor,a),this.initNormals=!0,this.setAttributes({position:t,color:e,pickingColor:i}),this.initNormals=!1}function Ba(t,e,i,n,r){var o=r||{},a=d(o.sphereDetail,1);this.geo=new wn(1,a),this._radius=i,za.call(this,t,e,n,o)}function Ua(t){this.size=this.count,this.attributeSize=this.count*this.mappingSize;var e=this.count*this.mappingIndicesSize,i=this.attributeSize>65535?Uint32Array:Uint16Array;this.index=new i(e),this.makeIndex(),Oa.call(this,null,null,this.index,null,t),this.addAttributes({mapping:{type:this.mappingType,value:null}})}function ja(t){this.mapping=new Float32Array([-1,1,-1,-1,1,1,1,-1]),this.mappingIndices=new Uint16Array([0,1,2,1,3,2]),this.mappingIndicesSize=6,this.mappingType="v2",this.mappingSize=4,this.mappingItemSize=2,Ua.call(this,t)}function $a(t,e,i,n,r){this.impostor=!0,this.count=t.length/3,this.vertexShader="SphereImpostor.vert",this.fragmentShader="SphereImpostor.frag",ja.call(this,r),this.addUniforms({projectionMatrixInverse:{value:new O},ortho:{value:0}}),this.addAttributes({radius:{type:"f",value:null}}),this.setAttributes({position:t,color:e,radius:i}),n&&(this.addAttributes({pickingColor:{type:"c",value:null}}),this.setAttributes({pickingColor:n}),this.pickable=!0),this.makeMapping()}function Va(t,e,i,n,r){var o=r||{};return!Mv||o.disableImpostor?new Ba(t,e,i,n,r):new $a(t,e,i,n,r)}function Ga(t,e,i,n,r,o,a){var s=a||{},c=d(s.sphereDetail,2);this.updateNormals=!0,this.geo=new wn(1,c),this._radius=i,this._majorAxis=n,this._minorAxis=r,za.call(this,t,e,o,s)}function Ha(t,e,i,n,r,o,a){return new Ga(t,e,i,n,r,o,a)}function Wa(t,e,i,n,r,o,a,s){var c=s||{},u=d(c.radialSegments,10),h=d(c.openEnded,!0);this.updateNormals=!0;var l=(new O).makeRotationX(Math.PI/2);this.geo=new yn(1,1,1,u,1,h),this.geo.applyMatrix(l);var f=t.length,p=r.length;this._position=new Float32Array(2*f),this._color=new Float32Array(2*f),this._pickingColor=new Float32Array(2*f),this._from=new Float32Array(2*f),this._to=new Float32Array(2*f),this._radius=new Float32Array(2*p),this.__center=new Float32Array(f),za.call(this,this._position,this._color,this._pickingColor,c),this.setAttributes({position1:t,position2:e,color:i,color2:n,radius:r,pickingColor:o,pickingColor2:a})}function Xa(t){this.mapping=new Float32Array([-1,1,-1,-1,-1,-1,1,1,-1,1,1,1,1,-1,-1,1,-1,1]),this.mappingIndices=new Uint16Array([0,1,2,1,4,2,2,4,3,4,5,3]),this.mappingIndicesSize=12,this.mappingType="v3",this.mappingSize=6,this.mappingItemSize=3,Ua.call(this,t)}function qa(t,e,i,n,r,o,a,s){var c=s||{};this.openEnded=d(c.openEnded,!1),this.impostor=!0,this.count=t.length/3,this.vertexShader="CylinderImpostor.vert",this.fragmentShader="CylinderImpostor.frag",Xa.call(this,c);var u=new rn(new O).onUpdate(function(t){this.value.getInverse(t.modelViewMatrix)});this.addUniforms({modelViewMatrixInverse:u,ortho:{value:0}}),this.addAttributes({position1:{type:"v3",value:null},position2:{type:"v3",value:null},color2:{type:"c",value:null},radius:{type:"f",value:null}}),this.setAttributes({position1:t,position2:e,color:i,color2:n,radius:r}),o&&(this.addAttributes({pickingColor:{type:"c",value:null},pickingColor2:{type:"c",value:null}}),this.setAttributes({pickingColor:o,pickingColor2:a}),this.pickable=!0),this.makeMapping()}function Ya(t,e,i,n,r,o,a,s){var c=s||{};return!Mv||c.disableImpostor?new Wa(t,e,i,n,r,o,a,s):new qa(t,e,i,n,r,o,a,s)}function Za(t,e,i,n,r,o){var a=o||{},s=d(a.radialSegments,60),c=d(a.openEnded,!1);this.updateNormals=!0;var u=(new O).makeRotationX(-Math.PI/2);this.geo=new Tn(1,1,s,1,c),this.geo.applyMatrix(u);var h=t.length,l=n.length;this._position=new Float32Array(h),this._from=new Float32Array(h),this._to=new Float32Array(h),this._radius=new Float32Array(l),za.call(this,this._position,i,r,a),this.setAttributes({position1:t,position2:e,color:i,radius:n,pickingColor:r})}function Ka(t,e,i,n,r,o){return new Za(t,e,i,n,r,o)}function Qa(t,e,i,n,r,o){function a(t){var e,i,n={};if(t.radius){for(e=0,i=p.length;e<i;++e)p[e]=t.radius[e]/c;n.cylinderRadius=p,n.coneRadius=t.radius}if(t.from&&t.to){var r=new N,o=new N,a=new N,s=new N;for(e=0,i=f.length;e<i;e+=3){r.fromArray(t.from,e),o.fromArray(t.to,e),a.subVectors(r,o);var u=a.length(),h=p[e/3]*c*2,l=Math.min(u,h);a.setLength(l),s.copy(o).add(a),s.toArray(f,e)}n.cylinderFrom=t.from,n.cylinderTo=f,n.coneFrom=f,n.coneTo=t.to}return t.color&&(n.cylinderColor=t.color,n.cylinderColor2=t.color,n.coneColor=t.color),t.pickingColor&&(n.cylinderPickingColor=t.pickingColor,n.cylinderPickingColor2=t.pickingColor,n.conePickingColor=t.pickingColor),n}var s=o||{},c=d(s.aspectRatio,1.5),u=d(s.radialSegments,50),h=d(s.openEnded,!1),l=d(s.disableImpostor,!1),f=new Float32Array(t.length),p=new Float32Array(n.length),m=a({from:t,to:e,color:i,radius:n,pickingColor:r}),g=new Ya(m.cylinderFrom,m.cylinderTo,m.cylinderColor,m.cylinderColor2,m.cylinderRadius,m.cylinderPickingColor,m.cylinderPickingColor2,{radialSegments:u,openEnded:h,disableImpostor:l}),v=new Ka(m.coneFrom,m.coneTo,m.coneColor,m.coneRadius,m.conePickingColor,{radialSegments:u,openEnded:h,disableImpostor:l});this.geometry=[g.geometry,v.geometry],this.wireframe=d(s.wireframe,!1),this.group=new We,this.wireframeGroup=new We,this.pickingGroup=new We,this.getMesh=function(t){return(new We).add(g.getMesh(t),v.getMesh(t))},this.getWireframeMesh=function(){return(new We).add(g.getWireframeMesh(),v.getWireframeMesh())},this.getPickingMesh=function(){return(new We).add(g.getPickingMesh(),v.getPickingMesh())},this.setAttributes=function(t){var e=a(t);g.setAttributes({
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Et,S=[],A=[],M=[],P=[],C=[],T=[],E=[],I=[],L=[],R=[],O=[],D=[],k=[],F=[],z=[],B=[],U=[],j=[],$=[],V=[],G=[];Object.defineProperties(this,{center:{get:function(){return x.center(b)}}}),this.boundingBox=x,this.addBuffer=n,this.addMesh=r,this.addSphere=o,this.addEllipsoid=a,this.addCylinder=s,this.addCone=c,this.addArrow=u,this.getBufferList=h,this.dispose=l}function ts(t,e,i){this.viewer=e,this.gidPool=i?i.gidPool:void 0,this.tasks=new wr,this.queue=new Ca(this.make.bind(this)),this.bufferList=[],this.init(i)}function es(t,e,i){Array.isArray(t)||(t=[t]),ts.call(this,t,e,i),this.buffer=t,this.build()}function is(){Da.apply(this,arguments)}function ns(t){this.size=t.size,this.side=t.side,this.wireframe=t.wireframe,this.visible=t.visible,this.geometry=t.geometry,this.pickable=t.pickable,this.background=t.background,this.group=new We,this.wireframeGroup=new We,this.pickingGroup=new We;var e=[],i=[],n=t,r=new t.constructor;n.makeMaterial(),r.makeMaterial(),r.geometry=t.geometry,r.wireframeGeometry=t.wireframeGeometry,r.size=t.size,r.attributeSize=t.attributeSize,r.pickable=t.pickable,r.setParameters(t.getParameters()),r.updateShader(),n.setParameters({side:"front"}),r.setParameters({side:"back",opacity:r.opacity}),this.getMesh=function(t){var o,a;return t?(a=r.getPickingMesh(),o=n.getPickingMesh()):(a=r.getMesh(),o=n.getMesh()),e.push(o),i.push(a),this.setParameters({side:this.side}),(new We).add(a,o)},this.getWireframeMesh=function(){return t.getWireframeMesh()},this.getPickingMesh=function(){return this.getMesh(!0)},this.setAttributes=function(e){t.setAttributes(e)},this.setParameters=function(t){t=Object.assign({},t),"front"===t.side?(e.forEach(function(t){t.visible=!0}),i.forEach(function(t){t.visible=!1})):"back"===t.side?(e.forEach(function(t){t.visible=!1}),i.forEach(function(t){t.visible=!0})):"double"===t.side&&(e.forEach(function(t){t.visible=!0}),i.forEach(function(t){t.visible=!0})),void 0!==t.side&&(this.side=t.side),delete t.side,n.setParameters(t),void 0!==t.wireframe&&(this.wireframe=t.wireframe,this.setVisibility(this.visible)),delete t.wireframe,r.setParameters(t)},this.setVisibility=Oa.prototype.setVisibility,this.dispose=function(){n.dispose(),r.dispose()}}function rs(t,e,i){ts.call(this,t,e,i),t instanceof Pa?(this.surface=void 0,this.volume=t):(this.surface=t,this.volume=void 0),this.boxCenter=new N,this.__boxCenter=new N,this.box=new Et,this.__box=new Et,this.setBox=function(){var t=new N;return function(){var i=e.controls.target,n=e.rotationGroup.position;t.copy(n).negate().add(i),t.equals(this.boxCenter)||this.setParameters({boxCenter:t})}.bind(this)}.bind(this)(),this.viewer.signals.orientationChanged.add(this.setBox),this.build()}function os(t){function e(t,e,i){return Math.min(Math.max(t,e),i)}function i(t,e,i,n){var r=i-t,o=n-e;return Math.sqrt(r*r+o*o)}function n(t,i,n){return n=e((n-t)/(i-t),0,1),n*n*(3-2*n)}for(var r=Object.assign({},t),o=d(r.width,256),a=d(r.height,256),s=[o/2,a/2],c=Math.min(o/2,a/2),u=d(r.delta,1/(c+1))*c,h=0,l=0,f=new Uint8Array(o*a*4),p=0,m=f.length;p<m;p+=4){var g=i(h,l,s[0],s[1]),v=1-n(c-u,c,g);f[p]=255*v,f[p+1]=255*v,f[p+2]=255*v,f[p+3]=255*v,++h===o&&(h=0,l++)}var y=new Fe(f,o,a);return y.needsUpdate=!0,y}function as(t,e,i){var n=i||{};this.point=!0,this.pointSize=d(n.pointSize,1),this.sizeAttenuation=d(n.sizeAttenuation,!0),this.sortParticles=d(n.sortParticles,!1),this.alphaTest=d(n.alphaTest,.5),this.useTexture=d(n.useTexture,!1),this.forceTransparent=d(n.forceTransparent,!1),this.edgeBleach=d(n.edgeBleach,0),this.size=t.length/3,this.attributeSize=this.size,this.vertexShader="Point.vert",this.fragmentShader="Point.frag",Oa.call(this,t,e,void 0,void 0,n),this.addUniforms({size:{value:this.pointSize},canvasHeight:{value:1},pixelRatio:{value:1},map:{value:null}})}function ss(t,e,i){ts.call(this,t,e,i),t instanceof Pa?(this.surface=void 0,this.volume=t):(this.surface=t,this.volume=void 0),this.build()}function cs(t,e,i,n,r){var o=r||{};this.size=4,this.attributeSize=this.size,this.vertexShader="Image.vert",this.fragmentShader="Image.frag",Oa.call(this,t,void 0,ny,void 0,o),this.forceTransparent=!0,this.filter=d(o.filter,"nearest"),this.tex=new Fe(e,i,n),this.tex.flipY=!0,this.addUniforms({map:{value:null},mapSize:{value:new I(i,n)}}),this.geometry.addAttribute("uv",new Kt(ry,2))}function us(t,e,i){ts.call(this,t,e,i),this.volume=t,this.build()}function hs(t,e,i){var n=i||{};if(this.selection=new On(n.sele),this.dataList=[],this.structure=t,this.structureView=this.structure.getView(this.selection),ts.call(this,t,e,n),t.biomolDict){var r={default:"default","":t.unitcell?"AU":"FULL"};Object.keys(t.biomolDict).forEach(function(t){r[t]=t}),this.parameters.assembly={type:"select",options:r,rebuild:!0}}else this.parameters.assembly=null;this.selection.signals.stringChanged.add(function(){this.build()}.bind(this)),this.build()}function ls(t,e,i,n,r){var o=r||{};this.size=t.length/3,this.vertexShader="Line.vert",this.fragmentShader="Line.frag",this.line=!0;var a=this.size,s=2*a*2;this.attributeSize=s,this.linePosition=new Float32Array(3*s),this.lineColor=new Float32Array(3*s),Oa.call(this,this.linePosition,this.lineColor,void 0,void 0,o),this.setAttributes({from:t,to:e,color:i,color2:n})}function ds(t,e,i){this.manualAttach=!0,this.trajectory=t,hs.call(this,t.structure,e,i)}function fs(t){Pv.error("makeRepresentation: representation type "+t+" unknown")}function ps(e,i,n,r){t.Debug&&Pv.time("makeRepresentation "+e);var o;if(i instanceof fa){if(o=Lv.get(e),!o)return void fs(e)}else if(i instanceof pa)if("surface"===e)o=rs;else{if("dot"!==e)return void fs(e);o=ss}else if(i instanceof Pa)if("surface"===e)o=rs;else if("dot"===e)o=ss;else{if("slice"!==e)return void fs(e);o=us}else if(i instanceof La)o=ds;else if(i instanceof Ja)o=es,i=i.getBufferList();else{if("buffer"!==e)return void Pv.error("makeRepresentation: object "+i+" unknown");o=es}var a=new o(i,n,r);return t.Debug&&Pv.timeEnd("makeRepresentation "+e),a}function ms(t,e){Object.defineProperty(this,"id",{value:oy++});var i=e||{};this.name=i.name,this.uuid=tm(),this.visible=void 0===i.visible||i.visible;var n=Object.keys(this.signals);this.signals={},n.forEach(function(t){this.signals[t]=new Rn},this),this.stage=t,this.viewer=t.viewer,this.reprList=[]}function gs(t,e,i,n){var r=i||{};r.name=d(r.name,e.type),ms.call(this,t,r),this.parent=n,this.setRepresentation(e)}function vs(t){this.list=t||[];for(var e=this.list.length,i=0;i<e;++i){var n=this.list[i];n.signals.disposed.add(this._remove,this)}}function ys(t){vs.call(this,t)}function bs(t){vs.call(this,t)}function xs(t,e){return t instanceof RegExp?null!==e.name.match(t):e.name===t}function ws(t,e){if(this.signals={parametersChanged:new Rn,fullscreenChanged:new Rn,componentAdded:new Rn,componentRemoved:new Rn,clicked:new Rn,hovered:new Rn},this.tasks=new wr,this.gidPool=new _r,this.compList=[],this.defaultFileParams={},this.viewer=new Ur(t),this.viewer.renderer){this.pickingControls=new Yv(this),this.pickingControls.signals.clicked.add(this.signals.clicked.dispatch),this.pickingControls.signals.hovered.add(this.signals.hovered.dispatch);var i=Object.assign({impostor:!0,quality:"medium",sampleLevel:0,backgroundColor:"black",rotateSpeed:2,zoomSpeed:1.2,panSpeed:.8,clipNear:0,clipFar:100,clipDist:10,fogNear:50,fogFar:100,cameraFov:40,cameraType:"perspective",lightColor:14540253,lightIntensity:1,ambientColor:14540253,ambientIntensity:.2,hoverTimeout:500},e);this.parameters=g(ws.prototype.parameters),this.setParameters(i),this.viewer.animate()}}function _s(t,e,i,n,r){this.signals={startedRunning:new Rn,haltedRunning:new Rn},t.signals.playerChanged.add(function(t){t!==this&&this.pause()},this);var o=t.numframes;this.traj=t,this.step=d(e,Math.ceil((o+1)/100)),this.timeout=d(i,50),this.start=d(n,0),this.end=Math.min(d(r,o-1),o-1),this.interpolateType="",this.interpolateStep=5,this.mode="loop",this.direction="forward",this._stopFlag=!1,this._running=!1}function Ss(t,e,i,n,r){this.seq1=t,this.seq2=e,this.gapPenalty=i||-10,this.gapExtensionPenalty=n||-1,this.substMatrix=r||"blosum62",this.substMatrix&&(this.substMatrix=ay[this.substMatrix])}function As(t,e,i,n,r){i=d(i,!1),n=d(n,""),r=d(r,"");var o,a,s,c,u;if(i){var h=t,l=e;n&&r&&(h=t.getView(new On(n)),l=e.getView(new On(r)));var f=h.getSequence(),p=l.getSequence(),m=new Ss(f.join(""),p.join(""));m.calc(),m.trace();var g,v,y,b,x;o=0,a=0,s=m.ali1.length;var w=[],_=[];for(g=0;g<s;++g)b=m.ali1[g],x=m.ali2[g],v=0,y=0,"-"===b?_[a]=!1:(_[a]=!0,v=1),"-"===x?w[o]=!1:(w[o]=!0,y=1),o+=v,a+=y;var S=[],A=[],M=h.getAtomProxy(),P=l.getAtomProxy();o=0,h.eachResidue(function(t){void 0!==t.traceAtomIndex&&t.traceAtomIndex===t.getAtomIndexByName("CA")&&(w[o]&&(M.index=t.getAtomIndexByName("CA"),S.push(M.x,M.y,M.z)),o+=1)}),o=0,l.eachResidue(function(t){void 0!==t.traceAtomIndex&&t.traceAtomIndex===t.getAtomIndexByName("CA")&&(_[o]&&(P.index=t.getAtomIndexByName("CA"),A.push(P.x,P.y,P.z)),o+=1)}),c=new 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Ts(t,e,i){this.name=t.name,this.path=t.path,this.frames=t.coordinates,this.boxes=t.boxes,La.call(this,"",e,i)}function Es(t,e,i){t="",La.call(this,t,e,i)}function Is(t,e,i){La.call(this,t,e,i)}function Ls(t,e,i){var n;return n=t&&"Frames"===t.type?new Ts(t,e,i):!t&&e.frames?new Es(t,e,i):new Is(t,e,i)}function Rs(t,e){this.signals={refreshed:new Rn},this.structure=t,this.selection=e,this.center=new N,this.boundingBox=new Et,this.init(),this.refresh()}function Os(t,e,i){var n=i||{};n.name=d(n.name,e.name),ms.call(this,t,n),this.structure=e,this.trajList=[],this.initSelection(n.sele),this.setDefaultAssembly(n.assembly||""),this.stage.gidPool.addObject(this.structure)}function Ds(t,e,i){var n=i||{};n.name=d(n.name,e.name),ms.call(this,t,n),this.surface=e}function Ns(t,e,i){var n=i||{};n.name=d(n.name,e.name),ms.call(this,t,n),this.volume=e,this.stage.gidPool.addObject(this.volume)}function ks(t,e,i){hs.call(this,t,e,i)}function Fs(t,e,i){hs.call(this,t,e,i)}function 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s=e,c=s-1,h=o||0,l=0;l<c;++l)u(g,i,n,r,h),h+=3*t;a&&(u(g,i,n,r,h),h+=3*t),b.toArray(r,h),y.toArray(n,h)},this.getNormalDir=function(e,i,n,r,o,a,s,u){e.reset(),i.reset();var h=new N,l=new N,d=new N,f=new N,p=new N,m=(new N).copy(e.next()),g=(new N).copy(e.next()),v=(new N).copy(e.next()),w=new N,_=(new N).copy(i.next()),S=(new N).copy(i.next()),A=(new N).copy(i.next());y.set(0,0,1);for(var M=e.size,P=M-1,C=a||0,T=0;T<P;++T)p.copy(m),m.copy(g),g.copy(v),v.copy(e.next()),w.copy(_),_.copy(S),S.copy(A),A.copy(i.next()),0===T?(h.subVectors(w,p),l.subVectors(_,m),h.dot(l)<0&&(l.multiplyScalar(-1),_.addVectors(m,l)),d.subVectors(S,g),l.dot(d)<0&&(d.multiplyScalar(-1),S.addVectors(g,d))):d.copy(f),f.subVectors(A,v),d.dot(f)<0&&(f.multiplyScalar(-1),A.addVectors(v,f)),c(p,m,g,v,w,_,S,A,n,r,o,C,u),C+=3*t;if(s&&(p.copy(e.get(M-2)),m.copy(e.get(M-1)),g.copy(e.get(0)),v.copy(e.get(1)),w.copy(i.get(M-2)),_.copy(i.get(M-1)),S.copy(i.get(0)),A.copy(i.get(1)),d.copy(f),f.subVectors(A,v),d.dot(f)<0&&(f.multiplyScalar(-1),A.addVectors(v,f)),c(p,m,g,v,w,_,S,A,n,r,o,C,u),C+=3*t),u){b.fromArray(o,3*x),y.fromArray(r,3*x);for(var E=0;E<x;++E)b.toArray(o,3*E),y.toArray(r,3*E)}else b.toArray(o,C),y.toArray(r,C)},this.getColor=function(e,i,n,r,o,a,s){e.reset();for(var c=e.next(),u=e.next(),l=e.size,d=l-1,f=a||0,p=0;p<d;++p)c=u,u=e.next(),h(c,u,i,n,r,o,f),f+=3*t;s&&(c=e.get(l-1),u=e.get(0),h(c,u,i,n,r,o,f),f+=3*t),r[f]=r[f-3],r[f+1]=r[f-2],r[f+2]=r[f-1],o[f]=o[f-3],o[f+1]=o[f-2],o[f+2]=o[f-1]},this.getSize=function(e,i,n,r,o){e.reset();for(var a=e.next(),s=e.next(),c=e.size,u=c-1,h=r||0,d=0;d<u;++d)a=s,s=e.next(),l(a,s,i,n,h),h+=t;o&&(a=e.get(c-1),s=e.get(0),l(a,s,i,n,h),h+=t),n[h]=n[h-1]}}function js(t,e){this.polymer=t,this.size=t.residueCount;var i=e||{};this.directional=i.directional||!1,this.positionIterator=i.positionIterator||!1,this.subdiv=i.subdiv||1,this.smoothSheet=i.smoothSheet||!1,isNaN(i.tension)?this.tension=this.polymer.isNucleic()?.5:.9:this.tension=i.tension||.5,this.interpolator=new Us(this.subdiv,this.tension)}function $s(t,e,i,n,r,o,a,s){var c=s||{};this.aspectRatio=d(c.aspectRatio,1),this.radialSegments=d(c.radialSegments,4),this.capped=d(c.capped,!1),this.capVertices=this.capped?this.radialSegments:0,this.capTriangles=this.capped?this.radialSegments-2:0;var u=t.length/3,h=u-1,l=u*this.radialSegments*3+2*this.capVertices*3;this.size2=u,this.meshPosition=new Float32Array(l),this.meshColor=new Float32Array(l),this.meshNormal=new Float32Array(l),this.meshPickingColor=a?new Float32Array(l):void 0;var f=2*h*this.radialSegments*3+2*this.capTriangles*3,p=this.meshPosition.length/3>65535?Uint32Array:Uint16Array;this.meshIndex=new p(f),this.makeIndex(),Da.call(this,this.meshPosition,this.meshColor,this.meshIndex,this.meshNormal,this.meshPickingColor,c),this.setAttributes({position:t,normal:e,binormal:i,tangent:n,color:r,size:o,pickingColor:a})}function Vs(t,e,i){hs.call(this,t,e,i)}function Gs(t,e){this.sview1=t,this.sview2=e,this.kdtree2=new Vo(e)}function Hs(t,e,i){e=e||3.5,i=i||40;for(var n=new On("( ARG and ( .NE or .NH1 or 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if("N"===h.atomname||"N"===l.atomname){var w,_;if("N"===h.atomname?(w=h,_=l):(w=l,_=h),p.index=w.residueIndex,d.index=p.getAtomIndexByName("CA"),void 0===d.index)continue;var S=p.getPreviousConnectedResidue(m);if(void 0===S)continue;if(f.index=S.getAtomIndexByName("C"),void 0===f.index)continue;g.subVectors(w,f),v.subVectors(w,d),g.add(v).multiplyScalar(.5),v.subVectors(_,w),Nn(g.angleTo(v))>i&&c.bondSet.flip_unsafe(b)}else("OH"===h.atomname&&"TYR"===h.resname||"OH"===l.atomname&&"TYR"===l.resname)&&(y(h,l,"OH","CZ")||c.bondSet.flip_unsafe(b));return{atomSet:c.atomSet,bondSet:c.bondSet,bondStore:c.bondStore}}function Ws(t,e,i){e=e||3.5,i=i||40;for(var n=new On("( PROTEIN and .N )"),r=new On("( PROTEIN and .O )"),o=t.getView(n),a=t.getView(r),s=new Gs(o,a),c=s.within(e),u=c.bondStore,h=t.getAtomProxy(),l=t.getAtomProxy(),d=t.getAtomProxy(),f=t.getAtomProxy(),p=t.getResidueProxy(),m=t.getResidueProxy(),g=new N,v=new N,y=0,b=u.count;y<b;++y){h.index=u.atomIndex1[y],l.index=u.atomIndex2[y];var x,w;if("N"===h.atomname?(x=h,w=l):(x=l,w=h),p.index=x.residueIndex,d.index=p.getAtomIndexByName("CA"),void 0!==d.index){var _=p.getPreviousConnectedResidue(m);void 0!==_&&(f.index=_.getAtomIndexByName("C"),void 0!==f.index&&(g.subVectors(x,f),v.subVectors(x,d),g.add(v).multiplyScalar(.5),v.subVectors(w,x),Nn(g.angleTo(v))>i&&c.bondSet.flip_unsafe(y)))}}return{atomSet:c.atomSet,bondSet:c.bondSet,bondStore:c.bondStore}}function Xs(t,e,i){hs.call(this,t,e,i)}function qs(t){var e=Object.assign({},t);if(this.font=d(e.font,["sans-serif"]),this.size=d(e.size,36),this.style=d(e.style,"normal"),this.variant=d(e.variant,"normal"),this.weight=d(e.weight,"normal"),this.outline=d(e.outline,0),this.width=d(e.width,1024),this.height=d(e.height,1024),this.gamma=1,"undefined"!=typeof navigator){var i=navigator.userAgent;i.match(/Chrome/)&&i.match(/OS X/)&&(this.gamma=.5)}this.mapped={},this.scratchW=0,this.scratchH=0,this.currentX=0,this.currentY=0,this.build(),this.populate(),this.texture=new qe(this.canvas2),this.texture.flipY=!1,this.texture.needsUpdate=!0}function Ys(t,e,i,n,r){var o=r||{};o.forceTransparent=!0,this.fontFamily=d(o.fontFamily,"sans-serif"),this.fontStyle=d(o.fontStyle,"normal"),this.fontWeight=d(o.fontWeight,"bold"),this.fontSize=d(o.fontSize,48),this.sdf=d(o.sdf,"Chrome"===_v),this.xOffset=d(o.xOffset,0),this.yOffset=d(o.yOffset,0),this.zOffset=d(o.zOffset,.5),this.attachment=d(o.attachment,"bottom-left"),this.showBorder=d(o.showBorder,!1),this.borderColor=d(o.borderColor,"lightgrey"),this.borderWidth=d(o.borderWidth,.15),this.showBackground=d(o.showBackground,!1),this.backgroundColor=d(o.backgroundColor,"lightgrey"),this.backgroundMargin=d(o.backgroundMargin,.5),this.backgroundOpacity=d(o.backgroundOpacity,1);for(var a=t.length/3,s=0,c=0;c<a;++c)s+=n[c].length;this.text=n,this.count=s,this.showBackground&&(this.count+=a),this.positionCount=a,this.vertexShader="SDFFont.vert",this.fragmentShader="SDFFont.frag",ja.call(this,o),this.addUniforms({fontTexture:{value:null},xOffset:{value:this.xOffset},yOffset:{value:this.yOffset},zOffset:{value:this.zOffset},ortho:{value:!1},showBorder:{value:this.showBorder},borderColor:{value:new Ct(this.borderColor)},borderWidth:{value:this.borderWidth},backgroundColor:{value:new Ct(this.backgroundColor)},backgroundOpacity:{value:this.backgroundOpacity}}),this.addAttributes({inputTexCoord:{type:"v2",value:null},inputSize:{type:"f",value:null}}),this.setAttributes({position:t,size:e,color:i}),this.makeTexture(),this.makeMapping()}function Zs(t,e,i){hs.call(this,t,e,i)}function Ks(t,e,i){var n=i||{};this.size=t.length/3,this.vertexShader="Line.vert",this.fragmentShader="Line.frag",this.line=!0;var r=this.size,o=2*r;this.attributeSize=o,this.scale=n.scale||1;var a=new Ct(n.color||"grey");this.linePosition=new Float32Array(3*o),this.lineColor=Lr(o,a.r,a.g,a.b),Oa.call(this,this.linePosition,this.lineColor,void 0,void 0,n),this.setAttributes({position:t,vector:e})}function Qs(t,e,i){hs.call(this,t,e,i)}function Js(t,e,i){Fs.call(this,t,e,i)}function tc(t){this.mapping=new Float32Array([-1,-1,-1,1,-1,-1,1,-1,1,-1,-1,1,-1,1,-1,1,1,-1,1,1,1,-1,1,1]),this.mappingIndices=new Uint16Array([0,1,2,0,2,3,1,5,6,1,6,2,4,6,5,4,7,6,0,7,4,0,3,7,0,5,1,0,4,5,3,2,6,3,6,7]),this.mappingIndicesSize=36,this.mappingType="v3",this.mappingSize=8,this.mappingItemSize=3,Ua.call(this,t)}function ec(t,e){var i=t.material.uniforms;i.modelViewMatrixInverse&&i.modelViewMatrixInverse.value.getInverse(t.modelViewMatrix),i.modelViewMatrixInverseTranspose&&(i.modelViewMatrixInverse?i.modelViewMatrixInverseTranspose.value.copy(i.modelViewMatrixInverse.value).transpose():i.modelViewMatrixInverseTranspose.value.getInverse(t.modelViewMatrix).transpose()),i.modelViewProjectionMatrix&&i.modelViewProjectionMatrix.value.multiplyMatrices(e.projectionMatrix,t.modelViewMatrix),i.modelViewProjectionMatrixInverse&&(i.modelViewProjectionMatrix?(cy.copy(i.modelViewProjectionMatrix.value),i.modelViewProjectionMatrixInverse.value.getInverse(cy)):(cy.multiplyMatrices(e.projectionMatrix,t.modelViewMatrix),i.modelViewProjectionMatrixInverse.value.getInverse(cy)))}function ic(t,e,i,n,r,o,a,s,c){var u=c||{},h=d(u.shrink,.14);this.impostor=!0,this.count=t.length/3,this.vertexShader="HyperballStickImpostor.vert",this.fragmentShader="HyperballStickImpostor.frag",tc.call(this,u);var l=new rn(new O).onUpdate(ec),f=new rn(new O).onUpdate(ec),p=new rn(new O).onUpdate(ec);this.addUniforms({modelViewProjectionMatrix:l,modelViewProjectionMatrixInverse:f,modelViewMatrixInverseTranspose:p,shrink:{value:h}}),this.addAttributes({color:{type:"c",value:null},color2:{type:"c",value:null},radius:{type:"f",value:null},radius2:{type:"f",value:null},position1:{type:"v3",value:null},position2:{type:"v3",value:null}}),this.setAttributes({color:i,color2:n,radius:r,radius2:o,position1:t,position2:e,position:Er(t,e)}),a&&(this.addAttributes({pickingColor:{type:"c",value:null},pickingColor2:{type:"c",value:null}}),this.setAttributes({pickingColor:a,pickingColor2:s}),this.pickable=!0),this.makeMapping()}function nc(t,e,i,n,r,o,a,s,c){var u=c||{};return!Mv||u.disableImpostor?new Wa(t,e,i,n,Rr(r,o),a,s,c):new ic(t,e,i,n,r,o,a,s,c)}function rc(t,e,i){Js.call(this,t,e,i),this.defaultScale.vdw=.2}function oc(t,e){this.type=t,this.text=e||{}}function ac(t,e,i){hs.call(this,t,e,i)}function sc(t,e,i){hs.call(this,t,e,i)}function cc(t,e,i,n,r){function o(t,n,o){return((t*e+n)*i+o)*r}n=n||Int32Array,r=r||1;var a,s=new n(t*e*i*r);this.data=s,this.index=o,this.set=function(t,e,i){var n=o(t,e,i);for(a=0;a<r;++a)s[n+a]=arguments[3+a]},this.toArray=function(t,e,i,n,c){var u=o(t,e,i);for(void 0===n&&(n=[]),void 0===c&&(c=0),a=0;a<r;++a)n[a]=s[u+a]},this.fromArray=function(t,e,i,n,c){var u=o(t,e,i);for(void 0===c&&(c=0),a=0;a<r;++a)s[u+a]=n[c+a]},this.copy=function(t){this.data.set(t.data)},this.clone=function(){return new cc(t,e,i,n,r).copy(this)}}function uc(t,e,i){function n(t,e,i,n,o){m=e||1.4,g=i||2,P=o||!0;var a=0;for(var s in f)a=Math.max(a,s);var c=Aa(I,L,a,g,t?m:0);y=c.dim[0],b=c.dim[1],x=c.dim[2],w=c.matrix,_=c.tran,g=c.scaleFactor,S={},A={},r(t),M=m*g,v=n?n:m/g,C=new Uint8Array(y*b*x),t&&(T=new Float64Array(y*b*x)),P&&(E=new Int32Array(y*b*x))}function r(t){var e,i,n,r,o,a,s,c,u,h;for(var l in f)if(e=f[l],!S[l]){for(s=t?(e+m)*g+.5:e*g+.5,a=s*s,c=Math.floor(s)+1,u=new Int32Array(c*c),h=0,i=0;i<c;++i)for(n=0;n<c;++n)r=i*i+n*n,r>a?u[h]=-1:(o=Math.sqrt(a-r),u[h]=Math.floor(o)),++h;A[l]=c,S[l]=u}}function o(i){var n,r,o,a,s,c,u,h,l,d,f,p,m,v,w,M,T,I,L=3*i,O=i;n=Math.floor(.5+g*(t[L]+_[0])),r=Math.floor(.5+g*(t[L+1]+_[1])),o=Math.floor(.5+g*(t[L+2]+_[2]));var D,N=e[O],k=S[N],F=0,z=b*x,B=A[N];for(d=0;d<B;++d)for(f=0;f<B;++f){if(D=k[F],D!=-1)for(M=-1;M<2;++M)for(T=-1;T<2;++T)for(I=-1;I<2;++I)if(0!==M&&0!==T&&0!==I)for(u=M*d,l=I*f,p=0;p<=D;++p)if(h=p*T,m=n+u,v=r+h,w=o+l,!(m<0||v<0||w<0||m>=y||v>=b||w>=x)){var U=m*z+v*x+w;if(P)if(C[U]&R){if(C[U]&R){var j=E[U];j!==L&&(a=n+u-Math.floor(.5+g*(t[j]+_[0])),s=r+h-Math.floor(.5+g*(t[j+1]+_[1])),c=o+l-Math.floor(.5+g*(t[j+2]+_[2])),u*u+h*h+l*l<a*a+s*s+c*c&&(E[U]=i))}}else C[U]|=R,E[U]=i;else C[U]|=R}F++}}function a(e){console.time("EDTSurface fillvoxels");var i,n;for(i=0,n=C.length;i<n;++i)C[i]=0,e&&(T[i]=-1),P&&(E[i]=-1);for(i=0,n=t.length/3;i<n;++i)o(i);for(i=0,n=C.length;i<n;++i)C[i]&R&&(C[i]|=O);console.timeEnd("EDTSurface fillvoxels")}function s(i){var n,r,o,a,s,c,u,h,l,d,f,p,m,v,w,M,T,I,L,R=3*i,D=i,N=0;n=Math.floor(.5+g*(t[R]+_[0])),r=Math.floor(.5+g*(t[R+1]+_[1])),o=Math.floor(.5+g*(t[R+2]+_[2]));var k=e[D],F=b*x;for(m=0,L=A[k];m<L;++m)for(v=0;v<L;++v){if(S[k][N]!=-1)for(M=-1;M<2;++M)for(T=-1;T<2;++T)for(I=-1;I<2;++I)if(0!==M&&0!==T&&0!==I)for(u=M*m,l=I*v,w=0;w<=S[k][N];++w)if(h=w*T,d=n+u,f=r+h,p=o+l,!(d<0||f<0||p<0||d>=y||f>=b||p>=x)){var z=d*F+f*x+p;if(C[z]&O){if(P){var B=E[z];a=Math.floor(.5+g*(t[B]+_[0])),s=Math.floor(.5+g*(t[B+1]+_[1])),c=Math.floor(.5+g*(t[B+2]+_[2])),u*u+h*h+l*l<a*a+s*s+c*c&&(E[z]=i)}}else C[z]|=O,P&&(E[z]=i)}N++}}function c(){var e,i;for(e=0,i=C.length;e<i;++e)C[e]&=~O;for(e=0,i=t.length/3;e<i;++e)s(e)}function u(){var t,e,i,n=b*x;for(t=0;t<y;++t)for(e=0;e<x;++e)for(i=0;i<b;++i){var r=t*n+i*x+e;if(C[r]&R)for(var o=0;o<26;){var a=t+N[o][0],s=e+N[o][2],c=i+N[o][1];if(a>-1&&a<y&&c>-1&&c<b&&s>-1&&s<x&&!(C[a*n+c*x+s]&R)){C[r]|=D;break}o++}}}function h(){console.time("EDTSurface fastdistancemap");var t,e,i,n,r,o=new cc(y,b,x,Uint16Array,3),a=b*x,s=M*M,c=0;for(t=0;t<y;++t)for(e=0;e<b;++e)for(i=0;i<x;++i)r=t*a+e*x+i,C[r]&=~O,C[r]&R&&C[r]&D&&(o.set(t,e,i,t,e,i),T[r]=0,C[r]|=O,c+=1);var u=new Int32Array(3*c),h=0,d=new Int32Array(3*c),f=0;for(t=0;t<y;++t)for(e=0;e<b;++e)for(i=0;i<x;++i)r=t*a+e*x+i,C[r]&D&&(u[h]=t,u[h+1]=e,u[h+2]=i,h+=3,C[r]&=~D);do for(f=l(u,o,h,d),h=0,t=0,n=f;t<n;t+=3)r=a*d[t]+x*d[t+1]+d[t+2],C[r]&=~D,T[r]<=1.0404*s&&(u[h]=d[t],u[h+1]=d[t+1],u[h+2]=d[t+2],h+=3);while(h>0);var p,m=v*v,g=new Uint16Array(3);for(t=0;t<y;++t)for(e=0;e<b;++e)for(i=0;i<x;++i)r=t*a+e*x+i,C[r]&=~D,C[r]&R&&(C[r]&O&&!(C[r]&O&&T[r]>=m)||(C[r]|=D,P&&C[r]&O&&(o.toArray(t,e,i,g),p=g[0]*a+g[1]*x+g[2],E[r]=E[p])));console.timeEnd("EDTSurface fastdistancemap")}function l(t,e,i,n){var r,o,a,s,c,u,h,l,d,f,p,m,g=new Uint16Array(3),v=0;if(0===i)return v;var w=-1,_=-1,S=-1,A=b*x;for(h=0,d=i;h<d;h+=3)for(r=t[h],o=t[h+1],a=t[h+2],e.toArray(r,o,a,g),l=0;l<6;++l)m=N[l],w=r+m[0],_=o+m[1],S=a+m[2],w<y&&w>-1&&_<b&&_>-1&&S<x&&S>-1&&(p=w*A+x*_+S,C[p]&R&&!(C[p]&O)?(e.fromArray(w,_,S,g),s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,T[p]=f,C[p]|=O,C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3):C[p]&R&&C[p]&O&&(s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,f<T[p]&&(e.fromArray(w,_,S,g),T[p]=f,C[p]&D||(C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3))));for(h=0,d=i;h<d;h+=3)for(r=t[h],o=t[h+1],a=t[h+2],e.toArray(r,o,a,g),l=6;l<18;l++)m=N[l],w=r+m[0],_=o+m[1],S=a+m[2],w<y&&w>-1&&_<b&&_>-1&&S<x&&S>-1&&(p=w*A+x*_+S,C[p]&R&&!(C[p]&O)?(e.fromArray(w,_,S,g),s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,T[p]=f,C[p]|=O,C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3):C[p]&R&&C[p]&O&&(s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,f<T[p]&&(e.fromArray(w,_,S,g),T[p]=f,C[p]&D||(C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3))));for(h=0,d=i;h<d;h+=3)for(r=t[h],o=t[h+1],a=t[h+2],e.toArray(r,o,a,g),l=18;l<26;l++)m=N[l],w=r+m[0],_=o+m[1],S=a+m[2],w<y&&w>-1&&_<b&&_>-1&&S<x&&S>-1&&(p=w*A+x*_+S,C[p]&R&&!(C[p]&O)?(e.fromArray(w,_,S,g),s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,T[p]=f,C[p]|=O,C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3):C[p]&R&&C[p]&O&&(s=w-g[0],c=_-g[1],u=S-g[2],f=s*s+c*c+u*u,f<T[p]&&(e.fromArray(w,_,S,g),T[p]=f,C[p]&D||(C[p]|=D,n[v]=w,n[v+1]=_,n[v+2]=S,v+=3))));return v}function d(t){var e,i=C.length;if("vws"===t)for(e=0;e<i;++e)C[e]&=~D,C[e]=C[e]&O?1:0;else if("ms"===t)for(e=0;e<i;++e)C[e]&=~O,C[e]&D&&(C[e]|=O),C[e]&=~D,C[e]=C[e]&O?1:0;else if("ses"===t)for(e=0;e<i;++e)C[e]&D&&C[e]&O?C[e]&=~D:C[e]&D&&!(C[e]&O)&&(C[e]|=O),C[e]=C[e]&O?1:0;else if("sas"===t)for(e=0;e<i;++e)C[e]&=~D,C[e]=C[e]&O?1:0}var f=Sa(e),p=Hr(t);0===t.length&&(p[0].set([0,0,0]),p[1].set([0,0,0]));var m,g,v,y,b,x,w,_,S,A,M,P,C,T,E,I=p[0],L=p[1],R=1,O=2,D=4,N=[new Int32Array([1,0,0]),new Int32Array([-1,0,0]),new Int32Array([0,1,0]),new Int32Array([0,-1,0]),new Int32Array([0,0,1]),new Int32Array([0,0,-1]),new Int32Array([1,1,0]),new Int32Array([1,-1,0]),new Int32Array([-1,1,0]),new Int32Array([-1,-1,0]),new Int32Array([1,0,1]),new Int32Array([1,0,-1]),new Int32Array([-1,0,1]),new Int32Array([-1,0,-1]),new Int32Array([0,1,1]),new Int32Array([0,1,-1]),new Int32Array([0,-1,1]),new Int32Array([0,-1,-1]),new Int32Array([1,1,1]),new Int32Array([1,1,-1]),new Int32Array([1,-1,1]),new Int32Array([-1,1,1]),new Int32Array([1,-1,-1]),new Int32Array([-1,-1,1]),new Int32Array([-1,1,-1]),new Int32Array([-1,-1,-1])];
-this.getVolume=function(t,e,o,s,l){console.time("EDTSurface.getVolume");var f="vws"!==t;n(f,e,o,s,l),a(f),u(),"ms"!==t&&"ses"!==t||h(),"ses"===t&&(r(!1),c()),d(t);for(var p=0,m=E.length;p<m;++p)E[p]=i[E[p]];return console.timeEnd("EDTSurface.getVolume"),{data:C,nx:x,ny:b,nz:y,atomindex:E}},this.getSurface=function(t,e,i,n,r,o,a){var s=this.getVolume(t,e,i,n,r),c=new Ma(s.data,s.nx,s.ny,s.nz,s.atomindex);return c.getSurface(1,o,void 0,w,a)}}function hc(t,e,i,n,r,o,a){function s(t,e){return Math.floor((t-e)/a)}for(var c=t.length,u=r[0],h=r[1],l=r[2],d=o[0],f=o[1],p=o[2],m=s(d,u)+1,g=s(f,h)+1,v=s(p,l)+1,y=m*g*v,b=g*v,x=function(t,e,i){return(s(t,u)*g+s(e,h))*v+s(i,l)},w=[],_=0;_<c;_++){var S=x(t[_],e[_],i[_]);void 0===w[S]?w[S]=[_]:w[S].push(_)}var A=new Uint32Array(y),M=new Uint16Array(y),P=new Uint32Array(c),C=0,T=0;for(_=0;_<y;_++){var E=A[_]=C,I=w[_];if(void 0!==I)for(var L=0;L<I.length;L++)P[C]=I[L],C++;var R=C-E;M[_]=R,R>T&&(T=R)}this.neighbourListLength=27*T+1,this.withinRadii=function(r,o,a,c,d){for(var f=0,p=s(r,u),y=s(o,h),x=s(a,l),w=Math.max(0,p-1),_=Math.max(0,y-1),S=Math.max(0,x-1),C=Math.min(m,p+1),T=Math.min(g,y+1),E=Math.min(v,x+1),I=w;I<=C;++I)for(var L=I*b,R=_;R<=T;++R)for(var O=R*v,D=S;D<=E;++D)for(var N=L+O+D,k=A[N],F=k+M[N],z=k;z<F;z++){var B=P[z],U=t[B]-r,j=e[B]-o,$=i[B]-a,V=n[B]+c;U*U+j*j+$*$<=V*V&&(d[f++]=P[z])}d[f]=-1}}function lc(t,e,i){function n(t,i,n,r){T=d(t,1.4),E=d(i,2),I=d(n,!0),L=d(r,30),M=new Float32Array(y),P=new Float32Array(y);for(var c=0;c<M.length;++c){var u=e[c]+T;M[c]=u,P[c]=u*u}C=0;for(var h=0;h<M.length;++h)M[h]>C&&(C=M[h]);o(),a(),s(),W=-1}function r(t,e,i){for(var n=0;n<t.length;n++)t[n]=e+i*n}function o(){var t=Aa(G,H,C,E,0);E=t.scaleFactor,R=t.dim,O=t.matrix,V=Math.min(5,2+Math.floor(T*E)),D=Ir(R[0]*R[1]*R[2],-1001),N=new Int32Array(D.length),k=new Float32Array(R[0]),F=new Float32Array(R[1]),z=new Float32Array(R[2]),r(k,G[0],1/E),r(F,G[1],1/E),r(z,G[2],1/E)}function a(){var t=0,e=2*Math.PI/L;U=new Float32Array(L),B=new Float32Array(L);for(var i=0;i<L;i++)U[i]=Math.cos(t),B[i]=Math.sin(t),t+=e}function s(){j=new hc(b,x,w,M,G,H,2.01*C),$=new Int32Array(j.neighbourListLength)}function c(t,e,i,n,r){var o;if(W!==-1){if(o=W,o!==n&&o!==r&&u(o,t,e,i))return o;W=-1}var a=0;for(o=$[a];o>=0;){if(o!==n&&o!==r&&u(o,t,e,i))return W=o,o;o=$[++a]}return W=-1,-1}function u(e,i,n,r){var o=3*e,a=P[e],s=t[o]-i,c=t[o+1]-n,u=t[o+2]-r,h=s*s+c*c+u*u;return h<a}function h(){for(var t=0;t<y;t++){var e=b[t],i=x[t],n=w[t],r=M[t],o=P[t];j.withinRadii(e,i,n,r,$);for(var a=Math.ceil(r*E),s=Math.floor(E*(e-G[0])),u=Math.floor(E*(i-G[1])),h=Math.floor(E*(n-G[2])),l=Math.max(0,s-a),d=Math.max(0,u-a),f=Math.max(0,h-a),p=Math.min(R[0],s+a+2),m=Math.min(R[1],u+a+2),g=Math.min(R[2],h+a+2),v=l;v<p;v++)for(var _=k[v]-e,S=R[1]*R[2]*v,A=d;A<m;A++)for(var C=F[A]-i,T=_*_+C*C,L=S+R[2]*A,O=f;O<g;O++){var B=z[O]-n,U=T+B*B;if(U<o){var V=O+L;D[V]<0&&(D[V]=-D[V]);var H=Math.sqrt(U),W=r/H,X=_*W,q=C*W,Y=B*W;if(X+=e,q+=i,Y+=n,c(X,q,Y,t,-1)===-1){var Z=r-H;Z<D[V]&&(D[V]=Z,I&&(N[V]=t))}}}}}function l(){for(var t=0;t<y;t++){j.withinRadii(b[t],x[t],w[t],M[t],$);for(var e=0,i=$[e];i>=0;)t<i&&f(t,i),i=$[++e]}}function f(t,e){var i=M[t],n=M[e],r=X[0]=b[e]-b[t],o=X[1]=x[e]-x[t],a=X[2]=w[e]-w[t],s=r*r+o*o+a*a,u=Math.sqrt(s),h=(i*i+u*u-n*n)/(2*i*u),l=i*h;io(X,X),p(q,X),io(q,q),Zr(Y,X,q),io(Y,Y);var d=Math.sqrt(i*i-l*l);eo(q,q,d),eo(Y,Y,d),eo(X,X,l),X[0]+=b[t],X[1]+=x[t],X[2]+=w[t],W=-1;for(var f=V,m=0;m<L;m++){var g=U[m],v=B[m],y=X[0]+g*q[0]+v*Y[0],_=X[1]+g*q[1]+v*Y[1],S=X[2]+g*q[2]+v*Y[2];if(c(y,_,S,t,e)==-1)for(var A=Math.floor(E*(y-G[0])),P=Math.floor(E*(_-G[1])),C=Math.floor(E*(S-G[2])),T=Math.max(0,A-f),O=Math.max(0,P-f),j=Math.max(0,C-f),$=Math.min(R[0],A+f+2),H=Math.min(R[1],P+f+2),Z=Math.min(R[2],C+f+2),K=T;K<$;K++){r=y-k[K];for(var Q=R[1]*R[2]*K,J=O;J<H;J++){o=_-F[J];for(var tt=r*r+o*o,et=Q+R[2]*J,it=j;it<Z;it++){a=S-z[it],s=tt+a*a;var nt=it+et,rt=D[nt];rt>0&&s<rt*rt&&(D[nt]=Math.sqrt(s),I&&(N[nt]=t))}}}}}function p(t,e){return t[0]=t[1]=t[2]=1,0!=e[0]?t[0]=(e[1]+e[2])/-e[0]:0!=e[1]?t[1]=(e[0]+e[2])/-e[1]:0!=e[2]&&(t[2]=(e[0]+e[1])/-e[2]),t}function m(){for(var t=0;t<D.length;t++)D[t]<0&&(D[t]=0)}function g(){for(var t=0;t<N.length;t++)N[t]=i[N[t]]}function v(t,e,i){console.time("AVSurface.getVolume"),console.time("AVSurface.init"),n(t,e,i),console.timeEnd("AVSurface.init"),console.time("AVSurface.projectPoints"),h(),console.timeEnd("AVSurface.projectPoints"),console.time("AVSurface.projectTorii"),l(),console.timeEnd("AVSurface.projectTorii"),m(),g(),console.timeEnd("AVSurface.getVolume")}for(var y=e.length,b=new Float32Array(y),x=new Float32Array(y),w=new Float32Array(y),_=0;_<y;_++){var S=3*_;b[_]=t[S],x[_]=t[S+1],w[_]=t[S+2]}var A=Hr(t);0===t.length&&(A[0].set([0,0,0]),A[1].set([0,0,0]));var M,P,C,T,E,I,L,R,O,D,N,k,F,z,B,U,j,$,V,G=A[0],H=A[1],W=-1,X=new Float32Array([0,0,0]),q=new Float32Array([0,0,0]),Y=new Float32Array([0,0,0]);this.getSurface=function(t,e,i,n,r,o,a){v(e,i,r);var s=new Ma(D,R[2],R[1],R[0],N);return s.getSurface(e,!1,void 0,O,a)}}function dc(t){this.structure=t}function fc(t,e,i,n){var r=n||{};this.size=t.length/3,this.vertexShader="Line.vert",this.fragmentShader="Line.frag",this.line=!0,this.attributeSize=this.size,Oa.call(this,t,e,i,void 0,r)}function pc(t,e,i){this.__infoList=[],hs.call(this,t,e,i),this.structure.signals.refreshed.add(function(){this.__forceNewMolsurf=!0},this)}function mc(t,e,i){hs.call(this,t,e,i)}function gc(t,e,i,n,r,o,a){var s=a||{},c=t.length/3-1,u=4*c,h=3*u;this.meshPosition=new Float32Array(h),this.meshColor=new Float32Array(h),this.meshNormal=new Float32Array(h),this.meshPickingColor=o?new Float32Array(h):void 0;var l=this.meshPosition.length/3>65535?Uint32Array:Uint16Array;this.meshIndex=new l(h),this.makeIndex(),Da.call(this,this.meshPosition,this.meshColor,this.meshIndex,this.meshNormal,this.meshPickingColor,s),this.vertexShader="Ribbon.vert",this.fragmentShader="Mesh.frag",this.geometry.addAttribute("dir",new Kt(new Float32Array(h),3)),this.geometry.addAttribute("size",new Kt(new Float32Array(u),1)),this.setAttributes({position:t,normal:e,dir:i,color:n,size:r,pickingColor:o})}function vc(t,e,i){hs.call(this,t,e,i),this.defaultScale.sstruc*=3}function yc(t,e,i){this.helixbundleList=[],hs.call(this,t,e,i)}function bc(t,e,i){Vs.call(this,t,e,i)}function xc(t,e,i){hs.call(this,t,e,i)}function wc(t,e,i){var n=i||{};this.size=t.length/3,this.vertexShader="Line.vert",this.fragmentShader="Line.frag",this.line=!0;var r=this.size,o=r-1;this.attributeSize=2*o,this.linePosition=new Float32Array(3*o*2),this.lineColor=new Float32Array(3*o*2),Oa.call(this,this.linePosition,this.lineColor,void 0,void 0,n),this.setAttributes({position:t,color:e})}function _c(t,e,i){hs.call(this,t,e,i)}function Sc(t,e,i){Vs.call(this,t,e,i)}function Ac(t,e,i){hs.call(this,t,e,i)}function Mc(t,e){var i=e||{};this.streamer=t,this.name=d(i.name,""),this.path=d(i.path,"")}function Pc(t){function e(t){for(var e=l.atomCount[t],r=l.atomOffset[t],o=new Array(e),a=0;a<e;++a)o[a]=h.atomTypeId[r+a];l.residueTypeId[t]=p.add(i,o,n)}var i,n,r=null,o=null,a=null,s=null,c=null,u=null,h=t.atomStore,l=t.residueStore,d=t.chainStore,f=t.modelStore,p=t.residueMap,m=-1,g=-1,v=-1,y=-1;this.addAtom=function(t,p,b,x,w,_,S,A){var M=!1,P=!1,C=!1;r!==t?(M=!0,P=!0,C=!0,y+=1,v+=1,g+=1):o!==b?(P=!0,C=!0,v+=1,g+=1):s===w&&a===x&&c===A||(C=!0,g+=1),m+=1,M&&(f.growIfFull(),f.chainOffset[y]=v,f.chainCount[y]=0,f.count+=1,d.modelIndex[v]=y),P&&(d.growIfFull(),d.setChainname(v,p),d.setChainid(v,b),d.residueOffset[v]=g,d.residueCount[v]=0,d.count+=1,d.modelIndex[v]=y,f.chainCount[y]+=1,l.chainIndex[g]=v),C&&(i=a,n=u,g>0&&e(g-1),l.growIfFull(),l.resno[g]=w,void 0!==S&&(l.sstruc[g]=S.charCodeAt(0)),void 0!==A&&(l.inscode[g]=A.charCodeAt(0)),l.atomOffset[g]=m,l.atomCount[g]=0,l.count+=1,l.chainIndex[g]=v,d.residueCount[v]+=1),h.count+=1,h.residueIndex[m]=g,l.atomCount[g]+=1,r=t,o=b,a=x,s=w,c=A,u=_},this.finalize=function(){i=a,n=u,g>-1&&e(g)}}function Cc(t,e){var i=e||{};this.firstModelOnly=d(i.firstModelOnly,!1),this.asTrajectory=d(i.asTrajectory,!1),this.cAlphaOnly=d(i.cAlphaOnly,!1),Mc.call(this,t,i),this.structure=new fa(this.name,this.path),this.structureBuilder=new Pc(this.structure)}function Tc(t,e,i,n,r,o,a,s){this.a=t||1,this.b=e||1,this.c=i||1,this.alpha=n||90,this.beta=r||90,this.gamma=o||90,this.spacegroup=a||"P 1";var c=Dn(this.alpha),u=Dn(this.beta),h=Dn(this.gamma),l=Math.cos(c),d=Math.cos(u),f=Math.cos(h),p=Math.sin(u),m=Math.sin(h);if(this.volume=this.a*this.b*this.c*Math.sqrt(1-l*l-d*d-f*f+2*l*d*f),void 0===s){var g=this.a*this.b*m/this.volume,v=(d*f-l)/(p*m);this.fracToCart=(new O).set(this.a,0,0,0,this.b*f,this.b*m,0,0,this.c*d,-this.c*p*v,1/g,0,0,0,0,1).transpose(),this.cartToFrac=(new O).getInverse(this.fracToCart)}else this.cartToFrac=s,this.fracToCart=(new O).getInverse(this.cartToFrac)}function Ec(t,e){Cc.call(this,t,e)}function Ic(t){switch(t=t.toLowerCase()){case"polymer":return im;case"non-polymer":return nm;case"macrolide":return rm;case"water":return om;default:return em}}function Lc(t,e,i,n,r){this.structure=t,this.index=e,this.description=i||"",this.entityType=Ic(n||""),this.chainIndexList=r||[],r.forEach(function(i){t.chainStore.entityIndex[i]=e})}function Rc(t,e){Cc.call(this,t,e)}function Oc(t,e){Cc.call(this,t,e)}function Dc(t,e){Array.isArray(t[e])||Object.keys(t).forEach(function(e){t[e]=[t[e]]})}function Nc(t){return"?"!==t}function kc(t,e){return Nc(t)?t:e}function Fc(t){switch(t.toLowerCase()){case"?":case"sing":return 1;case"doub":return 2;case"trip":return 3;case"quad":return 4}return 0}function zc(t,e,i){var n,r,o=e.atomStore,a=e.atomMap,s=t.chem_comp,c=t.chem_comp_atom,u=t.chem_comp_bond;s&&(s.name&&(e.title=s.name.trim().replace(fy,"")),s.id&&(e.id=s.id.trim().replace(fy,"")));var h={};if(c){var l,d,f,p;for(r=c.comp_id.length,n=0;n<r;++n)o.growIfFull(),l=c.atom_id[n].replace(dy,""),d=c.type_symbol[n],h[l]=n,o.atomTypeId[n]=a.add(l,d),o.x[n]=c.model_Cartn_x[n],o.y[n]=c.model_Cartn_y[n],o.z[n]=c.model_Cartn_z[n],o.serial[n]=n,f=c.pdbx_component_comp_id[n],p=c.pdbx_residue_numbering?c.pdbx_residue_numbering[n]:1,i.addAtom(0,"","",f,p,1);for(n=0;n<r;++n){var m=n+r;o.growIfFull(),l=c.atom_id[n].replace(dy,""),d=c.type_symbol[n],o.atomTypeId[m]=a.add(l,d),o.x[m]=c.pdbx_model_Cartn_x_ideal[n],o.y[m]=c.pdbx_model_Cartn_y_ideal[n],o.z[m]=c.pdbx_model_Cartn_z_ideal[n],o.serial[m]=m,f=c.pdbx_component_comp_id[n],p=c.pdbx_residue_numbering?c.pdbx_residue_numbering[n]:1,i.addAtom(1,"","",f,p,1)}}if(c&&u){var g,v,y;r=u.comp_id.length;var b=c.comp_id.length,x=e.getAtomProxy(),w=e.getAtomProxy();for(n=0;n<r;++n)g=u.atom_id_1[n].replace(dy,""),v=u.atom_id_2[n].replace(dy,""),y=Fc(u.value_order[n]),x.index=h[g],w.index=h[v],e.bondStore.growIfFull(),e.bondStore.addBond(x,w,y),x.index+=b,w.index+=b,e.bondStore.growIfFull(),e.bondStore.addBond(x,w,y)}}function Bc(t,e,i){var n,r,o,a,s=[],c=[],u=t.struct_conf;if(u)for(Dc(u,"id"),n=0,r=u.beg_auth_seq_id.length;n<r;++n){var h=parseInt(u.pdbx_PDB_helix_class[n]);Number.isNaN(h)||(o=u.pdbx_beg_PDB_ins_code[n],a=u.pdbx_end_PDB_ins_code[n],s.push([i[u.beg_label_asym_id[n]],parseInt(u.beg_auth_seq_id[n]),kc(o,""),i[u.end_label_asym_id[n]],parseInt(u.end_auth_seq_id[n]),kc(a,""),(uy[h]||uy[""]).charCodeAt(0)]))}var l=t.struct_sheet_range;if(l)for(Dc(l,"id"),n=0,r=l.beg_auth_seq_id.length;n<r;++n)o=l.pdbx_beg_PDB_ins_code[n],a=l.pdbx_end_PDB_ins_code[n],c.push([i[l.beg_label_asym_id[n]],parseInt(l.beg_auth_seq_id[n]),kc(o,""),i[l.end_label_asym_id[n]],parseInt(l.end_auth_seq_id[n]),kc(a,"")]);return!(!u&&!l)&&{helices:s,sheets:c}}function Uc(t,e,i){var n={},r=e.biomolDict;if(t.pdbx_struct_oper_list){var o=t.pdbx_struct_oper_list;Dc(o,"id"),o.id.forEach(function(t,e){var i=new O,r=i.elements;r[0]=parseFloat(o["matrix[1][1]"][e]),r[1]=parseFloat(o["matrix[1][2]"][e]),r[2]=parseFloat(o["matrix[1][3]"][e]),r[4]=parseFloat(o["matrix[2][1]"][e]),r[5]=parseFloat(o["matrix[2][2]"][e]),r[6]=parseFloat(o["matrix[2][3]"][e]),r[8]=parseFloat(o["matrix[3][1]"][e]),r[9]=parseFloat(o["matrix[3][2]"][e]),r[10]=parseFloat(o["matrix[3][3]"][e]),r[3]=parseFloat(o["vector[1]"][e]),r[7]=parseFloat(o["vector[2]"][e]),r[11]=parseFloat(o["vector[3]"][e]),i.transpose(),n[t]=i})}if(t.pdbx_struct_assembly_gen){var a=t.pdbx_struct_assembly_gen;Dc(a,"assembly_id");var s=function(t){var e={},i=t.replace(/[\(\)']/g,"").split(",");return i.forEach(function(t){if(t.includes("-"))for(var i=t.split("-"),r=parseInt(i[0]),o=parseInt(i[1]);r<=o;++r)e[r]=n[r];else e[t]=n[t]}),e};a.assembly_id.forEach(function(t,e){var n={},o=a.oper_expression[e].replace(/'\(|'/g,"");if(o.includes(")(")||o.indexOf("(")>0){o=o.split("(");var c=s(o[0]),u=s(o[1]);Object.keys(c).forEach(function(t){Object.keys(u).forEach(function(e){var i=new O;i.multiplyMatrices(c[t],u[e]),n[t+"x"+e]=i})})}else n=s(o);var h=[];for(var l in n)h.push(n[l]);var d=t;/^(0|[1-9][0-9]*)$/.test(d)&&(d="BU"+d);for(var f=a.asym_id_list[e].split(","),p=0,m=f.length;p<m;++p)f[p]=i[f[p]];void 0===r[d]&&(r[d]=new Wo(d)),r[d].addPart(h,f)})}if(t.struct_ncs_oper){var c=t.struct_ncs_oper;Dc(c,"id");var u="NCS";r[u]=new Wo(u);var h=r[u].addPart();c.id.forEach(function(t,e){if("given"!==c.code[e]){var i=new O,n=i.elements;n[0]=parseFloat(c["matrix[1][1]"][e]),n[1]=parseFloat(c["matrix[1][2]"][e]),n[2]=parseFloat(c["matrix[1][3]"][e]),n[4]=parseFloat(c["matrix[2][1]"][e]),n[5]=parseFloat(c["matrix[2][2]"][e]),n[6]=parseFloat(c["matrix[2][3]"][e]),n[8]=parseFloat(c["matrix[3][1]"][e]),n[9]=parseFloat(c["matrix[3][2]"][e]),n[10]=parseFloat(c["matrix[3][3]"][e]),n[3]=parseFloat(c["vector[1]"][e]),n[7]=parseFloat(c["vector[2]"][e]),n[11]=parseFloat(c["vector[3]"][e]),i.transpose(),h.matrixList.push(i)}}),0===h.matrixList.length&&delete r[u]}var l={};if(t.cell){var d=t.cell,f=parseFloat(d.length_a),p=parseFloat(d.length_b),m=parseFloat(d.length_c),g=new Float32Array(9);g[0]=f,g[4]=p,g[8]=m,e.boxes.push(g),l.a=f,l.b=p,l.c=m,l.alpha=parseFloat(d.angle_alpha),l.beta=parseFloat(d.angle_beta),l.gamma=parseFloat(d.angle_gamma)}if(t.symmetry){var v=t.symmetry,y=v["space_group_name_H-M"];y[0]!==y[y.length-1]||"'"!==y[0]&&'"'!==y[0]||(y=y.substring(1,y.length-1)),l.spacegroup=y}var b=new O;if(t.database_PDB_matrix){var x=t.database_PDB_matrix,w=b.elements;w[0]=parseFloat(x["origx[1][1]"]),w[1]=parseFloat(x["origx[1][2]"]),w[2]=parseFloat(x["origx[1][3]"]),w[4]=parseFloat(x["origx[2][1]"]),w[5]=parseFloat(x["origx[2][2]"]),w[6]=parseFloat(x["origx[2][3]"]),w[8]=parseFloat(x["origx[3][1]"]),w[9]=parseFloat(x["origx[3][2]"]),w[10]=parseFloat(x["origx[3][3]"]),w[3]=parseFloat(x["origx_vector[1]"]),w[7]=parseFloat(x["origx_vector[2]"]),w[11]=parseFloat(x["origx_vector[3]"]),b.transpose(),l.origx=b}var _=new O;if(t.atom_sites){var S=t.atom_sites,A=_.elements;A[0]=parseFloat(S["fract_transf_matrix[1][1]"]),A[1]=parseFloat(S["fract_transf_matrix[1][2]"]),A[2]=parseFloat(S["fract_transf_matrix[1][3]"]),A[4]=parseFloat(S["fract_transf_matrix[2][1]"]),A[5]=parseFloat(S["fract_transf_matrix[2][2]"]),A[6]=parseFloat(S["fract_transf_matrix[2][3]"]),A[8]=parseFloat(S["fract_transf_matrix[3][1]"]),A[9]=parseFloat(S["fract_transf_matrix[3][2]"]),A[10]=parseFloat(S["fract_transf_matrix[3][3]"]),A[3]=parseFloat(S["fract_transf_vector[1]"]),A[7]=parseFloat(S["fract_transf_vector[2]"]),A[11]=parseFloat(S["fract_transf_vector[3]"]),_.transpose(),l.scale=_}void 0!==l.a?e.unitcell=new Tc(l.a,l.b,l.c,l.alpha,l.beta,l.gamma,l.spacegroup,l.scale):e.unitcell=void 0}function jc(t,e,i){var n=t.struct_conn;if(n){Dc(n,"id");for(var r=/"/g,o=e.getAtomProxy(),a=e.getAtomProxy(),s={},c=0,u=n.id.length;c<u;++c){var h=n.conn_type_id[c];if("hydrog"!==h&&"mismat"!==h&&"saltbr"!==h&&"1_555"===n.ptnr1_symmetry[c]&&"1_555"===n.ptnr2_symmetry[c]){var l=n.pdbx_ptnr1_PDB_ins_code[c],d=n.pdbx_ptnr1_label_alt_id[c],f=n.ptnr1_auth_seq_id[c]+(Nc(l)?"^"+l:"")+":"+i[n.ptnr1_label_asym_id[c]]+"."+n.ptnr1_label_atom_id[c].replace(r,"")+(Nc(d)?"%"+d:""),p=s[f];if(!p){var m=new On(f);if(m.selection.error){Pv.warn("invalid selection for connection",f);continue}p=e.getAtomIndices(m),s[f]=p}var g=n.pdbx_ptnr2_PDB_ins_code[c],v=n.pdbx_ptnr2_label_alt_id[c],y=n.ptnr2_auth_seq_id[c]+(Nc(g)?"^"+g:"")+":"+i[n.ptnr2_label_asym_id[c]]+"."+n.ptnr2_label_atom_id[c].replace(r,"")+(Nc(v)?"%"+v:""),b=s[y];if(!b){var x=new On(y);if(x.selection.error){Pv.warn("invalid selection for connection",y);continue}b=e.getAtomIndices(x),s[y]=b}var w=p.length,_=b.length;if(w>_){var S=w;w=_,_=S;var A=p;p=b,b=A}if(0!==w&&0!==_)for(var M=0;M<_;++M)o.index=p[M%w],a.index=b[M],o&&a?e.bondStore.addBond(o,a,Fc(n.pdbx_value_order[c])):Pv.log("atoms 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r=65535&t|0,o=t>>>16&65535|0,a=0;0!==i;){a=i>2e3?2e3:i,i-=a;do r=r+e[n++]|0,o=o+r|0;while(--a);r%=65521,o%=65521}return r|o<<16|0}function zu(){for(var t,e=[],i=0;i<256;i++){t=i;for(var n=0;n<8;n++)t=1&t?3988292384^t>>>1:t>>>1;e[i]=t}return e}function Bu(t,e,i,n){var r=xy,o=n+i;t^=-1;for(var a=n;a<o;a++)t=t>>>8^r[255&(t^e[a])];return t^-1}function Uu(t,e){var i,n,r,o,a,s,c,u,h,l,d,f,p,m,g,v,y,b,x,w,_,S,A,M,P;i=t.state,n=t.next_in,M=t.input,r=n+(t.avail_in-5),o=t.next_out,P=t.output,a=o-(e-t.avail_out),s=o+(t.avail_out-257),c=i.dmax,u=i.wsize,h=i.whave,l=i.wnext,d=i.window,f=i.hold,p=i.bits,m=i.lencode,g=i.distcode,v=(1<<i.lenbits)-1,y=(1<<i.distbits)-1;t:do{p<15&&(f+=M[n++]<<p,p+=8,f+=M[n++]<<p,p+=8),b=m[f&v];e:for(;;){if(x=b>>>24,f>>>=x,p-=x,x=b>>>16&255,0===x)P[o++]=65535&b;else{if(!(16&x)){if(0===(64&x)){b=m[(65535&b)+(f&(1<<x)-1)];continue e}if(32&x){i.mode=_y;break t}t.msg="invalid literal/length code",i.mode=wy;break t}w=65535&b,x&=15,x&&(p<x&&(f+=M[n++]<<p,p+=8),w+=f&(1<<x)-1,f>>>=x,p-=x),p<15&&(f+=M[n++]<<p,p+=8,f+=M[n++]<<p,p+=8),b=g[f&y];i:for(;;){if(x=b>>>24,f>>>=x,p-=x,x=b>>>16&255,!(16&x)){if(0===(64&x)){b=g[(65535&b)+(f&(1<<x)-1)];continue i}t.msg="invalid distance code",i.mode=wy;break t}if(_=65535&b,x&=15,p<x&&(f+=M[n++]<<p,p+=8,p<x&&(f+=M[n++]<<p,p+=8)),_+=f&(1<<x)-1,_>c){t.msg="invalid distance too far back",i.mode=wy;break t}if(f>>>=x,p-=x,x=o-a,_>x){if(x=_-x,x>h&&i.sane){t.msg="invalid distance too far back",i.mode=wy;break t}if(S=0,A=d,0===l){if(S+=u-x,x<w){w-=x;do P[o++]=d[S++];while(--x);S=o-_,A=P}}else if(l<x){if(S+=u+l-x,x-=l,x<w){w-=x;do P[o++]=d[S++];while(--x);if(S=0,l<w){x=l,w-=x;do P[o++]=d[S++];while(--x);S=o-_,A=P}}}else if(S+=l-x,x<w){w-=x;do P[o++]=d[S++];while(--x);S=o-_,A=P}for(;w>2;)P[o++]=A[S++],P[o++]=A[S++],P[o++]=A[S++],w-=3;w&&(P[o++]=A[S++],w>1&&(P[o++]=A[S++]))}else{S=o-_;do 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$y;i=t.state,i.mode===rb&&(i.mode=ob),a=t.next_out,r=t.output,c=t.avail_out,o=t.next_in,n=t.input,s=t.avail_in,u=i.hold,h=i.bits,l=s,d=c,S=By;t:for(;;)switch(i.mode){case Xy:if(0===i.wrap){i.mode=ob;break}for(;h<16;){if(0===s)break t;s--,u+=n[o++]<<h,h+=8}if(2&i.wrap&&35615===u){i.check=0,C[0]=255&u,C[1]=u>>>8&255,i.check=Bu(i.check,C,2,0),u=0,h=0,i.mode=qy;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&u)<<8)+(u>>8))%31){t.msg="incorrect header check",i.mode=_b;break}if((15&u)!==Wy){t.msg="unknown compression method",i.mode=_b;break}if(u>>>=4,h-=4,_=(15&u)+8,0===i.wbits)i.wbits=_;else if(_>i.wbits){t.msg="invalid window size",i.mode=_b;break}i.dmax=1<<_,t.adler=i.check=1,i.mode=512&u?ib:rb,u=0,h=0;break;case qy:for(;h<16;){if(0===s)break t;s--,u+=n[o++]<<h,h+=8}if(i.flags=u,(255&i.flags)!==Wy){t.msg="unknown compression method",i.mode=_b;break}if(57344&i.flags){t.msg="unknown header flags 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m=s*u,g=s*h,v=c*u,y=c*h;e[0]=m-y*a,e[4]=-o*h,e[8]=v+g*a,e[1]=g+v*a,e[5]=o*u,e[9]=y-m*a,e[2]=-o*c,e[6]=a,e[10]=o*s}else if("ZYX"===t.order){var l=o*u,d=o*h,f=a*u,p=a*h;e[0]=s*u,e[4]=f*c-d,e[8]=l*c+p,e[1]=s*h,e[5]=p*c+l,e[9]=d*c-f,e[2]=-c,e[6]=a*s,e[10]=o*s}else if("YZX"===t.order){var b=o*s,x=o*c,w=a*s,_=a*c;e[0]=s*u,e[4]=_-b*h,e[8]=w*h+x,e[1]=h,e[5]=o*u,e[9]=-a*u,e[2]=-c*u,e[6]=x*h+w,e[10]=b-_*h}else if("XZY"===t.order){var b=o*s,x=o*c,w=a*s,_=a*c;e[0]=s*u,e[4]=-h,e[8]=c*u,e[1]=b*h+_,e[5]=o*u,e[9]=x*h-w,e[2]=w*h-x,e[6]=a*u,e[10]=_*h+b}return e[3]=0,e[7]=0,e[11]=0,e[12]=0,e[13]=0,e[14]=0,e[15]=1,this},makeRotationFromQuaternion:function(t){var e=this.elements,i=t.x,n=t.y,r=t.z,o=t.w,a=i+i,s=n+n,c=r+r,u=i*a,h=i*s,l=i*c,d=n*s,f=n*c,p=r*c,m=o*a,g=o*s,v=o*c;return e[0]=1-(d+p),e[4]=h-v,e[8]=l+g,e[1]=h+v,e[5]=1-(u+p),e[9]=f-m,e[2]=l-g,e[6]=f+m,e[10]=1-(u+d),e[3]=0,e[7]=0,e[11]=0,e[12]=0,e[13]=0,e[14]=0,e[15]=1,this},lookAt:function(){var t,e,i;return function(n,r,o){void 0===t&&(t=new N,e=new N,i=new N);var a=this.elements;return i.subVectors(n,r).normalize(),0===i.lengthSq()&&(i.z=1),t.crossVectors(o,i).normalize(),0===t.lengthSq()&&(i.z+=1e-4,t.crossVectors(o,i).normalize()),e.crossVectors(i,t),a[0]=t.x,a[4]=e.x,a[8]=i.x,a[1]=t.y,a[5]=e.y,a[9]=i.y,a[2]=t.z,a[6]=e.z,a[10]=i.z,this}}(),multiply:function(t,e){return void 0!==e?(console.warn("THREE.Matrix4: .multiply() now only accepts one argument. Use .multiplyMatrices( a, b ) instead."),this.multiplyMatrices(t,e)):this.multiplyMatrices(this,t)},premultiply:function(t){return this.multiplyMatrices(t,this)},multiplyMatrices:function(t,e){var i=t.elements,n=e.elements,r=this.elements,o=i[0],a=i[4],s=i[8],c=i[12],u=i[1],h=i[5],l=i[9],d=i[13],f=i[2],p=i[6],m=i[10],g=i[14],v=i[3],y=i[7],b=i[11],x=i[15],w=n[0],_=n[4],S=n[8],A=n[12],M=n[1],P=n[5],C=n[9],T=n[13],E=n[2],I=n[6],L=n[10],R=n[14],O=n[3],D=n[7],N=n[11],k=n[15];return r[0]=o*w+a*M+s*E+c*O,r[4]=o*_+a*P+s*I+c*D,r[8]=o*S+a*C+s*L+c*N,r[12]=o*A+a*T+s*R+c*k,r[1]=u*w+h*M+l*E+d*O,r[5]=u*_+h*P+l*I+d*D,r[9]=u*S+h*C+l*L+d*N,r[13]=u*A+h*T+l*R+d*k,r[2]=f*w+p*M+m*E+g*O,r[6]=f*_+p*P+m*I+g*D,r[10]=f*S+p*C+m*L+g*N,r[14]=f*A+p*T+m*R+g*k,r[3]=v*w+y*M+b*E+x*O,r[7]=v*_+y*P+b*I+x*D,r[11]=v*S+y*C+b*L+x*N,r[15]=v*A+y*T+b*R+x*k,this},multiplyToArray:function(t,e,i){var n=this.elements;return this.multiplyMatrices(t,e),i[0]=n[0],i[1]=n[1],i[2]=n[2],i[3]=n[3],i[4]=n[4],i[5]=n[5],i[6]=n[6],i[7]=n[7],i[8]=n[8],i[9]=n[9],i[10]=n[10],i[11]=n[11],i[12]=n[12],i[13]=n[13],i[14]=n[14],i[15]=n[15],this},multiplyScalar:function(t){var e=this.elements;return e[0]*=t,e[4]*=t,e[8]*=t,e[12]*=t,e[1]*=t,e[5]*=t,e[9]*=t,e[13]*=t,e[2]*=t,e[6]*=t,e[10]*=t,e[14]*=t,e[3]*=t,e[7]*=t,e[11]*=t,e[15]*=t,this},applyToVector3Array:function(){var t;return function(e,i,n){void 0===t&&(t=new N),void 0===i&&(i=0),void 0===n&&(n=e.length);for(var r=0,o=i;r<n;r+=3,o+=3)t.fromArray(e,o),t.applyMatrix4(this),t.toArray(e,o);return e}}(),applyToBuffer:function(){var t;return function(e,i,n){void 0===t&&(t=new N),void 0===i&&(i=0),void 0===n&&(n=e.length/e.itemSize);for(var r=0,o=i;r<n;r++,o++)t.x=e.getX(o),t.y=e.getY(o),t.z=e.getZ(o),t.applyMatrix4(this),e.setXYZ(t.x,t.y,t.z);return e}}(),determinant:function(){var t=this.elements,e=t[0],i=t[4],n=t[8],r=t[12],o=t[1],a=t[5],s=t[9],c=t[13],u=t[2],h=t[6],l=t[10],d=t[14],f=t[3],p=t[7],m=t[11],g=t[15];return f*(+r*s*h-n*c*h-r*a*l+i*c*l+n*a*d-i*s*d)+p*(+e*s*d-e*c*l+r*o*l-n*o*d+n*c*u-r*s*u)+m*(+e*c*h-e*a*d-r*o*h+i*o*d+r*a*u-i*c*u)+g*(-n*a*u-e*s*h+e*a*l+n*o*h-i*o*l+i*s*u)},transpose:function(){var t,e=this.elements;return t=e[1],e[1]=e[4],e[4]=t,t=e[2],e[2]=e[8],e[8]=t,t=e[6],e[6]=e[9],e[9]=t,t=e[3],e[3]=e[12],e[12]=t,t=e[7],e[7]=e[13],e[13]=t,t=e[11],e[11]=e[14],e[14]=t,this},flattenToArrayOffset:function(t,e){return console.warn("THREE.Matrix3: .flattenToArrayOffset is deprecated - just use .toArray instead."),this.toArray(t,e)},getPosition:function(){var t;return function(){return void 0===t&&(t=new N),console.warn("THREE.Matrix4: .getPosition() has been removed. Use Vector3.setFromMatrixPosition( matrix ) instead."),t.setFromMatrixColumn(this,3)}}(),setPosition:function(t){var e=this.elements;return e[12]=t.x,e[13]=t.y,e[14]=t.z,this},getInverse:function(t,e){var i=this.elements,n=t.elements,r=n[0],o=n[1],a=n[2],s=n[3],c=n[4],u=n[5],h=n[6],l=n[7],d=n[8],f=n[9],p=n[10],m=n[11],g=n[12],v=n[13],y=n[14],b=n[15],x=f*y*l-v*p*l+v*h*m-u*y*m-f*h*b+u*p*b,w=g*p*l-d*y*l-g*h*m+c*y*m+d*h*b-c*p*b,_=d*v*l-g*f*l+g*u*m-c*v*m-d*u*b+c*f*b,S=g*f*h-d*v*h-g*u*p+c*v*p+d*u*y-c*f*y,A=r*x+o*w+a*_+s*S;if(0===A){var M="THREE.Matrix4.getInverse(): can't invert matrix, determinant is 0";if(e===!0)throw new Error(M);return console.warn(M),this.identity()}var P=1/A;return i[0]=x*P,i[1]=(v*p*s-f*y*s-v*a*m+o*y*m+f*a*b-o*p*b)*P,i[2]=(u*y*s-v*h*s+v*a*l-o*y*l-u*a*b+o*h*b)*P,i[3]=(f*h*s-u*p*s-f*a*l+o*p*l+u*a*m-o*h*m)*P,i[4]=w*P,i[5]=(d*y*s-g*p*s+g*a*m-r*y*m-d*a*b+r*p*b)*P,i[6]=(g*h*s-c*y*s-g*a*l+r*y*l+c*a*b-r*h*b)*P,i[7]=(c*p*s-d*h*s+d*a*l-r*p*l-c*a*m+r*h*m)*P,i[8]=_*P,i[9]=(g*f*s-d*v*s-g*o*m+r*v*m+d*o*b-r*f*b)*P,i[10]=(c*v*s-g*u*s+g*o*l-r*v*l-c*o*b+r*u*b)*P,i[11]=(d*u*s-c*f*s-d*o*l+r*f*l+c*o*m-r*u*m)*P,i[12]=S*P,i[13]=(d*v*a-g*f*a+g*o*p-r*v*p-d*o*y+r*f*y)*P,i[14]=(g*u*a-c*v*a-g*o*h+r*v*h+c*o*y-r*u*y)*P,i[15]=(c*f*a-d*u*a+d*o*h-r*f*h-c*o*p+r*u*p)*P,this},scale:function(t){var e=this.elements,i=t.x,n=t.y,r=t.z;return e[0]*=i,e[4]*=n,e[8]*=r,e[1]*=i,e[5]*=n,e[9]*=r,e[2]*=i,e[6]*=n,e[10]*=r,e[3]*=i,e[7]*=n,e[11]*=r,this},getMaxScaleOnAxis:function(){var t=this.elements,e=t[0]*t[0]+t[1]*t[1]+t[2]*t[2],i=t[4]*t[4]+t[5]*t[5]+t[6]*t[6],n=t[8]*t[8]+t[9]*t[9]+t[10]*t[10];return Math.sqrt(Math.max(e,i,n))},makeTranslation:function(t,e,i){return this.set(1,0,0,t,0,1,0,e,0,0,1,i,0,0,0,1),this},makeRotationX:function(t){var e=Math.cos(t),i=Math.sin(t);return this.set(1,0,0,0,0,e,-i,0,0,i,e,0,0,0,0,1),
-this},makeRotationY:function(t){var e=Math.cos(t),i=Math.sin(t);return this.set(e,0,i,0,0,1,0,0,-i,0,e,0,0,0,0,1),this},makeRotationZ:function(t){var e=Math.cos(t),i=Math.sin(t);return this.set(e,-i,0,0,i,e,0,0,0,0,1,0,0,0,0,1),this},makeRotationAxis:function(t,e){var i=Math.cos(e),n=Math.sin(e),r=1-i,o=t.x,a=t.y,s=t.z,c=r*o,u=r*a;return this.set(c*o+i,c*a-n*s,c*s+n*a,0,c*a+n*s,u*a+i,u*s-n*o,0,c*s-n*a,u*s+n*o,r*s*s+i,0,0,0,0,1),this},makeScale:function(t,e,i){return this.set(t,0,0,0,0,e,0,0,0,0,i,0,0,0,0,1),this},compose:function(t,e,i){return this.makeRotationFromQuaternion(e),this.scale(i),this.setPosition(t),this},decompose:function(){var t,e;return function(i,n,r){void 0===t&&(t=new N,e=new O);var o=this.elements,a=t.set(o[0],o[1],o[2]).length(),s=t.set(o[4],o[5],o[6]).length(),c=t.set(o[8],o[9],o[10]).length(),u=this.determinant();u<0&&(a=-a),i.x=o[12],i.y=o[13],i.z=o[14],e.elements.set(this.elements);var h=1/a,l=1/s,d=1/c;return e.elements[0]*=h,e.elements[1]*=h,e.elements[2]*=h,e.elements[4]*=l,e.elements[5]*=l,e.elements[6]*=l,e.elements[8]*=d,e.elements[9]*=d,e.elements[10]*=d,n.setFromRotationMatrix(e),r.x=a,r.y=s,r.z=c,this}}(),makeFrustum:function(t,e,i,n,r,o){var a=this.elements,s=2*r/(e-t),c=2*r/(n-i),u=(e+t)/(e-t),h=(n+i)/(n-i),l=-(o+r)/(o-r),d=-2*o*r/(o-r);return a[0]=s,a[4]=0,a[8]=u,a[12]=0,a[1]=0,a[5]=c,a[9]=h,a[13]=0,a[2]=0,a[6]=0,a[10]=l,a[14]=d,a[3]=0,a[7]=0,a[11]=-1,a[15]=0,this},makePerspective:function(t,e,i,n){var r=i*Math.tan(Ed.DEG2RAD*t*.5),o=-r,a=o*e,s=r*e;return this.makeFrustum(a,s,o,r,i,n)},makeOrthographic:function(t,e,i,n,r,o){var a=this.elements,s=1/(e-t),c=1/(i-n),u=1/(o-r),h=(e+t)*s,l=(i+n)*c,d=(o+r)*u;return a[0]=2*s,a[4]=0,a[8]=0,a[12]=-h,a[1]=0,a[5]=2*c,a[9]=0,a[13]=-l,a[2]=0,a[6]=0,a[10]=-2*u,a[14]=-d,a[3]=0,a[7]=0,a[11]=0,a[15]=1,this},equals:function(t){for(var e=this.elements,i=t.elements,n=0;n<16;n++)if(e[n]!==i[n])return!1;return!0},fromArray:function(t){return this.elements.set(t),this},toArray:function(t,e){void 0===t&&(t=[]),void 0===e&&(e=0);var i=this.elements;return t[e]=i[0],t[e+1]=i[1],t[e+2]=i[2],t[e+3]=i[3],t[e+4]=i[4],t[e+5]=i[5],t[e+6]=i[6],t[e+7]=i[7],t[e+8]=i[8],t[e+9]=i[9],t[e+10]=i[10],t[e+11]=i[11],t[e+12]=i[12],t[e+13]=i[13],t[e+14]=i[14],t[e+15]=i[15],t}},D.prototype={constructor:D,get x(){return this._x},set x(t){this._x=t,this.onChangeCallback()},get y(){return this._y},set y(t){this._y=t,this.onChangeCallback()},get z(){return this._z},set z(t){this._z=t,this.onChangeCallback()},get w(){return this._w},set w(t){this._w=t,this.onChangeCallback()},set:function(t,e,i,n){return this._x=t,this._y=e,this._z=i,this._w=n,this.onChangeCallback(),this},clone:function(){return new this.constructor(this._x,this._y,this._z,this._w)},copy:function(t){return this._x=t.x,this._y=t.y,this._z=t.z,this._w=t.w,this.onChangeCallback(),this},setFromEuler:function(t,e){if((t&&t.isEuler)===!1)throw new Error("THREE.Quaternion: .setFromEuler() now expects a Euler rotation rather than a Vector3 and order.");var i=Math.cos(t._x/2),n=Math.cos(t._y/2),r=Math.cos(t._z/2),o=Math.sin(t._x/2),a=Math.sin(t._y/2),s=Math.sin(t._z/2),c=t.order;return"XYZ"===c?(this._x=o*n*r+i*a*s,this._y=i*a*r-o*n*s,this._z=i*n*s+o*a*r,this._w=i*n*r-o*a*s):"YXZ"===c?(this._x=o*n*r+i*a*s,this._y=i*a*r-o*n*s,this._z=i*n*s-o*a*r,this._w=i*n*r+o*a*s):"ZXY"===c?(this._x=o*n*r-i*a*s,this._y=i*a*r+o*n*s,this._z=i*n*s+o*a*r,this._w=i*n*r-o*a*s):"ZYX"===c?(this._x=o*n*r-i*a*s,this._y=i*a*r+o*n*s,this._z=i*n*s-o*a*r,this._w=i*n*r+o*a*s):"YZX"===c?(this._x=o*n*r+i*a*s,this._y=i*a*r+o*n*s,this._z=i*n*s-o*a*r,this._w=i*n*r-o*a*s):"XZY"===c&&(this._x=o*n*r-i*a*s,this._y=i*a*r-o*n*s,this._z=i*n*s+o*a*r,this._w=i*n*r+o*a*s),e!==!1&&this.onChangeCallback(),this},setFromAxisAngle:function(t,e){var i=e/2,n=Math.sin(i);return this._x=t.x*n,this._y=t.y*n,this._z=t.z*n,this._w=Math.cos(i),this.onChangeCallback(),this},setFromRotationMatrix:function(t){var e,i=t.elements,n=i[0],r=i[4],o=i[8],a=i[1],s=i[5],c=i[9],u=i[2],h=i[6],l=i[10],d=n+s+l;return d>0?(e=.5/Math.sqrt(d+1),this._w=.25/e,this._x=(h-c)*e,this._y=(o-u)*e,this._z=(a-r)*e):n>s&&n>l?(e=2*Math.sqrt(1+n-s-l),this._w=(h-c)/e,this._x=.25*e,this._y=(r+a)/e,this._z=(o+u)/e):s>l?(e=2*Math.sqrt(1+s-n-l),this._w=(o-u)/e,this._x=(r+a)/e,this._y=.25*e,this._z=(c+h)/e):(e=2*Math.sqrt(1+l-n-s),this._w=(a-r)/e,this._x=(o+u)/e,this._y=(c+h)/e,this._z=.25*e),this.onChangeCallback(),this},setFromUnitVectors:function(){var t,e,i=1e-6;return function(n,r){return void 0===t&&(t=new N),e=n.dot(r)+1,e<i?(e=0,Math.abs(n.x)>Math.abs(n.z)?t.set(-n.y,n.x,0):t.set(0,-n.z,n.y)):t.crossVectors(n,r),this._x=t.x,this._y=t.y,this._z=t.z,this._w=e,this.normalize()}}(),inverse:function(){return this.conjugate().normalize()},conjugate:function(){return this._x*=-1,this._y*=-1,this._z*=-1,this.onChangeCallback(),this},dot:function(t){return this._x*t._x+this._y*t._y+this._z*t._z+this._w*t._w},lengthSq:function(){return this._x*this._x+this._y*this._y+this._z*this._z+this._w*this._w},length:function(){return Math.sqrt(this._x*this._x+this._y*this._y+this._z*this._z+this._w*this._w)},normalize:function(){var t=this.length();return 0===t?(this._x=0,this._y=0,this._z=0,this._w=1):(t=1/t,this._x=this._x*t,this._y=this._y*t,this._z=this._z*t,this._w=this._w*t),this.onChangeCallback(),this},multiply:function(t,e){return void 0!==e?(console.warn("THREE.Quaternion: .multiply() now only accepts one argument. Use .multiplyQuaternions( a, b ) instead."),this.multiplyQuaternions(t,e)):this.multiplyQuaternions(this,t)},premultiply:function(t){return this.multiplyQuaternions(t,this)},multiplyQuaternions:function(t,e){var i=t._x,n=t._y,r=t._z,o=t._w,a=e._x,s=e._y,c=e._z,u=e._w;return this._x=i*u+o*a+n*c-r*s,this._y=n*u+o*s+r*a-i*c,this._z=r*u+o*c+i*s-n*a,this._w=o*u-i*a-n*s-r*c,this.onChangeCallback(),this},slerp:function(t,e){if(0===e)return this;if(1===e)return this.copy(t);var i=this._x,n=this._y,r=this._z,o=this._w,a=o*t._w+i*t._x+n*t._y+r*t._z;if(a<0?(this._w=-t._w,this._x=-t._x,this._y=-t._y,this._z=-t._z,a=-a):this.copy(t),a>=1)return this._w=o,this._x=i,this._y=n,this._z=r,this;var s=Math.sqrt(1-a*a);if(Math.abs(s)<.001)return this._w=.5*(o+this._w),this._x=.5*(i+this._x),this._y=.5*(n+this._y),this._z=.5*(r+this._z),this;var c=Math.atan2(s,a),u=Math.sin((1-e)*c)/s,h=Math.sin(e*c)/s;return this._w=o*u+this._w*h,this._x=i*u+this._x*h,this._y=n*u+this._y*h,this._z=r*u+this._z*h,this.onChangeCallback(),this},equals:function(t){return t._x===this._x&&t._y===this._y&&t._z===this._z&&t._w===this._w},fromArray:function(t,e){return void 0===e&&(e=0),this._x=t[e],this._y=t[e+1],this._z=t[e+2],this._w=t[e+3],this.onChangeCallback(),this},toArray:function(t,e){return void 0===t&&(t=[]),void 0===e&&(e=0),t[e]=this._x,t[e+1]=this._y,t[e+2]=this._z,t[e+3]=this._w,t},onChange:function(t){return this.onChangeCallback=t,this},onChangeCallback:function(){}},Object.assign(D,{slerp:function(t,e,i,n){return i.copy(t).slerp(e,n)},slerpFlat:function(t,e,i,n,r,o,a){var s=i[n+0],c=i[n+1],u=i[n+2],h=i[n+3],l=r[o+0],d=r[o+1],f=r[o+2],p=r[o+3];if(h!==p||s!==l||c!==d||u!==f){var m=1-a,g=s*l+c*d+u*f+h*p,v=g>=0?1:-1,y=1-g*g;if(y>Number.EPSILON){var b=Math.sqrt(y),x=Math.atan2(b,g*v);m=Math.sin(m*x)/b,a=Math.sin(a*x)/b}var w=a*v;if(s=s*m+l*w,c=c*m+d*w,u=u*m+f*w,h=h*m+p*w,m===1-a){var _=1/Math.sqrt(s*s+c*c+u*u+h*h);s*=_,c*=_,u*=_,h*=_}}t[e]=s,t[e+1]=c,t[e+2]=u,t[e+3]=h}}),N.prototype={constructor:N,isVector3:!0,set:function(t,e,i){return this.x=t,this.y=e,this.z=i,this},setScalar:function(t){return this.x=t,this.y=t,this.z=t,this},setX:function(t){return this.x=t,this},setY:function(t){return this.y=t,this},setZ:function(t){return this.z=t,this},setComponent:function(t,e){switch(t){case 0:this.x=e;break;case 1:this.y=e;break;case 2:this.z=e;break;default:throw new Error("index is out of range: "+t)}},getComponent:function(t){switch(t){case 0:return this.x;case 1:return this.y;case 2:return this.z;default:throw new Error("index is out of range: "+t)}},clone:function(){return new this.constructor(this.x,this.y,this.z)},copy:function(t){return this.x=t.x,this.y=t.y,this.z=t.z,this},add:function(t,e){return void 0!==e?(console.warn("THREE.Vector3: .add() now only accepts one argument. Use .addVectors( a, b ) instead."),this.addVectors(t,e)):(this.x+=t.x,this.y+=t.y,this.z+=t.z,this)},addScalar:function(t){return this.x+=t,this.y+=t,this.z+=t,this},addVectors:function(t,e){return this.x=t.x+e.x,this.y=t.y+e.y,this.z=t.z+e.z,this},addScaledVector:function(t,e){return this.x+=t.x*e,this.y+=t.y*e,this.z+=t.z*e,this},sub:function(t,e){return void 0!==e?(console.warn("THREE.Vector3: .sub() now only accepts one argument. Use .subVectors( a, b ) instead."),this.subVectors(t,e)):(this.x-=t.x,this.y-=t.y,this.z-=t.z,this)},subScalar:function(t){return this.x-=t,this.y-=t,this.z-=t,this},subVectors:function(t,e){return this.x=t.x-e.x,this.y=t.y-e.y,this.z=t.z-e.z,this},multiply:function(t,e){return void 0!==e?(console.warn("THREE.Vector3: .multiply() now only accepts one argument. Use .multiplyVectors( a, b ) instead."),this.multiplyVectors(t,e)):(this.x*=t.x,this.y*=t.y,this.z*=t.z,this)},multiplyScalar:function(t){return isFinite(t)?(this.x*=t,this.y*=t,this.z*=t):(this.x=0,this.y=0,this.z=0),this},multiplyVectors:function(t,e){return this.x=t.x*e.x,this.y=t.y*e.y,this.z=t.z*e.z,this},applyEuler:function(){var t;return function(e){return(e&&e.isEuler)===!1&&console.error("THREE.Vector3: .applyEuler() now expects an Euler rotation rather than a Vector3 and order."),void 0===t&&(t=new D),this.applyQuaternion(t.setFromEuler(e))}}(),applyAxisAngle:function(){var t;return function(e,i){return void 0===t&&(t=new D),this.applyQuaternion(t.setFromAxisAngle(e,i))}}(),applyMatrix3:function(t){var e=this.x,i=this.y,n=this.z,r=t.elements;return this.x=r[0]*e+r[3]*i+r[6]*n,this.y=r[1]*e+r[4]*i+r[7]*n,this.z=r[2]*e+r[5]*i+r[8]*n,this},applyMatrix4:function(t){var e=this.x,i=this.y,n=this.z,r=t.elements;return this.x=r[0]*e+r[4]*i+r[8]*n+r[12],this.y=r[1]*e+r[5]*i+r[9]*n+r[13],this.z=r[2]*e+r[6]*i+r[10]*n+r[14],this},applyProjection:function(t){var e=this.x,i=this.y,n=this.z,r=t.elements,o=1/(r[3]*e+r[7]*i+r[11]*n+r[15]);return this.x=(r[0]*e+r[4]*i+r[8]*n+r[12])*o,this.y=(r[1]*e+r[5]*i+r[9]*n+r[13])*o,this.z=(r[2]*e+r[6]*i+r[10]*n+r[14])*o,this},applyQuaternion:function(t){var e=this.x,i=this.y,n=this.z,r=t.x,o=t.y,a=t.z,s=t.w,c=s*e+o*n-a*i,u=s*i+a*e-r*n,h=s*n+r*i-o*e,l=-r*e-o*i-a*n;return this.x=c*s+l*-r+u*-a-h*-o,this.y=u*s+l*-o+h*-r-c*-a,this.z=h*s+l*-a+c*-o-u*-r,this},project:function(){var t;return function(e){return void 0===t&&(t=new O),t.multiplyMatrices(e.projectionMatrix,t.getInverse(e.matrixWorld)),this.applyProjection(t)}}(),unproject:function(){var t;return function(e){return void 0===t&&(t=new O),t.multiplyMatrices(e.matrixWorld,t.getInverse(e.projectionMatrix)),this.applyProjection(t)}}(),transformDirection:function(t){var e=this.x,i=this.y,n=this.z,r=t.elements;return this.x=r[0]*e+r[4]*i+r[8]*n,this.y=r[1]*e+r[5]*i+r[9]*n,this.z=r[2]*e+r[6]*i+r[10]*n,this.normalize()},divide:function(t){return this.x/=t.x,this.y/=t.y,this.z/=t.z,this},divideScalar:function(t){return this.multiplyScalar(1/t)},min:function(t){return this.x=Math.min(this.x,t.x),this.y=Math.min(this.y,t.y),this.z=Math.min(this.z,t.z),this},max:function(t){return this.x=Math.max(this.x,t.x),this.y=Math.max(this.y,t.y),this.z=Math.max(this.z,t.z),this},clamp:function(t,e){return this.x=Math.max(t.x,Math.min(e.x,this.x)),this.y=Math.max(t.y,Math.min(e.y,this.y)),this.z=Math.max(t.z,Math.min(e.z,this.z)),this},clampScalar:function(){var t,e;return function(i,n){return void 0===t&&(t=new N,e=new N),t.set(i,i,i),e.set(n,n,n),this.clamp(t,e)}}(),clampLength:function(t,e){var i=this.length();return this.multiplyScalar(Math.max(t,Math.min(e,i))/i)},floor:function(){return this.x=Math.floor(this.x),this.y=Math.floor(this.y),this.z=Math.floor(this.z),this},ceil:function(){return this.x=Math.ceil(this.x),this.y=Math.ceil(this.y),this.z=Math.ceil(this.z),this},round:function(){return this.x=Math.round(this.x),this.y=Math.round(this.y),this.z=Math.round(this.z),this},roundToZero:function(){return this.x=this.x<0?Math.ceil(this.x):Math.floor(this.x),this.y=this.y<0?Math.ceil(this.y):Math.floor(this.y),this.z=this.z<0?Math.ceil(this.z):Math.floor(this.z),this},negate:function(){return this.x=-this.x,this.y=-this.y,this.z=-this.z,this},dot:function(t){return this.x*t.x+this.y*t.y+this.z*t.z},lengthSq:function(){return this.x*this.x+this.y*this.y+this.z*this.z},length:function(){return Math.sqrt(this.x*this.x+this.y*this.y+this.z*this.z)},lengthManhattan:function(){return Math.abs(this.x)+Math.abs(this.y)+Math.abs(this.z)},normalize:function(){return this.divideScalar(this.length())},setLength:function(t){return this.multiplyScalar(t/this.length())},lerp:function(t,e){return this.x+=(t.x-this.x)*e,this.y+=(t.y-this.y)*e,this.z+=(t.z-this.z)*e,this},lerpVectors:function(t,e,i){return this.subVectors(e,t).multiplyScalar(i).add(t)},cross:function(t,e){if(void 0!==e)return console.warn("THREE.Vector3: .cross() now only accepts one argument. Use .crossVectors( a, b ) instead."),this.crossVectors(t,e);var i=this.x,n=this.y,r=this.z;return this.x=n*t.z-r*t.y,this.y=r*t.x-i*t.z,this.z=i*t.y-n*t.x,this},crossVectors:function(t,e){var i=t.x,n=t.y,r=t.z,o=e.x,a=e.y,s=e.z;return this.x=n*s-r*a,this.y=r*o-i*s,this.z=i*a-n*o,this},projectOnVector:function(t){var e=t.dot(this)/t.lengthSq();return this.copy(t).multiplyScalar(e)},projectOnPlane:function(){var t;return function(e){return void 0===t&&(t=new N),t.copy(this).projectOnVector(e),this.sub(t)}}(),reflect:function(){var t;return function(e){return void 0===t&&(t=new N),this.sub(t.copy(e).multiplyScalar(2*this.dot(e)))}}(),angleTo:function(t){var e=this.dot(t)/Math.sqrt(this.lengthSq()*t.lengthSq());return Math.acos(Ed.clamp(e,-1,1))},distanceTo:function(t){return Math.sqrt(this.distanceToSquared(t))},distanceToSquared:function(t){var e=this.x-t.x,i=this.y-t.y,n=this.z-t.z;return e*e+i*i+n*n},distanceToManhattan:function(t){return Math.abs(this.x-t.x)+Math.abs(this.y-t.y)+Math.abs(this.z-t.z)},setFromSpherical:function(t){var e=Math.sin(t.phi)*t.radius;return this.x=e*Math.sin(t.theta),this.y=Math.cos(t.phi)*t.radius,this.z=e*Math.cos(t.theta),this},setFromMatrixPosition:function(t){return this.setFromMatrixColumn(t,3)},setFromMatrixScale:function(t){var e=this.setFromMatrixColumn(t,0).length(),i=this.setFromMatrixColumn(t,1).length(),n=this.setFromMatrixColumn(t,2).length();return this.x=e,this.y=i,this.z=n,this},setFromMatrixColumn:function(t,e){if("number"==typeof t){console.warn("THREE.Vector3: setFromMatrixColumn now expects ( matrix, index ).");var i=t;t=e,e=i}return this.fromArray(t.elements,4*e)},equals:function(t){return t.x===this.x&&t.y===this.y&&t.z===this.z},fromArray:function(t,e){return void 0===e&&(e=0),this.x=t[e],this.y=t[e+1],this.z=t[e+2],this},toArray:function(t,e){return void 0===t&&(t=[]),void 0===e&&(e=0),t[e]=this.x,t[e+1]=this.y,t[e+2]=this.z,t},fromAttribute:function(t,e,i){return void 0===i&&(i=0),e=e*t.itemSize+i,this.x=t.array[e],this.y=t.array[e+1],this.z=t.array[e+2],this}},F.prototype={constructor:F,set:function(t,e){return this.min.copy(t),this.max.copy(e),this},setFromPoints:function(t){this.makeEmpty();for(var e=0,i=t.length;e<i;e++)this.expandByPoint(t[e]);return this},setFromCenterAndSize:function(){var t=new I;return function(e,i){var n=t.copy(i).multiplyScalar(.5);return this.min.copy(e).sub(n),this.max.copy(e).add(n),this}}(),clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.min.copy(t.min),this.max.copy(t.max),this},makeEmpty:function(){return this.min.x=this.min.y=+(1/0),this.max.x=this.max.y=-(1/0),this},isEmpty:function(){return this.max.x<this.min.x||this.max.y<this.min.y},center:function(t){var e=t||new I;return e.addVectors(this.min,this.max).multiplyScalar(.5)},size:function(t){var e=t||new I;return e.subVectors(this.max,this.min)},expandByPoint:function(t){return this.min.min(t),this.max.max(t),this},expandByVector:function(t){return this.min.sub(t),this.max.add(t),this},expandByScalar:function(t){return this.min.addScalar(-t),this.max.addScalar(t),this},containsPoint:function(t){return!(t.x<this.min.x||t.x>this.max.x||t.y<this.min.y||t.y>this.max.y)},containsBox:function(t){return this.min.x<=t.min.x&&t.max.x<=this.max.x&&this.min.y<=t.min.y&&t.max.y<=this.max.y},getParameter:function(t,e){var i=e||new I;return i.set((t.x-this.min.x)/(this.max.x-this.min.x),(t.y-this.min.y)/(this.max.y-this.min.y))},intersectsBox:function(t){return!(t.max.x<this.min.x||t.min.x>this.max.x||t.max.y<this.min.y||t.min.y>this.max.y)},clampPoint:function(t,e){var i=e||new I;return i.copy(t).clamp(this.min,this.max)},distanceToPoint:function(){var t=new I;return function(e){var i=t.copy(e).clamp(this.min,this.max);return i.sub(e).length()}}(),intersect:function(t){return this.min.max(t.min),this.max.min(t.max),this},union:function(t){return this.min.min(t.min),this.max.max(t.max),this},translate:function(t){return this.min.add(t),this.max.add(t),this},equals:function(t){return t.min.equals(this.min)&&t.max.equals(this.max)}},B.prototype=Object.create(L.prototype),B.prototype.constructor=B,B.prototype.isCubeTexture=!0,Object.defineProperty(B.prototype,"images",{get:function(){return this.image},set:function(t){this.image=t}});var Ld=new L,Rd=new B,Od=[],Dd=[];gt.prototype.setValue=function(t,e){for(var i=this.seq,n=0,r=i.length;n!==r;++n){var o=i[n];o.setValue(t,e[o.id])}};var Nd=/([\w\d_]+)(\])?(\[|\.)?/g;bt.prototype.setValue=function(t,e,i){var n=this.map[e];void 0!==n&&n.setValue(t,i,this.renderer)},bt.prototype.set=function(t,e,i){var n=this.map[i];void 0!==n&&n.setValue(t,e[i],this.renderer)},bt.prototype.setOptional=function(t,e,i){var n=e[i];void 0!==n&&this.setValue(t,i,n)},bt.upload=function(t,e,i,n){for(var r=0,o=e.length;r!==o;++r){var a=e[r],s=i[a.id];s.needsUpdate!==!1&&a.setValue(t,s.value,n)}},bt.seqWithValue=function(t,e){for(var i=[],n=0,r=t.length;n!==r;++n){var o=t[n];o.id in e&&i.push(o)}return i},bt.splitDynamic=function(t,e){for(var i=null,n=t.length,r=0,o=0;o!==n;++o){var a=t[o],s=e[a.id];s&&s.dynamic===!0?(null===i&&(i=[]),i.push(a)):(r<o&&(t[r]=a),++r)}return r<n&&(t.length=r),i},bt.evalDynamic=function(t,e,i,n){for(var r=0,o=t.length;r!==o;++r){var a=e[t[r].id],s=a.onUpdateCallback;void 0!==s&&s.call(a,i,n)}},wt.prototype={constructor:wt,isVector4:!0,set:function(t,e,i,n){return this.x=t,this.y=e,this.z=i,this.w=n,this},setScalar:function(t){return this.x=t,this.y=t,this.z=t,this.w=t,this},setX:function(t){return this.x=t,this},setY:function(t){return this.y=t,this},setZ:function(t){return this.z=t,this},setW:function(t){return this.w=t,this},setComponent:function(t,e){switch(t){case 0:this.x=e;break;case 1:this.y=e;break;case 2:this.z=e;break;case 3:this.w=e;break;default:throw new Error("index is out of range: "+t)}},getComponent:function(t){switch(t){case 0:return this.x;case 1:return this.y;case 2:return this.z;case 3:return this.w;default:throw new Error("index is out of range: "+t)}},clone:function(){return new this.constructor(this.x,this.y,this.z,this.w)},copy:function(t){return this.x=t.x,this.y=t.y,this.z=t.z,this.w=void 0!==t.w?t.w:1,this},add:function(t,e){return void 0!==e?(console.warn("THREE.Vector4: .add() now only accepts one argument. Use .addVectors( a, b ) instead."),this.addVectors(t,e)):(this.x+=t.x,this.y+=t.y,this.z+=t.z,this.w+=t.w,this)},addScalar:function(t){return this.x+=t,this.y+=t,this.z+=t,this.w+=t,this},addVectors:function(t,e){return this.x=t.x+e.x,this.y=t.y+e.y,this.z=t.z+e.z,this.w=t.w+e.w,this},addScaledVector:function(t,e){return this.x+=t.x*e,this.y+=t.y*e,this.z+=t.z*e,this.w+=t.w*e,this},sub:function(t,e){return void 0!==e?(console.warn("THREE.Vector4: .sub() now only accepts one argument. Use .subVectors( a, b ) instead."),this.subVectors(t,e)):(this.x-=t.x,this.y-=t.y,this.z-=t.z,this.w-=t.w,this)},subScalar:function(t){return this.x-=t,this.y-=t,this.z-=t,this.w-=t,this},subVectors:function(t,e){return this.x=t.x-e.x,this.y=t.y-e.y,this.z=t.z-e.z,this.w=t.w-e.w,this},multiplyScalar:function(t){return isFinite(t)?(this.x*=t,this.y*=t,this.z*=t,this.w*=t):(this.x=0,this.y=0,this.z=0,this.w=0),this},applyMatrix4:function(t){var e=this.x,i=this.y,n=this.z,r=this.w,o=t.elements;return this.x=o[0]*e+o[4]*i+o[8]*n+o[12]*r,this.y=o[1]*e+o[5]*i+o[9]*n+o[13]*r,this.z=o[2]*e+o[6]*i+o[10]*n+o[14]*r,this.w=o[3]*e+o[7]*i+o[11]*n+o[15]*r,this},divideScalar:function(t){return this.multiplyScalar(1/t)},setAxisAngleFromQuaternion:function(t){this.w=2*Math.acos(t.w);var e=Math.sqrt(1-t.w*t.w);return e<1e-4?(this.x=1,this.y=0,this.z=0):(this.x=t.x/e,this.y=t.y/e,this.z=t.z/e),this},setAxisAngleFromRotationMatrix:function(t){var e,i,n,r,o=.01,a=.1,s=t.elements,c=s[0],u=s[4],h=s[8],l=s[1],d=s[5],f=s[9],p=s[2],m=s[6],g=s[10];if(Math.abs(u-l)<o&&Math.abs(h-p)<o&&Math.abs(f-m)<o){if(Math.abs(u+l)<a&&Math.abs(h+p)<a&&Math.abs(f+m)<a&&Math.abs(c+d+g-3)<a)return this.set(1,0,0,0),this;e=Math.PI;var v=(c+1)/2,y=(d+1)/2,b=(g+1)/2,x=(u+l)/4,w=(h+p)/4,_=(f+m)/4;return v>y&&v>b?v<o?(i=0,n=.707106781,r=.707106781):(i=Math.sqrt(v),n=x/i,r=w/i):y>b?y<o?(i=.707106781,n=0,r=.707106781):(n=Math.sqrt(y),i=x/n,r=_/n):b<o?(i=.707106781,n=.707106781,r=0):(r=Math.sqrt(b),i=w/r,n=_/r),this.set(i,n,r,e),this}var S=Math.sqrt((m-f)*(m-f)+(h-p)*(h-p)+(l-u)*(l-u));return Math.abs(S)<.001&&(S=1),this.x=(m-f)/S,this.y=(h-p)/S,this.z=(l-u)/S,this.w=Math.acos((c+d+g-1)/2),this},min:function(t){return this.x=Math.min(this.x,t.x),this.y=Math.min(this.y,t.y),this.z=Math.min(this.z,t.z),this.w=Math.min(this.w,t.w),this},max:function(t){return this.x=Math.max(this.x,t.x),this.y=Math.max(this.y,t.y),this.z=Math.max(this.z,t.z),this.w=Math.max(this.w,t.w),this},clamp:function(t,e){return this.x=Math.max(t.x,Math.min(e.x,this.x)),this.y=Math.max(t.y,Math.min(e.y,this.y)),this.z=Math.max(t.z,Math.min(e.z,this.z)),this.w=Math.max(t.w,Math.min(e.w,this.w)),this},clampScalar:function(){var t,e;return function(i,n){return void 0===t&&(t=new wt,e=new wt),t.set(i,i,i,i),e.set(n,n,n,n),this.clamp(t,e)}}(),floor:function(){return this.x=Math.floor(this.x),this.y=Math.floor(this.y),this.z=Math.floor(this.z),this.w=Math.floor(this.w),this},ceil:function(){return this.x=Math.ceil(this.x),this.y=Math.ceil(this.y),this.z=Math.ceil(this.z),this.w=Math.ceil(this.w),this},round:function(){return this.x=Math.round(this.x),this.y=Math.round(this.y),this.z=Math.round(this.z),this.w=Math.round(this.w),this},roundToZero:function(){return this.x=this.x<0?Math.ceil(this.x):Math.floor(this.x),this.y=this.y<0?Math.ceil(this.y):Math.floor(this.y),this.z=this.z<0?Math.ceil(this.z):Math.floor(this.z),this.w=this.w<0?Math.ceil(this.w):Math.floor(this.w),this},negate:function(){return this.x=-this.x,this.y=-this.y,this.z=-this.z,this.w=-this.w,this},dot:function(t){return this.x*t.x+this.y*t.y+this.z*t.z+this.w*t.w},lengthSq:function(){return this.x*this.x+this.y*this.y+this.z*this.z+this.w*this.w},length:function(){return Math.sqrt(this.x*this.x+this.y*this.y+this.z*this.z+this.w*this.w)},lengthManhattan:function(){return Math.abs(this.x)+Math.abs(this.y)+Math.abs(this.z)+Math.abs(this.w)},normalize:function(){return this.divideScalar(this.length())},setLength:function(t){return this.multiplyScalar(t/this.length())},lerp:function(t,e){return this.x+=(t.x-this.x)*e,this.y+=(t.y-this.y)*e,this.z+=(t.z-this.z)*e,this.w+=(t.w-this.w)*e,this},lerpVectors:function(t,e,i){return this.subVectors(e,t).multiplyScalar(i).add(t)},equals:function(t){return t.x===this.x&&t.y===this.y&&t.z===this.z&&t.w===this.w},fromArray:function(t,e){return void 0===e&&(e=0),this.x=t[e],this.y=t[e+1],this.z=t[e+2],this.w=t[e+3],this},toArray:function(t,e){return void 0===t&&(t=[]),void 0===e&&(e=0),t[e]=this.x,t[e+1]=this.y,t[e+2]=this.z,t[e+3]=this.w,t},fromAttribute:function(t,e,i){return void 0===i&&(i=0),e=e*t.itemSize+i,this.x=t.array[e],this.y=t.array[e+1],this.z=t.array[e+2],this.w=t.array[e+3],this}},Object.assign(St.prototype,E.prototype,{isWebGLRenderTarget:!0,setSize:function(t,e){this.width===t&&this.height===e||(this.width=t,this.height=e,this.dispose()),this.viewport.set(0,0,t,e),this.scissor.set(0,0,t,e)},clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.width=t.width,this.height=t.height,this.viewport.copy(t.viewport),this.texture=t.texture.clone(),this.depthBuffer=t.depthBuffer,this.stencilBuffer=t.stencilBuffer,this.depthTexture=t.depthTexture,this},dispose:function(){this.dispatchEvent({type:"dispose"})}}),At.prototype={constructor:At,isMaterial:!0,get needsUpdate(){return this._needsUpdate},set needsUpdate(t){t===!0&&this.update(),this._needsUpdate=t},setValues:function(t){if(void 0!==t)for(var e in t){var i=t[e];if(void 0!==i){var n=this[e];void 0!==n?n&&n.isColor?n.set(i):n&&n.isVector3&&i&&i.isVector3?n.copy(i):"overdraw"===e?this[e]=Number(i):this[e]=i:console.warn("THREE."+this.type+": '"+e+"' is not a property of this material.")}else console.warn("THREE.Material: '"+e+"' parameter is undefined.")}},toJSON:function(t){function e(t){var e=[];for(var i in t){var n=t[i];delete n.metadata,e.push(n)}return e}var i=void 0===t;i&&(t={textures:{},images:{}});var n={metadata:{version:4.4,type:"Material",generator:"Material.toJSON"}};if(n.uuid=this.uuid,n.type=this.type,""!==this.name&&(n.name=this.name),this.color&&this.color.isColor&&(n.color=this.color.getHex()),void 0!==this.roughness&&(n.roughness=this.roughness),void 0!==this.metalness&&(n.metalness=this.metalness),this.emissive&&this.emissive.isColor&&(n.emissive=this.emissive.getHex()),this.specular&&this.specular.isColor&&(n.specular=this.specular.getHex()),void 0!==this.shininess&&(n.shininess=this.shininess),this.map&&this.map.isTexture&&(n.map=this.map.toJSON(t).uuid),this.alphaMap&&this.alphaMap.isTexture&&(n.alphaMap=this.alphaMap.toJSON(t).uuid),this.lightMap&&this.lightMap.isTexture&&(n.lightMap=this.lightMap.toJSON(t).uuid),this.bumpMap&&this.bumpMap.isTexture&&(n.bumpMap=this.bumpMap.toJSON(t).uuid,n.bumpScale=this.bumpScale),this.normalMap&&this.normalMap.isTexture&&(n.normalMap=this.normalMap.toJSON(t).uuid,n.normalScale=this.normalScale.toArray()),this.displacementMap&&this.displacementMap.isTexture&&(n.displacementMap=this.displacementMap.toJSON(t).uuid,n.displacementScale=this.displacementScale,n.displacementBias=this.displacementBias),this.roughnessMap&&this.roughnessMap.isTexture&&(n.roughnessMap=this.roughnessMap.toJSON(t).uuid),this.metalnessMap&&this.metalnessMap.isTexture&&(n.metalnessMap=this.metalnessMap.toJSON(t).uuid),this.emissiveMap&&this.emissiveMap.isTexture&&(n.emissiveMap=this.emissiveMap.toJSON(t).uuid),this.specularMap&&this.specularMap.isTexture&&(n.specularMap=this.specularMap.toJSON(t).uuid),this.envMap&&this.envMap.isTexture&&(n.envMap=this.envMap.toJSON(t).uuid,n.reflectivity=this.reflectivity),void 0!==this.size&&(n.size=this.size),void 0!==this.sizeAttenuation&&(n.sizeAttenuation=this.sizeAttenuation),this.blending!==Dh&&(n.blending=this.blending),this.shading!==Eh&&(n.shading=this.shading),this.side!==Mh&&(n.side=this.side),this.vertexColors!==Ih&&(n.vertexColors=this.vertexColors),this.opacity<1&&(n.opacity=this.opacity),this.transparent===!0&&(n.transparent=this.transparent),n.depthFunc=this.depthFunc,n.depthTest=this.depthTest,n.depthWrite=this.depthWrite,this.alphaTest>0&&(n.alphaTest=this.alphaTest),this.premultipliedAlpha===!0&&(n.premultipliedAlpha=this.premultipliedAlpha),this.wireframe===!0&&(n.wireframe=this.wireframe),this.wireframeLinewidth>1&&(n.wireframeLinewidth=this.wireframeLinewidth),"round"!==this.wireframeLinecap&&(n.wireframeLinecap=this.wireframeLinecap),"round"!==this.wireframeLinejoin&&(n.wireframeLinejoin=this.wireframeLinejoin),n.skinning=this.skinning,n.morphTargets=this.morphTargets,i){var r=e(t.textures),o=e(t.images);r.length>0&&(n.textures=r),o.length>0&&(n.images=o)}return n},clone:function(){return(new this.constructor).copy(this)},copy:function(t){this.name=t.name,this.fog=t.fog,this.lights=t.lights,this.blending=t.blending,this.side=t.side,this.shading=t.shading,this.vertexColors=t.vertexColors,this.opacity=t.opacity,this.transparent=t.transparent,this.blendSrc=t.blendSrc,this.blendDst=t.blendDst,this.blendEquation=t.blendEquation,this.blendSrcAlpha=t.blendSrcAlpha,this.blendDstAlpha=t.blendDstAlpha,this.blendEquationAlpha=t.blendEquationAlpha,this.depthFunc=t.depthFunc,this.depthTest=t.depthTest,this.depthWrite=t.depthWrite,this.colorWrite=t.colorWrite,this.precision=t.precision,this.polygonOffset=t.polygonOffset,this.polygonOffsetFactor=t.polygonOffsetFactor,this.polygonOffsetUnits=t.polygonOffsetUnits,this.alphaTest=t.alphaTest,this.premultipliedAlpha=t.premultipliedAlpha,this.overdraw=t.overdraw,this.visible=t.visible,this.clipShadows=t.clipShadows;var e=t.clippingPlanes,i=null;if(null!==e){var n=e.length;i=new Array(n);for(var r=0;r!==n;++r)i[r]=e[r].clone()}return this.clippingPlanes=i,this},update:function(){this.dispatchEvent({type:"update"})},dispose:function(){this.dispatchEvent({type:"dispose"})}},Object.assign(At.prototype,E.prototype);var kd=0,Fd={merge:function(t){for(var e={},i=0;i<t.length;i++){var n=this.clone(t[i]);for(var r in n)e[r]=n[r]}return e},clone:function(t){var e={};for(var i in t){e[i]={};for(var n in t[i]){var r=t[i][n];r&&r.isColor||r&&r.isVector2||r&&r.isVector3||r&&r.isVector4||r&&r.isMatrix3||r&&r.isMatrix4||r&&r.isTexture?e[i][n]=r.clone():Array.isArray(r)?e[i][n]=r.slice():e[i][n]=r}}return e}};Pt.prototype=Object.create(At.prototype),Pt.prototype.constructor=Pt,Pt.prototype.isShaderMaterial=!0,Pt.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.fragmentShader=t.fragmentShader,this.vertexShader=t.vertexShader,this.uniforms=Fd.clone(t.uniforms),this.defines=t.defines,this.wireframe=t.wireframe,this.wireframeLinewidth=t.wireframeLinewidth,this.lights=t.lights,this.clipping=t.clipping,this.skinning=t.skinning,this.morphTargets=t.morphTargets,this.morphNormals=t.morphNormals,this.extensions=t.extensions,this},Pt.prototype.toJSON=function(t){var e=At.prototype.toJSON.call(this,t);return e.uniforms=this.uniforms,e.vertexShader=this.vertexShader,e.fragmentShader=this.fragmentShader,e};var zd="#ifdef USE_ALPHAMAP\n\tdiffuseColor.a *= texture2D( alphaMap, vUv ).g;\n#endif\n",Bd="#ifdef USE_ALPHAMAP\n\tuniform sampler2D alphaMap;\n#endif\n",Ud="#ifdef ALPHATEST\n\tif ( diffuseColor.a < ALPHATEST ) discard;\n#endif\n",jd="#ifdef USE_AOMAP\n\tfloat ambientOcclusion = ( texture2D( aoMap, vUv2 ).r - 1.0 ) * aoMapIntensity + 1.0;\n\treflectedLight.indirectDiffuse *= ambientOcclusion;\n\t#if defined( USE_ENVMAP ) && defined( PHYSICAL )\n\t\tfloat dotNV = saturate( dot( geometry.normal, geometry.viewDir ) );\n\t\treflectedLight.indirectSpecular *= computeSpecularOcclusion( dotNV, ambientOcclusion, material.specularRoughness );\n\t#endif\n#endif\n",$d="#ifdef USE_AOMAP\n\tuniform sampler2D aoMap;\n\tuniform float aoMapIntensity;\n#endif",Vd="\nvec3 transformed = vec3( position );\n",Gd="\nvec3 objectNormal = vec3( normal );\n",Hd="bool testLightInRange( const in float lightDistance, const in float cutoffDistance ) {\n\treturn any( bvec2( cutoffDistance == 0.0, lightDistance < cutoffDistance ) );\n}\nfloat punctualLightIntensityToIrradianceFactor( const in float lightDistance, const in float cutoffDistance, const in float decayExponent ) {\n\t\tif( decayExponent > 0.0 ) {\n#if defined ( PHYSICALLY_CORRECT_LIGHTS )\n\t\t\tfloat distanceFalloff = 1.0 / max( pow( lightDistance, decayExponent ), 0.01 );\n\t\t\tfloat maxDistanceCutoffFactor = pow2( saturate( 1.0 - pow4( lightDistance / cutoffDistance ) ) );\n\t\t\treturn distanceFalloff * maxDistanceCutoffFactor;\n#else\n\t\t\treturn pow( saturate( -lightDistance / cutoffDistance + 1.0 ), decayExponent );\n#endif\n\t\t}\n\t\treturn 1.0;\n}\nvec3 BRDF_Diffuse_Lambert( const in vec3 diffuseColor ) {\n\treturn RECIPROCAL_PI * diffuseColor;\n}\nvec3 F_Schlick( const in vec3 specularColor, const in float dotLH ) {\n\tfloat fresnel = exp2( ( -5.55473 * dotLH - 6.98316 ) * dotLH );\n\treturn ( 1.0 - specularColor ) * fresnel + specularColor;\n}\nfloat G_GGX_Smith( const in float alpha, const in float dotNL, const in float dotNV ) {\n\tfloat a2 = pow2( alpha );\n\tfloat gl = dotNL + sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNL ) );\n\tfloat gv = dotNV + sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNV ) );\n\treturn 1.0 / ( gl * gv );\n}\nfloat G_GGX_SmithCorrelated( const in float alpha, const in float dotNL, const in float dotNV ) {\n\tfloat a2 = pow2( alpha );\n\tfloat gv = dotNL * sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNV ) );\n\tfloat gl = dotNV * sqrt( a2 + ( 1.0 - a2 ) * pow2( dotNL ) );\n\treturn 0.5 / max( gv + gl, EPSILON );\n}\nfloat D_GGX( const in float alpha, const in float dotNH ) {\n\tfloat a2 = pow2( alpha );\n\tfloat denom = pow2( dotNH ) * ( a2 - 1.0 ) + 1.0;\n\treturn RECIPROCAL_PI * a2 / pow2( denom );\n}\nvec3 BRDF_Specular_GGX( const in IncidentLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float roughness ) {\n\tfloat alpha = pow2( roughness );\n\tvec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\n\tfloat dotNL = saturate( dot( geometry.normal, incidentLight.direction ) );\n\tfloat dotNV = saturate( dot( geometry.normal, geometry.viewDir ) );\n\tfloat dotNH = saturate( dot( geometry.normal, halfDir ) );\n\tfloat dotLH = saturate( dot( incidentLight.direction, halfDir ) );\n\tvec3 F = F_Schlick( specularColor, dotLH );\n\tfloat G = G_GGX_SmithCorrelated( alpha, dotNL, dotNV );\n\tfloat D = D_GGX( alpha, dotNH );\n\treturn F * ( G * D );\n}\nvec3 BRDF_Specular_GGX_Environment( const in GeometricContext geometry, const in vec3 specularColor, const in float roughness ) {\n\tfloat dotNV = saturate( dot( geometry.normal, geometry.viewDir ) );\n\tconst vec4 c0 = vec4( - 1, - 0.0275, - 0.572, 0.022 );\n\tconst vec4 c1 = vec4( 1, 0.0425, 1.04, - 0.04 );\n\tvec4 r = roughness * c0 + c1;\n\tfloat a004 = min( r.x * r.x, exp2( - 9.28 * dotNV ) ) * r.x + r.y;\n\tvec2 AB = vec2( -1.04, 1.04 ) * a004 + r.zw;\n\treturn specularColor * AB.x + AB.y;\n}\nfloat G_BlinnPhong_Implicit( ) {\n\treturn 0.25;\n}\nfloat D_BlinnPhong( const in float shininess, const in float dotNH ) {\n\treturn RECIPROCAL_PI * ( shininess * 0.5 + 1.0 ) * pow( dotNH, shininess );\n}\nvec3 BRDF_Specular_BlinnPhong( const in IncidentLight incidentLight, const in GeometricContext geometry, const in vec3 specularColor, const in float shininess ) {\n\tvec3 halfDir = normalize( incidentLight.direction + geometry.viewDir );\n\tfloat dotNH = saturate( dot( geometry.normal, halfDir ) );\n\tfloat dotLH = saturate( dot( incidentLight.direction, halfDir ) );\n\tvec3 F = F_Schlick( specularColor, dotLH );\n\tfloat G = G_BlinnPhong_Implicit( );\n\tfloat D = D_BlinnPhong( shininess, dotNH );\n\treturn F * ( G * D );\n}\nfloat GGXRoughnessToBlinnExponent( const in float ggxRoughness ) {\n\treturn ( 2.0 / pow2( ggxRoughness + 0.0001 ) - 2.0 );\n}\nfloat BlinnExponentToGGXRoughness( const in float blinnExponent ) {\n\treturn sqrt( 2.0 / ( blinnExponent + 2.0 ) );\n}\n",Wd="#ifdef USE_BUMPMAP\n\tuniform sampler2D bumpMap;\n\tuniform float bumpScale;\n\tvec2 dHdxy_fwd() {\n\t\tvec2 dSTdx = dFdx( vUv );\n\t\tvec2 dSTdy = dFdy( vUv );\n\t\tfloat Hll = bumpScale * texture2D( bumpMap, vUv ).x;\n\t\tfloat dBx = bumpScale * texture2D( bumpMap, vUv + dSTdx ).x - Hll;\n\t\tfloat dBy = bumpScale * texture2D( bumpMap, vUv + dSTdy ).x - Hll;\n\t\treturn vec2( dBx, dBy );\n\t}\n\tvec3 perturbNormalArb( vec3 surf_pos, vec3 surf_norm, vec2 dHdxy ) {\n\t\tvec3 vSigmaX = dFdx( surf_pos );\n\t\tvec3 vSigmaY = dFdy( surf_pos );\n\t\tvec3 vN = surf_norm;\n\t\tvec3 R1 = cross( vSigmaY, vN );\n\t\tvec3 R2 = cross( vN, vSigmaX );\n\t\tfloat fDet = dot( vSigmaX, R1 );\n\t\tvec3 vGrad = sign( fDet ) * ( dHdxy.x * R1 + dHdxy.y * R2 );\n\t\treturn normalize( abs( fDet ) * surf_norm - vGrad );\n\t}\n#endif\n",Xd="#if NUM_CLIPPING_PLANES > 0\n\tfor ( int i = 0; i < NUM_CLIPPING_PLANES; ++ i ) {\n\t\tvec4 plane = clippingPlanes[ i ];\n\t\tif ( dot( vViewPosition, plane.xyz ) > plane.w ) discard;\n\t}\n#endif\n",qd="#if NUM_CLIPPING_PLANES > 0\n\t#if ! defined( PHYSICAL ) && ! defined( PHONG )\n\t\tvarying vec3 vViewPosition;\n\t#endif\n\tuniform vec4 clippingPlanes[ NUM_CLIPPING_PLANES ];\n#endif\n",Yd="#if NUM_CLIPPING_PLANES > 0 && ! defined( PHYSICAL ) && ! defined( PHONG )\n\tvarying vec3 vViewPosition;\n#endif\n",Zd="#if NUM_CLIPPING_PLANES > 0 && ! defined( PHYSICAL ) && ! defined( PHONG )\n\tvViewPosition = - mvPosition.xyz;\n#endif\n",Kd="#ifdef USE_COLOR\n\tdiffuseColor.rgb *= vColor;\n#endif",Qd="#ifdef USE_COLOR\n\tvarying vec3 vColor;\n#endif\n",Jd="#ifdef USE_COLOR\n\tvarying vec3 vColor;\n#endif",tf="#ifdef USE_COLOR\n\tvColor.xyz = color.xyz;\n#endif",ef="#define PI 3.14159265359\n#define PI2 6.28318530718\n#define RECIPROCAL_PI 0.31830988618\n#define RECIPROCAL_PI2 0.15915494\n#define LOG2 1.442695\n#define EPSILON 1e-6\n#define saturate(a) clamp( a, 0.0, 1.0 )\n#define whiteCompliment(a) ( 1.0 - saturate( a ) )\nfloat pow2( const in float x ) { return x*x; }\nfloat pow3( const in float x ) { return x*x*x; }\nfloat pow4( const in float x ) { float x2 = x*x; return x2*x2; }\nfloat average( const in vec3 color ) { return dot( color, vec3( 0.3333 ) ); }\nhighp float rand( const in vec2 uv ) {\n\tconst highp float a = 12.9898, b = 78.233, c = 43758.5453;\n\thighp float dt = dot( uv.xy, vec2( a,b ) ), sn = mod( dt, PI );\n\treturn fract(sin(sn) * c);\n}\nstruct IncidentLight {\n\tvec3 color;\n\tvec3 direction;\n\tbool visible;\n};\nstruct ReflectedLight {\n\tvec3 directDiffuse;\n\tvec3 directSpecular;\n\tvec3 indirectDiffuse;\n\tvec3 indirectSpecular;\n};\nstruct GeometricContext {\n\tvec3 position;\n\tvec3 normal;\n\tvec3 viewDir;\n};\nvec3 transformDirection( in vec3 dir, in mat4 matrix ) {\n\treturn normalize( ( matrix * vec4( dir, 0.0 ) ).xyz );\n}\nvec3 inverseTransformDirection( in vec3 dir, in mat4 matrix ) {\n\treturn normalize( ( vec4( dir, 0.0 ) * matrix ).xyz );\n}\nvec3 projectOnPlane(in vec3 point, in vec3 pointOnPlane, in vec3 planeNormal ) {\n\tfloat distance = dot( planeNormal, point - pointOnPlane );\n\treturn - distance * planeNormal + point;\n}\nfloat sideOfPlane( in vec3 point, in vec3 pointOnPlane, in vec3 planeNormal ) {\n\treturn sign( dot( point - pointOnPlane, planeNormal ) );\n}\nvec3 linePlaneIntersect( in vec3 pointOnLine, in vec3 lineDirection, in vec3 pointOnPlane, in vec3 planeNormal ) {\n\treturn lineDirection * ( dot( planeNormal, pointOnPlane - pointOnLine ) / dot( planeNormal, lineDirection ) ) + pointOnLine;\n}\n",nf="#ifdef ENVMAP_TYPE_CUBE_UV\n#define cubeUV_textureSize (1024.0)\nint getFaceFromDirection(vec3 direction) {\n\tvec3 absDirection = abs(direction);\n\tint face = -1;\n\tif( absDirection.x > absDirection.z ) {\n\t\tif(absDirection.x > absDirection.y )\n\t\t\tface = direction.x > 0.0 ? 0 : 3;\n\t\telse\n\t\t\tface = direction.y > 0.0 ? 1 : 4;\n\t}\n\telse {\n\t\tif(absDirection.z > absDirection.y )\n\t\t\tface = direction.z > 0.0 ? 2 : 5;\n\t\telse\n\t\t\tface = direction.y > 0.0 ? 1 : 4;\n\t}\n\treturn face;\n}\n#define cubeUV_maxLods1  (log2(cubeUV_textureSize*0.25) - 1.0)\n#define cubeUV_rangeClamp (exp2((6.0 - 1.0) * 2.0))\nvec2 MipLevelInfo( vec3 vec, float roughnessLevel, float roughness ) {\n\tfloat scale = exp2(cubeUV_maxLods1 - roughnessLevel);\n\tfloat dxRoughness = dFdx(roughness);\n\tfloat dyRoughness = dFdy(roughness);\n\tvec3 dx = dFdx( vec * scale * dxRoughness );\n\tvec3 dy = dFdy( vec * scale * dyRoughness );\n\tfloat d = max( dot( dx, dx ), dot( dy, dy ) );\n\td = clamp(d, 1.0, cubeUV_rangeClamp);\n\tfloat mipLevel = 0.5 * log2(d);\n\treturn vec2(floor(mipLevel), fract(mipLevel));\n}\n#define cubeUV_maxLods2 (log2(cubeUV_textureSize*0.25) - 2.0)\n#define cubeUV_rcpTextureSize (1.0 / cubeUV_textureSize)\nvec2 getCubeUV(vec3 direction, float roughnessLevel, float mipLevel) {\n\tmipLevel = roughnessLevel > cubeUV_maxLods2 - 3.0 ? 0.0 : mipLevel;\n\tfloat a = 16.0 * cubeUV_rcpTextureSize;\n\tvec2 exp2_packed = exp2( vec2( roughnessLevel, mipLevel ) );\n\tvec2 rcp_exp2_packed = vec2( 1.0 ) / exp2_packed;\n\tfloat powScale = exp2_packed.x * exp2_packed.y;\n\tfloat scale = rcp_exp2_packed.x * rcp_exp2_packed.y * 0.25;\n\tfloat mipOffset = 0.75*(1.0 - rcp_exp2_packed.y) * rcp_exp2_packed.x;\n\tbool bRes = mipLevel == 0.0;\n\tscale =  bRes && (scale < a) ? a : scale;\n\tvec3 r;\n\tvec2 offset;\n\tint face = getFaceFromDirection(direction);\n\tfloat rcpPowScale = 1.0 / powScale;\n\tif( face == 0) {\n\t\tr = vec3(direction.x, -direction.z, direction.y);\n\t\toffset = vec2(0.0+mipOffset,0.75 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  a : offset.y;\n\t}\n\telse if( face == 1) {\n\t\tr = vec3(direction.y, direction.x, direction.z);\n\t\toffset = vec2(scale+mipOffset, 0.75 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  a : offset.y;\n\t}\n\telse if( face == 2) {\n\t\tr = vec3(direction.z, direction.x, direction.y);\n\t\toffset = vec2(2.0*scale+mipOffset, 0.75 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  a : offset.y;\n\t}\n\telse if( face == 3) {\n\t\tr = vec3(direction.x, direction.z, direction.y);\n\t\toffset = vec2(0.0+mipOffset,0.5 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  0.0 : offset.y;\n\t}\n\telse if( face == 4) {\n\t\tr = vec3(direction.y, direction.x, -direction.z);\n\t\toffset = vec2(scale+mipOffset, 0.5 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  0.0 : offset.y;\n\t}\n\telse {\n\t\tr = vec3(direction.z, -direction.x, direction.y);\n\t\toffset = vec2(2.0*scale+mipOffset, 0.5 * rcpPowScale);\n\t\toffset.y = bRes && (offset.y < 2.0*a) ?  0.0 : offset.y;\n\t}\n\tr = normalize(r);\n\tfloat texelOffset = 0.5 * cubeUV_rcpTextureSize;\n\tvec2 s = ( r.yz / abs( r.x ) + vec2( 1.0 ) ) * 0.5;\n\tvec2 base = offset + vec2( texelOffset );\n\treturn base + s * ( scale - 2.0 * texelOffset );\n}\n#define cubeUV_maxLods3 (log2(cubeUV_textureSize*0.25) - 3.0)\nvec4 textureCubeUV(vec3 reflectedDirection, float roughness ) {\n\tfloat roughnessVal = roughness* cubeUV_maxLods3;\n\tfloat r1 = floor(roughnessVal);\n\tfloat r2 = r1 + 1.0;\n\tfloat t = fract(roughnessVal);\n\tvec2 mipInfo = MipLevelInfo(reflectedDirection, r1, roughness);\n\tfloat s = mipInfo.y;\n\tfloat level0 = mipInfo.x;\n\tfloat level1 = level0 + 1.0;\n\tlevel1 = level1 > 5.0 ? 5.0 : level1;\n\tlevel0 += min( floor( s + 0.5 ), 5.0 );\n\tvec2 uv_10 = getCubeUV(reflectedDirection, r1, level0);\n\tvec4 color10 = envMapTexelToLinear(texture2D(envMap, uv_10));\n\tvec2 uv_20 = getCubeUV(reflectedDirection, r2, level0);\n\tvec4 color20 = envMapTexelToLinear(texture2D(envMap, uv_20));\n\tvec4 result = mix(color10, color20, t);\n\treturn vec4(result.rgb, 1.0);\n}\n#endif\n",rf="#ifdef FLIP_SIDED\n\tobjectNormal = -objectNormal;\n#endif\nvec3 transformedNormal = normalMatrix * objectNormal;\n",of="#ifdef USE_DISPLACEMENTMAP\n\tuniform sampler2D displacementMap;\n\tuniform float displacementScale;\n\tuniform float displacementBias;\n#endif\n",af="#ifdef USE_DISPLACEMENTMAP\n\ttransformed += normal * ( texture2D( displacementMap, uv ).x * displacementScale + displacementBias );\n#endif\n",sf="#ifdef USE_EMISSIVEMAP\n\tvec4 emissiveColor = texture2D( emissiveMap, vUv );\n\temissiveColor.rgb = emissiveMapTexelToLinear( emissiveColor ).rgb;\n\ttotalEmissiveRadiance *= emissiveColor.rgb;\n#endif\n",cf="#ifdef USE_EMISSIVEMAP\n\tuniform sampler2D emissiveMap;\n#endif\n",uf="  gl_FragColor = linearToOutputTexel( gl_FragColor );\n",hf="\nvec4 LinearToLinear( in vec4 value ) {\n  return value;\n}\nvec4 GammaToLinear( in vec4 value, in float gammaFactor ) {\n  return vec4( pow( value.xyz, vec3( gammaFactor ) ), value.w );\n}\nvec4 LinearToGamma( in vec4 value, in float gammaFactor ) {\n  return vec4( pow( value.xyz, vec3( 1.0 / gammaFactor ) ), value.w );\n}\nvec4 sRGBToLinear( in vec4 value ) {\n  return vec4( mix( pow( value.rgb * 0.9478672986 + vec3( 0.0521327014 ), vec3( 2.4 ) ), value.rgb * 0.0773993808, vec3( lessThanEqual( value.rgb, vec3( 0.04045 ) ) ) ), value.w );\n}\nvec4 LinearTosRGB( in vec4 value ) {\n  return vec4( mix( pow( value.rgb, vec3( 0.41666 ) ) * 1.055 - vec3( 0.055 ), value.rgb * 12.92, vec3( lessThanEqual( value.rgb, vec3( 0.0031308 ) ) ) ), value.w );\n}\nvec4 RGBEToLinear( in vec4 value ) {\n  return vec4( value.rgb * exp2( value.a * 255.0 - 128.0 ), 1.0 );\n}\nvec4 LinearToRGBE( in vec4 value ) {\n  float maxComponent = max( max( value.r, value.g ), value.b );\n  float fExp = clamp( ceil( log2( maxComponent ) ), -128.0, 127.0 );\n  return vec4( value.rgb / exp2( fExp ), ( fExp + 128.0 ) / 255.0 );\n}\nvec4 RGBMToLinear( in vec4 value, in float maxRange ) {\n  return vec4( value.xyz * value.w * maxRange, 1.0 );\n}\nvec4 LinearToRGBM( in vec4 value, in float maxRange ) {\n  float maxRGB = max( value.x, max( value.g, value.b ) );\n  float M      = clamp( maxRGB / maxRange, 0.0, 1.0 );\n  M            = ceil( M * 255.0 ) / 255.0;\n  return vec4( value.rgb / ( M * maxRange ), M );\n}\nvec4 RGBDToLinear( in vec4 value, in float maxRange ) {\n    return vec4( value.rgb * ( ( maxRange / 255.0 ) / value.a ), 1.0 );\n}\nvec4 LinearToRGBD( in vec4 value, in float maxRange ) {\n    float maxRGB = max( value.x, max( value.g, value.b ) );\n    float D      = max( maxRange / maxRGB, 1.0 );\n    D            = min( floor( D ) / 255.0, 1.0 );\n    return vec4( value.rgb * ( D * ( 255.0 / maxRange ) ), D );\n}\nconst mat3 cLogLuvM = mat3( 0.2209, 0.3390, 0.4184, 0.1138, 0.6780, 0.7319, 0.0102, 0.1130, 0.2969 );\nvec4 LinearToLogLuv( in vec4 value )  {\n  vec3 Xp_Y_XYZp = value.rgb * cLogLuvM;\n  Xp_Y_XYZp = max(Xp_Y_XYZp, vec3(1e-6, 1e-6, 1e-6));\n  vec4 vResult;\n  vResult.xy = Xp_Y_XYZp.xy / Xp_Y_XYZp.z;\n  float Le = 2.0 * log2(Xp_Y_XYZp.y) + 127.0;\n  vResult.w = fract(Le);\n  vResult.z = (Le - (floor(vResult.w*255.0))/255.0)/255.0;\n  return vResult;\n}\nconst mat3 cLogLuvInverseM = mat3( 6.0014, -2.7008, -1.7996, -1.3320, 3.1029, -5.7721, 0.3008, -1.0882, 5.6268 );\nvec4 LogLuvToLinear( in vec4 value ) {\n  float Le = value.z * 255.0 + value.w;\n  vec3 Xp_Y_XYZp;\n  Xp_Y_XYZp.y = exp2((Le - 127.0) / 2.0);\n  Xp_Y_XYZp.z = Xp_Y_XYZp.y / value.y;\n  Xp_Y_XYZp.x = value.x * Xp_Y_XYZp.z;\n  vec3 vRGB = Xp_Y_XYZp.rgb * cLogLuvInverseM;\n  return vec4( max(vRGB, 0.0), 1.0 );\n}\n",lf="#ifdef USE_ENVMAP\n\t#if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG )\n\t\tvec3 cameraToVertex = normalize( vWorldPosition - cameraPosition );\n\t\tvec3 worldNormal = inverseTransformDirection( normal, viewMatrix );\n\t\t#ifdef ENVMAP_MODE_REFLECTION\n\t\t\tvec3 reflectVec = reflect( cameraToVertex, worldNormal );\n\t\t#else\n\t\t\tvec3 reflectVec = refract( cameraToVertex, worldNormal, refractionRatio );\n\t\t#endif\n\t#else\n\t\tvec3 reflectVec = vReflect;\n\t#endif\n\t#ifdef ENVMAP_TYPE_CUBE\n\t\tvec4 envColor = textureCube( envMap, flipNormal * vec3( flipEnvMap * reflectVec.x, reflectVec.yz ) );\n\t#elif defined( ENVMAP_TYPE_EQUIREC )\n\t\tvec2 sampleUV;\n\t\tsampleUV.y = saturate( flipNormal * reflectVec.y * 0.5 + 0.5 );\n\t\tsampleUV.x = atan( flipNormal * reflectVec.z, flipNormal * reflectVec.x ) * RECIPROCAL_PI2 + 0.5;\n\t\tvec4 envColor = texture2D( envMap, sampleUV );\n\t#elif defined( ENVMAP_TYPE_SPHERE )\n\t\tvec3 reflectView = flipNormal * normalize( ( viewMatrix * vec4( reflectVec, 0.0 ) ).xyz + vec3( 0.0, 0.0, 1.0 ) );\n\t\tvec4 envColor = texture2D( envMap, reflectView.xy * 0.5 + 0.5 );\n\t#else\n\t\tvec4 envColor = vec4( 0.0 );\n\t#endif\n\tenvColor = envMapTexelToLinear( envColor );\n\t#ifdef ENVMAP_BLENDING_MULTIPLY\n\t\toutgoingLight = mix( outgoingLight, outgoingLight * envColor.xyz, specularStrength * reflectivity );\n\t#elif defined( ENVMAP_BLENDING_MIX )\n\t\toutgoingLight = mix( outgoingLight, envColor.xyz, specularStrength * reflectivity );\n\t#elif defined( ENVMAP_BLENDING_ADD )\n\t\toutgoingLight += envColor.xyz * specularStrength * reflectivity;\n\t#endif\n#endif\n",df="#if defined( USE_ENVMAP ) || defined( PHYSICAL )\n\tuniform float reflectivity;\n\tuniform float envMapIntenstiy;\n#endif\n#ifdef USE_ENVMAP\n\t#if ! defined( PHYSICAL ) && ( defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG ) )\n\t\tvarying vec3 vWorldPosition;\n\t#endif\n\t#ifdef ENVMAP_TYPE_CUBE\n\t\tuniform samplerCube envMap;\n\t#else\n\t\tuniform sampler2D envMap;\n\t#endif\n\tuniform float flipEnvMap;\n\t#if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG ) || defined( PHYSICAL )\n\t\tuniform float refractionRatio;\n\t#else\n\t\tvarying vec3 vReflect;\n\t#endif\n#endif\n",ff="#ifdef USE_ENVMAP\n\t#if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG )\n\t\tvarying vec3 vWorldPosition;\n\t#else\n\t\tvarying vec3 vReflect;\n\t\tuniform float refractionRatio;\n\t#endif\n#endif\n",pf="#ifdef USE_ENVMAP\n\t#if defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( PHONG )\n\t\tvWorldPosition = worldPosition.xyz;\n\t#else\n\t\tvec3 cameraToVertex = normalize( worldPosition.xyz - cameraPosition );\n\t\tvec3 worldNormal = inverseTransformDirection( transformedNormal, viewMatrix );\n\t\t#ifdef ENVMAP_MODE_REFLECTION\n\t\t\tvReflect = reflect( cameraToVertex, worldNormal );\n\t\t#else\n\t\t\tvReflect = refract( cameraToVertex, worldNormal, refractionRatio );\n\t\t#endif\n\t#endif\n#endif\n",mf="#ifdef USE_FOG\n\t#ifdef USE_LOGDEPTHBUF_EXT\n\t\tfloat depth = gl_FragDepthEXT / gl_FragCoord.w;\n\t#else\n\t\tfloat depth = gl_FragCoord.z / gl_FragCoord.w;\n\t#endif\n\t#ifdef FOG_EXP2\n\t\tfloat fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );\n\t#else\n\t\tfloat fogFactor = smoothstep( fogNear, fogFar, depth );\n\t#endif\n\tgl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );\n#endif\n",gf="#ifdef USE_FOG\n\tuniform vec3 fogColor;\n\t#ifdef FOG_EXP2\n\t\tuniform float fogDensity;\n\t#else\n\t\tuniform float fogNear;\n\t\tuniform float fogFar;\n\t#endif\n#endif",vf="#ifdef USE_LIGHTMAP\n\treflectedLight.indirectDiffuse += PI * texture2D( lightMap, vUv2 ).xyz * lightMapIntensity;\n#endif\n",yf="#ifdef USE_LIGHTMAP\n\tuniform sampler2D lightMap;\n\tuniform float lightMapIntensity;\n#endif",bf="vec3 diffuse = vec3( 1.0 );\nGeometricContext geometry;\ngeometry.position = mvPosition.xyz;\ngeometry.normal = normalize( transformedNormal );\ngeometry.viewDir = normalize( -mvPosition.xyz );\nGeometricContext backGeometry;\nbackGeometry.position = geometry.position;\nbackGeometry.normal = -geometry.normal;\nbackGeometry.viewDir = geometry.viewDir;\nvLightFront = vec3( 0.0 );\n#ifdef DOUBLE_SIDED\n\tvLightBack = vec3( 0.0 );\n#endif\nIncidentLight directLight;\nfloat dotNL;\nvec3 directLightColor_Diffuse;\n#if NUM_POINT_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_POINT_LIGHTS; i ++ ) {\n\t\tgetPointDirectLightIrradiance( pointLights[ i ], geometry, directLight );\n\t\tdotNL = dot( geometry.normal, directLight.direction );\n\t\tdirectLightColor_Diffuse = PI * directLight.color;\n\t\tvLightFront += saturate( dotNL ) * directLightColor_Diffuse;\n\t\t#ifdef DOUBLE_SIDED\n\t\t\tvLightBack += saturate( -dotNL ) * directLightColor_Diffuse;\n\t\t#endif\n\t}\n#endif\n#if NUM_SPOT_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_SPOT_LIGHTS; i ++ ) {\n\t\tgetSpotDirectLightIrradiance( spotLights[ i ], geometry, directLight );\n\t\tdotNL = dot( geometry.normal, directLight.direction );\n\t\tdirectLightColor_Diffuse = PI * directLight.color;\n\t\tvLightFront += saturate( dotNL ) * directLightColor_Diffuse;\n\t\t#ifdef DOUBLE_SIDED\n\t\t\tvLightBack += saturate( -dotNL ) * directLightColor_Diffuse;\n\t\t#endif\n\t}\n#endif\n#if NUM_DIR_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\n\t\tgetDirectionalDirectLightIrradiance( directionalLights[ i ], geometry, directLight );\n\t\tdotNL = dot( geometry.normal, directLight.direction );\n\t\tdirectLightColor_Diffuse = PI * directLight.color;\n\t\tvLightFront += saturate( dotNL ) * directLightColor_Diffuse;\n\t\t#ifdef DOUBLE_SIDED\n\t\t\tvLightBack += saturate( -dotNL ) * directLightColor_Diffuse;\n\t\t#endif\n\t}\n#endif\n#if NUM_HEMI_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_HEMI_LIGHTS; i ++ ) {\n\t\tvLightFront += getHemisphereLightIrradiance( hemisphereLights[ i ], geometry );\n\t\t#ifdef DOUBLE_SIDED\n\t\t\tvLightBack += getHemisphereLightIrradiance( hemisphereLights[ i ], backGeometry );\n\t\t#endif\n\t}\n#endif\n",xf="uniform vec3 ambientLightColor;\nvec3 getAmbientLightIrradiance( const in vec3 ambientLightColor ) {\n\tvec3 irradiance = ambientLightColor;\n\t#ifndef PHYSICALLY_CORRECT_LIGHTS\n\t\tirradiance *= PI;\n\t#endif\n\treturn irradiance;\n}\n#if NUM_DIR_LIGHTS > 0\n\tstruct DirectionalLight {\n\t\tvec3 direction;\n\t\tvec3 color;\n\t\tint shadow;\n\t\tfloat shadowBias;\n\t\tfloat shadowRadius;\n\t\tvec2 shadowMapSize;\n\t};\n\tuniform DirectionalLight directionalLights[ NUM_DIR_LIGHTS ];\n\tvoid getDirectionalDirectLightIrradiance( const in DirectionalLight directionalLight, const in GeometricContext geometry, out IncidentLight directLight ) {\n\t\tdirectLight.color = directionalLight.color;\n\t\tdirectLight.direction = directionalLight.direction;\n\t\tdirectLight.visible = true;\n\t}\n#endif\n#if NUM_POINT_LIGHTS > 0\n\tstruct PointLight {\n\t\tvec3 position;\n\t\tvec3 color;\n\t\tfloat distance;\n\t\tfloat decay;\n\t\tint shadow;\n\t\tfloat shadowBias;\n\t\tfloat shadowRadius;\n\t\tvec2 shadowMapSize;\n\t};\n\tuniform PointLight pointLights[ NUM_POINT_LIGHTS ];\n\tvoid getPointDirectLightIrradiance( const in PointLight pointLight, const in GeometricContext geometry, out IncidentLight directLight ) {\n\t\tvec3 lVector = pointLight.position - geometry.position;\n\t\tdirectLight.direction = normalize( lVector );\n\t\tfloat lightDistance = length( lVector );\n\t\tif ( testLightInRange( lightDistance, pointLight.distance ) ) {\n\t\t\tdirectLight.color = pointLight.color;\n\t\t\tdirectLight.color *= punctualLightIntensityToIrradianceFactor( lightDistance, pointLight.distance, pointLight.decay );\n\t\t\tdirectLight.visible = true;\n\t\t} else {\n\t\t\tdirectLight.color = vec3( 0.0 );\n\t\t\tdirectLight.visible = false;\n\t\t}\n\t}\n#endif\n#if NUM_SPOT_LIGHTS > 0\n\tstruct SpotLight {\n\t\tvec3 position;\n\t\tvec3 direction;\n\t\tvec3 color;\n\t\tfloat distance;\n\t\tfloat decay;\n\t\tfloat coneCos;\n\t\tfloat penumbraCos;\n\t\tint shadow;\n\t\tfloat shadowBias;\n\t\tfloat shadowRadius;\n\t\tvec2 shadowMapSize;\n\t};\n\tuniform SpotLight spotLights[ NUM_SPOT_LIGHTS ];\n\tvoid getSpotDirectLightIrradiance( const in SpotLight spotLight, const in GeometricContext geometry, out IncidentLight directLight  ) {\n\t\tvec3 lVector = spotLight.position - geometry.position;\n\t\tdirectLight.direction = normalize( lVector );\n\t\tfloat lightDistance = length( lVector );\n\t\tfloat angleCos = dot( directLight.direction, spotLight.direction );\n\t\tif ( all( bvec2( angleCos > spotLight.coneCos, testLightInRange( lightDistance, spotLight.distance ) ) ) ) {\n\t\t\tfloat spotEffect = smoothstep( spotLight.coneCos, spotLight.penumbraCos, angleCos );\n\t\t\tdirectLight.color = spotLight.color;\n\t\t\tdirectLight.color *= spotEffect * punctualLightIntensityToIrradianceFactor( lightDistance, spotLight.distance, spotLight.decay );\n\t\t\tdirectLight.visible = true;\n\t\t} else {\n\t\t\tdirectLight.color = vec3( 0.0 );\n\t\t\tdirectLight.visible = false;\n\t\t}\n\t}\n#endif\n#if NUM_HEMI_LIGHTS > 0\n\tstruct HemisphereLight {\n\t\tvec3 direction;\n\t\tvec3 skyColor;\n\t\tvec3 groundColor;\n\t};\n\tuniform HemisphereLight hemisphereLights[ NUM_HEMI_LIGHTS ];\n\tvec3 getHemisphereLightIrradiance( const in HemisphereLight hemiLight, const in GeometricContext geometry ) {\n\t\tfloat dotNL = dot( geometry.normal, hemiLight.direction );\n\t\tfloat hemiDiffuseWeight = 0.5 * dotNL + 0.5;\n\t\tvec3 irradiance = mix( hemiLight.groundColor, hemiLight.skyColor, hemiDiffuseWeight );\n\t\t#ifndef PHYSICALLY_CORRECT_LIGHTS\n\t\t\tirradiance *= PI;\n\t\t#endif\n\t\treturn irradiance;\n\t}\n#endif\n#if defined( USE_ENVMAP ) && defined( PHYSICAL )\n\tvec3 getLightProbeIndirectIrradiance( const in GeometricContext geometry, const in int maxMIPLevel ) {\n\t\t#include <normal_flip>\n\t\tvec3 worldNormal = inverseTransformDirection( geometry.normal, viewMatrix );\n\t\t#ifdef ENVMAP_TYPE_CUBE\n\t\t\tvec3 queryVec = flipNormal * vec3( flipEnvMap * worldNormal.x, worldNormal.yz );\n\t\t\t#ifdef TEXTURE_LOD_EXT\n\t\t\t\tvec4 envMapColor = textureCubeLodEXT( envMap, queryVec, float( maxMIPLevel ) );\n\t\t\t#else\n\t\t\t\tvec4 envMapColor = textureCube( envMap, queryVec, float( maxMIPLevel ) );\n\t\t\t#endif\n\t\t\tenvMapColor.rgb = envMapTexelToLinear( envMapColor ).rgb;\n\t\t#elif defined( ENVMAP_TYPE_CUBE_UV )\n\t\t\tvec3 queryVec = flipNormal * vec3( flipEnvMap * worldNormal.x, worldNormal.yz );\n\t\t\tvec4 envMapColor = textureCubeUV( queryVec, 1.0 );\n\t\t#else\n\t\t\tvec4 envMapColor = vec4( 0.0 );\n\t\t#endif\n\t\treturn PI * envMapColor.rgb * envMapIntensity;\n\t}\n\tfloat getSpecularMIPLevel( const in float blinnShininessExponent, const in int maxMIPLevel ) {\n\t\tfloat maxMIPLevelScalar = float( maxMIPLevel );\n\t\tfloat desiredMIPLevel = maxMIPLevelScalar - 0.79248 - 0.5 * log2( pow2( blinnShininessExponent ) + 1.0 );\n\t\treturn clamp( desiredMIPLevel, 0.0, maxMIPLevelScalar );\n\t}\n\tvec3 getLightProbeIndirectRadiance( const in GeometricContext geometry, const in float blinnShininessExponent, const in int maxMIPLevel ) {\n\t\t#ifdef ENVMAP_MODE_REFLECTION\n\t\t\tvec3 reflectVec = reflect( -geometry.viewDir, geometry.normal );\n\t\t#else\n\t\t\tvec3 reflectVec = refract( -geometry.viewDir, geometry.normal, refractionRatio );\n\t\t#endif\n\t\t#include <normal_flip>\n\t\treflectVec = inverseTransformDirection( reflectVec, viewMatrix );\n\t\tfloat specularMIPLevel = getSpecularMIPLevel( blinnShininessExponent, maxMIPLevel );\n\t\t#ifdef ENVMAP_TYPE_CUBE\n\t\t\tvec3 queryReflectVec = flipNormal * vec3( flipEnvMap * reflectVec.x, reflectVec.yz );\n\t\t\t#ifdef TEXTURE_LOD_EXT\n\t\t\t\tvec4 envMapColor = textureCubeLodEXT( envMap, queryReflectVec, specularMIPLevel );\n\t\t\t#else\n\t\t\t\tvec4 envMapColor = textureCube( envMap, queryReflectVec, specularMIPLevel );\n\t\t\t#endif\n\t\t\tenvMapColor.rgb = envMapTexelToLinear( envMapColor ).rgb;\n\t\t#elif defined( ENVMAP_TYPE_CUBE_UV )\n\t\t\tvec3 queryReflectVec = flipNormal * vec3( flipEnvMap * reflectVec.x, reflectVec.yz );\n\t\t\tvec4 envMapColor = textureCubeUV(queryReflectVec, BlinnExponentToGGXRoughness(blinnShininessExponent));\n\t\t#elif defined( ENVMAP_TYPE_EQUIREC )\n\t\t\tvec2 sampleUV;\n\t\t\tsampleUV.y = saturate( flipNormal * reflectVec.y * 0.5 + 0.5 );\n\t\t\tsampleUV.x = atan( flipNormal * reflectVec.z, flipNormal * reflectVec.x ) * RECIPROCAL_PI2 + 0.5;\n\t\t\t#ifdef TEXTURE_LOD_EXT\n\t\t\t\tvec4 envMapColor = texture2DLodEXT( envMap, sampleUV, specularMIPLevel );\n\t\t\t#else\n\t\t\t\tvec4 envMapColor = texture2D( envMap, sampleUV, specularMIPLevel );\n\t\t\t#endif\n\t\t\tenvMapColor.rgb = envMapTexelToLinear( envMapColor ).rgb;\n\t\t#elif defined( ENVMAP_TYPE_SPHERE )\n\t\t\tvec3 reflectView = flipNormal * normalize( ( viewMatrix * vec4( reflectVec, 0.0 ) ).xyz + vec3( 0.0,0.0,1.0 ) );\n\t\t\t#ifdef TEXTURE_LOD_EXT\n\t\t\t\tvec4 envMapColor = texture2DLodEXT( envMap, reflectView.xy * 0.5 + 0.5, specularMIPLevel );\n\t\t\t#else\n\t\t\t\tvec4 envMapColor = texture2D( envMap, reflectView.xy * 0.5 + 0.5, specularMIPLevel );\n\t\t\t#endif\n\t\t\tenvMapColor.rgb = envMapTexelToLinear( envMapColor ).rgb;\n\t\t#endif\n\t\treturn envMapColor.rgb * envMapIntensity;\n\t}\n#endif\n",wf="BlinnPhongMaterial material;\nmaterial.diffuseColor = diffuseColor.rgb;\nmaterial.specularColor = specular;\nmaterial.specularShininess = shininess;\nmaterial.specularStrength = specularStrength;\n",_f="varying vec3 vViewPosition;\n#ifndef FLAT_SHADED\n\tvarying vec3 vNormal;\n#endif\nstruct BlinnPhongMaterial {\n\tvec3\tdiffuseColor;\n\tvec3\tspecularColor;\n\tfloat\tspecularShininess;\n\tfloat\tspecularStrength;\n};\nvoid RE_Direct_BlinnPhong( const in IncidentLight directLight, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\n\tfloat dotNL = saturate( dot( geometry.normal, directLight.direction ) );\n\tvec3 irradiance = dotNL * directLight.color;\n\t#ifndef PHYSICALLY_CORRECT_LIGHTS\n\t\tirradiance *= PI;\n\t#endif\n\treflectedLight.directDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\n\treflectedLight.directSpecular += irradiance * BRDF_Specular_BlinnPhong( directLight, geometry, material.specularColor, material.specularShininess ) * material.specularStrength;\n}\nvoid RE_IndirectDiffuse_BlinnPhong( const in vec3 irradiance, const in GeometricContext geometry, const in BlinnPhongMaterial material, inout ReflectedLight reflectedLight ) {\n\treflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\n}\n#define RE_Direct\t\t\t\tRE_Direct_BlinnPhong\n#define RE_IndirectDiffuse\t\tRE_IndirectDiffuse_BlinnPhong\n#define Material_LightProbeLOD( material )\t(0)\n",Sf="PhysicalMaterial material;\nmaterial.diffuseColor = diffuseColor.rgb * ( 1.0 - metalnessFactor );\nmaterial.specularRoughness = clamp( roughnessFactor, 0.04, 1.0 );\n#ifdef STANDARD\n\tmaterial.specularColor = mix( vec3( DEFAULT_SPECULAR_COEFFICIENT ), diffuseColor.rgb, metalnessFactor );\n#else\n\tmaterial.specularColor = mix( vec3( MAXIMUM_SPECULAR_COEFFICIENT * pow2( reflectivity ) ), diffuseColor.rgb, metalnessFactor );\n\tmaterial.clearCoat = saturate( clearCoat );\tmaterial.clearCoatRoughness = clamp( clearCoatRoughness, 0.04, 1.0 );\n#endif\n",Af="struct PhysicalMaterial {\n\tvec3\tdiffuseColor;\n\tfloat\tspecularRoughness;\n\tvec3\tspecularColor;\n\t#ifndef STANDARD\n\t\tfloat clearCoat;\n\t\tfloat clearCoatRoughness;\n\t#endif\n};\n#define MAXIMUM_SPECULAR_COEFFICIENT 0.16\n#define DEFAULT_SPECULAR_COEFFICIENT 0.04\nfloat clearCoatDHRApprox( const in float roughness, const in float dotNL ) {\n\treturn DEFAULT_SPECULAR_COEFFICIENT + ( 1.0 - DEFAULT_SPECULAR_COEFFICIENT ) * ( pow( 1.0 - dotNL, 5.0 ) * pow( 1.0 - roughness, 2.0 ) );\n}\nvoid RE_Direct_Physical( const in IncidentLight directLight, const in GeometricContext geometry, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) {\n\tfloat dotNL = saturate( dot( geometry.normal, directLight.direction ) );\n\tvec3 irradiance = dotNL * directLight.color;\n\t#ifndef PHYSICALLY_CORRECT_LIGHTS\n\t\tirradiance *= PI;\n\t#endif\n\t#ifndef STANDARD\n\t\tfloat clearCoatDHR = material.clearCoat * clearCoatDHRApprox( material.clearCoatRoughness, dotNL );\n\t#else\n\t\tfloat clearCoatDHR = 0.0;\n\t#endif\n\treflectedLight.directSpecular += ( 1.0 - clearCoatDHR ) * irradiance * BRDF_Specular_GGX( directLight, geometry, material.specularColor, material.specularRoughness );\n\treflectedLight.directDiffuse += ( 1.0 - clearCoatDHR ) * irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\n\t#ifndef STANDARD\n\t\treflectedLight.directSpecular += irradiance * material.clearCoat * BRDF_Specular_GGX( directLight, geometry, vec3( DEFAULT_SPECULAR_COEFFICIENT ), material.clearCoatRoughness );\n\t#endif\n}\nvoid RE_IndirectDiffuse_Physical( const in vec3 irradiance, const in GeometricContext geometry, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) {\n\treflectedLight.indirectDiffuse += irradiance * BRDF_Diffuse_Lambert( material.diffuseColor );\n}\nvoid RE_IndirectSpecular_Physical( const in vec3 radiance, const in vec3 clearCoatRadiance, const in GeometricContext geometry, const in PhysicalMaterial material, inout ReflectedLight reflectedLight ) {\n\t#ifndef STANDARD\n\t\tfloat dotNV = saturate( dot( geometry.normal, geometry.viewDir ) );\n\t\tfloat dotNL = dotNV;\n\t\tfloat clearCoatDHR = material.clearCoat * clearCoatDHRApprox( material.clearCoatRoughness, dotNL );\n\t#else\n\t\tfloat clearCoatDHR = 0.0;\n\t#endif\n\treflectedLight.indirectSpecular += ( 1.0 - clearCoatDHR ) * radiance * BRDF_Specular_GGX_Environment( geometry, material.specularColor, material.specularRoughness );\n\t#ifndef STANDARD\n\t\treflectedLight.indirectSpecular += clearCoatRadiance * material.clearCoat * BRDF_Specular_GGX_Environment( geometry, vec3( DEFAULT_SPECULAR_COEFFICIENT ), material.clearCoatRoughness );\n\t#endif\n}\n#define RE_Direct\t\t\t\tRE_Direct_Physical\n#define RE_IndirectDiffuse\t\tRE_IndirectDiffuse_Physical\n#define RE_IndirectSpecular\t\tRE_IndirectSpecular_Physical\n#define Material_BlinnShininessExponent( material )   GGXRoughnessToBlinnExponent( material.specularRoughness )\n#define Material_ClearCoat_BlinnShininessExponent( material )   GGXRoughnessToBlinnExponent( material.clearCoatRoughness )\nfloat computeSpecularOcclusion( const in float dotNV, const in float ambientOcclusion, const in float roughness ) {\n\treturn saturate( pow( dotNV + ambientOcclusion, exp2( - 16.0 * roughness - 1.0 ) ) - 1.0 + ambientOcclusion );\n}\n",Mf="\nGeometricContext geometry;\ngeometry.position = - vViewPosition;\ngeometry.normal = normal;\ngeometry.viewDir = normalize( vViewPosition );\nIncidentLight directLight;\n#if ( NUM_POINT_LIGHTS > 0 ) && defined( RE_Direct )\n\tPointLight pointLight;\n\tfor ( int i = 0; i < NUM_POINT_LIGHTS; i ++ ) {\n\t\tpointLight = pointLights[ i ];\n\t\tgetPointDirectLightIrradiance( pointLight, geometry, directLight );\n\t\t#ifdef USE_SHADOWMAP\n\t\tdirectLight.color *= all( bvec2( pointLight.shadow, directLight.visible ) ) ? getPointShadow( pointShadowMap[ i ], pointLight.shadowMapSize, pointLight.shadowBias, pointLight.shadowRadius, vPointShadowCoord[ i ] ) : 1.0;\n\t\t#endif\n\t\tRE_Direct( directLight, geometry, material, reflectedLight );\n\t}\n#endif\n#if ( NUM_SPOT_LIGHTS > 0 ) && defined( RE_Direct )\n\tSpotLight spotLight;\n\tfor ( int i = 0; i < NUM_SPOT_LIGHTS; i ++ ) {\n\t\tspotLight = spotLights[ i ];\n\t\tgetSpotDirectLightIrradiance( spotLight, geometry, directLight );\n\t\t#ifdef USE_SHADOWMAP\n\t\tdirectLight.color *= all( bvec2( spotLight.shadow, directLight.visible ) ) ? getShadow( spotShadowMap[ i ], spotLight.shadowMapSize, spotLight.shadowBias, spotLight.shadowRadius, vSpotShadowCoord[ i ] ) : 1.0;\n\t\t#endif\n\t\tRE_Direct( directLight, geometry, material, reflectedLight );\n\t}\n#endif\n#if ( NUM_DIR_LIGHTS > 0 ) && defined( RE_Direct )\n\tDirectionalLight directionalLight;\n\tfor ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\n\t\tdirectionalLight = directionalLights[ i ];\n\t\tgetDirectionalDirectLightIrradiance( directionalLight, geometry, directLight );\n\t\t#ifdef USE_SHADOWMAP\n\t\tdirectLight.color *= all( bvec2( directionalLight.shadow, directLight.visible ) ) ? getShadow( directionalShadowMap[ i ], directionalLight.shadowMapSize, directionalLight.shadowBias, directionalLight.shadowRadius, vDirectionalShadowCoord[ i ] ) : 1.0;\n\t\t#endif\n\t\tRE_Direct( directLight, geometry, material, reflectedLight );\n\t}\n#endif\n#if defined( RE_IndirectDiffuse )\n\tvec3 irradiance = getAmbientLightIrradiance( ambientLightColor );\n\t#ifdef USE_LIGHTMAP\n\t\tvec3 lightMapIrradiance = texture2D( lightMap, vUv2 ).xyz * lightMapIntensity;\n\t\t#ifndef PHYSICALLY_CORRECT_LIGHTS\n\t\t\tlightMapIrradiance *= PI;\n\t\t#endif\n\t\tirradiance += lightMapIrradiance;\n\t#endif\n\t#if ( NUM_HEMI_LIGHTS > 0 )\n\t\tfor ( int i = 0; i < NUM_HEMI_LIGHTS; i ++ ) {\n\t\t\tirradiance += getHemisphereLightIrradiance( hemisphereLights[ i ], geometry );\n\t\t}\n\t#endif\n\t#if defined( USE_ENVMAP ) && defined( PHYSICAL ) && defined( ENVMAP_TYPE_CUBE_UV )\n\t \tirradiance += getLightProbeIndirectIrradiance( geometry, 8 );\n\t#endif\n\tRE_IndirectDiffuse( irradiance, geometry, material, reflectedLight );\n#endif\n#if defined( USE_ENVMAP ) && defined( RE_IndirectSpecular )\n\tvec3 radiance = getLightProbeIndirectRadiance( geometry, Material_BlinnShininessExponent( material ), 8 );\n\t#ifndef STANDARD\n\t\tvec3 clearCoatRadiance = getLightProbeIndirectRadiance( geometry, Material_ClearCoat_BlinnShininessExponent( material ), 8 );\n\t#else\n\t\tvec3 clearCoatRadiance = vec3( 0.0 );\n\t#endif\n\t\t\n\tRE_IndirectSpecular( radiance, clearCoatRadiance, geometry, material, reflectedLight );\n#endif\n",Pf="#if defined(USE_LOGDEPTHBUF) && defined(USE_LOGDEPTHBUF_EXT)\n\tgl_FragDepthEXT = log2(vFragDepth) * logDepthBufFC * 0.5;\n#endif",Cf="#ifdef USE_LOGDEPTHBUF\n\tuniform float logDepthBufFC;\n\t#ifdef USE_LOGDEPTHBUF_EXT\n\t\tvarying float vFragDepth;\n\t#endif\n#endif\n",Tf="#ifdef USE_LOGDEPTHBUF\n\t#ifdef USE_LOGDEPTHBUF_EXT\n\t\tvarying float vFragDepth;\n\t#endif\n\tuniform float logDepthBufFC;\n#endif",Ef="#ifdef USE_LOGDEPTHBUF\n\tgl_Position.z = log2(max( EPSILON, gl_Position.w + 1.0 )) * logDepthBufFC;\n\t#ifdef USE_LOGDEPTHBUF_EXT\n\t\tvFragDepth = 1.0 + gl_Position.w;\n\t#else\n\t\tgl_Position.z = (gl_Position.z - 1.0) * gl_Position.w;\n\t#endif\n#endif\n",If="#ifdef USE_MAP\n\tvec4 texelColor = texture2D( map, vUv );\n\ttexelColor = mapTexelToLinear( texelColor );\n\tdiffuseColor *= texelColor;\n#endif\n",Lf="#ifdef USE_MAP\n\tuniform sampler2D map;\n#endif\n",Rf="#ifdef USE_MAP\n\tvec4 mapTexel = texture2D( map, vec2( gl_PointCoord.x, 1.0 - gl_PointCoord.y ) * offsetRepeat.zw + offsetRepeat.xy );\n\tdiffuseColor *= mapTexelToLinear( mapTexel );\n#endif\n",Of="#ifdef USE_MAP\n\tuniform vec4 offsetRepeat;\n\tuniform sampler2D map;\n#endif\n",Df="float metalnessFactor = metalness;\n#ifdef USE_METALNESSMAP\n\tvec4 texelMetalness = texture2D( metalnessMap, vUv );\n\tmetalnessFactor *= texelMetalness.r;\n#endif\n",Nf="#ifdef USE_METALNESSMAP\n\tuniform sampler2D metalnessMap;\n#endif",kf="#ifdef USE_MORPHNORMALS\n\tobjectNormal += ( morphNormal0 - normal ) * morphTargetInfluences[ 0 ];\n\tobjectNormal += ( morphNormal1 - normal ) * morphTargetInfluences[ 1 ];\n\tobjectNormal += ( morphNormal2 - normal ) * morphTargetInfluences[ 2 ];\n\tobjectNormal += ( morphNormal3 - normal ) * morphTargetInfluences[ 3 ];\n#endif\n",Ff="#ifdef USE_MORPHTARGETS\n\t#ifndef USE_MORPHNORMALS\n\tuniform float morphTargetInfluences[ 8 ];\n\t#else\n\tuniform float morphTargetInfluences[ 4 ];\n\t#endif\n#endif",zf="#ifdef USE_MORPHTARGETS\n\ttransformed += ( morphTarget0 - position ) * morphTargetInfluences[ 0 ];\n\ttransformed += ( morphTarget1 - position ) * morphTargetInfluences[ 1 ];\n\ttransformed += ( morphTarget2 - position ) * morphTargetInfluences[ 2 ];\n\ttransformed += ( morphTarget3 - position ) * morphTargetInfluences[ 3 ];\n\t#ifndef USE_MORPHNORMALS\n\ttransformed += ( morphTarget4 - position ) * morphTargetInfluences[ 4 ];\n\ttransformed += ( morphTarget5 - position ) * morphTargetInfluences[ 5 ];\n\ttransformed += ( morphTarget6 - position ) * morphTargetInfluences[ 6 ];\n\ttransformed += ( morphTarget7 - position ) * morphTargetInfluences[ 7 ];\n\t#endif\n#endif\n",Bf="#ifdef DOUBLE_SIDED\n\tfloat flipNormal = ( float( gl_FrontFacing ) * 2.0 - 1.0 );\n#else\n\tfloat flipNormal = 1.0;\n#endif\n",Uf="#ifdef FLAT_SHADED\n\tvec3 fdx = vec3( dFdx( vViewPosition.x ), dFdx( vViewPosition.y ), dFdx( vViewPosition.z ) );\n\tvec3 fdy = vec3( dFdy( vViewPosition.x ), dFdy( vViewPosition.y ), dFdy( vViewPosition.z ) );\n\tvec3 normal = normalize( cross( fdx, fdy ) );\n#else\n\tvec3 normal = normalize( vNormal ) * flipNormal;\n#endif\n#ifdef USE_NORMALMAP\n\tnormal = perturbNormal2Arb( -vViewPosition, normal );\n#elif defined( USE_BUMPMAP )\n\tnormal = perturbNormalArb( -vViewPosition, normal, dHdxy_fwd() );\n#endif\n",jf="#ifdef USE_NORMALMAP\n\tuniform sampler2D normalMap;\n\tuniform vec2 normalScale;\n\tvec3 perturbNormal2Arb( vec3 eye_pos, vec3 surf_norm ) {\n\t\tvec3 q0 = dFdx( eye_pos.xyz );\n\t\tvec3 q1 = dFdy( eye_pos.xyz );\n\t\tvec2 st0 = dFdx( vUv.st );\n\t\tvec2 st1 = dFdy( vUv.st );\n\t\tvec3 S = normalize( q0 * st1.t - q1 * st0.t );\n\t\tvec3 T = normalize( -q0 * st1.s + q1 * st0.s );\n\t\tvec3 N = normalize( surf_norm );\n\t\tvec3 mapN = texture2D( normalMap, vUv ).xyz * 2.0 - 1.0;\n\t\tmapN.xy = normalScale * mapN.xy;\n\t\tmat3 tsn = mat3( S, T, N );\n\t\treturn normalize( tsn * mapN );\n\t}\n#endif\n",$f="vec3 packNormalToRGB( const in vec3 normal ) {\n  return normalize( normal ) * 0.5 + 0.5;\n}\nvec3 unpackRGBToNormal( const in vec3 rgb ) {\n  return 1.0 - 2.0 * rgb.xyz;\n}\nconst float PackUpscale = 256. / 255.;const float UnpackDownscale = 255. / 256.;\nconst vec3 PackFactors = vec3( 256. * 256. * 256., 256. * 256.,  256. );\nconst vec4 UnpackFactors = UnpackDownscale / vec4( PackFactors, 1. );\nconst float ShiftRight8 = 1. / 256.;\nvec4 packDepthToRGBA( const in float v ) {\n\tvec4 r = vec4( fract( v * PackFactors ), v );\n\tr.yzw -= r.xyz * ShiftRight8;\treturn r * PackUpscale;\n}\nfloat unpackRGBAToDepth( const in vec4 v ) {\n\treturn dot( v, UnpackFactors );\n}\nfloat viewZToOrthographicDepth( const in float viewZ, const in float near, const in float far ) {\n  return ( viewZ + near ) / ( near - far );\n}\nfloat orthographicDepthToViewZ( const in float linearClipZ, const in float near, const in float far ) {\n  return linearClipZ * ( near - far ) - near;\n}\nfloat viewZToPerspectiveDepth( const in float viewZ, const in float near, const in float far ) {\n  return (( near + viewZ ) * far ) / (( far - near ) * viewZ );\n}\nfloat perspectiveDepthToViewZ( const in float invClipZ, const in float near, const in float far ) {\n  return ( near * far ) / ( ( far - near ) * invClipZ - far );\n}\n",Vf="#ifdef PREMULTIPLIED_ALPHA\n\tgl_FragColor.rgb *= gl_FragColor.a;\n#endif\n",Gf="#ifdef USE_SKINNING\n\tvec4 mvPosition = modelViewMatrix * skinned;\n#else\n\tvec4 mvPosition = modelViewMatrix * vec4( transformed, 1.0 );\n#endif\ngl_Position = projectionMatrix * mvPosition;\n",Hf="float roughnessFactor = roughness;\n#ifdef USE_ROUGHNESSMAP\n\tvec4 texelRoughness = texture2D( roughnessMap, vUv );\n\troughnessFactor *= texelRoughness.r;\n#endif\n",Wf="#ifdef USE_ROUGHNESSMAP\n\tuniform sampler2D roughnessMap;\n#endif",Xf="#ifdef USE_SHADOWMAP\n\t#if NUM_DIR_LIGHTS > 0\n\t\tuniform sampler2D directionalShadowMap[ NUM_DIR_LIGHTS ];\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\n\t#endif\n\t#if NUM_SPOT_LIGHTS > 0\n\t\tuniform sampler2D spotShadowMap[ NUM_SPOT_LIGHTS ];\n\t\tvarying vec4 vSpotShadowCoord[ NUM_SPOT_LIGHTS ];\n\t#endif\n\t#if NUM_POINT_LIGHTS > 0\n\t\tuniform sampler2D pointShadowMap[ NUM_POINT_LIGHTS ];\n\t\tvarying vec4 vPointShadowCoord[ NUM_POINT_LIGHTS ];\n\t#endif\n\tfloat texture2DCompare( sampler2D depths, vec2 uv, float compare ) {\n\t\treturn step( compare, unpackRGBAToDepth( texture2D( depths, uv ) ) );\n\t}\n\tfloat texture2DShadowLerp( sampler2D depths, vec2 size, vec2 uv, float compare ) {\n\t\tconst vec2 offset = vec2( 0.0, 1.0 );\n\t\tvec2 texelSize = vec2( 1.0 ) / size;\n\t\tvec2 centroidUV = floor( uv * size + 0.5 ) / size;\n\t\tfloat lb = texture2DCompare( depths, centroidUV + texelSize * offset.xx, compare );\n\t\tfloat lt = texture2DCompare( depths, centroidUV + texelSize * offset.xy, compare );\n\t\tfloat rb = texture2DCompare( depths, centroidUV + texelSize * offset.yx, compare );\n\t\tfloat rt = texture2DCompare( depths, centroidUV + texelSize * offset.yy, compare );\n\t\tvec2 f = fract( uv * size + 0.5 );\n\t\tfloat a = mix( lb, lt, f.y );\n\t\tfloat b = mix( rb, rt, f.y );\n\t\tfloat c = mix( a, b, f.x );\n\t\treturn c;\n\t}\n\tfloat getShadow( sampler2D shadowMap, vec2 shadowMapSize, float shadowBias, float shadowRadius, vec4 shadowCoord ) {\n\t\tshadowCoord.xyz /= shadowCoord.w;\n\t\tshadowCoord.z += shadowBias;\n\t\tbvec4 inFrustumVec = bvec4 ( shadowCoord.x >= 0.0, shadowCoord.x <= 1.0, shadowCoord.y >= 0.0, shadowCoord.y <= 1.0 );\n\t\tbool inFrustum = all( inFrustumVec );\n\t\tbvec2 frustumTestVec = bvec2( inFrustum, shadowCoord.z <= 1.0 );\n\t\tbool frustumTest = all( frustumTestVec );\n\t\tif ( frustumTest ) {\n\t\t#if defined( SHADOWMAP_TYPE_PCF )\n\t\t\tvec2 texelSize = vec2( 1.0 ) / shadowMapSize;\n\t\t\tfloat dx0 = - texelSize.x * shadowRadius;\n\t\t\tfloat dy0 = - texelSize.y * shadowRadius;\n\t\t\tfloat dx1 = + texelSize.x * shadowRadius;\n\t\t\tfloat dy1 = + texelSize.y * shadowRadius;\n\t\t\treturn (\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\n\t\t\t\ttexture2DCompare( shadowMap, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\n\t\t\t) * ( 1.0 / 9.0 );\n\t\t#elif defined( SHADOWMAP_TYPE_PCF_SOFT )\n\t\t\tvec2 texelSize = vec2( 1.0 ) / shadowMapSize;\n\t\t\tfloat dx0 = - texelSize.x * shadowRadius;\n\t\t\tfloat dy0 = - texelSize.y * shadowRadius;\n\t\t\tfloat dx1 = + texelSize.x * shadowRadius;\n\t\t\tfloat dy1 = + texelSize.y * shadowRadius;\n\t\t\treturn (\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx0, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( 0.0, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx1, dy0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx0, 0.0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy, shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx1, 0.0 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx0, dy1 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( 0.0, dy1 ), shadowCoord.z ) +\n\t\t\t\ttexture2DShadowLerp( shadowMap, shadowMapSize, shadowCoord.xy + vec2( dx1, dy1 ), shadowCoord.z )\n\t\t\t) * ( 1.0 / 9.0 );\n\t\t#else\n\t\t\treturn texture2DCompare( shadowMap, shadowCoord.xy, shadowCoord.z );\n\t\t#endif\n\t\t}\n\t\treturn 1.0;\n\t}\n\tvec2 cubeToUV( vec3 v, float texelSizeY ) {\n\t\tvec3 absV = abs( v );\n\t\tfloat scaleToCube = 1.0 / max( absV.x, max( absV.y, absV.z ) );\n\t\tabsV *= scaleToCube;\n\t\tv *= scaleToCube * ( 1.0 - 2.0 * texelSizeY );\n\t\tvec2 planar = v.xy;\n\t\tfloat almostATexel = 1.5 * texelSizeY;\n\t\tfloat almostOne = 1.0 - almostATexel;\n\t\tif ( absV.z >= almostOne ) {\n\t\t\tif ( v.z > 0.0 )\n\t\t\t\tplanar.x = 4.0 - v.x;\n\t\t} else if ( absV.x >= almostOne ) {\n\t\t\tfloat signX = sign( v.x );\n\t\t\tplanar.x = v.z * signX + 2.0 * signX;\n\t\t} else if ( absV.y >= almostOne ) {\n\t\t\tfloat signY = sign( v.y );\n\t\t\tplanar.x = v.x + 2.0 * signY + 2.0;\n\t\t\tplanar.y = v.z * signY - 2.0;\n\t\t}\n\t\treturn vec2( 0.125, 0.25 ) * planar + vec2( 0.375, 0.75 );\n\t}\n\tfloat getPointShadow( sampler2D shadowMap, vec2 shadowMapSize, float shadowBias, float shadowRadius, vec4 shadowCoord ) {\n\t\tvec2 texelSize = vec2( 1.0 ) / ( shadowMapSize * vec2( 4.0, 2.0 ) );\n\t\tvec3 lightToPosition = shadowCoord.xyz;\n\t\tvec3 bd3D = normalize( lightToPosition );\n\t\tfloat dp = ( length( lightToPosition ) - shadowBias ) / 1000.0;\n\t\t#if defined( SHADOWMAP_TYPE_PCF ) || defined( SHADOWMAP_TYPE_PCF_SOFT )\n\t\t\tvec2 offset = vec2( - 1, 1 ) * shadowRadius * texelSize.y;\n\t\t\treturn (\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.xyy, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.yyy, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.xyx, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.yyx, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.xxy, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.yxy, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.xxx, texelSize.y ), dp ) +\n\t\t\t\ttexture2DCompare( shadowMap, cubeToUV( bd3D + offset.yxx, texelSize.y ), dp )\n\t\t\t) * ( 1.0 / 9.0 );\n\t\t#else\n\t\t\treturn texture2DCompare( shadowMap, cubeToUV( bd3D, texelSize.y ), dp );\n\t\t#endif\n\t}\n#endif\n",qf="#ifdef USE_SHADOWMAP\n\t#if NUM_DIR_LIGHTS > 0\n\t\tuniform mat4 directionalShadowMatrix[ NUM_DIR_LIGHTS ];\n\t\tvarying vec4 vDirectionalShadowCoord[ NUM_DIR_LIGHTS ];\n\t#endif\n\t#if NUM_SPOT_LIGHTS > 0\n\t\tuniform mat4 spotShadowMatrix[ NUM_SPOT_LIGHTS ];\n\t\tvarying vec4 vSpotShadowCoord[ NUM_SPOT_LIGHTS ];\n\t#endif\n\t#if NUM_POINT_LIGHTS > 0\n\t\tuniform mat4 pointShadowMatrix[ NUM_POINT_LIGHTS ];\n\t\tvarying vec4 vPointShadowCoord[ NUM_POINT_LIGHTS ];\n\t#endif\n#endif\n",Yf="#ifdef USE_SHADOWMAP\n\t#if NUM_DIR_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\n\t\tvDirectionalShadowCoord[ i ] = directionalShadowMatrix[ i ] * worldPosition;\n\t}\n\t#endif\n\t#if NUM_SPOT_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_SPOT_LIGHTS; i ++ ) {\n\t\tvSpotShadowCoord[ i ] = spotShadowMatrix[ i ] * worldPosition;\n\t}\n\t#endif\n\t#if NUM_POINT_LIGHTS > 0\n\tfor ( int i = 0; i < NUM_POINT_LIGHTS; i ++ ) {\n\t\tvPointShadowCoord[ i ] = pointShadowMatrix[ i ] * worldPosition;\n\t}\n\t#endif\n#endif\n",Zf="float getShadowMask() {\n\tfloat shadow = 1.0;\n\t#ifdef USE_SHADOWMAP\n\t#if NUM_DIR_LIGHTS > 0\n\tDirectionalLight directionalLight;\n\tfor ( int i = 0; i < NUM_DIR_LIGHTS; i ++ ) {\n\t\tdirectionalLight = directionalLights[ i ];\n\t\tshadow *= bool( directionalLight.shadow ) ? getShadow( directionalShadowMap[ i ], directionalLight.shadowMapSize, directionalLight.shadowBias, directionalLight.shadowRadius, vDirectionalShadowCoord[ i ] ) : 1.0;\n\t}\n\t#endif\n\t#if NUM_SPOT_LIGHTS > 0\n\tSpotLight spotLight;\n\tfor ( int i = 0; i < NUM_SPOT_LIGHTS; i ++ ) {\n\t\tspotLight = spotLights[ i ];\n\t\tshadow *= bool( spotLight.shadow ) ? getShadow( spotShadowMap[ i ], spotLight.shadowMapSize, spotLight.shadowBias, spotLight.shadowRadius, vSpotShadowCoord[ i ] ) : 1.0;\n\t}\n\t#endif\n\t#if NUM_POINT_LIGHTS > 0\n\tPointLight pointLight;\n\tfor ( int i = 0; i < NUM_POINT_LIGHTS; i ++ ) {\n\t\tpointLight = pointLights[ i ];\n\t\tshadow *= bool( pointLight.shadow ) ? getPointShadow( pointShadowMap[ i ], pointLight.shadowMapSize, pointLight.shadowBias, pointLight.shadowRadius, vPointShadowCoord[ i ] ) : 1.0;\n\t}\n\t#endif\n\t#endif\n\treturn shadow;\n}\n",Kf="#ifdef USE_SKINNING\n\tmat4 boneMatX = getBoneMatrix( skinIndex.x );\n\tmat4 boneMatY = getBoneMatrix( skinIndex.y );\n\tmat4 boneMatZ = getBoneMatrix( skinIndex.z );\n\tmat4 boneMatW = getBoneMatrix( skinIndex.w );\n#endif",Qf="#ifdef USE_SKINNING\n\tuniform mat4 bindMatrix;\n\tuniform mat4 bindMatrixInverse;\n\t#ifdef BONE_TEXTURE\n\t\tuniform sampler2D boneTexture;\n\t\tuniform int boneTextureWidth;\n\t\tuniform int boneTextureHeight;\n\t\tmat4 getBoneMatrix( const in float i ) {\n\t\t\tfloat j = i * 4.0;\n\t\t\tfloat x = mod( j, float( boneTextureWidth ) );\n\t\t\tfloat y = floor( j / float( boneTextureWidth ) );\n\t\t\tfloat dx = 1.0 / float( boneTextureWidth );\n\t\t\tfloat dy = 1.0 / float( boneTextureHeight );\n\t\t\ty = dy * ( y + 0.5 );\n\t\t\tvec4 v1 = texture2D( boneTexture, vec2( dx * ( x + 0.5 ), y ) );\n\t\t\tvec4 v2 = texture2D( boneTexture, vec2( dx * ( x + 1.5 ), y ) );\n\t\t\tvec4 v3 = texture2D( boneTexture, vec2( dx * ( x + 2.5 ), y ) );\n\t\t\tvec4 v4 = texture2D( boneTexture, vec2( dx * ( x + 3.5 ), y ) );\n\t\t\tmat4 bone = mat4( v1, v2, v3, v4 );\n\t\t\treturn bone;\n\t\t}\n\t#else\n\t\tuniform mat4 boneMatrices[ MAX_BONES ];\n\t\tmat4 getBoneMatrix( const in float i ) {\n\t\t\tmat4 bone = boneMatrices[ int(i) ];\n\t\t\treturn bone;\n\t\t}\n\t#endif\n#endif\n",Jf="#ifdef USE_SKINNING\n\tvec4 skinVertex = bindMatrix * vec4( transformed, 1.0 );\n\tvec4 skinned = vec4( 0.0 );\n\tskinned += boneMatX * skinVertex * skinWeight.x;\n\tskinned += boneMatY * skinVertex * skinWeight.y;\n\tskinned += boneMatZ * skinVertex * skinWeight.z;\n\tskinned += boneMatW * skinVertex * skinWeight.w;\n\tskinned  = bindMatrixInverse * skinned;\n#endif\n",tp="#ifdef USE_SKINNING\n\tmat4 skinMatrix = mat4( 0.0 );\n\tskinMatrix += skinWeight.x * boneMatX;\n\tskinMatrix += skinWeight.y * boneMatY;\n\tskinMatrix += skinWeight.z * boneMatZ;\n\tskinMatrix += skinWeight.w * boneMatW;\n\tskinMatrix  = bindMatrixInverse * skinMatrix * bindMatrix;\n\tobjectNormal = vec4( skinMatrix * vec4( objectNormal, 0.0 ) ).xyz;\n#endif\n",ep="float specularStrength;\n#ifdef USE_SPECULARMAP\n\tvec4 texelSpecular = texture2D( specularMap, vUv );\n\tspecularStrength = texelSpecular.r;\n#else\n\tspecularStrength = 1.0;\n#endif",ip="#ifdef USE_SPECULARMAP\n\tuniform sampler2D specularMap;\n#endif",np="#if defined( TONE_MAPPING )\n  gl_FragColor.rgb = toneMapping( gl_FragColor.rgb );\n#endif\n",rp="#define saturate(a) clamp( a, 0.0, 1.0 )\nuniform float toneMappingExposure;\nuniform float toneMappingWhitePoint;\nvec3 LinearToneMapping( vec3 color ) {\n  return toneMappingExposure * color;\n}\nvec3 ReinhardToneMapping( vec3 color ) {\n  color *= toneMappingExposure;\n  return saturate( color / ( vec3( 1.0 ) + color ) );\n}\n#define Uncharted2Helper( x ) max( ( ( x * ( 0.15 * x + 0.10 * 0.50 ) + 0.20 * 0.02 ) / ( x * ( 0.15 * x + 0.50 ) + 0.20 * 0.30 ) ) - 0.02 / 0.30, vec3( 0.0 ) )\nvec3 Uncharted2ToneMapping( vec3 color ) {\n  color *= toneMappingExposure;\n  return saturate( Uncharted2Helper( color ) / Uncharted2Helper( vec3( toneMappingWhitePoint ) ) );\n}\nvec3 OptimizedCineonToneMapping( vec3 color ) {\n  color *= toneMappingExposure;\n  color = max( vec3( 0.0 ), color - 0.004 );\n  return pow( ( color * ( 6.2 * color + 0.5 ) ) / ( color * ( 6.2 * color + 1.7 ) + 0.06 ), vec3( 2.2 ) );\n}\n",op="#if defined( USE_MAP ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( USE_SPECULARMAP ) || defined( USE_ALPHAMAP ) || defined( USE_EMISSIVEMAP ) || defined( USE_ROUGHNESSMAP ) || defined( USE_METALNESSMAP )\n\tvarying vec2 vUv;\n#endif",ap="#if defined( USE_MAP ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( USE_SPECULARMAP ) || defined( USE_ALPHAMAP ) || defined( USE_EMISSIVEMAP ) || defined( USE_ROUGHNESSMAP ) || defined( USE_METALNESSMAP )\n\tvarying vec2 vUv;\n\tuniform vec4 offsetRepeat;\n#endif\n",sp="#if defined( USE_MAP ) || defined( USE_BUMPMAP ) || defined( USE_NORMALMAP ) || defined( USE_SPECULARMAP ) || defined( USE_ALPHAMAP ) || defined( USE_EMISSIVEMAP ) || defined( USE_ROUGHNESSMAP ) || defined( USE_METALNESSMAP )\n\tvUv = uv * offsetRepeat.zw + offsetRepeat.xy;\n#endif",cp="#if defined( USE_LIGHTMAP ) || defined( USE_AOMAP )\n\tvarying vec2 vUv2;\n#endif",up="#if defined( USE_LIGHTMAP ) || defined( USE_AOMAP )\n\tattribute vec2 uv2;\n\tvarying vec2 vUv2;\n#endif",hp="#if defined( USE_LIGHTMAP ) || defined( USE_AOMAP )\n\tvUv2 = uv2;\n#endif",lp="#if defined( USE_ENVMAP ) || defined( PHONG ) || defined( PHYSICAL ) || defined( LAMBERT ) || defined ( USE_SHADOWMAP )\n\t#ifdef USE_SKINNING\n\t\tvec4 worldPosition = modelMatrix * skinned;\n\t#else\n\t\tvec4 worldPosition = modelMatrix * vec4( transformed, 1.0 );\n\t#endif\n#endif\n",dp="uniform samplerCube tCube;\nuniform float tFlip;\nuniform float opacity;\nvarying vec3 vWorldPosition;\n#include <common>\nvoid main() {\n\tgl_FragColor = textureCube( tCube, vec3( tFlip * vWorldPosition.x, vWorldPosition.yz ) );\n\tgl_FragColor.a *= opacity;\n}\n",fp="varying vec3 vWorldPosition;\n#include <common>\nvoid main() {\n\tvWorldPosition = transformDirection( position, modelMatrix );\n\t#include <begin_vertex>\n\t#include <project_vertex>\n}\n",pp="#if DEPTH_PACKING == 3200\n\tuniform float opacity;\n#endif\n#include <common>\n#include <packing>\n#include <uv_pars_fragment>\n#include <map_pars_fragment>\n#include <alphamap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec4 diffuseColor = vec4( 1.0 );\n\t#if DEPTH_PACKING == 3200\n\t\tdiffuseColor.a = opacity;\n\t#endif\n\t#include <map_fragment>\n\t#include <alphamap_fragment>\n\t#include <alphatest_fragment>\n\t#include <logdepthbuf_fragment>\n\t#if DEPTH_PACKING == 3200\n\t\tgl_FragColor = vec4( vec3( gl_FragCoord.z ), opacity );\n\t#elif DEPTH_PACKING == 3201\n\t\tgl_FragColor = packDepthToRGBA( gl_FragCoord.z );\n\t#endif\n}\n",mp="#include <common>\n#include <uv_pars_vertex>\n#include <displacementmap_pars_vertex>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <uv_vertex>\n\t#include <skinbase_vertex>\n\t#include <begin_vertex>\n\t#include <displacementmap_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n}\n",gp="uniform vec3 lightPos;\nvarying vec4 vWorldPosition;\n#include <common>\n#include <packing>\n#include <clipping_planes_pars_fragment>\nvoid main () {\n\t#include <clipping_planes_fragment>\n\tgl_FragColor = packDepthToRGBA( length( vWorldPosition.xyz - lightPos.xyz ) / 1000.0 );\n}\n",vp="varying vec4 vWorldPosition;\n#include <common>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <skinbase_vertex>\n\t#include <begin_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <worldpos_vertex>\n\t#include <clipping_planes_vertex>\n\tvWorldPosition = worldPosition;\n}\n",yp="uniform sampler2D tEquirect;\nuniform float tFlip;\nvarying vec3 vWorldPosition;\n#include <common>\nvoid main() {\n\tvec3 direction = normalize( vWorldPosition );\n\tvec2 sampleUV;\n\tsampleUV.y = saturate( tFlip * direction.y * -0.5 + 0.5 );\n\tsampleUV.x = atan( direction.z, direction.x ) * RECIPROCAL_PI2 + 0.5;\n\tgl_FragColor = texture2D( tEquirect, sampleUV );\n}\n",bp="varying vec3 vWorldPosition;\n#include <common>\nvoid main() {\n\tvWorldPosition = transformDirection( position, modelMatrix );\n\t#include <begin_vertex>\n\t#include <project_vertex>\n}\n",xp="uniform vec3 diffuse;\nuniform float opacity;\nuniform float dashSize;\nuniform float totalSize;\nvarying float vLineDistance;\n#include <common>\n#include <color_pars_fragment>\n#include <fog_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tif ( mod( vLineDistance, totalSize ) > dashSize ) {\n\t\tdiscard;\n\t}\n\tvec3 outgoingLight = vec3( 0.0 );\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\t#include <logdepthbuf_fragment>\n\t#include <color_fragment>\n\toutgoingLight = diffuseColor.rgb;\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",wp="uniform float scale;\nattribute float lineDistance;\nvarying float vLineDistance;\n#include <common>\n#include <color_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <color_vertex>\n\tvLineDistance = scale * lineDistance;\n\tvec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\n\tgl_Position = projectionMatrix * mvPosition;\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n}\n",_p="uniform vec3 diffuse;\nuniform float opacity;\n#ifndef FLAT_SHADED\n\tvarying vec3 vNormal;\n#endif\n#include <common>\n#include <color_pars_fragment>\n#include <uv_pars_fragment>\n#include <uv2_pars_fragment>\n#include <map_pars_fragment>\n#include <alphamap_pars_fragment>\n#include <aomap_pars_fragment>\n#include <envmap_pars_fragment>\n#include <fog_pars_fragment>\n#include <specularmap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\t#include <logdepthbuf_fragment>\n\t#include <map_fragment>\n\t#include <color_fragment>\n\t#include <alphamap_fragment>\n\t#include <alphatest_fragment>\n\t#include <specularmap_fragment>\n\tReflectedLight reflectedLight;\n\treflectedLight.directDiffuse = vec3( 0.0 );\n\treflectedLight.directSpecular = vec3( 0.0 );\n\treflectedLight.indirectDiffuse = diffuseColor.rgb;\n\treflectedLight.indirectSpecular = vec3( 0.0 );\n\t#include <aomap_fragment>\n\tvec3 outgoingLight = reflectedLight.indirectDiffuse;\n\t#include <normal_flip>\n\t#include <envmap_fragment>\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",Sp="#include <common>\n#include <uv_pars_vertex>\n#include <uv2_pars_vertex>\n#include <envmap_pars_vertex>\n#include <color_pars_vertex>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <uv_vertex>\n\t#include <uv2_vertex>\n\t#include <color_vertex>\n\t#include <skinbase_vertex>\n\t#ifdef USE_ENVMAP\n\t#include <beginnormal_vertex>\n\t#include <morphnormal_vertex>\n\t#include <skinnormal_vertex>\n\t#include <defaultnormal_vertex>\n\t#endif\n\t#include <begin_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <worldpos_vertex>\n\t#include <clipping_planes_vertex>\n\t#include <envmap_vertex>\n}\n",Ap="uniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float opacity;\nvarying vec3 vLightFront;\n#ifdef DOUBLE_SIDED\n\tvarying vec3 vLightBack;\n#endif\n#include <common>\n#include <packing>\n#include <color_pars_fragment>\n#include <uv_pars_fragment>\n#include <uv2_pars_fragment>\n#include <map_pars_fragment>\n#include <alphamap_pars_fragment>\n#include <aomap_pars_fragment>\n#include <lightmap_pars_fragment>\n#include <emissivemap_pars_fragment>\n#include <envmap_pars_fragment>\n#include <bsdfs>\n#include <lights_pars>\n#include <fog_pars_fragment>\n#include <shadowmap_pars_fragment>\n#include <shadowmask_pars_fragment>\n#include <specularmap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\tReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\n\tvec3 totalEmissiveRadiance = emissive;\n\t#include <logdepthbuf_fragment>\n\t#include <map_fragment>\n\t#include <color_fragment>\n\t#include <alphamap_fragment>\n\t#include <alphatest_fragment>\n\t#include <specularmap_fragment>\n\t#include <emissivemap_fragment>\n\treflectedLight.indirectDiffuse = getAmbientLightIrradiance( ambientLightColor );\n\t#include <lightmap_fragment>\n\treflectedLight.indirectDiffuse *= BRDF_Diffuse_Lambert( diffuseColor.rgb );\n\t#ifdef DOUBLE_SIDED\n\t\treflectedLight.directDiffuse = ( gl_FrontFacing ) ? vLightFront : vLightBack;\n\t#else\n\t\treflectedLight.directDiffuse = vLightFront;\n\t#endif\n\treflectedLight.directDiffuse *= BRDF_Diffuse_Lambert( diffuseColor.rgb ) * getShadowMask();\n\t#include <aomap_fragment>\n\tvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + totalEmissiveRadiance;\n\t#include <normal_flip>\n\t#include <envmap_fragment>\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",Mp="#define LAMBERT\nvarying vec3 vLightFront;\n#ifdef DOUBLE_SIDED\n\tvarying vec3 vLightBack;\n#endif\n#include <common>\n#include <uv_pars_vertex>\n#include <uv2_pars_vertex>\n#include <envmap_pars_vertex>\n#include <bsdfs>\n#include <lights_pars>\n#include <color_pars_vertex>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <shadowmap_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <uv_vertex>\n\t#include <uv2_vertex>\n\t#include <color_vertex>\n\t#include <beginnormal_vertex>\n\t#include <morphnormal_vertex>\n\t#include <skinbase_vertex>\n\t#include <skinnormal_vertex>\n\t#include <defaultnormal_vertex>\n\t#include <begin_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n\t#include <worldpos_vertex>\n\t#include <envmap_vertex>\n\t#include <lights_lambert_vertex>\n\t#include <shadowmap_vertex>\n}\n",Pp="#define PHONG\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform vec3 specular;\nuniform float shininess;\nuniform float opacity;\n#include <common>\n#include <packing>\n#include <color_pars_fragment>\n#include <uv_pars_fragment>\n#include <uv2_pars_fragment>\n#include <map_pars_fragment>\n#include <alphamap_pars_fragment>\n#include <aomap_pars_fragment>\n#include <lightmap_pars_fragment>\n#include <emissivemap_pars_fragment>\n#include <envmap_pars_fragment>\n#include <fog_pars_fragment>\n#include <bsdfs>\n#include <lights_pars>\n#include <lights_phong_pars_fragment>\n#include <shadowmap_pars_fragment>\n#include <bumpmap_pars_fragment>\n#include <normalmap_pars_fragment>\n#include <specularmap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\tReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\n\tvec3 totalEmissiveRadiance = emissive;\n\t#include <logdepthbuf_fragment>\n\t#include <map_fragment>\n\t#include <color_fragment>\n\t#include <alphamap_fragment>\n\t#include <alphatest_fragment>\n\t#include <specularmap_fragment>\n\t#include <normal_flip>\n\t#include <normal_fragment>\n\t#include <emissivemap_fragment>\n\t#include <lights_phong_fragment>\n\t#include <lights_template>\n\t#include <aomap_fragment>\n\tvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveRadiance;\n\t#include <envmap_fragment>\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",Cp="#define PHONG\nvarying vec3 vViewPosition;\n#ifndef FLAT_SHADED\n\tvarying vec3 vNormal;\n#endif\n#include <common>\n#include <uv_pars_vertex>\n#include <uv2_pars_vertex>\n#include <displacementmap_pars_vertex>\n#include <envmap_pars_vertex>\n#include <color_pars_vertex>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <shadowmap_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <uv_vertex>\n\t#include <uv2_vertex>\n\t#include <color_vertex>\n\t#include <beginnormal_vertex>\n\t#include <morphnormal_vertex>\n\t#include <skinbase_vertex>\n\t#include <skinnormal_vertex>\n\t#include <defaultnormal_vertex>\n#ifndef FLAT_SHADED\n\tvNormal = normalize( transformedNormal );\n#endif\n\t#include <begin_vertex>\n\t#include <displacementmap_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n\tvViewPosition = - mvPosition.xyz;\n\t#include <worldpos_vertex>\n\t#include <envmap_vertex>\n\t#include <shadowmap_vertex>\n}\n",Tp="#define PHYSICAL\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float roughness;\nuniform float metalness;\nuniform float opacity;\n#ifndef STANDARD\n\tuniform float clearCoat;\n\tuniform float clearCoatRoughness;\n#endif\nuniform float envMapIntensity;\nvarying vec3 vViewPosition;\n#ifndef FLAT_SHADED\n\tvarying vec3 vNormal;\n#endif\n#include <common>\n#include <packing>\n#include <color_pars_fragment>\n#include <uv_pars_fragment>\n#include <uv2_pars_fragment>\n#include <map_pars_fragment>\n#include <alphamap_pars_fragment>\n#include <aomap_pars_fragment>\n#include <lightmap_pars_fragment>\n#include <emissivemap_pars_fragment>\n#include <envmap_pars_fragment>\n#include <fog_pars_fragment>\n#include <bsdfs>\n#include <cube_uv_reflection_fragment>\n#include <lights_pars>\n#include <lights_physical_pars_fragment>\n#include <shadowmap_pars_fragment>\n#include <bumpmap_pars_fragment>\n#include <normalmap_pars_fragment>\n#include <roughnessmap_pars_fragment>\n#include <metalnessmap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\tReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\n\tvec3 totalEmissiveRadiance = emissive;\n\t#include <logdepthbuf_fragment>\n\t#include <map_fragment>\n\t#include <color_fragment>\n\t#include <alphamap_fragment>\n\t#include <alphatest_fragment>\n\t#include <specularmap_fragment>\n\t#include <roughnessmap_fragment>\n\t#include <metalnessmap_fragment>\n\t#include <normal_flip>\n\t#include <normal_fragment>\n\t#include <emissivemap_fragment>\n\t#include <lights_physical_fragment>\n\t#include <lights_template>\n\t#include <aomap_fragment>\n\tvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveRadiance;\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",Ep="#define PHYSICAL\nvarying vec3 vViewPosition;\n#ifndef FLAT_SHADED\n\tvarying vec3 vNormal;\n#endif\n#include <common>\n#include <uv_pars_vertex>\n#include <uv2_pars_vertex>\n#include <displacementmap_pars_vertex>\n#include <color_pars_vertex>\n#include <morphtarget_pars_vertex>\n#include <skinning_pars_vertex>\n#include <shadowmap_pars_vertex>\n#include <specularmap_pars_fragment>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <uv_vertex>\n\t#include <uv2_vertex>\n\t#include <color_vertex>\n\t#include <beginnormal_vertex>\n\t#include <morphnormal_vertex>\n\t#include <skinbase_vertex>\n\t#include <skinnormal_vertex>\n\t#include <defaultnormal_vertex>\n#ifndef FLAT_SHADED\n\tvNormal = normalize( transformedNormal );\n#endif\n\t#include <begin_vertex>\n\t#include <displacementmap_vertex>\n\t#include <morphtarget_vertex>\n\t#include <skinning_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n\tvViewPosition = - mvPosition.xyz;\n\t#include <worldpos_vertex>\n\t#include <shadowmap_vertex>\n}\n",Ip="uniform float opacity;\nvarying vec3 vNormal;\n#include <common>\n#include <packing>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tgl_FragColor = vec4( packNormalToRGB( vNormal ), opacity );\n\t#include <logdepthbuf_fragment>\n}\n",Lp="varying vec3 vNormal;\n#include <common>\n#include <morphtarget_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\tvNormal = normalize( normalMatrix * normal );\n\t#include <begin_vertex>\n\t#include <morphtarget_vertex>\n\t#include <project_vertex>\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n}\n",Rp="uniform vec3 diffuse;\nuniform float opacity;\n#include <common>\n#include <packing>\n#include <color_pars_fragment>\n#include <map_particle_pars_fragment>\n#include <fog_pars_fragment>\n#include <shadowmap_pars_fragment>\n#include <logdepthbuf_pars_fragment>\n#include <clipping_planes_pars_fragment>\nvoid main() {\n\t#include <clipping_planes_fragment>\n\tvec3 outgoingLight = vec3( 0.0 );\n\tvec4 diffuseColor = vec4( diffuse, opacity );\n\t#include <logdepthbuf_fragment>\n\t#include <map_particle_fragment>\n\t#include <color_fragment>\n\t#include <alphatest_fragment>\n\toutgoingLight = diffuseColor.rgb;\n\tgl_FragColor = vec4( outgoingLight, diffuseColor.a );\n\t#include <premultiplied_alpha_fragment>\n\t#include <tonemapping_fragment>\n\t#include <encodings_fragment>\n\t#include <fog_fragment>\n}\n",Op="uniform float size;\nuniform float scale;\n#include <common>\n#include <color_pars_vertex>\n#include <shadowmap_pars_vertex>\n#include <logdepthbuf_pars_vertex>\n#include <clipping_planes_pars_vertex>\nvoid main() {\n\t#include <color_vertex>\n\t#include <begin_vertex>\n\t#include <project_vertex>\n\t#ifdef USE_SIZEATTENUATION\n\t\tgl_PointSize = size * ( scale / - mvPosition.z );\n\t#else\n\t\tgl_PointSize = size;\n\t#endif\n\t#include <logdepthbuf_vertex>\n\t#include <clipping_planes_vertex>\n\t#include <worldpos_vertex>\n\t#include <shadowmap_vertex>\n}\n",Dp="uniform float opacity;\n#include <common>\n#include <packing>\n#include <bsdfs>\n#include <lights_pars>\n#include <shadowmap_pars_fragment>\n#include <shadowmask_pars_fragment>\nvoid main() {\n\tgl_FragColor = vec4( 0.0, 0.0, 0.0, opacity * ( 1.0  - getShadowMask() ) );\n}\n",Np="#include <shadowmap_pars_vertex>\nvoid main() {\n\t#include <begin_vertex>\n\t#include <project_vertex>\n\t#include <worldpos_vertex>\n\t#include <shadowmap_vertex>\n}\n",kp={
-alphamap_fragment:zd,alphamap_pars_fragment:Bd,alphatest_fragment:Ud,aomap_fragment:jd,aomap_pars_fragment:$d,begin_vertex:Vd,beginnormal_vertex:Gd,bsdfs:Hd,bumpmap_pars_fragment:Wd,clipping_planes_fragment:Xd,clipping_planes_pars_fragment:qd,clipping_planes_pars_vertex:Yd,clipping_planes_vertex:Zd,color_fragment:Kd,color_pars_fragment:Qd,color_pars_vertex:Jd,color_vertex:tf,common:ef,cube_uv_reflection_fragment:nf,defaultnormal_vertex:rf,displacementmap_pars_vertex:of,displacementmap_vertex:af,emissivemap_fragment:sf,emissivemap_pars_fragment:cf,encodings_fragment:uf,encodings_pars_fragment:hf,envmap_fragment:lf,envmap_pars_fragment:df,envmap_pars_vertex:ff,envmap_vertex:pf,fog_fragment:mf,fog_pars_fragment:gf,lightmap_fragment:vf,lightmap_pars_fragment:yf,lights_lambert_vertex:bf,lights_pars:xf,lights_phong_fragment:wf,lights_phong_pars_fragment:_f,lights_physical_fragment:Sf,lights_physical_pars_fragment:Af,lights_template:Mf,logdepthbuf_fragment:Pf,logdepthbuf_pars_fragment:Cf,logdepthbuf_pars_vertex:Tf,logdepthbuf_vertex:Ef,map_fragment:If,map_pars_fragment:Lf,map_particle_fragment:Rf,map_particle_pars_fragment:Of,metalnessmap_fragment:Df,metalnessmap_pars_fragment:Nf,morphnormal_vertex:kf,morphtarget_pars_vertex:Ff,morphtarget_vertex:zf,normal_flip:Bf,normal_fragment:Uf,normalmap_pars_fragment:jf,packing:$f,premultiplied_alpha_fragment:Vf,project_vertex:Gf,roughnessmap_fragment:Hf,roughnessmap_pars_fragment:Wf,shadowmap_pars_fragment:Xf,shadowmap_pars_vertex:qf,shadowmap_vertex:Yf,shadowmask_pars_fragment:Zf,skinbase_vertex:Kf,skinning_pars_vertex:Qf,skinning_vertex:Jf,skinnormal_vertex:tp,specularmap_fragment:ep,specularmap_pars_fragment:ip,tonemapping_fragment:np,tonemapping_pars_fragment:rp,uv_pars_fragment:op,uv_pars_vertex:ap,uv_vertex:sp,uv2_pars_fragment:cp,uv2_pars_vertex:up,uv2_vertex:hp,worldpos_vertex:lp,cube_frag:dp,cube_vert:fp,depth_frag:pp,depth_vert:mp,distanceRGBA_frag:gp,distanceRGBA_vert:vp,equirect_frag:yp,equirect_vert:bp,linedashed_frag:xp,linedashed_vert:wp,meshbasic_frag:_p,meshbasic_vert:Sp,meshlambert_frag:Ap,meshlambert_vert:Mp,meshphong_frag:Pp,meshphong_vert:Cp,meshphysical_frag:Tp,meshphysical_vert:Ep,normal_frag:Ip,normal_vert:Lp,points_frag:Rp,points_vert:Op,shadow_frag:Dp,shadow_vert:Np};Ct.prototype={constructor:Ct,isColor:!0,r:1,g:1,b:1,set:function(t){return t&&t.isColor?this.copy(t):"number"==typeof t?this.setHex(t):"string"==typeof t&&this.setStyle(t),this},setScalar:function(t){this.r=t,this.g=t,this.b=t},setHex:function(t){return t=Math.floor(t),this.r=(t>>16&255)/255,this.g=(t>>8&255)/255,this.b=(255&t)/255,this},setRGB:function(t,e,i){return this.r=t,this.g=e,this.b=i,this},setHSL:function(){function t(t,e,i){return i<0&&(i+=1),i>1&&(i-=1),i<1/6?t+6*(e-t)*i:i<.5?e:i<2/3?t+6*(e-t)*(2/3-i):t}return function(e,i,n){if(e=Ed.euclideanModulo(e,1),i=Ed.clamp(i,0,1),n=Ed.clamp(n,0,1),0===i)this.r=this.g=this.b=n;else{var r=n<=.5?n*(1+i):n+i-n*i,o=2*n-r;this.r=t(o,r,e+1/3),this.g=t(o,r,e),this.b=t(o,r,e-1/3)}return this}}(),setStyle:function(t){function e(e){void 0!==e&&parseFloat(e)<1&&console.warn("THREE.Color: Alpha component of "+t+" will be ignored.")}var i;if(i=/^((?:rgb|hsl)a?)\(\s*([^\)]*)\)/.exec(t)){var n,r=i[1],o=i[2];switch(r){case"rgb":case"rgba":if(n=/^(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*(,\s*([0-9]*\.?[0-9]+)\s*)?$/.exec(o))return this.r=Math.min(255,parseInt(n[1],10))/255,this.g=Math.min(255,parseInt(n[2],10))/255,this.b=Math.min(255,parseInt(n[3],10))/255,e(n[5]),this;if(n=/^(\d+)\%\s*,\s*(\d+)\%\s*,\s*(\d+)\%\s*(,\s*([0-9]*\.?[0-9]+)\s*)?$/.exec(o))return this.r=Math.min(100,parseInt(n[1],10))/100,this.g=Math.min(100,parseInt(n[2],10))/100,this.b=Math.min(100,parseInt(n[3],10))/100,e(n[5]),this;break;case"hsl":case"hsla":if(n=/^([0-9]*\.?[0-9]+)\s*,\s*(\d+)\%\s*,\s*(\d+)\%\s*(,\s*([0-9]*\.?[0-9]+)\s*)?$/.exec(o)){var a=parseFloat(n[1])/360,s=parseInt(n[2],10)/100,c=parseInt(n[3],10)/100;return e(n[5]),this.setHSL(a,s,c)}}}else if(i=/^\#([A-Fa-f0-9]+)$/.exec(t)){var u=i[1],h=u.length;if(3===h)return this.r=parseInt(u.charAt(0)+u.charAt(0),16)/255,this.g=parseInt(u.charAt(1)+u.charAt(1),16)/255,this.b=parseInt(u.charAt(2)+u.charAt(2),16)/255,this;if(6===h)return this.r=parseInt(u.charAt(0)+u.charAt(1),16)/255,this.g=parseInt(u.charAt(2)+u.charAt(3),16)/255,this.b=parseInt(u.charAt(4)+u.charAt(5),16)/255,this}if(t&&t.length>0){var u=Fp[t];void 0!==u?this.setHex(u):console.warn("THREE.Color: Unknown color "+t)}return this},clone:function(){return new this.constructor(this.r,this.g,this.b)},copy:function(t){return this.r=t.r,this.g=t.g,this.b=t.b,this},copyGammaToLinear:function(t,e){return void 0===e&&(e=2),this.r=Math.pow(t.r,e),this.g=Math.pow(t.g,e),this.b=Math.pow(t.b,e),this},copyLinearToGamma:function(t,e){void 0===e&&(e=2);var i=e>0?1/e:1;return this.r=Math.pow(t.r,i),this.g=Math.pow(t.g,i),this.b=Math.pow(t.b,i),this},convertGammaToLinear:function(){var t=this.r,e=this.g,i=this.b;return this.r=t*t,this.g=e*e,this.b=i*i,this},convertLinearToGamma:function(){return this.r=Math.sqrt(this.r),this.g=Math.sqrt(this.g),this.b=Math.sqrt(this.b),this},getHex:function(){return 255*this.r<<16^255*this.g<<8^255*this.b<<0},getHexString:function(){return("000000"+this.getHex().toString(16)).slice(-6)},getHSL:function(t){var e,i,n=t||{h:0,s:0,l:0},r=this.r,o=this.g,a=this.b,s=Math.max(r,o,a),c=Math.min(r,o,a),u=(c+s)/2;if(c===s)e=0,i=0;else{var h=s-c;switch(i=u<=.5?h/(s+c):h/(2-s-c),s){case r:e=(o-a)/h+(o<a?6:0);break;case o:e=(a-r)/h+2;break;case a:e=(r-o)/h+4}e/=6}return n.h=e,n.s=i,n.l=u,n},getStyle:function(){return"rgb("+(255*this.r|0)+","+(255*this.g|0)+","+(255*this.b|0)+")"},offsetHSL:function(t,e,i){var n=this.getHSL();return n.h+=t,n.s+=e,n.l+=i,this.setHSL(n.h,n.s,n.l),this},add:function(t){return this.r+=t.r,this.g+=t.g,this.b+=t.b,this},addColors:function(t,e){return this.r=t.r+e.r,this.g=t.g+e.g,this.b=t.b+e.b,this},addScalar:function(t){return this.r+=t,this.g+=t,this.b+=t,this},sub:function(t){return this.r=Math.max(0,this.r-t.r),this.g=Math.max(0,this.g-t.g),this.b=Math.max(0,this.b-t.b),this},multiply:function(t){return 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function(e,i,n){void 0===t&&(t=new N),void 0===i&&(i=0),void 0===n&&(n=e.length/e.itemSize);for(var r=0,o=i;r<n;r++,o++)t.x=e.getX(o),t.y=e.getY(o),t.z=e.getZ(o),t.applyMatrix3(this),e.setXYZ(t.x,t.y,t.z);return e}}(),multiplyScalar:function(t){var e=this.elements;return e[0]*=t,e[3]*=t,e[6]*=t,e[1]*=t,e[4]*=t,e[7]*=t,e[2]*=t,e[5]*=t,e[8]*=t,this},determinant:function(){var t=this.elements,e=t[0],i=t[1],n=t[2],r=t[3],o=t[4],a=t[5],s=t[6],c=t[7],u=t[8];return e*o*u-e*a*c-i*r*u+i*a*s+n*r*c-n*o*s},getInverse:function(t,e){t&&t.isMatrix4&&console.error("THREE.Matrix3.getInverse no longer takes a Matrix4 argument.");var i=t.elements,n=this.elements,r=i[0],o=i[1],a=i[2],s=i[3],c=i[4],u=i[5],h=i[6],l=i[7],d=i[8],f=d*c-u*l,p=u*h-d*s,m=l*s-c*h,g=r*f+o*p+a*m;if(0===g){var v="THREE.Matrix3.getInverse(): can't invert matrix, determinant is 0";if(e===!0)throw new Error(v);return console.warn(v),this.identity()}var y=1/g;return n[0]=f*y,n[1]=(a*l-d*o)*y,n[2]=(u*o-a*c)*y,n[3]=p*y,n[4]=(d*r-a*h)*y,n[5]=(a*s-u*r)*y,n[6]=m*y,n[7]=(o*h-l*r)*y,n[8]=(c*r-o*s)*y,this},transpose:function(){var t,e=this.elements;return t=e[1],e[1]=e[3],e[3]=t,t=e[2],e[2]=e[6],e[6]=t,t=e[5],e[5]=e[7],e[7]=t,this},flattenToArrayOffset:function(t,e){return console.warn("THREE.Matrix3: .flattenToArrayOffset is deprecated - just use .toArray instead."),this.toArray(t,e)},getNormalMatrix:function(t){return this.setFromMatrix4(t).getInverse(this).transpose()},transposeIntoArray:function(t){var e=this.elements;return t[0]=e[0],t[1]=e[3],t[2]=e[6],t[3]=e[1],t[4]=e[4],t[5]=e[7],t[6]=e[2],t[7]=e[5],t[8]=e[8],this},fromArray:function(t){return this.elements.set(t),this},toArray:function(t,e){void 0===t&&(t=[]),void 0===e&&(e=0);var i=this.elements;return t[e]=i[0],t[e+1]=i[1],t[e+2]=i[2],t[e+3]=i[3],t[e+4]=i[4],t[e+5]=i[5],t[e+6]=i[6],t[e+7]=i[7],t[e+8]=i[8],t}},Rt.prototype={constructor:Rt,set:function(t,e){return this.normal.copy(t),this.constant=e,this},setComponents:function(t,e,i,n){return this.normal.set(t,e,i),this.constant=n,this},setFromNormalAndCoplanarPoint:function(t,e){return this.normal.copy(t),this.constant=-e.dot(this.normal),this},setFromCoplanarPoints:function(){var t=new N,e=new N;return function(i,n,r){var o=t.subVectors(r,n).cross(e.subVectors(i,n)).normalize();return this.setFromNormalAndCoplanarPoint(o,i),this}}(),clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.normal.copy(t.normal),this.constant=t.constant,this},normalize:function(){var t=1/this.normal.length();return this.normal.multiplyScalar(t),this.constant*=t,this},negate:function(){return this.constant*=-1,this.normal.negate(),this},distanceToPoint:function(t){return this.normal.dot(t)+this.constant},distanceToSphere:function(t){return this.distanceToPoint(t.center)-t.radius},projectPoint:function(t,e){return this.orthoPoint(t,e).sub(t).negate()},orthoPoint:function(t,e){var i=this.distanceToPoint(t),n=e||new N;return n.copy(this.normal).multiplyScalar(i)},intersectLine:function(){var t=new N;return function(e,i){var n=i||new N,r=e.delta(t),o=this.normal.dot(r);if(0!==o){var a=-(e.start.dot(this.normal)+this.constant)/o;if(!(a<0||a>1))return n.copy(r).multiplyScalar(a).add(e.start)}else if(0===this.distanceToPoint(e.start))return n.copy(e.start)}}(),intersectsLine:function(t){var e=this.distanceToPoint(t.start),i=this.distanceToPoint(t.end);return e<0&&i>0||i<0&&e>0},intersectsBox:function(t){return t.intersectsPlane(this)},intersectsSphere:function(t){return t.intersectsPlane(this)},coplanarPoint:function(t){var e=t||new N;return e.copy(this.normal).multiplyScalar(-this.constant)},applyMatrix4:function(){var t=new N,e=new Lt;return function(i,n){var r=this.coplanarPoint(t).applyMatrix4(i),o=n||e.getNormalMatrix(i),a=this.normal.applyMatrix3(o).normalize();return this.constant=-r.dot(a),this}}(),translate:function(t){return this.constant=this.constant-t.dot(this.normal),this},equals:function(t){return t.normal.equals(this.normal)&&t.constant===this.constant}},Ot.prototype={constructor:Ot,set:function(t,e,i,n,r,o){var a=this.planes;return a[0].copy(t),a[1].copy(e),a[2].copy(i),a[3].copy(n),a[4].copy(r),a[5].copy(o),this},clone:function(){return(new this.constructor).copy(this)},copy:function(t){for(var e=this.planes,i=0;i<6;i++)e[i].copy(t.planes[i]);return this},setFromMatrix:function(t){var e=this.planes,i=t.elements,n=i[0],r=i[1],o=i[2],a=i[3],s=i[4],c=i[5],u=i[6],h=i[7],l=i[8],d=i[9],f=i[10],p=i[11],m=i[12],g=i[13],v=i[14],y=i[15];return e[0].setComponents(a-n,h-s,p-l,y-m).normalize(),e[1].setComponents(a+n,h+s,p+l,y+m).normalize(),e[2].setComponents(a+r,h+c,p+d,y+g).normalize(),e[3].setComponents(a-r,h-c,p-d,y-g).normalize(),e[4].setComponents(a-o,h-u,p-f,y-v).normalize(),e[5].setComponents(a+o,h+u,p+f,y+v).normalize(),this},intersectsObject:function(){var t=new It;return function(e){var i=e.geometry;return null===i.boundingSphere&&i.computeBoundingSphere(),t.copy(i.boundingSphere).applyMatrix4(e.matrixWorld),this.intersectsSphere(t)}}(),intersectsSprite:function(){var t=new It;return function(e){return t.center.set(0,0,0),t.radius=.7071067811865476,t.applyMatrix4(e.matrixWorld),this.intersectsSphere(t)}}(),intersectsSphere:function(t){for(var e=this.planes,i=t.center,n=-t.radius,r=0;r<6;r++){var o=e[r].distanceToPoint(i);if(o<n)return!1}return!0},intersectsBox:function(){var t=new N,e=new N;return function(i){for(var n=this.planes,r=0;r<6;r++){var o=n[r];t.x=o.normal.x>0?i.min.x:i.max.x,e.x=o.normal.x>0?i.max.x:i.min.x,t.y=o.normal.y>0?i.min.y:i.max.y,e.y=o.normal.y>0?i.max.y:i.min.y,t.z=o.normal.z>0?i.min.z:i.max.z,e.z=o.normal.z>0?i.max.z:i.min.z;var a=o.distanceToPoint(t),s=o.distanceToPoint(e);if(a<0&&s<0)return!1}return!0}}(),containsPoint:function(t){for(var e=this.planes,i=0;i<6;i++)if(e[i].distanceToPoint(t)<0)return!1;return!0}};var Up=0;Kt.prototype={constructor:Kt,isBufferAttribute:!0,get count(){return this.array.length/this.itemSize},set needsUpdate(t){t===!0&&this.version++},setDynamic:function(t){return this.dynamic=t,this},copy:function(t){return this.array=new t.array.constructor(t.array),this.itemSize=t.itemSize,this.normalized=t.normalized,this.dynamic=t.dynamic,this},copyAt:function(t,e,i){t*=this.itemSize,i*=e.itemSize;for(var n=0,r=this.itemSize;n<r;n++)this.array[t+n]=e.array[i+n];return this},copyArray:function(t){return this.array.set(t),this},copyColorsArray:function(t){for(var e=this.array,i=0,n=0,r=t.length;n<r;n++){var o=t[n];void 0===o&&(console.warn("THREE.BufferAttribute.copyColorsArray(): color is undefined",n),o=new Ct),e[i++]=o.r,e[i++]=o.g,e[i++]=o.b}return this},copyIndicesArray:function(t){for(var e=this.array,i=0,n=0,r=t.length;n<r;n++){var o=t[n];e[i++]=o.a,e[i++]=o.b,e[i++]=o.c}return this},copyVector2sArray:function(t){for(var e=this.array,i=0,n=0,r=t.length;n<r;n++){var o=t[n];void 0===o&&(console.warn("THREE.BufferAttribute.copyVector2sArray(): vector is undefined",n),o=new I),e[i++]=o.x,e[i++]=o.y}return this},copyVector3sArray:function(t){for(var e=this.array,i=0,n=0,r=t.length;n<r;n++){var o=t[n];void 0===o&&(console.warn("THREE.BufferAttribute.copyVector3sArray(): vector is undefined",n),o=new N),e[i++]=o.x,e[i++]=o.y,e[i++]=o.z}return this},copyVector4sArray:function(t){for(var e=this.array,i=0,n=0,r=t.length;n<r;n++){var o=t[n];void 0===o&&(console.warn("THREE.BufferAttribute.copyVector4sArray(): vector is undefined",n),o=new wt),e[i++]=o.x,e[i++]=o.y,e[i++]=o.z,e[i++]=o.w}return this},set:function(t,e){return void 0===e&&(e=0),this.array.set(t,e),this},getX:function(t){return this.array[t*this.itemSize]},setX:function(t,e){return this.array[t*this.itemSize]=e,this},getY:function(t){return this.array[t*this.itemSize+1]},setY:function(t,e){return this.array[t*this.itemSize+1]=e,this},getZ:function(t){return this.array[t*this.itemSize+2]},setZ:function(t,e){return this.array[t*this.itemSize+2]=e,this},getW:function(t){return this.array[t*this.itemSize+3]},setW:function(t,e){return this.array[t*this.itemSize+3]=e,this},setXY:function(t,e,i){return t*=this.itemSize,this.array[t+0]=e,this.array[t+1]=i,this},setXYZ:function(t,e,i,n){return t*=this.itemSize,this.array[t+0]=e,this.array[t+1]=i,this.array[t+2]=n,this},setXYZW:function(t,e,i,n,r){return t*=this.itemSize,this.array[t+0]=e,this.array[t+1]=i,this.array[t+2]=n,this.array[t+3]=r,this},clone:function(){return(new this.constructor).copy(this)}},ee.prototype={constructor:ee,clone:function(){return(new this.constructor).copy(this)},copy:function(t){this.a=t.a,this.b=t.b,this.c=t.c,this.normal.copy(t.normal),this.color.copy(t.color),this.materialIndex=t.materialIndex;for(var e=0,i=t.vertexNormals.length;e<i;e++)this.vertexNormals[e]=t.vertexNormals[e].clone();for(var e=0,i=t.vertexColors.length;e<i;e++)this.vertexColors[e]=t.vertexColors[e].clone();return this}},ie.RotationOrders=["XYZ","YZX","ZXY","XZY","YXZ","ZYX"],ie.DefaultOrder="XYZ",ie.prototype={constructor:ie,isEuler:!0,get x(){return this._x},set x(t){this._x=t,this.onChangeCallback()},get y(){return this._y},set y(t){this._y=t,this.onChangeCallback()},get z(){return this._z},set z(t){this._z=t,this.onChangeCallback()},get order(){return this._order},set order(t){this._order=t,this.onChangeCallback()},set:function(t,e,i,n){return this._x=t,this._y=e,this._z=i,this._order=n||this._order,this.onChangeCallback(),this},clone:function(){return new this.constructor(this._x,this._y,this._z,this._order)},copy:function(t){return this._x=t._x,this._y=t._y,this._z=t._z,this._order=t._order,this.onChangeCallback(),this},setFromRotationMatrix:function(t,e,i){var n=Ed.clamp,r=t.elements,o=r[0],a=r[4],s=r[8],c=r[1],u=r[5],h=r[9],l=r[2],d=r[6],f=r[10];return e=e||this._order,"XYZ"===e?(this._y=Math.asin(n(s,-1,1)),Math.abs(s)<.99999?(this._x=Math.atan2(-h,f),this._z=Math.atan2(-a,o)):(this._x=Math.atan2(d,u),this._z=0)):"YXZ"===e?(this._x=Math.asin(-n(h,-1,1)),Math.abs(h)<.99999?(this._y=Math.atan2(s,f),this._z=Math.atan2(c,u)):(this._y=Math.atan2(-l,o),this._z=0)):"ZXY"===e?(this._x=Math.asin(n(d,-1,1)),Math.abs(d)<.99999?(this._y=Math.atan2(-l,f),this._z=Math.atan2(-a,u)):(this._y=0,this._z=Math.atan2(c,o))):"ZYX"===e?(this._y=Math.asin(-n(l,-1,1)),Math.abs(l)<.99999?(this._x=Math.atan2(d,f),this._z=Math.atan2(c,o)):(this._x=0,this._z=Math.atan2(-a,u))):"YZX"===e?(this._z=Math.asin(n(c,-1,1)),Math.abs(c)<.99999?(this._x=Math.atan2(-h,u),this._y=Math.atan2(-l,o)):(this._x=0,this._y=Math.atan2(s,f))):"XZY"===e?(this._z=Math.asin(-n(a,-1,1)),Math.abs(a)<.99999?(this._x=Math.atan2(d,u),this._y=Math.atan2(s,o)):(this._x=Math.atan2(-h,f),this._y=0)):console.warn("THREE.Euler: .setFromRotationMatrix() given unsupported order: "+e),this._order=e,i!==!1&&this.onChangeCallback(),this},setFromQuaternion:function(){var t;return function(e,i,n){return void 0===t&&(t=new O),t.makeRotationFromQuaternion(e),this.setFromRotationMatrix(t,i,n)}}(),setFromVector3:function(t,e){return this.set(t.x,t.y,t.z,e||this._order)},reorder:function(){var t=new D;return function(e){return t.setFromEuler(this),this.setFromQuaternion(t,e)}}(),equals:function(t){return t._x===this._x&&t._y===this._y&&t._z===this._z&&t._order===this._order},fromArray:function(t){return this._x=t[0],this._y=t[1],this._z=t[2],void 0!==t[3]&&(this._order=t[3]),this.onChangeCallback(),this},toArray:function(t,e){return void 0===t&&(t=[]),void 0===e&&(e=0),t[e]=this._x,t[e+1]=this._y,t[e+2]=this._z,t[e+3]=this._order,t},toVector3:function(t){return t?t.set(this._x,this._y,this._z):new N(this._x,this._y,this._z)},onChange:function(t){return this.onChangeCallback=t,this},onChangeCallback:function(){}},ne.prototype={constructor:ne,set:function(t){this.mask=1<<t},enable:function(t){this.mask|=1<<t},toggle:function(t){this.mask^=1<<t},disable:function(t){this.mask&=~(1<<t)},test:function(t){return 0!==(this.mask&t.mask)}},re.DefaultUp=new N(0,1,0),
-re.DefaultMatrixAutoUpdate=!0,Object.assign(re.prototype,E.prototype,{isObject3D:!0,applyMatrix:function(t){this.matrix.multiplyMatrices(t,this.matrix),this.matrix.decompose(this.position,this.quaternion,this.scale)},setRotationFromAxisAngle:function(t,e){this.quaternion.setFromAxisAngle(t,e)},setRotationFromEuler:function(t){this.quaternion.setFromEuler(t,!0)},setRotationFromMatrix:function(t){this.quaternion.setFromRotationMatrix(t)},setRotationFromQuaternion:function(t){this.quaternion.copy(t)},rotateOnAxis:function(){var t=new D;return function(e,i){return t.setFromAxisAngle(e,i),this.quaternion.multiply(t),this}}(),rotateX:function(){var t=new N(1,0,0);return function(e){return this.rotateOnAxis(t,e)}}(),rotateY:function(){var t=new N(0,1,0);return function(e){return this.rotateOnAxis(t,e)}}(),rotateZ:function(){var t=new N(0,0,1);return function(e){return this.rotateOnAxis(t,e)}}(),translateOnAxis:function(){var t=new N;return function(e,i){return t.copy(e).applyQuaternion(this.quaternion),this.position.add(t.multiplyScalar(i)),this}}(),translateX:function(){var t=new N(1,0,0);return function(e){return this.translateOnAxis(t,e)}}(),translateY:function(){var t=new N(0,1,0);return function(e){return this.translateOnAxis(t,e)}}(),translateZ:function(){var t=new N(0,0,1);return function(e){return this.translateOnAxis(t,e)}}(),localToWorld:function(t){return t.applyMatrix4(this.matrixWorld)},worldToLocal:function(){var t=new O;return function(e){return e.applyMatrix4(t.getInverse(this.matrixWorld))}}(),lookAt:function(){var t=new O;return function(e){t.lookAt(e,this.position,this.up),this.quaternion.setFromRotationMatrix(t)}}(),add:function(t){if(arguments.length>1){for(var e=0;e<arguments.length;e++)this.add(arguments[e]);return this}return t===this?(console.error("THREE.Object3D.add: object can't be added as a child of itself.",t),this):(t&&t.isObject3D?(null!==t.parent&&t.parent.remove(t),t.parent=this,t.dispatchEvent({type:"added"}),this.children.push(t)):console.error("THREE.Object3D.add: object not an instance of THREE.Object3D.",t),this)},remove:function(t){if(arguments.length>1)for(var e=0;e<arguments.length;e++)this.remove(arguments[e]);var i=this.children.indexOf(t);i!==-1&&(t.parent=null,t.dispatchEvent({type:"removed"}),this.children.splice(i,1))},getObjectById:function(t){return this.getObjectByProperty("id",t)},getObjectByName:function(t){return this.getObjectByProperty("name",t)},getObjectByProperty:function(t,e){if(this[t]===e)return this;for(var i=0,n=this.children.length;i<n;i++){var r=this.children[i],o=r.getObjectByProperty(t,e);if(void 0!==o)return o}},getWorldPosition:function(t){var e=t||new N;return this.updateMatrixWorld(!0),e.setFromMatrixPosition(this.matrixWorld)},getWorldQuaternion:function(){var t=new N,e=new N;return function(i){var n=i||new D;return this.updateMatrixWorld(!0),this.matrixWorld.decompose(t,n,e),n}}(),getWorldRotation:function(){var t=new D;return function(e){var i=e||new ie;return this.getWorldQuaternion(t),i.setFromQuaternion(t,this.rotation.order,!1)}}(),getWorldScale:function(){var t=new N,e=new D;return function(i){var n=i||new N;return this.updateMatrixWorld(!0),this.matrixWorld.decompose(t,e,n),n}}(),getWorldDirection:function(){var t=new D;return function(e){var i=e||new N;return this.getWorldQuaternion(t),i.set(0,0,1).applyQuaternion(t)}}(),raycast:function(){},traverse:function(t){t(this);for(var e=this.children,i=0,n=e.length;i<n;i++)e[i].traverse(t)},traverseVisible:function(t){if(this.visible!==!1){t(this);for(var e=this.children,i=0,n=e.length;i<n;i++)e[i].traverseVisible(t)}},traverseAncestors:function(t){var e=this.parent;null!==e&&(t(e),e.traverseAncestors(t))},updateMatrix:function(){this.matrix.compose(this.position,this.quaternion,this.scale),this.matrixWorldNeedsUpdate=!0},updateMatrixWorld:function(t){this.matrixAutoUpdate===!0&&this.updateMatrix(),this.matrixWorldNeedsUpdate!==!0&&t!==!0||(null===this.parent?this.matrixWorld.copy(this.matrix):this.matrixWorld.multiplyMatrices(this.parent.matrixWorld,this.matrix),this.matrixWorldNeedsUpdate=!1,t=!0);for(var e=this.children,i=0,n=e.length;i<n;i++)e[i].updateMatrixWorld(t)},toJSON:function(t){function e(t){var e=[];for(var i in t){var n=t[i];delete n.metadata,e.push(n)}return e}var i=void 0===t||""===t,n={};i&&(t={geometries:{},materials:{},textures:{},images:{}},n.metadata={version:4.4,type:"Object",generator:"Object3D.toJSON"});var r={};if(r.uuid=this.uuid,r.type=this.type,""!==this.name&&(r.name=this.name),"{}"!==JSON.stringify(this.userData)&&(r.userData=this.userData),this.castShadow===!0&&(r.castShadow=!0),this.receiveShadow===!0&&(r.receiveShadow=!0),this.visible===!1&&(r.visible=!1),r.matrix=this.matrix.toArray(),void 0!==this.geometry&&(void 0===t.geometries[this.geometry.uuid]&&(t.geometries[this.geometry.uuid]=this.geometry.toJSON(t)),r.geometry=this.geometry.uuid),void 0!==this.material&&(void 0===t.materials[this.material.uuid]&&(t.materials[this.material.uuid]=this.material.toJSON(t)),r.material=this.material.uuid),this.children.length>0){r.children=[];for(var o=0;o<this.children.length;o++)r.children.push(this.children[o].toJSON(t).object)}if(i){var a=e(t.geometries),s=e(t.materials),c=e(t.textures),u=e(t.images);a.length>0&&(n.geometries=a),s.length>0&&(n.materials=s),c.length>0&&(n.textures=c),u.length>0&&(n.images=u)}return n.object=r,n},clone:function(t){return(new this.constructor).copy(this,t)},copy:function(t,e){if(void 0===e&&(e=!0),this.name=t.name,this.up.copy(t.up),this.position.copy(t.position),this.quaternion.copy(t.quaternion),this.scale.copy(t.scale),this.matrix.copy(t.matrix),this.matrixWorld.copy(t.matrixWorld),this.matrixAutoUpdate=t.matrixAutoUpdate,this.matrixWorldNeedsUpdate=t.matrixWorldNeedsUpdate,this.visible=t.visible,this.castShadow=t.castShadow,this.receiveShadow=t.receiveShadow,this.frustumCulled=t.frustumCulled,this.renderOrder=t.renderOrder,this.userData=JSON.parse(JSON.stringify(t.userData)),e===!0)for(var i=0;i<t.children.length;i++){var n=t.children[i];this.add(n.clone())}return this}});var jp=0;Object.assign(ae.prototype,E.prototype,{isGeometry:!0,applyMatrix:function(t){for(var e=(new Lt).getNormalMatrix(t),i=0,n=this.vertices.length;i<n;i++){var r=this.vertices[i];r.applyMatrix4(t)}for(var i=0,n=this.faces.length;i<n;i++){var o=this.faces[i];o.normal.applyMatrix3(e).normalize();for(var a=0,s=o.vertexNormals.length;a<s;a++)o.vertexNormals[a].applyMatrix3(e).normalize()}return null!==this.boundingBox&&this.computeBoundingBox(),null!==this.boundingSphere&&this.computeBoundingSphere(),this.verticesNeedUpdate=!0,this.normalsNeedUpdate=!0,this},rotateX:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationX(e),this.applyMatrix(t),this}}(),rotateY:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationY(e),this.applyMatrix(t),this}}(),rotateZ:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationZ(e),this.applyMatrix(t),this}}(),translate:function(){var t;return function(e,i,n){return void 0===t&&(t=new O),t.makeTranslation(e,i,n),this.applyMatrix(t),this}}(),scale:function(){var t;return function(e,i,n){return void 0===t&&(t=new O),t.makeScale(e,i,n),this.applyMatrix(t),this}}(),lookAt:function(){var t;return function(e){void 0===t&&(t=new re),t.lookAt(e),t.updateMatrix(),this.applyMatrix(t.matrix)}}(),fromBufferGeometry:function(t){function e(t,e,n,r){var o=void 0!==a?[h[t].clone(),h[e].clone(),h[n].clone()]:[],f=void 0!==s?[i.colors[t].clone(),i.colors[e].clone(),i.colors[n].clone()]:[],p=new ee(t,e,n,o,f,r);i.faces.push(p),void 0!==c&&i.faceVertexUvs[0].push([l[t].clone(),l[e].clone(),l[n].clone()]),void 0!==u&&i.faceVertexUvs[1].push([d[t].clone(),d[e].clone(),d[n].clone()])}var i=this,n=null!==t.index?t.index.array:void 0,r=t.attributes,o=r.position.array,a=void 0!==r.normal?r.normal.array:void 0,s=void 0!==r.color?r.color.array:void 0,c=void 0!==r.uv?r.uv.array:void 0,u=void 0!==r.uv2?r.uv2.array:void 0;void 0!==u&&(this.faceVertexUvs[1]=[]);for(var h=[],l=[],d=[],f=0,p=0;f<o.length;f+=3,p+=2)i.vertices.push(new N(o[f],o[f+1],o[f+2])),void 0!==a&&h.push(new N(a[f],a[f+1],a[f+2])),void 0!==s&&i.colors.push(new Ct(s[f],s[f+1],s[f+2])),void 0!==c&&l.push(new I(c[p],c[p+1])),void 0!==u&&d.push(new I(u[p],u[p+1]));if(void 0!==n){var m=t.groups;if(m.length>0)for(var f=0;f<m.length;f++)for(var g=m[f],v=g.start,y=g.count,p=v,b=v+y;p<b;p+=3)e(n[p],n[p+1],n[p+2],g.materialIndex);else for(var f=0;f<n.length;f+=3)e(n[f],n[f+1],n[f+2])}else for(var f=0;f<o.length/3;f+=3)e(f,f+1,f+2);return this.computeFaceNormals(),null!==t.boundingBox&&(this.boundingBox=t.boundingBox.clone()),null!==t.boundingSphere&&(this.boundingSphere=t.boundingSphere.clone()),this},center:function(){this.computeBoundingBox();var t=this.boundingBox.center().negate();return this.translate(t.x,t.y,t.z),t},normalize:function(){this.computeBoundingSphere();var t=this.boundingSphere.center,e=this.boundingSphere.radius,i=0===e?1:1/e,n=new O;return n.set(i,0,0,-i*t.x,0,i,0,-i*t.y,0,0,i,-i*t.z,0,0,0,1),this.applyMatrix(n),this},computeFaceNormals:function(){for(var t=new N,e=new N,i=0,n=this.faces.length;i<n;i++){var r=this.faces[i],o=this.vertices[r.a],a=this.vertices[r.b],s=this.vertices[r.c];t.subVectors(s,a),e.subVectors(o,a),t.cross(e),t.normalize(),r.normal.copy(t)}},computeVertexNormals:function(t){void 0===t&&(t=!0);var e,i,n,r,o,a;for(a=new Array(this.vertices.length),e=0,i=this.vertices.length;e<i;e++)a[e]=new N;if(t){var s,c,u,h=new N,l=new N;for(n=0,r=this.faces.length;n<r;n++)o=this.faces[n],s=this.vertices[o.a],c=this.vertices[o.b],u=this.vertices[o.c],h.subVectors(u,c),l.subVectors(s,c),h.cross(l),a[o.a].add(h),a[o.b].add(h),a[o.c].add(h)}else for(n=0,r=this.faces.length;n<r;n++)o=this.faces[n],a[o.a].add(o.normal),a[o.b].add(o.normal),a[o.c].add(o.normal);for(e=0,i=this.vertices.length;e<i;e++)a[e].normalize();for(n=0,r=this.faces.length;n<r;n++){o=this.faces[n];var d=o.vertexNormals;3===d.length?(d[0].copy(a[o.a]),d[1].copy(a[o.b]),d[2].copy(a[o.c])):(d[0]=a[o.a].clone(),d[1]=a[o.b].clone(),d[2]=a[o.c].clone())}this.faces.length>0&&(this.normalsNeedUpdate=!0)},computeMorphNormals:function(){var t,e,i,n,r;for(i=0,n=this.faces.length;i<n;i++)for(r=this.faces[i],r.__originalFaceNormal?r.__originalFaceNormal.copy(r.normal):r.__originalFaceNormal=r.normal.clone(),r.__originalVertexNormals||(r.__originalVertexNormals=[]),t=0,e=r.vertexNormals.length;t<e;t++)r.__originalVertexNormals[t]?r.__originalVertexNormals[t].copy(r.vertexNormals[t]):r.__originalVertexNormals[t]=r.vertexNormals[t].clone();var o=new ae;for(o.faces=this.faces,t=0,e=this.morphTargets.length;t<e;t++){if(!this.morphNormals[t]){this.morphNormals[t]={},this.morphNormals[t].faceNormals=[],this.morphNormals[t].vertexNormals=[];var a,s,c=this.morphNormals[t].faceNormals,u=this.morphNormals[t].vertexNormals;for(i=0,n=this.faces.length;i<n;i++)a=new N,s={a:new N,b:new N,c:new N},c.push(a),u.push(s)}var h=this.morphNormals[t];o.vertices=this.morphTargets[t].vertices,o.computeFaceNormals(),o.computeVertexNormals();var a,s;for(i=0,n=this.faces.length;i<n;i++)r=this.faces[i],a=h.faceNormals[i],s=h.vertexNormals[i],a.copy(r.normal),s.a.copy(r.vertexNormals[0]),s.b.copy(r.vertexNormals[1]),s.c.copy(r.vertexNormals[2])}for(i=0,n=this.faces.length;i<n;i++)r=this.faces[i],r.normal=r.__originalFaceNormal,r.vertexNormals=r.__originalVertexNormals},computeTangents:function(){console.warn("THREE.Geometry: .computeTangents() has been removed.")},computeLineDistances:function(){for(var t=0,e=this.vertices,i=0,n=e.length;i<n;i++)i>0&&(t+=e[i].distanceTo(e[i-1])),this.lineDistances[i]=t},computeBoundingBox:function(){null===this.boundingBox&&(this.boundingBox=new Et),this.boundingBox.setFromPoints(this.vertices)},computeBoundingSphere:function(){null===this.boundingSphere&&(this.boundingSphere=new It),this.boundingSphere.setFromPoints(this.vertices)},merge:function(t,e,i){if((t&&t.isGeometry)===!1)return void console.error("THREE.Geometry.merge(): geometry not an instance of THREE.Geometry.",t);var n,r=this.vertices.length,o=this.vertices,a=t.vertices,s=this.faces,c=t.faces,u=this.faceVertexUvs[0],h=t.faceVertexUvs[0];void 0===i&&(i=0),void 0!==e&&(n=(new Lt).getNormalMatrix(e));for(var l=0,d=a.length;l<d;l++){var f=a[l],p=f.clone();void 0!==e&&p.applyMatrix4(e),o.push(p)}for(l=0,d=c.length;l<d;l++){var m,g,v,y=c[l],b=y.vertexNormals,x=y.vertexColors;m=new ee(y.a+r,y.b+r,y.c+r),m.normal.copy(y.normal),void 0!==n&&m.normal.applyMatrix3(n).normalize();for(var w=0,_=b.length;w<_;w++)g=b[w].clone(),void 0!==n&&g.applyMatrix3(n).normalize(),m.vertexNormals.push(g);m.color.copy(y.color);for(var w=0,_=x.length;w<_;w++)v=x[w],m.vertexColors.push(v.clone());m.materialIndex=y.materialIndex+i,s.push(m)}for(l=0,d=h.length;l<d;l++){var S=h[l],A=[];if(void 0!==S){for(var w=0,_=S.length;w<_;w++)A.push(S[w].clone());u.push(A)}}},mergeMesh:function(t){return(t&&t.isMesh)===!1?void console.error("THREE.Geometry.mergeMesh(): mesh not an instance of THREE.Mesh.",t):(t.matrixAutoUpdate&&t.updateMatrix(),void this.merge(t.geometry,t.matrix))},mergeVertices:function(){var t,e,i,n,r,o,a,s,c={},u=[],h=[],l=4,d=Math.pow(10,l);for(i=0,n=this.vertices.length;i<n;i++)t=this.vertices[i],e=Math.round(t.x*d)+"_"+Math.round(t.y*d)+"_"+Math.round(t.z*d),void 0===c[e]?(c[e]=i,u.push(this.vertices[i]),h[i]=u.length-1):h[i]=h[c[e]];var f=[];for(i=0,n=this.faces.length;i<n;i++){r=this.faces[i],r.a=h[r.a],r.b=h[r.b],r.c=h[r.c],o=[r.a,r.b,r.c];for(var p=-1,m=0;m<3;m++)if(o[m]===o[(m+1)%3]){p=m,f.push(i);break}}for(i=f.length-1;i>=0;i--){var g=f[i];for(this.faces.splice(g,1),a=0,s=this.faceVertexUvs.length;a<s;a++)this.faceVertexUvs[a].splice(g,1)}var v=this.vertices.length-u.length;return this.vertices=u,v},sortFacesByMaterialIndex:function(){function t(t,e){return t.materialIndex-e.materialIndex}for(var e=this.faces,i=e.length,n=0;n<i;n++)e[n]._id=n;e.sort(t);var r,o,a=this.faceVertexUvs[0],s=this.faceVertexUvs[1];a&&a.length===i&&(r=[]),s&&s.length===i&&(o=[]);for(var n=0;n<i;n++){var c=e[n]._id;r&&r.push(a[c]),o&&o.push(s[c])}r&&(this.faceVertexUvs[0]=r),o&&(this.faceVertexUvs[1]=o)},toJSON:function(){function t(t,e,i){return i?t|1<<e:t&~(1<<e)}function e(t){var e=t.x.toString()+t.y.toString()+t.z.toString();return void 0!==d[e]?d[e]:(d[e]=l.length/3,l.push(t.x,t.y,t.z),d[e])}function i(t){var e=t.r.toString()+t.g.toString()+t.b.toString();return void 0!==p[e]?p[e]:(p[e]=f.length,f.push(t.getHex()),p[e])}function n(t){var e=t.x.toString()+t.y.toString();return void 0!==g[e]?g[e]:(g[e]=m.length/2,m.push(t.x,t.y),g[e])}var r={metadata:{version:4.4,type:"Geometry",generator:"Geometry.toJSON"}};if(r.uuid=this.uuid,r.type=this.type,""!==this.name&&(r.name=this.name),void 0!==this.parameters){var o=this.parameters;for(var a in o)void 0!==o[a]&&(r[a]=o[a]);return r}for(var s=[],c=0;c<this.vertices.length;c++){var u=this.vertices[c];s.push(u.x,u.y,u.z)}for(var h=[],l=[],d={},f=[],p={},m=[],g={},c=0;c<this.faces.length;c++){var v=this.faces[c],y=!0,b=!1,x=void 0!==this.faceVertexUvs[0][c],w=v.normal.length()>0,_=v.vertexNormals.length>0,S=1!==v.color.r||1!==v.color.g||1!==v.color.b,A=v.vertexColors.length>0,M=0;if(M=t(M,0,0),M=t(M,1,y),M=t(M,2,b),M=t(M,3,x),M=t(M,4,w),M=t(M,5,_),M=t(M,6,S),M=t(M,7,A),h.push(M),h.push(v.a,v.b,v.c),h.push(v.materialIndex),x){var P=this.faceVertexUvs[0][c];h.push(n(P[0]),n(P[1]),n(P[2]))}if(w&&h.push(e(v.normal)),_){var C=v.vertexNormals;h.push(e(C[0]),e(C[1]),e(C[2]))}if(S&&h.push(i(v.color)),A){var T=v.vertexColors;h.push(i(T[0]),i(T[1]),i(T[2]))}}return r.data={},r.data.vertices=s,r.data.normals=l,f.length>0&&(r.data.colors=f),m.length>0&&(r.data.uvs=[m]),r.data.faces=h,r},clone:function(){return(new ae).copy(this)},copy:function(t){this.vertices=[],this.faces=[],this.faceVertexUvs=[[]];for(var e=t.vertices,i=0,n=e.length;i<n;i++)this.vertices.push(e[i].clone());for(var r=t.faces,i=0,n=r.length;i<n;i++)this.faces.push(r[i].clone());for(var i=0,n=t.faceVertexUvs.length;i<n;i++){var o=t.faceVertexUvs[i];void 0===this.faceVertexUvs[i]&&(this.faceVertexUvs[i]=[]);for(var a=0,s=o.length;a<s;a++){for(var c=o[a],u=[],h=0,l=c.length;h<l;h++){var d=c[h];u.push(d.clone())}this.faceVertexUvs[i].push(u)}}return this},dispose:function(){this.dispatchEvent({type:"dispose"})}});var $p=0;Object.assign(ce.prototype,E.prototype,{computeBoundingBox:ae.prototype.computeBoundingBox,computeBoundingSphere:ae.prototype.computeBoundingSphere,computeFaceNormals:function(){console.warn("THREE.DirectGeometry: computeFaceNormals() is not a method of this type of geometry.")},computeVertexNormals:function(){console.warn("THREE.DirectGeometry: computeVertexNormals() is not a method of this type of geometry.")},computeGroups:function(t){for(var e,i,n=[],r=t.faces,o=0;o<r.length;o++){var a=r[o];a.materialIndex!==i&&(i=a.materialIndex,void 0!==e&&(e.count=3*o-e.start,n.push(e)),e={start:3*o,materialIndex:i})}void 0!==e&&(e.count=3*o-e.start,n.push(e)),this.groups=n},fromGeometry:function(t){var e,i=t.faces,n=t.vertices,r=t.faceVertexUvs,o=r[0]&&r[0].length>0,a=r[1]&&r[1].length>0,s=t.morphTargets,c=s.length;if(c>0){e=[];for(var u=0;u<c;u++)e[u]=[];this.morphTargets.position=e}var h,l=t.morphNormals,d=l.length;if(d>0){h=[];for(var u=0;u<d;u++)h[u]=[];this.morphTargets.normal=h}for(var f=t.skinIndices,p=t.skinWeights,m=f.length===n.length,g=p.length===n.length,u=0;u<i.length;u++){var v=i[u];this.vertices.push(n[v.a],n[v.b],n[v.c]);var y=v.vertexNormals;if(3===y.length)this.normals.push(y[0],y[1],y[2]);else{var b=v.normal;this.normals.push(b,b,b)}var x=v.vertexColors;if(3===x.length)this.colors.push(x[0],x[1],x[2]);else{var w=v.color;this.colors.push(w,w,w)}if(o===!0){var _=r[0][u];void 0!==_?this.uvs.push(_[0],_[1],_[2]):(console.warn("THREE.DirectGeometry.fromGeometry(): Undefined vertexUv ",u),this.uvs.push(new I,new I,new I))}if(a===!0){var _=r[1][u];void 0!==_?this.uvs2.push(_[0],_[1],_[2]):(console.warn("THREE.DirectGeometry.fromGeometry(): Undefined vertexUv2 ",u),this.uvs2.push(new I,new I,new I))}for(var S=0;S<c;S++){var A=s[S].vertices;e[S].push(A[v.a],A[v.b],A[v.c])}for(var S=0;S<d;S++){var M=l[S].vertexNormals[u];h[S].push(M.a,M.b,M.c)}m&&this.skinIndices.push(f[v.a],f[v.b],f[v.c]),g&&this.skinWeights.push(p[v.a],p[v.b],p[v.c])}return this.computeGroups(t),this.verticesNeedUpdate=t.verticesNeedUpdate,this.normalsNeedUpdate=t.normalsNeedUpdate,this.colorsNeedUpdate=t.colorsNeedUpdate,this.uvsNeedUpdate=t.uvsNeedUpdate,this.groupsNeedUpdate=t.groupsNeedUpdate,this},dispose:function(){this.dispatchEvent({type:"dispose"})}}),Object.assign(ue.prototype,E.prototype,{isBufferGeometry:!0,getIndex:function(){return this.index},setIndex:function(t){this.index=t},addAttribute:function(t,e){return(e&&e.isBufferAttribute)===!1&&(e&&e.isInterleavedBufferAttribute)===!1?(console.warn("THREE.BufferGeometry: .addAttribute() now expects ( name, attribute )."),void this.addAttribute(t,new Kt(arguments[1],arguments[2]))):"index"===t?(console.warn("THREE.BufferGeometry.addAttribute: Use .setIndex() for index attribute."),void this.setIndex(e)):(this.attributes[t]=e,this)},getAttribute:function(t){return this.attributes[t]},removeAttribute:function(t){return delete this.attributes[t],this},addGroup:function(t,e,i){this.groups.push({start:t,count:e,materialIndex:void 0!==i?i:0})},clearGroups:function(){this.groups=[]},setDrawRange:function(t,e){this.drawRange.start=t,this.drawRange.count=e},applyMatrix:function(t){var e=this.attributes.position;void 0!==e&&(t.applyToVector3Array(e.array),e.needsUpdate=!0);var i=this.attributes.normal;if(void 0!==i){var n=(new Lt).getNormalMatrix(t);n.applyToVector3Array(i.array),i.needsUpdate=!0}return null!==this.boundingBox&&this.computeBoundingBox(),null!==this.boundingSphere&&this.computeBoundingSphere(),this},rotateX:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationX(e),this.applyMatrix(t),this}}(),rotateY:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationY(e),this.applyMatrix(t),this}}(),rotateZ:function(){var t;return function(e){return void 0===t&&(t=new O),t.makeRotationZ(e),this.applyMatrix(t),this}}(),translate:function(){var t;return function(e,i,n){return void 0===t&&(t=new O),t.makeTranslation(e,i,n),this.applyMatrix(t),this}}(),scale:function(){var t;return function(e,i,n){return void 0===t&&(t=new O),t.makeScale(e,i,n),this.applyMatrix(t),this}}(),lookAt:function(){var t;return function(e){void 0===t&&(t=new re),t.lookAt(e),t.updateMatrix(),this.applyMatrix(t.matrix)}}(),center:function(){this.computeBoundingBox();var t=this.boundingBox.center().negate();return this.translate(t.x,t.y,t.z),t},setFromObject:function(t){var e=t.geometry;if(t&&t.isPoints||t&&t.isLine){var i=new te(3*e.vertices.length,3),n=new te(3*e.colors.length,3);if(this.addAttribute("position",i.copyVector3sArray(e.vertices)),this.addAttribute("color",n.copyColorsArray(e.colors)),e.lineDistances&&e.lineDistances.length===e.vertices.length){var r=new te(e.lineDistances.length,1);this.addAttribute("lineDistance",r.copyArray(e.lineDistances))}null!==e.boundingSphere&&(this.boundingSphere=e.boundingSphere.clone()),null!==e.boundingBox&&(this.boundingBox=e.boundingBox.clone())}else t&&t.isMesh&&e&&e.isGeometry&&this.fromGeometry(e);return this},updateFromObject:function(t){var e=t.geometry;if(t&&t.isMesh){var i=e.__directGeometry;if(e.elementsNeedUpdate===!0&&(i=void 0,e.elementsNeedUpdate=!1),void 0===i)return this.fromGeometry(e);i.verticesNeedUpdate=e.verticesNeedUpdate,i.normalsNeedUpdate=e.normalsNeedUpdate,i.colorsNeedUpdate=e.colorsNeedUpdate,i.uvsNeedUpdate=e.uvsNeedUpdate,i.groupsNeedUpdate=e.groupsNeedUpdate,e.verticesNeedUpdate=!1,e.normalsNeedUpdate=!1,e.colorsNeedUpdate=!1,e.uvsNeedUpdate=!1,e.groupsNeedUpdate=!1,e=i}var n;return e.verticesNeedUpdate===!0&&(n=this.attributes.position,void 0!==n&&(n.copyVector3sArray(e.vertices),n.needsUpdate=!0),e.verticesNeedUpdate=!1),e.normalsNeedUpdate===!0&&(n=this.attributes.normal,void 0!==n&&(n.copyVector3sArray(e.normals),n.needsUpdate=!0),e.normalsNeedUpdate=!1),e.colorsNeedUpdate===!0&&(n=this.attributes.color,void 0!==n&&(n.copyColorsArray(e.colors),n.needsUpdate=!0),e.colorsNeedUpdate=!1),e.uvsNeedUpdate&&(n=this.attributes.uv,void 0!==n&&(n.copyVector2sArray(e.uvs),n.needsUpdate=!0),e.uvsNeedUpdate=!1),e.lineDistancesNeedUpdate&&(n=this.attributes.lineDistance,void 0!==n&&(n.copyArray(e.lineDistances),n.needsUpdate=!0),e.lineDistancesNeedUpdate=!1),e.groupsNeedUpdate&&(e.computeGroups(t.geometry),this.groups=e.groups,e.groupsNeedUpdate=!1),this},fromGeometry:function(t){return t.__directGeometry=(new ce).fromGeometry(t),this.fromDirectGeometry(t.__directGeometry)},fromDirectGeometry:function(t){var e=new Float32Array(3*t.vertices.length);if(this.addAttribute("position",new Kt(e,3).copyVector3sArray(t.vertices)),t.normals.length>0){var i=new Float32Array(3*t.normals.length);this.addAttribute("normal",new Kt(i,3).copyVector3sArray(t.normals))}if(t.colors.length>0){var n=new Float32Array(3*t.colors.length);this.addAttribute("color",new Kt(n,3).copyColorsArray(t.colors))}if(t.uvs.length>0){var r=new Float32Array(2*t.uvs.length);this.addAttribute("uv",new Kt(r,2).copyVector2sArray(t.uvs))}if(t.uvs2.length>0){var o=new Float32Array(2*t.uvs2.length);this.addAttribute("uv2",new Kt(o,2).copyVector2sArray(t.uvs2))}if(t.indices.length>0){var a=t.vertices.length>65535?Uint32Array:Uint16Array,s=new a(3*t.indices.length);this.setIndex(new Kt(s,1).copyIndicesArray(t.indices))}this.groups=t.groups;for(var c in t.morphTargets){for(var u=[],h=t.morphTargets[c],l=0,d=h.length;l<d;l++){var f=h[l],p=new te(3*f.length,3);u.push(p.copyVector3sArray(f))}this.morphAttributes[c]=u}if(t.skinIndices.length>0){var m=new te(4*t.skinIndices.length,4);this.addAttribute("skinIndex",m.copyVector4sArray(t.skinIndices))}if(t.skinWeights.length>0){var g=new te(4*t.skinWeights.length,4);this.addAttribute("skinWeight",g.copyVector4sArray(t.skinWeights))}return null!==t.boundingSphere&&(this.boundingSphere=t.boundingSphere.clone()),null!==t.boundingBox&&(this.boundingBox=t.boundingBox.clone()),this},computeBoundingBox:function(){null===this.boundingBox&&(this.boundingBox=new Et);var t=this.attributes.position.array;void 0!==t?this.boundingBox.setFromArray(t):this.boundingBox.makeEmpty(),(isNaN(this.boundingBox.min.x)||isNaN(this.boundingBox.min.y)||isNaN(this.boundingBox.min.z))&&console.error('THREE.BufferGeometry.computeBoundingBox: Computed min/max have NaN values. The "position" attribute is likely to have NaN values.',this)},computeBoundingSphere:function(){var t=new Et,e=new N;return function(){null===this.boundingSphere&&(this.boundingSphere=new It);var i=this.attributes.position;if(i){var n=i.array,r=this.boundingSphere.center;t.setFromArray(n),t.center(r);for(var o=0,a=0,s=n.length;a<s;a+=3)e.fromArray(n,a),o=Math.max(o,r.distanceToSquared(e));this.boundingSphere.radius=Math.sqrt(o),isNaN(this.boundingSphere.radius)&&console.error('THREE.BufferGeometry.computeBoundingSphere(): Computed radius is NaN. The "position" attribute is likely to have NaN values.',this)}}}(),computeFaceNormals:function(){},computeVertexNormals:function(){var t=this.index,e=this.attributes,i=this.groups;if(e.position){var n=e.position.array;if(void 0===e.normal)this.addAttribute("normal",new Kt(new Float32Array(n.length),3));else for(var r=e.normal.array,o=0,a=r.length;o<a;o++)r[o]=0;var s,c,u,h=e.normal.array,l=new N,d=new N,f=new N,p=new N,m=new N;if(t){var g=t.array;0===i.length&&this.addGroup(0,g.length);for(var v=0,y=i.length;v<y;++v)for(var b=i[v],x=b.start,w=b.count,o=x,a=x+w;o<a;o+=3)s=3*g[o+0],c=3*g[o+1],u=3*g[o+2],l.fromArray(n,s),d.fromArray(n,c),f.fromArray(n,u),p.subVectors(f,d),m.subVectors(l,d),p.cross(m),h[s]+=p.x,h[s+1]+=p.y,h[s+2]+=p.z,h[c]+=p.x,h[c+1]+=p.y,h[c+2]+=p.z,h[u]+=p.x,h[u+1]+=p.y,h[u+2]+=p.z}else for(var o=0,a=n.length;o<a;o+=9)l.fromArray(n,o),d.fromArray(n,o+3),f.fromArray(n,o+6),p.subVectors(f,d),m.subVectors(l,d),p.cross(m),h[o]=p.x,h[o+1]=p.y,h[o+2]=p.z,h[o+3]=p.x,h[o+4]=p.y,h[o+5]=p.z,h[o+6]=p.x,h[o+7]=p.y,h[o+8]=p.z;this.normalizeNormals(),e.normal.needsUpdate=!0}},merge:function(t,e){if((t&&t.isBufferGeometry)===!1)return void console.error("THREE.BufferGeometry.merge(): geometry not an instance of THREE.BufferGeometry.",t);void 0===e&&(e=0);var i=this.attributes;for(var n in i)if(void 0!==t.attributes[n])for(var r=i[n],o=r.array,a=t.attributes[n],s=a.array,c=a.itemSize,u=0,h=c*e;u<s.length;u++,h++)o[h]=s[u];return this},normalizeNormals:function(){for(var t,e,i,n,r=this.attributes.normal.array,o=0,a=r.length;o<a;o+=3)t=r[o],e=r[o+1],i=r[o+2],n=1/Math.sqrt(t*t+e*e+i*i),r[o]*=n,r[o+1]*=n,r[o+2]*=n},toNonIndexed:function(){if(null===this.index)return console.warn("THREE.BufferGeometry.toNonIndexed(): Geometry is already non-indexed."),this;var t=new ue,e=this.index.array,i=this.attributes;for(var n in i){for(var r=i[n],o=r.array,a=r.itemSize,s=new o.constructor(e.length*a),c=0,u=0,h=0,l=e.length;h<l;h++){c=e[h]*a;for(var d=0;d<a;d++)s[u++]=o[c++]}t.addAttribute(n,new Kt(s,a))}return t},toJSON:function(){var t={metadata:{version:4.4,type:"BufferGeometry",generator:"BufferGeometry.toJSON"}};if(t.uuid=this.uuid,t.type=this.type,""!==this.name&&(t.name=this.name),void 0!==this.parameters){var e=this.parameters;for(var i in e)void 0!==e[i]&&(t[i]=e[i]);return t}t.data={attributes:{}};var n=this.index;if(null!==n){var r=Array.prototype.slice.call(n.array);t.data.index={type:n.array.constructor.name,array:r}}var o=this.attributes;for(var i in o){var a=o[i],r=Array.prototype.slice.call(a.array);t.data.attributes[i]={itemSize:a.itemSize,type:a.array.constructor.name,array:r,normalized:a.normalized}}var s=this.groups;s.length>0&&(t.data.groups=JSON.parse(JSON.stringify(s)));var c=this.boundingSphere;return null!==c&&(t.data.boundingSphere={center:c.center.toArray(),radius:c.radius}),t},clone:function(){return(new ue).copy(this)},copy:function(t){var e=t.index;null!==e&&this.setIndex(e.clone());var i=t.attributes;for(var n in i){var r=i[n];this.addAttribute(n,r.clone())}for(var o=t.groups,a=0,s=o.length;a<s;a++){var c=o[a];this.addGroup(c.start,c.count,c.materialIndex)}return this},dispose:function(){this.dispatchEvent({type:"dispose"})}}),ue.MaxIndex=65535,ye.prototype=Object.create(St.prototype),ye.prototype.constructor=ye,ye.prototype.isWebGLRenderTargetCube=!0,be.prototype=Object.create(ue.prototype),be.prototype.constructor=be,xe.prototype={constructor:xe,set:function(t,e){return this.origin.copy(t),this.direction.copy(e),this},clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.origin.copy(t.origin),this.direction.copy(t.direction),this},at:function(t,e){var i=e||new N;return i.copy(this.direction).multiplyScalar(t).add(this.origin)},lookAt:function(t){return this.direction.copy(t).sub(this.origin).normalize(),this},recast:function(){var t=new N;return function(e){return this.origin.copy(this.at(e,t)),this}}(),closestPointToPoint:function(t,e){var i=e||new N;i.subVectors(t,this.origin);var n=i.dot(this.direction);return n<0?i.copy(this.origin):i.copy(this.direction).multiplyScalar(n).add(this.origin)},distanceToPoint:function(t){return Math.sqrt(this.distanceSqToPoint(t))},distanceSqToPoint:function(){var t=new N;return function(e){var i=t.subVectors(e,this.origin).dot(this.direction);return i<0?this.origin.distanceToSquared(e):(t.copy(this.direction).multiplyScalar(i).add(this.origin),t.distanceToSquared(e))}}(),distanceSqToSegment:function(){var t=new N,e=new N,i=new N;return function(n,r,o,a){t.copy(n).add(r).multiplyScalar(.5),e.copy(r).sub(n).normalize(),i.copy(this.origin).sub(t);var s,c,u,h,l=.5*n.distanceTo(r),d=-this.direction.dot(e),f=i.dot(this.direction),p=-i.dot(e),m=i.lengthSq(),g=Math.abs(1-d*d);if(g>0)if(s=d*p-f,c=d*f-p,h=l*g,s>=0)if(c>=-h)if(c<=h){var v=1/g;s*=v,c*=v,u=s*(s+d*c+2*f)+c*(d*s+c+2*p)+m}else c=l,s=Math.max(0,-(d*c+f)),u=-s*s+c*(c+2*p)+m;else c=-l,s=Math.max(0,-(d*c+f)),u=-s*s+c*(c+2*p)+m;else c<=-h?(s=Math.max(0,-(-d*l+f)),c=s>0?-l:Math.min(Math.max(-l,-p),l),u=-s*s+c*(c+2*p)+m):c<=h?(s=0,c=Math.min(Math.max(-l,-p),l),u=c*(c+2*p)+m):(s=Math.max(0,-(d*l+f)),c=s>0?l:Math.min(Math.max(-l,-p),l),u=-s*s+c*(c+2*p)+m);else c=d>0?-l:l,s=Math.max(0,-(d*c+f)),u=-s*s+c*(c+2*p)+m;return o&&o.copy(this.direction).multiplyScalar(s).add(this.origin),a&&a.copy(e).multiplyScalar(c).add(t),u}}(),intersectSphere:function(){var t=new N;return function(e,i){t.subVectors(e.center,this.origin);var n=t.dot(this.direction),r=t.dot(t)-n*n,o=e.radius*e.radius;if(r>o)return null;var a=Math.sqrt(o-r),s=n-a,c=n+a;return s<0&&c<0?null:s<0?this.at(c,i):this.at(s,i)}}(),intersectsSphere:function(t){return this.distanceToPoint(t.center)<=t.radius},distanceToPlane:function(t){var e=t.normal.dot(this.direction);if(0===e)return 0===t.distanceToPoint(this.origin)?0:null;var i=-(this.origin.dot(t.normal)+t.constant)/e;return i>=0?i:null},intersectPlane:function(t,e){var i=this.distanceToPlane(t);return null===i?null:this.at(i,e)},intersectsPlane:function(t){var e=t.distanceToPoint(this.origin);if(0===e)return!0;var i=t.normal.dot(this.direction);return i*e<0},intersectBox:function(t,e){var i,n,r,o,a,s,c=1/this.direction.x,u=1/this.direction.y,h=1/this.direction.z,l=this.origin;return c>=0?(i=(t.min.x-l.x)*c,n=(t.max.x-l.x)*c):(i=(t.max.x-l.x)*c,n=(t.min.x-l.x)*c),u>=0?(r=(t.min.y-l.y)*u,o=(t.max.y-l.y)*u):(r=(t.max.y-l.y)*u,o=(t.min.y-l.y)*u),i>o||r>n?null:((r>i||i!==i)&&(i=r),(o<n||n!==n)&&(n=o),h>=0?(a=(t.min.z-l.z)*h,s=(t.max.z-l.z)*h):(a=(t.max.z-l.z)*h,s=(t.min.z-l.z)*h),i>s||a>n?null:((a>i||i!==i)&&(i=a),(s<n||n!==n)&&(n=s),n<0?null:this.at(i>=0?i:n,e)))},intersectsBox:function(){var t=new N;return function(e){return null!==this.intersectBox(e,t)}}(),intersectTriangle:function(){var t=new N,e=new N,i=new N,n=new N;return function(r,o,a,s,c){e.subVectors(o,r),i.subVectors(a,r),n.crossVectors(e,i);var u,h=this.direction.dot(n);if(h>0){if(s)return null;u=1}else{if(!(h<0))return null;
-u=-1,h=-h}t.subVectors(this.origin,r);var l=u*this.direction.dot(i.crossVectors(t,i));if(l<0)return null;var d=u*this.direction.dot(e.cross(t));if(d<0)return null;if(l+d>h)return null;var f=-u*t.dot(n);return f<0?null:this.at(f/h,c)}}(),applyMatrix4:function(t){return this.direction.add(this.origin).applyMatrix4(t),this.origin.applyMatrix4(t),this.direction.sub(this.origin),this.direction.normalize(),this},equals:function(t){return t.origin.equals(this.origin)&&t.direction.equals(this.direction)}},we.prototype={constructor:we,set:function(t,e){return this.start.copy(t),this.end.copy(e),this},clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.start.copy(t.start),this.end.copy(t.end),this},center:function(t){var e=t||new N;return e.addVectors(this.start,this.end).multiplyScalar(.5)},delta:function(t){var e=t||new N;return e.subVectors(this.end,this.start)},distanceSq:function(){return this.start.distanceToSquared(this.end)},distance:function(){return this.start.distanceTo(this.end)},at:function(t,e){var i=e||new N;return this.delta(i).multiplyScalar(t).add(this.start)},closestPointToPointParameter:function(){var t=new N,e=new N;return function(i,n){t.subVectors(i,this.start),e.subVectors(this.end,this.start);var r=e.dot(e),o=e.dot(t),a=o/r;return n&&(a=Ed.clamp(a,0,1)),a}}(),closestPointToPoint:function(t,e,i){var n=this.closestPointToPointParameter(t,e),r=i||new N;return this.delta(r).multiplyScalar(n).add(this.start)},applyMatrix4:function(t){return this.start.applyMatrix4(t),this.end.applyMatrix4(t),this},equals:function(t){return t.start.equals(this.start)&&t.end.equals(this.end)}},_e.normal=function(){var t=new N;return function(e,i,n,r){var o=r||new N;o.subVectors(n,i),t.subVectors(e,i),o.cross(t);var a=o.lengthSq();return a>0?o.multiplyScalar(1/Math.sqrt(a)):o.set(0,0,0)}}(),_e.barycoordFromPoint=function(){var t=new N,e=new N,i=new N;return function(n,r,o,a,s){t.subVectors(a,r),e.subVectors(o,r),i.subVectors(n,r);var c=t.dot(t),u=t.dot(e),h=t.dot(i),l=e.dot(e),d=e.dot(i),f=c*l-u*u,p=s||new N;if(0===f)return p.set(-2,-1,-1);var m=1/f,g=(l*h-u*d)*m,v=(c*d-u*h)*m;return p.set(1-g-v,v,g)}}(),_e.containsPoint=function(){var t=new N;return function(e,i,n,r){var o=_e.barycoordFromPoint(e,i,n,r,t);return o.x>=0&&o.y>=0&&o.x+o.y<=1}}(),_e.prototype={constructor:_e,set:function(t,e,i){return this.a.copy(t),this.b.copy(e),this.c.copy(i),this},setFromPointsAndIndices:function(t,e,i,n){return this.a.copy(t[e]),this.b.copy(t[i]),this.c.copy(t[n]),this},clone:function(){return(new this.constructor).copy(this)},copy:function(t){return this.a.copy(t.a),this.b.copy(t.b),this.c.copy(t.c),this},area:function(){var t=new N,e=new N;return function(){return t.subVectors(this.c,this.b),e.subVectors(this.a,this.b),.5*t.cross(e).length()}}(),midpoint:function(t){var e=t||new N;return e.addVectors(this.a,this.b).add(this.c).multiplyScalar(1/3)},normal:function(t){return _e.normal(this.a,this.b,this.c,t)},plane:function(t){var e=t||new Rt;return e.setFromCoplanarPoints(this.a,this.b,this.c)},barycoordFromPoint:function(t,e){return _e.barycoordFromPoint(t,this.a,this.b,this.c,e)},containsPoint:function(t){return _e.containsPoint(t,this.a,this.b,this.c)},closestPointToPoint:function(){var t,e,i,n;return function(r,o){void 0===t&&(t=new Rt,e=[new we,new we,new we],i=new N,n=new N);var a=o||new N,s=1/0;if(t.setFromCoplanarPoints(this.a,this.b,this.c),t.projectPoint(r,i),this.containsPoint(i)===!0)a.copy(i);else{e[0].set(this.a,this.b),e[1].set(this.b,this.c),e[2].set(this.c,this.a);for(var c=0;c<e.length;c++){e[c].closestPointToPoint(i,!0,n);var u=i.distanceToSquared(n);u<s&&(s=u,a.copy(n))}}return a}}(),equals:function(t){return t.a.equals(this.a)&&t.b.equals(this.b)&&t.c.equals(this.c)}},Se.prototype=Object.create(At.prototype),Se.prototype.constructor=Se,Se.prototype.isMeshBasicMaterial=!0,Se.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.color.copy(t.color),this.map=t.map,this.aoMap=t.aoMap,this.aoMapIntensity=t.aoMapIntensity,this.specularMap=t.specularMap,this.alphaMap=t.alphaMap,this.envMap=t.envMap,this.combine=t.combine,this.reflectivity=t.reflectivity,this.refractionRatio=t.refractionRatio,this.wireframe=t.wireframe,this.wireframeLinewidth=t.wireframeLinewidth,this.wireframeLinecap=t.wireframeLinecap,this.wireframeLinejoin=t.wireframeLinejoin,this.skinning=t.skinning,this.morphTargets=t.morphTargets,this},Ae.prototype=Object.assign(Object.create(re.prototype),{constructor:Ae,isMesh:!0,setDrawMode:function(t){this.drawMode=t},copy:function(t){return re.prototype.copy.call(this,t),this.drawMode=t.drawMode,this},updateMorphTargets:function(){if(void 0!==this.geometry.morphTargets&&this.geometry.morphTargets.length>0){this.morphTargetBase=-1,this.morphTargetInfluences=[],this.morphTargetDictionary={};for(var t=0,e=this.geometry.morphTargets.length;t<e;t++)this.morphTargetInfluences.push(0),this.morphTargetDictionary[this.geometry.morphTargets[t].name]=t}},getMorphTargetIndexByName:function(t){return void 0!==this.morphTargetDictionary[t]?this.morphTargetDictionary[t]:(console.warn("THREE.Mesh.getMorphTargetIndexByName: morph target "+t+" does not exist. Returning 0."),0)},raycast:function(){function t(t,e,i,n,r,o,a){return _e.barycoordFromPoint(t,e,i,n,m),r.multiplyScalar(m.x),o.multiplyScalar(m.y),a.multiplyScalar(m.z),r.add(o).add(a),r.clone()}function e(t,e,i,n,r,o,a){var s,c=t.material;if(s=c.side===Ph?i.intersectTriangle(o,r,n,!0,a):i.intersectTriangle(n,r,o,c.side!==Ch,a),null===s)return null;v.copy(a),v.applyMatrix4(t.matrixWorld);var u=e.ray.origin.distanceTo(v);return u<e.near||u>e.far?null:{distance:u,point:v.clone(),object:t}}function i(i,n,r,o,u,h,l,m){a.fromArray(o,3*h),s.fromArray(o,3*l),c.fromArray(o,3*m);var v=e(i,n,r,a,s,c,g);return v&&(u&&(d.fromArray(u,2*h),f.fromArray(u,2*l),p.fromArray(u,2*m),v.uv=t(g,a,s,c,d,f,p)),v.face=new ee(h,l,m,_e.normal(a,s,c)),v.faceIndex=h),v}var n=new O,r=new xe,o=new It,a=new N,s=new N,c=new N,u=new N,h=new N,l=new N,d=new I,f=new I,p=new I,m=new N,g=new N,v=new N;return function(m,v){var y=this.geometry,b=this.material,x=this.matrixWorld;if(void 0!==b&&(null===y.boundingSphere&&y.computeBoundingSphere(),o.copy(y.boundingSphere),o.applyMatrix4(x),m.ray.intersectsSphere(o)!==!1&&(n.getInverse(x),r.copy(m.ray).applyMatrix4(n),null===y.boundingBox||r.intersectsBox(y.boundingBox)!==!1))){var w,_;if(y&&y.isBufferGeometry){var S,A,M,P=y.index,C=y.attributes,T=C.position.array;if(void 0!==C.uv&&(w=C.uv.array),null!==P)for(var E=P.array,I=0,L=E.length;I<L;I+=3)S=E[I],A=E[I+1],M=E[I+2],_=i(this,m,r,T,w,S,A,M),_&&(_.faceIndex=Math.floor(I/3),v.push(_));else for(var I=0,L=T.length;I<L;I+=9)S=I/3,A=S+1,M=S+2,_=i(this,m,r,T,w,S,A,M),_&&(_.index=S,v.push(_))}else if(y&&y.isGeometry){var R,O,D,N=b&&b.isMultiMaterial,k=N===!0?b.materials:null,F=y.vertices,z=y.faces,B=y.faceVertexUvs[0];B.length>0&&(w=B);for(var U=0,j=z.length;U<j;U++){var $=z[U],V=N===!0?k[$.materialIndex]:b;if(void 0!==V){if(R=F[$.a],O=F[$.b],D=F[$.c],V.morphTargets===!0){var G=y.morphTargets,H=this.morphTargetInfluences;a.set(0,0,0),s.set(0,0,0),c.set(0,0,0);for(var W=0,X=G.length;W<X;W++){var q=H[W];if(0!==q){var Y=G[W].vertices;a.addScaledVector(u.subVectors(Y[$.a],R),q),s.addScaledVector(h.subVectors(Y[$.b],O),q),c.addScaledVector(l.subVectors(Y[$.c],D),q)}}a.add(R),s.add(O),c.add(D),R=a,O=s,D=c}if(_=e(this,m,r,R,O,D,g)){if(w){var Z=w[U];d.copy(Z[0]),f.copy(Z[1]),p.copy(Z[2]),_.uv=t(g,R,O,D,d,f,p)}_.face=$,_.faceIndex=U,v.push(_)}}}}}}}(),clone:function(){return new this.constructor(this.geometry,this.material).copy(this)}}),Me.prototype=Object.create(ue.prototype),Me.prototype.constructor=Me,Pe.prototype=Object.create(re.prototype),Pe.prototype.constructor=Pe,Pe.prototype.isCamera=!0,Pe.prototype.getWorldDirection=function(){var t=new D;return function(e){var i=e||new N;return this.getWorldQuaternion(t),i.set(0,0,-1).applyQuaternion(t)}}(),Pe.prototype.lookAt=function(){var t=new O;return function(e){t.lookAt(this.position,e,this.up),this.quaternion.setFromRotationMatrix(t)}}(),Pe.prototype.clone=function(){return(new this.constructor).copy(this)},Pe.prototype.copy=function(t){return re.prototype.copy.call(this,t),this.matrixWorldInverse.copy(t.matrixWorldInverse),this.projectionMatrix.copy(t.projectionMatrix),this},Ce.prototype=Object.assign(Object.create(Pe.prototype),{constructor:Ce,isPerspectiveCamera:!0,copy:function(t){return Pe.prototype.copy.call(this,t),this.fov=t.fov,this.zoom=t.zoom,this.near=t.near,this.far=t.far,this.focus=t.focus,this.aspect=t.aspect,this.view=null===t.view?null:Object.assign({},t.view),this.filmGauge=t.filmGauge,this.filmOffset=t.filmOffset,this},setFocalLength:function(t){var e=.5*this.getFilmHeight()/t;this.fov=2*Ed.RAD2DEG*Math.atan(e),this.updateProjectionMatrix()},getFocalLength:function(){var t=Math.tan(.5*Ed.DEG2RAD*this.fov);return.5*this.getFilmHeight()/t},getEffectiveFOV:function(){return 2*Ed.RAD2DEG*Math.atan(Math.tan(.5*Ed.DEG2RAD*this.fov)/this.zoom)},getFilmWidth:function(){return this.filmGauge*Math.min(this.aspect,1)},getFilmHeight:function(){return this.filmGauge/Math.max(this.aspect,1)},setViewOffset:function(t,e,i,n,r,o){this.aspect=t/e,this.view={fullWidth:t,fullHeight:e,offsetX:i,offsetY:n,width:r,height:o},this.updateProjectionMatrix()},clearViewOffset:function(){this.view=null,this.updateProjectionMatrix()},updateProjectionMatrix:function(){var t=this.near,e=t*Math.tan(.5*Ed.DEG2RAD*this.fov)/this.zoom,i=2*e,n=this.aspect*i,r=-.5*n,o=this.view;if(null!==o){var a=o.fullWidth,s=o.fullHeight;r+=o.offsetX*n/a,e-=o.offsetY*i/s,n*=o.width/a,i*=o.height/s}var c=this.filmOffset;0!==c&&(r+=t*c/this.getFilmWidth()),this.projectionMatrix.makeFrustum(r,r+n,e-i,e,t,this.far)},toJSON:function(t){var e=re.prototype.toJSON.call(this,t);return e.object.fov=this.fov,e.object.zoom=this.zoom,e.object.near=this.near,e.object.far=this.far,e.object.focus=this.focus,e.object.aspect=this.aspect,null!==this.view&&(e.object.view=Object.assign({},this.view)),e.object.filmGauge=this.filmGauge,e.object.filmOffset=this.filmOffset,e}}),Te.prototype=Object.assign(Object.create(Pe.prototype),{constructor:Te,isOrthographicCamera:!0,copy:function(t){return Pe.prototype.copy.call(this,t),this.left=t.left,this.right=t.right,this.top=t.top,this.bottom=t.bottom,this.near=t.near,this.far=t.far,this.zoom=t.zoom,this.view=null===t.view?null:Object.assign({},t.view),this},setViewOffset:function(t,e,i,n,r,o){this.view={fullWidth:t,fullHeight:e,offsetX:i,offsetY:n,width:r,height:o},this.updateProjectionMatrix()},clearViewOffset:function(){this.view=null,this.updateProjectionMatrix()},updateProjectionMatrix:function(){var t=(this.right-this.left)/(2*this.zoom),e=(this.top-this.bottom)/(2*this.zoom),i=(this.right+this.left)/2,n=(this.top+this.bottom)/2,r=i-t,o=i+t,a=n+e,s=n-e;if(null!==this.view){var c=this.zoom/(this.view.width/this.view.fullWidth),u=this.zoom/(this.view.height/this.view.fullHeight),h=(this.right-this.left)/this.view.width,l=(this.top-this.bottom)/this.view.height;r+=h*(this.view.offsetX/c),o=r+h*(this.view.width/c),a-=l*(this.view.offsetY/u),s=a-l*(this.view.height/u)}this.projectionMatrix.makeOrthographic(r,o,a,s,this.near,this.far)},toJSON:function(t){var e=re.prototype.toJSON.call(this,t);return e.object.zoom=this.zoom,e.object.left=this.left,e.object.right=this.right,e.object.top=this.top,e.object.bottom=this.bottom,e.object.near=this.near,e.object.far=this.far,null!==this.view&&(e.object.view=Object.assign({},this.view)),e}}),Ie.prototype.isFogExp2=!0,Ie.prototype.clone=function(){return new Ie(this.color.getHex(),this.density)},Ie.prototype.toJSON=function(t){return{type:"FogExp2",color:this.color.getHex(),density:this.density}},Le.prototype.isFog=!0,Le.prototype.clone=function(){return new Le(this.color.getHex(),this.near,this.far)},Le.prototype.toJSON=function(t){return{type:"Fog",color:this.color.getHex(),near:this.near,far:this.far}},Re.prototype=Object.create(re.prototype),Re.prototype.constructor=Re,Re.prototype.copy=function(t,e){return re.prototype.copy.call(this,t,e),null!==t.background&&(this.background=t.background.clone()),null!==t.fog&&(this.fog=t.fog.clone()),null!==t.overrideMaterial&&(this.overrideMaterial=t.overrideMaterial.clone()),this.autoUpdate=t.autoUpdate,this.matrixAutoUpdate=t.matrixAutoUpdate,this},Re.prototype.toJSON=function(t){var e=re.prototype.toJSON.call(this,t);return null!==this.background&&(e.object.background=this.background.toJSON(t)),null!==this.fog&&(e.object.fog=this.fog.toJSON()),e},Oe.prototype=Object.assign(Object.create(re.prototype),{constructor:Oe,isLensFlare:!0,copy:function(t){re.prototype.copy.call(this,t),this.positionScreen.copy(t.positionScreen),this.customUpdateCallback=t.customUpdateCallback;for(var e=0,i=t.lensFlares.length;e<i;e++)this.lensFlares.push(t.lensFlares[e]);return this},add:function(t,e,i,n,r,o){void 0===e&&(e=-1),void 0===i&&(i=0),void 0===o&&(o=1),void 0===r&&(r=new Ct(16777215)),void 0===n&&(n=Dh),i=Math.min(i,Math.max(0,i)),this.lensFlares.push({texture:t,size:e,distance:i,x:0,y:0,z:0,scale:1,rotation:0,opacity:o,color:r,blending:n})},updateLensFlares:function(){var t,e,i=this.lensFlares.length,n=2*-this.positionScreen.x,r=2*-this.positionScreen.y;for(t=0;t<i;t++)e=this.lensFlares[t],e.x=this.positionScreen.x+n*e.distance,e.y=this.positionScreen.y+r*e.distance,e.wantedRotation=e.x*Math.PI*.25,e.rotation+=.25*(e.wantedRotation-e.rotation)}}),De.prototype=Object.create(At.prototype),De.prototype.constructor=De,De.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.color.copy(t.color),this.map=t.map,this.rotation=t.rotation,this},Ne.prototype=Object.assign(Object.create(re.prototype),{constructor:Ne,isSprite:!0,raycast:function(){var t=new N;return function(e,i){t.setFromMatrixPosition(this.matrixWorld);var n=e.ray.distanceSqToPoint(t),r=this.scale.x*this.scale.y/4;n>r||i.push({distance:Math.sqrt(n),point:this.position,face:null,object:this})}}(),clone:function(){return new this.constructor(this.material).copy(this)}}),ke.prototype=Object.assign(Object.create(re.prototype),{constructor:ke,copy:function(t){re.prototype.copy.call(this,t,!1);for(var e=t.levels,i=0,n=e.length;i<n;i++){var r=e[i];this.addLevel(r.object.clone(),r.distance)}return this},addLevel:function(t,e){void 0===e&&(e=0),e=Math.abs(e);for(var i=this.levels,n=0;n<i.length&&!(e<i[n].distance);n++);i.splice(n,0,{distance:e,object:t}),this.add(t)},getObjectForDistance:function(t){for(var e=this.levels,i=1,n=e.length;i<n&&!(t<e[i].distance);i++);return e[i-1].object},raycast:function(){var t=new N;return function(e,i){t.setFromMatrixPosition(this.matrixWorld);var n=e.ray.origin.distanceTo(t);this.getObjectForDistance(n).raycast(e,i)}}(),update:function(){var t=new N,e=new N;return function(i){var n=this.levels;if(n.length>1){t.setFromMatrixPosition(i.matrixWorld),e.setFromMatrixPosition(this.matrixWorld);var r=t.distanceTo(e);n[0].object.visible=!0;for(var o=1,a=n.length;o<a&&r>=n[o].distance;o++)n[o-1].object.visible=!1,n[o].object.visible=!0;for(;o<a;o++)n[o].object.visible=!1}}}(),toJSON:function(t){var e=re.prototype.toJSON.call(this,t);e.object.levels=[];for(var i=this.levels,n=0,r=i.length;n<r;n++){var o=i[n];e.object.levels.push({object:o.object.uuid,distance:o.distance})}return e}}),Fe.prototype=Object.create(L.prototype),Fe.prototype.constructor=Fe,Fe.prototype.isDataTexture=!0,Object.assign(ze.prototype,{calculateInverses:function(){this.boneInverses=[];for(var t=0,e=this.bones.length;t<e;t++){var i=new O;this.bones[t]&&i.getInverse(this.bones[t].matrixWorld),this.boneInverses.push(i)}},pose:function(){for(var t,e=0,i=this.bones.length;e<i;e++)t=this.bones[e],t&&t.matrixWorld.getInverse(this.boneInverses[e]);for(var e=0,i=this.bones.length;e<i;e++)t=this.bones[e],t&&(t.parent&&t.parent.isBone?(t.matrix.getInverse(t.parent.matrixWorld),t.matrix.multiply(t.matrixWorld)):t.matrix.copy(t.matrixWorld),t.matrix.decompose(t.position,t.quaternion,t.scale))},update:function(){var t=new O;return function(){for(var e=0,i=this.bones.length;e<i;e++){var n=this.bones[e]?this.bones[e].matrixWorld:this.identityMatrix;t.multiplyMatrices(n,this.boneInverses[e]),t.toArray(this.boneMatrices,16*e)}this.useVertexTexture&&(this.boneTexture.needsUpdate=!0)}}(),clone:function(){return new ze(this.bones,this.boneInverses,this.useVertexTexture)}}),Be.prototype=Object.assign(Object.create(re.prototype),{constructor:Be,isBone:!0,copy:function(t){return re.prototype.copy.call(this,t),this.skin=t.skin,this}}),Ue.prototype=Object.assign(Object.create(Ae.prototype),{constructor:Ue,isSkinnedMesh:!0,bind:function(t,e){this.skeleton=t,void 0===e&&(this.updateMatrixWorld(!0),this.skeleton.calculateInverses(),e=this.matrixWorld),this.bindMatrix.copy(e),this.bindMatrixInverse.getInverse(e)},pose:function(){this.skeleton.pose()},normalizeSkinWeights:function(){if(this.geometry&&this.geometry.isGeometry)for(var t=0;t<this.geometry.skinWeights.length;t++){var e=this.geometry.skinWeights[t],i=1/e.lengthManhattan();i!==1/0?e.multiplyScalar(i):e.set(1,0,0,0)}else if(this.geometry&&this.geometry.isBufferGeometry)for(var n=new wt,r=this.geometry.attributes.skinWeight,t=0;t<r.count;t++){n.x=r.getX(t),n.y=r.getY(t),n.z=r.getZ(t),n.w=r.getW(t);var i=1/n.lengthManhattan();i!==1/0?n.multiplyScalar(i):n.set(1,0,0,0),r.setXYZW(t,n.x,n.y,n.z,n.w)}},updateMatrixWorld:function(t){Ae.prototype.updateMatrixWorld.call(this,!0),"attached"===this.bindMode?this.bindMatrixInverse.getInverse(this.matrixWorld):"detached"===this.bindMode?this.bindMatrixInverse.getInverse(this.bindMatrix):console.warn("THREE.SkinnedMesh unrecognized bindMode: "+this.bindMode)},clone:function(){return new this.constructor(this.geometry,this.material,this.skeleton.useVertexTexture).copy(this)}}),je.prototype=Object.create(At.prototype),je.prototype.constructor=je,je.prototype.isLineBasicMaterial=!0,je.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.color.copy(t.color),this.linewidth=t.linewidth,this.linecap=t.linecap,this.linejoin=t.linejoin,this},$e.prototype=Object.assign(Object.create(re.prototype),{constructor:$e,isLine:!0,raycast:function(){var t=new O,e=new xe,i=new It;return function(n,r){var o=n.linePrecision,a=o*o,s=this.geometry,c=this.matrixWorld;if(null===s.boundingSphere&&s.computeBoundingSphere(),i.copy(s.boundingSphere),i.applyMatrix4(c),n.ray.intersectsSphere(i)!==!1){t.getInverse(c),e.copy(n.ray).applyMatrix4(t);var u=new N,h=new N,l=new N,d=new N,f=this&&this.isLineSegments?2:1;if(s&&s.isBufferGeometry){var p=s.index,m=s.attributes,g=m.position.array;if(null!==p)for(var v=p.array,y=0,b=v.length-1;y<b;y+=f){var x=v[y],w=v[y+1];u.fromArray(g,3*x),h.fromArray(g,3*w);var _=e.distanceSqToSegment(u,h,d,l);if(!(_>a)){d.applyMatrix4(this.matrixWorld);var S=n.ray.origin.distanceTo(d);S<n.near||S>n.far||r.push({distance:S,point:l.clone().applyMatrix4(this.matrixWorld),index:y,face:null,faceIndex:null,object:this})}}else for(var y=0,b=g.length/3-1;y<b;y+=f){u.fromArray(g,3*y),h.fromArray(g,3*y+3);var _=e.distanceSqToSegment(u,h,d,l);if(!(_>a)){d.applyMatrix4(this.matrixWorld);var S=n.ray.origin.distanceTo(d);S<n.near||S>n.far||r.push({distance:S,point:l.clone().applyMatrix4(this.matrixWorld),index:y,face:null,faceIndex:null,object:this})}}}else if(s&&s.isGeometry)for(var A=s.vertices,M=A.length,y=0;y<M-1;y+=f){var _=e.distanceSqToSegment(A[y],A[y+1],d,l);if(!(_>a)){d.applyMatrix4(this.matrixWorld);var S=n.ray.origin.distanceTo(d);S<n.near||S>n.far||r.push({distance:S,point:l.clone().applyMatrix4(this.matrixWorld),index:y,face:null,faceIndex:null,object:this})}}}}}(),clone:function(){return new this.constructor(this.geometry,this.material).copy(this)}}),Ve.prototype=Object.assign(Object.create($e.prototype),{constructor:Ve,isLineSegments:!0}),Ge.prototype=Object.create(At.prototype),Ge.prototype.constructor=Ge,Ge.prototype.isPointsMaterial=!0,Ge.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.color.copy(t.color),this.map=t.map,this.size=t.size,this.sizeAttenuation=t.sizeAttenuation,this},He.prototype=Object.assign(Object.create(re.prototype),{constructor:He,isPoints:!0,raycast:function(){var t=new O,e=new xe,i=new It;return function(n,r){function o(t,i){var o=e.distanceSqToPoint(t);if(o<l){var s=e.closestPointToPoint(t);s.applyMatrix4(c);var u=n.ray.origin.distanceTo(s);if(u<n.near||u>n.far)return;r.push({distance:u,distanceToRay:Math.sqrt(o),point:s.clone(),index:i,face:null,object:a})}}var a=this,s=this.geometry,c=this.matrixWorld,u=n.params.Points.threshold;if(null===s.boundingSphere&&s.computeBoundingSphere(),i.copy(s.boundingSphere),i.applyMatrix4(c),n.ray.intersectsSphere(i)!==!1){t.getInverse(c),e.copy(n.ray).applyMatrix4(t);var h=u/((this.scale.x+this.scale.y+this.scale.z)/3),l=h*h,d=new N;if(s&&s.isBufferGeometry){var f=s.index,p=s.attributes,m=p.position.array;if(null!==f)for(var g=f.array,v=0,y=g.length;v<y;v++){var b=g[v];d.fromArray(m,3*b),o(d,b)}else for(var v=0,x=m.length/3;v<x;v++)d.fromArray(m,3*v),o(d,v)}else for(var w=s.vertices,v=0,x=w.length;v<x;v++)o(w[v],v)}}}(),clone:function(){return new this.constructor(this.geometry,this.material).copy(this)}}),We.prototype=Object.assign(Object.create(re.prototype),{constructor:We}),Xe.prototype=Object.create(L.prototype),Xe.prototype.constructor=Xe,Xe.prototype.isCompressedTexture=!0,qe.prototype=Object.create(L.prototype),qe.prototype.constructor=qe,Ye.prototype=Object.create(At.prototype),Ye.prototype.constructor=Ye,Ye.prototype.isMeshStandardMaterial=!0,Ye.prototype.copy=function(t){return At.prototype.copy.call(this,t),this.defines={STANDARD:""},this.color.copy(t.color),this.roughness=t.roughness,this.metalness=t.metalness,this.map=t.map,this.lightMap=t.lightMap,this.lightMapIntensity=t.lightMapIntensity,this.aoMap=t.aoMap,this.aoMapIntensity=t.aoMapIntensity,this.emissive.copy(t.emissive),this.emissiveMap=t.emissiveMap,this.emissiveIntensity=t.emissiveIntensity,this.bumpMap=t.bumpMap,this.bumpScale=t.bumpScale,this.normalMap=t.normalMap,this.normalScale.copy(t.normalScale),this.displacementMap=t.displacementMap,this.displacementScale=t.displacementScale,this.displacementBias=t.displacementBias,this.roughnessMap=t.roughnessMap,this.metalnessMap=t.metalnessMap,this.alphaMap=t.alphaMap,this.envMap=t.envMap,this.envMapIntensity=t.envMapIntensity,this.refractionRatio=t.refractionRatio,this.wireframe=t.wireframe,this.wireframeLinewidth=t.wireframeLinewidth,this.wireframeLinecap=t.wireframeLinecap,this.wireframeLinejoin=t.wireframeLinejoin,this.skinning=t.skinning,this.morphTargets=t.morphTargets,this.morphNormals=t.morphNormals,this};var Vp={enabled:!1,files:{},add:function(t,e){this.enabled!==!1&&(this.files[t]=e)},get:function(t){if(this.enabled!==!1)return this.files[t]},remove:function(t){delete this.files[t]},clear:function(){this.files={}}},Gp=new Ze;Object.assign(Ke.prototype,{load:function(t,e,i,n){void 0!==this.path&&(t=this.path+t);var r=this,o=Vp.get(t);if(void 0!==o)return r.manager.itemStart(t),setTimeout(function(){e&&e(o),r.manager.itemEnd(t)},0),o;var a=new XMLHttpRequest;return a.open("GET",t,!0),a.addEventListener("load",function(i){var o=i.target.response;Vp.add(t,o),200===this.status?(e&&e(o),r.manager.itemEnd(t)):0===this.status?(console.warn("THREE.XHRLoader: HTTP Status 0 received."),e&&e(o),r.manager.itemEnd(t)):(n&&n(i),r.manager.itemError(t))},!1),void 0!==i&&a.addEventListener("progress",function(t){i(t)},!1),a.addEventListener("error",function(e){n&&n(e),r.manager.itemError(t)},!1),void 0!==this.responseType&&(a.responseType=this.responseType),void 0!==this.withCredentials&&(a.withCredentials=this.withCredentials),a.overrideMimeType&&a.overrideMimeType("text/plain"),a.send(null),r.manager.itemStart(t),a},setPath:function(t){return this.path=t,this},setResponseType:function(t){return this.responseType=t,this},setWithCredentials:function(t){return this.withCredentials=t,this}}),Object.assign(Qe.prototype,{load:function(t,e,i,n){function r(r){c.load(t[r],function(t){var i=o._parser(t,!0);a[r]={width:i.width,height:i.height,format:i.format,mipmaps:i.mipmaps},u+=1,6===u&&(1===i.mipmapCount&&(s.minFilter=Ll),s.format=i.format,s.needsUpdate=!0,e&&e(s))},i,n)}var o=this,a=[],s=new Xe;s.image=a;var c=new Ke(this.manager);if(c.setPath(this.path),c.setResponseType("arraybuffer"),Array.isArray(t))for(var u=0,h=0,l=t.length;h<l;++h)r(h);else c.load(t,function(t){var i=o._parser(t,!0);if(i.isCubemap)for(var n=i.mipmaps.length/i.mipmapCount,r=0;r<n;r++){a[r]={mipmaps:[]};for(var c=0;c<i.mipmapCount;c++)a[r].mipmaps.push(i.mipmaps[r*i.mipmapCount+c]),a[r].format=i.format,a[r].width=i.width,a[r].height=i.height}else s.image.width=i.width,s.image.height=i.height,s.mipmaps=i.mipmaps;1===i.mipmapCount&&(s.minFilter=Ll),s.format=i.format,s.needsUpdate=!0,e&&e(s)},i,n);return s},setPath:function(t){return this.path=t,this}}),Object.assign(Je.prototype,{load:function(t,e,i,n){var r=this,o=new Fe,a=new Ke(this.manager);return a.setResponseType("arraybuffer"),a.load(t,function(t){var i=r._parser(t);i&&(void 0!==i.image?o.image=i.image:void 0!==i.data&&(o.image.width=i.width,o.image.height=i.height,o.image.data=i.data),o.wrapS=void 0!==i.wrapS?i.wrapS:Pl,o.wrapT=void 0!==i.wrapT?i.wrapT:Pl,o.magFilter=void 0!==i.magFilter?i.magFilter:Ll,o.minFilter=void 0!==i.minFilter?i.minFilter:Ol,o.anisotropy=void 0!==i.anisotropy?i.anisotropy:1,void 0!==i.format&&(o.format=i.format),void 0!==i.type&&(o.type=i.type),void 0!==i.mipmaps&&(o.mipmaps=i.mipmaps),1===i.mipmapCount&&(o.minFilter=Ll),o.needsUpdate=!0,e&&e(o,i))},i,n),o}}),Object.assign(ti.prototype,{load:function(t,e,i,n){var r=this,o=document.createElementNS("http://www.w3.org/1999/xhtml","img");if(o.onload=function(){URL.revokeObjectURL(o.src),e&&e(o),r.manager.itemEnd(t)},0===t.indexOf("data:"))o.src=t;else{var a=new Ke;a.setPath(this.path),a.setResponseType("blob"),a.setWithCredentials(this.withCredentials),a.load(t,function(t){o.src=URL.createObjectURL(t)},i,n)}return r.manager.itemStart(t),o},setCrossOrigin:function(t){return this.crossOrigin=t,this},setWithCredentials:function(t){return this.withCredentials=t,this},setPath:function(t){return this.path=t,this}}),Object.assign(ei.prototype,{load:function(t,e,i,n){function r(i){a.load(t[i],function(t){o.images[i]=t,s++,6===s&&(o.needsUpdate=!0,e&&e(o))},void 0,n)}var o=new B,a=new ti(this.manager);a.setCrossOrigin(this.crossOrigin),a.setPath(this.path);for(var s=0,c=0;c<t.length;++c)r(c);return o},setCrossOrigin:function(t){return this.crossOrigin=t,this},setPath:function(t){return this.path=t,this}}),Object.assign(ii.prototype,{load:function(t,e,i,n){var r=new L,o=new ti(this.manager);return o.setCrossOrigin(this.crossOrigin),o.setWithCredentials(this.withCredentials),o.setPath(this.path),o.load(t,function(i){var n=t.search(/\.(jpg|jpeg)$/)>0||0===t.search(/^data\:image\/jpeg/);r.format=n?Xl:ql,r.image=i,r.needsUpdate=!0,void 0!==e&&e(r)},i,n),r},setCrossOrigin:function(t){return this.crossOrigin=t,this},setWithCredentials:function(t){return this.withCredentials=t,this},setPath:function(t){return this.path=t,this}}),ni.prototype=Object.assign(Object.create(re.prototype),{constructor:ni,isLight:!0,copy:function(t){return re.prototype.copy.call(this,t),this.color.copy(t.color),this.intensity=t.intensity,this},toJSON:function(t){var e=re.prototype.toJSON.call(this,t);return e.object.color=this.color.getHex(),e.object.intensity=this.intensity,void 0!==this.groundColor&&(e.object.groundColor=this.groundColor.getHex()),void 0!==this.distance&&(e.object.distance=this.distance),void 0!==this.angle&&(e.object.angle=this.angle),void 0!==this.decay&&(e.object.decay=this.decay),void 0!==this.penumbra&&(e.object.penumbra=this.penumbra),void 0!==this.shadow&&(e.object.shadow=this.shadow.toJSON()),e}}),ri.prototype=Object.assign(Object.create(ni.prototype),{constructor:ri,isHemisphereLight:!0,copy:function(t){return ni.prototype.copy.call(this,t),this.groundColor.copy(t.groundColor),this}}),Object.assign(oi.prototype,{copy:function(t){return this.camera=t.camera.clone(),this.bias=t.bias,this.radius=t.radius,this.mapSize.copy(t.mapSize),this},clone:function(){return(new this.constructor).copy(this)},toJSON:function(){var t={};return 0!==this.bias&&(t.bias=this.bias),1!==this.radius&&(t.radius=this.radius),512===this.mapSize.x&&512===this.mapSize.y||(t.mapSize=this.mapSize.toArray()),t.camera=this.camera.toJSON(!1).object,delete t.camera.matrix,t}}),ai.prototype=Object.assign(Object.create(oi.prototype),{constructor:ai,isSpotLightShadow:!0,update:function(t){var e=2*Ed.RAD2DEG*t.angle,i=this.mapSize.width/this.mapSize.height,n=t.distance||500,r=this.camera;e===r.fov&&i===r.aspect&&n===r.far||(r.fov=e,r.aspect=i,r.far=n,r.updateProjectionMatrix())}}),si.prototype=Object.assign(Object.create(ni.prototype),{constructor:si,isSpotLight:!0,copy:function(t){return ni.prototype.copy.call(this,t),this.distance=t.distance,this.angle=t.angle,this.penumbra=t.penumbra,this.decay=t.decay,this.target=t.target.clone(),this.shadow=t.shadow.clone(),this}}),ci.prototype=Object.assign(Object.create(ni.prototype),{constructor:ci,isPointLight:!0,copy:function(t){return ni.prototype.copy.call(this,t),this.distance=t.distance,this.decay=t.decay,this.shadow=t.shadow.clone(),this}}),ui.prototype=Object.assign(Object.create(oi.prototype),{constructor:ui}),hi.prototype=Object.assign(Object.create(ni.prototype),{constructor:hi,isDirectionalLight:!0,copy:function(t){return ni.prototype.copy.call(this,t),this.target=t.target.clone(),this.shadow=t.shadow.clone(),this}}),li.prototype=Object.assign(Object.create(ni.prototype),{constructor:li,isAmbientLight:!0});var Hp={arraySlice:function(t,e,i){return Hp.isTypedArray(t)?new t.constructor(t.subarray(e,i)):t.slice(e,i)},convertArray:function(t,e,i){return!t||!i&&t.constructor===e?t:"number"==typeof e.BYTES_PER_ELEMENT?new e(t):Array.prototype.slice.call(t)},isTypedArray:function(t){return ArrayBuffer.isView(t)&&!(t instanceof DataView)},getKeyframeOrder:function(t){function e(e,i){return t[e]-t[i]}for(var i=t.length,n=new Array(i),r=0;r!==i;++r)n[r]=r;return n.sort(e),n},sortedArray:function(t,e,i){for(var n=t.length,r=new t.constructor(n),o=0,a=0;a!==n;++o)for(var s=i[o]*e,c=0;c!==e;++c)r[a++]=t[s+c];return r},flattenJSON:function(t,e,i,n){for(var r=1,o=t[0];void 0!==o&&void 0===o[n];)o=t[r++];if(void 0!==o){var a=o[n];if(void 0!==a)if(Array.isArray(a)){do a=o[n],void 0!==a&&(e.push(o.time),i.push.apply(i,a)),o=t[r++];while(void 0!==o)}else if(void 0!==a.toArray){do a=o[n],void 0!==a&&(e.push(o.time),a.toArray(i,i.length)),o=t[r++];while(void 0!==o)}else do a=o[n],void 0!==a&&(e.push(o.time),i.push(a)),o=t[r++];while(void 0!==o)}}};di.prototype={constructor:di,evaluate:function(t){var e=this.parameterPositions,i=this._cachedIndex,n=e[i],r=e[i-1];t:{e:{var o;i:{n:if(!(t<n)){for(var a=i+2;;){if(void 0===n){if(t<r)break n;return i=e.length,this._cachedIndex=i,this.afterEnd_(i-1,t,r)}if(i===a)break;if(r=n,n=e[++i],t<n)break e}o=e.length;break i}{if(t>=r)break t;var s=e[1];t<s&&(i=2,r=s);for(var a=i-2;;){if(void 0===r)return this._cachedIndex=0,this.beforeStart_(0,t,n);if(i===a)break;if(n=r,r=e[--i-1],t>=r)break e}o=i,i=0}}for(;i<o;){var c=i+o>>>1;t<e[c]?o=c:i=c+1}if(n=e[i],r=e[i-1],void 0===r)return this._cachedIndex=0,this.beforeStart_(0,t,n);if(void 0===n)return i=e.length,this._cachedIndex=i,this.afterEnd_(i-1,r,t)}this._cachedIndex=i,this.intervalChanged_(i,r,n)}return this.interpolate_(i,r,t,n)},settings:null,DefaultSettings_:{},getSettings_:function(){return this.settings||this.DefaultSettings_},copySampleValue_:function(t){for(var e=this.resultBuffer,i=this.sampleValues,n=this.valueSize,r=t*n,o=0;o!==n;++o)e[o]=i[r+o];return e},interpolate_:function(t,e,i,n){throw new Error("call to abstract method")},intervalChanged_:function(t,e,i){}},Object.assign(di.prototype,{beforeStart_:di.prototype.copySampleValue_,afterEnd_:di.prototype.copySampleValue_}),fi.prototype=Object.assign(Object.create(di.prototype),{constructor:fi,
-DefaultSettings_:{endingStart:pd,endingEnd:pd},intervalChanged_:function(t,e,i){var n=this.parameterPositions,r=t-2,o=t+1,a=n[r],s=n[o];if(void 0===a)switch(this.getSettings_().endingStart){case md:r=t,a=2*e-i;break;case gd:r=n.length-2,a=e+n[r]-n[r+1];break;default:r=t,a=i}if(void 0===s)switch(this.getSettings_().endingEnd){case md:o=t,s=2*i-e;break;case gd:o=1,s=i+n[1]-n[0];break;default:o=t-1,s=e}var c=.5*(i-e),u=this.valueSize;this._weightPrev=c/(e-a),this._weightNext=c/(s-i),this._offsetPrev=r*u,this._offsetNext=o*u},interpolate_:function(t,e,i,n){for(var r=this.resultBuffer,o=this.sampleValues,a=this.valueSize,s=t*a,c=s-a,u=this._offsetPrev,h=this._offsetNext,l=this._weightPrev,d=this._weightNext,f=(i-e)/(n-e),p=f*f,m=p*f,g=-l*m+2*l*p-l*f,v=(1+l)*m+(-1.5-2*l)*p+(-.5+l)*f+1,y=(-1-d)*m+(1.5+d)*p+.5*f,b=d*m-d*p,x=0;x!==a;++x)r[x]=g*o[u+x]+v*o[c+x]+y*o[s+x]+b*o[h+x];return r}}),pi.prototype=Object.assign(Object.create(di.prototype),{constructor:pi,interpolate_:function(t,e,i,n){for(var r=this.resultBuffer,o=this.sampleValues,a=this.valueSize,s=t*a,c=s-a,u=(i-e)/(n-e),h=1-u,l=0;l!==a;++l)r[l]=o[c+l]*h+o[s+l]*u;return r}}),mi.prototype=Object.assign(Object.create(di.prototype),{constructor:mi,interpolate_:function(t,e,i,n){return this.copySampleValue_(t-1)}});var Wp;Wp={TimeBufferType:Float32Array,ValueBufferType:Float32Array,DefaultInterpolation:dd,InterpolantFactoryMethodDiscrete:function(t){return new mi(this.times,this.values,this.getValueSize(),t)},InterpolantFactoryMethodLinear:function(t){return new pi(this.times,this.values,this.getValueSize(),t)},InterpolantFactoryMethodSmooth:function(t){return new fi(this.times,this.values,this.getValueSize(),t)},setInterpolation:function(t){var e;switch(t){case ld:e=this.InterpolantFactoryMethodDiscrete;break;case dd:e=this.InterpolantFactoryMethodLinear;break;case fd:e=this.InterpolantFactoryMethodSmooth}if(void 0===e){var i="unsupported interpolation for "+this.ValueTypeName+" keyframe track named "+this.name;if(void 0===this.createInterpolant){if(t===this.DefaultInterpolation)throw new Error(i);this.setInterpolation(this.DefaultInterpolation)}return void console.warn(i)}this.createInterpolant=e},getInterpolation:function(){switch(this.createInterpolant){case this.InterpolantFactoryMethodDiscrete:return ld;case this.InterpolantFactoryMethodLinear:return dd;case this.InterpolantFactoryMethodSmooth:return fd}},getValueSize:function(){return this.values.length/this.times.length},shift:function(t){if(0!==t)for(var e=this.times,i=0,n=e.length;i!==n;++i)e[i]+=t;return this},scale:function(t){if(1!==t)for(var e=this.times,i=0,n=e.length;i!==n;++i)e[i]*=t;return this},trim:function(t,e){for(var i=this.times,n=i.length,r=0,o=n-1;r!==n&&i[r]<t;)++r;for(;o!==-1&&i[o]>e;)--o;if(++o,0!==r||o!==n){r>=o&&(o=Math.max(o,1),r=o-1);var a=this.getValueSize();this.times=Hp.arraySlice(i,r,o),this.values=Hp.arraySlice(this.values,r*a,o*a)}return this},validate:function(){var t=!0,e=this.getValueSize();e-Math.floor(e)!==0&&(console.error("invalid value size in track",this),t=!1);var i=this.times,n=this.values,r=i.length;0===r&&(console.error("track is empty",this),t=!1);for(var o=null,a=0;a!==r;a++){var s=i[a];if("number"==typeof s&&isNaN(s)){console.error("time is not a valid number",this,a,s),t=!1;break}if(null!==o&&o>s){console.error("out of order keys",this,a,s,o),t=!1;break}o=s}if(void 0!==n&&Hp.isTypedArray(n))for(var a=0,c=n.length;a!==c;++a){var u=n[a];if(isNaN(u)){console.error("value is not a valid number",this,a,u),t=!1;break}}return t},optimize:function(){for(var t=this.times,e=this.values,i=this.getValueSize(),n=1,r=1,o=t.length-1;r<=o;++r){var a=!1,s=t[r],c=t[r+1];if(s!==c&&(1!==r||s!==s[0]))for(var u=r*i,h=u-i,l=u+i,d=0;d!==i;++d){var f=e[u+d];if(f!==e[h+d]||f!==e[l+d]){a=!0;break}}if(a){if(r!==n){t[n]=t[r];for(var p=r*i,m=n*i,d=0;d!==i;++d)e[m+d]=e[p+d]}++n}}return n!==t.length&&(this.times=Hp.arraySlice(t,0,n),this.values=Hp.arraySlice(e,0,n*i)),this}},vi.prototype=Object.assign(Object.create(Wp),{constructor:vi,ValueTypeName:"vector"}),yi.prototype=Object.assign(Object.create(di.prototype),{constructor:yi,interpolate_:function(t,e,i,n){for(var r=this.resultBuffer,o=this.sampleValues,a=this.valueSize,s=t*a,c=(i-e)/(n-e),u=s+a;s!==u;s+=4)D.slerpFlat(r,0,o,s-a,o,s,c);return r}}),bi.prototype=Object.assign(Object.create(Wp),{constructor:bi,ValueTypeName:"quaternion",DefaultInterpolation:dd,InterpolantFactoryMethodLinear:function(t){return new yi(this.times,this.values,this.getValueSize(),t)},InterpolantFactoryMethodSmooth:void 0}),xi.prototype=Object.assign(Object.create(Wp),{constructor:xi,ValueTypeName:"number"}),wi.prototype=Object.assign(Object.create(Wp),{constructor:wi,ValueTypeName:"string",ValueBufferType:Array,DefaultInterpolation:ld,InterpolantFactoryMethodLinear:void 0,InterpolantFactoryMethodSmooth:void 0}),_i.prototype=Object.assign(Object.create(Wp),{constructor:_i,ValueTypeName:"bool",ValueBufferType:Array,DefaultInterpolation:ld,InterpolantFactoryMethodLinear:void 0,InterpolantFactoryMethodSmooth:void 0}),Si.prototype=Object.assign(Object.create(Wp),{constructor:Si,ValueTypeName:"color"}),Ai.prototype=Wp,Wp.constructor=Ai,Object.assign(Ai,{parse:function(t){if(void 0===t.type)throw new Error("track type undefined, can not parse");var e=Ai._getTrackTypeForValueTypeName(t.type);if(void 0===t.times){var i=[],n=[];Hp.flattenJSON(t.keys,i,n,"value"),t.times=i,t.values=n}return void 0!==e.parse?e.parse(t):new e(t.name,t.times,t.values,t.interpolation)},toJSON:function(t){var e,i=t.constructor;if(void 0!==i.toJSON)e=i.toJSON(t);else{e={name:t.name,times:Hp.convertArray(t.times,Array),values:Hp.convertArray(t.values,Array)};var n=t.getInterpolation();n!==t.DefaultInterpolation&&(e.interpolation=n)}return e.type=t.ValueTypeName,e},_getTrackTypeForValueTypeName:function(t){switch(t.toLowerCase()){case"scalar":case"double":case"float":case"number":case"integer":return xi;case"vector":case"vector2":case"vector3":case"vector4":return vi;case"color":return Si;case"quaternion":return bi;case"bool":case"boolean":return _i;case"string":return wi}throw new Error("Unsupported typeName: "+t)}}),Mi.prototype={constructor:Mi,resetDuration:function(){for(var t=this.tracks,e=0,i=0,n=t.length;i!==n;++i){var r=this.tracks[i];e=Math.max(e,r.times[r.times.length-1])}this.duration=e},trim:function(){for(var t=0;t<this.tracks.length;t++)this.tracks[t].trim(0,this.duration);return this},optimize:function(){for(var t=0;t<this.tracks.length;t++)this.tracks[t].optimize();return this}},Object.assign(Mi,{parse:function(t){for(var e=[],i=t.tracks,n=1/(t.fps||1),r=0,o=i.length;r!==o;++r)e.push(Ai.parse(i[r]).scale(n));return new Mi(t.name,t.duration,e)},toJSON:function(t){for(var e=[],i=t.tracks,n={name:t.name,duration:t.duration,tracks:e},r=0,o=i.length;r!==o;++r)e.push(Ai.toJSON(i[r]));return n},CreateFromMorphTargetSequence:function(t,e,i,n){for(var r=e.length,o=[],a=0;a<r;a++){var s=[],c=[];s.push((a+r-1)%r,a,(a+1)%r),c.push(0,1,0);var u=Hp.getKeyframeOrder(s);s=Hp.sortedArray(s,1,u),c=Hp.sortedArray(c,1,u),n||0!==s[0]||(s.push(r),c.push(c[0])),o.push(new xi(".morphTargetInfluences["+e[a].name+"]",s,c).scale(1/i))}return new Mi(t,-1,o)},findByName:function(t,e){var i=t;if(!Array.isArray(t)){var n=t;i=n.geometry&&n.geometry.animations||n.animations}for(var r=0;r<i.length;r++)if(i[r].name===e)return i[r];return null},CreateClipsFromMorphTargetSequences:function(t,e,i){for(var n={},r=/^([\w-]*?)([\d]+)$/,o=0,a=t.length;o<a;o++){var s=t[o],c=s.name.match(r);if(c&&c.length>1){var u=c[1],h=n[u];h||(n[u]=h=[]),h.push(s)}}var l=[];for(var u in n)l.push(Mi.CreateFromMorphTargetSequence(u,n[u],e,i));return l},parseAnimation:function(t,e,i){if(!t)return console.error("  no animation in JSONLoader data"),null;for(var n=function(t,e,i,n,r){if(0!==i.length){var o=[],a=[];Hp.flattenJSON(i,o,a,n),0!==o.length&&r.push(new t(e,o,a))}},r=[],o=t.name||"default",a=t.length||-1,s=t.fps||30,c=t.hierarchy||[],u=0;u<c.length;u++){var h=c[u].keys;if(h&&0!==h.length)if(h[0].morphTargets){for(var l={},d=0;d<h.length;d++)if(h[d].morphTargets)for(var f=0;f<h[d].morphTargets.length;f++)l[h[d].morphTargets[f]]=-1;for(var p in l){for(var m=[],g=[],f=0;f!==h[d].morphTargets.length;++f){var v=h[d];m.push(v.time),g.push(v.morphTarget===p?1:0)}r.push(new xi(".morphTargetInfluence["+p+"]",m,g))}a=l.length*(s||1)}else{var y=".bones["+e[u].name+"]";n(vi,y+".position",h,"pos",r),n(bi,y+".quaternion",h,"rot",r),n(vi,y+".scale",h,"scl",r)}}if(0===r.length)return null;var b=new Mi(o,a,r);return b}}),Object.assign(Pi.prototype,{load:function(t,e,i,n){var r=this,o=new Ke(r.manager);o.load(t,function(t){e(r.parse(JSON.parse(t)))},i,n)},setTextures:function(t){this.textures=t},parse:function(t){function e(t){return void 0===i[t]&&console.warn("THREE.MaterialLoader: Undefined texture",t),i[t]}var i=this.textures,n=new THREE[t.type];if(void 0!==t.uuid&&(n.uuid=t.uuid),void 0!==t.name&&(n.name=t.name),void 0!==t.color&&n.color.setHex(t.color),void 0!==t.roughness&&(n.roughness=t.roughness),void 0!==t.metalness&&(n.metalness=t.metalness),void 0!==t.emissive&&n.emissive.setHex(t.emissive),void 0!==t.specular&&n.specular.setHex(t.specular),void 0!==t.shininess&&(n.shininess=t.shininess),void 0!==t.uniforms&&(n.uniforms=t.uniforms),void 0!==t.vertexShader&&(n.vertexShader=t.vertexShader),void 0!==t.fragmentShader&&(n.fragmentShader=t.fragmentShader),void 0!==t.vertexColors&&(n.vertexColors=t.vertexColors),void 0!==t.fog&&(n.fog=t.fog),void 0!==t.shading&&(n.shading=t.shading),void 0!==t.blending&&(n.blending=t.blending),void 0!==t.side&&(n.side=t.side),void 0!==t.opacity&&(n.opacity=t.opacity),void 0!==t.transparent&&(n.transparent=t.transparent),void 0!==t.alphaTest&&(n.alphaTest=t.alphaTest),void 0!==t.depthTest&&(n.depthTest=t.depthTest),void 0!==t.depthWrite&&(n.depthWrite=t.depthWrite),void 0!==t.colorWrite&&(n.colorWrite=t.colorWrite),void 0!==t.wireframe&&(n.wireframe=t.wireframe),void 0!==t.wireframeLinewidth&&(n.wireframeLinewidth=t.wireframeLinewidth),void 0!==t.wireframeLinecap&&(n.wireframeLinecap=t.wireframeLinecap),void 0!==t.wireframeLinejoin&&(n.wireframeLinejoin=t.wireframeLinejoin),void 0!==t.skinning&&(n.skinning=t.skinning),void 0!==t.morphTargets&&(n.morphTargets=t.morphTargets),void 0!==t.size&&(n.size=t.size),void 0!==t.sizeAttenuation&&(n.sizeAttenuation=t.sizeAttenuation),void 0!==t.map&&(n.map=e(t.map)),void 0!==t.alphaMap&&(n.alphaMap=e(t.alphaMap),n.transparent=!0),void 0!==t.bumpMap&&(n.bumpMap=e(t.bumpMap)),void 0!==t.bumpScale&&(n.bumpScale=t.bumpScale),void 0!==t.normalMap&&(n.normalMap=e(t.normalMap)),void 0!==t.normalScale){var r=t.normalScale;Array.isArray(r)===!1&&(r=[r,r]),n.normalScale=(new I).fromArray(r)}if(void 0!==t.displacementMap&&(n.displacementMap=e(t.displacementMap)),void 0!==t.displacementScale&&(n.displacementScale=t.displacementScale),void 0!==t.displacementBias&&(n.displacementBias=t.displacementBias),void 0!==t.roughnessMap&&(n.roughnessMap=e(t.roughnessMap)),void 0!==t.metalnessMap&&(n.metalnessMap=e(t.metalnessMap)),void 0!==t.emissiveMap&&(n.emissiveMap=e(t.emissiveMap)),void 0!==t.emissiveIntensity&&(n.emissiveIntensity=t.emissiveIntensity),void 0!==t.specularMap&&(n.specularMap=e(t.specularMap)),void 0!==t.envMap&&(n.envMap=e(t.envMap)),void 0!==t.reflectivity&&(n.reflectivity=t.reflectivity),void 0!==t.lightMap&&(n.lightMap=e(t.lightMap)),void 0!==t.lightMapIntensity&&(n.lightMapIntensity=t.lightMapIntensity),void 0!==t.aoMap&&(n.aoMap=e(t.aoMap)),void 0!==t.aoMapIntensity&&(n.aoMapIntensity=t.aoMapIntensity),void 0!==t.materials)for(var o=0,a=t.materials.length;o<a;o++)n.materials.push(this.parse(t.materials[o]));return n}}),Object.assign(Ci.prototype,{load:function(t,e,i,n){var r=this,o=new Ke(r.manager);o.load(t,function(t){e(r.parse(JSON.parse(t)))},i,n)},parse:function(t){var e=new ue,i=t.data.index,n={Int8Array:Int8Array,Uint8Array:Uint8Array,Uint8ClampedArray:Uint8ClampedArray,Int16Array:Int16Array,Uint16Array:Uint16Array,Int32Array:Int32Array,Uint32Array:Uint32Array,Float32Array:Float32Array,Float64Array:Float64Array};if(void 0!==i){var r=new n[i.type](i.array);e.setIndex(new Kt(r,1))}var o=t.data.attributes;for(var a in o){var s=o[a],r=new n[s.type](s.array);e.addAttribute(a,new Kt(r,s.itemSize,s.normalized))}var c=t.data.groups||t.data.drawcalls||t.data.offsets;if(void 0!==c)for(var u=0,h=c.length;u!==h;++u){var l=c[u];e.addGroup(l.start,l.count,l.materialIndex)}var d=t.data.boundingSphere;if(void 0!==d){var f=new N;void 0!==d.center&&f.fromArray(d.center),e.boundingSphere=new It(f,d.radius)}return e}}),Ti.prototype={constructor:Ti,crossOrigin:void 0,extractUrlBase:function(t){var e=t.split("/");return 1===e.length?"./":(e.pop(),e.join("/")+"/")},initMaterials:function(t,e,i){for(var n=[],r=0;r<t.length;++r)n[r]=this.createMaterial(t[r],e,i);return n},createMaterial:function(){var t,e,i;return function(n,r,o){function a(t,i,n,a,c){var u,h=r+t,l=Ti.Handlers.get(h);null!==l?u=l.load(h):(e.setCrossOrigin(o),u=e.load(h)),void 0!==i&&(u.repeat.fromArray(i),1!==i[0]&&(u.wrapS=Ml),1!==i[1]&&(u.wrapT=Ml)),void 0!==n&&u.offset.fromArray(n),void 0!==a&&("repeat"===a[0]&&(u.wrapS=Ml),"mirror"===a[0]&&(u.wrapS=Cl),"repeat"===a[1]&&(u.wrapT=Ml),"mirror"===a[1]&&(u.wrapT=Cl)),void 0!==c&&(u.anisotropy=c);var d=Ed.generateUUID();return s[d]=u,d}void 0===t&&(t=new Ct),void 0===e&&(e=new ii),void 0===i&&(i=new Pi);var s={},c={uuid:Ed.generateUUID(),type:"MeshLambertMaterial"};for(var u in n){var h=n[u];switch(u){case"DbgColor":case"DbgIndex":case"opticalDensity":case"illumination":break;case"DbgName":c.name=h;break;case"blending":c.blending=THREE[h];break;case"colorAmbient":case"mapAmbient":console.warn("THREE.Loader.createMaterial:",u,"is no longer supported.");break;case"colorDiffuse":c.color=t.fromArray(h).getHex();break;case"colorSpecular":c.specular=t.fromArray(h).getHex();break;case"colorEmissive":c.emissive=t.fromArray(h).getHex();break;case"specularCoef":c.shininess=h;break;case"shading":"basic"===h.toLowerCase()&&(c.type="MeshBasicMaterial"),"phong"===h.toLowerCase()&&(c.type="MeshPhongMaterial"),"standard"===h.toLowerCase()&&(c.type="MeshStandardMaterial");break;case"mapDiffuse":c.map=a(h,n.mapDiffuseRepeat,n.mapDiffuseOffset,n.mapDiffuseWrap,n.mapDiffuseAnisotropy);break;case"mapDiffuseRepeat":case"mapDiffuseOffset":case"mapDiffuseWrap":case"mapDiffuseAnisotropy":break;case"mapEmissive":c.emissiveMap=a(h,n.mapEmissiveRepeat,n.mapEmissiveOffset,n.mapEmissiveWrap,n.mapEmissiveAnisotropy);break;case"mapEmissiveRepeat":case"mapEmissiveOffset":case"mapEmissiveWrap":case"mapEmissiveAnisotropy":break;case"mapLight":c.lightMap=a(h,n.mapLightRepeat,n.mapLightOffset,n.mapLightWrap,n.mapLightAnisotropy);break;case"mapLightRepeat":case"mapLightOffset":case"mapLightWrap":case"mapLightAnisotropy":break;case"mapAO":c.aoMap=a(h,n.mapAORepeat,n.mapAOOffset,n.mapAOWrap,n.mapAOAnisotropy);break;case"mapAORepeat":case"mapAOOffset":case"mapAOWrap":case"mapAOAnisotropy":break;case"mapBump":c.bumpMap=a(h,n.mapBumpRepeat,n.mapBumpOffset,n.mapBumpWrap,n.mapBumpAnisotropy);break;case"mapBumpScale":c.bumpScale=h;break;case"mapBumpRepeat":case"mapBumpOffset":case"mapBumpWrap":case"mapBumpAnisotropy":break;case"mapNormal":c.normalMap=a(h,n.mapNormalRepeat,n.mapNormalOffset,n.mapNormalWrap,n.mapNormalAnisotropy);break;case"mapNormalFactor":c.normalScale=[h,h];break;case"mapNormalRepeat":case"mapNormalOffset":case"mapNormalWrap":case"mapNormalAnisotropy":break;case"mapSpecular":c.specularMap=a(h,n.mapSpecularRepeat,n.mapSpecularOffset,n.mapSpecularWrap,n.mapSpecularAnisotropy);break;case"mapSpecularRepeat":case"mapSpecularOffset":case"mapSpecularWrap":case"mapSpecularAnisotropy":break;case"mapMetalness":c.metalnessMap=a(h,n.mapMetalnessRepeat,n.mapMetalnessOffset,n.mapMetalnessWrap,n.mapMetalnessAnisotropy);break;case"mapMetalnessRepeat":case"mapMetalnessOffset":case"mapMetalnessWrap":case"mapMetalnessAnisotropy":break;case"mapRoughness":c.roughnessMap=a(h,n.mapRoughnessRepeat,n.mapRoughnessOffset,n.mapRoughnessWrap,n.mapRoughnessAnisotropy);break;case"mapRoughnessRepeat":case"mapRoughnessOffset":case"mapRoughnessWrap":case"mapRoughnessAnisotropy":break;case"mapAlpha":c.alphaMap=a(h,n.mapAlphaRepeat,n.mapAlphaOffset,n.mapAlphaWrap,n.mapAlphaAnisotropy);break;case"mapAlphaRepeat":case"mapAlphaOffset":case"mapAlphaWrap":case"mapAlphaAnisotropy":break;case"flipSided":c.side=Ph;break;case"doubleSided":c.side=Ch;break;case"transparency":console.warn("THREE.Loader.createMaterial: transparency has been renamed to opacity"),c.opacity=h;break;case"depthTest":case"depthWrite":case"colorWrite":case"opacity":case"reflectivity":case"transparent":case"visible":case"wireframe":c[u]=h;break;case"vertexColors":h===!0&&(c.vertexColors=Rh),"face"===h&&(c.vertexColors=Lh);break;default:console.error("THREE.Loader.createMaterial: Unsupported",u,h)}}return"MeshBasicMaterial"===c.type&&delete c.emissive,"MeshPhongMaterial"!==c.type&&delete c.specular,c.opacity<1&&(c.transparent=!0),i.setTextures(s),i.parse(c)}}()},Ti.Handlers={handlers:[],add:function(t,e){this.handlers.push(t,e)},get:function(t){for(var e=this.handlers,i=0,n=e.length;i<n;i+=2){var r=e[i],o=e[i+1];if(r.test(t))return o}return null}},Object.assign(Ei.prototype,{load:function(t,e,i,n){var r=this,o=this.texturePath&&"string"==typeof this.texturePath?this.texturePath:Ti.prototype.extractUrlBase(t),a=new Ke(this.manager);a.setWithCredentials(this.withCredentials),a.load(t,function(i){var n=JSON.parse(i),a=n.metadata;if(void 0!==a){var s=a.type;if(void 0!==s){if("object"===s.toLowerCase())return void console.error("THREE.JSONLoader: "+t+" should be loaded with THREE.ObjectLoader instead.");if("scene"===s.toLowerCase())return void console.error("THREE.JSONLoader: "+t+" should be loaded with THREE.SceneLoader instead.")}}var c=r.parse(n,o);e(c.geometry,c.materials)},i,n)},setTexturePath:function(t){this.texturePath=t},parse:function(t,e){function i(e){function i(t,e){return t&1<<e}var n,r,o,s,c,u,h,l,d,f,p,m,g,v,y,b,x,w,_,S,A,M,P,C,T,E,L,R=t.faces,O=t.vertices,D=t.normals,k=t.colors,F=0;if(void 0!==t.uvs){for(n=0;n<t.uvs.length;n++)t.uvs[n].length&&F++;for(n=0;n<F;n++)a.faceVertexUvs[n]=[]}for(s=0,c=O.length;s<c;)w=new N,w.x=O[s++]*e,w.y=O[s++]*e,w.z=O[s++]*e,a.vertices.push(w);for(s=0,c=R.length;s<c;)if(f=R[s++],p=i(f,0),m=i(f,1),g=i(f,3),v=i(f,4),y=i(f,5),b=i(f,6),x=i(f,7),p){if(S=new ee,S.a=R[s],S.b=R[s+1],S.c=R[s+3],A=new ee,A.a=R[s+1],A.b=R[s+2],A.c=R[s+3],s+=4,m&&(d=R[s++],S.materialIndex=d,A.materialIndex=d),o=a.faces.length,g)for(n=0;n<F;n++)for(C=t.uvs[n],a.faceVertexUvs[n][o]=[],a.faceVertexUvs[n][o+1]=[],r=0;r<4;r++)l=R[s++],E=C[2*l],L=C[2*l+1],T=new I(E,L),2!==r&&a.faceVertexUvs[n][o].push(T),0!==r&&a.faceVertexUvs[n][o+1].push(T);if(v&&(h=3*R[s++],S.normal.set(D[h++],D[h++],D[h]),A.normal.copy(S.normal)),y)for(n=0;n<4;n++)h=3*R[s++],P=new N(D[h++],D[h++],D[h]),2!==n&&S.vertexNormals.push(P),0!==n&&A.vertexNormals.push(P);if(b&&(u=R[s++],M=k[u],S.color.setHex(M),A.color.setHex(M)),x)for(n=0;n<4;n++)u=R[s++],M=k[u],2!==n&&S.vertexColors.push(new Ct(M)),0!==n&&A.vertexColors.push(new Ct(M));a.faces.push(S),a.faces.push(A)}else{if(_=new ee,_.a=R[s++],_.b=R[s++],_.c=R[s++],m&&(d=R[s++],_.materialIndex=d),o=a.faces.length,g)for(n=0;n<F;n++)for(C=t.uvs[n],a.faceVertexUvs[n][o]=[],r=0;r<3;r++)l=R[s++],E=C[2*l],L=C[2*l+1],T=new I(E,L),a.faceVertexUvs[n][o].push(T);if(v&&(h=3*R[s++],_.normal.set(D[h++],D[h++],D[h])),y)for(n=0;n<3;n++)h=3*R[s++],P=new N(D[h++],D[h++],D[h]),_.vertexNormals.push(P);if(b&&(u=R[s++],_.color.setHex(k[u])),x)for(n=0;n<3;n++)u=R[s++],_.vertexColors.push(new Ct(k[u]));a.faces.push(_)}}function n(){var e=void 0!==t.influencesPerVertex?t.influencesPerVertex:2;if(t.skinWeights)for(var i=0,n=t.skinWeights.length;i<n;i+=e){var r=t.skinWeights[i],o=e>1?t.skinWeights[i+1]:0,s=e>2?t.skinWeights[i+2]:0,c=e>3?t.skinWeights[i+3]:0;a.skinWeights.push(new wt(r,o,s,c))}if(t.skinIndices)for(var i=0,n=t.skinIndices.length;i<n;i+=e){var u=t.skinIndices[i],h=e>1?t.skinIndices[i+1]:0,l=e>2?t.skinIndices[i+2]:0,d=e>3?t.skinIndices[i+3]:0;a.skinIndices.push(new wt(u,h,l,d))}a.bones=t.bones,a.bones&&a.bones.length>0&&(a.skinWeights.length!==a.skinIndices.length||a.skinIndices.length!==a.vertices.length)&&console.warn("When skinning, number of vertices ("+a.vertices.length+"), skinIndices ("+a.skinIndices.length+"), and skinWeights ("+a.skinWeights.length+") should match.")}function r(e){if(void 0!==t.morphTargets)for(var i=0,n=t.morphTargets.length;i<n;i++){a.morphTargets[i]={},a.morphTargets[i].name=t.morphTargets[i].name,a.morphTargets[i].vertices=[];for(var r=a.morphTargets[i].vertices,o=t.morphTargets[i].vertices,s=0,c=o.length;s<c;s+=3){var u=new N;u.x=o[s]*e,u.y=o[s+1]*e,u.z=o[s+2]*e,r.push(u)}}if(void 0!==t.morphColors&&t.morphColors.length>0){console.warn('THREE.JSONLoader: "morphColors" no longer supported. Using them as face colors.');for(var h=a.faces,l=t.morphColors[0].colors,i=0,n=h.length;i<n;i++)h[i].color.fromArray(l,3*i)}}function o(){var e=[],i=[];void 0!==t.animation&&i.push(t.animation),void 0!==t.animations&&(t.animations.length?i=i.concat(t.animations):i.push(t.animations));for(var n=0;n<i.length;n++){var r=Mi.parseAnimation(i[n],a.bones);r&&e.push(r)}if(a.morphTargets){var o=Mi.CreateClipsFromMorphTargetSequences(a.morphTargets,10);e=e.concat(o)}e.length>0&&(a.animations=e)}var a=new ae,s=void 0!==t.scale?1/t.scale:1;if(i(s),n(),r(s),o(),a.computeFaceNormals(),a.computeBoundingSphere(),void 0===t.materials||0===t.materials.length)return{geometry:a};var c=Ti.prototype.initMaterials(t.materials,e,this.crossOrigin);return{geometry:a,materials:c}}}),Object.assign(Ii.prototype,{load:function(t,e,i,n){""===this.texturePath&&(this.texturePath=t.substring(0,t.lastIndexOf("/")+1));var r=this,o=new Ke(r.manager);o.load(t,function(t){r.parse(JSON.parse(t),e)},i,n)},setTexturePath:function(t){this.texturePath=t},setCrossOrigin:function(t){this.crossOrigin=t},parse:function(t,e){var i=this.parseGeometries(t.geometries),n=this.parseImages(t.images,function(){void 0!==e&&e(a)}),r=this.parseTextures(t.textures,n),o=this.parseMaterials(t.materials,r),a=this.parseObject(t.object,i,o);return t.animations&&(a.animations=this.parseAnimations(t.animations)),void 0!==t.images&&0!==t.images.length||void 0!==e&&e(a),a},parseGeometries:function(t){var e={};if(void 0!==t)for(var i=new Ei,n=new Ci,r=0,o=t.length;r<o;r++){var a,s=t[r];switch(s.type){case"PlaneGeometry":case"PlaneBufferGeometry":a=new THREE[s.type](s.width,s.height,s.widthSegments,s.heightSegments);break;case"BoxGeometry":case"BoxBufferGeometry":case"CubeGeometry":a=new THREE[s.type](s.width,s.height,s.depth,s.widthSegments,s.heightSegments,s.depthSegments);break;case"CircleGeometry":case"CircleBufferGeometry":a=new THREE[s.type](s.radius,s.segments,s.thetaStart,s.thetaLength);break;case"CylinderGeometry":case"CylinderBufferGeometry":a=new THREE[s.type](s.radiusTop,s.radiusBottom,s.height,s.radialSegments,s.heightSegments,s.openEnded,s.thetaStart,s.thetaLength);break;case"ConeGeometry":case"ConeBufferGeometry":a=new THREE[s.type](s.radius,s.height,s.radialSegments,s.heightSegments,s.openEnded,s.thetaStart,s.thetaLength);break;case"SphereGeometry":case"SphereBufferGeometry":a=new THREE[s.type](s.radius,s.widthSegments,s.heightSegments,s.phiStart,s.phiLength,s.thetaStart,s.thetaLength);break;case"DodecahedronGeometry":case"IcosahedronGeometry":case"OctahedronGeometry":case"TetrahedronGeometry":a=new THREE[s.type](s.radius,s.detail);break;case"RingGeometry":case"RingBufferGeometry":a=new THREE[s.type](s.innerRadius,s.outerRadius,s.thetaSegments,s.phiSegments,s.thetaStart,s.thetaLength);break;case"TorusGeometry":case"TorusBufferGeometry":a=new THREE[s.type](s.radius,s.tube,s.radialSegments,s.tubularSegments,s.arc);break;case"TorusKnotGeometry":case"TorusKnotBufferGeometry":a=new THREE[s.type](s.radius,s.tube,s.tubularSegments,s.radialSegments,s.p,s.q);break;case"LatheGeometry":case"LatheBufferGeometry":a=new THREE[s.type](s.points,s.segments,s.phiStart,s.phiLength);break;case"BufferGeometry":a=n.parse(s);break;case"Geometry":a=i.parse(s.data,this.texturePath).geometry;break;default:console.warn('THREE.ObjectLoader: Unsupported geometry type "'+s.type+'"');continue}a.uuid=s.uuid,void 0!==s.name&&(a.name=s.name),e[s.uuid]=a}return e},parseMaterials:function(t,e){var i={};if(void 0!==t){var n=new Pi;n.setTextures(e);for(var r=0,o=t.length;r<o;r++){var a=n.parse(t[r]);i[a.uuid]=a}}return i},parseAnimations:function(t){for(var e=[],i=0;i<t.length;i++){var n=Mi.parse(t[i]);e.push(n)}return e},parseImages:function(t,e){function i(t){return n.manager.itemStart(t),a.load(t,function(){n.manager.itemEnd(t)},void 0,function(){n.manager.itemError(t)})}var n=this,r={};if(void 0!==t&&t.length>0){var o=new Ze(e),a=new ti(o);a.setCrossOrigin(this.crossOrigin);for(var s=0,c=t.length;s<c;s++){var u=t[s],h=/^(\/\/)|([a-z]+:(\/\/)?)/i.test(u.url)?u.url:n.texturePath+u.url;r[u.uuid]=i(h)}}return r},parseTextures:function(t,e){function i(t){return"number"==typeof t?t:(console.warn("THREE.ObjectLoader.parseTexture: Constant should be in numeric form.",t),THREE[t])}var n={};if(void 0!==t)for(var r=0,o=t.length;r<o;r++){var a=t[r];void 0===a.image&&console.warn('THREE.ObjectLoader: No "image" specified for',a.uuid),void 0===e[a.image]&&console.warn("THREE.ObjectLoader: Undefined image",a.image);var s=new L(e[a.image]);s.needsUpdate=!0,s.uuid=a.uuid,void 0!==a.name&&(s.name=a.name),void 0!==a.mapping&&(s.mapping=i(a.mapping)),void 0!==a.offset&&s.offset.fromArray(a.offset),void 0!==a.repeat&&s.repeat.fromArray(a.repeat),void 0!==a.wrap&&(s.wrapS=i(a.wrap[0]),s.wrapT=i(a.wrap[1])),void 0!==a.minFilter&&(s.minFilter=i(a.minFilter)),void 0!==a.magFilter&&(s.magFilter=i(a.magFilter)),void 0!==a.anisotropy&&(s.anisotropy=a.anisotropy),void 0!==a.flipY&&(s.flipY=a.flipY),n[a.uuid]=s}return n},parseObject:function(){var t=new O;return function(e,i,n){function r(t){return void 0===i[t]&&console.warn("THREE.ObjectLoader: Undefined geometry",t),i[t]}function o(t){if(void 0!==t)return void 0===n[t]&&console.warn("THREE.ObjectLoader: Undefined material",t),n[t]}var a;switch(e.type){case"Scene":a=new Re,void 0!==e.background&&Number.isInteger(e.background)&&(a.background=new THREE.Color(e.background)),void 0!==e.fog&&("Fog"===e.fog.type?a.fog=new Le(e.fog.color,e.fog.near,e.fog.far):"FogExp2"===e.fog.type&&(a.fog=new Ie(e.fog.color,e.fog.density)));break;case"PerspectiveCamera":a=new Ce(e.fov,e.aspect,e.near,e.far),void 0!==e.focus&&(a.focus=e.focus),void 0!==e.zoom&&(a.zoom=e.zoom),void 0!==e.filmGauge&&(a.filmGauge=e.filmGauge),void 0!==e.filmOffset&&(a.filmOffset=e.filmOffset),void 0!==e.view&&(a.view=Object.assign({},e.view));break;case"OrthographicCamera":a=new Te(e.left,e.right,e.top,e.bottom,e.near,e.far);break;case"AmbientLight":a=new li(e.color,e.intensity);break;case"DirectionalLight":a=new hi(e.color,e.intensity);break;case"PointLight":a=new ci(e.color,e.intensity,e.distance,e.decay);break;case"SpotLight":a=new si(e.color,e.intensity,e.distance,e.angle,e.penumbra,e.decay);break;case"HemisphereLight":a=new ri(e.color,e.groundColor,e.intensity);break;case"Mesh":var s=r(e.geometry),c=o(e.material);a=s.bones&&s.bones.length>0?new Ue(s,c):new Ae(s,c);break;case"LOD":a=new ke;break;case"Line":a=new $e(r(e.geometry),o(e.material),e.mode);break;case"LineSegments":a=new Ve(r(e.geometry),o(e.material));break;case"PointCloud":case"Points":a=new He(r(e.geometry),o(e.material));break;case"Sprite":a=new Ne(o(e.material));break;case"Group":a=new We;break;default:a=new re}if(a.uuid=e.uuid,void 0!==e.name&&(a.name=e.name),void 0!==e.matrix?(t.fromArray(e.matrix),t.decompose(a.position,a.quaternion,a.scale)):(void 0!==e.position&&a.position.fromArray(e.position),void 0!==e.rotation&&a.rotation.fromArray(e.rotation),void 0!==e.quaternion&&a.quaternion.fromArray(e.quaternion),void 0!==e.scale&&a.scale.fromArray(e.scale)),void 0!==e.castShadow&&(a.castShadow=e.castShadow),void 0!==e.receiveShadow&&(a.receiveShadow=e.receiveShadow),e.shadow&&(void 0!==e.shadow.bias&&(a.shadow.bias=e.shadow.bias),void 0!==e.shadow.radius&&(a.shadow.radius=e.shadow.radius),void 0!==e.shadow.mapSize&&a.shadow.mapSize.fromArray(e.shadow.mapSize),void 0!==e.shadow.camera&&(a.shadow.camera=this.parseObject(e.shadow.camera))),void 0!==e.visible&&(a.visible=e.visible),void 0!==e.userData&&(a.userData=e.userData),void 0!==e.children)for(var u in e.children)a.add(this.parseObject(e.children[u],i,n));if("LOD"===e.type)for(var h=e.levels,l=0;l<h.length;l++){var d=h[l],u=a.getObjectByProperty("uuid",d.object);void 0!==u&&a.addLevel(u,d.distance)}return a}}()});var Xp={area:function(t){for(var e=t.length,i=0,n=e-1,r=0;r<e;n=r++)i+=t[n].x*t[r].y-t[r].x*t[n].y;return.5*i},triangulate:function(){function t(t,e,i,n,r,o){var a,s,c,u,h,l,d,f,p;if(s=t[o[e]].x,c=t[o[e]].y,u=t[o[i]].x,h=t[o[i]].y,l=t[o[n]].x,d=t[o[n]].y,Number.EPSILON>(u-s)*(d-c)-(h-c)*(l-s))return!1;var m,g,v,y,b,x,w,_,S,A,M,P,C,T,E;for(m=l-u,g=d-h,v=s-l,y=c-d,b=u-s,x=h-c,a=0;a<r;a++)if(f=t[o[a]].x,p=t[o[a]].y,!(f===s&&p===c||f===u&&p===h||f===l&&p===d)&&(w=f-s,_=p-c,S=f-u,A=p-h,M=f-l,P=p-d,E=m*A-g*S,C=b*_-x*w,T=v*P-y*M,E>=-Number.EPSILON&&T>=-Number.EPSILON&&C>=-Number.EPSILON))return!1;return!0}return function(e,i){var n=e.length;if(n<3)return null;var r,o,a,s=[],c=[],u=[];if(Xp.area(e)>0)for(o=0;o<n;o++)c[o]=o;else for(o=0;o<n;o++)c[o]=n-1-o;var h=n,l=2*h;for(o=h-1;h>2;){if(l--<=0)return console.warn("THREE.ShapeUtils: Unable to triangulate polygon! in 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n,o,a,s,c;for(n=0;n<b.length;n++)for(o=e[b[n]],a=0;a<o.length;a++)if(s=a+1,s%=o.length,c=r(t,i,o[a],o[s],!0),c.length>0)return!0;return!1}for(var s,c,u,h,l,d,f,p,m,g,v,y=t.concat(),b=[],x=[],w=0,_=e.length;w<_;w++)b.push(w);for(var S=0,A=2*b.length;b.length>0;){if(A--,A<0){console.log("Infinite Loop! Holes left:"+b.length+", Probably Hole outside Shape!");break}for(u=S;u<y.length;u++){h=y[u],c=-1;for(var w=0;w<b.length;w++)if(d=b[w],f=h.x+":"+h.y+":"+d,void 0===x[f]){s=e[d];for(var M=0;M<s.length;M++)if(l=s[M],i(u,M)&&!n(h,l)&&!a(h,l)){c=M,b.splice(w,1),p=y.slice(0,u+1),
-m=y.slice(u),g=s.slice(c),v=s.slice(0,c+1),y=p.concat(g).concat(v).concat(m),S=u;break}if(c>=0)break;x[f]=!0}if(c>=0)break}}return y}i(t),e.forEach(i);for(var s,c,u,h,l,d,f={},p=t.concat(),m=0,g=e.length;m<g;m++)Array.prototype.push.apply(p,e[m]);for(s=0,c=p.length;s<c;s++)l=p[s].x+":"+p[s].y,void 0!==f[l]&&console.warn("THREE.ShapeUtils: Duplicate point",l,s),f[l]=s;var v=a(t,e),y=Xp.triangulate(v,!1);for(s=0,c=y.length;s<c;s++)for(h=y[s],u=0;u<3;u++)l=h[u].x+":"+h[u].y,d=f[l],void 0!==d&&(h[u]=d);return y.concat()},isClockWise:function(t){return Xp.area(t)<0},b2:function(){function t(t,e){var i=1-t;return i*i*e}function e(t,e){return 2*(1-t)*t*e}function i(t,e){return t*t*e}return function(n,r,o,a){return t(n,r)+e(n,o)+i(n,a)}}(),b3:function(){function t(t,e){var i=1-t;return i*i*i*e}function e(t,e){var i=1-t;return 3*i*i*t*e}function i(t,e){var i=1-t;return 3*i*t*t*e}function n(t,e){return t*t*t*e}return function(r,o,a,s,c){return t(r,o)+e(r,a)+i(r,s)+n(r,c)}}()};Li.prototype={constructor:Li,getPoint:function(t){return console.warn("THREE.Curve: Warning, getPoint() not implemented!"),null},getPointAt:function(t){var e=this.getUtoTmapping(t);return this.getPoint(e)},getPoints:function(t){t||(t=5);for(var e=[],i=0;i<=t;i++)e.push(this.getPoint(i/t));return e},getSpacedPoints:function(t){t||(t=5);for(var e=[],i=0;i<=t;i++)e.push(this.getPointAt(i/t));return e},getLength:function(){var t=this.getLengths();return t[t.length-1]},getLengths:function(t){if(t||(t=this.__arcLengthDivisions?this.__arcLengthDivisions:200),this.cacheArcLengths&&this.cacheArcLengths.length===t+1&&!this.needsUpdate)return this.cacheArcLengths;this.needsUpdate=!1;var e,i,n=[],r=this.getPoint(0),o=0;for(n.push(0),i=1;i<=t;i++)e=this.getPoint(i/t),o+=e.distanceTo(r),n.push(o),r=e;return this.cacheArcLengths=n,n},updateArcLengths:function(){this.needsUpdate=!0,this.getLengths()},getUtoTmapping:function(t,e){var i,n=this.getLengths(),r=0,o=n.length;i=e?e:t*n[o-1];for(var a,s=0,c=o-1;s<=c;)if(r=Math.floor(s+(c-s)/2),a=n[r]-i,a<0)s=r+1;else{if(!(a>0)){c=r;break}c=r-1}if(r=c,n[r]===i){var u=r/(o-1);return u}var h=n[r],l=n[r+1],d=l-h,f=(i-h)/d,u=(r+f)/(o-1);return u},getTangent:function(t){var e=1e-4,i=t-e,n=t+e;i<0&&(i=0),n>1&&(n=1);var r=this.getPoint(i),o=this.getPoint(n),a=o.clone().sub(r);return a.normalize()},getTangentAt:function(t){var e=this.getUtoTmapping(t);return this.getTangent(e)}},Li.create=function(t,e){return t.prototype=Object.create(Li.prototype),t.prototype.constructor=t,t.prototype.getPoint=e,t},Ri.prototype=Object.create(Li.prototype),Ri.prototype.constructor=Ri,Ri.prototype.isLineCurve=!0,Ri.prototype.getPoint=function(t){if(1===t)return this.v2.clone();var e=this.v2.clone().sub(this.v1);return e.multiplyScalar(t).add(this.v1),e},Ri.prototype.getPointAt=function(t){return this.getPoint(t)},Ri.prototype.getTangent=function(t){var e=this.v2.clone().sub(this.v1);return e.normalize()},Oi.prototype=Object.assign(Object.create(Li.prototype),{constructor:Oi,add:function(t){this.curves.push(t)},closePath:function(){var t=this.curves[0].getPoint(0),e=this.curves[this.curves.length-1].getPoint(1);t.equals(e)||this.curves.push(new Ri(e,t))},getPoint:function(t){for(var e=t*this.getLength(),i=this.getCurveLengths(),n=0;n<i.length;){if(i[n]>=e){var r=i[n]-e,o=this.curves[n],a=o.getLength(),s=0===a?0:1-r/a;return o.getPointAt(s)}n++}return null},getLength:function(){var t=this.getCurveLengths();return t[t.length-1]},updateArcLengths:function(){this.needsUpdate=!0,this.cacheLengths=null,this.getLengths()},getCurveLengths:function(){if(this.cacheLengths&&this.cacheLengths.length===this.curves.length)return this.cacheLengths;for(var t=[],e=0,i=0,n=this.curves.length;i<n;i++)e+=this.curves[i].getLength(),t.push(e);return this.cacheLengths=t,t},getSpacedPoints:function(t){t||(t=40);for(var e=[],i=0;i<=t;i++)e.push(this.getPoint(i/t));return this.autoClose&&e.push(e[0]),e},getPoints:function(t){t=t||12;for(var e,i=[],n=0,r=this.curves;n<r.length;n++)for(var o=r[n],a=o&&o.isEllipseCurve?2*t:o&&o.isLineCurve?1:o&&o.isSplineCurve?t*o.points.length:t,s=o.getPoints(a),c=0;c<s.length;c++){var u=s[c];e&&e.equals(u)||(i.push(u),e=u)}return this.autoClose&&i.length>1&&!i[i.length-1].equals(i[0])&&i.push(i[0]),i},createPointsGeometry:function(t){var e=this.getPoints(t);return this.createGeometry(e)},createSpacedPointsGeometry:function(t){var e=this.getSpacedPoints(t);return this.createGeometry(e)},createGeometry:function(t){for(var e=new ae,i=0,n=t.length;i<n;i++){var r=t[i];e.vertices.push(new N(r.x,r.y,r.z||0))}return e}}),Di.prototype=Object.create(Li.prototype),Di.prototype.constructor=Di,Di.prototype.isEllipseCurve=!0,Di.prototype.getPoint=function(t){for(var e=2*Math.PI,i=this.aEndAngle-this.aStartAngle,n=Math.abs(i)<Number.EPSILON;i<0;)i+=e;for(;i>e;)i-=e;i<Number.EPSILON&&(i=n?0:e),this.aClockwise!==!0||n||(i===e?i=-e:i-=e);var r=this.aStartAngle+t*i,o=this.aX+this.xRadius*Math.cos(r),a=this.aY+this.yRadius*Math.sin(r);if(0!==this.aRotation){var s=Math.cos(this.aRotation),c=Math.sin(this.aRotation),u=o-this.aX,h=a-this.aY;o=u*s-h*c+this.aX,a=u*c+h*s+this.aY}return new I(o,a)};var qp={tangentQuadraticBezier:function(t,e,i,n){return 2*(1-t)*(i-e)+2*t*(n-i)},tangentCubicBezier:function(t,e,i,n,r){return-3*e*(1-t)*(1-t)+3*i*(1-t)*(1-t)-6*t*i*(1-t)+6*t*n*(1-t)-3*t*t*n+3*t*t*r},tangentSpline:function(t,e,i,n,r){var o=6*t*t-6*t,a=3*t*t-4*t+1,s=-6*t*t+6*t,c=3*t*t-2*t;return o+a+s+c},interpolate:function(t,e,i,n,r){var o=.5*(i-t),a=.5*(n-e),s=r*r,c=r*s;return(2*e-2*i+o+a)*c+(-3*e+3*i-2*o-a)*s+o*r+e}};Ni.prototype=Object.create(Li.prototype),Ni.prototype.constructor=Ni,Ni.prototype.isSplineCurve=!0,Ni.prototype.getPoint=function(t){var e=this.points,i=(e.length-1)*t,n=Math.floor(i),r=i-n,o=e[0===n?n:n-1],a=e[n],s=e[n>e.length-2?e.length-1:n+1],c=e[n>e.length-3?e.length-1:n+2],u=qp.interpolate;return new I(u(o.x,a.x,s.x,c.x,r),u(o.y,a.y,s.y,c.y,r))},ki.prototype=Object.create(Li.prototype),ki.prototype.constructor=ki,ki.prototype.getPoint=function(t){var e=Xp.b3;return new I(e(t,this.v0.x,this.v1.x,this.v2.x,this.v3.x),e(t,this.v0.y,this.v1.y,this.v2.y,this.v3.y))},ki.prototype.getTangent=function(t){var e=qp.tangentCubicBezier;return new I(e(t,this.v0.x,this.v1.x,this.v2.x,this.v3.x),e(t,this.v0.y,this.v1.y,this.v2.y,this.v3.y)).normalize()},Fi.prototype=Object.create(Li.prototype),Fi.prototype.constructor=Fi,Fi.prototype.getPoint=function(t){var e=Xp.b2;return new I(e(t,this.v0.x,this.v1.x,this.v2.x),e(t,this.v0.y,this.v1.y,this.v2.y))},Fi.prototype.getTangent=function(t){var e=qp.tangentQuadraticBezier;return new I(e(t,this.v0.x,this.v1.x,this.v2.x),e(t,this.v0.y,this.v1.y,this.v2.y)).normalize()};var Yp=Object.assign(Object.create(Oi.prototype),{fromPoints:function(t){this.moveTo(t[0].x,t[0].y);for(var e=1,i=t.length;e<i;e++)this.lineTo(t[e].x,t[e].y)},moveTo:function(t,e){this.currentPoint.set(t,e)},lineTo:function(t,e){var i=new Ri(this.currentPoint.clone(),new I(t,e));this.curves.push(i),this.currentPoint.set(t,e)},quadraticCurveTo:function(t,e,i,n){var r=new Fi(this.currentPoint.clone(),new I(t,e),new I(i,n));this.curves.push(r),this.currentPoint.set(i,n)},bezierCurveTo:function(t,e,i,n,r,o){var a=new ki(this.currentPoint.clone(),new I(t,e),new I(i,n),new I(r,o));this.curves.push(a),this.currentPoint.set(r,o)},splineThru:function(t){var e=[this.currentPoint.clone()].concat(t),i=new Ni(e);this.curves.push(i),this.currentPoint.copy(t[t.length-1])},arc:function(t,e,i,n,r,o){var a=this.currentPoint.x,s=this.currentPoint.y;this.absarc(t+a,e+s,i,n,r,o)},absarc:function(t,e,i,n,r,o){this.absellipse(t,e,i,i,n,r,o)},ellipse:function(t,e,i,n,r,o,a,s){var c=this.currentPoint.x,u=this.currentPoint.y;this.absellipse(t+c,e+u,i,n,r,o,a,s)},absellipse:function(t,e,i,n,r,o,a,s){var c=new Di(t,e,i,n,r,o,a,s);if(this.curves.length>0){var u=c.getPoint(0);u.equals(this.currentPoint)||this.lineTo(u.x,u.y)}this.curves.push(c);var h=c.getPoint(1);this.currentPoint.copy(h)}});zi.prototype=Object.create(ae.prototype),zi.prototype.constructor=zi,zi.NoTaper=function(t){return 1},zi.SinusoidalTaper=function(t){return Math.sin(Math.PI*t)},zi.FrenetFrames=function(t,e,i){function n(){f[0]=new N,p[0]=new N,o=Number.MAX_VALUE,a=Math.abs(d[0].x),s=Math.abs(d[0].y),c=Math.abs(d[0].z),a<=o&&(o=a,l.set(1,0,0)),s<=o&&(o=s,l.set(0,1,0)),c<=o&&l.set(0,0,1),m.crossVectors(d[0],l).normalize(),f[0].crossVectors(d[0],m),p[0].crossVectors(d[0],f[0])}var r,o,a,s,c,u,h,l=new N,d=[],f=[],p=[],m=new N,g=new O,v=e+1;for(this.tangents=d,this.normals=f,this.binormals=p,u=0;u<v;u++)h=u/(v-1),d[u]=t.getTangentAt(h),d[u].normalize();for(n(),u=1;u<v;u++)f[u]=f[u-1].clone(),p[u]=p[u-1].clone(),m.crossVectors(d[u-1],d[u]),m.length()>Number.EPSILON&&(m.normalize(),r=Math.acos(Ed.clamp(d[u-1].dot(d[u]),-1,1)),f[u].applyMatrix4(g.makeRotationAxis(m,r))),p[u].crossVectors(d[u],f[u]);if(i)for(r=Math.acos(Ed.clamp(f[0].dot(f[v-1]),-1,1)),r/=v-1,d[0].dot(m.crossVectors(f[0],f[v-1]))>0&&(r=-r),u=1;u<v;u++)f[u].applyMatrix4(g.makeRotationAxis(d[u],r*u)),p[u].crossVectors(d[u],f[u])},Bi.prototype=Object.create(ae.prototype),Bi.prototype.constructor=Bi,Bi.prototype.addShapeList=function(t,e){for(var i=t.length,n=0;n<i;n++){var r=t[n];this.addShape(r,e)}},Bi.prototype.addShape=function(t,e){function i(t,e,i){return e||console.error("THREE.ExtrudeGeometry: vec does not exist"),e.clone().multiplyScalar(i).add(t)}function n(t,e,i){var n,r,o=1,a=t.x-e.x,s=t.y-e.y,c=i.x-t.x,u=i.y-t.y,h=a*a+s*s,l=a*u-s*c;if(Math.abs(l)>Number.EPSILON){var d=Math.sqrt(h),f=Math.sqrt(c*c+u*u),p=e.x-s/d,m=e.y+a/d,g=i.x-u/f,v=i.y+c/f,y=((g-p)*u-(v-m)*c)/(a*u-s*c);n=p+a*y-t.x,r=m+s*y-t.y;var b=n*n+r*r;if(b<=2)return new I(n,r);o=Math.sqrt(b/2)}else{var x=!1;a>Number.EPSILON?c>Number.EPSILON&&(x=!0):a<-Number.EPSILON?c<-Number.EPSILON&&(x=!0):Math.sign(s)===Math.sign(u)&&(x=!0),x?(n=-s,r=a,o=Math.sqrt(h)):(n=a,r=s,o=Math.sqrt(h/2))}return new I(n/o,r/o)}function r(){if(b){var t=0,e=G*t;for(X=0;X<H;X++)V=k[X],c(V[2]+e,V[1]+e,V[0]+e);for(t=w+2*y,e=G*t,X=0;X<H;X++)V=k[X],c(V[0]+e,V[1]+e,V[2]+e)}else{for(X=0;X<H;X++)V=k[X],c(V[2],V[1],V[0]);for(X=0;X<H;X++)V=k[X],c(V[0]+G*w,V[1]+G*w,V[2]+G*w)}}function o(){var t=0;for(a(F,t),t+=F.length,P=0,C=O.length;P<C;P++)M=O[P],a(M,t),t+=M.length}function a(t,e){var i,n;for(X=t.length;--X>=0;){i=X,n=X-1,n<0&&(n=t.length-1);var r=0,o=w+2*y;for(r=0;r<o;r++){var a=G*r,s=G*(r+1),c=e+i+a,h=e+n+a,l=e+n+s,d=e+i+s;u(c,h,l,d,t,r,o,i,n)}}}function s(t,e,i){T.vertices.push(new N(t,e,i))}function c(t,e,i){t+=E,e+=E,i+=E,T.faces.push(new ee(t,e,i,null,null,0));var n=A.generateTopUV(T,t,e,i);T.faceVertexUvs[0].push(n)}function u(t,e,i,n,r,o,a,s,c){t+=E,e+=E,i+=E,n+=E,T.faces.push(new ee(t,e,n,null,null,1)),T.faces.push(new ee(e,i,n,null,null,1));var u=A.generateSideWallUV(T,t,e,i,n);T.faceVertexUvs[0].push([u[0],u[1],u[3]]),T.faceVertexUvs[0].push([u[1],u[2],u[3]])}var h,l,d,f,p,m=void 0!==e.amount?e.amount:100,g=void 0!==e.bevelThickness?e.bevelThickness:6,v=void 0!==e.bevelSize?e.bevelSize:g-2,y=void 0!==e.bevelSegments?e.bevelSegments:3,b=void 0===e.bevelEnabled||e.bevelEnabled,x=void 0!==e.curveSegments?e.curveSegments:12,w=void 0!==e.steps?e.steps:1,_=e.extrudePath,S=!1,A=void 0!==e.UVGenerator?e.UVGenerator:Bi.WorldUVGenerator;_&&(h=_.getSpacedPoints(w),S=!0,b=!1,l=void 0!==e.frames?e.frames:new zi.FrenetFrames(_,w,!1),d=new N,f=new N,p=new N),b||(y=0,g=0,v=0);var M,P,C,T=this,E=this.vertices.length,L=t.extractPoints(x),R=L.shape,O=L.holes,D=!Xp.isClockWise(R);if(D){for(R=R.reverse(),P=0,C=O.length;P<C;P++)M=O[P],Xp.isClockWise(M)&&(O[P]=M.reverse());D=!1}var k=Xp.triangulateShape(R,O),F=R;for(P=0,C=O.length;P<C;P++)M=O[P],R=R.concat(M);for(var z,B,U,j,$,V,G=R.length,H=k.length,W=[],X=0,q=F.length,Y=q-1,Z=X+1;X<q;X++,Y++,Z++)Y===q&&(Y=0),Z===q&&(Z=0),W[X]=n(F[X],F[Y],F[Z]);var K,Q=[],J=W.concat();for(P=0,C=O.length;P<C;P++){for(M=O[P],K=[],X=0,q=M.length,Y=q-1,Z=X+1;X<q;X++,Y++,Z++)Y===q&&(Y=0),Z===q&&(Z=0),K[X]=n(M[X],M[Y],M[Z]);Q.push(K),J=J.concat(K)}for(z=0;z<y;z++){for(U=z/y,j=g*Math.cos(U*Math.PI/2),B=v*Math.sin(U*Math.PI/2),X=0,q=F.length;X<q;X++)$=i(F[X],W[X],B),s($.x,$.y,-j);for(P=0,C=O.length;P<C;P++)for(M=O[P],K=Q[P],X=0,q=M.length;X<q;X++)$=i(M[X],K[X],B),s($.x,$.y,-j)}for(B=v,X=0;X<G;X++)$=b?i(R[X],J[X],B):R[X],S?(f.copy(l.normals[0]).multiplyScalar($.x),d.copy(l.binormals[0]).multiplyScalar($.y),p.copy(h[0]).add(f).add(d),s(p.x,p.y,p.z)):s($.x,$.y,0);var tt;for(tt=1;tt<=w;tt++)for(X=0;X<G;X++)$=b?i(R[X],J[X],B):R[X],S?(f.copy(l.normals[tt]).multiplyScalar($.x),d.copy(l.binormals[tt]).multiplyScalar($.y),p.copy(h[tt]).add(f).add(d),s(p.x,p.y,p.z)):s($.x,$.y,m/w*tt);for(z=y-1;z>=0;z--){for(U=z/y,j=g*Math.cos(U*Math.PI/2),B=v*Math.sin(U*Math.PI/2),X=0,q=F.length;X<q;X++)$=i(F[X],W[X],B),s($.x,$.y,m+j);for(P=0,C=O.length;P<C;P++)for(M=O[P],K=Q[P],X=0,q=M.length;X<q;X++)$=i(M[X],K[X],B),S?s($.x,$.y+h[w-1].y,h[w-1].x+j):s($.x,$.y,m+j)}r(),o()},Bi.WorldUVGenerator={generateTopUV:function(t,e,i,n){var r=t.vertices,o=r[e],a=r[i],s=r[n];return[new I(o.x,o.y),new I(a.x,a.y),new I(s.x,s.y)]},generateSideWallUV:function(t,e,i,n,r){var o=t.vertices,a=o[e],s=o[i],c=o[n],u=o[r];return Math.abs(a.y-s.y)<.01?[new I(a.x,1-a.z),new I(s.x,1-s.z),new I(c.x,1-c.z),new I(u.x,1-u.z)]:[new I(a.y,1-a.z),new I(s.y,1-s.z),new I(c.y,1-c.z),new I(u.y,1-u.z)]}},Ui.prototype=Object.create(ae.prototype),Ui.prototype.constructor=Ui,Ui.prototype.addShapeList=function(t,e){for(var i=0,n=t.length;i<n;i++)this.addShape(t[i],e);return this},Ui.prototype.addShape=function(t,e){void 0===e&&(e={});var i,n,r,o=void 0!==e.curveSegments?e.curveSegments:12,a=e.material,s=void 0===e.UVGenerator?Bi.WorldUVGenerator:e.UVGenerator,c=this.vertices.length,u=t.extractPoints(o),h=u.shape,l=u.holes,d=!Xp.isClockWise(h);if(d){for(h=h.reverse(),i=0,n=l.length;i<n;i++)r=l[i],Xp.isClockWise(r)&&(l[i]=r.reverse());d=!1}var f=Xp.triangulateShape(h,l);for(i=0,n=l.length;i<n;i++)r=l[i],h=h.concat(r);var p,m,g=h.length,v=f.length;for(i=0;i<g;i++)p=h[i],this.vertices.push(new N(p.x,p.y,0));for(i=0;i<v;i++){m=f[i];var y=m[0]+c,b=m[1]+c,x=m[2]+c;this.faces.push(new ee(y,b,x,null,null,a)),this.faceVertexUvs[0].push(s.generateTopUV(this,y,b,x))}},ji.prototype=Object.assign(Object.create(Yp),{constructor:ji,extrude:function(t){return new Bi(this,t)},makeGeometry:function(t){return new Ui(this,t)},getPointsHoles:function(t){for(var e=[],i=0,n=this.holes.length;i<n;i++)e[i]=this.holes[i].getPoints(t);return e},extractAllPoints:function(t){return{shape:this.getPoints(t),holes:this.getPointsHoles(t)}},extractPoints:function(t){return this.extractAllPoints(t)}}),$i.prototype=Yp,Yp.constructor=$i,Vi.prototype={moveTo:function(t,e){this.currentPath=new $i,this.subPaths.push(this.currentPath),this.currentPath.moveTo(t,e)},lineTo:function(t,e){this.currentPath.lineTo(t,e)},quadraticCurveTo:function(t,e,i,n){this.currentPath.quadraticCurveTo(t,e,i,n)},bezierCurveTo:function(t,e,i,n,r,o){this.currentPath.bezierCurveTo(t,e,i,n,r,o)},splineThru:function(t){this.currentPath.splineThru(t)},toShapes:function(t,e){function i(t){for(var e=[],i=0,n=t.length;i<n;i++){var r=t[i],o=new ji;o.curves=r.curves,e.push(o)}return e}function n(t,e){for(var i=e.length,n=!1,r=i-1,o=0;o<i;r=o++){var a=e[r],s=e[o],c=s.x-a.x,u=s.y-a.y;if(Math.abs(u)>Number.EPSILON){if(u<0&&(a=e[o],c=-c,s=e[r],u=-u),t.y<a.y||t.y>s.y)continue;if(t.y===a.y){if(t.x===a.x)return!0}else{var h=u*(t.x-a.x)-c*(t.y-a.y);if(0===h)return!0;if(h<0)continue;n=!n}}else{if(t.y!==a.y)continue;if(s.x<=t.x&&t.x<=a.x||a.x<=t.x&&t.x<=s.x)return!0}}return n}var r=Xp.isClockWise,o=this.subPaths;if(0===o.length)return[];if(e===!0)return i(o);var a,s,c,u=[];if(1===o.length)return s=o[0],c=new ji,c.curves=s.curves,u.push(c),u;var h=!r(o[0].getPoints());h=t?!h:h;var l,d=[],f=[],p=[],m=0;f[m]=void 0,p[m]=[];for(var g=0,v=o.length;g<v;g++)s=o[g],l=s.getPoints(),a=r(l),a=t?!a:a,a?(!h&&f[m]&&m++,f[m]={s:new ji,p:l},f[m].s.curves=s.curves,h&&m++,p[m]=[]):p[m].push({h:s,p:l[0]});if(!f[0])return i(o);if(f.length>1){for(var y=!1,b=[],x=0,w=f.length;x<w;x++)d[x]=[];for(var x=0,w=f.length;x<w;x++)for(var _=p[x],S=0;S<_.length;S++){for(var A=_[S],M=!0,P=0;P<f.length;P++)n(A.p,f[P].p)&&(x!==P&&b.push({froms:x,tos:P,hole:S}),M?(M=!1,d[P].push(A)):y=!0);M&&d[x].push(A)}b.length>0&&(y||(p=d))}for(var C,g=0,T=f.length;g<T;g++){c=f[g].s,u.push(c),C=p[g];for(var E=0,I=C.length;E<I;E++)c.holes.push(C[E].h)}return u}},Object.assign(Gi.prototype,{isFont:!0,generateShapes:function(t,e,i){function n(t){for(var i=String(t).split(""),n=e/o.resolution,a=0,s=[],c=0;c<i.length;c++){var u=r(i[c],n,a);a+=u.offset,s.push(u.path)}return s}function r(t,e,n){var r=o.glyphs[t]||o.glyphs["?"];if(r){var a,s,c,u,h,l,d,f,p,m,g,v=new Vi,y=[],b=Xp.b2,x=Xp.b3;if(r.o)for(var w=r._cachedOutline||(r._cachedOutline=r.o.split(" ")),_=0,S=w.length;_<S;){var A=w[_++];switch(A){case"m":a=w[_++]*e+n,s=w[_++]*e,v.moveTo(a,s);break;case"l":a=w[_++]*e+n,s=w[_++]*e,v.lineTo(a,s);break;case"q":if(c=w[_++]*e+n,u=w[_++]*e,d=w[_++]*e+n,f=w[_++]*e,v.quadraticCurveTo(d,f,c,u),g=y[y.length-1]){h=g.x,l=g.y;for(var M=1;M<=i;M++){var P=M/i;b(P,h,d,c),b(P,l,f,u)}}break;case"b":if(c=w[_++]*e+n,u=w[_++]*e,d=w[_++]*e+n,f=w[_++]*e,p=w[_++]*e+n,m=w[_++]*e,v.bezierCurveTo(d,f,p,m,c,u),g=y[y.length-1]){h=g.x,l=g.y;for(var M=1;M<=i;M++){var P=M/i;x(P,h,d,p,c),x(P,l,f,m,u)}}}}return{offset:r.ha*e,path:v}}}void 0===e&&(e=100),void 0===i&&(i=4);for(var o=this.data,a=n(t),s=[],c=0,u=a.length;c<u;c++)Array.prototype.push.apply(s,a[c].toShapes());return s}}),Object.assign(Hi.prototype,{load:function(t,e,i,n){var r=this,o=new Ke(this.manager);o.load(t,function(t){var i;try{i=JSON.parse(t)}catch(e){console.warn("THREE.FontLoader: typeface.js support is being deprecated. Use typeface.json instead."),i=JSON.parse(t.substring(65,t.length-2))}var n=r.parse(i);e&&e(n)},i,n)},parse:function(t){return new Gi(t)}});var Zp;Object.assign(Xi.prototype,{load:function(t,e,i,n){var r=new Ke(this.manager);r.setResponseType("arraybuffer"),r.load(t,function(t){var i=Wi();i.decodeAudioData(t,function(t){e(t)})},i,n)}}),Object.assign(qi.prototype,{update:function(){var t,e,i,n,r,o=new O,a=new O;return function(s){var c=t!==s.focus||e!==s.fov||i!==s.aspect*this.aspect||n!==s.near||r!==s.far;if(c){t=s.focus,e=s.fov,i=s.aspect*this.aspect,n=s.near,r=s.far;var u,h,l=s.projectionMatrix.clone(),d=this.eyeSep/2,f=d*n/t,p=n*Math.tan(Ed.DEG2RAD*e*.5);a.elements[12]=-d,o.elements[12]=d,u=-p*i+f,h=p*i+f,l.elements[0]=2*n/(h-u),l.elements[8]=(h+u)/(h-u),this.cameraL.projectionMatrix.copy(l),u=-p*i-f,h=p*i-f,l.elements[0]=2*n/(h-u),l.elements[8]=(h+u)/(h-u),this.cameraR.projectionMatrix.copy(l)}this.cameraL.matrixWorld.copy(s.matrixWorld).multiply(a),this.cameraR.matrixWorld.copy(s.matrixWorld).multiply(o)}}()}),Yi.prototype=Object.assign(Object.create(re.prototype),{constructor:Yi,getInput:function(){return this.gain},removeFilter:function(){null!==this.filter&&(this.gain.disconnect(this.filter),this.filter.disconnect(this.context.destination),this.gain.connect(this.context.destination),this.filter=null)},getFilter:function(){return this.filter},setFilter:function(t){null!==this.filter?(this.gain.disconnect(this.filter),this.filter.disconnect(this.context.destination)):this.gain.disconnect(this.context.destination),this.filter=t,this.gain.connect(this.filter),this.filter.connect(this.context.destination)},getMasterVolume:function(){return this.gain.gain.value},setMasterVolume:function(t){this.gain.gain.value=t},updateMatrixWorld:function(){var t=new N,e=new D,i=new N,n=new N;return function(r){re.prototype.updateMatrixWorld.call(this,r);var o=this.context.listener,a=this.up;this.matrixWorld.decompose(t,e,i),n.set(0,0,-1).applyQuaternion(e),o.setPosition(t.x,t.y,t.z),o.setOrientation(n.x,n.y,n.z,a.x,a.y,a.z)}}()}),Zi.prototype=Object.assign(Object.create(re.prototype),{constructor:Zi,getOutput:function(){return this.gain},setNodeSource:function(t){return this.hasPlaybackControl=!1,this.sourceType="audioNode",this.source=t,this.connect(),this},setBuffer:function(t){return this.source.buffer=t,this.sourceType="buffer",this.autoplay&&this.play(),this},play:function(){if(this.isPlaying===!0)return void console.warn("THREE.Audio: Audio is already playing.");if(this.hasPlaybackControl===!1)return void console.warn("THREE.Audio: this Audio has no playback control.");var t=this.context.createBufferSource();return t.buffer=this.source.buffer,t.loop=this.source.loop,t.onended=this.source.onended,t.start(0,this.startTime),t.playbackRate.value=this.playbackRate,this.isPlaying=!0,this.source=t,this.connect()},pause:function(){return this.hasPlaybackControl===!1?void console.warn("THREE.Audio: this Audio has no playback control."):(this.source.stop(),this.startTime=this.context.currentTime,this.isPlaying=!1,this)},stop:function(){return this.hasPlaybackControl===!1?void console.warn("THREE.Audio: this Audio has no playback control."):(this.source.stop(),this.startTime=0,this.isPlaying=!1,this)},connect:function(){if(this.filters.length>0){this.source.connect(this.filters[0]);for(var t=1,e=this.filters.length;t<e;t++)this.filters[t-1].connect(this.filters[t]);this.filters[this.filters.length-1].connect(this.getOutput())}else this.source.connect(this.getOutput());return this},disconnect:function(){if(this.filters.length>0){this.source.disconnect(this.filters[0]);for(var t=1,e=this.filters.length;t<e;t++)this.filters[t-1].disconnect(this.filters[t]);this.filters[this.filters.length-1].disconnect(this.getOutput())}else this.source.disconnect(this.getOutput());return this},getFilters:function(){return this.filters},setFilters:function(t){return t||(t=[]),this.isPlaying===!0?(this.disconnect(),this.filters=t,this.connect()):this.filters=t,this},getFilter:function(){return this.getFilters()[0]},setFilter:function(t){return this.setFilters(t?[t]:[])},setPlaybackRate:function(t){return this.hasPlaybackControl===!1?void console.warn("THREE.Audio: this Audio has no playback control."):(this.playbackRate=t,this.isPlaying===!0&&(this.source.playbackRate.value=this.playbackRate),this)},getPlaybackRate:function(){return this.playbackRate},onEnded:function(){this.isPlaying=!1},getLoop:function(){return this.hasPlaybackControl===!1?(console.warn("THREE.Audio: this Audio has no playback control."),!1):this.source.loop},setLoop:function(t){return this.hasPlaybackControl===!1?void console.warn("THREE.Audio: this Audio has no playback control."):void(this.source.loop=t)},getVolume:function(){return this.gain.gain.value},setVolume:function(t){return this.gain.gain.value=t,this}}),Ki.prototype=Object.assign(Object.create(Zi.prototype),{constructor:Ki,getOutput:function(){return this.panner},getRefDistance:function(){return this.panner.refDistance},setRefDistance:function(t){this.panner.refDistance=t},getRolloffFactor:function(){return this.panner.rolloffFactor},setRolloffFactor:function(t){this.panner.rolloffFactor=t},getDistanceModel:function(){return this.panner.distanceModel},setDistanceModel:function(t){this.panner.distanceModel=t},getMaxDistance:function(){return this.panner.maxDistance},setMaxDistance:function(t){this.panner.maxDistance=t},updateMatrixWorld:function(){var t=new N;return function(e){re.prototype.updateMatrixWorld.call(this,e),t.setFromMatrixPosition(this.matrixWorld),this.panner.setPosition(t.x,t.y,t.z)}}()}),Object.assign(Qi.prototype,{getFrequencyData:function(){return this.analyser.getByteFrequencyData(this.data),this.data},getAverageFrequency:function(){for(var t=0,e=this.getFrequencyData(),i=0;i<e.length;i++)t+=e[i];return t/e.length}}),Ji.prototype={constructor:Ji,accumulate:function(t,e){var i=this.buffer,n=this.valueSize,r=t*n+n,o=this.cumulativeWeight;if(0===o){for(var a=0;a!==n;++a)i[r+a]=i[a];o=e}else{o+=e;var s=e/o;this._mixBufferRegion(i,r,0,s,n)}this.cumulativeWeight=o},apply:function(t){var e=this.valueSize,i=this.buffer,n=t*e+e,r=this.cumulativeWeight,o=this.binding;if(this.cumulativeWeight=0,r<1){var a=3*e;this._mixBufferRegion(i,n,a,1-r,e)}for(var s=e,c=e+e;s!==c;++s)if(i[s]!==i[s+e]){o.setValue(i,n);break}},saveOriginalState:function(){var t=this.binding,e=this.buffer,i=this.valueSize,n=3*i;t.getValue(e,n);for(var r=i,o=n;r!==o;++r)e[r]=e[n+r%i];this.cumulativeWeight=0},restoreOriginalState:function(){var t=3*this.valueSize;this.binding.setValue(this.buffer,t)},_select:function(t,e,i,n,r){if(n>=.5)for(var o=0;o!==r;++o)t[e+o]=t[i+o]},_slerp:function(t,e,i,n,r){D.slerpFlat(t,e,t,e,t,i,n)},_lerp:function(t,e,i,n,r){for(var o=1-n,a=0;a!==r;++a){var s=e+a;t[s]=t[s]*o+t[i+a]*n}}},tn.prototype={constructor:tn,getValue:function(t,e){this.bind(),this.getValue(t,e)},setValue:function(t,e){this.bind(),this.setValue(t,e)},bind:function(){var t=this.node,e=this.parsedPath,i=e.objectName,n=e.propertyName,r=e.propertyIndex;if(t||(t=tn.findNode(this.rootNode,e.nodeName)||this.rootNode,this.node=t),this.getValue=this._getValue_unavailable,this.setValue=this._setValue_unavailable,!t)return void console.error("  trying to update node for track: "+this.path+" but it wasn't found.");if(i){var o=e.objectIndex;switch(i){case"materials":if(!t.material)return void console.error("  can not bind to material as node does not have a material",this);if(!t.material.materials)return void console.error("  can not bind to material.materials as node.material does not have a materials array",this);t=t.material.materials;break;case"bones":if(!t.skeleton)return void console.error("  can not bind to bones as node does not have a skeleton",this);t=t.skeleton.bones;for(var a=0;a<t.length;a++)if(t[a].name===o){o=a;break}break;default:if(void 0===t[i])return void console.error("  can not bind to objectName of node, undefined",this);t=t[i]}if(void 0!==o){if(void 0===t[o])return void console.error("  trying to bind to objectIndex of objectName, but is undefined:",this,t);t=t[o]}}var s=t[n];if(void 0===s){var c=e.nodeName;return void console.error("  trying to update property for track: "+c+"."+n+" but it wasn't found.",t)}var u=this.Versioning.None;void 0!==t.needsUpdate?(u=this.Versioning.NeedsUpdate,this.targetObject=t):void 0!==t.matrixWorldNeedsUpdate&&(u=this.Versioning.MatrixWorldNeedsUpdate,this.targetObject=t);var h=this.BindingType.Direct;if(void 0!==r){if("morphTargetInfluences"===n){if(!t.geometry)return void console.error("  can not bind to morphTargetInfluences becasuse node does not have a geometry",this);if(!t.geometry.morphTargets)return void console.error("  can not bind to morphTargetInfluences becasuse node does not have a geometry.morphTargets",this);for(var a=0;a<this.node.geometry.morphTargets.length;a++)if(t.geometry.morphTargets[a].name===r){r=a;break}}h=this.BindingType.ArrayElement,this.resolvedProperty=s,this.propertyIndex=r}else void 0!==s.fromArray&&void 0!==s.toArray?(h=this.BindingType.HasFromToArray,this.resolvedProperty=s):void 0!==s.length?(h=this.BindingType.EntireArray,this.resolvedProperty=s):this.propertyName=n;this.getValue=this.GetterByBindingType[h],this.setValue=this.SetterByBindingTypeAndVersioning[h][u]},unbind:function(){this.node=null,this.getValue=this._getValue_unbound,this.setValue=this._setValue_unbound}},Object.assign(tn.prototype,{_getValue_unavailable:function(){},_setValue_unavailable:function(){},_getValue_unbound:tn.prototype.getValue,_setValue_unbound:tn.prototype.setValue,BindingType:{Direct:0,EntireArray:1,ArrayElement:2,HasFromToArray:3},Versioning:{None:0,NeedsUpdate:1,MatrixWorldNeedsUpdate:2},GetterByBindingType:[function(t,e){t[e]=this.node[this.propertyName]},function(t,e){for(var i=this.resolvedProperty,n=0,r=i.length;n!==r;++n)t[e++]=i[n]},function(t,e){t[e]=this.resolvedProperty[this.propertyIndex]},function(t,e){this.resolvedProperty.toArray(t,e)}],SetterByBindingTypeAndVersioning:[[function(t,e){this.node[this.propertyName]=t[e]},function(t,e){this.node[this.propertyName]=t[e],this.targetObject.needsUpdate=!0},function(t,e){this.node[this.propertyName]=t[e],this.targetObject.matrixWorldNeedsUpdate=!0}],[function(t,e){for(var i=this.resolvedProperty,n=0,r=i.length;n!==r;++n)i[n]=t[e++]},function(t,e){for(var i=this.resolvedProperty,n=0,r=i.length;n!==r;++n)i[n]=t[e++];this.targetObject.needsUpdate=!0},function(t,e){for(var i=this.resolvedProperty,n=0,r=i.length;n!==r;++n)i[n]=t[e++];this.targetObject.matrixWorldNeedsUpdate=!0}],[function(t,e){this.resolvedProperty[this.propertyIndex]=t[e]},function(t,e){this.resolvedProperty[this.propertyIndex]=t[e],this.targetObject.needsUpdate=!0},function(t,e){this.resolvedProperty[this.propertyIndex]=t[e],this.targetObject.matrixWorldNeedsUpdate=!0}],[function(t,e){this.resolvedProperty.fromArray(t,e)},function(t,e){this.resolvedProperty.fromArray(t,e),this.targetObject.needsUpdate=!0},function(t,e){this.resolvedProperty.fromArray(t,e),this.targetObject.matrixWorldNeedsUpdate=!0}]]}),tn.Composite=function(t,e,i){var n=i||tn.parseTrackName(e);this._targetGroup=t,this._bindings=t.subscribe_(e,n)},tn.Composite.prototype={constructor:tn.Composite,getValue:function(t,e){this.bind();var i=this._targetGroup.nCachedObjects_,n=this._bindings[i];void 0!==n&&n.getValue(t,e)},setValue:function(t,e){for(var i=this._bindings,n=this._targetGroup.nCachedObjects_,r=i.length;n!==r;++n)i[n].setValue(t,e)},bind:function(){for(var t=this._bindings,e=this._targetGroup.nCachedObjects_,i=t.length;e!==i;++e)t[e].bind()},unbind:function(){for(var t=this._bindings,e=this._targetGroup.nCachedObjects_,i=t.length;e!==i;++e)t[e].unbind()}},tn.create=function(t,e,i){return t&&t.isAnimationObjectGroup?new tn.Composite(t,e,i):new tn(t,e,i)},tn.parseTrackName=function(t){var e=/^((?:\w+\/)*)(\w+)?(?:\.(\w+)(?:\[(.+)\])?)?\.(\w+)(?:\[(.+)\])?$/,i=e.exec(t);if(!i)throw new Error("cannot parse trackName at all: "+t);var n={nodeName:i[2],objectName:i[3],objectIndex:i[4],propertyName:i[5],propertyIndex:i[6]};if(null===n.propertyName||0===n.propertyName.length)throw new Error("can not parse propertyName from trackName: "+t);return n},tn.findNode=function(t,e){if(!e||""===e||"root"===e||"."===e||e===-1||e===t.name||e===t.uuid)return t;if(t.skeleton){var i=function(t){for(var i=0;i<t.bones.length;i++){var n=t.bones[i];if(n.name===e)return n}return null},n=i(t.skeleton);if(n)return n}if(t.children){var r=function(t){for(var i=0;i<t.length;i++){var n=t[i];if(n.name===e||n.uuid===e)return n;var o=r(n.children);if(o)return o}return null},o=r(t.children);if(o)return o}return null},en.prototype={constructor:en,play:function(){return this._mixer._activateAction(this),this},stop:function(){return this._mixer._deactivateAction(this),this.reset()},reset:function(){return this.paused=!1,this.enabled=!0,this.time=0,this._loopCount=-1,this._startTime=null,this.stopFading().stopWarping()},isRunning:function(){return this.enabled&&!this.paused&&0!==this.timeScale&&null===this._startTime&&this._mixer._isActiveAction(this)},isScheduled:function(){return this._mixer._isActiveAction(this)},startAt:function(t){return this._startTime=t,this},setLoop:function(t,e){return this.loop=t,this.repetitions=e,this},setEffectiveWeight:function(t){return this.weight=t,this._effectiveWeight=this.enabled?t:0,this.stopFading()},getEffectiveWeight:function(){return this._effectiveWeight},fadeIn:function(t){return this._scheduleFading(t,0,1)},fadeOut:function(t){return this._scheduleFading(t,1,0)},crossFadeFrom:function(t,e,i){if(t.fadeOut(e),this.fadeIn(e),i){var n=this._clip.duration,r=t._clip.duration,o=r/n,a=n/r;t.warp(1,o,e),this.warp(a,1,e)}return this},crossFadeTo:function(t,e,i){return t.crossFadeFrom(this,e,i)},stopFading:function(){var t=this._weightInterpolant;return null!==t&&(this._weightInterpolant=null,this._mixer._takeBackControlInterpolant(t)),this},setEffectiveTimeScale:function(t){return this.timeScale=t,this._effectiveTimeScale=this.paused?0:t,this.stopWarping()},getEffectiveTimeScale:function(){return this._effectiveTimeScale},setDuration:function(t){return this.timeScale=this._clip.duration/t,this.stopWarping()},syncWith:function(t){return this.time=t.time,this.timeScale=t.timeScale,this.stopWarping()},halt:function(t){return this.warp(this._effectiveTimeScale,0,t);
-},warp:function(t,e,i){var n=this._mixer,r=n.time,o=this._timeScaleInterpolant,a=this.timeScale;null===o&&(o=n._lendControlInterpolant(),this._timeScaleInterpolant=o);var s=o.parameterPositions,c=o.sampleValues;return s[0]=r,s[1]=r+i,c[0]=t/a,c[1]=e/a,this},stopWarping:function(){var t=this._timeScaleInterpolant;return null!==t&&(this._timeScaleInterpolant=null,this._mixer._takeBackControlInterpolant(t)),this},getMixer:function(){return this._mixer},getClip:function(){return this._clip},getRoot:function(){return this._localRoot||this._mixer._root},_update:function(t,e,i,n){var r=this._startTime;if(null!==r){var o=(t-r)*i;if(o<0||0===i)return;this._startTime=null,e=i*o}e*=this._updateTimeScale(t);var a=this._updateTime(e),s=this._updateWeight(t);if(s>0)for(var c=this._interpolants,u=this._propertyBindings,h=0,l=c.length;h!==l;++h)c[h].evaluate(a),u[h].accumulate(n,s)},_updateWeight:function(t){var e=0;if(this.enabled){e=this.weight;var i=this._weightInterpolant;if(null!==i){var n=i.evaluate(t)[0];e*=n,t>i.parameterPositions[1]&&(this.stopFading(),0===n&&(this.enabled=!1))}}return this._effectiveWeight=e,e},_updateTimeScale:function(t){var e=0;if(!this.paused){e=this.timeScale;var i=this._timeScaleInterpolant;if(null!==i){var n=i.evaluate(t)[0];e*=n,t>i.parameterPositions[1]&&(this.stopWarping(),0===e?this.paused=!0:this.timeScale=e)}}return this._effectiveTimeScale=e,e},_updateTime:function(t){var e=this.time+t;if(0===t)return e;var i=this._clip.duration,n=this.loop,r=this._loopCount;if(n===cd){r===-1&&(this.loopCount=0,this._setEndings(!0,!0,!1));t:{if(e>=i)e=i;else{if(!(e<0))break t;e=0}this.clampWhenFinished?this.paused=!0:this.enabled=!1,this._mixer.dispatchEvent({type:"finished",action:this,direction:t<0?-1:1})}}else{var o=n===hd;if(r===-1&&(t>=0?(r=0,this._setEndings(!0,0===this.repetitions,o)):this._setEndings(0===this.repetitions,!0,o)),e>=i||e<0){var a=Math.floor(e/i);e-=i*a,r+=Math.abs(a);var s=this.repetitions-r;if(s<0)this.clampWhenFinished?this.paused=!0:this.enabled=!1,e=t>0?i:0,this._mixer.dispatchEvent({type:"finished",action:this,direction:t>0?1:-1});else{if(0===s){var c=t<0;this._setEndings(c,!c,o)}else this._setEndings(!1,!1,o);this._loopCount=r,this._mixer.dispatchEvent({type:"loop",action:this,loopDelta:a})}}if(o&&1===(1&r))return this.time=e,i-e}return this.time=e,e},_setEndings:function(t,e,i){var n=this._interpolantSettings;i?(n.endingStart=md,n.endingEnd=md):(t?n.endingStart=this.zeroSlopeAtStart?md:pd:n.endingStart=gd,e?n.endingEnd=this.zeroSlopeAtEnd?md:pd:n.endingEnd=gd)},_scheduleFading:function(t,e,i){var n=this._mixer,r=n.time,o=this._weightInterpolant;null===o&&(o=n._lendControlInterpolant(),this._weightInterpolant=o);var a=o.parameterPositions,s=o.sampleValues;return a[0]=r,s[0]=e,a[1]=r+t,s[1]=i,this}},Object.assign(nn.prototype,E.prototype,{clipAction:function(t,e){var i=e||this._root,n=i.uuid,r="string"==typeof t?Mi.findByName(i,t):t,o=null!==r?r.uuid:t,a=this._actionsByClip[o],s=null;if(void 0!==a){var c=a.actionByRoot[n];if(void 0!==c)return c;s=a.knownActions[0],null===r&&(r=s._clip)}if(null===r)return null;var u=new en(this,r,e);return this._bindAction(u,s),this._addInactiveAction(u,o,n),u},existingAction:function(t,e){var i=e||this._root,n=i.uuid,r="string"==typeof t?Mi.findByName(i,t):t,o=r?r.uuid:t,a=this._actionsByClip[o];return void 0!==a?a.actionByRoot[n]||null:null},stopAllAction:function(){var t=this._actions,e=this._nActiveActions,i=this._bindings,n=this._nActiveBindings;this._nActiveActions=0,this._nActiveBindings=0;for(var r=0;r!==e;++r)t[r].reset();for(var r=0;r!==n;++r)i[r].useCount=0;return this},update:function(t){t*=this.timeScale;for(var e=this._actions,i=this._nActiveActions,n=this.time+=t,r=Math.sign(t),o=this._accuIndex^=1,a=0;a!==i;++a){var s=e[a];s.enabled&&s._update(n,t,r,o)}for(var c=this._bindings,u=this._nActiveBindings,a=0;a!==u;++a)c[a].apply(o);return this},getRoot:function(){return this._root},uncacheClip:function(t){var e=this._actions,i=t.uuid,n=this._actionsByClip,r=n[i];if(void 0!==r){for(var o=r.knownActions,a=0,s=o.length;a!==s;++a){var c=o[a];this._deactivateAction(c);var u=c._cacheIndex,h=e[e.length-1];c._cacheIndex=null,c._byClipCacheIndex=null,h._cacheIndex=u,e[u]=h,e.pop(),this._removeInactiveBindingsForAction(c)}delete n[i]}},uncacheRoot:function(t){var e=t.uuid,i=this._actionsByClip;for(var n in i){var r=i[n].actionByRoot,o=r[e];void 0!==o&&(this._deactivateAction(o),this._removeInactiveAction(o))}var a=this._bindingsByRootAndName,s=a[e];if(void 0!==s)for(var c in s){var u=s[c];u.restoreOriginalState(),this._removeInactiveBinding(u)}},uncacheAction:function(t,e){var i=this.existingAction(t,e);null!==i&&(this._deactivateAction(i),this._removeInactiveAction(i))}}),Object.assign(nn.prototype,{_bindAction:function(t,e){var i=t._localRoot||this._root,n=t._clip.tracks,r=n.length,o=t._propertyBindings,a=t._interpolants,s=i.uuid,c=this._bindingsByRootAndName,u=c[s];void 0===u&&(u={},c[s]=u);for(var h=0;h!==r;++h){var l=n[h],d=l.name,f=u[d];if(void 0!==f)o[h]=f;else{if(f=o[h],void 0!==f){null===f._cacheIndex&&(++f.referenceCount,this._addInactiveBinding(f,s,d));continue}var p=e&&e._propertyBindings[h].binding.parsedPath;f=new Ji(tn.create(i,d,p),l.ValueTypeName,l.getValueSize()),++f.referenceCount,this._addInactiveBinding(f,s,d),o[h]=f}a[h].resultBuffer=f.buffer}},_activateAction:function(t){if(!this._isActiveAction(t)){if(null===t._cacheIndex){var e=(t._localRoot||this._root).uuid,i=t._clip.uuid,n=this._actionsByClip[i];this._bindAction(t,n&&n.knownActions[0]),this._addInactiveAction(t,i,e)}for(var r=t._propertyBindings,o=0,a=r.length;o!==a;++o){var s=r[o];0===s.useCount++&&(this._lendBinding(s),s.saveOriginalState())}this._lendAction(t)}},_deactivateAction:function(t){if(this._isActiveAction(t)){for(var e=t._propertyBindings,i=0,n=e.length;i!==n;++i){var r=e[i];0===--r.useCount&&(r.restoreOriginalState(),this._takeBackBinding(r))}this._takeBackAction(t)}},_initMemoryManager:function(){this._actions=[],this._nActiveActions=0,this._actionsByClip={},this._bindings=[],this._nActiveBindings=0,this._bindingsByRootAndName={},this._controlInterpolants=[],this._nActiveControlInterpolants=0;var t=this;this.stats={actions:{get total(){return t._actions.length},get inUse(){return t._nActiveActions}},bindings:{get total(){return t._bindings.length},get inUse(){return t._nActiveBindings}},controlInterpolants:{get total(){return t._controlInterpolants.length},get inUse(){return t._nActiveControlInterpolants}}}},_isActiveAction:function(t){var e=t._cacheIndex;return null!==e&&e<this._nActiveActions},_addInactiveAction:function(t,e,i){var n=this._actions,r=this._actionsByClip,o=r[e];if(void 0===o)o={knownActions:[t],actionByRoot:{}},t._byClipCacheIndex=0,r[e]=o;else{var a=o.knownActions;t._byClipCacheIndex=a.length,a.push(t)}t._cacheIndex=n.length,n.push(t),o.actionByRoot[i]=t},_removeInactiveAction:function(t){var e=this._actions,i=e[e.length-1],n=t._cacheIndex;i._cacheIndex=n,e[n]=i,e.pop(),t._cacheIndex=null;var r=t._clip.uuid,o=this._actionsByClip,a=o[r],s=a.knownActions,c=s[s.length-1],u=t._byClipCacheIndex;c._byClipCacheIndex=u,s[u]=c,s.pop(),t._byClipCacheIndex=null;var h=a.actionByRoot,l=(e._localRoot||this._root).uuid;delete h[l],0===s.length&&delete o[r],this._removeInactiveBindingsForAction(t)},_removeInactiveBindingsForAction:function(t){for(var e=t._propertyBindings,i=0,n=e.length;i!==n;++i){var r=e[i];0===--r.referenceCount&&this._removeInactiveBinding(r)}},_lendAction:function(t){var e=this._actions,i=t._cacheIndex,n=this._nActiveActions++,r=e[n];t._cacheIndex=n,e[n]=t,r._cacheIndex=i,e[i]=r},_takeBackAction:function(t){var e=this._actions,i=t._cacheIndex,n=--this._nActiveActions,r=e[n];t._cacheIndex=n,e[n]=t,r._cacheIndex=i,e[i]=r},_addInactiveBinding:function(t,e,i){var n=this._bindingsByRootAndName,r=n[e],o=this._bindings;void 0===r&&(r={},n[e]=r),r[i]=t,t._cacheIndex=o.length,o.push(t)},_removeInactiveBinding:function(t){var e=this._bindings,i=t.binding,n=i.rootNode.uuid,r=i.path,o=this._bindingsByRootAndName,a=o[n],s=e[e.length-1],c=t._cacheIndex;s._cacheIndex=c,e[c]=s,e.pop(),delete a[r];t:{for(var u in a)break t;delete o[n]}},_lendBinding:function(t){var e=this._bindings,i=t._cacheIndex,n=this._nActiveBindings++,r=e[n];t._cacheIndex=n,e[n]=t,r._cacheIndex=i,e[i]=r},_takeBackBinding:function(t){var e=this._bindings,i=t._cacheIndex,n=--this._nActiveBindings,r=e[n];t._cacheIndex=n,e[n]=t,r._cacheIndex=i,e[i]=r},_lendControlInterpolant:function(){var t=this._controlInterpolants,e=this._nActiveControlInterpolants++,i=t[e];return void 0===i&&(i=new pi(new Float32Array(2),new 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v=a.attributes.position,y=a.attributes.normal,u=0,f=0,p=v.count;f<p;f++)t.set(v.getX(f),v.getY(f),v.getZ(f)).applyMatrix4(r),e.set(y.getX(f),y.getY(f),y.getZ(f)),e.applyMatrix3(i).normalize().multiplyScalar(this.size).add(t),o.setXYZ(u,t.x,t.y,t.z),u+=1,o.setXYZ(u,e.x,e.y,e.z),u+=1;return o.needsUpdate=!0,this}}(),cn.prototype=Object.create(re.prototype),cn.prototype.constructor=cn,cn.prototype.dispose=function(){this.cone.geometry.dispose(),this.cone.material.dispose()},cn.prototype.update=function(){var t=new N,e=new N;return function(){var i=this.light.distance?this.light.distance:1e3,n=i*Math.tan(this.light.angle);this.cone.scale.set(n,n,i),t.setFromMatrixPosition(this.light.matrixWorld),e.setFromMatrixPosition(this.light.target.matrixWorld),this.cone.lookAt(e.sub(t)),this.cone.material.color.copy(this.light.color).multiplyScalar(this.light.intensity)}}(),un.prototype=Object.create(ue.prototype),un.prototype.constructor=un,hn.prototype=Object.create(ae.prototype),hn.prototype.constructor=hn,ln.prototype=Object.create(re.prototype),ln.prototype.constructor=ln,ln.prototype.dispose=function(){this.lightSphere.geometry.dispose(),this.lightSphere.material.dispose()},ln.prototype.update=function(){var t=new N;return function(){this.colors[0].copy(this.light.color).multiplyScalar(this.light.intensity),this.colors[1].copy(this.light.groundColor).multiplyScalar(this.light.intensity),this.lightSphere.lookAt(t.setFromMatrixPosition(this.light.matrixWorld).negate()),this.lightSphere.geometry.colorsNeedUpdate=!0}}(),dn.prototype=Object.create(Ve.prototype),dn.prototype.constructor=dn,dn.prototype.update=function(){var t=new N,e=new N,i=new Lt;return function(){this.object.updateMatrixWorld(!0),i.getNormalMatrix(this.object.matrixWorld);for(var n=this.object.matrixWorld,r=this.geometry.attributes.position,o=this.object.geometry,a=o.vertices,s=o.faces,c=0,u=0,h=s.length;u<h;u++){var l=s[u],d=l.normal;t.copy(a[l.a]).add(a[l.b]).add(a[l.c]).divideScalar(3).applyMatrix4(n),e.copy(d).applyMatrix3(i).normalize().multiplyScalar(this.size).add(t),r.setXYZ(c,t.x,t.y,t.z),c+=1,r.setXYZ(c,e.x,e.y,e.z),c+=1}return r.needsUpdate=!0,this}}(),fn.prototype=Object.create(ue.prototype),fn.prototype.constructor=fn,pn.prototype=Object.create(re.prototype),pn.prototype.constructor=pn,pn.prototype.dispose=function(){var t=this.children[0],e=this.children[1];t.geometry.dispose(),t.material.dispose(),e.geometry.dispose(),e.material.dispose()},pn.prototype.update=function(){var t=new N,e=new N,i=new N;return function(){t.setFromMatrixPosition(this.light.matrixWorld),e.setFromMatrixPosition(this.light.target.matrixWorld),i.subVectors(e,t);var n=this.children[0],r=this.children[1];n.lookAt(i),n.material.color.copy(this.light.color).multiplyScalar(this.light.intensity),r.lookAt(i),r.scale.z=i.length()}}(),mn.prototype=Object.create(Ve.prototype),mn.prototype.constructor=mn,mn.prototype.update=function(){function t(t,o,a,s){n.set(o,a,s).unproject(r);var c=i[t];if(void 0!==c)for(var u=0,h=c.length;u<h;u++)e.vertices[c[u]].copy(n)}var e,i,n=new N,r=new Pe;return function(){e=this.geometry,i=this.pointMap;var n=1,o=1;r.projectionMatrix.copy(this.camera.projectionMatrix),t("c",0,0,-1),t("t",0,0,1),t("n1",-n,-o,-1),t("n2",n,-o,-1),t("n3",-n,o,-1),t("n4",n,o,-1),t("f1",-n,-o,1),t("f2",n,-o,1),t("f3",-n,o,1),t("f4",n,o,1),t("u1",.7*n,1.1*o,-1),t("u2",.7*-n,1.1*o,-1),t("u3",0,2*o,-1),t("cf1",-n,0,1),t("cf2",n,0,1),t("cf3",0,-o,1),t("cf4",0,o,1),t("cn1",-n,0,-1),t("cn2",n,0,-1),t("cn3",0,-o,-1),t("cn4",0,o,-1),e.verticesNeedUpdate=!0}}(),gn.prototype=Object.create(ae.prototype),gn.prototype.constructor=gn,vn.prototype=Object.create(Ve.prototype),vn.prototype.constructor=vn,vn.prototype.update=function(){var t=new Et;return function(e){if(e&&e.isBox3?t.copy(e):t.setFromObject(e),!t.isEmpty()){var i=t.min,n=t.max,r=this.geometry.attributes.position,o=r.array;o[0]=n.x,o[1]=n.y,o[2]=n.z,o[3]=i.x,o[4]=n.y,o[5]=n.z,o[6]=i.x,o[7]=i.y,o[8]=n.z,o[9]=n.x,o[10]=i.y,o[11]=n.z,o[12]=n.x,o[13]=n.y,o[14]=i.z,o[15]=i.x,o[16]=n.y,o[17]=i.z,o[18]=i.x,o[19]=i.y,o[20]=i.z,o[21]=n.x,o[22]=i.y,o[23]=i.z,r.needsUpdate=!0,this.geometry.computeBoundingSphere()}}}(),yn.prototype=Object.create(ue.prototype),yn.prototype.constructor=yn;var Kp=new ue;Kp.addAttribute("position",new te([0,0,0,0,1,0],3));var Qp=new yn(0,.5,1,5,1);Qp.translate(0,-.5,0),bn.prototype=Object.create(re.prototype),bn.prototype.constructor=bn,bn.prototype.setDirection=function(){var t,e=new N;return function(i){i.y>.99999?this.quaternion.set(0,0,0,1):i.y<-.99999?this.quaternion.set(1,0,0,0):(e.set(i.z,0,-i.x).normalize(),t=Math.acos(i.y),this.quaternion.setFromAxisAngle(e,t))}}(),bn.prototype.setLength=function(t,e,i){void 0===e&&(e=.2*t),void 0===i&&(i=.2*e),this.line.scale.set(1,Math.max(0,t-e),1),this.line.updateMatrix(),this.cone.scale.set(i,e,i),this.cone.position.y=t,this.cone.updateMatrix()},bn.prototype.setColor=function(t){this.line.material.color.copy(t),this.cone.material.color.copy(t)},xn.prototype=Object.create(ae.prototype),xn.prototype.constructor=xn,wn.prototype=Object.create(xn.prototype),wn.prototype.constructor=wn,_n.prototype=Object.create(ue.prototype),_n.prototype.constructor=_n,Sn.prototype=Object.create(ue.prototype),Sn.prototype.constructor=Sn,An.prototype=Object.create(ue.prototype),An.prototype.constructor=An,Mn.prototype=Object.create(ae.prototype),Mn.prototype.constructor=Mn,Pn.prototype=Object.create(ue.prototype),Pn.prototype.constructor=Pn,Cn.prototype=Object.create(ae.prototype),Cn.prototype.constructor=Cn,Tn.prototype=Object.create(ue.prototype),Tn.prototype.constructor=Tn,En.prototype=Object.create(ue.prototype),En.prototype.constructor=En;(function(){function t(){}var e=new N,i=new t,n=new t,r=new t;return t.prototype.init=function(t,e,i,n){this.c0=t,this.c1=i,this.c2=-3*t+3*e-2*i-n,this.c3=2*t-2*e+i+n},t.prototype.initNonuniformCatmullRom=function(t,e,i,n,r,o,a){var s=(e-t)/r-(i-t)/(r+o)+(i-e)/o,c=(i-e)/o-(n-e)/(o+a)+(n-i)/a;s*=o,c*=o,this.init(e,i,s,c)},t.prototype.initCatmullRom=function(t,e,i,n,r){this.init(e,i,r*(i-t),r*(n-e))},t.prototype.calc=function(t){var e=t*t,i=e*t;return this.c0+this.c1*t+this.c2*e+this.c3*i},Li.create(function(t){this.points=t||[],this.closed=!1},function(t){var o,a,s,c,u=this.points;c=u.length,c<2&&console.log("duh, you need at least 2 points"),o=(c-(this.closed?0:1))*t,a=Math.floor(o),s=o-a,this.closed?a+=a>0?0:(Math.floor(Math.abs(a)/u.length)+1)*u.length:0===s&&a===c-1&&(a=c-2,s=1);var h,l,d,f;if(this.closed||a>0?h=u[(a-1)%c]:(e.subVectors(u[0],u[1]).add(u[0]),h=e),l=u[a%c],d=u[(a+1)%c],this.closed||a+2<c?f=u[(a+2)%c]:(e.subVectors(u[c-1],u[c-2]).add(u[c-1]),f=e),void 0===this.type||"centripetal"===this.type||"chordal"===this.type){var p="chordal"===this.type?.5:.25,m=Math.pow(h.distanceToSquared(l),p),g=Math.pow(l.distanceToSquared(d),p),v=Math.pow(d.distanceToSquared(f),p);g<1e-4&&(g=1),m<1e-4&&(m=g),v<1e-4&&(v=g),i.initNonuniformCatmullRom(h.x,l.x,d.x,f.x,m,g,v),n.initNonuniformCatmullRom(h.y,l.y,d.y,f.y,m,g,v),r.initNonuniformCatmullRom(h.z,l.z,d.z,f.z,m,g,v)}else if("catmullrom"===this.type){var y=void 0!==this.tension?this.tension:.5;i.initCatmullRom(h.x,l.x,d.x,f.x,y),n.initCatmullRom(h.y,l.y,d.y,f.y,y),r.initCatmullRom(h.z,l.z,d.z,f.z,y)}var b=new N(i.calc(s),n.calc(s),r.calc(s));return b})})(),Li.create(function(t){console.warn("THREE.SplineCurve3 will be deprecated. 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e.subVectors(this.v2,this.v1),e.multiplyScalar(t),e.add(this.v1),e});Object.defineProperty(t,"AudioContext",{get:function(){return t.getAudioContext()}}),In.prototype={active:!0,params:null,execute:function(t){var e,i;return this.active&&this._listener&&(i=this.params?this.params.concat(t):t,e=this._listener.apply(this.context,i),this._isOnce&&this.detach()),e},detach:function(){return this.isBound()?this._signal.remove(this._listener,this.context):null},isBound:function(){return!!this._signal&&!!this._listener},isOnce:function(){return this._isOnce},getListener:function(){return this._listener},getSignal:function(){return this._signal},_destroy:function(){delete this._signal,delete this._listener,delete this.context},toString:function(){return"[SignalBinding isOnce:"+this._isOnce+", isBound:"+this.isBound()+", active:"+this.active+"]"}},Rn.prototype={VERSION:"1.0.0",memorize:!1,_shouldPropagate:!0,active:!0,_registerListener:function(t,e,i,n){var r,o=this._indexOfListener(t,i);if(o!==-1){if(r=this._bindings[o],r.isOnce()!==e)throw new Error("You cannot add"+(e?"":"Once")+"() then add"+(e?"Once":"")+"() the same listener without removing the relationship first.")}else r=new In(this,t,e,i,n),this._addBinding(r);return this.memorize&&this._prevParams&&r.execute(this._prevParams),r},_addBinding:function(t){var e=this._bindings.length;do--e;while(this._bindings[e]&&t._priority<=this._bindings[e]._priority);this._bindings.splice(e+1,0,t)},_indexOfListener:function(t,e){for(var i,n=this._bindings.length;n--;)if(i=this._bindings[n],i._listener===t&&i.context===e)return n;return-1},has:function(t,e){return this._indexOfListener(t,e)!==-1},add:function(t,e,i){return Ln(t,"add"),this._registerListener(t,!1,e,i)},addOnce:function(t,e,i){return Ln(t,"addOnce"),this._registerListener(t,!0,e,i)},remove:function(t,e){Ln(t,"remove");var i=this._indexOfListener(t,e);return i!==-1&&(this._bindings[i]._destroy(),this._bindings.splice(i,1)),t},removeAll:function(){for(var t=this._bindings.length;t--;)this._bindings[t]._destroy();this._bindings.length=0},getNumListeners:function(){return this._bindings.length},halt:function(){this._shouldPropagate=!1},dispatch:function(t){if(this.active){var e,i=Array.prototype.slice.call(arguments),n=this._bindings.length;if(this.memorize&&(this._prevParams=i),n){e=this._bindings.slice(),this._shouldPropagate=!0;do n--;while(e[n]&&this._shouldPropagate&&e[n].execute(i)!==!1)}}},forget:function(){this._prevParams=null},dispose:function(){this.removeAll(),delete this._bindings,delete this._prevParams},toString:function(){return"[Signal active:"+this.active+" numListeners:"+this.getNumListeners()+"]"}};var Jp={PROTEIN:1,NUCLEIC:2,RNA:3,DNA:4,POLYMER:5,WATER:6,HELIX:7,SHEET:8,BACKBONE:9,SIDECHAIN:10,ALL:11,HETERO:12,ION:13,SACCHARIDE:14};On.prototype={constructor:On,type:"selection",setString:function(t,e){if(void 0===t&&(t=this.string||""),t!==this.string){try{this.parse(t)}catch(t){this.selection={error:t.message}}this.string=t,this.test=this.makeAtomTest(),this.residueTest=this.makeResidueTest(),this.chainTest=this.makeChainTest(),this.modelTest=this.makeModelTest(),this.atomOnlyTest=this.makeAtomTest(!0),this.residueOnlyTest=this.makeResidueTest(!0),this.chainOnlyTest=this.makeChainTest(!0),this.modelOnlyTest=this.makeModelTest(!0),e||this.signals.stringChanged.dispatch(this.string)}},parse:function(t){if(this.selection={operator:void 0,rules:[]},t){var e,i,n=this,r=this.selection,o=[];t=t.replace(/\(/g," ( ").replace(/\)/g," ) ").trim(),"("===t.charAt(0)&&")"===t.substr(-1)&&(t=t.slice(1,-1).trim());var a,s,c,u,h,l,d,f,p,m,g=t.split(/\s+/),v=["*","","ALL"],y=function(t){e={operator:t,rules:[]},void 0===r?(r=e,n.selection=e):(r.rules.push(e),o.push(r),r=e)},b=function(t){i=r,r=o.pop(),void 0===r&&(y(t),x(i))},x=function(t){r.rules.push(t)};for(c=0;c<g.length;++c)if(a=g[c],"("!==a)if(")"!==a){if(u>0)if("NOT"===a.toUpperCase())u=1;else if(1===u)u=2;else{if(2!==u)throw new Error("something went wrong with 'not'");u=!1,b()}if("AND"!==a.toUpperCase())if("OR"!==a.toUpperCase())if("NOT"!==a.toUpperCase())if(s={},"HETERO"!==a.toUpperCase())if("WATER"!==a.toUpperCase())if("PROTEIN"!==a.toUpperCase())if("NUCLEIC"!==a.toUpperCase())if("RNA"!==a.toUpperCase())if("DNA"!==a.toUpperCase())if("POLYMER"!==a.toUpperCase())if("ION"!==a.toUpperCase())if("SACCHARIDE"!==a.toUpperCase()&&"SUGAR"!==a.toUpperCase())if("HYDROGEN"!==a.toUpperCase())if("SMALL"!==a.toUpperCase())if("NUCLEOPHILIC"!==a.toUpperCase())if("HYDROPHOBIC"!==a.toUpperCase())if("AROMATIC"!==a.toUpperCase())if("AMIDE"!==a.toUpperCase())if("ACIDIC"!==a.toUpperCase())if("BASIC"!==a.toUpperCase())if("CHARGED"!==a.toUpperCase())if("POLAR"!==a.toUpperCase())if("NONPOLAR"!==a.toUpperCase())if("HELIX"!==a.toUpperCase())if("SHEET"!==a.toUpperCase())if("TURN"!==a.toUpperCase())if("BACKBONE"!==a.toUpperCase())if("SIDECHAIN"!==a.toUpperCase())if("SIDECHAINATTACHED"!==a.toUpperCase())if(v.indexOf(a.toUpperCase())===-1)if("@"!==a.charAt(0))if("#"!==a.charAt(0))if("["!==a[0]||"]"!==a[a.length-1])if(a.length>=1&&a.length<=4&&"^"!==a[0]&&":"!==a[0]&&"."!==a[0]&&"%"!==a[0]&&"/"!==a[0]&&isNaN(parseInt(a)))s.resname=a.toUpperCase(),x(s);else{if(s={operator:"AND",rules:[]},d=a.split("/"),d.length>1&&d[1]){if(isNaN(parseInt(d[1])))throw new Error("model must be an integer");s.rules.push({model:parseInt(d[1])})}if(p=d[0].split("%"),p.length>1&&s.rules.push({altloc:p[1]}),h=p[0].split("."),h.length>1&&h[1]){if(h[1].length>4)throw new Error("atomname must be one to four characters");s.rules.push({atomname:h[1].substring(0,4).toUpperCase()})}if(l=h[0].split(":"),l.length>1&&l[1]&&s.rules.push({chainname:l[1]}),m=l[0].split("^"),m.length>1&&s.rules.push({inscode:m[1]}),m[0]){var w,_;if("-"===m[0][0]&&(m[0]=m[0].substr(1),w=!0),m[0].includes("--")&&(m[0]=m[0].replace("--","-"),_=!0),f=m[0].split("-"),1===f.length){if(f=parseInt(f[0]),isNaN(f))throw new Error("resi must be an integer");w&&(f*=-1),s.rules.push({resno:f})}else{if(2!==f.length)throw new Error("resi range must contain one '-'");w&&(f[0]*=-1),_&&(f[1]*=-1),s.rules.push({resno:[parseInt(f[0]),parseInt(f[1])]})}}if(1===s.rules.length)x(s.rules[0]);else{if(!(s.rules.length>1))throw new Error("empty selection chunk");x(s)}}else s.resname=a.substr(1,a.length-2).toUpperCase(),x(s);else s.element=a.substr(1).toUpperCase(),x(s);else{for(var S=a.substr(1).split(","),A=0,M=S.length;A<M;++A)S[A]=parseInt(S[A]);S.sort(function(t,e){return t-e}),s.atomindex=S,s.atomindexFirst=S[0],s.atomindexLast=S[S.length-1],x(s)}else s.keyword=Jp.ALL,x(s);else s={operator:"OR",rules:[{keyword:Jp.SIDECHAIN},{operator:"AND",negate:!1,rules:[{keyword:Jp.PROTEIN},{operator:"OR",negate:!1,rules:[{atomname:"CA"},{atomname:"BB"}]}]},{operator:"AND",negate:!1,rules:[{resname:"PRO"},{atomname:"N"}]},{operator:"AND",negate:!1,rules:[{keyword:Jp.NUCLEIC},{operator:"OR",negate:!0,rules:[{atomname:"P"},{atomname:"OP1"},{atomname:"OP2"},{atomname:"O3'"},{atomname:"O3*"},{atomname:"O5'"},{atomname:"O5*"},{atomname:"C5'"},{atomname:"C5*"}]}]}]},x(s);else s.keyword=Jp.SIDECHAIN,x(s);else s.keyword=Jp.BACKBONE,x(s);else s={operator:"AND",rules:[{operator:"OR",negate:!0,rules:[{keyword:Jp.HELIX},{keyword:Jp.SHEET}]},{operator:"OR",rules:[{keyword:Jp.PROTEIN},{sstruc:"s"},{sstruc:"t"},{sstruc:"l"}]}]},x(s);else s.keyword=Jp.SHEET,x(s);else s.keyword=Jp.HELIX,x(s);else s={operator:"OR",rules:[{resname:"ALA"},{resname:"CYS"},{resname:"GLY"},{resname:"ILE"},{resname:"LEU"},{resname:"MET"},{resname:"PHE"},{resname:"PRO"},{resname:"VAL"},{resname:"TRP"}]},x(s);else s={operator:"OR",rules:[{resname:"ASP"},{resname:"GLU"},{resname:"HIS"},{resname:"LYS"},{resname:"ARG"},{resname:"ASN"},{resname:"GLN"},{resname:"SER"},{resname:"THR"},{resname:"TYR"}]},x(s);else s={operator:"OR",rules:[{resname:"ASP"},{resname:"GLU"},{resname:"HIS"},{resname:"LYS"},{resname:"ARG"}]},x(s);else s={operator:"OR",rules:[{resname:"HIS"},{resname:"LYS"},{resname:"ARG"}]},x(s);else s={operator:"OR",rules:[{resname:"ASP"},{resname:"GLU"}]},x(s);else s={operator:"OR",rules:[{resname:"ASN"},{resname:"GLN"}]},x(s);else s={operator:"OR",rules:[{resname:"PHE"},{resname:"TYR"},{resname:"TRP"}]},x(s);else s={operator:"OR",rules:[{resname:"VAL"},{resname:"LEU"},{resname:"ILE"},{resname:"MET"},{resname:"PRO"}]},x(s);else s={operator:"OR",rules:[{resname:"SER"},{resname:"THR"},{resname:"CYS"}]},x(s);else s={operator:"OR",rules:[{resname:"GLY"},{resname:"ALA"}]},x(s);else s.element="H",x(s);else s.keyword=Jp.SACCHARIDE,x(s);else s.keyword=Jp.ION,x(s);else s.keyword=Jp.POLYMER,x(s);else s.keyword=Jp.DNA,x(s);else s.keyword=Jp.RNA,x(s);else s.keyword=Jp.NUCLEIC,x(s);else s.keyword=Jp.PROTEIN,x(s);else s.keyword=Jp.WATER,x(s);else s.keyword=Jp.HETERO,x(s);else u=1,y(),r.negate=!0;else"AND"===r.operator?b("OR"):r.operator="OR";else if("OR"===r.operator){var P=r.rules.pop();y("AND"),x(P)}else r.operator="AND"}else b(),r.negate&&b();else u=!1,y();void 0===this.selection.operator&&1===this.selection.rules.length&&this.selection.rules[0].hasOwnProperty("operator")&&(this.selection=this.selection.rules[0])}},_makeTest:function(t,e){if(void 0===e&&(e=this.selection),null===e)return!1;if(e.error)return!1;var i=e.rules.length;if(0===i)return!1;for(var n,r,o,a,s=!e.negate,c=!!e.negate,u=[],h=0;h<i;++h)n=e.rules[h],n.hasOwnProperty("operator")&&(u[h]=this._makeTest(t,n));return function(h){r="AND"===e.operator,a=!1;for(var l=0;l<i;++l)if(n=e.rules[l],n.hasOwnProperty("operator")){if(o=u[l]?u[l](h):-1,o===-1){a=!0;continue}if(o===!0){if(r)continue;return s}if(r)return c}else{if(n.keyword===Jp.ALL){if(r)continue;return s}if(o=t(h,n),o!==-1){if(o===!0){if(r)continue;return s}if(r)return c}else a=!0}return a?-1:r?s:c}},_filter:function(t,e){if(void 0===e&&(e=this.selection),e.error)return e;var i=e.rules.length;if(0===i)return e;var n={operator:e.operator,rules:[]};e.hasOwnProperty("negate")&&(n.negate=e.negate);for(var r=0;r<i;++r){var o=e.rules[r];if(o.hasOwnProperty("operator")){var a=this._filter(t,o);null!==a&&n.rules.push(a)}else t(o)||n.rules.push(o)}return n.rules.length>0?e:null},makeAtomTest:function(t){var e,i=["h","g","i"],n=["e","b"];e=t?this._filter(function(t){return void 0!==t.keyword&&t.keyword!==Jp.BACKBONE&&t.keyword!==Jp.SIDECHAIN||(void 0!==t.model||(void 0!==t.chainname||(void 0!==t.resname||(void 0!==t.resno||void 0!==t.sstruc))))}):this.selection;var r=function(t,e){if(void 0===e.atomname&&void 0===e.element&&void 0===e.altloc&&void 0===e.atomindex&&void 0===e.keyword&&void 0===e.inscode&&void 0===e.resname&&void 0===e.sstruc&&void 0===e.resno&&void 0===e.chainname&&void 0===e.model)return-1;if(void 0!==e.keyword){if(e.keyword===Jp.BACKBONE&&!t.isBackbone())return!1;if(e.keyword===Jp.SIDECHAIN&&!t.isSidechain())return!1;if(e.keyword===Jp.HETERO&&!t.isHetero())return!1;if(e.keyword===Jp.PROTEIN&&!t.isProtein())return!1;if(e.keyword===Jp.NUCLEIC&&!t.isNucleic())return!1;if(e.keyword===Jp.RNA&&!t.isRna())return!1;if(e.keyword===Jp.DNA&&!t.isDna())return!1;if(e.keyword===Jp.POLYMER&&!t.isPolymer())return!1;if(e.keyword===Jp.WATER&&!t.isWater())return!1;if(e.keyword===Jp.HELIX&&i.indexOf(t.sstruc)===-1)return!1;if(e.keyword===Jp.SHEET&&n.indexOf(t.sstruc)===-1)return!1;if(e.keyword===Jp.ION&&!t.isIon())return!1;if(e.keyword===Jp.SACCHARIDE&&!t.isSaccharide())return!1}if(void 0!==e.atomname&&e.atomname!==t.atomname)return!1;if(void 0!==e.element&&e.element!==t.element)return!1;if(void 0!==e.altloc&&e.altloc!==t.altloc)return!1;if(void 0!==e.atomindex&&vh(e.atomindex,t.index)<0)return!1;if(void 0!==e.resname&&e.resname!==t.resname)return!1;if(void 0!==e.sstruc&&e.sstruc!==t.sstruc)return!1;if(void 0!==e.resno)if(Array.isArray(e.resno)&&2===e.resno.length){if(e.resno[0]>t.resno||e.resno[1]<t.resno)return!1}else if(e.resno!==t.resno)return!1;return(void 0===e.inscode||e.inscode===t.inscode)&&((void 0===e.chainname||e.chainname===t.chainname)&&(void 0===e.model||e.model===t.modelIndex))};return this._makeTest(r,e)},makeResidueTest:function(t){var e,i=["h","g","i"],n=["e","b"];e=t?this._filter(function(t){return t.keyword===Jp.BACKBONE||t.keyword===Jp.SIDECHAIN||(void 0!==t.model||(void 0!==t.chainname||(void 0!==t.atomname||(void 0!==t.element||void 0!==t.altloc))))}):this.selection;var r=function(t,e){if(void 0===e.resname&&void 0===e.resno&&void 0===e.inscode&&void 0===e.sstruc&&void 0===e.model&&void 0===e.chainname&&void 0===e.atomindex&&(void 0===e.keyword||e.keyword===Jp.BACKBONE||e.keyword===Jp.SIDECHAIN))return-1;if(void 0!==e.keyword){if(e.keyword===Jp.HETERO&&!t.isHetero())return!1;if(e.keyword===Jp.PROTEIN&&!t.isProtein())return!1;if(e.keyword===Jp.NUCLEIC&&!t.isNucleic())return!1;if(e.keyword===Jp.RNA&&!t.isRna())return!1;if(e.keyword===Jp.DNA&&!t.isDna())return!1;if(e.keyword===Jp.POLYMER&&!t.isPolymer())return!1;if(e.keyword===Jp.WATER&&!t.isWater())return!1;if(e.keyword===Jp.HELIX&&i.indexOf(t.sstruc)===-1)return!1;if(e.keyword===Jp.SHEET&&n.indexOf(t.sstruc)===-1)return!1;if(e.keyword===Jp.ION&&!t.isIon())return!1;if(e.keyword===Jp.SACCHARIDE&&!t.isSaccharide())return!1}if(void 0!==e.atomindex&&(t.atomOffset>e.atomindexLast||t.atomEnd<e.atomindexFirst))return!1;if(void 0!==e.resname&&e.resname!==t.resname)return!1;if(void 0!==e.sstruc&&e.sstruc!==t.sstruc)return!1;if(void 0!==e.resno)if(Array.isArray(e.resno)&&2===e.resno.length){if(e.resno[0]>t.resno||e.resno[1]<t.resno)return!1;
-}else if(e.resno!==t.resno)return!1;return(void 0===e.inscode||e.inscode===t.inscode)&&((void 0===e.chainname||e.chainname===t.chainname)&&(void 0===e.model||e.model===t.modelIndex))};return this._makeTest(r,e)},makeChainTest:function(t){var e,i=[Jp.HETERO,Jp.PROTEIN,Jp.NUCLEIC,Jp.RNA,Jp.DNA,Jp.POLYMER,Jp.WATER,Jp.ION,Jp.SACCHARIDE];e=t?this._filter(function(t){return void 0!==t.keyword&&!i.includes(t.keyword)||(void 0!==t.resname||(void 0!==t.resno||(void 0!==t.atomname||(void 0!==t.element||(void 0!==t.altloc||(void 0!==t.sstruc||void 0!==t.inscode))))))}):this.selection;var n=function(t,e){if(void 0===e.chainname&&void 0===e.model&&void 0===e.atomindex&&(void 0===e.keyword||!i.includes(e.keyword)))return-1;if(void 0!==e.keyword){if(e.keyword===Jp.HETERO&&!t.isHetero())return!1;if(e.keyword===Jp.PROTEIN&&!t.isProtein())return!1;if(e.keyword===Jp.NUCLEIC&&!t.isNucleic())return!1;if(e.keyword===Jp.RNA&&!t.isRna())return!1;if(e.keyword===Jp.DNA&&!t.isDna())return!1;if(e.keyword===Jp.POLYMER&&!t.isPolymer())return!1;if(e.keyword===Jp.WATER&&!t.isWater())return!1;if(e.keyword===Jp.ION&&!t.isIon())return!1;if(e.keyword===Jp.SACCHARIDE&&!t.isSaccharide())return!1}return(void 0===e.atomindex||!(t.atomOffset>e.atomindexLast||t.atomEnd<e.atomindexFirst))&&((void 0===e.chainname||e.chainname===t.chainname)&&(void 0===e.model||e.model===t.modelIndex))};return this._makeTest(n,e)},makeModelTest:function(t){var e;e=t?this._filter(function(t){return void 0!==t.keyword||(void 0!==t.chainname||(void 0!==t.resname||(void 0!==t.resno||(void 0!==t.atomname||(void 0!==t.element||(void 0!==t.altloc||(void 0!==t.sstruc||void 0!==t.inscode)))))))}):this.selection;var i=function(t,e){return void 0===e.model&&void 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n=hv(arguments),t=n[0],e=n[1],i=n[2],t=kg(t),e=kg(e),i=kg(i),.2126*t+.7152*e+.0722*i},kg=function(t){return t/=255,t<=.03928?t/12.92:Vg((t+.055)/1.055,2.4)},tg=[],Sg=function(t,e,i,n){var r,o,a,s;for(null==i&&(i=.5),null==n&&(n="rgb"),"object"!==uv(t)&&(t=cg(t)),"object"!==uv(e)&&(e=cg(e)),a=0,o=tg.length;a<o;a++)if(r=tg[a],n===r[0]){s=r[1](t,e,i,n);break}if(null==s)throw"color mode "+n+" is not supported";return s.alpha(t.alpha()+i*(e.alpha()-t.alpha())),s},cg.interpolate=Sg,Gm.prototype.interpolate=function(t,e,i){return Sg(this,t,e,i)},cg.mix=Sg,Gm.prototype.mix=Gm.prototype.interpolate,Cg=function(t,e,i,n){var r,o;return r=t._rgb,o=e._rgb,new Gm(r[0]+i*(o[0]-r[0]),r[1]+i*(o[1]-r[1]),r[2]+i*(o[2]-r[2]),n)},tg.push(["rgb",Cg]),Gm.prototype.luminance=function(t,e){var i,n,r,o;return null==e&&(e="rgb"),arguments.length?(0===t?this._rgb=[0,0,0,this._rgb[3]]:1===t?this._rgb=[255,255,255,this._rgb[3]]:(n=1e-7,r=20,o=function(i,a){var s,c;return 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e=this.allocateGidRange(t);return e&&(this.objectList.push(t),this.rangeList.push(e)),this},removeObject:function(t){t=this.getBaseObject(t);var e=this.objectList.indexOf(t);return e!==-1&&(this.objectList.splice(e,1),this.rangeList.splice(e,1),0===this.objectList.length&&(this.nextGid=1)),this},updateObject:function(t,e){t=this.getBaseObject(t);var i=this.objectList.indexOf(t);if(i!==-1){var n=this.rangeList[i];if(n[1]===this.nextGid){var r=this.getGidCount(t);this.nextGid+=r-(n[1]-n[0]),n[1]=this.nextGid}else this.rangeList[i]=this.allocateGidRange(t)}else e||Pv.warn("GidPool.updateObject: object not found.");return this},getGidCount:function(t){t=this.getBaseObject(t);var e=0;return"Structure"===t.type?e=t.atomStore.count+t.bondStore.count+t.backboneBondStore.count+t.rungBondStore.count:"Volume"===t.type?e=t.__data.length:Pv.warn("GidPool.getGidCount: unknown object type"),e},allocateGidRange:function(t){t=this.getBaseObject(t);var e=this.getGidCount(t);if(e>Math.pow(10,7))return Pv.warn("GidPool.allocateGidRange: gidCount too large"),null;var i=this.nextGid;return this.nextGid+=e,this.nextGid>Math.pow(2,24)&&Pv.error("GidPool.allocateGidRange: GidPool overflown"),[i,this.nextGid]},getNextGid:function(){return this.nextGid++},getGid:function(t,e){t=this.getBaseObject(t),e=e||0;var i=0,n=this.objectList.indexOf(t);if(n!==-1){var r=this.rangeList[n],o=r[0];i=o+e}else Pv.warn("GidPool.getGid: object not found.");return i},getByGid:function(t){var e;return this.objectList.forEach(function(i,n){var r=this.rangeList[n];if(!(t<r[0]||t>=r[1])){var 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e=s.renderer.domElement.getBoundingClientRect(),i=t.clientX-e.left,n=t.clientY-e.top;f.canvasPosition.set(i,e.height-n)}};o(),s.renderer.domElement.addEventListener("mousemove",function(t){t.preventDefault(),f.moving=!0,f.hovering=!1,f.lastMoved=performance.now(),f.position.set(t.layerX,t.layerY),f.setCanvasPosition(t)}),s.renderer.domElement.addEventListener("mousedown",function(t){t.preventDefault(),f.moving=!1,f.hovering=!1,f.down.set(t.layerX,t.layerY),f.which=t.which,f.setCanvasPosition(t)}),s.renderer.domElement.addEventListener("mouseup",function(e){if(e.preventDefault(),!(f.distance()>3||e.which===qv)){var i=r(f,!0);f.which=void 0,h.clicked.dispatch(i),t.Debug&&Pv.log("clicked",i)}}),s.renderer.domElement.addEventListener("mousewheel",a),s.renderer.domElement.addEventListener("wheel",a),s.renderer.domElement.addEventListener("MozMousePixelScroll",a),this.signals=h,this.setParameters=n};jr.prototype.add=function(t){this.count<<5<=t&&this.resize(t),this.words[t>>>5]|=1<<t},jr.prototype.add_unsafe=function(t){this.words[t>>>5]|=1<<t},jr.prototype.flip=function(t){this.count<<5<=t&&this.resize(t),this.words[t>>>5]^=1<<t},jr.prototype.flip_unsafe=function(t){this.words[t>>>5]^=1<<t},jr.prototype.flip_all=function(){for(var t=this.count,e=0;e+7<t;e+=8)this.words[e]=~this.words[e],this.words[e+1]=~this.words[e+1],this.words[e+2]=~this.words[e+2],this.words[e+3]=~this.words[e+3],this.words[e+4]=~this.words[e+4],this.words[e+5]=~this.words[e+5],this.words[e+6]=~this.words[e+6],this.words[e+7]=~this.words[e+7];for(;e<t;++e)this.words[e]=~this.words[e];return this},jr.prototype.set_all=function(t){return this.length<=0?this:(this.set_range(0,this.length-1,t),this)},jr.prototype.set_range=function(t,e,i){i=i?4294967295:0;for(var n=(t>>>5)+1,r=(e>>>5)-1,o=0|n;o+7<r;o+=8)this.words[o]=i,this.words[o+1]=i,this.words[o+2]=i,this.words[o+3]=i,this.words[o+4]=i,this.words[o+5]=i,this.words[o+6]=i,this.words[o+7]=i;for(;o<r;++o)this.words[o]=i;var a,s;if(i){for(a=t,s=(n<<5)+1;a<s;++a)this.words[a>>>5]|=1<<a;for(a=r<<5,s=e+1;a<s;++a)this.words[a>>>5]|=1<<a}else{for(a=t,s=(n<<5)+1;a<s;++a)this.words[a>>>5]&=~(1<<a);for(a=r<<5,s=e+1;a<s;++a)this.words[a>>>5]&=~(1<<a)}return this},jr.prototype.clear=function(){return this.count=0,this.length=0,this.words=new Uint32Array(this.count),this},jr.prototype.remove=function(t){this.count<<5<=t&&this.resize(t),this.words[t>>>5]&=~(1<<t)},jr.prototype.remove_unsafe=function(t){this.words[t>>>5]&=~(1<<t)},jr.prototype.isEmpty=function(){for(var t=this.count,e=0;e<t;e++)if(0!==this.words[e])return!1;return!0},jr.prototype.has=function(t){return 0!==(this.words[t>>>5]&1<<t)},jr.prototype.trim=function(){for(;this.count>0;)0===this.words[this.count-1]&&this.count--;this.words=this.words.slice(0,this.count)},jr.prototype.resize=function(t){if(this.length=t,!(this.count<<5>t)&&(this.count=t+32>>>5,this.words.length<<5<=t)){var e=new Uint32Array(this.count<<1);e.set(this.words),this.words=e}},jr.prototype.hammingWeight=function(t){return t-=t>>>1&1431655765,t=(858993459&t)+(t>>>2&858993459),16843009*(t+(t>>>4)&252645135)>>>24},jr.prototype.size=function(){for(var t=0,e=this.count,i=0;i<e;i++)t+=this.hammingWeight(0|this.words[i]);return Math.min(t,this.length)},jr.prototype.sizeRange=function(t,e){var i=0,n=t+e;return this.forEach(function(e){e>=t&&e<n&&++i}),i},jr.prototype.array=function(){for(var t=new Array(this.size()),e=0,i=0|this.count,n=0;n<i;++n)for(var r=this.words[n];0!==r;){var o=r&-r;t[e++]=(n<<5)+this.hammingWeight(o-1|0),r^=o}return t},jr.prototype.forEach=function(t){for(var e=0|this.count,i=0,n=0;n<e;++n)for(var r=this.words[n];0!==r;){var o=r&-r,a=(n<<5)+this.hammingWeight(o-1|0);a<this.length&&t(a,i),r^=o,i+=1}},jr.forEach=function(t,e,i){for(var n=0|Math.min(e.count,i.count),r=0;r<n;++r)for(var o=e.words[r],a=i.words[r];0!==o&&0!==a;){var s=o&-o,c=a&-a,u=r<<5;t(u+e.hammingWeight(s-1|0),u+i.hammingWeight(c-1|0)),o^=s,a^=c}},jr.prototype.clone=function(){var t=Object.create(jr.prototype);return t.count=this.count,t.length=this.length,t.words=new Uint32Array(this.words),t},jr.prototype.intersects=function(t){for(var e=Math.min(this.count,t.count),i=0;i<e;++i)if(0!==(this.words[i]&t.words[i]))return!0;return!1},jr.prototype.intersection=function(t){for(var e=Math.min(this.count,t.count),i=0;i+7<e;i+=8)this.words[i]&=t.words[i],this.words[i+1]&=t.words[i+1],this.words[i+2]&=t.words[i+2],this.words[i+3]&=t.words[i+3],this.words[i+4]&=t.words[i+4],this.words[i+5]&=t.words[i+5],this.words[i+6]&=t.words[i+6],this.words[i+7]&=t.words[i+7];for(;i<e;++i)this.words[i]&=t.words[i];var n=this.count;for(i=e;i<n;++i)this.words[i]=0;return this.count=e,this},jr.prototype.intersection_size=function(t){for(var e=Math.min(this.count,t.count),i=0,n=0;n<e;++n)i+=this.hammingWeight(this.words[n]&t.words[n]);return i},jr.prototype.new_intersection=function(t){var e=Object.create(jr.prototype);e.count=Math.min(this.count,t.count),e.words=new Uint32Array(e.count),e.length=Math.min(this.length,t.length);for(var i=e.count,n=0;n<i;++n)e.words[n]=this.words[n]&t.words[n];return e},jr.prototype.equals=function(t){var e,i,n=Math.min(this.count,t.count);for(e=0;e<n;++e)if(this.words[e]!=t.words[e])return!1;if(this.count<t.count){for(i=t.count,e=this.count;e<i;++e)if(0!==t.words[e])return!1}else if(t.count<this.count)for(i=this.count,e=t.count;e<i;++e)if(0!==this.words[e])return!1;return!0},jr.prototype.difference=function(t){for(var e=Math.min(this.count,t.count),i=0;i+7<e;i+=8)this.words[i]&=~t.words[i],this.words[i+1]&=~t.words[i+1],this.words[i+2]&=~t.words[i+2],this.words[i+3]&=~t.words[i+3],this.words[i+4]&=~t.words[i+4],this.words[i+5]&=~t.words[i+5],this.words[i+6]&=~t.words[i+6],this.words[i+7]&=~t.words[i+7];for(;i<e;++i)this.words[i]&=~t.words[i];return this},jr.prototype.difference_size=function(t){for(var e=Math.min(this.count,t.count),i=0,n=0;n<e;++n)i+=this.hammingWeight(this.words[n]&~t.words[n]);for(var r=this.count;n<r;++n)i+=this.hammingWeight(this.words[n]);return i},jr.prototype.toString=function(){return"{"+this.array().join(",")+"}"},jr.prototype.union=function(t){for(var e=Math.min(this.count,t.count),i=0;i+7<e;i+=8)this.words[i]|=t.words[i],this.words[i+1]|=t.words[i+1],this.words[i+2]|=t.words[i+2],this.words[i+3]|=t.words[i+3],this.words[i+4]|=t.words[i+4],this.words[i+5]|=t.words[i+5],this.words[i+6]|=t.words[i+6],this.words[i+7]|=t.words[i+7];for(;i<e;++i)this.words[i]|=t.words[i];if(this.count<t.count){this.resize((t.count<<5)-1);var n=t.count;for(i=e;i<n;++i)this.words[i]=t.words[i];this.count=t.count}return this},jr.prototype.new_union=function(t){var e=Object.create(jr.prototype);e.count=Math.max(this.count,t.count),e.words=new Uint32Array(e.count);var i,n=Math.min(this.count,t.count);for(i=0;i<n;++i)e.words[i]=this.words[i]|t.words[i];var r=this.count;for(i=n;i<r;++i)e.words[i]=this.words[i];var o=t.count;for(i=n;i<o;++i)e.words[i]=t.words[i];return e},jr.prototype.new_difference=function(t){return this.clone().difference(t)},jr.prototype.union_size=function(t){var e,i,n=Math.min(this.count,t.count),r=0;for(e=0;e<n;++e)r+=this.hammingWeight(this.words[e]|t.words[e]);if(this.count<t.count)for(i=t.count,e=this.count;e<i;++e)r+=this.hammingWeight(0|t.words[e]);else for(i=this.count,e=t.count;e<i;++e)r+=this.hammingWeight(0|this.words[e]);return r},jr.prototype.getTransferable=function(){return[this.words]},jr.prototype.toJSON=function(){return{count:this.count,length:this.length,words:this.words}},jr.prototype.fromJSON=function(t){return this.count=t.count,this.length=t.length,this.words=t.words,this},jr.prototype.toSeleString=function(){var t=this.array().join(",");return t?"@"+t:"NONE"},jr.prototype.type="Bitset";var Zv=jr;$r.prototype={constructor:$r,atomRadius:function(t){var e,i=this.type,n=this.scale;switch(i){case"vdw":e=Cm[t.element]||Tm;break;case"covalent":e=Em[t.element]||Im;break;case"bfactor":e=t.bfactor||1;break;case"sstruc":var r=t.sstruc;e="h"===r?.25:"g"===r?.25:"i"===r?.25:"e"===r?.25:"b"===r?.25:$m.includes(t.atomname)?.4:.1;break;default:e=i||1}return Math.min(e*n,this.max)}},$r.types={"":"",vdw:"by vdW radius",covalent:"by covalent radius",sstruc:"by secondary structure",bfactor:"by bfactor",size:"size"},to.__deps=[eo],io.__deps=[eo,Jr],co.prototype={copyTo:function(t){t.data.set(this.data)}};var Kv=1.192092896e-7,Qv=1e-37;Po.__deps=[Ao],Co.__deps=[Ao],To.__deps=[Ao],Io.__deps=[Yr,Zr],Oo.prototype={constructor:Oo,type:"Store",init:function(t){this.length=t,this.count=0;for(var e=0,i=this.__fields.length;e<i;++e){var n=this.__fields[e][0],r=this.__fields[e][1],o=this.__fields[e][2],a=this.length*r;switch(o){case"int8":this[n]=new Int8Array(a);break;case"int16":this[n]=new Int16Array(a);break;case"int32":this[n]=new Int32Array(a);break;case"uint8":this[n]=new Uint8Array(a);break;case"uint16":this[n]=new Uint16Array(a);break;case"uint32":this[n]=new Uint32Array(a);break;case"float32":this[n]=new Float32Array(a);break;default:Pv.warn("arrayType unknown: "+o)}}},resize:function(t){this.length=Math.round(t||0),this.count=Math.min(this.count,this.length);for(var e=0,i=this.__fields.length;e<i;++e){var n=this.__fields[e][0],r=this.__fields[e][1],o=this.length*r,a=new this[n].constructor(o);this[n].length>o?a.set(this[n].subarray(0,o)):a.set(this[n]),this[n]=a}},growIfFull:function(){if(this.count>=this.length){var t=Math.round(1.5*this.length);this.resize(Math.max(256,t))}},copyFrom:function(t,e,i,n){for(var r=0,o=this.__fields.length;r<o;++r)for(var a=this.__fields[r][0],s=this.__fields[r][1],c=this[a],u=t[a],h=0;h<n;++h)for(var l=s*(e+h),d=s*(i+h),f=0;f<s;++f)c[l+f]=u[d+f]},copyWithin:function(t,e,i){for(var n=0,r=this.__fields.length;n<r;++n)for(var o=this.__fields[n][0],a=this.__fields[n][1],s=this[o],c=0;c<i;++c)for(var u=a*(t+c),h=a*(e+c),l=0;l<a;++l)s[u+l]=s[h+l]},sort:function(t){function e(t,e){t!==e&&(r.copyFrom(n,0,t,1),n.copyWithin(t,e,1),n.copyFrom(r,e,0,1))}function i(n,r){if(n<r){var o=Math.floor((n+r)/2),a=n,s=r;do{for(;t(a,o)<0;)a+=1;for(;t(s,o)>0;)s-=1;a<=s&&(a===o?o=s:s===o&&(o=a),e(a,s),a+=1,s-=1)}while(a<=s);i(n,s),i(a,r)}}Pv.time("Store.sort");var n=this,r=new this.constructor(1);i(0,this.count-1),Pv.timeEnd("Store.sort")},clear:function(){this.count=0},dispose:function(){delete this.length,delete this.count;for(var t=0,e=this.__fields.length;t<e;++t){var i=this.__fields[t][0];delete this[i]}}},Do.prototype=Object.assign(Object.create(Oo.prototype),{constructor:Do,type:"BondStore",__fields:[["atomIndex1",1,"int32"],["atomIndex2",1,"int32"],["bondOrder",1,"int8"]],addBond:function(t,e,i){this.growIfFull();var n=this.count,r=t.index,o=e.index;r<o?(this.atomIndex1[n]=r,this.atomIndex2[n]=o):(this.atomIndex2[n]=r,this.atomIndex1[n]=o),i&&(this.bondOrder[n]=i),this.count+=1},addBondIfConnected:function(t,e,i){return!!t.connectedTo(e)&&(this.addBond(t,e,i),!0)}}),No.prototype=Object.assign(Object.create(Oo.prototype),{constructor:No,type:"AtomStore",__fields:[["residueIndex",1,"uint32"],["atomTypeId",1,"uint16"],["x",1,"float32"],["y",1,"float32"],["z",1,"float32"],["serial",1,"int32"],["bfactor",1,"float32"],["altloc",1,"uint8"],["occupancy",1,"float32"]],setAltloc:function(t,e){this.altloc[t]=e.charCodeAt(0)},getAltloc:function(t){var e=this.altloc[t];return e?String.fromCharCode(e):""}}),ko.prototype=Object.assign(Object.create(Oo.prototype),{constructor:ko,type:"ResidueStore",__fields:[["chainIndex",1,"uint32"],["atomOffset",1,"uint32"],["atomCount",1,"uint16"],["residueTypeId",1,"uint16"],["resno",1,"int32"],["sstruc",1,"uint8"],["inscode",1,"uint8"]],setSstruc:function(t,e){this.sstruc[t]=e.charCodeAt(0)},getSstruc:function(t){var e=this.sstruc[t];return e?String.fromCharCode(e):""},setInscode:function(t,e){this.inscode[t]=e.charCodeAt(0)},getInscode:function(t){var e=this.inscode[t];return e?String.fromCharCode(e):""}}),Fo.prototype=Object.assign(Object.create(Oo.prototype),{constructor:Fo,type:"ChainStore",__fields:[["entityIndex",1,"uint16"],["modelIndex",1,"uint16"],["residueOffset",1,"uint32"],["residueCount",1,"uint32"],["chainname",4,"uint8"],["chainid",4,"uint8"]],setChainname:function(t,e){var i=4*t;this.chainname[i]=e.charCodeAt(0),this.chainname[i+1]=e.charCodeAt(1),this.chainname[i+2]=e.charCodeAt(2),this.chainname[i+3]=e.charCodeAt(3)},getChainname:function(t){for(var e="",i=0;i<4;++i){var n=this.chainname[4*t+i];if(!n)break;e+=String.fromCharCode(n)}return e},setChainid:function(t,e){var i=4*t;this.chainid[i]=e.charCodeAt(0),this.chainid[i+1]=e.charCodeAt(1),this.chainid[i+2]=e.charCodeAt(2),this.chainid[i+3]=e.charCodeAt(3)},getChainid:function(t){for(var e="",i=0;i<4;++i){var n=this.chainid[4*t+i];if(!n)break;e+=String.fromCharCode(n)}return e}}),zo.prototype=Object.assign(Object.create(Oo.prototype),{constructor:zo,type:"ModelStore",__fields:[["chainOffset",1,"uint32"],["chainCount",1,"uint32"]]}),Bo.prototype={constructor:Bo,getCenterIterator:function(t){function e(){var t=this.get(s);return s+=1,t}function i(e){e=Math.min(o-1,Math.max(0,e));var i=c[a%4],n=3*e;if(i.fromArray(r,n),t){var s,u,h,l=Math.min(t,e,o-e-1);for(u=1;u<=l;++u)s=3*u,h=(l+1-u)/(l+1),i.x+=h*r[n-s+0]+h*r[n+s+0],i.y+=h*r[n-s+1]+h*r[n+s+1],i.z+=h*r[n-s+2]+h*r[n+s+2];i.x/=l+1,i.y/=l+1,i.z/=l+1}return a+=1,i}function n(){a=0,s=-1}var r=this.getPosition().center,o=r.length/3,a=0,s=-1,c=[new N,new N,new N,new N];return{size:o,next:e,get:i,reset:n}},getColor:function(t){var e=this.polymer,i=e.structure,n=e.residueCount,r=e.residueIndexStart,o=new Float32Array(3*n),a=new Float32Array(3*n),s=t||{};s.structure=i;for(var c=Ev.getScheme(s),u=Ev.getPickingScheme(s),h=i.getResidueProxy(),l=i.getAtomProxy(),d=0;d<n;++d){h.index=r+d,l.index=h.traceAtomIndex;var f=3*d;c.atomColorToArray(l,o,f),u.atomColorToArray(l,a,f)}return{color:o,pickingColor:a}},getSize:function(t,e){for(var i=this.polymer,n=i.structure,r=i.residueCount,o=i.residueIndexStart,a=new Float32Array(r),s=new $r(t,e),c=n.getResidueProxy(),u=n.getAtomProxy(),h=0;h<r;++h)c.index=o+h,u.index=c.traceAtomIndex,a[h]=s.atomRadius(u);return{size:a}},getPosition:function(){var t,e,i,n,r,o=this.polymer,a=o.structure,s=o.residueCount,c=s-3,u=new Float32Array(3*s),h=new Float32Array(3*s),l=new Float32Array(s),d=new Float32Array(s),f=new Float32Array(s),p=new Float32Array(s),m=new Float32Array(3*s),g=new N,v=new N,y=new N,b=new N,x=new N,w=new N,_=new N,S=new N,A=new N,M=new N,P=new N,C=new N(0,0,0),T="trace",E=a.getAtomProxy(),I=a.getAtomProxy(o.getAtomIndexByType(0,T)),L=a.getAtomProxy(o.getAtomIndexByType(1,T)),R=a.getAtomProxy(o.getAtomIndexByType(2,T));for(i=0;i<c;++i)E.index=I.index,I.index=L.index,L.index=R.index,R.index=o.getAtomIndexByType(i+3,T),e=3*i,g.subVectors(I,E),v.subVectors(L,I),y.subVectors(R,L),b.subVectors(g,v),x.subVectors(v,y),A.crossVectors(b,x).normalize(),A.toArray(h,e),i>0&&(l[i]=A.angleTo(M)),t=Math.cos(b.angleTo(x)),p[i]=180/Math.PI*Math.acos(t),n=b.length(),r=x.length(),d[i]=Math.sqrt(r*n)/Math.max(2,2*(1-t)),f[i]=Math.abs(v.dot(A)),w.copy(b).multiplyScalar(d[i]/n),_.copy(x).multiplyScalar(d[i]/r),w.subVectors(I,w),_.subVectors(L,_),w.toArray(u,e+3),_.toArray(u,e+6),P.subVectors(E,C),P.toArray(m,e),M.copy(A),C.copy(w);for(w.fromArray(u,3),_.fromArray(u,6),A.subVectors(w,_).normalize(),E.index=o.getAtomIndexByType(0,T),C.copy(E),S.copy(E),Gr(S,A,w),S.toArray(u,0),P.subVectors(C,w),P.toArray(m,0),w.fromArray(u,3*s-6),_.fromArray(u,3*s-9),A.subVectors(w,_).normalize(),E.index=o.getAtomIndexByType(s-1,T),C.copy(E),S.copy(E),Gr(S,A,w),S.toArray(u,3*s-3),i=s-3;i<s;++i)w.fromArray(u,3*i),E.index=o.getAtomIndexByType(i,T),C.copy(E),P.subVectors(C,w),P.toArray(m,3*i);var O=new Float32Array(s),D=new Float32Array(s),k=new Float32Array(s),F=new Float32Array(s);for(O[1]=d[0],D[1]=p[0],k[1]=d[0],i=2;i<s-2;++i)O[i]=.5*(d[i-2]+d[i-1]),D[i]=.5*(p[i-2]+p[i-1]),k[i]=.5*(f[i-2]+f[i-1]),w.fromArray(h,3*(i-2)),_.fromArray(h,3*(i-1)),F[i]=180/Math.PI*Math.acos(Math.cos(w.angleTo(_)));O[s-2]=d[s-4],D[s-2]=p[s-4],k[s-2]=f[s-4];var z=new Float32Array(3*s);for(Or(h,z,0,0,3),Or(h,z,0,3,3),i=2;i<s-2;++i)w.fromArray(h,3*(i-2)),_.fromArray(h,3*(i-1)),A.addVectors(_,w).multiplyScalar(.5).normalize(),A.toArray(z,3*i);return Or(h,z,3*s-12,3*s-6,3),Or(h,z,3*s-12,3*s-3,3),{center:u,axis:z,bending:F,radius:O,rise:k,twist:D,resdir:m}}},Uo.prototype={constructor:Uo,getAxis:function(t,e,i,n,r,o){t=t||30,e=e||2.5,i=void 0!==i&&i;var a=this.polymer,s=a.structure,c=a.residueCount,u=a.residueIndexStart,h=this.position,l=n||{};l.structure=s;for(var d,f,p=Ev.getScheme(l),m=Ev.getPickingScheme(l),g=new $r(r,o),v=0,y=0,b=[],x=[],w=[],_=[],S=[],A=[],M=[],P=[],C=[],T=[],E=[],I=new N,L=new 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t.eachChain(function(t){n.push(t.chainname)}),n=x(n),e.chainList.length===n.length},getBoundingBox:function(t){var e=new Et;return this.partList.forEach(function(i){var n=i.getBoundingBox(t);e.expandByPoint(n.min),e.expandByPoint(n.max)}),e},getSelection:function(){var t=[];return this.partList.forEach(function(e){t=t.concat(e.chainList)}),Ho(t)}},Xo.prototype={constructor:Xo,type:"AssemblyPart",getAtomCount:function(t){var e=0,i=this.chainList;return t.eachChain(function(t){(0===i.length||i.includes(t.chainname))&&(e+=t.atomCount)}),this.matrixList.length*e},getBoundingBox:function(t){var e=new Et,i=new Et,n=this.getSelection(),r=t.getBoundingBox(n);return this.matrixList.forEach(function(t){i.copy(r).applyMatrix4(t),e.expandByPoint(i.min),e.expandByPoint(i.max)}),e},getSelection:function(){return Ho(this.chainList)},getView:function(t){var e=this.getSelection();return e?t.getView(e):t},getInstanceList:function(){for(var t=[],e=0,i=this.matrixList.length;e<i;++e)t.push({id:e+1,name:e,matrix:this.matrixList[e]});return t}};var ey=function(){var e=function(t,e,i,n){for(var r=t.structure,o=t.residueIndexStart,a=r.getResidueProxy(),s=r.getResidueProxy(),c=r.getAtomProxy(),u=r.getAtomProxy(),h=Math.max(0,e-2);h<=e;++h)for(var l=2;l<5;++l)if(!(h+l>=t.residueCount)){a.index=o+h,s.index=o+h+l,c.index=a.traceAtomIndex,u.index=s.traceAtomIndex;var d=c.distanceTo(u);if(Math.abs(d-i[l-2])>n)return!1}return!0},i=function(t,i){var n=[5.45,5.18,6.37],r=2.1;return e(t,i,n,r)},n=function(t,i){var n=[6.1,10.4,13],r=1.42;return e(t,i,n,r)},r=function(t){for(var e=t.residueStore,r=t.residueIndexStart,o=0,a=t.residueCount;o<a;++o){var s="c";i(t,o)?s="h":n(t,o)&&(s="s"),e.sstruc[r+o]=s.charCodeAt(0)}},o=function(t){for(var e=20,i=2,n=t.residueStore,r=t.residueIndexStart,o=new Uo(t),a=o.position,s=new N,c=new N,u=0,h=t.residueCount;u<h;++u){s.fromArray(a.center,3*u),c.fromArray(a.center,3*u+3);var l=s.distanceTo(c);l<i&&l>1&&a.bending[u]<e&&(n.sstruc[r+u]="h".charCodeAt(0),n.sstruc[r+u+1]="h".charCodeAt(0))}};return function(e){t.Debug&&Pv.time("calculateSecondaryStructure"),e.eachPolymer(function(t){if(!(t.residueCount<4)){if(t.isCg())o(t);else{if(!t.isProtein())return;r(t)}var e,i=0;t.eachResidue(function(t){t.sstruc===e?i+=1:(1===i&&(t.index-=1,t.sstruc="c"),i=1,e=t.sstruc)})}}),t.Debug&&Pv.timeEnd("calculateSecondaryStructure")}}(),iy=function(){var t=["H","C","O","N","S","P"],e=["NA","CL"];return function(i){var n=i.trim().toUpperCase();parseInt(n.charAt(0))&&(n=n.substr(1)),parseInt(n.charAt(0))&&(n=n.substr(1));var r=n.length;if(0===r)return"";if(1===r)return n;if(2===r){if(e.indexOf(n)!==-1)return n;if(t.indexOf(n[0])!==-1)return n[0]}return r>=3&&t.indexOf(n[0])!==-1?n[0]:""}}();na.prototype={constructor:na,type:"AtomType",atomname:void 0,element:void 0,vdw:void 0,covalent:void 0},oa.prototype={constructor:oa,type:"ResidueType",resname:void 0,atomTypeIdList:void 0,atomCount:void 0,getBackboneIndexList:function(){var t,e=[];switch(this.moleculeType){case um:t=jm;break;case hm:case lm:t=$m;break;default:return e}for(var i=this.structure.atomMap,n=this.atomTypeIdList,r=0,o=this.atomCount;r<o;++r){var a=i.get(n[r]);t.includes(a.atomname)&&e.push(r)}return e},getMoleculeType:function(){return this.isProtein()?um:this.isRna()?hm:this.isDna()?lm:this.isWater()?sm:this.isIon()?cm:this.isSaccharide()?dm:am},getBackboneType:function(t){return this.hasProteinBackbone(t)?pm:this.hasRnaBackbone(t)?mm:this.hasDnaBackbone(t)?gm:this.hasCgProteinBackbone(t)?vm:this.hasCgRnaBackbone(t)?ym:this.hasCgDnaBackbone(t)?bm:fm},isProtein:function(){return this.chemCompType?xm.includes(this.chemCompType):this.hasAtomWithName("CA","C","N")||Dm.includes(this.resname)},isCg:function(){var t=this.backboneType;return t===vm||t===ym||t===bm},isNucleic:function(){return this.isRna()||this.isDna()},isRna:function(){return this.chemCompType?wm.includes(this.chemCompType):this.hasAtomWithName(["P","O3'","O3*"],["C4'","C4*"],["O2'","O2*","F2'","F2*"])||Nm.includes(this.resname)&&this.hasAtomWithName(["O2'","O2*","F2'","F2*"])},isDna:function(){return this.chemCompType?_m.includes(this.chemCompType):this.hasAtomWithName(["P","O3'","O3*"],["C3'","C3*"])&&!this.hasAtomWithName(["O2'","O2*","F2'","F2*"])||km.includes(this.resname)},isHetero:function(){return 1===this.hetero},isIon:function(){return Bm.includes(this.resname)},isWater:function(){return zm.includes(this.resname)},isSaccharide:function(){return this.chemCompType?Sm.includes(this.chemCompType):Um.includes(this.resname)},hasBackboneAtoms:function(t,e){var i=Vm[e];return t===-1?this.hasAtomWithName(i.trace,i.backboneEnd,i.direction1,i.direction2):0===t?this.hasAtomWithName(i.trace,i.direction1,i.direction2):1===t?this.hasAtomWithName(i.trace,i.backboneStart,i.direction1,i.direction2):this.hasAtomWithName(i.trace,i.backboneStart,i.backboneEnd,i.direction1,i.direction2)},hasProteinBackbone:function(t){return this.isProtein()&&this.hasBackboneAtoms(t,pm)},hasRnaBackbone:function(t){return this.isRna()&&this.hasBackboneAtoms(t,mm)},hasDnaBackbone:function(t){return this.isDna()&&this.hasBackboneAtoms(t,gm)},hasCgProteinBackbone:function(t){return this.isProtein()&&this.hasBackboneAtoms(t,vm)},hasCgRnaBackbone:function(t){return this.isRna()&&this.hasBackboneAtoms(t,ym)},hasCgDnaBackbone:function(t){return this.isDna()&&this.hasBackboneAtoms(t,bm)},hasBackbone:function(t){return this.hasProteinBackbone(t)||this.hasRnaBackbone(t)||this.hasDnaBackbone(t)||this.hasCgProteinBackbone(t)||this.hasCgRnaBackbone(t)||this.hasCgDnaBackbone(t)},getAtomIndexByName:function(t){var e,i,n=this.atomCount,r=this.structure.atomMap,o=this.atomTypeIdList;if(Array.isArray(t)){for(e=0;e<n;++e)if(i=o[e],t.includes(r.get(i).atomname))return e}else for(e=0;e<n;++e)if(i=o[e],t===r.get(i).atomname)return e},hasAtomWithName:function(){for(var t=arguments.length,e=0;e<t;++e)if(void 0!==arguments[e]&&void 0===this.getAtomIndexByName(arguments[e]))return!1;return!0},getBonds:function(t){return void 0===this.bonds&&(this.bonds=Ko(t)),this.bonds},getRings:function(){return void 0===this.rings&&this.calculateRings(),this.rings},getBondGraph:function(){return void 0===this.bondGraph&&this.calculateBondGraph(),this.bondGraph},calculateBondGraph:function(){for(var t,e,i=this.bondGraph={},n=this.getBonds(),r=n.atomIndices1.length,o=n.atomIndices1,a=n.atomIndices2,s=0;s<r;++s){t=o[s],e=a[s];var c=i[t]=i[t]||[];c.push(e);var u=i[e]=i[e]||[];u.push(t)}},calculateRings:function(){function t(a,s,c){if(i[a])throw Error("DFS revisited atom");i[a]=1,o.push(a);for(var u=s.length,h=0;h<u;++h){var l=s[h];if(0===i[l])e[l]&&e[l].length>=2?t(l,e[l],a):i[l]=2;else if(1===i[l]&&c&&c!=l){var d=[l];n[l]=1,r.push(d);for(var f=o.length-1;f>=0;--f){var p=o[f];if(p===l)break;d.push(p),n[p]=1}}}i[a]=2,o.pop()}for(var e=this.getBondGraph(),i=new Int8Array(this.atomCount),n=new Int8Array(this.atomCount),r=[],o=[],a=0;a<this.atomCount;++a)if(!i[a]){var s=e[a];!s||s.length<2?i[a]=2:(o.length=0,t(a,s))}this.rings={flags:n,rings:r}},assignBondReferenceAtomIndices:function(){var t,e,i,n,r,o=this.getBondGraph(),a=this.getRings(),s=a.flags,c=a.rings,u=this.bonds.atomIndices1,h=this.bonds.atomIndices2,l=this.bonds.bondOrders,d=this.bondReferenceAtomIndices,f=this.bonds.atomIndices1.length;for(d.length=0,t=0;t<f;++t)if(!(l[t]<=1)){if(i=u[t],n=h[t],s[i]&&s[n]){for(var p=0;p<c.length&&void 0===d[t];++p)for(var m=c[p],g=null,v=!1,y=0;y<m.length;++y)if(r=m[y],r===i||r===n?v=!0:g=r,v&&null!==g){d[t]=g;break}if(void 0!==d[t])continue}if(o[i].length>1){for(e=0;e<o[i].length;++e)if(r=o[i][e],r!==n){d[t]=r;break}}else if(o[n].length>1){for(e=0;e<o[n].length;++e)if(r=o[n][e],r!==i){d[t]=r;break}}else;}},getBondIndex:function(t,e){for(var i=this.bonds,n=i.atomIndices1,r=i.atomIndices2,o=n.indexOf(t),a=r.indexOf(e),s=a;o!==-1;){for(;a!==-1;){if(o===a)return o;a=r.indexOf(e,a+1)}o=n.indexOf(t,o+1),a=s}},getBondReferenceAtomIndex:function(t,e){var i=this.getBondIndex(t,e);if(void 0!==i)return 0===this.bondReferenceAtomIndices.length&&this.assignBondReferenceAtomIndices(),this.bondReferenceAtomIndices[i]}},sa.prototype={constructor:sa,type:"BondProxy",structure:void 0,bondStore:void 0,index:void 0,get atom1(){return this.structure.getAtomProxy(this.atomIndex1)},get atom2(){return this.structure.getAtomProxy(this.atomIndex2)},get atomIndex1(){return this.bondStore.atomIndex1[this.index]},set atomIndex1(t){this.bondStore.atomIndex1[this.index]=t},get atomIndex2(){return this.bondStore.atomIndex2[this.index]},set atomIndex2(t){this.bondStore.atomIndex2[this.index]=t},get bondOrder(){return this.bondStore.bondOrder[this.index]},set bondOrder(t){this.bondStore.bondOrder[this.index]=t},getReferenceAtomIndex:function(){var t=this._ap1,e=this._ap2;if(t.index=this.atomIndex1,e.index=this.atomIndex2,t.residueIndex===e.residueIndex){var i=t.index-t.residueAtomOffset,n=e.index-e.residueAtomOffset,r=t.residueType,o=r.getBondReferenceAtomIndex(i,n);return void 0!==o?o+t.residueAtomOffset:void console.warn("No reference atom found",t.index,e.index)}},calculateShiftDir:function(t){t||(t=new N);var e=this._ap1,i=this._ap2,n=this._ap3,r=this._v12,o=this._v13;e.index=this.atomIndex1,i.index=this.atomIndex2;var a=this.getReferenceAtomIndex();r.subVectors(e,i).normalize(),void 0!==a?(n.index=a,o.subVectors(e,n)):o.copy(e),o.normalize();var s=r.dot(o);return 1-Math.abs(s)<1e-5&&(o.set(1,0,0),s=r.dot(o),1-Math.abs(s)<1e-5&&(o.set(0,1,0),s=r.dot(o))),t.copy(o.sub(r.multiplyScalar(s))).normalize()},qualifiedName:function(){return this.atomIndex1+"="+this.atomIndex2},clone:function(){return new this.constructor(this.structure,this.index)},toObject:function(){return{atomIndex1:this.atomIndex1,atomIndex2:this.atomIndex2,bondOrder:this.bondOrder}}},ca.prototype={constructor:ca,type:"AtomProxy",structure:void 0,chainStore:void 0,residueStore:void 0,atomStore:void 0,index:void 0,get entity(){return this.structure.entityList[this.entityIndex]},get entityIndex(){return this.chainStore.entityIndex[this.chainIndex]},get modelIndex(){return this.chainStore.modelIndex[this.chainIndex]},get chainIndex(){return this.residueStore.chainIndex[this.residueIndex]},get residue(){return console.warn("residue - might be expensive"),this.structure.getResidueProxy(this.residueIndex)},get residueIndex(){return this.atomStore.residueIndex[this.index]},set residueIndex(t){this.atomStore.residueIndex[this.index]=t},get sstruc(){return this.residueStore.getSstruc(this.residueIndex)},get inscode(){return this.residueStore.getInscode(this.residueIndex)},get resno(){return this.residueStore.resno[this.residueIndex]},get chainname(){return this.chainStore.getChainname(this.chainIndex)},get chainid(){return this.chainStore.getChainid(this.chainIndex)},get residueType(){return this.residueMap.get(this.residueStore.residueTypeId[this.residueIndex])},get atomType(){return this.atomMap.get(this.atomStore.atomTypeId[this.index])},get residueAtomOffset(){return this.residueStore.atomOffset[this.residueIndex]},get resname(){return this.residueType.resname},get hetero(){return this.residueType.hetero},get atomname(){return this.atomType.atomname},get element(){return this.atomType.element},get vdw(){return this.atomType.vdw},get covalent(){return this.atomType.covalent},get x(){return this.atomStore.x[this.index]},set x(t){this.atomStore.x[this.index]=t},get y(){return this.atomStore.y[this.index]},set y(t){this.atomStore.y[this.index]=t},get z(){return this.atomStore.z[this.index]},set z(t){this.atomStore.z[this.index]=t},get serial(){return this.atomStore.serial[this.index]},set serial(t){this.atomStore.serial[this.index]=t},get bfactor(){return this.atomStore.bfactor[this.index]},set bfactor(t){this.atomStore.bfactor[this.index]=t},get occupancy(){return this.atomStore.occupancy[this.index]},set occupancy(t){this.atomStore.occupancy[this.index]=t},get altloc(){return this.atomStore.getAltloc(this.index)},set altloc(t){this.atomStore.setAltloc(this.index,t)},eachBond:function(t){for(var e=this.structure._bp,i=this.index,n=this.bondHash,r=n.indexArray,o=n.countArray[i],a=n.offsetArray[i],s=0;s<o;++s)e.index=r[a+s],t(e)},eachBondedAtom:function(t){var e=this.structure._ap,i=this.index;this.eachBond(function(n){i!==n.atomIndex1?e.index=n.atomIndex1:e.index=n.atomIndex2,t(e)})},isBackbone:function(){var t=this.residueType.backboneIndexList;if(t.length>0){var e=this.residueStore.atomOffset[this.residueIndex];return t.includes(this.index-e)}return!1},isPolymer:function(){if(this.structure.entityList.length>0)return this.entity.isPolymer();var t=this.residueType.moleculeType;return t===um||t===hm||t===lm},isSidechain:function(){return this.isPolymer()&&!this.isBackbone()},isCg:function(){var t=this.residueType.backboneType;return t===vm||t===ym||t===bm},isHetero:function(){return 1===this.residueType.hetero},isProtein:function(){return this.residueType.moleculeType===um},isNucleic:function(){var t=this.residueType.moleculeType;return t===hm||t===lm},isRna:function(){return this.residueType.moleculeType===hm},isDna:function(){return this.residueType.moleculeType===lm},isWater:function(){return this.residueType.moleculeType===sm},isIon:function(){return this.residueType.moleculeType===cm},isSaccharide:function(){return this.residueType.moleculeType===dm},isRing:function(){var t=this.residueType.getRings().flags;return 1===t[this.index-this.residueAtomOffset]},distanceTo:function(t){var e=this.atomStore,i=t.atomStore,n=this.index,r=t.index,o=e.x[n]-i.x[r],a=e.y[n]-i.y[r],s=e.z[n]-i.z[r],c=o*o+a*a+s*s;return Math.sqrt(c)},connectedTo:function(t){var e=this.atomStore,i=t.atomStore,n=this.index,r=t.index;if(e.altloc&&i.altloc){var o=e.altloc[n],a=i.altloc[r];if(0!==o&&0!==a&&32!==o&&32!==a&&o!==a)return!1}var s=e.x[n]-i.x[r],c=e.y[n]-i.y[r],u=e.z[n]-i.z[r],h=s*s+c*c+u*u;if(h<64&&this.isCg())return!0;if(isNaN(h))return!1;var l=this.covalent+t.covalent,d=l+.3,f=l-.5;return h<d*d&&h>f*f},positionFromArray:function(t,e){return void 0===e&&(e=0),this.x=t[e+0],this.y=t[e+1],this.z=t[e+2],this},positionToArray:function(t,e){void 0===t&&(t=[]),void 0===e&&(e=0);var i=this.index,n=this.atomStore;return t[e+0]=n.x[i],t[e+1]=n.y[i],t[e+2]=n.z[i],t},positionToVector3:function(t){return void 0===t&&(t=new N),t.x=this.x,t.y=this.y,t.z=this.z,t},positionFromVector3:function(t){return this.x=t.x,this.y=t.y,this.z=t.z,this},getResidueBonds:function(t){var e,i,n,r,o=this.residueAtomOffset,a=this.index-this.residueAtomOffset,s=this.residueType.getBonds(),c=s.atomIndices1,u=s.atomIndices2;for(t||(r=[]),e=c.indexOf(a);e!==-1;){if(n=u[e]+o,t)return n;r.push(n),e=c.indexOf(a,e+1)}for(i=u.indexOf(a);i!==-1;){if(n=c[i]+o,t)return n;r.push(n),i=u.indexOf(a,i+1)}return r},qualifiedName:function(t){var e="";return this.resname&&!t&&(e+="["+this.resname+"]"),void 0!==this.resno&&(e+=this.resno),this.inscode&&(e+="^"+this.inscode),this.chainname&&(e+=":"+this.chainname),this.atomname&&(e+="."+this.atomname),this.altloc&&(e+="%"+this.altloc),this.structure.modelStore.count>1&&(e+="/"+this.modelIndex),e},clone:function(){return new this.constructor(this.structure,this.index)},toObject:function(){return{index:this.index,residueIndex:this.residueIndex,atomno:this.atomno,resname:this.resname,x:this.x,y:this.y,z:this.z,element:this.element,chainname:this.chainname,resno:this.resno,serial:this.serial,vdw:this.vdw,covalent:this.covalent,hetero:this.hetero,bfactor:this.bfactor,altloc:this.altloc,atomname:this.atomname,modelindex:this.modelindex}}},ua.prototype={constructor:ua,type:"ResidueProxy",structure:void 0,chainStore:void 0,residueStore:void 0,atomStore:void 0,index:void 0,get entity(){return this.structure.entityList[this.entityIndex]},get entityIndex(){return this.chainStore.entityIndex[this.chainIndex]},get chain(){return this.structure.getChainProxy(this.chainIndex)},get chainIndex(){return this.residueStore.chainIndex[this.index]},set chainIndex(t){this.residueStore.chainIndex[this.index]=t},get atomOffset(){return this.residueStore.atomOffset[this.index]},set atomOffset(t){this.residueStore.atomOffset[this.index]=t},get atomCount(){return this.residueStore.atomCount[this.index]},set atomCount(t){this.residueStore.atomCount[this.index]=t},get atomEnd(){return this.atomOffset+this.atomCount-1},get modelIndex(){return this.chainStore.modelIndex[this.chainIndex]},get chainname(){return this.chainStore.getChainname(this.chainIndex)},get chainid(){return this.chainStore.getChainid(this.chainIndex)},get resno(){return this.residueStore.resno[this.index]},set resno(t){this.residueStore.resno[this.index]=t},get sstruc(){return this.residueStore.getSstruc(this.index)},set sstruc(t){this.residueStore.setSstruc(this.index,t)},get inscode(){return this.residueStore.getInscode(this.index)},set inscode(t){this.residueStore.getInscode(this.index,t)},get residueType(){return this.residueMap.get(this.residueStore.residueTypeId[this.index])},get resname(){return this.residueType.resname},get hetero(){return this.residueType.hetero},get moleculeType(){return this.residueType.moleculeType},get backboneType(){return this.residueType.backboneType},get backboneStartType(){return this.residueType.backboneStartType},get backboneEndType(){return this.residueType.backboneEndType},get traceAtomIndex(){return this.residueType.traceAtomIndex+this.atomOffset},get direction1AtomIndex(){return this.residueType.direction1AtomIndex+this.atomOffset},get direction2AtomIndex(){return this.residueType.direction2AtomIndex+this.atomOffset},get backboneStartAtomIndex(){return this.residueType.backboneStartAtomIndex+this.atomOffset},get backboneEndAtomIndex(){return this.residueType.backboneEndAtomIndex+this.atomOffset},get rungEndAtomIndex(){return this.residueType.rungEndAtomIndex+this.atomOffset},eachAtom:function(t,e){var i,n=this.atomCount,r=this.atomOffset,o=this.structure._ap,a=r+n;if(e&&e.atomOnlyTest){var s=e.atomOnlyTest;for(i=r;i<a;++i)o.index=i,s(o)&&t(o)}else for(i=r;i<a;++i)o.index=i,t(o)},isProtein:function(){return this.residueType.moleculeType===um},isNucleic:function(){var t=this.residueType.moleculeType;return t===hm||t===lm},isRna:function(){return this.residueType.moleculeType===hm},isDna:function(){return this.residueType.moleculeType===lm},isCg:function(){var t=this.residueType.backboneType;return t===vm||t===ym||t===bm},isPolymer:function(){if(this.structure.entityList.length>0)return this.entity.isPolymer();var t=this.residueType.moleculeType;return t===um||t===hm||t===lm},isHetero:function(){return 1===this.residueType.hetero},isWater:function(){return this.residueType.moleculeType===sm},isIon:function(){return this.residueType.moleculeType===cm},isSaccharide:function(){return this.residueType.moleculeType===dm},getAtomType:function(t){return this.atomMap.get(this.atomStore.atomTypeId[t])},getResname1:function(){return Om[this.resname.toUpperCase()]||"X"},getBackboneType:function(t){switch(t){case-1:return this.residueType.backboneStartType;case 1:return this.residueType.backboneEndType;default:return this.residueType.backboneType}},getAtomIndexByName:function(t){var e=this.residueType.getAtomIndexByName(t);return void 0!==e&&(e+=this.atomOffset),e},getAtomByName:function(t){return this.residueType.getAtomByName(t)},hasAtomWithName:function(t){return this.residueType.hasAtomWithName(t)},getAtomnameList:function(){console.warn("getAtomnameList - might be expensive");for(var t=this.atomCount,e=this.atomOffset,i=new Array(t),n=0;n<t;++n)i[n]=this.getAtomType(e+n).atomname;return i},connectedTo:function(t){var e=this.structure.getAtomProxy(this.backboneEndAtomIndex),i=this.structure.getAtomProxy(t.backboneStartAtomIndex);return!(!e||!i)&&e.connectedTo(i)},getNextConnectedResidue:function(){var t=this.chainStore.residueOffset[this.chainIndex],e=this.chainStore.residueCount[this.chainIndex],i=this.index+1;if(i<t+e){var n=this.structure.getResidueProxy(i);if(this.connectedTo(n))return n}else if(i===t+e){var r=this.structure.getResidueProxy(t);if(this.connectedTo(r))return r}},getPreviousConnectedResidue:function(t){var e=this.chainStore.residueOffset[this.chainIndex],i=this.index-1;if(i>=e){if(void 0===t&&(t=this.structure.getResidueProxy()),t.index=i,t.connectedTo(this))return t}else if(i===e-1){void 0===t&&(t=this.structure.getResidueProxy());var n=this.chainStore.residueCount[this.chainIndex];if(t.index=e+n-1,t.connectedTo(this))return t}},getBonds:function(){return this.residueType.getBonds(this)},getRings:function(){return this.residueType.getRings()},qualifiedName:function(t){var e="";return this.resname&&!t&&(e+="["+this.resname+"]"),void 0!==this.resno&&(e+=this.resno),this.inscode&&(e+="^"+this.inscode),this.chain&&(e+=":"+this.chainname),e+="/"+this.modelIndex},clone:function(){return new this.constructor(this.structure,this.index)},toObject:function(){return{index:this.index,chainIndex:this.chainIndex,atomOffset:this.atomOffset,atomCount:this.atomCount,resno:this.resno,resname:this.resname,sstruc:this.sstruc}}},ha.prototype={constructor:ha,type:"Polymer",structure:void 0,residueStore:void 0,atomStore:void 0,residueIndexStart:void 0,residueIndexEnd:void 0,residueCount:void 0,get chainIndex(){return this.residueStore.chainIndex[this.residueIndexStart]},get modelIndex(){return this.chainStore.modelIndex[this.chainIndex]},get chainname(){return this.chainStore.getChainname(this.chainIndex)},isProtein:function(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isProtein()},isCg:function(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isCg()},isNucleic:function(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.isNucleic()},getMoleculeType:function(){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.moleculeType},getBackboneType:function(t){return this.__residueProxy.index=this.residueIndexStart,this.__residueProxy.getBackboneType(t)},getAtomIndexByType:function(t,e){this.isCyclic?t===-1?t=this.residueCount-1:t===this.residueCount&&(t=0):(t!==-1||this.isPrevConnected||(t+=1),t!==this.residueCount||this.isNextNextConnected||(t-=1));var i=this.__residueProxy;i.index=this.residueIndexStart+t;var n;switch(e){case"trace":n=i.traceAtomIndex;break;case"direction1":n=i.direction1AtomIndex;break;case"direction2":n=i.direction2AtomIndex;break;default:var r=i.getAtomByName(e);n=r?r.index:void 0}return n},eachAtom:function(t,e){this.eachResidue(function(i){i.eachAtom(t,e)},e)},eachAtomN:function(t,e,i){var n,r=this.residueCount,o=new Array(t);for(n=0;n<t;++n)o[n]=this.structure.getAtomProxy(this.getAtomIndexByType(n,i));e.apply(this,o);for(var a=t;a<r;++a){for(n=1;n<t;++n)o[n-1].index=o[n].index;o[t-1].index=this.getAtomIndexByType(a,i),e.apply(this,o)}},eachAtomN2:function(t,e,i){var n=this.atomOffset,r=this.atomCount,o=n+r;if(!(r<t)){for(var a=new Array(t),s=0;s<t;++s)a[s]=this.structure.getAtomProxy();
-var c=this.structure.atomSetCache["__"+i];void 0===c&&(Pv.warn("no precomputed atomSet for: "+i),c=this.structure.getAtomSet(!1),this.eachResidue(function(t){var e=t.getAtomByName(i);c.add_unsafe(e.index)}));var u=0;c.forEach(function(i){if(i>=n&&i<o){for(var r=1;r<t;++r)a[r-1].index=a[r].index;a[t-1].index=i,u+=1,u>=t&&e.apply(this,a)}})}},eachDirectionAtomsN:function(t,e){var i=2*t,n=this.atomOffset,r=this.atomCount,o=n+r;if(!(r<t)){for(var a=new Array(i),s=0;s<i;++s)a[s]=this.structure.getAtomProxy();var c=this.structure.atomSetCache.__direction1,u=this.structure.atomSetCache.__direction2;if(void 0===c||void 0===u)return void Pv.error("no precomputed atomSet for direction1 or direction2");var h=0;Zv.forEach(function(i,r){if(i>=n&&i<o&&r>=n&&r<o){for(var s=1;s<t;++s)a[s-1].index=a[s].index,a[s-1+t].index=a[s+t].index;a[t-1].index=i,a[t-1+t].index=r,h+=1,h>=t&&e.apply(this,a)}},c,u)}},eachResidue:function(t){for(var e=this.structure.getResidueProxy(),i=this.residueCount,n=this.residueIndexStart,r=0;r<i;++r)e.index=n+r,t(e)},qualifiedName:function(){var t=this.structure.getResidueProxy(this.residueIndexStart),e=this.structure.getResidueProxy(this.residueIndexEnd);return t.qualifiedName()+" - "+e.qualifiedName()}},la.prototype={constructor:la,type:"ChainProxy",structure:void 0,chainStore:void 0,index:void 0,get entity(){return this.structure.entityList[this.entityIndex]},get model(){return this.structure.getModelProxy(this.modelIndex)},get entityIndex(){return this.chainStore.entityIndex[this.index]},set entityIndex(t){this.chainStore.entityIndex[this.index]=t},get modelIndex(){return this.chainStore.modelIndex[this.index]},set modelIndex(t){this.chainStore.modelIndex[this.index]=t},get residueOffset(){return this.chainStore.residueOffset[this.index]},set residueOffset(t){this.chainStore.residueOffset[this.index]=t},get residueCount(){return this.chainStore.residueCount[this.index]},set residueCount(t){this.chainStore.residueCount[this.index]=t},get residueEnd(){return this.residueOffset+this.residueCount-1},get atomOffset(){return this.residueStore.atomOffset[this.residueOffset]},get atomEnd(){return this.residueStore.atomOffset[this.residueEnd]+this.residueStore.atomCount[this.residueEnd]-1},get atomCount(){return 0===this.residueCount?0:this.atomEnd-this.atomOffset+1},get chainname(){return this.chainStore.getChainname(this.index)},set chainname(t){this.chainStore.setChainname(this.index,t)},get chainid(){return this.chainStore.getChainid(this.index)},set chainid(t){this.chainStore.setChainid(this.index,t)},get __firstResidueProxy(){return this.__residueProxy.index=this.residueOffset,this.__residueProxy},isProtein:function(){return this.__firstResidueProxy.isProtein()},isNucleic:function(){return this.__firstResidueProxy.isNucleic()},isRna:function(){return this.__firstResidueProxy.isRna()},isDna:function(){return this.__firstResidueProxy.isDna()},isPolymer:function(){return this.__firstResidueProxy.isPolymer()},isHetero:function(){return this.__firstResidueProxy.isHetero()},isWater:function(){return this.__firstResidueProxy.isWater()},isIon:function(){return this.__firstResidueProxy.isIon()},isSaccharide:function(){return this.__firstResidueProxy.isSaccharide()},eachAtom:function(t,e){this.eachResidue(function(i){i.eachAtom(t,e)},e)},eachResidue:function(t,e){var i,n=this.residueCount,r=this.residueOffset,o=this.structure._rp,a=r+n;if(e&&e.test){var s=e.residueOnlyTest;if(s)for(i=r;i<a;++i)o.index=i,s(o)&&t(o,e);else for(i=r;i<a;++i)o.index=i,t(o,e)}else for(i=r;i<a;++i)o.index=i,t(o)},eachResidueN:function(t,e){var i,n=this.residueCount,r=this.residueOffset,o=r+n;if(!(n<t)){var a=new Array(t);for(i=0;i<t;++i)a[i]=this.structure.getResidueProxy(r+i);e.apply(this,a);for(var s=r+t;s<o;++s){for(i=0;i<t;++i)a[i].index+=1;e.apply(this,a)}}},eachPolymer:function(t,e){for(var i,n,r=e?e.residueOnlyTest:void 0,o=this.model.structure,a=this.residueCount,s=this.residueOffset,c=s+a,u=this.structure.getResidueProxy(),h=this.structure.getResidueProxy(s),l=this.structure.getAtomProxy(),d=this.structure.getAtomProxy(),f=!0,p=s+1;p<c;++p){u.index=h.index,h.index=p,f&&(i=u.index,f=!1),n=h.index;var m=f?u.backboneEndType:u.backboneType,g=h.backboneType;m!==fm&&m===g?(l.index=u.backboneEndAtomIndex,d.index=h.backboneStartAtomIndex,l&&d&&l.connectedTo(d)&&(!r||r(u)&&r(h))||(u.index-i>1&&t(new ha(o,i,u.index)),i=n)):(m!==fm&&u.index-i>1&&t(new ha(o,i,u.index)),i=n)}n-i>1&&this.structure.getResidueProxy(i).backboneStartType&&t(new ha(o,i,n))},qualifiedName:function(){var t=":"+this.chainname+"/"+this.modelIndex;return t},clone:function(){return new this.constructor(this.structure,this.index)},toObject:function(){return{index:this.index,residueOffset:this.residueOffset,residueCount:this.residueCount,chainname:this.chainname}}},da.prototype={constructor:da,type:"ModelProxy",structure:void 0,modelStore:void 0,index:void 0,get chainOffset(){return this.modelStore.chainOffset[this.index]},set chainOffset(t){this.modelStore.chainOffset[this.index]=t},get chainCount(){return this.modelStore.chainCount[this.index]},set chainCount(t){this.modelStore.chainCount[this.index]=t},get residueOffset(){return this.chainStore.residueOffset[this.chainOffset]},get atomOffset(){return this.residueStore.atomOffset[this.residueOffset]},get chainEnd(){return this.chainOffset+this.chainCount-1},get residueEnd(){return this.chainStore.residueOffset[this.chainEnd]+this.chainStore.residueCount[this.chainEnd]-1},get atomEnd(){return this.residueStore.atomOffset[this.residueEnd]+this.residueStore.atomCount[this.residueEnd]-1},get residueCount(){return 0===this.chainCount?0:this.residueEnd-this.residueOffset+1},get atomCount(){return 0===this.residueCount?0:this.atomEnd-this.atomOffset+1},eachAtom:function(t,e){this.eachChain(function(i){i.eachAtom(t,e)},e)},eachResidue:function(t,e){this.eachChain(function(i){i.eachResidue(t,e)},e)},eachPolymer:function(t,e){if(e&&e.chainOnlyTest){var i=e.chainOnlyTest;this.eachChain(function(n){i(n)&&n.eachPolymer(t,e)})}else this.eachChain(function(i){i.eachPolymer(t,e)})},eachChain:function(t,e){var i,n=this.chainCount,r=this.chainOffset,o=this.structure._cp,a=r+n;if(e&&e.test){var s=e.chainOnlyTest;if(s)for(i=r;i<a;++i)o.index=i,s(o)&&t(o,e);else for(i=r;i<a;++i)o.index=i,t(o,e)}else for(i=r;i<a;++i)o.index=i,t(o)},qualifiedName:function(){var t="/"+this.index;return t},clone:function(){return new this.constructor(this.structure,this.index)},toObject:function(){return{index:this.index,chainOffset:this.chainOffset,chainCount:this.chainCount}}},fa.prototype={constructor:fa,type:"Structure",finalizeAtoms:function(){this.atomSet=this.getAtomSet(),this.atomCount=this.atomStore.count,this.boundingBox=this.getBoundingBox(),this.center=this.boundingBox.center(),this.spatialHash=new Lo(this.atomStore,this.boundingBox)},finalizeBonds:function(){this.bondSet=this.getBondSet(),this.bondCount=this.bondStore.count,this.bondHash=new Ro(this.bondStore,this.atomStore.count),this.atomSetCache={},this.atomSetDict.rung||(this.atomSetDict.rung=this.getAtomSet(!1));for(var t in this.atomSetDict){var e=this.atomSetDict[t],i=this.getAtomSet(!1);this.atomSetCache["__"+t]=i.intersection(e)}},getBondProxy:function(t){return new sa(this,t)},getAtomProxy:function(t){return new ca(this,t)},getResidueProxy:function(t){return new ua(this,t)},getChainProxy:function(t){return new la(this,t)},getModelProxy:function(t){return new da(this,t)},getBondSet:function(){t.Debug&&Pv.time("Structure.getBondSet");var e=this.bondStore.count,i=new Zv(e),n=this.atomSet;if(n)for(var r=this.getBondProxy(),o=0;o<e;++o)r.index=o,n.has(r.atomIndex1)&&n.has(r.atomIndex2)&&i.add_unsafe(r.index);else i.set_all(!0);return t.Debug&&Pv.timeEnd("Structure.getBondSet"),i},getBackboneBondSet:function(){t.Debug&&Pv.time("Structure.getBackboneBondSet");var e=this.backboneBondStore.count,i=new Zv(e),n=this.atomSetCache.__backbone;if(n){var r=this.getBondProxy();r.bondStore=this.backboneBondStore;for(var o=0;o<e;++o)r.index=o,n.has(r.atomIndex1)&&n.has(r.atomIndex2)&&i.add_unsafe(r.index)}else i.set_all(!0);return t.Debug&&Pv.timeEnd("Structure.getBackboneBondSet"),i},getRungBondSet:function(){t.Debug&&Pv.time("Structure.getRungBondSet");var e=this.rungBondStore.count,i=new Zv(e),n=this.atomSetCache.__rung;if(n){var r=this.getBondProxy();r.bondStore=this.rungBondStore;for(var o=0;o<e;++o)r.index=o,n.has(r.atomIndex1)&&n.has(r.atomIndex2)&&i.add_unsafe(r.index)}else i.set_all(!0);return t.Debug&&Pv.timeEnd("Structure.getRungBondSet"),i},getAtomSet:function(e){t.Debug&&Pv.time("Structure.getAtomSet");var i,n=this.atomStore.count;if(e&&"Bitset"===e.type)i=e;else if(e===!1)i=new Zv(n);else if(e===!0)i=new Zv(n),i.set_all(!0);else if(e&&e.test){var r=e.string;r in this.atomSetCache?i=this.atomSetCache[r]:(i=new Zv(n),this.eachAtom(function(t){i.add_unsafe(t.index)},e),this.atomSetCache[r]=i)}else i=new Zv(n),i.set_all(!0);return t.Debug&&Pv.timeEnd("Structure.getAtomSet"),i},getAtomSetWithinSelection:function(t,e){var i=this.spatialHash,n=this.getAtomSet(!1),r=this.getAtomProxy();return this.getAtomSet(t).forEach(function(t){r.index=t,i.within(r.x,r.y,r.z,e).forEach(function(t){n.add_unsafe(t)})}),n},getAtomSetWithinPoint:function(t,e){var i=t,n=this.getAtomSet(!1);return this.spatialHash.within(i.x,i.y,i.z,e).forEach(function(t){n.add_unsafe(t)}),n},getAtomSetWithinVolume:function(t,e,i,n,r){t.filterData(i,n,r);for(var o=t.dataPosition,a=o.length,s=t.matrix.getMaxScaleOnAxis(),c=this.getAtomSet(!1),u=0;u<a;u+=3)this.spatialHash.within(o[u],o[u+1],o[u+2],s).forEach(function(t){c.add_unsafe(t)});return c},getAtomSetWithinGroup:function(t){var e=this.atomStore.residueIndex,i=this.getAtomSet(!1),n=this.getResidueProxy();return this.getAtomSet(t).forEach(function(t){n.index=e[t];for(var r=n.atomOffset;r<=n.atomEnd;++r)i.add_unsafe(r)}),i},getSelection:function(){return!1},getStructure:function(){return this},eachEntity:function(t,e){this.entityList.forEach(function(i){void 0!==e&&i.getEntityType()!==e||t(i)})},eachBond:function(t,e){var i=this.getBondProxy(),n=this.bondSet;if(e&&e.test&&(n=n?n.new_intersection(this.getBondSet(e)):this.getBondSet(e)),n)n.forEach(function(e){i.index=e,t(i)});else for(var r=this.bondStore.count,o=0;o<r;++o)i.index=o,t(i)},eachAtom:function(t,e){if(e&&e.test)this.eachModel(function(i){i.eachAtom(t,e)},e);else for(var i=this.atomStore.count,n=this.getAtomProxy(),r=0;r<i;++r)n.index=r,t(n)},eachResidue:function(t,e){var i;if(e&&e.test){var n=this.modelStore.count,r=this.getModelProxy();if(e.modelOnlyTest){var o=e.modelOnlyTest;for(i=0;i<n;++i)r.index=i,o(r)&&r.eachResidue(t,e)}else for(i=0;i<n;++i)r.index=i,r.eachResidue(t,e)}else{var a=this.residueStore.count,s=this.getResidueProxy();for(i=0;i<a;++i)s.index=i,t(s)}},eachResidueN:function(t,e){var i,n,r=this.residueStore.count;if(!(r<t)){var o=new Array(t);for(i=0;i<t;++i)o[i]=this.getResidueProxy(i);for(e.apply(this,o),n=t;n<r;++n){for(i=0;i<t;++i)o[i].index+=1;e.apply(this,o)}}},eachPolymer:function(t,e){if(e&&e.modelOnlyTest){var i=e.modelOnlyTest;this.eachModel(function(n){i(n)&&n.eachPolymer(t,e)})}else this.eachModel(function(i){i.eachPolymer(t,e)})},eachChain:function(t,e){if(e&&e.test)this.eachModel(function(i){i.eachChain(t,e)});else for(var i=this.chainStore.count,n=this.getChainProxy(),r=0;r<i;++r)n.index=r,t(n)},eachModel:function(t,e){var i,n=this.modelStore.count,r=this.getModelProxy();if(e&&e.test){var o=e.modelOnlyTest;if(o)for(i=0;i<n;++i)r.index=i,o(r)&&t(r,e);else for(i=0;i<n;++i)r.index=i,t(r,e)}else for(i=0;i<n;++i)r.index=i,t(r)},getAtomData:function(t){var e=Object.assign({},t);e.colorParams&&(e.colorParams.structure=this.getStructure());var i,n,r,o,a,s,c,u,h=e.what,l=d(e.atomSet,this.atomSet),f={},p=this.getAtomProxy(),m=l.size();if(h&&!h.position||(o=new Float32Array(3*m),f.position=o),h&&!h.color||(a=new Float32Array(3*m),f.color=a,n=Ev.getScheme(e.colorParams)),!h||h.pickingColor){s=new Float32Array(3*m),f.pickingColor=s;var g=Object.assign(e.colorParams,{scheme:"picking"});r=Ev.getScheme(g)}return h&&!h.radius||(c=new Float32Array(m),f.radius=c,i=new $r(e.radiusParams.radius,e.radiusParams.scale)),h&&!h.index||(u=new Float32Array(m),f.index=u),l.forEach(function(t,e){var h=3*e;p.index=t,o&&p.positionToArray(o,h),a&&n.atomColorToArray(p,a,h),s&&r.atomColorToArray(p,s,h),c&&(c[e]=i.atomRadius(p)),u&&(u[e]=t)}),f},getBondData:function(t){var e=Object.assign({},t);e.colorParams&&(e.colorParams.structure=this.getStructure());var i,n,r,o,a,s,c,u,h,l,f,p=e.what,m=d(e.bondSet,this.bondSet),g=d(e.multipleBond,"off"),v="off"!==g,y="offset"===g,b=d(e.bondScale,.4),x=d(e.bondSpacing,1),w={},_=this.getBondProxy();e.bondStore&&(_.bondStore=e.bondStore);var S,A=this.getAtomProxy(),M=this.getAtomProxy();if(v){var P=_.bondStore.bondOrder;S=0,m.forEach(function(t){S+=P[t]})}else S=m.size();if(p&&!p.position||(o=new Float32Array(3*S),a=new Float32Array(3*S),w.position1=o,w.position2=a),p&&!p.color||(s=new Float32Array(3*S),c=new Float32Array(3*S),w.color1=s,w.color2=c,n=Ev.getScheme(e.colorParams)),!p||p.pickingColor){u=new Float32Array(3*S),h=new Float32Array(3*S),w.pickingColor1=u,w.pickingColor2=h;var C=Object.assign(e.colorParams,{scheme:"picking"});r=Ev.getScheme(C)}(!p||p.radius||v&&p.position)&&(i=new $r(e.radiusParams.radius,e.radiusParams.scale)),p&&!p.radius||(l=new Float32Array(S),e.radius2?(f=new Float32Array(S),w.radius1=l,w.radius2=f):w.radius=l);var T,E,I,L,R,O,D,k=0,F=new N,z=new N,B=new N;return m.forEach(function(t){if(E=3*k,_.index=t,A.index=_.atomIndex1,M.index=_.atomIndex2,L=_.bondOrder,o&&(v&&L>1?(R=i.atomRadius(A),O=R*b/(.5*L),_.calculateShiftDir(B),y?(D=2*x*R,B.multiplyScalar(D),B.negate(),z.subVectors(M,A).multiplyScalar(Math.max(.1,D/1.88)),A.positionToArray(o,E),M.positionToArray(a,E),L>=2&&(F.addVectors(A,B).add(z).toArray(o,E+3),F.addVectors(M,B).sub(z).toArray(a,E+3),L>=3&&(F.subVectors(A,B).add(z).toArray(o,E+6),F.subVectors(M,B).sub(z).toArray(a,E+6)))):(D=(x-b)*R,B.multiplyScalar(D),2===L?(F.addVectors(A,B).toArray(o,E),F.subVectors(A,B).toArray(o,E+3),F.addVectors(M,B).toArray(a,E),F.subVectors(M,B).toArray(a,E+3)):3===L?(A.positionToArray(o,E),F.addVectors(A,B).toArray(o,E+3),F.subVectors(A,B).toArray(o,E+6),M.positionToArray(a,E),F.addVectors(M,B).toArray(a,E+3),F.subVectors(M,B).toArray(a,E+6)):(A.positionToArray(o,E),M.positionToArray(a,E)))):(A.positionToArray(o,E),M.positionToArray(a,E))),s&&(n.bondColorToArray(_,1,s,E),n.bondColorToArray(_,0,c,E),v&&L>1))for(T=1;T<L;++T)I=3*T+E,Dr(s,E,I,3),Dr(c,E,I,3);if(u&&(r.bondColorToArray(_,1,u,E),r.bondColorToArray(_,0,h,E),v&&L>1))for(T=1;T<L;++T)I=3*T+E,Dr(u,E,I,3),Dr(h,E,I,3);if(l&&(l[k]=i.atomRadius(A),v&&L>1))for(O=l[k]*b/(y?1:.5*L),T=y?1:0;T<L;++T)l[k+T]=O;if(f&&(f[k]=i.atomRadius(M),v&&L>1))for(O=f[k]*b/(y?1:.5*L),T=y?1:0;T<L;++T)f[k+T]=O;k+=v?L:1}),w},getBackboneAtomData:function(t){return t=Object.assign({atomSet:this.atomSetCache.__backbone},t),this.getAtomData(t)},getBackboneBondData:function(t){return t=Object.assign({bondSet:this.getBackboneBondSet(),bondStore:this.backboneBondStore},t),this.getBondData(t)},getRungAtomData:function(t){return t=Object.assign({atomSet:this.atomSetCache.__rung},t),this.getAtomData(t)},getRungBondData:function(t){return t=Object.assign({bondSet:this.getRungBondSet(),bondStore:this.rungBondStore},t),this.getBondData(t)},getBoundingBox:function(e,i){t.Debug&&Pv.time("getBoundingBox"),i=i||new Et;var n=+(1/0),r=+(1/0),o=+(1/0),a=-(1/0),s=-(1/0),c=-(1/0);return this.eachAtom(function(t){var e=t.x,i=t.y,u=t.z;e<n&&(n=e),i<r&&(r=i),u<o&&(o=u),e>a&&(a=e),i>s&&(s=i),u>c&&(c=u)},e),i.min.set(n,r,o),i.max.set(a,s,c),t.Debug&&Pv.timeEnd("getBoundingBox"),i},getPrincipalAxes:function(e){t.Debug&&Pv.time("getPrincipalAxes");var i=0,n=new co(3,this.atomCount),r=n.data;return this.eachAtom(function(t){r[i+0]=t.x,r[i+1]=t.y,r[i+2]=t.z,i+=3},e),t.Debug&&Pv.timeEnd("getPrincipalAxes"),_o(n)},atomCenter:function(t){return t?this.getBoundingBox(t).center():this.center.clone()},getSequence:function(t){var e=[],i=this.getResidueProxy();return this.eachAtom(function(t){i.index=t.residueIndex,t.index===i.traceAtomIndex&&e.push(i.getResname1())},t),e},getAtomIndices:function(t){var e;if(t&&t.string)e=[],this.eachAtom(function(t){e.push(t.index)},t);else{var i={what:{index:!0}};e=this.getAtomData(i).index}return e},getChainnameCount:function(t){var e=new Set;return this.eachChain(function(t){t.residueCount&&e.add(t.chainname)},t),e.size},updatePosition:function(t){var e=0;this.eachAtom(function(i){i.positionFromArray(t,e),e+=3})},refreshPosition:function(){this.getBoundingBox(void 0,this.boundingBox),this.boundingBox.center(this.center),this.spatialHash=new Lo(this.atomStore,this.boundingBox)},dispose:function(){this.frames&&(this.frames.length=0),this.boxes&&(this.boxes.length=0),this.bondStore.dispose(),this.backboneBondStore.dispose(),this.rungBondStore.dispose(),this.atomStore.dispose(),this.residueStore.dispose(),this.chainStore.dispose(),this.modelStore.dispose(),delete this.bondStore,delete this.atomStore,delete this.residueStore,delete this.chainStore,delete this.modelStore,delete this.frames,delete this.boxes,delete this.cif,delete this.bondSet,delete this.atomSet}},pa.prototype={constructor:pa,type:"Surface",set:function(t,e,i,n,r,o){this.position=t,this.index=e,this.normal=i,this.color=n,this.atomindex=r,this.size=t.length/3,this.contour=o},fromGeometry:function(e){t.Debug&&Pv.time("GeometrySurface.fromGeometry");var i;e instanceof ae?(e.computeVertexNormals(!0),i=(new ue).fromGeometry(e)):i=e instanceof ue?e:e[0],i.boundingBox||i.computeBoundingBox(),this.center.copy(i.boundingBox.center()),this.boundingBox.copy(i.boundingBox);var n,r,o,a;if(i instanceof ue){var s=i.attributes,c=!!s.normal&&s.normal.array;(!c||0===c[0]&&0===c[1]&&0===c[2])&&i.computeVertexNormals(),n=s.position.array,o=s.index?s.index.array:null,a=s.normal.array}this.set(n,o,a,r,void 0),t.Debug&&Pv.timeEnd("GeometrySurface.setGeometry")},getPosition:function(){return this.position},getColor:function(t){var e,i,n,r=t||{},o=this.size;if("volume"===r.scheme){var a=new N,s=this.position;for(n=Ev.getScheme(r),i=new Float32Array(3*o),e=0;e<o;++e){var c=3*e;a.set(s[c],s[c+1],s[c+2]),n.positionColorToArray(a,i,c)}}else if(this.atomindex){r.surface=this,i=new Float32Array(3*o),n=Ev.getScheme(r);var u=r.structure.getAtomProxy(),h=this.atomindex;for(e=0;e<o;++e)u.index=h[e],n.atomColorToArray(u,i,3*e)}else{var l=new Ct(r.value);i=Lr(o,l.r,l.g,l.b)}return i},getPickingColor:function(t){var e=Object.assign(t||{});return e.scheme="picking",this.getColor(e)},getNormal:function(){return this.normal},getSize:function(t){return Ir(this.size,t)},getIndex:function(){return this.index},getFilteredIndex:function(t,e){if(t&&this.atomindex){for(var i,n=new On(t),r=e.getAtomSet(n),o=[],a=this.atomindex,s=this.index,c=s.length,u=0,h=this.contour?2:3,l=0;l<c;l+=h){var d=!0;for(i=0;i<h;i++){var f=s[l+i],p=a[f];if(!r.has(p)){d=!1;break}}if(d)for(i=0;i<h;i++,u++)o[u]=s[l+i]}var m=this.position.length/3>65535?Uint32Array:Uint16Array;return new m(o)}return this.index},getAtomindex:function(){return this.atomindex},dispose:function(){}},ma.prototype.constructor=ma,ga.prototype.constructor=ga,xa.__deps=[va,ya,ba],wa.__deps=[_a],_a.__deps=[Kr,Zr,Qr,qr],Aa.__deps=[Dn,no,ro,to,eo,oo,ao,Kr,so,So,Mo,Co,Po,To],Ma.__deps=[wa,_a,xa,Wr,Xr,Eo,Io],Tv.add("surf",function(t,e){var i=t.data.args,n=t.data.params;if(i&&(self.volsurf=new Ma(i[0],i[1],i[2],i[3],i[4])),n){var r=self.volsurf.getSurface(n.isolevel,n.smooth,n.box,n.matrix,n.contour),o=[r.position.buffer,r.index.buffer];r.normal&&o.push(r.normal.buffer),r.atomindex&&o.push(r.atomindex.buffer),e({sd:r,p:n},o)}},[Ma]),Pa.prototype={constructor:Pa,type:"Volume",setData:function(t,e,i,n,r){this.nx=e||1,this.ny=i||1,this.nz=n||1,this.data=t||new Float32Array(1),this.__data=this.data,this.setDataAtomindex(r),delete this.mc,delete this.__isolevel,delete this.__smooth,delete this.__minValue,delete this.__maxValue,delete this.__dataPositionBuffer,delete this.__dataPosition,delete this.__dataBuffer,delete this.__dataMin,delete this.__dataMax,delete this.__dataMean,delete this.__dataRms,this.worker&&this.worker.terminate()},setMatrix:function(t){this.matrix.copy(t);var e=this.boundingBox,i=this.center,n=this.nx-1,r=this.ny-1,o=this.nz-1;e.makeEmpty(),e.expandByPoint(i.set(n,r,o)),e.expandByPoint(i.set(n,r,0)),e.expandByPoint(i.set(n,0,o)),e.expandByPoint(i.set(n,0,0)),e.expandByPoint(i.set(0,r,o)),e.expandByPoint(i.set(0,0,o)),e.expandByPoint(i.set(0,r,0)),e.expandByPoint(i.set(0,0,0)),e.applyMatrix4(this.matrix),e.center(this.center);var a=this.matrix.elements,s=new N(a[0],a[1],a[2]),c=new N(a[4],a[5],a[6]),u=new N(a[8],a[9],a[10]),h=new N,l=this.normalMatrix.elements;h.crossVectors(c,u),l[0]=h.x,l[1]=h.y,l[2]=h.z,h.crossVectors(u,s),l[3]=h.x,l[4]=h.y,l[5]=h.z,h.crossVectors(s,c),l[6]=h.x,l[7]=h.y,l[8]=h.z,this.inverseMatrix.getInverse(this.matrix)},setDataAtomindex:function(t){this.dataAtomindex=t,this.__dataAtomindex=this.dataAtomindex,delete this.__dataAtomindexBuffer},getBox:function(t,e,i){return i||(i=new Et),i.set(t,t),i.expandByScalar(e),i.applyMatrix4(this.inverseMatrix),i.min.round(),i.max.round(),i},__getBox:function(t,e){if(t&&e){this.__box||(this.__box=new Et);var i=this.getBox(t,e,this.__box);return[i.min.toArray(),i.max.toArray()]}},makeSurface:function(t,e,i){var n=new pa("","",t);return n.info.isolevel=e,n.info.smooth=i,n},getSurface:function(t,e,i,n){t=isNaN(t)?this.getValueForSigma(2):t,e=e||0,void 0===this.volsurf&&(this.volsurf=new Ma(this.__data,this.nx,this.ny,this.nz,this.__dataAtomindex));var r=this.__getBox(i,n),o=this.volsurf.getSurface(t,e,r,this.matrix.elements);return this.makeSurface(o,t,e)},getSurfaceWorker:function(t,e,i,n,r){if(t=isNaN(t)?this.getValueForSigma(2):t,e=e||0,window.Worker){void 0===this.workerPool&&(this.workerPool=new ga("surf",2));var o={},a=this.workerPool.getNextWorker();0===a.postCount&&(o.args=[this.__data,this.nx,this.ny,this.nz,this.__dataAtomindex]),o.params={isolevel:t,smooth:e,box:this.__getBox(i,n),matrix:this.matrix.elements},a.post(o,void 0,function(t){var e=t.data.sd,i=t.data.p;r(this.makeSurface(e,i.isolevel,i.smooth))}.bind(this),function(o){console.warn("Volume.getSurfaceWorker error - trying without worker",o);var a=this.getSurface(t,e,i,n);r(a)}.bind(this))}else{var s=this.getSurface(t,e,i,n);r(s)}},getValueForSigma:function(t){return t=void 0!==t?t:2,this.getDataMean()+t*this.getDataRms()},getSigmaForValue:function(t){return t=void 0!==t?t:0,(t-this.getDataMean())/this.getDataRms()},filterData:function(t,e,i){isNaN(t)&&this.header&&(t=this.header.DMEAN+2*this.header.ARMS),t=void 0===t||isNaN(t)?-(1/0):t,e=void 0!==e?e:1/0,i=i||!1,this.dataPosition||this.makeDataPosition();var n=this.__dataPosition,r=this.__data;if(t!==this.__minValue||e!=this.__maxValue||i!==this.__outside){if(t===-(1/0)&&e===1/0)this.dataPosition=n,this.data=r;else{var o=r.length;this.__dataBuffer||(this.__dataPositionBuffer=new ArrayBuffer(3*o*4),this.__dataBuffer=new ArrayBuffer(4*o));for(var a=new Float32Array(this.__dataPositionBuffer),s=new Float32Array(this.__dataBuffer),c=0,u=0;u<o;++u){var h=3*u,l=r[u];if(!i&&l>=t&&l<=e||i&&(l<t||l>e)){var d=3*c;a[d+0]=n[h+0],a[d+1]=n[h+1],a[d+2]=n[h+2],s[c]=l,c+=1}}this.dataPosition=new Float32Array(this.__dataPositionBuffer,0,3*c),this.data=new Float32Array(this.__dataBuffer,0,c)}this.__minValue=t,this.__maxValue=e,this.__outside=i}},makeDataPosition:function(){for(var t=this.nz,e=this.ny,i=this.nx,n=new Float32Array(i*e*t*3),r=0,o=0;o<t;++o)for(var a=0;a<e;++a)for(var s=0;s<i;++s)n[r+0]=s,n[r+1]=a,n[r+2]=o,r+=3;this.matrix.applyToVector3Array(n),this.dataPosition=n,this.__dataPosition=n},getDataAtomindex:function(){return this.dataAtomindex},getDataPosition:function(){return this.dataPosition},getDataColor:function(t){var e=t||{};e.volume=this,e.scale=e.scale||"Spectral",e.domain=e.domain||[this.getDataMin(),this.getDataMax()];for(var i=Ev.getScheme(e),n=this.dataPosition.length/3,r=new Float32Array(3*n),o=0;o<n;++o)i.volumeColorToArray(o,r,3*o);return r},getPickingDataColor:function(t){var e=Object.assign(t||{});return e.scheme="picking",this.getDataColor(e)},getDataSize:function(t,e){var i,n,r=this.dataPosition.length/3;switch(t){case"value":n=new Float32Array(this.data);break;case"abs-value":for(n=new Float32Array(this.data),i=0;i<r;++i)n[i]=Math.abs(n[i]);break;case"value-min":n=new Float32Array(this.data);var o=this.getDataMin();for(i=0;i<r;++i)n[i]-=o;break;case"deviation":n=new Float32Array(this.data);break;default:n=Ir(r,t)}if(1!==e)for(i=0;i<r;++i)n[i]*=e;return n},getDataMin:function(){if(void 0===this.__dataMin){for(var t=this.__data,e=t.length,i=1/0,n=0;n<e;++n)i=Math.min(i,t[n]);this.__dataMin=i}return this.__dataMin},getDataMax:function(){if(void 0===this.__dataMax){for(var t=this.__data,e=t.length,i=-(1/0),n=0;n<e;++n)i=Math.max(i,t[n]);this.__dataMax=i}return this.__dataMax},getDataMean:function(){if(void 0===this.__dataMean){for(var t=this.__data,e=t.length,i=0,n=0;n<e;++n)i+=t[n];this.__dataMean=i/e}return this.__dataMean},getDataRms:function(){if(void 0===this.__dataRms){var t,e,i=this.__data,n=i.length,r=0;for(e=0;e<n;++e)t=i[e],r+=t*t;this.__dataRms=Math.sqrt(r/n)}return this.__dataRms},clone:function(){var t=new Pa(this.name,this.path,this.__data,this.nx,this.ny,this.nz,this.__dataAtomindex);return t.matrix.copy(this.matrix),this.header&&(t.header=Object.assign({},this.header)),t},dispose:function(){this.workerPool&&this.workerPool.terminate()}},Ta.prototype={constructor:Ta,_superpose:function(e,i){this.mean1=mo(e),this.mean2=mo(i),go(e,this.mean1),go(i,this.mean2),uo(this.coords1t,e),uo(this.coords2t,i),ho(this.A,this.coords2t,this.coords1t),wo(this.A,this.W,this.U,this.V),lo(this.V,this.VH),po(this.R,this.U,this.VH),fo(this.R)<0&&(t.Debug&&Pv.log("R not a right handed system"),po(this.tmp,this.c,this.VH),po(this.R,this.U,this.tmp))},prepCoords:function(t,e){var i=0,n=e.data;"function"==typeof t.eachAtom?t.eachAtom(function(t){n[i+0]=t.x,n[i+1]=t.y,n[i+2]=t.z,i+=3}):t instanceof Float32Array?n.set(t):Pv.warn("prepCoords: input type unknown")},transform:function(t){var e;"function"==typeof t.eachAtom?e=t.atomCount:t instanceof Float32Array&&(e=t.length/3);var i=new co(3,e),n=new co(e,3);this.prepCoords(t,i),go(i,this.mean1),ho(n,this.R,i),uo(i,n),vo(i,this.mean2);var r=0,o=i.data;"function"==typeof t.eachAtom?t.eachAtom(function(t){t.x=o[r+0],t.y=o[r+1],t.z=o[r+2],r+=3}):t instanceof Float32Array?t.set(o.subarray(0,3*e)):Pv.warn("transform: input type unknown")}},La.prototype={constructor:La,setStructure:function(t){this.structure=t,this.atomCount=t.atomCount,this.makeAtomIndices(),this.saveInitialStructure(),this.backboneIndices=this.getIndices(new On("backbone and not hydrogen")),this.makeIndices(),this.frameCache=[],this.boxCache=[],this.pathCache=[],this.frameCacheSize=0,this.currentFrame=-1},saveInitialStructure:function(){var t=0,e=new Float32Array(3*this.atomCount);this.structure.eachAtom(function(i){e[t+0]=i.x,e[t+1]=i.y,e[t+2]=i.z,t+=3}),this.initialStructure=e},setSelection:function(t){return this.selection.setString(t),this},getIndices:function(t){var e;if(t&&t.test){var i=0,n=t.test;e=[],this.structure.eachAtom(function(t){n(t)&&e.push(i),i+=1})}else e=this.structure.getAtomIndices(this.selection);return e},makeIndices:function(){this.indices=this.getIndices(this.selection);var t,e,i=3*this.indices.length;this.coords1=new Float32Array(i),this.coords2=new Float32Array(i);var n=this.initialStructure,r=this.coords2;for(t=0;t<i;t+=3)e=3*this.indices[t/3],r[t+0]=n[e+0],r[t+1]=n[e+1],r[t+2]=n[e+2]},makeAtomIndices:function(){Pv.error("Trajectory.makeAtomIndices not implemented")},getNumframes:function(){Pv.error("Trajectory.loadFrame not implemented")},resetCache:function(){return this.frameCache=[],this.boxCache=[],this.pathCache=[],this.frameCacheSize=0,this.setFrame(this.currentFrame),this},setParameters:function(t){var e=t,i=!1;void 0!==e.centerPbc&&e.centerPbc!==this.centerPbc&&(this.centerPbc=e.centerPbc,i=!0),void 0!==e.removePbc&&e.removePbc!==this.removePbc&&(this.removePbc=e.removePbc,i=!0),void 0!==e.superpose&&e.superpose!==this.superpose&&(this.superpose=e.superpose,i=!0),i&&this.resetCache()},setFrame:function(t,e){return void 0===t?this:(this.inProgress=!0,t=parseInt(t),t===-1||this.frameCache[t]?this.updateStructure(t,e):this.loadFrame(t,function(){this.updateStructure(t,e)}.bind(this)),this)},interpolate:function(){var t=function(t,e,i,n,r,o){var a=(i-t)*o,s=(n-e)*o,c=r*r,u=r*c;return(2*e-2*i+a+s)*u+(-3*e+3*i-2*a-s)*c+a*r+e},e=function(t,e,i){return t+(e-t)*i};return function(i,n,r,o,a,s,c){var u,h=this.frameCache,l=h[i],d=h[n],f=h[r],p=h[o],m=l.length,g=new Float32Array(m);if("spline"===s)for(u=0;u<m;u+=3)g[u+0]=t(p[u+0],f[u+0],d[u+0],l[u+0],a,1),g[u+1]=t(p[u+1],f[u+1],d[u+1],l[u+1],a,1),g[u+2]=t(p[u+2],f[u+2],d[u+2],l[u+2],a,1);else for(u=0;u<m;u+=3)g[u+0]=e(d[u+0],l[u+0],a),g[u+1]=e(d[u+1],l[u+1],a),g[u+2]=e(d[u+2],l[u+2],a);this.structure.updatePosition(g),this.currentFrame=i,this.signals.frameChanged.dispatch(i),"function"==typeof c&&c()}}(),setFrameInterpolated:function(t,e,i,n,r,o,a){if(void 0===t)return this;var s=this.frameCache,c=[];return s[n]||c.push(n),s[i]||c.push(i),s[e]||c.push(e),s[t]||c.push(t),c.length?this.loadFrame(c,function(){this.interpolate(t,e,i,n,r,o,a)}.bind(this)):this.interpolate(t,e,i,n,r,o,a),this},loadFrame:function(t,e){if(Array.isArray(t)){var i,n=function(t,n){this._loadFrame(t,n),0===i.length()&&"function"==typeof e&&e()}.bind(this);i=new Ca(n,t)}else this._loadFrame(t,e)},_loadFrame:function(t,e){Pv.error("Trajectory._loadFrame not implemented",t,e)},updateStructure:function(t,e){this._disposed||(t===-1?this.structure.updatePosition(this.initialStructure):this.structure.updatePosition(this.frameCache[t]),this.structure.trajectory={name:this.trajPath,frame:t},"function"==typeof e&&e(),this.currentFrame=t,this.inProgress=!1,this.signals.frameChanged.dispatch(t))},getCircularMean:function(t,e,i){return[Tr(e,i[0],3,0,t),Tr(e,i[1],3,1,t),Tr(e,i[2],3,2,t)]},doSuperpose:function(t){var e,i,n=3*this.indices.length,r=this.coords1,o=this.coords2;for(e=0;e<n;e+=3)i=3*this.indices[e/3],r[e+0]=t[i+0],r[e+1]=t[i+1],r[e+2]=t[i+2];var a=new Ta(r,o);a.transform(t)},process:function(t,e,i,n){if(this.setNumframes(n),e){if(this.backboneIndices.length>0&&this.centerPbc){var r=[e[0],e[4],e[8]],o=this.getCircularMean(this.backboneIndices,i,r);Ea(i,o,r)}this.removePbc&&Ia(i,e)}this.indices.length>0&&this.superpose&&this.doSuperpose(i),this.frameCache[t]=i,this.boxCache[t]=e,this.frameCacheSize+=1},setNumframes:function(t){t!==this.numframes&&(this.numframes=t,this.signals.gotNumframes.dispatch(t))},dispose:function(){this.frameCache=[],this._disposed=!0,this.player&&this.player.stop()},setPlayer:function(t){this.player=t,this.signals.playerChanged.dispatch(t)},getPath:function(t,e){Pv.error("Trajectory.getPath not implemented",t,e)}},Ov.add("shader/Mesh.vert","#define STANDARD\nuniform float nearClip;\nuniform vec3 clipCenter;\n#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )\nvarying vec3 vViewPosition;\n#endif\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#if defined( PICKING )\nattribute vec3 pickingColor;\nvarying vec3 vPickingColor;\n#elif defined( NOLIGHT )\nvarying vec3 vColor;\n#else\n#include color_pars_vertex\n#ifndef FLAT_SHADED\nvarying vec3 vNormal;\n#endif\n#endif\n#include common\nvoid main(){\n#if defined( PICKING )\nvPickingColor = pickingColor;\n#elif defined( NOLIGHT )\nvColor = color;\n#else\n#include color_vertex\n#include beginnormal_vertex\n#include defaultnormal_vertex\n#ifndef FLAT_SHADED\nvNormal = normalize( transformedNormal );\n#endif\n#endif\n#include begin_vertex\n#include project_vertex\n#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )\nvViewPosition = -mvPosition.xyz;\n#endif\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n#include nearclip_vertex\n}"),
-Ov.add("shader/Mesh.frag","#define STANDARD\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float roughness;\nuniform float metalness;\nuniform float opacity;\nuniform float nearClip;\nuniform float clipRadius;\n#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || ( !defined( PICKING ) && !defined( NOLIGHT ) )\nvarying vec3 vViewPosition;\n#endif\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#if defined( PICKING )\nuniform float objectId;\nvarying vec3 vPickingColor;\n#elif defined( NOLIGHT )\nvarying vec3 vColor;\n#else\n#ifndef FLAT_SHADED\nvarying vec3 vNormal;\n#endif\n#include common\n#include color_pars_fragment\n#include fog_pars_fragment\n#include bsdfs\n#include lights_pars\n#include lights_physical_pars_fragment\n#endif\nvoid main(){\n#include nearclip_fragment\n#include radiusclip_fragment\n#if defined( PICKING )\ngl_FragColor = vec4( vPickingColor, objectId );\n#elif defined( NOLIGHT )\ngl_FragColor = vec4( vColor, opacity );\n#else\nvec4 diffuseColor = vec4( diffuse, opacity );\nReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\nvec3 totalEmissiveLight = emissive;\n#include color_fragment\n#include roughnessmap_fragment\n#include metalnessmap_fragment\n#include normal_flip\n#include normal_fragment\n#include dull_interior_fragment\n#include lights_physical_fragment\n#include lights_template\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;\ngl_FragColor = vec4( outgoingLight, diffuseColor.a );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n#include opaque_back_fragment\n#endif\n}"),Oa.prototype={constructor:Oa,parameters:{opaqueBack:{updateShader:!0},dullInterior:{updateShader:!0},side:{updateShader:!0,property:!0},opacity:{uniform:!0},clipNear:{updateShader:!0,property:!0},clipRadius:{updateShader:!0,property:!0,uniform:!0},clipCenter:{uniform:!0},flatShaded:{updateShader:!0},background:{updateShader:!0},linewidth:{property:!0},wireframe:{updateVisibility:!0},roughness:{uniform:!0},metalness:{uniform:!0},diffuse:{uniform:!0}},get transparent(){return this.opacity<1||this.forceTransparent},makeMaterial:function(){var t=Ra(this.side);this.material=new Pt({uniforms:this.uniforms,vertexShader:"",fragmentShader:"",depthTest:!0,transparent:this.transparent,depthWrite:!0,lights:!0,fog:!0,side:t,linewidth:this.linewidth}),this.material.vertexColors=Rh,this.material.extensions.derivatives=this.flatShaded,this.material.extensions.fragDepth=this.impostor,this.material.clipNear=this.clipNear,this.wireframeMaterial=new Pt({uniforms:this.uniforms,vertexShader:"",fragmentShader:"",depthTest:!0,transparent:this.transparent,depthWrite:!0,lights:!1,fog:!0,side:t,linewidth:this.linewidth}),this.wireframeMaterial.vertexColors=Rh,this.wireframeMaterial.clipNear=this.clipNear,this.pickingMaterial=new Pt({uniforms:this.pickingUniforms,vertexShader:"",fragmentShader:"",depthTest:!0,transparent:!1,depthWrite:!0,lights:!1,fog:!1,side:t,linewidth:this.linewidth}),this.pickingMaterial.vertexColors=Rh,this.pickingMaterial.extensions.fragDepth=this.impostor,this.pickingMaterial.clipNear=this.clipNear,this.updateShader()},makeWireframeGeometry:function(){this.makeWireframeIndex();var t=this.geometry,e=this.wireframeIndex,i=new ue;i.attributes=t.attributes,e&&(i.setIndex(new Kt(e,1).setDynamic(this.dynamic)),i.setDrawRange(0,this.wireframeIndexCount)),this.wireframeGeometry=i},makeWireframeIndex:function(){function t(t,i){if(t>i){var n=t;t=i,i=n}var r=e[t];return void 0===r?(e[t]=[i],!0):!r.includes(i)&&(r.push(i),!0)}var e=[];return function(){var i=this.geometry.index;if(this.wireframe){if(i){var n=i.array,r=n.length;this.geometry.drawRange.count!==1/0&&(r=this.geometry.drawRange.count);var o;if(this.wireframeIndex&&this.wireframeIndex.length>2*r)o=this.wireframeIndex;else{var a=this.geometry.attributes.position.count,s=a>65535?Uint32Array:Uint16Array;o=new s(2*r)}var c=0;e.length=0;for(var u=0;u<r;u+=3){var h=n[u+0],l=n[u+1],d=n[u+2];t(h,l)&&(o[c+0]=h,o[c+1]=l,c+=2),t(l,d)&&(o[c+0]=l,o[c+1]=d,c+=2),t(d,h)&&(o[c+0]=d,o[c+1]=h,c+=2)}this.wireframeIndex=o,this.wireframeIndexCount=c,this.wireframeIndexVersion=this.indexVersion}}else this.wireframeIndex=new Uint16Array(0),this.wireframeIndexCount=0}}(),updateWireframeIndex:function(){if(this.wireframeGeometry.setDrawRange(0,1/0),this.wireframeIndexVersion<this.indexVersion&&this.makeWireframeIndex(),this.wireframeIndex.length>this.wireframeGeometry.index.array.length)this.wireframeGeometry.setIndex(new Kt(this.wireframeIndex,1).setDynamic(this.dynamic));else{var t=this.wireframeGeometry.getIndex();t.set(this.wireframeIndex),t.needsUpdate=this.wireframeIndexCount>0,t.updateRange.count=this.wireframeIndexCount}this.wireframeGeometry.setDrawRange(0,this.wireframeIndexCount)},getRenderOrder:function(){var t=0;return"text"===this.type?t=1:this.transparent&&(t="surface"===this.type?3:2),t},getMesh:function(){var t;return this.material||this.makeMaterial(),this.line?t=new Ve(this.geometry,this.material):this.point?(t=new He(this.geometry,this.material),this.sortParticles&&(t.sortParticles=!0)):t=new Ae(this.geometry,this.material),t.frustumCulled=!1,t.renderOrder=this.getRenderOrder(),t},getWireframeMesh:function(){var t;return this.material||this.makeMaterial(),this.wireframeGeometry||this.makeWireframeGeometry(),t=new Ve(this.wireframeGeometry,this.wireframeMaterial),t.frustumCulled=!1,t.renderOrder=this.getRenderOrder(),t},getPickingMesh:function(){var t;return this.material||this.makeMaterial(),t=new Ae(this.geometry,this.pickingMaterial),t.frustumCulled=!1,t.renderOrder=this.getRenderOrder(),t},getShader:function(t,e){return Pr(t,this.getDefines(e))},getVertexShader:function(t){return this.getShader(this.vertexShader,t)},getFragmentShader:function(t){return this.getShader(this.fragmentShader,t)},getDefines:function(t){var e={};return this.clipNear&&(e.NEAR_CLIP=1),this.clipRadius&&(e.RADIUS_CLIP=1),"picking"===t?e.PICKING=1:(("background"===t||this.background)&&(e.NOLIGHT=1),this.flatShaded&&(e.FLAT_SHADED=1),this.opaqueBack&&(e.OPAQUE_BACK=1),this.dullInterior&&(e.DULL_INTERIOR=1)),e},getParameters:function(){var t={};for(var e in this.parameters)t[e]=this[e];return t},addUniforms:function(t){this.uniforms=Fd.merge([this.uniforms,t]),this.pickingUniforms=Fd.merge([this.pickingUniforms,t])},addAttributes:function(t){var e={f:1,v2:2,v3:3,c:3};for(var i in t){var n,r=t[i];r.value?(this.attributeSize*e[r.type]!==r.value.length&&Pv.error("attribute value has wrong length",i),n=r.value):n=new Float32Array(this.attributeSize*e[r.type]),this.geometry.addAttribute(i,new Kt(n,e[r.type]).setDynamic(this.dynamic))}},updateRenderOrder:function(){function t(t){t.renderOrder=e}var e=this.getRenderOrder();this.group.children.forEach(t),this.pickingGroup&&this.pickingGroup.children.forEach(t)},updateShader:function(){var t=this.material,e=this.wireframeMaterial,i=this.pickingMaterial;t.vertexShader=this.getVertexShader(),t.fragmentShader=this.getFragmentShader(),t.needsUpdate=!0,e.vertexShader=this.getShader("Line.vert"),e.fragmentShader=this.getShader("Line.frag"),e.needsUpdate=!0,i.vertexShader=this.getVertexShader("picking"),i.fragmentShader=this.getFragmentShader("picking"),i.needsUpdate=!0},setParameters:function(t){if(t){var e=t,i=this.parameters,n={},r={},o=!1,a=!1;for(var s in e)void 0!==e[s]&&void 0!==i[s]&&(this[s]=e[s],i[s].property&&(i[s].property!==!0?n[i[s].property]=e[s]:n[s]=e[s]),i[s].uniform&&(i[s].uniform!==!0?r[i[s].uniform]=e[s]:r[s]=e[s]),i[s].updateShader&&(o=!0),i[s].updateVisibility&&(a=!0),this.dynamic&&"wireframe"===s&&e[s]===!0&&this.updateWireframeIndex(),"flatShaded"===s&&(this.material.extensions.derivatives=this.flatShaded),"forceTransparent"===s&&(n.transparent=this.transparent));this.setProperties(n),this.setUniforms(r),o&&this.updateShader(),a&&this.setVisibility(this.visible)}},setAttributes:function(t){var e=this.geometry,i=e.attributes;for(var n in t){var r=t[n],o=r.length;if("index"===n){var a=e.getIndex();e.setDrawRange(0,1/0),o>a.array.length?e.setIndex(new Kt(r,1).setDynamic(this.dynamic)):(a.set(r),a.needsUpdate=o>0,a.updateRange.count=o,e.setDrawRange(0,o)),this.indexVersion++,this.wireframe&&this.updateWireframeIndex()}else{var s=i[n];o>s.array.length?e.addAttribute(n,new Kt(r,s.itemSize).setDynamic(this.dynamic)):(i[n].set(r),i[n].needsUpdate=o>0,i[n].updateRange.count=o)}}},setUniforms:function(t){if(t){var e=this.material.uniforms,i=this.wireframeMaterial.uniforms,n=this.pickingMaterial.uniforms;for(var r in t)"opacity"===r&&this.setProperties({transparent:this.transparent}),void 0!==e[r]&&(e[r].value.isVector3?e[r].value.copy(t[r]):e[r].value.set?e[r].value.set(t[r]):e[r].value=t[r]),void 0!==i[r]&&(i[r].value.isVector3?i[r].value.copy(t[r]):i[r].value.set?i[r].value.set(t[r]):i[r].value=t[r]),void 0!==n[r]&&(n[r].value.isVector3?n[r].value.copy(t[r]):n[r].value.set?n[r].value.set(t[r]):n[r].value=t[r])}},setProperties:function(t){if(t){var e=this.material,i=this.wireframeMaterial,n=this.pickingMaterial;for(var r in t){var o=t[r];"transparent"===r?this.updateRenderOrder():"side"===r&&(o=Ra(o)),void 0!==e[r]&&(e[r]=o),void 0!==i[r]&&(i[r]=o),void 0!==n[r]&&(n[r]=o)}e.needsUpdate=!0,i.needsUpdate=!0,n.needsUpdate=!0}},setVisibility:function(t){this.visible=t,this.wireframe?(this.group.visible=!1,this.wireframeGroup.visible=t,this.pickable&&(this.pickingGroup.visible=!1)):(this.group.visible=t,this.wireframeGroup.visible=!1,this.pickable&&(this.pickingGroup.visible=t))},dispose:function(){this.material&&this.material.dispose(),this.wireframeMaterial&&this.wireframeMaterial.dispose(),this.pickingMaterial&&this.pickingMaterial.dispose(),this.geometry.dispose(),this.wireframeGeometry&&this.wireframeGeometry.dispose()}},Da.prototype=Object.assign(Object.create(Oa.prototype),{constructor:Da}),za.prototype=Object.assign(Object.create(Da.prototype),{constructor:za,applyPositionTransform:function(){},setAttributes:function(){var t=new O,e=new Lt;return function(i){var n,r,o,a,s,c,u,h,l,d,f,p=this.geometry.attributes;i.position&&(n=i.position,a=this.geoPosition,h=this.meshPosition,c=this.transformedGeoPosition,p.position.needsUpdate=!0),i.color&&(r=i.color,l=this.meshColor,p.color.needsUpdate=!0),i.pickingColor&&(o=i.pickingColor,d=this.meshPickingColor,p.pickingColor.needsUpdate=!0);var m=!(!this.updateNormals||!n),g=!(!this.initNormals||!n);(m||g)&&(s=this.geoNormal,f=this.meshNormal,u=this.transformedGeoNormal,p.normal.needsUpdate=!0);for(var v=this.positionCount,y=this.geoPositionCount,b=0;b<v;++b){var x,w,_=b*y*3,S=3*b;if(n&&(c.set(a),t.makeTranslation(n[S],n[S+1],n[S+2]),this.applyPositionTransform(t,b,S),t.applyToVector3Array(c),h.set(c,_)),m?(u.set(s),e.getNormalMatrix(t),e.applyToVector3Array(u),f.set(u,_)):g&&f.set(s,_),r)for(x=0;x<y;++x)w=_+3*x,l[w]=r[S],l[w+1]=r[S+1],l[w+2]=r[S+2];if(o)for(x=0;x<y;++x)w=_+3*x,d[w]=o[S],d[w+1]=o[S+1],d[w+2]=o[S+2]}}}(),makeIndex:function(){var t,e,i,n,r=this.geoIndex,o=this.meshIndex,a=this.positionCount,s=this.geoPositionCount,c=this.geoFacesCount,u=3*c;for(e=0;e<a;++e)for(i=e*u,n=i+u,o.set(r,i),t=i;t<n;++t)o[t]+=e*s}}),Ba.prototype=Object.assign(Object.create(za.prototype),{constructor:Ba,applyPositionTransform:function(){var t,e=new N;return function(i,n){t=this._radius[n],e.set(t,t,t),i.scale(e)}}(),setAttributes:function(t){t.radius&&(this._radius=t.radius),za.prototype.setAttributes.call(this,t)}}),Ov.add("shader/SphereImpostor.vert","uniform mat4 projectionMatrixInverse;\nuniform float nearClip;\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\nattribute vec2 mapping;\nattribute float radius;\n#ifdef PICKING\nattribute vec3 pickingColor;\nvarying vec3 vPickingColor;\n#else\n#include color_pars_vertex\n#endif\nconst mat4 D = mat4(\n1.0, 0.0, 0.0, 0.0,\n0.0, 1.0, 0.0, 0.0,\n0.0, 0.0, 1.0, 0.0,\n0.0, 0.0, 0.0, -1.0\n);\nmat4 transpose( in mat4 inMatrix ) {\nvec4 i0 = inMatrix[0];\nvec4 i1 = inMatrix[1];\nvec4 i2 = inMatrix[2];\nvec4 i3 = inMatrix[3];\nmat4 outMatrix = mat4(\nvec4(i0.x, i1.x, i2.x, i3.x),\nvec4(i0.y, i1.y, i2.y, i3.y),\nvec4(i0.z, i1.z, i2.z, i3.z),\nvec4(i0.w, i1.w, i2.w, i3.w)\n);\nreturn outMatrix;\n}\nvoid ComputePointSizeAndPositionInClipCoordSphere(){\nvec2 xbc;\nvec2 ybc;\nmat4 T = mat4(\nradius, 0.0, 0.0, 0.0,\n0.0, radius, 0.0, 0.0,\n0.0, 0.0, radius, 0.0,\nposition.x, position.y, position.z, 1.0\n);\nmat4 R = transpose( projectionMatrix * modelViewMatrix * T );\nfloat A = dot( R[ 3 ], D * R[ 3 ] );\nfloat B = -2.0 * dot( R[ 0 ], D * R[ 3 ] );\nfloat C = dot( R[ 0 ], D * R[ 0 ] );\nxbc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );\nxbc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );\nfloat sx = abs( xbc[ 0 ] - xbc[ 1 ] ) * 0.5;\nA = dot( R[ 3 ], D * R[ 3 ] );\nB = -2.0 * dot( R[ 1 ], D * R[ 3 ] );\nC = dot( R[ 1 ], D * R[ 1 ] );\nybc[ 0 ] = ( -B - sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );\nybc[ 1 ] = ( -B + sqrt( B * B - 4.0 * A * C ) ) / ( 2.0 * A );\nfloat sy = abs( ybc[ 0 ] - ybc[ 1 ] ) * 0.5;\ngl_Position.xy = vec2( 0.5 * ( xbc.x + xbc.y ), 0.5 * ( ybc.x + ybc.y ) );\ngl_Position.xy -= mapping * vec2( sx, sy );\ngl_Position.xy *= gl_Position.w;\n}\nvoid main(void){\n#ifdef PICKING\nvPickingColor = pickingColor;\n#else\n#include color_vertex\n#endif\nvec4 mvPosition = modelViewMatrix * vec4( position, 1.0 );\nmvPosition.z -= radius;\ngl_Position = projectionMatrix * vec4( mvPosition.xyz, 1.0 );\nComputePointSizeAndPositionInClipCoordSphere();\nvRadius = radius;\nvRadiusSq = radius * radius;\nvec4 vPoint4 = projectionMatrixInverse * gl_Position;\nvPoint = vPoint4.xyz / vPoint4.w;\nvPointViewPosition = -mvPosition.xyz / mvPosition.w;\n}"),Ov.add("shader/SphereImpostor.frag","#define STANDARD\n#define IMPOSTOR\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float roughness;\nuniform float metalness;\nuniform float opacity;\nuniform float nearClip;\nuniform mat4 projectionMatrix;\nuniform float ortho;\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n#ifdef PICKING\nuniform float objectId;\nvarying vec3 vPickingColor;\n#else\n#include common\n#include color_pars_fragment\n#include fog_pars_fragment\n#include bsdfs\n#include lights_pars\n#include lights_physical_pars_fragment\n#endif\nbool flag2 = false;\nbool interior = false;\nvec3 cameraPos;\nvec3 cameraNormal;\nfloat calcDepth( in vec3 cameraPos ){\nvec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw;\nreturn 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\nfloat calcClip( vec3 cameraPos ){\nreturn dot( vec4( cameraPos, 1.0 ), vec4( 0.0, 0.0, 1.0, nearClip - 0.5 ) );\n}\nbool Impostor( out vec3 cameraPos, out vec3 cameraNormal ){\nvec3 cameraSpherePos = -vPointViewPosition;\ncameraSpherePos.z += vRadius;\nvec3 rayOrigin = mix( vec3( 0.0, 0.0, 0.0 ), vPoint, ortho );\nvec3 rayDirection = mix( normalize( vPoint ), vec3( 0.0, 0.0, 1.0 ), ortho );\nvec3 cameraSphereDir = mix( cameraSpherePos, rayOrigin - cameraSpherePos, ortho );\nfloat B = dot( rayDirection, cameraSphereDir );\nfloat det = B * B + vRadiusSq - dot( cameraSphereDir, cameraSphereDir );\nif( det < 0.0 ){\ndiscard;\nreturn false;\n}else{\nfloat sqrtDet = sqrt( det );\nfloat posT = mix( B + sqrtDet, B + sqrtDet, ortho );\nfloat negT = mix( B - sqrtDet, sqrtDet - B, ortho );\ncameraPos = rayDirection * negT + rayOrigin;\n#ifdef NEAR_CLIP\nif( calcDepth( cameraPos ) <= 0.0 ){\ncameraPos = rayDirection * posT + rayOrigin;\ninterior = true;\nreturn false;\n}else if( calcClip( cameraPos ) > 0.0 ){\ncameraPos = rayDirection * posT + rayOrigin;\ninterior = true;\nflag2 = true;\nreturn false;\n}else{\ncameraNormal = normalize( cameraPos - cameraSpherePos );\n}\n#else\nif( calcDepth( cameraPos ) <= 0.0 ){\ncameraPos = rayDirection * posT + rayOrigin;\ninterior = true;\nreturn false;\n}else{\ncameraNormal = normalize( cameraPos - cameraSpherePos );\n}\n#endif\nreturn true;\n}\nreturn false;\n}\nvoid main(void){\nbool flag = Impostor( cameraPos, cameraNormal );\n#ifdef NEAR_CLIP\nif( calcClip( cameraPos ) > 0.0 )\ndiscard;\n#endif\ngl_FragDepthEXT = calcDepth( cameraPos );\nif( !flag ){\n#ifdef NEAR_CLIP\nif( flag2 ){\ngl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( nearClip - 0.5 ) ) ) + ( 0.0000001 / vRadius ) );\n}else if( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );\n}\n#else\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );\n}\n#endif\n}\nif (gl_FragDepthEXT < 0.0)\ndiscard;\nif (gl_FragDepthEXT > 1.0)\ndiscard;\n#ifdef PICKING\ngl_FragColor = vec4( vPickingColor, objectId );\n#else\nvec3 vNormal = cameraNormal;\nvec3 vViewPosition = -cameraPos;\nvec4 diffuseColor = vec4( diffuse, opacity );\nReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\nvec3 totalEmissiveLight = emissive;\n#include color_fragment\n#include roughnessmap_fragment\n#include metalnessmap_fragment\n#include normal_flip\n#include normal_fragment\nif( interior ){\nnormal = vec3( 0.0, 0.0, 0.4 );\n}\n#include lights_physical_fragment\n#include lights_template\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;\ngl_FragColor = vec4( outgoingLight, diffuseColor.a );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n#endif\n}"),Ua.prototype=Object.assign(Object.create(Oa.prototype),{constructor:Ua,setAttributes:function(t){var e,i,n,r,o,a,s,c=this.count,u=this.mappingSize,h=this.geometry.attributes;for(var l in t){i=t[l],e=h[l],n=e.itemSize,r=e.array;for(var d=0;d<c;++d){o=d*n,a=o*u;for(var f=0;f<u;++f){s=a+n*f;for(var p=0;p<n;++p)r[s+p]=i[o+p]}}e.needsUpdate=!0}},makeMapping:function(){for(var t=this.count,e=this.mapping,i=this.mappingSize,n=this.mappingItemSize,r=this.geometry.attributes.mapping.array,o=0;o<t;o++)r.set(e,o*n*i)},makeIndex:function(){for(var t,e,i=this.count,n=this.mappingSize,r=this.mappingIndices,o=this.mappingIndicesSize,a=this.index,s=0;s<i;s++){t=s*o,e=s*n,a.set(r,t);for(var c=0;c<o;++c)a[t+c]+=e}}}),ja.prototype=Object.assign(Object.create(Ua.prototype),{constructor:ja}),$a.prototype=Object.assign(Object.create(ja.prototype),{constructor:$a}),Ga.prototype=Object.assign(Object.create(za.prototype),{constructor:Ga,applyPositionTransform:function(){var t=new N,e=new N,i=new N,n=new N(0,0,0);return function(r,o,a){e.fromArray(this._majorAxis,a),i.fromArray(this._minorAxis,a),r.lookAt(n,e,i),t.set(this._radius[o],i.length(),e.length()),r.scale(t)}}(),setAttributes:function(t){t.majorAxis&&(this.majorAxis=t.majorAxis),t.minorAxis&&(this._minorAxis=t.minorAxis),za.prototype.setAttributes.call(this,t)}}),Wa.prototype=Object.assign(Object.create(za.prototype),{constructor:Wa,applyPositionTransform:function(){var t,e=new N,i=new N,n=new N,r=new N(0,1,0);return function(o,a,s){i.fromArray(this._from,s),n.fromArray(this._to,s),o.lookAt(i,n,r),t=this._radius[a],e.set(t,t,i.distanceTo(n)),o.scale(e)}}(),setAttributes:function(t){var e=this._position.length/2,i=this._radius.length/2,n={};t.position1&&t.position2&&(Er(t.position1,t.position2,this.__center),Er(t.position1,this.__center,this._position),Er(this.__center,t.position2,this._position,e),this._from.set(t.position1),this._from.set(this.__center,e),this._to.set(this.__center),this._to.set(t.position2,e),n.position=this._position),t.color&&t.color2&&(this._color.set(t.color),this._color.set(t.color2,e),n.color=this._color),t.pickingColor&&t.pickingColor2&&(this._pickingColor.set(t.pickingColor),this._pickingColor.set(t.pickingColor2,e),n.pickingColor=this._pickingColor),t.radius&&(this._radius.set(t.radius),this._radius.set(t.radius,i)),za.prototype.setAttributes.call(this,n)}}),Ov.add("shader/CylinderImpostor.vert","\nattribute vec3 mapping;\nattribute vec3 position1;\nattribute vec3 position2;\nattribute float radius;\nvarying vec3 axis;\nvarying vec4 base_radius;\nvarying vec4 end_b;\nvarying vec3 U;\nvarying vec3 V;\nvarying vec4 w;\n#ifdef PICKING\nattribute vec3 pickingColor;\nattribute vec3 pickingColor2;\nvarying vec3 vPickingColor;\nvarying vec3 vPickingColor2;\n#else\nattribute vec3 color2;\nvarying vec3 vColor1;\nvarying vec3 vColor2;\n#endif\nuniform mat4 modelViewMatrixInverse;\nuniform float ortho;\nvoid main(){\n#ifdef PICKING\nvPickingColor = pickingColor;\nvPickingColor2 = pickingColor2;\n#else\nvColor1 = color;\nvColor2 = color2;\n#endif\nbase_radius.w = radius;\nvec3 center = position;\nvec3 dir = normalize( position2 - position1 );\nfloat ext = length( position2 - position1 ) / 2.0;\nvec3 cam_dir;\nif( ortho == 0.0 ){\ncam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 0, 1 ) ).xyz - center;\n}else{\ncam_dir = ( modelViewMatrixInverse * vec4( 0, 0, 1, 0 ) ).xyz;\n}\ncam_dir = normalize( cam_dir );\nvec3 ldir;\nfloat b = dot( cam_dir, dir );\nend_b.w = b;\nif( b < 0.0 )\nldir = -ext * dir;\nelse\nldir = ext * dir;\nvec3 left = normalize( cross( cam_dir, ldir ) );\nleft = radius * left;\nvec3 up = radius * normalize( cross( left, ldir ) );\naxis = normalize( normalMatrix * ldir );\nU = normalize( normalMatrix * up );\nV = normalize( normalMatrix * left );\nvec4 base4 = modelViewMatrix * vec4( center - ldir, 1.0 );\nbase_radius.xyz = base4.xyz / base4.w;\nvec4 top_position = modelViewMatrix * vec4( center + ldir, 1.0 );\nvec4 end4 = top_position;\nend_b.xyz = end4.xyz / end4.w;\nw = modelViewMatrix * vec4(\ncenter + mapping.x*ldir + mapping.y*left + mapping.z*up, 1.0\n);\ngl_Position = projectionMatrix * w;\ngl_Position.z = 0.99;\n}"),Ov.add("shader/CylinderImpostor.frag","#define STANDARD\n#define IMPOSTOR\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float roughness;\nuniform float metalness;\nuniform float opacity;\nuniform float nearClip;\nuniform mat4 projectionMatrix;\nuniform float ortho;\nvarying vec3 axis;\nvarying vec4 base_radius;\nvarying vec4 end_b;\nvarying vec3 U;\nvarying vec3 V;\nvarying vec4 w;\n#ifdef PICKING\nuniform float objectId;\nvarying vec3 vPickingColor;\nvarying vec3 vPickingColor2;\n#else\nvarying vec3 vColor1;\nvarying vec3 vColor2;\n#include common\n#include fog_pars_fragment\n#include bsdfs\n#include lights_pars\n#include lights_physical_pars_fragment\n#endif\nbool interior = false;\nfloat distSq3( vec3 v3a, vec3 v3b ){\nreturn (\n( v3a.x - v3b.x ) * ( v3a.x - v3b.x ) +\n( v3a.y - v3b.y ) * ( v3a.y - v3b.y ) +\n( v3a.z - v3b.z ) * ( v3a.z - v3b.z )\n);\n}\nfloat calcDepth( in vec3 cameraPos ){\nvec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw;\nreturn 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\nfloat calcClip( vec3 cameraPos ){\nreturn dot( vec4( cameraPos, 1.0 ), vec4( 0.0, 0.0, 1.0, nearClip - 0.5 ) );\n}\nvoid main(){\nvec3 point = w.xyz / w.w;\nvec3 base = base_radius.xyz;\nfloat vRadius = base_radius.w;\nvec3 end = end_b.xyz;\nfloat b = end_b.w;\nvec3 end_cyl = end;\nvec3 surface_point = point;\nvec3 ray_target = surface_point;\nvec3 ray_origin = vec3(0.0);\nvec3 ray_direction = mix(normalize(ray_origin - ray_target), vec3(0.0, 0.0, 1.0), ortho);\nmat3 basis = mat3( U, V, axis );\nvec3 diff = ray_target - 0.5 * (base + end_cyl);\nvec3 P = diff * basis;\nfloat dz = dot( axis, ray_direction );\nfloat radius2 = vRadius*vRadius;\nvec3 D = vec3(dot(U, ray_direction),\ndot(V, ray_direction),\ndz);\nfloat a0 = P.x*P.x + P.y*P.y - radius2;\nfloat a1 = P.x*D.x + P.y*D.y;\nfloat a2 = D.x*D.x + D.y*D.y;\nfloat d = a1*a1 - a0*a2;\nif (d < 0.0)\ndiscard;\nfloat dist = (-a1 + sqrt(d)) / a2;\nvec3 new_point = ray_target + dist * ray_direction;\nvec3 tmp_point = new_point - base;\nvec3 _normal = normalize( tmp_point - axis * dot(tmp_point, axis) );\nray_origin = mix( ray_origin, surface_point, ortho );\nfloat front_cap_test = dot( tmp_point, axis );\nfloat end_cap_test = dot((new_point - end_cyl), axis);\n#ifndef CAP\nvec3 new_point2 = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;\nvec3 tmp_point2 = new_point2 - base;\n#endif\nif (front_cap_test < 0.0)\n{\nfloat dNV = dot(-axis, ray_direction);\nif (dNV < 0.0)\ndiscard;\nfloat near = dot(-axis, (base)) / dNV;\nvec3 front_point = ray_direction * near + ray_origin;\nif (dot(front_point - base, front_point-base) > radius2)\ndiscard;\n#ifdef CAP\nnew_point = front_point;\n_normal = axis;\n#else\nnew_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;\ndNV = dot(-axis, ray_direction);\nnear = dot(axis, end_cyl) / dNV;\nnew_point2 = ray_direction * near + ray_origin;\nif (dot(new_point2 - end_cyl, new_point2-base) < radius2)\ndiscard;\ninterior = true;\n#endif\n}\nif( end_cap_test > 0.0 )\n{\nfloat dNV = dot(axis, ray_direction);\nif (dNV < 0.0)\ndiscard;\nfloat near = dot(axis, end_cyl) / dNV;\nvec3 end_point = ray_direction * near + ray_origin;\nif( dot(end_point - end_cyl, end_point-base) > radius2 )\ndiscard;\n#ifdef CAP\nnew_point = end_point;\n_normal = axis;\n#else\nnew_point = ray_target + ( (-a1 - sqrt(d)) / a2 ) * ray_direction;\ndNV = dot(-axis, ray_direction);\nnear = dot(-axis, (base)) / dNV;\nnew_point2 = ray_direction * near + ray_origin;\nif (dot(new_point2 - base, new_point2-base) < radius2)\ndiscard;\ninterior = true;\n#endif\n}\ngl_FragDepthEXT = calcDepth( new_point );\n#ifdef NEAR_CLIP\nif( calcClip( new_point ) > 0.0 ){\ndist = (-a1 - sqrt(d)) / a2;\nnew_point = ray_target + dist * ray_direction;\nif( calcClip( new_point ) > 0.0 )\ndiscard;\ninterior = true;\ngl_FragDepthEXT = calcDepth( new_point );\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( nearClip - 0.5 ) ) ) + ( 0.0000001 / vRadius ) );\n}\n}else if( gl_FragDepthEXT <= 0.0 ){\ndist = (-a1 - sqrt(d)) / a2;\nnew_point = ray_target + dist * ray_direction;\ninterior = true;\ngl_FragDepthEXT = calcDepth( new_point );\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );\n}\n}\n#else\nif( gl_FragDepthEXT <= 0.0 ){\ndist = (-a1 - sqrt(d)) / a2;\nnew_point = ray_target + dist * ray_direction;\ninterior = true;\ngl_FragDepthEXT = calcDepth( new_point );\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / vRadius );\n}\n}\n#endif\nif (gl_FragDepthEXT < 0.0)\ndiscard;\nif (gl_FragDepthEXT > 1.0)\ndiscard;\n#ifdef PICKING\nif( distSq3( new_point, end_cyl ) < distSq3( new_point, base ) ){\nif( b < 0.0 ){\ngl_FragColor = vec4( vPickingColor, objectId );\n}else{\ngl_FragColor = vec4( vPickingColor2, objectId );\n}\n}else{\nif( b > 0.0 ){\ngl_FragColor = vec4( vPickingColor, objectId );\n}else{\ngl_FragColor = vec4( vPickingColor2, objectId );\n}\n}\n#else\nvec3 vViewPosition = -new_point;\nvec3 vNormal = _normal;\nvec3 vColor;\nif( distSq3( new_point, end_cyl ) < distSq3( new_point, base ) ){\nif( b < 0.0 ){\nvColor = vColor1;\n}else{\nvColor = vColor2;\n}\n}else{\nif( b > 0.0 ){\nvColor = vColor1;\n}else{\nvColor = vColor2;\n}\n}\nvec4 diffuseColor = vec4( diffuse, opacity );\nReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\nvec3 totalEmissiveLight = emissive;\n#include color_fragment\n#include roughnessmap_fragment\n#include metalnessmap_fragment\nvec3 normal = normalize( vNormal );\nif( interior ){\nnormal = vec3( 0.0, 0.0, 0.4 );\n}\n#include lights_physical_fragment\n#include lights_template\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;\ngl_FragColor = vec4( outgoingLight, diffuseColor.a );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n#endif\n}"),Xa.prototype=Object.assign(Object.create(Ua.prototype),{constructor:Xa}),qa.prototype=Object.assign(Object.create(Xa.prototype),{constructor:qa,parameters:Object.assign({openEnded:{updateShader:!0}},Xa.prototype.parameters),getDefines:function(t){var e=Xa.prototype.getDefines.call(this,t);return this.openEnded||(e.CAP=1),e},setAttributes:function(t){t&&t.position1&&t.position2&&(t.position=Er(t.position1,t.position2)),Xa.prototype.setAttributes.call(this,t)}}),Za.prototype=Object.assign(Object.create(za.prototype),{constructor:Za,applyPositionTransform:function(){var t,e=new N,i=new N,n=new N,r=new N(0,1,0);return function(o,a,s){i.fromArray(this._from,s),n.fromArray(this._to,s),o.lookAt(i,n,r),t=this._radius[a],e.set(t,t,i.distanceTo(n)),o.scale(e)}}(),setAttributes:function(t){var e={};t.position1&&t.position2&&(Er(t.position1,t.position2,this._position),this._from.set(t.position1),this._to.set(t.position2),e.position=this._position),t.color&&(e.color=t.color),t.pickingColor&&(e.pickingColor=t.pickingColor),t.radius&&this._radius.set(t.radius),za.prototype.setAttributes.call(this,e)}}),Ja.prototype.constructor=Ja,Ja.prototype.type="Shape",ts.prototype={constructor:ts,type:"",parameters:{lazy:{type:"boolean"},clipNear:{type:"range",step:1,max:100,min:0,buffer:!0},clipRadius:{type:"number",precision:1,max:1e3,min:0,buffer:!0},clipCenter:{type:"vector3",precision:1,buffer:!0},flatShaded:{type:"boolean",buffer:!0},opacity:{type:"range",step:.01,max:1,min:0,buffer:!0},side:{type:"select",buffer:!0,options:{front:"front",back:"back",double:"double"}},wireframe:{type:"boolean",buffer:!0},linewidth:{type:"integer",max:50,min:1,buffer:!0},colorScheme:{type:"select",update:"color",options:Ev.getTypes()},colorScale:{type:"select",update:"color",options:Ev.getScales()},colorValue:{type:"color",update:"color"},colorDomain:{type:"hidden",update:"color"},colorMode:{type:"select",update:"color",options:Ev.getModes()},roughness:{type:"range",step:.01,max:1,min:0,buffer:!0},metalness:{type:"range",step:.01,max:1,min:0,buffer:!0},diffuse:{type:"color",buffer:!0}},init:function(t){var e=t||{};this.clipNear=d(e.clipNear,0),this.clipRadius=d(e.clipRadius,0),this.clipCenter=d(e.clipCenter,new N),this.flatShaded=d(e.flatShaded,!1),this.side=d(e.side,"double"),this.opacity=d(e.opacity,1),this.wireframe=d(e.wireframe,!1),this.linewidth=d(e.linewidth,2),this.setColor(e.color,e),this.colorScheme=d(e.colorScheme,"uniform"),this.colorScale=d(e.colorScale,""),this.colorValue=d(e.colorValue,9474192),this.colorDomain=d(e.colorDomain,""),this.colorMode=d(e.colorMode,"hcl"),this.visible=d(e.visible,!0),this.quality=d(e.quality,void 0),this.roughness=d(e.roughness,.4),this.metalness=d(e.metalness,0),this.diffuse=d(e.diffuse,16777215),this.lazy=d(e.lazy,!1),this.lazyProps={build:!1,bufferParams:{},what:{}};var i=this.parameters;i.sphereDetail===!0&&(i.sphereDetail={type:"integer",max:3,min:0,rebuild:"impostor"}),i.radialSegments===!0&&(i.radialSegments={type:"integer",max:25,min:5,rebuild:"impostor"}),i.openEnded===!0&&(i.openEnded={type:"boolean",rebuild:"impostor",buffer:!0}),i.disableImpostor===!0&&(i.disableImpostor={type:"boolean",rebuild:!0}),"low"===e.quality?(i.sphereDetail&&(this.sphereDetail=0),i.radialSegments&&(this.radialSegments=5)):"medium"===e.quality?(i.sphereDetail&&(this.sphereDetail=1),i.radialSegments&&(this.radialSegments=10)):"high"===e.quality?(i.sphereDetail&&(this.sphereDetail=2),i.radialSegments&&(this.radialSegments=20)):(i.sphereDetail&&(this.sphereDetail=d(e.sphereDetail,1)),i.radialSegments&&(this.radialSegments=d(e.radialSegments,10))),i.openEnded&&(this.openEnded=d(e.openEnded,!0)),i.disableImpostor&&(this.disableImpostor=d(e.disableImpostor,!1))},getColorParams:function(t){return Object.assign({gidPool:this.gidPool,scheme:this.colorScheme,scale:this.colorScale,value:this.colorValue,domain:this.colorDomain,mode:this.colorMode},t)},getBufferParams:function(t){return Object.assign({clipNear:this.clipNear,clipRadius:this.clipRadius,clipCenter:this.clipCenter,flatShaded:this.flatShaded,opacity:this.opacity,side:this.side,wireframe:this.wireframe,
-linewidth:this.linewidth,roughness:this.roughness,metalness:this.metalness,diffuse:this.diffuse},t)},setColor:function(t,e){var i=Object.keys(Ev.getTypes());return i.includes(t)?e?e.colorScheme=t:this.setParameters({colorScheme:t}):void 0!==t&&(t=new Ct(t).getHex(),e?(e.colorScheme="uniform",e.colorValue=t):this.setParameters({colorScheme:"uniform",colorValue:t})),this},prepare:!1,create:function(){},update:function(){this.build()},build:function(t){return this.lazy&&!this.visible?void(this.lazyProps.build=!0):this.prepare?(this.queue.length()>0?(this.tasks.change(1-this.queue.length()),this.queue.kill()):this.tasks.increment(),void this.queue.push(t||!1)):(this.tasks.increment(),void this.make())},make:function(e,i){t.Debug&&Pv.time("Representation.make "+this.type);var n=function(){e?(this.update(e),this.viewer.requestRender(),this.tasks.decrement(),i&&i()):(this.clear(),this.create(),this.manualAttach||this.disposed||(t.Debug&&Pv.time("Representation.attach "+this.type),this.attach(function(){t.Debug&&Pv.timeEnd("Representation.attach "+this.type),this.tasks.decrement(),i&&i()}.bind(this)))),t.Debug&&Pv.timeEnd("Representation.make "+this.type)}.bind(this);this.prepare?this.prepare(n):n()},attach:function(t){this.setVisibility(this.visible),t()},setVisibility:function(t,e){if(this.visible=t,this.visible){var i=this.lazyProps,n=i.bufferParams,r=i.what;if(i.build)return i.build=!1,void this.build();(Object.keys(n).length||Object.keys(r).length)&&(i.bufferParams={},i.what={},this.updateParameters(n,r))}return this.bufferList.forEach(function(e){e.setVisibility(t)}),e||this.viewer.requestRender(),this},setParameters:function(t,e,i){var n=t||{},r=this.parameters;e=e||{},i=i||!1;var o={};for(var a in n)void 0!==n[a]&&void 0!==r[a]&&(r[a].int&&(n[a]=parseInt(n[a])),r[a].float&&(n[a]=parseFloat(n[a])),n[a]!==this[a]&&(this[a]=n[a],r[a].buffer&&(r[a].buffer===!0?o[a]=n[a]:o[r[a].buffer]=n[a]),r[a].update&&(e[r[a].update]=!0),!r[a].rebuild||"impostor"===r[a].rebuild&&Mv&&!this.disableImpostor||(i=!0)));return i?this.build():this.updateParameters(o,e),this},updateParameters:function(t,e){return this.lazy&&!this.visible?(Object.assign(this.lazyProps.bufferParams,t),void Object.assign(this.lazyProps.what,e)):(this.bufferList.forEach(function(e){e.setParameters(t)}),Object.keys(e).length&&this.update(e),void this.viewer.requestRender())},getParameters:function(){var t={lazy:this.lazy,visible:this.visible,quality:this.quality};return Object.keys(this.parameters).forEach(function(e){"button"===this.parameters.type?t[e]=this[e].bind(this):t[e]=this[e]},this),t},clear:function(){this.bufferList.forEach(function(t){this.viewer.remove(t),t.dispose()},this),this.bufferList.length=0,this.viewer.requestRender()},dispose:function(){this.disposed=!0,this.queue.kill(),this.tasks.dispose(),this.clear()}},es.prototype=Object.assign(Object.create(ts.prototype),{constructor:es,type:"buffer",parameters:Object.assign({},ts.prototype.parameters,{colorScheme:null,colorScale:null,colorValue:null,colorDomain:null,colorMode:null}),create:function(){this.bufferList.push.apply(this.bufferList,this.buffer)},attach:function(t){this.bufferList.forEach(function(t){this.viewer.add(t),t.setParameters(this.getBufferParams())},this),this.setVisibility(this.visible),t()}}),is.prototype=Object.assign(Object.create(Da.prototype),{constructor:is,type:"surface"}),ns.prototype.constructor=ns,rs.prototype=Object.assign(Object.create(ts.prototype),{constructor:rs,type:"surface",parameters:Object.assign({isolevelType:{type:"select",options:{value:"value",sigma:"sigma"}},isolevel:{type:"number",precision:2,max:1e3,min:-1e3},smooth:{type:"integer",precision:1,max:10,min:0},background:{type:"boolean",rebuild:!0},opaqueBack:{type:"boolean",buffer:!0},boxSize:{type:"integer",precision:1,max:100,min:0},useWorker:{type:"boolean",rebuild:!0}},ts.prototype.parameters),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"uniform"),e.colorValue=d(e.colorValue,14540253),this.isolevelType=d(e.isolevelType,"sigma"),this.isolevel=d(e.isolevel,2),this.smooth=d(e.smooth,0),this.background=d(e.background,!1),this.opaqueBack=d(e.opaqueBack,!0),this.boxSize=d(e.boxSize,0),this.useWorker=d(e.useWorker,!0),ts.prototype.init.call(this,e)},attach:function(t){this.bufferList.forEach(function(t){this.viewer.add(t)},this),this.setVisibility(this.visible),t()},prepare:function(t){if(this.volume){var e;if(e="sigma"===this.isolevelType?this.volume.getValueForSigma(this.isolevel):this.isolevel,!this.surface||this.__isolevel!==e||this.__smooth!==this.smooth||this.__boxSize!==this.boxSize||this.boxSize>0&&!this.__boxCenter.equals(this.boxCenter)){this.__isolevel=e,this.__smooth=this.smooth,this.__boxSize=this.boxSize,this.__boxCenter.copy(this.boxCenter),this.__box.copy(this.box);var i=function(e){this.surface=e,t()}.bind(this);this.useWorker?this.volume.getSurfaceWorker(e,this.smooth,this.boxCenter,this.boxSize,i):i(this.volume.getSurface(e,this.smooth,this.boxCenter,this.boxSize))}else t()}else t()},create:function(){var t=new is(this.surface.getPosition(),this.surface.getColor(this.getColorParams()),this.surface.getIndex(),this.surface.getNormal(),void 0,this.getBufferParams({background:this.background,opaqueBack:this.opaqueBack,dullInterior:!1})),e=new ns(t);this.bufferList.push(e)},update:function(t){if(0!==this.bufferList.length){t=t||{};var e={};t.position&&(e.position=this.surface.getPosition()),t.color&&(e.color=this.surface.getColor(this.getColorParams())),t.index&&(e.index=this.surface.getIndex()),t.normal&&(e.normal=this.surface.getNormal()),this.bufferList.forEach(function(t){t.setAttributes(e)})}},setParameters:function(t,e,i){return t&&void 0!==t.isolevelType&&this.volume&&("value"===this.isolevelType&&"sigma"===t.isolevelType?this.isolevel=this.volume.getSigmaForValue(this.isolevel):"sigma"===this.isolevelType&&"value"===t.isolevelType&&(this.isolevel=this.volume.getValueForSigma(this.isolevel)),this.isolevelType=t.isolevelType),t&&t.boxCenter&&(this.boxCenter.copy(t.boxCenter),delete t.boxCenter),ts.prototype.setParameters.call(this,t,e,i),this.volume&&this.volume.getBox(this.boxCenter,this.boxSize,this.box),this.surface&&(void 0!==t.isolevel||void 0!==t.smooth||void 0!==t.boxSize||this.boxSize>0&&!this.__box.equals(this.box))&&this.build({position:!0,color:!0,index:!0,normal:!0}),this},dispose:function(){this.viewer.signals.orientationChanged.remove(this.setBox),ts.prototype.dispose.call(this)}}),Ov.add("shader/Point.vert","uniform float nearClip;\nuniform float clipRadius;\nuniform vec3 clipCenter;\nuniform float size;\nuniform float canvasHeight;\nuniform float pixelRatio;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#include color_pars_vertex\n#include common\nvoid main(){\n#include color_vertex\n#include begin_vertex\n#include project_vertex\n#ifdef USE_SIZEATTENUATION\ngl_PointSize = size * pixelRatio * ( ( canvasHeight / 2.0 ) / -mvPosition.z );\n#else\ngl_PointSize = size * pixelRatio;\n#endif\nvViewPosition = -mvPosition.xyz;\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n#include nearclip_vertex\n#include radiusclip_vertex\n}"),Ov.add("shader/Point.frag","uniform vec3 diffuse;\nuniform float opacity;\nuniform float nearClip;\nuniform float clipRadius;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#ifdef USE_MAP\nuniform sampler2D map;\n#endif\n#include common\n#include color_pars_fragment\n#include fog_pars_fragment\nvoid main(){\n#include nearclip_fragment\n#include radiusclip_fragment\nvec3 outgoingLight = vec3( 0.0 );\nvec4 diffuseColor = vec4( diffuse, 1.0 );\n#ifdef USE_MAP\ndiffuseColor *= texture2D( map, vec2( gl_PointCoord.x, 1.0 - gl_PointCoord.y ) );\n#endif\n#include color_fragment\n#include alphatest_fragment\noutgoingLight = diffuseColor.rgb;\ngl_FragColor = vec4( outgoingLight, diffuseColor.a * opacity );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n}"),as.prototype=Object.assign(Object.create(Oa.prototype),{constructor:as,parameters:Object.assign({pointSize:{uniform:"size"},sizeAttenuation:{updateShader:!0},sortParticles:{},alphaTest:{updateShader:!0},useTexture:{updateShader:!0},forceTransparent:{},edgeBleach:{uniform:!0}},Oa.prototype.parameters),makeMaterial:function(){Oa.prototype.makeMaterial.call(this),this.makeTexture(),this.material.uniforms.map.value=this.tex,this.material.blending=Dh,this.material.needsUpdate=!0,this.wireframeMaterial.uniforms.map.value=this.tex,this.wireframeMaterial.blending=Dh,this.wireframeMaterial.needsUpdate=!0,this.pickingMaterial.uniforms.map.value=this.tex,this.pickingMaterial.blending=Dh,this.pickingMaterial.needsUpdate=!0},makeTexture:function(){this.tex&&this.tex.dispose(),this.tex=os({delta:this.edgeBleach})},getDefines:function(t){var e=Oa.prototype.getDefines.call(this,t);return this.sizeAttenuation&&(e.USE_SIZEATTENUATION=1),this.useTexture&&(e.USE_MAP=1),this.alphaTest>0&&this.alphaTest<=1&&(e.ALPHATEST=this.alphaTest.toPrecision(2)),e},setUniforms:function(t){t&&void 0!==t.edgeBleach&&(this.makeTexture(),t.map=this.tex),Oa.prototype.setUniforms.call(this,t)},dispose:function(){Oa.prototype.dispose.call(this),this.tex&&this.tex.dispose()}}),ss.prototype=Object.assign(Object.create(ts.prototype),{constructor:ss,type:"dot",parameters:Object.assign({thresholdType:{type:"select",rebuild:!0,options:{value:"value",sigma:"sigma"}},thresholdMin:{type:"number",precision:3,max:1/0,min:-(1/0),rebuild:!0},thresholdMax:{type:"number",precision:3,max:1/0,min:-(1/0),rebuild:!0},thresholdOut:{type:"boolean",rebuild:!0},dotType:{type:"select",rebuild:!0,options:{"":"",sphere:"sphere",point:"point"}},radiusType:{type:"select",options:{"":"",value:"value","abs-value":"abs-value","value-min":"value-min",deviation:"deviation",size:"size"}},radius:{type:"number",precision:3,max:10,min:.001,property:"size"},scale:{type:"number",precision:3,max:10,min:.001},sphereDetail:!0,disableImpostor:!0,pointSize:{type:"number",precision:1,max:100,min:0,buffer:!0},sizeAttenuation:{type:"boolean",buffer:!0},sortParticles:{type:"boolean",rebuild:!0},useTexture:{type:"boolean",buffer:!0},alphaTest:{type:"range",step:.001,max:1,min:0,buffer:!0},forceTransparent:{type:"boolean",buffer:!0},edgeBleach:{type:"range",step:.001,max:1,min:0,buffer:!0}},ts.prototype.parameters,{colorScheme:{type:"select",update:"color",options:{"":"",value:"value",uniform:"uniform"}}}),defaultSize:.1,init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"uniform"),e.colorValue=d(e.colorValue,14540253),this.thresholdType=d(e.thresholdType,"sigma"),this.thresholdMin=d(e.thresholdMin,2),this.thresholdMax=d(e.thresholdMax,1/0),this.thresholdOut=d(e.thresholdOut,!1),this.dotType=d(e.dotType,"point"),this.radius=d(e.radius,.1),this.scale=d(e.scale,1),this.pointSize=d(e.pointSize,1),this.sizeAttenuation=d(e.sizeAttenuation,!0),this.sortParticles=d(e.sortParticles,!1),this.useTexture=d(e.useTexture,!1),this.alphaTest=d(e.alphaTest,.5),this.forceTransparent=d(e.forceTransparent,!1),this.edgeBleach=d(e.edgeBleach,0),ts.prototype.init.call(this,e)},attach:function(t){this.bufferList.forEach(function(t){this.viewer.add(t)},this),this.setVisibility(this.visible),t()},create:function(){var t,e,i,n;if(this.volume){var r,o,a=this.volume;"sigma"===this.thresholdType?(r=a.getValueForSigma(this.thresholdMin),o=a.getValueForSigma(this.thresholdMax)):(r=this.thresholdMin,o=this.thresholdMax),a.filterData(r,o,this.thresholdOut),t=a.getDataPosition(),e=a.getDataColor(this.getColorParams()),i=a.getDataSize(this.radius,this.scale),n=a.getPickingDataColor(this.getColorParams())}else{var s=this.surface;t=s.getPosition(),e=s.getColor(this.getColorParams()),i=s.getSize(this.radius,this.scale),n=s.getPickingColor(this.getColorParams())}"sphere"===this.dotType?this.dotBuffer=new Va(t,e,i,n,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!1})):this.dotBuffer=new as(t,e,this.getBufferParams({pointSize:this.pointSize,sizeAttenuation:this.sizeAttenuation,sortParticles:this.sortParticles,useTexture:this.useTexture,alphaTest:this.alphaTest,forceTransparent:this.forceTransparent,edgeBleach:this.edgeBleach})),this.bufferList.push(this.dotBuffer)},update:function(t){if(0!==this.bufferList.length){t=t||{};var e={};t.color&&(this.volume?e.color=this.volume.getDataColor(this.getColorParams()):e.color=this.surface.getColor(this.getColorParams())),"sphere"===this.dotType&&(t.radius||t.scale)&&(this.volume?e.radius=this.volume.getDataSize(this.radius,this.scale):e.radius=this.surface.getSize(this.radius,this.scale)),this.dotBuffer.setAttributes(e)}},setParameters:function(t,e,i){return e=e||{},t&&void 0!==t.thresholdType&&this.volume instanceof Pa&&("value"===this.thresholdType&&"sigma"===t.thresholdType?(this.thresholdMin=this.volume.getSigmaForValue(this.thresholdMin),this.thresholdMax=this.volume.getSigmaForValue(this.thresholdMax)):"sigma"===this.thresholdType&&"value"===t.thresholdType&&(this.thresholdMin=this.volume.getValueForSigma(this.thresholdMin),this.thresholdMax=this.volume.getValueForSigma(this.thresholdMax)),this.thresholdType=t.thresholdType),t&&void 0!==t.radiusType&&("radius"===t.radiusType?this.radius=this.defaultSize:this.radius=t.radiusType,e.radius=!0,"sphere"!==this.dotType||Mv&&!this.disableImpostor||(i=!0)),t&&void 0!==t.radius&&(e.radius=!0,"sphere"!==this.dotType||Mv&&!this.disableImpostor||(i=!0)),t&&void 0!==t.scale&&(e.scale=!0,"sphere"!==this.dotType||Mv&&!this.disableImpostor||(i=!0)),ts.prototype.setParameters.call(this,t,e,i),this}}),Ov.add("shader/Image.vert","uniform float clipRadius;\nuniform vec3 clipCenter;\nvarying vec2 vUv;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\nvoid main() {\n#include begin_vertex\n#include project_vertex\nvUv = uv;\nvViewPosition = -mvPosition.xyz;\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n}"),Ov.add("shader/Image.frag","uniform sampler2D map;\nuniform float opacity;\nuniform vec2 mapSize;\nuniform float nearClip;\nuniform float clipRadius;\nvarying vec2 vUv;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#include fog_pars_fragment\n#if defined( CUBIC_INTERPOLATION )\n#if defined( CATMULROM_FILTER ) || defined( MITCHELL_FILTER )\n#if defined( CATMULROM_FILTER )\nconst float B = 0.0;\nconst float C = 0.5;\n#elif defined( MITCHELL_FILTER )\nconst float B = 0.333;\nconst float C = 0.333;\n#endif\nfloat filter( float x ){\nfloat f = x;\nif( f < 0.0 )\n{\nf = -f;\n}\nif( f < 1.0 )\n{\nreturn ( ( 12.0 - 9.0 * B - 6.0 * C ) * ( f * f * f ) +\n( -18.0 + 12.0 * B + 6.0 *C ) * ( f * f ) +\n( 6.0 - 2.0 * B ) ) / 6.0;\n}\nelse if( f >= 1.0 && f < 2.0 )\n{\nreturn ( ( -B - 6.0 * C ) * ( f * f * f )\n+ ( 6.0 * B + 30.0 * C ) * ( f *f ) +\n( - ( 12.0 * B ) - 48.0 * C ) * f +\n8.0 * B + 24.0 * C)/ 6.0;\n}\nelse\n{\nreturn 0.0;\n}\n}\n#elif defined( BSPLINE_FILTER )\nfloat filter( float x ){\nfloat f = x;\nif( f < 0.0 ){\nf = -f;\n}\nif( f >= 0.0 && f <= 1.0 ){\nreturn ( 2.0 / 3.0 ) + ( 0.5 ) * ( f*f*f ) - ( f*f );\n}else if( f > 1.0 && f <= 2.0 ){\nreturn 1.0 / 6.0 * pow( ( 2.0 - f ), 3.0 );\n}\nreturn 1.0;\n}\n#else\nfloat filter( float x ){\nreturn 1.0;\n}\n#endif\nvec4 biCubic( sampler2D tex, vec2 texCoord ){\nvec2 texelSize = 1.0 / mapSize;\ntexCoord -= texelSize / 2.0;\nvec4 nSum = vec4( 0.0 );\nfloat nDenom = 0.0;\nvec2 cell = fract( texCoord * mapSize );\nfor( float m = -1.0; m <= 2.0; ++m ){\nfor( float n = -1.0; n <= 2.0; ++n ){\nvec4 vecData = texture2D(\ntex, texCoord + texelSize * vec2( m, n )\n);\nfloat c = filter( m - cell.x ) * filter( -n + cell.y );\nnSum += vecData * c;\nnDenom += c;\n}\n}\nreturn nSum / nDenom;\n}\n#endif\nvoid main(){\n#include nearclip_fragment\n#include radiusclip_fragment\n#if defined( CUBIC_INTERPOLATION )\ngl_FragColor = biCubic( map, vUv );\n#else\ngl_FragColor = texture2D( map, vUv );\n#endif\ngl_FragColor.a *= opacity;\nif( gl_FragColor.a < 0.01 )\ndiscard;\n#include fog_fragment\n}");var ny=new Uint16Array([0,1,2,1,3,2]),ry=new Float32Array([0,1,0,0,1,1,1,0]);cs.prototype=Object.assign(Object.create(Oa.prototype),{constructor:cs,parameters:Object.assign({filter:{updateShader:!0,uniform:!0}},Oa.prototype.parameters),getDefines:function(t){var e=Oa.prototype.getDefines.call(this,t);return this.filter.startsWith("cubic")&&(e.CUBIC_INTERPOLATION=1,this.filter.endsWith("bspline")?e.BSPLINE_FILTER=1:this.filter.endsWith("catmulrom")?e.CATMULROM_FILTER=1:this.filter.endsWith("mitchell")&&(e.MITCHELL_FILTER=1)),e},updateTexture:function(){var t=this.tex;this.filter.startsWith("cubic")?(t.minFilter=Tl,t.magFilter=Tl):"linear"===this.filter?(t.minFilter=Ll,t.magFilter=Ll):(t.minFilter=Tl,t.magFilter=Tl),t.needsUpdate=!0},makeMaterial:function(){Oa.prototype.makeMaterial.call(this),this.updateTexture();var t=this.material;t.uniforms.map.value=this.tex,t.blending=Dh,t.needsUpdate=!0;var e=this.wireframeMaterial;e.uniforms.map.value=this.tex,e.blending=Dh,e.needsUpdate=!0;var i=this.pickingMaterial;i.uniforms.map.value=this.tex,i.blending=Dh,i.needsUpdate=!0},setUniforms:function(t){t&&void 0!==t.filter&&(this.updateTexture(),t.map=this.tex),Oa.prototype.setUniforms.call(this,t)}}),us.prototype=Object.assign(Object.create(ts.prototype),{constructor:us,type:"slice",parameters:Object.assign({filter:{type:"select",buffer:!0,options:{nearest:"nearest",linear:"linear","cubic-bspline":"cubic-bspline","cubic-catmulrom":"cubic-catmulrom","cubic-mitchell":"cubic-mitchell"}},position:{type:"range",step:.1,max:100,min:1,rebuild:!0},dimension:{type:"select",rebuild:!0,options:{x:"x",y:"y",z:"z"}},thresholdType:{type:"select",rebuild:!0,options:{value:"value",sigma:"sigma"}},thresholdMin:{type:"number",precision:3,max:1/0,min:-(1/0),rebuild:!0},thresholdMax:{type:"number",precision:3,max:1/0,min:-(1/0),rebuild:!0}},ts.prototype.parameters,{flatShaded:null,side:null,wireframe:null,linewidth:null,colorScheme:null,roughness:null,metalness:null,diffuse:null}),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"value"),e.colorScale=d(e.colorScale,"Spectral"),ts.prototype.init.call(this,e),this.colorScheme="value",this.dimension=d(e.dimension,"x"),this.filter=d(e.filter,"cubic-bspline"),this.position=d(e.position,30),this.thresholdType=d(e.thresholdType,"sigma"),this.thresholdMin=d(e.thresholdMin,-(1/0)),this.thresholdMax=d(e.thresholdMax,1/0)},attach:function(t){this.bufferList.forEach(function(t){this.viewer.add(t)},this),this.setVisibility(this.visible),t()},create:function(){function t(t){return Math.round(t/100*(i-1))}function e(t,e,i,r){return 3*(i*n.ny*n.nx+e*n.nx+t)+r}var i=this.position,n=this.volume;n.filterData(-(1/0),1/0,!1);var r,o,a,s,c,u=n.data,h=n.matrix,l=new Float32Array(12),d=0,f=0,p=0,m=n.nx,g=n.ny,v=n.nz,y=new N;"x"===this.dimension?(a=t(n.nx),s=n.ny-1,c=n.nz-1,r=n.nz,o=n.ny,d=a,m=d+1,y.set(a,0,0).applyMatrix4(h).toArray(l,0),y.set(a,s,0).applyMatrix4(h).toArray(l,3),y.set(a,0,c).applyMatrix4(h).toArray(l,6),y.set(a,s,c).applyMatrix4(h).toArray(l,9)):"y"===this.dimension?(a=n.nx-1,s=t(n.ny),c=n.nz-1,r=n.nz,o=n.nx,f=s,g=f+1,y.set(0,s,0).applyMatrix4(h).toArray(l,0),y.set(a,s,0).applyMatrix4(h).toArray(l,3),y.set(0,s,c).applyMatrix4(h).toArray(l,6),y.set(a,s,c).applyMatrix4(h).toArray(l,9)):"z"===this.dimension&&(a=n.nx-1,s=n.ny-1,c=t(n.nz),r=n.nx,o=n.ny,p=c,v=p+1,y.set(0,0,c).applyMatrix4(h).toArray(l,0),y.set(0,s,c).applyMatrix4(h).toArray(l,3),y.set(a,0,c).applyMatrix4(h).toArray(l,6),y.set(a,s,c).applyMatrix4(h).toArray(l,9));var b,x,w=0,_=new Uint8Array(r*o*4);"sigma"===this.thresholdType?(b=n.getValueForSigma(this.thresholdMin),x=n.getValueForSigma(this.thresholdMax)):(b=this.thresholdMin,x=this.thresholdMax);var S=this.getColorParams({volume:n});S.domain=[n.getDataMin(),n.getDataMax()];for(var A=Ev.getScheme(S),M=new Float32Array(3),P=f;P<g;++P)for(var C=d;C<m;++C)for(var T=p;T<v;++T){var E=e(C,P,T,0)/3,I=u[E];A.volumeColorToArray(E,M),_[w]=Math.round(255*M[0]),_[w+1]=Math.round(255*M[1]),_[w+2]=Math.round(255*M[2]),_[w+3]=I>b&&I<x?255:0,w+=4}var L=new cs(l,_,r,o,this.getBufferParams({filter:this.filter}));this.bufferList.push(L)}}),hs.prototype=Object.assign(Object.create(ts.prototype),{constructor:hs,type:"structure",parameters:Object.assign({radiusType:{type:"select",options:$r.types},radius:{type:"number",precision:3,max:10,min:.001},scale:{type:"number",precision:3,max:10,min:.001},assembly:null,defaultAssembly:{type:"hidden"}},ts.prototype.parameters),defaultScale:{vdw:1,covalent:1,bfactor:.01,sstruc:1},defaultSize:1,init:function(t){var e=t||{};if(e.colorScheme=d(e.colorScheme,"element"),this.radius=d(e.radius,"vdw"),this.scale=d(e.scale,1),this.assembly=d(e.assembly,"default"),this.defaultAssembly=d(e.defaultAssembly,""),"auto"===e.quality){var i,n=this.structureView,r=this.getAssembly();i=r?r.getAtomCount(n):n.atomCount,Sv&&(i*=4);var o=n.atomStore.count/n.residueStore.count<2;o&&(i*=10),i<15e3?e.quality="high":i<8e4?e.quality="medium":e.quality="low"}ts.prototype.init.call(this,e)},getAssembly:function(){var t="default"===this.assembly?this.defaultAssembly:this.assembly;return this.structure.biomolDict[t]},create:function(){if(0!==this.structureView.atomCount){var t=this.getAssembly();if(t)t.partList.forEach(function(t,e){var i=t.getView(this.structureView);if(0!==i.atomCount){var n=this.createData(i,e);n&&(n.sview=i,n.instanceList=t.getInstanceList(),this.dataList.push(n))}},this);else{var e=this.createData(this.structureView,0);e&&(e.sview=this.structureView,this.dataList.push(e))}}},createData:function(){console.error("createData not implemented")},update:function(t){return this.lazy&&!this.visible?void Object.assign(this.lazyProps.what,t):void this.dataList.forEach(function(e){e.bufferList.length>0&&this.updateData(t,e)},this)},updateData:function(){console.error("updateData not implemented")},getColorParams:function(){var t=ts.prototype.getColorParams.call(this);return t.structure=this.structure,t},getAtomParams:function(t,e){return Object.assign({what:t,colorParams:this.getColorParams(),radiusParams:{radius:this.radius,scale:this.scale}},e)},getBondParams:function(t,e){return Object.assign({what:t,colorParams:this.getColorParams(),radiusParams:{radius:this.radius,scale:this.scale}},e)},setSelection:function(t,e){return this.selection.setString(t,e),this},setParameters:function(t,e,i){return e=e||{},t&&void 0!==t.radiusType&&("size"===t.radiusType?this.radius=this.defaultSize:this.radius=t.radiusType,e.radius=!0,Mv&&!this.disableImpostor||(i=!0)),t&&void 0!==t.radius&&(e.radius=!0,Mv&&!this.disableImpostor||(i=!0)),t&&void 0!==t.scale&&(e.radius=!0,Mv&&!this.disableImpostor||(i=!0)),t&&void 0!==t.defaultAssembly&&(i=!0),ts.prototype.setParameters.call(this,t,e,i),this},getParameters:function(){var t=Object.assign(ts.prototype.getParameters.call(this),{sele:this.selection?this.selection.string:void 0,defaultAssembly:this.defaultAssembly});return t},attach:function(t){var e=this.viewer,i=this.bufferList;this.dataList.forEach(function(t){t.bufferList.forEach(function(n){i.push(n),e.add(n,t.instanceList)})}),this.setVisibility(this.visible),t()},clear:function(){this.dataList.length=0,ts.prototype.clear.call(this)},dispose:function(){this.structureView.dispose(),delete this.structure,delete this.structureView,ts.prototype.dispose.call(this)}}),Ov.add("shader/Line.vert","uniform float nearClip;\nuniform vec3 clipCenter;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#include color_pars_vertex\nvoid main(){\n#include color_vertex\n#include begin_vertex\n#include project_vertex\nvViewPosition = -mvPosition.xyz;\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n#include nearclip_vertex\n}"),Ov.add("shader/Line.frag","uniform float opacity;\nuniform float nearClip;\nuniform float clipRadius;\nvarying vec3 vViewPosition;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#include common\n#include color_pars_fragment\n#include fog_pars_fragment\nvoid main(){\n#include nearclip_fragment\n#include radiusclip_fragment\ngl_FragColor = vec4( vColor, opacity );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n}"),ls.prototype=Object.assign(Object.create(Oa.prototype),{constructor:ls,setAttributes:function(t){var e,i,n,r,o,a,s=this.geometry.attributes;t.from&&t.to&&(e=t.from,i=t.to,o=s.position.array,s.position.needsUpdate=!0),t.color&&t.color2&&(n=t.color,r=t.color2,a=s.color.array,s.color.needsUpdate=!0);for(var c,u,h,l,d,f,p,m,g,v,y,b,x=this.size,w=6*x,_=0;_<x;_++)u=3*_,c=2*_*3,h=c+w,e&&i&&(p=e[u],m=e[u+1],g=e[u+2],v=i[u],y=i[u+1],b=i[u+2],l=(p+v)/2,d=(m+y)/2,f=(g+b)/2,o[c]=p,o[c+1]=m,o[c+2]=g,o[c+3]=l,o[c+4]=d,o[c+5]=f,o[h]=l,o[h+1]=d,o[h+2]=f,o[h+3]=v,o[h+4]=y,o[h+5]=b),n&&r&&(a[c]=a[c+3]=n[u],a[c+1]=a[c+4]=n[u+1],a[c+2]=a[c+5]=n[u+2],a[h]=a[h+3]=r[u],a[h+1]=a[h+4]=r[u+1],a[h+2]=a[h+5]=r[u+2])}}),ds.prototype=Object.assign(Object.create(hs.prototype),{constructor:ds,type:"",parameters:Object.assign({drawLine:{type:"boolean",rebuild:!0},drawCylinder:{type:"boolean",rebuild:!0},drawPoint:{type:"boolean",rebuild:!0},drawSphere:{type:"boolean",rebuild:!0},linewidth:{type:"integer",max:20,min:1,rebuild:!0},pointSize:{type:"integer",max:20,min:1,rebuild:!0},sizeAttenuation:{type:"boolean",rebuild:!0},sort:{type:"boolean",rebuild:!0}},ts.prototype.parameters),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"uniform"),e.colorValue=d(e.colorValue,14540253),this.drawLine=d(e.drawLine,!0),this.drawCylinder=d(e.drawCylinder,!1),this.drawPoint=d(e.drawPoint,!1),this.drawSphere=d(e.drawSphere,!1),this.pointSize=d(e.pointSize,1),this.sizeAttenuation=d(e.sizeAttenuation,!1),this.sort=d(e.sort,!0),hs.prototype.init.call(this,e)},attach:function(t){this.bufferList.forEach(function(t){this.viewer.add(t)},this),this.setVisibility(this.visible),t()},prepare:function(t){t()},create:function(){if(0!==this.atomSet.atomCount){var t=this,e=this.atomSet.atoms[0].index;this.trajectory.getPath(e,function(e){var i=e.length/3,n=new Ct(t.colorValue);if(t.drawSphere){var r=new Va(e,Lr(i,n.r,n.g,n.b),Ir(i,.2),Lr(i,n.r,n.g,n.b),t.getBufferParams({sphereDetail:t.sphereDetail,dullInterior:!0,disableImpostor:t.disableImpostor}));t.bufferList.push(r)}if(t.drawCylinder){var o=new Ya(e.subarray(0,-3),e.subarray(3),Lr(i-1,n.r,n.g,n.b),Lr(i-1,n.r,n.g,n.b),Ir(i,.05),Lr(i-1,n.r,n.g,n.b),Lr(i-1,n.r,n.g,n.b),t.getBufferParams({openEnded:!1,radialSegments:t.radialSegments,disableImpostor:t.disableImpostor,dullInterior:!0}));t.bufferList.push(o)}if(t.drawPoint){var a=new as(e,Lr(i,n.r,n.g,n.b),t.getBufferParams({pointSize:t.pointSize,sizeAttenuation:t.sizeAttenuation,sort:t.sort}));t.bufferList.push(a)}if(t.drawLine){var s=new ls(e.subarray(0,-3),e.subarray(3),Lr(i-1,n.r,n.g,n.b),Lr(i-1,n.r,n.g,n.b),t.getBufferParams());t.bufferList.push(s)}t.attach()})}}});var oy=0;ms.prototype={constructor:ms,type:"component",signals:{representationAdded:null,representationRemoved:null,visibilityChanged:null,statusChanged:null,nameChanged:null,disposed:null},addRepresentation:function(t,e,i){var n=i||{},r=this.stage.getParameters();n.quality=n.quality||r.quality,n.disableImpostor=d(n.disableImpostor,!r.impostor),n.visible=d(n.visible,!0),n.gidPool=this.stage.gidPool;var o=Object.assign({},n,{visible:this.visible&&n.visible}),a=ps(t,e,this.viewer,o),s=this.__getRepresentationComponent(a,n);return this.reprList.push(s),this.signals.representationAdded.dispatch(s),s},addBufferRepresentation:function(t,e){return ms.prototype.addRepresentation.call(this,"buffer",t,e)},removeRepresentation:function(t){var e=this.reprList.indexOf(t);e!==-1&&this.reprList.splice(e,1),this.signals.representationRemoved.dispatch(t)},updateRepresentations:function(t){this.reprList.forEach(function(e){e.update(t)}),this.stage.viewer.requestRender()},clearRepresentations:function(){this.reprList.slice().forEach(function(t){t.dispose()})},dispose:function(){this.clearRepresentations(),delete this.reprList,this.signals.disposed.dispatch()},setVisibility:function(t){return this.visible=t,this.eachRepresentation(function(t){t.updateVisibility()}),this.signals.visibilityChanged.dispatch(t),this},setStatus:function(t){return this.status=t,this.signals.statusChanged.dispatch(t),this},setName:function(t){return this.name=t,this.signals.nameChanged.dispatch(t),this},getCenter:function(){},eachRepresentation:function(t){this.reprList.forEach(t)}},ms.prototype.__getRepresentationComponent=function(t,e){return new gs(this.stage,t,e,this)},gs.prototype=Object.assign(Object.create(ms.prototype),{constructor:gs,type:"representation",signals:Object.assign({parametersChanged:null},ms.prototype.signals),getType:function(){return this.repr.type},setRepresentation:function(t){this.disposeRepresentation(),this.repr=t,this.stage.tasks.listen(this.repr.tasks),this.updateVisibility()},addRepresentation:function(){},removeRepresentation:function(){},disposeRepresentation:function(){this.repr&&(this.stage.tasks.unlisten(this.repr.tasks),this.repr.dispose())},dispose:function(){this.parent&&this.parent.removeRepresentation(this),this.disposeRepresentation(),delete this.reprArgs,this.signals.disposed.dispatch()},setVisibility:function(t){return this.visible=t,this.updateVisibility(),this.signals.visibilityChanged.dispatch(this.visible),this},getVisibility:function(){return this.parent?this.parent.visible&&this.visible:this.visible},updateVisibility:function(){this.repr.setVisibility(this.getVisibility())},update:function(t){return this.repr.update(t),this},build:function(t){return this.repr.build(t),this},setSelection:function(t){return this.repr.setSelection(t),this},setParameters:function(t){return this.repr.setParameters(t),this.signals.parametersChanged.dispatch(this.repr.getParameters()),this},getParameters:function(){return this.repr.getParameters()},setColor:function(t){return this.repr.setColor(t),this},getCenter:function(){}}),vs.prototype={constructor:vs,_remove:function(t){var e=this.list.indexOf(t);e!==-1&&this.list.splice(e,1)},_invoke:function(t,e){for(var i=this.list.length,n=0;n<i;++n){var r=this.list[n],o=r[t];"function"==typeof o&&o.apply(r,e)}return this},setVisibility:function(t){return this._invoke("setVisibility",[t])},setSelection:function(t){return this._invoke("setSelection",[t])},dispose:function(){return this._invoke("dispose")}},ys.prototype=Object.assign(Object.create(vs.prototype),{constructor:ys,addRepresentation:function(t,e){return this._invoke("addRepresentation",[t,e])},centerView:function(t,e){return this._invoke("centerView",[t,e])}}),bs.prototype=Object.assign(Object.create(vs.prototype),{constructor:bs,setParameters:function(t){return this._invoke("setParameters",[t])},setColor:function(t){return this._invoke("setColor",[t])}}),ws.prototype={constructor:ws,parameters:{backgroundColor:{type:"color"},quality:{type:"select",options:{auto:"auto",low:"low",medium:"medium",high:"high"}},sampleLevel:{type:"range",step:1,max:5,min:-1},impostor:{type:"boolean"},rotateSpeed:{type:"number",precision:1,max:10,min:0},zoomSpeed:{type:"number",precision:1,max:10,min:0},panSpeed:{type:"number",precision:1,max:10,min:0},clipNear:{type:"range",step:1,max:100,min:0},clipFar:{type:"range",step:1,max:100,min:0},clipDist:{type:"integer",max:200,min:0},fogNear:{type:"range",step:1,max:100,min:0},fogFar:{type:"range",step:1,max:100,min:0},cameraType:{type:"select",options:{perspective:"perspective",orthographic:"orthographic"}},cameraFov:{type:"range",step:1,max:120,min:15},lightColor:{type:"color"},lightIntensity:{type:"number",precision:2,max:10,min:0},ambientColor:{type:"color"},ambientIntensity:{type:"number",precision:2,max:10,min:0},hoverTimeout:{type:"integer",
-max:1e4,min:10}},setParameters:function(t){var e=Object.assign({},t),i=this.parameters,n=this.viewer,r=n.controls,o=this.pickingControls;for(var a in e)void 0!==e[a]&&i[a]&&(i[a].int&&(e[a]=parseInt(e[a])),i[a].float&&(e[a]=parseFloat(e[a])),i[a].value=e[a]);return void 0!==e.quality&&this.setQuality(e.quality),void 0!==e.impostor&&this.setImpostor(e.impostor),void 0!==e.rotateSpeed&&(r.rotateSpeed=e.rotateSpeed),void 0!==e.zoomSpeed&&(r.zoomSpeed=e.zoomSpeed),void 0!==e.panSpeed&&(r.panSpeed=e.panSpeed),o.setParameters({hoverTimeout:e.hoverTimeout}),n.setClip(e.clipNear,e.clipFar,e.clipDist),n.setFog(void 0,e.fogNear,e.fogFar),n.setCamera(e.cameraType,e.cameraFov),n.setSampling(e.sampleLevel),n.setBackground(e.backgroundColor),n.setLight(e.lightColor,e.lightIntensity,e.ambientColor,e.ambientIntensity),this.signals.parametersChanged.dispatch(this.getParameters()),this},getParameters:function(){var t={};for(var e in this.parameters)t[e]=this.parameters[e].value;return t},defaultFileRepresentation:function(e){if("structure"===e.type){e.setSelection("/0");var i,n,r=e.structure;if(r.biomolDict.BU1){var o=r.biomolDict.BU1;i=o.getAtomCount(r),n=o.getInstanceCount(),e.setDefaultAssembly("BU1")}else i=r.getModelProxy(0).atomCount,n=1;Sv&&(i*=4);var a=r.atomStore.count/r.residueStore.count<2;a&&(i*=10);var s="chainname";if(1===r.getChainnameCount("polymer and /0")&&(s="residueindex"),t.Debug&&console.log(i,n,a),n>5&&i>15e3||i>7e5){var c=Math.min(1.5,Math.max(.1,2e3/(i/n)));a&&(c=Math.min(c,.15)),e.addRepresentation("surface",{sele:"polymer",surfaceType:"sas",probeRadius:1.4,scaleFactor:c,colorScheme:s,colorScale:"RdYlBu",useWorker:!1})}else i>25e4?e.addRepresentation("backbone",{lineOnly:!0,colorScheme:s,colorScale:"RdYlBu"}):i>1e5?e.addRepresentation("backbone",{quality:"low",disableImpostor:!0,colorScheme:s,colorScale:"RdYlBu",scale:2}):i>8e4?e.addRepresentation("backbone",{colorScheme:s,colorScale:"RdYlBu",scale:2}):(e.addRepresentation("cartoon",{color:s,colorScale:"RdYlBu",scale:.7,aspectRatio:5,quality:"auto"}),i<5e4&&e.addRepresentation("base",{color:s,colorScale:"RdYlBu",quality:"auto"}),e.addRepresentation("ball+stick",{sele:"hetero and not ( water or ion )",colorScheme:"element",scale:2,aspectRatio:1.5,bondScale:.3,bondSpacing:.75,quality:"auto"}));this.centerView(),e.structure.frames.length&&e.addTrajectory()}else"surface"!==e.type&&"volume"!==e.type||(e.addRepresentation("surface"),this.centerView())},loadFile:function(t,e){var i=Object.assign({},this.defaultFileParams,e),n=new ms(this,i);n.name=y(t).name,this.addComponent(n);var r=this.tasks;r.increment();var o,a=function(t){return this.removeComponent(n),n=this.addComponentFromObject(t,i),"script"===n.type&&n.run(),i.defaultRepresentation&&this.defaultFileRepresentation(n),r.decrement(),n}.bind(this),s=function(t){throw n.setStatus(t),r.decrement(),t},c=d(i.ext,y(t).ext);return o="dcd"===c?Promise.reject("loadFile: ext 'dcd' must be loaded into a structure component"):gr(t,i),o.then(a,s)},addComponent:function(t){return t?(this.compList.push(t),void this.signals.componentAdded.dispatch(t)):void Pv.warn("Stage.addComponent: no component given")},addComponentFromObject:function(t,e){var i=Nv.get(t.type);if(i){var n=new i(this,t,e);return this.addComponent(n),n}Pv.warn("no component for object type",t.type)},removeComponent:function(t){var e=this.compList.indexOf(t);e!==-1&&this.compList.splice(e,1),t.dispose(),this.signals.componentRemoved.dispatch(t)},removeAllComponents:function(t){this.compList.slice().forEach(function(e){t&&e.type!==t||this.removeComponent(e)},this)},handleResize:function(){this.viewer.handleResize()},toggleFullscreen:function(t){function e(){return document.fullscreenElement||document.mozFullScreenElement||document.webkitFullscreenElement||document.msFullscreenElement}function i(){if(!e()&&n.lastFullscreenElement){var t=n.lastFullscreenElement;t.style.width=t.dataset.normalWidth,t.style.height=t.dataset.normalHeight,document.removeEventListener("fullscreenchange",i),document.removeEventListener("mozfullscreenchange",i),document.removeEventListener("webkitfullscreenchange",i),document.removeEventListener("MSFullscreenChange",i),n.handleResize(),n.signals.fullscreenChanged.dispatch(!1)}}if(!(document.fullscreenEnabled||document.mozFullScreenEnabled||document.webkitFullscreenEnabled||document.msFullscreenEnabled))return void Pv.log("fullscreen mode (currently) not possible");var n=this;t=t||this.viewer.container,this.lastFullscreenElement=t,e()?document.exitFullscreen?document.exitFullscreen():document.msExitFullscreen?document.msExitFullscreen():document.mozCancelFullScreen?document.mozCancelFullScreen():document.webkitExitFullscreen&&document.webkitExitFullscreen():(t.dataset.normalWidth=t.style.width,t.dataset.normalHeight=t.style.height,t.style.width=screen.width+"px",t.style.height=screen.height+"px",t.requestFullscreen?t.requestFullscreen():t.msRequestFullscreen?t.msRequestFullscreen():t.mozRequestFullScreen?t.mozRequestFullScreen():t.webkitRequestFullscreen&&t.webkitRequestFullscreen(),document.addEventListener("fullscreenchange",i),document.addEventListener("mozfullscreenchange",i),document.addEventListener("webkitfullscreenchange",i),document.addEventListener("MSFullscreenChange",i),this.handleResize(),this.signals.fullscreenChanged.dispatch(!0),setTimeout(function(){n.handleResize()},100))},centerView:function(){if(this.tasks.count>0){var t=function(e,i){0===i&&this.tasks.signals.countChanged.remove(t,this),this.viewer.centerView(!0)};this.tasks.signals.countChanged.add(t,this)}this.viewer.centerView(!0)},setSpin:function(t,e){Array.isArray(t)&&(t=(new N).fromArray(t)),this.viewer.setSpin(t,e)},setOrientation:function(t){this.tasks.onZeroOnce(function(){this.viewer.setOrientation(t)},this)},getOrientation:function(){return this.viewer.getOrientation()},makeImage:function(t){var e=this.viewer,i=this.tasks;return new Promise(function(n,r){function o(){i.increment(),e.makeImage(t).then(function(t){i.decrement(),n(t)}).catch(function(t){i.decrement(),r(t)})}i.onZeroOnce(o)})},setImpostor:function(t){this.parameters.impostor.value=t;var e=["spacefill","ball+stick","licorice","hyperball","backbone","rocket","helixorient","contact","distance","dot"];this.eachRepresentation(function(i){if("script"!==i.type&&e.includes(i.getType())){var n=i.getParameters();n.disableImpostor=!t,i.build(n)}})},setQuality:function(t){this.parameters.quality.value=t;var e=["tube","cartoon","ribbon","trace","rope"],i=["spacefill","ball+stick","licorice","hyperball","backbone","rocket","helixorient","contact","distance","dot"];this.eachRepresentation(function(n){if("script"!==n.type){var r=n.getParameters();if(!e.includes(n.getType())){if(!i.includes(n.getType()))return;if(!r.disableImpostor)return void(n.repr.quality=t)}r.quality=t,n.build(r)}})},eachComponent:function(t,e){this.compList.forEach(function(i,n){e&&i.type!==e||t(i,n)})},eachRepresentation:function(t,e){this.eachComponent(function(e){e.reprList.forEach(function(i){t(i,e)})},e)},getComponentsByName:function(t,e){var i=[];return this.eachComponent(function(e){(void 0===t||xs(t,e))&&i.push(e)},e),new ys(i)},getRepresentationsByName:function(t,e){var i,n;"object"!=typeof t?(i=void 0,n=t):(i=t.comp,n=t.repr);var r=[];return this.eachRepresentation(function(t,e){(void 0===i||xs(i,e))&&(void 0===n||xs(n,t))&&r.push(t)},e),new bs(r)},getAnythingByName:function(t){var e=this.getComponentsByName(t).list,i=this.getRepresentationsByName(t).list;return new vs(e.concat(i))},dispose:function(){this.tasks.dispose()}},_s.prototype={constructor:_s,_animate:function(){var t;if(this._running=!0,this.traj.inProgress||this._stopFlag||(t="forward"===this.direction?this.traj.currentFrame+this.step:this.traj.currentFrame-this.step,(t>=this.end||t<this.start)&&("once"===this.mode?(this.pause(),t="forward"===this.direction?this.end:this.start):t="forward"===this.direction?this.start:this.end),this.interpolateType||this.traj.setFrame(t)),this._stopFlag)this._running=!1;else if(!this.traj.inProgress&&this.interpolateType){var e,i,n;"forward"===this.direction?(e=Math.max(this.start,t-this.step),i=Math.max(this.start,t-2*this.step),n=Math.max(this.start,t-3*this.step)):(e=Math.min(this.end,t+this.step),i=Math.min(this.end,t+2*this.step),n=Math.min(this.end,t+3*this.step)),this._interpolate(t,e,i,n,1/this.interpolateStep,0)}else setTimeout(this._animate.bind(this),this.timeout)},_interpolate:function(t,e,i,n,r,o){if(o+=r,o<=1){var a=Math.round(this.timeout*r);this.traj.setFrameInterpolated(t,e,i,n,o,this.interpolateType,function(){setTimeout(function(){this._interpolate(t,e,i,n,r,o)}.bind(this),a)}.bind(this))}else setTimeout(this._animate.bind(this),0)},toggle:function(){this._running?this.pause():this.play()},play:function(){if(!this._running){this.traj.player!==this&&this.traj.setPlayer(this);var t=this.traj.currentFrame,e=Math.ceil(t/this.step)*this.step;"forward"===this.direction&&t>=this.end?e=this.start:"backward"===this.direction&&t<=this.start&&(e=this.end),this.traj.setFrame(e),this._stopFlag=!1,this._animate(),this.signals.startedRunning.dispatch()}},pause:function(){this._running&&(this._stopFlag=!0,this.signals.haltedRunning.dispatch())},stop:function(){this.traj.setFrame(this.start),this.pause()}};var ay=function(){function t(t,e){var i,n=0,r={};return e.forEach(function(e){i=0;var o={};e.forEach(function(e){o[t[i++]]=e}),r[t[n++]]=o}),r}var e=[[4,0,-2,-1,-2,0,-2,-1,-1,-1,-1,-2,-1,-1,-1,1,0,0,-3,-2],[0,9,-3,-4,-2,-3,-3,-1,-3,-1,-1,-3,-3,-3,-3,-1,-1,-1,-2,-2],[-2,-3,6,2,-3,-1,-1,-3,-1,-4,-3,1,-1,0,-2,0,-1,-3,-4,-3],[-1,-4,2,5,-3,-2,0,-3,1,-3,-2,0,-1,2,0,0,-1,-2,-3,-2],[-2,-2,-3,-3,6,-3,-1,0,-3,0,0,-3,-4,-3,-3,-2,-2,-1,1,3],[0,-3,-1,-2,-3,6,-2,-4,-2,-4,-3,0,-2,-2,-2,0,-2,-3,-2,-3],[-2,-3,-1,0,-1,-2,8,-3,-1,-3,-2,1,-2,0,0,-1,-2,-3,-2,2],[-1,-1,-3,-3,0,-4,-3,4,-3,2,1,-3,-3,-3,-3,-2,-1,3,-3,-1],[-1,-3,-1,1,-3,-2,-1,-3,5,-2,-1,0,-1,1,2,0,-1,-2,-3,-2],[-1,-1,-4,-3,0,-4,-3,2,-2,4,2,-3,-3,-2,-2,-2,-1,1,-2,-1],[-1,-1,-3,-2,0,-3,-2,1,-1,2,5,-2,-2,0,-1,-1,-1,1,-1,-1],[-2,-3,1,0,-3,0,1,-3,0,-3,-2,6,-2,0,0,1,0,-3,-4,-2],[-1,-3,-1,-1,-4,-2,-2,-3,-1,-3,-2,-2,7,-1,-2,-1,-1,-2,-4,-3],[-1,-3,0,2,-3,-2,0,-3,1,-2,0,0,-1,5,1,0,-1,-2,-2,-1],[-1,-3,-2,0,-3,-2,0,-3,2,-2,-1,0,-2,1,5,-1,-1,-3,-3,-2],[1,-1,0,0,-2,0,-1,-2,0,-2,-1,1,-1,0,-1,4,1,-2,-3,-2],[0,-1,-1,-1,-2,-2,-2,-1,-1,-1,-1,0,-1,-1,-1,1,5,0,-2,-2],[0,-1,-3,-2,-1,-3,-3,3,-2,1,1,-3,-2,-2,-3,-2,0,4,-3,-1],[-3,-2,-4,-3,1,-2,-2,-3,-3,-2,-1,-4,-4,-2,-3,-3,-2,-3,11,2],[-2,-2,-3,-2,3,-3,2,-1,-2,-1,-1,-2,-3,-1,-2,-2,-2,-1,2,7]],i=[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1]],n="ACDEFGHIKLMNPQRSTVWY",r="ARNDCQEGHILKMFPSTWYVBZ?";return{blosum62:t(r,i),blosum62x:t(n,e)}}();Ss.prototype={constructor:Ss,initMatrices:function(){this.n=this.seq1.length,this.m=this.seq2.length,this.score=void 0,this.ali="",this.S=[],this.V=[],this.H=[];var t,e;for(t=0;t<=this.n;++t)for(this.S[t]=[],this.V[t]=[],this.H[t]=[],e=0;e<=this.m;++e)this.S[t][e]=0,this.V[t][e]=0,this.H[t][e]=0;for(t=0;t<=this.n;++t)this.S[t][0]=this.gap(0),this.H[t][0]=-(1/0);for(e=0;e<=this.m;++e)this.S[0][e]=this.gap(0),this.V[0][e]=-(1/0);this.S[0][0]=0},gap:function(t){return this.gapPenalty+t*this.gapExtensionPenalty},makeScoreFn:function(){var t,e,i=this.seq1,n=this.seq2,r=this.substMatrix;return r?function(o,a){t=i[o],e=n[a];try{return r[t][e]}catch(t){return-4}}:(Pv.warn("Alignment: no subst matrix"),function(r,o){return t=i[r],e=n[o],t===e?5:-3})},calc:function(){t.Debug&&Pv.time("Alignment.calc"),this.initMatrices();var e,i,n,r,o,a,s,c=this.gap(0),u=this.makeScoreFn(),h=this.gapExtensionPenalty,l=this.V,d=this.H,f=this.S,p=this.n,m=this.m;for(a=1;a<=p;++a)for(i=f[a-1],e=l[a-1],n=l[a],r=d[a],o=f[a],s=1;s<=m;++s)n[s]=Math.max(i[s]+c,e[s]+h),r[s]=Math.max(o[s-1]+c,r[s-1]+h),o[s]=Math.max(i[s-1]+u(a-1,s-1),n[s],r[s]);t.Debug&&Pv.timeEnd("Alignment.calc"),t.Debug&&Pv.log(this.S,this.V,this.H)},trace:function(){t.Debug&&Pv.time("Alignment.trace"),this.ali1="",this.ali2="";var e=this.makeScoreFn(),i=this.n,n=this.m,r="S";for(this.S[i][n]>=this.V[i][n]&&this.S[i][n]>=this.V[i][n]?(r="S",this.score=this.S[i][n]):this.V[i][n]>=this.H[i][n]?(r="V",this.score=this.V[i][n]):(r="H",this.score=this.H[i][n]),t.Debug&&Pv.log("Alignment: SCORE",this.score),t.Debug&&Pv.log("Alignment: S, V, H",this.S[i][n],this.V[i][n],this.H[i][n]);i>0&&n>0;)"S"===r?this.S[i][n]===this.S[i-1][n-1]+e(i-1,n-1)?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2=this.seq2[n-1]+this.ali2,--i,--n,r="S"):this.S[i][n]===this.V[i][n]?r="V":this.S[i][n]===this.H[i][n]?r="H":(--i,--n):"V"===r?this.V[i][n]===this.V[i-1][n]+this.gapExtensionPenalty?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i,r="V"):this.V[i][n]===this.S[i-1][n]+this.gap(0)?(this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i,r="S"):--i:"H"===r?this.H[i][n]===this.H[i][n-1]+this.gapExtensionPenalty?(this.ali1="-"+this.ali1,this.ali2=this.seq2[n-1]+this.ali2,--n,r="H"):this.H[i][n]===this.S[i][n-1]+this.gap(0)?(this.ali1="-"+this.ali1,this.ali2=this.seq2[n-1]+this.ali2,--n,r="S"):--n:Pv.error("Alignment: no matrix");for(;i>0;)this.ali1=this.seq1[i-1]+this.ali1,this.ali2="-"+this.ali2,--i;for(;n>0;)this.ali1="-"+this.ali1,this.ali2=this.seq2[n-1]+this.ali2,--n;t.Debug&&Pv.timeEnd("Alignment.trace"),t.Debug&&Pv.log([this.ali1,this.ali2])}},Ms.prototype=Object.assign(Object.create(ms.prototype),{constructor:Ms,type:"script",addRepresentation:function(){},removeRepresentation:function(){},run:function(){var t=this;this.setStatus("running"),this.script.call(this.stage,function(){t.setStatus("finished")}),this.setStatus("called")},dispose:function(){this.signals.disposed.dispatch()},setVisibility:function(){},getCenter:function(){}}),Nv.add("script",Ms),Ps.prototype=Object.assign(Object.create(ms.prototype),{constructor:Ps,type:"shape",addRepresentation:function(t,e){return ms.prototype.addRepresentation.call(this,t,this.shape,e)},centerView:function(t){t=d(t,!0);var e=this.getCenter();if(t){var i=this.shape.boundingBox,n=i.size(),r=Math.max(n.x,n.y,n.z),o=Math.min(n.x,n.y,n.z);t=Math.max(1,r+o/2)}return this.viewer.centerView(t,e),this},getCenter:function(){return this.shape.center},dispose:function(){this.shape.dispose(),ms.prototype.dispose.call(this)}}),Nv.add("shape",Ps),Cs.prototype=Object.assign(Object.create(ms.prototype),{constructor:Cs,type:"trajectory",signals:Object.assign({frameChanged:null,playerChanged:null,gotNumframes:null,parametersChanged:null},ms.prototype.signals),addRepresentation:function(t,e){return ms.prototype.addRepresentation.call(this,t,this.trajectory,e)},setFrame:function(t){this.trajectory.setFrame(t)},setParameters:function(t){return this.trajectory.setParameters(t),this.signals.parametersChanged.dispatch(t),this},dispose:function(){this.trajectory.dispose(),ms.prototype.dispose.call(this)},getCenter:function(){}}),Ts.prototype=Object.assign(Object.create(La.prototype),{constructor:Ts,type:"frames",makeAtomIndices:function(){"StructureView"===this.structure.type?this.atomIndices=this.structure.getAtomIndices():this.atomIndices=null},_loadFrame:function(t,e){var i,n=this.frames[t];if(this.atomIndices){var r=this.atomIndices,o=r.length;i=new Float32Array(3*o);for(var a=0;a<o;++a){var s=3*a,c=3*r[a];i[s+0]=n[c+0],i[s+1]=n[c+1],i[s+2]=n[c+2]}}else i=new Float32Array(n);var u=this.boxes[t],h=this.frames.length;this.process(t,u,i,h),"function"==typeof e&&e()},getNumframes:function(){this.frames&&this.setNumframes(this.frames.length)},getPath:function(t,e){var i,n,r,o=this.numframes,a=3*t,s=new Float32Array(3*o);for(i=0;i<o;++i)n=3*i,r=this.frames[i],s[n+0]=r[a+0],s[n+1]=r[a+1],s[n+2]=r[a+2];e(s)}}),Es.prototype=Object.assign(Object.create(La.prototype),{constructor:Es,type:"structure",makeAtomIndices:function(){this.structure.atomSet.size()<this.structure.atomStore.count?this.atomIndices=this.structure.getAtomIndices():this.atomIndices=null},_loadFrame:function(t,e){var i,n=this.structure,r=n.frames[t];if(this.atomIndices){var o=this.atomIndices,a=o.length;i=new Float32Array(3*a);for(var s=0;s<a;++s){var c=3*s,u=3*o[s];i[c+0]=r[u+0],i[c+1]=r[u+1],i[c+2]=r[u+2]}}else i=new Float32Array(r);var h=n.boxes[t],l=n.frames.length;this.process(t,h,i,l),"function"==typeof e&&e()},getNumframes:function(){this.setNumframes(this.structure.frames.length)},getPath:function(t,e){var i,n,r,o=this.numframes,a=3*t,s=new Float32Array(3*o);for(i=0;i<o;++i)n=3*i,r=this.structure.frames[i],s[n+0]=r[a+0],s[n+1]=r[a+1],s[n+2]=r[a+2];e(s)}}),Is.prototype=Object.assign(Object.create(La.prototype),{constructor:Is,type:"remote",makeAtomIndices:function(){var t=[];if("StructureView"===this.structure.type){var e,i,n=this.structure.getAtomIndices(),r=n[0],o=n[0],a=n.length;for(e=1;e<a;++e)i=n[e],o+1<i&&(t.push([r,o+1]),r=i),o=i;t.push([r,o+1])}else t.push([0,this.atomCount]);this.atomIndices=t},_loadFrame:function(t,e){var i=new XMLHttpRequest,n=Iv.trajectory,r=n.getFrameUrl(this.trajPath,t),o=n.getFrameParams(this.trajPath,this.atomIndices);i.open("POST",r,!0),i.responseType="arraybuffer",i.setRequestHeader("Content-type","application/x-www-form-urlencoded"),i.addEventListener("load",function(){var n=i.response;if(!n)return void Pv.error("empty arrayBuffer for '"+r+"'");var o=new Int32Array(n,0,1)[0],a=new Float32Array(n,8,9),s=new Float32Array(n,44);this.process(t,a,s,o),"function"==typeof e&&e()}.bind(this),!1),i.send(o)},getNumframes:function(){var t=new XMLHttpRequest,e=Iv.trajectory,i=e.getNumframesUrl(this.trajPath);t.open("GET",i,!0),t.addEventListener("load",function(){this.setNumframes(parseInt(t.response))}.bind(this),!1),t.send(null)},getPath:function(t,e){if(this.pathCache[t])return void e(this.pathCache[t]);Pv.time("loadPath");var i=new XMLHttpRequest,n=Iv.trajectory,r=n.getPathUrl(this.trajPath,t),o="";i.open("POST",r,!0),i.responseType="arraybuffer",i.setRequestHeader("Content-type","application/x-www-form-urlencoded"),i.addEventListener("load",function(){Pv.timeEnd("loadPath");var n=i.response;if(!n)return void Pv.error("empty arrayBuffer for '"+r+"'");var o=new Float32Array(n);this.pathCache[t]=o,e(o)}.bind(this),!1),i.send(o)}}),fa.prototype.getView=function(t){return new Rs(this,t)},Rs.prototype=Object.assign(Object.create(fa.prototype),{constructor:Rs,type:"StructureView",init:function(){Object.defineProperties(this,{name:{get:function(){return this.structure.name}},path:{get:function(){return this.structure.path}},title:{get:function(){return this.structure.title}},id:{get:function(){return this.structure.id}},atomSetDict:{get:function(){return this.structure.atomSetDict}},biomolDict:{get:function(){return this.structure.biomolDict}},entityList:{get:function(){return this.structure.entityList}},unitcell:{get:function(){return this.structure.unitcell}},frames:{get:function(){return this.structure.frames}},boxes:{get:function(){return this.structure.boxes}},bondStore:{get:function(){return this.structure.bondStore}},backboneBondStore:{get:function(){return this.structure.backboneBondStore}},rungBondStore:{get:function(){return this.structure.rungBondStore}},atomStore:{get:function(){return this.structure.atomStore}},residueStore:{get:function(){return this.structure.residueStore}},chainStore:{get:function(){return this.structure.chainStore}},modelStore:{get:function(){return this.structure.modelStore}},atomMap:{get:function(){return this.structure.atomMap}},residueMap:{get:function(){return this.structure.residueMap}},bondHash:{get:function(){return this.structure.bondHash}},spatialHash:{get:function(){return this.structure.spatialHash}}}),this._ap=this.getAtomProxy(),this._rp=this.getResidueProxy(),this._cp=this.getChainProxy(),this.selection&&this.selection.signals.stringChanged.add(this.refresh,this),this.structure.signals.refreshed.add(this.refresh,this)},refresh:function(){t.Debug&&Pv.time("StructureView.refresh"),this.atomSetCache={},this.atomSet=this.getAtomSet(this.selection,!0),this.structure.atomSet&&(t.Debug&&Pv.time("StructureView.refresh#atomSet.intersection"),this.atomSet=this.atomSet.intersection(this.structure.atomSet),t.Debug&&Pv.timeEnd("StructureView.refresh#atomSet.intersection")),this.bondSet=this.getBondSet(),t.Debug&&Pv.time("StructureView.refresh#atomSetDict.new_intersection");for(var e in this.atomSetDict){var i=this.atomSetDict[e];this.atomSetCache["__"+e]=i.new_intersection(this.atomSet)}t.Debug&&Pv.timeEnd("StructureView.refresh#atomSetDict.new_intersection"),t.Debug&&Pv.time("StructureView.refresh#size"),this.atomCount=this.atomSet.size(),this.bondCount=this.bondSet.size(),t.Debug&&Pv.timeEnd("StructureView.refresh#size"),this.boundingBox=this.getBoundingBox(),this.center=this.boundingBox.center(),t.Debug&&Pv.timeEnd("StructureView.refresh"),this.signals.refreshed.dispatch()},setSelection:function(t){this.selection=t,this.refresh()},getSelection:function(t){var e=[];t&&t.string&&e.push(t.string);var i=this.structure.getSelection();i&&i.string&&e.push(i.string),this.selection&&this.selection.string&&e.push(this.selection.string);var n="";return e.length>0&&(n="( "+e.join(" ) AND ( ")+" )"),new On(n)},getStructure:function(){return this.structure.getStructure()},eachBond:function(t,e){this.structure.eachBond(t,this.getSelection(e))},eachAtom:function(t,e){var i=this.getAtomProxy(),n=this.getAtomSet(e),r=this.atomStore.count;if(n&&n.size()<r)n.forEach(function(e){i.index=e,t(i)});else for(var o=0;o<r;++o)i.index=o,t(i)},eachResidue:function(t,e){this.structure.eachResidue(t,this.getSelection(e))},eachResidueN:function(){console.error("StructureView.eachResidueN() not implemented")},eachChain:function(t,e){this.structure.eachChain(t,this.getSelection(e))},eachModel:function(t,e){this.structure.eachModel(t,this.getSelection(e))},getAtomSet:function(e,i){t.Debug&&Pv.time("StructureView.getAtomSet");var n=this.structure.getAtomSet(e);return!i&&this.atomSet&&(n=n.new_intersection(this.atomSet)),t.Debug&&Pv.timeEnd("StructureView.getAtomSet"),n},getAtomIndices:function(t){return this.structure.getAtomIndices(this.getSelection(t))},refreshPosition:function(){return this.structure.refreshPosition()},dispose:function(){this.selection&&this.selection.signals.stringChanged.remove(this.refresh,this),this.structure.signals.refreshed.remove(this.refresh,this),delete this.structure,delete this.atomSet,delete this.bondSet,delete this.atomCount,delete this.bondCount}}),Os.prototype=Object.assign(Object.create(ms.prototype),{constructor:Os,type:"structure",signals:Object.assign({trajectoryAdded:null,trajectoryRemoved:null,defaultAssemblyChanged:null},ms.prototype.signals),initSelection:function(t){this.selection=new On(t),this.structureView=new Rs(this.structure,this.selection),this.selection.signals.stringChanged.add(function(){this.structureView.setSelection(this.selection),this.rebuildRepresentations(),this.rebuildTrajectories()},this)},setSelection:function(t){return this.selection.setString(t),this},setDefaultAssembly:function(t){this.defaultAssembly=t,this.reprList.forEach(function(t){t.setParameters({defaultAssembly:this.defaultAssembly})},this),this.signals.defaultAssemblyChanged.dispatch(t)},rebuildRepresentations:function(){this.reprList.forEach(function(t){t.build()})},rebuildTrajectories:function(){this.trajList.slice().forEach(function(t){t.trajectory.setStructure(this.structureView)},this)},addRepresentation:function(t,e){var i=e||{};return i.defaultAssembly=this.defaultAssembly,ms.prototype.addRepresentation.call(this,t,this.structureView,i)},addTrajectory:function(t,e){var i=Ls(t,this.structureView,e);i.signals.frameChanged.add(function(){this.updateRepresentations({position:!0})},this);var n=new Cs(this.stage,i,e,this);return this.trajList.push(n),this.signals.trajectoryAdded.dispatch(n),n},removeTrajectory:function(t){var e=this.trajList.indexOf(t);e!==-1&&this.trajList.splice(e,1),t.dispose(),this.signals.trajectoryRemoved.dispatch(t)},dispose:function(){this.stage.gidPool.removeObject(this.structure),this.trajList.slice().forEach(function(t){t.dispose()}),this.trajList.length=0,this.structure.dispose(),ms.prototype.dispose.call(this)},centerView:function(t,e){t=d(t,!0);var i=this.getCenter(e);if(t){var n;n=e?this.structureView.getBoundingBox(new On(e)):this.structureView.boundingBox;var r=n.size(),o=Math.max(r.x,r.y,r.z),a=Math.min(r.x,r.y,r.z);t=Math.max(1,o+a/2)}return this.viewer.centerView(t,i),this},getCenter:function(t){return t?this.structure.atomCenter(new On(t)):this.structure.center},superpose:function(t,e,i,n){return As(this.structureView,t.structureView,e,i,n),this.updateRepresentations({position:!0}),this},setVisibility:function(t){return ms.prototype.setVisibility.call(this,t),this.trajList.forEach(function(e){e.setVisibility(t)}),this}}),Nv.add("structure",Os),Ds.prototype=Object.assign(Object.create(ms.prototype),{constructor:Ds,type:"surface",addRepresentation:function(t,e){return ms.prototype.addRepresentation.call(this,t,this.surface,e)},dispose:function(){this.surface.dispose(),ms.prototype.dispose.call(this)},centerView:function(t){var e=this.surface.center;t&&(t=this.surface.boundingBox.size().length()),this.viewer.centerView(t,e)}}),Nv.add("surface",Ds),Ns.prototype=Object.assign(Object.create(ms.prototype),{constructor:Ns,type:"volume",addRepresentation:function(t,e){return ms.prototype.addRepresentation.call(this,t,this.volume,e)},dispose:function(){this.stage.gidPool.removeObject(this.volume),this.volume.dispose(),ms.prototype.dispose.call(this)},centerView:function(t){var e=this.volume.center;t&&(t=this.volume.boundingBox.size().length()),this.viewer.centerView(t,e)}}),Nv.add("volume",Ns),ks.prototype=Object.assign(Object.create(hs.prototype),{constructor:ks,type:"axes",parameters:Object.assign({radius:{type:"number",precision:3,max:10,min:.001},sphereDetail:!0,radialSegments:!0,disableImpostor:!0,align:{type:"button"},showAxes:{type:"boolean",rebuild:!0},showBox:{type:"boolean",rebuild:!0}},ts.prototype.parameters,{assembly:null}),init:function(t){var e=t||{};e.radius=d(e.radius,.5),e.colorValue=d(e.colorValue,"lightgreen"),hs.prototype.init.call(this,e),this.showAxes=d(e.showAxes,!0),this.showBox=d(e.showBox,!1)},getPrincipalAxes:function(){var t,e=this.getAssembly();return e&&(t=e.partList[0].getSelection()),this.structureView.getView(t).getPrincipalAxes()},align:function(){var t=this.getPrincipalAxes(this.structureView),e=(new N).copy(t[0][1]).sub(t[0][0]).normalize(),i=(new N).copy(t[2][1]).sub(t[2][0]).normalize();this.viewer.alignView(i,e,t[3],!0)},getAxesData:function(t){var e=this.getPrincipalAxes(t),i=new Ct(this.colorValue),n=0,r=0;this.showAxes&&(n+=6,r+=3),this.showBox&&(n+=8,r+=12);var o=new Float32Array(3*n),a=Lr(n,i.r,i.g,i.b),s=Ir(n,this.radius),c=new Float32Array(3*r),u=new Float32Array(3*r),h=Lr(r,i.r,i.g,i.b),l=Ir(r,this.radius),d=0;if(this.showAxes){var f=function(t,e){t.toArray(o,2*d),e.toArray(o,2*d+3),t.toArray(c,d),e.toArray(u,d),d+=3};f(e[0][0],e[0][1]),f(e[1][0],e[1][1]),f(e[2][0],e[2][1])}if(this.showBox){var p=(new N).subVectors(e[0][0],e[0][1]).normalize(),m=(new N).subVectors(e[1][0],e[1][1]).normalize(),g=(new N).subVectors(e[2][0],e[2][1]).normalize(),v=new N,y=new N,b=new N,x=new N,w=new N,_=-(1/0),S=-(1/0),A=-(1/0),M=-(1/0),P=-(1/0),C=-(1/0);t.eachAtom(function(t){Gr(v.copy(t),p,e[3]);var i=x.subVectors(v,e[3]).normalize().dot(p),n=v.distanceTo(e[3]);i>0?n>_&&(_=n):n>S&&(S=n),Gr(y.copy(t),m,e[3]);var r=x.subVectors(y,e[3]).normalize().dot(m),o=y.distanceTo(e[3]);r>0?o>A&&(A=o):o>M&&(M=o),Gr(b.copy(t),g,e[3]);var a=x.subVectors(b,e[3]).normalize().dot(g),s=b.distanceTo(e[3]);a>0?s>P&&(P=s):s>C&&(C=s)});var T=2*d,E=function(t,i,n){w.copy(e[3]).addScaledVector(p,t).addScaledVector(m,i).addScaledVector(g,n),w.toArray(o,T),T+=3};E(_,A,P),E(_,A,-C),E(_,-M,-C),E(_,-M,P),E(-S,-M,-C),E(-S,-M,P),E(-S,A,P),E(-S,A,-C);var I=d,L=function(t,e){w.fromArray(o,2*d+3*t).toArray(c,I),w.fromArray(o,2*d+3*e).toArray(u,I),I+=3};L(0,1),L(0,3),L(0,6),L(1,2),L(1,7),L(2,3),L(2,4),L(3,5),L(4,5),L(4,7),L(5,6),L(6,7)}return{vertexPosition:o,vertexColor:a,vertexRadius:s,edgePosition1:c,edgePosition2:u,edgeColor:h,edgeRadius:l}},create:function(){var t=this.getAxesData(this.structureView);this.sphereBuffer=new Va(t.vertexPosition,t.vertexColor,t.vertexRadius,void 0,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0})),this.cylinderBuffer=new Ya(t.edgePosition1,t.edgePosition2,t.edgeColor,t.edgeColor,t.edgeRadius,void 0,void 0,this.getBufferParams({openEnded:!0,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0})),this.dataList.push({sview:this.structureView,bufferList:[this.sphereBuffer,this.cylinderBuffer]})},updateData:function(t,e){var i=this.getAxesData(e.sview),n={},r={};t&&!t.position||(n.position=i.vertexPosition,r.position1=i.edgePosition1,r.position2=i.edgePosition2),t&&!t.color||(n.color=i.vertexColor,r.color=i.edgeColor,r.color2=i.edgeColor),t&&!t.radius||(n.radius=i.vertexRadius,r.radius=i.edgeRadius),this.sphereBuffer.setAttributes(n),this.cylinderBuffer.setAttributes(r)}}),Lv.add("axes",ks),Fs.prototype=Object.assign(Object.create(hs.prototype),{constructor:Fs,type:"ball+stick",defaultSize:.15,parameters:Object.assign({sphereDetail:!0,radialSegments:!0,openEnded:!0,disableImpostor:!0,aspectRatio:{type:"number",precision:1,max:10,min:1},lineOnly:{type:"boolean",rebuild:!0},cylinderOnly:{type:"boolean",rebuild:!0},multipleBond:{type:"select",rebuild:!0,options:{off:"off",symmetric:"symmetric",offset:"offset"}},bondScale:{type:"number",precision:2,max:1,min:.01},bondSpacing:{type:"number",precision:2,max:2,min:.5}},hs.prototype.parameters),init:function(t){var e=t||{};e.radius=d(e.radius,this.defaultSize),this.aspectRatio=d(e.aspectRatio,2),this.lineOnly=d(e.lineOnly,!1),this.cylinderOnly=d(e.cylinderOnly,!1),this.multipleBond=d(e.multipleBond,"off"),this.bondSpacing=d(e.bondSpacing,1),this.bondScale=d(e.bondScale,.4),hs.prototype.init.call(this,e)},getAtomParams:function(t,e){return e=Object.assign({radiusParams:{radius:this.radius,scale:this.scale*this.aspectRatio}},e),hs.prototype.getAtomParams.call(this,t,e)},getAtomData:function(t,e,i){return t.getAtomData(this.getAtomParams(e,i))},getBondParams:function(t,e){return e=Object.assign({multipleBond:this.multipleBond,bondSpacing:this.bondSpacing,bondScale:this.bondScale},e),hs.prototype.getBondParams.call(this,t,e)},getBondData:function(t,e,i){return t.getBondData(this.getBondParams(e,i))},createData:function(t){var e=this.getBondData(t),i=[];if(this.lineOnly)this.lineBuffer=new ls(e.position1,e.position2,e.color1,e.color2,this.getBufferParams()),
-i.push(this.lineBuffer);else{var n=new Ya(e.position1,e.position2,e.color1,e.color2,e.radius,e.pickingColor1,e.pickingColor2,this.getBufferParams({openEnded:this.openEnded,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0}));if(i.push(n),!this.cylinderOnly){var r=this.getAtomData(t),o=new Va(r.position,r.color,r.radius,r.pickingColor,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0}));i.push(o)}}return{bufferList:i}},updateData:function(t,e){"off"!==this.multipleBond&&t&&t.radius&&(t.position=!0);var i=this.getBondData(e.sview,t);if(this.lineOnly){var n={};t&&!t.position||(n.from=i.position1,n.to=i.position2),t&&!t.color||(n.color=i.color1,n.color2=i.color2),e.bufferList[0].setAttributes(n)}else{var r={};if(t&&!t.position||(r.position1=i.position1,r.position2=i.position2),t&&!t.color||(r.color=i.color1,r.color2=i.color2),t&&!t.radius||(r.radius=i.radius),e.bufferList[0].setAttributes(r),!this.cylinderOnly){var o=this.getAtomData(e.sview,t),a={};t&&!t.position||(a.position=o.position),t&&!t.color||(a.color=o.color),t&&!t.radius||(a.radius=o.radius),e.bufferList[1].setAttributes(a)}}},setParameters:function(t){var e=!1,i={};return t&&(t.aspectRatio||t.bondSpacing||t.bondScale)&&(i.radius=!0,Mv&&!this.disableImpostor||(e=!0)),hs.prototype.setParameters.call(this,t,i,e),this}}),Lv.add("ball+stick",Fs),zs.prototype=Object.assign(Object.create(Fs.prototype),{constructor:zs,type:"backbone",defaultSize:.25,parameters:Object.assign({},Fs.prototype.parameters,{multipleBond:null,bondSpacing:null}),init:function(t){var e=t||{};e.aspectRatio=d(e.aspectRatio,1),Fs.prototype.init.call(this,e)},getAtomData:function(t,e,i){return t.getBackboneAtomData(this.getAtomParams(e,i))},getBondData:function(t,e,i){var n=this.getBondParams(e,i);return n.colorParams.backbone=!0,t.getBackboneBondData(n)}}),Lv.add("backbone",zs),Bs.prototype=Object.assign(Object.create(Fs.prototype),{constructor:Bs,type:"base",defaultSize:.3,parameters:Object.assign({},Fs.prototype.parameters,{multipleBond:null,bondSpacing:null}),init:function(t){var e=t||{};e.aspectRatio=d(e.aspectRatio,1),Fs.prototype.init.call(this,e)},getAtomData:function(t,e,i){return t.getRungAtomData(this.getAtomParams(e,i))},getBondData:function(t,e,i){var n=this.getBondParams(e,i);return n.colorParams.rung=!0,t.getRungBondData(n)}}),Lv.add("base",Bs),js.prototype={constructor:js,getAtomIterator:function(t,e){function i(){var t=this.get(u);return u+=1,t}function n(i){var n=h[c%4];if(n.index=o.getAtomIndexByType(i,t),e&&i>0&&i<s&&"e"===n.sstruc){var r=l[c%4];return d.index=o.getAtomIndexByType(i+1,t),f.index=o.getAtomIndexByType(i-1,t),r.addVectors(d,f).add(n).add(n).multiplyScalar(.25),c+=1,r}return c+=1,n}function r(){c=0,u=-1}var o=this.polymer,a=o.structure,s=o.residueCount,c=0,u=-1,h=[a.getAtomProxy(),a.getAtomProxy(),a.getAtomProxy(),a.getAtomProxy()],l=[new N,new N,new N,new N],d=a.getAtomProxy(),f=a.getAtomProxy();return{size:s,next:i,get:n,reset:r}},getSubdividedColor:function(t){function e(t,e,i){d.atomColorToArray(t,e,i)}function i(t,e,i){f.atomColorToArray(t,e,i)}var n=this.subdiv,r=this.polymer,o=r.residueCount,a=o-1,s=a*n*3+3;r.isCyclic&&(s+=3*n);var c=new Float32Array(s),u=new Float32Array(s),h=this.getAtomIterator("trace"),l=t||{};l.structure=r.structure;var d=Ev.getScheme(l),f=Ev.getPickingScheme(l);return this.interpolator.getColor(h,e,i,c,u,0,r.isCyclic),{color:c,pickingColor:u}},getSubdividedPosition:function(){var t=this.getPosition();return{position:t}},getSubdividedOrientation:function(){var t=this.getTangent(),e=this.getNormals(t);return{tangent:t,normal:e.normal,binormal:e.binormal}},getSubdividedSize:function(t,e){function i(t){return h.atomRadius(t)}var n=this.subdiv,r=this.polymer,o=r.residueCount,a=o-1,s=a*n+1;r.isCyclic&&(s+=n);var c=new Float32Array(s),u=this.getAtomIterator("trace"),h=new $r(t,e);return this.interpolator.getSize(u,i,c,0,r.isCyclic),{size:c}},getPosition:function(){var t=this.subdiv,e=this.polymer,i=e.residueCount,n=i-1,r=n*t*3+3;e.isCyclic&&(r+=3*t);var o=new Float32Array(r),a=this.positionIterator||this.getAtomIterator("trace",this.smoothSheet);return this.interpolator.getPosition(a,o,0,e.isCyclic),o},getTangent:function(){var t=this.subdiv,e=this.polymer,i=this.size,n=i-1,r=n*t*3+3;e.isCyclic&&(r+=3*t);var o=new Float32Array(r),a=this.positionIterator||this.getAtomIterator("trace",this.smoothSheet);return this.interpolator.getTangent(a,o,0,e.isCyclic),o},getNormals:function(t){var e=this.subdiv,i=this.polymer,n=i.isProtein(),r=this.size,o=r-1,a=o*e*3+3;i.isCyclic&&(a+=3*e);var s=new Float32Array(a),c=new Float32Array(a);if(this.directional&&!this.polymer.isCg()){var u=this.getAtomIterator("direction1"),h=this.getAtomIterator("direction2");this.interpolator.getNormalDir(u,h,t,s,c,0,i.isCyclic,n)}else this.interpolator.getNormal(r,t,s,c,0,i.isCyclic,n);return{normal:s,binormal:c}}},$s.prototype=Object.assign(Object.create(Oa.prototype),{constructor:$s,setAttributes:function(){var t=new N,e=new N;return function(i){var n,r,o,a,s,c,u,h,l,d,f,p=this.aspectRatio,m=this.size2,g=m-1,v=this.radialSegments,y=this.geometry.attributes;i.position&&(n=i.position,r=i.normal,o=i.binormal,a=i.tangent,c=i.size,h=y.position.array,d=y.normal.array,y.position.needsUpdate=!0,y.normal.needsUpdate=!0),i.color&&(s=i.color,l=y.color.array,y.color.needsUpdate=!0),i.pickingColor&&(u=i.pickingColor,f=y.pickingColor.array,y.pickingColor.needsUpdate=!0);var b,x,w,_,S,A,M,P,C,T,E,I,L,R,O,D,N,k,F,z,B,U,j,$=[],V=[],G=[],H=[],W=[],X=[];if(n)for(x=0;x<v;++x)M=x/v*2*Math.PI,$[x]=p*Math.cos(M),V[x]=Math.sin(M),G[x]=p*Math.cos(M-.01),H[x]=Math.sin(M-.01),W[x]=p*Math.cos(M+.01),X[x]=Math.sin(M+.01);for(b=0;b<m;++b)for(w=3*b,_=w*v,n&&(t.set(a[w],a[w+1],a[w+2]),O=r[w],D=r[w+1],N=r[w+2],k=o[w],F=o[w+1],z=o[w+2],B=n[w],U=n[w+1],j=n[w+2],R=c[b]),x=0;x<v;++x)S=_+3*x,n&&(P=-R*$[x],C=R*V[x],T=-R*G[x],E=R*H[x],I=-R*W[x],L=R*X[x],h[S]=B+P*O+C*k,h[S+1]=U+P*D+C*F,h[S+2]=j+P*N+C*z,e.set(I*O+L*k-(T*O+E*k),I*D+L*F-(T*D+E*F),I*N+L*z-(T*N+E*z)).cross(t),d[S]=e.x,d[S+1]=e.y,d[S+2]=e.z),s&&(l[S]=s[w],l[S+1]=s[w+1],l[S+2]=s[w+2]),u&&(f[S]=u[w],f[S+1]=u[w+1],f[S+2]=u[w+2]);for(w=0,_=3*m*v,x=0;x<v;++x)S=w+3*x,A=_+3*x,n&&(h[A]=h[S],h[A+1]=h[S+1],h[A+2]=h[S+2],d[A]=a[w],d[A+1]=a[w+1],d[A+2]=a[w+2]),s&&(l[A]=l[S],l[A+1]=l[S+1],l[A+2]=l[S+2]),u&&(f[A]=f[S],f[A+1]=f[S+1],f[A+2]=f[S+2]);for(w=3*(m-1)*v,_=3*(m+1)*v,x=0;x<v;++x)S=w+3*x,A=_+3*x,n&&(h[A]=h[S],h[A+1]=h[S+1],h[A+2]=h[S+2],d[A]=a[3*g],d[A+1]=a[3*g+1],d[A+2]=a[3*g+2]),s&&(l[A]=l[S],l[A+1]=l[S+1],l[A+2]=l[S+2]),u&&(f[A]=f[S],f[A+1]=f[S+1],f[A+2]=f[S+2])}}(),makeIndex:function(){var t,e,i,n,r,o,a=this.meshIndex,s=this.size2,c=s-1,u=this.capTriangles,h=this.radialSegments,l=this.radialSegments+1;for(t=0;t<c;++t)for(e=t*h*3*2,i=t*h,n=(t+1)*h,o=0;o<h;++o)r=e+3*o*2,a[r]=i+o,a[r+1]=i+(o+1)%h,a[r+2]=n+o,a[r+3]=n+o,a[r+4]=i+(o+1)%h,a[r+5]=n+(o+1)%h;var d=[0];for(o=1;o<l/2;++o)d.push(o),h-o!==o&&d.push(h-o);for(r=c*h*3*2,e=s*h,o=0;o<d.length-2;++o)o%2===0?(a[r+3*o+0]=e+d[o+0],a[r+3*o+1]=e+d[o+1],a[r+3*o+2]=e+d[o+2]):(a[r+3*o+0]=e+d[o+2],a[r+3*o+1]=e+d[o+1],a[r+3*o+2]=e+d[o+0]);for(r=c*h*3*2+3*u,e=s*h+h,o=0;o<d.length-2;++o)o%2===0?(a[r+3*o+0]=e+d[o+0],a[r+3*o+1]=e+d[o+1],a[r+3*o+2]=e+d[o+2]):(a[r+3*o+0]=e+d[o+2],a[r+3*o+1]=e+d[o+1],a[r+3*o+2]=e+d[o+0])}}),Vs.prototype=Object.assign(Object.create(hs.prototype),{constructor:Vs,type:"cartoon",parameters:Object.assign({aspectRatio:{type:"number",precision:1,max:10,min:1},subdiv:{type:"integer",max:50,min:1,rebuild:!0},radialSegments:{type:"integer",max:50,min:1,rebuild:!0},tension:{type:"number",precision:1,max:1,min:.1},capped:{type:"boolean",rebuild:!0},smoothSheet:{type:"boolean",rebuild:!0}},hs.prototype.parameters),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"chainname"),e.colorScale=d(e.colorScale,"RdYlBu"),e.radius=d(e.radius,"sstruc"),e.scale=d(e.scale,.7),this.aspectRatio=d(e.aspectRatio,5),this.tension=d(e.tension,NaN),this.capped=d(e.capped,!0),this.smoothSheet=d(e.smoothSheet,!1),hs.prototype.init.call(this,e),"low"===e.quality?(this.subdiv=3,this.radialSegments=6):"medium"===e.quality?this.subdiv=6:"high"===e.quality?this.subdiv=12:this.subdiv=d(e.subdiv,6)},getSplineParams:function(t){return Object.assign({subdiv:this.subdiv,tension:this.tension,directional:1!==this.aspectRatio,smoothSheet:this.smoothSheet},t)},getSpline:function(t){return new js(t,this.getSplineParams())},getScale:function(t){return t.isCg()?this.scale*this.aspectRatio:this.scale},getAspectRatio:function(t){return t.isCg()?1:this.aspectRatio},createData:function(t){var e=[],i=[];return this.structure.eachPolymer(function(t){if(!(t.residueCount<4)){i.push(t);var n=this.getSpline(t),r=n.getSubdividedPosition(),o=n.getSubdividedOrientation(),a=n.getSubdividedColor(this.getColorParams()),s=n.getSubdividedSize(this.radius,this.getScale(t));e.push(new $s(r.position,o.normal,o.binormal,o.tangent,a.color,s.size,a.pickingColor,this.getBufferParams({radialSegments:this.radialSegments,aspectRatio:this.getAspectRatio(t),capped:this.capped,dullInterior:!0})))}}.bind(this),t.getSelection()),{bufferList:e,polymerList:i}},updateData:function(e,i){t.Debug&&Pv.time(this.type+" repr update"),e=e||{};for(var n=0,r=i.polymerList.length;n<r;++n){var o={},a=i.polymerList[n],s=this.getSpline(a);if(i.bufferList[n].aspectRatio=this.getAspectRatio(a),e.position||e.radius){var c=s.getSubdividedPosition(),u=s.getSubdividedOrientation(),h=s.getSubdividedSize(this.radius,this.getScale(a));o.position=c.position,o.normal=u.normal,o.binormal=u.binormal,o.tangent=u.tangent,o.size=h.size}if(e.color){var l=s.getSubdividedColor(this.getColorParams());o.color=l.color,o.pickingColor=l.pickingColor}i.bufferList[n].setAttributes(o)}t.Debug&&Pv.timeEnd(this.type+" repr update")},setParameters:function(t){var e=!1,i={};return t&&t.aspectRatio&&(i.radius=!0),t&&t.tension&&(i.position=!0),hs.prototype.setParameters.call(this,t,i,e),this}}),Lv.add("cartoon",Vs),Gs.prototype={within:function(t,e){Pv.time("Contact within");var i=this.kdtree2,n=this.sview1.getAtomProxy(),r=this.sview1.getAtomSet(!1),o=new Do;this.sview1.eachAtom(function(a){for(var s=!1,c=i.nearest(a,1/0,t),u=0,h=c.length;u<h;++u){var l=c[u];n.index=l.index,a.residueIndex!==n.residueIndex&&(!e||l.distance>e)&&(s=!0,r.add_unsafe(n.index),o.addBond(a,n,1))}s&&r.add_unsafe(a.index)});var a=new Zv(o.count);return a.set_all(!0),Pv.timeEnd("Contact within"),{atomSet:r,bondSet:a,bondStore:o}}},Xs.prototype=Object.assign(Object.create(hs.prototype),{constructor:Xs,type:"contact",defaultSize:.25,parameters:Object.assign({contactType:{type:"select",rebuild:!0,options:{polar:"polar",polarBackbone:"polar backbone"}},maxDistance:{type:"number",precision:1,max:10,min:.1,rebuild:!0},maxAngle:{type:"integer",max:180,min:0,rebuild:!0},radialSegments:!0,disableImpostor:!0},hs.prototype.parameters),init:function(t){var e=t||{};e.radius=d(e.radius,this.defaultSize),this.contactType=d(e.contactType,"polarBackbone"),this.maxDistance=d(e.maxDistance,3.5),this.maxAngle=d(e.maxAngle,40),hs.prototype.init.call(this,e)},getContactData:function(t){var e={polar:Hs,polarBackbone:Ws},i=e[this.contactType](t,this.maxDistance,this.maxAngle);return i},getBondData:function(t,e,i){return t.getBondData(this.getBondParams(e,i))},createData:function(t){var e=this.getContactData(t),i={bondSet:e.bondSet,bondStore:e.bondStore},n=this.getBondData(t,void 0,i),r=new Ya(n.position1,n.position2,n.color1,n.color2,n.radius,n.pickingColor1,n.pickingColor2,this.getBufferParams({openEnded:!1,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0}));return{bufferList:[r],bondSet:e.bondSet,bondStore:e.bondStore}},updateData:function(t,e){if(!t||t.position){var i=this.getContactData(e.sview);e.bondSet=i.bondSet,e.bondStore=i.bondStore}var n={bondSet:e.bondSet,bondStore:e.bondStore},r=this.getBondData(e.sview,t,n),o={};t&&!t.position||(o.position=Er(r.position1,r.position2),o.position1=r.position1,o.position2=r.position2),t&&!t.color||(o.color=r.color1,o.color2=r.color2),t&&!t.radius||(o.radius=r.radius),e.bufferList[0].setAttributes(o)}}),Lv.add("contact",Xs),Ov.add("shader/SDFFont.vert","uniform float nearClip;\nuniform float clipRadius;\nuniform vec3 clipCenter;\nuniform float xOffset;\nuniform float yOffset;\nuniform float zOffset;\nuniform bool ortho;\nvarying vec3 vViewPosition;\nvarying vec2 texCoord;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\nattribute vec2 mapping;\nattribute vec2 inputTexCoord;\nattribute float inputSize;\n#include color_pars_vertex\n#include common\nvoid main(void){\n#include color_vertex\ntexCoord = inputTexCoord;\nfloat _zOffset = zOffset;\nif( texCoord.x == 10.0 ){\n_zOffset -= 0.001;\n}\nvec3 pos = position;\nif( ortho ){\npos += normalize( cameraPosition ) * _zOffset;\n}\nvec4 cameraPos = modelViewMatrix * vec4( pos, 1.0 );\nvec4 cameraCornerPos = vec4( cameraPos.xyz, 1.0 );\ncameraCornerPos.xy += mapping * inputSize * 0.01;\ncameraCornerPos.x += xOffset;\ncameraCornerPos.y += yOffset;\nif( !ortho ){\ncameraCornerPos.xyz += normalize( -cameraCornerPos.xyz ) * _zOffset;\n}\ngl_Position = projectionMatrix * cameraCornerPos;\nvViewPosition = -cameraCornerPos.xyz;\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n#include nearclip_vertex\n#include radiusclip_vertex\n}"),Ov.add("shader/SDFFont.frag","uniform sampler2D fontTexture;\nuniform float opacity;\nuniform bool showBorder;\nuniform vec3 borderColor;\nuniform float borderWidth;\nuniform vec3 backgroundColor;\nuniform float backgroundOpacity;\nuniform float nearClip;\nuniform float clipRadius;\nvarying vec3 vViewPosition;\nvarying vec2 texCoord;\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\n#include common\n#include color_pars_fragment\n#include fog_pars_fragment\n#ifdef SDF\nconst float smoothness = 16.0;\n#else\nconst float smoothness = 256.0;\n#endif\nconst float gamma = 2.2;\nvoid main(){\n#include nearclip_fragment\n#include radiusclip_fragment\nif( texCoord.x > 1.0 ){\ngl_FragColor = vec4( backgroundColor, backgroundOpacity );\n}else{\nfloat sdf = texture2D( fontTexture, texCoord ).a;\nif( showBorder ) sdf += borderWidth;\nfloat w = clamp(\nsmoothness * ( abs( dFdx( texCoord.x ) ) + abs( dFdy( texCoord.y ) ) ),\n0.0,\n0.5\n);\nfloat a = smoothstep( 0.5 - w, 0.5 + w, sdf );\na = pow( a, 1.0 / gamma );\nif( a < 0.2 ) discard;\na *= opacity;\nvec3 outgoingLight = vColor;\nif( showBorder && sdf < ( 0.5 + borderWidth ) ){\noutgoingLight = borderColor;\n}\ngl_FragColor = vec4( outgoingLight, a );\n}\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n}");var sy=function(){var t={};return function(e){var i=JSON.stringify(e);return void 0===t[i]&&(t[i]=new qs(e)),t[i]}}();qs.prototype={constructor:qs,build:function(){var t=this.size+2*this.outline+Math.round(this.size/4),e=this.width/4,i=document.createElement("canvas");i.width=e,i.height=t;var n=i.getContext("2d");n.font=this.style+" "+this.variant+" "+this.weight+" "+this.size+"px "+this.font,n.fillStyle="#FF0000",n.textAlign="left",n.textBaseline="bottom",n.lineJoin="round";for(var r=[],o=3*this.outline,a=0;a<o;++a){var s=Math.max(0,8*-a+128-8*!a),c=("00"+s.toString(16)).slice(-2);r.push("#"+c+c+c)}var u=new Uint8Array(e*t*2);this.canvas=i,this.context=n,this.lineHeight=t,this.maxWidth=e,this.colors=r,this.scratch=u,this.data=new Uint8Array(this.width*this.height*4),this.canvas2=document.createElement("canvas"),this.canvas2.width=this.width,this.canvas2.height=this.height,this.context2=this.canvas2.getContext("2d")},map:function(t){return void 0===this.mapped[t]&&(this.draw(t),this.currentX+this.scratchW>this.width&&(this.currentX=0,this.currentY+=this.scratchH),this.currentY+this.scratchH>this.height&&console.warn("canvas to small"),this.mapped[t]={x:this.currentX,y:this.currentY,w:this.scratchW,h:this.scratchH},this.context2.drawImage(this.canvas,0,0,this.scratchW,this.scratchH,this.currentX,this.currentY,this.scratchW,this.scratchH),this.currentX+=this.scratchW),this.mapped[t]},draw:function(t){var e=this.lineHeight,i=this.outline,n=this.context,r=this.scratch,o=this.maxWidth,a=this.colors,s=i,c=e-this.outline,u=n.measureText(t),h=Math.min(o,Math.ceil(u.width+2*s+1));n.clearRect(0,0,h,e);var l,d,f,p,m;if(0===this.outline)for(n.fillText(t,s,c),p=n.getImageData(0,0,h,e),m=p.data,f=3,l=0,d=m.length/4;l<d;++l)r[l]=m[f],f+=4;else{for(n.globalCompositeOperation="source-over",l=i+1;l>0;--l)f=l>1?2*l-2:l,n.strokeStyle=a[f-1],n.lineWidth=f,n.strokeText(t,s,c);n.globalCompositeOperation="multiply",n.fillStyle="#FF00FF",n.fillText(t,s,c),p=n.getImageData(0,0,h,e),m=p.data,f=0;var g=this.gamma;for(l=0,d=m.length/4;l<d;++l){var v=m[f],y=v?m[f+1]/v:1;.5===g&&(y=Math.sqrt(y)),y=Math.min(1,Math.max(0,y));var b=256-v,x=b+(v-b)*y;r[l]=Math.max(0,Math.min(255,x+2)),m[f+3]=r[l],f+=4}}n.putImageData(p,0,0),this.scratchW=h,this.scratchH=e},populate:function(){for(var t=0;t<256;++t)this.map(String.fromCharCode(t))}},Ys.prototype=Object.assign(Object.create(ja.prototype),{constructor:Ys,type:"text",parameters:Object.assign({fontFamily:{uniform:!0},fontStyle:{uniform:!0},fontWeight:{uniform:!0},fontSize:{uniform:!0},sdf:{updateShader:!0,uniform:!0},xOffset:{uniform:!0},yOffset:{uniform:!0},zOffset:{uniform:!0},showBorder:{uniform:!0},borderColor:{uniform:!0},borderWidth:{uniform:!0},backgroundColor:{uniform:!0},backgroundOpacity:{uniform:!0}},Oa.prototype.parameters),makeMaterial:function(){Oa.prototype.makeMaterial.call(this);var t=this.texture,e=this.material;e.extensions.derivatives=!0,e.lights=!1,e.uniforms.fontTexture.value=t,e.needsUpdate=!0;var i=this.wireframeMaterial;i.extensions.derivatives=!0,i.lights=!1,i.uniforms.fontTexture.value=t,i.needsUpdate=!0;var n=this.pickingMaterial;n.extensions.derivatives=!0,n.lights=!1,n.uniforms.fontTexture.value=t,n.needsUpdate=!0},setAttributes:function(t){var e,i,n,r,o,a,s=this.text,c=this.geometry.attributes;t.position&&(e=t.position,r=c.position.array,c.position.needsUpdate=!0),t.size&&(i=t.size,o=c.inputSize.array,c.inputSize.needsUpdate=!0),t.color&&(n=t.color,a=c.color.array,c.color.needsUpdate=!0);for(var u,h,l,d,f,p=this.positionCount,m=0,g=0;g<p;++g)for(h=3*g,l=s[g],f=l.length,this.showBackground&&(f+=1),d=0;d<f;++d,++m)for(var v=0;v<4;v++)u=4*m*3+3*v,e&&(r[u]=e[h],r[u+1]=e[h+1],r[u+2]=e[h+2]),i&&(o[4*m+v]=i[g]),n&&(a[u]=n[h],a[u+1]=n[h+1],a[u+2]=n[h+2])},makeTexture:function(){this.textAtlas=sy({font:[this.fontFamily],style:this.fontStyle,weight:this.fontWeight,size:this.fontSize,outline:this.sdf?5:0}),this.texture=this.textAtlas.texture},makeMapping:function(){for(var t,e,i,n,r,o,a,s,c=this.textAtlas,u=this.text,h=this.attachment,l=c.lineHeight*this.backgroundMargin*.1-10,d=this.geometry.attributes.inputTexCoord.array,f=this.geometry.attributes.mapping.array,p=this.positionCount,m=0,g=0;g<p;++g){for(i=u[g],n=0,o=i.length,r=0;r<o;++r)t=c.mapped[i[r]],n+=t.w-2*c.outline;for(s=h.startsWith("top")?c.lineHeight/1.25:h.startsWith("middle")?c.lineHeight/2.5:0,a=h.endsWith("right")?n:h.endsWith("center")?n/2:0,a+=c.outline,s+=c.outline,this.showBackground&&(e=2*m*4,f[e+0]=-c.lineHeight/6-a-l,f[e+1]=c.lineHeight-s+l,f[e+2]=-c.lineHeight/6-a-l,f[e+3]=0-s-l,f[e+4]=n+c.lineHeight/6-a+2*c.outline+l,f[e+5]=c.lineHeight-s+l,f[e+6]=n+c.lineHeight/6-a+2*c.outline+l,f[e+7]=0-s-l,d[e+0]=10,d[e+2]=10,d[e+4]=10,d[e+6]=10,m+=1),n=0,r=0;r<o;++r,++m){t=c.mapped[i[r]],e=2*m*4,f[e+0]=n-a,f[e+1]=t.h-s,f[e+2]=n-a,f[e+3]=0-s,f[e+4]=n+t.w-a,f[e+5]=t.h-s,f[e+6]=n+t.w-a,f[e+7]=0-s;var v=c.width,y=c.height,b=[t.x/v,t.y/y,t.x/v,(t.y+t.h)/y,(t.x+t.w)/v,t.y/y,(t.x+t.w)/v,(t.y+t.h)/y];d.set(b,e),n+=t.w-2*c.outline}}this.geometry.attributes.inputTexCoord.needsUpdate=!0,this.geometry.attributes.mapping.needsUpdate=!0},getDefines:function(t){var e=Oa.prototype.getDefines.call(this,t);return this.sdf&&(e.SDF=1),e},setUniforms:function(t){!t||void 0===t.fontFamily&&void 0===t.fontStyle&&void 0===t.fontWeight&&void 0===t.fontSize&&void 0===t.sdf||(this.makeTexture(),this.makeMapping(),this.texture.needsUpdate=!0,t.fontTexture=this.texture),Oa.prototype.setUniforms.call(this,t)}}),Zs.prototype=Object.assign(Object.create(hs.prototype),{constructor:Zs,type:"distance",defaultSize:.15,parameters:Object.assign({labelSize:{type:"number",precision:3,max:10,min:.001},labelColor:{type:"color"},labelVisible:{type:"boolean"},labelZOffset:{type:"number",precision:1,max:20,min:-20,buffer:"zOffset"},atomPair:{type:"hidden",rebuild:!0},radialSegments:!0,disableImpostor:!0},hs.prototype.parameters,{flatShaded:null,assembly:null}),init:function(t){var e=t||{};e.radius=d(e.radius,this.defaultSize),this.fontFamily=d(e.fontFamily,"sans-serif"),this.fontStyle=d(e.fontStyle,"normal"),this.fontWeight=d(e.fontWeight,"bold"),this.sdf=d(e.sdf,"Firefox"!==_v),this.labelSize=d(e.labelSize,2),this.labelColor=d(e.labelColor,16777215),this.labelVisible=d(e.labelVisible,!0),this.labelZOffset=d(e.labelZOffset,.5),this.atomPair=d(e.atomPair,[]),hs.prototype.init.call(this,e)},getDistanceData:function(t,e){var i=e.length,n=new Array(i),r=new Float32Array(3*i),o=new On,a=new On,s=new Do,c=t.getAtomProxy(),u=t.getAtomProxy(),h=0;e.forEach(function(e,i){var l=e[0],d=e[1];if(Number.isInteger(l)&&Number.isInteger(d))c.index=l,u.index=d;else{o.setString(l),a.setString(d);var f=t.getAtomIndices(o),p=t.getAtomIndices(a);if(!f.length||!p.length)return void(h+=1);c.index=f[0],u.index=p[0]}s.addBond(c,u,1),i-=h,n[i]=c.distanceTo(u).toFixed(2);var m=3*i;r[m+0]=(c.x+u.x)/2,r[m+1]=(c.y+u.y)/2,r[m+2]=(c.z+u.z)/2},this),h>0&&(i-=h,r=r.subarray(0,3*i));var l=new Zv(s.count);return l.set_all(!0),{text:n,position:r,bondSet:l,bondStore:s}},getBondData:function(t,e,i){return t.getBondData(this.getBondParams(e,i))},create:function(){if(0!==this.structureView.atomCount){var t=this.atomPair.length;if(0!==t){var e=this.getDistanceData(this.structureView,this.atomPair),i=new Ct(this.labelColor);this.textBuffer=new Ys(e.position,Ir(t,this.labelSize),Lr(t,i.r,i.g,i.b),e.text,this.getBufferParams({fontFamily:this.fontFamily,fontStyle:this.fontStyle,fontWeight:this.fontWeight,sdf:this.sdf,zOffset:this.labelZOffset,opacity:1,visible:this.labelVisible}));var n={bondSet:e.bondSet,bondStore:e.bondStore},r=this.getBondData(this.structureView,void 0,n);this.cylinderBuffer=new Ya(r.position1,r.position2,r.color1,r.color2,r.radius,void 0,void 0,this.getBufferParams({openEnded:!1,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0})),this.dataList.push({sview:this.structureView,bondSet:e.bondSet,bondStore:e.bondStore,position:e.position,bufferList:[this.textBuffer,this.cylinderBuffer]})}}},update:function(t){t.position?this.build():hs.prototype.update.call(this,t)},updateData:function(t,e){var i={bondSet:e.bondSet,bondStore:e.bondStore},n=this.getBondData(e.sview,t,i),r={},o={},a=this.atomPair.length;if(t.labelSize&&(o.size=Ir(a,this.labelSize)),t.labelColor){var s=new Ct(this.labelColor);o.color=Lr(a,s.r,s.g,s.b)}t.color&&(r.color=n.color1,r.color2=n.color2),(t.radius||t.scale)&&(r.radius=n.radius),this.textBuffer.setAttributes(o),this.cylinderBuffer.setAttributes(r)},setVisibility:function(t,e){return hs.prototype.setVisibility.call(this,t,!0),this.textBuffer&&this.textBuffer.setVisibility(this.labelVisible&&this.visible),e||this.viewer.requestRender(),this},setParameters:function(t){var e=!1,i={};return t&&t.labelSize&&(i.labelSize=!0),t&&t.labelColor&&(i.labelColor=!0),hs.prototype.setParameters.call(this,t,i,e),t&&void 0!==t.labelVisible&&this.setVisibility(this.visible),this}}),Lv.add("distance",Zs),Ks.prototype=Object.assign(Object.create(Oa.prototype),{constructor:Ks,setAttributes:function(t){var e,i,n,r=this.geometry.attributes;t.position&&t.vector&&(e=t.position,i=t.vector,n=r.position.array,r.position.needsUpdate=!0);var o,a,s=this.size,c=this.scale;if(t.position&&t.vector)for(var u=0;u<s;u++)o=2*u*3,a=3*u,n[o+0]=e[a+0],n[o+1]=e[a+1],n[o+2]=e[a+2],n[o+3]=e[a+0]+i[a+0]*c,n[o+4]=e[a+1]+i[a+1]*c,n[o+5]=e[a+2]+i[a+2]*c}}),Qs.prototype=Object.assign(Object.create(hs.prototype),{constructor:Qs,type:"helixorient",parameters:Object.assign({sphereDetail:!0,disableImpostor:!0},hs.prototype.parameters),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"sstruc"),e.radius=d(e.radius,.15),e.scale=d(e.scale,1),hs.prototype.init.call(this,e)},createData:function(t){var e=[],i=[];return this.structure.eachPolymer(function(t){if(!(t.residueCount<4)){i.push(t);var n=new Bo(t),r=n.getPosition(),o=n.getColor(this.getColorParams()),a=n.getSize(this.radius,this.scale);e.push(new Va(r.center,o.color,a.size,o.pickingColor,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0})),new Ks(r.center,r.axis,this.getBufferParams({color:"skyblue",scale:1})),new Ks(r.center,r.resdir,this.getBufferParams({color:"lightgreen",scale:1})))}}.bind(this),t.getSelection()),{bufferList:e,polymerList:i}},updateData:function(e,i){t.Debug&&Pv.time(this.type+" repr update"),e=e||{};for(var n=0,r=i.polymerList.length;n<r;++n){var o=3*n,a={},s=i.polymerList[n],c=new Bo(s);if(e.position){var u=c.getPosition();a.position=u.center,i.bufferList[o+1].setAttributes({position:u.center,vector:u.axis}),i.bufferList[o+2].setAttributes({position:u.center,vector:u.resdir})}i.bufferList[o].setAttributes(a)}t.Debug&&Pv.timeEnd(this.type+" repr update")}}),Lv.add("helixorient",Qs),Js.prototype=Object.assign(Object.create(Fs.prototype),{constructor:Js,type:"licorice",parameters:Object.assign({},Fs.prototype.parameters,{aspectRatio:null}),init:function(t){var e=t||{};e.aspectRatio=1,Fs.prototype.init.call(this,e)}}),Lv.add("licorice",Js),Ov.add("shader/HyperballStickImpostor.vert","\nattribute vec3 mapping;\nattribute float radius;\nattribute float radius2;\nattribute vec3 position1;\nattribute vec3 position2;\nvarying mat4 matrix_near;\nvarying vec4 prime1;\nvarying vec4 prime2;\nvarying float vRadius;\nvarying float vRadius2;\n#ifdef PICKING\nattribute vec3 pickingColor;\nattribute vec3 pickingColor2;\nvarying vec3 vPickingColor;\nvarying vec3 vPickingColor2;\n#else\nattribute vec3 color2;\nvarying vec3 vColor1;\nvarying vec3 vColor2;\n#endif\nuniform float shrink;\nuniform mat4 modelViewProjectionMatrix;\nuniform mat4 modelViewProjectionMatrixInverse;\nvoid main(){\nvRadius = radius;\nvRadius2 = radius2;\nvec4 spaceposition;\nvec3 position_atom1;\nvec3 position_atom2;\nvec4 vertex_position;\n#ifdef PICKING\nvPickingColor = pickingColor;\nvPickingColor2 = pickingColor2;\n#else\nvColor1 = color;\nvColor2 = color2;\n#endif\nfloat radius1 = radius;\nposition_atom1 = position1;\nposition_atom2 = position2;\nfloat distance = distance( position_atom1, position_atom2 );\nspaceposition.z = mapping.z * distance;\nif (radius1 > radius2) {\nspaceposition.y = mapping.y * 1.5 * radius1;\nspaceposition.x = mapping.x * 1.5 * radius1;\n} else {\nspaceposition.y = mapping.y * 1.5 * radius2;\nspaceposition.x = mapping.x * 1.5 * radius2;\n}\nspaceposition.w = 1.0;\nvec4 e3 = vec4( 1.0 );\nvec3 e1, e1_temp, e2, e2_temp;\ne3.xyz = normalize(position_atom1-position_atom2);\nif (e3.z == 0.0) { e3.z = 0.0000000000001;}\nif ( (position_atom1.x - position_atom2.x) == 0.0) { position_atom1.x += 0.001;}\nif ( (position_atom1.y - position_atom2.y) == 0.0) { position_atom1.y += 0.001;}\nif ( (position_atom1.z - position_atom2.z) == 0.0) { position_atom1.z += 0.001;}\nvec4 focus = vec4( 1.0 );\nfocus.x = ( position_atom1.x*position_atom1.x - position_atom2.x*position_atom2.x +\n( radius2*radius2 - radius1*radius1 )*e3.x*e3.x/shrink )/(2.0*(position_atom1.x - position_atom2.x));\nfocus.y = ( position_atom1.y*position_atom1.y - position_atom2.y*position_atom2.y +\n( radius2*radius2 - radius1*radius1 )*e3.y*e3.y/shrink )/(2.0*(position_atom1.y - position_atom2.y));\nfocus.z = ( position_atom1.z*position_atom1.z - position_atom2.z*position_atom2.z +\n( radius2*radius2 - radius1*radius1 )*e3.z*e3.z/shrink )/(2.0*(position_atom1.z - position_atom2.z));\ne1.x = 1.0;\ne1.y = 1.0;\ne1.z = ( (e3.x*focus.x + e3.y*focus.y + e3.z*focus.z) - e1.x*e3.x - e1.y*e3.y)/e3.z;\ne1_temp = e1 - focus.xyz;\ne1 = normalize(e1_temp);\ne2_temp = e1.yzx * e3.zxy - e1.zxy * e3.yzx;\ne2 = normalize(e2_temp);\nmat3 R= mat3( e1.xyz, e2.xyz, e3.xyz );\nvertex_position.xyz = R * spaceposition.xyz;\nvertex_position.w = 1.0;\nvertex_position.x += (position_atom1.x+position_atom2.x) / 2.0;\nvertex_position.y += (position_atom1.y+position_atom2.y) / 2.0;\nvertex_position.z += (position_atom1.z+position_atom2.z) / 2.0;\ngl_Position = modelViewProjectionMatrix * vertex_position;\nvec4 i_near, i_far;\nvec4 near = gl_Position;\nnear.z = 0.0 ;\nnear = modelViewProjectionMatrixInverse * near;\ni_near = near;\nvec4 far = gl_Position;\nfar.z = far.w ;\ni_far = modelViewProjectionMatrixInverse * far;\nprime1 = vec4( position_atom1 - (position_atom1 - focus.xyz)*shrink, 1.0 );\nprime2 = vec4( position_atom2 - (position_atom2 - focus.xyz)*shrink, 1.0 );\nfloat Rsquare = (radius1*radius1/shrink) - (\n(position_atom1.x - focus.x)*(position_atom1.x - focus.x) +\n(position_atom1.y - focus.y)*(position_atom1.y - focus.y) +\n(position_atom1.z - focus.z)*(position_atom1.z - focus.z)\n);\nfocus.w = Rsquare;\nmatrix_near = mat4( i_near, i_far, focus, e3 );\ngl_Position.z = 1.0;\n}"),Ov.add("shader/HyperballStickImpostor.frag","#define STANDARD\n#define IMPOSTOR\nuniform vec3 diffuse;\nuniform vec3 emissive;\nuniform float roughness;\nuniform float metalness;\nuniform float opacity;\nuniform float nearClip;\nuniform float shrink;\nuniform mat4 modelViewMatrix;\nuniform mat4 modelViewProjectionMatrix;\nuniform mat4 modelViewMatrixInverseTranspose;\nuniform mat4 projectionMatrix;\nvarying mat4 matrix_near;\nvarying vec4 prime1;\nvarying vec4 prime2;\nvarying float vRadius;\nvarying float vRadius2;\n#ifdef PICKING\nuniform float objectId;\nvarying vec3 vPickingColor;\nvarying vec3 vPickingColor2;\n#else\nvarying vec3 vColor1;\nvarying vec3 vColor2;\n#include common\n#include fog_pars_fragment\n#include bsdfs\n#include lights_pars\n#include lights_physical_pars_fragment\n#endif\nbool interior = false;\nfloat calcClip( vec4 cameraPos ){\nreturn dot( cameraPos, vec4( 0.0, 0.0, 1.0, nearClip - 0.5 ) );\n}\nfloat calcClip( vec3 cameraPos ){\nreturn calcClip( vec4( cameraPos, 1.0 ) );\n}\nfloat calcDepth( in vec3 cameraPos ){\nvec2 clipZW = cameraPos.z * projectionMatrix[2].zw + projectionMatrix[3].zw;\nreturn 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\nstruct Ray {\nvec3 origin ;\nvec3 direction ;\n};\nbool cutoff_plane (vec3 M, vec3 cutoff, vec3 x3){\nfloat a = x3.x;\nfloat b = x3.y;\nfloat c = x3.z;\nfloat d = -x3.x*cutoff.x-x3.y*cutoff.y-x3.z*cutoff.z;\nfloat l = a*M.x+b*M.y+c*M.z+d;\nif (l<0.0) {return true;}\nelse{return false;}\n}\nvec3 isect_surf(Ray r, mat4 matrix_coef){\nvec4 direction = vec4(r.direction, 0.0);\nvec4 origin = vec4(r.origin, 1.0);\nfloat a = dot(direction,(matrix_coef*direction));\nfloat b = dot(origin,(matrix_coef*direction));\nfloat c = dot(origin,(matrix_coef*origin));\nfloat delta =b*b-a*c;\ngl_FragColor.a = 1.0;\nif (delta<0.0){\ndiscard;\n}\nfloat t1 =(-b-sqrt(delta))/a;\nreturn r.origin+t1*r.direction;\n}\nvec3 isect_surf2(Ray r, mat4 matrix_coef){\nvec4 direction = vec4(r.direction, 0.0);\nvec4 origin = vec4(r.origin, 1.0);\nfloat a = dot(direction,(matrix_coef*direction));\nfloat b = dot(origin,(matrix_coef*direction));\nfloat c = dot(origin,(matrix_coef*origin));\nfloat delta =b*b-a*c;\ngl_FragColor.a = 1.0;\nif (delta<0.0){\ndiscard;\n}\nfloat t2 =(-b+sqrt(delta))/a;\nreturn r.origin+t2*r.direction;\n}\nRay primary_ray(vec4 near1, vec4 far1){\nvec3 near=near1.xyz/near1.w;\nvec3 far=far1.xyz/far1.w;\nreturn Ray(near,far-near);\n}\nfloat update_z_buffer(vec3 M, mat4 ModelViewP){\nfloat depth1;\nvec4 Ms=(ModelViewP*vec4(M,1.0));\nreturn depth1=(1.0+Ms.z/Ms.w)/2.0;\n}\nvoid main(){\nfloat radius = max( vRadius, vRadius2 );\nvec4 i_near, i_far, focus;\nvec3 e3, e1, e1_temp, e2;\ni_near = vec4(matrix_near[0][0],matrix_near[0][1],matrix_near[0][2],matrix_near[0][3]);\ni_far = vec4(matrix_near[1][0],matrix_near[1][1],matrix_near[1][2],matrix_near[1][3]);\nfocus = vec4(matrix_near[2][0],matrix_near[2][1],matrix_near[2][2],matrix_near[2][3]);\ne3 = vec3(matrix_near[3][0],matrix_near[3][1],matrix_near[3][2]);\ne1.x = 1.0;\ne1.y = 1.0;\ne1.z = ( (e3.x*focus.x + e3.y*focus.y + e3.z*focus.z) - e1.x*e3.x - e1.y*e3.y)/e3.z;\ne1_temp = e1 - focus.xyz;\ne1 = normalize(e1_temp);\ne2 = normalize(cross(e1,e3));\nvec4 equation = focus;\nfloat shrinkfactor = shrink;\nfloat t1 = -1.0/(1.0-shrinkfactor);\nfloat t2 = 1.0/(shrinkfactor);\nvec4 colonne1, colonne2, colonne3, colonne4;\nmat4 mat;\nvec3 equation1 = vec3(t2,t2,t1);\nfloat A1 = - e1.x*equation.x - e1.y*equation.y - e1.z*equation.z;\nfloat A2 = - e2.x*equation.x - e2.y*equation.y - e2.z*equation.z;\nfloat A3 = - e3.x*equation.x - e3.y*equation.y - e3.z*equation.z;\nfloat A11 = equation1.x*e1.x*e1.x + equation1.y*e2.x*e2.x + equation1.z*e3.x*e3.x;\nfloat A21 = equation1.x*e1.x*e1.y + equation1.y*e2.x*e2.y + equation1.z*e3.x*e3.y;\nfloat A31 = equation1.x*e1.x*e1.z + equation1.y*e2.x*e2.z + equation1.z*e3.x*e3.z;\nfloat A41 = equation1.x*e1.x*A1 + equation1.y*e2.x*A2 + equation1.z*e3.x*A3;\nfloat A22 = equation1.x*e1.y*e1.y + equation1.y*e2.y*e2.y + equation1.z*e3.y*e3.y;\nfloat A32 = equation1.x*e1.y*e1.z + equation1.y*e2.y*e2.z + equation1.z*e3.y*e3.z;\nfloat A42 = equation1.x*e1.y*A1 + equation1.y*e2.y*A2 + equation1.z*e3.y*A3;\nfloat A33 = equation1.x*e1.z*e1.z + equation1.y*e2.z*e2.z + equation1.z*e3.z*e3.z;\nfloat A43 = equation1.x*e1.z*A1 + equation1.y*e2.z*A2 + equation1.z*e3.z*A3;\nfloat A44 = equation1.x*A1*A1 + equation1.y*A2*A2 + equation1.z*A3*A3 - equation.w;\ncolonne1 = vec4(A11,A21,A31,A41);\ncolonne2 = vec4(A21,A22,A32,A42);\ncolonne3 = vec4(A31,A32,A33,A43);\ncolonne4 = vec4(A41,A42,A43,A44);\nmat = mat4(colonne1,colonne2,colonne3,colonne4);\nRay ray = primary_ray(i_near,i_far) ;\nvec3 M;\nM = isect_surf(ray, mat);\nif (cutoff_plane(M, prime1.xyz, -e3) || cutoff_plane(M, prime2.xyz, e3)){ discard; }\nvec4 M1 = vec4(M,1.0);\nvec4 M2 = mat*M1;\nvec3 _normal = ( modelViewMatrixInverseTranspose * M2 ).xyz;\ngl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ;\n#ifdef NEAR_CLIP\nif( calcClip( modelViewMatrix * vec4( M, 1.0 ) ) > 0.0 ){\nM = isect_surf2(ray, mat);\nif( calcClip( modelViewMatrix * vec4( M, 1.0 ) ) > 0.0 )\ndiscard;\ninterior = true;\ngl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ;\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = max( 0.0, calcDepth( vec3( - ( nearClip - 0.5 ) ) ) + ( 0.0000001 / radius ) );\n}\n}else if( gl_FragDepthEXT <= 0.0 ){\nM = isect_surf2(ray, mat);\ninterior = true;\ngl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix);\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / radius );\n}\n}\n#else\nif( gl_FragDepthEXT <= 0.0 ){\nM = isect_surf2(ray, mat);\ninterior = true;\ngl_FragDepthEXT = update_z_buffer(M, modelViewProjectionMatrix) ;\nif( gl_FragDepthEXT >= 0.0 ){\ngl_FragDepthEXT = 0.0 + ( 0.0000001 / radius );\n}\n}\n#endif\nif (cutoff_plane(M, prime1.xyz, -e3) || cutoff_plane(M, prime2.xyz, e3)){ discard; }\nif (gl_FragDepthEXT < 0.0)\ndiscard;\nif (gl_FragDepthEXT > 1.0)\ndiscard;\nfloat distance_ratio = ((M.x-prime2.x)*e3.x + (M.y-prime2.y)*e3.y +(M.z-prime2.z)*e3.z) /\ndistance(prime2.xyz,prime1.xyz);\n#ifdef PICKING\nif( distance_ratio > 0.5 ){\ngl_FragColor = vec4( vPickingColor, objectId );\n}else{\ngl_FragColor = vec4( vPickingColor2, objectId );\n}\n#else\nvec3 vViewPosition = -( modelViewMatrix * vec4( M, 1.0 ) ).xyz;\nvec3 vNormal = _normal;\nvec3 vColor;\nif( distance_ratio>0.5 ){\nvColor = vColor1;\n}else{\nvColor = vColor2;\n}\nvec4 diffuseColor = vec4( diffuse, opacity );\nReflectedLight reflectedLight = ReflectedLight( vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ), vec3( 0.0 ) );\nvec3 totalEmissiveLight = emissive;\n#include color_fragment\n#include roughnessmap_fragment\n#include metalnessmap_fragment\nvec3 normal = normalize( vNormal );\nif( interior ){\nnormal = vec3( 0.0, 0.0, 0.4 );\n}\n#include lights_physical_fragment\n#include lights_template\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular + totalEmissiveLight;\ngl_FragColor = vec4( outgoingLight, diffuseColor.a );\n#include premultiplied_alpha_fragment\n#include tonemapping_fragment\n#include encodings_fragment\n#include fog_fragment\n#endif\n}"),
-tc.prototype=Object.assign(Object.create(Ua.prototype),{constructo:tc});var cy=new O;ic.prototype=Object.assign(Object.create(tc.prototype),{constructor:ic,parameters:Object.assign({shrink:{uniform:!0}},tc.prototype.parameters)}),rc.prototype=Object.assign(Object.create(Js.prototype),{constructor:rc,type:"hyperball",defaultSize:1,parameters:Object.assign({shrink:{type:"number",precision:3,max:1,min:.001,buffer:!0}},Js.prototype.parameters,{multipleBond:null,bondSpacing:null}),init:function(t){var e=t||{};e.scale=d(e.scale,.2),e.radius=d(e.radius,"vdw"),this.shrink=d(e.shrink,.12),Js.prototype.init.call(this,e)},getBondParams:function(t,e){return t&&!t.radius||(e=Object.assign({radius2:!0},e)),Js.prototype.getBondParams.call(this,t,e)},createData:function(t){var e=t.getAtomData(this.getAtomParams()),i=t.getBondData(this.getBondParams()),n=new Va(e.position,e.color,e.radius,e.pickingColor,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0}));this.__center=new Float32Array(3*t.bondCount);var r=new nc(i.position1,i.position2,i.color1,i.color2,i.radius1,i.radius2,i.pickingColor1,i.pickingColor2,this.getBufferParams({shrink:this.shrink,radialSegments:this.radialSegments,dullInterior:!0}),this.disableImpostor);return{bufferList:[n,r]}},updateData:function(t,e){var i=e.sview.getAtomData(this.getAtomParams()),n=e.sview.getBondData(this.getBondParams()),r={},o={};if(!t||t.position){r.position=i.position;var a=n.position1,s=n.position2;o.position=Er(a,s,this.__center),o.position1=a,o.position2=s}t&&!t.color||(r.color=i.color,o.color=n.color1,o.color2=n.color2),t&&!t.radius||(r.radius=i.radius,o.radius=n.radius1,o.radius2=n.radius2),e.bufferList[0].setAttributes(r),e.bufferList[1].setAttributes(o)}}),Lv.add("hyperball",rc),oc.prototype={constructor:oc,atomLabel:function(t){var e,i=this.type;switch(i){case"atomname":e=t.atomname;break;case"atomindex":e=""+t.index;break;case"occupancy":e=t.occupancy.toFixed(2);break;case"bfactor":e=t.bfactor.toFixed(2);break;case"serial":e=""+t.serial;break;case"element":e=t.element;break;case"atom":e=t.atomname+"|"+t.index;break;case"resname":e=t.resname;break;case"resno":e=""+t.resno;break;case"res":var n=t.resname.toUpperCase();e=(Om[n]||n)+t.resno;break;case"text":e=this.text[t.index];break;default:e=t.qualifiedName()}return void 0===e?"":e}},oc.types={"":"",atomname:"atom name",atomindex:"atom index",occupancy:"occupancy",bfactor:"b-factor",serial:"serial",element:"element",atom:"atom name + index",resname:"residue name",resno:"residue no",res:"residue name + no",text:"text",qualified:"qualified name"},ac.prototype=Object.assign(Object.create(hs.prototype),{constructor:ac,type:"label",parameters:Object.assign({labelType:{type:"select",options:oc.types,rebuild:!0},labelText:{type:"hidden",rebuild:!0},fontFamily:{type:"select",options:{"sans-serif":"sans-serif",monospace:"monospace",serif:"serif"},buffer:!0},fontStyle:{type:"select",options:{normal:"normal",italic:"italic"},buffer:!0},fontWeight:{type:"select",options:{normal:"normal",bold:"bold"},buffer:!0},sdf:{type:"boolean",buffer:!0},xOffset:{type:"number",precision:1,max:20,min:-20,buffer:!0},yOffset:{type:"number",precision:1,max:20,min:-20,buffer:!0},zOffset:{type:"number",precision:1,max:20,min:-20,buffer:!0},attachment:{type:"select",options:{"bottom-left":"bottom-left","bottom-center":"bottom-center","bottom-right":"bottom-right","middle-left":"middle-left","middle-center":"middle-center","middle-right":"middle-right","top-left":"top-left","top-center":"top-center","top-right":"top-right"},rebuild:!0},showBorder:{type:"boolean",buffer:!0},borderColor:{type:"color",buffer:!0},borderWidth:{type:"number",precision:2,max:.3,min:0,buffer:!0},showBackground:{type:"boolean",rebuild:!0},backgroundColor:{type:"color",buffer:!0},backgroundMargin:{type:"number",precision:2,max:2,min:0,rebuild:!0},backgroundOpacity:{type:"range",step:.01,max:1,min:0,buffer:!0}},hs.prototype.parameters,{side:null,flatShaded:null,wireframe:null,linewidth:null,roughness:null,metalness:null,diffuse:null}),init:function(t){var e=t||{};this.labelType=d(e.labelType,"res"),this.labelText=d(e.labelText,{}),this.fontFamily=d(e.fontFamily,"sans-serif"),this.fontStyle=d(e.fontStyle,"normal"),this.fontWeight=d(e.fontWeight,"bold"),this.sdf=d(e.sdf,"Chrome"===_v),this.xOffset=d(e.xOffset,0),this.yOffset=d(e.yOffset,0),this.zOffset=d(e.zOffset,.5),this.attachment=d(e.attachment,"bottom-left"),this.showBorder=d(e.showBorder,!1),this.borderColor=d(e.borderColor,"lightgrey"),this.borderWidth=d(e.borderWidth,.15),this.showBackground=d(e.showBackground,!1),this.backgroundColor=d(e.backgroundColor,"lightgrey"),this.backgroundMargin=d(e.backgroundMargin,.5),this.backgroundOpacity=d(e.backgroundOpacity,1),hs.prototype.init.call(this,e)},createData:function(t){var e={position:!0,color:!0,radius:!0},i=t.getAtomData(this.getAtomParams(e)),n=[],r=new oc(this.labelType,this.labelText);t.eachAtom(function(t){n.push(r.atomLabel(t))});var o=new Ys(i.position,i.radius,i.color,n,this.getBufferParams({fontFamily:this.fontFamily,fontStyle:this.fontStyle,fontWeight:this.fontWeight,sdf:this.sdf,xOffset:this.xOffset,yOffset:this.yOffset,zOffset:this.zOffset,attachment:this.attachment,showBorder:this.showBorder,borderColor:this.borderColor,borderWidth:this.borderWidth,showBackground:this.showBackground,backgroundColor:this.backgroundColor,backgroundMargin:this.backgroundMargin,backgroundOpacity:this.backgroundOpacity}));return{bufferList:[o]}},updateData:function(t,e){var i=e.sview.getAtomData(this.getAtomParams(t)),n={};t&&!t.position||(n.position=i.position),t&&!t.radius||(n.size=i.radius),t&&!t.color||(n.color=i.color),e.bufferList[0].setAttributes(n)}}),Lv.add("label",ac),sc.prototype=Object.assign(Object.create(hs.prototype),{constructor:sc,type:"line",parameters:Object.assign({multipleBond:{type:"select",rebuild:!0,options:{off:"off",symmetric:"symmetric",offset:"offset"}},bondSpacing:{type:"number",precision:2,max:2,min:.5}},ts.prototype.parameters,{flatShaded:null,side:null,wireframe:null,roughness:null,metalness:null,diffuse:null}),init:function(t){var e=t||{};this.multipleBond=d(e.multipleBond,"off"),this.bondSpacing=d(e.bondSpacing,1),hs.prototype.init.call(this,e)},getBondParams:function(t,e){return e=Object.assign({multipleBond:this.multipleBond,bondSpacing:this.bondSpacing,radiusParams:{radius:.1,scale:1}},e),hs.prototype.getBondParams.call(this,t,e)},createData:function(t){var e={position:!0,color:!0},i=t.getBondData(this.getBondParams(e)),n=new ls(i.position1,i.position2,i.color1,i.color2,this.getBufferParams());return{bufferList:[n]}},updateData:function(t,e){var i=e.sview.getBondData(this.getBondParams(t)),n={};t&&!t.position||(n.from=i.position1,n.to=i.position2),t&&!t.color||(n.color=i.color1,n.color2=i.color2),e.bufferList[0].setAttributes(n)},setParameters:function(t){var e=!1,i={};return t&&t.bondSpacing&&(i.position=!0),hs.prototype.setParameters.call(this,t,i,e),this}}),Lv.add("line",sc),uc.__deps=[Aa,Sa,Ma,Hr,cc],lc.__deps=[Aa,Ma,Ir,Hr,eo,Zr,io,hc,d],Tv.add("molsurf",function(t,e){var i=t.data.args,n=t.data.params;if(i&&n){var r="av"===n.type?lc:uc,o=new r(i.coordList,i.radiusList,i.indexList),a=o.getSurface(n.type,n.probeRadius,n.scaleFactor,n.cutoff,!0,n.smooth,n.contour),s=[a.position.buffer,a.index.buffer];a.normal&&s.push(a.normal.buffer),a.atomindex&&s.push(a.atomindex.buffer),e({sd:a,p:n},s)}},[uc,lc]),dc.prototype={getAtomData:function(){return this.structure.getAtomData({what:{position:!0,radius:!0,index:!0},radiusParams:{radius:"vdw",scale:1}})},makeSurface:function(t,e){var i=new pa("","",t);return i.info.type=e.type,i.info.probeRadius=e.probeRadius,i.info.scaleFactor=e.scaleFactor,i.info.smooth=e.smooth,i.info.cutoff=e.cutoff,i},getSurface:function(t){var e=t||{},i=this.getAtomData(),n=i.position,r=i.radius,o=i.index,a="av"===e.type?lc:uc,s=new a(n,r,o),c=s.getSurface(e.type,e.probeRadius,e.scaleFactor,e.cutoff,!0,e.smooth,e.contour);return this.makeSurface(c,e)},getSurfaceWorker:function(t,e){var i=Object.assign({},t);if(window.Worker){void 0===this.worker&&(this.worker=new ma("molsurf"));var n=this.getAtomData(),r=n.position,o=n.radius,a=n.index,s={args:{coordList:r,radiusList:o,indexList:a},params:i},c=[r.buffer,o.buffer,a.buffer];this.worker.post(s,c,function(t){var n=t.data.sd;e(this.makeSurface(n,i))}.bind(this),function(t){console.warn("MolecularSurface.getSurfaceWorker error - trying without worker",t),this.worker.terminate(),this.worker=void 0;var n=this.getSurface(i);e(n)}.bind(this))}else{var u=this.getSurface(i);e(u)}},dispose:function(){this.worker&&this.worker.terminate()}},fc.prototype=Object.assign(Object.create(Oa.prototype),{constructor:fc,setAttributes:function(t){var e=this.geometry.attributes;t.color&&(e.color.array.set(t.color),e.color.needsUpdate=!0),t.index&&(e.index.array.set(t.index),e.index.needsUpdate=!0)}}),pc.prototype=Object.assign(Object.create(hs.prototype),{constructor:pc,type:"surface",parameters:Object.assign({surfaceType:{type:"select",rebuild:!0,options:{vws:"vws",sas:"sas",ms:"ms",ses:"ses",av:"av"}},probeRadius:{type:"number",precision:1,max:20,min:0,rebuild:!0},smooth:{type:"integer",precision:1,max:10,min:0,rebuild:!0},scaleFactor:{type:"number",precision:1,max:5,min:0,rebuild:!0},cutoff:{type:"number",precision:2,max:50,min:0,rebuild:!0},contour:{type:"boolean",rebuild:!0},background:{type:"boolean",rebuild:!0},opaqueBack:{type:"boolean",buffer:!0},filterSele:{type:"text",rebuild:!0},volume:{type:"hidden"},useWorker:{type:"boolean",rebuild:!0}},hs.prototype.parameters,{radiusType:null,radius:null,scale:null}),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"uniform"),e.colorValue=d(e.colorValue,14540253),this.surfaceType=d(e.surfaceType,"ms"),this.probeRadius=d(e.probeRadius,1.4),this.smooth=d(e.smooth,2),this.scaleFactor=d(e.scaleFactor,2),this.cutoff=d(e.cutoff,0),this.contour=d(e.contour,!1),this.background=d(e.background,!1),this.opaqueBack=d(e.opaqueBack,!0),this.filterSele=d(e.filterSele,""),this.volume=d(e.volume,void 0),this.useWorker=d(e.useWorker,!0),hs.prototype.init.call(this,t)},prepareData:function(t,e,i){var n=this.__infoList[e];if(n||(n={},this.__infoList[e]=n),n.molsurf&&n.sele===t.selection.string)i(e);else{if(this.filterSele){var r=t.structure.getView(new On(this.filterSele)),o=r.boundingBox.size(),a=Math.max(o.x,o.y,o.z),s=t.getAtomSetWithinPoint(r.center,a/2);t=t.getView(new On(t.getAtomSetWithinSelection(s,3).toSeleString()))}n.sele=t.selection.string,n.molsurf=new dc(t);var c=this.getSurfaceParams(),u=function(t){n.surface=t,i(e)};this.useWorker?n.molsurf.getSurfaceWorker(c,u):u(n.molsurf.getSurface(c))}},prepare:function(t){if((this.__forceNewMolsurf||this.__sele!==this.selection.string||this.__surfaceParams!==JSON.stringify(this.getSurfaceParams()))&&(this.__infoList.forEach(function(t){t.molsurf.dispose()}.bind(this)),this.__infoList.length=0),0===this.structureView.atomCount)return void t();var e=function(){this.__sele=this.selection.string,this.__surfaceParams=JSON.stringify(this.getSurfaceParams()),this.__forceNewMolsurf=!1,t()}.bind(this),i="default"===this.assembly?this.defaultAssembly:this.assembly,n=this.structure.biomolDict[i];n?n.partList.forEach(function(t,i){var r=t.getView(this.structureView);this.prepareData(r,i,function(t){t===n.partList.length-1&&e()}.bind(this))},this):this.prepareData(this.structureView,0,e)},createData:function(t,e){var i=this.__infoList[e],n=i.surface.getPosition(),r=i.surface.getColor(this.getColorParams()),o=i.surface.getFilteredIndex(this.filterSele,t);if(i.surface.contour){var a=new fc(n,r,o,this.getBufferParams({wireframe:!1}));return{bufferList:[a],info:i}}var s=new is(n,r,o,i.surface.getNormal(),i.surface.getPickingColor(this.getColorParams()),this.getBufferParams({background:this.background,opaqueBack:this.opaqueBack,dullInterior:!1})),c=new ns(s);return{bufferList:[c],info:i}},updateData:function(t,e){var i={};return t.position?(this.__forceNewMolsurf=!0,void this.build()):(t.color&&(i.color=e.info.surface.getColor(this.getColorParams())),t.index&&(i.index=e.info.surface.getFilteredIndex(this.filterSele,e.sview)),void e.bufferList[0].setAttributes(i))},setParameters:function(t,e,i){return e=e||{},t&&t.filterSele&&(e.index=!0),t&&void 0!==t.volume&&(e.color=!0),t&&t.wireframe&&(t.contour||void 0===t.contour&&this.contour)&&(t.wireframe=!1),hs.prototype.setParameters.call(this,t,e,i),this},getSurfaceParams:function(t){var e=Object.assign({type:this.surfaceType,probeRadius:this.probeRadius,scaleFactor:this.scaleFactor,smooth:this.smooth&&!this.contour,cutoff:this.cutoff,contour:this.contour,useWorker:this.useWorker},t);return e},getColorParams:function(){var t=hs.prototype.getColorParams.call(this);return t.volume=this.volume,t},clear:function(){hs.prototype.clear.call(this)},dispose:function(){this.__infoList.forEach(function(t){t.molsurf.dispose()}.bind(this)),this.__infoList.length=0,hs.prototype.dispose.call(this)}}),Lv.add("surface",pc),mc.prototype=Object.assign(Object.create(hs.prototype),{constructor:mc,type:"point",parameters:Object.assign({pointSize:{type:"number",precision:1,max:100,min:0,buffer:!0},sizeAttenuation:{type:"boolean",buffer:!0},sortParticles:{type:"boolean",rebuild:!0},useTexture:{type:"boolean",buffer:!0},alphaTest:{type:"range",step:.001,max:1,min:0,buffer:!0},forceTransparent:{type:"boolean",buffer:!0},edgeBleach:{type:"range",step:.001,max:1,min:0,buffer:!0}},ts.prototype.parameters,{flatShaded:null,wireframe:null,linewidth:null,roughness:null,metalness:null}),init:function(t){var e=t||{};this.pointSize=d(e.pointSize,1),this.sizeAttenuation=d(e.sizeAttenuation,!0),this.sortParticles=d(e.sortParticles,!1),this.useTexture=d(e.useTexture,!1),this.alphaTest=d(e.alphaTest,.5),this.forceTransparent=d(e.forceTransparent,!1),this.edgeBleach=d(e.edgeBleach,0),hs.prototype.init.call(this,e)},createData:function(t){var e={position:!0,color:!0},i=t.getAtomData(this.getAtomParams(e)),n=new as(i.position,i.color,this.getBufferParams({pointSize:this.pointSize,sizeAttenuation:this.sizeAttenuation,sortParticles:this.sortParticles,useTexture:this.useTexture,alphaTest:this.alphaTest,forceTransparent:this.forceTransparent,edgeBleach:this.edgeBleach}));return{bufferList:[n]}},updateData:function(t,e){var i=e.sview.getAtomData(this.getAtomParams(t)),n={};t&&!t.position||(n.position=i.position),t&&!t.color||(n.color=i.color),e.bufferList[0].setAttributes(n)}}),Lv.add("point",mc),Ov.add("shader/Ribbon.vert","#define STANDARD\nuniform float nearClip;\nuniform vec3 clipCenter;\n#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING )\nvarying vec3 vViewPosition;\n#endif\n#if defined( RADIUS_CLIP )\nvarying vec3 vClipCenter;\n#endif\nattribute vec3 dir;\nattribute float size;\n#ifdef PICKING\nattribute vec3 pickingColor;\nvarying vec3 vPickingColor;\n#else\n#include color_pars_vertex\n#ifndef FLAT_SHADED\nvarying vec3 vNormal;\n#endif\n#endif\n#include common\nvoid main(void){\n#ifdef PICKING\nvPickingColor = pickingColor;\n#else\n#include color_vertex\n#include beginnormal_vertex\n#include defaultnormal_vertex\n#ifndef FLAT_SHADED\nvNormal = normalize( transformedNormal );\n#endif\n#endif\n#include begin_vertex\ntransformed += normalize( dir ) * size;\n#include project_vertex\n#if defined( NEAR_CLIP ) || defined( RADIUS_CLIP ) || !defined( PICKING )\nvViewPosition = -mvPosition.xyz;\n#endif\n#if defined( RADIUS_CLIP )\nvClipCenter = -( modelViewMatrix * vec4( clipCenter, 1.0 ) ).xyz;\n#endif\n#include nearclip_vertex\n}"),gc.prototype=Object.assign(Object.create(Oa.prototype),{constructor:gc,setAttributes:function(t){var e,i,n,r,o,a,s,c,u,h,l,d,f=this.size,p=f/4,m=this.geometry.attributes;t.position&&(e=t.position,s=m.position.array,m.position.needsUpdate=!0),t.normal&&(i=t.normal,c=m.normal.array,m.normal.needsUpdate=!0),t.size&&(n=t.size,u=m.size.array,m.size.needsUpdate=!0),t.dir&&(r=t.dir,h=m.dir.array,m.dir.needsUpdate=!0),t.color&&(o=t.color,l=m.color.array,m.color.needsUpdate=!0),t.pickingColor&&(a=t.pickingColor,d=m.pickingColor.array,m.pickingColor.needsUpdate=!0);var g,v,y,b,x,w,_,S=n?n[0]:null;for(g=0;g<p;++g){for(w=3*g,y=3*g*4,x=4*g,e&&(s[y]=s[y+3]=e[w],s[y+1]=s[y+4]=e[w+1],s[y+2]=s[y+5]=e[w+2],s[y+6]=s[y+9]=e[w+3],s[y+7]=s[y+10]=e[w+4],s[y+8]=s[y+11]=e[w+5]),i&&(c[y]=c[y+3]=-i[w],c[y+1]=c[y+4]=-i[w+1],c[y+2]=c[y+5]=-i[w+2],c[y+6]=c[y+9]=-i[w+3],c[y+7]=c[y+10]=-i[w+4],c[y+8]=c[y+11]=-i[w+5]),v=0;v<4;++v)b=y+3*v,o&&(l[b]=o[w],l[b+1]=o[w+1],l[b+2]=o[w+2]),a&&(d[b]=a[w],d[b+1]=a[w+1],d[b+2]=a[w+2]);n&&(_=n[g],S!==n[g]?(u[x]=S,u[x+1]=S,u[x+2]=_,u[x+3]=_):(u[x]=_,u[x+1]=_,u[x+2]=_,u[x+3]=_),S=_),r&&(h[y]=r[w],h[y+1]=r[w+1],h[y+2]=r[w+2],h[y+3]=-r[w],h[y+4]=-r[w+1],h[y+5]=-r[w+2],h[y+6]=r[w+3],h[y+7]=r[w+4],h[y+8]=r[w+5],h[y+9]=-r[w+3],h[y+10]=-r[w+4],h[y+11]=-r[w+5])}},makeIndex:function(){var t,e,i,n,r=this.meshIndex,o=r.length/4/3,a=new Uint16Array([0,1,2,1,3,2]);for(e=0;e<o;++e)for(i=6*e,n=4*e,r.set(a,i),t=0;t<6;++t)r[i+t]+=n}}),vc.prototype=Object.assign(Object.create(hs.prototype),{constructor:vc,type:"ribbon",parameters:Object.assign({subdiv:{type:"integer",max:50,min:1,rebuild:!0},tension:{type:"number",precision:1,max:1,min:.1},smoothSheet:{type:"boolean",rebuild:!0}},hs.prototype.parameters,{side:null,wireframe:null,linewidth:null}),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"chainname"),e.colorScale=d(e.colorScale,"RdYlBu"),e.radius=d(e.radius,"sstruc"),e.scale=d(e.scale,4),"low"===e.quality?this.subdiv=3:"medium"===e.quality?this.subdiv=6:"high"===e.quality?this.subdiv=12:this.subdiv=d(e.subdiv,6),this.tension=d(e.tension,NaN),this.smoothSheet=d(e.smoothSheet,!1),hs.prototype.init.call(this,e)},getSplineParams:function(t){return Object.assign({subdiv:this.subdiv,tension:this.tension,directional:!0,smoothSheet:this.smoothSheet},t)},createData:function(t){var e=[],i=[];return this.structure.eachPolymer(function(t){if(!(t.residueCount<4)){i.push(t);var n=new js(t,this.getSplineParams()),r=n.getSubdividedPosition(),o=n.getSubdividedOrientation(),a=n.getSubdividedColor(this.getColorParams()),s=n.getSubdividedSize(this.radius,this.scale);e.push(new gc(r.position,o.binormal,o.normal,a.color,s.size,a.pickingColor,this.getBufferParams()))}}.bind(this),t.getSelection()),{bufferList:e,polymerList:i}},updateData:function(t,e){t=t||{};var i=0,n=e.polymerList.length;for(i=0;i<n;++i){var r={},o=new js(e.polymerList[i],this.getSplineParams());if(t.position){var a=o.getSubdividedPosition(),s=o.getSubdividedOrientation();r.position=a.position,r.normal=s.binormal,r.dir=s.normal}if(t.radius||t.scale){var c=o.getSubdividedSize(this.radius,this.scale);r.size=c.size}if(t.color){var u=o.getSubdividedColor(this.getColorParams());r.color=u.color}e.bufferList[i].setAttributes(r)}},setParameters:function(t){var e=!1,i={};return t&&t.tension&&(i.position=!0),hs.prototype.setParameters.call(this,t,i,e),this}}),Lv.add("ribbon",vc),yc.prototype=Object.assign(Object.create(hs.prototype),{constructor:yc,type:"rocket",parameters:Object.assign({localAngle:{type:"integer",max:180,min:0,rebuild:!0},centerDist:{type:"number",precision:1,max:10,min:0,rebuild:!0},ssBorder:{type:"boolean",rebuild:!0},radialSegments:!0,openEnded:!0,disableImpostor:!0},hs.prototype.parameters),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"sstruc"),e.radius=d(e.radius,1.5),e.scale=d(e.scale,1),e.openEnded=d(e.openEnded,!1),this.localAngle=d(e.localAngle,30),this.centerDist=d(e.centerDist,2.5),this.ssBorder=d(e.ssBorder,!1),hs.prototype.init.call(this,e)},createData:function(t){var e=0,i=[],n=[];this.structure.eachPolymer(function(t){if(!(t.residueCount<4||t.isNucleic())){var r=new Uo(t),o=r.getAxis(this.localAngle,this.centerDist,this.ssBorder,this.getColorParams(),this.radius,this.scale);e+=o.size.length,i.push(o),n.push(r)}}.bind(this),t.getSelection());var r={begin:new Float32Array(3*e),end:new Float32Array(3*e),size:new Float32Array(e),color:new Float32Array(3*e),pickingColor:new Float32Array(3*e)},o=0;i.forEach(function(t){r.begin.set(t.begin,3*o),r.end.set(t.end,3*o),r.size.set(t.size,o),r.color.set(t.color,3*o),r.pickingColor.set(t.pickingColor,3*o),o+=t.size.length});var a=new Ya(r.begin,r.end,r.color,r.color,r.size,r.pickingColor,r.pickingColor,this.getBufferParams({openEnded:this.openEnded,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0}));return{bufferList:[a],axisList:i,helixbundleList:n,axisData:r}},updateData:function(t,e){if(t=t||{},t.position)return void this.build();var i={};if(t.color||t.radius){var n=0;e.helixbundleList.forEach(function(i){var r=i.getAxis(this.localAngle,this.centerDist,this.ssBorder,this.getColorParams(),this.radius,this.scale);t.color&&e.axisData.color.set(r.color,3*n),(t.radius||t.scale)&&e.axisData.size.set(r.size,n),n+=r.size.length}.bind(this)),t.color&&(i.color=e.axisData.color,i.color2=e.axisData.color),(t.radius||t.scale)&&(i.radius=e.axisData.size)}e.bufferList[0].setAttributes(i)}}),Lv.add("rocket",yc),bc.prototype=Object.assign(Object.create(Vs.prototype),{constructor:bc,type:"rope",parameters:Object.assign({smooth:{type:"integer",max:15,min:0,rebuild:!0}},Vs.prototype.parameters,{aspectRatio:null,smoothSheet:null}),init:function(t){var e=t||{};e.aspectRatio=1,e.tension=d(e.tension,.5),e.scale=d(e.scale,5),e.smoothSheet=!1,this.smooth=d(e.smooth,2),Vs.prototype.init.call(this,e)},getSpline:function(t){var e=new Bo(t);return new js(t,this.getSplineParams({directional:!1,positionIterator:e.getCenterIterator(this.smooth)}))}}),Lv.add("rope",bc),xc.prototype=Object.assign(Object.create(hs.prototype),{constructor:xc,type:"spacefill",parameters:Object.assign({sphereDetail:!0,disableImpostor:!0},hs.prototype.parameters),init:function(t){var e=t||{};hs.prototype.init.call(this,e)},createData:function(t){var e=t.getAtomData(this.getAtomParams()),i=new Va(e.position,e.color,e.radius,e.pickingColor,this.getBufferParams({sphereDetail:this.sphereDetail,dullInterior:!0,disableImpostor:this.disableImpostor}));return{bufferList:[i]}},updateData:function(t,e){var i=e.sview.getAtomData(this.getAtomParams(t)),n={};t&&!t.position||(n.position=i.position),t&&!t.color||(n.color=i.color),t&&!t.radius||(n.radius=i.radius),e.bufferList[0].setAttributes(n)}}),Lv.add("spacefill",xc),wc.prototype=Object.assign(Object.create(Oa.prototype),{constructor:wc,setAttributes:function(t){var e,i,n,r,o=this.geometry.attributes;if(t.position&&(e=t.position,n=o.position.array,o.position.needsUpdate=!0),t.color&&(i=t.color,r=o.color.array,o.color.needsUpdate=!0),!e&&!i)return void Pv.warn("TraceBuffer.prototype.setAttributes no data");for(var a,s,c=this.size,u=c-1,h=0;h<u;++h)a=3*h,s=3*h*2,e&&(n[s]=e[a],n[s+1]=e[a+1],n[s+2]=e[a+2],n[s+3]=e[a+3],n[s+4]=e[a+4],n[s+5]=e[a+5]),i&&(r[s]=i[a],r[s+1]=i[a+1],r[s+2]=i[a+2],r[s+3]=i[a+3],r[s+4]=i[a+4],r[s+5]=i[a+5])}}),_c.prototype=Object.assign(Object.create(hs.prototype),{constructor:_c,type:"trace",parameters:Object.assign({subdiv:{type:"integer",max:50,min:1,rebuild:!0},tension:{type:"number",precision:1,max:1,min:.1},smoothSheet:{type:"boolean",rebuild:!0}},ts.prototype.parameters,{flatShaded:null,side:null,wireframe:null}),init:function(t){var e=t||{};e.colorScheme=d(e.colorScheme,"chainname"),e.colorScale=d(e.colorScale,"RdYlBu"),"low"===e.quality?this.subdiv=3:"medium"===e.quality?this.subdiv=6:"high"===e.quality?this.subdiv=12:this.subdiv=d(e.subdiv,6),this.tension=d(e.tension,NaN),this.smoothSheet=d(e.smoothSheet,!1),hs.prototype.init.call(this,e)},getSplineParams:function(t){return Object.assign({subdiv:this.subdiv,tension:this.tension,directional:!1,smoothSheet:this.smoothSheet},t)},createData:function(t){var e=[],i=[];return this.structure.eachPolymer(function(t){if(!(t.residueCount<4)){i.push(t);var n=new js(t,this.getSplineParams()),r=n.getSubdividedPosition(),o=n.getSubdividedColor(this.getColorParams());e.push(new wc(r.position,o.color,this.getBufferParams()))}}.bind(this),t.getSelection()),{bufferList:e,polymerList:i}},updateData:function(t,e){t=t||{};var i=0,n=e.polymerList.length;for(i=0;i<n;++i){var r={},o=new js(e.polymerList[i],this.getSplineParams());if(t.position){var a=o.getSubdividedPosition();r.position=a.position}if(t.color){var s=o.getSubdividedColor(this.getColorParams());r.color=s.color}e.bufferList[i].setAttributes(r)}},setParameters:function(t){var e=!1,i={};return t&&t.tension&&(i.position=!0),hs.prototype.setParameters.call(this,t,i,e),this}}),Lv.add("trace",_c),Sc.prototype=Object.assign(Object.create(Vs.prototype),{constructor:Sc,type:"tube",parameters:Object.assign({},Vs.prototype.parameters,{aspectRatio:null}),init:function(t){var e=t||{};e.aspectRatio=1,e.scale=d(e.scale,2),Vs.prototype.init.call(this,e),"low"===e.quality&&(this.radialSegments=5)},getSplineParams:function(){return Vs.prototype.getSplineParams.call(this,{directional:!1})}}),Lv.add("tube",Sc),Ac.prototype=Object.assign(Object.create(hs.prototype),{constructor:Ac,type:"unitcell",parameters:Object.assign({radius:{type:"number",precision:3,max:10,min:.001},sphereDetail:!0,radialSegments:!0,disableImpostor:!0},ts.prototype.parameters,{assembly:null}),init:function(t){var e=t||{},i=.5;this.structure.unitcell&&(i=Math.cbrt(this.structure.unitcell.volume)/200),e.radius=d(e.radius,i),e.colorValue=d(e.colorValue,"orange"),hs.prototype.init.call(this,e)},getUnitcellData:function(t){function e(t,e,i){f.set(t,e,i).multiply(d).applyMatrix4(l.fracToCart).toArray(r,p),p+=3}function i(t,e){f.fromArray(r,3*t).toArray(s,m),f.fromArray(r,3*e).toArray(c,m),m+=3}var n=new Ct(this.colorValue),r=new Float32Array(24),o=Lr(8,n.r,n.g,n.b),a=Ir(8,this.radius),s=new Float32Array(36),c=new Float32Array(36),u=Lr(12,n.r,n.g,n.b),h=Ir(12,this.radius),l=t.unitcell,d=t.center.clone().applyMatrix4(l.cartToFrac).floor().multiplyScalar(2).addScalar(1),f=new N,p=0;e(0,0,0),e(1,0,0),e(0,1,0),e(0,0,1),e(1,1,0),e(1,0,1),e(0,1,1),e(1,1,1);var m=0;return i(0,1),i(0,2),i(0,3),i(1,4),i(1,5),i(2,6),i(3,5),i(4,7),i(5,7),i(2,4),i(7,6),i(3,6),{vertexPosition:r,vertexColor:o,vertexRadius:a,edgePosition1:s,edgePosition2:c,edgeColor:u,edgeRadius:h}},create:function(){var t=this.structureView.getStructure();if(t.unitcell){var e=this.getUnitcellData(t);this.sphereBuffer=new Va(e.vertexPosition,e.vertexColor,e.vertexRadius,void 0,this.getBufferParams({sphereDetail:this.sphereDetail,disableImpostor:this.disableImpostor,dullInterior:!0})),this.cylinderBuffer=new Ya(e.edgePosition1,e.edgePosition2,e.edgeColor,e.edgeColor,e.edgeRadius,void 0,void 0,this.getBufferParams({openEnded:!0,radialSegments:this.radialSegments,disableImpostor:this.disableImpostor,dullInterior:!0})),this.dataList.push({sview:this.structureView,bufferList:[this.sphereBuffer,this.cylinderBuffer]})}},updateData:function(t,e){var i=e.sview.getStructure(),n=this.getUnitcellData(i),r={},o={};t&&!t.position||(r.position=n.vertexPosition,o.position1=n.edgePosition1,o.position2=n.edgePosition2),t&&!t.color||(r.color=n.vertexColor,o.color=n.edgeColor,o.color2=n.edgeColor),t&&!t.radius||(r.radius=n.vertexRadius,o.radius=n.edgeRadius),this.sphereBuffer.setAttributes(r),this.cylinderBuffer.setAttributes(o)}}),Lv.add("unitcell",Ac),Mc.prototype={constructor:Mc,type:"",__objName:"",parse:function(t){return this.streamer.read(function(){this._beforeParse(),this._parse(),this._afterParse(),t(this[this.__objName])}.bind(this)),this[this.__objName]},_parse:function(){},_beforeParse:function(){},_afterParse:function(){t.Debug&&Pv.log(this[this.__objName])}},Cc.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Cc,type:"structure",__objName:"structure"}),Tc.prototype={constructor:Tc},Ec.prototype=Object.assign(Object.create(Cc.prototype),{constructor:Ec,type:"gro",_parse:function(){function e(t,e,r){for(var l=t;l<e;++l){++C;var g=C-1,T=r[l];if(T)if(g%_===0)s&&(i=new Float32Array(3*w),u.push(i),n=0);else if(g%_===1);else if(g%_===_-1){var E=T.trim().split(/\s+/),I=new Float32Array(9);if(I[0]=10*parseFloat(E[0]),I[4]=10*parseFloat(E[1]),I[8]=10*parseFloat(E[2]),h.push(I),a)return!0;P+=1}else{if(d=T.substr(10,5).trim(),c&&"CA"!==d)continue;var L=10*parseFloat(T.substr(y,v)),R=10*parseFloat(T.substr(b,v)),O=10*parseFloat(T.substr(x,v));if(s){var D=3*n;if(i[D+0]=L,i[D+1]=R,i[D+2]=O,n+=1,g>_)continue}f=T.substr(5,5).trim(),p=parseInt(T.substr(0,5)),m=parseInt(T.substr(15,5)),A.growIfFull(),A.atomTypeId[M]=S.add(d),A.x[M]=L,A.y[M]=R,A.z[M]=O,A.serial[M]=m,o.addAtom(P,"","",f,p,0,"l"),M+=1}}}t.Debug&&Pv.time("GroParser._parse "+this.name);var i,n,r=this.structure,o=this.structureBuilder,a=this.firstModelOnly,s=this.asTrajectory,c=this.cAlphaOnly,u=r.frames,h=r.boxes,l=this.streamer.peekLines(3);r.title=l[0].trim();var d,f,p,m,g=l[2].length-l[2].lastIndexOf(".")-1,v=5+g,y=20,b=20+v,x=20+2*v,w=parseInt(l[1]),_=w+3,S=r.atomMap,A=r.atomStore;A.resize(w);var M=0,P=0,C=0;this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)}),r.unitcell=new Tc(h[0][0],h[0][4],h[0][8],90,90,90,"P 1"),o.finalize(),r.finalizeAtoms(),Yo(r),Zo(r),r.finalizeBonds(),ey(r),ea(r),t.Debug&&Pv.timeEnd("GroParser._parse "+this.name)}}),Rv.add("gro",Ec),Lc.prototype={constructor:Lc,type:"Entity",getEntityType:function(){return this.entityType},isPolymer:function(){return this.entityType===im},isNonPolymer:function(){return this.entityType===nm},isMacrolide:function(){return this.entityType===rm},isWater:function(){return this.entityType===om},eachChain:function(t){var e=this.structure.getChainProxy();this.chainIndexList.forEach(function(i){e.index=i,t(e)})}};var uy={1:"h",2:"h",3:"i",4:"h",5:"g",6:"h",7:"h",8:"h",9:"h",10:"h","":"h"};Rc.prototype=Object.assign(Object.create(Cc.prototype),{constructor:Rc,type:"pdb",_parse:function(){function e(t,e,J){for(var ut,ht,lt=t;lt<e;++lt)if(s=J[lt],c=s.substr(0,6),"ATOM  "===c||"HETATM"===c){if(ct&&(U?(G?(i=new Float32Array(3*nt.count),$.push(i)):i=[],n=0):B||(W={}),C=1,T=C.toString(),E=!0,ct=!1),B&&st>0)continue;var dt,ft,pt,mt,gt;if(N){if(mt=s.split(k),gt=10===mt.length?1:0,m=mt[2],j&&"CA"!==m)continue;dt=parseFloat(mt[6-gt]),ft=parseFloat(mt[7-gt]),pt=parseFloat(mt[8-gt])}else{if(m=s.substr(12,4).trim(),j&&"CA"!==m)continue;dt=parseFloat(s.substr(30,8)),ft=parseFloat(s.substr(38,8)),pt=parseFloat(s.substr(46,8))}if(U&&(ut=3*n,i[ut+0]=dt,i[ut+1]=ft,i[ut+2]=pt,n+=1,G))continue;var vt;N?(u=parseInt(mt[1]),vt="",g="H"===s[0]?1:0,h=gt?"":mt[4],l=parseInt(mt[5-gt]),p="",d=mt[3],v=parseFloat(mt[9-gt]),y="",f=0):(u=parseInt(s.substr(6,5)),vt=s.substr(76,2).trim(),g="H"===s[0]?1:0,h=s[21].trim()||s.substr(72,4).trim(),l=parseInt(s.substr(22,4)),p=s[26].trim(),d=s.substr(17,4).trim(),v=parseFloat(s.substr(60,6)),y=s[16].trim(),f=parseFloat(s.substr(54,6))),nt.growIfFull(),nt.atomTypeId[at]=it.add(m,vt),nt.x[at]=dt,nt.y[at]=ft,nt.z[at]=pt,nt.serial[at]=u,nt.bfactor[at]=isNaN(v)?0:v,nt.altloc[at]=y.charCodeAt(0),nt.occupancy[at]=isNaN(f)?0:f,g?I===h&&R===d&&(zm.includes(d)||L===l&&D===p)||(C+=1,T=C.toString(),L=l,R=d,D=p):E||I===h||(C+=1,T=C.toString()),z.addAtom(st,h,T,d,l,g,void 0,p),W[u]=at,at+=1,E=!1,I=h}else if("CONECT"===c){var yt=W[parseInt(s.substr(6,5))],bt=[11,16,21,26],xt={};if(void 0===yt)continue;for(ut=0;ut<4;++ut){var wt=parseInt(s.substr(bt[ut],5));if(!Number.isNaN(wt)&&(wt=W[wt],void 0!==wt))if(yt<wt?(rt.index=yt,ot.index=wt):(rt.index=wt,ot.index=yt),void 0!==xt[wt])F.bondStore.bondOrder[xt[wt]]+=1;else{var _t=rt.index+"|"+ot.index;void 0===q[_t]&&(q[_t]=!0,xt[wt]=F.bondStore.count,F.bondStore.addBond(rt,ot,1))}}}else if("HELIX "===c){b=s[19].trim(),x=parseInt(s.substr(21,4)),w=s[25].trim(),_=s[31].trim(),S=parseInt(s.substr(33,4)),A=s[37].trim();var St=parseInt(s.substr(39,1));St=(uy[St]||uy[""]).charCodeAt(0),tt.push([b,x,w,_,S,A,St])}else if("SHEET "===c)b=s[21].trim(),x=parseInt(s.substr(22,4)),w=s[26].trim(),_=s[32].trim(),S=parseInt(s.substr(33,4)),A=s[37].trim(),et.push([b,x,w,_,S,A]);else if("HETNAM"===c)Q[s.substr(11,3)]=s.substr(15).trim();else if("COMPND"===c){var At,Mt=s.substr(10,70).trim(),Pt=Mt.indexOf(":"),Ct=Mt.substring(0,Pt);
-Z.includes(Ct)?(P=Ct,At=Mt.substring(Pt+2)):At=Mt,At=At.replace(/;$/,""),"MOL_ID"===P?(M={chainList:[],name:""},Y.push(M)):"MOLECULE"===P?(M.name&&(M.name+=" "),M.name+=At):"CHAIN"===P&&Array.prototype.push.apply(M.chainList,At.split(/\s*,\s*/))}else if(s.startsWith("TER")){var Tt=F.getChainProxy(F.chainStore.count-1);K[Tt.chainname]=Tt.index,C+=1,T=C.toString(),E=!0}else if("REMARK"===c&&"350"===s.substr(7,3)){if("BIOMOLECULE:"===s.substr(11,12)){var Et=s.substr(23).trim();/^(0|[1-9][0-9]*)$/.test(Et)&&(Et="BU"+Et),r=new Wo(Et),H[Et]=r}else if("BIOMT"===s.substr(13,5)){var It=s.split(/\s+/),Lt=parseInt(s[18])-1;0===Lt&&(a=new O,o.matrixList.push(a));var Rt=a.elements;Rt[0+Lt]=parseFloat(It[4]),Rt[4+Lt]=parseFloat(It[5]),Rt[8+Lt]=parseFloat(It[6]),Rt[12+Lt]=parseFloat(It[7])}else if("APPLY THE FOLLOWING TO CHAINS:"===s.substr(11,30)||"                   AND CHAINS:"===s.substr(11,30)){"APPLY"===s.substr(11,5)&&(o=r.addPart());var Ot=s.substr(41,30).split(",");for(ht=Ot.length;ut<ht;++ut){var Dt=Ot[ut].trim();Dt&&o.chainList.push(Dt)}}}else if("HEADER"===c)F.id=s.substr(62,4);else if("TITLE "===c)F.title+=(F.title?" ":"")+s.substr(10,70).trim();else if("MODEL "===c)ct=!0;else if("ENDMDL"===c||s.startsWith("END")){if(ct)continue;U&&!G&&($.push(new Float32Array(i)),G=!0),st+=1,ct=!0}else if("MTRIX"===s.substr(0,5)){if("1"===s[59])continue;var Nt=s.split(/\s+/),kt=Nt[1].trim();if("1"===s[5]&&"1"===kt){var Ft="NCS";r=new Wo(Ft),H[Ft]=r,o=r.addPart()}var zt=parseInt(s[5])-1;0===zt&&(a=new O,o.matrixList.push(a));var Bt=a.elements;Bt[0+zt]=parseFloat(Nt[2]),Bt[4+zt]=parseFloat(Nt[3]),Bt[8+zt]=parseFloat(Nt[4]),Bt[12+zt]=parseFloat(Nt[5])}else if("ORIGX"===s.substr(0,5)){X.origx||(X.origx=new O);var Ut=s.split(/\s+/),jt=parseInt(s[5])-1,$t=X.origx.elements;$t[0+jt]=parseFloat(Ut[1]),$t[4+jt]=parseFloat(Ut[2]),$t[8+jt]=parseFloat(Ut[3]),$t[12+jt]=parseFloat(Ut[4])}else if("SCALE"===s.substr(0,5)){X.scale||(X.scale=new O);var Vt=s.split(/\s+/),Gt=parseInt(s[5])-1,Ht=X.scale.elements;Ht[0+Gt]=parseFloat(Vt[1]),Ht[4+Gt]=parseFloat(Vt[2]),Ht[8+Gt]=parseFloat(Vt[3]),Ht[12+Gt]=parseFloat(Vt[4])}else if("CRYST1"===c){var Wt=parseFloat(s.substr(6,9)),Xt=parseFloat(s.substr(15,9)),qt=parseFloat(s.substr(24,9)),Yt=parseFloat(s.substr(33,7)),Zt=parseFloat(s.substr(40,7)),Kt=parseFloat(s.substr(47,7)),Qt=s.substr(55,11).trim(),Jt=new Float32Array(9);Jt[0]=Wt,Jt[4]=Xt,Jt[8]=qt,V.push(Jt),0===st&&(X.a=Wt,X.b=Xt,X.c=qt,X.alpha=Yt,X.beta=Zt,X.gamma=Kt,X.spacegroup=Qt)}}t.Debug&&Pv.time("PdbParser._parse "+this.name);var i,n,r,o,a,s,c,u,h,l,d,f,p,m,g,v,y,b,x,w,_,S,A,M,P,C,T,E,I,L,R,D,N="pqr"===this.type,k=/\s+/,F=this.structure,z=this.structureBuilder,B=this.firstModelOnly,U=this.asTrajectory,j=this.cAlphaOnly,$=F.frames,V=F.boxes,G=!1,H=F.biomolDict,W={},X={},q={},Y=[],Z=["MOL_ID","MOLECULE","CHAIN","FRAGMENT","SYNONYM","EC","ENGINEERED","MUTATION","OTHER_DETAILS"],K={},Q={},J={helices:[],sheets:[]},tt=J.helices,et=J.sheets,it=F.atomMap,nt=F.atomStore;nt.resize(Math.round(this.streamer.data.length/80));var rt=F.getAtomProxy(),ot=F.getAtomProxy(),at=0,st=0,ct=!0;this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)});var ut=Y.length;if(Y.length){F.eachChain(function(t){t.entityIndex=ut}),Y.forEach(function(t,e){var i=t.chainList.map(function(t){return K[t]});F.entityList.push(new Lc(F,e,t.name,"polymer",i))});var ht=Y.length,lt=F.getResidueProxy(),dt={};F.eachChain(function(t){t.entityIndex===ut&&(lt.index=t.residueOffset,dt[lt.resname]||(dt[lt.resname]=[]),dt[lt.resname].push(t.index))}),Object.keys(dt).forEach(function(t){var e=dt[t],i="non-polymer",n=Q[t]||t;zm.includes(t)&&(n="water",i="water"),F.entityList.push(new Lc(F,ht,n,i,e)),ht+=1})}void 0!==X.a?F.unitcell=new Tc(X.a,X.b,X.c,X.alpha,X.beta,X.gamma,X.spacegroup,X.scale):F.unitcell=void 0,z.finalize(),F.finalizeAtoms(),Yo(F),Zo(F),F.finalizeBonds(),tt.length||et.length?qo(F,J):ey(F),ea(F),t.Debug&&Pv.timeEnd("PdbParser._parse "+this.name)}}),Rv.add("pdb",Rc),Rv.add("pdb1",Rc),Rv.add("ent",Rc),Oc.prototype=Object.assign(Object.create(Rc.prototype),{constructor:Oc,type:"pqr"}),Rv.add("pqr",Oc);var hy=/\s+/,ly=/'((?:(?!'\s).)*)'|"((?:(?!"\s).)*)"|(\S+)/g,dy=/"/g,fy=/^['"]+|['"]+$/g;Vc.prototype=Object.assign(Object.create(Cc.prototype),{constructor:Vc,type:"cif",_parse:function(){function e(e,q,Y){for(var Z=e;Z<q;++Z)if(r=Y[Z],o=r.trim(),(o||R||N)&&"#"!==o[0])if("data_"===o.substring(0,5));else if(";"===o[0])R?(N?(z===F.length&&(z=0),F[z].push(O),z+=1):U===!1?E[B]=O:E[B][U]=O,R=!1,O=null):(R=!0,O=o.substring(1));else if("loop_"===o)N=!0,k=!0,F.length=0,$.length=0,z=0;else if("_"===o[0]){var K,Q,J;if(N&&!k&&(N=!1),N)K=o.split("."),Q=K[0].substring(1),J=K[1],1===K.length?(J=!1,E[Q]||(E[Q]=[]),F.push(E[Q])):(E[Q]||(E[Q]={}),E[Q][J]?Pv.warn(Q,J,"already exists"):(E[Q][J]=[],F.push(E[Q][J]),$.push(J))),B=Q,U=J,j=!0;else{var tt=o.match(ly),et=tt[0],it=tt[1];K=et.split("."),Q=K[0].substring(1),J=K[1],1===K.length?(J=!1,E[Q]=it):(E[Q]||(E[Q]={}),E[Q][J]?Pv.warn(Q,J,"already exists"):E[Q][J]=it),it||(D=!0),B=Q,U=J}}else if(R)O+=r;else if(N){var nt,rt;if(!o)continue;if("atom_site"===B){nt=$.length,rt=o.split(hy),j&&(a=$.indexOf("auth_asym_id"),s=$.indexOf("auth_seq_id"),c=$.indexOf("label_atom_id"),u=$.indexOf("label_comp_id"),h=$.indexOf("label_asym_id"),l=$.indexOf("label_entity_id"),d=$.indexOf("label_alt_id"),y=$.indexOf("Cartn_x"),b=$.indexOf("Cartn_y"),x=$.indexOf("Cartn_z"),p=$.indexOf("id"),m=$.indexOf("type_symbol"),f=$.indexOf("group_PDB"),w=$.indexOf("B_iso_or_equiv"),g=$.indexOf("pdbx_PDB_model_num"),v=$.indexOf("pdbx_PDB_ins_code"),_=$.indexOf("occupancy"),j=!1,H=parseInt(rt[g]),P&&(i=[],n=0));var ot=parseInt(rt[g]);if(H!==ot&&(P&&(0===X&&T.push(new Float32Array(i)),i=new Float32Array(3*G.count),T.push(i),n=0),X+=1),H=ot,M&&X>0)continue;var at=rt[c].replace(dy,"");if(C&&"CA"!==at)continue;var st=parseFloat(rt[y]),ct=parseFloat(rt[b]),ut=parseFloat(rt[x]);if(P){var ht=3*n;if(i[ht+0]=st,i[ht+1]=ct,i[ht+2]=ut,n+=1,X>0)continue}var lt=rt[u],dt=parseInt(rt[s]),ft=rt[v];ft="?"===ft?"":ft;var pt=rt[a],mt=rt[h],gt="H"===rt[f][0]?1:0,vt=rt[m],yt=parseFloat(rt[w]),bt=parseFloat(rt[_]),xt=rt[d];if(xt="."===xt?"":xt,G.growIfFull(),G.atomTypeId[W]=V.add(at,vt),G.x[W]=st,G.y[W]=ct,G.z[W]=ut,G.serial[W]=parseInt(rt[p]),G.bfactor[W]=isNaN(yt)?0:yt,G.occupancy[W]=isNaN(bt)?0:bt,G.altloc[W]=xt.charCodeAt(0),A.addAtom(X,pt,mt,lt,dt,gt,void 0,ft),t.Debug){var wt=I[mt];void 0!==wt&&wt!==pt&&Pv.warn(wt,pt)}I[mt]=pt;var _t=rt[l];L[_t]||(L[_t]=new Set),L[_t].add(S.chainStore.count-1),W+=1}else{rt=o.match(ly),nt=rt.length,z===F.length&&(z=0);for(var St=0;St<nt;++St)F[z+St].push(rt[St]);z+=nt}k=!1}else if("'"===o[0]&&"'"===o[o.length-1]){var At=o.substring(1,o.length-1);U===!1?E[B]=At:E[B][U]=At}else D?U===!1?E[B]=o:E[B][U]=o:t.Debug&&Pv.log("CifParser._parse: unknown state",o);else R=!1,N=!1,D=!1,F.length=0,z=null,B=null,U=null,j=null,$.length=0}Pv.time("CifParser._parse "+this.name);var i,n,r,o,a,s,c,u,h,l,d,f,p,m,g,v,y,b,x,w,_,S=this.structure,A=this.structureBuilder,M=this.firstModelOnly,P=this.asTrajectory,C=this.cAlphaOnly,T=S.frames,E={},I={},L={},R=!1,O=null,D=!1,N=!1,k=!1,F=[],z=null,B=null,U=null,j=null,$=[],V=S.atomMap,G=S.atomStore;G.resize(this.streamer.data.length/100);var H,W=0,X=0;if(this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)}),E.chem_comp&&E.chem_comp_atom)zc(E,S,A),A.finalize(),S.finalizeAtoms(),S.finalizeBonds(),ia(S);else{var q=Bc(E,S,I);if(Uc(E,S,I),jc(E,S,I),$c(E,S,L),E.struct&&E.struct.title&&(S.title=E.struct.title.trim().replace(fy,"")),E.entry&&E.entry.id&&(S.id=E.entry.id.trim().replace(fy,"")),E.database_PDB_rev){if(E.database_PDB_rev.date){Dc(E.database_PDB_rev,"date");var Y=E.database_PDB_rev.date.filter(Nc);Y.length&&(S.header.releaseDate=Y[Y.length-1])}if(E.database_PDB_rev.date_original){Dc(E.database_PDB_rev,"date_original");var Z=E.database_PDB_rev.date_original.filter(Nc);Z.length&&(S.header.depositionDate=Z[Z.length-1])}}E.reflns&&E.reflns.d_resolution_high?Nc(E.reflns.d_resolution_high)&&(S.header.resolution=parseFloat(E.reflns.d_resolution_high)):E.refine&&E.refine.ls_d_res_high&&Nc(E.refine.ls_d_res_high)&&(S.header.resolution=parseFloat(E.refine.ls_d_res_high)),E.refine&&E.refine.ls_R_factor_R_free&&Nc(E.refine.ls_R_factor_R_free)&&(S.header.rFree=parseFloat(E.refine.ls_R_factor_R_free)),E.refine&&E.refine.ls_R_factor_R_work&&Nc(E.refine.ls_R_factor_R_work)&&(S.header.rWork=parseFloat(E.refine.ls_R_factor_R_work)),E.exptl&&E.exptl.method&&(Dc(E.exptl,"method"),S.header.experimentalMethods=E.exptl.method.map(function(t){return t.replace(fy,"")})),A.finalize(),S.finalizeAtoms(),Zo(S),S.finalizeBonds(),q?qo(S,q):ey(S),ea(S)}t.Debug&&Pv.timeEnd("CifParser._parse "+this.name)}}),Rv.add("cif",Vc),Rv.add("mcif",Vc),Rv.add("mmcif",Vc),Gc.prototype=Object.assign(Object.create(Cc.prototype),{constructor:Gc,type:"sdf",_parse:function(){function e(t,e,a){for(var M=t;M<e;++M){var P=a[M];if("$$$$"===P.substr(0,4)&&(_=-1,++S,A=d.count),3===_&&(f=parseInt(P.substr(0,3)),p=parseInt(P.substr(3,3)),m=4,g=m+f,v=g,y=v+p,o&&(c=0,s=new Float32Array(3*f),u.push(s),S>0&&(h=!0))),_>=m&&_<g){if(r&&S>0)continue;var C=parseFloat(P.substr(0,10)),T=parseFloat(P.substr(10,10)),E=parseFloat(P.substr(20,10));if(o){var I=3*c;if(s[I+0]=C,s[I+1]=T,s[I+2]=E,c+=1,h)continue}var L=P.substr(31,3).trim(),R=L+(w+1);d.growIfFull(),d.atomTypeId[w]=l.add(R,L),d.x[w]=C,d.y[w]=T,d.z[w]=E,d.serial[w]=w,n.addAtom(S,"","","HET",1,1),w+=1}if(_>=v&&_<y){if(r&&S>0)continue;if(o&&S>0)continue;b.index=parseInt(P.substr(0,3))-1+A,x.index=parseInt(P.substr(3,3))-1+A;var O=parseInt(P.substr(6,3));i.bondStore.addBond(b,x,O)}++_}}t.Debug&&Pv.time("SdfParser._parse "+this.name);var i=this.structure,n=this.structureBuilder,r=this.firstModelOnly,o=this.asTrajectory,a=this.streamer.peekLines(2);i.id=a[0].trim(),i.title=a[1].trim();var s,c,u=i.frames,h=!1,l=i.atomMap,d=i.atomStore;d.resize(Math.round(this.streamer.data.length/50));var f,p,m,g,v,y,b=i.getAtomProxy(),x=i.getAtomProxy(),w=0,_=0,S=0,A=0;this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)}),n.finalize(),i.finalizeAtoms(),i.finalizeBonds(),ia(i),t.Debug&&Pv.timeEnd("SdfParser._parse "+this.name)},_postProcess:function(){ia(this.structure)}}),Rv.add("sdf",Gc),Hc.prototype=Object.assign(Object.create(Cc.prototype),{constructor:Hc,type:"mol2",_parse:function(){function e(t,e,M){for(var P,C=t;C<e;++C){var T=M[C].trim();if(""!==T&&"#"!==T[0])if("@"===T[0])"@<TRIPOS>MOLECULE"===T?(y=b,p=0,++g):"@<TRIPOS>ATOM"===T?(y=x,m=d.count,c&&(n=0,i=new Float32Array(3*v),u.push(i),g>0&&(h=!0))):y="@<TRIPOS>BOND"===T?w:0;else if(y===b)0===p?(o.title=T,o.id=T):1===p&&(P=T.split(r),v=parseInt(P[0])),++p;else if(y===x){if(P=T.split(r),s&&g>0)continue;var E=parseFloat(P[2]),I=parseFloat(P[3]),L=parseFloat(P[4]);if(c){var R=3*n;if(i[R+0]=E,i[R+1]=I,i[R+2]=L,n+=1,h)continue}var O=P[0],D=P[1],N=P[5].split(".")[0],k=P[6]?parseInt(P[6]):1,F=P[7]?P[7]:"",z=P[8]?parseFloat(P[8]):0;d.growIfFull(),d.atomTypeId[f]=l.add(D,N),d.x[f]=E,d.y[f]=I,d.z[f]=L,d.serial[f]=O,d.bfactor[f]=z,a.addAtom(g,"","",F,k,1),f+=1}else if(y===w){if(s&&g>0)continue;if(c&&g>0)continue;P=T.split(r),_.index=parseInt(P[1])-1+m,S.index=parseInt(P[2])-1+m;var B=A[P[3]];o.bondStore.addBond(_,S,B)}}}t.Debug&&Pv.time("Mol2Parser._parse "+this.name);var i,n,r=/\s+/,o=this.structure,a=this.structureBuilder,s=this.firstModelOnly,c=this.asTrajectory,u=o.frames,h=!1,l=o.atomMap,d=o.atomStore;d.resize(Math.round(this.streamer.data.length/60));var f=0,p=0,m=0,g=-1,v=0,y=0,b=1,x=2,w=3,_=o.getAtomProxy(),S=o.getAtomProxy(),A={1:1,2:2,3:3,am:1,ar:1,du:1,un:1,nc:0};this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)}),a.finalize(),o.finalizeAtoms(),Yo(o),Jo(o,!0),ta(o,!0),o.finalizeBonds(),ia(o),ey(o),t.Debug&&Pv.timeEnd("Mol2Parser._parse "+this.name)}}),Rv.add("mol2",Hc);var py=["mmtfVersion","mmtfProducer","unitCell","spaceGroup","structureId","title","depositionDate","releaseDate","experimentalMethods","resolution","rFree","rWork","bioAssemblyList","ncsOperatorList","entityList","groupList","numBonds","numAtoms","numGroups","numChains","numModels","groupsPerChain","chainsPerModel"],my=["xCoordList","yCoordList","zCoordList","groupIdList","groupTypeList","chainIdList","bFactorList","atomIdList","altLocList","occupancyList","secStructList","insCodeList","sequenceIndexList","chainNameList","bondAtomList","bondOrderList"],gy=py.concat(my),vy={0:"i".charCodeAt(0),1:"s".charCodeAt(0),2:"h".charCodeAt(0),3:"e".charCodeAt(0),4:"g".charCodeAt(0),5:"b".charCodeAt(0),6:"t".charCodeAt(0),7:"l".charCodeAt(0),"-1":"".charCodeAt(0)};pu.prototype=Object.assign(Object.create(Cc.prototype),{constructor:pu,type:"mmtf",_parse:function(){t.Debug&&Pv.time("MmtfParser._parse "+this.name);var e,i,n,r,o,a=this.structure,s=fu(lu(this.streamer.data)),c=["depositionDate","releaseDate","resolution","rFree","rWork","experimentalMethods"];c.forEach(function(t){void 0!==s[t]&&(a.header[t]=s[t])});var u,h,l,d,f,p;if(a.id=s.structureId,a.title=s.title,this.firstModelOnly||this.asTrajectory){for(f=1,d=s.chainsPerModel[0],l=0,e=0,i=d;e<i;++e)l+=s.groupsPerChain[e];for(h=0,e=0,i=l;e<i;++e)o=s.groupList[s.groupTypeList[e]],h+=o.atomNameList.length;u=s.numBonds,p=[d]}else u=s.numBonds,h=s.numAtoms,l=s.numGroups,d=s.numChains,f=s.numModels,p=s.chainsPerModel;if(u+=l,this.asTrajectory)for(e=0,i=s.numModels;e<i;++e){var m=new Float32Array(3*h),g=h*e;for(n=0;n<h;++n){var v=3*n,y=n+g;m[v]=s.xCoordList[y],m[v+1]=s.yCoordList[y],m[v+2]=s.zCoordList[y]}a.frames.push(m)}var b=new Uint32Array(u),x=new Uint32Array(u),w=new Uint8Array(u),_=new Uint32Array(h),S=new Uint32Array(l),A=new Uint32Array(l),M=new Uint16Array(l),P=new Uint16Array(d),C=new Uint32Array(d),T=new Uint32Array(d),E=new Uint32Array(f),I=new Uint32Array(f),L=0;for(e=0,i=f;e<i;++e){var R=p[e];for(E[e]=L,I[e]=R,n=0;n<R;++n)P[n+L]=e;L+=R}var D=s.groupsPerChain,N=0;for(e=0,i=d;e<i;++e){var k=D[e];for(C[e]=N,T[e]=k,n=0;n<k;++n)S[n+N]=e;N+=k}var F=0,z=0;for(e=0,i=l;e<i;++e){o=s.groupList[s.groupTypeList[e]];var B=o.atomNameList.length,U=o.bondAtomList,j=o.bondOrderList;for(n=0,r=j.length;n<r;++n)b[z]=F+U[2*n],x[z]=F+U[2*n+1],w[z]=j[n],z+=1;for(A[e]=F,M[e]=B,n=0;n<B;++n)_[F]=e,F+=1}var $=s.bondAtomList;if($)for(s.bondOrderList&&w.set(s.bondOrderList,z),e=0,i=$.length;e<i;e+=2){var V=$[e],G=$[e+1];V<h&&G<h&&(b[z]=V,x[z]=G,z+=1)}a.bondStore.length=w.length,a.bondStore.count=z,a.bondStore.atomIndex1=b,a.bondStore.atomIndex2=x,a.bondStore.bondOrder=w,a.atomStore.length=h,a.atomStore.count=h,a.atomStore.residueIndex=_,a.atomStore.atomTypeId=new Uint16Array(h),a.atomStore.x=s.xCoordList.subarray(0,h),a.atomStore.y=s.yCoordList.subarray(0,h),a.atomStore.z=s.zCoordList.subarray(0,h),a.atomStore.serial=s.atomIdList.subarray(0,h),a.atomStore.bfactor=s.bFactorList.subarray(0,h),a.atomStore.altloc=s.altLocList.subarray(0,h),a.atomStore.occupancy=s.occupancyList.subarray(0,h),a.residueStore.length=l,a.residueStore.count=l,a.residueStore.chainIndex=S,a.residueStore.residueTypeId=s.groupTypeList,a.residueStore.atomOffset=A,a.residueStore.atomCount=M,a.residueStore.resno=s.groupIdList.subarray(0,l),a.residueStore.sstruc=s.secStructList.subarray(0,l),a.residueStore.inscode=s.insCodeList.subarray(0,l),a.chainStore.length=d,a.chainStore.count=d,a.chainStore.entityIndex=new Uint16Array(d),a.chainStore.modelIndex=P,a.chainStore.residueOffset=C,a.chainStore.residueCount=T,a.chainStore.chainname=s.chainNameList.subarray(0,4*d),a.chainStore.chainid=s.chainIdList.subarray(0,4*d),a.modelStore.length=f,a.modelStore.count=f,a.modelStore.chainOffset=E,a.modelStore.chainCount=I;var H={};for(e=0,i=s.groupList.length;e<i;++e){var W=s.groupList[e],X=[];for(n=0,r=W.atomNameList.length;n<r;++n){var q=W.elementList[n].toUpperCase(),Y=W.atomNameList[n];X.push(a.atomMap.add(Y,q))}var Z=W.chemCompType.toUpperCase(),K=Pm.includes(Z),Q=W.bondOrderList.length,J=new Array(Q),tt=new Array(Q);for(n=0;n<Q;++n)J[n]=W.bondAtomList[2*n],tt[n]=W.bondAtomList[2*n+1];var et={atomIndices1:J,atomIndices2:tt,bondOrders:W.bondOrderList};H[e]=a.residueMap.add(W.groupName,X,K,Z,et)}for(e=0,i=l;e<i;++e)a.residueStore.residueTypeId[e]=H[a.residueStore.residueTypeId[e]];for(e=0,i=a.atomStore.count;e<i;++e){var it=a.atomStore.residueIndex[e],nt=a.residueMap.list[a.residueStore.residueTypeId[it]],rt=a.residueStore.atomOffset[it];a.atomStore.atomTypeId[e]=nt.atomTypeIdList[e-rt]}if(s.secStructList){var ot=s.secStructList.length;for(e=0,i=a.residueStore.count;e<i;++e){var at=vy[a.residueStore.sstruc[e%ot]];void 0!==at&&(a.residueStore.sstruc[e]=at)}}if(s.entityList&&s.entityList.forEach(function(t,e){a.entityList[e]=new Lc(a,e,t.description,t.type,t.chainIndexList)}),s.bioAssemblyList&&s.bioAssemblyList.forEach(function(t,e){var i=e+1,n=new Wo(i);a.biomolDict["BU"+i]=n;var r={};t.transformList.forEach(function(t){var e=(new O).fromArray(t.matrix).transpose(),i=t.chainIndexList.map(function(t){for(var e="",i=0;i<4;++i){var n=s.chainNameList[4*t+i];if(!n)break;e+=String.fromCharCode(n)}return e}),o=r[i];o?o.matrixList.push(e):r[i]=n.addPart([e],i)})}),s.ncsOperatorList){var st="NCS",ct=new Wo(st),ut=ct.addPart();s.ncsOperatorList.forEach(function(t){var e=(new O).fromArray(t).transpose();ut.matrixList.push(e)}),ut.matrixList.length>0&&(a.biomolDict[st]=ct)}s.unitCell&&Array.isArray(s.unitCell)&&s.unitCell[0]?a.unitcell=new Tc(s.unitCell[0],s.unitCell[1],s.unitCell[2],s.unitCell[3],s.unitCell[4],s.unitCell[5],s.spaceGroup):a.unitcell=void 0,t.Debug&&Pv.timeEnd("MmtfParser._parse "+this.name),ta(a,!0),Jo(a,!0),a.finalizeAtoms(),a.finalizeBonds(),ea(a)}}),Rv.add("mmtf",pu),mu.prototype={constructor:mu,type:"Frames"},gu.prototype=Object.assign(Object.create(Mc.prototype),{constructor:gu,type:"trajectory",__objName:"frames"}),vu.prototype=Object.assign(Object.create(gu.prototype),{constructor:vu,type:"dcd",_parse:function(){t.Debug&&Pv.time("DcdParser._parse "+this.name);var e=this.streamer.data;e instanceof Uint8Array&&(e=e.buffer);var i,n,r=new DataView(e),o=this.frames,a=o.coordinates,s=o.boxes,c={},u=0,h=new Int32Array(e,0,23),l=h[0]!==r.getInt32(0);if(84!==h[0])for(n=e.byteLength,i=0;i<n;i+=4)r.setFloat32(i,r.getFloat32(i),!0);84!==h[0]&&Pv.error("dcd bad format, header block start");var d=String.fromCharCode(r.getUint8(4),r.getUint8(5),r.getUint8(6),r.getUint8(7));"CORD"!==d&&Pv.error("dcd bad format, format string");var f=!1,p=!1,m=!1;0!==h[22]&&(f=!0,0!==h[12]&&(p=!0),1===h[13]&&(m=!0)),c.NSET=h[2],c.ISTART=h[3],c.NSAVC=h[4],c.NAMNF=h[10],f?c.DELTA=r.getFloat32(44,l):c.DELTA=r.getFloat64(44,l),84!==h[22]&&Pv.error("dcd bad format, header block end"),u=u+84+8;var g=r.getInt32(u,l),v=u+1;if((g-4)%80!==0&&Pv.error("dcd bad format, title block start"),c.TITLE=w(new Uint8Array(e,v,g)),r.getInt32(v+g+4-1,l)!==g&&Pv.error("dcd bad format, title block end"),u=u+g+8,4!==r.getInt32(u,l)&&Pv.error("dcd bad format, natom block start"),c.NATOM=r.getInt32(u+4,l),4!==r.getInt32(u+8,l)&&Pv.error("dcd bad format, natom block end"),u=u+4+8,c.NAMNF>0)return void Pv.error("dcd format with fixed atoms unsupported, aborting");var y=c.NATOM,b=4*y;for(i=0,n=c.NSET;i<n;++i){if(p){u+=4;var x=new Float32Array(9);x[0]=r.getFloat64(u,l),x[4]=r.getFloat64(u+16,l),x[8]=r.getFloat64(u+40,l),s.push(x),u+=48,u+=4}for(var _=new Float32Array(3*y),S=0;S<3;++S){r.getInt32(u,l)!==b&&Pv.error("dcd bad format, coord block start",i,S),u+=4;for(var A=new Float32Array(e,u,y),M=0;M<y;++M)_[3*M+S]=A[M];u+=b,r.getInt32(u,l)!==b&&Pv.error("dcd bad format, coord block end",i,S),u+=4}if(a.push(_),m){var P=r.getInt32(u,l);u+=4+P+4}}t.Debug&&Pv.timeEnd("DcdParser._parse "+this.name)}}),Rv.add("dcd",vu),yu.prototype=Object.assign(Object.create(Mc.prototype),{constructor:yu,type:"volume",__objName:"volume",_afterParse:function(){this.volume.setMatrix(this.getMatrix())},getMatrix:function(){return new O}}),bu.prototype=Object.assign(Object.create(yu.prototype),{constructor:bu,type:"mrc",_parse:function(){t.Debug&&Pv.time("MrcParser._parse "+this.name);var e=this.streamer.data;e instanceof Uint8Array&&(e=e.buffer);var i=this.volume,n={},r=new Int32Array(e,0,56),o=new Float32Array(e,0,56),a=new DataView(e);if(n.MAP=String.fromCharCode(a.getUint8(208),a.getUint8(209),a.getUint8(210),a.getUint8(211)),n.MACHST=[a.getUint8(212),a.getUint8(213)],17===n.MACHST[0]&&17===n.MACHST[1])for(var s=e.byteLength,c=0;c<s;c+=4)a.setFloat32(c,a.getFloat32(c),!0);n.NX=r[0],n.NY=r[1],n.NZ=r[2],n.MODE=r[3],n.NXSTART=r[4],n.NYSTART=r[5],n.NZSTART=r[6],n.MX=r[7],n.MY=r[8],n.MZ=r[9],n.xlen=o[10],n.ylen=o[11],n.zlen=o[12],n.alpha=o[13],n.beta=o[14],n.gamma=o[15],n.MAPC=r[16],n.MAPR=r[17],n.MAPS=r[18],n.DMIN=o[19],n.DMAX=o[20],n.DMEAN=o[21],n.ISPG=r[22],n.NSYMBT=r[23],n.LSKFLG=r[24],n.originX=o[49],n.originY=o[50],n.originZ=o[51],n.ARMS=o[54],i.header=n;var u;if(2===n.MODE)u=new Float32Array(e,1024+n.NSYMBT,n.NX*n.NY*n.NZ);else if(0===n.MODE){u=new Float32Array(new Int8Array(e,1024+n.NSYMBT,n.NX*n.NY*n.NZ));var h=1,l=0;if(r[39]===-128&&127===r[40]){h=(n.DMAX-n.DMIN)/255,l=.5*(n.DMIN+n.DMAX+h);for(var d=0,f=u.length;d<f;++d)u[d]=h*u[d]+l}}else console.error("MrcParser unknown mode",n.MODE);i.setData(u,n.NX,n.NY,n.NZ),t.Debug&&Pv.timeEnd("MrcParser._parse "+this.name)},getMatrix:function(){var t=this.volume.header,e=[t.xlen,0,0],i=[t.ylen*Math.cos(Math.PI/180*t.gamma),t.ylen*Math.sin(Math.PI/180*t.gamma),0],n=[t.zlen*Math.cos(Math.PI/180*t.beta),t.zlen*(Math.cos(Math.PI/180*t.alpha)-Math.cos(Math.PI/180*t.gamma)*Math.cos(Math.PI/180*t.beta))/Math.sin(Math.PI/180*t.gamma),0];n[2]=Math.sqrt(t.zlen*t.zlen*Math.sin(Math.PI/180*t.beta)*Math.sin(Math.PI/180*t.beta)-n[1]*n[1]);var r=[0,e,i,n],o=[0,t.MX,t.MY,t.MZ],a=[0,t.MAPC,t.MAPR,t.MAPS],s=new O;return s.set(r[a[1]][0]/o[a[1]],r[a[2]][0]/o[a[2]],r[a[3]][0]/o[a[3]],0,r[a[1]][1]/o[a[1]],r[a[2]][1]/o[a[2]],r[a[3]][1]/o[a[3]],0,r[a[1]][2]/o[a[1]],r[a[2]][2]/o[a[2]],r[a[3]][2]/o[a[3]],0,0,0,0,1),s.setPosition(new N(t.originX,t.originY,t.originZ)),s.multiply((new O).makeTranslation(t.NXSTART,t.NYSTART,t.NZSTART)),s}}),Rv.add("mrc",bu),Rv.add("ccp4",bu),Rv.add("map",bu),xu.prototype=Object.assign(Object.create(yu.prototype),{constructor:xu,type:"cube",_parse:function(){function e(t,e){var i=r[t].trim().split(a)[e];return parseFloat(i)}function i(t,e,i){for(var n=t;n<e;++n){var r=i[n].trim();if(""!==r&&h>=o.atomCount+6+l){r=r.split(a);for(var s=0,d=r.length;s<d;++s)1!==r.length&&(c[u]=parseFloat(r[s]),++u)}++h}}t.Debug&&Pv.time("CubeParser._parse "+this.name);var n=this.volume,r=this.streamer.peekLines(6),o={},a=/\s+/,s=.529177210859;o.atomCount=Math.abs(e(2,0)),o.originX=e(2,1)*s,o.originY=e(2,2)*s,o.originZ=e(2,3)*s,o.NVX=e(3,0),o.NVY=e(4,0),o.NVZ=e(5,0),o.AVX=e(3,1)*s,o.AVY=e(4,2)*s,o.AVZ=e(5,3)*s;var c=new Float32Array(o.NVX*o.NVY*o.NVZ),u=0,h=0,l=e(2,0)>0?0:1;this.streamer.eachChunkOfLines(function(t){i(0,t.length,t)}),n.header=o,n.setData(c,o.NVZ,o.NVY,o.NVX),t.Debug&&Pv.timeEnd("CubeParser._parse "+this.name)},getMatrix:function(){var t=this.volume.header,e=new O;return e.multiply((new O).makeRotationY(Dn(90))),e.multiply((new O).makeTranslation(-t.originZ,t.originY,t.originX)),e.multiply((new O).makeScale(-t.AVZ,t.AVY,t.AVX)),e}}),Rv.add("cub",xu),Rv.add("cube",xu),wu.prototype=Object.assign(Object.create(yu.prototype),{constructor:wu,type:"dx",_parse:function(){function e(t,e,i){for(var n=t;n<e;++n){if(h<c&&l>a){var r=i[n].trim();if(""!==r)for(var o=r.split(s),d=0,f=o.length;d<f;++d)u[h]=parseFloat(o[d]),++h}++l}}t.Debug&&Pv.time("DxParser._parse "+this.name);var i=this.volume,n=this.streamer.peekLines(30),r=this.parseHeaderLines(n),o=this.volume.header,a=r.dataLineStart,s=/\s+/,c=o.nx*o.ny*o.nz,u=new Float32Array(c),h=0,l=0;this.streamer.eachChunkOfLines(function(t){e(0,t.length,t)}),i.setData(u,o.nz,o.ny,o.nx),t.Debug&&Pv.timeEnd("DxParser._parse "+this.name)},parseHeaderLines:function(t){for(var e={},i=/\s+/,n=t.length,r=0,o=0,a=0,s=0;s<n;++s){var c,u=t[s];if(u.startsWith("object 1"))c=u.split(i),e.nx=parseInt(c[5]),e.ny=parseInt(c[6]),e.nz=parseInt(c[7]);else if(u.startsWith("origin"))c=u.split(i),e.xmin=parseFloat(c[1]),e.ymin=parseFloat(c[2]),e.zmin=parseFloat(c[3]);else if(u.startsWith("delta"))c=u.split(i),0===a?e.hx=parseFloat(c[1]):1===a?e.hy=parseFloat(c[2]):2===a&&(e.hz=parseFloat(c[3])),a+=1;else if(u.startsWith("object 3")){r=s,o+=u.length+1;break}o+=u.length+1}return this.volume.header=e,{dataLineStart:r,headerByteCount:o}},getMatrix:function(){var t=this.volume.header,e=new O;return e.multiply((new O).makeRotationY(Dn(90))),e.multiply((new O).makeTranslation(-t.zmin,t.ymin,t.xmin)),e.multiply((new O).makeScale(-t.hz,t.hy,t.hx)),e}}),Rv.add("dx",wu),_u.prototype=Object.assign(Object.create(wu.prototype),{constructor:_u,type:"dxbin",_parse:function(){t.Debug&&Pv.time("DxbinParser._parse "+this.name);var e=this.streamer.data;e instanceof Uint8Array&&(e=e.buffer);for(var i=_(new Uint8Array(e,0,1e3)),n=this.parseHeaderLines(i),r=this.volume.header,o=n.headerByteCount,a=r.nx*r.ny*r.nz,s=new DataView(e),c=new Float32Array(a),u=0;u<a;++u)c[u]=s.getFloat64(8*u+o,!0);this.volume.setData(c,r.nz,r.ny,r.nx),t.Debug&&Pv.timeEnd("DxbinParser._parse "+this.name)}}),Rv.add("dxbin",_u),Su.prototype=Object.assign(Object.create(yu.prototype),{constructor:Su,type:"xplor",_parse:function(){function e(t){return t.trim().split(s).map(parseFloat)}function i(t,e,i){for(var n=t;n<e;++n){var r=i[n];if(v>=c&&(v-c)%y!==0&&g<p)for(var o=0,a=6;o<a;++o)m[g]=parseFloat(r.substr(12*o,12)),++g;++v}}t.Debug&&Pv.time("XplorParser._parse "+this.name);var n,r=this.volume,o=this.streamer.peekLines(8),a={},s=/\s+/;n=o[2].startsWith("REMARKS")?parseInt(o[1].substring(0,8))+2:5;var c=n+3,u=e(o[n]);a.NA=u[0],a.AMIN=u[1],a.AMAX=u[2],a.NB=u[3],a.BMIN=u[4],a.BMAX=u[5],a.NC=u[6],a.CMIN=u[7],a.CMAX=u[8];var h=e(o[n+1]);a.a=h[0],a.b=h[1],a.c=h[2],a.alpha=h[3],a.beta=h[4],a.gamma=h[5];var l=a.AMAX-a.AMIN+1,d=a.BMAX-a.BMIN+1,f=a.CMAX-a.CMIN+1,p=l*d*f,m=new Float32Array(p),g=0,v=0,y=1+l*d/6;this.streamer.eachChunkOfLines(function(t){i(0,t.length,t)}),r.header=a,r.setData(m,l,d,f),t.Debug&&Pv.timeEnd("XplorParser._parse "+this.name)},getMatrix:function(){var t=this.volume.header,e=[t.a,0,0],i=[t.b*Math.cos(Math.PI/180*t.gamma),t.b*Math.sin(Math.PI/180*t.gamma),0],n=[t.c*Math.cos(Math.PI/180*t.beta),t.c*(Math.cos(Math.PI/180*t.alpha)-Math.cos(Math.PI/180*t.gamma)*Math.cos(Math.PI/180*t.beta))/Math.sin(Math.PI/180*t.gamma),0];n[2]=Math.sqrt(t.c*t.c*Math.sin(Math.PI/180*t.beta)*Math.sin(Math.PI/180*t.beta)-n[1]*n[1]);var r=[0,e,i,n],o=[0,t.NA,t.NB,t.NC],a=[0,1,2,3],s=new O;return s.set(r[a[1]][0]/o[a[1]],r[a[2]][0]/o[a[2]],r[a[3]][0]/o[a[3]],0,r[a[1]][1]/o[a[1]],r[a[2]][1]/o[a[2]],r[a[3]][1]/o[a[3]],0,r[a[1]][2]/o[a[1]],r[a[2]][2]/o[a[2]],r[a[3]][2]/o[a[3]],0,0,0,0,1),s.multiply((new O).makeTranslation(t.AMIN,t.BMIN,t.CMIN)),s}}),Rv.add("xplor",Su),Rv.add("cns",Su),Au.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Au,type:"surface",__objName:"surface",_parse:function(){var t=this.loader.parse(this.streamer.asText());this.surface.fromGeometry(t)}}),Mu.prototype={constructor:Mu,setPropertyNameMapping:function(t){this.propertyNameMapping=t},bin2str:function(t){for(var e=new Uint8Array(t),i="",n=0;n<t.byteLength;n++)i+=String.fromCharCode(e[n]);return i},isASCII:function(t){var e=this.parseHeader(this.bin2str(t));return"ascii"===e.format},parse:function(t){return t instanceof ArrayBuffer?this.isASCII(t)?this.parseASCII(this.bin2str(t)):this.parseBinary(t):this.parseASCII(t)},parseHeader:function(t){function e(t,e){var i={type:t[0]};return"list"===i.type?(i.name=t[3],i.countType=t[1],i.itemType=t[2]):i.name=t[1],i.name in e&&(i.name=e[i.name]),i}var i=/ply([\s\S]*)end_header\s/,n="",r=0,o=i.exec(t);null!==o&&(n=o[1],r=o[0].length);for(var a,s,c,u={comments:[],elements:[],headerLength:r},h=n.split("\n"),l=0;l<h.length;l++){var d=h[l];if(d=d.trim(),""!==d)switch(c=d.split(/\s+/),s=c.shift(),d=c.join(" "),s){case"format":u.format=c[0],u.version=c[1];break;case"comment":u.comments.push(d);break;case"element":void 0!==a&&u.elements.push(a),a={},a.name=c[0],a.count=parseInt(c[1]),a.properties=[];break;case"property":a.properties.push(e(c,this.propertyNameMapping));break;default:console.log("unhandled",s,c)}}return void 0!==a&&u.elements.push(a),u},parseASCIINumber:function(t,e){switch(e){case"char":case"uchar":case"short":case"ushort":case"int":case"uint":case"int8":case"uint8":case"int16":case"uint16":case"int32":case"uint32":return parseInt(t);case"float":case"double":case"float32":case"float64":return parseFloat(t)}},parseASCIIElement:function(t,e){for(var i=e.split(/\s+/),n={},r=0;r<t.length;r++)if("list"===t[r].type){for(var o=[],a=this.parseASCIINumber(i.shift(),t[r].countType),s=0;s<a;s++)o.push(this.parseASCIINumber(i.shift(),t[r].itemType));n[t[r].name]=o}else n[t[r].name]=this.parseASCIINumber(i.shift(),t[r].type);return n},parseASCII:function(t){var e,i=new ae,n=this.parseHeader(t),r=/end_header\s([\s\S]*)$/,o="";null!==(e=r.exec(t))&&(o=e[1]);var a=o.split("\n"),s=0,c=0;i.useColor=!1;for(var u=0;u<a.length;u++){var h=a[u];if(h=h.trim(),""!==h){c>=n.elements[s].count&&(s++,c=0);var l=this.parseASCIIElement(n.elements[s].properties,h);this.handleElement(i,n.elements[s].name,l),c++}}return this.postProcess(i)},postProcess:function(t){if(t.useColor){for(var e=0;e<t.faces.length;e++)t.faces[e].vertexColors=[t.colors[t.faces[e].a],t.colors[t.faces[e].b],t.colors[t.faces[e].c]];t.elementsNeedUpdate=!0}return t.computeBoundingSphere(),t},handleElement:function(t,e,i){if("vertex"===e){if(t.vertices.push(new N(i.x,i.y,i.z)),"red"in i&&"green"in i&&"blue"in i){t.useColor=!0;var n=new Ct;n.setRGB(i.red/255,i.green/255,i.blue/255),t.colors.push(n)}}else if("face"===e){var r=i.vertex_indices;3===r.length?t.faces.push(new ee(r[0],r[1],r[2])):4===r.length&&t.faces.push(new ee(r[0],r[1],r[3]),new ee(r[1],r[2],r[3]))}},binaryRead:function(t,e,i,n){switch(i){case"int8":case"char":return[t.getInt8(e),1];case"uint8":case"uchar":return[t.getUint8(e),1];case"int16":case"short":return[t.getInt16(e,n),2];case"uint16":case"ushort":return[t.getUint16(e,n),2];case"int32":case"int":return[t.getInt32(e,n),4];case"uint32":case"uint":return[t.getUint32(e,n),4];case"float32":case"float":return[t.getFloat32(e,n),4];case"float64":case"double":return[t.getFloat64(e,n),8]}},binaryReadElement:function(t,e,i,n){for(var r,o={},a=0,s=0;s<i.length;s++)if("list"===i[s].type){var c=[];r=this.binaryRead(t,e+a,i[s].countType,n);var u=r[0];a+=r[1];for(var h=0;h<u;h++)r=this.binaryRead(t,e+a,i[s].itemType,n),c.push(r[0]),a+=r[1];o[i[s].name]=c}else r=this.binaryRead(t,e+a,i[s].type,n),o[i[s].name]=r[0],a+=r[1];return[o,a]},parseBinary:function(t){for(var e,i=new ae,n=this.parseHeader(this.bin2str(t)),r="binary_little_endian"===n.format,o=new DataView(t,n.headerLength),a=0,s=0;s<n.elements.length;s++)for(var c=0;c<n.elements[s].count;c++){e=this.binaryReadElement(o,a,n.elements[s].properties,r),a+=e[1];var u=e[0];this.handleElement(i,n.elements[s].name,u)}return this.postProcess(i)}},Pu.prototype=Object.assign(Object.create(Au.prototype),{constructor:Pu,type:"ply"}),Rv.add("ply",Pu),Cu.prototype={constructor:Cu,setPath:function(t){this.path=t},_createParserState:function(){var t={objects:[],object:{},vertices:[],normals:[],startObject:function(t,e){return this.object&&this.object.fromDeclaration===!1?(this.object.name=t,void(this.object.fromDeclaration=e!==!1)):(this.object={name:t||"",geometry:{vertices:[],normals:[]},fromDeclaration:e!==!1},void this.objects.push(this.object))},parseVertexIndex:function(t,e){var i=parseInt(t,10);return 3*(i>=0?i-1:i+e/3)},parseNormalIndex:function(t,e){var i=parseInt(t,10);return 3*(i>=0?i-1:i+e/3)},addVertex:function(t,e,i){var n=this.vertices,r=this.object.geometry.vertices;r.push(n[t+0]),r.push(n[t+1]),r.push(n[t+2]),r.push(n[e+0]),r.push(n[e+1]),r.push(n[e+2]),r.push(n[i+0]),r.push(n[i+1]),r.push(n[i+2])},addVertexLine:function(t){var e=this.vertices,i=this.object.geometry.vertices;i.push(e[t+0]),i.push(e[t+1]),i.push(e[t+2])},addNormal:function(t,e,i){var n=this.normals,r=this.object.geometry.normals;
-r.push(n[t+0]),r.push(n[t+1]),r.push(n[t+2]),r.push(n[e+0]),r.push(n[e+1]),r.push(n[e+2]),r.push(n[i+0]),r.push(n[i+1]),r.push(n[i+2])},addFace:function(t,e,i,n,r,o,a,s){var c,u=this.vertices.length,h=this.parseVertexIndex(t,u),l=this.parseVertexIndex(e,u),d=this.parseVertexIndex(i,u);if(void 0===n?this.addVertex(h,l,d):(c=this.parseVertexIndex(n,u),this.addVertex(h,l,c),this.addVertex(l,d,c)),void 0!==r){var f=this.normals.length;h=this.parseNormalIndex(r,f),l=r===o?h:this.parseNormalIndex(o,f),d=r===a?h:this.parseNormalIndex(a,f),void 0===n?this.addNormal(h,l,d):(c=this.parseNormalIndex(s,f),this.addNormal(h,l,c),this.addNormal(l,d,c))}},addLineGeometry:function(t){this.object.geometry.type="Line";for(var e=this.vertices.length,i=0,n=t.length;i<n;i++)this.addVertexLine(this.parseVertexIndex(t[i],e))}};return t.startObject("",!1),t},parse:function(t){var e=this._createParserState();t.indexOf("\r\n")!==-1&&(t=t.replace(/\r\n/g,"\n")),t.indexOf("\\\n")!==-1&&(t=t.replace(/\\\n/g,""));var i,n,r=t.split("\n"),o="",a="",s="",c=0,u=[],h="function"==typeof"".trimLeft;for(i=0,n=r.length;i<n;i++)if(o=r[i],o=h?o.trimLeft():o.trim(),c=o.length,0!==c&&(a=o.charAt(0),"#"!==a))if("v"===a){if(s=o.charAt(1)," "===s&&null!==(u=this.regexp.vertex_pattern.exec(o)))e.vertices.push(parseFloat(u[1]),parseFloat(u[2]),parseFloat(u[3]));else if("n"===s&&null!==(u=this.regexp.normal_pattern.exec(o)))e.normals.push(parseFloat(u[1]),parseFloat(u[2]),parseFloat(u[3]));else if("t"!==s||null===(u=this.regexp.uv_pattern.exec(o)))throw new Error("Unexpected vertex/normal/uv line: '"+o+"'")}else if("f"===a)if(null!==(u=this.regexp.face_vertex_uv_normal.exec(o)))e.addFace(u[1],u[4],u[7],u[10],u[3],u[6],u[9],u[12]);else if(null!==(u=this.regexp.face_vertex_uv.exec(o)));else if(null!==(u=this.regexp.face_vertex_normal.exec(o)))e.addFace(u[1],u[3],u[5],u[7],u[2],u[4],u[6],u[8]);else{if(null===(u=this.regexp.face_vertex.exec(o)))throw new Error("Unexpected face line: '"+o+"'");e.addFace(u[1],u[2],u[3],u[4])}else if("l"===a){var l=o.substring(1).trim().split(" "),d=[],f=[];if(o.indexOf("/")===-1)d=l;else for(var p=0,m=l.length;p<m;p++){var g=l[p].split("/");""!==g[0]&&d.push(g[0]),""!==g[1]&&f.push(g[1])}e.addLineGeometry(d,f)}else if(null!==(u=this.regexp.object_pattern.exec(o))){var v=u[0].substr(1).trim();e.startObject(v)}else if(this.regexp.material_use_pattern.test(o));else if(this.regexp.material_library_pattern.test(o));else if(null===(u=this.regexp.smoothing_pattern.exec(o))){if("\0"===o)continue;throw new Error("Unexpected line: '"+o+"'")}var y=[];for(i=0,n=e.objects.length;i<n;i++){var b=e.objects[i],x=b.geometry;if(0!==x.vertices.length){var w=new ue;w.addAttribute("position",new Kt(new Float32Array(x.vertices),3)),x.normals.length>0?w.addAttribute("normal",new Kt(new Float32Array(x.normals),3)):w.computeVertexNormals(),y.push(w)}}return y}},Tu.prototype=Object.assign(Object.create(Au.prototype),{constructor:Tu,type:"obj"}),Rv.add("obj",Tu),Eu.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Eu,type:"text",__objName:"text",_parse:function(){this.text.data=this.streamer.asText()}}),Rv.add("txt",Eu),Rv.add("text",Eu),Iu.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Iu,type:"csv",__objName:"table",_parse:function(){var t=this.table.data,e=/\s*,\s*/;this.streamer.eachChunkOfLines(function(i,n){for(var r=i.length,o=0;o<r;++o){var a=i[o].trim(),s=a.split(e);0===n&&0===o?this.table.colNames=s:a&&t.push(s)}}.bind(this))}}),Rv.add("csv",Iu),Lu.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Lu,type:"json",__objName:"json",_parse:function(){this.streamer.isBinary()||this.string?this.json.data=JSON.parse(this.streamer.asText()):this.json.data=this.streamer.data}}),Rv.add("json",Lu),Ru.prototype=Object.assign(Object.create(Mc.prototype),{constructor:Ru,type:"xml",__objName:"xml",__xmlParser:function(t){function e(){return{declaration:i(),root:n()}}function i(){var t=s(/^<\?xml\s*/);if(t){for(var e={attributes:{}};!c()&&!u("?>");){var i=o();if(!i)return e;e.attributes[i.name]=i.value}return s(/\?>\s*/),e}}function n(){var t=s(/^<([\w-:.]+)\s*/);if(t){for(var e={name:t[1],attributes:{},children:[]};!(c()||u(">")||u("?>")||u("/>"));){var i=o();if(!i)return e;e.attributes[i.name]=i.value}if(s(/^\s*\/>\s*/))return e;s(/\??>\s*/),e.content=r();for(var a;a=n();)e.children.push(a);return s(/^<\/[\w-:.]+>\s*/),e}}function r(){var t=s(/^([^<]*)/);return t?t[1]:""}function o(){var t=s(/([\w:-]+)\s*=\s*("[^"]*"|'[^']*'|\w+)\s*/);if(t)return{name:t[1],value:a(t[2])}}function a(t){return t.replace(/^['"]|['"]$/g,"")}function s(e){var i=t.match(e);if(i)return t=t.slice(i[0].length),i}function c(){return 0===t.length}function u(e){return 0===t.indexOf(e)}return t=t.trim(),t=t.replace(/<!--[\s\S]*?-->/g,""),e()},__domParser:function(t){var e=new window.DOMParser;return e.parseFromString(t,"text/xml")},_parse:function(){t.Debug&&Pv.time("XmlParser._parse "+this.name),this.useDomParser?this.streamer.isBinary()||this.string?this.xml.data=this.__domParser(this.streamer.asText()):this.xml.data=this.streamer.data:this.xml.data=this.__xmlParser(this.streamer.asText()),t.Debug&&Pv.timeEnd("XmlParser._parse "+this.name)}}),Rv.add("xml",Ru);var yy,by,xy=zu(),wy=30,_y=12,Sy=15,Ay=852,My=592,Py=0,Cy=1,Ty=2,Ey=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],Iy=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],Ly=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],Ry=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64],Oy=0,Dy=1,Ny=2,ky=4,Fy=5,zy=6,By=0,Uy=1,jy=2,$y=-2,Vy=-3,Gy=-4,Hy=-5,Wy=8,Xy=1,qy=2,Yy=3,Zy=4,Ky=5,Qy=6,Jy=7,tb=8,eb=9,ib=10,nb=11,rb=12,ob=13,ab=14,sb=15,cb=16,ub=17,hb=18,lb=19,db=20,fb=21,pb=22,mb=23,gb=24,vb=25,yb=26,bb=27,xb=28,wb=29,_b=30,Sb=31,Ab=32,Mb=852,Pb=592,Cb=!0,Tb=!0,Eb=!0;try{String.fromCharCode.apply(null,[0])}catch(t){Tb=!1}try{String.fromCharCode.apply(null,new Uint8Array(1))}catch(t){Eb=!1}for(var Ib=new Uint8Array(256),Lb=0;Lb<256;Lb++)Ib[Lb]=Lb>=252?6:Lb>=248?5:Lb>=240?4:Lb>=224?3:Lb>=192?2:1;Ib[254]=Ib[254]=1;var Rb=0,Ob=2,Db=4,Nb=0,kb=1,Fb=2,zb=-5,Bb={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"},Ub=Object.prototype.toString;sh.prototype.push=function(t,e){var i,n,r,o,a,s,c=this.strm,u=this.options.chunkSize,h=this.options.dictionary,l=!1;if(this.ended)return!1;n=e===~~e?e:e===!0?Db:Rb,"string"==typeof t?c.input=ih(t):"[object ArrayBuffer]"===Ub.call(t)?c.input=new Uint8Array(t):c.input=t,c.next_in=0,c.avail_in=c.input.length;do{if(0===c.avail_out&&(c.output=new Uint8Array(u),c.next_out=0,c.avail_out=u),i=Zu(c,Rb),i===Fb&&h&&(s="string"==typeof h?th(h):"[object ArrayBuffer]"===Ub.call(h)?new Uint8Array(h):h,i=Ju(this.strm,s)),i===zb&&l===!0&&(i=Nb,l=!1),i!==kb&&i!==Nb)return this.onEnd(i),this.ended=!0,!1;c.next_out&&(0!==c.avail_out&&i!==kb&&(0!==c.avail_in||n!==Db&&n!==Ob)||("string"===this.options.to?(r=rh(c.output,c.next_out),o=c.next_out-r,a=nh(c.output,r),c.next_out=o,c.avail_out=u-o,o&&Nu(c.output,c.output,r,o,0),this.onData(a)):this.onData(Du(c.output,c.next_out)))),0===c.avail_in&&0===c.avail_out&&(l=!0)}while((c.avail_in>0||0===c.avail_out)&&i!==kb);return i===kb&&(n=Db),n===Db?(i=Ku(this.strm),this.onEnd(i),this.ended=!0,i===Nb):n!==Ob||(this.onEnd(Nb),c.avail_out=0,!0)},sh.prototype.onData=function(t){this.chunks.push(t)},sh.prototype.onEnd=function(t){t===Nb&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=ku(this.chunks)),this.chunks=[],this.err=t,this.msg=this.strm.msg},Dv.add("gz",uh);var jb="//files.rcsb.org/download/",$b="//mmtf.rcsb.org/v1.0/",Vb=$b+"full/",Gb=$b+"reduced/";Iv.add("rcsb",new hh);var Hb="//pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/",Wb="/SDF?record_type=3d";Iv.add("pubchem",new lh),Iv.add("ftp",new dh),Iv.add("http",new dh),Iv.add("https",new dh);var Xb="0.10.0-dev.5";"undefined"==typeof window||window.Promise||(window.Promise=n),t.Version=Xb,t.setDebug=ar,t.DatasourceRegistry=Iv,t.StaticDatasource=fh,t.ParserRegistry=Rv,t.autoLoad=gr,t.RepresentationRegistry=Lv,t.ColorMakerRegistry=Ev,t.ColorMaker=Fn,t.Selection=On,t.PdbWriter=xr,t.Stage=ws,t.Collection=vs,t.ComponentCollection=ys,t.RepresentationCollection=bs,t.Assembly=Wo,t.TrajectoryPlayer=_s,t.superpose=As,t.guessElement=iy,t.Queue=Ca,t.Counter=wr,t.throttle=b,t.download=v,t.getQuery=h,t.getDataInfo=mr,t.getFileInfo=y,t.uniqueArray=x,t.BufferRepresentation=es,t.SphereBuffer=Va,t.EllipsoidBuffer=Ha,t.CylinderBuffer=Ya,t.ConeBuffer=Ka,t.ArrowBuffer=Qa,t.Shape=Ja,t.Kdtree=Vo,t.SpatialHash=Lo,t.Signal=Rn,t.Matrix3=Lt,t.Matrix4=O,t.Vector2=I,t.Vector3=N,t.Box3=Et,t.Quaternion=D,t.Plane=Rt,t.Color=Ct,Object.defineProperty(t,"__esModule",{value:!0})});
-
diff --git a/config/plugins/visualizations/openlayers/config/openlayers.xml b/config/plugins/visualizations/openlayers/config/openlayers.xml
index 19b89de75375b815748fba917f9b4fefc3e785a5..2fb0ae6ca4281df26d1946594dde56660fc30594 100644
--- a/config/plugins/visualizations/openlayers/config/openlayers.xml
+++ b/config/plugins/visualizations/openlayers/config/openlayers.xml
@@ -6,14 +6,17 @@
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
             <test test_attr="ext" result_type="datatype">geojson</test>
-           <test test_attr="ext" result_type="datatype">shp</test>
+            <test test_attr="ext" result_type="datatype">shp</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="ol.css"/>
+    <requirements>
+        <requirement type="npm" version="0.0.0" package="@galaxyproject/openlayers"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
         <input>
             <label>Types of geometry</label>
@@ -21,7 +24,7 @@
             <help>Select a geometry type.</help>
             <type>select</type>
             <display>radio</display>
-            <value>circle</value>
+            <value>Circle</value>
             <data>
                 <data>
                     <label>None</label>
diff --git a/config/plugins/visualizations/openlayers/package.json b/config/plugins/visualizations/openlayers/package.json
deleted file mode 100644
index 17f1cb6c590f45df196a569c2a06ede43a930b72..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/openlayers/package.json
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.1.0",
-    "description": "Map visualization using OpenLayers",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "axios": "^0.19.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "file-saver": "^2.0.2",
-        "jquery": "^3.3.1",
-        "jszip": "^3.2.2",
-        "jszip-utils": "^0.1.0",
-        "ol": "^5.3.3",
-        "proj4": "^2.5.0",
-        "shpjs": "^3.4.3",
-        "underscore": "^1.8.3"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static --no-source-maps"
-    },
-    "devDependencies": {
-        "buffer": "^6.0.3",
-        "parcel": "^2.12.0",
-        "process": "^0.11.10",
-        "string_decoder": "^1.3.0"
-    }
-}
diff --git a/config/plugins/visualizations/openlayers/src/script.js b/config/plugins/visualizations/openlayers/src/script.js
deleted file mode 100644
index 90922403fa7f839fa367568fbf1a8afa9aa72e09..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/openlayers/src/script.js
+++ /dev/null
@@ -1,260 +0,0 @@
-import $ from "jquery";
-import _ from "underscore";
-
-import { Map, View, Graticule } from "ol";
-import { OSM, Vector } from "ol/source";
-import { GeoJSON } from "ol/format";
-import * as interaction from "ol/interaction";
-import * as style from "ol/style";
-import * as layer from "ol/layer";
-import * as control from "ol/control";
-import { saveAs } from "file-saver";
-
-import shp from "shpjs";
-import axios from "axios";
-
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
-var MapViewer = (function(mv) {
-    mv.gMap = null;
-
-    /** Set the style properties of shapes */
-    mv.setStyle = selectedColor => {
-        const styles = {
-            Polygon: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            Circle: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            Point: new style.Style({
-                image: new style.Circle({
-                    radius: 5,
-                    fill: new style.Fill({
-                        color: "rgba(0, 0, 255, 0.1)"
-                    }),
-                    stroke: new style.Stroke({ color: selectedColor, width: 1 })
-                })
-            }),
-            LineString: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                })
-            }),
-            MultiLineString: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                })
-            }),
-            MultiPoint: new style.Style({
-                image: new style.Circle({
-                    radius: 5,
-                    fill: new style.Fill({
-                        color: "rgba(0, 0, 255, 0.1)"
-                    }),
-                    stroke: new style.Stroke({ color: selectedColor, width: 1 })
-                })
-            }),
-            MultiPolygon: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            GeometryCollection: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: selectedColor
-                }),
-                image: new style.Circle({
-                    radius: 10,
-                    fill: null,
-                    stroke: new style.Stroke({
-                        color: selectedColor
-                    })
-                })
-            })
-        };
-        return styles;
-    };
-
-    /** Set up events and methods for interactions with map view*/
-    mv.setInteractions = (source, options) => {
-        const geometryType = options.chart.settings.get("geometry_type");
-        const geometryColor = options.chart.settings.get("geometry_color");
-        let drawInteraction;
-
-        const addInteraction = () => {
-            if (geometryType !== "None") {
-                drawInteraction = new interaction.Draw({
-                    source: source,
-                    type: geometryType,
-                    freehand: true
-                });
-                drawInteraction.on("drawstart", event => {
-                    const sty = new style.Style({
-                        stroke: new style.Stroke({
-                            color: geometryColor,
-                            width: 2
-                        }),
-                        fill: new style.Fill({
-                            color: "rgba(0, 0, 255, 0.1)"
-                        })
-                    });
-                    event.feature.setStyle(sty);
-                });
-                mv.gMap.addInteraction(drawInteraction);
-            }
-        };
-        addInteraction();
-    };
-
-    /** Export the map view to PNG image*/
-    mv.exportMap = () => {
-        mv.gMap.once("rendercomplete", event => {
-            const canvas = event.context.canvas;
-            let fileName = Math.random()
-                .toString(11)
-                .replace("0.", "");
-            fileName += ".png";
-            if (navigator.msSaveBlob) {
-                navigator.msSaveBlob(canvas.msToBlob(), fileName);
-            } else {
-                canvas.toBlob(blob => {
-                    saveAs(blob, fileName);
-                });
-            }
-        });
-        mv.gMap.renderSync();
-    };
-
-    /** Create the map view */
-    mv.setMap = (vSource, target, options, styleFunction) => {
-        const tile = new layer.Tile({ source: new OSM() });
-        // add fullscreen handle
-        const fullScreen = new control.FullScreen();
-        // add scale to the map
-        const scaleLineControl = new control.ScaleLine();
-        // create vector with styles
-        const vectorLayer = new layer.Vector({
-            source: vSource,
-            style: styleFunction
-        });
-
-        const view = new View({
-            center: [0, 0],
-            zoom: 2
-        });
-
-        // create map view
-        mv.gMap = new Map({
-            controls: control.defaults().extend([scaleLineControl, fullScreen]),
-            interactions: interaction.defaults().extend([new interaction.DragRotateAndZoom()]),
-            layers: [tile, vectorLayer],
-            target: target,
-            loadTilesWhileInteracting: true,
-            view: view
-        });
-
-        // add grid lines
-        const graticule = new Graticule({
-            strokeStyle: new style.Stroke({
-                color: "rgba(255, 120, 0, 0.9)",
-                width: 2,
-                lineDash: [0.5, 4]
-            }),
-            showLabels: true
-        });
-
-        mv.gMap.addInteraction(new interaction.Modify({ source: vSource }));
-        mv.gMap.addControl(new control.ZoomSlider());
-        graticule.setMap(mv.gMap);
-        mv.setInteractions(vSource, options);
-    };
-
-    /** Load the map GeoJson and Shapefiles*/
-    mv.loadFile = (filePath, fileType, options, chart) => {
-        const target = options.target;
-        const formatType = new GeoJSON();
-        const toExport = options.chart.settings.get("export_map");
-        const geometryColor = options.chart.settings.get("geometry_color");
-        const selectedStyles = mv.setStyle(geometryColor);
-        const styleFunction = feature => {
-            return selectedStyles[feature.getGeometry().getType()];
-        };
-
-        if (toExport === "export") {
-            mv.exportMap();
-        }
-
-        if (fileType === "geojson") {
-            const sourceVec = new Vector({ format: formatType, url: filePath, wrapX: false });
-            mv.createMap(filePath, sourceVec, options, chart, styleFunction, target);
-        } else if (fileType === "shp") {
-            axios.get(filePath, { responseType: "arraybuffer" }).then(shpfile => {
-                console.debug(shpfile);
-                shp(shpfile.data).then(
-                    geojson => {
-                        const url = window.URL.createObjectURL(
-                            new Blob([JSON.stringify(geojson)], { type: "application/json" })
-                        );
-                        const sourceVec = new Vector({ format: formatType, url: url, wrapX: false });
-                        mv.createMap(url, sourceVec, options, chart, styleFunction, target);
-                    },
-                    failure => {
-                        console.debug("FAILURE!", failure);
-                    }
-                );
-            });
-        }
-    };
-
-    mv.createMap = (filePath, sourceVec, options, chart, styleFunction, target) => {
-        mv.setMap(sourceVec, target, options, styleFunction);
-        chart.state("ok", "Chart drawn.");
-        options.process.resolve();
-    };
-
-    return mv;
-})(MapViewer || {});
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    const chart = options.chart;
-    const dataset = options.dataset;
-    const downloadUrl = prefixedDownloadUrl(options.root, dataset.download_url);
-    $.ajax({
-        url: downloadUrl,
-        success: () => {
-            MapViewer.loadFile(downloadUrl, dataset.extension, options, chart);
-        },
-        error: () => {
-            chart.state("failed", "Failed to access dataset.");
-            options.process.resolve();
-        }
-    });
-}
diff --git a/config/plugins/visualizations/openlayers/static/logo.png b/config/plugins/visualizations/openlayers/static/logo.png
deleted file mode 100644
index 29a440ff2bdb266f0857dbf5e5175232d2d55f8a..0000000000000000000000000000000000000000
Binary files a/config/plugins/visualizations/openlayers/static/logo.png and /dev/null differ
diff --git a/config/plugins/visualizations/openlayers/static/logo.svg b/config/plugins/visualizations/openlayers/static/logo.svg
new file mode 100644
index 0000000000000000000000000000000000000000..6295e16b8a358a2696f4677d190633715c949ed9
--- /dev/null
+++ b/config/plugins/visualizations/openlayers/static/logo.svg
@@ -0,0 +1 @@
+<svg width="2471" height="2500" viewBox="0 0 256 259" xmlns="http://www.w3.org/2000/svg" preserveAspectRatio="xMinYMin meet"><path d="M94.029 57.213c18.682-15.559 49.26-15.562 67.945 0l80.016 66.632c18.68 15.561 18.683 41.015-.003 56.577l-80.013 66.63c-18.69 15.564-49.266 15.56-67.945 0l-80.016-66.63c-18.683-15.56-18.683-41.016-.003-56.577l80.019-66.632z" fill="#015965"/><path d="M94.029 35.561c18.682-15.559 49.26-15.562 67.945 0l80.016 66.633c18.68 15.562 18.683 41.017-.003 56.578l-80.013 66.63c-18.69 15.564-49.266 15.56-67.945 0l-80.016-66.63c-18.683-15.56-18.683-41.016-.003-56.578L94.029 35.56z" fill="#E5E5E5"/><path d="M161.974 12.319L241.99 78.95c18.68 15.562 18.683 41.017-.003 56.578l-80.013 66.63c-18.69 15.565-49.266 15.56-67.945 0l-80.016-66.63C-4.67 119.97-4.67 94.513 14.01 78.951l80.019-66.632c18.682-15.56 49.26-15.563 67.945 0z" fill="#35BBCE"/><path d="M244.31 81.1a42.693 42.693 0 0 0-2.3-2.077L161.99 12.33c-18.688-15.577-49.267-15.574-67.952 0L14.011 79.023c-18.681 15.58-18.681 41.058.003 56.634l8.612 7.176C45.142 115.79 121.074 40.853 244.31 81.1z" opacity=".15" fill="#FFF"/></svg>
\ No newline at end of file
diff --git a/config/plugins/visualizations/openlayers/static/ol.css b/config/plugins/visualizations/openlayers/static/ol.css
deleted file mode 100644
index 79d87d00a509d45d67c8900a137c41484c78ac84..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/openlayers/static/ol.css
+++ /dev/null
@@ -1,251 +0,0 @@
-.ol-box {
-  box-sizing: border-box;
-  border-radius: 2px;
-  border: 2px solid blue;
-}
-
-.ol-mouse-position {
-  top: 8px;
-  right: 8px;
-  position: absolute;
-}
-
-.ol-scale-line {
-  background: rgba(0,60,136,0.3);
-  border-radius: 4px;
-  bottom: 8px;
-  left: 8px;
-  padding: 2px;
-  position: absolute;
-}
-.ol-scale-line-inner {
-  border: 1px solid #eee;
-  border-top: none;
-  color: #eee;
-  font-size: 10px;
-  text-align: center;
-  margin: 1px;
-  will-change: contents, width;
-}
-.ol-overlay-container {
-  will-change: left,right,top,bottom;
-}
-
-.ol-unsupported {
-  display: none;
-}
-.ol-viewport, .ol-unselectable {
-  -webkit-touch-callout: none;
-  -webkit-user-select: none;
-  -moz-user-select: none;
-  -ms-user-select: none;
-  user-select: none;
-  -webkit-tap-highlight-color: rgba(0,0,0,0);
-}
-.ol-selectable {
-  -webkit-touch-callout: default;
-  -webkit-user-select: text;
-  -moz-user-select: text;
-  -ms-user-select: text;
-  user-select: text;
-}
-.ol-grabbing {
-  cursor: -webkit-grabbing;
-  cursor: -moz-grabbing;
-  cursor: grabbing;
-}
-.ol-grab {
-  cursor: move;
-  cursor: -webkit-grab;
-  cursor: -moz-grab;
-  cursor: grab;
-}
-.ol-control {
-  position: absolute;
-  background-color: rgba(255,255,255,0.4);
-  border-radius: 4px;
-  padding: 2px;
-}
-.ol-control:hover {
-  background-color: rgba(255,255,255,0.6);
-}
-.ol-zoom {
-  top: .5em;
-  left: .5em;
-}
-.ol-rotate {
-  top: .5em;
-  right: .5em;
-  transition: opacity .25s linear, visibility 0s linear;
-}
-.ol-rotate.ol-hidden {
-  opacity: 0;
-  visibility: hidden;
-  transition: opacity .25s linear, visibility 0s linear .25s;
-}
-.ol-zoom-extent {
-  top: 4.643em;
-  left: .5em;
-}
-.ol-full-screen {
-  right: .5em;
-  top: .5em;
-}
-@media print {
-  .ol-control {
-    display: none;
-  }
-}
-
-.ol-control button {
-  display: block;
-  margin: 1px;
-  padding: 0;
-  color: white;
-  font-size: 1.14em;
-  font-weight: bold;
-  text-decoration: none;
-  text-align: center;
-  height: 1.375em;
-  width: 1.375em;
-  line-height: .4em;
-  background-color: rgba(0,60,136,0.5);
-  border: none;
-  border-radius: 2px;
-}
-.ol-control button::-moz-focus-inner {
-  border: none;
-  padding: 0;
-}
-.ol-zoom-extent button {
-  line-height: 1.4em;
-}
-.ol-compass {
-  display: block;
-  font-weight: normal;
-  font-size: 1.2em;
-  will-change: transform;
-}
-.ol-touch .ol-control button {
-  font-size: 1.5em;
-}
-.ol-touch .ol-zoom-extent {
-  top: 5.5em;
-}
-.ol-control button:hover,
-.ol-control button:focus {
-  text-decoration: none;
-  background-color: rgba(0,60,136,0.7);
-}
-.ol-zoom .ol-zoom-in {
-  border-radius: 2px 2px 0 0;
-}
-.ol-zoom .ol-zoom-out {
-  border-radius: 0 0 2px 2px;
-}
-
-
-.ol-attribution {
-  text-align: right;
-  bottom: .5em;
-  right: .5em;
-  max-width: calc(100% - 1.3em);
-}
-
-.ol-attribution ul {
-  margin: 0;
-  padding: 0 .5em;
-  font-size: .7rem;
-  line-height: 1.375em;
-  color: #000;
-  text-shadow: 0 0 2px #fff;
-}
-.ol-attribution li {
-  display: inline;
-  list-style: none;
-  line-height: inherit;
-}
-.ol-attribution li:not(:last-child):after {
-  content: " ";
-}
-.ol-attribution img {
-  max-height: 2em;
-  max-width: inherit;
-  vertical-align: middle;
-}
-.ol-attribution ul, .ol-attribution button {
-  display: inline-block;
-}
-.ol-attribution.ol-collapsed ul {
-  display: none;
-}
-.ol-attribution:not(.ol-collapsed) {
-  background: rgba(255,255,255,0.8);
-}
-.ol-attribution.ol-uncollapsible {
-  bottom: 0;
-  right: 0;
-  border-radius: 4px 0 0;
-  height: 1.1em;
-  line-height: 1em;
-}
-.ol-attribution.ol-uncollapsible img {
-  margin-top: -.2em;
-  max-height: 1.6em;
-}
-.ol-attribution.ol-uncollapsible button {
-  display: none;
-}
-
-.ol-zoomslider {
-  top: 4.5em;
-  left: .5em;
-  height: 200px;
-}
-.ol-zoomslider button {
-  position: relative;
-  height: 10px;
-}
-
-.ol-touch .ol-zoomslider {
-  top: 5.5em;
-}
-
-.ol-overviewmap {
-  left: 0.5em;
-  bottom: 0.5em;
-}
-.ol-overviewmap.ol-uncollapsible {
-  bottom: 0;
-  left: 0;
-  border-radius: 0 4px 0 0;
-}
-.ol-overviewmap .ol-overviewmap-map,
-.ol-overviewmap button {
-  display: inline-block;
-}
-.ol-overviewmap .ol-overviewmap-map {
-  border: 1px solid #7b98bc;
-  height: 150px;
-  margin: 2px;
-  width: 150px;
-}
-.ol-overviewmap:not(.ol-collapsed) button{
-  bottom: 1px;
-  left: 2px;
-  position: absolute;
-}
-.ol-overviewmap.ol-collapsed .ol-overviewmap-map,
-.ol-overviewmap.ol-uncollapsible button {
-  display: none;
-}
-.ol-overviewmap:not(.ol-collapsed) {
-  background: rgba(255,255,255,0.8);
-}
-.ol-overviewmap-box {
-  border: 2px dotted rgba(0,60,136,0.7);
-}
-
-.ol-overviewmap .ol-overviewmap-box:hover {
-  cursor: move;
-}
diff --git a/config/plugins/visualizations/phylocanvas/package.json b/config/plugins/visualizations/phylocanvas/package.json
index 24d6e23f0fb532b56f6557650ebae57ccf0a7f9c..efee4654d8d62a441ba9efb6172a012459d97487 100644
--- a/config/plugins/visualizations/phylocanvas/package.json
+++ b/config/plugins/visualizations/phylocanvas/package.json
@@ -15,6 +15,7 @@
         "build": "parcel build src/script.js --dist-dir static"
     },
     "devDependencies": {
+        "buffer": "^6.0.3",
         "parcel": "^2.12.0",
         "process": "^0.11.10"
     }
diff --git a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
index 99763daa554fa6025acd44fb63e54feedd515c83..84d14366f62cd444d572121348f306651855aa47 100644
--- a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
+++ b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
@@ -1,18 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
 <visualization name="Tiff Viewer">
-    <description>Basic Tiff Image visualization</description>
+    <description>Tiff Image Viewer</description>
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
-
             <test type="isinstance" test_attr="datatype" result_type="datatype">images.Tiff</test>
-
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="script.css"/>
+    <entry_point entry_point_type="script" src="script.js" css="script.css"/>
 </visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/tiffviewer/src/script.js b/config/plugins/visualizations/tiffviewer/src/script.js
index a16a82253d1acd932983d8e8cc465ef90daeba6f..f97bf19d255abb04e4cd9a4cfcb46959ccf23af4 100644
--- a/config/plugins/visualizations/tiffviewer/src/script.js
+++ b/config/plugins/visualizations/tiffviewer/src/script.js
@@ -8,22 +8,15 @@ const App = (props) => {
     return <TIFFViewer tiff={props.dataset_url} paginate="bottom" />;
 };
 
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
+const { root, visualization_config } = JSON.parse(document.getElementById("app").dataset.incoming);
 
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    const dataset = options.dataset;
-    const url = prefixedDownloadUrl(options.root, dataset.download_url);
-    const root = createRoot(document.getElementById(options.target));
-    root.render(
-        <StrictMode>
-            <App dataset_url={url} />
-        </StrictMode>
-    );
-    options.chart.state("ok", "Done.");
-    options.process.resolve();
-};
+const datasetId = visualization_config.dataset_id;
+
+const url = window.location.origin + root + "api/datasets/" + datasetId + "/display";
+
+const rootElement = createRoot(document.getElementById("app"));
+rootElement.render(
+    <StrictMode>
+        <App dataset_url={url} />
+    </StrictMode>
+);
diff --git a/config/plugins/visualizations/venn/config/venn.xml b/config/plugins/visualizations/venn/config/venn.xml
index a46fa31a9aa068f5b9d432f5901c9d7d0766c71a..1e9140135ea95aeb0cc11b3602944255a915ee4b 100644
--- a/config/plugins/visualizations/venn/config/venn.xml
+++ b/config/plugins/visualizations/venn/config/venn.xml
@@ -13,8 +13,11 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="script.css"/>
-    <groups>
+    <requirements>
+        <requirement type="npm" version="0.0.3" package="@galaxyproject/venn"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <tracks>
         <input>
             <label>Provide a label</label>
             <name>key</name>
@@ -28,5 +31,5 @@
             <type>data_column</type>
             <is_label>true</is_label>
         </input>
-    </groups>
+    </tracks>
 </visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/package.json b/config/plugins/visualizations/venn/package.json
deleted file mode 100644
index 2ed9970cabb54fed2669bc42b50a0c82c97862a6..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/venn/package.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.2.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "@galaxyproject/charts": "^0.1.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "d3": "^3.4.5",
-        "jquery": "^3.1.1",
-        "underscore": "^1.13.1"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "2.11.0"
-    }
-}
diff --git a/config/plugins/visualizations/venn/src/script.js b/config/plugins/visualizations/venn/src/script.js
deleted file mode 100644
index bd24659752c1ce024103eea118cbfe4faf9aaeb3..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/venn/src/script.js
+++ /dev/null
@@ -1,93 +0,0 @@
-import * as Venn from "./venn";
-import * as d3 from "d3";
-import _ from "underscore";
-window.d3 = d3;
-import { request as requestDatasets } from "@galaxyproject/charts/lib/utilities/datasets";
-
-function _combinations( current, remaining, results ) {
-    _.each( remaining, function( value, index ) {
-        var new_current = current.slice();
-        var new_remaining = remaining.slice();
-        new_remaining.splice( 0, index + 1 );
-        new_current.push( value );
-        results.push( new_current );
-        _combinations( new_current, new_remaining, results );
-    });
-};
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    requestDatasets({
-        root            : options.root,
-        chart           : options.chart,
-        dataset_id      : options.chart.get( 'dataset_id' ),
-        dataset_groups  : options.chart.groups,
-        success         : function( result ) {
-            var group_keys   = [];
-            var group_values = [];
-            var all_values   = {};
-            var set_size     = {};
-            var group_ids    = [];
-            _.each( result, function( group, i ) {
-                var group_index = {};
-                _.each( group.values, function( d ) {
-                    all_values[ d.observation ] = group_index[ d.observation ] = true;
-                });
-                group_keys.push( group.key );
-                group_values.push( group_index );
-                group_ids.push( i );
-            });
-            var combos = [];
-            _combinations( [], group_ids, combos );
-            var sets = [];
-            _.each( combos, function( c ) {
-                var size = 0;
-                for ( var value in all_values ) {
-                    var found = 0;
-                    _.each( c, function( group_id ) {
-                        if ( group_values[ group_id ][ value ] ) {
-                            found++;
-                        }
-                    });
-                    if ( found == c.length ) {
-                        size++;
-                    }
-                }
-                if ( size > 0 ) {
-                    var set_labels = [];
-                    _.each( c, function( id ) {
-                        set_labels.push( group_keys[ id ]);
-                    });
-                    sets.push( { sets: set_labels, size: size } );
-                }
-            });
-            $('#' + options.target).append("<svg/>")
-                                   .attr("id", "svg-" + options.target)
-                                   .css("height", "100%")
-                                   .css("width", "100%");
-            var svg = d3.select( '#svg-' + options.target ).datum( sets ).call( Venn.VennDiagram() );
-            var tooltip = null;
-            svg.selectAll( 'g' )
-                .on( 'mouseover', function( d, i ) {
-                    Venn.sortAreas( svg, d );
-                    tooltip = d3.select( 'body' ).append( 'div' ).attr( 'class', 'venntooltip' );
-                    tooltip.transition().duration( 400 ).style( 'opacity', .9 );
-                    tooltip.text(d.size );
-                    var selection = d3.select( this ).transition( 'tooltip' ).duration( 400 );
-                    selection.select( 'path' )
-                                .style( 'stroke-width', 3 )
-                                .style( 'fill-opacity', d.sets.length == 1 ? .4 : .1 )
-                                .style( 'stroke-opacity', 1 );
-                })
-                .on( 'mousemove', function() {
-                    tooltip.style( 'left', ( d3.event.pageX ) + 'px')
-                            .style( 'top', ( d3.event.pageY - 28 ) + 'px');
-                })
-                .on( 'mouseout', function( d, i ) {
-                    tooltip.remove();
-                });
-            options.chart.state( 'ok', 'Venn diagram drawn.' );
-            options.process.resolve();
-        }
-    });
-}
diff --git a/config/plugins/visualizations/venn/src/venn.js b/config/plugins/visualizations/venn/src/venn.js
deleted file mode 100644
index 58a29e784b3f12184c6f905e6b460f4861457456..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/venn/src/venn.js
+++ /dev/null
@@ -1,1789 +0,0 @@
-(function (global, factory) {
-    typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) :
-    typeof define === 'function' && define.amd ? define(['exports'], factory) :
-    factory((global.venn = {}),global.d3,global.d3);
-}(this, function (exports) { 'use strict';
-
-    /** finds the zeros of a function, given two starting points (which must
-     * have opposite signs */
-    function bisect(f, a, b, parameters) {
-        parameters = parameters || {};
-        var maxIterations = parameters.maxIterations || 100,
-            tolerance = parameters.tolerance || 1e-10,
-            fA = f(a),
-            fB = f(b),
-            delta = b - a;
-
-        if (fA * fB > 0) {
-            throw "Initial bisect points must have opposite signs";
-        }
-
-        if (fA === 0) return a;
-        if (fB === 0) return b;
-
-        for (var i = 0; i < maxIterations; ++i) {
-            delta /= 2;
-            var mid = a + delta,
-                fMid = f(mid);
-
-            if (fMid * fA >= 0) {
-                a = mid;
-            }
-
-            if ((Math.abs(delta) < tolerance) || (fMid === 0)) {
-                return mid;
-            }
-        }
-        return a + delta;
-    }
-
-    // need some basic operations on vectors, rather than adding a dependency,
-    // just define here
-    function zeros(x) { var r = new Array(x); for (var i = 0; i < x; ++i) { r[i] = 0; } return r; }
-    function zerosM(x,y) { return zeros(x).map(function() { return zeros(y); }); }
-
-    function dot(a, b) {
-        var ret = 0;
-        for (var i = 0; i < a.length; ++i) {
-            ret += a[i] * b[i];
-        }
-        return ret;
-    }
-
-    function norm2(a)  {
-        return Math.sqrt(dot(a, a));
-    }
-
-    function multiplyBy(a, c) {
-        for (var i = 0; i < a.length; ++i) {
-            a[i] *= c;
-        }
-    }
-
-    function weightedSum(ret, w1, v1, w2, v2) {
-        for (var j = 0; j < ret.length; ++j) {
-            ret[j] = w1 * v1[j] + w2 * v2[j];
-        }
-    }
-
-    /** minimizes a function using the downhill simplex method */
-    function fmin(f, x0, parameters) {
-        parameters = parameters || {};
-
-        var maxIterations = parameters.maxIterations || x0.length * 200,
-            nonZeroDelta = parameters.nonZeroDelta || 1.1,
-            zeroDelta = parameters.zeroDelta || 0.001,
-            minErrorDelta = parameters.minErrorDelta || 1e-6,
-            minTolerance = parameters.minErrorDelta || 1e-5,
-            rho = parameters.rho || 1,
-            chi = parameters.chi || 2,
-            psi = parameters.psi || -0.5,
-            sigma = parameters.sigma || 0.5,
-            callback = parameters.callback,
-            maxDiff,
-            temp;
-
-        // initialize simplex.
-        var N = x0.length,
-            simplex = new Array(N + 1);
-        simplex[0] = x0;
-        simplex[0].fx = f(x0);
-        for (var i = 0; i < N; ++i) {
-            var point = x0.slice();
-            point[i] = point[i] ? point[i] * nonZeroDelta : zeroDelta;
-            simplex[i+1] = point;
-            simplex[i+1].fx = f(point);
-        }
-
-        var sortOrder = function(a, b) { return a.fx - b.fx; };
-
-        var centroid = x0.slice(),
-            reflected = x0.slice(),
-            contracted = x0.slice(),
-            expanded = x0.slice();
-
-        for (var iteration = 0; iteration < maxIterations; ++iteration) {
-            simplex.sort(sortOrder);
-            if (callback) {
-                callback(simplex);
-            }
-
-            maxDiff = 0;
-            for (i = 0; i < N; ++i) {
-                maxDiff = Math.max(maxDiff, Math.abs(simplex[0][i] - simplex[1][i]));
-            }
-
-            if ((Math.abs(simplex[0].fx - simplex[N].fx) < minErrorDelta) &&
-                (maxDiff < minTolerance)) {
-                break;
-            }
-
-            // compute the centroid of all but the worst point in the simplex
-            for (i = 0; i < N; ++i) {
-                centroid[i] = 0;
-                for (var j = 0; j < N; ++j) {
-                    centroid[i] += simplex[j][i];
-                }
-                centroid[i] /= N;
-            }
-
-            // reflect the worst point past the centroid  and compute loss at reflected
-            // point
-            var worst = simplex[N];
-            weightedSum(reflected, 1+rho, centroid, -rho, worst);
-            reflected.fx = f(reflected);
-
-            // if the reflected point is the best seen, then possibly expand
-            if (reflected.fx <= simplex[0].fx) {
-                weightedSum(expanded, 1+chi, centroid, -chi, worst);
-                expanded.fx = f(expanded);
-                if (expanded.fx < reflected.fx) {
-                    temp = simplex[N];
-                    simplex[N] = expanded;
-                    expanded = temp;
-                }  else {
-                    temp = simplex[N];
-                    simplex[N] = reflected;
-                    reflected = temp;
-                }
-            }
-
-            // if the reflected point is worse than the second worst, we need to
-            // contract
-            else if (reflected.fx >= simplex[N-1].fx) {
-                var shouldReduce = false;
-
-                if (reflected.fx > worst.fx) {
-                    // do an inside contraction
-                    weightedSum(contracted, 1+psi, centroid, -psi, worst);
-                    contracted.fx = f(contracted);
-                    if (contracted.fx < worst.fx) {
-                        temp = simplex[N];
-                        simplex[N] = contracted;
-                        contracted = temp;
-                    } else {
-                        shouldReduce = true;
-                    }
-                } else {
-                    // do an outside contraction
-                    weightedSum(contracted, 1-psi * rho, centroid, psi*rho, worst);
-                    contracted.fx = f(contracted);
-                    if (contracted.fx <= reflected.fx) {
-                        temp = simplex[N];
-                        simplex[N] = contracted;
-                        contracted = temp;
-                    } else {
-                        shouldReduce = true;
-                    }
-                }
-
-                if (shouldReduce) {
-                    // do reduction. doesn't actually happen that often
-                    for (i = 1; i < simplex.length; ++i) {
-                        weightedSum(simplex[i], 1 - sigma, simplex[0], sigma, simplex[i]);
-                        simplex[i].fx = f(simplex[i]);
-                    }
-                }
-            } else {
-                temp = simplex[N];
-                simplex[N] = reflected;
-                reflected = temp;
-            }
-
-        }
-
-        simplex.sort(sortOrder);
-        return {f : simplex[0].fx,
-                solution : simplex[0]};
-    }
-
-    function minimizeConjugateGradient(f, initial, params) {
-        // allocate all memory up front here, keep out of the loop for perfomance
-        // reasons
-        var current = {x: initial.slice(), fx: 0, fxprime: initial.slice()},
-            next = {x: initial.slice(), fx: 0, fxprime: initial.slice()},
-            yk = initial.slice(),
-            pk, temp,
-            a = 1,
-            maxIterations;
-
-        params = params || {};
-        maxIterations = params.maxIterations || initial.length * 5;
-
-        current.fx = f(current.x, current.fxprime);
-        pk = current.fxprime.slice();
-        multiplyBy(pk, -1);
-
-        for (var i = 0; i < maxIterations; ++i) {
-            if (params.history) {
-                params.history.push({x: current.x.slice(),
-                                     fx: current.fx,
-                                     fxprime: current.fxprime.slice()});
-            }
-
-            a = wolfeLineSearch(f, pk, current, next, a);
-            if (!a) {
-                // faiiled to find point that satifies wolfe conditions.
-                // reset direction for next iteration
-                for (var j = 0; j < pk.length; ++j) {
-                    pk[j] = -1 * current.fxprime[j];
-                }
-            } else {
-                // update direction using Polak–Ribiere CG method
-                weightedSum(yk, 1, next.fxprime, -1, current.fxprime);
-
-                var delta_k = dot(current.fxprime, current.fxprime),
-                    beta_k = Math.max(0, dot(yk, next.fxprime) / delta_k);
-
-                weightedSum(pk, beta_k, pk, -1, next.fxprime);
-
-                temp = current;
-                current = next;
-                next = temp;
-            }
-
-            if (norm2(current.fxprime) <= 1e-5) {
-                break;
-            }
-        }
-
-        if (params.history) {
-            params.history.push({x: current.x.slice(),
-                                 fx: current.fx,
-                                 fxprime: current.fxprime.slice()});
-        }
-
-        return current;
-    }
-
-    var c1 = 1e-6;
-    var c2 = 0.1;
-    /// searches along line 'pk' for a point that satifies the wolfe conditions
-    /// See 'Numerical Optimization' by Nocedal and Wright p59-60
-    function wolfeLineSearch(f, pk, current, next, a) {
-        var phi0 = current.fx, phiPrime0 = dot(current.fxprime, pk),
-            phi = phi0, phi_old = phi0,
-            phiPrime = phiPrime0,
-            a0 = 0;
-
-        a = a || 1;
-
-        function zoom(a_lo, a_high, phi_lo) {
-            for (var iteration = 0; iteration < 16; ++iteration) {
-                a = (a_lo + a_high)/2;
-                weightedSum(next.x, 1.0, current.x, a, pk);
-                phi = next.fx = f(next.x, next.fxprime);
-                phiPrime = dot(next.fxprime, pk);
-
-                if ((phi > (phi0 + c1 * a * phiPrime0)) ||
-                    (phi >= phi_lo)) {
-                    a_high = a;
-
-                } else  {
-                    if (Math.abs(phiPrime) <= -c2 * phiPrime0) {
-                        return a;
-                    }
-
-                    if (phiPrime * (a_high - a_lo) >=0) {
-                        a_high = a_lo;
-                    }
-
-                    a_lo = a;
-                    phi_lo = phi;
-                }
-            }
-
-            return 0;
-        }
-
-        for (var iteration = 0; iteration < 10; ++iteration) {
-            weightedSum(next.x, 1.0, current.x, a, pk);
-            phi = next.fx = f(next.x, next.fxprime);
-            phiPrime = dot(next.fxprime, pk);
-            if ((phi > (phi0 + c1 * a * phiPrime0)) ||
-                (iteration && (phi >= phi_old))) {
-                return zoom(a0, a, phi_old);
-            }
-
-            if (Math.abs(phiPrime) <= -c2 * phiPrime0) {
-                return a;
-            }
-
-            if (phiPrime >= 0 ) {
-                return zoom(a, a0, phi);
-            }
-
-            phi_old = phi;
-            a0 = a;
-            a *= 2;
-        }
-
-        return 0;
-    }
-
-    var SMALL = 1e-10;
-
-    /** Returns the intersection area of a bunch of circles (where each circle
-     is an object having an x,y and radius property) */
-    function intersectionArea(circles, stats) {
-        // get all the intersection points of the circles
-        var intersectionPoints = getIntersectionPoints(circles);
-
-        // filter out points that aren't included in all the circles
-        var innerPoints = intersectionPoints.filter(function (p) {
-            return containedInCircles(p, circles);
-        });
-
-        var arcArea = 0, polygonArea = 0, arcs = [], i;
-
-        // if we have intersection points that are within all the circles,
-        // then figure out the area contained by them
-        if (innerPoints.length > 1) {
-            // sort the points by angle from the center of the polygon, which lets
-            // us just iterate over points to get the edges
-            var center = getCenter(innerPoints);
-            for (i = 0; i < innerPoints.length; ++i ) {
-                var p = innerPoints[i];
-                p.angle = Math.atan2(p.x - center.x, p.y - center.y);
-            }
-            innerPoints.sort(function(a,b) { return b.angle - a.angle;});
-
-            // iterate over all points, get arc between the points
-            // and update the areas
-            var p2 = innerPoints[innerPoints.length - 1];
-            for (i = 0; i < innerPoints.length; ++i) {
-                var p1 = innerPoints[i];
-
-                // polygon area updates easily ...
-                polygonArea += (p2.x + p1.x) * (p1.y - p2.y);
-
-                // updating the arc area is a little more involved
-                var midPoint = {x : (p1.x + p2.x) / 2,
-                                y : (p1.y + p2.y) / 2},
-                    arc = null;
-
-                for (var j = 0; j < p1.parentIndex.length; ++j) {
-                    if (p2.parentIndex.indexOf(p1.parentIndex[j]) > -1) {
-                        // figure out the angle halfway between the two points
-                        // on the current circle
-                        var circle = circles[p1.parentIndex[j]],
-                            a1 = Math.atan2(p1.x - circle.x, p1.y - circle.y),
-                            a2 = Math.atan2(p2.x - circle.x, p2.y - circle.y);
-
-                        var angleDiff = (a2 - a1);
-                        if (angleDiff < 0) {
-                            angleDiff += 2*Math.PI;
-                        }
-
-                        // and use that angle to figure out the width of the
-                        // arc
-                        var a = a2 - angleDiff/2,
-                            width = distance(midPoint, {
-                                x : circle.x + circle.radius * Math.sin(a),
-                                y : circle.y + circle.radius * Math.cos(a)
-                            });
-
-                        // pick the circle whose arc has the smallest width
-                        if ((arc === null) || (arc.width > width)) {
-                            arc = { circle : circle,
-                                    width : width,
-                                    p1 : p1,
-                                    p2 : p2};
-                        }
-                    }
-                }
-
-                if (arc !== null) {
-                    arcs.push(arc);
-                    arcArea += circleArea(arc.circle.radius, arc.width);
-                    p2 = p1;
-                }
-            }
-        } else {
-            // no intersection points, is either disjoint - or is completely
-            // overlapped. figure out which by examining the smallest circle
-            var smallest = circles[0];
-            for (i = 1; i < circles.length; ++i) {
-                if (circles[i].radius < smallest.radius) {
-                    smallest = circles[i];
-                }
-            }
-
-            // make sure the smallest circle is completely contained in all
-            // the other circles
-            var disjoint = false;
-            for (i = 0; i < circles.length; ++i) {
-                if (distance(circles[i], smallest) > Math.abs(smallest.radius - circles[i].radius)) {
-                    disjoint = true;
-                    break;
-                }
-            }
-
-            if (disjoint) {
-                arcArea = polygonArea = 0;
-
-            } else {
-                arcArea = smallest.radius * smallest.radius * Math.PI;
-                arcs.push({circle : smallest,
-                           p1: { x: smallest.x,        y : smallest.y + smallest.radius},
-                           p2: { x: smallest.x - SMALL, y : smallest.y + smallest.radius},
-                           width : smallest.radius * 2 });
-            }
-        }
-
-        polygonArea /= 2;
-        if (stats) {
-            stats.area = arcArea + polygonArea;
-            stats.arcArea = arcArea;
-            stats.polygonArea = polygonArea;
-            stats.arcs = arcs;
-            stats.innerPoints = innerPoints;
-            stats.intersectionPoints = intersectionPoints;
-        }
-
-        return arcArea + polygonArea;
-    }
-
-    /** returns whether a point is contained by all of a list of circles */
-    function containedInCircles(point, circles) {
-        for (var i = 0; i < circles.length; ++i) {
-            if (distance(point, circles[i]) > circles[i].radius + SMALL) {
-                return false;
-            }
-        }
-        return true;
-    }
-
-    /** Gets all intersection points between a bunch of circles */
-    function getIntersectionPoints(circles) {
-        var ret = [];
-        for (var i = 0; i < circles.length; ++i) {
-            for (var j = i + 1; j < circles.length; ++j) {
-                var intersect = circleCircleIntersection(circles[i],
-                                                              circles[j]);
-                for (var k = 0; k < intersect.length; ++k) {
-                    var p = intersect[k];
-                    p.parentIndex = [i,j];
-                    ret.push(p);
-                }
-            }
-        }
-        return ret;
-    }
-
-    function circleIntegral(r, x) {
-        var y = Math.sqrt(r * r - x * x);
-        return x * y + r * r * Math.atan2(x, y);
-    }
-
-    /** Returns the area of a circle of radius r - up to width */
-    function circleArea(r, width) {
-        return circleIntegral(r, width - r) - circleIntegral(r, -r);
-    }
-
-    /** euclidean distance between two points */
-    function distance(p1, p2) {
-        return Math.sqrt((p1.x - p2.x) * (p1.x - p2.x) +
-                         (p1.y - p2.y) * (p1.y - p2.y));
-    }
-
-
-    /** Returns the overlap area of two circles of radius r1 and r2 - that
-    have their centers separated by distance d. Simpler faster
-    circle intersection for only two circles */
-    function circleOverlap(r1, r2, d) {
-        // no overlap
-        if (d >= r1 + r2) {
-            return 0;
-        }
-
-        // completely overlapped
-        if (d <= Math.abs(r1 - r2)) {
-            return Math.PI * Math.min(r1, r2) * Math.min(r1, r2);
-        }
-
-        var w1 = r1 - (d * d - r2 * r2 + r1 * r1) / (2 * d),
-            w2 = r2 - (d * d - r1 * r1 + r2 * r2) / (2 * d);
-        return circleArea(r1, w1) + circleArea(r2, w2);
-    }
-
-    /** Given two circles (containing a x/y/radius attributes),
-    returns the intersecting points if possible.
-    note: doesn't handle cases where there are infinitely many
-    intersection points (circles are equivalent):, or only one intersection point*/
-    function circleCircleIntersection(p1, p2) {
-        var d = distance(p1, p2),
-            r1 = p1.radius,
-            r2 = p2.radius;
-
-        // if to far away, or self contained - can't be done
-        if ((d >= (r1 + r2)) || (d <= Math.abs(r1 - r2))) {
-            return [];
-        }
-
-        var a = (r1 * r1 - r2 * r2 + d * d) / (2 * d),
-            h = Math.sqrt(r1 * r1 - a * a),
-            x0 = p1.x + a * (p2.x - p1.x) / d,
-            y0 = p1.y + a * (p2.y - p1.y) / d,
-            rx = -(p2.y - p1.y) * (h / d),
-            ry = -(p2.x - p1.x) * (h / d);
-
-        return [{x: x0 + rx, y : y0 - ry },
-                {x: x0 - rx, y : y0 + ry }];
-    }
-
-    /** Returns the center of a bunch of points */
-    function getCenter(points) {
-        var center = {x: 0, y: 0};
-        for (var i =0; i < points.length; ++i ) {
-            center.x += points[i].x;
-            center.y += points[i].y;
-        }
-        center.x /= points.length;
-        center.y /= points.length;
-        return center;
-    }
-
-    /** given a list of set objects, and their corresponding overlaps.
-    updates the (x, y, radius) attribute on each set such that their positions
-    roughly correspond to the desired overlaps */
-    function venn(areas, parameters) {
-        parameters = parameters || {};
-        parameters.maxIterations = parameters.maxIterations || 500;
-        var initialLayout = parameters.initialLayout || bestInitialLayout;
-
-        // add in missing pairwise areas as having 0 size
-        areas = addMissingAreas(areas);
-
-        // initial layout is done greedily
-        var circles = initialLayout(areas);
-
-        // transform x/y coordinates to a vector to optimize
-        var initial = [], setids = [], setid;
-        for (setid in circles) {
-            if (circles.hasOwnProperty(setid)) {
-                initial.push(circles[setid].x);
-                initial.push(circles[setid].y);
-                setids.push(setid);
-            }
-        }
-
-        // optimize initial layout from our loss function
-        var totalFunctionCalls = 0;
-        var solution = fmin(
-            function(values) {
-                totalFunctionCalls += 1;
-                var current = {};
-                for (var i = 0; i < setids.length; ++i) {
-                    var setid = setids[i];
-                    current[setid] = {x: values[2 * i],
-                                      y: values[2 * i + 1],
-                                      radius : circles[setid].radius,
-                                     // size : circles[setid].size
-                                     };
-                }
-                return lossFunction(current, areas);
-            },
-            initial,
-            parameters);
-
-        // transform solution vector back to x/y points
-        var positions = solution.solution;
-        for (var i = 0; i < setids.length; ++i) {
-            setid = setids[i];
-            circles[setid].x = positions[2 * i];
-            circles[setid].y = positions[2 * i + 1];
-        }
-
-        return circles;
-    }
-
-    var SMALL$1 = 1e-10;
-
-    /** Returns the distance necessary for two circles of radius r1 + r2 to
-    have the overlap area 'overlap' */
-    function distanceFromIntersectArea(r1, r2, overlap) {
-        // handle complete overlapped circles
-        if (Math.min(r1, r2) * Math.min(r1,r2) * Math.PI <= overlap + SMALL$1) {
-            return Math.abs(r1 - r2);
-        }
-
-        return bisect(function(distance) {
-            return circleOverlap(r1, r2, distance) - overlap;
-        }, 0, r1 + r2);
-    }
-
-    /** Missing pair-wise intersection area data can cause problems:
-     treating as an unknown means that sets will be laid out overlapping,
-     which isn't what people expect. To reflect that we want disjoint sets
-     here, set the overlap to 0 for all missing pairwise set intersections */
-    function addMissingAreas(areas) {
-        areas = areas.slice();
-
-        // two circle intersections that aren't defined
-        var ids = [], pairs = {}, i, j, a, b;
-        for (i = 0; i < areas.length; ++i) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                ids.push(area.sets[0]);
-            } else if (area.sets.length == 2) {
-                a = area.sets[0];
-                b = area.sets[1];
-                pairs[[a, b]] = true;
-                pairs[[b, a]] = true;
-            }
-        }
-        ids.sort(function(a, b) { return a > b; });
-
-        for (i = 0; i < ids.length; ++i) {
-            a = ids[i];
-            for (j = i + 1; j < ids.length; ++j) {
-                b = ids[j];
-                if (!([a, b] in pairs)) {
-                    areas.push({'sets': [a, b],
-                                'size': 0});
-                }
-            }
-        }
-        return areas;
-    }
-
-    /// Returns two matrices, one of the euclidean distances between the sets
-    /// and the other indicating if there are subset or disjoint set relationships
-    function getDistanceMatrices(areas, sets, setids) {
-        // initialize an empty distance matrix between all the points
-        var distances = zerosM(sets.length, sets.length),
-            constraints = zerosM(sets.length, sets.length);
-
-        // compute required distances between all the sets such that
-        // the areas match
-        areas.filter(function(x) { return x.sets.length == 2; })
-            .map(function(current) {
-            var left = setids[current.sets[0]],
-                right = setids[current.sets[1]],
-                r1 = Math.sqrt(sets[left].size / Math.PI),
-                r2 = Math.sqrt(sets[right].size / Math.PI),
-                distance = distanceFromIntersectArea(r1, r2, current.size);
-
-            distances[left][right] = distances[right][left] = distance;
-
-            // also update constraints to indicate if its a subset or disjoint
-            // relationship
-            var c = 0;
-            if (current.size + 1e-10 >= Math.min(sets[left].size,
-                                                 sets[right].size)) {
-                c = 1;
-            } else if (current.size <= 1e-10) {
-                c = -1;
-            }
-            constraints[left][right] = constraints[right][left] = c;
-        });
-
-        return {distances: distances, constraints: constraints};
-    }
-
-    /// computes the gradient and loss simulatenously for our constrained MDS optimizer
-    function constrainedMDSGradient(x, fxprime, distances, constraints) {
-        var loss = 0, i;
-        for (i = 0; i < fxprime.length; ++i) {
-            fxprime[i] = 0;
-        }
-
-        for (i = 0; i < distances.length; ++i) {
-            var xi = x[2 * i], yi = x[2 * i + 1];
-            for (var j = i + 1; j < distances.length; ++j) {
-                var xj = x[2 * j], yj = x[2 * j + 1],
-                    dij = distances[i][j],
-                    constraint = constraints[i][j];
-
-                var squaredDistance = (xj - xi) * (xj - xi) + (yj - yi) * (yj - yi),
-                    distance = Math.sqrt(squaredDistance),
-                    delta = squaredDistance - dij * dij;
-
-                if (((constraint > 0) && (distance <= dij)) ||
-                    ((constraint < 0) && (distance >= dij))) {
-                    continue;
-                }
-
-                loss += 2 * delta * delta;
-
-                fxprime[2*i]     += 4 * delta * (xi - xj);
-                fxprime[2*i + 1] += 4 * delta * (yi - yj);
-
-                fxprime[2*j]     += 4 * delta * (xj - xi);
-                fxprime[2*j + 1] += 4 * delta * (yj - yi);
-            }
-        }
-        return loss;
-    }
-
-    /// takes the best working variant of either constrained MDS or greedy
-    function bestInitialLayout(areas, params) {
-        var initial = greedyLayout(areas, params);
-
-        // greedylayout is sufficient for all 2/3 circle cases. try out
-        // constrained MDS for higher order problems, take its output
-        // if it outperforms. (greedy is aesthetically better on 2/3 circles
-        // since it axis aligns)
-        if (areas.length >= 8) {
-            var constrained  = constrainedMDSLayout(areas, params),
-                constrainedLoss = lossFunction(constrained, areas),
-                greedyLoss = lossFunction(initial, areas);
-
-            if (constrainedLoss + 1e-8 < greedyLoss) {
-                initial = constrained;
-            }
-        }
-        return initial;
-    }
-
-    /// use the constrained MDS variant to generate an initial layout
-    function constrainedMDSLayout(areas, params) {
-        params = params || {};
-        var restarts = params.restarts || 10;
-
-        // bidirectionally map sets to a rowid  (so we can create a matrix)
-        var sets = [], setids = {}, i;
-        for (i = 0; i < areas.length; ++i ) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                setids[area.sets[0]] = sets.length;
-                sets.push(area);
-            }
-        }
-
-        var matrices = getDistanceMatrices(areas, sets, setids),
-            distances = matrices.distances,
-            constraints = matrices.constraints;
-
-        // keep distances bounded, things get messed up otherwise.
-        // TODO: proper preconditioner?
-        var norm = norm2(distances.map(norm2))/(distances.length);
-        distances = distances.map(function (row) {
-            return row.map(function (value) { return value / norm; });});
-
-        var obj = function(x, fxprime) {
-            return constrainedMDSGradient(x, fxprime, distances, constraints);
-        };
-
-        var best, current;
-        for (i = 0; i < restarts; ++i) {
-            var initial = zeros(distances.length*2).map(Math.random);
-
-            current = minimizeConjugateGradient(obj, initial, params);
-            if (!best || (current.fx < best.fx)) {
-                best = current;
-            }
-        }
-        var positions = best.x;
-
-        // translate rows back to (x,y,radius) coordinates
-        var circles = {};
-        for (i = 0; i < sets.length; ++i) {
-            var set = sets[i];
-            circles[set.sets[0]] = {
-                x: positions[2*i] * norm,
-                y: positions[2*i + 1] * norm,
-                radius:  Math.sqrt(set.size / Math.PI)
-            };
-        }
-
-        if (params.history) {
-            for (i = 0; i < params.history.length; ++i) {
-                multiplyBy(params.history[i].x, norm);
-            }
-        }
-        return circles;
-    }
-
-    /** Lays out a Venn diagram greedily, going from most overlapped sets to
-    least overlapped, attempting to position each new set such that the
-    overlapping areas to already positioned sets are basically right */
-    function greedyLayout(areas) {
-        // define a circle for each set
-        var circles = {}, setOverlaps = {}, set;
-        for (var i = 0; i < areas.length; ++i) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                set = area.sets[0];
-                circles[set] = {x: 1e10, y: 1e10,
-                                rowid: circles.length,
-                                size: area.size,
-                                radius: Math.sqrt(area.size / Math.PI)};
-                setOverlaps[set] = [];
-            }
-        }
-        areas = areas.filter(function(a) { return a.sets.length == 2; });
-
-        // map each set to a list of all the other sets that overlap it
-        for (i = 0; i < areas.length; ++i) {
-            var current = areas[i];
-            var weight = current.hasOwnProperty('weight') ? current.weight : 1.0;
-            var left = current.sets[0], right = current.sets[1];
-
-            // completely overlapped circles shouldn't be positioned early here
-            if (current.size + SMALL$1 >= Math.min(circles[left].size,
-                                                 circles[right].size)) {
-                weight = 0;
-            }
-
-            setOverlaps[left].push ({set:right, size:current.size, weight:weight});
-            setOverlaps[right].push({set:left,  size:current.size, weight:weight});
-        }
-
-        // get list of most overlapped sets
-        var mostOverlapped = [];
-        for (set in setOverlaps) {
-            if (setOverlaps.hasOwnProperty(set)) {
-                var size = 0;
-                for (i = 0; i < setOverlaps[set].length; ++i) {
-                    size += setOverlaps[set][i].size * setOverlaps[set][i].weight;
-                }
-
-                mostOverlapped.push({set: set, size:size});
-            }
-        }
-
-        // sort by size desc
-        function sortOrder(a,b) {
-            return b.size - a.size;
-        }
-        mostOverlapped.sort(sortOrder);
-
-        // keep track of what sets have been laid out
-        var positioned = {};
-        function isPositioned(element) {
-            return element.set in positioned;
-        }
-
-        // adds a point to the output
-        function positionSet(point, index) {
-            circles[index].x = point.x;
-            circles[index].y = point.y;
-            positioned[index] = true;
-        }
-
-        // add most overlapped set at (0,0)
-        positionSet({x: 0, y: 0}, mostOverlapped[0].set);
-
-        // get distances between all points. TODO, necessary?
-        // answer: probably not
-        // var distances = venn.getDistanceMatrices(circles, areas).distances;
-        for (i = 1; i < mostOverlapped.length; ++i) {
-            var setIndex = mostOverlapped[i].set,
-                overlap = setOverlaps[setIndex].filter(isPositioned);
-            set = circles[setIndex];
-            overlap.sort(sortOrder);
-
-            if (overlap.length === 0) {
-                // this shouldn't happen anymore with addMissingAreas
-                throw "ERROR: missing pairwise overlap information";
-            }
-
-            var points = [];
-            for (var j = 0; j < overlap.length; ++j) {
-                // get appropriate distance from most overlapped already added set
-                var p1 = circles[overlap[j].set],
-                    d1 = distanceFromIntersectArea(set.radius, p1.radius,
-                                                   overlap[j].size);
-
-                // sample positions at 90 degrees for maximum aesthetics
-                points.push({x : p1.x + d1, y : p1.y});
-                points.push({x : p1.x - d1, y : p1.y});
-                points.push({y : p1.y + d1, x : p1.x});
-                points.push({y : p1.y - d1, x : p1.x});
-
-                // if we have at least 2 overlaps, then figure out where the
-                // set should be positioned analytically and try those too
-                for (var k = j + 1; k < overlap.length; ++k) {
-                    var p2 = circles[overlap[k].set],
-                        d2 = distanceFromIntersectArea(set.radius, p2.radius,
-                                                       overlap[k].size);
-
-                    var extraPoints = circleCircleIntersection(
-                        { x: p1.x, y: p1.y, radius: d1},
-                        { x: p2.x, y: p2.y, radius: d2});
-
-                    for (var l = 0; l < extraPoints.length; ++l) {
-                        points.push(extraPoints[l]);
-                    }
-                }
-            }
-
-            // we have some candidate positions for the set, examine loss
-            // at each position to figure out where to put it at
-            var bestLoss = 1e50, bestPoint = points[0];
-            for (j = 0; j < points.length; ++j) {
-                circles[setIndex].x = points[j].x;
-                circles[setIndex].y = points[j].y;
-                var loss = lossFunction(circles, areas);
-                if (loss < bestLoss) {
-                    bestLoss = loss;
-                    bestPoint = points[j];
-                }
-            }
-
-            positionSet(bestPoint, setIndex);
-        }
-
-        return circles;
-    }
-
-    /** Given a bunch of sets, and the desired overlaps between these sets - computes
-    the distance from the actual overlaps to the desired overlaps. Note that
-    this method ignores overlaps of more than 2 circles */
-    function lossFunction(sets, overlaps) {
-        var output = 0;
-
-        function getCircles(indices) {
-            return indices.map(function(i) { return sets[i]; });
-        }
-
-        for (var i = 0; i < overlaps.length; ++i) {
-            var area = overlaps[i], overlap;
-            if (area.sets.length == 1) {
-                continue;
-            } else if (area.sets.length == 2) {
-                var left = sets[area.sets[0]],
-                    right = sets[area.sets[1]];
-                overlap = circleOverlap(left.radius, right.radius,
-                                        distance(left, right));
-            } else {
-                overlap = intersectionArea(getCircles(area.sets));
-            }
-
-            var weight = area.hasOwnProperty('weight') ? area.weight : 1.0;
-            output += weight * (overlap - area.size) * (overlap - area.size);
-        }
-
-        return output;
-    }
-
-    // orientates a bunch of circles to point in orientation
-    function orientateCircles(circles, orientation, orientationOrder) {
-        if (orientationOrder === null) {
-            circles.sort(function (a, b) { return b.radius - a.radius; });
-        } else {
-            circles.sort(orientationOrder);
-        }
-
-        var i;
-        // shift circles so largest circle is at (0, 0)
-        if (circles.length > 0) {
-            var largestX = circles[0].x,
-                largestY = circles[0].y;
-
-            for (i = 0; i < circles.length; ++i) {
-                circles[i].x -= largestX;
-                circles[i].y -= largestY;
-            }
-        }
-
-        // rotate circles so that second largest is at an angle of 'orientation'
-        // from largest
-        if (circles.length > 1) {
-            var rotation = Math.atan2(circles[1].x, circles[1].y) - orientation,
-                c = Math.cos(rotation),
-                s = Math.sin(rotation), x, y;
-
-            for (i = 0; i < circles.length; ++i) {
-                x = circles[i].x;
-                y = circles[i].y;
-                circles[i].x = c * x - s * y;
-                circles[i].y = s * x + c * y;
-            }
-        }
-
-        // mirror solution if third solution is above plane specified by
-        // first two circles
-        if (circles.length > 2) {
-            var angle = Math.atan2(circles[2].x, circles[2].y) - orientation;
-            while (angle < 0) { angle += 2* Math.PI; }
-            while (angle > 2*Math.PI) { angle -= 2* Math.PI; }
-            if (angle > Math.PI) {
-                var slope = circles[1].y / (1e-10 + circles[1].x);
-                for (i = 0; i < circles.length; ++i) {
-                    var d = (circles[i].x + slope * circles[i].y) / (1 + slope*slope);
-                    circles[i].x = 2 * d - circles[i].x;
-                    circles[i].y = 2 * d * slope - circles[i].y;
-                }
-            }
-        }
-    }
-
-    function disjointCluster(circles) {
-        // union-find clustering to get disjoint sets
-        circles.map(function(circle) { circle.parent = circle; });
-
-        // path compression step in union find
-        function find(circle) {
-            if (circle.parent !== circle) {
-                circle.parent = find(circle.parent);
-            }
-            return circle.parent;
-        }
-
-        function union(x, y) {
-            var xRoot = find(x), yRoot = find(y);
-            xRoot.parent = yRoot;
-        }
-
-        // get the union of all overlapping sets
-        for (var i = 0; i < circles.length; ++i) {
-            for (var j = i + 1; j < circles.length; ++j) {
-                var maxDistance = circles[i].radius + circles[j].radius;
-                if (distance(circles[i], circles[j]) + 1e-10 < maxDistance) {
-                    union(circles[j], circles[i]);
-                }
-            }
-        }
-
-        // find all the disjoint clusters and group them together
-        var disjointClusters = {}, setid;
-        for (i = 0; i < circles.length; ++i) {
-            setid = find(circles[i]).parent.setid;
-            if (!(setid in disjointClusters)) {
-                disjointClusters[setid] = [];
-            }
-            disjointClusters[setid].push(circles[i]);
-        }
-
-        // cleanup bookkeeping
-        circles.map(function(circle) { delete circle.parent; });
-
-        // return in more usable form
-        var ret = [];
-        for (setid in disjointClusters) {
-            if (disjointClusters.hasOwnProperty(setid)) {
-                ret.push(disjointClusters[setid]);
-            }
-        }
-        return ret;
-    }
-
-    function getBoundingBox(circles) {
-        var minMax = function(d) {
-            var hi = Math.max.apply(null, circles.map(
-                                    function(c) { return c[d] + c.radius; } )),
-                lo = Math.min.apply(null, circles.map(
-                                    function(c) { return c[d] - c.radius;} ));
-            return {max:hi, min:lo};
-        };
-
-        return {xRange: minMax('x'), yRange: minMax('y')};
-    }
-
-    function normalizeSolution(solution, orientation, orientationOrder) {
-        if (orientation === null){
-            orientation = Math.PI/2;
-        }
-
-        // work with a list instead of a dictionary, and take a copy so we
-        // don't mutate input
-        var circles = [], i, setid;
-        for (setid in solution) {
-            if (solution.hasOwnProperty(setid)) {
-                var previous = solution[setid];
-                circles.push({x: previous.x,
-                              y: previous.y,
-                              radius: previous.radius,
-                              setid: setid});
-            }
-        }
-
-        // get all the disjoint clusters
-        var clusters = disjointCluster(circles);
-
-        // orientate all disjoint sets, get sizes
-        for (i = 0; i < clusters.length; ++i) {
-            orientateCircles(clusters[i], orientation, orientationOrder);
-            var bounds = getBoundingBox(clusters[i]);
-            clusters[i].size = (bounds.xRange.max - bounds.xRange.min) * (bounds.yRange.max - bounds.yRange.min);
-            clusters[i].bounds = bounds;
-        }
-        clusters.sort(function(a, b) { return b.size - a.size; });
-
-        // orientate the largest at 0,0, and get the bounds
-        circles = clusters[0];
-        var returnBounds = circles.bounds;
-
-        var spacing = (returnBounds.xRange.max - returnBounds.xRange.min)/50;
-
-        function addCluster(cluster, right, bottom) {
-            if (!cluster) return;
-
-            var bounds = cluster.bounds, xOffset, yOffset, centreing;
-
-            if (right) {
-                xOffset = returnBounds.xRange.max  - bounds.xRange.min + spacing;
-            } else {
-                xOffset = returnBounds.xRange.max  - bounds.xRange.max;
-                centreing = (bounds.xRange.max - bounds.xRange.min) / 2 -
-                            (returnBounds.xRange.max - returnBounds.xRange.min) / 2;
-                if (centreing < 0) xOffset += centreing;
-            }
-
-            if (bottom) {
-                yOffset = returnBounds.yRange.max  - bounds.yRange.min + spacing;
-            } else {
-                yOffset = returnBounds.yRange.max  - bounds.yRange.max;
-                centreing = (bounds.yRange.max - bounds.yRange.min) / 2 -
-                            (returnBounds.yRange.max - returnBounds.yRange.min) / 2;
-                if (centreing < 0) yOffset += centreing;
-            }
-
-            for (var j = 0; j < cluster.length; ++j) {
-                cluster[j].x += xOffset;
-                cluster[j].y += yOffset;
-                circles.push(cluster[j]);
-            }
-        }
-
-        var index = 1;
-        while (index < clusters.length) {
-            addCluster(clusters[index], true, false);
-            addCluster(clusters[index+1], false, true);
-            addCluster(clusters[index+2], true, true);
-            index += 3;
-
-            // have one cluster (in top left). lay out next three relative
-            // to it in a grid
-            returnBounds = getBoundingBox(circles);
-        }
-
-        // convert back to solution form
-        var ret = {};
-        for (i = 0; i < circles.length; ++i) {
-            ret[circles[i].setid] = circles[i];
-        }
-        return ret;
-    }
-
-    /** Scales a solution from venn.venn or venn.greedyLayout such that it fits in
-    a rectangle of width/height - with padding around the borders. also
-    centers the diagram in the available space at the same time */
-    function scaleSolution(solution, width, height, padding) {
-        var circles = [], setids = [];
-        for (var setid in solution) {
-            if (solution.hasOwnProperty(setid)) {
-                setids.push(setid);
-                circles.push(solution[setid]);
-            }
-        }
-
-        width -= 2*padding;
-        height -= 2*padding;
-
-        var bounds = getBoundingBox(circles),
-            xRange = bounds.xRange,
-            yRange = bounds.yRange,
-            xScaling = width  / (xRange.max - xRange.min),
-            yScaling = height / (yRange.max - yRange.min),
-            scaling = Math.min(yScaling, xScaling),
-
-            // while we're at it, center the diagram too
-            xOffset = (width -  (xRange.max - xRange.min) * scaling) / 2,
-            yOffset = (height - (yRange.max - yRange.min) * scaling) / 2;
-
-        var scaled = {};
-        for (var i = 0; i < circles.length; ++i) {
-            var circle = circles[i];
-            scaled[setids[i]] = {
-                radius: scaling * circle.radius,
-                x: padding + xOffset + (circle.x - xRange.min) * scaling,
-                y: padding + yOffset + (circle.y - yRange.min) * scaling,
-            };
-        }
-
-        return scaled;
-    }
-
-    /*global console:true*/
-
-    function VennDiagram() {
-        var width = 600,
-            height = 350,
-            padding = 15,
-            duration = 1000,
-            orientation = Math.PI / 2,
-            normalize = true,
-            wrap = true,
-            styled = true,
-            fontSize = null,
-            orientationOrder = null,
-
-            // mimic the behaviour of d3.scale.category10 from the previous
-            // version of d3
-            colourMap = {},
-
-            // so this is the same as d3.schemeCategory10, which is only defined in d3 4.0
-            // since we can support older versions of d3 as long as we don't force this,
-            // I'm hackily redefining below. TODO: remove this and change to d3.schemeCategory10
-            colourScheme = ["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"],
-            colourIndex = 0,
-            colours = function(key) {
-                if (key in colourMap) {
-                    return colourMap[key];
-                }
-                var ret = colourMap[key] = colourScheme[colourIndex];
-                colourIndex += 1;
-                if (colourIndex >= colourScheme.length) {
-                    colourIndex = 0;
-                }
-                return ret;
-            },
-            layoutFunction = venn;
-
-        function chart(selection) {
-            var data = selection.datum();
-            var solution = layoutFunction(data);
-            if (normalize) {
-                solution = normalizeSolution(solution,
-                                             orientation,
-                                             orientationOrder);
-            }
-            var circles = scaleSolution(solution, width, height, padding);
-            var textCentres = computeTextCentres(circles, data);
-
-            // create svg if not already existing
-            selection.selectAll("svg").data([circles]).enter().append("svg");
-
-            var svg = selection.select("svg")
-                .attr("width", width)
-                .attr("height", height);
-
-            // to properly transition intersection areas, we need the
-            // previous circles locations. load from elements
-            var previous = {}, hasPrevious = false;
-            svg.selectAll("g path").each(function (d) {
-                var path = d3.select(this).attr("d");
-                if ((d.sets.length == 1) && path) {
-                    hasPrevious = true;
-                    previous[d.sets[0]] = circleFromPath(path);
-                }
-            });
-
-            // interpolate intersection area paths between previous and
-            // current paths
-            var pathTween = function(d) {
-                return function(t) {
-                    var c = d.sets.map(function(set) {
-                        var start = previous[set], end = circles[set];
-                        if (!start) {
-                            start = {x : width/2, y : height/2, radius : 1};
-                        }
-                        if (!end) {
-                            end = {x : width/2, y : height/2, radius : 1};
-                        }
-                        return {'x' : start.x * (1 - t) + end.x * t,
-                                'y' : start.y * (1 - t) + end.y * t,
-                                'radius' : start.radius * (1 - t) + end.radius * t};
-                    });
-                    return intersectionAreaPath(c);
-                };
-            };
-
-            // update data, joining on the set ids
-            var nodes = svg.selectAll("g")
-                .data(data, function(d) { return d.sets; });
-
-            // create new nodes
-            var enter = nodes.enter()
-                .append('g')
-                .attr("class", function(d) {
-                    return "venn-area venn-" +
-                        (d.sets.length == 1 ? "circle" : "intersection");
-                })
-                .attr("data-venn-sets", function(d) {
-                    return d.sets.join("_");
-                });
-
-            var enterPath = enter.append("path"),
-                enterText = enter.append("text")
-                .attr("class", "label")
-                .text(function (d) { return label(d); } )
-                .attr("text-anchor", "middle")
-                .attr("dy", ".35em")
-                .attr("x", width/2)
-                .attr("y", height/2);
-
-
-            // apply minimal style if wanted
-            if (styled) {
-                enterPath.style("fill-opacity", "0")
-                    .filter(function (d) { return d.sets.length == 1; } )
-                    .style("fill", function(d) { return colours(label(d)); })
-                    .style("fill-opacity", ".25");
-
-                enterText
-                    .style("fill", function(d) { return d.sets.length == 1 ? colours(label(d)) : "#444"; });
-            }
-
-            // update existing, using pathTween if necessary
-            var update = selection;
-            if (hasPrevious) {
-                update = selection.transition("venn").duration(duration);
-                update.selectAll("path")
-                    .attrTween("d", pathTween);
-            } else {
-                update.selectAll("path")
-                    .attr("d", function(d) {
-                        return intersectionAreaPath(d.sets.map(function (set) { return circles[set]; }));
-                    });
-            }
-
-            var updateText = update.selectAll("text")
-                .filter(function (d) { return d.sets in textCentres; })
-                .text(function (d) { return label(d); } )
-                .attr("x", function(d) { return Math.floor(textCentres[d.sets].x);})
-                .attr("y", function(d) { return Math.floor(textCentres[d.sets].y);});
-
-            if (wrap) {
-                if (hasPrevious) {
-                    // d3 4.0 uses 'on' for events on transitions,
-                    // but d3 3.0 used 'each' instead. switch appropiately
-                    if ('on' in updateText) {
-                        updateText.on("end", wrapText(circles, label));
-                    } else {
-                        updateText.each("end", wrapText(circles, label));
-                    }
-                } else {
-                    updateText.each(wrapText(circles, label));
-                }
-            }
-
-            // remove old
-            var exit = nodes.exit().transition('venn').duration(duration).remove();
-            exit.selectAll("path")
-                .attrTween("d", pathTween);
-
-            var exitText = exit.selectAll("text")
-                .attr("x", width/2)
-                .attr("y", height/2);
-
-            // if we've been passed a fontSize explicitly, use it to
-            // transition
-            if (fontSize !== null) {
-                enterText.style("font-size", "0px");
-                updateText.style("font-size", fontSize);
-                exitText.style("font-size", "0px");
-            }
-
-
-            return {'circles': circles,
-                    'textCentres': textCentres,
-                    'nodes': nodes,
-                    'enter': enter,
-                    'update': update,
-                    'exit': exit};
-        }
-
-        function label(d) {
-            if (d.label) {
-                return d.label;
-            }
-            if (d.sets.length == 1) {
-                return '' + d.sets[0];
-            }
-        }
-
-        chart.wrap = function(_) {
-            if (!arguments.length) return wrap;
-            wrap = _;
-            return chart;
-        };
-
-        chart.width = function(_) {
-            if (!arguments.length) return width;
-            width = _;
-            return chart;
-        };
-
-        chart.height = function(_) {
-            if (!arguments.length) return height;
-            height = _;
-            return chart;
-        };
-
-        chart.padding = function(_) {
-            if (!arguments.length) return padding;
-            padding = _;
-            return chart;
-        };
-
-        chart.colours = function(_) {
-            if (!arguments.length) return colours;
-            colours = _;
-            return chart;
-        };
-
-        chart.fontSize = function(_) {
-            if (!arguments.length) return fontSize;
-            fontSize = _;
-            return chart;
-        };
-
-        chart.duration = function(_) {
-            if (!arguments.length) return duration;
-            duration = _;
-            return chart;
-        };
-
-        chart.layoutFunction = function(_) {
-            if (!arguments.length) return layoutFunction;
-            layoutFunction = _;
-            return chart;
-        };
-
-        chart.normalize = function(_) {
-            if (!arguments.length) return normalize;
-            normalize = _;
-            return chart;
-        };
-
-        chart.styled = function(_) {
-            if (!arguments.length) return styled;
-            styled = _;
-            return chart;
-        };
-
-        chart.orientation = function(_) {
-            if (!arguments.length) return orientation;
-            orientation = _;
-            return chart;
-        };
-
-        chart.orientationOrder = function(_) {
-            if (!arguments.length) return orientationOrder;
-            orientationOrder = _;
-            return chart;
-        };
-
-        return chart;
-    }
-    // sometimes text doesn't fit inside the circle, if thats the case lets wrap
-    // the text here such that it fits
-    // todo: looks like this might be merged into d3 (
-    // https://github.com/mbostock/d3/issues/1642),
-    // also worth checking out is
-    // http://engineering.findthebest.com/wrapping-axis-labels-in-d3-js/
-    // this seems to be one of those things that should be easy but isn't
-    function wrapText(circles, labeller) {
-        return function() {
-            var text = d3.select(this),
-                data = text.datum(),
-                width = circles[data.sets[0]].radius || 50,
-                label = labeller(data) || '';
-
-                var words = label.split(/\s+/).reverse(),
-                maxLines = 3,
-                minChars = (label.length + words.length) / maxLines,
-                word = words.pop(),
-                line = [word],
-                joined,
-                lineNumber = 0,
-                lineHeight = 1.1, // ems
-                tspan = text.text(null).append("tspan").text(word);
-
-            while (true) {
-                word = words.pop();
-                if (!word) break;
-                line.push(word);
-                joined = line.join(" ");
-                tspan.text(joined);
-                if (joined.length > minChars && tspan.node().getComputedTextLength() > width) {
-                    line.pop();
-                    tspan.text(line.join(" "));
-                    line = [word];
-                    tspan = text.append("tspan").text(word);
-                    lineNumber++;
-                }
-            }
-
-            var initial = 0.35 - lineNumber * lineHeight / 2,
-                x = text.attr("x"),
-                y = text.attr("y");
-
-            text.selectAll("tspan")
-                .attr("x", x)
-                .attr("y", y)
-                .attr("dy", function(d, i) {
-                     return (initial + i * lineHeight) + "em";
-                });
-        };
-    }
-
-    function circleMargin(current, interior, exterior) {
-        var margin = interior[0].radius - distance(interior[0], current), i, m;
-        for (i = 1; i < interior.length; ++i) {
-            m = interior[i].radius - distance(interior[i], current);
-            if (m <= margin) {
-                margin = m;
-            }
-        }
-
-        for (i = 0; i < exterior.length; ++i) {
-            m = distance(exterior[i], current) - exterior[i].radius;
-            if (m <= margin) {
-                margin = m;
-            }
-        }
-        return margin;
-    }
-
-    // compute the center of some circles by maximizing the margin of
-    // the center point relative to the circles (interior) after subtracting
-    // nearby circles (exterior)
-    function computeTextCentre(interior, exterior) {
-        // get an initial estimate by sampling around the interior circles
-        // and taking the point with the biggest margin
-        var points = [], i;
-        for (i = 0; i < interior.length; ++i) {
-            var c = interior[i];
-            points.push({x: c.x, y: c.y});
-            points.push({x: c.x + c.radius/2, y: c.y});
-            points.push({x: c.x - c.radius/2, y: c.y});
-            points.push({x: c.x, y: c.y + c.radius/2});
-            points.push({x: c.x, y: c.y - c.radius/2});
-        }
-        var initial = points[0], margin = circleMargin(points[0], interior, exterior);
-        for (i = 1; i < points.length; ++i) {
-            var m = circleMargin(points[i], interior, exterior);
-            if (m >= margin) {
-                initial = points[i];
-                margin = m;
-            }
-        }
-
-        // maximize the margin numerically
-        var solution = fmin(
-                    function(p) { return -1 * circleMargin({x: p[0], y: p[1]}, interior, exterior); },
-                    [initial.x, initial.y],
-                    {maxIterations:500, minErrorDelta:1e-10}).solution;
-        var ret = {x: solution[0], y: solution[1]};
-
-        // check solution, fallback as needed (happens if fully overlapped
-        // etc)
-        var valid = true;
-        for (i = 0; i < interior.length; ++i) {
-            if (distance(ret, interior[i]) > interior[i].radius) {
-                valid = false;
-                break;
-            }
-        }
-
-        for (i = 0; i < exterior.length; ++i) {
-            if (distance(ret, exterior[i]) < exterior[i].radius) {
-                valid = false;
-                break;
-            }
-        }
-
-        if (!valid) {
-            if (interior.length == 1) {
-                ret = {x: interior[0].x, y: interior[0].y};
-            } else {
-                var areaStats = {};
-                intersectionArea(interior, areaStats);
-
-                if (areaStats.arcs.length === 0) {
-                    ret = {'x': 0, 'y': -1000, disjoint:true};
-
-                } else if (areaStats.arcs.length == 1) {
-                    ret = {'x': areaStats.arcs[0].circle.x,
-                           'y': areaStats.arcs[0].circle.y};
-
-                } else if (exterior.length) {
-                    // try again without other circles
-                    ret = computeTextCentre(interior, []);
-
-                } else {
-                    // take average of all the points in the intersection
-                    // polygon. this should basically never happen
-                    // and has some issues:
-                    // https://github.com/benfred/venn.js/issues/48#issuecomment-146069777
-                    ret = getCenter(areaStats.arcs.map(function (a) { return a.p1; }));
-                }
-            }
-        }
-
-        return ret;
-    }
-
-    // given a dictionary of {setid : circle}, returns
-    // a dictionary of setid to list of circles that completely overlap it
-    function getOverlappingCircles(circles) {
-        var ret = {}, circleids = [];
-        for (var circleid in circles) {
-            circleids.push(circleid);
-            ret[circleid] = [];
-        }
-        for (var i  = 0; i < circleids.length; i++) {
-            var a = circles[circleids[i]];
-            for (var j = i + 1; j < circleids.length; ++j) {
-                var b = circles[circleids[j]],
-                    d = distance(a, b);
-
-                if (d + b.radius <= a.radius + 1e-10) {
-                    ret[circleids[j]].push(circleids[i]);
-
-                } else if (d + a.radius <= b.radius + 1e-10) {
-                    ret[circleids[i]].push(circleids[j]);
-                }
-            }
-        }
-        return ret;
-    }
-
-    function computeTextCentres(circles, areas) {
-        var ret = {}, overlapped = getOverlappingCircles(circles);
-        for (var i = 0; i < areas.length; ++i) {
-            var area = areas[i].sets, areaids = {}, exclude = {};
-            for (var j = 0; j < area.length; ++j) {
-                areaids[area[j]] = true;
-                var overlaps = overlapped[area[j]];
-                // keep track of any circles that overlap this area,
-                // and don't consider for purposes of computing the text
-                // centre
-                for (var k = 0; k < overlaps.length; ++k) {
-                    exclude[overlaps[k]] = true;
-                }
-            }
-
-            var interior = [], exterior = [];
-            for (var setid in circles) {
-                if (setid in areaids) {
-                    interior.push(circles[setid]);
-                } else if (!(setid in exclude)) {
-                    exterior.push(circles[setid]);
-                }
-            }
-            var centre = computeTextCentre(interior, exterior);
-            ret[area] = centre;
-            if (centre.disjoint && (areas[i].size > 0)) {
-                console.log("WARNING: area " + area + " not represented on screen");
-            }
-        }
-        return  ret;
-    }
-
-    // sorts all areas in the venn diagram, so that
-    // a particular area is on top (relativeTo) - and
-    // all other areas are so that the smallest areas are on top
-    function sortAreas(div, relativeTo) {
-
-        // figure out sets that are completly overlapped by relativeTo
-        var overlaps = getOverlappingCircles(div.selectAll("svg").datum());
-        var exclude = {};
-        for (var i = 0; i < relativeTo.sets.length; ++i) {
-            var check = relativeTo.sets[i];
-            for (var setid in overlaps) {
-                var overlap = overlaps[setid];
-                for (var j = 0; j < overlap.length; ++j) {
-                    if (overlap[j] == check) {
-                        exclude[setid] = true;
-                        break;
-                    }
-                }
-            }
-        }
-
-        // checks that all sets are in exclude;
-        function shouldExclude(sets) {
-            for (var i = 0; i < sets.length; ++i) {
-                if (!(sets[i] in exclude)) {
-                    return false;
-                }
-            }
-            return true;
-        }
-
-        // need to sort div's so that Z order is correct
-        div.selectAll("g").sort(function (a, b) {
-            // highest order set intersections first
-            if (a.sets.length != b.sets.length) {
-                return a.sets.length - b.sets.length;
-            }
-
-            if (a == relativeTo) {
-                return shouldExclude(b.sets) ? -1 : 1;
-            }
-            if (b == relativeTo) {
-                return shouldExclude(a.sets) ? 1 : -1;
-            }
-
-            // finally by size
-            return b.size - a.size;
-        });
-    }
-
-    function circlePath(x, y, r) {
-        var ret = [];
-        ret.push("\nM", x, y);
-        ret.push("\nm", -r, 0);
-        ret.push("\na", r, r, 0, 1, 0, r *2, 0);
-        ret.push("\na", r, r, 0, 1, 0,-r *2, 0);
-        return ret.join(" ");
-    }
-
-    // inverse of the circlePath function, returns a circle object from an svg path
-    function circleFromPath(path) {
-        var tokens = path.split(' ');
-        return {'x' : parseFloat(tokens[1]),
-                'y' : parseFloat(tokens[2]),
-                'radius' : -parseFloat(tokens[4])
-                };
-    }
-
-    /** returns a svg path of the intersection area of a bunch of circles */
-    function intersectionAreaPath(circles) {
-        var stats = {};
-        intersectionArea(circles, stats);
-        var arcs = stats.arcs;
-
-        if (arcs.length === 0) {
-            return "M 0 0";
-
-        } else if (arcs.length == 1) {
-            var circle = arcs[0].circle;
-            return circlePath(circle.x, circle.y, circle.radius);
-
-        } else {
-            // draw path around arcs
-            var ret = ["\nM", arcs[0].p2.x, arcs[0].p2.y];
-            for (var i = 0; i < arcs.length; ++i) {
-                var arc = arcs[i], r = arc.circle.radius, wide = arc.width > r;
-                ret.push("\nA", r, r, 0, wide ? 1 : 0, 1,
-                         arc.p1.x, arc.p1.y);
-            }
-            return ret.join(" ");
-        }
-    }
-
-    exports.fmin = fmin;
-    exports.minimizeConjugateGradient = minimizeConjugateGradient;
-    exports.bisect = bisect;
-    exports.intersectionArea = intersectionArea;
-    exports.circleCircleIntersection = circleCircleIntersection;
-    exports.circleOverlap = circleOverlap;
-    exports.circleArea = circleArea;
-    exports.distance = distance;
-    exports.circleIntegral = circleIntegral;
-    exports.venn = venn;
-    exports.greedyLayout = greedyLayout;
-    exports.scaleSolution = scaleSolution;
-    exports.normalizeSolution = normalizeSolution;
-    exports.bestInitialLayout = bestInitialLayout;
-    exports.lossFunction = lossFunction;
-    exports.disjointCluster = disjointCluster;
-    exports.distanceFromIntersectArea = distanceFromIntersectArea;
-    exports.VennDiagram = VennDiagram;
-    exports.wrapText = wrapText;
-    exports.computeTextCentres = computeTextCentres;
-    exports.computeTextCentre = computeTextCentre;
-    exports.sortAreas = sortAreas;
-    exports.circlePath = circlePath;
-    exports.circleFromPath = circleFromPath;
-    exports.intersectionAreaPath = intersectionAreaPath;
-
-}));
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/static/logo.png b/config/plugins/visualizations/venn/static/logo.png
deleted file mode 100644
index 3d0b70624c8d5340b7ef314286e98f3e863b8118..0000000000000000000000000000000000000000
Binary files a/config/plugins/visualizations/venn/static/logo.png and /dev/null differ
diff --git a/config/plugins/visualizations/venn/static/logo.svg b/config/plugins/visualizations/venn/static/logo.svg
new file mode 100644
index 0000000000000000000000000000000000000000..2d851c8a414cc3894bd475d3642ea40ec0bbb8ae
--- /dev/null
+++ b/config/plugins/visualizations/venn/static/logo.svg
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" height="280" width="380" stroke="#FFFFFF" stroke-width="10">
+ <rect x="2.5" y="2.5" width="375" height="275" fill="#E30A17" rx="50" ry="50"/>
+ <circle cx="140" cy="140" r="100" fill="#FFFFFF"/>
+ <circle cx="240" cy="140" r="100" fill="#E30A17"/>
+ <circle cx="140" cy="140" r="100" fill="none"/>
+</svg>
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/static/script.css b/config/plugins/visualizations/venn/static/script.css
deleted file mode 100644
index 235c2555cee755e87f2a72a119b04781167931da..0000000000000000000000000000000000000000
--- a/config/plugins/visualizations/venn/static/script.css
+++ /dev/null
@@ -1,14 +0,0 @@
-.venntooltip {
-    position: absolute;
-    text-align: center;
-    width: 128px;
-    height: 22px;
-    background: #333;
-    color: #ddd;
-    border: 0px;
-    border-radius: 8px;
-    opacity: 0;
-}
-.venn-area > .label {
-    font-size: 1em;
-}
\ No newline at end of file
diff --git a/config/plugins/visualizations/visualization.dtd b/config/plugins/visualizations/visualization.dtd
index dec57f0310ced77b60a1f4b3f544de3140b7cee1..a4640e9ca6759cbb933e3b0174dfe2220bd227c3 100644
--- a/config/plugins/visualizations/visualization.dtd
+++ b/config/plugins/visualizations/visualization.dtd
@@ -54,11 +54,18 @@
                 if result_type is 'datatype' the registry will assume the text is a datatype class name
                 and parse it into the proper class before the test (often 'isinstance') is run.
                 DEFAULT: no parsing (result should be a string)
+        allow_uri_if_protocol: used in conjunction with type='isinstance' and test_attr='datatype'. Let you define
+                a list of protocols or schemes (e.g. 's3,https') that, in the case of a deferred target (e.g. currently only HDAs),
+                the registry will allow the test to pass if the the source URI has a scheme in the list.
+                This is useful for visualizations that can work directly with URIs.
+                DEFAULT: []
+                
     -->
     <!ATTLIST test
-        type        CDATA #IMPLIED
-        test_attr   CDATA #IMPLIED
-        result_type CDATA #IMPLIED
+        type                    CDATA #IMPLIED
+        test_attr               CDATA #IMPLIED
+        result_type             CDATA #IMPLIED
+        allow_uri_if_protocol   CDATA #IMPLIED
     >
 
     <!ELEMENT to_param (#PCDATA)>
diff --git a/config/plugins/visualizations/vizarr/config/vizarr.xml b/config/plugins/visualizations/vizarr/config/vizarr.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a6bc313c20de85ae3285c3b68207538643c8b79e
--- /dev/null
+++ b/config/plugins/visualizations/vizarr/config/vizarr.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Vizarr Viewer">
+    <description>Basic visualization for Zarr-based images like OME-Zarr</description>
+    <requirements>
+        <requirement type="npm" version="0.1.6" package="@galaxyproject/vizarr"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+
+            <test type="isinstance" test_attr="datatype" result_type="datatype" allow_uri_if_protocol="https,http">data.ZarrDirectory</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype" allow_uri_if_protocol="https,http">images.OMEZarr</test>
+
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+</visualization>
diff --git a/config/plugins/visualizations/vizarr/static/logo.svg b/config/plugins/visualizations/vizarr/static/logo.svg
new file mode 100644
index 0000000000000000000000000000000000000000..83a5214086ea27fa8d145c393d443e6074a59078
--- /dev/null
+++ b/config/plugins/visualizations/vizarr/static/logo.svg
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 145.65 126.13">
+  <defs>
+    <style>
+      .cls-1 {
+        fill: #ef4136;
+      }
+
+      .cls-1, .cls-2, .cls-3 {
+        mix-blend-mode: multiply;
+        stroke-width: 0px;
+      }
+
+      .cls-2 {
+        fill: #27aae1;
+      }
+
+      .cls-3 {
+        fill: #39b54a;
+      }
+
+      .cls-4 {
+        isolation: isolate;
+      }
+    </style>
+  </defs>
+  <g class="cls-4">
+    <g id="Layer_2" data-name="Layer 2">
+      <g id="Layer_1-2" data-name="Layer 1">
+        <polygon class="cls-2" points="72.82 40.61 49.38 0 7.5 0 72.82 113.14 138.15 0 96.27 0 72.82 40.61"/>
+        <polygon class="cls-1" points="102.06 12.99 72.82 63.62 43.59 12.99 15 12.99 80.32 126.13 145.65 12.99 102.06 12.99"/>
+        <polygon class="cls-3" points="72.82 63.62 43.59 12.99 0 12.99 65.32 126.13 130.65 12.99 102.06 12.99 72.82 63.62"/>
+      </g>
+    </g>
+  </g>
+</svg>
\ No newline at end of file
diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
index e34a9ba89afd231551bf9184fe3d3310cb2da81b..11092bb8451596eb1637f654f42ba427ebf3c77e 100644
--- a/doc/parse_gx_xsd.py
+++ b/doc/parse_gx_xsd.py
@@ -83,28 +83,20 @@ def _build_tag(tag, hide_attributes):
             assertions_buffer.write(_doc_or_none(assertions_tag))
             assertions_buffer.write("\n\n")
 
-            assertion_groups = assertions_tag.xpath(
-                "xs:choice/xs:group", namespaces={"xs": "http://www.w3.org/2001/XMLSchema"}
+            assertion_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}group[@name='TestAssertion']")
+            elements = assertion_tag.findall(
+                "{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element"
             )
-            for group in assertion_groups:
-                ref = group.attrib["ref"]
-                assertion_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}group[@name='" + ref + "']")
-                doc = _doc_or_none(assertion_tag)
-                assertions_buffer.write(f"### {doc}\n\n")
-                elements = assertion_tag.findall(
-                    "{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element"
-                )
-                for element in elements:
+            for element in elements:
+                doc = _doc_or_none(element)
+                if doc is None:
                     doc = _doc_or_none(element)
-                    if doc is None:
-                        doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
-                    doc = doc.strip()
-
-                    element_el = _find_tag_el(element)
-                    element_attributes = _find_attributes(element_el)
-                    doc = _replace_attribute_list(element_el, doc, element_attributes)
-                    assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
+                assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
+                doc = doc.strip()
+
+                element_attributes = _find_attributes(element)
+                doc = _replace_attribute_list(element, doc, element_attributes)
+                assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
             text = text.replace(line, assertions_buffer.getvalue())
     tag_help.write(text)
     if best_practices := _get_bp_link(annotation_el):
diff --git a/doc/schema_template.md b/doc/schema_template.md
index d08c7a4a0d06d56ec5dcf05c7e2642b8d46e154d..d6577843ba2f80df8ec355d3019be7075562de19 100644
--- a/doc/schema_template.md
+++ b/doc/schema_template.md
@@ -31,6 +31,7 @@ $tag:tool|creator|organization://complexType[@name='Organization']
 $tag:tool|requirements://complexType[@name='Requirements']
 $tag:tool|requirements|requirement://complexType[@name='Requirement']
 $tag:tool|requirements|container://complexType[@name='Container']
+$tag:tool|requirements|resource://complexType[@name='Resource']
 $tag:tool|required_files://complexType[@name='RequiredFiles']
 $tag:tool|required_files|include://complexType[@name='RequiredFileInclude']
 $tag:tool|required_files|exclude://complexType[@name='RequiredFileExclude']
diff --git a/doc/source/admin/data.md b/doc/source/admin/data.md
index 1e9a3ea909524575c48010f20229dfa8364570c8..15fbecbade4a25a0d083436ccc0a3a992c63c20f 100644
--- a/doc/source/admin/data.md
+++ b/doc/source/admin/data.md
@@ -13,13 +13,13 @@ This document is going to discuss two of these (file sources and object stores)
 File sources in Galaxy are a sprawling concept but essentially they provide users access to simple files (stored hierarchically into folders) that can be navigated and imported into Galaxy. Importing a "file" into Galaxy generally creates a copy of that file into a Galaxy "object store". Once these files are stored in Galaxy,
 they become "datasets". A Galaxy dataset is much more than a simple file - Galaxy datasets include various generic metadata a datatype, datatype specific metadata, and ownership and sharing rules managed by Galaxy.
 
-Galaxy object stores (called "storage locations" in the UI) store datasets and global (accessible to all users) object stores are configured with the ``galaxy.yml`` property ``object_store_config_file`` (or  ``object_store_config`` for a configuration embedded right in ``galaxy.yml``) that defaults to ``object_store_conf.xml`` or ``object_store_conf.yml`` if either is present in Galaxy's configuration directory. Galaxy file sources provide users access to raw files and global files sources are configured with the ``galaxy.yml`` property ``file_sources_config_file`` (or ``file_sources`` for embedded configurations) that defaults to ``file_sources_conf.yml`` if that file is present in Galaxy's configuration directory.
+Galaxy object stores (called "storage locations" in the UI) store datasets and global (accessible to all users) object stores are configured with the `galaxy.yml` property `object_store_config_file` (or `object_store_config` for a configuration embedded right in `galaxy.yml`) that defaults to `object_store_conf.xml` or `object_store_conf.yml` if either is present in Galaxy's configuration directory. Galaxy file sources provide users access to raw files and global files sources are configured with the `galaxy.yml` property `file_sources_config_file` (or `file_sources` for embedded configurations) that defaults to `file_sources_conf.yml` if that file is present in Galaxy's configuration directory.
 
-Some of Galaxy's most updated and complete administrator documentation can be found in configuration sample files - this is definitely the case for object stores and file sources. The relevant sample configuration files include  [file_sources_conf.yml.sample](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/file_sources_conf.yml.sample) and [object_store_conf.sample.yml](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/object_store_conf.sample.yml).
+Some of Galaxy's most updated and complete administrator documentation can be found in configuration sample files - this is definitely the case for object stores and file sources. The relevant sample configuration files include [file_sources_conf.yml.sample](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/file_sources_conf.yml.sample) and [object_store_conf.sample.yml](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/object_store_conf.sample.yml).
 
-File sources and object stores configured with the above files essentially are available to all users of your Galaxy instance - hence this document describes them as "global" file sources and object  stores. File source configurations do allow some templating that does allow the a global file source to be materialized differently for different users. For instance, you as an admin may setup a Dropbox file source and may explicitly add custom user properties that allow that single Dropbox file source to read from a user's preferences. Since there is just one Dropbox service and most people only have a single Dropbox account, this use case can be somewhat adequately addressed by the global file source and the global user preferences file. For a use case like Amazon S3 buckets though for instance, a single bucket file source that is parameterized one way is probably more clearly inadequate. For instance, users would very likely want to attach different buckets for different projects.  Additionally, the Galaxy user interface doesn't tie the user preferences to the particular file source and so this method introduces a huge education burden on your Galaxy instance. Finally, the templating available to file sources are not available for object stores - and allowing users to describe how they would like datasets stored and to pay for their own dataset storage are important use cases.
+File sources and object stores configured with the above files essentially are available to all users of your Galaxy instance - hence this document describes them as "global" file sources and object stores. File source configurations do allow some templating that does allow the a global file source to be materialized differently for different users. For instance, you as an admin may setup a Dropbox file source and may explicitly add custom user properties that allow that single Dropbox file source to read from a user's preferences. Since there is just one Dropbox service and most people only have a single Dropbox account, this use case can be somewhat adequately addressed by the global file source and the global user preferences file. For a use case like Amazon S3 buckets though for instance, a single bucket file source that is parameterized one way is probably more clearly inadequate. For instance, users would very likely want to attach different buckets for different projects. Additionally, the Galaxy user interface doesn't tie the user preferences to the particular file source and so this method introduces a huge education burden on your Galaxy instance. Finally, the templating available to file sources are not available for object stores - and allowing users to describe how they would like datasets stored and to pay for their own dataset storage are important use cases.
 
-This document is going to describe Galaxy configuration template libraries that allow the 
+This document is going to describe Galaxy configuration template libraries that allow the
 administrator to setup templates for file sources and object stores that your users may instantiate
 as they see fit. User's can instantiate multiple instances of any template, the template concept
 can apply to both file source and object store plugins, and the user interface is unified from the
@@ -29,10 +29,10 @@ your users do not need to navigate seemingly unrelated preferences to get plugin
 ## Object Store Templates
 
 Galaxy's object store templates are configured as a YAML list of template objects. This list
-can be placed ``object_store_templates.yml`` in Galaxy configuration directory (or any path
-pointed to by the configuration option ``object_store_templates_config_file`` in ``galaxy.yml``).
-Alternatively, the  configuration can be placed directly into ``galaxy.yml`` using the
-``object_store_templates`` configuration option.
+can be placed `object_store_templates.yml` in Galaxy configuration directory (or any path
+pointed to by the configuration option `object_store_templates_config_file` in `galaxy.yml`).
+Alternatively, the configuration can be placed directly into `galaxy.yml` using the
+`object_store_templates` configuration option.
 
 :::{admonition} Warning
 :class: warning
@@ -40,8 +40,8 @@ Alternatively, the  configuration can be placed directly into ``galaxy.yml`` usi
 Object store selection within Galaxy is available only when the primary object store is a
 distributed object store. All the other object stores provide stronger guarantees about how
 datasets are stored. Object Store Templates will not currently work if the primary
-object store (usually defined by ``object_store_config_file``) is a simple disk object
-store, a hierarchal object store, or anything other than a ``distributed`` object store.
+object store (usually defined by `object_store_config_file`) is a simple disk object
+store, a hierarchal object store, or anything other than a `distributed` object store.
 
 Ongoing discussion on this topic can be found at [this Galaxy Discussions post (#18157)](https://github.com/galaxyproject/galaxy/discussions/18157).
 :::
@@ -54,7 +54,7 @@ A minimal object store template might look something like:
 
 ### Object Store Types
 
-#### ``disk``
+#### `disk`
 
 This is the most basic sort of object store template that just makes disk paths available to users
 for storing data. Paths can be built up from the user supplied variables, user details, supplied
@@ -67,20 +67,20 @@ user's username to produce a unique path for each user defined object store.
 
 These sorts of object stores have no quota so be careful.
 
-The syntax for the ``configuration`` section of ``disk`` templates looks like this.
+The syntax for the `configuration` section of `disk` templates looks like this.
 
 ![](object_store_disk_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's object store infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``object_store_conf.yml`` (Galaxy's global object
+of what you'd be able to add directly to `object_store_conf.yml` (Galaxy's global object
 store configuration).
 
 ![](object_store_disk_configuration.png)
 
-#### ``boto3``
+#### `boto3`
 
-Object stores of the type ``boto3`` can be used to access a wide variety of S3
+Object stores of the type `boto3` can be used to access a wide variety of S3
 compatible storage services including AWS S3. How you template them can result in widely
 different experiences for your users and can result in addressing a wide variety of use cases.
 
@@ -116,18 +116,18 @@ and easily as possible that templates might look like this:
 :language: yaml
 ```
 
-The syntax for the ``configuration`` section of ``boto3`` templates looks like this.
+The syntax for the `configuration` section of `boto3` templates looks like this.
 
 ![](object_store_boto3_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's object store infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``object_store_conf.yml`` (Galaxy's global object
+of what you'd be able to add directly to `object_store_conf.yml` (Galaxy's global object
 store configuration).
 
 ![](object_store_boto3_configuration.png)
 
-#### ``azure_blob``
+#### `azure_blob`
 
 Here is a "production grade" Azure template that can be essentially used to connect to any
 Azure storage container.
@@ -147,47 +147,46 @@ This example is a little contrived though, if a small lab or institution has jus
 it would likely be a much easier user experience to just wrap them all in a Galaxy hierarchical
 object store, document them there, and make them available to your whole Galaxy instance.
 
-The syntax for the ``configuration`` section of ``azure_blob`` templates looks like this.
+The syntax for the `configuration` section of `azure_blob` templates looks like this.
 
 ![](object_store_azure_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's object store infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``object_store_conf.yml`` (Galaxy's global object
+of what you'd be able to add directly to `object_store_conf.yml` (Galaxy's global object
 store configuration).
 
 ![](object_store_azure_configuration.png)
 
-#### ``aws_s3`` (Legacy)
+#### `aws_s3` (Legacy)
 
-Object stores of the type ``aws_s3`` are be used to treat AWS Simple Storage Service (S3) buckets
+Object stores of the type `aws_s3` are be used to treat AWS Simple Storage Service (S3) buckets
 as Galaxy object stores. See Amazon documentation for information on [S3](https://aws.amazon.com/s3/)
 and [how to create buckets](https://docs.aws.amazon.com/AmazonS3/latest/userguide/create-bucket-overview.html)
 and [how to create access keys](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
 
-
 ```{literalinclude} ../../../lib/galaxy/objectstore/templates/examples/production_aws_s3_legacy.yml
 :language: yaml
 ```
 
-The ``aws_s3`` object store is older and more well tested than the ``boto3`` object store, but
-the ``boto3`` object store is built using a newer, more robust, and more feature-rich client
+The `aws_s3` object store is older and more well tested than the `boto3` object store, but
+the `boto3` object store is built using a newer, more robust, and more feature-rich client
 library so it should probably be the object store you use instead of this.
 
-The syntax for the ``configuration`` section of ``aws_s3`` templates looks like this.
+The syntax for the `configuration` section of `aws_s3` templates looks like this.
 
 ![](object_store_aws_s3_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's object store infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``object_store_conf.yml`` (Galaxy's global object
+of what you'd be able to add directly to `object_store_conf.yml` (Galaxy's global object
 store configuration).
 
 ![](object_store_aws_s3_configuration.png)
 
-#### ``generic_s3`` (Legacy)
+#### `generic_s3` (Legacy)
 
-Object stores of the type ``generic_s3`` can be used to access a wide variety of S3
+Object stores of the type `generic_s3` can be used to access a wide variety of S3
 compatible storage services. How you template them can result in widely different
 experiences for your users and can result in addressing a wide variety of use cases.
 
@@ -216,13 +215,13 @@ your user's to define individual buckets by name:
 :language: yaml
 ```
 
-The syntax for the ``configuration`` section of ``generic_s3`` templates looks like this.
+The syntax for the `configuration` section of `generic_s3` templates looks like this.
 
 ![](object_store_generic_s3_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's object store infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``object_store_conf.yml`` (Galaxy's global object
+of what you'd be able to add directly to `object_store_conf.yml` (Galaxy's global object
 store configuration).
 
 ![](object_store_generic_s3_configuration.png)
@@ -261,7 +260,6 @@ and you're comfortable with it storing your user's secrets.
 
 ![Screenshot](user_object_store_form_full_aws_s3.png)
 
-
 #### Allow Users to Define Google Cloud Provider S3 Interop Storage Buckets as Object Stores
 
 This template includes descriptions of how to generate HMAC keys used by this interoperability
@@ -276,28 +274,27 @@ layer provided by Google and lots of links to relevant Google Cloud Storage docu
 ## File Source Templates
 
 Galaxy's file source templates are configured as a YAML list of template objects. This list
-can be placed ``file_source_templates.yml`` in Galaxy configuration directory (or any path
-pointed to by the configuration option ``file_source_templates_config_file`` in ``galaxy.yml``).
-Alternatively, the  configuration can be placed directly into ``galaxy.yml`` using the
-``file_source_templates`` configuration option.
-
+can be placed `file_source_templates.yml` in Galaxy configuration directory (or any path
+pointed to by the configuration option `file_source_templates_config_file` in `galaxy.yml`).
+Alternatively, the configuration can be placed directly into `galaxy.yml` using the
+`file_source_templates` configuration option.
 
 ### File Source Types
 
-#### ``posix``
+#### `posix`
 
-The syntax for the ``configuration`` section of ``posix`` templates looks like this.
+The syntax for the `configuration` section of `posix` templates looks like this.
 
 ![](file_source_posix_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``file_sources_conf.yml`` (Galaxy's global file source
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
 configuration).
 
 ![](file_source_posix_configuration.png)
 
-#### ``s3fs``
+#### `s3fs`
 
 ```{literalinclude} ../../../lib/galaxy/files/templates/examples/production_s3fs.yml
 :language: yaml
@@ -313,43 +310,69 @@ configuration).
 
 ![](file_source_s3fs_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``file_sources_conf.yml`` (Galaxy's global file source
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
 configuration).
 
 ![](file_source_s3fs_configuration.png)
 
-#### ``ftp``
+#### `ftp`
 
 ```{literalinclude} ../../../lib/galaxy/files/templates/examples/production_ftp.yml
 :language: yaml
 ```
 
-The syntax for the ``configuration`` section of ``ftp`` templates looks like this.
+The syntax for the `configuration` section of `ftp` templates looks like this.
 
 ![](file_source_ftp_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``file_sources_conf.yml`` (Galaxy's global file source
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
 configuration).
 
 ![](file_source_ftp_configuration.png)
 
-#### ``azure``
+#### `azure`
 
-The syntax for the ``configuration`` section of ``azure`` templates looks like this.
+The syntax for the `configuration` section of `azure` templates looks like this.
 
 ![](file_source_azure_configuration_template.png)
 
-At runtime, after the ``configuration`` template is expanded, the resulting dictionary
+At runtime, after the `configuration` template is expanded, the resulting dictionary
 passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
-of what you'd be able to add directly to ``file_sources_conf.yml`` (Galaxy's global file source
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
 configuration).
 
 ![](file_source_azure_configuration.png)
 
+#### `webdav`
+
+The syntax for the `configuration` section of `webdav` templates looks like this.
+
+![](file_source_webdav_configuration_template.png)
+
+At runtime, after the `configuration` template is expanded, the resulting dictionary
+passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
+configuration).
+
+![](file_source_webdav_configuration.png)
+
+#### `dropbox`
+
+The syntax for the `configuration` section of `dropbox` templates looks like this.
+
+![](file_source_dropbox_configuration_template.png)
+
+At runtime, after the `configuration` template is expanded, the resulting dictionary
+passed to Galaxy's file source plugin infrastructure looks like this and should match a subset
+of what you'd be able to add directly to `file_sources_conf.yml` (Galaxy's global file source
+configuration).
+
+![](file_source_dropbox_configuration.png)
+
 ### YAML Syntax
 
 ![galaxy.files.templates.models](file_source_templates.png)
@@ -398,30 +421,106 @@ and you are comfortable with it storing your user's secrets.
 :language: yaml
 ```
 
+#### Allow Users to Define WebDAV Servers as File Sources
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/production_webdav.yml
+:language: yaml
+```
+
+![Screenshot](user_file_source_form_full_webdav.png)
+
+### Production OAuth 2.0 File Source Templates
+
+Unlike the examples in the previous section. These examples will require a bit of
+configuration on the part of the admin. This is to obtain client credentials from the
+external service and register an OAuth 2.0 redirection callback with the remote service.
+
+#### Dropbox
+
+Once you have OAuth 2.0 client credentials from Dropbox (called `oauth2_client_id` and
+`oauth2_client_secret` here), the following configuration can be used configure your Galaxy
+instance to enable Dropbox.
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/production_dropbox.yml
+:language: yaml
+```
+
+To use this template - you'll need to make your credentials available to Galaxy's
+web and job handler processes using the environment variables `GALAXY_DROPBOX_APP_CLIENT_ID`
+and `GALAXY_DROPBOX_APP_CLIENT_SECRET`. Your jobs themselves do not require
+these secrets to be set and will not be given the secrets.
+
+If you'd like to configure these secrets explicit - you can configure them explicitly
+in the configuration. If your configuration file is managed by Ansible, these secrets
+could potentially be populated from your Ansible vault.
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/dropbox_client_secrets_explicit.yml
+:language: yaml
+```
+
+To obtain the OAuth 2.0 credentials from Dropbox, you'll need to navigate to your
+[Dropbox Apps](https://www.dropbox.com/developers/apps) and create a new app
+for your Galaxy instance with the "Create app" button.
+
+![Screenshot of Dropbox](dropbox_create_button.png)
+
+The only option available is "Scoped access" and this works fine for typical
+Galaxy use cases. You will however want to click "Full Dropbox" to request
+full access to your user's account. You will also need to give your "App" a name
+here, this should likely be something related to your Galaxy instances name.
+
+![Screenshot of Dropbox](dropbox_create_app_options_1.png)
+
+After your app is created, you'll be presented with a management screen for it.
+The first thing you'll want to do is navigate to the permissions tab and enable
+permissions to read and write to files and directories so the file source plugin
+works properly:
+
+![Screenshot of Dropbox](dropbox_scopes.png)
+
+Next, navigate back to the "Settings" tab. You'll need to register a callback
+for your Galaxy instance (it will need HTTPS enabled). This should be the URL
+to your Galaxy instance with `oauth2_callback` appended to it.
+
+![Screenshot of Dropbox](dropbox_callback.png)
+
+Finally you'll be able to find the `oauth2_client_id` and `oauth2_client_secret`
+to configured your Galaxy with on this settings page.
+
+![Screenshot of Dropbox](dropbox_client_creds.png)
+
+Until you have 50 users, your App will be considered a "development" application.
+The upshot of this is that your user's will get a scary message during authorization
+but there seems to be no way around this. 50 users would definitely be considered
+a production Galaxy instance but Dropbox operates on a different scale.
+
+For more information on what Dropbox considers a "development" app versus a "production"
+app - checkout the [Dropbox documentation](https://www.dropbox.com/developers/reference/developer-guide#production-approval).
+
 ## Playing Nicer with Ansible
 
 Many large instances of Galaxy are configured with Ansible and much of the existing administrator
 documentation leverages Ansible. The configuration template files using Jinja templating and so
-does Ansible by default. This might result in a lack of clarity of when templates (strings 
-starting with ``{{`` and ending with ``}}``) are being evaluated. Ansible templates are evaluated
+does Ansible by default. This might result in a lack of clarity of when templates (strings
+starting with `{{` and ending with `}}`) are being evaluated. Ansible templates are evaluated
 at deploy time and the configuration objects describing plugins are evaluated at Galaxy runtime.
 
 The easiest way to fix this is probably to store these templates files in your Ansible as plain files
 and not templates. If you'd like to use Ansible templating to build up these files you'll very
-likely need to tell either Galaxy or Ansible to use something other than ``{{`` and ``}}`` for 
+likely need to tell either Galaxy or Ansible to use something other than `{{` and `}}` for
 templating variables. This can be done by placing a directive at the top of your template that
-is consumed by Ansible. For instance, to have ``[%`` and ``%]`` used instead of ``{{`` and ``}}``
+is consumed by Ansible. For instance, to have `[%` and `%]` used instead of `{{` and `}}`
 by Ansible at deploy time, the file could start with:
 
 ```
 #jinja2:variable_start_string:'[%' , variable_end_string:'%]'
 ```
 
-In this case, variables wrapped by ``[%`` and ``%]`` are expanded by Ansible and use the Ansible
-environment and ``{{`` and ``}}`` are reserved for Galaxy templating.
+In this case, variables wrapped by `[%` and `%]` are expanded by Ansible and use the Ansible
+environment and `{{` and `}}` are reserved for Galaxy templating.
 
 Alternatively, Galaxy can be configured to use a custom template on a per-configuration
-object basis by setting the ``template_start`` and/or ``template_end`` variables.
+object basis by setting the `template_start` and/or `template_end` variables.
 
 The following template chunk shows how to override the templating Galaxy does for a
 particular object store configuration. Similar templating overrides work for file source
@@ -431,8 +530,8 @@ plugin templates.
 :language: yaml
 ```
 
-- https://github.com/ansible/ansible/pull/75306
-- https://stackoverflow.com/questions/12083319/add-custom-tokens-in-jinja2-e-g-somevar
+-   https://github.com/ansible/ansible/pull/75306
+-   https://stackoverflow.com/questions/12083319/add-custom-tokens-in-jinja2-e-g-somevar
 
 ## Jinja Template Reference
 
@@ -449,21 +548,21 @@ allows and implements. The only relevant Jinja documentation you'll need in thes
 is probably just those documents on [variables](https://jinja.palletsprojects.com/en/3.0.x/templates/#variables), [filters](https://jinja.palletsprojects.com/en/3.0.x/templates/#filters),
 and the [list of builtin filters](https://jinja.palletsprojects.com/en/3.0.x/templates/#list-of-builtin-filters).
 
-### ``variables``
+### `variables`
 
-This is a typed dictionary object is populated with user supplied values defined via the the ``variables`` section of the configuration template and filled in by the user when they
+This is a typed dictionary object is populated with user supplied values defined via the the `variables` section of the configuration template and filled in by the user when they
 created a new object store or file source.
 
-### ``secrets``
+### `secrets`
 
-This is a dictionary of strings populated with user supplied secrets defined via the the ``secrets`` section of the configuration template and filled in by the user when they
+This is a dictionary of strings populated with user supplied secrets defined via the the `secrets` section of the configuration template and filled in by the user when they
 created a new object store or file source.
 
 A deep dive into these can be found in the [User Secrets](#user-secrets) section of this document.
 
-### ``environment``
+### `environment`
 
-This dictionary object is populated with admin-supplied values defined via the the ``environment``
+This dictionary object is populated with admin-supplied values defined via the the `environment`
 section of the configuration template.
 
 A deep dive into these can be found in the [Admin Secrets](#admin-secrets) section of this document.
@@ -472,18 +571,17 @@ A deep dive into these can be found in the [Admin Secrets](#admin-secrets) secti
 :language: yaml
 ```
 
-### ``user``
+### `user`
 
 This dictionary object exposes information about user configuring and using a target template
-configuration. These values are populated from the ``galaxy_user`` table of the Galaxy database.
+configuration. These values are populated from the `galaxy_user` table of the Galaxy database.
 The current properties exposed include:
 
-| Key          | Description                                               | 
-|--------------|-----------------------------------------------------------|
-| ``username`` | string corresponding the username of the Galaxy user      |
-| ``email``    | string corresponding the email of the Galaxy user         |
-| ``id``       | integer primary key of user object in the Galaxy database |
-
+| Key        | Description                                               |
+| ---------- | --------------------------------------------------------- |
+| `username` | string corresponding the username of the Galaxy user      |
+| `email`    | string corresponding the email of the Galaxy user         |
+| `id`       | integer primary key of user object in the Galaxy database |
 
 The simple example of project scratch storage used to describe these concepts made
 use the Galaxy user's username to generate unique paths.
@@ -492,16 +590,16 @@ use the Galaxy user's username to generate unique paths.
 :language: yaml
 ```
 
-### ``ensure_path_component``
+### `ensure_path_component`
 
 This [Jinja filter](https://jinja.palletsprojects.com/en/3.0.x/templates/#filters)
 will fail template evaluation if the value it is applied to is not
-a simple directory name. If it contain ``..`` or ``/`` or in some other way might
+a simple directory name. If it contain `..` or `/` or in some other way might
 be used to attempt path exploitation of cause odd path-related bugs. This is
-useful when producing paths for ``disk`` object stores or ``posix`` file sources.
+useful when producing paths for `disk` object stores or `posix` file sources.
 
-When taking inputs from users, setting the type of ``path_component`` instead of
-``string`` allows the client to validate potential issues way before this point,
+When taking inputs from users, setting the type of `path_component` instead of
+`string` allows the client to validate potential issues way before this point,
 but many path components might be built from environment variables or usernames
 or sources like this that are not explicitly user inputs.
 
@@ -513,27 +611,27 @@ documentation above.
 :language: yaml
 ```
 
-### ``asbool``
+### `asbool`
 
 This [Jinja filter](https://jinja.palletsprojects.com/en/3.0.x/templates/#filters)
 will use Galaxy configuration style logic to convert string values into boolean ones.
 
-When taking inputs from users, setting the type of ``boolean`` is sufficient to ensure
+When taking inputs from users, setting the type of `boolean` is sufficient to ensure
 a variable is boolean, but "secrets" and environment variables and many other things
 are likely to be of type string but should be used in a template that expects boolean
 values.
 
-An example of an object store template that uses this is ``secure`` environment parameter
+An example of an object store template that uses this is `secure` environment parameter
 on the simple minio example.
 
 ```{literalinclude} ../../../lib/galaxy/objectstore/templates/examples/minio_example.yml
 :language: yaml
 ```
 
-
 ## Connecting Configuration Templates to Secrets
 
 (user-secrets)=
+
 ### User Secrets
 
 Most of the examples in this document use secrets of one kind or another. For instance, in the FTP
@@ -555,8 +653,8 @@ storing and updating secrets. The Vault key for this password will be something
 /galaxy/user/<user_id>/file_source_config/<file_source_instance_uuid>/password
 ```
 
-Here ``user_id`` is the primary key of the User object in the database and 
-``file_source_instance_uuid`` is the ``uuid`` value corresponding to the ``user_file_source``
+Here `user_id` is the primary key of the User object in the database and
+`file_source_instance_uuid` is the `uuid` value corresponding to the `user_file_source`
 table in the database.
 
 User defined object stores are stored in a similar fashion but at:
@@ -576,19 +674,19 @@ individually in the "Secrets" tab.
 
 ![](config-template-secrets-edit.png)
 
-
 (admin-secrets)=
+
 ### Admin Secrets
 
 Administrators may define secrets that are available to all users and aren't parameterized
 on a per-instance basis. These secrets can be injected into template instances through Vault
 keys or through environment variables.
 
-Each template may optionally define an ``environment`` key where these can be defined. The
+Each template may optionally define an `environment` key where these can be defined. The
 following template entry describes a file source that injects the environment variable
-``GALAXY_SECRET_HOME_VAR`` into the template as ``environment.var`` and injects the Vault
-key ``secret_directory_file_source/my_secret`` into the template as ``environment.var``.
-This template uses these variables to construct a root path for a ``posix`` file source
+`GALAXY_SECRET_HOME_VAR` into the template as `environment.var` and injects the Vault
+key `secret_directory_file_source/my_secret` into the template as `environment.var`.
+This template uses these variables to construct a root path for a `posix` file source
 but the same secrets could just as easily store cloud keys and configure an S3 object store.
 
 ```{literalinclude} ../../../lib/galaxy/files/templates/examples/admin_secrets.yml
@@ -597,10 +695,77 @@ but the same secrets could just as easily store cloud keys and configure an S3 o
 
 If you'd like to make the target secrets optional, default values can also be setup.
 The following block demonstrates the same configuration but with default values of
-``default_var`` for the default ``var`` value and ``default_sec`` for the default ``sec``
+`default_var` for the default `var` value and `default_sec` for the default `sec`
 value. These will be used in the target Vault keys are absent or the target environment
 variable is not defined at runtime.
 
 ```{literalinclude} ../../../lib/galaxy/files/templates/examples/admin_secrets_with_defaults.yml
 :language: yaml
 ```
+
+## OAuth 2.0 Enabled Configurations
+
+[OAuth 2.0](https://oauth.net/2/) has become an industry standard for allowing users
+of various services (e.g. Dropbox or Google Drive) to authorize other services (e.g. Galaxy)
+fine grained access to the services. There is a bit of a dance the services need to do
+but the result can be a fairly nice end-user experience. The framework for configuring
+user defined data access templates can support OAuth 2.0.
+
+Galaxy keeps track of which plugin `type`s (currently only file source types) require
+OAuth2 to work properly and will take care of authorization redirection, saving refresh tokens,
+etc.. implicitly. One such `type` is `dropbox`. Here is the production Dropbox
+template distributed with Galaxy.
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/production_dropbox.yml
+:language: yaml
+```
+
+OAuth2 enabled plugin types include template definitions that include `oauth2_client_id`
+and `oauth2_client_secret` in the configuration (as shown in the following specification
+and in the above examples).
+
+![](file_source_dropbox_configuration_template.png)
+
+The above example defines these secrets using environment variables but they can stored in
+Galaxy's Vault explicitly by the admin or written right to the configuration files as shown
+in the next two examples:
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/dropbox_client_secrets_in_vault.yml
+:language: yaml
+```
+
+```{literalinclude} ../../../lib/galaxy/files/templates/examples/dropbox_client_secrets_explicit.yml
+:language: yaml
+```
+
+Looking at the configuration objects that get generated at runtime
+from these templates though - `oauth2_client_id` and `oauth2_client_secret` no longer
+appear and instead have been replaced with a `oauth2_access_token` parameter.
+Galaxy will take care of stripping out the client (e.g. Galaxy server) information and
+replacing it with short-term access tokens generated for the user's resources.
+
+![](file_source_dropbox_configuration.png)
+
+Normally, a UUID is created for each user configured instance object and this is used
+to store the template's explicitly listed secrets in Galaxy's Vault. For OAuth 2.0
+plugin types - before user's are even prompted for configuration metadata they are redirected
+to the remote service and prompted to authorize Galaxy to act on their behalf when using
+the remote service. If they authorize this, the remote service will send an [`authorization
+code`](https://oauth.net/2/grant-types/authorization-code/) to `https://<galaxy_url>/oauth2_callback` along with state information
+to recover which instance is being configured. At this point, Galaxy will fetch a [`refresh token`](https://oauth.net/2/refresh-tokens/) from the remote resource using the
+supplied authorization code. The refresh token is stored in the Vault in key associated with
+the UUID of the object that will be created when the user finishes the creation process.
+Specifically it is stored at
+
+```
+/galaxy/user/<user_id>/file_source_config/<file_source_instance_uuid>/_oauth2_refresh_token
+```
+
+Here is the prefix at the end of `_` is indicating that Galaxy is managing this instead of
+it being listed explicitly in a `secrets` section of the template configuration like the
+explicit Vault secrets discussed in this document.
+
+Galaxy knows how to fetch an [`access token`](https://oauth.net/2/access-tokens/) from this
+refresh token that is actually used to interact with the remote resource. This is the property
+`oauth2_access_token` that is injected into the configuration object shown above and passed
+along to the actual object store or file source plugin implementation.
diff --git a/doc/source/admin/db_migration.md b/doc/source/admin/db_migration.md
index b3edf508496cf4bcc284284e2bb496a94a3e9523..3b29abf53f9abd6b13ae12afc16342cbd83e1317 100644
--- a/doc/source/admin/db_migration.md
+++ b/doc/source/admin/db_migration.md
@@ -542,6 +542,12 @@ After that, run the upgrade script: `./manage_db.sh upgrade`. And you're done!
 
 ## Troubleshooting
 
+### Deadlock detected
+
+If you see a deadlock error, that may have been caused by a migration script requiring exclusive access
+to a database object, such as a row or a table. To avoid this error, it is recommended to shut down
+all Galaxy processes during database migration.
+
 ### How to handle migrations.IncorrectVersionError
 
 If you see this error, you'll need to upgrade or downgrade your database *before* upgrading to
@@ -552,4 +558,3 @@ is 181. Please see [this issue](https://github.com/galaxyproject/galaxy/issues/1
 
 #### Please help us improve this page:
 If you encounter any migration-related errors or issues, please [open an issue](https://github.com/galaxyproject/galaxy/issues/new?assignees=&labels=&template=bug_report.md&title=), and we will add the solution with any relevant context to this page.
-
diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst
index 19862f4c7c2384fade6516fc29874e453315fb84..88821e74fa5d2d424d7813c231d7caf1126251c1 100644
--- a/doc/source/admin/dependency_resolvers.rst
+++ b/doc/source/admin/dependency_resolvers.rst
@@ -207,7 +207,7 @@ debug
 ensure_channels
     Conda channels to enable by default. See https://conda.io/docs/user-guide/tasks/manage-channels.html for more
     information about channels. This defaults to the value of the global ``conda_ensure_channels`` option or
-    ``iuc,conda-forge,bioconda,defaults`` otherwise.  This order should be consistent with the `Bioconda prescribed
+    ``conda-forge,bioconda`` otherwise.  This order should be consistent with the `Bioconda prescribed
     order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__ if it includes ``bioconda``.
 
 auto_install
diff --git a/doc/source/admin/dropbox_callback.png b/doc/source/admin/dropbox_callback.png
new file mode 100644
index 0000000000000000000000000000000000000000..0125e94fec455e2a2b8087ed8ac6331b54720ee6
Binary files /dev/null and b/doc/source/admin/dropbox_callback.png differ
diff --git a/doc/source/admin/dropbox_client_creds.png b/doc/source/admin/dropbox_client_creds.png
new file mode 100644
index 0000000000000000000000000000000000000000..3a029cd3c85aa109f4d84b78d6fbe4c92a7b7972
Binary files /dev/null and b/doc/source/admin/dropbox_client_creds.png differ
diff --git a/doc/source/admin/dropbox_create_app_options_1.png b/doc/source/admin/dropbox_create_app_options_1.png
new file mode 100644
index 0000000000000000000000000000000000000000..839060a05783bebd575d54b26c7dff80b220063f
Binary files /dev/null and b/doc/source/admin/dropbox_create_app_options_1.png differ
diff --git a/doc/source/admin/dropbox_create_button.png b/doc/source/admin/dropbox_create_button.png
new file mode 100644
index 0000000000000000000000000000000000000000..6082eb17498199bac218986787da534bda8e14d9
Binary files /dev/null and b/doc/source/admin/dropbox_create_button.png differ
diff --git a/doc/source/admin/dropbox_scopes.png b/doc/source/admin/dropbox_scopes.png
new file mode 100644
index 0000000000000000000000000000000000000000..5a2643d0a0ff61ebdc7133c1ca836a1700102b0e
Binary files /dev/null and b/doc/source/admin/dropbox_scopes.png differ
diff --git a/doc/source/admin/file_source_azure_configuration.png b/doc/source/admin/file_source_azure_configuration.png
index 99aa460e639a8f29664812289fbc0318d285aac1..e9e778a32a9352760f16765d42e4e22b4e4a0928 100644
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diff --git a/doc/source/admin/file_source_ftp_configuration.png b/doc/source/admin/file_source_ftp_configuration.png
index 72f93e280fd738f862bf4c1b42db968bf54eccb6..712685ce9f56a6b4bbadac69af01e5bd0ab2d007 100644
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diff --git a/doc/source/admin/file_source_posix_configuration.png b/doc/source/admin/file_source_posix_configuration.png
index 4fcd0a0e7f5a1867139e494e6e45d2e912a2c0da..9186f93be05b999501ac4eefd1a54008e9aa3bab 100644
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diff --git a/doc/source/admin/file_source_s3fs_configuration.png b/doc/source/admin/file_source_s3fs_configuration.png
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diff --git a/doc/source/admin/file_source_templates.png b/doc/source/admin/file_source_templates.png
index 5d1556b69269dabd33e10621e2e53f6ed84521e2..fd48cee0eeef12427df4a4301bdf575cc103ad6d 100644
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diff --git a/doc/source/admin/file_source_webdav_configuration.png b/doc/source/admin/file_source_webdav_configuration.png
new file mode 100644
index 0000000000000000000000000000000000000000..1f636147d6fa4a60baf3c1c162820ff5385c2693
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diff --git a/doc/source/admin/file_source_webdav_configuration_template.png b/doc/source/admin/file_source_webdav_configuration_template.png
new file mode 100644
index 0000000000000000000000000000000000000000..26f709677b710465c60960c6f73f6b5c61225aca
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diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst
index 12613a31d46085c4684ef194b6cf7df76fb75597..c142f71cc840c960b2ca84f4fdf639f522d66e4a 100644
--- a/doc/source/admin/framework_dependencies.rst
+++ b/doc/source/admin/framework_dependencies.rst
@@ -185,7 +185,7 @@ Adding additional Galaxy dependencies
 -------------------------------------
 
 New packages can be added to Galaxy, or the versions of existing packages can be
-updated, using `poetry`_ and `Wheelforge`_.
+updated, using `uv`_ and `Wheelforge`_.
 
 If wheels already exist on PyPI for all platforms and Python versions supported
 by Galaxy, you can skip to step 3 in the process below.
@@ -195,11 +195,13 @@ by Galaxy, you can skip to step 3 in the process below.
 
 2. Submit a pull request to `Wheelforge`_.
 
-3. Add the new dependency to the `[tool.poetry.dependencies]` (or to `[tool.poetry.group.dev.dependencies]` if only needed for Galaxy development) section of `pyproject.toml` .
-4. Run `make update-dependencies` to update the requirements file in `lib/galaxy/dependencies`_.
+3. Add the new dependency to the ``dependencies`` list in the ``[project]``
+   section (or to ``dev`` list in the ``[dependency-groups]`` section if only
+   needed for Galaxy development) of `pyproject.toml`_ .
+4. Run ``make update-dependencies`` to update the requirements files in `lib/galaxy/dependencies`_.
 5. Submit a pull request to Galaxy with your changes.
 
-.. _poetry: https://python-poetry.org/
+.. _uv: https://docs.astral.sh/uv/
 .. _Wheelforge: https://github.com/galaxyproject/wheelforge/
-.. _Pull Request #4891: https://github.com/galaxyproject/galaxy/pull/4891
+.. _pyproject.toml: https://github.com/galaxyproject/galaxy/blob/dev/pyproject.toml
 .. _lib/galaxy/dependencies: https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/dependencies
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 45a9ba31a851bc1db5b29c174570a965fcf230b4..c5531e40ab77571621fccaae1f9a3e7fbbd7a108 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -477,7 +477,7 @@
 :Description:
     conda channels to enable by default
     (https://conda.io/docs/user-guide/tasks/manage-channels.html)
-:Default: ``conda-forge,bioconda,defaults``
+:Default: ``conda-forge,bioconda``
 :Type: str
 
 
@@ -509,8 +509,9 @@
 :Description:
     Set to true to instruct Galaxy to install Conda from the web
     automatically if it cannot find a local copy and conda_exec is not
-    configured.
-:Default: ``true``
+    configured. The default is true if running Galaxy from source, and
+    false if running from installed packages.
+:Default: ``None``
 :Type: bool
 
 
@@ -1590,8 +1591,8 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Default cache size for caching object stores if cache not
-    configured for that object store entry.
+    Default cache size, in GB, for caching object stores if the cache
+    is not configured for that object store entry.
 :Default: ``-1``
 :Type: int
 
@@ -1825,7 +1826,7 @@
     registering multiple accounts.  Applies mostly for the main Galaxy
     instance. If no message specified the warning box will not be
     shown.
-:Default: ``Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.``
+:Default: ``Please register only one account to ensure fair sharing of computational resources. Multiple registrations are monitored and will result in account termination and data deletion.``
 :Type: str
 
 
@@ -2044,7 +2045,7 @@
     defaults to "GLOBAL" if not set or the
     `geographical_server_location_code` value is invalid or
     unsupported. To see a full list of supported locations, visit
-    https://galaxyproject.org/admin/carbon_emissions
+    https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
 :Default: ``GLOBAL``
 :Type: str
 
@@ -2112,13 +2113,34 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Map for interactivetool proxy.
+    Map for the interactivetool proxy. Mappings are stored in a SQLite
+    database file located on this path. As an alternative, you may
+    also store them in any other RDBMS supported by SQLAlchemy using
+    the option ``interactivetoolsproxy_map``, which overrides this
+    one.
     The value of this option will be resolved with respect to
     <data_dir>.
 :Default: ``interactivetools_map.sqlite``
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``interactivetoolsproxy_map``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Use a database supported by SQLAlchemy as map for the
+    interactivetool proxy. When this option is set, the value of
+    ``interactivetools_map`` is ignored. The value of this option must
+    be a `SQLAlchemy database URL
+    <https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls>`_.
+    Mappings are written to the table "gxitproxy" within the database.
+    This value cannot match ``database_connection`` nor
+    ``install_database_connection``.
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``interactivetools_prefix``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -5126,6 +5148,26 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``workflow_scheduling_separate_materialization_iteration``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Workflows launched with URI/URL inputs that are not marked as
+    'deferred' are "materialized" (or undeferred) by the workflow
+    scheduler. This might be a lengthy process. Setting this to 'True'
+    will place the invocation back in the queue after materialization
+    before scheduling the workflow so it is less likely to starve
+    other workflow scheduling. Ideally, Galaxy would allow more fine
+    grain control of handlers but until then, this provides a way to
+    tip the balance between "doing more work" and "being more fair".
+    The default here is pretty arbitrary - it has been to False to
+    optimize Galaxy for automated, single user applications where
+    "fairness" is mostly irrelevant.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~
 ``cache_user_job_count``
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -5356,6 +5398,27 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~
+``openai_api_key``
+~~~~~~~~~~~~~~~~~~
+
+:Description:
+    API key for OpenAI (https://openai.com/) to enable the wizard (or
+    more?)
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~
+``openai_model``
+~~~~~~~~~~~~~~~~
+
+:Description:
+    OpenAI model to enable the wizard.
+:Default: ``gpt-4o``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``enable_tool_recommendations``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -5627,4 +5690,38 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_temp_dir``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Directory to store temporary files for file sources. This defaults
+    to new_file_path if not set.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_webdav_use_temp_files``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Default value for use_temp_files for webdav plugins that don't
+    explicitly declare this.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``file_source_listings_expiry_time``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Number of seconds before file source content listings are
+    refreshed. Shorter times will result in more queries while
+    browsing a file sources. Longer times will result in fewer
+    requests to file sources but outdated contents might be displayed
+    to the user. Currently only affects s3fs file sources.
+:Default: ``60``
+:Type: int
 
diff --git a/doc/source/admin/gen_diagrams.py b/doc/source/admin/gen_diagrams.py
index 2627420177ebff1660ccc6c514534f0f4e059b9b..3e1d57a53be49913b1a578bc199350db4496809f 100644
--- a/doc/source/admin/gen_diagrams.py
+++ b/doc/source/admin/gen_diagrams.py
@@ -8,6 +8,8 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 from galaxy.files.templates.models import (
     AzureFileSourceConfiguration,
     AzureFileSourceTemplateConfiguration,
+    DropboxFileSourceConfiguration,
+    DropboxFileSourceTemplateConfiguration,
     FileSourceTemplate,
     FtpFileSourceConfiguration,
     FtpFileSourceTemplateConfiguration,
@@ -15,6 +17,8 @@ from galaxy.files.templates.models import (
     PosixFileSourceTemplateConfiguration,
     S3FSFileSourceConfiguration,
     S3FSFileSourceTemplateConfiguration,
+    WebdavFileSourceConfiguration,
+    WebdavFileSourceTemplateConfiguration,
 )
 from galaxy.objectstore.templates.models import (
     AwsS3ObjectStoreConfiguration,
@@ -47,12 +51,16 @@ class_to_diagram = {
     FileSourceTemplate: "file_source_templates",
     AzureFileSourceTemplateConfiguration: "file_source_azure_configuration_template",
     AzureFileSourceConfiguration: "file_source_azure_configuration",
+    DropboxFileSourceTemplateConfiguration: "file_source_dropbox_configuration_template",
+    DropboxFileSourceConfiguration: "file_source_dropbox_configuration",
     PosixFileSourceTemplateConfiguration: "file_source_posix_configuration_template",
     PosixFileSourceConfiguration: "file_source_posix_configuration",
     S3FSFileSourceTemplateConfiguration: "file_source_s3fs_configuration_template",
     S3FSFileSourceConfiguration: "file_source_s3fs_configuration",
     FtpFileSourceTemplateConfiguration: "file_source_ftp_configuration_template",
     FtpFileSourceConfiguration: "file_source_ftp_configuration",
+    WebdavFileSourceTemplateConfiguration: "file_source_webdav_configuration_template",
+    WebdavFileSourceConfiguration: "file_source_webdav_configuration",
 }
 
 for clazz, diagram_name in class_to_diagram.items():
diff --git a/doc/source/admin/object_store_aws_s3_configuration.png b/doc/source/admin/object_store_aws_s3_configuration.png
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diff --git a/doc/source/admin/object_store_azure_configuration.png b/doc/source/admin/object_store_azure_configuration.png
index bbf2528f772c3181910cbc86181f7e540a4927f1..edbed59cda8863058e3dd6ba1e0388897eb9c789 100644
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diff --git a/doc/source/admin/object_store_boto3_configuration.png b/doc/source/admin/object_store_boto3_configuration.png
index cd8d8ef4ef0a1b30e46ec8c249ea505a8d3fe49a..71b92a84c42f5ddcbcc077da7ceadbb089825d7e 100644
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diff --git a/doc/source/admin/object_store_boto3_configuration_template.png b/doc/source/admin/object_store_boto3_configuration_template.png
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Binary files a/doc/source/admin/object_store_boto3_configuration_template.png and b/doc/source/admin/object_store_boto3_configuration_template.png differ
diff --git a/doc/source/admin/object_store_disk_configuration.png b/doc/source/admin/object_store_disk_configuration.png
index 836e13d6f59ac9a4418cf2ead86575b07fe95118..fe95bd28f70aa95c10ca1e7cceb41f4574eb289a 100644
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diff --git a/doc/source/admin/object_store_disk_configuration_template.png b/doc/source/admin/object_store_disk_configuration_template.png
index d851772ed4221d5b6c074e19473c0587863cb71a..f9868ee220911d255c3d081452481027edbbdb0b 100644
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diff --git a/doc/source/admin/object_store_generic_s3_configuration.png b/doc/source/admin/object_store_generic_s3_configuration.png
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diff --git a/doc/source/admin/object_store_generic_s3_configuration_template.png b/doc/source/admin/object_store_generic_s3_configuration_template.png
index 04b50dd5049e59d97e2c3c18e1fc5b9c9f23ebb1..678f1c7357fe822ddcc807b7b0fc6a5e291f96b2 100644
Binary files a/doc/source/admin/object_store_generic_s3_configuration_template.png and b/doc/source/admin/object_store_generic_s3_configuration_template.png differ
diff --git a/doc/source/admin/object_store_templates.png b/doc/source/admin/object_store_templates.png
index a43b5acf260efa8aa69902055ac080b505363710..5c7e8d1bb71ce85a827c2ba7519a2fe47c62f763 100644
Binary files a/doc/source/admin/object_store_templates.png and b/doc/source/admin/object_store_templates.png differ
diff --git a/doc/source/admin/search_for_new_screenshots.py b/doc/source/admin/search_for_new_screenshots.py
index 95f0ac2cbc69616b77e29e8e7828103dbe8a503b..ea09034da8d49e298ef6f7b1ceff259926a4467f 100644
--- a/doc/source/admin/search_for_new_screenshots.py
+++ b/doc/source/admin/search_for_new_screenshots.py
@@ -22,6 +22,7 @@ SEARCH_FOR = [
     "user_file_source_form_full_aws_public.png",
     "user_file_source_form_full_azure.png",
     "user_file_source_form_full_ftp.png",
+    "user_file_source_form_full_webdav.png",
 ]
 
 
diff --git a/doc/source/admin/special_topics/interactivetools.rst b/doc/source/admin/special_topics/interactivetools.rst
index 6d032c02d05cf78de1f23a3ceb50faaaecaa8788..f66d895e8725c8e3c3448e5c7663371498bf9c66 100644
--- a/doc/source/admin/special_topics/interactivetools.rst
+++ b/doc/source/admin/special_topics/interactivetools.rst
@@ -102,6 +102,19 @@ The ``gx-it-proxy`` config relates to an important service in the InteractiveToo
 proxy. ``gx-it-proxy`` runs as a separate process listening at port 4002 (by default). HTTP requests are decoded based on
 the URL and headers, then somewhat massaged, and finally forwarded to the correct entry point port of the target InteractiveTool.
 
+.. note::
+
+    Entry point mappings used by the proxy are stored on a SQLite database file located at ``interactivetools_map``. In
+    `some situations <https://www.sqlite.org/whentouse.html#situations_where_a_client_server_rdbms_may_work_better>`_,
+    SQLite may not be the best choice. A common case is a high-availability production setup, meaning that multiple
+    copies of Galaxy are running on different servers behind a load balancer.
+
+    For these situations, there exists an optional |configuration option interactivetoolsproxy_map|_ that allows using
+    any database supported by SQLAlchemy (it overrides ``interactivetools_map``).
+
+.. |configuration option interactivetoolsproxy_map| replace:: configuration option ``interactivetoolsproxy_map``
+.. _configuration option interactivetoolsproxy_map: ../config.html#interactivetoolsproxy-map
+
 .. note::
 
     A previous config option ``interactivetools_shorten_url`` was removed in commit `#73100de <https://github.com/galaxyproject/galaxy/pull/16795/commits/73100de17149ca3486c83b8c6ded74987c68a836>`_
diff --git a/doc/source/admin/user_file_source_form_full_webdav.png b/doc/source/admin/user_file_source_form_full_webdav.png
new file mode 100755
index 0000000000000000000000000000000000000000..6e5ed85b5096744143056006b4e73e3e6b587d6e
Binary files /dev/null and b/doc/source/admin/user_file_source_form_full_webdav.png differ
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 05b2c75f2e1b3bb092758494ecb5655b81c61a8e..57f71026b150d4cb0c3bc3bc89f9dc936706c236 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -162,9 +162,6 @@ html_theme_options = {
     "navigation_depth": 2,
 }
 
-# Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 # html_title = None
diff --git a/doc/source/dev/create_release.rst b/doc/source/dev/create_release.rst
index 75d1ff7d469d3efb498563b7691152cc800cbcf6..22f4783be918b8635627ecc849d0f0663a7708ab 100644
--- a/doc/source/dev/create_release.rst
+++ b/doc/source/dev/create_release.rst
@@ -36,11 +36,12 @@ and that you have configured your remotes so that you can push to the configured
 The script should abort gracefully if that is not the case.
 
 Follow these steps:
+    0. Enable the push URL of the galaxyproject git remote if you have disabled it (e.g. `git remote set-url --push upstream git@github.com:galaxyproject/galaxy.git`) and disable any pre-commit hooks you might have
     1. Check out the branch from which you want to create a release, e.g. release_23.0: `git checkout release_23.0`
     2. Activate your local virtualenv with Galaxy's dev requirements: `. .venv/bin/activate`
     3. Update Galaxy's dev dependencies (if you haven't done this in a while): `pip install -r lib/galaxy/dependencies/dev-requirements.txt`
     4. You need a personal access token from github (only needs public read permissions).
-    5. `GITHUB_AUTH=$YOUR_PAT_FROM_STEP_3 galaxy-release-util create-release --new-version 23.0.1 --last-commit v23.0`
+    5. `GITHUB_AUTH=$YOUR_PAT_FROM_STEP_4 galaxy-release-util create-release --new-version 23.0.1 --last-commit v23.0`
     6. Follow along the prompts and make sure the proposed changes look correct
 
 When the script is finished you should find a new tag in the GitHub interface, as well as updated release and dev branches.
diff --git a/doc/source/dev/data_types.md b/doc/source/dev/data_types.md
index fb03c4fe5d04dee0b09f36b860b9bbb2ad3aeb9d..16b970290be2e2bc1b406cb7e5c7e6ecd9065e1d 100644
--- a/doc/source/dev/data_types.md
+++ b/doc/source/dev/data_types.md
@@ -36,7 +36,8 @@ tag section of the `datatypes_conf.xml` file. Sample
 where
 
 - `extension` - the data type's Dataset file extension (e.g., `ab1`, `bed`,
-  `gff`, `qual`, etc.)
+  `gff`, `qual`, etc.). The extension must consist only of lowercase letters,
+  numbers, `_`, `-`, and `.`.
 - `type` - the path to the class for that data type.
 - `mimetype` - if present (it's optional), the data type's mime type
 - `display_in_upload` - if present (it's optional and defaults to False), the
diff --git a/doc/source/dev/image.Makefile b/doc/source/dev/image.Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..75cb5e1910e47b6f39d62376455e7709ee63762c
--- /dev/null
+++ b/doc/source/dev/image.Makefile
@@ -0,0 +1,11 @@
+MINDMAPS := $(wildcard *.mindmap.yml)
+INPUTS := $(wildcard *.plantuml.txt)
+OUTPUTS := $(INPUTS:.txt=.svg)
+
+all: plantuml.jar $(MINDMAPS) $(OUTPUTS)
+
+$(OUTPUTS): $(INPUTS) $(MINDMAPS)
+	java -jar plantuml.jar -c plantuml_options.txt -tsvg $(INPUTS)
+
+plantuml.jar:
+	wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar || curl --output plantuml.jar http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
diff --git a/doc/source/dev/index.rst b/doc/source/dev/index.rst
index 0957dfc5aeec0ad6e58321a52a67fd809eb5d83c..21a2760c24b4453716ca95c25ed2f373f6eca599 100644
--- a/doc/source/dev/index.rst
+++ b/doc/source/dev/index.rst
@@ -17,6 +17,7 @@ A multi-hour long video playlist covering these slides can be found at
   build_a_job_runner
   finding_and_improving_slow_code
   data_managers
+  data_source
   data_types
   faq
   writing_tests
diff --git a/doc/source/dev/plantuml_options.txt b/doc/source/dev/plantuml_options.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70424ef26736335d7520967e78c300170cdca251
--- /dev/null
+++ b/doc/source/dev/plantuml_options.txt
@@ -0,0 +1,51 @@
+' skinparam handwritten true
+' skinparam roundcorner 20
+
+skinparam class {
+    ArrowFontColor DarkOrange
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam object {
+    ArrowFontColor DarkOrange
+    BackgroundColor #FFEFD5
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam ComponentBackgroundColor #FFEFD5
+skinparam ComponentBorderColor DarkOrange
+
+skinparam DatabaseBackgroundColor #FFEFD5
+skinparam DatabaseBorderColor DarkOrange
+
+skinparam StorageBackgroundColor #FFEFD5
+skinparam StorageBorderColor DarkOrange
+
+skinparam QueueBackgroundColor #FFEFD5
+skinparam QueueBorderColor DarkOrange
+
+skinparam note {
+    BackgroundColor #FFEFD5
+    BorderColor #BF5700
+}
+
+skinparam sequence {
+    ArrowColor Orange
+    ArrowFontColor DarkOrange
+    ActorBorderColor DarkOrange
+    ActorBackgroundColor #FFEFD5
+
+    ParticipantBorderColor DarkOrange
+    ParticipantBackgroundColor #FFEFD5
+
+    LifeLineBorderColor DarkOrange
+    LifeLineBackgroundColor #FFEFD5
+
+    DividerBorderColor DarkOrange
+    GroupBorderColor DarkOrange
+}
+
diff --git a/doc/source/dev/plantuml_style.txt b/doc/source/dev/plantuml_style.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18911d622b75db7110f16c6f736cf78fd2860622
--- /dev/null
+++ b/doc/source/dev/plantuml_style.txt
@@ -0,0 +1,9 @@
+<style>
+mindmapDiagram {
+    node {
+        BackgroundColor #FFEFD5
+        BorderColor DarkOrange
+        LineColor Orange
+    }
+}
+</style>
diff --git a/doc/source/dev/tool_state_api.plantuml.svg b/doc/source/dev/tool_state_api.plantuml.svg
new file mode 100644
index 0000000000000000000000000000000000000000..3aaf86c1ee004f7fc5f6a3a88c0cb066355c460c
--- /dev/null
+++ b/doc/source/dev/tool_state_api.plantuml.svg
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="530px" preserveAspectRatio="none" style="width:732px;height:530px;background:#FFFFFF;" version="1.1" viewBox="0 0 732 530" width="732px" zoomAndPan="magnify"><defs/><g><line style="stroke:#181818;stroke-width:0.5;stroke-dasharray:5.0,5.0;" x1="52" x2="52" y1="67.4883" y2="451.5254"/><line style="stroke:#181818;stroke-width:0.5;stroke-dasharray:5.0,5.0;" x1="196" x2="196" y1="67.4883" y2="451.5254"/><line style="stroke:#181818;stroke-width:0.5;stroke-dasharray:5.0,5.0;" x1="340.5" x2="340.5" y1="67.4883" y2="451.5254"/><line style="stroke:#181818;stroke-width:0.5;stroke-dasharray:5.0,5.0;" x1="583" x2="583" y1="67.4883" y2="451.5254"/><line style="stroke:#181818;stroke-width:0.5;stroke-dasharray:5.0,5.0;" x1="676" x2="676" y1="67.4883" y2="451.5254"/><rect fill="#E2E2F0" height="30.4883" rx="2.5" ry="2.5" 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style="stroke:#181818;stroke-width:1.0;" x1="382.5" x2="382.5" y1="257.3516" y2="270.3516"/><line style="stroke:#181818;stroke-width:1.0;" x1="341.5" x2="382.5" y1="270.3516" y2="270.3516"/><polygon fill="#181818" points="351.5,266.3516,341.5,270.3516,351.5,274.3516,347.5,270.3516" style="stroke:#181818;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="166" x="347.5" y="237.2988">decode() RequestToolState</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="186" x="347.5" y="252.6094">into RequestInternalToolState</text><polygon fill="#181818" points="571.5,295.6621,581.5,299.6621,571.5,303.6621,575.5,299.6621" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="340.5" x2="577.5" y1="299.6621" y2="299.6621"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="213" x="347.5" y="294.9199">Serialize RequestInternalToolState</text><polygon fill="#181818" points="664.5,340.2832,674.5,344.2832,664.5,348.2832,668.5,344.2832" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="340.5" x2="670.5" y1="344.2832" y2="344.2832"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="221" x="347.5" y="324.2305">Queue QueueJobs with reference to</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="219" x="347.5" y="339.541">persisted RequestInternalToolState</text><polygon fill="#181818" points="207.5,384.9043,197.5,388.9043,207.5,392.9043,203.5,388.9043" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="201.5" x2="339.5" y1="388.9043" y2="388.9043"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="120" x="213.5" y="368.8516">JobCreateResponse</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="105" x="217.5" y="384.1621">(pydantic model)</text><polygon fill="#181818" points="63.5,429.5254,53.5,433.5254,63.5,437.5254,59.5,433.5254" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="57.5" x2="195.5" y1="433.5254" y2="433.5254"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="120" x="69.5" y="413.4727">JobCreateResponse</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="53" x="73.5" y="428.7832">(as json)</text><!--MD5=[d339d14969a14a06d7ae0fd7df2a6dba]
+@startuml
+
+'!include plantuml_options.txt
+participant "API Request" as apireq
+boundary    "Jobs API"    as api
+participant     "Job Service" as service
+database    Database    as database
+queue       TaskQueue   as queue
+apireq -> api : HTTP JSON
+api -> service : To boundary
+service -> service : Build RequestToolState
+service -> service : Validate RequestToolState (pydantic)
+service -> service : decode() RequestToolState \ninto RequestInternalToolState
+service -> database : Serialize RequestInternalToolState
+service -> queue : Queue QueueJobs with reference to\npersisted RequestInternalToolState
+service -> api : JobCreateResponse\n (pydantic model)
+api -> apireq : JobCreateResponse\n (as json)
+@enduml
+
+@startuml
+
+participant "API Request" as apireq
+boundary    "Jobs API"    as api
+participant     "Job Service" as service
+database    Database    as database
+queue       TaskQueue   as queue
+apireq -> api : HTTP JSON
+api -> service : To boundary
+service -> service : Build RequestToolState
+service -> service : Validate RequestToolState (pydantic)
+service -> service : decode() RequestToolState \ninto RequestInternalToolState
+service -> database : Serialize RequestInternalToolState
+service -> queue : Queue QueueJobs with reference to\npersisted RequestInternalToolState
+service -> api : JobCreateResponse\n (pydantic model)
+api -> apireq : JobCreateResponse\n (as json)
+@enduml
+
+PlantUML version 1.2022.8(Sun Sep 25 05:00:33 EDT 2022)
+(GPL source distribution)
+Java Runtime: Java(TM) SE Runtime Environment
+JVM: Java HotSpot(TM) 64-Bit Server VM
+Default Encoding: UTF-8
+Language: en
+Country: US
+--></g></svg>
\ No newline at end of file
diff --git a/doc/source/dev/tool_state_api.plantuml.txt b/doc/source/dev/tool_state_api.plantuml.txt
new file mode 100644
index 0000000000000000000000000000000000000000..060b4c5bdb9e517f1fe6ce3f1d6198aa91e2e908
--- /dev/null
+++ b/doc/source/dev/tool_state_api.plantuml.txt
@@ -0,0 +1,17 @@
+@startuml
+'!include plantuml_options.txt
+participant "API Request" as apireq
+boundary    "Jobs API"    as api
+participant     "Job Service" as service
+database    Database    as database
+queue       TaskQueue   as queue
+apireq -> api : HTTP JSON
+api -> service : To boundary
+service -> service : Build RequestToolState
+service -> service : Validate RequestToolState (pydantic)
+service -> service : decode() RequestToolState \ninto RequestInternalToolState
+service -> database : Serialize RequestInternalToolState
+service -> queue : Queue QueueJobs with reference to\npersisted RequestInternalToolState
+service -> api : JobCreateResponse\n (pydantic model)
+api -> apireq : JobCreateResponse\n (as json)
+@enduml
diff --git a/doc/source/dev/tool_state_state_classes.plantuml.svg b/doc/source/dev/tool_state_state_classes.plantuml.svg
new file mode 100644
index 0000000000000000000000000000000000000000..28c7da1c909219967d8dc6ad2a2c8348aad6108f
--- /dev/null
+++ b/doc/source/dev/tool_state_state_classes.plantuml.svg
@@ -0,0 +1,174 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="610px" preserveAspectRatio="none" style="width:1812px;height:610px;background:#FFFFFF;" version="1.1" viewBox="0 0 1812 610" width="1812px" zoomAndPan="magnify"><defs/><g><!--MD5=[85f7edf671c9ca26ac4c2dd7910a1a26]
+cluster galaxy.tool_util.parameters.state--><g id="cluster_galaxy.tool_util.parameters.state"><path d="M8.5,6 L242.5,6 A3.75,3.75 0 0 1 245,8.5 L252,28.4883 L1802.5,28.4883 A2.5,2.5 0 0 1 1805,30.9883 L1805,600.65 A2.5,2.5 0 0 1 1802.5,603.15 L8.5,603.15 A2.5,2.5 0 0 1 6,600.65 L6,8.5 A2.5,2.5 0 0 1 8.5,6 " fill="none" style="stroke:#FF8C00;stroke-width:1.5;"/><line style="stroke:#FF8C00;stroke-width:1.5;" x1="6" x2="252" y1="28.4883" y2="28.4883"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="233" x="10" y="21.5352">galaxy.tool_util.parameters.state</text></g><!--MD5=[001dd53740ce1259671441135e7c1cd4]
+class ToolState--><g id="elem_ToolState"><rect codeLine="5" fill="#FFEFD5" height="113.9531" id="ToolState" rx="2.5" ry="2.5" style="stroke:#FF8C00;stroke-width:0.5;" width="573" x="822.5" y="41"/><ellipse cx="1072.25" cy="57" fill="#ADD1B2" rx="11" ry="11" style="stroke:#181818;stroke-width:1.0;"/><path d="M1074.7231,63.1431 Q1074.1421,63.4419 1073.5029,63.5913 Q1072.8638,63.7407 1072.1582,63.7407 Q1069.6514,63.7407 1068.3315,62.0889 Q1067.0117,60.437 1067.0117,57.3159 Q1067.0117,54.1865 1068.3315,52.5347 Q1069.6514,50.8828 1072.1582,50.8828 Q1072.8638,50.8828 1073.5112,51.0322 Q1074.1587,51.1816 1074.7231,51.4805 L1074.7231,54.2031 Q1074.0923,53.6221 1073.4988,53.3523 Q1072.9053,53.0825 1072.2744,53.0825 Q1070.9297,53.0825 1070.2449,54.1492 Q1069.5601,55.2158 1069.5601,57.3159 Q1069.5601,59.4077 1070.2449,60.4744 Q1070.9297,61.541 1072.2744,61.541 Q1072.9053,61.541 1073.4988,61.2712 Q1074.0923,61.0015 1074.7231,60.4204 Z " fill="#000000"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="65" x="1092.75" y="62.291">ToolState</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="823.5" x2="1394.5" y1="73" y2="73"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="167" x="828.5" y="90.5352">state_representation: str</text><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="172" x="828.5" y="107.0234">input_state: Dict[str, Any]</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="823.5" x2="1394.5" y1="113.9766" y2="113.9766"/><ellipse cx="833.5" cy="127.7207" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="297" x="842.5" y="131.5117">validate(parameters: ToolParameterBundle)</text><ellipse cx="833.5" cy="144.209" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" font-style="italic" lengthAdjust="spacing" textLength="547" x="842.5" y="148">_to_base_model(parameters: ToolParameterBundle): Optional[Type[BaseModel]]</text></g><!--MD5=[93f66f43011efc5ae11c3d66e5c838fe]
+class RequestToolState--><g id="elem_RequestToolState"><rect codeLine="12" fill="#FFEFD5" height="80.9766" id="RequestToolState" rx="2.5" ry="2.5" style="stroke:#FF8C00;stroke-width:0.5;" width="504" x="22" y="215.95"/><ellipse cx="209.75" cy="231.95" fill="#ADD1B2" rx="11" ry="11" style="stroke:#181818;stroke-width:1.0;"/><path d="M212.2231,238.0931 Q211.6421,238.3919 211.0029,238.5413 Q210.3638,238.6907 209.6582,238.6907 Q207.1514,238.6907 205.8315,237.0389 Q204.5117,235.387 204.5117,232.2659 Q204.5117,229.1365 205.8315,227.4847 Q207.1514,225.8328 209.6582,225.8328 Q210.3638,225.8328 211.0112,225.9822 Q211.6587,226.1316 212.2231,226.4305 L212.2231,229.1531 Q211.5923,228.5721 210.9988,228.3023 Q210.4053,228.0325 209.7744,228.0325 Q208.4297,228.0325 207.7449,229.0992 Q207.0601,230.1658 207.0601,232.2659 Q207.0601,234.3577 207.7449,235.4244 Q208.4297,236.491 209.7744,236.491 Q210.4053,236.491 210.9988,236.2212 Q211.5923,235.9515 212.2231,235.3704 Z " fill="#000000"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="120" x="230.25" y="237.241">RequestToolState</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="23" x2="525" y1="247.95" y2="247.95"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="222" x="28" y="265.4852">state_representation = "request"</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="23" x2="525" y1="272.4383" y2="272.4383"/><ellipse cx="33" cy="286.1824" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="478" x="42" y="289.9734">_to_base_model(parameters: ToolParameterBundle): Type[BaseModel]</text></g><g id="elem_GMN5"><path d="M55.5,386.45 L55.5,442.3816 A0,0 0 0 0 55.5,442.3816 L298.5,442.3816 A0,0 0 0 0 298.5,442.3816 L298.5,396.45 L288.5,386.45 L198.04,386.45 L249.27,297.21 L190.04,386.45 L55.5,386.45 A0,0 0 0 0 55.5,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><path d="M288.5,386.45 L288.5,396.45 L298.5,396.45 L288.5,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="185" x="61.5" y="404.0184">Object references of the form</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="192" x="61.5" y="419.3289">{src: "hda", id: &lt;encoded_id&gt;}.</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="218" x="65.5" y="434.6395">Allow mapping/reduce constructs.</text></g><!--MD5=[93d581e844301c3bb0d1bdd786d99f81]
+class RequestInternalToolState--><g id="elem_RequestInternalToolState"><rect codeLine="18" fill="#FFEFD5" height="80.9766" id="RequestInternalToolState" rx="2.5" ry="2.5" style="stroke:#FF8C00;stroke-width:0.5;" width="504" x="621" y="215.95"/><ellipse cx="782.25" cy="231.95" fill="#ADD1B2" rx="11" ry="11" style="stroke:#181818;stroke-width:1.0;"/><path d="M784.7231,238.0931 Q784.1421,238.3919 783.5029,238.5413 Q782.8638,238.6907 782.1582,238.6907 Q779.6514,238.6907 778.3315,237.0389 Q777.0117,235.387 777.0117,232.2659 Q777.0117,229.1365 778.3315,227.4847 Q779.6514,225.8328 782.1582,225.8328 Q782.8638,225.8328 783.5112,225.9822 Q784.1587,226.1316 784.7231,226.4305 L784.7231,229.1531 Q784.0923,228.5721 783.4988,228.3023 Q782.9053,228.0325 782.2744,228.0325 Q780.9297,228.0325 780.2449,229.0992 Q779.5601,230.1658 779.5601,232.2659 Q779.5601,234.3577 780.2449,235.4244 Q780.9297,236.491 782.2744,236.491 Q782.9053,236.491 783.4988,236.2212 Q784.0923,235.9515 784.7231,235.3704 Z " fill="#000000"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="173" x="802.75" y="237.241">RequestInternalToolState</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="622" x2="1124" y1="247.95" y2="247.95"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="282" x="627" y="265.4852">state_representation = "request_internal"</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="622" x2="1124" y1="272.4383" y2="272.4383"/><ellipse cx="632" cy="286.1824" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="478" x="641" y="289.9734">_to_base_model(parameters: ToolParameterBundle): Type[BaseModel]</text></g><g id="elem_GMN9"><path d="M333,386.45 L333,442.3816 A0,0 0 0 0 333,442.3816 L709,442.3816 A0,0 0 0 0 709,442.3816 L709,396.45 L699,386.45 L586.96,386.45 L782.81,297.41 L578.96,386.45 L333,386.45 A0,0 0 0 0 333,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><path d="M699,386.45 L699,396.45 L709,396.45 L699,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="185" x="339" y="404.0184">Object references of the form</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="192" x="339" y="419.3289">{src: "hda", id: &lt;decoded_id&gt;}.</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="351" x="343" y="434.6395">Allow mapping/reduce constructs. Allows URI src dicts.</text></g><!--MD5=[f215adf382bf0ace6a358f4944a6558b]
+class RequestInternalDereferencedToolState--><g id="elem_RequestInternalDereferencedToolState"><rect codeLine="24" fill="#FFEFD5" height="80.9766" id="RequestInternalDereferencedToolState" rx="2.5" ry="2.5" style="stroke:#FF8C00;stroke-width:0.5;" width="504" x="1248" y="215.95"/><ellipse cx="1363.25" cy="231.95" fill="#ADD1B2" rx="11" ry="11" style="stroke:#181818;stroke-width:1.0;"/><path d="M1365.7231,238.0931 Q1365.1421,238.3919 1364.5029,238.5413 Q1363.8638,238.6907 1363.1582,238.6907 Q1360.6514,238.6907 1359.3315,237.0389 Q1358.0117,235.387 1358.0117,232.2659 Q1358.0117,229.1365 1359.3315,227.4847 Q1360.6514,225.8328 1363.1582,225.8328 Q1363.8638,225.8328 1364.5112,225.9822 Q1365.1587,226.1316 1365.7231,226.4305 L1365.7231,229.1531 Q1365.0923,228.5721 1364.4988,228.3023 Q1363.9053,228.0325 1363.2744,228.0325 Q1361.9297,228.0325 1361.2449,229.0992 Q1360.5601,230.1658 1360.5601,232.2659 Q1360.5601,234.3577 1361.2449,235.4244 Q1361.9297,236.491 1363.2744,236.491 Q1363.9053,236.491 1364.4988,236.2212 Q1365.0923,235.9515 1365.7231,235.3704 Z " fill="#000000"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="265" x="1383.75" y="237.241">RequestInternalDereferencedToolState</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="1249" x2="1751" y1="247.95" y2="247.95"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="282" x="1254" y="265.4852">state_representation = "request_internal"</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="1249" x2="1751" y1="272.4383" y2="272.4383"/><ellipse cx="1259" cy="286.1824" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="478" x="1268" y="289.9734">_to_base_model(parameters: ToolParameterBundle): Type[BaseModel]</text></g><g id="elem_GMN13"><path d="M744,386.45 L744,442.3816 A0,0 0 0 0 744,442.3816 L1250,442.3816 A0,0 0 0 0 1250,442.3816 L1250,396.45 L1240,386.45 L1089.54,386.45 L1371.12,297.41 L1081.54,386.45 L744,386.45 A0,0 0 0 0 744,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><path d="M1240,386.45 L1240,396.45 L1250,396.45 L1240,386.45 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="185" x="750" y="404.0184">Object references of the form</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="192" x="750" y="419.3289">{src: "hda", id: &lt;decoded_id&gt;}.</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="481" x="754" y="434.6395">Allow mapping/reduce constructs. No URI src dicts - all converted to HDAs.</text></g><!--MD5=[48b694eadbf7bc2510a32379c1b70352]
+class JobInternalToolState--><g id="elem_JobInternalToolState"><rect codeLine="30" fill="#FFEFD5" height="80.9766" id="JobInternalToolState" rx="2.5" ry="2.5" style="stroke:#FF8C00;stroke-width:0.5;" width="504" x="1285" y="373.93"/><ellipse cx="1462.75" cy="389.93" fill="#ADD1B2" rx="11" ry="11" style="stroke:#181818;stroke-width:1.0;"/><path d="M1465.2231,396.0731 Q1464.6421,396.3719 1464.0029,396.5213 Q1463.3638,396.6707 1462.6582,396.6707 Q1460.1514,396.6707 1458.8315,395.0189 Q1457.5117,393.367 1457.5117,390.2459 Q1457.5117,387.1165 1458.8315,385.4647 Q1460.1514,383.8128 1462.6582,383.8128 Q1463.3638,383.8128 1464.0112,383.9622 Q1464.6587,384.1116 1465.2231,384.4105 L1465.2231,387.1331 Q1464.5923,386.5521 1463.9988,386.2823 Q1463.4053,386.0125 1462.7744,386.0125 Q1461.4297,386.0125 1460.7449,387.0792 Q1460.0601,388.1458 1460.0601,390.2459 Q1460.0601,392.3377 1460.7449,393.4044 Q1461.4297,394.471 1462.7744,394.471 Q1463.4053,394.471 1463.9988,394.2012 Q1464.5923,393.9315 1465.2231,393.3504 Z " fill="#000000"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="140" x="1483.25" y="395.221">JobInternalToolState</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="1286" x2="1788" y1="405.93" y2="405.93"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="1291" y="423.4652">state_representation = "job_internal"</text><line style="stroke:#FF8C00;stroke-width:0.5;" x1="1286" x2="1788" y1="430.4183" y2="430.4183"/><ellipse cx="1296" cy="444.1624" fill="#84BE84" rx="3" ry="3" style="stroke:#038048;stroke-width:1.0;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="478" x="1305" y="447.9534">_to_base_model(parameters: ToolParameterBundle): Type[BaseModel]</text></g><g id="elem_GMN17"><path d="M1415,515.91 L1415,587.1522 A0,0 0 0 0 1415,587.1522 L1659,587.1522 A0,0 0 0 0 1659,587.1522 L1659,525.91 L1649,515.91 L1541,515.91 L1537,455.23 L1533,515.91 L1415,515.91 A0,0 0 0 0 1415,515.91 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><path d="M1649,515.91 L1649,525.91 L1659,525.91 L1649,515.91 " fill="#FFEFD5" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="185" x="1421" y="533.4784">Object references of the form</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="192" x="1421" y="548.7889">{src: "hda", id: &lt;decoded_id&gt;}.</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="219" x="1425" y="564.0995">Mapping constructs expanded out.</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="144" x="1425" y="579.41">(Defaults are inserted?)</text></g><!--MD5=[269f52e8487e2a76b96d386d755c75d8]
+reverse link ToolState to RequestToolState--><g id="link_ToolState_RequestToolState"><path codeLine="37" d="M801.15,156.66 C696.82,176.21 582.66,197.61 487.33,215.47 " fill="none" id="ToolState-backto-RequestToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="none" points="799.79,149.8,820.74,152.99,802.37,163.56,799.79,149.8" style="stroke:#FFA500;stroke-width:1.0;"/></g><!--MD5=[dd93b154e0c0c396ba5562a34580b1a6]
+reverse link ToolState to RequestInternalToolState--><g id="link_ToolState_RequestInternalToolState"><path codeLine="38" d="M1006.55,166.9 C981.47,183.53 955.45,200.78 933.1,215.6 " fill="none" id="ToolState-backto-RequestInternalToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="none" points="1002.33,161.3,1022.87,156.08,1010.07,172.97,1002.33,161.3" style="stroke:#FFA500;stroke-width:1.0;"/></g><!--MD5=[0358dda221f8b059da8053d6fb03640e]
+reverse link ToolState to RequestInternalDereferencedToolState--><g id="link_ToolState_RequestInternalDereferencedToolState"><path codeLine="39" d="M1269.66,163.27 C1313.89,180.97 1360.57,199.65 1400.26,215.53 " fill="none" id="ToolState-backto-RequestInternalDereferencedToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="none" points="1267.26,169.85,1251.29,155.92,1272.46,156.85,1267.26,169.85" style="stroke:#FFA500;stroke-width:1.0;"/></g><!--MD5=[36305bbce111c7e7d9f6236ae242d2c7]
+reverse link ToolState to JobInternalToolState--><g id="link_ToolState_JobInternalToolState"><path codeLine="40" d="M1416.95,115.94 C1566.33,131.28 1723.47,160.47 1770,215.95 C1793.13,243.53 1788.92,266.32 1770,296.93 C1748.66,331.46 1713.65,356.09 1677.17,373.53 " fill="none" id="ToolState-backto-JobInternalToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="none" points="1416.66,122.95,1397.44,114.02,1418.03,109.02,1416.66,122.95" style="stroke:#FFA500;stroke-width:1.0;"/></g><!--MD5=[7b766fbe81ea9c5eae779649ae0bfd4b]
+link RequestToolState to RequestInternalToolState--><g id="link_RequestToolState_RequestInternalToolState"><path codeLine="42" d="M526.29,256.44 C557.47,256.44 589.34,256.44 620.52,256.44 " fill="none" id="RequestToolState-RequestInternalToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="#FF8C00" points="553.5,245.0953,544.4549,242.1563,544.4549,248.0342,553.5,245.0953" style="stroke:#FF8C00;stroke-width:1.0;"/><text fill="#FF8C00" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="45" x="557.5" y="250.0084">decode</text></g><!--MD5=[fba7cd1c751470181daccad9648ff09d]
+link RequestInternalToolState to RequestInternalDereferencedToolState--><g id="link_RequestInternalToolState_RequestInternalDereferencedToolState"><path codeLine="44" d="M1125.31,256.44 C1165.64,256.44 1207.37,256.44 1247.69,256.44 " fill="none" id="RequestInternalToolState-RequestInternalDereferencedToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="#FF8C00" points="1152.5,245.0953,1143.4549,242.1563,1143.4549,248.0342,1152.5,245.0953" style="stroke:#FF8C00;stroke-width:1.0;"/><text fill="#FF8C00" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="73" x="1156.5" y="250.0084">dereference</text></g><!--MD5=[eaac149cd52357b54ad3c2582b313d87]
+reverse link RequestInternalDereferencedToolState to JobInternalToolState--><g id="link_RequestInternalDereferencedToolState_JobInternalToolState"><path codeLine="46" d="M1512.76,311.21 C1517.6,331.64 1523.03,354.53 1527.52,373.46 " fill="none" id="RequestInternalDereferencedToolState-backto-JobInternalToolState" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="none" points="1509.78,298.68,1507.2733,305.4414,1512.5505,310.3558,1515.0572,303.5944,1509.78,298.68" style="stroke:#FFA500;stroke-width:1.0;"/><polygon fill="#FF8C00" points="1525.1536,340.4504,1525.9264,330.9713,1520.2071,332.3274,1525.1536,340.4504" style="stroke:#FF8C00;stroke-width:1.0;"/><text fill="#FF8C00" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="46" x="1533" y="340.4984">expand</text></g><!--MD5=[ec4fa4eb858d20753965cdb606e0251f]
+@startuml
+
+!include plantuml_options.txt
+
+package galaxy.tool_util.parameters.state {
+
+class ToolState {
+state_representation: str
+input_state: Dict[str, Any]
++ validate(parameters: ToolParameterBundle)
++ {abstract} _to_base_model(parameters: ToolParameterBundle): Optional[Type[BaseModel]]
+}
+
+class RequestToolState {
+state_representation = "request"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <encoded_id>}.\n Allow mapping/reduce constructs.
+
+class RequestInternalToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. Allows URI src dicts.
+
+class RequestInternalDereferencedToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. No URI src dicts - all converted to HDAs.
+
+class JobInternalToolState {
+state_representation = "job_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Mapping constructs expanded out.\n (Defaults are inserted?)
+
+ToolState <|- - RequestToolState
+ToolState <|- - RequestInternalToolState
+ToolState <|- - RequestInternalDereferencedToolState
+ToolState <|- - JobInternalToolState
+
+RequestToolState - RequestInternalToolState : decode >
+
+RequestInternalToolState - RequestInternalDereferencedToolState : dereference > 
+
+RequestInternalDereferencedToolState o- - JobInternalToolState : expand >
+
+}
+@enduml
+
+@startuml
+
+
+skinparam class {
+    ArrowFontColor DarkOrange
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam object {
+    ArrowFontColor DarkOrange
+    BackgroundColor #FFEFD5
+    BackgroundColor #FFEFD5
+    ArrowColor Orange
+    BorderColor DarkOrange
+}
+
+skinparam ComponentBackgroundColor #FFEFD5
+skinparam ComponentBorderColor DarkOrange
+
+skinparam DatabaseBackgroundColor #FFEFD5
+skinparam DatabaseBorderColor DarkOrange
+
+skinparam StorageBackgroundColor #FFEFD5
+skinparam StorageBorderColor DarkOrange
+
+skinparam QueueBackgroundColor #FFEFD5
+skinparam QueueBorderColor DarkOrange
+
+skinparam note {
+    BackgroundColor #FFEFD5
+    BorderColor #BF5700
+}
+
+skinparam sequence {
+    ArrowColor Orange
+    ArrowFontColor DarkOrange
+    ActorBorderColor DarkOrange
+    ActorBackgroundColor #FFEFD5
+
+    ParticipantBorderColor DarkOrange
+    ParticipantBackgroundColor #FFEFD5
+
+    LifeLineBorderColor DarkOrange
+    LifeLineBackgroundColor #FFEFD5
+
+    DividerBorderColor DarkOrange
+    GroupBorderColor DarkOrange
+}
+
+
+package galaxy.tool_util.parameters.state {
+
+class ToolState {
+state_representation: str
+input_state: Dict[str, Any]
++ validate(parameters: ToolParameterBundle)
++ {abstract} _to_base_model(parameters: ToolParameterBundle): Optional[Type[BaseModel]]
+}
+
+class RequestToolState {
+state_representation = "request"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <encoded_id>}.\n Allow mapping/reduce constructs.
+
+class RequestInternalToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. Allows URI src dicts.
+
+class RequestInternalDereferencedToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. No URI src dicts - all converted to HDAs.
+
+class JobInternalToolState {
+state_representation = "job_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Mapping constructs expanded out.\n (Defaults are inserted?)
+
+ToolState <|- - RequestToolState
+ToolState <|- - RequestInternalToolState
+ToolState <|- - RequestInternalDereferencedToolState
+ToolState <|- - JobInternalToolState
+
+RequestToolState - RequestInternalToolState : decode >
+
+RequestInternalToolState - RequestInternalDereferencedToolState : dereference > 
+
+RequestInternalDereferencedToolState o- - JobInternalToolState : expand >
+
+}
+@enduml
+
+PlantUML version 1.2022.8(Sun Sep 25 05:00:33 EDT 2022)
+(GPL source distribution)
+Java Runtime: Java(TM) SE Runtime Environment
+JVM: Java HotSpot(TM) 64-Bit Server VM
+Default Encoding: UTF-8
+Language: en
+Country: US
+--></g></svg>
\ No newline at end of file
diff --git a/doc/source/dev/tool_state_state_classes.plantuml.txt b/doc/source/dev/tool_state_state_classes.plantuml.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c2c82951eb37ea1294f5889cfe3efc4015c8322
--- /dev/null
+++ b/doc/source/dev/tool_state_state_classes.plantuml.txt
@@ -0,0 +1,50 @@
+@startuml
+!include plantuml_options.txt
+
+package galaxy.tool_util.parameters.state {
+
+class ToolState {
+state_representation: str
+input_state: Dict[str, Any]
++ validate(parameters: ToolParameterBundle)
++ {abstract} _to_base_model(parameters: ToolParameterBundle): Optional[Type[BaseModel]]
+}
+
+class RequestToolState {
+state_representation = "request"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <encoded_id>}.\n Allow mapping/reduce constructs.
+
+class RequestInternalToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. Allows URI src dicts.
+
+class RequestInternalDereferencedToolState {
+state_representation = "request_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Allow mapping/reduce constructs. No URI src dicts - all converted to HDAs.
+
+class JobInternalToolState {
+state_representation = "job_internal"
++ _to_base_model(parameters: ToolParameterBundle): Type[BaseModel]
+
+}
+note bottom: Object references of the form \n{src: "hda", id: <decoded_id>}.\n Mapping constructs expanded out.\n (Defaults are inserted?)
+
+ToolState <|-- RequestToolState
+ToolState <|-- RequestInternalToolState
+ToolState <|-- RequestInternalDereferencedToolState
+ToolState <|-- JobInternalToolState
+
+RequestToolState - RequestInternalToolState : decode >
+
+RequestInternalToolState - RequestInternalDereferencedToolState : dereference > 
+
+RequestInternalDereferencedToolState o-- JobInternalToolState : expand >
+
+}
+@enduml
\ No newline at end of file
diff --git a/doc/source/dev/tool_state_task.plantuml.svg b/doc/source/dev/tool_state_task.plantuml.svg
new file mode 100644
index 0000000000000000000000000000000000000000..e4a4aa911d3a09fffacd50d8e423fcde14389f65
--- /dev/null
+++ b/doc/source/dev/tool_state_task.plantuml.svg
@@ -0,0 +1,62 @@
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style="stroke:#181818;stroke-width:0.5;" width="147" x="1357.5" y="5"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="133" x="1364.5" y="25.5352">ToolAction.execute</text><rect fill="#E2E2F0" height="30.4883" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1357.5" y="393.9043"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="133" x="1364.5" y="414.4395">ToolAction.execute</text><polygon fill="#181818" points="164.5,63.7988,174.5,67.7988,164.5,71.7988,168.5,67.7988" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="53.5" x2="170.5" y1="67.7988" y2="67.7988"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="99" x="60.5" y="63.0566">&lt;Launch Task&gt;</text><polygon fill="#181818" points="356.5,93.1094,366.5,97.1094,356.5,101.1094,360.5,97.1094" 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y="297.541">JobInternalToolState[]</text><path d="M863,317.2832 L937,317.2832 L937,324.5938 L927,334.5938 L863,334.5938 L863,317.2832 " fill="#EEEEEE" style="stroke:#000000;stroke-width:1.5;"/><rect fill="none" height="60.6211" style="stroke:#000000;stroke-width:1.5;" width="651.5" x="863" y="317.2832"/><text fill="#000000" font-family="sans-serif" font-size="13" font-weight="bold" lengthAdjust="spacing" textLength="29" x="878" y="330.8516">loop</text><text fill="#000000" font-family="sans-serif" font-size="11" font-weight="bold" lengthAdjust="spacing" textLength="173" x="952" y="329.918">[over expanded job tool states]</text><polygon fill="#181818" points="1419,336.5938,1429,340.5938,1419,344.5938,1423,340.5938" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="965" x2="1425" y1="340.5938" y2="340.5938"/><polygon fill="#181818" points="976,365.9043,966,369.9043,976,373.9043,972,369.9043" style="stroke:#181818;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.0;" x1="970" x2="1430" y1="369.9043" y2="369.9043"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="79" x="982" y="365.1621">A Galaxy Job</text><!--MD5=[63fdddff037208bb1e78aa28f3606777]
+@startuml
+
+'!include plantuml_options.txt
+queue       TaskQueue   as queue
+participant     "queue_jobs Task" as task
+participant     "JobSubmitter.queue_jobs" as queue_jobs
+participant     "JobSubmitter.dereference" as dereference
+participant     "materialize Task" as materialize_task
+participant     "Tool.handle_input_async" as handle_input
+participant     "expand_meta_parameters_async" as expand
+participant     "ToolAction.execute" as tool_action
+
+queue -> task : <Launch Task>
+task -> queue_jobs : QueueJobs pydantic model
+queue_jobs -> dereference : RequestInternalToolState
+dereference -> queue_jobs : RequestInternalDereferencedToolState
+queue_jobs -> materialize_task : HDA (with state deferred)
+materialize_task -> queue_jobs : return when state is okay
+queue_jobs -> handle_input : RequestInternalDereferencedToolState
+handle_input -> expand : RequestInternalDereferencedToolState
+expand -> handle_input : JobInternalToolState[]
+loop over expanded job tool states
+    handle_input -> tool_action :
+    tool_action -> handle_input : A Galaxy Job
+end
+@enduml
+
+@startuml
+
+queue       TaskQueue   as queue
+participant     "queue_jobs Task" as task
+participant     "JobSubmitter.queue_jobs" as queue_jobs
+participant     "JobSubmitter.dereference" as dereference
+participant     "materialize Task" as materialize_task
+participant     "Tool.handle_input_async" as handle_input
+participant     "expand_meta_parameters_async" as expand
+participant     "ToolAction.execute" as tool_action
+
+queue -> task : <Launch Task>
+task -> queue_jobs : QueueJobs pydantic model
+queue_jobs -> dereference : RequestInternalToolState
+dereference -> queue_jobs : RequestInternalDereferencedToolState
+queue_jobs -> materialize_task : HDA (with state deferred)
+materialize_task -> queue_jobs : return when state is okay
+queue_jobs -> handle_input : RequestInternalDereferencedToolState
+handle_input -> expand : RequestInternalDereferencedToolState
+expand -> handle_input : JobInternalToolState[]
+loop over expanded job tool states
+    handle_input -> tool_action :
+    tool_action -> handle_input : A Galaxy Job
+end
+@enduml
+
+PlantUML version 1.2022.8(Sun Sep 25 05:00:33 EDT 2022)
+(GPL source distribution)
+Java Runtime: Java(TM) SE Runtime Environment
+JVM: Java HotSpot(TM) 64-Bit Server VM
+Default Encoding: UTF-8
+Language: en
+Country: US
+--></g></svg>
\ No newline at end of file
diff --git a/doc/source/dev/tool_state_task.plantuml.txt b/doc/source/dev/tool_state_task.plantuml.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64286f2f5ed51729706dac1a8f1a1b4aedd861de
--- /dev/null
+++ b/doc/source/dev/tool_state_task.plantuml.txt
@@ -0,0 +1,25 @@
+@startuml
+'!include plantuml_options.txt
+queue       TaskQueue   as queue
+participant     "queue_jobs Task" as task
+participant     "JobSubmitter.queue_jobs" as queue_jobs
+participant     "JobSubmitter.dereference" as dereference
+participant     "materialize Task" as materialize_task
+participant     "Tool.handle_input_async" as handle_input
+participant     "expand_meta_parameters_async" as expand
+participant     "ToolAction.execute" as tool_action
+
+queue -> task : <Launch Task>
+task -> queue_jobs : QueueJobs pydantic model
+queue_jobs -> dereference : RequestInternalToolState
+dereference -> queue_jobs : RequestInternalDereferencedToolState
+queue_jobs -> materialize_task : HDA (with state deferred)
+materialize_task -> queue_jobs : return when state is okay
+queue_jobs -> handle_input : RequestInternalDereferencedToolState
+handle_input -> expand : RequestInternalDereferencedToolState
+expand -> handle_input : JobInternalToolState[]
+loop over expanded job tool states
+    handle_input -> tool_action :
+    tool_action -> handle_input : A Galaxy Job
+end
+@enduml
diff --git a/doc/source/project/organization.rst b/doc/source/project/organization.rst
index 1670165cd8afe20195a9da3c57993aa7e71488a9..c52de6597e9dc4b75b100a9245b448135ddfa8c8 100644
--- a/doc/source/project/organization.rst
+++ b/doc/source/project/organization.rst
@@ -46,7 +46,6 @@ Members
 - Dannon Baker (@dannon)
 - Matthias Bernt (@bernt-matthias)
 - Daniel Blankenberg (@blankenberg)
-- Dave Bouvier (@davebx)
 - Martin Čech (@martenson)
 - John Chilton (@jmchilton)
 - Nate Coraor (@natefoo)
@@ -55,6 +54,7 @@ Members
 - Nuwan Goonasekera (@nuwang)
 - Björn Grüning (@bgruening)
 - Aysam Guerler (@guerler)
+- Alireza Heidari (@itisAliRH)
 - Jennifer Hillman Jackson (@jennaj)
 - David López (@davelopez)
 - Laila Los (@ElectronicBlueberry)
diff --git a/doc/source/releases/24.2.rst b/doc/source/releases/24.2.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e4b9c6666fc3b45351426be0658c334bc152063d
--- /dev/null
+++ b/doc/source/releases/24.2.rst
@@ -0,0 +1,1047 @@
+
+.. to_doc
+
+24.2
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+.. major_feature
+
+.. feature
+
+Features
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Backport of Workflow Editor Activity Bar
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19212`_
+* Add onedata templates
+  (thanks to `@bwalkowi <https://github.com/bwalkowi>`__).
+  `Pull Request 18457`_
+* Add linter to check validity of output filters
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19114`_
+* FITS file table graph visualization plugin
+  (thanks to `@francoismg <https://github.com/francoismg>`__).
+  `Pull Request 19003`_
+* Experimental galactic wizard
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 15860`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration)
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18272`_
+* Add job metrics per invocation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19048`_
+* Feature - stdout live reporting
+  (thanks to `@gecage952 <https://github.com/gecage952>`__).
+  `Pull Request 16975`_
+
+.. enhancement_tag_viz
+
+Vizualization enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Fix MSA viz, new dependency specification options
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18760`_
+* Parse stored config details to script-based visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18651`_
+* Migrate NGL viewer to npm package
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18946`_
+* Support deferred datasets in visualizations
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19097`_
+* Openlayer update to npm package
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 19134`_
+* Replace static Cytoscape plugin with npm package
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 19127`_
+* Update tiff viewer to use script entry_point
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19151`_
+* Migrate Venn Diagram to Script-Tag
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19153`_
+* Remove OpenLayers legacy files and add SVG logo
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19135`_
+
+.. enhancement_tag_datatypes
+
+Datatype enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Add pod5 datatype
+  (thanks to `@TomHarrop <https://github.com/TomHarrop>`__).
+  `Pull Request 18419`_
+* Handle compressed content in dataset preview for all sequence classes
+  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
+  `Pull Request 18776`_
+* Improve usability of Directory datatype
+  (thanks to `@wm75 <https://github.com/wm75>`__).
+  `Pull Request 17614`_
+* Add some Zarr-based datatypes
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19040`_
+* Add XML based `vtk` datatype
+  (thanks to `@tStehling <https://github.com/tStehling>`__).
+  `Pull Request 19104`_
+
+.. enhancement_tag_tools
+
+Tool enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Update GPU JupyterLab tool
+  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
+  `Pull Request 18220`_
+* Add Tool-Centric APIs to the Tool Shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18524`_
+* Add BlobToolkit to the list of interactive tools
+  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
+  `Pull Request 18630`_
+* Remove some unused dynamic drill down options
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18892`_
+* Add filter null collection operation tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18928`_
+* Jupyter Interactive Tool 1.0.1/24.07
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 18861`_
+* Add Interactive Tool Ilastik
+  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
+  `Pull Request 16837`_
+
+.. enhancement_tag_workflows
+
+* Fix problem with multiple layers in workflow metrics
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19283`_
+* Fix workflow metrics chart style
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19291`_
+Workflow enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Fix usability of workflow best practice attribute checking.
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19230`_
+* Workflow Inputs Activity
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19252`_
+* Fix default value handling for parameters connected to required parameters
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19219`_
+* Allow connecting text param into data column parameter
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18674`_
+* Allow specifying multi-select workflow parameters
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18715`_
+* Allow access to invocation via shared or published history
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18707`_
+* Modelling for Test Assertions
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18787`_
+* Implement Pydantic model for workflow test format.
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18884`_
+* Improvements to Planemo test format based on feedback/discussions
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18889`_
+* Allow CORS requests to /api/workflow_landings
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18963`_
+* Workflow landing improvements
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18979`_
+* Always validate hashes when provided
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19110`_
+* Workflow Landing Requests
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18807`_
+* Implement Declarative Testing for Workflow Behaviors
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18542`_
+* Allow recovering a normalized version of workflow request state from API
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18985`_
+
+.. enhancement_tag_ui
+
+UI enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Enable verbatimModuleSyntax, fix jest usage
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18595`_
+* Make vite tool shed client proxy configurable
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18988`_
+* Upgrade `openapi-typescript` to 7.0.2 + swap to `openapi-fetch`
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18532`_
+
+.. enhancement_tag_jobs
+
+Job enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Record container id and type in core job metrics
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18579`_
+* Add type annotations to ``JobRunnerMapper`` and related code
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19115`_
+* Allow to overwrite `real_system_username` per destination
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18945`_
+
+.. enhancement_tag_admin
+
+Admin enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Remove `defaults` channel for conda usage
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18757`_
+* Allow setting a few global defaults for file source plugin types
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18909`_
+* Bring your own file sources: Add the WebDAV template and configuration
+  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
+  `Pull Request 18598`_
+* Decouple user email from role name
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18966`_
+* Support high-availability setups for the interactive tools proxy
+  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
+  `Pull Request 18481`_
+* Minor config documentation enhancements
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 18499`_
+* Better cleanup of sharing roles on user purge
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 19096`_
+
+.. enhancement
+
+* List private file sources first in Remote Files Dialog
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19455`_
+* Various list of pairs builder usability fixes
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19248`_
+* Fix to not display upload when creating collections from existing datasets
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19373`_
+Misc. enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Activity bar add new workflow button
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19281`_
+* Guide users to collection builders
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 18857`_
+* Updates the About Page
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18461`_
+* Moves Libraries from Masthead to Activity Bar
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18468`_
+* Adds an option to restore activity bar defaults
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18469`_
+* Add errors fast api
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18093`_
+* Add task expiration to persistent task monitor
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18551`_
+* Improve datasets permissions API schema typing
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18563`_
+* Group tool templating exceptions in sentry
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18570`_
+* Add a new version of the production s3fs file source template with the writable configuration variable added
+  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
+  `Pull Request 18575`_
+* Move history multiview item actions to top
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 18265`_
+* Improve update user API payload schema
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18602`_
+* Improve update history payload schema
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18618`_
+* Rev pinned gxformat2
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18624`_
+* Improve typing for archived histories API schema
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18586`_
+* Reduce unnecessary requests when browsing tool repositories in Admin Panel
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18632`_
+* Improve types around User in schema and client
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18645`_
+* Rip repository_registry out of tool shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18647`_
+* Improve accept header API schema
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18668`_
+* Another round of parameter model improvements
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18673`_
+* Another round of parameter model enhancements and tool tests
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18678`_
+* Dynamic Models for Tool Test Validation
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18679`_
+* Implement tool upgrade assistant
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18728`_
+* Cache pip directory as part of `setup-python` action
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18789`_
+* Refactor FolderTopBar to TypeScript
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18488`_
+* Update Visualization FastAPI
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18792`_
+* Add Alireza to committers group
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18613`_
+* Improvements to help terms & tool help
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18722`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 18578`_
+* Add wizard-like export view for workflow invocations
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18796`_
+* Improvements to parameter models for test case inputs
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18743`_
+* Add docs on indexing for filter column
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18844`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 18864`_
+* Add unique constraints to the email and username fields in the galaxy_user table
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18493`_
+* Replace History Dataset Picker in Library Folder
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18518`_
+* Allow using tracks and groups in visualization xml
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18779`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 18904`_
+* Add support for arbitrarily ordered image axes in image content assertions
+  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
+  `Pull Request 18891`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 18943`_
+* Add BioBlend tests
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18975`_
+* Optimize to_history_dataset_association in create_datasets_from_library_folder
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18970`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 18982`_
+* Add workflow to update PR title based on target branch version
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18835`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 19031`_
+* Enable extra user preferences for remotely authorized users
+  (thanks to `@maartenschermer <https://github.com/maartenschermer>`__).
+  `Pull Request 18887`_
+* UI Improvements for Tool Shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19041`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 19062`_
+* Annotate ``DatasetAssociationManager`` as generic type
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19063`_
+* Better logging around tool loading
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19029`_
+* Add `galaxy-upload` link to `UploadModal`
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19055`_
+* Do not skip CI tests on missing tools
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19002`_
+* Add a filter for `labels` (tags) in Tool Search
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19076`_
+* Replace poetry with uv
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19075`_
+* Add Python 3.13 support
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18449`_
+* Allow deferred datasets to behave as URIs
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19077`_
+* uv: Do not recalculate dependencies when exporting
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19099`_
+* Test hash validation also for upload by path
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19109`_
+* Integrate Tool Parameter Modeling into Linting (for Planemo)
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19073`_
+* Better search stuff in Tool Shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19047`_
+* Enable specifying dataset hash in test jobs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19113`_
+* Access public history in job cache / job search
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19108`_
+* Update Python dependencies
+  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
+  `Pull Request 19123`_
+* Also use miniforge docker for container building
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19128`_
+* Silence the quota manager for updates
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19046`_
+* Enhance relabel_from_file to work with any column pair in mapping file
+  (thanks to `@wm75 <https://github.com/wm75>`__).
+  `Pull Request 19022`_
+* Irods ssl connection
+  (thanks to `@pauldg <https://github.com/pauldg>`__).
+  `Pull Request 19014`_
+* Update Japanese locale.js
+  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
+  `Pull Request 19101`_
+* Update vizarr version to 0.1.5
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19142`_
+* Fix word wrapping in invocation panel list items
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19141`_
+* Add Workflow Title and Annotation sections
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 18762`_
+* Assert that `data_column` parameters have a valid `data_ref`
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18949`_
+* Switch update annotate image to new script entry_point
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19150`_
+* Workflow license and creator edit keyboard access
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18936`_
+* More data access tests, some refactoring and cleanup
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18312`_
+* Add hint to the tool schema about runtime conditional changes
+  (thanks to `@martenson <https://github.com/martenson>`__).
+  `Pull Request 18996`_
+* Undo stack UI
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 18548`_
+* Run installed Galaxy with no config and a simplified entry point
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 19050`_
+* A variety of improvements around tool parameter modeling (second try)
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19027`_
+* Parameter Model Improvements
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18641`_
+* Masthead Revision
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 17927`_
+* Workflow Invocation view improvements
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 18615`_
+* Add linters for datatypes
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17600`_
+
+.. small_enhancement
+
+* Release testing - selenium tests for workflow invocation export
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19262`_
+* Update versions of GitHub actions
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18197`_
+* Update openapi-typescript dependency to version 6.7.6
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18519`_
+* Mixed enhancements from CWL branch
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18539`_
+* Fix some Toolshed 2.0 development paper-cuts
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18538`_
+* Improvements to Tool Test Parsing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18560`_
+* Drop unused datasets controller methods
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18568`_
+* Consistent type imports, fixes and linting
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18589`_
+* Tighten user notification API response types
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18599`_
+* More tool test typing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18590`_
+* Remove unused functions in dataset managers
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18631`_
+* Better Typing for Tool Execution Plumbing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18626`_
+* De-couple XML from tool interface for test collections
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18676`_
+* Update ExportToRemoteModal.vue to use TypeScript
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18706`_
+* More typing, docs, and decomposition around tool execution
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18758`_
+* Migrate Visualizations API to FastAPI
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18721`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18773`_
+* Update Mypy to 1.11.2 and fix new signature override errors
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18811`_
+* Remove Build Dataset Pair option from history actions
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18740`_
+* Backend handling of setting user-role, user-group, and group-role associations
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18777`_
+* Refactor migration testing setup code
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18886`_
+* Enable ``ignore-without-code`` mypy error code
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18898`_
+* Raise exception if CompressedFile used on incompatible file
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18888`_
+* Type annotations and fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18911`_
+* Remove outdated fimo wrapper and galaxy-sequence-utils dependency
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18937`_
+* Migrate Library Contents API to FastAPI
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18838`_
+* Fix extra files path type hint
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18958`_
+* Move TRS import into WorkflowContentManager
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19070`_
+* More concise, readable tool execution testing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18977`_
+* Libraries Modernisation: Directory Dataset Picker
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18638`_
+
+
+Fixes
+-------------------------------
+
+.. major_bug
+
+
+.. bug_tag_viz
+
+* Prevent cycling through failing conversion jobs in trackster
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19494`_
+Vizualization fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Update visualizations package versions
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19232`_
+* Install npm-package viz to the package prefix explicitly
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18950`_
+* Restore access to saved visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19136`_
+
+.. bug_tag_datatypes
+
+Datatype fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Add gtf to auto_compressed_types
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19175`_
+
+.. bug_tag_tools
+
+Tool fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Drop "Send to cloud" tool and associated cloudauthz code
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18196`_
+* Fix commas that shouldn't be in biotools_mappings.tsv
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18919`_
+
+.. bug_tag_workflows
+
+* Fix error message when subworkflow input connection missing
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19526`_
+* Also check `trs_tool_id` for imported workflow indicator
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19460`_
+* Set a hard limit of 100 invocations per request in api/invocations
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19497`_
+* Fix import of previously-deleted TRS workflow
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19311`_
+Workflow fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Fix workflows with optional non-default parameter input
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19332`_
+* Fix cancellation of workflow scheduling
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19238`_
+* Fix collection type drag and drop validation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18623`_
+
+.. bug_tag_ui
+
+UI fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Bump requirejs from 2.3.6 to 2.3.7 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18610`_
+* Bump axios from 1.6.2 to 1.7.4 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18717`_
+* Bump webpack from 5.89.0 to 5.94.0 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18768`_
+* Bump express from 4.19.2 to 4.21.0 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18808`_
+* Bump dompurify from 3.0.6 to 3.1.3 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18821`_
+* Bump http-proxy-middleware from 2.0.6 to 2.0.7 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 19060`_
+* Bump dompurify from 2.3.10 to 3.1.6 in /client
+  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
+  `Pull Request 18880`_
+
+.. bug_tag_jobs
+
+* Use instance wide default ``real_system_username`` if not defined on destination
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19544`_
+* Fix job parameter summary for inputs without label
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19427`_
+* Serialize message exceptions on execution error
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19483`_
+* Partial backport of `#19331 <https://github.com/galaxyproject/galaxy/issues/19331>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19342`_
+* Fixes for console logging
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19381`_
+Job fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Fixes random job failures in kubernetes
+  (thanks to `@mapk-amazon <https://github.com/mapk-amazon>`__).
+  `Pull Request 19001`_
+
+.. bug_tag_admin
+
+* Downgrade 'InteractiveTools are not enabled' to warning
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19518`_
+.. bug
+
+* Use visualizations api in trackster
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19495`_
+* Fix extracting workflows from purged and deleted histories
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19525`_
+* Fix WSGI response status handling in controller methods
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19520`_
+* Fix remap for parameter called id
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19532`_
+* Fix admin cancel job message not being displayed to the user
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19537`_
+* Provide guidance in case of deadlock during db migration
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 19551`_
+* Update 24.2 db revision tags
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 19550`_
+* Fix to only show ChatGXY when available
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19389`_
+* Display upload help highlight only once and include Rule-based upload info
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19393`_
+* Show message for mixed extensions in collection creator
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19404`_
+* Fix Activity Bar state lost on page reload
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19426`_
+* Show Keycloak provider label in UI
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19447`_
+* `mulled-build-tool` fix for packages wo version
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19450`_
+* Fix parsing of validators with inf limits
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19459`_
+* Fix help text overflow breaking tool inspector
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19465`_
+* Fix object not found handling
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19468`_
+* Remove print statement
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19469`_
+* Bump typescript target to es2020
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19473`_
+* Fail with error message when submitting invalid request
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19489`_
+* Fix invocation query in JobInformation.vue component
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19496`_
+* Fix minor typo in event name in collection creator
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19499`_
+* Fix library dataset current user potentially null
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19505`_
+* Fix workflowID assignment in Markdown.vue
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19507`_
+* Skip token refresh without refresh token in psa
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19514`_
+* Fix tool search constantly loading bug
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19528`_
+* Add tool_id index on job table
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19543`_
+* Outputs filter linter fixes
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19208`_
+* Fix some collection builder help and language choices
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19244`_
+* Only allow moving activity bar icons when editing the bar
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19258`_
+* Fix CollectionCreatorModal being reopened on history
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19276`_
+* Fix invocation metrics usability by providing job context
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19279`_
+* Fix inconsistent tab handling in invocation view
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19298`_
+* Don't show published workflows in workflow activity of workflow editor
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19312`_
+* Fix timeout handling for planemo / galaxy-tool-util
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19384`_
+* Fix for empty string in regex validator message
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19387`_
+Misc. fixes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Fix handling of step id offsets when duplicating selections
+  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
+  `Pull Request 19351`_
+* Fix simple activity panel item style
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19350`_
+* Fixes window manager scrolling and resizing
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19308`_
+* Fix activity-bar-id handling wrt activityStore
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19316`_
+* Login redirect followup
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19251`_
+* Build collection only if populated in collection builder
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19250`_
+* Avoid a class of unhelpful accepted format drop downs
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19241`_
+* Improve the empty history message for guiding users to collections.
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19242`_
+* Fix PSA Redirect
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19247`_
+* release testing - UI tests for new workflow parameters
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19182`_
+* Return generic message for password reset email
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 18479`_
+* Raise Message Exception when displaying binary data
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18503`_
+* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18510`_
+* Follow-up on `#18212 <https://github.com/galaxyproject/galaxy/issues/18212>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18516`_
+* Fix "worklfow" typo here and there
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 18523`_
+* Fix MessageException handling in get_edit
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18529`_
+* Fix bugs in tool shed tool API
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18558`_
+* Fix Archive header encoding
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18583`_
+* Fix for not-null in 'column_list' object
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 18553`_
+* Fix API key reveals on mouse hover
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18593`_
+* Fix for Numeric form field to allow Null min/max values in validation methods
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 18585`_
+* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18605`_
+* Fixes for errors reported by mypy 1.11.0
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18608`_
+* Bug fix for invalid duplicate id in function test tools
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18644`_
+* Handle output parsing when tool is not available for tool-centric API
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18643`_
+* Restore interactive tools watcher
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18581`_
+* Strip whitespace when listifying admin users
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18656`_
+* Update mercurial
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18686`_
+* Restore repository update in the tool shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18655`_
+* Fix "Latest Updates" order in tool shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 16894`_
+* Replace types-pkg-resources with types-setuptools
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18708`_
+* Update ruff to 0.6.1
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18716`_
+* Fix new flake8-bugbear B039 and mypy type-var errors
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18755`_
+* Fixing RegisterForm.vue not appending prefix when set
+  (thanks to `@mcuaya1 <https://github.com/mcuaya1>`__).
+  `Pull Request 18786`_
+* Fix response if dataset requested by display application is deleted
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18803`_
+* Fix alert handling in workflow label handler
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18836`_
+* Fix transiently failing selenium tooltip issues
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18847`_
+* Fix flaky `test/integration_selenium/test_toolbox_filters.py::TestToolboxFiltersSeleniumIntegration::test_toolbox_filters`
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 18854`_
+* Fix migration data fixes tests
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18885`_
+* data_column params: offer same columns with and without use_header_names
+  (thanks to `@wm75 <https://github.com/wm75>`__).
+  `Pull Request 18879`_
+* Allow users with 'can_modify_folder' permission to delete items in libraries
+  (thanks to `@npinter <https://github.com/npinter>`__).
+  `Pull Request 18924`_
+* Fix `WorkflowInvocationHeader` import type and current user errors
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 18956`_
+* Explicitly display dataset preview in pages and workflow reports
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18968`_
+* Ignore preflight options in API schema
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18983`_
+* Define environment variables in ``env:`` section
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18987`_
+* Fix the bioblend test failures
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18991`_
+* Fix job directory not being cleaned up
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18997`_
+* Fix job search statement building
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19010`_
+* Fix test_stock.py unit test
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19037`_
+* add data source doc to the list in index
+  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
+  `Pull Request 18742`_
+* Fix auto-detect metadata from Edit Dataset Attributes panel
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19025`_
+* Fix numerous issues with tool input format "21.01"
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 19030`_
+* Prevent purged users from logging in
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 19094`_
+* Fixes and tests for data fetch models
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18834`_
+* Run ``uv lock`` under Python 3.9
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 19111`_
+* Allow modes `z` and `Z` for docker volumes
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18998`_
+* Fix handling of v2 hashes
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 18522`_
+* Dynamics options add library dataset
+  (thanks to `@gagayuan <https://github.com/gagayuan>`__).
+  `Pull Request 18198`_
+* Add merge migration to merge 2 heads
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 19163`_
+* Disallow /tool_runner? in robots.txt
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19020`_
+* Avoid possible negative offset in LibraryFolder
+  (thanks to `@martenson <https://github.com/martenson>`__).
+  `Pull Request 19090`_
+* Fix backend role sharing bug
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18942`_
+* Update a localized word with a more appropriate one
+  (thanks to `@mpalmada <https://github.com/mpalmada>`__).
+  `Pull Request 18910`_
+* Fix tag processing in library upload
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 18714`_
+* Update plausible script name in mako templates
+  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
+  `Pull Request 18458`_
+* Fix issue with generating slug for sharing
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 18986`_
+* Consolidate tag validation
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 19166`_
+* Move invocation view running actions and improve styling of annotation section
+  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
+  `Pull Request 19168`_
+* Fix mulled_hash
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19199`_
+* Add requirement/resource to schema docs
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 19172`_
+* Normalize usernames to lowercase in OIDC authentication
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 19131`_
+
+.. include:: 24.2_prs.rst
+
diff --git a/doc/source/releases/24.2_announce.rst b/doc/source/releases/24.2_announce.rst
index 112bddcd20d5bd5237ee0d360ce7ede9583a4b22..ca20109db1c53b7c445ad46b22441ce7292b2862 100644
--- a/doc/source/releases/24.2_announce.rst
+++ b/doc/source/releases/24.2_announce.rst
@@ -1,12 +1,361 @@
 
-:orphan:
+===========================================================
+24.2 Galaxy Release (February 2025)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+
+
+**A Wizard-like Export View for Workflow Invocations**. The workflow invocation
+export process has been enhanced with a new wizard-like interface, making it
+more guided and user-friendly. This interface simplifies complex processes with
+many options, providing a step-by-step approach to exporting workflow
+invocations.
+
+**Workflow Editor Enhancements: Activity Bar and Undo Stack UI**. The Activity
+Bar is now present in the Workflow Editor along side multiple interface
+improvements.
+
+**Masthead Revision and Activity Bar Improvements**. The Galaxy masthead has
+been revised to achieve consistency and reduce redundancy, aligning its
+functionality with the Activity Bar.
+
+**Improved Navigation and Usability of Collection Builders**. To guide users
+towards creating collections of the correct type, Galaxy now provides better
+navigation via buttons directly on data collection parameters. Users can create
+a collection with the required structure for the input, with pre-filtered items
+from their current history, also ensuring compatibility with required file
+extensions. Additionally, users can upload datasets directly to the collection
+builder.
+
+**Enhanced Workflow Invocation View**. The Workflow Invocation View, introduced
+in the previous release has been significantly refined to improve the usability
+and visualization of workflow runs.
+
+**Display Metrics for Workflow Invocations**. Galaxy now provides a Metrics tab
+in the Workflow Invocation View, allowing users to quickly summarize runtime,
+memory usage, and core allocation per invocation. This enhancement helps users
+better understand the resource usage of their workflows.
+
+**Libraries Modernization: Directory Dataset Picker**. The dataset picker for
+user and import directories has been modernized, providing a more intuitive and
+user-friendly interface. Users can now easily import files or folders from
+their user directory or import directory into a library.
+
+**Live Reporting of Job Console Outputs**. If enabled by the Galaxy
+administrators, it will now be possible to view live console output for running
+jobs. The job output will be available on the Job Information page where these
+logs have always been available for completed jobs.
+
+**ChatGXY - Job Error Wizard**. With this release, we're excited to introduce
+ChatGXY — AI assistance built directly into the Galaxy interface. The first
+functionality being rolled out is an AI-driven job error diagnoser that
+automatically inspects errored jobs and provides actionable insights. Users on
+supported servers can access this feature through the Dataset Error interface,
+where ChatGXY offers targeted suggestions to help diagnose and resolve job
+errors quickly and efficiently.
+
+
+Please see the `24.2 user release notes <24.2_announce_user.html>`__ for a summary of new user features.
+
+Get Galaxy
+===========================================================
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_24.2 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_24.2 && git pull --ff-only origin release_24.2
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
+
+Upcoming Deprecation Notices
+===========================================================
+
+**Deprecation of support for Python 3.8 in Galaxy release 25.0**
+  This Galaxy release (24.2) will be the last release that supports Python 3.8.
+  We encourage updating to a newer version of Python if possible.
+
+Admin Notes
+===========================================================
+
+* Migrating the database to 24.2 may require a short downtime. The 24.2
+  database migrations require exclusive access to the `galaxy_user` table.
+  Therefore, it is recommended to shut down all Galaxy procesess while
+  upgrading the database.
+* Database migration `04288b6a5b25 (make dataset uuids unique)` requires
+  function `gen_random_uuid()` which was added in PostgreSQL version 13.0.
+  Prior to version 13.0, UUID generation functions were available in the
+  external modules uuid-ossp and pgcrypto (see `PostgreSQL 13.0 release notes
+  <https://www.postgresql.org/docs/release/13.0/>`__). Thus, you need to
+  upgrade your database to version 13.0 or newer, or, alternatively, load the
+  pgcrypto extension (see `this solution on Stackoverflow
+  <https://stackoverflow.com/a/35960732/1382596>`__).  * A user's email address
+  is no longer used as the name of their private role;
+  instead, the association between a user and their private role is handled
+  through a foreign key at the database level. Although a role name is no
+  longer required to be unique in the database (automatically generated private
+  roles have the generic name "private role"), manually created roles still
+  must have a unique name; this prevents from accidentally creating duplicate
+  roles.
+* The user/role/group association tables in the database have been given
+  additional constraints which prevent accidental creation of duplicate or
+  incomplete records. In addition to these changes to the database schema, the
+  database upgrade includes data migration scripts (executed as part of the
+  upgrade) which will automatically fix any inconsistent data in these tables.
+  [`#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`__]
+* OAuth 2.0 enabled plugin for Dropbox has been added to the user defined file
+  sources framework. See `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`__
+  for updates to the admin documentation on how to build and configure a
+  Dropbox app within Dropbox for a Galaxy instance.
+* Support has been added for high-availability setups for the interactive tools proxy.
+  [`#18481 <https://github.com/galaxyproject/galaxy/pull/18481>`__]
+
+
+Configuration Changes
+===========================================================
+
+
+Added
+-----
+
+The following configuration options are new
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.galaxy.mapping.file_source_listings_expiry_time
+-  mapping.galaxy.mapping.file_source_temp_dir
+-  mapping.galaxy.mapping.file_source_webdav_use_temp_files
+-  mapping.galaxy.mapping.interactivetoolsproxy_map
+-  mapping.galaxy.mapping.openai_api_key
+-  mapping.galaxy.mapping.openai_model
+-  mapping.galaxy.mapping.workflow_scheduling_separate_materialization_iteration
+
+
+Changed
+-------
+
+The following configuration options have been changed
+
+config/user_preferences_extra_conf.yml.sample
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  preferences.onedata.inputs has changed from
+
+   ::
+
+    {'name': 'onezone_domain', 'label': 'Domain of the Onezone service (e.g. datahub.egi.eu)', 'type': 'text', 'required': False}
+    {'name': 'access_token', 'label': 'Your access token, suitable for REST API access in a Oneprovider service', 'type': 'password', 'required': False}
+    {'name': 'disable_tls_certificate_validation', 'label': 'Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.', 'type': 'boolean', 'required': False, 'value': False}
+
+   to
+
+   ::
+
+    {'name': 'onezone_domain', 'label': 'Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4.', 'type': 'text', 'required': False}
+    {'name': 'access_token', 'label': 'Your access token, suitable for REST API access in a Oneprovider service', 'type': 'password', 'required': False}
+    {'name': 'disable_tls_certificate_validation', 'label': 'Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.', 'type': 'boolean', 'required': False, 'value': False}
+
+
 
+config/file_sources_conf.yml.sample
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-   has changed from
+
+   ::
+
+    {'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'access_token': "${user.preferences['dropbox|access_token']}"}
+    {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}", 'temp_path': '/your/temp/path', 'writable': False}
+    {'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'}
+    {'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'}
+    {'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222}
+    {'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
+    {'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True}
+    {'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True}
+    {'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True}
+    {'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True}
+    {'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True}
+    {'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True}
+    {'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True}
+    {'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True}
+    {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}
+    {'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True}
+    {'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True}
+    {'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True}
+    {'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
+    {'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
+    {'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
+    {'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
+    {'type': 'inveniordm', 'id': 'invenio_sandbox', 'doc': 'This is the Sandbox instance of Invenio. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Invenio RDM Sandbox Repository (TESTING ONLY)', 'url': 'https://inveniordm.web.cern.ch/', 'token': "${user.user_vault.read_secret('preferences/invenio_sandbox/token')}", 'public_name': "${user.preferences['invenio_sandbox|public_name']}", 'writable': True}
+    {'type': 'zenodo', 'id': 'zenodo', 'doc': 'Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable.', 'label': 'Zenodo', 'url': 'https://zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo/token')}", 'public_name': "${user.preferences['zenodo|public_name']}", 'writable': True}
+    {'type': 'zenodo', 'id': 'zenodo_sandbox', 'doc': 'This is the Sandbox instance of Zenodo. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Zenodo Sandbox (TESTING ONLY)', 'url': 'https://sandbox.zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo_sandbox/token')}", 'public_name': "${user.preferences['zenodo_sandbox|public_name']}", 'writable': True}
+    {'type': 'onedata', 'id': 'onedata1', 'label': 'Onedata', 'doc': 'Your Onedata files - configure an access token via user preferences', 'accessToken': "${user.preferences['onedata|access_token']}", 'onezoneDomain': "${user.preferences['onedata|onezone_domain']}", 'disableTlsCertificateValidation': "${user.preferences['onedata|disable_tls_certificate_validation']}"}
+
+   to
+
+   ::
+
+    {'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'access_token': "${user.preferences['dropbox|access_token']}"}
+    {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}", 'temp_path': '/your/temp/path', 'writable': False}
+    {'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'}
+    {'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'}
+    {'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
+    {'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222}
+    {'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
+    {'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True}
+    {'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True}
+    {'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True}
+    {'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True}
+    {'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True}
+    {'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True}
+    {'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True}
+    {'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True}
+    {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}
+    {'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True}
+    {'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True}
+    {'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True}
+    {'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
+    {'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
+    {'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
+    {'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
+    {'type': 'inveniordm', 'id': 'invenio_sandbox', 'doc': 'This is the Sandbox instance of Invenio. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Invenio RDM Sandbox Repository (TESTING ONLY)', 'url': 'https://inveniordm.web.cern.ch/', 'token': "${user.user_vault.read_secret('preferences/invenio_sandbox/token')}", 'public_name': "${user.preferences['invenio_sandbox|public_name']}", 'writable': True}
+    {'type': 'zenodo', 'id': 'zenodo', 'doc': 'Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable.', 'label': 'Zenodo', 'url': 'https://zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo/token')}", 'public_name': "${user.preferences['zenodo|public_name']}", 'writable': True}
+    {'type': 'zenodo', 'id': 'zenodo_sandbox', 'doc': 'This is the Sandbox instance of Zenodo. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Zenodo Sandbox (TESTING ONLY)', 'url': 'https://sandbox.zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo_sandbox/token')}", 'public_name': "${user.preferences['zenodo_sandbox|public_name']}", 'writable': True}
+    {'type': 'onedata', 'id': 'onedata1', 'label': 'Onedata', 'doc': 'Your Onedata files - configure an access token via user preferences', 'access_token': "${user.preferences['onedata|access_token']}", 'onezone_domain': "${user.preferences['onedata|onezone_domain']}", 'disable_tls_certificate_validation': "${user.preferences['onedata|disable_tls_certificate_validation']}"}
+
+
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.galaxy.mapping.conda_auto_init.desc has changed from
+
+   ::
+
+    Set to true to instruct Galaxy to install Conda from the web automatically
+    if it cannot find a local copy and conda_exec is not configured.
+
+   to
+
+   ::
+
+    Set to true to instruct Galaxy to install Conda from the web automatically
+    if it cannot find a local copy and conda_exec is not configured. The default is
+    true if running Galaxy from source, and false if running from installed packages.
+
+
+-  mapping.galaxy.mapping.geographical_server_location_code.desc has changed from
+
+   ::
+
+    The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code.
+    This is used to make carbon emissions estimates more accurate as the location effects the
+    carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the
+    `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations,
+    visit https://galaxyproject.org/admin/carbon_emissions
+
+   to
+
+   ::
+
+    The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code.
+    This is used to make carbon emissions estimates more accurate as the location effects the
+    carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the
+    `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations,
+    visit https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
+
+
+-  mapping.galaxy.mapping.interactivetools_map.desc has changed from
+
+   ::
+
+    Map for interactivetool proxy.
+
+   to
+
+   ::
+
+    Map for the interactivetool proxy. Mappings are stored in a SQLite database file
+    located on this path. As an alternative, you may also store them in any other RDBMS
+    supported by SQLAlchemy using the option ``interactivetoolsproxy_map``, which
+    overrides this one.
+
+
+-  mapping.galaxy.mapping.object_store_cache_size.desc has changed from
+
+   ::
+
+    Default cache size for caching object stores if cache not configured for
+    that object store entry.
+
+   to
+
+   ::
+
+    Default cache size, in GB, for caching object stores if the cache is not
+    configured for that object store entry.
+
+
+Removed
+-------
+
+The following configuration options have been completely removed
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.galaxy.mapping.conda_auto_init
+
+
+Developer Notes
 ===========================================================
-October 2024 Galaxy Release (v 24.2)
+
+* More concise, readable tool execution testing: infrastructure and some examples. [`#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`__]
+* More examples of new data access tests. [`#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`__]
+* Poetry replaced: Galaxy's Python dependency management is now handled with uv. [`#19075 <https://github.com/galaxyproject/galaxy/pull/19075>`__]
+* Upgrades to openapi-typescript cause some breaking changes. See `#18532 <https://github.com/galaxyproject/galaxy/pull/18532>`__ for more details.
+
+
+Release Notes
 ===========================================================
 
+.. include:: 24.2.rst
+   :start-after: announce_start
 
-Schedule
+Release Team
 ===========================================================
- * Planned Freeze Date: 2024-10-07
- * Planned Release Date: 2024-10-28
+
+Release manager:  `John Davis <https://github.com/jdavcs>`__, `Ahmed Awan <https://github.com/ahmedhamidawan>`__
+
+Release testing:
+
+* `Patrik Smeds <https://github.com/Smeds>`__
+* `Junhao Qiu <https://github.com/qchiujunhao>`__
+* `Mina Hojat Ansari <https://github.com/Minamehr>`__
+* `John Chilton <https://github.com/jmchilton>`__
+* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__
+* `Aysam Guerler <https://github.com/guerler>`__
+* `Srividya Ramakrishnan <https://github.com/Srividya22>`__
+
+A special thank you goes to everyone who helped test the new release after its deployment on usegalaxy.org.
+
+----
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/24.2_announce_user.rst b/doc/source/releases/24.2_announce_user.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c42460e00ce8c53ccf6cf5dee165b11b5ff7ab6a
--- /dev/null
+++ b/doc/source/releases/24.2_announce_user.rst
@@ -0,0 +1,297 @@
+
+===========================================================
+24.2 Galaxy Release (January 2025)
+===========================================================
+
+.. include:: _header.rst
+
+Please see the full :doc:`24.2 release notes <24.2_announce>` for more details.
+
+Highlights
+===========================================================
+
+A Wizard-like Export View for Workflow Invocations
+-----------------------------------------------------------
+
+The workflow invocation export process has been enhanced with a new wizard-like interface,
+making it more guided and user-friendly. This interface simplifies complex processes with many
+options, providing a step-by-step approach to exporting workflow invocations.
+
+- **Select export format**. Choose from various formats such as RO Crate, BioCompute Object,
+  or Compressed File.
+- **Choose export destination**. Options include temporary direct download, remote file source,
+  or RDM repository.
+- **Export**! Finalize and complete the export process with ease.
+
+This new interface aims to improve the user experience and may be extended to other complex
+processes in Galaxy in the future.
+[`#18796 <https://github.com/galaxyproject/galaxy/pull/18796>`__]
+
+.. figure:: images/24.2-export-invocation-wizard.gif
+   :alt: Export invocation wizard.
+
+Workflow Editor Enhancements: Activity Bar and Undo Stack UI
+-----------------------------------------------------------
+
+The Activity Bar is now present in the Workflow Editor along side multiple interface
+improvements.
+[`#18729 <https://github.com/galaxyproject/galaxy/pull/18729>`__]
+[`#18548 <https://github.com/galaxyproject/galaxy/pull/18548>`__]
+
+- **No more double side bars**. Inspecting a step now has it's own floating window,
+  which can be easily expanded and remembers it's size. All other features were moved to the
+  left side-bar.
+- **Undo redo UI**. A new interactive way of viewing recent changes. Click a change to scroll
+  backwards and forwards in time.
+- **Layout anything with ease**. The auto-layout feature was moved to the Editor Tool Bar. It
+  now aligns to the grid, untangles connections, and sorts Workflow Comments along with steps.
+- **Find your workflows**. Workflows now have their own dedicated interface, from which you can
+  find, copy into, and inserts Sub-Workflows into your Workflow.
+- **Inputs** are not tools, and are now no longer treated as such. Find inputs in their own
+  interface, and easily add input sub-types directly.
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/42HZQkC7PHY" title="Galaxy 24.2 - Workflow Editor Enhancements: Activity Bar and Undo Stack UI" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Masthead Revision and Activity Bar Improvements
+-----------------------------------------------------------
+
+The Galaxy masthead has been revised to achieve consistency and reduce redundancy, aligning its
+functionality with the Activity Bar.
+
+- **New "More" activity**. Hidden and less frequently used activities are now accessible through
+  a new "More" activity, allowing users to add or remove items from the activity bar and navigate
+  directly to any activity.
+- **Username visible in masthead**. The username is now visible in the masthead, with user
+  preferences and logout options accessible through the user dropdown.
+- **A compact masthead**. The masthead has been streamlined, removing redundant links and only
+  displaying essential items such as storage and the username on the right end.
+
+These changes enhance the user experience by making the interface more intuitive and reducing
+clutter.
+[`#17927 <https://github.com/galaxyproject/galaxy/pull/17927>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/5NMkcpj-1w8" title="Galaxy 24.2 - Masthead Revision and Activity Bar Improvements" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Improved Navigation and Usability of Collection Builders
+-----------------------------------------------------------
+
+To guide users towards creating collections of the correct type, Galaxy now provides
+better navigation via buttons directly on data collection parameters. Users can create a
+collection with the required structure for the input, with pre-filtered items from their
+current history, also ensuring compatibility with required file extensions. Additionally, users
+can upload datasets directly to the collection builder. These updates will improve the user
+experience of opening a workflow run form, creating appropriate collection(s) for its inputs
+and running the workflow in one seamless iteration.
+[`#18857 <https://github.com/galaxyproject/galaxy/pull/18857>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/y4gNThU_BZE" title="Galaxy 24.2 - Improved Navigation and Usability of Collection Builders" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Enhanced Workflow Invocation View
+-----------------------------------------------------------
+
+The Workflow Invocation View, introduced in the `previous release <24.1_announce_user.html>`__
+has been significantly refined to improve the usability and visualization of workflow runs.
+[`#18615 <https://github.com/galaxyproject/galaxy/pull/18615>`__]
+
+Updates include:
+
+- **Workflow steps moved to a separate tab**, allocating maximum space for the graph.
+- **Progress bars relocated to the header** for a cleaner layout.
+- **Workflow inputs displayed directly on the graph**, eliminating the need for clicking
+  and investigating each input.
+- **The Invocations panel also toggles out on mouse leave**, providing an uncluttered view when
+  exploring runs.
+
+.. list-table::
+   :header-rows: 1
+
+   * - Before
+     - After
+   * - .. image:: images/24.2-invocation-view-improvements-before.png
+          :alt: Invocation view improvements before
+          :width: 100%
+     - .. image:: images/24.2-invocation-view-improvements-after.png
+          :alt: Invocation view improvements after
+          :width: 100%
+   * - Steps show on the right, the progress bars are within the `Overview` tab
+     - Only the currently active step shows below, leaving full width for graph, progress
+       bars in the Header
+
+Display Metrics for Workflow Invocations
+-----------------------------------------------------------
+
+Galaxy now provides a Metrics tab in the Workflow Invocation View, allowing users to quickly
+summarize runtime, memory usage, and core allocation per invocation. This enhancement helps users
+better understand the resource usage of their workflows. The Metrics tab displays runtime in
+seconds and core allocation for each step and tool in the workflow.
+[`#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`__]
+
+.. figure:: images/24.2-workflow-invocation-metrics.png
+   :alt: Metrics tab in the Workflow Invocation View.
+
+Libraries Modernization: Directory Dataset Picker
+-----------------------------------------------------------
+
+The dataset picker for user and import directories has been modernized, providing a more
+intuitive and user-friendly interface. Users can now easily import files or folders from their
+user directory or import directory into a library. Admins can also import datasets from a
+specified path. Additionally, the new History Dataset Picker allows users to explore their
+histories and select datasets to add to the library, streamlining the dataset management process.
+[`#18638 <https://github.com/galaxyproject/galaxy/pull/18638>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/i8AHdv5sU5A" title="Galaxy 24.2 - Libraries Modernization: Directory Dataset Picker" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Live Reporting of Job Console Outputs
+-----------------------------------------------------------
+
+If enabled by the Galaxy administrators, it will now be possible to view live console output
+for running jobs. The job output will be available on the Job Information page where these
+logs have always been available for completed jobs. The job information view has also been
+updated with scrollable code blocks, a more intuitive expand/collapse feature,
+and an auto-scroll function for seamless log viewing. This should allow you to debug issues with
+running jobs faster and track the progress of running jobs in realtime in a way that has never
+been an option in Galaxy. A huge thanks to Gregory Cage at Oak Ridge National Laboratory for
+this valuable contribution!
+[`#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`__]
+
+
+ChatGXY - Job Error Wizard
+-----------------------------------------------------------
+
+With this release, we're excited to introduce ChatGXY — AI assistance built
+directly into the Galaxy interface. The first functionality being rolled out is
+an AI-driven job error diagnoser that automatically inspects errored jobs and
+provides actionable insights. Users on supported servers can access this
+feature through the Dataset Error interface, where ChatGXY offers targeted
+suggestions to help diagnose and resolve job errors quickly and efficiently.
+[`#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`__]
+
+Visualizations
+===========================================================
+
+.. visualizations
+* Prevent cycling through failing conversion jobs in trackster
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19494`_
+* Update visualizations package versions
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19232`_
+* Fix MSA viz, new dependency specification options
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18760`_
+* Parse stored config details to script-based visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18651`_
+* Install npm-package viz to the package prefix explicitly
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18950`_
+* Migrate NGL viewer to npm package
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18946`_
+* Support deferred datasets in visualizations
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19097`_
+* Openlayer update to npm package
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 19134`_
+* Replace static Cytoscape plugin with npm package
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 19127`_
+* Update tiff viewer to use script entry_point
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19151`_
+* Migrate Venn Diagram to Script-Tag
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19153`_
+* FITS file table graph visualization plugin
+  (thanks to `@francoismg <https://github.com/francoismg>`__).
+  `Pull Request 19003`_
+* Restore access to saved visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19136`_
+* Remove OpenLayers legacy files and add SVG logo
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19135`_
+
+Datatypes
+===========================================================
+
+.. datatypes
+* Add pod5 datatype
+  (thanks to `@TomHarrop <https://github.com/TomHarrop>`__).
+  `Pull Request 18419`_
+* Handle compressed content in dataset preview for all sequence classes
+  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
+  `Pull Request 18776`_
+* Type annotations and fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18911`_
+* Improve usability of Directory datatype
+  (thanks to `@wm75 <https://github.com/wm75>`__).
+  `Pull Request 17614`_
+* Add some Zarr-based datatypes
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19040`_
+* Add XML based `vtk` datatype
+  (thanks to `@tStehling <https://github.com/tStehling>`__).
+  `Pull Request 19104`_
+* Add gtf to auto_compressed_types
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19175`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Drop "Send to cloud" tool and associated cloudauthz code
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18196`_
+* Update GPU JupyterLab tool
+  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
+  `Pull Request 18220`_
+* Improvements to Tool Test Parsing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18560`_
+* Add Tool-Centric APIs to the Tool Shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18524`_
+* Add BlobToolkit to the list of interactive tools
+  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
+  `Pull Request 18630`_
+* Enable ``ignore-without-code`` mypy error code
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18898`_
+* Remove some unused dynamic drill down options
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18892`_
+* Fix commas that shouldn't be in biotools_mappings.tsv
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18919`_
+* Add filter null collection operation tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18928`_
+* Remove outdated fimo wrapper and galaxy-sequence-utils dependency
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18937`_
+* Jupyter Interactive Tool 1.0.1/24.07
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 18861`_
+* Add Interactive Tool Ilastik
+  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
+  `Pull Request 16837`_
+
+Please see the full :doc:`24.2 release notes <24.2_announce>` for more details.
+
+.. include:: 24.2_prs.rst
+
+----
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/24.2_prs.rst b/doc/source/releases/24.2_prs.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c537e74380cf80dfb55bdc8b9b981f9b13c223a5
--- /dev/null
+++ b/doc/source/releases/24.2_prs.rst
@@ -0,0 +1,324 @@
+
+.. github_links
+.. _Pull Request 19471: https://github.com/galaxyproject/galaxy/pull/19471
+.. _Pull Request 19495: https://github.com/galaxyproject/galaxy/pull/19495
+.. _Pull Request 19525: https://github.com/galaxyproject/galaxy/pull/19525
+.. _Pull Request 19520: https://github.com/galaxyproject/galaxy/pull/19520
+.. _Pull Request 19494: https://github.com/galaxyproject/galaxy/pull/19494
+.. _Pull Request 19532: https://github.com/galaxyproject/galaxy/pull/19532
+.. _Pull Request 19537: https://github.com/galaxyproject/galaxy/pull/19537
+.. _Pull Request 19526: https://github.com/galaxyproject/galaxy/pull/19526
+.. _Pull Request 19544: https://github.com/galaxyproject/galaxy/pull/19544
+.. _Pull Request 19551: https://github.com/galaxyproject/galaxy/pull/19551
+.. _Pull Request 19550: https://github.com/galaxyproject/galaxy/pull/19550
+.. _Pull Request 19389: https://github.com/galaxyproject/galaxy/pull/19389
+.. _Pull Request 19393: https://github.com/galaxyproject/galaxy/pull/19393
+.. _Pull Request 19404: https://github.com/galaxyproject/galaxy/pull/19404
+.. _Pull Request 19426: https://github.com/galaxyproject/galaxy/pull/19426
+.. _Pull Request 19427: https://github.com/galaxyproject/galaxy/pull/19427
+.. _Pull Request 19447: https://github.com/galaxyproject/galaxy/pull/19447
+.. _Pull Request 19450: https://github.com/galaxyproject/galaxy/pull/19450
+.. _Pull Request 19455: https://github.com/galaxyproject/galaxy/pull/19455
+.. _Pull Request 19459: https://github.com/galaxyproject/galaxy/pull/19459
+.. _Pull Request 19460: https://github.com/galaxyproject/galaxy/pull/19460
+.. _Pull Request 19465: https://github.com/galaxyproject/galaxy/pull/19465
+.. _Pull Request 19468: https://github.com/galaxyproject/galaxy/pull/19468
+.. _Pull Request 19469: https://github.com/galaxyproject/galaxy/pull/19469
+.. _Pull Request 19473: https://github.com/galaxyproject/galaxy/pull/19473
+.. _Pull Request 19483: https://github.com/galaxyproject/galaxy/pull/19483
+.. _Pull Request 19489: https://github.com/galaxyproject/galaxy/pull/19489
+.. _Pull Request 19496: https://github.com/galaxyproject/galaxy/pull/19496
+.. _Pull Request 19497: https://github.com/galaxyproject/galaxy/pull/19497
+.. _Pull Request 19499: https://github.com/galaxyproject/galaxy/pull/19499
+.. _Pull Request 19505: https://github.com/galaxyproject/galaxy/pull/19505
+.. _Pull Request 19507: https://github.com/galaxyproject/galaxy/pull/19507
+.. _Pull Request 19514: https://github.com/galaxyproject/galaxy/pull/19514
+.. _Pull Request 19518: https://github.com/galaxyproject/galaxy/pull/19518
+.. _Pull Request 19528: https://github.com/galaxyproject/galaxy/pull/19528
+.. _Pull Request 19543: https://github.com/galaxyproject/galaxy/pull/19543
+.. _Pull Request 19208: https://github.com/galaxyproject/galaxy/pull/19208
+.. _Pull Request 19244: https://github.com/galaxyproject/galaxy/pull/19244
+.. _Pull Request 19248: https://github.com/galaxyproject/galaxy/pull/19248
+.. _Pull Request 19254: https://github.com/galaxyproject/galaxy/pull/19254
+.. _Pull Request 19258: https://github.com/galaxyproject/galaxy/pull/19258
+.. _Pull Request 19262: https://github.com/galaxyproject/galaxy/pull/19262
+.. _Pull Request 19276: https://github.com/galaxyproject/galaxy/pull/19276
+.. _Pull Request 19279: https://github.com/galaxyproject/galaxy/pull/19279
+.. _Pull Request 19283: https://github.com/galaxyproject/galaxy/pull/19283
+.. _Pull Request 19284: https://github.com/galaxyproject/galaxy/pull/19284
+.. _Pull Request 19288: https://github.com/galaxyproject/galaxy/pull/19288
+.. _Pull Request 19291: https://github.com/galaxyproject/galaxy/pull/19291
+.. _Pull Request 19298: https://github.com/galaxyproject/galaxy/pull/19298
+.. _Pull Request 19311: https://github.com/galaxyproject/galaxy/pull/19311
+.. _Pull Request 19312: https://github.com/galaxyproject/galaxy/pull/19312
+.. _Pull Request 19342: https://github.com/galaxyproject/galaxy/pull/19342
+.. _Pull Request 19373: https://github.com/galaxyproject/galaxy/pull/19373
+.. _Pull Request 19381: https://github.com/galaxyproject/galaxy/pull/19381
+.. _Pull Request 19384: https://github.com/galaxyproject/galaxy/pull/19384
+.. _Pull Request 19387: https://github.com/galaxyproject/galaxy/pull/19387
+.. _Pull Request 19351: https://github.com/galaxyproject/galaxy/pull/19351
+.. _Pull Request 19332: https://github.com/galaxyproject/galaxy/pull/19332
+.. _Pull Request 19350: https://github.com/galaxyproject/galaxy/pull/19350
+.. _Pull Request 19232: https://github.com/galaxyproject/galaxy/pull/19232
+.. _Pull Request 19399: https://github.com/galaxyproject/galaxy/pull/19399
+.. _Pull Request 19308: https://github.com/galaxyproject/galaxy/pull/19308
+.. _Pull Request 19316: https://github.com/galaxyproject/galaxy/pull/19316
+.. _Pull Request 19281: https://github.com/galaxyproject/galaxy/pull/19281
+.. _Pull Request 19251: https://github.com/galaxyproject/galaxy/pull/19251
+.. _Pull Request 19250: https://github.com/galaxyproject/galaxy/pull/19250
+.. _Pull Request 19230: https://github.com/galaxyproject/galaxy/pull/19230
+.. _Pull Request 19252: https://github.com/galaxyproject/galaxy/pull/19252
+.. _Pull Request 19238: https://github.com/galaxyproject/galaxy/pull/19238
+.. _Pull Request 18857: https://github.com/galaxyproject/galaxy/pull/18857
+.. _Pull Request 19241: https://github.com/galaxyproject/galaxy/pull/19241
+.. _Pull Request 19242: https://github.com/galaxyproject/galaxy/pull/19242
+.. _Pull Request 19247: https://github.com/galaxyproject/galaxy/pull/19247
+.. _Pull Request 19212: https://github.com/galaxyproject/galaxy/pull/19212
+.. _Pull Request 19219: https://github.com/galaxyproject/galaxy/pull/19219
+.. _Pull Request 19182: https://github.com/galaxyproject/galaxy/pull/19182
+.. _Pull Request 18197: https://github.com/galaxyproject/galaxy/pull/18197
+.. _Pull Request 18196: https://github.com/galaxyproject/galaxy/pull/18196
+.. _Pull Request 18220: https://github.com/galaxyproject/galaxy/pull/18220
+.. _Pull Request 18386: https://github.com/galaxyproject/galaxy/pull/18386
+.. _Pull Request 18461: https://github.com/galaxyproject/galaxy/pull/18461
+.. _Pull Request 18479: https://github.com/galaxyproject/galaxy/pull/18479
+.. _Pull Request 18503: https://github.com/galaxyproject/galaxy/pull/18503
+.. _Pull Request 18419: https://github.com/galaxyproject/galaxy/pull/18419
+.. _Pull Request 18468: https://github.com/galaxyproject/galaxy/pull/18468
+.. _Pull Request 18510: https://github.com/galaxyproject/galaxy/pull/18510
+.. _Pull Request 18516: https://github.com/galaxyproject/galaxy/pull/18516
+.. _Pull Request 18523: https://github.com/galaxyproject/galaxy/pull/18523
+.. _Pull Request 18519: https://github.com/galaxyproject/galaxy/pull/18519
+.. _Pull Request 18539: https://github.com/galaxyproject/galaxy/pull/18539
+.. _Pull Request 18469: https://github.com/galaxyproject/galaxy/pull/18469
+.. _Pull Request 18538: https://github.com/galaxyproject/galaxy/pull/18538
+.. _Pull Request 18093: https://github.com/galaxyproject/galaxy/pull/18093
+.. _Pull Request 18529: https://github.com/galaxyproject/galaxy/pull/18529
+.. _Pull Request 18558: https://github.com/galaxyproject/galaxy/pull/18558
+.. _Pull Request 18560: https://github.com/galaxyproject/galaxy/pull/18560
+.. _Pull Request 18551: https://github.com/galaxyproject/galaxy/pull/18551
+.. _Pull Request 18563: https://github.com/galaxyproject/galaxy/pull/18563
+.. _Pull Request 18568: https://github.com/galaxyproject/galaxy/pull/18568
+.. _Pull Request 18524: https://github.com/galaxyproject/galaxy/pull/18524
+.. _Pull Request 18583: https://github.com/galaxyproject/galaxy/pull/18583
+.. _Pull Request 18570: https://github.com/galaxyproject/galaxy/pull/18570
+.. _Pull Request 18575: https://github.com/galaxyproject/galaxy/pull/18575
+.. _Pull Request 18553: https://github.com/galaxyproject/galaxy/pull/18553
+.. _Pull Request 18589: https://github.com/galaxyproject/galaxy/pull/18589
+.. _Pull Request 18593: https://github.com/galaxyproject/galaxy/pull/18593
+.. _Pull Request 18599: https://github.com/galaxyproject/galaxy/pull/18599
+.. _Pull Request 18265: https://github.com/galaxyproject/galaxy/pull/18265
+.. _Pull Request 18602: https://github.com/galaxyproject/galaxy/pull/18602
+.. _Pull Request 18590: https://github.com/galaxyproject/galaxy/pull/18590
+.. _Pull Request 18579: https://github.com/galaxyproject/galaxy/pull/18579
+.. _Pull Request 18610: https://github.com/galaxyproject/galaxy/pull/18610
+.. _Pull Request 18623: https://github.com/galaxyproject/galaxy/pull/18623
+.. _Pull Request 18618: https://github.com/galaxyproject/galaxy/pull/18618
+.. _Pull Request 18624: https://github.com/galaxyproject/galaxy/pull/18624
+.. _Pull Request 18585: https://github.com/galaxyproject/galaxy/pull/18585
+.. _Pull Request 18605: https://github.com/galaxyproject/galaxy/pull/18605
+.. _Pull Request 18608: https://github.com/galaxyproject/galaxy/pull/18608
+.. _Pull Request 18586: https://github.com/galaxyproject/galaxy/pull/18586
+.. _Pull Request 18632: https://github.com/galaxyproject/galaxy/pull/18632
+.. _Pull Request 18644: https://github.com/galaxyproject/galaxy/pull/18644
+.. _Pull Request 18631: https://github.com/galaxyproject/galaxy/pull/18631
+.. _Pull Request 18643: https://github.com/galaxyproject/galaxy/pull/18643
+.. _Pull Request 18645: https://github.com/galaxyproject/galaxy/pull/18645
+.. _Pull Request 18647: https://github.com/galaxyproject/galaxy/pull/18647
+.. _Pull Request 18626: https://github.com/galaxyproject/galaxy/pull/18626
+.. _Pull Request 18581: https://github.com/galaxyproject/galaxy/pull/18581
+.. _Pull Request 18656: https://github.com/galaxyproject/galaxy/pull/18656
+.. _Pull Request 18668: https://github.com/galaxyproject/galaxy/pull/18668
+.. _Pull Request 18673: https://github.com/galaxyproject/galaxy/pull/18673
+.. _Pull Request 18676: https://github.com/galaxyproject/galaxy/pull/18676
+.. _Pull Request 18674: https://github.com/galaxyproject/galaxy/pull/18674
+.. _Pull Request 18686: https://github.com/galaxyproject/galaxy/pull/18686
+.. _Pull Request 18655: https://github.com/galaxyproject/galaxy/pull/18655
+.. _Pull Request 18706: https://github.com/galaxyproject/galaxy/pull/18706
+.. _Pull Request 16894: https://github.com/galaxyproject/galaxy/pull/16894
+.. _Pull Request 18708: https://github.com/galaxyproject/galaxy/pull/18708
+.. _Pull Request 18716: https://github.com/galaxyproject/galaxy/pull/18716
+.. _Pull Request 18717: https://github.com/galaxyproject/galaxy/pull/18717
+.. _Pull Request 18678: https://github.com/galaxyproject/galaxy/pull/18678
+.. _Pull Request 18679: https://github.com/galaxyproject/galaxy/pull/18679
+.. _Pull Request 18715: https://github.com/galaxyproject/galaxy/pull/18715
+.. _Pull Request 18728: https://github.com/galaxyproject/galaxy/pull/18728
+.. _Pull Request 18746: https://github.com/galaxyproject/galaxy/pull/18746
+.. _Pull Request 18707: https://github.com/galaxyproject/galaxy/pull/18707
+.. _Pull Request 18755: https://github.com/galaxyproject/galaxy/pull/18755
+.. _Pull Request 18768: https://github.com/galaxyproject/galaxy/pull/18768
+.. _Pull Request 18457: https://github.com/galaxyproject/galaxy/pull/18457
+.. _Pull Request 18630: https://github.com/galaxyproject/galaxy/pull/18630
+.. _Pull Request 18776: https://github.com/galaxyproject/galaxy/pull/18776
+.. _Pull Request 18758: https://github.com/galaxyproject/galaxy/pull/18758
+.. _Pull Request 18789: https://github.com/galaxyproject/galaxy/pull/18789
+.. _Pull Request 18488: https://github.com/galaxyproject/galaxy/pull/18488
+.. _Pull Request 18721: https://github.com/galaxyproject/galaxy/pull/18721
+.. _Pull Request 18786: https://github.com/galaxyproject/galaxy/pull/18786
+.. _Pull Request 18794: https://github.com/galaxyproject/galaxy/pull/18794
+.. _Pull Request 18773: https://github.com/galaxyproject/galaxy/pull/18773
+.. _Pull Request 18760: https://github.com/galaxyproject/galaxy/pull/18760
+.. _Pull Request 18792: https://github.com/galaxyproject/galaxy/pull/18792
+.. _Pull Request 18613: https://github.com/galaxyproject/galaxy/pull/18613
+.. _Pull Request 18722: https://github.com/galaxyproject/galaxy/pull/18722
+.. _Pull Request 18803: https://github.com/galaxyproject/galaxy/pull/18803
+.. _Pull Request 18651: https://github.com/galaxyproject/galaxy/pull/18651
+.. _Pull Request 18811: https://github.com/galaxyproject/galaxy/pull/18811
+.. _Pull Request 18578: https://github.com/galaxyproject/galaxy/pull/18578
+.. _Pull Request 18787: https://github.com/galaxyproject/galaxy/pull/18787
+.. _Pull Request 18740: https://github.com/galaxyproject/galaxy/pull/18740
+.. _Pull Request 18836: https://github.com/galaxyproject/galaxy/pull/18836
+.. _Pull Request 18595: https://github.com/galaxyproject/galaxy/pull/18595
+.. _Pull Request 18808: https://github.com/galaxyproject/galaxy/pull/18808
+.. _Pull Request 18847: https://github.com/galaxyproject/galaxy/pull/18847
+.. _Pull Request 18796: https://github.com/galaxyproject/galaxy/pull/18796
+.. _Pull Request 18743: https://github.com/galaxyproject/galaxy/pull/18743
+.. _Pull Request 18844: https://github.com/galaxyproject/galaxy/pull/18844
+.. _Pull Request 18852: https://github.com/galaxyproject/galaxy/pull/18852
+.. _Pull Request 18860: https://github.com/galaxyproject/galaxy/pull/18860
+.. _Pull Request 18864: https://github.com/galaxyproject/galaxy/pull/18864
+.. _Pull Request 18854: https://github.com/galaxyproject/galaxy/pull/18854
+.. _Pull Request 18821: https://github.com/galaxyproject/galaxy/pull/18821
+.. _Pull Request 18757: https://github.com/galaxyproject/galaxy/pull/18757
+.. _Pull Request 18777: https://github.com/galaxyproject/galaxy/pull/18777
+.. _Pull Request 18493: https://github.com/galaxyproject/galaxy/pull/18493
+.. _Pull Request 18885: https://github.com/galaxyproject/galaxy/pull/18885
+.. _Pull Request 18879: https://github.com/galaxyproject/galaxy/pull/18879
+.. _Pull Request 18884: https://github.com/galaxyproject/galaxy/pull/18884
+.. _Pull Request 18886: https://github.com/galaxyproject/galaxy/pull/18886
+.. _Pull Request 18898: https://github.com/galaxyproject/galaxy/pull/18898
+.. _Pull Request 18888: https://github.com/galaxyproject/galaxy/pull/18888
+.. _Pull Request 18889: https://github.com/galaxyproject/galaxy/pull/18889
+.. _Pull Request 18518: https://github.com/galaxyproject/galaxy/pull/18518
+.. _Pull Request 18911: https://github.com/galaxyproject/galaxy/pull/18911
+.. _Pull Request 18779: https://github.com/galaxyproject/galaxy/pull/18779
+.. _Pull Request 18904: https://github.com/galaxyproject/galaxy/pull/18904
+.. _Pull Request 18923: https://github.com/galaxyproject/galaxy/pull/18923
+.. _Pull Request 18892: https://github.com/galaxyproject/galaxy/pull/18892
+.. _Pull Request 18919: https://github.com/galaxyproject/galaxy/pull/18919
+.. _Pull Request 18928: https://github.com/galaxyproject/galaxy/pull/18928
+.. _Pull Request 18891: https://github.com/galaxyproject/galaxy/pull/18891
+.. _Pull Request 18937: https://github.com/galaxyproject/galaxy/pull/18937
+.. _Pull Request 18943: https://github.com/galaxyproject/galaxy/pull/18943
+.. _Pull Request 18909: https://github.com/galaxyproject/galaxy/pull/18909
+.. _Pull Request 18838: https://github.com/galaxyproject/galaxy/pull/18838
+.. _Pull Request 18924: https://github.com/galaxyproject/galaxy/pull/18924
+.. _Pull Request 18950: https://github.com/galaxyproject/galaxy/pull/18950
+.. _Pull Request 18956: https://github.com/galaxyproject/galaxy/pull/18956
+.. _Pull Request 18958: https://github.com/galaxyproject/galaxy/pull/18958
+.. _Pull Request 18963: https://github.com/galaxyproject/galaxy/pull/18963
+.. _Pull Request 18975: https://github.com/galaxyproject/galaxy/pull/18975
+.. _Pull Request 18968: https://github.com/galaxyproject/galaxy/pull/18968
+.. _Pull Request 18970: https://github.com/galaxyproject/galaxy/pull/18970
+.. _Pull Request 18983: https://github.com/galaxyproject/galaxy/pull/18983
+.. _Pull Request 18982: https://github.com/galaxyproject/galaxy/pull/18982
+.. _Pull Request 18598: https://github.com/galaxyproject/galaxy/pull/18598
+.. _Pull Request 18987: https://github.com/galaxyproject/galaxy/pull/18987
+.. _Pull Request 18988: https://github.com/galaxyproject/galaxy/pull/18988
+.. _Pull Request 18991: https://github.com/galaxyproject/galaxy/pull/18991
+.. _Pull Request 18997: https://github.com/galaxyproject/galaxy/pull/18997
+.. _Pull Request 18835: https://github.com/galaxyproject/galaxy/pull/18835
+.. _Pull Request 19010: https://github.com/galaxyproject/galaxy/pull/19010
+.. _Pull Request 19019: https://github.com/galaxyproject/galaxy/pull/19019
+.. _Pull Request 19001: https://github.com/galaxyproject/galaxy/pull/19001
+.. _Pull Request 18946: https://github.com/galaxyproject/galaxy/pull/18946
+.. _Pull Request 19037: https://github.com/galaxyproject/galaxy/pull/19037
+.. _Pull Request 19031: https://github.com/galaxyproject/galaxy/pull/19031
+.. _Pull Request 18887: https://github.com/galaxyproject/galaxy/pull/18887
+.. _Pull Request 18979: https://github.com/galaxyproject/galaxy/pull/18979
+.. _Pull Request 18742: https://github.com/galaxyproject/galaxy/pull/18742
+.. _Pull Request 19041: https://github.com/galaxyproject/galaxy/pull/19041
+.. _Pull Request 19062: https://github.com/galaxyproject/galaxy/pull/19062
+.. _Pull Request 19025: https://github.com/galaxyproject/galaxy/pull/19025
+.. _Pull Request 19063: https://github.com/galaxyproject/galaxy/pull/19063
+.. _Pull Request 19029: https://github.com/galaxyproject/galaxy/pull/19029
+.. _Pull Request 19055: https://github.com/galaxyproject/galaxy/pull/19055
+.. _Pull Request 19060: https://github.com/galaxyproject/galaxy/pull/19060
+.. _Pull Request 19002: https://github.com/galaxyproject/galaxy/pull/19002
+.. _Pull Request 19076: https://github.com/galaxyproject/galaxy/pull/19076
+.. _Pull Request 19070: https://github.com/galaxyproject/galaxy/pull/19070
+.. _Pull Request 17614: https://github.com/galaxyproject/galaxy/pull/17614
+.. _Pull Request 19075: https://github.com/galaxyproject/galaxy/pull/19075
+.. _Pull Request 18449: https://github.com/galaxyproject/galaxy/pull/18449
+.. _Pull Request 19030: https://github.com/galaxyproject/galaxy/pull/19030
+.. _Pull Request 19077: https://github.com/galaxyproject/galaxy/pull/19077
+.. _Pull Request 19097: https://github.com/galaxyproject/galaxy/pull/19097
+.. _Pull Request 19099: https://github.com/galaxyproject/galaxy/pull/19099
+.. _Pull Request 19094: https://github.com/galaxyproject/galaxy/pull/19094
+.. _Pull Request 19109: https://github.com/galaxyproject/galaxy/pull/19109
+.. _Pull Request 19073: https://github.com/galaxyproject/galaxy/pull/19073
+.. _Pull Request 19047: https://github.com/galaxyproject/galaxy/pull/19047
+.. _Pull Request 18834: https://github.com/galaxyproject/galaxy/pull/18834
+.. _Pull Request 19111: https://github.com/galaxyproject/galaxy/pull/19111
+.. _Pull Request 19113: https://github.com/galaxyproject/galaxy/pull/19113
+.. _Pull Request 19108: https://github.com/galaxyproject/galaxy/pull/19108
+.. _Pull Request 19110: https://github.com/galaxyproject/galaxy/pull/19110
+.. _Pull Request 19114: https://github.com/galaxyproject/galaxy/pull/19114
+.. _Pull Request 19123: https://github.com/galaxyproject/galaxy/pull/19123
+.. _Pull Request 19128: https://github.com/galaxyproject/galaxy/pull/19128
+.. _Pull Request 18998: https://github.com/galaxyproject/galaxy/pull/18998
+.. _Pull Request 19046: https://github.com/galaxyproject/galaxy/pull/19046
+.. _Pull Request 19115: https://github.com/galaxyproject/galaxy/pull/19115
+.. _Pull Request 19040: https://github.com/galaxyproject/galaxy/pull/19040
+.. _Pull Request 18522: https://github.com/galaxyproject/galaxy/pull/18522
+.. _Pull Request 18945: https://github.com/galaxyproject/galaxy/pull/18945
+.. _Pull Request 18198: https://github.com/galaxyproject/galaxy/pull/18198
+.. _Pull Request 19134: https://github.com/galaxyproject/galaxy/pull/19134
+.. _Pull Request 19022: https://github.com/galaxyproject/galaxy/pull/19022
+.. _Pull Request 19014: https://github.com/galaxyproject/galaxy/pull/19014
+.. _Pull Request 18880: https://github.com/galaxyproject/galaxy/pull/18880
+.. _Pull Request 18861: https://github.com/galaxyproject/galaxy/pull/18861
+.. _Pull Request 19101: https://github.com/galaxyproject/galaxy/pull/19101
+.. _Pull Request 19142: https://github.com/galaxyproject/galaxy/pull/19142
+.. _Pull Request 19127: https://github.com/galaxyproject/galaxy/pull/19127
+.. _Pull Request 19141: https://github.com/galaxyproject/galaxy/pull/19141
+.. _Pull Request 18762: https://github.com/galaxyproject/galaxy/pull/18762
+.. _Pull Request 18949: https://github.com/galaxyproject/galaxy/pull/18949
+.. _Pull Request 16837: https://github.com/galaxyproject/galaxy/pull/16837
+.. _Pull Request 19150: https://github.com/galaxyproject/galaxy/pull/19150
+.. _Pull Request 19151: https://github.com/galaxyproject/galaxy/pull/19151
+.. _Pull Request 19104: https://github.com/galaxyproject/galaxy/pull/19104
+.. _Pull Request 19153: https://github.com/galaxyproject/galaxy/pull/19153
+.. _Pull Request 18936: https://github.com/galaxyproject/galaxy/pull/18936
+.. _Pull Request 19003: https://github.com/galaxyproject/galaxy/pull/19003
+.. _Pull Request 19163: https://github.com/galaxyproject/galaxy/pull/19163
+.. _Pull Request 19136: https://github.com/galaxyproject/galaxy/pull/19136
+.. _Pull Request 19020: https://github.com/galaxyproject/galaxy/pull/19020
+.. _Pull Request 19170: https://github.com/galaxyproject/galaxy/pull/19170
+.. _Pull Request 15860: https://github.com/galaxyproject/galaxy/pull/15860
+.. _Pull Request 18272: https://github.com/galaxyproject/galaxy/pull/18272
+.. _Pull Request 19048: https://github.com/galaxyproject/galaxy/pull/19048
+.. _Pull Request 18977: https://github.com/galaxyproject/galaxy/pull/18977
+.. _Pull Request 18966: https://github.com/galaxyproject/galaxy/pull/18966
+.. _Pull Request 18807: https://github.com/galaxyproject/galaxy/pull/18807
+.. _Pull Request 18481: https://github.com/galaxyproject/galaxy/pull/18481
+.. _Pull Request 18312: https://github.com/galaxyproject/galaxy/pull/18312
+.. _Pull Request 18542: https://github.com/galaxyproject/galaxy/pull/18542
+.. _Pull Request 19135: https://github.com/galaxyproject/galaxy/pull/19135
+.. _Pull Request 19090: https://github.com/galaxyproject/galaxy/pull/19090
+.. _Pull Request 18996: https://github.com/galaxyproject/galaxy/pull/18996
+.. _Pull Request 18942: https://github.com/galaxyproject/galaxy/pull/18942
+.. _Pull Request 18910: https://github.com/galaxyproject/galaxy/pull/18910
+.. _Pull Request 18866: https://github.com/galaxyproject/galaxy/pull/18866
+.. _Pull Request 18714: https://github.com/galaxyproject/galaxy/pull/18714
+.. _Pull Request 18638: https://github.com/galaxyproject/galaxy/pull/18638
+.. _Pull Request 18548: https://github.com/galaxyproject/galaxy/pull/18548
+.. _Pull Request 18499: https://github.com/galaxyproject/galaxy/pull/18499
+.. _Pull Request 18458: https://github.com/galaxyproject/galaxy/pull/18458
+.. _Pull Request 19050: https://github.com/galaxyproject/galaxy/pull/19050
+.. _Pull Request 19027: https://github.com/galaxyproject/galaxy/pull/19027
+.. _Pull Request 18985: https://github.com/galaxyproject/galaxy/pull/18985
+.. _Pull Request 18641: https://github.com/galaxyproject/galaxy/pull/18641
+.. _Pull Request 18532: https://github.com/galaxyproject/galaxy/pull/18532
+.. _Pull Request 17927: https://github.com/galaxyproject/galaxy/pull/17927
+.. _Pull Request 18615: https://github.com/galaxyproject/galaxy/pull/18615
+.. _Pull Request 18986: https://github.com/galaxyproject/galaxy/pull/18986
+.. _Pull Request 19096: https://github.com/galaxyproject/galaxy/pull/19096
+.. _Pull Request 16975: https://github.com/galaxyproject/galaxy/pull/16975
+.. _Pull Request 19166: https://github.com/galaxyproject/galaxy/pull/19166
+.. _Pull Request 17600: https://github.com/galaxyproject/galaxy/pull/17600
+.. _Pull Request 19168: https://github.com/galaxyproject/galaxy/pull/19168
+.. _Pull Request 19199: https://github.com/galaxyproject/galaxy/pull/19199
+.. _Pull Request 19175: https://github.com/galaxyproject/galaxy/pull/19175
+.. _Pull Request 19172: https://github.com/galaxyproject/galaxy/pull/19172
+.. _Pull Request 19131: https://github.com/galaxyproject/galaxy/pull/19131
diff --git a/doc/source/releases/25.0_announce.rst b/doc/source/releases/25.0_announce.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4f1ce6ad647879a3069caeb89d89653c5c0f1ea9
--- /dev/null
+++ b/doc/source/releases/25.0_announce.rst
@@ -0,0 +1,6 @@
+
+:orphan:
+
+===========================================================
+25.0 Galaxy Release
+===========================================================
diff --git a/doc/source/releases/images/24.2-export-invocation-wizard.gif b/doc/source/releases/images/24.2-export-invocation-wizard.gif
new file mode 100644
index 0000000000000000000000000000000000000000..5c03c995613db288aeb9f63dfe8749fbc32e191b
Binary files /dev/null and b/doc/source/releases/images/24.2-export-invocation-wizard.gif differ
diff --git a/doc/source/releases/images/24.2-invocation-view-improvements-after.png b/doc/source/releases/images/24.2-invocation-view-improvements-after.png
new file mode 100644
index 0000000000000000000000000000000000000000..9212b6a39db36830d31b97572904bb9e3d8253af
Binary files /dev/null and b/doc/source/releases/images/24.2-invocation-view-improvements-after.png differ
diff --git a/doc/source/releases/images/24.2-invocation-view-improvements-before.png b/doc/source/releases/images/24.2-invocation-view-improvements-before.png
new file mode 100644
index 0000000000000000000000000000000000000000..bc7d9077d1333660a40f94bf329c1074efd716fb
Binary files /dev/null and b/doc/source/releases/images/24.2-invocation-view-improvements-before.png differ
diff --git a/doc/source/releases/images/24.2-workflow-invocation-metrics.png b/doc/source/releases/images/24.2-workflow-invocation-metrics.png
new file mode 100644
index 0000000000000000000000000000000000000000..2b9e43b319309acee43e1e1dec1831dcb4c0acb3
Binary files /dev/null and b/doc/source/releases/images/24.2-workflow-invocation-metrics.png differ
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 5e9d65038a4f6c86cb80a8fb01df683c3af093b2..2a84a59df414004958d50596e2ebaceae44415ce 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   24.2_announce_user
    24.1_announce_user
    24.0_announce_user
    23.2_announce_user
diff --git a/dockerfiles/Dockerfile.full b/dockerfiles/Dockerfile.full
index afb44a8ce8400c5fa81a8326212d4799710cbb1f..b72fcaf59f2e0157d9276e181d28c5699b343726 100644
--- a/dockerfiles/Dockerfile.full
+++ b/dockerfiles/Dockerfile.full
@@ -1,4 +1,4 @@
-FROM python:3.8
+FROM python:3.10
 
 
 RUN apt update && apt install -y ffmpeg && curl -fsSL https://get.docker.com -o get-docker.sh && sh ./get-docker.sh
@@ -10,6 +10,6 @@ COPY . /galaxy
 
 RUN /galaxy/scripts/common_startup.sh
 RUN mkdir -p /galaxy/database/dependencies
-RUN . /galaxy/.venv/bin/activate && python ./scripts/manage_tool_dependencies.py init_if_needed && pip install rucio-clients
+RUN . /galaxy/.venv/bin/activate && python ./scripts/manage_tool_dependencies.py init_if_needed && pip install rucio-clients==33.6.0
 
 
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 72b651e1869a818515eae43a3885be35be5ed841..8afb8d4f227520e574980ba95a20760f46d89bab 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -5,22 +5,18 @@ Contains library functions
 import json
 import logging
 import os.path
-from typing import Optional
 
 from markupsafe import escape
 
-from galaxy import util
-from galaxy.exceptions import (
-    AdminRequiredException,
-    ConfigDoesNotAllowException,
-    ItemAccessibilityException,
-    ObjectNotFound,
-    RequestParameterInvalidException,
+from galaxy import (
+    exceptions,
+    util,
 )
-from galaxy.model import (
-    LibraryDataset,
-    LibraryFolder,
+from galaxy.managers.collections_util import (
+    api_payload_to_create_params,
+    dictify_dataset_collection_instance,
 )
+from galaxy.model import LibraryFolder
 from galaxy.model.base import transaction
 from galaxy.tools.actions import upload_common
 from galaxy.tools.parameters import populate_state
@@ -35,17 +31,19 @@ log = logging.getLogger(__name__)
 
 def validate_server_directory_upload(trans, server_dir):
     if server_dir in [None, "None", ""]:
-        raise RequestParameterInvalidException("Invalid or unspecified server_dir parameter")
+        raise exceptions.RequestParameterInvalidException("Invalid or unspecified server_dir parameter")
 
     if trans.user_is_admin:
         import_dir = trans.app.config.library_import_dir
         import_dir_desc = "library_import_dir"
         if not import_dir:
-            raise ConfigDoesNotAllowException('"library_import_dir" is not set in the Galaxy configuration')
+            raise exceptions.ConfigDoesNotAllowException('"library_import_dir" is not set in the Galaxy configuration')
     else:
         import_dir = trans.app.config.user_library_import_dir
         if not import_dir:
-            raise ConfigDoesNotAllowException('"user_library_import_dir" is not set in the Galaxy configuration')
+            raise exceptions.ConfigDoesNotAllowException(
+                '"user_library_import_dir" is not set in the Galaxy configuration'
+            )
         if server_dir != trans.user.email:
             import_dir = os.path.join(import_dir, trans.user.email)
         import_dir_desc = "user_library_import_dir"
@@ -75,17 +73,21 @@ def validate_server_directory_upload(trans, server_dir):
         )
         unsafe = True
     if unsafe:
-        raise RequestParameterInvalidException("Invalid server_dir specified")
+        raise exceptions.RequestParameterInvalidException("Invalid server_dir specified")
 
     return full_dir, import_dir_desc
 
 
 def validate_path_upload(trans):
     if not trans.app.config.allow_library_path_paste:
-        raise ConfigDoesNotAllowException('"allow_path_paste" is not set to True in the Galaxy configuration file')
+        raise exceptions.ConfigDoesNotAllowException(
+            '"allow_path_paste" is not set to True in the Galaxy configuration file'
+        )
 
     if not trans.user_is_admin:
-        raise AdminRequiredException("Uploading files via filesystem paths can only be performed by administrators")
+        raise exceptions.AdminRequiredException(
+            "Uploading files via filesystem paths can only be performed by administrators"
+        )
 
 
 class LibraryActions:
@@ -93,96 +95,87 @@ class LibraryActions:
     Mixin for controllers that provide library functionality.
     """
 
-    def _upload_dataset(self, trans, folder_id: int, replace_dataset: Optional[LibraryDataset] = None, **kwd):
+    def _upload_dataset(self, trans, folder_id: int, payload):
         # Set up the traditional tool state/params
         cntrller = "api"
         tool_id = "upload1"
-        message = None
-        file_type = kwd.get("file_type")
-        try:
-            upload_common.validate_datatype_extension(datatypes_registry=trans.app.datatypes_registry, ext=file_type)
-        except RequestParameterInvalidException as e:
-            return (400, util.unicodify(e))
+        upload_common.validate_datatype_extension(
+            datatypes_registry=trans.app.datatypes_registry, ext=payload.file_type
+        )
         tool = trans.app.toolbox.get_tool(tool_id)
         state = tool.new_state(trans)
-        populate_state(trans, tool.inputs, kwd, state.inputs)
+        populate_state(trans, tool.inputs, payload.model_dump(), state.inputs)
         tool_params = state.inputs
         dataset_upload_inputs = []
         for input in tool.inputs.values():
             if input.type == "upload_dataset":
                 dataset_upload_inputs.append(input)
         # Library-specific params
-        server_dir = kwd.get("server_dir", "")
-        upload_option = kwd.get("upload_option", "upload_file")
-        response_code = 200
-        if upload_option == "upload_directory":
-            full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
-            message = "Select a directory"
-        elif upload_option == "upload_paths":
+        if payload.upload_option == "upload_directory":
+            full_dir, import_dir_desc = validate_server_directory_upload(trans, payload.server_dir)
+        elif payload.upload_option == "upload_paths":
             # Library API already checked this - following check isn't actually needed.
             validate_path_upload(trans)
         # Some error handling should be added to this method.
         try:
-            # FIXME: instead of passing params here ( which have been processed by util.Params(), the original kwd
+            # FIXME: instead of passing params here ( which have been processed by util.Params(), the original payload
             # should be passed so that complex objects that may have been included in the initial request remain.
-            library_bunch = upload_common.handle_library_params(trans, kwd, folder_id, replace_dataset)
+            library_bunch = upload_common.handle_library_params(trans, payload.model_dump(), folder_id, None)
         except Exception:
-            response_code = 500
-            message = "Unable to parse upload parameters, please report this error."
+            raise exceptions.InvalidFileFormatError("Invalid folder specified")
         # Proceed with (mostly) regular upload processing if we're still errorless
-        if response_code == 200:
-            if upload_option == "upload_file":
-                tool_params = upload_common.persist_uploads(tool_params, trans)
-                uploaded_datasets = upload_common.get_uploaded_datasets(
-                    trans, cntrller, tool_params, dataset_upload_inputs, library_bunch=library_bunch
-                )
-            elif upload_option == "upload_directory":
-                uploaded_datasets, response_code, message = self._get_server_dir_uploaded_datasets(
-                    trans, kwd, full_dir, import_dir_desc, library_bunch, response_code, message
-                )
-            elif upload_option == "upload_paths":
-                uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(
-                    trans, kwd, library_bunch, response_code, message
-                )
-            if upload_option == "upload_file" and not uploaded_datasets:
-                response_code = 400
-                message = "Select a file, enter a URL or enter text"
-        if response_code != 200:
-            return (response_code, message)
+        if payload.upload_option == "upload_file":
+            if payload.upload_files:
+                for i, upload_dataset in enumerate(tool_params["files"]):
+                    upload_dataset["file_data"] = payload.upload_files[i]
+            tool_params = upload_common.persist_uploads(tool_params, trans)
+            uploaded_datasets = upload_common.get_uploaded_datasets(
+                trans, cntrller, tool_params, dataset_upload_inputs, library_bunch=library_bunch
+            )
+        elif payload.upload_option == "upload_directory":
+            uploaded_datasets = self._get_server_dir_uploaded_datasets(
+                trans, payload, full_dir, import_dir_desc, library_bunch
+            )
+        elif payload.upload_option == "upload_paths":
+            uploaded_datasets, response_code, message = self._get_path_paste_uploaded_datasets(
+                trans, payload.model_dump(), library_bunch, 200, None
+            )
+            if response_code != 200:
+                raise exceptions.RequestParameterInvalidException(message)
+        if payload.upload_option == "upload_file" and not uploaded_datasets:
+            raise exceptions.RequestParameterInvalidException("Select a file, enter a URL or enter text")
         json_file_path = upload_common.create_paramfile(trans, uploaded_datasets)
         data_list = [ud.data for ud in uploaded_datasets]
         job_params = {}
-        job_params["link_data_only"] = json.dumps(kwd.get("link_data_only", "copy_files"))
-        job_params["uuid"] = json.dumps(kwd.get("uuid", None))
+        job_params["link_data_only"] = json.dumps(payload.link_data_only)
+        job_params["uuid"] = json.dumps(payload.uuid)
         job, output = upload_common.create_job(
             trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params
         )
         trans.app.job_manager.enqueue(job, tool=tool)
+        if not output:
+            raise exceptions.RequestParameterInvalidException("Upload failed")
         return output
 
-    def _get_server_dir_uploaded_datasets(
-        self, trans, params, full_dir, import_dir_desc, library_bunch, response_code, message
-    ):
-        dir_response = self._get_server_dir_files(params, full_dir, import_dir_desc)
-        files = dir_response[0]
-        if not files:
-            return dir_response
+    def _get_server_dir_uploaded_datasets(self, trans, payload, full_dir, import_dir_desc, library_bunch):
+        files = self._get_server_dir_files(payload, full_dir, import_dir_desc)
         uploaded_datasets = []
         for file in files:
             name = os.path.basename(file)
             uploaded_datasets.append(
-                self._make_library_uploaded_dataset(trans, params, name, file, "server_dir", library_bunch)
+                self._make_library_uploaded_dataset(
+                    trans, payload.model_dump(), name, file, "server_dir", library_bunch
+                )
             )
-        return uploaded_datasets, 200, None
+        return uploaded_datasets
 
-    def _get_server_dir_files(self, params, full_dir, import_dir_desc):
+    def _get_server_dir_files(self, payload, full_dir, import_dir_desc):
         files = []
         try:
             for entry in os.listdir(full_dir):
                 # Only import regular files
                 path = os.path.join(full_dir, entry)
-                link_data_only = params.get("link_data_only", "copy_files")
-                if os.path.islink(full_dir) and link_data_only == "link_to_files":
+                if os.path.islink(full_dir) and payload.link_data_only == "link_to_files":
                     # If we're linking instead of copying and the
                     # sub-"directory" in the import dir is actually a symlink,
                     # dereference the symlink, but not any of its contents.
@@ -191,7 +184,7 @@ class LibraryActions:
                         path = os.path.join(link_path, entry)
                     else:
                         path = os.path.abspath(os.path.join(link_path, entry))
-                elif os.path.islink(path) and os.path.isfile(path) and link_data_only == "link_to_files":
+                elif os.path.islink(path) and os.path.isfile(path) and payload.link_data_only == "link_to_files":
                     # If we're linking instead of copying and the "file" in the
                     # sub-directory of the import dir is actually a symlink,
                     # dereference the symlink (one dereference only, Vasili).
@@ -203,14 +196,12 @@ class LibraryActions:
                 if os.path.isfile(path):
                     files.append(path)
         except Exception as e:
-            message = f"Unable to get file list for configured {import_dir_desc}, error: {util.unicodify(e)}"
-            response_code = 500
-            return None, response_code, message
+            raise exceptions.InternalServerError(
+                f"Unable to get file list for configured {import_dir_desc}, error: {util.unicodify(e)}"
+            )
         if not files:
-            message = f"The directory '{full_dir}' contains no valid files"
-            response_code = 400
-            return None, response_code, message
-        return files, None, None
+            raise exceptions.ObjectAttributeMissingException(f"The directory '{full_dir}' contains no valid files")
+        return files
 
     def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, response_code, message):
         preserve_dirs = util.string_as_bool(params.get("preserve_dirs", False))
@@ -307,15 +298,37 @@ class LibraryActions:
                 trans.sa_session.commit()
         return uploaded_dataset
 
-    def _create_folder(self, trans, parent_id: int, **kwd):
+    def _upload_library_dataset(self, trans, payload):
         is_admin = trans.user_is_admin
         current_user_roles = trans.get_current_user_roles()
-        parent_folder = trans.sa_session.get(LibraryFolder, parent_id)
+        folder = trans.sa_session.get(LibraryFolder, payload.folder_id)
+        if not folder:
+            raise exceptions.RequestParameterInvalidException("Invalid folder id specified.")
+        self._check_access(trans, is_admin, folder, current_user_roles)
+        self._check_add(trans, is_admin, folder, current_user_roles)
+        if payload.roles:
+            # Check to see if the user selected roles to associate with the DATASET_ACCESS permission
+            # on the dataset that would cause accessibility issues.
+            vars = dict(DATASET_ACCESS_in=payload.roles)
+            permissions, in_roles, error, message = trans.app.security_agent.derive_roles_from_access(
+                trans, folder.parent_library.id, "api", library=True, **vars
+            )
+            if error:
+                raise exceptions.RequestParameterInvalidException(message)
+        created_outputs_dict = self._upload_dataset(trans, folder.id, payload)
+        return created_outputs_dict
+
+    def _create_folder(self, trans, payload):
+        is_admin = trans.user_is_admin
+        current_user_roles = trans.get_current_user_roles()
+        parent_folder = trans.sa_session.get(LibraryFolder, payload.folder_id)
+        if not parent_folder:
+            raise exceptions.RequestParameterInvalidException("Invalid folder id specified.")
         # Check the library which actually contains the user-supplied parent folder, not the user-supplied
         # library, which could be anything.
         self._check_access(trans, is_admin, parent_folder, current_user_roles)
         self._check_add(trans, is_admin, parent_folder, current_user_roles)
-        new_folder = LibraryFolder(name=kwd.get("name", ""), description=kwd.get("description", ""))
+        new_folder = LibraryFolder(name=payload.name, description=payload.description)
         # We are associating the last used genome build with folders, so we will always
         # initialize a new folder with the first dbkey in genome builds list which is currently
         # ?    unspecified (?)
@@ -326,25 +339,39 @@ class LibraryActions:
             trans.sa_session.commit()
         # New folders default to having the same permissions as their parent folder
         trans.app.security_agent.copy_library_permissions(trans, parent_folder, new_folder)
-        return 200, dict(created=new_folder)
+        new_folder_dict = dict(created=new_folder)
+        return new_folder_dict
+
+    def _create_collection(self, trans, payload, parent):
+        # Not delegating to library_common, so need to check access to parent folder here.
+        self.check_user_can_add_to_library_item(trans, parent, check_accessible=True)
+        create_params = api_payload_to_create_params(payload.model_dump())
+        # collection_manager.create needs trans as one of the params
+        create_params["trans"] = trans
+        create_params["parent"] = parent
+        dataset_collection_instance = self.collection_manager.create(**create_params)
+        dataset_collection = dictify_dataset_collection_instance(
+            dataset_collection_instance, security=trans.security, url_builder=trans.url_builder, parent=parent
+        )
+        return [dataset_collection]
 
     def _check_access(self, trans, is_admin, item, current_user_roles):
         if isinstance(item, trans.model.HistoryDatasetAssociation):
             # Make sure the user has the DATASET_ACCESS permission on the history_dataset_association.
             if not item:
                 message = f"Invalid history dataset ({escape(str(item))}) specified."
-                raise ObjectNotFound(message)
+                raise exceptions.ObjectNotFound(message)
             elif (
                 not trans.app.security_agent.can_access_dataset(current_user_roles, item.dataset)
                 and item.user == trans.user
             ):
                 message = f"You do not have permission to access the history dataset with id ({str(item.id)})."
-                raise ItemAccessibilityException(message)
+                raise exceptions.ItemAccessibilityException(message)
         else:
             # Make sure the user has the LIBRARY_ACCESS permission on the library item.
             if not item:
                 message = f"Invalid library item ({escape(str(item))}) specified."
-                raise ObjectNotFound(message)
+                raise exceptions.ObjectNotFound(message)
             elif not (
                 is_admin or trans.app.security_agent.can_access_library_item(current_user_roles, item, trans.user)
             ):
@@ -355,10 +382,10 @@ class LibraryActions:
                 else:
                     item_type = "(unknown item type)"
                 message = f"You do not have permission to access the {escape(item_type)} with id ({str(item.id)})."
-                raise ItemAccessibilityException(message)
+                raise exceptions.ItemAccessibilityException(message)
 
     def _check_add(self, trans, is_admin, item, current_user_roles):
         # Deny access if the user is not an admin and does not have the LIBRARY_ADD permission.
         if not (is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, item)):
             message = f"You are not authorized to add an item to ({escape(item.name)})."
-            raise ItemAccessibilityException(message)
+            raise exceptions.ItemAccessibilityException(message)
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 58e122c6b9c8445180b8f1008236efbdea3fcf12..285e2eed8a1cff4be9324c3cc4b9643dbd823e7a 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -34,6 +34,7 @@ from galaxy.celery.base_task import (
     GalaxyTaskBeforeStartUserRateLimitPostgres,
     GalaxyTaskBeforeStartUserRateLimitStandard,
 )
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.config_watchers import ConfigWatchers
 from galaxy.datatypes.registry import Registry
 from galaxy.files import (
@@ -147,6 +148,7 @@ from galaxy.tools.cache import ToolCache
 from galaxy.tools.data import ToolDataTableManager
 from galaxy.tools.data_manager.manager import DataManagers
 from galaxy.tools.error_reports import ErrorReports
+from galaxy.tools.evaluation import ToolTemplatingException
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tools.special_tools import load_lib_tools
 from galaxy.tours import (
@@ -205,7 +207,7 @@ class HaltableContainer(Container):
 
 
 class SentryClientMixin:
-    config: config.GalaxyAppConfiguration
+    config: GalaxyAppConfiguration
     application_stack: ApplicationStack
 
     def configure_sentry_client(self):
@@ -227,12 +229,34 @@ class SentryClientMixin:
                 level=logging.INFO,  # Capture info and above as breadcrumbs
                 event_level=getattr(logging, event_level),  # Send errors as events
             )
+
+            def before_send(event, hint):
+                if "exc_info" in hint:
+                    exc_type, exc_value, tb = hint["exc_info"]
+                    if isinstance(exc_value, ToolTemplatingException):
+                        # We set a custom fingerprint that may look like:
+                        # ["Error occurred while {action_str.lower()} for tool '{tool.id}'",
+                        #  "1.0",
+                        #  "cannot find 'file_name' while searching for 'species_chromosomes.file_name'"]
+                        # If we don't do this issues are never properly grouped since by default the calling stack is inspected,
+                        # and that is always unique in cheetah as it is dynamically generated.
+                        event["fingerprint"] = [str(exc_value), str(exc_value.tool_version), str(exc_value.__cause__)]
+                        event.setdefault("tags", {}).update(
+                            {
+                                "tool_is_latest": exc_value.is_latest,
+                                "tool_id": str(exc_value.tool_id),
+                                "tool_version": exc_value.tool_version,
+                            }
+                        )
+                return event
+
             self.sentry_client = sentry_sdk.init(
                 self.config.sentry_dsn,
                 release=f"{self.config.version_major}.{self.config.version_minor}",
                 integrations=[sentry_logging],
                 traces_sample_rate=self.config.sentry_traces_sample_rate,
                 ca_certs=self.config.sentry_ca_certs,
+                before_send=before_send,
             )
 
 
@@ -240,7 +264,7 @@ class MinimalGalaxyApplication(BasicSharedApp, HaltableContainer, SentryClientMi
     """Encapsulates the state of a minimal Galaxy application"""
 
     model: GalaxyModelMapping
-    config: config.GalaxyAppConfiguration
+    config: GalaxyAppConfiguration
     tool_cache: ToolCache
     job_config: jobs.JobConfiguration
     toolbox_search: ToolBoxSearch
@@ -264,7 +288,7 @@ class MinimalGalaxyApplication(BasicSharedApp, HaltableContainer, SentryClientMi
         self.name = "galaxy"
         self.is_webapp = False
         # Read config file and check for errors
-        self.config = self._register_singleton(config.GalaxyAppConfiguration, config.GalaxyAppConfiguration(**kwargs))
+        self.config = self._register_singleton(GalaxyAppConfiguration, GalaxyAppConfiguration(**kwargs))
         self.config.check()
         config_file = kwargs.get("global_conf", {}).get("__file__", None)
         if config_file:
@@ -632,7 +656,7 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication, Inst
         # Load security policy.
         self.security_agent = self.model.security_agent
         self.host_security_agent = galaxy.model.security.HostAgent(
-            model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions
+            self.security_agent.sa_session, permitted_actions=self.security_agent.permitted_actions
         )
 
         # We need the datatype registry for running certain tasks that modify HDAs, and to build the registry we need
@@ -642,6 +666,7 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication, Inst
             InstalledRepositoryManager, InstalledRepositoryManager(self)
         )
         self.dynamic_tool_manager = self._register_singleton(DynamicToolManager)
+        self.trs_proxy = self._register_singleton(TrsProxy, TrsProxy(self.config))
         self._configure_datatypes_registry(
             use_converters=use_converters,
             use_display_applications=use_display_applications,
@@ -796,16 +821,6 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
             self.authnz_manager = managers.AuthnzManager(
                 self, self.config.oidc_config_file, self.config.oidc_backends_config_file
             )
-            if self.is_webapp:
-                self.refresh_oidc_tokens_task = IntervalTask(
-                    func=lambda: self.authnz_manager.refresh_expiring_oidc_tokens(self.model.session),
-                    name="RefreshOIDCTokensTask",
-                    interval=self.config.oidc_refresh_tokens_interval,
-                    immediate_start=True,
-                    time_execution=True,
-                )
-                self.application_stack.register_postfork_function(self.refresh_oidc_tokens_task.start)
-                self.haltables.append(("RefreshOIDCTokensTask", self.refresh_oidc_tokens_task.shutdown))
 
             # If there is only a single external authentication provider in use
             # TODO: Future work will expand on this and provide an interface for
@@ -824,21 +839,20 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication):
             )
             self.application_stack.register_postfork_function(self.prune_history_audit_task.start)
             self.haltables.append(("HistoryAuditTablePruneTask", self.prune_history_audit_task.shutdown))
-        # Start the job manager
-        self.application_stack.register_postfork_function(self.job_manager.start)
         self.proxy_manager = ProxyManager(self.config)
 
         # Must be initialized after job_config.
         self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager(self)
 
-        self.trs_proxy = self._register_singleton(TrsProxy, TrsProxy(self.config))
+        # We need InteractiveToolManager before the job handler starts
+        self.interactivetool_manager = InteractiveToolManager(self)
+        # Start the job manager
+        self.application_stack.register_postfork_function(self.job_manager.start)
         # Must be initialized after any component that might make use of stack messaging is configured. Alternatively if
         # it becomes more commonly needed we could create a prefork function registration method like we do with
         # postfork functions.
         self.application_stack.init_late_prefork()
 
-        self.interactivetool_manager = InteractiveToolManager(self)
-
         # Configure handling of signals
         handlers = {}
         if self.heartbeat:
diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
index 8fe611ea78b5c7b5ede55ee54abaf26e4afbc8d4..69048e042aa6751a71185f66d65684f9574e06a4 100644
--- a/lib/galaxy/app_unittest_utils/galaxy_mock.py
+++ b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -158,6 +158,7 @@ class MockApp(di.Container, GalaxyDataTestApp):
         )
         self.is_job_handler = False
         self.biotools_metadata_source = None
+        self.trs_proxy = Bunch()
         set_thread_app(self)
 
         def url_for(*args, **kwds):
@@ -331,7 +332,7 @@ class MockTrans:
         self.security = self.app.security
         self.history = history
 
-        self.request: Any = Bunch(headers={}, is_body_readable=False, host="request.host")
+        self.request: Any = Bunch(headers={}, is_body_readable=False, host="request.host", url_path="mock/url/path")
         self.response: Any = Bunch(headers={}, set_content_type=lambda i: None)
 
     @property
@@ -432,8 +433,17 @@ class MockDir:
 
 
 class MockTemplateHelpers:
-    def js(*js_files):
+    def css(*css_files):
         pass
 
-    def css(*css_files):
+    def dumps(*kwargs):
+        return {}
+
+    def js(*js_files):
         pass
+
+    def is_url(*kwargs):
+        return True
+
+    def url_for(*kwargs):
+        return "/"
diff --git a/lib/galaxy/app_unittest_utils/tools_support.py b/lib/galaxy/app_unittest_utils/tools_support.py
index e29b96dc0299875b9e90f9e5004adacb78ef6c7f..f2f880da07045813352e22f6af14118418740417 100644
--- a/lib/galaxy/app_unittest_utils/tools_support.py
+++ b/lib/galaxy/app_unittest_utils/tools_support.py
@@ -20,6 +20,7 @@ from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.tool_util.parser import get_tool_source
 from galaxy.tools import create_tool_from_source
 from galaxy.util.bunch import Bunch
+from galaxy.util.path import StrPath
 
 datatypes_registry = galaxy.datatypes.registry.Registry()
 datatypes_registry.load_datatypes()
@@ -83,10 +84,10 @@ class UsesTools(UsesApp):
         tool_id="test_tool",
         extra_file_contents=None,
         extra_file_path=None,
-        tool_path=None,
+        tool_path: Optional[StrPath] = None,
     ):
         if tool_path is None:
-            self.tool_file = os.path.join(self.test_directory, filename)
+            self.tool_file: StrPath = os.path.join(self.test_directory, filename)
             contents_template = string.Template(tool_contents)
             tool_contents = contents_template.safe_substitute(dict(version=version, profile=profile, tool_id=tool_id))
             self.__write_tool(tool_contents)
@@ -96,7 +97,7 @@ class UsesTools(UsesApp):
             self.tool_file = tool_path
         return self.__setup_tool()
 
-    def _init_tool_for_path(self, tool_file):
+    def _init_tool_for_path(self, tool_file: StrPath):
         self.tool_file = tool_file
         return self.__setup_tool()
 
@@ -106,9 +107,13 @@ class UsesTools(UsesApp):
         self.app.config.tool_secret = "testsecret"
         self.app.config.track_jobs_in_database = False
 
-    def __setup_tool(self):
+    @property
+    def tool_source(self):
         tool_source = get_tool_source(self.tool_file)
-        self.tool = create_tool_from_source(self.app, tool_source, config_file=self.tool_file)
+        return tool_source
+
+    def __setup_tool(self):
+        self.tool = create_tool_from_source(self.app, self.tool_source, config_file=self.tool_file)
         if getattr(self, "tool_action", None):
             self.tool.tool_action = self.tool_action
         return self.tool
diff --git a/lib/galaxy/authnz/__init__.py b/lib/galaxy/authnz/__init__.py
index 5f8ab21b88b9b2f69f8806dcac1beacb7547da1f..b17ec78b88c94270910b6e9f19c1ce5b8dedb878 100644
--- a/lib/galaxy/authnz/__init__.py
+++ b/lib/galaxy/authnz/__init__.py
@@ -43,7 +43,7 @@ class IdentityProvider:
     def refresh(self, session, token, skip_old_tokens_threshold_days):
         raise NotImplementedError()
 
-    def authenticate(self, provider, trans):
+    def authenticate(self, trans, idphint=None):
         """Runs for authentication process. Checks the database if a
         valid identity exists in the database; if yes, then the  user
         is authenticated, if not, it generates a provider-specific
@@ -72,7 +72,7 @@ class IdentityProvider:
         """
         raise NotImplementedError()
 
-    def disconnect(self, provider, trans, disconnect_redirect_url=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         raise NotImplementedError()
 
     def logout(self, trans, post_user_logout_href=None):
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index cdd25943a750bf616d6e6678df77ebbf76b9960d..c69b415673baa71cc2db185adf926fe5cc12bf2d 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -63,6 +63,7 @@ class CustosAuthnzConfiguration:
     pkce_support: bool
     accepted_audiences: List[str]
     extra_params: Optional[dict]
+    extra_scopes: List[str]
     authorization_endpoint: Optional[str]
     token_endpoint: Optional[str]
     end_session_endpoint: Optional[str]
@@ -100,6 +101,7 @@ class OIDCAuthnzBase(IdentityProvider):
                 )
             ),
             extra_params={},
+            extra_scopes=oidc_backend_config.get("extra_scopes", []),
             authorization_endpoint=None,
             token_endpoint=None,
             end_session_endpoint=None,
@@ -119,7 +121,7 @@ class OIDCAuthnzBase(IdentityProvider):
         if custos_authnz_token is None:
             raise exceptions.AuthenticationFailed("cannot find authorized user while refreshing token")
         id_token_decoded = self._decode_token_no_signature(custos_authnz_token.id_token)
-        # do not refresh tokens if they didn't reach their half lifetime
+        # do not refresh tokens if the id_token didn't reach its half-life
         if int(id_token_decoded["iat"]) + int(id_token_decoded["exp"]) > 2 * int(time.time()):
             return False
 
@@ -172,6 +174,7 @@ class OIDCAuthnzBase(IdentityProvider):
     def authenticate(self, trans, idphint=None):
         base_authorize_url = self.config.authorization_endpoint
         scopes = ["openid", "email", "profile"]
+        scopes.extend(self.config.extra_scopes)
         scopes.extend(self._get_provider_specific_scopes())
         oauth2_session = self._create_oauth2_session(scope=scopes)
         nonce = generate_nonce()
@@ -388,7 +391,7 @@ class OIDCAuthnzBase(IdentityProvider):
             trans.sa_session.commit()
         return login_redirect_url, user
 
-    def disconnect(self, provider, trans, email=None, disconnect_redirect_url=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         try:
             user = trans.user
             index = 0
@@ -529,7 +532,7 @@ class OIDCAuthnzBase(IdentityProvider):
         username = userinfo.get("preferred_username", userinfo.get("username", userinfo["email"]))
         if "@" in username:
             username = username.split("@")[0]  # username created from username portion of email
-        username = util.ready_name_for_url(username)
+        username = util.ready_name_for_url(username).lower()
         if trans.sa_session.query(trans.app.model.User).filter_by(username=username).first():
             # if username already exists in database, append integer and iterate until unique username found
             count = 0
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 81ce4ce662eb7edc5481ca132ac504707da2418a..98d3bc3ad45ad610d1fdf1d301202ae8347df79b 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -1,18 +1,6 @@
 import builtins
-import copy
-import json
 import logging
-import os
-import random
-import string
-from datetime import (
-    datetime,
-    timedelta,
-)
-
-from cloudauthz import CloudAuthz
-from cloudauthz.exceptions import CloudAuthzBaseException
-from sqlalchemy import select
+import fcntl
 
 from galaxy import (
     exceptions,
@@ -23,7 +11,6 @@ from galaxy.util import (
     etree,
     listify,
     parse_xml,
-    requests,
     string_as_bool,
     unicodify,
 )
@@ -37,10 +24,7 @@ from .custos_authnz import (
 )
 from .psa_authnz import (
     BACKENDS_NAME,
-    on_the_fly_config,
     PSAAuthnz,
-    Storage,
-    Strategy,
 )
 
 OIDC_BACKEND_SCHEMA = resource_path(__package__, "xsd/oidc_backends_config.xsd")
@@ -113,8 +97,8 @@ class AuthnzManager:
     def _get_idp_icon(self, idp):
         return self.oidc_backends_config[idp].get("icon") or DEFAULT_OIDC_IDP_ICONS.get(idp)
 
-    def _get_idp_alias(self, idp):
-        return self.oidc_backends_config[idp].get("alias") or None
+    def _get_idp_button_text(self, idp):
+        return self.oidc_backends_config[idp].get("custom_button_text")
 
     def _parse_oidc_backends_config(self, config_file):
         self.oidc_backends_config = {}
@@ -142,11 +126,17 @@ class AuthnzManager:
                 if idp in BACKENDS_NAME:
                     self.oidc_backends_config[idp] = self._parse_idp_config(child)
                     self.oidc_backends_implementation[idp] = "psa"
-                    self.app.config.oidc[idp] = {"icon": self._get_idp_icon(idp), "alias": self._get_idp_alias(idp)}
+                    self.app.config.oidc[idp] = {
+                        "icon": self._get_idp_icon(idp),
+                        "custom_button_text": self._get_idp_button_text(idp),
+                    }
                 elif idp in KEYCLOAK_BACKENDS:
                     self.oidc_backends_config[idp] = self._parse_custos_config(child)
                     self.oidc_backends_implementation[idp] = "custos"
-                    self.app.config.oidc[idp] = {"icon": self._get_idp_icon(idp), "alias": self._get_idp_alias(idp)}
+                    self.app.config.oidc[idp] = {
+                        "icon": self._get_idp_icon(idp),
+                        "label": self.oidc_backends_config[idp].get("label", idp),
+                    }
                 else:
                     raise etree.ParseError("Unknown provider specified")
             if len(self.oidc_backends_config) == 0:
@@ -179,6 +169,10 @@ class AuthnzManager:
             rtv["extra_scopes"] = listify(config_xml.find("extra_scopes").text)
         if config_xml.find("tenant_id") is not None:
             rtv["tenant_id"] = config_xml.find("tenant_id").text
+        if config_xml.find("oidc_endpoint") is not None:
+            rtv["oidc_endpoint"] = config_xml.find("oidc_endpoint").text
+        if config_xml.find("custom_button_text") is not None:
+            rtv["custom_button_text"] = config_xml.find("custom_button_text").text
         if config_xml.find("pkce_support") is not None:
             rtv["pkce_support"] = asbool(config_xml.find("pkce_support").text)
         if config_xml.find("accepted_audiences") is not None:
@@ -186,13 +180,10 @@ class AuthnzManager:
         # this is a EGI Check-in specific config
         if config_xml.find("checkin_env") is not None:
             rtv["checkin_env"] = config_xml.find("checkin_env").text
-        if config_xml.find("alias") is not None:
-            rtv["alias"] = config_xml.find("alias").text
         if config_xml.find("well_known_oidc_config_uri") is not None:
             rtv["well_known_oidc_config_uri"] = config_xml.find("well_known_oidc_config_uri").text
         if config_xml.find("required_scope") is not None:
             rtv["required_scope"] = config_xml.find("required_scope").text
-
         return rtv
 
     def _parse_custos_config(self, config_xml):
@@ -217,14 +208,14 @@ class AuthnzManager:
             rtv["ca_bundle"] = config_xml.find("ca_bundle").text
         if config_xml.find("icon") is not None:
             rtv["icon"] = config_xml.find("icon").text
+        if config_xml.find("extra_scopes") is not None:
+            rtv["extra_scopes"] = listify(config_xml.find("extra_scopes").text)
         if config_xml.find("pkce_support") is not None:
             rtv["pkce_support"] = asbool(config_xml.find("pkce_support").text)
-        if config_xml.find("alias") is not None:
-            rtv["alias"] = config_xml.find("alias").text
-        if config_xml.find("user_extra_authorization_script") is not None:
-            rtv["user_extra_authorization_script"] = config_xml.find("user_extra_authorization_script").text
         if config_xml.find("accepted_audiences") is not None:
             rtv["accepted_audiences"] = config_xml.find("accepted_audiences").text
+        if config_xml.find("user_extra_authorization_script") is not None:
+            rtv["user_extra_authorization_script"] = config_xml.find("user_extra_authorization_script").text
         if config_xml.find("required_scope") is not None:
             rtv["required_scope"] = config_xml.find("required_scope").text
         return rtv
@@ -283,35 +274,6 @@ class AuthnzManager:
         else:
             return None
 
-    def _extend_cloudauthz_config(self, cloudauthz, request, sa_session, user_id):
-        config = copy.deepcopy(cloudauthz.config)
-        if cloudauthz.provider == "aws":
-            success, message, backend = self._get_authnz_backend(cloudauthz.authn.provider)
-            strategy = Strategy(request, None, Storage, backend.config)
-            on_the_fly_config(sa_session)
-            try:
-                config["id_token"] = cloudauthz.authn.get_id_token(strategy)
-            except requests.exceptions.HTTPError as e:
-                msg = (
-                    f"Sign-out from Galaxy and remove its access from `{self._unify_provider_name(cloudauthz.authn.provider)}`, "
-                    "then log back in using `{cloudauthz.authn.uid}` account."
-                )
-                log.debug(
-                    "Failed to get/refresh ID token for user with ID `%s` for assuming authz_id `%s`. "
-                    "User may not have a refresh token. If the problem persists, set the `prompt` key to "
-                    "`consent` in `oidc_backends_config.xml`, then restart Galaxy and ask user to: %s"
-                    "Error Message: `%s`",
-                    user_id,
-                    cloudauthz.id,
-                    msg,
-                    e.response.text,
-                )
-                raise exceptions.AuthenticationFailed(
-                    err_msg=f"An error occurred getting your ID token. {msg}. If the problem persists, please "
-                    "contact Galaxy admin."
-                )
-        return config
-
     @staticmethod
     def can_user_assume_authn(trans, authn_id):
         qres = trans.sa_session.query(model.UserAuthnzToken).get(authn_id)
@@ -327,64 +289,36 @@ class AuthnzManager:
             log.warning(msg)
             raise exceptions.ItemAccessibilityException(msg)
 
-    @staticmethod
-    def try_get_authz_config(sa_session, user_id, authz_id):
-        """
-        It returns a cloudauthz config (see model.CloudAuthz) with the
-        given ID; and raise an exception if either a config with given
-        ID does not exist, or the configuration is defined for a another
-        user than trans.user.
-
-        :type  trans:       galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans:       Galaxy web transaction
-
-        :type  authz_id:    int
-        :param authz_id:    The ID of a CloudAuthz configuration to be used for
-                            getting temporary credentials.
-
-        :rtype :            model.CloudAuthz
-        :return:            a cloudauthz configuration.
-        """
-        qres = sa_session.query(model.CloudAuthz).get(authz_id)
-        if qres is None:
-            raise exceptions.ObjectNotFound("An authorization configuration with given ID not found.")
-        if user_id != qres.user_id:
-            msg = (
-                f"The request authorization configuration (with ID:`{qres.id}`) is not accessible for user with "
-                f"ID:`{user_id}`."
-            )
-            log.warning(msg)
-            raise exceptions.ItemAccessibilityException(msg)
-        return qres
-
-    def refresh_expiring_oidc_tokens_for_provider(self, sa_session, auth):
-        try:
-            success, message, backend = self._get_authnz_backend(auth.provider)
-            if success is False:
-                msg = f"An error occurred when getting backend for `{auth.provider}` identity provider: {message}"
-                log.error(msg)
+    def refresh_expiring_oidc_tokens_for_provider(self, trans, auth):
+        with open("/dev/null", "w") as lock:
+            try:
+                fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB)
+                success, message, backend = self._get_authnz_backend(auth.provider)
+                if success is False:
+                    msg = f"An error occurred when refreshing user token on `{auth.provider}` identity provider: {message}"
+                    log.error(msg)
+                    return False
+                refreshed = backend.refresh(trans, auth, 30)
+                if refreshed:
+                    log.debug(f"Refreshed user token via `{auth.provider}` identity provider")
+                return True
+            except BlockingIOError:
+                log.debug("Another process is refreshing, skipping")
+                return True
+            except Exception:
+                log.exception("An error occurred when refreshing user token")
                 return False
-            backend.refresh(sa_session, auth, skip_old_tokens_threshold_days=30)
-            return True
-        except Exception:
-            log.exception("An error occurred when refreshing user token")
-            return False
-
-    def refresh_expiring_oidc_tokens(self, sa_session):
-        # Galaxy starts multiple RefreshOIDCTokensTask (one for each handler and workes). Until we found a better way
-        # to deal with it, we check the server name here and only run refresh for one worker.
-        if (
-            self.app.config.server_name != self.app.config.base_server_name
-            and self.app.config.server_name != f"{self.app.config.base_server_name}.1"
-        ):
-            return
 
-        all_users = sa_session.scalars(select(model.User)).all()
-        for user in all_users:
-            for auth in user.custos_auth or []:
-                self.refresh_expiring_oidc_tokens_for_provider(sa_session, auth)
-            for auth in user.social_auth or []:
-                self.refresh_expiring_oidc_tokens_for_provider(sa_session, auth)
+    def refresh_expiring_oidc_tokens(self, trans, user=None):
+        user = trans.user or user
+        if not isinstance(user, model.User):
+            return True
+        success = False
+        for auth in user.custos_auth or []:
+            success |= self.refresh_expiring_oidc_tokens_for_provider(trans, auth)
+        for auth in user.social_auth or []:
+            success |= self.refresh_expiring_oidc_tokens_for_provider(trans, auth)
+        return success
 
     def authenticate(self, provider, trans, idphint=None):
         """
@@ -419,13 +353,6 @@ class AuthnzManager:
             log.exception(msg)
             return False, msg, None
 
-    def _validate_permissions(self, user, jwt, provider):
-        # Get required scope if provided in config, else use the configured scope prefix
-        required_scopes = [
-            f"{self.oidc_backends_config[provider].get('required_scope', f'{self.app.config.oidc_scope_prefix}:*')}"
-        ]
-        self._assert_jwt_contains_scopes(user, jwt, required_scopes)
-
     def callback(self, provider, state_token, authz_code, trans, login_redirect_url, idphint=None):
         try:
             success, message, backend = self._get_authnz_backend(provider, idphint=idphint)
@@ -459,12 +386,18 @@ class AuthnzManager:
                 err_msg=f"User: {user.username} does not have the required scopes: [{required_scopes}]"
             )
         scopes = f"{jwt.get('scope')} {jwt.get('scp')}" or ""
-
         if not set(required_scopes).issubset(scopes.split(" ")):
             raise exceptions.AuthenticationFailed(
                 err_msg=f"User: {user.username} has JWT with scopes: [{scopes}] but not required scopes: [{required_scopes}]"
             )
 
+    def _validate_permissions(self, user, jwt, provider):
+        # Get required scope if provided in config, else use the configured scope prefix
+        required_scopes = [
+            f"{self.oidc_backends_config[provider].get('required_scope', f'{self.app.config.oidc_scope_prefix}:*')}"
+        ]
+        self._assert_jwt_contains_scopes(user, jwt, required_scopes)
+
     def _match_access_token_to_user_in_provider(self, sa_session, provider, access_token):
         try:
             success, message, backend = self._get_authnz_backend(provider)
@@ -532,104 +465,9 @@ class AuthnzManager:
             if success is False:
                 return False, message, None
             elif provider in KEYCLOAK_BACKENDS:
-                return backend.disconnect(provider, trans, email, disconnect_redirect_url)
+                return backend.disconnect(provider, trans, disconnect_redirect_url, email=email)
             return backend.disconnect(provider, trans, disconnect_redirect_url)
         except Exception:
             msg = f"An error occurred when disconnecting authentication with `{provider}` identity provider for user `{trans.user.username}`"
             log.exception(msg)
             return False, msg, None
-
-    def get_cloud_access_credentials(self, cloudauthz, sa_session, user_id, request=None):
-        """
-        This method leverages CloudAuthz (https://github.com/galaxyproject/cloudauthz)
-        to request a cloud-based resource provider (e.g., Amazon AWS, Microsoft Azure)
-        for temporary access credentials to a given resource.
-
-        It first checks if a cloudauthz config with the given ID (`authz_id`) is
-        available and can be assumed by the user, and raises an exception if either
-        is false. Otherwise, it then extends the cloudauthz configuration as required
-        by the CloudAuthz library for the provider specified in the configuration.
-        For instance, it adds on-the-fly values such as a valid OpenID Connect
-        identity token, as required by CloudAuthz for AWS. Then requests temporary
-        credentials from the CloudAuthz library using the updated configuration.
-
-        :type  cloudauthz:  CloudAuthz
-        :param cloudauthz:  an instance of CloudAuthz to be used for getting temporary
-                            credentials.
-
-        :type   sa_session: sqlalchemy.orm.scoping.scoped_session
-        :param  sa_session: SQLAlchemy database handle.
-
-        :type   user_id:    int
-        :param  user_id:    Decoded Galaxy user ID.
-
-        :type   request:    galaxy.web.framework.base.Request
-        :param  request:    Encapsulated HTTP(S) request.
-
-        :rtype:             dict
-        :return:            a dictionary containing credentials to access a cloud-based
-                            resource provider. See CloudAuthz (https://github.com/galaxyproject/cloudauthz)
-                            for details on the content of this dictionary.
-        """
-        config = self._extend_cloudauthz_config(cloudauthz, request, sa_session, user_id)
-        try:
-            ca = CloudAuthz()
-            log.info(
-                "Requesting credentials using CloudAuthz with config id `%s` on be half of user `%s`.",
-                cloudauthz.id,
-                user_id,
-            )
-            credentials = ca.authorize(cloudauthz.provider, config)
-            return credentials
-        except CloudAuthzBaseException as e:
-            log.info(e)
-            raise exceptions.AuthenticationFailed(e)
-        except NotImplementedError as e:
-            log.info(e)
-            raise exceptions.RequestParameterInvalidException(e)
-
-    def get_cloud_access_credentials_in_file(self, new_file_path, cloudauthz, sa_session, user_id, request=None):
-        """
-        This method leverages CloudAuthz (https://github.com/galaxyproject/cloudauthz)
-        to request a cloud-based resource provider (e.g., Amazon AWS, Microsoft Azure)
-        for temporary access credentials to a given resource.
-
-        This method uses the `get_cloud_access_credentials` method to obtain temporary
-        credentials, and persists them to a (temporary) file, and returns the file path.
-
-        :type  new_file_path:   str
-        :param new_file_path:   Where dataset files are saved on temporary storage.
-                                See `app.config.new_file_path`.
-
-        :type  cloudauthz:      CloudAuthz
-        :param cloudauthz:      an instance of CloudAuthz to be used for getting temporary
-                                credentials.
-
-        :type  sa_session:      sqlalchemy.orm.scoping.scoped_session
-        :param sa_session:      SQLAlchemy database handle.
-
-        :type  user_id:         int
-        :param user_id:         Decoded Galaxy user ID.
-
-        :type  request:         galaxy.web.framework.base.Request
-        :param request:         [Optional] Encapsulated HTTP(S) request.
-
-        :rtype:                 str
-        :return:                The filename to which credentials are written.
-        """
-        filename = os.path.abspath(
-            os.path.join(
-                new_file_path,
-                "cd_"
-                + "".join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(11)),
-            )
-        )
-        credentials = self.get_cloud_access_credentials(cloudauthz, sa_session, user_id, request)
-        log.info(
-            "Writing credentials generated using CloudAuthz with config id `%s` to the following file: `%s`",
-            cloudauthz.id,
-            filename,
-        )
-        with open(filename, "w") as f:
-            f.write(json.dumps(credentials))
-        return filename
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index bfdcd31d6f0635a712e28f25348d2a1704f1d5b5..65ef74f312708956188462dd4af0d228e1a26897 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -45,6 +45,7 @@ BACKENDS = {
     "okta": "social_core.backends.okta_openidconnect.OktaOpenIdConnect",
     "azure": "social_core.backends.azuread_tenant.AzureADV2TenantOAuth2",
     "egi_checkin": "social_core.backends.egi_checkin.EGICheckinOpenIdConnect",
+    "oidc": "social_core.backends.open_id_connect.OpenIdConnectAuth",
 }
 
 BACKENDS_NAME = {
@@ -54,6 +55,7 @@ BACKENDS_NAME = {
     "okta": "okta-openidconnect",
     "azure": "azuread-v2-tenant-oauth2",
     "egi_checkin": "egi-checkin",
+    "oidc": "oidc",
 }
 
 AZURE_USERINFO_ENDPOINT = "https://graph.microsoft.com/oidc/userinfo"
@@ -137,6 +139,8 @@ class PSAAuthnz(IdentityProvider):
         self.config["TENANT_ID"] = oidc_backend_config.get("tenant_id")
         self.config["redirect_uri"] = oidc_backend_config.get("redirect_uri")
         self.config["EXTRA_SCOPES"] = oidc_backend_config.get("extra_scopes")
+        if oidc_backend_config.get("oidc_endpoint"):
+            self.config["OIDC_ENDPOINT"] = oidc_backend_config["oidc_endpoint"]
         if oidc_backend_config.get("prompt") is not None:
             self.config[setting_name("AUTH_EXTRA_ARGUMENTS")]["prompt"] = oidc_backend_config.get("prompt")
         if oidc_backend_config.get("api_url") is not None:
@@ -176,7 +180,7 @@ class PSAAuthnz(IdentityProvider):
         extra_data["expires"] = int(expires - time.time())
         user_authnz_token.set_extra_data(extra_data)
 
-    def refresh(self, sa_session, user_authnz_token, skip_old_tokens_threshold_days):
+    def refresh(self, trans, user_authnz_token, skip_old_tokens_threshold_days):
         if not user_authnz_token or not user_authnz_token.extra_data:
             return False
         # refresh tokens if they reached their half lifetime
@@ -194,14 +198,14 @@ class PSAAuthnz(IdentityProvider):
             return False
 
         if int(user_authnz_token.extra_data["auth_time"]) + int(expires) / 2 <= int(time.time()):
-            on_the_fly_config(sa_session)
+            on_the_fly_config(trans.sa_session)
             log.debug(
                 f"Refreshing user token for {user_authnz_token.uid} via `{user_authnz_token.provider}` identity provider"
             )
             if self.config["provider"] == "azure":
                 self.refresh_azure(user_authnz_token)
             else:
-                strategy = Strategy(None, sa_session, Storage, self.config)
+                strategy = Strategy(None, trans.sa_session, Storage, self.config)
                 user_authnz_token.refresh_token(strategy)
             log.debug(
                 f"Refreshed user token for {user_authnz_token.uid} via `{user_authnz_token.provider}` identity provider"
@@ -211,7 +215,7 @@ class PSAAuthnz(IdentityProvider):
 
         return False
 
-    def authenticate(self, trans):
+    def authenticate(self, trans, idphint=None):
         on_the_fly_config(trans.sa_session)
         strategy = Strategy(trans.request, trans.session, Storage, self.config)
         backend = self._load_backend(strategy, self.config["redirect_uri"])
@@ -242,7 +246,7 @@ class PSAAuthnz(IdentityProvider):
 
         return redirect_url, self.config.get("user", None)
 
-    def disconnect(self, provider, trans, disconnect_redirect_url=None, association_id=None):
+    def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
         on_the_fly_config(trans.sa_session)
         self.config[setting_name("DISCONNECT_REDIRECT_URL")] = (
             disconnect_redirect_url if disconnect_redirect_url is not None else ()
@@ -399,19 +403,6 @@ class Strategy(BaseStrategy):
     def render_html(self, tpl=None, html=None, context=None):
         raise NotImplementedError("Not implemented.")
 
-    def start(self):
-        self.clean_partial_pipeline()
-        if self.backend.uses_redirect():
-            return self.redirect(self.backend.auth_url())
-        else:
-            return self.html(self.backend.auth_html())
-
-    def complete(self, *args, **kwargs):
-        return self.backend.auth_complete(*args, **kwargs)
-
-    def continue_pipeline(self, *args, **kwargs):
-        return self.backend.continue_pipeline(*args, **kwargs)
-
 
 class Storage:
     user = UserAuthnzToken
diff --git a/lib/galaxy/authnz/xsd/oidc_backends_config.xsd b/lib/galaxy/authnz/xsd/oidc_backends_config.xsd
index 3f24b6cc9407cf60fa87c5d60986dcf8e9651dea..b2a40b868ac5fa9c8564e69123c4ff53aab2ca90 100644
--- a/lib/galaxy/authnz/xsd/oidc_backends_config.xsd
+++ b/lib/galaxy/authnz/xsd/oidc_backends_config.xsd
@@ -121,6 +121,20 @@
                                     </xs:documentation>
                                 </xs:annotation>
                             </xs:element>
+                            <xs:element name="oidc_endpoint" minOccurs="0" type="xs:anyURI">
+                                <xs:annotation>
+                                    <xs:documentation>
+                                        OIDC endpoint for the IdP
+                                    </xs:documentation>
+                                </xs:annotation>
+                            </xs:element>
+                            <xs:element name="custom_button_text" minOccurs="0" type="xs:string">
+                                <xs:annotation>
+                                    <xs:documentation>
+                                        Can be used to set a custom text value for the "Sign in with " button for your chosen IdP.
+                                    </xs:documentation>
+                                </xs:annotation>
+                            </xs:element>
                             <xs:element name="pkce_support" minOccurs="0" type="xs:boolean">
                                 <xs:annotation>
                                     <xs:documentation>
diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py
index 11432481529cb53d1bd4cddc6c488ebe2e4609dc..120df3c28906e200f871bdbe8a56cd23373312e1 100644
--- a/lib/galaxy/celery/__init__.py
+++ b/lib/galaxy/celery/__init__.py
@@ -220,7 +220,7 @@ def config_celery_app(config, celery_app):
     if config.celery_conf:
         celery_app.conf.update(config.celery_conf)
     # Handle special cases
-    if not celery_app.conf.broker_url:
+    if not config.celery_conf.get("broker_url"):
         celery_app.conf.broker_url = config.amqp_internal_connection
 
 
diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 94bb8d75956f1d451dc4b90c8dadc4df59b6dedf..c4e986cc94b6d0bfb090aedc99c82bb733e6f7f9 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -80,7 +80,7 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     We take advantage of efficiencies in its dialect.
     """
 
-    def calculate_task_start_time(  # type: ignore
+    def calculate_task_start_time(
         self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         with transaction(sa_session):
diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py
index da57277a32e9cd33260234952e1f32ab22d8d6d4..552215798cd4e91842e4a78e051560ad57198183 100644
--- a/lib/galaxy/celery/tasks.py
+++ b/lib/galaxy/celery/tasks.py
@@ -1,4 +1,6 @@
+import datetime
 import json
+import shutil
 from concurrent.futures import TimeoutError
 from functools import lru_cache
 from pathlib import Path
@@ -21,6 +23,7 @@ from galaxy.celery import (
 from galaxy.config import GalaxyAppConfiguration
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry as DatatypesRegistry
+from galaxy.exceptions import ObjectNotFound
 from galaxy.jobs import MinimalJobWrapper
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.datasets import (
@@ -75,10 +78,8 @@ def setup_data_table_manager(app):
 
 
 @lru_cache
-def cached_create_tool_from_representation(app, raw_tool_source):
-    return create_tool_from_representation(
-        app=app, raw_tool_source=raw_tool_source, tool_dir="", tool_source_class="XmlToolSource"
-    )
+def cached_create_tool_from_representation(app: MinimalManagerApp, raw_tool_source: str):
+    return create_tool_from_representation(app=app, raw_tool_source=raw_tool_source, tool_source_class="XmlToolSource")
 
 
 @galaxy_task(action="recalculate a user's disk usage")
@@ -308,7 +309,7 @@ def _fetch_data(setup_return):
     working_directory = Path(tool_job_working_directory) / "working"
     datatypes_registry = DatatypesRegistry()
     datatypes_registry.load_datatypes(
-        galaxy_directory,
+        galaxy_directory(),
         config=Path(tool_job_working_directory) / "metadata" / "registry.xml",
         use_build_sites=False,
         use_converters=False,
@@ -512,3 +513,35 @@ def dispatch_pending_notifications(notification_manager: NotificationManager):
     count = notification_manager.dispatch_pending_notifications_via_channels()
     if count:
         log.info(f"Successfully dispatched {count} notifications.")
+
+
+@galaxy_task(action="clean up job working directories")
+def cleanup_jwds(sa_session: galaxy_scoped_session, object_store: BaseObjectStore, days: int = 5):
+    """Cleanup job working directories for failed jobs that are older than X days"""
+
+    def get_failed_jobs():
+        return sa_session.query(model.Job.id).filter(
+            model.Job.state == "error",
+            model.Job.update_time < datetime.datetime.now() - datetime.timedelta(days=days),
+            model.Job.object_store_id.isnot(None),
+        )
+
+    def delete_jwd(job):
+        try:
+            # Get job working directory from object store
+            path = object_store.get_filename(job, base_dir="job_work", dir_only=True, obj_dir=True)
+            shutil.rmtree(path)
+        except ObjectNotFound:
+            # job working directory already deleted
+            pass
+        except OSError as e:
+            log.error(f"Error deleting job working directory: {path} : {e.strerror}")
+
+    failed_jobs = get_failed_jobs()
+
+    if not failed_jobs:
+        log.info("No failed jobs found within the last %s days", days)
+
+    for job in failed_jobs:
+        delete_jwd(job)
+        log.info("Deleted job working directory for job %s", job.id)
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 554018472dc9066c082862e47ef611f279606c77..bb998f885efb2be1b3d28d15f7d91d59d4ce9b54 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -115,6 +115,14 @@ LOGGING_CONFIG_DEFAULT: Dict[str, Any] = {
             "level": "INFO",
             "qualname": "watchdog.observers.inotify_buffer",
         },
+        "py.warnings": {
+            "level": "ERROR",
+            "qualname": "py.warnings",
+        },
+        "celery.utils.functional": {
+            "level": "INFO",
+            "qualname": "celery.utils.functional",
+        },
     },
     "filters": {
         "stack": {
@@ -301,7 +309,7 @@ class BaseAppConfiguration(HasDynamicProperties):
 
     def _set_config_base(self, config_kwargs):
         def _set_global_conf():
-            self.config_file = config_kwargs.get("__file__", None)
+            self.config_file = config_kwargs.get("__file__") or config_kwargs.get("config_file")
             self.global_conf = config_kwargs.get("global_conf")
             self.global_conf_parser = configparser.ConfigParser()
             if not self.config_file and self.global_conf and "__file__" in self.global_conf:
@@ -503,10 +511,10 @@ class BaseAppConfiguration(HasDynamicProperties):
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
+            if path:
                 path = os.path.join(parent_path, path)  # resolve path
             else:
-                path = parent_path  # or use parent path
+                log.warning("Trying to resolve path for the '%s' option but it's empty/None", key)
 
             setattr(self, key, path)  # update property
             _cache[key] = path  # cache it!
@@ -530,7 +538,7 @@ class BaseAppConfiguration(HasDynamicProperties):
             if self.is_set(key) and self.paths_to_check_against_root and key in self.paths_to_check_against_root:
                 self._check_against_root(key)
 
-    def _check_against_root(self, key):
+    def _check_against_root(self, key: str):
         def get_path(current_path, initial_path):
             # if path does not exist and was set as relative:
             if not self._path_exists(current_path) and not os.path.isabs(initial_path):
@@ -549,6 +557,8 @@ class BaseAppConfiguration(HasDynamicProperties):
             return current_path
 
         current_value = getattr(self, key)  # resolved path or list of resolved paths
+        if not current_value:
+            return
         if isinstance(current_value, list):
             initial_paths = listify(self._raw_config[key], do_strip=True)  # initial unresolved paths
             updated_paths = []
@@ -597,7 +607,7 @@ class CommonConfigurationMixin:
     @admin_users.setter
     def admin_users(self, value):
         self._admin_users = value
-        self.admin_users_list = listify(value)
+        self.admin_users_list = listify(value, do_strip=True)
 
     def is_admin_user(self, user: Optional["User"]) -> bool:
         """Determine if the provided user is listed in `admin_users`."""
@@ -704,6 +714,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     drmaa_external_runjob_script: str
     email_from: Optional[str]
     enable_tool_shed_check: bool
+    file_source_temp_dir: str
     galaxy_data_manager_data_path: str
     galaxy_infrastructure_url: str
     hours_between_check: int
@@ -981,6 +992,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             # self, populate config_dict
             self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
 
+        if kwargs.get("conda_auto_init") is None:
+            self.config_dict["conda_auto_init"] = running_from_source
+
         if self.container_resolvers_config_file:
             self.container_resolvers_config_file = self._in_config_dir(self.container_resolvers_config_file)
 
@@ -1079,6 +1093,10 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         self._process_celery_config()
 
+        # load in the chat_prompts if openai api key is configured
+        if self.openai_api_key:
+            self._load_chat_prompts()
+
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
             with open(self.user_preferences_extra_conf_path) as stream:
@@ -1103,10 +1121,46 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         self.proxy_session_map = self.dynamic_proxy_session_map
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
-        # InteractiveTools propagator mapping file
-        self.interactivetools_map = self._in_root_dir(
-            kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite"))
-        )
+        # Interactive tools proxy mapping
+        if self.interactivetoolsproxy_map is None:
+            self.interactivetools_map = "sqlite:///" + self._in_root_dir(
+                kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite"))
+            )
+        else:
+            self.interactivetools_map = None  # overridden by `self.interactivetoolsproxy_map`
+
+            # ensure the database URL for the SQLAlchemy map does not match that of a Galaxy DB
+            urls = {
+                setting: urlparse(value)
+                for setting, value in (
+                    ("interactivetoolsproxy_map", self.interactivetoolsproxy_map),
+                    ("database_connection", self.database_connection),
+                    ("install_database_connection", self.install_database_connection),
+                )
+                if value is not None
+            }
+
+            def is_in_conflict(url1, url2):
+                return all(
+                    (
+                        url1.scheme == url2.scheme,
+                        url1.hostname == url2.hostname,
+                        url1.port == url2.port,
+                        url1.path == url2.path,
+                    )
+                )
+
+            conflicting_settings = {
+                setting
+                for setting, url in tuple(urls.items())[1:]  # exclude "interactivetoolsproxy_map"
+                if is_in_conflict(url, list(urls.values())[0])  # compare with "interactivetoolsproxy_map"
+            }
+
+            if conflicting_settings:
+                raise ConfigurationError(
+                    f"Option `{tuple(urls)[0]}` cannot take the same value as: %s"
+                    % ", ".join(f"`{setting}`" for setting in conflicting_settings)
+                )
 
         # Compliance/Policy variables
         self.redact_username_during_deletion = False
@@ -1200,6 +1254,25 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         else:
             _load_theme(self.themes_config_file, self.themes)
 
+        if self.file_source_temp_dir:
+            self.file_source_temp_dir = os.path.abspath(self.file_source_temp_dir)
+
+    def _load_chat_prompts(self):
+        current_dir = os.path.dirname(os.path.abspath(__file__))
+        chat_prompts_path = os.path.join(current_dir, "chat_prompts.json")
+
+        if os.path.exists(chat_prompts_path):
+            try:
+                with open(chat_prompts_path, encoding="utf-8") as file:
+                    data = json.load(file)
+                    self.chat_prompts = data.get("prompts", {})
+            except json.JSONDecodeError as e:
+                log.error(f"JSON decoding error in chat prompts file: {e}")
+            except Exception as e:
+                log.error(f"An error occurred while reading chat prompts file: {e}")
+        else:
+            log.warning(f"Chat prompts file not found at {chat_prompts_path}")
+
     def _process_celery_config(self):
         if self.celery_conf and self.celery_conf.get("result_backend") is None:
             # If the result_backend is not set, use a SQLite database in the data directory
@@ -1227,6 +1300,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         try_parsing(self.database_connection, "database_connection")
         try_parsing(self.install_database_connection, "install_database_connection")
+        if self.interactivetoolsproxy_map is not None:
+            try_parsing(self.interactivetoolsproxy_map, "interactivetoolsproxy_map")
         try_parsing(self.amqp_internal_connection, "amqp_internal_connection")
 
     def _configure_dataset_storage(self):
@@ -1310,6 +1385,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.template_cache_path,
             self.tool_data_path,
             self.user_library_import_dir,
+            self.file_source_temp_dir,
         ]
         for path in paths_to_check:
             self._ensure_directory(path)
diff --git a/lib/galaxy/config/chat_prompts.json b/lib/galaxy/config/chat_prompts.json
new file mode 100644
index 0000000000000000000000000000000000000000..93ff8e058ee798f006afb320dc781192e5c2ede2
--- /dev/null
+++ b/lib/galaxy/config/chat_prompts.json
@@ -0,0 +1,8 @@
+{
+   "prompts": {
+       "tool_error": "Adopt the persona of a galaxy project expert who is able to easily explain complex error messages to novice users in a serious manner.\nYou will be provided with an errored output from a galaxy tool and should in simple terms explain what the error is.\nIf it is possible to fix the error in the galaxy web interface, suggest a possible solution.\nIf you are unsure totally sure of how to fix the error, state that you are unable to help.\nPlease ensure your response is in well-formatted markdown."
+   }
+}
+
+
+ 
\ No newline at end of file
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0e026b5a7b0ab7b7237d18b85872325aaeb728e8..b0f67d6d2c732acc275e8eb2ec2c65d8f59ba7c6 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -190,7 +190,7 @@
     <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
     <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
     <datatype extension="graph_dot" type="galaxy.datatypes.data:Text" subclass="true"/>
-    <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
+    <datatype extension="gtf" auto_compressed_types="gz" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
       <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
       <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <display file="igb/gtf.xml"/>
@@ -202,6 +202,7 @@
     <datatype extension="grib" type="galaxy.datatypes.binary:Grib" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="h5mu" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="MuData is a format analogous to Anndata for multimodal datasets and is based on HDF5" description_url="https://github.com/scverse/mudata"/>
     <datatype extension="visium.tar.gz" type="galaxy.datatypes.binary:Visium" subclass="true" display_in_upload="true" description="Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file." />
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
@@ -230,6 +231,7 @@
     <datatype extension="fastk_ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="fastk_hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="fastk_prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_ktab_tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" description="Associated hidden ktab files that are essential for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="npy" type="galaxy.datatypes.binary:Numpy" description="Standard format for saving numpy arrays" display_in_upload="true" description_url="https://numpy.org/devdocs/reference/generated/numpy.lib.format.html"/>
 
     <!-- ISA data types -->
@@ -288,13 +290,23 @@
       <display file="qiime/qiime2/q2view.xml"/>
     </datatype>
     <datatype extension='qiime2.tabular' type="galaxy.datatypes.qiime2:QIIME2Metadata" display_in_upload="true"/>
-    <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"/>
+    <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="directory" />
+    </datatype>
     <datatype extension="ncbi_genome_dataset.zip" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
-    <datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
-      <converter file="tar_to_directory.xml" target_datatype="directory"/>
+    <datatype extension="zarr.zip" type="galaxy.datatypes.binary:CompressedZarrZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="zarr" />
+    </datatype>
+    <datatype extension="ome_zarr.zip" type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="ome_zarr" />
     </datatype>
-    <datatype extension="directory" type="galaxy.datatypes.data:Directory">
+    <datatype extension="tar" auto_compressed_types="gz,bz2" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
+      <converter file="archive_to_directory.xml" target_datatype="directory"/>
     </datatype>
+    <datatype extension="directory" type="galaxy.datatypes.data:Directory"/>
+    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>
+    <datatype extension="zarr" type="galaxy.datatypes.data:ZarrDirectory" />
+    <datatype extension="ome_zarr" type="galaxy.datatypes.images:OMEZarr" />
     <datatype extension="yaml" type="galaxy.datatypes.text:Yaml" display_in_upload="true" />
     <!-- Proteomics Datatypes -->
     <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
@@ -520,7 +532,7 @@
     <datatype extension="juicer_medium_tabix.gz" type="galaxy.datatypes.interval:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true"/>
+    <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>
@@ -720,6 +732,7 @@
     <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
     <datatype extension="rdata.se" type="galaxy.datatypes.hdf5:HDF5SummarizedExperiment"  mimetype="text/html" display_in_upload="true"/>
     <datatype extension="rdock_as" type="galaxy.datatypes.binary:Binary" description="rDock active site format" subclass="true" display_in_upload="true"/>
+    <datatype extension="prm" type="galaxy.datatypes.text:Prm" mimetype="text/plain" description="rDock prm format for system definition files, scoring function definition files and search protocol definition files" description_url="https://rdock.github.io/documentation/html_docs/reference-guide/file-formats.html" display_in_upload="true" />
     <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxlits" type="galaxy.datatypes.binary:OxliTagSet" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -975,6 +988,7 @@
     <datatype extension="gmsh.msh" type="galaxy.datatypes.constructive_solid_geometry:GmshMsh" display_in_upload="true"/>
     <datatype extension="gmsh.geo" type="galaxy.datatypes.constructive_solid_geometry:GmshGeo" display_in_upload="true"/>
     <datatype extension="zset.geof" type="galaxy.datatypes.constructive_solid_geometry:ZsetGeof" display_in_upload="true"/>
+    <datatype extension="vtkxml" type="galaxy.datatypes.constructive_solid_geometry:VtkXml" display_in_upload="true"/>
     <datatype extension="stl" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" description="STL is a file format native to the stereolithography CAD software created by 3D Systems."/>
     <!-- Povray script -->
     <datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
@@ -1007,6 +1021,7 @@
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
     <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
     <datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
+    <datatype extension="bcsp" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="Binary format of k-mer hash table which is only compatible with Fairy"/>
   </registration>
   <sniffers>
     <!--
@@ -1033,6 +1048,7 @@
     <sniffer type="galaxy.datatypes.mothur:Axes"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
+    <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkXml"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTess"/>
@@ -1107,6 +1123,8 @@
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:Pretext"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 534e7773654188a967dd2be8478c1890a0edf981..0bc5e9e10aed85716b908649c56cc701c5f34d1b 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -235,6 +235,6 @@
   id: onedata1
   label: Onedata
   doc: Your Onedata files - configure an access token via user preferences
-  accessToken: ${user.preferences['onedata|access_token']}
-  onezoneDomain: ${user.preferences['onedata|onezone_domain']}
-  disableTlsCertificateValidation: ${user.preferences['onedata|disable_tls_certificate_validation']}
+  access_token: ${user.preferences['onedata|access_token']}
+  onezone_domain: ${user.preferences['onedata|onezone_domain']}
+  disable_tls_certificate_validation: ${user.preferences['onedata|disable_tls_certificate_validation']}
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 9cf7bc3caf9b5b4fb403ae4a6e6d614432ae2a22..9b88819707573067067d5f75369a37cabacb59d5 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -578,7 +578,7 @@ galaxy:
 
   # conda channels to enable by default
   # (https://conda.io/docs/user-guide/tasks/manage-channels.html)
-  #conda_ensure_channels: conda-forge,bioconda,defaults
+  #conda_ensure_channels: conda-forge,bioconda
 
   # Use locally-built conda packages.
   #conda_use_local: false
@@ -589,8 +589,9 @@ galaxy:
 
   # Set to true to instruct Galaxy to install Conda from the web
   # automatically if it cannot find a local copy and conda_exec is not
-  # configured.
-  #conda_auto_init: true
+  # configured. The default is true if running Galaxy from source, and
+  # false if running from installed packages.
+  #conda_auto_init: false
 
   # You must set this to true if conda_prefix and job_working_directory
   # are not on the same volume, or some conda dependencies will fail to
@@ -1104,8 +1105,8 @@ galaxy:
   # <cache_dir>.
   #object_store_cache_path: object_store_cache
 
-  # Default cache size for caching object stores if cache not configured
-  # for that object store entry.
+  # Default cache size, in GB, for caching object stores if the cache is
+  # not configured for that object store entry.
   #object_store_cache_size: -1
 
   # Set this to true to indicate in the UI that a user's object store
@@ -1219,7 +1220,7 @@ galaxy:
   # Registration warning message is used to discourage people from
   # registering multiple accounts.  Applies mostly for the main Galaxy
   # instance. If no message specified the warning box will not be shown.
-  #registration_warning_message: Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.
+  #registration_warning_message: Please register only one account to ensure fair sharing of computational resources. Multiple registrations are monitored and will result in account termination and data deletion.
 
   # User account activation feature global flag.  If set to false, the
   # rest of the Account activation configuration is ignored and user
@@ -1348,11 +1349,24 @@ galaxy:
   # subdomain. Defaults to "/".
   #interactivetools_base_path: /
 
-  # Map for interactivetool proxy.
+  # Map for the interactivetool proxy. Mappings are stored in a SQLite
+  # database file located on this path. As an alternative, you may also
+  # store them in any other RDBMS supported by SQLAlchemy using the
+  # option ``interactivetoolsproxy_map``, which overrides this one.
   # The value of this option will be resolved with respect to
   # <data_dir>.
   #interactivetools_map: interactivetools_map.sqlite
 
+  # Use a database supported by SQLAlchemy as map for the
+  # interactivetool proxy. When this option is set, the value of
+  # ``interactivetools_map`` is ignored. The value of this option must
+  # be a `SQLAlchemy database URL
+  # <https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls>`_.
+  # Mappings are written to the table "gxitproxy" within the database.
+  # This value cannot match ``database_connection`` nor
+  # ``install_database_connection``.
+  #interactivetoolsproxy_map: null
+
   # Prefix to use in the formation of the subdomain or path for
   # interactive tools
   #interactivetools_prefix: interactivetool
@@ -2746,6 +2760,19 @@ galaxy:
   # <config_dir>.
   #workflow_schedulers_config_file: workflow_schedulers_conf.xml
 
+  # Workflows launched with URI/URL inputs that are not marked as
+  # 'deferred' are "materialized" (or undeferred) by the workflow
+  # scheduler. This might be a lengthy process. Setting this to 'True'
+  # will place the invocation back in the queue after materialization
+  # before scheduling the workflow so it is less likely to starve other
+  # workflow scheduling. Ideally, Galaxy would allow more fine grain
+  # control of handlers but until then, this provides a way to tip the
+  # balance between "doing more work" and "being more fair". The default
+  # here is pretty arbitrary - it has been to False to optimize Galaxy
+  # for automated, single user applications where "fairness" is mostly
+  # irrelevant.
+  #workflow_scheduling_separate_materialization_iteration: false
+
   # If using job concurrency limits (configured in job_config_file),
   # several extra database queries must be performed to determine the
   # number of jobs a user has dispatched to a given destination.  By
@@ -2866,6 +2893,13 @@ galaxy:
   # as threshold (above threshold: regular select fields will be used)
   #select_type_workflow_threshold: -1
 
+  # API key for OpenAI (https://openai.com/) to enable the wizard (or
+  # more?)
+  #openai_api_key: null
+
+  # OpenAI model to enable the wizard.
+  #openai_model: gpt-4o
+
   # Allow the display of tool recommendations in workflow editor and
   # after tool execution. If it is enabled and set to true, please
   # enable 'tool_recommendation_model_path' as well
@@ -2977,3 +3011,18 @@ galaxy:
   # This requires the help_forum_api_url to be set.
   #enable_help_forum_tool_panel_integration: false
 
+  # Directory to store temporary files for file sources. This defaults
+  # to new_file_path if not set.
+  #file_source_temp_dir: null
+
+  # Default value for use_temp_files for webdav plugins that don't
+  # explicitly declare this.
+  #file_source_webdav_use_temp_files: true
+
+  # Number of seconds before file source content listings are refreshed.
+  # Shorter times will result in more queries while browsing a file
+  # sources. Longer times will result in fewer requests to file sources
+  # but outdated contents might be displayed to the user. Currently only
+  # affects s3fs file sources.
+  #file_source_listings_expiry_time: 60
+
diff --git a/lib/galaxy/config/sample/object_store_conf.sample.yml b/lib/galaxy/config/sample/object_store_conf.sample.yml
index afbcfc22323b066f449d5a0214e638dce3f149d6..4ea83f3f2d7eec7d830ca9793cce70dc10eb1fdb 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -220,21 +220,24 @@ extra_dirs:
 
 type: onedata
 auth:
-  # an access token suitable for data access (allowing calls to the Oneprovider REST API).
+  # An access token suitable for data access (allowing calls to the Oneprovider REST API).
   access_token: ...
 connection:
-  # the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
-  # devel instances (see above).
+  # The domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
+  # devel instances (see above). The minimal supported Onezone version is 21.02.4.
   onezone_domain: datahub.egi.eu
   # Allows connection to Onedata servers that do not present trusted SSL certificates. 
   # SHOULD NOT be used unless you really know what you are doing.
   disable_tls_certificate_validation: false
 space:
-  # the name of the Onedata space where the Galaxy data will be stored.
+  # The name of the Onedata space where the Galaxy data will be stored.
+  # If there is more than one space with the same name, you can explicitly
+  # specify which one to select by using the format <space_name>@<space_id>
+  # (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
   name: demo-space
-  # the relative directory path in the space under which the Galaxy data will be stored.
+  # The relative directory path in the space at which the Galaxy data will be stored.
   # Optional, if not provided, the data will be stored in the root of space.
-  path: galaxy-data
+  galaxy_root_dir: galaxy-data
 cache:
   path: database/object_store_cache_s3
   size: 1000
@@ -261,6 +264,20 @@ connection:
   timeout: 30
   refresh_time: 300
   connection_pool_monitor_interval: 3600
+# ssl section is optional
+ssl:
+  client_server_negotiation: request_server_negotiation
+  client_server_policy: CS_NEG_REQUIRE
+  encryption_algorithm: AES-256-CBC
+  encryption_key_size: 32
+  encryption_num_hash_rounds: 16
+  encryption_salt_size: 8
+  ssl_verify_server: cert
+  ssl_ca_certificate_file: /etc/irods/ssl/irods.crt
+# The logical section is optional and is meant for defining the remote path
+# if not defined the default path is: /zone_name/home/username
+logical:
+  path: /tempZone/home/rods
 cache:
   path: database/object_store_cache_irods
   size: 1000
diff --git a/lib/galaxy/config/sample/object_store_conf.xml.sample b/lib/galaxy/config/sample/object_store_conf.xml.sample
index 1b9d997271e97bb121a14a8be7e84953e0f9cb93..f8746ff7cee69c4c290d2edc90121f0d55309261 100644
--- a/lib/galaxy/config/sample/object_store_conf.xml.sample
+++ b/lib/galaxy/config/sample/object_store_conf.xml.sample
@@ -166,7 +166,7 @@
 
     //connection/@onezone_domain -
         the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
-        devel instances (see above).
+        devel instances (see above). The minimal supported Onezone version is 21.02.4.
 
     //connection/@disable_tls_certificate_validation - 
         Allows connection to Onedata servers that do not present trusted SSL certificates. 
@@ -174,16 +174,19 @@
 
     //space/@name -
         the name of the Onedata space where the Galaxy data will be stored.
+        If there is more than one space with the same name, you can explicitly
+        specify which one to select by using the format <space_name>@<space_id>
+        (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
 
-    //space/@path -
-        the relative directory path in the space under which the Galaxy data will be stored.
+    //space/@galaxy_root_dir -
+        the relative directory path in the space at which the Galaxy data will be stored.
         Optional, if not provided, the data will be stored in the root of space.
 -->
 <!--
 <object_store type="onedata">
     <auth access_token="..." />
     <connection onezone_domain="datahub.egi.eu" disable_tls_certificate_validation="False"/>
-    <space name="demo-space" path="galaxy-data" />
+    <space name="demo-space" galaxy_root_dir="galaxy-data" />
     <cache path="database/object_store_cache" size="1000" cache_updated_data="True" />
     <extra_dir type="job_work" path="database/job_working_directory_onedata"/>
     <extra_dir type="temp" path="database/tmp_onedata"/>
@@ -192,6 +195,10 @@
 
 <!--
     Sample iRODS Object Store
+
+    The ssl section is optional
+    The logical section is optional and is meant for defining the remote path
+    if not defined the default path is: /zone_name/home/username
 -->
 <!--
 <object_store type="irods">
@@ -199,6 +206,10 @@
     <resource name="demoResc" />
     <zone name="tempZone" />
     <connection host="localhost" port="1247" timeout="30" refresh_time="300" connection_pool_monitor_interval="3600"/>
+    <ssl client_server_negotiation="request_server_negotiation" client_server_policy="CS_NEG_REQUIRE" 
+         encryption_algorithm="AES-256-CBC" encryption_key_size="32" encryption_num_hash_rounds="16" 
+         encryption_salt_size="8" ssl_verify_server="cert" ssl_ca_certificate_file="/etc/irods/ssl/irods.crt" />
+    <logical path="/tempZone/home/rods" />
     <cache path="database/object_store_cache_irods" size="1000" cache_updated_data="True" />
     <extra_dir type="job_work" path="database/job_working_directory_irods"/>
     <extra_dir type="temp" path="database/tmp_irods"/>
diff --git a/lib/galaxy/config/sample/oidc_backends_config.xml.sample b/lib/galaxy/config/sample/oidc_backends_config.xml.sample
index ce8e8e1d0b27e5db5d55782a5660d78e89ffbe1c..4244efd5b88892b1bd1e0b24e1d28377efc45d45 100644
--- a/lib/galaxy/config/sample/oidc_backends_config.xml.sample
+++ b/lib/galaxy/config/sample/oidc_backends_config.xml.sample
@@ -201,6 +201,26 @@ Please mind `http` and `https`.
         <tenant_id> ... </tenant_id>
     </provider>
 
+    <provider name="oidc">
+        <!-- This example section uses the generic OIDC backend from python-social-auth. This should work with any provider that
+        supports the OIDC standard.
+        -->
+        <client_id> ... </client_id>
+        <client_secret> ... </client_secret>
+        <redirect_uri>http://localhost:8080/authnz/oidc/callback</redirect_uri>
+        <oidc_endpoint> ... </oidc_endpoint>
+        <!-- enter the url of a OIDC endpoint that supports autoconfiguration here. Enter the URL minus the ".well-known/openid-configuration" part.
+        For example: If the complete url pointing to your endpoint's autoconfig file is "https:example.com/my-realm/.well-known/openid-configuration",
+        then simply enter "https://example.com/my-realm".
+         -->
+         <custom_button_text> ... </custom_button_text>
+         <!-- This is an optional field where you can provide a custom text for the sign in button on the Galaxy front page
+          that you can click to authenticate with your IdP. If you don't provide a custom button text, the sign in button
+          will just read the default value of your IdP name. For example: "Sign in with oidc" or "Sign in with Azure".
+          However, if for example you enter the value "your university account" here, the button will display "Sign in with your university account".
+         -->
+    </provider>
+
     <!-- Documentation: https://docs.egi.eu/providers/check-in/sp -->
     <provider name="egi_checkin">
 	<!-- Client id and secret can be obtained by registering your client at EGI Check-in
diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index 153b5ae314d43e1cd8fb9355a82ce3b3c7336c01..7c7cbd6a2646bead300a56ea959c9772245a7a02 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -32,6 +32,7 @@
     <tool file="${model_tools_path}/zip_collection.xml" />
     <tool file="${model_tools_path}/filter_failed_collection.xml" />
     <tool file="${model_tools_path}/filter_empty_collection.xml" />
+    <tool file="${model_tools_path}/filter_null.xml" />
     <tool file="${model_tools_path}/flatten_collection.xml" />
     <tool file="${model_tools_path}/merge_collection.xml" />
     <tool file="${model_tools_path}/relabel_from_file.xml" />
@@ -134,11 +135,13 @@
   <section id="interactivetools" name="Interactive tools">
     <tool file="interactive/interactivetool_askomics.xml" />
     <tool file="interactive/interactivetool_bam_iobio.xml" />
+    <tool file="interactive/interactivetool_blobtoolkit.xml" />
     <tool file="interactive/interactivetool_cellxgene_0.16.2.xml" />
     <tool file="interactive/interactivetool_cellxgene_1.1.1.xml" />
     <tool file="interactive/interactivetool_ethercalc.xml" />
     <tool file="interactive/interactivetool_guacamole_desktop.xml" />
     <tool file="interactive/interactivetool_hicbrowser.xml" />
+    <tool file="interactive/interactivetool_jupyter_notebook_1.0.1.xml" />
     <tool file="interactive/interactivetool_jupyter_notebook_1.0.0.xml" />
     <tool file="interactive/interactivetool_jupyter_notebook.xml" />
     <tool file="interactive/interactivetool_neo4j.xml" />
diff --git a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
index 6d8c50ac82c94411fa57612c1d952173735f76d4..244a77477e4aebdd38919918a356a9040e485335 100644
--- a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
@@ -110,6 +110,10 @@
         <columns>value, name, url</columns>
         <file path="tool-data/icn3d_simple_display.loc" />
     </table>
+    <table name="sift_db" comment_char="#" allow_duplicate_entries="False">
+        <columns>dbkey, value</columns>
+        <file path="tool-data/sift_db.loc" />
+    </table>
     <!-- Refgenie __dbkeys__ -->
     <table name="__dbkeys__" type="refgenie" asset="fasta" >
         <file from_config="refgenie_config_file" />
diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index bf16f6bfabab54879dd354780a6f1d90c91b4b59..d0a8aa456cccab220d3b9a01730e5c620ce261bb 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -54,6 +54,9 @@ tool_shed:
   # options.
   #whoosh_index_dir: database/toolshed_whoosh_indexes
 
+  # Cache directory for Pydantic model objects.
+  #model_cache_dir: database/model_cache
+
   # For searching repositories at /api/repositories:
   #repo_name_boost: 0.9
 
diff --git a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
index 72689e31bf44117f35f699e11c40e74be27de4db..9f38f40bba1d760687f497730fe3b4a0aa942891 100644
--- a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
+++ b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
@@ -141,7 +141,7 @@ preferences:
         description: Your Onedata account
         inputs:
             - name: onezone_domain
-              label: Domain of the Onezone service (e.g. datahub.egi.eu)
+              label: Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4.
               type: text
               required: False
             - name: access_token
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 79c456009762aa5ebf74d4f8cd06053f98feceb7..a6dbbd35a678347c6abd3d2fc2b0fe71746970cd 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -359,7 +359,7 @@ mapping:
 
       conda_ensure_channels:
         type: str
-        default: conda-forge,bioconda,defaults
+        default: conda-forge,bioconda
         required: false
         desc: |
           conda channels to enable by default
@@ -382,11 +382,11 @@ mapping:
 
       conda_auto_init:
         type: bool
-        default: true
         required: false
         desc: |
           Set to true to instruct Galaxy to install Conda from the web automatically
-          if it cannot find a local copy and conda_exec is not configured.
+          if it cannot find a local copy and conda_exec is not configured. The default is
+          true if running Galaxy from source, and false if running from installed packages.
 
       conda_copy_dependencies:
         type: bool
@@ -1146,8 +1146,8 @@ mapping:
         default: -1
         required: false
         desc: |
-          Default cache size for caching object stores if cache not configured for
-          that object store entry.
+          Default cache size, in GB, for caching object stores if the cache is not
+          configured for that object store entry.
 
       object_store_always_respect_user_selection:
         type: bool
@@ -1306,9 +1306,9 @@ mapping:
       registration_warning_message:
         type: str
         default: >-
-          Please register only one account - we provide this service free of charge and have limited
-          computational resources. Multi-accounts are tracked and will be subjected to account
-          termination and data deletion.
+          Please register only one account to ensure fair sharing of
+          computational resources. Multiple registrations are monitored and will
+          result in account termination and data deletion.
         required: false
         desc: |
           Registration warning message is used to discourage people from registering
@@ -1474,7 +1474,7 @@ mapping:
           This is used to make carbon emissions estimates more accurate as the location effects the
           carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the
           `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations,
-          visit https://galaxyproject.org/admin/carbon_emissions
+          visit https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
 
       power_usage_effectiveness:
         type: float
@@ -1520,7 +1520,21 @@ mapping:
         default: interactivetools_map.sqlite
         path_resolves_to: data_dir
         desc: |
-          Map for interactivetool proxy.
+          Map for the interactivetool proxy. Mappings are stored in a SQLite database file
+          located on this path. As an alternative, you may also store them in any other RDBMS
+          supported by SQLAlchemy using the option ``interactivetoolsproxy_map``, which
+          overrides this one.
+
+      interactivetoolsproxy_map:
+        type: str
+        required: false
+        desc: |
+          Use a database supported by SQLAlchemy as map for the interactivetool proxy.
+          When this option is set, the value of ``interactivetools_map`` is ignored. The
+          value of this option must be a
+          `SQLAlchemy database URL <https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls>`_.
+          Mappings are written to the table "gxitproxy" within the database. This value cannot match
+          ``database_connection`` nor ``install_database_connection``.
 
       interactivetools_prefix:
         type: str
@@ -3748,6 +3762,21 @@ mapping:
           Optional configuration file similar to `job_config_file` to specify
           which Galaxy processes should schedule workflows.
 
+      workflow_scheduling_separate_materialization_iteration:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Workflows launched with URI/URL inputs that are not marked as 'deferred'
+          are "materialized" (or undeferred) by the workflow scheduler. This might be
+          a lengthy process. Setting this to 'True' will place the invocation back in
+          the queue after materialization before scheduling the workflow so it is less
+          likely to starve other workflow scheduling. Ideally, Galaxy would allow more
+          fine grain control of handlers but until then, this provides a way to tip the
+          balance between "doing more work" and "being more fair". The default here is
+          pretty arbitrary - it has been to False to optimize Galaxy for automated,
+          single user applications where "fairness" is mostly irrelevant.
+
       cache_user_job_count:
         type: bool
         default: false
@@ -3853,7 +3882,7 @@ mapping:
           `result_backend` option in the `celery_conf` option to a valid Celery result
           backend URL. By default, Galaxy uses an SQLite database at '<data_dir>/results.sqlite' for storing task results.
           For details, see https://docs.galaxyproject.org/en/master/admin/production.html#use-celery-for-asynchronous-tasks
-          
+
       celery_conf:
         type: any
         required: false
@@ -3918,6 +3947,19 @@ mapping:
           use -1 (default) in order to always use the regular select fields,
           use any other positive number as threshold (above threshold: regular select fields will be used)
 
+      openai_api_key:
+        type: str
+        required: false
+        desc: |
+          API key for OpenAI (https://openai.com/) to enable the wizard (or more?)
+
+      openai_model:
+        type: str
+        default: gpt-4o
+        required: false
+        desc: |
+          OpenAI model to enable the wizard.
+
       enable_tool_recommendations:
         type: bool
         default: false
@@ -4106,3 +4148,23 @@ mapping:
         required: false
         desc: |
           Disable the batch input mode for all tools. This will remove the "Multiple Datasets" and "Dataset Collection" input types from single dataset inputs in all tools.
+
+      file_source_temp_dir:
+        type: str
+        required: false
+        desc: |
+          Directory to store temporary files for file sources. This defaults to new_file_path if not set.
+
+      file_source_webdav_use_temp_files:
+        type: bool
+        default: true
+        desc: |
+          Default value for use_temp_files for webdav plugins that don't explicitly declare this.
+
+      file_source_listings_expiry_time:
+        type: int
+        default: 60
+        desc: |
+          Number of seconds before file source content listings are refreshed. Shorter times will result in more
+          queries while browsing a file sources. Longer times will result in fewer requests to file sources but
+          outdated contents might be displayed to the user. Currently only affects s3fs file sources.
diff --git a/lib/galaxy/config/schemas/tool_shed_config_schema.yml b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
index 42ea164d9d5f6a5f0395ec5b0c0bf1cb374d1659..b7b6bfee049e5c5cbe92a962c88942f6c908e518 100644
--- a/lib/galaxy/config/schemas/tool_shed_config_schema.yml
+++ b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
@@ -102,6 +102,13 @@ mapping:
           the repositories and tools within the Tool Shed given that you specify
           the following two config options.
 
+      model_cache_dir:
+        type: str
+        default: database/model_cache
+        required: false
+        desc: |
+          Cache directory for Pydantic model objects.
+
       repo_name_boost:
         type: float
         default: 0.9
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 2633594a09b4673af13bc81b43f07c9549c7eb7e..66beb9d47bc95a04212a05948061378cc9278492 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -441,6 +441,103 @@ class CompressedZipArchive(CompressedArchive):
         return False
 
 
+class CompressedZarrZipArchive(CompressedZipArchive):
+    """A zarr store compressed in a zip file.
+
+    The zarr store must be in the root of the zip file.
+    """
+
+    file_ext = "zarr.zip"
+
+    MetadataElement(
+        name="zarr_format",
+        default=None,
+        desc="Zarr format version",
+        readonly=True,
+        optional=False,
+        visible=False,
+    )
+
+    MetadataElement(
+        name="compression",
+        default=None,
+        desc="Compression type used in the Zip zarr store",
+        readonly=True,
+        optional=False,
+        visible=False,
+    )
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.blurb = f"{nice_size(dataset.get_size())}"
+            dataset.blurb += f"\nFormat v{dataset.metadata.zarr_format}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        with zipfile.ZipFile(dataset.get_file_name()) as zf:
+            dataset.metadata.compression = zf.compression
+            meta_file = self._find_zarr_metadata_file(zf)
+            if meta_file:
+                with zf.open(meta_file) as f:
+                    meta = json.load(f)
+                    format_version = meta.get("zarr_format")
+                    if not format_version:
+                        log.debug("Could not determine Zarr format version")
+                        return
+                    dataset.metadata.zarr_format = format_version
+
+    def sniff(self, filename: str) -> bool:
+        # Check if the zip file contains a zarr store.
+        # In theory, the zarr store must be in the root of the zip file.
+        # See: https://github.com/zarr-developers/zarr-python/issues/756#issuecomment-852134901
+        # But in practice, many examples online have the zarr store in a subfolder in the zip file,
+        # so we will check for that as well.
+        meta_file = None
+        with zipfile.ZipFile(filename) as zf:
+            meta_file = self._find_zarr_metadata_file(zf)
+        return meta_file is not None
+
+    def _find_zarr_metadata_file(self, zip_file: zipfile.ZipFile) -> Optional[str]:
+        """Returns the path to the metadata file in the Zarr store if found."""
+        # Depending on the Zarr version, the metadata file can be in different locations
+        # In v1 the metadata is in a file named "meta" https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html
+        # In v2 it can be in .zarray or .zgroup https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html
+        # In v3 the metadata is in a file named "zarr.json" https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html
+        possible_meta_files = ["meta", ".zarray", ".zgroup", "zarr.json"]
+        for file in zip_file.namelist():
+            if any(file.endswith(meta_file) for meta_file in possible_meta_files):
+                return file
+        return None
+
+
+class CompressedOMEZarrZipArchive(CompressedZarrZipArchive):
+    file_ext = "ome_zarr.zip"
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = "OME-Zarr directory"
+            dataset.blurb = f"{nice_size(dataset.get_size())}"
+            dataset.blurb += f"\nZarr Format v{dataset.metadata.zarr_format}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def sniff(self, filename: str) -> bool:
+        meta_file = None
+        with zipfile.ZipFile(filename) as zf:
+            meta_file = self._find_ome_zarr_metadata_file(zf)
+        return meta_file is not None
+
+    def _find_ome_zarr_metadata_file(self, zip_file: zipfile.ZipFile) -> Optional[str]:
+        expected_meta_file_name = "OME/METADATA.ome.xml"
+        for file in zip_file.namelist():
+            if file.endswith(expected_meta_file_name):
+                return file
+        return None
+
+
 class GenericAsn1Binary(Binary):
     """Class for generic ASN.1 binary format"""
 
@@ -570,7 +667,7 @@ class BamNative(CompressedArchive, _BamOrSam):
         :param split_files: List of bam file paths to merge
         :param output_file: Write merged bam file to this location
         """
-        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined]
+        pysam.merge("-O", "BAM", output_file, *split_files)  # type: ignore[attr-defined, unused-ignore]
 
     def init_meta(self, dataset: HasMetadata, copy_from: Optional[HasMetadata] = None) -> None:
         Binary.init_meta(self, dataset, copy_from=copy_from)
@@ -639,7 +736,7 @@ class BamNative(CompressedArchive, _BamOrSam):
             [f"-@{slots}", file_name, "-T", tmp_sorted_dataset_file_name_prefix, "-O", "BAM", "-o", sorted_file_name]
         )
         try:
-            pysam.sort(*sort_args)  # type: ignore[attr-defined]
+            pysam.sort(*sort_args)  # type: ignore[attr-defined, unused-ignore]
         except Exception:
             shutil.rmtree(tmp_dir, ignore_errors=True)
             raise
@@ -836,11 +933,12 @@ class Bam(BamNative):
             index_file = dataset.metadata.spec[spec_key].param.new_file(
                 dataset=dataset, metadata_tmp_files_dir=metadata_tmp_files_dir
             )
+        extra_threads = int(os.environ.get("GALAXY_SLOTS", 1)) - 1
         if index_flag == "-b":
             # IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
-            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
         else:
-            pysam.index(index_flag, "-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index(index_flag, "-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
         dataset.metadata.bam_index = index_file
 
     def sniff(self, filename: str) -> bool:
@@ -1030,8 +1128,9 @@ class CRAM(Binary):
             return -1, -1
 
     def set_index_file(self, dataset: HasFileName, index_file) -> bool:
+        extra_threads = int(os.environ.get("GALAXY_SLOTS", 1)) - 1
         try:
-            pysam.index("-o", index_file.get_file_name(), dataset.get_file_name())  # type: ignore [attr-defined]
+            pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())  # type: ignore[attr-defined, unused-ignore]
             return True
         except Exception as exc:
             log.warning("%s, set_index_file Exception: %s", self, exc)
@@ -1301,7 +1400,7 @@ class Loom(H5):
 
     def sniff(self, filename: str) -> bool:
         if super().sniff(filename):
-            with h5py.File(filename, "r") as loom_file:
+            with h5py.File(filename, "r", locking=False) as loom_file:
                 # Check the optional but distinctive LOOM_SPEC_VERSION attribute
                 if bool(loom_file.attrs.get("LOOM_SPEC_VERSION")):
                     return True
@@ -1330,7 +1429,7 @@ class Loom(H5):
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.get_file_name(), "r") as loom_file:
+            with h5py.File(dataset.get_file_name(), "r", locking=False) as loom_file:
                 dataset.metadata.title = loom_file.attrs.get("title")
                 dataset.metadata.description = loom_file.attrs.get("description")
                 dataset.metadata.url = loom_file.attrs.get("url")
@@ -1466,7 +1565,7 @@ class Anndata(H5):
     def sniff(self, filename: str) -> bool:
         if super().sniff(filename):
             try:
-                with h5py.File(filename, "r") as f:
+                with h5py.File(filename, "r", locking=False) as f:
                     return all(attr in f for attr in ["X", "obs", "var"])
             except Exception:
                 return False
@@ -1474,7 +1573,7 @@ class Anndata(H5):
 
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
         super().set_meta(dataset, overwrite=overwrite, **kwd)
-        with h5py.File(dataset.get_file_name(), "r") as anndata_file:
+        with h5py.File(dataset.get_file_name(), "r", locking=False) as anndata_file:
             dataset.metadata.title = anndata_file.attrs.get("title")
             dataset.metadata.description = anndata_file.attrs.get("description")
             dataset.metadata.url = anndata_file.attrs.get("url")
@@ -1517,7 +1616,10 @@ class Anndata(H5):
                 obs = get_index_value(tmp)
                 # Determine cell labels
                 if obs is not None:
-                    dataset.metadata.obs_names = [n.decode() for n in obs]
+                    # This is super expensive because the number of observations is unbounded.
+                    # https://github.com/galaxyproject/tools-iuc/blob/8341270dd36185ebf59d15282bc79f1215e936a4/tools/anndata/import.xml#L53
+                    # seems to be the only tool to consume this in the IUC. drop and make tool compute this?
+                    dataset.metadata.obs_names = [util.unicodify(n) for n in obs]
                 else:
                     log.warning("Could not determine observation index for %s", self)
 
@@ -1824,7 +1926,7 @@ class Biom2(H5):
         False
         """
         if super().sniff(filename):
-            with h5py.File(filename, "r") as f:
+            with h5py.File(filename, "r", locking=False) as f:
                 required_fields = {"id", "format-url", "type", "generated-by", "creation-date", "nnz", "shape"}
                 return required_fields.issubset(f.attrs.keys())
         return False
@@ -1832,7 +1934,7 @@ class Biom2(H5):
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.get_file_name(), "r") as f:
+            with h5py.File(dataset.get_file_name(), "r", locking=False) as f:
                 attributes = f.attrs
 
                 dataset.metadata.id = util.unicodify(attributes["id"])
@@ -1855,7 +1957,7 @@ class Biom2(H5):
         if not dataset.dataset.purged:
             lines = ["Biom2 (HDF5) file"]
             try:
-                with h5py.File(dataset.get_file_name()) as f:
+                with h5py.File(dataset.get_file_name(), locking=False) as f:
                     for k, v in f.attrs.items():
                         lines.append(f"{k}:  {util.unicodify(v)}")
             except Exception as e:
@@ -1902,7 +2004,7 @@ class Cool(H5):
 
         if super().sniff(filename):
             keys = ["chroms", "bins", "pixels", "indexes"]
-            with h5py.File(filename, "r") as handle:
+            with h5py.File(filename, "r", locking=False) as handle:
                 fmt = util.unicodify(handle.attrs.get("format"))
                 url = util.unicodify(handle.attrs.get("format-url"))
                 if fmt == MAGIC or url == URL:
@@ -1958,7 +2060,7 @@ class MCool(H5):
 
         if super().sniff(filename):
             keys0 = ["resolutions"]
-            with h5py.File(filename, "r") as handle:
+            with h5py.File(filename, "r", locking=False) as handle:
                 if not all(name in handle.keys() for name in keys0):
                     return False
                 res0 = next(iter(handle["resolutions"].keys()))
@@ -2024,7 +2126,7 @@ class H5MLM(H5):
                 params_file = dataset.metadata.spec[spec_key].param.new_file(
                     dataset=dataset, metadata_tmp_files_dir=metadata_tmp_files_dir
                 )
-            with h5py.File(dataset.get_file_name(), "r") as handle:
+            with h5py.File(dataset.get_file_name(), "r", locking=False) as handle:
                 hyper_params = handle[self.HYPERPARAMETER][()]
             hyper_params = json.loads(util.unicodify(hyper_params))
             with open(params_file.get_file_name(), "w") as f:
@@ -2038,7 +2140,7 @@ class H5MLM(H5):
     def sniff(self, filename: str) -> bool:
         if super().sniff(filename):
             keys = [self.CONFIG]
-            with h5py.File(filename, "r") as handle:
+            with h5py.File(filename, "r", locking=False) as handle:
                 if not all(name in handle.keys() for name in keys):
                     return False
                 url = util.unicodify(handle.attrs.get(self.URL))
@@ -2048,7 +2150,7 @@ class H5MLM(H5):
 
     def get_attribute(self, filename: str, attr_key: str) -> str:
         try:
-            with h5py.File(filename, "r") as handle:
+            with h5py.File(filename, "r", locking=False) as handle:
                 attr = util.unicodify(handle.attrs.get(attr_key))
             return attr
         except Exception as e:
@@ -2071,7 +2173,7 @@ class H5MLM(H5):
 
     def get_config_string(self, filename: str) -> str:
         try:
-            with h5py.File(filename, "r") as handle:
+            with h5py.File(filename, "r", locking=False) as handle:
                 config = util.unicodify(handle[self.CONFIG][()])
             return config
         except Exception as e:
@@ -2112,7 +2214,7 @@ class H5MLM(H5):
         out_dict: Dict = {}
         fname = dataset.get_file_name(user=trans.user)
         try:
-            with h5py.File(fname, "r") as handle:
+            with h5py.File(fname, "r", locking=False) as handle:
                 out_dict["Attributes"] = {}
                 attributes = handle.attrs
                 for k in set(attributes.keys()) - {self.HTTP_REPR, self.REPR, self.URL}:
@@ -2202,7 +2304,7 @@ class HexrdMaterials(H5):
     def sniff(self, filename: str) -> bool:
         if super().sniff(filename):
             req = {"AtomData", "Atomtypes", "CrystalSystem", "LatticeParameters"}
-            with h5py.File(filename, "r") as mat_file:
+            with h5py.File(filename, "r", locking=False) as mat_file:
                 for k in mat_file.keys():
                     if isinstance(mat_file[k], h5py._hl.group.Group) and set(mat_file[k].keys()) >= req:
                         return True
@@ -2211,7 +2313,7 @@ class HexrdMaterials(H5):
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
         super().set_meta(dataset, overwrite=overwrite, **kwd)
         try:
-            with h5py.File(dataset.get_file_name(), "r") as mat_file:
+            with h5py.File(dataset.get_file_name(), "r", locking=False) as mat_file:
                 dataset.metadata.materials = list(mat_file.keys())
                 sgn = {}
                 lp = {}
diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py
index 73973abb65a5843e7a37a82b8e9924407d5a818d..9ef0e84ae9ea48f126726d34693e0653ad315a9c 100644
--- a/lib/galaxy/datatypes/constructive_solid_geometry.py
+++ b/lib/galaxy/datatypes/constructive_solid_geometry.py
@@ -5,6 +5,7 @@ Constructive Solid Geometry file formats.
 """
 
 import abc
+import re
 from typing import (
     List,
     Optional,
@@ -29,6 +30,7 @@ from galaxy.datatypes.sniff import (
     FilePrefix,
 )
 from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.xml import GenericXml
 
 if TYPE_CHECKING:
     from io import TextIOBase
@@ -189,9 +191,6 @@ class Vtk:
 
     Binary data must be placed into the file immediately after the newline
     ('\\n') character from the previous ASCII keyword and parameter sequence.
-
-    TODO: only legacy formats are currently supported and support for XML formats
-    should be added.
     """
 
     subtype = ""
@@ -813,3 +812,59 @@ def get_next_line(fh):
         # Discard the rest of the line
         fh.readline()
     return line.strip()
+
+
+class VtkXml(GenericXml):
+    """Format for defining VTK (XML based) and its sub-datatypes. https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html"""
+
+    edam_format = "edam:format_2332"
+    file_ext = "vtkxml"
+
+    # The same MetadataElements are also available for legacy VTK datatypes.
+    MetadataElement(name="vtk_version", default=None, desc="Vtk version", readonly=True, optional=True, visible=True)
+    MetadataElement(name="file_format", default=None, desc="File format", readonly=True, optional=True, visible=True)
+    MetadataElement(name="dataset_type", default=None, desc="Dataset type", readonly=True, optional=True, visible=True)
+
+    def extract_version(self, line: str) -> str:
+        match = re.search(r'version="([^"]+)"', line)
+        if match:
+            return match.group(1)
+        return "?"
+
+    def extract_type(self, line: str) -> str:
+        match = re.search(r'type="([^"]+)"', line)
+        if match:
+            return match.group(1)
+        return "?"
+
+    def set_meta(self, dataset: DatasetProtocol, **kwd) -> None:
+        dataset.metadata.file_format = "XML"
+        with open(dataset.get_file_name(), errors="ignore") as file:
+            # first line might be the xml header, so we take two
+            first_line = file.readline()
+            if first_line.startswith("<?xml"):
+                first_line = file.readline()
+            dataset.metadata.vtk_version = self.extract_version(first_line)
+            dataset.metadata.dataset_type = self.extract_type(first_line)
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        """Set the peek and blurb text for VTK dataset files."""
+        if not dataset.dataset.purged:
+            dataset.peek = "VTK Dataset file"
+            dataset.blurb = f"type {dataset.metadata.dataset_type} version {dataset.metadata.vtk_version}"
+        else:
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disk"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """Check for the key string 'VTKFile' to determine if this is a VTK dataset file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('data.vtu')
+        >>> VtkXml().sniff(fname)
+        True
+        >>> fname = get_test_fname('1.phyloxml')
+        >>> VtkXml().sniff(fname)
+        False
+        """
+        return self._has_root_element_in_prefix(file_prefix, "VTKFile")
diff --git a/lib/galaxy/datatypes/converters/archive_to_directory.xml b/lib/galaxy/datatypes/converters/archive_to_directory.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b9fe422aaa32d1a80399e9fc9df58664f8673b9c
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/archive_to_directory.xml
@@ -0,0 +1,39 @@
+<tool id="CONVERTER_archive_to_directory" name="Unpack archive to directory" version="1.0.0" profile="21.09">
+    <!-- Use compression_utils instead of shell commands (tar/unzip) so we can verify safety of results -->
+    <requirements>
+        <requirement type="package" version="23.2.1">galaxy-util</requirement>
+    </requirements>
+    <command><![CDATA[
+        mkdir '$output1.files_path' &&
+        cd '$output1.files_path' &&
+        python -c "from galaxy.util.compression_utils import CompressedFile; CompressedFile('$input1').extract('.')"
+    ]]></command>
+    <configfiles>
+        <configfile filename="metadata_json"><![CDATA[{
+    "output1": {
+        "name": "$input1.name unpacked to $__target_datatype__",
+        "ext": "$__target_datatype__"
+    }
+}]]></configfile>
+    </configfiles>
+    <inputs>
+        <param format="tar,zip" name="input1" type="data"/>
+        <param name="__target_datatype__" type="select" label="Target data type">
+            <option value="directory">directory</option>
+            <option value="zarr">zarr</option>
+            <option value="ome_zarr">ome_zarr</option>
+        </param>
+    </inputs>
+    <outputs provided_metadata_file="metadata_json">
+        <data format="auto" name="output1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" ftype="tar" value="testdir1.tar"/>
+            <param name="__target_datatype__" value="directory"/>
+            <output name="output1" ftype="directory" value="testdir1.tar.directory"/>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
index 2f94c32737c25f6527071fefe6aa4078b7e1793a..dd16fe1a2fa744a20d6fc3b9377e10af4ef667c9 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
@@ -5,7 +5,7 @@
     </requirements>
     <command><![CDATA[
         ln -s '$bgzip' input.bgz &&
-        tabix 
+        tabix
         #if $input1.is_of_type('bed')
             -p bed
         #elif $input1.is_of_type('vcf')
@@ -23,7 +23,7 @@
         if [ ! -s input.bgz.tbi ]; then
             >&2 echo "The converted tabix index file is empty, meaning the input data is invalid.";
             exit 1;
-        fi 
+        fi
         &&
         tabix -l input.bgz
     ]]></command>
@@ -40,12 +40,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" ftype="bed" value="droPer1.bed"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="133"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="bed" value="droPer1.bed" />
+            <param name="bgzip" ftype="bgzip" value="droPer1.bed.gz" />
             <assert_command>
                 <has_text text="-p bed"/>
             </assert_command>
@@ -54,12 +50,8 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="110" delta="10"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="encodepeak" value="encode.broad.peak" />
+            <param name="bgzip" ftype="bgzip" value="encode.broad.peak.gz" />
             <assert_command>
                 <has_text text="-p" negate="true"/>
             </assert_command>
@@ -68,12 +60,8 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="120"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff" />
+            <param name="bgzip" ftype="bgzip" value="gff_filter_by_feature_count_out2.gff.gz" />
             <assert_command>
                 <has_text text="-p gff"/>
             </assert_command>
@@ -82,12 +70,8 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="input1" ftype="interval" value="2.interval"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="247"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="interval" value="2.interval" />
+            <param name="bgzip" ftype="bgzip" value="2.interval.gz" />
             <assert_command>
                 <has_text text="-p" negate="true"/>
             </assert_command>
@@ -96,12 +80,8 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="143"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf" />
+            <param name="bgzip" ftype="bgzip" value="vcf_to_maf_in.vcf.gz" />
             <assert_command>
                 <has_text text="-p vcf"/>
             </assert_command>
@@ -110,16 +90,15 @@
             </assert_stdout>
         </test>
         <test>
-            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
-            <output name="output1" ftype="tabix">
-                <assert_contents>
-                    <has_size value="125"/>
-                </assert_contents>
-            </output>
+            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf" />
+            <param name="bgzip" ftype="bgzip" value="cufflinks_out1.gtf.gz" />
             <assert_command>
-                <has_text text="-p gff"/>
+                <has_text text="-p gff" />
             </assert_command>
-        </test>        
+            <assert_stdout>
+                <has_line line="test_chromosome" />
+            </assert_stdout>
+        </test>
     </tests>
     <help>
     </help>
diff --git a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
index 0da3c04f42f18434ef9623e7c4a5bb9bbd123cbf..7b95b9a296148704f1fcdef46d3ceac999cb896d 100644
--- a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
+++ b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
@@ -15,7 +15,9 @@
   <tests>
     <test>
       <!-- TODO mock test? $output1 should be the html primary file? -->
-      <param name="input1" ftype="neostore.zip" value="neostore.zip"/>
+      <param name="input1" value="" ftype="neostore.zip">
+        <composite_data value="neostore.zip" />
+      </param>
       <output name="output1" ftype="neostore">
         <assert_contents>
           <has_n_lines n="2"/>
diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index 59354b39b5fdcaea93da87c8e7b48be8081e5113..0160746283dae2bf15670ad9ffdc5fddfb47496d 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
     <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
     <requirements>
-        <requirement type="package" version="23.1">galaxy-util</requirement>
+        <requirement type="package" version="23.2.1">galaxy-util</requirement>
     </requirements>
     <command>
         mkdir '$output1.files_path';
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 984f187c835744ed8f5b999958270781aaada63a..f74003f1dd897ae8d46ed5960c0db0202a2c2b8b 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -1,3 +1,4 @@
+import json
 import logging
 import mimetypes
 import os
@@ -49,6 +50,7 @@ from galaxy.util import (
     FILENAME_VALID_CHARS,
     inflector,
     iter_start_of_line,
+    to_content_disposition,
     unicodify,
     UNKNOWN,
 )
@@ -58,7 +60,6 @@ from galaxy.util.markdown import (
     indicate_data_truncated,
     literal_via_fence,
 )
-from galaxy.util.sanitize_html import sanitize_html
 from galaxy.util.zipstream import ZipstreamWrapper
 from . import (
     dataproviders as p_dataproviders,
@@ -171,7 +172,7 @@ def _get_max_peek_size(data):
 
     max_peek_size = DEFAULT_MAX_PEEK_SIZE  # 1 MB
     if isinstance(data.datatype, text.Html):
-        max_peek_size = 10000000  # 10 MB for html
+        max_peek_size = 50000000  # 50 MB for html
     elif isinstance(data.datatype, binary.Binary):
         max_peek_size = 100000  # 100 KB for binary
     return max_peek_size
@@ -208,6 +209,7 @@ class Data(metaclass=DataMeta):
     edam_data = "data_0006"
     edam_format = "format_1915"
     file_ext = "data"
+    is_subclass = False
     # Data is not chunkable by default.
     CHUNKABLE = False
 
@@ -437,7 +439,7 @@ class Data(metaclass=DataMeta):
             element_identifier=kwd.get("element_identifier"),
             filename_pattern=kwd.get("filename_pattern"),
         )
-        headers["Content-Disposition"] = f'attachment; filename="{filename}"'
+        headers["Content-Disposition"] = to_content_disposition(filename)
         return open(dataset.get_file_name(), mode="rb"), headers
 
     def to_archive(self, dataset: DatasetProtocol, name: str = "", user=None) -> Iterable:
@@ -467,6 +469,8 @@ class Data(metaclass=DataMeta):
         composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
         composite_extensions.append("html")  # for archiving composite datatypes
         composite_extensions.append("data_manager_json")  # for downloading bundles if bundled.
+        composite_extensions.append("directory")  # for downloading directories.
+        composite_extensions.append("zarr")  # for downloading zarr directories.
 
         if data.extension in composite_extensions:
             return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get("do_action", "zip"))
@@ -482,7 +486,8 @@ class Data(metaclass=DataMeta):
             headers["content-type"] = (
                 "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
             )
-            headers["Content-Disposition"] = f'attachment; filename="{filename}"'
+
+            headers["Content-Disposition"] = to_content_disposition(filename)
             return open(data.get_file_name(user=trans.user), "rb"), headers
 
     def _serve_binary_file_contents_as_text(self, trans, data, headers, file_size, max_peek_size):
@@ -636,21 +641,18 @@ class Data(metaclass=DataMeta):
         return result
 
     def _yield_user_file_content(self, trans, from_dataset: HasCreatingJob, filename: str, headers: Headers) -> IO:
-        """This method is responsible for sanitizing the HTML if needed."""
+        """This method sets the content type header to text/plain if we don't trust html content."""
         if trans.app.config.sanitize_all_html and headers.get("content-type", None) == "text/html":
-            # Sanitize anytime we respond with plain text/html content.
             # Check to see if this dataset's parent job is allowlisted
             # We cannot currently trust imported datasets for rendering.
-            if not from_dataset.creating_job.imported and from_dataset.creating_job.tool_id.startswith(
-                tuple(trans.app.config.sanitize_allowlist)
-            ):
-                return open(filename, mode="rb")
-
-            # This is returning to the browser, it needs to be encoded.
-            # TODO Ideally this happens a layer higher, but this is a bad
-            # issue affecting many tools
-            with open(filename) as f:
-                return sanitize_html(f.read()).encode("utf-8")
+            content_type = "text/html"
+            if from_dataset.creating_job.imported:
+                content_type = "text/plain"
+                headers["x-sanitized-job-imported"] = True
+            if not from_dataset.creating_job.tool_id.startswith(tuple(trans.app.config.sanitize_allowlist)):
+                content_type = "text/plain"
+                headers["x-sanitized-tool-id"] = from_dataset.creating_job.tool_id
+            headers["content-type"] = content_type
 
         return open(filename, mode="rb")
 
@@ -662,16 +664,13 @@ class Data(metaclass=DataMeta):
         element_identifier: Optional[str] = None,
         filename_pattern: Optional[str] = None,
     ) -> str:
-        def escape(raw_identifier):
-            return "".join(c in FILENAME_VALID_CHARS and c or "_" for c in raw_identifier)[0:150]
-
         if not to_ext or to_ext == "data":
             # If a client requests to_ext with the extension 'data', they are
             # deferring to the server, set it based on datatype.
             to_ext = dataset.extension
 
         template_values = {
-            "name": escape(dataset.name),
+            "name": dataset.name,
             "ext": to_ext,
             "hid": dataset.hid,
         }
@@ -684,8 +683,9 @@ class Data(metaclass=DataMeta):
 
         if hdca is not None:
             # Use collection context to build up filename.
-            template_values["element_identifier"] = element_identifier
-            template_values["hdca_name"] = escape(hdca.name)
+            if element_identifier is not None:
+                template_values["element_identifier"] = element_identifier
+            template_values["hdca_name"] = hdca.name
             template_values["hdca_hid"] = hdca.hid
 
         return string.Template(filename_pattern).substitute(**template_values)
@@ -853,7 +853,11 @@ class Data(metaclass=DataMeta):
         job, converted_datasets, *_ = converter.execute(
             trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
         )
+        # We should only have a single converted output, but let's be defensive here
+        n_converted_datasets = len(converted_datasets)
         for converted_dataset in converted_datasets.values():
+            if converted_dataset.extension == "auto" and n_converted_datasets == 1:
+                converted_dataset.extension = target_type
             original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
         trans.app.job_manager.enqueue(job, tool=converter)
         if len(params) > 0:
@@ -1217,6 +1221,142 @@ class Text(Data):
 class Directory(Data):
     """Class representing a directory of files."""
 
+    file_ext = "directory"
+
+    def _archive_main_file(
+        self, archive: ZipstreamWrapper, display_name: str, data_filename: str
+    ) -> Tuple[bool, str, str]:
+        """Overwrites the method to not do anything.
+
+        No main file gets added to a directory archive.
+        """
+        error, msg, messagetype = False, "", ""
+        return error, msg, messagetype
+
+
+class ZarrDirectory(Directory):
+    """Class representing a zarr-format structure with general-purpose numeric content."""
+
+    edam_format = "format_3915"
+    file_ext = "zarr"
+
+    # This wouldn't be needed if the CompressedFile.extract function didn't
+    # create an extra folder under the dataset's extra_files_path.
+    # Maybe this can be avoided somehow?
+    MetadataElement(
+        name="store_root",
+        default=None,
+        desc="Name of the root folder where the zarr store is located",
+        readonly=True,
+        optional=False,
+        visible=False,
+    )
+
+    MetadataElement(
+        name="zarr_format",
+        default=None,
+        desc="Zarr format version",
+        readonly=True,
+        optional=False,
+        visible=False,
+    )
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.blurb = f"Format v{dataset.metadata.zarr_format}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        store_root_folder = self._find_store_root_folder_name(dataset)
+        if store_root_folder is None:
+            log.debug("Directory structure does not look like Zarr format")
+            return
+        dataset.metadata.store_root = store_root_folder
+
+        root_directory = os.path.join(dataset.extra_files_path, store_root_folder)
+        format_version = self._get_format_version(root_directory)
+        if not format_version:
+            log.debug("Could not determine Zarr format version")
+            return
+        dataset.metadata.zarr_format = format_version
+
+    def sniff(self, filename: str) -> bool:
+        # TO DO: Can we access extra files path from here? Otherwise it cannot be auto-detected.
+        return False
+
+    def display_data(
+        self,
+        trans,
+        dataset: DatasetHasHidProtocol,
+        preview: bool = False,
+        filename: Optional[str] = None,
+        to_ext: Optional[str] = None,
+        **kwd,
+    ):
+        if preview:
+            store_root_path = os.path.join(dataset.extra_files_path, dataset.metadata.store_root)
+            metadata_file_path = self._find_zarr_metadata_file(store_root_path)
+            if metadata_file_path:
+                headers = kwd.get("headers", {})
+                headers["content-type"] = "application/json"
+                return self._yield_user_file_content(trans, dataset, metadata_file_path, headers), headers
+
+        return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)
+
+    def _find_store_root_folder_name(self, dataset: DatasetProtocol) -> Optional[str]:
+        """Returns the name of the root folder where the Zarr store is located.
+
+        The Zarr store can be directly in the extra files folder or in a subfolder.
+        """
+        extra_files_path = dataset.extra_files_path
+        if self._find_zarr_metadata_file(extra_files_path):
+            return ""  # The store is in the root of the extra files folder
+        items_in_path = os.listdir(extra_files_path)
+        sub_folder_name = items_in_path[0]
+        zarr_store_path = os.path.join(extra_files_path, sub_folder_name)
+        if (
+            len(items_in_path) == 1
+            and os.path.isdir(zarr_store_path)
+            and self._find_zarr_metadata_file(zarr_store_path)
+        ):
+            return sub_folder_name  # The store is in a subfolder of the extra files folder
+        return None  # The directory structure does not look like Zarr format
+
+    def _load_zarr_metadata_file(self, store_root_path: str) -> Optional[Dict[str, Any]]:
+        """Returns the path to the metadata file in the Zarr store."""
+        meta_file = self._find_zarr_metadata_file(store_root_path)
+        if meta_file:
+            with open(meta_file) as f:
+                return json.load(f)
+        return None
+
+    def _find_zarr_metadata_file(self, store_root_path: str) -> Optional[str]:
+        """Returns the path to the metadata file in the Zarr store."""
+        meta_file = None
+        files_in_store = os.listdir(store_root_path)
+
+        # Depending on the Zarr version, the metadata file can be in different locations
+        # In v1 the metadata is in a file named "meta" https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html
+        # In v2 it can be in .zarray or .zgroup https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html
+        # In v3 the metadata is in a file named "zarr.json" https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html
+        for meta_filename in ["meta", ".zarray", ".zgroup", "zarr.json"]:
+            if meta_filename in files_in_store:
+                meta_file = os.path.join(store_root_path, meta_filename)
+                break
+
+        if meta_file and os.path.isfile(meta_file):
+            return meta_file
+        return None
+
+    def _get_format_version(self, store_root_path: str) -> Optional[str]:
+        """Returns the Zarr format version from the metadata file in the Zarr store."""
+        metadata_file = self._load_zarr_metadata_file(store_root_path)
+        if metadata_file:
+            return metadata_file.get("zarr_format")
+        return None
+
 
 class GenericAsn1(Text):
     """Class for generic ASN.1 text format"""
diff --git a/lib/galaxy/datatypes/dataproviders/base.py b/lib/galaxy/datatypes/dataproviders/base.py
index c1239f86b9ff790e3eb4b591eb3c8bdab8256a3a..a271437f184e58e2f859e06e4241676a8d2dee9f 100644
--- a/lib/galaxy/datatypes/dataproviders/base.py
+++ b/lib/galaxy/datatypes/dataproviders/base.py
@@ -36,6 +36,7 @@ datasets API entry point:
         Building a giant list by sweeping all possible dprov classes doesn't make sense
     For now - I'm burying them in the class __init__s - but I don't like that
 """
+MAX_LIMIT = 10000
 
 
 # ----------------------------------------------------------------------------- base classes
@@ -233,21 +234,20 @@ class LimitedOffsetDataProvider(FilteredDataProvider):
     settings = {"limit": "int", "offset": "int"}
 
     # TODO: may want to squash this into DataProvider
-    def __init__(self, source, offset=0, limit=None, **kwargs):
+    def __init__(self, source, offset=0, limit=MAX_LIMIT, **kwargs):
         """
         :param offset:  the number of data to skip before providing.
         :param limit:   the final number of data to provide.
         """
         super().__init__(source, **kwargs)
 
-        # how many valid data to skip before we start outputing data - must be positive
-        #   (diff to support neg. indeces - must be pos.)
-        self.offset = max(offset, 0)
+        # how many valid data to skip before we start outputting data - must be positive
+        self.offset = offset
 
-        # how many valid data to return - must be positive (None indicates no limit)
+        # how many valid data to return - must be positive
+        if limit is None:
+            limit = MAX_LIMIT
         self.limit = limit
-        if self.limit is not None:
-            self.limit = max(self.limit, 0)
 
     def __iter__(self):
         """
diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py
index bd2d46262d5b3e55a4116e24ff038953892a565c..392b102b2892744cca7d41386b1fb3d92e03e7e2 100644
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -14,6 +14,7 @@ from bx import (
     wiggle as bx_wig,
 )
 
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.util import sqlite
 from galaxy.util.compression_utils import get_fileobj
 from . import (
@@ -716,7 +717,11 @@ class SQliteDataProvider(base.DataProvider):
 
     def __init__(self, source, query=None, **kwargs):
         self.query = query
-        self.connection = sqlite.connect(source.dataset.get_file_name())
+        datatype = source.datatype
+        file_name = source.dataset.get_file_name()
+        if not datatype.sniff(file_name):
+            raise RequestParameterInvalidException("Dataset is not a SQlite file, cannot fetch data.")
+        self.connection = sqlite.connect(file_name)
         super().__init__(source, **kwargs)
 
     def __iter__(self):
diff --git a/lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml b/lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml
index 787a4b3ef4dcb924aed92464d49cf287d63032f1..4c5d4e10f1597b95ec578e47ead62b7350607572 100644
--- a/lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml
+++ b/lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml
@@ -2,6 +2,6 @@
 <display id="biom_simple" version="1.0.0" name="view biom at">
     <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name">
         <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url>
-        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" />
+        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" allow_cors="true" />
     </dynamic_links>
 </display>
diff --git a/lib/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml b/lib/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml
index 1035cbb679a05690aab1ecb80f77b8973a311fed..5cbba046610c2d65ab20887b8c439abbe1560700 100644
--- a/lib/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml
+++ b/lib/galaxy/datatypes/display_applications/configs/qiime/qiime2/q2view.xml
@@ -2,6 +2,6 @@
 <display id="q2view" version="1.0.0" name="view at">
     <dynamic_links from_data_table="q2view_display" skip_startswith="#" id="value" name="name">
         <url>${ url % { 'q2view_file_url_qp': $q2view_file.qp } }</url>
-        <param type="data" name="q2view_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
+        <param type="data" name="q2view_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" allow_cors="true"/>
     </dynamic_links>
 </display>
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 83136fcb7b9e212b05b5415b978477a74ef5b2c9..1ce24261aebffaceddfab852fbc0190b5c4cd092 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -334,7 +334,6 @@ class Rgenetics(Html):
         ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            f, e = os.path.splitext(fname)
             rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append("</ul></body></html>")
         with open(dataset.get_file_name(), "w") as f:
@@ -864,16 +863,15 @@ class RexpBase(Html):
         pp = os.path.join(dataset.extra_files_path, pn)
         dataset.metadata.pheno_path = pp
         try:
-            with open(pp) as f:
-                pf = f.readlines()  # read the basename.phenodata in the extra_files_path
+            with open(pp) as file:
+                pf = file.readlines()  # read the basename.phenodata in the extra_files_path
         except Exception:
             pf = None
         if pf:
-            h = pf[0].strip()
-            h = h.split("\t")  # hope is header
-            h = [escape(x) for x in h]
-            dataset.metadata.column_names = h
-            dataset.metadata.columns = len(h)
+            header = pf[0].strip()
+            columns = [escape(x) for x in header.split("\t")]  # hope is header
+            dataset.metadata.column_names = columns
+            dataset.metadata.columns = len(columns)
             dataset.peek = "".join(pf[:5])
         else:
             dataset.metadata.column_names = []
diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py
index e61efeaca05a4a837315e762ba2c251740e05c52..c44a294f07f29a81d611f94ca63b56920106d94d 100644
--- a/lib/galaxy/datatypes/images.py
+++ b/lib/galaxy/datatypes/images.py
@@ -127,6 +127,24 @@ class OMETiff(Tiff):
         return False
 
 
+class OMEZarr(data.ZarrDirectory):
+    """OME-Zarr is a format for storing multi-dimensional image data in Zarr format.
+
+    It is technically a Zarr directory with custom metadata but stores image information
+    so it is an Image datatype.
+    """
+
+    file_ext = "ome_zarr"
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = "OME-Zarr directory"
+            dataset.blurb = f"Zarr Format v{dataset.metadata.zarr_format}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+
 class Hamamatsu(Image):
     file_ext = "vms"
 
diff --git a/lib/galaxy/datatypes/isa.py b/lib/galaxy/datatypes/isa.py
index 5d1b88d30d942ceb8fab60eaef7983eeb54bc659..c2c710a229fbe8b10559f45246790540e93c6478 100644
--- a/lib/galaxy/datatypes/isa.py
+++ b/lib/galaxy/datatypes/isa.py
@@ -17,12 +17,22 @@ from typing import (
     TYPE_CHECKING,
 )
 
-# Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
-logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
-from isatools import (
-    isajson,
-    isatab_meta,
-)
+logger = logging.getLogger(__name__)
+
+ISA_MISSING_MODULE_MESSAGE = "Please install the missing isatools dependency from `isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master`"
+
+try:
+    # Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
+    logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
+    from isatools import (
+        isajson,
+        isatab_meta,
+    )
+except ImportError:
+    isajson = None
+    isatab_meta = None
+    logger.exception(ISA_MISSING_MODULE_MESSAGE)
+
 from markupsafe import escape
 
 from galaxy import util
@@ -39,9 +49,6 @@ from galaxy.util.sanitize_html import sanitize_html
 if TYPE_CHECKING:
     from isatools.model import Investigation
 
-# CONSTANTS {{{1
-################################################################
-
 # Main files regex
 JSON_FILE_REGEX = re.compile(r"^.*\.json$", flags=re.IGNORECASE)
 INVESTIGATION_FILE_REGEX = re.compile(r"^i_\w+\.txt$", flags=re.IGNORECASE)
@@ -52,18 +59,6 @@ ISA_ARCHIVE_NAME = "archive"
 # Set max number of lines of the history peek
 _MAX_LINES_HISTORY_PEEK = 11
 
-# Configure logger {{{1
-################################################################
-
-logger = logging.getLogger(__name__)
-
-# Function for opening correctly a CSV file for csv.reader() for both Python 2 and 3 {{{1
-################################################################
-
-
-# ISA class {{{1
-################################################################
-
 
 class _Isa(Data):
     """Base class for implementing ISA datatypes"""
@@ -71,15 +66,9 @@ class _Isa(Data):
     composite_type = "auto_primary_file"
     is_binary = True
 
-    # Make investigation instance {{{2
-    ################################################################
-
     def _make_investigation_instance(self, filename: str) -> "Investigation":
         raise NotImplementedError()
 
-    # Constructor {{{2
-    ################################################################
-
     def __init__(self, main_file_regex: re.Pattern, **kwd) -> None:
         super().__init__(**kwd)
         self._main_file_regex = main_file_regex
@@ -87,57 +76,34 @@ class _Isa(Data):
         # Add the archive file as the only composite file
         self.add_composite_file(ISA_ARCHIVE_NAME, is_binary=True, optional=True)
 
-    # Get ISA folder path {{{2
-    ################################################################
-
     def _get_isa_folder_path(self, dataset: HasExtraFilesPath) -> str:
         isa_folder = dataset.extra_files_path
         if not isa_folder:
             raise Exception("Unvalid dataset object, or no extra files path found for this dataset.")
         return isa_folder
 
-    # Get main file {{{2
-    ################################################################
-
-    def _get_main_file(self, dataset: HasExtraFilesPath) -> Optional[str]:
+    def _get_main_file(self, dataset: HasExtraFilesPath) -> str:
         """Get the main file of the ISA archive. Either the investigation file i_*.txt for ISA-Tab, or the JSON file for ISA-JSON."""
 
         main_file = None
         isa_folder = self._get_isa_folder_path(dataset)
+        assert os.path.exists(isa_folder)
 
-        if os.path.exists(isa_folder):
-            # Get ISA archive older
-            isa_files = os.listdir(isa_folder)
+        # Get ISA archive older
+        isa_files = os.listdir(isa_folder)
 
-            # Try to find main file
-            main_file = self._find_main_file_in_archive(isa_files)
+        main_file = self._find_main_file_in_archive(isa_files)
+        # Make full path
+        return os.path.join(isa_folder, main_file)
 
-            if main_file is None:
-                raise Exception("Invalid ISA archive. No main file found.")
-
-            # Make full path
-            assert main_file
-            main_file = os.path.join(isa_folder, main_file)
-
-        return main_file
-
-    # Get investigation {{{2
-    ################################################################
-
-    def _get_investigation(self, dataset: HasExtraFilesPath) -> Optional["Investigation"]:
+    def _get_investigation(self, dataset: HasExtraFilesPath) -> "Investigation":
         """Create a contained instance specific to the exact ISA type (Tab or Json).
         We will use it to parse and access information from the archive."""
 
-        investigation = None
-        if (main_file := self._get_main_file(dataset)) is not None:
-            investigation = self._make_investigation_instance(main_file)
-
-        return investigation
-
-    # Find main file in archive {{{2
-    ################################################################
+        main_file = self._get_main_file(dataset)
+        return self._make_investigation_instance(main_file)
 
-    def _find_main_file_in_archive(self, files_list: List) -> Optional[str]:
+    def _find_main_file_in_archive(self, files_list: List) -> str:
         """Find the main file inside the ISA archive."""
 
         found_file = None
@@ -150,24 +116,17 @@ class _Isa(Data):
                     found_file = matched if isinstance(matched, str) else matched[0]
                 else:
                     raise Exception(
-                        'More than one file match the pattern "',
-                        str(self._main_file_regex),
-                        '" to identify the investigation file',
+                        f"More than one file match the pattern '{self._main_file_regex}' to identify the investigation file"
                     )
-
+        if found_file is None:
+            raise Exception("Invalid ISA archive. No main file found.")
         return found_file
 
-    # Set peek {{{2
-    ################################################################
-
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
         """Set the peek and blurb text. Get first lines of the main file and set it as the peek."""
 
         main_file = self._get_main_file(dataset)
 
-        if main_file is None:
-            raise RuntimeError("Unable to find the main file within the 'files_path' folder")
-
         # Read first lines of main file
         with open(main_file, encoding="utf-8") as f:
             data: List = []
@@ -183,9 +142,6 @@ class _Isa(Data):
                 dataset.peek = "file does not exist"
                 dataset.blurb = "file purged from disk"
 
-    # Display peek {{{2
-    ################################################################
-
     def display_peek(self, dataset: DatasetProtocol) -> str:
         """Create the HTML table used for displaying peek, from the peek text found by set_peek() method."""
 
@@ -204,9 +160,6 @@ class _Isa(Data):
         except Exception as exc:
             return f"Can't create peek: {util.unicodify(exc)}"
 
-    # Generate primary file {{{2
-    ################################################################
-
     def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         """Generate the primary file. It is an HTML file containing description of the composite dataset
         as well as a list of the composite files that it contains."""
@@ -223,16 +176,10 @@ class _Isa(Data):
             return "\n".join(rval)
         return "<div>No dataset available</div>"
 
-    # Dataset content needs grooming {{{2
-    ################################################################
-
     def dataset_content_needs_grooming(self, file_name: str) -> bool:
         """This function is called on an output dataset file after the content is initially generated."""
         return os.path.basename(file_name) == ISA_ARCHIVE_NAME
 
-    # Groom dataset content {{{2
-    ################################################################
-
     def groom_dataset_content(self, file_name: str) -> None:
         """This method is called by Galaxy to extract files contained in a composite data type."""
         # XXX Is the right place to extract files? Should this step not be a cleaning step instead?
@@ -260,9 +207,6 @@ class _Isa(Data):
             else:
                 shutil.move(temp_folder, output_path)
 
-    # Display data {{{2
-    ################################################################
-
     def display_data(
         self,
         trans,
@@ -287,8 +231,10 @@ class _Isa(Data):
         dataset.get_file_name(user=trans.user)
 
         # prepare the preview of the ISA dataset
-        investigation = self._get_investigation(dataset)
-        if investigation is None:
+        try:
+            investigation = self._get_investigation(dataset)
+        except Exception:
+            logger.exception(f"Failed to display dataset {dataset.id}")
             html = """<html><header><title>Error while reading ISA archive.</title></header>
                    <body>
                         <h1>An error occurred while reading content of ISA archive.</h1>
@@ -332,23 +278,15 @@ class _Isa(Data):
         return sanitize_html(html).encode("utf-8"), headers
 
 
-# ISA-Tab class {{{1
-################################################################
-
-
 class IsaTab(_Isa):
     file_ext = "isa-tab"
 
-    # Constructor {{{2
-    ################################################################
-
     def __init__(self, **kwd):
         super().__init__(main_file_regex=INVESTIGATION_FILE_REGEX, **kwd)
 
-    # Make investigation instance {{{2
-    ################################################################
-
-    def _make_investigation_instance(self, filename: str) -> "Investigation":
+    def _make_investigation_instance(self, filename: str):
+        if not isatab_meta:
+            raise Exception(ISA_MISSING_MODULE_MESSAGE)
         # Parse ISA-Tab investigation file
         parser = isatab_meta.InvestigationParser()
         isa_dir = os.path.dirname(filename)
@@ -365,23 +303,15 @@ class IsaTab(_Isa):
         return isa
 
 
-# ISA-JSON class {{{1
-################################################################
-
-
 class IsaJson(_Isa):
     file_ext = "isa-json"
 
-    # Constructor {{{2
-    ################################################################
-
     def __init__(self, **kwd):
         super().__init__(main_file_regex=JSON_FILE_REGEX, **kwd)
 
-    # Make investigation instance {{{2
-    ################################################################
-
-    def _make_investigation_instance(self, filename: str) -> "Investigation":
+    def _make_investigation_instance(self, filename: str):
+        if not isajson:
+            raise Exception(ISA_MISSING_MODULE_MESSAGE)
         # Parse JSON file
         with open(filename, newline="", encoding="utf8") as fp:
             isa = isajson.load(fp)
diff --git a/lib/galaxy/datatypes/protocols.py b/lib/galaxy/datatypes/protocols.py
index ae3df71a6ccfa6fcddecc7dab4992d4a476d5c65..db922fa6ce0b2fae6c8bc12cd8165bd9c820b5a9 100644
--- a/lib/galaxy/datatypes/protocols.py
+++ b/lib/galaxy/datatypes/protocols.py
@@ -27,7 +27,7 @@ class HasExt(Protocol):
 
 class HasExtraFilesPath(Protocol):
     @property
-    def extra_files_path(self): ...
+    def extra_files_path(self) -> str: ...
 
 
 class HasFileName(Protocol):
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 671f30d82e168446f1dd9f66ca88553fb14c3306..0789b0dd9ee5c9eb8d10e25185e57c90c8e1fd42 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -6,15 +6,16 @@ import importlib.util
 import logging
 import os
 import pkgutil
-from pathlib import Path
 from string import Template
 from typing import (
+    Any,
     cast,
     Dict,
     Iterable,
     List,
     Optional,
     Tuple,
+    Type,
     TYPE_CHECKING,
     Union,
 )
@@ -24,8 +25,12 @@ import yaml
 import galaxy.util
 from galaxy.datatypes.protocols import DatasetProtocol
 from galaxy.tool_util.edam_util import load_edam_tree
-from galaxy.util import RW_R__R__
+from galaxy.util import (
+    Element,
+    RW_R__R__,
+)
 from galaxy.util.bunch import Bunch
+from galaxy.util.path import StrPath
 from . import (
     binary,
     coverage,
@@ -43,6 +48,7 @@ from .display_applications.application import DisplayApplication
 
 if TYPE_CHECKING:
     from galaxy.datatypes.data import Data
+    from galaxy.tool_util.toolbox.base import AbstractToolBox
 
 
 class ConfigurationError(Exception):
@@ -65,7 +71,7 @@ class Registry:
         self.log.addHandler(logging.NullHandler())
         self.config = config
         self.edam = edam
-        self.datatypes_by_extension = {}
+        self.datatypes_by_extension: Dict[str, Data] = {}
         self.datatypes_by_suffix_inferences = {}
         self.mimetypes_by_extension = {}
         self.datatype_converters = {}
@@ -75,7 +81,7 @@ class Registry:
         self.converter_deps = {}
         self.available_tracks = []
         self.set_external_metadata_tool = None
-        self.sniff_order = []
+        self.sniff_order: List[Data] = []
         self.upload_file_formats = []
         # Datatype elements defined in local datatypes_conf.xml that contain display applications.
         self.display_app_containers = []
@@ -92,7 +98,7 @@ class Registry:
         self.inherit_display_application_by_class = []
         self.datatype_elems = []
         self.datatype_info_dicts = []
-        self.sniffer_elems = []
+        self.sniffer_elems: List[Element] = []
         self._registry_xml_string = None
         self._edam_formats_mapping = None
         self._edam_data_mapping = None
@@ -104,13 +110,13 @@ class Registry:
 
     def load_datatypes(
         self,
-        root_dir=None,
-        config=None,
-        override=True,
-        use_converters=True,
-        use_display_applications=True,
-        use_build_sites=True,
-    ):
+        root_dir: Optional[StrPath] = None,
+        config: Optional[Union[Element, StrPath]] = None,
+        override: bool = True,
+        use_converters: bool = True,
+        use_display_applications: bool = True,
+        use_build_sites: bool = True,
+    ) -> None:
         """
         Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within
         an installed Tool Shed repository.
@@ -127,8 +133,8 @@ class Registry:
             return module
 
         if root_dir and config:
-            compressed_sniffers = {}
-            if isinstance(config, (str, Path)):
+            compressed_sniffers: Dict[Type[Data], List[Data]] = {}
+            if isinstance(config, (str, os.PathLike)):
                 # Parse datatypes_conf.xml
                 tree = galaxy.util.parse_xml(config)
                 root = tree.getroot()
@@ -137,6 +143,7 @@ class Registry:
             else:
                 root = config
             registration = root.find("registration")
+            assert registration is not None
             # Set default paths defined in local datatypes_conf.xml.
             if use_converters:
                 if not self.converters_path:
@@ -167,7 +174,6 @@ class Registry:
 
             for elem in registration.findall("datatype"):
                 # Keep a status of the process steps to enable stopping the process of handling the datatype if necessary.
-                ok = True
                 extension = self.get_extension(elem)
                 dtype = elem.get("type", None)
                 type_extension = elem.get("type_extension", None)
@@ -199,7 +205,9 @@ class Registry:
                         if override or extension not in self.datatypes_by_extension:
                             can_process_datatype = True
                 if can_process_datatype:
+                    datatype_class: Optional[Type[Data]] = None
                     if dtype is not None:
+                        ok = True
                         try:
                             fields = dtype.split(":")
                             datatype_module = fields[0]
@@ -208,21 +216,18 @@ class Registry:
                             self.log.exception("Error parsing datatype definition for dtype %s", str(dtype))
                             ok = False
                         if ok:
-                            datatype_class = None
-                            if datatype_class is None:
-                                try:
-                                    # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
-                                    fields = datatype_module.split(".")[1:]
-                                    module = __import__(datatype_module)
-                                    for mod in fields:
-                                        module = getattr(module, mod)
-                                    datatype_class = getattr(module, datatype_class_name)
-                                    self.log.debug(
-                                        f"Retrieved datatype module {str(datatype_module)}:{datatype_class_name} from the datatype registry for extension {extension}."
-                                    )
-                                except Exception:
-                                    self.log.exception("Error importing datatype module %s", str(datatype_module))
-                                    ok = False
+                            try:
+                                # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
+                                fields = datatype_module.split(".")[1:]
+                                module = __import__(datatype_module)
+                                for mod in fields:
+                                    module = getattr(module, mod)
+                                datatype_class = getattr(module, datatype_class_name)
+                                self.log.debug(
+                                    f"Retrieved datatype module {str(datatype_module)}:{datatype_class_name} from the datatype registry for extension {extension}."
+                                )
+                            except Exception:
+                                self.log.exception("Error importing datatype module %s", str(datatype_module))
                     elif type_extension is not None:
                         try:
                             datatype_class = self.datatypes_by_extension[type_extension].__class__
@@ -233,8 +238,7 @@ class Registry:
                             self.log.exception(
                                 "Error determining datatype_class for type_extension %s", str(type_extension)
                             )
-                            ok = False
-                    if ok:
+                    if datatype_class:
                         # A new tool shed repository that contains custom datatypes is being installed, and since installation is
                         # occurring after the datatypes registry has been initialized at server startup, its contents cannot be
                         # overridden by new introduced conflicting data types unless the value of override is True.
@@ -262,7 +266,7 @@ class Registry:
                         for upload_warning_el in upload_warning_els:
                             if upload_warning_template is not None:
                                 raise NotImplementedError("Multiple upload_warnings not implemented")
-                            upload_warning_template = Template(upload_warning_el.text)
+                            upload_warning_template = Template(upload_warning_el.text or "")
                         datatype_instance = datatype_class()
                         self.datatypes_by_extension[extension] = datatype_instance
                         if mimetype is None:
@@ -282,9 +286,9 @@ class Registry:
                         # compressed files in the future (e.g. maybe some day faz will be a compressed fasta
                         # or something along those lines)
                         for infer_from in elem.findall("infer_from"):
-                            suffix = infer_from.get("suffix", None)
+                            suffix = infer_from.get("suffix")
                             if suffix is None:
-                                raise Exception("Failed to parse infer_from datatype element")
+                                raise ConfigurationError("Failed to parse infer_from datatype element")
                             infer_from_suffixes.append(suffix)
                             self.datatypes_by_suffix_inferences[suffix] = datatype_instance
                         for converter in elem.findall("converter"):
@@ -300,9 +304,11 @@ class Registry:
                                 self.converters.append((converter_config, extension, target_datatype))
                         # Add composite files.
                         for composite_file in elem.findall("composite_file"):
-                            name = composite_file.get("name", None)
+                            name = composite_file.get("name")
                             if name is None:
-                                self.log.warning(f"You must provide a name for your composite_file ({composite_file}).")
+                                raise ConfigurationError(
+                                    f"You must provide a name for your composite_file ({composite_file})."
+                                )
                             optional = composite_file.get("optional", False)
                             mimetype = composite_file.get("mimetype", None)
                             self.datatypes_by_extension[extension].add_composite_file(
@@ -321,8 +327,8 @@ class Registry:
                         composite_files = datatype_instance.get_composite_files()
                         if composite_files:
                             _composite_files = []
-                            for name, composite_file in composite_files.items():
-                                _composite_file = composite_file.dict()
+                            for name, composite_file_bunch in composite_files.items():
+                                _composite_file = composite_file_bunch.dict()
                                 _composite_file["name"] = name
                                 _composite_files.append(_composite_file)
                             datatype_info_dict["composite_files"] = _composite_files
@@ -332,16 +338,18 @@ class Registry:
                             compressed_extension = f"{extension}.{auto_compressed_type}"
                             upper_compressed_type = auto_compressed_type[0].upper() + auto_compressed_type[1:]
                             auto_compressed_type_name = datatype_class_name + upper_compressed_type
-                            attributes = {}
+                            attributes: Dict[str, Any] = {}
                             if auto_compressed_type == "gz":
-                                dynamic_parent = binary.GzDynamicCompressedArchive
+                                dynamic_parent: Type[binary.DynamicCompressedArchive] = (
+                                    binary.GzDynamicCompressedArchive
+                                )
                             elif auto_compressed_type == "bz2":
                                 dynamic_parent = binary.Bz2DynamicCompressedArchive
                             else:
-                                raise Exception(f"Unknown auto compression type [{auto_compressed_type}]")
+                                raise ConfigurationError(f"Unknown auto compression type [{auto_compressed_type}]")
                             attributes["file_ext"] = compressed_extension
                             attributes["uncompressed_datatype_instance"] = datatype_instance
-                            compressed_datatype_class = type(
+                            compressed_datatype_class: Type[Data] = type(
                                 auto_compressed_type_name,
                                 (
                                     datatype_class,
@@ -411,7 +419,7 @@ class Registry:
                 self._load_build_sites(root)
         self.set_default_values()
 
-        def append_to_sniff_order():
+        def append_to_sniff_order() -> None:
             sniff_order_classes = {type(_) for _ in self.sniff_order}
             for datatype in self.datatypes_by_extension.values():
                 # Add a datatype only if it is not already in sniff_order, it
@@ -482,7 +490,12 @@ class Registry:
     def get_display_sites(self, site_type):
         return self.display_sites.get(site_type, [])
 
-    def load_datatype_sniffers(self, root, override=False, compressed_sniffers=None):
+    def load_datatype_sniffers(
+        self,
+        root: Element,
+        override: bool = False,
+        compressed_sniffers: Optional[Dict[Type["Data"], List["Data"]]] = None,
+    ) -> None:
         """
         Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy
         distributed config) or contained within an installed Tool Shed repository.
@@ -514,17 +527,15 @@ class Registry:
                                 ok = False
                         if ok:
                             try:
-                                aclass = getattr(module, datatype_class_name)()
+                                aclass = getattr(module, datatype_class_name)
                             except Exception:
-                                self.log.exception(
-                                    "Error calling method %s from class %s", str(datatype_class_name), str(module)
-                                )
+                                self.log.exception("Error getting class %s from module %s", datatype_class_name, module)
                                 ok = False
                             if ok:
                                 # We are loading new sniffer, so see if we have a conflicting sniffer already loaded.
                                 conflict = False
-                                for conflict_loc, sniffer_class in enumerate(self.sniff_order):
-                                    if sniffer_class.__class__ == aclass.__class__:
+                                for conflict_loc, sniffer_datatype_instance in enumerate(self.sniff_order):
+                                    if sniffer_datatype_instance.__class__ == aclass:
                                         # We have a conflicting sniffer, so replace the one previously loaded.
                                         conflict = True
                                         if override:
@@ -532,16 +543,15 @@ class Registry:
                                             self.log.debug(f"Removed conflicting sniffer for datatype '{dtype}'")
                                         break
                                 if not conflict or override:
-                                    if compressed_sniffers and aclass.__class__ in compressed_sniffers:
-                                        for compressed_sniffer in compressed_sniffers[aclass.__class__]:
+                                    if compressed_sniffers and aclass in compressed_sniffers:
+                                        for compressed_sniffer in compressed_sniffers[aclass]:
                                             self.sniff_order.append(compressed_sniffer)
-                                    self.sniff_order.append(aclass)
+                                    self.sniff_order.append(aclass())
                                     self.log.debug(f"Loaded sniffer for datatype '{dtype}'")
                                 # Processing the new sniffer elem is now complete, so make sure the element defining it is loaded if necessary.
-                                sniffer_class = elem.get("type", None)
-                                if sniffer_class is not None:
-                                    if sniffer_class not in sniffer_elem_classes:
-                                        self.sniffer_elems.append(elem)
+                                sniffer_class = elem.get("type")
+                                if sniffer_class is not None and sniffer_class not in sniffer_elem_classes:
+                                    self.sniffer_elems.append(elem)
 
     def get_datatype_from_filename(self, name):
         max_extension_parts = 3
@@ -614,7 +624,7 @@ class Registry:
                 data.init_meta(copy_from=data)
         return data
 
-    def load_datatype_converters(self, toolbox, use_cached=False):
+    def load_datatype_converters(self, toolbox: "AbstractToolBox", use_cached: bool = False):
         """
         Add datatype converters from self.converters to the calling app's toolbox.
         """
@@ -864,7 +874,7 @@ class Registry:
             ext = dataset_or_ext
             dataset = None
 
-        accepted_datatypes: List["Data"] = []
+        accepted_datatypes: List[Data] = []
         for accepted_format in accepted_formats:
             if isinstance(accepted_format, str):
                 accepted_datatype = self.get_datatype_by_extension(accepted_format)
@@ -881,7 +891,16 @@ class Registry:
         if datatype and datatype.matches_any(accepted_datatypes):
             return True, None, None
 
-        for convert_ext in self.get_converters_by_datatype(ext):
+        converter_extensions = self.get_converters_by_datatype(ext)
+        uncompressed_instance = getattr(datatype, "uncompressed_datatype_instance", None)
+        if uncompressed_instance and uncompressed_instance.file_ext in converter_extensions:
+            # sort uncompressed instance ahead of other possible conversions
+            converter_extensions = [
+                uncompressed_instance.file_ext,
+                *(ext for ext in converter_extensions if ext != uncompressed_instance.file_ext),
+            ]
+
+        for convert_ext in converter_extensions:
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
                 self.log.warning(
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 79a05c31a18c6ed1af405f8747774dff2460d104..844934021a78dd4b583b30f2de04f36a435e1f32 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -41,6 +41,7 @@ from galaxy.datatypes.sniff import (
     get_headers,
     iter_headers,
 )
+from galaxy.exceptions import InvalidFileFormatError
 from galaxy.util import (
     compression_utils,
     nice_size,
@@ -317,6 +318,34 @@ class Sequence(data.Text):
 
         return [cmd]
 
+    def display_data(
+        self,
+        trans,
+        dataset: DatasetHasHidProtocol,
+        preview: bool = False,
+        filename: Optional[str] = None,
+        to_ext: Optional[str] = None,
+        **kwd,
+    ):
+        headers = kwd.get("headers", {})
+        if preview:
+            with compression_utils.get_fileobj(dataset.get_file_name()) as fh:
+                max_peek_size = 100000
+                try:
+                    chunk = fh.read(max_peek_size + 1)
+                except UnicodeDecodeError:
+                    raise InvalidFileFormatError("Dataset appears to contain binary data, cannot display.")
+                if len(chunk) <= max_peek_size:
+                    mime = "text/plain"
+                    self._clean_and_set_mime_type(trans, mime, headers)
+                    return chunk[:-1], headers
+                return (
+                    trans.fill_template_mako("/dataset/large_file.mako", truncated_data=chunk[:-1], data=dataset),
+                    headers,
+                )
+        else:
+            return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)
+
 
 class Alignment(data.Text):
     """Class describing an alignment"""
@@ -763,32 +792,6 @@ class BaseFastq(Sequence):
             return False
         return self.check_first_block(file_prefix)
 
-    def display_data(
-        self,
-        trans,
-        dataset: DatasetHasHidProtocol,
-        preview: bool = False,
-        filename: Optional[str] = None,
-        to_ext: Optional[str] = None,
-        **kwd,
-    ):
-        headers = kwd.get("headers", {})
-        if preview:
-            with compression_utils.get_fileobj(dataset.get_file_name(user=trans.user)) as fh:
-                max_peek_size = 1000000  # 1 MB
-                if os.stat(dataset.get_file_name(user=trans.user)).st_size < max_peek_size:
-                    mime = "text/plain"
-                    self._clean_and_set_mime_type(trans, mime, headers)
-                    return fh.read(), headers
-                return (
-                    trans.fill_template_mako(
-                        "/dataset/large_file.mako", truncated_data=fh.read(max_peek_size), data=dataset
-                    ),
-                    headers,
-                )
-        else:
-            return Sequence.display_data(self, trans, dataset, preview, filename, to_ext, **kwd)
-
     @classmethod
     def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py
index 12a6550bdf6df7c2d4cad9504a1311b9d705fd0c..310ee9d21c7fac7702b9591c7865db2a8dab2e9c 100644
--- a/lib/galaxy/datatypes/sniff.py
+++ b/lib/galaxy/datatypes/sniff.py
@@ -17,8 +17,10 @@ from typing import (
     Callable,
     Dict,
     IO,
+    Iterable,
     NamedTuple,
     Optional,
+    TYPE_CHECKING,
     Union,
 )
 
@@ -37,9 +39,15 @@ from galaxy.util.checkers import (
 )
 from galaxy.util.path import StrPath
 
-import pylibmagic  # noqa: F401  # isort:skip
+try:
+    import pylibmagic  # noqa: F401  # isort:skip
+except ImportError:
+    # Not available in conda, but docker image contains libmagic
+    pass
 import magic  # isort:skip
 
+if TYPE_CHECKING:
+    from .data import Data
 
 log = logging.getLogger(__name__)
 
@@ -685,7 +693,7 @@ def _get_file_prefix(filename_or_file_prefix: Union[str, FilePrefix], auto_decom
     return filename_or_file_prefix
 
 
-def run_sniffers_raw(file_prefix: FilePrefix, sniff_order):
+def run_sniffers_raw(file_prefix: FilePrefix, sniff_order: Iterable["Data"]):
     """Run through sniffers specified by sniff_order, return None of None match."""
     fname = file_prefix.filename
     file_ext = None
@@ -714,15 +722,16 @@ def run_sniffers_raw(file_prefix: FilePrefix, sniff_order):
                 continue
         try:
             if hasattr(datatype, "sniff_prefix"):
-                if file_prefix.compressed_format and getattr(datatype, "compressed_format", None):
+                datatype_compressed_format = getattr(datatype, "compressed_format", None)
+                if file_prefix.compressed_format and datatype_compressed_format:
                     # Compare the compressed format detected
                     # to the expected.
-                    if file_prefix.compressed_format != datatype.compressed_format:
+                    if file_prefix.compressed_format != datatype_compressed_format:
                         continue
                 if datatype.sniff_prefix(file_prefix):
                     file_ext = datatype.file_ext
                     break
-            elif datatype.sniff(fname):
+            elif hasattr(datatype, "sniff") and datatype.sniff(fname):
                 file_ext = datatype.file_ext
                 break
         except Exception:
diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py
index 80193155ffbb701af0edc7b6f48276e9e444c1c2..47e0cedcc26816f489b2eca74f2d114d6a570011 100644
--- a/lib/galaxy/datatypes/spaln.py
+++ b/lib/galaxy/datatypes/spaln.py
@@ -91,7 +91,6 @@ class _SpalnDb(Data):
         ]
         for fname in flist:
             sfname = os.path.split(fname)[-1]
-            f, e = os.path.splitext(fname)
             rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
         rval.append("</ul></body></html>")
         with open(dataset.get_file_name(), "w") as f:
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index ef807b64e23f9013d393c6f4ed5a60f7a768d44d..ffa56173593cfeb8da40e00dea9557217bc8d83c 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -65,6 +65,7 @@ from galaxy.datatypes.sniff import (
     iter_headers,
     validate_tabular,
 )
+from galaxy.exceptions import InvalidFileFormatError
 from galaxy.util import compression_utils
 from galaxy.util.compression_utils import (
     FileObjType,
@@ -157,12 +158,15 @@ class TabularData(Text):
     def _read_chunk(self, trans, dataset: HasFileName, offset: int, ck_size: Optional[int] = None):
         with compression_utils.get_fileobj(dataset.get_file_name()) as f:
             f.seek(offset)
-            ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
-            if ck_data and ck_data[-1] != "\n":
-                cursor = f.read(1)
-                while cursor and cursor != "\n":
-                    ck_data += cursor
+            try:
+                ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
+                if ck_data and ck_data[-1] != "\n":
                     cursor = f.read(1)
+                    while cursor and cursor != "\n":
+                        ck_data += cursor
+                        cursor = f.read(1)
+            except UnicodeDecodeError:
+                raise InvalidFileFormatError("Dataset appears to contain binary data, cannot display.")
             last_read = f.tell()
         return ck_data, last_read
 
diff --git a/lib/galaxy/datatypes/test/data.vtu b/lib/galaxy/datatypes/test/data.vtu
new file mode 100644
index 0000000000000000000000000000000000000000..f9483ba6c0f5b3cbe3bf56d82e12cab5875c7a73
--- /dev/null
+++ b/lib/galaxy/datatypes/test/data.vtu
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="21" NumberOfCells="21">
+      <PointData>
+        <DataArray type="Float64" Name="P_BC_FLOW" format="binary" RangeMin="-2" RangeMax="0">
+          AQAAAACAAACoAAAAFgAAAA==eJxjYCAKHCBAE1JPqvno4gwABYYGwQ==
+        </DataArray>
+        <DataArray type="UInt64" Name="bulk_node_ids" format="binary" RangeMin="0" RangeMax="70">
+          AQAAAACAAACoAAAAOwAAAA==eJwtxRECgDAAAMBJkDQomQySBk2SYNKg/v+kQXdyIfySJ2fP3r34cHTx6tObqy/fbn7c/frzAL7YAwQ=
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="42.42640687119285" RangeMax="94.33981132056604">
+          AQAAAACAAAD4AQAAYwAAAA==eJxjYAABOwcw1RAIoeEAXVzlAIo4gx929XBxqHq4fjT1GOLo6j1xqPdEVQ+31wWHe2Di6OajqccQRzffDlU9hjiaerh5Jmjm+KGKY4QDurgnqjiGv9DVu+BQbwcXBwAoLCke
+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              42.426406871
+            </Value>
+            <Value index="1">
+              94.339811321
+            </Value>
+          </InformationKey>
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="20">
+          AQAAAACAAACoAAAAMQAAAA==eJwtxUECQCAAALAQRSLx/7d2sF0Wwm/y7MXRqzcnZ+8+XHy6+vLt5sfdrz8PMMgA0w==
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="1" RangeMax="21">
+          AQAAAACAAACoAAAAMgAAAA==eJwtxbcBgCAAADArFsAC8v+rDiRLxqGbPHvx6uDNuw+fjk7Ovnz78evi6s/NPzgAAOg=
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="1" RangeMax="1">
+          AQAAAACAAAAVAAAACwAAAA==eJxjZMQCAAD8ABY=
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>
diff --git a/lib/galaxy/datatypes/test/test.prm b/lib/galaxy/datatypes/test/test.prm
new file mode 100644
index 0000000000000000000000000000000000000000..b7c2114e148da414b2755ff20bf984804a244b31
--- /dev/null
+++ b/lib/galaxy/datatypes/test/test.prm
@@ -0,0 +1,26 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE R_1YET
+RECEPTOR_FILE R_1YET_protein.mol2
+RECEPTOR_FLEX 3.0
+
+##################################################################
+### CAVITY DEFINITION: REFERENCE LIGAND METHOD
+##################################################################
+SECTION MAPPER
+        SITE_MAPPER RbtLigandSiteMapper
+        REF_MOL 1YET_c.sd
+        RADIUS 6.0
+        SMALL_SPHERE 1.0
+        MIN_VOLUME 100
+        MAX_CAVITIES 1
+        VOL_INCR 0.0
+        GRIDSTEP 0.5
+END_SECTION
+
+#################################
+#CAVITY RESTRAINT PENALTY
+#################################
+SECTION CAVITY
+        SCORING_FUNCTION        RbtCavityGridSF
+        WEIGHT                  1.0
+END_SECTION
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 194e05fdee26611941ad493f2a14b3b006196583..58a37f5c7defedfc579bc2874891eda42cc88dc0 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -139,6 +139,7 @@ class DataManagerJson(Json):
     MetadataElement(
         name="data_tables", default=None, desc="Data tables represented by this dataset", readonly=True, visible=True
     )
+    MetadataElement(name="is_bundle", default=False, desc="Dataset represents bundle", readonly=True, visible=True)
 
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd):
         super().set_meta(dataset=dataset, overwrite=overwrite, **kwd)
@@ -1560,3 +1561,29 @@ class FormattedDensity(Text):
             (lines[9].strip() == end_header and lines[10].strip() == grid_points)
             or (lines[9].strip() == end_header_spin and lines[10].strip() == grid_points_spin)
         )
+
+
+@build_sniff_from_prefix
+class Prm(Text):
+    """rDock prm format
+
+    For system definition files, scoring function definition files and search
+    protocol definition files.
+    """
+
+    file_ext = "prm"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """
+        Determines whether the file is in prm format, according to
+        https://rdock.github.io/documentation/html_docs/reference-guide/file-formats.html
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname("test.prm")
+        >>> Prm().sniff(fname)
+        True
+        >>> fname = get_test_fname("larch_potentials.inp")
+        >>> Prm().sniff(fname)
+        False
+        """
+        return file_prefix.startswith("RBT_PARAMETER_FILE_V1.00")
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index bd5e7ef44637241b7ef77f028f7e4e8b2563860a..08e47b124e06974467bce94cae59afdd582eb0a5 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -13,6 +13,7 @@ from os.path import (
 import yaml
 from dparse import parse
 
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.util import (
     asbool,
     etree,
@@ -41,6 +42,7 @@ class ConditionalDependencies:
             self.config = load_app_properties(config_file=self.config_file)
         else:
             self.config = config
+        self.config_object = GalaxyAppConfiguration(config_file=self.config_file, override_tempdir=False, **self.config)
         self.parse_configs()
         self.get_conditional_requirements()
 
@@ -58,7 +60,7 @@ class ConditionalDependencies:
         if "job_config" in self.config:
             load_job_config_dict(self.config.get("job_config"))
         else:
-            job_conf_path = self.config.get("job_config_file")
+            job_conf_path = self.config_object.job_config_file
             if not job_conf_path:
                 job_conf_path = join(dirname(self.config_file), "job_conf.yml")
                 if not exists(job_conf_path):
@@ -85,9 +87,7 @@ class ConditionalDependencies:
                 except OSError:
                     pass
 
-        object_store_conf_path = self.config.get(
-            "object_store_config_file", join(dirname(self.config_file), "object_store_conf.xml")
-        )
+        object_store_conf_path = self.config_object.object_store_config_file
         try:
             if ".xml" in object_store_conf_path:
                 for store in parse_xml(object_store_conf_path).iter("object_store"):
@@ -117,7 +117,7 @@ class ConditionalDependencies:
             pass
 
         # Parse auth conf
-        auth_conf_xml = self.config.get("auth_config_file", join(dirname(self.config_file), "auth_conf.xml"))
+        auth_conf_xml = self.config_object.auth_config_file
         try:
             for auth in parse_xml(auth_conf_xml).findall("authenticator"):
                 auth_type = auth.find("type")
@@ -128,9 +128,7 @@ class ConditionalDependencies:
 
         # Parse oidc_backends_config_file specifically for PKCE support.
         self.pkce_support = False
-        oidc_backend_conf_xml = self.config.get(
-            "oidc_backends_config_file", join(dirname(self.config_file), "oidc_backends_config.xml")
-        )
+        oidc_backend_conf_xml = self.config_object.oidc_backends_config_file
         try:
             for pkce_support_element in parse_xml(oidc_backend_conf_xml).iterfind("./provider/pkce_support"):
                 if pkce_support_element.text == "true":
@@ -140,7 +138,7 @@ class ConditionalDependencies:
             pass
 
         # Parse error report config
-        error_report_yml = self.config.get("error_report_file", join(dirname(self.config_file), "error_report.yml"))
+        error_report_yml = self.config_object.error_report_file
         try:
             with open(error_report_yml) as f:
                 error_reporters = yaml.safe_load(f)
@@ -149,9 +147,8 @@ class ConditionalDependencies:
             pass
 
         # Parse file sources config
-        file_sources_conf_yml = self.config.get(
-            "file_sources_config_file", join(dirname(self.config_file), "file_sources_conf.yml")
-        )
+        file_sources_conf_yml = self.config_object.file_sources_config_file
+
         if exists(file_sources_conf_yml):
             with open(file_sources_conf_yml) as f:
                 file_sources_conf = yaml.safe_load(f)
@@ -160,7 +157,7 @@ class ConditionalDependencies:
         self.file_sources = [c.get("type", None) for c in file_sources_conf]
 
         # Parse vault config
-        vault_conf_yml = self.config.get("vault_config_file", join(dirname(self.config_file), "vault_conf.yml"))
+        vault_conf_yml = self.config_object.vault_config_file
         if exists(vault_conf_yml):
             with open(vault_conf_yml) as f:
                 vault_conf = yaml.safe_load(f)
@@ -293,6 +290,9 @@ class ConditionalDependencies:
     def check_tensorflow(self):
         return asbool(self.config["enable_tool_recommendations"])
 
+    def check_openai(self):
+        return self.config.get("openai_api_key", None) is not None
+
     def check_weasyprint(self):
         # See notes in ./conditional-requirements.txt for more information.
         return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 35b7e38eade512de0c9bf34fea6c4fcf3f0a058b..c9d989c356a224c6296097cc3696685d7505e8b5 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -1,5 +1,5 @@
 # These dependencies are only required when certain config options are set
-psycopg2-binary==2.9.9
+psycopg2-binary==2.9.10
 mysqlclient
 fluent-logger
 sentry-sdk[fastapi]
@@ -14,17 +14,18 @@ python-pam
 galaxycloudrunner
 pkce
 total-perspective-vortex>=2.3.2,<3
+openai
 
 # For file sources plugins
 fs.webdavfs>=0.4.2  # type: webdav
-fs.dropboxfs>=1.0  # type: dropbox
+fs.dropboxfs>=1.0.3  # type: dropbox
 fs.sshfs  # type: ssh
 fs.anvilfs # type: anvil
 fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
 # fs-gcsfs doesn't pin google-cloud-storage, and old versions log noisy exceptions and break test discovery
 google-cloud-storage>=2.8.0  # type: googlecloudstorage
-fs.onedatarestfs==21.2.5.1 # type: onedata, depends on onedatafilerestclient
+fs.onedatarestfs==21.2.5.2 # type: onedata, depends on onedatafilerestclient
 fs-basespace # type: basespace
 fs-azureblob # type: azure
 
@@ -39,7 +40,7 @@ rucio-clients==33.6.0
 chronos-python==1.2.1
 
 # Kubernetes job runner
-pykube-ng==21.3.0
+pykube-ng==23.6.0
 
 # Synnefo / Pithos+ object store client
 kamaki
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index c7c95fe3832b35fdd4303fec53937a04bd68068d..c782e31842e26f7182710fa2bf7a2a5f9574c439 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,180 +1,188 @@
-aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
-aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
-ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
-async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
-attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
-axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
-babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
-backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
-backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
-boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
-cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
-click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
-codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
-colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
-contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
-cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
-darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
-decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
-defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
-deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
-docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
-dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
-exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
-frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-galaxy-release-util==0.1.9 ; python_version >= "3.8" and python_version < "3.13"
-graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
-h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
-httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
-idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
-imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
-iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
-isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
-jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
-jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
-junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13"
-kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
-lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
-markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
-markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
-markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
-matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "3.13"
-mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
-mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
-mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
-msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
-nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
-numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
-onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
-outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
-pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
-pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
-pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
-pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
-prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13"
-pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
-pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
-pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
-pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
-pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
-pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13"
-pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13"
-pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
-python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
-python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
-pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
-rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
-requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
-rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
-ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
-ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
-scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
-secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
-seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
-six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
-sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-sphinx-rtd-theme==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-htmlhelp==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-jquery==4.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
-statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
-stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13"
-tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
-testfixtures==8.2.0 ; python_version >= "3.8" and python_version < "3.13"
-text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
-tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
-toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
-trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
-tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
-twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
-wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
-werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
-wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
-yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
+# This file was autogenerated by uv via the following command:
+#    uv export --frozen --no-hashes --only-group=dev
+aiohappyeyeballs==2.4.3
+aiohttp==3.10.11
+aiosignal==1.3.1
+alabaster==0.7.13
+anyio==4.5.2
+ase==3.23.0
+async-timeout==5.0.1 ; python_full_version < '3.11'
+attrs==24.2.0
+axe-selenium-python==2.1.6
+babel==2.16.0
+backports-tarfile==1.2.0 ; python_full_version < '3.12'
+backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
+black==24.8.0
+boto3==1.35.36
+botocore==1.35.36
+build==1.2.2.post1
+cachecontrol==0.14.1
+certifi==2024.8.30
+cffi==1.17.1
+charset-normalizer==3.4.0
+click==8.1.7
+codespell==2.3.0
+colorama==0.4.6 ; (platform_system != 'Windows' and sys_platform == 'win32') or platform_system == 'Windows' or os_name == 'nt'
+contourpy==1.1.1 ; python_full_version < '3.9'
+contourpy==1.3.0 ; python_full_version >= '3.9'
+coverage==7.6.1
+cryptography==43.0.3
+cwltest==2.5.20240906231108
+cycler==0.12.1
+darker==2.1.1
+darkgraylib==1.2.1
+decorator==5.1.1 ; python_full_version >= '3.9'
+defusedxml==0.7.1
+deprecated==1.2.15
+docutils==0.20.1
+dogpile-cache==1.3.3 ; python_full_version >= '3.9'
+exceptiongroup==1.2.2 ; python_full_version < '3.11'
+filelock==3.16.1
+fluent-logger==0.11.1
+fonttools==4.55.0
+frozenlist==1.5.0
+galaxy-release-util==0.1.11
+graylint==1.1.1
+greenlet==3.1.1
+h11==0.14.0
+httpcore==1.0.7
+httpx==0.27.2
+idna==3.10
+imagesize==1.4.1
+importlib-metadata==8.5.0
+importlib-resources==6.4.5 ; python_full_version < '3.10'
+iniconfig==2.0.0
+isodate==0.6.1
+isort==5.13.2
+jaraco-classes==3.4.0
+jaraco-context==6.0.1
+jaraco-functools==4.1.0
+jeepney==0.8.0 ; sys_platform == 'linux'
+jinja2==3.1.4
+jmespath==1.0.1
+jsonschema==4.23.0 ; python_full_version >= '3.9'
+jsonschema-specifications==2023.12.1 ; python_full_version >= '3.9'
+junit-xml==1.9
+keyring==25.5.0
+kiwisolver==1.4.7
+lxml==5.3.0
+markdown-it-py==3.0.0
+markdown-it-reporter==0.0.2
+markupsafe==2.1.5
+matplotlib==3.7.5 ; python_full_version < '3.9'
+matplotlib==3.9.2 ; python_full_version >= '3.9'
+mdit-py-plugins==0.4.2
+mdurl==0.1.2
+mirakuru==2.5.2
+mistune==3.0.2
+more-itertools==10.5.0
+msgpack==1.1.0
+multidict==6.1.0
+mypy-extensions==1.0.0
+myst-parser==3.0.1
+nh3==0.2.18
+numpy==1.24.4 ; python_full_version < '3.9'
+numpy==2.0.2 ; python_full_version == '3.9.*'
+numpy==2.1.3 ; python_full_version >= '3.10'
+onedatafilerestclient==21.2.5.2
+outcome==1.3.0.post0
+packaging==24.2
+pathspec==0.12.1
+pbr==6.1.0 ; python_full_version >= '3.9'
+pillow==10.4.0
+pkce==1.0.3
+pkginfo==1.10.0
+pkgutil-resolve-name==1.3.10 ; python_version < '0'
+platformdirs==4.3.6
+playwright==1.48.0
+pluggy==1.5.0
+port-for==0.7.3
+prettytable==3.11.0
+propcache==0.2.0
+psutil==6.1.0 ; sys_platform != 'cygwin'
+psycopg==3.2.3
+pycparser==2.22
+pyee==12.0.0
+pygithub==2.5.0
+pygments==2.18.0
+pyjwt==2.9.0
+pynacl==1.5.0
+pyparsing==3.1.4
+pyproject-hooks==1.2.0
+pysocks==1.7.1
+pytest==7.4.4
+pytest-asyncio==0.23.8
+pytest-base-url==2.1.0
+pytest-cov==5.0.0
+pytest-html==4.1.1
+pytest-httpserver==1.1.0
+pytest-json-report==1.5.0
+pytest-metadata==3.1.1
+pytest-mock==3.14.0
+pytest-playwright==0.5.2
+pytest-postgresql==6.1.1
+pytest-shard==0.1.2
+python-dateutil==2.9.0.post0
+python-irodsclient==2.2.0
+python-slugify==8.0.4
+pytz==2024.2 ; python_full_version < '3.9'
+pywin32-ctypes==0.2.3 ; sys_platform == 'win32'
+pyyaml==6.0.2
+rdflib==6.3.2
+readme-renderer==43.0
+referencing==0.35.1 ; python_full_version >= '3.9'
+requests==2.32.3
+requests-toolbelt==1.0.0
+responses==0.25.3
+rfc3986==2.0.0
+rich==13.9.4
+rpds-py==0.20.1 ; python_full_version >= '3.9'
+ruamel-yaml==0.18.6
+ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
+rucio-clients==35.5.0 ; python_full_version >= '3.9'
+s3transfer==0.10.3
+schema-salad==8.7.20241010092723
+scipy==1.10.1 ; python_full_version < '3.9'
+scipy==1.13.1 ; python_full_version == '3.9.*'
+scipy==1.14.1 ; python_full_version >= '3.10'
+secretstorage==3.3.3 ; sys_platform == 'linux'
+selenium==4.26.1
+seletools==1.5.0
+setuptools==75.3.0
+six==1.16.0
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sortedcontainers==2.4.0
+sphinx==7.1.2
+sphinx-rtd-theme==3.0.2
+sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+statsd==4.0.1
+stevedore==5.3.0 ; python_full_version >= '3.9'
+tabulate==0.9.0 ; python_full_version >= '3.9'
+testfixtures==8.3.0
+text-unidecode==1.3
+tinydb==4.8.2
+toml==0.10.2
+tomli==2.1.0 ; python_full_version <= '3.11'
+trio==0.27.0
+trio-websocket==0.11.1
+tuspy==1.0.3
+twill==3.3
+twine==5.1.1
+typing-extensions==4.12.2
+tzdata==2024.2 ; sys_platform == 'win32'
+urllib3==1.26.20
+watchdog==4.0.2
+wcwidth==0.2.13
+websocket-client==1.8.0
+werkzeug==3.0.6
+wrapt==1.16.0
+wsproto==1.2.0
+yarl==1.15.2
+zipp==3.20.2
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 805eda6a8a58be9551c5d5123365af20b4b63f6c..f0afdffeb3c3342a32ced1bd377239fc7735fec1 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,7 @@
-attrs==23.2.0
-flake8==7.0.0
-flake8-bugbear==24.4.26
+attrs==24.2.0
+flake8==7.1.1
+flake8-bugbear==24.10.31
 mccabe==0.7.0
-pycodestyle==2.11.1
+pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.4.4
+ruff==0.7.4
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 52b17eaba1c919a913acd713a38a96c867e977e4..1def9bb621ed210fbd15ee10b0483e518fd38994 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -1,217 +1,219 @@
---extra-index-url https://wheels.galaxyproject.org/simple
-
-a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
-adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13"
-aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
-aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
-aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
-aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
-amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
-aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
-annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
-apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
-appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
-arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
-argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
-async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
-attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
-attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
-babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
-backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
-bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13"
-bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
-beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
-billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
-bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
-boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
-boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
-cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
-cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
-circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
-click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
-click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
-click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
-cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
-colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
-coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
-conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
-cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
-cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
-cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
-decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
-defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
-deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
-dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
-dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13"
-docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
-docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
-dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
-edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
-email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
-exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
-fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
-fsspec==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
-future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
-galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
-graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13"
-graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"
-graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
-graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
-gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
-greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32")
-gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
-gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
-h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
-h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
-humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
-idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
-isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
-#isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
-isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
-jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
-jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
-jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
-jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13"
-jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
-kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13"
-lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
-lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
-mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13"
-markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
-markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
-markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
-mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13"
-mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
-mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
-msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-networkx==2.5 ; python_version >= "3.8" and python_version < "3.13"
-nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
-numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
-oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
-orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13"
-oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
-paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
-parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
-paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13"
-pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
-pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
-promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
-prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
-prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
-psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
-pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
-pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
-pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
-pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
-pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
-pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
-pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
-pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
-pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
-pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13"
-python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
-python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
-python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
-pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
-pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13"
-rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13"
-refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
-regex==2024.5.15 ; python_version >= "3.8" and python_version < "3.13"
-repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
-requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
-requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
-requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
-rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
-routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
-ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
-ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
-setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
-shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
-six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
-sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13"
-sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
-sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
-starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
-starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13"
-supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13"
-svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
-tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
-tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
-tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
-tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13"
-tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
-tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
-ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
-urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13"
-uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"
-vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
-wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
-webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13"
-whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
-wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
-yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
-yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
-zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
-zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
+# This file was autogenerated by uv via the following command:
+#    uv export --frozen --no-hashes --no-dev
+a2wsgi==1.10.7
+adal==1.2.7
+aiobotocore==2.15.2
+aiodataloader==0.4.0
+aiofiles==24.1.0
+aiohappyeyeballs==2.4.3
+aiohttp==3.10.11
+aioitertools==0.12.0
+aiosignal==1.3.1
+alembic==1.14.0
+amqp==5.3.1
+annotated-types==0.7.0
+anyio==4.5.2
+apispec==6.6.1
+appdirs==1.4.4
+arcp==0.2.1
+argcomplete==3.5.1
+async-timeout==5.0.1 ; python_full_version < '3.11'
+attmap==0.13.2
+attrs==24.2.0
+babel==2.16.0
+backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
+bagit==1.8.1
+bagit-profile==1.3.1
+bcrypt==4.2.0
+bdbag==1.7.3
+beaker==1.13.0
+billiard==4.2.1
+bioblend==1.4.0
+bleach==6.1.0
+boltons==24.1.0
+boto==2.49.0
+botocore==1.35.36
+bx-python==0.13.0
+cachecontrol==0.14.1
+celery==5.4.0
+certifi==2024.8.30
+cffi==1.17.1
+charset-normalizer==3.4.0
+circus==0.18.0
+click==8.1.7
+click-didyoumean==0.3.1
+click-plugins==1.1.1
+click-repl==0.3.0
+cloudauthz==0.6.0
+cloudbridge==3.2.0
+colorama==0.4.6 ; platform_system == 'Windows'
+coloredlogs==15.0.1
+conda-package-streaming==0.11.0
+cryptography==43.0.3
+ct3==3.3.3.post1
+cwl-upgrader==1.2.11
+cwl-utils==0.35
+cwltool==3.1.20241007082533
+defusedxml==0.7.1
+deprecation==2.1.0
+dictobj==0.4
+dnspython==2.6.1
+docopt==0.6.2
+docutils==0.20.1
+dparse==0.6.4
+edam-ontology==1.25.2
+email-validator==2.2.0
+exceptiongroup==1.2.2 ; python_full_version < '3.11'
+fastapi-slim==0.115.5
+filelock==3.16.1
+fissix==24.4.24 ; python_full_version >= '3.13'
+frozenlist==1.5.0
+fs==2.4.16
+fsspec==2024.10.0
+future==1.0.0
+galaxy2cwl==0.1.4
+graphene==3.4.3
+graphene-sqlalchemy==3.0.0rc1
+graphql-core==3.2.5
+graphql-relay==3.2.0
+gravity==1.0.6
+greenlet==3.1.1 ; (python_full_version < '3.13' and platform_machine == 'AMD64') or (python_full_version < '3.13' and platform_machine == 'WIN32') or (python_full_version < '3.13' and platform_machine == 'aarch64') or (python_full_version < '3.13' and platform_machine == 'amd64') or (python_full_version < '3.13' and platform_machine == 'ppc64le') or (python_full_version < '3.13' and platform_machine == 'win32') or (python_full_version < '3.13' and platform_machine == 'x86_64')
+gunicorn==23.0.0
+gxformat2==0.20.0
+h11==0.14.0
+h5grove==2.3.0
+h5py==3.11.0 ; python_full_version < '3.9'
+h5py==3.12.1 ; python_full_version >= '3.9'
+humanfriendly==10.0
+idna==3.10
+importlib-metadata==8.5.0
+importlib-resources==6.4.5 ; python_full_version < '3.9'
+isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef
+isal==1.7.1
+isodate==0.6.1
+jinja2==3.1.4
+jmespath==1.0.1
+jsonref==1.1.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kombu==5.4.2
+lagom==2.6.0
+legacy-cgi==2.6.1 ; python_full_version >= '3.13'
+lxml==5.3.0
+mako==1.3.6
+markdown==3.7
+markdown-it-py==3.0.0
+markupsafe==2.1.5
+mdurl==0.1.2
+mercurial==6.8.2
+mistune==3.0.2
+mrcfile==1.5.3
+msal==1.31.0
+msgpack==1.1.0
+multidict==6.1.0
+mypy-extensions==1.0.0
+networkx==3.1
+nodeenv==1.9.1
+numpy==1.24.4 ; python_full_version < '3.9'
+numpy==2.0.2 ; python_full_version == '3.9.*'
+numpy==2.1.3 ; python_full_version >= '3.10'
+oauthlib==3.2.2
+orjson==3.10.11
+oyaml==1.0
+packaging==24.2
+paramiko==3.5.0
+parsley==1.3
+paste==3.10.1
+pastedeploy==3.1.0
+pebble==5.0.7
+pillow==10.4.0
+pkgutil-resolve-name==1.3.10 ; python_full_version < '3.9'
+promise==2.3
+prompt-toolkit==3.0.48
+propcache==0.2.0
+prov==1.5.1
+psutil==6.1.0
+pulsar-galaxy-lib==0.15.7
+pycparser==2.22
+pycryptodome==3.21.0
+pydantic==2.9.2
+pydantic-core==2.23.4
+pydantic-tes==0.1.5
+pydot==2.0.0
+pyeventsystem==0.1.0
+pyfaidx==0.8.1.3
+pygments==2.18.0
+pyjwt==2.9.0
+pykwalify==1.8.0
+pylibmagic==0.5.0
+pynacl==1.5.0
+pyparsing==3.1.4
+pyreadline3==3.5.4 ; sys_platform == 'win32'
+pysam==0.22.1
+python-dateutil==2.9.0.post0
+python-magic==0.4.27
+python-multipart==0.0.17
+python-slugify==8.0.4
+python3-openid==3.2.0
+pytz==2024.2
+pyyaml==6.0.2
+pyzmq==26.2.0
+rdflib==6.3.2
+referencing==0.35.1
+refgenconf==0.12.2
+regex==2024.11.6
+repoze-lru==0.7
+requests==2.32.3
+requests-oauthlib==2.0.0
+requests-toolbelt==1.0.0
+requests-unixsocket==0.3.0
+rich==13.9.4
+rocrate==0.11.0
+routes==2.5.1
+rpds-py==0.20.1
+ruamel-yaml==0.18.6
+ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
+s3fs==2024.10.0
+schema-salad==8.7.20241010092723
+setuptools==75.3.0
+setuptools-scm==5.0.2
+six==1.16.0
+sniffio==1.3.1
+social-auth-core==4.5.4
+sortedcontainers==2.4.0
+spython==0.3.14
+sqlalchemy==2.0.35
+sqlitedict==2.1.0
+sqlparse==0.5.2
+starlette==0.41.2
+starlette-context==0.3.6
+starlette-graphene3==0.6.0
+supervisor==4.2.5
+svgwrite==1.4.3
+tenacity==9.0.0
+text-unidecode==1.3
+tifffile==2023.7.10
+tinydb==4.8.2
+tomli==2.1.0 ; python_full_version < '3.11'
+tornado==6.4.1
+tqdm==4.67.0
+tuspy==1.0.3
+tuswsgi==0.5.5
+typing-extensions==4.12.2
+tzdata==2024.2
+tzlocal==5.2
+ubiquerg==0.8.0
+urllib3==1.26.20
+uvicorn==0.32.0
+uvloop==0.21.0
+vine==5.1.0
+wcwidth==0.2.13
+webencodings==0.5.1
+webob==1.8.9
+whoosh==2.7.4
+wrapt==1.16.0
+yacman==0.9.3
+yarl==1.15.2
+zipp==3.20.2
+zipstream-new==1.1.8
+zstandard==0.23.0
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index d4cb93e53f3f3e8067881e22fae2da468a0a6d26..ad5c1328d2c8deefc66ea82326255eea4ac86430 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,30 +1,33 @@
-annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.34.108 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.34.94 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
-lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13"
-mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
-types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
-types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
-types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
-types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.21.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
-types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
-types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
-types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
-types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
-types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
-types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
-types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13"
-types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
+# This file was autogenerated by uv via the following command:
+#    uv export --frozen --no-hashes --only-group=typecheck
+annotated-types==0.7.0
+boto3-stubs==1.35.63
+botocore-stubs==1.35.63
+cffi==1.17.1 ; platform_python_implementation != 'PyPy'
+cryptography==43.0.3
+lxml-stubs==0.5.1
+mypy==1.13.0
+mypy-boto3-s3==1.35.61
+mypy-extensions==1.0.0
+pycparser==2.22 ; platform_python_implementation != 'PyPy'
+pydantic==2.9.2
+pydantic-core==2.23.4
+tomli==2.1.0 ; python_full_version < '3.11'
+types-awscrt==0.23.0
+types-bleach==6.1.0.20240331
+types-boto==2.49.18.20241019
+types-contextvars==2.4.7.3
+types-dataclasses==0.6.6
+types-docutils==0.21.0.20241005
+types-html5lib==1.1.11.20241018
+types-markdown==3.7.0.20240822
+types-paramiko==3.5.0.20240928
+types-python-dateutil==2.9.0.20241003
+types-python-slugify==8.0.2.20240310
+types-pyyaml==6.0.12.20240917
+types-requests==2.31.0.6
+types-s3transfer==0.10.3
+types-setuptools==75.5.0.20241116
+types-six==1.16.21.20241105
+types-urllib3==1.26.25.14
+typing-extensions==4.12.2
diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
index 6bb140e8f0785020aae3bf6c04459423b58f174a..201f510ee9b6ab404899f52c1f63b516efec30d8 100755
--- a/lib/galaxy/dependencies/update.sh
+++ b/lib/galaxy/dependencies/update.sh
@@ -1,25 +1,25 @@
 #!/bin/sh
 
-# This script installs poetry if it's not already installed in the user account.
-# It then runs poetry inside Galaxy's root directory, potentially updating 
-# pyproject.toml and poetry.lock, and the pinned and dev requirements files.
+# This script installs uv if it's not already installed in the user account.
+# It then runs uv inside Galaxy's root directory, potentially updating
+# pyproject.toml and uv.lock, and the pinned requirements files.
 
 set -e
 
-SUPPORTED_PYTHON_VERSIONS="3.8 3.9 3.10 3.11 3.12"
-NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.13"
-
 this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
 usage() {
-    printf "Usage: %s: [-a] [pkg_spec...]\n" "${0##*/}" >&2
+    printf "Usage: %s: [-p pkg]\n" "${0##*/}" >&2
 }
 
-add=
-while getopts 'a' OPTION
+pkg=
+while getopts 'p:h' OPTION
 do
     case $OPTION in
-        a) add=1
+        p) pkg="$OPTARG"
+           ;;
+        h) usage
+           exit 0
            ;;
         ?) usage
            exit 2
@@ -28,67 +28,20 @@ do
 done
 shift $((OPTIND - 1))
 
-if [ -n "$add" ] && [ $# -eq 0 ]; then
-    printf "When adding (-a), you must provide at least one package specification.\n" >&2
-    usage
-    exit 2
-fi
-
-# Install the latest version of poetry into the user account
-curl -sSL https://install.python-poetry.org | python3 -
-poetry self add 'poetry-plugin-export!=1.7.0'  # https://github.com/python-poetry/poetry-plugin-export/issues/269
+# Create a virtual environment in a tmp directory and install uv into it
+uv_venv=$(mktemp -d "${TMPDIR:-/tmp}/uv_venv.XXXXXXXXXX")
+python3 -m venv "${uv_venv}"
+"${uv_venv}/bin/python" -m pip install uv
+uv="${uv_venv}/bin/uv"
 
-# Run poetry (this may update pyproject.toml and poetry.lock).
-if [ -z "$add" ]; then
-    poetry update -vv --lock "$@"
+# Run uv (this may update pyproject.toml and uv.lock).
+if [ -n "$pkg" ]; then
+    ${uv} lock --upgrade-package "$pkg"
 else
-    poetry add -vv --lock "$@"
+    ${uv} lock --upgrade
 fi
 
 # Update pinned requirements files.
-PINNED_REQUIREMENTS_FILE=$this_directory/pinned-requirements.txt
-PINNED_DEV_REQUIREMENTS_FILE=$this_directory/dev-requirements.txt
-poetry export -f requirements.txt --without-hashes --output "$PINNED_REQUIREMENTS_FILE"
-poetry export --only dev -f requirements.txt --without-hashes --output "$PINNED_DEV_REQUIREMENTS_FILE"
-poetry export --only typecheck -f requirements.txt --without-hashes --output "$this_directory/pinned-typecheck-requirements.txt"
-
-# Fix requirements
-
-latest_package_version_for_python_version () {
-    PIP_INDEX_OUT=$(pip index versions --python-version "$2" "$1")
-    echo "$PIP_INDEX_OUT" | head -n 1 | sed -e 's/.* (\(.*\)).*/\1/'
-}
-
-split_requirement () {
-    PACKAGE_NAME=$1
-
-    if ! pip index version --help >/dev/null; then
-        echo "pip >= 21.2.1 required for the 'index' command"
-        exit 1
-    fi
-
-    NEW_REQUIREMENTS=
-    PREVIOUS_LATEST_PACKAGE_VERSION=
-    for PYTHON_VERSION in $SUPPORTED_PYTHON_VERSIONS; do
-        LATEST_PACKAGE_VERSION=$(latest_package_version_for_python_version "$PACKAGE_NAME" "$PYTHON_VERSION")
-        if [ -z "$NEW_REQUIREMENTS" ]; then
-            NEW_REQUIREMENTS="$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
-        elif [ "$LATEST_PACKAGE_VERSION" != "$PREVIOUS_LATEST_PACKAGE_VERSION" ]; then
-            NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$PYTHON_VERSION\"\n$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\""
-        fi
-        PREVIOUS_LATEST_PACKAGE_VERSION=$LATEST_PACKAGE_VERSION
-    done
-    if [ -n "$NOT_SUPPORTED_NEXT_PYTHON_VERSION" ]; then
-        NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$NOT_SUPPORTED_NEXT_PYTHON_VERSION\""
-    fi
-
-    sed -i.orig -e "s/^$PACKAGE_NAME==.*/$NEW_REQUIREMENTS/" "$PINNED_REQUIREMENTS_FILE" "$PINNED_DEV_REQUIREMENTS_FILE"
-}
-
-# For some packages there is no recent version that works on all Python versions
-# supported by Galaxy, so Poetry resorts to an old version. Here we replace any
-# such requirement with multiple Python-version-specific requirements.
-# Packages which specify a maximum Python version pin:
-split_requirement matplotlib
-split_requirement numpy
-split_requirement scipy
+${uv} export --frozen --no-hashes --no-dev > "$this_directory/pinned-requirements.txt"
+${uv} export --frozen --no-hashes --only-group=dev > "$this_directory/dev-requirements.txt"
+${uv} export --frozen --no-hashes --only-group=typecheck > "$this_directory/pinned-typecheck-requirements.txt"
diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index e52ec14db7fe8dbe0325116c26d77625f4f21daf..46bc28adf7a182462a53f22174432cc01f9abd71 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -154,10 +154,13 @@ class ToolInputsNotReadyException(MessageException):
 
 
 class ToolInputsNotOKException(MessageException):
-    def __init__(self, err_msg: Optional[str] = None, type="info", *, src: str, id: int, **extra_error_info):
-        super().__init__(err_msg, type, **extra_error_info)
+    def __init__(
+        self, err_msg: Optional[str] = None, type="info", *, src: str, id: str, input_name: str, **extra_error_info
+    ):
+        super().__init__(err_msg, type, src=src, id=id, input_name=input_name, **extra_error_info)
         self.src = src
         self.id = id
+        self.input_name = input_name
 
     status_code = 400
     error_code = error_codes_by_name["TOOL_INPUTS_NOT_OK"]
@@ -224,6 +227,11 @@ class UserActivationRequiredException(MessageException):
     err_code = error_codes_by_name["USER_ACTIVATION_REQUIRED"]
 
 
+class ItemAlreadyClaimedException(MessageException):
+    status_code = 403
+    err_code = error_codes_by_name["ITEM_IS_CLAIMED"]
+
+
 class ObjectNotFound(MessageException):
     """Accessed object was not found"""
 
@@ -236,6 +244,10 @@ class Conflict(MessageException):
     err_code = error_codes_by_name["CONFLICT"]
 
 
+class ItemMustBeClaimed(Conflict):
+    err_code = error_codes_by_name["MUST_CLAIM"]
+
+
 class DeprecatedMethod(MessageException):
     """
     Method (or a particular form/arg signature) has been removed and won't be available later
@@ -255,6 +267,11 @@ class InconsistentDatabase(MessageException):
     err_code = error_codes_by_name["INCONSISTENT_DATABASE"]
 
 
+class InconsistentApplicationState(MessageException):
+    status_code = 500
+    err_code = error_codes_by_name["INCONSISTENT_APPLICATION_STATE"]
+
+
 class InternalServerError(MessageException):
     status_code = 500
     err_code = error_codes_by_name["INTERNAL_SERVER_ERROR"]
diff --git a/lib/galaxy/exceptions/error_codes.json b/lib/galaxy/exceptions/error_codes.json
index 5eea7fbbe9d3fd58b46e512cc2972451b168c1c7..6c349f2218d96dd1fd612f30563152ee990e2b04 100644
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -144,6 +144,11 @@
         "code": 403007,
         "message": "Action requires account activation."
     },
+    {
+        "name": "ITEM_IS_CLAIMED",
+        "code": 403008,
+        "message": "This item has already been claimed and cannot be re-claimed."
+    },
     {
         "name": "USER_REQUIRED",
         "code": 403008,
@@ -159,6 +164,11 @@
         "code": 409001,
         "message": "Database conflict prevented fulfilling the request."
     },
+    {
+        "name": "MUST_CLAIM",
+        "code": 409010,
+        "message": "Private request must be claimed before use"
+    },
     {
         "name": "DEPRECATED_API_CALL",
         "code": 410001,
@@ -194,6 +204,11 @@
         "code": 500006,
         "message": "Reference data required for program execution failed to load."
     },
+    {
+        "name": "INCONSISTENT_APPLICATION_STATE",
+        "code": 500007,
+        "message": "Inconsistent application state (likely not dbms related) prevented fulfilling the request."
+    },
     {
         "name": "NOT_IMPLEMENTED",
         "code": 501001,
diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index b13b2e1db8c8a4e48b822c4fa2ee03e771c7b3e2..d3cb2c6174099adfe6aacb7b638d0fa357efc5f3 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -396,7 +396,11 @@ class ProvidesFileSourcesUserContext(FileSourcesUserContext, FileSourceDictifiab
     def role_names(self) -> Set[str]:
         """The set of role names of this user."""
         user = self.trans.user
-        return {ura.role.name for ura in user.roles} if user else set()
+        role_names = set()
+        if user:
+            role_names = {ura.role.name for ura in user.roles}
+            role_names.add(user.email)  # User's private role may have a generic name, so add user's email explicitly.
+        return role_names
 
     @property
     def group_names(self) -> Set[str]:
diff --git a/lib/galaxy/files/plugins.py b/lib/galaxy/files/plugins.py
index 4f9c182f846abcf669bb306e3dbf8e8660e60ca1..fcbee3fdeaf86a9aa37c518acf303c693c81c0fc 100644
--- a/lib/galaxy/files/plugins.py
+++ b/lib/galaxy/files/plugins.py
@@ -24,6 +24,9 @@ class FileSourcePluginsConfig:
     user_library_import_dir: Optional[str]
     ftp_upload_dir: Optional[str]
     ftp_upload_purge: bool
+    tmp_dir: Optional[str]
+    webdav_use_temp_files: Optional[bool]
+    listings_expiry_time: Optional[int]
 
     def __init__(
         self,
@@ -33,6 +36,9 @@ class FileSourcePluginsConfig:
         user_library_import_dir=None,
         ftp_upload_dir=None,
         ftp_upload_purge=True,
+        tmp_dir=None,
+        webdav_use_temp_files=None,
+        listings_expiry_time=None,
     ):
         symlink_allowlist = symlink_allowlist or []
         fetch_url_allowlist = fetch_url_allowlist or []
@@ -42,6 +48,9 @@ class FileSourcePluginsConfig:
         self.user_library_import_dir = user_library_import_dir
         self.ftp_upload_dir = ftp_upload_dir
         self.ftp_upload_purge = ftp_upload_purge
+        self.tmp_dir = tmp_dir
+        self.webdav_use_temp_files = webdav_use_temp_files
+        self.listings_expiry_time = listings_expiry_time
 
     @staticmethod
     def from_app_config(config):
@@ -54,6 +63,10 @@ class FileSourcePluginsConfig:
         kwds["user_library_import_dir"] = config.user_library_import_dir
         kwds["ftp_upload_dir"] = config.ftp_upload_dir
         kwds["ftp_upload_purge"] = config.ftp_upload_purge
+        kwds["tmp_dir"] = config.file_source_temp_dir
+        kwds["webdav_use_temp_files"] = config.file_source_webdav_use_temp_files
+        kwds["listings_expiry_time"] = config.file_source_listings_expiry_time
+
         return FileSourcePluginsConfig(**kwds)
 
     def to_dict(self):
@@ -64,6 +77,9 @@ class FileSourcePluginsConfig:
             "user_library_import_dir": self.user_library_import_dir,
             "ftp_upload_dir": self.ftp_upload_dir,
             "ftp_upload_purge": self.ftp_upload_purge,
+            "tmp_dir": self.tmp_dir,
+            "webdav_use_temp_files": self.webdav_use_temp_files,
+            "listings_expiry_time": self.listings_expiry_time,
         }
 
     @staticmethod
@@ -75,6 +91,10 @@ class FileSourcePluginsConfig:
             user_library_import_dir=as_dict["user_library_import_dir"],
             ftp_upload_dir=as_dict["ftp_upload_dir"],
             ftp_upload_purge=as_dict["ftp_upload_purge"],
+            # Always provided for new jobs, remove in 25.0
+            tmp_dir=as_dict.get("tmp_dir"),
+            webdav_use_temp_files=as_dict.get("webdav_use_temp_files"),
+            listings_expiry_time=as_dict.get("listings_expiry_time"),
         )
 
 
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 19fcc1b214751b817179ad8df7e2d90a1e9bbc1a..fd1e846701733fde874a29f3552e68aeaa03aa69 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -277,6 +277,10 @@ class SingleFileSource(metaclass=abc.ABCMeta):
         context doesn't need to be present after the plugin is re-hydrated.
         """
 
+    @abc.abstractmethod
+    def prefer_links(self) -> bool:
+        """Prefer linking to files."""
+
 
 class SupportsBrowsing(metaclass=abc.ABCMeta):
     """An interface indicating that this filesource is browsable.
@@ -351,6 +355,9 @@ class BaseFilesSource(FilesSource):
             or (self._user_has_required_roles(user_context) and self._user_has_required_groups(user_context))
         )
 
+    def prefer_links(self) -> bool:
+        return False
+
     @property
     def user_context_required(self) -> bool:
         return self.requires_roles is not None or self.requires_groups is not None
diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py
index afcff2884961340737ca7a742540b5850985cccb..5b3add6e61197449a84c6976a5daa600e723a118 100644
--- a/lib/galaxy/files/sources/_pyfilesystem2.py
+++ b/lib/galaxy/files/sources/_pyfilesystem2.py
@@ -38,6 +38,7 @@ class PyFilesystem2FilesSource(BaseFilesSource):
     required_package: ClassVar[str]
     supports_pagination = True
     supports_search = True
+    allow_key_error_on_empty_directories = False  # work around a bug in webdav
 
     def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         if self.required_module is None:
@@ -65,10 +66,14 @@ class PyFilesystem2FilesSource(BaseFilesSource):
             with self._open_fs(user_context=user_context, opts=opts) as h:
                 if recursive:
                     recursive_result: List[AnyRemoteEntry] = []
-                    for p, dirs, files in h.walk(path, namespaces=["details"]):
-                        to_dict = functools.partial(self._resource_info_to_dict, p)
-                        recursive_result.extend(map(to_dict, dirs))
-                        recursive_result.extend(map(to_dict, files))
+                    try:
+                        for p, dirs, files in h.walk(path, namespaces=["details"]):
+                            to_dict = functools.partial(self._resource_info_to_dict, p)
+                            recursive_result.extend(map(to_dict, dirs))
+                            recursive_result.extend(map(to_dict, files))
+                    except KeyError:
+                        if not self.allow_key_error_on_empty_directories:
+                            raise
                     return recursive_result, len(recursive_result)
                 else:
                     page = self._to_page(limit, offset)
diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 1848cf57cb244e27e7cd3f94ccd512e109887399..691e5ba8d90bcec874f890f793a56703b76ada0c 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -201,11 +201,8 @@ class RDMFilesSource(BaseFilesSource):
         return effective_props
 
     def get_authorization_token(self, user_context: OptionalUserContext) -> Optional[str]:
-        token = None
-        if user_context:
-            effective_props = self._serialization_props(user_context)
-            token = effective_props.get("token")
-        return token
+        effective_props = self._serialization_props(user_context)
+        return effective_props.get("token")
 
     def get_public_name(self, user_context: OptionalUserContext) -> Optional[str]:
         effective_props = self._serialization_props(user_context)
diff --git a/lib/galaxy/files/sources/dropbox.py b/lib/galaxy/files/sources/dropbox.py
index 70c994e3e2e47d89c285ad879c0aa3c4ec1fcccd..e8bad36d281293a9a877c662a5bde2c87f7f0113 100644
--- a/lib/galaxy/files/sources/dropbox.py
+++ b/lib/galaxy/files/sources/dropbox.py
@@ -30,6 +30,8 @@ class DropboxFilesSource(PyFilesystem2FilesSource):
         # accessToken has been renamed to access_token in fs.dropboxfs 1.0
         if "accessToken" in props:
             props["access_token"] = props.pop("accessToken")
+        if "oauth2_access_token" in props:
+            props["access_token"] = props.pop("oauth2_access_token")
 
         try:
             handle = DropboxFS(**{**props, **extra_props})
diff --git a/lib/galaxy/files/sources/googledrive.py b/lib/galaxy/files/sources/googledrive.py
index c5e777d6b78d729587280c2b713c7063d4baa803..e809d4cd03bfe8fc3b56024e2ec66588e0a7ad5a 100644
--- a/lib/galaxy/files/sources/googledrive.py
+++ b/lib/galaxy/files/sources/googledrive.py
@@ -17,6 +17,9 @@ class GoogleDriveFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
+        access_token = props.pop("oauth2_access_token")
+        if access_token:
+            props["token"] = access_token
         credentials = Credentials(**props)
         handle = GoogleDriveFS(credentials)
         return handle
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 146d63d0b641bf8e3f0d4a1cb51549b86c853537..329507cf1862d518685ef7e392711b38b0dd6769 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -347,12 +347,10 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
         if is_draft_record:
             file_details_url = self._to_draft_url(file_details_url)
             download_file_content_url = self._to_draft_url(download_file_content_url)
-        file_details = self._get_response(user_context, file_details_url)
-        if not self._can_download_from_api(file_details):
-            # TODO: This is a temporary workaround for the fact that the "content" API
-            # does not support downloading files from S3 or other remote storage classes.
-            # More info: https://inveniordm.docs.cern.ch/reference/file_storage/#remote-files-r
-            download_file_content_url = f"{file_details_url.replace('/api', '')}?download=1"
+        # Downloading through the API is only supported for local files and depends on how
+        # the InvenioRDM instance file storage is configured.
+        # So this is the most reliable way to download files for now it.
+        download_file_content_url = f"{file_details_url.replace('/api', '')}?download=1"
         return download_file_content_url
 
     def _is_api_url(self, url: str) -> bool:
@@ -361,11 +359,6 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
     def _to_draft_url(self, url: str) -> str:
         return url.replace("/files/", "/draft/files/")
 
-    def _can_download_from_api(self, file_details: dict) -> bool:
-        # Only files stored locally seems to be fully supported by the API for now
-        # More info: https://inveniordm.docs.cern.ch/reference/file_storage/
-        return file_details["storage_class"] == "L"
-
     def _is_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
         request_url = self._get_draft_record_url(record_id)
         headers = self._get_request_headers(user_context)
diff --git a/lib/galaxy/files/sources/onedata.py b/lib/galaxy/files/sources/onedata.py
index af7c104c9eaff1a91013107b965e7d9bcb4d47a6..87f455c68dd95ce28f9df89f30be7b578eef707d 100644
--- a/lib/galaxy/files/sources/onedata.py
+++ b/lib/galaxy/files/sources/onedata.py
@@ -5,6 +5,7 @@ except ImportError:
 
 from typing import Optional
 
+from galaxy.util import mapped_chars
 from . import FilesSourceOptions
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
@@ -22,11 +23,20 @@ class OnedataFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
-        onezone_domain = props.pop("onezoneDomain", "") or ""
+
+        access_token = props.pop("access_token", "") or ""
+        onezone_domain = props.pop("onezone_domain", "") or ""
         onezone_domain = remove_prefix("http://", remove_prefix("https://", onezone_domain))
-        access_token = props.pop("accessToken", "") or ""
-        disable_tls_certificate_validation = props.pop("disableTlsCertificateValidation", False) or False
-        handle = OnedataRESTFS(onezone_domain, access_token, verify_ssl=not disable_tls_certificate_validation)
+        disable_tls_certificate_validation = props.pop("disable_tls_certificate_validation", False) or False
+
+        alt_space_fqn_separators = [mapped_chars["@"]] if "@" in mapped_chars else None
+
+        handle = OnedataRESTFS(
+            onezone_domain,
+            access_token,
+            alt_space_fqn_separators=alt_space_fqn_separators,
+            verify_ssl=not disable_tls_certificate_validation,
+        )
         return handle
 
 
diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index 8768b5b5ca9ce1843ad30c1b1f49b0ad0fd317bf..258d5ef20a692369dfd9d9894f4a5c03eb001100 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -26,6 +26,7 @@ from . import (
 DEFAULT_ENFORCE_SYMLINK_SECURITY = True
 DEFAULT_DELETE_ON_REALIZE = False
 DEFAULT_ALLOW_SUBDIR_CREATION = True
+DEFAULT_PREFER_LINKS = False
 
 
 class PosixFilesSourceProperties(FilesSourceProperties, total=False):
@@ -33,6 +34,7 @@ class PosixFilesSourceProperties(FilesSourceProperties, total=False):
     enforce_symlink_security: bool
     delete_on_realize: bool
     allow_subdir_creation: bool
+    prefer_links: bool
 
 
 class PosixFilesSource(BaseFilesSource):
@@ -53,6 +55,10 @@ class PosixFilesSource(BaseFilesSource):
         self.enforce_symlink_security = props.get("enforce_symlink_security", DEFAULT_ENFORCE_SYMLINK_SECURITY)
         self.delete_on_realize = props.get("delete_on_realize", DEFAULT_DELETE_ON_REALIZE)
         self.allow_subdir_creation = props.get("allow_subdir_creation", DEFAULT_ALLOW_SUBDIR_CREATION)
+        self._prefer_links = props.get("prefer_links", DEFAULT_PREFER_LINKS)
+
+    def prefer_links(self) -> bool:
+        return self._prefer_links
 
     def _list(
         self,
@@ -182,6 +188,7 @@ class PosixFilesSource(BaseFilesSource):
             "enforce_symlink_security": self.enforce_symlink_security,
             "delete_on_realize": self.delete_on_realize,
             "allow_subdir_creation": self.allow_subdir_creation,
+            "prefer_links": self._prefer_links,
         }
 
     @property
diff --git a/lib/galaxy/files/sources/s3fs.py b/lib/galaxy/files/sources/s3fs.py
index 6967f4a5b6a74bb79e4e2426ed0dbc5d504b4da1..c6a7dedc96d3f951eb870c5abab4e43d96a071a3 100644
--- a/lib/galaxy/files/sources/s3fs.py
+++ b/lib/galaxy/files/sources/s3fs.py
@@ -8,7 +8,10 @@ from typing import (
     Tuple,
 )
 
-from typing_extensions import Unpack
+from typing_extensions import (
+    NotRequired,
+    Unpack,
+)
 
 from galaxy.files import OptionalUserContext
 from . import (
@@ -35,6 +38,7 @@ class S3FsFilesSourceProperties(FilesSourceProperties, total=False):
     endpoint_url: int
     user: str
     passwd: str
+    listings_expiry_time: NotRequired[Optional[int]]
     client_kwargs: dict  # internally computed. Should not be specified in config file
 
 
@@ -45,6 +49,14 @@ class S3FsFilesSource(BaseFilesSource):
         if s3fs is None:
             raise Exception("Package s3fs unavailable but required for this file source plugin.")
         props: S3FsFilesSourceProperties = cast(S3FsFilesSourceProperties, self._parse_common_config_opts(kwd))
+        file_sources_config = self._file_sources_config
+        if (
+            props.get("listings_expiry_time") is None
+            and file_sources_config
+            and file_sources_config.listings_expiry_time
+        ):
+            if file_sources_config.listings_expiry_time:
+                props["listings_expiry_time"] = file_sources_config.listings_expiry_time
         # There is a possibility that the bucket name could be parameterized: e.g.
         # bucket: ${user.preferences['generic_s3|bucket']}
         # that's ok, because we evaluate the bucket name again later. The bucket property here will only
diff --git a/lib/galaxy/files/sources/util.py b/lib/galaxy/files/sources/util.py
index 3704aaa7a71b210df482e33b249cdf8d47e5e392..a3af04f6bff4b19cde9789bc0dc802ae74d47482 100644
--- a/lib/galaxy/files/sources/util.py
+++ b/lib/galaxy/files/sources/util.py
@@ -1,10 +1,8 @@
 import time
-from os import PathLike
 from typing import (
     List,
     Optional,
     Tuple,
-    Union,
 )
 
 from galaxy import exceptions
@@ -20,8 +18,7 @@ from galaxy.util import (
     requests,
 )
 from galaxy.util.config_parsers import IpAllowedListEntryT
-
-TargetPathT = Union[str, PathLike]
+from galaxy.util.path import StrPath
 
 
 def _not_implemented(drs_uri: str, desc: str) -> NotImplementedError:
@@ -79,7 +76,7 @@ def _get_access_info(obj_url: str, access_method: dict, headers=None) -> Tuple[s
 
 def fetch_drs_to_file(
     drs_uri: str,
-    target_path: TargetPathT,
+    target_path: StrPath,
     user_context: Optional[FileSourcesUserContext],
     force_http=False,
     retry_options: Optional[RetryOptions] = None,
diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py
index 2e11a51d98b267f0d0694ce869afcade66367fb6..9aec17fdbdc4ddfeb2592b63de3622088b4ee6a5 100644
--- a/lib/galaxy/files/sources/webdav.py
+++ b/lib/galaxy/files/sources/webdav.py
@@ -5,10 +5,13 @@ except ImportError:
 
 import tempfile
 from typing import (
+    cast,
     Optional,
     Union,
 )
 
+from typing_extensions import NotRequired
+
 from . import (
     FilesSourceOptions,
     FilesSourceProperties,
@@ -16,18 +19,35 @@ from . import (
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
+class WebDavFilesSourceProperties(FilesSourceProperties, total=False):
+    use_temp_files: NotRequired[Optional[bool]]
+    temp_path: NotRequired[Optional[str]]
+
+
 class WebDavFilesSource(PyFilesystem2FilesSource):
     plugin_type = "webdav"
     required_module = WebDAVFS
     required_package = "fs.webdavfs"
+    allow_key_error_on_empty_directories = True
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
-        props = self._serialization_props(user_context)
+        props = cast(WebDavFilesSourceProperties, self._serialization_props(user_context))
+        file_sources_config = self._file_sources_config
         use_temp_files = props.pop("use_temp_files", None)
+        if use_temp_files is None and file_sources_config and file_sources_config.webdav_use_temp_files is not None:
+            use_temp_files = file_sources_config.webdav_use_temp_files
         if use_temp_files is None:
             # Default to True to avoid memory issues with large files.
-            props["use_temp_files"] = True
-            props["temp_path"] = props.get("temp_path", tempfile.TemporaryDirectory(prefix="webdav_"))
+            use_temp_files = True
+
+        if use_temp_files:
+            temp_path = props.get("temp_path")
+            if temp_path is None and file_sources_config and file_sources_config.tmp_dir:
+                temp_path = file_sources_config.tmp_dir
+            if temp_path is None:
+                temp_path = tempfile.mkdtemp(prefix="webdav_")
+            props["temp_path"] = temp_path
+        props["use_temp_files"] = use_temp_files
         extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
         handle = WebDAVFS(**{**props, **extra_props})
         return handle
diff --git a/lib/galaxy/files/templates/__init__.py b/lib/galaxy/files/templates/__init__.py
index aa8faf85fd30881cb026b0646d90e1a58bef4cf0..2aef4eb906ed339fb0bbde34093f2306dd9dd45a 100644
--- a/lib/galaxy/files/templates/__init__.py
+++ b/lib/galaxy/files/templates/__init__.py
@@ -4,6 +4,8 @@ from .models import (
     FileSourceTemplate,
     FileSourceTemplateSummaries,
     FileSourceTemplateType,
+    get_oauth2_config,
+    get_oauth2_config_or_none,
     template_to_configuration,
 )
 
@@ -13,5 +15,7 @@ __all__ = (
     "FileSourceTemplate",
     "FileSourceTemplateSummaries",
     "FileSourceTemplateType",
+    "get_oauth2_config",
+    "get_oauth2_config_or_none",
     "template_to_configuration",
 )
diff --git a/lib/galaxy/files/templates/examples/admin_secrets.yml b/lib/galaxy/files/templates/examples/admin_secrets.yml
index 5c421b2278e22d2f45a20e2960fa0229d666dfce..494ca04b5ab590a4be7326ef40824af3be3351b7 100644
--- a/lib/galaxy/files/templates/examples/admin_secrets.yml
+++ b/lib/galaxy/files/templates/examples/admin_secrets.yml
@@ -1,4 +1,5 @@
 - id: admin_secret_directory
+  version: 0
   name: Secret Directory
   description: An directory constructed from admin secrets.
   configuration:
diff --git a/lib/galaxy/files/templates/examples/admin_secrets_with_defaults.yml b/lib/galaxy/files/templates/examples/admin_secrets_with_defaults.yml
index 2cbec347ce8cd7d6e1b6611ab9bf700b91427b11..ab3a6fdf769e02ed98e618686d14474365dc43b3 100644
--- a/lib/galaxy/files/templates/examples/admin_secrets_with_defaults.yml
+++ b/lib/galaxy/files/templates/examples/admin_secrets_with_defaults.yml
@@ -1,4 +1,5 @@
 - id: admin_secret_directory
+  version: 0
   name: Secret Directory with Defaults
   description: An directory constructed from admin secrets or defaults.
   configuration:
diff --git a/lib/galaxy/files/templates/examples/dropbox_client_secrets_explicit.yml b/lib/galaxy/files/templates/examples/dropbox_client_secrets_explicit.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4206e9997b6286f1511b80d1e580f57b6a02e54d
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/dropbox_client_secrets_explicit.yml
@@ -0,0 +1,7 @@
+- id: dropbox
+  name: Dropbox
+  description: Connect to your Dropbox account to download and upload files.
+  configuration:
+    type: dropbox
+    oauth2_client_id: abcdefgh
+    oauth2_client_secret: ijklmnopqr
diff --git a/lib/galaxy/files/templates/examples/dropbox_client_secrets_in_vault.yml b/lib/galaxy/files/templates/examples/dropbox_client_secrets_in_vault.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4ed3be1ec510b5230b233fac1401de205d636e2f
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/dropbox_client_secrets_in_vault.yml
@@ -0,0 +1,15 @@
+- id: dropbox
+  name: Dropbox
+  description: Connect to your Dropbox account to download and upload files.
+  configuration:
+    type: dropbox
+    oauth2_client_id: "{{ environment.oauth2_client_id }}"
+    oauth2_client_secret: "{{ environment.oauth2_client_secret }}"
+    writable: true
+  environment:
+    oauth2_client_id:
+      type: secret
+      vault_key: "dropbox_file_source/client_id"
+    oauth2_client_secret:
+      type: secret
+      vault_key: "dropbox_file_source/client_secret"
diff --git a/lib/galaxy/files/templates/examples/onedata.yml b/lib/galaxy/files/templates/examples/onedata.yml
new file mode 100644
index 0000000000000000000000000000000000000000..97e950377580bcf47e28f09d9dcafa07ab752c1a
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/onedata.yml
@@ -0,0 +1,44 @@
+- id: onedata
+  version: 0
+  name: Onedata Storage
+  description: |
+    If you have an account in Onedata, you can use such a file source to upload
+    your data directly from Onedata to Galaxy. You can also perform
+    an "Export datasets to remote files source" of a dataset from Galaxy to
+    Onedata.
+
+    The minimal supported Onezone version is 21.02.4.
+    More information on Onedata can be found on [Onedata's website](https://onedata.org/#/home).
+  variables:
+    onezone_domain:
+      label: Onezone domain
+      type: string
+      help: Domain of the Onezone service (e.g. datahub.egi.eu) to connect to.
+    disable_tls_certificate_validation:
+      label: Disable tls certificate validation?
+      type: boolean
+      help: |
+        Allows connection to Onedata servers that do not present trusted SSL certificates.
+        SHOULD NOT be used unless you really know what you are doing.
+      default: False
+    writable:
+      label: Writable?
+      type: boolean
+      help: |
+        Allow Galaxy to write data to this Onedata storage.
+        Requires an access token with write data access.
+      default: False
+  secrets:
+    access_token:
+      label: Access Token
+      help: |
+        Your [access token](https://onedata.org/#/home/documentation/topic/stable/tokens),
+        suitable for REST API access in a Oneprovider service. May be confined
+        to read-only data access, unless you wish to use the
+        "Export datasets to remote files source" tool (write permissions are needed then).
+  configuration:
+    type: onedata
+    access_token: "{{ secrets.access_token }}"
+    onezone_domain: "{{ variables.onezone_domain }}"
+    disable_tls_certificate_validation: "{{ variables.disable_tls_certificate_validation }}"
+    writable: "{{ variables.writable }}"
diff --git a/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml b/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml
index 81e62afa16ad4361db66c1e6ec24802bb21f90a7..600bbdebb09e81d2d800bad4b44fcabdbf49df15 100644
--- a/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml
+++ b/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml
@@ -1,12 +1,13 @@
 - id: aws_private
+  version: 0
   name: Amazon Web Services Private Bucket
-  description: Setup access to a private AWS bucket using a secret access key. 
+  description: Setup access to a private AWS bucket using a secret access key.
   configuration:
     type: s3fs
-    bucket: "{{ bucket }}"
-    writable: "{{ writable }}"
-    secret: "{{ secret_key }}"
-    key: "{{ access_key }}"
+    bucket: "{{ variables.bucket }}"
+    writable: "{{ variables.writable }}"
+    secret: "{{ secrets.secret_key }}"
+    key: "{{ variables.access_key }}"
   variables:
     access_key:
       label: Access Key ID
@@ -26,5 +27,5 @@
   secrets:
     secret_key:
       label: Secret Access Key
-      help: |        
+      help: |
         The "secret access key" as defined in the [Amazon Documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
diff --git a/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml b/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml
index fd1493e726f4b60f31506367be4cdf4989346244..22ee645b3e3757fe40df8514ef17a449ae752ff8 100644
--- a/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml
+++ b/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml
@@ -1,6 +1,7 @@
 - id: aws_public
+  version: 0
   name: Amazon Web Services Public Bucket
-  description: Setup anonymous access to a public AWS bucket. 
+  description: Setup anonymous access to a public AWS bucket.
   configuration:
     type: s3fs
     bucket: "{{ variables.bucket }}"
diff --git a/lib/galaxy/files/templates/examples/production_dropbox.yml b/lib/galaxy/files/templates/examples/production_dropbox.yml
new file mode 100644
index 0000000000000000000000000000000000000000..61ac82ad1041d2e2dccda2717bff039ebb04ce82
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/production_dropbox.yml
@@ -0,0 +1,15 @@
+- id: dropbox
+  name: Dropbox
+  description: Connect to your Dropbox account to download and upload files.
+  configuration:
+    type: dropbox
+    oauth2_client_id: "{{ environment.oauth2_client_id }}"
+    oauth2_client_secret: "{{ environment.oauth2_client_secret }}"
+    writable: true
+  environment:
+    oauth2_client_id:
+      type: variable
+      variable: GALAXY_DROPBOX_APP_CLIENT_ID
+    oauth2_client_secret:
+      type: variable
+      variable: GALAXY_DROPBOX_APP_CLIENT_SECRET
diff --git a/lib/galaxy/files/templates/examples/production_google_drive.yml b/lib/galaxy/files/templates/examples/production_google_drive.yml
new file mode 100644
index 0000000000000000000000000000000000000000..164b162ef3868059428ed2c9d32a856cce743f90
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/production_google_drive.yml
@@ -0,0 +1,15 @@
+- id: google_drive
+  name: Export to Google Drive
+  description: This file source allows export to your Google Drive but can only read files uploaded by this Galaxy instance.
+  configuration:
+    type: googledrive
+    oauth2_client_id: "{{ environment.oauth2_client_id }}"
+    oauth2_client_secret: "{{ environment.oauth2_client_secret }}"
+    writable: true
+  environment:
+    oauth2_client_id:
+      type: variable
+      variable: GALAXY_GOOGLE_DRIVE_APP_CLIENT_ID
+    oauth2_client_secret:
+      type: variable
+      variable: GALAXY_GOOGLE_DRIVE_APP_CLIENT_SECRET
diff --git a/lib/galaxy/files/templates/examples/production_s3fs.yml b/lib/galaxy/files/templates/examples/production_s3fs.yml
index 19cea3e41dcb16041deea3b73ee5888f9b275abb..d0aeb928d24595d7eaf9938fc0cab79a4570d818 100644
--- a/lib/galaxy/files/templates/examples/production_s3fs.yml
+++ b/lib/galaxy/files/templates/examples/production_s3fs.yml
@@ -1,4 +1,5 @@
 - id: s3fs
+  version: 0
   name: S3 Compatible Storage with Credentials
   description: |
     The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
@@ -19,7 +20,64 @@
         that is accessing the data. The [Amazon documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/security-creds.html)
         calls these an "access key ID", the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
         describes these as ``aws_access_key_id``.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. How to setup buckets for your storage will vary from service to service
+        but all S3 compatible storage services should have the concept of a bucket to namespace
+        a grouping of your data together with.
+    endpoint_url:
+      label: S3-Compatible API Endpoint
+      type: string
+      help: |
+        If the documentation for your storage service has something called an ``endpoint_url``,
+        For instance, the CloudFlare documentation describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
+        you would substitute your CloudFlare account ID into the endpoint url and use that value.
+        So if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
+        The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
+        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
+        this value would be entered here.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        The secret key used to connect to the S3 compatible storage with for the given access key.
+
+        The [Amazon documentation] calls these an "secret access key" and
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
+        this the ``secret_key``.
+  configuration:
+    type: s3fs
+    endpoint_url: '{{ variables.endpoint_url }}'
+    key: '{{ variables.access_key }}'
+    secret: '{{ secrets.secret_key }}'
+    bucket: '{{ variables.bucket }}'
+
+- id: s3fs
+  version: 1
+  name: S3 Compatible Storage with Credentials
+  description: |
+    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
+    of an unofficial standard for cloud storage across a variety of vendors and services.
+    Many vendors offer storage APIs compatible with S3. This template configuration allows
+    using such service as a Galaxy storage location as long as you are able to find the
+    connection details and have the relevant credentials.
 
+    Given the amount of information needed to connect to such a service, this is a bit of an
+    advanced template and probably should not be used to connect to a service if a more
+    specific template is available.
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        The less secure part of your access tokens or access keys that describe the user
+        that is accessing the data. The [Amazon documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/security-creds.html)
+        calls these an "access key ID", the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_access_key_id``.
     bucket:
       label: Bucket
       type: string
@@ -39,6 +97,10 @@
         The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
         documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
         this value would be entered here.
+    writable:
+      label: Writable?
+      type: boolean
+      help: Is this a bucket you have permission to write to?
   secrets:
     secret_key:
       label: Secret Access Key
@@ -55,3 +117,4 @@
     key: '{{ variables.access_key }}'
     secret: '{{ secrets.secret_key }}'
     bucket: '{{ variables.bucket }}'
+    writable: '{{ variables.writable }}'
diff --git a/lib/galaxy/files/templates/examples/production_webdav.yml b/lib/galaxy/files/templates/examples/production_webdav.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0767dc550867e68ee6dbf42e3b3cfc334adaf936
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/production_webdav.yml
@@ -0,0 +1,42 @@
+- id: webdav
+  version: 0
+  name: WebDAV
+  description: |
+    The WebDAV protocol is a simple way to access files over the internet. This template
+    configuration allows you to connect to a WebDAV server.
+  variables:
+    url:
+      label: Server Domain (e.g. https://myowncloud.org)
+      type: string
+      help: |
+        The domain of the WebDAV server you are connecting to. This should be the full URL
+        including the protocol (http or https) and the domain name.
+    root:
+      label: WebDAV server Path (should end with /remote.php/webdav, e.g. /a/sub/path/remote.php/webdav)
+      type: string
+      help: |
+        The full server path to the WebDAV service. Ensure the path includes /remote.php/webdav.
+    login:
+      label: Username
+      type: string
+      help: |
+        The username to use to connect to the WebDAV server. This should be the username you use
+        to log in to the WebDAV server.
+    writable:
+      label: Writable?
+      type: boolean
+      default: false
+      help: Allow Galaxy to write data to this WebDAV server.
+  secrets:
+    password:
+      label: Password
+      help: |
+        The password to use to connect to the WebDAV server. This should be the password you use
+        to log in to the WebDAV server.
+  configuration:
+    type: webdav
+    url: '{{ variables.url }}'
+    root: '{{ variables.root }}'
+    login: '{{ variables.login }}'
+    writable: '{{ variables.writable }}'
+    password: '{{ secrets.password }}'
diff --git a/lib/galaxy/files/templates/examples/s3fs_by_host_and_port.yml b/lib/galaxy/files/templates/examples/s3fs_by_host_and_port.yml
index 3381d2357a6e218fb210d9f5b497b45b889ab5ac..dc457ad3238f20893d4a536c5bf48e5f8575706c 100644
--- a/lib/galaxy/files/templates/examples/s3fs_by_host_and_port.yml
+++ b/lib/galaxy/files/templates/examples/s3fs_by_host_and_port.yml
@@ -1,4 +1,5 @@
 - id: s3fs
+  version: 0
   name: S3 Compatible Storage with Credentials
   description: |
     The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
@@ -19,7 +20,6 @@
         that is accessing the data. The [Amazon documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/security-creds.html)
         calls these an "access key ID", the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
         describes these as ``aws_access_key_id``.
-
     bucket:
       label: Bucket
       type: string
@@ -34,13 +34,12 @@
       help: |
         The [hostname](https://en.wikipedia.org/wiki/Hostname) used to connect to the target
         S3 compatible service.
-        
+
         If the documentation for your storage service has something called an ``endpoint_url``,
         this can be used to determine this value. For instance, the CloudFlare documentation
         describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
         you would substitute your CloudFlare account ID into the endpoint and shave off the ``https://``,
         so if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
-
     port:
       label: Connection Port
       type: integer
diff --git a/lib/galaxy/files/templates/examples/templating_override.yml b/lib/galaxy/files/templates/examples/templating_override.yml
index ad11b3265ebf7fee5fa2661cc6408fcfeee70bda..03d5a8497c45f3080ebe586fefaba82fe6d5f056 100644
--- a/lib/galaxy/files/templates/examples/templating_override.yml
+++ b/lib/galaxy/files/templates/examples/templating_override.yml
@@ -1,4 +1,5 @@
 - id: project_disk
+  version: 0
   name: Project Disk
   description: |
     Disk in our institutional ``/data`` directory for you user's project.""
diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py
index 2e22cc904c3067ac7e2d42a77a0cfc24838a4c9a..967d83ea0894973303653950985fbdb57d198d13 100644
--- a/lib/galaxy/files/templates/models.py
+++ b/lib/galaxy/files/templates/models.py
@@ -11,9 +11,14 @@ from typing import (
 from pydantic import RootModel
 
 from galaxy.util.config_templates import (
+    ConfiguredOAuth2Sources,
     EnvironmentDict,
     expand_raw_config,
+    get_oauth2_config_from,
+    ImplicitConfigurationParameters,
     MarkdownContent,
+    merge_implicit_parameters,
+    OAuth2Configuration,
     populate_default_variables,
     SecretsDict,
     StrictModel,
@@ -25,7 +30,7 @@ from galaxy.util.config_templates import (
     UserDetailsDict,
 )
 
-FileSourceTemplateType = Literal["ftp", "posix", "s3fs", "azure"]
+FileSourceTemplateType = Literal["ftp", "posix", "s3fs", "azure", "onedata", "webdav", "dropbox", "googledrive"]
 
 
 class PosixFileSourceTemplateConfiguration(StrictModel):
@@ -42,6 +47,54 @@ class PosixFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class OAuth2TemplateConfiguration:
+    oauth2_client_id: Union[str, TemplateExpansion]
+    oauth2_client_secret: Union[str, TemplateExpansion]
+
+
+class DropboxFileSourceTemplateConfiguration(OAuth2TemplateConfiguration, StrictModel):
+    type: Literal["dropbox"]
+    writable: Union[bool, TemplateExpansion] = False
+    oauth2_client_id: Union[str, TemplateExpansion]
+    oauth2_client_secret: Union[str, TemplateExpansion]
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class OAuth2FileSourceConfiguration:
+    oauth2_access_token: str
+
+
+class DropboxFileSourceConfiguration(OAuth2FileSourceConfiguration, StrictModel):
+    type: Literal["dropbox"]
+    writable: bool = False
+    oauth2_access_token: str
+
+
+class GoogleDriveFileSourceTemplateConfiguration(OAuth2TemplateConfiguration, StrictModel):
+    type: Literal["googledrive"]
+    writable: Union[bool, TemplateExpansion] = False
+    oauth2_client_id: Union[str, TemplateExpansion]
+    oauth2_client_secret: Union[str, TemplateExpansion]
+    # Will default to https://www.googleapis.com/auth/drive.file, which provides
+    # access to a folder specific to your Galaxy instance. Ideally we would use
+    # https://www.googleapis.com/auth/drive but that would require becoming
+    # Google verified - https://support.google.com/cloud/answer/13464321#ss-rs-requirements.
+    # That seems like a onerous process and I don't know how it would
+    # work in the context of an open source project like Galaxy, I am
+    # adding the extension point here for the brave individual that would like
+    # to use it but I expect it isn't practical for the typical admin.
+    oauth2_scope: Optional[Union[str, TemplateExpansion]] = None
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class GoogleDriveFileSourceConfiguration(OAuth2FileSourceConfiguration, StrictModel):
+    type: Literal["googledrive"]
+    writable: bool = False
+    oauth2_access_token: str
+
+
 class S3FSFileSourceTemplateConfiguration(StrictModel):
     type: Literal["s3fs"]
     endpoint_url: Optional[Union[str, TemplateExpansion]] = None
@@ -104,17 +157,63 @@ class AzureFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class OnedataFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["onedata"]
+    access_token: Union[str, TemplateExpansion]
+    onezone_domain: Union[str, TemplateExpansion]
+    disable_tls_certificate_validation: Union[bool, TemplateExpansion] = False
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class OnedataFileSourceConfiguration(StrictModel):
+    type: Literal["onedata"]
+    access_token: str
+    onezone_domain: str
+    disable_tls_certificate_validation: bool = False
+    writable: bool = False
+
+
+class WebdavFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["webdav"]
+    url: Union[str, TemplateExpansion]
+    root: Union[str, TemplateExpansion]
+    login: Union[str, TemplateExpansion]
+    password: Union[str, TemplateExpansion]
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class WebdavFileSourceConfiguration(StrictModel):
+    type: Literal["webdav"]
+    url: str
+    root: str
+    login: str
+    password: str
+    writable: bool = False
+
+
 FileSourceTemplateConfiguration = Union[
     PosixFileSourceTemplateConfiguration,
     S3FSFileSourceTemplateConfiguration,
     FtpFileSourceTemplateConfiguration,
     AzureFileSourceTemplateConfiguration,
+    OnedataFileSourceTemplateConfiguration,
+    WebdavFileSourceTemplateConfiguration,
+    DropboxFileSourceTemplateConfiguration,
+    GoogleDriveFileSourceTemplateConfiguration,
 ]
 FileSourceConfiguration = Union[
     PosixFileSourceConfiguration,
     S3FSFileSourceConfiguration,
     FtpFileSourceConfiguration,
     AzureFileSourceConfiguration,
+    OnedataFileSourceConfiguration,
+    WebdavFileSourceConfiguration,
+    DropboxFileSourceConfiguration,
+    GoogleDriveFileSourceConfiguration,
 ]
 
 
@@ -149,6 +248,10 @@ class FileSourceTemplate(FileSourceTemplateBase):
     configuration: FileSourceTemplateConfiguration
     environment: Optional[List[TemplateEnvironmentEntry]] = None
 
+    @property
+    def type(self):
+        return self.configuration.type
+
 
 FileSourceTemplateCatalog = RootModel[List[FileSourceTemplate]]
 
@@ -163,10 +266,12 @@ def template_to_configuration(
     secrets: SecretsDict,
     user_details: UserDetailsDict,
     environment: EnvironmentDict,
+    implicit: Optional[ImplicitConfigurationParameters] = None,
 ) -> FileSourceConfiguration:
     configuration_template = template.configuration
     populate_default_variables(template.variables, variables)
     raw_config = expand_raw_config(configuration_template, variables, secrets, user_details, environment)
+    merge_implicit_parameters(raw_config, implicit)
     return to_configuration_object(raw_config)
 
 
@@ -175,9 +280,38 @@ TypesToConfigurationClasses: Dict[FileSourceTemplateType, Type[FileSourceConfigu
     "posix": PosixFileSourceConfiguration,
     "s3fs": S3FSFileSourceConfiguration,
     "azure": AzureFileSourceConfiguration,
+    "onedata": OnedataFileSourceConfiguration,
+    "webdav": WebdavFileSourceConfiguration,
+    "dropbox": DropboxFileSourceConfiguration,
+    "googledrive": GoogleDriveFileSourceConfiguration,
 }
 
 
+OAUTH2_CONFIGURED_SOURCES: ConfiguredOAuth2Sources = {
+    "dropbox": OAuth2Configuration(
+        authorize_url="https://www.dropbox.com/oauth2/authorize",
+        authorize_params={"token_access_type": "offline"},
+        token_url="https://api.dropbox.com/oauth2/token",
+    ),
+    "googledrive": OAuth2Configuration(
+        authorize_url="https://accounts.google.com/o/oauth2/v2/auth",
+        authorize_params={"access_type": "offline", "prompt": "consent"},
+        token_url="https://oauth2.googleapis.com/token",
+        scope="https://www.googleapis.com/auth/drive.file",
+    ),
+}
+
+
+def get_oauth2_config(template: FileSourceTemplate) -> OAuth2Configuration:
+    return get_oauth2_config_from(template, OAUTH2_CONFIGURED_SOURCES)
+
+
+def get_oauth2_config_or_none(template: FileSourceTemplate) -> Optional[OAuth2Configuration]:
+    if template.configuration.type not in OAUTH2_CONFIGURED_SOURCES:
+        return None
+    return get_oauth2_config(template)
+
+
 def to_configuration_object(configuration_dict: Dict[str, Any]) -> FileSourceConfiguration:
     if "type" not in configuration_dict:
         raise KeyError("Configuration objects require a file source 'type' key, none found.")
diff --git a/lib/galaxy/files/uris.py b/lib/galaxy/files/uris.py
index d35e51d696c4ee73c27566e7f14721bc6b19761a..9d48853294d6d98db40760dde44c7f8240e49ea2 100644
--- a/lib/galaxy/files/uris.py
+++ b/lib/galaxy/files/uris.py
@@ -49,8 +49,7 @@ def stream_url_to_file(
     target_path: Optional[str] = None,
     file_source_opts: Optional[FilesSourceOptions] = None,
 ) -> str:
-    if file_sources is None:
-        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    file_sources = ensure_file_sources(file_sources)
     file_source, rel_path = file_sources.get_file_source_path(url)
     if file_source:
         if not target_path:
@@ -62,6 +61,12 @@ def stream_url_to_file(
         raise NoMatchingFileSource(f"Could not find a matching handler for: {url}")
 
 
+def ensure_file_sources(file_sources: Optional["ConfiguredFileSources"]) -> "ConfiguredFileSources":
+    if file_sources is None:
+        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    return file_sources
+
+
 def stream_to_file(stream, suffix="", prefix="", dir=None, text=False, **kwd):
     """Writes a stream to a temporary file, returns the temporary file's name"""
     fd, temp_name = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir, text=text)
diff --git a/lib/galaxy/job_execution/compute_environment.py b/lib/galaxy/job_execution/compute_environment.py
index de81b0d4e2ffc82a59437025527e808539355cc5..bdd5b2ed96e7e817cb783c9dac5cb1adf0ace7b9 100644
--- a/lib/galaxy/job_execution/compute_environment.py
+++ b/lib/galaxy/job_execution/compute_environment.py
@@ -8,6 +8,7 @@ from typing import (
     Dict,
 )
 
+from galaxy.job_execution.datasets import DeferrableObjectsT
 from galaxy.job_execution.setup import JobIO
 from galaxy.model import Job
 
@@ -22,6 +23,9 @@ class ComputeEnvironment(metaclass=ABCMeta):
     compute server.
     """
 
+    def __init__(self):
+        self.materialized_objects: Dict[str, DeferrableObjectsT] = {}
+
     @abstractmethod
     def output_names(self):
         """Output unqualified filenames defined by job."""
diff --git a/lib/galaxy/job_execution/container_monitor.py b/lib/galaxy/job_execution/container_monitor.py
index dfed37daf8d0b8feeebe134e1bc76b794756ce57..0590ce715db94a7323a87e4d3f7d90843612b9c1 100644
--- a/lib/galaxy/job_execution/container_monitor.py
+++ b/lib/galaxy/job_execution/container_monitor.py
@@ -75,7 +75,8 @@ def main():
                         if ports[key]["host"] == "0.0.0.0":
                             ports[key]["host"] = host_ip
                 if callback_url:
-                    requests.post(callback_url, json={"container_runtime": ports}, timeout=DEFAULT_SOCKET_TIMEOUT)
+                    r = requests.post(callback_url, json={"container_runtime": ports}, timeout=DEFAULT_SOCKET_TIMEOUT)
+                    r.raise_for_status()
                 else:
                     with open("container_runtime.json", "w") as f:
                         json.dump(ports, f)
diff --git a/lib/galaxy/job_execution/datasets.py b/lib/galaxy/job_execution/datasets.py
index 69ed7a9022460f89d04f56e7f52bf1aa6564cc50..529f54832a5813791dce02671b43e95a83b6bbb5 100644
--- a/lib/galaxy/job_execution/datasets.py
+++ b/lib/galaxy/job_execution/datasets.py
@@ -7,6 +7,15 @@ from abc import (
     ABCMeta,
     abstractmethod,
 )
+from typing import Union
+
+from galaxy.model import (
+    DatasetCollectionElement,
+    DatasetInstance,
+    HistoryDatasetCollectionAssociation,
+)
+
+DeferrableObjectsT = Union[DatasetInstance, HistoryDatasetCollectionAssociation, DatasetCollectionElement]
 
 
 def dataset_path_rewrites(dataset_paths):
diff --git a/lib/galaxy/job_execution/setup.py b/lib/galaxy/job_execution/setup.py
index 7458be012d094a4f882ac7a424b9d17b2e825183..57b5492ca8d399af21953f65cb2dcafe57437d7f 100644
--- a/lib/galaxy/job_execution/setup.py
+++ b/lib/galaxy/job_execution/setup.py
@@ -22,6 +22,7 @@ from galaxy.files import (
 from galaxy.job_execution.datasets import (
     DatasetPath,
     DatasetPathRewriter,
+    DeferrableObjectsT,
     get_path_rewriter,
 )
 from galaxy.model import (
@@ -31,7 +32,7 @@ from galaxy.model import (
     MetadataFile,
 )
 from galaxy.util import safe_makedirs
-from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.dictifiable import UsesDictVisibleKeys
 
 TOOL_PROVIDED_JOB_METADATA_FILE = "galaxy.json"
 TOOL_PROVIDED_JOB_METADATA_KEYS = ["name", "info", "dbkey", "created_from_basename"]
@@ -62,7 +63,7 @@ class JobOutputs(threading.local):
         self.output_hdas_and_paths = {t.output_name: (t.dataset, t.dataset_path) for t in job_outputs}
 
 
-class JobIO(Dictifiable):
+class JobIO(UsesDictVisibleKeys):
     dict_collection_visible_keys = (
         "job_id",
         "working_directory",
@@ -148,7 +149,7 @@ class JobIO(Dictifiable):
         self._dataset_path_rewriter: Optional[DatasetPathRewriter] = None
 
     @property
-    def job(self):
+    def job(self) -> Job:
         return self.sa_session.get(Job, self.job_id)
 
     @classmethod
@@ -168,7 +169,7 @@ class JobIO(Dictifiable):
         return cls(sa_session=sa_session, **io_dict)
 
     def to_dict(self):
-        io_dict = super().to_dict()
+        io_dict = super()._dictify_view_keys()
         # dict_for will always add `model_class`, we don't need or want it
         io_dict.pop("model_class")
         io_dict["user_context"] = self.user_context.to_dict()
@@ -217,11 +218,19 @@ class JobIO(Dictifiable):
             filenames.append(ds.dataset.extra_files_path)
         return filenames
 
-    def get_input_datasets(self) -> List[DatasetInstance]:
+    def get_input_datasets(
+        self, materialized_objects: Optional[Dict[str, DeferrableObjectsT]] = None
+    ) -> List[DatasetInstance]:
         job = self.job
-        return [
-            da.dataset for da in job.input_datasets + job.input_library_datasets if da.dataset
-        ]  # da is JobToInputDatasetAssociation object
+        datasets: List[DatasetInstance] = []
+        for da in job.input_datasets + job.input_library_datasets:
+            if materialized_objects and da.name in materialized_objects:
+                materialized_object = materialized_objects[da.name]
+                if isinstance(materialized_object, DatasetInstance):
+                    datasets.append(materialized_object)
+            elif da.dataset:
+                datasets.append(da.dataset)
+        return datasets
 
     def get_input_fnames(self) -> List[str]:
         filenames = []
@@ -229,9 +238,9 @@ class JobIO(Dictifiable):
             filenames.extend(self.get_input_dataset_fnames(ds))
         return filenames
 
-    def get_input_paths(self) -> List[DatasetPath]:
+    def get_input_paths(self, materialized_objects: Optional[Dict[str, DeferrableObjectsT]]) -> List[DatasetPath]:
         paths = []
-        for ds in self.get_input_datasets():
+        for ds in self.get_input_datasets(materialized_objects):
             paths.append(self.get_input_path(ds))
         return paths
 
diff --git a/lib/galaxy/job_metrics/instrumenters/core.py b/lib/galaxy/job_metrics/instrumenters/core.py
index a08ad8f8de5e72f6a999a9b0b14c5d24ecbc7a79..76cd4053ffd2b28433e8e435a0747702a4a20a84 100644
--- a/lib/galaxy/job_metrics/instrumenters/core.py
+++ b/lib/galaxy/job_metrics/instrumenters/core.py
@@ -1,5 +1,6 @@
 """The module describes the ``core`` job metrics plugin."""
 
+import json
 import logging
 import time
 from typing import (
@@ -23,10 +24,16 @@ GALAXY_MEMORY_MB_KEY = "galaxy_memory_mb"
 START_EPOCH_KEY = "start_epoch"
 END_EPOCH_KEY = "end_epoch"
 RUNTIME_SECONDS_KEY = "runtime_seconds"
+CONTAINER_ID = "container_id"
+CONTAINER_TYPE = "container_type"
 
 
 class CorePluginFormatter(JobMetricFormatter):
     def format(self, key: str, value: Any) -> FormattedMetric:
+        if key == CONTAINER_ID:
+            return FormattedMetric("Container ID", value)
+        if key == CONTAINER_TYPE:
+            return FormattedMetric("Container Type", value)
         value = int(value)
         if key == GALAXY_SLOTS_KEY:
             return FormattedMetric("Cores Allocated", "%d" % value)
@@ -73,12 +80,23 @@ class CorePlugin(InstrumentPlugin):
         properties[GALAXY_MEMORY_MB_KEY] = self.__read_integer(galaxy_memory_mb_file)
         start = self.__read_seconds_since_epoch(job_directory, "start")
         end = self.__read_seconds_since_epoch(job_directory, "end")
+        properties.update(self.__read_container_details(job_directory))
         if start is not None and end is not None:
             properties[START_EPOCH_KEY] = start
             properties[END_EPOCH_KEY] = end
             properties[RUNTIME_SECONDS_KEY] = end - start
         return properties
 
+    def get_container_file_path(self, job_directory):
+        return self._instrument_file_path(job_directory, "container")
+
+    def __read_container_details(self, job_directory) -> Dict[str, str]:
+        try:
+            with open(self.get_container_file_path(job_directory)) as fh:
+                return json.load(fh)
+        except FileNotFoundError:
+            return {}
+
     def __record_galaxy_slots_command(self, job_directory):
         galaxy_slots_file = self.__galaxy_slots_file(job_directory)
         return f"""echo "$GALAXY_SLOTS" > '{galaxy_slots_file}' """
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 8edea4a407283d53334ca5a7dba2cb93ca264ac4..2a0161109405f725d806dc26b94d8b5086105423 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -14,19 +14,29 @@ import shutil
 import sys
 import time
 import traceback
+from dataclasses import (
+    dataclass,
+    field,
+)
 from json import loads
 from typing import (
     Any,
     Dict,
     Iterable,
     List,
+    Optional,
     TYPE_CHECKING,
 )
 
 import yaml
 from packaging.version import Version
 from pulsar.client.staging import COMMAND_VERSION_FILENAME
-from sqlalchemy import select
+from sqlalchemy import (
+    and_,
+    func,
+    select,
+    update,
+)
 
 from galaxy import (
     model,
@@ -70,6 +80,7 @@ from galaxy.model.base import transaction
 from galaxy.model.store import copy_dataset_instance_metadata_attributes
 from galaxy.model.store.discover import MaxDiscoveredFilesExceededError
 from galaxy.objectstore import (
+    is_user_object_store,
     ObjectStorePopulator,
     serialize_static_object_store_config,
 )
@@ -99,6 +110,7 @@ from galaxy.work.context import WorkRequestContext
 
 if TYPE_CHECKING:
     from galaxy.jobs.handler import JobHandlerQueue
+    from galaxy.tools import Tool
 
 log = logging.getLogger(__name__)
 
@@ -293,6 +305,18 @@ def job_config_xml_to_dict(config, root):
     return config_dict
 
 
+@dataclass
+class JobConfigurationLimits:
+    registered_user_concurrent_jobs: Optional[int] = None
+    anonymous_user_concurrent_jobs: Optional[int] = None
+    walltime: Optional[str] = None
+    walltime_delta: Optional[datetime.timedelta] = None
+    total_walltime: Dict[str, Any] = field(default_factory=dict)
+    output_size: Optional[int] = None
+    destination_user_concurrent_jobs: Dict[str, int] = field(default_factory=dict)
+    destination_total_concurrent_jobs: Dict[str, int] = field(default_factory=dict)
+
+
 class JobConfiguration(ConfiguresHandlers):
     """A parser and interface to advanced job management features.
 
@@ -326,7 +350,7 @@ class JobConfiguration(ConfiguresHandlers):
         """Parse the job configuration XML."""
         self.app = app
         self.runner_plugins = []
-        self.dynamic_params = None
+        self.dynamic_params: Optional[Dict[str, Any]] = None
         self.handlers = {}
         self.handler_runner_plugins = {}
         self.default_handler_id = None
@@ -341,16 +365,7 @@ class JobConfiguration(ConfiguresHandlers):
         self.resource_groups = {}
         self.default_resource_group = None
         self.resource_parameters = {}
-        self.limits = Bunch(
-            registered_user_concurrent_jobs=None,
-            anonymous_user_concurrent_jobs=None,
-            walltime=None,
-            walltime_delta=None,
-            total_walltime={},
-            output_size=None,
-            destination_user_concurrent_jobs={},
-            destination_total_concurrent_jobs={},
-        )
+        self.limits = JobConfigurationLimits()
 
         default_resubmits = []
         default_resubmit_condition = self.app.config.default_job_resubmission_condition
@@ -382,6 +397,8 @@ class JobConfiguration(ConfiguresHandlers):
                             f" release of Galaxy. Please convert to YAML at {self.app.config.job_config_file} or"
                             f" explicitly set `job_config_file` to {job_config_file} to remove this message"
                         )
+                if not job_config_file:
+                    raise OSError()
                 if ".xml" in job_config_file:
                     tree = load(job_config_file)
                     job_config_dict = self.__parse_job_conf_xml(tree)
@@ -430,7 +447,7 @@ class JobConfiguration(ConfiguresHandlers):
                 continue
             self.runner_plugins.append(runner_info)
         if "dynamic" in job_config_dict:
-            self.dynamic_params = job_config_dict.get("dynamic", None)
+            self.dynamic_params = job_config_dict["dynamic"]
 
         # Parse handlers
         handling_config_dict = job_config_dict.get("handling", {})
@@ -828,12 +845,12 @@ class JobConfiguration(ConfiguresHandlers):
         """
         return self.destinations.get(id_or_tag, [])
 
-    def get_job_runner_plugins(self, handler_id):
+    def get_job_runner_plugins(self, handler_id: str):
         """Load all configured job runner plugins
 
         :returns: list of job runner plugins
         """
-        rval = {}
+        rval: Dict[str, BaseJobRunner] = {}
         if handler_id in self.handler_runner_plugins:
             plugins_to_load = [rp for rp in self.runner_plugins if rp["id"] in self.handler_runner_plugins[handler_id]]
             log.info(
@@ -869,11 +886,9 @@ class JobConfiguration(ConfiguresHandlers):
                     # If the name included a '.' or loading from the static runners path failed, try the original name
                     module = __import__(load)
                     module_name = load
-            if module is None:
-                # Module couldn't be loaded, error should have already been displayed
-                continue
             for comp in module_name.split(".")[1:]:
                 module = getattr(module, comp)
+            assert module  # make mypy happy
             if not class_names:
                 # If there's not a ':', we check <module>.__all__ for class names
                 try:
@@ -984,11 +999,17 @@ class MinimalJobWrapper(HasResourceParameters):
 
     is_task = False
 
-    def __init__(self, job: model.Job, app: MinimalManagerApp, use_persisted_destination: bool = False, tool=None):
+    def __init__(
+        self,
+        job: model.Job,
+        app: MinimalManagerApp,
+        use_persisted_destination: bool = False,
+        tool: Optional["Tool"] = None,
+    ):
         self.job_id = job.id
         self.session_id = job.session_id
         self.user_id = job.user_id
-        self.app: MinimalManagerApp = app
+        self.app = app
         self.tool = tool
         self.sa_session = self.app.model.context
         self.extra_filenames: List[str] = []
@@ -1249,10 +1270,6 @@ class MinimalJobWrapper(HasResourceParameters):
             self.__prepare_upload_paramfile(job)
 
         tool_evaluator = self._get_tool_evaluator(job)
-        if hasattr(self.app, "interactivetool_manager"):
-            self.interactivetools = tool_evaluator.populate_interactivetools()
-            self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
-            job.interactive_url = self.app.interactivetool_manager.get_job_subdomain(job)
         compute_environment = compute_environment or self.default_compute_environment(job)
         tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
         (
@@ -1260,6 +1277,7 @@ class MinimalJobWrapper(HasResourceParameters):
             self.version_command_line,
             self.extra_filenames,
             self.environment_variables,
+            self.interactivetools,
         ) = tool_evaluator.build()
         job.command_line = self.command_line
 
@@ -1322,7 +1340,7 @@ class MinimalJobWrapper(HasResourceParameters):
             )
         return self.__working_directory
 
-    def working_directory_exists(self):
+    def working_directory_exists(self) -> bool:
         job = self.get_job()
         return self.app.object_store.exists(job, base_dir="job_work", dir_only=True, obj_dir=True)
 
@@ -1382,7 +1400,15 @@ class MinimalJobWrapper(HasResourceParameters):
                 util.umask_fix_perms(path, self.app.config.umask, 0o666, self.app.config.gid)
 
     def fail(
-        self, message, exception=False, tool_stdout="", tool_stderr="", exit_code=None, job_stdout=None, job_stderr=None
+        self,
+        message,
+        exception=False,
+        tool_stdout="",
+        tool_stderr="",
+        exit_code=None,
+        job_stdout=None,
+        job_stderr=None,
+        job_metrics_directory=None,
     ):
         """
         Indicate job failure by setting state and message on all output
@@ -1409,6 +1435,10 @@ class MinimalJobWrapper(HasResourceParameters):
         message = str(message)
         working_directory_exists = self.working_directory_exists()
 
+        if not job.tasks and working_directory_exists:
+            # If job was composed of tasks, don't attempt to recollect statistics
+            self._collect_metrics(job, job_metrics_directory)
+
         # if the job was deleted, don't fail it
         if not job.state == job.states.DELETED:
             # Check if the failure is due to an exception
@@ -1484,6 +1514,7 @@ class MinimalJobWrapper(HasResourceParameters):
             pjaa.post_job_action for pjaa in job.post_job_actions if pjaa.post_job_action.action_type == "EmailAction"
         ]:
             ActionBox.execute(self.app, self.sa_session, pja, job)
+
         # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up
         if self.tool:
             try:
@@ -1499,7 +1530,7 @@ class MinimalJobWrapper(HasResourceParameters):
             job = self.get_job()
         if message is None:
             message = "Execution of this dataset's job is paused"
-        if job.state == job.states.NEW:
+        if job.state in (job.states.NEW, job.states.QUEUED):
             for dataset_assoc in job.output_datasets + job.output_library_datasets:
                 dataset_assoc.dataset.dataset.state = dataset_assoc.dataset.dataset.states.PAUSED
                 dataset_assoc.dataset.info = message
@@ -1591,18 +1622,157 @@ class MinimalJobWrapper(HasResourceParameters):
         dest_params = self.job_destination.params
         return self.get_job().get_destination_configuration(dest_params, self.app.config, key, default)
 
+    def queue_with_limit(self, job: Job, job_destination: JobDestination):
+        anonymous_user_concurrent_jobs = self.app.job_config.limits.anonymous_user_concurrent_jobs
+        registered_user_concurrent_jobs = self.app.job_config.limits.registered_user_concurrent_jobs
+        destination_total_concurrent_jobs = self.app.job_config.limits.destination_total_concurrent_jobs
+        destination_total_limit = self.app.job_config.limits.destination_total_concurrent_jobs.get(job_destination.id)
+        destination_user_limit = self.app.job_config.limits.destination_user_concurrent_jobs.get(job_destination.id)
+        destination_tag_limits = {}
+        if job_destination.tags:
+            for tag in job_destination.tags:
+                if tag_limit := destination_total_concurrent_jobs.get(tag):
+                    destination_tag_limits[tag] = tag_limit
+
+        conditions = [model.Job.table.c.id == job.id]
+
+        if job.user_id:
+            user_job_count = (
+                select(func.count(model.Job.table.c.id))
+                .where(
+                    and_(
+                        model.Job.table.c.state.in_(
+                            [
+                                model.Job.states.QUEUED,
+                                model.Job.states.RUNNING,
+                                model.Job.states.RESUBMITTED,
+                            ]
+                        ),
+                        model.Job.table.c.user_id == job.user_id,
+                    )
+                )
+                .scalar_subquery()
+            )
+
+            if registered_user_concurrent_jobs is not None:
+                conditions.append(user_job_count < registered_user_concurrent_jobs)
+            if destination_user_limit is not None:
+                destination_job_count = (
+                    select(func.count(model.Job.table.c.id))
+                    .where(
+                        and_(
+                            model.Job.table.c.state.in_(
+                                [
+                                    model.Job.states.QUEUED,
+                                    model.Job.states.RUNNING,
+                                    model.Job.states.RESUBMITTED,
+                                ]
+                            ),
+                            model.Job.table.c.destination_id == job_destination.id,
+                            model.Job.table.c.user_id == job.user_id,
+                        )
+                    )
+                    .scalar_subquery()
+                )
+                conditions.append(destination_job_count < destination_user_limit)
+
+        elif anonymous_user_concurrent_jobs and job.galaxy_session and job.galaxy_session.id:
+            anon_job_count = (
+                select(func.count(model.Job.table.c.id))
+                .where(
+                    and_(
+                        model.Job.table.c.state.in_(
+                            [
+                                model.Job.states.QUEUED,
+                                model.Job.states.RUNNING,
+                                model.Job.states.RESUBMITTED,
+                            ]
+                        ),
+                        model.Job.table.c.session_id == job.galaxy_session.id,
+                    )
+                )
+                .scalar_subquery()
+            )
+            conditions.append(anon_job_count < anonymous_user_concurrent_jobs)
+
+        if destination_total_limit is not None:
+            destination_total_count = (
+                select(func.count(model.Job.table.c.id))
+                .where(
+                    and_(
+                        model.Job.table.c.state.in_(
+                            [
+                                model.Job.states.QUEUED,
+                                model.Job.states.RUNNING,
+                                model.Job.states.RESUBMITTED,
+                            ]
+                        ),
+                        model.Job.table.c.destination_id == job_destination.id,
+                    )
+                )
+                .scalar_subquery()
+            )
+            conditions.append(destination_total_count < destination_total_limit)
+
+        if destination_tag_limits:
+            for tag, limit in destination_tag_limits.items():
+                destination_ids = {destination.id for destination in self.app.job_config.get_destinations(tag)}
+                tag_count = (
+                    select(func.count(model.Job.table.c.id))
+                    .where(
+                        and_(
+                            model.Job.table.c.state.in_(
+                                [
+                                    model.Job.states.QUEUED,
+                                    model.Job.states.RUNNING,
+                                    model.Job.states.RESUBMITTED,
+                                ]
+                            ),
+                            model.Job.table.c.destination_id.in_(destination_ids),
+                        )
+                    )
+                    .scalar_subquery()
+                )
+                conditions.append(tag_count < limit)
+
+        update_stmt = (
+            update(model.Job)
+            .where(*conditions)
+            .values(
+                state=model.Job.states.QUEUED,
+                destination_id=job_destination.id,
+                destination_params=job_destination.params,
+                job_runner_name=job_destination.runner,
+            )
+        )
+
+        result = self.sa_session.execute(update_stmt)
+        self.sa_session.commit()
+
+        return result.rowcount > 0
+
     def enqueue(self):
         job = self.get_job()
         # Change to queued state before handing to worker thread so the runner won't pick it up again
-        self.change_state(model.Job.states.QUEUED, flush=False, job=job)
-        # Persist the destination so that the job will be included in counts if using concurrency limits
-        self.set_job_destination(self.job_destination, None, flush=False, job=job)
+        if self.is_task:
+            self.change_state(model.Job.states.QUEUED, flush=False, job=job)
+        elif not self.queue_with_limit(job, self.job_destination):
+            return False
+        job.update_output_states(self.app.application_stack.supports_skip_locked())
         # Set object store after job destination so can leverage parameters...
         self._set_object_store_ids(job)
+        # Now that we have the object store id, check if we are over the limit
+        self._pause_job_if_over_quota(job)
         with transaction(self.sa_session):
             self.sa_session.commit()
         return True
 
+    def _pause_job_if_over_quota(self, job):
+        if self.app.quota_agent.is_over_quota(self.app, job, self.job_destination):
+            log.info("(%d) User (%s) is over quota: job paused" % (job.id, job.user_id))
+            message = "Execution of this dataset's job is paused because you were over your disk quota at the time it was ready to run"
+            self.pause(job, message)
+
     def set_job_destination(self, job_destination, external_id=None, flush=True, job=None):
         """Subclasses should implement this to persist a destination, if necessary."""
 
@@ -1844,6 +2014,7 @@ class MinimalJobWrapper(HasResourceParameters):
                 job_stdout=job_stdout,
                 job_stderr=job_stderr,
                 exception=exception,
+                job_metrics_directory=job_metrics_directory,
             )
 
         # TODO: After failing here, consider returning from the function.
@@ -2127,7 +2298,7 @@ class MinimalJobWrapper(HasResourceParameters):
 
         return state
 
-    def cleanup(self, delete_files=True):
+    def cleanup(self, delete_files: bool = True) -> None:
         # At least one of these tool cleanup actions (job import), is needed
         # for the tool to work properly, that is why one might want to run
         # cleanup but not delete files.
@@ -2148,7 +2319,13 @@ class MinimalJobWrapper(HasResourceParameters):
 
     def _collect_metrics(self, has_metrics, job_metrics_directory=None):
         job = has_metrics.get_job()
-        job_metrics_directory = job_metrics_directory or self.working_directory
+        if job_metrics_directory is None:
+            try:
+                # working directory might have been purged already
+                job_metrics_directory = self.working_directory
+            except Exception:
+                log.exception("Could not recover job metrics")
+                return
         per_plugin_properties = self.app.job_metrics.collect_properties(
             job.destination_id, self.job_id, job_metrics_directory
         )
@@ -2313,7 +2490,7 @@ class MinimalJobWrapper(HasResourceParameters):
         required_user_object_store_uris = set()
         for out_dataset_instance in out_data.values():
             object_store_id = out_dataset_instance.dataset.object_store_id
-            if object_store_id and object_store_id.startswith("user_objects://"):
+            if is_user_object_store(object_store_id):
                 required_user_object_store_uris.add(object_store_id)
 
         job_metadata = os.path.join(self.tool_working_directory, self.tool.provided_metadata_file)
@@ -2496,7 +2673,9 @@ class MinimalJobWrapper(HasResourceParameters):
     def user_system_pwent(self):
         if self.__user_system_pwent is None:
             job = self.get_job()
-            self.__user_system_pwent = job.user.system_user_pwent(self.app.config.real_system_username)
+            self.__user_system_pwent = job.user.system_user_pwent(
+                self.get_destination_configuration("real_system_username", self.app.config.real_system_username)
+            )
         return self.__user_system_pwent
 
     @property
@@ -2538,10 +2717,15 @@ class MinimalJobWrapper(HasResourceParameters):
 
 
 class JobWrapper(MinimalJobWrapper):
-    def __init__(self, job, queue: "JobHandlerQueue", use_persisted_destination=False, app=None):
-        super().__init__(job, app=queue.app, use_persisted_destination=use_persisted_destination)
+    def __init__(self, job, queue: "JobHandlerQueue", use_persisted_destination=False):
+        app = queue.app
+        super().__init__(
+            job,
+            app=app,
+            use_persisted_destination=use_persisted_destination,
+            tool=app.toolbox.get_tool(job.tool_id, job.tool_version, exact=True),
+        )
         self.queue = queue
-        self.tool = self.app.toolbox.get_tool(job.tool_id, job.tool_version, exact=True)
         self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)
diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 2a70911b239ad6332a29a5174a2965a0f59d9502..3e596240e0ded3cabc3ea133a54c348e1646d628 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -1,7 +1,10 @@
 import json
 import typing
 from logging import getLogger
-from os import getcwd
+from os import (
+    getcwd,
+    makedirs,
+)
 from os.path import (
     abspath,
     join,
@@ -82,8 +85,16 @@ def build_command(
         __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)
 
     __handle_task_splitting(commands_builder, job_wrapper)
-
     for_pulsar = "pulsar_version" in remote_command_params
+    if container:
+        if core_job_metric_plugin := runner.app.job_metrics.default_job_instrumenter.get_configured_plugin("core"):
+            directory = join(job_wrapper.working_directory, "metadata") if for_pulsar else job_wrapper.working_directory
+            makedirs(directory, exist_ok=True)
+            container_file_path = core_job_metric_plugin.get_container_file_path(directory)
+            with open(container_file_path, "w") as container_file:
+                container_file.write(
+                    json.dumps({"container_id": container.container_id, "container_type": container.container_type})
+                )
     if (container and modify_command_for_container) or job_wrapper.commands_in_new_shell:
         if container and modify_command_for_container:
             # Many Docker containers do not have /bin/bash.
@@ -132,6 +143,7 @@ def build_command(
 
     if job_wrapper.is_cwl_job:
         # Minimal metadata needed by the relocate script
+        assert job_wrapper.tool
         cwl_metadata_params = {
             "job_metadata": join("working", job_wrapper.tool.provided_metadata_file),
             "job_id_tag": job_wrapper.get_id_tag(),
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index c445e137ceb3c30a9e6434d9f272b7a0925fca47..ea9d91cc8780d936631b47b4374d8a7aeaee5062 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -123,6 +123,7 @@ class ItemGrabber:
         self.self_handler_tags = self_handler_tags
         self.max_grab = max_grab
         self.handler_tags = handler_tags
+        self._grab_conn_opts = {}
         self._grab_query = None
         self._supports_returning = self.app.application_stack.supports_returning()
 
@@ -130,7 +131,13 @@ class ItemGrabber:
         if self.grab_model is model.Job:
             grab_condition = self.grab_model.state == self.grab_model.states.NEW
         elif self.grab_model is model.WorkflowInvocation:
-            grab_condition = self.grab_model.state.in_((self.grab_model.states.NEW, self.grab_model.states.CANCELLING))
+            grab_condition = self.grab_model.state.in_(
+                (
+                    self.grab_model.states.NEW,
+                    self.grab_model.states.REQUIRES_MATERIALIZATION,
+                    self.grab_model.states.CANCELLING,
+                )
+            )
         else:
             raise NotImplementedError(f"Grabbing {self.grab_model.__name__} not implemented")
         subq = (
@@ -187,6 +194,7 @@ class ItemGrabber:
             self.setup_query()
 
         with self.app.model.engine.connect() as conn:
+            conn.execution_options(**self._grab_conn_opts)
             with conn.begin() as trans:
                 try:
                     proxy = conn.execute(self._grab_query)
@@ -225,7 +233,7 @@ class StopSignalException(Exception):
 class BaseJobHandlerQueue(Monitors):
     STOP_SIGNAL = object()
 
-    def __init__(self, app: MinimalManagerApp, dispatcher):
+    def __init__(self, app: MinimalManagerApp, dispatcher: "DefaultJobDispatcher"):
         """
         Initializes the Queue, creates (unstarted) monitoring thread.
         """
@@ -303,12 +311,15 @@ class JobHandlerQueue(BaseJobHandlerQueue):
             with transaction(session):
                 session.commit()
 
-    def _check_job_at_startup(self, job):
+    def _check_job_at_startup(self, job: model.Job):
+        assert job.tool_id is not None
         if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
             log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to recover job")
             self.job_wrapper(job).fail(
                 "This tool was disabled before the job completed.  Please contact your Galaxy administrator."
             )
+        elif job.copied_from_job_id:
+            self.queue.put((job.id, job.tool_id))
         elif job.job_runner_name is not None and job.job_runner_external_id is None:
             # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
             log.debug(f"({job.id}) Job runner assigned but no external ID recorded, adding to the job handler queue")
@@ -507,6 +518,9 @@ class JobHandlerQueue(BaseJobHandlerQueue):
                 pass
         # Ensure that we get new job counts on each iteration
         self.__clear_job_count()
+        self.__cache_total_job_count_per_destination()
+        self.__cache_user_job_count_per_destination()
+        self.__cache_user_job_count()
         # Check resubmit jobs first so that limits of new jobs will still be enforced
         for job in resubmit_jobs:
             log.debug("(%s) Job was resubmitted and is being dispatched immediately", job.id)
@@ -553,18 +567,12 @@ class JobHandlerQueue(BaseJobHandlerQueue):
                     log.info("(%d) Job deleted by user while still queued" % job.id)
                 elif job_state == JOB_ADMIN_DELETED:
                     log.info("(%d) Job deleted by admin while still queued" % job.id)
-                elif job_state in (JOB_USER_OVER_QUOTA, JOB_USER_OVER_TOTAL_WALLTIME):
-                    if job_state == JOB_USER_OVER_QUOTA:
-                        log.info("(%d) User (%s) is over quota: job paused" % (job.id, job.user_id))
-                        what = "your disk quota"
-                    else:
-                        log.info("(%d) User (%s) is over total walltime limit: job paused" % (job.id, job.user_id))
-                        what = "your total job runtime"
-
+                elif job_state == JOB_USER_OVER_TOTAL_WALLTIME:
+                    log.info("(%d) User (%s) is over total walltime limit: job paused" % (job.id, job.user_id))
                     job.set_state(model.Job.states.PAUSED)
                     for dataset_assoc in job.output_datasets + job.output_library_datasets:
                         dataset_assoc.dataset.dataset.state = model.Dataset.states.PAUSED
-                        dataset_assoc.dataset.info = f"Execution of this dataset's job is paused because you were over {what} at the time it was ready to run"
+                        dataset_assoc.dataset.info = "Execution of this dataset's job is paused because you were over your total job runtime at the time it was ready to run"
                         self.sa_session.add(dataset_assoc.dataset.dataset)
                     self.sa_session.add(job)
                 elif job_state == JOB_ERROR:
@@ -738,8 +746,6 @@ class JobHandlerQueue(BaseJobHandlerQueue):
 
         if state == JOB_READY:
             state = self.__check_user_jobs(job, job_wrapper)
-        if state == JOB_READY and self.app.quota_agent.is_over_quota(self.app, job, job_destination):
-            return JOB_USER_OVER_QUOTA, job_destination
         # Check total walltime limits
         if state == JOB_READY and "delta" in self.app.job_config.limits.total_walltime:
             jobs_to_check = self.sa_session.query(model.Job).filter(
@@ -821,7 +827,6 @@ class JobHandlerQueue(BaseJobHandlerQueue):
         self.total_job_count_per_destination = None
 
     def get_user_job_count(self, user_id):
-        self.__cache_user_job_count()
         # This could have been incremented by a previous job dispatched on this iteration, even if we're not caching
         rval = self.user_job_count.get(user_id, 0)
         if not self.app.config.cache_user_job_count:
@@ -862,7 +867,6 @@ class JobHandlerQueue(BaseJobHandlerQueue):
             self.user_job_count = {}
 
     def get_user_job_count_per_destination(self, user_id):
-        self.__cache_user_job_count_per_destination()
         cached = self.user_job_count_per_destination.get(user_id, {})
         if self.app.config.cache_user_job_count:
             rval = cached
@@ -1003,7 +1007,6 @@ class JobHandlerQueue(BaseJobHandlerQueue):
                 self.total_job_count_per_destination[row["destination_id"]] = row["job_count"]
 
     def get_total_job_count_per_destination(self):
-        self.__cache_total_job_count_per_destination()
         # Always use caching (at worst a job will have to wait one iteration,
         # and this would be more fair anyway as it ensures FIFO scheduling,
         # insofar as FIFO would be fair...)
@@ -1199,7 +1202,7 @@ class DefaultJobDispatcher:
         for runner in self.job_runners.values():
             runner.start()
 
-    def url_to_destination(self, url):
+    def url_to_destination(self, url: str):
         """This is used by the runner mapper (a.k.a. dynamic runner) and
         recovery methods to have runners convert URLs to destinations.
 
@@ -1260,10 +1263,11 @@ class DefaultJobDispatcher:
             runner_name = job_runner_name.split(":", 1)[0]
             log.debug(f"Stopping job {job_wrapper.get_id_tag()} in {runner_name} runner")
             try:
-                try:
-                    self.job_runners[runner_name].stop_job(job_wrapper, soft_kill=soft_kill)
-                except:
-                    self.job_runners[runner_name].stop_job(job_wrapper)
+                if job.state != model.Job.states.NEW:
+                    try:
+                        self.job_runners[runner_name].stop_job(job_wrapper, soft_kill=soft_kill)
+                    except:
+                        self.job_runners[runner_name].stop_job(job_wrapper)
             except KeyError:
                 log.error(f"stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}")
                 # Job and output dataset states have already been updated, so nothing is done here.
diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py
index f5bac4e684075eeaf83a5dbaad829baf92e1d19d..66edbc10867e46bf0b41c5b888b167810f7b0474 100644
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -2,6 +2,10 @@ import importlib
 import logging
 from inspect import getfullargspec
 from types import ModuleType
+from typing import (
+    Callable,
+    TYPE_CHECKING,
+)
 
 import galaxy.jobs.rules
 from galaxy.jobs import stock_rules
@@ -9,6 +13,13 @@ from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
 from galaxy.util.submodules import import_submodules
 from .rule_helper import RuleHelper
 
+if TYPE_CHECKING:
+    from galaxy.jobs import (
+        JobConfiguration,
+        JobDestination,
+        JobWrapper,
+    )
+
 log = logging.getLogger(__name__)
 
 DYNAMIC_RUNNER_NAME = "dynamic"
@@ -52,7 +63,12 @@ class JobRunnerMapper:
 
     rules_module: ModuleType
 
-    def __init__(self, job_wrapper, url_to_destination, job_config):
+    def __init__(
+        self,
+        job_wrapper: "JobWrapper",
+        url_to_destination: Callable[[str], "JobDestination"],
+        job_config: "JobConfiguration",
+    ):
         self.job_wrapper = job_wrapper
         self.url_to_destination = url_to_destination
         self.job_config = job_config
@@ -129,7 +145,7 @@ class JobRunnerMapper:
         param_values = job.get_param_values(app, ignore_errors=True)
         return param_values
 
-    def __convert_url_to_destination(self, url):
+    def __convert_url_to_destination(self, url: str):
         """
         Job runner URLs are deprecated, but dynamic mapper functions may still
         be returning them.  Runners are expected to be able to convert these to
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 9f42f7a0f27c80090427334cf94983d0ae4651e0..70f3b265052e0aa7bfad40d025059d3ab6aa551b 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -11,12 +11,18 @@ import sys
 import threading
 import time
 import traceback
-import typing
 import uuid
 from queue import (
     Empty,
     Queue,
 )
+from typing import (
+    Any,
+    Dict,
+    Optional,
+    TYPE_CHECKING,
+    Union,
+)
 
 import jwt
 from sqlalchemy import select
@@ -61,7 +67,7 @@ from galaxy.util.custom_logging import get_logger
 from galaxy.util.monitors import Monitors
 from .state_handler_factory import build_state_handlers
 
-if typing.TYPE_CHECKING:
+if TYPE_CHECKING:
     from galaxy.app import GalaxyManagerApplication
     from galaxy.jobs import (
         JobDestination,
@@ -186,7 +192,7 @@ class BaseJobRunner:
                         # Prevent fail_job cycle in the work_queue
                         self.work_queue.put((self.fail_job, job_state))
 
-    def _ensure_db_session(self, arg: typing.Union["JobWrapper", "JobState"]) -> None:
+    def _ensure_db_session(self, arg: Union["JobWrapper", "JobState"]) -> None:
         """Ensure Job object belongs to current session."""
         try:
             job_wrapper = arg.job_wrapper  # type: ignore[union-attr]
@@ -267,7 +273,7 @@ class BaseJobRunner:
         """
         return galaxy.jobs.JobDestination(runner=url.split(":")[0])
 
-    def parse_destination_params(self, params: typing.Dict[str, typing.Any]):
+    def parse_destination_params(self, params: Dict[str, Any]):
         """Parse the JobDestination ``params`` dict and return the runner's native representation of those params."""
         raise NotImplementedError()
 
@@ -350,8 +356,8 @@ class BaseJobRunner:
     def get_work_dir_outputs(
         self,
         job_wrapper: "MinimalJobWrapper",
-        job_working_directory: typing.Optional[str] = None,
-        tool_working_directory: typing.Optional[str] = None,
+        job_working_directory: Optional[str] = None,
+        tool_working_directory: Optional[str] = None,
     ):
         """
         Returns list of pairs (source_file, destination) describing path
@@ -505,6 +511,7 @@ class BaseJobRunner:
             env_setup_commands.append(env_to_statement(env))
         command_line = job_wrapper.runner_command_line
         tmp_dir_creation_statement = job_wrapper.tmp_dir_creation_statement
+        assert job_wrapper.tool
         options = dict(
             tmp_dir_creation_statement=tmp_dir_creation_statement,
             job_instrumenter=job_instrumenter,
@@ -572,10 +579,10 @@ class BaseJobRunner:
     def _find_container(
         self,
         job_wrapper: "MinimalJobWrapper",
-        compute_working_directory: typing.Optional[str] = None,
-        compute_tool_directory: typing.Optional[str] = None,
-        compute_job_directory: typing.Optional[str] = None,
-        compute_tmp_directory: typing.Optional[str] = None,
+        compute_working_directory: Optional[str] = None,
+        compute_tool_directory: Optional[str] = None,
+        compute_job_directory: Optional[str] = None,
+        compute_tmp_directory: Optional[str] = None,
     ):
         job_directory_type = "galaxy" if compute_working_directory is None else "pulsar"
         if not compute_working_directory:
@@ -584,13 +591,14 @@ class BaseJobRunner:
         if not compute_job_directory:
             compute_job_directory = job_wrapper.working_directory
 
+        tool = job_wrapper.tool
+        assert tool
         if not compute_tool_directory:
-            compute_tool_directory = job_wrapper.tool.tool_dir
+            compute_tool_directory = str(tool.tool_dir) if tool.tool_dir is not None else None
 
         if not compute_tmp_directory:
             compute_tmp_directory = job_wrapper.tmp_directory()
 
-        tool = job_wrapper.tool
         guest_ports = job_wrapper.guest_ports
         tool_info = ToolInfo(
             tool.containers,
@@ -630,7 +638,8 @@ class BaseJobRunner:
             log.exception("Caught exception in runner state handler")
 
     def fail_job(self, job_state: "JobState", exception=False, message="Job failed", full_status=None):
-        if getattr(job_state, "stop_job", True):
+        job = job_state.job_wrapper.get_job()
+        if getattr(job_state, "stop_job", True) and job.state != model.Job.states.NEW:
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
         self._handle_runner_state("failure", job_state)
@@ -647,7 +656,7 @@ class BaseJobRunner:
                 fail_message, tool_stdout=tool_stdout, tool_stderr=tool_stderr, exception=exception
             )
 
-    def mark_as_resubmitted(self, job_state: "JobState", info: typing.Optional[str] = None):
+    def mark_as_resubmitted(self, job_state: "JobState", info: Optional[str] = None):
         job_state.job_wrapper.mark_as_resubmitted(info=info)
         if not self.app.config.track_jobs_in_database:
             job_state.job_wrapper.change_state(model.Job.states.QUEUED)
diff --git a/lib/galaxy/jobs/runners/aws.py b/lib/galaxy/jobs/runners/aws.py
index 5f301b078975625bff54ff9fc23068b0287d683a..72b0782075911e0fe6883e0cbc762e81d90011df 100644
--- a/lib/galaxy/jobs/runners/aws.py
+++ b/lib/galaxy/jobs/runners/aws.py
@@ -401,11 +401,13 @@ class AWSBatchJobRunner(AsynchronousJobRunner):
         msg = "(name!r/runner!r) is still in {state!s} state, adding to the runner monitor queue"
         job_id = job.get_job_runner_external_id()
         job_name = self.JOB_NAME_PREFIX + job_wrapper.get_id_tag()
-        ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
-        ajs.job_id = str(job_id)
-        ajs.job_name = job_name
-        ajs.job_wrapper = job_wrapper
-        ajs.job_destination = job_wrapper.job_destination
+        ajs = AsynchronousJobState(
+            files_dir=job_wrapper.working_directory,
+            job_wrapper=job_wrapper,
+            job_id=str(job_id),
+            job_name=job_name,
+            job_destination=job_wrapper.job_destination,
+        )
         if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
             log.debug(msg.format(name=job.id, runner=job.job_runner_name, state=job.state))
             ajs.old_state = model.Job.states.RUNNING
@@ -417,14 +419,21 @@ class AWSBatchJobRunner(AsynchronousJobRunner):
             ajs.running = False
             self.monitor_queue.put(ajs)
 
-    def fail_job(self, job_state, exception=False):
-        if getattr(job_state, "stop_job", True):
+    def fail_job(self, job_state: JobState, exception=False, message="Job failed", full_status=None):
+        job = job_state.job_wrapper.get_job()
+        if getattr(job_state, "stop_job", True) and job.state != model.Job.states.NEW:
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
         self._handle_runner_state("failure", job_state)
         if not job_state.runner_state_handled:
-            job_state.job_wrapper.fail(getattr(job_state, "fail_message", "Job failed"), exception=exception)
-            self._finish_or_resubmit_job(job_state, "", job_state.fail_message, job_id=job_state.job_id)
+            full_status = full_status or {}
+            tool_stdout = full_status.get("stdout")
+            tool_stderr = full_status.get("stderr")
+            fail_message = getattr(job_state, "fail_message", message)
+            job_state.job_wrapper.fail(
+                fail_message, tool_stdout=tool_stdout, tool_stderr=tool_stderr, exception=exception
+            )
+            self._finish_or_resubmit_job(job_state, "", fail_message)
             if job_state.job_wrapper.cleanup_job == "always":
                 job_state.cleanup()
 
diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py
index 56fef20a0ecb4c8d4cc91afe15e1235b29e3b4b1..b09fb0b5c7f9728e0a980d74fa12e5e32173c475 100644
--- a/lib/galaxy/jobs/runners/kubernetes.py
+++ b/lib/galaxy/jobs/runners/kubernetes.py
@@ -8,6 +8,7 @@ import math
 import os
 import re
 import time
+from dataclasses import dataclass
 from datetime import datetime
 
 import yaml
@@ -20,6 +21,7 @@ from galaxy.jobs.runners import (
 )
 from galaxy.jobs.runners.util.pykube_util import (
     deduplicate_entries,
+    DEFAULT_INGRESS_API_VERSION,
     DEFAULT_JOB_API_VERSION,
     delete_ingress,
     delete_job,
@@ -34,6 +36,7 @@ from galaxy.jobs.runners.util.pykube_util import (
     HTTPError,
     Ingress,
     ingress_object_dict,
+    is_pod_running,
     is_pod_unschedulable,
     Job,
     job_object_dict,
@@ -42,6 +45,7 @@ from galaxy.jobs.runners.util.pykube_util import (
     produce_k8s_job_prefix,
     pull_policy,
     pykube_client_from_dict,
+    reload_job,
     Service,
     service_object_dict,
 )
@@ -53,6 +57,18 @@ log = logging.getLogger(__name__)
 __all__ = ("KubernetesJobRunner",)
 
 
+@dataclass
+class RetryableDeleteJobState(JobState):
+    def __init__(self, job_state, k8s_job, max_retries=5, attempts=0):
+        self.__dict__ = job_state.__dict__.copy()
+        self.init_retryable_job(max_retries, attempts)
+        self.k8s_job = k8s_job
+
+    def init_retryable_job(self, max_retries, attempts):
+        self.max_retries: int = max_retries
+        self.attempts: int = attempts
+
+
 class KubernetesJobRunner(AsynchronousJobRunner):
     """
     Job runner backed by a finite pool of worker threads. FIFO scheduling
@@ -109,6 +125,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             k8s_interactivetools_use_ssl=dict(map=bool, default=False),
             k8s_interactivetools_ingress_annotations=dict(map=str),
             k8s_interactivetools_ingress_class=dict(map=str, default=None),
+            k8s_interactivetools_tls_secret=dict(map=str, default=None),
+            k8s_ingress_api_version=dict(map=str, default=DEFAULT_INGRESS_API_VERSION),
         )
 
         if "runner_param_specs" not in kwargs:
@@ -121,10 +139,6 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         self._pykube_api = pykube_client_from_dict(self.runner_params)
         self._galaxy_instance_id = self.__get_galaxy_instance_id()
 
-        self._run_as_user_id = self.__get_run_as_user_id()
-        self._run_as_group_id = self.__get_run_as_group_id()
-        self._supplemental_group = self.__get_supplemental_group()
-        self._fs_group = self.__get_fs_group()
         self._default_pull_policy = self.__get_pull_policy()
 
         self.setup_base_volumes()
@@ -149,11 +163,11 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         self.runner_params["k8s_volumes"].extend(get_volume_mounts_for("k8s_working_volume_claim")[0])
 
     def queue_job(self, job_wrapper):
-        """Create job script and submit it to Kubernetes cluster"""
-        # prepare the job
+        """Create a Galaxy job script and submit it to Kubernetes cluster"""
+        # prepare the Galaxy job
         # We currently don't need to include_metadata or include_work_dir_outputs, as working directory is the same
         # where galaxy will expect results.
-        log.debug(f"Starting queue_job for job {job_wrapper.get_id_tag()}")
+        log.debug(f"Starting queue_job for Galaxy job {job_wrapper.get_id_tag()}")
 
         ajs = AsynchronousJobState(
             files_dir=job_wrapper.working_directory,
@@ -180,8 +194,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         try:
             self.write_executable_script(ajs.job_file, script, job_io=job_wrapper.job_io)
         except Exception:
-            job_wrapper.fail("failure preparing job script", exception=True)
-            log.exception(f"({job_wrapper.get_id_tag()}) failure writing job script")
+            job_wrapper.fail("Failure preparing Galaxy job script", exception=True)
+            log.exception(f"({job_wrapper.get_id_tag()}) failure writing Galaxy job script")
             return
 
         # Construction of Kubernetes objects follow: https://kubernetes.io/docs/concepts/workloads/controllers/job/
@@ -198,27 +212,27 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         k8s_job_prefix = self.__produce_k8s_job_prefix()
         k8s_job_obj = job_object_dict(self.runner_params, k8s_job_prefix, self.__get_k8s_job_spec(ajs))
 
-        job = Job(self._pykube_api, k8s_job_obj)
+        k8s_job = Job(self._pykube_api, k8s_job_obj)
         try:
-            job.create()
+            k8s_job.create()
         except HTTPError:
-            log.exception("Kubernetes failed to create job, HTTP exception encountered")
+            log.exception("Kubernetes failed to create a job, HTTP exception encountered")
             ajs.runner_state = JobState.runner_states.UNKNOWN_ERROR
-            ajs.fail_message = "Kubernetes failed to create job."
+            ajs.fail_message = "Kubernetes failed to create a job; HTTP exception encountered."
             self.mark_as_failed(ajs)
             return
-        if not job.name:
-            log.exception(f"Kubernetes failed to create job, empty name encountered: [{job.obj}]")
+        if not k8s_job.name:
+            log.exception(f"Kubernetes failed to create a job, empty name encountered: [{k8s_job.obj}]")
             ajs.runner_state = JobState.runner_states.UNKNOWN_ERROR
-            ajs.fail_message = "Kubernetes failed to create job."
+            ajs.fail_message = "Kubernetes failed to create a job; empty name encountered."
             self.mark_as_failed(ajs)
             return
-        job_id = job.name
+        k8s_job_id = k8s_job.name
 
         # define job attributes in the AsyncronousJobState for follow-up
-        ajs.job_id = job_id
+        ajs.job_id = k8s_job_id
         # store runner information for tracking if Galaxy restarts
-        job_wrapper.set_external_id(job_id)
+        job_wrapper.set_external_id(k8s_job_id)
         self.monitor_queue.put(ajs)
 
     def __has_guest_ports(self, job_wrapper):
@@ -249,71 +263,35 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         service = Service(self._pykube_api, k8s_service_obj)
         service.create()
         ingress = Ingress(self._pykube_api, k8s_ingress_obj)
+        ingress.version = self.runner_params["k8s_ingress_api_version"]
         ingress.create()
 
     def __get_overridable_params(self, job_wrapper, param_key):
-        dest_params = self.__get_destination_params(job_wrapper)
-        return dest_params.get(param_key, self.runner_params[param_key])
+        try:
+            return job_wrapper.job_destination.params[param_key]
+        except KeyError:
+            return self.runner_params[param_key]
 
     def __get_pull_policy(self):
         return pull_policy(self.runner_params)
 
-    def __get_run_as_user_id(self):
-        if self.runner_params.get("k8s_run_as_user_id") or self.runner_params.get("k8s_run_as_user_id") == 0:
-            run_as_user = self.runner_params["k8s_run_as_user_id"]
-            if run_as_user == "$uid":
+    def __get_user_group_param_or_default(self, job_wrapper, param_name):
+        substitutable_user_group_id = self.__get_overridable_params(job_wrapper, param_name)
+        if substitutable_user_group_id or substitutable_user_group_id == 0:
+            if substitutable_user_group_id == "$uid":
                 return os.getuid()
-            else:
-                try:
-                    return int(self.runner_params["k8s_run_as_user_id"])
-                except Exception:
-                    log.warning(
-                        'User ID passed for Kubernetes runner needs to be an integer or "$uid", value %s passed is invalid',
-                        self.runner_params["k8s_run_as_user_id"],
-                    )
-                    return None
-        return None
-
-    def __get_run_as_group_id(self):
-        if self.runner_params.get("k8s_run_as_group_id") or self.runner_params.get("k8s_run_as_group_id") == 0:
-            run_as_group = self.runner_params["k8s_run_as_group_id"]
-            if run_as_group == "$gid":
+            elif substitutable_user_group_id == "$gid":
                 return self.app.config.gid
             else:
                 try:
-                    return int(self.runner_params["k8s_run_as_group_id"])
+                    return int(substitutable_user_group_id)
                 except Exception:
                     log.warning(
-                        'Group ID passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
-                        self.runner_params["k8s_run_as_group_id"],
+                        'param %s passed to Kubernetes runner needs to be an integer or the strings "$uid" or "$gid". Value %s is invalid',
+                        param_name,
+                        substitutable_user_group_id,
                     )
-        return None
-
-    def __get_supplemental_group(self):
-        if (
-            self.runner_params.get("k8s_supplemental_group_id")
-            or self.runner_params.get("k8s_supplemental_group_id") == 0
-        ):
-            try:
-                return int(self.runner_params["k8s_supplemental_group_id"])
-            except Exception:
-                log.warning(
-                    'Supplemental group passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
-                    self.runner_params["k8s_supplemental_group_id"],
-                )
-                return None
-        return None
-
-    def __get_fs_group(self):
-        if self.runner_params.get("k8s_fs_group_id") or self.runner_params.get("k8s_fs_group_id") == 0:
-            try:
-                return int(self.runner_params["k8s_fs_group_id"])
-            except Exception:
-                log.warning(
-                    'FS group passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
-                    self.runner_params["k8s_fs_group_id"],
-                )
-                return None
+                    return None
         return None
 
     def __get_galaxy_instance_id(self):
@@ -387,7 +365,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         }
         # TODO include other relevant elements that people might want to use from
         # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec
-        k8s_spec_template["spec"]["securityContext"] = self.__get_k8s_security_context()
+        k8s_spec_template["spec"]["securityContext"] = self.__get_k8s_security_context(ajs.job_wrapper)
         extra_metadata = self.runner_params["k8s_job_metadata"] or "{}"
         if isinstance(extra_metadata, str):
             extra_metadata = yaml.safe_load(extra_metadata)
@@ -429,6 +407,54 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         }
         return k8s_spec_template
 
+    def __get_k8s_ingress_rules_spec(self, ajs, entry_points):
+        """This represents the template for the "rules" portion of the Ingress spec."""
+        if "v1beta1" in self.runner_params["k8s_ingress_api_version"]:
+            rules_spec = [
+                {
+                    "host": ep["domain"],
+                    "http": {
+                        "paths": [
+                            {
+                                "backend": {
+                                    "serviceName": self.__get_k8s_job_name(
+                                        self.__produce_k8s_job_prefix(), ajs.job_wrapper
+                                    ),
+                                    "servicePort": int(ep["tool_port"]),
+                                },
+                                "path": ep.get("entry_path", "/"),
+                                "pathType": "Prefix",
+                            }
+                        ]
+                    },
+                }
+                for ep in entry_points
+            ]
+        else:
+            rules_spec = [
+                {
+                    "host": ep["domain"],
+                    "http": {
+                        "paths": [
+                            {
+                                "backend": {
+                                    "service": {
+                                        "name": self.__get_k8s_job_name(
+                                            self.__produce_k8s_job_prefix(), ajs.job_wrapper
+                                        ),
+                                        "port": {"number": int(ep["tool_port"])},
+                                    }
+                                },
+                                "path": ep.get("entry_path", "/"),
+                                "pathType": "ImplementationSpecific",
+                            }
+                        ]
+                    },
+                }
+                for ep in entry_points
+            ]
+        return rules_spec
+
     def __get_k8s_ingress_spec(self, ajs):
         """The k8s spec template is nothing but a Ingress spec, except that it is nested and does not have an apiversion
         nor kind."""
@@ -466,54 +492,41 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 },
                 "annotations": {"app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id},
             },
-            "spec": {
-                "rules": [
-                    {
-                        "host": ep["domain"],
-                        "http": {
-                            "paths": [
-                                {
-                                    "backend": {
-                                        "service": {
-                                            "name": self.__get_k8s_job_name(
-                                                self.__produce_k8s_job_prefix(), ajs.job_wrapper
-                                            ),
-                                            "port": {"number": int(ep["tool_port"])},
-                                        }
-                                    },
-                                    "path": ep.get("entry_path", "/"),
-                                    "pathType": "Prefix",
-                                }
-                            ]
-                        },
-                    }
-                    for ep in entry_points
-                ],
-            },
+            "spec": {"rules": self.__get_k8s_ingress_rules_spec(ajs, entry_points)},
         }
         default_ingress_class = self.runner_params.get("k8s_interactivetools_ingress_class")
         if default_ingress_class:
             k8s_spec_template["spec"]["ingressClassName"] = default_ingress_class
         if self.runner_params.get("k8s_interactivetools_use_ssl"):
             domains = list({e["domain"] for e in entry_points})
-            k8s_spec_template["spec"]["tls"] = [
-                {"hosts": [domain], "secretName": re.sub("[^a-z0-9-]", "-", domain)} for domain in domains
-            ]
+            override_secret = self.runner_params.get("k8s_interactivetools_tls_secret")
+            if override_secret:
+                k8s_spec_template["spec"]["tls"] = [
+                    {"hosts": [domain], "secretName": override_secret} for domain in domains
+                ]
+            else:
+                k8s_spec_template["spec"]["tls"] = [
+                    {"hosts": [domain], "secretName": re.sub("[^a-z0-9-]", "-", domain)} for domain in domains
+                ]
         if self.runner_params.get("k8s_interactivetools_ingress_annotations"):
             new_ann = yaml.safe_load(self.runner_params.get("k8s_interactivetools_ingress_annotations"))
             k8s_spec_template["metadata"]["annotations"].update(new_ann)
         return k8s_spec_template
 
-    def __get_k8s_security_context(self):
+    def __get_k8s_security_context(self, job_wrapper):
         security_context = {}
-        if self._run_as_user_id or self._run_as_user_id == 0:
-            security_context["runAsUser"] = self._run_as_user_id
-        if self._run_as_group_id or self._run_as_group_id == 0:
-            security_context["runAsGroup"] = self._run_as_group_id
-        if self._supplemental_group and self._supplemental_group > 0:
-            security_context["supplementalGroups"] = [self._supplemental_group]
-        if self._fs_group and self._fs_group > 0:
-            security_context["fsGroup"] = self._fs_group
+        run_as_user_id = self.__get_user_group_param_or_default(job_wrapper, "k8s_run_as_user_id")
+        run_as_group_id = self.__get_user_group_param_or_default(job_wrapper, "k8s_run_as_group_id")
+        supplemental_group = self.__get_user_group_param_or_default(job_wrapper, "k8s_supplemental_group_id")
+        fs_group = self.__get_user_group_param_or_default(job_wrapper, "k8s_fs_group_id")
+        if run_as_user_id or run_as_user_id == 0:
+            security_context["runAsUser"] = run_as_user_id
+        if run_as_group_id or run_as_group_id == 0:
+            security_context["runAsGroup"] = run_as_group_id
+        if supplemental_group and supplemental_group > 0:
+            security_context["supplementalGroups"] = [supplemental_group]
+        if fs_group and fs_group > 0:
+            security_context["fsGroup"] = fs_group
         return security_context
 
     def __get_k8s_restart_policy(self, job_wrapper):
@@ -699,22 +712,12 @@ class KubernetesJobRunner(AsynchronousJobRunner):
     def __get_k8s_job_name(self, prefix, job_wrapper):
         return f"{prefix}-{self.__force_label_conformity(job_wrapper.get_id_tag())}"
 
-    def __get_destination_params(self, job_wrapper):
-        """Obtains allowable runner param overrides from the destination"""
-        job_destination = job_wrapper.job_destination
-        OVERRIDABLE_PARAMS = ["k8s_node_selector", "k8s_affinity", "k8s_extra_job_envs"]
-        new_params = {}
-        for each_param in OVERRIDABLE_PARAMS:
-            if each_param in job_destination.params:
-                new_params[each_param] = job_destination.params[each_param]
-        return new_params
-
     def check_watched_item(self, job_state):
         """Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState"""
         jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
 
         if len(jobs.response["items"]) == 1:
-            job = Job(self._pykube_api, jobs.response["items"][0])
+            k8s_job = Job(self._pykube_api, jobs.response["items"][0])
             job_destination = job_state.job_wrapper.job_destination
             succeeded = 0
             active = 0
@@ -731,19 +734,22 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             # would wait forever for a pod that never gets sent.
             max_pod_retries = min(max_pod_retries, self.runner_params["k8s_job_spec_back_off_limit"])
 
-            # Check if job.obj['status'] is empty,
+            # Check if k8s_job.obj['status'] is empty,
             # return job_state unchanged if this is the case
             # as probably this means that the k8s API server hasn't
             # had time to fill in the object status since the
             # job was created only too recently.
-            if len(job.obj["status"]) == 0:
+            # It is possible that k8s didn't account for the status of the pods
+            # and they are in the uncountedTerminatedPods status. In this
+            # case we also need to wait a moment
+            if len(k8s_job.obj["status"]) == 0 or k8s_job.obj["status"].get("uncountedTerminatedPods"):
                 return job_state
-            if "succeeded" in job.obj["status"]:
-                succeeded = job.obj["status"]["succeeded"]
-            if "active" in job.obj["status"]:
-                active = job.obj["status"]["active"]
-            if "failed" in job.obj["status"]:
-                failed = job.obj["status"]["failed"]
+            if "succeeded" in k8s_job.obj["status"]:
+                succeeded = k8s_job.obj["status"]["succeeded"]
+            if "active" in k8s_job.obj["status"]:
+                active = k8s_job.obj["status"]["active"]
+            if "failed" in k8s_job.obj["status"]:
+                failed = k8s_job.obj["status"]["failed"]
 
             job_persisted_state = job_state.job_wrapper.get_state()
 
@@ -751,26 +757,30 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             if succeeded > 0 or job_state == model.Job.states.STOPPED:
                 job_state.running = False
                 self.mark_as_finished(job_state)
-                log.debug(f"Job id: {job_state.job_id} with k8s id: {job.name} succeeded")
+                log.debug(f"Job id: {job_state.job_id} with k8s id: {k8s_job.name} succeeded")
                 return None
             elif active > 0 and failed < max_pod_retries + 1:
                 if not job_state.running:
                     if self.__job_pending_due_to_unschedulable_pod(job_state):
-                        log.debug(f"Job id: {job_state.job_id} with k8s id: {job.name}  pending...")
+                        log.debug(f"Job id: {job_state.job_id} with k8s id: {k8s_job.name} pending...")
                         if self.runner_params.get("k8s_unschedulable_walltime_limit"):
-                            creation_time_str = job.obj["metadata"].get("creationTimestamp")
+                            creation_time_str = k8s_job.obj["metadata"].get("creationTimestamp")
                             creation_time = datetime.strptime(creation_time_str, "%Y-%m-%dT%H:%M:%SZ")
                             elapsed_seconds = (datetime.utcnow() - creation_time).total_seconds()
                             if elapsed_seconds > self.runner_params["k8s_unschedulable_walltime_limit"]:
-                                return self._handle_unschedulable_job(job, job_state)
+                                return self._handle_unschedulable_job(k8s_job, job_state)
                             else:
                                 pass
                         else:
                             pass
-                    else:
-                        log.debug("Job set to running...")
+                    elif self.__check_job_pod_running(job_state):
+                        log.debug(f"Job {k8s_job.name} set to running...")
                         job_state.running = True
                         job_state.job_wrapper.change_state(model.Job.states.RUNNING)
+                    else:
+                        log.debug(
+                            f"Job id: {job_state.job_id} with k8s id: {k8s_job.name} scheduled and is waiting to start..."
+                        )
                 return job_state
             elif job_persisted_state == model.Job.states.DELETED:
                 # Job has been deleted via stop_job and job has not been deleted,
@@ -783,7 +793,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 log.debug(
                     f"Job id: {job_state.job_id} failed and it is not a deletion case. Current state: {job_state.job_wrapper.get_state()}"
                 )
-                if self._handle_job_failure(job, job_state):
+                if self._handle_job_failure(k8s_job, job_state):
                     # changes for resubmission (removed self.mark_as_failed from handle_job_failure)
                     self.work_queue.put((self.mark_as_failed, job_state))
                 else:
@@ -821,7 +831,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             # job is no longer viable - remove from watched jobs
             return None
 
-    def _handle_unschedulable_job(self, job, job_state):
+    def _handle_unschedulable_job(self, k8s_job, job_state):
         # Handle unschedulable job that exceeded deadline
         job_state.fail_message = "Job was unschedulable longer than specified deadline"
         job_state.runner_state = JobState.runner_states.WALLTIME_REACHED
@@ -829,13 +839,14 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         self.mark_as_failed(job_state)
         try:
             if self.__has_guest_ports(job_state.job_wrapper):
-                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, job)
-            self.__cleanup_k8s_job(job)
+                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, k8s_job)
+            # Wrap the k8s job before we put it in the work queue so it can be retried a few times
+            self.work_queue.put((self.__cleanup_k8s_job, RetryableDeleteJobState(job_state=job_state, k8s_job=k8s_job)))
         except Exception:
-            log.exception("Could not clean up k8s batch job. Ignoring...")
+            log.exception("Could not clean up an unschedulable k8s batch job. Ignoring...")
         return None
 
-    def _handle_job_failure(self, job, job_state):
+    def _handle_job_failure(self, k8s_job, job_state):
         # Figure out why job has failed
         mark_failed = True
         with open(job_state.error_file, "a") as error_file:
@@ -845,7 +856,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 error_file.write("Job killed after running out of memory. Try with more memory.\n")
                 job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory."
                 job_state.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
-            elif self.__job_failed_due_to_walltime_limit(job):
+            elif self.__job_failed_due_to_walltime_limit(k8s_job):
                 log.debug(f"Walltime limit reached for job: {job_state.job_id}")
                 error_file.write("DeadlineExceeded")
                 job_state.fail_message = "Job was active longer than specified deadline"
@@ -861,22 +872,51 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 log.debug(msg)
                 error_file.write(msg)
                 job_state.fail_message = (
-                    "An unknown error occurered with this job. See standard output within the info section for details."
+                    "An unknown error occurred with this job. See standard output within the info section for details."
                 )
         # changes for resubmission
         # job_state.running = False
         # self.mark_as_failed(job_state)
         try:
             if self.__has_guest_ports(job_state.job_wrapper):
-                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, job)
-            self.__cleanup_k8s_job(job)
+                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, k8s_job)
+            # Wrap the k8s job before we put it in the work queue so it can be retried a few times
+            self.work_queue.put((self.__cleanup_k8s_job, RetryableDeleteJobState(job_state=job_state, k8s_job=k8s_job)))
         except Exception:
-            log.exception("Could not clean up k8s batch job. Ignoring...")
+            log.exception("Could not clean up a failed k8s batch job. Ignoring...")
         return mark_failed
 
-    def __cleanup_k8s_job(self, job):
+    def __cleanup_k8s_job(self, retryable_delete_k8s_job_state: RetryableDeleteJobState):
+        k8s_job = retryable_delete_k8s_job_state.k8s_job
+        log.debug(
+            f"Cleaning up job with K8s id {k8s_job.name} (attempt {retryable_delete_k8s_job_state.attempts + 1})."
+        )
         k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
-        delete_job(job, k8s_cleanup_job)
+        try:
+            delete_job(k8s_job, k8s_cleanup_job)
+        except HTTPError as exc:
+            # If job not found, then previous deletion was successful
+            if exc.code == 404 and retryable_delete_k8s_job_state.attempts >= 1:
+                log.warning(
+                    f"Cleanup job with K8s id {k8s_job.name} skipped as it is no longer available (404) and a previous deletion was triggered."
+                )
+                return
+            if retryable_delete_k8s_job_state.max_retries <= retryable_delete_k8s_job_state.attempts:
+                log.error(
+                    f"Failed to cleanup job with K8s id {k8s_job.name} after {retryable_delete_k8s_job_state.attempts} of {retryable_delete_k8s_job_state.max_retries} attempts; giving up."
+                )
+                raise exc
+            else:
+                # Refresh the job to resolve object & cluster conflicts
+                reload_job(k8s_job)
+                # Try the cleanup again
+                new_retryable_job_state = RetryableDeleteJobState(
+                    job_state=retryable_delete_k8s_job_state,
+                    k8s_job=k8s_job,
+                    max_retries=retryable_delete_k8s_job_state.max_retries,
+                    attempts=retryable_delete_k8s_job_state.attempts + 1,
+                )
+                self.work_queue.put((self.__cleanup_k8s_job, new_retryable_job_state))
 
     def __cleanup_k8s_ingress(self, ingress, job_failed=False):
         k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
@@ -886,8 +926,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         k8s_cleanup_job = self.runner_params["k8s_cleanup_job"]
         delete_service(service, k8s_cleanup_job, job_failed)
 
-    def __job_failed_due_to_walltime_limit(self, job):
-        conditions = job.obj["status"].get("conditions") or []
+    def __job_failed_due_to_walltime_limit(self, k8s_job):
+        conditions = k8s_job.obj["status"].get("conditions") or []
         return any(True for c in conditions if c["type"] == "Failed" and c["reason"] == "DeadlineExceeded")
 
     def _get_pod_for_job(self, job_state):
@@ -921,6 +961,17 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
         return False
 
+    def __check_job_pod_running(self, job_state):
+        """
+        checks the state of the pod to see if it is running.
+        """
+        pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params["k8s_namespace"])
+        if not pods.response["items"]:
+            return False
+
+        pod = Pod(self._pykube_api, pods.response["items"][0])
+        return is_pod_running(self._pykube_api, pod, self.runner_params["k8s_namespace"])
+
     def __job_pending_due_to_unschedulable_pod(self, job_state):
         """
         checks the state of the pod to see if it is unschedulable.
@@ -978,39 +1029,48 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def stop_job(self, job_wrapper):
         """Attempts to delete a dispatched job to the k8s cluster"""
-        job = job_wrapper.get_job()
+        gxy_job = job_wrapper.get_job()
         try:
-            log.debug(f"Attempting to stop job {job.id} ({job.job_runner_external_id})")
+            log.debug(f"Attempting to stop job {gxy_job.id} ({gxy_job.job_runner_external_id})")
             job_to_delete = find_job_object_by_name(
-                self._pykube_api, job.get_job_runner_external_id(), self.runner_params["k8s_namespace"]
+                self._pykube_api, gxy_job.get_job_runner_external_id(), self.runner_params["k8s_namespace"]
             )
             if job_to_delete and len(job_to_delete.response["items"]) > 0:
                 k8s_job = Job(self._pykube_api, job_to_delete.response["items"][0])
-                log.debug(f"Found job with id {job.get_job_runner_external_id()} to delete")
+                log.debug(f"Found job with id {gxy_job.get_job_runner_external_id()} to delete")
                 # For interactive jobs, at this point because the job stopping has been partly handled by the
                 # interactive tool manager, the job wrapper no longer shows any guest ports. We need another way
                 # to check if the job is an interactive job.
                 if self.__has_guest_ports(job_wrapper):
-                    log.debug(f"Job {job.id} ({job.job_runner_external_id}) has guest ports, cleaning them up")
+                    log.debug(f"Job {gxy_job.id} ({gxy_job.job_runner_external_id}) has guest ports, cleaning them up")
                     self.__cleanup_k8s_guest_ports(job_wrapper, k8s_job)
-                self.__cleanup_k8s_job(k8s_job)
+                # Wrap the k8s job before we put it in the work queue so it can be retried a few times
+                self.work_queue.put(
+                    (
+                        self.__cleanup_k8s_job,
+                        RetryableDeleteJobState(
+                            job_state=JobState(job_wrapper=job_wrapper, job_destination=job_wrapper.job_destination),
+                            k8s_job=k8s_job,
+                        ),
+                    )
+                )
             else:
-                log.debug(f"Could not find job with id {job.get_job_runner_external_id()} to delete")
+                log.debug(f"Could not find job with id {gxy_job.get_job_runner_external_id()} to delete")
             # TODO assert whether job parallelism == 0
             # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
-            log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
+            log.debug(f"({gxy_job.id}/{gxy_job.job_runner_external_id}) terminated at user's request")
 
         except Exception as e:
             log.exception(
                 "(%s/%s) User killed running job, but error encountered during termination: %s",
-                job.id,
-                job.get_job_runner_external_id(),
+                gxy_job.id,
+                gxy_job.get_job_runner_external_id(),
                 e,
             )
 
-    def recover(self, job, job_wrapper):
+    def recover(self, gxy_job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""
-        job_id = job.get_job_runner_external_id()
+        job_id = gxy_job.get_job_runner_external_id()
         log.debug(f"k8s trying to recover job: {job_id}")
         if job_id is None:
             self.put(job_wrapper)
@@ -1021,22 +1081,22 @@ class KubernetesJobRunner(AsynchronousJobRunner):
             job_id=job_id,
             job_destination=job_wrapper.job_destination,
         )
-        ajs.command_line = job.command_line
-        if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
+        ajs.command_line = gxy_job.command_line
+        if gxy_job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
             log.debug(
                 "(%s/%s) is still in %s state, adding to the runner monitor queue",
-                job.id,
-                job.job_runner_external_id,
-                job.state,
+                gxy_job.id,
+                gxy_job.job_runner_external_id,
+                gxy_job.state,
             )
             ajs.old_state = model.Job.states.RUNNING
             ajs.running = True
             self.monitor_queue.put(ajs)
-        elif job.state == model.Job.states.QUEUED:
+        elif gxy_job.state == model.Job.states.QUEUED:
             log.debug(
                 "(%s/%s) is still in queued state, adding to the runner monitor queue",
-                job.id,
-                job.job_runner_external_id,
+                gxy_job.id,
+                gxy_job.job_runner_external_id,
             )
             ajs.old_state = model.Job.states.QUEUED
             ajs.running = False
@@ -1045,7 +1105,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
     # added to make sure that stdout and stderr is captured for Kubernetes
     def fail_job(self, job_state: "JobState", exception=False, message="Job failed", full_status=None):
         log.debug("PP Getting into fail_job in k8s runner")
-        job = job_state.job_wrapper.get_job()
+        gxy_job = job_state.job_wrapper.get_job()
 
         # Get STDOUT and STDERR from the job and tool to be stored in the database #
         # This is needed because when calling finish_job on a failed job, the check_output method
@@ -1066,7 +1126,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
                 if which_try == self.app.config.retry_job_output_collection:
                     job_stdout = ""
                     job_stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
-                    log.error(f"{job.id}/{job.job_runner_external_id} {job_stderr}: {unicodify(e)}")
+                    log.error(f"{gxy_job.id}/{gxy_job.job_runner_external_id} {job_stderr}: {unicodify(e)}")
                 else:
                     time.sleep(1)
                 which_try += 1
@@ -1101,10 +1161,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
         # full status empty leaves the UI without stderr/stdout
         full_status = {"stderr": tool_stderr, "stdout": tool_stdout}
-        log.debug(f"({job.id}/{job.job_runner_external_id}) tool_stdout: {tool_stdout}")
-        log.debug(f"({job.id}/{job.job_runner_external_id}) tool_stderr: {tool_stderr}")
-        log.debug(f"({job.id}/{job.job_runner_external_id}) job_stdout: {job_stdout}")
-        log.debug(f"({job.id}/{job.job_runner_external_id}) job_stderr: {job_stderr}")
+        log.debug(f"({gxy_job.id}/{gxy_job.job_runner_external_id}) tool_stdout: {tool_stdout}")
+        log.debug(f"({gxy_job.id}/{gxy_job.job_runner_external_id}) tool_stderr: {tool_stderr}")
+        log.debug(f"({gxy_job.id}/{gxy_job.job_runner_external_id}) job_stdout: {job_stdout}")
+        log.debug(f"({gxy_job.id}/{gxy_job.job_runner_external_id}) job_stderr: {job_stderr}")
 
         # run super method
         super().fail_job(job_state, exception, message, full_status)
@@ -1122,7 +1182,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         elif len(jobs.response["items"]) == 0:
             log.warning("No k8s job found which matches job id '%s'. Ignoring...", job_state.job_id)
         else:
-            job = Job(self._pykube_api, jobs.response["items"][0])
+            k8s_job = Job(self._pykube_api, jobs.response["items"][0])
             if self.__has_guest_ports(job_state.job_wrapper):
-                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, job)
-            self.__cleanup_k8s_job(job)
+                self.__cleanup_k8s_guest_ports(job_state.job_wrapper, k8s_job)
+            # Wrap the k8s job before we put it in the work queue so it can be retried a few times
+            self.work_queue.put((self.__cleanup_k8s_job, RetryableDeleteJobState(job_state=job_state, k8s_job=k8s_job)))
diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py
index 98438a155ef64f298fbff5fdad21f798bf0f329a..eb1853eb01bfcd09ef01ad4adc93508cd85edba5 100644
--- a/lib/galaxy/jobs/runners/local.py
+++ b/lib/galaxy/jobs/runners/local.py
@@ -57,7 +57,7 @@ class LocalJobRunner(BaseJobRunner):
 
         super().__init__(app, nworkers)
 
-    def __command_line(self, job_wrapper: "MinimalJobWrapper") -> Tuple[str, str]:
+    def _command_line(self, job_wrapper: "MinimalJobWrapper") -> Tuple[str, str]:
         """ """
         command_line = job_wrapper.runner_command_line
 
@@ -90,7 +90,7 @@ class LocalJobRunner(BaseJobRunner):
         stderr = stdout = ""
 
         # command line has been added to the wrapper by prepare_job()
-        job_file, exit_code_path = self.__command_line(job_wrapper)
+        job_file, exit_code_path = self._command_line(job_wrapper)
         job_id = job_wrapper.get_id_tag()
 
         try:
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index 2202c71d4e36a0741d79b42d03d5f7a144ee3232..3317da5f2f065f6ed89f557a2963d1c1ddb58011 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -371,7 +371,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 output_names = compute_environment.output_names()
 
                 client_inputs_list = []
-                for input_dataset_wrapper in job_wrapper.job_io.get_input_paths():
+                for input_dataset_wrapper in job_wrapper.job_io.get_input_paths(
+                    compute_environment.materialized_objects
+                ):
                     # str here to resolve false_path if set on a DatasetPath object.
                     path = str(input_dataset_wrapper)
                     object_store_ref = {
@@ -457,9 +459,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             job = job_wrapper.get_job()
             # Set the job destination here (unlike other runners) because there are likely additional job destination
             # params from the Pulsar client.
-            # Flush with change_state.
-            job_wrapper.set_job_destination(job_destination, external_id=external_job_id, flush=False, job=job)
-            job_wrapper.change_state(model.Job.states.QUEUED, job=job)
+            job_wrapper.set_job_destination(job_destination, external_id=external_job_id, flush=True, job=job)
         except Exception:
             job_wrapper.fail("failure running job", exception=True)
             log.exception("failure running job %d", job_wrapper.job_id)
@@ -670,13 +670,13 @@ class PulsarJobRunner(AsynchronousJobRunner):
             client = self.get_client_from_state(job_state)
             run_results = client.full_status()
             remote_metadata_directory = run_results.get("metadata_directory", None)
-            tool_stdout = run_results.get("stdout", "")
-            tool_stderr = run_results.get("stderr", "")
+            tool_stdout = unicodify(run_results.get("stdout", ""), strip_null=True)
+            tool_stderr = unicodify(run_results.get("stderr", ""), strip_null=True)
             for file in ("tool_stdout", "tool_stderr"):
                 if tool_stdout and tool_stderr:
                     pass
                 try:
-                    file_path = Path(job_wrapper.working_directory) / "outputs" / file
+                    file_path = os.path.join(job_wrapper.working_directory, "outputs", file)
                     file_content = open(file_path)
                     if tool_stdout is None and file == "tool_stdout":
                         tool_stdout = file_content.read()
@@ -725,16 +725,9 @@ class PulsarJobRunner(AsynchronousJobRunner):
             ) as exit_code_file:
                 exit_code_file.write(str(exit_code))
             self._handle_metadata_externally(job_wrapper, resolve_requirements=True)
+        job_metrics_directory = os.path.join(job_wrapper.working_directory, "metadata")
         # Finish the job
         try:
-            job_metrics_directory = os.path.join(job_wrapper.working_directory, "metadata")
-            # Following check is a hack for jobs started during 19.01 or earlier release
-            # and finishing with a 19.05 code base. Eliminate the hack in 19.09 or later
-            # along with hacks for legacy metadata compute strategy.
-            if not os.path.exists(job_metrics_directory) or not any(
-                "__instrument" in f for f in os.listdir(job_metrics_directory)
-            ):
-                job_metrics_directory = job_wrapper.working_directory
             job_wrapper.finish(
                 tool_stdout,
                 tool_stderr,
@@ -746,7 +739,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
             )
         except Exception:
             log.exception("Job wrapper finish method failed")
-            job_wrapper.fail("Unable to finish job", exception=True)
+            job_wrapper.fail("Unable to finish job", exception=True, job_metrics_directory=job_metrics_directory)
 
     def check_pid(self, pid):
         try:
@@ -1068,7 +1061,7 @@ class PulsarMQJobRunner(PulsarJobRunner):
 
 
 DEFAULT_PULSAR_CONTAINER = "galaxy/pulsar-pod-staging:0.15.0.2"
-COEXECUTION_DESTENTATION_DEFAULTS = {
+COEXECUTION_DESTINATION_DEFAULTS = {
     "default_file_action": "remote_transfer",
     "rewrite_parameters": "true",
     "jobs_directory": "/pulsar_staging",
@@ -1080,7 +1073,7 @@ COEXECUTION_DESTENTATION_DEFAULTS = {
 
 
 class PulsarCoexecutionJobRunner(PulsarMQJobRunner):
-    destination_defaults = COEXECUTION_DESTENTATION_DEFAULTS
+    destination_defaults = COEXECUTION_DESTINATION_DEFAULTS
 
     def _populate_parameter_defaults(self, job_destination):
         super()._populate_parameter_defaults(job_destination)
@@ -1094,7 +1087,7 @@ class PulsarCoexecutionJobRunner(PulsarMQJobRunner):
             pulsar_app_config["staging_directory"] = params.get("jobs_directory")
 
 
-KUBERNETES_DESTINATION_DEFAULTS: Dict[str, Any] = {"k8s_enabled": True, **COEXECUTION_DESTENTATION_DEFAULTS}
+KUBERNETES_DESTINATION_DEFAULTS: Dict[str, Any] = {"k8s_enabled": True, **COEXECUTION_DESTINATION_DEFAULTS}
 
 
 class PulsarKubernetesJobRunner(PulsarCoexecutionJobRunner):
@@ -1102,14 +1095,14 @@ class PulsarKubernetesJobRunner(PulsarCoexecutionJobRunner):
     poll = True  # Poll so we can check API for pod IP for ITs.
 
 
-TES_DESTENTATION_DEFAULTS: Dict[str, Any] = {
+TES_DESTINATION_DEFAULTS: Dict[str, Any] = {
     "tes_url": PARAMETER_SPECIFICATION_REQUIRED,
-    **COEXECUTION_DESTENTATION_DEFAULTS,
+    **COEXECUTION_DESTINATION_DEFAULTS,
 }
 
 
 class PulsarTesJobRunner(PulsarCoexecutionJobRunner):
-    destination_defaults = TES_DESTENTATION_DEFAULTS
+    destination_defaults = TES_DESTINATION_DEFAULTS
 
 
 class PulsarRESTJobRunner(PulsarJobRunner):
diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py
index db1ed9b3d002375db978bd693f74e75830254c38..b64b54c4c9db8032e1f3cbb0b34ef4097a8e6daf 100644
--- a/lib/galaxy/jobs/runners/slurm.py
+++ b/lib/galaxy/jobs/runners/slurm.py
@@ -138,16 +138,8 @@ class SlurmJobRunner(DRMAAJobRunner):
                         ajs.job_wrapper.get_id_tag(),
                         ajs.job_id,
                     )
-                    ajs.job_wrapper.change_state(
-                        model.Job.states.QUEUED, info="Job was resubmitted due to node failure"
-                    )
-                    try:
-                        self.queue_job(ajs.job_wrapper)
-                        return
-                    except Exception:
-                        ajs.fail_message = (
-                            "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
-                        )
+                    self.mark_as_resubmitted(ajs, info="Job was resubmitted due to node failure")
+                    return
                 elif slurm_state == "OUT_OF_MEMORY":
                     log.info(
                         "(%s/%s) Job hit memory limit (SLURM state: OUT_OF_MEMORY)",
diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py
index 6fc2c039f7414b64d55fbe8672883adedc7a2e23..6206a94c7a87715c7ef5b6caecd925d6a1459cbb 100644
--- a/lib/galaxy/jobs/runners/util/pykube_util.py
+++ b/lib/galaxy/jobs/runners/util/pykube_util.py
@@ -7,7 +7,10 @@ from pathlib import PurePath
 
 try:
     from pykube.config import KubeConfig
-    from pykube.exceptions import HTTPError
+    from pykube.exceptions import (
+        HTTPError,
+        ObjectDoesNotExist,
+    )
     from pykube.http import HTTPClient
     from pykube.objects import (
         Ingress,
@@ -94,6 +97,13 @@ def find_pod_object_by_name(pykube_api, job_name, namespace=None):
     return Pod.objects(pykube_api).filter(selector=f"job-name={job_name}", namespace=namespace)
 
 
+def is_pod_running(pykube_api, pod, namespace=None):
+    if pod.obj["status"].get("phase") == "Running":
+        return True
+
+    return False
+
+
 def is_pod_unschedulable(pykube_api, pod, namespace=None):
     is_unschedulable = any(c.get("reason") == "Unschedulable" for c in pod.obj["status"].get("conditions", []))
     if pod.obj["status"].get("phase") == "Pending" and is_unschedulable:
@@ -105,7 +115,12 @@ def is_pod_unschedulable(pykube_api, pod, namespace=None):
 def delete_job(job, cleanup="always"):
     job_failed = job.obj["status"]["failed"] > 0 if "failed" in job.obj["status"] else False
     # Scale down the job just in case even if cleanup is never
-    job.scale(replicas=0)
+    try:
+        job.scale(replicas=0)
+    except ObjectDoesNotExist as e:
+        # Okay, job does no longer exist
+        log.info(e)
+
     api_delete = cleanup == "always"
     if not api_delete and cleanup == "onsuccess" and not job_failed:
         api_delete = True
@@ -311,6 +326,7 @@ __all__ = (
     "find_pod_object_by_name",
     "galaxy_instance_id",
     "HTTPError",
+    "is_pod_running",
     "is_pod_unschedulable",
     "Job",
     "Service",
@@ -328,3 +344,13 @@ __all__ = (
     "get_volume_mounts_for_job",
     "parse_pvc_param_line",
 )
+
+
+def reload_job(job):
+    try:
+        job.reload()
+    except HTTPError as e:
+        if e.code == 404:
+            pass
+        else:
+            raise e
diff --git a/lib/galaxy/managers/_config_templates.py b/lib/galaxy/managers/_config_templates.py
index 2b0583a4c887b05b39d30291cff8dc9b2adc662c..22d798a22076b545218039de721e124c5c103445 100644
--- a/lib/galaxy/managers/_config_templates.py
+++ b/lib/galaxy/managers/_config_templates.py
@@ -1,17 +1,24 @@
 import logging
 import os
 from typing import (
+    Any,
     cast,
     Dict,
     List,
     Optional,
+    Type,
     TypeVar,
     Union,
 )
 
-from pydantic import BaseModel
+from pydantic import (
+    BaseModel,
+    UUID4,
+)
+from typing_extensions import TypedDict
 
 from galaxy.exceptions import (
+    InconsistentDatabase,
     ObjectNotFound,
     RequestParameterInvalidException,
     RequestParameterMissingException,
@@ -30,19 +37,26 @@ from galaxy.security.vault import (
     UserVaultWrapper,
     Vault,
 )
+from galaxy.util import config_templates  # defer get_token_from_refresh_raw access for monkey patching
 from galaxy.util.config_templates import (
     EnvironmentDict,
     find_template_by,
+    ImplicitConfigurationParameters,
+    OAuth2ClientPair,
+    OAuth2Configuration,
+    PluginAspectStatus,
     secrets_as_dict,
     SecretsDict,
     Template,
     TemplateEnvironmentEntry,
     TemplateEnvironmentSecret,
     TemplateEnvironmentVariable,
+    TemplateReference,
     TemplateVariableValueType,
     validate_no_extra_variables_defined,
     validate_specified_datatypes_variables,
 )
+from galaxy.work.context import SessionRequestContext
 
 log = logging.getLogger(__name__)
 
@@ -57,6 +71,7 @@ class CreateInstancePayload(BaseModel):
     template_version: int
     variables: SuppliedVariables
     secrets: SuppliedSecrets
+    uuid: Optional[UUID4] = None
 
 
 class UpdateInstancePayload(BaseModel):
@@ -78,14 +93,56 @@ class UpgradeInstancePayload(BaseModel):
     secrets: SuppliedSecrets
 
 
+class TestUpdateInstancePayload(BaseModel):
+    variables: Optional[SuppliedVariables] = None
+
+
+class TestUpgradeInstancePayload(BaseModel):
+    template_version: int
+    variables: SuppliedVariables
+    secrets: SuppliedSecrets
+
+
+class UpgradeTestTarget:
+    instance: HasConfigTemplate
+    payload: TestUpgradeInstancePayload
+
+    def __init__(self, instance: HasConfigTemplate, payload: TestUpgradeInstancePayload):
+        self.instance = instance
+        self.payload = payload
+
+
+class UpdateTestTarget:
+    instance: HasConfigTemplate
+    payload: TestUpdateInstancePayload
+
+    def __init__(self, instance: HasConfigTemplate, payload: TestUpdateInstancePayload):
+        self.instance = instance
+        self.payload = payload
+
+
+class CreateTestTarget:
+    payload: CreateInstancePayload
+    instance_class: Type[HasConfigSecrets]
+
+    def __init__(self, payload: CreateInstancePayload, instance_class: Type[HasConfigSecrets]):
+        self.payload = payload
+        self.instance_class = instance_class
+
+
 ModifyInstancePayload = Union[UpdateInstanceSecretPayload, UpgradeInstancePayload, UpdateInstancePayload]
+TestModifyInstancePayload = Union[TestUpgradeInstancePayload, TestUpdateInstancePayload]
+CanTestPluginStatus = Union[HasConfigTemplate, CreateTestTarget, UpgradeTestTarget, UpdateTestTarget]
 
 
 def recover_secrets(
-    user_object_store: HasConfigSecrets, vault: Vault, app_config: UsesTemplatesAppConfig
+    user_object_store: HasConfigSecrets, vault: Union[UserVaultWrapper, Vault], app_config: UsesTemplatesAppConfig
 ) -> SecretsDict:
-    user: User = user_object_store.user
-    user_vault = UserVaultWrapper(vault, user)
+    if isinstance(vault, UserVaultWrapper):
+        user_vault = vault
+    else:
+        user: User = user_object_store.user
+        user_vault = UserVaultWrapper(vault, user)
     secrets: SecretsDict = {}
     # now we could recover the list of secrets to fetch from...
     # ones recorded as written in the persisted object, the ones
@@ -100,6 +157,111 @@ def recover_secrets(
     return secrets
 
 
+class TemplateParameters(TypedDict):
+    secrets: SuppliedSecrets
+    variables: SuppliedVariables
+    environment: EnvironmentDict
+    user_details: Dict[str, Any]
+    implicit: Optional[ImplicitConfigurationParameters]
+
+
+class TemplateServerConfiguration:
+    """Extra configuration relevant to a given template.
+
+    For state defined in the server but not defined in the template JSON/YAML directly.
+    Currently this only contains optional oauth2 client credentials and oauth2 configuration
+    information (provider URLs and provider specific configuration for the oauth2 flow).
+    """
+
+    oauth2_client_pair: Optional[OAuth2ClientPair]
+    oauth2_configuration: Optional[OAuth2Configuration]
+
+    def __init__(
+        self,
+        oauth2_client_pair: Optional[OAuth2ClientPair] = None,
+        oauth2_configuration: Optional[OAuth2Configuration] = None,
+        oauth2_scope: Optional[str] = None,
+    ):
+        self.oauth2_client_pair = oauth2_client_pair
+        self.oauth2_configuration = oauth2_configuration
+        self.oauth2_scope = oauth2_scope
+
+    @property
+    def uses_oauth2(self):
+        return self.oauth2_configuration is not None
+
+
+def prepare_template_parameters_for_testing(
+    trans: ProvidesUserContext,
+    template: Template,
+    template_server_configuration: TemplateServerConfiguration,
+    target: CanTestPluginStatus,
+    vault: Vault,
+    app_config: UsesTemplatesAppConfig,
+) -> TemplateParameters:
+    secrets = _secrets_for_plugin_status_test(target, trans.user_vault, app_config)
+    variables = _variables_for_plugin_status_test(target)
+    environment = prepare_environment_from_root(template.environment, vault, app_config)
+    user_details = trans.user.config_template_details()
+    implicit = implicit_parameters_for_testing(
+        trans,
+        template_server_configuration,
+        target,
+        app_config,
+    )
+    return TemplateParameters(
+        {
+            "secrets": secrets,
+            "variables": variables,
+            "environment": environment,
+            "user_details": user_details,
+            "implicit": implicit,
+        }
+    )
+
+
+def _variables_for_plugin_status_test(target: CanTestPluginStatus) -> SuppliedVariables:
+    if isinstance(target, CreateTestTarget):
+        return target.payload.variables
+    elif isinstance(target, UpgradeTestTarget) or isinstance(target, UpdateTestTarget):
+        if target.instance.template_variables:
+            variables = target.instance.template_variables.copy()
+        else:
+            variables = {}
+        new_variables = target.payload.variables or {}
+        for new_variable in new_variables:
+            variables[new_variable] = new_variables[new_variable]
+        return new_variables
+    else:
+        return target.template_variables or {}
+
+
+def _secrets_for_plugin_status_test(
+    target: CanTestPluginStatus, user_vault: UserVaultWrapper, app_config: UsesTemplatesAppConfig
+) -> SecretsDict:
+    if isinstance(target, CreateTestTarget):
+        payload = target.payload
+        secrets = payload.secrets.copy()
+        return secrets
+    elif isinstance(target, UpgradeTestTarget):
+        secrets = recover_secrets(target.instance, user_vault, app_config)
+        new_secrets = target.payload.secrets or {}
+        for new_secret in new_secrets:
+            secrets[new_secret] = new_secrets[new_secret]
+        return secrets
+    elif isinstance(target, UpdateTestTarget):
+        secrets = recover_secrets(target.instance, user_vault, app_config)
+        return secrets
+    else:
+        secrets = recover_secrets(target, user_vault, app_config)
+        return secrets
+
+
+def to_template_reference(persisted_instance: HasConfigTemplate) -> TemplateReference:
+    # for mypy convert Mapped[X] -> X
+    return cast(TemplateReference, persisted_instance)
+
+
 def prepare_environment(
     configuration_template: HasConfigEnvironment, vault: Vault, app_config: UsesTemplatesAppConfig
 ) -> EnvironmentDict:
@@ -108,7 +270,7 @@ def prepare_environment(
 
 def prepare_environment_from_root(
     root: Optional[List[TemplateEnvironmentEntry]], vault: Vault, app_config: UsesTemplatesAppConfig
-):
+) -> EnvironmentDict:
     environment: EnvironmentDict = {}
     for environment_entry in root or []:
         e_type = environment_entry.type
@@ -279,3 +441,95 @@ def sort_templates(config, catalog: List[T], instance: HasConfigTemplate) -> Lis
     else:
         templates = [stored_template]
     return templates
+
+
+def implicit_parameters_for_testing(
+    trans: ProvidesUserContext,
+    template_server_configuration: TemplateServerConfiguration,
+    target: CanTestPluginStatus,
+    app_config: UsesTemplatesAppConfig,
+) -> Optional[ImplicitConfigurationParameters]:
+    implicit: ImplicitConfigurationParameters = {}
+    if template_server_configuration.oauth2_configuration:
+        refresh_token_key = None
+        oauth2_refresh_token = None
+        if isinstance(target, CreateTestTarget):
+            if target.payload.uuid:
+                refresh_token_key = target.instance_class.vault_key_from_uuid(
+                    target.payload.uuid, "_oauth2_refresh_token", app_config
+                )
+        else:
+            if isinstance(target, (UpgradeTestTarget, UpdateTestTarget)):
+                instance = target.instance
+            else:
+                instance = target
+            refresh_token_key = instance.vault_key_from_uuid(instance.uuid, "_oauth2_refresh_token", app_config)
+        oauth2_refresh_token = trans.user_vault.read_secret(refresh_token_key)
+        if not oauth2_refresh_token:
+            raise InconsistentDatabase(
+                f"Failed to recover oauth2 refresh token from vault at location {refresh_token_key}, Galaxy is in an inconsistent state and probably requires admin intervention"
+            )
+        _inject_oauth2_access_token(implicit, oauth2_refresh_token, template_server_configuration)
+
+    return implicit
+
+
+def implicit_parameters_for_instance(
+    user_instance: HasConfigSecrets,
+    template_server_configuration: TemplateServerConfiguration,
+    vault: Vault,
+    app_config: UsesTemplatesAppConfig,
+) -> ImplicitConfigurationParameters:
+    implicit: ImplicitConfigurationParameters = {}
+
+    if template_server_configuration.oauth2_configuration:
+        refresh_token_key = user_instance.__class__.vault_key_from_uuid(
+            str(user_instance.uuid), "_oauth2_refresh_token", app_config
+        )
+        user_vault = UserVaultWrapper(vault, user_instance.user)
+        oauth2_refresh_token = user_vault.read_secret(refresh_token_key)
+        if not oauth2_refresh_token:
+            raise Exception("null refresh token key read from user vault")
+        _inject_oauth2_access_token(implicit, oauth2_refresh_token, template_server_configuration)
+
+    return implicit
+
+
+def _inject_oauth2_access_token(
+    implicit: ImplicitConfigurationParameters,
+    oauth2_refresh_token: str,
+    template_server_configuration: TemplateServerConfiguration,
+) -> None:
+    oauth2_client_pair = template_server_configuration.oauth2_client_pair
+    oauth2_configuration = template_server_configuration.oauth2_configuration
+    assert oauth2_client_pair
+    assert oauth2_configuration
+    response = config_templates.get_token_from_refresh_raw(
+        oauth2_refresh_token, oauth2_client_pair, oauth2_configuration
+    )
+    response.raise_for_status()
+    implicit["oauth2_access_token"] = response.json()["access_token"]
+
+
+def oauth2_refresh_token_status(
+    template_server_configuration: TemplateServerConfiguration, exception: Optional[Exception]
+) -> Optional[PluginAspectStatus]:
+    if not template_server_configuration.uses_oauth2:
+        # no oauth enabled, don't report a status associated with
+        return None
+    else:
+        if not exception:
+            return PluginAspectStatus(
+                state="ok", message="OAuth2 secret refresh token generated an access token for this resource"
+            )
+        else:
+            return PluginAspectStatus(
+                state="not_ok",
+                message=f"OAuth2 secret refresh token failed to generate an access token for this resource: {exception}",
+            )
+
+
+def oauth2_redirect_uri(trans: SessionRequestContext) -> str:
+    galaxy_root = trans.request.url_path
+    redirect_uri = f"{galaxy_root}oauth2_callback"
+    return redirect_uri
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 6629e69112677e46b1779141d06a8b6617edb144..135616fbed5aa14ca44e1dc1ad1164735f4fe184 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -110,6 +110,8 @@ def security_check(trans, item, check_ownership=False, check_accessible=False):
             raise exceptions.ItemOwnershipException(
                 f"{item.__class__.__name__} is not owned by the current user", type="error"
             )
+        # no need to check accessibility if we're the owner
+        return item
 
     # Verify accessible:
     #   if it's part of a lib - can they access via security
@@ -501,18 +503,18 @@ class ModelManager(Generic[U]):
         """
         raise exceptions.NotImplemented("Abstract method")
 
-    def update(self, item, new_values, flush=True, **kwargs) -> U:
+    def update(self, item: U, new_values: Dict[str, Any], flush: bool = True, **kwargs) -> U:
         """
         Given a dictionary of new values, update `item` and return it.
 
         ..note: NO validation or deserialization occurs here.
         """
-        self.session().add(item)
         for key, value in new_values.items():
             if hasattr(item, key):
                 setattr(item, key, value)
+        session = self.session()
+        session.add(item)
         if flush:
-            session = self.session()
             with transaction(session):
                 session.commit()
         return item
@@ -697,7 +699,7 @@ class ModelSerializer(HasAModelManager[T]):
                 try:
                     returned[key] = self.serializers[key](item, key, **context)
                 except SkipAttribute:
-                    # dont add this key if the deserializer threw this
+                    # don't add this key if the serializer threw this
                     pass
             elif key in self.serializable_keyset:
                 returned[key] = self.default_serializer(item, key, **context)
@@ -1292,13 +1294,6 @@ def raise_filter_err(attr, op, val, msg):
     raise exceptions.RequestParameterInvalidException(msg, column=attr, operation=op, val=val)
 
 
-def is_valid_slug(slug):
-    """Returns true iff slug is valid."""
-
-    VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
-    return VALID_SLUG_RE.match(slug)
-
-
 class SortableManager:
     """A manager interface for parsing order_by strings into actual 'order by' queries."""
 
diff --git a/lib/galaxy/managers/chat.py b/lib/galaxy/managers/chat.py
new file mode 100644
index 0000000000000000000000000000000000000000..ecf651602684fcf274bfa780102a9a0584af27ab
--- /dev/null
+++ b/lib/galaxy/managers/chat.py
@@ -0,0 +1,99 @@
+from typing import Union
+
+from sqlalchemy import (
+    and_,
+    select,
+)
+from sqlalchemy.exc import (
+    MultipleResultsFound,
+    NoResultFound,
+)
+
+from galaxy.exceptions import (
+    InconsistentDatabase,
+    InternalServerError,
+    RequestParameterInvalidException,
+)
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.model import ChatExchange
+from galaxy.model.base import transaction
+from galaxy.util import unicodify
+
+
+class ChatManager:
+    """
+    Business logic for chat exchanges.
+    """
+
+    def create(self, trans: ProvidesUserContext, job_id: int, message: str) -> ChatExchange:
+        """
+        Create a new chat exchange in the DB.  Currently these are *only* job-based chat exchanges, will need to generalize down the road.
+        :param  job_id:      id of the job to associate the response with
+        :type   job_id:      int
+        :param  response:    the response to save in the DB
+        :type   response:    str
+        :returns:   the created ChatExchange object
+        :rtype:     galaxy.model.ChatExchange
+        :raises: InternalServerError
+        """
+        chat_exchange = ChatExchange(user=trans.user, job_id=job_id, message=message)
+        trans.sa_session.add(chat_exchange)
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+        return chat_exchange
+
+    def get(self, trans: ProvidesUserContext, job_id: int) -> Union[ChatExchange, None]:
+        """
+        Returns the chat response from the DB based on the given job id.
+        :param  job_id:      id of the job to load a response for from the DB
+        :type   job_id:      int
+        :returns:   the loaded ChatExchange object
+        :rtype:     galaxy.model.ChatExchange
+        :raises: InconsistentDatabase, InternalServerError
+        """
+        try:
+            stmt = select(ChatExchange).where(
+                and_(ChatExchange.job_id == job_id, ChatExchange.user_id == trans.user.id)
+            )
+            chat_response = trans.sa_session.execute(stmt).scalar_one()
+        except MultipleResultsFound:
+            # TODO: Unsure about this, isn't this more applicable when we're getting the response for response.id instead of response.
+            raise InconsistentDatabase("Multiple chat responses found with the same job id.")
+        except NoResultFound:
+            # TODO: Would there be cases where we raise an exception here? Or, is there a better way to return None?
+            # raise RequestParameterInvalidException("No accessible response found with the id provided.")
+            return None
+        except Exception as e:
+            raise InternalServerError(f"Error loading from the database.{unicodify(e)}")
+        return chat_response
+
+    def set_feedback_for_job(self, trans: ProvidesUserContext, job_id: int, feedback: int) -> ChatExchange:
+        """
+        Set the feedback for a chat response.
+        :param  message_id:      id of the job to associate the feedback with
+        :type   message_id:      int
+        :param  feedback:    the feedback to save in the DB (0 or 1)
+        :type   feedback:    int
+        :returns:   the updated ChatExchange object
+        :rtype:     galaxy.model.ChatExchange
+        :raises: RequestParameterInvalidException
+        """
+
+        # TODO: Set feedback for specific messages as we allow multiple messages per exchange, not this method targeting job.
+
+        # Validate the feedback; it should be 0 or 1
+        if feedback not in [0, 1]:
+            raise RequestParameterInvalidException("Feedback should be 0 or 1.")
+
+        chat_exchange = self.get(trans, job_id)
+
+        if not chat_exchange:
+            raise RequestParameterInvalidException("No accessible response found with the id provided.")
+
+        # There is only one message in an exchange currently, so we can set the feedback on the first message
+        chat_exchange.messages[0].feedback = feedback
+
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+
+        return chat_exchange
diff --git a/lib/galaxy/managers/citations.py b/lib/galaxy/managers/citations.py
index a76e38aea9b7617180d11cc66b80ef51361ef573..e23403e8a3c4e22fd747db4a45000081369993a4 100644
--- a/lib/galaxy/managers/citations.py
+++ b/lib/galaxy/managers/citations.py
@@ -1,10 +1,17 @@
 import functools
 import logging
+from typing import (
+    Dict,
+    Optional,
+    Type,
+    Union,
+)
 
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
 
 from galaxy.structured_app import BasicSharedApp
+from galaxy.tool_util.parser.interface import Citation
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     requests,
@@ -12,6 +19,9 @@ from galaxy.util import (
 
 log = logging.getLogger(__name__)
 
+CitationT = Union["BibtexCitation", "DoiCitation"]
+OptionalCitationT = Optional[CitationT]
+
 
 class CitationsManager:
     def __init__(self, app: BasicSharedApp) -> None:
@@ -29,8 +39,8 @@ class CitationsManager:
                 citation_collection.add(citation)
         return citation_collection.citations
 
-    def parse_citation(self, citation_elem):
-        return parse_citation(citation_elem, self)
+    def parse_citation(self, citation_model: Citation) -> OptionalCitationT:
+        return parse_citation(citation_model, self)
 
     def _get_tool(self, tool_id):
         tool = self.app.toolbox.get_tool(tool_id)
@@ -67,19 +77,19 @@ class DoiCache:
         return self._cache.get(key=doi, createfunc=createfunc)
 
 
-def parse_citation(elem, citation_manager):
+def parse_citation(citation_model: Citation, citation_manager) -> OptionalCitationT:
     """
     Parse an abstract citation entry from the specified XML element.
     """
-    citation_type = elem.attrib.get("type", None)
+    citation_type = citation_model.type
     citation_class = CITATION_CLASSES.get(citation_type, None)
     if not citation_class:
         log.warning(f"Unknown or unspecified citation type: {citation_type}")
         return None
     try:
-        citation = citation_class(elem, citation_manager)
+        citation = citation_class(citation_model, citation_manager)
     except Exception as e:
-        raise Exception(f"Invalid citation of type '{citation_type}' with content '{elem.text}': {e}")
+        raise Exception(f"Invalid citation of type '{citation_type}' with content '{citation_model.content}': {e}")
     return citation
 
 
@@ -126,20 +136,22 @@ class BaseCitation:
 
 
 class BibtexCitation(BaseCitation):
-    def __init__(self, elem, citation_manager):
-        self.raw_bibtex = elem.text.strip()
+    def __init__(self, citation_model: Citation, citation_manager: CitationsManager):
+        self.raw_bibtex = citation_model.content
 
-    def to_bibtex(self):
+    def to_bibtex(self) -> str:
         return self.raw_bibtex
 
 
+BIBTEX_UNSET = object()
+
+
 class DoiCitation(BaseCitation):
-    BIBTEX_UNSET = object()
 
-    def __init__(self, elem, citation_manager):
-        self.__doi = elem.text.strip()
+    def __init__(self, citation_model: Citation, citation_manager: CitationsManager):
+        self.__doi = citation_model.content
         self.doi_cache = citation_manager.doi_cache
-        self.raw_bibtex = DoiCitation.BIBTEX_UNSET
+        self.raw_bibtex = BIBTEX_UNSET
 
     def has_doi(self):
         return True
@@ -147,23 +159,23 @@ class DoiCitation(BaseCitation):
     def doi(self):
         return self.__doi
 
-    def to_bibtex(self):
-        if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
+    def to_bibtex(self) -> str:
+        if self.raw_bibtex is BIBTEX_UNSET:
             try:
                 self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi)
             except Exception:
                 log.debug("Failed to fetch bibtex for DOI %s", self.__doi)
 
-        if self.raw_bibtex is DoiCitation.BIBTEX_UNSET:
+        if self.raw_bibtex is BIBTEX_UNSET:
             return f"""@MISC{{{self.__doi},
                 DOI = {{{self.__doi}}},
                 note = {{Failed to fetch BibTeX for DOI.}}
             }}"""
         else:
-            return self.raw_bibtex
+            return str(self.raw_bibtex)
 
 
-CITATION_CLASSES = dict(
+CITATION_CLASSES: Dict[str, Type[CitationT]] = dict(
     bibtex=BibtexCitation,
     doi=DoiCitation,
 )
diff --git a/lib/galaxy/managers/cloud.py b/lib/galaxy/managers/cloud.py
deleted file mode 100644
index 813b5690b7ee8485b307b4fd15b7ff51e0a2a9d9..0000000000000000000000000000000000000000
--- a/lib/galaxy/managers/cloud.py
+++ /dev/null
@@ -1,400 +0,0 @@
-"""
-Manager and serializer for cloud-based storages.
-"""
-
-import json
-import logging
-
-from galaxy import (
-    model,
-    util,
-)
-from galaxy.exceptions import (
-    ItemAccessibilityException,
-    MessageException,
-    ObjectNotFound,
-    RequestParameterInvalidException,
-    RequestParameterMissingException,
-)
-from galaxy.managers import sharable
-from galaxy.util import Params
-
-try:
-    from cloudbridge.factory import (
-        CloudProviderFactory,
-        ProviderList,
-    )
-except ImportError:
-    CloudProviderFactory = None
-    ProviderList = None
-
-log = logging.getLogger(__name__)
-
-NO_CLOUDBRIDGE_ERROR_MESSAGE = (
-    "Cloud ObjectStore is configured, but no CloudBridge dependency available."
-    "Please install CloudBridge or modify ObjectStore configuration."
-)
-
-# Any change to this list, MUST be reflected in the SEND_TOOL wrapper
-# (tools/cloud/send.xml).
-SUPPORTED_PROVIDERS = {"aws": 0, "azure": 1}
-
-SEND_TOOL = "send_to_cloud"
-SEND_TOOL_VERSION = "0.1.0"
-
-# TODO: this configuration should be set in a config file.
-SINGED_URL_TTL = 3600
-
-
-class CloudManager(sharable.SharableModelManager):
-    # This manager does not manage a history; however,
-    # some of its functions require operations
-    # on history objects using methods from the base
-    # manager class (e.g., get_accessible), which requires
-    # setting this property.
-    model_class = model.History
-
-    @staticmethod
-    def configure_provider(provider, credentials):
-        """
-        Given a provider name and required credentials, it configures and returns a cloudbridge
-        connection to the provider.
-
-        :type  provider: string
-        :param provider: the name of cloud-based resource provided. A list of supported providers is given in
-                         `SUPPORTED_PROVIDERS` variable.
-
-        :type  credentials: dict
-        :param credentials: a dictionary containing all the credentials required to authenticated to the
-                            specified provider.
-
-        :rtype: provider specific, e.g., `cloudbridge.cloud.providers.aws.provider.AWSCloudProvider` for AWS.
-        :return: a cloudbridge connection to the specified provider.
-        """
-        missing_credentials = []
-        if provider == "aws":
-            access = credentials.get("access_key", None)
-            if access is None:
-                access = credentials.get("AccessKeyId", None)
-                if access is None:
-                    missing_credentials.append("access_key")
-            secret = credentials.get("secret_key", None)
-            if secret is None:
-                secret = credentials.get("SecretAccessKey", None)
-                if secret is None:
-                    missing_credentials.append("secret_key")
-            if len(missing_credentials) > 0:
-                raise RequestParameterMissingException(
-                    "The following required key(s) are missing from the provided "
-                    f"credentials object: {missing_credentials}"
-                )
-            session_token = credentials.get("SessionToken")
-            config = {"aws_access_key": access, "aws_secret_key": secret, "aws_session_token": session_token}
-            connection = CloudProviderFactory().create_provider(ProviderList.AWS, config)
-        elif provider == "azure":
-            subscription = credentials.get("subscription_id", None)
-            if subscription is None:
-                missing_credentials.append("subscription_id")
-            client = credentials.get("client_id", None)
-            if client is None:
-                missing_credentials.append("client_id")
-            secret = credentials.get("secret", None)
-            if secret is None:
-                missing_credentials.append("secret")
-            tenant = credentials.get("tenant", None)
-            if tenant is None:
-                missing_credentials.append("tenant")
-            if len(missing_credentials) > 0:
-                raise RequestParameterMissingException(
-                    "The following required key(s) are missing from the provided "
-                    f"credentials object: {missing_credentials}"
-                )
-
-            config = {
-                "azure_subscription_id": subscription,
-                "azure_client_id": client,
-                "azure_secret": secret,
-                "azure_tenant": tenant,
-            }
-            storage_account = credentials.get("storage_account")
-            if storage_account:
-                config["azure_storage_account"] = storage_account
-            resource_group = credentials.get("resource_group")
-            if resource_group:
-                config["azure_resource_group"] = resource_group
-            connection = CloudProviderFactory().create_provider(ProviderList.AZURE, config)
-        elif provider == "openstack":
-            username = credentials.get("username", None)
-            if username is None:
-                missing_credentials.append("username")
-            password = credentials.get("password", None)
-            if password is None:
-                missing_credentials.append("password")
-            auth_url = credentials.get("auth_url", None)
-            if auth_url is None:
-                missing_credentials.append("auth_url")
-            prj_name = credentials.get("project_name", None)
-            if prj_name is None:
-                missing_credentials.append("project_name")
-            prj_domain_name = credentials.get("project_domain_name", None)
-            if prj_domain_name is None:
-                missing_credentials.append("project_domain_name")
-            user_domain_name = credentials.get("user_domain_name", None)
-            if user_domain_name is None:
-                missing_credentials.append("user_domain_name")
-            if len(missing_credentials) > 0:
-                raise RequestParameterMissingException(
-                    "The following required key(s) are missing from the provided "
-                    f"credentials object: {missing_credentials}"
-                )
-            config = {
-                "os_username": username,
-                "os_password": password,
-                "os_auth_url": auth_url,
-                "os_project_name": prj_name,
-                "os_project_domain_name": prj_domain_name,
-                "os_user_domain_name": user_domain_name,
-            }
-            connection = CloudProviderFactory().create_provider(ProviderList.OPENSTACK, config)
-        elif provider == "gcp":
-            config = {"gcp_service_creds_dict": credentials}
-            connection = CloudProviderFactory().create_provider(ProviderList.GCP, config)
-        else:
-            raise RequestParameterInvalidException(
-                f"Unrecognized provider '{provider}'; the following are the supported "
-                f"providers: {SUPPORTED_PROVIDERS.keys()}."
-            )
-
-        # The authorization-assertion mechanism of Cloudbridge assumes a user has an elevated privileges,
-        # such as Admin-level access to all resources (see https://github.com/CloudVE/cloudbridge/issues/135).
-        # As a result, a user who wants to authorize Galaxy to read/write an Amazon S3 bucket, need to
-        # also authorize Galaxy with full permission to Amazon EC2 (because Cloudbridge leverages EC2-specific
-        # operation to assert credentials). While the EC2 authorization is not required by Galaxy to
-        # read/write a S3 bucket, it can cause this exception.
-        #
-        # Until Cloudbridge implements an authorization-specific credentials assertion, we are not asserting
-        # the authorization/validity of the credentials, in order to avoid asking users to grant Galaxy with an
-        # elevated, yet unnecessary, privileges.
-        #
-        # Note, if user's credentials are invalid/expired to perform the authorized action, that can cause
-        # exceptions which we capture separately in related read/write attempts.
-        return connection
-
-    @staticmethod
-    def _get_inputs(obj, key, input_args):
-        space_to_tab = None
-        if input_args.get("space_to_tab", "").lower() == "true":
-            space_to_tab = "Yes"
-        elif input_args.get("space_to_tab", "").lower() not in ["false", ""]:
-            raise RequestParameterInvalidException(
-                "The valid values for `space_to_tab` argument are `true` and `false`; received {}".format(
-                    input_args.get("space_to_tab")
-                )
-            )
-
-        to_posix_lines = None
-        if input_args.get("to_posix_lines", "").lower() == "true":
-            to_posix_lines = "Yes"
-        elif input_args.get("to_posix_lines", "").lower() not in ["false", ""]:
-            raise RequestParameterInvalidException(
-                "The valid values for `to_posix_lines` argument are `true` and `false`; received {}".format(
-                    input_args.get("to_posix_lines")
-                )
-            )
-
-        return {
-            "dbkey": input_args.get("dbkey", "?"),
-            "file_type": input_args.get("file_type", "auto"),
-            "files_0|type": "upload_dataset",
-            "files_0|space_to_tab": space_to_tab,
-            "files_0|to_posix_lines": to_posix_lines,
-            "files_0|NAME": obj,
-            "files_0|url_paste": key.generate_url(expires_in=SINGED_URL_TTL),
-        }
-
-    def get(self, trans, history_id, bucket_name, objects, authz_id, input_args=None):
-        """
-        Implements the logic of getting a file from a cloud-based storage (e.g., Amazon S3)
-        and persisting it as a Galaxy dataset.
-
-        This manager does NOT require use credentials, instead, it uses a more secure method,
-        which leverages CloudAuthz (https://github.com/galaxyproject/cloudauthz) and automatically
-        requests temporary credentials to access the defined resources.
-
-        :type  trans:       galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans:       Galaxy web transaction
-
-        :type  history_id:  string
-        :param history_id:  the (decoded) id of history to which the object should be received to.
-
-        :type  bucket_name: string
-        :param bucket_name: the name of a bucket from which data should be fetched (e.g., a bucket name on AWS S3).
-
-        :type  objects:     list of string
-        :param objects:     the name of objects to be fetched.
-
-        :type  authz_id:    int
-        :param authz_id:    the ID of CloudAuthz to be used for authorizing access to the resource provider. You may
-                            get a list of the defined authorizations sending GET to `/api/cloud/authz`. Also, you can
-                            POST to `/api/cloud/authz` to define a new authorization.
-
-        :type  input_args:  dict
-        :param input_args:  a [Optional] a dictionary of input parameters:
-                            dbkey, file_type, space_to_tab, to_posix_lines (see galaxy/webapps/galaxy/api/cloud.py)
-
-        :rtype:             list of galaxy.model.Dataset
-        :return:            a list of datasets created for the fetched files.
-        """
-        if CloudProviderFactory is None:
-            raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
-
-        if input_args is None:
-            input_args = {}
-
-        if not hasattr(trans.app, "authnz_manager"):
-            err_msg = (
-                "The OpenID Connect protocol, a required feature for getting data from cloud, "
-                "is not enabled on this Galaxy instance."
-            )
-            log.debug(err_msg)
-            raise MessageException(err_msg)
-
-        cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
-        credentials = trans.app.authnz_manager.get_cloud_access_credentials(
-            cloudauthz, trans.sa_session, trans.user.id, trans.request
-        )
-        connection = self.configure_provider(cloudauthz.provider, credentials)
-        try:
-            bucket = connection.storage.buckets.get(bucket_name)
-            if bucket is None:
-                raise RequestParameterInvalidException(f"The bucket `{bucket_name}` not found.")
-        except Exception as e:
-            raise ItemAccessibilityException(f"Could not get the bucket `{bucket_name}`: {util.unicodify(e)}")
-
-        datasets = []
-        for obj in objects:
-            try:
-                key = bucket.objects.get(obj)
-            except Exception as e:
-                raise MessageException(
-                    f"The following error occurred while getting the object {obj}: {util.unicodify(e)}"
-                )
-            if key is None:
-                log.exception(
-                    "Could not get object `%s` for user `%s`. Object may not exist, or the provided credentials are "
-                    "invalid or not authorized to read the bucket/object.",
-                    obj,
-                    trans.user.id,
-                )
-                raise ObjectNotFound(
-                    f"Could not get the object `{obj}`. Please check if the object exists, and credentials are valid and "
-                    "authorized to read the bucket and object. "
-                )
-
-            params = Params(self._get_inputs(obj, key, input_args), sanitize=False)
-            incoming = params.__dict__
-            history = trans.sa_session.get(model.History, history_id)
-            if not history:
-                raise ObjectNotFound("History with the ID provided was not found.")
-            output = trans.app.toolbox.get_tool("upload1").handle_input(trans, incoming, history=history)
-
-            job_errors = output.get("job_errors", [])
-            if job_errors:
-                raise ValueError(
-                    f"Following error occurred while getting the given object(s) from {cloudauthz.provider}: {job_errors}"
-                )
-            else:
-                for d in output["out_data"]:
-                    datasets.append(d[1].dataset)
-
-        return datasets
-
-    def send(self, trans, history_id, bucket_name, authz_id, dataset_ids=None, overwrite_existing=False):
-        """
-        Implements the logic of sending dataset(s) from a given history to a given cloud-based storage
-        (e.g., Amazon S3).
-
-        :type  trans:               galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans:               Galaxy web transaction
-
-        :type  history_id:          string
-        :param history_id:          the (encoded) id of history from which the object should be sent.
-
-        :type  bucket_name:         string
-        :param bucket_name:         the name of a bucket to which data should be sent (e.g., a bucket
-                                    name on AWS S3).
-
-        :type  authz_id:            int
-        :param authz_id:            the ID of CloudAuthz to be used for authorizing access to the resource provider.
-                                    You may get a list of the defined authorizations via `/api/cloud/authz`. Also,
-                                    you can use `/api/cloud/authz/create` to define a new authorization.
-
-        :type  dataset_ids:         set
-        :param dataset_ids:         [Optional] The list of (decoded) dataset ID(s) belonging to the given
-                                    history which should be sent to the given provider. If not provided,
-                                    Galaxy sends all the datasets belonging to the given history.
-
-        :type  overwrite_existing:  boolean
-        :param overwrite_existing:  [Optional] If set to "True", and an object with same name of the
-                                    dataset to be sent already exist in the bucket, Galaxy replaces
-                                    the existing object with the dataset to be sent. If set to
-                                    "False", Galaxy appends datetime to the dataset name to prevent
-                                    overwriting the existing object.
-
-        :rtype:                     tuple
-        :return:                    A tuple of two lists of labels of the objects that were successfully and
-                                    unsuccessfully sent to cloud.
-        """
-        if CloudProviderFactory is None:
-            raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
-
-        if not hasattr(trans.app, "authnz_manager"):
-            err_msg = (
-                "The OpenID Connect protocol, a required feature for sending data to cloud, "
-                "is not enabled on this Galaxy instance."
-            )
-            log.debug(err_msg)
-            raise MessageException(err_msg)
-
-        cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
-
-        history = trans.sa_session.get(model.History, history_id)
-        if not history:
-            raise ObjectNotFound("History with the provided ID not found.")
-
-        sent = []
-        failed = []
-        for hda in history.datasets:
-            if hda.deleted or hda.purged or hda.state != "ok" or hda.creating_job.tool_id == SEND_TOOL:
-                continue
-            if dataset_ids is None or hda.dataset.id in dataset_ids:
-                try:
-                    object_label = hda.name.replace(" ", "_")
-                    args = {
-                        # We encode ID here because the tool wrapper expects
-                        # an encoded ID and attempts decoding it.
-                        "authz_id": trans.security.encode_id(cloudauthz.id),
-                        "bucket": bucket_name,
-                        "object_label": object_label,
-                        "filename": hda,
-                        "overwrite_existing": overwrite_existing,
-                    }
-                    incoming = (util.Params(args, sanitize=False)).__dict__
-                    d2c = trans.app.toolbox.get_tool(SEND_TOOL, SEND_TOOL_VERSION)
-                    if not d2c:
-                        log.debug(f"Failed to get the `send` tool per user `{trans.user.id}` request.")
-                        failed.append(json.dumps({"object": object_label, "error": "Unable to get the `send` tool."}))
-                        continue
-                    res = d2c.execute(trans, incoming, history=history)
-                    job = res[0]
-                    sent.append(json.dumps({"object": object_label, "job_id": trans.app.security.encode_id(job.id)}))
-                except Exception as e:
-                    err_msg = f"maybe invalid or unauthorized credentials. {util.unicodify(e)}"
-                    log.debug(
-                        "Failed to send the dataset `%s` per user `%s` request to cloud, %s",
-                        object_label,
-                        trans.user.id,
-                        err_msg,
-                    )
-                    failed.append(json.dumps({"object": object_label, "error": err_msg}))
-        return sent, failed
diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py
deleted file mode 100644
index bf4e0aa4caa2be049d8845200a099aadad41ae15..0000000000000000000000000000000000000000
--- a/lib/galaxy/managers/cloudauthzs.py
+++ /dev/null
@@ -1,127 +0,0 @@
-"""
-Manager and (de)serializer for cloud authorizations (cloudauthzs).
-"""
-
-import logging
-from typing import Dict
-
-from galaxy import model
-from galaxy.exceptions import InternalServerError
-from galaxy.managers import (
-    base,
-    sharable,
-)
-
-log = logging.getLogger(__name__)
-
-
-class CloudAuthzManager(sharable.SharableModelManager):
-    model_class = model.CloudAuthz
-    foreign_key_name = "cloudauthz"
-
-
-class CloudAuthzsSerializer(base.ModelSerializer):
-    """
-    Interface/service object for serializing cloud authorizations (cloudauthzs) into dictionaries.
-    """
-
-    model_manager_class = CloudAuthzManager
-
-    def __init__(self, app, **kwargs):
-        super().__init__(app, **kwargs)
-        self.cloudauthzs_manager = self.manager
-
-        self.default_view = "summary"
-        self.add_view(
-            "summary",
-            [
-                "id",
-                "model_class",
-                "user_id",
-                "provider",
-                "config",
-                "authn_id",
-                "last_update",
-                "last_activity",
-                "create_time",
-                "description",
-            ],
-        )
-
-    def add_serializers(self):
-        super().add_serializers()
-
-        # Arguments of the following lambda functions:
-        # i  : an instance of galaxy.model.CloudAuthz.
-        # k  : serialized dictionary key (e.g., 'model_class', 'provider').
-        # **c: a dictionary containing 'trans' and 'user' objects.
-        serializers: Dict[str, base.Serializer] = {
-            "id": lambda item, key, **context: self.app.security.encode_id(item.id),
-            "model_class": lambda item, key, **context: "CloudAuthz",
-            "user_id": lambda item, key, **context: self.app.security.encode_id(item.user_id),
-            "provider": lambda item, key, **context: str(item.provider),
-            "config": lambda item, key, **context: item.config,
-            "authn_id": lambda item, key, **context: (
-                self.app.security.encode_id(item.authn_id) if item.authn_id else None
-            ),
-            "last_update": lambda item, key, **context: str(item.last_update),
-            "last_activity": lambda item, key, **context: str(item.last_activity),
-            "create_time": lambda item, key, **context: item.create_time.isoformat(),
-            "description": lambda item, key, **context: str(item.description),
-        }
-        self.serializers.update(serializers)
-
-
-class CloudAuthzsDeserializer(base.ModelDeserializer):
-    """
-    Service object for validating and deserializing dictionaries that
-    update/alter cloudauthz configurations.
-    """
-
-    model_manager_class = CloudAuthzManager
-
-    def add_deserializers(self):
-        super().add_deserializers()
-        self.deserializers.update(
-            {
-                "authn_id": self.deserialize_and_validate_authn_id,
-                "provider": self.default_deserializer,
-                "config": self.default_deserializer,
-                "description": self.default_deserializer,
-            }
-        )
-
-    def deserialize_and_validate_authn_id(self, item, key, val, **context):
-        """
-        Deserializes an authentication ID (authn_id), and asserts if the
-        current user can assume that authentication.
-
-        :type  item:    galaxy.model.CloudAuthz
-        :param item:    an instance of cloudauthz
-
-        :type  key:     string
-        :param key:     `authn_id` attribute of the cloudauthz object (i.e., the `item` param).
-
-        :type  val:     string
-        :param val:     the value of `authn_id` attribute of the cloudauthz object (i.e., the `item` param).
-
-        :type  context: dict
-        :param context: a dictionary object containing Galaxy `trans`.
-
-        :rtype:         string
-        :return:        decoded authentication ID.
-        """
-
-        decoded_authn_id = self.app.security.decode_id(val, object_name="authz")
-
-        trans = context.get("trans")
-        if trans is None:
-            log.debug("Not found expected `trans` when deserializing CloudAuthz.")
-            raise InternalServerError
-
-        try:
-            trans.app.authnz_manager.can_user_assume_authn(trans, decoded_authn_id)
-        except Exception as e:
-            raise e
-
-        return decoded_authn_id
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 58fb252aed5753b6da0e20b0f9ed710c231a6aa7..68f312a3dfb536a21e608f24bbffb5cde2e4c2d8 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -104,8 +104,8 @@ class ConfigSerializer(base.ModelSerializer):
         self.default_view = "all"
         self.add_view("all", list(self.serializers.keys()))
 
-    def default_serializer(self, config, key):
-        return getattr(config, key, None)
+    def default_serializer(self, item, key, **context):
+        return getattr(item, key, None)
 
     def add_serializers(self):
         def _defaults_to(default) -> base.Serializer:
@@ -232,6 +232,7 @@ class ConfigSerializer(base.ModelSerializer):
             "help_forum_api_url": _use_config,
             "enable_help_forum_tool_panel_integration": _use_config,
             "disable_batch_input": _use_config,
+            "llm_api_configured": lambda item, key, **context: bool(item.openai_api_key),
         }
 
 
diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index 24c29567a80b337bde1d4fd7e09efd4784a118f5..89a9c32c890219dadaa5184e8b8d6ed4436487c0 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -39,10 +39,13 @@ import abc
 import string
 from json import dumps
 from typing import (
+    Any,
     Callable,
     cast,
+    Dict,
     List,
     Optional,
+    Tuple,
 )
 
 from sqlalchemy import select
@@ -79,11 +82,13 @@ class ProvidesAppContext:
     Mixed in class must provide `app` property.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def app(self) -> MinimalManagerApp:
         """Provide access to the Galaxy ``app`` object."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def url_builder(self) -> Optional[Callable[..., str]]:
         """
         Provide access to Galaxy URLs (if available).
@@ -204,6 +209,13 @@ class ProvidesUserContext(ProvidesAppContext):
 
     galaxy_session: Optional[GalaxySession] = None
     _tag_handler: Optional[GalaxyTagHandlerSession] = None
+    _short_term_cache: Dict[Tuple[str, ...], Any]
+
+    def set_cache_value(self, args: Tuple[str, ...], value: Any):
+        self._short_term_cache[args] = value
+
+    def get_cache_value(self, args: Tuple[str, ...], default: Any = None) -> Any:
+        return self._short_term_cache.get(args, default)
 
     @property
     def tag_handler(self):
@@ -217,7 +229,8 @@ class ProvidesUserContext(ProvidesAppContext):
             raise AuthenticationRequired("The async task requires user authentication.")
         return RequestUser(user_id=self.user.id)
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def user(self):
         """Provide access to the user object."""
 
@@ -290,7 +303,8 @@ class ProvidesHistoryContext(ProvidesUserContext):
     properties.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def history(self) -> Optional[History]:
         """Provide access to the user's current history model object.
 
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index 8c63932ecb787d8903879fad4fea09a868d968f3..6bd28821ff3a920ae14e14273c1055e4b6486eed 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -8,8 +8,10 @@ import os
 from typing import (
     Any,
     Dict,
+    Generic,
     List,
     Optional,
+    Set,
     Type,
     TypeVar,
 )
@@ -31,8 +33,11 @@ from galaxy.managers import (
 from galaxy.model import (
     Dataset,
     DatasetHash,
+    DatasetInstance,
+    HistoryDatasetAssociation,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.schema.tasks import (
     ComputeDatasetHashTaskRequest,
     PurgeDatasetsTaskRequest,
@@ -45,12 +50,12 @@ log = logging.getLogger(__name__)
 T = TypeVar("T")
 
 
-class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManagerMixin, deletable.PurgableManagerMixin):
+class DatasetManager(base.ModelManager[Dataset], secured.AccessibleManagerMixin, deletable.PurgableManagerMixin):
     """
     Manipulate datasets: the components contained in DatasetAssociations/DatasetInstances/HDAs/LDDAs
     """
 
-    model_class = model.Dataset
+    model_class = Dataset
     foreign_key_name = "dataset"
     app: MinimalManagerApp
 
@@ -62,45 +67,28 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager
         # needed for admin test
         self.user_manager = users.UserManager(app)
         self.quota_agent = app.quota_agent
-        self.security_agent = app.model.security_agent
 
-    def create(self, manage_roles=None, access_roles=None, flush=True, **kwargs):
-        """
-        Create and return a new Dataset object.
-        """
-        # default to NEW state on new datasets
-        kwargs.update(dict(state=(kwargs.get("state", model.Dataset.states.NEW))))
-        dataset = model.Dataset(**kwargs)
-        self.session().add(dataset)
-
-        self.permissions.set(dataset, manage_roles, access_roles, flush=False)
-
-        if flush:
-            session = self.session()
-            with transaction(session):
-                session.commit()
-        return dataset
-
-    def copy(self, dataset, **kwargs):
+    def copy(self, item, **kwargs):
         raise exceptions.NotImplemented("Datasets cannot be copied")
 
-    def purge(self, dataset, flush=True, user=None):
+    def purge(self, item, flush=True, user=None, **kwargs):
         """
         Remove the object_store/file for this dataset from storage and mark
         as purged.
 
         :raises exceptions.ConfigDoesNotAllowException: if the instance doesn't allow
         """
-        self.error_unless_dataset_purge_allowed(dataset)
+        self.error_unless_dataset_purge_allowed(item)
 
         # the following also marks dataset as purged and deleted
-        dataset.full_delete(user=user)
-        self.session().add(dataset)
+
+        item.full_delete(user=user)
+        self.session().add(item)
         if flush:
             session = self.session()
             with transaction(session):
                 session.commit()
-        return dataset
+        return item
 
     def purge_datasets(self, request: PurgeDatasetsTaskRequest, user: Optional[model.User]):
         """
@@ -141,7 +129,7 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager
 
     def has_access_permission(self, dataset, user):
         """
-        Return T/F if the user has role-based access to the dataset.
+        Whether the user has role-based access to the dataset.
         """
         roles = user.all_roles_exploiting_cache() if user else []
         return self.app.security_agent.can_access_dataset(roles, dataset)
@@ -159,7 +147,7 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager
                 "Cannot swap object store IDs for object stores that don't share a device ID."
             )
 
-        if not self.security_agent.can_change_object_store_id(trans.user, dataset):
+        if not self.app.security_agent.can_change_object_store_id(trans.user, dataset):
             # TODO: probably want separate exceptions for doesn't own the dataset and dataset
             # has been shared.
             raise exceptions.InsufficientPermissionsException("Cannot change dataset permissions...")
@@ -169,7 +157,7 @@ class DatasetManager(base.ModelManager[model.Dataset], secured.AccessibleManager
             new_label = quota_source_map.get_quota_source_label(new_object_store_id)
             if old_label != new_label:
                 self.quota_agent.relabel_quota_for_dataset(dataset, old_label, new_label)
-        sa_session = self.app.model.context
+        sa_session = self.session()
         with transaction(sa_session):
             dataset.object_store_id = new_object_store_id
             sa_session.add(dataset)
@@ -336,12 +324,15 @@ class DatasetSerializer(base.ModelSerializer[DatasetManager], deletable.Purgable
         return permissions
 
 
-# ============================================================================= AKA DatasetInstanceManager
+U = TypeVar("U", bound=DatasetInstance)
+
+
 class DatasetAssociationManager(
-    base.ModelManager[model.DatasetInstance],
+    base.ModelManager[DatasetInstance],
     secured.AccessibleManagerMixin,
     secured.OwnableManagerMixin,
     deletable.PurgableManagerMixin,
+    Generic[U],
 ):
     """
     DatasetAssociation/DatasetInstances are intended to be working
@@ -355,18 +346,18 @@ class DatasetAssociationManager(
 
     # NOTE: model_manager_class should be set in HDA/LDA subclasses
 
-    def __init__(self, app):
+    def __init__(self, app: MinimalManagerApp):
         super().__init__(app)
         self.dataset_manager = DatasetManager(app)
 
-    def is_accessible(self, item, user: Optional[model.User], **kwargs: Any) -> bool:
+    def is_accessible(self, item: U, user: Optional[model.User], **kwargs: Any) -> bool:
         """
         Is this DA accessible to `user`?
         """
         # defer to the dataset
         return self.dataset_manager.is_accessible(item.dataset, user, **kwargs)
 
-    def delete(self, item, flush: bool = True, stop_job: bool = False, **kwargs):
+    def delete(self, item: U, flush: bool = True, stop_job: bool = False, **kwargs):
         """
         Marks this dataset association as deleted.
         If `stop_job` is True, will stop the creating job if all other outputs are deleted.
@@ -376,7 +367,7 @@ class DatasetAssociationManager(
             self.stop_creating_job(item, flush=flush)
         return item
 
-    def purge(self, dataset_assoc, flush=True):
+    def purge(self, item: U, flush=True, **kwargs):
         """
         Purge this DatasetInstance and the dataset underlying it.
         """
@@ -388,21 +379,21 @@ class DatasetAssociationManager(
         # so that job cleanup associated with stop_creating_job will see
         # the dataset as purged.
         flush_required = not self.app.config.track_jobs_in_database
-        super().purge(dataset_assoc, flush=flush or flush_required)
+        super().purge(item, flush=flush or flush_required, **kwargs)
 
-        # stop any jobs outputing the dataset_assoc
-        self.stop_creating_job(dataset_assoc, flush=True)
+        # stop any jobs outputing the dataset association
+        self.stop_creating_job(item, flush=True)
 
         # more importantly, purge underlying dataset as well
-        if dataset_assoc.dataset.user_can_purge:
-            self.dataset_manager.purge(dataset_assoc.dataset, user=dataset_assoc.user)
-        return dataset_assoc
+        if item.dataset.user_can_purge:
+            self.dataset_manager.purge(item.dataset, flush=flush, user=item.user, **kwargs)
+        return item
 
     def by_user(self, user):
         raise exceptions.NotImplemented("Abstract Method")
 
     # .... associated job
-    def creating_job(self, dataset_assoc):
+    def creating_job(self, dataset_assoc: U):
         """
         Return the `Job` that created this dataset or None if not found.
         """
@@ -414,14 +405,14 @@ class DatasetAssociationManager(
             break
         return job
 
-    def stop_creating_job(self, dataset_assoc, flush=False):
+    def stop_creating_job(self, dataset_assoc: U, flush=False):
         """
         Stops an dataset_assoc's creating job if all the job's other outputs are deleted.
         """
 
         # Optimize this to skip other checks if this dataset is terminal - we can infer the
         # job is already complete.
-        if dataset_assoc.state in model.Dataset.terminal_states:
+        if dataset_assoc.state in Dataset.terminal_states:
             return False
 
         if dataset_assoc.parent_id is None and len(dataset_assoc.creating_job_associations) > 0:
@@ -441,7 +432,7 @@ class DatasetAssociationManager(
                     return True
         return False
 
-    def is_composite(self, dataset_assoc):
+    def is_composite(self, dataset_assoc: U):
         """
         Return True if this hda/ldda is a composite type dataset.
 
@@ -449,13 +440,13 @@ class DatasetAssociationManager(
         """
         return dataset_assoc.extension in self.app.datatypes_registry.get_composite_extensions()
 
-    def extra_files(self, dataset_assoc):
+    def extra_files(self, dataset_assoc: U):
         """Return a list of file paths for composite files, an empty list otherwise."""
         if not self.is_composite(dataset_assoc):
             return []
         return glob.glob(os.path.join(dataset_assoc.dataset.extra_files_path, "*"))
 
-    def serialize_dataset_association_roles(self, trans, dataset_assoc):
+    def serialize_dataset_association_roles(self, dataset_assoc: U):
         if hasattr(dataset_assoc, "library_dataset_dataset_association"):
             library_dataset = dataset_assoc
             dataset = library_dataset.library_dataset_dataset_association.dataset
@@ -463,42 +454,50 @@ class DatasetAssociationManager(
             library_dataset = None
             dataset = dataset_assoc.dataset
 
+        private_role_emails = get_private_role_user_emails_dict(self.session())
+
         # Omit duplicated roles by converting to set
-        security_agent = trans.app.security_agent
-        access_roles = set(dataset.get_access_roles(security_agent))
-        manage_roles = set(dataset.get_manage_permissions_roles(security_agent))
-
-        access_dataset_role_list = [
-            (access_role.name, trans.security.encode_id(access_role.id)) for access_role in access_roles
-        ]
-        manage_dataset_role_list = [
-            (manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles
-        ]
+        access_roles = set(dataset.get_access_roles(self.app.security_agent))
+        manage_roles = set(dataset.get_manage_permissions_roles(self.app.security_agent))
+
+        def make_tuples(roles: Set):
+            tuples = []
+            for role in roles:
+                # use role name for non-private roles, and user.email from private rules
+                displayed_name = private_role_emails.get(role.id, role.name)
+                role_tuple = (displayed_name, self.app.security.encode_id(role.id))
+                tuples.append(role_tuple)
+            return tuples
+
+        access_dataset_role_list = make_tuples(access_roles)
+        manage_dataset_role_list = make_tuples(manage_roles)
+
         rval = dict(access_dataset_roles=access_dataset_role_list, manage_dataset_roles=manage_dataset_role_list)
         if library_dataset is not None:
             modify_roles = set(
-                security_agent.get_roles_for_action(
-                    library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY
+                self.app.security_agent.get_roles_for_action(
+                    library_dataset, self.app.security_agent.permitted_actions.LIBRARY_MODIFY
                 )
             )
-            modify_item_role_list = [
-                (modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles
-            ]
+            modify_item_role_list = make_tuples(modify_roles)
             rval["modify_item_roles"] = modify_item_role_list
         return rval
 
-    def ensure_dataset_on_disk(self, trans, dataset):
+    def ensure_dataset_on_disk(self, trans, dataset: U):
         # Not a guarantee data is really present, but excludes a lot of expected cases
         if not dataset.dataset:
             raise exceptions.InternalServerError("Item has no associated dataset.")
         if dataset.purged or dataset.dataset.purged:
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been purged.")
-        elif dataset.deleted and not (trans.user_is_admin or self.is_owner(dataset, trans.get_user())):
+        elif dataset.deleted and not (
+            trans.user_is_admin
+            or (isinstance(dataset, HistoryDatasetAssociation) and self.is_owner(dataset, trans.get_user()))  # type: ignore[arg-type]
+        ):
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been deleted.")
         elif dataset.state == Dataset.states.UPLOAD:
             raise exceptions.Conflict("Please wait until this dataset finishes uploading before attempting to view it.")
-        elif dataset.state == Dataset.states.NEW:
-            raise exceptions.Conflict("The dataset you are attempting to view is new and has no data.")
+        elif dataset.state in (Dataset.states.NEW, Dataset.states.QUEUED):
+            raise exceptions.Conflict(f"The dataset you are attempting to view is {dataset.state} and has no data.")
         elif dataset.state == Dataset.states.DISCARDED:
             raise exceptions.ItemDeletionException("The dataset you are attempting to view has been discarded.")
         elif dataset.state == Dataset.states.DEFERRED:
@@ -509,8 +508,16 @@ class DatasetAssociationManager(
             raise exceptions.Conflict(
                 "The dataset you are attempting to view is in paused state. One of the inputs for the job that creates this dataset has failed."
             )
+        elif dataset.state == Dataset.states.RUNNING:
+            if not self.app.object_store.exists(dataset.dataset):
+                raise exceptions.Conflict(
+                    "The dataset you are attempting to view is still being created and has no data yet."
+                )
+        elif dataset.state == Dataset.states.ERROR:
+            if not self.app.object_store.exists(dataset.dataset):
+                raise exceptions.RequestParameterInvalidException("The dataset is in error and has no data.")
 
-    def ensure_can_change_datatype(self, dataset: model.DatasetInstance, raiseException: bool = True) -> bool:
+    def ensure_can_change_datatype(self, dataset: U, raiseException: bool = True) -> bool:
         if not dataset.datatype.is_datatype_change_allowed():
             if not raiseException:
                 return False
@@ -519,7 +526,7 @@ class DatasetAssociationManager(
             )
         return True
 
-    def ensure_can_set_metadata(self, dataset: model.DatasetInstance, raiseException: bool = True) -> bool:
+    def ensure_can_set_metadata(self, dataset: U, raiseException: bool = True) -> bool:
         if not dataset.ok_to_edit_metadata():
             if not raiseException:
                 return False
@@ -528,29 +535,29 @@ class DatasetAssociationManager(
             )
         return True
 
-    def detect_datatype(self, trans, dataset_assoc):
+    def detect_datatype(self, trans, dataset_assoc: U):
         """Sniff and assign the datatype to a given dataset association (ldda or hda)"""
-        data = trans.sa_session.get(self.model_class, dataset_assoc.id)
-        self.ensure_can_change_datatype(data)
-        self.ensure_can_set_metadata(data)
-        path = data.dataset.get_file_name()
-        datatype = sniff.guess_ext(path, trans.app.datatypes_registry.sniff_order)
-        trans.app.datatypes_registry.change_datatype(data, datatype)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        session = self.session()
+        self.ensure_can_change_datatype(dataset_assoc)
+        self.ensure_can_set_metadata(dataset_assoc)
+        assert dataset_assoc.dataset
+        path = dataset_assoc.dataset.get_file_name()
+        datatype = sniff.guess_ext(path, self.app.datatypes_registry.sniff_order)
+        self.app.datatypes_registry.change_datatype(dataset_assoc, datatype)
+        with transaction(session):
+            session.commit()
         self.set_metadata(trans, dataset_assoc)
 
-    def set_metadata(self, trans, dataset_assoc, overwrite=False, validate=True):
+    def set_metadata(self, trans, dataset_assoc: U, overwrite: bool = False, validate: bool = True) -> None:
         """Trigger a job that detects and sets metadata on a given dataset association (ldda or hda)"""
-        data = trans.sa_session.get(self.model_class, dataset_assoc.id)
-        self.ensure_can_set_metadata(data)
+        self.ensure_can_set_metadata(dataset_assoc)
         if overwrite:
-            self.overwrite_metadata(data)
+            self.overwrite_metadata(dataset_assoc)
 
-        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_trans(
             self.app.datatypes_registry.set_external_metadata_tool,
             trans,
-            incoming={"input1": data, "validate": validate},
+            incoming={"input1": dataset_assoc, "validate": validate},
             overwrite=overwrite,
         )
         self.app.job_manager.enqueue(job, tool=self.app.datatypes_registry.set_external_metadata_tool)
@@ -562,7 +569,7 @@ class DatasetAssociationManager(
                 if spec.get("default"):
                     setattr(data.metadata, name, spec.unwrap(spec.get("default")))
 
-    def update_permissions(self, trans, dataset_assoc, **kwd):
+    def update_permissions(self, trans, dataset_assoc: U, **kwd):
         action = kwd.get("action", "set_permissions")
         if action not in ["remove_restrictions", "make_private", "set_permissions"]:
             raise exceptions.RequestParameterInvalidException(
@@ -577,26 +584,26 @@ class DatasetAssociationManager(
             dataset = dataset_assoc.dataset
 
         current_user_roles = trans.get_current_user_roles()
-        can_manage = trans.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin
+        can_manage = self.app.security_agent.can_manage_dataset(current_user_roles, dataset) or trans.user_is_admin
         if not can_manage:
             raise exceptions.InsufficientPermissionsException(
                 "You do not have proper permissions to manage permissions on this dataset."
             )
 
         if action == "remove_restrictions":
-            trans.app.security_agent.make_dataset_public(dataset)
-            if not trans.app.security_agent.dataset_is_public(dataset):
+            self.app.security_agent.make_dataset_public(dataset)
+            if not self.app.security_agent.dataset_is_public(dataset):
                 raise exceptions.InternalServerError("An error occurred while making dataset public.")
         elif action == "make_private":
-            if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
-                private_role = trans.app.security_agent.get_private_user_role(trans.user)
-                dp = trans.app.model.DatasetPermissions(
-                    trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role
+            if not self.app.security_agent.dataset_is_private_to_user(trans, dataset):
+                private_role = self.app.security_agent.get_private_user_role(trans.user)
+                dp = self.app.model.DatasetPermissions(
+                    self.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role
                 )
                 trans.sa_session.add(dp)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            if not trans.app.security_agent.dataset_is_private_to_user(trans, dataset):
+            if not self.app.security_agent.dataset_is_private_to_user(trans, dataset):
                 # Check again and inform the user if dataset is not private.
                 raise exceptions.InternalServerError("An error occurred and the dataset is NOT private.")
         elif action == "set_permissions":
@@ -616,7 +623,7 @@ class DatasetAssociationManager(
 
             self._set_permissions(trans, dataset_assoc, role_ids_dict)
 
-    def _set_permissions(self, trans, dataset_assoc, roles_dict):
+    def _set_permissions(self, trans, dataset_assoc: U, roles_dict):
         raise exceptions.NotImplemented()
 
 
@@ -648,7 +655,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
             "file_size": lambda item, key, **context: self.serializers["size"](item, key, **context),
             "nice_size": lambda item, key, **context: item.get_size(nice_size=True, calculate_size=False),
             # common to lddas and hdas - from mapping.py
-            "copied_from_history_dataset_association_id": self.serialize_id,
+            "copied_from_history_dataset_association_id": lambda item, key, **context: item.id,
             "copied_from_library_dataset_dataset_association_id": self.serialize_id,
             "info": lambda item, key, **context: item.info.strip() if isinstance(item.info, str) else item.info,
             "blurb": lambda item, key, **context: item.blurb,
@@ -782,7 +789,7 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
         # remove the single nesting key here
         del self.serializers["metadata"]
 
-    def serialize(self, dataset_assoc, keys, **context):
+    def serialize(self, item, keys, **context):
         """
         Override to add metadata as flattened keys on the serialized DatasetInstance.
         """
@@ -790,11 +797,11 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
         # TODO: remove these when metadata is sub-object
         KEYS_HANDLED_SEPARATELY = ("metadata",)
         left_to_handle = self._pluck_from_list(keys, KEYS_HANDLED_SEPARATELY)
-        serialized = super().serialize(dataset_assoc, keys, **context)
+        serialized = super().serialize(item, keys, **context)
 
         # add metadata directly to the dict instead of as a sub-object
         if "metadata" in left_to_handle:
-            metadata = self._prefixed_metadata(dataset_assoc)
+            metadata = self._prefixed_metadata(item)
             serialized.update(metadata)
         return serialized
 
@@ -883,10 +890,10 @@ class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableD
         assert (
             trans
         ), "Logic error in Galaxy, deserialize_datatype not send a transation object"  # TODO: restructure this for stronger typing
-        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
+        job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_trans(
             self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={"input1": item}, overwrite=False
         )  # overwrite is False as per existing behavior
-        trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
+        self.app.job_manager.enqueue(job, tool=self.app.datatypes_registry.set_external_metadata_tool)
         return item.datatype
 
 
diff --git a/lib/galaxy/managers/file_source_instances.py b/lib/galaxy/managers/file_source_instances.py
index f364110828cd44f778b87eaa3bd90d6e42e93a75..4572eafc8c66f2e429aab50e2be94ea7d49a8c0b 100644
--- a/lib/galaxy/managers/file_source_instances.py
+++ b/lib/galaxy/managers/file_source_instances.py
@@ -8,6 +8,7 @@ from typing import (
     Optional,
     Set,
     Tuple,
+    Union,
 )
 from uuid import uuid4
 
@@ -18,8 +19,11 @@ from pydantic import (
 )
 
 from galaxy.exceptions import (
+    Conflict,
     ItemOwnershipException,
+    ObjectNotFound,
     RequestParameterInvalidException,
+    RequestParameterMissingException,
 )
 from galaxy.files import (
     FileSourceScore,
@@ -44,6 +48,7 @@ from galaxy.files.templates import (
     FileSourceTemplate,
     FileSourceTemplateSummaries,
     FileSourceTemplateType,
+    get_oauth2_config_or_none,
     template_to_configuration,
 )
 from galaxy.managers.context import ProvidesUserContext
@@ -52,34 +57,55 @@ from galaxy.model import (
     UserFileSource,
 )
 from galaxy.model.scoped_session import galaxy_scoped_session
+from galaxy.schema.schema import OAuth2State
 from galaxy.security.vault import Vault
+from galaxy.util import config_templates  # defer acess to a couple methods to allow monkeypatching in testing
 from galaxy.util.config_templates import (
     connection_exception_to_status,
+    get_authorize_url,
+    OAuth2Info,
     PluginAspectStatus,
     PluginStatus,
+    read_oauth2_info_from_configuration,
     settings_exception_to_status,
     status_template_definition,
+    TemplateReference,
     TemplateVariableValueType,
     validate_no_extra_secrets_defined,
     validate_no_extra_variables_defined,
 )
 from galaxy.util.plugin_config import plugin_source_from_dict
+from galaxy.work.context import SessionRequestContext
 from ._config_templates import (
+    CanTestPluginStatus,
     CreateInstancePayload,
+    CreateTestTarget,
+    implicit_parameters_for_instance,
     ModifyInstancePayload,
+    oauth2_redirect_uri,
+    oauth2_refresh_token_status,
     prepare_environment,
     prepare_environment_from_root,
+    prepare_template_parameters_for_testing,
     purge_template_instance,
     recover_secrets,
     save_template_instance,
     sort_templates,
+    TemplateParameters,
+    TemplateServerConfiguration,
+    TestModifyInstancePayload,
+    TestUpdateInstancePayload,
+    TestUpgradeInstancePayload,
+    to_template_reference,
     update_instance_secret,
     update_template_instance,
     updated_template_variables,
     UpdateInstancePayload,
     UpdateInstanceSecretPayload,
+    UpdateTestTarget,
     upgrade_secrets,
     UpgradeInstancePayload,
+    UpgradeTestTarget,
 )
 
 log = logging.getLogger(__name__)
@@ -139,6 +165,73 @@ class FileSourceInstancesManager:
     def summaries(self) -> FileSourceTemplateSummaries:
         return self._catalog.summaries
 
+    def template_oauth2(self, trans: SessionRequestContext, template_id: str, template_version: int) -> OAuth2Info:
+        redirect_uri = oauth2_redirect_uri(trans)
+        template_server_configuration = self._resolver.template_server_configuration(
+            trans.user, template_id, template_version
+        )
+        if template_server_configuration.oauth2_client_pair is None:
+            raise ObjectNotFound(f"Could not find oauth2 configuration for specified plugin template id {template_id}")
+
+        oauth2_configuration = template_server_configuration.oauth2_configuration
+        if not oauth2_configuration:
+            raise Exception(
+                "Configuration error - attempting to template an oauth2 configuration but not configuration found."
+            )
+
+        state = OAuth2State(
+            route=f"file_source_instances/{template_id}/{template_version}",
+            nonce="TODO",
+        ).encode()
+        return OAuth2Info(
+            authorize_url=get_authorize_url(
+                template_server_configuration.oauth2_client_pair,
+                oauth2_configuration,
+                redirect_uri=redirect_uri,
+                state=state,
+                scope=template_server_configuration.oauth2_scope,
+            )
+        )
+
+    def handle_authorization_code(self, trans: SessionRequestContext, code: str, state: OAuth2State) -> str:
+        route = state.route
+        _, template_id, template_version = route.split("/", 3)
+        redirect_uri = oauth2_redirect_uri(trans)
+        template_server_configuration = self._resolver.template_server_configuration(
+            trans.user, template_id, int(template_version)
+        )
+        if template_server_configuration.oauth2_client_pair is None:
+            raise ObjectNotFound(f"Could not find oauth2 configuration for specified plugin template id {template_id}")
+
+        oauth2_configuration = template_server_configuration.oauth2_configuration
+        if not oauth2_configuration:
+            raise Exception(
+                "Configuration error - attempting to template an oauth2 configuration but not configuration found."
+            )
+
+        response = config_templates.get_token_from_code_raw(
+            code,
+            template_server_configuration.oauth2_client_pair,
+            oauth2_configuration,
+            redirect_uri,
+        )
+        response.raise_for_status()  # DO BETTER!
+        user_vault = trans.user_vault
+        new_object_uuid = str(uuid4().hex)
+        refresh_token = response.json()["refresh_token"]
+        refresh_token_vault_key = UserFileSource.vault_key_from_uuid(
+            new_object_uuid, "_oauth2_refresh_token", self._app_config
+        )
+        if not refresh_token:
+            raise RequestParameterMissingException("Missing refresh_token in response from remote resource")
+        user_vault.write_secret(refresh_token_vault_key, refresh_token)
+        return f"file_source_templates/{template_id}/new?uuid={new_object_uuid}"
+
+    def _redirect_uri(self, trans: SessionRequestContext) -> str:
+        galaxy_root = trans.request.url_path
+        redirect_uri = f"{galaxy_root}/oauth2_callback"
+        return redirect_uri
+
     def index(self, trans: ProvidesUserContext) -> List[UserFileSourceModel]:
         stores = self._sa_session.query(UserFileSource).filter(UserFileSource.user_id == trans.user.id).all()
         return [self._to_model(trans, s) for s in stores]
@@ -166,9 +259,7 @@ class FileSourceInstancesManager:
         self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload
     ) -> UserFileSourceModel:
         persisted_file_source = self._get(trans, id)
-        template = self._get_template(persisted_file_source, payload.template_version)
-        validate_no_extra_variables_defined(payload.variables, template)
-        validate_no_extra_secrets_defined(payload.secrets, template)
+        template = self._get_and_validate_target_upgrade_template(persisted_file_source, payload)
         persisted_file_source.template_version = template.version
         persisted_file_source.template_definition = template.model_dump()
         actual_variables = updated_template_variables(
@@ -181,6 +272,14 @@ class FileSourceInstancesManager:
         self._save(persisted_file_source)
         return self._to_model(trans, persisted_file_source)
 
+    def _get_and_validate_target_upgrade_template(
+        self, persisted_file_source: UserFileSource, payload: Union[UpgradeInstancePayload, TestUpgradeInstancePayload]
+    ) -> FileSourceTemplate:
+        template = self._get_template(persisted_file_source, payload.template_version)
+        validate_no_extra_variables_defined(payload.variables, template)
+        validate_no_extra_secrets_defined(payload.secrets, template)
+        return template
+
     def _update_instance(
         self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload
     ) -> UserFileSourceModel:
@@ -206,7 +305,12 @@ class FileSourceInstancesManager:
         persisted_file_source = UserFileSource()
         persisted_file_source.user_id = trans.user.id
         assert persisted_file_source.user_id
-        persisted_file_source.uuid = uuid4().hex
+        if payload.uuid:
+            # created a UUID during oauth2 callback to save refresh token
+            self._ensure_no_object_with_uuid(payload.uuid)
+            persisted_file_source.uuid = payload.uuid
+        else:
+            persisted_file_source.uuid = uuid4().hex
         persisted_file_source.template_definition = template.model_dump()
         persisted_file_source.template_id = template.id
         persisted_file_source.template_version = template.version
@@ -230,14 +334,64 @@ class FileSourceInstancesManager:
         self._save(persisted_file_source)
         return self._to_model(trans, persisted_file_source)
 
+    def test_modify_instance(
+        self, trans: ProvidesUserContext, id: UUID4, payload: TestModifyInstancePayload
+    ) -> PluginStatus:
+        persisted_file_source = self._get(trans, id)
+        if isinstance(payload, TestUpgradeInstancePayload):
+            return self._plugin_status_for_upgrade(trans, payload, persisted_file_source)
+        else:
+            assert isinstance(payload, TestUpdateInstancePayload)
+            return self._plugin_status_for_update(trans, payload, persisted_file_source)
+
+    def _plugin_status_for_update(
+        self, trans: ProvidesUserContext, payload: TestUpdateInstancePayload, persisted_file_source: UserFileSource
+    ) -> PluginStatus:
+        template = self._get_template(persisted_file_source)
+        target = UpdateTestTarget(persisted_file_source, payload)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def _plugin_status_for_upgrade(
+        self, trans: ProvidesUserContext, payload: TestUpgradeInstancePayload, persisted_file_source: UserFileSource
+    ) -> PluginStatus:
+        template = self._get_and_validate_target_upgrade_template(persisted_file_source, payload)
+        target = UpgradeTestTarget(persisted_file_source, payload)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def plugin_status_for_instance(self, trans: ProvidesUserContext, id: UUID4):
+        persisted_file_source = self._get(trans, id)
+        return self._plugin_status(trans, persisted_file_source, to_template_reference(persisted_file_source))
+
     def plugin_status(self, trans: ProvidesUserContext, payload: CreateInstancePayload) -> PluginStatus:
-        template = self._catalog.find_template(payload)
+        target = CreateTestTarget(payload, UserFileSource)
+        return self._plugin_status(trans, target, payload)
+
+    def _plugin_status(
+        self, trans: ProvidesUserContext, target: CanTestPluginStatus, template_reference: TemplateReference
+    ):
+        template = self._catalog.find_template(template_reference)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def _plugin_status_for_template(
+        self, trans: ProvidesUserContext, payload: CanTestPluginStatus, template: FileSourceTemplate
+    ):
         template_definition_status = status_template_definition(template)
         status_kwds = {"template_definition": template_definition_status}
         if template_definition_status.is_not_ok:
             return PluginStatus(**status_kwds)
         assert template
-        configuration, template_settings_status = self._template_settings_status(trans, payload, template)
+        template_parameters, oauth2_access_token_generation_status = self._template_parameter_generation(
+            trans, payload, template
+        )
+        if oauth2_access_token_generation_status is not None:
+            status_kwds["oauth2_access_token_generation"] = oauth2_access_token_generation_status
+        if not template_parameters or (
+            oauth2_access_token_generation_status and oauth2_access_token_generation_status.is_not_ok
+        ):
+            return PluginStatus(**status_kwds)
+        configuration, template_settings_status = self._template_settings_status(
+            trans, payload, template, template_parameters
+        )
         status_kwds["template_settings"] = template_settings_status
         if template_settings_status.is_not_ok:
             return PluginStatus(**status_kwds)
@@ -252,41 +406,62 @@ class FileSourceInstancesManager:
         # locally.
         return PluginStatus(**status_kwds)
 
+    def _template_parameter_generation(
+        self,
+        trans: ProvidesUserContext,
+        payload: CanTestPluginStatus,
+        template: FileSourceTemplate,
+    ) -> Tuple[Optional[TemplateParameters], Optional[PluginAspectStatus]]:
+        template_server_configuration = self._resolver.template_server_configuration(
+            trans.user, template.id, template.version
+        )
+        template_parameters = None
+        exception = None
+        try:
+            template_parameters = prepare_template_parameters_for_testing(
+                trans, template, template_server_configuration, payload, self._app_vault, self._app_config
+            )
+        except Exception as e:
+            if template_server_configuration.uses_oauth2:
+                exception = e
+            else:
+                raise
+        return template_parameters, oauth2_refresh_token_status(template_server_configuration, exception)
+
     def _template_settings_status(
         self,
         trans: ProvidesUserContext,
-        payload: CreateInstancePayload,
+        payload: CanTestPluginStatus,
         template: FileSourceTemplate,
+        template_parameters: TemplateParameters,
     ) -> Tuple[Optional[FileSourceConfiguration], PluginAspectStatus]:
-        secrets = payload.secrets
-        variables = payload.variables
-        environment = prepare_environment_from_root(template.environment, self._app_vault, self._app_config)
-        user_details = trans.user.config_template_details()
-
         configuration = None
         exception = None
         try:
-            configuration = template_to_configuration(
-                template,
-                variables=variables,
-                secrets=secrets,
-                user_details=user_details,
-                environment=environment,
-            )
+            configuration = template_to_configuration(template, **template_parameters)
         except Exception as e:
             exception = e
         return configuration, settings_exception_to_status(exception)
 
     def _connection_status(
-        self, trans: ProvidesUserContext, payload: CreateInstancePayload, configuration: FileSourceConfiguration
+        self, trans: ProvidesUserContext, target: CanTestPluginStatus, configuration: FileSourceConfiguration
     ) -> Tuple[Optional[BaseFilesSource], PluginAspectStatus]:
         file_source = None
         exception = None
+        if isinstance(target, (UpgradeTestTarget, UpdateTestTarget)):
+            label = target.instance.name
+            doc = target.instance.description
+        elif isinstance(target, (CreateTestTarget)):
+            label = target.payload.name
+            doc = target.payload.description
+        else:
+            label = target.name
+            doc = target.description
         try:
             file_source_properties = configuration_to_file_source_properties(
                 configuration,
-                label=payload.name,
-                doc=payload.description,
+                label=label,
+                doc=doc,
                 id=uuid4().hex,
             )
             file_source = self._resolver._file_source(file_source_properties)
@@ -304,6 +479,12 @@ class FileSourceInstancesManager:
     def _index_filter(self, uuid: UUID4):
         return UserFileSource.__table__.c.uuid == uuid
 
+    def _ensure_no_object_with_uuid(self, uuid: UUID4):
+        filter = UserFileSource.__table__.c.uuid == uuid
+        user_file_source = self._sa_session.query(UserFileSource).filter(filter).one_or_none()
+        if user_file_source is not None:
+            raise Conflict()
+
     def _get(self, trans: ProvidesUserContext, uuid: UUID4) -> UserFileSource:
         filter = self._index_filter(uuid)
         user_file_source = self._sa_session.query(UserFileSource).filter(filter).one_or_none()
@@ -393,13 +574,19 @@ class UserDefinedFileSourcesImpl(UserDefinedFileSources):
     def _file_source_properties(self, user_file_source: UserFileSource) -> FilesSourceProperties:
         secrets = recover_secrets(user_file_source, self._app_vault, self._app_config)
         environment = prepare_environment(user_file_source, self._app_vault, self._app_config)
+        template_server_configuration = self.template_server_configuration(
+            user_file_source.user, user_file_source.template_id, user_file_source.template_version
+        )
+        implicit = implicit_parameters_for_instance(
+            user_file_source, template_server_configuration, self._app_vault, self._app_config
+        )
         templates = sort_templates(
             self._app_config,
             self._catalog.catalog.root,
             user_file_source,
         )
         file_source_configuration: FileSourceConfiguration = user_file_source.file_source_configuration(
-            secrets=secrets, environment=environment, templates=templates
+            secrets=secrets, environment=environment, implicit=implicit, templates=templates
         )
         return configuration_to_file_source_properties(
             file_source_configuration,
@@ -447,6 +634,31 @@ class UserDefinedFileSourcesImpl(UserDefinedFileSources):
             all_file_source_properties.append(files_source_properties)
         return all_file_source_properties
 
+    def template_server_configuration(
+        self, user, template_id: str, template_version: int
+    ) -> TemplateServerConfiguration:
+        catalog = self._catalog
+        template = catalog.find_template_by(template_id, template_version)
+        oauth2_configuration = get_oauth2_config_or_none(template)
+        oauth2_scope = None
+        if oauth2_configuration is not None:
+            environment = prepare_environment_from_root(template.environment, self._app_vault, self._app_config)
+            user_details = user.config_template_details()
+            oauth2_client_pair_obj, oauth2_scope = read_oauth2_info_from_configuration(
+                template.configuration, user_details, environment
+            )
+            # most configuration definitions won't include this, the default for the
+            # plugin type is the fallback and the typical case here
+            if oauth2_scope is None:
+                oauth2_scope = oauth2_configuration.scope
+        else:
+            oauth2_client_pair_obj = None
+        return TemplateServerConfiguration(
+            oauth2_client_pair=oauth2_client_pair_obj,
+            oauth2_configuration=oauth2_configuration,
+            oauth2_scope=oauth2_scope,
+        )
+
     def user_file_sources_to_dicts(
         self,
         for_serialization: bool,
@@ -504,6 +716,9 @@ __all__ = (
     "CreateInstancePayload",
     "FileSourceInstancesManager",
     "ModifyInstancePayload",
+    "TestModifyInstancePayload",
+    "TestUpgradeInstancePayload",
+    "TestUpdateInstancePayload",
     "UpdateInstancePayload",
     "UpdateInstanceSecretPayload",
     "UpgradeInstancePayload",
diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py
index fcbbed0cb9c5dca195bbb6abb1b7ff9c3927fe73..e7ccfcf55a10b4084e9654d8a683f7244279021e 100644
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -7,6 +7,7 @@ from dataclasses import dataclass
 from typing import (
     List,
     Optional,
+    Set,
     Tuple,
     Union,
 )
@@ -49,6 +50,7 @@ from galaxy.model import (
     LibraryFolderPermissions,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.schema.schema import LibraryFolderContentsIndexQueryPayload
 from galaxy.security import RBACAgent
@@ -295,6 +297,8 @@ class FolderManager:
         :returns:   dict of current roles for all available permission types
         :rtype:     dictionary
         """
+        private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+
         # Omit duplicated roles by converting to set
         modify_roles = set(
             trans.app.security_agent.get_roles_for_action(
@@ -312,17 +316,19 @@ class FolderManager:
             )
         )
 
-        modify_folder_role_list = [
-            (modify_role.name, trans.security.encode_id(modify_role.id)) for modify_role in modify_roles
-        ]
-        manage_folder_role_list = [
-            (manage_role.name, trans.security.encode_id(manage_role.id)) for manage_role in manage_roles
-        ]
-        add_library_item_role_list = [(add_role.name, trans.security.encode_id(add_role.id)) for add_role in add_roles]
+        def make_tuples(roles: Set):
+            tuples = []
+            for role in roles:
+                # use role name for non-private roles, and user.email from private rules
+                displayed_name = private_role_emails.get(role.id, role.name)
+                role_tuple = (displayed_name, trans.security.encode_id(role.id))
+                tuples.append(role_tuple)
+            return tuples
+
         return dict(
-            modify_folder_role_list=modify_folder_role_list,
-            manage_folder_role_list=manage_folder_role_list,
-            add_library_item_role_list=add_library_item_role_list,
+            modify_folder_role_list=make_tuples(modify_roles),
+            manage_folder_role_list=make_tuples(manage_roles),
+            add_library_item_role_list=make_tuples(add_roles),
         )
 
     def can_add_item(self, trans, folder):
@@ -505,7 +511,7 @@ class FolderManager:
             stmt = stmt.where(
                 or_(
                     func.lower(ldda.name).contains(search_text, autoescape=True),
-                    func.lower(ldda.message).contains(search_text, autoescape=True),  # type:ignore[attr-defined]
+                    func.lower(ldda.message).contains(search_text, autoescape=True),
                 )
             )
         sort_column = LDDA_SORT_COLUMN_MAP[payload.order_by](ldda, associated_dataset)
diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
index ce742e7c6d96fedbff0973fbd70fbd7d65095804..8d2bd2e8d5765aefdab24a1ca35405153dab8d80 100644
--- a/lib/galaxy/managers/genomes.py
+++ b/lib/galaxy/managers/genomes.py
@@ -10,13 +10,17 @@ from sqlalchemy import (
     text,
 )
 
-from galaxy import model as m
 from galaxy.exceptions import (
     ReferenceDataError,
     RequestParameterInvalidException,
 )
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.structured_app import StructuredApp
+from galaxy.model import User
+from galaxy.model.database_utils import is_postgres
+from galaxy.structured_app import (
+    MinimalManagerApp,
+    StructuredApp,
+)
 from .base import raise_filter_err
 
 if TYPE_CHECKING:
@@ -28,10 +32,10 @@ class GenomesManager:
         self._app = app
         self.genomes = app.genomes
 
-    def get_dbkeys(self, user: Optional[m.User], chrom_info: bool) -> List[List[str]]:
+    def get_dbkeys(self, user: Optional[User], chrom_info: bool) -> List[List[str]]:
         return self.genomes.get_dbkeys(user, chrom_info)
 
-    def is_registered_dbkey(self, dbkey: str, user: Optional[m.User]) -> bool:
+    def is_registered_dbkey(self, dbkey: str, user: Optional[User]) -> bool:
         dbkeys = self.get_dbkeys(user, chrom_info=False)
         for _, key in dbkeys:
             if dbkey == key:
@@ -78,8 +82,8 @@ class GenomesManager:
 
 
 class GenomeFilterMixin:
+    app: MinimalManagerApp
     orm_filter_parsers: "OrmFilterParsersType"
-    database_connection: str
     valid_ops = ("eq", "contains", "has")
 
     def create_genome_filter(self, attr, op, val):
@@ -91,8 +95,7 @@ class GenomeFilterMixin:
             # Doesn't filter genome_build for collections
             if model_class.__name__ == "HistoryDatasetCollectionAssociation":
                 return False
-            # TODO: should use is_postgres(self.database_connection) in 23.2
-            if self.database_connection.startswith("postgres"):
+            if is_postgres(self.app.config.database_connection):
                 column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
             else:
                 column = func.json_extract(model_class.table.c._metadata, "$.dbkey")  # type:ignore[assignment]
@@ -106,6 +109,5 @@ class GenomeFilterMixin:
 
         return _create_genome_filter
 
-    def _add_parsers(self, database_connection: str):
-        self.database_connection = database_connection
+    def _add_parsers(self):
         self.orm_filter_parsers.update({"genome_build": self.create_genome_filter})
diff --git a/lib/galaxy/managers/groups.py b/lib/galaxy/managers/groups.py
index 40623159bbc9f56c99018933a4d596d2b4700f2b..e0d6cd1777319579ee4f4f7000c9cdd9ed0e41d7 100644
--- a/lib/galaxy/managers/groups.py
+++ b/lib/galaxy/managers/groups.py
@@ -11,8 +11,6 @@ from galaxy.exceptions import (
     RequestParameterInvalidException,
 )
 from galaxy.managers.context import ProvidesAppContext
-from galaxy.managers.roles import get_roles_by_ids
-from galaxy.managers.users import get_users_by_ids
 from galaxy.model import Group
 from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
@@ -54,13 +52,11 @@ class GroupsManager:
 
         group = model.Group(name=name)
         sa_session.add(group)
-        user_ids = payload.user_ids
-        users = get_users_by_ids(sa_session, user_ids)
-        role_ids = payload.role_ids
-        roles = get_roles_by_ids(sa_session, role_ids)
-        trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
-        with transaction(sa_session):
-            sa_session.commit()
+
+        trans.app.security_agent.set_group_user_and_role_associations(
+            group, user_ids=payload.user_ids, role_ids=payload.role_ids
+        )
+        sa_session.commit()
 
         encoded_id = Security.security.encode_id(group.id)
         item = group.to_dict(view="element")
@@ -88,23 +84,12 @@ class GroupsManager:
         if name := payload.name:
             self._check_duplicated_group_name(sa_session, name)
             group.name = name
-            sa_session.add(group)
-
-        users = None
-        if payload.user_ids is not None:
-            users = get_users_by_ids(sa_session, payload.user_ids)
-
-        roles = None
-        if payload.role_ids is not None:
-            roles = get_roles_by_ids(sa_session, payload.role_ids)
+            sa_session.commit()
 
-        self._app.security_agent.set_entity_group_associations(
-            groups=[group], roles=roles, users=users, delete_existing_assocs=False
+        self._app.security_agent.set_group_user_and_role_associations(
+            group, user_ids=payload.user_ids, role_ids=payload.role_ids
         )
 
-        with transaction(sa_session):
-            sa_session.commit()
-
         encoded_id = Security.security.encode_id(group.id)
         item = group.to_dict(view="element")
         item["url"] = self._url_for(trans, "show_group", group_id=encoded_id)
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 073e435ded06c03e09b08ff5276963524755985c..4ff14c5511efd16329b123f41ec4b9375c34cdbc 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -44,13 +44,16 @@ from galaxy.managers import (
     taggable,
     users,
 )
+from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model import (
+    HistoryDatasetAssociation,
     Job,
     JobStateHistory,
     JobToOutputDatasetAssociation,
 )
 from galaxy.model.base import transaction
 from galaxy.model.deferred import materializer_factory
+from galaxy.model.dereference import dereference_to_model
 from galaxy.schema.schema import DatasetSourceType
 from galaxy.schema.storage_cleaner import (
     CleanableItemsSummary,
@@ -68,6 +71,7 @@ from galaxy.structured_app import (
     MinimalManagerApp,
     StructuredApp,
 )
+from galaxy.tool_util.parameters import DataRequestUri
 from galaxy.util.compression_utils import get_fileobj
 
 log = logging.getLogger(__name__)
@@ -78,7 +82,7 @@ class HistoryDatasetAssociationNoHistoryException(Exception):
 
 
 class HDAManager(
-    datasets.DatasetAssociationManager,
+    datasets.DatasetAssociationManager[HistoryDatasetAssociation],
     secured.OwnableManagerMixin,
     annotatable.AnnotatableManagerMixin,
 ):
@@ -86,7 +90,7 @@ class HDAManager(
     Interface/service object for interacting with HDAs.
     """
 
-    model_class = model.HistoryDatasetAssociation
+    model_class = HistoryDatasetAssociation
     foreign_key_name = "history_dataset_association"
 
     tag_assoc = model.HistoryDatasetAssociationTagAssociation
@@ -115,22 +119,11 @@ class HDAManager(
         return self.list(filters=filters)
 
     # .... security and permissions
-    def is_accessible(self, item: model.HistoryDatasetAssociation, user: Optional[model.User], **kwargs: Any) -> bool:
-        """
-        Override to allow owners (those that own the associated history).
-        """
-        # this, apparently, is not True:
-        #   if I have a copy of a dataset and anyone who manages permissions on it revokes my access
-        #   I can not access that dataset even if it's in my history
-        # if self.is_owner( hda, user, **kwargs ):
-        #     return True
-        return super().is_accessible(item, user, **kwargs)
-
     def is_owner(self, item, user: Optional[model.User], current_history=None, **kwargs: Any) -> bool:
         """
         Use history to see if current user owns HDA.
         """
-        if not isinstance(item, model.HistoryDatasetAssociation):
+        if not isinstance(item, HistoryDatasetAssociation):
             raise TypeError('"item" must be of type HistoryDatasetAssociation.')
         if self.user_manager.is_admin(user, trans=kwargs.get("trans", None)):
             return True
@@ -141,15 +134,13 @@ class HDAManager(
         # TODO: some dup here with historyManager.is_owner but prevents circ import
         # TODO: awkward kwarg (which is my new band name); this may not belong here - move to controller?
         if self.user_manager.is_anonymous(user):
-            if current_history and history == current_history:
-                return True
-            return False
+            return current_history is not None and history == current_history
         return history.user == user
 
     # .... create and copy
     def create(
         self, flush: bool = True, history=None, dataset=None, *args: Any, **kwargs: Any
-    ) -> model.HistoryDatasetAssociation:
+    ) -> HistoryDatasetAssociation:
         """
         Create a new hda optionally passing in it's history and dataset.
 
@@ -158,9 +149,7 @@ class HDAManager(
         """
         if not dataset:
             kwargs["create_dataset"] = True
-        hda = model.HistoryDatasetAssociation(
-            history=history, dataset=dataset, sa_session=self.app.model.context, **kwargs
-        )
+        hda = HistoryDatasetAssociation(history=history, dataset=dataset, sa_session=self.app.model.context, **kwargs)
 
         if history:
             history.add_dataset(hda, set_hid=("hid" not in kwargs))
@@ -173,7 +162,7 @@ class HDAManager(
                 session.commit()
         return hda
 
-    def materialize(self, request: MaterializeDatasetInstanceTaskRequest) -> None:
+    def materialize(self, request: MaterializeDatasetInstanceTaskRequest, in_place: bool = False) -> bool:
         request_user: RequestUser = request.user
         materializer = materializer_factory(
             True,  # attached...
@@ -187,19 +176,23 @@ class HDAManager(
         else:
             dataset_instance = self.ldda_manager.get_accessible(request.content, user)
         history = self.app.history_manager.by_id(request.history_id)
-        new_hda = materializer.ensure_materialized(dataset_instance, target_history=history)
-        history.add_dataset(new_hda, set_hid=True)
+        new_hda = materializer.ensure_materialized(dataset_instance, target_history=history, in_place=in_place)
+        if not in_place:
+            history.add_dataset(new_hda, set_hid=True)
+        else:
+            new_hda.set_total_size()
         session = self.session()
         with transaction(session):
             session.commit()
+        return new_hda.is_ok
 
     def copy(
         self, item: Any, history=None, hide_copy: bool = False, flush: bool = True, **kwargs: Any
-    ) -> model.HistoryDatasetAssociation:
+    ) -> HistoryDatasetAssociation:
         """
         Copy hda, including annotation and tags, add to history and return the given HDA.
         """
-        if not isinstance(item, model.HistoryDatasetAssociation):
+        if not isinstance(item, HistoryDatasetAssociation):
             raise TypeError()
         hda = item
         copy = hda.copy(
@@ -228,14 +221,14 @@ class HDAManager(
         return copy
 
     # .... deletion and purging
-    def purge(self, hda, flush=True, **kwargs):
+    def purge(self, item, flush=True, **kwargs):
         if self.app.config.enable_celery_tasks:
             from galaxy.celery.tasks import purge_hda
 
             user = kwargs.get("user")
-            return purge_hda.delay(hda_id=hda.id, task_user_id=getattr(user, "id", None))
+            return purge_hda.delay(hda_id=item.id, task_user_id=getattr(user, "id", None))
         else:
-            self._purge(hda, flush=flush)
+            self._purge(item, flush=flush)
 
     def _purge(self, hda, flush=True):
         """
@@ -342,29 +335,41 @@ class HDAManager(
                 raise exceptions.RequestParameterInvalidException(error)
 
 
+def dereference_input(
+    trans: ProvidesHistoryContext, data_request: DataRequestUri, history: Optional[model.History] = None
+) -> HistoryDatasetAssociation:
+    target_history = history or trans.history
+    hda = dereference_to_model(trans.sa_session, trans.user, target_history, data_request)
+    permissions = trans.app.security_agent.history_get_default_permissions(target_history)
+    trans.app.security_agent.set_all_dataset_permissions(hda.dataset, permissions, new=True, flush=False)
+    with transaction(trans.sa_session):
+        trans.sa_session.commit()
+    return hda
+
+
 class HDAStorageCleanerManager(base.StorageCleanerManager):
     def __init__(self, hda_manager: HDAManager, dataset_manager: datasets.DatasetManager):
         self.hda_manager = hda_manager
         self.dataset_manager = dataset_manager
         self.sort_map = {
-            StoredItemOrderBy.NAME_ASC: asc(model.HistoryDatasetAssociation.name),
-            StoredItemOrderBy.NAME_DSC: desc(model.HistoryDatasetAssociation.name),
+            StoredItemOrderBy.NAME_ASC: asc(HistoryDatasetAssociation.name),
+            StoredItemOrderBy.NAME_DSC: desc(HistoryDatasetAssociation.name),
             StoredItemOrderBy.SIZE_ASC: nulls_first(asc(model.Dataset.total_size)),
             StoredItemOrderBy.SIZE_DSC: nulls_last(desc(model.Dataset.total_size)),
-            StoredItemOrderBy.UPDATE_TIME_ASC: asc(model.HistoryDatasetAssociation.update_time),
-            StoredItemOrderBy.UPDATE_TIME_DSC: desc(model.HistoryDatasetAssociation.update_time),
+            StoredItemOrderBy.UPDATE_TIME_ASC: asc(HistoryDatasetAssociation.update_time),
+            StoredItemOrderBy.UPDATE_TIME_DSC: desc(HistoryDatasetAssociation.update_time),
         }
 
     def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
         stmt = (
-            select(func.sum(model.Dataset.total_size), func.count(model.HistoryDatasetAssociation.id))
-            .select_from(model.HistoryDatasetAssociation)
-            .join(model.Dataset, model.HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)
-            .join(model.History, model.HistoryDatasetAssociation.table.c.history_id == model.History.id)
+            select(func.sum(model.Dataset.total_size), func.count(HistoryDatasetAssociation.id))
+            .select_from(HistoryDatasetAssociation)
+            .join(model.Dataset, HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)
+            .join(model.History, HistoryDatasetAssociation.table.c.history_id == model.History.id)
             .where(
                 and_(
-                    model.HistoryDatasetAssociation.deleted == true(),
-                    model.HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
+                    HistoryDatasetAssociation.deleted == true(),
+                    HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
                     model.History.user_id == user.id,
                 )
             )
@@ -383,18 +388,18 @@ class HDAStorageCleanerManager(base.StorageCleanerManager):
     ) -> List[StoredItem]:
         stmt = (
             select(
-                model.HistoryDatasetAssociation.id,
-                model.HistoryDatasetAssociation.name,
-                model.HistoryDatasetAssociation.update_time,
+                HistoryDatasetAssociation.id,
+                HistoryDatasetAssociation.name,
+                HistoryDatasetAssociation.update_time,
                 model.Dataset.total_size,
             )
-            .select_from(model.HistoryDatasetAssociation)
-            .join(model.Dataset, model.HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)
-            .join(model.History, model.HistoryDatasetAssociation.table.c.history_id == model.History.id)
+            .select_from(HistoryDatasetAssociation)
+            .join(model.Dataset, HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)
+            .join(model.History, HistoryDatasetAssociation.table.c.history_id == model.History.id)
             .where(
                 and_(
-                    model.HistoryDatasetAssociation.deleted == true(),
-                    model.HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
+                    HistoryDatasetAssociation.deleted == true(),
+                    HistoryDatasetAssociation.purged == false(),  # type:ignore[arg-type]
                     model.History.user_id == user.id,
                 )
             )
@@ -420,7 +425,7 @@ class HDAStorageCleanerManager(base.StorageCleanerManager):
 
         for hda_id in item_ids:
             try:
-                hda: model.HistoryDatasetAssociation = self.hda_manager.get_owned(hda_id, user)
+                hda: HistoryDatasetAssociation = self.hda_manager.get_owned(hda_id, user)
                 hda.deleted = True
                 quota_amount = int(hda.quota_amount(user))
                 hda.purge_usage_from_quota(user, hda.dataset.quota_source_info)
@@ -614,14 +619,14 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         }
         self.serializers.update(serializers)
 
-    def serialize(self, hda, keys, user=None, **context):
+    def serialize(self, item, keys, user=None, **context):
         """
         Override to hide information to users not able to access.
         """
         # TODO: to DatasetAssociationSerializer
-        if not self.manager.is_accessible(hda, user, **context):
+        if not self.manager.is_accessible(item, user, **context):
             keys = self._view_to_keys("inaccessible")
-        return super().serialize(hda, keys, user=user, **context)
+        return super().serialize(item, keys, user=user, **context)
 
     def serialize_display_apps(self, item, key, trans=None, **context):
         """
@@ -629,7 +634,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         """
         hda = item
         display_apps: List[Dict[str, Any]] = []
-        if hda.state == model.HistoryDatasetAssociation.states.OK and not hda.deleted:
+        if hda.state == HistoryDatasetAssociation.states.OK and not hda.deleted:
             for display_app in hda.get_display_applications(trans).values():
                 app_links = []
                 for link_app in display_app.links.values():
@@ -653,7 +658,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         display_apps: List[Dict[str, Any]] = []
         if (
             self.app.config.enable_old_display_applications
-            and hda.state == model.HistoryDatasetAssociation.states.OK
+            and hda.state == HistoryDatasetAssociation.states.OK
             and not hda.deleted
         ):
             display_link_fn = hda.datatype.get_display_links
@@ -740,7 +745,7 @@ class HDAFilterParser(
     datasets.DatasetAssociationFilterParser, taggable.TaggableFilterMixin, annotatable.AnnotatableFilterMixin
 ):
     model_manager_class = HDAManager
-    model_class = model.HistoryDatasetAssociation
+    model_class = HistoryDatasetAssociation
 
     def _add_parsers(self):
         super()._add_parsers()
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 84db5dd38c2fb8067d1f7a99057d1cf825929351..392c3601679130e4cd6b886635d573d5320915be 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -237,12 +237,6 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
             stmt = stmt.offset(payload.offset)
         return trans.sa_session.scalars(stmt), total_matches  # type:ignore[return-value]
 
-    def copy(self, history, user, **kwargs):
-        """
-        Copy and return the given `history`.
-        """
-        return history.copy(target_user=user, **kwargs)
-
     # .... sharable
     # overriding to handle anonymous users' current histories in both cases
     def by_user(
@@ -269,9 +263,7 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         """
         # anon users are only allowed to view their current history
         if self.user_manager.is_anonymous(user):
-            if current_history and item == current_history:
-                return True
-            return False
+            return current_history is not None and item == current_history
         return super().is_owner(item, user)
 
     # TODO: possibly to sharable or base
@@ -289,19 +281,19 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
         return self.session().scalars(stmt).first()
 
     # .... purgable
-    def purge(self, history, flush=True, **kwargs):
+    def purge(self, item, flush=True, **kwargs):
         """
         Purge this history and all HDAs, Collections, and Datasets inside this history.
         """
-        self.error_unless_mutable(history)
+        self.error_unless_mutable(item)
         self.hda_manager.dataset_manager.error_unless_dataset_purge_allowed()
         # First purge all the datasets
-        for hda in history.datasets:
+        for hda in item.datasets:
             if not hda.purged:
                 self.hda_manager.purge(hda, flush=True, **kwargs)
 
         # Now mark the history as purged
-        super().purge(history, flush=flush, **kwargs)
+        super().purge(item, flush=flush, **kwargs)
 
     # .... current
     # TODO: make something to bypass the anon user + current history permissions issue
@@ -424,7 +416,7 @@ class HistoryManager(sharable.SharableModelManager, deletable.PurgableManagerMix
 
         # Run job to do export.
         history_exp_tool = trans.app.toolbox.get_tool(export_tool_id)
-        job, *_ = history_exp_tool.execute(trans, incoming=params, history=history, set_output_hid=True)
+        job, *_ = history_exp_tool.execute(trans, incoming=params, history=history)
         trans.app.job_manager.enqueue(job, tool=history_exp_tool)
         return job
 
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 638a0c4561811cf7c2e7acdb5da8623d4183ded0..0db49a4536e887e8f0a485ff70d79dda46cd8fc4 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -637,9 +637,8 @@ class HistoryContentsFilters(
 
     def _add_parsers(self):
         super()._add_parsers()
-        database_connection: str = self.app.config.database_connection
         annotatable.AnnotatableFilterMixin._add_parsers(self)
-        genomes.GenomeFilterMixin._add_parsers(self, database_connection)
+        genomes.GenomeFilterMixin._add_parsers(self)
         deletable.PurgableFiltersMixin._add_parsers(self)
         taggable.TaggableFilterMixin._add_parsers(self)
         tools.ToolFilterMixin._add_parsers(self)
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index 223851149cc929382ed6844d9b7d671a4f3cb339..5a8ebcfda3ddbef9083f2601f8d489fc0a1fb416 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -1,14 +1,21 @@
 import json
 import logging
-import sqlite3
 from urllib.parse import (
     urlsplit,
     urlunsplit,
 )
 
 from sqlalchemy import (
-    or_,
+    Column,
+    create_engine,
+    delete,
+    insert,
+    Integer,
+    MetaData,
     select,
+    String,
+    Table,
+    Text,
 )
 
 from galaxy import exceptions
@@ -18,88 +25,67 @@ from galaxy.model import (
 )
 from galaxy.model.base import transaction
 from galaxy.security.idencoding import IdAsLowercaseAlphanumEncodingHelper
-from galaxy.util.filelock import FileLock
 
 log = logging.getLogger(__name__)
 
-DATABASE_TABLE_NAME = "gxitproxy"
-
-
-class InteractiveToolSqlite:
-    def __init__(self, sqlite_filename, encode_id):
-        self.sqlite_filename = sqlite_filename
-        self.encode_id = encode_id
-
-    def get(self, key, key_type):
-        with FileLock(self.sqlite_filename):
-            conn = sqlite3.connect(self.sqlite_filename)
-            try:
-                c = conn.cursor()
-                select = f"""SELECT token, host, port, info, protocol,
-                            FROM {DATABASE_TABLE_NAME}
-                            WHERE key=? and key_type=?"""
-                c.execute(
-                    select,
-                    (
-                        key,
-                        key_type,
-                    ),
-                )
-                try:
-                    token, host, port, info, protocol = c.fetchone()
-                except TypeError:
-                    log.warning("get(): invalid key: %s key_type %s", key, key_type)
-                    return None
-                return dict(key=key, key_type=key_type, token=token, host=host, port=port, info=info, protocol=protocol)
-            finally:
-                conn.close()
-
-    def save(self, key, key_type, token, host, port, info=None, protocol=None):
+gxitproxy = Table(
+    "gxitproxy",
+    MetaData(),
+    Column("key", String(16), primary_key=True),
+    Column("key_type", Text(), primary_key=True),
+    Column("token", String(32)),
+    Column("host", Text()),
+    Column("port", Integer()),
+    Column("info", Text()),
+)
+
+
+class InteractiveToolPropagatorSQLAlchemy:
+    """
+    Propagator for InteractiveToolManager implemented using SQLAlchemy.
+    """
+
+    def __init__(self, database_url, encode_id):
+        """
+        Constructor that sets up the propagator using a SQLAlchemy database URL.
+
+        :param database_url: SQLAlchemy database URL, read more on the SQLAlchemy documentation
+                             https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls.
+        :param encode_id: A helper class that can encode ids as lowercase alphanumeric strings and vice versa.
+        """
+        self._engine = create_engine(database_url)
+        self._encode_id = encode_id
+
+    def save(self, key, key_type, token, host, port, info=None):
         """
-        Writeout a key, key_type, token, value store that is can be used for coordinating
-        with external resources.
+        Write out a key, key_type, token, value store that is can be used for coordinating with external resources.
         """
         assert key, ValueError("A non-zero length key is required.")
         assert key_type, ValueError("A non-zero length key_type is required.")
         assert token, ValueError("A non-zero length token is required.")
-        with FileLock(self.sqlite_filename):
-            conn = sqlite3.connect(self.sqlite_filename)
-            try:
-                c = conn.cursor()
-                try:
-                    # Create table
-                    c.execute(
-                        f"""CREATE TABLE {DATABASE_TABLE_NAME}
-                                 (key text,
-                                  key_type text,
-                                  token text,
-                                  host text,
-                                  port integer,
-                                  info text,
-                                  protocol text,
-                                  PRIMARY KEY (key, key_type)
-                                  )"""
-                    )
-                except Exception:
-                    pass
-                delete = f"""DELETE FROM {DATABASE_TABLE_NAME} WHERE key=? and key_type=?"""
-                c.execute(
-                    delete,
-                    (
-                        key,
-                        key_type,
-                    ),
-                )
-                insert = f"""INSERT INTO {DATABASE_TABLE_NAME}
-                            (key, key_type, token, host, port, info, protocol)
-                            VALUES (?, ?, ?, ?, ?, ?, ?)"""
-                c.execute(
-                    insert,
-                    (key, key_type, token, host, port, info, protocol),
-                )
-                conn.commit()
-            finally:
-                conn.close()
+        with self._engine.connect() as conn:
+            # create database table if not exists
+            gxitproxy.create(conn, checkfirst=True)
+
+            # delete existing data with same key
+            stmt_delete = delete(gxitproxy).where(
+                gxitproxy.c.key == key,
+                gxitproxy.c.key_type == key_type,
+            )
+            conn.execute(stmt_delete)
+
+            # save data
+            stmt_insert = insert(gxitproxy).values(
+                key=key,
+                key_type=key_type,
+                token=token,
+                host=host,
+                port=port,
+                info=info,
+            )
+            conn.execute(stmt_insert)
+
+            conn.commit()
 
     def remove(self, **kwd):
         """
@@ -107,30 +93,17 @@ class InteractiveToolSqlite:
         with external resources. Remove entries that match all provided key=values
         """
         assert kwd, ValueError("You must provide some values to key upon")
-        delete = f"DELETE FROM {DATABASE_TABLE_NAME} WHERE"
-        value_list = []
-        for i, (key, value) in enumerate(kwd.items()):
-            if i != 0:
-                delete += " and"
-            delete += f" {key}=?"
-            value_list.append(value)
-        with FileLock(self.sqlite_filename):
-            conn = sqlite3.connect(self.sqlite_filename)
-            try:
-                c = conn.cursor()
-                try:
-                    # Delete entry
-                    c.execute(delete, tuple(value_list))
-                except Exception as e:
-                    log.debug("Error removing entry (%s): %s", delete, e)
-                conn.commit()
-            finally:
-                conn.close()
+        with self._engine.connect() as conn:
+            stmt = delete(gxitproxy).where(
+                *(gxitproxy.c[key] == value for key, value in kwd.items()),
+            )
+            conn.execute(stmt)
+            conn.commit()
 
     def save_entry_point(self, entry_point):
         """Convenience method to easily save an entry_point."""
         return self.save(
-            self.encode_id(entry_point.id),
+            self._encode_id(entry_point.id),
             entry_point.__class__.__name__.lower(),
             entry_point.token,
             entry_point.host,
@@ -141,12 +114,11 @@ class InteractiveToolSqlite:
                     "requires_path_in_header_named": entry_point.requires_path_in_header_named,
                 }
             ),
-            protocol=entry_point.protocol,
         )
 
     def remove_entry_point(self, entry_point):
         """Convenience method to easily remove an entry_point."""
-        return self.remove(key=self.encode_id(entry_point.id), key_type=entry_point.__class__.__name__.lower())
+        return self.remove(key=self._encode_id(entry_point.id), key_type=entry_point.__class__.__name__.lower())
 
 
 class InteractiveToolManager:
@@ -161,7 +133,10 @@ class InteractiveToolManager:
         self.sa_session = app.model.context
         self.job_manager = app.job_manager
         self.encoder = IdAsLowercaseAlphanumEncodingHelper(app.security)
-        self.propagator = InteractiveToolSqlite(app.config.interactivetools_map, self.encoder.encode_id)
+        self.propagator = InteractiveToolPropagatorSQLAlchemy(
+            app.config.interactivetoolsproxy_map or app.config.interactivetools_map,
+            self.encoder.encode_id,
+        )
 
     def create_entry_points(self, job, tool, entry_points=None, flush=True):
         entry_points = entry_points or tool.ports
@@ -173,7 +148,6 @@ class InteractiveToolManager:
                 name=entry["name"],
                 label=entry["label"],
                 requires_domain=entry["requires_domain"],
-                protocol=entry["protocol"],
                 requires_path_in_url=entry["requires_path_in_url"],
                 requires_path_in_header_named=entry["requires_path_in_header_named"],
             )
@@ -182,15 +156,6 @@ class InteractiveToolManager:
             with transaction(self.sa_session):
                 self.sa_session.commit()
 
-    def get_job_subdomain(self, job):
-        # returns the url for the first entry point
-        for entry_point in job.interactivetool_entry_points:
-            entry_point_encoded_id = self.app.security.encode_id(entry_point.id)
-            entry_point_class = entry_point.__class__.__name__.lower()
-            entry_point_prefix = self.app.config.interactivetools_prefix
-            entry_point_token = entry_point.token
-            return f"{entry_point_encoded_id}-{entry_point_token}.{entry_point_class}.{entry_point_prefix}"
-
     def configure_entry_point(self, job, tool_port=None, host=None, port=None, protocol=None):
         return self.configure_entry_points(
             job, {tool_port: dict(tool_port=tool_port, host=host, port=port, protocol=protocol)}
@@ -237,18 +202,15 @@ class InteractiveToolManager:
         if trans.user is None and trans.get_galaxy_session() is None:
             return []
 
-        def build_subquery():
-            if trans.user:
-                stmt = select(Job.id).where(Job.user == trans.user)
-            else:
-                stmt = select(Job.id).where(Job.session_id == trans.get_galaxy_session().id)
-            filters = []
-            for state in Job.non_ready_states:
-                filters.append(Job.state == state)
-            stmt = stmt.where(or_(*filters))
-            return stmt.subquery()
-
-        stmt = select(InteractiveToolEntryPoint).where(InteractiveToolEntryPoint.job_id.in_(build_subquery()))
+        stmt = (
+            select(InteractiveToolEntryPoint)
+            .join(Job, InteractiveToolEntryPoint.job_id == Job.id)
+            .where(Job.state.in_(Job.non_ready_states))
+        )
+        if trans.user:
+            stmt = stmt.where(Job.user == trans.user)
+        else:
+            stmt = stmt.where(Job.session_id == trans.get_galaxy_session().id)
         return trans.sa_session.scalars(stmt)
 
     def can_access_job(self, trans, job):
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index b46f1f2be3586cab427e8ff1c8b30c7465db3fe4..eb3aabc02eefeea1c1d1ab7e8972a1a13236816e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -6,10 +6,12 @@ from datetime import (
 )
 from pathlib import Path
 from typing import (
+    Any,
     cast,
     Dict,
     List,
     Optional,
+    Union,
 )
 
 import sqlalchemy
@@ -32,6 +34,7 @@ from typing_extensions import TypedDict
 
 from galaxy import model
 from galaxy.exceptions import (
+    ConfigDoesNotAllowException,
     ItemAccessibilityException,
     ObjectNotFound,
     RequestParameterInvalidException,
@@ -42,7 +45,10 @@ from galaxy.job_metrics import (
     Safety,
 )
 from galaxy.managers.collections import DatasetCollectionManager
-from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.context import (
+    ProvidesHistoryContext,
+    ProvidesUserContext,
+)
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.lddas import LDDAManager
@@ -50,11 +56,13 @@ from galaxy.model import (
     ImplicitCollectionJobs,
     ImplicitCollectionJobsJobAssociation,
     Job,
+    JobMetricNumeric,
     JobParameter,
     User,
     Workflow,
     WorkflowInvocation,
     WorkflowInvocationStep,
+    WorkflowStep,
     YIELD_PER_ROWS,
 )
 from galaxy.model.base import transaction
@@ -69,10 +77,15 @@ from galaxy.schema.schema import (
 )
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.structured_app import StructuredApp
+from galaxy.tools._types import (
+    ToolStateDumpedToJsonInternalT,
+    ToolStateJobInstancePopulatedT,
+)
 from galaxy.util import (
     defaultdict,
     ExecutionTimer,
     listify,
+    string_as_bool_or_none,
 )
 from galaxy.util.search import (
     FilteredTerm,
@@ -82,6 +95,10 @@ from galaxy.util.search import (
 
 log = logging.getLogger(__name__)
 
+JobStateT = str
+JobStatesT = Union[JobStateT, List[JobStateT]]
+
+
 STDOUT_LOCATION = "outputs/tool_stdout"
 STDERR_LOCATION = "outputs/tool_stderr"
 
@@ -292,14 +309,19 @@ class JobManager:
         if job is None:
             raise ObjectNotFound()
 
+        # Check job destination params to see if stdout reporting is enabled
+        dest_params = job.destination_params
+        if not string_as_bool_or_none(dest_params.get("live_tool_output_reporting", False)):
+            raise ConfigDoesNotAllowException()
+
         # If stdout_length and stdout_position are good values, then load standard out and add it to status
-        console_output = dict()
+        console_output = {}
         console_output["state"] = job.state
         if job.state == job.states.RUNNING:
             working_directory = trans.app.object_store.get_filename(
                 job, base_dir="job_work", dir_only=True, obj_dir=True
             )
-            if stdout_length > 0 and stdout_position > -1:
+            if stdout_length > -1 and stdout_position > -1:
                 try:
                     stdout_path = Path(working_directory) / STDOUT_LOCATION
                     stdout_file = open(stdout_path)
@@ -308,7 +330,7 @@ class JobManager:
                 except Exception as e:
                     log.error("Could not read STDOUT: %s", e)
                     console_output["stdout"] = ""
-            if stderr_length > 0 and stderr_position > -1:
+            if stderr_length > -1 and stderr_position > -1:
                 try:
                     stderr_path = Path(working_directory) / STDERR_LOCATION
                     stderr_file = open(stderr_path)
@@ -324,7 +346,7 @@ class JobManager:
 
     def stop(self, job, message=None):
         if not job.finished:
-            job.mark_deleted(self.app.config.track_jobs_in_database)
+            job.mark_deleted(self.app.config.track_jobs_in_database, message)
             session = self.app.model.session
             with transaction(session):
                 session.commit()
@@ -361,7 +383,15 @@ class JobSearch:
         self.ldda_manager = ldda_manager
         self.decode_id = id_encoding_helper.decode_id
 
-    def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state="ok"):
+    def by_tool_input(
+        self,
+        trans: ProvidesHistoryContext,
+        tool_id: str,
+        tool_version: Optional[str],
+        param: ToolStateJobInstancePopulatedT,
+        param_dump: ToolStateDumpedToJsonInternalT,
+        job_state: Optional[JobStatesT] = "ok",
+    ):
         """Search for jobs producing same results using the 'inputs' part of a tool POST."""
         user = trans.user
         input_data = defaultdict(list)
@@ -373,7 +403,12 @@ class JobSearch:
                 current_case = param_dump
                 for p in path:
                     current_case = current_case[p]
-                src = current_case["src"]
+                src = current_case.get("src")
+                if src is None:
+                    # just a parameter named id.
+                    # TODO: dispatch on tool parameter type instead of values,
+                    # maybe with tool state variant
+                    return key, value
                 current_case = param
                 for i, p in enumerate(path):
                     if p == "values" and i == len(path) - 2:
@@ -403,7 +438,14 @@ class JobSearch:
         )
 
     def __search(
-        self, tool_id, tool_version, user, input_data, job_state=None, param_dump=None, wildcard_param_dump=None
+        self,
+        tool_id: str,
+        tool_version: Optional[str],
+        user: model.User,
+        input_data,
+        job_state: Optional[JobStatesT],
+        param_dump: ToolStateDumpedToJsonInternalT,
+        wildcard_param_dump=None,
     ):
         search_timer = ExecutionTimer()
 
@@ -418,9 +460,7 @@ class JobSearch:
                 return key, value
             return key, value
 
-        stmt_sq = self._build_job_subquery(tool_id, user.id, tool_version, job_state, wildcard_param_dump)
-
-        stmt = select(Job.id).select_from(Job.table.join(stmt_sq, stmt_sq.c.id == Job.id))
+        stmt = self._build_job_query(tool_id, user.id, tool_version, job_state, wildcard_param_dump)
 
         data_conditions: List = []
 
@@ -452,7 +492,7 @@ class JobSearch:
                 else:
                     return []
 
-            stmt = stmt.where(*data_conditions).group_by(model.Job.id, *used_ids).order_by(model.Job.id.desc())
+        stmt = stmt.where(*data_conditions).group_by(model.Job.id, *used_ids).order_by(model.Job.id.desc())
 
         for job in self.sa_session.execute(stmt):
             # We found a job that is equal in terms of tool_id, user, state and input datasets,
@@ -512,13 +552,20 @@ class JobSearch:
         log.info("No equivalent jobs found %s", search_timer)
         return None
 
-    def _build_job_subquery(self, tool_id, user_id, tool_version, job_state, wildcard_param_dump):
+    def _build_job_query(self, tool_id: str, user_id: int, tool_version: Optional[str], job_state, wildcard_param_dump):
         """Build subquery that selects a job with correct job parameters."""
-        stmt = select(model.Job.id).where(
-            and_(
-                model.Job.tool_id == tool_id,
-                model.Job.user_id == user_id,
-                model.Job.copied_from_job_id.is_(None),  # Always pick original job
+        stmt = (
+            select(model.Job.id)
+            .join(model.History, model.Job.history_id == model.History.id)
+            .where(
+                and_(
+                    model.Job.tool_id == tool_id,
+                    or_(
+                        model.Job.user_id == user_id,
+                        model.History.published == true(),
+                    ),
+                    model.Job.copied_from_job_id.is_(None),  # Always pick original job
+                )
             )
         )
         if tool_version:
@@ -534,7 +581,7 @@ class JobSearch:
             if isinstance(job_state, str):
                 stmt = stmt.where(Job.state == job_state)
             elif isinstance(job_state, list):
-                stmt = stmt.where(or_(*[Job.state == s for s in job_state]))
+                stmt = stmt.where(Job.state.in_(job_state))
 
         # exclude jobs with deleted outputs
         stmt = stmt.where(
@@ -573,7 +620,7 @@ class JobSearch:
                     )
                 )
 
-        return stmt.subquery()
+        return stmt
 
     def _build_stmt_for_hda(self, stmt, data_conditions, used_ids, k, v, identifier):
         a = aliased(model.JobToInputDatasetAssociation)
@@ -751,6 +798,43 @@ def invocation_job_source_iter(sa_session, invocation_id):
             yield ("ImplicitCollectionJobs", row[1], row[2])
 
 
+def get_job_metrics_for_invocation(sa_session: galaxy_scoped_session, invocation_id: int):
+    single_job_stmnt = (
+        select(WorkflowStep.order_index, Job.id, Job.tool_id, WorkflowStep.label, JobMetricNumeric)
+        .join(Job, JobMetricNumeric.job_id == Job.id)
+        .join(
+            WorkflowInvocationStep,
+            and_(
+                WorkflowInvocationStep.workflow_invocation_id == invocation_id, WorkflowInvocationStep.job_id == Job.id
+            ),
+        )
+        .join(WorkflowStep, WorkflowStep.id == WorkflowInvocationStep.workflow_step_id)
+    )
+    collection_job_stmnt = (
+        select(WorkflowStep.order_index, Job.id, Job.tool_id, WorkflowStep.label, JobMetricNumeric)
+        .join(Job, JobMetricNumeric.job_id == Job.id)
+        .join(ImplicitCollectionJobsJobAssociation, Job.id == ImplicitCollectionJobsJobAssociation.job_id)
+        .join(
+            ImplicitCollectionJobs,
+            ImplicitCollectionJobs.id == ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id,
+        )
+        .join(
+            WorkflowInvocationStep,
+            and_(
+                WorkflowInvocationStep.workflow_invocation_id == invocation_id,
+                WorkflowInvocationStep.implicit_collection_jobs_id == ImplicitCollectionJobs.id,
+            ),
+        )
+        .join(WorkflowStep, WorkflowStep.id == WorkflowInvocationStep.workflow_step_id)
+    )
+    # should be sa_session.execute(single_job_stmnt.union(collection_job_stmnt)).all() but that returns
+    # columns instead of the job metrics ORM instance.
+    return sorted(
+        (*sa_session.execute(single_job_stmnt).all(), *sa_session.execute(collection_job_stmnt).all()),
+        key=lambda row: row[0],
+    )
+
+
 def fetch_job_states(sa_session, job_source_ids, job_source_types):
     assert len(job_source_ids) == len(job_source_types)
     job_ids = set()
@@ -933,6 +1017,10 @@ def summarize_job_metrics(trans, job):
     Precondition: the caller has verified the job is accessible to the user
     represented by the trans parameter.
     """
+    return summarize_metrics(trans, job.metrics)
+
+
+def summarize_metrics(trans: ProvidesUserContext, job_metrics):
     safety_level = Safety.SAFE
     if trans.user_is_admin:
         safety_level = Safety.UNSAFE
@@ -944,7 +1032,7 @@ def summarize_job_metrics(trans, job):
             m.metric_value,
             m.plugin,
         )
-        for m in job.metrics
+        for m in job_metrics
     ]
     dictifiable_metrics = trans.app.job_metrics.dictifiable_metrics(raw_metrics, safety_level)
     return [d.dict() for d in dictifiable_metrics]
@@ -1008,7 +1096,11 @@ def summarize_job_parameters(trans, job: Job):
                         is_valid = False
                     if is_valid:
                         rval.append(
-                            dict(text=input.test_param.label, depth=depth, value=input.cases[current_case].value)
+                            dict(
+                                text=input.test_param.label or input.test_param.name,
+                                depth=depth,
+                                value=input.cases[current_case].value,
+                            )
                         )
                         rval.extend(
                             inputs_recursive(
@@ -1040,16 +1132,17 @@ def summarize_job_parameters(trans, job: Job):
                     or input.type == "data_collection"
                     or isinstance(input_value, model.HistoryDatasetAssociation)
                 ):
-                    value = []
+                    value: List[Union[Dict[str, Any], None]] = []
                     for element in listify(input_value):
-                        element_id = element.id
                         if isinstance(element, model.HistoryDatasetAssociation):
                             hda = element
-                            value.append({"src": "hda", "id": element_id, "hid": hda.hid, "name": hda.name})
+                            value.append({"src": "hda", "id": element.id, "hid": hda.hid, "name": hda.name})
                         elif isinstance(element, model.DatasetCollectionElement):
-                            value.append({"src": "dce", "id": element_id, "name": element.element_identifier})
+                            value.append({"src": "dce", "id": element.id, "name": element.element_identifier})
                         elif isinstance(element, model.HistoryDatasetCollectionAssociation):
-                            value.append({"src": "hdca", "id": element_id, "hid": element.hid, "name": element.name})
+                            value.append({"src": "hdca", "id": element.id, "hid": element.hid, "name": element.name})
+                        elif element is None:
+                            value.append(None)
                         else:
                             raise Exception(
                                 f"Unhandled data input parameter type encountered {element.__class__.__name__}"
@@ -1167,7 +1260,7 @@ def get_jobs_to_check_at_startup(session: galaxy_scoped_session, track_jobs_in_d
         # Filter out the jobs of inactive users.
         stmt = stmt.outerjoin(User).filter(or_((Job.user_id == null()), (User.active == true())))
 
-    return session.scalars(stmt)
+    return session.scalars(stmt).all()
 
 
 def get_job(session, *where_clauses):
diff --git a/lib/galaxy/managers/landing.py b/lib/galaxy/managers/landing.py
new file mode 100644
index 0000000000000000000000000000000000000000..5012d22801341e2b7b15552d5a61468836a0262f
--- /dev/null
+++ b/lib/galaxy/managers/landing.py
@@ -0,0 +1,203 @@
+from typing import (
+    Optional,
+    Union,
+)
+from uuid import uuid4
+
+from pydantic import UUID4
+from sqlalchemy import select
+
+from galaxy.exceptions import (
+    InsufficientPermissionsException,
+    ItemAlreadyClaimedException,
+    ItemMustBeClaimed,
+    ObjectNotFound,
+    RequestParameterMissingException,
+)
+from galaxy.managers.workflows import WorkflowContentsManager
+from galaxy.model import (
+    ToolLandingRequest as ToolLandingRequestModel,
+    WorkflowLandingRequest as WorkflowLandingRequestModel,
+)
+from galaxy.model.base import transaction
+from galaxy.model.scoped_session import galaxy_scoped_session
+from galaxy.schema.schema import (
+    ClaimLandingPayload,
+    CreateToolLandingRequestPayload,
+    CreateWorkflowLandingRequestPayload,
+    LandingRequestState,
+    ToolLandingRequest,
+    WorkflowLandingRequest,
+)
+from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.structured_app import StructuredApp
+from galaxy.util import safe_str_cmp
+from .context import ProvidesUserContext
+
+LandingRequestModel = Union[ToolLandingRequestModel, WorkflowLandingRequestModel]
+
+
+class LandingRequestManager:
+
+    def __init__(
+        self,
+        sa_session: galaxy_scoped_session,
+        security: IdEncodingHelper,
+        workflow_contents_manager: WorkflowContentsManager,
+    ):
+        self.sa_session = sa_session
+        self.security = security
+        self.workflow_contents_manager = workflow_contents_manager
+
+    def create_tool_landing_request(self, payload: CreateToolLandingRequestPayload, user_id=None) -> ToolLandingRequest:
+        model = ToolLandingRequestModel()
+        model.tool_id = payload.tool_id
+        model.tool_version = payload.tool_version
+        model.request_state = payload.request_state
+        model.uuid = uuid4()
+        model.client_secret = payload.client_secret
+        model.public = payload.public
+        if user_id:
+            model.user_id = user_id
+        self._save(model)
+        return self._tool_response(model)
+
+    def create_workflow_landing_request(self, payload: CreateWorkflowLandingRequestPayload) -> WorkflowLandingRequest:
+        model = WorkflowLandingRequestModel()
+        if payload.workflow_target_type == "stored_workflow":
+            model.stored_workflow_id = self.security.decode_id(payload.workflow_id)
+        elif payload.workflow_target_type == "workflow":
+            model.workflow_id = self.security.decode_id(payload.workflow_id)
+        elif payload.workflow_target_type == "trs_url":
+            model.workflow_source_type = "trs_url"
+            # validate this ?
+            model.workflow_source = payload.workflow_id
+        model.uuid = uuid4()
+        model.client_secret = payload.client_secret
+        model.request_state = payload.request_state
+        model.public = payload.public
+        self._save(model)
+        return self._workflow_response(model)
+
+    def claim_tool_landing_request(
+        self, trans: ProvidesUserContext, uuid: UUID4, claim: Optional[ClaimLandingPayload]
+    ) -> ToolLandingRequest:
+        request = self._get_tool_landing_request(uuid)
+        self._check_can_claim(trans, request, claim)
+        request.user_id = trans.user.id
+        self._save(request)
+        return self._tool_response(request)
+
+    def claim_workflow_landing_request(
+        self, trans: ProvidesUserContext, uuid: UUID4, claim: Optional[ClaimLandingPayload]
+    ) -> WorkflowLandingRequest:
+        request = self._get_workflow_landing_request(uuid)
+        self._check_can_claim(trans, request, claim)
+        self._ensure_workflow(trans, request)
+        request.user_id = trans.user.id
+        self._save(request)
+        return self._workflow_response(request)
+
+    def _ensure_workflow(self, trans: ProvidesUserContext, request: WorkflowLandingRequestModel):
+        if request.workflow_source_type == "trs_url" and isinstance(trans.app, StructuredApp):
+            # trans is always structured app except for unit test
+            assert request.workflow_source
+            workflow = self.workflow_contents_manager.get_or_create_workflow_from_trs(
+                trans, trs_url=request.workflow_source
+            )
+            request.workflow_id = workflow.latest_workflow_id
+
+    def get_tool_landing_request(self, trans: ProvidesUserContext, uuid: UUID4) -> ToolLandingRequest:
+        request = self._get_claimed_tool_landing_request(trans, uuid)
+        return self._tool_response(request)
+
+    def get_workflow_landing_request(self, trans: ProvidesUserContext, uuid: UUID4) -> WorkflowLandingRequest:
+        request = self._get_claimed_workflow_landing_request(trans, uuid)
+        self._ensure_workflow(trans, request)
+        return self._workflow_response(request)
+
+    def _check_can_claim(
+        self, trans: ProvidesUserContext, request: LandingRequestModel, claim: Optional[ClaimLandingPayload]
+    ):
+        if request.client_secret is not None:
+            if claim is None or not claim.client_secret:
+                raise RequestParameterMissingException()
+            if not safe_str_cmp(request.client_secret, claim.client_secret):
+                raise InsufficientPermissionsException()
+        if request.user_id is not None:
+            raise ItemAlreadyClaimedException()
+
+    def _get_tool_landing_request(self, uuid: UUID4) -> ToolLandingRequestModel:
+        request = self.sa_session.scalars(
+            select(ToolLandingRequestModel).where(ToolLandingRequestModel.uuid == str(uuid))
+        ).one_or_none()
+        if request is None:
+            raise ObjectNotFound()
+        return request
+
+    def _get_workflow_landing_request(self, uuid: UUID4) -> WorkflowLandingRequestModel:
+        request = self.sa_session.scalars(
+            select(WorkflowLandingRequestModel).where(WorkflowLandingRequestModel.uuid == str(uuid))
+        ).one_or_none()
+        if request is None:
+            raise ObjectNotFound()
+        return request
+
+    def _get_claimed_tool_landing_request(self, trans: ProvidesUserContext, uuid: UUID4) -> ToolLandingRequestModel:
+        request = self._get_tool_landing_request(uuid)
+        self._check_ownership(trans, request)
+        return request
+
+    def _get_claimed_workflow_landing_request(
+        self, trans: ProvidesUserContext, uuid: UUID4
+    ) -> WorkflowLandingRequestModel:
+        request = self._get_workflow_landing_request(uuid)
+        self._check_ownership(trans, request)
+        return request
+
+    def _tool_response(self, model: ToolLandingRequestModel) -> ToolLandingRequest:
+        response_model = ToolLandingRequest(
+            tool_id=model.tool_id,
+            tool_version=model.tool_version,
+            request_state=model.request_state,
+            uuid=model.uuid,
+            state=self._state(model),
+        )
+        return response_model
+
+    def _workflow_response(self, model: WorkflowLandingRequestModel) -> WorkflowLandingRequest:
+
+        workflow_id: Optional[Union[int, str]] = None
+        if model.stored_workflow_id is not None:
+            workflow_id = model.stored_workflow_id
+            target_type = "stored_workflow"
+        elif model.workflow_id is not None:
+            workflow_id = model.workflow_id
+            target_type = "workflow"
+        elif model.workflow_source_type == "trs_url":
+            target_type = model.workflow_source_type
+            workflow_id = model.workflow_source
+        assert workflow_id
+        response_model = WorkflowLandingRequest(
+            workflow_id=self.security.encode_id(workflow_id) if isinstance(workflow_id, int) else workflow_id,
+            workflow_target_type=target_type,
+            request_state=model.request_state,
+            uuid=model.uuid,
+            state=self._state(model),
+        )
+        return response_model
+
+    def _check_ownership(self, trans: ProvidesUserContext, model: LandingRequestModel):
+        if not model.public and self._state(model) == LandingRequestState.UNCLAIMED:
+            raise ItemMustBeClaimed
+        if model.user_id and model.user_id != trans.user.id:
+            raise InsufficientPermissionsException()
+
+    def _state(self, model: LandingRequestModel) -> LandingRequestState:
+        return LandingRequestState.UNCLAIMED if model.user_id is None else LandingRequestState.CLAIMED
+
+    def _save(self, model: LandingRequestModel):
+        sa_session = self.sa_session
+        sa_session.add(model)
+        with transaction(sa_session):
+            sa_session.commit()
diff --git a/lib/galaxy/managers/lddas.py b/lib/galaxy/managers/lddas.py
index 1cb2fe6da3f07b94817c2eaba727559bd8cfd149..7e56010c31cad690e0cc15b323710a9e102a9f5d 100644
--- a/lib/galaxy/managers/lddas.py
+++ b/lib/galaxy/managers/lddas.py
@@ -1,19 +1,26 @@
 import logging
+from typing import (
+    Any,
+    Optional,
+)
 
-from galaxy import model
 from galaxy.managers import base as manager_base
 from galaxy.managers.datasets import DatasetAssociationManager
+from galaxy.model import (
+    LibraryDatasetDatasetAssociation,
+    User,
+)
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
 
 
-class LDDAManager(DatasetAssociationManager):
+class LDDAManager(DatasetAssociationManager[LibraryDatasetDatasetAssociation]):
     """
     A fairly sparse manager for LDDAs.
     """
 
-    model_class = model.LibraryDatasetDatasetAssociation
+    model_class = LibraryDatasetDatasetAssociation
 
     def __init__(self, app: MinimalManagerApp):
         """
@@ -21,11 +28,20 @@ class LDDAManager(DatasetAssociationManager):
         """
         super().__init__(app)
 
-    def get(self, trans, id: int, check_accessible=True) -> model.LibraryDatasetDatasetAssociation:
+    def get(self, trans, id: int, check_accessible=True) -> LibraryDatasetDatasetAssociation:
         return manager_base.get_object(
             trans, id, "LibraryDatasetDatasetAssociation", check_ownership=False, check_accessible=check_accessible
         )
 
+    def is_owner(self, item, user: Optional[User], **kwargs: Any) -> bool:
+        """
+        Return True if user owns the item.
+        """
+        assert isinstance(item, LibraryDatasetDatasetAssociation)
+        if self.app.config.is_admin_user(user):
+            return True
+        return item.user == user
+
     def _set_permissions(self, trans, library_dataset, role_ids_dict):
         # Check Git history for an older broken implementation, but it was broken
         # and security related and had not test coverage so it was deleted.
diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py
index 3acb16a522d67e701d93df34388c51d1830796e3..ba3d9f48c3d428c61502b892ec3e79a8830ec445 100644
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -10,15 +10,6 @@ from typing import (
     Tuple,
 )
 
-from sqlalchemy import (
-    asc,
-    false,
-    func,
-    not_,
-    or_,
-    select,
-    true,
-)
 from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
@@ -29,10 +20,17 @@ from galaxy import exceptions
 from galaxy.managers.folders import FolderManager
 from galaxy.model import (
     Library,
-    LibraryPermissions,
     Role,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.library import (
+    get_libraries_by_name,
+    get_libraries_for_admins,
+    get_libraries_for_nonadmins,
+    get_library_ids,
+    get_library_permissions_by_role,
+)
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.util import (
     pretty_print_time_interval,
     unicodify,
@@ -60,7 +58,7 @@ class LibraryManager:
         :rtype:     galaxy.model.Library
         """
         try:
-            library = get_library(trans.sa_session, decoded_library_id)
+            library = trans.sa_session.get(Library, decoded_library_id)
         except MultipleResultsFound:
             raise exceptions.InconsistentDatabase("Multiple libraries found with the same id.")
         except NoResultFound:
@@ -280,26 +278,26 @@ class LibraryManager:
         :rtype:     dictionary
         :returns:   dict of current roles for all available permission types
         """
-        access_library_role_list = [
-            (access_role.name, trans.security.encode_id(access_role.id))
-            for access_role in self.get_access_roles(trans, library)
-        ]
-        modify_library_role_list = [
-            (modify_role.name, trans.security.encode_id(modify_role.id))
-            for modify_role in self.get_modify_roles(trans, library)
-        ]
-        manage_library_role_list = [
-            (manage_role.name, trans.security.encode_id(manage_role.id))
-            for manage_role in self.get_manage_roles(trans, library)
-        ]
-        add_library_item_role_list = [
-            (add_role.name, trans.security.encode_id(add_role.id)) for add_role in self.get_add_roles(trans, library)
-        ]
+        private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+        access_roles = self.get_access_roles(trans, library)
+        modify_roles = self.get_modify_roles(trans, library)
+        manage_roles = self.get_manage_roles(trans, library)
+        add_roles = self.get_add_roles(trans, library)
+
+        def make_tuples(roles: Set):
+            tuples = []
+            for role in roles:
+                # use role name for non-private roles, and user.email from private rules
+                displayed_name = private_role_emails.get(role.id, role.name)
+                role_tuple = (displayed_name, trans.security.encode_id(role.id))
+                tuples.append(role_tuple)
+            return tuples
+
         return dict(
-            access_library_role_list=access_library_role_list,
-            modify_library_role_list=modify_library_role_list,
-            manage_library_role_list=manage_library_role_list,
-            add_library_item_role_list=add_library_item_role_list,
+            access_library_role_list=make_tuples(access_roles),
+            modify_library_role_list=make_tuples(modify_roles),
+            manage_library_role_list=make_tuples(manage_roles),
+            add_library_item_role_list=make_tuples(add_roles),
         )
 
     def get_access_roles(self, trans, library: Library) -> Set[Role]:
@@ -358,52 +356,8 @@ def get_containing_library_from_library_dataset(trans, library_dataset) -> Optio
     while folder.parent:
         folder = folder.parent
     # We have folder set to the library's root folder, which has the same name as the library
-    stmt = select(Library).where(Library.deleted == false()).where(Library.name == folder.name)
-    for library in trans.sa_session.scalars(stmt):
+    for library in get_libraries_by_name(trans.sa_session, folder.name):
         # Just to double-check
         if library.root_folder == folder:
             return library
     return None
-
-
-def get_library(session, library_id):
-    stmt = select(Library).where(Library.id == library_id)
-    return session.execute(stmt).scalar_one()
-
-
-def get_library_ids(session, library_access_action):
-    stmt = select(LibraryPermissions.library_id).where(LibraryPermissions.action == library_access_action).distinct()
-    return session.scalars(stmt)
-
-
-def get_library_permissions_by_role(session, role_ids):
-    stmt = select(LibraryPermissions).where(LibraryPermissions.role_id.in_(role_ids))
-    return session.scalars(stmt)
-
-
-def get_libraries_for_admins(session, deleted):
-    stmt = select(Library)
-    if deleted is None:
-        #  Flag is not specified, do not filter on it.
-        pass
-    elif deleted:
-        stmt = stmt.where(Library.deleted == true())
-    else:
-        stmt = stmt.where(Library.deleted == false())
-    stmt = stmt.order_by(asc(func.lower(Library.name)))
-    return session.scalars(stmt)
-
-
-def get_libraries_for_nonadmins(session, restricted_library_ids, accessible_restricted_library_ids):
-    stmt = (
-        select(Library)
-        .where(Library.deleted == false())
-        .where(
-            or_(
-                not_(Library.id.in_(restricted_library_ids)),
-                Library.id.in_(accessible_restricted_library_ids),
-            )
-        )
-    )
-    stmt = stmt.order_by(asc(func.lower(Library.name)))
-    return session.scalars(stmt)
diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py
index 3666838b2bb0614e0990ad8eb879ef23c0414f9d..29005f42c65164cb3a2ec91e24f04b0663d4b251 100644
--- a/lib/galaxy/managers/library_datasets.py
+++ b/lib/galaxy/managers/library_datasets.py
@@ -1,23 +1,26 @@
 """Manager and Serializer for library datasets."""
 
 import logging
+from typing import (
+    Any,
+    Dict,
+)
 
 from sqlalchemy import select
 
-from galaxy import (
-    model,
-    util,
-)
+from galaxy import util
 from galaxy.exceptions import (
     InsufficientPermissionsException,
     InternalServerError,
     ObjectNotFound,
     RequestParameterInvalidException,
 )
-from galaxy.managers import datasets
+from galaxy.managers.base import ModelManager
 from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.lddas import LDDAManager
 from galaxy.model import (
     LibraryDataset,
+    LibraryDatasetDatasetAssociation,
     LibraryFolder,
 )
 from galaxy.model.base import transaction
@@ -27,15 +30,16 @@ from galaxy.util import validation
 log = logging.getLogger(__name__)
 
 
-class LibraryDatasetsManager(datasets.DatasetAssociationManager):
+class LibraryDatasetsManager(ModelManager[LibraryDataset]):
     """Interface/service object for interacting with library datasets."""
 
-    model_class = model.LibraryDatasetDatasetAssociation
+    model_class = LibraryDataset
 
     def __init__(self, app: MinimalManagerApp):
-        self.app = app
+        super().__init__(app)
+        self.ldda_manager = LDDAManager(app)
 
-    def get(self, trans, decoded_library_dataset_id, check_accessible=True):
+    def get(self, trans, decoded_library_dataset_id, check_accessible=True) -> LibraryDataset:
         """
         Get the library dataset from the DB.
 
@@ -54,14 +58,14 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         ld = self.secure(trans, ld, check_accessible)
         return ld
 
-    def update(self, trans, ld, payload):
+    def update(self, item: LibraryDataset, new_values: Dict[str, Any], flush: bool = True, **kwargs) -> LibraryDataset:
         """
         Update the given library dataset - the latest linked ldda.
         Updating older lddas (versions) is not allowed.
 
-        :param  ld:                 library dataset to change
-        :type   ld:                 LibraryDataset
-        :param  payload:            dictionary structure containing::
+        :param  item:               library dataset to change
+        :type   item:               LibraryDataset
+        :param  new_values:         dictionary structure containing::
             :param name:            new ld's name, must be longer than 0
             :type  name:            str
             :param misc_info:       new ld's misc info
@@ -72,19 +76,27 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
             :type  genome_build:    str
             :param tags:            list of dataset tags
             :type  tags:            list
-        :type   payload: dict
+        :type   new_values: dict
 
         :returns:   the changed library dataset
         :rtype:     galaxy.model.LibraryDataset
         """
-        self.check_modifiable(trans, ld)
+        trans = kwargs.get("trans")
+        if not trans:
+            raise ValueError("Missing trans parameter")
         # we are going to operate on the actual latest ldda
-        ldda = ld.library_dataset_dataset_association
-        payload = self._validate_and_parse_update_payload(payload)
-        self._set_from_dict(trans, ldda, payload)
-        return ld
-
-    def _set_from_dict(self, trans: ProvidesUserContext, ldda, new_data):
+        ldda = item.library_dataset_dataset_association
+        new_values = self._validate_and_parse_update_payload(new_values)
+        self._set_from_dict(trans, ldda, new_values, flush=flush)
+        return item
+
+    def _set_from_dict(
+        self,
+        trans: ProvidesUserContext,
+        ldda: LibraryDatasetDatasetAssociation,
+        new_data: Dict[str, Any],
+        flush: bool = True,
+    ) -> None:
         changed = False
         new_name = new_data.get("name", None)
         if new_name is not None and new_name != ldda.name:
@@ -100,10 +112,10 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
             changed = True
         new_file_ext = new_data.get("file_ext", None)
         if new_file_ext == "auto":
-            self.detect_datatype(trans, ldda)
+            self.ldda_manager.detect_datatype(trans, ldda)
         elif new_file_ext is not None and new_file_ext != ldda.extension:
             ldda.extension = new_file_ext
-            self.set_metadata(trans, ldda)
+            self.ldda_manager.set_metadata(trans, ldda)
             changed = True
         new_genome_build = new_data.get("genome_build", None)
         if new_genome_build is not None and new_genome_build != ldda.dbkey:
@@ -118,10 +130,11 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
             changed = True
         if changed:
             ldda.update_parent_folder_update_times()
-            trans.sa_session.add(ldda)
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-        return changed
+            session = self.session()
+            session.add(ldda)
+            if flush:
+                with transaction(session):
+                    session.commit()
 
     def _validate_and_parse_update_payload(self, payload):
         MINIMUM_STRING_LENGTH = 1
@@ -129,7 +142,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         for key, val in payload.items():
             if val is None:
                 continue
-            if key in ("name"):
+            if key in ("name",):
                 if len(val) < MINIMUM_STRING_LENGTH:
                     raise RequestParameterInvalidException(
                         f"{key} must have at least length of {MINIMUM_STRING_LENGTH}"
@@ -139,19 +152,19 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
             if key in ("misc_info", "message"):
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ("file_ext"):
+            if key in ("file_ext",):
                 datatype = self.app.datatypes_registry.get_datatype_by_extension(val)
                 if datatype is None and val not in ("auto",):
                     raise RequestParameterInvalidException(f"This Galaxy does not recognize the datatype of: {val}")
                 validated_payload[key] = val
-            if key in ("genome_build"):
+            if key in ("genome_build",):
                 if len(val) < MINIMUM_STRING_LENGTH:
                     raise RequestParameterInvalidException(
                         f"{key} must have at least length of {MINIMUM_STRING_LENGTH}"
                     )
                 val = validation.validate_and_sanitize_basestring(key, val)
                 validated_payload[key] = val
-            if key in ("tags"):
+            if key in ("tags",):
                 val = validation.validate_and_sanitize_basestring_list(key, util.listify(val))
                 validated_payload[key] = val
         return validated_payload
@@ -187,7 +200,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
 
         :raises:    ObjectNotFound
         """
-        if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), ld, trans.user):
+        if not self.app.security_agent.can_access_library_item(trans.get_current_user_roles(), ld, trans.user):
             raise ObjectNotFound("Library dataset with the id provided was not found.")
         elif ld.deleted:
             raise ObjectNotFound("Library dataset with the id provided is deleted.")
@@ -210,27 +223,27 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
             raise ObjectNotFound("Library dataset with the id provided is deleted.")
         elif trans.user_is_admin:
             return ld
-        if not trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), ld):
+        if not self.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), ld):
             raise InsufficientPermissionsException("You do not have proper permission to modify this library dataset.")
         else:
             return ld
 
-    def serialize(self, trans, ld):
+    def serialize(self, trans, ld: LibraryDataset) -> Dict[str, Any]:
         """Serialize the library dataset into a dictionary."""
         current_user_roles = trans.get_current_user_roles()
 
         # Build the full path for breadcrumb purposes.
         full_path = self._build_path(trans, ld.folder)
-        dataset_item = (trans.security.encode_id(ld.id), ld.name)
+        dataset_item = (self.app.security.encode_id(ld.id), ld.name)
         full_path.insert(0, dataset_item)
         full_path = full_path[::-1]
 
         # Find expired versions of the library dataset
         expired_ldda_versions = []
         for expired_ldda in ld.expired_datasets:
-            expired_ldda_versions.append((trans.security.encode_id(expired_ldda.id), expired_ldda.name))
+            expired_ldda_versions.append((self.app.security.encode_id(expired_ldda.id), expired_ldda.name))
 
-        rval = trans.security.encode_all_ids(ld.to_dict())
+        rval = self.app.security.encode_all_ids(ld.to_dict())
         if len(expired_ldda_versions) > 0:
             rval["has_versions"] = True
             rval["expired_versions"] = expired_ldda_versions
@@ -249,14 +262,14 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         rval["file_size"] = util.nice_size(int(ldda.get_size(calculate_size=False)))
         rval["date_uploaded"] = ldda.create_time.isoformat()
         rval["update_time"] = ldda.update_time.isoformat()
-        rval["can_user_modify"] = trans.user_is_admin or trans.app.security_agent.can_modify_library_item(
+        rval["can_user_modify"] = trans.user_is_admin or self.app.security_agent.can_modify_library_item(
             current_user_roles, ld
         )
-        rval["is_unrestricted"] = trans.app.security_agent.dataset_is_public(ldda.dataset)
+        rval["is_unrestricted"] = self.app.security_agent.dataset_is_public(ldda.dataset)
         rval["tags"] = trans.tag_handler.get_tags_list(ldda.tags)
 
         #  Manage dataset permission is always attached to the dataset itself, not the ld or ldda to maintain consistency
-        rval["can_user_manage"] = trans.user_is_admin or trans.app.security_agent.can_manage_dataset(
+        rval["can_user_manage"] = trans.user_is_admin or self.app.security_agent.can_manage_dataset(
             current_user_roles, ldda.dataset
         )
         return rval
@@ -275,15 +288,15 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
         path_to_root = []
         if folder.parent_id is None:
             # We are almost in root
-            path_to_root.append((f"F{trans.security.encode_id(folder.id)}", folder.name))
+            path_to_root.append((f"F{self.app.security.encode_id(folder.id)}", folder.name))
         else:
             # We add the current folder and traverse up one folder.
-            path_to_root.append((f"F{trans.security.encode_id(folder.id)}", folder.name))
+            path_to_root.append((f"F{self.app.security.encode_id(folder.id)}", folder.name))
             upper_folder = trans.sa_session.get(LibraryFolder, folder.parent_id)
             path_to_root.extend(self._build_path(trans, upper_folder))
         return path_to_root
 
 
-def get_library_dataset(session, library_dataset_id):
+def get_library_dataset(session, library_dataset_id) -> LibraryDataset:
     stmt = select(LibraryDataset).where(LibraryDataset.id == library_dataset_id)
     return session.scalars(stmt).one()
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index 009aae3ea7629f255475ce2ef3c61eb549e0fce8..02545399e997d68785c41acdc7145fa677831c32 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -215,7 +215,9 @@ class GalaxyInternalMarkdownDirectiveHandler(metaclass=abc.ABCMeta):
                 url = trans.app.config.organization_url
                 rval = self.handle_instance_organization_link(line, title, url)
             elif container == "invocation_time":
-                invocation = workflow_manager.get_invocation(trans, object_id)
+                invocation = workflow_manager.get_invocation(
+                    trans, object_id, check_ownership=False, check_accessible=True
+                )
                 rval = self.handle_invocation_time(line, invocation)
             elif container == "visualization":
                 rval = None
diff --git a/lib/galaxy/managers/notification.py b/lib/galaxy/managers/notification.py
index 7c7ea171f69476d82bf134fc254bba9c9c36ba19..6bd99278e59a7ca5f6641c63dc22840f3262c66d 100644
--- a/lib/galaxy/managers/notification.py
+++ b/lib/galaxy/managers/notification.py
@@ -414,16 +414,14 @@ class NotificationManager:
 
     def get_user_notification_preferences(self, user: User) -> UserNotificationPreferences:
         """Gets the user's current notification preferences or the default ones if no preferences are set."""
-        current_notification_preferences = (
-            user.preferences[NOTIFICATION_PREFERENCES_SECTION_NAME]
-            if NOTIFICATION_PREFERENCES_SECTION_NAME in user.preferences
-            else None
-        )
-        try:
-            return UserNotificationPreferences.model_validate_json(current_notification_preferences)
-        except ValidationError:
-            # Gracefully return default preferences is they don't exist or get corrupted
-            return UserNotificationPreferences.default()
+        current_notification_preferences = user.preferences.get(NOTIFICATION_PREFERENCES_SECTION_NAME)
+        if current_notification_preferences:
+            try:
+                return UserNotificationPreferences.model_validate_json(current_notification_preferences)
+            except ValidationError:
+                pass
+        # Gracefully return default preferences is they don't exist or get corrupted
+        return UserNotificationPreferences.default()
 
     def update_user_notification_preferences(
         self, user: User, request: UpdateUserNotificationPreferencesRequest
diff --git a/lib/galaxy/managers/object_store_instances.py b/lib/galaxy/managers/object_store_instances.py
index b0163c7be249891be24171f0408c8a5985204e72..2473c39b117b3527c0f5ff6703f24b07b7179803 100644
--- a/lib/galaxy/managers/object_store_instances.py
+++ b/lib/galaxy/managers/object_store_instances.py
@@ -13,6 +13,7 @@ from typing import (
     List,
     Optional,
     Tuple,
+    Union,
 )
 from uuid import uuid4
 
@@ -31,6 +32,7 @@ from galaxy.objectstore import (
     build_test_object_store_from_user_config,
     ConcreteObjectStoreModel,
     QuotaModel,
+    USER_OBJECTS_SCHEME,
     UserObjectStoresAppConfig,
 )
 from galaxy.objectstore.badges import serialize_badges
@@ -49,26 +51,36 @@ from galaxy.util.config_templates import (
     PluginStatus,
     settings_exception_to_status,
     status_template_definition,
+    TemplateReference,
     TemplateVariableValueType,
     validate_no_extra_secrets_defined,
     validate_no_extra_variables_defined,
 )
 from ._config_templates import (
+    CanTestPluginStatus,
     CreateInstancePayload,
+    CreateTestTarget,
     ModifyInstancePayload,
     prepare_environment,
-    prepare_environment_from_root,
+    prepare_template_parameters_for_testing,
     purge_template_instance,
     recover_secrets,
     save_template_instance,
     sort_templates,
+    TemplateServerConfiguration,
+    TestModifyInstancePayload,
+    TestUpdateInstancePayload,
+    TestUpgradeInstancePayload,
+    to_template_reference,
     update_instance_secret,
     update_template_instance,
     updated_template_variables,
     UpdateInstancePayload,
     UpdateInstanceSecretPayload,
+    UpdateTestTarget,
     upgrade_secrets,
     UpgradeInstancePayload,
+    UpgradeTestTarget,
 )
 
 log = logging.getLogger(__name__)
@@ -126,11 +138,9 @@ class ObjectStoreInstancesManager:
         self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload
     ) -> UserConcreteObjectStoreModel:
         persisted_object_store = self._get(trans, id)
-        template = self._get_template(persisted_object_store, payload.template_version)
+        template = self._get_and_validate_target_upgrade_template(persisted_object_store, payload)
         persisted_object_store.template_version = template.version
         persisted_object_store.template_definition = template.model_dump()
-        validate_no_extra_variables_defined(payload.variables, template)
-        validate_no_extra_secrets_defined(payload.secrets, template)
         actual_variables = updated_template_variables(
             payload.variables,
             persisted_object_store,
@@ -141,6 +151,16 @@ class ObjectStoreInstancesManager:
         self._save(persisted_object_store)
         return self._to_model(trans, persisted_object_store)
 
+    def _get_and_validate_target_upgrade_template(
+        self,
+        persisted_object_store: UserObjectStore,
+        payload: Union[UpgradeInstancePayload, TestUpgradeInstancePayload],
+    ) -> ObjectStoreTemplate:
+        template = self._get_template(persisted_object_store, payload.template_version)
+        validate_no_extra_variables_defined(payload.variables, template)
+        validate_no_extra_secrets_defined(payload.secrets, template)
+        return template
+
     def _update_instance(
         self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload
     ) -> UserConcreteObjectStoreModel:
@@ -218,8 +238,47 @@ class ObjectStoreInstancesManager:
             raise ItemOwnershipException()
         return user_object_store
 
+    def test_modify_instance(
+        self, trans: ProvidesUserContext, id: UUID4, payload: TestModifyInstancePayload
+    ) -> PluginStatus:
+        persisted_object_store = self._get(trans, id)
+        if isinstance(payload, TestUpgradeInstancePayload):
+            return self._plugin_status_for_upgrade(trans, payload, persisted_object_store)
+        else:
+            assert isinstance(payload, TestUpdateInstancePayload)
+            return self._plugin_status_for_update(trans, payload, persisted_object_store)
+
+    def _plugin_status_for_update(
+        self, trans: ProvidesUserContext, payload: TestUpdateInstancePayload, persisted_object_store: UserObjectStore
+    ) -> PluginStatus:
+        template = self._get_template(persisted_object_store)
+        target = UpdateTestTarget(persisted_object_store, payload)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def _plugin_status_for_upgrade(
+        self, trans: ProvidesUserContext, payload: TestUpgradeInstancePayload, persisted_object_store: UserObjectStore
+    ) -> PluginStatus:
+        template = self._get_and_validate_target_upgrade_template(persisted_object_store, payload)
+        target = UpgradeTestTarget(persisted_object_store, payload)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def plugin_status_for_instance(self, trans: ProvidesUserContext, id: UUID4):
+        persisted_object_store = self._get(trans, id)
+        return self._plugin_status(trans, persisted_object_store, to_template_reference(persisted_object_store))
+
     def plugin_status(self, trans: ProvidesUserContext, payload: CreateInstancePayload) -> PluginStatus:
-        template = self._catalog.find_template(payload)
+        target = CreateTestTarget(payload, UserObjectStore)
+        return self._plugin_status(trans, target, payload)
+
+    def _plugin_status(
+        self, trans: ProvidesUserContext, target: CanTestPluginStatus, template_reference: TemplateReference
+    ):
+        template = self._catalog.find_template(template_reference)
+        return self._plugin_status_for_template(trans, target, template)
+
+    def _plugin_status_for_template(
+        self, trans: ProvidesUserContext, payload: CanTestPluginStatus, template: ObjectStoreTemplate
+    ):
         template_definition_status = status_template_definition(template)
         status_kwds = {"template_definition": template_definition_status}
         if template_definition_status.is_not_ok:
@@ -243,30 +302,23 @@ class ObjectStoreInstancesManager:
     def _template_settings_status(
         self,
         trans: ProvidesUserContext,
-        payload: CreateInstancePayload,
+        payload: CanTestPluginStatus,
         template: ObjectStoreTemplate,
     ) -> Tuple[Optional[ObjectStoreConfiguration], PluginAspectStatus]:
-        secrets = payload.secrets
-        variables = payload.variables
-        environment = prepare_environment_from_root(template.environment, self._app_vault, self._app_config)
-        user_details = trans.user.config_template_details()
+        template_parameters = prepare_template_parameters_for_testing(
+            trans, template, TemplateServerConfiguration(), payload, self._app_vault, self._app_config
+        )
 
         configuration = None
         exception = None
         try:
-            configuration = template_to_configuration(
-                template,
-                variables=variables,
-                secrets=secrets,
-                user_details=user_details,
-                environment=environment,
-            )
+            configuration = template_to_configuration(template, **template_parameters)
         except Exception as e:
             exception = e
         return configuration, settings_exception_to_status(exception)
 
     def _connection_status(
-        self, trans: ProvidesUserContext, payload: CreateInstancePayload, configuration: ObjectStoreConfiguration
+        self, trans: ProvidesUserContext, payload: CanTestPluginStatus, configuration: ObjectStoreConfiguration
     ) -> Tuple[Optional[BaseObjectStore], PluginAspectStatus]:
         object_store = None
         exception = None
@@ -300,7 +352,7 @@ class ObjectStoreInstancesManager:
         )
         secrets = persisted_object_store.template_secrets or []
         uuid = str(persisted_object_store.uuid)
-        object_store_id = f"user_objects://{uuid}"
+        object_store_id = f"{USER_OBJECTS_SCHEME}{uuid}"
 
         return UserConcreteObjectStoreModel(
             uuid=uuid,
@@ -354,6 +406,9 @@ class UserObjectStoreResolverImpl(BaseUserObjectStoreResolver):
 __all__ = (
     "CreateInstancePayload",
     "ModifyInstancePayload",
+    "TestUpgradeInstancePayload",
+    "TestUpdateInstancePayload",
+    "TestModifyInstancePayload",
     "UpdateInstancePayload",
     "UpdateInstanceSecretPayload",
     "UpgradeInstancePayload",
diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py
index 581b5b93562b3749ad16ab0d4fbf784da57cadb7..101d785c688e580d1c127a988bf38959c8ea79b8 100644
--- a/lib/galaxy/managers/pages.py
+++ b/lib/galaxy/managers/pages.py
@@ -248,7 +248,7 @@ class PageManager(sharable.SharableModelManager, UsesAnnotations):
             raise exceptions.ObjectAttributeMissingException("Page name is required")
         elif not payload.slug:
             raise exceptions.ObjectAttributeMissingException("Page id is required")
-        elif not base.is_valid_slug(payload.slug):
+        elif not sharable.SlugBuilder.is_valid_slug(payload.slug):
             raise exceptions.ObjectAttributeInvalidException(
                 "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
             )
diff --git a/lib/galaxy/managers/quotas.py b/lib/galaxy/managers/quotas.py
index 31e7fcc48e6dc3ef22ab6ffaa9911fa65b1297ea..932e77a91348c2cdb3157842af863a9790b9e4af 100644
--- a/lib/galaxy/managers/quotas.py
+++ b/lib/galaxy/managers/quotas.py
@@ -12,7 +12,10 @@ from typing import (
     Union,
 )
 
-from sqlalchemy import select
+from sqlalchemy import (
+    and_,
+    select,
+)
 
 from galaxy import (
     model,
@@ -114,11 +117,11 @@ class QuotaManager:
         except ValueError:
             return False
 
-    def rename_quota(self, quota, params) -> str:
-        stmt = select(Quota).where(Quota.name == params.name).limit(1)
+    def rename_quota(self, quota, params) -> Optional[str]:
+        stmt = select(Quota).where(and_(Quota.name == params.name, Quota.id != quota.id)).limit(1)
         if not params.name:
             raise ActionInputError("Enter a valid name.")
-        elif params.name != quota.name and self.sa_session.scalars(stmt).first():
+        elif self.sa_session.scalars(stmt).first():
             raise ActionInputError("A quota with that name already exists.")
         else:
             old_name = quota.name
@@ -128,10 +131,12 @@ class QuotaManager:
             self.sa_session.add(quota)
             with transaction(self.sa_session):
                 self.sa_session.commit()
-            message = f"Quota '{old_name}' has been renamed to '{params.name}'."
-            return message
+            if old_name != params.name:
+                return f"Quota '{old_name}' has been renamed to '{params.name}'."
+            else:
+                return None
 
-    def manage_users_and_groups_for_quota(self, quota, params, decode_id=None) -> str:
+    def manage_users_and_groups_for_quota(self, quota, params, decode_id=None) -> Optional[str]:
         if quota.default:
             raise ActionInputError("Default quotas cannot be associated with specific users and groups.")
         else:
@@ -148,10 +153,16 @@ class QuotaManager:
                 raise ActionInputError("One or more invalid group id has been provided.")
             self.quota_agent.set_entity_quota_associations(quotas=[quota], users=in_users, groups=in_groups)
             self.sa_session.refresh(quota)
-            message = f"Quota '{quota.name}' has been updated with {len(in_users)} associated users and {len(in_groups)} associated groups."
-            return message
+            if len(quota.users) != len(in_users) and len(quota.groups) != len(in_groups):
+                return f"Quota '{quota.name}' has been updated with {len(in_users)} associated users and {len(in_groups)} associated groups."
+            elif len(quota.users) != len(in_users):
+                return f"Quota '{quota.name}' has been updated with {len(in_users)} associated users."
+            elif len(quota.groups) != len(in_groups):
+                return f"Quota '{quota.name}' has been updated with {len(in_groups)} associated groups."
+            else:
+                return None
 
-    def edit_quota(self, quota, params) -> str:
+    def edit_quota(self, quota, params) -> Optional[str]:
         if params.amount.lower() in ("unlimited", "none", "no limit"):
             new_amount = None
         else:
@@ -166,42 +177,43 @@ class QuotaManager:
         elif params.operation not in model.Quota.valid_operations:
             raise ActionInputError("Enter a valid operation.")
         else:
+            old_display_amount = quota.display_amount
+            old_operation = quota.operation
             quota.amount = new_amount
             quota.operation = params.operation
             self.sa_session.add(quota)
             with transaction(self.sa_session):
                 self.sa_session.commit()
-            message = f"Quota '{quota.name}' is now '{quota.operation}{quota.display_amount}'."
-            return message
+            if old_display_amount != quota.display_amount or old_operation != quota.operation:
+                return f"Quota '{quota.name}' is now '{quota.operation}{quota.display_amount}'."
+            else:
+                return None
 
-    def set_quota_default(self, quota, params) -> str:
+    def set_quota_default(self, quota, params) -> Optional[str]:
         if params.default != "no" and params.default not in model.DefaultQuotaAssociation.types.__members__.values():
             raise ActionInputError("Enter a valid default type.")
         else:
+            message = None
             if params.default != "no":
                 self.quota_agent.set_default_quota(params.default, quota)
                 message = f"Quota '{quota.name}' is now the default for {params.default} users."
-            else:
-                if quota.default:
-                    message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
-                    for dqa in quota.default:
-                        self.sa_session.delete(dqa)
-                    with transaction(self.sa_session):
-                        self.sa_session.commit()
-                else:
-                    message = f"Quota '{quota.name}' is not a default."
+            elif quota.default:
+                message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
+                for dqa in quota.default:
+                    self.sa_session.delete(dqa)
+                with transaction(self.sa_session):
+                    self.sa_session.commit()
             return message
 
-    def unset_quota_default(self, quota, params=None) -> str:
-        if not quota.default:
-            raise ActionInputError(f"Quota '{quota.name}' is not a default.")
-        else:
+    def unset_quota_default(self, quota, params=None) -> Optional[str]:
+        message = None
+        if quota.default:
             message = f"Quota '{quota.name}' is no longer the default for {quota.default[0].type} users."
             for dqa in quota.default:
                 self.sa_session.delete(dqa)
             with transaction(self.sa_session):
                 self.sa_session.commit()
-            return message
+        return message
 
     def delete_quota(self, quota, params=None) -> str:
         quotas = util.listify(quota)
@@ -245,7 +257,7 @@ class QuotaManager:
         message += ", ".join(names)
         return message
 
-    def purge_quota(self, quota, params=None):
+    def purge_quota(self, quota, params=None) -> str:
         """
         This method should only be called for a Quota that has previously been deleted.
         Purging a deleted Quota deletes all of the following from the database:
diff --git a/lib/galaxy/managers/rbac_secured.py b/lib/galaxy/managers/rbac_secured.py
index a63cd036447bf37491aaba7d0e1df0eea54a5741..41f24da248097c6e3f7d294fcd9da787da117cda 100644
--- a/lib/galaxy/managers/rbac_secured.py
+++ b/lib/galaxy/managers/rbac_secured.py
@@ -42,10 +42,10 @@ class RBACPermission:
             error_info = dict(model_class=item.__class__, id=getattr(item, "id", None))
             raise self.permission_failed_error_class(**error_info)
 
-    def grant(self, item, user, flush=True):
+    def grant(self, item, user, flush: bool = True):
         raise NotImplementedError("abstract parent class")
 
-    def revoke(self, item, user, flush=True):
+    def revoke(self, item, user, flush: bool = True):
         raise NotImplementedError("abstract parent class")
 
     def _role_is_permitted(self, item, role):
@@ -197,13 +197,13 @@ class ManageDatasetRBACPermission(DatasetRBACPermission):
                 return True
         return False
 
-    def grant(self, dataset, user, flush=True):
+    def grant(self, item, user, flush: bool = True):
         private_role = self._user_private_role(user)
-        return self._grant_role(dataset, private_role, flush=flush)
+        return self._grant_role(item, private_role, flush=flush)
 
-    def revoke(self, dataset, user, flush=True):
+    def revoke(self, item, user, flush: bool = True):
         private_role = self._user_private_role(user)
-        return self._revoke_role(dataset, private_role, flush=flush)
+        return self._revoke_role(item, private_role, flush=flush)
 
     # ---- private
     def _role_is_permitted(self, dataset, role):
@@ -253,13 +253,13 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
             or self._user_has_all_roles(user, current_roles)
         )
 
-    def grant(self, item, user):
+    def grant(self, item, user, flush: bool = True):
         pass
         # not so easy
         # need to check for a sharing role
         # then add the new user to it
 
-    def revoke(self, item, user):
+    def revoke(self, item, user, flush: bool = True):
         pass
         # not so easy
 
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index e9a18a60e91ed9792d05ca2d85516bd110975fe0..4787946243137483b96914ec8ad6305f4826b112 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -3,15 +3,9 @@ Manager and Serializer for Roles.
 """
 
 import logging
-from typing import (
-    List,
-    Sequence,
-)
+from typing import List
 
-from sqlalchemy import (
-    false,
-    select,
-)
+from sqlalchemy import select
 from sqlalchemy.exc import (
     MultipleResultsFound,
     NoResultFound,
@@ -29,7 +23,7 @@ from galaxy.managers import base
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import Role
 from galaxy.model.base import transaction
-from galaxy.model.scoped_session import galaxy_scoped_session
+from galaxy.model.db.role import get_displayable_roles
 from galaxy.schema.schema import RoleDefinitionModel
 from galaxy.util import unicodify
 
@@ -75,12 +69,7 @@ class RoleManager(base.ModelManager[model.Role]):
         return role
 
     def list_displayable_roles(self, trans: ProvidesUserContext) -> List[Role]:
-        roles = []
-        stmt = select(Role).where(Role.deleted == false())
-        for role in trans.sa_session.scalars(stmt):
-            if trans.user_is_admin or trans.app.security_agent.ok_to_display(trans.user, role):
-                roles.append(role)
-        return roles
+        return get_displayable_roles(trans.sa_session, trans.user, trans.user_is_admin, trans.app.security_agent)
 
     def create_role(self, trans: ProvidesUserContext, role_definition_model: RoleDefinitionModel) -> model.Role:
         name = role_definition_model.name
@@ -165,8 +154,3 @@ class RoleManager(base.ModelManager[model.Role]):
         with transaction(trans.sa_session):
             trans.sa_session.commit()
         return role
-
-
-def get_roles_by_ids(session: galaxy_scoped_session, role_ids: List[int]) -> Sequence[Role]:
-    stmt = select(Role).where(Role.id.in_(role_ids))
-    return session.scalars(stmt).all()
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 1f607f5d2589632548563e55407147631838df2b..cfdcda372e9729fcb1ba7154730112e5b4e6a9f2 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -11,7 +11,6 @@ A sharable Galaxy object:
 """
 
 import logging
-import re
 from typing import (
     Any,
     List,
@@ -20,6 +19,7 @@ from typing import (
     Type,
 )
 
+from slugify import slugify
 from sqlalchemy import (
     exists,
     false,
@@ -291,7 +291,7 @@ class SharableModelManager(
         Validate and set the new slug for `item`.
         """
         # precondition: has been validated
-        if not self.is_valid_slug(new_slug):
+        if not SlugBuilder.is_valid_slug(new_slug):
             raise exceptions.RequestParameterInvalidException("Invalid slug", slug=new_slug)
 
         if item.slug == new_slug:
@@ -309,23 +309,6 @@ class SharableModelManager(
                 session.commit()
         return item
 
-    def is_valid_slug(self, slug):
-        """
-        Returns true if `slug` is valid.
-        """
-        VALID_SLUG_RE = re.compile(r"^[a-z0-9\-]+$")
-        return VALID_SLUG_RE.match(slug)
-
-    def _slugify(self, start_with):
-        # Replace whitespace with '-'
-        slug_base = re.sub(r"\s+", "-", start_with)
-        # Remove all non-alphanumeric characters.
-        slug_base = re.sub(r"[^a-zA-Z0-9\-]", "", slug_base)
-        # Remove trailing '-'.
-        if slug_base.endswith("-"):
-            slug_base = slug_base[:-1]
-        return slug_base
-
     def _default_slug_base(self, item):
         # override in subclasses
         if hasattr(item, "title"):
@@ -341,7 +324,7 @@ class SharableModelManager(
 
         # Setup slug base.
         if cur_slug is None or cur_slug == "":
-            slug_base = self._slugify(self._default_slug_base(item))
+            slug_base = slugify(self._default_slug_base(item), allow_unicode=True)
         else:
             slug_base = cur_slug
 
@@ -580,6 +563,11 @@ class SlugBuilder:
         item.slug = new_slug
         return item.slug == cur_slug
 
+    @classmethod
+    def is_valid_slug(self, slug):
+        """Returns true if slug is valid."""
+        return slugify(slug, allow_unicode=True) == slug
+
 
 def slug_exists(session, model_class, user, slug, ignore_deleted=False):
     stmt = select(exists().where(model_class.user == user).where(model_class.slug == slug))
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 8d3012553924acb37a04599d186b7ce3a236663a..d1f24e4cb0b6f779a2917d67b161821e46ac3579 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -14,7 +14,6 @@ from typing import (
     Dict,
     List,
     Optional,
-    Sequence,
 )
 
 from markupsafe import escape
@@ -46,7 +45,11 @@ from galaxy.model import (
     UserQuotaUsage,
 )
 from galaxy.model.base import transaction
-from galaxy.model.scoped_session import galaxy_scoped_session
+from galaxy.model.db.user import (
+    _cleanup_nonprivate_user_roles,
+    get_user_by_email,
+    get_user_by_username,
+)
 from galaxy.security.validate_user_input import (
     VALID_EMAIL_RE,
     validate_email,
@@ -212,10 +215,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         # Delete UserGroupAssociations
         for uga in user.groups:
             self.session().delete(uga)
-        # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE
-        for ura in user.roles:
-            if ura.role_id != private_role.id:
-                self.session().delete(ura)
+        _cleanup_nonprivate_user_roles(self.session(), user, private_role.id)
         # Delete UserAddresses
         for address in user.addresses:
             self.session().delete(address)
@@ -656,11 +656,8 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             remote_user_email = remote_user_email.lower()
         user = get_user_by_email(self.session(), remote_user_email, self.app.model.User)
         if user:
-            # GVK: June 29, 2009 - This is to correct the behavior of a previous bug where a private
-            # role and default user / history permissions were not set for remote users.  When a
-            # remote user authenticates, we'll look for this information, and if missing, create it.
-            if not self.app.security_agent.get_private_user_role(user):
-                self.app.security_agent.create_private_user_role(user)
+            # Ensure a private role and default permissions are set for remote users (remote user creation bug existed prior to 2009)
+            self.app.security_agent.get_private_user_role(user, auto_create=True)
             if self.app_type == "galaxy":
                 if not user.default_permissions:
                     self.app.security_agent.user_set_default_permissions(user)
@@ -866,28 +863,6 @@ class AdminUserFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMix
         self.fn_filter_parsers.update({})
 
 
-def get_users_by_ids(session: galaxy_scoped_session, user_ids: List[int]) -> Sequence[User]:
-    stmt = select(User).where(User.id.in_(user_ids))
-    return session.scalars(stmt).all()
-
-
-# The get_user_by_email and get_user_by_username functions may be called from
-# the tool_shed app, which has its own User model, which is different from
-# galaxy.model.User. In that case, the tool_shed user model should be passed as
-# the model_class argument.
-def get_user_by_email(session, email: str, model_class=User, case_sensitive=True):
-    filter_clause = model_class.email == email
-    if not case_sensitive:
-        filter_clause = func.lower(model_class.email) == func.lower(email)
-    stmt = select(model_class).where(filter_clause).limit(1)
-    return session.scalars(stmt).first()
-
-
-def get_user_by_username(session, username: str, model_class=User):
-    stmt = select(model_class).filter(model_class.username == username).limit(1)
-    return session.scalars(stmt).first()
-
-
 def username_from_email(session, email, model_class=User):
     """Get next available username generated based on email"""
     username = email.split("@", 1)[0].lower()
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 1259dd7719add0f8ed63f10ddb8905ac330bc24b..140167e15757d76179067b1f1503a6ccfb1f14bb 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -14,6 +14,7 @@ from typing import (
 )
 
 import sqlalchemy
+import yaml
 from gxformat2 import (
     from_galaxy_native,
     ImporterGalaxyInterface,
@@ -29,6 +30,7 @@ from pydantic import (
     WrapSerializer,
 )
 from sqlalchemy import (
+    and_,
     desc,
     false,
     func,
@@ -53,7 +55,10 @@ from galaxy.managers import (
     deletable,
     sharable,
 )
-from galaxy.managers.base import decode_id
+from galaxy.managers.base import (
+    decode_id,
+    security_check,
+)
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.executables import artifact_class
 from galaxy.model import (
@@ -64,6 +69,7 @@ from galaxy.model import (
     StoredWorkflow,
     StoredWorkflowTagAssociation,
     StoredWorkflowUserShareAssociation,
+    to_json,
     User,
     Workflow,
     WorkflowInvocation,
@@ -130,6 +136,7 @@ from galaxy.workflow.steps import (
     attach_ordered_steps,
     has_cycles,
 )
+from galaxy.workflow.trs_proxy import TrsProxy
 
 log = logging.getLogger(__name__)
 
@@ -238,6 +245,12 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
                                 message = "Can only use tag is:shared_with_me if show_shared parameter also true."
                                 raise exceptions.RequestParameterInvalidException(message)
                             stmt = stmt.where(StoredWorkflowUserShareAssociation.user == user)
+                        elif q == "bookmarked":
+                            stmt = (
+                                stmt.join(model.StoredWorkflowMenuEntry)
+                                .where(model.StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id)
+                                .where(model.StoredWorkflowMenuEntry.user_id == user.id)
+                            )
                 elif isinstance(term, RawTextTerm):
                     tf = w_tag_filter(term.text, False)
                     alias = aliased(User)
@@ -347,10 +360,10 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         if isinstance(has_workflow, model.WorkflowInvocation):
             # We use the owner of the history that is associated to the invocation as a proxy
             # for the owner of the invocation.
-            if trans.user != has_workflow.history.user and not trans.user_is_admin:
-                raise exceptions.ItemOwnershipException()
-            else:
-                return True
+            security_check(
+                trans, has_workflow.history, check_ownership=check_ownership, check_accessible=check_accessible
+            )
+            return True
 
         # stored workflow contains security stuff - follow that workflow to
         # that unless given a stored workflow.
@@ -404,20 +417,26 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         workflow_canvas.add_steps()
         return workflow_canvas.finish(for_embed=for_embed)
 
-    def get_invocation(self, trans, decoded_invocation_id: int, eager=False) -> WorkflowInvocation:
+    def get_invocation(
+        self, trans, decoded_invocation_id: int, eager=False, check_ownership=True, check_accessible=True
+    ) -> WorkflowInvocation:
         workflow_invocation = _get_invocation(trans.sa_session, eager, decoded_invocation_id)
         if not workflow_invocation:
             encoded_wfi_id = trans.security.encode_id(decoded_invocation_id)
             message = f"'{encoded_wfi_id}' is not a valid workflow invocation id"
             raise exceptions.ObjectNotFound(message)
-        self.check_security(trans, workflow_invocation, check_ownership=True, check_accessible=False)
+        self.check_security(
+            trans, workflow_invocation, check_ownership=check_ownership, check_accessible=check_accessible
+        )
         return workflow_invocation
 
     def get_invocation_report(self, trans, invocation_id, **kwd):
         decoded_workflow_invocation_id = (
             trans.security.decode_id(invocation_id) if isinstance(invocation_id, str) else invocation_id
         )
-        workflow_invocation = self.get_invocation(trans, decoded_workflow_invocation_id)
+        workflow_invocation = self.get_invocation(
+            trans, decoded_workflow_invocation_id, check_ownership=False, check_accessible=True
+        )
         generator_plugin_type = kwd.get("generator_plugin_type")
         runtime_report_config_json = kwd.get("runtime_report_config_json")
         invocation_markdown = kwd.get("invocation_markdown", None)
@@ -433,7 +452,7 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         )
 
     def request_invocation_cancellation(self, trans, decoded_invocation_id: int):
-        workflow_invocation = self.get_invocation(trans, decoded_invocation_id)
+        workflow_invocation = self.get_invocation(trans, decoded_invocation_id, check_ownership=True)
         cancelled = workflow_invocation.cancel()
 
         if cancelled:
@@ -445,13 +464,18 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
 
         return workflow_invocation
 
-    def get_invocation_step(self, trans, decoded_workflow_invocation_step_id):
+    def get_invocation_step(
+        self, trans, decoded_workflow_invocation_step_id, check_ownership=True, check_accessible=True
+    ):
         try:
             workflow_invocation_step = trans.sa_session.get(WorkflowInvocationStep, decoded_workflow_invocation_step_id)
         except Exception:
             raise exceptions.ObjectNotFound()
         self.check_security(
-            trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False
+            trans,
+            workflow_invocation_step.workflow_invocation,
+            check_ownership=check_ownership,
+            check_accessible=check_accessible,
         )
         return workflow_invocation_step
 
@@ -490,6 +514,7 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         sort_by=None,
         sort_desc=None,
         include_nested_invocations=True,
+        check_ownership=True,
     ) -> Tuple[List, int]:
         """Get invocations owned by the current user."""
 
@@ -536,7 +561,7 @@ class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManager
         invocations = [
             inv
             for inv in trans.sa_session.scalars(stmt)
-            if self.check_security(trans, inv, check_ownership=True, check_accessible=False)
+            if self.check_security(trans, inv, check_ownership=check_ownership, check_accessible=True)
         ]
         return invocations, total_matches
 
@@ -571,8 +596,10 @@ class WorkflowSerializer(sharable.SharableModelSerializer):
 
 
 class WorkflowContentsManager(UsesAnnotations):
-    def __init__(self, app: MinimalManagerApp):
+
+    def __init__(self, app: MinimalManagerApp, trs_proxy: TrsProxy):
         self.app = app
+        self.trs_proxy = trs_proxy
         self._resource_mapper_function = get_resource_mapper_function(app)
 
     def ensure_raw_description(self, dict_or_raw_description):
@@ -591,7 +618,7 @@ class WorkflowContentsManager(UsesAnnotations):
         import_options = ImportOptions()
         import_options.deduplicate_subworkflows = True
         as_dict = python_to_workflow(as_dict, galaxy_interface, workflow_directory=None, import_options=import_options)
-        raw_description = RawWorkflowDescription(as_dict, path)
+        raw_description = RawWorkflowDescription(as_dict)
         created_workflow = self.build_workflow_from_raw_description(trans, raw_description, WorkflowCreateOptions())
         return created_workflow.workflow
 
@@ -620,9 +647,12 @@ class WorkflowContentsManager(UsesAnnotations):
             galaxy_interface = Format2ConverterGalaxyInterface()
             import_options = ImportOptions()
             import_options.deduplicate_subworkflows = True
-            as_dict = python_to_workflow(
-                as_dict, galaxy_interface, workflow_directory=workflow_directory, import_options=import_options
-            )
+            try:
+                as_dict = python_to_workflow(
+                    as_dict, galaxy_interface, workflow_directory=workflow_directory, import_options=import_options
+                )
+            except yaml.scanner.ScannerError as e:
+                raise exceptions.MalformedContents(str(e))
 
         return RawWorkflowDescription(as_dict, workflow_path)
 
@@ -784,18 +814,17 @@ class WorkflowContentsManager(UsesAnnotations):
         workflow.license = data.get("license")
         workflow.creator_metadata = data.get("creator")
 
-        if hasattr(workflow_state_resolution_options, "archive_source"):
-            if workflow_state_resolution_options.archive_source:
-                source_metadata = {}
-                if workflow_state_resolution_options.archive_source == "trs_tool":
-                    source_metadata["trs_tool_id"] = workflow_state_resolution_options.trs_tool_id
-                    source_metadata["trs_version_id"] = workflow_state_resolution_options.trs_version_id
-                    source_metadata["trs_server"] = workflow_state_resolution_options.trs_server
-                    source_metadata["trs_url"] = workflow_state_resolution_options.trs_url
-                elif not workflow_state_resolution_options.archive_source.startswith("file://"):  # URL import
-                    source_metadata["url"] = workflow_state_resolution_options.archive_source
-                workflow_state_resolution_options.archive_source = None  # so trs_id is not set for subworkflows
-                workflow.source_metadata = source_metadata  # type:ignore[assignment]
+        if getattr(workflow_state_resolution_options, "archive_source", None):
+            source_metadata = {}
+            if workflow_state_resolution_options.archive_source in ("trs_tool", "trs_url"):
+                source_metadata["trs_tool_id"] = workflow_state_resolution_options.trs_tool_id
+                source_metadata["trs_version_id"] = workflow_state_resolution_options.trs_version_id
+                source_metadata["trs_server"] = workflow_state_resolution_options.trs_server
+                source_metadata["trs_url"] = workflow_state_resolution_options.trs_url
+            elif not workflow_state_resolution_options.archive_source.startswith("file://"):  # URL import
+                source_metadata["url"] = workflow_state_resolution_options.archive_source
+            workflow_state_resolution_options.archive_source = None  # so trs_id is not set for subworkflows
+            workflow.source_metadata = source_metadata
 
         # Assume no errors until we find a step that has some
         workflow.has_errors = False
@@ -927,8 +956,9 @@ class WorkflowContentsManager(UsesAnnotations):
         return wf_dict
 
     def _sync_stored_workflow(self, trans, stored_workflow):
-        workflow_path = stored_workflow.from_path
-        self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)
+        if trans.user_is_admin:
+            workflow_path = stored_workflow.from_path
+            self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)
 
     def store_workflow_artifacts(self, directory, filename_base, workflow, **kwd):
         modern_workflow_path = os.path.join(directory, f"{filename_base}.gxwf.yml")
@@ -1047,6 +1077,7 @@ class WorkflowContentsManager(UsesAnnotations):
             step_models.append(step_model)
         return {
             "id": trans.app.security.encode_id(stored.id),
+            "workflow_id": trans.app.security.encode_id(workflow.id),
             "history_id": trans.app.security.encode_id(history.id) if history else None,
             "name": stored.name,
             "owner": stored.user.username,
@@ -1635,7 +1666,7 @@ class WorkflowContentsManager(UsesAnnotations):
         inputs = {}
         for step in workflow.input_steps:
             step_type = step.type
-            step_label = step.label or step.tool_inputs.get("name")
+            step_label = step.label or step.tool_inputs and step.tool_inputs.get("name")
             if step_label:
                 label = step_label
             elif step_type == "data_input":
@@ -1909,10 +1940,12 @@ class WorkflowContentsManager(UsesAnnotations):
                         if "output_name" not in conn_dict or "id" not in conn_dict:
                             template = "Invalid connection [%s] - must be dict with output_name and id fields."
                             message = template % conn_dict
-                            raise exceptions.MessageException(message)
+                            raise exceptions.MalformedContents(message)
                         external_id = conn_dict["id"]
                         if external_id not in steps_by_external_id:
-                            raise KeyError(f"Failed to find external id {external_id} in {steps_by_external_id.keys()}")
+                            raise exceptions.MalformedContents(
+                                f"Invalid connection. Failed to find input step id {external_id}"
+                            )
                         output_step = steps_by_external_id[external_id]
 
                         output_name = conn_dict["output_name"]
@@ -1929,7 +1962,7 @@ class WorkflowContentsManager(UsesAnnotations):
         to the actual `label` attribute which is available for all module types, unique, and mapped to its own database column.
         """
         if not module.label and module.type in ["data_input", "data_collection_input"]:
-            new_state = safe_loads(state)
+            new_state = safe_loads(state) or {}
             default_label = new_state.get("name")
             if default_label and util.unicodify(default_label).lower() not in [
                 "input dataset",
@@ -1950,7 +1983,7 @@ class WorkflowContentsManager(UsesAnnotations):
             dry_run=refactor_request.dry_run,
         )
 
-        module_injector = WorkflowModuleInjector(trans)
+        module_injector = WorkflowModuleInjector(trans, allow_tool_state_corrections=True)
         refactor_executor = WorkflowRefactorExecutor(raw_workflow_description, workflow, module_injector)
         action_executions = refactor_executor.refactor(refactor_request)
         refactored_workflow, errors = self.update_workflow_from_raw_description(
@@ -1986,6 +2019,73 @@ class WorkflowContentsManager(UsesAnnotations):
                 tools.extend(self.get_all_tools(step.subworkflow))
         return tools
 
+    def get_or_create_workflow_from_trs(
+        self,
+        trans: ProvidesUserContext,
+        trs_url: Optional[str],
+        trs_id: Optional[str] = None,
+        trs_version: Optional[str] = None,
+        trs_server: Optional[str] = None,
+    ):
+        user_id = trans.user and trans.user.id
+        assert user_id, "Cannot create workflow for anonymous user"
+        if not trs_url:
+            assert trs_server and trs_id and trs_version, "trs_url or trs_server, trs_version and trs_id must be passed"
+            server = self.trs_proxy.get_server(trs_server)
+            trs_url = server.get_trs_url(trs_id, trs_version)
+        else:
+            _, trs_id, trs_version = self.trs_proxy.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
+        assert trs_id and trs_version and trs_url
+
+        workflow = self.get_workflow_by_trs_id_and_version(trs_id=trs_id, trs_version=trs_version, user_id=user_id)
+        if not workflow:
+            workflow = self.create_workflow_from_trs_url(trans, trs_url, trs_server)
+        return workflow
+
+    def create_workflow_from_trs_url(
+        self, trans: ProvidesUserContext, trs_url: str, trs_server: Optional[str] = None
+    ) -> StoredWorkflow:
+        _, trs_tool_id, trs_version_id = self.trs_proxy.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
+        data = self.trs_proxy.get_version_from_trs_url(trs_url)
+        as_dict = yaml.safe_load(data)
+        raw_workflow_description = self.normalize_workflow_format(trans, as_dict)
+        created_workflow = self.build_workflow_from_raw_description(
+            trans,
+            raw_workflow_description,
+            WorkflowCreateOptions(
+                trs_tool_id=trs_tool_id,
+                trs_version_id=trs_version_id,
+                trs_url=trs_url,
+                trs_server=trs_server,
+                archive_source="trs_url",
+            ),
+        )
+        return created_workflow.stored_workflow
+
+    def get_workflow_by_trs_id_and_version(
+        self, trs_id: str, trs_version: str, user_id: Optional[int] = None
+    ) -> Optional[model.StoredWorkflow]:
+        sa_session = self.app.model.session
+
+        stmnt = (
+            select(model.StoredWorkflow)
+            .join(model.Workflow, model.Workflow.id == model.StoredWorkflow.latest_workflow_id)
+            .filter(
+                and_(
+                    model.StoredWorkflow.deleted == false(),
+                    to_json(sa_session, model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
+                    to_json(sa_session, model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
+                )
+            )
+        )
+        if user_id:
+            stmnt = stmnt.filter(
+                model.StoredWorkflow.user_id == user_id,
+            )
+        else:
+            stmnt = stmnt.filter(model.StoredWorkflow.importable == true())
+        return sa_session.execute(stmnt.order_by(model.StoredWorkflow.id.desc()).limit(1)).scalar()
+
 
 class RefactorRequest(RefactorActions):
     style: str = "export"
@@ -2041,11 +2141,11 @@ class WorkflowCreateOptions(WorkflowStateResolutionOptions):
     shed_tool_conf: Optional[str] = None
 
     # for workflows imported by archive source
-    archive_source: Optional[str] = ""
-    trs_tool_id: str = ""
-    trs_version_id: str = ""
-    trs_server: str = ""
-    trs_url: str = ""
+    archive_source: Optional[str] = None
+    trs_tool_id: Optional[str] = None
+    trs_version_id: Optional[str] = None
+    trs_server: Optional[str] = None
+    trs_url: Optional[str] = None
 
     @property
     def is_importable(self):
diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index eae836844ddc511cfa5f7ff0eee4a658a2f4f989..3f0117dcba5580e7bb9e9113a7216684cb792226 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -476,9 +476,10 @@ def set_metadata_portable(
                     # Can't happen, but type system doesn't know
                     raise Exception("object_store not built")
                 if not is_deferred and not link_data_only:
-                    object_store_update_actions.append(
-                        partial(push_if_necessary, object_store, dataset, external_filename)
-                    )
+                    if dataset_instance_id not in unnamed_id_to_path:
+                        object_store_update_actions.append(
+                            partial(push_if_necessary, object_store, dataset, external_filename)
+                        )
                     object_store_update_actions.append(partial(reset_external_filename, dataset))
                 object_store_update_actions.append(partial(dataset.set_total_size))
                 object_store_update_actions.append(partial(export_store.add_dataset, dataset))
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index ddd0b3024a5cd047a5d5fb44d452e40bc436cf67..7f04f987f813ebade0767cec99df300664dbe598 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -18,6 +18,7 @@ import random
 import string
 from collections import defaultdict
 from collections.abc import Callable
+from dataclasses import dataclass
 from datetime import (
     datetime,
     timedelta,
@@ -29,6 +30,7 @@ from string import Template
 from typing import (
     Any,
     cast,
+    ClassVar,
     Dict,
     Generic,
     Iterable,
@@ -66,8 +68,10 @@ from sqlalchemy import (
     bindparam,
     Boolean,
     case,
+    Cast,
     Column,
     column,
+    ColumnElement,
     DateTime,
     delete,
     desc,
@@ -98,7 +102,11 @@ from sqlalchemy import (
     update,
     VARCHAR,
 )
-from sqlalchemy.exc import OperationalError
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.exc import (
+    CompileError,
+    OperationalError,
+)
 from sqlalchemy.ext import hybrid
 from sqlalchemy.ext.associationproxy import (
     association_proxy,
@@ -159,7 +167,7 @@ from galaxy.model.item_attrs import (
 )
 from galaxy.model.orm.now import now
 from galaxy.model.orm.util import add_object_to_object_session
-from galaxy.objectstore import ObjectStorePopulator
+from galaxy.objectstore import USER_OBJECTS_SCHEME
 from galaxy.objectstore.templates import (
     ObjectStoreConfiguration,
     ObjectStoreTemplate,
@@ -176,6 +184,7 @@ from galaxy.schema.schema import (
     DatasetValidatedState,
     InvocationsStateCounts,
     JobState,
+    ToolRequestState,
 )
 from galaxy.schema.workflow.comments import WorkflowCommentModel
 from galaxy.security import get_permitted_actions
@@ -192,6 +201,7 @@ from galaxy.util import (
 )
 from galaxy.util.config_templates import (
     EnvironmentDict,
+    ImplicitConfigurationParameters,
     SecretsDict,
     Template as ConfigTemplate,
     TemplateEnvironment,
@@ -212,6 +222,7 @@ from galaxy.util.form_builder import (
     WorkflowMappingField,
 )
 from galaxy.util.hash_util import (
+    HashFunctionNameEnum,
     md5_hash_str,
     new_insecure_hash,
 )
@@ -219,6 +230,13 @@ from galaxy.util.json import safe_loads
 from galaxy.util.sanitize_html import sanitize_html
 
 if TYPE_CHECKING:
+    from sqlalchemy.sql.expression import BindParameter
+
+    from galaxy.objectstore import (
+        BaseObjectStore,
+        ObjectStorePopulator,
+        QuotaSourceMap,
+    )
     from galaxy.schema.invocation import InvocationMessageUnion
 
 log = logging.getLogger(__name__)
@@ -305,6 +323,19 @@ def get_uuid(uuid: Optional[Union[UUID, str]] = None) -> UUID:
     return UUID(str(uuid))
 
 
+def to_json(sa_session, column, keys: List[str]):
+    assert sa_session.bind
+    if sa_session.bind.dialect.name == "postgresql":
+        cast: Union[ColumnElement[Any], Cast[Any]] = func.cast(func.convert_from(column, "UTF8"), JSONB)
+        for key in keys:
+            cast = cast.__getitem__(key)
+        return cast.astext
+    else:
+        for key in keys:
+            column = func.json_extract(column, f"$.{key}")
+        return column
+
+
 class Base(DeclarativeBase, _HasTable):
     __abstract__ = True
     metadata = MetaData(naming_convention=NAMING_CONVENTION)
@@ -641,13 +672,14 @@ FROM dataset
 LEFT OUTER JOIN library_dataset_dataset_association ON dataset.id = library_dataset_dataset_association.dataset_id
 WHERE dataset.id IN (SELECT dataset_id FROM per_hist_hdas)
     AND library_dataset_dataset_association.id IS NULL
+    AND (dataset.object_store_id NOT LIKE '{user_objects_scheme}%' OR dataset.object_store_id IS NULL)
     {and_dataset_condition}
 """
 
 
-def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False):
+def calculate_user_disk_usage_statements(user_id: int, quota_source_map: "QuotaSourceMap", for_sqlite: bool = False):
     """Standalone function so can be reused for postgres directly in pgcleanup.py."""
-    statements = []
+    statements: List[Tuple[str, Dict[str, Any]]] = []
     default_quota_enabled = quota_source_map.default_quota_enabled
     default_exclude_ids = quota_source_map.default_usage_excluded_ids()
     default_cond = "dataset.object_store_id IS NULL" if default_quota_enabled and default_exclude_ids else ""
@@ -656,12 +688,14 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     default_usage_dataset_condition = f"{default_cond} {use_or} {exclude_cond}"
     if default_usage_dataset_condition.strip():
         default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )"
-    default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)
+    default_usage = UNIQUE_DATASET_USER_USAGE.format(
+        and_dataset_condition=default_usage_dataset_condition, user_objects_scheme=USER_OBJECTS_SCHEME
+    )
     default_usage = f"""
 UPDATE galaxy_user SET disk_usage = ({default_usage})
 WHERE id = :id
 """
-    params = {"id": user_id}
+    params: Dict[str, Any] = {"id": user_id}
     if default_exclude_ids:
         params["exclude_object_store_ids"] = default_exclude_ids
     statements.append((default_usage, params))
@@ -670,7 +704,8 @@ WHERE id = :id
     # the object_store_id to quota_source_label into a temp table of values
     for quota_source_label, object_store_ids in source.items():
         label_usage = UNIQUE_DATASET_USER_USAGE.format(
-            and_dataset_condition="AND ( dataset.object_store_id IN :include_object_store_ids )"
+            and_dataset_condition="AND ( dataset.object_store_id IN :include_object_store_ids )",
+            user_objects_scheme=USER_OBJECTS_SCHEME,
         )
         if for_sqlite:
             # hacky alternative for older sqlite
@@ -776,7 +811,7 @@ class User(Base, Dictifiable, RepresentById):
     id: Mapped[int] = mapped_column(primary_key=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
-    email: Mapped[str] = mapped_column(TrimmedString(255), index=True)
+    email: Mapped[str] = mapped_column(TrimmedString(255), index=True, unique=True)
     username: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True, unique=True)
     password: Mapped[str] = mapped_column(TrimmedString(255))
     last_password_change: Mapped[Optional[datetime]] = mapped_column(default=now)
@@ -793,8 +828,8 @@ class User(Base, Dictifiable, RepresentById):
     addresses: Mapped[List["UserAddress"]] = relationship(
         back_populates="user", order_by=lambda: desc(UserAddress.update_time), cascade_backrefs=False
     )
-    cloudauthz: Mapped[List["CloudAuthz"]] = relationship(back_populates="user")
     custos_auth: Mapped[List["CustosAuthnzToken"]] = relationship(back_populates="user")
+    chat_exchanges: Mapped[List["ChatExchange"]] = relationship(back_populates="user")
     default_permissions: Mapped[List["DefaultUserPermissions"]] = relationship(back_populates="user")
     groups: Mapped[List["UserGroupAssociation"]] = relationship(back_populates="user")
     histories: Mapped[List["History"]] = relationship(
@@ -846,14 +881,6 @@ class User(Base, Dictifiable, RepresentById):
     all_notifications: Mapped[List["UserNotificationAssociation"]] = relationship(
         back_populates="user", cascade_backrefs=False
     )
-    non_private_roles: Mapped[List["UserRoleAssociation"]] = relationship(
-        viewonly=True,
-        primaryjoin=(
-            lambda: (User.id == UserRoleAssociation.user_id)
-            & (UserRoleAssociation.role_id == Role.id)
-            & not_(Role.name == User.email)
-        ),
-    )
 
     preferences: AssociationProxy[Any]
 
@@ -895,8 +922,8 @@ class User(Base, Dictifiable, RepresentById):
                 Dataset.state == "ok",
                 # excludes data manager runs that actually populated tables.
                 # maybe track this formally by creating a different datatype for bundles ?
-                Dataset.total_size != Dataset.file_size,
                 HistoryDatasetAssociation._metadata.contains(data_table),
+                to_json(session, HistoryDatasetAssociation._metadata, ["is_bundle"]) == "true",
             )
             .order_by(HistoryDatasetAssociation.id)
         )
@@ -1123,7 +1150,9 @@ ON CONFLICT
             if exclude_objectstore_ids
             else ""
         )
-        default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)
+        default_usage = UNIQUE_DATASET_USER_USAGE.format(
+            and_dataset_condition=default_usage_dataset_condition, user_objects_scheme=USER_OBJECTS_SCHEME
+        )
         sql_calc = text(default_usage)
         params = {"id": self.id}
         bindparams = [bindparam("id")]
@@ -1135,13 +1164,13 @@ ON CONFLICT
         usage = sa_session.scalar(sql_calc, params)
         return usage
 
-    def calculate_and_set_disk_usage(self, object_store):
+    def calculate_and_set_disk_usage(self, object_store: "BaseObjectStore"):
         """
         Calculates and sets user disk usage.
         """
         self._calculate_or_set_disk_usage(object_store=object_store)
 
-    def _calculate_or_set_disk_usage(self, object_store):
+    def _calculate_or_set_disk_usage(self, object_store: "BaseObjectStore"):
         """
         Utility to calculate and return the disk usage.  If dryrun is False,
         the new value is set immediately.
@@ -1149,11 +1178,13 @@ ON CONFLICT
         assert object_store is not None
         quota_source_map = object_store.get_quota_source_map()
         sa_session = object_session(self)
+        assert sa_session
+        assert sa_session.bind
         for_sqlite = "sqlite" in sa_session.bind.dialect.name
         statements = calculate_user_disk_usage_statements(self.id, quota_source_map, for_sqlite)
         for sql, args in statements:
             statement = text(sql)
-            binds = []
+            binds: List[BindParameter] = []
             for key, _ in args.items():
                 expand_binding = key.endswith("s")
                 binds.append(bindparam(key, expanding=expand_binding))
@@ -1230,10 +1261,7 @@ ON CONFLICT
 
     def attempt_create_private_role(self):
         session = object_session(self)
-        role_name = self.email
-        role_desc = f"Private Role for {self.email}"
-        role_type = Role.types.PRIVATE
-        role = Role(name=role_name, description=role_desc, type=role_type)
+        role = Role(type=Role.types.PRIVATE)
         assoc = UserRoleAssociation(self, role)
         session.add(assoc)
         with transaction(session):
@@ -1333,6 +1361,30 @@ class PasswordResetToken(Base):
         self.expiration_time = now() + timedelta(hours=24)
 
 
+class ToolSource(Base, Dictifiable, RepresentById):
+    __tablename__ = "tool_source"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    hash: Mapped[Optional[str]] = mapped_column(Unicode(255))
+    source: Mapped[dict] = mapped_column(JSONType)
+
+
+class ToolRequest(Base, Dictifiable, RepresentById):
+    __tablename__ = "tool_request"
+
+    states: TypeAlias = ToolRequestState
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    tool_source_id: Mapped[int] = mapped_column(ForeignKey("tool_source.id"), index=True)
+    history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)
+    request: Mapped[dict] = mapped_column(JSONType)
+    state: Mapped[Optional[str]] = mapped_column(TrimmedString(32), index=True)
+    state_message: Mapped[Optional[str]] = mapped_column(JSONType, index=True)
+
+    tool_source: Mapped["ToolSource"] = relationship()
+    history: Mapped[Optional["History"]] = relationship(back_populates="tool_requests")
+
+
 class DynamicTool(Base, Dictifiable, RepresentById):
     __tablename__ = "dynamic_tool"
 
@@ -1429,7 +1481,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, index=True, nullable=True)
     history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)
     library_folder_id: Mapped[Optional[int]] = mapped_column(ForeignKey("library_folder.id"), index=True)
-    tool_id: Mapped[Optional[str]] = mapped_column(String(255))
+    tool_id: Mapped[Optional[str]] = mapped_column(String(255), index=True)
     tool_version: Mapped[Optional[str]] = mapped_column(TEXT, default="1.0.0")
     galaxy_version: Mapped[Optional[str]] = mapped_column(String(64), default=None)
     dynamic_tool_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dynamic_tool.id"), index=True)
@@ -1460,7 +1512,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     preferred_object_store_id: Mapped[Optional[str]] = mapped_column(String(255))
     object_store_id_overrides: Mapped[Optional[STR_TO_STR_DICT]] = mapped_column(JSONType)
     stopped: Mapped[Optional[bool]] = mapped_column(default=False, index=True)
+    tool_request_id: Mapped[Optional[int]] = mapped_column(ForeignKey("tool_request.id"), index=True)
 
+    tool_request: Mapped[Optional["ToolRequest"]] = relationship()
     user: Mapped[Optional["User"]] = relationship()
     galaxy_session: Mapped[Optional["GalaxySession"]] = relationship()
     history: Mapped[Optional["History"]] = relationship(back_populates="jobs")
@@ -1523,6 +1577,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         "galaxy_version",
         "command_version",
         "copied_from_job_id",
+        "user_id",
     ]
 
     _numeric_metric = JobMetricNumeric
@@ -1871,7 +1926,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
             self.state = Job.states.STOPPED
         self.stopped = True
 
-    def mark_deleted(self, track_jobs_in_database=False):
+    def mark_deleted(self, track_jobs_in_database=False, message=None):
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
@@ -1882,7 +1937,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
             self.state = Job.states.DELETING
         else:
             self.state = Job.states.DELETED
-        self.info = "Job output deleted by user before job completed."
+        info = message or "Job output deleted by user before job completed."
+        self.info = info
         for jtoda in self.output_datasets:
             output_hda = jtoda.dataset
             output_hda.deleted = True
@@ -1892,7 +1948,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
                 shared_hda.deleted = True
                 shared_hda.blurb = "deleted"
                 shared_hda.peek = "Job deleted"
-                shared_hda.info = "Job output deleted by user before job completed"
+                shared_hda.info = info
 
     def mark_failed(self, info="Job execution failed", blurb=None, peek=None):
         """
@@ -2630,7 +2686,7 @@ class PostJobAction(Base, RepresentById):
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
     action_type: Mapped[str] = mapped_column(String(255))
     output_name: Mapped[Optional[str]] = mapped_column(String(255))
-    action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    _action_arguments: Mapped[Optional[Dict[str, Any]]] = mapped_column("action_arguments", MutableJSONType)
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(
         back_populates="post_job_actions",
         primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id),
@@ -2643,6 +2699,18 @@ class PostJobAction(Base, RepresentById):
         self.workflow_step = workflow_step
         ensure_object_added_to_session(self, object_in_session=workflow_step)
 
+    @property
+    def action_arguments(self):
+        if self.action_type in ("HideDatasetAction", "DeleteIntermediatesAction") and self._action_arguments is True:
+            # Fix up broken workflows resulting from imports with gxformat2 <= 0.20.0
+            return {}
+        else:
+            return self._action_arguments
+
+    @action_arguments.setter
+    def action_arguments(self, value: Dict[str, Any]):
+        self._action_arguments = value
+
 
 class PostJobActionAssociation(Base, RepresentById):
     __tablename__ = "post_job_action_association"
@@ -2712,11 +2780,13 @@ class JobExternalOutputMetadata(Base, RepresentById):
 class FakeDatasetAssociation:
     fake_dataset_association = True
 
-    def __init__(self, dataset=None):
+    def __init__(self, dataset: Optional["Dataset"] = None) -> None:
         self.dataset = dataset
-        self.metadata = {}
+        self.metadata: Dict = {}
+        self.has_deferred_data = False
 
-    def get_file_name(self, sync_cache=True, user=None):
+    def get_file_name(self, sync_cache: bool = True, user=None) -> str:
+        assert self.dataset
         return self.dataset.get_file_name(sync_cache, user)
 
     def __eq__(self, other):
@@ -2916,8 +2986,7 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
     @property
     def active(self):
         if self.configured and not self.deleted:
-            # FIXME: don't included queued?
-            return not self.job.finished
+            return self.job.running
         return False
 
     @property
@@ -2945,6 +3014,43 @@ class GenomeIndexToolData(Base, RepresentById):  # TODO: params arg is lost
     user: Mapped[Optional["User"]] = relationship()
 
 
+class ChatExchange(Base, RepresentById):
+
+    __tablename__ = "chat_exchange"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=False)
+    job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True, nullable=True)
+
+    user: Mapped["User"] = relationship(back_populates="chat_exchanges")
+    messages: Mapped[List["ChatExchangeMessage"]] = relationship(back_populates="chat_exchange")
+
+    def __init__(self, user, job_id=None, message=None, **kwargs):
+        self.user = user
+        self.job_id = job_id
+        self.messages = []
+        if message:
+            self.add_message(message)
+
+    def add_message(self, message):
+        self.messages.append(ChatExchangeMessage(message=message))
+
+
+class ChatExchangeMessage(Base, RepresentById):
+    __tablename__ = "chat_exchange_message"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    chat_exchange_id: Mapped[int] = mapped_column(ForeignKey("chat_exchange.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(default=now)
+    message: Mapped[str] = mapped_column(Text)
+    feedback: Mapped[Optional[int]] = mapped_column(Integer)
+    chat_exchange: Mapped["ChatExchange"] = relationship("ChatExchange", back_populates="messages")
+
+    def __init__(self, message, feedback=None):
+        self.message = message
+        self.feedback = feedback
+
+
 class Group(Base, Dictifiable, RepresentById):
     __tablename__ = "galaxy_group"
 
@@ -2967,10 +3073,11 @@ class Group(Base, Dictifiable, RepresentById):
 
 class UserGroupAssociation(Base, RepresentById):
     __tablename__ = "user_group_association"
+    __table_args__ = (UniqueConstraint("user_id", "group_id"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    group_id: Mapped[int] = mapped_column(ForeignKey("galaxy_group.id"), index=True, nullable=True)
+    user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    group_id: Mapped[int] = mapped_column(ForeignKey("galaxy_group.id"), index=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
     user: Mapped["User"] = relationship(back_populates="groups")
@@ -3184,6 +3291,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
     )
     user: Mapped[Optional["User"]] = relationship(back_populates="histories")
     jobs: Mapped[List["Job"]] = relationship(back_populates="history", cascade_backrefs=False)
+    tool_requests: Mapped[List["ToolRequest"]] = relationship(back_populates="history")
 
     update_time = column_property(
         select(func.max(HistoryAudit.update_time)).where(HistoryAudit.history_id == id).scalar_subquery(),
@@ -3283,16 +3391,21 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         table = self.__table__
         history_id = cached_id(self)
         update_stmt = update(table).where(table.c.id == history_id).values(hid_counter=table.c.hid_counter + n)
+        update_returning_stmnt = update_stmt.returning(table.c.hid_counter)
 
-        with engine.begin() as conn:
-            if engine.name in ["postgres", "postgresql"]:
-                stmt = update_stmt.returning(table.c.hid_counter)
-                updated_hid = conn.execute(stmt).scalar()
-                hid = updated_hid - n
-            else:
-                select_stmt = select(table.c.hid_counter).where(table.c.id == history_id).with_for_update()
-                hid = conn.execute(select_stmt).scalar()
-                conn.execute(update_stmt)
+        if engine.name != "sqlite":
+            with engine.begin() as conn:
+                hid = conn.execute(update_returning_stmnt).scalar() - n
+        else:
+            try:
+                hid = session.execute(update_returning_stmnt).scalar() - n
+            except (CompileError, OperationalError):
+                # The RETURNING clause was added to SQLite in version 3.35.0.
+                # Not using FOR UPDATE either, since that was added in 3.45.0,
+                # and anyway does a whole-table lock
+                select_stmt = select(table.c.hid_counter).where(table.c.id == history_id)
+                hid = session.execute(select_stmt).scalar()
+                session.execute(update_stmt)
 
         session.expire(self, ["hid_counter"])
         return hid
@@ -3619,6 +3732,10 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         """Return all active contents ordered by hid."""
         return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)
 
+    @property
+    def visible_contents(self):
+        return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)
+
     def contents_iter(self, **kwds):
         """
         Fetch filtered list of contents of history.
@@ -3685,10 +3802,11 @@ class HistoryUserShareAssociation(Base, UserShareAssociation):
 
 class UserRoleAssociation(Base, RepresentById):
     __tablename__ = "user_role_association"
+    __table_args__ = (UniqueConstraint("user_id", "role_id"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True, nullable=True)
-    role_id: Mapped[int] = mapped_column(ForeignKey("role.id"), index=True, nullable=True)
+    user_id: Mapped[int] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    role_id: Mapped[int] = mapped_column(ForeignKey("role.id"), index=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
 
@@ -3703,10 +3821,11 @@ class UserRoleAssociation(Base, RepresentById):
 
 class GroupRoleAssociation(Base, RepresentById):
     __tablename__ = "group_role_association"
+    __table_args__ = (UniqueConstraint("group_id", "role_id"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    group_id: Mapped[int] = mapped_column(ForeignKey("galaxy_group.id"), index=True, nullable=True)
-    role_id: Mapped[int] = mapped_column(ForeignKey("role.id"), index=True, nullable=True)
+    group_id: Mapped[int] = mapped_column(ForeignKey("galaxy_group.id"), index=True)
+    role_id: Mapped[int] = mapped_column(ForeignKey("role.id"), index=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
     group: Mapped["Group"] = relationship(back_populates="roles")
@@ -3724,7 +3843,7 @@ class Role(Base, Dictifiable, RepresentById):
     id: Mapped[int] = mapped_column(primary_key=True)
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, nullable=True)
-    name: Mapped[Optional[str]] = mapped_column(String(255), index=True, unique=True)
+    name: Mapped[str] = mapped_column(String(255), index=True)
     description: Mapped[Optional[str]] = mapped_column(TEXT)
     type: Mapped[Optional[str]] = mapped_column(String(40), index=True)
     deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False)
@@ -3743,8 +3862,12 @@ class Role(Base, Dictifiable, RepresentById):
         ADMIN = "admin"
         SHARING = "sharing"
 
+    @staticmethod
+    def default_name(role_type):
+        return f"{role_type.value} role"
+
     def __init__(self, name=None, description=None, type=types.SYSTEM, deleted=False):
-        self.name = name
+        self.name = name or Role.default_name(type)
         self.description = description
         self.type = type
         self.deleted = deleted
@@ -4045,12 +4168,13 @@ class StorableObject:
                 sa_session.commit()
 
 
-def setup_global_object_store_for_models(object_store):
+def setup_global_object_store_for_models(object_store: "BaseObjectStore") -> None:
     Dataset.object_store = object_store
 
 
 class Dataset(Base, StorableObject, Serializable):
     __tablename__ = "dataset"
+    __table_args__ = (UniqueConstraint("uuid", name="uq_uuid_column"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
     job_id: Mapped[Optional[int]] = mapped_column(ForeignKey("job.id"), index=True)
@@ -4066,7 +4190,7 @@ class Dataset(Base, StorableObject, Serializable):
     created_from_basename: Mapped[Optional[str]] = mapped_column(TEXT)
     file_size: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0))
     total_size: Mapped[Optional[Decimal]] = mapped_column(Numeric(15, 0))
-    uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType())
+    uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType(), unique=True)
 
     actions: Mapped[List["DatasetPermissions"]] = relationship(back_populates="dataset")
     job: Mapped[Optional["Job"]] = relationship(primaryjoin=(lambda: Dataset.job_id == Job.id))
@@ -4114,7 +4238,9 @@ class Dataset(Base, StorableObject, Serializable):
 
     non_ready_states = (states.NEW, states.UPLOAD, states.QUEUED, states.RUNNING, states.SETTING_METADATA)
     ready_states = tuple(set(states.__members__.values()) - set(non_ready_states))
-    valid_input_states = tuple(set(states.__members__.values()) - {states.ERROR, states.DISCARDED})
+    valid_input_states = tuple(
+        set(states.__members__.values()) - {states.ERROR, states.DISCARDED, states.FAILED_METADATA}
+    )
     no_data_states = (states.PAUSED, states.DEFERRED, states.DISCARDED, *non_ready_states)
     terminal_states = (
         states.OK,
@@ -4137,7 +4263,9 @@ class Dataset(Base, StorableObject, Serializable):
 
     permitted_actions = get_permitted_actions(filter="DATASET")
     file_path = "/tmp/"
-    object_store = None  # This get initialized in mapping.py (method init) by app.py
+    object_store: ClassVar[Optional["BaseObjectStore"]] = (
+        None  # This get initialized in mapping.py (method init) by app.py
+    )
     engine = None
 
     def __init__(
@@ -4171,7 +4299,7 @@ class Dataset(Base, StorableObject, Serializable):
         return self.state in self.ready_states
 
     @property
-    def shareable(self):
+    def shareable(self) -> bool:
         """Return True if placed into an objectstore not labeled as ``private``."""
         if self.external_filename:
             return True
@@ -4183,7 +4311,7 @@ class Dataset(Base, StorableObject, Serializable):
         if not self.shareable:
             raise Exception(CANNOT_SHARE_PRIVATE_DATASET_MESSAGE)
 
-    def get_file_name(self, sync_cache=True, user=None):
+    def get_file_name(self, sync_cache: bool = True, user=None) -> str:
         if self.purged:
             log.warning(f"Attempt to get file name of purged dataset {self.id}")
             return ""
@@ -4229,20 +4357,19 @@ class Dataset(Base, StorableObject, Serializable):
         else:
             self.external_filename = filename
 
-    def _assert_object_store_set(self):
-        assert self.object_store is not None, f"Object Store has not been initialized for dataset {self.id}"
+    def _assert_object_store_set(self) -> "BaseObjectStore":
+        assert self.object_store is not None, "Object Store has not been initialized"
         return self.object_store
 
-    def get_extra_files_path(self):
+    def get_extra_files_path(self) -> str:
         # Unlike get_file_name - external_extra_files_path is not backed by an
         # actual database column so if SA instantiates this object - the
         # attribute won't exist yet.
         if not getattr(self, "external_extra_files_path", None):
-            if self.object_store.exists(self, dir_only=True, extra_dir=self._extra_files_rel_path):
-                return self.object_store.get_filename(self, dir_only=True, extra_dir=self._extra_files_rel_path)
-            return self.object_store.construct_path(
-                self, dir_only=True, extra_dir=self._extra_files_rel_path, in_cache=True
-            )
+            object_store = self._assert_object_store_set()
+            if object_store.exists(self, dir_only=True, extra_dir=self._extra_files_rel_path):
+                return object_store.get_filename(self, dir_only=True, extra_dir=self._extra_files_rel_path)
+            return object_store.construct_path(self, dir_only=True, extra_dir=self._extra_files_rel_path, in_cache=True)
         else:
             return os.path.abspath(self.external_extra_files_path)
 
@@ -4287,7 +4414,7 @@ class Dataset(Base, StorableObject, Serializable):
             except OSError:
                 return 0
         assert self.object_store
-        return self.object_store.size(self)  # type:ignore[unreachable]
+        return self.object_store.size(self)
 
     @overload
     def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int: ...
@@ -4465,7 +4592,17 @@ class DatasetSource(Base, Dictifiable, Serializable):
         return new_source
 
 
-class DatasetSourceHash(Base, Serializable):
+class HasHashFunctionName:
+    hash_function: Mapped[Optional[str]]
+
+    @property
+    def hash_func_name(self) -> HashFunctionNameEnum:
+        as_str = self.hash_function
+        assert as_str
+        return HashFunctionNameEnum(self.hash_function)
+
+
+class DatasetSourceHash(Base, Serializable, HasHashFunctionName):
     __tablename__ = "dataset_source_hash"
 
     id: Mapped[int] = mapped_column(primary_key=True)
@@ -4490,7 +4627,7 @@ class DatasetSourceHash(Base, Serializable):
         return new_hash
 
 
-class DatasetHash(Base, Dictifiable, Serializable):
+class DatasetHash(Base, Dictifiable, Serializable, HasHashFunctionName):
     __tablename__ = "dataset_hash"
 
     id: Mapped[int] = mapped_column(primary_key=True)
@@ -4519,6 +4656,15 @@ class DatasetHash(Base, Dictifiable, Serializable):
         new_hash.extra_files_path = self.extra_files_path
         return new_hash
 
+    @property
+    def hash_func_name(self) -> HashFunctionNameEnum:
+        as_str = self.hash_function
+        assert as_str
+        return HashFunctionNameEnum(self.hash_function)
+
+
+DescribesHash = Union[DatasetSourceHash, DatasetHash]
+
 
 def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
     if extension is not None:
@@ -4535,7 +4681,7 @@ def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
 
 
 class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
-    """A base class for all 'dataset instances', HDAs, LDAs, etc"""
+    """A base class for all 'dataset instances', HDAs, LDDAs, etc"""
 
     states = Dataset.states
     _state: Optional[str]
@@ -4545,6 +4691,9 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
     creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]
     copied_from_history_dataset_association: Optional["HistoryDatasetAssociation"]
     copied_from_library_dataset_dataset_association: Optional["LibraryDatasetDatasetAssociation"]
+    dependent_jobs: List[JobToInputLibraryDatasetAssociation]
+    implicitly_converted_datasets: List["ImplicitlyConvertedDatasetAssociation"]
+    implicitly_converted_parent_datasets: List["ImplicitlyConvertedDatasetAssociation"]
 
     validated_states = DatasetValidatedState
 
@@ -4633,6 +4782,13 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
     def has_deferred_data(self):
         return self.dataset.state == Dataset.states.DEFERRED
 
+    @property
+    def deferred_source_uri(self):
+        if self.has_deferred_data and self.sources:
+            # Assuming the first source is the deferred source
+            return self.sources[0].source_uri
+        return None
+
     @property
     def state(self):
         # self._state holds state that should only affect this particular dataset association, not the dataset state itself
@@ -4665,18 +4821,21 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
 
     quota_source_label = property(get_quota_source_label)
 
-    def set_skipped(self, object_store_populator: ObjectStorePopulator):
+    def set_skipped(self, object_store_populator: "ObjectStorePopulator") -> None:
         assert self.dataset
         object_store_populator.set_object_store_id(self)
         self.extension = "expression.json"
         self.state = self.states.OK
         self.blurb = "skipped"
         self.visible = False
+        null = json.dumps(None)
         with open(self.dataset.get_file_name(), "w") as out:
-            out.write(json.dumps(None))
+            out.write(null)
+        self.peek = null
         self.set_total_size()
 
-    def get_file_name(self, sync_cache=True, user=None) -> str:
+
+    def get_file_name(self, sync_cache: bool = True, user=None) -> str:
         if self.dataset.purged:
             return ""
         return self.dataset.get_file_name(sync_cache=sync_cache, user=user)
@@ -4869,12 +5028,17 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
     def display_info(self):
         return self.datatype.display_info(self)
 
-    def get_converted_files_by_type(self, file_type):
+    def get_converted_files_by_type(self, file_type, include_errored=False):
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and assoc.type == file_type:
-                if assoc.dataset:
-                    return assoc.dataset
-                return assoc.dataset_ldda
+                item = assoc.dataset or assoc.dataset_ldda
+                valid_states = (
+                    (Dataset.states.ERROR, *Dataset.valid_input_states)
+                    if include_errored
+                    else Dataset.valid_input_states
+                )
+                if not item.deleted and item.state in valid_states:
+                    return item
         return None
 
     def get_converted_dataset_deps(self, trans, target_ext):
@@ -4888,7 +5052,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
             depends_list = []
         return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}
 
-    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
+    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):
         """
         Return converted dataset(s) if they exist, along with a dict of dependencies.
         If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -4900,7 +5064,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
         converted_dataset = self.get_metadata_dataset(target_ext)
         if converted_dataset:
             return converted_dataset
-        converted_dataset = self.get_converted_files_by_type(target_ext)
+        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)
         if converted_dataset:
             return converted_dataset
         deps = {}
@@ -5124,7 +5288,8 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
 
         # Get converted dataset; this will start the conversion if necessary.
         try:
-            converted_dataset = self.get_converted_dataset(trans, target_type)
+            # Include errored datasets here, we let user chose to retry or view error
+            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)
         except NoConverterException:
             return self.conversion_messages.NO_CONVERTER
         except ConverterDependencyException as dep_error:
@@ -5276,6 +5441,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         if include_tags and self.history:
             self.copy_tags_from(self.user, other_hda)
         self.dataset = new_dataset or other_hda.dataset
+        self.copied_from_history_dataset_association_id = other_hda.id
         if old_dataset:
             old_dataset.full_delete(user=self.user)
 
@@ -5335,7 +5501,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
         roles=None,
         ldda_message="",
         element_identifier=None,
-    ):
+    ) -> "LibraryDatasetDatasetAssociation":
         """
         Copy this HDA to a library optionally replacing an existing LDDA.
         """
@@ -5369,7 +5535,9 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             user=user,
         )
         library_dataset.library_dataset_dataset_association = ldda
-        object_session(self).add(library_dataset)
+        session = object_session(self)
+        assert session
+        session.add(library_dataset)
         # If roles were selected on the upload form, restrict access to the Dataset to those roles
         roles = roles or []
         for role in roles:
@@ -5379,7 +5547,6 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             trans.sa_session.add(dp)
         # Must set metadata after ldda flushed, as MetadataFiles require ldda.id
         if self.set_metadata_requires_flush:
-            session = object_session(self)
             with transaction(session):
                 session.commit()
         ldda.metadata = self.metadata
@@ -5388,10 +5555,9 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             ldda.message = ldda_message
         if not replace_dataset:
             target_folder.add_library_dataset(library_dataset, genome_build=ldda.dbkey)
-            object_session(self).add(target_folder)
-        object_session(self).add(library_dataset)
+            session.add(target_folder)
+        session.add(library_dataset)
 
-        session = object_session(self)
         with transaction(session):
             session.commit()
 
@@ -5985,6 +6151,8 @@ class LibraryDataset(Base, Serializable):
 
 
 class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
+    message: Mapped[Optional[str]]
+    tags: Mapped[List["LibraryDatasetDatasetAssociationTagAssociation"]]
 
     def __init__(
         self,
@@ -5999,7 +6167,9 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
         self.library_dataset = library_dataset
         self.user = user
 
-    def to_history_dataset_association(self, target_history, parent_id=None, add_to_history=False, visible=None):
+    def to_history_dataset_association(
+        self, target_history, parent_id=None, add_to_history=False, visible=None, commit=True
+    ):
         sa_session = object_session(self)
         hda = HistoryDatasetAssociation(
             name=self.name,
@@ -6023,9 +6193,12 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
         sa_session.add(hda)
         hda.metadata = self.metadata
         if add_to_history and target_history:
-            target_history.add_dataset(hda)
-        with transaction(sa_session):
-            sa_session.commit()
+            target_history.stage_addition(hda)
+            if commit:
+                target_history.add_pending_items()
+        if commit:
+            with transaction(sa_session):
+                sa_session.commit()
         return hda
 
     def copy(self, parent_id=None, target_folder=None, flush=True):
@@ -6895,11 +7068,6 @@ class HistoryDatasetCollectionAssociation(
         primaryjoin=copied_from_history_dataset_collection_association_id == id,
         remote_side=[id],
         uselist=False,
-        back_populates="copied_to_history_dataset_collection_association",
-    )
-    copied_to_history_dataset_collection_association = relationship(
-        "HistoryDatasetCollectionAssociation",
-        back_populates="copied_from_history_dataset_collection_association",
     )
     implicit_input_collections: Mapped[List["ImplicitlyCreatedDatasetCollectionInput"]] = relationship(
         primaryjoin=(
@@ -7604,7 +7772,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
         order_by=lambda: -Workflow.id,
         cascade_backrefs=False,
     )
-    latest_workflow = relationship(
+    latest_workflow: Mapped["Workflow"] = relationship(
         "Workflow",
         post_update=True,
         primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),
@@ -7645,6 +7813,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
 
     dict_collection_visible_keys = [
         "id",
+        "latest_workflow_id",
         "name",
         "create_time",
         "update_time",
@@ -7655,6 +7824,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
     ]
     dict_element_visible_keys = [
         "id",
+        "latest_workflow_id",
         "name",
         "create_time",
         "update_time",
@@ -7694,6 +7864,16 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
             raise galaxy.exceptions.RequestParameterInvalidException("Version does not exist")
         return list(reversed(self.workflows))[version]
 
+    def get_internal_version_by_id(self, workflow_instance_id: int):
+        sa_session = object_session(self)
+        assert sa_session
+        workflow = sa_session.get(Workflow, workflow_instance_id)
+        if not workflow:
+            raise galaxy.exceptions.ObjectNotFound()
+        elif workflow.stored_workflow != self:
+            raise galaxy.exceptions.RequestParameterInvalidException()
+        return workflow
+
     def version_of(self, workflow):
         for version, workflow_instance in enumerate(reversed(self.workflows)):
             if workflow_instance.id == workflow.id:
@@ -7710,7 +7890,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
         )
         return bool(sa_session.scalar(stmt))
 
-    def copy_tags_from(self, target_user, source_workflow):
+    def copy_tags_from(self, target_user, source_workflow: "StoredWorkflow"):
         # Override to only copy owner tags.
         for src_swta in source_workflow.owner_tags:
             new_swta = src_swta.copy()
@@ -7760,12 +7940,12 @@ class Workflow(Base, Dictifiable, RepresentById):
     has_cycles: Mapped[Optional[bool]]
     has_errors: Mapped[Optional[bool]]
     reports_config: Mapped[Optional[bytes]] = mapped_column(JSONType)
-    creator_metadata: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    creator_metadata: Mapped[Optional[List[Dict[str, Any]]]] = mapped_column(JSONType)
     license: Mapped[Optional[str]] = mapped_column(TEXT)
-    source_metadata: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    source_metadata: Mapped[Optional[Dict[str, str]]] = mapped_column(JSONType)
     uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)
 
-    steps = relationship(
+    steps: Mapped[List["WorkflowStep"]] = relationship(
         "WorkflowStep",
         back_populates="workflow",
         primaryjoin=(lambda: Workflow.id == WorkflowStep.workflow_id),
@@ -7816,7 +7996,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         return rval
 
     @property
-    def steps_by_id(self):
+    def steps_by_id(self) -> Dict[int, "WorkflowStep"]:
         steps = {}
         for step in self.steps:
             step_id = step.id
@@ -7883,7 +8063,7 @@ class Workflow(Base, Dictifiable, RepresentById):
         """
         return self.top_level_workflow.stored_workflow
 
-    def copy(self, user=None):
+    def copy(self, user: User):
         """Copy a workflow for a new StoredWorkflow object.
 
         Pass user if user-specific information needed.
@@ -7960,11 +8140,11 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
     type: Mapped[Optional[str]] = mapped_column(String(64))
     tool_id: Mapped[Optional[str]] = mapped_column(TEXT)
     tool_version: Mapped[Optional[str]] = mapped_column(TEXT)
-    tool_inputs: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    tool_inputs: Mapped[Optional[Dict[str, Any]]] = mapped_column(JSONType)
     tool_errors: Mapped[Optional[bytes]] = mapped_column(JSONType)
     position: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     config: Mapped[Optional[bytes]] = mapped_column(JSONType)
-    order_index: Mapped[Optional[int]]
+    order_index: Mapped[int]
     when_expression: Mapped[Optional[bytes]] = mapped_column(JSONType)
     uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType)
     label: Mapped[Optional[str]] = mapped_column(Unicode(255))
@@ -7991,7 +8171,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         back_populates="workflow_step",
     )
     post_job_actions = relationship("PostJobAction", back_populates="workflow_step", cascade_backrefs=False)
-    inputs = relationship("WorkflowStepInput", back_populates="workflow_step")
+    inputs: Mapped[List["WorkflowStepInput"]] = relationship("WorkflowStepInput", back_populates="workflow_step")
     workflow_outputs: Mapped[List["WorkflowOutput"]] = relationship(
         back_populates="workflow_step", cascade_backrefs=False
     )
@@ -8017,8 +8197,8 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         self._inputs_by_name = None
         # Injected attributes
         # TODO: code using these should be refactored to not depend on these non-persistent fields
-        self.module: Optional["WorkflowModule"]
-        self.state: Optional["DefaultToolState"]
+        self.module: Optional[WorkflowModule]
+        self.state: Optional[DefaultToolState]
         self.upgrade_messages: Optional[Dict]
 
     @reconstructor
@@ -8031,15 +8211,13 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         return self.dynamic_tool and self.dynamic_tool.uuid
 
     @property
-    def input_type(self):
-        assert (
-            self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE
-        ), "step.input_type can only be called on input step types"
-        return self.STEP_TYPE_TO_INPUT_TYPE[self.type]
+    def is_input_type(self) -> bool:
+        return bool(self.type and self.type in self.STEP_TYPE_TO_INPUT_TYPE)
 
     @property
-    def input_default_value(self):
-        self.get_input_default_value(None)
+    def input_type(self):
+        assert self.is_input_type, "step.input_type can only be called on input step types"
+        return self.STEP_TYPE_TO_INPUT_TYPE[self.type]
 
     def get_input_default_value(self, default_default):
         # parameter_input and the data parameters handle this slightly differently
@@ -8064,17 +8242,18 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
         # Ensure input_connections has already been set.
 
         # Make connection information available on each step by input name.
-        inputs_by_name = {}
+        inputs_by_name: Dict[str, Any] = {}
         for step_input in self.inputs:
             input_name = step_input.name
             assert input_name not in inputs_by_name
             inputs_by_name[input_name] = step_input
         self._inputs_by_name = inputs_by_name
+        return inputs_by_name
 
     @property
     def inputs_by_name(self):
         if self._inputs_by_name is None:
-            self.setup_inputs_by_name()
+            return self.setup_inputs_by_name()
         return self._inputs_by_name
 
     def get_input(self, input_name):
@@ -8194,7 +8373,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
                 break
         return target_output
 
-    def copy_to(self, copied_step, step_mapping, user=None):
+    def copy_to(self, copied_step: "WorkflowStep", step_mapping: Dict[int, "WorkflowStep"], user: User):
         copied_step.order_index = self.order_index
         copied_step.type = self.type
         copied_step.tool_id = self.tool_id
@@ -8224,16 +8403,17 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
             if stored_subworkflow and stored_subworkflow.user == user:
                 # This should be fine and reduces the number of stored subworkflows
                 copied_step.subworkflow = subworkflow
+                copied_subworkflow = subworkflow
             else:
-                # Can this even happen, building a workflow with a subworkflow you don't own ?
-                copied_subworkflow = subworkflow.copy()
+                # Importing a shared workflow with a subworkflow step
+                copied_subworkflow = subworkflow.copy(user=user)
                 stored_workflow = StoredWorkflow(
-                    user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
+                    user=user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True
                 )
                 copied_subworkflow.stored_workflow = stored_workflow
                 copied_step.subworkflow = copied_subworkflow
-                for subworkflow_step, copied_subworkflow_step in zip(subworkflow.steps, copied_subworkflow.steps):
-                    subworkflow_step_mapping[subworkflow_step.id] = copied_subworkflow_step
+            for subworkflow_step, copied_subworkflow_step in zip(subworkflow.steps, copied_subworkflow.steps):
+                subworkflow_step_mapping[subworkflow_step.id] = copied_subworkflow_step
 
         for old_conn, new_conn in zip(self.input_connections, copied_step.input_connections):
             new_conn.input_step_input = copied_step.get_or_add_input(old_conn.input_name)
@@ -8254,6 +8434,17 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime):
             f"WorkflowStep[index={self.order_index},type={self.type},label={self.label},uuid={self.uuid},id={self.id}]"
         )
 
+    @property
+    def effective_label(self) -> Optional[str]:
+        label = self.label
+        if label is not None:
+            return label
+        elif self.is_input_type:
+            tool_inputs = self.tool_inputs
+            if tool_inputs is not None:
+                return cast(Optional[str], tool_inputs.get("name"))
+        return None
+
     def clear_module_extras(self):
         # the module code adds random dynamic state to the step, this
         # attempts to clear that.
@@ -8324,16 +8515,16 @@ class WorkflowStepConnection(Base, RepresentById):
     output_name: Mapped[Optional[str]] = mapped_column(TEXT)
     input_subworkflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
 
-    input_step_input = relationship(
+    input_step_input: Mapped["WorkflowStepInput"] = relationship(
         "WorkflowStepInput",
         back_populates="connections",
         cascade="all",
         primaryjoin=(lambda: WorkflowStepConnection.input_step_input_id == WorkflowStepInput.id),
     )
-    input_subworkflow_step = relationship(
+    input_subworkflow_step: Mapped[Optional["WorkflowStep"]] = relationship(
         "WorkflowStep", primaryjoin=(lambda: WorkflowStepConnection.input_subworkflow_step_id == WorkflowStep.id)
     )
-    output_step = relationship(
+    output_step: Mapped["WorkflowStep"] = relationship(
         "WorkflowStep",
         back_populates="output_connections",
         cascade="all",
@@ -8357,7 +8548,7 @@ class WorkflowStepConnection(Base, RepresentById):
 
     @property
     def input_step(self) -> Optional[WorkflowStep]:
-        return self.input_step_input and self.input_step_input.workflow_step
+        return self.input_step_input.workflow_step
 
     @property
     def input_step_id(self):
@@ -8519,6 +8710,18 @@ class StoredWorkflowMenuEntry(Base, RepresentById):
     )
 
 
+@dataclass
+class InputWithRequest:
+    input: Any
+    request: Dict[str, Any]
+
+
+@dataclass
+class InputToMaterialize:
+    hda: "HistoryDatasetAssociation"
+    input_dataset: "WorkflowRequestToInputDatasetAssociation"
+
+
 class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     __tablename__ = "workflow_invocation"
 
@@ -8529,7 +8732,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
     state: Mapped[Optional[str]] = mapped_column(TrimmedString(64), index=True)
     scheduler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
     handler: Mapped[Optional[str]] = mapped_column(TrimmedString(255), index=True)
-    uuid: Mapped[Optional[Union[UUID, str]]] = mapped_column(UUIDType())
+    uuid: Mapped[Optional[Union[UUID]]] = mapped_column(UUIDType())
     history_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history.id"), index=True)
 
     history = relationship("History", back_populates="workflow_invocations")
@@ -8562,7 +8765,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         order_by=lambda: WorkflowInvocationStep.order_index,
         cascade_backrefs=False,
     )
-    workflow = relationship("Workflow")
+    workflow: Mapped[Workflow] = relationship("Workflow")
     output_dataset_collections = relationship(
         "WorkflowInvocationOutputDatasetCollectionAssociation",
         back_populates="workflow_invocation",
@@ -8750,6 +8953,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         and_conditions = [
             or_(
                 WorkflowInvocation.state == WorkflowInvocation.states.NEW,
+                WorkflowInvocation.state == WorkflowInvocation.states.REQUIRES_MATERIALIZATION,
                 WorkflowInvocation.state == WorkflowInvocation.states.READY,
                 WorkflowInvocation.state == WorkflowInvocation.states.CANCELLING,
             ),
@@ -8841,6 +9045,21 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
             inputs.append(input_dataset_collection_assoc)
         return inputs
 
+    def inputs_requiring_materialization(self) -> List[InputToMaterialize]:
+        hdas_to_materialize: List[InputToMaterialize] = []
+        for input_dataset_assoc in self.input_datasets:
+            request = input_dataset_assoc.request
+            if request:
+                deferred = request.get("deferred", False)
+                if not deferred:
+                    hdas_to_materialize.append(
+                        InputToMaterialize(
+                            input_dataset_assoc.dataset,
+                            input_dataset_assoc,
+                        )
+                    )
+        return hdas_to_materialize
+
     def _serialize(self, id_encoder, serialization_options):
         invocation_attrs = dict_for(self)
         invocation_attrs["state"] = self.state
@@ -9003,23 +9222,75 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
             else:
                 request_to_content.workflow_step = step
 
+        request: Optional[Dict[str, Any]] = None
+        if isinstance(content, InputWithRequest):
+            request = content.request
+            content = content.input
+
         history_content_type = getattr(content, "history_content_type", None)
         if history_content_type == "dataset":
             request_to_content = WorkflowRequestToInputDatasetAssociation()
             request_to_content.dataset = content
+            request_to_content.request = request
             attach_step(request_to_content)
             self.input_datasets.append(request_to_content)
         elif history_content_type == "dataset_collection":
             request_to_content = WorkflowRequestToInputDatasetCollectionAssociation()
             request_to_content.dataset_collection = content
+            request_to_content.request = request
             attach_step(request_to_content)
             self.input_dataset_collections.append(request_to_content)
         else:
             request_to_content = WorkflowRequestInputStepParameter()
             request_to_content.parameter_value = content
+            request_to_content.request = request
             attach_step(request_to_content)
             self.input_step_parameters.append(request_to_content)
 
+    def recover_inputs(self) -> Tuple[Dict[str, Any], str]:
+        inputs = {}
+        inputs_by = "name"
+
+        have_referenced_steps_by_order_index = False
+
+        def best_step_reference(workflow_step: "WorkflowStep") -> str:
+            label = workflow_step.effective_label
+            if label is not None:
+                return label
+            nonlocal have_referenced_steps_by_order_index
+            have_referenced_steps_by_order_index = True
+            return str(workflow_step.order_index)
+
+        def ensure_step(step: Optional["WorkflowStep"]) -> "WorkflowStep":
+            if step is None:
+                raise galaxy.exceptions.InconsistentDatabase(
+                    "workflow input found without step definition, this should not happen"
+                )
+            assert step
+            return step
+
+        for input_dataset_assoc in self.input_datasets:
+            workflow_step = ensure_step(input_dataset_assoc.workflow_step)
+            input_dataset = input_dataset_assoc.dataset
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = input_dataset
+
+        for input_dataset_collection_assoc in self.input_dataset_collections:
+            workflow_step = ensure_step(input_dataset_collection_assoc.workflow_step)
+            input_dataset_collection = input_dataset_collection_assoc.dataset_collection
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = input_dataset_collection
+
+        for input_step_parameter_assoc in self.input_step_parameters:
+            workflow_step = ensure_step(input_step_parameter_assoc.workflow_step)
+            value = input_step_parameter_assoc.parameter_value
+            input_index = best_step_reference(workflow_step)
+            inputs[input_index] = value
+
+        if have_referenced_steps_by_order_index:
+            inputs_by = "name|step_index"
+        return inputs, inputs_by
+
     def add_message(self, message: "InvocationMessageUnion"):
         self.messages.append(
             WorkflowInvocationMessage(  # type:ignore[abstract]
@@ -9186,7 +9457,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
     )
     action: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
 
-    workflow_step = relationship("WorkflowStep")
+    workflow_step: Mapped[WorkflowStep] = relationship("WorkflowStep")
     job: Mapped[Optional["Job"]] = relationship(back_populates="workflow_invocation_step", uselist=False)
     implicit_collection_jobs = relationship("ImplicitCollectionJobs", uselist=False)
     output_dataset_collections = relationship(
@@ -9417,7 +9688,7 @@ class WorkflowRequestStepState(Base, Dictifiable, Serializable):
         ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE"), index=True
     )
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"))
-    value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    value: Mapped[Optional[Dict[str, Any]]] = mapped_column(MutableJSONType)
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()
     workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="step_states")
 
@@ -9440,6 +9711,7 @@ class WorkflowRequestToInputDatasetAssociation(Base, Dictifiable, Serializable):
     workflow_invocation_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_invocation.id"), index=True)
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"))
     dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True)
+    request: Mapped[Optional[Dict]] = mapped_column(JSONType)
 
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()
     dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship()
@@ -9475,6 +9747,7 @@ class WorkflowRequestToInputDatasetCollectionAssociation(Base, Dictifiable, Seri
     workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(
         back_populates="input_dataset_collections"
     )
+    request: Mapped[Optional[Dict]] = mapped_column(JSONType)
 
     history_content_type = "dataset_collection"
     dict_collection_visible_keys = ["id", "workflow_invocation_id", "workflow_step_id", "dataset_collection_id", "name"]
@@ -9498,6 +9771,7 @@ class WorkflowRequestInputStepParameter(Base, Dictifiable, Serializable):
     workflow_invocation_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_invocation.id"), index=True)
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"))
     parameter_value: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    request: Mapped[Optional[Dict]] = mapped_column(JSONType)
 
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()
     workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="input_step_parameters")
@@ -9521,7 +9795,6 @@ class WorkflowInvocationOutputDatasetAssociation(Base, Dictifiable, Serializable
     workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
     dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("history_dataset_association.id"), index=True)
     workflow_output_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_output.id"), index=True)
-
     workflow_invocation: Mapped[Optional["WorkflowInvocation"]] = relationship(back_populates="output_datasets")
     workflow_step: Mapped[Optional["WorkflowStep"]] = relationship()
     dataset: Mapped[Optional["HistoryDatasetAssociation"]] = relationship()
@@ -9701,16 +9974,18 @@ class MetadataFile(Base, StorableObject, Serializable):
                 alt_name=os.path.basename(self.get_file_name()),
             )
 
-    def get_file_name(self, sync_cache=True, user=None):
+
+    def get_file_name(self, sync_cache: bool = True, user=None) -> str:
         # Ensure the directory structure and the metadata file object exist
         try:
             da = self.history_dataset or self.library_dataset
-            if self.object_store_id is None and da is not None:
+            assert da is not None
+            if self.object_store_id is None:
                 self.object_store_id = da.dataset.object_store_id
             object_store = da.dataset.object_store
             store_by = object_store.get_store_by(da.dataset)
             if store_by == "id" and self.id is None:
-                self.flush()
+                self.flush()  # type:ignore[unreachable]
             identifier = getattr(self, store_by)
             alt_name = f"metadata_{identifier}.dat"
             if not object_store.exists(self, extra_dir="_metadata_files", extra_dir_at_root=True, alt_name=alt_name):
@@ -9724,7 +9999,7 @@ class MetadataFile(Base, StorableObject, Serializable):
                 user=user,
             )
             return path
-        except AttributeError:
+        except (AssertionError, AttributeError):
             assert (
                 self.id is not None
             ), "ID must be set before MetadataFile used without an HDA/LDDA (commit the object)"
@@ -9898,12 +10173,12 @@ class PSAAssociation(Base, AssociationMixin, RepresentById):
     __tablename__ = "psa_association"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
-    handle: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
-    secret: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
-    issued: Mapped[Optional[int]]
-    lifetime: Mapped[Optional[int]]
-    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
+    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment, unused-ignore]  # needed for social-auth-core Mixin class attributes. unused-ignore needed for older social-auth-core on Python 3.8
+    handle: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment, unused-ignore]
+    secret: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment, unused-ignore]
+    issued: Mapped[Optional[int]]  # type:ignore[assignment, unused-ignore]
+    lifetime: Mapped[Optional[int]]  # type:ignore[assignment, unused-ignore]
+    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))  # type:ignore[assignment, unused-ignore]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9962,8 +10237,8 @@ class PSACode(Base, CodeMixin, RepresentById):
     __table_args__ = (UniqueConstraint("code", "email"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    email: Mapped[Optional[str]] = mapped_column(VARCHAR(200))
-    code: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
+    email: Mapped[Optional[str]] = mapped_column(VARCHAR(200))  # type:ignore[assignment, unused-ignore]
+    code: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment, unused-ignore]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -9990,9 +10265,9 @@ class PSANonce(Base, NonceMixin, RepresentById):
     __tablename__ = "psa_nonce"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
-    timestamp: Mapped[Optional[int]]
-    salt: Mapped[Optional[str]] = mapped_column(VARCHAR(40))
+    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment, unused-ignore]
+    timestamp: Mapped[Optional[int]]  # type:ignore[assignment, unused-ignore]
+    salt: Mapped[Optional[str]] = mapped_column(VARCHAR(40))  # type:ignore[assignment, unused-ignore]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10028,10 +10303,10 @@ class PSAPartial(Base, PartialMixin, RepresentById):
     __tablename__ = "psa_partial"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    token: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
-    data: Mapped[Optional[str]] = mapped_column(TEXT)
-    next_step: Mapped[Optional[int]]
-    backend: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
+    token: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment, unused-ignore]
+    data: Mapped[Optional[str]] = mapped_column(TEXT)  # type:ignore[assignment, unused-ignore]
+    next_step: Mapped[Optional[int]]  # type:ignore[assignment, unused-ignore]
+    backend: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment, unused-ignore]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10073,12 +10348,14 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
-    uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))
-    provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))
+    uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment, unused-ignore]
+    provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment, unused-ignore]
     extra_data: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
     lifetime: Mapped[Optional[int]]
     assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
-    user: Mapped[Optional["User"]] = relationship(back_populates="social_auth")
+    user: Mapped[Optional["User"]] = relationship(
+        back_populates="social_auth"
+    )  # type:ignore[assignment, unused-ignore]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10246,42 +10523,6 @@ class CustosAuthnzToken(Base, RepresentById):
     user: Mapped["User"] = relationship("User", back_populates="custos_auth")
 
 
-class CloudAuthz(Base):
-    __tablename__ = "cloudauthz"
-
-    id: Mapped[int] = mapped_column(primary_key=True)
-    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
-    provider: Mapped[Optional[str]] = mapped_column(String(255))
-    config: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
-    authn_id: Mapped[Optional[int]] = mapped_column(ForeignKey("oidc_user_authnz_tokens.id"), index=True)
-    tokens: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
-    last_update: Mapped[Optional[datetime]]
-    last_activity: Mapped[Optional[datetime]]
-    description: Mapped[Optional[str]] = mapped_column(TEXT)
-    create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
-    user: Mapped[Optional["User"]] = relationship(back_populates="cloudauthz")
-    authn: Mapped[Optional["UserAuthnzToken"]] = relationship()
-
-    def __init__(self, user_id, provider, config, authn_id, description=None):
-        self.user_id = user_id
-        self.provider = provider
-        self.config = config
-        self.authn_id = authn_id
-        self.last_update = now()
-        self.last_activity = now()
-        self.description = description
-
-    def equals(self, user_id, provider, authn_id, config):
-        return (
-            self.user_id == user_id
-            and self.provider == provider
-            and self.authn_id
-            and self.authn_id == authn_id
-            and len({k: self.config[k] for k in self.config if k in config and self.config[k] == config[k]})
-            == len(self.config)
-        )
-
-
 class Page(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpdateTime):
     __tablename__ = "page"
     __table_args__ = (Index("ix_page_slug", "slug", mysql_length=200),)
@@ -11023,6 +11264,10 @@ class HasConfigSecrets(RepresentById):
     uuid: Mapped[Union[UUID, str]]
     user: Mapped["User"]
 
+    @classmethod
+    def vault_key_from_uuid(clazz, uuid: Union[str, UUID], secret: str, app_config: UsesTemplatesAppConfig) -> str:
+        return f"{clazz.secret_config_type}/{str(get_uuid(uuid))}/{secret}"
+
     def vault_id_prefix(self, app_config: UsesTemplatesAppConfig) -> str:
         id_str = str(self.uuid)
         user_vault_id_prefix = f"{self.secret_config_type}/{id_str}"
@@ -11177,7 +11422,11 @@ class UserFileSource(Base, HasConfigTemplate):
         return FileSourceTemplate(**self.template_definition or {})
 
     def file_source_configuration(
-        self, secrets: SecretsDict, environment: EnvironmentDict, templates: Optional[List[FileSourceTemplate]] = None
+        self,
+        secrets: SecretsDict,
+        environment: EnvironmentDict,
+        implicit: ImplicitConfigurationParameters,
+        templates: Optional[List[FileSourceTemplate]] = None,
     ) -> FileSourceConfiguration:
         if templates is None:
             templates = [self.template]
@@ -11192,6 +11441,7 @@ class UserFileSource(Base, HasConfigTemplate):
                     secrets=secrets,
                     user_details=user_details,
                     environment=environment,
+                    implicit=implicit,
                 )
             except Exception as e:
                 if first_exception is None:
@@ -11203,6 +11453,47 @@ class UserFileSource(Base, HasConfigTemplate):
         raise ValueError("No template sent to file_source_configuration")
 
 
+# TODO: add link from tool_request to this
+class ToolLandingRequest(Base):
+    __tablename__ = "tool_landing_request"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
+    update_time: Mapped[Optional[datetime]] = mapped_column(index=True, default=now, onupdate=now, nullable=True)
+    uuid: Mapped[Union[UUID, str]] = mapped_column(UUIDType(), index=True)
+    tool_id: Mapped[str] = mapped_column(String(255))
+    tool_version: Mapped[Optional[str]] = mapped_column(String(255), default=None)
+    request_state: Mapped[Optional[Dict]] = mapped_column(JSONType)
+    client_secret: Mapped[Optional[str]] = mapped_column(String(255), default=None)
+    public: Mapped[bool] = mapped_column(Boolean)
+
+    user: Mapped[Optional["User"]] = relationship()
+
+
+# TODO: add link from workflow_invocation to this
+class WorkflowLandingRequest(Base):
+    __tablename__ = "workflow_landing_request"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
+    workflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("stored_workflow.id"), nullable=True)
+    stored_workflow_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow.id"), nullable=True)
+
+    create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
+    update_time: Mapped[Optional[datetime]] = mapped_column(index=True, default=now, onupdate=now, nullable=True)
+    uuid: Mapped[Union[UUID, str]] = mapped_column(UUIDType(), index=True)
+    request_state: Mapped[Optional[Dict]] = mapped_column(JSONType)
+    client_secret: Mapped[Optional[str]] = mapped_column(String(255), default=None)
+    workflow_source: Mapped[Optional[str]] = mapped_column(String(255), default=None)
+    workflow_source_type: Mapped[Optional[str]] = mapped_column(String(255), default=None)
+    public: Mapped[bool] = mapped_column(Boolean)
+
+    user: Mapped[Optional["User"]] = relationship()
+    stored_workflow: Mapped[Optional["StoredWorkflow"]] = relationship()
+    workflow: Mapped[Optional["Workflow"]] = relationship()
+
+
 class UserAction(Base, RepresentById):
     __tablename__ = "user_action"
 
diff --git a/lib/galaxy/model/base.py b/lib/galaxy/model/base.py
index db82a2f9ca78ab537ebe8679244c4c6e38ed6d1e..e1243dda67f548f37d4e4223d5443981bb14cb90 100644
--- a/lib/galaxy/model/base.py
+++ b/lib/galaxy/model/base.py
@@ -38,8 +38,7 @@ log = logging.getLogger(__name__)
 # of a request (which run within a threadpool) to see changes to the ContextVar
 # state. See https://github.com/tiangolo/fastapi/issues/953#issuecomment-586006249
 # for details
-_request_state: Dict[str, str] = {}
-REQUEST_ID = ContextVar("request_id", default=_request_state.copy())
+REQUEST_ID: ContextVar[Union[Dict[str, str], None]] = ContextVar("request_id", default=None)
 
 
 @contextlib.contextmanager
@@ -112,12 +111,12 @@ class ModelMapping(Bunch):
 
     def request_scopefunc(self):
         """
-        Return a value that is used as dictionary key for sqlalchemy's ScopedRegistry.
+        Return a value that is used as dictionary key for SQLAlchemy's ScopedRegistry.
 
         This ensures that threads or request contexts will receive a single identical session
         from the ScopedRegistry.
         """
-        return REQUEST_ID.get().get("request") or threading.get_ident()
+        return REQUEST_ID.get({}).get("request") or threading.get_ident()
 
     @staticmethod
     def set_request_id(request_id):
diff --git a/test/integration/cloudauthz/__init__.py b/lib/galaxy/model/db/__init__.py
similarity index 100%
rename from test/integration/cloudauthz/__init__.py
rename to lib/galaxy/model/db/__init__.py
diff --git a/lib/galaxy/model/db/library.py b/lib/galaxy/model/db/library.py
new file mode 100644
index 0000000000000000000000000000000000000000..b88fa28433dbeeeaaccdb6eff8cbbdeb1972bd87
--- /dev/null
+++ b/lib/galaxy/model/db/library.py
@@ -0,0 +1,57 @@
+from sqlalchemy import (
+    asc,
+    false,
+    func,
+    not_,
+    or_,
+    select,
+    true,
+)
+
+from galaxy.model import (
+    Library,
+    LibraryPermissions,
+)
+
+
+def get_library_ids(session, library_access_action):
+    stmt = select(LibraryPermissions.library_id).where(LibraryPermissions.action == library_access_action).distinct()
+    return session.scalars(stmt)
+
+
+def get_library_permissions_by_role(session, role_ids):
+    stmt = select(LibraryPermissions).where(LibraryPermissions.role_id.in_(role_ids))
+    return session.scalars(stmt)
+
+
+def get_libraries_for_admins(session, deleted):
+    stmt = select(Library)
+    if deleted is None:
+        #  Flag is not specified, do not filter on it.
+        pass
+    elif deleted:
+        stmt = stmt.where(Library.deleted == true())
+    else:
+        stmt = stmt.where(Library.deleted == false())
+    stmt = stmt.order_by(asc(func.lower(Library.name)))
+    return session.scalars(stmt)
+
+
+def get_libraries_for_nonadmins(session, restricted_library_ids, accessible_restricted_library_ids):
+    stmt = (
+        select(Library)
+        .where(Library.deleted == false())
+        .where(
+            or_(
+                not_(Library.id.in_(restricted_library_ids)),
+                Library.id.in_(accessible_restricted_library_ids),
+            )
+        )
+    )
+    stmt = stmt.order_by(asc(func.lower(Library.name)))
+    return session.scalars(stmt)
+
+
+def get_libraries_by_name(session, name):
+    stmt = select(Library).where(Library.deleted == false()).where(Library.name == name)
+    return session.scalars(stmt)
diff --git a/lib/galaxy/model/db/role.py b/lib/galaxy/model/db/role.py
new file mode 100644
index 0000000000000000000000000000000000000000..8362767c93b0d45e554a09ce5514f147d15e6836
--- /dev/null
+++ b/lib/galaxy/model/db/role.py
@@ -0,0 +1,62 @@
+from typing import Dict
+
+from sqlalchemy import (
+    and_,
+    false,
+    select,
+)
+
+from galaxy.model import (
+    Role,
+    User,
+    UserRoleAssociation,
+)
+from galaxy.model.scoped_session import galaxy_scoped_session
+
+
+def get_npns_roles(session):
+    """
+    non-private, non-sharing roles
+    """
+    stmt = (
+        select(Role)
+        .where(and_(Role.deleted == false(), Role.type != Role.types.PRIVATE, Role.type != Role.types.SHARING))
+        .order_by(Role.name)
+    )
+    return session.scalars(stmt)
+
+
+def get_private_user_role(user, session):
+    stmt = (
+        select(Role)
+        .where(
+            and_(
+                UserRoleAssociation.user_id == user.id,
+                Role.id == UserRoleAssociation.role_id,
+                Role.type == Role.types.PRIVATE,
+            )
+        )
+        .distinct()
+    )
+    return session.execute(stmt).scalar_one_or_none()
+
+
+def get_roles_by_ids(session: galaxy_scoped_session, role_ids):
+    stmt = select(Role).where(Role.id.in_(role_ids))
+    return session.scalars(stmt).all()
+
+
+def get_displayable_roles(session, trans_user, user_is_admin, security_agent):
+    roles = []
+    stmt = select(Role).where(Role.deleted == false())
+    for role in session.scalars(stmt):
+        if user_is_admin or security_agent.ok_to_display(trans_user, role):
+            roles.append(role)
+    return roles
+
+
+def get_private_role_user_emails_dict(session) -> Dict[int, str]:
+    """Return a mapping of private role ids to user emails."""
+    stmt = select(UserRoleAssociation.role_id, User.email).join(Role).join(User).where(Role.type == Role.types.PRIVATE)
+    roleid_email_tuples = session.execute(stmt).all()
+    return dict(roleid_email_tuples)
diff --git a/lib/galaxy/model/db/user.py b/lib/galaxy/model/db/user.py
new file mode 100644
index 0000000000000000000000000000000000000000..00f824f5e1ee803224668e8eb129fe7405f2ac97
--- /dev/null
+++ b/lib/galaxy/model/db/user.py
@@ -0,0 +1,92 @@
+from typing import Optional
+
+from sqlalchemy import (
+    false,
+    func,
+    or_,
+    select,
+    true,
+)
+
+from galaxy.model import (
+    Role,
+    User,
+)
+from galaxy.model.scoped_session import galaxy_scoped_session
+
+
+def get_users_by_ids(session: galaxy_scoped_session, user_ids):
+    stmt = select(User).where(User.id.in_(user_ids))
+    return session.scalars(stmt).all()
+
+
+# The get_user_by_email and get_user_by_username functions may be called from
+# the tool_shed app, which has its own User model, which is different from
+# galaxy.model.User. In that case, the tool_shed user model should be passed as
+# the model_class argument.
+def get_user_by_email(session, email: str, model_class=User, case_sensitive=True):
+    filter_clause = model_class.email == email
+    if not case_sensitive:
+        filter_clause = func.lower(model_class.email) == func.lower(email)
+    stmt = select(model_class).where(filter_clause).limit(1)
+    return session.scalars(stmt).first()
+
+
+def get_user_by_username(session, username: str, model_class=User):
+    stmt = select(model_class).filter(model_class.username == username).limit(1)
+    return session.scalars(stmt).first()
+
+
+def get_users_for_index(
+    session,
+    deleted: bool,
+    f_email: Optional[str] = None,
+    f_name: Optional[str] = None,
+    f_any: Optional[str] = None,
+    is_admin: bool = False,
+    expose_user_email: bool = False,
+    expose_user_name: bool = False,
+):
+    stmt = select(User)
+    if f_email and (is_admin or expose_user_email):
+        stmt = stmt.where(User.email.like(f"%{f_email}%"))
+    if f_name and (is_admin or expose_user_name):
+        stmt = stmt.where(User.username.like(f"%{f_name}%"))
+    if f_any:
+        if is_admin:
+            stmt = stmt.where(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
+        else:
+            if expose_user_email and expose_user_name:
+                stmt = stmt.where(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
+            elif expose_user_email:
+                stmt = stmt.where(User.email.like(f"%{f_any}%"))
+            elif expose_user_name:
+                stmt = stmt.where(User.username.like(f"%{f_any}%"))
+    if deleted:
+        stmt = stmt.where(User.deleted == true())
+    else:
+        stmt = stmt.where(User.deleted == false())
+    return session.scalars(stmt).all()
+
+
+def _cleanup_nonprivate_user_roles(session, user, private_role_id):
+    """
+    Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE;
+    Delete sharing roles that are associated with this user only;
+    Remove user email from sharing role names associated with multiple users.
+
+    Note: this method updates the session without flushing or committing.
+    """
+    user_roles = [ura for ura in user.roles if ura.role_id != private_role_id]
+    for user_role_assoc in user_roles:
+        role = user_role_assoc.role
+        if role.type == Role.types.SHARING:
+            if len(role.users) == 1:
+                # This role is associated with this user only, so we can delete it
+                session.delete(role)
+            elif user.email in role.name:
+                # Remove user email from sharing role's name
+                role.name = role.name.replace(user.email, "[USER PURGED]")
+                session.add(role)
+        # Delete user role association
+        session.delete(user_role_assoc)
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index d73517fb756a8c0550dfc4e14cc55810f92b4b6b..06eb995adc9366da8623bbadb82e3e2d02c21598 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -4,6 +4,7 @@ import os
 import shutil
 from typing import (
     cast,
+    List,
     NamedTuple,
     Optional,
     Union,
@@ -25,7 +26,9 @@ from galaxy.model import (
     Dataset,
     DatasetCollection,
     DatasetCollectionElement,
+    DatasetHash,
     DatasetSource,
+    DescribesHash,
     History,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
@@ -36,6 +39,7 @@ from galaxy.objectstore import (
     ObjectStore,
     ObjectStorePopulator,
 )
+from galaxy.util.hash_util import verify_hash
 
 log = logging.getLogger(__name__)
 
@@ -95,6 +99,7 @@ class DatasetInstanceMaterializer:
         self,
         dataset_instance: Union[HistoryDatasetAssociation, LibraryDatasetDatasetAssociation],
         target_history: Optional[History] = None,
+        in_place: bool = False,
     ) -> HistoryDatasetAssociation:
         """Create a new detached dataset instance from the supplied instance.
 
@@ -106,15 +111,21 @@ class DatasetInstanceMaterializer:
         if dataset.state != Dataset.states.DEFERRED and isinstance(dataset_instance, HistoryDatasetAssociation):
             return dataset_instance
 
-        materialized_dataset = Dataset()
-        materialized_dataset.state = Dataset.states.OK
-        materialized_dataset.deleted = False
-        materialized_dataset.purged = False
-        materialized_dataset.sources = [s.copy() for s in dataset.sources]
-        materialized_dataset.hashes = [h.copy() for h in dataset.hashes]
-
+        materialized_dataset_hashes = [h.copy() for h in dataset.hashes]
+        if in_place:
+            materialized_dataset = dataset_instance.dataset
+            materialized_dataset.state = Dataset.states.OK
+        else:
+            materialized_dataset = Dataset()
+            materialized_dataset.state = Dataset.states.OK
+            materialized_dataset.deleted = False
+            materialized_dataset.purged = False
+            materialized_dataset.sources = [s.copy() for s in dataset.sources]
+            materialized_dataset.hashes = materialized_dataset_hashes
         target_source = self._find_closest_dataset_source(dataset)
         transient_paths = None
+
+        exception_materializing: Optional[Exception] = None
         if attached:
             object_store_populator = self._object_store_populator
             assert object_store_populator
@@ -130,17 +141,24 @@ class DatasetInstanceMaterializer:
                 with transaction(sa_session):
                     sa_session.commit()
             object_store_populator.set_dataset_object_store_id(materialized_dataset)
-            path = self._stream_source(target_source, datatype=dataset_instance.datatype)
-            object_store.update_from_file(materialized_dataset, file_name=path)
+            try:
+                path = self._stream_source(target_source, dataset_instance.datatype, materialized_dataset_hashes)
+                object_store.update_from_file(materialized_dataset, file_name=path)
+                materialized_dataset.set_size()
+            except Exception as e:
+                exception_materializing = e
         else:
             transient_path_mapper = self._transient_path_mapper
             assert transient_path_mapper
             transient_paths = transient_path_mapper.transient_paths_for(dataset)
             # TODO: optimize this by streaming right to this path...
             # TODO: take into acount transform and ensure we are and are not modifying the file as appropriate.
-            path = self._stream_source(target_source, datatype=dataset_instance.datatype)
-            shutil.move(path, transient_paths.external_filename)
-            materialized_dataset.external_filename = transient_paths.external_filename
+            try:
+                path = self._stream_source(target_source, dataset_instance.datatype, materialized_dataset_hashes)
+                shutil.move(path, transient_paths.external_filename)
+                materialized_dataset.external_filename = transient_paths.external_filename
+            except Exception as e:
+                exception_materializing = e
 
         history = target_history
         if history is None and isinstance(dataset_instance, HistoryDatasetAssociation):
@@ -148,19 +166,31 @@ class DatasetInstanceMaterializer:
                 history = dataset_instance.history
             except DetachedInstanceError:
                 history = None
-        materialized_dataset_instance = HistoryDatasetAssociation(
-            create_dataset=False,  # is the default but lets make this really clear...
-            history=history,
-        )
+
+        materialized_dataset_instance: HistoryDatasetAssociation
+        if not in_place:
+            materialized_dataset_instance = HistoryDatasetAssociation(
+                create_dataset=False,  # is the default but lets make this really clear...
+                history=history,
+            )
+        else:
+            assert isinstance(dataset_instance, HistoryDatasetAssociation)
+            materialized_dataset_instance = cast(HistoryDatasetAssociation, dataset_instance)
+        if exception_materializing is not None:
+            materialized_dataset.state = Dataset.states.ERROR
+            materialized_dataset_instance.info = (
+                f"Failed to materialize deferred dataset with exception: {exception_materializing}"
+            )
         if attached:
             sa_session = self._sa_session
             if sa_session is None:
                 sa_session = object_session(dataset_instance)
             assert sa_session
             sa_session.add(materialized_dataset_instance)
-        materialized_dataset_instance.copy_from(
-            dataset_instance, new_dataset=materialized_dataset, include_tags=attached, include_metadata=True
-        )
+        if not in_place:
+            materialized_dataset_instance.copy_from(
+                dataset_instance, new_dataset=materialized_dataset, include_tags=attached, include_metadata=True
+            )
         require_metadata_regeneration = (
             materialized_dataset_instance.has_metadata_files or materialized_dataset_instance.metadata_deferred
         )
@@ -176,8 +206,15 @@ class DatasetInstanceMaterializer:
             materialized_dataset_instance.metadata_deferred = False
         return materialized_dataset_instance
 
-    def _stream_source(self, target_source: DatasetSource, datatype) -> str:
-        path = stream_url_to_file(target_source.source_uri, file_sources=self._file_sources)
+    def _stream_source(self, target_source: DatasetSource, datatype, dataset_hashes: List[DatasetHash]) -> str:
+        source_uri = target_source.source_uri
+        if source_uri is None:
+            raise Exception("Cannot stream from dataset source without specified source_uri")
+        path = stream_url_to_file(source_uri, file_sources=self._file_sources)
+        if target_source.hashes:
+            for source_hash in target_source.hashes:
+                _validate_hash(path, source_hash, "downloaded file")
+
         transform = target_source.transform or []
         to_posix_lines = False
         spaces_to_tabs = False
@@ -199,6 +236,11 @@ class DatasetInstanceMaterializer:
             path = convert_result.converted_path
         if datatype_groom:
             datatype.groom_dataset_content(path)
+
+        if dataset_hashes:
+            for dataset_hash in dataset_hashes:
+                _validate_hash(path, dataset_hash, "dataset contents")
+
         return path
 
     def _find_closest_dataset_source(self, dataset: Dataset) -> DatasetSource:
@@ -295,3 +337,9 @@ def materializer_factory(
         file_sources=file_sources,
         sa_session=sa_session,
     )
+
+
+def _validate_hash(path: str, describes_hash: DescribesHash, what: str) -> None:
+    hash_value = describes_hash.hash_value
+    if hash_value is not None:
+        verify_hash(path, hash_func_name=describes_hash.hash_func_name, hash_value=hash_value)
diff --git a/lib/galaxy/model/dereference.py b/lib/galaxy/model/dereference.py
new file mode 100644
index 0000000000000000000000000000000000000000..9d6993b81c8a347e5ee13271ee793d6e1f2b17db
--- /dev/null
+++ b/lib/galaxy/model/dereference.py
@@ -0,0 +1,46 @@
+import os.path
+from typing import List
+
+from galaxy.model import (
+    DatasetSource,
+    DatasetSourceHash,
+    HistoryDatasetAssociation,
+    TransformAction,
+)
+from galaxy.tool_util.parameters import DataRequestUri
+
+
+def dereference_to_model(sa_session, user, history, data_request_uri: DataRequestUri) -> HistoryDatasetAssociation:
+    name = data_request_uri.name or os.path.basename(data_request_uri.url)
+    dbkey = data_request_uri.dbkey or "?"
+    hda = HistoryDatasetAssociation(
+        name=name,
+        extension=data_request_uri.ext,
+        dbkey=dbkey,  # TODO
+        history=history,
+        create_dataset=True,
+        sa_session=sa_session,
+    )
+    hda.state = hda.states.DEFERRED
+    dataset_source = DatasetSource()
+    dataset_source.source_uri = data_request_uri.url
+    hashes = []
+    for dataset_hash in data_request_uri.hashes or []:
+        hash_object = DatasetSourceHash()
+        hash_object.hash_function = dataset_hash.hash_function
+        hash_object.hash_value = dataset_hash.hash_value
+        hashes.append(hash_object)
+    dataset_source.hashes = hashes
+    hda.dataset.sources = [dataset_source]
+    transform: List[TransformAction] = []
+    if data_request_uri.space_to_tab:
+        transform.append({"action": "spaces_to_tabs"})
+    elif data_request_uri.to_posix_lines:
+        transform.append({"action": "to_posix_lines"})
+    if len(transform) > 0:
+        dataset_source.transform = transform
+
+    sa_session.add(hda)
+    sa_session.add(dataset_source)
+    history.add_dataset(hda, genome_build=dbkey, quota=False)
+    return hda
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 053e177edd9f0690c0e09af647be3b61c8690ee5..707b20b7ca2f8eceb04780914ba688f92cc70579 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -3,6 +3,7 @@ from threading import local
 from typing import (
     Optional,
     Type,
+    TYPE_CHECKING,
 )
 
 from galaxy import model
@@ -16,6 +17,9 @@ from galaxy.model.orm.engine_factory import build_engine
 from galaxy.model.security import GalaxyRBACAgent
 from galaxy.model.triggers.update_audit_table import install as install_timestamp_triggers
 
+if TYPE_CHECKING:
+    from galaxy.objectstore import BaseObjectStore
+
 log = logging.getLogger(__name__)
 
 metadata = mapper_registry.metadata
@@ -93,14 +97,17 @@ def _build_model_mapping(engine, map_install_models, thread_local_log) -> Galaxy
         model_modules.append(tool_shed_install)
 
     model_mapping = GalaxyModelMapping(model_modules, engine)
-    model_mapping.security_agent = GalaxyRBACAgent(model_mapping)
+    model_mapping.security_agent = GalaxyRBACAgent(model_mapping.session)
     model_mapping.thread_local_log = thread_local_log
     return model_mapping
 
 
 def init_models_from_config(
-    config: GalaxyAppConfiguration, map_install_models=False, object_store=None, trace_logger=None
-):
+    config: GalaxyAppConfiguration,
+    map_install_models: bool = False,
+    object_store: Optional["BaseObjectStore"] = None,
+    trace_logger=None,
+) -> GalaxyModelMapping:
     model = init(
         config.file_path,
         config.database_connection,
diff --git a/lib/galaxy/model/migrations/alembic/env.py b/lib/galaxy/model/migrations/alembic/env.py
index 8ec793787d54c312835bc5bcd1d524cd5391ffec..b7766e4e20bfefdec82a22de301acc2dc88aa657 100644
--- a/lib/galaxy/model/migrations/alembic/env.py
+++ b/lib/galaxy/model/migrations/alembic/env.py
@@ -10,6 +10,7 @@ from alembic import context
 from alembic.script import ScriptDirectory
 from alembic.script.base import Script
 from sqlalchemy import create_engine
+from sqlalchemy.exc import OperationalError
 
 from galaxy.model import Base
 from galaxy.model.migrations import (
@@ -111,19 +112,30 @@ def _configure_and_run_migrations_offline(url: str) -> None:
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
     )
-    with context.begin_transaction():
-        context.run_migrations()
+    _run_migrations()
 
 
 def _configure_and_run_migrations_online(url) -> None:
     engine = create_engine(url)
     with engine.connect() as connection:
         context.configure(connection=connection, target_metadata=target_metadata)
-        with context.begin_transaction():
-            context.run_migrations()
+        _run_migrations()
     engine.dispose()
 
 
+def _run_migrations():
+    with context.begin_transaction():
+        try:
+            context.run_migrations()
+        except OperationalError as error:
+            if getattr(error.orig, "pgcode", None) == "40P01":  # PostgreSQL DeadlockDetected error detected
+                msg = """A deadlock has been detected. This may be due to a database
+revision requiring exclusive access to a database object. To avoid this error, it is recommended to
+shut down all Galaxy procesess during database migration."""
+                log.error(msg)
+                raise
+
+
 def _get_url_from_config() -> str:
     url = config.get_main_option("sqlalchemy.url")
     return cast(str, url)
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py b/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py
new file mode 100644
index 0000000000000000000000000000000000000000..a0572676503943960bd706138c85b8c862e4a250
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py
@@ -0,0 +1,330 @@
+"""make dataset uuids unique
+
+Revision ID: 04288b6a5b25
+Revises: c63848676caf
+Create Date: 2024-07-24 10:43:48.162813
+
+NOTE ON NAMING: In this script, the term "latest" refers to a dataset that has
+the smallest primary key in a group of datasets with duplicate UUIDs and,
+therefore, is the oldest/original dataset in this group.
+"""
+
+from alembic import op
+from sqlalchemy.sql import text
+
+from galaxy.model.migrations.util import (
+    _is_sqlite,
+    create_unique_constraint,
+    drop_constraint,
+    table_exists,
+)
+
+# revision identifiers, used by Alembic.
+revision = "04288b6a5b25"
+down_revision = "c63848676caf"
+branch_labels = None
+depends_on = None
+
+dataset_table_name = "dataset"
+uuid_column = "uuid"
+unique_constraint_name = "uq_uuid_column"
+
+DEBUG = False
+
+
+# sqlite isn't production - ignore the fake uuid please
+# https://stackoverflow.com/questions/17277735/using-uuids-in-sqlite
+def new_uuid():
+    return "lower(hex(randomblob(16)))" if _is_sqlite() else "REPLACE(gen_random_uuid()::text, '-', '')"
+
+
+def upgrade():
+    connection = op.get_bind()
+
+    op.execute("DROP TABLE IF EXISTS duplicate_datasets_by_uuid")
+    op.execute("DROP TABLE IF EXISTS temp_duplicates_counts")
+    op.execute("DROP VIEW IF EXISTS temp_duplicate_datasets_purged")
+    op.execute("DROP VIEW IF EXISTS temp_duplicate_datasets_active")
+    op.execute("DROP TABLE IF EXISTS temp_latest_active_duplicate")
+    op.execute("DROP TABLE IF EXISTS temp_active_mapping")
+    op.execute("DROP TABLE IF EXISTS hda_dataset_mapping_pre_uuid_condense")
+    op.execute("DROP TABLE IF EXISTS ldda_dataset_mapping_pre_uuid_condense")
+
+    # Find and store duplicate UUIDs - create table temp_duplicates_counts
+    _setup_duplicate_counts(connection)
+
+    # Backup all dataset info for duplicated dataset table in
+    # table duplicate_datasets_by_uuid
+    _setup_backup_datasets_for_duplicated_uuids(connection)
+
+    # create views temp_duplicate_datasets_purged and temp_duplicate_datasets_active to
+    # join against in subsequent queries inspect this data
+    _setup_duplicated_dataset_views_by_purged_status(connection)
+
+    _find_latest_active_dataset_for_each_uuid(connection)  # and record in temp_latest_active_duplicate
+
+    _map_active_uuids_to_latest(connection)  # in temp table temp_active_mapping
+
+    _preserve_old_dataset_association_mappings(connection)
+
+    _randomize_uuids_for_purged_datasets_with_duplicated_uuids(connection)
+    _randomize_uuids_for_older_active_datasets_with_duplicated_uuids(connection)
+
+    _update_dataset_associations_to_point_to_latest_active_datasets(connection)
+
+    # cleanup all working tables except backups required to undo migration prcoess - these backups are
+    # duplicate_datasets_by_uuid, ldda_dataset_mapping_pre_uuid_condense, hda_dataset_mapping_pre_uuid_condense
+    op.execute("DROP VIEW IF EXISTS temp_duplicate_datasets_purged")
+    op.execute("DROP VIEW IF EXISTS temp_duplicate_datasets_active")
+    op.execute("DROP TABLE IF EXISTS temp_active_mapping")
+    op.execute("DROP TABLE IF EXISTS temp_latest_active_duplicate")
+    op.execute("DROP TABLE IF EXISTS temp_duplicates_counts")
+
+    # Add a unique constraint to the UUID column
+    create_unique_constraint(unique_constraint_name, dataset_table_name, [uuid_column])
+
+
+def downgrade():
+    connection = op.get_bind()
+
+    drop_constraint(unique_constraint_name, dataset_table_name)
+
+    # restoring the old uuids requires untracked tables left by previous upgrade
+    # the unit tests do not set these up - so lets verify the tables we need exist
+    # before restoring the UUIDs.
+    if table_exists("hda_dataset_mapping_pre_uuid_condense", True):
+        _restore_old_mappings(connection)
+        _restore_dataset_uuids(connection)
+
+    # cleanup left behind untracked tables duplicate_datasets_by_uuid, ldda_dataset_mapping_pre_uuid_condense, hda_dataset_mapping_pre_uuid_condense
+    op.execute("DROP TABLE IF EXISTS duplicate_datasets_by_uuid")
+    op.execute("DROP TABLE IF EXISTS ldda_dataset_mapping_pre_uuid_condense")
+    op.execute("DROP TABLE IF EXISTS hda_dataset_mapping_pre_uuid_condense")
+
+
+def _restore_old_mappings(connection):
+    restore_hda_dataset_ids = text(
+        """
+        UPDATE history_dataset_association
+        SET dataset_id=mapping.old_dataset_id
+        FROM hda_dataset_mapping_pre_uuid_condense AS mapping
+        WHERE mapping.id = history_dataset_association.id
+        """
+    )
+    connection.execute(restore_hda_dataset_ids)
+    restore_ldda_dataset_ids = text(
+        """
+        UPDATE library_dataset_dataset_association
+        SET dataset_id=mapping.old_dataset_id
+        FROM ldda_dataset_mapping_pre_uuid_condense as mapping
+        WHERE mapping.id = library_dataset_dataset_association.id
+        """
+    )
+    connection.execute(restore_ldda_dataset_ids)
+
+
+def _restore_dataset_uuids(connection):
+    restore_ldda_dataset_ids = text(
+        f"""
+        UPDATE {dataset_table_name}
+        SET {uuid_column}=backup_datasets.{uuid_column}
+        FROM duplicate_datasets_by_uuid as backup_datasets
+        WHERE backup_datasets.id = {dataset_table_name}.id
+        """
+    )
+    connection.execute(restore_ldda_dataset_ids)
+
+
+def _setup_duplicate_counts(connection):
+    duplicate_counts_query = text(
+        f"""
+        CREATE TEMP TABLE temp_duplicates_counts AS
+        SELECT {uuid_column}, COUNT(*)
+        FROM {dataset_table_name}
+        GROUP BY {uuid_column}
+        HAVING COUNT(*) > 1
+        """
+    )
+    connection.execute(duplicate_counts_query)
+
+
+def _setup_backup_datasets_for_duplicated_uuids(connection):
+    duplicate_datasets = text(
+        f"""
+        CREATE TABLE duplicate_datasets_by_uuid AS
+        SELECT *
+        FROM {dataset_table_name}
+        WHERE {uuid_column} IN (select {uuid_column} from temp_duplicates_counts)
+        """
+    )
+    connection.execute(duplicate_datasets)
+
+
+def _setup_duplicated_dataset_views_by_purged_status(connection):
+    duplicate_purged_datasets_query = text(
+        """
+        CREATE TEMP VIEW temp_duplicate_datasets_purged AS
+        SELECT *
+        FROM duplicate_datasets_by_uuid
+        WHERE purged = true
+        """
+    )
+    connection.execute(duplicate_purged_datasets_query)
+
+    duplicate_active_datasets_query = text(
+        """
+        CREATE TEMP VIEW temp_duplicate_datasets_active AS
+        SELECT *
+        FROM duplicate_datasets_by_uuid
+        WHERE purged = false
+        """
+    )
+    connection.execute(duplicate_active_datasets_query)
+    _debug(connection, "purged duplicated", text("select count(*) from temp_duplicate_datasets_purged"))
+    _debug(connection, "active duplicated", text("select count(*) from temp_duplicate_datasets_active"))
+
+
+def _find_latest_active_dataset_for_each_uuid(connection):
+    latest_active_duplicate_query = text(
+        f"""
+        CREATE TEMP TABLE temp_latest_active_duplicate AS
+        SELECT {uuid_column}, MIN(id) as latest_dataset_id
+        FROM temp_duplicate_datasets_active
+        GROUP BY {uuid_column}
+        """
+    )
+    connection.execute(latest_active_duplicate_query)
+    debug_query = text("select * from temp_latest_active_duplicate")
+    _debug(connection, "latest active table", debug_query)
+
+
+def _map_active_uuids_to_latest(connection):
+    active_mapping_query = text(
+        f"""
+        CREATE TEMP TABLE temp_active_mapping AS
+        SELECT d.id as from_dataset_id, l.latest_dataset_id as to_dataset_id, l.{uuid_column} as uuid
+        FROM temp_duplicate_datasets_active as d
+        LEFT JOIN temp_latest_active_duplicate l ON d.{uuid_column} = l.{uuid_column}
+        """
+    )
+    connection.execute(active_mapping_query)
+    debug_query = text("select * from temp_active_mapping")
+    _debug(connection, "temp active mapping", debug_query)
+    debug_query = text("select * from temp_active_mapping as m where m.from_dataset_id != m.to_dataset_id")
+    _debug(connection, "temp active mapping older...", debug_query)
+
+
+def _randomize_uuids_for_purged_datasets_with_duplicated_uuids(connection):
+    updated_purged_uuids = text(
+        f"""
+        UPDATE {dataset_table_name}
+        SET uuid={new_uuid()}
+        WHERE {uuid_column} IN (SELECT {uuid_column} FROM temp_duplicate_datasets_purged) AND purged = true
+        """
+    )
+    connection.execute(updated_purged_uuids)
+
+
+def _randomize_uuids_for_older_active_datasets_with_duplicated_uuids(connection):
+    # sanity check...
+    duplicate_datasets_with_uuid_of_latest_active_uuid = text(
+        f"""
+        SELECT COUNT(*)
+        FROM {dataset_table_name} as d
+        INNER JOIN temp_active_mapping AS a ON d.uuid = a.uuid
+        GROUP BY d.{uuid_column}
+        HAVING COUNT(*) > 1
+        """
+    )
+    _debug(
+        connection,
+        "(before) duplicate_datasets_with_uuid_of_latest_active_uuid",
+        duplicate_datasets_with_uuid_of_latest_active_uuid,
+    )
+
+    update_older_datasets = text(
+        f"""
+        UPDATE {dataset_table_name}
+        SET uuid={new_uuid()}
+        WHERE EXISTS
+            (
+                SELECT *
+                FROM temp_active_mapping as m
+                where m.from_dataset_id = {dataset_table_name}.id and m.from_dataset_id != m.to_dataset_id
+            )
+        """
+    )
+    connection.execute(update_older_datasets)
+
+    _debug(
+        connection,
+        "(after) duplicate_datasets_with_uuid_of_latest_active_uuid",
+        duplicate_datasets_with_uuid_of_latest_active_uuid,
+    )
+
+    duplicate_active_count = text(
+        """
+        SELECT COUNT(*)
+        FROM temp_active_mapping
+        """
+    )
+    _debug(connection, "(after) duplicate_active_count", duplicate_active_count)
+    datasets_with_originally_duplicated_uuids = text(
+        f"""
+        SELECT COUNT(*)
+        FROM {dataset_table_name} as d
+        INNER JOIN temp_active_mapping AS a ON d.uuid = a.uuid
+        """
+    )
+    _debug(connection, "(after) datasets_with_originally_duplicated_uuids", datasets_with_originally_duplicated_uuids)
+
+
+def _update_dataset_associations_to_point_to_latest_active_datasets(connection):
+    # for others select one dataset to represent the dataset in HDAs/LDDAs
+    update_hda_links = text(
+        """
+        UPDATE history_dataset_association
+        SET dataset_id=t.to_dataset_id
+        FROM temp_active_mapping t
+        WHERE t.from_dataset_id = dataset_id
+        """
+    )
+    connection.execute(update_hda_links)
+    update_ldda_links = text(
+        """
+        UPDATE library_dataset_dataset_association
+        SET dataset_id=t.to_dataset_id
+        FROM temp_active_mapping t
+        WHERE t.from_dataset_id = dataset_id
+        """
+    )
+    connection.execute(update_ldda_links)
+
+
+def _preserve_old_dataset_association_mappings(connection):
+    old_hda_mappings = text(
+        f"""
+        CREATE TABLE hda_dataset_mapping_pre_uuid_condense AS
+        SELECT DISTINCT h.id as id, d.id as old_dataset_id
+         FROM history_dataset_association AS h
+         INNER JOIN dataset AS d ON h.dataset_id = d.id
+         INNER JOIN duplicate_datasets_by_uuid AS duplicates ON d.{uuid_column} = duplicates.{uuid_column}
+        """
+    )
+    connection.execute(old_hda_mappings)
+    old_ldda_mappings = text(
+        f"""
+        CREATE TABLE ldda_dataset_mapping_pre_uuid_condense AS
+         SELECT l.id as id, d.id as old_dataset_id
+         FROM library_dataset_dataset_association aS l
+         INNER JOIN dataset AS d ON l.dataset_id = d.id
+         INNER JOIN duplicate_datasets_by_uuid AS duplicates ON d.{uuid_column} = duplicates.{uuid_column}
+        """
+    )
+    connection.execute(old_ldda_mappings)
+
+
+def _debug(connection, log_msg, query):
+    if DEBUG:
+        result = connection.execute(query)
+        print(f"{log_msg} {result.all()}")
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/13fe10b8e35b_add_not_null_constraints_to_user_group_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/13fe10b8e35b_add_not_null_constraints_to_user_group_.py
new file mode 100644
index 0000000000000000000000000000000000000000..822a0229a4bcfa8eba03db57107c3d9f8ae94e08
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/13fe10b8e35b_add_not_null_constraints_to_user_group_.py
@@ -0,0 +1,42 @@
+"""Add not-null constraints to user_group_association
+
+Revision ID: 13fe10b8e35b
+Revises: 56ddf316dbd0
+Create Date: 2024-09-09 21:26:26.032842
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import UserGroupAssociationNullFix
+from galaxy.model.migrations.util import (
+    alter_column,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "13fe10b8e35b"
+down_revision = "56ddf316dbd0"
+branch_labels = None
+depends_on = None
+
+table_name = "user_group_association"
+
+
+def upgrade():
+    with transaction():
+        _remove_records_with_nulls()
+        alter_column(table_name, "user_id", nullable=False)
+        alter_column(table_name, "group_id", nullable=False)
+
+
+def downgrade():
+    with transaction():
+        alter_column(table_name, "user_id", nullable=True)
+        alter_column(table_name, "group_id", nullable=True)
+
+
+def _remove_records_with_nulls():
+    """Remove associations having null as user_id or group_id"""
+    connection = op.get_bind()
+    UserGroupAssociationNullFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/1cf595475b58_email_column_unique_constraint.py b/lib/galaxy/model/migrations/alembic/versions_gxy/1cf595475b58_email_column_unique_constraint.py
new file mode 100644
index 0000000000000000000000000000000000000000..ba356b1c770d26dad095c396b5f19c7194d881a0
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/1cf595475b58_email_column_unique_constraint.py
@@ -0,0 +1,52 @@
+"""Email column unique constraint
+
+Revision ID: 1cf595475b58
+Revises: d619fdfa6168
+Create Date: 2024-07-03 19:53:22.443016
+"""
+
+from alembic import op
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.data_fixes.user_table_fixer import EmailDeduplicator
+from galaxy.model.migrations.util import (
+    create_index,
+    drop_index,
+    index_exists,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "1cf595475b58"
+down_revision = "d619fdfa6168"
+branch_labels = None
+depends_on = None
+
+
+table_name = "galaxy_user"
+column_name = "email"
+index_name = build_index_name(table_name, [column_name])
+
+
+def upgrade():
+    with transaction():
+        _fix_duplicate_emails()
+        # Existing databases may have an existing index we no longer need
+        # New databases will not have that index, so we must check.
+        if index_exists(index_name, table_name, False):
+            drop_index(index_name, table_name)
+        # Create a UNIQUE index
+        create_index(index_name, table_name, [column_name], unique=True)
+
+
+def downgrade():
+    with transaction():
+        drop_index(index_name, table_name)
+        # Restore a non-unique index
+        create_index(index_name, table_name, [column_name])
+
+
+def _fix_duplicate_emails():
+    """Fix records with duplicate usernames"""
+    connection = op.get_bind()
+    EmailDeduplicator(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/1fdd615f2cdb_add_not_null_constraints_to_user_role_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/1fdd615f2cdb_add_not_null_constraints_to_user_role_.py
new file mode 100644
index 0000000000000000000000000000000000000000..4fb6f5262f8e0364a47b5a96a0d879e3e5161cf2
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/1fdd615f2cdb_add_not_null_constraints_to_user_role_.py
@@ -0,0 +1,42 @@
+"""Add not-null constraints to user_role_association
+
+Revision ID: 1fdd615f2cdb
+Revises: 349dd9d9aac9
+Create Date: 2024-09-09 21:28:11.987054
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import UserRoleAssociationNullFix
+from galaxy.model.migrations.util import (
+    alter_column,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "1fdd615f2cdb"
+down_revision = "349dd9d9aac9"
+branch_labels = None
+depends_on = None
+
+table_name = "user_role_association"
+
+
+def upgrade():
+    with transaction():
+        _remove_records_with_nulls()
+        alter_column(table_name, "user_id", nullable=False)
+        alter_column(table_name, "role_id", nullable=False)
+
+
+def downgrade():
+    with transaction():
+        alter_column(table_name, "user_id", nullable=True)
+        alter_column(table_name, "role_id", nullable=True)
+
+
+def _remove_records_with_nulls():
+    """Remove associations having null as user_id or role_id"""
+    connection = op.get_bind()
+    UserRoleAssociationNullFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/25b092f7938b_add_not_null_constraints_to_group_role_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/25b092f7938b_add_not_null_constraints_to_group_role_.py
new file mode 100644
index 0000000000000000000000000000000000000000..f57dd446d0cb10bde3ab88f377c5822a081ec1bf
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/25b092f7938b_add_not_null_constraints_to_group_role_.py
@@ -0,0 +1,42 @@
+"""Add not-null constraints to group_role_association
+
+Revision ID: 25b092f7938b
+Revises: 9ef6431f3a4e
+Create Date: 2024-09-09 16:17:26.652865
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import GroupRoleAssociationNullFix
+from galaxy.model.migrations.util import (
+    alter_column,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "25b092f7938b"
+down_revision = "9ef6431f3a4e"
+branch_labels = None
+depends_on = None
+
+table_name = "group_role_association"
+
+
+def upgrade():
+    with transaction():
+        _remove_records_with_nulls()
+        alter_column(table_name, "group_id", nullable=True)
+        alter_column(table_name, "role_id", nullable=False)
+
+
+def downgrade():
+    with transaction():
+        alter_column(table_name, "group_id", nullable=True)
+        alter_column(table_name, "role_id", nullable=True)
+
+
+def _remove_records_with_nulls():
+    """Remove associations having null as group_id or role_id"""
+    connection = op.get_bind()
+    GroupRoleAssociationNullFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py
index 14c990e3086a63a795c5ab1c24047c16528fc1b8..be5e3c0ae1bb2e56fb9203c5efa7ab26f34081bb 100644
--- a/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py
@@ -10,6 +10,7 @@ from galaxy.model.database_object_names import build_index_name
 from galaxy.model.migrations.util import (
     create_index,
     drop_index,
+    index_exists,
 )
 
 # revision identifiers, used by Alembic.
@@ -32,7 +33,8 @@ workflow_comment_parent_comment_index_name = build_index_name(
 
 def upgrade():
     create_index(workflow_step_parent_comment_index_name, workflow_step_table_name, [parent_comment_id_column_name])
-    create_index(workflow_comment_workflow_id_index_name, workflow_comment_table_name, [workflow_id_column_name])
+    if not index_exists(workflow_comment_workflow_id_index_name, workflow_comment_table_name, False):
+        create_index(workflow_comment_workflow_id_index_name, workflow_comment_table_name, [workflow_id_column_name])
     create_index(
         workflow_comment_parent_comment_index_name, workflow_comment_table_name, [parent_comment_id_column_name]
     )
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/349dd9d9aac9_add_unique_constraint_to_user_role_assoc.py b/lib/galaxy/model/migrations/alembic/versions_gxy/349dd9d9aac9_add_unique_constraint_to_user_role_assoc.py
new file mode 100644
index 0000000000000000000000000000000000000000..26245f4a9c8788385ea1ec40b5910bf4a68da67a
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/349dd9d9aac9_add_unique_constraint_to_user_role_assoc.py
@@ -0,0 +1,45 @@
+"""Add unique constraint to user_role_association
+
+Revision ID: 349dd9d9aac9
+Revises: 1cf595475b58
+Create Date: 2024-09-09 16:14:58.278850
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import UserRoleAssociationDuplicateFix
+from galaxy.model.migrations.util import (
+    create_unique_constraint,
+    drop_constraint,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "349dd9d9aac9"
+down_revision = "1cf595475b58"
+branch_labels = None
+depends_on = None
+
+table_name = "user_role_association"
+constraint_column_names = ["user_id", "role_id"]
+unique_constraint_name = (
+    "user_role_association_user_id_key"  # This is what the model's naming convention will generate.
+)
+
+
+def upgrade():
+    with transaction():
+        _remove_duplicate_records()
+        create_unique_constraint(unique_constraint_name, table_name, constraint_column_names)
+
+
+def downgrade():
+    with transaction():
+        drop_constraint(unique_constraint_name, table_name)
+
+
+def _remove_duplicate_records():
+    """Remove duplicate associations"""
+    connection = op.get_bind()
+    UserRoleAssociationDuplicateFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/56ddf316dbd0_add_unique_constraint_to_user_group_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/56ddf316dbd0_add_unique_constraint_to_user_group_.py
new file mode 100644
index 0000000000000000000000000000000000000000..4a50ddcfcbe0d11a4227a0a03e51fae0d4405537
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/56ddf316dbd0_add_unique_constraint_to_user_group_.py
@@ -0,0 +1,45 @@
+"""Add unique constraint to user_group_association
+
+Revision ID: 56ddf316dbd0
+Revises: 1fdd615f2cdb
+Create Date: 2024-09-09 16:10:37.081834
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import UserGroupAssociationDuplicateFix
+from galaxy.model.migrations.util import (
+    create_unique_constraint,
+    drop_constraint,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "56ddf316dbd0"
+down_revision = "1fdd615f2cdb"
+branch_labels = None
+depends_on = None
+
+table_name = "user_group_association"
+constraint_column_names = ["user_id", "group_id"]
+unique_constraint_name = (
+    "user_group_association_user_id_key"  # This is what the model's naming convention will generate.
+)
+
+
+def upgrade():
+    with transaction():
+        _remove_duplicate_records()
+        create_unique_constraint(unique_constraint_name, table_name, constraint_column_names)
+
+
+def downgrade():
+    with transaction():
+        drop_constraint(unique_constraint_name, table_name)
+
+
+def _remove_duplicate_records():
+    """Remove duplicate associations"""
+    connection = op.get_bind()
+    UserGroupAssociationDuplicateFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/570bce1e82f9_drop_cloudauthz_table.py b/lib/galaxy/model/migrations/alembic/versions_gxy/570bce1e82f9_drop_cloudauthz_table.py
new file mode 100644
index 0000000000000000000000000000000000000000..1afe2dbe505827a352aa3da928839c08af1d2e2e
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/570bce1e82f9_drop_cloudauthz_table.py
@@ -0,0 +1,47 @@
+"""drop cloudauthz table
+
+Revision ID: 570bce1e82f9
+Revises: c14a3c93d66b
+Create Date: 2024-05-21 15:53:06.430082
+
+"""
+
+import sqlalchemy as sa
+
+from galaxy.model.custom_types import MutableJSONType
+from galaxy.model.migrations.util import (
+    create_table,
+    drop_table,
+    transaction,
+)
+from galaxy.model.orm.now import now
+
+# revision identifiers, used by Alembic.
+revision = "570bce1e82f9"
+down_revision = "c14a3c93d66b"
+branch_labels = None
+depends_on = None
+
+CLOUDAUTHZ_TABLE_NAME = "cloudauthz"
+
+
+def upgrade():
+    with transaction():
+        drop_table(CLOUDAUTHZ_TABLE_NAME)
+
+
+def downgrade():
+    with transaction():
+        create_table(
+            CLOUDAUTHZ_TABLE_NAME,
+            sa.Column("id", sa.Integer, primary_key=True),
+            sa.Column("user_id", sa.Integer, sa.ForeignKey("galaxy_user.id"), index=True),
+            sa.Column("provider", sa.String(255)),
+            sa.Column("config", MutableJSONType),
+            sa.Column("authn_id", sa.Integer, sa.ForeignKey("oidc_user_authnz_tokens.id"), index=True),
+            sa.Column("tokens", MutableJSONType),
+            sa.Column("last_update", sa.DateTime),
+            sa.Column("last_activity", sa.DateTime),
+            sa.Column("description", sa.Text),
+            sa.Column("create_time", sa.DateTime, default=now),
+        )
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/75348cfb3715_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/75348cfb3715_.py
new file mode 100644
index 0000000000000000000000000000000000000000..e031447c4bbdad622f78793c1c5327f35814af4f
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/75348cfb3715_.py
@@ -0,0 +1,21 @@
+"""Merge head revisions
+
+Revision ID: 75348cfb3715
+Revises: 9a5207190a4d, cbc46035eba0
+Create Date: 2024-11-19 11:48:02.273303
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = "75348cfb3715"
+down_revision = ("9a5207190a4d", "cbc46035eba0")
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/7ffd33d5d144_implement_structured_tool_state.py b/lib/galaxy/model/migrations/alembic/versions_gxy/7ffd33d5d144_implement_structured_tool_state.py
new file mode 100644
index 0000000000000000000000000000000000000000..027338dac2792a02cc51fc1e2ab11438e10641c8
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/7ffd33d5d144_implement_structured_tool_state.py
@@ -0,0 +1,178 @@
+"""implement structured tool state
+
+Revision ID: 7ffd33d5d144
+Revises: 25b092f7938b
+Create Date: 2022-11-09 15:53:11.451185
+
+"""
+
+from sqlalchemy import (
+    Column,
+    DateTime,
+    Integer,
+    String,
+)
+
+from galaxy.model.custom_types import (
+    JSONType,
+    UUIDType,
+)
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.util import (
+    add_column,
+    create_foreign_key,
+    create_index,
+    create_table,
+    drop_column,
+    drop_index,
+    drop_table,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "7ffd33d5d144"
+down_revision = "25b092f7938b"
+branch_labels = None
+depends_on = None
+
+job_table_name = "job"
+tool_source_table_name = "tool_source"
+tool_request_table_name = "tool_request"
+request_column_name = "tool_request_id"
+job_request_index_name = build_index_name(job_table_name, request_column_name)
+workflow_request_to_input_dataset_table_name = "workflow_request_to_input_dataset"
+workflow_request_to_input_collection_table_name = "workflow_request_to_input_collection_dataset"
+workflow_request_to_input_parameter_table_name = "workflow_request_input_step_parameter"
+workflow_input_request_column_name = "request"
+workflow_landing_request_table_name = "workflow_landing_request"
+tool_landing_request_table_name = "tool_landing_request"
+
+
+def upgrade():
+    with transaction():
+        create_table(
+            tool_landing_request_table_name,
+            Column("id", Integer, primary_key=True),
+            Column("user_id", Integer, index=True, nullable=True),
+            Column("create_time", DateTime),
+            Column("update_time", DateTime, nullable=True),
+            Column("request_state", JSONType),
+            Column("client_secret", String(255), nullable=True),
+            Column("uuid", UUIDType, nullable=False, index=True),
+        )
+
+        create_table(
+            workflow_landing_request_table_name,
+            Column("id", Integer, primary_key=True),
+            Column("user_id", Integer, index=True, nullable=True),
+            Column("stored_workflow_id", Integer, index=True),
+            Column("workflow_id", Integer, index=True),
+            Column("create_time", DateTime),
+            Column("update_time", DateTime, nullable=True),
+            Column("request_state", JSONType),
+            Column("client_secret", String(255), nullable=True),
+            Column("uuid", UUIDType, nullable=False, index=True),
+        )
+
+        create_foreign_key(
+            "foreign_key_user_id",
+            tool_landing_request_table_name,
+            "galaxy_user",
+            ["user_id"],
+            ["id"],
+        )
+        create_foreign_key(
+            "foreign_key_user_id",
+            workflow_landing_request_table_name,
+            "galaxy_user",
+            ["user_id"],
+            ["id"],
+        )
+        create_foreign_key(
+            "foreign_key_stored_workflow_id",
+            workflow_landing_request_table_name,
+            "stored_workflow",
+            ["stored_workflow_id"],
+            ["id"],
+        )
+        create_foreign_key(
+            "foreign_key_workflow_id",
+            workflow_landing_request_table_name,
+            "workflow",
+            ["workflow_id"],
+            ["id"],
+        )
+
+        create_table(
+            tool_source_table_name,
+            Column("id", Integer, primary_key=True),
+            Column("hash", String(255), index=True),
+            Column("source", JSONType),
+        )
+        create_table(
+            tool_request_table_name,
+            Column("id", Integer, primary_key=True),
+            Column("request", JSONType),
+            Column("state", String(32)),
+            Column("state_message", JSONType),
+            Column("tool_source_id", Integer, index=True),
+            Column("history_id", Integer, index=True),
+        )
+
+        create_foreign_key(
+            "foreign_key_tool_source_id",
+            tool_request_table_name,
+            tool_source_table_name,
+            ["tool_source_id"],
+            ["id"],
+        )
+
+        create_foreign_key(
+            "foreign_key_history_id",
+            tool_request_table_name,
+            "history",
+            ["history_id"],
+            ["id"],
+        )
+
+        add_column(
+            job_table_name,
+            Column(request_column_name, Integer, default=None),
+        )
+
+        create_foreign_key(
+            "foreign_key_tool_request_id",
+            job_table_name,
+            tool_request_table_name,
+            ["tool_request_id"],
+            ["id"],
+        )
+
+        create_index(job_request_index_name, job_table_name, [request_column_name])
+
+        add_column(
+            workflow_request_to_input_dataset_table_name,
+            Column(workflow_input_request_column_name, JSONType, default=None),
+        )
+        add_column(
+            workflow_request_to_input_collection_table_name,
+            Column(workflow_input_request_column_name, JSONType, default=None),
+        )
+        add_column(
+            workflow_request_to_input_parameter_table_name,
+            Column(workflow_input_request_column_name, JSONType, default=None),
+        )
+
+
+def downgrade():
+    with transaction():
+        drop_column(workflow_request_to_input_dataset_table_name, workflow_input_request_column_name)
+        drop_column(workflow_request_to_input_collection_table_name, workflow_input_request_column_name)
+        drop_column(workflow_request_to_input_parameter_table_name, workflow_input_request_column_name)
+        drop_index(job_request_index_name, job_table_name)
+        drop_column(job_table_name, request_column_name)
+        drop_table(tool_request_table_name)
+        drop_table(tool_source_table_name)
+
+        drop_table(tool_landing_request_table_name)
+        drop_table(workflow_landing_request_table_name)
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/9a5207190a4d_remove_unique_constraint_from_role_name.py b/lib/galaxy/model/migrations/alembic/versions_gxy/9a5207190a4d_remove_unique_constraint_from_role_name.py
new file mode 100644
index 0000000000000000000000000000000000000000..36893551e7a46fa92b55d99a6e64fb5ee6063ab9
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/9a5207190a4d_remove_unique_constraint_from_role_name.py
@@ -0,0 +1,56 @@
+"""Remove unique constraint from role name, add not null constraint
+
+Revision ID: 9a5207190a4d
+Revises: a99a5b52ccb8
+Create Date: 2024-10-08 14:08:28.418055
+
+"""
+
+import logging
+
+from alembic import op
+from sqlalchemy import text
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.util import (
+    alter_column,
+    create_index,
+    drop_index,
+    transaction,
+)
+
+log = logging.getLogger(__name__)
+
+# revision identifiers, used by Alembic.
+revision = "9a5207190a4d"
+down_revision = "a99a5b52ccb8"
+branch_labels = None
+depends_on = None
+
+
+table_name = "role"
+column_name = "name"
+index_name = build_index_name(table_name, [column_name])
+
+
+def upgrade():
+    with transaction():
+        drop_index(index_name, table_name)
+        alter_column(table_name, column_name, nullable=False)
+        create_index(index_name, table_name, [column_name])
+
+
+def downgrade():
+    with transaction():
+        alter_column(table_name, column_name, nullable=True)
+
+        stmt = text("SELECT 1 FROM role GROUP BY name HAVING count(*) > 1")
+        has_nonunique_values = op.get_bind().scalar(stmt)
+        if not has_nonunique_values:
+            drop_index(index_name, table_name)
+            create_index(index_name, table_name, [column_name], unique=True)
+        else:
+            msg = f"""This downgrade requires creating a unique index on the `{table_name}.{column_name}` field.
+This operation cannot proceed due to the existence of non-unique values in that column, which are the result of Galaxy v24.2 (and above)
+operating under normal conditions. The current non-unique index will remain unchanged."""
+            log.error(msg)
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/9ef6431f3a4e_add_unique_constraint_to_group_role_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/9ef6431f3a4e_add_unique_constraint_to_group_role_.py
new file mode 100644
index 0000000000000000000000000000000000000000..f84d09d5b04367020448a19b1e0282d1d416c7ad
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/9ef6431f3a4e_add_unique_constraint_to_group_role_.py
@@ -0,0 +1,45 @@
+"""Add unique constraint to group_role_association
+
+Revision ID: 9ef6431f3a4e
+Revises: 13fe10b8e35b
+Create Date: 2024-09-09 15:01:20.426534
+
+"""
+
+from alembic import op
+
+from galaxy.model.migrations.data_fixes.association_table_fixer import GroupRoleAssociationDuplicateFix
+from galaxy.model.migrations.util import (
+    create_unique_constraint,
+    drop_constraint,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "9ef6431f3a4e"
+down_revision = "13fe10b8e35b"
+branch_labels = None
+depends_on = None
+
+table_name = "group_role_association"
+constraint_column_names = ["group_id", "role_id"]
+unique_constraint_name = (
+    "group_role_association_group_id_key"  # This is what the model's naming convention will generate.
+)
+
+
+def upgrade():
+    with transaction():
+        _remove_duplicate_records()
+        create_unique_constraint(unique_constraint_name, table_name, constraint_column_names)
+
+
+def downgrade():
+    with transaction():
+        drop_constraint(unique_constraint_name, table_name)
+
+
+def _remove_duplicate_records():
+    """Remove duplicate associations"""
+    connection = op.get_bind()
+    GroupRoleAssociationDuplicateFix(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/a4c3ef999ab5_add_index_on_tool_id_column_of_job_table.py b/lib/galaxy/model/migrations/alembic/versions_gxy/a4c3ef999ab5_add_index_on_tool_id_column_of_job_table.py
new file mode 100644
index 0000000000000000000000000000000000000000..004ff6a875c601fc52ef97981986bc5ee15bde19
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/a4c3ef999ab5_add_index_on_tool_id_column_of_job_table.py
@@ -0,0 +1,32 @@
+"""Add index on tool_id column of job table
+
+Revision ID: a4c3ef999ab5
+Revises: 75348cfb3715
+Create Date: 2025-02-05 14:55:13.348044
+
+"""
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.util import (
+    create_index,
+    drop_index,
+)
+
+# revision identifiers, used by Alembic.
+revision = "a4c3ef999ab5"
+down_revision = "75348cfb3715"
+branch_labels = None
+depends_on = None
+
+
+table_name = "job"
+column_name = "tool_id"
+index_name = build_index_name(table_name, column_name)
+
+
+def upgrade():
+    create_index(index_name, table_name, [column_name])
+
+
+def downgrade():
+    drop_index(index_name, table_name)
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/a99a5b52ccb8_add_workflow_source_and_workflow_source_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/a99a5b52ccb8_add_workflow_source_and_workflow_source_.py
new file mode 100644
index 0000000000000000000000000000000000000000..275f11df8f8c9a080cee2dcaf96e4ed37c85053f
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/a99a5b52ccb8_add_workflow_source_and_workflow_source_.py
@@ -0,0 +1,47 @@
+"""Add workflow_source and workflow_source_type and public column
+
+Revision ID: a99a5b52ccb8
+Revises: 7ffd33d5d144
+Create Date: 2024-10-10 14:23:29.485113
+
+"""
+
+import sqlalchemy as sa
+
+from galaxy.model.migrations.util import (
+    add_column,
+    column_exists,
+    drop_column,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "a99a5b52ccb8"
+down_revision = "7ffd33d5d144"
+branch_labels = None
+depends_on = None
+
+workflow_table_name = "workflow_landing_request"
+tool_table_name = "tool_landing_request"
+
+
+def drop_if_exists(table_name: str, column_name: str):
+    if column_exists(table_name, column_name, True):
+        drop_column(table_name, column_name)
+
+
+def upgrade():
+    with transaction():
+        add_column(workflow_table_name, sa.Column("workflow_source", sa.String(255), nullable=True))
+        add_column(workflow_table_name, sa.Column("workflow_source_type", sa.String(255), nullable=True))
+        add_column(workflow_table_name, sa.Column("public", sa.Boolean, nullable=False, server_default=sa.false()))
+        add_column(tool_table_name, sa.Column("public", sa.Boolean, nullable=False, server_default=sa.false()))
+
+
+def downgrade():
+    with transaction():
+        drop_column(workflow_table_name, "workflow_source")
+        drop_column(workflow_table_name, "workflow_source_type")
+        # For test.galaxyproject.org which was deployed from PR branch that didn't contain public column
+        drop_if_exists(workflow_table_name, "public")
+        drop_if_exists(tool_table_name, "public")
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/cbc46035eba0_chat_exchange_storage.py b/lib/galaxy/model/migrations/alembic/versions_gxy/cbc46035eba0_chat_exchange_storage.py
new file mode 100644
index 0000000000000000000000000000000000000000..c5767ac7ace7e5750e50e50760f3950be00aed1b
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/cbc46035eba0_chat_exchange_storage.py
@@ -0,0 +1,52 @@
+"""Chat exchange storage.
+
+Revision ID: cbc46035eba0
+Revises: b855b714e8b8
+Create Date: 2023-06-05 13:23:42.050738
+
+"""
+
+# from alembic import op
+# import sqlalchemy as sa
+
+from sqlalchemy import (
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    Text,
+)
+
+from galaxy.model.migrations.util import (
+    create_table,
+    drop_table,
+)
+
+# revision identifiers, used by Alembic.
+revision = "cbc46035eba0"
+down_revision = "a99a5b52ccb8"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    create_table(
+        "chat_exchange",
+        Column("id", Integer, primary_key=True),
+        Column("user_id", Integer, ForeignKey("galaxy_user.id")),
+        Column("job_id", Integer, ForeignKey("job.id"), nullable=True),
+    )
+
+    create_table(
+        "chat_exchange_message",
+        Column("id", Integer, primary_key=True),
+        Column("chat_exchange_id", Integer, ForeignKey("chat_exchange.id")),
+        Column("create_time", DateTime),
+        Column("message", Text),
+        Column("feedback", Integer, nullable=True),
+    )
+
+
+def downgrade():
+    drop_table("chat_exchange_message")
+    drop_table("chat_exchange")
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/d2d8f51ebb7e_merge_uuid_migration_into_dev.py b/lib/galaxy/model/migrations/alembic/versions_gxy/d2d8f51ebb7e_merge_uuid_migration_into_dev.py
new file mode 100644
index 0000000000000000000000000000000000000000..90b99f933888c6b841bf61c9a6251e453d9e0fc9
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/d2d8f51ebb7e_merge_uuid_migration_into_dev.py
@@ -0,0 +1,21 @@
+"""Merge uuid migration into dev
+
+Revision ID: d2d8f51ebb7e
+Revises: 04288b6a5b25, eee9229a9765, d4a650f47a3c
+Create Date: 2024-09-20 10:52:07.695199
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = "d2d8f51ebb7e"
+down_revision = ("04288b6a5b25", "eee9229a9765")
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/d619fdfa6168_username_column_unique_constraint.py b/lib/galaxy/model/migrations/alembic/versions_gxy/d619fdfa6168_username_column_unique_constraint.py
new file mode 100644
index 0000000000000000000000000000000000000000..de09d29097bb02cbdd8ccb004d45a493916178d4
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/d619fdfa6168_username_column_unique_constraint.py
@@ -0,0 +1,51 @@
+"""Username column unique constraint
+
+Revision ID: d619fdfa6168
+Revises: d2d8f51ebb7e
+Create Date: 2024-07-02 13:13:10.325586
+"""
+
+from alembic import op
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.data_fixes.user_table_fixer import UsernameDeduplicator
+from galaxy.model.migrations.util import (
+    create_index,
+    drop_index,
+    index_exists,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "d619fdfa6168"
+down_revision = "d2d8f51ebb7e"
+branch_labels = None
+depends_on = None
+
+table_name = "galaxy_user"
+column_name = "username"
+index_name = build_index_name(table_name, [column_name])
+
+
+def upgrade():
+    with transaction():
+        _fix_duplicate_usernames()
+        # Existing databases may have an existing index we no longer need
+        # New databases will not have that index, so we must check.
+        if index_exists(index_name, table_name, False):
+            drop_index(index_name, table_name)
+        # Create a UNIQUE index
+        create_index(index_name, table_name, [column_name], unique=True)
+
+
+def downgrade():
+    with transaction():
+        drop_index(index_name, table_name)
+        # Restore a non-unique index
+        create_index(index_name, table_name, [column_name])
+
+
+def _fix_duplicate_usernames():
+    """Fix records with duplicate usernames"""
+    connection = op.get_bind()
+    UsernameDeduplicator(connection).run()
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/eee9229a9765_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/eee9229a9765_.py
new file mode 100644
index 0000000000000000000000000000000000000000..46eb08793c9a9be83d2f35bc5996d8b4d3dbaa2e
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/eee9229a9765_.py
@@ -0,0 +1,21 @@
+"""Merge 2 head revisions after pulling 24.1 into dev
+
+Revision ID: eee9229a9765
+Revises: 570bce1e82f9, c63848676caf
+Create Date: 2024-06-13 11:50:03.226676
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = "eee9229a9765"
+down_revision = ("570bce1e82f9", "c63848676caf")
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass
diff --git a/lib/galaxy/model/migrations/data_fixes/__init__.py b/lib/galaxy/model/migrations/data_fixes/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b48aef46800de0c6f2ddbd9299fc7e401a396f5
--- /dev/null
+++ b/lib/galaxy/model/migrations/data_fixes/__init__.py
@@ -0,0 +1,4 @@
+"""
+Package contains code for fixing inconsistent data in the database that must be
+run together with a migration script.
+"""
diff --git a/lib/galaxy/model/migrations/data_fixes/association_table_fixer.py b/lib/galaxy/model/migrations/data_fixes/association_table_fixer.py
new file mode 100644
index 0000000000000000000000000000000000000000..711f266c5be1aa97357a5af3354a7df15b8e17e4
--- /dev/null
+++ b/lib/galaxy/model/migrations/data_fixes/association_table_fixer.py
@@ -0,0 +1,200 @@
+from abc import (
+    ABC,
+    abstractmethod,
+)
+
+from sqlalchemy import (
+    delete,
+    func,
+    null,
+    or_,
+    select,
+)
+
+from galaxy.model import (
+    GroupRoleAssociation,
+    UserGroupAssociation,
+    UserRoleAssociation,
+)
+
+
+class AssociationNullFix(ABC):
+
+    def __init__(self, connection):
+        self.connection = connection
+        self.assoc_model = self.association_model()
+        self.assoc_name = self.assoc_model.__tablename__
+        self.where_clause = self.build_where_clause()
+
+    def run(self):
+        invalid_assocs = self.count_associations_with_nulls()
+        if invalid_assocs:
+            self.delete_associations_with_nulls()
+
+    def count_associations_with_nulls(
+        self,
+    ):
+        """
+        Retrieve association records where one or both associated item ids are null.
+        """
+        select_stmt = select(func.count()).where(self.where_clause)
+        return self.connection.scalar(select_stmt)
+
+    def delete_associations_with_nulls(self):
+        """
+        Delete association records where one or both associated item ids are null.
+        """
+        delete_stmt = delete(self.assoc_model).where(self.where_clause)
+        self.connection.execute(delete_stmt)
+
+    @abstractmethod
+    def association_model(self):
+        """Return model class"""
+
+    @abstractmethod
+    def build_where_clause(self):
+        """Build where clause for filtering records containing nulls instead of associated item ids"""
+
+
+class UserGroupAssociationNullFix(AssociationNullFix):
+
+    def association_model(self):
+        return UserGroupAssociation
+
+    def build_where_clause(self):
+        return or_(UserGroupAssociation.user_id == null(), UserGroupAssociation.group_id == null())
+
+
+class UserRoleAssociationNullFix(AssociationNullFix):
+
+    def association_model(self):
+        return UserRoleAssociation
+
+    def build_where_clause(self):
+        return or_(UserRoleAssociation.user_id == null(), UserRoleAssociation.role_id == null())
+
+
+class GroupRoleAssociationNullFix(AssociationNullFix):
+
+    def association_model(self):
+        return GroupRoleAssociation
+
+    def build_where_clause(self):
+        return or_(GroupRoleAssociation.group_id == null(), GroupRoleAssociation.role_id == null())
+
+
+class AssociationDuplicateFix(ABC):
+
+    def __init__(self, connection):
+        self.connection = connection
+        self.assoc_model = self.association_model()
+        self.assoc_name = self.assoc_model.__tablename__
+
+    def run(self):
+        duplicate_assocs = self.select_duplicate_associations()
+        if duplicate_assocs:
+            self.delete_duplicate_associations(duplicate_assocs)
+
+    def select_duplicate_associations(self):
+        """Retrieve duplicate association records."""
+        select_stmt = self.build_duplicate_tuples_statement()
+        return self.connection.execute(select_stmt).all()
+
+    @abstractmethod
+    def association_model(self):
+        """Return model class"""
+
+    @abstractmethod
+    def build_duplicate_tuples_statement(self):
+        """
+        Build select statement returning a list of tuples (item1_id, item2_id) that have counts > 1
+        """
+
+    @abstractmethod
+    def build_duplicate_ids_statement(self, item1_id, item2_id):
+        """
+        Build select statement returning a list of ids for duplicate records retrieved via build_duplicate_tuples_statement().
+        """
+
+    def delete_duplicate_associations(self, records):
+        """
+        Delete duplicate association records retaining oldest record in each group of duplicates.
+        """
+        to_delete = []
+        for item1_id, item2_id in records:
+            to_delete += self._get_duplicates_to_delete(item1_id, item2_id)
+        for id in to_delete:
+            delete_stmt = delete(self.assoc_model).where(self.assoc_model.id == id)
+            self.connection.execute(delete_stmt)
+
+    def _get_duplicates_to_delete(self, item1_id, item2_id):
+        stmt = self.build_duplicate_ids_statement(item1_id, item2_id)
+        duplicates = self.connection.scalars(stmt).all()
+        # IMPORTANT: we slice to skip the first item ([1:]), which is the oldest record and SHOULD NOT BE DELETED.
+        return duplicates[1:]
+
+
+class UserGroupAssociationDuplicateFix(AssociationDuplicateFix):
+
+    def association_model(self):
+        return UserGroupAssociation
+
+    def build_duplicate_tuples_statement(self):
+        stmt = (
+            select(UserGroupAssociation.user_id, UserGroupAssociation.group_id)
+            .group_by(UserGroupAssociation.user_id, UserGroupAssociation.group_id)
+            .having(func.count() > 1)
+        )
+        return stmt
+
+    def build_duplicate_ids_statement(self, user_id, group_id):
+        stmt = (
+            select(UserGroupAssociation.id)
+            .where(UserGroupAssociation.user_id == user_id, UserGroupAssociation.group_id == group_id)
+            .order_by(UserGroupAssociation.update_time)
+        )
+        return stmt
+
+
+class UserRoleAssociationDuplicateFix(AssociationDuplicateFix):
+
+    def association_model(self):
+        return UserRoleAssociation
+
+    def build_duplicate_tuples_statement(self):
+        stmt = (
+            select(UserRoleAssociation.user_id, UserRoleAssociation.role_id)
+            .group_by(UserRoleAssociation.user_id, UserRoleAssociation.role_id)
+            .having(func.count() > 1)
+        )
+        return stmt
+
+    def build_duplicate_ids_statement(self, user_id, role_id):
+        stmt = (
+            select(UserRoleAssociation.id)
+            .where(UserRoleAssociation.user_id == user_id, UserRoleAssociation.role_id == role_id)
+            .order_by(UserRoleAssociation.update_time)
+        )
+        return stmt
+
+
+class GroupRoleAssociationDuplicateFix(AssociationDuplicateFix):
+
+    def association_model(self):
+        return GroupRoleAssociation
+
+    def build_duplicate_tuples_statement(self):
+        stmt = (
+            select(GroupRoleAssociation.group_id, GroupRoleAssociation.role_id)
+            .group_by(GroupRoleAssociation.group_id, GroupRoleAssociation.role_id)
+            .having(func.count() > 1)
+        )
+        return stmt
+
+    def build_duplicate_ids_statement(self, group_id, role_id):
+        stmt = (
+            select(GroupRoleAssociation.id)
+            .where(GroupRoleAssociation.group_id == group_id, GroupRoleAssociation.role_id == role_id)
+            .order_by(GroupRoleAssociation.update_time)
+        )
+        return stmt
diff --git a/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py b/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py
new file mode 100644
index 0000000000000000000000000000000000000000..4b9054872cd0f92bb9251a4f09b56db9859e05ca
--- /dev/null
+++ b/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py
@@ -0,0 +1,112 @@
+import uuid
+
+from sqlalchemy import (
+    func,
+    Result,
+    select,
+    text,
+    update,
+)
+
+from galaxy.model import User
+
+
+class UsernameDeduplicator:
+
+    def __init__(self, connection):
+        self.connection = connection
+
+    def run(self):
+        """
+        Deduplicate usernames by generating a unique value for all duplicates, keeping
+        the username of the most recently created user unchanged.
+        Records updated with the generated value are marked as deleted.
+        """
+        duplicates = self._get_duplicate_username_data()
+        prev_username = None
+        for id, username, _ in duplicates:
+            if username == prev_username:
+                new_username = self._generate_next_available_username(username)
+                stmt = update(User).where(User.id == id).values(username=new_username, deleted=True)
+                self.connection.execute(stmt)
+            else:
+                prev_username = username
+
+    def _get_duplicate_username_data(self) -> Result:
+        # Duplicate usernames
+        duplicates_stmt = select(User.username).group_by(User.username).having(func.count() > 1)
+        # User data for records with duplicate usernames (ordering: newest to oldest)
+        stmt = (
+            select(User.id, User.username, User.create_time)
+            .where(User.username.in_(duplicates_stmt))
+            .order_by(User.username, User.create_time.desc())
+        )
+        return self.connection.execute(stmt)
+
+    def _generate_next_available_username(self, username):
+        i = 1
+        while self.connection.execute(select(User).where(User.username == f"{username}-{i}")).first():
+            i += 1
+        return f"{username}-{i}"
+
+
+class EmailDeduplicator:
+
+    def __init__(self, connection):
+        self.connection = connection
+
+    def run(self):
+        """
+        Deduplicate user emails by generating a unique value for all duplicates, keeping
+        the email of the most recently created user that has one or more history unchanged.
+        If such a user does not exist, keep the oldest user.
+        Records updated with the generated value are marked as deleted (we presume them
+        to be invalid, and the user should not be able to login).
+        """
+        stmt = select(User.email).group_by(User.email).having(func.count() > 1)
+        duplicate_emails = self.connection.scalars(stmt)
+        for email in duplicate_emails:
+            users = self._get_users_with_same_email(email)
+            user_with_history = self._find_oldest_user_with_history(users)
+            duplicates = self._get_users_to_deduplicate(users, user_with_history)
+            self._deduplicate_users(email, duplicates)
+
+    def _get_users_with_same_email(self, email: str):
+        sql = text(
+            """
+            SELECT u.id, EXISTS(SELECT h.id FROM history h WHERE h.user_id = u.id)
+            FROM galaxy_user u
+            WHERE u.email = :email
+            ORDER BY u.create_time
+            """
+        )
+        params = {"email": email}
+        return self.connection.execute(sql, params).all()
+
+    def _find_oldest_user_with_history(self, users):
+        for user_id, exists in users:
+            if exists:
+                return user_id
+        return None
+
+    def _get_users_to_deduplicate(self, users, user_with_history):
+        if user_with_history:
+            # Preserve the oldest user with a history
+            return [user_id for user_id, _ in users if user_id != user_with_history]
+        else:
+            # Preserve the oldest user
+            return [user_id for user_id, _ in users[1:]]
+
+    def _deduplicate_users(self, email, to_deduplicate):
+        for id in to_deduplicate:
+            new_email = self._generate_replacement_for_duplicate_email(email)
+            stmt = update(User).where(User.id == id).values(email=new_email, deleted=True)
+            self.connection.execute(stmt)
+
+    def _generate_replacement_for_duplicate_email(self, email: str) -> str:
+        """
+        Generate a replacement for a duplicate email value. The new value consists of the original
+        email and a unique suffix. Since the original email is part of the new value, it will be
+        possible to retrieve the user record based on this value, if needed.
+        """
+        return f"{email}-{uuid.uuid4()}"
diff --git a/lib/galaxy/model/migrations/dbscript.py b/lib/galaxy/model/migrations/dbscript.py
index 2e17c361d4f61c20d65c394eff8da071da5cde83..ec0180676db337abc993308f23c52ce3f1879667 100644
--- a/lib/galaxy/model/migrations/dbscript.py
+++ b/lib/galaxy/model/migrations/dbscript.py
@@ -42,8 +42,10 @@ REVISION_TAGS = {
     "23.2": "8a19186a6ee7",
     "release_24.0": "55f02fd8ab6c",
     "24.0": "55f02fd8ab6c",
-    "release_24.1": "c63848676caf",
-    "24.1": "c63848676caf",
+    "release_24.1": "04288b6a5b25",
+    "24.1": "04288b6a5b25",
+    "release_24.2": "a4c3ef999ab5",
+    "24.2": "a4c3ef999ab5",
 }
 
 
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index e48d639e92f61e24526e4355c72b61636f12c527..77dc660d69f27a6822801dfb05a3e5fc59460b36 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -28,6 +28,8 @@ DEFAULT_CONFIG_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.
 DEFAULT_CONFIG_NAMES = ["galaxy", "universe_wsgi"]
 DEFAULT_CONFIG_PREFIX = ""
 DEFAULT_DATABASE = "galaxy"
+ALEMBIC_CONFIG = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "migrations", "alembic.ini"))
+
 
 DATABASE = {
     "galaxy": {
@@ -163,6 +165,9 @@ def manage_db():
     _insert_x_argument("tsi_url", tsi_config.url)
     _insert_x_argument("gxy_url", gxy_config.url)
 
+    sys.argv.insert(1, "--config")
+    sys.argv.insert(2, ALEMBIC_CONFIG)
+
     if "heads" in sys.argv and "upgrade" in sys.argv:
         i = sys.argv.index("heads")
         sys.argv[i] = f"{GXY}@head"
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 9709ea77e4f0435da2430063d5052757696ed9ea..85fcb7be8532284b13431acd3c2e8dcd796a7ca7 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -1,33 +1,48 @@
 import logging
 import socket
+import sqlite3
 from datetime import (
     datetime,
     timedelta,
 )
-from typing import List
+from typing import (
+    List,
+    Optional,
+)
 
 from sqlalchemy import (
     and_,
+    delete,
     false,
     func,
+    insert,
     not_,
     or_,
     select,
+    text,
 )
+from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import joinedload
-from sqlalchemy.sql import text
 
 import galaxy.model
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model import (
     Dataset,
+    DatasetCollection,
     DatasetPermissions,
+    DefaultHistoryPermissions,
+    DefaultUserPermissions,
     Group,
     GroupRoleAssociation,
     HistoryDatasetAssociationDisplayAtAuthorization,
     Library,
     LibraryDataset,
+    LibraryDatasetCollectionAssociation,
     LibraryDatasetDatasetAssociation,
+    LibraryDatasetDatasetAssociationPermissions,
     LibraryDatasetPermissions,
+    LibraryFolder,
+    LibraryFolderPermissions,
     LibraryPermissions,
     Role,
     User,
@@ -35,6 +50,10 @@ from galaxy.model import (
     UserRoleAssociation,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.role import (
+    get_npns_roles,
+    get_private_user_role,
+)
 from galaxy.security import (
     Action,
     get_permitted_actions,
@@ -47,23 +66,18 @@ log = logging.getLogger(__name__)
 
 
 class GalaxyRBACAgent(RBACAgent):
-    def __init__(self, model, permitted_actions=None):
-        self.model = model
+    def __init__(self, sa_session, permitted_actions=None):
+        self.sa_session = sa_session
         if permitted_actions:
             self.permitted_actions = permitted_actions
         # List of "library_item" objects and their associated permissions and info template objects
         self.library_item_assocs = (
-            (self.model.Library, self.model.LibraryPermissions),
-            (self.model.LibraryFolder, self.model.LibraryFolderPermissions),
-            (self.model.LibraryDataset, self.model.LibraryDatasetPermissions),
-            (self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions),
+            (Library, LibraryPermissions),
+            (LibraryFolder, LibraryFolderPermissions),
+            (LibraryDataset, LibraryDatasetPermissions),
+            (LibraryDatasetDatasetAssociation, LibraryDatasetDatasetAssociationPermissions),
         )
 
-    @property
-    def sa_session(self):
-        """Returns a SQLAlchemy session"""
-        return self.model.context
-
     def sort_by_attr(self, seq, attr):
         """
         Sort the sequence of objects by object's attribute
@@ -80,22 +94,11 @@ class GalaxyRBACAgent(RBACAgent):
         intermed.sort()
         return [_[-1] for _ in intermed]
 
-    def _get_npns_roles(self, trans):
-        """
-        non-private, non-sharing roles
-        """
-        stmt = (
-            select(Role)
-            .where(and_(Role.deleted == false(), Role.type != Role.types.PRIVATE, Role.type != Role.types.SHARING))
-            .order_by(Role.name)
-        )
-        return trans.sa_session.scalars(stmt)
-
     def get_all_roles(self, trans, cntrller):
         admin_controller = cntrller in ["library_admin"]
         roles = set()
         if not trans.user:
-            return self._get_npns_roles(trans)
+            return get_npns_roles(trans.sa_session)
         if admin_controller:
             # The library is public and the user is an admin, so all roles are legitimate
             stmt = select(Role).where(Role.deleted == false()).order_by(Role.name)
@@ -108,7 +111,7 @@ class GalaxyRBACAgent(RBACAgent):
             for role in self.get_sharing_roles(trans.user):
                 roles.add(role)
             # Add all remaining non-private, non-sharing roles
-            for role in self._get_npns_roles(trans):
+            for role in get_npns_roles(trans.sa_session):
                 roles.add(role)
         return self.sort_by_attr(list(roles), "name")
 
@@ -146,41 +149,19 @@ class GalaxyRBACAgent(RBACAgent):
         else:
             limit = None
         total_count = None
-        if isinstance(item, self.model.Library) and self.library_is_public(item):
+        if isinstance(item, Library) and self.library_is_public(item):
             is_public_item = True
-        elif isinstance(item, self.model.Dataset) and self.dataset_is_public(item):
+        elif isinstance(item, Dataset) and self.dataset_is_public(item):
             is_public_item = True
-        elif isinstance(item, self.model.LibraryFolder):
+        elif isinstance(item, LibraryFolder):
             is_public_item = True
         else:
             is_public_item = False
         # Admins can always choose from all non-deleted roles
         if trans.user_is_admin or trans.app.config.expose_user_email:
-            if trans.user_is_admin:
-                stmt = select(Role).where(Role.deleted == false())
-            else:
-                # User is not an admin but the configuration exposes all private roles to all users.
-                stmt = select(Role).where(and_(Role.deleted == false(), Role.type == Role.types.PRIVATE))
-            if search_query:
-                stmt = stmt.where(Role.name.like(search_query, escape="/"))
-
-            count_stmt = select(func.count()).select_from(stmt)
-            total_count = trans.sa_session.scalar(count_stmt)
-
-            if limit is not None:
-                # Takes the least number of results from beginning that includes the requested page
-                stmt = stmt.order_by(Role.name).limit(limit)
-                page_start = (page * page_limit) - page_limit
-                page_end = page_start + page_limit
-                if total_count < page_start + 1:
-                    # Return empty list if there are less results than the requested position
-                    roles = []
-                else:
-                    roles = trans.sa_session.scalars(stmt).all()
-                    roles = roles[page_start:page_end]
-            else:
-                stmt = stmt.order_by(Role.name)
-                roles = trans.sa_session.scalars(stmt).all()
+            roles = _get_valid_roles_exposed(
+                trans.sa_session, search_query, trans.user_is_admin, limit, page, page_limit
+            )
         # Non-admin and public item
         elif is_public_item:
             # Add the current user's private role
@@ -189,7 +170,7 @@ class GalaxyRBACAgent(RBACAgent):
             for role in self.get_sharing_roles(trans.user):
                 roles.append(role)
             # Add all remaining non-private, non-sharing roles
-            for role in self._get_npns_roles(trans):
+            for role in get_npns_roles(trans.sa_session):
                 roles.append(role)
         # User will see all the roles derived from the access roles on the item
         else:
@@ -245,8 +226,8 @@ class GalaxyRBACAgent(RBACAgent):
         """
         admin_controller = cntrller in ["library_admin"]
         roles = set()
-        if (isinstance(item, self.model.Library) and self.library_is_public(item)) or (
-            isinstance(item, self.model.Dataset) and self.dataset_is_public(item)
+        if (isinstance(item, Library) and self.library_is_public(item)) or (
+            isinstance(item, Dataset) and self.dataset_is_public(item)
         ):
             return self.get_all_roles(trans, cntrller)
         # If item has roles associated with the access permission, we need to start with them.
@@ -279,13 +260,13 @@ class GalaxyRBACAgent(RBACAgent):
         """
         role_type = role.type
         if user:
-            if role_type == self.model.Role.types.PRIVATE:
+            if role_type == Role.types.PRIVATE:
                 return role == self.get_private_user_role(user)
-            if role_type == self.model.Role.types.SHARING:
+            if role_type == Role.types.SHARING:
                 return role in self.get_sharing_roles(user)
             # If role_type is neither private nor sharing, it's ok to display
             return True
-        return role_type != self.model.Role.types.PRIVATE and role_type != self.model.Role.types.SHARING
+        return role_type != Role.types.PRIVATE and role_type != Role.types.SHARING
 
     def allow_action(self, roles, action, item):
         """
@@ -336,7 +317,7 @@ class GalaxyRBACAgent(RBACAgent):
         ret_permissions = {}
         if len(permission_items) > 0:
             # SM: NB: LibraryDatasets became Datasets for some odd reason.
-            if isinstance(permission_items[0], trans.model.LibraryDataset):
+            if isinstance(permission_items[0], LibraryDataset):
                 ids = [item.library_dataset_id for item in permission_items]
                 stmt = select(LibraryDatasetPermissions).where(
                     and_(
@@ -355,7 +336,7 @@ class GalaxyRBACAgent(RBACAgent):
                     ret_permissions[item.library_dataset_id] = []
                 for permission in permissions:
                     ret_permissions[permission.library_dataset_id].append(permission)
-            elif isinstance(permission_items[0], trans.model.Dataset):
+            elif isinstance(permission_items[0], Dataset):
                 ids = [item.id for item in permission_items]
 
                 stmt = select(DatasetPermissions).where(
@@ -506,7 +487,7 @@ class GalaxyRBACAgent(RBACAgent):
     def item_permission_map_for_add(self, trans, user_roles, libitems):
         return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems)
 
-    def can_access_dataset(self, user_roles, dataset: galaxy.model.Dataset):
+    def can_access_dataset(self, user_roles, dataset: Dataset):
         # SM: dataset_is_public will access dataset.actions, which is a
         # backref that causes a query to be made to DatasetPermissions
         retval = self.dataset_is_public(dataset) or self.allow_action(
@@ -525,7 +506,7 @@ class GalaxyRBACAgent(RBACAgent):
 
         return True
 
-    def can_access_collection(self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection):
+    def can_access_collection(self, user_roles: List[Role], collection: DatasetCollection):
         action_tuples = collection.dataset_action_tuples
         if not self.can_access_datasets(user_roles, action_tuples):
             return False
@@ -606,21 +587,21 @@ class GalaxyRBACAgent(RBACAgent):
         return False
 
     def can_access_library_item(self, roles, item, user):
-        if isinstance(item, self.model.Library):
+        if isinstance(item, Library):
             return self.can_access_library(roles, item)
-        elif isinstance(item, self.model.LibraryFolder):
+        elif isinstance(item, LibraryFolder):
             return (
                 self.can_access_library(roles, item.parent_library) and self.check_folder_contents(user, roles, item)[0]
             )
-        elif isinstance(item, self.model.LibraryDataset):
+        elif isinstance(item, LibraryDataset):
             return self.can_access_library(roles, item.folder.parent_library) and self.can_access_dataset(
                 roles, item.library_dataset_dataset_association.dataset
             )
-        elif isinstance(item, self.model.LibraryDatasetDatasetAssociation):
+        elif isinstance(item, LibraryDatasetDatasetAssociation):
             return self.can_access_library(
                 roles, item.library_dataset.folder.parent_library
             ) and self.can_access_dataset(roles, item.dataset)
-        elif isinstance(item, self.model.LibraryDatasetCollectionAssociation):
+        elif isinstance(item, LibraryDatasetCollectionAssociation):
             return self.can_access_library(roles, item.folder.parent_library)
         else:
             log.warning(f"Unknown library item type: {type(item)}")
@@ -665,7 +646,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         datasets = datasets or []
         perms = {}
         for dataset in datasets:
-            if not isinstance(dataset, self.model.Dataset):
+            if not isinstance(dataset, Dataset):
                 dataset = dataset.dataset
             these_perms = {}
             # initialize blank perms
@@ -707,43 +688,29 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     perms[action].extend([_ for _ in role_ids if _ not in perms[action]])
         return perms
 
-    def associate_components(self, **kwd):
-        if "user" in kwd:
-            if "group" in kwd:
-                return self.associate_user_group(kwd["user"], kwd["group"])
-            elif "role" in kwd:
-                return self.associate_user_role(kwd["user"], kwd["role"])
-        elif "role" in kwd:
-            if "group" in kwd:
-                return self.associate_group_role(kwd["group"], kwd["role"])
-        if "action" in kwd:
-            if "dataset" in kwd and "role" in kwd:
-                return self.associate_action_dataset_role(kwd["action"], kwd["dataset"], kwd["role"])
-        raise Exception(f"No valid method of associating provided components: {kwd}")
-
     def associate_user_group(self, user, group):
-        assoc = self.model.UserGroupAssociation(user, group)
+        assoc = UserGroupAssociation(user, group)
         self.sa_session.add(assoc)
         with transaction(self.sa_session):
             self.sa_session.commit()
         return assoc
 
     def associate_user_role(self, user, role):
-        assoc = self.model.UserRoleAssociation(user, role)
+        assoc = UserRoleAssociation(user, role)
         self.sa_session.add(assoc)
         with transaction(self.sa_session):
             self.sa_session.commit()
         return assoc
 
     def associate_group_role(self, group, role):
-        assoc = self.model.GroupRoleAssociation(group, role)
+        assoc = GroupRoleAssociation(group, role)
         self.sa_session.add(assoc)
         with transaction(self.sa_session):
             self.sa_session.commit()
         return assoc
 
     def associate_action_dataset_role(self, action, dataset, role):
-        assoc = self.model.DatasetPermissions(action, dataset, role)
+        assoc = DatasetPermissions(action, dataset, role)
         self.sa_session.add(assoc)
         with transaction(self.sa_session):
             self.sa_session.commit()
@@ -768,34 +735,20 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         if auto_create and user.id is None:
             # New user, directly create private role
             return self.create_private_user_role(user)
-        stmt = (
-            select(Role)
-            .where(
-                and_(
-                    UserRoleAssociation.user_id == user.id,
-                    Role.id == UserRoleAssociation.role_id,
-                    Role.type == Role.types.PRIVATE,
-                )
-            )
-            .distinct()
-        )
-        role = self.sa_session.execute(stmt).scalar_one_or_none()
-        if not role:
-            if auto_create:
-                return self.create_private_user_role(user)
-            else:
-                return None
+        role = get_private_user_role(user, self.sa_session)
+        if not role and auto_create:
+            role = self.create_private_user_role(user)
         return role
 
     def get_role(self, name, type=None):
-        type = type or self.model.Role.types.SYSTEM
+        type = type or Role.types.SYSTEM
         # will raise exception if not found
         stmt = select(Role).where(and_(Role.name == name, Role.type == type))
         return self.sa_session.execute(stmt).scalar_one()
 
     def create_role(self, name, description, in_users, in_groups, create_group_for_role=False, type=None):
-        type = type or self.model.Role.types.SYSTEM
-        role = self.model.Role(name=name, description=description, type=type)
+        type = type or Role.types.SYSTEM
+        role = Role(name=name, description=description, type=type)
         self.sa_session.add(role)
         # Create the UserRoleAssociations
         for user in [self.sa_session.get(User, x) for x in in_users]:
@@ -805,7 +758,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
             self.associate_group_role(group, role)
         if create_group_for_role:
             # Create the group
-            group = self.model.Group(name=name)
+            group = Group(name=name)
             self.sa_session.add(group)
             # Associate the group with the role
             self.associate_group_role(group, role)
@@ -817,10 +770,13 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         return role, num_in_groups
 
     def get_sharing_roles(self, user):
-        stmt = select(Role).where(
-            and_((Role.name).like(f"Sharing role for: %{user.email}%"), Role.type == Role.types.SHARING)
+        stmt = (
+            select(Role)
+            .join(Role.users)
+            .where(UserRoleAssociation.user_id == user.id)
+            .where(Role.type == Role.types.SHARING)
         )
-        return self.sa_session.scalars(stmt)
+        return self.sa_session.scalars(stmt).all()
 
     def user_set_default_permissions(
         self,
@@ -852,7 +808,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         for action, roles in permissions.items():
             if isinstance(action, Action):
                 action = action.action
-            for dup in [self.model.DefaultUserPermissions(user, action, role) for role in roles]:
+            for dup in [DefaultUserPermissions(user, action, role) for role in roles]:
                 self.sa_session.add(dup)
                 flush_needed = True
         if flush_needed:
@@ -892,7 +848,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         for action, roles in permissions.items():
             if isinstance(action, Action):
                 action = action.action
-            for dhp in [self.model.DefaultHistoryPermissions(history, action, role) for role in roles]:
+            for dhp in [DefaultHistoryPermissions(history, action, role) for role in roles]:
                 self.sa_session.add(dhp)
                 flush_needed = True
         if flush_needed:
@@ -943,7 +899,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
             for _, roles in _walk_action_roles(permissions, self.permitted_actions.DATASET_ACCESS):
                 dataset_access_roles.extend(roles)
 
-            if len(dataset_access_roles) != 1 or dataset_access_roles[0].type != self.model.Role.types.PRIVATE:
+            if len(dataset_access_roles) != 1 or dataset_access_roles[0].type != Role.types.PRIVATE:
                 return galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE
 
         flush_needed = False
@@ -961,7 +917,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     role_id = role.id
                 else:
                     role_id = role
-                dp = self.model.DatasetPermissions(action, dataset, role_id=role_id)
+                dp = DatasetPermissions(action, dataset, role_id=role_id)
                 self.sa_session.add(dp)
                 flush_needed = True
         if flush_needed and flush:
@@ -991,7 +947,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     self.sa_session.delete(dp)
                     flush_needed = True
             # Add the new specific permission on the dataset
-            for dp in [self.model.DatasetPermissions(action, dataset, role) for role in roles]:
+            for dp in [DatasetPermissions(action, dataset, role) for role in roles]:
                 self.sa_session.add(dp)
                 flush_needed = True
         if flush_needed:
@@ -1014,9 +970,9 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         return permissions
 
     def copy_dataset_permissions(self, src, dst, flush=True):
-        if not isinstance(src, self.model.Dataset):
+        if not isinstance(src, Dataset):
             src = src.dataset
-        if not isinstance(dst, self.model.Dataset):
+        if not isinstance(dst, Dataset):
             dst = dst.dataset
         self.set_all_dataset_permissions(dst, self.get_permissions(src), flush=flush)
 
@@ -1025,7 +981,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         intersect = None
         users = users or []
         for user in users:
-            roles = [ura.role for ura in user.roles if ura.role.type == self.model.Role.types.SHARING]
+            roles = [ura.role for ura in user.roles if ura.role.type == Role.types.SHARING]
             if intersect is None:
                 intersect = roles
             else:
@@ -1042,16 +998,18 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     sharing_role = role
                     break
         if sharing_role is None:
-            sharing_role = self.model.Role(
-                name=f"Sharing role for: {', '.join(u.email for u in users)}", type=self.model.Role.types.SHARING
-            )
-            self.sa_session.add(sharing_role)
-            with transaction(self.sa_session):
-                self.sa_session.commit()
-            for user in users:
-                self.associate_components(user=user, role=sharing_role)
+            sharing_role = self._create_sharing_role(users)
         self.set_dataset_permission(dataset, {self.permitted_actions.DATASET_ACCESS: [sharing_role]})
 
+    def _create_sharing_role(self, users):
+        sharing_role = Role(name=f"Sharing role for: {', '.join(u.email for u in users)}", type=Role.types.SHARING)
+        self.sa_session.add(sharing_role)
+        with transaction(self.sa_session):
+            self.sa_session.commit()
+        for user in users:
+            self.associate_user_role(user, sharing_role)
+        return sharing_role
+
     def set_all_library_permissions(self, trans, library_item, permissions=None):
         # Set new permissions on library_item, eliminating all current permissions
         flush_needed = False
@@ -1068,7 +1026,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     for role_assoc in [permission_class(action, library_item, role) for role in roles]:
                         self.sa_session.add(role_assoc)
                         flush_needed = True
-                    if isinstance(library_item, self.model.LibraryDatasetDatasetAssociation):
+                    if isinstance(library_item, LibraryDatasetDatasetAssociation):
                         # Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
                         # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
                         # permission.  In this case, we'll reset this permission to the library_item user's private role.
@@ -1107,14 +1065,12 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     self.sa_session.delete(item_permission)
                     flush_needed = True
             # Add the new specific permission on the library item
-            if isinstance(library_item, self.model.LibraryDataset):
-                for item_permission in [
-                    self.model.LibraryDatasetPermissions(action, library_item, role) for role in roles
-                ]:
+            if isinstance(library_item, LibraryDataset):
+                for item_permission in [LibraryDatasetPermissions(action, library_item, role) for role in roles]:
                     self.sa_session.add(item_permission)
                     flush_needed = True
-            elif isinstance(library_item, self.model.LibraryPermissions):
-                for item_permission in [self.model.LibraryPermissions(action, library_item, role) for role in roles]:
+            elif isinstance(library_item, LibraryPermissions):
+                for item_permission in [LibraryPermissions(action, library_item, role) for role in roles]:
                     self.sa_session.add(item_permission)
                     flush_needed = True
         if flush_needed:
@@ -1172,7 +1128,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
             if not dataset.purged and not self.dataset_is_public(dataset):
                 self.make_dataset_public(dataset)
 
-    def dataset_is_public(self, dataset: galaxy.model.Dataset):
+    def dataset_is_public(self, dataset: Dataset):
         """
         A dataset is considered public if there are no "access" actions
         associated with it.  Any other actions ( 'manage permissions',
@@ -1215,7 +1171,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
             return False
         else:
             access_role = access_roles[0]
-            return access_role.type == self.model.Role.types.PRIVATE
+            return access_role.type == Role.types.PRIVATE
 
     def datasets_are_public(self, trans, datasets):
         """
@@ -1315,7 +1271,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     # permission on this dataset, or the dataset is not accessible.
                     # Since we have more than 1 role, none of them can be private.
                     for role in in_roles:
-                        if role.type == self.model.Role.types.PRIVATE:
+                        if role.type == Role.types.PRIVATE:
                             private_role_found = True
                             break
                 if len(in_roles) == 1:
@@ -1379,7 +1335,7 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                     f"Invalid class ({target_library_item.__class__}) specified for target_library_item ({target_library_item.__class__.__name__})"
                 )
             # Make sure user's private role is included
-            private_role = self.model.security_agent.get_private_user_role(user)
+            private_role = self.get_private_user_role(user)
             for action in self.permitted_actions.values():
                 if not found_permission_class.filter_by(role_id=private_role.id, action=action.action).first():
                     lp = found_permission_class(action.action, target_library_item, private_role)
@@ -1428,9 +1384,9 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         for action in actions_to_check:
             if self.allow_action(roles, action, library_item):
                 return True, hidden_folder_ids
-        if isinstance(library_item, self.model.Library):
+        if isinstance(library_item, Library):
             return self.show_library_item(user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids="")
-        if isinstance(library_item, self.model.LibraryFolder):
+        if isinstance(library_item, LibraryFolder):
             for folder in library_item.active_folders:
                 can_show, hidden_folder_ids = self.show_library_item(
                     user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids
@@ -1454,11 +1410,11 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
         """
         hidden_folder_ids = hidden_folder_ids or []
         showable_folders = showable_folders or []
-        if isinstance(library_item, self.model.Library):
+        if isinstance(library_item, Library):
             return self.get_showable_folders(
                 user, roles, library_item.root_folder, actions_to_check, showable_folders=[]
             )
-        if isinstance(library_item, self.model.LibraryFolder):
+        if isinstance(library_item, LibraryFolder):
             if library_item.id not in hidden_folder_ids:
                 for action in actions_to_check:
                     if self.allow_action(roles, action, library_item):
@@ -1468,62 +1424,170 @@ WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :
                 self.get_showable_folders(user, roles, folder, actions_to_check, showable_folders=showable_folders)
         return showable_folders
 
-    def set_entity_user_associations(self, users=None, roles=None, groups=None, delete_existing_assocs=True):
-        users = users or []
-        roles = roles or []
-        groups = groups or []
-        for user in users:
-            if delete_existing_assocs:
-                flush_needed = False
-                for a in user.non_private_roles + user.groups:
-                    self.sa_session.delete(a)
-                    flush_needed = True
-                if flush_needed:
-                    with transaction(self.sa_session):
-                        self.sa_session.commit()
-            self.sa_session.refresh(user)
-            for role in roles:
-                # Make sure we are not creating an additional association with a PRIVATE role
-                if role not in [x.role for x in user.roles]:
-                    self.associate_components(user=user, role=role)
-            for group in groups:
-                self.associate_components(user=user, group=group)
+    def set_user_group_and_role_associations(
+        self,
+        user: User,
+        *,
+        group_ids: Optional[List[int]] = None,
+        role_ids: Optional[List[int]] = None,
+    ) -> None:
+        """
+        Set user groups and user roles, replacing current associations.
 
-    def set_entity_group_associations(self, groups=None, users=None, roles=None, delete_existing_assocs=True):
-        users = users or []
-        roles = roles or []
-        groups = groups or []
-        for group in groups:
-            if delete_existing_assocs:
-                flush_needed = False
-                for a in group.roles + group.users:
-                    self.sa_session.delete(a)
-                    flush_needed = True
-                if flush_needed:
-                    with transaction(self.sa_session):
-                        self.sa_session.commit()
-            for role in roles:
-                self.associate_components(group=group, role=role)
-            for user in users:
-                self.associate_components(group=group, user=user)
+        Associations are set only if a list of new associations is provided.
+        If the provided list is empty, existing associations will be removed.
+        If the provided value is None, existing associations will not be updated.
+        """
+        self._persist_new_model(user)
+        if group_ids is not None:
+            self._set_user_groups(user, group_ids)
+        if role_ids is not None:
+            self._set_user_roles(user, role_ids)
+        # Commit only if both user groups and user roles have been set.
+        self.sa_session.commit()
+
+    def set_group_user_and_role_associations(
+        self,
+        group: Group,
+        *,
+        user_ids: Optional[List[int]] = None,
+        role_ids: Optional[List[int]] = None,
+    ) -> None:
+        """
+        Set group users and group roles, replacing current associations.
 
-    def set_entity_role_associations(self, roles=None, users=None, groups=None, delete_existing_assocs=True):
-        users = users or []
-        roles = roles or []
-        groups = groups or []
-        for role in roles:
-            if delete_existing_assocs:
-                flush_needed = False
-                for a in role.users + role.groups:
-                    self.sa_session.delete(a)
-                    flush_needed = True
-                if flush_needed:
-                    with transaction(self.sa_session):
-                        self.sa_session.commit()
-            for user in users:
-                self.associate_components(user=user, role=role)
-            for group in groups:
-                self.associate_components(group=group, role=role)
+        Associations are set only if a list of new associations is provided.
+        If the provided list is empty, existing associations will be removed.
+        If the provided value is None, existing associations will not be updated.
+        """
+        self._persist_new_model(group)
+        if user_ids is not None:
+            self._set_group_users(group, user_ids)
+        if role_ids is not None:
+            self._set_group_roles(group, role_ids)
+        # Commit only if both group users and group roles have been set.
+        self.sa_session.commit()
+
+    def set_role_user_and_group_associations(
+        self,
+        role: Role,
+        *,
+        user_ids: Optional[List[int]] = None,
+        group_ids: Optional[List[int]] = None,
+    ) -> None:
+        """
+        Set role users and role groups, replacing current associations.
+
+        Associations are set only if a list of new associations is provided.
+        If the provided list is empty, existing associations will be removed.
+        If the provided value is None, existing associations will not be updated.
+        """
+        self._persist_new_model(role)
+        if user_ids is not None:
+            self._set_role_users(role, user_ids)
+        if group_ids is not None:
+            self._set_role_groups(role, group_ids)
+        # Commit only if both role users and role groups have been set.
+        self.sa_session.commit()
+
+    def _set_user_groups(self, user, group_ids):
+        delete_stmt = delete(UserGroupAssociation).where(UserGroupAssociation.user_id == user.id)
+        insert_values = [{"user_id": user.id, "group_id": group_id} for group_id in group_ids]
+        self._set_associations(user, UserGroupAssociation, delete_stmt, insert_values)
+
+    def _set_user_roles(self, user, role_ids):
+        # Do not include user's private role association in delete statement.
+        delete_stmt = delete(UserRoleAssociation).where(UserRoleAssociation.user_id == user.id)
+        private_role = get_private_user_role(user, self.sa_session)
+        if not private_role:
+            log.warning("User %s does not have a private role assigned", user)
+        else:
+            delete_stmt = delete_stmt.where(UserRoleAssociation.role_id != private_role.id)
+        role_ids = self._filter_private_roles(role_ids)
+
+        insert_values = [{"user_id": user.id, "role_id": role_id} for role_id in role_ids]
+        self._set_associations(user, UserRoleAssociation, delete_stmt, insert_values)
+
+    def _filter_private_roles(self, role_ids):
+        """Filter out IDs of private roles: those should not be assignable via UI"""
+        stmt = select(Role.id).where(Role.id.in_(role_ids)).where(Role.type == Role.types.PRIVATE)
+        private_role_ids = self.sa_session.scalars(stmt).all()
+        # We could simply select only private roles; however, that would get rid of potential duplicates
+        # and invalid role_ids; which would hide any bugs that should be caught in the _set_associations() method.
+        return [role_id for role_id in role_ids if role_id not in private_role_ids]
+
+    def _set_group_users(self, group, user_ids):
+        delete_stmt = delete(UserGroupAssociation).where(UserGroupAssociation.group_id == group.id)
+        insert_values = [{"group_id": group.id, "user_id": user_id} for user_id in user_ids]
+        self._set_associations(group, UserGroupAssociation, delete_stmt, insert_values)
+
+    def _set_group_roles(self, group, role_ids):
+        delete_stmt = delete(GroupRoleAssociation).where(GroupRoleAssociation.group_id == group.id)
+        insert_values = [{"group_id": group.id, "role_id": role_id} for role_id in role_ids]
+        self._set_associations(group, GroupRoleAssociation, delete_stmt, insert_values)
+
+    def _set_role_users(self, role, user_ids):
+        # Do not set users if the role is private
+        # Even though we do not expect to be handling a private role here, the following code is
+        # a safeguard against deleting a user-role-association record for a private role.
+        if role.type == Role.types.PRIVATE:
+            return
+
+        # First, check previously associated users to:
+        # - delete DefaultUserPermissions for users that are being removed from this role;
+        # - delete DefaultHistoryPermissions for histories associated with users that are being removed from this role.
+        for ura in role.users:
+            if ura.user_id not in user_ids:  # If a user will be removed from this role, then:
+                user = self.sa_session.get(User, ura.user_id)
+                # Delete DefaultUserPermissions for this user
+                for dup in user.default_permissions:
+                    if role == dup.role:
+                        self.sa_session.delete(dup)
+                # Delete DefaultHistoryPermissions for histories associated with this user
+                for history in user.histories:
+                    for dhp in history.default_permissions:
+                        if role == dhp.role:
+                            self.sa_session.delete(dhp)
+
+        delete_stmt = delete(UserRoleAssociation).where(UserRoleAssociation.role_id == role.id)
+        insert_values = [{"role_id": role.id, "user_id": user_id} for user_id in user_ids]
+        self._set_associations(role, UserRoleAssociation, delete_stmt, insert_values)
+
+    def _set_role_groups(self, role, group_ids):
+        delete_stmt = delete(GroupRoleAssociation).where(GroupRoleAssociation.role_id == role.id)
+        insert_values = [{"role_id": role.id, "group_id": group_id} for group_id in group_ids]
+        self._set_associations(role, GroupRoleAssociation, delete_stmt, insert_values)
+
+    def _persist_new_model(self, model_instance):
+        # If model_instance is new, it may have not been assigned a database id yet, which is required
+        # for creating association records. Flush if that's the case.
+        if model_instance.id is None:
+            self.sa_session.flush([model_instance])
+
+    def _set_associations(self, parent_model, assoc_model, delete_stmt, insert_values):
+        """
+        Delete current associations for assoc_model, then insert new associations if values are provided.
+        """
+        # Ensure sqlite respects foreign key constraints.
+        if self.sa_session.bind.dialect.name == "sqlite":
+            self.sa_session.execute(text("PRAGMA foreign_keys = ON;"))
+        self.sa_session.execute(delete_stmt)
+        if not insert_values:
+            return
+        try:
+            self.sa_session.execute(insert(assoc_model), insert_values)
+        except IntegrityError as ie:
+            self.sa_session.rollback()
+            if is_unique_constraint_violation(ie):
+                msg = f"Attempting to create a duplicate {assoc_model} record ({insert_values})"
+                log.exception(msg)
+                raise RequestParameterInvalidException()
+            elif is_foreign_key_violation(ie):
+                msg = f"Attempting to create an invalid {assoc_model} record ({insert_values})"
+                log.exception(msg)
+                raise RequestParameterInvalidException()
+            else:
+                raise
 
     def get_component_associations(self, **kwd):
         assert len(kwd) == 2, "You must specify exactly 2 Galaxy security components to check for associations."
@@ -1615,16 +1679,11 @@ class HostAgent(RBACAgent):
         ucsc_archaea=("lowepub.cse.ucsc.edu",),
     )
 
-    def __init__(self, model, permitted_actions=None):
-        self.model = model
+    def __init__(self, sa_session, permitted_actions=None):
+        self.sa_session = sa_session
         if permitted_actions:
             self.permitted_actions = permitted_actions
 
-    @property
-    def sa_session(self):
-        """Returns a SQLAlchemy session"""
-        return self.model.context
-
     def allow_action(self, addr, action, **kwd):
         if "dataset" in kwd and action == self.permitted_actions.DATASET_ACCESS:
             hda = kwd["dataset"]
@@ -1685,7 +1744,7 @@ class HostAgent(RBACAgent):
         if hdadaa:
             hdadaa.update_time = datetime.utcnow()
         else:
-            hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization(hda=hda, user=user, site=site)
+            hdadaa = HistoryDatasetAssociationDisplayAtAuthorization(hda=hda, user=user, site=site)
         self.sa_session.add(hdadaa)
         with transaction(self.sa_session):
             self.sa_session.commit()
@@ -1698,3 +1757,74 @@ def _walk_action_roles(permissions, query_action):
                 yield action, roles
         elif action == query_action.action and roles:
             yield action, roles
+
+
+def is_unique_constraint_violation(error):
+    # A more elegant way to handle sqlite iw this:
+    #   if hasattr(error.orig, "sqlite_errorname"):
+    #       return error.orig.sqlite_errorname == "SQLITE_CONSTRAINT_UNIQUE"
+    # However, that's only possible with Python 3.11+
+    # https://docs.python.org/3/library/sqlite3.html#sqlite3.Error.sqlite_errorcode
+    if isinstance(error.orig, sqlite3.IntegrityError):
+        return error.orig.args[0].startswith("UNIQUE constraint failed")
+    else:
+        # If this is a PostgreSQL unique constraint, then error.orig is an instance of psycopg2.errors.UniqueViolation
+        # and should have an attribute `pgcode` = 23505.
+        return int(getattr(error.orig, "pgcode", -1)) == 23505
+
+
+def is_foreign_key_violation(error):
+    # A more elegant way to handle sqlite iw this:
+    #   if hasattr(error.orig, "sqlite_errorname"):
+    #       return error.orig.sqlite_errorname == "SQLITE_CONSTRAINT_UNIQUE"
+    # However, that's only possible with Python 3.11+
+    # https://docs.python.org/3/library/sqlite3.html#sqlite3.Error.sqlite_errorcode
+    if isinstance(error.orig, sqlite3.IntegrityError):
+        return error.orig.args[0] == "FOREIGN KEY constraint failed"
+    else:
+        # If this is a PostgreSQL foreign key error, then error.orig is an instance of psycopg2.errors.ForeignKeyViolation
+        # and should have an attribute `pgcode` = 23503.
+        return int(getattr(error.orig, "pgcode", -1)) == 23503
+
+
+def _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit):
+    """Case: trans.user_is_admin or trans.app.config.expose_user_email"""
+    stmt = select(Role).where(Role.deleted == false())
+
+    if not is_admin:
+        # User is not an admin but the configuration exposes all private roles to all users,
+        # so only private roles are returned.
+        stmt = stmt.where(Role.type == Role.types.PRIVATE)
+
+    if search_query:
+        stmt = stmt.where(Role.name.like(search_query, escape="/"))
+
+        # Also check against user emails for associated users of private roles ONLY
+        stmt2 = (
+            select(Role)
+            .join(Role.users)
+            .join(User)
+            .where(and_(Role.type == Role.types.PRIVATE, User.email.like(search_query, escape="/")))
+        )
+        stmt = stmt.union(stmt2)
+
+    count_stmt = select(func.count()).select_from(stmt)
+    total_count = session.scalar(count_stmt)
+
+    stmt = stmt.order_by(Role.name)
+
+    if limit is not None:
+        # Takes the least number of results from beginning that includes the requested page
+        stmt = stmt.limit(limit)
+        page_start = (page * page_limit) - page_limit
+        page_end = page_start + page_limit
+        if total_count < page_start + 1:
+            # Return empty list if there are less results than the requested position
+            return []
+
+    stmt = select(Role).from_statement(stmt)
+    roles = session.scalars(stmt).all()
+    if limit is not None:
+        roles = roles[page_start:page_end]
+
+    return roles
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index d093e3c24838f95df298b54f986d9e4ca74acf89..c68d9919d9d393c73af4dc6d8900eef7e496fe3e 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -578,10 +578,11 @@ class ModelImportStore(metaclass=abc.ABCMeta):
                 self._attach_raw_id_if_editing(dataset_instance, dataset_attrs)
 
                 # Older style...
-                if "uuid" in dataset_attrs:
-                    dataset_instance.dataset.uuid = dataset_attrs["uuid"]
-                if "dataset_uuid" in dataset_attrs:
-                    dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
+                if self.import_options.allow_edit:
+                    if "uuid" in dataset_attrs:
+                        dataset_instance.dataset.uuid = dataset_attrs["uuid"]
+                    if "dataset_uuid" in dataset_attrs:
+                        dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
 
                 self._session_add(dataset_instance)
 
@@ -998,14 +999,16 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             # sense.
             hdca_copied_from_sinks = object_import_tracker.hdca_copied_from_sinks
             if copied_from_object_key in object_import_tracker.hdcas_by_key:
-                hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
-                    copied_from_object_key
-                ]
+                source_hdca = object_import_tracker.hdcas_by_key[copied_from_object_key]
+                if source_hdca is not hdca:
+                    # We may not have the copied source, in which case the first included HDCA in the chain
+                    # acts as the source, so here we make sure we don't create a cycle.
+                    hdca.copied_from_history_dataset_collection_association = source_hdca
             else:
                 if copied_from_object_key in hdca_copied_from_sinks:
-                    hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
-                        hdca_copied_from_sinks[copied_from_object_key]
-                    ]
+                    source_hdca = object_import_tracker.hdcas_by_key[hdca_copied_from_sinks[copied_from_object_key]]
+                    if source_hdca is not hdca:
+                        hdca.copied_from_history_dataset_collection_association = source_hdca
                 else:
                     hdca_copied_from_sinks[copied_from_object_key] = dataset_collection_key
 
@@ -1022,7 +1025,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
 
             if object_import_tracker.copy_hid_for:
                 # in an if to avoid flush if unneeded
-                for from_dataset, to_dataset in object_import_tracker.copy_hid_for.items():
+                for from_dataset, to_dataset in object_import_tracker.copy_hid_for:
                     to_dataset.hid = from_dataset.hid
                     self._session_add(to_dataset)
                 self._flush()
@@ -1071,7 +1074,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             for step_attrs in invocation_attrs["steps"]:
                 imported_invocation_step = model.WorkflowInvocationStep()
                 imported_invocation_step.workflow_invocation = imported_invocation
-                ensure_object_added_to_session(imported_invocation, session=self.sa_session)
+                ensure_object_added_to_session(imported_invocation_step, session=self.sa_session)
                 attach_workflow_step(imported_invocation_step, step_attrs)
                 restore_times(imported_invocation_step, step_attrs)
                 imported_invocation_step.action = step_attrs["action"]
@@ -1275,18 +1278,24 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             metadata_safe = False
             idc = model.ImplicitlyConvertedDatasetAssociation(metadata_safe=metadata_safe, for_import=True)
             idc.type = idc_attrs["file_type"]
-            if idc_attrs.get("parent_hda"):
-                idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]]
+            # We may not have exported the parent, so only set the parent_hda attribute if we did.
+            if (parent_hda_id := idc_attrs.get("parent_hda")) and (
+                parent_hda := object_import_tracker.hdas_by_key.get(parent_hda_id)
+            ):
+                # exports created prior to 24.2 may not have a parent if the parent had been purged
+                idc.parent_hda = parent_hda
             if idc_attrs.get("hda"):
                 idc.dataset = object_import_tracker.hdas_by_key[idc_attrs["hda"]]
 
-            # we have a the dataset and the parent, lets ensure they land up with the same HID
-            if idc.dataset and idc.parent_hda and idc.parent_hda in object_import_tracker.requires_hid:
+            # we have the dataset and the parent, lets ensure they land up with the same HID
+            if idc.dataset and idc.parent_hda:
                 try:
                     object_import_tracker.requires_hid.remove(idc.dataset)
                 except ValueError:
                     pass  # we wanted to remove it anyway.
-                object_import_tracker.copy_hid_for[idc.parent_hda] = idc.dataset
+                # A HDA can be the parent of multiple implicitly converted dataset,
+                # that's thy we use [(source, target)] here
+                object_import_tracker.copy_hid_for.append((idc.parent_hda, idc.dataset))
 
             self._session_add(idc)
 
@@ -1369,7 +1378,7 @@ class ObjectImportTracker:
     hdca_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType]
     jobs_by_key: Dict[ObjectKeyType, model.Job]
     requires_hid: List["HistoryItem"]
-    copy_hid_for: Dict["HistoryItem", "HistoryItem"]
+    copy_hid_for: List[Tuple["HistoryItem", "HistoryItem"]]
 
     def __init__(self) -> None:
         self.libraries_by_key = {}
@@ -1387,7 +1396,7 @@ class ObjectImportTracker:
         self.implicit_collection_jobs_by_key: Dict[str, ImplicitCollectionJobs] = {}
         self.workflows_by_key: Dict[str, model.Workflow] = {}
         self.requires_hid = []
-        self.copy_hid_for = {}
+        self.copy_hid_for = []
 
         self.new_history: Optional[model.History] = None
 
@@ -1919,12 +1928,14 @@ class DirectoryModelExportStore(ModelExportStore):
         self.export_files = export_files
         self.included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]] = {}
         self.dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation] = {}
-        self.included_collections: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
+        self.included_collections: Dict[
+            Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
+            Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
+        ] = {}
         self.included_libraries: List[model.Library] = []
         self.included_library_folders: List[model.LibraryFolder] = []
         self.included_invocations: List[model.WorkflowInvocation] = []
         self.collection_datasets: Set[int] = set()
-        self.collections_attrs: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
         self.dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]] = {}
 
         self.job_output_dataset_associations: Dict[int, Dict[str, model.DatasetInstance]] = {}
@@ -2291,8 +2302,7 @@ class DirectoryModelExportStore(ModelExportStore):
     def add_dataset_collection(
         self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
     ) -> None:
-        self.collections_attrs.append(collection)
-        self.included_collections.append(collection)
+        self.included_collections[collection] = collection
 
     def add_implicit_conversion_dataset(
         self,
@@ -2300,6 +2310,14 @@ class DirectoryModelExportStore(ModelExportStore):
         include_files: bool,
         conversion: model.ImplicitlyConvertedDatasetAssociation,
     ) -> None:
+        parent_hda = conversion.parent_hda
+        if parent_hda and parent_hda not in self.included_datasets:
+            # We should always include the parent of an implicit conversion
+            # to avoid holes in the provenance.
+            self.included_datasets[parent_hda] = (parent_hda, include_files)
+            grand_parent_association = parent_hda.implicitly_converted_parent_datasets
+            if grand_parent_association and (grand_parent_hda := grand_parent_association[0].parent_hda):
+                self.add_implicit_conversion_dataset(grand_parent_hda, include_files, grand_parent_association[0])
         self.included_datasets[dataset] = (dataset, include_files)
         self.dataset_implicit_conversions[dataset] = conversion
 
@@ -2347,7 +2365,7 @@ class DirectoryModelExportStore(ModelExportStore):
 
         collections_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_COLLECTIONS)
         with open(collections_attrs_filename, "w") as collections_attrs_out:
-            collections_attrs_out.write(to_json(self.collections_attrs))
+            collections_attrs_out.write(to_json(self.included_collections.values()))
 
         conversions_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_CONVERSIONS)
         with open(conversions_attrs_filename, "w") as conversions_attrs_out:
@@ -2368,12 +2386,12 @@ class DirectoryModelExportStore(ModelExportStore):
             #
 
             # Get all jobs associated with included HDAs.
-            jobs_dict: Dict[str, model.Job] = {}
+            jobs_dict: Dict[int, model.Job] = {}
             implicit_collection_jobs_dict = {}
 
             def record_job(job):
-                if not job:
-                    # No viable job.
+                if not job or job.id in jobs_dict:
+                    # No viable job or job already recorded.
                     return
 
                 jobs_dict[job.id] = job
@@ -2399,10 +2417,11 @@ class DirectoryModelExportStore(ModelExportStore):
                     )
                 job_hda = hda
                 while job_hda.copied_from_history_dataset_association:  # should this check library datasets as well?
+                    # record job (if one exists) even if dataset was copied
+                    # copy could have been created manually through UI/API or using database operation tool,
+                    # in which case we have a relevant job to export.
+                    record_associated_jobs(job_hda)
                     job_hda = job_hda.copied_from_history_dataset_association
-                if not job_hda.creating_job_associations:
-                    # No viable HDA found.
-                    continue
 
                 record_associated_jobs(job_hda)
 
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 6ddf292534f514ba213076a0b867b1cceefe176b..cdaf545a3f7d369ed5cda79acabf3497be1d4510 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -80,6 +80,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         name,
         filename=None,
         extra_files=None,
+        metadata=None,
         metadata_source_name=None,
         info=None,
         library_folder=None,
@@ -132,11 +133,6 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                 )
                 self.persist_object(primary_data)
 
-                if init_from:
-                    self.permission_provider.copy_dataset_permissions(init_from, primary_data)
-                    primary_data.state = init_from.state
-                else:
-                    self.permission_provider.set_default_hda_permissions(primary_data)
             else:
                 ld = galaxy.model.LibraryDataset(folder=library_folder, name=name)
                 ldda = galaxy.model.LibraryDatasetDatasetAssociation(
@@ -157,6 +153,12 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         #        if final_job_state == galaxy.model.Job.states.ERROR and not self.get_implicit_collection_jobs_association_id():
         #            primary_data.visible = True
 
+        if metadata:
+            for key, value in metadata.items():
+                metadata_element = primary_data.datatype.metadata_spec.get(key)
+                if metadata_element and metadata_element.set_in_upload:
+                    setattr(primary_data.metadata, key, value)
+
         for source_dict in sources:
             source = galaxy.model.DatasetSource()
             source.source_uri = source_dict["source_uri"]
@@ -208,6 +210,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                     filename=filename,
                     link_data=link_data,
                     output_name=output_name,
+                    init_from=init_from,
                 )
             else:
                 storage_callbacks.append(
@@ -218,11 +221,14 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
                         filename=filename,
                         link_data=link_data,
                         output_name=output_name,
+                        init_from=init_from,
                     )
                 )
         return primary_data
 
-    def finalize_storage(self, primary_data, dataset_attributes, extra_files, filename, link_data, output_name):
+    def finalize_storage(
+        self, primary_data, dataset_attributes, extra_files, filename, link_data, output_name, init_from
+    ):
         if primary_data.dataset.purged:
             # metadata won't be set, maybe we should do that, then purge ?
             primary_data.dataset.file_size = 0
@@ -243,6 +249,12 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta):
         else:
             # We are sure there are no extra files, so optimize things that follow by settting total size also.
             primary_data.set_size(no_extra_files=True)
+
+        if init_from:
+            self.permission_provider.copy_dataset_permissions(init_from, primary_data)
+        else:
+            self.permission_provider.set_default_hda_permissions(primary_data)
+
         # TODO: this might run set_meta after copying the file to the object store, which could be inefficient if job working directory is closer to the node.
         self.set_datasets_metadata(datasets=[primary_data], datasets_attributes=[dataset_attributes])
 
@@ -855,6 +867,7 @@ def persist_hdas(elements, model_persistence_context, final_job_state="ok"):
                     name=name,
                     filename=discovered_file.path,
                     extra_files=extra_files,
+                    metadata=element.get("metadata"),
                     info=info,
                     tag_list=tag_list,
                     link_data=link_data,
@@ -925,9 +938,7 @@ def replace_request_syntax_sugar(obj):
                     new_hashes.append({"hash_function": key, "hash_value": obj[key.lower()]})
                     del obj[key.lower()]
 
-            if "hashes" not in obj:
-                obj["hashes"] = []
-            obj["hashes"].extend(new_hashes)
+            obj.setdefault("hashes", []).extend(new_hashes)
 
 
 class DiscoveredFile(NamedTuple):
diff --git a/lib/galaxy/model/store/ro_crate_utils.py b/lib/galaxy/model/store/ro_crate_utils.py
index f3592ac04ab9ff2f390ed46c37963c2e949336bd..33072d27baa14535e4aa5c5e04300c4c6d919eec 100644
--- a/lib/galaxy/model/store/ro_crate_utils.py
+++ b/lib/galaxy/model/store/ro_crate_utils.py
@@ -123,25 +123,27 @@ class WorkflowRunCrateProfileBuilder:
     def _add_files(self, crate: ROCrate):
         for wfda in self.invocation.input_datasets:
             if not self.file_entities.get(wfda.dataset.dataset.id):
+                dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
+                crate.mainEntity.append_to("input", dataset_formal_param)
                 properties = {
-                    "exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
+                    "exampleOfWork": {"@id": dataset_formal_param.id},
                 }
                 file_entity = self._add_file(wfda.dataset, properties, crate)
-                dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
-                crate.mainEntity.append_to("input", dataset_formal_param)
                 self.create_action.append_to("object", file_entity)
 
         for wfda in self.invocation.output_datasets:
             if not self.file_entities.get(wfda.dataset.dataset.id):
+                dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
+                crate.mainEntity.append_to("output", dataset_formal_param)
                 properties = {
-                    "exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
+                    "exampleOfWork": {"@id": dataset_formal_param.id},
                 }
                 file_entity = self._add_file(wfda.dataset, properties, crate)
-                dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
-                crate.mainEntity.append_to("output", dataset_formal_param)
                 self.create_action.append_to("result", file_entity)
 
-    def _add_collection(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate) -> ContextEntity:
+    def _add_collection(
+        self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate, collection_formal_param: ContextEntity
+    ) -> ContextEntity:
         name = hdca.name
         dataset_ids = []
         for hda in hdca.dataset_instances:
@@ -158,7 +160,7 @@ class WorkflowRunCrateProfileBuilder:
             "@type": "Collection",
             "additionalType": self._get_collection_additional_type(hdca.collection.collection_type),
             "hasPart": dataset_ids,
-            "exampleOfWork": {"@id": f"#{hdca.type_id}-param"},
+            "exampleOfWork": {"@id": collection_formal_param.id},
         }
         collection_entity = crate.add(
             ContextEntity(
@@ -185,14 +187,14 @@ class WorkflowRunCrateProfileBuilder:
 
     def _add_collections(self, crate: ROCrate):
         for wfdca in self.invocation.input_dataset_collections:
-            collection_entity = self._add_collection(wfdca.dataset_collection, crate)
             collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
+            collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
             crate.mainEntity.append_to("input", collection_formal_param)
             self.create_action.append_to("object", collection_entity)
 
         for wfdca in self.invocation.output_dataset_collections:
-            collection_entity = self._add_collection(wfdca.dataset_collection, crate)
             collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
+            collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
             crate.mainEntity.append_to("output", collection_formal_param)
             self.create_action.append_to("result", collection_entity)
 
@@ -336,30 +338,14 @@ class WorkflowRunCrateProfileBuilder:
     def _add_parameters(self, crate: ROCrate):
         for step in self.invocation.steps:
             if step.workflow_step.type == "parameter_input":
-                property_value = self._add_step_parameter_pv(step, crate)
-                formal_param = self._add_step_parameter_fp(step, crate)
-                crate.mainEntity.append_to("input", formal_param)
+                property_value = self._add_step_parameter(step, crate)
                 self.create_action.append_to("object", property_value)
 
-    def _add_step_parameter_pv(self, step: WorkflowInvocationStep, crate: ROCrate):
-        param_id = step.workflow_step.label
-        return crate.add(
-            ContextEntity(
-                crate,
-                f"{param_id}-pv",
-                properties={
-                    "@type": "PropertyValue",
-                    "name": f"{param_id}",
-                    "value": step.output_value.value,
-                    "exampleOfWork": {"@id": f"#{param_id}-param"},
-                },
-            )
-        )
-
-    def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
+    def _add_step_parameter(self, step: WorkflowInvocationStep, crate: ROCrate) -> ContextEntity:
         param_id = step.workflow_step.label
+        assert step.workflow_step.tool_inputs
         param_type = step.workflow_step.tool_inputs["parameter_type"]
-        return crate.add(
+        formal_param = crate.add(
             ContextEntity(
                 crate,
                 f"{param_id}-param",
@@ -372,18 +358,16 @@ class WorkflowRunCrateProfileBuilder:
                 },
             )
         )
-
-    def _add_step_tool_pv(self, step: WorkflowInvocationStep, tool_input: str, crate: ROCrate):
-        param_id = tool_input
+        crate.mainEntity.append_to("input", formal_param)
         return crate.add(
             ContextEntity(
                 crate,
                 f"{param_id}-pv",
                 properties={
                     "@type": "PropertyValue",
-                    "name": f"{step.workflow_step.label}",
-                    "value": step.workflow_step.tool_inputs[tool_input],
-                    "exampleOfWork": {"@id": f"#{param_id}-param"},
+                    "name": f"{param_id}",
+                    "value": step.output_value.value,
+                    "exampleOfWork": {"@id": formal_param.id},
                 },
             )
         )
@@ -417,7 +401,9 @@ class WorkflowRunCrateProfileBuilder:
             )
         )
 
-    def _add_collection_formal_parameter(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate):
+    def _add_collection_formal_parameter(
+        self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate
+    ) -> ContextEntity:
         return crate.add(
             ContextEntity(
                 crate,
diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index 14d8d6b73cecebb8175c92944e3b75a98d46dc29..bffb0de77794dcdbc43afac9970f58f11f15bc98 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -61,7 +61,7 @@ class TagHandler:
         self.item_tag_assoc_info: Dict[str, ItemTagAssocInfo] = {}
         # Can't include type annotation in signature, because lagom will attempt to look up
         # GalaxySession, but can't find it due to the circular import
-        self.galaxy_session: Optional["GalaxySession"] = galaxy_session
+        self.galaxy_session: Optional[GalaxySession] = galaxy_session
 
     def create_tag_handler_session(self, galaxy_session: Optional["GalaxySession"]):
         # Creates a transient tag handler that avoids repeated flushes
@@ -502,7 +502,7 @@ class GalaxyTagHandlerSession(GalaxyTagHandler):
 
     def __init__(self, sa_session, galaxy_session: Optional["GalaxySession"]):
         super().__init__(sa_session, galaxy_session)
-        self.created_tags: Dict[str, "Tag"] = {}
+        self.created_tags: Dict[str, Tag] = {}
 
     def _get_tag(self, tag_name):
         """Get tag from cache or database."""
diff --git a/lib/galaxy/model/unittest_utils/data_app.py b/lib/galaxy/model/unittest_utils/data_app.py
index 75e5101eca8073dcaa08ed147624bc494cbcbd81..0d424cca3623c34d66dd950c8bbafde9537e972e 100644
--- a/lib/galaxy/model/unittest_utils/data_app.py
+++ b/lib/galaxy/model/unittest_utils/data_app.py
@@ -79,6 +79,10 @@ class GalaxyDataTestConfig(Bunch):
         self.ftp_upload_dir = None
         self.ftp_upload_purge = False
 
+        self.file_source_temp_dir = None
+        self.file_source_webdav_use_temp_files = False
+        self.file_source_listings_expiry_time = 60
+
     def __del__(self):
         if self._remove_root:
             shutil.rmtree(self.root)
diff --git a/lib/galaxy/model/unittest_utils/db_helpers.py b/lib/galaxy/model/unittest_utils/db_helpers.py
new file mode 100644
index 0000000000000000000000000000000000000000..6c56d83278b32a455cba9e82a12ac19c9538a3d5
--- /dev/null
+++ b/lib/galaxy/model/unittest_utils/db_helpers.py
@@ -0,0 +1,12 @@
+from sqlalchemy import select
+
+from galaxy import model
+
+
+def get_hdca_by_name(session, name):
+    stmt = (
+        select(model.HistoryDatasetCollectionAssociation)
+        .where(model.HistoryDatasetCollectionAssociation.name == name)
+        .limit(1)
+    )
+    return session.scalars(stmt).first()
diff --git a/lib/galaxy/model/unittest_utils/store_fixtures.py b/lib/galaxy/model/unittest_utils/store_fixtures.py
index d779e79d698e2efc54aa9584d612c87d0adc811e..153303c12c8131de96c1d6d23c917ff517efc489 100644
--- a/lib/galaxy/model/unittest_utils/store_fixtures.py
+++ b/lib/galaxy/model/unittest_utils/store_fixtures.py
@@ -11,7 +11,8 @@ from galaxy.model.orm.now import now
 TEST_SOURCE_URI = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/2.bed"
 TEST_SOURCE_URI_BAM = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bam"
 TEST_HASH_FUNCTION = "MD5"
-TEST_HASH_VALUE = "moocowpretendthisisahas"
+TEST_HASH_VALUE = "f568c29421792b1b1df4474dafae01f1"
+TEST_HASH_VALUE_BAM = "34693a376f9878cbe53166db083e0e26"
 TEST_HISTORY_NAME = "My history in a model store"
 TEST_EXTENSION = "bed"
 TEST_LIBRARY_NAME = "My cool library"
@@ -339,7 +340,7 @@ def deferred_hda_model_store_dict_bam(
     dataset_hash = dict(
         model_class="DatasetHash",
         hash_function=TEST_HASH_FUNCTION,
-        hash_value=TEST_HASH_VALUE,
+        hash_value=TEST_HASH_VALUE_BAM,
         extra_files_path=None,
     )
     dataset_source: Dict[str, Any] = dict(
diff --git a/lib/galaxy/model/unittest_utils/utils.py b/lib/galaxy/model/unittest_utils/utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..c558b52b51de896e275ab4cf995650303ef4f965
--- /dev/null
+++ b/lib/galaxy/model/unittest_utils/utils.py
@@ -0,0 +1,13 @@
+import random
+import string
+
+
+def random_str() -> str:
+    alphabet = string.ascii_lowercase + string.digits
+    size = random.randint(5, 10)
+    return "".join(random.choices(alphabet, k=size))
+
+
+def random_email() -> str:
+    text = random_str()
+    return f"{text}@galaxy.testing"
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 4b15e24d67272839a24088bcb4523ad223919d2a..14e796390ed94b6fc1dc9116b8812426ea72b23b 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -75,9 +75,15 @@ DEFAULT_PRIVATE = False
 DEFAULT_QUOTA_SOURCE = None  # Just track quota right on user object in Galaxy.
 DEFAULT_QUOTA_ENABLED = True  # enable quota tracking in object stores by default
 DEFAULT_DEVICE_ID = None
+USER_OBJECTS_SCHEME = "user_objects://"
+
 log = logging.getLogger(__name__)
 
 
+def is_user_object_store(object_store_id: Optional[str]) -> bool:
+    return object_store_id is not None and object_store_id.startswith(USER_OBJECTS_SCHEME)
+
+
 class UserObjectStoreResolver(Protocol):
     def resolve_object_store_uri_config(self, uri: str) -> ObjectStoreConfiguration:
         pass
@@ -143,19 +149,43 @@ class ObjectStore(metaclass=abc.ABCMeta):
     """
 
     @abc.abstractmethod
-    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def exists(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+    ) -> bool:
         """Return True if the object identified by `obj` exists, False otherwise."""
         raise NotImplementedError()
 
     @abc.abstractmethod
     def construct_path(
-        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None
-    ):
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        in_cache: bool = False,
+    ) -> str:
         raise NotImplementedError()
 
     @abc.abstractmethod
     def create(
-        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
     ):
         """
         Mark the object (`obj`) as existing in the store, but with no content.
@@ -169,7 +199,9 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def empty(
+        self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False
+    ) -> bool:
         """
         Test if the object identified by `obj` has content.
 
@@ -178,7 +210,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False) -> int:
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False) -> int:
         """
         Return size of the object identified by `obj`.
 
@@ -190,13 +222,15 @@ class ObjectStore(metaclass=abc.ABCMeta):
     def delete(
         self,
         obj,
-        entire_dir=False,
+        entire_dir: bool = False,
         base_dir=None,
+        dir_only=False,
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
-    ):
+        obj_dir: bool = False,
+        user = None,
+    ) -> bool:
         """
         Delete the object identified by `obj`.
 
@@ -218,7 +252,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
+        obj_dir: bool = False,
     ):
         """
         Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
@@ -242,11 +276,11 @@ class ObjectStore(metaclass=abc.ABCMeta):
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
-        sync_cache=False,
+        obj_dir: bool = False,
+        sync_cache: bool = True,
         user=None,
         auth_token=None,
-    ):
+    ) -> str:
         """
         Get the expected filename with absolute path for object with id `obj.id`.
 
@@ -262,11 +296,11 @@ class ObjectStore(metaclass=abc.ABCMeta):
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
+        obj_dir: bool = False,
         file_name=None,
-        create=False,
-        preserve_symlinks=False,
-    ):
+        create: bool = False,
+        preserve_symlinks: bool = False,
+    ) -> None:
         """
         Inform the store that the file associated with `obj.id` has been updated.
 
@@ -285,7 +319,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False):
         """
         Return the URL for direct access if supported, otherwise return None.
 
@@ -320,7 +354,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
         """Return a list of dictified badges summarizing the object store configuration."""
 
     @abc.abstractmethod
-    def is_private(self, obj):
+    def is_private(self, obj) -> bool:
         """Return True iff supplied object is stored in private ConcreteObjectStore."""
 
     def object_store_ids(self, private=None):
@@ -372,7 +406,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def get_quota_source_map(self):
+    def get_quota_source_map(self) -> "QuotaSourceMap":
         """Return QuotaSourceMap describing mapping of object store IDs to quota sources."""
 
     @abc.abstractmethod
@@ -460,35 +494,196 @@ class BaseObjectStore(ObjectStore):
     def _invoke(self, delegate, obj=None, **kwargs):
         return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
 
-    def exists(self, obj, **kwargs):
-        return self._invoke("exists", obj, **kwargs)
+    def exists(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+    ) -> bool:
+        return self._invoke(
+            "exists",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def construct_path(self, obj, **kwargs):
-        return self._invoke("construct_path", obj, **kwargs)
+    def construct_path(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        in_cache: bool = False,
+    ) -> str:
+        return self._invoke(
+            "construct_path",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            in_cache=in_cache,
+        )
 
-    def create(self, obj, **kwargs):
-        return self._invoke("create", obj, **kwargs)
+    def create(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+    ):
+        return self._invoke(
+            "create",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def empty(self, obj, **kwargs):
-        return self._invoke("empty", obj, **kwargs)
+    def empty(
+        self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False
+    ) -> bool:
+        return self._invoke(
+            "empty",
+            obj,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def size(self, obj, **kwargs):
-        return self._invoke("size", obj, **kwargs)
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False) -> int:
+        return self._invoke(
+            "size", obj, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, obj_dir=obj_dir
+        )
 
-    def delete(self, obj, **kwargs):
-        return self._invoke("delete", obj, **kwargs)
+    def delete(
+        self,
+        obj,
+        entire_dir: bool = False,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        user=None,
+    ) -> bool:
+        return self._invoke(
+            "delete",
+            obj,
+            entire_dir=entire_dir,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            user=user,
+        )
 
-    def get_data(self, obj, **kwargs):
-        return self._invoke("get_data", obj, **kwargs)
+    def get_data(
+        self,
+        obj,
+        start=0,
+        count=-1,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+    ):
+        return self._invoke(
+            "get_data",
+            obj,
+            start=start,
+            count=count,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
-    def get_filename(self, obj, **kwargs):
-        return self._invoke("get_filename", obj, **kwargs)
+    def get_filename(
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        sync_cache: bool = True,
+        user: str = None,
+    ) -> str:
+        return self._invoke(
+            "get_filename",
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            sync_cache=sync_cache,
+            user=user,
+        )
 
-    def update_from_file(self, obj, **kwargs):
-        return self._invoke("update_from_file", obj, **kwargs)
+    def update_from_file(
+        self,
+        obj,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        file_name=None,
+        create: bool = False,
+        preserve_symlinks: bool = False,
+    ) -> None:
+        return self._invoke(
+            "update_from_file",
+            obj,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            file_name=file_name,
+            create=create,
+            preserve_symlinks=preserve_symlinks,
+        )
 
-    def get_object_url(self, obj, **kwargs):
-        return self._invoke("get_object_url", obj, **kwargs)
+    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir: bool = False):
+        return self._invoke(
+            "get_object_url",
+            obj,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
     def get_concrete_store_name(self, obj):
         return self._invoke("get_concrete_store_name", obj)
@@ -505,7 +700,7 @@ class BaseObjectStore(ObjectStore):
     def get_store_by(self, obj, **kwargs):
         return self._invoke("get_store_by", obj, **kwargs)
 
-    def is_private(self, obj):
+    def is_private(self, obj) -> bool:
         return self._invoke("is_private", obj)
 
     def cache_targets(self) -> List[CacheTarget]:
@@ -527,7 +722,7 @@ class BaseObjectStore(ObjectStore):
             badges.append({"type": type, "message": message})
         return badges
 
-    def get_quota_source_map(self):
+    def get_quota_source_map(self) -> "QuotaSourceMap":
         # I'd rather keep this abstract... but register_singleton wants it to be instantiable...
         raise NotImplementedError()
 
@@ -619,7 +814,7 @@ class ConcreteObjectStore(BaseObjectStore):
     def _get_store_by(self, obj):
         return self.store_by
 
-    def _is_private(self, obj):
+    def _is_private(self, obj) -> bool:
         return self.private
 
     @property
@@ -717,8 +912,15 @@ class DiskObjectStore(ConcreteObjectStore):
         return as_dict
 
     def __get_filename(
-        self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False
-    ):
+        self,
+        obj,
+        base_dir=None,
+        dir_only=False,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+    ) -> str:
         """
         Return the absolute path for the file corresponding to the `obj.id`.
 
@@ -736,30 +938,33 @@ class DiskObjectStore(ConcreteObjectStore):
         )
         # For backward compatibility: check the old style root path first;
         # otherwise construct hashed path.
-        if not os.path.exists(path):
-            return self._construct_path(
-                obj,
-                base_dir=base_dir,
-                dir_only=dir_only,
-                extra_dir=extra_dir,
-                extra_dir_at_root=extra_dir_at_root,
-                alt_name=alt_name,
-            )
+        if os.path.exists(path):
+            return path
+        return self._construct_path(
+            obj,
+            base_dir=base_dir,
+            dir_only=dir_only,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+        )
 
     # TODO: rename to _disk_path or something like that to avoid conflicts with
     # children that'll use the local_extra_dirs decorator, e.g. S3
     def _construct_path(
         self,
         obj,
-        old_style=False,
         base_dir=None,
         dir_only=False,
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
-        **kwargs,
-    ):
+        obj_dir: bool = False,
+        in_cache: bool = False,
+        old_style=False,
+        user=None
+    ) -> str:
         """
         Construct the absolute path for accessing the object identified by `obj.id`.
 
@@ -826,7 +1031,7 @@ class DiskObjectStore(ConcreteObjectStore):
             path = os.path.join(path, alt_name if alt_name else f"dataset_{obj_id}.dat")
         return os.path.abspath(path)
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         """Override `ObjectStore`'s stub and check on disk."""
         if self.check_old_style:
             path = self._construct_path(obj, old_style=True, **kwargs)
@@ -851,9 +1056,9 @@ class DiskObjectStore(ConcreteObjectStore):
                 umask_fix_perms(path, self.config.umask, 0o666)
         return self
 
-    def _empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs) -> bool:
         """Override `ObjectStore`'s stub by checking file size on disk."""
-        return self.size(obj, **kwargs) == 0
+        return self._size(obj, **kwargs) == 0
 
     def _size(self, obj, **kwargs) -> int:
         """Override `ObjectStore`'s stub by return file size on disk.
@@ -875,7 +1080,7 @@ class DiskObjectStore(ConcreteObjectStore):
         else:
             return 0
 
-    def _delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir: bool = False, **kwargs) -> bool:
         """Override `ObjectStore`'s stub; delete the file or folder on disk."""
         path = self._get_filename(obj, **kwargs)
         extra_dir = kwargs.get("extra_dir", None)
@@ -894,7 +1099,7 @@ class DiskObjectStore(ConcreteObjectStore):
             # and another process writes files into that directory.
             # If the path doesn't exist anymore, another rmtree call was successful.
             path = self.__get_filename(obj, **kwargs)
-            if path is None:
+            if not os.path.exists(path):
                 return True
             else:
                 log.critical(f"{path} delete error {ex}", exc_info=True)
@@ -908,7 +1113,7 @@ class DiskObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def _get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, sync_cache: bool = True, **kwargs) -> str:
         """
         Override `ObjectStore`'s stub.
 
@@ -926,9 +1131,10 @@ class DiskObjectStore(ConcreteObjectStore):
             raise ObjectNotFound
         return path
 
-    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(
+        self, obj, file_name=None, create: bool = False, preserve_symlinks: bool = False, **kwargs
+    ) -> None:
         """`create` parameter is not used in this implementation."""
-        preserve_symlinks = kwargs.pop("preserve_symlinks", False)
         # FIXME: symlinks and the object store model may not play well together
         # these should be handled better, e.g. registering the symlink'd file
         # as an object
@@ -971,6 +1177,8 @@ class NestedObjectStore(BaseObjectStore):
     Example: DistributedObjectStore, HierarchicalObjectStore
     """
 
+    backends: Dict
+
     def __init__(self, config, config_xml=None):
         """Extend `ObjectStore`'s constructor."""
         super().__init__(config)
@@ -982,7 +1190,7 @@ class NestedObjectStore(BaseObjectStore):
             store.shutdown()
         super().shutdown()
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         """Determine if the `obj` exists in any of the backends."""
         return self._call_method("_exists", obj, False, False, **kwargs)
 
@@ -998,15 +1206,15 @@ class NestedObjectStore(BaseObjectStore):
         # TODO: merge more intelligently - de-duplicate paths and handle conflicting sizes/percents
         return cache_targets
 
-    def _empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs) -> bool:
         """For the first backend that has this `obj`, determine if it is empty."""
         return self._call_method("_empty", obj, True, False, **kwargs)
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         """For the first backend that has this `obj`, return its size."""
         return self._call_method("_size", obj, 0, False, **kwargs)
 
-    def _delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs) -> bool:
         """For the first backend that has this `obj`, delete it."""
         return self._call_method("_delete", obj, False, False, **kwargs)
 
@@ -1014,16 +1222,46 @@ class NestedObjectStore(BaseObjectStore):
         """For the first backend that has this `obj`, get data from it."""
         return self._call_method("_get_data", obj, ObjectNotFound, True, **kwargs)
 
-    def _get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs) -> str:
         """For the first backend that has this `obj`, get its filename."""
         return self._call_method("_get_filename", obj, ObjectNotFound, True, **kwargs)
 
-    def _update_from_file(self, obj, **kwargs):
+    def _update_from_file(
+        self,
+        obj,
+        base_dir=None,
+        extra_dir=None,
+        extra_dir_at_root=False,
+        alt_name=None,
+        obj_dir: bool = False,
+        file_name=None,
+        create: bool = False,
+        preserve_symlinks: bool = False,
+    ) -> None:
         """For the first backend that has this `obj`, update it from the given file."""
-        if kwargs.get("create", False):
-            self._create(obj, **kwargs)
-            kwargs["create"] = False
-        return self._call_method("_update_from_file", obj, ObjectNotFound, True, **kwargs)
+        if create:
+            self._create(
+                obj,
+                base_dir=base_dir,
+                extra_dir=extra_dir,
+                extra_dir_at_root=extra_dir_at_root,
+                alt_name=alt_name,
+                obj_dir=obj_dir,
+            )
+        return self._call_method(
+            "_update_from_file",
+            obj,
+            ObjectNotFound,
+            True,
+            base_dir=base_dir,
+            extra_dir=extra_dir,
+            extra_dir_at_root=extra_dir_at_root,
+            alt_name=alt_name,
+            obj_dir=obj_dir,
+            file_name=file_name,
+            create=False,
+            preserve_symlinks=preserve_symlinks,
+        )
 
     def _get_object_url(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its URL."""
@@ -1038,7 +1276,7 @@ class NestedObjectStore(BaseObjectStore):
     def _get_concrete_store_badges(self, obj) -> List[BadgeDict]:
         return self._call_method("_get_concrete_store_badges", obj, [], False)
 
-    def _is_private(self, obj):
+    def _is_private(self, obj) -> bool:
         return self._call_method("_is_private", obj, False, False)
 
     def _get_store_by(self, obj):
@@ -1054,8 +1292,22 @@ class NestedObjectStore(BaseObjectStore):
 
     def _call_method(self, method, obj, default, default_is_exception, **kwargs):
         """Check all children object stores for the first one with the dataset."""
+        base_dir = kwargs.get("base_dir", None)
+        dir_only = kwargs.get("dir_only", False)
+        extra_dir = kwargs.get("extra_dir", None)
+        extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+        alt_name = kwargs.get("alt_name", None)
+        obj_dir = kwargs.get("obj_dir", False)
         for store in self.backends.values():
-            if store.exists(obj, **kwargs):
+            if store.exists(
+                obj,
+                base_dir=base_dir,
+                dir_only=dir_only,
+                extra_dir=extra_dir,
+                extra_dir_at_root=extra_dir_at_root,
+                alt_name=alt_name,
+                obj_dir=obj_dir,
+            ):
                 return store.__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
             raise default(
@@ -1085,6 +1337,7 @@ class DistributedObjectStore(NestedObjectStore):
     with weighting.
     """
 
+    backends: Dict[str, Any]  # BaseObjectStore or ConcreteObjectStore?
     store_type = "distributed"
     _quota_source_map: Optional["QuotaSourceMap"]
     _device_source_map: Optional["DeviceSourceMap"]
@@ -1109,7 +1362,6 @@ class DistributedObjectStore(NestedObjectStore):
         super().__init__(config, config_dict)
         self._quota_source_map = None
         self._device_source_map = None
-        self.backends = {}
         self.weighted_backend_ids = []
         self.original_weighted_backend_ids = []
         self.max_percent_full = {}
@@ -1119,22 +1371,22 @@ class DistributedObjectStore(NestedObjectStore):
 
         user_selection_allowed = []
         for backend_def in config_dict["backends"]:
-            backened_id = backend_def["id"]
+            backend_id = backend_def["id"]
             maxpctfull = backend_def.get("max_percent_full", 0)
             weight = backend_def["weight"]
             allow_selection = backend_def.get("allow_selection")
             if allow_selection:
-                user_selection_allowed.append(backened_id)
+                user_selection_allowed.append(backend_id)
             backend = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
 
-            self.backends[backened_id] = backend
-            self.max_percent_full[backened_id] = maxpctfull
+            self.backends[backend_id] = backend
+            self.max_percent_full[backend_id] = maxpctfull
 
             for _ in range(0, weight):
                 # The simplest way to do weighting: add backend ids to a
                 # sequence the number of times equalling weight, then randomly
                 # choose a backend from that sequence at creation
-                self.weighted_backend_ids.append(backened_id)
+                self.weighted_backend_ids.append(backend_id)
 
         self.original_weighted_backend_ids = self.weighted_backend_ids
         self.user_object_store_resolver = user_object_store_resolver
@@ -1254,7 +1506,7 @@ class DistributedObjectStore(NestedObjectStore):
             self.weighted_backend_ids = new_weighted_backend_ids
             sleeper.sleep(120)  # Test free space every 2 minutes
 
-    def _construct_path(self, obj, **kwargs):
+    def _construct_path(self, obj, **kwargs) -> str:
         return self._resolve_backend(obj.object_store_id).construct_path(obj, **kwargs)
 
     def _create(self, obj, **kwargs):
@@ -1298,7 +1550,7 @@ class DistributedObjectStore(NestedObjectStore):
         try:
             return self.backends[object_store_id]
         except KeyError:
-            if object_store_id.startswith("user_objects://") and self.user_object_store_resolver:
+            if is_user_object_store(object_store_id) and self.user_object_store_resolver:
                 return self.user_object_store_resolver.resolve_object_store_uri(object_store_id)
             raise
 
@@ -1336,7 +1588,7 @@ class DistributedObjectStore(NestedObjectStore):
 
     def __get_store_id_for(self, obj, **kwargs):
         if obj.object_store_id is not None:
-            if obj.object_store_id in self.backends or obj.object_store_id.startswith("user_objects://"):
+            if obj.object_store_id in self.backends or is_user_object_store(obj.object_store_id):
                 return obj.object_store_id
             else:
                 log.warning(
@@ -1349,8 +1601,22 @@ class DistributedObjectStore(NestedObjectStore):
             # if this instance has been switched from a non-distributed to a
             # distributed object store, or if the object's store id is invalid,
             # try to locate the object
+            base_dir = kwargs.get("base_dir", None)
+            dir_only = kwargs.get("dir_only", False)
+            extra_dir = kwargs.get("extra_dir", None)
+            extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
+            alt_name = kwargs.get("alt_name", None)
+            obj_dir = kwargs.get("obj_dir", False)
             for id, store in self.backends.items():
-                if store.exists(obj, **kwargs):
+                if store.exists(
+                    obj,
+                    base_dir=base_dir,
+                    dir_only=dir_only,
+                    extra_dir=extra_dir,
+                    extra_dir_at_root=extra_dir_at_root,
+                    alt_name=alt_name,
+                    obj_dir=obj_dir,
+                ):
                     log.warning(
                         f"{obj.__class__.__name__} object with ID {obj.id} found in backend object store with ID {id}"
                     )
@@ -1375,7 +1641,7 @@ class DistributedObjectStore(NestedObjectStore):
         if parent_check or object_store_id is None:
             return parent_check
         # user selection allowed and object_store_id is not None
-        if object_store_id.startswith("user_objects://"):
+        if is_user_object_store(object_store_id):
             if not user:
                 return "Supplied object store id is not accessible"
             rest_of_uri = object_store_id.split("://", 1)[1]
@@ -1405,13 +1671,13 @@ class HierarchicalObjectStore(NestedObjectStore):
     When creating objects only the first store is used.
     """
 
+    backends: Dict[int, BaseObjectStore]
     store_type = "hierarchical"
 
     def __init__(self, config, config_dict, fsmon=False):
         """The default constructor. Extends `NestedObjectStore`."""
         super().__init__(config, config_dict)
 
-        backends: Dict[int, ObjectStore] = {}
         is_private = config_dict.get("private", DEFAULT_PRIVATE)
         for order, backend_def in enumerate(config_dict["backends"]):
             backend_is_private = backend_def.get("private")
@@ -1426,9 +1692,8 @@ class HierarchicalObjectStore(NestedObjectStore):
                 assert backend_quota.get("source", DEFAULT_QUOTA_SOURCE) == DEFAULT_QUOTA_SOURCE
                 assert backend_quota.get("enabled", DEFAULT_QUOTA_ENABLED) == DEFAULT_QUOTA_ENABLED
 
-            backends[order] = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
+            self.backends[order] = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
 
-        self.backends = backends
         self.private = is_private
         quota_config = config_dict.get("quota", {})
         self.quota_source = quota_config.get("source", DEFAULT_QUOTA_SOURCE)
@@ -1460,21 +1725,21 @@ class HierarchicalObjectStore(NestedObjectStore):
         as_dict["private"] = self.private
         return as_dict
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         """Check all child object stores."""
         for store in self.backends.values():
             if store.exists(obj, **kwargs):
                 return True
         return False
 
-    def _construct_path(self, obj, **kwargs):
+    def _construct_path(self, obj, **kwargs) -> str:
         return self.backends[0].construct_path(obj, **kwargs)
 
     def _create(self, obj, **kwargs):
         """Call the primary object store."""
         return self.backends[0].create(obj, **kwargs)
 
-    def _is_private(self, obj):
+    def _is_private(self, obj) -> bool:
         # Unlink the DistributedObjectStore - the HierarchicalObjectStore does not use
         # object_store_id - so all the contained object stores need to define is_private
         # the same way.
@@ -1766,12 +2031,16 @@ class QuotaSourceMap:
         self.default_quota_source = source
         self.default_quota_enabled = enabled
         self.info = QuotaSourceInfo(self.default_quota_source, self.default_quota_enabled)
+        # User defined sources are provided by the user and the quota is not tracked
+        self.user_defined_source_info = QuotaSourceInfo(label=None, use=False)
         self.backends = {}
         self._labels = None
 
-    def get_quota_source_info(self, object_store_id):
+    def get_quota_source_info(self, object_store_id: Optional[str]) -> QuotaSourceInfo:
         if object_store_id in self.backends:
             return self.backends[object_store_id].get_quota_source_info(object_store_id)
+        elif is_user_object_store(object_store_id):
+            return self.user_defined_source_info
         else:
             return self.info
 
@@ -1850,17 +2119,16 @@ class ObjectStorePopulator:
         self.object_store_id = None
         self.user = user
 
-    def set_object_store_id(self, data, require_shareable=False):
+    def set_object_store_id(self, data: "DatasetInstance", require_shareable: bool = False) -> None:
         self.set_dataset_object_store_id(data.dataset, require_shareable=require_shareable)
 
-    def set_dataset_object_store_id(self, dataset, require_shareable=True):
+    def set_dataset_object_store_id(self, dataset: "Dataset", require_shareable: bool = True) -> None:
         # Create an empty file immediately.  The first dataset will be
         # created in the "default" store, all others will be created in
         # the same store as the first.
         dataset.object_store_id = self.object_store_id
         try:
-            ensure_non_private = require_shareable
-            concrete_store = self.object_store.create(dataset, ensure_non_private=ensure_non_private)
+            concrete_store = self.object_store.create(dataset)
             if concrete_store.private and require_shareable:
                 raise ObjectCreationProblemSharingDisabled()
         except ObjectInvalid:
diff --git a/lib/galaxy/objectstore/_caching_base.py b/lib/galaxy/objectstore/_caching_base.py
index 066fc9077e345eaab0659ec4b4ef6a19913e523b..b4f825580434ec37c9c66ec1c8101ffd2f6f9633 100644
--- a/lib/galaxy/objectstore/_caching_base.py
+++ b/lib/galaxy/objectstore/_caching_base.py
@@ -57,10 +57,10 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
-        obj_dir=False,
-        in_cache=False,
+        obj_dir: bool = False,
+        in_cache: bool = False,
         **kwargs,
-    ):
+    ) -> str:
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot
         if extra_dir and extra_dir != os.path.normpath(extra_dir):
@@ -112,7 +112,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         cache_path = self._get_cache_path(rel_path)
         return os.path.exists(cache_path)
 
-    def _pull_into_cache(self, rel_path) -> bool:
+    def _pull_into_cache(self, rel_path, **kwargs) -> bool:
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
         rel_path_dir = os.path.dirname(rel_path)
         if not os.path.exists(self._get_cache_path(rel_path_dir)):
@@ -129,7 +129,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
-            self._pull_into_cache(rel_path)
+            self._pull_into_cache(rel_path, **kwargs)
         # Read the file content from cache
         data_file = open(self._get_cache_path(rel_path))
         data_file.seek(start)
@@ -137,7 +137,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         in_cache = exists_remotely = False
         rel_path = self._construct_path(obj, **kwargs)
         dir_only = kwargs.get("dir_only", False)
@@ -248,7 +248,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
             )
             return success
 
-    def _empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs) -> bool:
         if self._exists(obj, **kwargs):
             return self._size(obj, **kwargs) == 0
         else:
@@ -257,7 +257,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
     def _get_size_in_cache(self, rel_path):
         return os.path.getsize(self._get_cache_path(rel_path))
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
@@ -269,11 +269,10 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def _get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, sync_cache: bool = True, **kwargs) -> str:
         base_dir = kwargs.get("base_dir", None)
         dir_only = kwargs.get("dir_only", False)
         obj_dir = kwargs.get("obj_dir", False)
-        sync_cache = kwargs.get("sync_cache", True)
 
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -298,7 +297,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
                 self._download_directory_into_cache(rel_path, cache_path)
                 return cache_path
             else:
-                if self._pull_into_cache(rel_path):
+                if self._pull_into_cache(rel_path, **kwargs):
                     return cache_path
         raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
 
@@ -313,7 +312,7 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
         # object stores should definitely override this.
         pass
 
-    def _delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir: bool = False, **kwargs) -> bool:
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get("extra_dir", None)
         base_dir = kwargs.get("base_dir", None)
@@ -342,7 +341,9 @@ class CachingConcreteObjectStore(ConcreteObjectStore):
             log.exception("%s delete error", self._get_filename(obj, **kwargs))
         return False
 
-    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(
+        self, obj, file_name=None, create: bool = False, preserve_symlinks: bool = False, **kwargs
+    ) -> None:
         if create:
             self._create(obj, **kwargs)
 
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 9241c1efe75cd24e63f63d1d153f7c060994f4d4..7a0d415a3a6a6cbac14c3f517f8a6a64a8b7f187 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -5,6 +5,7 @@ Object Store plugin for the Integrated Rule-Oriented Data System (iRODS)
 import logging
 import os
 import shutil
+import ssl
 import threading
 from datetime import datetime
 from pathlib import Path
@@ -40,7 +41,7 @@ def _config_xml_error(tag):
 
 
 def _config_dict_error(key):
-    msg = "No {key} key in config dictionary".forma(key=key)
+    msg = f"No {key} key in config dictionary"
     raise Exception(msg)
 
 
@@ -52,6 +53,26 @@ def parse_config_xml(config_xml):
         username = a_xml[0].get("username")
         password = a_xml[0].get("password")
 
+        s_xml = config_xml.findall("ssl")
+        if s_xml:
+            client_server_negotiation = s_xml[0].get("client_server_negotiation", None)
+            client_server_policy = s_xml[0].get("client_server_policy", None)
+            encryption_algorithm = s_xml[0].get("encryption_algorithm", None)
+            encryption_key_size = int(s_xml[0].get("encryption_key_size", None))
+            encryption_num_hash_rounds = int(s_xml[0].get("encryption_num_hash_rounds", None))
+            encryption_salt_size = int(s_xml[0].get("encryption_salt_size", None))
+            ssl_verify_server = s_xml[0].get("ssl_verify_server", None)
+            ssl_ca_certificate_file = s_xml[0].get("ssl_ca_certificate_file", None)
+        else:
+            client_server_negotiation = None
+            client_server_policy = None
+            encryption_algorithm = None
+            encryption_key_size = None
+            encryption_num_hash_rounds = None
+            encryption_salt_size = None
+            ssl_verify_server = None
+            ssl_ca_certificate_file = None
+
         r_xml = config_xml.findall("resource")
         if not r_xml:
             _config_xml_error("resource")
@@ -71,6 +92,12 @@ def parse_config_xml(config_xml):
         refresh_time = int(c_xml[0].get("refresh_time", 300))
         connection_pool_monitor_interval = int(c_xml[0].get("connection_pool_monitor_interval", -1))
 
+        l_xml = config_xml.findall("logical")
+        if l_xml:
+            logical_path = l_xml[0].get("path", None)
+        else:
+            logical_path = None
+
         c_xml = config_xml.findall("cache")
         if not c_xml:
             _config_xml_error("cache")
@@ -89,6 +116,16 @@ def parse_config_xml(config_xml):
                 "username": username,
                 "password": password,
             },
+            "ssl": {
+                "client_server_negotiation": client_server_negotiation,
+                "client_server_policy": client_server_policy,
+                "encryption_algorithm": encryption_algorithm,
+                "encryption_key_size": encryption_key_size,
+                "encryption_num_hash_rounds": encryption_num_hash_rounds,
+                "encryption_salt_size": encryption_salt_size,
+                "ssl_verify_server": ssl_verify_server,
+                "ssl_ca_certificate_file": ssl_ca_certificate_file,
+            },
             "resource": {
                 "name": resource_name,
             },
@@ -102,6 +139,9 @@ def parse_config_xml(config_xml):
                 "refresh_time": refresh_time,
                 "connection_pool_monitor_interval": connection_pool_monitor_interval,
             },
+            "logical": {
+                "path": logical_path,
+            },
             "cache": {
                 "size": cache_size,
                 "path": staging_path,
@@ -139,6 +179,17 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         if self.password is None:
             _config_dict_error("auth->password")
 
+        ssl_dict = config_dict.get("ssl") or {}
+
+        self.client_server_negotiation = ssl_dict.get("client_server_negotiation")
+        self.client_server_policy = ssl_dict.get("client_server_policy")
+        self.encryption_algorithm = ssl_dict.get("encryption_algorithm")
+        self.encryption_key_size = ssl_dict.get("encryption_key_size")
+        self.encryption_num_hash_rounds = ssl_dict.get("encryption_num_hash_rounds")
+        self.encryption_salt_size = ssl_dict.get("encryption_salt_size")
+        self.ssl_verify_server = ssl_dict.get("ssl_verify_server")
+        self.ssl_ca_certificate_file = ssl_dict.get("ssl_ca_certificate_file")
+
         resource_dict = config_dict["resource"]
         if resource_dict is None:
             _config_dict_error("resource")
@@ -172,6 +223,11 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         if self.connection_pool_monitor_interval is None:
             _config_dict_error("connection->connection_pool_monitor_interval")
 
+        logical_dict = config_dict.get("logical") or {}
+        self.logical_path = logical_dict.get("path") or f"/{self.zone}/home/{self.username}"
+        if self.logical_path is None:
+            _config_dict_error("logical->path")
+
         cache_dict = config_dict.get("cache") or {}
         self.cache_size = cache_dict.get("size") or self.config.object_store_cache_path
         if self.cache_size is None:
@@ -189,19 +245,29 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         if irods is None:
             raise Exception(IRODS_IMPORT_MESSAGE)
 
-        self.home = f"/{self.zone}/home/{self.username}"
-
         if irods is None:
             raise Exception(IRODS_IMPORT_MESSAGE)
 
-        self.session = iRODSSession(
-            host=self.host,
-            port=self.port,
-            user=self.username,
-            password=self.password,
-            zone=self.zone,
-            refresh_time=self.refresh_time,
-        )
+        session_params = {
+            "host": self.host,
+            "port": self.port,
+            "user": self.username,
+            "password": self.password,
+            "zone": self.zone,
+            "refresh_time": self.refresh_time,
+            "client_server_negotiation": self.client_server_negotiation,
+            "client_server_policy": self.client_server_policy,
+            "encryption_algorithm": self.encryption_algorithm,
+            "encryption_key_size": self.encryption_key_size,
+            "encryption_num_hash_rounds": self.encryption_num_hash_rounds,
+            "encryption_salt_size": self.encryption_salt_size,
+            "ssl_verify_server": self.ssl_verify_server,
+            "ssl_ca_certificate_file": self.ssl_ca_certificate_file,
+            "ssl_context": ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH),
+        }
+
+        self.session = iRODSSession(**session_params)
+
         # Set connection timeout
         self.session.connection_timeout = self.timeout
 
@@ -285,6 +351,16 @@ class IRODSObjectStore(CachingConcreteObjectStore):
                 "username": self.username,
                 "password": self.password,
             },
+            "ssl": {
+                "client_server_negotiation": self.client_server_negotiation,
+                "client_server_policy": self.client_server_policy,
+                "encryption_algorithm": self.encryption_algorithm,
+                "encryption_key_size": self.encryption_key_size,
+                "encryption_num_hash_rounds": self.encryption_num_hash_rounds,
+                "encryption_salt_size": self.encryption_salt_size,
+                "ssl_verify_server": self.ssl_verify_server,
+                "ssl_ca_certificate_file": self.ssl_ca_certificate_file,
+            },
             "resource": {
                 "name": self.resource,
             },
@@ -298,6 +374,9 @@ class IRODSObjectStore(CachingConcreteObjectStore):
                 "refresh_time": self.refresh_time,
                 "connection_pool_monitor_interval": self.connection_pool_monitor_interval,
             },
+            "logical": {
+                "path": self.logical_path,
+            },
             "cache": {
                 "size": self.cache_size,
                 "path": self.staging_path,
@@ -312,7 +391,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{subcollection_name}"
+        collection_path = f"{self.logical_path}/{subcollection_name}"
         data_object_path = f"{collection_path}/{data_object_name}"
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
@@ -332,7 +411,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{subcollection_name}"
+        collection_path = f"{self.logical_path}/{subcollection_name}"
         data_object_path = f"{collection_path}/{data_object_name}"
         options = {kw.DEST_RESC_NAME_KW: self.resource}
 
@@ -354,7 +433,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         data_object_name = p.stem + p.suffix
         subcollection_name = p.parent
 
-        collection_path = f"{self.home}/{subcollection_name}"
+        collection_path = f"{self.logical_path}/{subcollection_name}"
         data_object_path = f"{collection_path}/{data_object_name}"
         # we need to allow irods to override already existing zero-size output files created
         # in object store cache during job setup (see also https://github.com/galaxyproject/galaxy/pull/17025#discussion_r1394517033)
@@ -395,7 +474,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
             return False
 
         # Check if the data object exists in iRODS
-        collection_path = f"{self.home}/{subcollection_name}"
+        collection_path = f"{self.logical_path}/{subcollection_name}"
         data_object_path = f"{collection_path}/{data_object_name}"
         exists = False
 
@@ -450,7 +529,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
         finally:
             log.debug("irods_pt _push_to_storage: %s", ipt_timer)
 
-    def _delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir: bool = False, **kwargs) -> bool:
         ipt_timer = ExecutionTimer()
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get("extra_dir", None)
@@ -473,7 +552,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path), ignore_errors=True)
 
-                col_path = f"{self.home}/{rel_path}"
+                col_path = f"{self.logical_path}/{rel_path}"
                 col = None
                 try:
                     col = self.session.collections.get(col_path)
@@ -501,7 +580,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
                 data_object_name = p.stem + p.suffix
                 subcollection_name = p.parent
 
-                collection_path = f"{self.home}/{subcollection_name}"
+                collection_path = f"{self.logical_path}/{subcollection_name}"
                 data_object_path = f"{collection_path}/{data_object_name}"
 
                 try:
@@ -527,7 +606,7 @@ class IRODSObjectStore(CachingConcreteObjectStore):
             data_object_name = p.stem + p.suffix
             subcollection_name = p.parent
 
-            collection_path = f"{self.home}/{subcollection_name}"
+            collection_path = f"{self.logical_path}/{subcollection_name}"
             data_object_path = f"{collection_path}/{data_object_name}"
 
             return data_object_path
diff --git a/lib/galaxy/objectstore/onedata.py b/lib/galaxy/objectstore/onedata.py
index 7fc8d5b72c275a036ea05a906c0f740ebe05493c..80f45a365d788e1546033bdc2c5494059ad3b72c 100644
--- a/lib/galaxy/objectstore/onedata.py
+++ b/lib/galaxy/objectstore/onedata.py
@@ -15,7 +15,10 @@ try:
 except ImportError:
     OnedataFileRESTClient = None
 
-from galaxy.util import string_as_bool
+from galaxy.util import (
+    mapped_chars,
+    string_as_bool,
+)
 from ._caching_base import CachingConcreteObjectStore
 from .caching import (
     enable_cache_monitor,
@@ -44,7 +47,7 @@ def _parse_config_xml(config_xml):
 
         space_xml = _get_config_xml_elements(config_xml, "space")[0]
         space_name = space_xml.get("name")
-        galaxy_root_dir = space_xml.get("path", "")
+        galaxy_root_dir = space_xml.get("galaxy_root_dir", "")
 
         cache_dict = parse_caching_config_dict_from_xml(config_xml)
 
@@ -107,8 +110,8 @@ class OnedataObjectStore(CachingConcreteObjectStore):
 
         cache_dict = config_dict.get("cache") or {}
         self.enable_cache_monitor, self.cache_monitor_interval = enable_cache_monitor(config, config_dict)
-        self.cache_size = cache_dict["size"] or self.config.object_store_cache_size
-        self.staging_path = cache_dict["path"] or self.config.object_store_cache_path
+        self.cache_size = cache_dict.get("size") or self.config.object_store_cache_size
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
         self.cache_updated_data = cache_dict.get("cache_updated_data", True)
 
         extra_dirs = {e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])}
@@ -125,8 +128,14 @@ class OnedataObjectStore(CachingConcreteObjectStore):
             f"(disable_tls_certificate_validation={self.disable_tls_certificate_validation})"
         )
 
+        alt_space_fqn_separators = [mapped_chars["@"]] if "@" in mapped_chars else None
         verify_ssl = not self.disable_tls_certificate_validation
-        self._client = OnedataFileRESTClient(self.onezone_domain, self.access_token, verify_ssl=verify_ssl)
+        self._client = OnedataFileRESTClient(
+            self.onezone_domain,
+            self.access_token,
+            alt_space_fqn_separators=alt_space_fqn_separators,
+            verify_ssl=verify_ssl,
+        )
 
         self._ensure_staging_path_writable()
         self._start_cache_monitor_if_needed()
diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py
index 43697062d9d06b409fe027bac9d0097dab2f4cab..45e95f4fa57381561d480cb8814c1ff672578316 100644
--- a/lib/galaxy/objectstore/pithos.py
+++ b/lib/galaxy/objectstore/pithos.py
@@ -149,7 +149,7 @@ class PithosObjectStore(CachingConcreteObjectStore):
 
     # No need to overwrite "shutdown"
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         """Check if file exists, fix if file in cache and not on Pithos+
         :returns: weather the file exists remotely or in cache
         """
diff --git a/lib/galaxy/objectstore/pulsar.py b/lib/galaxy/objectstore/pulsar.py
index 04eab33d5fa4876c551c02c2596316c889cef0b8..7444cc49d82f3c31d6d267f261102ce690481afc 100644
--- a/lib/galaxy/objectstore/pulsar.py
+++ b/lib/galaxy/objectstore/pulsar.py
@@ -24,7 +24,7 @@ class PulsarObjectStore(BaseObjectStore):
     def __init__(self, config, config_xml):
         self.pulsar_client = self.__build_pulsar_client(config_xml)
 
-    def _exists(self, obj, **kwds):
+    def _exists(self, obj, **kwds) -> bool:
         return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds))
 
     def file_ready(self, obj, **kwds):
@@ -33,23 +33,23 @@ class PulsarObjectStore(BaseObjectStore):
     def _create(self, obj, **kwds):
         return self.pulsar_client.create(**self.__build_kwds(obj, **kwds))
 
-    def _empty(self, obj, **kwds):
+    def _empty(self, obj, **kwds) -> bool:
         return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds))
 
-    def _size(self, obj, **kwds):
+    def _size(self, obj, **kwds) -> int:
         return self.pulsar_client.size(**self.__build_kwds(obj, **kwds))
 
-    def _delete(self, obj, **kwds):
+    def _delete(self, obj, **kwds) -> bool:
         return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds))
 
     # TODO: Optimize get_data.
     def _get_data(self, obj, **kwds):
         return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds))
 
-    def _get_filename(self, obj, **kwds):
+    def _get_filename(self, obj, **kwds) -> str:
         return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds))
 
-    def _update_from_file(self, obj, **kwds):
+    def _update_from_file(self, obj, **kwds) -> None:
         return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds))
 
     def _get_store_usage_percent(self):
diff --git a/lib/galaxy/objectstore/rucio.py b/lib/galaxy/objectstore/rucio.py
index 8056106cdc322c93f82989cea1fe98ec8389c013..97d1bd9f8e143b7850aea61188631607845cfd30 100644
--- a/lib/galaxy/objectstore/rucio.py
+++ b/lib/galaxy/objectstore/rucio.py
@@ -2,6 +2,7 @@ import hashlib
 import logging
 import os
 import shutil
+from typing import Optional
 
 try:
     import rucio.common
@@ -237,8 +238,15 @@ class RucioBroker:
                 }
             items = [item]
             download_client = self.get_rucio_download_client(auth_token=auth_token)
-            res = download_client.download_dids(items)
-            os.replace(res[0]["dest_file_paths"][0], dest_path)
+            try:
+                res = download_client.download_dids(items)
+                os.replace(res[0]["dest_file_paths"][0], dest_path)
+            except Exception as e:
+                if os.path.exists(dest_path):
+                    log.debug("File was already downloaded")
+                else:
+                    log.exception(f"Cannot download file: {str(e)}")
+                    return False
         except Exception as e:
             log.exception(f"Cannot download file: {str(e)}")
             return False
@@ -253,12 +261,12 @@ class RucioBroker:
         except Exception:
             return False
 
-    def get_size(self, key):
+    def get_size(self, key) -> int:
         key = _encode_key(key)
         dids = [{"scope": self.scope, "name": key}]
         try:
             repl = next(self.get_rucio_client().list_replicas(dids))
-            return repl["bytes"]
+            return int(repl["bytes"])
         except Exception:
             return 0
 
@@ -311,7 +319,7 @@ class RucioObjectStore(CachingConcreteObjectStore):
             self._ensure_staging_path_writable()
         self._start_cache_monitor_if_needed()
 
-    def _pull_into_cache(self, rel_path, auth_token):
+    def _pull_into_cache(self, rel_path, **kwargs) -> bool:
         log.debug("rucio _pull_into_cache: %s", rel_path)
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
         rel_path_dir = os.path.dirname(rel_path)
@@ -319,6 +327,7 @@ class RucioObjectStore(CachingConcreteObjectStore):
             os.makedirs(self._get_cache_path(rel_path_dir), exist_ok=True)
         # Now pull in the file
         dest = self._get_cache_path(rel_path)
+        auth_token = self._get_token(**kwargs)
         file_ok = self.rucio_broker.download(rel_path, dest, auth_token)
         self._fix_permissions(self._get_cache_path(rel_path_dir))
         return file_ok
@@ -339,7 +348,7 @@ class RucioObjectStore(CachingConcreteObjectStore):
 
     # "interfaces to implement"
 
-    def _exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs) -> bool:
         rel_path = self._construct_path(obj, **kwargs)
         log.debug("rucio _exists: %s", rel_path)
 
@@ -392,26 +401,27 @@ class RucioObjectStore(CachingConcreteObjectStore):
             log.debug("rucio _create: %s", rel_path)
         return self
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         rel_path = self._construct_path(obj, **kwargs)
         log.debug("rucio _size: %s", rel_path)
 
         if self._in_cache(rel_path):
+            size: Optional[int] = None
             try:
                 size = os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try iRODS. Error: %s", rel_path, ex)
-            if size != 0:
+            if size is not None:
                 return size
         if self._exists(obj, **kwargs):
             return self._get_remote_size(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def _get_remote_size(self, rel_path):
+    def _get_remote_size(self, rel_path) -> int:
         return self.rucio_broker.get_size(rel_path)
 
-    def _delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir: bool = False, **kwargs) -> bool:
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get("extra_dir", None)
         base_dir = kwargs.get("base_dir", None)
@@ -457,16 +467,14 @@ class RucioObjectStore(CachingConcreteObjectStore):
                 tokens = user.get_oidc_tokens(backend)
                 if tokens["id"]:
                     return tokens["id"]
-        except Exception as e:
-            log.debug("Failed to get auth token: %s", e)
+        except Exception:
             return None
 
-    def _get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, sync_cache: bool = True, **kwargs) -> str:
         base_dir = kwargs.get("base_dir", None)
         dir_only = kwargs.get("dir_only", False)
         auth_token = self._get_token(**kwargs)
         rel_path = self._construct_path(obj, **kwargs)
-        sync_cache = kwargs.get("sync_cache", True)
 
         log.debug("rucio _get_filename: %s", rel_path)
 
@@ -498,7 +506,7 @@ class RucioObjectStore(CachingConcreteObjectStore):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
-                if self._pull_into_cache(rel_path, auth_token):
+                if self._pull_into_cache(rel_path, auth_token=auth_token):
                     return cache_path
         raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
 
@@ -515,7 +523,9 @@ class RucioObjectStore(CachingConcreteObjectStore):
         log.debug("rucio _register_file: %s", file_name)
         return
 
-    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(
+        self, obj, file_name=None, create: bool = False, preserve_symlinks: bool = False, **kwargs
+    ) -> None:
         rel_path = self._construct_path(obj, **kwargs)
         log.debug("rucio _update_from_file: %s", rel_path)
 
diff --git a/lib/galaxy/objectstore/templates/examples/cloudflare.yml b/lib/galaxy/objectstore/templates/examples/cloudflare.yml
index df6732104c12f6eddef49b57525fc5bb6e3f4589..73db6d20866a6b5e73d71558f6aa93c16b174ded 100644
--- a/lib/galaxy/objectstore/templates/examples/cloudflare.yml
+++ b/lib/galaxy/objectstore/templates/examples/cloudflare.yml
@@ -1,5 +1,6 @@
 # https://developers.cloudflare.com/r2/examples/aws/boto3/
 - id: cloudflare
+  version: 0
   name: CloudFlare R2
   description: |
     This template can be used to connect to your [CloudFlare R2](https://developers.cloudflare.com/r2/)
@@ -7,7 +8,6 @@
     [CloudFlare R2 access tokens](https://developers.cloudflare.com/r2/api/s3/tokens/).
     Following that tutorial, you should have an "Account ID", and "Access Key ID", and a
     "Secret Access Key".
-
   variables:
     access_key:
       label: Access Key ID
@@ -15,13 +15,11 @@
       help: |
         An Access Key ID generated according to the
         [CloudFlare R2 access tokens documentation](https://developers.cloudflare.com/r2/api/s3/tokens/).
-
     account_id:
       label: Account ID
       type: string
       help: |
         Your account ID as available in the [CloudFlare dashboard](https://developers.cloudflare.com/fundamentals/setup/find-account-and-zone-ids/).
-
     bucket:
       label: Bucket
       type: string
@@ -34,7 +32,6 @@
       help: |
         A Secret Access Key generated according to the
         [CloudFlare R2 access tokens documentation](https://developers.cloudflare.com/r2/api/s3/tokens/).
-
   configuration:
     type: boto3
     auth:
diff --git a/lib/galaxy/objectstore/templates/examples/cloudflare_legacy.yml b/lib/galaxy/objectstore/templates/examples/cloudflare_legacy.yml
index df143e20a1f35f36578515095a786f485bd5cbc0..2aa7915c461c4f838e120f7b65a18885b4ec84a4 100644
--- a/lib/galaxy/objectstore/templates/examples/cloudflare_legacy.yml
+++ b/lib/galaxy/objectstore/templates/examples/cloudflare_legacy.yml
@@ -1,5 +1,6 @@
 # https://developers.cloudflare.com/r2/examples/aws/boto3/
 - id: cloudflare_legacy
+  version: 0
   name: CloudFlare R2
   description: |
     This template can be used to connect to your [CloudFlare R2](https://developers.cloudflare.com/r2/)
@@ -7,7 +8,6 @@
     [CloudFlare R2 access tokens](https://developers.cloudflare.com/r2/api/s3/tokens/).
     Following that tutorial, you should have an "Account ID", and "Access Key ID", and a
     "Secret Access Key".
-
   variables:
     access_key:
       label: Access Key ID
@@ -15,13 +15,11 @@
       help: |
         An Access Key ID generated according to the
         [CloudFlare R2 access tokens documentation](https://developers.cloudflare.com/r2/api/s3/tokens/).
-
     account_id:
       label: Account ID
       type: string
       help: |
         Your account ID as available in the [CloudFlare dashboard](https://developers.cloudflare.com/fundamentals/setup/find-account-and-zone-ids/).
-
     bucket:
       label: Bucket
       type: string
@@ -34,7 +32,6 @@
       help: |
         A Secret Access Key generated according to the
         [CloudFlare R2 access tokens documentation](https://developers.cloudflare.com/r2/api/s3/tokens/).
-
   configuration:
     type: generic_s3
     auth:
diff --git a/lib/galaxy/objectstore/templates/examples/minio_example.yml b/lib/galaxy/objectstore/templates/examples/minio_example.yml
index 2694b4f8ed3bd39a4ce50e002421673c7a6d0b5e..792de26330a2314636eb237424b7e1ae99861475 100644
--- a/lib/galaxy/objectstore/templates/examples/minio_example.yml
+++ b/lib/galaxy/objectstore/templates/examples/minio_example.yml
@@ -1,4 +1,5 @@
 - id: minio
+  version: 0
   name: Institutional S3 Storage
   description: Connect to our institutional MinIO storage service.
   variables:
diff --git a/lib/galaxy/objectstore/templates/examples/minio_just_buckets.yml b/lib/galaxy/objectstore/templates/examples/minio_just_buckets.yml
index 0996e45f7d39be3db79d8f3d6955be0546fef167..78828494aebad4b8df4de2978226e0b5f4cd95d2 100644
--- a/lib/galaxy/objectstore/templates/examples/minio_just_buckets.yml
+++ b/lib/galaxy/objectstore/templates/examples/minio_just_buckets.yml
@@ -1,4 +1,5 @@
 - id: lab_minio_storage
+  version: 0
   name: Lab Storage
   description: Connect to our lab's local MinIO storage service.
   variables:
diff --git a/lib/galaxy/objectstore/templates/examples/minio_just_buckets_legacy.yml b/lib/galaxy/objectstore/templates/examples/minio_just_buckets_legacy.yml
index b91f196e4051de754737e6b7cf6b50fee6154c31..85c55e4b01824b4ac833eb8f4880e4bd5b4d6c82 100644
--- a/lib/galaxy/objectstore/templates/examples/minio_just_buckets_legacy.yml
+++ b/lib/galaxy/objectstore/templates/examples/minio_just_buckets_legacy.yml
@@ -1,4 +1,5 @@
 - id: lab_minio_storage_legacy
+  version: 0
   name: Lab Storage (Legacy)
   description: Connect to our lab's local MinIO storage service.
   variables:
diff --git a/lib/galaxy/objectstore/templates/examples/onedata.yml b/lib/galaxy/objectstore/templates/examples/onedata.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f50a137da44700428a355cb5e962483b2c6ae91a
--- /dev/null
+++ b/lib/galaxy/objectstore/templates/examples/onedata.yml
@@ -0,0 +1,55 @@
+- id: onedata
+  name: Onedata Storage
+  version: 0
+  description: |
+    If you have an account in Onedata, you can use such an object store as
+    a storage location for your Galaxy datasets; they will be stored in
+    the Onedata space of your choice.
+
+    The minimal supported Onezone version is 21.02.4.
+    More information on Onedata can be found on [Onedata's website](https://onedata.org/#/home).
+  variables:
+    onezone_domain:
+      label: Onezone Domain
+      type: string
+      help: Domain of the Onezone service (e.g. datahub.egi.eu) to connect to.
+    disable_tls_certificate_validation:
+      label: Disable tls certificate validation?
+      type: boolean
+      help: |
+        Allows connection to Onedata servers that do not present trusted SSL certificates.
+        SHOULD NOT be used unless you really know what you are doing.
+      default: False
+    space_name:
+      label: Space Name
+      type: string
+      help: |
+        The name of the Onedata space where the Galaxy data will be stored.
+        If there is more than one space with the same name, you can explicitly
+        specify which one to select by using the format <space_name>@<space_id>
+        (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
+    galaxy_root_dir:
+      label: Galaxy root directory
+      type: string
+      help: |
+        The relative directory path in the space at which the Galaxy data
+        will be stored. If empty, the data will be stored in the space's
+        root directory.
+      default: ""
+  secrets:
+    access_token:
+      label: Access Token
+      help: |
+        Your [access token](https://onedata.org/#/home/documentation/topic/stable/tokens),
+        suitable for REST API access in a Oneprovider service. Must allow both
+        read and write data access.
+  configuration:
+    type: onedata
+    auth:
+      access_token: '{{ secrets.access_token }}'
+    connection:
+      onezone_domain: "{{ variables.onezone_domain }}"
+      disable_tls_certificate_validation: "{{ variables.disable_tls_certificate_validation }}"
+    space:
+      name: "{{ variables.space_name }}"
+      galaxy_root_dir: "{{ variables.galaxy_root_dir }}"
diff --git a/lib/galaxy/objectstore/templates/examples/production_aws_s3.yml b/lib/galaxy/objectstore/templates/examples/production_aws_s3.yml
index 77eabc10cc10432d38b8856fabe369c3a9a4f04b..c87026d1069c2e2924872561b75d80d1f1aa4e90 100644
--- a/lib/galaxy/objectstore/templates/examples/production_aws_s3.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_aws_s3.yml
@@ -1,4 +1,5 @@
 - id: aws_s3
+  version: 0
   name: Amazon Web Services S3 Storage
   description: |
     Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
@@ -10,7 +11,7 @@
       help: |
         A security credential for interacting with AWS services can be created from your
         AWS web console. Creating an "Access Key" creates a pair of keys used to identify
-        and authenticate access to your AWS account - the first part of the pair  is 
+        and authenticate access to your AWS account - the first part of the pair  is
         "Access Key ID" and should be entered here. The second part of your key is the secret
         part called the "Secret Access Key". Place that in the secure part of this form below.
     bucket:
@@ -25,7 +26,6 @@
       label: Secret Access Key
       help: |
         See the documentation above used "Access Key ID" for information about access key pairs.
-
   configuration:
     type: boto3
     auth:
diff --git a/lib/galaxy/objectstore/templates/examples/production_aws_s3_legacy.yml b/lib/galaxy/objectstore/templates/examples/production_aws_s3_legacy.yml
index 1bc8f66cf43277727fd94f24520eebdd5bb7ace7..1a3730897c56018bb2efaf67b88f1af5795a8940 100644
--- a/lib/galaxy/objectstore/templates/examples/production_aws_s3_legacy.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_aws_s3_legacy.yml
@@ -1,4 +1,5 @@
 - id: aws_s3_legacy
+  version: 0
   name: Amazon Web Services S3 Storage (Legacy)
   description: |
     Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
@@ -10,7 +11,7 @@
       help: |
         A security credential for interacting with AWS services can be created from your
         AWS web console. Creating an "Access Key" creates a pair of keys used to identify
-        and authenticate access to your AWS account - the first part of the pair  is 
+        and authenticate access to your AWS account - the first part of the pair  is
         "Access Key ID" and should be entered here. The second part of your key is the secret
         part called the "Secret Access Key". Place that in the secure part of this form below.
     bucket:
diff --git a/lib/galaxy/objectstore/templates/examples/production_azure_blob.yml b/lib/galaxy/objectstore/templates/examples/production_azure_blob.yml
index f7afbe7ed52adc5ef76f01e9cc6612e26643e5a8..ee57eaf74852369f2b471f3fc88592a45534a1a4 100644
--- a/lib/galaxy/objectstore/templates/examples/production_azure_blob.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_azure_blob.yml
@@ -8,10 +8,8 @@
     auth:
       account_name: '{{ variables.account_name }}'
       account_key: '{{ secrets.account_key}}'
-
     container:
       name: '{{ variables.container_name }}'
-
   variables:
     container_name:
       label: Container Name
@@ -25,7 +23,6 @@
       help: |
         The name of your Azure Blob Storage account. More information on containers can be found in the
         [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-overview).
-
   secrets:
     account_key:
       label: Account Key
diff --git a/lib/galaxy/objectstore/templates/examples/production_gcp_s3.yml b/lib/galaxy/objectstore/templates/examples/production_gcp_s3.yml
index da7622fc01d5548dff566c2288ab04546df0a300..95a14a634b5909880ab1d4be2a0cd3b712611a46 100644
--- a/lib/galaxy/objectstore/templates/examples/production_gcp_s3.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_gcp_s3.yml
@@ -1,5 +1,6 @@
 # https://cloud.google.com/storage/docs/aws-simple-migration
 - id: gcp_s3_interop
+  version: 0
   name: Google Cloud Storage
   description: |
     This template can be used to connect to your [Google Cloud Storage](https://cloud.google.com/storage).
@@ -16,7 +17,6 @@
       help: |
         This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
         to use your storage.
-
     bucket:
       label: Bucket
       type: string
@@ -30,7 +30,6 @@
         This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
         to use your storage. It should be 40 characters long and look something like the example used
         the Google documentation - `bGoa+V7g/yqDXvKRqq+JTFn4uQZbPiQJo4pf9RzJ`.
-
   configuration:
     type: boto3
     auth:
diff --git a/lib/galaxy/objectstore/templates/examples/production_generic_s3.yml b/lib/galaxy/objectstore/templates/examples/production_generic_s3.yml
index 4d8bdefdc24df89e75a63a3a03496b382a7a67b9..8a9c02e37eeb95c106b6ff1442ccb206fa3f86da 100644
--- a/lib/galaxy/objectstore/templates/examples/production_generic_s3.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_generic_s3.yml
@@ -1,4 +1,5 @@
 - id: generic_s3
+  version: 0
   name: Any S3 Compatible Storage
   description: |
     The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
@@ -20,7 +21,6 @@
         the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
         describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
         this the ``access_key``.
-
     bucket:
       label: Bucket
       type: string
diff --git a/lib/galaxy/objectstore/templates/examples/production_generic_s3_legacy.yml b/lib/galaxy/objectstore/templates/examples/production_generic_s3_legacy.yml
index 3e325e827463b2f5cb97cc50344adfffd9f4dc05..0894205b38a27d6f41c51b67087fd9f8d3efcd74 100644
--- a/lib/galaxy/objectstore/templates/examples/production_generic_s3_legacy.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_generic_s3_legacy.yml
@@ -1,4 +1,5 @@
 - id: generic_s3_legacy
+  version: 0
   name: Any S3 Compatible Storage (Legacy)
   description: |
     The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
@@ -20,7 +21,6 @@
         the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
         describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
         this the ``access_key``.
-
     bucket:
       label: Bucket
       type: string
@@ -35,13 +35,12 @@
       help: |
         The [hostname](https://en.wikipedia.org/wiki/Hostname) used to connect to the target
         S3 compatible service.
-        
+
         If the documentation for your storage service has something called an ``endpoint_url``,
         this can be used to determine this value. For instance, the CloudFlare documentation
         describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
         you would substitute your CloudFlare account ID into the endpoint and shave off the ``https://``,
         so if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
-
     port:
       label: Connection Port
       type: integer
diff --git a/lib/galaxy/objectstore/templates/models.py b/lib/galaxy/objectstore/templates/models.py
index dcbabb760434bd4c130b1e61db69cf8d04c89d71..3a5e041addafa1ffec5b2d4d98fdceea51487c99 100644
--- a/lib/galaxy/objectstore/templates/models.py
+++ b/lib/galaxy/objectstore/templates/models.py
@@ -17,7 +17,9 @@ from galaxy.objectstore.badges import (
 from galaxy.util.config_templates import (
     EnvironmentDict,
     expand_raw_config,
+    ImplicitConfigurationParameters,
     MarkdownContent,
+    merge_implicit_parameters,
     populate_default_variables,
     SecretsDict,
     StrictModel,
@@ -32,7 +34,7 @@ from galaxy.util.config_templates import (
 
 ObjectStoreTemplateVariableType = TemplateVariableType
 ObjectStoreTemplateVariableValueType = TemplateVariableValueType
-ObjectStoreTemplateType = Literal["aws_s3", "azure_blob", "boto3", "disk", "generic_s3"]
+ObjectStoreTemplateType = Literal["aws_s3", "azure_blob", "boto3", "disk", "generic_s3", "onedata"]
 
 
 class S3AuthTemplate(StrictModel):
@@ -266,12 +268,59 @@ class GenericS3ObjectStoreConfiguration(StrictModel):
     badges: BadgeList = None
 
 
+class OnedataAuthTemplate(StrictModel):
+    access_token: Union[str, TemplateExpansion]
+
+
+class OnedataAuth(StrictModel):
+    access_token: str
+
+
+class OnedataConnectionTemplate(StrictModel):
+    onezone_domain: Union[str, TemplateExpansion]
+    disable_tls_certificate_validation: Union[bool, TemplateExpansion] = False
+
+
+class OnedataConnection(StrictModel):
+    onezone_domain: str
+    disable_tls_certificate_validation: bool = False
+
+
+class OnedataSpaceTemplate(StrictModel):
+    name: Union[str, TemplateExpansion]
+    galaxy_root_dir: Optional[Union[str, TemplateExpansion]] = ""
+
+
+class OnedataSpace(StrictModel):
+    name: str
+    galaxy_root_dir: str
+
+
+class OnedataObjectStoreTemplateConfiguration(StrictModel):
+    type: Literal["onedata"]
+    auth: OnedataAuthTemplate
+    connection: OnedataConnectionTemplate
+    space: OnedataSpaceTemplate
+    badges: BadgeList = None
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class OnedataObjectStoreConfiguration(StrictModel):
+    type: Literal["onedata"]
+    auth: OnedataAuth
+    connection: OnedataConnection
+    space: OnedataSpace
+    badges: BadgeList = None
+
+
 ObjectStoreTemplateConfiguration = Union[
     AwsS3ObjectStoreTemplateConfiguration,
     Boto3ObjectStoreTemplateConfiguration,
     GenericS3ObjectStoreTemplateConfiguration,
     DiskObjectStoreTemplateConfiguration,
     AzureObjectStoreTemplateConfiguration,
+    OnedataObjectStoreTemplateConfiguration,
 ]
 ObjectStoreConfiguration = Union[
     AwsS3ObjectStoreConfiguration,
@@ -279,6 +328,7 @@ ObjectStoreConfiguration = Union[
     DiskObjectStoreConfiguration,
     AzureObjectStoreConfiguration,
     GenericS3ObjectStoreConfiguration,
+    OnedataObjectStoreConfiguration,
 ]
 
 
@@ -318,6 +368,10 @@ class ObjectStoreTemplate(ObjectStoreTemplateBase):
     configuration: ObjectStoreTemplateConfiguration
     environment: Optional[List[TemplateEnvironmentEntry]] = None
 
+    @property
+    def type(self):
+        return self.configuration.type
+
 
 ObjectStoreTemplateCatalog = RootModel[List[ObjectStoreTemplate]]
 
@@ -332,10 +386,12 @@ def template_to_configuration(
     secrets: SecretsDict,
     user_details: UserDetailsDict,
     environment: EnvironmentDict,
+    implicit: Optional[ImplicitConfigurationParameters] = None,
 ) -> ObjectStoreConfiguration:
     configuration_template = template.configuration
     populate_default_variables(template.variables, variables)
     raw_config = expand_raw_config(configuration_template, variables, secrets, user_details, environment)
+    merge_implicit_parameters(raw_config, implicit)
     return to_configuration_object(raw_config)
 
 
@@ -345,6 +401,7 @@ TypesToConfigurationClasses: Dict[ObjectStoreTemplateType, Type[ObjectStoreConfi
     "generic_s3": GenericS3ObjectStoreConfiguration,
     "azure_blob": AzureObjectStoreConfiguration,
     "disk": DiskObjectStoreConfiguration,
+    "onedata": OnedataObjectStoreConfiguration,
 }
 
 
diff --git a/lib/galaxy/quota/__init__.py b/lib/galaxy/quota/__init__.py
index 3f0b55cda645c939ee9f805284d8db770295c009..83fc8392762e6b473044c5b13305f1cf7625d119 100644
--- a/lib/galaxy/quota/__init__.py
+++ b/lib/galaxy/quota/__init__.py
@@ -8,6 +8,7 @@ from sqlalchemy.sql import text
 
 import galaxy.util
 from galaxy.model.base import transaction
+from galaxy.objectstore import is_user_object_store
 
 log = logging.getLogger(__name__)
 
@@ -378,8 +379,8 @@ WHERE default_quota_association.type = :default_type
                 self.sa_session.commit()
 
     def is_over_quota(self, app, job, job_destination):
-        # Doesn't work because job.object_store_id until inside handler :_(
-        # quota_source_label = job.quota_source_label
+        if is_user_object_store(job.object_store_id):
+            return False  # User object stores are not subject to quotas
         if job_destination is not None:
             object_store_id = job_destination.params.get("object_store_id", None)
             object_store = app.object_store
diff --git a/lib/galaxy/schema/cloud.py b/lib/galaxy/schema/cloud.py
deleted file mode 100644
index 86a4f11a41ab6005fdc664af32a152d3a6e196c6..0000000000000000000000000000000000000000
--- a/lib/galaxy/schema/cloud.py
+++ /dev/null
@@ -1,131 +0,0 @@
-from typing import (
-    List,
-    Optional,
-    Union,
-)
-
-from pydantic import (
-    Field,
-    RootModel,
-)
-from typing_extensions import Literal
-
-from galaxy.schema.fields import DecodedDatabaseIdField
-from galaxy.schema.schema import (
-    DatasetSummary,
-    Model,
-)
-
-
-class InputArguments(Model):
-    dbkey: Optional[str] = Field(
-        default="?",
-        title="Database Key",
-        description="Sets the database key of the objects being fetched to Galaxy.",
-    )
-    file_type: Optional[str] = Field(
-        default="auto",
-        title="File Type",
-        description="Sets the Galaxy datatype (e.g., `bam`) for the objects being fetched to Galaxy. See the following link for a complete list of Galaxy data types: https://galaxyproject.org/learn/datatypes/.",
-    )
-    to_posix_lines: Optional[Union[Literal["Yes"], bool]] = Field(
-        default="Yes",
-        title="POSIX line endings",
-        description="A boolean value ('true' or 'false'); if 'Yes', converts universal line endings to POSIX line endings. Set to 'False' if you upload a gzip, bz2 or zip archive containing a binary file.",
-    )
-    space_to_tab: Optional[bool] = Field(
-        default=False,
-        title="Spaces to tabs",
-        description="A boolean value ('true' or 'false') that sets if spaces should be converted to tab in the objects being fetched to Galaxy. Applicable only if `to_posix_lines` is True",
-    )
-
-
-class CloudObjects(Model):
-    history_id: DecodedDatabaseIdField = Field(
-        default=...,
-        title="History ID",
-        description="The ID of history to which the object should be received to.",
-    )
-    bucket: str = Field(
-        default=...,
-        title="Bucket",
-        description="The name of a bucket from which data should be fetched from (e.g., a bucket name on AWS S3).",
-    )
-    objects: List[str] = Field(
-        default=...,
-        title="Objects",
-        description="A list of the names of objects to be fetched.",
-    )
-    authz_id: DecodedDatabaseIdField = Field(
-        default=...,
-        title="Authentication ID",
-        description="The ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations via `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define a new authorization.",
-    )
-    input_args: Optional[InputArguments] = Field(
-        default=None,
-        title="Input arguments",
-        description="A summary of the input arguments, which is optional and will default to {}.",
-    )
-
-
-class CloudDatasets(Model):
-    history_id: DecodedDatabaseIdField = Field(
-        default=...,
-        title="History ID",
-        description="The ID of history from which the object should be downloaded",
-    )
-    bucket: str = Field(
-        default=...,
-        title="Bucket",
-        description="The name of a bucket to which data should be sent (e.g., a bucket name on AWS S3).",
-    )
-    authz_id: DecodedDatabaseIdField = Field(
-        default=...,
-        title="Authentication ID",
-        description="The ID of CloudAuthz to be used for authorizing access to the resource provider. You may get a list of the defined authorizations via `/api/cloud/authz`. Also, you can use `/api/cloud/authz/create` to define a new authorization.",
-    )
-    dataset_ids: Optional[List[DecodedDatabaseIdField]] = Field(
-        default=None,
-        title="Objects",
-        description="A list of dataset IDs belonging to the specified history that should be sent to the given bucket. If not provided, Galaxy sends all the datasets belonging the specified history.",
-    )
-    overwrite_existing: Optional[bool] = Field(
-        default=False,
-        title="Spaces to tabs",
-        description="A boolean value. If set to 'True', and an object with same name of the dataset to be sent already exist in the bucket, Galaxy replaces the existing object with the dataset to be sent. If set to 'False', Galaxy appends datetime to the dataset name to prevent overwriting an existing object.",
-    )
-
-
-class CloudDatasetsResponse(Model):
-    sent_dataset_labels: List[str] = Field(
-        default=...,
-        title="Send datasets",
-        description="The datasets for which Galaxy succeeded to create (and queue) send job",
-    )
-    failed_dataset_labels: List[str] = Field(
-        default=...,
-        title="Failed datasets",
-        description="The datasets for which Galaxy failed to create (and queue) send job",
-    )
-    bucket_name: str = Field(
-        default=...,
-        title="Bucket",
-        description="The name of bucket to which the listed datasets are queued to be sent",
-    )
-
-
-class StatusCode(Model):
-    detail: str = Field(
-        default=...,
-        title="Detail",
-        description="The detail to expand on the status code",
-    )
-    status: int = Field(
-        default=...,
-        title="Code",
-        description="The actual status code",
-    )
-
-
-class DatasetSummaryList(RootModel):
-    root: List[DatasetSummary]
diff --git a/lib/galaxy/schema/fetch_data.py b/lib/galaxy/schema/fetch_data.py
index 2603b1471ea5448b263a21cc1995e3c7ca14f89b..daf9c905dfed256918455b14b35b7e5d74c5c905 100644
--- a/lib/galaxy/schema/fetch_data.py
+++ b/lib/galaxy/schema/fetch_data.py
@@ -1,6 +1,8 @@
 import json
 from enum import Enum
 from typing import (
+    Any,
+    Dict,
     List,
     Optional,
     Union,
@@ -101,6 +103,13 @@ class ExtraFiles(FetchBaseModel):
     )
 
 
+class FetchDatasetHash(Model):
+    hash_function: Literal["MD5", "SHA-1", "SHA-256", "SHA-512"]
+    hash_value: str
+
+    model_config = ConfigDict(extra="forbid")
+
+
 class BaseDataElement(FetchBaseModel):
     name: Optional[CoercedStringType] = None
     dbkey: str = Field("?")
@@ -116,6 +125,10 @@ class BaseDataElement(FetchBaseModel):
     items_from: Optional[ElementsFromType] = Field(None, alias="elements_from")
     collection_type: Optional[str] = None
     MD5: Optional[str] = None
+    SHA1: Optional[str] = Field(None, alias="SHA-1")
+    SHA256: Optional[str] = Field(None, alias="SHA-256")
+    SHA512: Optional[str] = Field(None, alias="SHA-512")
+    hashes: Optional[List[FetchDatasetHash]] = None
     description: Optional[str] = None
     model_config = ConfigDict(extra="forbid")
 
@@ -170,6 +183,7 @@ class PathDataElement(BaseDataElement):
 class CompositeDataElement(BaseDataElement):
     src: Literal["composite"]
     composite: "CompositeItems"
+    metadata: Optional[Dict[str, Any]] = None
 
 
 class CompositeItems(FetchBaseModel):
diff --git a/lib/galaxy/schema/fields.py b/lib/galaxy/schema/fields.py
index 311a0cf105e548d5cd817bd25cc5bf42e295e048..eb332962e0f026ecc4fe66ceacf516f7f07e6a5f 100644
--- a/lib/galaxy/schema/fields.py
+++ b/lib/galaxy/schema/fields.py
@@ -133,3 +133,15 @@ def ModelClassField(default_value):
         description="The name of the database model class.",
         json_schema_extra={"const": literal_to_value(default_value), "type": "string"},
     )
+
+
+def accept_wildcard_defaults_to_json(v):
+    assert isinstance(v, str)
+    # Accept header can have multiple comma separated values.
+    # If any of these values is the wildcard - we default to application/json.
+    if "*/*" in v:
+        return "application/json"
+    return v
+
+
+AcceptHeaderValidator = BeforeValidator(accept_wildcard_defaults_to_json)
diff --git a/lib/galaxy/schema/generics.py b/lib/galaxy/schema/generics.py
index 6eca44835054c9c6a612da83157f89c0bc35bf6e..7312a4b328692e0a3a0c6684f754c88e05dd05de 100644
--- a/lib/galaxy/schema/generics.py
+++ b/lib/galaxy/schema/generics.py
@@ -1,5 +1,7 @@
+import sys
 from typing import (
     Any,
+    Generic,
     Tuple,
     Type,
     TypeVar,
@@ -7,6 +9,7 @@ from typing import (
 
 from pydantic import BaseModel
 from pydantic.json_schema import GenerateJsonSchema
+from typing_extensions import override
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
@@ -50,3 +53,46 @@ class CustomJsonSchema(GenerateJsonSchema):
             for i, choice in enumerate(choices):
                 choices[i] = choice.replace(choices[0], ref_to_name[ref])  # type: ignore[call-overload]
         return full_def
+
+
+class PatchGenericPickle:
+    """A mixin that allows generic pydantic models to be serialized and deserialized with pickle.
+
+    Notes
+    ----
+    In general, pickle shouldn't be encouraged as a means of serialization since there are better,
+    safer options. In some cases e.g. Streamlit's `@st.cache_data there's no getting around
+    needing to use pickle.
+
+    As of Pydantic 2.7, generics don't properly work with pickle. The core issue is the following
+    1. For each specialized generic, pydantic creates a new subclass at runtime. This class
+       has a `__qualname__` that contains the type var argument e.g. `"MyGeneric[str]"` for a
+       `class MyGeneric(BaseModel, Generic[T])`.
+    2. Pickle attempts to find a symbol with the value of `__qualname__` in the module where the
+       class was defined, which fails since Pydantic defines that class dynamically at runtime.
+       Pydantic does attempt to register these dynamic classes but currently only for classes
+       defined at the top-level of the interpreter.
+
+    See Also
+    --------
+    - https://github.com/pydantic/pydantic/issues/9390
+    """
+
+    @classmethod
+    @override
+    def __init_subclass__(cls, **kwargs):
+        # Note: we're still in __init_subclass__, not yet in __pydantic_init_subclass__
+        #  not all model_fields are available at this point.
+        super().__init_subclass__(**kwargs)
+
+        if not issubclass(cls, BaseModel):
+            raise TypeError("PatchGenericPickle can only be used with subclasses of pydantic.BaseModel")
+        if not issubclass(cls, Generic):  # type: ignore [arg-type]
+            raise TypeError("PatchGenericPickle can only be used with Generic models")
+
+        qualname = cls.__qualname__
+        declaring_module = sys.modules[cls.__module__]
+        if qualname not in declaring_module.__dict__:
+            # This should work in all cases, but we might need to make this check and update more
+            # involved e.g. see pydantic._internal._generics.create_generic_submodel
+            declaring_module.__dict__[qualname] = cls
diff --git a/lib/galaxy/schema/groups.py b/lib/galaxy/schema/groups.py
index 1a4bde58f764505ed3ad910e370736691d25968c..b513ba26fa417e0d284986fce184413b63a19098 100644
--- a/lib/galaxy/schema/groups.py
+++ b/lib/galaxy/schema/groups.py
@@ -73,5 +73,18 @@ class GroupCreatePayload(Model):
 
 
 @partial_model()
-class GroupUpdatePayload(GroupCreatePayload):
-    pass
+class GroupUpdatePayload(Model):
+    """Payload schema for updating a group."""
+
+    name: str = Field(
+        ...,
+        title="name of the group",
+    )
+    user_ids: Optional[List[DecodedDatabaseIdField]] = Field(
+        None,
+        title="user IDs",
+    )
+    role_ids: Optional[List[DecodedDatabaseIdField]] = Field(
+        None,
+        title="role IDs",
+    )
diff --git a/lib/galaxy/schema/help.py b/lib/galaxy/schema/help.py
index ebe2da9370db27122e7cccbdc6a9e7ea5a209ddb..6ecb83513b496fd09cf3f611148100d75b864c1c 100644
--- a/lib/galaxy/schema/help.py
+++ b/lib/galaxy/schema/help.py
@@ -27,14 +27,14 @@ class HelpForumPost(HelpTempBaseModel):
     """Model for a post in the help forum."""
 
     id: Annotated[int, Field(description="The ID of the post.")]
-    name: Annotated[str, Field(description="The name of the post.")]
-    username: Annotated[str, Field(description="The username of the post author.")]
-    avatar_template: Annotated[str, Field(description="The avatar template of the user.")]
-    created_at: Annotated[str, Field(description="The creation date of the post.")]
-    like_count: Annotated[int, Field(description="The number of likes of the post.")]
-    blurb: Annotated[str, Field(description="The blurb of the post.")]
-    post_number: Annotated[int, Field(description="The post number of the post.")]
-    topic_id: Annotated[int, Field(description="The ID of the topic of the post.")]
+    name: Annotated[Optional[str], Field(description="The name of the post.")]
+    username: Annotated[Optional[str], Field(description="The username of the post author.")]
+    avatar_template: Annotated[Optional[str], Field(description="The avatar template of the user.")]
+    created_at: Annotated[Optional[str], Field(description="The creation date of the post.")]
+    like_count: Annotated[Optional[int], Field(description="The number of likes of the post.")]
+    blurb: Annotated[Optional[str], Field(description="The blurb of the post.")]
+    post_number: Annotated[Optional[int], Field(description="The post number of the post.")]
+    topic_id: Annotated[Optional[int], Field(description="The ID of the topic of the post.")]
 
 
 class HelpForumTopic(Model):
diff --git a/lib/galaxy/schema/invocation.py b/lib/galaxy/schema/invocation.py
index 1d433fa5584a3c2de8c8af02aa14b0d6c6f0a94a..76d7ca72761f6808d5227d3d3340a32a9572f842 100644
--- a/lib/galaxy/schema/invocation.py
+++ b/lib/galaxy/schema/invocation.py
@@ -20,6 +20,7 @@ from pydantic import (
 from typing_extensions import (
     Annotated,
     Literal,
+    TypeAliasType,
 )
 
 from galaxy.schema import schema
@@ -46,6 +47,19 @@ from galaxy.schema.schema import (
     UpdateTimeField,
     WithModelClass,
 )
+from .workflows import (
+    INPUTS_BY_DESCRIPTION,
+    PreferredIntermediateObjectStoreIdField,
+    PreferredObjectStoreIdField,
+    PreferredOutputsObjectStoreIdField,
+    ReplacementParametersField,
+    ResourceParametersField,
+    STEP_PARAMETERS_DESCRIPTION,
+    STEP_PARAMETERS_NORMALIZED_DESCRIPTION,
+    STEP_PARAMETERS_NORMALIZED_TITLE,
+    STEP_PARAMETERS_TITLE,
+    UseCachedJobField,
+)
 
 INVOCATION_STEP_OUTPUT_SRC = Literal["hda"]
 INVOCATION_STEP_COLLECTION_OUTPUT_SRC = Literal["hdca"]
@@ -76,6 +90,7 @@ class FailureReason(str, Enum):
     expression_evaluation_failed = "expression_evaluation_failed"
     when_not_boolean = "when_not_boolean"
     unexpected_failure = "unexpected_failure"
+    workflow_parameter_invalid = "workflow_parameter_invalid"
 
 
 # The reasons below are attached to the invocation and user-actionable.
@@ -211,6 +226,14 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     )
 
 
+class GenericInvocationFailureWorkflowParameterInvalid(InvocationFailureMessageBase[DatabaseIdT], Generic[DatabaseIdT]):
+    reason: Literal[FailureReason.workflow_parameter_invalid]
+    workflow_step_id: int = Field(
+        ..., title="Workflow parameter step that failed validation", validation_alias="workflow_step_index"
+    )
+    details: str = Field(..., description="Message raised by validator")
+
+
 InvocationCancellationReviewFailed = GenericInvocationCancellationReviewFailed[int]
 InvocationCancellationHistoryDeleted = GenericInvocationCancellationHistoryDeleted[int]
 InvocationCancellationUserRequest = GenericInvocationCancellationUserRequest[int]
@@ -222,6 +245,7 @@ InvocationFailureExpressionEvaluationFailed = GenericInvocationFailureExpression
 InvocationFailureWhenNotBoolean = GenericInvocationFailureWhenNotBoolean[int]
 InvocationUnexpectedFailure = GenericInvocationUnexpectedFailure[int]
 InvocationWarningWorkflowOutputNotFound = GenericInvocationEvaluationWarningWorkflowOutputNotFound[int]
+InvocationFailureWorkflowParameterInvalid = GenericInvocationFailureWorkflowParameterInvalid[int]
 
 InvocationMessageUnion = Union[
     InvocationCancellationReviewFailed,
@@ -235,6 +259,7 @@ InvocationMessageUnion = Union[
     InvocationFailureWhenNotBoolean,
     InvocationUnexpectedFailure,
     InvocationWarningWorkflowOutputNotFound,
+    InvocationFailureWorkflowParameterInvalid,
 ]
 
 InvocationCancellationReviewFailedResponseModel = GenericInvocationCancellationReviewFailed[EncodedDatabaseIdField]
@@ -252,8 +277,11 @@ InvocationUnexpectedFailureResponseModel = GenericInvocationUnexpectedFailure[En
 InvocationWarningWorkflowOutputNotFoundResponseModel = GenericInvocationEvaluationWarningWorkflowOutputNotFound[
     EncodedDatabaseIdField
 ]
+InvocationFailureWorkflowParameterInvalidResponseModel = GenericInvocationFailureWorkflowParameterInvalid[
+    EncodedDatabaseIdField
+]
 
-InvocationMessageResponseUnion = Annotated[
+_InvocationMessageResponseUnion = Annotated[
     Union[
         InvocationCancellationReviewFailedResponseModel,
         InvocationCancellationHistoryDeletedResponseModel,
@@ -266,10 +294,13 @@ InvocationMessageResponseUnion = Annotated[
         InvocationFailureWhenNotBooleanResponseModel,
         InvocationUnexpectedFailureResponseModel,
         InvocationWarningWorkflowOutputNotFoundResponseModel,
+        InvocationFailureWorkflowParameterInvalidResponseModel,
     ],
     Field(discriminator="reason"),
 ]
 
+InvocationMessageResponseUnion = TypeAliasType("InvocationMessageResponseUnion", _InvocationMessageResponseUnion)
+
 
 class InvocationMessageResponseModel(RootModel):
     root: InvocationMessageResponseUnion
@@ -278,6 +309,7 @@ class InvocationMessageResponseModel(RootModel):
 
 class InvocationState(str, Enum):
     NEW = "new"  # Brand new workflow invocation... maybe this should be same as READY
+    REQUIRES_MATERIALIZATION = "requires_materialization"  # an otherwise NEW or READY workflow that requires inputs to be materialized (undeferred)
     READY = "ready"  # Workflow ready for another iteration of scheduling.
     SCHEDULED = "scheduled"  # Workflow has been scheduled.
     CANCELLED = "cancelled"
@@ -527,13 +559,16 @@ class InvocationOutputCollection(InvocationIOBase):
     )
 
 
+InvocationWorkflowIdField = Field(
+    title="Workflow ID", description="The encoded Workflow ID associated with the invocation."
+)
+
+
 class WorkflowInvocationCollectionView(Model, WithModelClass):
     id: EncodedDatabaseIdField = InvocationIdField
     create_time: datetime = CreateTimeField
     update_time: datetime = UpdateTimeField
-    workflow_id: EncodedDatabaseIdField = Field(
-        title="Workflow ID", description="The encoded Workflow ID associated with the invocation."
-    )
+    workflow_id: EncodedDatabaseIdField = InvocationWorkflowIdField
     history_id: EncodedDatabaseIdField = Field(
         default=...,
         title="History ID",
@@ -579,6 +614,48 @@ class WorkflowInvocationResponse(RootModel):
     ]
 
 
+class WorkflowInvocationRequestModel(Model):
+    """Model a workflow invocation request (InvokeWorkflowPayload) for an existing invocation."""
+
+    history_id: str = Field(
+        ...,
+        title="History ID",
+        description="The encoded history id the workflow was run in.",
+    )
+    workflow_id: str = Field(title="Workflow ID", description="The encoded Workflow ID associated with the invocation.")
+    inputs: Dict[str, Any] = Field(
+        ...,
+        title="Inputs",
+        description="Values for inputs",
+    )
+    inputs_by: str = Field(
+        ...,
+        title="Inputs by",
+        description=INPUTS_BY_DESCRIPTION,
+    )
+    replacement_params: Optional[Dict[str, Any]] = ReplacementParametersField
+    resource_params: Optional[Dict[str, Any]] = ResourceParametersField
+    use_cached_job: bool = UseCachedJobField
+    preferred_object_store_id: Optional[str] = PreferredObjectStoreIdField
+    preferred_intermediate_object_store_id: Optional[str] = PreferredIntermediateObjectStoreIdField
+    preferred_outputs_object_store_id: Optional[str] = PreferredOutputsObjectStoreIdField
+    parameters_normalized: Literal[True] = Field(
+        True,
+        title=STEP_PARAMETERS_NORMALIZED_TITLE,
+        description=STEP_PARAMETERS_NORMALIZED_DESCRIPTION,
+    )
+    parameters: Optional[Dict[str, Any]] = Field(
+        None,
+        title=STEP_PARAMETERS_TITLE,
+        description=f"{STEP_PARAMETERS_DESCRIPTION} If these are set, the workflow was not executed in a best-practice fashion and we the resulting invocation request may not fully reflect the executed workflow state.",
+    )
+    instance: Literal[True] = Field(
+        True,
+        title="Is instance",
+        description="This API yields a particular workflow instance, newer workflows belonging to the same storedworkflow may have different state.",
+    )
+
+
 class InvocationJobsSummaryBaseModel(Model):
     id: EncodedDatabaseIdField = InvocationIdField
     states: Dict[JobState, int] = Field(
diff --git a/lib/galaxy/schema/jobs.py b/lib/galaxy/schema/jobs.py
index b48e92f51f90938a381169e4e25040c9ffa7496b..fbca9e281a2d55b37cbaf7308cab9cd6915f3fde 100644
--- a/lib/galaxy/schema/jobs.py
+++ b/lib/galaxy/schema/jobs.py
@@ -191,6 +191,7 @@ class EncodedJobDetails(JobSummary):
         title="Output collections",
         description="",
     )
+    user_id: Optional[EncodedDatabaseIdField] = Field(default=None, description="User ID of user that ran this job")
 
 
 class JobDestinationParams(Model):
@@ -213,9 +214,9 @@ class JobOutput(Model):
 
 
 class JobConsoleOutput(Model):
-    state: str = Field(None, title="Job State", description="The current job's state")
-    stdout: Optional[str] = Field(None, title="STDOUT", description="Job STDOUT text")
-    stderr: Optional[str] = Field(None, title="STDERR", description="Job STDERR text")
+    state: Optional[JobState] = Field(None, title="Job State", description="The current job's state")
+    stdout: Optional[str] = Field(None, title="STDOUT", description="Tool STDOUT from job.")
+    stderr: Optional[str] = Field(None, title="STDERR", description="Tool STDERR from job.")
 
 
 class JobParameter(Model):
@@ -229,7 +230,7 @@ class JobParameter(Model):
         title="Depth",
         description="The depth of the job parameter.",
     )
-    value: Optional[Union[List[EncodedJobParameterHistoryItem], float, int, bool, str]] = Field(
+    value: Optional[Union[List[Optional[EncodedJobParameterHistoryItem]], float, int, bool, str]] = Field(
         default=None, title="Value", description="The values of the job parameter", union_mode="left_to_right"
     )
     notes: Optional[str] = Field(default=None, title="Notes", description="Notes associated with the job parameter.")
diff --git a/lib/galaxy/schema/library_contents.py b/lib/galaxy/schema/library_contents.py
new file mode 100644
index 0000000000000000000000000000000000000000..52b41c7c82d19bfa29b0ff3de53e12f56205b07b
--- /dev/null
+++ b/lib/galaxy/schema/library_contents.py
@@ -0,0 +1,328 @@
+import json
+from enum import Enum
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from pydantic import (
+    ConfigDict,
+    Field,
+    RootModel,
+)
+from pydantic.functional_validators import field_validator
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
+
+from galaxy.schema.fields import (
+    DecodedDatabaseIdField,
+    EncodedDatabaseIdField,
+    EncodedLibraryFolderDatabaseIdField,
+    LibraryFolderDatabaseIdField,
+    ModelClassField,
+)
+from galaxy.schema.schema import (
+    Model,
+    TagCollection,
+)
+
+
+class UploadOption(str, Enum):
+    upload_file = "upload_file"
+    upload_paths = "upload_paths"
+    upload_directory = "upload_directory"
+
+
+class CreateType(str, Enum):
+    file = "file"
+    folder = "folder"
+    collection = "collection"
+
+
+class LinkDataOnly(str, Enum):
+    copy_files = "copy_files"
+    link_to_files = "link_to_files"
+
+
+class LibraryContentsCreatePayload(Model):
+    create_type: CreateType = Field(
+        ...,
+        description="the type of item to create",
+    )
+    upload_option: UploadOption = Field(
+        UploadOption.upload_file,
+        description="the method to use for uploading files",
+        deprecated=True,
+    )
+    folder_id: LibraryFolderDatabaseIdField = Field(
+        ...,
+        description="the encoded id of the parent folder of the new item",
+    )
+    tag_using_filenames: bool = Field(
+        False,
+        description="create tags on datasets using the file's original name",
+    )
+    tags: List[str] = Field(
+        [],
+        description="create the given list of tags on datasets",
+    )
+    from_hda_id: Optional[DecodedDatabaseIdField] = Field(
+        None,
+        description="(only if create_type is 'file') the encoded id of an accessible HDA to copy into the library",
+    )
+    from_hdca_id: Optional[DecodedDatabaseIdField] = Field(
+        None,
+        description="(only if create_type is 'file') the encoded id of an accessible HDCA to copy into the library",
+    )
+    ldda_message: str = Field(
+        "",
+        description="the new message attribute of the LDDA created",
+    )
+    extended_metadata: Optional[Dict[str, Any]] = Field(
+        None,
+        description="sub-dictionary containing any extended metadata to associate with the item",
+    )
+
+    @field_validator("tags", mode="before", check_fields=False)
+    @classmethod
+    def tags_string_to_json(cls, v):
+        if isinstance(v, str):
+            return json.loads(v)
+        return v
+
+
+class LibraryContentsFileCreatePayload(LibraryContentsCreatePayload):
+    dbkey: Union[str, list] = Field(
+        "?",
+        title="database key",
+    )
+    roles: str = Field(
+        "",
+        title="user selected roles",
+    )
+    file_type: Optional[str] = Field(
+        None,
+        title="file type",
+    )
+    server_dir: str = Field(
+        "",
+        description="(only if upload_option is 'upload_directory') relative path of the "
+        "subdirectory of Galaxy ``library_import_dir`` (if admin) or "
+        "``user_library_import_dir`` (if non-admin) to upload. "
+        "All and only the files (i.e. no subdirectories) contained "
+        "in the specified directory will be uploaded.",
+    )
+    filesystem_paths: str = Field(
+        "",
+        description="(only if upload_option is 'upload_paths' and the user is an admin) "
+        "file paths on the Galaxy server to upload to the library, one file per line",
+    )
+    link_data_only: LinkDataOnly = Field(
+        LinkDataOnly.copy_files,
+        description="(only when upload_option is 'upload_directory' or 'upload_paths')."
+        "Setting to 'link_to_files' symlinks instead of copying the files",
+    )
+    uuid: Optional[str] = Field(
+        None,
+        title="UUID of the dataset to upload",
+    )
+    upload_files: Optional[List[Dict[str, Any]]] = Field(
+        None,
+        title="list of the uploaded files",
+    )
+
+    # uploaded file fields
+    model_config = ConfigDict(extra="allow")
+
+
+class LibraryContentsFolderCreatePayload(LibraryContentsCreatePayload):
+    name: str = Field(
+        "",
+        title="name of the folder to create",
+    )
+    description: str = Field(
+        "",
+        title="description of the folder to create",
+    )
+
+
+class LibraryContentsCollectionCreatePayload(LibraryContentsCreatePayload):
+    collection_type: str = Field(
+        ...,
+        title="the type of collection to create",
+    )
+    element_identifiers: List[Dict[str, Any]] = Field(
+        ...,
+        title="list of dictionaries containing the element identifiers for the collection",
+    )
+    name: Optional[str] = Field(
+        None,
+        title="the name of the collection",
+    )
+    hide_source_items: bool = Field(
+        False,
+        description="if True, hide the source items in the collection",
+    )
+    copy_elements: bool = Field(
+        False,
+        description="if True, copy the elements into the collection",
+    )
+
+
+class LibraryContentsUpdatePayload(Model):
+    converted_dataset_id: Optional[DecodedDatabaseIdField] = Field(
+        None,
+        title="the decoded id of the dataset",
+    )
+
+
+class LibraryContentsDeletePayload(Model):
+    purge: bool = Field(
+        False,
+        description="if True, purge the library dataset",
+    )
+
+
+class LibraryContentsIndexResponse(Model):
+    type: str
+    name: str
+    url: str
+
+
+class LibraryContentsIndexFolderResponse(LibraryContentsIndexResponse):
+    id: EncodedLibraryFolderDatabaseIdField
+
+
+class LibraryContentsIndexDatasetResponse(LibraryContentsIndexResponse):
+    id: EncodedDatabaseIdField
+
+
+class LibraryContentsIndexListResponse(RootModel):
+    root: List[Union[LibraryContentsIndexFolderResponse, LibraryContentsIndexDatasetResponse]]
+
+
+class LibraryContentsShowResponse(Model):
+    name: str
+    genome_build: Optional[str]
+    update_time: str
+    parent_library_id: EncodedDatabaseIdField
+
+
+class LibraryContentsShowFolderResponse(LibraryContentsShowResponse):
+    model_class: Annotated[Literal["LibraryFolder"], ModelClassField(Literal["LibraryFolder"])]
+    id: EncodedLibraryFolderDatabaseIdField
+    parent_id: Optional[EncodedLibraryFolderDatabaseIdField]
+    description: str
+    item_count: int
+    deleted: bool
+    library_path: List[str]
+
+
+class LibraryContentsShowDatasetResponse(LibraryContentsShowResponse):
+    model_class: Annotated[Literal["LibraryDataset"], ModelClassField(Literal["LibraryDataset"])]
+    id: EncodedDatabaseIdField
+    ldda_id: EncodedDatabaseIdField
+    folder_id: EncodedLibraryFolderDatabaseIdField
+    state: str
+    file_name: str
+    created_from_basename: Optional[str]
+    uploaded_by: Optional[str]
+    message: Optional[str]
+    date_uploaded: str
+    file_size: int
+    file_ext: str
+    data_type: str
+    misc_info: Optional[str]
+    misc_blurb: Optional[str]
+    peek: Optional[str]
+    uuid: str
+    tags: TagCollection
+
+    # metadata fields
+    model_config = ConfigDict(extra="allow")
+
+
+class LibraryContentsCreateResponse(Model):
+    name: str
+    url: str
+
+
+class LibraryContentsCreateFolderResponse(LibraryContentsCreateResponse):
+    id: EncodedLibraryFolderDatabaseIdField
+
+
+class LibraryContentsCreateFileResponse(LibraryContentsCreateResponse):
+    id: EncodedDatabaseIdField
+
+
+class LibraryContentsCreateFolderListResponse(RootModel):
+    root: List[LibraryContentsCreateFolderResponse]
+
+
+class LibraryContentsCreateFileListResponse(RootModel):
+    root: List[LibraryContentsCreateFileResponse]
+
+
+class LibraryContentsCreateDatasetResponse(Model):
+    # id, library_dataset_id, parent_library_id should change to EncodedDatabaseIdField latter
+    # because they are encoded ids in _copy_hda_to_library_folder and _copy_hdca_to_library_folder
+    # functions that are shared by LibraryFolderContentsService too
+    id: str
+    hda_ldda: str
+    model_class: Annotated[
+        Literal["LibraryDatasetDatasetAssociation"], ModelClassField(Literal["LibraryDatasetDatasetAssociation"])
+    ]
+    name: str
+    deleted: bool
+    visible: bool
+    state: str
+    library_dataset_id: str
+    file_size: int
+    file_name: str
+    update_time: str
+    file_ext: str
+    data_type: str
+    genome_build: str
+    misc_info: Optional[str]
+    misc_blurb: Optional[str]
+    created_from_basename: Optional[str]
+    uuid: str
+    parent_library_id: str
+
+    # metadata fields
+    model_config = ConfigDict(extra="allow")
+
+
+class LibraryContentsCreateDatasetCollectionResponse(RootModel):
+    root: List[LibraryContentsCreateDatasetResponse]
+
+
+class LibraryContentsDeleteResponse(Model):
+    id: EncodedDatabaseIdField
+    deleted: bool
+
+
+class LibraryContentsPurgedResponse(LibraryContentsDeleteResponse):
+    purged: bool
+
+
+AnyLibraryContentsShowResponse = Union[
+    LibraryContentsShowFolderResponse,
+    LibraryContentsShowDatasetResponse,
+]
+
+AnyLibraryContentsCreatePayload = Union[
+    LibraryContentsFolderCreatePayload, LibraryContentsFileCreatePayload, LibraryContentsCollectionCreatePayload
+]
+
+AnyLibraryContentsCreateResponse = Union[
+    LibraryContentsCreateFolderListResponse,
+    LibraryContentsCreateFileListResponse,
+    LibraryContentsCreateDatasetCollectionResponse,
+    LibraryContentsCreateDatasetResponse,
+]
diff --git a/lib/galaxy/schema/notifications.py b/lib/galaxy/schema/notifications.py
index 941752dc25e7f88e89c403325a5c17b618565bb6..1c8204a2369b62e4ce396fa38dc2c7b0298eeb4e 100644
--- a/lib/galaxy/schema/notifications.py
+++ b/lib/galaxy/schema/notifications.py
@@ -26,6 +26,7 @@ from galaxy.schema.fields import (
 from galaxy.schema.generics import (
     DatabaseIdT,
     GenericModel,
+    PatchGenericPickle,
 )
 from galaxy.schema.schema import Model
 from galaxy.schema.types import (
@@ -118,20 +119,30 @@ class NewSharedItemNotificationContent(Model):
     slug: str = Field(..., title="Slug", description="The slug of the shared item. Used for the link to the item.")
 
 
-AnyNotificationContent = Annotated[
+NotificationContentField = Field(
+    default=...,
+    discriminator="category",
+    title="Content",
+    description="The content of the notification. The structure depends on the category.",
+)
+
+AnyUserNotificationContent = Annotated[
     Union[
         MessageNotificationContent,
         NewSharedItemNotificationContent,
+    ],
+    NotificationContentField,
+]
+
+AnyNotificationContent = Annotated[
+    Union[
+        AnyUserNotificationContent,
         BroadcastNotificationContent,
     ],
-    Field(
-        default=...,
-        discriminator="category",
-        title="Content",
-        description="The content of the notification. The structure depends on the category.",
-    ),
+    NotificationContentField,
 ]
 
+
 NotificationIdField = Field(
     ...,
     title="ID",
@@ -200,6 +211,7 @@ class UserNotificationResponse(NotificationResponse):
     """A notification response specific to the user."""
 
     category: PersonalNotificationCategory = NotificationCategoryField
+    content: AnyUserNotificationContent
     seen_time: Optional[datetime] = Field(
         None,
         title="Seen time",
@@ -264,7 +276,7 @@ class NotificationCreateData(Model):
     )
 
 
-class GenericNotificationRecipients(GenericModel, Generic[DatabaseIdT]):
+class GenericNotificationRecipients(GenericModel, Generic[DatabaseIdT], PatchGenericPickle):
     """The recipients of a notification. Can be a combination of users, groups and roles."""
 
     user_ids: List[DatabaseIdT] = Field(
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 0d1ebed8f83479eb4d6d51ce17ce6dc7f0b1c338..fd294d869086e01d5193d0a4f0adac6552fa2235 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1,5 +1,6 @@
 """This module contains general pydantic models and common schema field annotations for them."""
 
+import base64
 from datetime import (
     date,
     datetime,
@@ -28,6 +29,7 @@ from pydantic import (
     RootModel,
     UUID4,
 )
+from pydantic_core import core_schema
 from typing_extensions import (
     Annotated,
     Literal,
@@ -48,6 +50,7 @@ from galaxy.schema.types import (
     OffsetNaiveDatetime,
     RelativeUrl,
 )
+from galaxy.util.sanitize_html import sanitize_html
 
 USER_MODEL_CLASS = Literal["User"]
 GROUP_MODEL_CLASS = Literal["Group"]
@@ -88,6 +91,7 @@ class DatasetState(str, Enum):
     # be able to have history contents associated (normal HDAs?)
     DEFERRED = "deferred"
     DISCARDED = "discarded"
+    STOPPED = "stopped"
 
     @classmethod
     def values(self):
@@ -362,7 +366,7 @@ class CreatedUserModel(UserModel, DiskUsageUserModel):
 
 
 class AnonUserModel(DiskUsageUserModel):
-    quota_percent: Any = QuotaPercentField
+    quota_percent: Optional[float] = QuotaPercentField
 
 
 class DetailedUserModel(BaseUserModel, AnonUserModel):
@@ -371,10 +375,18 @@ class DetailedUserModel(BaseUserModel, AnonUserModel):
     preferences: Dict[Any, Any] = Field(default=..., title="Preferences", description="Preferences of the user")
     preferred_object_store_id: Optional[str] = PreferredObjectStoreIdField
     quota: str = Field(default=..., title="Quota", description="Quota applicable to the user")
-    quota_bytes: Any = Field(default=..., title="Quota in bytes", description="Quota applicable to the user in bytes.")
+    quota_bytes: Optional[int] = Field(
+        default=None, title="Quota in bytes", description="Quota applicable to the user in bytes."
+    )
     tags_used: List[str] = Field(default=..., title="Tags used", description="Tags used by the user")
 
 
+class UserUpdatePayload(Model):
+    active: Annotated[Optional[bool], Field(None, title="Active", description="User is active")]
+    username: Annotated[Optional[str], Field(None, title="Username", description="The name of the user.")]
+    preferred_object_store_id: Annotated[Optional[str], PreferredObjectStoreIdField]
+
+
 class UserCreationPayload(Model):
     password: str = Field(default=..., title="user_password", description="The password of the user.")
     email: str = UserEmailField
@@ -902,6 +914,9 @@ class HDADetailed(HDASummary, WithModelClass):
             description="The list of sources associated with this dataset.",
         ),
     ]
+    copied_from_history_dataset_association_id: Annotated[
+        Optional[EncodedDatabaseIdField], Field(None, description="ID of HDA this HDA was copied from.")
+    ]
 
 
 class HDAExtended(HDADetailed):
@@ -1104,6 +1119,9 @@ class HDCASummary(HDCACommon, WithModelClass):
     populated_state: DatasetCollectionPopulatedState = PopulatedStateField
     populated_state_message: Optional[str] = PopulatedStateMessageField
     element_count: ElementCountField
+    elements_datatypes: Set[str] = Field(
+        ..., description="A set containing all the different element datatypes in the collection."
+    )
     job_source_id: Optional[EncodedDatabaseIdField] = Field(
         None,
         title="Job Source ID",
@@ -1128,9 +1146,6 @@ class HDCADetailed(HDCASummary):
 
     populated: PopulatedField
     elements: List[DCESummary] = ElementsField
-    elements_datatypes: Set[str] = Field(
-        ..., description="A set containing all the different element datatypes in the collection."
-    )
     implicit_collection_jobs_id: Optional[EncodedDatabaseIdField] = Field(
         None,
         description="Encoded ID for the ICJ object describing the collection of jobs corresponding to this collection",
@@ -1439,6 +1454,18 @@ AnyHistoryView = Annotated[
 ]
 
 
+class UpdateHistoryPayload(Model):
+    name: Optional[str] = None
+    annotation: Optional[str] = None
+    tags: Optional[TagCollection] = None
+    published: Optional[bool] = None
+    importable: Optional[bool] = None
+    deleted: Optional[bool] = None
+    purged: Optional[bool] = None
+    genome_build: Optional[str] = None
+    preferred_object_store_id: Optional[str] = None
+
+
 class ExportHistoryArchivePayload(Model):
     gzip: Optional[bool] = Field(
         default=True,
@@ -1890,12 +1917,24 @@ class ArchivedHistoryDetailed(HistoryDetailed, ExportAssociationData):
     pass
 
 
-AnyArchivedHistoryView = Union[
-    ArchivedHistorySummary,
-    ArchivedHistoryDetailed,
-    # Any will cover those cases in which only specific `keys` are requested
-    # otherwise the validation will fail because the required fields are not returned
-    Any,
+@partial_model()
+class CustomArchivedHistoryView(CustomHistoryView, ExportAssociationData):
+    """Archived History Response with all optional fields.
+
+    It is used for serializing only specific attributes using the "keys"
+    query parameter.
+    """
+
+    pass
+
+
+AnyArchivedHistoryView = Annotated[
+    Union[
+        CustomArchivedHistoryView,
+        ArchivedHistoryDetailed,
+        ArchivedHistorySummary,
+    ],
+    Field(union_mode="left_to_right"),
 ]
 
 
@@ -2133,6 +2172,13 @@ class JobMetric(Model):
     )
 
 
+class WorkflowJobMetric(JobMetric):
+    tool_id: str
+    job_id: str
+    step_index: int
+    step_label: Optional[str]
+
+
 class JobMetricCollection(RootModel):
     """Represents a collection of metrics associated with a Job."""
 
@@ -3080,7 +3126,7 @@ class LibraryAvailablePermissions(Model):
     roles: List[BasicRoleModel] = Field(
         ...,
         title="Roles",
-        description="A list available roles that can be assigned to a particular permission.",
+        description="A list containing available roles that can be assigned to a particular permission.",
     )
     page: int = Field(
         ...,
@@ -3229,30 +3275,65 @@ class DatasetAssociationRoles(Model):
     )
 
 
-class UpdateDatasetPermissionsPayload(Model):
+class UpdateDatasetPermissionsPayloadBase(Model):
     action: Optional[DatasetPermissionAction] = Field(
         DatasetPermissionAction.set_permissions,
         title="Action",
         description="Indicates what action should be performed on the dataset.",
     )
-    access_ids: Optional[RoleIdList] = Field(
-        [],
-        alias="access_ids[]",  # Added for backward compatibility but it looks really ugly...
+
+
+AccessIdsField = Annotated[
+    Optional[RoleIdList],
+    Field(
+        default=None,
         title="Access IDs",
         description="A list of role encoded IDs defining roles that should have access permission on the dataset.",
-    )
-    manage_ids: Optional[RoleIdList] = Field(
-        [],
-        alias="manage_ids[]",
+    ),
+]
+
+ManageIdsField = Annotated[
+    Optional[RoleIdList],
+    Field(
+        default=None,
         title="Manage IDs",
         description="A list of role encoded IDs defining roles that should have manage permission on the dataset.",
-    )
-    modify_ids: Optional[RoleIdList] = Field(
-        [],
-        alias="modify_ids[]",
+    ),
+]
+
+ModifyIdsField = Annotated[
+    Optional[RoleIdList],
+    Field(
+        default=None,
         title="Modify IDs",
         description="A list of role encoded IDs defining roles that should have modify permission on the dataset.",
-    )
+    ),
+]
+
+
+class UpdateDatasetPermissionsPayload(UpdateDatasetPermissionsPayloadBase):
+    access_ids: Annotated[Optional[RoleIdList], Field(default=None, alias="access_ids[]")] = None
+    manage_ids: Annotated[Optional[RoleIdList], Field(default=None, alias="manage_ids[]")] = None
+    modify_ids: Annotated[Optional[RoleIdList], Field(default=None, alias="modify_ids[]")] = None
+
+
+class UpdateDatasetPermissionsPayloadAliasB(UpdateDatasetPermissionsPayloadBase):
+    access: AccessIdsField = None
+    manage: ManageIdsField = None
+    modify: ModifyIdsField = None
+
+
+class UpdateDatasetPermissionsPayloadAliasC(UpdateDatasetPermissionsPayloadBase):
+    access_ids: AccessIdsField = None
+    manage_ids: ManageIdsField = None
+    modify_ids: ModifyIdsField = None
+
+
+UpdateDatasetPermissionsPayloadAliases = Union[
+    UpdateDatasetPermissionsPayload,
+    UpdateDatasetPermissionsPayloadAliasB,
+    UpdateDatasetPermissionsPayloadAliasC,
+]
 
 
 @partial_model()
@@ -3266,7 +3347,7 @@ class HDACustom(HDADetailed):
     # TODO: Fix this workaround for partial_model not supporting UUID fields for some reason.
     # The error otherwise is: `PydanticUserError: 'UuidVersion' cannot annotate 'nullable'.`
     # Also ignoring mypy complaints about the type redefinition.
-    uuid: Optional[UUID4]  # type: ignore
+    uuid: Optional[UUID4]  # type: ignore[assignment]
 
     # Add fields that are not part of any view here
     visualizations: Annotated[
@@ -3283,8 +3364,17 @@ class HDACustom(HDADetailed):
     model_config = ConfigDict(extra="allow")
 
 
+@partial_model()
+class HDCACustom(HDCADetailed):
+    """Can contain any serializable property of an HDCA.
+
+    Allows arbitrary custom keys to be specified in the serialization
+    parameters without a particular view (predefined set of keys).
+    """
+
+
 AnyHDA = Union[HDACustom, HDADetailed, HDASummary, HDAInaccessible]
-AnyHDCA = Union[HDCADetailed, HDCASummary]
+AnyHDCA = Union[HDCACustom, HDCADetailed, HDCASummary]
 AnyHistoryContentItem = Annotated[
     Union[
         AnyHDA,
@@ -3596,7 +3686,7 @@ class PageSummaryBase(Model):
         ...,  # Required
         title="Identifier",
         description="The title slug for the page URL, must be unique.",
-        pattern=r"^[a-z0-9\-]+$",
+        pattern=r"^[^/:?#]+$",
     )
 
 
@@ -3619,6 +3709,19 @@ class MaterializeDatasetInstanceRequest(MaterializeDatasetInstanceAPIRequest):
     history_id: DecodedDatabaseIdField
 
 
+class ChatPayload(Model):
+    query: str = Field(
+        ...,
+        title="Query",
+        description="The query to be sent to the chatbot.",
+    )
+    context: Optional[str] = Field(
+        default="",
+        title="Context",
+        description="The context for the chatbot.",
+    )
+
+
 class CreatePagePayload(PageSummaryBase):
     content_format: PageContentFormat = ContentFormatField
     content: Optional[str] = ContentField
@@ -3656,6 +3759,22 @@ class AsyncTaskResultSummary(Model):
     )
 
 
+ToolRequestIdField = Field(title="ID", description="Encoded ID of the role")
+
+
+class ToolRequestState(str, Enum):
+    NEW = "new"
+    SUBMITTED = "submitted"
+    FAILED = "failed"
+
+
+class ToolRequestModel(Model):
+    id: EncodedDatabaseIdField = ToolRequestIdField
+    request: Dict[str, Any]
+    state: ToolRequestState
+    state_message: Optional[str]
+
+
 class AsyncFile(Model):
     storage_request_id: UUID
     task: AsyncTaskResultSummary
@@ -3720,6 +3839,18 @@ GenerateTimeField = Field(
 )
 
 
+class OAuth2State(BaseModel):
+    route: str
+    nonce: str
+
+    def encode(self) -> str:
+        return base64.b64encode(self.model_dump_json().encode("utf-8")).decode("utf-8")
+
+    @staticmethod
+    def decode(base64_param: str) -> "OAuth2State":
+        return OAuth2State.model_validate_json(base64.b64decode(base64_param.encode("utf-8")))
+
+
 class PageDetails(PageSummary):
     content_format: PageContentFormat = ContentFormatField
     content: Optional[str] = ContentField
@@ -3735,14 +3866,74 @@ class PageSummaryList(RootModel):
     )
 
 
-class DatasetSummary(Model):
-    id: EncodedDatabaseIdField
-    create_time: Optional[datetime] = CreateTimeField
-    update_time: Optional[datetime] = UpdateTimeField
-    state: DatasetStateField
-    deleted: bool
-    purged: bool
-    purgable: bool
-    file_size: int
-    total_size: int
+class LandingRequestState(str, Enum):
+    UNCLAIMED = "unclaimed"
+    CLAIMED = "claimed"
+
+
+ToolLandingRequestIdField = Field(title="ID", description="Encoded ID of the tool landing request")
+WorkflowLandingRequestIdField = Field(title="ID", description="Encoded ID of the workflow landing request")
+
+
+class CreateToolLandingRequestPayload(Model):
+    tool_id: str
+    tool_version: Optional[str] = None
+    request_state: Optional[Dict[str, Any]] = None
+    client_secret: Optional[str] = None
+    public: bool = False
+
+
+class CreateWorkflowLandingRequestPayload(Model):
+    workflow_id: str
+    workflow_target_type: Literal["stored_workflow", "workflow", "trs_url"]
+    request_state: Optional[Dict[str, Any]] = None
+    client_secret: Optional[str] = None
+    public: bool = Field(
+        False,
+        description="If workflow landing request is public anyone with the uuid can use the landing request. If not public the request must be claimed before use and additional verification might occur.",
+    )
+
+
+class ClaimLandingPayload(Model):
+    client_secret: Optional[str] = None
+
+
+class ToolLandingRequest(Model):
+    uuid: UuidField
+    tool_id: str
+    tool_version: Optional[str] = None
+    request_state: Optional[Dict[str, Any]] = None
+    state: LandingRequestState
+
+
+class WorkflowLandingRequest(Model):
     uuid: UuidField
+    workflow_id: str
+    workflow_target_type: Literal["stored_workflow", "workflow", "trs_url"]
+    request_state: Dict[str, Any]
+    state: LandingRequestState
+
+
+class MessageExceptionModel(BaseModel):
+    err_msg: str
+    err_code: int
+
+
+class SanitizedString(str):
+    @classmethod
+    def __get_validators__(cls):
+        yield cls.validate
+
+    @classmethod
+    def validate(cls, value):
+        if isinstance(value, str):
+            return cls(sanitize_html(value))
+        raise TypeError("string required")
+
+    @classmethod
+    def __get_pydantic_core_schema__(cls, source_type, handler):
+        return core_schema.no_info_after_validator_function(
+            cls.validate,
+            core_schema.str_schema(),
+            serialization=core_schema.to_string_ser_schema(),
+        )
diff --git a/lib/galaxy/schema/tasks.py b/lib/galaxy/schema/tasks.py
index 022d82666aedd04fa422287d3337892593912667..313ec9f1dad06dca181a21e253d058e4598bfef2 100644
--- a/lib/galaxy/schema/tasks.py
+++ b/lib/galaxy/schema/tasks.py
@@ -104,8 +104,8 @@ class MaterializeDatasetInstanceTaskRequest(Model):
         title="Content",
         description=(
             "Depending on the `source` it can be:\n"
-            "- The encoded id of the source library dataset\n"
-            "- The encoded id of the HDA\n"
+            "- The decoded id of the source library dataset\n"
+            "- The decoded id of the HDA\n"
         ),
     )
 
diff --git a/lib/galaxy/schema/visualization.py b/lib/galaxy/schema/visualization.py
index 0488bf249c9e30a7823862df5a2ac80e82a47f0b..45a693b21f8eccc1a429d55de137fe5ff0aa8808 100644
--- a/lib/galaxy/schema/visualization.py
+++ b/lib/galaxy/schema/visualization.py
@@ -1,7 +1,9 @@
 from datetime import datetime
 from typing import (
+    Dict,
     List,
     Optional,
+    Union,
 )
 
 from pydantic import (
@@ -14,16 +16,22 @@ from typing_extensions import Literal
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
     EncodedDatabaseIdField,
+    ModelClassField,
 )
 from galaxy.schema.schema import (
     CreateTimeField,
     Model,
+    SanitizedString,
     TagCollection,
     UpdateTimeField,
+    WithModelClass,
 )
 
 VisualizationSortByEnum = Literal["create_time", "title", "update_time", "username"]
 
+VISUALIZATION_MODEL_CLASS = Literal["Visualization"]
+VISUALIZATION_REVISION_MODEL_CLASS = Literal["VisualizationRevision"]
+
 
 class VisualizationIndexQueryPayload(Model):
     deleted: bool = False
@@ -100,3 +108,247 @@ class VisualizationSummaryList(RootModel):
         default=[],
         title="List with detailed information of Visualizations.",
     )
+
+
+class VisualizationRevisionResponse(Model, WithModelClass):
+    model_class: VISUALIZATION_REVISION_MODEL_CLASS = ModelClassField(VISUALIZATION_REVISION_MODEL_CLASS)
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization Revision.",
+    )
+    visualization_id: EncodedDatabaseIdField = Field(
+        ...,
+        title="Visualization ID",
+        description="Encoded ID of the Visualization.",
+    )
+    title: str = Field(
+        ...,
+        title="Title",
+        description="The name of the visualization revision.",
+    )
+    dbkey: Optional[str] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    config: Dict = Field(
+        ...,
+        title="Config",
+        description="The config of the visualization revision.",
+    )
+
+
+class VisualizationPluginResponse(Model):
+    name: str = Field(
+        ...,
+        title="Name",
+        description="The name of the plugin.",
+    )
+    html: str = Field(
+        ...,
+        title="HTML",
+        description="The HTML of the plugin.",
+    )
+    description: str = Field(
+        ...,
+        title="Description",
+        description="The description of the plugin.",
+    )
+    logo: Optional[str] = Field(
+        None,
+        title="Logo",
+        description="The logo of the plugin.",
+    )
+    title: Optional[str] = Field(
+        None,
+        title="Title",
+        description="The title of the plugin.",
+    )
+    target: str = Field(
+        ...,
+        title="Target",
+        description="The target of the plugin.",
+    )
+    embeddable: bool = Field(
+        ...,
+        title="Embeddable",
+        description="Whether the plugin is embeddable.",
+    )
+    entry_point: Dict = Field(
+        ...,
+        title="Entry Point",
+        description="The entry point of the plugin.",
+    )
+    settings: List[Dict] = Field(
+        ...,
+        title="Settings",
+        description="The settings of the plugin.",
+    )
+    groups: Optional[List[Dict]] = Field(
+        None,
+        title="Groups",
+        description="The groups of the plugin.",
+    )
+    specs: Optional[Dict] = Field(
+        None,
+        title="Specs",
+        description="The specs of the plugin.",
+    )
+    href: str = Field(
+        ...,
+        title="Href",
+        description="The href of the plugin.",
+    )
+
+
+class VisualizationShowResponse(Model, WithModelClass):
+    model_class: VISUALIZATION_MODEL_CLASS = ModelClassField(VISUALIZATION_MODEL_CLASS)
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+    title: str = Field(
+        ...,
+        title="Title",
+        description="The name of the visualization.",
+    )
+    type: str = Field(
+        ...,
+        title="Type",
+        description="The type of the visualization.",
+    )
+    user_id: EncodedDatabaseIdField = Field(
+        ...,
+        title="User ID",
+        description="The ID of the user owning this Visualization.",
+    )
+    dbkey: Optional[str] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    slug: Optional[str] = Field(
+        None,
+        title="Slug",
+        description="The slug of the visualization.",
+    )
+    latest_revision: VisualizationRevisionResponse = Field(
+        ...,
+        title="Latest Revision",
+        description="The latest revision of this Visualization.",
+    )
+    revisions: List[EncodedDatabaseIdField] = Field(
+        ...,
+        title="Revisions",
+        description="A list of encoded IDs of the revisions of this Visualization.",
+    )
+    url: str = Field(
+        ...,
+        title="URL",
+        description="The URL of the visualization.",
+    )
+    username: str = Field(
+        ...,
+        title="Username",
+        description="The name of the user owning this Visualization.",
+    )
+    email_hash: str = Field(
+        ...,
+        title="Email Hash",
+        description="The hash of the email of the user owning this Visualization.",
+    )
+    tags: Optional[TagCollection] = Field(
+        None,
+        title="Tags",
+        description="A list of tags to add to this item.",
+    )
+    annotation: Optional[str] = Field(
+        None,
+        title="Annotation",
+        description="The annotation of this Visualization.",
+    )
+    plugin: Optional[VisualizationPluginResponse] = Field(
+        None,
+        title="Plugin",
+        description="The plugin of this Visualization.",
+    )
+
+
+class VisualizationCreateResponse(Model):
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+
+
+class VisualizationUpdateResponse(Model):
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+    revision: EncodedDatabaseIdField = Field(
+        ...,
+        title="Revision",
+        description="Encoded ID of the Visualization Revision.",
+    )
+
+
+class VisualizationCreatePayload(Model):
+    type: str = Field(
+        ...,
+        title="Type",
+        description="The type of the visualization.",
+    )
+    title: Optional[SanitizedString] = Field(
+        SanitizedString("Untitled Visualization"),
+        title="Title",
+        description="The name of the visualization.",
+        min_length=3,
+    )
+    dbkey: Optional[SanitizedString] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    slug: Optional[SanitizedString] = Field(
+        None,
+        title="Slug",
+        description="The slug of the visualization.",
+    )
+    annotation: Optional[SanitizedString] = Field(
+        None,
+        title="Annotation",
+        description="The annotation of the visualization.",
+    )
+    config: Optional[dict] = Field(
+        {},
+        title="Config",
+        description="The config of the visualization.",
+    )
+
+
+class VisualizationUpdatePayload(Model):
+    title: Optional[SanitizedString] = Field(
+        None,
+        title="Title",
+        description="The name of the visualization.",
+    )
+    dbkey: Optional[SanitizedString] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    deleted: Optional[bool] = Field(
+        False,
+        title="Deleted",
+        description="Whether this Visualization has been deleted.",
+    )
+    config: Optional[Union[dict, bytes]] = Field(
+        {},
+        title="Config",
+        description="The config of the visualization.",
+    )
diff --git a/lib/galaxy/schema/workflows.py b/lib/galaxy/schema/workflows.py
index f679fd47818d1d243674d20c8cd138ee12ca43f4..960e2dc3e978da6e5667c45e7f14c66cff950359 100644
--- a/lib/galaxy/schema/workflows.py
+++ b/lib/galaxy/schema/workflows.py
@@ -1,6 +1,7 @@
 import json
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
@@ -8,9 +9,11 @@ from typing import (
 )
 
 from pydantic import (
+    AfterValidator,
     Field,
     field_validator,
 )
+from typing_extensions import Annotated
 
 from galaxy.schema.schema import (
     AnnotationField,
@@ -21,13 +24,73 @@ from galaxy.schema.schema import (
     Organization,
     PauseStep,
     Person,
-    PreferredObjectStoreIdField,
     StoredWorkflowSummary,
     SubworkflowStep,
     ToolStep,
     WorkflowInput,
 )
 
+TargetHistoryIdField = Field(
+    None,
+    title="History ID",
+    # description="The history to import the workflow into.",
+    description="The encoded history id into which to import.",
+)
+INPUTS_BY_DESCRIPTION = (
+    "How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps."
+)
+STEP_PARAMETERS_NORMALIZED_TITLE = "Legacy Step Parameters Normalized"
+STEP_PARAMETERS_NORMALIZED_DESCRIPTION = "Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID."
+STEP_PARAMETERS_TITLE = "Legacy Step Parameters"
+STEP_PARAMETERS_DESCRIPTION = "Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead."
+ReplacementParametersField = Field(
+    {},
+    title="Replacement Parameters",
+    description="Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters",
+)
+UseCachedJobField = Field(
+    False,
+    title="Use cached job",
+    description="Indicated whether to use a cached job for workflow invocation.",
+)
+PreferredObjectStoreIdField = Field(
+    default=None,
+    title="Preferred Object Store ID",
+    description="The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences",
+)
+PreferredIntermediateObjectStoreIdField = Field(
+    None,
+    title="Preferred Intermediate Object Store ID",
+    description="The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences",
+)
+PreferredOutputsObjectStoreIdField = Field(
+    None,
+    title="Preferred Outputs Object Store ID",
+    description="The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.",
+)
+ResourceParametersField = Field(
+    {},
+    title="Resource Parameters",
+    description="If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.",
+)
+
+VALID_INPUTS_BY_ITEMS = ["step_id", "step_index", "step_uuid", "name"]
+
+
+def validateInputsBy(inputsBy: Optional[str]) -> Optional[str]:
+    if inputsBy is not None:
+        if not isinstance(inputsBy, str):
+            raise ValueError(f"Invalid type for inputsBy {inputsBy}")
+        inputsByStr = cast(str, inputsBy)
+        inputsByArray: List[str] = inputsByStr.split("|")
+        for inputsByItem in inputsByArray:
+            if inputsByItem not in VALID_INPUTS_BY_ITEMS:
+                raise ValueError(f"Invalid inputsBy delineation {inputsByItem}")
+    return inputsBy
+
+
+InputsByValidator = AfterValidator(validateInputsBy)
+
 
 class GetTargetHistoryPayload(Model):
     # TODO - Are the descriptions correct?
@@ -37,12 +100,7 @@ class GetTargetHistoryPayload(Model):
         # description="The encoded history id - passed exactly like this 'hist_id=...' -  to import the workflow into. Or the name of the new history to import the workflow into.",
         description="The encoded history id - passed exactly like this 'hist_id=...' -  into which to import. Or the name of the new history into which to import.",
     )
-    history_id: Optional[str] = Field(
-        None,
-        title="History ID",
-        # description="The history to import the workflow into.",
-        description="The encoded history id into which to import.",
-    )
+    history_id: Optional[str] = TargetHistoryIdField
     new_history_name: Optional[str] = Field(
         None,
         title="New History Name",
@@ -84,15 +142,11 @@ class InvokeWorkflowPayload(GetTargetHistoryPayload):
         title="Allow tool state corrections",
         description="Indicates if tool state corrections are allowed for workflow invocation.",
     )
-    use_cached_job: Optional[bool] = Field(
-        False,
-        title="Use cached job",
-        description="Indicated whether to use a cached job for workflow invocation.",
-    )
+    use_cached_job: Optional[bool] = UseCachedJobField
     parameters_normalized: Optional[bool] = Field(
         False,
-        title="Parameters Normalized",
-        description="Indicates if parameters are already normalized for workflow invocation.",
+        title=STEP_PARAMETERS_NORMALIZED_TITLE,
+        description=STEP_PARAMETERS_NORMALIZED_DESCRIPTION,
     )
 
     @field_validator(
@@ -101,7 +155,6 @@ class InvokeWorkflowPayload(GetTargetHistoryPayload):
         "ds_map",
         "resource_params",
         "replacement_params",
-        "step_parameters",
         mode="before",
         check_fields=False,
     )
@@ -113,34 +166,22 @@ class InvokeWorkflowPayload(GetTargetHistoryPayload):
 
     parameters: Optional[Dict[str, Any]] = Field(
         {},
-        title="Parameters",
-        description="The raw parameters for the workflow invocation.",
+        title=STEP_PARAMETERS_TITLE,
+        description=STEP_PARAMETERS_DESCRIPTION,
     )
     inputs: Optional[Dict[str, Any]] = Field(
         None,
         title="Inputs",
-        description="TODO",
+        description="Specify values for formal inputs to the workflow",
     )
     ds_map: Optional[Dict[str, Dict[str, Any]]] = Field(
         {},
-        title="Dataset Map",
-        description="TODO",
-    )
-    resource_params: Optional[Dict[str, Any]] = Field(
-        {},
-        title="Resource Parameters",
-        description="TODO",
-    )
-    replacement_params: Optional[Dict[str, Any]] = Field(
-        {},
-        title="Replacement Parameters",
-        description="TODO",
-    )
-    step_parameters: Optional[Dict[str, Any]] = Field(
-        None,
-        title="Step Parameters",
-        description="TODO",
+        title="Legacy Dataset Map",
+        description="An older alternative to specifying inputs using database IDs, do not use this and use inputs instead",
+        deprecated=True,
     )
+    resource_params: Optional[Dict[str, Any]] = ResourceParametersField
+    replacement_params: Optional[Dict[str, Any]] = ReplacementParametersField
     no_add_to_history: Optional[bool] = Field(
         False,
         title="No Add to History",
@@ -151,11 +192,11 @@ class InvokeWorkflowPayload(GetTargetHistoryPayload):
         title="Legacy",
         description="Indicating if to use legacy workflow invocation.",
     )
-    inputs_by: Optional[str] = Field(
+    inputs_by: Annotated[Optional[str], InputsByValidator] = Field(
         None,
         title="Inputs By",
         # lib/galaxy/workflow/run_request.py - see line 60
-        description="How inputs maps to inputs (datasets/collections) to workflows steps.",
+        description=INPUTS_BY_DESCRIPTION,
     )
     effective_outputs: Optional[Any] = Field(
         None,
@@ -163,17 +204,9 @@ class InvokeWorkflowPayload(GetTargetHistoryPayload):
         # lib/galaxy/workflow/run_request.py - see line 455
         description="TODO",
     )
-    preferred_intermediate_object_store_id: Optional[str] = Field(
-        None,
-        title="Preferred Intermediate Object Store ID",
-        description="The ID of the ? object store that should be used to store ? datasets in this history.",
-    )
-    preferred_outputs_object_store_id: Optional[str] = Field(
-        None,
-        title="Preferred Outputs Object Store ID",
-        description="The ID of the object store that should be used to store ? datasets in this history.",
-    )
     preferred_object_store_id: Optional[str] = PreferredObjectStoreIdField
+    preferred_intermediate_object_store_id: Optional[str] = PreferredIntermediateObjectStoreIdField
+    preferred_outputs_object_store_id: Optional[str] = PreferredOutputsObjectStoreIdField
 
 
 class StoredWorkflowDetailed(StoredWorkflowSummary):
@@ -194,19 +227,21 @@ class StoredWorkflowDetailed(StoredWorkflowSummary):
     )
     steps: Dict[
         int,
-        Union[
-            InputDataStep,
-            InputDataCollectionStep,
-            InputParameterStep,
-            PauseStep,
-            ToolStep,
-            SubworkflowStep,
+        Annotated[
+            Union[
+                InputDataStep,
+                InputDataCollectionStep,
+                InputParameterStep,
+                PauseStep,
+                ToolStep,
+                SubworkflowStep,
+            ],
+            Field(discriminator="type"),
         ],
     ] = Field(
         {},
         title="Steps",
         description="A dictionary with information about all the steps of the workflow.",
-        discriminator="type",
     )
     importable: Optional[bool] = Field(
         ...,
diff --git a/lib/galaxy/security/__init__.py b/lib/galaxy/security/__init__.py
index 0c1082830259e1de4805f00b12f96502604bc157..94e8948042b43347a2251a57a0569af3342c9fad 100644
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -95,9 +95,6 @@ class RBACAgent:
     def can_manage_library_item(self, roles, item):
         raise Exception("Unimplemented Method")
 
-    def associate_components(self, **kwd):
-        raise Exception(f"No valid method of associating provided components: {kwd}")
-
     def create_private_user_role(self, user):
         raise Exception("Unimplemented Method")
 
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index 9e6ed7d4afc3a808e3b6d27f21f0444d03cb3615..a984a21017475545b46fb61acd80f42865c78e2e 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -43,6 +43,11 @@ FILL_CHAR = "-"
 PASSWORD_MIN_LEN = 6
 
 
+def is_valid_email_str(email):
+    """Validates a string containing an email address and returns a boolean result."""
+    return validate_email_str(email) == ""
+
+
 def validate_email_str(email):
     """Validates a string containing an email address."""
     if not email:
diff --git a/lib/galaxy/selenium/cli.py b/lib/galaxy/selenium/cli.py
index f52f3b3a73321af7cbcc9f5dd2f18491f3271f08..109343ea5961582223ac138aee8bcb995ff2f998 100644
--- a/lib/galaxy/selenium/cli.py
+++ b/lib/galaxy/selenium/cli.py
@@ -73,7 +73,7 @@ class DriverWrapper(NavigatesGalaxy):
         self.driver = driver
         self.target_url = args.galaxy_url
 
-    def build_url(self, url=""):
+    def build_url(self, url="", for_selenium: bool = True):
         return urljoin(self.target_url, url)
 
     def screenshot(self, label: str) -> None:
diff --git a/lib/galaxy/selenium/has_driver.py b/lib/galaxy/selenium/has_driver.py
index 9fae270ca7b8f0ffcd0eefdd8026cc377755aba0..d0ab5ed98ca303a590e0e0b17b418aab3d71f102 100644
--- a/lib/galaxy/selenium/has_driver.py
+++ b/lib/galaxy/selenium/has_driver.py
@@ -116,6 +116,9 @@ class HasDriver:
     def element_absent(self, selector_template: Target) -> bool:
         return len(self.find_elements(selector_template)) == 0
 
+    def switch_to_frame(self, name: str = "frame"):
+        return self._wait_on(ec.frame_to_be_available_and_switch_to_it((By.NAME, name)))
+
     def wait_for_xpath(self, xpath: str, **kwds) -> WebElement:
         element = self._wait_on(
             ec.presence_of_element_located((By.XPATH, xpath)), f"XPATH selector [{xpath}] to become present", **kwds
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index cfb53b38bf7cef470578f2615ed352266dde5849..26785d1fd8ae5d5b98c9c29d69493441742b2522 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -299,6 +299,13 @@ class NavigatesGalaxy(HasDriver):
         except SeleniumTimeoutException as e:
             raise ClientBuildException(e)
 
+    def go_to_workflow_landing(self, uuid: str, public: Literal["false", "true"], client_secret: Optional[str]):
+        path = f"workflow_landings/{uuid}?public={public}"
+        if client_secret:
+            path = f"{path}&client_secret={client_secret}"
+        self.driver.get(self.build_url(path))
+        self.components.workflow_run.run_workflow.wait_for_visible()
+
     def go_to_trs_search(self) -> None:
         self.driver.get(self.build_url("workflows/trs_search"))
         self.components.masthead._.wait_for_visible()
@@ -785,31 +792,6 @@ class NavigatesGalaxy(HasDriver):
         elif assert_valid:
             self.wait_for_logged_in()
 
-            # Code below previously was needed because there was a bug that would prevent the masthead from changing,
-            # the bug seems maybe to be fixed though - so we could consider eliminating these extra checks to speed
-            # up tests.
-            self.home()
-            self.wait_for_logged_in()
-            self.click_masthead_user()
-            # Make sure the user menu was dropped down
-            user_menu = self.components.masthead.user_menu.wait_for_visible()
-            try:
-                username_element = self.components.masthead.username.wait_for_visible()
-            except SeleniumTimeoutException as e:
-                menu_items = user_menu.find_elements(By.CSS_SELECTOR, "li a")
-                menu_text = [mi.text for mi in menu_items]
-                message = f"Failed to find logged in message in menu items {', '.join(menu_text)}"
-                raise self.prepend_timeout_message(e, message)
-
-            text = username_element.text
-            assert username in text
-            user_object = self.get_logged_in_user()
-            assert user_object and "email" in user_object
-            assert user_object["email"] == email
-
-            # clicking away no longer closes menu post Masthead -> VueJS
-            self.click_masthead_user()
-
     def wait_for_logged_in(self):
         try:
             self.components.masthead.logged_in_only.wait_for_visible()
@@ -894,7 +876,7 @@ class NavigatesGalaxy(HasDriver):
 
         self.upload_start()
 
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
     def perform_upload_of_composite_dataset_pasted_data(self, ext, paste_content):
         self.home()
@@ -932,8 +914,7 @@ class NavigatesGalaxy(HasDriver):
         if not hide_source_items:
             self.collection_builder_hide_originals()
 
-        self.collection_builder_clear_filters()
-        # TODO: generalize and loop these clicks so we don't need the assert
+        self.ensure_collection_builder_filters_cleared()
         assert len(test_paths) == 2
         self.collection_builder_click_paired_item("forward", 0)
         self.collection_builder_click_paired_item("reverse", 1)
@@ -1221,17 +1202,30 @@ class NavigatesGalaxy(HasDriver):
         text_area_elem.clear()
         text_area_elem.send_keys(json)
 
-    def workflow_editor_set_license(self, license: str) -> None:
+    def workflow_editor_add_input(self, item_name="data_input"):
         editor = self.components.workflow_editor
-        editor.edit_license_link.wait_for_and_click()
-        select = editor.license_select.wait_for_select()
-        select.select_by_value(license)
-        editor.license_save.wait_for_and_click()
+
+        # Make sure we're on the workflow editor and not clicking the main tool panel.
+        editor.canvas_body.wait_for_visible()
+
+        if editor.inputs.activity_panel.is_absent:
+            editor.inputs.activity_button.wait_for_and_click()
+
+        editor.inputs.input(id=item_name).wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+    def workflow_editor_set_license(self, license: str) -> None:
+        license_selector = self.components.workflow_editor.license_selector
+        license_selector.wait_for_and_click()
+        license_selector.wait_for_and_send_keys(license)
+
+        license_selector_option = self.components.workflow_editor.license_selector_option
+        license_selector_option.wait_for_and_click()
 
     def workflow_editor_click_option(self, option_label):
         self.workflow_editor_click_options()
         menu_element = self.workflow_editor_options_menu_element()
-        option_elements = menu_element.find_elements(By.CSS_SELECTOR, "a")
+        option_elements = menu_element.find_elements(By.CSS_SELECTOR, "button")
         assert len(option_elements) > 0, "Failed to find workflow editor options"
         self.sleep_for(WAIT_TYPES.UX_RENDER)
         found_option = False
@@ -1248,10 +1242,10 @@ class NavigatesGalaxy(HasDriver):
             raise Exception(f"Failed to find workflow editor option with label [{option_label}]")
 
     def workflow_editor_click_options(self):
-        return self.wait_for_and_click_selector("#workflow-options-button")
+        return self.wait_for_and_click_selector("#activity-settings")
 
     def workflow_editor_options_menu_element(self):
-        return self.wait_for_selector_visible("#workflow-options-button")
+        return self.wait_for_selector_visible(".activity-settings")
 
     def workflow_editor_click_run(self):
         return self.wait_for_and_click_selector("#workflow-run-button")
@@ -1260,49 +1254,70 @@ class NavigatesGalaxy(HasDriver):
         self.wait_for_and_click_selector("#workflow-save-button")
         self.sleep_for(self.wait_types.DATABASE_OPERATION)
 
+    def workflow_editor_search_for_workflow(self, name: str):
+        self.wait_for_and_click(self.components.workflow_editor.workflow_activity)
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        input = self.wait_for_selector(".activity-panel input")
+        input.send_keys(name)
+
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+    def workflow_editor_add_steps(self, name: str):
+        self.workflow_editor_search_for_workflow(name)
+
+        insert_button = self.components.workflows.workflow_card_button(name=name, title="Copy steps into workflow")
+        insert_button.wait_for_and_click()
+
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+    def workflow_editor_add_subworkflow(self, name: str):
+        self.workflow_editor_search_for_workflow(name)
+
+        insert_button = self.components.workflows.workflow_card_button(name=name, title="Insert as sub-workflow")
+        insert_button.wait_for_and_click()
+
+        self.components.workflow_editor.node._(label=name).wait_for_present()
+
+        self.sleep_for(self.wait_types.UX_RENDER)
+
     def navigate_to_histories_page(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.histories.wait_for_and_click()
+        self.components.histories.activity.wait_for_and_click()
         self.components.histories.histories.wait_for_present()
 
     def navigate_to_histories_shared_with_me_page(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.histories.wait_for_and_click()
+        self.components.histories.activity.wait_for_and_click()
         self.components.shared_histories.tab.wait_for_and_click()
 
     def navigate_to_user_preferences(self):
         self.home()
-        self.click_masthead_user()
+        self.components.masthead.user.wait_for_and_click()
         self.components.masthead.preferences.wait_for_and_click()
 
-    def navigate_to_invocations(self):
+    def navigate_to_invocations_grid(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.invocations.wait_for_and_click()
+        self.components.invocations.activity.wait_for_and_click()
+        self.components.invocations.activity_expand.wait_for_and_click()
 
     def navigate_to_pages(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.pages.wait_for_and_click()
+        self.components.pages.activity.wait_for_and_click()
 
     def navigate_to_published_workflows(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.workflows.wait_for_and_click()
+        self.components.workflows.activity.wait_for_and_click()
         self.components.workflows.published_tab.wait_for_and_click()
 
     def navigate_to_published_histories(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.histories.wait_for_and_click()
+        self.components.histories.activity.wait_for_and_click()
         self.components.published_histories.tab.wait_for_and_click()
 
-    def navigate_to_published_pages(self):
+    def navigate_to_tools(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.pages.wait_for_and_click()
+        self.components.tools.activity.wait_for_and_click()
 
     def admin_open(self):
         self.components.admin.activity.wait_for_and_click()
@@ -1354,8 +1369,7 @@ class NavigatesGalaxy(HasDriver):
 
     def libraries_open(self):
         self.home()
-        self.click_masthead_data()
-        self.components.masthead.libraries.wait_for_and_click()
+        self.components.libraries.activity.wait_for_and_click()
         self.components.libraries.selector.wait_for_visible()
 
     def libraries_open_with_name(self, name):
@@ -1427,25 +1441,36 @@ class NavigatesGalaxy(HasDriver):
         self.libraries_click_dataset_import()
         self.wait_for_and_click(btn)
 
+    def libraries_dataset_import_from_history_search_for(self, search_term=None):
+        return self._inline_search_for(
+            self.navigation.libraries.folder.selectors.import_datasets_from_history_modal_history_search,
+            search_term,
+        )
+
     def libraries_dataset_import_from_history_select(self, to_select_items):
-        self.wait_for_visible(self.navigation.libraries.folder.selectors.import_history_content)
-        history_elements = self.find_elements(self.navigation.libraries.folder.selectors.import_history_contents_items)
+        self.wait_for_visible(
+            self.navigation.libraries.folder.selectors.import_datasets_from_history_modal_list_is_ready
+        )
         for to_select_item in to_select_items:
             found = False
-            for history_element in history_elements:
-                if to_select_item in history_element.text:
-                    history_element.find_element(By.CSS_SELECTOR, "input").click()
-                    found = True
-                    break
-
-            if not found:
-                raise Exception(f"Failed to find history item [{to_select_item}] to select")
+            self._inline_search_for(
+                self.navigation.libraries.folder.selectors.import_datasets_from_history_modal_dataset_search,
+                to_select_item,
+            )
+            self.components.libraries.folder.import_datasets_from_history_modal_select_list_item_by_index(
+                row_index=1
+            ).wait_for_and_click()
+            found = True
+        if not found:
+            raise Exception(f"Failed to find history item [{to_select_item}] to select")
 
     def libraries_dataset_import_from_history_click_ok(self, wait=True):
-        self.wait_for_and_click(self.navigation.libraries.folder.selectors.import_datasets_ok_button)
+        self.wait_for_and_click(self.navigation.libraries.folder.selectors.import_datasets_from_history_modal_ok)
         if wait:
             # Let the progress bar disappear...
-            self.wait_for_absent_or_hidden(self.navigation.libraries.folder.selectors.import_progress_bar)
+            self.wait_for_absent_or_hidden(
+                self.navigation.libraries.folder.selectors.import_datasets_from_history_modal
+            )
 
     def libraries_table_elements(self):
         tbody_element = self.wait_for_selector_visible("#folder_list_body > tbody")
@@ -1478,7 +1503,7 @@ class NavigatesGalaxy(HasDriver):
 
     def workflow_index_open(self):
         self.home()
-        self.click_masthead_workflow()
+        self.click_activity_workflow()
 
     def workflow_shared_with_me_open(self):
         self.workflow_index_open()
@@ -1631,7 +1656,9 @@ class NavigatesGalaxy(HasDriver):
             workflow_run.expand_form_link.wait_for_and_click()
             workflow_run.expanded_form.wait_for_visible()
 
-    def workflow_create_new(self, annotation=None, clear_placeholder=False, save_workflow=True):
+    def workflow_create_new(
+        self, annotation: Optional[str] = None, clear_placeholder: bool = False, save_workflow: bool = True
+    ):
         self.workflow_index_open()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.click_button_new_workflow()
@@ -1656,7 +1683,26 @@ class NavigatesGalaxy(HasDriver):
         invocations.invocations_table.wait_for_visible()
         return invocations.invocations_table_rows.all()
 
+    def open_toolbox(self):
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        if self.element_absent(self.components.tools.tools_activity_workflow_editor):
+            if self.element_absent(self.components._.toolbox_panel):
+                self.components.tools.activity.wait_for_and_click()
+        else:
+            if self.element_absent(self.components._.toolbox_panel):
+                self.components.tools.tools_activity_workflow_editor.wait_for_and_click()
+
+        self.sleep_for(self.wait_types.UX_RENDER)
+
     def tool_open(self, tool_id, outer=False):
+        self.open_toolbox()
+
+        self.components.tools.clear_search.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        self.components.tools.search.wait_for_and_send_keys(f"id:{tool_id}")
+
         if outer:
             tool_link = self.components.tool_panel.outer_tool_link(tool_id=tool_id)
         else:
@@ -1738,14 +1784,8 @@ class NavigatesGalaxy(HasDriver):
     def tool_form_execute(self):
         self.components.tool_form.execute.wait_for_and_click()
 
-    def click_masthead_user(self):
-        self.components.masthead.user.wait_for_and_click()
-
-    def click_masthead_data(self):
-        self.components.masthead.data.wait_for_and_click()
-
-    def click_masthead_workflow(self):
-        self.components.masthead.workflow.wait_for_and_click()
+    def click_activity_workflow(self):
+        self.components.workflows.activity.wait_for_and_click()
 
     def click_button_new_workflow(self):
         self.wait_for_and_click(self.navigation.workflows.selectors.new_button)
@@ -2006,13 +2046,20 @@ class NavigatesGalaxy(HasDriver):
         target_element.send_keys(text)
 
     def collection_builder_hide_originals(self):
-        self.wait_for_and_click_selector("input.hide-originals")
+        self.wait_for_and_click_selector('[data-description="hide original elements"]')
 
     def collection_builder_create(self):
         self.wait_for_and_click_selector("button.create-collection")
 
+    def ensure_collection_builder_filters_cleared(self):
+        clear_filters = self.components.collection_builders.clear_filters
+        element = clear_filters.wait_for_present()
+        if "disabled" not in element.get_attribute("class").split(" "):
+            self.collection_builder_clear_filters()
+
     def collection_builder_clear_filters(self):
-        self.wait_for_and_click_selector("a.clear-filters-link")
+        clear_filters = self.components.collection_builders.clear_filters
+        clear_filters.wait_for_and_click()
 
     def collection_builder_click_paired_item(self, forward_or_reverse, item):
         assert forward_or_reverse in ["forward", "reverse"]
@@ -2027,7 +2074,7 @@ class NavigatesGalaxy(HasDriver):
 
     def logout(self):
         self.components.masthead.logged_in_only.wait_for_visible()
-        self.click_masthead_user()
+        self.components.masthead.user.wait_for_and_click()
         self.components.masthead.logout.wait_for_and_click()
         try:
             self.components.masthead.logged_out_only.wait_for_visible()
@@ -2083,10 +2130,26 @@ class NavigatesGalaxy(HasDriver):
         )
         return element
 
+    def _clear_tooltip(self, tooltip_component):
+        last_timeout: Optional[SeleniumTimeoutException] = None
+        for _ in range(2):
+            if not tooltip_component.is_absent:
+                move_away_chain = self.action_chains()
+                move_away_chain.move_by_offset(100, 100)
+                move_away_chain.perform()
+            try:
+                tooltip_component.wait_for_absent()
+                return
+            except SeleniumTimeoutException as e:
+                last_timeout = e
+
+        assert last_timeout
+        message = "Failed to force current tool tip off screen, cannot test next tooltip."
+        raise self.prepend_timeout_message(last_timeout, message)
+
     def get_tooltip_text(self, element, sleep=0, click_away=True):
         tooltip_balloon = self.components._.tooltip_balloon
-        tooltip_balloon.wait_for_absent()
-
+        self._clear_tooltip(tooltip_balloon)
         action_chains = self.action_chains()
         action_chains.move_to_element(element)
         action_chains.perform()
diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index 7ab7bcba397796a4e58e64dc69b3213e0ca6ef36..1d1986dee1a8ff0fce8cd6562b9e6a4c3ec23c88 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -46,7 +46,10 @@ if TYPE_CHECKING:
     from galaxy.managers.collections import DatasetCollectionManager
     from galaxy.managers.hdas import HDAManager
     from galaxy.managers.histories import HistoryManager
-    from galaxy.managers.workflows import WorkflowsManager
+    from galaxy.managers.workflows import (
+        WorkflowContentsManager,
+        WorkflowsManager,
+    )
     from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
     from galaxy.tools import ToolBox
     from galaxy.tools.cache import ToolCache
@@ -110,7 +113,7 @@ class MinimalManagerApp(MinimalApp):
     history_manager: "HistoryManager"
     hda_manager: "HDAManager"
     workflow_manager: "WorkflowsManager"
-    workflow_contents_manager: Any  # 'galaxy.managers.workflows.WorkflowContentsManager'
+    workflow_contents_manager: "WorkflowContentsManager"
     library_folder_manager: Any  # 'galaxy.managers.folders.FolderManager'
     library_manager: Any  # 'galaxy.managers.libraries.LibraryManager'
     role_manager: Any  # 'galaxy.managers.roles.RoleManager'
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index e2ed787bdba29b62b135f587fcdf22eb3c99d91d..02272ddfe06f2bf9e8a6283d7d7762a24db6d7c1 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -192,7 +192,9 @@ class InstalledRepositoryMetadataManager(GalaxyMetadataGenerator):
             status = "error"
         return message, status
 
-    def set_repository(self, repository):
+    def set_repository(
+        self, repository, relative_install_dir: Optional[str] = None, changeset_revision: Optional[str] = None
+    ):
         super().set_repository(repository)
         self.repository_clone_url = common_util.generate_clone_url_for_installed_repository(self.app, repository)
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
index d4f2157f82d534b366a7bd2859726f2bea72e9c4..c870829bf994a2b00d4eef10d91b2c3579f2f2ff 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py
@@ -74,7 +74,7 @@ class DataManagerHandler:
         repository,
         repository_tools_tups,
     ) -> List["DataManagerInterface"]:
-        rval: List["DataManagerInterface"] = []
+        rval: List[DataManagerInterface] = []
         if "data_manager" in metadata_dict:
             tpm = tool_panel_manager.ToolPanelManager(self.app)
             repository_tools_by_guid = {}
diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 4c439ada7a9955750e8f51e8ef360a410ce17af3..90d374bec7266514a23a8f6de747550df43d93a2 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -12,7 +12,10 @@ from typing import (
     Union,
 )
 
-from typing_extensions import Protocol
+from typing_extensions import (
+    Protocol,
+    TypedDict,
+)
 
 from galaxy import util
 from galaxy.model.tool_shed_install import ToolShedRepository
@@ -64,6 +67,21 @@ NOT_TOOL_CONFIGS = [
 ]
 
 
+class RepositoryMetadataToolDict(TypedDict):
+    id: str
+    guid: str
+    name: str
+    version: str
+    profile: str
+    description: Optional[str]
+    version_string_cmd: Optional[str]
+    tool_config: str
+    tool_type: str
+    requirements: Optional[Any]
+    tests: Optional[Any]
+    add_to_tool_panel: bool
+
+
 class RepositoryProtocol(Protocol):
     name: str
     id: str
@@ -597,7 +615,7 @@ class BaseMetadataGenerator:
         # should not be displayed in the tool panel are datatypes converters and DataManager tools
         # (which are of type 'manage_data').
         add_to_tool_panel_attribute = self._set_add_to_tool_panel_attribute_for_tool(tool)
-        tool_dict = dict(
+        tool_dict = RepositoryMetadataToolDict(
             id=tool.id,
             guid=guid,
             name=tool.name,
diff --git a/lib/galaxy/tool_shed/tools/tool_validator.py b/lib/galaxy/tool_shed/tools/tool_validator.py
index a73af2230c9e7a8f39ed58997760d924317e6a7f..428601c651133fd47a9da52056c4de6c732eb2f9 100644
--- a/lib/galaxy/tool_shed/tools/tool_validator.py
+++ b/lib/galaxy/tool_shed/tools/tool_validator.py
@@ -97,7 +97,7 @@ class ToolValidator:
             tool = None
             valid = False
             error_message = (
-                f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file.  Upload a file '
+                f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file. Upload a file '
             )
             error_message += (
                 "named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct "
diff --git a/lib/galaxy/tool_util/client/landing.py b/lib/galaxy/tool_util/client/landing.py
new file mode 100644
index 0000000000000000000000000000000000000000..e089ae268689f24697b13d58c79d33273932a818
--- /dev/null
+++ b/lib/galaxy/tool_util/client/landing.py
@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+
+# . .venv/bin/activate; PYTHONPATH=lib python lib/galaxy/tool_util/client/landing.py -g http://localhost:8081 simple_workflow
+
+import argparse
+import random
+import string
+import sys
+from dataclasses import dataclass
+from typing import Optional
+
+import requests
+import yaml
+
+from galaxy.util.resources import resource_string
+
+DESCRIPTION = """
+A small utility for demoing creation of tool and workflow landing endpoints.
+
+This allows an external developer to create tool and workflow forms with
+pre-populated parameters and handing them off with URLs to their clients/users.
+"""
+RANDOM_SECRET_LENGTH = 10
+
+
+def load_default_catalog():
+    catalog_yaml = resource_string("galaxy.tool_util.client", "landing_catalog.sample.yml")
+    return yaml.safe_load(catalog_yaml)
+
+
+@dataclass
+class Request:
+    template_id: str
+    catalog: str
+    client_secret: Optional[str]
+    galaxy_url: str
+
+
+@dataclass
+class Response:
+    landing_url: str
+
+
+def generate_claim_url(request: Request) -> Response:
+    template_id = request.template_id
+    catalog_path = request.catalog
+    galaxy_url = request.galaxy_url
+    client_secret = request.client_secret
+    if client_secret == "__GEN__":
+        client_secret = "".join(
+            random.choice(string.ascii_lowercase + string.digits) for _ in range(RANDOM_SECRET_LENGTH)
+        )
+    if catalog_path:
+        with open(catalog_path) as f:
+            catalog = yaml.safe_load(f)
+    else:
+        catalog = load_default_catalog()
+    template = catalog[template_id]
+    template_type = "tool" if "tool_id" in template else "workflow"
+    if client_secret:
+        template["client_secret"] = client_secret
+
+    landing_request_url = f"{galaxy_url}/api/{template_type}_landings"
+    raw_response = requests.post(
+        landing_request_url,
+        json=template,
+    )
+    try:
+        raw_response.raise_for_status()
+    except Exception:
+        raise Exception("Request failed: %s", raw_response.text)
+    response = raw_response.json()
+    url = f"{galaxy_url}/{template_type}_landings/{response['uuid']}"
+    if client_secret:
+        url = url + f"?secret={client_secret}"
+    return Response(url)
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument("template_id")
+    parser.add_argument(
+        "-g",
+        "--galaxy-url",
+        dest="galaxy_url",
+        default="https://usegalaxy.org/",
+        help="Galxy target for the landing request",
+    )
+    parser.add_argument(
+        "-c",
+        "--catalog",
+        dest="catalog",
+        default=None,
+        help="YAML catalog to load landing request templates from.",
+    )
+    parser.add_argument(
+        "-s",
+        "--secret",
+        dest="secret",
+        default=None,
+        help="An optional client secret to verify the request against, set to __GEN__ to generate one at random for this request.",
+    )
+    return parser
+
+
+def main(argv=None) -> None:
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = arg_parser().parse_args(argv)
+    request = Request(
+        args.template_id,
+        args.catalog,
+        args.secret,
+        args.galaxy_url,
+    )
+    response = generate_claim_url(request)
+    print(f"Your customized form is located at {response.landing_url}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/tool_util/client/landing_library.catalog.yml b/lib/galaxy/tool_util/client/landing_library.catalog.yml
new file mode 100644
index 0000000000000000000000000000000000000000..71a1c6e03f622a177b39ad3c0b317940c5c016d6
--- /dev/null
+++ b/lib/galaxy/tool_util/client/landing_library.catalog.yml
@@ -0,0 +1,21 @@
+# Catalog of artifacts that the landing script can generate landing URLs for against
+# the target Galaxy.
+simple_workflow:
+  # Encoded ID for a workflow to target - if workflow_target_type is stored_workflow this
+  # will always be the latest version of that workflow and stored workflow ID should be provided.
+  # If instead workflow_target_type is workflow - this is a particular version of a workflow and
+  # the workflow ID should be provided.
+  workflow_id: f2db41e1fa331b3e
+  workflow_target_type: stored_workflow
+  # request state provides prepopulated parameters for this workflow or stored workflow when the
+  # user navigates to the landing URL.
+  request_state:
+    myinput:
+      src: url
+      url: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed
+      ext: txt
+int_workflow:
+  workflow_id: f597429621d6eb2b
+  workflow_target_type: stored_workflow
+  request_state:
+    int_input: 8
diff --git a/lib/galaxy/tool_util/client/staging.py b/lib/galaxy/tool_util/client/staging.py
index 8156dd123f58b83a916a0f639b273ce4a44e58af..1bfd68b32c43ab41a082b891da1454d17e213413 100644
--- a/lib/galaxy/tool_util/client/staging.py
+++ b/lib/galaxy/tool_util/client/staging.py
@@ -11,11 +11,13 @@ import os
 from typing import (
     Any,
     BinaryIO,
+    Callable,
     Dict,
     List,
     Optional,
     Tuple,
     TYPE_CHECKING,
+    Union,
 )
 
 import yaml
@@ -84,9 +86,10 @@ class StagingInterface(metaclass=abc.ABCMeta):
         use_path_paste: bool = LOAD_TOOLS_FROM_PATH,
         to_posix_lines: bool = True,
         job_dir: str = ".",
+        resolve_data: Optional[Callable[[str], Optional[str]]] = None,
     ) -> Tuple[Dict[str, Any], List[Dict[str, Any]]]:
         def upload_func_fetch(upload_target: UploadTarget) -> Dict[str, Any]:
-            def _attach_file(upload_payload: Dict[str, Any], uri: str, index: int = 0) -> Dict[str, str]:
+            def _attach_file(upload_payload: Dict[str, Any], uri: str, index: int = 0) -> Dict[str, Union[str, bool]]:
                 uri = path_or_uri_to_uri(uri)
                 is_path = uri.startswith("file://")
                 if not is_path or use_path_paste:
@@ -107,6 +110,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
                     dbkey=dbkey,
                     to_posix_lines=to_posix_lines,
                     decompress=upload_target.properties.get("decompress") or DEFAULT_DECOMPRESS,
+                    hashes=upload_target.properties.get("hashes"),
                 )
                 name = _file_path_to_name(file_path)
                 if file_path is not None:
@@ -118,6 +122,8 @@ class StagingInterface(metaclass=abc.ABCMeta):
                     for i, composite_data in enumerate(upload_target.composite_data):
                         composite_item_src = _attach_file(fetch_payload, composite_data, index=i)
                         composite_items.append(composite_item_src)
+                    if "metadata" in upload_target.properties:
+                        fetch_payload["targets"][0]["elements"][0]["metadata"] = upload_target.properties["metadata"]
                     fetch_payload["targets"][0]["elements"][0]["src"] = "composite"
                     fetch_payload["targets"][0]["elements"][0]["composite"] = {
                         "items": composite_items,
@@ -141,11 +147,18 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 if tags:
                     fetch_payload["targets"][0]["elements"][0]["tags"] = tags
             elif isinstance(upload_target, DirectoryUploadTarget):
-                fetch_payload = _fetch_payload(history_id, file_type="directory")
-                fetch_payload["targets"][0].pop("elements")
+                fetch_payload = _fetch_payload(history_id, file_type=upload_target.file_type)
+                element = fetch_payload["targets"][0]["elements"][0]
+                element["name"] = upload_target.name
                 tar_path = upload_target.tar_path
-                src = _attach_file(fetch_payload, tar_path)
-                fetch_payload["targets"][0]["elements_from"] = src
+                extra_files = _attach_file(fetch_payload, tar_path)
+                extra_files["fuzzy_root"] = False
+                extra_files["items_from"] = "archive"
+                # {"src": "pasted", "paste_content": ""} because
+                # we need some primary file even if we don't have one
+                element["src"] = "pasted"
+                element["paste_content"] = ""
+                element["extra_files"] = extra_files
             elif isinstance(upload_target, ObjectUploadTarget):
                 content = json.dumps(upload_target.object)
                 fetch_payload = _fetch_payload(history_id, file_type="expression.json")
@@ -177,11 +190,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 file_path = upload_target.path
                 file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
                 dbkey = upload_target.properties.get("dbkey", None) or DEFAULT_DBKEY
-                upload_payload = _upload_payload(
-                    history_id,
-                    file_type=file_type,
-                    to_posix_lines=dbkey,
-                )
+                upload_payload = _upload_payload(history_id, file_type=file_type, to_posix_lines=dbkey)
                 name = _file_path_to_name(file_path)
                 upload_payload["inputs"]["files_0|auto_decompress"] = False
                 upload_payload["inputs"]["auto_decompress"] = False
@@ -266,6 +275,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
             upload,
             create_collection_func,
             tool_or_workflow,
+            resolve_data=resolve_data,
         )
 
     # extension point for planemo to override logging
@@ -334,6 +344,8 @@ def _fetch_payload(history_id, file_type=DEFAULT_FILE_TYPE, dbkey=DEFAULT_DBKEY,
     for arg in ["to_posix_lines", "space_to_tab"]:
         if arg in kwd:
             element[arg] = kwd[arg]
+    if kwd.get("hashes"):
+        element["hashes"] = kwd["hashes"]
     if "file_name" in kwd:
         element["name"] = kwd["file_name"]
     if "decompress" in kwd:
diff --git a/lib/galaxy/tool_util/cwl/__init__.py b/lib/galaxy/tool_util/cwl/__init__.py
index bb55b897519efb1fa2eedd883e67f6c0bd76af6c..e932c0fa725e5dbb70851574831d1ff5b8f0f634 100644
--- a/lib/galaxy/tool_util/cwl/__init__.py
+++ b/lib/galaxy/tool_util/cwl/__init__.py
@@ -1,7 +1,4 @@
-from .cwltool_deps import (
-    needs_shell_quoting,
-    shellescape,
-)
+from .cwltool_deps import needs_shell_quoting
 from .parser import (
     tool_proxy,
     tool_proxy_from_persistent_representation,
@@ -21,5 +18,4 @@ __all__ = (
     "to_cwl_job",
     "to_galaxy_parameters",
     "needs_shell_quoting",
-    "shellescape",
 )
diff --git a/lib/galaxy/tool_util/cwl/cwltool_deps.py b/lib/galaxy/tool_util/cwl/cwltool_deps.py
index 414c516caf8bbaddc56d2c6233d7b26564c3a491..3606319db46c38dd84cb69d1362496067c8d1c2d 100644
--- a/lib/galaxy/tool_util/cwl/cwltool_deps.py
+++ b/lib/galaxy/tool_util/cwl/cwltool_deps.py
@@ -71,11 +71,6 @@ except ImportError:
     visit_class = None  # type: ignore[assignment]
     normalizeFilesDirs = None  # type: ignore[assignment]
 
-try:
-    import shellescape
-except ImportError:
-    shellescape = None
-
 try:
     import schema_salad
     from schema_salad import (
@@ -105,7 +100,7 @@ def ensure_cwltool_available():
 
     Throw an ImportError with a description of the problem if they do not exist.
     """
-    if main is None or workflow is None or shellescape is None:
+    if main is None or workflow is None:
         message = "This feature requires cwltool and dependencies to be available, they are not."
         if main is None:
             message += " cwltool is not unavailable."
@@ -113,8 +108,6 @@ def ensure_cwltool_available():
             message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
         if requests is None:
             message += " Library 'requests' unavailable."
-        if shellescape is None:
-            message += " Library 'shellescape' unavailable."
         if schema_salad is None:
             message += " Library 'schema_salad' unavailable."
         raise ImportError(message)
@@ -137,7 +130,6 @@ __all__ = (
     "resolve_and_validate_document",
     "RuntimeContext",
     "schema_salad",
-    "shellescape",
     "sourceline",
     "StdFsAccess",
     "visit_class",
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index 674b3abcc3576b9808072383d648df4a8e99ba9c..e4a4ff83fb2063e89b98e389e0bb94a42617b283 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -144,6 +144,10 @@ class ToolProxy(metaclass=ABCMeta):
             tool_id = tool_id[1:]
         return tool_id
 
+    @abstractmethod
+    def input_fields(self) -> list:
+        """Return InputInstance objects describing mapping to Galaxy inputs."""
+
     @abstractmethod
     def input_instances(self):
         """Return InputInstance objects describing mapping to Galaxy inputs."""
@@ -236,7 +240,7 @@ class CommandLineToolProxy(ToolProxy):
         else:
             return ""
 
-    def input_fields(self):
+    def input_fields(self) -> list:
         input_records_schema = self._eval_schema(self._tool.inputs_record_schema)
         if input_records_schema["type"] != "record":
             raise Exception("Unhandled CWL tool input structure")
@@ -903,7 +907,7 @@ def split_step_references(step_references, workflow_id=None, multiple=True):
     if multiple:
         return split_references
     else:
-        assert len(split_references) == 1
+        assert len(split_references) == 1, split_references
         return split_references[0]
 
 
diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index 4d2dc2977d11408a043d62375f42c6d6decff820..a57342a8bb1eac72a357bfe263140cae3a6ace1c 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -100,11 +100,15 @@ def _handle_pseudo_location(properties, pseudo_location):
         properties["location"] = properties["basename"]
 
 
-def abs_path_or_uri(path_or_uri: str, relative_to: str) -> str:
+def abs_path_or_uri(path_or_uri: str, relative_to: str, resolve_data: Optional[Callable[[str], Optional[str]]]) -> str:
     """Return the absolute path if this isn't a URI, otherwise keep the URI the same."""
     if "://" in path_or_uri:
         return path_or_uri
     abs_path_ = os.path.abspath(os.path.join(relative_to, path_or_uri))
+    if resolve_data and not os.path.exists(abs_path_):
+        resolved_data = resolve_data(path_or_uri)
+        if resolved_data:
+            abs_path_ = resolved_data
     _ensure_file_exists(abs_path_)
     return abs_path_
 
@@ -136,6 +140,7 @@ def galactic_job_json(
     upload_func: Callable[["UploadTarget"], Dict[str, Any]],
     collection_create_func: Callable[[List[Dict[str, Any]], str], Dict[str, Any]],
     tool_or_workflow: Literal["tool", "workflow"] = "workflow",
+    resolve_data: Optional[Callable[[str], Optional[str]]] = None,
 ) -> Tuple[Dict[str, Any], List[Dict[str, Any]]]:
     """Adapt a CWL job object to the Galaxy API.
 
@@ -159,7 +164,7 @@ def galactic_job_json(
         return {"src": "hda", "id": dataset_id}
 
     def upload_file(file_path: str, secondary_files: Optional[str], **kwargs) -> Dict[str, str]:
-        file_path = abs_path_or_uri(file_path, test_data_directory)
+        file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
         target = FileUploadTarget(file_path, secondary_files, **kwargs)
         upload_response = upload_func(target)
         return response_to_hda(target, upload_response)
@@ -169,18 +174,18 @@ def galactic_job_json(
         upload_response = upload_func(target)
         return response_to_hda(target, upload_response)
 
-    def upload_tar(file_path: str) -> Dict[str, str]:
-        file_path = abs_path_or_uri(file_path, test_data_directory)
-        target = DirectoryUploadTarget(file_path)
+    def upload_tar(file_path: str, file_type: str = "directory", name: str = "uploaded tar file") -> Dict[str, str]:
+        file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
+        target = DirectoryUploadTarget(file_path, file_type=file_type, name=name)
         upload_response = upload_func(target)
         return response_to_hda(target, upload_response)
 
     def upload_file_with_composite_data(file_path: Optional[str], composite_data, **kwargs) -> Dict[str, str]:
         if file_path is not None:
-            file_path = abs_path_or_uri(file_path, test_data_directory)
+            file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
         composite_data_resolved = []
         for cd in composite_data:
-            composite_data_resolved.append(abs_path_or_uri(cd, test_data_directory))
+            composite_data_resolved.append(abs_path_or_uri(cd, test_data_directory, resolve_data=resolve_data))
         target = FileUploadTarget(file_path, composite_data=composite_data_resolved, **kwargs)
         upload_response = upload_func(target)
         return response_to_hda(target, upload_response)
@@ -235,6 +240,10 @@ def galactic_job_json(
             kwd["dbkey"] = value.get("dbkey")
         if "decompress" in value:
             kwd["decompress"] = value["decompress"]
+        if value.get("hashes"):
+            kwd["hashes"] = value["hashes"]
+        if value.get("metadata"):
+            kwd["metadata"] = value["metadata"]
         if composite_data_raw:
             composite_data = []
             for entry in composite_data_raw:
@@ -281,16 +290,17 @@ def galactic_job_json(
         file_path = value.get("location", None) or value.get("path", None)
         if file_path is None:
             return value
-
         if not os.path.isabs(file_path):
             file_path = os.path.join(test_data_directory, file_path)
 
+        file_type = value.get("filetype", None) or value.get("format", None) or "directory"
+
         tmp = tempfile.NamedTemporaryFile(delete=False)
         tf = tarfile.open(fileobj=tmp, mode="w:")
         tf.add(file_path, ".")
         tf.close()
 
-        return upload_tar(tmp.name)
+        return upload_tar(tmp.name, file_type=file_type, name=os.path.basename(file_path))
 
     def replacement_list(value) -> Dict[str, str]:
         collection_element_identifiers = []
@@ -425,8 +435,10 @@ class ObjectUploadTarget(UploadTarget):
 
 
 class DirectoryUploadTarget(UploadTarget):
-    def __init__(self, tar_path: str) -> None:
+    def __init__(self, tar_path: str, file_type: str = "directory", name: str = "uploaded directory") -> None:
         self.tar_path = tar_path
+        self.file_type = file_type
+        self.name = name
 
     def __str__(self) -> str:
         return f"DirectoryUploadTarget[tar_path={self.tar_path}]"
diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py
index 4905b6091e3e095710167a4da11b81a25bc9ab32..6a80d4b5efb5c42c63c0f7dc7f1b9e431ef8cc90 100644
--- a/lib/galaxy/tool_util/deps/conda_util.py
+++ b/lib/galaxy/tool_util/deps/conda_util.py
@@ -48,7 +48,7 @@ IS_OS_X = sys.platform == "darwin"
 VERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@(.*)")
 UNVERSIONED_ENV_DIR_NAME = re.compile(r"__(.*)@_uv_")
 USE_PATH_EXEC_DEFAULT = False
-CONDA_PACKAGE_SPECS = ("conda>=23.7.0", "conda-libmamba-solver", "'pyopenssl>=22.1.0'")
+CONDA_PACKAGE_SPECS = ("conda>=23.7.0", "conda-libmamba-solver", "pyopenssl>=22.1.0")
 CONDA_BUILD_SPECS = ("conda-build>=3.22.0",)
 USE_LOCAL_DEFAULT = False
 
@@ -60,13 +60,10 @@ def conda_link() -> str:
         else:
             url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh"
     else:
-        if sys.maxsize > 2**32:
-            if "arm64" in platform.platform():
-                url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
-            else:
-                url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
+        if "arm64" in platform.platform():
+            url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
         else:
-            url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh"
+            url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
     return url
 
 
@@ -75,21 +72,12 @@ def find_conda_prefix() -> str:
     for Miniconda installs.
     """
     home = os.path.expanduser("~")
-    miniconda_2_dest = os.path.join(home, "miniconda2")
-    miniconda_3_dest = os.path.join(home, "miniconda3")
-    anaconda_2_dest = os.path.join(home, "anaconda2")
-    anaconda_3_dest = os.path.join(home, "anaconda3")
-    # Prefer miniconda3 install if both available
-    if os.path.exists(miniconda_3_dest):
-        return miniconda_3_dest
-    elif os.path.exists(miniconda_2_dest):
-        return miniconda_2_dest
-    elif os.path.exists(anaconda_3_dest):
-        return anaconda_3_dest
-    elif os.path.exists(anaconda_2_dest):
-        return anaconda_2_dest
-    else:
-        return miniconda_3_dest
+    destinations = ["miniforge3", "miniconda3", "miniconda2", "anaconda3", "anaconda2"]
+    for destination in destinations:
+        destination = os.path.join(home, destination)
+        if os.path.exists(destination):
+            return destination
+    return os.path.join(home, "miniforge3")
 
 
 class CondaContext(installable.InstallableContext):
@@ -101,7 +89,7 @@ class CondaContext(installable.InstallableContext):
     def __init__(
         self,
         conda_prefix: Optional[str] = None,
-        conda_exec: Optional[str] = None,
+        conda_exec: Optional[Union[str, List[str]]] = None,
         shell_exec: Optional[Callable[..., int]] = None,
         debug: bool = False,
         ensure_channels: Union[str, List[str]] = "",
@@ -204,11 +192,12 @@ class CondaContext(installable.InstallableContext):
 
     def is_conda_installed(self) -> bool:
         """
-        Check if conda_exec exists
+        Check if conda_info() works
         """
-        if os.path.exists(self.conda_exec):
+        try:
+            self.conda_info()
             return True
-        else:
+        except Exception:
             return False
 
     def can_install_conda(self) -> bool:
@@ -218,6 +207,7 @@ class CondaContext(installable.InstallableContext):
         If conda_exec equals conda_prefix/bin/conda, we can install conda if either conda_prefix
         does not exist or is empty.
         """
+        assert isinstance(self.conda_exec, str), "conda_exec is not a str"
         conda_exec = os.path.abspath(self.conda_exec)
         conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, "bin/conda"))
         if conda_exec == conda_prefix_plus_exec:
@@ -437,7 +427,7 @@ class CondaTarget:
     def __init__(
         self, package: str, version: Optional[str] = None, build: Optional[str] = None, channel: Optional[str] = None
     ) -> None:
-        if SHELL_UNSAFE_PATTERN.search(package) is not None:
+        if SHELL_UNSAFE_PATTERN.search(package) is not None or not package:
             raise ValueError(f"Invalid package [{package}] encountered.")
         self.capitalized_package = package
         self.package = package.lower()
diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
index 6544399e3743c52479821aba1ffb95cbcc709aa3..4a4f9551ba6874e7c9ab82433494f6e3a4b0a4bd 100644
--- a/lib/galaxy/tool_util/deps/container_classes.py
+++ b/lib/galaxy/tool_util/deps/container_classes.py
@@ -194,6 +194,10 @@ class Volume:
         ('A', 'B', 'rw')
         >>> Volume.parse_volume_str('A:ro')
         ('A', 'A', 'ro')
+        >>> Volume.parse_volume_str('A:z')
+        ('A', 'A', 'z')
+        >>> Volume.parse_volume_str('A:Z')
+        ('A', 'A', 'Z')
         >>> Volume.parse_volume_str('A')
         ('A', 'A', 'rw')
         >>> Volume.parse_volume_str(' ')
@@ -216,7 +220,9 @@ class Volume:
             target = volume_parts[1]
             mode = volume_parts[2]
         elif len(volume_parts) == 2:
-            if volume_parts[1] not in ("rw", "ro", "default_ro"):
+            # not really parsing/checking mode here, just figuring out if the 2nd component is target or mode
+            mode_parts = volume_parts[1].split(",")
+            if any(mode_part not in ("rw", "ro", "default_ro", "z", "Z") for mode_part in mode_parts):
                 source = volume_parts[0]
                 target = volume_parts[1]
                 mode = "rw"
@@ -409,6 +415,18 @@ class HasDockerLikeVolumes:
         return volumes_str
 
 
+def _parse_volumes(volumes_raw: str, container_type: str) -> List[DockerVolume]:
+    """
+    >>> volumes_raw = "$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:z,$default_file_path:z"
+    >>> volumes = _parse_volumes(volumes_raw, "docker")
+    >>> [str(v) for v in volumes]
+    ['"$galaxy_root:$galaxy_root:ro"', '"$tool_directory:$tool_directory:ro"', '"$job_directory:$job_directory:ro"', '"$working_directory:$working_directory:z"', '"$default_file_path:$default_file_path:z"']
+    """
+    preprocessed_volumes_list = preprocess_volumes(volumes_raw, container_type)
+    # TODO: Remove redundant volumes...
+    return [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+
+
 class DockerContainer(Container, HasDockerLikeVolumes):
     container_type = DOCKER_CONTAINER_TYPE
 
@@ -448,9 +466,7 @@ class DockerContainer(Container, HasDockerLikeVolumes):
             raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
 
         volumes_raw = self._expand_volume_str(self.destination_info.get("docker_volumes", "$defaults"))
-        preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
-        # TODO: Remove redundant volumes...
-        volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+        volumes = _parse_volumes(volumes_raw, self.container_type)
         volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
 
         docker_host_props = self.docker_host_props
@@ -584,8 +600,7 @@ class SingularityContainer(Container, HasDockerLikeVolumes):
             raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
 
         volumes_raw = self._expand_volume_str(self.destination_info.get("singularity_volumes", "$defaults"))
-        preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
-        volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+        volumes = _parse_volumes(volumes_raw, self.container_type)
 
         run_command = singularity_util.build_singularity_run_command(
             command,
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/__init__.py b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
index 6407ba2fa609ee3027fe3e999dbfa96cefeae176..8a5682a3b39f79a54ac4377b047aa54059cb4388 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/__init__.py
@@ -3,7 +3,6 @@
 from abc import (
     ABCMeta,
     abstractmethod,
-    abstractproperty,
 )
 from typing import (
     Any,
@@ -65,7 +64,8 @@ class ContainerResolver(Dictifiable, metaclass=ABCMeta):
         of the tool and its requirements.
         """
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def resolver_type(self) -> str:
         """Short label for the type of container resolution."""
 
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
index b976662ccf6b3ca5000453b0eede65fe6c91acd1..f22c81842b417a45f4ea4ec5412d0a64a6c194d1 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -42,13 +42,13 @@ from ..container_classes import (
 )
 from ..docker_util import build_docker_images_command
 from ..mulled.mulled_build import (
-    DEFAULT_CHANNELS,
     ensure_installed,
     InvolucroContext,
     mull_targets,
 )
 from ..mulled.mulled_build_tool import requirements_to_mulled_targets
 from ..mulled.util import (
+    DEFAULT_CHANNELS,
     default_mulled_conda_channels_from_env,
     mulled_tags_for,
     split_tag,
@@ -738,7 +738,7 @@ class BuildMulledDockerContainerResolver(CliContainerResolver):
             "namespace": namespace,
             "hash_func": self.hash_func,
             "command": "build-and-test",
-            "use_mamba": True,
+            "use_mamba": False,
         }
         self._mulled_kwds["channels"] = default_mulled_conda_channels_from_env() or self._get_config_option(
             "mulled_channels", DEFAULT_CHANNELS
@@ -789,7 +789,7 @@ class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
             "namespace": "local",
             "singularity": True,
             "singularity_image_dir": self.cache_directory.path,
-            "use_mamba": True,
+            "use_mamba": False,
         }
         self.involucro_context = InvolucroContext(**self._involucro_context_kwds)
         auto_init = self._get_config_option("involucro_auto_init", True)
diff --git a/lib/galaxy/tool_util/deps/container_volumes.py b/lib/galaxy/tool_util/deps/container_volumes.py
index 2e969a3b4b6352080096962f4f922e1d10ec8378..01747bba15b8a3a304cfdb64436f75dd2cfab00c 100644
--- a/lib/galaxy/tool_util/deps/container_volumes.py
+++ b/lib/galaxy/tool_util/deps/container_volumes.py
@@ -7,7 +7,7 @@ from typing import Optional
 
 
 class ContainerVolume(metaclass=ABCMeta):
-    valid_modes = frozenset({"ro", "rw"})
+    valid_modes = frozenset({"ro", "rw", "z", "Z"})
 
     def __init__(self, path: str, host_path: Optional[str] = None, mode: Optional[str] = None):
         self.path = path
@@ -50,7 +50,7 @@ class DockerVolume(ContainerVolume):
             kwds["path"] = kwds["host_path"]
         elif len(parts) == 2:
             # /host_path:mode is not (or is no longer?) valid Docker volume syntax
-            if parts[1] in DockerVolume.valid_modes:
+            if all(mode_part in DockerVolume.valid_modes for mode_part in parts[1].split(",")):
                 kwds["mode"] = parts[1]
                 kwds["path"] = kwds["host_path"]
             else:
diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
index 4791c6d9506e2a0bf9ba6a8510121fbb9cc7f180..bfd2f19cf86f2aaaf21ae67892b3b9605baa4dac 100644
--- a/lib/galaxy/tool_util/deps/dependencies.py
+++ b/lib/galaxy/tool_util/deps/dependencies.py
@@ -12,7 +12,7 @@ from galaxy.tool_util.deps.requirements import (
     ToolRequirements,
 )
 from galaxy.util import bunch
-from .mulled.mulled_build import DEFAULT_CHANNELS
+from .mulled.util import DEFAULT_CHANNELS
 
 
 class AppInfo:
diff --git a/lib/galaxy/tool_util/deps/installable.py b/lib/galaxy/tool_util/deps/installable.py
index 3488f4a0a1401e807e8ee33b61828a342778b38e..a8d239259c0530cdc1b463ab528cc1de9175abaf 100644
--- a/lib/galaxy/tool_util/deps/installable.py
+++ b/lib/galaxy/tool_util/deps/installable.py
@@ -34,7 +34,7 @@ class InstallableContext(metaclass=abc.ABCMeta):
         """Return parent path of the location the installable will be created within."""
 
 
-def ensure_installed(installable_context, install_func, auto_init):
+def ensure_installed(installable_context: InstallableContext, install_func, auto_init):
     """Make sure target is installed - handle multiple processes potentially attempting installation."""
     parent_path = installable_context.parent_path
     desc = installable_context.installable_description
diff --git a/lib/galaxy/tool_util/deps/mulled/get_tests.py b/lib/galaxy/tool_util/deps/mulled/get_tests.py
index 33a83cc67c4ad15550b0d73ee08c85a4f90e837b..6f042c67c341cd1e416b8613ebbff6ee21d2b1ac 100644
--- a/lib/galaxy/tool_util/deps/mulled/get_tests.py
+++ b/lib/galaxy/tool_util/deps/mulled/get_tests.py
@@ -26,12 +26,17 @@ except ImportError:
     Template = None  # type: ignore[assignment,misc]
     UndefinedError = Exception  # type: ignore[assignment,misc]
 
+from galaxy.tool_util.deps.conda_util import (
+    best_search_result,
+    CondaTarget,
+)
 from galaxy.util import (
     check_github_api_response_rate_limit,
     unicodify,
 )
 from galaxy.util.commands import argv_to_str
 from .util import (
+    CondaInDockerContext,
     get_files_from_conda_package,
     MULLED_SOCKET_TIMEOUT,
     split_container_name,
@@ -299,20 +304,19 @@ def hashed_test_search(
     targets = concatenated_targets.split(",")
     packages = [target.split("=") for target in targets]
 
+    conda_context = CondaInDockerContext(ensure_channels=[anaconda_channel])
     containers = []
-    for package in packages:
-        r = requests.get(f"https://anaconda.org/bioconda/{package[0]}/files", timeout=MULLED_SOCKET_TIMEOUT)
-        r.raise_for_status()
-        p = "-".join(package)
-        for line in r.text.split("\n"):
-            # include only linux-64 builds since that is hardcoded in get_anaconda_url and the only target for container builds
-            if p in line and "linux-64" in line:
-                build = line.split(p)[1].split(".tar.bz2")[0]
-                if build == "":
-                    containers.append(f"{package[0]}:{package[1]}")
-                else:
-                    containers.append(f"{package[0]}:{package[1]}-{build}")
-                break
+    for package_name, package_version in packages:
+        conda_target = CondaTarget(package_name, package_version)
+        # include only linux-64 builds since that is hardcoded in get_anaconda_url and the only target for container builds
+        hit, exact = best_search_result(conda_target, conda_context, platform="linux-64")
+        if not hit or not exact:
+            raise Exception(f"Could not find {conda_target}")
+        build = hit["build"]
+        if build:
+            containers.append(f"{package_name}:{package_version}--{build}")
+        else:
+            containers.append(f"{package_name}:{package_version}")
 
     for container in containers:
         tests = main_test_search(container, recipes_path, deep, anaconda_channel, github_repo)
diff --git a/lib/galaxy/tool_util/deps/mulled/invfile.lua b/lib/galaxy/tool_util/deps/mulled/invfile.lua
index 38ddc860cc3be44c1090e4abb6c248ddf7dd5129..f7bef84d18b54c1b827a81312f88e7e4bee176bd 100644
--- a/lib/galaxy/tool_util/deps/mulled/invfile.lua
+++ b/lib/galaxy/tool_util/deps/mulled/invfile.lua
@@ -42,7 +42,7 @@ end
 
 local conda_image = VAR.CONDA_IMAGE
 if conda_image == '' then
-    conda_image = 'quay.io/condaforge/mambaforge:latest'
+    conda_image = 'quay.io/condaforge/miniforge3:latest'
 end
 
 local conda_bin = VAR.CONDA_BIN
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index be956c84a8b969493a9fac3f1d80216b98039020..0d00de2e8ff5ae7443b2760b4aad9cb1166e16c2 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -33,7 +33,6 @@ from galaxy.tool_util.deps.conda_util import (
     CondaContext,
     CondaTarget,
 )
-from galaxy.tool_util.deps.docker_util import command_list as docker_command_list
 from galaxy.util import (
     commands,
     download_to_file,
@@ -45,8 +44,10 @@ from ._cli import arg_parser
 from .util import (
     build_target,
     conda_build_target_str,
+    CONDA_IMAGE,
+    CondaInDockerContext,
     create_repository,
-    default_mulled_conda_channels_from_env,
+    DEFAULT_CHANNELS,
     get_files_from_conda_package,
     PrintProgress,
     quay_repository,
@@ -62,14 +63,12 @@ DEFAULT_BASE_IMAGE = os.environ.get("DEFAULT_BASE_IMAGE", "quay.io/bioconda/base
 DEFAULT_EXTENDED_BASE_IMAGE = os.environ.get(
     "DEFAULT_EXTENDED_BASE_IMAGE", "quay.io/bioconda/base-glibc-debian-bash:latest"
 )
-DEFAULT_CHANNELS = default_mulled_conda_channels_from_env() or ["conda-forge", "bioconda"]
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
 DEFAULT_WORKING_DIR = "/source/"
 IS_OS_X = _platform == "darwin"
 INVOLUCRO_VERSION = "1.1.2"
 DEST_BASE_IMAGE = os.environ.get("DEST_BASE_IMAGE", None)
-CONDA_IMAGE = os.environ.get("CONDA_IMAGE", None)
 
 SINGULARITY_TEMPLATE = """Bootstrap: docker
 From: %(base_image)s
@@ -314,11 +313,11 @@ def mull_targets(
         if conda_version is not None:
             specs.append(f"conda={conda_version}")
         if mamba_version is not None:
-            specs.append(f"mamba={mamba_version}")
             if mamba_version == "" and not specs:
                 # If nothing but mamba without a specific version is requested,
                 # then only run conda install if mamba is not already installed.
                 mamba_test = "[ '[]' = \"$( conda list --json --full-name mamba )\" ]"
+            specs.append(f"mamba={mamba_version}")
         conda_install = f"""conda install {verbose} --yes {" ".join(f"'{spec}'" for spec in specs)}"""
         involucro_args.extend(["-set", f"PREINSTALL=if {mamba_test} ; then {conda_install} ; fi"])
 
@@ -363,34 +362,6 @@ def context_from_args(args):
     return InvolucroContext(involucro_bin=args.involucro_path, verbose=verbose)
 
 
-class CondaInDockerContext(CondaContext):
-    def __init__(
-        self,
-        conda_prefix=None,
-        conda_exec=None,
-        shell_exec=None,
-        debug=False,
-        ensure_channels=DEFAULT_CHANNELS,
-        condarc_override=None,
-    ):
-        if not conda_exec:
-            conda_image = CONDA_IMAGE or "continuumio/miniconda3:latest"
-            binds = []
-            for channel in ensure_channels:
-                if channel.startswith("file://"):
-                    bind_path = channel[7:]
-                    binds.extend(["-v", f"{bind_path}:{bind_path}"])
-            conda_exec = docker_command_list("run", binds + [conda_image, "conda"])
-        super().__init__(
-            conda_prefix=conda_prefix,
-            conda_exec=conda_exec,
-            shell_exec=shell_exec,
-            debug=debug,
-            ensure_channels=ensure_channels,
-            condarc_override=condarc_override,
-        )
-
-
 class InvolucroContext(installable.InstallableContext):
     installable_description = "Involucro"
 
@@ -527,8 +498,8 @@ def add_single_image_arguments(parser):
     )
 
 
-def target_str_to_targets(targets_raw):
-    def parse_target(target_str):
+def target_str_to_targets(targets_raw: str) -> List[CondaTarget]:
+    def parse_target(target_str: str) -> CondaTarget:
         if "=" in target_str:
             package_name, version = target_str.split("=", 1)
             build = None
@@ -541,8 +512,10 @@ def target_str_to_targets(targets_raw):
             target = build_target(target_str)
         return target
 
-    targets = [parse_target(_) for _ in targets_raw.split(",")]
-    return targets
+    if targets_raw.strip() == "":
+        return []
+    else:
+        return [parse_target(_) for _ in targets_raw.split(",")]
 
 
 def args_to_mull_targets_kwds(args):
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
index a469bcd5eac9e6cadce9e113cb544d5e52ad6821..6be1a2de4a5ed8e6349ea780c7e72c31e0b9ec0c 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
@@ -20,13 +20,21 @@ from .mulled_build import (
     add_single_image_arguments,
     args_to_mull_targets_kwds,
     mull_targets,
+    target_str_to_targets,
 )
-from .util import build_target
 
 if TYPE_CHECKING:
     from galaxy.tool_util.deps.conda_util import CondaTarget
 
 
+def _mulled_build_tool(tool, args):
+    tool_source = get_tool_source(tool)
+    requirements, *_ = tool_source.parse_requirements_and_containers()
+    targets = requirements_to_mulled_targets(requirements)
+    kwds = args_to_mull_targets_kwds(args)
+    mull_targets(targets, **kwds)
+
+
 def main(argv=None) -> None:
     """Main entry-point for the CLI tool."""
     parser = arg_parser(argv, globals())
@@ -35,11 +43,7 @@ def main(argv=None) -> None:
     parser.add_argument("command", metavar="COMMAND", help="Command (build-and-test, build, all)")
     parser.add_argument("tool", metavar="TOOL", default=None, help="Path to tool to build mulled image for.")
     args = parser.parse_args()
-    tool_source = get_tool_source(args.tool)
-    requirements, *_ = tool_source.parse_requirements_and_containers()
-    targets = requirements_to_mulled_targets(requirements)
-    kwds = args_to_mull_targets_kwds(args)
-    mull_targets(targets, **kwds)
+    _mulled_build_tool(args.tool, args)
 
 
 def requirements_to_mulled_targets(requirements) -> List["CondaTarget"]:
@@ -48,7 +52,8 @@ def requirements_to_mulled_targets(requirements) -> List["CondaTarget"]:
     Only package requirements are retained.
     """
     package_requirements = [r for r in requirements if r.type == "package"]
-    targets = [build_target(r.name, r.version) for r in package_requirements]
+    target_str = ",".join(f"{r.name}={r.version}" if r.version else r.name for r in package_requirements)
+    targets = target_str_to_targets(target_str)
     return targets
 
 
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
index 691e4ab7e7494fe98b91b3a7e316ebbf2a827b47..1cd87d5a3d09d784e24c5d7563fbc2e7a7651f26 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
@@ -7,6 +7,7 @@ Produce a mulled hash with:
 
     mulled-hash samtools=1.3.1,bedtools=2.22
 """
+from typing_extensions import Literal
 
 from ._cli import arg_parser
 from .mulled_build import target_str_to_targets
@@ -16,6 +17,18 @@ from .util import (
 )
 
 
+def _mulled_hash(hash: Literal["v1", "v2"], targets_str: str):
+    """
+    >>> _mulled_hash("v2", "samtools=1.3.1,bedtools=2.26.0")
+    'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619'
+    >>> _mulled_hash("v2", "samtools=1.3.1=h9071d68_10,bedtools=2.26.0=0")
+    'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619'
+    """
+    targets = target_str_to_targets(targets_str)
+    image_name = v2_image_name if hash == "v2" else v1_image_name
+    return image_name(targets)
+
+
 def main(argv=None):
     """Main entry-point for the CLI tool."""
     parser = arg_parser(argv, globals())
@@ -24,9 +37,7 @@ def main(argv=None):
     )
     parser.add_argument("--hash", dest="hash", choices=["v1", "v2"], default="v2")
     args = parser.parse_args()
-    targets = target_str_to_targets(args.targets)
-    image_name = v2_image_name if args.hash == "v2" else v1_image_name
-    print(image_name(targets))
+    print(_mulled_hash(args.hash, args.targets))
 
 
 __all__ = ("main",)
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_search.py b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
index d936802a08405aca985780af59504e278d0dce4c..cf350f76cd9c4426ecadd20c871cbb7bf8862202 100755
--- a/lib/galaxy/tool_util/deps/mulled/mulled_search.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
@@ -5,6 +5,10 @@ import json
 import logging
 import sys
 import tempfile
+from typing import (
+    Dict,
+    List,
+)
 
 from galaxy.tool_util.deps.conda_util import CondaContext
 from galaxy.util import (
@@ -122,7 +126,7 @@ class CondaSearch:
     def __init__(self, channel):
         self.channel = channel
 
-    def get_json(self, search_string):
+    def get_json(self, search_string) -> List[Dict[str, str]]:
         """
         Function takes search_string variable and returns results from the bioconda channel in JSON format
 
@@ -135,8 +139,16 @@ class CondaSearch:
         except Exception as e:
             logging.info(f"Search failed with: {e}")
             return []
+        header_found = False
+        lines_fields: List[List[str]] = []
+        for line in raw_out.splitlines():
+            if line.startswith("#"):
+                header_found = True
+            elif header_found:
+                lines_fields.append(line.split())
         return [
-            {"package": n.split()[0], "version": n.split()[1], "build": n.split()[2]} for n in raw_out.split("\n")[2:-1]
+            {"package": line_fields[0], "version": line_fields[1], "build": line_fields[2]}
+            for line_fields in lines_fields
         ]
 
 
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py b/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
index deb62f0b24b82cdf66e7651daabba5aabaa04fdc..b1fd62feed801fef903fbe9b2de4113a233a82f9 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import argparse
-import os
 import os.path
 import subprocess
 import tempfile
@@ -11,10 +10,10 @@ from typing import (
     Any,
     Dict,
     List,
-    Union,
 )
 
 from galaxy.util import unicodify
+from galaxy.util.path import StrPath
 from .get_tests import (
     hashed_test_search,
     import_test_to_command_list,
@@ -46,7 +45,7 @@ def docker_to_singularity(container, installation, filepath, no_sudo=False):
 
 
 def singularity_container_test(
-    tests: Dict[str, Dict[str, Any]], installation: str, filepath: Union[str, os.PathLike]
+    tests: Dict[str, Dict[str, Any]], installation: str, filepath: StrPath
 ) -> Dict[str, List]:
     """
     Run tests, record if they pass or fail
diff --git a/lib/galaxy/tool_util/deps/mulled/util.py b/lib/galaxy/tool_util/deps/mulled/util.py
index a7eacb33806c1da9d1d56e8cbf3dd3f3ba8011a8..6ad094a8ce50ff9684cd15686c289e54258cff7c 100644
--- a/lib/galaxy/tool_util/deps/mulled/util.py
+++ b/lib/galaxy/tool_util/deps/mulled/util.py
@@ -9,6 +9,7 @@ import sys
 import threading
 from typing import (
     Any,
+    Callable,
     Dict,
     Iterable,
     List,
@@ -23,7 +24,11 @@ from conda_package_streaming.url import stream_conda_info as stream_conda_info_f
 from packaging.version import Version
 from requests import Session
 
-from galaxy.tool_util.deps.conda_util import CondaTarget
+from galaxy.tool_util.deps.conda_util import (
+    CondaContext,
+    CondaTarget,
+)
+from galaxy.tool_util.deps.docker_util import command_list as docker_command_list
 from galaxy.tool_util.version import (
     LegacyVersion,
     parse_version,
@@ -41,6 +46,7 @@ MULLED_SOCKET_TIMEOUT = 12
 QUAY_VERSIONS_CACHE_EXPIRY = 300
 NAMESPACE_HAS_REPO_NAME_KEY = "galaxy.tool_util.deps.container_resolvers.mulled.util:namespace_repo_names"
 TAG_CACHE_KEY = "galaxy.tool_util.deps.container_resolvers.mulled.util:tag_cache"
+CONDA_IMAGE = os.environ.get("CONDA_IMAGE", "quay.io/condaforge/miniforge3:latest")
 
 
 class PARSED_TAG(NamedTuple):
@@ -57,6 +63,36 @@ def default_mulled_conda_channels_from_env() -> Optional[List[str]]:
         return None
 
 
+DEFAULT_CHANNELS = default_mulled_conda_channels_from_env() or ["conda-forge", "bioconda"]
+
+
+class CondaInDockerContext(CondaContext):
+    def __init__(
+        self,
+        conda_prefix: Optional[str] = None,
+        conda_exec: Optional[Union[str, List[str]]] = None,
+        shell_exec: Optional[Callable[..., int]] = None,
+        debug: bool = False,
+        ensure_channels: Union[str, List[str]] = DEFAULT_CHANNELS,
+        condarc_override: Optional[str] = None,
+    ):
+        if not conda_exec:
+            binds = []
+            for channel in ensure_channels:
+                if channel.startswith("file://"):
+                    bind_path = channel[7:]
+                    binds.extend(["-v", f"{bind_path}:{bind_path}"])
+            conda_exec = docker_command_list("run", binds + [CONDA_IMAGE, "conda"])
+        super().__init__(
+            conda_prefix=conda_prefix,
+            conda_exec=conda_exec,
+            shell_exec=shell_exec,
+            debug=debug,
+            ensure_channels=ensure_channels,
+            condarc_override=condarc_override,
+        )
+
+
 def create_repository(namespace: str, repo_name: str, oauth_token: str) -> None:
     assert oauth_token
     headers = {"Authorization": f"Bearer {oauth_token}"}
@@ -335,7 +371,11 @@ def v2_image_name(
     >>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
     >>> v2_image_name(multi_targets_versionless)
     'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'
+    >>> targets_version_with_build = [build_target("samtools", version="1.3.1", build="h9071d68_10"), build_target("bedtools", version="2.26.0", build="0")]
+    >>> v2_image_name(targets_version_with_build)
+    'mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619'
     """
+
     if name_override is not None:
         print(
             "WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result."
@@ -436,7 +476,10 @@ image_name = v1_image_name  # deprecated
 
 __all__ = (
     "build_target",
+    "CONDA_IMAGE",
     "conda_build_target_str",
+    "CondaInDockerContext",
+    "DEFAULT_CHANNELS",
     "get_files_from_conda_package",
     "image_name",
     "mulled_tags_for",
diff --git a/lib/galaxy/tool_util/deps/resolvers/__init__.py b/lib/galaxy/tool_util/deps/resolvers/__init__.py
index 492219665e0d9700f53a1b7f0d846dbe268dd531..707e3e1cfa149ec5f54cc77176c919e4eb04cd1e 100644
--- a/lib/galaxy/tool_util/deps/resolvers/__init__.py
+++ b/lib/galaxy/tool_util/deps/resolvers/__init__.py
@@ -5,7 +5,6 @@ import os.path
 from abc import (
     ABCMeta,
     abstractmethod,
-    abstractproperty,
 )
 from typing import (
     Any,
@@ -237,7 +236,8 @@ class SpecificationAwareDependencyResolver(metaclass=ABCMeta):
 class SpecificationPatternDependencyResolver(SpecificationAwareDependencyResolver):
     """Implement the :class:`SpecificationAwareDependencyResolver` with a regex pattern."""
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def _specification_pattern(self):
         """Pattern of URI to match against."""
 
@@ -275,7 +275,8 @@ class Dependency(Dictifiable, metaclass=ABCMeta):
         Return shell commands to enable this dependency.
         """
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def exact(self):
         """Return true if version information wasn't discarded to resolve
         the dependency.
diff --git a/lib/galaxy/tool_util/deps/resolvers/conda.py b/lib/galaxy/tool_util/deps/resolvers/conda.py
index d28fca78b42c3a229828b78aab63b41e5e096b19..450e0c1b6fddd9f8f060519205eb62fb25c5573c 100644
--- a/lib/galaxy/tool_util/deps/resolvers/conda.py
+++ b/lib/galaxy/tool_util/deps/resolvers/conda.py
@@ -45,7 +45,7 @@ DEFAULT_BASE_PATH_DIRECTORY = "_conda"
 DEFAULT_CONDARC_OVERRIDE = "_condarc"
 # Conda channel order from highest to lowest, following the one used in
 # https://github.com/bioconda/bioconda-recipes/blob/master/config.yml
-DEFAULT_ENSURE_CHANNELS = "conda-forge,bioconda,defaults"
+DEFAULT_ENSURE_CHANNELS = "conda-forge,bioconda"
 CONDA_SOURCE_CMD = """[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '{environment_path}')" ] || {{
 MAX_TRIES=3
 COUNT=0
diff --git a/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
index 30a8a1bcc39895a282892410e74b459901b2136e..137edf56a6e96e98eb956117fbac7fdbbee64ced 100644
--- a/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/tool_shed_packages.py
@@ -31,7 +31,7 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use
         else:
             return NullDependency(version=version, name=name)
 
-    def _find_dep_default(self, name, type="package", **kwds):
+    def _find_dep_default(self, name, type="package", exact=True, **kwds):
         if type == "set_environment" and kwds.get("installed_tool_dependencies", None):
             installed_tool_dependency = self._get_installed_dependency(name, type, version=None, **kwds)
             if installed_tool_dependency:
diff --git a/lib/galaxy/tool_util/linters/cwl.py b/lib/galaxy/tool_util/linters/cwl.py
index f4e7f367ba5656ced9f9270d83db7b823daac25b..ed68c512d9a3da1a51e2d4d99fd52ec5d783b91d 100644
--- a/lib/galaxy/tool_util/linters/cwl.py
+++ b/lib/galaxy/tool_util/linters/cwl.py
@@ -20,7 +20,7 @@ class CWLValid(Linter):
             schema_loader.process_definition(raw_reference)
         except Exception:
             return
-        lint_ctx.info("CWL appears to be valid.")
+        lint_ctx.info("CWL appears to be valid.", linter=cls.name())
 
 
 class CWLInValid(Linter):
@@ -30,7 +30,7 @@ class CWLInValid(Linter):
         try:
             schema_loader.process_definition(raw_reference)
         except Exception as e:
-            lint_ctx.error(f"Failed to valdiate CWL artifact: {e}")
+            lint_ctx.error(f"Failed to valdiate CWL artifact: {e}", linter=cls.name())
 
 
 class CWLVersionMissing(Linter):
@@ -39,7 +39,7 @@ class CWLVersionMissing(Linter):
         raw_reference = schema_loader.raw_process_reference(tool_source.source_path)
         cwl_version = raw_reference.process_object.get("cwlVersion", None)
         if cwl_version is None:
-            lint_ctx.error("CWL file does not contain a 'cwlVersion'")
+            lint_ctx.error("CWL file does not contain a 'cwlVersion'", linter=cls.name())
 
 
 class CWLVersionUnknown(Linter):
@@ -48,7 +48,9 @@ class CWLVersionUnknown(Linter):
         raw_reference = schema_loader.raw_process_reference(tool_source.source_path)
         cwl_version = raw_reference.process_object.get("cwlVersion", None)
         if cwl_version not in ["v1.0"]:
-            lint_ctx.warn(f"CWL version [{cwl_version}] is unknown, we recommend the v1.0 the stable release.")
+            lint_ctx.warn(
+                f"CWL version [{cwl_version}] is unknown, we recommend the v1.0 the stable release.", linter=cls.name()
+            )
 
 
 class CWLVersionGood(Linter):
@@ -57,7 +59,7 @@ class CWLVersionGood(Linter):
         raw_reference = schema_loader.raw_process_reference(tool_source.source_path)
         cwl_version = raw_reference.process_object.get("cwlVersion", None)
         if cwl_version in ["v1.0"]:
-            lint_ctx.info(f"Modern CWL version [{cwl_version}].")
+            lint_ctx.info(f"Modern CWL version [{cwl_version}].", linter=cls.name())
 
 
 class CWLDockerMissing(Linter):
@@ -65,7 +67,7 @@ class CWLDockerMissing(Linter):
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         _, containers, *_ = tool_source.parse_requirements_and_containers()
         if len(containers) == 0:
-            lint_ctx.warn("Tool does not specify a DockerPull source.")
+            lint_ctx.warn("Tool does not specify a DockerPull source.", linter=cls.name())
 
 
 class CWLDockerGood(Linter):
@@ -74,7 +76,7 @@ class CWLDockerGood(Linter):
         _, containers, *_ = tool_source.parse_requirements_and_containers()
         if len(containers) > 0:
             identifier = containers[0].identifier
-            lint_ctx.info(f"Tool will run in Docker image [{identifier}].")
+            lint_ctx.info(f"Tool will run in Docker image [{identifier}].", linter=cls.name())
 
 
 class CWLDescriptionMissing(Linter):
@@ -82,12 +84,12 @@ class CWLDescriptionMissing(Linter):
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         help = tool_source.parse_help()
         if not help:
-            lint_ctx.warn("Description of tool is empty or absent.")
+            lint_ctx.warn("Description of tool is empty or absent.", linter=cls.name())
 
 
 class CWLHelpTODO(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         help = tool_source.parse_help()
-        if help and "TODO" in help:
-            lint_ctx.warn("Help contains TODO text.")
+        if help and "TODO" in help.content:
+            lint_ctx.warn("Help contains TODO text.", linter=cls.name())
diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py
new file mode 100644
index 0000000000000000000000000000000000000000..ec2d5e6299fb92f6660d88654cbf4d987d86cac1
--- /dev/null
+++ b/lib/galaxy/tool_util/linters/datatypes.py
@@ -0,0 +1,97 @@
+import os.path
+from typing import (
+    Set,
+    TYPE_CHECKING,
+    Union,
+)
+
+# from galaxy import config
+from galaxy.tool_util.lint import Linter
+from galaxy.util import (
+    listify,
+    parse_xml,
+)
+from galaxy.util.resources import resource_path
+
+if TYPE_CHECKING:
+    from galaxy.tool_util.lint import LintContext
+    from galaxy.tool_util.parser import ToolSource
+    from galaxy.util.resources import Traversable
+
+DATATYPES_CONF = resource_path(__package__, "datatypes_conf.xml.sample")
+
+
+def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]:
+    datatypes = set()
+    tree = parse_xml(datatype_conf_path)
+    root = tree.getroot()
+    for elem in root.findall("./registration/datatype"):
+        extension = elem.get("extension", "")
+        datatypes.add(extension)
+        auto_compressed_types = listify(elem.get("auto_compressed_types", ""))
+        for act in auto_compressed_types:
+            datatypes.add(f"{extension}.{act}")
+    return datatypes
+
+
+class DatatypesCustomConf(Linter):
+    """
+    Check if a custom datatypes_conf.xml is present
+    """
+
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        if not tool_source.source_path:
+            return
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        tool_node = tool_xml.getroot()
+        tool_dir = os.path.dirname(tool_source.source_path)
+        datatypes_conf_path = os.path.join(tool_dir, "datatypes_conf.xml")
+        if os.path.exists(datatypes_conf_path):
+            lint_ctx.warn(
+                "Tool uses a custom datatypes_conf.xml which is discouraged",
+                linter=cls.name(),
+                node=tool_node,
+            )
+
+
+class ValidDatatypes(Linter):
+    """
+    Check that used datatypes are available
+    """
+
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        # get Galaxy built-in dataypes
+        datatypes = _parse_datatypes(DATATYPES_CONF)
+        # add custom tool data types
+        if tool_source.source_path:
+            tool_dir = os.path.dirname(tool_source.source_path)
+            datatypes_conf_path = os.path.join(tool_dir, "datatypes_conf.xml")
+            if os.path.exists(datatypes_conf_path):
+                datatypes |= _parse_datatypes(datatypes_conf_path)
+        for attrib in ["format", "ftype", "ext"]:
+            for elem in tool_xml.findall(f".//*[@{attrib}]"):
+                formats = elem.get(attrib, "").split(",")
+                # Certain elements (e.g. `data`) can only have one format. This
+                # is checked separately by linting against the XSD.
+                if "auto" in formats:
+                    if elem.tag == "param":
+                        lint_ctx.error(
+                            "Format [auto] can not be used for tool or tool test inputs",
+                            linter=cls.name(),
+                            node=elem,
+                        )
+                    continue
+                for format in formats:
+                    if format not in datatypes:
+                        lint_ctx.error(
+                            f"Unknown datatype [{format}] used in {elem.tag} element",
+                            linter=cls.name(),
+                            node=elem,
+                        )
diff --git a/lib/galaxy/tool_util/linters/datatypes_conf.xml.sample b/lib/galaxy/tool_util/linters/datatypes_conf.xml.sample
new file mode 120000
index 0000000000000000000000000000000000000000..6a8d2e1034819328b95b40d3059e7a35bd2831bf
--- /dev/null
+++ b/lib/galaxy/tool_util/linters/datatypes_conf.xml.sample
@@ -0,0 +1 @@
+../../config/sample/datatypes_conf.xml.sample
\ No newline at end of file
diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
index e4fd04694dec8d0985ca1d11fdb7cfe267806309..79c1aefb3ba1cba681d518afbb66073dbd534ad5 100644
--- a/lib/galaxy/tool_util/linters/inputs.py
+++ b/lib/galaxy/tool_util/linters/inputs.py
@@ -710,12 +710,14 @@ class InputsSelectOptionsDefinesOptions(Linter):
             # TODO check if input param is present for from_dataset
             from_dataset = options.get("from_dataset", None)
             from_data_table = options.get("from_data_table", None)
+            from_url = options.get("from_url", None)
 
             if (
                 from_file is None
                 and from_parameter is None
                 and from_dataset is None
                 and from_data_table is None
+                and from_url is None
                 and not filter_adds_options
             ):
                 lint_ctx.error(
diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index 37ebab7343d428ea5d09ea35f68a5ff07c4c131c..b1d48fd2a60dc0ad7ed9936600331565a2febafb 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -1,5 +1,6 @@
 """This module contains a linting functions for tool outputs."""
 
+import ast
 from typing import TYPE_CHECKING
 
 from packaging.version import Version
@@ -76,6 +77,23 @@ class OutputsNameDuplicated(Linter):
             names.add(name)
 
 
+class OutputsFilterExpression(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        for filter in tool_xml.findall("./outputs/*/filter"):
+            try:
+                ast.parse(filter.text.strip(), mode="eval")
+            except Exception as e:
+                lint_ctx.warn(
+                    f"Filter '{filter.text}' is no valid expression: {str(e)}",
+                    linter=cls.name(),
+                    node=filter,
+                )
+
+
 class OutputsLabelDuplicatedFilter(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index 90cec700b06bfb44861e9468d78574113cfba630..49f4c78185c235cd73132615cc6b658a676a1864 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -1,5 +1,6 @@
 """This module contains a linting functions for tool tests."""
 
+from io import StringIO
 from typing import (
     Iterator,
     List,
@@ -7,7 +8,11 @@ from typing import (
     TYPE_CHECKING,
 )
 
+from packaging.version import Version
+
 from galaxy.tool_util.lint import Linter
+from galaxy.tool_util.parameters import validate_test_cases_for_tool_source
+from galaxy.tool_util.verify.assertion_models import assertion_list
 from galaxy.util import asbool
 from ._util import is_datasource
 
@@ -134,6 +139,69 @@ class TestsAssertsHasSizeOrValueQuant(Linter):
                     )
 
 
+class TestsAssertionValidation(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        try:
+            raw_tests_dict = tool_source.parse_tests_to_dict()
+        except Exception:
+            lint_ctx.warn("Failed to parse test dictionaries from tool - cannot lint assertions")
+            return
+        assert "tests" in raw_tests_dict
+        for test_idx, test in enumerate(raw_tests_dict["tests"], start=1):
+            # TODO: validate command, command_version, element tests. What about children?
+            for output in test["outputs"]:
+                asserts_raw = output.get("attributes", {}).get("assert_list") or []
+                to_yaml_assertions = []
+                for raw_assert in asserts_raw:
+                    to_yaml_assertions.append({"that": raw_assert["tag"], **raw_assert.get("attributes", {})})
+                try:
+                    assertion_list.model_validate(to_yaml_assertions)
+                except Exception as e:
+                    error_str = _cleanup_pydantic_error(e)
+                    lint_ctx.warn(
+                        f"Test {test_idx}: failed to validate assertions. Validation errors are [{error_str}]",
+                        linter=cls.name(),
+                    )
+
+
+class TestsCaseValidation(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        profile = tool_source.parse_profile()
+        lint_log = lint_ctx.warn if Version(profile) < Version("24.2") else lint_ctx.error
+
+        try:
+            validation_results = validate_test_cases_for_tool_source(tool_source, use_latest_profile=True)
+        except Exception as e:
+            lint_log(
+                f"Serious problem parsing tool source or tests - cannot validate test cases. The exception is [{e}]",
+                linter=cls.name(),
+            )
+            return
+        for test_idx, validation_result in enumerate(validation_results, start=1):
+            error = validation_result.validation_error
+            if error:
+                error_str = _cleanup_pydantic_error(error)
+                lint_log(
+                    f"Test {test_idx}: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [{error_str}]",
+                    linter=cls.name(),
+                )
+
+
+def _cleanup_pydantic_error(error) -> str:
+    full_validation_error = f"{error}"
+    new_error = StringIO("")
+    for line in full_validation_error.splitlines():
+        # this repeated over and over isn't useful in the context of how we're building the dynamic models,
+        # tool authors should not be looking up pydantic docs on models they cannot even really inspect
+        if line.strip().startswith("For further information visit https://errors.pydantic"):
+            continue
+        else:
+            new_error.write(f"{line}\n")
+    return new_error.getvalue().strip()
+
+
 class TestsExpectNumOutputs(Linter):
     @classmethod
     def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
diff --git a/lib/galaxy/tool_util/models.py b/lib/galaxy/tool_util/models.py
new file mode 100644
index 0000000000000000000000000000000000000000..858b509389423ebebea34b6c4a810c83443eb19e
--- /dev/null
+++ b/lib/galaxy/tool_util/models.py
@@ -0,0 +1,193 @@
+"""Define the ParsedTool model representing metadata extracted from a tool's source.
+
+This is abstraction exported by newer tool shed APIS (circa 2024) and should be sufficient
+for reasoning about tool state externally from Galaxy.
+"""
+
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from pydantic import (
+    AfterValidator,
+    AnyUrl,
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+)
+from typing_extensions import (
+    Annotated,
+    Literal,
+    NotRequired,
+    TypedDict,
+)
+
+from .parameters import (
+    input_models_for_tool_source,
+    ToolParameterT,
+)
+from .parser.interface import (
+    Citation,
+    HelpContent,
+    OutputCompareType,
+    ToolSource,
+    XrefDict,
+)
+from .parser.output_models import (
+    from_tool_source,
+    ToolOutput,
+)
+from .verify.assertion_models import assertions
+
+
+class ParsedTool(BaseModel):
+    id: str
+    version: Optional[str]
+    name: str
+    description: Optional[str]
+    inputs: List[ToolParameterT]
+    outputs: List[ToolOutput]
+    citations: List[Citation]
+    license: Optional[str]
+    profile: Optional[str]
+    edam_operations: List[str]
+    edam_topics: List[str]
+    xrefs: List[XrefDict]
+    help: Optional[HelpContent]
+
+
+def parse_tool(tool_source: ToolSource) -> ParsedTool:
+    id = tool_source.parse_id()
+    version = tool_source.parse_version()
+    name = tool_source.parse_name()
+    description = tool_source.parse_description()
+    inputs = input_models_for_tool_source(tool_source).parameters
+    outputs = from_tool_source(tool_source)
+    citations = tool_source.parse_citations()
+    license = tool_source.parse_license()
+    profile = tool_source.parse_profile()
+    edam_operations = tool_source.parse_edam_operations()
+    edam_topics = tool_source.parse_edam_topics()
+    xrefs = tool_source.parse_xrefs()
+    help = tool_source.parse_help()
+
+    return ParsedTool(
+        id=id,
+        version=version,
+        name=name,
+        description=description,
+        profile=profile,
+        inputs=inputs,
+        outputs=outputs,
+        license=license,
+        citations=citations,
+        edam_operations=edam_operations,
+        edam_topics=edam_topics,
+        xrefs=xrefs,
+        help=help,
+    )
+
+
+class StrictModel(BaseModel):
+
+    model_config = ConfigDict(
+        extra="forbid",
+    )
+
+
+class BaseTestOutputModel(StrictModel):
+    file: Optional[str] = None
+    path: Optional[str] = None
+    location: Optional[AnyUrl] = None
+    ftype: Optional[str] = None
+    sort: Optional[bool] = None
+    compare: Optional[OutputCompareType] = None
+    checksum: Optional[str] = None
+    metadata: Optional[Dict[str, Any]] = None
+    asserts: Optional[assertions] = None
+    delta: Optional[int] = None
+    delta_frac: Optional[float] = None
+    lines_diff: Optional[int] = None
+    decompress: Optional[bool] = None
+
+
+class TestDataOutputAssertions(BaseTestOutputModel):
+    class_: Optional[Literal["File"]] = Field("File", alias="class")
+
+
+class TestCollectionCollectionElementAssertions(StrictModel):
+    elements: Optional[Dict[str, "TestCollectionElementAssertion"]] = None
+    element_tests: Optional[Dict[str, "TestCollectionElementAssertion"]] = None
+
+
+class TestCollectionDatasetElementAssertions(BaseTestOutputModel):
+    pass
+
+
+TestCollectionElementAssertion = Union[
+    TestCollectionDatasetElementAssertions, TestCollectionCollectionElementAssertions
+]
+TestCollectionCollectionElementAssertions.model_rebuild()
+
+
+def _check_collection_type(v: str) -> str:
+    if len(v) == 0:
+        raise ValueError("Invalid empty collection_type specified.")
+    collection_levels = v.split(":")
+    for collection_level in collection_levels:
+        if collection_level not in ["list", "paired"]:
+            raise ValueError(f"Invalid collection_type specified [{v}]")
+    return v
+
+
+CollectionType = Annotated[Optional[str], AfterValidator(_check_collection_type)]
+
+
+class CollectionAttributes(StrictModel):
+    collection_type: CollectionType = None
+
+
+class TestCollectionOutputAssertions(StrictModel):
+    class_: Optional[Literal["Collection"]] = Field("Collection", alias="class")
+    elements: Optional[Dict[str, TestCollectionElementAssertion]] = None
+    element_tests: Optional[Dict[str, "TestCollectionElementAssertion"]] = None
+    element_count: Optional[int] = None
+    attributes: Optional[CollectionAttributes] = None
+    collection_type: CollectionType = None
+
+
+TestOutputLiteral = Union[bool, int, float, str]
+
+TestOutputAssertions = Union[TestCollectionOutputAssertions, TestDataOutputAssertions, TestOutputLiteral]
+
+JobDict = Dict[str, Any]
+
+
+class TestJob(StrictModel):
+    doc: Optional[str]
+    job: JobDict
+    outputs: Dict[str, TestOutputAssertions]
+    expect_failure: Optional[bool] = False
+
+
+Tests = RootModel[List[TestJob]]
+
+# TODO: typed dict versions of all thee above for verify code - make this Dict[str, Any] here more
+# specific.
+OutputChecks = Union[TestOutputLiteral, Dict[str, Any]]
+OutputsDict = Dict[str, OutputChecks]
+
+
+class TestJobDict(TypedDict):
+    doc: NotRequired[str]
+    job: NotRequired[JobDict]
+    expect_failure: NotRequired[bool]
+    outputs: OutputsDict
+
+
+TestDicts = List[TestJobDict]
diff --git a/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv b/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
index bb23dd9fc7cbff71518ad47f1fa6fec384f9f2c7..edb75127595ddab112327d0823db1e018402caf2 100644
--- a/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
+++ b/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
@@ -44,6 +44,7 @@ gffcompare	gffcompare
 sample_seqs	biopython
 seq_filter_by_id	biopython
 rxlr_motifs	signalp
+rxlr_motifs	hmmer2
 crossmap_bam	crossmap
 samtools_bam_to_cram	samtools
 crossmap_region	crossmap
@@ -132,7 +133,6 @@ samtools_fixmate	samtools
 samtool_filter2	samtools
 ngsutils_bam_filter	ngsutils
 samtools_rmdup	samtools
-sam_merge2	Broken link in tool shed
 bamhash	bamhash
 bedtools_annotatebed	bedtools
 bedtools_bed12tobed6	bedtools
@@ -260,7 +260,6 @@ fraggenescan	fraggenescan
 repeatmodeler	repeatmodeler
 promoter2	promoter
 Psortb	psortb
-rxlr_motifs	signalp hmmer2
 signalp3	signalp
 tmhmm2	tmhmm
 wolf_psort	wolf_psort
@@ -965,23 +964,23 @@ stacks2_tsv2bam	stacks
 stacks2_sstacks	stacks
 BayeScan	bayescan
 stacks2_cstacks	stacks
-NSPDK_candidateClust	graphclust, GraphClust2
-structure_to_gspan	graphclust, GraphClust2
-preproc	graphclust, GraphClust3
-preMloc	graphclust, GraphClust4
-nspdk_sparse	graphclust, GraphClust5
-locarna_best_subtree	graphclust, GraphClust6
-gspan	graphclust, GraphClust7
-glob_report	graphclust, GraphClust8
-cmFinder	graphclust, GraphClust9
-graphclust_align_cluster	graphclust, GraphClust10
-graphclust_aggregate_alignments	graphclust, GraphClust11
-graphclust_glob_report_no_align	graphclust, GraphClust12
-motifFinderPlot	graphclust, GraphClust13
+NSPDK_candidateClust	graphclust
+structure_to_gspan	graphclust
+preproc	graphclust
+preMloc	graphclust
+nspdk_sparse	graphclust
+locarna_best_subtree	graphclust
+gspan	graphclust
+glob_report	graphclust
+cmFinder	graphclust
+graphclust_align_cluster	graphclust
+graphclust_aggregate_alignments	graphclust
+graphclust_glob_report_no_align	graphclust
+motifFinderPlot	graphclust
 infernal_cmbuild	infernal
 infernal_cmsearch	infernal
 infernal_cmstat	infernal
-customize_metaphlan_database	metaphlan, seqtk
+customize_metaphlan_database	metaphlan
 merge_metaphlan_tables	metaphlan
 metabat2_jgi_summarize_bam_contig_depths	MetaBAT_2
 est_abundance	bracken
@@ -1898,10 +1897,10 @@ gatk_count_covariates	gatk
 spring_model	spring
 spring_minz	spring
 spring_cross	spring
-pubmed_by_queries	pubmed, simtext
-text_to_wordmatrix	pubmed, simtext
-abstracts_by_pmids	pubmed, simtext
-pmids_to_pubtator_matrix	pubmed, simtext
+pubmed_by_queries	pubmed
+text_to_wordmatrix	pubmed
+abstracts_by_pmids	pubmed
+pmids_to_pubtator_matrix	pubmed
 spring_model_all	spring
 spring_map	spring
 spring_mcc	spring
diff --git a/lib/galaxy/tool_util/ontologies/ontology_data.py b/lib/galaxy/tool_util/ontologies/ontology_data.py
index 9903031c17906ef02f3a7a77efcd8d58e339db6e..63a4d573b4d78955a5f5004482bc084ddac918b6 100644
--- a/lib/galaxy/tool_util/ontologies/ontology_data.py
+++ b/lib/galaxy/tool_util/ontologies/ontology_data.py
@@ -1,3 +1,4 @@
+from collections import defaultdict
 from typing import (
     cast,
     Dict,
@@ -8,7 +9,10 @@ from typing import (
 )
 
 from galaxy.tool_util.biotools import BiotoolsMetadataSource
-from galaxy.tool_util.parser import ToolSource
+from galaxy.tool_util.parser import (
+    ToolSource,
+    XrefDict,
+)
 from galaxy.util.resources import resource_string
 
 
@@ -31,13 +35,11 @@ EDAM_OPERATION_MAPPING_FILENAME = "edam_operation_mappings.tsv"
 EDAM_TOPIC_MAPPING_FILENAME = "edam_topic_mappings.tsv"
 
 BIOTOOLS_MAPPING_CONTENT = _read_ontology_data_text(BIOTOOLS_MAPPING_FILENAME)
-BIOTOOLS_MAPPING: Dict[str, str] = dict(
-    [
-        cast(Tuple[str, str], tuple(x.split("\t")))
-        for x in BIOTOOLS_MAPPING_CONTENT.splitlines()
-        if not x.startswith("#")
-    ]
-)
+BIOTOOLS_MAPPING: Dict[str, List[str]] = defaultdict(list)
+for line in BIOTOOLS_MAPPING_CONTENT.splitlines():
+    if not line.startswith("#"):
+        tool_id, xref = line.split("\t")
+        BIOTOOLS_MAPPING[tool_id].append(xref)
 EDAM_OPERATION_MAPPING_CONTENT = _read_ontology_data_text(EDAM_OPERATION_MAPPING_FILENAME)
 EDAM_OPERATION_MAPPING: Dict[str, List[str]] = _multi_dict_mapping(EDAM_OPERATION_MAPPING_CONTENT)
 
@@ -46,7 +48,7 @@ EDAM_TOPIC_MAPPING: Dict[str, List[str]] = _multi_dict_mapping(EDAM_TOPIC_MAPPIN
 
 
 class OntologyData(NamedTuple):
-    xrefs: List[Dict[str, str]]
+    xrefs: List[XrefDict]
     edam_operations: Optional[List[str]]
     edam_topics: Optional[List[str]]
 
@@ -58,11 +60,11 @@ def biotools_reference(xrefs):
     return None
 
 
-def legacy_biotools_external_reference(all_ids: List[str]) -> Optional[str]:
+def legacy_biotools_external_reference(all_ids: List[str]) -> List[str]:
     for tool_id in all_ids:
         if tool_id in BIOTOOLS_MAPPING:
             return BIOTOOLS_MAPPING[tool_id]
-    return None
+    return []
 
 
 def expand_ontology_data(
@@ -71,9 +73,9 @@ def expand_ontology_data(
     xrefs = tool_source.parse_xrefs()
     has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
     if not has_biotools_reference:
-        legacy_biotools_ref = legacy_biotools_external_reference(all_ids)
-        if legacy_biotools_ref is not None:
-            xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
+        for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
+            if legacy_biotools_ref is not None:
+                xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
 
     edam_operations = tool_source.parse_edam_operations()
     edam_topics = tool_source.parse_edam_topics()
diff --git a/lib/galaxy/tool_util/parameters/__init__.py b/lib/galaxy/tool_util/parameters/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..22dd7e6053aabd1aa6856b59058d1f2f39958b77
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/__init__.py
@@ -0,0 +1,165 @@
+from .case import (
+    test_case_state,
+    validate_test_cases_for_tool_source,
+)
+from .convert import (
+    decode,
+    dereference,
+    encode,
+    encode_test,
+    fill_static_defaults,
+    landing_decode,
+    landing_encode,
+)
+from .factory import (
+    from_input_source,
+    input_models_for_pages,
+    input_models_for_tool_source,
+    input_models_from_json,
+    ParameterDefinitionError,
+    tool_parameter_bundle_from_json,
+)
+from .json import to_json_schema_string
+from .models import (
+    BooleanParameterModel,
+    ColorParameterModel,
+    ConditionalParameterModel,
+    ConditionalWhen,
+    CwlBooleanParameterModel,
+    CwlDirectoryParameterModel,
+    CwlFileParameterModel,
+    CwlFloatParameterModel,
+    CwlIntegerParameterModel,
+    CwlNullParameterModel,
+    CwlStringParameterModel,
+    CwlUnionParameterModel,
+    DataCollectionParameterModel,
+    DataCollectionRequest,
+    DataParameterModel,
+    DataRequest,
+    DataRequestHda,
+    DataRequestInternalHda,
+    DataRequestUri,
+    FloatParameterModel,
+    HiddenParameterModel,
+    IntegerParameterModel,
+    LabelValue,
+    RawStateDict,
+    RepeatParameterModel,
+    RulesParameterModel,
+    SelectParameterModel,
+    TextParameterModel,
+    ToolParameterBundle,
+    ToolParameterBundleModel,
+    ToolParameterModel,
+    ToolParameterT,
+    validate_against_model,
+    validate_internal_job,
+    validate_internal_landing_request,
+    validate_internal_request,
+    validate_internal_request_dereferenced,
+    validate_landing_request,
+    validate_request,
+    validate_test_case,
+    validate_workflow_step,
+    validate_workflow_step_linked,
+    ValidationFunctionT,
+)
+from .state import (
+    JobInternalToolState,
+    LandingRequestInternalToolState,
+    LandingRequestToolState,
+    RequestInternalDereferencedToolState,
+    RequestInternalToolState,
+    RequestToolState,
+    TestCaseToolState,
+    ToolState,
+    WorkflowStepLinkedToolState,
+    WorkflowStepToolState,
+)
+from .visitor import (
+    flat_state_path,
+    keys_starting_with,
+    repeat_inputs_to_array,
+    validate_explicit_conditional_test_value,
+    visit_input_values,
+    VISITOR_NO_REPLACEMENT,
+)
+
+__all__ = (
+    "from_input_source",
+    "input_models_for_pages",
+    "input_models_for_tool_source",
+    "tool_parameter_bundle_from_json",
+    "input_models_from_json",
+    "ParameterDefinitionError",
+    "JobInternalToolState",
+    "ToolParameterBundle",
+    "ToolParameterBundleModel",
+    "DataRequest",
+    "DataRequestInternalHda",
+    "DataRequestHda",
+    "DataRequestUri",
+    "DataCollectionRequest",
+    "ToolParameterModel",
+    "IntegerParameterModel",
+    "BooleanParameterModel",
+    "CwlFileParameterModel",
+    "CwlFloatParameterModel",
+    "CwlIntegerParameterModel",
+    "CwlStringParameterModel",
+    "CwlNullParameterModel",
+    "CwlUnionParameterModel",
+    "CwlBooleanParameterModel",
+    "CwlDirectoryParameterModel",
+    "TextParameterModel",
+    "FloatParameterModel",
+    "HiddenParameterModel",
+    "ColorParameterModel",
+    "RulesParameterModel",
+    "DataParameterModel",
+    "DataCollectionParameterModel",
+    "LabelValue",
+    "SelectParameterModel",
+    "ConditionalParameterModel",
+    "ConditionalWhen",
+    "RepeatParameterModel",
+    "RawStateDict",
+    "ValidationFunctionT",
+    "validate_against_model",
+    "validate_internal_job",
+    "validate_internal_landing_request",
+    "validate_internal_request",
+    "validate_internal_request_dereferenced",
+    "validate_landing_request",
+    "validate_request",
+    "validate_test_case",
+    "validate_workflow_step",
+    "validate_workflow_step_linked",
+    "validate_explicit_conditional_test_value",
+    "ToolState",
+    "TestCaseToolState",
+    "ToolParameterT",
+    "to_json_schema_string",
+    "test_case_state",
+    "validate_test_cases_for_tool_source",
+    "RequestToolState",
+    "RequestInternalToolState",
+    "RequestInternalDereferencedToolState",
+    "LandingRequestToolState",
+    "LandingRequestInternalToolState",
+    "flat_state_path",
+    "keys_starting_with",
+    "visit_input_values",
+    "repeat_inputs_to_array",
+    "VISITOR_NO_REPLACEMENT",
+    "decode",
+    "encode",
+    "encode_test",
+    "fill_static_defaults",
+    "landing_decode",
+    "landing_encode",
+    "dereference",
+    "WorkflowStepToolState",
+    "WorkflowStepLinkedToolState",
+)
diff --git a/lib/galaxy/tool_util/parameters/_types.py b/lib/galaxy/tool_util/parameters/_types.py
new file mode 100644
index 0000000000000000000000000000000000000000..64fa9a3274fc0db439c597eb99dc7fc5ad328c89
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/_types.py
@@ -0,0 +1,59 @@
+"""Type utilities for building pydantic models for tool parameters.
+
+Lots of mypy exceptions in here - this code is all well tested and the exceptions
+are fine otherwise because we're using the typing system to interact with pydantic
+and build runtime models not to use mypy to type check static code.
+"""
+
+from typing import (
+    Any,
+    cast,
+    List,
+    Optional,
+    Type,
+    Union,
+)
+
+# https://stackoverflow.com/questions/56832881/check-if-a-field-is-typing-optional
+from typing_extensions import (
+    Annotated,
+    get_args,
+    get_origin,
+)
+
+
+def optional(type: Type) -> Type:
+    return_type: Type = Optional[type]  # type: ignore[assignment]
+    return return_type
+
+
+def optional_if_needed(type: Type, is_optional: bool) -> Type:
+    return_type: Type = type
+    if is_optional:
+        return_type = optional(type)
+    return return_type
+
+
+def union_type(args: List[Type]) -> Type:
+    return Union[tuple(args)]  # type: ignore[return-value]
+
+
+def list_type(arg: Type) -> Type:
+    return List[arg]  # type: ignore[valid-type]
+
+
+def cast_as_type(arg) -> Type:
+    return cast(Type, arg)
+
+
+def is_optional(field) -> bool:
+    return get_origin(field) is Union and type(None) in get_args(field)
+
+
+def expand_annotation(field: Type, new_annotations: List[Any]) -> Type:
+    is_annotation = get_origin(field) is Annotated
+    if is_annotation:
+        args = get_args(field)  # noqa: F841
+        return Annotated[tuple([args[0], *args[1:], *new_annotations])]  # type: ignore[return-value]
+    else:
+        return Annotated[tuple([field, *new_annotations])]  # type: ignore[return-value]
diff --git a/lib/galaxy/tool_util/parameters/case.py b/lib/galaxy/tool_util/parameters/case.py
new file mode 100644
index 0000000000000000000000000000000000000000..c371d5e3b12ecdab7d2099ef61a5284fa3ef16c9
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/case.py
@@ -0,0 +1,340 @@
+from dataclasses import dataclass
+from re import compile
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Set,
+)
+
+from packaging.version import Version
+
+from galaxy.tool_util.parser.interface import (
+    TestCollectionDef,
+    ToolSource,
+    ToolSourceTest,
+    ToolSourceTestInput,
+    ToolSourceTestInputs,
+    xml_data_input_to_json,
+    XmlTestCollectionDefDict,
+)
+from galaxy.util import asbool
+from .factory import input_models_for_tool_source
+from .models import (
+    BooleanParameterModel,
+    ConditionalParameterModel,
+    ConditionalWhen,
+    DataCollectionParameterModel,
+    DataColumnParameterModel,
+    DataParameterModel,
+    FloatParameterModel,
+    IntegerParameterModel,
+    RepeatParameterModel,
+    SectionParameterModel,
+    ToolParameterT,
+)
+from .state import TestCaseToolState
+from .visitor import (
+    flat_state_path,
+    repeat_inputs_to_array,
+    validate_explicit_conditional_test_value,
+)
+
+INTEGER_STR_PATTERN = compile(r"^(\d+)$")
+INTEGERS_STR_PATTERN = compile(r"^(\d+)(\s*,\s*(\d+))*$")
+COLUMN_NAME_STR_PATTERN = compile(r"^c(\d+): .*$")
+# In an effort to squeeze all the ambiguity out of test cases - at some point Marius and John
+# agree tools should be using value_json for typed inputs to parameters but John has come around on
+# this now that we're validating the parameters as a whole on load. The models are ensuring only
+# unambigious test cases are being loaded.
+WARN_ON_UNTYPED_XML_STRINGS = False
+
+
+@dataclass
+class TestCaseStateAndWarnings:
+    tool_state: TestCaseToolState
+    warnings: List[str]
+    unhandled_inputs: List[str]
+
+
+@dataclass
+class TestCaseStateValidationResult:
+    tool_state: TestCaseToolState
+    warnings: List[str]
+    validation_error: Optional[Exception]
+    tool_parameter_bundle: List[ToolParameterT]
+    profile: str
+
+    def to_dict(self):
+        tool_state_json = self.tool_state.input_state
+        warnings = self.warnings
+        validation_error = str(self.validation_error) if self.validation_error else None
+        return {
+            "tool_state": tool_state_json,
+            "warnings": warnings,
+            "validation_error": validation_error,
+            "validated_with_profile": self.profile,
+        }
+
+
+def legacy_from_string(parameter: ToolParameterT, value: Optional[Any], warnings: List[str], profile: str) -> Any:
+    """Convert string values in XML test cases into typed variants.
+
+    This should only be used when parsing XML test cases into a TestCaseToolState object.
+    We have to maintain backward compatibility on these for older Galaxy tool profile versions.
+    """
+    result_value: Any = value
+    if isinstance(value, str):
+        value_str = cast(str, value)
+        if isinstance(parameter, (IntegerParameterModel,)):
+            if WARN_ON_UNTYPED_XML_STRINGS:
+                warnings.append(
+                    f"Implicitly converted {parameter.name} to an integer from a string value, please use 'value_json' to define this test input parameter value instead."
+                )
+            result_value = int(value_str)
+        elif isinstance(parameter, (FloatParameterModel,)):
+            if WARN_ON_UNTYPED_XML_STRINGS:
+                warnings.append(
+                    f"Implicitly converted {parameter.name} to a floating point number from a string value, please use 'value_json' to define this test input parameter value instead."
+                )
+            result_value = float(value_str)
+        elif isinstance(parameter, (BooleanParameterModel,)):
+            if WARN_ON_UNTYPED_XML_STRINGS:
+                warnings.append(
+                    f"Implicitly converted {parameter.name} to a boolean from a string value, please use 'value_json' to define this test input parameter value instead."
+                )
+            try:
+                result_value = asbool(value_str)
+            except ValueError:
+                warnings.append(
+                    "Likely using deprected truevalue/falsevalue in tool parameter - switch to 'true' or 'false'"
+                )
+        elif isinstance(parameter, (DataColumnParameterModel,)):
+            if parameter.multiple:
+                integers_match = INTEGER_STR_PATTERN.match(value_str)
+                if integers_match:
+                    if WARN_ON_UNTYPED_XML_STRINGS:
+                        warnings.append(
+                            f"Implicitly converted {parameter.name} to a column index integer from a string value, please use 'value_json' to define this test input parameter value instead."
+                        )
+                    result_value = [int(v.strip()) for v in value_str.split(",")]
+            else:
+                integer_match = INTEGER_STR_PATTERN.match(value_str)
+                if integer_match:
+                    if WARN_ON_UNTYPED_XML_STRINGS:
+                        warnings.append(
+                            f"Implicitly converted {parameter.name} to a column index integer from a string value, please use 'value_json' to define this test input parameter value instead."
+                        )
+                    result_value = int(value_str)
+                elif Version(profile) < Version("24.2"):
+                    # allow this for older tools but new tools will just require the integer index
+                    warnings.append(
+                        f"Using column names as test case values is deprecated, please adjust {parameter.name} to just use an integer column index."
+                    )
+                    column_name_value_match = COLUMN_NAME_STR_PATTERN.match(value_str)
+                    if column_name_value_match:
+                        column_part = column_name_value_match.group(1)
+                        result_value = int(column_part)
+    return result_value
+
+
+def test_case_state(
+    test_dict: ToolSourceTest, tool_parameter_bundle: List[ToolParameterT], profile: str, validate: bool = True
+) -> TestCaseStateAndWarnings:
+    warnings: List[str] = []
+    inputs: ToolSourceTestInputs = test_dict["inputs"]
+    unhandled_inputs = []
+    state: Dict[str, Any] = {}
+
+    handled_inputs = _merge_level_into_state(tool_parameter_bundle, inputs, state, profile, warnings, None)
+
+    for test_input in inputs:
+        input_name = test_input["name"]
+        if input_name not in handled_inputs:
+            unhandled_inputs.append(input_name)
+
+    tool_state = TestCaseToolState(state)
+    if validate:
+        tool_state.validate(tool_parameter_bundle)
+        for input_name in unhandled_inputs:
+            raise Exception(f"Invalid parameter name found {input_name}")
+    return TestCaseStateAndWarnings(tool_state, warnings, unhandled_inputs)
+
+
+def test_case_validation(
+    test_dict: ToolSourceTest, tool_parameter_bundle: List[ToolParameterT], profile: str, name: Optional[str] = None
+) -> TestCaseStateValidationResult:
+    test_case_state_and_warnings = test_case_state(test_dict, tool_parameter_bundle, profile, validate=False)
+    exception: Optional[Exception] = None
+    try:
+        test_case_state_and_warnings.tool_state.validate(tool_parameter_bundle, name=name)
+        for input_name in test_case_state_and_warnings.unhandled_inputs:
+            raise Exception(f"Invalid parameter name found {input_name}")
+    except Exception as e:
+        exception = e
+    return TestCaseStateValidationResult(
+        test_case_state_and_warnings.tool_state,
+        test_case_state_and_warnings.warnings,
+        exception,
+        tool_parameter_bundle,
+        profile,
+    )
+
+
+def _merge_level_into_state(
+    tool_inputs: List[ToolParameterT],
+    inputs: ToolSourceTestInputs,
+    state_at_level: dict,
+    profile: str,
+    warnings: List[str],
+    prefix: Optional[str],
+) -> Set[str]:
+    handled_inputs: Set[str] = set()
+    for tool_input in tool_inputs:
+        handled_inputs.update(_merge_into_state(tool_input, inputs, state_at_level, profile, warnings, prefix))
+
+    return handled_inputs
+
+
+def _inputs_as_dict(inputs: ToolSourceTestInputs) -> Dict[str, ToolSourceTestInput]:
+    as_dict: Dict[str, ToolSourceTestInput] = {}
+    for input in inputs:
+        as_dict[input["name"]] = input
+
+    return as_dict
+
+
+def _merge_into_state(
+    tool_input: ToolParameterT,
+    inputs: ToolSourceTestInputs,
+    state_at_level: dict,
+    profile: str,
+    warnings: List[str],
+    prefix: Optional[str],
+) -> Set[str]:
+    handled_inputs = set()
+
+    input_name = tool_input.name
+    state_path = flat_state_path(input_name, prefix)
+    handled_inputs.add(state_path)
+
+    if isinstance(tool_input, (ConditionalParameterModel,)):
+        conditional_state = state_at_level.get(input_name, {})
+        if input_name not in state_at_level:
+            state_at_level[input_name] = conditional_state
+
+        conditional = cast(ConditionalParameterModel, tool_input)
+        when: ConditionalWhen = _select_which_when(conditional, conditional_state, inputs, state_path)
+        test_parameter = conditional.test_parameter
+        handled_inputs.update(
+            _merge_into_state(test_parameter, inputs, conditional_state, profile, warnings, state_path)
+        )
+        handled_inputs.update(
+            _merge_level_into_state(when.parameters, inputs, conditional_state, profile, warnings, state_path)
+        )
+    elif isinstance(tool_input, (RepeatParameterModel,)):
+        repeat_state_array = state_at_level.get(input_name, [])
+        if input_name not in state_at_level:
+            state_at_level[input_name] = repeat_state_array
+
+        repeat = cast(RepeatParameterModel, tool_input)
+        repeat_instance_inputs = repeat_inputs_to_array(state_path, _inputs_as_dict(inputs))
+        for i, _ in enumerate(repeat_instance_inputs):
+            while len(repeat_state_array) <= i:
+                repeat_state_array.append({})
+
+            repeat_instance_prefix = f"{state_path}_{i}"
+            handled_inputs.update(
+                _merge_level_into_state(
+                    repeat.parameters, inputs, repeat_state_array[i], profile, warnings, repeat_instance_prefix
+                )
+            )
+    elif isinstance(tool_input, (SectionParameterModel,)):
+        section_state = state_at_level.get(input_name, {})
+        if input_name not in state_at_level:
+            state_at_level[input_name] = section_state
+
+        section = cast(SectionParameterModel, tool_input)
+        handled_inputs.update(
+            _merge_level_into_state(section.parameters, inputs, section_state, profile, warnings, state_path)
+        )
+    else:
+        test_input = _input_for(state_path, inputs)
+        if test_input is not None:
+            input_value: Any
+            if isinstance(tool_input, (DataCollectionParameterModel,)):
+                input_value = TestCollectionDef.from_dict(
+                    cast(XmlTestCollectionDefDict, test_input.get("attributes", {}).get("collection"))
+                ).test_format_to_dict()
+            elif isinstance(tool_input, (DataParameterModel,)):
+                data_tool_input = cast(DataParameterModel, tool_input)
+                if data_tool_input.multiple:
+                    value = test_input["value"]
+                    input_value_list = []
+                    if value:
+                        test_input_values = cast(str, value).split(",")
+                        for test_input_value in test_input_values:
+                            instance_test_input = test_input.copy()
+                            instance_test_input["value"] = test_input_value
+                            input_value_json = xml_data_input_to_json(instance_test_input)
+                            input_value_list.append(input_value_json)
+                    input_value = input_value_list
+                else:
+                    input_value = xml_data_input_to_json(test_input)
+            else:
+                input_value = test_input["value"]
+                input_value = legacy_from_string(tool_input, input_value, warnings, profile)
+
+            state_at_level[input_name] = input_value
+
+    return handled_inputs
+
+
+def _select_which_when(
+    conditional: ConditionalParameterModel, state: dict, inputs: ToolSourceTestInputs, prefix: str
+) -> ConditionalWhen:
+    test_parameter = conditional.test_parameter
+    is_boolean = test_parameter.parameter_type == "gx_boolean"
+    test_parameter_name = test_parameter.name
+    test_parameter_flat_path = flat_state_path(test_parameter_name, prefix)
+
+    test_input = _input_for(test_parameter_flat_path, inputs)
+    explicit_test_value = test_input["value"] if test_input else None
+    if is_boolean and isinstance(explicit_test_value, str):
+        explicit_test_value = asbool(explicit_test_value)
+    test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
+    for when in conditional.whens:
+        if test_value is None and when.is_default_when:
+            return when
+        elif test_value == when.discriminator:
+            return when
+    else:
+        raise Exception(f"Invalid conditional test value ({explicit_test_value}) for parameter ({test_parameter_name})")
+
+
+def _input_for(flat_state_path: str, inputs: ToolSourceTestInputs) -> Optional[ToolSourceTestInput]:
+    for input in inputs:
+        if input["name"] == flat_state_path:
+            return input
+    else:
+        return None
+
+
+def validate_test_cases_for_tool_source(
+    tool_source: ToolSource, use_latest_profile: bool = False, name: Optional[str] = None
+) -> List[TestCaseStateValidationResult]:
+    name = name or f"PydanticModelFor[{tool_source.parse_id()}]"
+    tool_parameter_bundle = input_models_for_tool_source(tool_source)
+    if use_latest_profile:
+        # this might get old but it is fine, just needs to be updated when test case changes are made
+        profile = "24.2"
+    else:
+        profile = tool_source.parse_profile()
+    test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]
+    results_by_test: List[TestCaseStateValidationResult] = []
+    for test_case in test_cases:
+        validation_result = test_case_validation(test_case, tool_parameter_bundle.parameters, profile, name=name)
+        results_by_test.append(validation_result)
+    return results_by_test
diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
new file mode 100644
index 0000000000000000000000000000000000000000..63dbb9ab58b97cab332bd4b5315493d0c3c92e4d
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/convert.py
@@ -0,0 +1,407 @@
+"""Utilities for converting between request states.
+"""
+
+import logging
+from typing import (
+    Any,
+    Callable,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from galaxy.tool_util.parser.interface import (
+    JsonTestCollectionDefDict,
+    JsonTestDatasetDefDict,
+)
+from .models import (
+    BooleanParameterModel,
+    ConditionalParameterModel,
+    ConditionalWhen,
+    DataCollectionRequest,
+    DataColumnParameterModel,
+    DataParameterModel,
+    DataRequestHda,
+    DataRequestInternalHda,
+    DataRequestUri,
+    DiscriminatorType,
+    DrillDownParameterModel,
+    FloatParameterModel,
+    GenomeBuildParameterModel,
+    HiddenParameterModel,
+    IntegerParameterModel,
+    RepeatParameterModel,
+    SectionParameterModel,
+    SelectParameterModel,
+    ToolParameterBundle,
+    ToolParameterT,
+)
+from .state import (
+    JobInternalToolState,
+    LandingRequestInternalToolState,
+    LandingRequestToolState,
+    RequestInternalDereferencedToolState,
+    RequestInternalToolState,
+    RequestToolState,
+    TestCaseToolState,
+)
+from .visitor import (
+    Callback,
+    validate_explicit_conditional_test_value,
+    visit_input_values,
+    VISITOR_NO_REPLACEMENT,
+)
+
+log = logging.getLogger(__name__)
+
+
+DecodeFunctionT = Callable[[str], int]
+EncodeFunctionT = Callable[[int], str]
+DereferenceCallable = Callable[[DataRequestUri], DataRequestInternalHda]
+# interfaces for adapting test data dictionaries to tool request dictionaries
+# e.g. {class: File, path: foo.bed} => {src: hda, id: ab1235cdfea3}
+AdaptDatasets = Callable[[JsonTestDatasetDefDict], DataRequestHda]
+AdaptCollections = Callable[[JsonTestCollectionDefDict], DataCollectionRequest]
+
+
+def decode(
+    external_state: RequestToolState, input_models: ToolParameterBundle, decode_id: Callable[[str], int]
+) -> RequestInternalToolState:
+    """Prepare an internal representation of tool state (request_internal) for storing in the database."""
+
+    external_state.validate(input_models)
+    decode_callback = _decode_callback_for(decode_id)
+    internal_state_dict = visit_input_values(
+        input_models,
+        external_state,
+        decode_callback,
+    )
+
+    internal_request_state = RequestInternalToolState(internal_state_dict)
+    internal_request_state.validate(input_models)
+    return internal_request_state
+
+
+def encode(
+    internal_state: RequestInternalToolState, input_models: ToolParameterBundle, encode_id: EncodeFunctionT
+) -> RequestToolState:
+    """Prepare an external representation of tool state (request) from persisted state in the database (request_internal)."""
+
+    encode_callback = _encode_callback_for(encode_id)
+    request_state_dict = visit_input_values(
+        input_models,
+        internal_state,
+        encode_callback,
+    )
+    request_state = RequestToolState(request_state_dict)
+    request_state.validate(input_models)
+    return request_state
+
+
+def landing_decode(
+    external_state: LandingRequestToolState, input_models: ToolParameterBundle, decode_id: Callable[[str], int]
+) -> LandingRequestInternalToolState:
+    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+
+    external_state.validate(input_models)
+    decode_callback = _decode_callback_for(decode_id)
+    internal_state_dict = visit_input_values(
+        input_models,
+        external_state,
+        decode_callback,
+    )
+
+    internal_request_state = LandingRequestInternalToolState(internal_state_dict)
+    internal_request_state.validate(input_models)
+    return internal_request_state
+
+
+def landing_encode(
+    internal_state: LandingRequestInternalToolState, input_models: ToolParameterBundle, encode_id: EncodeFunctionT
+) -> LandingRequestToolState:
+    """Prepare an external representation of tool state (request) for storing in the database (request_internal)."""
+
+    encode_callback = _encode_callback_for(encode_id)
+    request_state_dict = visit_input_values(
+        input_models,
+        internal_state,
+        encode_callback,
+    )
+    request_state = LandingRequestToolState(request_state_dict)
+    request_state.validate(input_models)
+    return request_state
+
+
+def dereference(
+    internal_state: RequestInternalToolState, input_models: ToolParameterBundle, dereference: DereferenceCallable
+) -> RequestInternalDereferencedToolState:
+
+    def derefrence_dict(src_dict: dict):
+        src = src_dict.get("src")
+        if src == "url":
+            data_request_uri: DataRequestUri = DataRequestUri.model_validate(src_dict)
+            data_request_hda: DataRequestInternalHda = dereference(data_request_uri)
+            return data_request_hda.model_dump()
+        else:
+            return src_dict
+
+    def dereference_callback(parameter: ToolParameterT, value: Any):
+        if parameter.parameter_type == "gx_data":
+            if value is None:
+                return VISITOR_NO_REPLACEMENT
+            data_parameter = cast(DataParameterModel, parameter)
+            if data_parameter.multiple:
+                assert isinstance(value, list), str(value)
+                return list(map(derefrence_dict, value))
+            else:
+                assert isinstance(value, dict), str(value)
+                return derefrence_dict(value)
+        else:
+            return VISITOR_NO_REPLACEMENT
+
+    request_state_dict = visit_input_values(
+        input_models,
+        internal_state,
+        dereference_callback,
+    )
+    request_state = RequestInternalDereferencedToolState(request_state_dict)
+    request_state.validate(input_models)
+    return request_state
+
+
+def encode_test(
+    test_case_state: TestCaseToolState,
+    input_models: ToolParameterBundle,
+    adapt_datasets: AdaptDatasets,
+    adapt_collections: AdaptCollections,
+):
+
+    def encode_callback(parameter: ToolParameterT, value: Any):
+        if parameter.parameter_type == "gx_data":
+            data_parameter = cast(DataParameterModel, parameter)
+            if value is not None:
+                if data_parameter.multiple:
+                    assert isinstance(value, list), str(value)
+                    test_datasets = cast(List[JsonTestDatasetDefDict], value)
+                    return [d.model_dump() for d in map(adapt_datasets, test_datasets)]
+                else:
+                    assert isinstance(value, dict), str(value)
+                    test_dataset = cast(JsonTestDatasetDefDict, value)
+                    return adapt_datasets(test_dataset).model_dump()
+        elif parameter.parameter_type == "gx_data_collection":
+            # data_collection_parameter = cast(DataCollectionParameterModel, parameter)
+            if value is not None:
+                assert isinstance(value, dict), str(value)
+                test_collection = cast(JsonTestCollectionDefDict, value)
+                return adapt_collections(test_collection).model_dump()
+        elif parameter.parameter_type == "gx_select":
+            select_parameter = cast(SelectParameterModel, parameter)
+            if select_parameter.multiple and value is not None:
+                return [v.strip() for v in value.split(",")]
+            else:
+                return VISITOR_NO_REPLACEMENT
+        elif parameter.parameter_type == "gx_drill_down":
+            drilldown = cast(DrillDownParameterModel, parameter)
+            if drilldown.multiple and value is not None:
+                return [v.strip() for v in value.split(",")]
+            else:
+                return VISITOR_NO_REPLACEMENT
+        elif parameter.parameter_type == "gx_data_column":
+            data_column = cast(DataColumnParameterModel, parameter)
+            is_multiple = data_column.multiple
+            if is_multiple and value is not None and isinstance(value, (str,)):
+                return [int(v.strip()) for v in value.split(",")]
+            else:
+                return VISITOR_NO_REPLACEMENT
+
+        return VISITOR_NO_REPLACEMENT
+
+    request_state_dict = visit_input_values(
+        input_models,
+        test_case_state,
+        encode_callback,
+    )
+    request_state = RequestToolState(request_state_dict)
+    request_state.validate(input_models)
+    return request_state
+
+
+def fill_static_defaults(
+    tool_state: Dict[str, Any], input_models: ToolParameterBundle, profile: float, partial: bool = True
+) -> Dict[str, Any]:
+    """If additional defaults might stem from Galaxy runtime, partial should be true.
+
+    Setting partial to True, prevents runtime validation.
+    """
+    _fill_defaults(tool_state, input_models)
+
+    if not partial:
+        internal_state = JobInternalToolState(tool_state)
+        internal_state.validate(input_models)
+    return tool_state
+
+
+def _fill_defaults(tool_state: Dict[str, Any], input_models: ToolParameterBundle) -> None:
+    for parameter in input_models.parameters:
+        _fill_default_for(tool_state, parameter)
+
+
+def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) -> None:
+    parameter_name = parameter.name
+    parameter_type = parameter.parameter_type
+    if parameter_type == "gx_boolean":
+        boolean = cast(BooleanParameterModel, parameter)
+        if parameter_name not in tool_state:
+            # even optional parameters default to false if not in the body of the request :_(
+            # see test_tools.py -> expression_null_handling_boolean or test cases for gx_boolean_optional.xml
+            tool_state[parameter_name] = boolean.value or False
+
+    if parameter_type in ["gx_integer", "gx_float", "gx_hidden"]:
+        has_value_parameter = cast(
+            Union[
+                IntegerParameterModel,
+                FloatParameterModel,
+                HiddenParameterModel,
+            ],
+            parameter,
+        )
+        if parameter_name not in tool_state:
+            tool_state[parameter_name] = has_value_parameter.value
+    elif parameter_type == "gx_genomebuild":
+        genomebuild = cast(GenomeBuildParameterModel, parameter)
+        if parameter_name not in tool_state and genomebuild.optional:
+            tool_state[parameter_name] = None
+    elif parameter_type == "gx_select":
+        select = cast(SelectParameterModel, parameter)
+        # don't fill in dynamic parameters - wait for runtime to specify the default
+        if select.dynamic_options:
+            return
+
+        if parameter_name not in tool_state:
+            if not select.multiple:
+                tool_state[parameter_name] = select.default_value
+            else:
+                tool_state[parameter_name] = None
+    elif parameter_type == "gx_drill_down":
+        if parameter_name not in tool_state:
+            drilldown = cast(DrillDownParameterModel, parameter)
+            if drilldown.multiple:
+                options = drilldown.default_options
+                if options is not None:
+                    tool_state[parameter_name] = options
+            else:
+                option = drilldown.default_option
+                if option is not None:
+                    tool_state[parameter_name] = option
+    elif parameter_type in ["gx_conditional"]:
+        if parameter_name not in tool_state:
+            tool_state[parameter_name] = {}
+
+        raw_conditional_state = tool_state[parameter_name]
+        assert isinstance(raw_conditional_state, dict)
+        conditional_state = cast(Dict[str, Any], raw_conditional_state)
+
+        conditional = cast(ConditionalParameterModel, parameter)
+        test_parameter = conditional.test_parameter
+        test_parameter_name = test_parameter.name
+
+        explicit_test_value: Optional[DiscriminatorType] = (
+            conditional_state[test_parameter_name] if test_parameter_name in conditional_state else None
+        )
+        test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
+        when = _select_which_when(conditional, test_value, conditional_state)
+        _fill_default_for(conditional_state, test_parameter)
+        _fill_defaults(conditional_state, when)
+    elif parameter_type in ["gx_repeat"]:
+        if parameter_name not in tool_state:
+            tool_state[parameter_name] = []
+        repeat_instances = cast(List[Dict[str, Any]], tool_state[parameter_name])
+        repeat = cast(RepeatParameterModel, parameter)
+        if repeat.min:
+            while len(repeat_instances) < repeat.min:
+                repeat_instances.append({})
+
+        for instance_state in tool_state[parameter_name]:
+            _fill_defaults(instance_state, repeat)
+    elif parameter_type in ["gx_section"]:
+        if parameter_name not in tool_state:
+            tool_state[parameter_name] = {}
+        section_state = cast(Dict[str, Any], tool_state[parameter_name])
+        section = cast(SectionParameterModel, parameter)
+        _fill_defaults(section_state, section)
+
+
+def _select_which_when(
+    conditional: ConditionalParameterModel, test_value: Optional[DiscriminatorType], conditional_state: Dict[str, Any]
+) -> ConditionalWhen:
+    for when in conditional.whens:
+        if test_value is None and when.is_default_when:
+            return when
+        elif test_value == when.discriminator:
+            return when
+    else:
+        raise Exception(
+            f"Invalid conditional test value ({test_value}) for parameter ({conditional.test_parameter.name})"
+        )
+
+
+def _encode_callback_for(encode_id: EncodeFunctionT) -> Callback:
+
+    def encode_src_dict(src_dict: dict):
+        if "id" in src_dict:
+            encoded_dict = src_dict.copy()
+            encoded_dict["id"] = encode_id(src_dict["id"])
+            return encoded_dict
+        else:
+            return src_dict
+
+    def encode_callback(parameter: ToolParameterT, value: Any):
+        if parameter.parameter_type == "gx_data":
+            data_parameter = cast(DataParameterModel, parameter)
+            if data_parameter.multiple:
+                assert isinstance(value, list), str(value)
+                return list(map(encode_src_dict, value))
+            else:
+                assert isinstance(value, dict), str(value)
+                return encode_src_dict(value)
+        elif parameter.parameter_type == "gx_data_collection":
+            assert isinstance(value, dict), str(value)
+            return encode_src_dict(value)
+        else:
+            return VISITOR_NO_REPLACEMENT
+
+    return encode_callback
+
+
+def _decode_callback_for(decode_id: DecodeFunctionT) -> Callback:
+
+    def decode_src_dict(src_dict: dict):
+        if "id" in src_dict:
+            decoded_dict = src_dict.copy()
+            decoded_dict["id"] = decode_id(src_dict["id"])
+            return decoded_dict
+        else:
+            return src_dict
+
+    def decode_callback(parameter: ToolParameterT, value: Any):
+        if parameter.parameter_type == "gx_data":
+            if value is None:
+                return VISITOR_NO_REPLACEMENT
+            data_parameter = cast(DataParameterModel, parameter)
+            if data_parameter.multiple:
+                assert isinstance(value, list), str(value)
+                return list(map(decode_src_dict, value))
+            else:
+                assert isinstance(value, dict), str(value)
+                return decode_src_dict(value)
+        elif parameter.parameter_type == "gx_data_collection":
+            if value is None:
+                return VISITOR_NO_REPLACEMENT
+            assert isinstance(value, dict), str(value)
+            return decode_src_dict(value)
+        else:
+            return VISITOR_NO_REPLACEMENT
+
+    return decode_callback
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
new file mode 100644
index 0000000000000000000000000000000000000000..a659992aa5ecd580f86c2951ef779feda219e8be
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/factory.py
@@ -0,0 +1,444 @@
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from galaxy.tool_util.parser.cwl import CwlInputSource
+from galaxy.tool_util.parser.interface import (
+    InputSource,
+    PageSource,
+    PagesSource,
+    ToolSource,
+)
+from galaxy.tool_util.parser.parameter_validators import (
+    EmptyFieldParameterValidatorModel,
+    ExpressionParameterValidatorModel,
+    InRangeParameterValidatorModel,
+    LengthParameterValidatorModel,
+    NoOptionsParameterValidatorModel,
+    RegexParameterValidatorModel,
+    static_validators,
+)
+from galaxy.tool_util.parser.util import (
+    parse_profile_version,
+    text_input_is_optional,
+)
+from galaxy.util import string_as_bool
+from .models import (
+    BaseUrlParameterModel,
+    BooleanParameterModel,
+    ColorParameterModel,
+    cond_test_parameter_default_value,
+    ConditionalParameterModel,
+    ConditionalWhen,
+    CwlBooleanParameterModel,
+    CwlDirectoryParameterModel,
+    CwlFileParameterModel,
+    CwlFloatParameterModel,
+    CwlIntegerParameterModel,
+    CwlNullParameterModel,
+    CwlStringParameterModel,
+    CwlUnionParameterModel,
+    DataCollectionParameterModel,
+    DataColumnParameterModel,
+    DataParameterModel,
+    DirectoryUriParameterModel,
+    DrillDownParameterModel,
+    FloatParameterModel,
+    GenomeBuildParameterModel,
+    GroupTagParameterModel,
+    HiddenParameterModel,
+    IntegerParameterModel,
+    LabelValue,
+    NumberCompatiableValidators,
+    RepeatParameterModel,
+    RulesParameterModel,
+    SectionParameterModel,
+    SelectCompatiableValidators,
+    SelectParameterModel,
+    TextCompatiableValidators,
+    TextParameterModel,
+    ToolParameterBundle,
+    ToolParameterBundleModel,
+    ToolParameterT,
+)
+
+
+class ParameterDefinitionError(Exception):
+    pass
+
+
+class UnknownParameterTypeError(ParameterDefinitionError):
+    pass
+
+
+def get_color_value(input_source: InputSource) -> str:
+    return input_source.get("value", "#000000")
+
+
+def _from_input_source_galaxy(input_source: InputSource, profile: float) -> ToolParameterT:
+    input_type = input_source.parse_input_type()
+    if input_type == "param":
+        param_type = input_source.get("type")
+        if param_type == "integer":
+            optional = input_source.parse_optional()
+            value = input_source.get("value")
+            int_value: Optional[int]
+            if value:
+                int_value = int(value)
+            elif optional:
+                int_value = None
+            elif value == "" or value is None:
+                # A truly required parameter: https://github.com/galaxyproject/galaxy/pull/16966/files
+                int_value = None
+            else:
+                raise ParameterDefinitionError()
+            static_validator_models = static_validators(input_source.parse_validators())
+            int_validators: List[NumberCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "in_range":
+                    int_validators.append(cast(InRangeParameterValidatorModel, static_validator))
+            min_raw = input_source.get("min", None)
+            max_raw = input_source.get("max", None)
+            min_int = int(min_raw) if min_raw is not None else None
+            max_int = int(max_raw) if max_raw is not None else None
+            return IntegerParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                value=int_value,
+                min=min_int,
+                max=max_int,
+                validators=int_validators,
+            )
+        elif param_type == "boolean":
+            nullable = input_source.parse_optional()
+            value = input_source.get_bool_or_none("checked", None if nullable else False)
+            return BooleanParameterModel(
+                name=input_source.parse_name(),
+                optional=nullable,
+                value=value,
+            )
+        elif param_type == "text":
+            optional, optionality_inferred = text_input_is_optional(input_source)
+            text_validators: List[TextCompatiableValidators] = _text_validators(input_source)
+            return TextParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                validators=text_validators,
+            )
+        elif param_type == "float":
+            optional = input_source.parse_optional()
+            value = input_source.get("value")
+            float_value: Optional[float]
+            if value:
+                float_value = float(value)
+            elif optional:
+                float_value = None
+            elif value == "" or value is None:
+                # See note above for matching integer handling.
+                float_value = None
+            else:
+                raise ParameterDefinitionError()
+            static_validator_models = static_validators(input_source.parse_validators())
+            float_validators: List[NumberCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "in_range":
+                    float_validators.append(cast(InRangeParameterValidatorModel, static_validator))
+            min_raw = input_source.get("min", None)
+            max_raw = input_source.get("max", None)
+            min_float = float(min_raw) if min_raw is not None else None
+            max_float = float(max_raw) if max_raw is not None else None
+            return FloatParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                value=float_value,
+                min=min_float,
+                max=max_float,
+                validators=float_validators,
+            )
+        elif param_type == "hidden":
+            optional = input_source.parse_optional()
+            value = input_source.get("value")
+            hidden_validators: List[TextCompatiableValidators] = _text_validators(input_source)
+            return HiddenParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                value=value,
+                validators=hidden_validators,
+            )
+        elif param_type == "color":
+            optional = input_source.parse_optional()
+            return ColorParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                value=get_color_value(input_source),
+            )
+        elif param_type == "rules":
+            return RulesParameterModel(
+                name=input_source.parse_name(),
+            )
+        elif param_type == "data":
+            optional = input_source.parse_optional()
+            multiple = input_source.get_bool("multiple", False)
+            return DataParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                multiple=multiple,
+            )
+        elif param_type == "data_collection":
+            optional = input_source.parse_optional()
+            default_value = input_source.parse_default()
+            return DataCollectionParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                value=default_value,
+            )
+        elif param_type == "select":
+            # Function... example in devteam cummeRbund.
+            optional = input_source.parse_optional()
+            dynamic_options_config = input_source.parse_dynamic_options()
+            is_static = dynamic_options_config is None
+            multiple = input_source.get_bool("multiple", False)
+            options: Optional[List[LabelValue]] = None
+            if is_static:
+                options = []
+                for option_label, option_value, selected in input_source.parse_static_options():
+                    options.append(LabelValue(label=option_label, value=option_value, selected=selected))
+            static_validator_models = static_validators(input_source.parse_validators())
+            select_validators: List[SelectCompatiableValidators] = []
+            for static_validator in static_validator_models:
+                if static_validator.type == "no_options":
+                    select_validators.append(cast(NoOptionsParameterValidatorModel, static_validator))
+            return SelectParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                options=options,
+                multiple=multiple,
+                validators=select_validators,
+            )
+        elif param_type == "drill_down":
+            multiple = input_source.get_bool("multiple", False)
+            hierarchy = input_source.get("hierarchy", "exact")
+            dynamic_options = input_source.parse_drill_down_dynamic_options()
+            static_options = None
+            if dynamic_options is None:
+                static_options = input_source.parse_drill_down_static_options()
+            return DrillDownParameterModel(
+                name=input_source.parse_name(),
+                multiple=multiple,
+                hierarchy=hierarchy,
+                options=static_options,
+            )
+        elif param_type == "data_column":
+            multiple = input_source.get_bool("multiple", False)
+            optional = input_source.parse_optional()
+            return DataColumnParameterModel(
+                name=input_source.parse_name(),
+                multiple=multiple,
+                optional=optional,
+            )
+        elif param_type == "group_tag":
+            multiple = input_source.get_bool("multiple", False)
+            optional = input_source.parse_optional()
+            return GroupTagParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                multiple=multiple,
+            )
+        elif param_type == "baseurl":
+            return BaseUrlParameterModel(
+                name=input_source.parse_name(),
+            )
+        elif param_type == "genomebuild":
+            optional = input_source.parse_optional()
+            multiple = input_source.get_bool("multiple", False)
+            return GenomeBuildParameterModel(
+                name=input_source.parse_name(),
+                optional=optional,
+                multiple=multiple,
+            )
+        elif param_type == "directory_uri":
+            directory_uri_validators: List[TextCompatiableValidators] = _text_validators(input_source)
+            return DirectoryUriParameterModel(
+                name=input_source.parse_name(),
+                validators=directory_uri_validators,
+            )
+        else:
+            raise UnknownParameterTypeError(f"Unknown Galaxy parameter type {param_type}")
+    elif input_type == "conditional":
+        test_param_input_source = input_source.parse_test_input_source()
+        test_parameter = cast(
+            Union[BooleanParameterModel, SelectParameterModel],
+            _from_input_source_galaxy(test_param_input_source, profile),
+        )
+        whens = []
+        default_test_value = cond_test_parameter_default_value(test_parameter)
+        for value, case_inputs_sources in input_source.parse_when_input_sources():
+            if isinstance(test_parameter, BooleanParameterModel):
+                true_value = test_param_input_source.get("truevalue")
+                false_value = test_param_input_source.get("falsevalue")
+                if isinstance(value, str) and value == true_value:
+                    value = True
+                elif isinstance(value, str) and value == false_value:
+                    value = False
+                typed_value = string_as_bool(value)
+            else:
+                typed_value = value
+
+            tool_parameter_models = input_models_for_page(case_inputs_sources, profile)
+            is_default_when = False
+            if typed_value == default_test_value:
+                is_default_when = True
+            whens.append(
+                ConditionalWhen(
+                    discriminator=typed_value, parameters=tool_parameter_models, is_default_when=is_default_when
+                )
+            )
+        return ConditionalParameterModel(
+            name=input_source.parse_name(),
+            test_parameter=test_parameter,
+            whens=whens,
+        )
+    elif input_type == "repeat":
+        name = input_source.get("name")
+        # title = input_source.get("title")
+        # help = input_source.get("help", None)
+        instance_sources = input_source.parse_nested_inputs_source()
+        instance_tool_parameter_models = input_models_for_page(instance_sources, profile)
+        min_raw = input_source.get("min", None)
+        max_raw = input_source.get("max", None)
+        min = int(min_raw) if min_raw is not None else None
+        max = int(max_raw) if max_raw is not None else None
+        return RepeatParameterModel(
+            name=name,
+            parameters=instance_tool_parameter_models,
+            min=min,
+            max=max,
+        )
+    elif input_type == "section":
+        name = input_source.get("name")
+        instance_sources = input_source.parse_nested_inputs_source()
+        instance_tool_parameter_models = input_models_for_page(instance_sources, profile)
+        return SectionParameterModel(
+            name=name,
+            parameters=instance_tool_parameter_models,
+        )
+    else:
+        raise Exception(
+            f"Cannot generate tool parameter model for supplied tool source - unknown input_type {input_type}"
+        )
+
+
+def _simple_cwl_type_to_model(simple_type: str, input_source: CwlInputSource):
+    if simple_type == "int":
+        return CwlIntegerParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "float":
+        return CwlFloatParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "null":
+        return CwlNullParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "string":
+        return CwlStringParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "boolean":
+        return CwlBooleanParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "org.w3id.cwl.cwl.File":
+        return CwlFileParameterModel(
+            name=input_source.parse_name(),
+        )
+    elif simple_type == "org.w3id.cwl.cwl.Directory":
+        return CwlDirectoryParameterModel(
+            name=input_source.parse_name(),
+        )
+    raise NotImplementedError(
+        f"Cannot generate tool parameter model for this CWL artifact yet - contains unknown type {simple_type}."
+    )
+
+
+def _text_validators(input_source: InputSource) -> List[TextCompatiableValidators]:
+    static_validator_models = static_validators(input_source.parse_validators())
+    text_validators: List[TextCompatiableValidators] = []
+    for static_validator in static_validator_models:
+        if static_validator.type == "length":
+            text_validators.append(cast(LengthParameterValidatorModel, static_validator))
+        elif static_validator.type == "regex":
+            text_validators.append(cast(RegexParameterValidatorModel, static_validator))
+        elif static_validator.type == "expression":
+            text_validators.append(cast(ExpressionParameterValidatorModel, static_validator))
+        elif static_validator.type == "empty_field":
+            text_validators.append(cast(EmptyFieldParameterValidatorModel, static_validator))
+    return text_validators
+
+
+def _from_input_source_cwl(input_source: CwlInputSource) -> ToolParameterT:
+    schema_salad_field = input_source.field
+    if schema_salad_field is None:
+        raise NotImplementedError("Cannot generate tool parameter model for this CWL artifact yet.")
+    if "type" not in schema_salad_field:
+        raise NotImplementedError("Cannot generate tool parameter model for this CWL artifact yet.")
+    schema_salad_type = schema_salad_field["type"]
+    if isinstance(schema_salad_type, str):
+        return _simple_cwl_type_to_model(schema_salad_type, input_source)
+    elif isinstance(schema_salad_type, list):
+        return CwlUnionParameterModel(
+            name=input_source.parse_name(),
+            parameters=[_simple_cwl_type_to_model(t, input_source) for t in schema_salad_type],
+        )
+    else:
+        raise NotImplementedError("Cannot generate tool parameter model for this CWL artifact yet.")
+
+
+def input_models_from_json(json: List[Dict[str, Any]]) -> ToolParameterBundle:
+    return ToolParameterBundleModel(parameters=json)
+
+
+def tool_parameter_bundle_from_json(json: Dict[str, Any]) -> ToolParameterBundleModel:
+    return ToolParameterBundleModel(**json)
+
+
+def input_models_for_tool_source(tool_source: ToolSource) -> ToolParameterBundleModel:
+    pages = tool_source.parse_input_pages()
+    profile = parse_profile_version(tool_source)
+    return ToolParameterBundleModel(parameters=input_models_for_pages(pages, profile))
+
+
+def input_models_for_pages(pages: PagesSource, profile: float) -> List[ToolParameterT]:
+    input_models = []
+    if pages.inputs_defined:
+        for page_source in pages.page_sources:
+            input_models.extend(input_models_for_page(page_source, profile))
+
+    return input_models
+
+
+def input_models_for_page(page_source: PageSource, profile: float) -> List[ToolParameterT]:
+    input_models = []
+    for input_source in page_source.parse_input_sources():
+        input_type = input_source.parse_input_type()
+        if input_type == "display":
+            # not a real input... just skip this. Should this be handled in the parser layer better?
+            continue
+        tool_parameter_model = from_input_source(input_source, profile)
+        input_models.append(tool_parameter_model)
+    return input_models
+
+
+def from_input_source(input_source: InputSource, profile: float) -> ToolParameterT:
+    tool_parameter: ToolParameterT
+    if isinstance(input_source, CwlInputSource):
+        tool_parameter = _from_input_source_cwl(input_source)
+    else:
+        tool_parameter = _from_input_source_galaxy(input_source, profile)
+    return tool_parameter
diff --git a/lib/galaxy/tool_util/parameters/json.py b/lib/galaxy/tool_util/parameters/json.py
new file mode 100644
index 0000000000000000000000000000000000000000..6796353a4fb7380c9fe5401febb3104809cb64d2
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/json.py
@@ -0,0 +1,27 @@
+import json
+from typing import (
+    Any,
+    Dict,
+)
+
+from pydantic.json_schema import GenerateJsonSchema
+from typing_extensions import Literal
+
+MODE = Literal["validation", "serialization"]
+DEFAULT_JSON_SCHEMA_MODE: MODE = "validation"
+
+
+class CustomGenerateJsonSchema(GenerateJsonSchema):
+
+    def generate(self, schema, mode: MODE = DEFAULT_JSON_SCHEMA_MODE):
+        json_schema = super().generate(schema, mode=mode)
+        json_schema["$schema"] = self.schema_dialect
+        return json_schema
+
+
+def to_json_schema(model, mode: MODE = DEFAULT_JSON_SCHEMA_MODE) -> Dict[str, Any]:
+    return model.model_json_schema(schema_generator=CustomGenerateJsonSchema, mode=mode)
+
+
+def to_json_schema_string(model, mode: MODE = DEFAULT_JSON_SCHEMA_MODE) -> str:
+    return json.dumps(to_json_schema(model, mode=mode), indent=4)
diff --git a/lib/galaxy/tool_util/parameters/models.py b/lib/galaxy/tool_util/parameters/models.py
new file mode 100644
index 0000000000000000000000000000000000000000..9979d4ffd985a3241c3522c6d98ec2f9f7afa15f
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/models.py
@@ -0,0 +1,1576 @@
+# attempt to model requires_value...
+# conditional can descend...
+from abc import abstractmethod
+from typing import (
+    Any,
+    Callable,
+    cast,
+    Dict,
+    Iterable,
+    List,
+    Mapping,
+    NamedTuple,
+    Optional,
+    Sequence,
+    Type,
+    TypeVar,
+    Union,
+)
+
+from pydantic import (
+    AfterValidator,
+    AnyUrl,
+    BaseModel,
+    ConfigDict,
+    create_model,
+    Discriminator,
+    Field,
+    field_validator,
+    HttpUrl,
+    RootModel,
+    StrictBool,
+    StrictFloat,
+    StrictInt,
+    StrictStr,
+    Tag,
+    ValidationError,
+)
+from typing_extensions import (
+    Annotated,
+    Literal,
+    Protocol,
+)
+
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.tool_util.parser.interface import (
+    DrillDownOptionsDict,
+    JsonTestCollectionDefDict,
+    JsonTestDatasetDefDict,
+)
+from galaxy.tool_util.parser.parameter_validators import (
+    EmptyFieldParameterValidatorModel,
+    ExpressionParameterValidatorModel,
+    InRangeParameterValidatorModel,
+    LengthParameterValidatorModel,
+    NoOptionsParameterValidatorModel,
+    RegexParameterValidatorModel,
+    StaticValidatorModel,
+)
+from ._types import (
+    cast_as_type,
+    expand_annotation,
+    is_optional,
+    list_type,
+    optional,
+    optional_if_needed,
+    union_type,
+)
+
+# TODO:
+# - implement data_ref on rules and implement some cross model validation
+
+# + request: Return info needed to build request pydantic model at runtime.
+# + request_internal: This is a pydantic model to validate what Galaxy expects to find in the database,
+# in particular dataset and collection references should be decoded integers.
+StateRepresentationT = Literal[
+    "request",
+    "request_internal",
+    "request_internal_dereferenced",
+    "landing_request",
+    "landing_request_internal",
+    "job_internal",
+    "test_case_xml",
+    "workflow_step",
+    "workflow_step_linked",
+]
+
+DEFAULT_MODEL_NAME = "DynamicModelForTool"
+RawStateDict = Dict[str, Any]
+
+
+# could be made more specific - validators need to be classmethod
+ValidatorDictT = Dict[str, Callable]
+
+
+class DynamicModelInformation(NamedTuple):
+    name: str
+    definition: tuple
+    validators: ValidatorDictT
+
+
+class StrictModel(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+
+class ConnectedValue(BaseModel):
+    discriminator: Literal["ConnectedValue"] = Field(alias="__class__")
+
+
+def allow_connected_value(type: Type):
+    return union_type([type, ConnectedValue])
+
+
+def allow_batching(job_template: DynamicModelInformation, batch_type: Optional[Type] = None) -> DynamicModelInformation:
+    job_py_type: Type = job_template.definition[0]
+    default_value = job_template.definition[1]
+    batch_type = batch_type or job_py_type
+
+    class BatchRequest(StrictModel):
+        meta_class: Literal["Batch"] = Field(..., alias="__class__")
+        values: List[batch_type]  # type: ignore[valid-type]
+
+    request_type = union_type([job_py_type, BatchRequest])
+
+    return DynamicModelInformation(
+        job_template.name,
+        (request_type, default_value),
+        {},  # should we modify these somehow?
+    )
+
+
+class Validators:
+    def validate_not_none(cls, v):
+        assert v is not None, "null is an invalid value for attribute"
+        return v
+
+
+class ParamModel(Protocol):
+    @property
+    def name(self) -> str: ...
+
+    @property
+    def request_requires_value(self) -> bool:
+        # if this is a non-optional type and no default is defined - an
+        # input value MUST be specified.
+        ...
+
+
+def safe_field_name(name: str) -> str:
+    if name.startswith("_"):
+        return f"X{name}"
+    return name
+
+
+def dynamic_model_information_from_py_type(
+    param_model: ParamModel, py_type: Type, requires_value: Optional[bool] = None, validators=None
+):
+    name = safe_field_name(param_model.name)
+    if requires_value is None:
+        requires_value = param_model.request_requires_value
+    initialize = ... if requires_value else None
+    py_type_is_optional = is_optional(py_type)
+    validators = validators or {}
+    if not py_type_is_optional and not requires_value:
+        validators["not_null"] = field_validator(name)(Validators.validate_not_none)
+
+    return DynamicModelInformation(
+        name,
+        (py_type, Field(initialize, alias=param_model.name if param_model.name != name else None)),
+        validators,
+    )
+
+
+# We probably need incoming (parameter def) and outgoing (parameter value as transmitted) models,
+# where value in the incoming model means "default value" and value in the outgoing model is the actual
+# value a user has set. (incoming/outgoing from the client perspective).
+class BaseToolParameterModelDefinition(BaseModel):
+    name: str
+    parameter_type: str
+
+    @abstractmethod
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        """Return info needed to build Pydantic model at runtime for validation."""
+
+
+class BaseGalaxyToolParameterModelDefinition(BaseToolParameterModelDefinition):
+    hidden: bool = False
+    label: Optional[str] = None
+    help: Optional[str] = None
+    argument: Optional[str] = None
+    is_dynamic: bool = False
+    optional: bool = False
+
+
+class LabelValue(BaseModel):
+    label: str
+    value: str
+    selected: bool
+
+
+TextCompatiableValidators = Union[
+    LengthParameterValidatorModel,
+    RegexParameterValidatorModel,
+    ExpressionParameterValidatorModel,
+    EmptyFieldParameterValidatorModel,
+]
+
+
+def pydantic_to_galaxy_type(value: Any) -> Any:
+    """We use advanced Pydantic types like URL but the Galaxy validators only expect strings for these."""
+    if isinstance(value, AnyUrl):
+        return str(value)
+
+    return value
+
+
+VT = TypeVar("VT", bound=StaticValidatorModel)
+
+
+def decorate_type_with_validators_if_needed(py_type: Type, static_validator_models: Sequence[VT]) -> Type:
+    pydantic_validator = pydantic_validator_for(static_validator_models)
+    if pydantic_validator:
+        return expand_annotation(py_type, [pydantic_validator])
+    else:
+        return py_type
+
+
+# Looks like Annotated only work with one PlainValidator so condensing all static validators
+# into a single PlainValidator for pydantic.
+def pydantic_validator_for(static_validator_models: Sequence[VT]) -> Optional[AfterValidator]:
+
+    if static_validator_models:
+
+        def validator(v: Any) -> Any:
+            gx_val = pydantic_to_galaxy_type(v)
+
+            for static_validator_model in static_validator_models:
+                static_validator_model.statically_validate(gx_val)
+            return v
+
+        return AfterValidator(validator)
+    else:
+        return None
+
+
+class TextParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_text"] = "gx_text"
+    area: bool = False
+    default_value: Optional[str] = Field(default=None, alias="value")
+    default_options: List[LabelValue] = []
+    validators: List[TextCompatiableValidators] = []
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(StrictStr, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = decorate_type_with_validators_if_needed(self.py_type, self.validators)
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False
+
+
+NumberCompatiableValidators = Union[InRangeParameterValidatorModel,]
+
+
+class IntegerParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_integer"] = "gx_integer"
+    optional: bool
+    value: Optional[int] = None
+    min: Optional[int] = None
+    max: Optional[int] = None
+    validators: List[NumberCompatiableValidators] = []
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(StrictInt, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        validators = self.validators[:]
+        if self.min is not None or self.max is not None:
+            validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
+        py_type = decorate_type_with_validators_if_needed(py_type, validators)
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return not self.optional and self.value is None
+
+
+class FloatParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_float"] = "gx_float"
+    value: Optional[float] = None
+    min: Optional[float] = None
+    max: Optional[float] = None
+    validators: List[NumberCompatiableValidators] = []
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(union_type([StrictInt, StrictFloat]), self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
+        validators = self.validators[:]
+        if self.min is not None or self.max is not None:
+            validators.append(InRangeParameterValidatorModel(min=self.min, max=self.max, implicit=True))
+        py_type = decorate_type_with_validators_if_needed(py_type, validators)
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False
+
+
+DataSrcT = Literal["hda", "ldda"]
+MultiDataSrcT = Literal["hda", "ldda", "hdca"]
+CollectionStrT = Literal["hdca"]
+
+TestCaseDataSrcT = Literal["File"]
+
+
+class DataRequestHda(StrictModel):
+    src: Literal["hda"] = "hda"
+    id: StrictStr
+
+
+class DataRequestLdda(StrictModel):
+    src: Literal["ldda"] = "ldda"
+    id: StrictStr
+
+
+class DataRequestHdca(StrictModel):
+    src: Literal["hdca"] = "hdca"
+    id: StrictStr
+
+
+class DatasetHash(StrictModel):
+    hash_function: Literal["MD5", "SHA-1", "SHA-256", "SHA-512"]
+    hash_value: StrictStr
+
+
+class DataRequestUri(StrictModel):
+    # calling it url instead of uri to match data fetch schema...
+    src: Literal["url"] = "url"
+    url: StrictStr
+    name: Optional[StrictStr] = None
+    ext: StrictStr
+    dbkey: StrictStr = "?"
+    deferred: StrictBool = False
+    created_from_basename: Optional[StrictStr] = None
+    info: Optional[StrictStr] = None
+    hashes: Optional[List[DatasetHash]] = None
+    space_to_tab: bool = False
+    to_posix_lines: bool = False
+    # to implement:
+    # tags
+
+
+DataRequest: Type = cast(
+    Type, Annotated[union_type([DataRequestHda, DataRequestLdda, DataRequestUri]), Field(discriminator="src")]
+)
+
+
+class BatchDataInstance(StrictModel):
+    src: MultiDataSrcT
+    id: StrictStr
+
+
+MultiDataInstance: Type = cast(
+    Type,
+    Annotated[
+        union_type([DataRequestHda, DataRequestLdda, DataRequestHdca, DataRequestUri]), Field(discriminator="src")
+    ],
+)
+MultiDataRequest: Type = cast(Type, union_type([MultiDataInstance, list_type(MultiDataInstance)]))
+
+
+class DataRequestInternalHda(StrictModel):
+    src: Literal["hda"] = "hda"
+    id: StrictInt
+
+
+class DataRequestInternalLdda(StrictModel):
+    src: Literal["ldda"] = "ldda"
+    id: StrictInt
+
+
+class DataRequestInternalHdca(StrictModel):
+    src: Literal["hdca"] = "hdca"
+    id: StrictInt
+
+
+DataRequestInternal: Type = cast(
+    Type, Annotated[Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestUri], Field(discriminator="src")]
+)
+DataRequestInternalDereferenced: Type = cast(
+    Type, Annotated[Union[DataRequestInternalHda, DataRequestInternalLdda], Field(discriminator="src")]
+)
+DataJobInternal = DataRequestInternalDereferenced
+
+
+class BatchDataInstanceInternal(StrictModel):
+    src: MultiDataSrcT
+    id: StrictInt
+
+
+MultiDataInstanceInternal: Type = cast(
+    Type,
+    Annotated[
+        Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca, DataRequestUri],
+        Field(discriminator="src"),
+    ],
+)
+MultiDataInstanceInternalDereferenced: Type = cast(
+    Type,
+    Annotated[
+        Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca], Field(discriminator="src")
+    ],
+)
+
+MultiDataRequestInternal: Type = union_type([MultiDataInstanceInternal, list_type(MultiDataInstanceInternal)])
+MultiDataRequestInternalDereferenced: Type = union_type(
+    [MultiDataInstanceInternalDereferenced, list_type(MultiDataInstanceInternalDereferenced)]
+)
+
+
+class DataParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_data"] = "gx_data"
+    extensions: List[str] = ["data"]
+    multiple: bool = False
+    min: Optional[int] = None
+    max: Optional[int] = None
+
+    @property
+    def py_type(self) -> Type:
+        base_model: Type
+        if self.multiple:
+            base_model = MultiDataRequest
+        else:
+            base_model = DataRequest
+        return optional_if_needed(base_model, self.optional)
+
+    @property
+    def py_type_internal(self) -> Type:
+        base_model: Type
+        if self.multiple:
+            base_model = MultiDataRequestInternal
+        else:
+            base_model = DataRequestInternal
+        return optional_if_needed(base_model, self.optional)
+
+    @property
+    def py_type_internal_dereferenced(self) -> Type:
+        base_model: Type
+        if self.multiple:
+            base_model = MultiDataRequestInternalDereferenced
+        else:
+            base_model = DataRequestInternalDereferenced
+        return optional_if_needed(base_model, self.optional)
+
+    @property
+    def py_type_test_case(self) -> Type:
+        base_model: Type
+        if self.multiple:
+            base_model = list_type(JsonTestDatasetDefDict)
+        else:
+            base_model = JsonTestDatasetDefDict
+        return optional_if_needed(base_model, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        if state_representation == "request":
+            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type), BatchDataInstance)
+        if state_representation == "landing_request":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type, requires_value=False), BatchDataInstance
+            )
+        elif state_representation == "request_internal":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal), BatchDataInstanceInternal
+            )
+        elif state_representation == "landing_request_internal":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False),
+                BatchDataInstanceInternal,
+            )
+        elif state_representation == "request_internal_dereferenced":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal_dereferenced),
+                BatchDataInstanceInternal,
+            )
+        elif state_representation == "job_internal":
+            return dynamic_model_information_from_py_type(self, self.py_type_internal_dereferenced, requires_value=True)
+        elif state_representation == "test_case_xml":
+            return dynamic_model_information_from_py_type(self, self.py_type_test_case)
+        elif state_representation == "workflow_step":
+            return dynamic_model_information_from_py_type(self, type(None), requires_value=False)
+        elif state_representation == "workflow_step_linked":
+            return dynamic_model_information_from_py_type(self, ConnectedValue)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return not self.optional
+
+
+class DataCollectionRequest(StrictModel):
+    src: CollectionStrT
+    id: StrictStr
+
+
+class DataCollectionRequestInternal(StrictModel):
+    src: CollectionStrT
+    id: StrictInt
+
+
+class DataCollectionParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_data_collection"] = "gx_data_collection"
+    collection_type: Optional[str] = None
+    extensions: List[str] = ["data"]
+    value: Optional[Dict[str, Any]]
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(DataCollectionRequest, self.optional)
+
+    @property
+    def py_type_internal(self) -> Type:
+        return optional_if_needed(DataCollectionRequestInternal, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        if state_representation == "request":
+            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type))
+        elif state_representation == "landing_request":
+            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type, requires_value=False))
+        elif state_representation == "landing_request_internal":
+            return allow_batching(
+                dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=False)
+            )
+        elif state_representation in ["request_internal", "request_internal_dereferenced"]:
+            return allow_batching(dynamic_model_information_from_py_type(self, self.py_type_internal))
+        elif state_representation == "job_internal":
+            return dynamic_model_information_from_py_type(self, self.py_type_internal, requires_value=True)
+        elif state_representation == "workflow_step":
+            return dynamic_model_information_from_py_type(self, type(None), requires_value=False)
+        elif state_representation == "workflow_step_linked":
+            return dynamic_model_information_from_py_type(self, ConnectedValue)
+        elif state_representation == "test_case_xml":
+            return dynamic_model_information_from_py_type(self, JsonTestCollectionDefDict)
+        else:
+            raise NotImplementedError(
+                f"Have not implemented data collection parameter models for state representation {state_representation}"
+            )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return not self.optional and self.value is None
+
+
+class HiddenParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_hidden"] = "gx_hidden"
+    value: Optional[str]
+    validators: List[TextCompatiableValidators] = []
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(StrictStr, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        requires_value = not self.optional and self.value is None
+        py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        elif state_representation == "workflow_step" and not self.optional:
+            # allow it to be linked in so force allow optional...
+            py_type = optional(py_type)
+            requires_value = False
+        elif state_representation == "job_internal":
+            requires_value = True
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return not self.optional and self.value is None
+
+
+def ensure_color_valid(value: Optional[Any]):
+    if value is None:
+        return
+    if not isinstance(value, str):
+        raise ValueError(f"Invalid color value type {value.__class__} encountered.")
+    value_str: str = value
+    message = f"Invalid color value string format {value_str} encountered."
+    if len(value_str) != 7:
+        raise ValueError(message + "0")
+    if value_str[0] != "#":
+        raise ValueError(message + "1")
+    for byte_str in value_str[1:]:
+        if byte_str not in "0123456789abcdef":
+            raise ValueError(message + "2")
+
+
+class ColorParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_color"] = "gx_color"
+    value: Optional[str] = None
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(StrictStr, self.optional)
+
+    @staticmethod
+    def validate_color_str(value) -> str:
+        ensure_color_valid(value)
+        return value
+
+    @staticmethod
+    def validate_color_str_if_value(value) -> str:
+        if value:
+            ensure_color_valid(value)
+        return value
+
+    @staticmethod
+    def validate_color_str_or_connected_value(value) -> str:
+        if not isinstance(value, ConnectedValue):
+            ensure_color_valid(value)
+        return value
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        initialize: Any = ...
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+            validators = {
+                "color_format": field_validator(self.name)(ColorParameterModel.validate_color_str_or_connected_value)
+            }
+        elif state_representation == "workflow_step":
+            initialize = None
+            validators = {"color_format": field_validator(self.name)(ColorParameterModel.validate_color_str_if_value)}
+        else:
+            validators = {"color_format": field_validator(self.name)(ColorParameterModel.validate_color_str)}
+        return DynamicModelInformation(
+            self.name,
+            (py_type, initialize),
+            validators,
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False
+
+
+class BooleanParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_boolean"] = "gx_boolean"
+    value: Optional[bool] = False
+    truevalue: Optional[str] = None
+    falsevalue: Optional[str] = None
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(StrictBool, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        # these parameters always have an implicit default - either None if
+        # if it is optional or 'checked' if not (itself defaulting to False).
+        return False
+
+
+class DirectoryUriParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_directory_uri"] = "gx_directory_uri"
+    validators: List[TextCompatiableValidators] = []
+
+    @property
+    def py_type(self) -> Type:
+        return AnyUrl
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type
+        py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
+        if state_representation == "workflow_step_linked":
+            py_type = allow_connected_value(py_type)
+        requires_value = self.request_requires_value
+        if _is_landing_request(state_representation):
+            requires_value = False
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class RulesMapping(StrictModel):
+    type: str
+    columns: List[StrictInt]
+
+
+class RulesModel(StrictModel):
+    rules: List[Dict[str, Any]]
+    mappings: List[RulesMapping]
+
+
+class RulesParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_rules"] = "gx_rules"
+
+    @property
+    def py_type(self) -> Type:
+        return RulesModel
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+SelectCompatiableValidators = Union[NoOptionsParameterValidatorModel,]
+
+
+class SelectParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_select"] = "gx_select"
+    options: Optional[List[LabelValue]] = None
+    multiple: bool
+    validators: List[SelectCompatiableValidators]
+
+    @staticmethod
+    def split_str(cls, data: Any) -> Any:
+        if isinstance(data, str):
+            return [x.strip() for x in data.split(",")]
+
+        return data
+
+    def py_type_if_required(self, allow_connections: bool = False) -> Type:
+        if self.options is not None:
+            if len(self.options) > 0:
+                literal_options: List[Type] = [cast_as_type(Literal[o.value]) for o in self.options]
+                py_type = union_type(literal_options)
+            else:
+                py_type = type(None)
+        else:
+            py_type = StrictStr
+        if self.multiple:
+            if allow_connections:
+                py_type = list_type(allow_connected_value(py_type))
+            else:
+                py_type = list_type(py_type)
+        elif allow_connections:
+            py_type = allow_connected_value(py_type)
+        return py_type
+
+    @property
+    def py_type(self) -> Type:
+        return optional_if_needed(self.py_type_if_required(), self.optional or self.multiple)
+
+    @property
+    def py_type_workflow_step(self) -> Type:
+        # this is always optional in this context
+        return optional(self.py_type_if_required())
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        validators = {}
+        requires_value = self.request_requires_value
+        py_type = None
+        if state_representation == "workflow_step":
+            py_type = self.py_type_workflow_step
+        elif state_representation == "workflow_step_linked":
+            py_type = self.py_type_if_required(allow_connections=True)
+            py_type = optional_if_needed(py_type, self.optional or self.multiple)
+        elif state_representation == "test_case_xml":
+            # in a YAML test case representation this can be string, in XML we are still expecting a comma separated string
+            py_type = self.py_type_if_required(allow_connections=False)
+            if self.multiple:
+                validators = {"from_string": field_validator(self.name, mode="before")(SelectParameterModel.split_str)}
+            py_type = optional_if_needed(py_type, self.optional)
+        elif state_representation == "job_internal":
+            requires_value = True
+            py_type = self.py_type
+        else:
+            py_type = self.py_type
+
+        py_type = decorate_type_with_validators_if_needed(py_type, self.validators)
+        return dynamic_model_information_from_py_type(
+            self, py_type, validators=validators, requires_value=requires_value
+        )
+
+    @property
+    def has_selected_static_option(self):
+        return self.options is not None and any(o.selected for o in self.options)
+
+    @property
+    def default_value(self) -> Optional[str]:
+        if self.options:
+            for option in self.options:
+                if option.selected:
+                    return option.value
+            # single value pick up first value
+            if not self.optional:
+                return self.options[0].value
+
+        return None
+
+    @property
+    def request_requires_value(self) -> bool:
+        # API will allow an empty value and just grab the first static option
+        # see API Tests -> test_tools.py -> test_select_first_by_default
+        # If it is multiple - it will also always just allow null regardless of
+        # optional - see test_select_multiple_null_handling
+        return False
+
+    @property
+    def dynamic_options(self) -> bool:
+        return self.options is None
+
+
+class GenomeBuildParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_genomebuild"] = "gx_genomebuild"
+    multiple: bool
+
+    @property
+    def py_type(self) -> Type:
+        py_type: Type = StrictStr
+        if self.multiple:
+            py_type = list_type(py_type)
+        return optional_if_needed(py_type, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        # assumes it uses behavior of select parameters - an API test to reference for this would be nice
+        return self.multiple and not self.optional
+
+
+DrillDownHierarchyT = Literal["recurse", "exact"]
+
+
+def drill_down_possible_values(
+    options: List[DrillDownOptionsDict], multiple: bool, hierarchy: DrillDownHierarchyT
+) -> List[str]:
+    possible_values = []
+
+    def add_value(option: str, is_leaf: bool):
+        if not multiple and not is_leaf and hierarchy == "recurse":
+            return
+        possible_values.append(option)
+
+    def walk_selection(option: DrillDownOptionsDict):
+        child_options = option["options"]
+        is_leaf = not child_options
+        add_value(option["value"], is_leaf)
+        if not is_leaf:
+            for child_option in child_options:
+                walk_selection(child_option)
+
+    for option in options:
+        walk_selection(option)
+
+    return possible_values
+
+
+class DrillDownParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_drill_down"] = "gx_drill_down"
+    options: Optional[List[DrillDownOptionsDict]] = None
+    multiple: bool
+    hierarchy: DrillDownHierarchyT
+
+    @property
+    def py_type(self) -> Type:
+        if self.options is not None:
+            literal_options: List[Type] = [
+                cast_as_type(Literal[o])
+                for o in drill_down_possible_values(self.options, self.multiple, self.hierarchy)
+            ]
+            py_type = union_type(literal_options)
+        else:
+            py_type = StrictStr
+
+        if self.multiple:
+            py_type = list_type(py_type)
+
+        return py_type
+
+    @property
+    def py_type_test_case_xml(self) -> Type:
+        base_model = str
+        return optional_if_needed(base_model, not self.request_requires_value)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        py_type = self.py_type_test_case_xml if state_representation == "test_case_xml" else self.py_type
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+
+        return dynamic_model_information_from_py_type(self, py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        options = self.options
+        if options:
+            # if any of these are selected, they seem to serve as defaults - check out test_tools -> test_drill_down_first_by_default
+            return not any_drill_down_options_selected(options)
+        else:
+            # I'm not sure how to handle dynamic options... they might or might not be required?
+            # do we need to default to assuming they're not required?
+            return False
+
+    @property
+    def default_option(self) -> Optional[str]:
+        options = self.options
+        if options:
+            selected_options = selected_drill_down_options(options)
+            if len(selected_options) > 0:
+                return selected_options[0]
+        return None
+
+    @property
+    def default_options(self) -> Optional[List[str]]:
+        options = self.options
+        if options:
+            selected_options = selected_drill_down_options(options)
+            return selected_options
+
+        return None
+
+
+def any_drill_down_options_selected(options: List[DrillDownOptionsDict]) -> bool:
+    for option in options:
+        selected = option.get("selected")
+        if selected:
+            return True
+        child_options = option.get("options", [])
+        if any_drill_down_options_selected(child_options):
+            return True
+
+    return False
+
+
+def selected_drill_down_options(options: List[DrillDownOptionsDict]) -> List[str]:
+    selected_options: List[str] = []
+    for option in options:
+        selected = option.get("selected")
+        value = option.get("value")
+        if selected and value:
+            selected_options.append(value)
+        child_options = option.get("options", [])
+        selected_options.extend(selected_drill_down_options(child_options))
+
+    return selected_options
+
+
+class DataColumnParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_data_column"] = "gx_data_column"
+    multiple: bool
+
+    @staticmethod
+    def split_str(cls, data: Any) -> Any:
+        if isinstance(data, str):
+            return [int(x.strip()) for x in data.split(",")]
+        elif isinstance(data, int):
+            return [data]
+
+        return data
+
+    @property
+    def py_type(self) -> Type:
+        py_type: Type = StrictInt
+        if self.multiple:
+            py_type = list_type(py_type)
+        return optional_if_needed(py_type, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        if state_representation == "test_case_xml":
+            if self.multiple:
+                validators = {
+                    "from_string": field_validator(self.name, mode="before")(DataColumnParameterModel.split_str)
+                }
+            else:
+                validators = {}
+            return dynamic_model_information_from_py_type(self, self.py_type, validators=validators)
+        else:
+            requires_value = self.request_requires_value
+            if state_representation == "job_internal":
+                requires_value = True
+            return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return self.multiple and not self.optional
+
+
+class GroupTagParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_group_tag"] = "gx_group_tag"
+    multiple: bool
+
+    @property
+    def py_type(self) -> Type:
+        py_type: Type = StrictStr
+        if self.multiple:
+            py_type = list_type(py_type)
+        return optional_if_needed(py_type, self.optional)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        return dynamic_model_information_from_py_type(self, self.py_type, requires_value=requires_value)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return not self.optional
+
+
+class BaseUrlParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_baseurl"] = "gx_baseurl"
+
+    @property
+    def py_type(self) -> Type:
+        return HttpUrl
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+DiscriminatorType = Union[bool, str]
+
+
+def cond_test_parameter_default_value(
+    test_parameter: Union["BooleanParameterModel", "SelectParameterModel"]
+) -> Optional[DiscriminatorType]:
+    default_value: Optional[DiscriminatorType] = None
+    if isinstance(test_parameter, BooleanParameterModel):
+        default_value = test_parameter.value
+    elif isinstance(test_parameter, SelectParameterModel):
+        select_parameter = cast(SelectParameterModel, test_parameter)
+        select_default_value = select_parameter.default_value
+        if select_default_value is not None:
+            default_value = select_default_value
+    return default_value
+
+
+class ConditionalWhen(StrictModel):
+    discriminator: DiscriminatorType
+    parameters: List["ToolParameterT"]
+    is_default_when: bool
+
+
+class ConditionalParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_conditional"] = "gx_conditional"
+    test_parameter: Union[BooleanParameterModel, SelectParameterModel]
+    whens: List[ConditionalWhen]
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        is_boolean = isinstance(self.test_parameter, BooleanParameterModel)
+        test_param_name = self.test_parameter.name
+        test_info = self.test_parameter.pydantic_template(state_representation)
+        extra_validators = test_info.validators
+        if state_representation == "job_internal":
+            test_parameter_requires_value = True
+        else:
+            test_parameter_requires_value = self.test_parameter.request_requires_value
+        when_types: List[Type[BaseModel]] = []
+        default_type = None
+        for when in self.whens:
+            discriminator = when.discriminator
+            parameters = when.parameters
+            if test_parameter_requires_value:
+                initialize_test = ...
+            else:
+                initialize_test = None
+            tag = str(discriminator) if not is_boolean else str(discriminator).lower()
+            extra_kwd = {test_param_name: (Union[str, bool], initialize_test)}
+            when_types.append(
+                cast(
+                    Type[BaseModel],
+                    Annotated[
+                        create_field_model(
+                            parameters,
+                            f"When_{test_param_name}_{discriminator}",
+                            state_representation,
+                            extra_kwd=extra_kwd,
+                            extra_validators=extra_validators,
+                        ),
+                        Tag(tag),
+                    ],
+                )
+            )
+            # job_internal requires parameters are filled in - so don't allow the absent branch
+            # here that most other state representations allow
+            if state_representation != "job_internal":
+                if when.is_default_when:
+                    extra_kwd = {}
+                    default_type = create_field_model(
+                        parameters,
+                        f"When_{test_param_name}___absent",
+                        state_representation,
+                        extra_kwd=extra_kwd,
+                        extra_validators={},
+                    )
+                    when_types.append(cast(Type[BaseModel], Annotated[default_type, Tag("__absent__")]))
+
+        def model_x_discriminator(v: Any) -> Optional[str]:
+            # returning None causes a validation error, this is what we would want if
+            # if the conditional state is not a dictionary.
+            if not isinstance(v, dict):
+                return None
+            if test_param_name not in v:
+                return "__absent__"
+            else:
+                test_param_val = v[test_param_name]
+                if test_param_val is True:
+                    return "true"
+                elif test_param_val is False:
+                    return "false"
+                else:
+                    return str(test_param_val)
+
+        py_type: Type
+
+        if len(when_types) > 1:
+            cond_type = union_type(when_types)
+
+            class ConditionalType(RootModel):
+                root: cond_type = Field(..., discriminator=Discriminator(model_x_discriminator))  # type: ignore[valid-type]
+
+            if default_type is not None:
+                initialize_cond = None
+            else:
+                initialize_cond = ...
+
+            py_type = ConditionalType
+
+        else:
+            py_type = when_types[0]
+            # a better check here would be if any of the parameters below this have a required value,
+            # in the case of job_internal though this is correct
+            if state_representation == "job_internal":
+                initialize_cond = ...
+            else:
+                initialize_cond = None
+
+        return DynamicModelInformation(
+            self.name,
+            (py_type, initialize_cond),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False  # TODO
+
+
+class RepeatParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_repeat"] = "gx_repeat"
+    parameters: List["ToolParameterT"]
+    min: Optional[int] = None
+    max: Optional[int] = None
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        # Maybe validators for min and max...
+        instance_class: Type[BaseModel] = create_field_model(
+            self.parameters, f"Repeat_{self.name}", state_representation
+        )
+        min_length = self.min
+        max_length = self.max
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        elif _is_landing_request(state_representation):
+            requires_value = False
+            min_length = 0  # in a landing request - parameters can be partially filled
+
+        initialize_repeat: Any
+        if requires_value:
+            initialize_repeat = ...
+        else:
+            initialize_repeat = None
+
+        class RepeatType(RootModel):
+            root: List[instance_class] = Field(initialize_repeat, min_length=min_length, max_length=max_length)  # type: ignore[valid-type]
+
+        return DynamicModelInformation(
+            self.name,
+            (RepeatType, initialize_repeat),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        if self.min is None or self.min == 0:
+            return False
+        # so we know we need at least one value, but maybe none of the parameters in the list
+        # are required
+        for parameter in self.parameters:
+            if parameter.request_requires_value:
+                return True
+        return False
+
+
+class SectionParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_section"] = "gx_section"
+    parameters: List["ToolParameterT"]
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        instance_class: Type[BaseModel] = create_field_model(
+            self.parameters, f"Section_{self.name}", state_representation
+        )
+        requires_value = self.request_requires_value
+        if state_representation == "job_internal":
+            requires_value = True
+        if requires_value:
+            initialize_section = ...
+        else:
+            initialize_section = None
+        return DynamicModelInformation(
+            self.name,
+            (instance_class, initialize_section),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        any_request_parameters_required = False
+        for parameter in self.parameters:
+            if parameter.request_requires_value:
+                any_request_parameters_required = True
+                break
+        return any_request_parameters_required
+
+
+LiteralNone: Type = Literal[None]  # type: ignore[assignment]
+
+
+class CwlNullParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_null"] = "cwl_null"
+
+    @property
+    def py_type(self) -> Type:
+        return LiteralNone
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False
+
+
+class CwlStringParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_string"] = "cwl_string"
+
+    @property
+    def py_type(self) -> Type:
+        return StrictStr
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class CwlIntegerParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_integer"] = "cwl_integer"
+
+    @property
+    def py_type(self) -> Type:
+        return StrictInt
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class CwlFloatParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_float"] = "cwl_float"
+
+    @property
+    def py_type(self) -> Type:
+        return union_type([StrictFloat, StrictInt])
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class CwlBooleanParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_boolean"] = "cwl_boolean"
+
+    @property
+    def py_type(self) -> Type:
+        return StrictBool
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class CwlUnionParameterModel(BaseToolParameterModelDefinition):
+    parameter_type: Literal["cwl_union"] = "cwl_union"
+    parameters: List["CwlParameterT"]
+
+    @property
+    def py_type(self) -> Type:
+        union_of_cwl_types: List[Type] = []
+        for parameter in self.parameters:
+            union_of_cwl_types.append(parameter.py_type)
+        return union_type(union_of_cwl_types)
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return DynamicModelInformation(
+            self.name,
+            (self.py_type, ...),
+            {},
+        )
+
+    @property
+    def request_requires_value(self) -> bool:
+        return False  # TODO:
+
+
+class CwlFileParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["cwl_file"] = "cwl_file"
+
+    @property
+    def py_type(self) -> Type:
+        return DataRequest
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+class CwlDirectoryParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["cwl_directory"] = "cwl_directory"
+
+    @property
+    def py_type(self) -> Type:
+        return DataRequest
+
+    def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
+        return dynamic_model_information_from_py_type(self, self.py_type)
+
+    @property
+    def request_requires_value(self) -> bool:
+        return True
+
+
+CwlParameterT = Union[
+    CwlIntegerParameterModel,
+    CwlFloatParameterModel,
+    CwlStringParameterModel,
+    CwlBooleanParameterModel,
+    CwlNullParameterModel,
+    CwlFileParameterModel,
+    CwlDirectoryParameterModel,
+    CwlUnionParameterModel,
+]
+
+GalaxyParameterT = Union[
+    TextParameterModel,
+    IntegerParameterModel,
+    FloatParameterModel,
+    BooleanParameterModel,
+    HiddenParameterModel,
+    SelectParameterModel,
+    DataParameterModel,
+    DataCollectionParameterModel,
+    DataColumnParameterModel,
+    DirectoryUriParameterModel,
+    RulesParameterModel,
+    DrillDownParameterModel,
+    GroupTagParameterModel,
+    BaseUrlParameterModel,
+    GenomeBuildParameterModel,
+    ColorParameterModel,
+    ConditionalParameterModel,
+    RepeatParameterModel,
+    SectionParameterModel,
+]
+
+ToolParameterT = Union[
+    CwlParameterT,
+    GalaxyParameterT,
+]
+
+
+class ToolParameterModel(RootModel):
+    root: ToolParameterT = Field(..., discriminator="parameter_type")
+
+
+ConditionalWhen.model_rebuild()
+ConditionalParameterModel.model_rebuild()
+RepeatParameterModel.model_rebuild()
+CwlUnionParameterModel.model_rebuild()
+
+
+class ToolParameterBundle(Protocol):
+    """An object having a dictionary of input models (i.e. a 'Tool')"""
+
+    parameters: List[ToolParameterT]
+
+
+class ToolParameterBundleModel(BaseModel):
+    parameters: List[ToolParameterT]
+
+
+def to_simple_model(input_parameter: Union[ToolParameterModel, ToolParameterT]) -> ToolParameterT:
+    if input_parameter.__class__ == ToolParameterModel:
+        assert isinstance(input_parameter, ToolParameterModel)
+        return cast(ToolParameterT, input_parameter.root)
+    else:
+        return cast(ToolParameterT, input_parameter)
+
+
+def simple_input_models(parameters: Union[List[ToolParameterModel], List[ToolParameterT]]) -> Iterable[ToolParameterT]:
+    return [to_simple_model(m) for m in parameters]
+
+
+def create_model_strict(*args, **kwd) -> Type[BaseModel]:
+    # proteted_namespaces here prevents tool with model_ parameter names from issueing warnings
+    model_config = ConfigDict(extra="forbid", protected_namespaces=())
+
+    return create_model(*args, __config__=model_config, **kwd)
+
+
+def create_model_factory(state_representation: StateRepresentationT):
+
+    def create_method(tool: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_field_model(tool.parameters, name or DEFAULT_MODEL_NAME, state_representation)
+
+    return create_method
+
+
+create_request_model = create_model_factory("request")
+create_request_internal_model = create_model_factory("request_internal")
+create_request_internal_dereferenced_model = create_model_factory("request_internal_dereferenced")
+create_landing_request_model = create_model_factory("landing_request")
+create_landing_request_internal_model = create_model_factory("landing_request_internal")
+create_job_internal_model = create_model_factory("job_internal")
+create_test_case_model = create_model_factory("test_case_xml")
+create_workflow_step_model = create_model_factory("workflow_step")
+create_workflow_step_linked_model = create_model_factory("workflow_step_linked")
+
+
+def create_field_model(
+    tool_parameter_models: Union[List[ToolParameterModel], List[ToolParameterT]],
+    name: str,
+    state_representation: StateRepresentationT,
+    extra_kwd: Optional[Mapping[str, tuple]] = None,
+    extra_validators: Optional[ValidatorDictT] = None,
+) -> Type[BaseModel]:
+    kwd: Dict[str, tuple] = {}
+    if extra_kwd:
+        kwd.update(extra_kwd)
+    model_validators = (extra_validators or {}).copy()
+
+    for input_model in tool_parameter_models:
+        input_model = to_simple_model(input_model)
+        pydantic_request_template = input_model.pydantic_template(state_representation)
+        input_name = pydantic_request_template.name
+        kwd[input_name] = pydantic_request_template.definition
+        input_validators = pydantic_request_template.validators
+        for validator_name, validator_callable in input_validators.items():
+            model_validators[f"{input_name}_{validator_name}"] = validator_callable
+
+    pydantic_model = create_model_strict(name, __validators__=model_validators, **kwd)
+    return pydantic_model
+
+
+def _is_landing_request(state_representation: StateRepresentationT):
+    return state_representation in ["landing_request", "landing_request_internal"]
+
+
+def validate_against_model(pydantic_model: Type[BaseModel], parameter_state: Dict[str, Any]) -> None:
+    try:
+        pydantic_model(**parameter_state)
+    except ValidationError as e:
+        # TODO: Improve this or maybe add a handler for this in the FastAPI exception
+        # handler.
+        raise RequestParameterInvalidException(str(e))
+
+
+class ValidationFunctionT(Protocol):
+
+    def __call__(self, tool: ToolParameterBundle, request: RawStateDict, name: Optional[str] = None) -> None: ...
+
+
+def validate_model_type_factory(state_representation: StateRepresentationT) -> ValidationFunctionT:
+
+    def validate_request(tool: ToolParameterBundle, request: Dict[str, Any], name: Optional[str] = None) -> None:
+        name = name or DEFAULT_MODEL_NAME
+        pydantic_model = create_field_model(tool.parameters, name=name, state_representation=state_representation)
+        validate_against_model(pydantic_model, request)
+
+    return validate_request
+
+
+validate_request = validate_model_type_factory("request")
+validate_internal_request = validate_model_type_factory("request_internal")
+validate_internal_request_dereferenced = validate_model_type_factory("request_internal_dereferenced")
+validate_landing_request = validate_model_type_factory("landing_request")
+validate_internal_landing_request = validate_model_type_factory("landing_request_internal")
+validate_internal_job = validate_model_type_factory("job_internal")
+validate_test_case = validate_model_type_factory("test_case_xml")
+validate_workflow_step = validate_model_type_factory("workflow_step")
+validate_workflow_step_linked = validate_model_type_factory("workflow_step_linked")
diff --git a/tools/meme/__init__.py b/lib/galaxy/tool_util/parameters/scripts/__init__.py
similarity index 100%
rename from tools/meme/__init__.py
rename to lib/galaxy/tool_util/parameters/scripts/__init__.py
diff --git a/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py b/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py
new file mode 100644
index 0000000000000000000000000000000000000000..958135f5331a504b6b9b44d89878cf4fcd3676df
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/scripts/validate_test_cases.py
@@ -0,0 +1,152 @@
+import argparse
+import json
+import os
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+from typing import (
+    List,
+    Optional,
+)
+
+from galaxy.tool_util.parameters.case import (
+    TestCaseStateValidationResult,
+    validate_test_cases_for_tool_source,
+)
+from galaxy.tool_util.parser import get_tool_source
+
+DESCRIPTION = """
+A small utility to load a Galaxy tool file and run tool test validation code on it.
+
+This is not meant to be an end-user application or part of the typical tool developer tool
+chain. This functionality will be integrated into Planemo with the typical polish that
+entails. This purpose of this utility is for Galaxy developers and people wishing to
+make informed decisions about the tool test schema and best practices to apply the tool
+state validation code in isolation. This script can also be used to integrate this functionality
+in non-Python tool chains.
+"""
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument("tool_source")
+    parser.add_argument(
+        "-l",
+        "--latest",
+        dest="latest",
+        default=False,
+        action="store_true",
+        help="Validate test against latest tool profile version regardless of explicit tool profile version specified in tool source file.",
+    )
+    parser.add_argument(
+        "-j",
+        "--json",
+        default=False,
+        action="store_true",
+        help="Output validation results as JSON.",
+    )
+    return parser
+
+
+@dataclass
+class ToolTestValidationResults:
+    tool_id: str
+    tool_version: Optional[str]
+    tool_profile: str
+    tool_path: str
+    results: List[TestCaseStateValidationResult]
+    load_error: Optional[Exception]
+
+    def to_dict(self):
+        return {
+            "tool_id": self.tool_id,
+            "tool_version": self.tool_version,
+            "tool_path": str(self.tool_path),
+            "results": [r.to_dict() for r in self.results],
+            "load_error": str(self.load_error) if self.load_error else None,
+        }
+
+
+def report_results(results_for_tool: ToolTestValidationResults) -> None:
+    test_results = results_for_tool.results
+    print(
+        f"Found {len(test_results)} test cases to validate for tool {results_for_tool.tool_id} / {results_for_tool.tool_version} (@ {results_for_tool.tool_path})"
+    )
+    for i, result in enumerate(test_results):
+        if result.validation_error is not None:
+            print(f"Test Case {i + 1}: validation failed - {str(result.validation_error)}")
+        elif len(result.warnings) == 0:
+            print(f"Test Case {i + 1}: validated")
+        else:
+            print(f"Test case {i + 1}: test case validated with warnings:")
+            for test_warning in result.warnings:
+                print(f"- {test_warning}")
+
+
+class NotValidToolException(Exception):
+    pass
+
+
+def validate_tool(tool_path, latest) -> ToolTestValidationResults:
+    try:
+        tool_source = get_tool_source(tool_path)
+    except Exception:
+        # probably not a Galaxy tool... just skip
+        raise NotValidToolException()
+    tool_id = tool_source.parse_id()
+    if tool_id is None:
+        raise NotValidToolException()
+    load_error: Optional[Exception] = None
+    try:
+        results = validate_test_cases_for_tool_source(tool_source, use_latest_profile=latest)
+    except Exception as e:
+        load_error = e
+        results = []
+    return ToolTestValidationResults(
+        tool_id,
+        tool_source.parse_version(),
+        tool_source.parse_profile(),
+        tool_path,
+        results,
+        load_error,
+    )
+
+
+def validate_test_cases(args):
+    path = args.tool_source
+    latest = args.latest
+    if not os.path.isdir(path):
+        results = validate_tool(path, latest)
+        if args.json:
+            print(json.dumps(results.to_dict()))
+        else:
+            report_results(results)
+    else:
+        xml_files = Path(path).glob("**/*.xml")
+        all_results = []
+        for xml_file in xml_files:
+            if "test-data" in str(xml_file):
+                continue
+            try:
+                results = validate_tool(xml_file, latest)
+                all_results.append(results)
+            except NotValidToolException:
+                continue
+
+        if args.json:
+            print(json.dumps([r.to_dict() for r in all_results], indent=4))
+        else:
+            for results in all_results:
+                report_results(results)
+
+
+def main(argv=None) -> None:
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = arg_parser().parse_args(argv)
+    validate_test_cases(args)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/tool_util/parameters/state.py b/lib/galaxy/tool_util/parameters/state.py
new file mode 100644
index 0000000000000000000000000000000000000000..df040e1803ca1d8f68240d0f4c87e4fd8da71c4c
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/state.py
@@ -0,0 +1,144 @@
+from abc import (
+    ABC,
+    abstractmethod,
+)
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Type,
+    Union,
+)
+
+from pydantic import BaseModel
+from typing_extensions import Literal
+
+from .models import (
+    create_job_internal_model,
+    create_landing_request_internal_model,
+    create_landing_request_model,
+    create_request_internal_dereferenced_model,
+    create_request_internal_model,
+    create_request_model,
+    create_test_case_model,
+    create_workflow_step_linked_model,
+    create_workflow_step_model,
+    StateRepresentationT,
+    ToolParameterBundle,
+    ToolParameterBundleModel,
+    ToolParameterT,
+    validate_against_model,
+)
+
+HasToolParameters = Union[List[ToolParameterT], ToolParameterBundle]
+
+
+class ToolState(ABC):
+    input_state: Dict[str, Any]
+
+    def __init__(self, input_state: Dict[str, Any]):
+        self.input_state = input_state
+
+    def _validate(self, pydantic_model: Type[BaseModel]) -> None:
+        validate_against_model(pydantic_model, self.input_state)
+
+    def validate(self, parameters: HasToolParameters, name: Optional[str] = None) -> None:
+        base_model = self.parameter_model_for(parameters, name=name)
+        if base_model is None:
+            raise NotImplementedError(
+                f"Validating tool state against state representation {self.state_representation} is not implemented."
+            )
+        self._validate(base_model)
+
+    @property
+    @abstractmethod
+    def state_representation(self) -> StateRepresentationT:
+        """Get state representation of the inputs."""
+
+    @classmethod
+    def parameter_model_for(cls, parameters: HasToolParameters, name: Optional[str] = None) -> Type[BaseModel]:
+        bundle: ToolParameterBundle
+        if isinstance(parameters, list):
+            bundle = ToolParameterBundleModel(parameters=parameters)
+        else:
+            bundle = parameters
+        return cls._parameter_model_for(bundle, name=name)
+
+    @classmethod
+    @abstractmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        """Return a model type for this tool state kind."""
+
+
+class RequestToolState(ToolState):
+    state_representation: Literal["request"] = "request"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_request_model(parameters, name)
+
+
+class RequestInternalToolState(ToolState):
+    state_representation: Literal["request_internal"] = "request_internal"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_request_internal_model(parameters, name)
+
+
+class LandingRequestToolState(ToolState):
+    state_representation: Literal["landing_request"] = "landing_request"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_landing_request_model(parameters, name)
+
+
+class LandingRequestInternalToolState(ToolState):
+    state_representation: Literal["landing_request_internal"] = "landing_request_internal"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_landing_request_internal_model(parameters, name)
+
+
+class RequestInternalDereferencedToolState(ToolState):
+    state_representation: Literal["request_internal_dereferenced"] = "request_internal_dereferenced"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_request_internal_dereferenced_model(parameters, name)
+
+
+class JobInternalToolState(ToolState):
+    state_representation: Literal["job_internal"] = "job_internal"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_job_internal_model(parameters, name)
+
+
+class TestCaseToolState(ToolState):
+    state_representation: Literal["test_case_xml"] = "test_case_xml"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        # implement a test case model...
+        return create_test_case_model(parameters, name)
+
+
+class WorkflowStepToolState(ToolState):
+    state_representation: Literal["workflow_step"] = "workflow_step"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_workflow_step_model(parameters, name)
+
+
+class WorkflowStepLinkedToolState(ToolState):
+    state_representation: Literal["workflow_step_linked"] = "workflow_step_linked"
+
+    @classmethod
+    def _parameter_model_for(cls, parameters: ToolParameterBundle, name: Optional[str] = None) -> Type[BaseModel]:
+        return create_workflow_step_linked_model(parameters, name)
diff --git a/lib/galaxy/tool_util/parameters/visitor.py b/lib/galaxy/tool_util/parameters/visitor.py
new file mode 100644
index 0000000000000000000000000000000000000000..35d4bc176a3ea1273e3b8ada07a3eda2dc09c395
--- /dev/null
+++ b/lib/galaxy/tool_util/parameters/visitor.py
@@ -0,0 +1,185 @@
+from typing import (
+    Any,
+    cast,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    TypeVar,
+    Union,
+)
+
+from typing_extensions import Protocol
+
+from .models import (
+    ConditionalParameterModel,
+    ConditionalWhen,
+    RepeatParameterModel,
+    SectionParameterModel,
+    simple_input_models,
+    ToolParameterBundle,
+    ToolParameterT,
+)
+from .state import ToolState
+
+
+class VisitorNoReplacement:
+    pass
+
+
+class VisitorUndefined:
+    pass
+
+
+VISITOR_NO_REPLACEMENT = VisitorNoReplacement()
+VISITOR_UNDEFINED = VisitorUndefined()
+
+
+class Callback(Protocol):
+    def __call__(self, parameter: ToolParameterT, value: Any):
+        pass
+
+
+def visit_input_values(
+    input_models: ToolParameterBundle,
+    tool_state: ToolState,
+    callback: Callback,
+    no_replacement_value=VISITOR_NO_REPLACEMENT,
+) -> Dict[str, Any]:
+    return _visit_input_values(
+        simple_input_models(input_models.parameters),
+        tool_state.input_state,
+        callback=callback,
+        no_replacement_value=no_replacement_value,
+    )
+
+
+def _visit_input_values(
+    input_models: Iterable[ToolParameterT],
+    input_values: Dict[str, Any],
+    callback: Callback,
+    no_replacement_value=VISITOR_NO_REPLACEMENT,
+) -> Dict[str, Any]:
+
+    def _callback(name: str, old_values: Dict[str, Any], new_values: Dict[str, Any]):
+        input_value = old_values.get(name, VISITOR_UNDEFINED)
+        if input_value is VISITOR_UNDEFINED:
+            return
+        replacement = callback(model, input_value)
+        if replacement != no_replacement_value:
+            new_values[name] = replacement
+        else:
+            new_values[name] = input_value
+
+    new_input_values: Dict[str, Any] = {}
+    for model in input_models:
+        name = model.name
+        parameter_type = model.parameter_type
+        input_value = input_values.get(name, VISITOR_UNDEFINED)
+        if input_value is VISITOR_UNDEFINED:
+            continue
+
+        if parameter_type == "gx_repeat":
+            repeat_parameter = cast(RepeatParameterModel, model)
+            repeat_parameters = repeat_parameter.parameters
+            repeat_values = cast(list, input_value)
+            new_repeat_values = []
+            for repeat_instance_values in repeat_values:
+                new_repeat_values.append(
+                    _visit_input_values(
+                        repeat_parameters, repeat_instance_values, callback, no_replacement_value=no_replacement_value
+                    )
+                )
+            new_input_values[name] = new_repeat_values
+        elif parameter_type == "gx_section":
+            section_parameter = cast(SectionParameterModel, model)
+            section_parameters = section_parameter.parameters
+            section_values = cast(dict, input_value)
+            new_section_values = _visit_input_values(
+                section_parameters, section_values, callback, no_replacement_value=no_replacement_value
+            )
+            new_input_values[name] = new_section_values
+        elif parameter_type == "gx_conditional":
+            conditional_parameter = cast(ConditionalParameterModel, model)
+            test_parameter = conditional_parameter.test_parameter
+            test_parameter_name = test_parameter.name
+
+            conditional_values = cast(dict, input_value)
+            when: ConditionalWhen = _select_which_when(conditional_parameter, conditional_values)
+            new_conditional_values = _visit_input_values(
+                when.parameters, conditional_values, callback, no_replacement_value=no_replacement_value
+            )
+            if test_parameter_name in conditional_values:
+                _callback(test_parameter_name, conditional_values, new_conditional_values)
+            new_input_values[name] = new_conditional_values
+        else:
+            _callback(name, input_values, new_input_values)
+    return new_input_values
+
+
+def _select_which_when(conditional: ConditionalParameterModel, state: dict) -> ConditionalWhen:
+    test_parameter = conditional.test_parameter
+    test_parameter_name = test_parameter.name
+    explicit_test_value = state.get(test_parameter_name)
+    test_value = validate_explicit_conditional_test_value(test_parameter_name, explicit_test_value)
+    for when in conditional.whens:
+        print(when.discriminator)
+        print(type(when.discriminator))
+        if test_value is None and when.is_default_when:
+            return when
+        elif test_value == when.discriminator:
+            return when
+    else:
+        raise Exception(f"Invalid conditional test value ({explicit_test_value}) for parameter ({test_parameter_name})")
+
+
+def flat_state_path(has_name: Union[str, ToolParameterT], prefix: Optional[str] = None) -> str:
+    """Given a parameter name or model and an optional prefix, give 'flat' name for parameter in tree."""
+    if hasattr(has_name, "name"):
+        name = cast(ToolParameterT, has_name).name
+    else:
+        name = cast(str, has_name)
+    return name if prefix is None else f"{prefix}|{name}"
+
+
+KVT = TypeVar("KVT")
+
+
+def keys_starting_with(flat_tree: Dict[str, KVT], flat_state_path: str) -> Dict[str, KVT]:
+    subset: Dict[str, KVT] = {}
+    for key, value in flat_tree.items():
+        if key.startswith(flat_state_path):
+            subset[key] = value
+    return subset
+
+
+def repeat_inputs_to_array(flat_state_path: str, inputs: Dict[str, KVT]) -> List[Dict[str, KVT]]:
+    repeat_inputs = keys_starting_with(inputs, flat_state_path + "_")
+    highest_count = -1
+    for key in repeat_inputs.keys():
+        repeat_num_str = key[len(flat_state_path) + 1 :].split("|")[0]
+        try:
+            repeat_num = int(repeat_num_str)
+            if repeat_num > highest_count:
+                highest_count = repeat_num
+        except ValueError:
+            continue
+
+    params: List[Dict[str, KVT]] = []
+    for _ in range(highest_count + 1):
+        instance_params: Dict[str, KVT] = {}
+        params.append(instance_params)
+    for key, value in repeat_inputs.items():
+        repeat_num_str = key[len(flat_state_path) + 1 :].split("|")[0]
+        try:
+            repeat_num = int(repeat_num_str)
+            params[repeat_num][key] = value
+        except ValueError:
+            continue
+    return params
+
+
+def validate_explicit_conditional_test_value(test_parameter_name: str, value: Any) -> Optional[Union[str, bool]]:
+    if value is not None and not isinstance(value, (str, bool)):
+        raise Exception(f"Invalid conditional test value ({value}) for parameter ({test_parameter_name})")
+    return cast(Optional[Union[str, bool]], value)
diff --git a/lib/galaxy/tool_util/parser/__init__.py b/lib/galaxy/tool_util/parser/__init__.py
index 509a6c066b31dbc2a34c6bdec4d7d40d0ef9b611..0a67935df53c16f1f830d9c389fe2dabf3f88fe2 100644
--- a/lib/galaxy/tool_util/parser/__init__.py
+++ b/lib/galaxy/tool_util/parser/__init__.py
@@ -9,6 +9,7 @@ from .factory import (
 from .interface import (
     RequiredFiles,
     ToolSource,
+    XrefDict,
 )
 from .output_objects import ToolOutputCollectionPart
 
@@ -19,4 +20,5 @@ __all__ = (
     "RequiredFiles",
     "ToolOutputCollectionPart",
     "ToolSource",
+    "XrefDict",
 )
diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index 1647c39aa7010073d06d8ca2e64a0e429fb23f28..26d2fdfdc16c56611d775e32468407312ba14a0b 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -11,6 +11,7 @@ from galaxy.tool_util.cwl.parser import (
 )
 from galaxy.tool_util.deps import requirements
 from .interface import (
+    HelpContent,
     PageSource,
     PagesSource,
     ToolSource,
@@ -80,7 +81,11 @@ class CwlToolSource(ToolSource):
         return []
 
     def parse_help(self):
-        return self.tool_proxy.doc()
+        doc = self.tool_proxy.doc()
+        if doc:
+            return HelpContent(format="plain_text", content=doc)
+        else:
+            return None
 
     def parse_sanitize(self):
         return False
@@ -113,7 +118,7 @@ class CwlToolSource(ToolSource):
     def parse_interactivetool(self):
         return []
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> PagesSource:
         page_source = CwlPageSource(self.tool_proxy)
         return PagesSource([page_source])
 
@@ -179,18 +184,41 @@ class CwlToolSource(ToolSource):
         return json.dumps(self.tool_proxy.to_persistent_representation())
 
 
+class CwlInputSource(YamlInputSource):
+    def __init__(self, as_dict, as_field):
+        super().__init__(as_dict)
+        self._field = as_field
+
+    @property
+    def field(self):
+        return self._field
+
+
 class CwlPageSource(PageSource):
     def __init__(self, tool_proxy):
         cwl_instances = tool_proxy.input_instances()
-        self._input_list = list(map(self._to_input_source, cwl_instances))
+        input_fields = tool_proxy.input_fields()
+        input_list = []
+        for cwl_instance in cwl_instances:
+            name = cwl_instance.name
+            input_field = None
+            for field in input_fields:
+                if field["name"] == name:
+                    input_field = field
+            input_list.append(CwlInputSource(cwl_instance.to_dict(), input_field))
+
+        self._input_list = input_list
 
     def _to_input_source(self, input_instance):
         as_dict = input_instance.to_dict()
-        return YamlInputSource(as_dict)
+        return CwlInputSource(as_dict)
 
     def parse_input_sources(self):
         return self._input_list
 
+    def input_fields(self):
+        return self._input_fields
+
 
 __all__ = (
     "CwlToolSource",
diff --git a/lib/galaxy/tool_util/parser/factory.py b/lib/galaxy/tool_util/parser/factory.py
index 6a88f7b9d960abe611e1c4172be4e7e1e55c96c5..ce403638f7f02fe674d5db28d15bea97989d9c23 100644
--- a/lib/galaxy/tool_util/parser/factory.py
+++ b/lib/galaxy/tool_util/parser/factory.py
@@ -15,6 +15,7 @@ from galaxy.util import (
     ElementTree,
     parse_xml_string_to_etree,
 )
+from galaxy.util.path import StrPath
 from galaxy.util.yaml_util import ordered_load
 from .cwl import (
     CwlToolSource,
@@ -59,7 +60,7 @@ TOOL_SOURCE_FACTORIES: Dict[str, Callable[[str], ToolSource]] = {
 
 
 def get_tool_source(
-    config_file: Optional[str] = None,
+    config_file: Optional[StrPath] = None,
     xml_tree: Optional[ElementTree] = None,
     enable_beta_formats: bool = True,
     tool_location_fetcher: Optional[ToolLocationFetcher] = None,
@@ -85,6 +86,8 @@ def get_tool_source(
         tool_location_fetcher = ToolLocationFetcher()
 
     assert config_file
+    config_file = str(config_file)
+
     config_file = tool_location_fetcher.to_tool_path(config_file)
     if not enable_beta_formats:
         tree, macro_paths = load_tool_with_refereces(config_file)
@@ -116,17 +119,22 @@ def get_tool_source_from_representation(tool_format, tool_representation):
         raise Exception(f"Unknown tool representation format [{tool_format}].")
 
 
-def get_input_source(content):
+def get_input_source(content, trusted: bool = True):
     """Wrap dicts or XML elements as InputSource if needed.
 
     If the supplied content is already an InputSource object,
     it is simply returned. This allow Galaxy to uniformly
     consume using the tool input source interface.
+
+    Setting trusted to false indicates that no dynamic code should be
+    executed - no eval. This should be used for user-defined tools (in
+    the future) and for workflow inputs.
     """
     if not isinstance(content, InputSource):
         if isinstance(content, dict):
-            content = YamlInputSource(content)
+            content = YamlInputSource(content, trusted=trusted)
         else:
+            assert trusted  # trust is not implemented for XML inputs
             content = XmlInputSource(content)
     return content
 
diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
index 0572b8b57960f1201f74dea3902065f3a0839ec1..af72bf4a482506c0d4923e065e565239f5682589 100644
--- a/lib/galaxy/tool_util/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -5,9 +5,11 @@ from abc import (
     ABCMeta,
     abstractmethod,
 )
+from enum import Enum
 from os.path import join
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
@@ -17,9 +19,16 @@ from typing import (
 )
 
 import packaging.version
-from typing_extensions import TypedDict
+from pydantic import BaseModel
+from typing_extensions import (
+    Literal,
+    NotRequired,
+    TypedDict,
+)
 
+from galaxy.util import Element
 from galaxy.util.path import safe_walk
+from .parameter_validators import AnyValidatorModel
 from .util import _parse_name
 
 if TYPE_CHECKING:
@@ -42,10 +51,63 @@ AssertionList = Optional[List[AssertionDict]]
 XmlInt = Union[str, int]
 
 
+class OutputCompareType(str, Enum):
+    diff = "diff"
+    re_match = "re_match"
+    sim_size = "sim_size"
+    re_match_multiline = "re_match_multiline"
+    contains = "contains"
+    image_diff = "image_diff"
+
+
+class ToolSourceTestOutputAttributes(TypedDict):
+    object: NotRequired[Optional[Any]]
+    compare: OutputCompareType
+    lines_diff: int
+    delta: int
+    delta_frac: Optional[float]
+    sort: bool
+    decompress: bool
+    location: NotRequired[Optional[str]]
+    ftype: NotRequired[Optional[str]]
+    eps: float
+    metric: str
+    pin_labels: Optional[Any]
+    count: Optional[int]
+    metadata: Dict[str, Any]
+    md5: Optional[str]
+    checksum: Optional[str]
+    primary_datasets: Dict[str, Any]
+    elements: Dict[str, Any]
+    assert_list: AssertionList
+    extra_files: List[Dict[str, Any]]
+
+
+class ToolSourceTestOutput(TypedDict):
+    name: str
+    value: Optional[str]
+    attributes: ToolSourceTestOutputAttributes
+
+
+# The unfortunate 'attrib = dict(param_elem.attrib)' makes this difficult to type.
+ToolSourceTestInputAttributes = Dict[str, Any]
+
+
+class ToolSourceTestInput(TypedDict):
+    name: str
+    value: Optional[Any]
+    attributes: ToolSourceTestInputAttributes
+
+
+ToolSourceTestInputs = List[ToolSourceTestInput]
+ToolSourceTestOutputs = List[ToolSourceTestOutput]
+TestSourceTestOutputColllection = Any
+
+
 class ToolSourceTest(TypedDict):
-    inputs: Any
-    outputs: Any
-    output_collections: List[Any]
+    inputs: ToolSourceTestInputs
+    outputs: ToolSourceTestOutputs
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: AssertionList
     stderr: AssertionList
     expect_exit_code: Optional[XmlInt]
@@ -61,6 +123,21 @@ class ToolSourceTests(TypedDict):
     tests: List[ToolSourceTest]
 
 
+class XrefDict(TypedDict):
+    value: str
+    reftype: str
+
+
+class Citation(BaseModel):
+    type: str
+    content: str
+
+
+class HelpContent(BaseModel):
+    format: Literal["restructuredtext", "plain_text", "markdown"]
+    content: str
+
+
 class ToolSource(metaclass=ABCMeta):
     """This interface represents an abstract source to parse tool
     information from.
@@ -76,10 +153,10 @@ class ToolSource(metaclass=ABCMeta):
         """
 
     @abstractmethod
-    def parse_version(self):
+    def parse_version(self) -> Optional[str]:
         """Parse a version describing the abstract tool."""
 
-    def parse_tool_module(self):
+    def parse_tool_module(self) -> Optional[Tuple[str, str]]:
         """Load Tool class from a custom module. (Optional).
 
         If not None, return pair containing module and class (as strings).
@@ -93,17 +170,20 @@ class ToolSource(metaclass=ABCMeta):
         """
         return None
 
-    def parse_tool_type(self):
+    def parse_tool_type(self) -> Optional[str]:
         """Load simple tool type string (e.g. 'data_source', 'default')."""
         return None
 
     @abstractmethod
-    def parse_name(self):
+    def parse_name(self) -> str:
         """Parse a short name for tool (required)."""
 
     @abstractmethod
-    def parse_description(self):
-        """Parse a description for tool. Longer than name, shorted than help."""
+    def parse_description(self) -> str:
+        """Parse a description for tool. Longer than name, shorted than help.
+
+        We parse this out as "" if it isn't explicitly declared.
+        """
 
     def parse_edam_operations(self) -> List[str]:
         """Parse list of edam operation codes."""
@@ -114,7 +194,7 @@ class ToolSource(metaclass=ABCMeta):
         return []
 
     @abstractmethod
-    def parse_xrefs(self) -> List[Dict[str, str]]:
+    def parse_xrefs(self) -> List[XrefDict]:
         """Parse list of external resource URIs and types."""
 
     def parse_display_interface(self, default):
@@ -231,7 +311,7 @@ class ToolSource(metaclass=ABCMeta):
         """Return triple of ToolRequirement, ContainerDescription and ResourceRequirement lists."""
 
     @abstractmethod
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> "PagesSource":
         """Return a PagesSource representing inputs by page for tool."""
 
     def parse_provided_metadata_style(self):
@@ -270,19 +350,25 @@ class ToolSource(metaclass=ABCMeta):
         return [], []
 
     @abstractmethod
-    def parse_help(self) -> Optional[str]:
-        """Return RST definition of help text for tool or None if the tool
-        doesn't define help text.
+    def parse_help(self) -> Optional[HelpContent]:
+        """Return help text for tool or None if the tool doesn't define help text.
+
+        The returned object contains the help text and an indication if it is reStructuredText
+        (``restructuredtext``), Markdown (``markdown``), or plain text (``plain_text``).
         """
 
     @abstractmethod
-    def parse_profile(self):
+    def parse_profile(self) -> str:
         """Return tool profile version as Galaxy major e.g. 16.01 or 16.04."""
 
     @abstractmethod
-    def parse_license(self):
+    def parse_license(self) -> Optional[str]:
         """Return license corresponding to tool wrapper."""
 
+    def parse_citations(self) -> List[Citation]:
+        """Return a list of citations."""
+        return []
+
     @abstractmethod
     def parse_python_template_version(self) -> Optional[packaging.version.Version]:
         """
@@ -341,6 +427,34 @@ class PagesSource:
         return True
 
 
+class DynamicOptions(metaclass=ABCMeta):
+
+    def elem(self) -> Element:
+        # For things in transition that still depend on XML - provide a way
+        # to grab it and just throw an error if feature is attempted to be
+        # used with other tool sources.
+        raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
+
+    @abstractmethod
+    def get_dynamic_options_code(self) -> Optional[str]:
+        """If dynamic options are a piece of code to eval, return it."""
+
+    @abstractmethod
+    def get_data_table_name(self) -> Optional[str]:
+        """If dynamic options are loaded from a data table, return the name."""
+
+    @abstractmethod
+    def get_index_file_name(self) -> Optional[str]:
+        """If dynamic options are loaded from an index file, return the name."""
+
+
+class DrillDownDynamicOptions(metaclass=ABCMeta):
+
+    @abstractmethod
+    def from_code_block(self) -> Optional[str]:
+        """Get a code block to do an eval on."""
+
+
 class InputSource(metaclass=ABCMeta):
     default_optional = False
 
@@ -362,6 +476,12 @@ class InputSource(metaclass=ABCMeta):
         keys to be supported depend on the parameter type.
         """
 
+    @abstractmethod
+    def get_bool_or_none(self, key, default):
+        """Return simple named properties as boolean or none for this input source.
+        keys to be supported depend on the parameter type.
+        """
+
     def parse_label(self):
         return self.get("label")
 
@@ -387,7 +507,7 @@ class InputSource(metaclass=ABCMeta):
         """
         return None
 
-    def parse_validator_elems(self):
+    def parse_validators(self) -> List[AnyValidatorModel]:
         """Return an XML description of sanitizers. This is a stop gap
         until we can rework galaxy.tools.parameters.validation to not
         explicitly depend on XML.
@@ -400,16 +520,30 @@ class InputSource(metaclass=ABCMeta):
             default = self.default_optional
         return self.get_bool("optional", default)
 
-    def parse_dynamic_options_elem(self):
-        """Return an XML elemnt describing dynamic options."""
+    def parse_dynamic_options(self) -> Optional[DynamicOptions]:
+        """Return an optional element describing dynamic options.
+
+        These options are still very XML based but as they are adapted to the infrastructure, the return
+        type here will evolve.
+        """
+        return None
+
+    def parse_drill_down_dynamic_options(
+        self, tool_data_path: Optional[str] = None
+    ) -> Optional["DrillDownDynamicOptions"]:
         return None
 
-    def parse_static_options(self):
+    def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         """Return list of static options if this is a select type without
         defining a dynamic options.
         """
         return []
 
+    def parse_drill_down_static_options(
+        self, tool_data_path: Optional[str] = None
+    ) -> Optional[List["DrillDownOptionsDict"]]:
+        return None
+
     def parse_conversion_tuples(self):
         """Return list of (name, extension) to describe explicit conversions."""
         return []
@@ -438,8 +572,126 @@ class PageSource(metaclass=ABCMeta):
         """Return a list of InputSource objects."""
 
 
+AnyTestCollectionDefDict = Union["JsonTestCollectionDefDict", "XmlTestCollectionDefDict"]
+TestCollectionDefElementObject = Union[AnyTestCollectionDefDict, "ToolSourceTestInput"]
+TestCollectionAttributeDict = Dict[str, Any]
+CollectionType = str
+
+
+class TestCollectionDefElementDict(TypedDict):
+    element_identifier: str
+    element_definition: TestCollectionDefElementObject
+
+
+class TestCollectionDefElementInternal(TypedDict):
+    element_identifier: str
+    element_definition: Union["TestCollectionDef", "ToolSourceTestInput"]
+
+
+# two versions of collection inputs can be parsed out, XmlTestCollectionDefDict is historically
+# used by tools and Galaxy internals and exposed in the API via the test definition endpoints for
+# tool execution. JsonTestCollectionDefDict is the format consumed by Planemo that mirrors a CWL
+# way of defining inputs.
+class XmlTestCollectionDefDict(TypedDict):
+    model_class: Literal["TestCollectionDef"]
+    attributes: TestCollectionAttributeDict
+    collection_type: CollectionType
+    elements: List[TestCollectionDefElementDict]
+    name: str
+
+
+JsonTestDatasetDefDict = TypedDict(
+    "JsonTestDatasetDefDict",
+    {
+        "class": Literal["File"],
+        "path": NotRequired[Optional[str]],
+        "location": NotRequired[Optional[str]],
+        "name": NotRequired[Optional[str]],
+        "dbkey": NotRequired[Optional[str]],
+        "filetype": NotRequired[Optional[str]],
+        "composite_data": NotRequired[Optional[List[str]]],
+        "tags": NotRequired[Optional[List[str]]],
+    },
+)
+
+JsonTestCollectionDefElementDict = Union[
+    "JsonTestCollectionDefDatasetElementDict", "JsonTestCollectionDefCollectionElementDict"
+]
+JsonTestCollectionDefDatasetElementDict = TypedDict(
+    "JsonTestCollectionDefDatasetElementDict",
+    {
+        "identifier": str,
+        "class": Literal["File"],
+        "path": NotRequired[Optional[str]],
+        "location": NotRequired[Optional[str]],
+        "name": NotRequired[Optional[str]],
+        "dbkey": NotRequired[Optional[str]],
+        "filetype": NotRequired[Optional[str]],
+        "composite_data": NotRequired[Optional[List[str]]],
+        "tags": NotRequired[Optional[List[str]]],
+    },
+)
+BaseJsonTestCollectionDefCollectionElementDict = TypedDict(
+    "BaseJsonTestCollectionDefCollectionElementDict",
+    {
+        "class": Literal["Collection"],
+        "collection_type": str,
+        "elements": NotRequired[Optional[List[JsonTestCollectionDefElementDict]]],
+    },
+)
+JsonTestCollectionDefCollectionElementDict = TypedDict(
+    "JsonTestCollectionDefCollectionElementDict",
+    {
+        "identifier": str,
+        "class": Literal["Collection"],
+        "collection_type": str,
+        "elements": NotRequired[Optional[List[JsonTestCollectionDefElementDict]]],
+    },
+)
+JsonTestCollectionDefDict = TypedDict(
+    "JsonTestCollectionDefDict",
+    {
+        "class": Literal["Collection"],
+        "collection_type": str,
+        "elements": NotRequired[Optional[List[JsonTestCollectionDefElementDict]]],
+        "name": NotRequired[Optional[str]],
+    },
+)
+
+
+def xml_data_input_to_json(xml_input: ToolSourceTestInput) -> Optional["JsonTestDatasetDefDict"]:
+    attributes = xml_input["attributes"]
+    value = xml_input["value"]
+    if value is None and attributes.get("location") is None:
+        return None
+    as_dict: JsonTestDatasetDefDict = {
+        "class": "File",
+    }
+    if value:
+        as_dict["path"] = value
+    _copy_if_exists(attributes, as_dict, "location")
+    _copy_if_exists(attributes, as_dict, "dbkey")
+    _copy_if_exists(attributes, as_dict, "ftype", "filetype")
+    _copy_if_exists(attributes, as_dict, "composite_data", only_if_value=True)
+    tags = attributes.get("tags")
+    if tags:
+        as_dict["tags"] = [t.strip() for t in tags.split(",")]
+    return as_dict
+
+
+def _copy_if_exists(attributes, as_dict, name: str, as_name: Optional[str] = None, only_if_value: bool = False):
+    if name in attributes:
+        value = attributes[name]
+        if not value and only_if_value:
+            return
+        if as_name is None:
+            as_name = name
+        as_dict[as_name] = value
+
+
 class TestCollectionDef:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
+    elements: List[TestCollectionDefElementInternal]
 
     def __init__(self, attrib, name, collection_type, elements):
         self.attrib = attrib
@@ -447,30 +699,46 @@ class TestCollectionDef:
         self.elements = elements
         self.name = name
 
-    @staticmethod
-    def from_xml(elem, parse_param_elem):
-        elements = []
-        attrib = dict(elem.attrib)
-        collection_type = attrib["type"]
-        name = attrib.get("name", "Unnamed Collection")
-        for element in elem.findall("element"):
-            element_attrib = dict(element.attrib)
-            element_identifier = element_attrib["name"]
-            nested_collection_elem = element.find("collection")
-            if nested_collection_elem is not None:
-                element_definition = TestCollectionDef.from_xml(nested_collection_elem, parse_param_elem)
+    def _test_format_to_dict(self) -> "BaseJsonTestCollectionDefCollectionElementDict":
+
+        def to_element(xml_element_dict: "TestCollectionDefElementInternal") -> "JsonTestCollectionDefElementDict":
+            identifier = xml_element_dict["element_identifier"]
+            element_object = xml_element_dict["element_definition"]
+            as_dict: JsonTestCollectionDefElementDict
+
+            if isinstance(element_object, TestCollectionDef):
+                as_dict = JsonTestCollectionDefCollectionElementDict(
+                    identifier=identifier, **element_object._test_format_to_dict()
+                )
             else:
-                element_definition = parse_param_elem(element)
-            elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
-
-        return TestCollectionDef(
-            attrib=attrib,
-            collection_type=collection_type,
-            elements=elements,
-            name=name,
+                input_as_dict: Optional[JsonTestDatasetDefDict] = xml_data_input_to_json(
+                    cast(ToolSourceTestInput, element_object)
+                )
+                if input_as_dict is not None:
+                    as_dict = JsonTestCollectionDefDatasetElementDict(
+                        identifier=identifier,
+                        **input_as_dict,
+                    )
+                else:
+                    raise Exception("Invalid empty test element...")
+            return as_dict
+
+        test_format_dict = BaseJsonTestCollectionDefCollectionElementDict(
+            {
+                "class": "Collection",
+                "elements": list(map(to_element, self.elements)),
+                "collection_type": self.collection_type,
+            }
         )
+        return test_format_dict
 
-    def to_dict(self):
+    def test_format_to_dict(self) -> JsonTestCollectionDefDict:
+        test_format_dict = JsonTestCollectionDefDict(**self._test_format_to_dict())
+        if self.name:
+            test_format_dict["name"] = self.name
+        return test_format_dict
+
+    def to_dict(self) -> XmlTestCollectionDefDict:
         def element_to_dict(element_dict):
             element_identifier, element_def = element_dict["element_identifier"], element_dict["element_definition"]
             if isinstance(element_def, TestCollectionDef):
@@ -489,23 +757,53 @@ class TestCollectionDef:
         }
 
     @staticmethod
-    def from_dict(as_dict):
-        assert as_dict["model_class"] == "TestCollectionDef"
-
-        def element_from_dict(element_dict):
-            if "element_definition" not in element_dict:
-                raise Exception(f"Invalid element_dict {element_dict}")
-            element_def = element_dict["element_definition"]
-            if element_def.get("model_class", None) == "TestCollectionDef":
-                element_def = TestCollectionDef.from_dict(element_def)
-            return {"element_identifier": element_dict["element_identifier"], "element_definition": element_def}
-
-        return TestCollectionDef(
-            attrib=as_dict["attributes"],
-            name=as_dict["name"],
-            elements=list(map(element_from_dict, as_dict["elements"] or [])),
-            collection_type=as_dict["collection_type"],
-        )
+    def from_dict(
+        as_dict: Union[AnyTestCollectionDefDict, JsonTestCollectionDefCollectionElementDict]
+    ) -> "TestCollectionDef":
+        if "model_class" in as_dict:
+            xml_as_dict = cast(XmlTestCollectionDefDict, as_dict)
+            assert xml_as_dict["model_class"] == "TestCollectionDef"
+
+            def element_from_dict(element_dict) -> TestCollectionDefElementInternal:
+                if "element_definition" not in element_dict:
+                    raise Exception(f"Invalid element_dict {element_dict}")
+                element_def = element_dict["element_definition"]
+                if element_def.get("model_class", None) == "TestCollectionDef":
+                    element_def = TestCollectionDef.from_dict(element_def)
+                return {"element_identifier": element_dict["element_identifier"], "element_definition": element_def}
+
+            return TestCollectionDef(
+                attrib=xml_as_dict["attributes"],
+                name=xml_as_dict.get("name", "Unnamed Collection"),
+                elements=list(map(element_from_dict, xml_as_dict["elements"] or [])),
+                collection_type=xml_as_dict["collection_type"],
+            )
+        else:
+            json_as_dict = cast(JsonTestCollectionDefDict, as_dict)
+
+            def element_from_dict_json(
+                element_dict: JsonTestCollectionDefElementDict,
+            ) -> TestCollectionDefElementInternal:
+                element_class = element_dict.get("class")
+                identifier = element_dict["identifier"]
+                element_def: Union[TestCollectionDef, ToolSourceTestInput]
+                if element_class == "Collection":
+                    collection_element_dict = cast(JsonTestCollectionDefCollectionElementDict, element_dict)
+                    element_def = TestCollectionDef.from_dict(collection_element_dict)
+                else:
+                    dataset_element_dict = cast(JsonTestCollectionDefDatasetElementDict, element_dict)
+                    value = dataset_element_dict["path"]  # todo handle location
+                    name = dataset_element_dict.get("name") or "Unnamed Collection"
+                    element_def = {"name": name, "value": value, "attributes": {}}
+                return TestCollectionDefElementInternal(element_identifier=identifier, element_definition=element_def)
+
+            elements = list(map(element_from_dict_json, json_as_dict.get("elements") or []))
+            return TestCollectionDef(
+                attrib={},
+                name=json_as_dict.get("name") or "Unnamed Collection",
+                elements=elements,
+                collection_type=json_as_dict["collection_type"],
+            )
 
     def collect_inputs(self):
         inputs = []
@@ -568,10 +866,13 @@ class RequiredFiles:
 class TestCollectionOutputDef:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
-    def __init__(self, name, attrib, element_tests):
+    def __init__(self, name, attrib, element_tests, element_count: Optional[int] = None):
         self.name = name
         self.collection_type = attrib.get("type", None)
-        count = attrib.get("count", None)
+        if element_count is not None:
+            count = element_count
+        else:
+            count = attrib.get("count")
         self.count = int(count) if count is not None else None
         self.attrib = attrib
         self.element_tests = element_tests
@@ -581,8 +882,29 @@ class TestCollectionOutputDef:
         return TestCollectionOutputDef(
             name=as_dict["name"],
             attrib=as_dict.get("attributes", {}),
-            element_tests=as_dict["element_tests"],
+            element_tests=as_dict.get("element_tests"),
+            element_count=as_dict.get("element_count"),
         )
 
+    @staticmethod
+    def from_yaml_test_format(as_dict):
+        if "attributes" not in as_dict:
+            as_dict["attributes"] = {}
+        attributes = as_dict["attributes"]
+        # setup preferred name "elements" in accordance with work in https://github.com/galaxyproject/planemo/pull/1417
+        # TODO: test this works recursively...
+        if "elements" in as_dict and "element_tests" not in as_dict:
+            as_dict["element_tests"] = as_dict["elements"]
+        if "collection_type" in as_dict:
+            attributes["type"] = as_dict["collection_type"]
+        return TestCollectionOutputDef.from_dict(as_dict)
+
     def to_dict(self):
-        return dict(name=self.name, attributes=self.attrib, element_tests=self.element_tests)
+        return dict(name=self.name, attributes=self.attrib, element_tests=self.element_tests, element_count=self.count)
+
+
+class DrillDownOptionsDict(TypedDict):
+    name: Optional[str]
+    value: str
+    options: List["DrillDownOptionsDict"]
+    selected: bool
diff --git a/lib/galaxy/tool_util/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
index baf61c520cdbdc92d2d97a670f9dc3e473c6da94..81675de7159fdf45f6bf1465dfebf030280de633 100644
--- a/lib/galaxy/tool_util/parser/output_collection_def.py
+++ b/lib/galaxy/tool_util/parser/output_collection_def.py
@@ -2,9 +2,21 @@
 dataset collection after jobs are finished.
 """
 
-from typing import List
+import abc
+from typing import (
+    List,
+    Optional,
+)
 
 from galaxy.util import asbool
+from .output_models import (
+    DatasetCollectionDescriptionT,
+    DiscoverViaT,
+    FilePatternDatasetCollectionDescription as FilePatternDatasetCollectionDescriptionModel,
+    SortCompT,
+    SortKeyT,
+    ToolProvidedMetadataDatasetCollection as ToolProvidedMetadataDatasetCollectionModel,
+)
 from .util import is_dict
 
 DEFAULT_EXTRA_FILENAME_PATTERN = (
@@ -81,7 +93,15 @@ def dataset_collection_description(**kwargs):
         return FilePatternDatasetCollectionDescription(**kwargs)
 
 
-class DatasetCollectionDescription:
+class DatasetCollectionDescription(metaclass=abc.ABCMeta):
+    discover_via: DiscoverViaT
+    default_ext: Optional[str]
+    default_visible: bool
+    assign_primary_output: bool
+    directory: Optional[str]
+    recurse: bool
+    match_relative_path: bool
+
     def __init__(self, **kwargs):
         self.default_dbkey = kwargs.get("dbkey", INPUT_DBKEY_TOKEN)
         self.default_ext = kwargs.get("ext", None)
@@ -91,9 +111,9 @@ class DatasetCollectionDescription:
         self.assign_primary_output = asbool(kwargs.get("assign_primary_output", False))
         self.directory = kwargs.get("directory", None)
         self.recurse = False
-        self.match_relative_path = kwargs.get("match_relative_path", False)
+        self.match_relative_path = asbool(kwargs.get("match_relative_path", False))
 
-    def to_dict(self):
+    def _common_model_props(self):
         return {
             "discover_via": self.discover_via,
             "dbkey": self.default_dbkey,
@@ -105,6 +125,12 @@ class DatasetCollectionDescription:
             "match_relative_path": self.match_relative_path,
         }
 
+    @abc.abstractmethod
+    def to_model(self) -> DatasetCollectionDescriptionT: ...
+
+    def to_dict(self) -> dict:
+        return self.to_model().model_dump()
+
     @property
     def discover_patterns(self) -> List[str]:
         return []
@@ -113,9 +139,27 @@ class DatasetCollectionDescription:
 class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
     discover_via = "tool_provided_metadata"
 
+    def to_model(self) -> ToolProvidedMetadataDatasetCollectionModel:
+        return ToolProvidedMetadataDatasetCollectionModel(
+            discover_via=self.discover_via,
+            dbkey=self.default_dbkey,
+            format=self.default_ext,
+            visible=self.default_visible,
+            assign_primary_output=self.assign_primary_output,
+            directory=self.directory,
+            recurse=self.recurse,
+            match_relative_path=self.match_relative_path,
+        )
+
+    def to_dict(self) -> dict:
+        return self.to_model().model_dump()
+
 
 class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
     discover_via = "pattern"
+    sort_key: SortKeyT
+    sort_comp: SortCompT
+    pattern: str
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
@@ -140,18 +184,21 @@ class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
         self.sort_key = sort_by
         self.sort_comp = sort_comp
 
-    def to_dict(self):
-        as_dict = super().to_dict()
-        as_dict.update(
-            {
-                "sort_key": self.sort_key,
-                "sort_comp": self.sort_comp,
-                "pattern": self.pattern,
-                "recurse": self.recurse,
-                "sort_by": self.sort_by,
-            }
+    def to_model(self) -> FilePatternDatasetCollectionDescriptionModel:
+        return FilePatternDatasetCollectionDescriptionModel(
+            discover_via=self.discover_via,
+            dbkey=self.default_dbkey,
+            format=self.default_ext,
+            visible=self.default_visible,
+            assign_primary_output=self.assign_primary_output,
+            directory=self.directory,
+            recurse=self.recurse,
+            match_relative_path=self.match_relative_path,
+            sort_key=self.sort_key,
+            sort_comp=self.sort_comp,
+            pattern=self.pattern,
+            sort_by=self.sort_by,
         )
-        return as_dict
 
     @property
     def discover_patterns(self) -> List[str]:
diff --git a/lib/galaxy/tool_util/parser/output_models.py b/lib/galaxy/tool_util/parser/output_models.py
new file mode 100644
index 0000000000000000000000000000000000000000..c16d423443a90801ecd4a66779451d501a21380e
--- /dev/null
+++ b/lib/galaxy/tool_util/parser/output_models.py
@@ -0,0 +1,115 @@
+"""Modern pydantic based descriptions of Galaxy tool output objects.
+
+output_objects.py is still used for internals and contain references to the actual tool object
+but the goal here is to switch to using these overtime at least for external APIs and in library
+code where actual tool objects aren't created.
+"""
+
+from typing import (
+    List,
+    Optional,
+    Union,
+)
+
+from pydantic import (
+    BaseModel,
+    Field,
+)
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
+
+from .interface import ToolSource
+
+
+class ToolOutputBaseModel(BaseModel):
+    name: str
+    label: Optional[str]
+    hidden: bool
+
+
+class ToolOutputDataset(ToolOutputBaseModel):
+    type: Literal["data"]
+    format: str
+    format_source: Optional[str]
+    metadata_source: Optional[str]
+    discover_datasets: Optional[List["DatasetCollectionDescriptionT"]]
+
+
+class ToolOutputCollectionStructure(BaseModel):
+    collection_type: Optional[str]
+    collection_type_source: Optional[str]
+    collection_type_from_rules: Optional[str]
+    structured_like: Optional[str]
+    discover_datasets: Optional[List["DatasetCollectionDescriptionT"]]
+
+
+class ToolOutputCollection(ToolOutputBaseModel):
+    type: Literal["collection"]
+    structure: ToolOutputCollectionStructure
+
+
+class ToolOutputSimple(ToolOutputBaseModel):
+    pass
+
+
+class ToolOutputText(ToolOutputSimple):
+    type: Literal["text"]
+
+
+class ToolOutputInteger(ToolOutputSimple):
+    type: Literal["integer"]
+
+
+class ToolOutputFloat(ToolOutputSimple):
+    type: Literal["float"]
+
+
+class ToolOutputBoolean(ToolOutputSimple):
+    type: Literal["boolean"]
+
+
+DiscoverViaT = Literal["tool_provided_metadata", "pattern"]
+SortKeyT = Literal["filename", "name", "designation", "dbkey"]
+SortCompT = Literal["lexical", "numeric"]
+
+
+class DatasetCollectionDescription(BaseModel):
+    discover_via: DiscoverViaT
+    format: Optional[str]
+    visible: bool
+    assign_primary_output: bool
+    directory: Optional[str]
+    recurse: bool
+    match_relative_path: bool
+
+
+class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
+    discover_via: Literal["tool_provided_metadata"]
+
+
+class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
+    discover_via: Literal["pattern"]
+    sort_key: SortKeyT
+    sort_comp: SortCompT
+    pattern: str
+
+
+DatasetCollectionDescriptionT = Union[FilePatternDatasetCollectionDescription, ToolProvidedMetadataDatasetCollection]
+
+
+ToolOutputT = Union[
+    ToolOutputDataset, ToolOutputCollection, ToolOutputText, ToolOutputInteger, ToolOutputFloat, ToolOutputBoolean
+]
+ToolOutput = Annotated[ToolOutputT, Field(discriminator="type")]
+
+
+def from_tool_source(tool_source: ToolSource) -> List[ToolOutput]:
+    tool_outputs, tool_output_collections = tool_source.parse_outputs(None)
+    outputs = []
+    for tool_output in tool_outputs.values():
+        outputs.append(tool_output.to_model())
+    # for tool_output_collection in tool_output_collections.values():
+    #    outputs.append(tool_output_collection.to_model())
+    return outputs
diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index 27d06ca29c2b9b4f5ef360959ef1960306efd337..63148c1fb9465560f05bb9ad50747eec248d5c93 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -3,6 +3,8 @@ from typing import (
     Dict,
     List,
     Optional,
+    Type,
+    Union,
 )
 
 from typing_extensions import TypedDict
@@ -14,6 +16,16 @@ from .output_collection_def import (
     dataset_collector_descriptions_from_output_dict,
     DatasetCollectionDescription,
 )
+from .output_models import (
+    ToolOutputBoolean as ToolOutputBooleanModel,
+    ToolOutputCollection as ToolOutputCollectionModel,
+    ToolOutputCollectionStructure as ToolOutputCollectionStructureModel,
+    ToolOutputDataset as ToolOutputDataModel,
+    ToolOutputFloat as ToolOutputFloatModel,
+    ToolOutputInteger as ToolOutputIntegerModel,
+    ToolOutputT as ToolOutputModel,
+    ToolOutputText as ToolOutputTextModel,
+)
 
 
 class ChangeFormatModel(TypedDict):
@@ -25,6 +37,10 @@ class ChangeFormatModel(TypedDict):
 
 
 class ToolOutputBase(Dictifiable):
+    name: str
+    label: Optional[str]
+    hidden: bool
+
     def __init__(
         self,
         name: str,
@@ -128,9 +144,24 @@ class ToolOutput(ToolOutputBase):
             as_dict["edam_format"] = edam_format
             edam_data = app.datatypes_registry.edam_data.get(self.format)
             as_dict["edam_data"] = edam_data
-        as_dict["discover_datasets"] = [d.to_dict() for d in self.dataset_collector_descriptions]
+        if self.dataset_collector_descriptions:
+            as_dict["discover_datasets"] = [d.to_dict() for d in self.dataset_collector_descriptions]
+        else:
+            as_dict["discover_datasets"] = []
         return as_dict
 
+    def to_model(self) -> ToolOutputDataModel:
+        return ToolOutputDataModel(
+            type="data",
+            name=self.name,
+            label=self.label,
+            hidden=self.hidden,
+            format=self.format,
+            format_source=self.format_source,
+            metadata_source=self.metadata_source or None,  # model is decorated as Optional
+            discover_datasets=[d.to_model() for d in self.dataset_collector_descriptions],
+        )
+
     @staticmethod
     def from_dict(name: str, output_dict: Dict[str, Any], tool: Optional[object] = None) -> "ToolOutput":
         output = ToolOutput(name)
@@ -175,6 +206,31 @@ class ToolExpressionOutput(ToolOutputBase):
         self.implicit = False
         self.from_work_dir = None
 
+    def to_model(self) -> ToolOutputModel:
+        model_class: Union[
+            Type[ToolOutputIntegerModel],
+            Type[ToolOutputFloatModel],
+            Type[ToolOutputBooleanModel],
+            Type[ToolOutputTextModel],
+        ]
+        model_type = self.output_type
+        if self.output_type == "integer":
+            model_class = ToolOutputIntegerModel
+        elif self.output_type == "float":
+            model_class = ToolOutputFloatModel
+        elif self.output_type == "bool":
+            model_class = ToolOutputBooleanModel
+            model_type = "boolean"
+        elif self.output_type == "text":
+            model_class = ToolOutputTextModel
+        assert model_class
+        return model_class(
+            type=model_type,
+            name=self.name,
+            label=self.label,
+            hidden=self.hidden,
+        )
+
 
 class ToolOutputCollection(ToolOutputBase):
     """
@@ -300,6 +356,15 @@ class ToolOutputCollection(ToolOutputBase):
         as_dict["structure"] = self.structure.to_dict()
         return as_dict
 
+    def to_model(self) -> ToolOutputCollectionModel:
+        return ToolOutputCollectionModel(
+            type="collection",
+            name=self.name,
+            label=self.label,
+            hidden=self.hidden,
+            structure=self.structure.to_model(),
+        )
+
     @staticmethod
     def from_dict(name, output_dict, tool=None) -> "ToolOutputCollection":
         structure = ToolOutputCollectionStructure.from_dict(output_dict["structure"])
@@ -323,6 +388,13 @@ class ToolOutputCollection(ToolOutputBase):
 
 
 class ToolOutputCollectionStructure:
+    collection_type: Optional[str]
+    collection_type_source: Optional[str]
+    collection_type_from_rules: Optional[str]
+    structured_like: Optional[str]
+    dataset_collector_descriptions: Optional[List[DatasetCollectionDescription]]
+    dynamic: bool
+
     def __init__(
         self,
         collection_type: Optional[str],
@@ -366,13 +438,19 @@ class ToolOutputCollectionStructure:
         return collection_prototype
 
     def to_dict(self):
-        return {
-            "collection_type": self.collection_type,
-            "collection_type_source": self.collection_type_source,
-            "collection_type_from_rules": self.collection_type_from_rules,
-            "structured_like": self.structured_like,
-            "discover_datasets": [d.to_dict() for d in self.dataset_collector_descriptions],
-        }
+        return self.to_model().dict()
+
+    def to_model(self) -> ToolOutputCollectionStructureModel:
+        discover_datasets = []
+        if self.dataset_collector_descriptions:
+            discover_datasets = [d.to_model() for d in self.dataset_collector_descriptions]
+        return ToolOutputCollectionStructureModel(
+            collection_type=self.collection_type,
+            collection_type_source=self.collection_type_source,
+            collection_type_from_rules=self.collection_type_from_rules,
+            structured_like=self.structured_like,
+            discover_datasets=discover_datasets,
+        )
 
     @staticmethod
     def from_dict(as_dict) -> "ToolOutputCollectionStructure":
diff --git a/lib/galaxy/tool_util/parser/parameter_validators.py b/lib/galaxy/tool_util/parser/parameter_validators.py
new file mode 100644
index 0000000000000000000000000000000000000000..7d2fd77204ed01109fa29518c290a9c3b8a9a3c7
--- /dev/null
+++ b/lib/galaxy/tool_util/parser/parameter_validators.py
@@ -0,0 +1,748 @@
+import json
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Sequence,
+    Union,
+)
+
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    model_validator,
+    PrivateAttr,
+    TypeAdapter,
+)
+from typing_extensions import (
+    Annotated,
+    get_args,
+    Literal,
+    Protocol,
+    Self,
+)
+
+from galaxy.util import (
+    asbool,
+    Element,
+)
+
+try:
+    import regex
+except ImportError:
+    import re as regex
+
+
+class ValidationArgument:
+    doc: Optional[str]
+    xml_body: bool
+    xml_allow_json_load: bool
+
+    def __init__(
+        self,
+        doc: Optional[str],
+        xml_body: bool = False,
+        xml_allow_json_load: bool = False,
+    ):
+        self.doc = doc
+        self.xml_body = xml_body
+        self.xml_allow_json_load = xml_allow_json_load
+
+
+Negate = Annotated[
+    bool,
+    ValidationArgument("Negates the result of the validator."),
+]
+NEGATE_DEFAULT = False
+SPLIT_DEFAULT = "\t"
+DEFAULT_VALIDATOR_MESSAGE = "Parameter validation error."
+
+ValidatorType = Literal[
+    "expression",
+    "regex",
+    "in_range",
+    "length",
+    "metadata",
+    "dataset_metadata_equal",
+    "unspecified_build",
+    "no_options",
+    "empty_field",
+    "empty_dataset",
+    "empty_extra_files_path",
+    "dataset_metadata_in_data_table",
+    "dataset_metadata_not_in_data_table",
+    "dataset_metadata_in_range",
+    "value_in_data_table",
+    "value_not_in_data_table",
+    "dataset_ok_validator",
+    "dataset_metadata_in_file",
+]
+
+
+class StrictModel(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+
+class ParameterValidatorModel(StrictModel):
+    type: ValidatorType
+    message: Annotated[
+        Optional[str],
+        ValidationArgument(
+            """The error message displayed on the tool form if validation fails. A placeholder string ``%s`` will be repaced by the ``value``"""
+        ),
+    ] = None
+    # track validators setup by other input parameters and not validation explicitly
+    implicit: bool = False
+    _static: bool = PrivateAttr(False)
+    _deprecated: bool = PrivateAttr(False)
+    # validators must be explicitly set as 'safe' to operate as user-defined workflow parameters or to be used
+    # within future user-defined tool parameters
+    _safe: bool = PrivateAttr(False)
+
+    @model_validator(mode="after")
+    def set_default_message(self) -> Self:
+        if self.message is None:
+            self.message = self.default_message
+        return self
+
+    @property
+    def default_message(self) -> str:
+        return DEFAULT_VALIDATOR_MESSAGE
+
+
+class StaticValidatorModel(ParameterValidatorModel):
+    _static: bool = PrivateAttr(True)
+
+    def statically_validate(self, v: Any) -> None: ...
+
+
+class ExpressionParameterValidatorModel(StaticValidatorModel):
+    """Check if a one line python expression given expression evaluates to True.
+
+    The expression is given is the content of the validator tag."""
+
+    type: Literal["expression"] = "expression"
+    negate: Negate = NEGATE_DEFAULT
+    expression: Annotated[str, ValidationArgument("Python expression to validate.", xml_body=True)]
+
+    def statically_validate(self, value: Any) -> None:
+        ExpressionParameterValidatorModel.expression_validation(self.expression, value, self)
+
+    @staticmethod
+    def ensure_compiled(expression: Union[str, Any]) -> Any:
+        if isinstance(expression, str):
+            return compile(expression, "<string>", "eval")
+        else:
+            return expression
+
+    @staticmethod
+    def expression_validation(
+        expression: str, value: Any, validator: "ValidatorDescription", compiled_expression: Optional[Any] = None
+    ):
+        if compiled_expression is None:
+            compiled_expression = ExpressionParameterValidatorModel.ensure_compiled(expression)
+        message = None
+        try:
+            evalresult = eval(compiled_expression, dict(value=value))
+        except Exception:
+            message = f"Validator '{expression}' could not be evaluated on '{value}'"
+            evalresult = False
+
+        raise_error_if_valiation_fails(bool(evalresult), validator, message=message, value_to_show=value)
+
+    @property
+    def default_message(self) -> str:
+        return f"Value '%s' does not evaluate to {'True' if not self.negate else 'False'} for '{self.expression}'"
+
+
+class RegexParameterValidatorModel(StaticValidatorModel):
+    """Check if a regular expression **matches** the value, i.e. appears
+    at the beginning of the value. To enforce a match of the complete value use
+    ``$`` at the end of the expression. The expression is given is the content
+    of the validator tag. Note that for ``selects`` each option is checked
+    separately."""
+
+    type: Literal["regex"] = "regex"
+    negate: Negate = NEGATE_DEFAULT
+    expression: Annotated[str, ValidationArgument("Regular expression to validate against.", xml_body=True)]
+    _safe: bool = PrivateAttr(True)
+
+    @property
+    def default_message(self) -> str:
+        return f"Value '%s' does {'not ' if not self.negate else ''}match regular expression '{self.expression.replace('%', '%%')}'"
+
+    def statically_validate(self, value: Any) -> None:
+        if value and not isinstance(value, str):
+            raise ValueError(f"Wrong type found value {value}")
+        RegexParameterValidatorModel.regex_validation(self.expression, value, self)
+
+    @staticmethod
+    def regex_validation(expression: str, value: Any, validator: "ValidatorDescription"):
+        if not isinstance(value, list):
+            value = [value]
+        for val in value:
+            match = regex.match(expression, val or "")
+            raise_error_if_valiation_fails(match is not None, validator, value_to_show=val)
+
+
+class InRangeParameterValidatorModel(StaticValidatorModel):
+    type: Literal["in_range"] = "in_range"
+    min: Optional[Union[float, int]] = None
+    max: Optional[Union[float, int]] = None
+    exclude_min: bool = False
+    exclude_max: bool = False
+    negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
+
+    def statically_validate(self, value: Any):
+        if isinstance(value, (int, float)):
+            validates = True
+            if self.min is not None and value == self.min and self.exclude_min:
+                validates = False
+            elif self.min is not None and value < self.min:
+                validates = False
+            elif self.max is not None and value == self.max and self.exclude_max:
+                validates = False
+            if self.max is not None and value > self.max:
+                validates = False
+            raise_error_if_valiation_fails(validates, self)
+
+    @property
+    def default_message(self) -> str:
+        op1 = "<="
+        op2 = "<="
+        if self.exclude_min:
+            op1 = "<"
+        if self.exclude_max:
+            op2 = "<"
+        min_str = str(self.min) if self.min is not None else "-infinity"
+        max_str = str(self.max) if self.max is not None else "+infinity"
+        range_description_str = f"({min_str} {op1} value {op2} {max_str})"
+        return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"
+
+
+class LengthParameterValidatorModel(StaticValidatorModel):
+    type: Literal["length"] = "length"
+    min: Optional[int] = None
+    max: Optional[int] = None
+    negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
+
+    def statically_validate(self, value: Any):
+        if isinstance(value, str):
+            length = len(value)
+            validates = True
+            if self.min is not None and length < self.min:
+                validates = False
+            if self.max is not None and length > self.max:
+                validates = False
+            raise_error_if_valiation_fails(validates, self)
+
+    @property
+    def default_message(self) -> str:
+        return f"Must {'not ' if self.negate else ''}have length of at least {self.min} and at most {self.max}"
+
+
+class MetadataParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["metadata"] = "metadata"
+    check: Optional[List[str]] = None
+    skip: Optional[List[str]] = None
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        check = self.check
+        skip = self.skip
+        message = DEFAULT_VALIDATOR_MESSAGE
+        if not self.negate:
+            message = "Metadata '%s' missing, click the pencil icon in the history item to edit / save the metadata attributes"
+        else:
+            if check:
+                message = f"""At least one of the checked metadata '{",".join(check)}' is set, click the pencil icon in the history item to edit / save the metadata attributes"""
+            elif skip:
+                message = f"""At least one of the non skipped metadata '{",".join(skip)}' is set, click the pencil icon in the history item to edit / save the metadata attributes"""
+        return message
+
+
+class DatasetMetadataEqualParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_metadata_equal"] = "dataset_metadata_equal"
+    metadata_name: str
+    value: Annotated[Any, ValidationArgument("Value to test against", xml_allow_json_load=True)]
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        if not self.negate:
+            message = f"Metadata value for '{self.metadata_name}' must be '{self.value}', but it is '%s'."
+        else:
+            message = f"Metadata value for '{self.metadata_name}' must not be '{self.value}' but it is."
+        return message
+
+
+class UnspecifiedBuildParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["unspecified_build"] = "unspecified_build"
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return f"{'Unspecified' if not self.negate else 'Specified'} genome build, click the pencil icon in the history item to {'set' if not self.negate else 'remove'} the genome build"
+
+
+class NoOptionsParameterValidatorModel(StaticValidatorModel):
+    type: Literal["no_options"] = "no_options"
+    negate: Negate = NEGATE_DEFAULT
+
+    @staticmethod
+    def no_options_validate(value: Any, validator: "ValidatorDescription"):
+        raise_error_if_valiation_fails(value is not None, validator)
+
+    def statically_validate(self, value: Any) -> None:
+        NoOptionsParameterValidatorModel.no_options_validate(value, self)
+
+    @property
+    def default_message(self) -> str:
+        return f"{'No options' if not self.negate else 'Options'} available for selection"
+
+
+class EmptyFieldParameterValidatorModel(StaticValidatorModel):
+    type: Literal["empty_field"] = "empty_field"
+    negate: Negate = NEGATE_DEFAULT
+
+    @staticmethod
+    def empty_validate(value: Any, validator: "ValidatorDescription"):
+        raise_error_if_valiation_fails((value not in ("", None)), validator)
+
+    def statically_validate(self, value: Any) -> None:
+        EmptyFieldParameterValidatorModel.empty_validate(value, self)
+
+    @property
+    def default_message(self) -> str:
+        if not self.negate:
+            message = "Field requires a value"
+        else:
+            message = "Field must not set a value"
+        return message
+
+
+class EmptyDatasetParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["empty_dataset"] = "empty_dataset"
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return f"The selected dataset is {'non-' if self.negate else ''}empty, this tool expects {'non-' if not self.negate else ''}empty files."
+
+
+class EmptyExtraFilesPathParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["empty_extra_files_path"] = "empty_extra_files_path"
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        negate = self.negate
+        return f"The selected dataset's extra_files_path directory is {'non-' if negate else ''}empty or does {'not ' if not negate else ''}exist, this tool expects {'non-' if not negate else ''}empty extra_files_path directories associated with the selected input."
+
+
+class DatasetMetadataInDataTableParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_metadata_in_data_table"] = "dataset_metadata_in_data_table"
+    table_name: str
+    metadata_name: str
+    metadata_column: Union[int, str]
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return f"Value for metadata {self.metadata_name} was not found in {self.table_name}."
+
+
+class DatasetMetadataNotInDataTableParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_metadata_not_in_data_table"] = "dataset_metadata_not_in_data_table"
+    table_name: str
+    metadata_name: str
+    metadata_column: Union[int, str]
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return f"Value for metadata {self.metadata_name} was not found in {self.table_name}."
+
+
+class DatasetMetadataInRangeParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_metadata_in_range"] = "dataset_metadata_in_range"
+    metadata_name: str
+    min: Optional[Union[float, int]] = None
+    max: Optional[Union[float, int]] = None
+    exclude_min: bool = False
+    exclude_max: bool = False
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        op1 = "<="
+        op2 = "<="
+        if self.exclude_min:
+            op1 = "<"
+        if self.exclude_max:
+            op2 = "<"
+        range_description_str = f"({self.min} {op1} value {op2} {self.max})"
+        return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"
+
+
+class ValueInDataTableParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["value_in_data_table"] = "value_in_data_table"
+    table_name: str
+    metadata_column: Union[int, str]
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return "Value for metadata not found."
+
+
+class ValueNotInDataTableParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["value_not_in_data_table"] = "value_not_in_data_table"
+    table_name: str
+    metadata_column: Union[int, str]
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        return f"Value was not found in {self.table_name}."
+
+
+class DatasetOkValidatorParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_ok_validator"] = "dataset_ok_validator"
+    negate: Negate = NEGATE_DEFAULT
+
+    @property
+    def default_message(self) -> str:
+        if not self.negate:
+            message = (
+                "The selected dataset is still being generated, select another dataset or wait until it is completed"
+            )
+        else:
+            message = "The selected dataset must not be in state OK"
+        return message
+
+
+class DatasetMetadataInFileParameterValidatorModel(ParameterValidatorModel):
+    type: Literal["dataset_metadata_in_file"] = "dataset_metadata_in_file"
+    filename: str
+    metadata_name: str
+    metadata_column: Union[int, str]
+    line_startswith: Optional[str] = None
+    split: str = SPLIT_DEFAULT
+    negate: Negate = NEGATE_DEFAULT
+    _deprecated: bool = PrivateAttr(True)
+
+    @property
+    def default_message(self) -> str:
+        return f"Value for metadata {self.metadata_name} was not found in {self.filename}."
+
+
+AnyValidatorModel = Annotated[
+    Union[
+        ExpressionParameterValidatorModel,
+        RegexParameterValidatorModel,
+        InRangeParameterValidatorModel,
+        LengthParameterValidatorModel,
+        MetadataParameterValidatorModel,
+        DatasetMetadataEqualParameterValidatorModel,
+        UnspecifiedBuildParameterValidatorModel,
+        NoOptionsParameterValidatorModel,
+        EmptyFieldParameterValidatorModel,
+        EmptyDatasetParameterValidatorModel,
+        EmptyExtraFilesPathParameterValidatorModel,
+        DatasetMetadataInDataTableParameterValidatorModel,
+        DatasetMetadataNotInDataTableParameterValidatorModel,
+        DatasetMetadataInRangeParameterValidatorModel,
+        ValueInDataTableParameterValidatorModel,
+        ValueNotInDataTableParameterValidatorModel,
+        DatasetOkValidatorParameterValidatorModel,
+        DatasetMetadataInFileParameterValidatorModel,
+    ],
+    Field(discriminator="type"),
+]
+
+
+DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
+
+
+def parse_dict_validators(validator_dicts: List[Dict[str, Any]], trusted: bool) -> List[AnyValidatorModel]:
+    validator_models = []
+    for validator_dict in validator_dicts:
+        validator = DiscriminatedAnyValidatorModel.validate_python(validator_dict)
+        if not trusted:
+            # Don't risk instantiating unsafe validators for user-defined code
+            assert validator._safe
+        validator_models.append(validator)
+    return validator_models
+
+
+def parse_xml_validators(input_elem: Element) -> List[AnyValidatorModel]:
+    validator_els: List[Element] = input_elem.findall("validator") or []
+    models = []
+    for validator_el in validator_els:
+        models.append(parse_xml_validator(validator_el))
+    return models
+
+
+def static_validators(validator_models: List[AnyValidatorModel]) -> List[AnyValidatorModel]:
+    static_validators = []
+    for validator_model in validator_models:
+        if validator_model._static:
+            static_validators.append(validator_model)
+    return static_validators
+
+
+def parse_xml_validator(validator_el: Element) -> AnyValidatorModel:
+    _type = validator_el.get("type")
+    if _type is None:
+        raise ValueError("Required 'type' attribute missing from validator")
+    valid_types = get_args(ValidatorType)
+    if _type not in valid_types:
+        raise ValueError(f"Unknown 'type' attribute in validator {_type}")
+    validator_type: ValidatorType = cast(ValidatorType, _type)
+    if validator_type == "expression":
+        return ExpressionParameterValidatorModel(
+            type="expression",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+            expression=validator_el.text,
+        )
+    elif validator_type == "regex":
+        return RegexParameterValidatorModel(
+            type="regex",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+            expression=validator_el.text,
+        )
+    elif validator_type == "in_range":
+        return InRangeParameterValidatorModel(
+            type="in_range",
+            message=_parse_message(validator_el),
+            min=_parse_number(validator_el, "min"),
+            max=_parse_number(validator_el, "max"),
+            exclude_min=_parse_bool(validator_el, "exclude_min", False),
+            exclude_max=_parse_bool(validator_el, "exclude_max", False),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "length":
+        return LengthParameterValidatorModel(
+            type="length",
+            min=_parse_int(validator_el, "min"),
+            max=_parse_int(validator_el, "max"),
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "metadata":
+        return MetadataParameterValidatorModel(
+            type="metadata",
+            message=_parse_message(validator_el),
+            check=_parse_str_list(validator_el, "check"),
+            skip=_parse_str_list(validator_el, "skip"),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_metadata_equal":
+        return DatasetMetadataEqualParameterValidatorModel(
+            type="dataset_metadata_equal",
+            metadata_name=validator_el.get("metadata_name"),
+            value=_parse_json_value(validator_el),
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "unspecified_build":
+        return UnspecifiedBuildParameterValidatorModel(
+            type="unspecified_build",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "no_options":
+        return NoOptionsParameterValidatorModel(
+            type="no_options",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "empty_field":
+        return EmptyFieldParameterValidatorModel(
+            type="empty_field",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "empty_dataset":
+        return EmptyDatasetParameterValidatorModel(
+            type="empty_dataset",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "empty_extra_files_path":
+        return EmptyExtraFilesPathParameterValidatorModel(
+            type="empty_extra_files_path",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_metadata_in_data_table":
+        return DatasetMetadataInDataTableParameterValidatorModel(
+            type="dataset_metadata_in_data_table",
+            message=_parse_message(validator_el),
+            table_name=validator_el.get("table_name"),
+            metadata_name=validator_el.get("metadata_name"),
+            metadata_column=_parse_metadata_column(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_metadata_not_in_data_table":
+        return DatasetMetadataNotInDataTableParameterValidatorModel(
+            type="dataset_metadata_not_in_data_table",
+            message=_parse_message(validator_el),
+            table_name=validator_el.get("table_name"),
+            metadata_name=validator_el.get("metadata_name"),
+            metadata_column=_parse_metadata_column(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_metadata_in_range":
+        return DatasetMetadataInRangeParameterValidatorModel(
+            type="dataset_metadata_in_range",
+            message=_parse_message(validator_el),
+            metadata_name=validator_el.get("metadata_name"),
+            min=_parse_number(validator_el, "min"),
+            max=_parse_number(validator_el, "max"),
+            exclude_min=_parse_bool(validator_el, "exclude_min", False),
+            exclude_max=_parse_bool(validator_el, "exclude_max", False),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "value_in_data_table":
+        return ValueInDataTableParameterValidatorModel(
+            type="value_in_data_table",
+            message=_parse_message(validator_el),
+            table_name=validator_el.get("table_name"),
+            metadata_column=_parse_metadata_column(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "value_not_in_data_table":
+        return ValueNotInDataTableParameterValidatorModel(
+            type="value_not_in_data_table",
+            message=_parse_message(validator_el),
+            table_name=validator_el.get("table_name"),
+            metadata_column=_parse_metadata_column(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_ok_validator":
+        return DatasetOkValidatorParameterValidatorModel(
+            type="dataset_ok_validator",
+            message=_parse_message(validator_el),
+            negate=_parse_negate(validator_el),
+        )
+    elif validator_type == "dataset_metadata_in_file":
+        filename = validator_el.get("filename")
+        return DatasetMetadataInFileParameterValidatorModel(
+            type="dataset_metadata_in_file",
+            message=_parse_message(validator_el),
+            filename=filename,
+            metadata_name=validator_el.get("metadata_name"),
+            metadata_column=_parse_metadata_column(validator_el),
+            line_startswith=validator_el.get("line_startswith"),
+            split=validator_el.get("split", SPLIT_DEFAULT),
+            negate=_parse_negate(validator_el),
+        )
+    else:
+        raise ValueError(f"Unhandled 'type' attribute in validator {validator_type}")
+
+
+class ValidatorDescription(Protocol):
+
+    @property
+    def negate(self) -> bool: ...
+
+    @property
+    def message(self) -> Optional[str]: ...
+
+
+def raise_error_if_valiation_fails(
+    value: bool, validator: ValidatorDescription, message: Optional[str] = None, value_to_show: Optional[str] = None
+):
+    if not isinstance(value, bool):
+        raise AssertionError("Validator logic problem - computed validation value must be boolean")
+    if message is None:
+        message = validator.message
+    if not message:
+        message = DEFAULT_VALIDATOR_MESSAGE
+    assert message is not None
+    if value_to_show and "%s" in message:
+        message = message % value_to_show
+    negate = validator.negate
+    if (not negate and value) or (negate and not value):
+        return
+    else:
+        raise ValueError(message)
+
+
+def _parse_message(xml_el: Element) -> Optional[str]:
+    message = cast(Optional[str], xml_el.get("message"))
+    return message
+
+
+def _parse_int(xml_el: Element, attribute: str) -> Optional[int]:
+    raw_value = xml_el.get(attribute)
+    if raw_value:
+        return int(raw_value)
+    else:
+        return None
+
+
+def _parse_number(xml_el: Element, attribute: str) -> Optional[Union[float, int]]:
+    raw_value = xml_el.get(attribute)
+    if raw_value and ("." in raw_value or "e" in raw_value or "inf" in raw_value):
+        return float(raw_value)
+    elif raw_value:
+        return int(raw_value)
+    else:
+        return None
+
+
+def _parse_negate(xml_el: Element) -> bool:
+    return _parse_bool(xml_el, "negate", False)
+
+
+def _parse_bool(xml_el: Element, attribute: str, default_value: bool) -> bool:
+    return asbool(xml_el.get(attribute, default_value))
+
+
+def _parse_str_list(xml_el: Element, attribute: str) -> List[str]:
+    raw_value = xml_el.get(attribute)
+    if not raw_value:
+        return []
+    else:
+        return [v.strip() for v in raw_value.split(",")]
+
+
+def _parse_json_value(xml_el: Element) -> Any:
+    value = xml_el.get("value", None) or json.loads(xml_el.get("value_json", "null"))
+    return value
+
+
+def _parse_metadata_column(xml_el: Element) -> Union[int, str]:
+    column = xml_el.get("metadata_column", 0)
+    try:
+        return int(column)
+    except ValueError:
+        return column
+
+
+def static_tool_validators(validators: Sequence[ParameterValidatorModel]) -> List[StaticValidatorModel]:
+    static_validators: List[StaticValidatorModel] = []
+    for validator in validators:
+        if isinstance(validator, StaticValidatorModel):
+            static_validators.append(validator)
+    return static_validators
+
+
+def statically_validates(validators: Sequence[ParameterValidatorModel], value: Any) -> bool:
+    for validator in static_tool_validators(validators):
+        try:
+            validator.statically_validate(value)
+        except ValueError:
+            return False
+    return True
diff --git a/lib/galaxy/tool_util/parser/util.py b/lib/galaxy/tool_util/parser/util.py
index 46cd012809a057c235a7f1f9647a756c8acd5517..34f3e0943eeab93424e2e7e1deddea259a40e989 100644
--- a/lib/galaxy/tool_util/parser/util.py
+++ b/lib/galaxy/tool_util/parser/util.py
@@ -1,4 +1,21 @@
 from collections import OrderedDict
+from typing import (
+    Optional,
+    Tuple,
+    TYPE_CHECKING,
+    Union,
+)
+
+from packaging.version import Version
+
+from galaxy.util import string_as_bool
+from .parameter_validators import statically_validates
+
+if TYPE_CHECKING:
+    from .interface import (
+        InputSource,
+        ToolSource,
+    )
 
 DEFAULT_DELTA = 10000
 DEFAULT_DELTA_FRAC = None
@@ -6,6 +23,8 @@ DEFAULT_DELTA_FRAC = None
 DEFAULT_METRIC = "mae"
 DEFAULT_EPS = 0.01
 DEFAULT_PIN_LABELS = None
+DEFAULT_SORT = False
+DEFAULT_DECOMPRESS = False
 
 
 def is_dict(item):
@@ -23,3 +42,74 @@ def _parse_name(name, argument):
             raise ValueError("parameter must specify a 'name' or 'argument'.")
         name = argument.lstrip("-").replace("-", "_")
     return name
+
+
+def parse_profile_version(tool_source: "ToolSource") -> float:
+    return float(tool_source.parse_profile())
+
+
+def parse_tool_version_with_defaults(
+    id: Optional[str], tool_source: "ToolSource", profile: Optional[Version] = None
+) -> str:
+    if profile is None:
+        profile = Version(tool_source.parse_profile())
+
+    version = tool_source.parse_version()
+    if not version:
+        if profile < Version("16.04"):
+            # For backward compatibility, some tools may not have versions yet.
+            version = "1.0.0"
+        else:
+            raise Exception(f"Missing tool 'version' for tool with id '{id}' at '{tool_source}'")
+    return version
+
+
+def boolean_is_checked(input_source: "InputSource"):
+    nullable = input_source.get_bool("optional", False)
+    return input_source.get_bool("checked", None if nullable else False)
+
+
+def boolean_true_and_false_values(input_source, profile: Optional[Union[float, str]] = None) -> Tuple[str, str]:
+    truevalue = input_source.get("truevalue", "true")
+    falsevalue = input_source.get("falsevalue", "false")
+    if profile and Version(str(profile)) >= Version("23.1"):
+        if truevalue == falsevalue:
+            raise ParameterParseException("Cannot set true and false to the same value")
+        if truevalue.lower() == "false":
+            raise ParameterParseException(
+                f"Cannot set truevalue to [{truevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case."
+            )
+        if falsevalue.lower() == "true":
+            raise ParameterParseException(
+                f"Cannot set falsevalue to [{falsevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case."
+            )
+    return (truevalue, falsevalue)
+
+
+def text_input_is_optional(input_source: "InputSource") -> Tuple[bool, bool]:
+    # Optionality not explicitly defined, default to False
+    optional: Optional[bool] = False
+    optionality_inferred: bool = False
+
+    optional = input_source.get("optional", None)
+    if optional is not None:
+        optional = string_as_bool(optional)
+    else:
+        # A text parameter that doesn't raise a validation error on empty string
+        # is considered to be optional
+        if statically_validates(input_source.parse_validators(), ""):
+            optional = True
+            optionality_inferred = True
+        else:
+            optional = False
+
+    assert isinstance(optional, bool)
+    return optional, optionality_inferred
+
+
+class ParameterParseException(Exception):
+    message: str
+
+    def __init__(self, message):
+        super().__init__(message)
+        self.message = message
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 4c09c6fa4963b164530b8cda3019039973cdb00b..929bb56b891798dc6013c7cb185e4a5139627b45 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -11,36 +11,56 @@ from typing import (
     Iterable,
     List,
     Optional,
+    Tuple,
 )
 
 from packaging.version import Version
 
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import (
+    DEFAULT_DECOMPRESS,
     DEFAULT_DELTA,
     DEFAULT_DELTA_FRAC,
     DEFAULT_EPS,
     DEFAULT_METRIC,
     DEFAULT_PIN_LABELS,
+    DEFAULT_SORT,
 )
 from galaxy.util import (
     Element,
     ElementTree,
     string_as_bool,
+    string_as_bool_or_none,
+    XML,
     xml_text,
     xml_to_string,
 )
 from .interface import (
     AssertionList,
+    Citation,
+    DrillDownDynamicOptions,
+    DrillDownOptionsDict,
+    DynamicOptions,
+    HelpContent,
     InputSource,
+    OutputCompareType,
     PageSource,
     PagesSource,
     RequiredFiles,
-    TestCollectionDef,
+    TestCollectionDefElementDict,
+    TestCollectionDefElementObject,
     TestCollectionOutputDef,
     ToolSource,
     ToolSourceTest,
+    ToolSourceTestInput,
+    ToolSourceTestInputAttributes,
+    ToolSourceTestInputs,
+    ToolSourceTestOutput,
+    ToolSourceTestOutputAttributes,
+    ToolSourceTestOutputs,
     ToolSourceTests,
+    XmlTestCollectionDefDict,
+    XrefDict,
 )
 from .output_actions import ToolOutputActionGroup
 from .output_collection_def import dataset_collector_descriptions_from_elem
@@ -51,6 +71,10 @@ from .output_objects import (
     ToolOutputCollection,
     ToolOutputCollectionStructure,
 )
+from .parameter_validators import (
+    AnyValidatorModel,
+    parse_xml_validators,
+)
 from .stdio import (
     aggressive_error_checks,
     error_on_exit_code,
@@ -142,7 +166,7 @@ class XmlToolSource(ToolSource):
         self.root = None
         self._xml_tree = None
 
-    def parse_version(self):
+    def parse_version(self) -> Optional[str]:
         return self.root.get("version", None)
 
     def parse_id(self):
@@ -170,11 +194,10 @@ class XmlToolSource(ToolSource):
 
     def parse_tool_type(self):
         root = self.root
-        if root.get("tool_type", None) is not None:
-            return root.get("tool_type")
+        return root.get("tool_type")
 
     def parse_name(self):
-        return self.root.get("name")
+        return self.root.get("name") or self.parse_id()
 
     def parse_edam_operations(self):
         edam_ops = self.root.find("edam_operations")
@@ -188,17 +211,17 @@ class XmlToolSource(ToolSource):
             return []
         return [edam_topic.text for edam_topic in edam_topics.findall("edam_topic")]
 
-    def parse_xrefs(self):
+    def parse_xrefs(self) -> List[XrefDict]:
         xrefs = self.root.find("xrefs")
         if xrefs is None:
             return []
         return [
-            dict(value=xref.text.strip(), reftype=xref.attrib["type"])
+            XrefDict(value=xref.text.strip(), reftype=str(xref.attrib["type"]))
             for xref in xrefs.findall("xref")
-            if xref.get("type")
+            if xref.get("type") and xref.text
         ]
 
-    def parse_description(self):
+    def parse_description(self) -> str:
         return xml_text(self.root, "description")
 
     def parse_display_interface(self, default):
@@ -362,6 +385,10 @@ class XmlToolSource(ToolSource):
     def _command_el(self):
         return self.root.find("command")
 
+    @property
+    def _outputs_el(self):
+        return self.root.find("outputs")
+
     def _get_attribute_as_bool(self, attribute, default, elem=None):
         if elem is None:
             elem = self.root
@@ -392,12 +419,12 @@ class XmlToolSource(ToolSource):
     def parse_requirements_and_containers(self):
         return requirements.parse_requirements_from_xml(self.root, parse_resources=True)
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> "XmlPagesSource":
         return XmlPagesSource(self.root)
 
     def parse_provided_metadata_style(self):
         style = None
-        out_elem = self.root.find("outputs")
+        out_elem = self._outputs_el
         if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
             style = out_elem.attrib["provided_metadata_style"]
 
@@ -415,7 +442,7 @@ class XmlToolSource(ToolSource):
 
         return provided_metadata_file
 
-    def parse_outputs(self, tool):
+    def parse_outputs(self, tool=None):
         out_elem = self.root.find("outputs")
         outputs = {}
         output_collections = {}
@@ -539,7 +566,7 @@ class XmlToolSource(ToolSource):
         output.default_identifier_source = data_elem.get("default_identifier_source", "None")
         output.metadata_source = data_elem.get("metadata_source", default_metadata_source)
         output.parent = data_elem.get("parent", None)
-        output.label = xml_text(data_elem, "label")
+        output.label = xml_text(data_elem, "label", None)
         output.count = int(data_elem.get("count", 1))
         output.filters = data_elem.findall("filter")
         output.tool = tool
@@ -550,7 +577,12 @@ class XmlToolSource(ToolSource):
             # This ensures that old tools continue to work.
             output.from_work_dir = output.from_work_dir.strip()
         output.hidden = string_as_bool(data_elem.get("hidden", ""))
-        output.actions = ToolOutputActionGroup(output, data_elem.find("actions"))
+        if tool is not None:
+            # poor design here driven entirely by pragmatism in refactoring, ToolOutputActionGroup
+            # belongs in galaxy-tool because it uses app heavily. Breaking the output objects
+            # into app-aware things and dumb models would be a large project but superior design
+            # and decomposition.
+            output.actions = ToolOutputActionGroup(output, data_elem.find("actions"))
         output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(
             data_elem, legacy=self.legacy_defaults
         )
@@ -565,7 +597,7 @@ class XmlToolSource(ToolSource):
             from_expression,
         )
         output.path = output_elem.get("value")
-        output.label = xml_text(output_elem, "label")
+        output.label = xml_text(output_elem, "label", None)
 
         output.hidden = string_as_bool(output_elem.get("hidden", ""))
         output.actions = ToolOutputActionGroup(output, output_elem.find("actions"))
@@ -630,9 +662,14 @@ class XmlToolSource(ToolSource):
         else:
             return string_as_bool(default)
 
-    def parse_help(self):
+    def parse_help(self) -> Optional[HelpContent]:
         help_elem = self.root.find("help")
-        return help_elem.text if help_elem is not None else None
+        if help_elem is None:
+            return None
+
+        help_format = help_elem.get("format", "restructuredtext")
+        content = help_elem.text or ""
+        return HelpContent(format=help_format, content=content)
 
     @property
     def macro_paths(self):
@@ -663,9 +700,24 @@ class XmlToolSource(ToolSource):
         # - Enable buggy interpreter attribute.
         return self.root.get("profile", "16.01")
 
-    def parse_license(self):
+    def parse_license(self) -> Optional[str]:
         return self.root.get("license")
 
+    def parse_citations(self) -> List[Citation]:
+        """Return a list of citations."""
+        citations: List[Citation] = []
+        root = self.root
+        citations_elem = root.find("citations")
+        if citations_elem is None:
+            return citations
+
+        for citation_elem in citations_elem:
+            citation = parse_citation_elem(citation_elem)
+            if citation:
+                citations.append(citation)
+
+        return citations
+
     def parse_python_template_version(self):
         python_template_version = self.root.get("python_template_version")
         if python_template_version is not None:
@@ -711,21 +763,21 @@ def _test_elem_to_dict(test_elem, i, profile=None) -> ToolSourceTest:
     return rval
 
 
-def __parse_input_elems(test_elem, i):
+def __parse_input_elems(test_elem, i) -> ToolSourceTestInputs:
     __expand_input_elems(test_elem)
     return __parse_inputs_elems(test_elem, i)
 
 
-def __parse_output_elems(test_elem):
-    outputs = []
+def __parse_output_elems(test_elem) -> ToolSourceTestOutputs:
+    outputs: ToolSourceTestOutputs = []
     for output_elem in test_elem.findall("output"):
         name, file, attributes = __parse_output_elem(output_elem)
-        outputs.append({"name": name, "value": file, "attributes": attributes})
+        outputs.append(ToolSourceTestOutput({"name": name, "value": file, "attributes": attributes}))
     return outputs
 
 
 def __parse_output_elem(output_elem):
-    attrib = dict(output_elem.attrib)
+    attrib = _element_to_dict(output_elem)
     name = attrib.pop("name", None)
     if name is None:
         raise Exception("Test output does not have a 'name'")
@@ -747,7 +799,7 @@ def __parse_output_collection_elems(test_elem, profile=None):
 
 
 def __parse_output_collection_elem(output_collection_elem, profile=None):
-    attrib = dict(output_collection_elem.attrib)
+    attrib = _element_to_dict(output_collection_elem)
     name = attrib.pop("name", None)
     if name is None:
         raise Exception("Test output collection does not have a 'name'")
@@ -758,7 +810,7 @@ def __parse_output_collection_elem(output_collection_elem, profile=None):
 def __parse_element_tests(parent_element, profile=None):
     element_tests = {}
     for idx, element in enumerate(parent_element.findall("element")):
-        element_attrib = dict(element.attrib)
+        element_attrib: dict = _element_to_dict(element)
         identifier = element_attrib.pop("name", None)
         if identifier is None:
             raise Exception("Test primary dataset does not have a 'identifier'")
@@ -771,59 +823,65 @@ def __parse_element_tests(parent_element, profile=None):
     return element_tests
 
 
-def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False, profile=None):
+VALUE_OBJECT_UNSET = object()
+
+
+def __parse_test_attributes(
+    output_elem, attrib, parse_elements=False, parse_discovered_datasets=False, profile=None
+) -> Tuple[Optional[str], ToolSourceTestOutputAttributes]:
     assert_list = __parse_assert_list(output_elem)
 
     # Allow either file or value to specify a target file to compare result with
     # file was traditionally used by outputs and value by extra files.
-    file = attrib.pop("file", attrib.pop("value", None))
+    file: Optional[str] = attrib.pop("file", attrib.pop("value", None))
 
     # File no longer required if an list of assertions was present.
-    attributes = {}
 
+    value_object: Any = VALUE_OBJECT_UNSET
     if "value_json" in attrib:
-        attributes["object"] = json.loads(attrib.pop("value_json"))
+        value_object = json.loads(attrib.pop("value_json"))
 
     # Method of comparison
-    attributes["compare"] = attrib.pop("compare", "diff").lower()
+    compare: OutputCompareType = cast(OutputCompareType, attrib.pop("compare", "diff").lower())
     # Number of lines to allow to vary in logs (for dates, etc)
-    attributes["lines_diff"] = int(attrib.pop("lines_diff", "0"))
+    lines_diff: int = int(attrib.pop("lines_diff", "0"))
     # Allow a file size to vary if sim_size compare
-    attributes["delta"] = int(attrib.pop("delta", DEFAULT_DELTA))
-    attributes["delta_frac"] = float(attrib["delta_frac"]) if "delta_frac" in attrib else DEFAULT_DELTA_FRAC
-    attributes["sort"] = string_as_bool(attrib.pop("sort", False))
-    attributes["decompress"] = string_as_bool(attrib.pop("decompress", False))
+    delta: int = int(attrib.pop("delta", DEFAULT_DELTA))
+    delta_frac: Optional[float] = float(attrib["delta_frac"]) if "delta_frac" in attrib else DEFAULT_DELTA_FRAC
+    sort: bool = string_as_bool(attrib.pop("sort", DEFAULT_SORT))
+    decompress: bool = string_as_bool(attrib.pop("decompress", DEFAULT_DECOMPRESS))
     # `location` may contain an URL to a remote file that will be used to download `file` (if not already present on disk).
-    location = attrib.get("location")
-    # Parameters for "image_diff" comparison
-    attributes["metric"] = attrib.pop("metric", DEFAULT_METRIC)
-    attributes["eps"] = float(attrib.pop("eps", DEFAULT_EPS))
-    attributes["pin_labels"] = attrib.pop("pin_labels", DEFAULT_PIN_LABELS)
+    location: Optional[str] = attrib.get("location")
     if location and file is None:
         file = os.path.basename(location)  # If no file specified, try to get filename from URL last component
-    attributes["location"] = location
+    # Parameters for "image_diff" comparison
+    metric: str = attrib.pop("metric", DEFAULT_METRIC)
+    eps: float = float(attrib.pop("eps", DEFAULT_EPS))
+    pin_labels: Optional[Any] = attrib.pop("pin_labels", DEFAULT_PIN_LABELS)
+    count: Optional[int] = None
     try:
-        attributes["count"] = int(attrib.pop("count"))
+        count = int(attrib.pop("count"))
     except KeyError:
-        attributes["count"] = None
-    extra_files = []
+        pass
+    extra_files: List[Dict[str, Any]] = []
+    ftype: Optional[str] = None
     if "ftype" in attrib:
-        attributes["ftype"] = attrib["ftype"]
+        ftype = attrib["ftype"]
     for extra in output_elem.findall("extra_files"):
         extra_files.append(__parse_extra_files_elem(extra))
-    metadata = {}
+    metadata: Dict[str, Any] = {}
     for metadata_elem in output_elem.findall("metadata"):
         metadata[metadata_elem.get("name")] = metadata_elem.get("value")
     md5sum = attrib.get("md5", None)
     checksum = attrib.get("checksum", None)
-    element_tests = {}
+    element_tests: Dict[str, Any] = {}
     if parse_elements:
         element_tests = __parse_element_tests(output_elem, profile=profile)
 
-    primary_datasets = {}
+    primary_datasets: Dict[str, Any] = {}
     if parse_discovered_datasets:
         for primary_elem in output_elem.findall("discovered_dataset") or []:
-            primary_attrib = dict(primary_elem.attrib)
+            primary_attrib = _element_to_dict(primary_elem)
             designation = primary_attrib.pop("designation", None)
             if designation is None:
                 raise Exception("Test primary dataset does not have a 'designation'")
@@ -831,22 +889,38 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
 
     has_checksum = md5sum or checksum
     has_nested_tests = extra_files or element_tests or primary_datasets
-    has_object = "object" in attributes
+    has_object = value_object is not VALUE_OBJECT_UNSET
     if not (assert_list or file or metadata or has_checksum or has_nested_tests or has_object):
         raise Exception(
             "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)"
         )
-    attributes["assert_list"] = assert_list
-    attributes["extra_files"] = extra_files
-    attributes["metadata"] = metadata
-    attributes["md5"] = md5sum
-    attributes["checksum"] = checksum
-    attributes["elements"] = element_tests
-    attributes["primary_datasets"] = primary_datasets
+    attributes = ToolSourceTestOutputAttributes(
+        ftype=ftype,
+        compare=compare,
+        lines_diff=lines_diff,
+        delta=delta,
+        delta_frac=delta_frac,
+        sort=sort,
+        decompress=decompress,
+        metric=metric,
+        eps=eps,
+        pin_labels=pin_labels,
+        location=location,
+        count=count,
+        metadata=metadata,
+        md5=md5sum,
+        checksum=checksum,
+        primary_datasets=primary_datasets,
+        elements=element_tests,
+        assert_list=assert_list,
+        extra_files=extra_files,
+    )
+    if value_object is not VALUE_OBJECT_UNSET:
+        attributes["object"] = value_object
     return file, attributes
 
 
-def __parse_assert_list(output_elem):
+def __parse_assert_list(output_elem) -> AssertionList:
     assert_elem = output_elem.find("assert_contents")
     return __parse_assert_list_from_elem(assert_elem)
 
@@ -857,7 +931,7 @@ def __parse_assert_list_from_elem(assert_elem) -> AssertionList:
     def convert_elem(elem):
         """Converts and XML element to a dictionary format, used by assertion checking code."""
         tag = elem.tag
-        attributes = dict(elem.attrib)
+        attributes = _element_to_dict(elem)
         converted_children = []
         for child_elem in elem:
             converted_children.append(convert_elem(child_elem))
@@ -874,7 +948,7 @@ def __parse_assert_list_from_elem(assert_elem) -> AssertionList:
 def __parse_extra_files_elem(extra):
     # File or directory, when directory, compare basename
     # by basename
-    attrib = dict(extra.attrib)
+    attrib = _element_to_dict(extra)
     extra_type = attrib.pop("type", "file")
     extra_name = attrib.pop("name", None)
     assert (
@@ -937,16 +1011,41 @@ def _copy_to_dict_if_present(elem, rval, attributes):
     return rval
 
 
-def __parse_inputs_elems(test_elem, i):
-    raw_inputs = []
+def __parse_inputs_elems(test_elem, i) -> ToolSourceTestInputs:
+    raw_inputs: ToolSourceTestInputs = []
     for param_elem in test_elem.findall("param"):
         raw_inputs.append(__parse_param_elem(param_elem, i))
 
     return raw_inputs
 
 
-def __parse_param_elem(param_elem, i=0):
-    attrib = dict(param_elem.attrib)
+def _test_collection_def_dict(elem: Element) -> XmlTestCollectionDefDict:
+    elements: List[TestCollectionDefElementDict] = []
+    attrib: Dict[str, Any] = _element_to_dict(elem)
+    collection_type = attrib["type"]
+    name = attrib.get("name", "Unnamed Collection")
+    for element in elem.findall("element"):
+        element_attrib: Dict[str, Any] = _element_to_dict(element)
+        element_identifier = element_attrib["name"]
+        nested_collection_elem = element.find("collection")
+        element_definition: TestCollectionDefElementObject
+        if nested_collection_elem is not None:
+            element_definition = _test_collection_def_dict(nested_collection_elem)
+        else:
+            element_definition = __parse_param_elem(element)
+        elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
+
+    return XmlTestCollectionDefDict(
+        model_class="TestCollectionDef",
+        attributes=attrib,
+        collection_type=collection_type,
+        elements=elements,
+        name=name,
+    )
+
+
+def __parse_param_elem(param_elem, i=0) -> ToolSourceTestInput:
+    attrib: ToolSourceTestInputAttributes = dict(param_elem.attrib)
     if "values" in attrib:
         value = attrib["values"].split(",")
     elif "value" in attrib:
@@ -983,7 +1082,7 @@ def __parse_param_elem(param_elem, i=0):
             elif child.tag == "edit_attributes":
                 attrib["edit_attributes"].append(child)
             elif child.tag == "collection":
-                attrib["collection"] = TestCollectionDef.from_xml(child, __parse_param_elem)
+                attrib["collection"] = _test_collection_def_dict(child)
         if composite_data_name:
             # Composite datasets need implicit renaming;
             # inserted at front of list so explicit declarations
@@ -1203,6 +1302,27 @@ class XmlPageSource(PageSource):
         return list(map(XmlInputSource, self.parent_elem))
 
 
+class XmlDynamicOptions(DynamicOptions):
+
+    def __init__(self, options_elem: Element, dynamic_option_code: Optional[str]):
+        self._options_elem = options_elem
+        self._dynamic_options_code = dynamic_option_code
+
+    def elem(self) -> Element:
+        return self._options_elem
+
+    def get_dynamic_options_code(self) -> Optional[str]:
+        """If dynamic options are a piece of code to eval, return it."""
+        return self._dynamic_options_code
+
+    def get_data_table_name(self) -> Optional[str]:
+        """If dynamic options are loaded from a data table, return the name."""
+        return self._options_elem.get("from_data_table") if self._options_elem is not None else None
+
+    def get_index_file_name(self) -> Optional[str]:
+        return self._options_elem.get("from_file") if self._options_elem is not None else None
+
+
 class XmlInputSource(InputSource):
     def __init__(self, input_elem):
         self.input_elem = input_elem
@@ -1220,6 +1340,9 @@ class XmlInputSource(InputSource):
     def get_bool(self, key, default):
         return string_as_bool(self.get(key, default))
 
+    def get_bool_or_none(self, key, default):
+        return string_as_bool_or_none(self.get(key, default))
+
     def parse_label(self):
         return xml_text(self.input_elem, "label")
 
@@ -1229,17 +1352,20 @@ class XmlInputSource(InputSource):
     def parse_sanitizer_elem(self):
         return self.input_elem.find("sanitizer")
 
-    def parse_validator_elems(self):
-        return self.input_elem.findall("validator")
+    def parse_validators(self) -> List[AnyValidatorModel]:
+        return parse_xml_validators(self.input_elem)
 
-    def parse_dynamic_options_elem(self):
-        """Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
-        if appropriate.
-        """
+    def parse_dynamic_options(self) -> Optional[XmlDynamicOptions]:
+        """Return a XmlDynamicOptions to describe dynamic options if options elem is available."""
         options_elem = self.input_elem.find("options")
-        return options_elem
+        dynamic_option_code = self.input_elem.get("dynamic_options")
+        is_dynamic = options_elem is not None or dynamic_option_code is not None
+        if is_dynamic:
+            return XmlDynamicOptions(options_elem, dynamic_option_code)
+        else:
+            return None
 
-    def parse_static_options(self):
+    def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         """
         >>> from galaxy.util import parse_xml_string_to_etree
         >>> xml = '<param><option value="a">A</option><option value="b">B</option></param>'
@@ -1262,6 +1388,40 @@ class XmlInputSource(InputSource):
             deduplicated_static_options[value] = (text, value, selected)
         return list(deduplicated_static_options.values())
 
+    def parse_drill_down_dynamic_options(
+        self, tool_data_path: Optional[str] = None
+    ) -> Optional[DrillDownDynamicOptions]:
+        elem = self.input_elem
+        dynamic_options_raw = elem.get("dynamic_options", None)
+        dynamic_options: Optional[str] = str(dynamic_options_raw) if dynamic_options_raw else None
+        if dynamic_options is None:
+            return None
+        else:
+            return XmlDrillDownDynamicOptions(code_block=dynamic_options)
+
+    def parse_drill_down_static_options(
+        self, tool_data_path: Optional[str] = None
+    ) -> Optional[List[DrillDownOptionsDict]]:
+        from_file = self.input_elem.get("from_file", None)
+        if from_file:
+            if not os.path.isabs(from_file):
+                assert tool_data_path, "This tool cannot be parsed outside of a Galaxy context"
+                from_file = os.path.join(tool_data_path, from_file)
+            elem = XML(f"<root>{open(from_file).read()}</root>")
+        else:
+            elem = self.input_elem
+
+        dynamic_options_elem = elem.get("dynamic_options", None)
+        filter_elem = elem.get("filter", None)
+        if dynamic_options_elem is not None and filter_elem is not None:
+            return None
+
+        root_options: List[DrillDownOptionsDict] = []
+        options_elem = elem.find("options")
+        assert options_elem, "Non-dynamic drilldown parameters must supply an options element"
+        _recurse_drill_down_elems(root_options, options_elem.findall("option"))
+        return root_options
+
     def parse_optional(self, default=None):
         """Return boolean indicating whether parameter is optional."""
         elem = self.input_elem
@@ -1376,3 +1536,52 @@ class ParallelismInfo:
             # legacy basic mode - provide compatible defaults
             self.attributes["split_size"] = 20
             self.attributes["split_mode"] = "number_of_parts"
+
+
+def parse_citation_elem(citation_elem: Element) -> Optional[Citation]:
+    if citation_elem.tag != "citation":
+        return None
+
+    citation_type = citation_elem.attrib.get("type", None)
+    citation_raw_text = citation_elem.text
+    assert citation_raw_text
+    content = citation_raw_text.strip()
+
+    return Citation(
+        type=citation_type,
+        content=content,
+    )
+
+
+class XmlDrillDownDynamicOptions(DrillDownDynamicOptions):
+
+    def __init__(self, code_block: Optional[str]):
+        self._code_block = code_block
+
+    def from_code_block(self) -> Optional[str]:
+        """Get a code block to do an eval on."""
+        return self._code_block
+
+
+def _element_to_dict(elem: Element) -> Dict[str, Any]:
+    # every call to this function needs to be replaced with something more type safe and with
+    # an actual typed dictionary - but centralizing this hack for now.
+    return dict(elem.attrib)  # type: ignore [arg-type]
+
+
+def _recurse_drill_down_elems(options: List[DrillDownOptionsDict], option_elems: List[Element]):
+    for option_elem in option_elems:
+        selected = string_as_bool(option_elem.get("selected", False))
+        nested_options: List[DrillDownOptionsDict] = []
+        value = option_elem.get("value")
+        assert value
+        current_option: DrillDownOptionsDict = DrillDownOptionsDict(
+            {
+                "name": option_elem.get("name"),
+                "value": value,
+                "options": nested_options,
+                "selected": selected,
+            }
+        )
+        _recurse_drill_down_elems(nested_options, option_elem.findall("option"))
+        options.append(current_option)
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 020f0019e99e582bc1620cd456eddcae03685963..88be9c72846afab205177917524e96b5ade09823 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -4,24 +4,29 @@ from typing import (
     Dict,
     List,
     Optional,
+    Tuple,
 )
 
 import packaging.version
 
 from galaxy.tool_util.deps import requirements
 from galaxy.tool_util.parser.util import (
+    DEFAULT_DECOMPRESS,
     DEFAULT_DELTA,
     DEFAULT_DELTA_FRAC,
+    DEFAULT_SORT,
 )
 from .interface import (
     AssertionDict,
     AssertionList,
+    HelpContent,
     InputSource,
     PageSource,
     PagesSource,
     ToolSource,
     ToolSourceTest,
     ToolSourceTests,
+    XrefDict,
 )
 from .output_collection_def import dataset_collector_descriptions_from_output_dict
 from .output_objects import (
@@ -29,6 +34,10 @@ from .output_objects import (
     ToolOutputCollection,
     ToolOutputCollectionStructure,
 )
+from .parameter_validators import (
+    AnyValidatorModel,
+    parse_dict_validators,
+)
 from .stdio import error_on_exit_code
 from .util import is_dict
 
@@ -51,24 +60,27 @@ class YamlToolSource(ToolSource):
     def parse_id(self):
         return self.root_dict.get("id")
 
-    def parse_version(self):
-        return str(self.root_dict.get("version"))
+    def parse_version(self) -> Optional[str]:
+        version_raw = self.root_dict.get("version")
+        return str(version_raw) if version_raw is not None else None
 
-    def parse_name(self):
-        return self.root_dict.get("name")
+    def parse_name(self) -> str:
+        rval = self.root_dict.get("name") or self.parse_id()
+        assert rval
+        return str(rval)
 
-    def parse_description(self):
+    def parse_description(self) -> str:
         return self.root_dict.get("description", "")
 
-    def parse_edam_operations(self):
+    def parse_edam_operations(self) -> List[str]:
         return self.root_dict.get("edam_operations", [])
 
-    def parse_edam_topics(self):
+    def parse_edam_topics(self) -> List[str]:
         return self.root_dict.get("edam_topics", [])
 
-    def parse_xrefs(self):
+    def parse_xrefs(self) -> List[XrefDict]:
         xrefs = self.root_dict.get("xrefs", [])
-        return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
+        return [XrefDict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
 
     def parse_sanitize(self):
         return self.root_dict.get("sanitize", True)
@@ -105,7 +117,7 @@ class YamlToolSource(ToolSource):
             resource_requirements=[r for r in mixed_requirements if r.get("type") == "resource"],
         )
 
-    def parse_input_pages(self):
+    def parse_input_pages(self) -> PagesSource:
         # All YAML tools have only one page (feature is deprecated)
         page_source = YamlPageSource(self.root_dict.get("inputs", {}))
         return PagesSource([page_source])
@@ -117,8 +129,12 @@ class YamlToolSource(ToolSource):
     def parse_stdio(self):
         return error_on_exit_code()
 
-    def parse_help(self):
-        return self.root_dict.get("help", None)
+    def parse_help(self) -> Optional[HelpContent]:
+        content = self.root_dict.get("help", None)
+        if content:
+            return HelpContent(format="markdown", content=content)
+        else:
+            return None
 
     def parse_outputs(self, tool):
         outputs = self.root_dict.get("outputs", {})
@@ -191,10 +207,10 @@ class YamlToolSource(ToolSource):
 
         return rval
 
-    def parse_profile(self):
+    def parse_profile(self) -> str:
         return self.root_dict.get("profile", "16.04")
 
-    def parse_license(self):
+    def parse_license(self) -> Optional[str]:
         return self.root_dict.get("license")
 
     def parse_interactivetool(self):
@@ -245,7 +261,8 @@ def _parse_test(i, test_dict) -> ToolSourceTest:
             "lines_diff": 0,
             "delta": DEFAULT_DELTA,
             "delta_frac": DEFAULT_DELTA_FRAC,
-            "sort": False,
+            "sort": DEFAULT_SORT,
+            "decompress": DEFAULT_DECOMPRESS,
         }
         # TODO
         attributes["extra_files"] = []
@@ -302,6 +319,8 @@ def to_test_assert_list(assertions) -> AssertionList:
     return assert_list or None  # XML variant is None if no assertions made
 
 
+# Planemo depends on this and was never updated unfortunately.
+# https://github.com/galaxyproject/planemo/blob/master/planemo/test/_check_output.py
 __to_test_assert_list = to_test_assert_list
 
 
@@ -314,8 +333,9 @@ class YamlPageSource(PageSource):
 
 
 class YamlInputSource(InputSource):
-    def __init__(self, input_dict):
+    def __init__(self, input_dict, trusted: bool = True):
         self.input_dict = input_dict
+        self.trusted = trusted
 
     def get(self, key, default=None):
         return self.input_dict.get(key, default)
@@ -323,6 +343,9 @@ class YamlInputSource(InputSource):
     def get_bool(self, key, default):
         return self.input_dict.get(key, default)
 
+    def get_bool_or_none(self, key, default):
+        return self.input_dict.get(key, default)
+
     def parse_input_type(self):
         input_type = self.input_dict["type"]
         if input_type == "repeat":
@@ -360,7 +383,10 @@ class YamlInputSource(InputSource):
             sources.append((value, case_page_source))
         return sources
 
-    def parse_static_options(self):
+    def parse_validators(self) -> List[AnyValidatorModel]:
+        return parse_dict_validators(self.input_dict.get("validators", []), trusted=self.trusted)
+
+    def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         static_options = []
         input_dict = self.input_dict
         for option in input_dict.get("options", {}):
diff --git a/lib/galaxy/tool_util/toolbox/__init__.py b/lib/galaxy/tool_util/toolbox/__init__.py
index 34c2070b09f143d46cc6b416cd1bb3e2377a1a00..e73ead24118b1c222dd268f7580949197c2626f0 100644
--- a/lib/galaxy/tool_util/toolbox/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/__init__.py
@@ -3,6 +3,8 @@
 from .base import (
     AbstractToolBox,
     AbstractToolTagManager,
+    ToolLoadConfigurationConflict,
+    ToolLoadError,
 )
 from .panel import (
     panel_item_types,
@@ -14,6 +16,8 @@ __all__ = (
     "AbstractToolBox",
     "AbstractToolTagManager",
     "panel_item_types",
+    "ToolLoadConfigurationConflict",
+    "ToolLoadError",
     "ToolSection",
     "ToolSectionLabel",
 )
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 3f50c28ceceac659fff2af501251d09e837e78d2..ae7ce9a2458414c6892174bcde35046f3fe3a367 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -33,7 +33,6 @@ from galaxy.util import (
     unicodify,
 )
 from galaxy.util.bunch import Bunch
-from galaxy.util.dictifiable import Dictifiable
 from .filters import FilterFactory
 from .integrated_panel import ManagesIntegratedToolPanelMixin
 from .lineages import LineageMap
@@ -134,7 +133,15 @@ class NullToolTagManager(AbstractToolTagManager):
         return None
 
 
-class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
+class ToolLoadError(Exception):
+    pass
+
+
+class ToolLoadConfigurationConflict(Exception):
+    pass
+
+
+class AbstractToolBox(ManagesIntegratedToolPanelMixin):
     """
     Abstract container for managing a ToolPanel - containing tools and
     workflows optionally in labelled sections.
@@ -246,7 +253,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
             config_value = getattr(config, "default_panel_view", None)
         return config_value or self.__default_panel_view
 
-    def create_tool(self, config_file, tool_shed_repository=None, guid=None, **kwds):
+    def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
         raise NotImplementedError()
 
     def create_dynamic_tool(self, dynamic_tool):
@@ -1074,6 +1081,12 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                     self._load_tool_panel_views()
                     self._save_integrated_tool_panel()
                 return tool.id
+            except ToolLoadConfigurationConflict as e:
+                log.warning(f"Configuration does not permit loading tool {tool_file} - {e}")
+            except ToolLoadError as e:
+                # no need for full stack trace - ToolLoadError corresponds to a known load
+                # error with defined cause that is included in the message
+                log.error(f"Failed to load potential tool {tool_file} - {e}")
             except Exception:
                 log.exception("Failed to load potential tool %s.", tool_file)
                 return None
@@ -1106,10 +1119,10 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         if not tool or guid and guid != tool.guid:
             try:
                 tool = self.create_tool(
-                    config_file=config_file,
+                    config_file,
+                    tool_cache_data_dir=tool_cache_data_dir,
                     tool_shed_repository=tool_shed_repository,
                     guid=guid,
-                    tool_cache_data_dir=tool_cache_data_dir,
                     **kwds,
                 )
             except Exception:
diff --git a/lib/galaxy/tool_util/toolbox/panel.py b/lib/galaxy/tool_util/toolbox/panel.py
index 0dd2fbbb3525608e657ca512f25d33a066b39284..85ebdaa06d0de988aaa4b27598fb76f3688aeee6 100644
--- a/lib/galaxy/tool_util/toolbox/panel.py
+++ b/lib/galaxy/tool_util/toolbox/panel.py
@@ -6,7 +6,7 @@ from typing import (
     Tuple,
 )
 
-from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.dictifiable import UsesDictVisibleKeys
 from galaxy.util.odict import odict
 from .parser import ensure_tool_conf_item
 
@@ -44,7 +44,7 @@ class HasPanelItems:
             yield (panel_key, panel_type, panel_value)
 
 
-class ToolSection(Dictifiable, HasPanelItems):
+class ToolSection(UsesDictVisibleKeys, HasPanelItems):
     """
     A group of tools with similar type/purpose that will be displayed as a
     group in the user interface.
@@ -107,7 +107,7 @@ class ToolSection(Dictifiable, HasPanelItems):
         `section.elems`
         """
 
-        section_dict = super().to_dict()
+        section_dict = super()._dictify_view_keys()
         section_elts = []
         kwargs = dict(trans=trans, link_details=link_details, tool_help=tool_help)
         for elt in self.elems.values():
@@ -131,7 +131,7 @@ class ToolSection(Dictifiable, HasPanelItems):
         return self.elems
 
 
-class ToolSectionLabel(Dictifiable):
+class ToolSectionLabel(UsesDictVisibleKeys):
     """
     A label for a set of tools that can be displayed above groups of tools
     and sections in the user interface
@@ -151,7 +151,7 @@ class ToolSectionLabel(Dictifiable):
         self.links = item.get("links", None)
 
     def to_dict(self, **kwds):
-        return super().to_dict()
+        return super()._dictify_view_keys()
 
 
 class ToolPanelElements(odict, HasPanelItems):
diff --git a/lib/galaxy/tool_util/unittest_utils/__init__.py b/lib/galaxy/tool_util/unittest_utils/__init__.py
index d9814f09d5788589ec048de551e8da2295a844cd..05849a7bedd8f3066790a1b2ea69cb984424c155 100644
--- a/lib/galaxy/tool_util/unittest_utils/__init__.py
+++ b/lib/galaxy/tool_util/unittest_utils/__init__.py
@@ -1,3 +1,4 @@
+import os
 from typing import (
     Callable,
     Dict,
@@ -6,6 +7,8 @@ from typing import (
 )
 from unittest.mock import Mock
 
+from galaxy.util import galaxy_directory
+
 
 def mock_trans(has_user=True, is_admin=False):
     """A mock ``trans`` object for exposing user info to toolbox filter unit tests."""
@@ -26,3 +29,11 @@ def t_data_downloader_for(content: Union[Dict[Optional[str], bytes], bytes]) ->
             return content
 
     return get_content
+
+
+def functional_test_tool_directory() -> str:
+    return os.path.join(galaxy_directory(), "test/functional/tools")
+
+
+def functional_test_tool_path(test_path: str) -> str:
+    return os.path.join(functional_test_tool_directory(), test_path)
diff --git a/lib/galaxy/tool_util/unittest_utils/parameters.py b/lib/galaxy/tool_util/unittest_utils/parameters.py
new file mode 100644
index 0000000000000000000000000000000000000000..906dc4e5cfcd6447bad3b4d9651e096e6a7533ff
--- /dev/null
+++ b/lib/galaxy/tool_util/unittest_utils/parameters.py
@@ -0,0 +1,45 @@
+import os
+
+from galaxy.tool_util.parameters import (
+    input_models_for_tool_source,
+    ToolParameterBundle,
+    ToolParameterBundleModel,
+    ToolParameterT,
+)
+from galaxy.tool_util.parser import (
+    get_tool_source,
+    ToolSource,
+)
+from galaxy.util import galaxy_directory
+from . import functional_test_tool_path
+
+
+class ParameterBundle(ToolParameterBundle):
+
+    def __init__(self, parameter: ToolParameterT):
+        self.parameters = [parameter]
+
+
+def parameter_bundle(parameter: ToolParameterT) -> ParameterBundle:
+    return ParameterBundle(parameter)
+
+
+def parameter_bundle_for_framework_tool(filename: str) -> ToolParameterBundleModel:
+    path = functional_test_tool_path(filename)
+    tool_source = get_tool_source(path, macro_paths=[])
+    return input_models_for_tool_source(tool_source)
+
+
+def parameter_bundle_for_file(filename: str) -> ToolParameterBundleModel:
+    tool_source = parameter_tool_source(filename)
+    return input_models_for_tool_source(tool_source)
+
+
+def parameter_tool_source(basename: str) -> ToolSource:
+    path_prefix = os.path.join(galaxy_directory(), "test/functional/tools/parameters", basename)
+    if os.path.exists(f"{path_prefix}.xml"):
+        path = f"{path_prefix}.xml"
+    else:
+        path = f"{path_prefix}.cwl"
+    tool_source = get_tool_source(path, macro_paths=[])
+    return tool_source
diff --git a/lib/galaxy/tool_util/unittest_utils/sample_data.py b/lib/galaxy/tool_util/unittest_utils/sample_data.py
index d4b6ddb6f027d13e685f176718b903c5132dfa0e..e9b19283401aa14c9e03907bf9f479a0ccb907c4 100644
--- a/lib/galaxy/tool_util/unittest_utils/sample_data.py
+++ b/lib/galaxy/tool_util/unittest_utils/sample_data.py
@@ -17,3 +17,56 @@ SIMPLE_MACRO = Template(
 </macros>
 """
 )
+
+VALID_XML_VALIDATORS = [
+    """<validator type="empty_dataset" />""",
+    """<validator type="empty_dataset" message="foobar" />""",
+    """<validator type="empty_dataset" message="foobar" negate="true" />""",
+    """<validator type="expression">value == 7</validator>""",
+    """<validator type="regex">mycoolexpression</validator>""",
+    """<validator type="in_range" min="3.1" max="3.8" />""",
+    """<validator type="in_range" min="3.1" />""",
+    """<validator type="in_range" min="3.1" max="3.8" exclude_min="false" exclude_max="true" />""",
+    """<validator type="length" min="3" />""",
+    """<validator type="length" max="7" />""",
+    """<validator type="length" min="2" max="7" negate="true" />""",
+    """<validator type="empty_field" />""",
+    """<validator type="empty_extra_files_path" />""",
+    """<validator type="no_options" />""",
+    """<validator type="unspecified_build" />""",
+    """<validator type="dataset_ok_validator" />""",
+    """<validator type="metadata" check="foo, bar" />""",
+    """<validator type="metadata" skip="name, dbkey" />""",
+    """<validator type="dataset_metadata_equal" metadata_name="foobar" value="moocow" />""",
+    """<validator type="dataset_metadata_equal" metadata_name="foobar" value_json="null" />""",
+    """<validator type="dataset_metadata_in_range" metadata_name="foobar" min="4.5" max="7.8" />""",
+    """<validator type="dataset_metadata_in_range" metadata_name="foobar" min="4.5" max="7.8" include_min="true" />""",
+    """<validator type="dataset_metadata_in_data_table" metadata_name="foobar" metadata_column="3" table_name="mycooltable" />""",
+    """<validator type="dataset_metadata_not_in_data_table" metadata_name="foobar" metadata_column="3" table_name="mycooltable" />""",
+    """<validator type="value_in_data_table" metadata_column="3" table_name="mycooltable" />""",
+    """<validator type="value_in_data_table" table_name="mycooltable" />""",
+    """<validator type="value_not_in_data_table" metadata_column="3" table_name="mycooltable" />""",
+    """<validator type="value_not_in_data_table" table_name="mycooltable" />""",
+]
+
+INVALID_XML_VALIDATORS = [
+    """<validator type="unknown" />""",
+    """<validator type="empty_datasetx" />""",
+    """<validator type="expression" />""",
+    """<validator type="empty_dataset" message="foobar" negate="NOTABOOLVALUE" />""",
+    """<validator type="regex" />""",
+    """<validator type="in_range" min="3.1" max="3.8" exclude_min="false" exclude_max="foobar" />""",
+    """<validator type="in_range" min="notanumber" max="3.8" />""",
+    """<validator type="length" min="notanumber" />""",
+    """<validator type="length" max="notanumber" />""",
+    """<validator type="length" min="2" max="7" negate="notabool" />""",
+    """<validator type="dataset_metadata_equal" />""",
+    """<validator type="dataset_metadata_equal" metadaata_name="foobar" />""",
+    """<validator type="dataset_metadata_equal" metadaata_name="foobar" value_json="undefined" />""",
+    """<validator type="dataset_metadata_in_range" metadata_name="foobar" min="4.5" max="7.8" include_min="notabool" />"""
+    """<validator type="dataset_metadata_in_range"  min="4.5" max="7.8" />"""
+    """<validator type="dataset_metadata_in_data_table" metadata_name="foobar" metadata_column="3" />""",
+    """<validator type="dataset_metadata_in_data_table" metadata_column="3" table_name="mycooltable" />""",
+    """<validator type="dataset_metadata_not_in_data_table" metadata_name="foobar" metadata_column="3" />""",
+    """<validator type="dataset_metadata_not_in_data_table" metadata_column="3" table_name="mycooltable" />""",
+]
diff --git a/lib/galaxy/tool_util/upgrade/__init__.py b/lib/galaxy/tool_util/upgrade/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..41be4988d0c43f24532071f536b3a0e50f3f2a7e
--- /dev/null
+++ b/lib/galaxy/tool_util/upgrade/__init__.py
@@ -0,0 +1,319 @@
+# Documented profile changes not covered.
+# - Allow invalid values. @mvdbeek any clue what to say here. The PR is here:
+# - https://github.com/galaxyproject/galaxy/pull/6264
+#
+# I don't want to declare these TODO but somethings could be more percise.
+# - We could inspect the XML source and tell when tools are using galaxy.json and improve
+#   the messaging on 17.09 for that. We can't be absolutely sure these would or would not be
+#   problems but we can be more confident they might be.
+# - Ditto for $HOME and the 18.01 migration.
+# - We could try to walk parameters and give more specific advice on structured_like qualification.
+from json import loads
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Type,
+)
+
+from typing_extensions import (
+    Literal,
+    NotRequired,
+    TypedDict,
+)
+
+from galaxy.tool_util.parameters.case import validate_test_cases_for_tool_source
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.parser.xml import XmlToolSource
+from galaxy.util import Element
+from galaxy.util.resources import resource_string
+
+TOOL_TOO_NEW = "Target tool has a profile that is too new, consider upgrading this script for the latest advice."
+TARGET_TOO_NEW = (
+    "Target upgrade version is too new for this script, consider upgrading this script for the latest advice."
+)
+
+TYPE_LEVEL = Literal["must_fix", "consider", "ready", "info"]
+
+
+class AdviceCode(TypedDict):
+    name: str
+    level: TYPE_LEVEL
+    message: str
+    niche: NotRequired[bool]
+    url: NotRequired[str]
+
+
+upgrade_codes_json = resource_string(__package__, "upgrade_codes.json")
+upgrade_codes_by_name: Dict[str, AdviceCode] = {}
+
+for name, upgrade_object in loads(upgrade_codes_json).items():
+    upgrade_object["name"] = name
+    upgrade_codes_by_name[name] = cast(AdviceCode, upgrade_object)
+
+
+class Advice:
+    advice_code: AdviceCode
+    message: Optional[str]
+
+    def __init__(self, advice_code: AdviceCode, message: Optional[str]):
+        self.advice_code = advice_code
+        self.message = message
+
+    @property
+    def url(self) -> Optional[str]:
+        return self.advice_code.get("url")
+
+    @property
+    def level(self) -> TYPE_LEVEL:
+        return self.advice_code["level"]
+
+    @property
+    def niche(self) -> bool:
+        return self.advice_code.get("niche", False)
+
+    @property
+    def advice_code_message(self) -> str:
+        return self.advice_code["message"]
+
+    def to_dict(self) -> Dict[str, Any]:
+        as_dict = cast(Dict[str, Any], self.advice_code.copy())
+        as_dict["advice_code_message"] = self.advice_code_message
+        as_dict["message"] = self.message
+        return as_dict
+
+
+class AdviceCollection:
+    _advice: List[Advice]
+
+    def __init__(self):
+        self._advice = []
+
+    def add(self, code: str, message: Optional[str] = None):
+        self._advice.append(Advice(upgrade_codes_by_name[code], message))
+
+    def to_list(self) -> List[Advice]:
+        return self._advice
+
+
+class ProfileMigration:
+    """A class offering advice on upgrading a Galaxy tool between two profile versions."""
+
+    from_version: str
+    to_version: str
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        return None
+
+
+class ProfileMigration16_04(ProfileMigration):
+    from_version = "16.01"
+    to_version = "16.04"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        interpreter = tool_source.parse_interpreter()
+        if interpreter:
+            advice_collection.add("16_04_fix_interpreter")
+        else:
+            advice_collection.add("16_04_ready_interpreter")
+        advice_collection.add("16_04_consider_implicit_extra_file_collection")
+
+        if _has_matching_xpath(tool_source, ".//data[@format = 'input']"):
+            advice_collection.add("16_04_fix_output_format")
+
+        if not _has_matching_xpath(tool_source, ".//stdio") and not _has_matching_xpath(
+            tool_source, ".//command[@detect_errors]"
+        ):
+            advice_collection.add("16_04_exit_code")
+
+
+class ProfileMigration17_09(ProfileMigration):
+    from_version = "16.04"
+    to_version = "17.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        outputs_el = tool_source._outputs_el
+        if outputs_el is not None and outputs_el.get("`provided_metadata_style`", None) is not None:
+            advice_collection.add("17_09_consider_provided_metadata_style")
+
+
+class ProfileMigration18_01(ProfileMigration):
+    from_version = "17.09"
+    to_version = "18.01"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        command_el = tool_source._command_el
+        if command_el is not None and command_el.get("use_shared_home", None) is None:
+            advice_collection.add("18_01_consider_home_directory")
+
+        if _has_matching_xpath(tool_source, ".//outputs/collection[@structured_like]"):
+            advice_collection.add("18_01_consider_structured_like")
+
+
+class ProfileMigration18_09(ProfileMigration):
+    from_version = "18.01"
+    to_version = "18.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "manage_data":
+            advice_collection.add("18_09_consider_python_environment")
+
+
+class ProfileMigration20_05(ProfileMigration):
+    from_version = "18.09"
+    to_version = "20.05"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        if _has_matching_xpath(tool_source, ".//configfiles/inputs"):
+            advice_collection.add("20_05_consider_inputs_as_json_changes")
+
+
+class ProfileMigration20_09(ProfileMigration):
+    from_version = "20.05"
+    to_version = "20.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        tests = tool_source.parse_tests_to_dict()
+        for test in tests["tests"]:
+            output_collections = test.get("output_collections")
+            if not output_collections:
+                continue
+
+            for output_collection in output_collections:
+                if output_collection.get("element_tests"):
+                    advice_collection.add("20_09_consider_output_collection_order")
+
+        command_el = tool_source._command_el
+        if command_el is not None:
+            strict = command_el.get("strict", None)
+            if strict is None:
+                advice_collection.add("20_09_consider_set_e")
+
+
+class ProfileMigration21_09(ProfileMigration):
+    from_version = "20.09"
+    to_version = "21.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        for el in _find_all(tool_source, ".//data[@from_work_dir]"):
+            from_work_dir = el.get("from_work_dir") or ""
+            if from_work_dir != from_work_dir.strip():
+                advice_collection.add("")
+
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "data_source":
+            advice_collection.add("21_09_consider_python_environment")
+
+
+class ProfileMigration23_0(ProfileMigration):
+    from_version = "21.09"
+    to_version = "23.0"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        for text_param in _find_all(tool_source, ".//input[@type='text']"):
+            optional_tag_set = text_param.get("optional", None) is not None
+            if not optional_tag_set:
+                advice_collection.add("23_0_consider_optional_text")
+
+
+class ProfileMigration24_0(ProfileMigration):
+    from_version = "23.0"
+    to_version = "24.0"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "data_source_async":
+            advice_collection.add("24_0_consider_python_environment")
+        if tool_type in ["data_source_async", "data_source"]:
+            advice_collection.add("24_0_request_cleaning")
+
+
+class ProfileMigration24_2(ProfileMigration):
+    from_version = "24.0"
+    to_version = "24.2"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        results = validate_test_cases_for_tool_source(tool_source, use_latest_profile=True)
+        for result in results:
+            if result.validation_error:
+                advice_collection.add("24_2_fix_test_case_validation", str(result.validation_error))
+
+
+profile_migrations: List[Type[ProfileMigration]] = [
+    ProfileMigration16_04,
+    ProfileMigration17_09,
+    ProfileMigration18_01,
+    ProfileMigration18_09,
+    ProfileMigration20_05,
+    ProfileMigration20_09,
+    ProfileMigration21_09,
+    ProfileMigration23_0,
+    ProfileMigration24_0,
+    ProfileMigration24_2,
+]
+
+latest_supported_version = "24.2"
+
+
+def advise_on_upgrade(xml_file: str, to_version: Optional[str] = None) -> List[Advice]:
+    to_version = to_version or latest_supported_version
+    tool_source = _xml_tool_source(xml_file)
+    initial_version = tool_source.parse_profile()
+    if initial_version > latest_supported_version:
+        raise Exception(TOOL_TOO_NEW)
+    elif to_version > latest_supported_version:
+        raise Exception(TARGET_TOO_NEW)
+    advice_collection = AdviceCollection()
+
+    for migration in profile_migrations:
+        if migration.to_version < initial_version:
+            # tool started past here... just skip this advice
+            continue
+        if migration.to_version > to_version:
+            # we're not advising on upgrading past this point
+            break
+        migration.advise(advice_collection, xml_file)
+
+    return advice_collection.to_list()
+
+
+def _xml_tool_source(xml_file: str) -> XmlToolSource:
+    tool_source = get_tool_source(xml_file)
+    if not isinstance(tool_source, XmlToolSource):
+        raise Exception("Can only provide upgrade advice for XML tools.")
+    return cast(XmlToolSource, tool_source)
+
+
+def _has_matching_xpath(tool_source: XmlToolSource, xpath: str) -> bool:
+    return tool_source.xml_tree.find(xpath) is not None
+
+
+def _find_all(tool_source: XmlToolSource, xpath: str) -> List[Element]:
+    return cast(List[Element], tool_source.xml_tree.findall(".//data[@from_work_dir]") or [])
diff --git a/lib/galaxy/tool_util/upgrade/script.py b/lib/galaxy/tool_util/upgrade/script.py
new file mode 100755
index 0000000000000000000000000000000000000000..2778fc40c4845270a790b40259d0bd21ceb7cef9
--- /dev/null
+++ b/lib/galaxy/tool_util/upgrade/script.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+from json import dumps
+from textwrap import (
+    indent,
+    wrap,
+)
+from typing import List
+
+from galaxy.tool_util.upgrade import (
+    Advice,
+    advise_on_upgrade,
+    latest_supported_version,
+)
+
+LEVEL_TO_STRING = {
+    "must_fix": "❌",
+    "ready": "✅",
+    "consider": "🤔",
+    "info": "ℹ️",
+}
+DESCRIPTION = f"""
+A small utility to check for potential problems and provide advice when upgrading a tool's
+profile version. This version of the script can provide advice for upgrading tools through
+{latest_supported_version}.
+"""
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument("xml_file")
+    parser.add_argument(
+        "-p",
+        "--profile-version",
+        dest="profile_version",
+        default=latest_supported_version,
+        help="Provide upgrade advice up to this Galaxy tool profile version.",
+    )
+    parser.add_argument(
+        "-j",
+        "--json",
+        default=False,
+        action="store_true",
+        help="Output aadvice as JSON.",
+    )
+    parser.add_argument(
+        "-n",
+        "--niche",
+        default=False,
+        action="store_true",
+        help="Include advice about niche features that may not be relevant for most tools - including the use of 'galaxy.json' and writing global state in the $HOME directory.",
+    )
+    return parser
+
+
+def _print_advice(advice: Advice):
+    message = "\n".join(wrap(advice.advice_code_message, initial_indent="", subsequent_indent="    "))
+    level = advice.level
+    level_str = LEVEL_TO_STRING[level]
+    url = advice.url
+    print(f"- {level_str}{message}\n")
+    if advice.message:
+        print(indent(advice.message, "    "))
+        print("")
+    if url:
+        print(f"    More information at {url}")
+
+
+def _print_advice_list(advice_list: List[Advice]):
+    for advice in advice_list:
+        _print_advice(advice)
+
+
+def advise(xml_file: str, version: str, json: bool, niche: bool):
+    advice_list = advise_on_upgrade(xml_file, version)
+    if not niche:
+        advice_list = [a for a in advice_list if not a.niche]
+    if json:
+        print(dumps(a.to_dict() for a in advice_list))
+    else:
+        _print_advice_list(advice_list)
+
+
+def main(argv=None) -> None:
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = arg_parser().parse_args(argv)
+    advise(args.xml_file, args.profile_version, args.json, args.niche)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/tool_util/upgrade/upgrade_codes.json b/lib/galaxy/tool_util/upgrade/upgrade_codes.json
new file mode 100644
index 0000000000000000000000000000000000000000..342ca16ee0ed0484fc518d15b43761ad193fec32
--- /dev/null
+++ b/lib/galaxy/tool_util/upgrade/upgrade_codes.json
@@ -0,0 +1,94 @@
+{
+    "16_04_fix_interpreter": {
+        "level": "must_fix",
+        "message": "This tool uses an interpreter on the command block, this was disabled with 16.04. The command line needs to be rewritten to call the language runtime with a full path to the target script using `$tool_directory` to refer to the path to the tool and its script.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/1688"
+    },
+    "16_04_ready_interpreter": {
+        "level": "ready",
+        "message": "This tool follows best practice and does not specify an interpreter on the command block.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/1688"
+    },
+    "16_04_consider_implicit_extra_file_collection": {
+        "level": "consider",
+        "message": "Starting is with profile 16.04 tools, Galaxy no longer attempts to just find tool outputs keyed on the output ID in the working directory. Tool outputs need to be explicitly declared and dynamic outputs need to be specified in a 'galaxy.json' file or with a 'discover_datasets' block.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/1688",
+        "niche": true
+    },
+    "16_04_fix_output_format": {
+        "level": "must_fix",
+        "message": "Starting with 16.04 tools, having format='input' on a tool output is disabled. The behavior was not well defined for these outputs. Please add 'format_source=\"a_specific_input_name\" for a specific input to inherit the format from.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/1688"
+    },
+    "16_04_exit_code": {
+        "level": "consider",
+        "message": "Starting with 16.04 tools the exit code of the command executed will be used to detect errors by default. This tool previously would have discovered errors by checking if any content is written to standard error. Add '<stdio><regex match=\".*\" source=\"stderr\" level=\"fatal\" description=\"Unknown error encountered\" /></stdio>' to your tool to restore the legacy behavior or restructure your command block to rely on the exit code.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/1688"
+    },
+    "18_01_consider_structured_like": {
+        "level": "consider",
+        "message": "Starting with 18.01 tools, the 'structured_like` attribute must reference inputs in a fully qualified manner - using '|' to describe parent conditionals for instance.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/6162"
+    },
+    "20_05_consider_inputs_as_json_changes": {
+        "level": "consider",
+        "message": "Starting with 20.05, the format of data in 'inputs' config files changed slightly. Unselected optional `select` and `data_column` parameters get json null values instead of the string 'None' and multiple `select` and `data_column` parameters are lists (instead of comma separated strings).",
+        "url": "https://github.com/galaxyproject/galaxy/pull/9776/files"
+    },
+    "20_09_consider_output_collection_order": {
+        "level": "consider",
+        "message": "Starting in profile 20.09 tools, the order elements defined in tool test became relevant in order to verify collections are properly sorted. This may cause tool tests to fail after the upgrade, rearrange the elements defined in output collections if this occurs.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/10434"
+    },
+    "20_09_consider_set_e": {
+        "level": "consider",
+        "message": "Starting with profile 20.09 tools, tool scripts are executed with the 'set -e' instruction. The 'set -e' option instructs the shell to immediately exit if any command has a non-zero exit status. If your command uses multiple sub-commands and you'd like to allow them to execute with non-zero exit codes add 'strict=\"false\"' to the command tag to restore the tool's legacy behavior.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/9962"
+    },
+    "18_01_consider_home_directory": {
+        "level": "consider",
+        "message": "Starting with profile 18.01 tools, each job is given its own home directory. Most tools should not depend on global state in a home directory, if this is required though set 'use_shared_home=\"true\"' on the command tag of the tool.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/5193",
+        "niche": true
+    },
+    "18_09_consider_python_environment": {
+        "level": "consider",
+        "message": "Starting with profile 18.09 tools, data managers run without Galaxy's virtual environment. Be sure your requirements reflect all the data manager's dependencies.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/6466"
+    },
+    "17_09_consider_provided_metadata_style": {
+        "level": "consider",
+        "message": "Starting with 17.09 tools, the format of 'galaxy.json' (a rarely used file that can be used to dynamically collect datasets or metadata about datasets produced by the tool) changed - the original behavior can be restored by adding 'provided_metadata_style=\"legacy\"' to the tool's outputs tag.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/4437",
+        "niche": true
+    },
+    "21_09_fix_from_work_dir_whitespace": {
+        "level": "must_fix",
+        "message": "Starting with 21.09 tools, from_work_dir output file names are quoted so white space needs to be stripped out of attribute.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/12536"
+    },
+    "21_09_consider_python_environment": {
+        "level": "consider",
+        "message": "Starting with 21.09 data source tools, Galaxy's virtual environment is no longer included in the tool's runtime environment. Tools that require it, should include the galaxy-util package in their requirements.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/12515"
+    },
+    "23_0_consider_optional_text": {
+        "level": "consider",
+        "message": "Text parameters that are inferred to be optional (i.e the `optional` tag is not set, but the tool parameter accepts an empty string) are set to `None` for templating in Cheetah. Previous to this version tools would receive the empty string `\"\"` as the templated value.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/15491/files"
+    },
+    "24_0_consider_python_environment": {
+        "level": "consider",
+        "message": "Starting with 24.0 async data source tools, Galaxy's virtual environment is no longer included in the tool's runtime environment. Tools that require it, should include the galaxy-util package in their requirements.",
+        "url": "https://github.com/galaxyproject/galaxy/pull/17422"
+    },
+    "24_0_request_cleaning": {
+        "level": "consider",
+        "message": "Starting with 24.0 data source tools, Galaxy requires explicit `request_param_translation` for each parameter sent to the tool. If this tools depends on unspecified parameters - new xml elements will need to be added for these parameters."
+    },
+    "24_2_fix_test_case_validation": {
+        "level": "must_fix",
+        "message": "Starting with 24.2 tools, test cases must validate against a more stringent schema. Unknown parameters are disallowed (prevents misspellings), select parameters must be specified by value (to prevent ambiguity and match the API), column parameters must be specified as integers, and parameters must be full qualified ('|' separation to include parent repeat, cond, and sections).",
+        "url": "https://github.com/galaxyproject/galaxy/pull/18679"
+    }
+}
diff --git a/lib/galaxy/tool_util/validate_test_format.py b/lib/galaxy/tool_util/validate_test_format.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd9e055b378914ee0a69255421083caf1b623585
--- /dev/null
+++ b/lib/galaxy/tool_util/validate_test_format.py
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+
+import yaml
+
+from galaxy.tool_util.models import Tests
+
+DESCRIPTION = """
+A small utility to verify the Planemo test format.
+
+This script doesn't use semantic information about tools or workflows so only
+the structure of the file is checked and things like inputs matching up is not
+included.
+"""
+
+
+def validate_test_file(test_file: str) -> None:
+    with open(test_file) as f:
+        json = yaml.safe_load(f)
+    Tests.model_validate(json)
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument("test_file")
+    return parser
+
+
+def main(argv=None) -> None:
+    if argv is None:
+        argv = sys.argv[1:]
+
+    args = arg_parser().parse_args(argv)
+    validate_test_file(args.test_file)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index ec84f23ae345e966bd308c2543ab484b7764a40c..1fa55a0b2f204fef36f51ee1da79ae69e1e61707 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -45,8 +45,13 @@ from galaxy.tool_util.parser.util import (
     DEFAULT_METRIC,
     DEFAULT_PIN_LABELS,
 )
+from galaxy.tool_util.parser.yaml import to_test_assert_list
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
+from ._types import (
+    ExpandedToolInputsJsonified,
+    ToolTestDescriptionDict,
+)
 from .asserts import verify_assertions
 from .test_data import TestDataResolver
 
@@ -56,6 +61,8 @@ if TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 DEFAULT_TEST_DATA_RESOLVER = TestDataResolver()
+GetFilenameT = Optional[Callable[[str], str]]
+GetLocationT = Optional[Callable[[str], str]]
 
 
 def verify(
@@ -64,7 +71,7 @@ def verify(
     attributes: Optional[Dict[str, Any]],
     filename: Optional[str] = None,
     get_filecontent: Optional[Callable[[str], bytes]] = None,
-    get_filename: Optional[Callable[[str], str]] = None,
+    get_filename: GetFilenameT = None,
     keep_outputs_dir: Optional[str] = None,
     verify_extra_files: Optional[Callable] = None,
     mode="file",
@@ -279,7 +286,7 @@ def get_compressed_formats(attributes):
     return None if decompress else []
 
 
-def files_diff(file1, file2, attributes=None):
+def files_diff(file1: str, file2: str, attributes=None):
     """Check the contents of 2 files for differences."""
     attributes = attributes or {}
 
@@ -296,9 +303,9 @@ def files_diff(file1, file2, attributes=None):
         compressed_formats = get_compressed_formats(attributes)
         is_pdf = False
         try:
-            with get_fileobj(file2, compressed_formats=compressed_formats) as fh:
+            with get_fileobj(file2, compressed_formats=compressed_formats, mode="r") as fh:
                 history_data = fh.readlines()
-            with get_fileobj(file1, compressed_formats=compressed_formats) as fh:
+            with get_fileobj(file1, compressed_formats=compressed_formats, mode="r") as fh:
                 local_file = fh.readlines()
         except UnicodeDecodeError:
             if file1.endswith(".pdf") or file2.endswith(".pdf"):
@@ -464,8 +471,8 @@ def files_contains(file1, file2, attributes=None):
 
 
 def _singleobject_intersection_over_union(
-    mask1: "numpy.typing.NDArray",
-    mask2: "numpy.typing.NDArray",
+    mask1: "numpy.typing.NDArray[numpy.bool_]",
+    mask2: "numpy.typing.NDArray[numpy.bool_]",
 ) -> "numpy.floating":
     return numpy.logical_and(mask1, mask2).sum() / numpy.logical_or(mask1, mask2).sum()
 
@@ -476,7 +483,7 @@ def _multiobject_intersection_over_union(
     pin_labels: Optional[List[int]] = None,
     repeat_reverse: bool = True,
 ) -> List["numpy.floating"]:
-    iou_list = []
+    iou_list: List[numpy.floating] = []
     for label1 in numpy.unique(mask1):
         cc1 = mask1 == label1
 
@@ -487,13 +494,13 @@ def _multiobject_intersection_over_union(
 
         # Otherwise, use the object with the largest IoU value, excluding the pinned labels.
         else:
-            cc1_iou_list = []
+            cc1_iou_list: List[numpy.floating] = []
             for label2 in numpy.unique(mask2[cc1]):
                 if pin_labels is not None and label2 in pin_labels:
                     continue
                 cc2 = mask2 == label2
                 cc1_iou_list.append(_singleobject_intersection_over_union(cc1, cc2))
-            iou_list.append(max(cc1_iou_list))
+            iou_list.append(max(cc1_iou_list))  # type: ignore[type-var, unused-ignore]  # https://github.com/python/typeshed/issues/12562
 
     if repeat_reverse:
         iou_list.extend(_multiobject_intersection_over_union(mask2, mask1, pin_labels, repeat_reverse=False))
@@ -504,7 +511,7 @@ def _multiobject_intersection_over_union(
 def intersection_over_union(
     mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray", pin_labels: Optional[List[int]] = None
 ) -> "numpy.floating":
-    """Compute the intersection over union (IoU) for the objects in two masks containing lables.
+    """Compute the intersection over union (IoU) for the objects in two masks containing labels.
 
     The IoU is computed for each uniquely labeled image region (object), and the overall minimum value is returned (i.e. the worst value).
     To compute the IoU for each object, the corresponding object in the other mask needs to be determined.
@@ -522,7 +529,7 @@ def intersection_over_union(
         count = sum(label in mask for mask in (mask1, mask2))
         count_str = {1: "one", 2: "both"}
         assert count == 2, f"Label {label} is pinned but missing in {count_str[2 - count]} of the images."
-    return min(_multiobject_intersection_over_union(mask1, mask2, pin_labels))
+    return min(_multiobject_intersection_over_union(mask1, mask2, pin_labels))  # type: ignore[type-var, unused-ignore]  # https://github.com/python/typeshed/issues/12562
 
 
 def _parse_label_list(label_list_str: Optional[str]) -> List[int]:
@@ -585,3 +592,77 @@ def files_image_diff(file1: str, file2: str, attributes: Optional[Dict[str, Any]
     distance_eps = attributes.get("eps", DEFAULT_EPS)
     if distance > distance_eps:
         raise AssertionError(f"Image difference {distance} exceeds eps={distance_eps}.")
+
+
+# TODO: After tool-util with this included is published, fefactor planemo.test._check_output
+# to use this function. There is already a comment there about breaking fewer abstractions.
+# https://github.com/galaxyproject/planemo/blob/master/planemo/test/_check_output.py
+# TODO: Also migrate the logic for checking non-dictionaries out of Planemo - this function now
+# does that check also.
+def verify_file_path_against_dict(
+    get_filename: GetFilenameT,
+    get_location: GetLocationT,
+    path: str,
+    output_content: bytes,
+    test_properties,
+    test_data_target_dir: Optional[str] = None,
+) -> None:
+    with open(path, "rb") as f:
+        output_content = f.read()
+    item_label = f"Output with path {path}"
+    verify_file_contents_against_dict(
+        get_filename, get_location, item_label, output_content, test_properties, test_data_target_dir
+    )
+
+
+def verify_file_contents_against_dict(
+    get_filename: GetFilenameT,
+    get_location: GetLocationT,
+    item_label: str,
+    output_content: bytes,
+    test_properties,
+    test_data_target_dir: Optional[str] = None,
+) -> None:
+    expected_file: Optional[str] = None
+    if isinstance(test_properties, dict):
+        # Support Galaxy-like file location (using "file") or CWL-like ("path" or "location").
+        expected_file = test_properties.get("file", None)
+        if expected_file is None:
+            expected_file = test_properties.get("path", None)
+        if expected_file is None:
+            location = test_properties.get("location")
+            if location:
+                if location.startswith(("http://", "https://")):
+                    assert get_location
+                    expected_file = get_location(location)
+                else:
+                    expected_file = location.split("file://", 1)[-1]
+
+        if "asserts" in test_properties:
+            test_properties["assert_list"] = to_test_assert_list(test_properties["asserts"])
+        verify(
+            item_label,
+            output_content,
+            attributes=test_properties,
+            filename=expected_file,
+            get_filename=get_filename,
+            keep_outputs_dir=test_data_target_dir,
+            verify_extra_files=None,
+        )
+    else:
+        output_value = json.loads(output_content.decode("utf-8"))
+        if test_properties != output_value:
+            template = "Output [%s] value [%s] does not match expected value [%s]."
+            message = template % (item_label, output_value, test_properties)
+            raise AssertionError(message)
+
+
+__all__ = [
+    "DEFAULT_TEST_DATA_RESOLVER",
+    "ExpandedToolInputsJsonified",
+    "GetFilenameT",
+    "GetLocationT",
+    "ToolTestDescriptionDict",
+    "verify",
+    "verify_file_contents_against_dict",
+]
diff --git a/lib/galaxy/tool_util/verify/_types.py b/lib/galaxy/tool_util/verify/_types.py
new file mode 100644
index 0000000000000000000000000000000000000000..e5aa85f1ddb7263320309ed3ceaa5c05f63f2607
--- /dev/null
+++ b/lib/galaxy/tool_util/verify/_types.py
@@ -0,0 +1,54 @@
+"""Types used by interactor and test case processor."""
+
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
+
+from typing_extensions import (
+    NotRequired,
+    TypedDict,
+)
+
+from galaxy.tool_util.parser.interface import (
+    AssertionList,
+    TestSourceTestOutputColllection,
+    ToolSourceTestOutputs,
+)
+
+# inputs that have been processed with parse.py and expanded out
+ExpandedToolInputs = Dict[str, Any]
+# ExpandedToolInputs where any model objects have been json-ified with to_dict()
+ExpandedToolInputsJsonified = Dict[str, Any]
+ExtraFileInfoDictT = Dict[str, Any]
+RequiredFileTuple = Tuple[str, ExtraFileInfoDictT]
+RequiredFilesT = List[RequiredFileTuple]
+RequiredDataTablesT = List[str]
+RequiredLocFileT = List[str]
+
+
+class ToolTestDescriptionDict(TypedDict):
+    tool_id: str
+    tool_version: Optional[str]
+    name: str
+    test_index: int
+    inputs: ExpandedToolInputsJsonified
+    outputs: ToolSourceTestOutputs
+    output_collections: List[TestSourceTestOutputColllection]
+    stdout: Optional[AssertionList]
+    stderr: Optional[AssertionList]
+    expect_exit_code: Optional[int]
+    expect_failure: bool
+    expect_test_failure: bool
+    num_outputs: Optional[int]
+    command_line: Optional[AssertionList]
+    command_version: Optional[AssertionList]
+    required_files: List[Any]
+    required_data_tables: List[Any]
+    required_loc_files: List[str]
+    error: bool
+    exception: Optional[str]
+    maxseconds: NotRequired[Optional[int]]
diff --git a/lib/galaxy/tool_util/verify/assertion_models.py b/lib/galaxy/tool_util/verify/assertion_models.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b508e0d3172695f8b5af0e527da76ceb94a66a1
--- /dev/null
+++ b/lib/galaxy/tool_util/verify/assertion_models.py
@@ -0,0 +1,3641 @@
+"""This module is auto-generated, please do not modify."""
+
+import re
+import typing
+
+from pydantic import (
+    BaseModel,
+    BeforeValidator,
+    ConfigDict,
+    Field,
+    model_validator,
+    RootModel,
+    StrictFloat,
+    StrictInt,
+)
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
+
+BYTES_PATTERN = re.compile(r"^(0|[1-9][0-9]*)([kKMGTPE]i?)?$")
+
+
+class AssertionModel(BaseModel):
+    model_config = ConfigDict(
+        extra="forbid",
+    )
+
+
+def check_bytes(v: typing.Any) -> typing.Any:
+    if isinstance(v, str):
+        assert BYTES_PATTERN.match(v), "Not valid bytes string"
+    return v
+
+
+def check_center_of_mass(v: typing.Any):
+    assert isinstance(v, str)
+    split_parts = v.split(",")
+    assert len(split_parts) == 2
+    for part in split_parts:
+        assert float(part.strip())
+    return v
+
+
+def check_regex(v: typing.Any):
+    assert isinstance(v, str)
+    try:
+        re.compile(typing.cast(str, v))
+    except re.error:
+        raise AssertionError(f"Invalid regular expression {v}")
+    return v
+
+
+def check_non_negative_if_set(v: typing.Any):
+    if v is not None:
+        try:
+            assert float(v) >= 0
+        except TypeError:
+            raise AssertionError(f"Invalid type found {v}")
+    return v
+
+
+def check_non_negative_if_int(v: typing.Any):
+    if v is not None and isinstance(v, int):
+        assert typing.cast(int, v) >= 0
+    return v
+
+
+has_line_line_description = """The full line of text to search for in the output."""
+
+has_line_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_line_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_line_model(AssertionModel):
+    """base model for has_line describing attributes."""
+
+    line: str = Field(
+        ...,
+        description=has_line_line_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_line_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_line_negate_description,
+    )
+
+
+class base_has_line_model_relaxed(AssertionModel):
+    """base model for has_line describing attributes."""
+
+    line: str = Field(
+        ...,
+        description=has_line_line_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_line_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_line_negate_description,
+    )
+
+
+class has_line_model(base_has_line_model):
+    r"""Asserts the specified output contains the line specified by the
+    argument line. The exact number of occurrences can be optionally
+    specified by the argument n"""
+
+    that: Literal["has_line"] = "has_line"
+
+
+class has_line_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_line: base_has_line_model
+
+
+class has_line_model_relaxed(base_has_line_model_relaxed):
+    r"""Asserts the specified output contains the line specified by the
+    argument line. The exact number of occurrences can be optionally
+    specified by the argument n"""
+
+    that: Literal["has_line"] = "has_line"
+
+
+has_line_matching_expression_description = """The regular expressions to attempt match in the output."""
+
+has_line_matching_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_matching_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_line_matching_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_matching_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_line_matching_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_line_matching_model(AssertionModel):
+    """base model for has_line_matching describing attributes."""
+
+    expression: str = Field(
+        ...,
+        description=has_line_matching_expression_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_line_matching_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_line_matching_negate_description,
+    )
+
+
+class base_has_line_matching_model_relaxed(AssertionModel):
+    """base model for has_line_matching describing attributes."""
+
+    expression: str = Field(
+        ...,
+        description=has_line_matching_expression_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_line_matching_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_line_matching_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_line_matching_negate_description,
+    )
+
+
+class has_line_matching_model(base_has_line_matching_model):
+    r"""Asserts the specified output contains a line matching the
+    regular expression specified by the argument expression. If n is given
+    the assertion checks for exactly n occurences."""
+
+    that: Literal["has_line_matching"] = "has_line_matching"
+
+
+class has_line_matching_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_line_matching: base_has_line_matching_model
+
+
+class has_line_matching_model_relaxed(base_has_line_matching_model_relaxed):
+    r"""Asserts the specified output contains a line matching the
+    regular expression specified by the argument expression. If n is given
+    the assertion checks for exactly n occurences."""
+
+    that: Literal["has_line_matching"] = "has_line_matching"
+
+
+has_n_lines_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_lines_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_n_lines_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_lines_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_lines_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_n_lines_model(AssertionModel):
+    """base model for has_n_lines describing attributes."""
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_lines_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_lines_negate_description,
+    )
+
+
+class base_has_n_lines_model_relaxed(AssertionModel):
+    """base model for has_n_lines describing attributes."""
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_lines_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_lines_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_lines_negate_description,
+    )
+
+
+class has_n_lines_model(base_has_n_lines_model):
+    r"""Asserts the specified output contains ``n`` lines allowing
+    for a difference in the number of lines (delta)
+    or relative differebce in the number of lines"""
+
+    that: Literal["has_n_lines"] = "has_n_lines"
+
+
+class has_n_lines_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_n_lines: base_has_n_lines_model
+
+
+class has_n_lines_model_relaxed(base_has_n_lines_model_relaxed):
+    r"""Asserts the specified output contains ``n`` lines allowing
+    for a difference in the number of lines (delta)
+    or relative differebce in the number of lines"""
+
+    that: Literal["has_n_lines"] = "has_n_lines"
+
+
+has_text_text_description = """The text to search for in the output."""
+
+has_text_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_text_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_text_model(AssertionModel):
+    """base model for has_text describing attributes."""
+
+    text: str = Field(
+        ...,
+        description=has_text_text_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_text_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_text_negate_description,
+    )
+
+
+class base_has_text_model_relaxed(AssertionModel):
+    """base model for has_text describing attributes."""
+
+    text: str = Field(
+        ...,
+        description=has_text_text_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_text_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_text_negate_description,
+    )
+
+
+class has_text_model(base_has_text_model):
+    r"""Asserts specified output contains the substring specified by
+    the argument text. The exact number of occurrences can be
+    optionally specified by the argument n"""
+
+    that: Literal["has_text"] = "has_text"
+
+
+class has_text_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_text: base_has_text_model
+
+
+class has_text_model_relaxed(base_has_text_model_relaxed):
+    r"""Asserts specified output contains the substring specified by
+    the argument text. The exact number of occurrences can be
+    optionally specified by the argument n"""
+
+    that: Literal["has_text"] = "has_text"
+
+
+has_text_matching_expression_description = """The regular expressions to attempt match in the output."""
+
+has_text_matching_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_matching_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_text_matching_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_matching_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_text_matching_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_text_matching_model(AssertionModel):
+    """base model for has_text_matching describing attributes."""
+
+    expression: str = Field(
+        ...,
+        description=has_text_matching_expression_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_text_matching_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_text_matching_negate_description,
+    )
+
+
+class base_has_text_matching_model_relaxed(AssertionModel):
+    """base model for has_text_matching describing attributes."""
+
+    expression: str = Field(
+        ...,
+        description=has_text_matching_expression_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_text_matching_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_text_matching_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_text_matching_negate_description,
+    )
+
+
+class has_text_matching_model(base_has_text_matching_model):
+    r"""Asserts the specified output contains text matching the
+    regular expression specified by the argument expression.
+    If n is given the assertion checks for exacly n (nonoverlapping)
+    occurences."""
+
+    that: Literal["has_text_matching"] = "has_text_matching"
+
+
+class has_text_matching_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_text_matching: base_has_text_matching_model
+
+
+class has_text_matching_model_relaxed(base_has_text_matching_model_relaxed):
+    r"""Asserts the specified output contains text matching the
+    regular expression specified by the argument expression.
+    If n is given the assertion checks for exacly n (nonoverlapping)
+    occurences."""
+
+    that: Literal["has_text_matching"] = "has_text_matching"
+
+
+not_has_text_text_description = """The text to search for in the output."""
+
+
+class base_not_has_text_model(AssertionModel):
+    """base model for not_has_text describing attributes."""
+
+    text: str = Field(
+        ...,
+        description=not_has_text_text_description,
+    )
+
+
+class base_not_has_text_model_relaxed(AssertionModel):
+    """base model for not_has_text describing attributes."""
+
+    text: str = Field(
+        ...,
+        description=not_has_text_text_description,
+    )
+
+
+class not_has_text_model(base_not_has_text_model):
+    r"""Asserts specified output does not contain the substring
+    specified by the argument text"""
+
+    that: Literal["not_has_text"] = "not_has_text"
+
+
+class not_has_text_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    not_has_text: base_not_has_text_model
+
+
+class not_has_text_model_relaxed(base_not_has_text_model_relaxed):
+    r"""Asserts specified output does not contain the substring
+    specified by the argument text"""
+
+    that: Literal["not_has_text"] = "not_has_text"
+
+
+has_n_columns_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_columns_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_n_columns_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_columns_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_columns_sep_description = """Separator defining columns, default: tab"""
+
+has_n_columns_comment_description = (
+    """Comment character(s) used to skip comment lines (which should not be used for counting columns)"""
+)
+
+has_n_columns_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_n_columns_model(AssertionModel):
+    """base model for has_n_columns describing attributes."""
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_columns_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_max_description,
+    )
+
+    sep: str = Field(
+        "	",
+        description=has_n_columns_sep_description,
+    )
+
+    comment: str = Field(
+        "",
+        description=has_n_columns_comment_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_columns_negate_description,
+    )
+
+
+class base_has_n_columns_model_relaxed(AssertionModel):
+    """base model for has_n_columns describing attributes."""
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_columns_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_columns_max_description,
+    )
+
+    sep: str = Field(
+        "	",
+        description=has_n_columns_sep_description,
+    )
+
+    comment: str = Field(
+        "",
+        description=has_n_columns_comment_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_columns_negate_description,
+    )
+
+
+class has_n_columns_model(base_has_n_columns_model):
+    r"""Asserts tabular output  contains the specified
+    number (``n``) of columns.
+
+    For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
+    Number of columns can optionally also be specified with ``delta``. Alternatively the
+    range of expected occurences can be specified by ``min`` and/or ``max``.
+
+    Optionally a column separator (``sep``, default is ``       ``) `and comment character(s)
+    can be specified (``comment``, default is empty string). The first non-comment
+    line is used for determining the number of columns."""
+
+    that: Literal["has_n_columns"] = "has_n_columns"
+
+
+class has_n_columns_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_n_columns: base_has_n_columns_model
+
+
+class has_n_columns_model_relaxed(base_has_n_columns_model_relaxed):
+    r"""Asserts tabular output  contains the specified
+    number (``n``) of columns.
+
+    For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
+    Number of columns can optionally also be specified with ``delta``. Alternatively the
+    range of expected occurences can be specified by ``min`` and/or ``max``.
+
+    Optionally a column separator (``sep``, default is ``       ``) `and comment character(s)
+    can be specified (``comment``, default is empty string). The first non-comment
+    line is used for determining the number of columns."""
+
+    that: Literal["has_n_columns"] = "has_n_columns"
+
+
+attribute_is_path_description = """The Python xpath-like expression to find the target element."""
+
+attribute_is_attribute_description = """The XML attribute name to test against from the target XML element."""
+
+attribute_is_text_description = """The expected attribute value to test against on the target XML element"""
+
+attribute_is_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_attribute_is_model(AssertionModel):
+    """base model for attribute_is describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=attribute_is_path_description,
+    )
+
+    attribute: str = Field(
+        ...,
+        description=attribute_is_attribute_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=attribute_is_text_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=attribute_is_negate_description,
+    )
+
+
+class base_attribute_is_model_relaxed(AssertionModel):
+    """base model for attribute_is describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=attribute_is_path_description,
+    )
+
+    attribute: str = Field(
+        ...,
+        description=attribute_is_attribute_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=attribute_is_text_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=attribute_is_negate_description,
+    )
+
+
+class attribute_is_model(base_attribute_is_model):
+    r"""Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` is the specified ``text``.
+
+    For example:
+
+    ```xml
+    <attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["attribute_is"] = "attribute_is"
+
+
+class attribute_is_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    attribute_is: base_attribute_is_model
+
+
+class attribute_is_model_relaxed(base_attribute_is_model_relaxed):
+    r"""Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` is the specified ``text``.
+
+    For example:
+
+    ```xml
+    <attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["attribute_is"] = "attribute_is"
+
+
+attribute_matches_path_description = """The Python xpath-like expression to find the target element."""
+
+attribute_matches_attribute_description = """The XML attribute name to test against from the target XML element."""
+
+attribute_matches_expression_description = (
+    """The regular expressions to apply against the named attribute on the target XML element."""
+)
+
+attribute_matches_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_attribute_matches_model(AssertionModel):
+    """base model for attribute_matches describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=attribute_matches_path_description,
+    )
+
+    attribute: str = Field(
+        ...,
+        description=attribute_matches_attribute_description,
+    )
+
+    expression: Annotated[str, BeforeValidator(check_regex)] = Field(
+        ...,
+        description=attribute_matches_expression_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=attribute_matches_negate_description,
+    )
+
+
+class base_attribute_matches_model_relaxed(AssertionModel):
+    """base model for attribute_matches describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=attribute_matches_path_description,
+    )
+
+    attribute: str = Field(
+        ...,
+        description=attribute_matches_attribute_description,
+    )
+
+    expression: Annotated[str, BeforeValidator(check_regex)] = Field(
+        ...,
+        description=attribute_matches_expression_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=attribute_matches_negate_description,
+    )
+
+
+class attribute_matches_model(base_attribute_matches_model):
+    r"""Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` matches the regular expression specified by ``expression``.
+
+    For example:
+
+    ```xml
+    <attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["attribute_matches"] = "attribute_matches"
+
+
+class attribute_matches_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    attribute_matches: base_attribute_matches_model
+
+
+class attribute_matches_model_relaxed(base_attribute_matches_model_relaxed):
+    r"""Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` matches the regular expression specified by ``expression``.
+
+    For example:
+
+    ```xml
+    <attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["attribute_matches"] = "attribute_matches"
+
+
+element_text_path_description = """The Python xpath-like expression to find the target element."""
+
+element_text_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_element_text_model(AssertionModel):
+    """base model for element_text describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_path_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+    @model_validator(mode="before")
+    @classmethod
+    def validate_children(self, data: typing.Any):
+        if isinstance(data, dict) and "children" not in data and "asserts" not in data:
+            raise ValueError("At least one of 'children' or 'asserts' must be specified for this assertion type.")
+        return data
+
+
+class base_element_text_model_relaxed(AssertionModel):
+    """base model for element_text describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_path_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+    @model_validator(mode="before")
+    @classmethod
+    def validate_children(self, data: typing.Any):
+        if isinstance(data, dict) and "children" not in data and "asserts" not in data:
+            raise ValueError("At least one of 'children' or 'asserts' must be specified for this assertion type.")
+        return data
+
+
+class element_text_model(base_element_text_model):
+    r"""This tag allows the developer to recurisively specify additional assertions as
+    child elements about just the text contained in the element specified by the
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
+      <not_has_text text="EDK72998.1" />
+    </element_text>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the implicit assertions can be inverted.
+    The sub-assertions, which have their own ``negate`` attribute, are not affected
+    by ``negate``."""
+
+    that: Literal["element_text"] = "element_text"
+
+
+class element_text_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    element_text: base_element_text_model
+
+
+class element_text_model_relaxed(base_element_text_model_relaxed):
+    r"""This tag allows the developer to recurisively specify additional assertions as
+    child elements about just the text contained in the element specified by the
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
+      <not_has_text text="EDK72998.1" />
+    </element_text>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the implicit assertions can be inverted.
+    The sub-assertions, which have their own ``negate`` attribute, are not affected
+    by ``negate``."""
+
+    that: Literal["element_text"] = "element_text"
+
+
+element_text_is_path_description = """The Python xpath-like expression to find the target element."""
+
+element_text_is_text_description = (
+    """The expected element text (body of the XML tag) to test against on the target XML element"""
+)
+
+element_text_is_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_element_text_is_model(AssertionModel):
+    """base model for element_text_is describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_is_path_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=element_text_is_text_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_is_negate_description,
+    )
+
+
+class base_element_text_is_model_relaxed(AssertionModel):
+    """base model for element_text_is describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_is_path_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=element_text_is_text_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_is_negate_description,
+    )
+
+
+class element_text_is_model(base_element_text_is_model):
+    r"""Asserts the text of the XML element with the specified XPath-like ``path`` is
+    the specified ``text``.
+
+    For example:
+
+    ```xml
+    <element_text_is path="BlastOutput_program" text="blastp" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["element_text_is"] = "element_text_is"
+
+
+class element_text_is_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    element_text_is: base_element_text_is_model
+
+
+class element_text_is_model_relaxed(base_element_text_is_model_relaxed):
+    r"""Asserts the text of the XML element with the specified XPath-like ``path`` is
+    the specified ``text``.
+
+    For example:
+
+    ```xml
+    <element_text_is path="BlastOutput_program" text="blastp" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["element_text_is"] = "element_text_is"
+
+
+element_text_matches_path_description = """The Python xpath-like expression to find the target element."""
+
+element_text_matches_expression_description = """The regular expressions to apply against the target element."""
+
+element_text_matches_negate_description = (
+    """A boolean that can be set to true to negate the outcome of the assertion."""
+)
+
+
+class base_element_text_matches_model(AssertionModel):
+    """base model for element_text_matches describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_matches_path_description,
+    )
+
+    expression: Annotated[str, BeforeValidator(check_regex)] = Field(
+        ...,
+        description=element_text_matches_expression_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_matches_negate_description,
+    )
+
+
+class base_element_text_matches_model_relaxed(AssertionModel):
+    """base model for element_text_matches describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=element_text_matches_path_description,
+    )
+
+    expression: Annotated[str, BeforeValidator(check_regex)] = Field(
+        ...,
+        description=element_text_matches_expression_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=element_text_matches_negate_description,
+    )
+
+
+class element_text_matches_model(base_element_text_matches_model):
+    r"""Asserts the text of the XML element with the specified XPath-like ``path``
+    matches the regular expression defined by ``expression``.
+
+    For example:
+
+    ```xml
+    <element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["element_text_matches"] = "element_text_matches"
+
+
+class element_text_matches_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    element_text_matches: base_element_text_matches_model
+
+
+class element_text_matches_model_relaxed(base_element_text_matches_model_relaxed):
+    r"""Asserts the text of the XML element with the specified XPath-like ``path``
+    matches the regular expression defined by ``expression``.
+
+    For example:
+
+    ```xml
+    <element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected)."""
+
+    that: Literal["element_text_matches"] = "element_text_matches"
+
+
+has_element_with_path_path_description = """The Python xpath-like expression to find the target element."""
+
+has_element_with_path_negate_description = (
+    """A boolean that can be set to true to negate the outcome of the assertion."""
+)
+
+
+class base_has_element_with_path_model(AssertionModel):
+    """base model for has_element_with_path describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_element_with_path_path_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_element_with_path_negate_description,
+    )
+
+
+class base_has_element_with_path_model_relaxed(AssertionModel):
+    """base model for has_element_with_path describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_element_with_path_path_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_element_with_path_negate_description,
+    )
+
+
+class has_element_with_path_model(base_has_element_with_path_model):
+    r"""Asserts the XML output contains at least one element (or tag) with the specified
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
+    ```
+
+    With ``negate`` the result of the assertion can be inverted."""
+
+    that: Literal["has_element_with_path"] = "has_element_with_path"
+
+
+class has_element_with_path_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_element_with_path: base_has_element_with_path_model
+
+
+class has_element_with_path_model_relaxed(base_has_element_with_path_model_relaxed):
+    r"""Asserts the XML output contains at least one element (or tag) with the specified
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
+    ```
+
+    With ``negate`` the result of the assertion can be inverted."""
+
+    that: Literal["has_element_with_path"] = "has_element_with_path"
+
+
+has_n_elements_with_path_path_description = """The Python xpath-like expression to find the target element."""
+
+has_n_elements_with_path_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_n_elements_with_path_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_n_elements_with_path_min_description = (
+    """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_n_elements_with_path_max_description = (
+    """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_n_elements_with_path_negate_description = (
+    """A boolean that can be set to true to negate the outcome of the assertion."""
+)
+
+
+class base_has_n_elements_with_path_model(AssertionModel):
+    """base model for has_n_elements_with_path describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_n_elements_with_path_path_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_elements_with_path_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_elements_with_path_negate_description,
+    )
+
+
+class base_has_n_elements_with_path_model_relaxed(AssertionModel):
+    """base model for has_n_elements_with_path describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_n_elements_with_path_path_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_n_elements_with_path_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_n_elements_with_path_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_n_elements_with_path_negate_description,
+    )
+
+
+class has_n_elements_with_path_model(base_has_n_elements_with_path_model):
+    r"""Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or
+    tags) with the specified XPath-like ``path``.
+
+    For example:
+
+    ```xml
+    <has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
+    ```
+
+    Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
+    can be used to specify the range of the expected number of occurences.
+    With ``negate`` the result of the assertion can be inverted."""
+
+    that: Literal["has_n_elements_with_path"] = "has_n_elements_with_path"
+
+
+class has_n_elements_with_path_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_n_elements_with_path: base_has_n_elements_with_path_model
+
+
+class has_n_elements_with_path_model_relaxed(base_has_n_elements_with_path_model_relaxed):
+    r"""Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or
+    tags) with the specified XPath-like ``path``.
+
+    For example:
+
+    ```xml
+    <has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
+    ```
+
+    Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
+    can be used to specify the range of the expected number of occurences.
+    With ``negate`` the result of the assertion can be inverted."""
+
+    that: Literal["has_n_elements_with_path"] = "has_n_elements_with_path"
+
+
+class base_is_valid_xml_model(AssertionModel):
+    """base model for is_valid_xml describing attributes."""
+
+
+class base_is_valid_xml_model_relaxed(AssertionModel):
+    """base model for is_valid_xml describing attributes."""
+
+
+class is_valid_xml_model(base_is_valid_xml_model):
+    r"""Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``)."""
+
+    that: Literal["is_valid_xml"] = "is_valid_xml"
+
+
+class is_valid_xml_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    is_valid_xml: base_is_valid_xml_model
+
+
+class is_valid_xml_model_relaxed(base_is_valid_xml_model_relaxed):
+    r"""Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``)."""
+
+    that: Literal["is_valid_xml"] = "is_valid_xml"
+
+
+xml_element_path_description = """The Python xpath-like expression to find the target element."""
+
+xml_element_attribute_description = """The XML attribute name to test against from the target XML element."""
+
+xml_element_all_description = (
+    """Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first """
+)
+
+xml_element_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+xml_element_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+xml_element_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+xml_element_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+xml_element_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_xml_element_model(AssertionModel):
+    """base model for xml_element describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=xml_element_path_description,
+    )
+
+    attribute: typing.Optional[typing.Union[str]] = Field(
+        None,
+        description=xml_element_attribute_description,
+    )
+
+    all: typing.Union[bool, str] = Field(
+        False,
+        description=xml_element_all_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=xml_element_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=xml_element_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+
+class base_xml_element_model_relaxed(AssertionModel):
+    """base model for xml_element describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=xml_element_path_description,
+    )
+
+    attribute: typing.Optional[typing.Union[str]] = Field(
+        None,
+        description=xml_element_attribute_description,
+    )
+
+    all: typing.Union[bool, str] = Field(
+        False,
+        description=xml_element_all_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=xml_element_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=xml_element_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=xml_element_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+
+class xml_element_model(base_xml_element_model):
+    r"""Assert if the XML file contains element(s) or tag(s) with the specified
+    [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
+    or ``min`` and ``max`` are given also the number of occurences is checked.
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem"/>
+      <xml_element path="./elem/more[2]"/>
+      <xml_element path=".//more" n="3" delta="1"/>
+    </assert_contents>
+    ```
+
+    With ``negate="true"`` the outcome of the assertions wrt the precence and number
+    of ``path`` can be negated. If there are any sub assertions then check them against
+
+    - the content of the attribute ``attribute``
+    - the element's text if no attribute is given
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem/more[2]" attribute="name">
+        <has_text_matching expression="foo$"/>
+      </xml_element>
+    </assert_contents>
+    ```
+
+    Sub-assertions are not subject to the ``negate`` attribute of ``xml_element``.
+    If ``all`` is ``true`` then the sub assertions are checked for all occurences.
+
+    Note that all other XML assertions can be expressed by this assertion (Galaxy
+    also implements the other assertions by calling this one)."""
+
+    that: Literal["xml_element"] = "xml_element"
+
+
+class xml_element_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    xml_element: base_xml_element_model
+
+
+class xml_element_model_relaxed(base_xml_element_model_relaxed):
+    r"""Assert if the XML file contains element(s) or tag(s) with the specified
+    [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
+    or ``min`` and ``max`` are given also the number of occurences is checked.
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem"/>
+      <xml_element path="./elem/more[2]"/>
+      <xml_element path=".//more" n="3" delta="1"/>
+    </assert_contents>
+    ```
+
+    With ``negate="true"`` the outcome of the assertions wrt the precence and number
+    of ``path`` can be negated. If there are any sub assertions then check them against
+
+    - the content of the attribute ``attribute``
+    - the element's text if no attribute is given
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem/more[2]" attribute="name">
+        <has_text_matching expression="foo$"/>
+      </xml_element>
+    </assert_contents>
+    ```
+
+    Sub-assertions are not subject to the ``negate`` attribute of ``xml_element``.
+    If ``all`` is ``true`` then the sub assertions are checked for all occurences.
+
+    Note that all other XML assertions can be expressed by this assertion (Galaxy
+    also implements the other assertions by calling this one)."""
+
+    that: Literal["xml_element"] = "xml_element"
+
+
+has_json_property_with_text_property_description = """The property name to search the JSON document for."""
+
+has_json_property_with_text_text_description = """The expected text value of the target JSON attribute."""
+
+
+class base_has_json_property_with_text_model(AssertionModel):
+    """base model for has_json_property_with_text describing attributes."""
+
+    property: str = Field(
+        ...,
+        description=has_json_property_with_text_property_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=has_json_property_with_text_text_description,
+    )
+
+
+class base_has_json_property_with_text_model_relaxed(AssertionModel):
+    """base model for has_json_property_with_text describing attributes."""
+
+    property: str = Field(
+        ...,
+        description=has_json_property_with_text_property_description,
+    )
+
+    text: str = Field(
+        ...,
+        description=has_json_property_with_text_text_description,
+    )
+
+
+class has_json_property_with_text_model(base_has_json_property_with_text_model):
+    r"""Asserts the JSON document contains a property or key with the specified text (i.e. string) value.
+
+    ```xml
+    <has_json_property_with_text property="color" text="red" />
+    ```"""
+
+    that: Literal["has_json_property_with_text"] = "has_json_property_with_text"
+
+
+class has_json_property_with_text_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_json_property_with_text: base_has_json_property_with_text_model
+
+
+class has_json_property_with_text_model_relaxed(base_has_json_property_with_text_model_relaxed):
+    r"""Asserts the JSON document contains a property or key with the specified text (i.e. string) value.
+
+    ```xml
+    <has_json_property_with_text property="color" text="red" />
+    ```"""
+
+    that: Literal["has_json_property_with_text"] = "has_json_property_with_text"
+
+
+has_json_property_with_value_property_description = """The property name to search the JSON document for."""
+
+has_json_property_with_value_value_description = (
+    """The expected JSON value of the target JSON attribute (as a JSON encoded string)."""
+)
+
+
+class base_has_json_property_with_value_model(AssertionModel):
+    """base model for has_json_property_with_value describing attributes."""
+
+    property: str = Field(
+        ...,
+        description=has_json_property_with_value_property_description,
+    )
+
+    value: str = Field(
+        ...,
+        description=has_json_property_with_value_value_description,
+    )
+
+
+class base_has_json_property_with_value_model_relaxed(AssertionModel):
+    """base model for has_json_property_with_value describing attributes."""
+
+    property: str = Field(
+        ...,
+        description=has_json_property_with_value_property_description,
+    )
+
+    value: str = Field(
+        ...,
+        description=has_json_property_with_value_value_description,
+    )
+
+
+class has_json_property_with_value_model(base_has_json_property_with_value_model):
+    r"""Asserts the JSON document contains a property or key with the specified JSON value.
+
+    ```xml
+    <has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />
+    ```"""
+
+    that: Literal["has_json_property_with_value"] = "has_json_property_with_value"
+
+
+class has_json_property_with_value_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_json_property_with_value: base_has_json_property_with_value_model
+
+
+class has_json_property_with_value_model_relaxed(base_has_json_property_with_value_model_relaxed):
+    r"""Asserts the JSON document contains a property or key with the specified JSON value.
+
+    ```xml
+    <has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />
+    ```"""
+
+    that: Literal["has_json_property_with_value"] = "has_json_property_with_value"
+
+
+has_h5_attribute_key_description = """HDF5 attribute to check value of."""
+
+has_h5_attribute_value_description = """Expected value of HDF5 attribute to check."""
+
+
+class base_has_h5_attribute_model(AssertionModel):
+    """base model for has_h5_attribute describing attributes."""
+
+    key: str = Field(
+        ...,
+        description=has_h5_attribute_key_description,
+    )
+
+    value: str = Field(
+        ...,
+        description=has_h5_attribute_value_description,
+    )
+
+
+class base_has_h5_attribute_model_relaxed(AssertionModel):
+    """base model for has_h5_attribute describing attributes."""
+
+    key: str = Field(
+        ...,
+        description=has_h5_attribute_key_description,
+    )
+
+    value: str = Field(
+        ...,
+        description=has_h5_attribute_value_description,
+    )
+
+
+class has_h5_attribute_model(base_has_h5_attribute_model):
+    r"""Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.
+
+    ```xml
+    <has_h5_attribute key="nchroms" value="15" />
+    ```"""
+
+    that: Literal["has_h5_attribute"] = "has_h5_attribute"
+
+
+class has_h5_attribute_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_h5_attribute: base_has_h5_attribute_model
+
+
+class has_h5_attribute_model_relaxed(base_has_h5_attribute_model_relaxed):
+    r"""Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.
+
+    ```xml
+    <has_h5_attribute key="nchroms" value="15" />
+    ```"""
+
+    that: Literal["has_h5_attribute"] = "has_h5_attribute"
+
+
+has_h5_keys_keys_description = """HDF5 attributes to check value of as a comma-separated string."""
+
+
+class base_has_h5_keys_model(AssertionModel):
+    """base model for has_h5_keys describing attributes."""
+
+    keys: str = Field(
+        ...,
+        description=has_h5_keys_keys_description,
+    )
+
+
+class base_has_h5_keys_model_relaxed(AssertionModel):
+    """base model for has_h5_keys describing attributes."""
+
+    keys: str = Field(
+        ...,
+        description=has_h5_keys_keys_description,
+    )
+
+
+class has_h5_keys_model(base_has_h5_keys_model):
+    r"""Asserts the specified HDF5 output has the given keys."""
+
+    that: Literal["has_h5_keys"] = "has_h5_keys"
+
+
+class has_h5_keys_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_h5_keys: base_has_h5_keys_model
+
+
+class has_h5_keys_model_relaxed(base_has_h5_keys_model_relaxed):
+    r"""Asserts the specified HDF5 output has the given keys."""
+
+    that: Literal["has_h5_keys"] = "has_h5_keys"
+
+
+has_archive_member_path_description = """The regular expression specifying the archive member."""
+
+has_archive_member_all_description = (
+    """Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first"""
+)
+
+has_archive_member_n_description = """Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_archive_member_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_archive_member_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_archive_member_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_archive_member_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_archive_member_model(AssertionModel):
+    """base model for has_archive_member describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_archive_member_path_description,
+    )
+
+    all: typing.Union[bool, str] = Field(
+        False,
+        description=has_archive_member_all_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_archive_member_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_archive_member_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+
+class base_has_archive_member_model_relaxed(AssertionModel):
+    """base model for has_archive_member describing attributes."""
+
+    path: str = Field(
+        ...,
+        description=has_archive_member_path_description,
+    )
+
+    all: typing.Union[bool, str] = Field(
+        False,
+        description=has_archive_member_all_description,
+    )
+
+    n: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_n_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_archive_member_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_archive_member_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_archive_member_negate_description,
+    )
+
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+
+class has_archive_member_model(base_has_archive_member_model):
+    r"""This tag allows to check if ``path`` is contained in a compressed file.
+
+    The path is a regular expression that is matched against the full paths of the objects in
+    the compressed file (remember that "matching" means it is checked if a prefix of
+    the full path of an archive member is described by the regular expression).
+    Valid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that
+    depending on the archive creation method:
+
+    - full paths of the members may be prefixed with ``./``
+    - directories may be treated as empty files
+
+    ```xml
+    <has_archive_member path="./path/to/my-file.txt"/>
+    ```
+
+    With ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of
+    archive members matching ``path`` can be expressed. The following could be used,
+    e.g., to assert an archive containing n&plusmn;1 elements out of which at least
+    4 need to have a ``txt`` extension.
+
+    ```xml
+    <has_archive_member path=".*" n="10" delta="1"/>
+    <has_archive_member path=".*\.txt" min="4"/>
+    ```
+
+    In addition the tag can contain additional assertions as child elements about
+    the first member in the archive matching the regular expression ``path``. For
+    instance
+
+    ```xml
+    <has_archive_member path=".*/my-file.txt">
+      <not_has_text text="EDK72998.1"/>
+    </has_archive_member>
+    ```
+
+    If the ``all`` attribute is set to ``true`` then all archive members are subject
+    to the assertions. Note that, archive members matching the ``path`` are sorted
+    alphabetically.
+
+    The ``negate`` attribute of the ``has_archive_member`` assertion only affects
+    the asserts on the presence and number of matching archive members, but not any
+    sub-assertions (which can offer the ``negate`` attribute on their own).  The
+    check if the file is an archive at all, which is also done by the function, is
+    not affected."""
+
+    that: Literal["has_archive_member"] = "has_archive_member"
+
+
+class has_archive_member_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_archive_member: base_has_archive_member_model
+
+
+class has_archive_member_model_relaxed(base_has_archive_member_model_relaxed):
+    r"""This tag allows to check if ``path`` is contained in a compressed file.
+
+    The path is a regular expression that is matched against the full paths of the objects in
+    the compressed file (remember that "matching" means it is checked if a prefix of
+    the full path of an archive member is described by the regular expression).
+    Valid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that
+    depending on the archive creation method:
+
+    - full paths of the members may be prefixed with ``./``
+    - directories may be treated as empty files
+
+    ```xml
+    <has_archive_member path="./path/to/my-file.txt"/>
+    ```
+
+    With ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of
+    archive members matching ``path`` can be expressed. The following could be used,
+    e.g., to assert an archive containing n&plusmn;1 elements out of which at least
+    4 need to have a ``txt`` extension.
+
+    ```xml
+    <has_archive_member path=".*" n="10" delta="1"/>
+    <has_archive_member path=".*\.txt" min="4"/>
+    ```
+
+    In addition the tag can contain additional assertions as child elements about
+    the first member in the archive matching the regular expression ``path``. For
+    instance
+
+    ```xml
+    <has_archive_member path=".*/my-file.txt">
+      <not_has_text text="EDK72998.1"/>
+    </has_archive_member>
+    ```
+
+    If the ``all`` attribute is set to ``true`` then all archive members are subject
+    to the assertions. Note that, archive members matching the ``path`` are sorted
+    alphabetically.
+
+    The ``negate`` attribute of the ``has_archive_member`` assertion only affects
+    the asserts on the presence and number of matching archive members, but not any
+    sub-assertions (which can offer the ``negate`` attribute on their own).  The
+    check if the file is an archive at all, which is also done by the function, is
+    not affected."""
+
+    that: Literal["has_archive_member"] = "has_archive_member"
+
+
+has_size_value_description = """Deprecated alias for `size`"""
+
+has_size_size_description = """Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_size_delta_description = (
+    """Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+)
+
+has_size_min_description = """Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_size_max_description = """Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``"""
+
+has_size_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_size_model(AssertionModel):
+    """base model for has_size describing attributes."""
+
+    value: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_value_description,
+    )
+
+    size: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_size_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_size_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_size_negate_description,
+    )
+
+
+class base_has_size_model_relaxed(AssertionModel):
+    """base model for has_size describing attributes."""
+
+    value: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_value_description,
+    )
+
+    size: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_size_description,
+    )
+
+    delta: Annotated[
+        typing.Union[int, str], BeforeValidator(check_bytes), BeforeValidator(check_non_negative_if_int)
+    ] = Field(
+        0,
+        description=has_size_delta_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[str, int]],
+        BeforeValidator(check_bytes),
+        BeforeValidator(check_non_negative_if_int),
+    ] = Field(
+        None,
+        description=has_size_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_size_negate_description,
+    )
+
+
+class has_size_model(base_has_size_model):
+    r"""Asserts the specified output has a size of the specified value
+
+    Attributes size and value or synonyms though value is considered deprecated.
+    The size optionally allows for absolute (``delta``) difference."""
+
+    that: Literal["has_size"] = "has_size"
+
+
+class has_size_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_size: base_has_size_model
+
+
+class has_size_model_relaxed(base_has_size_model_relaxed):
+    r"""Asserts the specified output has a size of the specified value
+
+    Attributes size and value or synonyms though value is considered deprecated.
+    The size optionally allows for absolute (``delta``) difference."""
+
+    that: Literal["has_size"] = "has_size"
+
+
+has_image_center_of_mass_center_of_mass_description = """The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma)."""
+
+has_image_center_of_mass_channel_description = """Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel)."""
+
+has_image_center_of_mass_slice_description = (
+    """Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice)."""
+)
+
+has_image_center_of_mass_frame_description = """Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame)."""
+
+has_image_center_of_mass_eps_description = (
+    """The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``)."""
+)
+
+
+class base_has_image_center_of_mass_model(AssertionModel):
+    """base model for has_image_center_of_mass describing attributes."""
+
+    center_of_mass: Annotated[str, BeforeValidator(check_center_of_mass)] = Field(
+        ...,
+        description=has_image_center_of_mass_center_of_mass_description,
+    )
+
+    channel: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_center_of_mass_channel_description,
+    )
+
+    slice: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_center_of_mass_slice_description,
+    )
+
+    frame: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_center_of_mass_frame_description,
+    )
+
+    eps: Annotated[typing.Union[StrictInt, StrictFloat], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_center_of_mass_eps_description,
+    )
+
+
+class base_has_image_center_of_mass_model_relaxed(AssertionModel):
+    """base model for has_image_center_of_mass describing attributes."""
+
+    center_of_mass: Annotated[str, BeforeValidator(check_center_of_mass)] = Field(
+        ...,
+        description=has_image_center_of_mass_center_of_mass_description,
+    )
+
+    channel: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_center_of_mass_channel_description,
+    )
+
+    slice: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_center_of_mass_slice_description,
+    )
+
+    frame: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_center_of_mass_frame_description,
+    )
+
+    eps: Annotated[typing.Union[float, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_center_of_mass_eps_description,
+    )
+
+
+class has_image_center_of_mass_model(base_has_image_center_of_mass_model):
+    r"""Asserts the specified output is an image and has the specified center of mass.
+
+    Asserts the output is an image and has a specific center of mass,
+    or has an Euclidean distance of ``eps`` or less to that point (e.g.,
+    ``<has_image_center_of_mass center_of_mass="511.07, 223.34" />``)."""
+
+    that: Literal["has_image_center_of_mass"] = "has_image_center_of_mass"
+
+
+class has_image_center_of_mass_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_center_of_mass: base_has_image_center_of_mass_model
+
+
+class has_image_center_of_mass_model_relaxed(base_has_image_center_of_mass_model_relaxed):
+    r"""Asserts the specified output is an image and has the specified center of mass.
+
+    Asserts the output is an image and has a specific center of mass,
+    or has an Euclidean distance of ``eps`` or less to that point (e.g.,
+    ``<has_image_center_of_mass center_of_mass="511.07, 223.34" />``)."""
+
+    that: Literal["has_image_center_of_mass"] = "has_image_center_of_mass"
+
+
+has_image_channels_channels_description = """Expected number of channels of the image."""
+
+has_image_channels_delta_description = """Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``."""
+
+has_image_channels_min_description = """Minimum allowed number of channels."""
+
+has_image_channels_max_description = """Maximum allowed number of channels."""
+
+has_image_channels_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_channels_model(AssertionModel):
+    """base model for has_image_channels describing attributes."""
+
+    channels: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_channels_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_channels_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_channels_negate_description,
+    )
+
+
+class base_has_image_channels_model_relaxed(AssertionModel):
+    """base model for has_image_channels describing attributes."""
+
+    channels: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_channels_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_channels_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_channels_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_channels_negate_description,
+    )
+
+
+class has_image_channels_model(base_has_image_channels_model):
+    r"""Asserts the output is an image and has a specific number of channels.
+
+    The number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
+
+    Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_channels"] = "has_image_channels"
+
+
+class has_image_channels_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_channels: base_has_image_channels_model
+
+
+class has_image_channels_model_relaxed(base_has_image_channels_model_relaxed):
+    r"""Asserts the output is an image and has a specific number of channels.
+
+    The number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
+
+    Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_channels"] = "has_image_channels"
+
+
+has_image_depth_depth_description = """Expected depth of the image (number of slices)."""
+
+has_image_depth_delta_description = """Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``."""
+
+has_image_depth_min_description = """Minimum allowed depth of the image (number of slices)."""
+
+has_image_depth_max_description = """Maximum allowed depth of the image (number of slices)."""
+
+has_image_depth_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_depth_model(AssertionModel):
+    """base model for has_image_depth describing attributes."""
+
+    depth: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_depth_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_depth_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_depth_negate_description,
+    )
+
+
+class base_has_image_depth_model_relaxed(AssertionModel):
+    """base model for has_image_depth describing attributes."""
+
+    depth: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_depth_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_depth_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_depth_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_depth_negate_description,
+    )
+
+
+class has_image_depth_model(base_has_image_depth_model):
+    r"""Asserts the output is an image and has a specific depth (number of slices).
+
+    The depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth="512" delta="2" />``).
+    Alternatively the range of the expected depth can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_depth"] = "has_image_depth"
+
+
+class has_image_depth_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_depth: base_has_image_depth_model
+
+
+class has_image_depth_model_relaxed(base_has_image_depth_model_relaxed):
+    r"""Asserts the output is an image and has a specific depth (number of slices).
+
+    The depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth="512" delta="2" />``).
+    Alternatively the range of the expected depth can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_depth"] = "has_image_depth"
+
+
+has_image_frames_frames_description = """Expected number of frames in the image sequence (number of time steps)."""
+
+has_image_frames_delta_description = """Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``."""
+
+has_image_frames_min_description = """Minimum allowed number of frames in the image sequence (number of time steps)."""
+
+has_image_frames_max_description = """Maximum allowed number of frames in the image sequence (number of time steps)."""
+
+has_image_frames_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_frames_model(AssertionModel):
+    """base model for has_image_frames describing attributes."""
+
+    frames: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_frames_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_frames_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_frames_negate_description,
+    )
+
+
+class base_has_image_frames_model_relaxed(AssertionModel):
+    """base model for has_image_frames describing attributes."""
+
+    frames: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_frames_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_frames_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_frames_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_frames_negate_description,
+    )
+
+
+class has_image_frames_model(base_has_image_frames_model):
+    r"""Asserts the output is an image and has a specific number of frames (number of time steps).
+
+    The number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth="512" delta="2" />``).
+    Alternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_frames"] = "has_image_frames"
+
+
+class has_image_frames_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_frames: base_has_image_frames_model
+
+
+class has_image_frames_model_relaxed(base_has_image_frames_model_relaxed):
+    r"""Asserts the output is an image and has a specific number of frames (number of time steps).
+
+    The number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth="512" delta="2" />``).
+    Alternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_frames"] = "has_image_frames"
+
+
+has_image_height_height_description = """Expected height of the image (in pixels)."""
+
+has_image_height_delta_description = """Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``."""
+
+has_image_height_min_description = """Minimum allowed height of the image (in pixels)."""
+
+has_image_height_max_description = """Maximum allowed height of the image (in pixels)."""
+
+has_image_height_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_height_model(AssertionModel):
+    """base model for has_image_height describing attributes."""
+
+    height: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_height_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_height_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_height_negate_description,
+    )
+
+
+class base_has_image_height_model_relaxed(AssertionModel):
+    """base model for has_image_height describing attributes."""
+
+    height: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_height_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_height_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_height_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_height_negate_description,
+    )
+
+
+class has_image_height_model(base_has_image_height_model):
+    r"""Asserts the output is an image and has a specific height (in pixels).
+
+    The height is plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
+    Alternatively the range of the expected height can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_height"] = "has_image_height"
+
+
+class has_image_height_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_height: base_has_image_height_model
+
+
+class has_image_height_model_relaxed(base_has_image_height_model_relaxed):
+    r"""Asserts the output is an image and has a specific height (in pixels).
+
+    The height is plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
+    Alternatively the range of the expected height can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_height"] = "has_image_height"
+
+
+has_image_mean_intensity_channel_description = """Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel)."""
+
+has_image_mean_intensity_slice_description = (
+    """Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice)."""
+)
+
+has_image_mean_intensity_frame_description = """Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame)."""
+
+has_image_mean_intensity_mean_intensity_description = """The required mean value of the image intensities."""
+
+has_image_mean_intensity_eps_description = """The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``."""
+
+has_image_mean_intensity_min_description = """A lower bound of the required mean value of the image intensities."""
+
+has_image_mean_intensity_max_description = """An upper bound of the required mean value of the image intensities."""
+
+
+class base_has_image_mean_intensity_model(AssertionModel):
+    """base model for has_image_mean_intensity describing attributes."""
+
+    channel: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_intensity_channel_description,
+    )
+
+    slice: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_intensity_slice_description,
+    )
+
+    frame: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_intensity_frame_description,
+    )
+
+    mean_intensity: typing.Optional[typing.Union[StrictInt, StrictFloat]] = Field(
+        None,
+        description=has_image_mean_intensity_mean_intensity_description,
+    )
+
+    eps: Annotated[typing.Union[StrictInt, StrictFloat], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_mean_intensity_eps_description,
+    )
+
+    min: typing.Optional[typing.Union[StrictInt, StrictFloat]] = Field(
+        None,
+        description=has_image_mean_intensity_min_description,
+    )
+
+    max: typing.Optional[typing.Union[StrictInt, StrictFloat]] = Field(
+        None,
+        description=has_image_mean_intensity_max_description,
+    )
+
+
+class base_has_image_mean_intensity_model_relaxed(AssertionModel):
+    """base model for has_image_mean_intensity describing attributes."""
+
+    channel: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_intensity_channel_description,
+    )
+
+    slice: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_intensity_slice_description,
+    )
+
+    frame: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_intensity_frame_description,
+    )
+
+    mean_intensity: typing.Optional[typing.Union[float, str]] = Field(
+        None,
+        description=has_image_mean_intensity_mean_intensity_description,
+    )
+
+    eps: Annotated[typing.Union[float, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_mean_intensity_eps_description,
+    )
+
+    min: typing.Optional[typing.Union[float, str]] = Field(
+        None,
+        description=has_image_mean_intensity_min_description,
+    )
+
+    max: typing.Optional[typing.Union[float, str]] = Field(
+        None,
+        description=has_image_mean_intensity_max_description,
+    )
+
+
+class has_image_mean_intensity_model(base_has_image_mean_intensity_model):
+    r"""Asserts the output is an image and has a specific mean intensity value.
+
+    The mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity="0.83" />``).
+    Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_mean_intensity"] = "has_image_mean_intensity"
+
+
+class has_image_mean_intensity_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_mean_intensity: base_has_image_mean_intensity_model
+
+
+class has_image_mean_intensity_model_relaxed(base_has_image_mean_intensity_model_relaxed):
+    r"""Asserts the output is an image and has a specific mean intensity value.
+
+    The mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity="0.83" />``).
+    Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_mean_intensity"] = "has_image_mean_intensity"
+
+
+has_image_mean_object_size_channel_description = """Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel)."""
+
+has_image_mean_object_size_slice_description = (
+    """Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice)."""
+)
+
+has_image_mean_object_size_frame_description = """Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame)."""
+
+has_image_mean_object_size_labels_description = """List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``."""
+
+has_image_mean_object_size_exclude_labels_description = """List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``."""
+
+has_image_mean_object_size_mean_object_size_description = """The required mean size of the uniquely labeled objects."""
+
+has_image_mean_object_size_eps_description = """The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``."""
+
+has_image_mean_object_size_min_description = (
+    """A lower bound of the required mean size of the uniquely labeled objects."""
+)
+
+has_image_mean_object_size_max_description = (
+    """An upper bound of the required mean size of the uniquely labeled objects."""
+)
+
+
+class base_has_image_mean_object_size_model(AssertionModel):
+    """base model for has_image_mean_object_size describing attributes."""
+
+    channel: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_object_size_channel_description,
+    )
+
+    slice: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_object_size_slice_description,
+    )
+
+    frame: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_mean_object_size_frame_description,
+    )
+
+    labels: typing.Optional[typing.List[int]] = Field(
+        None,
+        description=has_image_mean_object_size_labels_description,
+    )
+
+    exclude_labels: typing.Optional[typing.List[int]] = Field(
+        None,
+        description=has_image_mean_object_size_exclude_labels_description,
+    )
+
+    mean_object_size: Annotated[
+        typing.Optional[typing.Union[StrictInt, StrictFloat]], BeforeValidator(check_non_negative_if_set)
+    ] = Field(
+        None,
+        description=has_image_mean_object_size_mean_object_size_description,
+    )
+
+    eps: Annotated[typing.Union[StrictInt, StrictFloat], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_mean_object_size_eps_description,
+    )
+
+    min: Annotated[
+        typing.Optional[typing.Union[StrictInt, StrictFloat]], BeforeValidator(check_non_negative_if_set)
+    ] = Field(
+        None,
+        description=has_image_mean_object_size_min_description,
+    )
+
+    max: Annotated[
+        typing.Optional[typing.Union[StrictInt, StrictFloat]], BeforeValidator(check_non_negative_if_set)
+    ] = Field(
+        None,
+        description=has_image_mean_object_size_max_description,
+    )
+
+
+class base_has_image_mean_object_size_model_relaxed(AssertionModel):
+    """base model for has_image_mean_object_size describing attributes."""
+
+    channel: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_object_size_channel_description,
+    )
+
+    slice: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_object_size_slice_description,
+    )
+
+    frame: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_mean_object_size_frame_description,
+    )
+
+    labels: typing.Optional[typing.Union[str, typing.List[int]]] = Field(
+        None,
+        description=has_image_mean_object_size_labels_description,
+    )
+
+    exclude_labels: typing.Optional[typing.Union[str, typing.List[int]]] = Field(
+        None,
+        description=has_image_mean_object_size_exclude_labels_description,
+    )
+
+    mean_object_size: Annotated[
+        typing.Optional[typing.Union[float, str]], BeforeValidator(check_non_negative_if_set)
+    ] = Field(
+        None,
+        description=has_image_mean_object_size_mean_object_size_description,
+    )
+
+    eps: Annotated[typing.Union[float, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0.01,
+        description=has_image_mean_object_size_eps_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[float, str]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_mean_object_size_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[float, str]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_mean_object_size_max_description,
+    )
+
+
+class has_image_mean_object_size_model(base_has_image_mean_object_size_model):
+    r"""Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),
+
+    The mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
+
+    The labels must be unique."""
+
+    that: Literal["has_image_mean_object_size"] = "has_image_mean_object_size"
+
+
+class has_image_mean_object_size_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_mean_object_size: base_has_image_mean_object_size_model
+
+
+class has_image_mean_object_size_model_relaxed(base_has_image_mean_object_size_model_relaxed):
+    r"""Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),
+
+    The mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
+
+    The labels must be unique."""
+
+    that: Literal["has_image_mean_object_size"] = "has_image_mean_object_size"
+
+
+has_image_n_labels_channel_description = """Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel)."""
+
+has_image_n_labels_slice_description = (
+    """Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice)."""
+)
+
+has_image_n_labels_frame_description = """Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame)."""
+
+has_image_n_labels_labels_description = """List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``."""
+
+has_image_n_labels_exclude_labels_description = """List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``."""
+
+has_image_n_labels_n_description = """Expected number of labels."""
+
+has_image_n_labels_delta_description = """Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``."""
+
+has_image_n_labels_min_description = """Minimum allowed number of labels."""
+
+has_image_n_labels_max_description = """Maximum allowed number of labels."""
+
+has_image_n_labels_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_n_labels_model(AssertionModel):
+    """base model for has_image_n_labels describing attributes."""
+
+    channel: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_n_labels_channel_description,
+    )
+
+    slice: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_n_labels_slice_description,
+    )
+
+    frame: typing.Optional[StrictInt] = Field(
+        None,
+        description=has_image_n_labels_frame_description,
+    )
+
+    labels: typing.Optional[typing.List[int]] = Field(
+        None,
+        description=has_image_n_labels_labels_description,
+    )
+
+    exclude_labels: typing.Optional[typing.List[int]] = Field(
+        None,
+        description=has_image_n_labels_exclude_labels_description,
+    )
+
+    n: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_n_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_n_labels_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_n_labels_negate_description,
+    )
+
+
+class base_has_image_n_labels_model_relaxed(AssertionModel):
+    """base model for has_image_n_labels describing attributes."""
+
+    channel: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_n_labels_channel_description,
+    )
+
+    slice: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_n_labels_slice_description,
+    )
+
+    frame: typing.Optional[typing.Union[str, int]] = Field(
+        None,
+        description=has_image_n_labels_frame_description,
+    )
+
+    labels: typing.Optional[typing.Union[str, typing.List[int]]] = Field(
+        None,
+        description=has_image_n_labels_labels_description,
+    )
+
+    exclude_labels: typing.Optional[typing.Union[str, typing.List[int]]] = Field(
+        None,
+        description=has_image_n_labels_exclude_labels_description,
+    )
+
+    n: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_n_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_n_labels_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_n_labels_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_n_labels_negate_description,
+    )
+
+
+class has_image_n_labels_model(base_has_image_n_labels_model):
+    r"""Asserts the output is an image and has the specified labels.
+
+    Labels can be a number of labels or unique values (e.g.,
+    ``<has_image_n_labels n="187" exclude_labels="0" />``).
+
+    The primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects."""
+
+    that: Literal["has_image_n_labels"] = "has_image_n_labels"
+
+
+class has_image_n_labels_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_n_labels: base_has_image_n_labels_model
+
+
+class has_image_n_labels_model_relaxed(base_has_image_n_labels_model_relaxed):
+    r"""Asserts the output is an image and has the specified labels.
+
+    Labels can be a number of labels or unique values (e.g.,
+    ``<has_image_n_labels n="187" exclude_labels="0" />``).
+
+    The primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects."""
+
+    that: Literal["has_image_n_labels"] = "has_image_n_labels"
+
+
+has_image_width_width_description = """Expected width of the image (in pixels)."""
+
+has_image_width_delta_description = """Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``."""
+
+has_image_width_min_description = """Minimum allowed width of the image (in pixels)."""
+
+has_image_width_max_description = """Maximum allowed width of the image (in pixels)."""
+
+has_image_width_negate_description = """A boolean that can be set to true to negate the outcome of the assertion."""
+
+
+class base_has_image_width_model(AssertionModel):
+    """base model for has_image_width describing attributes."""
+
+    width: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_width_description,
+    )
+
+    delta: Annotated[StrictInt, BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_width_delta_description,
+    )
+
+    min: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_min_description,
+    )
+
+    max: Annotated[typing.Optional[StrictInt], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_width_negate_description,
+    )
+
+
+class base_has_image_width_model_relaxed(AssertionModel):
+    """base model for has_image_width describing attributes."""
+
+    width: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_width_description,
+    )
+
+    delta: Annotated[typing.Union[int, str], BeforeValidator(check_non_negative_if_set)] = Field(
+        0,
+        description=has_image_width_delta_description,
+    )
+
+    min: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_min_description,
+    )
+
+    max: Annotated[typing.Optional[typing.Union[str, int]], BeforeValidator(check_non_negative_if_set)] = Field(
+        None,
+        description=has_image_width_max_description,
+    )
+
+    negate: typing.Union[bool, str] = Field(
+        False,
+        description=has_image_width_negate_description,
+    )
+
+
+class has_image_width_model(base_has_image_width_model):
+    r"""Asserts the output is an image and has a specific width (in pixels).
+
+    The width is plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
+    Alternatively the range of the expected width can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_width"] = "has_image_width"
+
+
+class has_image_width_model_nested(AssertionModel):
+    r"""Nested version of this assertion model."""
+
+    has_image_width: base_has_image_width_model
+
+
+class has_image_width_model_relaxed(base_has_image_width_model_relaxed):
+    r"""Asserts the output is an image and has a specific width (in pixels).
+
+    The width is plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
+    Alternatively the range of the expected width can be specified by ``min`` and/or ``max``."""
+
+    that: Literal["has_image_width"] = "has_image_width"
+
+
+any_assertion_model_flat = Annotated[
+    typing.Union[
+        has_line_model,
+        has_line_matching_model,
+        has_n_lines_model,
+        has_text_model,
+        has_text_matching_model,
+        not_has_text_model,
+        has_n_columns_model,
+        attribute_is_model,
+        attribute_matches_model,
+        element_text_model,
+        element_text_is_model,
+        element_text_matches_model,
+        has_element_with_path_model,
+        has_n_elements_with_path_model,
+        is_valid_xml_model,
+        xml_element_model,
+        has_json_property_with_text_model,
+        has_json_property_with_value_model,
+        has_h5_attribute_model,
+        has_h5_keys_model,
+        has_archive_member_model,
+        has_size_model,
+        has_image_center_of_mass_model,
+        has_image_channels_model,
+        has_image_depth_model,
+        has_image_frames_model,
+        has_image_height_model,
+        has_image_mean_intensity_model,
+        has_image_mean_object_size_model,
+        has_image_n_labels_model,
+        has_image_width_model,
+    ],
+    Field(discriminator="that"),
+]
+
+any_assertion_model_nested = typing.Union[
+    has_line_model_nested,
+    has_line_matching_model_nested,
+    has_n_lines_model_nested,
+    has_text_model_nested,
+    has_text_matching_model_nested,
+    not_has_text_model_nested,
+    has_n_columns_model_nested,
+    attribute_is_model_nested,
+    attribute_matches_model_nested,
+    element_text_model_nested,
+    element_text_is_model_nested,
+    element_text_matches_model_nested,
+    has_element_with_path_model_nested,
+    has_n_elements_with_path_model_nested,
+    is_valid_xml_model_nested,
+    xml_element_model_nested,
+    has_json_property_with_text_model_nested,
+    has_json_property_with_value_model_nested,
+    has_h5_attribute_model_nested,
+    has_h5_keys_model_nested,
+    has_archive_member_model_nested,
+    has_size_model_nested,
+    has_image_center_of_mass_model_nested,
+    has_image_channels_model_nested,
+    has_image_depth_model_nested,
+    has_image_frames_model_nested,
+    has_image_height_model_nested,
+    has_image_mean_intensity_model_nested,
+    has_image_mean_object_size_model_nested,
+    has_image_n_labels_model_nested,
+    has_image_width_model_nested,
+]
+
+any_assertion_model_flat_relaxed = Annotated[
+    typing.Union[
+        has_line_model_relaxed,
+        has_line_matching_model_relaxed,
+        has_n_lines_model_relaxed,
+        has_text_model_relaxed,
+        has_text_matching_model_relaxed,
+        not_has_text_model_relaxed,
+        has_n_columns_model_relaxed,
+        attribute_is_model_relaxed,
+        attribute_matches_model_relaxed,
+        element_text_model_relaxed,
+        element_text_is_model_relaxed,
+        element_text_matches_model_relaxed,
+        has_element_with_path_model_relaxed,
+        has_n_elements_with_path_model_relaxed,
+        is_valid_xml_model_relaxed,
+        xml_element_model_relaxed,
+        has_json_property_with_text_model_relaxed,
+        has_json_property_with_value_model_relaxed,
+        has_h5_attribute_model_relaxed,
+        has_h5_keys_model_relaxed,
+        has_archive_member_model_relaxed,
+        has_size_model_relaxed,
+        has_image_center_of_mass_model_relaxed,
+        has_image_channels_model_relaxed,
+        has_image_depth_model_relaxed,
+        has_image_frames_model_relaxed,
+        has_image_height_model_relaxed,
+        has_image_mean_intensity_model_relaxed,
+        has_image_mean_object_size_model_relaxed,
+        has_image_n_labels_model_relaxed,
+        has_image_width_model_relaxed,
+    ],
+    Field(discriminator="that"),
+]
+
+assertion_list = RootModel[typing.List[typing.Union[any_assertion_model_flat, any_assertion_model_nested]]]
+
+# used to model what the XML conversion should look like - not meant to be consumed outside of
+# of Galaxy internals / linting.
+relaxed_assertion_list = RootModel[typing.List[any_assertion_model_flat_relaxed]]
+
+
+class assertion_dict(AssertionModel):
+
+    has_line: typing.Optional[base_has_line_model] = None
+
+    has_line_matching: typing.Optional[base_has_line_matching_model] = None
+
+    has_n_lines: typing.Optional[base_has_n_lines_model] = None
+
+    has_text: typing.Optional[base_has_text_model] = None
+
+    has_text_matching: typing.Optional[base_has_text_matching_model] = None
+
+    not_has_text: typing.Optional[base_not_has_text_model] = None
+
+    has_n_columns: typing.Optional[base_has_n_columns_model] = None
+
+    attribute_is: typing.Optional[base_attribute_is_model] = None
+
+    attribute_matches: typing.Optional[base_attribute_matches_model] = None
+
+    element_text: typing.Optional[base_element_text_model] = None
+
+    element_text_is: typing.Optional[base_element_text_is_model] = None
+
+    element_text_matches: typing.Optional[base_element_text_matches_model] = None
+
+    has_element_with_path: typing.Optional[base_has_element_with_path_model] = None
+
+    has_n_elements_with_path: typing.Optional[base_has_n_elements_with_path_model] = None
+
+    is_valid_xml: typing.Optional[base_is_valid_xml_model] = None
+
+    xml_element: typing.Optional[base_xml_element_model] = None
+
+    has_json_property_with_text: typing.Optional[base_has_json_property_with_text_model] = None
+
+    has_json_property_with_value: typing.Optional[base_has_json_property_with_value_model] = None
+
+    has_h5_attribute: typing.Optional[base_has_h5_attribute_model] = None
+
+    has_h5_keys: typing.Optional[base_has_h5_keys_model] = None
+
+    has_archive_member: typing.Optional[base_has_archive_member_model] = None
+
+    has_size: typing.Optional[base_has_size_model] = None
+
+    has_image_center_of_mass: typing.Optional[base_has_image_center_of_mass_model] = None
+
+    has_image_channels: typing.Optional[base_has_image_channels_model] = None
+
+    has_image_depth: typing.Optional[base_has_image_depth_model] = None
+
+    has_image_frames: typing.Optional[base_has_image_frames_model] = None
+
+    has_image_height: typing.Optional[base_has_image_height_model] = None
+
+    has_image_mean_intensity: typing.Optional[base_has_image_mean_intensity_model] = None
+
+    has_image_mean_object_size: typing.Optional[base_has_image_mean_object_size_model] = None
+
+    has_image_n_labels: typing.Optional[base_has_image_n_labels_model] = None
+
+    has_image_width: typing.Optional[base_has_image_width_model] = None
+
+
+assertions = typing.Union[assertion_list, assertion_dict]
diff --git a/lib/galaxy/tool_util/verify/asserts/__init__.py b/lib/galaxy/tool_util/verify/asserts/__init__.py
index 10e0ce8909e4405caac8ba82b7c11400745fb632..532692c6198a0beade334145c4aee8436b43ea77 100644
--- a/lib/galaxy/tool_util/verify/asserts/__init__.py
+++ b/lib/galaxy/tool_util/verify/asserts/__init__.py
@@ -5,6 +5,11 @@ from inspect import (
     getmembers,
 )
 from tempfile import NamedTemporaryFile
+from typing import (
+    Callable,
+    Dict,
+    Tuple,
+)
 
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
@@ -13,11 +18,8 @@ log = logging.getLogger(__name__)
 
 assertion_module_names = ["text", "tabular", "xml", "json", "hdf5", "archive", "size", "image"]
 
-# Code for loading modules containing assertion checking functions, to
-# create a new module of assertion functions, create the needed python
-# source file "test/base/asserts/<MODULE_NAME>.py" and add
-# <MODULE_NAME> to the list of assertion module names defined above.
-assertion_functions = {}
+assertion_module_and_functions: Dict[str, Tuple[str, Callable]] = {}
+
 for assertion_module_name in assertion_module_names:
     full_assertion_module_name = f"galaxy.tool_util.verify.asserts.{assertion_module_name}"
     try:
@@ -29,10 +31,17 @@ for assertion_module_name in assertion_module_names:
         continue
     for member, value in getmembers(assertion_module):
         if member.startswith("assert_"):
-            assertion_functions[member] = value
+            assertion_module_and_functions[member] = (f"{full_assertion_module_name}.{member}", value)
+
+
+# Code for loading modules containing assertion checking functions, to
+# create a new module of assertion functions, create the needed python
+# source file "test/base/asserts/<MODULE_NAME>.py" and add
+# <MODULE_NAME> to the list of assertion module names defined above.
+assertion_functions: Dict[str, Callable] = {k: v[1] for (k, v) in assertion_module_and_functions.items()}
 
 
-def verify_assertions(data: bytes, assertion_description_list, decompress: bool = False):
+def verify_assertions(data: bytes, assertion_description_list: list, decompress: bool = False):
     """This function takes a list of assertions and a string to check
     these assertions against."""
     if decompress:
diff --git a/lib/galaxy/tool_util/verify/asserts/_types.py b/lib/galaxy/tool_util/verify/asserts/_types.py
new file mode 100644
index 0000000000000000000000000000000000000000..4b2f601f9d5a23baf2586a5f5092f79fbcc0fa8a
--- /dev/null
+++ b/lib/galaxy/tool_util/verify/asserts/_types.py
@@ -0,0 +1,102 @@
+from typing import (
+    Any,
+    List,
+    Optional,
+    Union,
+)
+
+from typing_extensions import (
+    Annotated,
+    Protocol,
+)
+
+
+class AssertionParameter:
+    doc: str
+    xml_type: Optional[str]
+    json_type: Optional[str]
+    deprecated: bool
+    validators: List[str]
+
+    def __init__(
+        self,
+        doc: Optional[str],
+        xml_type: Optional[str] = None,
+        json_type: Optional[str] = None,
+        deprecated: bool = False,
+        validators: Optional[List[str]] = None,
+    ):
+        self.doc = doc or ""
+        self.xml_type = xml_type
+        self.json_type = json_type
+        self.deprecated = deprecated
+        self.validators = validators or []
+
+
+XmlInt = Union[int, str]
+XmlFloat = Union[float, str]
+XmlBool = Union[bool, str]
+XmlRegex = str
+OptionalXmlInt = Optional[XmlInt]
+OptionalXmlFloat = Optional[XmlFloat]
+OptionalXmlBool = Optional[XmlBool]
+
+Output = Annotated[str, "The target output of a tool or workflow read as a UTF-8 string"]
+OutputBytes = Annotated[bytes, "The target output of a tool or workflow read as raw Python 'bytes'"]
+
+
+class VerifyAssertionsFunction(Protocol):
+
+    def __call__(self, data: bytes, assertion_description_list: list, decompress: bool = False):
+        """Callback for recursirve functions."""
+
+
+ChildAssertions = Annotated[Any, "Parsed child assertions"]
+Negate = Annotated[
+    XmlBool,
+    AssertionParameter(
+        "A boolean that can be set to true to negate the outcome of the assertion.", xml_type="PermissiveBoolean"
+    ),
+]
+NEGATE_DEFAULT = False
+
+N = Annotated[
+    Optional[XmlInt], AssertionParameter("Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``", xml_type="Bytes")
+]
+Delta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``", xml_type="Bytes"
+    ),
+]
+Min = Annotated[
+    Optional[XmlInt],
+    AssertionParameter("Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", xml_type="Bytes"),
+]
+Max = Annotated[
+    Optional[XmlInt],
+    AssertionParameter("Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``", xml_type="Bytes"),
+]
+
+
+__all__ = (
+    "Annotated",
+    "AssertionParameter",
+    "ChildAssertions",
+    "Delta",
+    "Max",
+    "Min",
+    "Negate",
+    "N",
+    "NEGATE_DEFAULT",
+    "OptionalXmlBool",
+    "OptionalXmlFloat",
+    "OptionalXmlInt",
+    "Output",
+    "OutputBytes",
+    "VerifyAssertionsFunction",
+    "XmlBool",
+    "XmlFloat",
+    "XmlInt",
+    "XmlRegex",
+)
diff --git a/lib/galaxy/tool_util/verify/asserts/archive.py b/lib/galaxy/tool_util/verify/asserts/archive.py
index 336b3ccfaee67ffc0460ffde913e4704c57692f6..6bf554c10fd04fbacccc648149f1bc81c05177b9 100644
--- a/lib/galaxy/tool_util/verify/asserts/archive.py
+++ b/lib/galaxy/tool_util/verify/asserts/archive.py
@@ -3,12 +3,22 @@ import re
 import tarfile
 import tempfile
 import zipfile
-from typing import (
-    Optional,
-    Union,
-)
 
 from galaxy.util import asbool
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    ChildAssertions,
+    Delta,
+    Max,
+    Min,
+    N,
+    Negate,
+    NEGATE_DEFAULT,
+    OutputBytes,
+    VerifyAssertionsFunction,
+    XmlBool,
+)
 from ._util import _assert_presence_number
 
 
@@ -55,21 +65,72 @@ def _list_from_zip(output_bytes, path):
     return sorted(lst)
 
 
+Path = Annotated[str, AssertionParameter("The regular expression specifying the archive member.")]
+All = Annotated[
+    XmlBool,
+    AssertionParameter(
+        "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first",
+        xml_type="PermissiveBoolean",
+    ),
+]
+
+
 def assert_has_archive_member(
-    output_bytes: bytes,
-    path: str,
-    verify_assertions_function,
-    children,
-    all: Union[bool, str] = False,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output_bytes: OutputBytes,
+    path: Path,
+    verify_assertions_function: VerifyAssertionsFunction,
+    children: ChildAssertions = None,
+    all: All = False,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """Recursively checks the specified children assertions against the text of
-    the first element matching the specified path found within the archive.
-    Currently supported formats: .zip, .tar, .tar.gz."""
+    """This tag allows to check if ``path`` is contained in a compressed file.
+
+    The path is a regular expression that is matched against the full paths of the objects in
+    the compressed file (remember that "matching" means it is checked if a prefix of
+    the full path of an archive member is described by the regular expression).
+    Valid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that
+    depending on the archive creation method:
+
+    - full paths of the members may be prefixed with ``./``
+    - directories may be treated as empty files
+
+    ```xml
+    <has_archive_member path="./path/to/my-file.txt"/>
+    ```
+
+    With ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of
+    archive members matching ``path`` can be expressed. The following could be used,
+    e.g., to assert an archive containing n&plusmn;1 elements out of which at least
+    4 need to have a ``txt`` extension.
+
+    ```xml
+    <has_archive_member path=".*" n="10" delta="1"/>
+    <has_archive_member path=".*\\.txt" min="4"/>
+    ```
+
+    In addition the tag can contain additional assertions as child elements about
+    the first member in the archive matching the regular expression ``path``. For
+    instance
+
+    ```xml
+    <has_archive_member path=".*/my-file.txt">
+      <not_has_text text="EDK72998.1"/>
+    </has_archive_member>
+    ```
+
+    If the ``all`` attribute is set to ``true`` then all archive members are subject
+    to the assertions. Note that, archive members matching the ``path`` are sorted
+    alphabetically.
+
+    The ``negate`` attribute of the ``has_archive_member`` assertion only affects
+    the asserts on the presence and number of matching archive members, but not any
+    sub-assertions (which can offer the ``negate`` attribute on their own).  The
+    check if the file is an archive at all, which is also done by the function, is
+    not affected."""
     all = asbool(all)
     extract_foo = None
     # from python 3.9 is_tarfile supports file like objects then we do not need
diff --git a/lib/galaxy/tool_util/verify/asserts/hdf5.py b/lib/galaxy/tool_util/verify/asserts/hdf5.py
index e94c61c3af04d9be8757bfe19b3854d42b872976..5cab5f3e1765a941fb41f95db01621ccdc64beba 100644
--- a/lib/galaxy/tool_util/verify/asserts/hdf5.py
+++ b/lib/galaxy/tool_util/verify/asserts/hdf5.py
@@ -5,27 +5,42 @@ try:
 except ImportError:
     h5py = None
 
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    OutputBytes,
+)
+
 IMPORT_MISSING_MESSAGE = "h5 assertion requires unavailable optional dependency h5py"
 
+Key = Annotated[str, AssertionParameter("HDF5 attribute to check value of.")]
+Value = Annotated[str, AssertionParameter("Expected value of HDF5 attribute to check.")]
+Keys = Annotated[str, AssertionParameter("HDF5 attributes to check value of as a comma-separated string.")]
+
 
 def _assert_h5py():
     if h5py is None:
         raise Exception(IMPORT_MISSING_MESSAGE)
 
 
-def assert_has_h5_attribute(output_bytes: bytes, key: str, value: str) -> None:
-    """Asserts the specified HDF5 output has a given key-value pair as HDF5
-    attribute"""
+def assert_has_h5_attribute(output_bytes: OutputBytes, key: Key, value: Value) -> None:
+    """Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.
+
+    ```xml
+    <has_h5_attribute key="nchroms" value="15" />
+    ```
+    """
     _assert_h5py()
     output_temp = io.BytesIO(output_bytes)
-    local_attrs = h5py.File(output_temp, "r").attrs
-    assert (
-        key in local_attrs and str(local_attrs[key]) == value
-    ), f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})"
+    with h5py.File(output_temp, "r", locking=False) as h5:
+        local_attrs = h5.attrs
+        assert (
+            key in local_attrs and str(local_attrs[key]) == value
+        ), f"Not a HDF5 file or H5 attributes do not match:\n\t{[(key, str(value)) for key, value in local_attrs.items()]}\n\n\t({key} : {value})"
 
 
 # TODO the function actually queries groups. so the function and argument name are misleading
-def assert_has_h5_keys(output_bytes: bytes, keys: str) -> None:
+def assert_has_h5_keys(output_bytes: OutputBytes, keys: Keys) -> None:
     """Asserts the specified HDF5 output has the given keys."""
     _assert_h5py()
     h5_keys = sorted([k.strip() for k in keys.strip().split(",")])
@@ -36,9 +51,10 @@ def assert_has_h5_keys(output_bytes: bytes, keys: str) -> None:
         local_keys.append(key)
         return None
 
-    h5py.File(output_temp, "r").visit(append_keys)
-    missing = 0
-    for key in h5_keys:
-        if key not in local_keys:
-            missing += 1
-    assert missing == 0, f"Not a HDF5 file or H5 keys missing:\n\t{local_keys}\n\t{h5_keys}"
+    with h5py.File(output_temp, "r", locking=False) as f:
+        f.visit(append_keys)
+        missing = 0
+        for key in h5_keys:
+            if key not in local_keys:
+                missing += 1
+        assert missing == 0, f"Not a HDF5 file or H5 keys missing:\n\t{local_keys}\n\t{h5_keys}"
diff --git a/lib/galaxy/tool_util/verify/asserts/image.py b/lib/galaxy/tool_util/verify/asserts/image.py
index 7513be700f5e037de21bb1c6f5de86550470ee84..d9972994d3fef6169132cb6e37358fa7a8920c67 100644
--- a/lib/galaxy/tool_util/verify/asserts/image.py
+++ b/lib/galaxy/tool_util/verify/asserts/image.py
@@ -8,6 +8,17 @@ from typing import (
     Union,
 )
 
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    Negate,
+    NEGATE_DEFAULT,
+    OptionalXmlFloat,
+    OptionalXmlInt,
+    OutputBytes,
+    XmlFloat,
+    XmlInt,
+)
 from ._util import _assert_number
 
 try:
@@ -27,6 +38,341 @@ if TYPE_CHECKING:
     import numpy.typing
 
 
+JSON_STRICT_NUMBER = "typing.Union[StrictInt, StrictFloat]"
+JSON_OPTIONAL_STRICT_NUMBER = f"typing.Optional[{JSON_STRICT_NUMBER}]"
+
+
+Width = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected width of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+Height = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected height of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+Channels = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected number of channels of the image.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+Depth = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected depth of the image (number of slices).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+Frames = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected number of frames in the image sequence (number of time steps).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+WidthDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+WidthMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed width of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+WidthMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed width of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+HeightDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+HeightMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed height of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+HeightMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed height of the image (in pixels).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+ChannelsDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+ChannelsMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed number of channels.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+ChannelsMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed number of channels.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+DepthDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+DepthMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed depth of the image (number of slices).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+DepthMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed depth of the image (number of slices).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+FramesDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+FramesMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed number of frames in the image sequence (number of time steps).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+FramesMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed number of frames in the image sequence (number of time steps).",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+MeanIntensity = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter("The required mean value of the image intensities.", json_type=JSON_OPTIONAL_STRICT_NUMBER),
+]
+MeanIntensityEps = Annotated[
+    XmlFloat,
+    AssertionParameter(
+        "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.",
+        json_type=JSON_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+MeanIntensityMin = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter(
+        "A lower bound of the required mean value of the image intensities.", json_type=JSON_OPTIONAL_STRICT_NUMBER
+    ),
+]
+MeanIntensityMax = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter(
+        "An upper bound of the required mean value of the image intensities.", json_type=JSON_OPTIONAL_STRICT_NUMBER
+    ),
+]
+NumLabels = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Expected number of labels.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+NumLabelsDelta = Annotated[
+    XmlInt,
+    AssertionParameter(
+        "Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.",
+        json_type="StrictInt",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+NumLabelsMin = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Minimum allowed number of labels.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+NumLabelsMax = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Maximum allowed number of labels.",
+        json_type="typing.Optional[StrictInt]",
+        xml_type="xs:nonNegativeInteger",
+        validators=["check_non_negative_if_set"],
+    ),
+]
+
+Channel = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).",
+        json_type="typing.Optional[StrictInt]",
+    ),
+]
+Slice = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).",
+        json_type="typing.Optional[StrictInt]",
+    ),
+]
+Frame = Annotated[
+    OptionalXmlInt,
+    AssertionParameter(
+        "Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).",
+        json_type="typing.Optional[StrictInt]",
+    ),
+]
+CenterOfMass = Annotated[
+    str,
+    AssertionParameter(
+        "The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).",
+        validators=["check_center_of_mass"],
+    ),
+]
+CenterOfMassEps = Annotated[
+    XmlFloat,
+    AssertionParameter(
+        "The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).",
+        json_type=JSON_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+Labels = Annotated[
+    Optional[Union[str, List[int]]],
+    AssertionParameter(
+        "List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.",
+        xml_type="xs:string",
+        json_type="typing.Optional[typing.List[int]]",
+    ),
+]
+ExcludeLabels = Annotated[
+    Optional[Union[str, List[int]]],
+    AssertionParameter(
+        "List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.",
+        xml_type="xs:string",
+        json_type="typing.Optional[typing.List[int]]",
+    ),
+]
+MeanObjectSize = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter(
+        "The required mean size of the uniquely labeled objects.",
+        xml_type="xs:float",
+        json_type=JSON_OPTIONAL_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+MeanObjectSizeEps = Annotated[
+    XmlFloat,
+    AssertionParameter(
+        "The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.",
+        xml_type="xs:float",
+        json_type=JSON_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+MeanObjectSizeMin = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter(
+        "A lower bound of the required mean size of the uniquely labeled objects.",
+        xml_type="xs:float",
+        json_type=JSON_OPTIONAL_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+MeanObjectSizeMax = Annotated[
+    OptionalXmlFloat,
+    AssertionParameter(
+        "An upper bound of the required mean size of the uniquely labeled objects.",
+        xml_type="xs:float",
+        json_type=JSON_OPTIONAL_STRICT_NUMBER,
+        validators=["check_non_negative_if_set"],
+    ),
+]
+
+
 def _assert_float(
     actual: float,
     label: str,
@@ -52,19 +398,22 @@ def _assert_float(
 
 
 def assert_has_image_width(
-    output_bytes: bytes,
-    width: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output_bytes: OutputBytes,
+    width: Width = None,
+    delta: WidthDelta = 0,
+    min: WidthMin = None,
+    max: WidthMax = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """
-    Asserts the specified output is an image and has a width of the specified value.
+    Asserts the output is an image and has a specific width (in pixels).
+
+    The width is plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
+    Alternatively the range of the expected width can be specified by ``min`` and/or ``max``.
     """
     im_arr = _get_image(output_bytes)
     _assert_number(
-        im_arr.shape[1],
+        im_arr.shape[3],  # Image axes are normalized like "TZYXC"
         width,
         delta,
         min,
@@ -77,18 +426,21 @@ def assert_has_image_width(
 
 def assert_has_image_height(
     output_bytes: bytes,
-    height: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    height: Height = None,
+    delta: HeightDelta = 0,
+    min: HeightMin = None,
+    max: HeightMax = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """
-    Asserts the specified output is an image and has a height of the specified value.
+    Asserts the output is an image and has a specific height (in pixels).
+
+    The height is plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
+    Alternatively the range of the expected height can be specified by ``min`` and/or ``max``.
     """
     im_arr = _get_image(output_bytes)
     _assert_number(
-        im_arr.shape[0],
+        im_arr.shape[2],  # Image axes are normalized like "TZYXC"
         height,
         delta,
         min,
@@ -101,19 +453,22 @@ def assert_has_image_height(
 
 def assert_has_image_channels(
     output_bytes: bytes,
-    channels: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    channels: Channels = None,
+    delta: ChannelsDelta = 0,
+    min: ChannelsMin = None,
+    max: ChannelsMax = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """
-    Asserts the specified output is an image and has the specified number of channels.
+    Asserts the output is an image and has a specific number of channels.
+
+    The number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
+
+    Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.
     """
     im_arr = _get_image(output_bytes)
-    n_channels = 1 if im_arr.ndim < 3 else im_arr.shape[2]  # we assume here that the image is a 2-D image
     _assert_number(
-        n_channels,
+        im_arr.shape[-1],  # Image axes are normalized like "TZYXC"
         channels,
         delta,
         min,
@@ -124,31 +479,168 @@ def assert_has_image_channels(
     )
 
 
+def assert_has_image_depth(
+    output_bytes: OutputBytes,
+    depth: Depth = None,
+    delta: DepthDelta = 0,
+    min: DepthMin = None,
+    max: DepthMax = None,
+    negate: Negate = NEGATE_DEFAULT,
+) -> None:
+    """
+    Asserts the output is an image and has a specific depth (number of slices).
+
+    The depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth="512" delta="2" />``).
+    Alternatively the range of the expected depth can be specified by ``min`` and/or ``max``.
+    """
+    im_arr = _get_image(output_bytes)
+    _assert_number(
+        im_arr.shape[1],  # Image axes are normalized like "TZYXC"
+        depth,
+        delta,
+        min,
+        max,
+        negate,
+        "{expected} depth {n}+-{delta}",
+        "{expected} depth to be in [{min}:{max}]",
+    )
+
+
+def assert_has_image_frames(
+    output_bytes: OutputBytes,
+    frames: Frames = None,
+    delta: FramesDelta = 0,
+    min: FramesMin = None,
+    max: FramesMax = None,
+    negate: Negate = NEGATE_DEFAULT,
+) -> None:
+    """
+    Asserts the output is an image and has a specific number of frames (number of time steps).
+
+    The number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth="512" delta="2" />``).
+    Alternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.
+    """
+    im_arr = _get_image(output_bytes)
+    _assert_number(
+        im_arr.shape[0],  # Image axes are normalized like "TZYXC"
+        frames,
+        delta,
+        min,
+        max,
+        negate,
+        "{expected} frames {n}+-{delta}",
+        "{expected} frames to be in [{min}:{max}]",
+    )
+
+
 def _compute_center_of_mass(im_arr: "numpy.typing.NDArray") -> Tuple[float, float]:
-    while im_arr.ndim > 2:
-        im_arr = im_arr.sum(axis=2)
-    im_arr = numpy.abs(im_arr)
-    if im_arr.sum() == 0:
+    im_arr_yx = im_arr.sum(axis=(0, 1, 4))  # Image axes are normalized like "TZYXC"
+    im_arr_yx = numpy.abs(im_arr_yx)
+    if im_arr_yx.sum() == 0:
         return (numpy.nan, numpy.nan)
-    im_arr = im_arr / im_arr.sum()
-    yy, xx = numpy.indices(im_arr.shape)
-    return (im_arr * xx).sum(), (im_arr * yy).sum()
+    im_arr_yx = im_arr_yx / im_arr_yx.sum()
+    yy, xx = numpy.indices(im_arr_yx.shape)
+    return (im_arr_yx * xx).sum(), (im_arr_yx * yy).sum()
+
+
+def _move_char(s: str, pos_src: int, pos_dst: int) -> str:
+    s_list = list(s)
+    c = s_list.pop(pos_src)
+    if pos_dst < 0:
+        pos_dst = len(s_list) + pos_dst + 1
+    s_list.insert(pos_dst, c)
+    return "".join(s_list)
+
+
+def _swap_char(s: str, pos1: int, pos2: int) -> str:
+    s_list = list(s)
+    s_list[pos1], s_list[pos2] = s_list[pos2], s_list[pos1]
+    return "".join(s_list)
 
 
 def _get_image(
     output_bytes: bytes,
     channel: Optional[Union[int, str]] = None,
+    slice: Optional[Union[int, str]] = None,
+    frame: Optional[Union[int, str]] = None,
 ) -> "numpy.typing.NDArray":
     """
-    Returns the output image or a specific channel.
+    Returns the output image with the axes ``TZYXC``, optionally restricted to a specific `channel`, `slice`,
+    `frame`, or a combination thereof.
 
-    The function tries to read the image using tifffile and Pillow.
+    The function tries to read the image using tifffile and Pillow. The image axes are normalized like ``TZYXC``,
+    treating sample axis ``S`` as an alias for the channel axis ``C``. For images which cannot be read by tifffile,
+    two- and three-dimensional data is supported. Two-dimensional images are assumed to be in ``YX`` axes order,
+    and three-dimensional images are assumed to be in ``YXC`` axes order.
     """
     buf = io.BytesIO(output_bytes)
 
     # Try reading with tifffile first. It fails if the file is not a TIFF.
     try:
-        im_arr = tifffile.imread(buf)
+        with tifffile.TiffFile(buf) as im_file:
+            assert len(im_file.series) == 1, f"Image has unsupported number of series: {len(im_file.series)}"
+            im_axes = im_file.series[0].axes
+
+            # Verify that the image format is supported
+            assert (
+                frozenset("YX") <= frozenset(im_axes) <= frozenset("TZYXCS")
+            ), f"Image has unsupported axes: {im_axes}"
+
+            # Treat sample axis "S" as channel axis "C" and fail if both are present
+            assert (
+                "C" not in im_axes or "S" not in im_axes
+            ), f"Image has sample and channel axes which is not supported: {im_axes}"
+            im_axes = im_axes.replace("S", "C")
+
+            # Read the image data
+            im_arr = im_file.asarray()
+
+            # Step 1. In the three steps below, the optional axes are added, of if they arent't there yet:
+
+            # (1.1) Append "C" axis if not present yet
+            if im_axes.find("C") == -1:
+                im_arr = im_arr[..., None]
+                im_axes += "C"
+
+            # (1.2) Append "Z" axis if not present yet
+            if im_axes.find("Z") == -1:
+                im_arr = im_arr[..., None]
+                im_axes += "Z"
+
+            # (1.3) Append "T" axis if not present yet
+            if im_axes.find("T") == -1:
+                im_arr = im_arr[..., None]
+                im_axes += "T"
+
+            # Step 2. All supported axes are there now. Normalize the order of the axes:
+
+            # (2.1) Normalize order of axes "Y" and "X"
+            ypos = im_axes.find("Y")
+            xpos = im_axes.find("X")
+            if ypos > xpos:
+                im_arr = im_arr.swapaxes(ypos, xpos)
+                im_axes = _swap_char(im_axes, xpos, ypos)
+
+            # (2.2) Normalize the position of the "C" axis (should be last)
+            cpos = im_axes.find("C")
+            if cpos < len(im_axes) - 1:
+                im_arr = numpy.moveaxis(im_arr, cpos, -1)
+                im_axes = _move_char(im_axes, cpos, -1)
+
+            # (2.3) Normalize the position of the "T" axis (should be first)
+            tpos = im_axes.find("T")
+            if tpos != 0:
+                im_arr = numpy.moveaxis(im_arr, tpos, 0)
+                im_axes = _move_char(im_axes, tpos, 0)
+
+            # (2.4) Normalize the position of the "Z" axis (should be second)
+            zpos = im_axes.find("Z")
+            if zpos != 1:
+                im_arr = numpy.moveaxis(im_arr, zpos, 1)
+                im_axes = _move_char(im_axes, zpos, 1)
+
+            # Verify that the normalizations were successful
+            assert im_axes == "TZYXC", f"Image axis normalization failed: {im_axes}"
 
     # If tifffile failed, then the file is not a tifffile. In that case, try with Pillow.
     except tifffile.TiffFileError:
@@ -156,26 +648,50 @@ def _get_image(
         with Image.open(buf) as im:
             im_arr = numpy.array(im)
 
+            # Verify that the image format is supported
+            assert im_arr.ndim in (2, 3), f"Image has unsupported dimension: {im_arr.ndim}"
+
+            # Normalize the axes
+            if im_arr.ndim == 2:  # Append "C" axis if not present yet
+                im_arr = im_arr[..., None]
+            im_arr = im_arr[None, None, ...]  # Prepend "T" and "Z" axes
+
+            # Verify that the normalizations were successful
+            assert im_arr.ndim == 5, "Image axis normalization failed"
+
     # Select the specified channel (if any).
     if channel is not None:
-        im_arr = im_arr[:, :, int(channel)]
+        im_arr = im_arr[..., [int(channel)]]
+
+    # Select the specified slice (if any).
+    if slice is not None:
+        im_arr = im_arr[:, [int(slice)], ...]
+
+    # Select the specified frame (if any).
+    if frame is not None:
+        im_arr = im_arr[[int(frame)], ...]
 
     # Return the image
     return im_arr
 
 
 def assert_has_image_mean_intensity(
-    output_bytes: bytes,
-    channel: Optional[Union[int, str]] = None,
-    mean_intensity: Optional[Union[float, str]] = None,
-    eps: Union[float, str] = 0.01,
-    min: Optional[Union[float, str]] = None,
-    max: Optional[Union[float, str]] = None,
+    output_bytes: OutputBytes,
+    channel: Channel = None,
+    slice: Slice = None,
+    frame: Frame = None,
+    mean_intensity: MeanIntensity = None,
+    eps: MeanIntensityEps = 0.01,
+    min: MeanIntensityMin = None,
+    max: MeanIntensityMax = None,
 ) -> None:
     """
-    Asserts the specified output is an image and has the specified mean intensity value.
+    Asserts the output is an image and has a specific mean intensity value.
+
+    The mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity="0.83" />``).
+    Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.
     """
-    im_arr = _get_image(output_bytes, channel)
+    im_arr = _get_image(output_bytes, channel, slice, frame)
     _assert_float(
         actual=im_arr.mean(),
         label="mean intensity",
@@ -187,22 +703,27 @@ def assert_has_image_mean_intensity(
 
 
 def assert_has_image_center_of_mass(
-    output_bytes: bytes,
-    center_of_mass: Union[Tuple[float, float], str],
-    channel: Optional[Union[int, str]] = None,
-    eps: Union[float, str] = 0.01,
+    output_bytes: OutputBytes,
+    center_of_mass: CenterOfMass,
+    channel: Channel = None,
+    slice: Slice = None,
+    frame: Frame = None,
+    eps: CenterOfMassEps = 0.01,
 ) -> None:
     """
     Asserts the specified output is an image and has the specified center of mass.
+
+    Asserts the output is an image and has a specific center of mass,
+    or has an Euclidean distance of ``eps`` or less to that point (e.g.,
+    ``<has_image_center_of_mass center_of_mass="511.07, 223.34" />``).
     """
-    im_arr = _get_image(output_bytes, channel)
-    if isinstance(center_of_mass, str):
-        center_of_mass_parts = [c.strip() for c in center_of_mass.split(",")]
-        assert len(center_of_mass_parts) == 2
-        center_of_mass = (float(center_of_mass_parts[0]), float(center_of_mass_parts[1]))
-    assert len(center_of_mass) == 2, "center_of_mass must have two components"
+    im_arr = _get_image(output_bytes, channel, slice, frame)
+    center_of_mass_parts = [c.strip() for c in center_of_mass.split(",")]
+    assert len(center_of_mass_parts) == 2
+    center_of_mass_tuple = (float(center_of_mass_parts[0]), float(center_of_mass_parts[1]))
+    assert len(center_of_mass_tuple) == 2, "center_of_mass must have two components"
     actual_center_of_mass = _compute_center_of_mass(im_arr)
-    distance = numpy.linalg.norm(numpy.subtract(center_of_mass, actual_center_of_mass))
+    distance = numpy.linalg.norm(numpy.subtract(center_of_mass_tuple, actual_center_of_mass))
     assert distance <= float(
         eps
     ), f"Wrong center of mass: {actual_center_of_mass} (expected {center_of_mass}, distance: {distance}, eps: {eps})"
@@ -211,6 +732,8 @@ def assert_has_image_center_of_mass(
 def _get_image_labels(
     output_bytes: bytes,
     channel: Optional[Union[int, str]] = None,
+    slice: Optional[Union[int, str]] = None,
+    frame: Optional[Union[int, str]] = None,
     labels: Optional[Union[str, List[int]]] = None,
     exclude_labels: Optional[Union[str, List[int]]] = None,
 ) -> Tuple["numpy.typing.NDArray", List[Any]]:
@@ -218,7 +741,7 @@ def _get_image_labels(
     Determines the unique labels in the output image or a specific channel.
     """
     assert labels is None or exclude_labels is None
-    im_arr = _get_image(output_bytes, channel)
+    im_arr = _get_image(output_bytes, channel, slice, frame)
 
     def cast_label(label):
         label = label.strip()
@@ -251,20 +774,27 @@ def _get_image_labels(
 
 
 def assert_has_image_n_labels(
-    output_bytes: bytes,
-    channel: Optional[Union[int, str]] = None,
-    labels: Optional[Union[str, List[int]]] = None,
-    exclude_labels: Optional[Union[str, List[int]]] = None,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output_bytes: OutputBytes,
+    channel: Channel = None,
+    slice: Slice = None,
+    frame: Frame = None,
+    labels: Labels = None,
+    exclude_labels: ExcludeLabels = None,
+    n: NumLabels = None,
+    delta: NumLabelsDelta = 0,
+    min: NumLabelsMin = None,
+    max: NumLabelsMax = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """
-    Asserts the specified output is an image and has the specified number of unique values (e.g., uniquely labeled objects).
+    Asserts the output is an image and has the specified labels.
+
+    Labels can be a number of labels or unique values (e.g.,
+    ``<has_image_n_labels n="187" exclude_labels="0" />``).
+
+    The primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.
     """
-    present_labels = _get_image_labels(output_bytes, channel, labels, exclude_labels)[1]
+    present_labels = _get_image_labels(output_bytes, channel, slice, frame, labels, exclude_labels)[1]
     _assert_number(
         len(present_labels),
         n,
@@ -278,20 +808,41 @@ def assert_has_image_n_labels(
 
 
 def assert_has_image_mean_object_size(
-    output_bytes: bytes,
-    channel: Optional[Union[int, str]] = None,
-    labels: Optional[Union[str, List[int]]] = None,
-    exclude_labels: Optional[Union[str, List[int]]] = None,
-    mean_object_size: Optional[Union[float, str]] = None,
-    eps: Union[float, str] = 0.01,
-    min: Optional[Union[float, str]] = None,
-    max: Optional[Union[float, str]] = None,
+    output_bytes: OutputBytes,
+    channel: Channel = None,
+    slice: Slice = None,
+    frame: Frame = None,
+    labels: Labels = None,
+    exclude_labels: ExcludeLabels = None,
+    mean_object_size: MeanObjectSize = None,
+    eps: MeanObjectSizeEps = 0.01,
+    min: MeanObjectSizeMin = None,
+    max: MeanObjectSizeMax = None,
 ) -> None:
     """
-    Asserts the specified output is an image with labeled objects which have the specified mean size (number of pixels).
+    Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),
+
+    The mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
+
+    The labels must be unique.
     """
-    im_arr, present_labels = _get_image_labels(output_bytes, channel, labels, exclude_labels)
-    actual_mean_object_size = sum((im_arr == label).sum() for label in present_labels) / len(present_labels)
+    im_arr, present_labels = _get_image_labels(output_bytes, channel, slice, frame, labels, exclude_labels)
+    assert (
+        im_arr.shape[-1] == 1
+    ), f"has_image_mean_object_size is undefined for multi-channel images (channels: {im_arr.shape[-1]})"
+
+    # Build list of all object sizes over all time-frames
+    object_sizes = sum(
+        [
+            # Iterate over all XYZC time-frames (axis C is singleton)
+            [(im_arr_t == label).sum() for label in present_labels]
+            for im_arr_t in im_arr
+        ],
+        [],
+    )
+
+    # Compute the mean object size and verify
+    actual_mean_object_size = numpy.mean([object_size for object_size in object_sizes if object_size > 0])
     _assert_float(
         actual=actual_mean_object_size,
         label="mean object size",
diff --git a/lib/galaxy/tool_util/verify/asserts/json.py b/lib/galaxy/tool_util/verify/asserts/json.py
index 1ba151ba26c073e485848128a180f54341a6940b..1f67e6b4608711ee11299aee7f6f01f14b94f247 100644
--- a/lib/galaxy/tool_util/verify/asserts/json.py
+++ b/lib/galaxy/tool_util/verify/asserts/json.py
@@ -5,8 +5,20 @@ from typing import (
     cast,
 )
 
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    Output,
+)
+
 PropertyVisitor = Callable[[str, Any], Any]
 
+Property = Annotated[str, AssertionParameter("The property name to search the JSON document for.")]
+Text = Annotated[str, AssertionParameter("The expected text value of the target JSON attribute.")]
+Value = Annotated[
+    str, AssertionParameter("The expected JSON value of the target JSON attribute (as a JSON encoded string).")
+]
+
 
 def any_in_tree(f: PropertyVisitor, json_tree: Any):
     if isinstance(json_tree, list):
@@ -25,13 +37,18 @@ def any_in_tree(f: PropertyVisitor, json_tree: Any):
 
 
 def assert_has_json_property_with_value(
-    output,
-    property: str,
-    value: str,
+    output: Output,
+    property: Property,
+    value: Value,
 ):
-    """Assert JSON tree contains the specified property with specified JSON-ified value."""
-    output_json = json.loads(output)
-    expected_value = json.loads(value)
+    """Asserts the JSON document contains a property or key with the specified JSON value.
+
+    ```xml
+    <has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />
+    ```
+    """
+    output_json = _assert_json_and_load(output)
+    expected_value = _assert_json_and_load(value)
 
     def is_property(key, value):
         return key == property and value == expected_value
@@ -40,14 +57,26 @@ def assert_has_json_property_with_value(
 
 
 def assert_has_json_property_with_text(
-    output,
-    property: str,
-    text: str,
+    output: Output,
+    property: Property,
+    text: Text,
 ):
-    """Assert JSON tree contains the specified property with specified JSON-ified value."""
-    output_json = json.loads(output)
+    """Asserts the JSON document contains a property or key with the specified text (i.e. string) value.
+
+    ```xml
+    <has_json_property_with_text property="color" text="red" />
+    ```
+    """
+    output_json = _assert_json_and_load(output)
 
     def is_property(key, value):
         return key == property and value == text
 
     assert any_in_tree(is_property, output_json), f"Failed to find property [{property}] with text [{text}]"
+
+
+def _assert_json_and_load(json_str: str):
+    try:
+        return json.loads(json_str)
+    except Exception:
+        raise AssertionError(f"Failed to parse JSON from {json_str[0:1024]}.")
diff --git a/lib/galaxy/tool_util/verify/asserts/size.py b/lib/galaxy/tool_util/verify/asserts/size.py
index 6eb6cb43094d8e4de163898a644bb96927cd980b..0e3eebe06f86a2806f438a3026dda4e5034a59a1 100644
--- a/lib/galaxy/tool_util/verify/asserts/size.py
+++ b/lib/galaxy/tool_util/verify/asserts/size.py
@@ -1,24 +1,35 @@
-from typing import (
-    Optional,
-    Union,
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    Delta,
+    Max,
+    Min,
+    Negate,
+    NEGATE_DEFAULT,
+    OptionalXmlInt,
+    OutputBytes,
 )
-
 from ._util import _assert_number
 
 
 def assert_has_size(
-    output_bytes: bytes,
-    value: Optional[Union[int, str]] = None,
-    size: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output_bytes: OutputBytes,
+    value: Annotated[OptionalXmlInt, AssertionParameter("Deprecated alias for `size`", xml_type="Bytes")] = None,
+    size: Annotated[
+        OptionalXmlInt,
+        AssertionParameter(
+            "Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``", xml_type="Bytes"
+        ),
+    ] = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """
-    Asserts the specified output has a size of the specified value
-    (size and value or synonyms),
-    allowing for absolute (delta) and relative (delta_frac) difference.
+    """Asserts the specified output has a size of the specified value
+
+    Attributes size and value or synonyms though value is considered deprecated.
+    The size optionally allows for absolute (``delta``) difference.
     """
     output_size = len(output_bytes)
     if size is None:
diff --git a/lib/galaxy/tool_util/verify/asserts/tabular.py b/lib/galaxy/tool_util/verify/asserts/tabular.py
index b7278ec1d979fc3ce3af79c4c7bb6b92be2ce451..9fc8e9f71c0573d6cd4e572e6afec1e5302a9a8f 100644
--- a/lib/galaxy/tool_util/verify/asserts/tabular.py
+++ b/lib/galaxy/tool_util/verify/asserts/tabular.py
@@ -1,11 +1,26 @@
 import re
-from typing import (
-    Optional,
-    Union,
-)
 
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    Delta,
+    Max,
+    Min,
+    N,
+    Negate,
+    NEGATE_DEFAULT,
+    Output,
+)
 from ._util import _assert_number
 
+Sep = Annotated[str, AssertionParameter("Separator defining columns, default: tab")]
+Comment = Annotated[
+    str,
+    AssertionParameter(
+        "Comment character(s) used to skip comment lines (which should not be used for counting columns)"
+    ),
+]
+
 
 def get_first_line(output: str, comment: str) -> str:
     """
@@ -22,19 +37,26 @@ def get_first_line(output: str, comment: str) -> str:
 
 
 def assert_has_n_columns(
-    output: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    sep: str = "\t",
-    comment: str = "",
-    negate: Union[bool, str] = False,
+    output: Output,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    sep: Sep = "\t",
+    comment: Comment = "",
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """Asserts the tabular output contains n columns. The optional
-    sep argument specifies the column seperator used to determine the
-    number of columns. The optional comment argument specifies
-    comment characters"""
+    """Asserts tabular output  contains the specified
+    number (``n``) of columns.
+
+    For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
+    Number of columns can optionally also be specified with ``delta``. Alternatively the
+    range of expected occurences can be specified by ``min`` and/or ``max``.
+
+    Optionally a column separator (``sep``, default is ``\t``) `and comment character(s)
+    can be specified (``comment``, default is empty string). The first non-comment
+    line is used for determining the number of columns.
+    """
     first_line = get_first_line(output, comment)
     n_columns = len(first_line.split(sep))
     _assert_number(
diff --git a/lib/galaxy/tool_util/verify/asserts/text.py b/lib/galaxy/tool_util/verify/asserts/text.py
index e7aa1bc37e4db8faf769638808ed05984b4077ac..8726535ce99954fa28b5c1f47ccec022f9196baa 100644
--- a/lib/galaxy/tool_util/verify/asserts/text.py
+++ b/lib/galaxy/tool_util/verify/asserts/text.py
@@ -1,23 +1,35 @@
 import re
-from typing import (
-    Optional,
-    Union,
-)
 
+from typing_extensions import Annotated
+
+from ._types import (
+    AssertionParameter,
+    Delta,
+    Max,
+    Min,
+    N,
+    Negate,
+    NEGATE_DEFAULT,
+    Output,
+)
 from ._util import (
     _assert_number,
     _assert_presence_number,
 )
 
+Text = Annotated[str, AssertionParameter("The text to search for in the output.")]
+Line = Annotated[str, AssertionParameter("The full line of text to search for in the output.")]
+Expression = Annotated[str, AssertionParameter("The regular expressions to attempt match in the output.")]
+
 
 def assert_has_text(
-    output: str,
-    text: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    text: Text,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """Asserts specified output contains the substring specified by
     the argument text. The exact number of occurrences can be
@@ -39,7 +51,7 @@ def assert_has_text(
     )
 
 
-def assert_not_has_text(output: str, text: str) -> None:
+def assert_not_has_text(output: Output, text: Text) -> None:
     """Asserts specified output does not contain the substring
     specified by the argument text"""
     assert output is not None, "Checking not_has_text assertion on empty output (None)"
@@ -47,13 +59,13 @@ def assert_not_has_text(output: str, text: str) -> None:
 
 
 def assert_has_line(
-    output: str,
-    line: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    line: Line,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """Asserts the specified output contains the line specified by the
     argument line. The exact number of occurrences can be optionally
@@ -76,12 +88,12 @@ def assert_has_line(
 
 
 def assert_has_n_lines(
-    output: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """Asserts the specified output contains ``n`` lines allowing
     for a difference in the number of lines (delta)
@@ -101,13 +113,13 @@ def assert_has_n_lines(
 
 
 def assert_has_text_matching(
-    output: str,
-    expression: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    expression: Expression,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
@@ -131,13 +143,13 @@ def assert_has_text_matching(
 
 
 def assert_has_line_matching(
-    output: str,
-    expression: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    expression: Expression,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
     """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given
diff --git a/lib/galaxy/tool_util/verify/asserts/xml.py b/lib/galaxy/tool_util/verify/asserts/xml.py
index b80798436e2ec5cbe0529f16d057ae6d84a108a0..848602f821ced74e69456b644341c8bb2227d8f6 100644
--- a/lib/galaxy/tool_util/verify/asserts/xml.py
+++ b/lib/galaxy/tool_util/verify/asserts/xml.py
@@ -1,8 +1,5 @@
 import re
-from typing import (
-    Optional,
-    Union,
-)
+from typing import Optional
 
 from lxml.etree import XMLSyntaxError
 
@@ -12,95 +9,247 @@ from galaxy.util import (
     parse_xml_string,
     unicodify,
 )
+from ._types import (
+    Annotated,
+    AssertionParameter,
+    ChildAssertions,
+    Delta,
+    Max,
+    Min,
+    N,
+    Negate,
+    NEGATE_DEFAULT,
+    Output,
+    VerifyAssertionsFunction,
+    XmlBool,
+    XmlRegex,
+)
+
+Path = Annotated[str, AssertionParameter("The Python xpath-like expression to find the target element.")]
+ElementExpression = Annotated[
+    XmlRegex,
+    AssertionParameter("The regular expressions to apply against the target element.", validators=["check_regex"]),
+]
+AttributeExpression = Annotated[
+    XmlRegex,
+    AssertionParameter(
+        "The regular expressions to apply against the named attribute on the target XML element.",
+        validators=["check_regex"],
+    ),
+]
+Attribute = Annotated[str, AssertionParameter("The XML attribute name to test against from the target XML element.")]
+OptionalAttribute = Annotated[
+    Optional[str], AssertionParameter("The XML attribute name to test against from the target XML element.")
+]
+ElementText = Annotated[
+    str, AssertionParameter("The expected element text (body of the XML tag) to test against on the target XML element")
+]
+AttributeText = Annotated[
+    str, AssertionParameter("The expected attribute value to test against on the target XML element")
+]
+All = Annotated[
+    XmlBool,
+    AssertionParameter(
+        "Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ",
+        xml_type="PermissiveBoolean",
+    ),
+]
 
 
-def assert_is_valid_xml(output: str) -> None:
-    """Simple assertion that just verifies the specified output
-    is valid XML."""
+def assert_is_valid_xml(output: Output) -> None:
+    """Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``)."""
     try:
         parse_xml_string(output)
     except XMLSyntaxError as e:
         raise AssertionError(f"Expected valid XML, but could not parse output. {unicodify(e)}")
 
 
-def assert_has_element_with_path(output: str, path: str, negate: Union[bool, str] = False) -> None:
-    """Asserts the specified output has at least one XML element with a
-    path matching the specified path argument. Valid paths are the
-    simplified subsets of XPath implemented by lxml.etree;
-    https://lxml.de/xpathxslt.html for more information."""
+def assert_has_element_with_path(output: Output, path: Path, negate: Negate = NEGATE_DEFAULT) -> None:
+    """Asserts the XML output contains at least one element (or tag) with the specified
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
+    ```
+
+    With ``negate`` the result of the assertion can be inverted."""
     assert_xml_element(output, path, negate=negate)
 
 
 def assert_has_n_elements_with_path(
-    output: str,
-    path: str,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    path: Path,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """Asserts the specified output has exactly n elements matching the
-    path specified."""
+    """Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or
+    tags) with the specified XPath-like ``path``.
+
+    For example:
+
+    ```xml
+    <has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
+    ```
+
+    Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
+    can be used to specify the range of the expected number of occurences.
+    With ``negate`` the result of the assertion can be inverted.
+    """
     assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
 
 
-def assert_element_text_matches(output: str, path: str, expression: str, negate: Union[bool, str] = False) -> None:
-    """Asserts the text of the first element matching the specified
-    path matches the specified regular expression."""
+def assert_element_text_matches(
+    output: Output, path: Path, expression: ElementExpression, negate: Negate = NEGATE_DEFAULT
+) -> None:
+    """Asserts the text of the XML element with the specified XPath-like ``path``
+    matches the regular expression defined by ``expression``.
+
+    For example:
+
+    ```xml
+    <element_text_matches path="BlastOutput_version" expression="BLASTP\\s+2\\.2.*"/>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected).
+    """
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub])
 
 
-def assert_element_text_is(output: str, path: str, text: str, negate: Union[bool, str] = False) -> None:
-    """Asserts the text of the first element matching the specified
-    path matches exactly the specified text."""
+def assert_element_text_is(output: Output, path: Path, text: ElementText, negate: Negate = NEGATE_DEFAULT) -> None:
+    """Asserts the text of the XML element with the specified XPath-like ``path`` is
+    the specified ``text``.
+
+    For example:
+
+    ```xml
+    <element_text_is path="BlastOutput_program" text="blastp" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected).
+    """
     assert_element_text_matches(output, path, re.escape(text) + "$", negate=negate)
 
 
 def assert_attribute_matches(
-    output: str, path: str, attribute, expression: str, negate: Union[bool, str] = False
+    output: Output,
+    path: Path,
+    attribute: Attribute,
+    expression: AttributeExpression,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """Asserts the specified attribute of the first element matching
-    the specified path matches the specified regular expression."""
+    """Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` matches the regular expression specified by ``expression``.
+
+    For example:
+
+    ```xml
+    <attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\\d+" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the matching) can be inverted (the
+    implicit assertion on the existence of the path is not affected).
+    """
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub], attribute=attribute)
 
 
-def assert_attribute_is(output: str, path: str, attribute: str, text, negate: Union[bool, str] = False) -> None:
-    """Asserts the specified attribute of the first element matching
-    the specified path matches exactly the specified text."""
+def assert_attribute_is(
+    output: Output, path: Path, attribute: Attribute, text: AttributeText, negate: Negate = NEGATE_DEFAULT
+) -> None:
+    """Asserts the XML ``attribute`` for the element (or tag) with the specified
+    XPath-like ``path`` is the specified ``text``.
+
+    For example:
+
+    ```xml
+    <attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the assertion (on the equality) can be inverted (the
+    implicit assertion on the existence of the path is not affected).
+    """
     assert_attribute_matches(output, path, attribute, re.escape(text) + "$", negate=negate)
 
 
 def assert_element_text(
-    output: str, path: str, verify_assertions_function, children, negate: Union[bool, str] = False
+    output: Output,
+    path: Path,
+    verify_assertions_function: VerifyAssertionsFunction,
+    children: ChildAssertions,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """Recursively checks the specified assertions against the text of
-    the first element matching the specified path."""
+    """This tag allows the developer to recurisively specify additional assertions as
+    child elements about just the text contained in the element specified by the
+    XPath-like ``path``, e.g.
+
+    ```xml
+    <element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
+      <not_has_text text="EDK72998.1" />
+    </element_text>
+    ```
+
+    The assertion implicitly also asserts that an element matching ``path`` exists.
+    With ``negate`` the result of the implicit assertions can be inverted.
+    The sub-assertions, which have their own ``negate`` attribute, are not affected
+    by ``negate``.
+    """
     assert_xml_element(output, path, verify_assertions_function, children, negate=negate)
 
 
 def assert_xml_element(
-    output: str,
-    path: str,
-    verify_assertions_function=None,
-    children=None,
-    attribute: Optional[str] = None,
-    all: Union[bool, str] = False,
-    n: Optional[Union[int, str]] = None,
-    delta: Union[int, str] = 0,
-    min: Optional[Union[int, str]] = None,
-    max: Optional[Union[int, str]] = None,
-    negate: Union[bool, str] = False,
+    output: Output,
+    path: Path,
+    verify_assertions_function: Optional[VerifyAssertionsFunction] = None,
+    children: ChildAssertions = None,
+    attribute: OptionalAttribute = None,
+    all: All = False,
+    n: N = None,
+    delta: Delta = 0,
+    min: Min = None,
+    max: Max = None,
+    negate: Negate = NEGATE_DEFAULT,
 ) -> None:
-    """
-    Check if path occurs in the xml. If n and delta or min and max are given
-    also the number of occurences is checked.
-    If there are any sub assertions then check them against
-    - the element's text if attribute is None
-    - the content of the attribute
-    If all is True then the sub assertions are checked for all occurences.
+    """Assert if the XML file contains element(s) or tag(s) with the specified
+    [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
+    or ``min`` and ``max`` are given also the number of occurences is checked.
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem"/>
+      <xml_element path="./elem/more[2]"/>
+      <xml_element path=".//more" n="3" delta="1"/>
+    </assert_contents>
+    ```
+
+    With ``negate="true"`` the outcome of the assertions wrt the precence and number
+    of ``path`` can be negated. If there are any sub assertions then check them against
+
+    - the content of the attribute ``attribute``
+    - the element's text if no attribute is given
+
+    ```xml
+    <assert_contents>
+      <xml_element path="./elem/more[2]" attribute="name">
+        <has_text_matching expression="foo$"/>
+      </xml_element>
+    </assert_contents>
+    ```
+
+    Sub-assertions are not subject to the ``negate`` attribute of ``xml_element``.
+    If ``all`` is ``true`` then the sub assertions are checked for all occurences.
+
+    Note that all other XML assertions can be expressed by this assertion (Galaxy
+    also implements the other assertions by calling this one).
     """
     children = children or []
     all = asbool(all)
@@ -131,7 +280,9 @@ def assert_xml_element(
         else:
             content = occ.attrib[attribute]  # type: ignore[assignment] # https://github.com/lxml/lxml-stubs/pull/99
         try:
-            verify_assertions_function(content, children)
+            if content is None:
+                raise AssertionError("Failed to find expected XML content")
+            verify_assertions_function(content.encode("utf-8"), children)
         except AssertionError as e:
             if attribute is not None and attribute != "":
                 raise AssertionError(f"Attribute '{attribute}' on element with path '{path}': {str(e)}")
diff --git a/lib/galaxy/tool_util/verify/codegen.py b/lib/galaxy/tool_util/verify/codegen.py
new file mode 100644
index 0000000000000000000000000000000000000000..64352c461823eb012e2ff9f4ce030cc3526ef324
--- /dev/null
+++ b/lib/galaxy/tool_util/verify/codegen.py
@@ -0,0 +1,500 @@
+#!/usr/bin/env python
+
+# how to use this function...
+# PYTHONPATH=lib python lib/galaxy/tool_util/verify/codegen.py
+
+import argparse
+import inspect
+import os
+from shutil import move
+from typing import (
+    cast,
+    List,
+    Optional,
+    Union,
+)
+
+import lxml.etree as ET
+from jinja2 import Environment
+from typing_extensions import (
+    Annotated,
+    get_args,
+    get_origin,
+    Literal,
+)
+
+from galaxy.tool_util.verify.asserts import assertion_module_and_functions
+from galaxy.tool_util.verify.asserts._types import AssertionParameter as AssertionParameterAnnotation
+from galaxy.util.commands import shell
+
+models_path = os.path.join(os.path.dirname(__file__), "assertion_models.py")
+galaxy_xsd_path = os.path.join(os.path.dirname(__file__), "..", "xsd", "galaxy.xsd")
+
+Children = Literal["allowed", "required", "forbidden"]
+
+DESCRIPTION = """This script synchronizes dynamic code artifacts against models in Galaxy.
+
+Right now this just synchronizes Galaxy's XSD file against documentation in Galaxy's assertion modules but
+in the future it will also build Pydantic models for these functions.
+"""
+
+assert_models_template = """
+'''This module is auto-generated, please do not modify.'''
+import typing
+import re
+
+from typing_extensions import (
+    Annotated,
+    Literal,
+)
+
+from pydantic import (
+    BaseModel,
+    BeforeValidator,
+    ConfigDict,
+    Field,
+    model_validator,
+    RootModel,
+    StrictFloat,
+    StrictInt,
+)
+
+BYTES_PATTERN = re.compile(r"^(0|[1-9][0-9]*)([kKMGTPE]i?)?$")
+
+
+class AssertionModel(BaseModel):
+    model_config = ConfigDict(
+        extra="forbid",
+    )
+
+
+def check_bytes(v: typing.Any) -> typing.Any:
+    if isinstance(v, str):
+        assert BYTES_PATTERN.match(v), "Not valid bytes string"
+    return v
+
+
+def check_center_of_mass(v: typing.Any):
+    assert isinstance(v, str)
+    split_parts = v.split(",")
+    assert len(split_parts) == 2
+    for part in split_parts:
+        assert float(part.strip())
+    return v
+
+
+def check_regex(v: typing.Any):
+    assert isinstance(v, str)
+    try:
+        re.compile(typing.cast(str, v))
+    except re.error:
+        raise AssertionError(f"Invalid regular expression {v}")
+    return v
+
+
+def check_non_negative_if_set(v: typing.Any):
+    if v is not None:
+        try:
+            assert float(v) >= 0
+        except TypeError:
+            raise AssertionError(f"Invalid type found {v}")
+    return v
+
+
+def check_non_negative_if_int(v: typing.Any):
+    if v is not None and isinstance(v, int):
+        assert typing.cast(int, v) >= 0
+    return v
+
+
+{% for assertion in assertions %}
+{% for parameter in assertion.parameters %}
+{{assertion.name}}_{{ parameter.name }}_description = '''{{ parameter.description }}'''
+{% endfor %}
+
+class base_{{assertion.name}}_model(AssertionModel):
+    '''base model for {{assertion.name}} describing attributes.'''
+{% for parameter in assertion.parameters %}
+{% if not parameter.is_deprecated %}
+    {{ parameter.name }}: {{ parameter.type_str }} = Field(
+        {{ parameter.field_default_str }},
+        description={{ assertion.name }}_{{ parameter.name }}_description,
+    )
+{% endif %}
+{% endfor %}
+{% if assertion.children in ["required", "allowed"] %}
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+{% if assertion.children == "required" %}
+    @model_validator(mode='before')
+    @classmethod
+    def validate_children(self, data: typing.Any):
+        if isinstance(data, dict) and 'children' not in data and 'asserts' not in data:
+            raise ValueError("At least one of 'children' or 'asserts' must be specified for this assertion type.")
+        return data
+{% endif %}
+{% endif %}
+
+
+class base_{{assertion.name}}_model_relaxed(AssertionModel):
+    '''base model for {{assertion.name}} describing attributes.'''
+{% for parameter in assertion.parameters %}
+{% if not parameter.is_deprecated %}
+    {{ parameter.name }}: {{ parameter.lax_type_str }} = Field(
+        {{ parameter.field_default_str }},
+        description={{ assertion.name }}_{{ parameter.name }}_description,
+    )
+{% endif %}
+{% endfor %}
+{% if assertion.children in ["required", "allowed"] %}
+    children: typing.Optional["assertion_list"] = None
+    asserts: typing.Optional["assertion_list"] = None
+
+{% if assertion.children == "required" %}
+    @model_validator(mode='before')
+    @classmethod
+    def validate_children(self, data: typing.Any):
+        if isinstance(data, dict) and 'children' not in data and 'asserts' not in data:
+            raise ValueError("At least one of 'children' or 'asserts' must be specified for this assertion type.")
+        return data
+{% endif %}
+{% endif %}
+
+
+class {{assertion.name}}_model(base_{{assertion.name}}_model):
+    r\"\"\"{{ assertion.docstring }}\"\"\"
+    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"
+
+class {{assertion.name}}_model_nested(AssertionModel):
+    r\"\"\"Nested version of this assertion model.\"\"\"
+    {{assertion.name}}: base_{{assertion.name}}_model
+
+class {{assertion.name}}_model_relaxed(base_{{assertion.name}}_model_relaxed):
+    r\"\"\"{{ assertion.docstring }}\"\"\"
+    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"
+{% endfor %}
+
+any_assertion_model_flat = Annotated[typing.Union[
+{% for assertion in assertions %}
+    {{assertion.name}}_model,
+{% endfor %}
+], Field(discriminator="that")]
+
+any_assertion_model_nested = typing.Union[
+{% for assertion in assertions %}
+    {{assertion.name}}_model_nested,
+{% endfor %}
+]
+
+any_assertion_model_flat_relaxed = Annotated[typing.Union[
+{% for assertion in assertions %}
+    {{assertion.name}}_model_relaxed,
+{% endfor %}
+], Field(discriminator="that")]
+
+assertion_list = RootModel[typing.List[typing.Union[any_assertion_model_flat, any_assertion_model_nested]]]
+
+# used to model what the XML conversion should look like - not meant to be consumed outside of
+# of Galaxy internals / linting.
+relaxed_assertion_list = RootModel[typing.List[any_assertion_model_flat_relaxed]]
+
+class assertion_dict(AssertionModel):
+{% for assertion in assertions %}
+    {{assertion.name}}: typing.Optional[base_{{assertion.name}}_model] = None
+{% endfor %}
+
+
+assertions = typing.Union[assertion_list, assertion_dict]
+"""
+
+
+def get_default_args(func):
+    signature = inspect.signature(func)
+    return {k: v.default for k, v in signature.parameters.items()}
+
+
+def main():
+    assertions = []
+    for function_name, (module_and_function, assertion_function) in assertion_module_and_functions.items():
+        if not function_name.startswith("assert_"):
+            continue
+        name = function_name[len("assert_") :]
+        docstring = inspect.cleandoc(assertion_function.__doc__ or "")
+        annotations = assertion_function.__annotations__
+        default_args = get_default_args(assertion_function)
+        parameters = []
+        children: Children = "forbidden"
+        for parameter_name, parameter_type in annotations.items():
+            if parameter_name == "return":
+                continue
+            elif parameter_name == "children":
+                if default_args.get("children", inspect._empty) is not inspect._empty:
+                    children = "allowed"
+                else:
+                    children = "required"
+                continue
+            elif parameter_name in ["output", "output_bytes", "verify_assertions_function"]:
+                continue
+
+            default_value = default_args.get(parameter_name)
+            parameters.append(AssertionParameter(parameter_name, parameter_type, default_value))
+        assertion = Assertion(name, docstring, parameters, children, module_and_function)
+        assertions.append(assertion)
+    rewrite_galaxy_xsd(assertions)
+    write_assertion_models(assertions)
+
+
+def _expand_template(template_str: str, assertions) -> str:
+    template = Environment().from_string(template_str)
+    return template.render(assertions=assertions)
+
+
+def write_assertion_models(assertions):
+    models_file_contents = _expand_template(assert_models_template, assertions)
+    with open(models_path, "w") as f:
+        f.write(models_file_contents)
+    shell(["isort", models_path])
+    shell(["black", models_path])
+
+
+def get_annotation(text: str, nsmap):
+    annotation = ET.Element("{http://www.w3.org/2001/XMLSchema}annotation")
+    documentation = ET.Element("{http://www.w3.org/2001/XMLSchema}documentation")
+    documentation.text = ET.CDATA(text)
+    documentation.attrib["{http://www.w3.org/XML/1998/namespace}lang"] = "en"
+    annotation.append(documentation)
+    return annotation
+
+
+def parameter_xsd_element(assertion_parameter, nsmap):
+    el = ET.Element("{http://www.w3.org/2001/XMLSchema}attribute", nsmap=nsmap)
+    el.attrib["name"] = assertion_parameter.name
+    el.attrib["type"] = assertion_parameter.xml_type_str
+    el.attrib["use"] = "required" if not assertion_parameter.has_default_value else "optional"
+    annotation = get_annotation(assertion_parameter.description, nsmap)
+    el.append(annotation)
+    return el
+
+
+def xsd_element(assertion, nsmap):
+    el = ET.Element("{http://www.w3.org/2001/XMLSchema}element", nsmap=nsmap)
+    el.attrib["name"] = assertion.name
+    annotation = get_annotation(assertion.docstring + "\n\n$attribute_list::5", nsmap)
+    complexType = ET.Element("{http://www.w3.org/2001/XMLSchema}complexType", nsmap=nsmap)
+    if assertion.children != "forbidden":
+        sequence = ET.Element("{http://www.w3.org/2001/XMLSchema}sequence", nsmap=nsmap)
+        group = ET.Element("{http://www.w3.org/2001/XMLSchema}group", nsmap=nsmap)
+        group.attrib["ref"] = "TestAssertion"
+        group.attrib["minOccurs"] = "0" if assertion.children == "allowed" else "1"
+        group.attrib["maxOccurs"] = "unbounded"
+        sequence.append(group)
+        complexType.append(sequence)
+    for parameter in assertion.parameters:
+        complexType.append(parameter_xsd_element(parameter, nsmap))
+    el.append(annotation)
+    el.append(complexType)
+    return el
+
+
+def xsd_elements(assertions, nsmap):
+    elements = []
+    for assertion in assertions:
+        elements.append(ET.Comment(f" XSD doc for element auto-generated from {assertion.module_and_function}"))
+        elements.append(xsd_element(assertion, nsmap))
+    return elements
+
+
+def rewrite_galaxy_xsd(assertions):
+    with open(galaxy_xsd_path, "rb") as f:
+        contents = f.read()
+    parser = ET.XMLParser(strip_cdata=False)
+    root = ET.fromstring(contents, parser=parser)
+    raw_element = root.find(
+        ".//{http://www.w3.org/2001/XMLSchema}group[@name='TestAssertion']/{http://www.w3.org/2001/XMLSchema}choice"
+    )
+    assert raw_element
+    element = cast(ET._Element, raw_element)
+    for el in element.iterchildren():
+        element.remove(el)
+    element.append(ET.Comment("The following block and all children are auto-generated - please do not modify."))
+    for xsd_element in xsd_elements(assertions, root.nsmap):
+        xsd_element.tail = "\n      "
+        element.append(xsd_element)
+    xml_new = ET.tostring(root).decode("utf-8")
+    with open(galaxy_xsd_path, "w") as f:
+        f.write('<?xml version="1.0" encoding="UTF-8"?>\n')
+        f.write(xml_new)
+        f.write("\n")
+    ret_code = shell(["xmllint", "--format", "--output", "galaxy-tmp.xsd", galaxy_xsd_path])
+    assert ret_code == 0
+    move("galaxy-tmp.xsd", galaxy_xsd_path)
+
+
+class AssertionParameter:
+
+    def __init__(self, name: str, type: str, default_value):
+        self.name = name
+        self.type = type
+        self.default_value = default_value
+
+    @property
+    def description(self) -> str:
+        type = self.type
+        if hasattr(type, "__metadata__"):
+            return type.__metadata__[0].doc
+        else:
+            return ""
+
+    @property
+    def type_str(self) -> str:
+        raw_type_str = as_type_str(self.type, strict=True)
+        validators = self.validators[:]
+        if self.xml_type_str == "Bytes":
+            validators.append("check_bytes")
+            validators.append("check_non_negative_if_int")
+        if len(validators) > 0:
+            validation_str = ",".join([f"BeforeValidator({v})" for v in validators])
+            return f"Annotated[{raw_type_str}, {validation_str}]"
+
+        return raw_type_str
+
+    @property
+    def lax_type_str(self) -> str:
+        raw_type_str = as_type_str(self.type, strict=False)
+        validators = self.validators[:]
+        if self.xml_type_str == "Bytes":
+            validators.append("check_bytes")
+            validators.append("check_non_negative_if_int")
+        if len(validators) > 0:
+            validation_str = ",".join([f"BeforeValidator({v})" for v in validators])
+            return f"Annotated[{raw_type_str}, {validation_str}]"
+
+        return raw_type_str
+
+    @property
+    def xml_type_str(self) -> str:
+        return as_xml_type(self.type)
+
+    @property
+    def field_default_str(self) -> str:
+        if not self.has_default_value:
+            return "..."
+        elif isinstance(self.default_value, str):
+            return f'''"{self.default_value}"'''
+        else:
+            return str(self.default_value)
+
+    @property
+    def has_default_value(self) -> bool:
+        return self.default_value is not inspect._empty
+
+    @property
+    def is_deprecated(self) -> bool:
+        assertion_parameter = self._get_type_annotation()
+        if assertion_parameter is not None:
+            return assertion_parameter.deprecated
+
+        return False
+
+    @property
+    def validators(self) -> List[str]:
+        assertion_parameter = self._get_type_annotation()
+        if assertion_parameter is not None:
+            return assertion_parameter.validators
+
+        return []
+
+    def _get_type_annotation(self) -> Optional[AssertionParameterAnnotation]:
+        target_type = self.type
+        if get_origin(target_type) is Annotated:
+            args = get_args(target_type)
+            if len(args) > 1:
+                return cast(AssertionParameterAnnotation, args[1])
+
+        return None
+
+
+def _is_none_type(target_type):
+    return target_type is type(None)
+
+
+def _non_optional_types(union_type):
+    return [t for t in get_args(union_type) if not _is_none_type(t)]
+
+
+def as_xml_type(target_type) -> str:
+    if get_origin(target_type) is Annotated:
+        args = get_args(target_type)
+        if len(args) > 1:
+            assertion_parameter = args[1]
+            if assertion_parameter.xml_type:
+                return assertion_parameter.xml_type
+
+        return as_xml_type(args[0])
+    elif get_origin(target_type) is Union:
+        types = _non_optional_types(target_type)
+        if len(types) == 2:
+            non_str_types = [t for t in types if t is not str]
+            if len(non_str_types) == 1 and non_str_types[0] is bool:
+                return "xs:boolean"
+            elif len(non_str_types) == 1 and non_str_types[0] is int:
+                return "xs:integer"
+            elif len(non_str_types) == 1 and non_str_types[0] is float:
+                return "xs:float"
+
+    return "xs:string"
+
+
+def as_type_str(target_type, strict=True):
+    if get_origin(target_type) is Annotated:
+        args = get_args(target_type)
+        if len(args) > 1:
+            if args[1].json_type and strict:
+                return args[1].json_type
+
+        return as_type_str(args[0])
+    elif get_origin(target_type) is Union:
+        is_optional = any(_is_none_type(t) for t in get_args(target_type))
+        types_as_str = ", ".join(map(as_type_str, _non_optional_types(target_type)))
+        union_type = f"typing.Union[{types_as_str}]"
+        if is_optional:
+            return f"typing.Optional[{union_type}]"
+        else:
+            return union_type
+    elif target_type is str:
+        return "str"
+    elif target_type is int:
+        return "int"
+    elif target_type is float:
+        return "float"
+    elif target_type is bool:
+        return "bool"
+    else:
+        return str(target_type)
+
+
+class Assertion:
+
+    def __init__(
+        self,
+        name: str,
+        docstring: str,
+        parameters: List[AssertionParameter],
+        children: Children,
+        module_and_function: str,
+    ):
+        self.name = name
+        self.parameters = parameters
+        self.docstring = docstring
+        self.children = children
+        self.module_and_function = module_and_function
+
+
+def arg_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    return parser
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index b51e2a33ad5ab24e9783b6e4f9659b0ad0c38e1f..2c859132e6188575d57282d9475cf7a53a59d085 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -8,6 +8,7 @@ import sys
 import tarfile
 import tempfile
 import time
+import traceback
 import urllib.parse
 import zipfile
 from json import dumps
@@ -35,11 +36,16 @@ from typing_extensions import (
 )
 
 from galaxy import util
+from galaxy.tool_util.client.staging import StagingInterface
 from galaxy.tool_util.parser.interface import (
     AssertionList,
     TestCollectionDef,
     TestCollectionOutputDef,
+    TestSourceTestOutputColllection,
+    ToolSourceTestOutputs,
+    XmlTestCollectionDefDict,
 )
+from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.util import requests
 from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import (
@@ -47,6 +53,14 @@ from galaxy.util.hash_util import (
     parse_checksum_hash,
 )
 from . import verify
+from ._types import (
+    ExpandedToolInputs,
+    ExpandedToolInputsJsonified,
+    RequiredDataTablesT,
+    RequiredFilesT,
+    RequiredLocFileT,
+    ToolTestDescriptionDict,
+)
 from .asserts import verify_assertions
 from .wait import wait_on
 
@@ -58,7 +72,7 @@ log = getLogger(__name__)
 VERBOSE_ERRORS = util.asbool(os.environ.get("GALAXY_TEST_VERBOSE_ERRORS", False))
 UPLOAD_ASYNC = util.asbool(os.environ.get("GALAXY_TEST_UPLOAD_ASYNC", True))
 ERROR_MESSAGE_DATASET_SEP = "--------------------------------------"
-DEFAULT_TOOL_TEST_WAIT = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400))
+DEFAULT_TOOL_TEST_WAIT: int = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 86400))
 CLEANUP_TEST_HISTORIES = "GALAXY_TEST_NO_CLEANUP" not in os.environ
 DEFAULT_TARGET_HISTORY = os.environ.get("GALAXY_TEST_HISTORY_ID", None)
 
@@ -90,21 +104,21 @@ JobDataCallbackT = Callable[[JobDataT], None]
 
 
 class ValidToolTestDict(TypedDict):
-    inputs: Any
-    outputs: Any
-    output_collections: List[Dict[str, Any]]
+    inputs: ExpandedToolInputs
+    outputs: ToolSourceTestOutputs
+    output_collections: List[TestSourceTestOutputColllection]
     stdout: NotRequired[AssertionList]
     stderr: NotRequired[AssertionList]
-    expect_exit_code: NotRequired[int]
+    expect_exit_code: NotRequired[Optional[Union[str, int]]]
     expect_failure: NotRequired[bool]
     expect_test_failure: NotRequired[bool]
-    maxseconds: NotRequired[int]
-    num_outputs: NotRequired[int]
+    maxseconds: NotRequired[Optional[int]]
+    num_outputs: NotRequired[Optional[Union[str, int]]]
     command_line: NotRequired[AssertionList]
     command_version: NotRequired[AssertionList]
-    required_files: NotRequired[List[Any]]
-    required_data_tables: NotRequired[List[Any]]
-    required_loc_files: NotRequired[List[str]]
+    required_files: NotRequired[RequiredFilesT]
+    required_data_tables: NotRequired[RequiredDataTablesT]
+    required_loc_files: NotRequired[RequiredLocFileT]
     error: Literal[False]
     tool_id: str
     tool_version: str
@@ -125,45 +139,42 @@ ToolTestDict = Union[ValidToolTestDict, InvalidToolTestDict]
 ToolTestDictsT = List[ToolTestDict]
 
 
+class PathOrLocation(NamedTuple):
+    name: str
+    path: Optional[str]
+    location: Optional[str]
+
+
 def stage_data_in_history(
     galaxy_interactor: "GalaxyInteractorApi",
     tool_id: str,
     all_test_data,
-    history=None,
+    history: str,
     force_path_paste=False,
     maxseconds=DEFAULT_TOOL_TEST_WAIT,
     tool_version=None,
+    test_data_resolver: Optional[TestDataResolver] = None,
 ):
-    # Upload any needed files
-    upload_waits = []
-
     assert tool_id
 
-    if UPLOAD_ASYNC:
-        for test_data in all_test_data:
-            upload_waits.append(
-                galaxy_interactor.stage_data_async(
-                    test_data,
-                    history,
-                    tool_id,
-                    force_path_paste=force_path_paste,
-                    maxseconds=maxseconds,
-                    tool_version=tool_version,
-                )
-            )
-        for upload_wait in upload_waits:
-            upload_wait()
-    else:
-        for test_data in all_test_data:
-            upload_wait = galaxy_interactor.stage_data_async(
-                test_data,
-                history,
-                tool_id,
-                force_path_paste=force_path_paste,
-                maxseconds=maxseconds,
-                tool_version=tool_version,
-            )
-            upload_wait()
+    staging_interface = InteractorStagingInterface(galaxy_interactor, maxseconds=maxseconds, upload_async=UPLOAD_ASYNC)
+    job = {}
+    for test_data in all_test_data:
+        test_dict = galaxy_interactor.remote_to_input(
+            test_data=test_data, tool_id=tool_id, force_path_paste=force_path_paste, tool_version=tool_version
+        )
+        job[test_data["fname"]] = test_dict
+    resolve_data = test_data_resolver.get_filename if test_data_resolver else None
+    staging_interface.stage(
+        "tool",
+        history_id=history,
+        job=job,
+        use_path_paste=force_path_paste,
+        resolve_data=resolve_data,
+    )
+    staging_interface.handle_jobs()
+    galaxy_interactor.uploads = job
+    return
 
 
 class RunToolResponse(NamedTuple):
@@ -173,6 +184,38 @@ class RunToolResponse(NamedTuple):
     jobs: List[Dict[str, Any]]
 
 
+class InteractorStagingInterface(StagingInterface):
+
+    def __init__(self, galaxy_interactor: "GalaxyInteractorApi", maxseconds: Optional[int], upload_async: bool) -> None:
+        super().__init__()
+        self.galaxy_interactor = galaxy_interactor
+        self.maxseconds = maxseconds or DEFAULT_TOOL_TEST_WAIT
+        self.upload_async = upload_async
+        self.job_responses: List[Dict[str, Any]] = []
+
+    def _post(self, api_path: str, payload: Dict[str, Any]) -> Dict[str, Any]:
+        response = self.galaxy_interactor._post(api_path, payload, json=True)
+        assert response.status_code == 200, f"Staging failed: {response.text}"
+        return response.json()
+
+    def _handle_job(self, job_response: Dict[str, Any]):
+        if not self.upload_async:
+            return self.galaxy_interactor.wait_for_job(
+                job_response["id"], job_response["history_id"], maxseconds=self.maxseconds
+            )
+        else:
+            self.job_responses.append(job_response)
+        return
+
+    def handle_jobs(self):
+        for job_response in self.job_responses:
+            self.galaxy_interactor.wait_for_job(job_response["id"], job_response["history_id"], self.maxseconds)
+
+    @property
+    def use_fetch_api(self):
+        return True
+
+
 class GalaxyInteractorApi:
     # api_key and cookies can also be manually set by UsesApiTestCaseMixin._different_user()
     api_key: Optional[str]
@@ -225,7 +268,7 @@ class GalaxyInteractorApi:
         assert response.status_code == 200, f"Non 200 response from tool tests available API. [{response.content}]"
         return response.json()
 
-    def get_tool_tests(self, tool_id: str, tool_version: Optional[str] = None) -> ToolTestDictsT:
+    def get_tool_tests(self, tool_id: str, tool_version: Optional[str] = None) -> List[ToolTestDescriptionDict]:
         url = f"tools/{tool_id}/test_data"
         params = {"tool_version": tool_version} if tool_version else None
         response = self._get(url, data=params)
@@ -337,18 +380,7 @@ class GalaxyInteractorApi:
         `dbkey` and `tags` all map to the API description directly. Other metadata attributes
         are assumed to be datatype-specific and mapped with a prefix of `metadata_`.
         """
-        metadata = attributes.get("metadata", {}).copy()
-        for key in metadata.copy().keys():
-            if key not in ["name", "info", "tags", "created_from_basename"]:
-                new_key = f"metadata_{key}"
-                metadata[new_key] = metadata[key]
-                del metadata[key]
-            elif key == "info":
-                metadata["misc_info"] = metadata["info"]
-                del metadata["info"]
-        expected_file_type = attributes.get("ftype", None)
-        if expected_file_type:
-            metadata["file_ext"] = expected_file_type
+        metadata = get_metadata_to_test(attributes)
 
         if metadata:
 
@@ -361,29 +393,7 @@ class GalaxyInteractorApi:
                     return None
 
             dataset = wait_on(wait_for_content, desc="dataset metadata", timeout=10)
-
-            for key, value in metadata.items():
-                try:
-                    dataset_value = dataset.get(key, None)
-
-                    def compare(val, expected):
-                        if str(val) != str(expected):
-                            raise Exception(
-                                f"Dataset metadata verification for [{key}] failed, expected [{value}] but found [{dataset_value}]. Dataset API value was [{dataset}]."  # noqa: B023
-                            )
-
-                    if isinstance(dataset_value, list):
-                        value = str(value).split(",")
-                        if len(value) != len(dataset_value):
-                            raise Exception(
-                                f"Dataset metadata verification for [{key}] failed, expected [{value}] but found [{dataset_value}], lists differ in length. Dataset API value was [{dataset}]."
-                            )
-                        for val, expected in zip(dataset_value, value):
-                            compare(val, expected)
-                    else:
-                        compare(dataset_value, value)
-                except KeyError:
-                    raise Exception(f"Failed to verify dataset metadata, metadata key [{key}] was not found.")
+            compare_expected_metadata_to_api_response(metadata, dataset)
 
     def wait_for_job(self, job_id: str, history_id: Optional[str] = None, maxseconds=DEFAULT_TOOL_TEST_WAIT) -> None:
         self.wait_for(lambda: self.__job_ready(job_id, history_id), maxseconds=maxseconds)
@@ -403,7 +413,7 @@ class GalaxyInteractorApi:
 
     def get_history(self, history_name: str = "test_history") -> Optional[Dict[str, Any]]:
         # Return the most recent non-deleted history matching the provided name
-        filters = urllib.parse.urlencode({"q": "name", "qv": history_name, "order": "update_time"})
+        filters = urllib.parse.urlencode({"q": "name", "qv": history_name, "order": "update_time", "show_own": "true"})
         response = self._get(f"histories?{filters}")
         try:
             return response.json()[-1]
@@ -412,14 +422,17 @@ class GalaxyInteractorApi:
 
     @contextlib.contextmanager
     def test_history(
-        self, require_new: bool = True, cleanup_callback: Optional[Callable[[str], None]] = None
+        self,
+        require_new: bool = True,
+        cleanup_callback: Optional[Callable[[str], None]] = None,
+        name: Optional[str] = None,
     ) -> Generator[str, None, None]:
         history_id = None
         if not require_new:
             history_id = DEFAULT_TARGET_HISTORY
 
         cleanup = CLEANUP_TEST_HISTORIES
-        history_id = history_id or self.new_history()
+        history_id = history_id or self.new_history(name)
         try:
             yield history_id
         except Exception:
@@ -429,7 +442,8 @@ class GalaxyInteractorApi:
             if cleanup and cleanup_callback is not None:
                 cleanup_callback(history_id)
 
-    def new_history(self, history_name: str = "test_history", publish_history: bool = False) -> str:
+    def new_history(self, history_name: Optional[str] = None, publish_history: bool = False) -> str:
+        history_name = history_name or "test_history"
         create_response = self._post("histories", {"name": history_name})
         try:
             create_response.raise_for_status()
@@ -452,16 +466,23 @@ class GalaxyInteractorApi:
             return result
         raise Exception(result["err_msg"])
 
-    def test_data_download(self, tool_id, filename, mode="file", is_output=True, tool_version=None):
-        result = None
-        local_path = None
+    def test_data_download(self, tool_id, filename, mode="file", is_output=True, tool_version=None, path_only=False):
+        result: Optional[Union[str, bytes]] = None
+        local_path: Optional[str] = None
 
         if self.supports_test_data_download:
             version_fragment = f"&tool_version={tool_version}" if tool_version else ""
             response = self._get(f"tools/{tool_id}/test_data_download?filename={filename}{version_fragment}")
             if response.status_code == 200:
                 if mode == "file":
-                    result = response.content
+                    if path_only:
+                        pardir = tempfile.mkdtemp()
+                        path = os.path.join(pardir, os.path.basename(filename))
+                        with open(path, "wb") as out:
+                            out.write(response.content)
+                        return out.name
+                    else:
+                        return response.content
                 elif mode == "directory":
                     prefix = os.path.basename(filename)
                     path = tempfile.mkdtemp(prefix=prefix)
@@ -474,6 +495,8 @@ class GalaxyInteractorApi:
                         with tarfile.open(fileobj=fileobj) as tar_contents:
                             tar_contents.extractall(path=path)
                     result = path
+                    if path_only:
+                        return result
         else:
             # We can only use local data
             local_path = self.test_data_path(tool_id, filename, tool_version=tool_version)
@@ -483,6 +506,8 @@ class GalaxyInteractorApi:
 
         if result is None and local_path is not None and os.path.exists(local_path):
             if mode == "file":
+                if path_only:
+                    return local_path
                 with open(local_path, mode="rb") as f:
                     result = f.read()
             elif mode == "directory":
@@ -518,95 +543,97 @@ class GalaxyInteractorApi:
             output_id = output_data
         return output_id
 
-    def stage_data_async(
-        self,
-        test_data: Dict[str, Any],
-        history_id: str,
-        tool_id: str,
-        force_path_paste: bool = False,
-        maxseconds: int = DEFAULT_TOOL_TEST_WAIT,
-        tool_version: Optional[str] = None,
-    ) -> Callable[[], None]:
+    def remote_to_input(
+        self, test_data, tool_id: str, force_path_paste: bool = False, tool_version: Optional[str] = None
+    ):
         fname = test_data["fname"]
+        tags = test_data.get("tags")
         tool_input = {
-            "file_type": test_data["ftype"],
+            "format": test_data["ftype"],
             "dbkey": test_data["dbkey"],
+            "class": test_data.get("class", "File"),
+            # Match legacy test behavior
+            "decompress": util.string_as_bool(test_data.get("decompress", True)),
         }
+        if tags:
+            if isinstance(tags, str):
+                tags = tags.split(",")
+            tool_input["tags"] = tags
+
         metadata = test_data.get("metadata", {})
         if not hasattr(metadata, "items"):
             raise Exception(f"Invalid metadata description found for input [{fname}] - [{metadata}]")
-        for name, value in test_data.get("metadata", {}).items():
-            tool_input[f"files_metadata|{name}"] = value
+        tool_input["metadata"] = metadata
 
         composite_data = test_data["composite_data"]
         if composite_data:
-            files = {}
-            for i, file_name in enumerate(composite_data):
-                if force_path_paste:
-                    file_path = self.test_data_path(tool_id, file_name, tool_version=tool_version)
-                    tool_input.update({f"files_{i}|url_paste": f"file://{file_path}"})
-                else:
-                    file_content = self.test_data_download(
-                        tool_id, file_name, is_output=False, tool_version=tool_version
-                    )
-                    files[f"files_{i}|file_data"] = file_content
-                tool_input.update(
-                    {
-                        f"files_{i}|type": "upload_dataset",
-                    }
-                )
-            name = test_data["name"]
+            tool_input["composite_data"] = [
+                self._get_path_or_location(
+                    fname=fname_,
+                    test_data={},
+                    tool_id=tool_id,
+                    tool_version=tool_version,
+                    force_path_paste=force_path_paste,
+                ).path
+                for fname_ in composite_data
+            ]
         else:
-            file_name = None
-            file_name_exists = False
-            location = self._ensure_valid_location_in(test_data)
-            if fname:
-                file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
-                file_name_exists = os.path.exists(f"{file_name}")
-            upload_from_location = not file_name_exists and location is not None
-            name = os.path.basename(location if upload_from_location else fname)
-            tool_input.update(
-                {
-                    "files_0|NAME": name,
-                    "files_0|type": "upload_dataset",
-                }
+            assert fname, "File path is required and cannot be empty string"
+            path_or_location = self._get_path_or_location(
+                fname,
+                test_data,
+                tool_id,
+                tool_version=tool_version,
+                mode="file" if tool_input["class"].lower() == "file" else "directory",
             )
-            files = {}
-            if upload_from_location:
-                tool_input.update({"files_0|url_paste": location})
-            elif force_path_paste:
-                file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
-                tool_input.update({"files_0|url_paste": f"file://{file_name}"})
+            if path_or_location.path:
+                tool_input["path"] = path_or_location.path
+            if path_or_location.location:
+                tool_input["location"] = path_or_location.location
+            tool_input["name"] = os.path.basename(path_or_location.name)
+        return tool_input
+
+    def _get_path_or_location(
+        self,
+        fname: str,
+        test_data: Dict[str, Any],
+        tool_id: str,
+        tool_version: Optional[str] = None,
+        force_path_paste: bool = False,
+        mode: Literal["file", "directory"] = "file",
+    ) -> PathOrLocation:
+        file_name = None
+        file_name_exists = False
+        location = self._ensure_valid_location_in(test_data)
+        if fname and force_path_paste:
+            file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
+            file_name_exists = os.path.exists(file_name)
+        if not file_name_exists and location is not None:
+            return PathOrLocation(name=location, location=location, path=None)
+        else:
+            if force_path_paste:
+                if file_name is None:
+                    file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
+                return PathOrLocation(name=fname, location=f"file://{file_name}", path=None)
             else:
-                file_content = self.test_data_download(tool_id, fname, is_output=False, tool_version=tool_version)
-                files = {"files_0|file_data": file_content}
-        submit_response_object = self.__submit_tool(
-            history_id, "upload1", tool_input, extra_data={"type": "upload_dataset"}, files=files
-        )
-        submit_response = ensure_tool_run_response_okay(submit_response_object, f"upload dataset {name}")
-        assert (
-            "outputs" in submit_response
-        ), f"Invalid response from server [{submit_response}], expecting outputs in response."
-        outputs = submit_response["outputs"]
-        assert len(outputs) > 0, f"Invalid response from server [{submit_response}], expecting an output dataset."
-        dataset = outputs[0]
-        hid = dataset["id"]
-        self.uploads[os.path.basename(fname)] = self.uploads[fname] = self.uploads[name] = {"src": "hda", "id": hid}
-        assert (
-            "jobs" in submit_response
-        ), f"Invalid response from server [{submit_response}], expecting jobs in response."
-        jobs = submit_response["jobs"]
-        assert len(jobs) > 0, f"Invalid response from server [{submit_response}], expecting a job."
-        return lambda: self.wait_for_job(jobs[0]["id"], history_id, maxseconds=maxseconds)
+                path = self.test_data_download(
+                    tool_id, fname, is_output=False, tool_version=tool_version, mode=mode, path_only=True
+                )
+                assert isinstance(path, str)
+                # Downloaded directories contain root directory
+                if path and mode == "directory":
+                    path = os.path.join(path, fname)
+                return PathOrLocation(name=fname, location=None, path=path)
 
     def _ensure_valid_location_in(self, test_data: dict) -> Optional[str]:
         location: Optional[str] = test_data.get("location")
-        has_valid_location = location and util.is_url(location)
-        if location and not has_valid_location:
+        if location and not util.is_url(location):
             raise ValueError(f"Invalid `location` URL: `{location}`")
         return location
 
-    def run_tool(self, testdef, history_id, resource_parameters=None) -> RunToolResponse:
+    def run_tool(
+        self, testdef: "ToolTestDescription", history_id: str, resource_parameters: Optional[Dict[str, Any]] = None
+    ) -> RunToolResponse:
         # We need to handle the case where we've uploaded a valid compressed file since the upload
         # tool will have uncompressed it on the fly.
         resource_parameters = resource_parameters or {}
@@ -686,7 +713,8 @@ class GalaxyInteractorApi:
                 element["name"] = element_identifier
                 tags = element_def.get("attributes").get("tags")
                 if tags:
-                    element["tags"] = tags.split(",")
+                    if isinstance(tags, str):
+                        element["tags"] = tags.split(",")
             element_identifiers.append(element)
         return element_identifiers
 
@@ -904,7 +932,7 @@ class GalaxyInteractorApi:
                 else:
                     break
 
-            assert response
+            assert response, f"Failed to fetch url '{url}'"
             response.raise_for_status()
             return response.content
 
@@ -1148,7 +1176,7 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
             raise AssertionError(message)
 
     expected_element_count = output_collection_def.count
-    if expected_element_count:
+    if expected_element_count is not None:
         actual_element_count = len(data_collection["elements"])
         if expected_element_count != actual_element_count:
             message = f"Output collection '{name}': expected to have {expected_element_count} elements, but it had {actual_element_count}."
@@ -1201,7 +1229,8 @@ def verify_collection(output_collection_def, data_collection, verify_dataset):
                     message = f"Output collection '{name}': identifier '{identifier}' found out of order, expected order of {expected_sort_order} for the tool generated collection elements {eo_ids}"
                     raise AssertionError(message)
 
-    verify_elements(data_collection["elements"], output_collection_def.element_tests)
+    if output_collection_def.element_tests:
+        verify_elements(data_collection["elements"], output_collection_def.element_tests)
 
 
 def _verify_composite_datatype_file_content(
@@ -1338,7 +1367,8 @@ def verify_tool(
     client_test_config: Optional[TestConfig] = None,
     skip_with_reference_data: bool = False,
     skip_on_dynamic_param_errors: bool = False,
-    _tool_test_dicts: Optional[ToolTestDictsT] = None,  # extension point only for tests
+    _tool_test_dicts: Optional[List[ToolTestDescriptionDict]] = None,  # extension point only for tests
+    test_data_resolver: Optional[TestDataResolver] = None,
 ):
     if resource_parameters is None:
         resource_parameters = {}
@@ -1379,7 +1409,7 @@ def verify_tool(
         return
 
     tool_test_dict.setdefault("maxseconds", maxseconds)
-    testdef = ToolTestDescription(cast(ToolTestDict, tool_test_dict))
+    testdef = ToolTestDescription(tool_test_dict)
     _handle_def_errors(testdef)
 
     created_history = False
@@ -1396,7 +1426,7 @@ def verify_tool(
     job_stdio = None
     job_output_exceptions = None
     tool_execution_exception: Optional[Exception] = None
-    input_staging_exception = None
+    input_staging_exc_info = None
     expected_failure_occurred = False
     begin_time = time.time()
     try:
@@ -1409,9 +1439,10 @@ def verify_tool(
                 force_path_paste=force_path_paste,
                 maxseconds=maxseconds,
                 tool_version=tool_version,
+                test_data_resolver=test_data_resolver,
             )
-        except Exception as e:
-            input_staging_exception = e
+        except Exception:
+            input_staging_exc_info = sys.exc_info()
             raise
         try:
             tool_response = galaxy_interactor.run_tool(testdef, test_history, resource_parameters=resource_parameters)
@@ -1461,8 +1492,10 @@ def verify_tool(
                         status = "skip"
                     else:
                         status = "error"
-            if input_staging_exception:
-                job_data["execution_problem"] = f"Input staging problem: {util.unicodify(input_staging_exception)}"
+            if input_staging_exc_info:
+                job_data["execution_problem"] = (
+                    f"Input staging problem: {''.join(traceback.format_exception(*input_staging_exc_info))}"
+                )
                 status = "error"
             job_data["status"] = status
             register_job_data(job_data)
@@ -1657,27 +1690,132 @@ class JobOutputsError(AssertionError):
         self.output_exceptions = output_exceptions
 
 
-class ToolTestDescriptionDict(TypedDict):
-    name: str
-    inputs: Any
-    outputs: Any
-    output_collections: List[Dict[str, Any]]
-    stdout: Optional[AssertionList]
-    stderr: Optional[AssertionList]
-    expect_exit_code: Optional[int]
-    expect_failure: bool
-    expect_test_failure: bool
-    num_outputs: Optional[int]
-    command_line: Optional[AssertionList]
-    command_version: Optional[AssertionList]
-    required_files: List[Any]
-    required_data_tables: List[Any]
-    required_loc_files: List[str]
-    error: bool
-    tool_id: str
-    tool_version: Optional[str]
-    test_index: int
-    exception: Optional[str]
+DEFAULT_NUM_OUTPUTS: Optional[int] = None
+DEFAULT_OUTPUT_COLLECTIONS: List[TestSourceTestOutputColllection] = []
+DEFAULT_REQUIRED_FILES: RequiredFilesT = []
+DEFAULT_REQUIRED_DATA_TABLES: RequiredDataTablesT = []
+DEFAULT_REQUIRED_LOC_FILES: RequiredLocFileT = []
+DEFAULT_COMMAND_LINE: Optional[AssertionList] = []
+DEFAULT_COMMAND_VERSION: Optional[AssertionList] = []
+DEFAULT_STDOUT: Optional[AssertionList] = []
+DEFAULT_STDERR: Optional[AssertionList] = []
+DEFAULT_OUTPUTS: ToolSourceTestOutputs = []
+DEFAULT_EXPECT_EXIT_CODE: Optional[int] = None
+DEFAULT_EXPECT_FAILURE: bool = False
+DEFAULT_EXPECT_TEST_FAILURE: bool = False
+DEFAULT_EXCEPTION: Optional[str] = None
+
+
+def adapt_tool_source_dict(processed_dict: ToolTestDict) -> ToolTestDescriptionDict:
+    """Convert the dictionaries parsed from tool sources (ToolTestDict) to a ToolTestDescriptionDict.
+
+    ToolTestDescription is used inside and outside of Galaxy, so convert the dictionaries to the format
+    produced by ToolTestDescription.to_dict() and then construct a ToolTestDescription from that.
+    """
+    test_index: int = _get_test_index(processed_dict)
+    name = _get_test_name(processed_dict, test_index)
+    error_in_test_definition = processed_dict["error"]
+
+    exception: Optional[str] = DEFAULT_EXCEPTION
+    output_collections: List[TestSourceTestOutputColllection] = []
+    num_outputs: Optional[int] = DEFAULT_NUM_OUTPUTS
+    required_files: RequiredFilesT = DEFAULT_REQUIRED_FILES
+    required_data_tables: RequiredDataTablesT = DEFAULT_REQUIRED_DATA_TABLES
+    required_loc_files: RequiredLocFileT = DEFAULT_REQUIRED_LOC_FILES
+    command_line: Optional[AssertionList] = DEFAULT_COMMAND_LINE
+    command_version: Optional[AssertionList] = DEFAULT_COMMAND_VERSION
+    stdout: Optional[AssertionList] = DEFAULT_STDERR
+    stderr: Optional[AssertionList] = DEFAULT_STDERR
+    outputs: ToolSourceTestOutputs = DEFAULT_OUTPUTS
+    expect_exit_code: Optional[int] = DEFAULT_EXPECT_EXIT_CODE
+    expect_failure: bool = DEFAULT_EXPECT_FAILURE
+    expect_test_failure: bool = DEFAULT_EXPECT_TEST_FAILURE
+    inputs: ExpandedToolInputsJsonified = {}
+    maxseconds: Optional[int] = None
+
+    if not error_in_test_definition:
+        processed_test_dict = cast(ValidToolTestDict, processed_dict)
+        maxseconds = processed_test_dict.get("maxseconds")
+        output_collections = processed_test_dict.get("output_collections", [])
+        if "num_outputs" in processed_test_dict and processed_test_dict["num_outputs"]:
+            num_outputs = int(processed_test_dict["num_outputs"])
+
+        required_files = processed_test_dict.get("required_files", DEFAULT_REQUIRED_FILES)
+        required_data_tables = processed_test_dict.get("required_data_tables", DEFAULT_REQUIRED_DATA_TABLES)
+        required_loc_files = processed_test_dict.get("required_loc_files", DEFAULT_REQUIRED_LOC_FILES)
+        command_line = processed_test_dict.get("command_line", DEFAULT_COMMAND_LINE)
+        command_version = processed_test_dict.get("command_version", DEFAULT_COMMAND_VERSION)
+        stdout = processed_test_dict.get("stdout", DEFAULT_STDOUT)
+        stderr = processed_test_dict.get("stderr", DEFAULT_STDERR)
+        outputs = processed_test_dict.get("outputs", DEFAULT_OUTPUTS)
+        raw_expect_exit_code: Optional[Union[str, int]] = processed_test_dict.get(
+            "expect_exit_code", DEFAULT_EXPECT_EXIT_CODE
+        )
+        if raw_expect_exit_code is not None:
+            expect_exit_code = int(raw_expect_exit_code)
+
+        expect_failure = processed_test_dict.get("expect_failure", DEFAULT_EXPECT_FAILURE)
+        expect_test_failure = processed_test_dict.get("expect_test_failure", DEFAULT_EXPECT_TEST_FAILURE)
+        inputs = processed_test_dict.get("inputs", {})
+    else:
+        invalid_test_dict = cast(InvalidToolTestDict, processed_dict)
+        maxseconds = DEFAULT_TOOL_TEST_WAIT
+        exception = invalid_test_dict.get("exception", DEFAULT_EXCEPTION)
+
+    return ToolTestDescriptionDict(
+        test_index=test_index,
+        name=name,
+        error=error_in_test_definition,
+        maxseconds=maxseconds,
+        tool_id=processed_dict["tool_id"],
+        tool_version=processed_dict.get("tool_version"),
+        exception=exception,
+        num_outputs=num_outputs,
+        required_files=required_files,
+        required_data_tables=required_data_tables,
+        required_loc_files=required_loc_files,
+        command_line=command_line,
+        command_version=command_version,
+        stdout=stdout,
+        stderr=stderr,
+        outputs=outputs,
+        output_collections=output_collections,
+        expect_exit_code=expect_exit_code,
+        expect_failure=expect_failure,
+        expect_test_failure=expect_test_failure,
+        inputs=inputs,
+    )
+
+
+def _get_test_index(test_dict: Union[ToolTestDict, ToolTestDescriptionDict]) -> int:
+    assert "test_index" in test_dict, "Invalid processed test description, must have a 'test_index' for naming, etc.."
+    return test_dict["test_index"]
+
+
+def _get_test_name(test_dict: Union[ToolTestDict, ToolTestDescriptionDict], test_index: int) -> str:
+    name = cast(str, test_dict.get("name", f"Test-{test_index + 1}"))
+    return name
+
+
+def expanded_inputs_from_json(expanded_inputs_json: ExpandedToolInputsJsonified) -> ExpandedToolInputs:
+    loaded_inputs: ExpandedToolInputs = {}
+    for key, value in expanded_inputs_json.items():
+        if isinstance(value, dict) and value.get("model_class"):
+            collection_def_dict = cast(XmlTestCollectionDefDict, value)
+            loaded_inputs[key] = TestCollectionDef.from_dict(collection_def_dict)
+        else:
+            loaded_inputs[key] = value
+    return loaded_inputs
+
+
+def expanded_inputs_to_json(expanded_inputs: ExpandedToolInputs) -> ExpandedToolInputsJsonified:
+    inputs_dict: ExpandedToolInputsJsonified = {}
+    for key, value in expanded_inputs.items():
+        if hasattr(value, "to_dict"):
+            inputs_dict[key] = value.to_dict()
+        else:
+            inputs_dict[key] = value
+    return inputs_dict
 
 
 class ToolTestDescription:
@@ -1688,70 +1826,53 @@ class ToolTestDescription:
     """
 
     name: str
+    tool_id: str
+    tool_version: Optional[str]
+    test_index: int
     num_outputs: Optional[int]
     stdout: Optional[AssertionList]
     stderr: Optional[AssertionList]
     command_line: Optional[AssertionList]
     command_version: Optional[AssertionList]
-    required_files: List[Any]
-    required_data_tables: List[Any]
-    required_loc_files: List[str]
+    required_files: RequiredFilesT
+    required_data_tables: RequiredDataTablesT
+    required_loc_files: RequiredLocFileT
     expect_exit_code: Optional[int]
     expect_failure: bool
     expect_test_failure: bool
     exception: Optional[str]
+    inputs: ExpandedToolInputs
+    outputs: ToolSourceTestOutputs
+    output_collections: List[TestCollectionOutputDef]
+    maxseconds: Optional[int]
 
-    def __init__(self, processed_test_dict: ToolTestDict):
-        assert (
-            "test_index" in processed_test_dict
-        ), "Invalid processed test description, must have a 'test_index' for naming, etc.."
-        test_index = processed_test_dict["test_index"]
-        name = cast(str, processed_test_dict.get("name", f"Test-{test_index + 1}"))
-        error_in_test_definition = processed_test_dict["error"]
-        if not error_in_test_definition:
-            processed_test_dict = cast(ValidToolTestDict, processed_test_dict)
-            maxseconds = int(processed_test_dict.get("maxseconds") or DEFAULT_TOOL_TEST_WAIT or 86400)
-            output_collections = processed_test_dict.get("output_collections", [])
-        else:
-            processed_test_dict = cast(InvalidToolTestDict, processed_test_dict)
-            maxseconds = DEFAULT_TOOL_TEST_WAIT
-            output_collections = []
-
-        self.test_index = test_index
-        assert (
-            "tool_id" in processed_test_dict
-        ), "Invalid processed test description, must have a 'tool_id' for naming, etc.."
-        self.tool_id = processed_test_dict["tool_id"]
-        self.tool_version = processed_test_dict.get("tool_version")
-        self.name = name
-        self.maxseconds = maxseconds
-        self.required_files = cast(List[Any], processed_test_dict.get("required_files", []))
-        self.required_data_tables = cast(List[Any], processed_test_dict.get("required_data_tables", []))
-        self.required_loc_files = cast(List[str], processed_test_dict.get("required_loc_files", []))
-
-        inputs = processed_test_dict.get("inputs", {})
-        loaded_inputs = {}
-        for key, value in inputs.items():
-            if isinstance(value, dict) and value.get("model_class"):
-                loaded_inputs[key] = TestCollectionDef.from_dict(value)
-            else:
-                loaded_inputs[key] = value
-
-        self.inputs = loaded_inputs
-        self.outputs = processed_test_dict.get("outputs", [])
-        self.num_outputs = cast(Optional[int], processed_test_dict.get("num_outputs", None))
-
-        self.error = processed_test_dict.get("error", False)
-        self.exception = cast(Optional[str], processed_test_dict.get("exception", None))
+    @staticmethod
+    def from_tool_source_dict(processed_test_dict: ToolTestDict) -> "ToolTestDescription":
+        return ToolTestDescription(adapt_tool_source_dict(processed_test_dict))
 
+    def __init__(self, json_dict: ToolTestDescriptionDict):
+        self.test_index = _get_test_index(json_dict)
+        self.name = _get_test_name(json_dict, self.test_index)
+        self.error = json_dict["error"]
+        self.exception = json_dict.get("exception", DEFAULT_EXCEPTION)
+        output_collections = json_dict.get("output_collections", DEFAULT_OUTPUT_COLLECTIONS)
         self.output_collections = [TestCollectionOutputDef.from_dict(d) for d in output_collections]
-        self.command_line = cast(Optional[AssertionList], processed_test_dict.get("command_line", None))
-        self.command_version = cast(Optional[AssertionList], processed_test_dict.get("command_version", None))
-        self.stdout = cast(Optional[AssertionList], processed_test_dict.get("stdout", None))
-        self.stderr = cast(Optional[AssertionList], processed_test_dict.get("stderr", None))
-        self.expect_exit_code = cast(Optional[int], processed_test_dict.get("expect_exit_code", None))
-        self.expect_failure = cast(bool, processed_test_dict.get("expect_failure", False))
-        self.expect_test_failure = cast(bool, processed_test_dict.get("expect_test_failure", False))
+        self.num_outputs = json_dict.get("num_outputs", DEFAULT_NUM_OUTPUTS)
+        self.required_files = json_dict.get("required_files", DEFAULT_REQUIRED_FILES)
+        self.required_data_tables = json_dict.get("required_data_tables", DEFAULT_REQUIRED_DATA_TABLES)
+        self.required_loc_files = json_dict.get("required_loc_files", DEFAULT_REQUIRED_LOC_FILES)
+        self.command_line = json_dict.get("command_line", DEFAULT_COMMAND_LINE)
+        self.command_version = json_dict.get("command_version", DEFAULT_COMMAND_VERSION)
+        self.stdout = json_dict.get("stdout", DEFAULT_STDOUT)
+        self.stderr = json_dict.get("stderr", DEFAULT_STDERR)
+        self.outputs = json_dict.get("outputs", DEFAULT_OUTPUTS)
+        self.expect_exit_code = json_dict.get("expect_exit_code", DEFAULT_EXPECT_EXIT_CODE)
+        self.expect_failure = json_dict.get("expect_failure", DEFAULT_EXPECT_FAILURE)
+        self.expect_test_failure = json_dict.get("expect_test_failure", DEFAULT_EXPECT_TEST_FAILURE)
+        self.inputs = expanded_inputs_from_json(json_dict.get("inputs", {}))
+        self.tool_id = json_dict["tool_id"]
+        self.tool_version = json_dict.get("tool_version")
+        self.maxseconds = json_dict.get("maxseconds")
 
     def test_data(self):
         """
@@ -1760,15 +1881,9 @@ class ToolTestDescription:
         return test_data_iter(self.required_files)
 
     def to_dict(self) -> ToolTestDescriptionDict:
-        inputs_dict = {}
-        for key, value in self.inputs.items():
-            if hasattr(value, "to_dict"):
-                inputs_dict[key] = value.to_dict()
-            else:
-                inputs_dict[key] = value
-
-        return {
-            "inputs": inputs_dict,
+        inputs = expanded_inputs_to_json(self.inputs)
+        test_description_def: ToolTestDescriptionDict = {
+            "inputs": inputs,
             "outputs": self.outputs,
             "output_collections": [_.to_dict() for _ in self.output_collections],
             "num_outputs": self.num_outputs,
@@ -1789,18 +1904,24 @@ class ToolTestDescription:
             "error": self.error,
             "exception": self.exception,
         }
+        if self.maxseconds is not None:
+            test_description_def["maxseconds"] = self.maxseconds
+        return ToolTestDescriptionDict(**test_description_def)
 
 
 def test_data_iter(required_files):
     for fname, extra in required_files:
-        data_dict = dict(
-            fname=fname,
-            metadata=extra.get("metadata", {}),
-            composite_data=extra.get("composite_data", []),
-            ftype=extra.get("ftype", DEFAULT_FTYPE),
-            dbkey=extra.get("dbkey", DEFAULT_DBKEY),
-            location=extra.get("location", None),
-        )
+        default_ftype = DEFAULT_FTYPE if extra.get("class", "File").lower() != "directory" else "directory"
+        data_dict = {
+            "fname": fname,
+            "class": extra.get("class", "File"),
+            "metadata": extra.get("metadata", {}),
+            "composite_data": extra.get("composite_data", []),
+            "ftype": extra.get("ftype", default_ftype),
+            "dbkey": extra.get("dbkey", DEFAULT_DBKEY),
+            "location": extra.get("location", None),
+            "tags": extra.get("tags", []),
+        }
         edit_attributes = extra.get("edit_attributes", [])
 
         # currently only renaming is supported
@@ -1813,3 +1934,45 @@ def test_data_iter(required_files):
                 raise Exception(f"edit_attributes type ({edit_att.get('type', None)}) is unimplemented")
 
         yield data_dict
+
+
+def compare_expected_metadata_to_api_response(metadata: dict, dataset: dict) -> None:
+    for key, value in metadata.items():
+        try:
+            dataset_value = dataset.get(key, None)
+
+            def compare(val, expected):
+                if str(val) != str(expected):
+                    raise Exception(
+                        f"Dataset metadata verification for [{key}] failed, expected [{value}] but found [{dataset_value}]. Dataset API value was [{dataset}]."  # noqa: B023
+                    )
+
+            if isinstance(dataset_value, list):
+                value = str(value).split(",")
+                if len(value) != len(dataset_value):
+                    raise Exception(
+                        f"Dataset metadata verification for [{key}] failed, expected [{value}] but found [{dataset_value}], lists differ in length. Dataset API value was [{dataset}]."
+                    )
+                for val, expected in zip(dataset_value, value):
+                    compare(val, expected)
+            else:
+                compare(dataset_value, value)
+        except KeyError:
+            raise Exception(f"Failed to verify dataset metadata, metadata key [{key}] was not found.")
+
+
+def get_metadata_to_test(test_properties: dict) -> dict:
+    """Fetch out metadata to test from test property dict and adapt it to keys the API produces."""
+    metadata = test_properties.get("metadata", {}).copy()
+    for key in metadata.copy().keys():
+        if key not in ["name", "info", "tags", "created_from_basename"]:
+            new_key = f"metadata_{key}"
+            metadata[new_key] = metadata[key]
+            del metadata[key]
+        elif key == "info":
+            metadata["misc_info"] = metadata["info"]
+            del metadata["info"]
+    expected_file_type = test_properties.get("ftype", None)
+    if expected_file_type:
+        metadata["file_ext"] = expected_file_type
+    return metadata
diff --git a/lib/galaxy/tool_util/verify/parse.py b/lib/galaxy/tool_util/verify/parse.py
new file mode 100644
index 0000000000000000000000000000000000000000..9bdc487c47e05070c5a85853fe110ce1c3e82147
--- /dev/null
+++ b/lib/galaxy/tool_util/verify/parse.py
@@ -0,0 +1,612 @@
+import logging
+import os
+import traceback
+from typing import (
+    Any,
+    Iterable,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+from packaging.version import Version
+
+from galaxy.tool_util.parameters import (
+    input_models_for_tool_source,
+    test_case_state as case_state,
+)
+from galaxy.tool_util.parser.interface import (
+    InputSource,
+    TestCollectionDef,
+    ToolSource,
+    ToolSourceTest,
+    ToolSourceTestInputs,
+    ToolSourceTests,
+)
+from galaxy.tool_util.parser.util import (
+    boolean_is_checked,
+    boolean_true_and_false_values,
+    parse_tool_version_with_defaults,
+)
+from galaxy.tool_util.parser.xml import __parse_assert_list_from_elem
+from galaxy.tool_util.verify.assertion_models import relaxed_assertion_list
+from galaxy.tool_util.verify.interactor import (
+    InvalidToolTestDict,
+    ToolTestDescription,
+    ValidToolTestDict,
+)
+from galaxy.util import (
+    string_as_bool,
+    string_as_bool_or_none,
+    unicodify,
+)
+from ._types import (
+    ExpandedToolInputs,
+    ExtraFileInfoDictT,
+    RequiredDataTablesT,
+    RequiredFilesT,
+    RequiredLocFileT,
+)
+
+log = logging.getLogger(__name__)
+
+AnyParamContext = Union["ParamContext", "RootParamContext"]
+
+
+def parse_tool_test_descriptions(
+    tool_source: ToolSource, tool_guid: Optional[str] = None
+) -> Iterable[ToolTestDescription]:
+    """
+    Build ToolTestDescription objects for each test description.
+    """
+    validate_on_load = Version(tool_source.parse_profile()) >= Version("24.2")
+    raw_tests_dict: ToolSourceTests = tool_source.parse_tests_to_dict()
+    tests: List[ToolTestDescription] = []
+
+    profile = tool_source.parse_profile()
+    for i, raw_test_dict in enumerate(raw_tests_dict.get("tests", [])):
+        validation_exception: Optional[Exception] = None
+        if validate_on_load:
+            tool_parameter_bundle = input_models_for_tool_source(tool_source)
+            try:
+                case_state(raw_test_dict, tool_parameter_bundle.parameters, profile, validate=True)
+            except Exception as e:
+                # TOOD: restrict types of validation exceptions a bit probably?
+                validation_exception = e
+
+        if validation_exception:
+            tool_id, tool_version = _tool_id_and_version(tool_source, tool_guid)
+            test = ToolTestDescription.from_tool_source_dict(
+                InvalidToolTestDict(
+                    {
+                        "tool_id": tool_id,
+                        "tool_version": tool_version,
+                        "test_index": i,
+                        "inputs": {},
+                        "error": True,
+                        "exception": unicodify(validation_exception),
+                        "maxseconds": None,
+                    }
+                )
+            )
+        else:
+            test = _description_from_tool_source(tool_source, raw_test_dict, i, tool_guid)
+        tests.append(test)
+    return tests
+
+
+def _description_from_tool_source(
+    tool_source: ToolSource, raw_test_dict: ToolSourceTest, test_index: int, tool_guid: Optional[str]
+) -> ToolTestDescription:
+    required_files: RequiredFilesT = []
+    required_data_tables: RequiredDataTablesT = []
+    required_loc_files: RequiredLocFileT = []
+
+    num_outputs = raw_test_dict.get("expect_num_outputs", None)
+    if num_outputs:
+        num_outputs = int(num_outputs)
+    maxseconds = raw_test_dict.get("maxseconds", None)
+    if maxseconds is not None:
+        maxseconds = int(maxseconds)
+
+    tool_id, tool_version = _tool_id_and_version(tool_source, tool_guid)
+    processed_test_dict: Union[ValidToolTestDict, InvalidToolTestDict]
+    try:
+        processed_inputs = _process_raw_inputs(
+            tool_source,
+            input_sources(tool_source),
+            raw_test_dict["inputs"],
+            required_files,
+            required_data_tables,
+            required_loc_files,
+        )
+        processed_test_dict = ValidToolTestDict(
+            {
+                "inputs": processed_inputs,
+                "outputs": raw_test_dict["outputs"],
+                "output_collections": raw_test_dict["output_collections"],
+                "num_outputs": num_outputs,
+                "command_line": raw_test_dict.get("command", None),
+                "command_version": raw_test_dict.get("command_version", None),
+                "stdout": raw_test_dict.get("stdout", None),
+                "stderr": raw_test_dict.get("stderr", None),
+                "expect_exit_code": raw_test_dict.get("expect_exit_code", None),
+                "expect_failure": raw_test_dict.get("expect_failure", False),
+                "expect_test_failure": raw_test_dict.get("expect_test_failure", False),
+                "required_files": required_files,
+                "required_data_tables": required_data_tables,
+                "required_loc_files": required_loc_files,
+                "tool_id": tool_id,
+                "tool_version": tool_version,
+                "test_index": test_index,
+                "maxseconds": maxseconds,
+                "error": False,
+            }
+        )
+    except Exception:
+        processed_test_dict = InvalidToolTestDict(
+            {
+                "tool_id": tool_id,
+                "tool_version": tool_version,
+                "test_index": test_index,
+                "inputs": {},
+                "error": True,
+                "exception": unicodify(traceback.format_exc()),
+                "maxseconds": maxseconds,
+            }
+        )
+
+    return ToolTestDescription.from_tool_source_dict(processed_test_dict)
+
+
+def _tool_id_and_version(tool_source: ToolSource, tool_guid: Optional[str]) -> Tuple[str, str]:
+    tool_id = tool_guid or tool_source.parse_id()
+    assert tool_id
+    tool_version = parse_tool_version_with_defaults(tool_id, tool_source)
+    return tool_id, tool_version
+
+
+def _process_raw_inputs(
+    tool_source: ToolSource,
+    input_sources: List[InputSource],
+    raw_inputs: ToolSourceTestInputs,
+    required_files: RequiredFilesT,
+    required_data_tables: RequiredDataTablesT,
+    required_loc_files: RequiredLocFileT,
+    parent_context: Optional[AnyParamContext] = None,
+) -> ExpandedToolInputs:
+    """
+    Recursively expand flat list of inputs into "tree" form of flat list
+    (| using to nest to new levels) structure and expand dataset
+    information as proceeding to populate self.required_files.
+    """
+    profile = tool_source.parse_profile()
+    allow_legacy_test_case_parameters = Version(profile) <= Version("24.1")
+    parent_context = parent_context or RootParamContext(allow_unqualified_access=allow_legacy_test_case_parameters)
+    expanded_inputs: ExpandedToolInputs = {}
+    for input_source in input_sources:
+        input_type = input_source.parse_input_type()
+        name = input_source.parse_name()
+        if input_type == "conditional":
+            cond_context = ParamContext(name=name, parent_context=parent_context)
+            test_param_input_source = input_source.parse_test_input_source()
+            case_name = test_param_input_source.parse_name()
+            case_context = ParamContext(name=case_name, parent_context=cond_context)
+            raw_input_dict = case_context.extract_value(raw_inputs)
+            case_value = raw_input_dict["value"] if raw_input_dict else None
+            case_when, case_input_sources = _matching_case_for_value(
+                tool_source, input_source, test_param_input_source, case_value, allow_legacy_test_case_parameters
+            )
+            if case_input_sources:
+                for case_input_source in case_input_sources.parse_input_sources():
+                    case_inputs = _process_raw_inputs(
+                        tool_source,
+                        [case_input_source],
+                        raw_inputs,
+                        required_files,
+                        required_data_tables,
+                        required_loc_files,
+                        parent_context=cond_context,
+                    )
+                    expanded_inputs.update(case_inputs)
+                expanded_case_value = split_if_str(case_when)
+                if case_value is not None:
+                    # A bit tricky here - we are growing inputs with value
+                    # that may be implicit (i.e. not defined by user just
+                    # a default defined in tool). So we do not want to grow
+                    # expanded_inputs and risk repeat block viewing this
+                    # as a new instance with value defined and hence enter
+                    # an infinite loop - hence the "case_value is not None"
+                    # check.
+                    processed_value = _process_simple_value(
+                        test_param_input_source,
+                        expanded_case_value,
+                        required_data_tables,
+                        required_loc_files,
+                        allow_legacy_test_case_parameters,
+                    )
+                    expanded_inputs[case_context.for_state()] = processed_value
+        elif input_type == "section":
+            context = ParamContext(name=name, parent_context=parent_context)
+            page_source = input_source.parse_nested_inputs_source()
+            for section_input_source in page_source.parse_input_sources():
+                expanded_input = _process_raw_inputs(
+                    tool_source,
+                    [section_input_source],
+                    raw_inputs,
+                    required_files,
+                    required_data_tables,
+                    required_loc_files,
+                    parent_context=context,
+                )
+                if expanded_input:
+                    expanded_inputs.update(expanded_input)
+        elif input_type == "repeat":
+            repeat_index = 0
+            while True:
+                context = ParamContext(name=name, parent_context=parent_context, index=repeat_index)
+                updated = False
+                page_source = input_source.parse_nested_inputs_source()
+                for r_value in page_source.parse_input_sources():
+                    expanded_input = _process_raw_inputs(
+                        tool_source,
+                        [r_value],
+                        raw_inputs,
+                        required_files,
+                        required_data_tables,
+                        required_loc_files,
+                        parent_context=context,
+                    )
+                    if expanded_input:
+                        expanded_inputs.update(expanded_input)
+                        updated = True
+                if not updated:
+                    break
+                repeat_index += 1
+        else:
+            context = ParamContext(name=name, parent_context=parent_context)
+            raw_input_dict = context.extract_value(raw_inputs)
+            param_type = input_source.get("type")
+            if raw_input_dict:
+                name = raw_input_dict["name"]
+                param_value = raw_input_dict["value"]
+                param_extra = raw_input_dict["attributes"]
+                location = param_extra.get("location")
+                if param_type != "text":
+                    param_value = split_if_str(param_value)
+                if param_type == "data":
+                    if location and input_source.get_bool("multiple", False):
+                        # We get the input/s from the location which can be a list of urls separated by commas
+                        locations = split_if_str(location)
+                        param_value = []
+                        for location in locations:
+                            v = os.path.basename(location)
+                            param_value.append(v)
+                            # param_extra should contain only the corresponding location
+                            extra = dict(param_extra)
+                            extra["location"] = location
+                            _add_uploaded_dataset(context.for_state(), v, extra, input_source, required_files)
+                    else:
+                        if not isinstance(param_value, list):
+                            param_value = [param_value]
+                        for v in param_value:
+                            _add_uploaded_dataset(context.for_state(), v, param_extra, input_source, required_files)
+                    processed_value = param_value
+                elif param_type == "data_collection":
+                    assert "collection" in param_extra
+                    collection_dict = param_extra["collection"]
+                    collection_def = TestCollectionDef.from_dict(collection_dict)
+                    for input_dict in collection_def.collect_inputs():
+                        name = input_dict["name"]
+                        value = input_dict["value"]
+                        attributes = input_dict["attributes"]
+                        require_file(name, value, attributes, required_files)
+                    processed_value = collection_def
+                else:
+                    processed_value = _process_simple_value(
+                        input_source,
+                        param_value,
+                        required_data_tables,
+                        required_loc_files,
+                        allow_legacy_test_case_parameters,
+                    )
+                expanded_inputs[context.for_state()] = processed_value
+    return expanded_inputs
+
+
+def input_sources(tool_source: ToolSource) -> List[InputSource]:
+    input_sources = []
+    pages_source = tool_source.parse_input_pages()
+    if pages_source.inputs_defined:
+        for page_source in pages_source.page_sources:
+            for input_source in page_source.parse_input_sources():
+                input_sources.append(input_source)
+    return input_sources
+
+
+class ParamContext:
+    """Capture the context of a parameter's position within the inputs tree of a tool."""
+
+    parent_context: AnyParamContext
+    name: str
+    # if in a repeat - what position in the repeat
+    index: Optional[int]
+    # we've encouraged the use of repeat/conditional tags to capture fully qualified paths
+    # to parameters in tools. This brings the parameters closer to the API and prevents a
+    # variety of possible ambiguities. Disable this for newer tools.
+    allow_unqualified_access: bool
+
+    def __init__(self, name: str, parent_context: AnyParamContext, index: Optional[int] = None):
+        self.parent_context = parent_context
+        self.name = name
+        self.index = None if index is None else int(index)
+        self.allow_unqualified_access = parent_context.allow_unqualified_access
+
+    def for_state(self) -> str:
+        name = self.name if self.index is None else "%s_%d" % (self.name, self.index)
+        parent_for_state = self.parent_context.for_state()
+        if parent_for_state:
+            return f"{parent_for_state}|{name}"
+        else:
+            return name
+
+    def __str__(self) -> str:
+        return f"Context[for_state={self.for_state()}]"
+
+    def param_names(self):
+        if not self.allow_unqualified_access:
+            yield self.for_state()
+        else:
+            for parent_context_param in self.parent_context.param_names():
+                if self.index is not None:
+                    yield "%s|%s_%d" % (parent_context_param, self.name, self.index)
+                else:
+                    yield f"{parent_context_param}|{self.name}"
+            if self.index is not None:
+                yield "%s_%d" % (self.name, self.index)
+            else:
+                yield self.name
+
+    def extract_value(self, raw_inputs: ToolSourceTestInputs):
+        for param_name in self.param_names():
+            value = self.__raw_param_found(param_name, raw_inputs)
+            if value:
+                return value
+        return None
+
+    def __raw_param_found(self, param_name: str, raw_inputs: ToolSourceTestInputs):
+        index = None
+        for i, raw_input_dict in enumerate(raw_inputs):
+            if raw_input_dict["name"] == param_name:
+                index = i
+        if index is not None:
+            raw_input_dict = raw_inputs[index]
+            del raw_inputs[index]
+            return raw_input_dict
+        else:
+            return None
+
+
+class RootParamContext:
+    allow_unqualified_access: bool
+
+    def __init__(self, allow_unqualified_access: bool):
+        self.allow_unqualified_access = allow_unqualified_access
+
+    def for_state(self):
+        return ""
+
+    def param_names(self):
+        return []
+
+    def get_index(self):
+        return 0
+
+
+def _process_simple_value(
+    param: InputSource,
+    param_value: Any,
+    required_data_tables: RequiredDataTablesT,
+    required_loc_files: RequiredLocFileT,
+    allow_legacy_test_case_parameters: bool,
+):
+    input_type = param.get("type")
+    if input_type == "select":
+        # Tests may specify values as either raw value or the value
+        # as they appear in the list - the API doesn't and shouldn't
+        # accept the text value - so we need to convert the text
+        # into the form value.
+        def process_param_value(param_value):
+            found_value = False
+            value_for_text = None
+            if allow_legacy_test_case_parameters:
+                # we used to allow selections based on text - this
+                # should really be only based on key
+                static_options = param.parse_static_options()
+                for text, opt_value, _ in static_options:
+                    if param_value == opt_value:
+                        found_value = True
+                    if value_for_text is None and param_value == text:
+                        value_for_text = opt_value
+            dynamic_options = param.parse_dynamic_options()
+            if dynamic_options:
+                data_table_name = dynamic_options.get_data_table_name()
+                index_file_name = dynamic_options.get_index_file_name()
+                if data_table_name:
+                    required_data_tables.append(data_table_name)
+                elif index_file_name:
+                    required_loc_files.append(index_file_name)
+            if not found_value and value_for_text is not None:
+                processed_value = value_for_text
+            else:
+                processed_value = param_value
+            return processed_value
+
+        # Do replacement described above for lists or singleton
+        # values.
+        if isinstance(param_value, list):
+            processed_value = list(map(process_param_value, param_value))
+        else:
+            processed_value = process_param_value(param_value)
+    elif input_type == "boolean":
+        # Like above, tests may use the tool define values of simply
+        # true/false.
+        processed_value = _process_bool_param_value(param, param_value, allow_legacy_test_case_parameters)
+    else:
+        processed_value = param_value
+    return processed_value
+
+
+def _matching_case_for_value(
+    tool_source: ToolSource,
+    cond: InputSource,
+    test_param: InputSource,
+    declared_value: Any,
+    allow_legacy_test_case_parameters: bool,
+):
+    tool_id = tool_source.parse_id()
+    cond_name = cond.parse_name()
+
+    assert test_param.parse_input_type() == "param"
+    test_param_type = test_param.get("type")
+
+    if test_param_type == "boolean":
+        if declared_value is None:
+            # No explicit value for param in test case, determine from default
+            query_value = boolean_is_checked(test_param)
+        else:
+            query_value = _process_bool_param_value(test_param, declared_value, allow_legacy_test_case_parameters)
+
+        def matches_declared_value(case_value):
+            return _process_bool_param_value(test_param, case_value, allow_legacy_test_case_parameters) == query_value
+
+    elif test_param_type == "select":
+        static_options = test_param.parse_static_options()
+        if declared_value is not None:
+            # Test case supplied explicit value to check against.
+
+            def matches_declared_value(case_value):
+                return case_value == declared_value
+
+        elif static_options:
+            # No explicit value in test case, not much to do if options are dynamic but
+            # if static options are available can find the one specified as default or
+            # fallback on top most option (like GUI).
+
+            for name, _, selected in static_options:
+                if selected:
+                    default_option = name
+            else:
+                first_option = static_options[0]
+                first_option_value = first_option[1]
+                default_option = first_option_value
+
+            def matches_declared_value(case_value):
+                return case_value == default_option
+
+        else:
+            # No explicit value for this param and cannot determine a
+            # default - give up. Previously this would just result in a key
+            # error exception.
+            msg = f"Failed to find test parameter value specification required for conditional {cond_name}"
+            raise Exception(msg)
+    else:
+        msg = f"Invalid conditional test type found {test_param_type}"
+        raise Exception(msg)
+
+    # Check the tool's defined cases against predicate to determine
+    # selected or default.
+    for case_when, case_input_sources in cond.parse_when_input_sources():
+        if matches_declared_value(case_when):
+            return case_when, case_input_sources
+    else:
+        msg_template = "%s - Failed to find case matching value (%s) for test parameter specification for conditional %s. Remainder of test behavior is unspecified."
+        msg = msg_template % (tool_id, declared_value, cond_name)
+        log.info(msg)
+    return None
+
+
+def _add_uploaded_dataset(
+    name: str,
+    value: Optional[str],
+    extra: ExtraFileInfoDictT,
+    input_parameter: InputSource,
+    required_files: RequiredFilesT,
+) -> Optional[str]:
+    if value is None:
+        assert (
+            input_parameter.parse_optional() or "composite_data" in extra
+        ), f"{name} is not optional. You must provide a valid filename."
+        return value
+    return require_file(name, value, extra, required_files)
+
+
+def require_file(name: str, value: str, extra: ExtraFileInfoDictT, required_files: RequiredFilesT) -> str:
+    if (value, extra) not in required_files:
+        required_files.append((value, extra))  # these files will be uploaded
+    name_changes = [att for att in extra.get("edit_attributes", []) if att.get("type") == "name"]
+    if name_changes:
+        name_change = name_changes[-1].get("value")  # only the last name change really matters
+        value = str(name_change)  # change value for select to renamed uploaded file for e.g. composite dataset
+    else:
+        for end in [".zip", ".gz"]:
+            if value.endswith(end):
+                value = value[: -len(end)]
+                break
+        value = os.path.basename(value)  # if uploading a file in a path other than root of test-data
+    return value
+
+
+def _process_bool_param_value(
+    input_source: InputSource, param_value: Any, allow_legacy_test_case_parameters: bool
+) -> Any:
+    truevalue, falsevalue = boolean_true_and_false_values(input_source)
+    optional = input_source.parse_optional()
+    return process_bool_param_value(truevalue, falsevalue, optional, param_value, allow_legacy_test_case_parameters)
+
+
+def process_bool_param_value(
+    truevalue: str, falsevalue: str, optional: bool, param_value: Any, allow_legacy_test_case_parameters: bool
+) -> Any:
+    was_list = False
+    if isinstance(param_value, list):
+        was_list = True
+        param_value = param_value[0]
+
+    if allow_legacy_test_case_parameters and truevalue == param_value:
+        processed_value = True
+    elif allow_legacy_test_case_parameters and falsevalue == param_value:
+        processed_value = False
+    else:
+        if optional:
+            processed_value = string_as_bool_or_none(param_value)
+        else:
+            processed_value = string_as_bool(param_value)
+    return [processed_value] if was_list else processed_value
+
+
+def split_if_str(value):
+    split = isinstance(value, str)
+    if split:
+        value = value.split(",")
+    return value
+
+
+# convert the sort internal structure used by the tool library {tag: string, attributes: dict, children: []}
+# into the YAML structure consumed by the test framework {that: string, **atributes}
+def tag_structure_to_that_structure(raw_assert):
+    as_json = {"that": raw_assert["tag"], **raw_assert.get("attributes", {})}
+    children = raw_assert.get("children")
+    if children:
+        as_json["children"] = list(map(tag_structure_to_that_structure, children))
+    return as_json
+
+
+def assertion_xml_els_to_models(asserts_raw) -> relaxed_assertion_list:
+    asserts_raw = __parse_assert_list_from_elem(asserts_raw)
+
+    to_yaml_assertions = []
+    for raw_assert in asserts_raw or []:
+        to_yaml_assertions.append(tag_structure_to_that_structure(raw_assert))
+    return relaxed_assertion_list.model_validate(to_yaml_assertions)
diff --git a/lib/galaxy/tool_util/verify/script.py b/lib/galaxy/tool_util/verify/script.py
index f14f0f68df4f5510f209fac5604d5e3641e240d8..fca086cf1325f51c3ba8b8dcec9ef6edd4f4a917 100644
--- a/lib/galaxy/tool_util/verify/script.py
+++ b/lib/galaxy/tool_util/verify/script.py
@@ -23,10 +23,10 @@ from typing import (
 
 import yaml
 
+from galaxy.tool_util.verify import ToolTestDescriptionDict
 from galaxy.tool_util.verify.interactor import (
     DictClientTestConfig,
     GalaxyInteractorApi,
-    ToolTestDictsT,
     verify_tool,
 )
 
@@ -341,9 +341,11 @@ def build_case_references(
                     test_references.append(test_reference)
     else:
         assert tool_id
-        tool_test_dicts: ToolTestDictsT = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
+        tool_test_dicts: List[ToolTestDescriptionDict] = galaxy_interactor.get_tool_tests(
+            tool_id, tool_version=tool_version
+        )
         for i, tool_test_dict in enumerate(tool_test_dicts):
-            this_tool_version = tool_test_dict.get("tool_version", tool_version)
+            this_tool_version = tool_test_dict.get("tool_version") or tool_version
             this_test_index = i
             if test_index == ALL_TESTS or i == test_index:
                 test_reference = TestReference(tool_id, this_tool_version, this_test_index)
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 7c17312c4f0b43286183513aefa42009b3674faa..b24627fb2b30dae9673a605520b153c291856b0f 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -1,15 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<xs:schema
-        xmlns:xs="http://www.w3.org/2001/XMLSchema"
-        xmlns:gxdocs="http://galaxyproject.org/xml/1.0"
-    elementFormDefault="qualified"
-    attributeFormDefault="unqualified"
-    >
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:gxdocs="http://galaxyproject.org/xml/1.0" elementFormDefault="qualified" attributeFormDefault="unqualified">
   <xs:annotation>
     <xs:appinfo>Galaxy Schema</xs:appinfo>
     <xs:documentation xml:lang="en">A Galaxy XML tool wrapper</xs:documentation>
   </xs:annotation>
-
   <xs:element name="tool">
     <xs:annotation gxdocs:best_practices="tools">
       <xs:documentation xml:lang="en"><![CDATA[
@@ -29,10 +23,14 @@ List of behavior changes associated with profile versions:
 - Disable default tool version of 1.0.0.
 - Use non zero exit code as default stdio error condition (before non-empty stderr).
 
+#### 17.09
+
+- Introduce `provided_metadata_style` with default `"default"`. Restore legacy behavior by setting
+  this to `"legacy"`.
+
 #### 18.01
 
 - Use a separate home directory for each job.
-- Introduce `provided_metadata_style` with default `"default"` before `"legacy"`.
 
 #### 18.09
 
@@ -70,6 +68,10 @@ List of behavior changes associated with profile versions:
 - Do not use Galaxy python environment for `data_source_async` tools.
 - Drop request parameters received by data source tools that are not declared in `<request_param_translation>` section.
 
+### 24.2
+
+- require a valid `data_ref` attribute for `data_column` parameters
+
 ### Examples
 
 A normal tool:
@@ -101,11 +103,11 @@ A ``data_source`` tool contains a few more relevant attributes.
         <xs:element name="macros" type="Macros" minOccurs="0"/>
         <xs:element name="edam_topics" type="EdamTopics" minOccurs="0"/>
         <xs:element name="edam_operations" type="EdamOperations" minOccurs="0"/>
-        <xs:element name="xrefs" type="xrefs" minOccurs="0" />
-        <xs:element name="creator" type="Creator" minOccurs="0" />
+        <xs:element name="xrefs" type="xrefs" minOccurs="0"/>
+        <xs:element name="creator" type="Creator" minOccurs="0"/>
         <xs:element name="requirements" type="Requirements" minOccurs="0"/>
         <xs:element name="required_files" type="RequiredFiles" minOccurs="0"/>
-        <xs:element name="entry_points" type="EntryPoints" minOccurs="0" maxOccurs="1" />
+        <xs:element name="entry_points" type="EntryPoints" minOccurs="0" maxOccurs="1"/>
         <xs:element name="description" type="xs:string" minOccurs="0">
           <xs:annotation gxdocs:best_practices="tool-descriptions">
             <xs:documentation xml:lang="en"><![CDATA[The value is displayed in
@@ -122,7 +124,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
         </xs:element>
         <xs:element name="parallelism" type="Parallelism" minOccurs="0"/>
         <xs:element name="version_command" type="VersionCommand" minOccurs="0"/>
-        <xs:element name="action" type="ToolAction" minOccurs="0" maxOccurs="1" />
+        <xs:element name="action" type="ToolAction" minOccurs="0" maxOccurs="1"/>
         <xs:element name="environment_variables" type="EnvironmentVariables" minOccurs="0" maxOccurs="1"/>
         <xs:element name="command" type="Command" minOccurs="0" maxOccurs="1"/>
         <xs:element name="expression" type="Expression" minOccurs="0" maxOccurs="1"/>
@@ -132,51 +134,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
         <xs:element name="inputs" type="Inputs" minOccurs="0"/>
         <xs:element name="tests" type="Tests" minOccurs="0"/>
         <xs:element name="stdio" type="Stdio" minOccurs="0"/>
-        <xs:element name="help" type="xs:string" minOccurs="0">
-          <xs:annotation gxdocs:best_practices="help-tag">
-            <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html).
-
-tag | details
---- | -------
-``.. class:: warningmark`` | a yellow warning symbol
-``.. class:: infomark`` | a blue information symbol
-``.. image:: path-of-the-file.png :height: 500 :width: 600`` | insert a png file of height 500 and width 600 at this position |
-``**bold**`` | bold
-``*italic*`` | italic
-``*`` | list
-``-`` | list
-``::`` | paragraph
-``-----`` | a horizontal line
-
-### Examples
-
-Show a warning sign to remind users that this tool accept fasta format files only, followed by an example of the query sequence and a figure.
-
-```xml
-<help>
-
-.. class:: warningmark
-
-'''TIP''' This tool requires *fasta* format.
-
-----
-
-'''Example'''
-
-Query sequence::
-    >seq1
-    ATCG...
-
-.. image:: my_figure.png
-    :height: 500
-    :width: 600
-
-</help>
-```
-
-]]></xs:documentation>
-          </xs:annotation>
-        </xs:element>
+        <xs:element name="help" type="Help" minOccurs="0" maxOccurs="1"/>
         <xs:element name="code" type="Code" minOccurs="0"/>
         <xs:element name="uihints" type="UIhints" minOccurs="0"/>
         <xs:element name="options" type="Options" minOccurs="0"/>
@@ -284,7 +242,6 @@ this attribute defined the HTTP request method to use when communicating with an
       </xs:attribute>
     </xs:complexType>
   </xs:element>
-
   <xs:complexType name="Macros">
     <xs:annotation>
       <xs:documentation xml:lang="en">Frequently, tools may require the same XML
@@ -306,8 +263,7 @@ Example:
 <macros>
     <import>macros.xml</import>
 </macros>
-````]]>
-          </xs:documentation>
+````]]></xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="token" type="xs:anyType" minOccurs="0" maxOccurs="unbounded">
@@ -327,14 +283,12 @@ Usage example:
 <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mypackage</requirement>
 </requirements>
-````]]>
-          </xs:documentation>
+````]]></xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="xml" type="xs:anyType" minOccurs="0" maxOccurs="unbounded">
         <xs:annotation>
-          <xs:documentation xml:lang="en">
-            <![CDATA[
+          <xs:documentation xml:lang="en"><![CDATA[
 The ``xml`` element, inside macros, allows defining a named XML fragment that can be reused (expanded) anywhere in the tool or tools that use the macro.
 
 Definition example:
@@ -357,20 +311,16 @@ Usage example:
       </xs:element>
       <xs:element name="macro" type="xs:anyType" minOccurs="0" maxOccurs="unbounded">
         <xs:annotation>
-          <xs:documentation xml:lang="en">
-            <![CDATA[
+          <xs:documentation xml:lang="en"><![CDATA[
 A generalisation for macro tokens, templates and xml macros, i.e.
 `<macro name="an_xml_macro" type="xml">` is identical to `<xml name="an_xml_macro">`,
 `<macro name="a_template" type="template">` is identical to `<template name="a_template">`, and
 `<macro name="a_token" type="xml">` is identical to `<token name="a_token">`.
-
-Note that 
        ]]></xs:documentation>
         </xs:annotation>
       </xs:element>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="EntryPoints">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -385,7 +335,6 @@ to a tool.
       <xs:element name="entry_point" type="EntryPoint" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="EntryPoint" mixed="true">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -409,24 +358,24 @@ to provide access to graphical tools in real-time.
       <xs:element name="port" type="EntryPointPort" minOccurs="1" maxOccurs="1"/>
       <xs:element name="url" type="EntryPointURL" minOccurs="0" maxOccurs="1"/>
     </xs:sequence>
-        <xs:attribute name="name" type="xs:string" use="required">
-          <xs:annotation>
-            <xs:documentation xml:lang="en">The name of the entry point.</xs:documentation>
-          </xs:annotation>
-        </xs:attribute>
-        <xs:attribute name="label" type="xs:string" use="optional">
-          <xs:annotation>
-            <xs:documentation xml:lang="en">A unique label to identify the entry point. Used by interactive client tools to connect.</xs:documentation>
-          </xs:annotation>
-        </xs:attribute>
-        <xs:attribute name="requires_domain" type="PermissiveBoolean" default="true">
-          <xs:annotation>
-            <xs:documentation xml:lang="en">Whether domain-based proxying is required for the entry point. Default is True.</xs:documentation>
-          </xs:annotation>
-        </xs:attribute>
-        <xs:attribute name="requires_path_in_url" type="PermissiveBoolean" default="false">
-          <xs:annotation>
-            <xs:documentation xml:lang="en"><![CDATA[
+    <xs:attribute name="name" type="xs:string" use="required">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">The name of the entry point.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="label" type="xs:string" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">A unique label to identify the entry point. Used by interactive client tools to connect.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="requires_domain" type="PermissiveBoolean" default="true">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Whether domain-based proxying is required for the entry point. Default is True.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="requires_path_in_url" type="PermissiveBoolean" default="false">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
 Whether the InteractiveTool proxy will add the entry point path to the URL provided to the interactive tool. Only
 relevant when path-based proxying is configured (``requires_domain=False``). A value of False implies that the web service
 for the interactive tool fully operates with relative links. A value of True implies that the unique entry point path,
@@ -435,21 +384,19 @@ into an environment variable by setting the attribute ``inject="entry_point_path
 Alternatively, the attribute ``requires_path_in_header_named`` can be set to provide the path in the specified HTTP header.
 The entry point path should in any case be used to configure the web service in the interactive tool to serve the content
 from the provided URL path. Default value of ``requires_path_in_url`` is False.
-]]>
-            </xs:documentation>
-          </xs:annotation>
-        </xs:attribute>
-        <xs:attribute name="requires_path_in_header_named" type="xs:string" default="">
-          <xs:annotation>
-            <xs:documentation xml:lang="en"><![CDATA[
+]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="requires_path_in_header_named" type="xs:string" default="">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
 Whether the InteractiveTool proxy will add the entry point path to an HTTP header. An empty string as value (default) means
 that the path will not be provided in an HTTP header. Any other string value will define the name of the HTTP header
 where the path will be injected by the proxy. See the documentation of ``requires_path_in_url`` for more information.
 Default value of ``requires_path_in_header_named`` is False.
-]]>
-            </xs:documentation>
-          </xs:annotation>
-        </xs:attribute>
+]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
   </xs:complexType>
   <xs:complexType name="EntryPointPort" mixed="true">
     <xs:annotation>
@@ -469,7 +416,6 @@ This tag set is contained within the ``<entry_point>`` tag set. It contains the
 ]]></xs:documentation>
     </xs:annotation>
   </xs:complexType>
-
   <xs:complexType name="ToolAction">
     <xs:annotation>
       <xs:documentation xml:lang="en">Describe the backend Python action to execute for this Galaxy tool.</xs:documentation>
@@ -481,7 +427,6 @@ This tag set is contained within the ``<entry_point>`` tag set. It contains the
     <xs:attribute name="class" type="xs:string" use="required">
     </xs:attribute>
   </xs:complexType>
-
   <xs:attributeGroup name="Thing">
     <xs:attribute name="name" type="xs:string" use="optional">
       <xs:annotation>
@@ -490,7 +435,7 @@ This tag set is contained within the ``<entry_point>`` tag set. It contains the
     </xs:attribute>
     <xs:attribute name="url" type="xs:string" use="optional">
       <xs:annotation>
-      <xs:documentation xml:lang="en">[schema.org/url](https://schema.org/url)</xs:documentation>
+        <xs:documentation xml:lang="en">[schema.org/url](https://schema.org/url)</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="identifier" type="xs:string" use="optional">
@@ -529,7 +474,6 @@ This tag set is contained within the ``<entry_point>`` tag set. It contains the
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
-
   <xs:complexType name="Person">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -563,7 +507,6 @@ Describes a person. Tries to stay close to [schema.org/Person](https://schema.or
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Organization">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -572,14 +515,12 @@ Describes an organization. Tries to stay close to [schema.org/Organization](http
     </xs:annotation>
     <xs:attributeGroup ref="Thing"/>
   </xs:complexType>
-
   <xs:group name="PersonOrOrganization">
     <xs:choice>
-      <xs:element name="person" type="Person" />
-      <xs:element name="organization" type="Organization" />
+      <xs:element name="person" type="Person"/>
+      <xs:element name="organization" type="Organization"/>
     </xs:choice>
   </xs:group>
-
   <xs:complexType name="Creator">
     <xs:annotation>
       <xs:documentation xml:lang="en">The creator(s) of this work. See [schema.org/creator](https://schema.org/creator).</xs:documentation>
@@ -588,7 +529,6 @@ Describes an organization. Tries to stay close to [schema.org/Organization](http
       <xs:group ref="PersonOrOrganization" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="RequiredFiles">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -615,7 +555,6 @@ practice.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:simpleType name="RequiredFileReferenceType">
     <xs:annotation>
       <xs:documentation xml:lang="en">How are files referenced in RequiredFileIncludes and RequiredFileExcludes. Paths are matched relative to the tool directory. `literal` must match the filename exactly. `prefix` will match paths based on their start. `glob` and `regex` use patterns to match files.</xs:documentation>
@@ -627,7 +566,6 @@ practice.
       <xs:enumeration value="regex"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:complexType name="RequiredFileInclude">
     <xs:annotation>
       <xs:documentation xml:lang="en">Describe files to include when relocating tool directory for remote execution.</xs:documentation>
@@ -643,7 +581,6 @@ practice.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="RequiredFileExclude">
     <xs:annotation>
       <xs:documentation xml:lang="en">Describe files to exclude when relocating tool directory for remote execution.</xs:documentation>
@@ -659,7 +596,6 @@ practice.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Requirements">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -739,6 +675,12 @@ resolver.
     </xs:simpleContent>
   </xs:complexType>
   <xs:complexType name="Resource">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
+Allows to describe a resource requirement of a tool. At the moment this tag is mostly descriptive,
+It can be used by dynamic job rules and serves to guide Galaxy admins.
+]]></xs:documentation>
+    </xs:annotation>
     <xs:simpleContent>
       <xs:extension base="xs:string">
         <xs:attribute name="type" type="ResourceType" use="required">
@@ -783,7 +725,69 @@ Read more about configuring Galaxy to run Docker jobs
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
+  <xs:simpleType name="HelpFormatType">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">Document type of tool help</xs:documentation>
+    </xs:annotation>
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="restructuredtext"/>
+      <xs:enumeration value="markdown"/>
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:complexType name="Help">
+    <xs:annotation gxdocs:best_practices="help-tag">
+      <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html).
+
+tag | details
+--- | -------
+``.. class:: warningmark`` | a yellow warning symbol
+``.. class:: infomark`` | a blue information symbol
+``.. image:: path-of-the-file.png :height: 500 :width: 600`` | insert a png file of height 500 and width 600 at this position |
+``**bold**`` | bold
+``*italic*`` | italic
+``*`` | list
+``-`` | list
+``::`` | paragraph
+``-----`` | a horizontal line
+
+### Examples
+
+Show a warning sign to remind users that this tool accept fasta format files only, followed by an example of the query sequence and a figure.
+
+```xml
+<help>
+
+.. class:: warningmark
+
+'''TIP''' This tool requires *fasta* format.
+
+----
+
+'''Example'''
+
+Query sequence::
+    >seq1
+    ATCG...
 
+.. image:: my_figure.png
+    :height: 500
+    :width: 600
+
+</help>
+```
+
+]]></xs:documentation>
+    </xs:annotation>
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute name="format" type="HelpFormatType">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Valid values are ``restructuredtext`` and ``markdown``</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+      </xs:extension>
+    </xs:simpleContent>
+  </xs:complexType>
   <xs:complexType name="Parallelism">
     <xs:annotation>
       <xs:documentation xml:lang="en">Documentation for Parallelism</xs:documentation>
@@ -987,7 +991,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
 The content of ``stdout`` and ``stderr`` are strings containing the output of the process.
 
 ]]></xs:documentation>
-
     </xs:annotation>
     <xs:sequence>
       <xs:element name="hook" type="CodeHook" minOccurs="0" maxOccurs="unbounded"/>
@@ -1018,7 +1021,6 @@ The content of ``stdout`` and ``stderr`` are strings containing the output of th
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Options">
     <xs:annotation>
       <xs:documentation xml:lang="en">This directive is used to specify some rarely modified options.</xs:documentation>
@@ -1034,32 +1036,29 @@ The content of ``stdout`` and ``stderr`` are strings containing the output of th
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="TracksterConf">
     <xs:annotation>
       <xs:documentation xml:lang="en">This directive is used to specify some rarely modified trackster options.</xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:element name="action" type="TracksterAction" minOccurs="0" maxOccurs="unbounded" />
+      <xs:element name="action" type="TracksterAction" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="TracksterAction">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:attribute name="name" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en"></xs:documentation>
+        <xs:documentation xml:lang="en"/>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="output_name" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en"></xs:documentation>
+        <xs:documentation xml:lang="en"/>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Tests">
     <xs:annotation gxdocs:best_practices="tests">
       <xs:documentation xml:lang="en"><![CDATA[
@@ -1082,7 +1081,6 @@ documentation or the much older wiki content for
       <xs:element name="test" type="Test" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="Test">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -1197,10 +1195,10 @@ that at least one of the assumptions of the test is not met. This is most useful
   </xs:complexType>
   <xs:group name="TestParamElement">
     <xs:choice>
-      <xs:element name="param" type="TestParam" />
-      <xs:element name="repeat" type="TestRepeat" />
-      <xs:element name="conditional" type="TestConditional" />
-      <xs:element name="section" type="TestSection" />
+      <xs:element name="param" type="TestParam"/>
+      <xs:element name="repeat" type="TestRepeat"/>
+      <xs:element name="conditional" type="TestConditional"/>
+      <xs:element name="section" type="TestSection"/>
       <xs:element name="output" type="TestOutput" minOccurs="0" maxOccurs="unbounded"/>
       <xs:element name="output_collection" type="TestOutputCollection"/>
       <xs:element name="assert_command" type="TestAssertions">
@@ -1278,11 +1276,10 @@ contains a test case demonstrating this block. This test case appears below:
 </test>
 ```
 
-]]>
-      </xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -1424,7 +1421,7 @@ shown below.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -1500,7 +1497,7 @@ allowing multiple instances of a single repeat to be specified.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -1552,9 +1549,9 @@ select an option for a test.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:element name="collection" type="TestCollection" minOccurs="0" maxOccurs="1" />
-      <xs:element name="composite_data" type="TestCompositeData" minOccurs="0" maxOccurs="unbounded" />
-      <xs:element name="metadata" type="TestParamMetadata" minOccurs="0" maxOccurs="unbounded" />
+      <xs:element name="collection" type="TestCollection" minOccurs="0" maxOccurs="1"/>
+      <xs:element name="composite_data" type="TestCompositeData" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="metadata" type="TestParamMetadata" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -1575,7 +1572,7 @@ used to load typed parameters. This string will be loaded as JSON and its type w
 attempt to be preserved through API requests to Galaxy.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="ftype" type="xs:string">
+    <xs:attribute name="ftype" type="Format">
       <xs:annotation>
         <xs:documentation xml:lang="en">This attribute name should be included
 only with parameters of ``type`` ``data`` for the tool. If this
@@ -1583,6 +1580,13 @@ attribute name is not included, the functional test framework will attempt to
 determine the data type for the input dataset using the data type sniffers.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
+    <xs:attribute name="class" type="Class">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">This attribute name should be included
+only with parameter of ``type`` ``data`` for the tool. If this attribute name is not included the test framework will
+assume that the dataset is a file. Set this to ``Directory`` to interpret and upload the value as a directory.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
     <xs:attribute name="dbkey" type="xs:string">
       <xs:annotation>
         <xs:documentation xml:lang="en">Specifies a ``dbkey`` value for the
@@ -1686,7 +1690,7 @@ by ``file`` using the ``compare`` attribute:
         ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="TestOutputElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="TestOutputElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <!-- TODO: This would be more percise if this was required if at the top-level. -->
     <xs:attribute name="name" type="xs:string">
@@ -1720,7 +1724,7 @@ generated as JSON. This can be useful for testing tool outputs that are not file
 ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="ftype" type="xs:string">
+    <xs:attribute name="ftype" type="Format">
       <xs:annotation>
         <xs:documentation xml:lang="en"><![CDATA[
 
@@ -1894,7 +1898,7 @@ The following demonstrates verifying XML content with XPath-like expressions.
         </xs:annotation>
       </xs:element>
       <!-- TODO: This would be more percise if this was only allowed at the top-level. -->
-      <xs:element name="extra_files" type="TestExtraFile" />
+      <xs:element name="extra_files" type="TestExtraFile"/>
       <xs:element name="metadata" type="TestOutputMetadata"/>
     </xs:choice>
   </xs:group>
@@ -2158,7 +2162,6 @@ This value is the same as the value of the ``name`` attribute of the
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="TestAssertions">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -2172,372 +2175,575 @@ can be found below.
 The implementation of these tags are simply Python functions defined in the
 [/lib/galaxy/tool_util/verify/asserts](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tool_util/verify/asserts)
 module.
-]]>
-      </xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:choice minOccurs="0" maxOccurs="unbounded">
-      <xs:group ref="TestAssertionsGeneral" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsText" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsTabular" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsArchive" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsXml" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsJson" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsH5" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsImage" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:group ref="TestAssertion"/>
     </xs:choice>
   </xs:complexType>
-  <xs:group name="TestAssertionsGeneral">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[General assertions]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_size" type="AssertHasSize"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsText">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for text data]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_text" type="AssertHasText"/>
-      <xs:element name="not_has_text" type="AssertNotHasText"/>
-      <xs:element name="has_text_matching" type="AssertHasTextMatching"/>
-      <xs:element name="has_line" type="AssertHasLine"/>
-      <xs:element name="has_line_matching" type="AssertHasLineMatching"/>
-      <xs:element name="has_n_lines" type="AssertHasNLines"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsTabular">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for tabular data]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_n_columns" type="AssertHasNColumns"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsArchive">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for archives (zip/tar)]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_archive_member" type="AssertHasArchiveMember"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsXml">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for XML data]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="is_valid_xml" type="AssertIsValidXML"/>
-      <xs:element name="xml_element" type="AssertXMLElement"/>
-      <xs:element name="has_element_with_path" type="AssertHasElementWithPath"/>
-      <xs:element name="has_n_elements_with_path" type="AssertHasNElementsWithPath"/>
-      <xs:element name="element_text_matches" type="AssertElementTextMatches"/>
-      <xs:element name="element_text_is" type="AssertElementTextIs"/>
-      <xs:element name="attribute_matches" type="AssertAttributeMatches"/>
-      <xs:element name="attribute_is" type="AssertAttributeIs"/>
-      <xs:element name="element_text" type="AssertElementText"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsJson">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for JSON data]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_json_property_with_value" type="AssertHasJsonPropertyWithValue"/>
-      <xs:element name="has_json_property_with_text" type="AssertHasJsonPropertyWithText"/>
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsImage">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for image data]]></xs:documentation>
-    </xs:annotation>
-    <xs:choice>
-      <xs:element name="has_image_width" type="AssertHasImageWidth" />
-      <xs:element name="has_image_height" type="AssertHasImageHeight" />
-      <xs:element name="has_image_channels" type="AssertHasImageChannels" />
-      <xs:element name="has_image_mean_intensity" type="AssertHasImageMeanIntensity" />
-      <xs:element name="has_image_center_of_mass" type="AssertHasImageCenterOfMass" />
-      <xs:element name="has_image_n_labels" type="AssertHasImageNLabels" />
-      <xs:element name="has_image_mean_object_size" type="AssertHasImageMeanObjectSize" />
-    </xs:choice>
-  </xs:group>
-  <xs:group name="TestAssertionsH5">
+  <xs:group name="TestAssertion">
     <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[Assertions for H5 data]]></xs:documentation>
+      <xs:documentation xml:lang="en">An individual test assertion definition.</xs:documentation>
     </xs:annotation>
     <xs:choice>
-      <xs:element name="has_h5_keys" type="AssertHasH5Keys"/>
-      <xs:element name="has_h5_attribute" type="AssertHasH5Attribute"/>
-    </xs:choice>
-  </xs:group>
-  <xs:complexType name="AssertHasSize">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output has a specific size (in bytes) of ``value`` plus minus
-``delta``, e.g. ``<has_size value="10000" delta="100" />``.
-Alternatively the range of the expected size can be specified by ``min`` and/or
-``max``.
+      <!--The following block and all children are auto-generated - please do not modify.-->
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_has_line-->
+      <xs:element name="has_line">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains the line specified by the
+argument line. The exact number of occurrences can be optionally
+specified by the argument n
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="size" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="value" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">An outdated alias for `size`</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed size difference (default is 0). The observed size has to be in the range ``value +- delta``. Can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum expected size, can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum expected size, can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasText">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the specified ``text`` appears in the output (e.g. ``<has_text
-text="chr7">``). If the ``text`` is expected to occur a particular number of
-times, this value can be specified using ``n``. Optionally also with a certain
-``delta``. Alternatively the range of expected occurences can be specified by
-``min`` and/or ``max``.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="text" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Text to check for</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertNotHasText">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the specified ``text`` does not appear in the output (e.g. ``<not_has_text text="chr8" />``).
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="line" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The full line of text to search for in the output.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_has_line_matching-->
+      <xs:element name="has_line_matching">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains a line matching the
+regular expression specified by the argument expression. If n is given
+the assertion checks for exactly n occurences.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="text" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Text to check for</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasTextMatching">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts text matching the specified regular expression (``expression``) appears
-in the output (e.g. ``<has_text_matching expression="1274\d+53" />`` ). If the
-regular expression is expected to match a particular number of times, this value
-can be specified using ``n``.  Note only non-overlapping occurences are counted.
-Optionally also with a certain ``delta``. Alternatively the range of expected
-occurences can be specified by ``min`` and/or ``max``.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="expression" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Regular expression to check for</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasLine">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts a line matching the specified string (``line``) appears in the output
-(e.g. ``<has_line line="A full example line." />``). If the ``line`` is expected
-to occur a particular number of times, this value can be specified using ``n``.
-Optionally also with a certain ``delta``. Alternatively the range of expected
-occurences can be specified by ``min`` and/or ``max``.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="line" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The line to check for</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasNLines">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts that an output contains ``n`` lines, allowing for a difference of
-``delta`` (default is 0), e.g. ``<has_n_lines n="3" delta="1"/>``.
-Alternatively the range of expected occurences can be specified by ``min``
-and/or ``max``.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="expression" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The regular expressions to attempt match in the output.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_has_n_lines-->
+      <xs:element name="has_n_lines">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains ``n`` lines allowing
+for a difference in the number of lines (delta)
+or relative differebce in the number of lines
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasLineMatching">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts a line matching the specified regular expression (``expression``)
-appears in the output (e.g. ``<has_line_matching expression=".*\s+127489808\s+127494553" />``).
-If a particular number of matching lines is expected, this value can be
-specified using ``n``.  Optionally also with ``delta``. Alternatively the range
-of expected occurences can be specified by ``min`` and/or ``max``.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="expression" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Regular expression to check for</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasNColumns">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts tabular output (actually only the first line) contains the specified
-number (``n``) of columns (e.g. ``<has_n_columns n="3"/>``) optionally also with
-``delta``. Alternatively the range of expected occurences can be specified by
-``min`` and/or ``max``.  Optionally a column separator (``sep``, default is
-``\t``) `and comment character(s) can be specified (``comment``, default is
-empty string), then the first non-comment line is used for determining the
-number of columns.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-    <xs:attribute name="sep" type="xs:string" default="&#009;">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Separator defining columns, default: tab</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="comment" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Comment character(s) used to skip comment lines (which should not be used for counting columns)</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasArchiveMember">
-    <xs:annotation>
-        <xs:documentation xml:lang="en"><![CDATA[
-This tag allows to check if ``path`` is contained in a compressed file. The path
-is a regular expression that is matched against the full paths of the objects in
-the compressed file (remember that "matching" means it is checked if a prefix of
-the full path of an archive member is described by the regular expression).
-Valid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that
-depending on the archive creation method:
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_has_text-->
+      <xs:element name="has_text">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts specified output contains the substring specified by
+the argument text. The exact number of occurrences can be
+optionally specified by the argument n
 
-- full paths of the members may be prefixed with ``./``
-- directories may be treated as empty files
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="text" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The text to search for in the output.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_has_text_matching-->
+      <xs:element name="has_text_matching">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output contains text matching the
+regular expression specified by the argument expression.
+If n is given the assertion checks for exacly n (nonoverlapping)
+occurences.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="expression" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The regular expressions to attempt match in the output.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.text.assert_not_has_text-->
+      <xs:element name="not_has_text">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts specified output does not contain the substring
+specified by the argument text
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="text" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The text to search for in the output.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.tabular.assert_has_n_columns-->
+      <xs:element name="has_n_columns">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts tabular output  contains the specified
+number (``n``) of columns.
+
+For instance, ``<has_n_columns n="3"/>``. The assertion tests only the first line.
+Number of columns can optionally also be specified with ``delta``. Alternatively the
+range of expected occurences can be specified by ``min`` and/or ``max``.
+
+Optionally a column separator (``sep``, default is ``       ``) `and comment character(s)
+can be specified (``comment``, default is empty string). The first non-comment
+line is used for determining the number of columns.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="sep" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Separator defining columns, default: tab]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="comment" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Comment character(s) used to skip comment lines (which should not be used for counting columns)]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_attribute_is-->
+      <xs:element name="attribute_is">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified
+XPath-like ``path`` is the specified ``text``.
+
+For example:
 
 ```xml
-<has_archive_member path="./path/to/my-file.txt"/>
+<attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
 ```
 
-With ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of
-archive members matching ``path`` can be expressed. The following could be used,
-e.g., to assert an archive containing n&plusmn;1 elements out of which at least
-4 need to have a ``txt`` extension.
+The assertion implicitly also asserts that an element matching ``path`` exists.
+With ``negate`` the result of the assertion (on the equality) can be inverted (the
+implicit assertion on the existence of the path is not affected).
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="attribute" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The XML attribute name to test against from the target XML element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="text" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The expected attribute value to test against on the target XML element]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_attribute_matches-->
+      <xs:element name="attribute_matches">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified
+XPath-like ``path`` matches the regular expression specified by ``expression``.
+
+For example:
 
 ```xml
-<has_archive_member path=".*" n="10" delta="1"/>
-<has_archive_member path=".*\.txt" min="4"/>
+<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />
 ```
 
-In addition the tag can contain additional assertions as child elements about
-the first member in the archive matching the regular expression ``path``. For
-instance
+The assertion implicitly also asserts that an element matching ``path`` exists.
+With ``negate`` the result of the assertion (on the matching) can be inverted (the
+implicit assertion on the existence of the path is not affected).
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="attribute" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The XML attribute name to test against from the target XML element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="expression" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The regular expressions to apply against the named attribute on the target XML element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_element_text-->
+      <xs:element name="element_text">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[This tag allows the developer to recurisively specify additional assertions as
+child elements about just the text contained in the element specified by the
+XPath-like ``path``, e.g.
 
 ```xml
-<has_archive_member path=".*/my-file.txt">
-  <not_has_text text="EDK72998.1"/>
-</has_archive_member>
+<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
+  <not_has_text text="EDK72998.1" />
+</element_text>
 ```
 
-If the ``all`` attribute is set to ``true`` then all archive members are subject
-to the assertions. Note that, archive members matching the ``path`` are sorted
-alphabetically.
+The assertion implicitly also asserts that an element matching ``path`` exists.
+With ``negate`` the result of the implicit assertions can be inverted.
+The sub-assertions, which have their own ``negate`` attribute, are not affected
+by ``negate``.
 
-The ``negate`` attribute of the ``has_archive_member`` assertion only affects
-the asserts on the presence and number of matching archive members, but not any
-sub-assertions (which can offer the ``negate`` attribute on their own).  The
-check if the file is an archive at all, which is also done by the function, is
-not affected.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:sequence>
+            <xs:group ref="TestAssertion" minOccurs="1" maxOccurs="unbounded"/>
+          </xs:sequence>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_element_text_is-->
+      <xs:element name="element_text_is">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path`` is
+the specified ``text``.
 
-$attribute_list::5
-]]></xs:documentation>
-    </xs:annotation>
-    <xs:sequence>
-      <xs:group ref="TestAssertionsGeneral" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsText" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsTabular" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsJson" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsXml" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsH5" minOccurs="0" maxOccurs="unbounded"/>
-      <xs:group ref="TestAssertionsImage" minOccurs="0" maxOccurs="unbounded"/>
-    </xs:sequence>
-    <xs:attribute name="path" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The regular expression specifying the archive member.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="all" type="PermissiveBoolean" default="false">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first </xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-  </xs:complexType>
-  <xs:complexType name="AssertIsValidXML">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).
+For example:
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-  </xs:complexType>
-  <xs:complexType name="AssertXMLElement">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Assert if the XML file contains element(s) or tag(s) with the specified
+```xml
+<element_text_is path="BlastOutput_program" text="blastp" />
+```
+
+The assertion implicitly also asserts that an element matching ``path`` exists.
+With ``negate`` the result of the assertion (on the equality) can be inverted (the
+implicit assertion on the existence of the path is not affected).
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="text" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The expected element text (body of the XML tag) to test against on the target XML element]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_element_text_matches-->
+      <xs:element name="element_text_matches">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path``
+matches the regular expression defined by ``expression``.
+
+For example:
+
+```xml
+<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>
+```
+
+The assertion implicitly also asserts that an element matching ``path`` exists.
+With ``negate`` the result of the assertion (on the matching) can be inverted (the
+implicit assertion on the existence of the path is not affected).
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="expression" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The regular expressions to apply against the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_has_element_with_path-->
+      <xs:element name="has_element_with_path">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML output contains at least one element (or tag) with the specified
+XPath-like ``path``, e.g.
+
+```xml
+<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
+```
+
+With ``negate`` the result of the assertion can be inverted.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_has_n_elements_with_path-->
+      <xs:element name="has_n_elements_with_path">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or
+tags) with the specified XPath-like ``path``.
+
+For example:
+
+```xml
+<has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
+```
+
+Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
+can be used to specify the range of the expected number of occurences.
+With ``negate`` the result of the assertion can be inverted.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_is_valid_xml-->
+      <xs:element name="is_valid_xml">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType/>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.xml.assert_xml_element-->
+      <xs:element name="xml_element">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Assert if the XML file contains element(s) or tag(s) with the specified
 [XPath-like ``path``](https://lxml.de/xpathxslt.html).  If ``n`` and ``delta``
 or ``min`` and ``max`` are given also the number of occurences is checked.
 
@@ -2569,593 +2775,685 @@ If ``all`` is ``true`` then the sub assertions are checked for all occurences.
 Note that all other XML assertions can be expressed by this assertion (Galaxy
 also implements the other assertions by calling this one).
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attribute name="all" type="PermissiveBoolean" default="false">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="attribute" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The name of the attribute to apply sub-assertion on. If not given then the element text is used</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasElementWithPath">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the XML output contains at least one element (or tag) with the specified
-XPath-like ``path``, e.g.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:sequence>
+            <xs:group ref="TestAssertion" minOccurs="0" maxOccurs="unbounded"/>
+          </xs:sequence>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The Python xpath-like expression to find the target element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="attribute" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The XML attribute name to test against from the target XML element.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="all" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first ]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.json.assert_has_json_property_with_text-->
+      <xs:element name="has_json_property_with_text">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the JSON document contains a property or key with the specified text (i.e. string) value.
 
 ```xml
-<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />
+<has_json_property_with_text property="color" text="red" />
 ```
 
-With ``negate`` the result of the assertion can be inverted.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasNElementsWithPath">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the XML output contains the specified number (``n``, optionally with ``delta``) of elements (or
-tags) with the specified XPath-like ``path``, e.g.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="property" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The property name to search the JSON document for.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="text" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The expected text value of the target JSON attribute.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.json.assert_has_json_property_with_value-->
+      <xs:element name="has_json_property_with_value">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the JSON document contains a property or key with the specified JSON value.
 
 ```xml
-<has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />
+<has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />
 ```
 
-Alternatively to ``n`` and ``delta`` also the ``min`` and ``max`` attributes
-can be used to specify the range of the expected number of occurences.
-With ``negate`` the result of the assertion can be inverted.
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attributeGroup ref="AssertAttributeN"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertElementTextMatches">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the text of the XML element with the specified XPath-like ``path``
-matches the regular expression defined by ``expression``, e.g.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="property" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The property name to search the JSON document for.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="value" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The expected JSON value of the target JSON attribute (as a JSON encoded string).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.hdf5.assert_has_h5_attribute-->
+      <xs:element name="has_h5_attribute">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.
 
 ```xml
-<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>
+<has_h5_attribute key="nchroms" value="15" />
 ```
 
-The assertion implicitly also asserts that an element matching ``path`` exists.
-With ``negate`` the result of the assertion (on the matching) can be inverted (the
-implicit assertion on the existence of the path is not affected).
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attribute name="expression" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The regular expression to use.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertElementTextIs">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the text of the XML element with the specified XPath-like ``path`` is
-the specified ``text``, e.g.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="key" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[HDF5 attribute to check value of.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="value" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected value of HDF5 attribute to check.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.hdf5.assert_has_h5_keys-->
+      <xs:element name="has_h5_keys">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified HDF5 output has the given keys.
 
-```xml
-<element_text_is path="BlastOutput_program" text="blastp" />
-```
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="keys" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[HDF5 attributes to check value of as a comma-separated string.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.archive.assert_has_archive_member-->
+      <xs:element name="has_archive_member">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[This tag allows to check if ``path`` is contained in a compressed file.
 
-The assertion implicitly also asserts that an element matching ``path`` exists.
-With ``negate`` the result of the assertion (on the equality) can be inverted (the
-implicit assertion on the existence of the path is not affected).
+The path is a regular expression that is matched against the full paths of the objects in
+the compressed file (remember that "matching" means it is checked if a prefix of
+the full path of an archive member is described by the regular expression).
+Valid archive formats include ``.zip``, ``.tar``, and ``.tar.gz``. Note that
+depending on the archive creation method:
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attribute name="text" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Text to check for.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertAttributeMatches">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the XML ``attribute`` for the element (or tag) with the specified
-XPath-like ``path`` matches the regular expression specified by ``expression``, e.g.
+- full paths of the members may be prefixed with ``./``
+- directories may be treated as empty files
 
 ```xml
-<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />
+<has_archive_member path="./path/to/my-file.txt"/>
 ```
 
-The assertion implicitly also asserts that an element matching ``path`` exists.
-With ``negate`` the result of the assertion (on the matching) can be inverted (the
-implicit assertion on the existence of the path is not affected).
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attribute name="expression" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The regular expression to use.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertAttributeIs">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the XML ``attribute`` for the element (or tag) with the specified
-XPath-like ``path`` is the specified ``text``, e.g.
+With ``n`` and ``delta`` (or ``min`` and ``max``) assertions on the number of
+archive members matching ``path`` can be expressed. The following could be used,
+e.g., to assert an archive containing n&plusmn;1 elements out of which at least
+4 need to have a ``txt`` extension.
 
 ```xml
-<attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />
+<has_archive_member path=".*" n="10" delta="1"/>
+<has_archive_member path=".*\.txt" min="4"/>
 ```
 
-The assertion implicitly also asserts that an element matching ``path`` exists.
-With ``negate`` the result of the assertion (on the equality) can be inverted (the
-implicit assertion on the existence of the path is not affected).
-
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attribute name="text" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Text to check for.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertElementText">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-This tag allows the developer to recurisively specify additional assertions as
-child elements about just the text contained in the element specified by the
-XPath-like ``path``, e.g.
+In addition the tag can contain additional assertions as child elements about
+the first member in the archive matching the regular expression ``path``. For
+instance
 
 ```xml
-<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def">
-  <not_has_text text="EDK72998.1" />
-</element_text>
+<has_archive_member path=".*/my-file.txt">
+  <not_has_text text="EDK72998.1"/>
+</has_archive_member>
 ```
 
-The assertion implicitly also asserts that an element matching ``path`` exists.
-With ``negate`` the result of the implicit assertions can be inverted.
-The sub-assertions, which have their own ``negate`` attribute, are not affected
-by ``negate``.
+If the ``all`` attribute is set to ``true`` then all archive members are subject
+to the assertions. Note that, archive members matching the ``path`` are sorted
+alphabetically.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:sequence>
-      <xs:group ref="TestAssertionsText" minOccurs="1" maxOccurs="unbounded"/>
-    </xs:sequence>
-    <xs:attributeGroup ref="AssertAttributePath"/>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageWidth">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image and has a specific width (in pixels),
-plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
-Alternatively the range of the expected width can be specified by ``min`` and/or ``max``.
+The ``negate`` attribute of the ``has_archive_member`` assertion only affects
+the asserts on the presence and number of matching archive members, but not any
+sub-assertions (which can offer the ``negate`` attribute on their own).  The
+check if the file is an archive at all, which is also done by the function, is
+not affected.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="width" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Expected width of the image (in pixels).`</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum allowed width of the image (in pixels).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed width of the image (in pixels).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageHeight">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image and has a specific height (in pixels),
-plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
-Alternatively the range of the expected height can be specified by ``min`` and/or ``max``.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:sequence>
+            <xs:group ref="TestAssertion" minOccurs="0" maxOccurs="unbounded"/>
+          </xs:sequence>
+          <xs:attribute name="path" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The regular expression specifying the archive member.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="all" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Check the sub-assertions for all paths matching the path. Default: false, i.e. only the first]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.size.assert_has_size-->
+      <xs:element name="has_size">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output has a size of the specified value
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="height" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Expected height of the image (in pixels).`</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum allowed height of the image (in pixels).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed height of the image (in pixels).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageChannels">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image and has a specific number of channels,
-plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
-Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.
+Attributes size and value or synonyms though value is considered deprecated.
+The size optionally allows for absolute (``delta``) difference.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="channels" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Expected number of channels of the image.`</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum allowed number of channels.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed number of channels.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageMeanIntensity">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image and has a specific mean intensity value,
-plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity="0.83" />``).
-Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="value" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Deprecated alias for `size`]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="size" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Desired size of the output (in bytes), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="Bytes" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_center_of_mass-->
+      <xs:element name="has_image_center_of_mass">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified output is an image and has the specified center of mass.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="mean_intensity" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The required mean value of the image intensities.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">A lower bound of the required mean value of the image intensities.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">An upper bound of the required mean value of the image intensities.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="channel" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageCenterOfMass">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
 Asserts the output is an image and has a specific center of mass,
 or has an Euclidean distance of ``eps`` or less to that point (e.g.,
 ``<has_image_center_of_mass center_of_mass="511.07, 223.34" />``).
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="center_of_mass" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="channel" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageNLabels">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image and has the specified number of labels, or unique values (e.g.,
-``<has_image_n_labels n="187" exclude_labels="0" />``).
-The primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="center_of_mass" type="xs:string" use="required">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="channel" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="slice" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="frame" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="eps" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_channels-->
+      <xs:element name="has_image_channels">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific number of channels.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="n" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Expected number of labels.`</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum allowed number of labels.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum allowed number of labels.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="channel" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel). Must be used with multi-channel imags.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="labels" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="exclude_labels" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attributeGroup ref="AssertAttributeNegate"/>
-  </xs:complexType>
-  <xs:complexType name="AssertHasImageMeanObjectSize">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),
-plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
-The labels must be unique.
+The number of channels is plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="mean_object_size" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The required mean size of the uniquely labeled objects.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">A lower bound of the required mean size of the uniquely labeled objects.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="xs:float" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">An upper bound of the required mean size of the uniquely labeled objects.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="channel" type="xs:integer" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel). Must be used with multi-channel imags.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="labels" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="exclude_labels" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasJsonPropertyWithValue">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the JSON document contains a property or key with the specified JSON value.
+Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.
 
-```xml
-<has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />
-```
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="channels" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected number of channels of the image.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the number of channels (default is 0). The observed number of channels has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed number of channels.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed number of channels.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_depth-->
+      <xs:element name="has_image_depth">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific depth (number of slices).
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributeProperty"/>
-    <xs:attribute name="value" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">JSON-ified value to search for. This will be converted from an XML string to JSON with Python's json.loads function.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasJsonPropertyWithText">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts the JSON document contains a property or key with the specified text (i.e. string) value.
+The depth is plus/minus ``delta`` (e.g., ``<has_image_depth depth="512" delta="2" />``).
+Alternatively the range of the expected depth can be specified by ``min`` and/or ``max``.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="depth" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected depth of the image (number of slices).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the image depth (number of slices, default is 0). The observed depth has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed depth of the image (number of slices).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed depth of the image (number of slices).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_frames-->
+      <xs:element name="has_image_frames">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific number of frames (number of time steps).
+
+The number of frames is plus/minus ``delta`` (e.g., ``<has_image_frames depth="512" delta="2" />``).
+Alternatively the range of the expected number of frames can be specified by ``min`` and/or ``max``.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="frames" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected number of frames in the image sequence (number of time steps).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the number of frames in the image sequence (number of time steps, default is 0). The observed number of frames has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed number of frames in the image sequence (number of time steps).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed number of frames in the image sequence (number of time steps).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_height-->
+      <xs:element name="has_image_height">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific height (in pixels).
+
+The height is plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
+Alternatively the range of the expected height can be specified by ``min`` and/or ``max``.
 
-```xml
-<has_json_property_with_text property="color" text="red" />
-```
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="height" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected height of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the image height (in pixels, default is 0). The observed height has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed height of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed height of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_mean_intensity-->
+      <xs:element name="has_image_mean_intensity">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific mean intensity value.
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attributeGroup ref="AssertAttributeProperty"/>
-    <xs:attribute name="text" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Text value to search for.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasH5Keys">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts HDF5 output has a set of attributes (``keys``), specified as a
-comma-separated list, e.g.
+The mean intensity value is plus/minus ``eps`` (e.g., ``<has_image_mean_intensity mean_intensity="0.83" />``).
+Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.
 
-```xml
-<has_h5_keys keys="bins,chroms,indexes,pixels,chroms/lengths" />
-```
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="keys" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Comma-separated list of HDF5 attributes to check for.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
-  <xs:complexType name="AssertHasH5Attribute">
-    <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-Asserts HDF5 output contains the specified ``value`` for an attribute (``key``), e.g.
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="channel" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="slice" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="frame" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="mean_intensity" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The required mean value of the image intensities.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="eps" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A lower bound of the required mean value of the image intensities.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[An upper bound of the required mean value of the image intensities.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_mean_object_size-->
+      <xs:element name="has_image_mean_object_size">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image with labeled objects which have the specified mean size (number of pixels),
 
-```xml
-<has_h5_attribute key="nchroms" value="15" />
-```
+The mean size is plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
 
-$attribute_list::5
-]]>
-      </xs:documentation>
-    </xs:annotation>
-    <xs:attribute name="key" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">HDF5 attribute to check value of.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="value" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Expected value of HDF5 attribute to check.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:complexType>
+The labels must be unique.
 
-  <xs:attributeGroup name="AssertAttributePath">
-    <xs:attribute name="path" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Path to check for. Valid paths are the simplified subsets of XPath implemented by lxml.etree; https://lxml.de/xpathxslt.html for more information.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:attributeGroup>
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="channel" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="slice" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="frame" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="labels" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="exclude_labels" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="mean_object_size" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The required mean size of the uniquely labeled objects.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="eps" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A lower bound of the required mean size of the uniquely labeled objects.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:float" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[An upper bound of the required mean size of the uniquely labeled objects.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_n_labels-->
+      <xs:element name="has_image_n_labels">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has the specified labels.
 
-  <xs:attributeGroup name="AssertAttributeProperty">
-    <xs:attribute name="property" type="xs:string" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">JSON property to search the target for.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:attributeGroup>
+Labels can be a number of labels or unique values (e.g.,
+``<has_image_n_labels n="187" exclude_labels="0" />``).
 
-  <xs:attributeGroup name="AssertAttributeNegate">
-    <xs:attribute name="negate" type="PermissiveBoolean" default="false">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Negate the outcome of the assertion.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:attributeGroup>
+The primary usage of this assertion is to verify the number of objects in images with uniquely labeled objects.
 
-  <xs:attributeGroup name="AssertAttributeN">
-    <xs:attribute name="n" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Desired number, can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="delta" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Allowed difference with respect to n (default: 0), can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="min" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Minimum number (default: -infinity), can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="max" type="Bytes" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Maximum number (default: infinity), can be suffixed by ``(k|M|G|T|P|E)i?``</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-  </xs:attributeGroup>
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="channel" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific channel of the image (where ``0`` corresponds to the first image channel).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="slice" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific slice of the image (where ``0`` corresponds to the first image slice).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="frame" type="xs:integer" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Restricts the assertion to a specific frame of the image sequence (where ``0`` corresponds to the first image frame).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="labels" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[List of labels, separated by a comma. Labels *not* on this list will be excluded from consideration. Cannot be used in combination with ``exclude_labels``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="exclude_labels" type="xs:string" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[List of labels to be excluded from consideration, separated by a comma. The primary usage of this attribute is to exclude the background of a label image. Cannot be used in combination with ``labels``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="n" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected number of labels.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the number of labels (default is 0). The observed number of labels has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed number of labels.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed number of labels.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+      <!-- XSD doc for element auto-generated from galaxy.tool_util.verify.asserts.image.assert_has_image_width-->
+      <xs:element name="has_image_width">
+        <xs:annotation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is an image and has a specific width (in pixels).
 
+The width is plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
+Alternatively the range of the expected width can be specified by ``min`` and/or ``max``.
+
+$attribute_list::5]]></xs:documentation>
+        </xs:annotation>
+        <xs:complexType>
+          <xs:attribute name="width" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Expected width of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="delta" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed difference of the image width (in pixels, default is 0). The observed width has to be in the range ``value +- delta``.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="min" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Minimum allowed width of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="max" type="xs:nonNegativeInteger" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[Maximum allowed width of the image (in pixels).]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+          <xs:attribute name="negate" type="PermissiveBoolean" use="optional">
+            <xs:annotation>
+              <xs:documentation xml:lang="en"><![CDATA[A boolean that can be set to true to negate the outcome of the assertion.]]></xs:documentation>
+            </xs:annotation>
+          </xs:attribute>
+        </xs:complexType>
+      </xs:element>
+    </xs:choice>
+  </xs:group>
   <xs:complexType name="Inputs">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Consists of all elements that define the
 tool's input parameters. Each [param](#tool-inputs-param) element contained in this element
 can be used as a command line parameter within the [command](#tool-command) text content. Most
-tools will not need to specify any attributes on this tag itself.]]>
-</xs:documentation>
+tools will not need to specify any attributes on this tag itself.]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
       <xs:group ref="InputElement" minOccurs="0" maxOccurs="unbounded"/>
@@ -3188,8 +3486,6 @@ Data source HTTP action (e.g. ``get`` or ``put``) to use.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
-
   <xs:group name="InputElement">
     <xs:choice>
       <xs:element name="param" type="Param"/>
@@ -3214,15 +3510,17 @@ Data source HTTP action (e.g. ``get`` or ``put``) to use.</xs:documentation>
     </xs:annotation>
     <xs:sequence/>
   </xs:complexType>
-
-
   <xs:complexType name="Conditional">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
 
-This is a container for conditional parameters in the tool (must contain 'when'
-tag sets) - the command line (or portions thereof) are then wrapped in an if-else
-statement. A good example tool that demonstrates many conditional parameters is
+This is a container for conditional parameters in the tool (must contain ``when``
+tag sets) - the command line is then wrapped in an if-else statement.
+
+Note that value of a conditional cannot be changed on the workflow run form.
+If you expect users to interact with the element during runtime consider using ``sections`` instead.
+
+An example tool that demonstrates conditional parameters is
 [biom_convert.xml](https://github.com/galaxyproject/tools-iuc/blob/main/tools/biom_format/biom_convert.xml).
 
 ```xml
@@ -3303,7 +3601,7 @@ between paired inputs of single stranded inputs.
     <xs:complexContent>
       <xs:extension base="InputType">
         <xs:sequence>
-          <xs:element name="param" type="Param" minOccurs="1" maxOccurs="1" />
+          <xs:element name="param" type="Param" minOccurs="1" maxOccurs="1"/>
           <xs:element name="when" type="ConditionalWhen" minOccurs="0" maxOccurs="unbounded"/>
         </xs:sequence>
         <xs:attribute name="name" type="xs:string" use="required">
@@ -3329,22 +3627,17 @@ Referenced parameter to pass method.]]></xs:documentation>
           <xs:annotation>
             <xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
 
-Is referenced parameter is the same group.]]></xs:documentation>
+Is referenced parameter in the same group.]]></xs:documentation>
           </xs:annotation>
         </xs:attribute>
-
         <xs:attribute name="label" type="xs:string">
           <xs:annotation>
             <xs:documentation xml:lang="en">Human readable description for the conditional, unused in the Galaxy UI currently.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
-
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-
-
-
   <xs:complexType name="ConditionalWhen">
     <xs:annotation>
       <xs:documentation xml:lang="en">This directive describes one potential
@@ -3362,9 +3655,6 @@ corresponding to this ``when`` block.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
-
-
   <xs:complexType name="Repeat">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -3482,7 +3772,6 @@ demonstrates both testing strategies.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-
   <xs:complexType name="Section">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -3572,7 +3861,6 @@ Further examples can be found in the [test case](https://github.com/galaxyprojec
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Param">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -3820,7 +4108,7 @@ types are more obsecure and less likely to be useful for most tool authors.
     <xs:complexContent>
       <xs:extension base="InputType">
         <xs:sequence>
-          <xs:group ref="ParamElement" minOccurs="0" maxOccurs="unbounded" />
+          <xs:group ref="ParamElement" minOccurs="0" maxOccurs="unbounded"/>
         </xs:sequence>
         <xs:attribute name="type" type="ParamType" use="required">
           <xs:annotation>
@@ -3839,7 +4127,7 @@ the tool form widget is different. Currently valid parameter types are:
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="name" type="xs:string">
-            <xs:annotation>
+          <xs:annotation>
             <xs:documentation xml:lang="en"><![CDATA[Name for this element. This ``name``
 is used as the Cheetah variable containing the user-supplied parameter name in
 ``command`` and ``configfile`` elements. The name should not contain pipes or
@@ -3927,7 +4215,7 @@ only when the ``type`` attribute value is ``data``, ``float``, or ``integer``.</
 only when the ``type`` attribute value is ``data``, ``float``, or ``integer``.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
-        <xs:attribute name="format" type="xs:string">
+        <xs:attribute name="format" type="FormatList">
           <xs:annotation>
             <xs:documentation xml:lang="en">The comma-separated list of accepted
 data formats for this input. The list of supported data formats is contained in the
@@ -4045,6 +4333,47 @@ template if the parameter is ``false`` or not checked by the user. Used only
 when the ``type`` attribute value is ``boolean``.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
+        <xs:attribute name="allow_uri_if_protocol" type="xs:string">
+          <xs:annotation>
+            <xs:documentation xml:lang="en"><![CDATA[
+When using `deferred` datasets, Galaxy will try to materialize them into files when
+running the tool. In case we don't want to download them, the `allow_uri_if_protocol` attribute
+can be used to avoid materialization and pass the URI as is to the tool.
+This is useful when the tool can handle the URI directly. Example:
+
+```xml
+<param name="input" type="data" format="txt" allow_uri_if_protocol="http,https,s3" />
+```
+
+You can specify multiple prefixes separated by comma or use the wildcard '*' to always
+treat deferred datasets as URIs. The source URI will be passed to the tool as is.
+
+This attribute is only valid for `data` parameters.
+
+### Handling the input in the tool
+
+Since the input can be a regular file or a URI, the tool should be able to handle both cases.
+The tool should check if the input ``is_deferred`` and if so, treat it as a URI, otherwise
+it should treat it as a regular file. Please note that only deferred datasets with the specified
+protocol will be passed as URIs, the rest will be materialized as files.
+
+Here is an example command section that handles the above sample input:
+
+```python
+<command>
+  ## We should handle the case where the input must be treated as a URI with a specific protocol.
+  #if $input.is_deferred:
+      ## Here, the input is a deferred dataset which source URI has the protocol 'https', 'http' or 's3'.
+      echo '$input' > '$output' ## The ouput will be the source URI of the input.
+  #else:
+      ## Here, the input is a regular dataset or a materialized dataset in case of a
+      ## deferred dataset which source URI has a protocol different than 'https', 'http' or 's3'.
+      cp '$input' '$output' ## The output will be a copy of the input content.
+</command>
+```
+         ]]></xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
         <xs:attribute name="size" type="xs:string" gxdocs:deprecated="true">
           <!-- TODO: can be integer or integerxinteger -->
           <xs:annotation>
@@ -4074,7 +4403,6 @@ allow access to Python code to generate options for a select list. See
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-
   <xs:group name="ParamElement">
     <xs:choice>
       <xs:element name="label" type="xs:string">
@@ -4082,12 +4410,12 @@ allow access to Python code to generate options for a select list. See
           <xs:documentation xml:lang="en">Documentation for label</xs:documentation>
         </xs:annotation>
       </xs:element>
-      <xs:element name="conversion" type="ParamConversion" />
-      <xs:element name="option" type="ParamSelectOption" />
+      <xs:element name="conversion" type="ParamConversion"/>
+      <xs:element name="option" type="ParamSelectOption"/>
       <xs:element name="options" type="ParamOptions"/>
-      <xs:element name="validator" type="Validator" />
+      <xs:element name="validator" type="Validator"/>
       <xs:element name="sanitizer" type="Sanitizer"/>
-      <xs:element name="default" type="ParamDefault" />
+      <xs:element name="default" type="ParamDefault"/>
       <xs:element name="help" type="xs:string">
         <xs:annotation>
           <xs:documentation xml:lang="en">Documentation for help</xs:documentation>
@@ -4095,7 +4423,6 @@ allow access to Python code to generate options for a select list. See
       </xs:element>
     </xs:choice>
   </xs:group>
-
   <xs:simpleType name="ParamType">
     <xs:annotation>
       <xs:documentation xml:lang="en">Documentation for ParamType</xs:documentation>
@@ -4117,11 +4444,9 @@ allow access to Python code to generate options for a select list. See
       <xs:enumeration value="drill_down"/>
       <xs:enumeration value="group_tag"/>
       <xs:enumeration value="data_collection"/>
-      <xs:enumeration value="directory_uri" />
+      <xs:enumeration value="directory_uri"/>
     </xs:restriction>
   </xs:simpleType>
-
-
   <xs:complexType name="Command">
     <xs:annotation gxdocs:best_practices="command-tag">
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4307,8 +4632,7 @@ The ``detect_errors`` attribute of ``command``, if present, loads a preset of er
 * ``default``: for non-legacy tools with absent stdio block non-zero exit codes are added. For legacy tools or if a stdio block is present nothing is added.
 * ``exit_code``: adds checks for non zero exit codes. The ``oom_exit_code`` parameter can be used to add an additional out of memory indicating exit code. This is the default when a tool specifies a ``profile`` >= 16.04.
 * ``aggressive``: adds checks for non zero exit codes, and checks for ``Exception:``, ``Error:`` in the standard error. Additionally checks for messages in the standard error that indicate an out of memory error (``MemoryError``, ``std::bad_alloc``, ``java.lang.OutOfMemoryError``, ``Out of memory``).
-]]>
-            </xs:documentation>
+]]></xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="oom_exit_code" type="xs:integer">
@@ -4328,13 +4652,12 @@ The ``detect_errors`` attribute of ``command``, if present, loads a preset of er
         </xs:attribute>
         <xs:attribute name="strict" type="xs:boolean">
           <xs:annotation>
-            <xs:documentation xml:lang="en">This boolean forces the ``#set -e`` directive on in shell scripts - so that in a multi-part command if any part fails the job exits with a non-zero exit code. This is enabled by default for tools with ``profile>=20.09`` and disabled on legacy tools.</xs:documentation>
+            <xs:documentation xml:lang="en">This boolean forces the ``#set -e`` directive on in shell scripts - so that in a multi-part command if any part fails the job exits with a non-zero exit code. This is enabled by default for tools with ``profile&gt;=20.09`` and disabled on legacy tools.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="Expression">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4353,26 +4676,23 @@ of "type" specified for this expression block.
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:simpleType name="ExpressionType">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:restriction base="xs:string">
-      <xs:enumeration value="ecma5.1" />
+      <xs:enumeration value="ecma5.1"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:simpleType name="RequestMethodType">
     <xs:annotation>
       <xs:documentation xml:lang="en">Select a request method, defaults to GET if unspecified</xs:documentation>
     </xs:annotation>
     <xs:restriction base="xs:string">
-      <xs:enumeration value="GET" />
-      <xs:enumeration value="POST" />
+      <xs:enumeration value="GET"/>
+      <xs:enumeration value="POST"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:complexType name="ParamSelectOption">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4411,8 +4731,7 @@ In general the values and the texts for the options need to be unique,
 but it is possible to specify an option two times if the 2nd has a different
 value for the ``selected`` attribute. This is handy if an option list is
 defined in a macro and different default value(s) are used.
-]]>
-</xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:simpleContent>
       <xs:extension base="xs:string">
@@ -4434,7 +4753,6 @@ if the corresponding option is selected by default (the default is ``false``).
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="ParamDrillDownOption">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4455,7 +4773,6 @@ See [drill_down.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/funct
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="ParamConversion">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4467,8 +4784,7 @@ This directive is optionally contained within the ``<param>`` tag when the
 ``type`` attribute value is ``data`` and is used to dynamically generated a converted
 dataset for the contained input of the type specified using the ``type`` tag.
 
-]]>
-</xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -4481,16 +4797,14 @@ dataset for the contained input of the type specified using the ``type`` tag.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="ParamDefault">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
-]]>
-</xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
       <!-- can have zero or one collection elements -->
-      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="collection_type" type="CollectionType" use="optional">
       <xs:annotation>
@@ -4502,7 +4816,6 @@ collection types (the most common types are ``list``, ``paired``,
         ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
-
     <xs:attribute name="location" type="xs:anyURI" gxdocs:added="23.2" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en"><![CDATA[
@@ -4510,14 +4823,11 @@ Galaxy-aware URI for the default file. This should only be used with parameters
         ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
-
   </xs:complexType>
-
   <xs:complexType name="ParamDefaultCollection">
     <xs:sequence>
-      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
-
     <xs:attribute name="collection_type" type="CollectionType" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en"><![CDATA[
@@ -4528,12 +4838,10 @@ collection types (the most common types are ``list``, ``paired``,
         ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
-
   </xs:complexType>
-
   <xs:complexType name="ParamDefaultElement">
     <xs:sequence>
-      <xs:element name="collection" type="ParamDefaultCollection" minOccurs="0" maxOccurs="1" />
+      <xs:element name="collection" type="ParamDefaultCollection" minOccurs="0" maxOccurs="1"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string">
       <xs:annotation>
@@ -4548,7 +4856,6 @@ Galaxy-aware URI for the default file for collection element.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="ParamOptions">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -4779,11 +5086,10 @@ wrappers for an example of these.
 Though deprecated and discouraged, [code](#tool-code) blocks can also be
 used to generate dynamic options.
 
-]]>
-</xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OptionsElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OptionsElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="from_dataset" type="xs:string">
       <xs:annotation>
@@ -4843,12 +5149,12 @@ used to generate dynamic options.
   </xs:complexType>
   <xs:group name="OptionsElement">
     <xs:choice>
-      <xs:element name="filter" type="Filter" minOccurs="0" maxOccurs="unbounded" />
-      <xs:element name="column" type="Column" minOccurs="0" maxOccurs="unbounded" />
-      <xs:element name="validator" type="Validator" minOccurs="0" maxOccurs="1" />
-      <xs:element name="postprocess_expression" type="Expression" minOccurs="0" maxOccurs="1" />
-      <xs:element name="request_body" type="RequestBody" minOccurs="0" maxOccurs="1" />
-      <xs:element name="request_headers" type="RequestHeaders" minOccurs="0" maxOccurs="1" />
+      <xs:element name="filter" type="Filter" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="column" type="Column" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="validator" type="Validator" minOccurs="0" maxOccurs="1"/>
+      <xs:element name="postprocess_expression" type="Expression" minOccurs="0" maxOccurs="1"/>
+      <xs:element name="request_body" type="RequestBody" minOccurs="0" maxOccurs="1"/>
+      <xs:element name="request_headers" type="RequestHeaders" minOccurs="0" maxOccurs="1"/>
       <xs:element name="file" type="xs:string" minOccurs="0" maxOccurs="unbounded">
         <xs:annotation>
           <xs:documentation xml:lang="en">Documentation for file</xs:documentation>
@@ -4920,7 +5226,6 @@ target file.</xs:documentation>
   </xs:complexType>
   <xs:complexType name="Validator">
     <xs:annotation>
-
       <xs:documentation xml:lang="en"><![CDATA[
 
 This tag set is contained within the ``<param>`` tag set - it applies a
@@ -5490,7 +5795,7 @@ Currently the filters in the ``filter_types`` dictionary in the module
     </xs:attribute>
     <xs:attribute name="column" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">Column targeted by this filter given as column index or a column name. Invalid if ``type`` is ``add_value`` or ``remove_value``.
+        <xs:documentation xml:lang="en">Column targeted by this filter given as 0-based column index or a column name. Invalid if ``type`` is ``add_value`` or ``remove_value``.
 </xs:documentation>
       </xs:annotation>
     </xs:attribute>
@@ -5624,22 +5929,21 @@ The default is ``galaxy.json``.
   </xs:complexType>
   <xs:group name="OutputsElement">
     <xs:choice>
-      <xs:element name="output" type="Output" />
+      <xs:element name="output" type="Output"/>
       <xs:element name="data" type="OutputData"/>
-      <xs:element name="collection" type="OutputCollection" />
+      <xs:element name="collection" type="OutputCollection"/>
     </xs:choice>
   </xs:group>
   <xs:group name="OutputDataElement">
     <xs:choice>
       <xs:element name="change_format" type="ChangeFormat"/>
-      <xs:element name="filter" type="OutputFilter" />
-      <xs:element name="discover_datasets" type="OutputDiscoverDatasets" />
+      <xs:element name="filter" type="OutputFilter"/>
+      <xs:element name="discover_datasets" type="OutputDiscoverDatasets"/>
       <xs:element name="actions" type="Actions"/>
     </xs:choice>
   </xs:group>
-
   <xs:attributeGroup name="OutputCommon">
-    <xs:attribute name="format" type="xs:string">
+    <xs:attribute name="format" type="Format">
       <xs:annotation>
         <xs:documentation xml:lang="en"><![CDATA[
 The short name for the output datatype. The valid values for format can be found in
@@ -5668,15 +5972,14 @@ above. The default label is ``${tool.name} on ${on_string}``.
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="name" type="xs:string" use="required">
-        <xs:annotation>
-          <xs:documentation xml:lang="en"><![CDATA[Name for this output. This
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[Name for this output. This
 ``name`` is used as the Cheetah variable containing the Galaxy assigned output
 path in ``command`` and ``configfile`` elements. The name should not contain
 pipes or periods (e.g. ``.``).]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
-
   <xs:attributeGroup name="OutputDataAttributes">
     <xs:attribute name="auto_format" type="PermissiveBoolean">
       <xs:annotation>
@@ -5714,7 +6017,6 @@ dataset in the history view. (Default is ``false``.)</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
-
   <xs:attributeGroup name="OutputCollectionAttributes">
     <xs:attribute name="structured_like" type="xs:string">
       <xs:annotation>
@@ -5733,7 +6035,6 @@ format of outputs from format of corresponding input.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
-
   <xs:complexType name="OutputData">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -5820,30 +6121,27 @@ on Human (hg18)``.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <!-- TODO: add a unique constraint for action. -->
     <xs:attributeGroup ref="OutputCommon"/>
     <xs:attributeGroup ref="OutputDataAttributes"/>
   </xs:complexType>
-
   <!-- Allowed tags included in collection-data -->
   <xs:group name="OutputCollectionDataElement">
     <xs:choice>
-      <xs:element name="actions" type="Actions" />
-      <xs:element name="change_format" type="ChangeFormat" />
+      <xs:element name="actions" type="Actions"/>
+      <xs:element name="change_format" type="ChangeFormat"/>
     </xs:choice>
   </xs:group>
-
   <!-- Allowed tags included in collection -->
   <xs:group name="OutputCollectionElement">
     <xs:choice>
-      <xs:element name="data" type="OutputCollectionData" />
-      <xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets" />
-      <xs:element name="filter" type="OutputFilter" />
+      <xs:element name="data" type="OutputCollectionData"/>
+      <xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets"/>
+      <xs:element name="filter" type="OutputFilter"/>
     </xs:choice>
   </xs:group>
-
   <xs:complexType name="OutputCollectionData">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -5853,12 +6151,11 @@ define the elements of a collection statically. See also [Planemo's documentatio
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OutputCollectionDataElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OutputCollectionDataElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
-    <xs:attributeGroup ref="OutputCommon" />
-    <xs:attributeGroup ref="OutputDataAttributes" />
+    <xs:attributeGroup ref="OutputCommon"/>
+    <xs:attributeGroup ref="OutputDataAttributes"/>
   </xs:complexType>
-
   <xs:complexType name="OutputCollection">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -5875,7 +6172,7 @@ Creating collections in tools is covered in-depth in
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attributeGroup ref="OutputCommon"/>
     <xs:attributeGroup ref="OutputCollectionAttributes"/>
@@ -5896,7 +6193,6 @@ derive collection's type (e.g. ``collection_type``) from.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Output">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -5905,7 +6201,7 @@ This tag describes an output to the tool.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attributeGroup ref="OutputCommon"/>
     <xs:attributeGroup ref="OutputCollectionAttributes"/>
@@ -5935,7 +6231,6 @@ collection types (the most common types are ``list``, ``paired``,
 derive collection's type (e.g. ``collection_type``) from.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
-
   </xs:complexType>
   <xs:complexType name="OutputFilter">
     <xs:annotation>
@@ -6010,7 +6305,6 @@ Therefore a filter for such a variable looks like the following example.
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:attributeGroup name="OutputDiscoverDatasetsCommon">
     <xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
       <xs:annotation>
@@ -6037,12 +6331,12 @@ Therefore a filter for such a variable looks like the following example.
         <xs:documentation xml:lang="en">Indicates that the entire path of the discovered dataset relative to the specified directory should be available for matching patterns.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="format" type="xs:string" use="optional">
+    <xs:attribute name="format" type="Format" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``ext``).</xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="ext" type="xs:string" use="optional">
+    <xs:attribute name="ext" type="Format" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``format``).</xs:documentation>
       </xs:annotation>
@@ -6052,7 +6346,7 @@ Therefore a filter for such a variable looks like the following example.
         <xs:documentation xml:lang="en"><![CDATA[
         A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements.
         `SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either
-        `lexical` or `numeric`. Default is lexical sorting by filename. 
+        `lexical` or `numeric`. Default is lexical sorting by filename.
         Note that lexical sorting is case sensitive, i.e. upper case characters come before lower case characters (e.g. "Apple" < "Banana" < "apple" < "banana").
         ]]></xs:documentation>
       </xs:annotation>
@@ -6063,9 +6357,8 @@ Therefore a filter for such a variable looks like the following example.
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
-
   <xs:complexType name="OutputDiscoverDatasets">
-     <xs:annotation>
+    <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
 
 Describe datasets to dynamically collect after the job complete.
@@ -6089,8 +6382,8 @@ More information can be found on Planemo's documentation for
     </xs:attribute>
   </xs:complexType>
   <xs:complexType name="OutputCollectionDiscoverDatasets">
-     <xs:annotation>
-       <xs:documentation xml:lang="en"><![CDATA[
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
 
 This tag allows one to describe the datasets contained within an output
 collection dynamically, such that the outputs are "discovered" based on regular
@@ -6272,8 +6565,7 @@ column="1" />`` tag does), then it should be changed to ``equCab2`` (which is th
     </action>
 </actions>
 ```
-]]>
-</xs:documentation>
+]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
       <xs:group ref="ActionsElement" minOccurs="0" maxOccurs="unbounded"/>
@@ -6394,7 +6686,7 @@ of this directive.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-        <xs:element name="when" type="ActionsConditionalWhen" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="when" type="ActionsConditionalWhen" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
@@ -6431,7 +6723,7 @@ e.g. ``True`` or ``False`` if the referred parameter is a boolean.</xs:documenta
   </xs:complexType>
   <xs:complexType name="ActionsConditionalFilter">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:attribute name="type" type="ActionsConditionalFilterType" use="required">
       <xs:annotation>
@@ -6600,10 +6892,9 @@ This directive should contain one or more ``environment_variable`` definition.
       </xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:element name="environment_variable" type="EnvironmentVariable" minOccurs="0" maxOccurs="unbounded" />
+      <xs:element name="environment_variable" type="EnvironmentVariable" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="EnvironmentVariable">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -6674,17 +6965,17 @@ define.</xs:documentation>
           <xs:annotation>
             <xs:documentation xml:lang="en">Whether to strip leading and trailing whitespace from the calculated value before exporting the environment variable.</xs:documentation>
           </xs:annotation>
-      </xs:attribute>
+        </xs:attribute>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
   <xs:simpleType name="EnvironmentVariableInject">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:restriction base="xs:string">
-      <xs:enumeration value="api_key" />
-      <xs:enumeration value="entry_point_path_for_label" />
+      <xs:enumeration value="api_key"/>
+      <xs:enumeration value="entry_point_path_for_label"/>
     </xs:restriction>
   </xs:simpleType>
   <xs:complexType name="ConfigFiles">
@@ -6696,10 +6987,9 @@ container for ``<configfile>`` and ``<inputs>`` tag sets - which can be used
 to setup configuration files for use by tools.]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="ConfigFilesElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="ConfigFilesElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:group name="ConfigFilesElement">
     <xs:choice>
       <xs:element name="inputs" type="ConfigInputs"/>
@@ -6707,7 +6997,6 @@ to setup configuration files for use by tools.]]></xs:documentation>
       <xs:element name="configfile" type="ConfigFile"/>
     </xs:choice>
   </xs:group>
-
   <xs:complexType name="ConfigFile">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -6777,7 +7066,6 @@ the path to the file created with this directive.</xs:documentation>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="ConfigInputs">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -6842,7 +7130,6 @@ response to this directive.
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="ConfigFileSources">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -6866,7 +7153,6 @@ response to this directive.
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="VersionCommand">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Specifies the command to be run in
@@ -6912,7 +7198,6 @@ Examples are included in the test tools directory including:
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:complexType name="RequestParameterTranslation">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[See [/tools/data_source/ucsc_tablebrowser.xml](https://github.com/galaxyproject/galaxy/blob/dev/tools/data_source/ucsc_tablebrowser.xml) for an example of how to use this tag set. This tag set is used only in "data_source" tools (i.e. whose ``tool_type`` attribute is ``data_source`` or ``data_source_async``). This tag set contains a set of [request_param](#tool-request-param-translation-request-param) elements.]]></xs:documentation>
@@ -6921,7 +7206,6 @@ Examples are included in the test tools directory including:
       <xs:element name="request_param" minOccurs="0" maxOccurs="unbounded" type="RequestParameter"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="RequestParameter">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Contained within the [request_param_translation](#tool-request-param-translation) tag set (used only in "data_source" tools). The external data source application may send back parameter names like "GENOME" which must be translated to "dbkey" in Galaxy.]]></xs:documentation>
@@ -6951,32 +7235,29 @@ Examples are included in the test tools directory including:
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:simpleType name="RequestParameterGalaxyNameType">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:restriction base="xs:string">
-      <xs:enumeration value="URL" />
-      <xs:enumeration value="URL_method" />
-      <xs:enumeration value="dbkey" />
-      <xs:enumeration value="organism" />
-      <xs:enumeration value="table" />
-      <xs:enumeration value="position" />
-      <xs:enumeration value="description" />
-      <xs:enumeration value="name" />
-      <xs:enumeration value="info" />
-      <xs:enumeration value="data_type" />
+      <xs:enumeration value="URL"/>
+      <xs:enumeration value="URL_method"/>
+      <xs:enumeration value="dbkey"/>
+      <xs:enumeration value="organism"/>
+      <xs:enumeration value="table"/>
+      <xs:enumeration value="position"/>
+      <xs:enumeration value="description"/>
+      <xs:enumeration value="name"/>
+      <xs:enumeration value="info"/>
+      <xs:enumeration value="data_type"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:group name="RequestParameterElement">
     <xs:choice>
-      <xs:element name="append_param" type="RequestParameterAppend" />
-      <xs:element name="value_translation" type="RequestParameterValueTranslation" />
+      <xs:element name="append_param" type="RequestParameterAppend"/>
+      <xs:element name="value_translation" type="RequestParameterValueTranslation"/>
     </xs:choice>
   </xs:group>
-
   <xs:complexType name="RequestParameterAppend">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Optionally contained within the [request_param](#tool-request-param-translation-request-param) element if ``galaxy_name="URL"``. Some remote data sources (e.g., Gbrowse, Biomart) send parameters back to Galaxy in the initial response that must be added to the value of "URL" prior to Galaxy sending the secondary request to the remote data source via URL.]]></xs:documentation>
@@ -7006,7 +7287,6 @@ The text to use to join the param name to its value (example ``join="="``).
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="RequestParameterAppendValue">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Contained within the [append_param](#tool-request-param-translation-request-param-append-param) tag set. Allows for appending a param name / value pair to the value of URL.
@@ -7037,7 +7317,6 @@ Any valid HTTP request parameter name. The name / value pair must be received fr
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="RequestParameterValueTranslation">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Optionally contained within the [request_param](#tool-request-param-translation-request-param) tag set. The parameter value received from a remote data source may be named differently in Galaxy, and this tag set allows for the value to be appropriately translated.]]></xs:documentation>
@@ -7046,7 +7325,6 @@ Any valid HTTP request parameter name. The name / value pair must be received fr
       <xs:element name="value" minOccurs="0" maxOccurs="unbounded" type="RequestParameterValueTranslationValue"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="RequestParameterValueTranslationValue">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Contained within the [value_translation](#tool-request-param-translation-request-param-value-translation) tag set - allows for changing the data type value to something supported by Galaxy.
@@ -7078,7 +7356,6 @@ The target value (e.g. for setting data format: the list of supported data forma
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Stdio">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Tools write the bulk of useful data to datasets, but they can also write messages to standard I/O (stdio) channels known as standard output (stdout) and standard error (stderr). Both stdout and stderr are typically written to the executing program's console or terminal. Previous versions of Galaxy checked stderr for execution errors - if any text showed up on stderr, then the tool's execution was marked as failed. However, many tools write messages to stderr that are not errors, and using stderr allows programs to redirect other interesting messages to a separate file. Programs may also exit with codes that indicate success or failure. One convention is for programs to return 0 on success and a non-zero exit code on failure.
@@ -7106,20 +7383,17 @@ configuration file, and regular expressions are also applied in the order in
 which they appear in the tool's configuration file. However, once a rule is
 triggered that causes a fatal error, no further rules are
 checked.]]></xs:documentation>
-
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="StdioElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="StdioElement" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:group name="StdioElement">
     <xs:choice>
       <xs:element name="regex" type="Regex"/>
       <xs:element name="exit_code" type="ExitCode"/>
     </xs:choice>
   </xs:group>
-
   <xs:complexType name="ExitCode">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -7180,8 +7454,6 @@ marked as having failed.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
-
   <xs:complexType name="Regex">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -7316,7 +7588,6 @@ description. Note the quoting of the ``<`` and ``>`` characters in XML.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="ChangeFormat">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -7389,7 +7660,7 @@ parameter (e.g. ``value="interval"`` above), or of the deprecated ``input_datase
 attribute.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="format" type="xs:string" use="required">
+    <xs:attribute name="format" type="Format" use="required">
       <xs:annotation>
         <xs:documentation xml:lang="en">This value must be a supported data type
 (e.g. ``format="interval"``). See
@@ -7408,7 +7679,6 @@ for a list of supported formats.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
-
   <xs:complexType name="Citations">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Tool files may declare one
@@ -7459,7 +7729,6 @@ will be available to the end user.
       <xs:element name="citation" type="Citation" minOccurs="0" maxOccurs="unbounded"/>
     </xs:sequence>
   </xs:complexType>
-
   <xs:complexType name="Citation">
     <xs:annotation>
       <xs:documentation xml:lang="en">Each citations element can contain one or
@@ -7477,7 +7746,6 @@ and ``bibtex`` are the only supported options.</xs:documentation>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
-
   <xs:simpleType name="CitationType">
     <xs:annotation>
       <xs:documentation xml:lang="en">Type of citation represented.</xs:documentation>
@@ -7487,7 +7755,6 @@ and ``bibtex`` are the only supported options.</xs:documentation>
       <xs:enumeration value="doi"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:simpleType name="RequirementType">
     <xs:annotation>
       <xs:documentation xml:lang="en">Documentation for RequirementType</xs:documentation>
@@ -7534,7 +7801,7 @@ and ``bibtex`` are the only supported options.</xs:documentation>
           <xs:documentation xml:lang="en">Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20 bytes), if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
         </xs:annotation>
       </xs:enumeration>
-       <xs:enumeration value="cuda_version_min">
+      <xs:enumeration value="cuda_version_min">
         <xs:annotation>
           <xs:documentation xml:lang="en">Minimum CUDA (runtime link library) runtime version, if runtime allows it (not yet implemented in Galaxy).</xs:documentation>
         </xs:annotation>
@@ -7659,7 +7926,7 @@ and ``bibtex`` are the only supported options.</xs:documentation>
   </xs:simpleType>
   <xs:simpleType name="FilterType">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:restriction base="xs:string">
       <xs:enumeration value="data_meta"/>
@@ -7676,7 +7943,7 @@ and ``bibtex`` are the only supported options.</xs:documentation>
   </xs:simpleType>
   <xs:simpleType name="ActionsConditionalFilterType">
     <xs:annotation>
-      <xs:documentation xml:lang="en"></xs:documentation>
+      <xs:documentation xml:lang="en"/>
     </xs:annotation>
     <xs:restriction base="xs:string">
       <xs:enumeration value="param_value"/>
@@ -7804,17 +8071,36 @@ favour of a ``has_size`` assertion.</xs:documentation>
       <xs:documentation xml:lang="en">Number of bytes allowing for suffix (k|K|M|G|P|E)i? </xs:documentation>
     </xs:annotation>
     <xs:union>
-       <xs:simpleType>
-         <xs:restriction base="xs:integer">
-         </xs:restriction>
-       </xs:simpleType>
-       <xs:simpleType>
-         <xs:restriction base="xs:string">
-          <xs:pattern value="(0|[1-9][0-9]*)([kKMGTPE]i?)?"></xs:pattern>
+      <xs:simpleType>
+        <xs:restriction base="xs:integer">
          </xs:restriction>
-       </xs:simpleType>
+      </xs:simpleType>
+      <xs:simpleType>
+        <xs:restriction base="xs:string">
+          <xs:pattern value="(0|[1-9][0-9]*)([kKMGTPE]i?)?"/>
+        </xs:restriction>
+      </xs:simpleType>
     </xs:union>
   </xs:simpleType>
+
+  <xs:simpleType name="Format">
+    <xs:restriction base="xs:string">
+      <xs:pattern value="[0-9a-z._-]+"/>
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:simpleType name="FormatList">
+    <xs:restriction base="xs:string">
+      <xs:pattern value="([a-z0-9._-]+)(,([a-z0-9._-]+))*"/>
+    </xs:restriction>
+  </xs:simpleType>
+
+  <xs:simpleType name="Class">
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="File"/>
+      <xs:enumeration value="Directory"/>
+    </xs:restriction>
+  </xs:simpleType>
+
   <xs:complexType name="EdamTopics">
     <xs:annotation gxdocs:best_practices="tool-annotations-edam">
       <xs:documentation xml:lang="en"><![CDATA[
@@ -7833,7 +8119,7 @@ A tool can have any number of EDAM topic references.
       <xs:element name="edam_topic" minOccurs="0" maxOccurs="unbounded">
         <xs:simpleType>
           <xs:restriction base="singleLineString">
-            <xs:pattern value="topic_[0-9]{4}"></xs:pattern>
+            <xs:pattern value="topic_[0-9]{4}"/>
           </xs:restriction>
         </xs:simpleType>
       </xs:element>
@@ -7858,7 +8144,7 @@ A tool can have any number of EDAM operation references.
       <xs:element name="edam_operation" minOccurs="0" maxOccurs="unbounded">
         <xs:simpleType>
           <xs:restriction base="singleLineString">
-            <xs:pattern value="operation_[0-9]{4}"></xs:pattern>
+            <xs:pattern value="operation_[0-9]{4}"/>
           </xs:restriction>
         </xs:simpleType>
       </xs:element>
@@ -7881,8 +8167,8 @@ A tool can refer multiple reference IDs.
 
 ]]></xs:documentation>
     </xs:annotation>
-      <xs:sequence>
-        <xs:element name="xref" type="xref" minOccurs="0" maxOccurs="unbounded">
+    <xs:sequence>
+      <xs:element name="xref" type="xref" minOccurs="0" maxOccurs="unbounded">
       </xs:element>
     </xs:sequence>
   </xs:complexType>
@@ -7913,13 +8199,11 @@ the only supported options.</xs:documentation>
       <!--xs:enumeration value="whatelse"/-->
     </xs:restriction>
   </xs:simpleType>
-
   <xs:simpleType name="MacroImportType">
     <xs:restriction base="singleLineString">
       <xs:pattern value="[a-zA-Z0-9_\-\.]+.xml"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:simpleType name="singleLineString">
     <xs:annotation>
       <xs:documentation xml:lang="en">A string without newline characters.</xs:documentation>
@@ -7928,7 +8212,6 @@ the only supported options.</xs:documentation>
       <xs:whiteSpace value="collapse"/>
     </xs:restriction>
   </xs:simpleType>
-
   <xs:simpleType name="DetectErrorType">
     <xs:restriction base="xs:string">
       <xs:enumeration value="default"/>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 570008c7c64bc353199b560805a335ca02457665..502cdad17290644a54c3bd730d66dddba1556a58 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -51,6 +51,7 @@ from galaxy.model import (
     StoredWorkflow,
 )
 from galaxy.model.base import transaction
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.tool_shed.util.repository_util import get_installed_repository
 from galaxy.tool_shed.util.shed_util_common import set_image_paths
 from galaxy.tool_util.deps import (
@@ -77,10 +78,19 @@ from galaxy.tool_util.parser import (
     ToolOutputCollectionPart,
 )
 from galaxy.tool_util.parser.interface import (
+    HelpContent,
     InputSource,
     PageSource,
     ToolSource,
 )
+from galaxy.tool_util.parser.output_objects import (
+    ToolOutput,
+    ToolOutputCollection,
+)
+from galaxy.tool_util.parser.util import (
+    parse_profile_version,
+    parse_tool_version_with_defaults,
+)
 from galaxy.tool_util.parser.xml import (
     XmlPageSource,
     XmlToolSource,
@@ -89,10 +99,13 @@ from galaxy.tool_util.provided_metadata import parse_tool_provided_metadata
 from galaxy.tool_util.toolbox import (
     AbstractToolBox,
     AbstractToolTagManager,
+    ToolLoadConfigurationConflict,
+    ToolLoadError,
     ToolSection,
 )
 from galaxy.tool_util.toolbox.views.sources import StaticToolBoxViewSources
 from galaxy.tool_util.verify.interactor import ToolTestDescription
+from galaxy.tool_util.verify.parse import parse_tool_test_descriptions
 from galaxy.tool_util.verify.test_data import TestDataNotFoundError
 from galaxy.tool_util.version import (
     LegacyVersion,
@@ -108,11 +121,14 @@ from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
 from galaxy.tools.cache import ToolDocumentCache
 from galaxy.tools.evaluation import global_tool_errors
+from galaxy.tools.execution_helpers import ToolExecutionCache
 from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper
 from galaxy.tools.parameters import (
     check_param,
     params_from_strings,
     params_to_incoming,
+    params_to_json,
+    params_to_json_internal,
     params_to_strings,
     populate_state,
     visit_input_values,
@@ -124,7 +140,6 @@ from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter,
     HiddenToolParameter,
-    ImplicitConversionRequired,
     SelectTagParameter,
     SelectToolParameter,
     ToolParameter,
@@ -143,9 +158,9 @@ from galaxy.tools.parameters.grouping import (
 )
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
+from galaxy.tools.parameters.populate_model import populate_model
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.tools.parameters.wrapped_json import json_wrap
-from galaxy.tools.test import parse_tests
 from galaxy.util import (
     in_directory,
     listify,
@@ -160,13 +175,14 @@ from galaxy.util import (
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.compression_utils import get_fileobj_raw
-from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.dictifiable import UsesDictVisibleKeys
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.form_builder import SelectField
 from galaxy.util.json import (
     safe_loads,
     swap_inf_nan,
 )
+from galaxy.util.path import StrPath
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import (
     fill_template,
@@ -177,14 +193,35 @@ from galaxy.util.tool_shed.common_util import (
     get_tool_shed_url_from_tool_shed_registry,
 )
 from galaxy.version import VERSION_MAJOR
-from galaxy.work.context import proxy_work_context_for_history
+from galaxy.work.context import (
+    proxy_work_context_for_history,
+    WorkRequestContext,
+)
+from ._types import (
+    InputFormatT,
+    ParameterValidationErrorsT,
+    ToolRequestT,
+    ToolStateDumpedToJsonInternalT,
+    ToolStateDumpedToJsonT,
+    ToolStateJobInstancePopulatedT,
+    ToolStateJobInstanceT,
+)
 from .execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    DEFAULT_USE_CACHED_JOB,
     execute as execute_job,
+    ExecutionSlice,
+    JobCallbackT,
     MappingParameters,
 )
 
 if TYPE_CHECKING:
     from galaxy.app import UniverseApplication
+    from galaxy.managers.context import ProvidesUserContext
     from galaxy.managers.jobs import JobSearch
     from galaxy.tools.actions.metadata import SetMetadataToolAction
 
@@ -307,6 +344,7 @@ WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
     "__BUILD_LIST__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
     "__APPLY_RULES__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
     "__EXTRACT_DATASET__": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "__RELABEL_FROM_FILE__": safe_update(parse_version("1.0.0"), parse_version("1.1.0")),
     "Grep1": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
     "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
@@ -340,15 +378,19 @@ class ToolNotFoundException(Exception):
     pass
 
 
-def create_tool_from_source(app, tool_source, config_file=None, **kwds):
+def create_tool_from_source(app, tool_source: ToolSource, config_file: Optional[StrPath] = None, **kwds):
     # Allow specifying a different tool subclass to instantiate
     if (tool_module := tool_source.parse_tool_module()) is not None:
         module, cls = tool_module
         mod = __import__(module, globals(), locals(), [cls])
         ToolClass = getattr(mod, cls)
-    elif tool_source.parse_tool_type():
-        tool_type = tool_source.parse_tool_type()
+    elif tool_type := tool_source.parse_tool_type():
         ToolClass = tool_types.get(tool_type)
+        if not ToolClass:
+            if tool_type == "cwl":
+                raise ToolLoadError("Runtime support for CWL tools is not implemented currently")
+            else:
+                raise ToolLoadError(f"Parsed unrecognized tool type ({tool_type}) from tool")
     else:
         # Normal tool
         root = getattr(tool_source, "root", None)
@@ -358,7 +400,7 @@ def create_tool_from_source(app, tool_source, config_file=None, **kwds):
 
 
 def create_tool_from_representation(
-    app, raw_tool_source: str, tool_dir: str, tool_source_class="XmlToolSource"
+    app, raw_tool_source: str, tool_dir: Optional[StrPath] = None, tool_source_class="XmlToolSource"
 ) -> "Tool":
     tool_source = get_tool_source(tool_source_class=tool_source_class, raw_tool_source=raw_tool_source)
     return create_tool_from_source(app, tool_source=tool_source, tool_dir=tool_dir)
@@ -530,7 +572,7 @@ class ToolBox(AbstractToolBox):
                 self.cache_regions[tool_cache_data_dir] = ToolDocumentCache(cache_dir=tool_cache_data_dir)
             return self.cache_regions[tool_cache_data_dir]
 
-    def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
+    def create_tool(self, config_file: str, tool_cache_data_dir=None, **kwds):
         cache = self.get_cache_region(tool_cache_data_dir)
         if config_file.endswith(".xml") and cache and not cache.disabled:
             tool_document = cache.get(config_file)
@@ -566,6 +608,8 @@ class ToolBox(AbstractToolBox):
     def create_dynamic_tool(self, dynamic_tool, **kwds):
         tool_format = dynamic_tool.tool_format
         tool_representation = dynamic_tool.value
+        if "name" not in tool_representation:
+            tool_representation["name"] = f"dynamic tool {dynamic_tool.uuid}"
         tool_source = get_tool_source_from_representation(
             tool_format=tool_format,
             tool_representation=tool_representation,
@@ -585,7 +629,6 @@ class ToolBox(AbstractToolBox):
         Retrieve all loaded versions of a tool from the toolbox and return a select list enabling
         selection of a different version, the list of the tool's loaded versions, and the specified tool.
         """
-        toolbox = self
         tool_version_select_field = None
         tools = []
         tool = None
@@ -597,11 +640,11 @@ class ToolBox(AbstractToolBox):
                 # Some data sources send back redirects ending with `/`, this takes care of that case
                 tool_id = tool_id[:-1]
             if get_loaded_tools_by_lineage:
-                tools = toolbox.get_loaded_tools_by_lineage(tool_id)
+                tools = self.get_loaded_tools_by_lineage(tool_id)
             else:
-                tools = toolbox.get_tool(tool_id, tool_version=tool_version, get_all_versions=True)
+                tools = self.get_tool(tool_id, tool_version=tool_version, get_all_versions=True)
             if tools:
-                tool = toolbox.get_tool(tool_id, tool_version=tool_version, get_all_versions=False)
+                tool = self.get_tool(tool_id, tool_version=tool_version, get_all_versions=False)
                 if len(tools) > 1:
                     tool_version_select_field = self.__build_tool_version_select_field(tools, tool.id, set_selected)
                 break
@@ -694,7 +737,7 @@ class DefaultToolState:
         """
         Convert the data to a string
         """
-        value = params_to_strings(tool.inputs, self.inputs, app, nested=nested)
+        value = cast(Dict[str, Any], params_to_strings(tool.inputs, self.inputs, app, nested=nested))
         value["__page__"] = self.page
         value["__rerun_remap_job_id__"] = self.rerun_remap_job_id
         return value
@@ -704,7 +747,7 @@ class DefaultToolState:
         Restore the state from a string
         """
         values = safe_loads(values) or {}
-        self.page = values.pop("__page__") if "__page__" in values else None
+        self.page = values.pop("__page__") if "__page__" in values else 0
         self.rerun_remap_job_id = values.pop("__rerun_remap_job_id__") if "__rerun_remap_job_id__" in values else None
         self.inputs = params_from_strings(tool.inputs, values, app, ignore_errors=True)
 
@@ -724,7 +767,7 @@ class _Options(Bunch):
     refresh: str
 
 
-class Tool(Dictifiable):
+class Tool(UsesDictVisibleKeys):
     """
     Represents a computational tool that can be executed through Galaxy.
     """
@@ -743,24 +786,22 @@ class Tool(Dictifiable):
 
     def __init__(
         self,
-        config_file,
+        config_file: Optional[StrPath],
         tool_source: ToolSource,
         app: "UniverseApplication",
-        guid=None,
+        guid: Optional[str] = None,
         repository_id=None,
         tool_shed_repository=None,
-        allow_code_files=True,
-        dynamic=False,
-        tool_dir=None,
+        allow_code_files: bool = True,
+        dynamic: bool = False,
+        tool_dir: Optional[StrPath] = None,
     ):
         """Load a tool from the config named by `config_file`"""
+        self.config_file = config_file
         # Determine the full path of the directory where the tool config is
         if config_file is not None:
-            self.config_file = config_file
-            self.tool_dir = tool_dir or os.path.dirname(config_file)
-        else:
-            self.config_file = None
-            self.tool_dir = tool_dir
+            tool_dir = tool_dir or os.path.dirname(config_file)
+        self.tool_dir = tool_dir
 
         self.app = app
         self.repository_id = repository_id
@@ -811,6 +852,8 @@ class Tool(Dictifiable):
         self.tool_errors = None
         # Parse XML element containing configuration
         self.tool_source = tool_source
+        self.outputs: Dict[str, ToolOutput] = {}
+        self.output_collections: Dict[str, ToolOutputCollection] = {}
         self._is_workflow_compatible = None
         self.__help = None
         self.__tests: Optional[str] = None
@@ -1000,11 +1043,11 @@ class Tool(Dictifiable):
             return False
         return True
 
-    def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
+    def parse(self, tool_source: ToolSource, guid: Optional[str] = None, dynamic: bool = False) -> None:
         """
         Read tool configuration from the element `root` and fill in `self`.
         """
-        self.profile = float(tool_source.parse_profile())
+        self.profile = parse_profile_version(tool_source)
         # Get the UNIQUE id for the tool
         self.old_id = tool_source.parse_id()
         if guid is None:
@@ -1030,18 +1073,13 @@ class Tool(Dictifiable):
 
         # Get the (user visible) name of the tool
         self.name = tool_source.parse_name()
-        if not self.name and dynamic:
+        if not self.name and dynamic and self.id:
             self.name = self.id
         if not dynamic and not self.name:
             raise Exception(f"Missing tool 'name' for tool with id '{self.id}' at '{tool_source}'")
 
-        self.version = tool_source.parse_version()
-        if not self.version:
-            if profile < Version("16.04"):
-                # For backward compatibility, some tools may not have versions yet.
-                self.version = "1.0.0"
-            else:
-                raise Exception(f"Missing tool 'version' for tool with id '{self.id}' at '{tool_source}'")
+        version = parse_tool_version_with_defaults(self.id, tool_source, profile)
+        self.version = version
 
         # Legacy feature, ignored by UI.
         self.force_history_refresh = False
@@ -1103,6 +1141,7 @@ class Tool(Dictifiable):
             version_cmd_interpreter = tool_source.parse_version_command_interpreter()
             if version_cmd_interpreter:
                 executable = self.version_string_cmd.split()[0]
+                assert self.tool_dir is not None
                 abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable))
                 command_line = self.version_string_cmd.replace(executable, abs_executable, 1)
                 self.version_string_cmd = f"{version_cmd_interpreter} {command_line}"
@@ -1222,7 +1261,7 @@ class Tool(Dictifiable):
 
         self._is_workflow_compatible = self.check_workflow_compatible(self.tool_source)
 
-    def __parse_legacy_features(self, tool_source):
+    def __parse_legacy_features(self, tool_source: ToolSource):
         self.code_namespace: Dict[str, str] = {}
         self.hook_map: Dict[str, str] = {}
         self.uihints: Dict[str, str] = {}
@@ -1241,6 +1280,7 @@ class Tool(Dictifiable):
                     # map hook to function
                     self.hook_map[key] = value
             file_name = code_elem.get("file")
+            assert self.tool_dir is not None
             code_path = os.path.join(self.tool_dir, file_name)
             if self._allow_code_files:
                 with open(code_path) as f:
@@ -1305,9 +1345,10 @@ class Tool(Dictifiable):
             self.trackster_conf = TracksterConfig.parse(trackster_conf)
 
     def parse_tests(self):
-        if tests_source := self.tool_source:
+        if self.tool_source:
+            test_descriptions = parse_tool_test_descriptions(self.tool_source, self.id)
             try:
-                self.__tests = json.dumps([t.to_dict() for t in parse_tests(self, tests_source)], indent=None)
+                self.__tests = json.dumps([t.to_dict() for t in test_descriptions], indent=None)
             except Exception:
                 self.__tests = None
                 log.exception("Failed to parse tool tests for tool '%s'", self.id)
@@ -1321,9 +1362,8 @@ class Tool(Dictifiable):
     @property
     def _repository_dir(self):
         """If tool shed installed tool, the base directory of the repository installed."""
-        repository_base_dir = None
-
         if getattr(self, "tool_shed", None):
+            assert self.tool_dir is not None
             tool_dir = Path(self.tool_dir)
             for repo_dir in itertools.chain([tool_dir], tool_dir.parents):
                 if repo_dir.name == self.repository_name and repo_dir.parent.name == self.installed_changeset_revision:
@@ -1331,7 +1371,7 @@ class Tool(Dictifiable):
             else:
                 log.error(f"Problem finding repository dir for tool '{self.id}'")
 
-        return repository_base_dir
+        return None
 
     def test_data_path(self, filename):
         test_data = None
@@ -1476,22 +1516,12 @@ class Tool(Dictifiable):
         self.stdio_regexes = regexes
 
     def _parse_citations(self, tool_source):
-        # TODO: Move following logic into ToolSource abstraction.
-        if not hasattr(tool_source, "root"):
-            return []
-
-        root = tool_source.root
-        citations: List[str] = []
-        citations_elem = root.find("citations")
-        if citations_elem is None:
-            return citations
-
-        for citation_elem in citations_elem:
-            if citation_elem.tag != "citation":
-                pass
-            citations_manager = getattr(self.app, "citations_manager", None)
-            if citations_manager is not None:
-                citation = citations_manager.parse_citation(citation_elem)
+        citation_models = tool_source.parse_citations()
+        citations_manager = getattr(self.app, "citations_manager", None)
+        citations = []
+        if citations_manager is not None:
+            for citation_model in citation_models:
+                citation = citations_manager.parse_citation(citation_model)
                 if citation:
                     citations.append(citation)
         return citations
@@ -1510,8 +1540,8 @@ class Tool(Dictifiable):
             # Repeat group
             input_type = input_source.parse_input_type()
             if input_type == "repeat":
-                group_r = Repeat()
-                group_r.name = input_source.get("name")
+                repeat_name = input_source.get("name")
+                group_r = Repeat(repeat_name)
                 group_r.title = input_source.get("title")
                 group_r.help = input_source.get("help", None)
                 page_source = input_source.parse_nested_inputs_source()
@@ -1527,15 +1557,17 @@ class Tool(Dictifiable):
                 group_r.default = cast(int, min(max(group_r.default, group_r.min), group_r.max))
                 rval[group_r.name] = group_r
             elif input_type == "conditional":
-                group_c = Conditional()
-                group_c.name = input_source.get("name")
-                group_c.value_ref = input_source.get("value_ref", None)
+                cond_name = input_source.get("name")
+                group_c = Conditional(cond_name)
+                value_ref = input_source.get("value_ref", None)
+                group_c.value_ref = value_ref
                 group_c.value_ref_in_group = input_source.get_bool("value_ref_in_group", True)
                 value_from = input_source.get("value_from", None)
                 if value_from:
                     value_from = value_from.split(":")
                     temp_value_from = locals().get(value_from[0])
-                    group_c.test_param = rval[group_c.value_ref]
+                    assert value_ref
+                    group_c.test_param = rval[value_ref]
                     assert isinstance(group_c.test_param, ToolParameter)
                     group_c.test_param.refresh_on_change = True
                     for attr in value_from[1].split("."):
@@ -1596,8 +1628,8 @@ class Tool(Dictifiable):
                         group_c.cases.append(case)
                 rval[group_c.name] = group_c
             elif input_type == "section":
-                group_s = Section()
-                group_s.name = input_source.get("name")
+                section_name = input_source.get("name")
+                group_s = Section(section_name)
                 group_s.title = input_source.get("title")
                 group_s.help = input_source.get("help", None)
                 group_s.expanded = input_source.get_bool("expanded", False)
@@ -1606,8 +1638,8 @@ class Tool(Dictifiable):
                 rval[group_s.name] = group_s
             elif input_type == "upload_dataset":
                 elem = input_source.elem()
-                group_u = UploadDataset()
-                group_u.name = elem.get("name")
+                upload_name = elem.get("name")
+                group_u = UploadDataset(upload_name)
                 group_u.title = elem.get("title")
                 group_u.file_type_name = elem.get("file_type_name", group_u.file_type_name)
                 group_u.default_file_type = elem.get("default_file_type", group_u.default_file_type)
@@ -1640,8 +1672,9 @@ class Tool(Dictifiable):
         # form when it changes
         for name in param.get_dependencies():
             # Let it throw exception, but give some hint what the problem might be
-            if name not in context:
-                log.error(f"Tool with id '{self.id}': Could not find dependency '{name}' of parameter '{param.name}'")
+            assert (
+                name in context
+            ), f"Tool with id '{self.id}': Could not find dependency '{name}' of parameter '{param.name}'"
             context[name].refresh_on_change = True
         return param
 
@@ -1674,9 +1707,12 @@ class Tool(Dictifiable):
 
     @property
     def help(self) -> Template:
+        help_content = self.raw_help
+        assert help_content
+        assert help_content.format == "restructuredtext"
         try:
             return Template(
-                rst_to_html(self.raw_help),
+                rst_to_html(help_content.content),
                 input_encoding="utf-8",
                 default_filters=["decode.utf8"],
                 encoding_errors="replace",
@@ -1693,23 +1729,25 @@ class Tool(Dictifiable):
         """
         return biotools_reference(self.xrefs)
 
-    def __get_help_with_images(self, raw_help: Optional[str]):
-        help_text = raw_help or ""
-        try:
-            if help_text.find(".. image:: ") >= 0 and (self.tool_shed_repository or self.repository_id):
-                return set_image_paths(
-                    self.app,
-                    help_text,
-                    encoded_repository_id=self.repository_id,
-                    tool_shed_repository=self.tool_shed_repository,
-                    tool_id=self.old_id,
-                    tool_version=self.version,
+    def __get_help_with_images(self, help_content: Optional[HelpContent]) -> Optional[HelpContent]:
+        if help_content and help_content.format == "restructuredtext":
+            help_text = help_content.content or ""
+            try:
+                if help_text.find(".. image:: ") >= 0 and (self.tool_shed_repository or self.repository_id):
+                    help_text = set_image_paths(
+                        self.app,
+                        help_text,
+                        encoded_repository_id=self.repository_id,
+                        tool_shed_repository=self.tool_shed_repository,
+                        tool_id=self.old_id,
+                        tool_version=self.version,
+                    )
+            except Exception:
+                log.exception(
+                    "Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id
                 )
-        except Exception:
-            log.exception(
-                "Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id
-            )
-        return help_text
+            help_content = HelpContent(format="restructuredtext", content=help_text)
+        return help_content
 
     def find_output_def(self, name):
         # name is JobToOutputDatasetAssociation name.
@@ -1792,74 +1830,37 @@ class Tool(Dictifiable):
         if self.check_values:
             visit_input_values(self.inputs, values, callback)
 
-    def expand_incoming(self, trans, incoming, request_context, input_format="legacy"):
-        rerun_remap_job_id = None
-        if "rerun_remap_job_id" in incoming:
-            try:
-                rerun_remap_job_id = trans.app.security.decode_id(incoming["rerun_remap_job_id"])
-            except Exception as exception:
-                log.error(str(exception))
-                raise exceptions.MessageException(
-                    "Failure executing tool with id '%s' (attempting to rerun invalid job).", self.id
-                )
-
+    def expand_incoming(
+        self, request_context: WorkRequestContext, incoming: ToolRequestT, input_format: InputFormatT = "legacy"
+    ) -> Tuple[
+        List[ToolStateJobInstancePopulatedT],
+        List[ToolStateJobInstancePopulatedT],
+        Optional[int],
+        Optional[MatchingCollections],
+    ]:
+        rerun_remap_job_id = _rerun_remap_job_id(request_context, incoming, self.id)
         set_dataset_matcher_factory(request_context, self)
 
         # Fixed set of input parameters may correspond to any number of jobs.
         # Expand these out to individual parameters for given jobs (tool executions).
-        expanded_incomings, collection_info = expand_meta_parameters(trans, self, incoming)
-
-        # Remapping a single job to many jobs doesn't make sense, so disable
-        # remap if multi-runs of tools are being used.
-        produces_multiple_jobs = len(expanded_incomings) > 1
-        if rerun_remap_job_id and produces_multiple_jobs:
-            raise exceptions.RequestParameterInvalidException(
-                f"Failure executing tool with id '{self.id}' (cannot create multiple jobs when remapping existing job)."
-            )
+        expanded_incomings: List[ToolStateJobInstanceT]
+        collection_info: Optional[MatchingCollections]
+        expanded_incomings, collection_info = expand_meta_parameters(
+            request_context, self, incoming, input_format=input_format
+        )
 
-        if self.input_translator and produces_multiple_jobs:
-            raise exceptions.RequestParameterInvalidException(
-                f"Failure executing tool with id '{self.id}' (cannot create multiple jobs with this type of data source tool)."
-            )
+        self._ensure_expansion_is_valid(expanded_incomings, rerun_remap_job_id)
 
         # Process incoming data
         validation_timer = self.app.execution_timer_factory.get_timer(
             "internals.galaxy.tools.validation",
             "Validated and populated state for tool request",
         )
-        all_errors = []
-        all_params = []
+        all_errors: List[ParameterValidationErrorsT] = []
+        all_params: List[ToolStateJobInstancePopulatedT] = []
+
         for expanded_incoming in expanded_incomings:
-            params = {}
-            errors: Dict[str, str] = {}
-            if self.input_translator:
-                self.input_translator.translate(expanded_incoming)
-            if not self.check_values:
-                # If `self.check_values` is false we don't do any checking or
-                # processing on input  This is used to pass raw values
-                # through to/from external sites.
-                params = expanded_incoming
-            else:
-                # Update state for all inputs on the current page taking new
-                # values from `incoming`.
-                populate_state(
-                    request_context,
-                    self.inputs,
-                    expanded_incoming,
-                    params,
-                    errors,
-                    simple_errors=False,
-                    input_format=input_format,
-                )
-                # If the tool provides a `validate_input` hook, call it.
-                validate_input = self.get_hook("validate_input")
-                if validate_input:
-                    # hooks are so terrible ... this is specifically for https://github.com/galaxyproject/tools-devteam/blob/main/tool_collections/gops/basecoverage/operation_filter.py
-                    legacy_non_dce_params = {
-                        k: v.hda if isinstance(v, model.DatasetCollectionElement) and v.hda else v
-                        for k, v in params.items()
-                    }
-                    validate_input(request_context, errors, legacy_non_dce_params, self.inputs)
+            params, errors = self._populate(request_context, expanded_incoming, input_format)
             all_errors.append(errors)
             all_params.append(params)
         unset_dataset_matcher_factory(request_context)
@@ -1867,14 +1868,97 @@ class Tool(Dictifiable):
         log.info(validation_timer)
         return all_params, all_errors, rerun_remap_job_id, collection_info
 
+    def _ensure_expansion_is_valid(
+        self, expanded_incomings: List[ToolStateJobInstanceT], rerun_remap_job_id: Optional[int]
+    ) -> None:
+        """If the request corresponds to multiple jobs but this doesn't work with request configuration - raise an error.
+
+        In particular check if this is a data source job or if we're remapping a single job - in either case we should
+        not have any expansion occuring.
+        """
+        produces_multiple_jobs = len(expanded_incomings) > 1
+        if rerun_remap_job_id and produces_multiple_jobs:
+            raise exceptions.RequestParameterInvalidException(
+                f"Failure executing tool with id '{self.id}' (cannot create multiple jobs when remapping existing job)."
+            )
+
+        if self.input_translator and produces_multiple_jobs:
+            raise exceptions.RequestParameterInvalidException(
+                f"Failure executing tool with id '{self.id}' (cannot create multiple jobs with this type of data source tool)."
+            )
+
+    def _populate(
+        self, request_context, expanded_incoming: ToolStateJobInstanceT, input_format: InputFormatT
+    ) -> Tuple[ToolStateJobInstancePopulatedT, ParameterValidationErrorsT]:
+        """Validate expanded parameters for a job to replace references with model objects.
+
+        So convert a ToolStateJobInstanceT to a ToolStateJobInstancePopulatedT.
+        """
+        params: ToolStateJobInstancePopulatedT = {}
+        errors: ParameterValidationErrorsT = {}
+        if self.input_translator:
+            self.input_translator.translate(expanded_incoming)
+        if not self.check_values:
+            # If `self.check_values` is false we don't do any checking or
+            # processing on input  This is used to pass raw values
+            # through to/from external sites.
+            params = cast(ToolStateJobInstancePopulatedT, expanded_incoming)
+        else:
+            # Update state for all inputs on the current page taking new
+            # values from `incoming`.
+            populate_state(
+                request_context,
+                self.inputs,
+                expanded_incoming,
+                params,
+                errors,
+                simple_errors=False,
+                input_format=input_format,
+            )
+            self._handle_validate_input_hook(request_context, params, errors)
+        return params, errors
+
+    def _handle_validate_input_hook(
+        self, request_context, params: ToolStateJobInstancePopulatedT, errors: ParameterValidationErrorsT
+    ):
+        # If the tool provides a `validate_input` hook, call it.
+        validate_input = self.get_hook("validate_input")
+        if validate_input:
+            # hooks are so terrible ... this is specifically for https://github.com/galaxyproject/tools-devteam/blob/main/tool_collections/gops/basecoverage/operation_filter.py
+            legacy_non_dce_params = {
+                k: v.hda if isinstance(v, model.DatasetCollectionElement) and v.hda else v for k, v in params.items()
+            }
+            validate_input(request_context, errors, legacy_non_dce_params, self.inputs)
+
+    def completed_jobs(
+        self, trans, use_cached_job: bool, all_params: List[ToolStateJobInstancePopulatedT]
+    ) -> Dict[int, Optional[model.Job]]:
+        completed_jobs: Dict[int, Optional[model.Job]] = {}
+        for i, param in enumerate(all_params):
+            if use_cached_job:
+                tool_id = self.id
+                assert tool_id
+                param_dump: ToolStateDumpedToJsonInternalT = params_to_json_internal(self.inputs, param, self.app)
+                completed_jobs[i] = self.job_search.by_tool_input(
+                    trans=trans,
+                    tool_id=tool_id,
+                    tool_version=self.version,
+                    param=param,
+                    param_dump=param_dump,
+                    job_state=None,
+                )
+            else:
+                completed_jobs[i] = None
+        return completed_jobs
+
     def handle_input(
         self,
         trans,
-        incoming,
-        history=None,
-        use_cached_job=False,
-        preferred_object_store_id: Optional[str] = None,
-        input_format="legacy",
+        incoming: ToolRequestT,
+        history: Optional[model.History] = None,
+        use_cached_job: bool = DEFAULT_USE_CACHED_JOB,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        input_format: InputFormatT = "legacy",
     ):
         """
         Process incoming parameters for this tool from the dict `incoming`,
@@ -1883,26 +1967,17 @@ class Tool(Dictifiable):
         there were no errors).
         """
         request_context = proxy_work_context_for_history(trans, history=history)
-        all_params, all_errors, rerun_remap_job_id, collection_info = self.expand_incoming(
-            trans=trans, incoming=incoming, request_context=request_context, input_format=input_format
-        )
+        expanded = self.expand_incoming(request_context, incoming=incoming, input_format=input_format)
+        all_params: List[ToolStateJobInstancePopulatedT] = expanded[0]
+        all_errors: List[ParameterValidationErrorsT] = expanded[1]
+        rerun_remap_job_id: Optional[int] = expanded[2]
+        collection_info: Optional[MatchingCollections] = expanded[3]
+
         # If there were errors, we stay on the same page and display them
         self.handle_incoming_errors(all_errors)
 
         mapping_params = MappingParameters(incoming, all_params)
-        completed_jobs: Dict[int, Optional[model.Job]] = {}
-        for i, param in enumerate(all_params):
-            if use_cached_job:
-                completed_jobs[i] = self.job_search.by_tool_input(
-                    trans=trans,
-                    tool_id=self.id,
-                    tool_version=self.version,
-                    param=param,
-                    param_dump=self.params_to_strings(param, self.app, nested=True),
-                    job_state=None,
-                )
-            else:
-                completed_jobs[i] = None
+        completed_jobs: Dict[int, Optional[model.Job]] = self.completed_jobs(trans, use_cached_job, all_params)
         execution_tracker = execute_job(
             trans,
             self,
@@ -1920,7 +1995,13 @@ class Tool(Dictifiable):
         raise_execution_exception = not execution_tracker.successful_jobs and len(all_params) > 0
 
         if raise_execution_exception:
-            raise exceptions.MessageException(execution_tracker.execution_errors[0])
+            example_error = execution_tracker.execution_errors[0]
+            assert example_error
+            if isinstance(example_error, exceptions.MessageException):
+                raise example_error
+            else:
+                # Fallback, though everything here should already be a MessageException.
+                raise exceptions.MessageException(str(example_error))
 
         return dict(
             out_data=execution_tracker.output_datasets,
@@ -1931,7 +2012,7 @@ class Tool(Dictifiable):
             implicit_collections=execution_tracker.implicit_collections,
         )
 
-    def handle_incoming_errors(self, all_errors):
+    def handle_incoming_errors(self, all_errors: List[ParameterValidationErrorsT]) -> None:
         if any(all_errors):
             # simple param_key -> message string for tool form.
             err_data = {key: unicodify(value) for d in all_errors for (key, value) in d.items()}
@@ -1950,23 +2031,23 @@ class Tool(Dictifiable):
     def handle_single_execution(
         self,
         trans,
-        rerun_remap_job_id,
-        execution_slice,
-        history,
-        execution_cache=None,
-        completed_job=None,
-        collection_info=None,
-        job_callback=None,
-        preferred_object_store_id=None,
-        flush_job=True,
-        skip=False,
+        rerun_remap_job_id: Optional[int],
+        execution_slice: ExecutionSlice,
+        history: model.History,
+        execution_cache: ToolExecutionCache,
+        completed_job: Optional[model.Job],
+        collection_info: Optional[MatchingCollections],
+        job_callback: Optional[JobCallbackT],
+        preferred_object_store_id: Optional[str],
+        flush_job: bool,
+        skip: bool,
     ):
         """
         Return a pair with whether execution is successful as well as either
         resulting output data or an error message indicating the problem.
         """
         try:
-            rval = self.execute(
+            rval = self._execute(
                 trans,
                 incoming=execution_slice.param_combination,
                 history=history,
@@ -2053,18 +2134,67 @@ class Tool(Dictifiable):
                 args[key] = param.get_initial_value(trans, None)
         return args
 
-    def execute(self, trans, incoming=None, set_output_hid=True, history=None, **kwargs):
+    def execute(
+        self,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[model.History] = None,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+    ):
         """
         Execute the tool using parameter values in `incoming`. This just
         dispatches to the `ToolAction` instance specified by
         `self.tool_action`. In general this will create a `Job` that
         when run will build the tool's outputs, e.g. `DefaultToolAction`.
+
+        _execute has many more options but should be accessed through
+        handle_single_execution. The public interface to execute should be
+        rarely used and in more specific ways.
         """
+        return self._execute(
+            trans,
+            incoming=incoming,
+            history=history,
+            set_output_hid=set_output_hid,
+            flush_job=flush_job,
+        )
+
+    def _execute(
+        self,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[model.History] = None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = None,
+        completed_job: Optional[model.Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ):
         if incoming is None:
             incoming = {}
         try:
             return self.tool_action.execute(
-                self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs
+                self,
+                trans,
+                incoming=incoming,
+                history=history,
+                job_params=None,
+                rerun_remap_job_id=rerun_remap_job_id,
+                execution_cache=execution_cache,
+                dataset_collection_elements=dataset_collection_elements,
+                completed_job=completed_job,
+                collection_info=collection_info,
+                job_callback=job_callback,
+                preferred_object_store_id=preferred_object_store_id,
+                set_output_hid=set_output_hid,
+                flush_job=flush_job,
+                skip=skip,
             )
         except exceptions.ToolExecutionError as exc:
             job = exc.job
@@ -2075,7 +2205,7 @@ class Tool(Dictifiable):
             log.error("Tool execution failed for job: %s", job_id)
             raise
 
-    def params_to_strings(self, params, app, nested=False):
+    def params_to_strings(self, params: ToolStateJobInstancePopulatedT, app, nested=False):
         return params_to_strings(self.inputs, params, app, nested)
 
     def params_from_strings(self, params, app, ignore_errors=False):
@@ -2239,7 +2369,7 @@ class Tool(Dictifiable):
     def exec_before_job(self, app, inp_data, out_data, param_dict=None):
         pass
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state: Optional[str] = None):
         pass
 
     def job_failed(self, job_wrapper, message, exception=False):
@@ -2295,16 +2425,16 @@ class Tool(Dictifiable):
         return collected
 
     def to_archive(self):
-        tool = self
         tarball_files = []
         temp_files = []
-        with open(os.path.abspath(tool.config_file)) as fh1:
+        assert self.config_file
+        with open(os.path.abspath(self.config_file)) as fh1:
             tool_xml = fh1.read()
         # Retrieve tool help images and rewrite the tool's xml into a temporary file with the path
         # modified to be relative to the repository root.
         image_found = False
-        if tool.help is not None:
-            tool_help = tool.help._source
+        if self.help is not None:
+            tool_help = self.help._source
             # Check each line of the rendered tool help for an image tag that points to a location under static/
             for help_line in tool_help.split("\n"):
                 image_regex = re.compile(r'img alt="[^"]+" src="\${static_path}/([^"]+)"')
@@ -2322,25 +2452,25 @@ class Tool(Dictifiable):
             with tempfile.NamedTemporaryFile(mode="w", suffix=".xml", delete=False) as fh2:
                 new_tool_config = fh2.name
                 fh2.write(tool_xml)
-            tool_tup = (new_tool_config, os.path.split(tool.config_file)[-1])
+            tool_tup = (new_tool_config, os.path.split(self.config_file)[-1])
             temp_files.append(new_tool_config)
         else:
-            tool_tup = (os.path.abspath(tool.config_file), os.path.split(tool.config_file)[-1])
+            tool_tup = (os.path.abspath(self.config_file), os.path.split(self.config_file)[-1])
         tarball_files.append(tool_tup)
         # TODO: This feels hacky.
-        tool_command = tool.command.strip().split()[0]
-        tool_path = os.path.dirname(os.path.abspath(tool.config_file))
+        tool_command = self.command.strip().split()[0]
+        tool_path = os.path.dirname(os.path.abspath(self.config_file))
         # Add the tool XML to the tuple that will be used to populate the tarball.
         if os.path.exists(os.path.join(tool_path, tool_command)):
             tarball_files.append((os.path.join(tool_path, tool_command), tool_command))
         # Find and add macros and code files.
-        for external_file in tool.get_externally_referenced_paths(os.path.abspath(tool.config_file)):
+        for external_file in self.get_externally_referenced_paths(os.path.abspath(self.config_file)):
             external_file_abspath = os.path.abspath(os.path.join(tool_path, external_file))
             tarball_files.append((external_file_abspath, external_file))
         if os.path.exists(os.path.join(tool_path, "Dockerfile")):
             tarball_files.append((os.path.join(tool_path, "Dockerfile"), "Dockerfile"))
         # Find tests, and check them for test data.
-        if (tests := tool.tests) is not None:
+        if (tests := self.tests) is not None:
             for test in tests:
                 # Add input file tuples to the list.
                 for input in test.inputs:
@@ -2356,7 +2486,7 @@ class Tool(Dictifiable):
                     if os.path.exists(output_filepath):
                         td_tup = (output_filepath, os.path.join("test-data", filename))
                         tarball_files.append(td_tup)
-        for param in tool.input_params:
+        for param in self.input_params:
             # Check for tool data table definitions.
             param_options = getattr(param, "options", None)
             if param_options is not None:
@@ -2405,7 +2535,7 @@ class Tool(Dictifiable):
         """Returns dict of tool."""
 
         # Basic information
-        tool_dict = super().to_dict()
+        tool_dict = self._dictify_view_keys()
 
         tool_dict["edam_operations"] = self.edam_operations
         tool_dict["edam_topics"] = self.edam_topics
@@ -2452,12 +2582,18 @@ class Tool(Dictifiable):
         if tool_help:
             # create tool help
             help_txt = ""
-            if self.help:
-                help_txt = self.help.render(
-                    static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
-                )
-                help_txt = unicodify(help_txt)
+            help_format = "restructuredtext"
+            help_content = self.raw_help
+            if help_content:
+                help_format = help_content.format
+                if help_format == "restructuredtext":
+                    help_txt = self.help.render(
+                        static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
+                    )
+                    help_txt = unicodify(help_txt)
+
             tool_dict["help"] = help_txt
+            tool_dict["help_format"] = help_format
 
         return tool_dict
 
@@ -2506,7 +2642,7 @@ class Tool(Dictifiable):
         set_dataset_matcher_factory(request_context, self)
         # create tool state
         state_inputs: Dict[str, str] = {}
-        state_errors: Dict[str, str] = {}
+        state_errors: ParameterValidationErrorsT = {}
         populate_state(request_context, self.inputs, params.__dict__, state_inputs, state_errors)
 
         # create tool model
@@ -2517,22 +2653,29 @@ class Tool(Dictifiable):
 
         # create tool help
         tool_help = ""
-        if self.help:
+        tool_help_format = "restructuredtext"
+        if self.raw_help and self.raw_help.format == "restructuredtext":
             tool_help = self.help.render(
                 static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
             )
             tool_help = unicodify(tool_help, "utf-8")
+        elif self.raw_help:
+            tool_help = self.raw_help.content
+            tool_help_format = self.raw_help.format
 
         if isinstance(self.action, tuple):
             action = self.action[0] + self.app.url_for(self.action[1])
         else:
             action = self.app.url_for(self.action)
 
+        state_inputs_json: ToolStateDumpedToJsonT = params_to_json(self.inputs, state_inputs, self.app)
+
         # update tool model
         tool_model.update(
             {
                 "id": self.id,
                 "help": tool_help,
+                "help_format": tool_help_format,
                 "citations": bool(self.citations),
                 "sharable_url": self.sharable_url,
                 "message": tool_message,
@@ -2541,7 +2684,7 @@ class Tool(Dictifiable):
                 "requirements": [{"name": r.name, "version": r.version} for r in self.requirements],
                 "errors": state_errors,
                 "tool_errors": self.tool_errors,
-                "state_inputs": params_to_strings(self.inputs, state_inputs, self.app, use_security=True, nested=True),
+                "state_inputs": state_inputs_json,
                 "job_id": trans.security.encode_id(job.id) if job else None,
                 "job_remap": job.remappable() if job else None,
                 "history_id": trans.security.encode_id(history.id) if history else None,
@@ -2559,63 +2702,13 @@ class Tool(Dictifiable):
         """
         Populates the tool model consumed by the client form builder.
         """
-        other_values = ExpressionContext(state_inputs, other_values)
-        for input_index, input in enumerate(inputs.values()):
-            tool_dict = None
-            group_state = state_inputs.get(input.name, {})
-            if input.type == "repeat":
-                tool_dict = input.to_dict(request_context)
-                group_size = len(group_state)
-                tool_dict["cache"] = [None] * group_size
-                group_cache: List[List[str]] = tool_dict["cache"]
-                for i in range(group_size):
-                    group_cache[i] = []
-                    self.populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
-            elif input.type == "conditional":
-                tool_dict = input.to_dict(request_context)
-                if "test_param" in tool_dict:
-                    test_param = tool_dict["test_param"]
-                    test_param["value"] = input.test_param.value_to_basic(
-                        group_state.get(
-                            test_param["name"], input.test_param.get_initial_value(request_context, other_values)
-                        ),
-                        self.app,
-                    )
-                    test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
-                    for i in range(len(tool_dict["cases"])):
-                        current_state = {}
-                        if i == group_state.get("__current_case__"):
-                            current_state = group_state
-                        self.populate_model(
-                            request_context,
-                            input.cases[i].inputs,
-                            current_state,
-                            tool_dict["cases"][i]["inputs"],
-                            other_values,
-                        )
-            elif input.type == "section":
-                tool_dict = input.to_dict(request_context)
-                self.populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
-            else:
-                try:
-                    initial_value = input.get_initial_value(request_context, other_values)
-                    tool_dict = input.to_dict(request_context, other_values=other_values)
-                    tool_dict["value"] = input.value_to_basic(
-                        state_inputs.get(input.name, initial_value), self.app, use_security=True
-                    )
-                    tool_dict["default_value"] = input.value_to_basic(initial_value, self.app, use_security=True)
-                    tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
-                except ImplicitConversionRequired:
-                    tool_dict = input.to_dict(request_context)
-                    # This hack leads client to display a text field
-                    tool_dict["textable"] = True
-                except Exception:
-                    tool_dict = input.to_dict(request_context)
-                    log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
-            if input_index >= len(group_inputs):
-                group_inputs.append(tool_dict)
-            else:
-                group_inputs[input_index] = tool_dict
+        populate_model(
+            request_context=request_context,
+            inputs=inputs,
+            state_inputs=state_inputs,
+            group_inputs=group_inputs,
+            other_values=other_values,
+        )
 
     def _map_source_to_history(self, trans, tool_inputs, params):
         # Need to remap dataset parameters. Job parameters point to original
@@ -2857,7 +2950,7 @@ class ExpressionTool(Tool):
         with open(expression_inputs_path, "w") as f:
             json.dump(expression_inputs, f)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         for key, val in self.outputs.items():
             if key not in out_data:
                 # Skip filtered outputs
@@ -2880,7 +2973,9 @@ class ExpressionTool(Tool):
                 # if change_datatype PJA is associated with expression tool output the new output already has
                 # the desired datatype, so we use it. If the extension is "data" there's no change_dataset PJA and
                 # we want to use the existing extension.
-                new_ext = output.extension if output.extension != "data" else copy_object.extension
+                new_ext = (
+                    output.extension if output.extension not in ("data", "expression.json") else copy_object.extension
+                )
                 require_metadata_regeneration = copy_object.extension != new_ext
                 output.copy_from(copy_object, include_metadata=not require_metadata_regeneration)
                 output.extension = new_ext
@@ -2895,8 +2990,12 @@ class ExpressionTool(Tool):
                     else:
                         # TODO: move exec_after_process into metadata script so this doesn't run on the headnode ?
                         output.init_meta()
-                        output.set_meta()
-                        output.set_metadata_success_state()
+                        try:
+                            output.set_meta()
+                            output.set_metadata_success_state()
+                        except Exception:
+                            output.state = model.HistoryDatasetAssociation.states.FAILED_METADATA
+                            log.exception("Exception occured while setting metdata")
 
     def parse_environment_variables(self, tool_source):
         """Setup environment variable for inputs file."""
@@ -3016,7 +3115,9 @@ class SetMetadataTool(Tool):
     requires_setting_metadata = False
     tool_action: "SetMetadataToolAction"
 
-    def regenerate_imported_metadata_if_needed(self, hda, history, user, session_id):
+    def regenerate_imported_metadata_if_needed(
+        self, hda: model.HistoryDatasetAssociation, history: model.History, user: model.User, session_id: int
+    ):
         if hda.has_metadata_files:
             job, *_ = self.tool_action.execute_via_app(
                 self,
@@ -3029,7 +3130,7 @@ class SetMetadataTool(Tool):
             )
             self.app.job_manager.enqueue(job=job, tool=self)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         working_directory = app.object_store.get_filename(job, base_dir="job_work", dir_only=True, obj_dir=True)
         for name, dataset in inp_data.items():
             external_metadata = get_metadata_compute_strategy(app.config, job.id, tool_id=self.id)
@@ -3087,8 +3188,8 @@ class ExportHistoryTool(Tool):
 class ImportHistoryTool(Tool):
     tool_type = "import_history"
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None, **kwds):
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         if final_job_state != DETECTED_JOB_STATE.OK:
             return
         JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job()
@@ -3099,9 +3200,10 @@ class InteractiveTool(Tool):
     produces_entry_points = True
 
     def __init__(self, config_file, tool_source, app, **kwd):
-        assert app.config.interactivetools_enable, ValueError(
-            "Trying to load an InteractiveTool, but InteractiveTools are not enabled."
-        )
+        if not app.config.interactivetools_enable:
+            raise ToolLoadConfigurationConflict(
+                "Trying to load an InteractiveTool, but InteractiveTools are not enabled."
+            )
         super().__init__(config_file, tool_source, app, **kwd)
 
     def __remove_interactivetool_by_job(self, job):
@@ -3112,9 +3214,8 @@ class InteractiveTool(Tool):
         else:
             log.warning("Could not determine job to stop InteractiveTool: %s", job)
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kwds):
-        # run original exec_after_process
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         self.__remove_interactivetool_by_job(job)
 
     def job_failed(self, job_wrapper, message, exception=False):
@@ -3133,12 +3234,11 @@ class DataManagerTool(OutputParameterJSONTool):
         if self.data_manager_id is None:
             self.data_manager_id = self.id
 
-    def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, final_job_state=None, **kwds):
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None):
         assert self.allow_user_access(job.user), "You must be an admin to access this tool."
         if final_job_state != DETECTED_JOB_STATE.OK:
             return
-        # run original exec_after_process
-        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
         # process results of tool
         data_manager_id = job.data_manager_association.data_manager_id
         data_manager = self.app.data_managers.get_manager(data_manager_id)
@@ -3161,6 +3261,7 @@ class DataManagerTool(OutputParameterJSONTool):
                     create=True,
                     preserve_symlinks=True,
                 )
+                hda.metadata.is_bundle = True
 
         else:
             raise Exception("Unknown data manager mode encountered type...")
@@ -3242,32 +3343,34 @@ class DatabaseOperationTool(Tool):
     def allow_errored_inputs(self):
         return not self.require_dataset_ok
 
-    def check_inputs_ready(self, input_datasets, input_dataset_collections):
-        def check_dataset_state(state):
+    def check_inputs_ready(self, input_datasets, input_dataset_collections, security):
+        def check_dataset_state(input_key, state):
             if self.require_terminal_states and state in model.Dataset.non_ready_states:
                 raise ToolInputsNotReadyException("An input dataset is pending.")
 
             if self.require_dataset_ok:
                 if state != model.Dataset.states.OK:
+                    # TODO: frontend component should intercept and point to problematic input
                     raise ToolInputsNotOKException(
-                        f"Tool requires inputs to be in valid state, but dataset {input_dataset} is in state '{input_dataset.state}'",
+                        f"Tool requires inputs to be in valid state, but dataset with hid {input_dataset.hid} is in state '{input_dataset.state}'",
                         src="hda",
                         id=input_dataset.id,
+                        input_name=input_key,
                     )
 
-        for input_dataset in input_datasets.values():
+        for input_key, input_dataset in input_datasets.items():
             if input_dataset:
                 # None is a possible input for optional inputs
-                check_dataset_state(input_dataset.state)
+                check_dataset_state(input_key, input_dataset.state)
 
-        for input_dataset_collection_pairs in input_dataset_collections.values():
+        for input_key, input_dataset_collection_pairs in input_dataset_collections.items():
             for input_dataset_collection, _ in input_dataset_collection_pairs:
                 if not input_dataset_collection.collection.populated_optimized:
                     raise ToolInputsNotReadyException("An input collection is not populated.")
 
             states, _ = input_dataset_collection.collection.dataset_states_and_extensions_summary
             for state in states:
-                check_dataset_state(state)
+                check_dataset_state(input_key, state)
 
     def _add_datasets_to_history(self, history, elements, datasets_visible=False):
         for element_object in elements:
@@ -3275,7 +3378,7 @@ class DatabaseOperationTool(Tool):
                 element_object.visible = datasets_visible
                 history.stage_addition(element_object)
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
+    def produce_outputs(self, trans: "ProvidesUserContext", out_data, output_collections, incoming, history, **kwds):
         return self._outputs_dict()
 
     def _outputs_dict(self):
@@ -3452,7 +3555,7 @@ class ExtractDatasetCollectionTool(DatabaseOperationTool):
     require_terminal_states = False
     require_dataset_ok = False
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tags=None, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         has_collection = incoming["input"]
         if hasattr(has_collection, "element_type"):
             # It is a DCE
@@ -3664,6 +3767,25 @@ class FilterEmptyDatasetsTool(FilterDatasetsTool):
         return False
 
 
+class FilterNullTool(FilterDatasetsTool):
+    tool_type = "filter_null"
+    require_dataset_ok = True
+
+    @staticmethod
+    def element_is_valid(element: model.DatasetCollectionElement):
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
+        if element_object.extension == "expression.json":
+            if element_object.peek == "null":
+                # shortcut
+                return False
+            else:
+                with open(element_object.get_file_name()) as fh:
+                    if fh.read(5) == "null":
+                        return False
+        return True
+
+
 class FlattenTool(DatabaseOperationTool):
     tool_type = "flatten_collection"
     require_terminal_states = False
@@ -3769,14 +3891,13 @@ class HarmonizeTool(DatabaseOperationTool):
         final_sorted_identifiers = [
             element.element_identifier for element in elements1 if element.element_identifier in old_elements2_dict
         ]
-        # Raise Exception if it is empty
         if len(final_sorted_identifiers) == 0:
             # Create empty collections:
             output_collections.create_collection(
-                next(iter(self.outputs.values())), "output1", elements={}, propagate_hda_tags=False
+                self.outputs["output1"], "output1", elements={}, propagate_hda_tags=False
             )
             output_collections.create_collection(
-                next(iter(self.outputs.values())), "output2", elements={}, propagate_hda_tags=False
+                self.outputs["output2"], "output2", elements={}, propagate_hda_tags=False
             )
             return
 
@@ -3794,7 +3915,7 @@ class HarmonizeTool(DatabaseOperationTool):
             self._add_datasets_to_history(history, new_elements.values())
             # Create collections:
             output_collections.create_collection(
-                next(iter(self.outputs.values())), output_label, elements=new_elements, propagate_hda_tags=False
+                self.outputs[output_label], output_label, elements=new_elements, propagate_hda_tags=False
             )
 
         # Create outputs:
@@ -3829,27 +3950,45 @@ class RelabelFromFileTool(DatabaseOperationTool):
             new_labels = fh.readlines(1024 * 1000000)
         if strict and len(hdca.collection.elements) != len(new_labels):
             raise exceptions.MessageException("Relabel mapping file contains incorrect number of identifiers")
-        if how_type == "tabular":
-            # We have a tabular file, where the first column is an existing element identifier,
-            # and the second column is the new element identifier.
+        if how_type in ["tabular", "tabular_extended"]:
+            # We have a tabular file, where one column lists existing element identifiers,
+            # another one the corresponding new element identifiers.
+            # In tabular_extended mode the two columns ("from" and "to") are user-specified,
+            # while in simple tabular mode they default to the first and second column and
+            # these must be the only two columns in the input.
+            from_index = int(incoming["how"].get("from", 1)) - 1
+            to_index = int(incoming["how"].get("to", 2)) - 1
+            if from_index < 0 or to_index < 0:
+                raise exceptions.MessageException(
+                    "Column < 1 specified for relabel mapping file. Column count starts at 1."
+                )
             new_labels_dict = {}
-            source_new_label = (line.strip().split("\t") for line in new_labels)
-            for i, label_pair in enumerate(source_new_label):
-                if not len(label_pair) == 2:
-                    raise exceptions.MessageException(
-                        f"Relabel mapping file line {i + 1} contains {len(label_pair)} columns, but 2 are required"
-                    )
-                new_labels_dict[label_pair[0]] = label_pair[1]
+            try:
+                for i, line in enumerate(new_labels, 1):
+                    cols = line.strip().split("\t")
+                    if how_type == "tabular" and len(cols) != 2:
+                        raise exceptions.MessageException(
+                            f"Relabel mapping file contains {len(cols)} columns on line {i}, but 2 are required"
+                        )
+                    new_labels_dict[cols[from_index]] = cols[to_index]
+            except IndexError:
+                raise exceptions.MessageException(
+                    f"Specified column number > number of columns [{len(cols)}] on line {i} of relabel mapping file."
+                )
             for dce in hdca.collection.elements:
                 dce_object = dce.element_object
                 element_identifier = dce.element_identifier
                 default = None if strict else element_identifier
                 new_label = new_labels_dict.get(element_identifier, default)
                 if not new_label:
-                    raise exceptions.MessageException(f"Failed to find new label for identifier [{element_identifier}]")
+                    raise exceptions.MessageException(f"Failed to find original identifier [{element_identifier}]")
                 add_copied_value_to_new_elements(new_label, dce_object)
         else:
             # If new_labels_dataset_assoc is not a two-column tabular dataset we label with the current line of the dataset
+            if hdca.collection.element_count > len(new_labels):
+                raise exceptions.MessageException(
+                    "Relabel mapping file contains less lines than there are collection elements to relabel."
+                )
             for i, dce in enumerate(hdca.collection.elements):
                 dce_object = dce.element_object
                 add_copied_value_to_new_elements(new_labels[i], dce_object)
@@ -3865,7 +4004,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
 class ApplyRulesTool(DatabaseOperationTool):
     tool_type = "apply_rules"
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
         rule_set = RuleSet(incoming["rules"])
         copied_datasets = []
@@ -3873,7 +4012,7 @@ class ApplyRulesTool(DatabaseOperationTool):
         def copy_dataset(dataset, tags):
             copied_dataset = dataset.copy(copy_tags=dataset.tags, flush=False)
             if tags is not None:
-                tag_handler.set_tags_from_list(
+                trans.tag_handler.set_tags_from_list(
                     trans.get_user(),
                     copied_dataset,
                     tags,
@@ -3902,7 +4041,7 @@ class TagFromFileTool(DatabaseOperationTool):
     # require_terminal_states = True
     # require_dataset_ok = False
 
-    def produce_outputs(self, trans, out_data, output_collections, incoming, history, tag_handler, **kwds):
+    def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
         how = incoming["how"]
         new_tags_dataset_assoc = incoming["tags"]
@@ -3910,6 +4049,7 @@ class TagFromFileTool(DatabaseOperationTool):
         new_datasets = []
 
         def add_copied_value_to_new_elements(new_tags_dict, dce):
+            tag_handler = trans.tag_handler
             if getattr(dce.element_object, "history_content_type", None) == "dataset":
                 copied_value = dce.element_object.copy(copy_tags=dce.element_object.tags, flush=False)
                 # copy should never be visible, since part of a collection
@@ -4030,7 +4170,6 @@ class DuplicateFileToCollectionTool(DatabaseOperationTool):
 
 
 # Populate tool_type to ToolClass mappings
-tool_types = {}
 TOOL_CLASSES: List[Type[Tool]] = [
     Tool,
     SetMetadataTool,
@@ -4050,11 +4189,24 @@ TOOL_CLASSES: List[Type[Tool]] = [
     ExtractDatasetCollectionTool,
     DataDestinationTool,
 ]
-for tool_class in TOOL_CLASSES:
-    tool_types[tool_class.tool_type] = tool_class
-
+tool_types = {tool_class.tool_type: tool_class for tool_class in TOOL_CLASSES}
 
 # ---- Utility classes to be factored out -----------------------------------
+
+
+def _rerun_remap_job_id(trans, incoming, tool_id: Optional[str]) -> Optional[int]:
+    rerun_remap_job_id = None
+    if "rerun_remap_job_id" in incoming:
+        try:
+            rerun_remap_job_id = trans.app.security.decode_id(incoming["rerun_remap_job_id"])
+        except Exception as exception:
+            log.error(str(exception))
+            raise exceptions.MessageException(
+                "Failure executing tool with id '%s' (attempting to rerun invalid job).", tool_id
+            )
+    return rerun_remap_job_id
+
+
 class TracksterConfig:
     """Trackster configuration encapsulation."""
 
diff --git a/lib/galaxy/tools/_types.py b/lib/galaxy/tools/_types.py
new file mode 100644
index 0000000000000000000000000000000000000000..635a86cf459d1754876263844200f3e6cb420840
--- /dev/null
+++ b/lib/galaxy/tools/_types.py
@@ -0,0 +1,65 @@
+"""
+Tool state goes through several different iterations that are difficult to follow I think,
+hopefully datatypes can be used as markers to describe what has been done - even if they don't
+provide strong traditional typing semantics.
+
++--------------------------------+------------+---------------------------------+------------+-----------+
+| Python Type                    | State for? | Object References               | Validated? | xref      |
++================================+============+=================================+============+===========+
+| ToolRequestT                   | request    | src dicts of encoded ids        | nope        |          |
+| ToolStateJobInstanceT          | a job      | src dicts of encoded ids        | nope        |          |
+| ToolStateJobInstancePopulatedT | a job      | model objs loaded from db       | check_param |          |
+| ToolStateDumpedToJsonT         | a job      | src dicts of encoded ids        | "           |          |
+|                                |            | (normalized into values attr)   | "           |          |
+| ToolStateDumpedToJsonInternalT | a job      | src dicts of decoded ids        | "           |          |
+|                                |            | (normalized into values attr)   | "           |          |
+| ToolStateDumpedToStringsT      | a job      | src dicts dumped to strs        | "           |          |
+|                                |            | (normalized into values attr)   | "           |          |
++--------------------------------+------------+---------------------------------+-------------+----------+
+"""
+
+from typing import (
+    Any,
+    Dict,
+    Union,
+)
+
+from typing_extensions import Literal
+
+# Input dictionary from the API, may include map/reduce instructions. Objects are referenced by "src"
+# dictionaries and encoded IDS.
+ToolRequestT = Dict[str, Any]
+
+# Input dictionary extracted from a tool request for running a tool individually as a single job. Objects are referenced
+# by "src" dictionaries with encoded IDs still but batch instructions have been pulled out. Parameters have not
+# been "checked" (check_param has not been called).
+ToolStateJobInstanceT = Dict[str, Any]
+
+# Input dictionary for an individual job where objects are their model objects and parameters have been
+# "checked" (check_param has been called).
+ToolStateJobInstancePopulatedT = Dict[str, Any]
+
+# Input dictionary for an individual where the state has been valiated and populated but then converted back down
+# to json. Object references are unified in the format of {"values": List["src" dictionary]} where the src dictionaries.
+# are decoded ids (ints).
+# See comments on galaxy.tools.parameters.params_to_strings for more information.
+ToolStateDumpedToJsonInternalT = Dict[str, Any]
+
+# Input dictionary for an individual where the state has been valiated and populated but then converted back down
+# to json. Object references are unified in the format of {"values": List["src" dictionary]} where src dictonaries
+# are encoded (ids). See comments on galaxy.tools.parameters.params_to_strings for more information.
+ToolStateDumpedToJsonT = Dict[str, Any]
+
+# Input dictionary for an individual where the state has been valiated and populated but then converted back down
+# to json. Object references are unified in the format of {"values": List["src" dictionary]} but dumped into
+# strings. See comments on galaxy.tools.parameters.params_to_strings for more information. This maybe should be
+# broken into separate types for encoded and decoded IDs in subsequent type refinements if both are used, it not
+# this comment should be updated to indicate which is used exclusively.
+ToolStateDumpedToStringsT = Dict[str, str]
+
+# A dictionary of error messages that occur while attempting to validate a ToolStateJobInstanceT and transform it
+# into a ToolStateJobInstancePopulatedT with model objects populated. Tool errors indicate the job should not be
+# further processed.
+ParameterValidationErrorsT = Dict[str, Union["ParameterValidationErrorsT", str, Exception]]
+
+InputFormatT = Literal["legacy", "21.01"]
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 1a16ed58af3cb8b03f32d72483dbaab69c8e2cd6..4da5b270545d463f76e127f2d261c25fe5906556 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -9,7 +9,9 @@ from typing import (
     cast,
     Dict,
     List,
+    Optional,
     Set,
+    Tuple,
     TYPE_CHECKING,
     Union,
 )
@@ -18,12 +20,14 @@ from packaging.version import Version
 
 from galaxy import model
 from galaxy.exceptions import (
+    AuthenticationRequired,
     ItemAccessibilityException,
     RequestParameterInvalidException,
 )
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model import (
+    History,
     HistoryDatasetAssociation,
     Job,
     LibraryDatasetDatasetAssociation,
@@ -31,8 +35,24 @@ from galaxy.model import (
 )
 from galaxy.model.base import transaction
 from galaxy.model.dataset_collections.builder import CollectionBuilder
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.model.none_like import NoneDataset
 from galaxy.objectstore import ObjectStorePopulator
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import (
+    filter_output,
+    on_text_for_names,
+    ToolExecutionCache,
+)
 from galaxy.tools.parameters import update_dataset_ids
 from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
@@ -54,32 +74,8 @@ if TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 
-class ToolExecutionCache:
-    """An object mean to cache calculation caused by repeatedly evaluting
-    the same tool by the same user with slightly different parameters.
-    """
-
-    def __init__(self, trans):
-        self.trans = trans
-        self.current_user_roles = trans.get_current_user_roles()
-        self.chrom_info = {}
-        self.cached_collection_elements = {}
-
-    def get_chrom_info(self, tool_id, input_dbkey):
-        genome_builds = self.trans.app.genome_builds
-        custom_build_hack_get_len_from_fasta_conversion = tool_id != "CONVERTER_fasta_to_len"
-        if custom_build_hack_get_len_from_fasta_conversion and input_dbkey in self.chrom_info:
-            return self.chrom_info[input_dbkey]
-
-        chrom_info_pair = genome_builds.get_chrom_info(
-            input_dbkey,
-            trans=self.trans,
-            custom_build_hack_get_len_from_fasta_conversion=custom_build_hack_get_len_from_fasta_conversion,
-        )
-        if custom_build_hack_get_len_from_fasta_conversion:
-            self.chrom_info[input_dbkey] = chrom_info_pair
-
-        return chrom_info_pair
+OutputDatasetsT = Dict[str, "DatasetInstance"]
+ToolActionExecuteResult = Union[Tuple[Job, OutputDatasetsT, Optional[History]], Tuple[Job, OutputDatasetsT]]
 
 
 class ToolAction:
@@ -89,14 +85,46 @@ class ToolAction:
     """
 
     @abstractmethod
-    def execute(self, tool, trans, incoming=None, set_output_hid=True, **kwargs):
-        pass
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
+        """Perform target tool action."""
+
+    @abstractmethod
+    def get_output_name(
+        self,
+        output,
+        dataset=None,
+        tool=None,
+        on_text=None,
+        trans=None,
+        incoming=None,
+        history=None,
+        params=None,
+        job_params=None,
+    ) -> str:
+        """Get name to assign a tool output."""
 
 
 class DefaultToolAction(ToolAction):
     """Default tool action is to run an external command"""
 
-    produces_real_jobs = True
+    produces_real_jobs: bool = True
 
     def _collect_input_datasets(
         self,
@@ -389,21 +417,20 @@ class DefaultToolAction(ToolAction):
         self,
         tool,
         trans,
-        incoming=None,
-        return_job=False,
-        set_output_hid=True,
-        history=None,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
         job_params=None,
-        rerun_remap_job_id=None,
-        execution_cache=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
         dataset_collection_elements=None,
-        completed_job=None,
-        collection_info=None,
-        job_callback=None,
-        preferred_object_store_id=None,
-        flush_job=True,
-        skip=False,
-    ):
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         """
         Executes a tool, creating job and tool outputs, associating them, and
         submitting the job to the job queue. If history is not specified, use
@@ -424,6 +451,7 @@ class DefaultToolAction(ToolAction):
             preserved_hdca_tags,
             all_permissions,
         ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
+        assert history  # tell type system we've set history and it is no longer optional
         # Build name for output datasets based on tool name and input names
         on_text = self._get_on_text(inp_data)
 
@@ -505,7 +533,7 @@ class DefaultToolAction(ToolAction):
                     output,
                     wrapped_params.params,
                     inp_data,
-                    inp_dataset_collections,
+                    input_collections,
                     input_ext,
                     python_template_version=tool.python_template_version,
                     execution_cache=execution_cache,
@@ -681,6 +709,7 @@ class DefaultToolAction(ToolAction):
                 output_collection.mark_as_populated()
             for hdca in output_collections.out_collection_instances.values():
                 hdca.visible = False
+                hdca.collection.mark_as_populated()
             object_store_populator = ObjectStorePopulator(trans.app, trans.user)
             for data in out_data.values():
                 data.set_skipped(object_store_populator)
@@ -698,14 +727,6 @@ class DefaultToolAction(ToolAction):
         # Remap any outputs if this is a rerun and the user chose to continue dependent jobs
         # This functionality requires tracking jobs in the database.
         if app.config.track_jobs_in_database and rerun_remap_job_id is not None:
-            # Need to flush here so that referencing outputs by id works
-            session = trans.sa_session()
-            try:
-                session.expire_on_commit = False
-                with transaction(session):
-                    session.commit()
-            finally:
-                session.expire_on_commit = True
             self._remap_job_on_rerun(
                 trans=trans,
                 galaxy_session=galaxy_session,
@@ -746,7 +767,14 @@ class DefaultToolAction(ToolAction):
 
         return job, out_data, history
 
-    def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current_job, out_data):
+    def _remap_job_on_rerun(
+        self,
+        trans: ProvidesHistoryContext,
+        galaxy_session: Optional[model.GalaxySession],
+        rerun_remap_job_id: int,
+        current_job: Job,
+        out_data,
+    ):
         """
         Re-connect dependent datasets for a job that is being rerun (because it failed initially).
 
@@ -754,22 +782,39 @@ class DefaultToolAction(ToolAction):
         To be able to resume jobs that depend on this jobs output datasets we change the dependent's job
         input datasets to be those of the job that is being rerun.
         """
+        old_job = trans.sa_session.get(Job, rerun_remap_job_id)
+        if not old_job:
+            # I don't think that can really happen
+            raise RequestParameterInvalidException("rerun_remap_job_id parameter is invalid")
+        old_tool = trans.app.toolbox.get_tool(old_job.tool_id, exact=False)
+        new_tool = trans.app.toolbox.get_tool(current_job.tool_id, exact=False)
+        if old_tool and new_tool and old_tool.old_id != new_tool.old_id:
+            # If we currently only have the old or new tool installed we'll find the other tool anyway with `exact=False`.
+            # If we don't have the tool at all we'll fail anyway, no need to worry here.
+            raise RequestParameterInvalidException(
+                f"Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})"
+            )
+        if trans.user is not None:
+            if old_job.user_id != trans.user.id:
+                raise RequestParameterInvalidException(
+                    "Cannot remap job dependencies for job not created by current user."
+                )
+        elif trans.user is None and galaxy_session:
+            if old_job.session_id != galaxy_session.id:
+                raise RequestParameterInvalidException(
+                    "Cannot remap job dependencies for job not created by current user."
+                )
+        else:
+            raise AuthenticationRequired("Authentication required to remap job dependencies")
+        # Need to flush here so that referencing outputs by id works
+        session = trans.sa_session()
+        try:
+            session.expire_on_commit = False
+            with transaction(session):
+                session.commit()
+        finally:
+            session.expire_on_commit = True
         try:
-            old_job = trans.sa_session.get(Job, rerun_remap_job_id)
-            assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid"
-            assert (
-                old_job.tool_id == current_job.tool_id
-            ), f"({old_job.id}/{current_job.id}): Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})"
-            if trans.user is not None:
-                assert (
-                    old_job.user_id == trans.user.id
-                ), f"({old_job.id}/{current_job.id}): Old user id ({old_job.user_id}) does not match rerun user id ({trans.user.id})"
-            elif trans.user is None and isinstance(galaxy_session, trans.model.GalaxySession):
-                assert (
-                    old_job.session_id == galaxy_session.id
-                ), f"({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})"
-            else:
-                raise Exception(f"({old_job.id}/{current_job.id}): Remapping via the API is not (yet) supported")
             # Start by hiding current job outputs before taking over the old job's (implicit) outputs.
             current_job.hide_outputs(flush=False)
             # Duplicate PJAs before remap.
@@ -791,7 +836,7 @@ class DefaultToolAction(ToolAction):
             for jtod in old_job.output_datasets:
                 for job_to_remap, jtid in [(jtid.job, jtid) for jtid in jtod.dataset.dependent_jobs]:
                     if (trans.user is not None and job_to_remap.user_id == trans.user.id) or (
-                        trans.user is None and job_to_remap.session_id == galaxy_session.id
+                        trans.user is None and galaxy_session and job_to_remap.session_id == galaxy_session.id
                     ):
                         self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
                         trans.sa_session.add(job_to_remap)
@@ -846,7 +891,7 @@ class DefaultToolAction(ToolAction):
 
         return on_text_for_names(input_names)
 
-    def _new_job_for_session(self, trans, tool, history):
+    def _new_job_for_session(self, trans, tool, history) -> Tuple[model.Job, Optional[model.GalaxySession]]:
         job = trans.app.model.Job()
         job.galaxy_version = trans.app.config.version_major
         galaxy_session = None
@@ -938,7 +983,7 @@ class DefaultToolAction(ToolAction):
         history=None,
         params=None,
         job_params=None,
-    ):
+    ) -> str:
         if output.label:
             params["tool"] = tool
             params["on_string"] = on_text
@@ -1097,40 +1142,6 @@ class OutputCollections:
             self.out_collection_instances[name] = hdca
 
 
-def on_text_for_names(input_names):
-    # input_names may contain duplicates... this is because the first value in
-    # multiple input dataset parameters will appear twice once as param_name
-    # and once as param_name1.
-    unique_names = []
-    for name in input_names:
-        if name not in unique_names:
-            unique_names.append(name)
-    input_names = unique_names
-
-    # Build name for output datasets based on tool name and input names
-    if len(input_names) == 0:
-        on_text = ""
-    elif len(input_names) == 1:
-        on_text = input_names[0]
-    elif len(input_names) == 2:
-        on_text = "{} and {}".format(*input_names)
-    elif len(input_names) == 3:
-        on_text = "{}, {}, and {}".format(*input_names)
-    else:
-        on_text = "{}, {}, and others".format(*input_names[:2])
-    return on_text
-
-
-def filter_output(tool, output, incoming):
-    for filter in output.filters:
-        try:
-            if not eval(filter.text.strip(), globals(), incoming):
-                return True  # do not create this dataset
-        except Exception as e:
-            log.debug(f"Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}")
-    return False
-
-
 def get_ext_or_implicit_ext(hda):
     if hda.implicitly_converted_parent_datasets:
         # implicitly_converted_parent_datasets is a list of ImplicitlyConvertedDatasetAssociation
@@ -1187,7 +1198,7 @@ def determine_output_format(
 
         if collection_name in input_dataset_collections:
             try:
-                input_collection = input_dataset_collections[collection_name][0][0]
+                input_collection = input_dataset_collections[collection_name]
                 input_collection_collection = input_collection.collection
                 if element_index is None:
                     # just pick the first HDA
diff --git a/lib/galaxy/tools/actions/data_manager.py b/lib/galaxy/tools/actions/data_manager.py
index ce7d69e1048cfe3e09bc9123f1a7a03ad9944743..d8786ad5a92117cdb9db680c9549a379acbcd324 100644
--- a/lib/galaxy/tools/actions/data_manager.py
+++ b/lib/galaxy/tools/actions/data_manager.py
@@ -1,7 +1,27 @@
 import logging
+from typing import Optional
 
+from galaxy.model import (
+    History,
+    Job,
+)
 from galaxy.model.base import transaction
-from . import DefaultToolAction
+from galaxy.model.dataset_collections.matching import MatchingCollections
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import ToolExecutionCache
+from . import (
+    DefaultToolAction,
+    ToolActionExecuteResult,
+)
 
 log = logging.getLogger(__name__)
 
@@ -9,8 +29,41 @@ log = logging.getLogger(__name__)
 class DataManagerToolAction(DefaultToolAction):
     """Tool action used for Data Manager Tools"""
 
-    def execute(self, tool, trans, **kwds):
-        rval = super().execute(tool, trans, **kwds)
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
+        rval = super().execute(
+            tool,
+            trans,
+            incoming=incoming,
+            history=history,
+            job_params=job_params,
+            rerun_remap_job_id=rerun_remap_job_id,
+            execution_cache=execution_cache,
+            dataset_collection_elements=dataset_collection_elements,
+            completed_job=completed_job,
+            collection_info=collection_info,
+            job_callback=job_callback,
+            preferred_object_store_id=preferred_object_store_id,
+            set_output_hid=set_output_hid,
+            flush_job=flush_job,
+            skip=skip,
+        )
         if isinstance(rval, tuple) and len(rval) >= 2 and isinstance(rval[0], trans.app.model.Job):
             assoc = trans.app.model.DataManagerJobAssociation(job=rval[0], data_manager_id=tool.data_manager_id)
             trans.sa_session.add(assoc)
diff --git a/lib/galaxy/tools/actions/history_imp_exp.py b/lib/galaxy/tools/actions/history_imp_exp.py
index d98764c405fdc3da3fbabd341a45d9dd26b81cd3..de502f3a11d72e41dadbef491e1129e6a081fc41 100644
--- a/lib/galaxy/tools/actions/history_imp_exp.py
+++ b/lib/galaxy/tools/actions/history_imp_exp.py
@@ -2,10 +2,30 @@ import datetime
 import logging
 import os
 import tempfile
+from typing import Optional
 
 from galaxy.job_execution.setup import create_working_directory_for_job
+from galaxy.model import (
+    History,
+    Job,
+)
 from galaxy.model.base import transaction
-from galaxy.tools.actions import ToolAction
+from galaxy.model.dataset_collections.matching import MatchingCollections
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
+from galaxy.tools.actions import (
+    ToolAction,
+    ToolActionExecuteResult,
+)
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import ToolExecutionCache
 from galaxy.tools.imp_exp import (
     JobExportHistoryArchiveWrapper,
     JobImportHistoryArchiveWrapper,
@@ -18,9 +38,26 @@ log = logging.getLogger(__name__)
 class ImportHistoryToolAction(ToolAction):
     """Tool action used for importing a history to an archive."""
 
-    produces_real_jobs = True
-
-    def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
+    produces_real_jobs: bool = True
+
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         #
         # Create job.
         #
@@ -78,9 +115,26 @@ class ImportHistoryToolAction(ToolAction):
 class ExportHistoryToolAction(ToolAction):
     """Tool action used for exporting a history to an archive."""
 
-    produces_real_jobs = True
-
-    def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs):
+    produces_real_jobs: bool = True
+
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         trans.check_user_activation()
         #
         # Get history to export.
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index 04db0ab30e1729c16ca9ae591d9a58bc0dc15297..2b46c6060ccdbf6286378c1f1a8a84ebac71a176 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -1,10 +1,32 @@
 import logging
 import os
 from json import dumps
+from typing import (
+    Any,
+    Dict,
+    Optional,
+)
 
 from galaxy.job_execution.datasets import DatasetPath
 from galaxy.metadata import get_metadata_compute_strategy
+from galaxy.model import (
+    History,
+    Job,
+    User,
+)
 from galaxy.model.base import transaction
+from galaxy.model.dataset_collections.matching import MatchingCollections
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import ToolExecutionCache
 from galaxy.util import asbool
 from . import ToolAction
 
@@ -14,47 +36,80 @@ log = logging.getLogger(__name__)
 class SetMetadataToolAction(ToolAction):
     """Tool action used for setting external metadata on an existing dataset"""
 
-    produces_real_jobs = False
+    produces_real_jobs: bool = False
+    set_output_hid: bool = False
 
     def execute(
-        self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
     ):
         """
         Execute using a web transaction.
         """
+        overwrite = True
+        job, odict = self.execute_via_trans(
+            tool,
+            trans,
+            incoming,
+            overwrite,
+            history,
+            job_params,
+        )
+        # FIXME: can remove this when logging in execute_via_app method.
+        trans.log_event(f"Added set external metadata job to the job queue, id: {str(job.id)}", tool_id=job.tool_id)
+        return job, odict
+
+    def execute_via_trans(
+        self,
+        tool,
+        trans,
+        incoming: Optional[Dict[str, Any]],
+        overwrite: bool = True,
+        history: Optional[History] = None,
+        job_params: Optional[Dict[str, Any]] = None,
+    ):
         trans.check_user_activation()
         session = trans.get_galaxy_session()
         session_id = session and session.id
         history_id = trans.history and trans.history.id
         incoming = incoming or {}
-        job, odict = self.execute_via_app(
+        return self.execute_via_app(
             tool,
             trans.app,
             session_id,
             history_id,
             trans.user,
             incoming,
-            set_output_hid,
             overwrite,
             history,
             job_params,
         )
-        # FIXME: can remove this when logging in execute_via_app method.
-        trans.log_event(f"Added set external metadata job to the job queue, id: {str(job.id)}", tool_id=job.tool_id)
-        return job, odict
 
     def execute_via_app(
         self,
         tool,
         app,
-        session_id,
-        history_id,
-        user=None,
-        incoming=None,
-        set_output_hid=False,
-        overwrite=True,
-        history=None,
-        job_params=None,
+        session_id: Optional[int],
+        history_id: Optional[int],
+        user: Optional[User] = None,
+        incoming: Optional[Dict[str, Any]] = None,
+        overwrite: bool = True,
+        history: Optional[History] = None,
+        job_params: Optional[Dict[str, Any]] = None,
     ):
         """
         Execute using application.
diff --git a/lib/galaxy/tools/actions/model_operations.py b/lib/galaxy/tools/actions/model_operations.py
index bedba42d4aa3cc5953124fe6709b1d92ce8730fe..85a7411532b5bc8b35df67d9eeb9e3ade1835fa8 100644
--- a/lib/galaxy/tools/actions/model_operations.py
+++ b/lib/galaxy/tools/actions/model_operations.py
@@ -1,12 +1,32 @@
 import logging
-from typing import TYPE_CHECKING
+from typing import (
+    Optional,
+    TYPE_CHECKING,
+)
 
+from galaxy.model import (
+    History,
+    Job,
+)
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.objectstore import ObjectStorePopulator
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
 from galaxy.tools.actions import (
     DefaultToolAction,
     OutputCollections,
-    ToolExecutionCache,
+    OutputDatasetsT,
+    ToolActionExecuteResult,
 )
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import ToolExecutionCache
 
 if TYPE_CHECKING:
     from galaxy.managers.context import ProvidesUserContext
@@ -15,7 +35,7 @@ log = logging.getLogger(__name__)
 
 
 class ModelOperationToolAction(DefaultToolAction):
-    produces_real_jobs = False
+    produces_real_jobs: bool = False
 
     def check_inputs_ready(self, tool, trans, incoming, history, execution_cache=None, collection_info=None):
         if execution_cache is None:
@@ -26,23 +46,26 @@ class ModelOperationToolAction(DefaultToolAction):
             tool, trans, incoming, history, current_user_roles, collection_info
         )
 
-        tool.check_inputs_ready(inp_data, inp_dataset_collections)
+        tool.check_inputs_ready(inp_data, inp_dataset_collections, security=trans.security)
 
     def execute(
         self,
         tool,
         trans,
-        incoming=None,
-        set_output_hid=False,
-        overwrite=True,
-        history=None,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
         job_params=None,
-        execution_cache=None,
-        collection_info=None,
-        job_callback=None,
-        skip=False,
-        **kwargs,
-    ):
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         incoming = incoming or {}
         trans.check_user_activation()
 
@@ -65,7 +88,7 @@ class ModelOperationToolAction(DefaultToolAction):
         # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
         wrapped_params = self._wrapped_params(trans, tool, incoming)
 
-        out_data = {}
+        out_data: OutputDatasetsT = {}
         input_collections = {k: v[0][0] for k, v in inp_dataset_collections.items()}
         output_collections = OutputCollections(
             trans,
@@ -73,7 +96,7 @@ class ModelOperationToolAction(DefaultToolAction):
             tool=tool,
             tool_action=self,
             input_collections=input_collections,
-            dataset_collection_elements=kwargs.get("dataset_collection_elements", None),
+            dataset_collection_elements=dataset_collection_elements,
             on_text=on_text,
             incoming=incoming,
             params=wrapped_params.params,
@@ -116,7 +139,6 @@ class ModelOperationToolAction(DefaultToolAction):
     def _produce_outputs(
         self, trans: "ProvidesUserContext", tool, out_data, output_collections, incoming, history, tags, hdca_tags, skip
     ):
-        tag_handler = trans.tag_handler
         tool.produce_outputs(
             trans,
             out_data,
@@ -125,7 +147,6 @@ class ModelOperationToolAction(DefaultToolAction):
             history=history,
             tags=tags,
             hdca_tags=hdca_tags,
-            tag_handler=tag_handler,
         )
         if mapped_over_elements := output_collections.dataset_collection_elements:
             for name, value in out_data.items():
diff --git a/lib/galaxy/tools/actions/upload.py b/lib/galaxy/tools/actions/upload.py
index ee3a47e05f7b5a05ace7d80e8244591cb3dc6aa9..651684a45a7c5ae61fa751d39afa07dbe50216b6 100644
--- a/lib/galaxy/tools/actions/upload.py
+++ b/lib/galaxy/tools/actions/upload.py
@@ -1,14 +1,34 @@
 import json
 import logging
 import os
+from typing import Optional
 
 from galaxy.exceptions import RequestParameterMissingException
+from galaxy.model import (
+    History,
+    Job,
+)
 from galaxy.model.base import transaction
+from galaxy.model.dataset_collections.matching import MatchingCollections
 from galaxy.model.dataset_collections.structure import UninitializedTree
+from galaxy.tools._types import ToolStateJobInstancePopulatedT
 from galaxy.tools.actions import upload_common
+from galaxy.tools.execute import (
+    DatasetCollectionElementsSliceT,
+    DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    DEFAULT_JOB_CALLBACK,
+    DEFAULT_PREFERRED_OBJECT_STORE_ID,
+    DEFAULT_RERUN_REMAP_JOB_ID,
+    DEFAULT_SET_OUTPUT_HID,
+    JobCallbackT,
+)
+from galaxy.tools.execution_helpers import ToolExecutionCache
 from galaxy.util import ExecutionTimer
 from galaxy.util.bunch import Bunch
-from . import ToolAction
+from . import (
+    ToolAction,
+    ToolActionExecuteResult,
+)
 
 log = logging.getLogger(__name__)
 
@@ -16,7 +36,24 @@ log = logging.getLogger(__name__)
 class BaseUploadToolAction(ToolAction):
     produces_real_jobs = True
 
-    def execute(self, tool, trans, incoming=None, history=None, **kwargs):
+    def execute(
+        self,
+        tool,
+        trans,
+        incoming: Optional[ToolStateJobInstancePopulatedT] = None,
+        history: Optional[History] = None,
+        job_params=None,
+        rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+        execution_cache: Optional[ToolExecutionCache] = None,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+        completed_job: Optional[Job] = None,
+        collection_info: Optional[MatchingCollections] = None,
+        job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+        preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
+        set_output_hid: bool = DEFAULT_SET_OUTPUT_HID,
+        flush_job: bool = True,
+        skip: bool = False,
+    ) -> ToolActionExecuteResult:
         trans.check_user_activation()
         incoming = incoming or {}
         dataset_upload_inputs = []
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index 8101af78b32438e5e0d0ab63e771b67594c63a89..1d6d1b9a4c10c72ce85bb56fc57c7718752d182e 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -195,8 +195,9 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, tag_h
         tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag_from_filename, flush=False)
 
     if tags_list := uploaded_dataset.get("tags", False):
-        for tag in tags_list:
-            tag_handler.apply_item_tag(item=ldda, user=trans.user, name="name", value=tag, flush=False)
+        new_tags = tag_handler.parse_tags_list(tags_list)
+        for tag in new_tags:
+            tag_handler.apply_item_tag(item=ldda, user=trans.user, name=tag[0], value=tag[1], flush=False)
 
     trans.sa_session.add(ldda)
     if state:
@@ -276,7 +277,13 @@ def new_upload(
                 )
     else:
         upload_target_dataset_instance = __new_history_upload(trans, uploaded_dataset, history=history, state=state)
-
+        tags_raw = getattr(uploaded_dataset, "tags", None)
+        if tags_raw:
+            new_tags = tag_handler.parse_tags_list(tags_raw.split(","))
+            for tag in new_tags:
+                tag_handler.apply_item_tag(
+                    user=trans.user, item=upload_target_dataset_instance, name=tag[0], value=tag[1], flush=True
+                )
     if tag_list:
         tag_handler.add_tags_from_list(trans.user, upload_target_dataset_instance, tag_list, flush=False)
 
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index a6786c725dc99be927b84be576f7923c39d9bdf5..459042e60c721a3b12c07d8d53660cdef1e550ab 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -23,6 +23,7 @@ from galaxy.datatypes.upload_util import (
     UploadProblemException,
 )
 from galaxy.files.uris import (
+    ensure_file_sources,
     stream_to_file,
     stream_url_to_file,
 )
@@ -34,7 +35,8 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.compression_utils import CompressedFile
 from galaxy.util.hash_util import (
     HASH_NAMES,
-    memory_bound_hexdigest,
+    HashFunctionNameEnum,
+    verify_hash,
 )
 
 DESCRIPTION = """Data Import Script"""
@@ -85,7 +87,7 @@ def _request_to_galaxy_json(upload_config: "UploadConfig", request):
     return {"__unnamed_outputs": fetched_targets}
 
 
-def _fetch_target(upload_config: "UploadConfig", target):
+def _fetch_target(upload_config: "UploadConfig", target: Dict[str, Any]):
     destination = target.get("destination", None)
     assert destination, "No destination defined."
 
@@ -96,13 +98,13 @@ def _fetch_target(upload_config: "UploadConfig", target):
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _directory_to_items(decompressed_directory)
             elif elements_from == "bagit":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _bagit_to_items(elements_from_path)
             elif elements_from == "bagit_archive":
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _bagit_to_items(decompressed_directory)
             elif elements_from == "directory":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _directory_to_items(elements_from_path)
             else:
                 raise Exception(f"Unknown elements from type encountered [{elements_from}]")
@@ -157,21 +159,28 @@ def _fetch_target(upload_config: "UploadConfig", target):
         registry = upload_config.registry
         datatype = registry.get_datatype_by_extension(requested_ext)
         composite = item.pop("composite", None)
+        validated_metadata = {}
         if datatype and datatype.composite_type:
             composite_type = datatype.composite_type
             assert composite_type == "auto_primary_file", "basic composite uploads not yet implemented"
+            provided_metadata = item.get("metadata")
+            if provided_metadata:
+                for key, value in provided_metadata.items():
+                    metadata_element = datatype.metadata_spec.get(key)
+                    if metadata_element and metadata_element.set_in_upload:
+                        validated_metadata[key] = value
 
             # get_composite_dataset_name finds dataset name from basename of contents
             # and such but we're not implementing that here yet. yagni?
             # also need name...
-            metadata = {
+            metadata = item.get("metadata") or {
                 composite_file.substitute_name_with_metadata: datatype.metadata_spec[
                     composite_file.substitute_name_with_metadata
                 ].default
                 for composite_file in datatype.composite_files.values()
                 if composite_file.substitute_name_with_metadata
             }
-            name = item.get("name") or "Composite Dataset"
+            name = metadata.get("base_name") or item.get("name") or "Composite Dataset"
             metadata["base_name"] = name
             dataset = Bunch(
                 name=name,
@@ -194,6 +203,8 @@ def _fetch_target(upload_config: "UploadConfig", target):
                 "hashes": [],
                 "extra_files": extra_files_path,
             }
+            if validated_metadata:
+                rval["metadata"] = validated_metadata
             _copy_and_validate_simple_attributes(item, rval)
             composite_items = composite.get("elements", [])
             keys = list(writable_files.keys())
@@ -204,7 +215,7 @@ def _fetch_target(upload_config: "UploadConfig", target):
                     pass
                 key = keys[composite_item_idx]
                 writable_file = writable_files[key]
-                _, src_target = _has_src_to_path(upload_config, composite_item)
+                _, src_target, _ = _has_src_to_path(upload_config, composite_item)
                 # do the writing
                 sniff.handle_composite_file(
                     datatype,
@@ -237,10 +248,23 @@ def _fetch_target(upload_config: "UploadConfig", target):
         converted_path = None
 
         deferred = upload_config.get_option(item, "deferred")
+
+        link_data_only = upload_config.link_data_only
+        link_data_only_explicit = upload_config.link_data_only_explicit
+        if "link_data_only" in item:
+            # Allow overriding this on a per file basis.
+            link_data_only, link_data_only_explicit = _link_data_only(item)
+
         name: str
         path: Optional[str]
+        default_in_place = False
         if not deferred:
-            name, path = _has_src_to_path(upload_config, item, is_dataset=True)
+            name, path, is_link = _has_src_to_path(
+                upload_config, item, is_dataset=True, link_data_only_explicitly_set=link_data_only_explicit
+            )
+            if is_link:
+                link_data_only = True
+                default_in_place = True
         else:
             name, path = _has_src_to_name(item) or "Deferred Dataset", None
         sources = []
@@ -250,20 +274,21 @@ def _fetch_target(upload_config: "UploadConfig", target):
         if url:
             sources.append(source_dict)
         hashes = item.get("hashes", [])
-        for hash_dict in hashes:
-            hash_function = hash_dict.get("hash_function")
-            hash_value = hash_dict.get("hash_value")
-            try:
-                _handle_hash_validation(upload_config, hash_function, hash_value, path)
-            except Exception as e:
-                error_message = str(e)
-                item["error_message"] = error_message
+        for hash_function in HASH_NAMES:
+            hash_value = item.get(hash_function)
+            if hash_value:
+                hashes.append({"hash_function": hash_function, "hash_value": hash_value})
+        if path:
+            for hash_dict in hashes:
+                hash_function = hash_dict.get("hash_function")
+                hash_value = hash_dict.get("hash_value")
+                try:
+                    _handle_hash_validation(hash_function, hash_value, path)
+                except Exception as e:
+                    error_message = str(e)
+                    item["error_message"] = error_message
 
         dbkey = item.get("dbkey", "?")
-        link_data_only = upload_config.link_data_only
-        if "link_data_only" in item:
-            # Allow overriding this on a per file basis.
-            link_data_only = _link_data_only(item)
 
         ext = "data"
         staged_extra_files = None
@@ -275,7 +300,7 @@ def _fetch_target(upload_config: "UploadConfig", target):
 
         effective_state = "ok"
         if not deferred and not error_message:
-            in_place = item.get("in_place", False)
+            in_place = item.get("in_place", default_in_place)
             purge_source = item.get("purge_source", True)
 
             registry = upload_config.registry
@@ -333,7 +358,7 @@ def _fetch_target(upload_config: "UploadConfig", target):
                                 item_prefix = os.path.join(prefix, name)
                             walk_extra_files(item.get("elements"), prefix=item_prefix)
                         else:
-                            src_name, src_path = _has_src_to_path(upload_config, item)
+                            src_name, src_path, _ = _has_src_to_path(upload_config, item)
                             if prefix:
                                 rel_path = os.path.join(prefix, src_name)
                             else:
@@ -418,8 +443,8 @@ def _bagit_to_items(directory):
     return items
 
 
-def _decompress_target(upload_config: "UploadConfig", target):
-    elements_from_name, elements_from_path = _has_src_to_path(upload_config, target, is_dataset=False)
+def _decompress_target(upload_config: "UploadConfig", target: Dict[str, Any]):
+    elements_from_name, elements_from_path, _ = _has_src_to_path(upload_config, target, is_dataset=False)
     # by default Galaxy will check for a directory with a single file and interpret that
     # as the new root for expansion, this is a good user experience for uploading single
     # files in a archive but not great from an API perspective. Allow disabling by setting
@@ -477,12 +502,33 @@ def _has_src_to_name(item) -> Optional[str]:
     return name
 
 
-def _has_src_to_path(upload_config, item, is_dataset=False) -> Tuple[str, str]:
+def _has_src_to_path(
+    upload_config: "UploadConfig",
+    item: Dict[str, Any],
+    is_dataset: bool = False,
+    link_data_only: bool = False,
+    link_data_only_explicitly_set: bool = False,
+) -> Tuple[str, str, bool]:
     assert "src" in item, item
     src = item.get("src")
     name = item.get("name")
+    is_link = False
     if src == "url":
         url = item.get("url")
+        file_sources = ensure_file_sources(upload_config.file_sources)
+        assert url, "url cannot be empty"
+        if not link_data_only_explicitly_set:
+            file_source, rel_path = file_sources.get_file_source_path(url)
+            prefer_links = file_source.prefer_links()
+            if prefer_links:
+                if rel_path.startswith("/"):
+                    rel_path = rel_path[1:]
+                path = os.path.abspath(os.path.join(file_source.root, rel_path))
+                if name is None:
+                    name = url.split("/")[-1]
+                is_link = True
+                return name, path, is_link
+
         try:
             path = stream_url_to_file(url, file_sources=upload_config.file_sources, dir=upload_config.working_directory)
         except Exception as e:
@@ -494,7 +540,7 @@ def _has_src_to_path(upload_config, item, is_dataset=False) -> Tuple[str, str]:
             for hash_function in HASH_NAMES:
                 hash_value = item.get(hash_function)
                 if hash_value:
-                    _handle_hash_validation(upload_config, hash_function, hash_value, path)
+                    _handle_hash_validation(hash_function, hash_value, path)
         if name is None:
             name = url.split("/")[-1]
     elif src == "pasted":
@@ -506,16 +552,11 @@ def _has_src_to_path(upload_config, item, is_dataset=False) -> Tuple[str, str]:
         path = item["path"]
         if name is None:
             name = os.path.basename(path)
-    return name, path
+    return name, path, is_link
 
 
-def _handle_hash_validation(upload_config, hash_function, hash_value, path):
-    if upload_config.validate_hashes:
-        calculated_hash_value = memory_bound_hexdigest(hash_func_name=hash_function, path=path)
-        if calculated_hash_value != hash_value:
-            raise Exception(
-                f"Failed to validate upload with [{hash_function}] - expected [{hash_value}] got [{calculated_hash_value}]"
-            )
+def _handle_hash_validation(hash_function: HashFunctionNameEnum, hash_value: str, path: str):
+    verify_hash(path, hash_func_name=hash_function, hash_value=hash_value, what="upload")
 
 
 def _arg_parser():
@@ -548,11 +589,11 @@ def get_file_sources(working_directory, file_sources_as_dict=None):
 class UploadConfig:
     def __init__(
         self,
-        request,
-        registry,
-        working_directory,
-        allow_failed_collections,
-        file_sources_dict=None,
+        request: Dict[str, Any],
+        registry: Registry,
+        working_directory: str,
+        allow_failed_collections: bool,
+        file_sources_dict: Optional[Dict] = None,
     ):
         self.registry = registry
         self.working_directory = working_directory
@@ -561,9 +602,8 @@ class UploadConfig:
         self.to_posix_lines = request.get("to_posix_lines", False)
         self.space_to_tab = request.get("space_to_tab", False)
         self.auto_decompress = request.get("auto_decompress", False)
-        self.validate_hashes = request.get("validate_hashes", False)
         self.deferred = request.get("deferred", False)
-        self.link_data_only = _link_data_only(request)
+        self.link_data_only, self.link_data_only_explicit = _link_data_only(request)
         self.file_sources_dict = file_sources_dict
         self._file_sources = None
 
@@ -615,12 +655,19 @@ class UploadConfig:
         return new_path
 
 
-def _link_data_only(has_config_dict):
-    link_data_only = has_config_dict.get("link_data_only", False)
-    if not isinstance(link_data_only, bool):
-        # Allow the older string values of 'copy_files' and 'link_to_files'
-        link_data_only = link_data_only == "copy_files"
-    return link_data_only
+def _link_data_only(has_config_dict) -> Tuple[bool, bool]:
+    if "link_data_only" in has_config_dict:
+        link_data_only_raw = has_config_dict["link_data_only"]
+        if not isinstance(link_data_only_raw, bool):
+            # Allow the older string values of 'copy_files' and 'link_to_files'
+            link_data_only = link_data_only_raw == "copy_files"
+        else:
+            link_data_only = link_data_only_raw
+        link_data_only_explicit = True
+    else:
+        link_data_only = False
+        link_data_only_explicit = False
+    return link_data_only, link_data_only_explicit
 
 
 def _for_each_src(f, obj):
diff --git a/lib/galaxy/tools/error_reports/plugins/__init__.py b/lib/galaxy/tools/error_reports/plugins/__init__.py
index 97de6441cb30ab7b1e98fb4cb2ca3da228784248..08e03097775e8dc36c8db6c2c8d09081bb54dea1 100644
--- a/lib/galaxy/tools/error_reports/plugins/__init__.py
+++ b/lib/galaxy/tools/error_reports/plugins/__init__.py
@@ -17,6 +17,6 @@ class ErrorPlugin(metaclass=ABCMeta):
     def plugin_type(self):
         """Short string providing labelling this plugin"""
 
-    def submit_report(self, dataset, job, tool, user_submission=False, **kwargs):
+    def submit_report(self, dataset, job, tool, **kwargs):
         """Submit the bug report and render a string to be displayed to the user."""
         return None
diff --git a/lib/galaxy/tools/error_reports/plugins/slack.py b/lib/galaxy/tools/error_reports/plugins/slack.py
index 53affb80bc1a0c458a7384e749a9bb487498e2c7..3c4f273ed034cc813d94204259a1f0f1b3b0350d 100644
--- a/lib/galaxy/tools/error_reports/plugins/slack.py
+++ b/lib/galaxy/tools/error_reports/plugins/slack.py
@@ -17,7 +17,7 @@ log = logging.getLogger(__name__)
 
 
 class SlackPlugin(BaseGitPlugin):
-    """Send error report to Sentry."""
+    """Send error report to Slack."""
 
     plugin_type = "slack"
 
diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py
index 771a7f5b856a0838d1973fc177fd06c1772af8cf..e42a5f68f9b7d5b2615d4b798b8b2f62e10afb32 100644
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -12,15 +12,15 @@ from typing import (
     Dict,
     List,
     Optional,
-    Union,
+    TYPE_CHECKING,
 )
-from urllib.parse import urlparse
 
 from packaging.version import Version
 
 from galaxy import model
 from galaxy.authnz.util import provider_name_to_backend
 from galaxy.job_execution.compute_environment import ComputeEnvironment
+from galaxy.job_execution.datasets import DeferrableObjectsT
 from galaxy.job_execution.setup import ensure_configs_directory
 from galaxy.model.deferred import (
     materialize_collection_input,
@@ -33,6 +33,7 @@ from galaxy.structured_app import (
     MinimalToolApp,
 )
 from galaxy.tool_util.data import TabularToolDataTable
+from galaxy.tools.actions import determine_output_format
 from galaxy.tools.parameters import (
     visit_input_values,
     wrapped_json,
@@ -71,6 +72,9 @@ from galaxy.util.template import (
 from galaxy.util.tree_dict import TreeDict
 from galaxy.work.context import WorkRequestContext
 
+if TYPE_CHECKING:
+    from galaxy.tools import Tool
+
 log = logging.getLogger(__name__)
 
 
@@ -90,18 +94,27 @@ class ToolErrorLog:
 global_tool_errors = ToolErrorLog()
 
 
-def global_tool_logs(func, config_file, action_str):
+class ToolTemplatingException(Exception):
+
+    def __init__(self, *args: object, tool_id: Optional[str], tool_version: str, is_latest: bool) -> None:
+        super().__init__(*args)
+        self.tool_id = tool_id
+        self.tool_version = tool_version
+        self.is_latest = is_latest
+
+
+def global_tool_logs(func, config_file: str, action_str: str, tool: "Tool"):
     try:
         return func()
     except Exception as e:
         # capture and log parsing errors
         global_tool_errors.add_error(config_file, action_str, e)
-        raise e
-
-
-DeferrableObjectsT = Union[
-    model.DatasetInstance, model.HistoryDatasetCollectionAssociation, model.DatasetCollectionElement
-]
+        raise ToolTemplatingException(
+            f"Error occurred while {action_str.lower()} for tool '{tool.id}'",
+            tool_id=tool.id,
+            tool_version=tool.version,
+            is_latest=tool.is_latest_version,
+        ) from e
 
 
 class ToolEvaluator:
@@ -150,6 +163,7 @@ class ToolEvaluator:
 
         # materialize deferred datasets
         materialized_objects = self._materialize_objects(deferred_objects, self.local_working_directory)
+        self.compute_environment.materialized_objects = materialized_objects
 
         # replace materialized objects back into tool input parameters
         self._replaced_deferred_objects(inp_data, incoming, materialized_objects)
@@ -169,6 +183,9 @@ class ToolEvaluator:
             out_data,
             output_collections=out_collections,
         )
+        # late update of format_source outputs
+        self._eval_format_source(job, inp_data, out_data)
+
         self.execute_tool_hooks(inp_data=inp_data, out_data=out_data, incoming=incoming)
 
     def execute_tool_hooks(self, inp_data, out_data, incoming):
@@ -199,11 +216,6 @@ class ToolEvaluator:
         if self._history:
             param_dict["__history_id__"] = self.app.security.encode_id(self._history.id)
         param_dict["__galaxy_url__"] = self.compute_environment.galaxy_url()
-        if hasattr(self.job, "interactive_url") and isinstance(self.job.interactive_url, str):
-            param_dict["__tool_url_prefix__"] = "".join(
-                [self.job.interactive_url, ".", urlparse(self.compute_environment.galaxy_url()).hostname]
-            )
-
         param_dict.update(self.tool.template_macro_params)
         # All parameters go into the param_dict
         param_dict.update(incoming)
@@ -263,6 +275,23 @@ class ToolEvaluator:
 
         return undeferred_objects
 
+    def _eval_format_source(
+        self,
+        job: model.Job,
+        inp_data: Dict[str, Optional[model.DatasetInstance]],
+        out_data: Dict[str, model.DatasetInstance],
+    ):
+        for output_name, output in out_data.items():
+            if (
+                (tool_output := self.tool.outputs.get(output_name))
+                and (tool_output.format_source or tool_output.change_format)
+                and output.extension == "expression.json"
+            ):
+                input_collections = {jtidca.name: jtidca.dataset_collection for jtidca in job.input_dataset_collections}
+                ext = determine_output_format(tool_output, self.param_dict, inp_data, input_collections, None)
+                if ext:
+                    output.extension = ext
+
     def _replaced_deferred_objects(
         self,
         inp_data: Dict[str, Optional[model.DatasetInstance]],
@@ -302,7 +331,8 @@ class ToolEvaluator:
         deferred_objects: Dict[str, DeferrableObjectsT] = {}
         for key, value in input_datasets.items():
             if value is not None and value.state == model.Dataset.states.DEFERRED:
-                deferred_objects[key] = value
+                if self._should_materialize_deferred_input(key, value):
+                    deferred_objects[key] = value
 
         def find_deferred_collections(input, value, context, prefixed_name=None, **kwargs):
             if (
@@ -315,6 +345,19 @@ class ToolEvaluator:
 
         return deferred_objects
 
+    def _should_materialize_deferred_input(self, input_name: str, input_value: DeferrableObjectsT) -> bool:
+        """
+        We can skip materializing some deferred datasets if the input can work with URIs that are prefixed
+        with a known prefix set in `allow_uri_if_protocol`.
+        """
+        deferred_input = self.tool.inputs.get(input_name)
+        if isinstance(deferred_input, DataToolParameter) and isinstance(input_value, model.DatasetInstance):
+            source_uri = input_value.deferred_source_uri or ""
+            for prefix in deferred_input.allow_uri_if_protocol:
+                if prefix == "*" or source_uri.startswith(prefix):
+                    return False
+        return True
+
     def __walk_inputs(self, inputs, input_values, func):
         def do_walk(inputs, input_values):
             """
@@ -526,10 +569,10 @@ class ToolEvaluator:
 
     def _create_interactivetools_entry_points(self):
         if hasattr(self.app, "interactivetool_manager"):
-            self.interactivetools = self.populate_interactivetools()
+            self.interactivetools = self._populate_interactivetools_template()
             self.app.interactivetool_manager.create_interactivetool(self.job, self.tool, self.interactivetools)
 
-    def populate_interactivetools(self):
+    def _populate_interactivetools_template(self):
         """
         Populate InteractiveTools templated values.
         """
@@ -542,7 +585,6 @@ class ToolEvaluator:
                 "label",
                 "url",
                 "requires_domain",
-                "protocol",
                 "requires_path_in_url",
                 "requires_path_in_header_named",
             ):
@@ -587,16 +629,25 @@ class ToolEvaluator:
         compute environment.
         """
         config_file = self.tool.config_file
-        global_tool_logs(self._build_config_files, config_file, "Building Config Files")
-        global_tool_logs(self._build_param_file, config_file, "Building Param File")
-        global_tool_logs(self._build_command_line, config_file, "Building Command Line")
-        global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
-        global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
+        global_tool_logs(
+            self._create_interactivetools_entry_points, config_file, "Building Interactive Tool Entry Points", self.tool
+        )
+        global_tool_logs(
+            self._build_config_files,
+            config_file,
+            "Building Config Files",
+            self.tool,
+        )
+        global_tool_logs(self._build_param_file, config_file, "Building Param File", self.tool)
+        global_tool_logs(self._build_command_line, config_file, "Building Command Line", self.tool)
+        global_tool_logs(self._build_version_command, config_file, "Building Version Command Line", self.tool)
+        global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables", self.tool)
         return (
             self.command_line,
             self.version_command_line,
             self.extra_filenames,
             self.environment_variables,
+            self.interactivetools,
         )
 
     def _build_command_line(self):
@@ -839,7 +890,7 @@ class PartialToolEvaluator(ToolEvaluator):
 
     def build(self):
         config_file = self.tool.config_file
-        global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
+        global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables", self.tool)
         return (
             self.command_line,
             self.version_command_line,
@@ -860,10 +911,10 @@ class RemoteToolEvaluator(ToolEvaluator):
 
     def build(self):
         config_file = self.tool.config_file
-        global_tool_logs(self._build_config_files, config_file, "Building Config Files")
-        global_tool_logs(self._build_param_file, config_file, "Building Param File")
-        global_tool_logs(self._build_command_line, config_file, "Building Command Line")
-        global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
+        global_tool_logs(self._build_config_files, config_file, "Building Config Files", self.tool)
+        global_tool_logs(self._build_param_file, config_file, "Building Param File", self.tool)
+        global_tool_logs(self._build_command_line, config_file, "Building Command Line", self.tool)
+        global_tool_logs(self._build_version_command, config_file, "Building Version Command Line", self.tool)
         return (
             self.command_line,
             self.version_command_line,
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index cca56529442854a0b0a25a627e469431df122df1..31369c948052532726eb1a4d0afa4015cd79a79d 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -15,6 +15,8 @@ from typing import (
     List,
     NamedTuple,
     Optional,
+    Tuple,
+    Union,
 )
 
 from boltons.iterutils import remap
@@ -29,12 +31,16 @@ from galaxy.model.dataset_collections.structure import (
     tool_output_to_structure,
 )
 from galaxy.tool_util.parser import ToolOutputCollectionPart
-from galaxy.tools.actions import (
+from galaxy.tools.execution_helpers import (
     filter_output,
     on_text_for_names,
     ToolExecutionCache,
 )
 from galaxy.tools.parameters.workflow_utils import is_runtime_value
+from ._types import (
+    ToolRequestT,
+    ToolStateJobInstancePopulatedT,
+)
 
 if typing.TYPE_CHECKING:
     from galaxy.tools import Tool
@@ -45,14 +51,26 @@ SINGLE_EXECUTION_SUCCESS_MESSAGE = "Tool ${tool_id} created job ${job_id}"
 BATCH_EXECUTION_MESSAGE = "Created ${job_count} job(s) for tool ${tool_id} request"
 
 
+CompletedJobsT = Dict[int, Optional[model.Job]]
+JobCallbackT = Callable
+WorkflowResourceParametersT = Dict[str, Any]
+DatasetCollectionElementsSliceT = Dict[str, model.DatasetCollectionElement]
+DEFAULT_USE_CACHED_JOB = False
+DEFAULT_PREFERRED_OBJECT_STORE_ID: Optional[str] = None
+DEFAULT_RERUN_REMAP_JOB_ID: Optional[int] = None
+DEFAULT_JOB_CALLBACK: Optional[JobCallbackT] = None
+DEFAULT_DATASET_COLLECTION_ELEMENTS: Optional[DatasetCollectionElementsSliceT] = None
+DEFAULT_SET_OUTPUT_HID: bool = True
+
+
 class PartialJobExecution(Exception):
-    def __init__(self, execution_tracker):
+    def __init__(self, execution_tracker: "ExecutionTracker"):
         self.execution_tracker = execution_tracker
 
 
 class MappingParameters(NamedTuple):
-    param_template: Dict[str, Any]
-    param_combinations: List[Dict[str, Any]]
+    param_template: ToolRequestT
+    param_combinations: List[ToolStateJobInstancePopulatedT]
 
 
 def execute(
@@ -60,15 +78,15 @@ def execute(
     tool: "Tool",
     mapping_params: MappingParameters,
     history: model.History,
-    rerun_remap_job_id: Optional[int] = None,
-    preferred_object_store_id: Optional[str] = None,
+    rerun_remap_job_id: Optional[int] = DEFAULT_RERUN_REMAP_JOB_ID,
+    preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
     collection_info: Optional[MatchingCollections] = None,
     workflow_invocation_uuid: Optional[str] = None,
     invocation_step: Optional[model.WorkflowInvocationStep] = None,
     max_num_jobs: Optional[int] = None,
-    job_callback: Optional[Callable] = None,
-    completed_jobs: Optional[Dict[int, Optional[model.Job]]] = None,
-    workflow_resource_parameters: Optional[Dict[str, Any]] = None,
+    job_callback: Optional[JobCallbackT] = DEFAULT_JOB_CALLBACK,
+    completed_jobs: Optional[CompletedJobsT] = None,
+    workflow_resource_parameters: Optional[WorkflowResourceParametersT] = None,
     validate_outputs: bool = False,
 ):
     """
@@ -95,7 +113,7 @@ def execute(
         )
     execution_cache = ToolExecutionCache(trans)
 
-    def execute_single_job(execution_slice, completed_job, skip=False):
+    def execute_single_job(execution_slice: "ExecutionSlice", completed_job: Optional[model.Job], skip: bool = False):
         job_timer = tool.app.execution_timer_factory.get_timer(
             "internals.galaxy.tools.execute.job_single", SINGLE_EXECUTION_SUCCESS_MESSAGE
         )
@@ -124,8 +142,8 @@ def execute(
             execution_cache,
             completed_job,
             collection_info,
-            job_callback=job_callback,
-            preferred_object_store_id=preferred_object_store_id,
+            job_callback,
+            preferred_object_store_id,
             flush_job=False,
             skip=skip,
         )
@@ -225,15 +243,41 @@ def execute(
 
 
 class ExecutionSlice:
-    def __init__(self, job_index, param_combination, dataset_collection_elements=None):
+    job_index: int
+    param_combination: ToolStateJobInstancePopulatedT
+    dataset_collection_elements: Optional[DatasetCollectionElementsSliceT]
+    history: Optional[model.History]
+
+    def __init__(
+        self,
+        job_index: int,
+        param_combination: ToolStateJobInstancePopulatedT,
+        dataset_collection_elements: Optional[DatasetCollectionElementsSliceT] = DEFAULT_DATASET_COLLECTION_ELEMENTS,
+    ):
         self.job_index = job_index
         self.param_combination = param_combination
         self.dataset_collection_elements = dataset_collection_elements
         self.history = None
 
 
+ExecutionErrorsT = Union[str, Exception]
+
+
 class ExecutionTracker:
-    def __init__(self, trans, tool, mapping_params, collection_info, completed_jobs=None):
+    execution_errors: List[ExecutionErrorsT]
+    successful_jobs: List[model.Job]
+    output_datasets: List[Tuple[str, model.HistoryDatasetAssociation]]
+    output_collections: List[Tuple[str, model.HistoryDatasetCollectionAssociation]]
+    implicit_collections: Dict[str, model.HistoryDatasetCollectionAssociation]
+
+    def __init__(
+        self,
+        trans,
+        tool: "Tool",
+        mapping_params: MappingParameters,
+        collection_info: Optional[MatchingCollections],
+        completed_jobs: Optional[CompletedJobsT] = None,
+    ):
         # Known ahead of time...
         self.trans = trans
         self.tool = tool
@@ -241,7 +285,7 @@ class ExecutionTracker:
         self.collection_info = collection_info
         self.completed_jobs = completed_jobs
 
-        self._on_text = None
+        self._on_text: Optional[str] = None
 
         # Populated as we go...
         self.failed_jobs = 0
@@ -278,9 +322,10 @@ class ExecutionTracker:
         self.execution_errors.append(error)
 
     @property
-    def on_text(self):
-        if self._on_text is None:
-            collection_names = ["collection %d" % c.hid for c in self.collection_info.collections.values()]
+    def on_text(self) -> Optional[str]:
+        collection_info = self.collection_info
+        if self._on_text is None and collection_info is not None:
+            collection_names = ["collection %d" % c.hid for c in collection_info.collections.values()]
             self._on_text = on_text_for_names(collection_names)
 
         return self._on_text
@@ -338,19 +383,23 @@ class ExecutionTracker:
         )
         subcollection_mapping_type = None
         if self.is_implicit_input(input_name):
-            subcollection_mapping_type = self.collection_info.subcollection_mapping_type(input_name)
+            collection_info = self.collection_info
+            assert collection_info
+            subcollection_mapping_type = collection_info.subcollection_mapping_type(input_name)
 
         return get_structure(
             input_collection, collection_type_description, leaf_subcollection_type=subcollection_mapping_type
         )
 
     def _structure_for_output(self, trans, tool_output):
-        structure = self.collection_info.structure
+        collection_info = self.collection_info
+        assert collection_info
+        structure = collection_info.structure
         if hasattr(tool_output, "default_identifier_source"):
             # Switch the structure for outputs if the output specified a default_identifier_source
             collection_type_descriptions = trans.app.dataset_collection_manager.collection_type_descriptions
 
-            source_collection = self.collection_info.collections.get(tool_output.default_identifier_source)
+            source_collection = collection_info.collections.get(tool_output.default_identifier_source)
             if source_collection:
                 collection_type_description = collection_type_descriptions.for_collection_type(
                     source_collection.collection.collection_type
@@ -390,10 +439,10 @@ class ExecutionTracker:
         # collection replaced with a specific dataset. Need to replace this
         # with the collection and wrap everything up so can evaluate output
         # label.
+        collection_info = self.collection_info
+        assert collection_info
         trans = self.trans
-        params.update(
-            self.collection_info.collections
-        )  # Replace datasets with source collections for labelling outputs.
+        params.update(collection_info.collections)  # Replace datasets with source collections for labelling outputs.
 
         collection_instances = {}
         implicit_inputs = self.implicit_inputs
@@ -465,6 +514,7 @@ class ExecutionTracker:
             completed_collections = {}
             if (
                 self.completed_jobs
+                and self.completed_jobs[0]
                 and self.implicit_collection_jobs
                 and len(self.completed_jobs) == len(self.successful_jobs)
             ):
@@ -485,13 +535,16 @@ class ExecutionTracker:
                     implicit_collection_jobs = implicit_collection.implicit_collection_jobs
                     implicit_collection_jobs.populated_state = "ok"
                     trans.sa_session.add(implicit_collection_jobs)
+                collection_info = self.collection_info
+                assert collection_info
                 implicit_collection.collection.finalize(
-                    collection_type_description=self.collection_info.structure.collection_type_description
+                    collection_type_description=collection_info.structure.collection_type_description
                 )
 
                 # Mark implicit HDCA as copied
-                completed_implicit_collection = implicit_collection and completed_collections.get(
-                    implicit_collection.implicit_output_name
+                implicit_output_name = implicit_collection.implicit_output_name
+                completed_implicit_collection = (
+                    implicit_collection and implicit_output_name and completed_collections.get(implicit_output_name)
                 )
                 if completed_implicit_collection:
                     implicit_collection.copied_from_history_dataset_collection_association_id = (
@@ -505,14 +558,20 @@ class ExecutionTracker:
 
     @property
     def implicit_inputs(self):
-        implicit_inputs = list(self.collection_info.collections.items())
+        collection_info = self.collection_info
+        assert collection_info
+        implicit_inputs = list(collection_info.collections.items())
         return implicit_inputs
 
     def is_implicit_input(self, input_name):
-        return input_name in self.collection_info.collections
+        collection_info = self.collection_info
+        assert collection_info
+        return input_name in collection_info.collections
 
     def walk_implicit_collections(self):
-        return self.collection_info.structure.walk_collections(self.implicit_collections)
+        collection_info = self.collection_info
+        assert collection_info
+        return collection_info.structure.walk_collections(self.implicit_collections)
 
     def new_execution_slices(self):
         if self.collection_info is None:
@@ -548,13 +607,22 @@ class ExecutionTracker:
 # Seperate these because workflows need to track their jobs belong to the invocation
 # in the database immediately and they can be recovered.
 class ToolExecutionTracker(ExecutionTracker):
-    def __init__(self, trans, tool, mapping_params, collection_info, completed_jobs=None):
+    def __init__(
+        self,
+        trans,
+        tool: "Tool",
+        mapping_params: MappingParameters,
+        collection_info: Optional[MatchingCollections],
+        completed_jobs: Optional[CompletedJobsT] = None,
+    ):
         super().__init__(trans, tool, mapping_params, collection_info, completed_jobs=completed_jobs)
 
         # New to track these things for tool output API response in the tool case,
         # in the workflow case we just write stuff to the database and forget about
         # it.
-        self.outputs_by_output_name = collections.defaultdict(list)
+        self.outputs_by_output_name: Dict[str, List[Union[model.DatasetInstance, model.DatasetCollection]]] = (
+            collections.defaultdict(list)
+        )
 
     def record_success(self, execution_slice, job, outputs):
         super().record_success(execution_slice, job, outputs)
@@ -580,7 +648,15 @@ class ToolExecutionTracker(ExecutionTracker):
 
 
 class WorkflowStepExecutionTracker(ExecutionTracker):
-    def __init__(self, trans, tool, mapping_params, collection_info, invocation_step, completed_jobs=None):
+    def __init__(
+        self,
+        trans,
+        tool: "Tool",
+        mapping_params: MappingParameters,
+        collection_info: Optional[MatchingCollections],
+        invocation_step: model.WorkflowInvocationStep,
+        completed_jobs: Optional[CompletedJobsT] = None,
+    ):
         super().__init__(trans, tool, mapping_params, collection_info, completed_jobs=completed_jobs)
         self.invocation_step = invocation_step
 
diff --git a/lib/galaxy/tools/execution_helpers.py b/lib/galaxy/tools/execution_helpers.py
new file mode 100644
index 0000000000000000000000000000000000000000..76413a5f6370c0f4c324de565290a791f08a6932
--- /dev/null
+++ b/lib/galaxy/tools/execution_helpers.py
@@ -0,0 +1,72 @@
+"""Helpers meant to assist tool execution.
+
+Lower-level things that prevent interwoven dependencies between tool code,
+tool execution code, and tool action code.
+"""
+
+import logging
+from typing import Collection
+
+log = logging.getLogger(__name__)
+
+
+class ToolExecutionCache:
+    """An object meant to cache calculation caused by repeatedly evaluting
+    the same tool by the same user with slightly different parameters.
+    """
+
+    def __init__(self, trans):
+        self.trans = trans
+        self.current_user_roles = trans.get_current_user_roles()
+        self.chrom_info = {}
+        self.cached_collection_elements = {}
+
+    def get_chrom_info(self, tool_id, input_dbkey):
+        genome_builds = self.trans.app.genome_builds
+        custom_build_hack_get_len_from_fasta_conversion = tool_id != "CONVERTER_fasta_to_len"
+        if custom_build_hack_get_len_from_fasta_conversion and input_dbkey in self.chrom_info:
+            return self.chrom_info[input_dbkey]
+
+        chrom_info_pair = genome_builds.get_chrom_info(
+            input_dbkey,
+            trans=self.trans,
+            custom_build_hack_get_len_from_fasta_conversion=custom_build_hack_get_len_from_fasta_conversion,
+        )
+        if custom_build_hack_get_len_from_fasta_conversion:
+            self.chrom_info[input_dbkey] = chrom_info_pair
+
+        return chrom_info_pair
+
+
+def filter_output(tool, output, incoming):
+    for filter in output.filters:
+        try:
+            if not eval(filter.text.strip(), globals(), incoming):
+                return True  # do not create this dataset
+        except Exception as e:
+            log.debug(f"Tool {tool.id} output {output.name}: dataset output filter ({filter.text}) failed: {e}")
+    return False
+
+
+def on_text_for_names(input_names: Collection[str]) -> str:
+    # input_names may contain duplicates... this is because the first value in
+    # multiple input dataset parameters will appear twice once as param_name
+    # and once as param_name1.
+    unique_names = []
+    for name in input_names:
+        if name not in unique_names:
+            unique_names.append(name)
+    input_names = unique_names
+
+    # Build name for output datasets based on tool name and input names
+    if len(input_names) == 0:
+        on_text = ""
+    elif len(input_names) == 1:
+        on_text = input_names[0]
+    elif len(input_names) == 2:
+        on_text = "{} and {}".format(*input_names)
+    elif len(input_names) == 3:
+        on_text = "{}, {}, and {}".format(*input_names)
+    else:
+        on_text = "{}, {}, and others".format(*input_names[:2])
+    return on_text
diff --git a/lib/galaxy/tools/filter_null.xml b/lib/galaxy/tools/filter_null.xml
new file mode 100644
index 0000000000000000000000000000000000000000..06fa4745ee94ab7088ec866a4f2bb0cf2bf18f57
--- /dev/null
+++ b/lib/galaxy/tools/filter_null.xml
@@ -0,0 +1,46 @@
+<tool id="__FILTER_NULL__" name="Filter null elements" version="1.0.0" tool_type="filter_null">
+    <description/>
+    <type class="FilterNullTool" module="galaxy.tools"/>
+    <action module="galaxy.tools.actions.model_operations" class="ModelOperationToolAction"/>
+    <edam_operations>
+        <edam_operation>operation_3695</edam_operation>
+    </edam_operations>
+    <inputs>
+        <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection"/>
+    </inputs>
+    <outputs>
+        <collection name="output" format_source="input" type_source="input" label="${on_string} (without null datasets)">
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="e1" value="simple_line.txt"/>
+                </collection>
+            </param>
+            <output_collection name="output" type="list" count="1">
+                <element name="e1">
+                    <assert_contents>
+                        <has_text_matching expression="^This is a line of text.\n$"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+========
+Synopsis
+========
+
+Removes null elements from a collection.
+
+This tool takes a dataset collection and filters out nulls. This is useful for removing elements that resulted from conditional execution of jobs.
+
+.. class:: infomark
+
+This tool will create new history datasets from your collection but your quota usage will not increase.
+
+      ]]></help>
+</tool>
diff --git a/lib/galaxy/tools/flatten_collection.xml b/lib/galaxy/tools/flatten_collection.xml
index 67a96252dfeb0c10fe3c4fb53ee6eb899a5226c2..a9cb4f04f075a13f5f84cdf2b6aa1ea71600b588 100644
--- a/lib/galaxy/tools/flatten_collection.xml
+++ b/lib/galaxy/tools/flatten_collection.xml
@@ -1,7 +1,7 @@
 <tool id="__FLATTEN__"
       name="Flatten collection"
       version="1.0.0"
-      tool_type="filter_collection">
+      tool_type="flatten_collection">
     <description></description>
     <type class="FlattenTool" module="galaxy.tools" />
     <action module="galaxy.tools.actions.model_operations"
diff --git a/lib/galaxy/tools/harmonize_two_collections_list.xml b/lib/galaxy/tools/harmonize_two_collections_list.xml
index 7828ec5138e616faf61ce45a7d73b5f613d930ad..3a12173f04e869f6e2df2ab012b957f93e711d05 100644
--- a/lib/galaxy/tools/harmonize_two_collections_list.xml
+++ b/lib/galaxy/tools/harmonize_two_collections_list.xml
@@ -171,6 +171,37 @@
             <output_collection name="output1" type="list" count="0"/>
             <output_collection name="output2" type="list" count="0"/>
         </test>
+        <!-- test that collection types get propagated to outputs correctly -->
+        <test>
+            <param name="input1">
+                <collection type="list">
+                    <element name="element_1" value="simple_line.txt" />
+                </collection>
+            </param>
+            <param name="input2">
+                <collection type="list:paired">
+                    <element name="element_1">
+                        <collection type="paired">
+                            <element name="forward" value="1.fastqsanger" ftype="fastqsanger" />
+                            <element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
+                         </collection>
+                    </element>
+                </collection>
+            </param>
+            <output_collection name="output1" type="list" count="1">
+                <element name="element_1">
+                    <assert_contents>
+                        <has_text_matching expression="^This is a line of text.\n$" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="output2" type="list:paired" count="1">
+                <element name="element_1">
+                    <element name="forward" file="1.fastqsanger" ftype="fastqsanger" />
+                    <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index 7e72bf3a9eb16a4f16c7f39c03d16665c1335919..86b19e25f4cc29eeec5ab58ada161512f687a88a 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -4,12 +4,15 @@ Classes encapsulating Galaxy tool parameters.
 
 from json import dumps
 from typing import (
+    cast,
     Dict,
+    Optional,
     Union,
 )
 
 from boltons.iterutils import remap
 
+from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.util import unicodify
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.json import safe_loads
@@ -29,15 +32,27 @@ from .grouping import (
 )
 from .workflow_utils import (
     is_runtime_value,
+    NO_REPLACEMENT,
     runtime_to_json,
 )
 from .wrapped import flat_to_nested_state
+from .._types import (
+    InputFormatT,
+    ParameterValidationErrorsT,
+    ToolStateDumpedToJsonInternalT,
+    ToolStateDumpedToJsonT,
+    ToolStateDumpedToStringsT,
+    ToolStateJobInstancePopulatedT,
+    ToolStateJobInstanceT,
+)
 
 REPLACE_ON_TRUTHY = object()
 
 # Some tools use the code tag and access the code base, expecting certain tool parameters to be available here.
 __all__ = ("DataCollectionToolParameter", "DataToolParameter", "SelectToolParameter")
 
+ToolInputsT = Dict[str, Union[Group, ToolParameter]]
+
 
 def visit_input_values(
     inputs,
@@ -49,6 +64,8 @@ def visit_input_values(
     context=None,
     no_replacement_value=REPLACE_ON_TRUTHY,
     replace_optional_connections=False,
+    allow_case_inference=False,
+    unset_value=None,
 ):
     """
     Given a tools parameter definition (`inputs`) and a specific set of
@@ -63,21 +80,20 @@ def visit_input_values(
     >>> from galaxy.tools.parameters.basic import TextToolParameter, BooleanToolParameter
     >>> from galaxy.tools.parameters.grouping import Repeat
     >>> a = TextToolParameter(None, XML('<param name="a"/>'))
-    >>> b = Repeat()
+    >>> b = Repeat('b')
     >>> c = TextToolParameter(None, XML('<param name="c"/>'))
-    >>> d = Repeat()
+    >>> d = Repeat('d')
     >>> e = TextToolParameter(None, XML('<param name="e"/>'))
-    >>> f = Conditional()
+    >>> f = Conditional('f')
     >>> g = BooleanToolParameter(None, XML('<param name="g"/>'))
     >>> h = TextToolParameter(None, XML('<param name="h"/>'))
     >>> i = TextToolParameter(None, XML('<param name="i"/>'))
     >>> j = TextToolParameter(None, XML('<param name="j"/>'))
-    >>> b.name = b.title = 'b'
+    >>> b.title = 'b'
     >>> b.inputs = dict([ ('c', c), ('d', d) ])
-    >>> d.name = d.title = 'd'
+    >>> d.title = 'd'
     >>> d.inputs = dict([ ('e', e), ('f', f) ])
     >>> f.test_param = g
-    >>> f.name = 'f'
     >>> f.cases = [Bunch(value='true', inputs= {'h': h}), Bunch(value='false', inputs= { 'i': i })]
     >>>
     >>> def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
@@ -146,7 +162,7 @@ def visit_input_values(
     """
 
     def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None):
-        value = input_values.get(input.name)
+        value = input_values.get(input.name, unset_value)
         args = {
             "input": input,
             "parent": input_values,
@@ -160,23 +176,55 @@ def visit_input_values(
         if input.name not in input_values:
             args["error"] = f"No value found for '{args.get('prefixed_label')}'."
         new_value = callback(**args)
+
+        # is this good enough ? feels very ugh
+        if new_value == [no_replacement_value]:
+            # Single unspecified value in multiple="true" input with a single null input, pretend it's a singular value
+            new_value = no_replacement_value
+        if isinstance(new_value, list):
+            # Maybe mixed input, I guess tool defaults don't really make sense here ?
+            # Would e.g. be default dataset in multiple="true" input, you wouldn't expect the default to be inserted
+            # if other inputs are connected and provided.
+            new_value = [item if not item == no_replacement_value else None for item in new_value]
+
         if no_replacement_value is REPLACE_ON_TRUTHY:
             replace = bool(new_value)
         else:
             replace = new_value != no_replacement_value
         if replace:
             input_values[input.name] = new_value
-        elif replace_optional_connections and is_runtime_value(value) and hasattr(input, "value"):
-            input_values[input.name] = input.value
+        elif replace_optional_connections:
+            # Only used in workflow context
+            has_default = hasattr(input, "value")
+            if new_value is value is NO_REPLACEMENT or is_runtime_value(value):
+                # NO_REPLACEMENT means value was connected but left unspecified
+                if has_default:
+                    # Use default if we have one
+                    input_values[input.name] = input.value
+                else:
+                    # Should fail if input is not optional and does not have default value
+                    # Effectively however depends on parameter implementation.
+                    # We might want to raise an exception here, instead of depending on a tool parameter value error.
+                    input_values[input.name] = None
 
     def get_current_case(input, input_values):
+        test_parameter = input.test_param
+        test_parameter_name = test_parameter.name
         try:
-            return input.get_current_case(input_values[input.test_param.name])
+            if test_parameter_name not in input_values and allow_case_inference:
+                return input.get_current_case(test_parameter.get_initial_value(None, input_values))
+            else:
+                return input.get_current_case(input_values[test_parameter_name])
         except (KeyError, ValueError):
             return -1
 
     context = ExpressionContext(input_values, context)
-    payload = {"context": context, "no_replacement_value": no_replacement_value}
+    payload = {
+        "context": context,
+        "no_replacement_value": no_replacement_value,
+        "allow_case_inference": allow_case_inference,
+        "unset_value": unset_value,
+    }
     for input in inputs.values():
         if isinstance(input, Repeat) or isinstance(input, UploadDataset):
             values = input_values[input.name] = input_values.get(input.name, [])
@@ -196,6 +244,10 @@ def visit_input_values(
         elif isinstance(input, Conditional):
             values = input_values[input.name] = input_values.get(input.name, {})
             new_name_prefix = f"{name_prefix + input.name}|"
+            if not isinstance(values, dict):
+                raise RequestParameterInvalidException(
+                    f"Invalid value '{values}' submitted for conditional parameter '{name_prefix + input.name}'."
+                )
             case_error = None if get_current_case(input, values) >= 0 else "The selected case is unavailable/invalid."
             callback_helper(
                 input.test_param,
@@ -253,15 +305,37 @@ def check_param(trans, param, incoming_value, param_values, simple_errors=True):
     return value, error
 
 
+def params_to_json_internal(
+    params: ToolInputsT, param_values: ToolStateJobInstancePopulatedT, app
+) -> ToolStateDumpedToJsonInternalT:
+    """Return ToolStateDumpedToJsonT for supplied validated and populated parameters."""
+    return cast(
+        ToolStateDumpedToJsonInternalT, params_to_strings(params, param_values, app, nested=True, use_security=False)
+    )
+
+
+def params_to_json(params: ToolInputsT, param_values: ToolStateJobInstancePopulatedT, app) -> ToolStateDumpedToJsonT:
+    """Return ToolStateDumpedToJsonT for supplied validated and populated parameters."""
+    return cast(ToolStateDumpedToJsonT, params_to_strings(params, param_values, app, nested=True, use_security=True))
+
+
 def params_to_strings(
-    params: Dict[str, Union[Group, ToolParameter]], param_values: Dict, app, nested=False, use_security=False
-) -> Dict:
+    params: ToolInputsT,
+    param_values: ToolStateJobInstancePopulatedT,
+    app,
+    nested=False,
+    use_security=False,
+) -> Union[ToolStateDumpedToJsonT, ToolStateDumpedToJsonInternalT, ToolStateDumpedToStringsT]:
     """
     Convert a dictionary of parameter values to a dictionary of strings
     suitable for persisting. The `value_to_basic` method of each parameter
     is called to convert its value to basic types, the result of which
     is then json encoded (this allowing complex nested parameters and
-    such).
+    such). If `nested` this will remain as a sort of JSON-ifiable dictionary
+    (ToolStateDumpedToJsonT), otherwise these will dumped into strings of the
+    JSON (ToolStateDumpedToStringsT). If use_security is False, this will return
+    object references with decoded (integer) IDs, otherwise they will be encoded
+    strings.
     """
     rval = {}
     for key, value in param_values.items():
@@ -344,67 +418,17 @@ def update_dataset_ids(input_values, translate_values, src):
 
 def populate_state(
     request_context,
-    inputs,
-    incoming,
-    state,
-    errors=None,
+    inputs: ToolInputsT,
+    incoming: ToolStateJobInstanceT,
+    state: ToolStateJobInstancePopulatedT,
+    errors: Optional[ParameterValidationErrorsT] = None,
     context=None,
     check=True,
     simple_errors=True,
-    input_format="legacy",
+    input_format: InputFormatT = "legacy",
 ):
     """
     Populates nested state dict from incoming parameter values.
-    >>> from galaxy.util import XML
-    >>> from galaxy.util.bunch import Bunch
-    >>> from galaxy.tools.parameters.basic import TextToolParameter, BooleanToolParameter
-    >>> from galaxy.tools.parameters.grouping import Repeat
-    >>> trans = Bunch(workflow_building_mode=False)
-    >>> a = TextToolParameter(None, XML('<param name="a"/>'))
-    >>> b = Repeat()
-    >>> b.min = 0
-    >>> b.max = 1
-    >>> c = TextToolParameter(None, XML('<param name="c"/>'))
-    >>> d = Repeat()
-    >>> d.min = 0
-    >>> d.max = 1
-    >>> e = TextToolParameter(None, XML('<param name="e"/>'))
-    >>> f = Conditional()
-    >>> g = BooleanToolParameter(None, XML('<param name="g"/>'))
-    >>> h = TextToolParameter(None, XML('<param name="h"/>'))
-    >>> i = TextToolParameter(None, XML('<param name="i"/>'))
-    >>> b.name = 'b'
-    >>> b.inputs = dict([('c', c), ('d', d)])
-    >>> d.name = 'd'
-    >>> d.inputs = dict([('e', e), ('f', f)])
-    >>> f.test_param = g
-    >>> f.name = 'f'
-    >>> f.cases = [Bunch(value='true', inputs= { 'h': h }), Bunch(value='false', inputs= { 'i': i })]
-    >>> inputs = dict([('a',a),('b',b)])
-    >>> flat = dict([('a', 1), ('b_0|c', 2), ('b_0|d_0|e', 3), ('b_0|d_0|f|h', 4), ('b_0|d_0|f|g', True)])
-    >>> state = {}
-    >>> populate_state(trans, inputs, flat, state, check=False)
-    >>> print(state['a'])
-    1
-    >>> print(state['b'][0]['c'])
-    2
-    >>> print(state['b'][0]['d'][0]['e'])
-    3
-    >>> print(state['b'][0]['d'][0]['f']['h'])
-    4
-    >>> # now test with input_format='21.01'
-    >>> nested = {'a': 1, 'b': [{'c': 2, 'd': [{'e': 3, 'f': {'h': 4, 'g': True}}]}]}
-    >>> state_new = {}
-    >>> populate_state(trans, inputs, nested, state_new, check=False, input_format='21.01')
-    >>> print(state_new['a'])
-    1
-    >>> print(state_new['b'][0]['c'])
-    2
-    >>> print(state_new['b'][0]['d'][0]['e'])
-    3
-    >>> print(state_new['b'][0]['d'][0]['f']['h'])
-    4
-
     """
     if errors is None:
         errors = {}
@@ -426,77 +450,87 @@ def populate_state(
             state[input.name] = input.get_initial_value(request_context, context)
             group_state = state[input.name]
             if input.type == "repeat":
-                if len(incoming[input.name]) > input.max or len(incoming[input.name]) < input.min:
-                    errors[input.name] = "The number of repeat elements is outside the range specified by the tool."
+                repeat_input = cast(Repeat, input)
+                repeat_name = repeat_input.name
+                repeat_incoming = incoming.get(repeat_name) or []
+                if repeat_incoming and (
+                    len(repeat_incoming) > repeat_input.max or len(repeat_incoming) < repeat_input.min
+                ):
+                    errors[repeat_name] = "The number of repeat elements is outside the range specified by the tool."
                 else:
                     del group_state[:]
-                    for rep in incoming[input.name]:
-                        new_state = {}
+                    for rep in repeat_incoming:
+                        new_state: ToolStateJobInstancePopulatedT = {}
                         group_state.append(new_state)
-                        new_errors = {}
+                        repeat_errors: ParameterValidationErrorsT = {}
                         populate_state(
                             request_context,
-                            input.inputs,
+                            repeat_input.inputs,
                             rep,
                             new_state,
-                            new_errors,
+                            repeat_errors,
                             context=context,
                             check=check,
                             simple_errors=simple_errors,
                             input_format=input_format,
                         )
-                        if new_errors:
-                            errors[input.name] = new_errors
+                        if repeat_errors:
+                            errors[repeat_input.name] = repeat_errors
 
             elif input.type == "conditional":
-                test_param_value = incoming.get(input.name, {}).get(input.test_param.name)
+                conditional_input = cast(Conditional, input)
+                test_param = cast(ToolParameter, conditional_input.test_param)
+                test_param_value = incoming.get(conditional_input.name, {}).get(test_param.name)
                 value, error = (
-                    check_param(
-                        request_context, input.test_param, test_param_value, context, simple_errors=simple_errors
-                    )
+                    check_param(request_context, test_param, test_param_value, context, simple_errors=simple_errors)
                     if check
                     else [test_param_value, None]
                 )
                 if error:
-                    errors[input.test_param.name] = error
+                    errors[test_param.name] = error
                 else:
                     try:
-                        current_case = input.get_current_case(value)
-                        group_state = state[input.name] = {}
-                        new_errors = {}
+                        current_case = conditional_input.get_current_case(value)
+                        group_state = state[conditional_input.name] = {}
+                        cast_errors: ParameterValidationErrorsT = {}
+                        incoming_for_conditional = cast(
+                            ToolStateJobInstanceT, incoming.get(conditional_input.name) or {}
+                        )
                         populate_state(
                             request_context,
-                            input.cases[current_case].inputs,
-                            incoming.get(input.name),
+                            conditional_input.cases[current_case].inputs,
+                            incoming_for_conditional,
                             group_state,
-                            new_errors,
+                            cast_errors,
                             context=context,
                             check=check,
                             simple_errors=simple_errors,
                             input_format=input_format,
                         )
-                        if new_errors:
-                            errors[input.name] = new_errors
+                        if cast_errors:
+                            errors[conditional_input.name] = cast_errors
                         group_state["__current_case__"] = current_case
                     except Exception:
-                        errors[input.test_param.name] = "The selected case is unavailable/invalid."
-                group_state[input.test_param.name] = value
+                        errors[test_param.name] = "The selected case is unavailable/invalid."
+                group_state[test_param.name] = value
 
             elif input.type == "section":
-                new_errors = {}
+                section_input = cast(Section, input)
+                section_errors: ParameterValidationErrorsT = {}
+                incoming_for_state = cast(ToolStateJobInstanceT, incoming.get(section_input.name) or {})
                 populate_state(
                     request_context,
-                    input.inputs,
-                    incoming.get(input.name),
+                    section_input.inputs,
+                    incoming_for_state,
                     group_state,
-                    new_errors,
+                    section_errors,
                     context=context,
                     check=check,
                     simple_errors=simple_errors,
                     input_format=input_format,
                 )
-                if new_errors:
-                    errors[input.name] = new_errors
+                if section_errors:
+                    errors[section_input.name] = section_errors
 
             elif input.type == "upload_dataset":
                 raise NotImplementedError
@@ -512,11 +546,21 @@ def populate_state(
                     errors[input.name] = error
                 state[input.name] = value
     else:
-        raise Exception(f"Input format {input_format} not recognized; input_format must be either legacy or 21.01.")
+        raise RequestParameterInvalidException(
+            f"Input format {input_format} not recognized; input_format must be either legacy or 21.01."
+        )
 
 
 def _populate_state_legacy(
-    request_context, inputs, incoming, state, errors, prefix="", context=None, check=True, simple_errors=True
+    request_context,
+    inputs: ToolInputsT,
+    incoming: ToolStateJobInstanceT,
+    state: ToolStateJobInstancePopulatedT,
+    errors,
+    prefix="",
+    context=None,
+    check=True,
+    simple_errors=True,
 ):
     if context is None:
         context = flat_to_nested_state(incoming)
@@ -527,22 +571,23 @@ def _populate_state_legacy(
         group_state = state[input.name]
         group_prefix = f"{key}|"
         if input.type == "repeat":
+            repeat_input = cast(Repeat, input)
             rep_index = 0
             del group_state[:]
             while True:
                 rep_prefix = "%s_%d" % (key, rep_index)
-                rep_min_default = input.default if input.default > input.min else input.min
+                rep_min_default = repeat_input.default if repeat_input.default > repeat_input.min else repeat_input.min
                 if (
                     not any(incoming_key.startswith(rep_prefix) for incoming_key in incoming.keys())
                     and rep_index >= rep_min_default
                 ):
                     break
-                if rep_index < input.max:
-                    new_state = {"__index__": rep_index}
+                if rep_index < repeat_input.max:
+                    new_state: ToolStateJobInstancePopulatedT = {"__index__": rep_index}
                     group_state.append(new_state)
                     _populate_state_legacy(
                         request_context,
-                        input.inputs,
+                        repeat_input.inputs,
                         incoming,
                         new_state,
                         errors,
@@ -553,13 +598,21 @@ def _populate_state_legacy(
                     )
                 rep_index += 1
         elif input.type == "conditional":
-            if input.value_ref and not input.value_ref_in_group:
-                test_param_key = prefix + input.test_param.name
+            conditional_input = cast(Conditional, input)
+            test_param = cast(ToolParameter, conditional_input.test_param)
+            if conditional_input.value_ref and not conditional_input.value_ref_in_group:
+                test_param_key = prefix + test_param.name
             else:
-                test_param_key = group_prefix + input.test_param.name
-            test_param_value = incoming.get(test_param_key, group_state.get(input.test_param.name))
+                test_param_key = group_prefix + test_param.name
+            test_param_value = incoming.get(test_param_key, group_state.get(test_param.name))
             value, error = (
-                check_param(request_context, input.test_param, test_param_value, context, simple_errors=simple_errors)
+                check_param(
+                    request_context,
+                    test_param,
+                    test_param_value,
+                    context,
+                    simple_errors=simple_errors,
+                )
                 if check
                 else [test_param_value, None]
             )
@@ -567,11 +620,11 @@ def _populate_state_legacy(
                 errors[test_param_key] = error
             else:
                 try:
-                    current_case = input.get_current_case(value)
-                    group_state = state[input.name] = {}
+                    current_case = conditional_input.get_current_case(value)
+                    group_state = state[conditional_input.name] = cast(ToolStateJobInstancePopulatedT, {})
                     _populate_state_legacy(
                         request_context,
-                        input.cases[current_case].inputs,
+                        conditional_input.cases[current_case].inputs,
                         incoming,
                         group_state,
                         errors,
@@ -583,11 +636,12 @@ def _populate_state_legacy(
                     group_state["__current_case__"] = current_case
                 except Exception:
                     errors[test_param_key] = "The selected case is unavailable/invalid."
-            group_state[input.test_param.name] = value
+            group_state[test_param.name] = value
         elif input.type == "section":
+            section_input = cast(Section, input)
             _populate_state_legacy(
                 request_context,
-                input.inputs,
+                section_input.inputs,
                 incoming,
                 group_state,
                 errors,
@@ -597,20 +651,21 @@ def _populate_state_legacy(
                 simple_errors=simple_errors,
             )
         elif input.type == "upload_dataset":
-            file_count = input.get_file_count(request_context, context)
+            dataset_input = cast(UploadDataset, input)
+            file_count = dataset_input.get_file_count(request_context, context)
             while len(group_state) > file_count:
                 del group_state[-1]
             while file_count > len(group_state):
-                new_state = {"__index__": len(group_state)}
-                for upload_item in input.inputs.values():
-                    new_state[upload_item.name] = upload_item.get_initial_value(request_context, context)
-                group_state.append(new_state)
+                new_state_upload: ToolStateJobInstancePopulatedT = {"__index__": len(group_state)}
+                for upload_item in dataset_input.inputs.values():
+                    new_state_upload[upload_item.name] = upload_item.get_initial_value(request_context, context)
+                group_state.append(new_state_upload)
             for rep_index, rep_state in enumerate(group_state):
                 rep_index = rep_state.get("__index__", rep_index)
                 rep_prefix = "%s_%d|" % (key, rep_index)
                 _populate_state_legacy(
                     request_context,
-                    input.inputs,
+                    dataset_input.inputs,
                     incoming,
                     rep_state,
                     errors,
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 279adde7a92ea016a97800c393e9003c502bfcc5..f33fba90b6deb88b39b3491ca14bf7fda02ff0fd 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -13,10 +13,11 @@ import urllib.parse
 from collections.abc import MutableMapping
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
-    Tuple,
+    Sequence,
     TYPE_CHECKING,
     Union,
 )
@@ -41,16 +42,27 @@ from galaxy.model import (
 )
 from galaxy.model.dataset_collections import builder
 from galaxy.schema.fetch_data import FilesPayload
+from galaxy.tool_util.parameters.factory import get_color_value
 from galaxy.tool_util.parser import get_input_source as ensure_input_source
-from galaxy.tools.parameters.workflow_utils import workflow_building_modes
+from galaxy.tool_util.parser.interface import DrillDownOptionsDict
+from galaxy.tool_util.parser.util import (
+    boolean_is_checked,
+    boolean_true_and_false_values,
+    ParameterParseException,
+    text_input_is_optional,
+)
+from galaxy.tools.parameters.options import ParameterOption
+from galaxy.tools.parameters.workflow_utils import (
+    NO_REPLACEMENT,
+    workflow_building_modes,
+)
 from galaxy.util import (
     sanitize_param,
     string_as_bool,
     string_as_bool_or_none,
     unicodify,
-    XML,
 )
-from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.dictifiable import UsesDictVisibleKeys
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.hash_util import HASH_NAMES
 from galaxy.util.rules_dsl import RuleSet
@@ -113,9 +125,17 @@ def is_runtime_context(trans, other_values):
 
 
 def parse_dynamic_options(param, input_source):
-    if (options_elem := input_source.parse_dynamic_options_elem()) is not None:
-        return dynamic_options.DynamicOptions(options_elem, param)
-    return None
+    dynamic_options_config = input_source.parse_dynamic_options()
+    if not dynamic_options_config:
+        return None
+    options_elem = dynamic_options_config.elem()
+    if options_elem is None:
+        return None
+    return dynamic_options.DynamicOptions(options_elem, param)
+
+
+def serialize_options(security: "IdEncodingHelper", options: Sequence[ParameterOption]):
+    return [option.serialize(security) for option in options]
 
 
 # Describe a parameter value error where there is no actual supplied
@@ -136,7 +156,7 @@ def assert_throws_param_value_error(message):
 
 class ParameterValueError(ValueError):
     def __init__(self, message_suffix, parameter_name, parameter_value=NO_PARAMETER_VALUE, is_dynamic=None):
-        message = f"parameter '{parameter_name}': {message_suffix}"
+        message = f"Parameter '{parameter_name}': {message_suffix}"
         super().__init__(message)
         self.message_suffix = message_suffix
         self.parameter_name = parameter_name
@@ -154,20 +174,22 @@ class ParameterValueError(ValueError):
         return as_dict
 
 
-class ToolParameter(Dictifiable):
+class ToolParameter(UsesDictVisibleKeys):
     """
     Describes a parameter accepted by a tool. This is just a simple stub at the
     moment but in the future should encapsulate more complex parameters (lists
     of valid choices, validation logic, ...)
 
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch(app=None)
+    >>> from galaxy.util import XML
+    >>> trans = Bunch(app=None, security=lambda x: x)
     >>> p = ToolParameter(None, XML('<param argument="--parameter-name" type="text" value="default" />'))
     >>> assert p.name == 'parameter_name'
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
     """
 
-    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "refresh_on_change"]
+    name: str
+    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "help_format", "refresh_on_change"]
 
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
@@ -178,17 +200,15 @@ class ToolParameter(Dictifiable):
         self.hidden = input_source.get_bool("hidden", False)
         self.refresh_on_change = input_source.get_bool("refresh_on_change", False)
         self.optional = input_source.parse_optional()
-        self.optionality_inferred = False
         self.is_dynamic = False
         self.label = input_source.parse_label()
         self.help = input_source.parse_help()
+        self.help_format = input_source.get("help_format") or "html"
         if (sanitizer_elem := input_source.parse_sanitizer_elem()) is not None:
             self.sanitizer = ToolParameterSanitizer.from_element(sanitizer_elem)
         else:
             self.sanitizer = None
-        self.validators = []
-        for elem in input_source.parse_validator_elems():
-            self.validators.append(validation.Validator.from_element(self, elem))
+        self.validators = validation.to_validators(tool.app if tool else None, input_source.parse_validators())
 
     @property
     def visible(self) -> bool:
@@ -199,7 +219,7 @@ class ToolParameter(Dictifiable):
         """Return user friendly name for the parameter"""
         return self.label if self.label else self.name
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         """
         Convert a value from an HTML POST into the parameters preferred value
         format.
@@ -237,6 +257,8 @@ class ToolParameter(Dictifiable):
     def value_to_basic(self, value, app, use_security=False):
         if is_runtime_value(value):
             return runtime_to_json(value)
+        elif value == NO_REPLACEMENT:
+            return {"__class__": "NoReplacement"}
         return self.to_json(value, app, use_security)
 
     def value_from_basic(self, value, app, ignore_errors=False):
@@ -245,8 +267,11 @@ class ToolParameter(Dictifiable):
             if isinstance(self, HiddenToolParameter):
                 raise ParameterValueError(message_suffix="Runtime Parameter not valid", parameter_name=self.name)
             return runtime_to_object(value)
-        elif isinstance(value, MutableMapping) and value.get("__class__") == "UnvalidatedValue":
-            return value["value"]
+        elif isinstance(value, MutableMapping):
+            if value.get("__class__") == "UnvalidatedValue":
+                return value["value"]
+            elif value.get("__class__") == "NoReplacement":
+                return NO_REPLACEMENT
         # Delegate to the 'to_python' method
         if ignore_errors:
             try:
@@ -265,6 +290,7 @@ class ToolParameter(Dictifiable):
         """
         Convert a value to a text representation suitable for displaying to
         the user
+        >>> from galaxy.util import XML
         >>> p = ToolParameter(None, XML('<param name="_name" />'))
         >>> print(p.to_text(None))
         Not available.
@@ -306,12 +332,12 @@ class ToolParameter(Dictifiable):
             try:
                 validator.validate(value, trans)
             except ValueError as e:
-                raise ValueError(f"Parameter {self.name}: {e}") from None
+                raise ParameterValueError(str(e), self.name, value) from None
 
     def to_dict(self, trans, other_values=None):
         """to_dict tool parameter. This can be overridden by subclasses."""
         other_values = other_values or {}
-        tool_dict = super().to_dict()
+        tool_dict = self._dictify_view_keys()
         tool_dict["model_class"] = self.__class__.__name__
         tool_dict["optional"] = self.optional
         tool_dict["hidden"] = self.hidden
@@ -349,18 +375,7 @@ class SimpleTextToolParameter(ToolParameter):
         else:
             # Optionality not explicitly defined, default to False
             optional = False
-            if self.type == "text":
-                # A text parameter that doesn't raise a validation error on empty string
-                # is considered to be optional
-                try:
-                    for validator in self.validators:
-                        validator.validate("")
-                    optional = True
-                    self.optionality_inferred = True
-                except ValueError:
-                    pass
         self.optional = optional
-
         if self.optional:
             self.value = None
         else:
@@ -368,11 +383,7 @@ class SimpleTextToolParameter(ToolParameter):
 
     def to_json(self, value, app, use_security):
         """Convert a value to a string representation suitable for persisting"""
-        if value is None:
-            rval = "" if not self.optional else None
-        else:
-            rval = unicodify(value)
-        return rval
+        return unicodify(value)
 
     def get_initial_value(self, trans, other_values):
         return self.value
@@ -383,20 +394,28 @@ class TextToolParameter(SimpleTextToolParameter):
     Parameter that can take on any text value.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None)
     >>> p = TextToolParameter(None, XML('<param name="_name" type="text" value="default" />'))
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
+    [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
     """
 
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
+        self.profile = tool.profile if tool else None
         self.datalist = []
         for title, value, _ in input_source.parse_static_options():
             self.datalist.append({"label": title, "value": value})
+
+        # why does Integer and Float subclass this :_(
+        if self.type == "text":
+            self.optional, self.optionality_inferred = text_input_is_optional(input_source)
+        else:
+            self.optionality_inferred = False
         self.value = input_source.get("value")
         self.area = input_source.get_bool("area", False)
 
@@ -409,6 +428,16 @@ class TextToolParameter(SimpleTextToolParameter):
         ):
             return super().validate(value, trans)
 
+    @property
+    def wrapper_default(self) -> Optional[str]:
+        """Handle change in default handling pre and post 23.0 profiles."""
+        profile = self.profile
+        legacy_behavior = profile is None or Version(str(profile)) < Version("23.0")
+        default_value = None
+        if self.optional and self.optionality_inferred and legacy_behavior:
+            default_value = ""
+        return default_value
+
     def to_dict(self, trans, other_values=None):
         d = super().to_dict(trans)
         other_values = other_values or {}
@@ -423,13 +452,14 @@ class IntegerToolParameter(TextToolParameter):
     Parameter that takes an integer value.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
     >>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
     >>> assert type(p.from_json("10", trans)) == int
-    >>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
+    >>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
     ...     p.from_json("_string", trans)
     """
 
@@ -455,7 +485,7 @@ class IntegerToolParameter(TextToolParameter):
             except ValueError:
                 raise ParameterValueError("attribute 'max' must be an integer", self.name, self.max)
         if self.min is not None or self.max is not None:
-            self.validators.append(validation.InRangeValidator(None, self.min, self.max))
+            self.validators.append(validation.InRangeValidator.simple_range_validator(self.min, self.max))
 
     def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
@@ -495,13 +525,14 @@ class FloatToolParameter(TextToolParameter):
     Parameter that takes a real number value.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
     >>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
     >>> assert type(p.from_json("36.1", trans)) == float
-    >>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
+    >>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
     ...     p.from_json("_string", trans)
     """
 
@@ -527,7 +558,7 @@ class FloatToolParameter(TextToolParameter):
             except ValueError:
                 raise ParameterValueError("attribute 'max' must be a real number", self.name, self.max)
         if self.min is not None or self.max is not None:
-            self.validators.append(validation.InRangeValidator(None, self.min, self.max))
+            self.validators.append(validation.InRangeValidator.simple_range_validator(self.min, self.max))
 
     def from_json(self, value, trans, other_values=None):
         other_values = other_values or {}
@@ -569,16 +600,17 @@ class BooleanToolParameter(ToolParameter):
     Parameter that takes one of two values.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch())
     >>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
-    >>> print(p.from_json('true'))
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
+    >>> print(p.from_json('true', trans))
     True
     >>> print(p.to_param_dict_string(True))
     _truevalue
-    >>> print(p.from_json('false'))
+    >>> print(p.from_json('false', trans))
     False
     >>> print(p.to_param_dict_string(False))
     _falsevalue
@@ -593,29 +625,16 @@ class BooleanToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        truevalue = input_source.get("truevalue", "true")
-        falsevalue = input_source.get("falsevalue", "false")
-        if tool and Version(str(tool.profile)) >= Version("23.1"):
-            if truevalue == falsevalue:
-                raise ParameterValueError("Cannot set true and false to the same value", self.name)
-            if truevalue.lower() == "false":
-                raise ParameterValueError(
-                    f"Cannot set truevalue to [{truevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case.",
-                    self.name,
-                )
-            if falsevalue.lower() == "true":
-                raise ParameterValueError(
-                    f"Cannot set falsevalue to [{falsevalue}], Galaxy state may encounter issues distinguishing booleans and strings in this case.",
-                    self.name,
-                )
-
+        try:
+            truevalue, falsevalue = boolean_true_and_false_values(input_source, tool and tool.profile)
+        except ParameterParseException as ppe:
+            raise ParameterValueError(ppe.message, self.name)
         self.truevalue = truevalue
         self.falsevalue = falsevalue
-        nullable = input_source.get_bool("optional", False)
-        self.optional = nullable
-        self.checked = input_source.get_bool("checked", None if nullable else False)
+        self.optional = input_source.get_bool("optional", False)
+        self.checked = boolean_is_checked(input_source)
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self.to_python(value)
 
     def to_python(self, value, app=None):
@@ -654,18 +673,19 @@ class FileToolParameter(ToolParameter):
     Parameter that takes an uploaded file as a value.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch())
     >>> p = FileToolParameter(None, XML('<param name="_name" type="file"/>'))
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
+    [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
     """
 
     def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
         if isinstance(value, FilesPayload):
@@ -727,12 +747,13 @@ class FTPFileToolParameter(ToolParameter):
     Parameter that takes a file uploaded via FTP as a value.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch(), user=None)
     >>> p = FTPFileToolParameter(None, XML('<param name="_name" type="ftpfile"/>'))
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
+    [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
     """
 
     def __init__(self, tool, input_source):
@@ -763,7 +784,7 @@ class FTPFileToolParameter(ToolParameter):
         else:
             return lst[0]
 
-    def from_json(self, value, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self.to_python(value, trans.app, validate=True)
 
     def to_json(self, value, app, use_security):
@@ -800,11 +821,12 @@ class HiddenToolParameter(ToolParameter):
     Parameter that takes one of two values.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch())
     >>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
     """
 
     def __init__(self, tool, input_source):
@@ -824,28 +846,29 @@ class ColorToolParameter(ToolParameter):
     Parameter that stores a color.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch())
     >>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff"/>'))
     >>> print(p.name)
     _name
     >>> print(p.to_param_dict_string("#ffffff"))
     #ffffff
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
     >>> p = ColorToolParameter(None, XML('<param name="_name" type="color"/>'))
     >>> print(p.get_initial_value(trans, {}))
     #000000
     >>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
     >>> print(p.to_param_dict_string("#ffffff"))
     (255, 255, 255)
-    >>> with assert_throws_param_value_error("parameter '_name': Failed to convert 'None' to RGB."):
+    >>> with assert_throws_param_value_error("Parameter '_name': Failed to convert 'None' to RGB."):
     ...      p.to_param_dict_string(None)
     """
 
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.value = input_source.get("value", "#000000")
-        self.rgb = input_source.get("rgb", False)
+        self.value = get_color_value(input_source)
+        self.rgb = input_source.get_bool("rgb", False)
 
     def get_initial_value(self, trans, other_values):
         if self.value is not None:
@@ -866,11 +889,12 @@ class BaseURLToolParameter(HiddenToolParameter):
     current server base url. Used in all redirects.
 
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> trans = Bunch(app=None, history=Bunch())
     >>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
     """
 
     def __init__(self, tool, input_source):
@@ -880,7 +904,7 @@ class BaseURLToolParameter(HiddenToolParameter):
     def get_initial_value(self, trans, other_values):
         return self._get_value(trans)
 
-    def from_json(self, value=None, trans=None, other_values=None):
+    def from_json(self, value, trans, other_values=None):
         return self._get_value(trans)
 
     def _get_value(self, trans):
@@ -907,7 +931,8 @@ class SelectToolParameter(ToolParameter):
     Parameter that takes on one (or many) or a specific set of values.
 
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=False)
+    >>> from galaxy.util import XML
+    >>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=False, security=lambda x: x)
     >>> p = SelectToolParameter(None, XML(
     ... '''
     ... <param name="_name" type="select">
@@ -919,7 +944,7 @@ class SelectToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
+    [('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
     >>> p = SelectToolParameter(None, XML(
     ... '''
     ... <param name="_name" type="select" multiple="true">
@@ -931,7 +956,7 @@ class SelectToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
+    [('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
     >>> print(p.to_param_dict_string(["y", "z"]))
     y,z
     """
@@ -965,13 +990,15 @@ class SelectToolParameter(ToolParameter):
             call_other_values.update(other_values.dict)
         return call_other_values
 
-    def get_options(self, trans, other_values):
+    def get_options(self, trans, other_values) -> Sequence[Union[ParameterOption, DrillDownOptionsDict]]:
         if self.options:
             return self.options.get_options(trans, other_values)
         elif self.dynamic_options:
             call_other_values = self._get_dynamic_options_call_other_values(trans, other_values)
             try:
-                return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
+                return [
+                    ParameterOption(*o) for o in eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
+                ]
             except Exception as e:
                 log.debug(
                     "Error determining dynamic options for parameter '%s' in tool '%s':",
@@ -981,24 +1008,26 @@ class SelectToolParameter(ToolParameter):
                 )
                 return []
         else:
-            return self.static_options
+            return [ParameterOption(*o) for o in self.static_options]
 
     def get_legal_values(self, trans, other_values, value):
         """
         determine the set of values of legal options
         """
-        return {
-            history_item_dict_to_python(v, trans.app, self.name) or v
-            for _, v, _ in self.get_options(trans, other_values)
-        }
+        options = cast(List[ParameterOption], self.get_options(trans, other_values))
+        return {option.dataset or option.value for option in options}
 
     def get_legal_names(self, trans, other_values):
         """
-        determine a mapping from names to values for all legal options
+        determine the set of values of legal options
         """
-        return {n: v for n, v, _ in self.get_options(trans, other_values)}
+        options = cast(List[ParameterOption], self.get_options(trans, other_values))
+        return {option.name: option.value for option in options}
+
+    def from_json(self, value, trans, other_values=None):
+        return self._select_from_json(value, trans, other_values=other_values, require_legal_value=True)
 
-    def from_json(self, value, trans, other_values=None, require_legal_value=True):
+    def _select_from_json(self, value, trans, other_values=None, require_legal_value=True):
         other_values = other_values or {}
         try:
             legal_values = self.get_legal_values(trans, other_values, value)
@@ -1115,17 +1144,17 @@ class SelectToolParameter(ToolParameter):
 
     def get_initial_value(self, trans, other_values):
         try:
-            options = list(self.get_options(trans, other_values))
+            options = cast(List[ParameterOption], self.get_options(trans, other_values))
         except ImplicitConversionRequired:
             return None
         if not options:
             return None
-        value = [optval for _, optval, selected in options if selected]
+        value = [option.value for option in options if option.selected]
         if len(value) == 0:
             if not self.optional and not self.multiple and options:
                 # Nothing selected, but not optional and not a multiple select, with some values,
                 # so we have to default to something (the HTML form will anyway)
-                value2 = options[0][1]
+                value2: Optional[Union[str, List[str]]] = options[0].value
             else:
                 value2 = None
         elif len(value) == 1 or not self.multiple:
@@ -1165,8 +1194,8 @@ class SelectToolParameter(ToolParameter):
         d = super().to_dict(trans, other_values)
 
         # Get options, value.
-        options = self.get_options(trans, other_values)
-        d["options"] = options
+        options = cast(List[ParameterOption], self.get_options(trans, other_values))
+        d["options"] = serialize_options(trans.security, options)
         d["display"] = self.display
         d["multiple"] = self.multiple
         d["textable"] = is_runtime_context(trans, other_values)
@@ -1190,7 +1219,8 @@ class GenomeBuildParameter(SelectToolParameter):
 
     >>> # Create a mock transaction with 'hg17' as the current build
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch(app=None, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None))
+    >>> from galaxy.util import XML
+    >>> trans = Bunch(app=None, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None), security=lambda x:x)
     >>> p = GenomeBuildParameter(None, XML('<param name="_name" type="genomebuild" value="hg17" />'))
     >>> print(p.name)
     _name
@@ -1210,12 +1240,14 @@ class GenomeBuildParameter(SelectToolParameter):
             self.static_options = [(value, key, False) for key, value in self._get_dbkey_names()]
         self.is_dynamic = True
 
-    def get_options(self, trans, other_values):
+    def get_options(self, trans, other_values) -> Sequence[ParameterOption]:
         last_used_build = object()
         if trans.history:
             last_used_build = trans.history.genome_build
-        for dbkey, build_name in self._get_dbkey_names(trans=trans):
-            yield build_name, dbkey, (dbkey == last_used_build)
+        return [
+            ParameterOption(build_name, dbkey, (dbkey == last_used_build))
+            for dbkey, build_name in self._get_dbkey_names(trans=trans)
+        ]
 
     def get_legal_values(self, trans, other_values, value):
         return {dbkey for dbkey, _ in self._get_dbkey_names(trans=trans)}
@@ -1225,16 +1257,16 @@ class GenomeBuildParameter(SelectToolParameter):
         d = ToolParameter.to_dict(self, trans)
 
         # Get options, value - options is a generator here, so compile to list
-        options = list(self.get_options(trans, {}))
-        value = options[0][1]
+        options = self.get_options(trans, {})
+        value = options[0].value
         for option in options:
-            if option[2]:
+            if option.selected:
                 # Found selected option.
-                value = option[1]
+                value = option.value
 
         d.update(
             {
-                "options": options,
+                "options": serialize_options(trans, options),
                 "value": value,
                 "display": self.display,
                 "multiple": self.multiple,
@@ -1296,7 +1328,7 @@ class SelectTagParameter(SelectToolParameter):
                 value = None
         # We skip requiring legal values -- this is similar to optional, but allows only subset of datasets to be positive
         # TODO: May not actually be required for (nested) collection input ?
-        return super().from_json(value, trans, other_values, require_legal_value=False)
+        return super()._select_from_json(value, trans, other_values, require_legal_value=False)
 
     def get_tag_list(self, other_values):
         """
@@ -1322,13 +1354,13 @@ class SelectTagParameter(SelectToolParameter):
                         tags.add(tag.user_value)
         return list(tags)
 
-    def get_options(self, trans, other_values):
+    def get_options(self, trans, other_values) -> Sequence[ParameterOption]:
         """
         Show tags
         """
         options = []
         for tag in self.get_tag_list(other_values):
-            options.append((f"Tags: {tag}", tag, False))
+            options.append(ParameterOption(f"Tags: {tag}", tag, False))
         return options
 
     def get_initial_value(self, trans, other_values):
@@ -1362,6 +1394,7 @@ class ColumnListParameter(SelectToolParameter):
     >>> # Mock up a history (not connected to database)
     >>> from galaxy.model import History, HistoryDatasetAssociation
     >>> from galaxy.util.bunch import Bunch
+    >>> from galaxy.util import XML
     >>> from galaxy.model.mapping import init
     >>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
     >>> hist = History()
@@ -1385,6 +1418,10 @@ class ColumnListParameter(SelectToolParameter):
         if self.accept_default:
             self.optional = True
         self.data_ref = input_source.get("data_ref", None)
+        profile = tool.profile if tool else None
+        assert (
+            profile is None or Version(str(profile)) < Version("24.2") or self.data_ref is not None
+        ), f"data_column parameter {self.name} requires a valid data_ref attribute"
         self.ref_input = None
         # Legacy style default value specification...
         self.default_value = input_source.get("default_value", None)
@@ -1436,10 +1473,9 @@ class ColumnListParameter(SelectToolParameter):
 
     @staticmethod
     def _strip_c(column):
-        if isinstance(column, str):
-            column = column.strip()
-            if column.startswith("c") and len(column) > 1 and all(c.isdigit() for c in column[1:]):
-                column = column.lower()[1:]
+        column = str(column).strip()
+        if column.startswith("c") and len(column) > 1 and all(c.isdigit() for c in column[1:]):
+            column = column.lower()[1:]
         return column
 
     def get_column_list(self, trans, other_values):
@@ -1457,8 +1493,8 @@ class ColumnListParameter(SelectToolParameter):
             # Use representative dataset if a dataset collection is parsed
             if isinstance(dataset, HistoryDatasetCollectionAssociation):
                 dataset = dataset.to_hda_representative()
-            if isinstance(dataset, DatasetCollectionElement) and dataset.hda:
-                dataset = dataset.hda
+            if isinstance(dataset, DatasetCollectionElement):
+                dataset = dataset.first_dataset_instance()
             if isinstance(dataset, HistoryDatasetAssociation) and self.ref_input and self.ref_input.formats:
                 direct_match, target_ext, converted_dataset = dataset.find_conversion_destination(
                     self.ref_input.formats
@@ -1491,11 +1527,14 @@ class ColumnListParameter(SelectToolParameter):
                 column_list = [c for c in column_list if c in this_column_list]
         return column_list
 
-    def get_options(self, trans, other_values):
+    def get_options(self, trans, other_values) -> Sequence[ParameterOption]:
         """
         Show column labels rather than c1..cn if use_header_names=True
         """
-        options: List[Tuple[str, Union[str, Tuple[str, str]], bool]] = []
+        options: Sequence[ParameterOption] = []
+        column_list = self.get_column_list(trans, other_values)
+        if not column_list:
+            return options
         # if available use column_names metadata for option names
         # otherwise read first row - assume is a header with tab separated names
         if self.usecolnames:
@@ -1505,29 +1544,26 @@ class ColumnListParameter(SelectToolParameter):
                 and hasattr(dataset.metadata, "column_names")
                 and dataset.metadata.element_is_set("column_names")
             ):
-                column_list = [
-                    ("%d" % (i + 1), "c%d: %s" % (i + 1, x)) for i, x in enumerate(dataset.metadata.column_names)
-                ]
+                try:
+                    options = [
+                        ParameterOption(f"c{c}: {dataset.metadata.column_names[int(c) - 1]}", c, False)
+                        for c in column_list
+                    ]
+                except IndexError:
+                    # ignore and rely on fallback
+                    pass
             else:
                 try:
                     with open(dataset.get_file_name()) as f:
                         head = f.readline()
                     cnames = head.rstrip("\n\r ").split("\t")
-                    column_list = [("%d" % (i + 1), "c%d: %s" % (i + 1, x)) for i, x in enumerate(cnames)]
+                    options = [ParameterOption(f"c{c}: {cnames[int(c) - 1]}", c, False) for c in column_list]
                 except Exception:
-                    column_list = self.get_column_list(trans, other_values)
-            if self.numerical:  # If numerical was requested, filter columns based on metadata
-                if hasattr(dataset, "metadata") and getattr(dataset.metadata, "column_types", None) is not None:
-                    if len(dataset.metadata.column_types) >= len(column_list):
-                        numerics = [i for i, x in enumerate(dataset.metadata.column_types) if x in ["int", "float"]]
-                        column_list = [column_list[i] for i in numerics]
-        else:
-            column_list = self.get_column_list(trans, other_values)
-        for col in column_list:
-            if isinstance(col, tuple) and len(col) == 2:
-                options.append((col[1], col[0], False))
-            else:
-                options.append((f"Column: {col}", col, False))
+                    # ignore and rely on fallback
+                    pass
+        if not options:
+            # fallback if no options list could be built so far
+            options = [ParameterOption(f"Column: {col}", col, False) for col in column_list]
         return options
 
     def get_initial_value(self, trans, other_values):
@@ -1553,9 +1589,13 @@ class ColumnListParameter(SelectToolParameter):
         for dataset in util.listify(other_values.get(self.data_ref)):
             # Use representative dataset if a dataset collection is parsed
             if isinstance(dataset, HistoryDatasetCollectionAssociation):
-                dataset = dataset.to_hda_representative()
+                if dataset.populated:
+                    dataset = dataset.to_hda_representative()
+                else:
+                    # That's fine, we'll check again on execution
+                    return True
             if isinstance(dataset, DatasetCollectionElement):
-                dataset = dataset.hda
+                dataset = dataset.first_dataset_instance()
             if isinstance(dataset, DatasetInstance):
                 return not dataset.has_data()
             if is_runtime_value(dataset):
@@ -1582,9 +1622,12 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     Parameter that takes on one (or many) of a specific set of values.
     Creating a hierarchical select menu, which allows users to 'drill down' a tree-like set of options.
 
+    >>> from galaxy.util import XML
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch(app=None, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None))
-    >>> p = DrillDownSelectToolParameter(None, XML(
+    >>> app = Bunch(config=Bunch(tool_data_path=None))
+    >>> tool = Bunch(app=app)
+    >>> trans = Bunch(app=app, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None), security=lambda x: x)
+    >>> p = DrillDownSelectToolParameter(tool, XML(
     ... '''
     ... <param name="_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
     ...   <options>
@@ -1622,58 +1665,26 @@ class DrillDownSelectToolParameter(SelectToolParameter):
     """
 
     def __init__(self, tool, input_source, context=None):
-        def recurse_option_elems(cur_options, option_elems):
-            for option_elem in option_elems:
-                selected = string_as_bool(option_elem.get("selected", False))
-                cur_options.append(
-                    {
-                        "name": option_elem.get("name"),
-                        "value": option_elem.get("value"),
-                        "options": [],
-                        "selected": selected,
-                    }
-                )
-                recurse_option_elems(cur_options[-1]["options"], option_elem.findall("option"))
-
         input_source = ensure_input_source(input_source)
         ToolParameter.__init__(self, tool, input_source)
-        # TODO: abstract XML out of here - so non-XML InputSources can
-        # specify DrillDown parameters.
-        elem = input_source.elem()
-        self.multiple = string_as_bool(elem.get("multiple", False))
-        self.display = elem.get("display", None)
-        self.hierarchy = elem.get("hierarchy", "exact")  # exact or recurse
-        self.separator = elem.get("separator", ",")
-        if from_file := elem.get("from_file", None):
-            if not os.path.isabs(from_file):
-                from_file = os.path.join(tool.app.config.tool_data_path, from_file)
-            elem = XML(f"<root>{open(from_file).read()}</root>")
-        self.dynamic_options = elem.get("dynamic_options", None)
-        if self.dynamic_options:
-            self.is_dynamic = True
-        self.options = []
-        self.filtered: Dict[str, Any] = {}
-        if elem.find("filter"):
+        self.multiple = input_source.get_bool("multiple", False)
+        self.display = input_source.get("display", None)
+        self.hierarchy = input_source.get("hierarchy", "exact")  # exact or recurse
+        self.separator = input_source.get("separator", ",")
+        tool_data_path = tool.app.config.tool_data_path
+        drill_down_dynamic_options = input_source.parse_drill_down_dynamic_options(tool_data_path)
+        if drill_down_dynamic_options is not None:
             self.is_dynamic = True
-            for filter in elem.findall("filter"):
-                # currently only filtering by metadata key matching input file is allowed
-                if filter.get("type") == "data_meta":
-                    if filter.get("data_ref") not in self.filtered:
-                        self.filtered[filter.get("data_ref")] = {}
-                    if filter.get("meta_key") not in self.filtered[filter.get("data_ref")]:
-                        self.filtered[filter.get("data_ref")][filter.get("meta_key")] = {}
-                    if filter.get("value") not in self.filtered[filter.get("data_ref")][filter.get("meta_key")]:
-                        self.filtered[filter.get("data_ref")][filter.get("meta_key")][filter.get("value")] = []
-                    recurse_option_elems(
-                        self.filtered[filter.get("data_ref")][filter.get("meta_key")][filter.get("value")],
-                        filter.find("options").findall("option"),
-                    )
-        elif not self.dynamic_options:
-            recurse_option_elems(self.options, elem.find("options").findall("option"))
+            self.dynamic_options = drill_down_dynamic_options.from_code_block()
+            self.options = []
+        else:
+            self.is_dynamic = False
+            self.dynamic_options = None
+            self.options = input_source.parse_drill_down_static_options(tool_data_path)
 
-    def _get_options_from_code(self, trans=None, value=None, other_values=None):
+    def _get_options_from_code(self, trans=None, other_values=None):
         assert self.dynamic_options, Exception("dynamic_options was not specifed")
-        call_other_values = ExpressionContext({"__trans__": trans, "__value__": value})
+        call_other_values = ExpressionContext({"__trans__": trans, "__value__": None})
         if other_values:
             call_other_values.parent = other_values.parent
             call_other_values.update(other_values.dict)
@@ -1682,32 +1693,17 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         except Exception:
             return []
 
-    def get_options(self, trans=None, value=None, other_values=None):
+    def get_options(self, trans=None, other_values=None) -> List[DrillDownOptionsDict]:
         other_values = other_values or {}
         if self.is_dynamic:
             if self.dynamic_options:
-                options = self._get_options_from_code(trans=trans, value=value, other_values=other_values)
-            else:
-                options = []
-            for filter_key, filter_value in self.filtered.items():
-                dataset = other_values.get(filter_key)
-                if dataset.__class__.__name__.endswith(
-                    "DatasetFilenameWrapper"
-                ):  # this is a bad way to check for this, but problems importing class (due to circular imports?)
-                    dataset = dataset.dataset
-                if dataset:
-                    for meta_key, meta_dict in filter_value.items():
-                        if hasattr(dataset, "metadata") and hasattr(dataset.metadata, "spec"):
-                            check_meta_val = dataset.metadata.spec[meta_key].param.to_string(
-                                dataset.metadata.get(meta_key)
-                            )
-                            if check_meta_val in meta_dict:
-                                options.extend(meta_dict[check_meta_val])
-            return options
+                return self._get_options_from_code(trans=trans, other_values=other_values)
+            return []
+
         return self.options
 
     def get_legal_values(self, trans, other_values, value):
-        def recurse_options(legal_values, options):
+        def recurse_options(legal_values, options: List[DrillDownOptionsDict]):
             for option in options:
                 legal_values.append(option["value"])
                 recurse_options(legal_values, option["options"])
@@ -1753,16 +1749,16 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         other_values = other_values or {}
 
         def get_options_list(value):
-            def get_base_option(value, options):
+            def get_base_option(value, options: List[DrillDownOptionsDict]):
                 for option in options:
                     if value == option["value"]:
                         return option
-                    rval = get_base_option(value, option["options"])
+                    rval = get_base_option(value, option["options"] or [])
                     if rval:
                         return rval
                 return None  # not found
 
-            def recurse_option(option_list, option):
+            def recurse_option(option_list, option: DrillDownOptionsDict):
                 if not option["options"]:
                     option_list.append(option["value"])
                 else:
@@ -1770,8 +1766,10 @@ class DrillDownSelectToolParameter(SelectToolParameter):
                         recurse_option(option_list, opt)
 
             rval: List[str] = []
-            base_option = get_base_option(value, self.get_options(other_values=other_values))
-            recurse_option(rval, base_option)
+            options = self.get_options(other_values=other_values)
+            base_option = get_base_option(value, options)
+            if base_option:
+                recurse_option(rval, base_option)
             return rval or [value]
 
         if value is None:
@@ -1797,11 +1795,11 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         return rval
 
     def get_initial_value(self, trans, other_values):
-        def recurse_options(initial_values, options):
+        def recurse_options(initial_values, options: List[DrillDownOptionsDict]):
             for option in options:
                 if option["selected"]:
                     initial_values.append(option["value"])
-                recurse_options(initial_values, option["options"])
+                recurse_options(initial_values, option["options"] or [])
 
         # More working around dynamic options for workflow
         options = self.get_options(trans=trans, other_values=other_values)
@@ -1814,11 +1812,11 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         return initial_values
 
     def to_text(self, value):
-        def get_option_display(value, options):
+        def get_option_display(value, options: List[DrillDownOptionsDict]):
             for option in options:
                 if value == option["value"]:
                     return option["name"]
-                rval = get_option_display(value, option["options"])
+                rval = get_option_display(value, option["options"] or [])
                 if rval:
                     return rval
             return None  # not found
@@ -1840,16 +1838,13 @@ class DrillDownSelectToolParameter(SelectToolParameter):
         else:
             rval = []
             for val in value:
-                rval.append(get_option_display(val, self.options) or val)
+                rval.append(get_option_display(val, self.options or val))
         if rval:
             return "\n".join(map(str, rval))
         return "Nothing selected."
 
     def get_dependencies(self):
-        """
-        Get the *names* of the other params this param depends on.
-        """
-        return list(self.filtered.keys())
+        return []
 
     def to_dict(self, trans, other_values=None):
         other_values = other_values or {}
@@ -1998,7 +1993,7 @@ class BaseDataToolParameter(ToolParameter):
                     try:
                         validator.validate(v, trans)
                     except ValueError as e:
-                        raise ValueError(f"Parameter {self.name}: {e}") from None
+                        raise ParameterValueError(str(e), self.name, v) from None
 
         dataset_count = 0
         if value:
@@ -2079,7 +2074,7 @@ class DataToolParameter(BaseDataToolParameter):
         self.load_contents = int(input_source.get("load_contents", 0))
         # Add metadata validator
         if not input_source.get_bool("no_validation", False):
-            self.validators.append(validation.MetadataValidator())
+            self.validators.append(validation.MetadataValidator.default_metadata_validator())
         self._parse_formats(trans, input_source)
         tag = input_source.get("tag")
         self.multiple = input_source.get_bool("multiple", False)
@@ -2096,6 +2091,7 @@ class DataToolParameter(BaseDataToolParameter):
         self.tag = tag
         self.is_dynamic = True
         self._parse_options(input_source)
+        self._parse_allow_uri_if_protocol(input_source)
         # Load conversions required for the dataset input
         self.conversions = []
         self.default_object = input_source.parse_default()
@@ -2117,6 +2113,12 @@ class DataToolParameter(BaseDataToolParameter):
                     )
                 self.conversions.append((name, conv_extension, [conv_type]))
 
+    def _parse_allow_uri_if_protocol(self, input_source):
+        # In case of deferred datasets, if the source URI is prefixed with one of the values in this list,
+        # the dataset will behave as an URI and will not be materialized into a file path.
+        allow_uri_if_protocol = input_source.get("allow_uri_if_protocol", None)
+        self.allow_uri_if_protocol = allow_uri_if_protocol.split(",") if allow_uri_if_protocol else []
+
     def from_json(self, value, trans, other_values=None):
         session = trans.sa_session
 
@@ -2370,13 +2372,27 @@ class DataToolParameter(BaseDataToolParameter):
         # add datasets
         hda_list = util.listify(other_values.get(self.name))
         # Prefetch all at once, big list of visible, non-deleted datasets.
+        matches_by_hid: Dict[int, List] = {}
         for hda in history.active_visible_datasets_and_roles:
             match = dataset_matcher.hda_match(hda)
             if match:
                 m = match.hda
                 hda_list = [h for h in hda_list if h != m and h != hda]
-                m_name = f"{match.original_hda.name} (as {match.target_ext})" if match.implicit_conversion else m.name
-                append(d["options"]["hda"], m, m_name, "hda")
+                if m.hid not in matches_by_hid:
+                    matches_by_hid[m.hid] = []
+                matches_by_hid[m.hid].append(match)
+
+        # Add only original HDAs to the options, implicit conversions will be skipped
+        for matches in matches_by_hid.values():
+            match = matches[0]
+            if len(matches) > 1:
+                # If there are multiple matches for the same hid, use the original HDA and skip the implicit conversions
+                match = next((m for m in matches if len(m.hda.implicitly_converted_parent_datasets) == 0), match)
+            m_name = (
+                f"{match.original_hda.name} (as {match.target_ext})" if match.implicit_conversion else match.hda.name
+            )
+            append(d["options"]["hda"], match.hda, m_name, "hda")
+
         for hda in hda_list:
             if hasattr(hda, "hid"):
                 if hda.deleted:
@@ -2667,6 +2683,14 @@ class DirectoryUriToolParameter(SimpleTextToolParameter):
         if not user_has_access:
             raise ParameterValueError(f"The user cannot access {value}.", self.name)
 
+    def to_param_dict_string(self, value, other_values=None) -> str:
+        """Called via __str__ when used in the Cheetah template"""
+        if value is None:
+            value = ""
+        elif not isinstance(value, str):
+            value = str(value)
+        return value
+
 
 class RulesListToolParameter(BaseJsonToolParameter):
     """
diff --git a/lib/galaxy/tools/parameters/cancelable_request.py b/lib/galaxy/tools/parameters/cancelable_request.py
index 794854a3ae627d9ee496aa0db84a9ae94d19e447..17964b80510801e894532b0370281bb6250d2135 100644
--- a/lib/galaxy/tools/parameters/cancelable_request.py
+++ b/lib/galaxy/tools/parameters/cancelable_request.py
@@ -23,7 +23,7 @@ async def fetch_url(
     method: REQUEST_METHOD = "GET",
 ):
     async with session.request(method=method, url=url, params=params, data=data, headers=headers) as response:
-        return await response.json()
+        return await response.json(content_type=None)
 
 
 async def async_request_with_timeout(
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
index b8cd20dab37dd41c036f980b661181afc7d8630c..4b14c798782d468c282fb3c329a4900a91b8fb57 100644
--- a/lib/galaxy/tools/parameters/dynamic_options.py
+++ b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -15,7 +15,10 @@ from typing import (
     cast,
     Dict,
     get_args,
+    List,
     Optional,
+    Sequence,
+    Set,
 )
 
 from typing_extensions import Literal
@@ -24,10 +27,12 @@ from galaxy.model import (
     DatasetCollectionElement,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
+    LibraryDatasetDatasetAssociation,
     MetadataFile,
     User,
 )
 from galaxy.tools.expressions import do_eval
+from galaxy.tools.parameters.options import ParameterOption
 from galaxy.tools.parameters.workflow_utils import (
     is_runtime_value,
     workflow_building_modes,
@@ -91,7 +96,7 @@ class StaticValueFilter(Filter):
         self.column = d_option.column_spec_to_index(column)
         self.keep = string_as_bool(elem.get("keep", "True"))
 
-    def filter_options(self, options, trans, other_values):
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
         rval = []
         filter_value = self.value
         try:
@@ -127,7 +132,7 @@ class RegexpFilter(Filter):
         self.column = d_option.column_spec_to_index(column)
         self.keep = string_as_bool(elem.get("keep", "True"))
 
-    def filter_options(self, options, trans, other_values):
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
         rval = []
         filter_value = self.value
         try:
@@ -183,7 +188,12 @@ class DataMetaFilter(Filter):
     def get_dependency_name(self):
         return self.ref_name
 
-    def filter_options(self, options, trans, other_values):
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
+        options = list(options)
+        if trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
+            # We're in the run form, can't possibly apply a data_meta filter.
+            return options
+
         def _add_meta(meta_value, m):
             if isinstance(m, list):
                 meta_value |= set(m)
@@ -223,7 +233,7 @@ class DataMetaFilter(Filter):
         # - for data sets: the meta data value
         # in both cases only meta data that is set (i.e. differs from the no_value)
         # is considered
-        meta_value = set()
+        meta_value: Set[Any] = set()
         for r in ref:
             if not r.metadata.element_is_set(self.key):
                 continue
@@ -235,7 +245,7 @@ class DataMetaFilter(Filter):
             return copy.deepcopy(options)
 
         if self.column is not None:
-            rval = []
+            rval: List[ParameterOption] = []
             for fields in options:
                 if compare_meta_value(fields[self.column], meta_value):
                     rval.append(fields)
@@ -245,7 +255,7 @@ class DataMetaFilter(Filter):
                 self.dynamic_option.columns = {"name": 0, "value": 1, "selected": 2}
                 self.dynamic_option.largest_index = 2
             for value in meta_value:
-                options.append((value, value, False))
+                options.append(ParameterOption(value, value, False))
             return options
 
 
@@ -285,15 +295,13 @@ class ParamValueFilter(Filter):
     def get_dependency_name(self):
         return self.ref_name
 
-    def filter_options(self, options, trans, other_values):
-        if trans is not None and trans.workflow_building_mode:
-            return []
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
         ref = other_values.get(self.ref_name, None)
-        if ref is None:
+        if ref is None or is_runtime_value(ref):
             ref = []
 
         # - for HDCAs the list of contained HDAs is extracted
-        # - single values are transformed in a single eleent list
+        # - single values are transformed in a single element list
         # - remaining cases are already lists (select and data parameters with multiple=true)
         if isinstance(ref, HistoryDatasetCollectionAssociation):
             ref = ref.to_hda_representative(multiple=True)
@@ -337,7 +345,7 @@ class UniqueValueFilter(Filter):
     def get_dependency_name(self):
         return self.dynamic_option.dataset_ref_name
 
-    def filter_options(self, options, trans, other_values):
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
         rval = []
         seen = set()
         for fields in options:
@@ -366,12 +374,17 @@ class MultipleSplitterFilter(Filter):
         assert columns is not None, "Required 'column' attribute missing from filter"
         self.columns = [d_option.column_spec_to_index(column) for column in columns.split(",")]
 
-    def filter_options(self, options, trans, other_values):
+    def filter_options(self, options: Sequence[ParameterOption], trans, other_values):
         rval = []
         for fields in options:
             for column in self.columns:
-                for field in fields[column].split(self.separator):
-                    rval.append(fields[0:column] + [field] + fields[column + 1 :])
+                field = fields[column]
+                if isinstance(field, str):
+                    for split_field in field.split(self.separator):
+                        new_options = list(fields[0:column]) + [split_field] + list(fields[column + 1 :])
+                        # tested in filter_multiple_splitter.xml
+                        option = tuple(new_options)
+                        rval.append(option)
         return rval
 
 
@@ -623,8 +636,9 @@ class DynamicOptions:
             self.filters.append(Filter.from_element(self, filter_elem))
 
         # Load Validators
-        for validator in elem.findall("validator"):
-            self.validators.append(validation.Validator.from_element(self.tool_param, validator))
+        validators = validation.parse_xml_validators(self.tool_param.tool.app, elem)
+        if validators:
+            self.validators = validators
 
         if self.dataset_ref_name:
             tool_param.data_ref = self.dataset_ref_name
@@ -766,6 +780,19 @@ class DynamicOptions:
             options = filter.filter_options(options, trans, other_values)
         return options
 
+    @staticmethod
+    def to_parameter_options(options):
+        rval: List[ParameterOption] = []
+        for option in options:
+            if isinstance(option, ParameterOption):
+                rval.append(option)
+            else:
+                if len(option) == 1:
+                    rval.append(ParameterOption(option[0], option[0]))
+                else:
+                    rval.append(ParameterOption(*option[:3]))
+        return rval
+
     def get_user_options(self, user: User):
         # stored metadata are key: value pairs, turn into flat lists of correct order
         fields = []
@@ -783,9 +810,19 @@ class DynamicOptions:
                 by_dbkey.update(table_entries)
             for data_table_entry in by_dbkey.values():
                 field_entry = []
+                if hda := data_table_entry.get("__hda__"):
+                    field_entry.append(hda)
+                missing_columns = False
                 for column_key in self.tool_data_table.columns.keys():
+                    if column_key not in data_table_entry:
+                        # currrent data table definition (as in self.tool_data_table)
+                        # may not match against the data manager bundle.
+                        # Breaking here fixes https://github.com/galaxyproject/galaxy/issues/18749.
+                        missing_columns = True
+                        break
                     field_entry.append(data_table_entry[column_key])
-                fields.append(field_entry)
+                if not missing_columns:
+                    fields.append(field_entry)
         return fields
 
     @staticmethod
@@ -797,7 +834,7 @@ class DynamicOptions:
             if path := value.get("path"):
                 # maybe a hack, should probably pass around dataset or src id combinations ?
                 value["path"] = os.path.join(hda.extra_files_path, path)
-                value["value"] = {"src": "hda", "id": hda.id}
+                value["__hda__"] = hda
         return table_entries
 
     def get_option_from_dataset(self, dataset):
@@ -834,12 +871,15 @@ class DynamicOptions:
                 rval.append(fields[field_index])
         return rval
 
-    def get_options(self, trans, other_values):
-        def to_triple(values):
+    def get_options(self, trans, other_values) -> Sequence[ParameterOption]:
+
+        rval: List[ParameterOption] = []
+
+        def to_option(values):
             if len(values) == 2:
-                return [str(values[0]), str(values[1]), False]
+                return ParameterOption(str(values[0]), str(values[1]), False)
             else:
-                return [str(values[0]), str(values[1]), bool(values[2])]
+                return ParameterOption(str(values[0]), str(values[1]), bool(values[2]))
 
         if from_url_options := self.from_url_options:
             context = User.user_template_environment(trans.user)
@@ -877,8 +917,7 @@ class DynamicOptions:
                     data = []
 
             # We only support the very specific ["name", "value", "selected"] format for now.
-            return [to_triple(d) for d in data]
-        rval = []
+            rval = [to_option(d) for d in data]
         if (
             self.file_fields is not None
             or self.tool_data_table is not None
@@ -887,11 +926,14 @@ class DynamicOptions:
         ):
             options = self.get_fields(trans, other_values)
             for fields in options:
-                rval.append((fields[self.columns["name"]], fields[self.columns["value"]], False))
+                name = fields[self.columns["name"]]
+                value = fields[self.columns["value"]]
+                hda = fields[-1] if isinstance(fields[-1], HistoryDatasetAssociation) else None
+                rval.append(ParameterOption(name, value, False, dataset=hda))
         else:
             for filter in self.filters:
                 rval = filter.filter_options(rval, trans, other_values)
-        return rval
+        return self.to_parameter_options(rval)
 
     def column_spec_to_index(self, column_spec):
         """
@@ -965,6 +1007,7 @@ def _get_ref_data(other_values, ref_name):
         (
             DatasetFilenameWrapper,
             HistoryDatasetAssociation,
+            LibraryDatasetDatasetAssociation,
             DatasetCollectionElement,
             DatasetListWrapper,
             HistoryDatasetCollectionAssociation,
@@ -976,7 +1019,7 @@ def _get_ref_data(other_values, ref_name):
         raise ValueError
     if isinstance(ref, DatasetCollectionElement) and ref.hda:
         ref = ref.hda
-    if isinstance(ref, (DatasetFilenameWrapper, HistoryDatasetAssociation)):
+    if isinstance(ref, (DatasetFilenameWrapper, HistoryDatasetAssociation, LibraryDatasetDatasetAssociation)):
         ref = [ref]
     elif isinstance(ref, HistoryDatasetCollectionAssociation):
         ref = ref.to_hda_representative(multiple=True)
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index ebf64542dd2e3343abe80390339e53a058a0e77f..26b4e171c0dec66b7aaa3eb68407abe89e59f9fb 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -6,6 +6,7 @@ import io
 import logging
 import os
 import unicodedata
+from math import inf
 from typing import (
     Any,
     Callable,
@@ -29,12 +30,13 @@ from galaxy.util import (
     sanitize_for_filename,
 )
 from galaxy.util.bunch import Bunch
-from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.dictifiable import UsesDictVisibleKeys
 from galaxy.util.expressions import ExpressionContext
 
 if TYPE_CHECKING:
     from galaxy.tools import Tool
     from galaxy.tools.parameter.basic import ToolParameter
+    from galaxy.tools.parameters import ToolInputsT
 
 log = logging.getLogger(__name__)
 URI_PREFIXES = [
@@ -55,12 +57,13 @@ URI_PREFIXES = [
 ]
 
 
-class Group(Dictifiable):
+class Group(UsesDictVisibleKeys):
     dict_collection_visible_keys = ["name", "type"]
     type: str
+    name: str
 
-    def __init__(self):
-        self.name = None
+    def __init__(self, name: str):
+        self.name = name
 
     @property
     def visible(self):
@@ -87,22 +90,25 @@ class Group(Dictifiable):
         raise TypeError("Not implemented")
 
     def to_dict(self, trans):
-        group_dict = super().to_dict()
+        group_dict = self._dictify_view_keys()
         return group_dict
 
 
 class Repeat(Group):
     dict_collection_visible_keys = ["name", "type", "title", "help", "default", "min", "max"]
     type = "repeat"
+    inputs: "ToolInputsT"
+    min: int
+    max: float
 
-    def __init__(self):
-        Group.__init__(self)
+    def __init__(self, name: str):
+        Group.__init__(self, name)
         self._title = None
-        self.inputs = None
+        self.inputs = {}
         self.help = None
         self.default = 0
-        self.min = None
-        self.max = None
+        self.min = 0
+        self.max = inf
 
     @property
     def title(self):
@@ -186,11 +192,12 @@ class Repeat(Group):
 class Section(Group):
     dict_collection_visible_keys = ["name", "type", "title", "help", "expanded"]
     type = "section"
+    inputs: "ToolInputsT"
 
-    def __init__(self):
-        Group.__init__(self)
+    def __init__(self, name: str):
+        Group.__init__(self, name)
         self.title = None
-        self.inputs = None
+        self.inputs = {}
         self.help = None
         self.expanded = False
 
@@ -266,11 +273,12 @@ class Dataset(Bunch):
 
 class UploadDataset(Group):
     type = "upload_dataset"
+    inputs: "ToolInputsT"
 
-    def __init__(self):
-        Group.__init__(self)
+    def __init__(self, name: str):
+        Group.__init__(self, name)
         self.title = None
-        self.inputs = None
+        self.inputs = {}
         self.file_type_name = "file_type"
         self.default_file_type = "txt"
         self.file_type_to_ext = {"auto": self.default_file_type}
@@ -735,12 +743,13 @@ class UploadDataset(Group):
 class Conditional(Group):
     type = "conditional"
     value_from: Callable[[ExpressionContext, "Conditional", "Tool"], Mapping[str, str]]
+    cases: List["ConditionalWhen"]
 
-    def __init__(self):
-        Group.__init__(self)
+    def __init__(self, name: str):
+        Group.__init__(self, name)
         self.test_param: Optional[ToolParameter] = None
         self.cases = []
-        self.value_ref = None
+        self.value_ref: Optional[str] = None
         self.value_ref_in_group = True  # When our test_param is not part of the conditional Group, this is False
 
     @property
@@ -761,7 +770,7 @@ class Conditional(Group):
     def value_to_basic(self, value, app, use_security=False):
         if self.test_param is None:
             raise Exception("Must set 'test_param' attribute to use.")
-        rval = {}
+        rval: Dict[str, Any] = {}
         rval[self.test_param.name] = self.test_param.value_to_basic(value[self.test_param.name], app)
         current_case = rval["__current_case__"] = self.get_current_case(value[self.test_param.name])
         for input in self.cases[current_case].inputs.values():
@@ -822,7 +831,7 @@ class Conditional(Group):
         return cond_dict
 
 
-class ConditionalWhen(Dictifiable):
+class ConditionalWhen(UsesDictVisibleKeys):
     dict_collection_visible_keys = ["value"]
 
     def __init__(self):
@@ -832,7 +841,7 @@ class ConditionalWhen(Dictifiable):
     def to_dict(self, trans):
         if self.inputs is None:
             raise Exception("Must set 'inputs' attribute to use.")
-        when_dict = super().to_dict()
+        when_dict = self._dictify_view_keys()
 
         def input_to_dict(input):
             return input.to_dict(trans)
diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py
index fee9f6d6079e6254ed54bb69fe20c7f1dbc9de2b..b74df54fa269d7cb376849acc98994ae87cf422a 100644
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -19,9 +19,22 @@ from galaxy.model.dataset_collections import (
     matching,
     subcollections,
 )
-from galaxy.util import permutations
+from galaxy.util.permutations import (
+    build_combos,
+    input_classification,
+    is_in_state,
+    state_copy,
+    state_get_value,
+    state_remove_value,
+    state_set_value,
+)
 from . import visit_input_values
 from .wrapped import process_key
+from .._types import (
+    InputFormatT,
+    ToolRequestT,
+    ToolStateJobInstanceT,
+)
 
 log = logging.getLogger(__name__)
 
@@ -154,10 +167,18 @@ def expand_workflow_inputs(param_inputs, inputs=None):
     return WorkflowParameterExpansion(param_combinations, params_keys, input_combinations)
 
 
-ExpandedT = Tuple[List[Dict[str, Any]], Optional[matching.MatchingCollections]]
+ExpandedT = Tuple[List[ToolStateJobInstanceT], Optional[matching.MatchingCollections]]
+
+
+def expand_flat_parameters_to_nested(incoming_copy: ToolRequestT) -> Dict[str, Any]:
+    nested_dict: Dict[str, Any] = {}
+    for incoming_key, incoming_value in incoming_copy.items():
+        if not incoming_key.startswith("__"):
+            process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
+    return nested_dict
 
 
-def expand_meta_parameters(trans, tool, incoming) -> ExpandedT:
+def expand_meta_parameters(trans, tool, incoming: ToolRequestT, input_format: InputFormatT) -> ExpandedT:
     """
     Take in a dictionary of raw incoming parameters and expand to a list
     of expanded incoming parameters (one set of parameters per tool
@@ -172,33 +193,24 @@ def expand_meta_parameters(trans, tool, incoming) -> ExpandedT:
     # order matters, so the following reorders incoming
     # according to tool.inputs (which is ordered).
     incoming_copy = incoming.copy()
-    nested_dict: Dict[str, Any] = {}
-    for incoming_key, incoming_value in incoming_copy.items():
-        if not incoming_key.startswith("__"):
-            process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
-
-    reordered_incoming = {}
-
-    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
-        if prefixed_name in incoming_copy:
-            reordered_incoming[prefixed_name] = incoming_copy[prefixed_name]
-            del incoming_copy[prefixed_name]
+    if input_format == "legacy":
+        nested_dict = expand_flat_parameters_to_nested(incoming_copy)
+    else:
+        nested_dict = incoming_copy
 
-    visit_input_values(inputs=tool.inputs, input_values=nested_dict, callback=visitor)
-    reordered_incoming.update(incoming_copy)
+    collections_to_match = matching.CollectionsToMatch()
 
-    def classifier(input_key):
-        value = incoming[input_key]
+    def classifier_from_value(value, input_key):
         if isinstance(value, dict) and "values" in value:
             # Explicit meta wrapper for inputs...
             is_batch = value.get("batch", False)
             is_linked = value.get("linked", True)
             if is_batch and is_linked:
-                classification = permutations.input_classification.MATCHED
+                classification = input_classification.MATCHED
             elif is_batch:
-                classification = permutations.input_classification.MULTIPLIED
+                classification = input_classification.MULTIPLIED
             else:
-                classification = permutations.input_classification.SINGLE
+                classification = input_classification.SINGLE
             if __collection_multirun_parameter(value):
                 collection_value = value["values"][0]
                 values = __expand_collection_parameter(
@@ -207,17 +219,29 @@ def expand_meta_parameters(trans, tool, incoming) -> ExpandedT:
             else:
                 values = value["values"]
         else:
-            classification = permutations.input_classification.SINGLE
+            classification = input_classification.SINGLE
             values = value
         return classification, values
 
-    collections_to_match = matching.CollectionsToMatch()
+    nested = input_format != "legacy"
+    if not nested:
+        reordered_incoming = reorder_parameters(tool, incoming_copy, nested_dict, nested)
+        incoming_template = reordered_incoming
+
+        def classifier_flat(input_key):
+            return classifier_from_value(incoming[input_key], input_key)
 
-    # Stick an unexpanded version of multirun keys so they can be replaced,
-    # by expand_mult_inputs.
-    incoming_template = reordered_incoming
+        single_inputs, matched_multi_inputs, multiplied_multi_inputs = split_inputs_flat(
+            incoming_template, classifier_flat
+        )
+    else:
+        reordered_incoming = reorder_parameters(tool, incoming_copy, nested_dict, nested)
+        incoming_template = reordered_incoming
+        single_inputs, matched_multi_inputs, multiplied_multi_inputs = split_inputs_nested(
+            tool.inputs, incoming_template, classifier_from_value
+        )
 
-    expanded_incomings = permutations.expand_multi_inputs(incoming_template, classifier)
+    expanded_incomings = build_combos(single_inputs, matched_multi_inputs, multiplied_multi_inputs, nested=nested)
     if collections_to_match.has_collections():
         collection_info = trans.app.dataset_collection_manager.match_collections(collections_to_match)
     else:
@@ -225,6 +249,84 @@ def expand_meta_parameters(trans, tool, incoming) -> ExpandedT:
     return expanded_incomings, collection_info
 
 
+def reorder_parameters(tool, incoming, nested_dict, nested):
+    # If we're going to multiply input dataset combinations
+    # order matters, so the following reorders incoming
+    # according to tool.inputs (which is ordered).
+    incoming_copy = state_copy(incoming, nested)
+
+    reordered_incoming = {}
+
+    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
+        if is_in_state(incoming_copy, prefixed_name, nested):
+            value_to_copy_over = state_get_value(incoming_copy, prefixed_name, nested)
+            state_set_value(reordered_incoming, prefixed_name, value_to_copy_over, nested)
+            state_remove_value(incoming_copy, prefixed_name, nested)
+
+    visit_input_values(inputs=tool.inputs, input_values=nested_dict, callback=visitor)
+
+    def merge_into(from_object, into_object):
+        if isinstance(from_object, dict):
+            for key, value in from_object.items():
+                if key not in into_object:
+                    into_object[key] = value
+                else:
+                    into_target = into_object[key]
+                    merge_into(value, into_target)
+        elif isinstance(from_object, list):
+            for index in from_object:
+                if len(into_object) <= index:
+                    into_object.append(from_object[index])
+                else:
+                    merge_into(from_object[index], into_object[index])
+
+    merge_into(incoming_copy, reordered_incoming)
+    return reordered_incoming
+
+
+def split_inputs_flat(inputs: Dict[str, Any], classifier):
+    single_inputs: Dict[str, Any] = {}
+    matched_multi_inputs: Dict[str, Any] = {}
+    multiplied_multi_inputs: Dict[str, Any] = {}
+
+    for input_key in inputs:
+        input_type, expanded_val = classifier(input_key)
+        if input_type == input_classification.SINGLE:
+            single_inputs[input_key] = expanded_val
+        elif input_type == input_classification.MATCHED:
+            matched_multi_inputs[input_key] = expanded_val
+        elif input_type == input_classification.MULTIPLIED:
+            multiplied_multi_inputs[input_key] = expanded_val
+
+    return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)
+
+
+def split_inputs_nested(inputs, nested_dict, classifier):
+    single_inputs: Dict[str, Any] = {}
+    matched_multi_inputs: Dict[str, Any] = {}
+    multiplied_multi_inputs: Dict[str, Any] = {}
+    unset_value = object()
+
+    def visitor(input, value, prefix, prefixed_name, prefixed_label, error, **kwargs):
+        if value is unset_value:
+            # don't want to inject extra nulls into state
+            return
+
+        input_type, expanded_val = classifier(value, prefixed_name)
+        if input_type == input_classification.SINGLE:
+            single_inputs[prefixed_name] = expanded_val
+        elif input_type == input_classification.MATCHED:
+            matched_multi_inputs[prefixed_name] = expanded_val
+        elif input_type == input_classification.MULTIPLIED:
+            multiplied_multi_inputs[prefixed_name] = expanded_val
+
+    visit_input_values(
+        inputs=inputs, input_values=nested_dict, callback=visitor, allow_case_inference=True, unset_value=unset_value
+    )
+    single_inputs_nested = expand_flat_parameters_to_nested(single_inputs)
+    return (single_inputs_nested, matched_multi_inputs, multiplied_multi_inputs)
+
+
 def __expand_collection_parameter(trans, input_key, incoming_val, collections_to_match, linked=False):
     # If subcollectin multirun of data_collection param - value will
     # be "hdca_id|subcollection_type" else it will just be hdca_id
diff --git a/lib/galaxy/tools/parameters/options.py b/lib/galaxy/tools/parameters/options.py
new file mode 100644
index 0000000000000000000000000000000000000000..4fd23c3fcaed526732fa2cb3b7002620d19739f7
--- /dev/null
+++ b/lib/galaxy/tools/parameters/options.py
@@ -0,0 +1,29 @@
+from typing import (
+    NamedTuple,
+    Optional,
+)
+
+from galaxy.model import (
+    DatasetInstance,
+    HistoryDatasetAssociation,
+)
+from galaxy.security.idencoding import IdEncodingHelper
+
+
+class ParameterOption(NamedTuple):
+    name: str
+    value: str
+    selected: bool = False
+    dataset: Optional["DatasetInstance"] = None
+
+    def serialize(self, security: "IdEncodingHelper"):
+        if self.dataset:
+            return (
+                self.name,
+                {
+                    "src": "hda" if isinstance(self.dataset, HistoryDatasetAssociation) else "ldda",
+                    "id": security.encode_id(self.dataset.id),
+                },
+                self.selected,
+            )
+        return (self.name, self.value, self.selected)
diff --git a/lib/galaxy/tools/parameters/populate_model.py b/lib/galaxy/tools/parameters/populate_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..41950bc3a03f82002061edddcee9797bf68d27af
--- /dev/null
+++ b/lib/galaxy/tools/parameters/populate_model.py
@@ -0,0 +1,74 @@
+import logging
+from typing import (
+    Any,
+    Dict,
+    List,
+)
+
+from galaxy.util.expressions import ExpressionContext
+from .basic import ImplicitConversionRequired
+
+log = logging.getLogger(__name__)
+
+
+def populate_model(request_context, inputs, state_inputs, group_inputs: List[Dict[str, Any]], other_values=None):
+    """
+    Populates the tool model consumed by the client form builder.
+    """
+    other_values = ExpressionContext(state_inputs, other_values)
+    for input_index, input in enumerate(inputs.values()):
+        tool_dict = None
+        group_state = state_inputs.get(input.name, {})
+        if input.type == "repeat":
+            tool_dict = input.to_dict(request_context)
+            group_size = len(group_state)
+            tool_dict["cache"] = [None] * group_size
+            group_cache: List[List[Dict[str, Any]]] = tool_dict["cache"]
+            for i in range(group_size):
+                group_cache[i] = []
+                populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
+        elif input.type == "conditional":
+            tool_dict = input.to_dict(request_context)
+            if "test_param" in tool_dict:
+                test_param = tool_dict["test_param"]
+                test_param["value"] = input.test_param.value_to_basic(
+                    group_state.get(
+                        test_param["name"], input.test_param.get_initial_value(request_context, other_values)
+                    ),
+                    request_context.app,
+                )
+                test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
+                for i in range(len(tool_dict["cases"])):
+                    current_state = {}
+                    if i == group_state.get("__current_case__"):
+                        current_state = group_state
+                    populate_model(
+                        request_context,
+                        input.cases[i].inputs,
+                        current_state,
+                        tool_dict["cases"][i]["inputs"],
+                        other_values,
+                    )
+        elif input.type == "section":
+            tool_dict = input.to_dict(request_context)
+            populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
+        else:
+            try:
+                initial_value = input.get_initial_value(request_context, other_values)
+                tool_dict = input.to_dict(request_context, other_values=other_values)
+                tool_dict["value"] = input.value_to_basic(
+                    state_inputs.get(input.name, initial_value), request_context.app, use_security=True
+                )
+                tool_dict["default_value"] = input.value_to_basic(initial_value, request_context.app, use_security=True)
+                tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
+            except ImplicitConversionRequired:
+                tool_dict = input.to_dict(request_context)
+                # This hack leads client to display a text field
+                tool_dict["textable"] = True
+            except Exception:
+                tool_dict = input.to_dict(request_context)
+                log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
+        if input_index >= len(group_inputs):
+            group_inputs.append(tool_dict)
+        else:
+            group_inputs[input_index] = tool_dict
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 6334fd95f8b835511f109b3219548df6ac24a539..57e0a6c45f1059a16f5792adf60b75072ada1527 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -3,16 +3,30 @@ Classes related to parameter validation.
 """
 
 import abc
-import json
 import logging
-import os.path
-
-import regex
+import os
+from typing import (
+    Any,
+    cast,
+    List,
+    Optional,
+    Union,
+)
 
 from galaxy import (
     model,
     util,
 )
+from galaxy.tool_util.parser.parameter_validators import (
+    AnyValidatorModel,
+    EmptyFieldParameterValidatorModel,
+    ExpressionParameterValidatorModel,
+    InRangeParameterValidatorModel,
+    MetadataParameterValidatorModel,
+    parse_xml_validators as parse_xml_validators_models,
+    raise_error_if_valiation_fails,
+    RegexParameterValidatorModel,
+)
 
 log = logging.getLogger(__name__)
 
@@ -24,27 +38,7 @@ class Validator(abc.ABC):
 
     requires_dataset_metadata = False
 
-    @classmethod
-    def from_element(cls, param, elem):
-        """
-        Initialize the appropriate Validator class
-
-        example call `validation.Validator.from_element(ToolParameter_object, Validator_object)`
-
-        needs to be implemented in the subclasses and should return the
-        corresponding Validator object by a call to `cls( ... )` which calls the
-        `__init__` method of the corresponding validator
-
-        param cls the Validator class
-        param param the element to be evaluated (which contains the validator)
-        param elem the validator element
-        return an object of a Validator subclass that corresponds to the type attribute of the validator element
-        """
-        _type = elem.get("type")
-        assert _type is not None, "Required 'type' attribute missing from validator"
-        return validator_types[_type].from_element(param, elem)
-
-    def __init__(self, message, negate=False):
+    def __init__(self, message: str, negate: bool = False):
         self.message = message
         self.negate = util.asbool(negate)
         super().__init__()
@@ -68,15 +62,7 @@ class Validator(abc.ABC):
 
         return None if positive validation, otherwise a ValueError is raised
         """
-        assert isinstance(value, bool), "value must be boolean"
-        if message is None:
-            message = self.message
-        if value_to_show and "%s" in message:
-            message = message % value_to_show
-        if (not self.negate and value) or (self.negate and not value):
-            return
-        else:
-            raise ValueError(message)
+        raise_error_if_valiation_fails(value, self, message=message, value_to_show=value_to_show)
 
 
 class RegexValidator(Validator):
@@ -84,24 +70,14 @@ class RegexValidator(Validator):
     Validator that evaluates a regular expression
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        return cls(elem.get("message"), elem.text, elem.get("negate", "false"))
-
-    def __init__(self, message, expression, negate):
-        if message is None:
-            message = f"Value '%s' does {'not ' if negate == 'false' else ''}match regular expression '{expression.replace('%', '%%')}'"
+    def __init__(self, message: str, expression: str, negate: bool):
         super().__init__(message, negate)
         # Compile later. RE objects used to not be thread safe. Not sure about
         # the sre module.
         self.expression = expression
 
     def validate(self, value, trans=None):
-        if not isinstance(value, list):
-            value = [value]
-        for val in value:
-            match = regex.match(self.expression, val or "")
-            super().validate(match is not None, value_to_show=val)
+        RegexParameterValidatorModel.regex_validation(self.expression, value, self)
 
 
 class ExpressionValidator(Validator):
@@ -109,24 +85,16 @@ class ExpressionValidator(Validator):
     Validator that evaluates a python expression using the value
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        return cls(elem.get("message"), elem.text, elem.get("negate", "false"))
-
-    def __init__(self, message, expression, negate):
-        if message is None:
-            message = f"Value '%s' does not evaluate to {'True' if negate == 'false' else 'False'} for '{expression}'"
+    def __init__(self, message: str, expression: str, negate: bool):
         super().__init__(message, negate)
         self.expression = expression
         # Save compiled expression, code objects are thread safe (right?)
-        self.compiled_expression = compile(expression, "<string>", "eval")
+        self.compiled_expression = ExpressionParameterValidatorModel.ensure_compiled(expression)
 
     def validate(self, value, trans=None):
-        try:
-            evalresult = eval(self.compiled_expression, dict(value=value))
-        except Exception:
-            super().validate(False, message=f"Validator '{self.expression}' could not be evaluated on '{value}'")
-        super().validate(bool(evalresult), value_to_show=value)
+        ExpressionParameterValidatorModel.expression_validation(
+            self.expression, value, self, compiled_expression=self.compiled_expression
+        )
 
 
 class InRangeValidator(ExpressionValidator):
@@ -134,18 +102,15 @@ class InRangeValidator(ExpressionValidator):
     Validator that ensures a number is in a specified range
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        return cls(
-            elem.get("message"),
-            elem.get("min"),
-            elem.get("max"),
-            elem.get("exclude_min", "false"),
-            elem.get("exclude_max", "false"),
-            elem.get("negate", "false"),
-        )
-
-    def __init__(self, message, range_min, range_max, exclude_min=False, exclude_max=False, negate=False):
+    def __init__(
+        self,
+        message: str,
+        min: Optional[float] = None,
+        max: Optional[float] = None,
+        exclude_min: bool = False,
+        exclude_max: bool = False,
+        negate: bool = False,
+    ):
         """
         When the optional exclude_min and exclude_max attributes are set
         to true, the range excludes the end points (i.e., min < value < max),
@@ -153,10 +118,10 @@ class InRangeValidator(ExpressionValidator):
         (1.e., min <= value <= max).  Combinations of exclude_min and exclude_max
         values are allowed.
         """
-        self.min = range_min if range_min is not None else "-inf"
-        self.exclude_min = util.asbool(exclude_min)
-        self.max = range_max if range_max is not None else "inf"
-        self.exclude_max = util.asbool(exclude_max)
+        self.min = str(min) if min is not None else "-inf"
+        self.exclude_min = exclude_min
+        self.max = str(max) if max is not None else "inf"
+        self.exclude_max = exclude_max
         assert float(self.min) <= float(self.max), "min must be less than or equal to max"
         # Remove unneeded 0s and decimal from floats to make message pretty.
         op1 = "<="
@@ -166,24 +131,23 @@ class InRangeValidator(ExpressionValidator):
         if self.exclude_max:
             op2 = "<"
         expression = f"float('{self.min}') {op1} float(value) {op2} float('{self.max}')"
-        if message is None:
-            message = f"Value ('%s') must {'not ' if negate == 'true' else ''}fulfill {expression}"
         super().__init__(message, expression, negate)
 
+    @staticmethod
+    def simple_range_validator(min: Optional[float], max: Optional[float]):
+        return cast(
+            InRangeParameterValidatorModel,
+            _to_validator(None, InRangeParameterValidatorModel(min=min, max=max, implicit=True)),
+        )
+
 
 class LengthValidator(InRangeValidator):
     """
     Validator that ensures the length of the provided string (value) is in a specific range
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        return cls(elem.get("message"), elem.get("min"), elem.get("max"), elem.get("negate", "false"))
-
-    def __init__(self, message, length_min, length_max, negate):
-        if message is None:
-            message = f"Must {'not ' if negate == 'true' else ''}have length of at least {length_min} and at most {length_max}"
-        super().__init__(message, range_min=length_min, range_max=length_max, negate=negate)
+    def __init__(self, message: str, min: float, max: float, negate: bool):
+        super().__init__(message, min=min, max=max, negate=negate)
 
     def validate(self, value, trans=None):
         if value is None:
@@ -196,16 +160,8 @@ class DatasetOkValidator(Validator):
     Validator that checks if a dataset is in an 'ok' state
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        negate = elem.get("negate", "false")
-        message = elem.get("message")
-        if message is None:
-            if negate == "false":
-                message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
-            else:
-                message = "The selected dataset must not be in state OK"
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
         if value:
@@ -217,13 +173,8 @@ class DatasetEmptyValidator(Validator):
     Validator that checks if a dataset has a positive file size.
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        negate = elem.get("negate", "false")
-        if not message:
-            message = f"The selected dataset is {'non-' if negate == 'true' else ''}empty, this tool expects {'non-' if negate == 'false' else ''}empty files."
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
         if value:
@@ -235,13 +186,8 @@ class DatasetExtraFilesPathEmptyValidator(Validator):
     Validator that checks if a dataset's extra_files_path exists and is not empty.
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        negate = elem.get("negate", "false")
-        if not message:
-            message = f"The selected dataset's extra_files_path directory is {'non-' if negate == 'true' else ''}empty or does {'not ' if negate == 'false' else ''}exist, this tool expects {'non-' if negate == 'false' else ''}empty extra_files_path directories associated with the selected input."
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
         if value:
@@ -255,25 +201,20 @@ class MetadataValidator(Validator):
 
     requires_dataset_metadata = True
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        return cls(
-            message=message, check=elem.get("check", ""), skip=elem.get("skip", ""), negate=elem.get("negate", "false")
-        )
-
-    def __init__(self, message=None, check="", skip="", negate="false"):
-        if not message:
-            if not util.asbool(negate):
-                message = "Metadata '%s' missing, click the pencil icon in the history item to edit / save the metadata attributes"
-            else:
-                if check != "":
-                    message = f"At least one of the checked metadata '{check}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
-                elif skip != "":
-                    message = f"At least one of the non skipped metadata '{skip}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
+    def __init__(
+        self,
+        message: str,
+        check: Optional[List[str]] = None,
+        skip: Optional[List[str]] = None,
+        negate: bool = False,
+    ):
         super().__init__(message, negate)
-        self.check = check.split(",") if check else None
-        self.skip = skip.split(",") if skip else None
+        self.check = check
+        self.skip = skip
+
+    @staticmethod
+    def default_metadata_validator() -> "MetadataValidator":
+        return cast(MetadataValidator, _to_validator(None, MetadataParameterValidatorModel(implicit=True)))
 
     def validate(self, value, trans=None):
         if value:
@@ -292,26 +233,11 @@ class MetadataEqualValidator(Validator):
 
     requires_dataset_metadata = True
 
-    def __init__(self, metadata_name=None, value=None, message=None, negate="false"):
-        if not message:
-            if not util.asbool(negate):
-                message = f"Metadata value for '{metadata_name}' must be '{value}', but it is '%s'."
-            else:
-                message = f"Metadata value for '{metadata_name}' must not be '{value}' but it is."
+    def __init__(self, metadata_name=None, value=None, message=None, negate: bool = False):
         super().__init__(message, negate)
         self.metadata_name = metadata_name
         self.value = value
 
-    @classmethod
-    def from_element(cls, param, elem):
-        value = elem.get("value", None) or json.loads(elem.get("value_json", "null"))
-        return cls(
-            metadata_name=elem.get("metadata_name", None),
-            value=value,
-            message=elem.get("message", None),
-            negate=elem.get("negate", "false"),
-        )
-
     def validate(self, value, trans=None):
         if value:
             metadata_value = getattr(value.metadata, self.metadata_name)
@@ -325,13 +251,8 @@ class UnspecifiedBuildValidator(Validator):
 
     requires_dataset_metadata = True
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        negate = elem.get("negate", "false")
-        if not message:
-            message = f"{'Unspecified' if negate == 'false' else 'Specified'} genome build, click the pencil icon in the history item to {'set' if negate == 'false' else 'remove'} the genome build"
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
         # if value is None, we cannot validate
@@ -348,13 +269,8 @@ class NoOptionsValidator(Validator):
     Validator that checks for empty select list
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        negate = elem.get("negate", "false")
-        if not message:
-            message = f"{'No options' if negate == 'false' else 'Options'} available for selection"
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
         super().validate(value is not None)
@@ -365,19 +281,11 @@ class EmptyTextfieldValidator(Validator):
     Validator that checks for empty text field
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        message = elem.get("message")
-        negate = elem.get("negate", "false")
-        if not message:
-            if negate == "false":
-                message = elem.get("message", "Field requires a value")
-            else:
-                message = elem.get("message", "Field must not set a value")
-        return cls(message, negate)
+    def __init__(self, message: str, negate: bool = False):
+        super().__init__(message, negate=negate)
 
     def validate(self, value, trans=None):
-        super().validate(value != "")
+        EmptyFieldParameterValidatorModel.empty_validate(value, self)
 
 
 class MetadataInFileColumnValidator(Validator):
@@ -391,35 +299,19 @@ class MetadataInFileColumnValidator(Validator):
 
     requires_dataset_metadata = True
 
-    @classmethod
-    def from_element(cls, param, elem):
-        filename = elem.get("filename")
-        assert filename, f"Required 'filename' attribute missing from {elem.get('type')} validator."
-        filename = f"{param.tool.app.config.tool_data_path}/{filename.strip()}"
-        assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
-        metadata_name = elem.get("metadata_name")
-        assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
-        metadata_name = metadata_name.strip()
-        metadata_column = int(elem.get("metadata_column", 0))
-        split = elem.get("split", "\t")
-        message = elem.get("message", f"Value for metadata {metadata_name} was not found in {filename}.")
-        line_startswith = elem.get("line_startswith")
-        if line_startswith:
-            line_startswith = line_startswith.strip()
-        negate = elem.get("negate", "false")
-        return cls(filename, metadata_name, metadata_column, message, line_startswith, split, negate)
-
     def __init__(
         self,
-        filename,
-        metadata_name,
-        metadata_column,
-        message="Value for metadata not found.",
-        line_startswith=None,
-        split="\t",
-        negate="false",
+        filename: str,
+        metadata_name: str,
+        metadata_column: int,
+        message: str,
+        line_startswith: Optional[str] = None,
+        split: str = "\t",
+        negate: bool = False,
     ):
         super().__init__(message, negate)
+        assert filename
+        assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
         self.metadata_name = metadata_name
         self.valid_values = set()
         with open(filename) as fh:
@@ -445,28 +337,20 @@ class ValueInDataTableColumnValidator(Validator):
     note: this is covered in a framework test (validation_value_in_datatable)
     """
 
-    @classmethod
-    def from_element(cls, param, elem):
-        table_name = elem.get("table_name")
-        assert table_name, f"Required 'table_name' attribute missing from {elem.get('type')} validator."
-        tool_data_table = param.tool.app.tool_data_tables[table_name]
-        column = elem.get("metadata_column", 0)
-        try:
-            column = int(column)
-        except ValueError:
-            pass
-        message = elem.get("message", f"Value was not found in {table_name}.")
-        negate = elem.get("negate", "false")
-        return cls(tool_data_table, column, message, negate)
-
-    def __init__(self, tool_data_table, column, message="Value not found.", negate="false"):
+    def __init__(
+        self,
+        tool_data_table,
+        metadata_column: Union[str, int],
+        message: str,
+        negate: bool = False,
+    ):
         super().__init__(message, negate)
-        self.valid_values = []
+        self.valid_values: List[Any] = []
         self._data_table_content_version = None
         self._tool_data_table = tool_data_table
-        if isinstance(column, str):
-            column = tool_data_table.columns[column]
-        self._column = column
+        if isinstance(metadata_column, str):
+            metadata_column = tool_data_table.columns[metadata_column]
+        self._column = metadata_column
         self._load_values()
 
     def _load_values(self):
@@ -496,7 +380,9 @@ class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
     note: this is covered in a framework test (validation_value_in_datatable)
     """
 
-    def __init__(self, tool_data_table, metadata_column, message="Value already present.", negate="false"):
+    def __init__(
+        self, tool_data_table, metadata_column: Union[str, int], message="Value already present.", negate: bool = False
+    ):
         super().__init__(tool_data_table, metadata_column, message, negate)
 
     def validate(self, value, trans=None):
@@ -517,26 +403,13 @@ class MetadataInDataTableColumnValidator(ValueInDataTableColumnValidator):
 
     requires_dataset_metadata = True
 
-    @classmethod
-    def from_element(cls, param, elem):
-        table_name = elem.get("table_name")
-        assert table_name, f"Required 'table_name' attribute missing from {elem.get('type')} validator."
-        tool_data_table = param.tool.app.tool_data_tables[table_name]
-        metadata_name = elem.get("metadata_name")
-        assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
-        metadata_name = metadata_name.strip()
-        # TODO rename to column?
-        metadata_column = elem.get("metadata_column", 0)
-        try:
-            metadata_column = int(metadata_column)
-        except ValueError:
-            pass
-        message = elem.get("message", f"Value for metadata {metadata_name} was not found in {table_name}.")
-        negate = elem.get("negate", "false")
-        return cls(tool_data_table, metadata_name, metadata_column, message, negate)
-
     def __init__(
-        self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"
+        self,
+        tool_data_table,
+        metadata_name: str,
+        metadata_column: Union[str, int],
+        message: str,
+        negate: bool = False,
     ):
         super().__init__(tool_data_table, metadata_column, message, negate)
         self.metadata_name = metadata_name
@@ -558,7 +431,12 @@ class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
     requires_dataset_metadata = True
 
     def __init__(
-        self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"
+        self,
+        tool_data_table,
+        metadata_name: str,
+        metadata_column: Union[str, int],
+        message: str,
+        negate: bool = False,
     ):
         super().__init__(tool_data_table, metadata_name, metadata_column, message, negate)
 
@@ -580,26 +458,18 @@ class MetadataInRangeValidator(InRangeValidator):
 
     requires_dataset_metadata = True
 
-    @classmethod
-    def from_element(cls, param, elem):
-        metadata_name = elem.get("metadata_name")
-        assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
-        metadata_name = metadata_name.strip()
-        ret = cls(
-            metadata_name,
-            elem.get("message"),
-            elem.get("min"),
-            elem.get("max"),
-            elem.get("exclude_min", "false"),
-            elem.get("exclude_max", "false"),
-            elem.get("negate", "false"),
-        )
-        ret.message = "Metadata: " + ret.message
-        return ret
-
-    def __init__(self, metadata_name, message, range_min, range_max, exclude_min, exclude_max, negate):
+    def __init__(
+        self,
+        metadata_name: str,
+        message: str,
+        min: Optional[float] = None,
+        max: Optional[float] = None,
+        exclude_min: bool = False,
+        exclude_max: bool = False,
+        negate: bool = False,
+    ):
         self.metadata_name = metadata_name
-        super().__init__(message, range_min, range_max, exclude_min, exclude_max, negate)
+        super().__init__(message, min, max, exclude_min, exclude_max, negate)
 
     def validate(self, value, trans=None):
         if value:
@@ -638,3 +508,29 @@ validator_types = dict(
 
 deprecated_validator_types = dict(dataset_metadata_in_file=MetadataInFileColumnValidator)
 validator_types.update(deprecated_validator_types)
+
+
+def parse_xml_validators(app, xml_el: util.Element) -> List[Validator]:
+    return to_validators(app, parse_xml_validators_models(xml_el))
+
+
+def to_validators(app, validator_models: List[AnyValidatorModel]) -> List[Validator]:
+    validators = []
+    for validator_model in validator_models:
+        validators.append(_to_validator(app, validator_model))
+    return validators
+
+
+def _to_validator(app, validator_model: AnyValidatorModel) -> Validator:
+    as_dict = validator_model.model_dump()
+    validator_type = as_dict.pop("type")
+    del as_dict["implicit"]
+    if "table_name" in as_dict and app is not None:
+        table_name = as_dict.pop("table_name")
+        tool_data_table = app.tool_data_tables[table_name]
+        as_dict["tool_data_table"] = tool_data_table
+    if "filename" in as_dict and app is not None:
+        filename = as_dict.pop("filename")
+        as_dict["filename"] = f"{app.config.tool_data_path}/{filename}"
+
+    return validator_types[validator_type](**as_dict)
diff --git a/lib/galaxy/tools/parameters/workflow_utils.py b/lib/galaxy/tools/parameters/workflow_utils.py
index 73fcb688dfa1a1f8ad535fe9875d9c4a295ae846..178f08a773a6dd8ef5f1357ae965ff53286e8c3c 100644
--- a/lib/galaxy/tools/parameters/workflow_utils.py
+++ b/lib/galaxy/tools/parameters/workflow_utils.py
@@ -1,6 +1,15 @@
 from collections.abc import MutableMapping
 
 
+class NoReplacement:
+
+    def __str__(self):
+        return "NO_REPLACEMENT singleton"
+
+
+NO_REPLACEMENT = NoReplacement()
+
+
 class workflow_building_modes:
     DISABLED = False
     ENABLED = True
diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py
index 11fa98c0e64462f638f5cbeec17d0bbb8b98d15c..d23e9be5edf91ecd2397f4efbd093ca18ce60ddd 100644
--- a/lib/galaxy/tools/parameters/wrapped.py
+++ b/lib/galaxy/tools/parameters/wrapped.py
@@ -25,6 +25,10 @@ from galaxy.tools.wrappers import (
     InputValueWrapper,
     SelectToolParameterWrapper,
 )
+from galaxy.util.permutations import (
+    looks_like_flattened_repeat_key,
+    split_flattened_repeat_key,
+)
 
 PARAMS_UNWRAPPED = object()
 
@@ -172,10 +176,9 @@ def process_key(incoming_key: str, incoming_value: Any, d: Dict[str, Any]):
             # In case we get an empty repeat after we already filled in a repeat element
             return
         d[incoming_key] = incoming_value
-    elif key_parts[0].rsplit("_", 1)[-1].isdigit():
+    elif looks_like_flattened_repeat_key(key_parts[0]):
         # Repeat
-        input_name, _index = key_parts[0].rsplit("_", 1)
-        index = int(_index)
+        input_name, index = split_flattened_repeat_key(key_parts[0])
         d.setdefault(input_name, [])
         newlist: List[Dict[Any, Any]] = [{} for _ in range(index + 1)]
         d[input_name].extend(newlist[len(d[input_name]) :])
diff --git a/lib/galaxy/tools/recommendations.py b/lib/galaxy/tools/recommendations.py
index 6d6aa1e9e3522f70f7d1d1d11c39ec310f28438a..62df298fcfb4bfe4222fe5b8a352fefafad85bfc 100644
--- a/lib/galaxy/tools/recommendations.py
+++ b/lib/galaxy/tools/recommendations.py
@@ -131,16 +131,16 @@ class ToolRecommendations:
         Create model and associated dictionaries for recommendations
         """
         self.tool_recommendation_model_path = self.__download_model(remote_model_url)
-        model_file = h5py.File(self.tool_recommendation_model_path, "r")
-        self.reverse_dictionary = json.loads(model_file["reverse_dict"][()].decode("utf-8"))
-        self.loaded_model = self.create_transformer_model(len(self.reverse_dictionary) + 1)
-        self.loaded_model.load_weights(self.tool_recommendation_model_path)
+        with h5py.File(self.tool_recommendation_model_path, "r", locking=False) as model_file:
+            self.reverse_dictionary = json.loads(model_file["reverse_dict"][()].decode("utf-8"))
+            self.loaded_model = self.create_transformer_model(len(self.reverse_dictionary) + 1)
+            self.loaded_model.load_weights(self.tool_recommendation_model_path)
 
-        self.model_data_dictionary = {v: k for k, v in self.reverse_dictionary.items()}
-        # set the list of compatible tools
-        self.compatible_tools = json.loads(model_file["compatible_tools"][()].decode("utf-8"))
-        tool_weights = json.loads(model_file["class_weights"][()].decode("utf-8"))
-        self.standard_connections = json.loads(model_file["standard_connections"][()].decode("utf-8"))
+            self.model_data_dictionary = {v: k for k, v in self.reverse_dictionary.items()}
+            # set the list of compatible tools
+            self.compatible_tools = json.loads(model_file["compatible_tools"][()].decode("utf-8"))
+            tool_weights = json.loads(model_file["class_weights"][()].decode("utf-8"))
+            self.standard_connections = json.loads(model_file["standard_connections"][()].decode("utf-8"))
         # sort the tools' usage dictionary
         tool_pos_sorted = [int(key) for key in tool_weights.keys()]
         for k in tool_pos_sorted:
diff --git a/lib/galaxy/tools/relabel_from_file.xml b/lib/galaxy/tools/relabel_from_file.xml
index 8b741d3b0b06be40e44963b684ff0d13edeee2a6..7f2687d35e70220de24b124abe50f5ee0a05b1ea 100644
--- a/lib/galaxy/tools/relabel_from_file.xml
+++ b/lib/galaxy/tools/relabel_from_file.xml
@@ -1,6 +1,6 @@
 <tool id="__RELABEL_FROM_FILE__"
       name="Relabel identifiers"
-      version="1.0.0"
+      version="1.1.0"
       tool_type="relabel_from_file">
     <description></description>
     <type class="RelabelFromFileTool" module="galaxy.tools" />
@@ -13,16 +13,23 @@
         <param type="data_collection" name="input" label="Input Collection" help="collection to change identifiers in"/>
         <conditional name="how">
             <param type="select" name="how_select" label="How should the new labels be specified?">
-                <option value="txt">Using lines in a simple text file.</option>
-                <option value="tabular">Map original identifiers to new ones using a two column table.</option>
+                <option value="txt">Use lines in a simple text file as new identifiers.</option>
+                <option value="tabular">Map original identifiers to new ones using a two-column table.</option>
+                <option value="tabular_extended">Use any two columns of a table for identifier mapping.</option>
             </param>
             <when value="txt">
                 <param type="data" name="labels" format="txt" label="New Identifiers" />
-                <param name="strict" type="boolean" label="Ensure strict mapping" help="If selected, the target file must contain exactly the correct number of lines." truevalue="true" falsevalue="false" />
+                <param name="strict" type="boolean" label="Ensure strict mapping" help="If selected, the text file must contain exactly the correct number of lines." truevalue="true" falsevalue="false" />
             </when>
             <when value="tabular">
-                <param type="data" name="labels" format="tabular" label="New Identifiers" />
-                <param name="strict" type="boolean" label="Ensure strict mapping" help="If checked, the target file must contain exactly the correct number of lines and each input identifier must match exactly one element of the input collection." truevalue="true" falsevalue="false" />
+                <param type="data" name="labels" format="tabular" label="Identifier mapping" />
+                <param name="strict" type="boolean" label="Ensure strict mapping" help="If checked, the table must contain exactly the correct number of lines and each original identifier must match exactly one element of the input collection." truevalue="true" falsevalue="false" />
+            </when>
+            <when value="tabular_extended">
+                <param type="data" name="labels" format="tabular" label="Identifier mapping" />
+                <param name="from" type="data_column" data_ref="labels" value="1" label="Column with current identifiers"/>
+                <param name="to" type="data_column" data_ref="labels" value="2" label="Column with new identifiers"/>
+                <param name="strict" type="boolean" label="Ensure strict mapping" help="If checked, the table must contain exactly the correct number of lines and each original identifier must match exactly one element of the input collection." truevalue="true" falsevalue="false" />
             </when>
         </conditional>
     </inputs>
@@ -87,6 +94,37 @@
               </element>
             </output_collection>
         </test>
+        <!-- test non-default columns -->
+        <test>
+            <param name="input">
+                <collection type="list:paired">
+                    <element name="i1">
+                        <collection type="paired">
+                            <element name="forward" value="simple_line.txt" />
+                            <element name="reverse" value="simple_line_alternative.txt" />
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="how_select" value="tabular_extended" />
+            <param name="labels" value="new_labels_3.txt" ftype="tabular" />
+            <param name="from" value="3" />
+            <param name="to" value="1" />
+            <output_collection name="output" type="list:paired">
+              <element name="new_i1">
+                <element name="forward">
+                  <assert_contents>
+                    <has_text_matching expression="^This is a line of text.\n$" />
+                  </assert_contents>
+                </element>
+                <element name="reverse">
+                  <assert_contents>
+                    <has_text_matching expression="^This is a different line of text.\n$" />
+                  </assert_contents>
+                </element>
+              </element>
+            </output_collection>
+        </test>
         <!-- test strict -->
         <test expect_failure="true">
             <param name="input">
@@ -147,9 +185,9 @@ Changes identifiers of datasets within a collection using identifiers from a sup
 Description
 ===========
 
-New identifiers can be supplied as either a simple list or a tab-delimited file mapping old identifier to the new ones. This is controlled using **How should the new identifiers be specified?** drop-down:
+New identifiers can be supplied as either a simple list or a tab-delimited file mapping old identifiers to new ones. This is controlled using **How should the new identifiers be specified?** drop-down:
 
-**Using lines in a simple text file**
+**Use lines in a simple text file as new identifiers**
 
 Given a collection::
 
@@ -175,7 +213,7 @@ the tool will return::
 
 -------
 
-**Map original identifiers to new ones using a two column table**
+**Map original identifiers to new ones using a two-column table**
 
 Given a collection::
 
@@ -183,7 +221,7 @@ Given a collection::
              [Dataset B] 
              [Dataset X]
 
-and a simple text file (you can see that entries do not have to be in order here)::
+and a simple tabular file (you can see that entries do not have to be in order here)::
 
              B Beta
              X Gamma
@@ -195,6 +233,13 @@ the tool will return::
              [Dataset Beta] 
              [Dataset Gamma]
 
+-------
+
+**Map original identifiers to new ones using a two-column table**
+
+This mode works exactly as the previous one, but the tabular mapping file is allowed to have more than two columns, and you can specify which of them holds the original and new element identifiers, respectively.
+
+-------
 
 .. class:: warningmark
 
diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py
index b07c6cf6a875a00e7d691a472adffd4c10bd4a62..6f2e273ffbe4d255ccb5ddc1703a39defcd66f06 100644
--- a/lib/galaxy/tools/remote_tool_eval.py
+++ b/lib/galaxy/tools/remote_tool_eval.py
@@ -72,7 +72,7 @@ class ToolApp(MinimalToolApp):
         self.security = None  # type: ignore[assignment]
 
 
-def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
+def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY) -> None:
     metadata_params = get_metadata_params(WORKING_DIRECTORY)
     datatypes_config = metadata_params["datatypes_config"]
     if not os.path.exists(datatypes_config):
diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index 3fcce2caab42e58d665ac73d43dd253b0068c724..9fa0c24baff43de35301078bf83e0275bcba1011 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -71,8 +71,7 @@ CanConvertToInt = Union[str, int, float]
 
 def get_or_create_index(index_dir, schema):
     """Get or create a reference to the index."""
-    if not os.path.exists(index_dir):
-        os.makedirs(index_dir)
+    os.makedirs(index_dir, exist_ok=True)
     if index.exists_in(index_dir):
         idx = index.open_dir(index_dir)
         if idx.schema == schema:
diff --git a/lib/galaxy/tools/stock.py b/lib/galaxy/tools/stock.py
new file mode 100644
index 0000000000000000000000000000000000000000..eead325e644a60fa253ae4cd0e700d52299a09bf
--- /dev/null
+++ b/lib/galaxy/tools/stock.py
@@ -0,0 +1,34 @@
+"""Reason about stock tools based on ToolSource abstractions."""
+
+from pathlib import Path
+
+from lxml.etree import XMLSyntaxError
+
+# Set GALAXY_INCLUDES_ROOT from tool shed to point this at a Galaxy root
+# (once we are running the tool shed from packages not rooted with Galaxy).
+import galaxy.tools
+from galaxy.tool_util.loader_directory import looks_like_a_tool_xml
+from galaxy.tool_util.parser import get_tool_source
+from galaxy.util import galaxy_directory
+from galaxy.util.resources import files
+
+
+def stock_tool_paths():
+    yield from _walk_directory_for_tools(files(galaxy.tools))
+    yield from _walk_directory_for_tools(Path(galaxy_directory()) / "test" / "functional" / "tools")
+
+
+def stock_tool_sources():
+    for stock_tool_path in stock_tool_paths():
+        try:
+            yield get_tool_source(str(stock_tool_path))
+        except XMLSyntaxError:
+            continue
+
+
+def _walk_directory_for_tools(path):
+    if path.is_file() and not path.name.endswith("tool_conf.xml") and looks_like_a_tool_xml(path):
+        yield path
+    elif path.is_dir():
+        for directory in path.iterdir():
+            yield from _walk_directory_for_tools(directory)
diff --git a/lib/galaxy/tools/test.py b/lib/galaxy/tools/test.py
deleted file mode 100644
index 41921dd4eaea4f07efd3104883da4ffc1f7248f8..0000000000000000000000000000000000000000
--- a/lib/galaxy/tools/test.py
+++ /dev/null
@@ -1,422 +0,0 @@
-import logging
-import os
-import os.path
-from typing import (
-    Iterable,
-    List,
-    Tuple,
-    Union,
-)
-
-import galaxy.tools.parameters.basic
-import galaxy.tools.parameters.grouping
-from galaxy.tool_util.verify.interactor import (
-    InvalidToolTestDict,
-    ToolTestDescription,
-    ValidToolTestDict,
-)
-from galaxy.util import (
-    string_as_bool,
-    string_as_bool_or_none,
-    unicodify,
-)
-
-log = logging.getLogger(__name__)
-
-
-def parse_tests(tool, tests_source) -> Iterable[ToolTestDescription]:
-    """
-    Build ToolTestDescription objects for each "<test>" elements and
-    return default interactor (if any).
-    """
-    raw_tests_dict = tests_source.parse_tests_to_dict()
-    tests: List[ToolTestDescription] = []
-    for i, raw_test_dict in enumerate(raw_tests_dict.get("tests", [])):
-        test = description_from_tool_object(tool, i, raw_test_dict)
-        tests.append(test)
-    return tests
-
-
-def description_from_tool_object(tool, test_index, raw_test_dict) -> ToolTestDescription:
-    required_files: List[Tuple[str, dict]] = []
-    required_data_tables: List[str] = []
-    required_loc_files: List[str] = []
-
-    num_outputs = raw_test_dict.get("expect_num_outputs", None)
-    if num_outputs:
-        num_outputs = int(num_outputs)
-    maxseconds = raw_test_dict.get("maxseconds", None)
-    if maxseconds is not None:
-        maxseconds = int(maxseconds)
-
-    processed_test_dict: Union[ValidToolTestDict, InvalidToolTestDict]
-    try:
-        processed_inputs = _process_raw_inputs(
-            tool, tool.inputs, raw_test_dict["inputs"], required_files, required_data_tables, required_loc_files
-        )
-
-        processed_test_dict = ValidToolTestDict(
-            {
-                "inputs": processed_inputs,
-                "outputs": raw_test_dict["outputs"],
-                "output_collections": raw_test_dict["output_collections"],
-                "num_outputs": num_outputs,
-                "command_line": raw_test_dict.get("command", None),
-                "command_version": raw_test_dict.get("command_version", None),
-                "stdout": raw_test_dict.get("stdout", None),
-                "stderr": raw_test_dict.get("stderr", None),
-                "expect_exit_code": raw_test_dict.get("expect_exit_code", None),
-                "expect_failure": raw_test_dict.get("expect_failure", False),
-                "expect_test_failure": raw_test_dict.get("expect_test_failure", False),
-                "required_files": required_files,
-                "required_data_tables": required_data_tables,
-                "required_loc_files": required_loc_files,
-                "tool_id": tool.id,
-                "tool_version": tool.version,
-                "test_index": test_index,
-                "maxseconds": maxseconds,
-                "error": False,
-            }
-        )
-    except Exception as e:
-        log.exception("Failed to load tool test number [%d] for %s" % (test_index, tool.id))
-        processed_test_dict = InvalidToolTestDict(
-            {
-                "tool_id": tool.id,
-                "tool_version": tool.version,
-                "test_index": test_index,
-                "inputs": {},
-                "error": True,
-                "exception": unicodify(e),
-                "maxseconds": maxseconds,
-            }
-        )
-
-    return ToolTestDescription(processed_test_dict)
-
-
-def _process_raw_inputs(
-    tool, tool_inputs, raw_inputs, required_files, required_data_tables, required_loc_files, parent_context=None
-):
-    """
-    Recursively expand flat list of inputs into "tree" form of flat list
-    (| using to nest to new levels) structure and expand dataset
-    information as proceeding to populate self.required_files.
-    """
-    parent_context = parent_context or RootParamContext()
-    expanded_inputs = {}
-    for value in tool_inputs.values():
-        if isinstance(value, galaxy.tools.parameters.grouping.Conditional):
-            cond_context = ParamContext(name=value.name, parent_context=parent_context)
-            assert value.test_param
-            case_context = ParamContext(name=value.test_param.name, parent_context=cond_context)
-            raw_input_dict = case_context.extract_value(raw_inputs)
-            case_value = raw_input_dict["value"] if raw_input_dict else None
-            case = _matching_case_for_value(tool, value, case_value)
-            if case:
-                for input_name, input_value in case.inputs.items():
-                    case_inputs = _process_raw_inputs(
-                        tool,
-                        {input_name: input_value},
-                        raw_inputs,
-                        required_files,
-                        required_data_tables,
-                        required_loc_files,
-                        parent_context=cond_context,
-                    )
-                    expanded_inputs.update(case_inputs)
-                if not value.type == "text":
-                    expanded_case_value = _split_if_str(case.value)
-                if case_value is not None:
-                    # A bit tricky here - we are growing inputs with value
-                    # that may be implicit (i.e. not defined by user just
-                    # a default defined in tool). So we do not want to grow
-                    # expanded_inputs and risk repeat block viewing this
-                    # as a new instance with value defined and hence enter
-                    # an infinite loop - hence the "case_value is not None"
-                    # check.
-                    processed_value = _process_simple_value(
-                        value.test_param, expanded_case_value, required_data_tables, required_loc_files
-                    )
-                    expanded_inputs[case_context.for_state()] = processed_value
-        elif isinstance(value, galaxy.tools.parameters.grouping.Section):
-            context = ParamContext(name=value.name, parent_context=parent_context)
-            assert value.inputs
-            for r_value in value.inputs.values():
-                expanded_input = _process_raw_inputs(
-                    tool,
-                    {context.for_state(): r_value},
-                    raw_inputs,
-                    required_files,
-                    required_data_tables,
-                    required_loc_files,
-                    parent_context=context,
-                )
-                if expanded_input:
-                    expanded_inputs.update(expanded_input)
-        elif isinstance(value, galaxy.tools.parameters.grouping.Repeat):
-            repeat_index = 0
-            while True:
-                context = ParamContext(name=value.name, index=repeat_index, parent_context=parent_context)
-                updated = False
-                assert value.inputs
-                for r_value in value.inputs.values():
-                    expanded_input = _process_raw_inputs(
-                        tool,
-                        {context.for_state(): r_value},
-                        raw_inputs,
-                        required_files,
-                        required_data_tables,
-                        required_loc_files,
-                        parent_context=context,
-                    )
-                    if expanded_input:
-                        expanded_inputs.update(expanded_input)
-                        updated = True
-                if not updated:
-                    break
-                repeat_index += 1
-        else:
-            context = ParamContext(name=value.name, parent_context=parent_context)
-            raw_input_dict = context.extract_value(raw_inputs)
-            if raw_input_dict:
-                name = raw_input_dict["name"]
-                param_value = raw_input_dict["value"]
-                param_extra = raw_input_dict["attributes"]
-                location = param_extra.get("location")
-                if not value.type == "text":
-                    param_value = _split_if_str(param_value)
-                if isinstance(value, galaxy.tools.parameters.basic.DataToolParameter):
-                    if location and value.multiple:
-                        # We get the input/s from the location which can be a list of urls separated by commas
-                        locations = _split_if_str(location)
-                        param_value = []
-                        for location in locations:
-                            v = os.path.basename(location)
-                            param_value.append(v)
-                            # param_extra should contain only the corresponding location
-                            extra = dict(param_extra)
-                            extra["location"] = location
-                            _add_uploaded_dataset(context.for_state(), v, extra, value, required_files)
-                    else:
-                        if not isinstance(param_value, list):
-                            param_value = [param_value]
-                        for v in param_value:
-                            _add_uploaded_dataset(context.for_state(), v, param_extra, value, required_files)
-                    processed_value = param_value
-                elif isinstance(value, galaxy.tools.parameters.basic.DataCollectionToolParameter):
-                    assert "collection" in param_extra
-                    collection_def = param_extra["collection"]
-                    for input_dict in collection_def.collect_inputs():
-                        name = input_dict["name"]
-                        value = input_dict["value"]
-                        attributes = input_dict["attributes"]
-                        require_file(name, value, attributes, required_files)
-                    processed_value = collection_def
-                else:
-                    processed_value = _process_simple_value(
-                        value, param_value, required_data_tables, required_loc_files
-                    )
-                expanded_inputs[context.for_state()] = processed_value
-    return expanded_inputs
-
-
-def _process_simple_value(param, param_value, required_data_tables, required_loc_files):
-    if isinstance(param, galaxy.tools.parameters.basic.SelectToolParameter):
-        # Tests may specify values as either raw value or the value
-        # as they appear in the list - the API doesn't and shouldn't
-        # accept the text value - so we need to convert the text
-        # into the form value.
-        def process_param_value(param_value):
-            found_value = False
-            value_for_text = None
-            for text, opt_value, _ in getattr(param, "static_options", []):
-                if param_value == opt_value:
-                    found_value = True
-                if value_for_text is None and param_value == text:
-                    value_for_text = opt_value
-            if param.options and not isinstance(param, galaxy.tools.parameters.basic.DrillDownSelectToolParameter):
-                if param.options.tool_data_table_name:
-                    required_data_tables.append(param.options.tool_data_table_name)
-                elif param.options.index_file:
-                    required_loc_files.append(param.options.index_file)
-            if not found_value and value_for_text is not None:
-                processed_value = value_for_text
-            else:
-                processed_value = param_value
-            return processed_value
-
-        # Do replacement described above for lists or singleton
-        # values.
-        if isinstance(param_value, list):
-            processed_value = list(map(process_param_value, param_value))
-        else:
-            processed_value = process_param_value(param_value)
-    elif isinstance(param, galaxy.tools.parameters.basic.BooleanToolParameter):
-        # Like above, tests may use the tool define values of simply
-        # true/false.
-        processed_value = _process_bool_param_value(param, param_value)
-    else:
-        processed_value = param_value
-    return processed_value
-
-
-def _matching_case_for_value(tool, cond, declared_value):
-    test_param = cond.test_param
-    if isinstance(test_param, galaxy.tools.parameters.basic.BooleanToolParameter):
-        if declared_value is None:
-            # No explicit value for param in test case, determine from default
-            query_value = test_param.checked
-        else:
-            query_value = _process_bool_param_value(test_param, declared_value)
-
-        def matches_declared_value(case_value):
-            return _process_bool_param_value(test_param, case_value) == query_value
-
-    elif isinstance(test_param, galaxy.tools.parameters.basic.SelectToolParameter):
-        if declared_value is not None:
-            # Test case supplied explicit value to check against.
-
-            def matches_declared_value(case_value):
-                return case_value == declared_value
-
-        elif test_param.static_options:
-            # No explicit value in test case, not much to do if options are dynamic but
-            # if static options are available can find the one specified as default or
-            # fallback on top most option (like GUI).
-            for name, _, selected in test_param.static_options:
-                if selected:
-                    default_option = name
-            else:
-                first_option = test_param.static_options[0]
-                first_option_value = first_option[1]
-                default_option = first_option_value
-
-            def matches_declared_value(case_value):
-                return case_value == default_option
-
-        else:
-            # No explicit value for this param and cannot determine a
-            # default - give up. Previously this would just result in a key
-            # error exception.
-            msg = f"Failed to find test parameter value specification required for conditional {cond.name}"
-            raise Exception(msg)
-
-    # Check the tool's defined cases against predicate to determine
-    # selected or default.
-    for case in cond.cases:
-        if matches_declared_value(case.value):
-            return case
-    else:
-        msg_template = "%s - Failed to find case matching value (%s) for test parameter specification for conditional %s. Remainder of test behavior is unspecified."
-        msg = msg_template % (tool.id, declared_value, cond.name)
-        log.info(msg)
-
-
-def _add_uploaded_dataset(name, value, extra, input_parameter, required_files):
-    if value is None:
-        assert input_parameter.optional, f"{name} is not optional. You must provide a valid filename."
-        return value
-    return require_file(name, value, extra, required_files)
-
-
-def _split_if_str(value):
-    split = isinstance(value, str)
-    if split:
-        value = value.split(",")
-    return value
-
-
-def _process_bool_param_value(param, param_value):
-    assert isinstance(param, galaxy.tools.parameters.basic.BooleanToolParameter)
-    was_list = False
-    if isinstance(param_value, list):
-        was_list = True
-        param_value = param_value[0]
-    if param.truevalue == param_value:
-        processed_value = True
-    elif param.falsevalue == param_value:
-        processed_value = False
-    else:
-        if param.optional:
-            processed_value = string_as_bool_or_none(param_value)
-        else:
-            processed_value = string_as_bool(param_value)
-    return [processed_value] if was_list else processed_value
-
-
-def require_file(name, value, extra, required_files):
-    if (value, extra) not in required_files:
-        required_files.append((value, extra))  # these files will be uploaded
-    name_change = [att for att in extra.get("edit_attributes", []) if att.get("type") == "name"]
-    if name_change:
-        name_change = name_change[-1].get("value")  # only the last name change really matters
-        value = name_change  # change value for select to renamed uploaded file for e.g. composite dataset
-    else:
-        for end in [".zip", ".gz"]:
-            if value.endswith(end):
-                value = value[: -len(end)]
-                break
-        value = os.path.basename(value)  # if uploading a file in a path other than root of test-data
-    return value
-
-
-class ParamContext:
-    def __init__(self, name, index=None, parent_context=None):
-        self.parent_context = parent_context
-        self.name = name
-        self.index = None if index is None else int(index)
-
-    def for_state(self):
-        name = self.name if self.index is None else "%s_%d" % (self.name, self.index)
-        if parent_for_state := self.parent_context.for_state():
-            return f"{parent_for_state}|{name}"
-        else:
-            return name
-
-    def __str__(self):
-        return f"Context[for_state={self.for_state()}]"
-
-    def param_names(self):
-        for parent_context_param in self.parent_context.param_names():
-            if self.index is not None:
-                yield "%s|%s_%d" % (parent_context_param, self.name, self.index)
-            else:
-                yield f"{parent_context_param}|{self.name}"
-        if self.index is not None:
-            yield "%s_%d" % (self.name, self.index)
-        else:
-            yield self.name
-
-    def extract_value(self, raw_inputs):
-        for param_name in self.param_names():
-            value = self.__raw_param_found(param_name, raw_inputs)
-            if value:
-                return value
-        return None
-
-    def __raw_param_found(self, param_name, raw_inputs):
-        index = None
-        for i, raw_input_dict in enumerate(raw_inputs):
-            if raw_input_dict["name"] == param_name:
-                index = i
-        if index is not None:
-            raw_input_dict = raw_inputs[index]
-            del raw_inputs[index]
-            return raw_input_dict
-        else:
-            return None
-
-
-class RootParamContext:
-    def __init__(self):
-        pass
-
-    def for_state(self):
-        return ""
-
-    def param_names(self):
-        return []
-
-    def get_index(self):
-        return 0
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 01e8e8491bbca02680637988594c2ec80b410a26..12d3d779cafcac0d7ec5c088f4d2e640e3da2faf 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -19,7 +19,6 @@ from typing import (
     Union,
 )
 
-from packaging.version import Version
 from typing_extensions import TypeAlias
 
 from galaxy.model import (
@@ -33,7 +32,10 @@ from galaxy.model import (
 from galaxy.model.metadata import FileParameter
 from galaxy.model.none_like import NoneDataset
 from galaxy.security.object_wrapper import wrap_with_safe_string
-from galaxy.tools.parameters.basic import BooleanToolParameter
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    TextToolParameter,
+)
 from galaxy.tools.parameters.wrapped_json import (
     data_collection_input_to_staging_path_and_source_path,
     data_input_to_staging_path_and_source_path,
@@ -126,15 +128,9 @@ class InputValueWrapper(ToolParameterValueWrapper):
         profile: Optional[float] = None,
     ) -> None:
         self.input = input
-        if (
-            value is None
-            and input.type == "text"
-            and input.optional
-            and input.optionality_inferred
-            and (profile is None or Version(str(profile)) < Version("23.0"))
-        ):
+        if value is None and input.type == "text":
             # Tools with old profile versions may treat an optional text parameter as `""`
-            value = ""
+            value = cast(TextToolParameter, input).wrapper_default
         self.value = value
         self._other_values: Dict[str, str] = other_values or {}
 
@@ -460,6 +456,10 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
     def is_collection(self) -> bool:
         return False
 
+    @property
+    def is_deferred(self) -> bool:
+        return self.unsanitized.has_deferred_data
+
     def is_of_type(self, *exts: str) -> bool:
         datatypes = []
         if not self.datatypes_registry:
@@ -475,6 +475,11 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         return self.dataset.datatype.matches_any(datatypes)
 
     def __str__(self) -> str:
+        return self._path_or_uri()
+
+    def _path_or_uri(self) -> str:
+        if self.is_deferred:
+            return self.unsanitized.deferred_source_uri or ""
         if self.false_path is not None:
             return self.false_path
         else:
@@ -806,6 +811,8 @@ class ElementIdentifierMapper:
             self.identifier_key_dict = {}
 
     def identifier(self, dataset_value: str, input_values: Dict[str, str]) -> Optional[str]:
+        if isinstance(dataset_value, list):
+            raise TypeError(f"Expected {dataset_value} to be hashable")
         element_identifier = None
         if identifier_key := self.identifier_key_dict.get(dataset_value, None):
             element_identifier = input_values.get(identifier_key, None)
diff --git a/lib/galaxy/tours/_impl.py b/lib/galaxy/tours/_impl.py
index 60ab97bfc80a8a451751abc94ff01c587bc82dd7..ab6f280f45e54df01decf90f6110b04d2d68ea17 100644
--- a/lib/galaxy/tours/_impl.py
+++ b/lib/galaxy/tours/_impl.py
@@ -4,10 +4,7 @@ This module manages loading/etc of Galaxy interactive tours.
 
 import logging
 import os
-from typing import (
-    List,
-    Union,
-)
+from typing import List
 
 import yaml
 from pydantic import parse_obj_as
@@ -15,6 +12,7 @@ from pydantic import parse_obj_as
 from galaxy.exceptions import ObjectNotFound
 from galaxy.navigation.data import load_root_component
 from galaxy.util import config_directories_from_setting
+from galaxy.util.path import StrPath
 from ._interface import ToursRegistry
 from ._schema import TourList
 
@@ -61,12 +59,12 @@ def load_tour_steps(contents_dict, warn=None, resolve_components=True):
             step["title"] = title_default
 
 
-def get_tour_id_from_path(tour_path: Union[str, os.PathLike]) -> str:
+def get_tour_id_from_path(tour_path: StrPath) -> str:
     filename = os.path.basename(tour_path)
     return os.path.splitext(filename)[0]
 
 
-def load_tour_from_path(tour_path: Union[str, os.PathLike], warn=None, resolve_components=True) -> dict:
+def load_tour_from_path(tour_path: StrPath, warn=None, resolve_components=True) -> dict:
     with open(tour_path) as f:
         tour = yaml.safe_load(f)
         load_tour_steps(tour, warn=warn, resolve_components=resolve_components)
@@ -80,7 +78,7 @@ def is_yaml(filename: str) -> bool:
     return False
 
 
-def tour_paths(target_path: Union[str, os.PathLike]) -> List[str]:
+def tour_paths(target_path: StrPath) -> List[str]:
     paths = []
     if os.path.isdir(target_path):
         for filename in os.listdir(target_path):
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index ca844c2358fc468e982c1e1a0008899caaa88087..797ba6f4428c6cfd99bf142620914fe15c8ef57b 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -30,8 +30,7 @@ from datetime import (
     timezone,
 )
 from decimal import Decimal
-from email.mime.multipart import MIMEMultipart
-from email.mime.text import MIMEText
+from email.message import EmailMessage
 from hashlib import md5
 from os.path import relpath
 from pathlib import Path
@@ -46,10 +45,12 @@ from typing import (
     Optional,
     overload,
     Tuple,
+    TYPE_CHECKING,
     TypeVar,
     Union,
 )
 from urllib.parse import (
+    quote,
     urlencode,
     urlparse,
     urlsplit,
@@ -75,6 +76,7 @@ except ImportError:
 LXML_AVAILABLE = True
 try:
     from lxml import etree
+    from lxml.etree import DocumentInvalid
 
     # lxml.etree.Element is a function that returns a new instance of the
     # lxml.etree._Element class. This class doesn't have a proper __init__()
@@ -123,6 +125,10 @@ except ImportError:
         XML,
     )
 
+    class DocumentInvalid(Exception):  # type: ignore[no-redef]
+        pass
+
+
 from . import requests
 from .custom_logging import get_logger
 from .inflection import Inflector
@@ -142,6 +148,9 @@ except AttributeError:
         return " ".join(map(shlex.quote, split_command))
 
 
+if TYPE_CHECKING:
+    from galaxy.util.resources import Traversable
+
 inflector = Inflector()
 
 log = get_logger(__name__)
@@ -333,7 +342,10 @@ def unique_id(KEY_SIZE=128):
 
 
 def parse_xml(
-    fname: StrPath, strip_whitespace=True, remove_comments=True, schemafname: Union[StrPath, None] = None
+    fname: Union[StrPath, "Traversable"],
+    strip_whitespace: bool = True,
+    remove_comments: bool = True,
+    schemafname: Union[StrPath, None] = None,
 ) -> ElementTree:
     """Returns a parsed xml tree"""
     parser = None
@@ -348,8 +360,10 @@ def parse_xml(
             schema_root = etree.XML(schema_file.read())
             schema = etree.XMLSchema(schema_root)
 
+    source = Path(fname) if isinstance(fname, (str, os.PathLike)) else fname
     try:
-        tree = cast(ElementTree, etree.parse(str(fname), parser=parser))
+        with source.open("rb") as f:
+            tree = cast(ElementTree, etree.parse(f, parser=parser))
         root = tree.getroot()
         if strip_whitespace:
             for elem in root.iter("*"):
@@ -359,15 +373,10 @@ def parse_xml(
                     elem.tail = elem.tail.strip()
         if schema:
             schema.assertValid(tree)
-    except OSError as e:
-        if e.errno is None and not os.path.exists(fname):  # type: ignore[unreachable]
-            # lxml doesn't set errno
-            e.errno = errno.ENOENT  # type: ignore[unreachable]
-        raise
     except etree.ParseError:
         log.exception("Error parsing file %s", fname)
         raise
-    except etree.DocumentInvalid:
+    except DocumentInvalid:
         log.exception("Validation of file %s failed", fname)
         raise
     return tree
@@ -996,7 +1005,7 @@ class Params:
         self.__dict__.update(values)
 
 
-def xml_text(root, name=None):
+def xml_text(root, name=None, default=""):
     """Returns the text inside an element"""
     if name is not None:
         # Try attribute first
@@ -1011,7 +1020,7 @@ def xml_text(root, name=None):
         text = "".join(elem.text.splitlines())
         return text.strip()
     # No luck, return empty string
-    return ""
+    return default
 
 
 def parse_resource_parameters(resource_param_file):
@@ -1134,7 +1143,7 @@ def commaify(amount):
 
 
 @overload
-def unicodify(  # type: ignore[overload-overlap]
+def unicodify(
     value: Literal[None],
     encoding: str = DEFAULT_ENCODING,
     error: str = "replace",
@@ -1634,10 +1643,8 @@ def send_mail(frm, to, subject, body, config, html=None, reply_to=None):
         return
 
     to = listify(to)
-    if html:
-        msg = MIMEMultipart("alternative")
-    else:
-        msg = MIMEText(body, "plain", "utf-8")
+    msg = EmailMessage()
+    msg.set_content(body)
 
     msg["To"] = ", ".join(to)
     msg["From"] = frm
@@ -1652,45 +1659,40 @@ def send_mail(frm, to, subject, body, config, html=None, reply_to=None):
         return
 
     if html:
-        mp_text = MIMEText(body, "plain", "utf-8")
-        mp_html = MIMEText(html, "html", "utf-8")
-        msg.attach(mp_text)
-        msg.attach(mp_html)
+        msg.add_alternative(html, subtype="html")
 
     smtp_ssl = asbool(getattr(config, "smtp_ssl", False))
     if smtp_ssl:
         s = smtplib.SMTP_SSL(config.smtp_server)
     else:
         s = smtplib.SMTP(config.smtp_server)
-    if not smtp_ssl:
-        try:
-            s.starttls()
-            log.debug("Initiated SSL/TLS connection to SMTP server: %s", config.smtp_server)
-        except RuntimeError as e:
-            log.warning("SSL/TLS support is not available to your Python interpreter: %s", unicodify(e))
-        except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPException as e:
-            log.warning("The server does not support the STARTTLS extension: %s", unicodify(e))
-    if config.smtp_username and config.smtp_password:
-        try:
-            s.login(config.smtp_username, config.smtp_password)
-        except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPAuthenticationError as e:
-            log.error("The server didn't accept the username/password combination: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPException as e:
-            log.error("No suitable authentication method was found: %s", unicodify(e))
-            s.close()
-            raise
-    s.sendmail(frm, to, msg.as_string())
-    s.quit()
+    try:
+        if not smtp_ssl:
+            try:
+                s.starttls()
+                log.debug("Initiated SSL/TLS connection to SMTP server: %s", config.smtp_server)
+            except RuntimeError as e:
+                log.warning("SSL/TLS support is not available to your Python interpreter: %s", e)
+            except smtplib.SMTPHeloError as e:
+                log.error("The server didn't reply properly to the HELO greeting: %s", e)
+                raise
+            except smtplib.SMTPException as e:
+                log.warning("The server does not support the STARTTLS extension: %s", e)
+        if config.smtp_username and config.smtp_password:
+            try:
+                s.login(config.smtp_username, config.smtp_password)
+            except smtplib.SMTPHeloError as e:
+                log.error("The server didn't reply properly to the HELO greeting: %s", e)
+                raise
+            except smtplib.SMTPAuthenticationError as e:
+                log.error("The server didn't accept the username/password combination: %s", e)
+                raise
+            except smtplib.SMTPException as e:
+                log.error("No suitable authentication method was found: %s", e)
+                raise
+        s.send_message(msg)
+    finally:
+        s.quit()
 
 
 def force_symlink(source, link_name):
@@ -1738,12 +1740,20 @@ def safe_str_cmp(a, b):
     return rv == 0
 
 
+# never load packages this way (won't work for installed packages),
+# but while we're working on packaging everything this can be a way to point
+# an installed Galaxy at a Galaxy root for things like tools. Ultimately
+# this all needs to be packaged, but we have some very old PRs working on this
+# that are pretty tricky and shouldn't slow current development.
+GALAXY_INCLUDES_ROOT = os.environ.get("GALAXY_INCLUDES_ROOT")
+
+
 #  Don't use this directly, prefer method version that "works" with packaged Galaxy.
-galaxy_root_path = Path(__file__).parent.parent.parent.parent
+galaxy_root_path = Path(GALAXY_INCLUDES_ROOT) if GALAXY_INCLUDES_ROOT else Path(__file__).parent.parent.parent.parent
 
 
 def galaxy_directory() -> str:
-    if in_packages():
+    if in_packages() and not GALAXY_INCLUDES_ROOT:
         # This will work only when running pytest from <galaxy_root>/packages/<package_name>/
         cwd = Path.cwd()
         path = cwd.parent.parent
@@ -2006,3 +2016,11 @@ def lowercase_alphanum_to_hex(lowercase_alphanum: str) -> str:
     import numpy as np
 
     return np.base_repr(int(lowercase_alphanum, 36), 16).lower()
+
+
+def to_content_disposition(target: str) -> str:
+    filename, ext = os.path.splitext(target)
+    character_limit = 255 - len(ext)
+    sanitized_filename = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in filename)[0:character_limit] + ext
+    utf8_encoded_filename = quote(re.sub(r'[\/\\\?%*:|"<>]', "_", filename), safe="")[0:character_limit] + ext
+    return f"attachment; filename=\"{sanitized_filename}\"; filename*=UTF-8''{utf8_encoded_filename}"
diff --git a/lib/galaxy/util/compression_utils.py b/lib/galaxy/util/compression_utils.py
index d54c0ffcbc24e286641f11be09ef25f0ca9a6734..4022a73b4802837aad5c34b1f99502c8eedbe5d4 100644
--- a/lib/galaxy/util/compression_utils.py
+++ b/lib/galaxy/util/compression_utils.py
@@ -184,10 +184,12 @@ class CompressedFile:
 
     def __init__(self, file_path: StrPath, mode: str = "r") -> None:
         file_path_str = str(file_path)
-        if tarfile.is_tarfile(file_path):
-            self.file_type = "tar"
-        elif zipfile.is_zipfile(file_path) and not file_path_str.endswith(".jar"):
+        if zipfile.is_zipfile(file_path) and not file_path_str.endswith(".jar"):
             self.file_type = "zip"
+        elif tarfile.is_tarfile(file_path):
+            self.file_type = "tar"
+        else:
+            raise Exception("File must be valid zip or tar file.")
         self.file_name = os.path.splitext(os.path.basename(file_path))[0]
         if self.file_name.endswith(".tar"):
             self.file_name = os.path.splitext(self.file_name)[0]
diff --git a/lib/galaxy/util/config_templates.py b/lib/galaxy/util/config_templates.py
index 79f0bed52ca9511d54758e019e3277a362d8e725..f193d762d20ed66c47c9adaa8532ce1572efd9cd 100644
--- a/lib/galaxy/util/config_templates.py
+++ b/lib/galaxy/util/config_templates.py
@@ -3,17 +3,22 @@
 This is capturing code shared by file source templates and object store templates.
 """
 
+import logging
 import os
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
+    Tuple,
     Type,
     TypeVar,
     Union,
 )
+from urllib.parse import urlencode
 
+import requests
 import yaml
 from boltons.iterutils import remap
 from pydantic import (
@@ -24,7 +29,9 @@ from pydantic import (
 )
 from typing_extensions import (
     Literal,
+    NotRequired,
     Protocol,
+    TypedDict,
 )
 
 try:
@@ -45,6 +52,8 @@ from galaxy.exceptions import (
 )
 from galaxy.util import asbool
 
+log = logging.getLogger(__name__)
+
 TemplateVariableType = Literal["string", "path_component", "boolean", "integer"]
 TemplateVariableValueType = Union[str, bool, int]
 TemplateExpansion = str
@@ -57,7 +66,7 @@ EnvironmentDict = Dict[str, str]
 
 
 class StrictModel(BaseModel):
-    model_config = ConfigDict(extra="forbid")
+    model_config = ConfigDict(extra="forbid", coerce_numbers_to_str=True)
 
 
 class BaseTemplateVariable(StrictModel):
@@ -178,6 +187,12 @@ def expand_raw_config(
         "environment": environment,
     }
 
+    return _expand_raw_config(template_configuration, template_variables)
+
+
+def _expand_raw_config(
+    template_configuration: TemplateConfiguration, template_variables: Dict[str, Any]
+) -> RawTemplateConfig:
     template_start = template_configuration.template_start or "{{"
     template_end = template_configuration.template_end or "}}"
 
@@ -193,6 +208,14 @@ def expand_raw_config(
     return raw_config
 
 
+def merge_implicit_parameters(raw_config: RawTemplateConfig, implicit: Optional["ImplicitConfigurationParameters"]):
+    if implicit:
+        raw_config.update(implicit)
+        raw_config.pop("oauth2_client_id", None)
+        raw_config.pop("oauth2_client_secret", None)
+        raw_config.pop("oauth2_scope", None)
+
+
 def verify_vault_configured_if_uses_secrets(catalog, vault_configured: bool, exception_message: str) -> None:
     if _catalog_uses_secrets(catalog) and not vault_configured:
         raise Exception(exception_message)
@@ -283,6 +306,9 @@ class Template(Protocol):
     @property
     def version(self) -> int: ...
 
+    @property
+    def type(self) -> str: ...
+
     @property
     def variables(self) -> Optional[List[TemplateVariable]]: ...
 
@@ -445,6 +471,7 @@ class PluginStatus(StrictModel):
 
     # TODO: Fill in writable checks.
     # writable: Optional[PluginAspectStatus] = None
+    oauth2_access_token_generation: Optional[PluginAspectStatus] = None
 
 
 def status_template_definition(template: Optional[Template]) -> PluginAspectStatus:
@@ -478,3 +505,106 @@ def connection_exception_to_status(what: str, exception: Optional[Exception]) ->
         message = f"Failed to connect to a {what} with supplied settings: {exception}"
         connection_status = PluginAspectStatus(state="not_ok", message=message)
     return connection_status
+
+
+class OAuth2Info(StrictModel):
+    authorize_url: str
+
+
+class OAuth2Configuration(StrictModel):
+    authorize_url: str
+    token_url: str
+    authorize_params: Optional[Dict[str, str]]
+    scope: Optional[str] = None
+
+
+ConfiguredOAuth2Sources = Dict[str, OAuth2Configuration]
+
+
+class OAuth2ClientPair(StrictModel):
+    client_id: str
+    client_secret: str
+
+
+def get_authorize_url(
+    client_id_or_pair: Union[str, OAuth2ClientPair],
+    config: OAuth2Configuration,
+    redirect_uri: Optional[str],
+    state: Optional[str] = None,
+    scope: Optional[str] = None,
+) -> str:
+    client_id = client_id_or_pair if isinstance(client_id_or_pair, str) else client_id_or_pair.client_id
+    query_data = dict(
+        client_id=client_id,
+        response_type="code",
+    )
+    if redirect_uri is not None:
+        query_data["redirect_uri"] = redirect_uri
+    if state is not None:
+        query_data["state"] = state
+    if scope is not None:
+        query_data["scope"] = scope
+    elif config.scope is not None:
+        query_data["scope"] = config.scope
+    query_data.update(config.authorize_params or {})
+    query = urlencode(query_data)
+    return f"{config.authorize_url}?{query}"
+
+
+def get_token_from_code_raw(
+    code: str, client_pair: OAuth2ClientPair, config: OAuth2Configuration, redirect_uri: Optional[str]
+) -> requests.Response:
+    data = {
+        "code": code,
+        "grant_type": "authorization_code",
+        "client_id": client_pair.client_id,
+        "client_secret": client_pair.client_secret,
+    }
+    if redirect_uri is not None:
+        data["redirect_uri"] = redirect_uri
+
+    return requests.post(config.token_url, data=data)
+
+
+def get_token_from_refresh_raw(
+    refresh_token: str, client_pair: OAuth2ClientPair, config: OAuth2Configuration
+) -> requests.Response:
+    data = {
+        "refresh_token": refresh_token,
+        "grant_type": "refresh_token",
+        "client_id": client_pair.client_id,
+        "client_secret": client_pair.client_secret,
+    }
+
+    return requests.post(config.token_url, data=data)
+
+
+def get_oauth2_config_from(template, sources: ConfiguredOAuth2Sources) -> OAuth2Configuration:
+    template_type = template.configuration.type
+    if template_type not in sources:
+        raise ObjectNotFound(f"oauth information not available for template type {template_type}")
+    return sources[template_type]
+
+
+def read_oauth2_info_from_configuration(
+    template_configuration: TemplateConfiguration,
+    user_details: UserDetailsDict,
+    environment: EnvironmentDict,
+) -> Tuple[OAuth2ClientPair, Optional[str]]:
+    template_variables = {
+        "user": user_details,
+        "environment": environment,
+    }
+
+    expanded_config = _expand_raw_config(template_configuration, template_variables)
+    oauth2_client_id = expanded_config["oauth2_client_id"]
+    oauth2_client_secret = expanded_config["oauth2_client_secret"]
+    oauth2_scope = cast(Optional[str], expanded_config.get("oauth2_scope"))
+    client_pair = OAuth2ClientPair(client_id=oauth2_client_id, client_secret=oauth2_client_secret)
+    return client_pair, oauth2_scope
+
+
+# Things added to configuration dictionary not managed by the template
+# but injected dynamically. Currently only `oauth2_access_token`.
+class ImplicitConfigurationParameters(TypedDict):
+    oauth2_access_token: NotRequired[str]
diff --git a/lib/galaxy/util/dictifiable.py b/lib/galaxy/util/dictifiable.py
index 4d099884424bbf0e8c415bad926cec0b36009709..d40c7f8f1f93260f7f322be5b348652c01518d1f 100644
--- a/lib/galaxy/util/dictifiable.py
+++ b/lib/galaxy/util/dictifiable.py
@@ -7,18 +7,26 @@ from typing import (
     Optional,
 )
 
+ValueMapperT = Dict[str, Callable]
+
 
 def dict_for(obj, **kwds):
     # Create dict to represent item.
     return dict(model_class=obj.__class__.__name__, **kwds)
 
 
-class Dictifiable:
-    """Mixin that enables objects to be converted to dictionaries. This is useful
-    when for sharing objects across boundaries, such as the API, tool scripts,
-    and JavaScript code."""
+class UsesDictVisibleKeys:
+    """Mixin used to implement to_dict methods that consume dict_{view}_visible_keys to produce dicts.
 
-    def to_dict(self, view: str = "collection", value_mapper: Optional[Dict[str, Callable]] = None) -> Dict[str, Any]:
+    For typical to_dict methods that just consume a view and value mapper use the Dictifable mixin instead
+    of this more low level mixin, but if you want to consume other things in your to_dict method that
+    are incompatible (such as required arguments) - inherit this lower level mixin and implement a custom
+    to_dict with whatever signature makes sense for the class.
+    """
+
+    def _dictify_view_keys(
+        self, view: str = "collection", value_mapper: Optional[ValueMapperT] = None
+    ) -> Dict[str, Any]:
         """
         Return item dictionary.
         """
@@ -70,3 +78,15 @@ class Dictifiable:
                 rval[key] = None
 
         return rval
+
+
+class Dictifiable(UsesDictVisibleKeys):
+    """Mixin that enables objects to be converted to dictionaries. This is useful
+    when for sharing objects across boundaries, such as the API, tool scripts,
+    and JavaScript code."""
+
+    def to_dict(self, view: str = "collection", value_mapper: Optional[ValueMapperT] = None) -> Dict[str, Any]:
+        """
+        Return item dictionary.
+        """
+        return self._dictify_view_keys(view=view, value_mapper=value_mapper)
diff --git a/lib/galaxy/util/hash_util.py b/lib/galaxy/util/hash_util.py
index 100adc23bcc4f1aefba9a045ac88e10f1a0e991e..efb5d0ce7e1baf684ef19650a1980a6d15d4a4fe 100644
--- a/lib/galaxy/util/hash_util.py
+++ b/lib/galaxy/util/hash_util.py
@@ -6,7 +6,6 @@ introduced hashlib which replaced sha in Python 2.4 and previous versions.
 import hashlib
 import hmac
 import logging
-import os
 from enum import Enum
 from typing import (
     Any,
@@ -19,6 +18,7 @@ from typing import (
 )
 
 from . import smart_str
+from .path import StrPath
 
 log = logging.getLogger(__name__)
 
@@ -82,7 +82,7 @@ def memory_bound_hexdigest(
         file.close()
 
 
-def md5_hash_file(path: Union[str, os.PathLike]) -> Optional[str]:
+def md5_hash_file(path: StrPath) -> Optional[str]:
     """
     Return a md5 hashdigest for a file or None if path could not be read.
     """
@@ -153,6 +153,14 @@ def parse_checksum_hash(checksum: str) -> Tuple[HashFunctionNameEnum, str]:
     return HashFunctionNameEnum(hash_name), hash_value
 
 
+def verify_hash(path: str, hash_func_name: HashFunctionNameEnum, hash_value: str, what: str = "path"):
+    calculated_hash_value = memory_bound_hexdigest(hash_func_name=hash_func_name, path=path)
+    if calculated_hash_value != hash_value:
+        raise Exception(
+            f"Failed to validate {what} with [{hash_func_name}] - expected [{hash_value}] got [{calculated_hash_value}]"
+        )
+
+
 __all__ = (
     "md5",
     "hashlib",
diff --git a/lib/galaxy/util/image_util.py b/lib/galaxy/util/image_util.py
index 3b11a50d2fda913d18b20eb9437988b8a0dae9b3..b8c26cf0ff549e231782e6db76aa69af84dbf20d 100644
--- a/lib/galaxy/util/image_util.py
+++ b/lib/galaxy/util/image_util.py
@@ -1,6 +1,5 @@
 """Provides utilities for working with image files."""
 
-import imghdr
 import logging
 from typing import (
     List,
@@ -22,11 +21,7 @@ def image_type(filename: str) -> Optional[str]:
             with Image.open(filename) as im:
                 fmt = im.format
         except Exception:
-            # We continue to try with imghdr, so this is a rare case of an
-            # exception we expect to happen frequently, so we're not logging
             pass
-    if not fmt:
-        fmt = imghdr.what(filename)
     if fmt:
         return fmt.upper()
     else:
diff --git a/lib/galaxy/util/odict.py b/lib/galaxy/util/odict.py
index aeb66cd2003916db412bde19b581f0b2f7b4f863..4b3fdbc2dc7f6edd14ff756a54004118bb7c5e88 100644
--- a/lib/galaxy/util/odict.py
+++ b/lib/galaxy/util/odict.py
@@ -71,10 +71,6 @@ class odict(UserDict):
             self._keys.append(key)
         return UserDict.setdefault(self, key, failobj)
 
-    def update(self, dict):
-        for key, val in dict.items():
-            self.__setitem__(key, val)
-
     def values(self):
         return map(self.get, self._keys)
 
diff --git a/lib/galaxy/util/permutations.py b/lib/galaxy/util/permutations.py
index 5dd1b11ee8fae38f558cde84626bbcc49cc24679..92573d8c6dbc2265a4934833fdc8e29505fc7b2e 100644
--- a/lib/galaxy/util/permutations.py
+++ b/lib/galaxy/util/permutations.py
@@ -7,10 +7,8 @@ Maybe this doesn't make sense and maybe much of this stuff could be replaced
 with itertools product and permutations. These are open questions.
 """
 
-from typing import (
-    Dict,
-    TypeVar,
-)
+import copy
+from typing import Tuple
 
 from galaxy.exceptions import MessageException
 from galaxy.util.bunch import Bunch
@@ -21,47 +19,20 @@ input_classification = Bunch(
     MULTIPLIED="multiplied",
 )
 
-# generic type of splitting input dictionary
-T = TypeVar("T")
-
 
 class InputMatchedException(MessageException):
     """Indicates problem matching inputs while building up inputs
     permutations."""
 
 
-def expand_multi_inputs(inputs: Dict[str, T], classifier, key_filter=None):
-    key_filter = key_filter or (lambda x: True)
-
-    single_inputs, matched_multi_inputs, multiplied_multi_inputs = __split_inputs(inputs, classifier, key_filter)
-
+def build_combos(single_inputs, matched_multi_inputs, multiplied_multi_inputs, nested):
     # Build up every combination of inputs to be run together.
-    input_combos = __extend_with_matched_combos(single_inputs, matched_multi_inputs)
-    input_combos = __extend_with_multiplied_combos(input_combos, multiplied_multi_inputs)
-
+    input_combos = __extend_with_matched_combos(single_inputs, matched_multi_inputs, nested)
+    input_combos = __extend_with_multiplied_combos(input_combos, multiplied_multi_inputs, nested)
     return input_combos
 
 
-def __split_inputs(inputs: Dict[str, T], classifier, key_filter):
-    key_filter = key_filter or (lambda x: True)
-
-    single_inputs: Dict[str, T] = {}
-    matched_multi_inputs: Dict[str, T] = {}
-    multiplied_multi_inputs: Dict[str, T] = {}
-
-    for input_key in filter(key_filter, inputs):
-        input_type, expanded_val = classifier(input_key)
-        if input_type == input_classification.SINGLE:
-            single_inputs[input_key] = expanded_val
-        elif input_type == input_classification.MATCHED:
-            matched_multi_inputs[input_key] = expanded_val
-        elif input_type == input_classification.MULTIPLIED:
-            multiplied_multi_inputs[input_key] = expanded_val
-
-    return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)
-
-
-def __extend_with_matched_combos(single_inputs, multi_inputs):
+def __extend_with_matched_combos(single_inputs, multi_inputs, nested):
     """
 
     {a => 1, b => 2} and {c => {3, 4}, d => {5, 6}}
@@ -81,7 +52,7 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
     first_multi_value = multi_inputs.get(first_multi_input_key)
 
     for value in first_multi_value:
-        new_inputs = __copy_and_extend_inputs(single_inputs, first_multi_input_key, value)
+        new_inputs = __copy_and_extend_inputs(single_inputs, first_multi_input_key, value, nested=nested)
         matched_multi_inputs.append(new_inputs)
 
     for multi_input_key, multi_input_values in multi_inputs.items():
@@ -94,12 +65,12 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
             )
 
         for index, value in enumerate(multi_input_values):
-            matched_multi_inputs[index][multi_input_key] = value
+            state_set_value(matched_multi_inputs[index], multi_input_key, value, nested)
 
     return matched_multi_inputs
 
 
-def __extend_with_multiplied_combos(input_combos, multi_inputs):
+def __extend_with_multiplied_combos(input_combos, multi_inputs, nested):
     combos = input_combos
 
     for multi_input_key, multi_input_value in multi_inputs.items():
@@ -107,7 +78,7 @@ def __extend_with_multiplied_combos(input_combos, multi_inputs):
 
         for combo in combos:
             for input_value in multi_input_value:
-                iter_combo = __copy_and_extend_inputs(combo, multi_input_key, input_value)
+                iter_combo = __copy_and_extend_inputs(combo, multi_input_key, input_value, nested)
                 iter_combos.append(iter_combo)
 
         combos = iter_combos
@@ -115,7 +86,84 @@ def __extend_with_multiplied_combos(input_combos, multi_inputs):
     return combos
 
 
-def __copy_and_extend_inputs(inputs, key, value):
-    new_inputs = dict(inputs)
-    new_inputs[key] = value
+def __copy_and_extend_inputs(inputs, key, value, nested):
+    # can't deepcopy dicts with our models for reason I don't understand,
+    # test_map_over_two_collections_unlinked breaks if I try to combine these two branches of the if
+    new_inputs = state_copy(inputs, nested)
+    state_set_value(new_inputs, key, value, nested)
     return new_inputs
+
+
+def state_copy(inputs, nested):
+    # can't deepcopy dicts with our models for reason I don't understand,
+    # test_map_over_two_collections_unlinked breaks if I try to combine these two branches of the if
+    if nested:
+        state_dict_copy = copy.deepcopy(inputs)
+    else:
+        state_dict_copy = dict(inputs)
+    return state_dict_copy
+
+
+def state_set_value(state_dict, key, value, nested):
+    if "|" not in key or not nested:
+        state_dict[key] = value
+    else:
+        first, rest = key.split("|", 1)
+        if first not in state_dict and looks_like_flattened_repeat_key(first):
+            repeat_name, index = split_flattened_repeat_key(first)
+            if repeat_name not in state_dict:
+                state_dict[repeat_name] = []
+            repeat_state = state_dict[repeat_name]
+            while len(repeat_state) <= index:
+                repeat_state.append({})
+            state_set_value(repeat_state[index], rest, value, nested)
+        else:
+            state_set_value(state_dict[first], rest, value, nested)
+
+
+def state_remove_value(state_dict, key, nested):
+    if "|" not in key or not nested:
+        del state_dict[key]
+    else:
+        first, rest = key.split("|", 1)
+        child_dict = state_dict[first]
+        # repeats?
+        if "|" in rest:
+            state_remove_value(child_dict, rest, nested)
+        else:
+            del child_dict[rest]
+            if len(child_dict) == 0:
+                del state_dict[first]
+
+
+def state_get_value(state_dict, key, nested):
+    if "|" not in key or not nested:
+        return state_dict[key]
+    else:
+        first, rest = key.split("|", 1)
+        if first not in state_dict and looks_like_flattened_repeat_key(first):
+            repeat_name, index = split_flattened_repeat_key(first)
+            return state_get_value(state_dict[repeat_name][index], rest, nested)
+        else:
+            return state_get_value(state_dict[first], rest, nested)
+
+
+def is_in_state(state_dict, key, nested):
+    if not state_dict:
+        return False
+    if "|" not in key or not nested:
+        return key in state_dict
+    else:
+        first, rest = key.split("|", 1)
+        # repeats?
+        is_in_state(state_dict.get(first), rest, nested)
+
+
+def looks_like_flattened_repeat_key(key: str) -> bool:
+    return key.rsplit("_", 1)[-1].isdigit()
+
+
+def split_flattened_repeat_key(key: str) -> Tuple[str, int]:
+    input_name, _index = key.rsplit("_", 1)
+    index = int(_index)
+    return input_name, index
diff --git a/lib/galaxy/util/plugin_config.py b/lib/galaxy/util/plugin_config.py
index 3b4bc405ebd449dfc12a37651cb8e4cd49ca591f..50852627e3e7eb694557c9cec3f3eb8e891a7a9e 100644
--- a/lib/galaxy/util/plugin_config.py
+++ b/lib/galaxy/util/plugin_config.py
@@ -1,4 +1,3 @@
-from pathlib import Path
 from types import ModuleType
 from typing import (
     Any,
@@ -16,9 +15,9 @@ from typing import (
 import yaml
 
 from galaxy.util import parse_xml
+from galaxy.util.path import StrPath
 from galaxy.util.submodules import import_submodules
 
-PathT = Union[str, Path]
 PluginDictConfigT = Dict[str, Any]
 PluginConfigsT = Union[PluginDictConfigT, List[PluginDictConfigT]]
 
@@ -132,7 +131,7 @@ def __load_plugins_from_dicts(
     return plugins
 
 
-def plugin_source_from_path(path: PathT) -> PluginConfigSource:
+def plugin_source_from_path(path: StrPath) -> PluginConfigSource:
     filename = str(path)
     if (
         filename.endswith(".yaml")
@@ -149,7 +148,7 @@ def plugin_source_from_dict(as_dict: PluginConfigsT) -> PluginConfigSource:
     return PluginConfigSource("dict", as_dict)
 
 
-def __read_yaml(path: PathT):
+def __read_yaml(path: StrPath):
     if yaml is None:
         raise ImportError("Attempting to read YAML configuration file - but PyYAML dependency unavailable.")
 
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index 7cf3b8710a75e8a0fdb4075f118076f3e9d26cbd..72a53dabd911cf9d7157c386e88386afa7727359 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -103,7 +103,7 @@ def load_app_properties(
         config_section = config_section or ini_section
 
     # read from file or init w/no file
-    if config_file:
+    if config_file and os.path.exists(config_file):
         properties = read_properties_from_file(config_file, config_section)
     else:
         properties = {"__file__": None}
@@ -208,6 +208,8 @@ def get_data_dir(properties):
     if data_dir is None:
         if running_from_source:
             data_dir = "./database"
+        elif properties["__file__"] is None:
+            data_dir = "./data"
         else:
             config_dir = properties.get("config_dir", os.path.dirname(properties["__file__"]))
             data_dir = os.path.join(config_dir, "data")
diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 9b7f7965592ec99c94c63110ab34c4fcded07dd7..01a2cd68c8400ad1616587460bd2261bc53d0b6a 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -1,18 +1,34 @@
 """Entry point for the usage of Cheetah templating within Galaxy."""
 
+import sys
 import traceback
-from lib2to3.refactor import RefactoringTool
 
 from Cheetah.Compiler import Compiler
 from Cheetah.NameMapper import NotFound
 from Cheetah.Parser import ParseError
 from Cheetah.Template import Template
 from packaging.version import Version
-from past.translation import myfixes
 
 from galaxy.util.tree_dict import TreeDict
 from . import unicodify
 
+if sys.version_info >= (3, 13):
+    import fissix
+    from fissix import (
+        fixes as fissix_fixes,
+        pgen2 as fissix_pgen2,
+        refactor as fissix_refactor,
+    )
+
+    sys.modules["lib2to3"] = fissix
+    sys.modules["lib2to3.fixes"] = fissix_fixes
+    sys.modules["lib2to3.pgen2"] = fissix_pgen2
+    sys.modules["lib2to3.refactor"] = fissix_refactor
+
+from lib2to3.refactor import RefactoringTool
+
+from past.translation import myfixes
+
 # Skip libpasteurize fixers, which make sure code is py2 and py3 compatible.
 # This is not needed, we only translate code on py3.
 myfixes = [f for f in myfixes if not f.startswith("libpasteurize")]
diff --git a/lib/galaxy/util/topsort.py b/lib/galaxy/util/topsort.py
index 64a1338fa1a404e58b72d499a6cb0bd99e2c0b8d..049cbee283667ab380b861852ed1767827f1bcc4 100644
--- a/lib/galaxy/util/topsort.py
+++ b/lib/galaxy/util/topsort.py
@@ -37,6 +37,8 @@ many methods to help analyze and break the cycles.  This requires
 a good deal more code than topsort itself!
 """
 
+from random import choice
+
 
 class CycleError(Exception):
     def __init__(self, sofar, numpreds, succs):
@@ -112,7 +114,6 @@ class CycleError(Exception):
         # crawl backward over the preds until we hit a duplicate, then
         # reverse the path.
         preds = self.get_preds()
-        from random import choice
 
         x = choice(remaining_elts)
         answer = []
diff --git a/lib/galaxy/util/zipstream.py b/lib/galaxy/util/zipstream.py
index 1cd1c77649e74977182d8611bc220aef447cd6bf..7b81d1c33f4bfaf2f735ec3ae1af8799beac870b 100644
--- a/lib/galaxy/util/zipstream.py
+++ b/lib/galaxy/util/zipstream.py
@@ -11,6 +11,7 @@ from urllib.parse import quote
 
 import zipstream
 
+from galaxy.util import to_content_disposition
 from .path import safe_walk
 
 CRC32_MIN = 1444
@@ -41,8 +42,7 @@ class ZipstreamWrapper:
     def get_headers(self) -> Dict[str, str]:
         headers = {}
         if self.archive_name:
-            archive_name = self.archive_name.encode("latin-1", "replace").decode("latin-1")
-            headers["Content-Disposition"] = f'attachment; filename="{archive_name}.zip"'
+            headers["Content-Disposition"] = to_content_disposition(f"{self.archive_name}.zip")
         if self.upstream_mod_zip:
             headers["X-Archive-Files"] = "zip"
         else:
diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index 127856da436fafdd9b3b9f4c4b4e8757abbb4ee6..7e5d63eca556c8c2df93fed20bdef0419c81fc4e 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
-VERSION_MAJOR = "24.1"
-VERSION_MINOR = "2.dev0"
+VERSION_MAJOR = "24.2"
+VERSION_MINOR = "4.dev0"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
diff --git a/lib/galaxy/visualization/data_providers/basic.py b/lib/galaxy/visualization/data_providers/basic.py
index 356bcebcc9c34cbd8552f2485264499bfe3f9d65..686b5e870c24bff0f349787a9b3776c3b1d2054b 100644
--- a/lib/galaxy/visualization/data_providers/basic.py
+++ b/lib/galaxy/visualization/data_providers/basic.py
@@ -1,6 +1,4 @@
-import sys
 from json import loads
-from typing import Iterator
 
 from galaxy.datatypes.tabular import Tabular
 from galaxy.model import DatasetInstance
@@ -30,42 +28,6 @@ class BaseDataProvider:
         self.dependencies = dependencies
         self.error_max_vals = error_max_vals
 
-    def has_data(self, **kwargs):
-        """
-        Returns true if dataset has data in the specified genome window, false
-        otherwise.
-        """
-        raise Exception("Unimplemented Function")
-
-    def get_iterator(self, data_file, chrom, start, end, **kwargs) -> Iterator[str]:
-        """
-        Returns an iterator that provides data in the region chrom:start-end
-        """
-        raise Exception("Unimplemented Function")
-
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
-        """
-        Process data from an iterator to a format that can be provided to client.
-        """
-        raise Exception("Unimplemented Function")
-
-    def get_data(self, chrom, start, end, start_val=0, max_vals=sys.maxsize, **kwargs):
-        """
-        Returns data as specified by kwargs. start_val is the first element to
-        return and max_vals indicates the number of values to return.
-
-        Return value must be a dictionary with the following attributes:
-            dataset_type, data
-        """
-        iterator = self.get_iterator(chrom, start, end)
-        return self.process_data(iterator, start_val, max_vals, **kwargs)
-
-    def write_data_to_file(self, filename, **kwargs):
-        """
-        Write data in region defined by chrom, start, and end to a file.
-        """
-        raise Exception("Unimplemented Function")
-
 
 class ColumnDataProvider(BaseDataProvider):
     """Data provider for columnar data"""
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index 9735167c38433a9a1c6d16e07c4080d4be19a1ae..02ace9373504879d45af813aceb79a547ae2c9eb 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -4,6 +4,7 @@ Data providers for genome visualizations.
 
 import abc
 import itertools
+import logging
 import math
 import os
 import random
@@ -44,6 +45,10 @@ from galaxy.model import DatasetInstance
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
 
+log = logging.getLogger(__name__)
+
+IntWebParam = Union[str, int]
+
 #
 # Utility functions.
 #
@@ -98,7 +103,10 @@ def _chrom_naming_matches(chrom1, chrom2):
     )
 
 
-class FeatureLocationIndexDataProvider(BaseDataProvider):
+# Was previously a BaseDataProvider but it doesn't have the same interface or use any of
+# the parent methods. It is also only used explicitly, constructed by name, and access with
+# get_data directly using a specified query.
+class FeatureLocationIndexDataProvider:
     """
     Reads/writes/queries feature location index (FLI) datasets.
     """
@@ -185,19 +193,13 @@ class GenomeDataProvider(BaseDataProvider):
             error_max_vals=error_max_vals,
         )
 
-    def write_data_to_file(self, regions, filename):
-        """
-        Write data in region defined by chrom, start, and end to a file.
-        """
-        raise Exception("Unimplemented Function")
-
     def valid_chroms(self):
         """
         Returns chroms/contigs that the dataset contains
         """
         return None  # by default
 
-    def has_data(self, chrom, start, end, **kwargs):
+    def has_data(self, chrom):
         """
         Returns true if dataset has data in the specified genome window, false
         otherwise.
@@ -217,13 +219,13 @@ class GenomeDataProvider(BaseDataProvider):
         """
         raise Exception("Unimplemented Function")
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Process data from an iterator to a format that can be provided to client.
         """
         raise Exception("Unimplemented Function")
 
-    def get_data(self, chrom=None, low=None, high=None, start_val=0, max_vals=sys.maxsize, **kwargs):
+    def get_data(self, chrom: str, start: IntWebParam, end: IntWebParam, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Returns data in region defined by chrom, start, and end. start_val and
         max_vals are used to denote the data to return: start_val is the first element to
@@ -232,10 +234,15 @@ class GenomeDataProvider(BaseDataProvider):
         Return value must be a dictionary with the following attributes:
             dataset_type, data
         """
-        start, end = int(low), int(high)
+        start, end = int(start), int(end)
         with self.open_data_file() as data_file:
             iterator = self.get_iterator(data_file, chrom, start, end, **kwargs)
-            data = self.process_data(iterator, start_val, max_vals, start=start, end=end, **kwargs)
+            try:
+                data = self.process_data(iterator, start_val, max_vals, start=start, end=end, **kwargs)
+            except ValueError as e:
+                err_msg = f"Could not return data, error was '{e}'"
+                log.warning(err_msg, exc_info=True)
+                raise MessageException(err_msg)
         return data
 
     def get_genome_data(self, chroms_info, **kwargs):
@@ -384,14 +391,6 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
 
         return iterator
 
-    def write_data_to_file(self, regions, filename):
-        with self.open_data_file() as data_file, open(filename, "w") as out:
-            for region in regions:
-                # Write data in region.
-                iterator = self.get_iterator(data_file, region.chrom, region.start, region.end)
-                for line in iterator:
-                    out.write(f"{line}\n")
-
 
 #
 # -- Interval data providers --
@@ -410,7 +409,7 @@ class IntervalDataProvider(GenomeDataProvider):
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         raise Exception("Unimplemented Function")
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Provides
         """
@@ -468,9 +467,6 @@ class IntervalDataProvider(GenomeDataProvider):
 
         return {"data": rval, "message": message}
 
-    def write_data_to_file(self, regions, filename):
-        raise Exception("Unimplemented Function")
-
 
 class IntervalTabixDataProvider(TabixDataProvider, IntervalDataProvider):
     """
@@ -495,7 +491,7 @@ class BedDataProvider(GenomeDataProvider):
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         raise Exception("Unimplemented Method")
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Provides
         """
@@ -561,18 +557,6 @@ class BedDataProvider(GenomeDataProvider):
 
         return {"data": rval, "dataset_type": self.dataset_type, "message": message}
 
-    def write_data_to_file(self, regions, filename):
-        with open(filename, "w") as out:
-            for region in regions:
-                # Write data in region.
-                chrom = region.chrom
-                start = region.start
-                end = region.end
-                with self.open_data_file() as data_file:
-                    iterator = self.get_iterator(data_file, chrom, start, end)
-                    for line in iterator:
-                        out.write(f"{line}\n")
-
 
 class BedTabixDataProvider(TabixDataProvider, BedDataProvider):
     """
@@ -645,7 +629,7 @@ class VcfDataProvider(GenomeDataProvider):
 
     dataset_type = "variant"
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Returns a dict with the following attributes::
 
@@ -757,15 +741,6 @@ class VcfDataProvider(GenomeDataProvider):
 
         return {"data": data, "message": message}
 
-    def write_data_to_file(self, regions, filename):
-        out = open(filename, "w")
-        with self.open_data_file() as data_file:
-            for region in regions:
-                # Write data in region.
-                iterator = self.get_iterator(data_file, region.chrom, region.start, region.end)
-                for line in iterator:
-                    out.write(f"{line}\n")
-
 
 class VcfTabixDataProvider(TabixDataProvider, VcfDataProvider):
     """
@@ -844,43 +819,6 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         filters.append({"name": "Mapping Quality", "type": "number", "index": filter_col})
         return filters
 
-    def write_data_to_file(self, regions, filename):
-        """
-        Write reads in regions to file.
-        """
-
-        # Open current BAM file using index.
-        bamfile = pysam.AlignmentFile(
-            self.original_dataset.get_file_name(), mode="rb", index_filename=self.converted_dataset.get_file_name()
-        )
-
-        # TODO: write headers as well?
-        new_bamfile = pysam.AlignmentFile(filename, template=bamfile, mode="wb")
-
-        for region in regions:
-            # Write data from region.
-            chrom = region.chrom
-            start = region.start
-            end = region.end
-
-            try:
-                data = bamfile.fetch(start=start, end=end, reference=chrom)
-            except ValueError:
-                # Try alternative chrom naming.
-                chrom = _convert_between_ucsc_and_ensemble_naming(chrom)
-                try:
-                    data = bamfile.fetch(start=start, end=end, reference=chrom)
-                except ValueError:
-                    return None
-
-            # Write reads in region.
-            for read in data:
-                new_bamfile.write(read)
-
-        # Cleanup.
-        new_bamfile.close()
-        bamfile.close()
-
     @contextmanager
     def open_data_file(self):
         # Attempt to open the BAM file with index
@@ -913,7 +851,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
         self,
         iterator,
         start_val=0,
-        max_vals=None,
+        max_vals=sys.maxsize,
         ref_seq=None,
         iterator_type="nth",
         mean_depth=None,
@@ -1189,7 +1127,7 @@ class BBIDataProvider(GenomeDataProvider):
         f.close()
         return all_dat is not None
 
-    def get_data(self, chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs):
+    def get_data(self, chrom: str, start, end, start_val=0, max_vals=sys.maxsize, **kwargs):
         start = int(start)
         end = int(end)
 
@@ -1261,7 +1199,7 @@ class BBIDataProvider(GenomeDataProvider):
             return result
 
         # Approach is different depending on region size.
-        num_samples = int(num_samples)
+        num_samples = int(kwargs.get("num_samples", 100))
         if end - start < num_samples:
             # Get values for individual bases in region, including start and end.
             # To do this, need to increase end to next base and request number of points.
@@ -1328,27 +1266,6 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
 
     dataset_type = "interval_index"
 
-    def write_data_to_file(self, regions, filename):
-        index = Indexes(self.converted_dataset.get_file_name())
-        with open(self.original_dataset.get_file_name()) as source, open(filename, "w") as out:
-            for region in regions:
-                # Write data from region.
-                chrom = region.chrom
-                start = region.start
-                end = region.end
-                for _start, _end, offset in index.find(chrom, start, end):
-                    source.seek(offset)
-
-                    # HACK: write differently depending on original dataset format.
-                    if self.original_dataset.ext not in ["gff", "gff3", "gtf"]:
-                        line = source.readline()
-                        out.write(line)
-                    else:
-                        reader = GFFReaderWrapper(source, fix_strand=True)
-                        feature = next(reader)
-                        for interval in feature.intervals:
-                            out.write("\t".join(interval.fields) + "\n")
-
     @contextmanager
     def open_data_file(self):
         i = Indexes(self.converted_dataset.get_file_name())
@@ -1364,7 +1281,7 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
 
         return data_file.find(chrom, start, end)
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         results = []
         message = None
         with open(self.original_dataset.get_file_name()) as source:
@@ -1438,7 +1355,7 @@ class RawGFFDataProvider(GenomeDataProvider):
 
         return features_in_region_iter()
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Process data from an iterator to a format that can be provided to client.
         """
@@ -1466,7 +1383,7 @@ class GtfTabixDataProvider(TabixDataProvider):
     Returns data from GTF datasets that are indexed via tabix.
     """
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         # Loop through lines and group by transcript_id; each group is a feature.
 
         # TODO: extend this code or use code in gff_util to process GFF/3 as well
@@ -1521,7 +1438,7 @@ class ENCODEPeakDataProvider(GenomeDataProvider):
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         raise Exception("Unimplemented Method")
 
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Provides
         """
@@ -1621,7 +1538,7 @@ class ENCODEPeakTabixDataProvider(TabixDataProvider, ENCODEPeakDataProvider):
 
 
 class ChromatinInteractionsDataProvider(GenomeDataProvider):
-    def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
+    def process_data(self, iterator, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Provides
         """
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 066785feae7a1bb669b7e228dcd40bf3c071ca34..d38996c52c32d33b3276edea83c067d479d18607 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -14,11 +14,11 @@ from galaxy.exceptions import (
     ObjectNotFound,
     ReferenceDataError,
 )
-from galaxy.managers.users import get_user_by_username
 from galaxy.model import (
     HistoryDatasetAssociation,
     User,
 )
+from galaxy.model.db.user import get_user_by_username
 from galaxy.structured_app import StructuredApp
 from galaxy.util.bunch import Bunch
 
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index 13fd42865695b2545c4641954daac35ba9b2346f..b7f90b26fdbcc6337fcba59bc03bbed258aa742f 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -6,7 +6,10 @@ from typing import (
 )
 
 import galaxy.model
-from galaxy.util import asbool
+from galaxy.util import (
+    asbool,
+    listify,
+)
 from galaxy.util.xml_macros import load
 
 log = logging.getLogger(__name__)
@@ -151,9 +154,9 @@ class VisualizationsConfigParser:
         if (specs_section := xml_tree.find("specs")) is not None:
             returned["specs"] = DictParser(specs_section)
 
-        # load group specifiers
-        if (groups_section := xml_tree.find("groups")) is not None:
-            returned["groups"] = ListParser(groups_section)
+        # load tracks specifiers (allow 'groups' section for backward compatibility)
+        if (tracks_section := xml_tree.find("tracks") or xml_tree.find("groups")) is not None:
+            returned["tracks"] = ListParser(tracks_section)
 
         # load settings specifiers
         if (settings_section := xml_tree.find("settings")) is not None:
@@ -221,7 +224,7 @@ class DataSourceParser:
         # when no tests are given, default to isinstance( object, model_class )
         returned["tests"] = self.parse_tests(xml_tree.findall("test"))
 
-        # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_clas, tests
+        # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_class, tests
         returned["to_params"] = {}
         if to_params := self.parse_to_params(xml_tree.findall("to_param")):
             returned["to_params"] = to_params
@@ -301,8 +304,16 @@ class DataSourceParser:
             # result type should tell the registry how to convert the result before the test
             test_result_type = test_elem.get("result_type", "string")
 
+            # allow_uri_if_protocol indicates that the visualization can work with deferred data_sources which source URI
+            # matches any of the given protocols in this list. This is useful for visualizations that can work with URIs.
+            # Can only be used with isinstance tests. By default, an empty list means that the visualization doesn't support
+            # deferred data_sources.
+            allow_uri_if_protocol = []
+
             # test functions should be sent an object to test, and the parsed result expected from the test
             if test_type == "isinstance":
+                allow_uri_if_protocol = listify(test_elem.get("allow_uri_if_protocol"))
+
                 # is test_attr attribute an instance of result
                 # TODO: wish we could take this further but it would mean passing in the datatypes_registry
                 def test_fn(o, result, getter=getter):
@@ -333,7 +344,15 @@ class DataSourceParser:
                 def test_fn(o, result, getter=getter):
                     return str(getter(o)) == result
 
-            tests.append({"type": test_type, "result": test_result, "result_type": test_result_type, "fn": test_fn})
+            tests.append(
+                {
+                    "type": test_type,
+                    "result": test_result,
+                    "result_type": test_result_type,
+                    "fn": test_fn,
+                    "allow_uri_if_protocol": allow_uri_if_protocol,
+                }
+            )
 
         return tests
 
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index dfe625e53dcb12e27073964b3c9998005e5a2be0..bcd8c57098c7f5bc25b979ae908c508583ba1f6b 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -80,12 +80,11 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         base_url = context.get("base_url", "")
         self.base_url = "/".join((base_url, self.name)) if base_url else self.name
         self.static_path = self._get_static_path(self.path)
-        if self.static_path and os.path.exists(os.path.join(self.static_path, "logo.png")):
-            self.config["logo"] = f"{self.static_path}/logo.png"
         template_cache_dir = context.get("template_cache_dir", None)
         additional_template_paths = context.get("additional_template_paths", [])
         self._set_up_template_plugin(template_cache_dir, additional_template_paths=additional_template_paths)
         self.resource_parser = resource_parser.ResourceParser(app)
+        self._set_logo()
 
     def render(self, trans=None, embedded=None, **kwargs):
         """
@@ -125,8 +124,8 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
             "embeddable": self.config.get("embeddable"),
             "entry_point": self.config.get("entry_point"),
             "settings": self.config.get("settings"),
-            "groups": self.config.get("groups"),
             "specs": self.config.get("specs"),
+            "tracks": self.config.get("tracks"),
             "href": self._get_url(),
         }
 
@@ -161,7 +160,7 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         render_vars.update(
             visualization_name=self.name,
             visualization_display_name=self.config["name"],
-            title=kwargs.get("title", None),
+            title=kwargs.get("title", "Unnamed Visualization"),
             saved_visualization=None,
             visualization_id=None,
             visualization_plugin=self.to_dict(),
@@ -232,6 +231,15 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
         # as is for now
         return embedded
 
+    def _set_logo(self):
+        if self.static_path:
+            supported_formats = ["png", "svg"]
+            for file_format in supported_formats:
+                logo_path = os.path.join(self.static_path, f"logo.{file_format}")
+                if os.path.isfile(logo_path):
+                    self.config["logo"] = logo_path
+                    return
+
 
 class ScriptVisualizationPlugin(VisualizationPlugin):
     """
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index 09a320c36d1feb8d4045de586cc2ed679489ab5b..16d785b38d987474c83dfe82f05c2f36ed6cdf13 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -8,6 +8,10 @@ Lower level of visualization framework which does three main things:
 import logging
 import os
 import weakref
+from typing import (
+    List,
+    Optional,
+)
 
 from galaxy.exceptions import ObjectNotFound
 from galaxy.util import (
@@ -268,6 +272,7 @@ class VisualizationsRegistry:
             result_type = test["result_type"]
             test_result = test["result"]
             test_fn = test["fn"]
+            supported_protocols = test.get("allow_uri_if_protocol", [])
             # log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
             #           test_type, result_type, test_result, test_fn )
 
@@ -286,8 +291,36 @@ class VisualizationsRegistry:
                         continue
 
             # NOTE: tests are OR'd, if any test passes - the visualization can be applied
-            if test_fn(target_object, test_result):
+            if test_fn(target_object, test_result) and self._check_uri_support(target_object, supported_protocols):
                 # log.debug( '\t test passed' )
                 return True
 
         return False
+
+    def _is_deferred(self, target_object) -> bool:
+        """Whether the target object is a deferred object."""
+        return getattr(target_object, "state", None) == "deferred"
+
+    def _deferred_source_uri(self, target_object) -> Optional[str]:
+        """Get the source uri from a deferred object."""
+        sources = getattr(target_object, "sources", None)
+        if sources and sources[0]:
+            return sources[0].source_uri
+        return None
+
+    def _check_uri_support(self, target_object, supported_protocols: List[str]) -> bool:
+        """Test if the target object is deferred and has a supported protocol."""
+        if not self._is_deferred(target_object):
+            return True  # not deferred, so no uri to check
+
+        if not supported_protocols:
+            return False  # no protocols defined, means no support for deferred objects
+
+        if "*" in supported_protocols:
+            return True  # wildcard support for all protocols
+
+        deferred_source_uri = self._deferred_source_uri(target_object)
+        if deferred_source_uri:
+            protocol = deferred_source_uri.split("://")[0]
+            return protocol in supported_protocols
+        return False
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index b0c72256d4110212829870c6e4ea0f17443a738f..c9bbfe8f9eaecad6edd461ab970c6ccae757abc9 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -492,7 +492,7 @@ class Response:
         """
         Create a new Response defaulting to HTML content and "200 OK" status
         """
-        self.status = "200 OK"
+        self.status: int = 200
         self.headers = HeaderDict({"content-type": "text/html; charset=UTF-8"})
         self.cookies = SimpleCookie()
 
diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py
index 7fde6906cf1919cd9c66232d9c789808c701909b..f6f90bc54820d6bf7e167d9f87d753ca606c89e4 100644
--- a/lib/galaxy/web/framework/helpers/__init__.py
+++ b/lib/galaxy/web/framework/helpers/__init__.py
@@ -6,6 +6,7 @@ visualizations in their mako files through the `$h` object, see
 GalaxyWebTransaction in galaxy/webapps/base/webapp.py
 """
 
+import re
 from datetime import (
     datetime,
     timedelta,
@@ -105,6 +106,22 @@ def is_true(val):
     return val is True or val in ["True", "true", "T", "t"]
 
 
+def is_url(val):
+    """
+    Regular expression to match common URL protocols
+
+    >>> assert is_url(None) == False
+    >>> assert is_url("is_url") == False
+    >>> assert is_url("http://is_url") == True
+    >>> assert is_url("https://is_url") == True
+    """
+    if val is not None:
+        url_pattern = re.compile(r"^(https?:\/\/|ftp:\/\/)")
+        return bool(url_pattern.match(val))
+    else:
+        return False
+
+
 def to_js_bool(val):
     """
     Prints javascript boolean for passed value.
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index ea01f1efd0985cffcb229ba49b647978718f3536..c839f7eff8ddce4bf0cc6a44b29f7e29629191b1 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -86,7 +86,7 @@ class GridData:
 
         # Process sort arguments.
         sort_by = kwargs.get("sort_by", self.default_sort_key)
-        sort_desc = string_as_bool(kwargs.get("sort_desc", True))
+        sort_desc = string_as_bool(kwargs.get("sort_desc", False))
         for column in self.columns:
             if column.key == sort_by:
                 query = column.sort(trans, query, not sort_desc, column_name=sort_by)
diff --git a/lib/galaxy/web/framework/middleware/remoteuser.py b/lib/galaxy/web/framework/middleware/remoteuser.py
index dc260ceb3958f6ca7474db1d7071da63181aa8c7..8e150917e436f62739a17a6e5e0c10164d781718 100644
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -165,6 +165,7 @@ class RemoteUser:
                 "/user/api_key",
                 "/user/edit_username",
                 "/user/dbkeys",
+                "/user/information",
                 "/user/logout",
                 "/user/toolbox_filters",
                 "/user/set_default_permissions",
diff --git a/lib/galaxy/web/framework/middleware/static.py b/lib/galaxy/web/framework/middleware/static.py
index d46ff6af592c85e8af10e00755d35da89a61265c..03e636e186bf7b2e49cde36e43bf2c0e9a788a31 100644
--- a/lib/galaxy/web/framework/middleware/static.py
+++ b/lib/galaxy/web/framework/middleware/static.py
@@ -18,10 +18,7 @@ class CacheableStaticURLParser(StaticURLParser):
 
     def __call__(self, environ, start_response):
         path_info = environ.get("PATH_INFO", "")
-        script_name = environ.get("SCRIPT_NAME", "")
-        if script_name == "/robots.txt" or script_name == "/favicon.ico":
-            filename = script_name.replace("/", "")
-        elif not path_info:
+        if not path_info:
             # See if this is a static file hackishly mapped.
             if os.path.exists(self.directory) and os.path.isfile(self.directory):
                 app = FileApp(self.directory)
diff --git a/lib/galaxy/web_stack/message.py b/lib/galaxy/web_stack/message.py
index f7ef7f7d2ddf9b8b94f712382da71cf62411ae55..15259b4cc50ee6cecb4bf00615f43ce032bfb51e 100644
--- a/lib/galaxy/web_stack/message.py
+++ b/lib/galaxy/web_stack/message.py
@@ -68,7 +68,9 @@ class ApplicationStackMessage(dict):
         names = set()
         for cls in reversed(self.__class__.mro()):
             names.update(
-                [x for x in dir(cls) if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple]
+                x
+                for x in dir(cls)
+                if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple  # noqa: E721
             )
         for name in names:
             setattr(self.__class__, name.lstrip("_"), property(lambda self, name=name: self._get_list_from_mro(name)))
diff --git a/lib/galaxy/webapps/base/api.py b/lib/galaxy/webapps/base/api.py
index 3da3ba3d39003b402471c9773035ace9f7f6b38b..2c8cc4b8b11c6805661ed4e61e542786c105b572 100644
--- a/lib/galaxy/webapps/base/api.py
+++ b/lib/galaxy/webapps/base/api.py
@@ -1,8 +1,16 @@
 import os
 import stat
-import typing
 import uuid
 from logging import getLogger
+from typing import (
+    Any,
+    Dict,
+    Mapping,
+    Optional,
+    Tuple,
+    TYPE_CHECKING,
+    Union,
+)
 
 import anyio
 from fastapi import (
@@ -26,10 +34,11 @@ from starlette_context.plugins import (
 
 from galaxy.exceptions import MessageException
 from galaxy.exceptions.utils import api_error_to_dict
+from galaxy.util.path import StrPath
 from galaxy.web.framework.base import walk_controller_modules
 from galaxy.web.framework.decorators import validation_error_to_message_exception
 
-if typing.TYPE_CHECKING:
+if TYPE_CHECKING:
     from starlette.background import BackgroundTask
     from starlette.types import (
         Receive,
@@ -37,12 +46,13 @@ if typing.TYPE_CHECKING:
         Send,
     )
 
+from galaxy.schema.schema import MessageExceptionModel
 
 log = getLogger(__name__)
 
 
 # Copied from https://github.com/tiangolo/fastapi/issues/1240#issuecomment-1055396884
-def _get_range_header(range_header: str, file_size: int) -> typing.Tuple[int, int]:
+def _get_range_header(range_header: str, file_size: int) -> Tuple[int, int]:
     def _invalid_range():
         return HTTPException(
             status.HTTP_416_REQUESTED_RANGE_NOT_SATISFIABLE,
@@ -66,19 +76,19 @@ class GalaxyFileResponse(FileResponse):
     Augments starlette FileResponse with x-accel-redirect/x-sendfile and byte-range handling.
     """
 
-    nginx_x_accel_redirect_base: typing.Optional[str] = None
-    apache_xsendfile: typing.Optional[bool] = None
+    nginx_x_accel_redirect_base: Optional[str] = None
+    apache_xsendfile: Optional[bool] = None
 
     def __init__(
         self,
-        path: typing.Union[str, "os.PathLike[str]"],
+        path: StrPath,
         status_code: int = 200,
-        headers: typing.Optional[typing.Mapping[str, str]] = None,
-        media_type: typing.Optional[str] = None,
-        background: typing.Optional["BackgroundTask"] = None,
-        filename: typing.Optional[str] = None,
-        stat_result: typing.Optional[os.stat_result] = None,
-        method: typing.Optional[str] = None,
+        headers: Optional[Mapping[str, str]] = None,
+        media_type: Optional[str] = None,
+        background: Optional["BackgroundTask"] = None,
+        filename: Optional[str] = None,
+        stat_result: Optional[os.stat_result] = None,
+        method: Optional[str] = None,
         content_disposition_type: str = "attachment",
     ) -> None:
         super().__init__(
@@ -183,8 +193,8 @@ def get_error_response_for_request(request: Request, exc: MessageException) -> J
     else:
         content = error_dict
 
-    retry_after: typing.Optional[int] = getattr(exc, "retry_after", None)
-    headers: typing.Dict[str, str] = {}
+    retry_after: Optional[int] = getattr(exc, "retry_after", None)
+    headers: Dict[str, str] = {}
     if retry_after:
         headers["Retry-After"] = str(retry_after)
     return JSONResponse(status_code=status_code, content=content, headers=headers)
@@ -236,7 +246,27 @@ def add_request_id_middleware(app: FastAPI):
 
 
 def include_all_package_routers(app: FastAPI, package_name: str):
+    responses: Dict[Union[int, str], Dict[str, Any]] = {
+        "4XX": {
+            "description": "Request Error",
+            "model": MessageExceptionModel,
+        },
+        "5XX": {
+            "description": "Server Error",
+            "model": MessageExceptionModel,
+        },
+    }
     for _, module in walk_controller_modules(package_name):
         router = getattr(module, "router", None)
         if router:
-            app.include_router(router)
+            app.include_router(router, responses=responses)
+
+    # handle CORS preflight requests - synchronize with wsgi behavior.
+    # this needs to happen last so it doesn't clobber routes with explicit cors handling
+    # it doesn't affect the CORS middleware since the middleware terminates the request handling before routing
+    @app.options("/api/{rest_of_path:path}", include_in_schema=False)
+    async def preflight_handler(request: Request, rest_of_path: str) -> Response:
+        response = Response()
+        response.headers["Access-Control-Allow-Headers"] = "*"
+        response.headers["Access-Control-Max-Age"] = "600"
+        return response
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index 83c3ae620560a264ba11cdc89cc1253a85a5d36a..e481a55038f8c0e85275fbd7a66d4e398e382aea 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -613,220 +613,6 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
 
     slug_builder = SlugBuilder()
 
-    def get_visualization(self, trans, id, check_ownership=True, check_accessible=False):
-        """
-        Get a Visualization from the database by id, verifying ownership.
-        """
-        # Load workflow from database
-        try:
-            visualization = trans.sa_session.get(model.Visualization, trans.security.decode_id(id))
-        except TypeError:
-            visualization = None
-        if not visualization:
-            error("Visualization not found")
-        else:
-            return self.security_check(trans, visualization, check_ownership, check_accessible)
-
-    def get_visualization_dict(self, visualization):
-        """
-        Return a set of detailed attributes for a visualization in dictionary form.
-        The visualization's latest_revision is returned in its own sub-dictionary.
-        NOTE: that encoding ids isn't done here should happen at the caller level.
-        """
-        return {
-            "model_class": "Visualization",
-            "id": visualization.id,
-            "title": visualization.title,
-            "type": visualization.type,
-            "user_id": visualization.user.id,
-            "dbkey": visualization.dbkey,
-            "slug": visualization.slug,
-            # to_dict only the latest revision (allow older to be fetched elsewhere)
-            "latest_revision": self.get_visualization_revision_dict(visualization.latest_revision),
-            "revisions": [r.id for r in visualization.revisions],
-        }
-
-    def get_visualization_revision_dict(self, revision):
-        """
-        Return a set of detailed attributes for a visualization in dictionary form.
-        NOTE: that encoding ids isn't done here should happen at the caller level.
-        """
-        return {
-            "model_class": "VisualizationRevision",
-            "id": revision.id,
-            "visualization_id": revision.visualization.id,
-            "title": revision.title,
-            "dbkey": revision.dbkey,
-            "config": revision.config,
-        }
-
-    def import_visualization(self, trans, id, user=None):
-        """
-        Copy the visualization with the given id and associate the copy
-        with the given user (defaults to trans.user).
-
-        Raises `ItemAccessibilityException` if `user` is not passed and
-        the current user is anonymous, and if the visualization is not `importable`.
-        Raises `ItemDeletionException` if the visualization has been deleted.
-        """
-        # default to trans.user, error if anon
-        if not user:
-            if not trans.user:
-                raise exceptions.ItemAccessibilityException("You must be logged in to import Galaxy visualizations")
-            user = trans.user
-
-        # check accessibility
-        visualization = self.get_visualization(trans, id, check_ownership=False)
-        if not visualization.importable:
-            raise exceptions.ItemAccessibilityException(
-                "The owner of this visualization has disabled imports via this link."
-            )
-        if visualization.deleted:
-            raise exceptions.ItemDeletionException("You can't import this visualization because it has been deleted.")
-
-        # copy vis and alter title
-        # TODO: need to handle custom db keys.
-        imported_visualization = visualization.copy(user=user, title=f"imported: {visualization.title}")
-        trans.sa_session.add(imported_visualization)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
-        return imported_visualization
-
-    def create_visualization(
-        self,
-        trans,
-        type,
-        title="Untitled Visualization",
-        slug=None,
-        dbkey=None,
-        annotation=None,
-        config=None,
-        save=True,
-    ):
-        """
-        Create visualiation and first revision.
-        """
-        config = config or {}
-        visualization = self._create_visualization(trans, title, type, dbkey, slug, annotation, save)
-        # TODO: handle this error structure better either in _create or here
-        if isinstance(visualization, dict):
-            err_dict = visualization
-            raise ValueError(err_dict["title_err"] or err_dict["slug_err"])
-
-        # Create and save first visualization revision
-        revision = trans.model.VisualizationRevision(
-            visualization=visualization, title=title, config=config, dbkey=dbkey
-        )
-        visualization.latest_revision = revision
-
-        if save:
-            session = trans.sa_session
-            session.add(revision)
-            with transaction(session):
-                session.commit()
-
-        return visualization
-
-    def add_visualization_revision(self, trans, visualization, config, title, dbkey):
-        """
-        Adds a new `VisualizationRevision` to the given `visualization` with
-        the given parameters and set its parent visualization's `latest_revision`
-        to the new revision.
-        """
-        # precondition: only add new revision on owned vis's
-        # TODO:?? should we default title, dbkey, config? to which: visualization or latest_revision?
-        revision = trans.model.VisualizationRevision(
-            visualization=visualization, title=title, dbkey=dbkey, config=config
-        )
-
-        visualization.latest_revision = revision
-        # TODO:?? does this automatically add revision to visualzation.revisions?
-        trans.sa_session.add(revision)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
-        return revision
-
-    def save_visualization(self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None):
-        session = trans.sa_session
-
-        # Create/get visualization.
-        if not id:
-            # Create new visualization.
-            vis = self._create_visualization(trans, title, type, dbkey, slug, annotation)
-        else:
-            decoded_id = trans.security.decode_id(id)
-            vis = session.get(model.Visualization, decoded_id)
-            # TODO: security check?
-
-        # Create new VisualizationRevision that will be attached to the viz
-        vis_rev = trans.model.VisualizationRevision()
-        vis_rev.visualization = vis
-        # do NOT alter the dbkey
-        vis_rev.dbkey = vis.dbkey
-        # do alter the title and config
-        vis_rev.title = title
-
-        # -- Validate config. --
-
-        if vis.type == "trackster":
-
-            def unpack_track(track_dict):
-                """Unpack a track from its json."""
-                dataset_dict = track_dict["dataset"]
-                return {
-                    "dataset_id": trans.security.decode_id(dataset_dict["id"]),
-                    "hda_ldda": dataset_dict.get("hda_ldda", "hda"),
-                    "track_type": track_dict["track_type"],
-                    "prefs": track_dict["prefs"],
-                    "mode": track_dict["mode"],
-                    "filters": track_dict["filters"],
-                    "tool_state": track_dict["tool_state"],
-                }
-
-            def unpack_collection(collection_json):
-                """Unpack a collection from its json."""
-                unpacked_drawables = []
-                drawables = collection_json["drawables"]
-                for drawable_json in drawables:
-                    if "track_type" in drawable_json:
-                        drawable = unpack_track(drawable_json)
-                    else:
-                        drawable = unpack_collection(drawable_json)
-                    unpacked_drawables.append(drawable)
-                return {
-                    "obj_type": collection_json["obj_type"],
-                    "drawables": unpacked_drawables,
-                    "prefs": collection_json.get("prefs", []),
-                    "filters": collection_json.get("filters", None),
-                }
-
-            # TODO: unpack and validate bookmarks:
-            def unpack_bookmarks(bookmarks_json):
-                return bookmarks_json
-
-            # Unpack and validate view content.
-            view_content = unpack_collection(config["view"])
-            bookmarks = unpack_bookmarks(config["bookmarks"])
-            vis_rev.config = {"view": view_content, "bookmarks": bookmarks}
-            # Viewport from payload
-            viewport = config.get("viewport")
-            if viewport:
-                chrom = viewport["chrom"]
-                start = viewport["start"]
-                end = viewport["end"]
-                overview = viewport["overview"]
-                vis_rev.config["viewport"] = {"chrom": chrom, "start": start, "end": end, "overview": overview}
-        else:
-            # Default action is to save the config as is with no validation.
-            vis_rev.config = config
-
-        vis.latest_revision = vis_rev
-        session.add(vis_rev)
-        with transaction(session):
-            session.commit()
-        encoded_id = trans.security.encode_id(vis.id)
-        return {"vis_id": encoded_id, "url": url_for(controller="visualization", action=vis.type, id=encoded_id)}
-
     def get_tool_def(self, trans, hda):
         """Returns definition of an interactive tool for an HDA."""
 
@@ -874,10 +660,14 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
             bookmarks = latest_revision.config.get("bookmarks", [])
 
             def pack_track(track_dict):
-                dataset_id = track_dict["dataset_id"]
+                unencoded_id = track_dict.get("dataset_id")
+                if unencoded_id:
+                    encoded_id = trans.security.encode_id(unencoded_id)
+                else:
+                    encoded_id = track_dict["dataset"]["id"]
                 hda_ldda = track_dict.get("hda_ldda", "hda")
-                dataset_id = trans.security.encode_id(dataset_id)
-                dataset = self.get_hda_or_ldda(trans, hda_ldda, dataset_id)
+
+                dataset = self.get_hda_or_ldda(trans, hda_ldda, encoded_id)
                 try:
                     prefs = track_dict["prefs"]
                 except KeyError:
@@ -1016,44 +806,6 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                 )
         return data
 
-    # -- Helper functions --
-
-    def _create_visualization(self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True):
-        """Create visualization but not first revision. Returns Visualization object."""
-        user = trans.get_user()
-
-        # Error checking.
-        title_err = slug_err = ""
-        if not title:
-            title_err = "visualization name is required"
-        elif slug and not managers_base.is_valid_slug(slug):
-            slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
-        elif slug and slug_exists(trans.sa_session, trans.model.Visualization, user, slug, ignore_deleted=True):
-            slug_err = "visualization identifier must be unique"
-
-        if title_err or slug_err:
-            return {"title_err": title_err, "slug_err": slug_err}
-
-        # Create visualization
-        visualization = trans.model.Visualization(user=user, title=title, dbkey=dbkey, type=type)
-        if slug:
-            visualization.slug = slug
-        else:
-            self.slug_builder.create_item_slug(trans.sa_session, visualization)
-        if annotation:
-            annotation = sanitize_html(annotation)
-            # TODO: if this is to stay in the mixin, UsesAnnotations should be added to the superclasses
-            #   right now this is depending on the classes that include this mixin to have UsesAnnotations
-            self.add_item_annotation(trans.sa_session, trans.user, visualization, annotation)
-
-        if save:
-            session = trans.sa_session
-            session.add(visualization)
-            with transaction(session):
-                session.commit()
-
-        return visualization
-
     def _get_genome_data(self, trans, dataset, dbkey=None):
         """
         Returns genome-wide data for dataset if available; if not, message is returned.
@@ -1144,7 +896,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
             except exceptions.ToolMissingException:
                 pass
 
-    def _import_shared_workflow(self, trans, stored):
+    def _import_shared_workflow(self, trans, stored: model.StoredWorkflow):
         """Imports a shared workflow"""
         # Copy workflow.
         imported_stored = model.StoredWorkflow()
@@ -1174,7 +926,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
         """
         Converts a workflow to a dict of attributes suitable for exporting.
         """
-        workflow_contents_manager = workflows.WorkflowContentsManager(self.app)
+        workflow_contents_manager = workflows.WorkflowContentsManager(self.app, self.app.trs_proxy)
         return workflow_contents_manager.workflow_to_dict(
             trans,
             stored,
@@ -1261,7 +1013,7 @@ class SharableMixin:
 
     def _is_valid_slug(self, slug):
         """Returns true if slug is valid."""
-        return managers_base.is_valid_slug(slug)
+        return SlugBuilder.is_valid_slug(slug)
 
     @web.expose
     @web.require_login("modify Galaxy items")
@@ -1294,6 +1046,11 @@ class SharableMixin:
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug, **kwargs):
         """Display item by username and slug."""
+        # Ensure slug is in the correct format.
+        slug = slug.encode("latin1").decode("utf-8")
+        self._display_by_username_and_slug(trans, username, slug, **kwargs)
+
+    def _display_by_username_and_slug(self, trans, username, slug, **kwargs):
         raise NotImplementedError()
 
     def get_item(self, trans, id):
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index e7c9cc3c6044ac2d15906bcee991f252c47a1735..6ccf47c842033eaabd54b963d9e04a88ff25c8b2 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -14,6 +14,7 @@ from typing import (
     Any,
     Dict,
     Optional,
+    Tuple,
 )
 from urllib.parse import urlparse
 
@@ -325,6 +326,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
         self.galaxy_session = None
         self.error_message = None
         self.host = self.request.host
+        self._short_term_cache: Dict[Tuple[str, ...], Any] = {}
 
         # set any cross origin resource sharing headers if configured to do so
         self.set_cors_headers()
@@ -345,6 +347,26 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo
             self._ensure_valid_session(session_cookie)
 
         if self.galaxy_session:
+            success = True
+            if hasattr(self.app, "authnz_manager") and self.app.authnz_manager:
+                success = self.app.authnz_manager.refresh_expiring_oidc_tokens(self)
+            if not success:
+                self.handle_user_logout()
+                if self.environ.get("is_api_request", False):
+                    self.response.status = 401
+                    self.user = None
+                    self.galaxy_session = None
+                else:
+                    self.response.send_redirect(
+                        url_for(
+                            controller="login",
+                            action="start",
+                            message="You have been logged from your identity provider.  Please log in again to continue using Galaxy.",
+                            status="info",
+                            use_panels=True,
+                        )
+                    )
+                return
             # When we've authenticated by session, we have to check the
             # following.
             # Prevent deleted users from accessing Galaxy
@@ -1151,19 +1173,34 @@ def build_url_map(app, global_conf, **local_conf):
     # Send to dynamic app by default
     urlmap["/"] = app
 
-    def get_static_from_config(option_name, default_path):
-        config_val = conf.get(option_name, default_url_path(default_path))
+    def get_static_from_config(option_name, default_path, sample=None):
+        config_val = conf.get(option_name)
+        default = default_url_path(default_path)
+        if not config_val:
+            if not os.path.exists(default) and sample:
+                config_val = os.path.abspath(f"{sample}")
+            else:
+                config_val = default
         per_host_config_option = f"{option_name}_by_host"
         per_host_config = conf.get(per_host_config_option)
         return Static(config_val, cache_time, directory_per_host=per_host_config)
 
     # Define static mappings from config
-    urlmap["/static"] = get_static_from_config("static_dir", "static/")
-    urlmap["/images"] = get_static_from_config("static_images_dir", "static/images")
-    urlmap["/static/scripts"] = get_static_from_config("static_scripts_dir", "static/scripts/")
-    urlmap["/static/welcome.html"] = get_static_from_config("static_welcome_html", "static/welcome.html")
-    urlmap["/favicon.ico"] = get_static_from_config("static_favicon_dir", "static/favicon.ico")
-    urlmap["/robots.txt"] = get_static_from_config("static_robots_txt", "static/robots.txt")
+    static_dir = get_static_from_config("static_dir", "static/")
+    static_dir_bare = static_dir.directory.rstrip("/")
+    urlmap["/static"] = static_dir
+    urlmap["/images"] = get_static_from_config("static_images_dir", f"{static_dir_bare}/images")
+    urlmap["/static/scripts"] = get_static_from_config("static_scripts_dir", f"{static_dir_bare}/scripts/")
+
+    urlmap["/static/welcome.html"] = get_static_from_config(
+        "static_welcome_html", f"{static_dir_bare}/welcome.html", sample=default_url_path("static/welcome.sample.html")
+    )
+    urlmap["/favicon.ico"] = get_static_from_config(
+        "static_favicon_dir", f"{static_dir_bare}/favicon.ico", sample=default_url_path("static/favicon.ico")
+    )
+    urlmap["/robots.txt"] = get_static_from_config(
+        "static_robots_txt", f"{static_dir_bare}/robots.txt", sample=default_url_path("static/robots.txt")
+    )
 
     if "static_local_dir" in conf:
         urlmap["/static_local"] = Static(conf["static_local_dir"], cache_time)
diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index 3b96292f955d48eddd23bbcdfc9997badd2e7018..95ec6cf4069aac648c8e331901d37777f7ac5271 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -8,6 +8,7 @@ from string import Template
 from typing import (
     Any,
     AsyncGenerator,
+    Callable,
     cast,
     NamedTuple,
     Optional,
@@ -26,6 +27,7 @@ from fastapi import (
     APIRouter,
     Form,
     Header,
+    Path,
     Query,
     Request,
     Response,
@@ -41,7 +43,10 @@ from fastapi.security import (
     HTTPAuthorizationCredentials,
     HTTPBearer,
 )
-from pydantic import ValidationError
+from pydantic import (
+    UUID4,
+    ValidationError,
+)
 from pydantic.main import BaseModel
 from routes import (
     Mapper,
@@ -375,6 +380,18 @@ def get_admin_user(trans: SessionRequestContext = DependsOnTrans):
 AdminUserRequired = Depends(get_admin_user)
 
 
+def cors_preflight(response: Response):
+    response.headers["Access-Control-Allow-Origin"] = "*"
+    # Only allow CORS safe-listed headers for now (https://developer.mozilla.org/en-US/docs/Glossary/CORS-safelisted_request_header)
+    response.headers["Access-Control-Allow-Headers"] = "Accept,Accept-Language,Content-Language,Content-Type,Range"
+    response.headers["Access-Control-Max-Age"] = "600"
+    response.status_code = 200
+    return response
+
+
+CORSPreflightRequired = Depends(cors_preflight)
+
+
 class BaseGalaxyAPIController(BaseAPIController):
     def __init__(self, app: StructuredApp):
         super().__init__(app)
@@ -397,7 +414,7 @@ class FrameworkRouter(APIRouter):
 
     def wrap_with_alias(self, verb: RestVerb, *args, alias: Optional[str] = None, **kwd):
         """
-        Wraps FastAPI methods with additional alias keyword and require_admin handling.
+        Wraps FastAPI methods with additional alias keyword, require_admin and CORS handling.
 
         @router.get("/api/thing", alias="/api/deprecated_thing") will then create
         routes for /api/thing and /api/deprecated_thing.
@@ -405,6 +422,13 @@ class FrameworkRouter(APIRouter):
         kwd = self._handle_galaxy_kwd(kwd)
         include_in_schema = kwd.pop("include_in_schema", True)
 
+        allow_cors = kwd.pop("allow_cors", False)
+        if allow_cors:
+            assert (
+                "route_class_override" not in kwd
+            ), "Cannot use allow_cors=True on route and specify `route_class_override`"
+            kwd["route_class_override"] = APICorsRoute
+
         def decorate_route(route, include_in_schema=include_in_schema):
             # Decorator solely exists to allow passing `route_class_override` to add_api_route
             def decorated_route(func):
@@ -415,6 +439,21 @@ class FrameworkRouter(APIRouter):
                     include_in_schema=include_in_schema,
                     **kwd,
                 )
+
+                if allow_cors:
+
+                    dependencies = kwd.pop("dependencies", [])
+                    dependencies.append(CORSPreflightRequired)
+
+                    self.add_api_route(
+                        route,
+                        endpoint=lambda: None,
+                        methods=[RestVerb.options],
+                        include_in_schema=False,
+                        dependencies=dependencies,
+                        **kwd,
+                    )
+
                 return func
 
             return decorated_route
@@ -500,6 +539,23 @@ class Router(FrameworkRouter):
     user_dependency = DependsOnUser
 
 
+class APICorsRoute(APIRoute):
+    """
+    Sends CORS headers
+    """
+
+    def get_route_handler(self) -> Callable:
+        original_route_handler = super().get_route_handler()
+
+        async def custom_route_handler(request: Request) -> Response:
+            response: Response = await original_route_handler(request)
+            response.headers["Access-Control-Allow-Origin"] = request.headers.get("Origin", "*")
+            response.headers["Access-Control-Max-Age"] = "600"
+            return response
+
+        return custom_route_handler
+
+
 class APIContentTypeRoute(APIRoute):
     """
     Determines endpoint to match using content-type.
@@ -618,3 +674,10 @@ def search_query_param(model_name: str, tags: list, free_text_fields: list) -> O
         title="Search query.",
         description=description,
     )
+
+
+LandingUuidPathParam: UUID4 = Path(
+    ...,
+    title="Landing UUID",
+    description="The UUID used to identify a persisted landing request.",
+)
diff --git a/lib/galaxy/webapps/galaxy/api/chat.py b/lib/galaxy/webapps/galaxy/api/chat.py
new file mode 100644
index 0000000000000000000000000000000000000000..8633954cd3dc3c8a3797ecb402a6c4eaa0e9e66f
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/api/chat.py
@@ -0,0 +1,142 @@
+"""
+API Controller providing Chat functionality
+"""
+
+import logging
+from typing import (
+    Optional,
+    Union,
+)
+
+from fastapi import Path
+from typing_extensions import Annotated
+
+from galaxy.config import GalaxyAppConfiguration
+from galaxy.exceptions import ConfigurationError
+from galaxy.managers.chat import ChatManager
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.jobs import JobManager
+from galaxy.model import User
+from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.schema import ChatPayload
+from galaxy.webapps.galaxy.api import (
+    depends,
+    DependsOnTrans,
+    DependsOnUser,
+    Router,
+)
+
+try:
+    import openai
+except ImportError:
+    openai = None
+
+log = logging.getLogger(__name__)
+
+router = Router(tags=["chat"])
+
+DEFAULT_PROMPT = """
+Please only say that something went wrong when configuing the ai prompt in your response.
+"""
+
+JobIdPathParam = Optional[
+    Annotated[
+        DecodedDatabaseIdField,
+        Path(title="Job ID", description="The Job ID the chat exchange is linked to."),
+    ]
+]
+
+
+@router.cbv
+class ChatAPI:
+    config: GalaxyAppConfiguration = depends(GalaxyAppConfiguration)
+    chat_manager: ChatManager = depends(ChatManager)
+    job_manager: JobManager = depends(JobManager)
+
+    @router.post("/api/chat")
+    def query(
+        self,
+        job_id: JobIdPathParam,
+        payload: ChatPayload,
+        trans: ProvidesUserContext = DependsOnTrans,
+        user: User = DependsOnUser,
+    ) -> str:
+        """We're off to ask the wizard"""
+        # Currently job-based chat exchanges are the only ones supported,
+        # and will only have the one message.
+        job = self.job_manager.get_accessible_job(trans, job_id)
+        if job:
+            # If there's an existing response for this job, just return that one for now.
+            # TODO: Support regenerating the response as a new message, and
+            # asking follow-up questions.
+            existing_response = self.chat_manager.get(trans, job.id)
+            if existing_response and existing_response.messages[0]:
+                return existing_response.messages[0].message
+
+        self._ensure_openai_configured()
+
+        messages = self._build_messages(payload, trans)
+        response = self._call_openai(messages)
+        answer = response.choices[0].message.content
+
+        if job:
+            self.chat_manager.create(trans, job.id, answer)
+
+        return answer
+
+    @router.put("/api/chat/{job_id}/feedback")
+    def feedback(
+        self,
+        job_id: JobIdPathParam,
+        feedback: int,
+        trans: ProvidesUserContext = DependsOnTrans,
+        user: User = DependsOnUser,
+    ) -> Union[int, None]:
+        """Provide feedback on the chatbot response."""
+        job = self.job_manager.get_accessible_job(trans, job_id)
+        chat_response = self.chat_manager.set_feedback_for_job(trans, job.id, feedback)
+        return chat_response.messages[0].feedback
+
+    def _ensure_openai_configured(self):
+        """Ensure OpenAI is available and configured with an API key."""
+        if openai is None:
+            raise ConfigurationError("OpenAI is not installed. Please install openai to use this feature.")
+        if self.config.openai_api_key is None:
+            raise ConfigurationError("OpenAI is not configured for this instance.")
+        openai.api_key = self.config.openai_api_key
+
+    def _get_system_prompt(self) -> str:
+        """Get the system prompt for OpenAI."""
+        return self.config.chat_prompts.get("tool_error", DEFAULT_PROMPT)
+
+    def _build_messages(self, payload: ChatPayload, trans: ProvidesUserContext) -> list:
+        """Build the message array to send to OpenAI."""
+        messages = [
+            {"role": "system", "content": self._get_system_prompt()},
+            {"role": "user", "content": payload.query},
+        ]
+
+        user_msg = self._get_user_context_message(trans)
+        if user_msg:
+            messages.append({"role": "system", "content": user_msg})
+
+        return messages
+
+    def _get_user_context_message(self, trans: ProvidesUserContext) -> str:
+        """Generate a user context message based on the user's information."""
+        user = trans.user
+        if user:
+            log.debug(f"CHATGPTuser: {user.username}")
+            return f"You will address the user as {user.username}"
+        return "You will address the user as Anonymous User"
+
+    def _call_openai(self, messages: list):
+        """Send a chat request to OpenAI and handle exceptions."""
+        try:
+            return openai.chat.completions.create(
+                model=self.config.openai_model,
+                messages=messages,
+            )
+        except Exception as e:
+            log.error(f"Error calling OpenAI: {e}")
+            raise ConfigurationError("An error occurred while communicating with OpenAI.")
diff --git a/lib/galaxy/webapps/galaxy/api/cloud.py b/lib/galaxy/webapps/galaxy/api/cloud.py
deleted file mode 100644
index 059b6732e04c46780fdd4ce35765da97c1466415..0000000000000000000000000000000000000000
--- a/lib/galaxy/webapps/galaxy/api/cloud.py
+++ /dev/null
@@ -1,84 +0,0 @@
-"""
-API operations on Cloud-based storages, such as Amazon Simple Storage Service (S3).
-"""
-
-import logging
-
-from fastapi import Body
-
-from galaxy.managers.cloud import CloudManager
-from galaxy.managers.context import ProvidesHistoryContext
-from galaxy.managers.datasets import DatasetSerializer
-from galaxy.schema.cloud import (
-    CloudDatasets,
-    CloudDatasetsResponse,
-    CloudObjects,
-    DatasetSummaryList,
-)
-from galaxy.webapps.galaxy.api import (
-    depends,
-    Router,
-)
-from . import DependsOnTrans
-
-log = logging.getLogger(__name__)
-
-router = Router(tags=["cloud"])
-
-
-@router.cbv
-class FastAPICloudController:
-    cloud_manager: CloudManager = depends(CloudManager)
-    datasets_serializer: DatasetSerializer = depends(DatasetSerializer)
-
-    @router.post(
-        "/api/cloud/storage/get",
-        summary="Gets given objects from a given cloud-based bucket to a Galaxy history.",
-        deprecated=True,
-    )
-    def get(
-        self,
-        payload: CloudObjects = Body(default=...),
-        trans: ProvidesHistoryContext = DependsOnTrans,
-    ) -> DatasetSummaryList:
-        datasets = self.cloud_manager.get(
-            trans=trans,
-            history_id=payload.history_id,
-            bucket_name=payload.bucket,
-            objects=payload.objects,
-            authz_id=payload.authz_id,
-            input_args=payload.input_args,
-        )
-        rtv = []
-        for dataset in datasets:
-            rtv.append(self.datasets_serializer.serialize_to_view(dataset, view="summary"))
-        return DatasetSummaryList.model_construct(root=rtv)
-
-    @router.post(
-        "/api/cloud/storage/send",
-        summary="Sends given dataset(s) in a given history to a given cloud-based bucket.",
-        deprecated=True,
-    )
-    def send(
-        self,
-        payload: CloudDatasets = Body(default=...),
-        trans: ProvidesHistoryContext = DependsOnTrans,
-    ) -> CloudDatasetsResponse:
-        log.info(
-            msg="Received api/send request for `{}` datasets using authnz with id `{}`, and history `{}`."
-            "".format(
-                "all the dataset in the given history" if not payload.dataset_ids else len(payload.dataset_ids),
-                payload.authz_id,
-                payload.history_id,
-            )
-        )
-
-        sent, failed = self.cloud_manager.send(
-            trans=trans,
-            history_id=payload.history_id,
-            bucket_name=payload.bucket,
-            authz_id=payload.authz_id,
-            dataset_ids=payload.dataset_ids,
-            overwrite_existing=payload.overwrite_existing,
-        )
-        return CloudDatasetsResponse(sent_dataset_labels=sent, failed_dataset_labels=failed, bucket_name=payload.bucket)
diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
deleted file mode 100644
index e3e1ced530612a645bd19ee648daad50b82ceaa8..0000000000000000000000000000000000000000
--- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py
+++ /dev/null
@@ -1,277 +0,0 @@
-"""
-API operations on defining cloud authorizations.
-
-Through means of cloud authorization a user is able to grant a Galaxy server a secure access to his/her
-cloud-based resources without sharing his/her long-lasting credentials.
-
-User provides a provider-specific configuration, which Galaxy users to request temporary credentials
-from the provider to access the user's resources.
-"""
-
-import logging
-
-from galaxy.exceptions import (
-    ActionInputError,
-    InternalServerError,
-    MalformedId,
-    RequestParameterInvalidException,
-    RequestParameterMissingException,
-)
-from galaxy.managers import cloudauthzs
-from galaxy.model.base import transaction
-from galaxy.structured_app import StructuredApp
-from galaxy.util import unicodify
-from galaxy.web import expose_api
-from . import BaseGalaxyAPIController
-
-log = logging.getLogger(__name__)
-
-
-class CloudAuthzController(BaseGalaxyAPIController):
-    """
-    RESTfull controller for defining cloud authorizations.
-    """
-
-    def __init__(self, app: StructuredApp):
-        super().__init__(app)
-        self.cloudauthz_manager = cloudauthzs.CloudAuthzManager(app)
-        self.cloudauthz_serializer = cloudauthzs.CloudAuthzsSerializer(app)
-        self.cloudauthz_deserializer = cloudauthzs.CloudAuthzsDeserializer(app)
-
-    @expose_api
-    def index(self, trans, **kwargs):
-        """
-        GET /api/cloud/authz
-
-        Lists all the cloud authorizations user has defined.
-
-        :type  trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans: Galaxy web transaction
-
-        :param kwargs: empty dict
-
-        :rtype: list of dict
-        :return: a list of cloud authorizations (each represented in key-value pair format) defined for the user.
-        """
-        rtv = []
-        for cloudauthz in trans.user.cloudauthz:
-            rtv.append(
-                self.cloudauthz_serializer.serialize_to_view(
-                    cloudauthz, user=trans.user, trans=trans, **self._parse_serialization_params(kwargs, "summary")
-                )
-            )
-        return rtv
-
-    @expose_api
-    def create(self, trans, payload, **kwargs):
-        """
-        * POST /api/cloud/authz
-            Request to store the payload as a cloudauthz (cloud authorization) configuration for a user.
-
-        :type  trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans: Galaxy web transaction
-
-        :type payload: dict
-        :param payload: A dictionary structure containing the following keys:
-            *   provider:       the cloud-based resource provider to which this configuration belongs to.
-
-            *   config:         a dictionary containing all the configuration required to request temporary credentials
-                                from the provider. See the following page for details:
-                                https://galaxyproject.org/authnz/
-
-            *   authn_id:       the (encoded) ID of a third-party authentication of a user. To have this ID, user must
-                                have logged-in to this Galaxy server using third-party identity (e.g., Google), or has
-                                associated his/her Galaxy account with a third-party OIDC-based identity. See this page:
-                                https://galaxyproject.org/authnz/config/
-
-            *   description:    [Optional] a brief description for this configuration.
-
-        :param kwargs: empty dict
-
-        :rtype: dict
-        :return: a dictionary with the following kvp:
-            *   status:     HTTP response code
-            *   message:    A message complementary to the response code.
-        """
-        msg_template = f"Rejected user `{trans.user.id}`'s request to create cloudauthz config because of {{}}."
-        if not isinstance(payload, dict):
-            raise ActionInputError(
-                "Invalid payload data type. The payload is expected to be a dictionary, but "
-                f"received data of type `{type(payload)}`."
-            )
-
-        missing_arguments = []
-        provider = payload.get("provider", None)
-        if provider is None:
-            missing_arguments.append("provider")
-
-        config = payload.get("config", None)
-        if config is None:
-            missing_arguments.append("config")
-
-        authn_id = payload.get("authn_id", None)
-        if authn_id is None and provider.lower() not in ["azure", "gcp"]:
-            missing_arguments.append("authn_id")
-
-        if len(missing_arguments) > 0:
-            log.debug(msg_template.format(f"missing required config {missing_arguments}"))
-            raise RequestParameterMissingException(
-                f"The following required arguments are missing in the payload: {missing_arguments}"
-            )
-
-        description = payload.get("description", "")
-
-        if not isinstance(config, dict):
-            log.debug(msg_template.format(f"invalid config type `{type(config)}`, expected `dict`"))
-            raise RequestParameterInvalidException(
-                f"Invalid type for the required `config` variable; expected `dict` but received `{type(config)}`."
-            )
-        if authn_id:
-            try:
-                decoded_authn_id = self.decode_id(authn_id)
-            except MalformedId as e:
-                log.debug(msg_template.format(f"cannot decode authz_id `{authn_id}`"))
-                raise e
-
-            try:
-                trans.app.authnz_manager.can_user_assume_authn(trans, decoded_authn_id)
-            except Exception as e:
-                raise e
-
-        # No two authorization configuration with
-        # exact same key/value should exist.
-        for ca in trans.user.cloudauthz:
-            if ca.equals(trans.user.id, provider, authn_id, config):
-                log.debug(
-                    "Rejected user `%s`'s request to create cloud authorization because a similar config "
-                    "already exists.",
-                    trans.user.id,
-                )
-                raise ActionInputError("A similar cloud authorization configuration is already defined.")
-
-        try:
-            new_cloudauthz = self.cloudauthz_manager.create(
-                user_id=trans.user.id, provider=provider, config=config, authn_id=authn_id, description=description
-            )
-            view = self.cloudauthz_serializer.serialize_to_view(
-                new_cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, "summary")
-            )
-            log.debug(f"Created a new cloudauthz record for the user id `{str(trans.user.id)}` ")
-            return view
-        except Exception as e:
-            log.exception(msg_template.format("exception while creating the new cloudauthz record"))
-            raise InternalServerError(
-                "An unexpected error has occurred while responding to the create request of the "
-                "cloudauthz API." + unicodify(e)
-            )
-
-    @expose_api
-    def delete(self, trans, encoded_authz_id, **kwargs):
-        """
-        * DELETE /api/cloud/authz/{encoded_authz_id}
-            Deletes the CloudAuthz record with the given ``encoded_authz_id`` from database.
-
-        :type  trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans: Galaxy web transaction
-
-        :type  encoded_authz_id:    string
-        :param encoded_authz_id:    The encoded ID of the CloudAuthz record to be marked deleted.
-
-        :rtype  JSON
-        :return The cloudauthz record marked as deleted, serialized as a JSON object.
-        """
-
-        msg_template = f"Rejected user `{str(trans.user.id)}`'s request to delete cloudauthz config because of {{}}."
-        try:
-            authz_id = self.decode_id(encoded_authz_id)
-        except MalformedId as e:
-            log.debug(msg_template.format(f"cannot decode authz_id `{encoded_authz_id}`"))
-            raise e
-
-        try:
-            cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
-            trans.sa_session.delete(cloudauthz)
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            log.debug(f"Deleted a cloudauthz record with id `{authz_id}` for the user id `{str(trans.user.id)}` ")
-            view = self.cloudauthz_serializer.serialize_to_view(
-                cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, "summary")
-            )
-            trans.response.status = "200"
-            return view
-        except Exception as e:
-            log.exception(
-                msg_template.format(f"exception while deleting the cloudauthz record with ID: `{encoded_authz_id}`.")
-            )
-            raise InternalServerError(
-                "An unexpected error has occurred while responding to the DELETE request of the "
-                "cloudauthz API." + unicodify(e)
-            )
-
-    @expose_api
-    def update(self, trans, encoded_authz_id, payload, **kwargs):
-        """
-        PUT /api/cloud/authz/{encoded_authz_id}
-
-        Updates the values for the cloudauthz configuration with the given ``encoded_authz_id``.
-
-        With this API only the following attributes of a cloudauthz configuration
-        can be updated: `authn_id`, `provider`, `config`, `deleted`.
-
-        :type  trans:               galaxy.webapps.base.webapp.GalaxyWebTransaction
-        :param trans:               Galaxy web transaction
-
-        :type  encoded_authz_id:    string
-        :param encoded_authz_id:    The encoded ID of the CloudAuthz record to be updated.
-
-        :type payload:              dict
-        :param payload:             A dictionary structure containing the attributes to modified with their new values.
-                                    It can contain any number of the following attributes:
-
-                                        *   provider:   the cloud-based resource provider
-                                                        to which this configuration belongs to.
-
-                                        *   authn_id:   the (encoded) ID of a third-party authentication of a user.
-                                                        To have this ID, user must have logged-in to this Galaxy server
-                                                        using third-party identity (e.g., Google), or has associated
-                                                        their Galaxy account with a third-party OIDC-based identity.
-                                                        See this page: https://galaxyproject.org/authnz/config/
-
-                                                        Note: A user can associate a cloudauthz record with their own
-                                                        authentications only. If the given authentication with authn_id
-                                                        belongs to a different user, Galaxy will throw the
-                                                        ItemAccessibilityException exception.
-
-                                        *   config:     a dictionary containing all the configuration required to
-                                                        request temporary credentials from the provider.
-                                                        See the following page for details:
-                                                        https://galaxyproject.org/authnz/
-
-                                        *   deleted:    a boolean type marking the specified cloudauthz as (un)deleted.
-
-        """
-
-        msg_template = f"Rejected user `{str(trans.user.id)}`'s request to delete cloudauthz config because of {{}}."
-        try:
-            authz_id = self.decode_id(encoded_authz_id)
-        except MalformedId as e:
-            log.debug(msg_template.format(f"cannot decode authz_id `{encoded_authz_id}`"))
-            raise e
-
-        try:
-            cloudauthz_to_update = trans.app.authnz_manager.try_get_authz_config(
-                trans.sa_session, trans.user.id, authz_id
-            )
-            self.cloudauthz_deserializer.deserialize(cloudauthz_to_update, payload, trans=trans)
-            self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view="summary")
-            return self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view="summary")
-        except MalformedId as e:
-            raise e
-        except Exception as e:
-            log.exception(
-                msg_template.format(f"exception while updating the cloudauthz record with ID: `{encoded_authz_id}`.")
-            )
-            raise InternalServerError(
-                "An unexpected error has occurred while responding to the PUT request of the "
-                "cloudauthz API." + unicodify(e)
-            )
diff --git a/lib/galaxy/webapps/galaxy/api/common.py b/lib/galaxy/webapps/galaxy/api/common.py
index 4ba9cedbe53eec8ede1569243a393fd2db8330bb..5ade80943bf8e058e064403289a66f1c9bf1d18d 100644
--- a/lib/galaxy/webapps/galaxy/api/common.py
+++ b/lib/galaxy/webapps/galaxy/api/common.py
@@ -2,13 +2,13 @@
 
 from typing import (
     Any,
-    Dict,
     List,
     Optional,
     Set,
 )
 
 from fastapi import (
+    Body,
     Path,
     Query,
     Request,
@@ -21,7 +21,10 @@ from galaxy.schema import (
     ValueFilterQueryParams,
 )
 from galaxy.schema.fields import DecodedDatabaseIdField
-from galaxy.schema.schema import UpdateDatasetPermissionsPayload
+from galaxy.schema.schema import (
+    UpdateDatasetPermissionsPayload,
+    UpdateDatasetPermissionsPayloadAliases,
+)
 from galaxy.util import listify
 
 HistoryIDPathParam = Annotated[
@@ -66,6 +69,20 @@ RoleIDPathParam = Annotated[
     Path(..., title="Role ID", description="The ID of the role."),
 ]
 
+UpdateDatasetPermissionsBody = Annotated[
+    UpdateDatasetPermissionsPayloadAliases,
+    Body(
+        ...,
+        examples=[
+            UpdateDatasetPermissionsPayload(
+                action="set_permissions",
+                access_ids=[],
+                manage_ids=[],
+                modify_ids=[],
+            ).model_dump()
+        ],
+    ),
+]
 
 LibraryIdPathParam = Annotated[
     DecodedDatabaseIdField,
@@ -194,16 +211,23 @@ def get_filter_query_params(
     )
 
 
-def get_update_permission_payload(payload: Dict[str, Any]) -> UpdateDatasetPermissionsPayload:
-    """Converts the generic payload dictionary into a UpdateDatasetPermissionsPayload model with custom parsing.
-    This is an attempt on supporting multiple aliases for the permissions params."""
-    # There are several allowed names for the same role list parameter, i.e.: `access`, `access_ids`, `access_ids[]`
-    # The `access_ids[]` name is not pydantic friendly, so this will be modelled as an alias but we can only set one alias
+def normalize_permission_payload(
+    payload_aliases: UpdateDatasetPermissionsPayloadAliases,
+) -> UpdateDatasetPermissionsPayload:
+    """Normalize the payload by choosing the first non-None value for each field.
+
+    This is an attempt on supporting multiple aliases for the permissions params.
+    There are several allowed names for the same role list parameter, i.e.: `access`, `access_ids`, `access_ids[]`
+    """
     # TODO: Maybe we should choose only one way/naming and deprecate the others?
-    payload["access_ids"] = payload.get("access_ids[]") or payload.get("access")
-    payload["manage_ids"] = payload.get("manage_ids[]") or payload.get("manage")
-    payload["modify_ids"] = payload.get("modify_ids[]") or payload.get("modify")
-    update_payload = UpdateDatasetPermissionsPayload(**payload)
+    payload = payload_aliases.model_dump()
+    normalized_payload = {
+        "action": payload.get("action"),
+        "access_ids": payload.get("access_ids") or payload.get("access_ids[]") or payload.get("access"),
+        "manage_ids": payload.get("manage_ids") or payload.get("manage_ids[]") or payload.get("manage"),
+        "modify_ids": payload.get("modify_ids") or payload.get("modify_ids[]") or payload.get("modify"),
+    }
+    update_payload = UpdateDatasetPermissionsPayload.model_construct(**normalized_payload)
     return update_payload
 
 
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index 5ef027c3978c8b8c415fe33ceeb8b492dde5686f..cecabb6e3c1700a3a85df367a37d800512ba0abc 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -5,6 +5,8 @@ from fastapi import (
     Body,
     Path,
     Query,
+    Response,
+    status,
 )
 from typing_extensions import Annotated
 
@@ -68,6 +70,7 @@ class FastAPIDatasetCollections:
     @router.post(
         "/api/dataset_collections/{id}/copy",
         summary="Copy the given collection datasets to a new collection using a new `dbkey` attribute.",
+        status_code=status.HTTP_204_NO_CONTENT,
     )
     def copy(
         self,
@@ -76,6 +79,7 @@ class FastAPIDatasetCollections:
         payload: UpdateCollectionAttributePayload = Body(...),
     ):
         self.service.copy(trans, id, payload)
+        return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.get(
         "/api/dataset_collections/{id}/attributes",
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index 53006b4ee8c182dbd035deba3ab2a65c08a8c9a8..eba6795100fd2968ebc1b396c56af69a5c735442 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -9,9 +9,7 @@ from io import (
     StringIO,
 )
 from typing import (
-    Any,
     cast,
-    Dict,
     List,
     Optional,
 )
@@ -29,6 +27,7 @@ from starlette.responses import (
 )
 from typing_extensions import Annotated
 
+from galaxy.datatypes.dataproviders.base import MAX_LIMIT
 from galaxy.schema import (
     FilterQueryParams,
     SerializationParams,
@@ -40,7 +39,6 @@ from galaxy.schema.schema import (
     AsyncTaskResultSummary,
     DatasetAssociationRoles,
     DatasetSourceType,
-    UpdateDatasetPermissionsPayload,
 )
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.webapps.base.api import GalaxyFileResponse
@@ -52,10 +50,11 @@ from galaxy.webapps.galaxy.api import (
 from galaxy.webapps.galaxy.api.common import (
     get_filter_query_params,
     get_query_parameters_from_request_excluding,
-    get_update_permission_payload,
     HistoryDatasetIDPathParam,
     HistoryIDPathParam,
+    normalize_permission_payload,
     query_serialization_params,
+    UpdateDatasetPermissionsBody,
 )
 from galaxy.webapps.galaxy.services.datasets import (
     ComputeDatasetHashPayload,
@@ -145,6 +144,7 @@ class FastAPIDatasets:
     )
     def index(
         self,
+        response: Response,
         trans=DependsOnTrans,
         history_id: Optional[DecodedDatabaseIdField] = Query(
             default=None,
@@ -153,7 +153,9 @@ class FastAPIDatasets:
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
     ) -> List[AnyHistoryContentItem]:
-        return self.service.index(trans, history_id, serialization_params, filter_query_params)
+        entries, total_matches = self.service.index(trans, history_id, serialization_params, filter_query_params)
+        response.headers["total_matches"] = str(total_matches)
+        return entries
 
     @router.get(
         "/api/datasets/{dataset_id}/storage",
@@ -235,15 +237,11 @@ class FastAPIDatasets:
     def update_permissions(
         self,
         dataset_id: HistoryDatasetIDPathParam,
+        payload: UpdateDatasetPermissionsBody,
         trans=DependsOnTrans,
-        # Using a generic Dict here as an attempt on supporting multiple aliases for the permissions params.
-        payload: Dict[str, Any] = Body(
-            default=...,
-            examples=[UpdateDatasetPermissionsPayload()],
-        ),
     ) -> DatasetAssociationRoles:
         """Set permissions of the given history dataset to the given role ids."""
-        update_payload = get_update_permission_payload(payload)
+        update_payload = normalize_permission_payload(payload)
         return self.service.update_permissions(trans, dataset_id, update_payload)
 
     @router.get(
@@ -432,18 +430,35 @@ class FastAPIDatasets:
                 "may return different responses."
             ),
         ),
+        limit: Annotated[
+            Optional[int],
+            Query(
+                ge=1,
+                le=MAX_LIMIT,
+                description="Maximum number of items to return. Currently only applies to `data_type=raw_data` requests",
+            ),
+        ] = MAX_LIMIT,
+        offset: Annotated[
+            Optional[int],
+            Query(
+                ge=0,
+                description="Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item. Currently only applies to `data_type=raw_data` requests",
+            ),
+        ] = 0,
         serialization_params: SerializationParams = Depends(query_serialization_params),
     ):
         """
-        **Note**: Due to the multipurpose nature of this endpoint, which can receive a wild variety of parameters
+        **Note**: Due to the multipurpose nature of this endpoint, which can receive a wide variety of parameters
         and return different kinds of responses, the documentation here will be limited.
         To get more information please check the source code.
         """
-        exclude_params = {"hda_ldda", "data_type"}
+        exclude_params = {"hda_ldda", "data_type", "limit", "offset"}
         exclude_params.update(SerializationParams.model_fields.keys())
         extra_params = get_query_parameters_from_request_excluding(request, exclude_params)
 
-        return self.service.show(trans, dataset_id, hda_ldda, serialization_params, data_type, **extra_params)
+        return self.service.show(
+            trans, dataset_id, hda_ldda, serialization_params, data_type, limit=limit, offset=offset, **extra_params
+        )
 
     @router.get(
         "/api/datasets/{dataset_id}/content/{content_type}",
diff --git a/lib/galaxy/webapps/galaxy/api/file_sources.py b/lib/galaxy/webapps/galaxy/api/file_sources.py
index 957da9b54092b452e475a5ae35fdf32437d7649c..4546e7b88ebce1c5739beb76fd0ab631529d8418 100644
--- a/lib/galaxy/webapps/galaxy/api/file_sources.py
+++ b/lib/galaxy/webapps/galaxy/api/file_sources.py
@@ -15,10 +15,15 @@ from galaxy.managers.file_source_instances import (
     CreateInstancePayload,
     FileSourceInstancesManager,
     ModifyInstancePayload,
+    TestModifyInstancePayload,
     UserFileSourceModel,
 )
 from galaxy.model import User
-from galaxy.util.config_templates import PluginStatus
+from galaxy.util.config_templates import (
+    OAuth2Info,
+    PluginStatus,
+)
+from galaxy.work.context import SessionRequestContext
 from . import (
     depends,
     DependsOnTrans,
@@ -35,6 +40,14 @@ UserFileSourceIdPathParam: UUID4 = Path(
     ..., title="User File Source UUID", description="The UUID index for a persisted UserFileSourceStore object."
 )
 
+TemplateIdPathParam: str = Path(
+    ..., title="Template ID", description="The template ID of the target file source template."
+)
+
+TemplateVersionPathParam = Path(
+    ..., title="Template Version", description="The template version of the target file source template."
+)
+
 
 @router.cbv
 class FastAPIFileSources:
@@ -53,6 +66,19 @@ class FastAPIFileSources:
     ) -> FileSourceTemplateSummaries:
         return self.file_source_instances_manager.summaries
 
+    @router.get(
+        "/api/file_source_templates/{template_id}/{template_version}/oauth2",
+        response_description="OAuth2 authorization url to redirect user to prior to creation.",
+        operation_id="file_sources__template_oauth2",
+    )
+    def template_oauth2(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        template_id: str = TemplateIdPathParam,
+        template_version: int = TemplateVersionPathParam,
+    ) -> OAuth2Info:
+        return self.file_source_instances_manager.template_oauth2(trans, template_id, template_version)
+
     @router.post(
         "/api/file_source_instances",
         summary="Create a user-bound file source.",
@@ -89,32 +115,57 @@ class FastAPIFileSources:
         return self.file_source_instances_manager.index(trans)
 
     @router.get(
-        "/api/file_source_instances/{user_file_source_id}",
+        "/api/file_source_instances/{uuid}",
         summary="Get a persisted user file source instance.",
         operation_id="file_sources__instances_get",
     )
     def instances_show(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
+        uuid: UUID4 = UserFileSourceIdPathParam,
     ) -> UserFileSourceModel:
-        return self.file_source_instances_manager.show(trans, user_file_source_id)
+        return self.file_source_instances_manager.show(trans, uuid)
+
+    @router.get(
+        "/api/file_source_instances/{uuid}/test",
+        summary="Test a file source instance and return status.",
+        operation_id="file_sources__instances_test_instance",
+    )
+    def instance_test(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        uuid: UUID4 = UserFileSourceIdPathParam,
+    ) -> PluginStatus:
+        return self.file_source_instances_manager.plugin_status_for_instance(trans, uuid)
 
     @router.put(
-        "/api/file_source_instances/{user_file_source_id}",
+        "/api/file_source_instances/{uuid}",
         summary="Update or upgrade user file source instance.",
         operation_id="file_sources__instances_update",
     )
     def update_instance(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
+        uuid: UUID4 = UserFileSourceIdPathParam,
         payload: ModifyInstancePayload = Body(...),
     ) -> UserFileSourceModel:
-        return self.file_source_instances_manager.modify_instance(trans, user_file_source_id, payload)
+        return self.file_source_instances_manager.modify_instance(trans, uuid, payload)
+
+    @router.post(
+        "/api/file_source_instances/{uuid}/test",
+        summary="Test updating or upgrading user file source instance.",
+        operation_id="file_sources__test_instances_update",
+    )
+    def test_update_instance(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        uuid: UUID4 = UserFileSourceIdPathParam,
+        payload: TestModifyInstancePayload = Body(...),
+    ) -> PluginStatus:
+        return self.file_source_instances_manager.test_modify_instance(trans, uuid, payload)
 
     @router.delete(
-        "/api/file_source_instances/{user_file_source_id}",
+        "/api/file_source_instances/{uuid}",
         summary="Purge user file source instance.",
         operation_id="file_sources__instances_purge",
         status_code=status.HTTP_204_NO_CONTENT,
@@ -122,7 +173,7 @@ class FastAPIFileSources:
     def purge_instance(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        user_file_source_id: UUID4 = UserFileSourceIdPathParam,
+        uuid: UUID4 = UserFileSourceIdPathParam,
     ):
-        self.file_source_instances_manager.purge_instance(trans, user_file_source_id)
+        self.file_source_instances_manager.purge_instance(trans, uuid)
         return Response(status_code=status.HTTP_204_NO_CONTENT)
diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py
index 4c215ed1cdaf9445e313f8ae153c0fa893c73108..c954ecf00d1b7a1d17027d9af05ef55f28e72861 100644
--- a/lib/galaxy/webapps/galaxy/api/group_roles.py
+++ b/lib/galaxy/webapps/galaxy/api/group_roles.py
@@ -3,9 +3,11 @@ API operations on Group objects.
 """
 
 import logging
+from typing import Optional
 
 from galaxy.managers.context import ProvidesAppContext
 from galaxy.managers.group_roles import GroupRolesManager
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.schema.fields import Security
 from galaxy.schema.schema import (
     GroupRoleListResponse,
@@ -26,11 +28,12 @@ log = logging.getLogger(__name__)
 router = Router(tags=["group_roles"])
 
 
-def group_role_to_model(trans, group_id: int, role) -> GroupRoleResponse:
+def group_role_to_model(trans, group_id: int, role, displayed_name: Optional[str] = None) -> GroupRoleResponse:
     encoded_group_id = Security.security.encode_id(group_id)
     encoded_role_id = Security.security.encode_id(role.id)
     url = trans.url_builder("group_role", group_id=encoded_group_id, role_id=encoded_role_id)
-    return GroupRoleResponse(id=role.id, name=role.name, url=url)
+    displayed_name = displayed_name or role.name
+    return GroupRoleResponse(id=role.id, name=displayed_name, url=url)
 
 
 @router.cbv
@@ -49,7 +52,13 @@ class FastAPIGroupRoles:
         trans: ProvidesAppContext = DependsOnTrans,
     ) -> GroupRoleListResponse:
         group_roles = self.manager.index(trans, group_id)
-        return GroupRoleListResponse(root=[group_role_to_model(trans, group_id, gr.role) for gr in group_roles])
+        private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+        data = []
+        for group in group_roles:
+            role = group.role
+            displayed_name = private_role_emails.get(role.id, role.name)
+            data.append(group_role_to_model(trans, group_id, role, displayed_name))
+        return GroupRoleListResponse(root=data)
 
     @router.get(
         "/api/groups/{group_id}/roles/{role_id}",
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 067dd425369a2b8e31299454bbc52d632ec22d87..57b18c1f1c179131080d1a76bde3f15f640cd92b 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -8,6 +8,7 @@ import logging
 from typing import (
     Any,
     List,
+    Literal,
     Optional,
     Union,
 )
@@ -33,7 +34,10 @@ from galaxy.schema import (
     FilterQueryParams,
     SerializationParams,
 )
-from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.fields import (
+    AcceptHeaderValidator,
+    DecodedDatabaseIdField,
+)
 from galaxy.schema.history import (
     HistoryIndexQueryPayload,
     HistorySortByEnum,
@@ -57,6 +61,7 @@ from galaxy.schema.schema import (
     ShareWithPayload,
     SharingStatus,
     StoreExportPayload,
+    UpdateHistoryPayload,
     WriteStoreToPayload,
 )
 from galaxy.schema.types import LatestLiteral
@@ -162,6 +167,16 @@ class CreateHistoryFormData(CreateHistoryPayload):
     """Uses Form data instead of JSON"""
 
 
+IndexExportsAcceptHeader = Annotated[
+    Literal[
+        "application/json",
+        "application/vnd.galaxy.task.export+json",
+    ],
+    AcceptHeaderValidator,
+    Header(description="Accept header to determine the response format. Default is 'application/json'."),
+]
+
+
 @router.cbv
 class FastAPIHistories:
     service: HistoriesService = depends(HistoriesService)
@@ -271,6 +286,7 @@ class FastAPIHistories:
     @router.get(
         "/api/histories/archived",
         summary="Get a list of all archived histories for the current user.",
+        response_model_exclude_unset=True,
     )
     def get_archived_histories(
         self,
@@ -457,13 +473,14 @@ class FastAPIHistories:
         self,
         history_id: HistoryIDPathParam,
         trans: ProvidesHistoryContext = DependsOnTrans,
-        payload: Any = Body(
+        payload: UpdateHistoryPayload = Body(
             ...,
             description="Object containing any of the editable fields of the history.",
         ),
         serialization_params: SerializationParams = Depends(query_serialization_params),
     ) -> AnyHistoryView:
-        return self.service.update(trans, history_id, payload, serialization_params)
+        data = payload.model_dump(exclude_unset=True)
+        return self.service.update(trans, history_id, data, serialization_params)
 
     @router.post(
         "/api/histories/from_store",
@@ -513,7 +530,7 @@ class FastAPIHistories:
         trans: ProvidesHistoryContext = DependsOnTrans,
         limit: Optional[int] = LimitQueryParam,
         offset: Optional[int] = OffsetQueryParam,
-        accept: str = Header(default="application/json", include_in_schema=False),
+        accept: IndexExportsAcceptHeader = "application/json",
     ) -> Union[JobExportHistoryArchiveListResponse, ExportTaskListResponse]:
         """
         By default the legacy job-based history exports (jeha) are returned.
@@ -613,6 +630,7 @@ class FastAPIHistories:
     @router.post(
         "/api/histories/{history_id}/archive",
         summary="Archive a history.",
+        response_model_exclude_unset=True,
     )
     def archive_history(
         self,
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 052ea3a2e465950da2459e78cfe205dde452e965..2386807211baa4f5ad416ebc20454cdc80fc1f2d 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -4,10 +4,10 @@ API operations on the contents of a history.
 
 import logging
 from typing import (
-    Any,
-    Dict,
     List,
+    Literal,
     Optional,
+    Set,
     Union,
 )
 
@@ -24,6 +24,7 @@ from starlette.responses import (
     Response,
     StreamingResponse,
 )
+from typing_extensions import Annotated
 
 from galaxy import util
 from galaxy.managers.context import ProvidesHistoryContext
@@ -32,7 +33,10 @@ from galaxy.schema import (
     SerializationParams,
     ValueFilterQueryParams,
 )
-from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.fields import (
+    AcceptHeaderValidator,
+    DecodedDatabaseIdField,
+)
 from galaxy.schema.schema import (
     AnyHistoryContentItem,
     AnyJobStateSummary,
@@ -51,7 +55,6 @@ from galaxy.schema.schema import (
     MaterializeDatasetInstanceAPIRequest,
     MaterializeDatasetInstanceRequest,
     StoreExportPayload,
-    UpdateDatasetPermissionsPayload,
     UpdateHistoryContentsBatchPayload,
     UpdateHistoryContentsPayload,
     WriteStoreToPayload,
@@ -64,12 +67,13 @@ from galaxy.webapps.galaxy.api import (
 )
 from galaxy.webapps.galaxy.api.common import (
     get_filter_query_params,
-    get_update_permission_payload,
     get_value_filter_query_params,
     HistoryHDCAIDPathParam,
     HistoryIDPathParam,
     HistoryItemIDPathParam,
+    normalize_permission_payload,
     query_serialization_params,
+    UpdateDatasetPermissionsBody,
 )
 from galaxy.webapps.galaxy.services.history_contents import (
     CreateHistoryContentFromStore,
@@ -332,11 +336,10 @@ def parse_content_types(types: Union[List[str], str]) -> List[HistoryContentType
 def parse_dataset_details(details: Optional[str]):
     """Parses the different values that the `dataset_details` parameter
     can have from a string."""
-    dataset_details = None
     if details is not None and details != "all":
-        dataset_details = set(util.listify(details))
+        dataset_details: Union[None, Set[str], str] = set(util.listify(details))
     else:  # either None or 'all'
-        dataset_details = details  # type: ignore
+        dataset_details = details
     return dataset_details
 
 
@@ -376,6 +379,32 @@ def parse_index_jobs_summary_params(
     return HistoryContentsIndexJobsSummaryParams(ids=util.listify(ids), types=util.listify(types))
 
 
+HistoryIndexAcceptContentTypes = Annotated[
+    Literal[
+        "application/json",
+        "application/vnd.galaxy.history.contents.stats+json",
+    ],
+    AcceptHeaderValidator,
+    Header(description="Accept header to determine the response format. Default is 'application/json'."),
+]
+
+HistoryIndexResponsesSchema = {
+    200: {
+        "description": ("The contents of the history that match the query."),
+        "content": {
+            "application/json": {
+                "schema": {"$ref": "#/components/schemas/HistoryContentsResult"},  # HistoryContentsResult.schema(),
+            },
+            HistoryContentsWithStatsResult.__accept_type__: {
+                "schema": {  # HistoryContentsWithStatsResult.schema(),
+                    "$ref": "#/components/schemas/HistoryContentsWithStatsResult"
+                },
+            },
+        },
+    },
+}
+
+
 @router.cbv
 class FastAPIHistoryContents:
     service: HistoriesContentsService = depends(HistoriesContentsService)
@@ -383,6 +412,7 @@ class FastAPIHistoryContents:
     @router.get(
         "/api/histories/{history_id}/contents/{type}s",
         summary="Returns the contents of the given history filtered by type.",
+        responses=HistoryIndexResponsesSchema,
         operation_id="history_contents__index_typed",
         response_model_exclude_unset=True,
     )
@@ -395,7 +425,7 @@ class FastAPIHistoryContents:
         legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
-        accept: str = Header(default="application/json", include_in_schema=False),
+        accept: HistoryIndexAcceptContentTypes = "application/json",
     ) -> Union[HistoryContentsResult, HistoryContentsWithStatsResult]:
         """
         Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
@@ -421,23 +451,7 @@ class FastAPIHistoryContents:
         "/api/histories/{history_id}/contents",
         name="history_contents",
         summary="Returns the contents of the given history.",
-        responses={
-            200: {
-                "description": ("The contents of the history that match the query."),
-                "content": {
-                    "application/json": {
-                        "schema": {  # HistoryContentsResult.schema(),
-                            "$ref": "#/components/schemas/HistoryContentsResult"
-                        },
-                    },
-                    HistoryContentsWithStatsResult.__accept_type__: {
-                        "schema": {  # HistoryContentsWithStatsResult.schema(),
-                            "$ref": "#/components/schemas/HistoryContentsWithStatsResult"
-                        },
-                    },
-                },
-            },
-        },
+        responses=HistoryIndexResponsesSchema,
         operation_id="history_contents__index",
         response_model_exclude_unset=True,
     )
@@ -450,7 +464,7 @@ class FastAPIHistoryContents:
         legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
-        accept: str = Header(default="application/json", include_in_schema=False),
+        accept: HistoryIndexAcceptContentTypes = "application/json",
     ) -> Union[HistoryContentsResult, HistoryContentsWithStatsResult]:
         """
         Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
@@ -727,15 +741,11 @@ class FastAPIHistoryContents:
         self,
         history_id: HistoryIDPathParam,
         dataset_id: HistoryItemIDPathParam,
+        payload: UpdateDatasetPermissionsBody,
         trans: ProvidesHistoryContext = DependsOnTrans,
-        # Using a generic Dict here as an attempt on supporting multiple aliases for the permissions params.
-        payload: Dict[str, Any] = Body(
-            default=...,
-            examples=[UpdateDatasetPermissionsPayload().model_dump()],
-        ),
     ) -> DatasetAssociationRoles:
         """Set permissions of the given history dataset to the given role ids."""
-        update_payload = get_update_permission_payload(payload)
+        update_payload = normalize_permission_payload(payload)
         return self.service.update_permissions(trans, dataset_id, update_payload)
 
     @router.put(
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index 68cb821e6a69aa250a7c3e6e199163962cba6a83..3d02ccfcf7bec38702ca76c3d4edde85a5f9bdaa 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -133,9 +133,9 @@ class JobFilesAPIController(BaseGalaxyAPIController):
         target_dir = os.path.dirname(path)
         util.safe_makedirs(target_dir)
         try:
-            if os.path.exists(path):
-                with open(path, "ab") as dest:
-                    shutil.copyfileobj(open(input_file.name, "rb"), dest)
+            if os.path.exists(path) and (path.endswith("tool_stdout") or path.endswith("tool_stderr")):
+                with open(path, "ab") as destination:
+                    shutil.copyfileobj(open(input_file.name, "rb"), destination)
             else:
                 shutil.move(input_file.name, path)
         finally:
diff --git a/lib/galaxy/webapps/galaxy/api/job_tokens.py b/lib/galaxy/webapps/galaxy/api/job_tokens.py
index fa2e3d6b05da7205bf78493d2b8b9a03d1cf65d9..8916ee16ae967830fa070289a35ccac70d9d3fe8 100644
--- a/lib/galaxy/webapps/galaxy/api/job_tokens.py
+++ b/lib/galaxy/webapps/galaxy/api/job_tokens.py
@@ -48,6 +48,7 @@ class FastAPIJobTokens:
         trans: ProvidesAppContext = DependsOnTrans,
     ) -> str:
         job = self.__authorize_job_access(trans, job_id, job_key)
+        trans.app.authnz_manager.refresh_expiring_oidc_tokens(trans, job.user)  # type: ignore[attr-defined]
         tokens = job.user.get_oidc_tokens(provider_name_to_backend(provider))
         return tokens["id"]
 
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index 98f1a43c1067c2d5ca18ec7265d2ba04e24d2224..806957f02e1f382d8b35535bb70b675c212e43fd 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -72,7 +72,7 @@ from galaxy.webapps.galaxy.services.jobs import (
     JobIndexViewEnum,
     JobsService,
 )
-from galaxy.work.context import WorkRequestContext
+from galaxy.work.context import proxy_work_context_for_history
 
 log = logging.getLogger(__name__)
 
@@ -373,7 +373,7 @@ class FastAPIJobs:
     @router.get(
         "/api/jobs/{job_id}/console_output",
         name="get_console_output",
-        summary="Returns STDOUT and STDERR from job.",
+        summary="Returns STDOUT and STDERR from the tool running in a specific job.",
     )
     def console_output(
         self,
@@ -385,7 +385,7 @@ class FastAPIJobs:
         trans: ProvidesUserContext = DependsOnTrans,
     ) -> JobConsoleOutput:
         """
-        Get the stdout and/or stderr of a job. The position parameters are the index
+        Get the stdout and/or stderr from the tool running in a specific job. The position parameters are the index
         of where to start reading stdout/stderr. The length parameters control how much
         stdout/stderr is read.
         """
@@ -490,9 +490,9 @@ class FastAPIJobs:
         summary="Finished a job regardless of execution status (ie early job finish)",
     )
     def finish(
-        self,
-        job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],
-        trans: ProvidesUserContext = DependsOnTrans,
+            self,
+            job_id: Annotated[DecodedDatabaseIdField, JobIdPathParam],
+            trans: ProvidesUserContext = DependsOnTrans,
     ) -> bool:
         job = self.service.get_job(trans=trans, job_id=job_id)
         if not job:
@@ -527,10 +527,8 @@ class FastAPIJobs:
         for k, v in payload.__annotations__.items():
             if k.startswith("files_") or k.startswith("__files_"):
                 inputs[k] = v
-        request_context = WorkRequestContext(app=trans.app, user=trans.user, history=trans.history)
-        all_params, all_errors, _, _ = tool.expand_incoming(
-            trans=trans, incoming=inputs, request_context=request_context
-        )
+        request_context = proxy_work_context_for_history(trans)
+        all_params, all_errors, _, _ = tool.expand_incoming(request_context, incoming=inputs)
         if any(all_errors):
             return []
         params_dump = [tool.params_to_strings(param, trans.app, nested=True) for param in all_params]
diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py
index dc3c5e120f342958040ac7bc8b872f6a4b953f4e..0a1c84d097d2410ac375fd521817b2089c6efd67 100644
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -3,506 +3,164 @@ API operations on the contents of a data library.
 """
 
 import logging
-from typing import Optional
+from typing import (
+    cast,
+    List,
+    Optional,
+)
+
+from fastapi import (
+    Body,
+    Depends,
+    Request,
+    UploadFile,
+)
+from starlette.datastructures import UploadFile as StarletteUploadFile
 
-from galaxy import (
-    exceptions,
-    managers,
-    util,
+from galaxy.managers.context import (
+    ProvidesHistoryContext,
+    ProvidesUserContext,
 )
-from galaxy.actions.library import (
-    LibraryActions,
-    validate_path_upload,
+from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.library_contents import (
+    AnyLibraryContentsCreatePayload,
+    AnyLibraryContentsCreateResponse,
+    AnyLibraryContentsShowResponse,
+    LibraryContentsDeletePayload,
+    LibraryContentsDeleteResponse,
+    LibraryContentsFileCreatePayload,
+    LibraryContentsIndexListResponse,
 )
-from galaxy.managers.collections_util import (
-    api_payload_to_create_params,
-    dictify_dataset_collection_instance,
+from galaxy.webapps.galaxy.api import (
+    depends,
+    DependsOnTrans,
+    Router,
 )
-from galaxy.model import (
-    ExtendedMetadata,
-    ExtendedMetadataIndex,
-    Library,
-    LibraryDataset,
-    LibraryFolder,
-    tags,
+from galaxy.webapps.galaxy.services.library_contents import (
+    LibraryContentsService,
+    MaybeLibraryFolderOrDatasetID,
 )
-from galaxy.model.base import transaction
-from galaxy.structured_app import StructuredApp
-from galaxy.web import expose_api
-from galaxy.webapps.base.controller import (
-    HTTPBadRequest,
-    url_for,
-    UsesFormDefinitionsMixin,
-    UsesLibraryMixinItems,
+from . import (
+    APIContentTypeRoute,
+    as_form,
 )
-from galaxy.webapps.galaxy.api import BaseGalaxyAPIController
 
 log = logging.getLogger(__name__)
 
-
-class LibraryContentsController(
-    BaseGalaxyAPIController, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions
-):
-    def __init__(self, app: StructuredApp, hda_manager: managers.hdas.HDAManager):
-        super().__init__(app)
-        self.hda_manager = hda_manager
-
-    @expose_api
-    def index(self, trans, library_id, **kwd):
-        """
-        GET /api/libraries/{library_id}/contents:
-
-        Return a list of library files and folders.
-
-        .. note:: This endpoint is slow for large libraries. Returns all content traversing recursively through all folders.
-        .. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a faster non-recursive solution
-
-        :param  library_id: the encoded id of the library
-        :type   library_id: str
-
-        :returns:   list of dictionaries of the form:
-
-            * id:   the encoded id of the library item
-            * name: the 'library path'
-                or relationship of the library item to the root
-            * type: 'file' or 'folder'
-            * url:  the url to get detailed information on the library item
-
-        :rtype:     list
-
-        :raises:  MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError
-        """
-        rval = []
-        current_user_roles = trans.get_current_user_roles()
-
-        def traverse(folder):
-            admin = trans.user_is_admin
-            rval = []
-            for subfolder in folder.active_folders:
-                if not admin:
-                    can_access, folder_ids = trans.app.security_agent.check_folder_contents(
-                        trans.user, current_user_roles, subfolder
-                    )
-                if (admin or can_access) and not subfolder.deleted:
-                    subfolder.api_path = f"{folder.api_path}/{subfolder.name}"
-                    subfolder.api_type = "folder"
-                    rval.append(subfolder)
-                    rval.extend(traverse(subfolder))
-            for ld in folder.datasets:
-                if not admin:
-                    can_access = trans.app.security_agent.can_access_dataset(
-                        current_user_roles, ld.library_dataset_dataset_association.dataset
-                    )
-                if (admin or can_access) and not ld.deleted:
-                    ld.api_path = f"{folder.api_path}/{ld.name}"
-                    ld.api_type = "file"
-                    rval.append(ld)
-            return rval
-
-        library = trans.sa_session.get(Library, self.decode_id(library_id))
-        if not library:
-            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
-        if not (trans.user_is_admin or trans.app.security_agent.can_access_library(current_user_roles, library)):
-            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
-        encoded_id = f"F{trans.security.encode_id(library.root_folder.id)}"
-        # appending root folder
-        rval.append(
-            dict(
-                id=encoded_id,
-                type="folder",
-                name="/",
-                url=url_for("library_content", library_id=library_id, id=encoded_id),
-            )
-        )
-        library.root_folder.api_path = ""
-        # appending all other items in the library recursively
-        for content in traverse(library.root_folder):
-            encoded_id = trans.security.encode_id(content.id)
-            if content.api_type == "folder":
-                encoded_id = f"F{encoded_id}"
-            rval.append(
-                dict(
-                    id=encoded_id,
-                    type=content.api_type,
-                    name=content.api_path,
-                    url=url_for(
-                        "library_content",
-                        library_id=library_id,
-                        id=encoded_id,
-                    ),
-                )
-            )
-        return rval
-
-    @expose_api
-    def show(self, trans, id, library_id, **kwd):
-        """
-        GET /api/libraries/{library_id}/contents/{id}
-
-        Returns information about library file or folder.
-
-        :param  id:         the encoded id of the library item to return
-        :type   id:         str
-
-        :param  library_id: the encoded id of the library that contains this item
-        :type   library_id: str
-
-        :returns:   detailed library item information
-        :rtype:     dict
-
-        .. seealso::
-            :func:`galaxy.model.LibraryDataset.to_dict` and
-            :attr:`galaxy.model.LibraryFolder.dict_element_visible_keys`
-        """
-        class_name, content_id = self._decode_library_content_id(id)
-        if class_name == "LibraryFolder":
-            content = self.get_library_folder(trans, content_id, check_ownership=False, check_accessible=True)
-            rval = content.to_dict(view="element", value_mapper={"id": trans.security.encode_id})
-            rval["id"] = f"F{str(rval['id'])}"
-            if rval["parent_id"] is not None:  # This can happen for root folders.
-                rval["parent_id"] = f"F{str(trans.security.encode_id(rval['parent_id']))}"
-            rval["parent_library_id"] = trans.security.encode_id(rval["parent_library_id"])
-        else:
-            content = self.get_library_dataset(trans, content_id, check_ownership=False, check_accessible=True)
-            rval = content.to_dict(view="element")
-            rval["id"] = trans.security.encode_id(rval["id"])
-            rval["ldda_id"] = trans.security.encode_id(rval["ldda_id"])
-            rval["folder_id"] = f"F{str(trans.security.encode_id(rval['folder_id']))}"
-            rval["parent_library_id"] = trans.security.encode_id(rval["parent_library_id"])
-
-            tag_manager = tags.GalaxyTagHandler(trans.sa_session)
-            rval["tags"] = tag_manager.get_tags_list(content.library_dataset_dataset_association.tags)
-        return rval
-
-    @expose_api
-    def create(self, trans, library_id, payload, **kwd):
-        """
-        POST /api/libraries/{library_id}/contents:
-
-        Create a new library file or folder.
-
-        To copy an HDA into a library send ``create_type`` of 'file' and
-        the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_message``).
-
-        To copy an HDCA into a library send ``create_type`` of 'file' and
-        the HDCA's encoded id in ``from_hdca_id`` (and optionally ``ldda_message``).
-
-        :type   library_id: str
-        :param  library_id: the encoded id of the library where to create the new item
-        :type   payload:    dict
-        :param  payload:    dictionary structure containing:
-
-            * folder_id:    the encoded id of the parent folder of the new item
-            * create_type:  the type of item to create ('file', 'folder' or 'collection')
-            * from_hda_id:  (optional, only if create_type is 'file') the
-                encoded id of an accessible HDA to copy into the library
-            * ldda_message: (optional) the new message attribute of the LDDA created
-            * extended_metadata: (optional) sub-dictionary containing any extended
-                metadata to associate with the item
-            * upload_option: (optional) one of 'upload_file' (default), 'upload_directory' or 'upload_paths'
-            * server_dir: (optional, only if upload_option is
-                'upload_directory') relative path of the subdirectory of Galaxy
-                ``library_import_dir`` (if admin) or ``user_library_import_dir``
-                (if non-admin) to upload. All and only the files (i.e.
-                no subdirectories) contained in the specified directory will be
-                uploaded.
-            * filesystem_paths: (optional, only if upload_option is
-                'upload_paths' and the user is an admin) file paths on the
-                Galaxy server to upload to the library, one file per line
-            * link_data_only: (optional, only when upload_option is
-                'upload_directory' or 'upload_paths') either 'copy_files'
-                (default) or 'link_to_files'. Setting to 'link_to_files'
-                symlinks instead of copying the files
-            * name: (optional, only if create_type is 'folder') name of the
-                folder to create
-            * description: (optional, only if create_type is 'folder')
-                description of the folder to create
-            * tag_using_filenames: (optional)
-                create tags on datasets using the file's original name
-            * tags: (optional)
-                create the given list of tags on datasets
-
-        :returns:   a dictionary describing the new item unless ``from_hdca_id`` is supplied,
-                    in that case a list of such dictionaries is returned.
-        :rtype:     object
-        """
-        if trans.user_is_bootstrap_admin:
-            raise exceptions.RealUserRequiredException("Only real users can create a new library file or folder.")
-        if "create_type" not in payload:
-            raise exceptions.RequestParameterMissingException("Missing required 'create_type' parameter.")
-        create_type = payload.pop("create_type")
-        if create_type not in ("file", "folder", "collection"):
-            raise exceptions.RequestParameterInvalidException(
-                f"Invalid value for 'create_type' parameter ( {create_type} ) specified."
-            )
-        if "upload_option" in payload and payload["upload_option"] not in (
-            "upload_file",
-            "upload_directory",
-            "upload_paths",
-        ):
-            raise exceptions.RequestParameterInvalidException(
-                f"Invalid value for 'upload_option' parameter ( {payload['upload_option']} ) specified."
-            )
-        if "folder_id" not in payload:
-            raise exceptions.RequestParameterMissingException("Missing required 'folder_id' parameter.")
-        folder_id = payload.pop("folder_id")
-        _, folder_id = self._decode_library_content_id(folder_id)
-        folder_id = trans.security.decode_id(folder_id)
-        # security is checked in the downstream controller
-        parent = self.get_library_folder(trans, folder_id, check_ownership=False, check_accessible=False)
-        # The rest of the security happens in the library_common controller.
-
-        payload["tag_using_filenames"] = util.string_as_bool(payload.get("tag_using_filenames", None))
-        payload["tags"] = util.listify(payload.get("tags", None))
-
-        # are we copying an HDA to the library folder?
-        #   we'll need the id and any message to attach, then branch to that private function
-        from_hda_id, from_hdca_id, ldda_message = (
-            payload.pop("from_hda_id", None),
-            payload.pop("from_hdca_id", None),
-            payload.pop("ldda_message", ""),
-        )
-        if create_type == "file":
-            if from_hda_id:
-                return self._copy_hda_to_library_folder(
-                    trans, self.hda_manager, self.decode_id(from_hda_id), folder_id, ldda_message
-                )
-            if from_hdca_id:
-                return self._copy_hdca_to_library_folder(
-                    trans, self.hda_manager, self.decode_id(from_hdca_id), folder_id, ldda_message
-                )
-
-        # check for extended metadata, store it and pop it out of the param
-        # otherwise sanitize_param will have a fit
-        ex_meta_payload = payload.pop("extended_metadata", None)
-
-        # Now create the desired content object, either file or folder.
-        if create_type == "file":
-            status, output = self._upload_library_dataset(trans, folder_id, **payload)
-        elif create_type == "folder":
-            status, output = self._create_folder(trans, folder_id, **payload)
-        elif create_type == "collection":
-            # Not delegating to library_common, so need to check access to parent
-            # folder here.
-            self.check_user_can_add_to_library_item(trans, parent, check_accessible=True)
-            create_params = api_payload_to_create_params(payload)
-            create_params["parent"] = parent
-            dataset_collection_manager = trans.app.dataset_collection_manager
-            dataset_collection_instance = dataset_collection_manager.create(**create_params)
-            return [
-                dictify_dataset_collection_instance(
-                    dataset_collection_instance, security=trans.security, url_builder=trans.url_builder, parent=parent
-                )
-            ]
-        if status != 200:
-            trans.response.status = status
-            return output
-        else:
-            rval = []
-            for v in output.values():
-                if ex_meta_payload is not None:
-                    # If there is extended metadata, store it, attach it to the dataset, and index it
-                    ex_meta = ExtendedMetadata(ex_meta_payload)
-                    trans.sa_session.add(ex_meta)
-                    v.extended_metadata = ex_meta
-                    trans.sa_session.add(v)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
-                    for path, value in self._scan_json_block(ex_meta_payload):
-                        meta_i = ExtendedMetadataIndex(ex_meta, path, value)
-                        trans.sa_session.add(meta_i)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
-                if isinstance(v, trans.app.model.LibraryDatasetDatasetAssociation):
-                    v = v.library_dataset
-                encoded_id = trans.security.encode_id(v.id)
-                if create_type == "folder":
-                    encoded_id = f"F{encoded_id}"
-                rval.append(
-                    dict(
-                        id=encoded_id, name=v.name, url=url_for("library_content", library_id=library_id, id=encoded_id)
-                    )
-                )
-            return rval
-
-    def _upload_library_dataset(self, trans, folder_id: int, **kwd):
-        replace_dataset: Optional[LibraryDataset] = None
-        upload_option = kwd.get("upload_option", "upload_file")
-        dbkey = kwd.get("dbkey", "?")
-        if isinstance(dbkey, list):
-            last_used_build = dbkey[0]
-        else:
-            last_used_build = dbkey
-        is_admin = trans.user_is_admin
-        current_user_roles = trans.get_current_user_roles()
-        folder = trans.sa_session.get(LibraryFolder, folder_id)
-        self._check_access(trans, is_admin, folder, current_user_roles)
-        self._check_add(trans, is_admin, folder, current_user_roles)
-        library = folder.parent_library
-        if folder and last_used_build in ["None", None, "?"]:
-            last_used_build = folder.genome_build
-        error = False
-        if upload_option == "upload_paths":
-            validate_path_upload(trans)  # Duplicate check made in _upload_dataset.
-        elif roles := kwd.get("roles", ""):
-            # Check to see if the user selected roles to associate with the DATASET_ACCESS permission
-            # on the dataset that would cause accessibility issues.
-            vars = dict(DATASET_ACCESS_in=roles)
-            permissions, in_roles, error, message = trans.app.security_agent.derive_roles_from_access(
-                trans, library.id, "api", library=True, **vars
-            )
-        if error:
-            return 400, message
-        else:
-            created_outputs_dict = self._upload_dataset(
-                trans, folder_id=folder.id, replace_dataset=replace_dataset, **kwd
-            )
-            if created_outputs_dict:
-                if isinstance(created_outputs_dict, str):
-                    return 400, created_outputs_dict
-                elif isinstance(created_outputs_dict, tuple):
-                    return created_outputs_dict[0], created_outputs_dict[1]
-                return 200, created_outputs_dict
-            else:
-                return 400, "Upload failed"
-
-    def _scan_json_block(self, meta, prefix=""):
-        """
-        Scan a json style data structure, and emit all fields and their values.
-        Example paths
-
-        Data
-        { "data" : [ 1, 2, 3 ] }
-
-        Path:
-        /data == [1,2,3]
-
-        /data/[0] == 1
-
-        """
-        if isinstance(meta, dict):
-            for a in meta:
-                yield from self._scan_json_block(meta[a], f"{prefix}/{a}")
-        elif isinstance(meta, list):
-            for i, a in enumerate(meta):
-                yield from self._scan_json_block(a, prefix + "[%d]" % (i))
-        else:
-            # BUG: Everything is cast to string, which can lead to false positives
-            # for cross type comparisions, ie "True" == True
-            yield prefix, (f"{meta}").encode()
-
-    @expose_api
-    def update(self, trans, id, library_id, payload, **kwd):
-        """
-        PUT /api/libraries/{library_id}/contents/{id}
-
-        Create an ImplicitlyConvertedDatasetAssociation.
-
-        .. seealso:: :class:`galaxy.model.ImplicitlyConvertedDatasetAssociation`
-
-        :type   id:         str
-        :param  id:         the encoded id of the library item to return
-        :type   library_id: str
-        :param  library_id: the encoded id of the library that contains this item
-        :type   payload:    dict
-        :param  payload:    dictionary structure containing::
-            'converted_dataset_id':
-
-        :rtype:     None
-        :returns:   None
-        """
-        if "converted_dataset_id" in payload:
-            converted_id = payload.pop("converted_dataset_id")
-            content = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=False)
-            content_conv = self.get_library_dataset(trans, converted_id, check_ownership=False, check_accessible=False)
-            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
-                parent=content.library_dataset_dataset_association,
-                dataset=content_conv.library_dataset_dataset_association,
-                file_type=content_conv.library_dataset_dataset_association.extension,
-                metadata_safe=True,
-            )
-            trans.sa_session.add(assoc)
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-
-    def _decode_library_content_id(self, content_id):
-        if len(content_id) % 16 == 0:
-            return "LibraryDataset", content_id
-        elif content_id.startswith("F"):
-            return "LibraryFolder", content_id[1:]
-        else:
-            raise HTTPBadRequest(f"Malformed library content id ( {str(content_id)} ) specified, unable to decode.")
-
-    @expose_api
-    def delete(self, trans, library_id, id, **kwd):
-        """
-        DELETE /api/libraries/{library_id}/contents/{id}
-
-        Delete the LibraryDataset with the given ``id``.
-
-        :type   id:     str
-        :param  id:     the encoded id of the library dataset to delete
-        :type   kwd:    dict
-        :param  kwd:    (optional) dictionary structure containing:
-
-            * payload:     a dictionary itself containing:
-                * purge:   if True, purge the LD
-
-        :rtype:     dict
-        :returns:   an error object if an error occurred or a dictionary containing:
-            * id:         the encoded id of the library dataset,
-            * deleted:    if the library dataset was marked as deleted,
-            * purged:     if the library dataset was purged
-        """
-        purge = False
-        if kwd.get("payload", None):
-            purge = util.string_as_bool(kwd["payload"].get("purge", False))
-
-        rval = {"id": id}
-        try:
-            ld = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=True)
-            user_is_admin = trans.user_is_admin
-            can_modify = trans.app.security_agent.can_modify_library_item(trans.user.all_roles(), ld)
-            log.debug("is_admin: %s, can_modify: %s", user_is_admin, can_modify)
-            if not (user_is_admin or can_modify):
-                trans.response.status = 403
-                rval.update({"error": "Unauthorized to delete or purge this library dataset"})
-                return rval
-
-            ld.deleted = True
-            if purge:
-                ld.purged = True
-                trans.sa_session.add(ld)
-                with transaction(trans.sa_session):
-                    trans.sa_session.commit()
-
-                # TODO: had to change this up a bit from Dataset.user_can_purge
-                dataset = ld.library_dataset_dataset_association.dataset
-                no_history_assoc = len(dataset.history_associations) == len(dataset.purged_history_associations)
-                no_library_assoc = dataset.library_associations == [ld.library_dataset_dataset_association]
-                can_purge_dataset = not dataset.purged and no_history_assoc and no_library_assoc
-
-                if can_purge_dataset:
-                    try:
-                        ld.library_dataset_dataset_association.dataset.full_delete()
-                        trans.sa_session.add(ld.dataset)
-                    except Exception:
-                        pass
-                    # flush now to preserve deleted state in case of later interruption
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
-                rval["purged"] = True
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            rval["deleted"] = True
-
-        except exceptions.httpexceptions.HTTPInternalServerError:
-            log.exception("Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s", id, str(kwd))
-            raise
-        except exceptions.httpexceptions.HTTPException:
-            raise
-        except Exception as exc:
-            log.exception("library_contents API, delete: uncaught exception: %s, %s", id, str(kwd))
-            trans.response.status = 500
-            rval.update({"error": util.unicodify(exc)})
-        return rval
+router = Router(tags=["libraries"])
+
+
+class FormDataApiRoute(APIContentTypeRoute):
+    match_content_type = "multipart/form-data"
+
+
+class JsonApiRoute(APIContentTypeRoute):
+    match_content_type = "application/json"
+
+
+LibraryContentsCreateForm = as_form(LibraryContentsFileCreatePayload)
+
+
+async def get_files(request: Request, files: Optional[List[UploadFile]] = None):
+    # FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
+    files2: List[StarletteUploadFile] = cast(List[StarletteUploadFile], files or [])
+    if not files2:
+        data = await request.form()
+        for value in data.values():
+            if isinstance(value, StarletteUploadFile):
+                files2.append(value)
+    return files2
+
+
+@router.cbv
+class FastAPILibraryContents:
+    service: LibraryContentsService = depends(LibraryContentsService)
+
+    @router.get(
+        "/api/libraries/{library_id}/contents",
+        summary="Return a list of library files and folders.",
+        deprecated=True,
+    )
+    def index(
+        self,
+        library_id: DecodedDatabaseIdField,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> LibraryContentsIndexListResponse:
+        """This endpoint is deprecated. Please use GET /api/folders/{folder_id}/contents instead."""
+        return self.service.index(trans, library_id)
+
+    @router.get(
+        "/api/libraries/{library_id}/contents/{id}",
+        name="library_content",
+        summary="Return a library file or folder.",
+        deprecated=True,
+    )
+    def show(
+        self,
+        library_id: DecodedDatabaseIdField,
+        id: MaybeLibraryFolderOrDatasetID,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> AnyLibraryContentsShowResponse:
+        """This endpoint is deprecated. Please use GET /api/libraries/datasets/{library_id} instead."""
+        return self.service.show(trans, id)
+
+    @router.post(
+        "/api/libraries/{library_id}/contents",
+        summary="Create a new library file or folder.",
+        deprecated=True,
+        route_class_override=JsonApiRoute,
+    )
+    def create_json(
+        self,
+        library_id: DecodedDatabaseIdField,
+        payload: AnyLibraryContentsCreatePayload,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+    ) -> AnyLibraryContentsCreateResponse:
+        """This endpoint is deprecated. Please use POST /api/folders/{folder_id} or POST /api/folders/{folder_id}/contents instead."""
+        return self.service.create(trans, library_id, payload)
+
+    @router.post(
+        "/api/libraries/{library_id}/contents",
+        summary="Create a new library file or folder.",
+        deprecated=True,
+        route_class_override=FormDataApiRoute,
+    )
+    def create_form(
+        self,
+        library_id: DecodedDatabaseIdField,
+        payload: LibraryContentsFileCreatePayload = Depends(LibraryContentsCreateForm.as_form),
+        files: List[StarletteUploadFile] = Depends(get_files),
+        trans: ProvidesHistoryContext = DependsOnTrans,
+    ) -> AnyLibraryContentsCreateResponse:
+        """This endpoint is deprecated. Please use POST /api/folders/{folder_id} or POST /api/folders/{folder_id}/contents instead."""
+        return self.service.create(trans, library_id, payload, files)
+
+    @router.put(
+        "/api/libraries/{library_id}/contents/{id}",
+        summary="Update a library file or folder.",
+        deprecated=True,
+    )
+    def update(
+        self,
+        library_id: DecodedDatabaseIdField,
+        id: DecodedDatabaseIdField,
+        payload,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> None:
+        """This endpoint is deprecated. Please use PATCH /api/libraries/datasets/{library_id} instead."""
+        return self.service.update(trans, id, payload)
+
+    @router.delete(
+        "/api/libraries/{library_id}/contents/{id}",
+        summary="Delete a library file or folder.",
+        deprecated=True,
+    )
+    def delete(
+        self,
+        library_id: DecodedDatabaseIdField,
+        id: DecodedDatabaseIdField,
+        payload: Optional[LibraryContentsDeletePayload] = Body(None),
+        trans: ProvidesHistoryContext = DependsOnTrans,
+    ) -> LibraryContentsDeleteResponse:
+        """This endpoint is deprecated. Please use DELETE /api/libraries/datasets/{library_id} instead."""
+        return self.service.delete(trans, id, payload or LibraryContentsDeletePayload())
diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py
index 35cc5ae350f9d0fce2e94515dd9fe9c4354d28c4..92eee9c5905bd493375935c645632a0efd7c07e4 100644
--- a/lib/galaxy/webapps/galaxy/api/library_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/library_datasets.py
@@ -27,6 +27,7 @@ from galaxy.managers import (
     roles,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.structured_app import StructuredApp
 from galaxy.tools.actions import upload_common
 from galaxy.tools.parameters import populate_state
@@ -150,10 +151,12 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                 page_limit = 10
             query = kwd.get("q", None)
             roles, total_roles = trans.app.security_agent.get_valid_roles(trans, dataset, query, page, page_limit)
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
             return_roles = []
             for role in roles:
                 role_id = trans.security.encode_id(role.id)
-                return_roles.append(dict(id=role_id, name=role.name, type=role.type))
+                displayed_name = private_role_emails.get(role.id, role.name)
+                return_roles.append(dict(id=role_id, name=displayed_name, type=role.type))
             return dict(roles=return_roles, page=page, page_limit=page_limit, total=total_roles)
         else:
             raise exceptions.RequestParameterInvalidException(
@@ -171,7 +174,7 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         :rtype:     dictionary
         :returns:   dict of current roles for all available permission types
         """
-        return self.ldda_manager.serialize_dataset_association_roles(trans, library_dataset)
+        return self.ldda_manager.serialize_dataset_association_roles(library_dataset)
 
     @expose_api
     def update(self, trans, encoded_dataset_id, payload=None, **kwd):
@@ -199,7 +202,8 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
         :rtype:     dictionary
         """
         library_dataset = self.ld_manager.get(trans, managers_base.decode_id(self.app, encoded_dataset_id))
-        updated = self.ld_manager.update(trans, library_dataset, payload)
+        self.ld_manager.check_modifiable(trans, library_dataset)
+        updated = self.ld_manager.update(library_dataset, payload, trans=trans)
         serialized = self.ld_manager.serialize(trans, updated)
         return serialized
 
@@ -486,9 +490,7 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin,
                     os.path.realpath(path),
                 )
                 raise exceptions.RequestParameterInvalidException("The given path is invalid.")
-            if trans.app.config.user_library_import_check_permissions and not full_path_permission_for_user(
-                full_dir, path, username
-            ):
+            if username is not None and not full_path_permission_for_user(full_dir, path, username):
                 log.error(
                     "User attempted to import a path that resolves to a path outside of their import dir: "
                     "%s -> %s and cannot be read by them.",
diff --git a/lib/galaxy/webapps/galaxy/api/oauth2_callback.py b/lib/galaxy/webapps/galaxy/api/oauth2_callback.py
new file mode 100644
index 0000000000000000000000000000000000000000..581571c284830878052a643fb3b1e529f231a578
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/api/oauth2_callback.py
@@ -0,0 +1,84 @@
+from typing import Optional
+
+from fastapi import Query
+from fastapi.responses import RedirectResponse
+
+from galaxy.exceptions import ObjectNotFound
+from galaxy.managers.file_source_instances import FileSourceInstancesManager
+from galaxy.schema.schema import OAuth2State
+from galaxy.webapps.galaxy.api import (
+    depends,
+    DependsOnTrans,
+    Router,
+)
+from galaxy.work.context import SessionRequestContext
+
+StateQueryParam: str = Query(
+    ...,
+    title="State information sent with auth request",
+    description="Base-64 encoded JSON used to route request within Galaxy.",
+)
+CodeQueryParam: Optional[str] = Query(
+    None,
+    title="OAuth2 Authorization Code from remote resource",
+)
+ErrorQueryParam: Optional[str] = Query(
+    None,
+    title="OAuth2 Error from remote resource",
+)
+
+router = Router(tags=["oauth2"])
+
+ERROR_REDIRECT_PATH = "file_source_instances/create"
+
+VALID_OAUTH2_ERROR_CODES = [
+    "access_denied",
+    "invalid_request",
+    "unauthorized_client",
+    "unsupported_response_type",
+    "invalid_scope",
+    "server_error",
+    "temporarily_unavailable",
+]
+
+
+@router.cbv
+class OAuth2Callback:
+    file_source_instances_manager: FileSourceInstancesManager = depends(FileSourceInstancesManager)
+
+    @router.get(
+        "/oauth2_callback",
+        summary="Callback entry point for remote resource responses with OAuth2 authorization codes",
+    )
+    def oauth2_callback(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        state: str = StateQueryParam,
+        code: Optional[str] = CodeQueryParam,
+        error: Optional[str] = ErrorQueryParam,
+    ):
+        if error:
+            error_code = self._ensure_valid_oauth_error_code(error)
+            return RedirectResponse(f"{trans.request.url_path}{ERROR_REDIRECT_PATH}?error={error_code}")
+        elif not code:
+            return RedirectResponse(
+                f"{trans.request.url_path}{ERROR_REDIRECT_PATH}?error=No credentials provided, please try again."
+            )
+
+        oauth2_state = OAuth2State.decode(state)
+        # TODO: save session information in cookie to verify not CSRF with oauth2_state.nonce
+        route = oauth2_state.route
+        if route.startswith("file_source_instances/"):
+            redirect = self.file_source_instances_manager.handle_authorization_code(trans, code, oauth2_state)
+        # implement other routes here as needed for other components
+        else:
+            raise ObjectNotFound(f"Could not find oauth2 callback for route {route}")
+
+        return RedirectResponse(f"{trans.request.url_path}{redirect}")
+
+    def _ensure_valid_oauth_error_code(self, error: str) -> str:
+        # if the error code is valid, return it as is so the client can
+        # handle it or display the appropriate error message
+        if error in VALID_OAUTH2_ERROR_CODES:
+            return error
+        return "Unknown OAuth2 error code"
diff --git a/lib/galaxy/webapps/galaxy/api/object_store.py b/lib/galaxy/webapps/galaxy/api/object_store.py
index 3927ff17b1d5c6a590b2e5455bb87ff89238cd9c..0963530e5818c2b516f6df1a71db79f12419c6e0 100644
--- a/lib/galaxy/webapps/galaxy/api/object_store.py
+++ b/lib/galaxy/webapps/galaxy/api/object_store.py
@@ -26,6 +26,7 @@ from galaxy.managers.object_store_instances import (
     CreateInstancePayload,
     ModifyInstancePayload,
     ObjectStoreInstancesManager,
+    TestModifyInstancePayload,
     UserConcreteObjectStoreModel,
 )
 from galaxy.model import User
@@ -129,7 +130,7 @@ class FastAPIObjectStore:
         return self.object_store_instance_manager.index(trans)
 
     @router.get(
-        "/api/object_store_instances/{user_object_store_id}",
+        "/api/object_store_instances/{uuid}",
         summary="Get a persisted user object store instance.",
         operation_id="object_stores__instances_get",
     )
@@ -137,9 +138,21 @@ class FastAPIObjectStore:
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         user: User = DependsOnUser,
-        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,
+        uuid: UUID4 = UserObjectStoreIdPathParam,
     ) -> UserConcreteObjectStoreModel:
-        return self.object_store_instance_manager.show(trans, user_object_store_id)
+        return self.object_store_instance_manager.show(trans, uuid)
+
+    @router.get(
+        "/api/object_store_instances/{uuid}/test",
+        summary="Get a persisted user object store instance.",
+        operation_id="object_stores__instances_test_instance",
+    )
+    def instance_test(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        uuid: UUID4 = UserObjectStoreIdPathParam,
+    ) -> PluginStatus:
+        return self.object_store_instance_manager.plugin_status_for_instance(trans, uuid)
 
     @router.get(
         "/api/object_stores/{object_store_id}",
@@ -153,7 +166,7 @@ class FastAPIObjectStore:
         return self._model_for(object_store_id)
 
     @router.put(
-        "/api/object_store_instances/{user_object_store_id}",
+        "/api/object_store_instances/{uuid}",
         summary="Update or upgrade user object store instance.",
         operation_id="object_stores__instances_update",
     )
@@ -161,13 +174,26 @@ class FastAPIObjectStore:
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         user: User = DependsOnUser,
-        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,
+        uuid: UUID4 = UserObjectStoreIdPathParam,
         payload: ModifyInstancePayload = Body(...),
     ) -> UserConcreteObjectStoreModel:
-        return self.object_store_instance_manager.modify_instance(trans, user_object_store_id, payload)
+        return self.object_store_instance_manager.modify_instance(trans, uuid, payload)
+
+    @router.post(
+        "/api/object_store_instances/{uuid}/test",
+        summary="Test updating or upgrading user object source instance.",
+        operation_id="object_stores__test_instances_update",
+    )
+    def test_update_instance(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        user_file_source_id: UUID4 = UserObjectStoreIdPathParam,
+        payload: TestModifyInstancePayload = Body(...),
+    ) -> PluginStatus:
+        return self.object_store_instance_manager.test_modify_instance(trans, user_file_source_id, payload)
 
     @router.delete(
-        "/api/object_store_instances/{user_object_store_id}",
+        "/api/object_store_instances/{uuid}",
         summary="Purge user object store instance.",
         operation_id="object_stores__instances_purge",
         status_code=status.HTTP_204_NO_CONTENT,
@@ -176,9 +202,9 @@ class FastAPIObjectStore:
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         user: User = DependsOnUser,
-        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,
+        uuid: UUID4 = UserObjectStoreIdPathParam,
     ):
-        self.object_store_instance_manager.purge_instance(trans, user_object_store_id)
+        self.object_store_instance_manager.purge_instance(trans, uuid)
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
     @router.get(
diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py
index 61aaea66ead006cec09502b50bdd160336038b95..a0b45e4056ef9c26be7f4525a8e4c5716f5926d5 100644
--- a/lib/galaxy/webapps/galaxy/api/pages.py
+++ b/lib/galaxy/webapps/galaxy/api/pages.py
@@ -103,7 +103,7 @@ class FastAPIPages:
         summary="Lists all Pages viewable by the user.",
         response_description="A list with summary page information.",
     )
-    async def index(
+    def index(
         self,
         response: Response,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -153,7 +153,7 @@ class FastAPIPages:
         summary="Marks the specific Page as deleted.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
-    async def delete(
+    def delete(
         self,
         id: PageIdPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -167,7 +167,7 @@ class FastAPIPages:
         summary="Undelete the specific Page.",
         status_code=status.HTTP_204_NO_CONTENT,
     )
-    async def undelete(
+    def undelete(
         self,
         id: PageIdPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -188,7 +188,7 @@ class FastAPIPages:
             501: {"description": "PDF conversion service not available."},
         },
     )
-    async def show_pdf(
+    def show_pdf(
         self,
         id: PageIdPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -210,7 +210,7 @@ class FastAPIPages:
             501: {"description": "PDF conversion service not available."},
         },
     )
-    async def prepare_pdf(
+    def prepare_pdf(
         self,
         id: PageIdPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -226,7 +226,7 @@ class FastAPIPages:
         summary="Return a page summary and the content of the last revision.",
         response_description="The page summary information.",
     )
-    async def show(
+    def show(
         self,
         id: PageIdPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index eaa16234432b9440aec5196cf0e2dcd3332229d4..c5a708d748bfe7cbc03b30cac7c8f2dad0b68138 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -128,7 +128,7 @@ class FastAPIRemoteFiles:
         deprecated=True,
         summary="Displays remote files available to the user. Please use /api/remote_files instead.",
     )
-    async def index(
+    def index(
         self,
         response: Response,
         user_ctx: ProvidesUserContext = DependsOnTrans,
@@ -157,7 +157,7 @@ class FastAPIRemoteFiles:
         summary="Display plugin information for each of the gxfiles:// URI targets available.",
         response_description="A list with details about each plugin.",
     )
-    async def plugins(
+    def plugins(
         self,
         user_ctx: ProvidesUserContext = DependsOnTrans,
         browsable_only: Annotated[Optional[bool], BrowsableQueryParam] = True,
@@ -176,7 +176,7 @@ class FastAPIRemoteFiles:
         "/api/remote_files",
         summary="Creates a new entry (directory/record) on the remote files source.",
     )
-    async def create_entry(
+    def create_entry(
         self,
         user_ctx: ProvidesUserContext = DependsOnTrans,
         payload: CreateEntryPayload = Body(
diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py
index 166860c92ffd823fc55b451b615fe7dff026732a..55f6d9bfece2cbb14630781f07059c6458ac58f5 100644
--- a/lib/galaxy/webapps/galaxy/api/roles.py
+++ b/lib/galaxy/webapps/galaxy/api/roles.py
@@ -7,22 +7,18 @@ import logging
 from fastapi import Body
 
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.managers.roles import RoleManager
-from galaxy.schema.fields import (
-    DecodedDatabaseIdField,
-    Security,
-)
+from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.schema import (
     RoleDefinitionModel,
     RoleListResponse,
     RoleModelResponse,
 )
-from galaxy.webapps.base.controller import url_for
 from galaxy.webapps.galaxy.api import (
     depends,
     DependsOnTrans,
     Router,
 )
+from galaxy.webapps.galaxy.services.roles import RolesService
 
 log = logging.getLogger(__name__)
 
@@ -32,48 +28,32 @@ log = logging.getLogger(__name__)
 router = Router(tags=["roles"])
 
 
-def role_to_model(role):
-    item = role.to_dict(view="element")
-    role_id = Security.security.encode_id(role.id)
-    item["url"] = url_for("role", id=role_id)
-    return RoleModelResponse(**item)
-
-
 @router.cbv
 class FastAPIRoles:
-    role_manager: RoleManager = depends(RoleManager)
+    service: RolesService = depends(RolesService)
 
     @router.get("/api/roles")
     def index(self, trans: ProvidesUserContext = DependsOnTrans) -> RoleListResponse:
-        roles = self.role_manager.list_displayable_roles(trans)
-        return RoleListResponse(root=[role_to_model(r) for r in roles])
+        return self.service.get_index(trans=trans)
 
     @router.get("/api/roles/{id}")
     def show(self, id: DecodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModelResponse:
-        role = self.role_manager.get(trans, id)
-        return role_to_model(role)
+        return self.service.show(trans, id)
 
     @router.post("/api/roles", require_admin=True)
     def create(
         self, trans: ProvidesUserContext = DependsOnTrans, role_definition_model: RoleDefinitionModel = Body(...)
     ) -> RoleModelResponse:
-        role = self.role_manager.create_role(trans, role_definition_model)
-        return role_to_model(role)
+        return self.service.create(trans, role_definition_model)
 
     @router.delete("/api/roles/{id}", require_admin=True)
     def delete(self, id: DecodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModelResponse:
-        role = self.role_manager.get(trans, id)
-        role = self.role_manager.delete(trans, role)
-        return role_to_model(role)
+        return self.service.delete(trans, id)
 
     @router.post("/api/roles/{id}/purge", require_admin=True)
     def purge(self, id: DecodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModelResponse:
-        role = self.role_manager.get(trans, id)
-        role = self.role_manager.purge(trans, role)
-        return role_to_model(role)
+        return self.service.purge(trans, id)
 
     @router.post("/api/roles/{id}/undelete", require_admin=True)
     def undelete(self, id: DecodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModelResponse:
-        role = self.role_manager.get(trans, id)
-        role = self.role_manager.undelete(trans, role)
-        return role_to_model(role)
+        return self.service.undelete(trans, id)
diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py
index 953c2909e5109352762deb40ab8bdbe2ac478dc7..1ba64f222071561bae53a041aafa7a69538b7012 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -67,7 +67,7 @@ class FastAPIToolData:
         summary="Import a data manager bundle",
         require_admin=True,
     )
-    async def create(
+    def create(
         self, tool_data_file_path: Optional[str] = None, import_bundle_model: ImportToolDataBundle = Body(...)
     ) -> AsyncTaskResultSummary:
         source = import_bundle_model.source
@@ -91,7 +91,7 @@ class FastAPIToolData:
         response_description="A description of the reloaded data table and its content",
         require_admin=True,
     )
-    async def reload(self, table_name: str = ToolDataTableName) -> ToolDataDetails:
+    def reload(self, table_name: str = ToolDataTableName) -> ToolDataDetails:
         """Reloads a data table and return its details."""
         return self.tool_data_manager.reload(table_name)
 
@@ -116,7 +116,7 @@ class FastAPIToolData:
         response_class=GalaxyFileResponse,
         require_admin=True,
     )
-    async def download_field_file(
+    def download_field_file(
         self,
         table_name: str = ToolDataTableName,
         field_name: str = ToolDataTableFieldName,
@@ -136,7 +136,7 @@ class FastAPIToolData:
         response_description="A description of the affected data table and its content",
         require_admin=True,
     )
-    async def delete(
+    def delete(
         self,
         payload: ToolDataItem,
         table_name: str = ToolDataTableName,
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index ea78cd9f56965fe25973a672280d6e1efa771895..dc27f7c3408efb24d4e529300512d02bc4cbe996 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -31,6 +31,7 @@ from galaxy.schema.fetch_data import (
     FetchDataFormPayload,
     FetchDataPayload,
 )
+from galaxy.tool_util.verify import ToolTestDescriptionDict
 from galaxy.tools.evaluation import global_tool_errors
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.web import (
@@ -73,12 +74,23 @@ router = Router(tags=["tools"])
 FetchDataForm = as_form(FetchDataFormPayload)
 
 
+async def get_files(request: Request, files: Optional[List[UploadFile]] = None):
+    # FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
+    files2: List[StarletteUploadFile] = cast(List[StarletteUploadFile], files or [])
+    if not files2:
+        data = await request.form()
+        for value in data.values():
+            if isinstance(value, StarletteUploadFile):
+                files2.append(value)
+    return files2
+
+
 @router.cbv
 class FetchTools:
     service: ToolsService = depends(ToolsService)
 
     @router.post("/api/tools/fetch", summary="Upload files to Galaxy", route_class_override=JsonApiRoute)
-    async def fetch_json(self, payload: FetchDataPayload = Body(...), trans: ProvidesHistoryContext = DependsOnTrans):
+    def fetch_json(self, payload: FetchDataPayload = Body(...), trans: ProvidesHistoryContext = DependsOnTrans):
         return self.service.create_fetch(trans, payload)
 
     @router.post(
@@ -86,22 +98,13 @@ class FetchTools:
         summary="Upload files to Galaxy",
         route_class_override=FormDataApiRoute,
     )
-    async def fetch_form(
+    def fetch_form(
         self,
-        request: Request,
         payload: FetchDataFormPayload = Depends(FetchDataForm.as_form),
-        files: Optional[List[UploadFile]] = None,
         trans: ProvidesHistoryContext = DependsOnTrans,
+        files: List[StarletteUploadFile] = Depends(get_files),
     ):
-        files2: List[StarletteUploadFile] = cast(List[StarletteUploadFile], files or [])
-
-        # FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
-        if not files2:
-            data = await request.form()
-            for value in data.values():
-                if isinstance(value, StarletteUploadFile):
-                    files2.append(value)
-        return self.service.create_fetch(trans, payload, files2)
+        return self.service.create_fetch(trans, payload, files)
 
 
 class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
@@ -316,7 +319,7 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
         return test_counts_by_tool
 
     @expose_api_anonymous_and_sessionless
-    def test_data(self, trans: GalaxyWebTransaction, id, **kwd):
+    def test_data(self, trans: GalaxyWebTransaction, id, **kwd) -> List[ToolTestDescriptionDict]:
         """
         GET /api/tools/{tool_id}/test_data?tool_version={tool_version}
 
diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py
index eb051f63ed97b084d90c9aa87393676d5f43d5e3..88374ef9312ef32084b67c1b27ef56da9a733fa8 100644
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -8,7 +8,6 @@ import logging
 import re
 from typing import (
     Any,
-    Dict,
     List,
     Optional,
     Union,
@@ -43,6 +42,7 @@ from galaxy.model import (
     UserQuotaUsage,
 )
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.schema import APIKeyModel
 from galaxy.schema.schema import (
     AnonUserModel,
@@ -58,9 +58,11 @@ from galaxy.schema.schema import (
     FlexibleUserIdType,
     MaybeLimitedUserModel,
     RemoteUserCreationPayload,
+    RoleListResponse,
     UserBeaconSetting,
     UserCreationPayload,
     UserDeletionPayload,
+    UserUpdatePayload,
 )
 from galaxy.security.validate_user_input import (
     validate_email,
@@ -395,17 +397,16 @@ class FastAPIUsers:
         user = self.service.get_user(trans, user_id)
         favorites = json.loads(user.preferences["favorites"]) if "favorites" in user.preferences else {}
         if object_type.value == "tools":
-            if "tools" in favorites:
-                favorite_tools = favorites["tools"]
-                if object_id in favorite_tools:
-                    del favorite_tools[favorite_tools.index(object_id)]
-                    favorites["tools"] = favorite_tools
-                    user.preferences["favorites"] = json.dumps(favorites)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
-                else:
-                    raise exceptions.ObjectNotFound("Given object is not in the list of favorites")
-        return favorites
+            favorite_tools = favorites.get("tools", [])
+            if object_id in favorite_tools:
+                del favorite_tools[favorite_tools.index(object_id)]
+                favorites["tools"] = favorite_tools
+                user.preferences["favorites"] = json.dumps(favorites)
+                with transaction(trans.sa_session):
+                    trans.sa_session.commit()
+            else:
+                raise exceptions.ObjectNotFound("Given object is not in the list of favorites")
+        return FavoriteObjectsSummary.model_validate(favorites)
 
     @router.put(
         "/api/users/{user_id}/favorites/{object_type}",
@@ -428,17 +429,14 @@ class FastAPIUsers:
                 raise exceptions.ObjectNotFound(f"Could not find tool with id '{tool_id}'.")
             if not tool.allow_user_access(user):
                 raise exceptions.AuthenticationFailed(f"Access denied for tool with id '{tool_id}'.")
-            if "tools" in favorites:
-                favorite_tools = favorites["tools"]
-            else:
-                favorite_tools = []
+            favorite_tools = favorites.get("tools", [])
             if tool_id not in favorite_tools:
                 favorite_tools.append(tool_id)
                 favorites["tools"] = favorite_tools
                 user.preferences["favorites"] = json.dumps(favorites)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-        return favorites
+        return FavoriteObjectsSummary.model_validate(favorites)
 
     @router.put(
         "/api/users/{user_id}/theme/{theme}",
@@ -674,13 +672,14 @@ class FastAPIUsers:
         self,
         trans: ProvidesUserContext = DependsOnTrans,
         user_id: FlexibleUserIdType = FlexibleUserIdPathParam,
-        payload: Dict[Any, Any] = UserUpdateBody,
+        payload: UserUpdatePayload = UserUpdateBody,
         deleted: Optional[bool] = UserDeletedQueryParam,
     ) -> DetailedUserModel:
         deleted = deleted or False
         current_user = trans.user
         user_to_update = self.service.get_non_anonymous_user_full(trans, user_id, deleted=deleted)
-        self.service.user_deserializer.deserialize(user_to_update, payload, user=current_user, trans=trans)
+        data = payload.model_dump(exclude_unset=True)
+        self.service.user_deserializer.deserialize(user_to_update, data, user=current_user, trans=trans)
         return self.service.user_to_detailed_model(user_to_update)
 
     @router.delete(
@@ -733,6 +732,19 @@ class FastAPIUsers:
         if not self.service.user_manager.send_activation_email(trans, user.email, user.username):
             raise exceptions.MessageException("Unable to send activation email.")
 
+    @router.get(
+        "/api/users/{user_id}/roles",
+        name="get user roles",
+        description="Return a list of roles associated with this user. Only admins can see user roles.",
+        require_admin=True,
+    )
+    def get_user_roles(
+        self,
+        user_id: UserIdPathParam,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> RoleListResponse:
+        return self.service.get_user_roles(trans=trans, user_id=user_id)
+
 
 class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController, UsesFormDefinitionsMixin):
     service: UsersService = depends(UsersService)
@@ -813,7 +825,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
             "username": username,
         }
         is_galaxy_app = trans.webapp.name == "galaxy"
-        if trans.app.config.enable_account_interface or not is_galaxy_app:
+        if (trans.app.config.enable_account_interface and not trans.app.config.use_remote_user) or not is_galaxy_app:
             inputs.append(
                 {
                     "id": "email_input",
@@ -825,7 +837,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                 }
             )
         if is_galaxy_app:
-            if trans.app.config.enable_account_interface:
+            if trans.app.config.enable_account_interface and not trans.app.config.use_remote_user:
                 inputs.append(
                     {
                         "id": "name_input",
@@ -979,6 +991,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         extra_user_pref_data = {}
         extra_pref_keys = self._get_extra_user_preferences(trans)
         user_vault = UserVaultWrapper(trans.app.vault, user)
+        current_extra_user_pref_data = json.loads(user.preferences.get("extra_user_preferences", "{}"))
         if extra_pref_keys is not None:
             for key in extra_pref_keys:
                 key_prefix = f"{key}|"
@@ -991,8 +1004,17 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                             input = matching_input[0]
                             if input.get("required") and payload[item] == "":
                                 raise exceptions.ObjectAttributeMissingException("Please fill the required field")
-                            if not (input.get("type") == "secret" and payload[item] == "__SECRET_PLACEHOLDER__"):
-                                if input.get("store") == "vault":
+                            input_type = input.get("type")
+                            is_secret_value_unchanged = (
+                                input_type == "secret" and payload[item] == "__SECRET_PLACEHOLDER__"
+                            )
+                            is_stored_in_vault = input.get("store") == "vault"
+                            if is_secret_value_unchanged:
+                                if not is_stored_in_vault:
+                                    # If the value is unchanged, keep the current value
+                                    extra_user_pref_data[item] = current_extra_user_pref_data.get(item, "")
+                            else:
+                                if is_stored_in_vault:
                                     user_vault.write_secret(f"preferences/{keys[0]}/{keys[1]}", str(payload[item]))
                                 else:
                                     extra_user_pref_data[item] = payload[item]
@@ -1070,7 +1092,16 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        roles = user.all_roles()
+
+        def get_role_tuples():
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+            role_tuples = set()
+            for role in user.all_roles():
+                displayed_name = private_role_emails.get(role.id, role.name)
+                role_tuples.add((displayed_name, role.id))
+            return list(role_tuples)
+
+        role_tuples = get_role_tuples()
         inputs = []
         for index, action in trans.app.model.Dataset.permitted_actions.items():
             inputs.append(
@@ -1081,7 +1112,7 @@ class UserAPIController(BaseGalaxyAPIController, UsesTagsMixin, BaseUIController
                     "name": index,
                     "label": action.action,
                     "help": action.description,
-                    "options": list({(r.name, r.id) for r in roles}),
+                    "options": role_tuples,
                     "value": [a.role.id for a in user.default_permissions if a.action == action.action],
                 }
             )
diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py
index 2e8283b03dcd10af9199c6448210aceaa1e3f491..559c10d9d330287b6ed92d9ba1e887337871c0f9 100644
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -5,7 +5,6 @@ NOTE!: this is a work in progress and functionality and data structures
 may change often.
 """
 
-import json
 import logging
 from typing import Optional
 
@@ -18,14 +17,7 @@ from fastapi import (
 )
 from typing_extensions import Annotated
 
-from galaxy import (
-    exceptions,
-    util,
-    web,
-)
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.model.base import transaction
-from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.schema import (
     SetSlugPayload,
@@ -34,16 +26,16 @@ from galaxy.schema.schema import (
     SharingStatus,
 )
 from galaxy.schema.visualization import (
+    VisualizationCreatePayload,
+    VisualizationCreateResponse,
     VisualizationIndexQueryPayload,
+    VisualizationShowResponse,
     VisualizationSortByEnum,
     VisualizationSummaryList,
+    VisualizationUpdatePayload,
+    VisualizationUpdateResponse,
 )
-from galaxy.util.hash_util import md5_hash_str
-from galaxy.web import expose_api
-from galaxy.webapps.base.controller import UsesVisualizationMixin
-from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from galaxy.webapps.galaxy.api import (
-    BaseGalaxyAPIController,
     depends,
     DependsOnTrans,
     IndexQueryTag,
@@ -120,7 +112,7 @@ class FastAPIVisualizations:
         "/api/visualizations",
         summary="Returns visualizations for the current user.",
     )
-    async def index(
+    def index(
         self,
         response: Response,
         trans: ProvidesUserContext = DependsOnTrans,
@@ -239,175 +231,44 @@ class FastAPIVisualizations:
         self.service.shareable_service.set_slug(trans, id, payload)
         return Response(status_code=status.HTTP_204_NO_CONTENT)
 
+    @router.get(
+        "/api/visualizations/{id}",
+        summary="Get a visualization by ID.",
+    )
+    def show(
+        self,
+        id: VisualizationIdPathParam,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> VisualizationShowResponse:
+        """Return the visualization."""
+        return self.service.show(trans, id)
 
-class VisualizationsController(BaseGalaxyAPIController, UsesVisualizationMixin, UsesAnnotations):
-    """
-    RESTful controller for interactions with visualizations.
-    """
-
-    service: VisualizationsService = depends(VisualizationsService)
-
-    @expose_api
-    def show(self, trans: GalaxyWebTransaction, id: str, **kwargs):
-        """
-        GET /api/visualizations/{viz_id}
-        """
-        # TODO: revisions should be a contents/nested controller like viz/xxx/r/xxx)?
-        # the important thing is the config
-        # TODO:?? /api/visualizations/registry -> json of registry.listings?
-        visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
-        dictionary = trans.security.encode_dict_ids(self.get_visualization_dict(visualization))
-        dictionary["url"] = web.url_for(
-            controller="visualization",
-            action="display_by_username_and_slug",
-            username=visualization.user.username,
-            slug=visualization.slug,
-        )
-        dictionary["username"] = visualization.user.username
-        dictionary["email_hash"] = md5_hash_str(visualization.user.email)
-        dictionary["tags"] = visualization.make_tag_string_list()
-        dictionary["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, visualization)
-        # need to encode ids in revisions as well
-        encoded_revisions = []
-        for revision in dictionary["revisions"]:
-            # NOTE: does not encode ids inside the configs
-            encoded_revisions.append(trans.security.encode_id(revision))
-        dictionary["revisions"] = encoded_revisions
-        dictionary["latest_revision"] = trans.security.encode_dict_ids(dictionary["latest_revision"])
-        if trans.app.visualizations_registry:
-            visualization = trans.app.visualizations_registry.get_plugin(dictionary["type"])
-            dictionary["plugin"] = visualization.to_dict()
-        return dictionary
-
-    @expose_api
-    def create(self, trans: GalaxyWebTransaction, payload: dict, **kwargs):
-        """
-        POST /api/visualizations
-        creates a new visualization using the given payload
-
-        POST /api/visualizations?import_id={encoded_visualization_id}
-        imports a copy of an existing visualization into the user's workspace
-        """
-        rval = None
-
-        if "import_id" in payload:
-            import_id = payload["import_id"]
-            visualization = self.import_visualization(trans, import_id, user=trans.user)
-
-        else:
-            payload = self._validate_and_parse_payload(payload)
-            # must have a type (I've taken this to be the visualization name)
-            if "type" not in payload:
-                raise exceptions.RequestParameterMissingException("key/value 'type' is required")
-            vis_type = payload.pop("type", False)
-
-            payload["save"] = True
-            try:
-                # generate defaults - this will err if given a weird key?
-                visualization = self.create_visualization(trans, vis_type, **payload)
-            except ValueError as val_err:
-                raise exceptions.RequestParameterMissingException(str(val_err))
-
-        rval = {"id": trans.security.encode_id(visualization.id)}
-
-        return rval
-
-    @expose_api
-    def update(self, trans: GalaxyWebTransaction, id: str, payload: dict, **kwargs):
-        """
-        PUT /api/visualizations/{encoded_visualization_id}
-        """
-        rval = None
-        payload = self._validate_and_parse_payload(payload)
-
-        # there's a differentiation here between updating the visualization and creating a new revision
-        # that needs to be handled clearly here or alternately, using a different controller
-        # like e.g. PUT /api/visualizations/{id}/r/{id}
-
-        # TODO: consider allowing direct alteration of revisions title (without a new revision)
-        #   only create a new revsion on a different config
-
-        # only update owned visualizations
-        visualization = self.get_visualization(trans, id, check_ownership=True)
-        title = payload.get("title", visualization.latest_revision.title)
-        dbkey = payload.get("dbkey", visualization.latest_revision.dbkey)
-        deleted = payload.get("deleted", visualization.deleted)
-        config = payload.get("config", visualization.latest_revision.config)
-
-        latest_config = visualization.latest_revision.config
-        if (
-            (title != visualization.latest_revision.title)
-            or (dbkey != visualization.latest_revision.dbkey)
-            or (json.dumps(config) != json.dumps(latest_config))
-        ):
-            revision = self.add_visualization_revision(trans, visualization, config, title, dbkey)
-            rval = {"id": id, "revision": revision.id}
-
-        # allow updating vis title
-        visualization.title = title
-        visualization.deleted = deleted
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
-
-        return rval
-
-    def _validate_and_parse_payload(self, payload):
+    @router.post(
+        "/api/visualizations",
+        summary="Create a new visualization.",
+    )
+    def create(
+        self,
+        payload: VisualizationCreatePayload = Body(...),
+        import_id: Optional[DecodedDatabaseIdField] = Query(
+            None, title="Import ID", description="The encoded database identifier of the Visualization to import."
+        ),
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> VisualizationCreateResponse:
         """
-        Validate and parse incomming data payload for a visualization.
+        Creates a new visualization using the given payload and does not require the import_id field.
+        If import_id given, it imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload.
         """
-        # This layer handles (most of the stricter idiot proofing):
-        #   - unknown/unallowed keys
-        #   - changing data keys from api key to attribute name
-        #   - protection against bad data form/type
-        #   - protection against malicious data content
-        # all other conversions and processing (such as permissions, etc.) should happen down the line
-
-        # keys listed here don't error when attempting to set, but fail silently
-        #   this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs
-        valid_but_uneditable_keys = (
-            "id",
-            "model_class",
-            # TODO: fill out when we create to_dict, get_dict, whatevs
-        )
-        # TODO: importable
-        ValidationError = exceptions.RequestParameterInvalidException
-
-        validated_payload = {}
-        for key, val in payload.items():
-            # TODO: validate types in VALID_TYPES/registry names at the mixin/model level?
-            if key == "type":
-                if not isinstance(val, str):
-                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
-                val = util.sanitize_html.sanitize_html(val)
-            elif key == "config":
-                if not isinstance(val, dict):
-                    raise ValidationError(f"{key} must be a dictionary: {str(type(val))}")
-            elif key == "annotation":
-                if not isinstance(val, str):
-                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
-                val = util.sanitize_html.sanitize_html(val)
-            elif key == "deleted":
-                if not isinstance(val, bool):
-                    raise ValidationError(f"{key} must be a bool: {str(type(val))}")
-
-            # these are keys that actually only be *updated* at the revision level and not here
-            #   (they are still valid for create, tho)
-            elif key == "title":
-                if not isinstance(val, str):
-                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
-                val = util.sanitize_html.sanitize_html(val)
-            elif key == "slug":
-                if not isinstance(val, str):
-                    raise ValidationError(f"{key} must be a string: {str(type(val))}")
-                val = util.sanitize_html.sanitize_html(val)
-            elif key == "dbkey":
-                if not isinstance(val, str):
-                    raise ValidationError(f"{key} must be a string or unicode: {str(type(val))}")
-                val = util.sanitize_html.sanitize_html(val)
-
-            elif key not in valid_but_uneditable_keys:
-                continue
-                # raise AttributeError( 'unknown key: %s' %( str( key ) ) )
+        return self.service.create(trans, import_id, payload)
 
-            validated_payload[key] = val
-        return validated_payload
+    @router.put(
+        "/api/visualizations/{id}",
+        summary="Update a visualization.",
+    )
+    def update(
+        self,
+        id: VisualizationIdPathParam,
+        payload: VisualizationUpdatePayload = Body(...),
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> Optional[VisualizationUpdateResponse]:
+        return self.service.update(trans, id, payload)
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 64d1d2a4c0bac928d0eb075a5e06a818c1c47758..bd1313d335a68e03d1d4838d3815e5aaf9f33e50 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -21,7 +21,7 @@ from fastapi import (
     Response,
     status,
 )
-from gxformat2._yaml import ordered_dump
+from gxformat2.yaml import ordered_dump
 from pydantic import (
     UUID1,
     UUID4,
@@ -42,6 +42,7 @@ from galaxy.managers.context import (
     ProvidesHistoryContext,
     ProvidesUserContext,
 )
+from galaxy.managers.landing import LandingRequestManager
 from galaxy.managers.workflows import (
     MissingToolsException,
     RefactorRequest,
@@ -63,17 +64,22 @@ from galaxy.schema.invocation import (
     InvocationStepJobsResponseJobModel,
     InvocationStepJobsResponseStepModel,
     InvocationUpdatePayload,
+    WorkflowInvocationRequestModel,
     WorkflowInvocationResponse,
 )
 from galaxy.schema.schema import (
     AsyncFile,
     AsyncTaskResultSummary,
+    ClaimLandingPayload,
+    CreateWorkflowLandingRequestPayload,
     InvocationSortByEnum,
     InvocationsStateCounts,
     SetSlugPayload,
     ShareWithPayload,
     ShareWithStatus,
     SharingStatus,
+    WorkflowJobMetric,
+    WorkflowLandingRequest,
     WorkflowSortByEnum,
 )
 from galaxy.schema.workflows import (
@@ -83,6 +89,7 @@ from galaxy.schema.workflows import (
 from galaxy.structured_app import StructuredApp
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tools import recommendations
+from galaxy.tools._types import ParameterValidationErrorsT
 from galaxy.tools.parameters import populate_state
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.web import (
@@ -100,7 +107,9 @@ from galaxy.webapps.galaxy.api import (
     BaseGalaxyAPIController,
     depends,
     DependsOnTrans,
+    DependsOnUser,
     IndexQueryTag,
+    LandingUuidPathParam,
     Router,
     search_query_param,
 )
@@ -238,27 +247,14 @@ class WorkflowsAPIController(
                     payload["workflow"] = workflow_src
                     return self.__api_import_new_workflow(trans, payload, **kwd)
                 elif archive_source == "trs_tool":
-                    server = None
-                    trs_tool_id = None
-                    trs_version_id = None
-                    import_source = None
-                    if "trs_url" in payload:
-                        parts = self.app.trs_proxy.match_url(payload["trs_url"])
-                        if parts:
-                            server = self.app.trs_proxy.server_from_url(parts["trs_base_url"])
-                            trs_tool_id = parts["tool_id"]
-                            trs_version_id = parts["version_id"]
-                            payload["trs_tool_id"] = trs_tool_id
-                            payload["trs_version_id"] = trs_version_id
-                        else:
-                            raise exceptions.MessageException("Invalid TRS URL.")
-                    else:
-                        trs_server = payload.get("trs_server")
-                        server = self.app.trs_proxy.get_server(trs_server)
-                        trs_tool_id = payload.get("trs_tool_id")
-                        trs_version_id = payload.get("trs_version_id")
-
-                    archive_data = server.get_version_descriptor(trs_tool_id, trs_version_id)
+                    workflow = self.workflow_contents_manager.get_or_create_workflow_from_trs(
+                        trans,
+                        trs_url=payload.get("trs_url"),
+                        trs_id=payload.get("trs_tool_id"),
+                        trs_version=payload.get("trs_version_id"),
+                        trs_server=payload.get("trs_server"),
+                    )
+                    return self.__api_import_response(workflow)
                 else:
                     try:
                         archive_data = stream_url_to_str(
@@ -535,12 +531,12 @@ class WorkflowsAPIController(
         inputs = payload.get("inputs", {})
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         module = module_factory.from_dict(trans, payload, from_tool_form=True)
-        if "tool_state" not in payload:
-            module_state: Dict[str, Any] = {}
-            errors: Dict[str, str] = {}
-            populate_state(trans, module.get_inputs(), inputs, module_state, errors=errors, check=True)
-            module.recover_state(module_state, from_tool_form=True)
-            module.check_and_update_state()
+
+        module_state: Dict[str, Any] = {}
+        errors: ParameterValidationErrorsT = {}
+        populate_state(trans, module.get_inputs(), inputs, module_state, errors=errors, check=True)
+        module.recover_state(module_state, from_tool_form=True)
+        module.check_and_update_state()
         step_dict = {
             "name": module.get_name(),
             "tool_state": module_state,
@@ -593,13 +589,15 @@ class WorkflowsAPIController(
         workflow, missing_tool_tups = self._workflow_from_dict(
             trans, raw_workflow_description, workflow_create_options, source=source
         )
-        workflow_id = workflow.id
-        workflow = workflow.latest_workflow
+        return self.__api_import_response(workflow)
 
+    def __api_import_response(self, stored_workflow: model.StoredWorkflow):
+        workflow = stored_workflow.latest_workflow
+        assert workflow
         response = {
             "message": f"Workflow '{workflow.name}' imported successfully.",
             "status": "success",
-            "id": trans.security.encode_id(workflow_id),
+            "id": self.app.security.encode_id(stored_workflow.id),
         }
         if workflow.has_errors:
             response["message"] = "Imported, but some steps in this workflow have validation errors."
@@ -855,9 +853,21 @@ query_tags = [
         "Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.",
     ),
     IndexQueryTag(
-        "is:share_with_me",
+        "is:importable",
+        "Include only importable workflows in the final result.",
+    ),
+    IndexQueryTag(
+        "is:deleted",
+        "Include only deleted workflows in the final result.",
+    ),
+    IndexQueryTag(
+        "is:shared_with_me",
         "Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.",
     ),
+    IndexQueryTag(
+        "is:bookmarked",
+        "Include only workflows bookmarked by the requesting user.",
+    ),
 ]
 
 SearchQueryParam: Optional[str] = search_query_param(
@@ -894,6 +904,7 @@ RefactorWorkflowBody = Annotated[
 @router.cbv
 class FastAPIWorkflows:
     service: WorkflowsService = depends(WorkflowsService)
+    landing_manager: LandingRequestManager = depends(LandingRequestManager)
 
     @router.get(
         "/api/workflows",
@@ -1144,6 +1155,33 @@ class FastAPIWorkflows:
     ) -> StoredWorkflowDetailed:
         return self.service.show_workflow(trans, workflow_id, instance, legacy, version)
 
+    @router.post("/api/workflow_landings", public=True, allow_cors=True)
+    def create_landing(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        workflow_landing_request: CreateWorkflowLandingRequestPayload = Body(...),
+    ) -> WorkflowLandingRequest:
+        return self.landing_manager.create_workflow_landing_request(workflow_landing_request)
+
+    @router.post("/api/workflow_landings/{uuid}/claim")
+    def claim_landing(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        uuid: UUID4 = LandingUuidPathParam,
+        payload: Optional[ClaimLandingPayload] = Body(...),
+        user: model.User = DependsOnUser,
+    ) -> WorkflowLandingRequest:
+        return self.landing_manager.claim_workflow_landing_request(trans, uuid, payload)
+
+    @router.get("/api/workflow_landings/{uuid}")
+    def get_landing(
+        self,
+        trans: ProvidesUserContext = DependsOnTrans,
+        uuid: UUID4 = LandingUuidPathParam,
+        user: model.User = DependsOnUser,
+    ) -> WorkflowLandingRequest:
+        return self.landing_manager.get_workflow_landing_request(trans, uuid)
+
 
 StepDetailQueryParam = Annotated[
     bool,
@@ -1227,6 +1265,7 @@ InvocationsLimitQueryParam = Annotated[
     Optional[int],
     Query(
         ge=1,
+        le=100,
         title="Limit",
         description="Limit the number of invocations to return.",
     ),
@@ -1290,7 +1329,7 @@ class FastAPIInvocations:
         sort_by: InvocationsSortByQueryParam = None,
         sort_desc: InvocationsSortDescQueryParam = False,
         include_terminal: InvocationsIncludeTerminalQueryParam = True,
-        limit: InvocationsLimitQueryParam = None,
+        limit: InvocationsLimitQueryParam = 20,
         offset: InvocationsOffsetQueryParam = None,
         instance: InvocationsInstanceQueryParam = False,
         view: SerializationViewQueryParam = None,
@@ -1344,7 +1383,7 @@ class FastAPIInvocations:
         sort_by: InvocationsSortByQueryParam = None,
         sort_desc: InvocationsSortDescQueryParam = False,
         include_terminal: InvocationsIncludeTerminalQueryParam = True,
-        limit: InvocationsLimitQueryParam = None,
+        limit: InvocationsLimitQueryParam = 20,
         offset: InvocationsOffsetQueryParam = None,
         instance: InvocationsInstanceQueryParam = False,
         view: SerializationViewQueryParam = None,
@@ -1415,6 +1454,17 @@ class FastAPIInvocations:
         )
         return self.invocations_service.show(trans, invocation_id, serialization_params, eager=True)
 
+    @router.get(
+        "/api/invocations/{invocation_id}/request",
+        summary="Get a description modeling an API request to invoke this workflow - this is recreated and will be more specific in some ways than the initial creation request.",
+    )
+    def invocation_as_request(
+        self,
+        invocation_id: InvocationIDPathParam,
+        trans: ProvidesUserContext = DependsOnTrans,
+    ) -> WorkflowInvocationRequestModel:
+        return self.invocations_service.as_request(trans, invocation_id)
+
     @router.get(
         "/api/workflows/{workflow_id}/invocations/{invocation_id}",
         summary="Get detailed description of a workflow invocation.",
@@ -1711,3 +1761,11 @@ class FastAPIInvocations:
     ) -> InvocationJobsResponse:
         """An alias for `GET /api/invocations/{invocation_id}/jobs_summary`. `workflow_id` is ignored."""
         return self.invocation_jobs_summary(trans=trans, invocation_id=invocation_id)
+
+    @router.get("/api/invocations/{invocation_id}/metrics")
+    def get_invocation_metrics(
+        self,
+        invocation_id: InvocationIDPathParam,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+    ) -> List[WorkflowJobMetric]:
+        return self.invocations_service.show_invocation_metrics(trans=trans, invocation_id=invocation_id)
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index c9d075756dc72d43c77638d3fd4b1f4ef2a6a7ee..759691ad7b8000d390d8880b754739ec79ced698 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -222,10 +222,13 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/admin/form/{form_id}")
     webapp.add_client_route("/admin/api_keys")
     webapp.add_client_route("/carbon_emissions_calculations")
+    webapp.add_client_route("/help/terms/{term_id}")
     webapp.add_client_route("/datatypes")
     webapp.add_client_route("/login/start")
     webapp.add_client_route("/tools/list")
     webapp.add_client_route("/tools/json")
+    webapp.add_client_route("/tool_landings/{uuid}")
+    webapp.add_client_route("/workflow_landings/{uuid}")
     webapp.add_client_route("/tours")
     webapp.add_client_route("/tours/{tour_id}")
     webapp.add_client_route("/user")
@@ -374,27 +377,6 @@ def populate_api_routes(webapp, app):
         parent_resources=dict(member_name="page", collection_name="pages"),
     )
 
-    webapp.mapper.connect("/api/cloud/authz/", action="index", controller="cloudauthz", conditions=dict(method=["GET"]))
-    webapp.mapper.connect(
-        "/api/cloud/authz/", action="create", controller="cloudauthz", conditions=dict(method=["POST"])
-    )
-
-    webapp.mapper.connect(
-        "delete_cloudauthz_item",
-        "/api/cloud/authz/{encoded_authz_id}",
-        action="delete",
-        controller="cloudauthz",
-        conditions=dict(method=["DELETE"]),
-    )
-
-    webapp.mapper.connect(
-        "upload_cloudauthz_item",
-        "/api/cloud/authz/{encoded_authz_id}",
-        action="update",
-        controller="cloudauthz",
-        conditions=dict(method=["PUT"]),
-    )
-
     # =======================
     # ====== TOOLS API ======
     # =======================
@@ -609,7 +591,6 @@ def populate_api_routes(webapp, app):
         conditions=dict(method=["POST"]),
     )
 
-    webapp.mapper.resource("visualization", "visualizations", path_prefix="/api")
     webapp.mapper.resource("plugins", "plugins", path_prefix="/api")
     webapp.mapper.connect("/api/workflows/build_module", action="build_module", controller="workflows")
     webapp.mapper.connect(
@@ -636,6 +617,7 @@ def populate_api_routes(webapp, app):
         "/plugins/visualizations/{visualization_name}/saved",
         controller="visualization",
         action="saved",
+        conditions={"method": ["GET"]},
     )
     # Deprecated in favor of POST /api/workflows with 'workflow' in payload.
     webapp.mapper.connect(
@@ -872,19 +854,6 @@ def populate_api_routes(webapp, app):
         conditions=dict(method=["POST", "GET"]),
     )
 
-    webapp.mapper.resource(
-        "content",
-        "contents",
-        controller="library_contents",
-        name_prefix="library_",
-        path_prefix="/api/libraries/{library_id}",
-        parent_resources=dict(member_name="library", collection_name="libraries"),
-    )
-
-    _add_item_extended_metadata_controller(
-        webapp, name_prefix="library_dataset_", path_prefix="/api/libraries/{library_id}/contents/{library_content_id}"
-    )
-
     webapp.mapper.connect(
         "build_for_rerun",
         "/api/jobs/{id}/build_for_rerun",
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index bd0ea3a0615853d4ac8a183c348c00f10a4a4edd..c6bf6506c75465d70aa014b2f5db417cdbcd31c9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -13,9 +13,13 @@ from galaxy import (
     util,
     web,
 )
-from galaxy.exceptions import ActionInputError
+from galaxy.exceptions import (
+    ActionInputError,
+    RequestParameterInvalidException,
+)
 from galaxy.managers.quotas import QuotaManager
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.model.index_filter_util import (
     raw_text_column_filter,
     text_column_filter,
@@ -187,6 +191,7 @@ class RoleListGrid(grids.GridData):
     ]
 
     def apply_query_filter(self, query, **kwargs):
+        # Note: we use Role._name (the column), not Role.name (which is a property)
         INDEX_SEARCH_FILTERS = {
             "description": "description",
             "name": "name",
@@ -201,7 +206,7 @@ class RoleListGrid(grids.GridData):
                     key = term.filter
                     q = term.text
                     if key == "name":
-                        query = query.filter(text_column_filter(self.model_class.name, term))
+                        query = query.filter(text_column_filter(self.model_class._name, term))
                     if key == "description":
                         query = query.filter(text_column_filter(self.model_class.description, term))
                     elif key == "is":
@@ -212,7 +217,7 @@ class RoleListGrid(grids.GridData):
                         raw_text_column_filter(
                             [
                                 self.model_class.description,
-                                self.model_class.name,
+                                self.model_class._name,
                             ],
                             term,
                         )
@@ -807,35 +812,17 @@ class AdminGalaxy(controller.JSAppLauncher):
                 ],
             }
         else:
-            in_users = [
-                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_users"))
-            ]
-            in_groups = [
-                trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_groups"))
-            ]
-            if None in in_users or None in in_groups:
+            user_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_users"))]
+            group_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_groups"))]
+            try:
+                trans.app.security_agent.set_role_user_and_group_associations(
+                    role, user_ids=user_ids, group_ids=group_ids
+                )
+                return {
+                    "message": f"Role '{role.name}' has been updated with {len(user_ids)} associated users and {len(group_ids)} associated groups."
+                }
+            except RequestParameterInvalidException:
                 return self.message_exception(trans, "One or more invalid user/group id has been provided.")
-            for ura in role.users:
-                user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
-                if user not in in_users:
-                    # Delete DefaultUserPermissions for previously associated users that have been removed from the role
-                    for dup in user.default_permissions:
-                        if role == dup.role:
-                            trans.sa_session.delete(dup)
-                    # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role
-                    for history in user.histories:
-                        for dhp in history.default_permissions:
-                            if role == dhp.role:
-                                trans.sa_session.delete(dhp)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
-            trans.app.security_agent.set_entity_role_associations(roles=[role], users=in_users, groups=in_groups)
-            trans.sa_session.refresh(role)
-            return {
-                "message": f"Role '{role.name}' has been updated with {len(in_users)} associated users and {len(in_groups)} associated groups."
-            }
 
     @web.legacy_expose_api
     @web.require_admin
@@ -893,6 +880,9 @@ class AdminGalaxy(controller.JSAppLauncher):
                 if user in [x.user for x in group.users]:
                     in_users.append(trans.security.encode_id(user.id))
                 all_users.append((user.email, trans.security.encode_id(user.id)))
+
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+
             for role in (
                 trans.sa_session.query(trans.app.model.Role)
                 .filter(trans.app.model.Role.deleted == false())
@@ -900,7 +890,8 @@ class AdminGalaxy(controller.JSAppLauncher):
             ):
                 if role in [x.role for x in group.roles]:
                     in_roles.append(trans.security.encode_id(role.id))
-                all_roles.append((role.name, trans.security.encode_id(role.id)))
+                displayed_name = private_role_emails.get(role.id, role.name)
+                all_roles.append((displayed_name, trans.security.encode_id(role.id)))
             return {
                 "title": f"Group '{group.name}'",
                 "message": "Group '%s' is currently associated with %d user(s) and %d role(s)."
@@ -912,21 +903,17 @@ class AdminGalaxy(controller.JSAppLauncher):
                 ],
             }
         else:
-            in_users = [
-                trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_users"))
-            ]
-            in_roles = [
-                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_roles"))
-            ]
-            if None in in_users or None in in_roles:
+            user_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_users"))]
+            role_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_roles"))]
+            try:
+                trans.app.security_agent.set_group_user_and_role_associations(
+                    group, user_ids=user_ids, role_ids=role_ids
+                )
+                return {
+                    "message": f"Group '{group.name}' has been updated with {len(user_ids)} associated users and {len(role_ids)} associated roles."
+                }
+            except RequestParameterInvalidException:
                 return self.message_exception(trans, "One or more invalid user/role id has been provided.")
-            trans.app.security_agent.set_entity_group_associations(groups=[group], users=in_users, roles=in_roles)
-            trans.sa_session.refresh(group)
-            return {
-                "message": f"Group '{group.name}' has been updated with {len(in_users)} associated users and {len(in_roles)} associated roles."
-            }
 
     @web.legacy_expose_api
     @web.require_admin
@@ -940,12 +927,16 @@ class AdminGalaxy(controller.JSAppLauncher):
                 .order_by(trans.app.model.User.table.c.email)
             ):
                 all_users.append((user.email, trans.security.encode_id(user.id)))
+
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+
             for role in (
                 trans.sa_session.query(trans.app.model.Role)
                 .filter(trans.app.model.Role.deleted == false())
                 .order_by(trans.app.model.Role.name)
             ):
-                all_roles.append((role.name, trans.security.encode_id(role.id)))
+                displayed_name = private_role_emails.get(role.id, role.name)
+                all_roles.append((displayed_name, trans.security.encode_id(role.id)))
             return {
                 "title": "Create Group",
                 "title_id": "create-group",
@@ -1099,28 +1090,18 @@ class AdminGalaxy(controller.JSAppLauncher):
                 ],
             }
         else:
-            in_roles = [
-                trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_roles"))
-            ]
-            in_groups = [
-                trans.sa_session.query(trans.app.model.Group).get(trans.security.decode_id(x))
-                for x in util.listify(payload.get("in_groups"))
-            ]
-            if None in in_groups or None in in_roles:
+            role_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_roles"))]
+            group_ids = [trans.security.decode_id(id) for id in util.listify(payload.get("in_groups"))]
+            try:
+                trans.app.security_agent.set_user_group_and_role_associations(
+                    user, group_ids=group_ids, role_ids=role_ids
+                )
+                return {
+                    "message": f"User '{user.email}' has been updated with {len(role_ids)} associated roles and {len(group_ids)} associated groups (private roles are not displayed)."
+                }
+            except RequestParameterInvalidException:
                 return self.message_exception(trans, "One or more invalid role/group id has been provided.")
 
-            # make sure the user is not dis-associating himself from his private role
-            private_role = trans.app.security_agent.get_private_user_role(user)
-            if private_role not in in_roles:
-                in_roles.append(private_role)
-
-            trans.app.security_agent.set_entity_user_associations(users=[user], roles=in_roles, groups=in_groups)
-            trans.sa_session.refresh(user)
-            return {
-                "message": f"User '{user.email}' has been updated with {len(in_roles) - 1} associated roles and {len(in_groups)} associated groups (private roles are not displayed)."
-            }
-
 
 # ---- Utility methods -------------------------------------------------------
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py
index 1abcc722ce65d46be37183c74b374ed5907be0e5..e4a07b28092e30ff76375a85455ba7548595b85a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/authnz.py
+++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py
@@ -19,6 +19,7 @@ from galaxy.webapps.base.controller import JSAppLauncher
 log = logging.getLogger(__name__)
 
 PROVIDER_COOKIE_NAME = "galaxy-oidc-provider"
+LOGIN_NEXT_COOKIE_NAME = "galaxy-oidc-login-next"
 
 
 class OIDC(JSAppLauncher):
@@ -52,10 +53,14 @@ class OIDC(JSAppLauncher):
                 userinfo = jwt.decode(
                     token.id_token, options={"verify_signature": False, "verify_aud": False, "verify_exp": False}
                 )
+                provider_label = trans.app.authnz_manager.oidc_backends_config.get(token.provider, {}).get(
+                    "label", token.provider
+                )
                 rtv.append(
                     {
                         "id": trans.app.security.encode_id(token.id),
                         "provider": token.provider,
+                        "provider_label": provider_label,
                         "email": userinfo["email"],
                         "expiration": str(datetime.datetime.utcfromtimestamp(userinfo["exp"])),
                     }
@@ -72,12 +77,17 @@ class OIDC(JSAppLauncher):
 
     @web.json
     @web.expose
-    def login(self, trans, provider, idphint=None):
+    def login(self, trans, provider, idphint=None, next=None):
         if not trans.app.config.enable_oidc:
             msg = "Login to Galaxy using third-party identities is not enabled on this Galaxy instance."
             log.debug(msg)
             return trans.show_error_message(msg)
-        success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans, idphint=idphint)
+        if next:
+            trans.set_cookie(value=next, name=LOGIN_NEXT_COOKIE_NAME, age=1)
+        else:
+            # If no next parameter is provided, ensure we unset any existing next cookie.
+            trans.set_cookie(value="/", name=LOGIN_NEXT_COOKIE_NAME)
+        success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans, idphint)
         if success:
             return {"redirect_uri": redirect_uri}
         else:
@@ -86,6 +96,7 @@ class OIDC(JSAppLauncher):
     @web.expose
     def callback(self, trans, provider, idphint=None, **kwargs):
         user = trans.user.username if trans.user is not None else "anonymous"
+        login_next = url_for(trans.get_cookie(name=LOGIN_NEXT_COOKIE_NAME) or "/")
         if not bool(kwargs):
             log.error(f"OIDC callback received no data for provider `{provider}` and user `{user}`")
             return trans.show_error_message(
@@ -110,7 +121,7 @@ class OIDC(JSAppLauncher):
                 kwargs.get("state", " "),
                 kwargs["code"],
                 trans,
-                login_redirect_url=url_for("/"),
+                login_redirect_url=login_next,
                 idphint=idphint,
             )
         except exceptions.AuthenticationFailed:
@@ -134,6 +145,8 @@ class OIDC(JSAppLauncher):
         trans.handle_user_login(user)
         # Record which idp provider was logged into, so we can logout of it later
         trans.set_cookie(value=provider, name=PROVIDER_COOKIE_NAME)
+        # Clear the login next cookie back to default.
+        trans.set_cookie(value="/", name=LOGIN_NEXT_COOKIE_NAME)
         return trans.response.send_redirect(url_for(redirect_url))
 
     @web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index ddfb8deb2176726896587158b85fbdee1e89b13a..40105d2460b98991ccb005725ee91d56c9e175f8 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -19,14 +19,18 @@ from galaxy.datatypes.display_applications.util import (
     encode_dataset_user,
 )
 from galaxy.datatypes.sniff import guess_ext
-from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.exceptions import (
+    InsufficientPermissionsException,
+    MessageException,
+    RequestParameterInvalidException,
+)
 from galaxy.managers.hdas import (
     HDADeserializer,
     HDAManager,
 )
 from galaxy.managers.histories import HistoryManager
-from galaxy.model import Dataset
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.model.item_attrs import (
     UsesAnnotations,
     UsesItemRatings,
@@ -39,11 +43,8 @@ from galaxy.util import (
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.web import form_builder
-from galaxy.web.framework.helpers import iff
 from galaxy.webapps.base.controller import (
     BaseUIController,
-    ERROR,
-    SUCCESS,
     url_for,
     UsesExtendedMetadataMixin,
 )
@@ -107,25 +108,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         if not data:
             raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
         if not self._can_access_dataset(trans, data):
-            return trans.show_error_message("You are not allowed to access this dataset")
-        if data.purged or data.dataset.purged:
-            return trans.show_error_message("The dataset you are attempting to view has been purged.")
-        elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.user)):
-            return trans.show_error_message("The dataset you are attempting to view has been deleted.")
-        elif data.state == Dataset.states.UPLOAD:
-            return trans.show_error_message(
-                "Please wait until this dataset finishes uploading before attempting to view it."
-            )
-        elif data.state == Dataset.states.DISCARDED:
-            return trans.show_error_message("The dataset you are attempting to view has been discarded.")
-        elif data.state == Dataset.states.DEFERRED:
-            return trans.show_error_message(
-                "The dataset you are attempting to view has deferred data. You can only use this dataset as input for jobs."
-            )
-        elif data.state == Dataset.states.PAUSED:
-            return trans.show_error_message(
-                "The dataset you are attempting to view is in paused state. One of the inputs for the job that creates this dataset has failed."
-            )
+            raise InsufficientPermissionsException("You are not allowed to access this dataset")
+        self.app.hda_manager.ensure_dataset_on_disk(trans, data)
         return data
 
     @web.expose
@@ -133,8 +117,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd
     ):
         data = self._check_dataset(trans, dataset_id)
-        if not isinstance(data, trans.app.model.DatasetInstance):
-            return data
         if "hdca" in kwd:
             raise RequestParameterInvalidException("Invalid request parameter 'hdca' encountered.")
         if hdca_id := kwd.get("hdca_id", None):
@@ -158,7 +140,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         trans.response.headers.update(headers)
         return display_data
 
-    @web.legacy_expose_api_anonymous
+    @web.expose_api_anonymous
     def get_edit(self, trans, dataset_id=None, **kwd):
         """Produces the input definitions available to modify dataset attributes"""
         status = None
@@ -168,8 +150,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
 
         if self._can_access_dataset(trans, data):
             if data.state == trans.model.Dataset.states.UPLOAD:
-                return self.message_exception(
-                    trans, "Please wait until this dataset finishes uploading before attempting to edit its metadata."
+                raise MessageException(
+                    "Please wait until this dataset finishes uploading before attempting to edit its metadata."
                 )
             # let's not overwrite the imported datatypes module with the variable datatypes?
             # the built-in 'id' is overwritten in lots of places as well
@@ -179,10 +161,13 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 if dtype_value.is_datatype_change_allowed()
             ]
             ldatatypes.sort()
-            all_roles = [
-                (r.name, trans.security.encode_id(r.id))
-                for r in trans.app.security_agent.get_legitimate_roles(trans, data.dataset, "root")
-            ]
+
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+            role_tuples = []
+            for role in trans.app.security_agent.get_legitimate_roles(trans, data.dataset, "root"):
+                displayed_name = private_role_emails.get(role.id, role.name)
+                role_tuples.append((displayed_name, trans.security.encode_id(role.id)))
+
             data_metadata = list(data.metadata.spec.items())
             converters_collection = [(key, value.name) for key, value in data.get_converter_types().items()]
             can_manage_dataset = trans.app.security_agent.can_manage_dataset(
@@ -292,7 +277,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                                 "name": index,
                                 "label": action.action,
                                 "help": help_text,
-                                "options": all_roles,
+                                "options": role_tuples,
                                 "value": in_roles.get(action.action),
                                 "readonly": not can_manage_dataset,
                             }
@@ -331,8 +316,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 "permission_disable": permission_disable,
             }
         else:
-            return self.message_exception(
-                trans, f"You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
+            raise MessageException(
+                "You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
             )
 
     @web.expose_api_anonymous
@@ -378,9 +363,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if data.datatype.is_datatype_change_allowed():
                 # prevent modifying datatype when dataset is queued or running as input/output
                 if not data.ok_to_edit_metadata():
-                    return self.message_exception(
-                        trans,
-                        "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them.",
+                    raise MessageException(
+                        "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them."
                     )
                 else:
                     path = data.dataset.get_file_name()
@@ -392,12 +376,11 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                         trans.app.datatypes_registry.set_external_metadata_tool,
                         trans,
                         incoming={"input1": data},
-                        overwrite=False,
-                    )  # overwrite is False as per existing behavior
+                    )
                     trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
                     message = f"Detection was finished and changed the datatype to {datatype}."
             else:
-                return self.message_exception(trans, f'Changing datatype "{data.extension}" is not allowed.')
+                raise MessageException(f'Changing datatype "{data.extension}" is not allowed.')
         elif operation == "autodetect":
             # The user clicked the Auto-detect button on the 'Edit Attributes' form
             self.hda_manager.set_metadata(trans, data, overwrite=True)
@@ -408,7 +391,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 try:
                     message = data.datatype.convert_dataset(trans, data, target_type)
                 except DatatypeConverterNotFoundException as e:
-                    return self.message_exception(trans, str(e))
+                    raise MessageException(str(e))
         elif operation == "permission":
             # Adapt form request to API - style.
             payload_permissions = {}
@@ -425,7 +408,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             )
             message = "Your changes completed successfully."
         else:
-            return self.message_exception(trans, f"Invalid operation identifier ({operation}).")
+            raise MessageException(f"Invalid operation identifier ({operation}).")
         return {"status": status, "message": sanitize_text(message)}
 
     def _get_dataset_for_edit(self, trans, dataset_id):
@@ -452,34 +435,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
         return data, None
 
-    @web.expose
-    def imp(self, trans, dataset_id=None, **kwd):
-        """Import another user's dataset via a shared URL; dataset is added to user's current history."""
-        # Set referer message.
-        referer = trans.request.referer
-        if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
-            referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>"
-        else:
-            referer_message = f"<a href='{url_for('/')}'>go to Galaxy's start page</a>"
-        # Error checking.
-        if not dataset_id:
-            return trans.show_error_message(
-                f"You must specify a dataset to import. You can {referer_message}.", use_panels=True
-            )
-        # Do import.
-        cur_history = trans.get_history(create=True)
-        status, message = self._copy_datasets(trans, [dataset_id], [cur_history], imported=True)
-        message = (
-            f"Dataset imported. <br>You can <a href='{url_for('/')}'>start using the dataset</a> or {referer_message}."
-        )
-        return trans.show_message(message, type=status, use_panels=True)
-
-    @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True, **kwargs):
+    def _display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True, **kwargs):
         """Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""
         dataset = self._check_dataset(trans, slug)
-        if not isinstance(dataset, trans.app.model.DatasetInstance):
-            return dataset
         # Filename used for composite types.
         if filename:
             return self.display(trans, dataset_id=slug, filename=filename)
@@ -510,34 +468,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 first_chunk=first_chunk,
             )
 
-    @web.expose
-    def annotate_async(self, trans, id, new_annotation=None, **kwargs):
-        # TODO:?? why is this an access check only?
-        decoded_id = self.decode_id(id)
-        dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
-        dataset = self.hda_manager.error_if_uploading(dataset)
-        if not dataset:
-            web.httpexceptions.HTTPNotFound()
-        if dataset and new_annotation:
-            # Sanitize annotation before adding it.
-            new_annotation = sanitize_html(new_annotation)
-            self.add_item_annotation(trans.sa_session, trans.get_user(), dataset, new_annotation)
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            return new_annotation
-
-    @web.expose
-    def get_annotation_async(self, trans, id):
-        decoded_id = self.decode_id(id)
-        dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
-        dataset = self.hda_manager.error_if_uploading(dataset)
-        if not dataset:
-            web.httpexceptions.HTTPNotFound()
-        annotation = self.get_item_annotation_str(trans.sa_session, trans.user, dataset)
-        if annotation and isinstance(annotation, str):
-            annotation = annotation.encode("ascii", "replace")  # paste needs ascii here
-        return annotation
-
     @web.expose
     def display_at(self, trans, dataset_id, filename=None, **kwd):
         """Sets up a dataset permissions so it is viewable at an external site"""
@@ -727,177 +657,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             "You do not have permission to view this dataset at an external display application."
         )
 
-    def _delete(self, trans, dataset_id):
-        message = None
-        status = "done"
-        id = None
-        try:
-            id = self.decode_id(dataset_id)
-            hda = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
-            self.hda_manager.error_unless_mutable(hda.history)
-            hda.mark_deleted()
-            hda.clear_associated_files()
-            trans.log_event(f"Dataset id {str(id)} marked as deleted")
-            self.hda_manager.stop_creating_job(hda, flush=True)
-        except Exception:
-            msg = f"HDA deletion failed (encoded: {dataset_id}, decoded: {id})"
-            log.exception(msg)
-            trans.log_event(msg)
-            message = "Dataset deletion failed"
-            status = "error"
-        return (message, status)
-
-    def _undelete(self, trans, dataset_id):
-        message = None
-        status = "done"
-        id = None
-        try:
-            id = self.decode_id(dataset_id)
-            item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
-            self.hda_manager.error_unless_mutable(item.history)
-            self.hda_manager.undelete(item)
-            trans.log_event(f"Dataset id {str(id)} has been undeleted")
-        except Exception:
-            msg = f"HDA undeletion failed (encoded: {dataset_id}, decoded: {id})"
-            log.exception(msg)
-            trans.log_event(msg)
-            message = "Dataset undeletion failed"
-            status = "error"
-        return (message, status)
-
-    def _unhide(self, trans, dataset_id):
-        try:
-            id = self.decode_id(dataset_id)
-            item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
-            self.hda_manager.error_unless_mutable(item.history)
-            item.mark_unhidden()
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            trans.log_event(f"Dataset id {str(id)} has been unhidden")
-            return True
-        except Exception:
-            return False
-
-    def _purge(self, trans, dataset_id):
-        message = None
-        status = "done"
-        try:
-            id = self.decode_id(dataset_id)
-            user = trans.get_user()
-            hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
-            # Invalid HDA
-            assert hda, "Invalid history dataset ID"
-
-            # If the user is anonymous, make sure the HDA is owned by the current session.
-            if not user:
-                current_history_id = trans.galaxy_session.current_history_id
-                assert hda.history.id == current_history_id, "Data does not belong to current user"
-            # If the user is known, make sure the HDA is owned by the current user.
-            else:
-                assert hda.history.user == user, "Data does not belong to current user"
-
-            # Ensure HDA is deleted
-            hda.deleted = True
-            # HDA is purgeable
-            # Decrease disk usage first
-            hda.purge_usage_from_quota(user, hda.dataset.quota_source_info)
-            # Mark purged
-            hda.purged = True
-            trans.sa_session.add(hda)
-            trans.log_event(f"HDA id {hda.id} has been purged")
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            # Don't delete anything if there are active HDAs or any LDDAs, even if
-            # the LDDAs are deleted.  Let the cleanup scripts get it in the latter
-            # case.
-            if hda.dataset.user_can_purge:
-                try:
-                    hda.dataset.full_delete(user=user)
-                    trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the purge of HDA id {hda.id}")
-                    trans.sa_session.add(hda.dataset)
-                except Exception:
-                    log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):")
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-        except Exception:
-            msg = f"HDA purge failed (encoded: {dataset_id}, decoded: {id})"
-            log.exception(msg)
-            trans.log_event(msg)
-            message = "Dataset removal from disk failed"
-            status = "error"
-        return (message, status)
-
-    @web.expose
-    def delete(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
-        message, status = self._delete(trans, dataset_id)
-        return trans.response.send_redirect(
-            web.url_for(
-                controller="root",
-                action="history",
-                show_deleted=show_deleted_on_refresh,
-                message=message,
-                status=status,
-            )
-        )
-
-    @web.expose
-    def delete_async(self, trans, dataset_id, filename):
-        message, status = self._delete(trans, dataset_id)
-        if status == "done":
-            return "OK"
-        else:
-            raise Exception(message)
-
-    @web.expose
-    def undelete(self, trans, dataset_id, filename):
-        message, status = self._undelete(trans, dataset_id)
-        return trans.response.send_redirect(
-            web.url_for(controller="root", action="history", show_deleted=True, message=message, status=status)
-        )
-
-    @web.expose
-    def undelete_async(self, trans, dataset_id, filename):
-        message, status = self._undelete(trans, dataset_id)
-        if status == "done":
-            return "OK"
-        else:
-            raise Exception(message)
-
-    @web.expose
-    def unhide(self, trans, dataset_id, filename):
-        if self._unhide(trans, dataset_id):
-            return trans.response.send_redirect(web.url_for(controller="root", action="history", show_hidden=True))
-        raise Exception("Error unhiding")
-
-    @web.expose
-    def purge(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
-        if trans.app.config.allow_user_dataset_purge:
-            message, status = self._purge(trans, dataset_id)
-        else:
-            message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
-            status = "error"
-        return trans.response.send_redirect(
-            web.url_for(
-                controller="root",
-                action="history",
-                show_deleted=show_deleted_on_refresh,
-                message=message,
-                status=status,
-            )
-        )
-
-    @web.expose
-    def purge_async(self, trans, dataset_id, filename):
-        if trans.app.config.allow_user_dataset_purge:
-            message, status = self._purge(trans, dataset_id)
-        else:
-            message = "Removal of datasets by users is not allowed in this Galaxy instance.  Please contact your Galaxy administrator."
-            status = "error"
-        if status == "done":
-            return "OK"
-        else:
-            raise Exception(message)
-
     @web.expose
     def copy_datasets(
         self,
@@ -1043,53 +802,3 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             error_msg=error_msg,
             refresh_frames=refresh_frames,
         )
-
-    def _copy_datasets(self, trans, dataset_ids, target_histories, imported=False):
-        """Helper method for copying datasets."""
-        user = trans.get_user()
-        done_msg = error_msg = ""
-
-        invalid_datasets = 0
-        if not dataset_ids or not target_histories:
-            error_msg = "You must provide both source datasets and target histories."
-        else:
-            # User must own target histories to copy datasets to them.
-            for history in target_histories:
-                if user != history.user:
-                    error_msg = (
-                        error_msg
-                        + "You do not have permission to add datasets to %i requested histories.  "
-                        % (len(target_histories))
-                    )
-            for dataset_id in dataset_ids:
-                decoded_id = self.decode_id(dataset_id)
-                data = self.hda_manager.get_accessible(decoded_id, trans.user)
-                data = self.hda_manager.error_if_uploading(data)
-
-                if data is None:
-                    error_msg = f"{error_msg}You tried to copy a dataset that does not exist or that you do not have access to.  "
-                    invalid_datasets += 1
-                else:
-                    for hist in target_histories:
-                        dataset_copy = data.copy()
-                        if imported:
-                            dataset_copy.name = f"imported: {dataset_copy.name}"
-                        hist.add_dataset(dataset_copy)
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
-            num_datasets_copied = len(dataset_ids) - invalid_datasets
-            done_msg = "%i dataset%s copied to %i histor%s." % (
-                num_datasets_copied,
-                iff(num_datasets_copied == 1, "", "s"),
-                len(target_histories),
-                iff(len(target_histories) == 1, "y", "ies"),
-            )
-            trans.sa_session.refresh(history)
-
-        if error_msg != "":
-            status = ERROR
-            message = error_msg
-        else:
-            status = SUCCESS
-            message = done_msg
-        return status, message
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index a9d5ff4bc8ab34457a782a0a40252c70a71827cf..55bb4e9bb809ef8e97ddd9d01fe1a7a324d2ed06 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -12,6 +12,7 @@ from galaxy.managers import histories
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.model import Role
 from galaxy.model.base import transaction
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.model.item_attrs import (
     UsesAnnotations,
     UsesItemRatings,
@@ -88,8 +89,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             "allow_user_dataset_purge": trans.app.config.allow_user_dataset_purge,
         }
 
-    @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, **kwargs):
+    def _display_by_username_and_slug(self, trans, username, slug, **kwargs):
         """
         Display history based on a username and slug.
         """
@@ -135,13 +135,20 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
         if trans.request.method == "GET":
             inputs = []
-            all_roles = trans.user.all_roles()
+            all_roles = set(trans.user.all_roles())
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
             current_actions = history.default_permissions
             for action_key, action in trans.app.model.Dataset.permitted_actions.items():
                 in_roles = set()
                 for a in current_actions:
                     if a.action == action.action:
                         in_roles.add(a.role)
+
+                role_tuples = []
+                for role in all_roles:
+                    displayed_name = private_role_emails.get(role.id, role.name)
+                    role_tuples.append((displayed_name, trans.security.encode_id(role.id)))
+
                 inputs.append(
                     {
                         "type": "select",
@@ -151,7 +158,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                         "name": action_key,
                         "label": action.action,
                         "help": action.description,
-                        "options": [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
+                        "options": role_tuples,
                         "value": [trans.security.encode_id(role.id) for role in in_roles],
                     }
                 )
@@ -244,7 +251,7 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             history = trans.get_history()
             if history:
                 history.resume_paused_jobs()
-                return trans.show_ok_message("Your jobs have been resumed.")
+                return {"message": "Your jobs have been resumed.", "status": "success"}
         raise exceptions.RequestParameterInvalidException(
             "You can currently only resume all the datasets of the current history."
         )
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index b222c7a6be3e5ae46ca5a9ca2d438fe5652c72cc..fac24d92648dc52f2d1f366dd5bae8077cf9dac9 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -13,9 +13,9 @@ from galaxy.managers.pages import (
     PageManager,
 )
 from galaxy.managers.sharable import SlugBuilder
-from galaxy.managers.users import get_user_by_username
 from galaxy.managers.workflows import WorkflowsManager
 from galaxy.model.base import transaction
+from galaxy.model.db.user import get_user_by_username
 from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.schema.schema import CreatePagePayload
 from galaxy.structured_app import StructuredApp
@@ -170,8 +170,7 @@ class PageController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, U
             raise web.httpexceptions.HTTPNotFound()
         return self.display_by_username_and_slug(trans, page.user.username, page.slug)
 
-    @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, **kwargs):
+    def _display_by_username_and_slug(self, trans, username, slug, **kwargs):
         """Display page based on a username and slug."""
 
         # Get page.
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index 7e4f1d52f137c821a81f21908e9aa254558fb591..0e3f61737edf01a8cd32dc88fca970c971e08120 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -6,7 +6,10 @@ import logging
 
 from webob.exc import HTTPNotFound
 
-from galaxy import web
+from galaxy import (
+    exceptions,
+    web,
+)
 from galaxy.managers.histories import HistoryManager
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.structured_app import StructuredApp
@@ -96,24 +99,29 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         """
         # TODO: unencoded id
         data = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
-        authz_method = "rbac"
-        if "authz_method" in kwd:
-            authz_method = kwd["authz_method"]
+        authz_method = kwd.get("authz_method", "rbac")
         if data:
             if authz_method == "rbac" and trans.app.security_agent.can_access_dataset(
                 trans.get_current_user_roles(), data.dataset
             ):
-                trans.response.set_content_type(data.get_mime())
-                trans.log_event(f"Formatted dataset id {str(id)} for display at {display_app}")
-                return data.as_display_type(display_app, **kwd)
+                pass
             elif authz_method == "display_at" and trans.app.host_security_agent.allow_action(
                 trans.request.remote_addr, data.permitted_actions.DATASET_ACCESS, dataset=data
             ):
-                trans.response.set_content_type(data.get_mime())
-                return data.as_display_type(display_app, **kwd)
+                pass
             else:
+                trans.response.status = 403
                 return "You are not allowed to access this dataset."
+            try:
+                self.app.hda_manager.ensure_dataset_on_disk(trans, data)
+            except exceptions.MessageException as e:
+                trans.response.status = e.status_code
+                return str(e)
+            trans.response.set_content_type(data.get_mime())
+            trans.log_event(f"Formatted dataset id {str(id)} for display at {display_app}")
+            return data.as_display_type(display_app, **kwd)
         else:
+            trans.response.status = 400
             return "No data with id=%d" % id
 
     @web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index eafcf5dbc7029328134a7f1da56679e070ba245f..9afc442292a46a78d68f8e991ed1bd0122f23320 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -18,8 +18,9 @@ from galaxy import (
 )
 from galaxy.exceptions import Conflict
 from galaxy.managers import users
-from galaxy.managers.users import get_user_by_email
+from galaxy.model.db.user import get_user_by_email
 from galaxy.security.validate_user_input import (
+    is_valid_email_str,
     validate_email,
     validate_publicname,
 )
@@ -161,6 +162,9 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
             message, user = self.__autoregistration(trans, login, password)
             if message:
                 return self.message_exception(trans, message)
+        elif user.purged:
+            message = "This account has been permanently deleted."
+            return self.message_exception(trans, message, sanitize=False)
         elif user.deleted:
             message = (
                 "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
@@ -280,25 +284,37 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
         Check whether token fits the user and then activate the user's account.
         """
         params = util.Params(kwd, sanitize=False)
-        email = params.get("email", None)
-        if email is not None:
-            email = unquote(email)
         activation_token = params.get("activation_token", None)
         index_url = web.url_for(controller="root", action="index")
+        invalid_link_message = f"You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='{index_url}'>Go to login page.</a>"
+
+        email = params.get("email", None)
+        if email is not None:
+            try:
+                email = unquote(email)
+            except AttributeError:
+                # A recurring error has been observed where the email parameter is a list of 2 items, where the second item is the email, and
+                # the first item has the shape "[email]?activation_token=[activation token]". This may happen if the user incorrectly copies and pastes
+                # the activation link into their browser. We try to handle this case here.
+                if (
+                    isinstance(email, list)
+                    and len(email) == 2
+                    and is_valid_email_str(email[1])
+                    and email[0].startswith(email[1])
+                ):
+                    email = unquote(email[1])
+                else:
+                    return trans.show_error_message(invalid_link_message)
 
         if email is None or activation_token is None:
             #  We don't have the email or activation_token, show error.
-            return trans.show_error_message(
-                f"You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='{index_url}'>Go to login page.</a>"
-            )
+            return trans.show_error_message(invalid_link_message)
         else:
             # Find the user
             user = get_user_by_email(trans.sa_session, email)
             if not user:
                 # Probably wrong email address
-                return trans.show_error_message(
-                    f"You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='{index_url}'>Go to login page.</a>"
-                )
+                return trans.show_error_message(invalid_link_message)
             # If the user is active already don't try to activate
             if user.active is True:
                 return trans.show_ok_message(
@@ -312,9 +328,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
                 )
             else:
                 #  Tokens don't match. Activation is denied.
-                return trans.show_error_message(
-                    f"You are using an invalid activation link. Try to log in and we will send you a new activation email. <br><a href='{index_url}'>Go to login page.</a>"
-                )
+                return trans.show_error_message(invalid_link_message)
 
     @expose_api_anonymous_and_sessionless
     def change_password(self, trans, payload=None, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 622a896ab2b95bb14425b91b0e49eef693d7bbfa..f57ca8d0e8fedec0699b3ed0f4d3d149ba753fc8 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -1,5 +1,4 @@
 import logging
-from json import loads
 
 from markupsafe import escape
 from paste.httpexceptions import (
@@ -41,6 +40,16 @@ class VisualizationController(
     def __init__(self, app: StructuredApp):
         super().__init__(app)
 
+    def get_visualization(self, trans, visualization_id, check_ownership=True, check_accessible=False):
+        """
+        Get a Visualization from the database by id, verifying ownership.
+        """
+        visualization = trans.sa_session.get(model.Visualization, trans.security.decode_id(visualization_id))
+        if not visualization:
+            raise MessageException("Visualization not found")
+        else:
+            return self.security_check(trans, visualization, check_ownership, check_accessible)
+
     #
     # -- Functions for operating on visualizations. --
     #
@@ -111,8 +120,7 @@ class VisualizationController(
                 use_panels=True,
             )
 
-    @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, **kwargs):
+    def _display_by_username_and_slug(self, trans, username, slug, **kwargs):
         """Display visualization based on a username and slug."""
 
         # Get visualization.
@@ -139,21 +147,6 @@ class VisualizationController(
             )
         )
 
-    @web.json
-    def save(self, trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None, **kwargs):
-        """
-        Save a visualization; if visualization does not have an ID, a new
-        visualization is created. Returns JSON of visualization.
-        """
-        # Get visualization attributes from kwargs or from config.
-        vis_config = loads(vis_json)
-        vis_type = type or vis_config["type"]
-        vis_id = id or vis_config.get("id", None)
-        vis_title = title or vis_config.get("title", None)
-        vis_dbkey = dbkey or vis_config.get("dbkey", None)
-        vis_annotation = annotation or vis_config.get("annotation", None)
-        return self.save_visualization(trans, vis_config, vis_type, vis_id, vis_title, vis_dbkey, vis_annotation)
-
     @web.legacy_expose_api
     @web.require_login("edit visualizations")
     def edit(self, trans, payload=None, **kwd):
@@ -275,12 +268,8 @@ class VisualizationController(
     @web.require_login("use Galaxy visualizations", use_panels=True)
     def saved(self, trans, id=None, revision=None, type=None, config=None, title=None, **kwargs):
         """
-        Save (on POST) or load (on GET) a visualization then render.
+        Load a visualization and render it.
         """
-        # TODO: consider merging saved and render at this point (could break saved URLs, tho)
-        if trans.request.method == "POST":
-            self._POST_to_saved(trans, id=id, revision=revision, type=type, config=config, title=title, **kwargs)
-
         # check the id and load the saved visualization
         if id is None:
             return HTTPBadRequest("A valid visualization id is required to load a visualization")
@@ -295,38 +284,6 @@ class VisualizationController(
         except Exception as exception:
             self._handle_plugin_error(trans, visualization.type, exception)
 
-    def _POST_to_saved(self, trans, id=None, revision=None, type=None, config=None, title=None, **kwargs):
-        """
-        Save the visualiztion info (revision, type, config, title, etc.) to
-        the Visualization at `id` or to a new Visualization if `id` is None.
-
-        Uses POST/redirect/GET after a successful save, redirecting to GET.
-        """
-        DEFAULT_VISUALIZATION_NAME = "Unnamed Visualization"
-
-        # post to saved in order to save a visualization
-        if type is None or config is None:
-            return HTTPBadRequest("A visualization type and config are required to save a visualization")
-        if isinstance(config, str):
-            config = loads(config)
-        title = title or DEFAULT_VISUALIZATION_NAME
-
-        # TODO: allow saving to (updating) a specific revision - should be part of UsesVisualization
-        # TODO: would be easier if this returned the visualization directly
-        # check security if posting to existing visualization
-        if id is not None:
-            self.get_visualization(trans, id, check_ownership=True, check_accessible=False)
-            # ??: on not owner: error raised, but not returned (status = 200)
-        # TODO: there's no security check in save visualization (if passed an id)
-        returned = self.save_visualization(trans, config, type, id, title)
-
-        # redirect to GET to prevent annoying 'Do you want to post again?' dialog on page reload
-        render_url = web.url_for(controller="visualization", action="saved", id=returned.get("vis_id"))
-        return trans.response.send_redirect(render_url)
-
-    #
-    # Visualizations.
-    #
     @web.expose
     @web.require_login()
     def trackster(self, trans, **kwargs):
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 085834f67ec07a1b2b523fa7422cb5df28e1c3be..770196cd2a20ccac5efa273fc6914be2a4c2c8a4 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1,8 +1,6 @@
 import logging
 
 from markupsafe import escape
-from sqlalchemy import desc
-from sqlalchemy.orm import joinedload
 
 from galaxy import (
     model,
@@ -38,8 +36,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     def __init__(self, app: StructuredApp):
         super().__init__(app)
 
-    @web.expose
-    def display_by_username_and_slug(self, trans, username, slug, format="html", **kwargs):
+    def _display_by_username_and_slug(self, trans, username, slug, format="html", **kwargs):
         """
         Display workflow based on a username and slug. Format can be html, json, or json-download.
         """
@@ -164,16 +161,6 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             else:
                 new_workflow = True
 
-        # The following query loads all user-owned workflows,
-        # So that they can be copied or inserted in the workflow editor.
-        workflows = (
-            trans.sa_session.query(model.StoredWorkflow)
-            .filter_by(user=trans.user, deleted=False, hidden=False)
-            .order_by(desc(model.StoredWorkflow.table.c.update_time))
-            .options(joinedload(model.StoredWorkflow.latest_workflow).joinedload(model.Workflow.steps))
-            .all()
-        )
-
         # create workflow module models
         module_sections = []
         for module_section in load_module_sections(trans).values():
@@ -216,27 +203,14 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
             # identify item tags
             item_tags = stored.make_tag_string_list()
 
-        # create workflow models
-        workflows = [
-            {
-                "id": trans.security.encode_id(workflow.id),
-                "latest_id": trans.security.encode_id(workflow.latest_workflow.id),
-                "step_count": len(workflow.latest_workflow.steps),
-                "name": workflow.name,
-            }
-            for workflow in workflows
-            if new_workflow or workflow.id != stored.id
-        ]
-
         # build workflow editor model
         editor_config = {
             "moduleSections": module_sections,
             "dataManagers": data_managers,
-            "workflows": workflows,
         }
 
         # for existing workflow add its data to the model
-        if new_workflow is False:
+        if stored:
             editor_config.update(
                 {
                     "id": trans.security.encode_id(stored.id),
@@ -276,7 +250,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         return self._workflow_to_dict(trans, stored)
 
     @web.json_pretty
-    def export_to_file(self, trans, id):
+    def export_to_file(self, trans, id, **kwds):
         """
         Get the latest Workflow for the StoredWorkflow identified by `id` and
         export it to a JSON file that can be imported back into Galaxy.
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index 02a191efe9a05b8b51f70e7369bafcfe61ab9cb2..143586156e8f83eacee40b00832fdd62310b2b44 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -10,7 +10,6 @@ from fastapi import (
 )
 from fastapi.openapi.constants import REF_TEMPLATE
 from starlette.middleware.cors import CORSMiddleware
-from starlette.responses import Response
 
 from galaxy.schema.generics import CustomJsonSchema
 from galaxy.version import VERSION
@@ -121,14 +120,6 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
             allow_methods=["*"],
             max_age=600,
         )
-    else:
-        # handle CORS preflight requests - synchronize with wsgi behavior.
-        @app.options("/api/{rest_of_path:path}")
-        async def preflight_handler(request: Request, rest_of_path: str) -> Response:
-            response = Response()
-            response.headers["Access-Control-Allow-Headers"] = "*"
-            response.headers["Access-Control-Max-Age"] = "600"
-            return response
 
 
 def include_legacy_openapi(app, gx_app):
diff --git a/lib/galaxy/webapps/galaxy/script.py b/lib/galaxy/webapps/galaxy/script.py
new file mode 100644
index 0000000000000000000000000000000000000000..4ca9d050bf7ebd2f5e732e43d93ad1110466c80b
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/script.py
@@ -0,0 +1,30 @@
+import os
+from argparse import ArgumentParser
+
+import uvicorn
+
+
+def main() -> None:
+    parser = ArgumentParser(
+        prog="galaxy-web",
+        description="Run Galaxy Web Server",
+    )
+    parser.add_argument("--config", "-c", help="Galaxy config file")
+    parser.add_argument("--single-user", "-s", help="Single user mode as user SINGLE_USER")
+    parser.add_argument("--bind", "-b", default="localhost:8080", help="Bind to <host>:<port>")
+    parser.add_argument(
+        "--client-path", "-n", default="node_modules/@galaxyproject/galaxy-client", help="Path to Galaxy client"
+    )
+    args = parser.parse_args()
+    if args.config:
+        os.environ["GALAXY_CONFIG_FILE"] = args.config
+    if args.single_user:
+        os.environ["GALAXY_CONFIG_SINGLE_USER"] = args.single_user
+        os.environ["GALAXY_CONFIG_ADMIN_USERS"] = args.single_user
+    os.environ["GALAXY_CONFIG_STATIC_DIR"] = args.client_path
+    uvicorn.run(
+        "galaxy.webapps.galaxy.fast_factory:factory",
+        factory=True,
+        host=args.bind.split(":")[0],
+        port=int(args.bind.split(":")[1]),
+    )
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 1b760e317871b22021af42cf1da970dcc2a3887c..e37335d829f00c75d5c85e1e3d0acc06c5cba271 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -252,7 +252,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
             raise exceptions.RequestParameterInvalidException(
                 "Parameter instance_type not being 'history' is not yet implemented."
             )
-        hdca: "HistoryDatasetCollectionAssociation" = self.collection_manager.get_dataset_collection_instance(
+        hdca: HistoryDatasetCollectionAssociation = self.collection_manager.get_dataset_collection_instance(
             trans, "history", hdca_id
         )
 
diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py
index b8d79bba04de67ad5802fc30824217e99e53d2c0..188eb9c3bae1c9c971f8d3f886f4521911c7fd85 100644
--- a/lib/galaxy/webapps/galaxy/services/datasets.py
+++ b/lib/galaxy/webapps/galaxy/services/datasets.py
@@ -325,7 +325,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         history_id: Optional[DecodedDatabaseIdField],
         serialization_params: SerializationParams,
         filter_query_params: FilterQueryParams,
-    ) -> List[AnyHistoryContentItem]:
+    ) -> Tuple[List[AnyHistoryContentItem], int]:
         """
         Search datasets or collections using a query system and returns a list
         containing summary of dataset or dataset_collection information.
@@ -345,12 +345,20 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             order_by=order_by,
             user_id=user.id,
         )
-        return [
-            self.serializer_by_type[content.history_content_type].serialize_to_view(
-                content, user=user, trans=trans, encode_id=False, **serialization_params.model_dump()
-            )
-            for content in contents
-        ]
+        total_matches = self.history_contents_manager.contents_count(
+            container=container,
+            filters=filters,
+            user_id=user.id,
+        )
+        return (
+            [
+                self.serializer_by_type[content.history_content_type].serialize_to_view(
+                    content, user=user, trans=trans, encode_id=False, **serialization_params.model_dump()
+                )
+                for content in contents
+            ],
+            total_matches,
+        )
 
     def show(
         self,
@@ -403,7 +411,11 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             # Default: return dataset as dict.
             if hda_ldda == DatasetSourceType.hda:
                 return self.hda_serializer.serialize_to_view(
-                    dataset, view=serialization_params.view or "detailed", user=trans.user, trans=trans
+                    dataset,
+                    view=serialization_params.view or "detailed",
+                    keys=serialization_params.keys,
+                    user=trans.user,
+                    trans=trans,
                 )
             else:
                 dataset_dict = dataset.to_dict()
@@ -569,7 +581,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
         dataset_manager = self.dataset_manager_by_type[hda_ldda]
         dataset = dataset_manager.get_accessible(dataset_id, trans.user)
         dataset_manager.update_permissions(trans, dataset, **payload_dict)
-        return dataset_manager.serialize_dataset_association_roles(trans, dataset)
+        return dataset_manager.serialize_dataset_association_roles(dataset)
 
     def extra_files(
         self,
@@ -735,7 +747,8 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
             try:
                 manager = self.dataset_manager_by_type[dataset.src]
                 dataset_instance = manager.get_owned(dataset.id, trans.user)
-                manager.error_unless_mutable(dataset_instance.history)
+                if hasattr(dataset_instance, "history"):
+                    manager.error_unless_mutable(dataset_instance.history)
                 if dataset.src == DatasetSourceType.hda:
                     self.hda_manager.error_if_uploading(dataset_instance)
                 if payload.purge:
diff --git a/lib/galaxy/webapps/galaxy/services/histories.py b/lib/galaxy/webapps/galaxy/services/histories.py
index d5a6a75ffba7e68e9760686748809ccffbf4cf49..32e8a9fa8a1c28edc3db7ea28f933112273c0b81 100644
--- a/lib/galaxy/webapps/galaxy/services/histories.py
+++ b/lib/galaxy/webapps/galaxy/services/histories.py
@@ -686,7 +686,7 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         history: model.History,
         serialization_params: SerializationParams,
         default_view: str = "detailed",
-    ) -> AnyHistoryView:
+    ):
         """
         Returns a dictionary with the corresponding values depending on the
         serialization parameters provided.
@@ -793,7 +793,10 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
             filters=filters, order_by=order_by, limit=filter_query_params.limit, offset=filter_query_params.offset
         )
 
-        histories = [self._serialize_archived_history(trans, history, serialization_params) for history in histories]
+        histories = [
+            self._serialize_archived_history(trans, history, serialization_params, default_view="summary")
+            for history in histories
+        ]
         return histories, total_matches
 
     def _serialize_archived_history(
@@ -801,14 +804,13 @@ class HistoriesService(ServiceBase, ConsumesModelStores, ServesExportStores):
         trans: ProvidesHistoryContext,
         history: model.History,
         serialization_params: Optional[SerializationParams] = None,
+        default_view: str = "detailed",
     ):
         if serialization_params is None:
-            serialization_params = SerializationParams(default_view="summary")
-        archived_history = self.serializer.serialize_to_view(
-            history, user=trans.user, trans=trans, **serialization_params.dict()
-        )
+            serialization_params = SerializationParams()
+        archived_history = self._serialize_history(trans, history, serialization_params, default_view)
         export_record_data = self._get_export_record_data(history)
-        archived_history["export_record_data"] = export_record_data.dict() if export_record_data else None
+        archived_history["export_record_data"] = export_record_data.model_dump() if export_record_data else None
         return archived_history
 
     def _get_export_record_data(self, history: model.History) -> Optional[WriteStoreToPayload]:
diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index 03bda2fa5aa9b00e18fb0b900aba93f0511dacc4..0f2069658fb07b70b362b27b8426a5c5db2c4f26 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -605,7 +605,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
         assert hda is not None
         self.history_manager.error_unless_mutable(hda.history)
         self.hda_manager.update_permissions(trans, hda, **payload_dict)
-        roles = self.hda_manager.serialize_dataset_association_roles(trans, hda)
+        roles = self.hda_manager.serialize_dataset_association_roles(hda)
         return DatasetAssociationRoles(**roles)
 
     def update(
@@ -698,7 +698,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
         history = self.history_manager.get_mutable(history_id, trans.user, current_history=trans.history)
         filters = self.history_contents_filters.parse_query_filters(filter_query_params)
         self._validate_bulk_operation_params(payload, trans.user, trans)
-        contents: List["HistoryItem"]
+        contents: List[HistoryItem]
         if payload.items:
             contents = self._get_contents_by_item_list(
                 trans,
@@ -1172,22 +1172,28 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
                         rval.append(ld)
                 return rval
 
-            for ld in traverse(folder):
-                hda = ld.library_dataset_dataset_association.to_history_dataset_association(
-                    history, add_to_history=True
+            hdas = [
+                ld.library_dataset_dataset_association.to_history_dataset_association(
+                    history, add_to_history=True, commit=False
                 )
+                for ld in traverse(folder)
+            ]
+            history.add_pending_items()
+
+            with transaction(trans.sa_session):
+                trans.sa_session.commit()
+
+            for hda in hdas:
                 hda_dict = self.hda_serializer.serialize_to_view(
                     hda, user=trans.user, trans=trans, encode_id=False, **serialization_params.model_dump()
                 )
                 rval.append(hda_dict)
+            return rval
+
         else:
             message = f"Invalid 'source' parameter in request: {source}"
             raise exceptions.RequestParameterInvalidException(message)
 
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
-        return rval
-
     def __create_dataset(
         self,
         trans,
@@ -1367,7 +1373,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
     def _get_contents_by_item_list(
         self, trans, history: History, items: List[HistoryContentItem]
     ) -> List["HistoryItem"]:
-        contents: List["HistoryItem"] = []
+        contents: List[HistoryItem] = []
 
         dataset_items = filter(lambda item: item.history_content_type == HistoryContentType.dataset, items)
         datasets_ids = (dataset.id for dataset in dataset_items)
diff --git a/lib/galaxy/webapps/galaxy/services/invocations.py b/lib/galaxy/webapps/galaxy/services/invocations.py
index 9b18db8f1b2db83f8cf86485139ad8319a33e2e7..9b7ef61cc1cec1a43e6f4224e1c0ae548494e530 100644
--- a/lib/galaxy/webapps/galaxy/services/invocations.py
+++ b/lib/galaxy/webapps/galaxy/services/invocations.py
@@ -1,3 +1,4 @@
+import json
 import logging
 from typing import (
     Any,
@@ -14,18 +15,27 @@ from galaxy.celery.tasks import (
 )
 from galaxy.exceptions import (
     AdminRequiredException,
+    InconsistentDatabase,
     ObjectNotFound,
 )
-from galaxy.managers.context import ProvidesHistoryContext
+from galaxy.managers.context import (
+    ProvidesHistoryContext,
+    ProvidesUserContext,
+)
 from galaxy.managers.histories import HistoryManager
 from galaxy.managers.jobs import (
     fetch_job_states,
+    get_job_metrics_for_invocation,
     invocation_job_source_iter,
+    summarize_metrics,
 )
 from galaxy.managers.workflows import WorkflowsManager
 from galaxy.model import (
+    HistoryDatasetAssociation,
+    HistoryDatasetCollectionAssociation,
     WorkflowInvocation,
     WorkflowInvocationStep,
+    WorkflowRequestInputParameter,
 )
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.invocation import (
@@ -33,6 +43,7 @@ from galaxy.schema.invocation import (
     InvocationSerializationParams,
     InvocationSerializationView,
     InvocationStep,
+    WorkflowInvocationRequestModel,
     WorkflowInvocationResponse,
 )
 from galaxy.schema.schema import (
@@ -122,14 +133,23 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
             sort_by=invocation_payload.sort_by,
             sort_desc=invocation_payload.sort_desc,
             include_nested_invocations=invocation_payload.include_nested_invocations,
+            check_ownership=False,
         )
         invocation_dict = self.serialize_workflow_invocations(invocations, serialization_params)
         return invocation_dict, total_matches
 
     def show(self, trans, invocation_id, serialization_params, eager=False):
-        wfi = self._workflows_manager.get_invocation(trans, invocation_id, eager)
+        wfi = self._workflows_manager.get_invocation(
+            trans, invocation_id, eager, check_ownership=False, check_accessible=True
+        )
         return self.serialize_workflow_invocation(wfi, serialization_params)
 
+    def as_request(self, trans: ProvidesUserContext, invocation_id) -> WorkflowInvocationRequestModel:
+        wfi = self._workflows_manager.get_invocation(
+            trans, invocation_id, True, check_ownership=True, check_accessible=True
+        )
+        return self.serialize_workflow_invocation_to_request(trans, wfi)
+
     def cancel(self, trans, invocation_id, serialization_params):
         wfi = self._workflows_manager.request_invocation_cancellation(trans, invocation_id)
         return self.serialize_workflow_invocation(wfi, serialization_params)
@@ -139,9 +159,34 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
         return wfi_report
 
     def show_invocation_step(self, trans, step_id) -> InvocationStep:
-        wfi_step = self._workflows_manager.get_invocation_step(trans, step_id)
+        wfi_step = self._workflows_manager.get_invocation_step(
+            trans, step_id, check_ownership=False, check_accessible=True
+        )
         return self.serialize_workflow_invocation_step(wfi_step)
 
+    def show_invocation_metrics(self, trans: ProvidesHistoryContext, invocation_id: int):
+        extended_job_metrics = get_job_metrics_for_invocation(trans.sa_session, invocation_id)
+        job_metrics = []
+        job_ids = []
+        tool_ids = []
+        step_indexes = []
+        step_labels = []
+        for row in extended_job_metrics:
+            step_indexes.append(row[0])
+            job_ids.append(row[1])
+            tool_ids.append(row[2])
+            step_labels.append(row[3])
+            job_metrics.append(row[4])
+        metrics_dict_list = summarize_metrics(trans, job_metrics)
+        for tool_id, job_id, step_index, step_label, metrics_dict in zip(
+            tool_ids, job_ids, step_indexes, step_labels, metrics_dict_list
+        ):
+            metrics_dict["tool_id"] = tool_id
+            metrics_dict["job_id"] = trans.security.encode_id(job_id)
+            metrics_dict["step_index"] = step_index
+            metrics_dict["step_label"] = step_label
+        return metrics_dict_list
+
     def update_invocation_step(self, trans, step_id, action):
         wfi_step = self._workflows_manager.update_invocation_step(trans, step_id, action)
         return self.serialize_workflow_invocation_step(wfi_step)
@@ -164,7 +209,9 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
     ) -> AsyncFile:
         ensure_celery_tasks_enabled(trans.app.config)
         model_store_format = payload.model_store_format
-        workflow_invocation = self._workflows_manager.get_invocation(trans, invocation_id, eager=True)
+        workflow_invocation = self._workflows_manager.get_invocation(
+            trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
+        )
         if not workflow_invocation:
             raise ObjectNotFound()
         try:
@@ -190,7 +237,9 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
         self, trans, invocation_id: DecodedDatabaseIdField, payload: WriteInvocationStoreToPayload
     ) -> AsyncTaskResultSummary:
         ensure_celery_tasks_enabled(trans.app.config)
-        workflow_invocation = self._workflows_manager.get_invocation(trans, invocation_id, eager=True)
+        workflow_invocation = self._workflows_manager.get_invocation(
+            trans, invocation_id, eager=True, check_ownership=False, check_accessible=True
+        )
         if not workflow_invocation:
             raise ObjectNotFound()
         request = WriteInvocationTo(
@@ -243,3 +292,71 @@ class InvocationsService(ServiceBase, ConsumesModelStores):
             history=history,
         )
         return self.serialize_workflow_invocations(object_tracker.invocations_by_key.values(), serialization_params)
+
+    def serialize_workflow_invocation_to_request(
+        self, trans: ProvidesUserContext, invocation: WorkflowInvocation
+    ) -> WorkflowInvocationRequestModel:
+        history_id = trans.security.encode_id(invocation.history.id)
+        workflow_id = trans.security.encode_id(invocation.workflow.id)
+        inputs, inputs_by = invocation.recover_inputs()
+        export_inputs = {}
+        for key, value in inputs.items():
+            if isinstance(value, HistoryDatasetAssociation):
+                export_inputs[key] = {"src": "hda", "id": trans.security.encode_id(value.id)}
+            elif isinstance(value, HistoryDatasetCollectionAssociation):
+                export_inputs[key] = {"src": "hdca", "id": trans.security.encode_id(value.id)}
+            else:
+                export_inputs[key] = value
+
+        param_types = WorkflowRequestInputParameter.types
+        steps_by_id = invocation.workflow.steps_by_id
+
+        replacement_dict = {}
+        resource_params = {}
+        use_cached_job = False
+        preferred_object_store_id = None
+        preferred_intermediate_object_store_id = None
+        preferred_outputs_object_store_id = None
+        step_param_map: Dict[str, Dict] = {}
+        for parameter in invocation.input_parameters:
+            parameter_type = parameter.type
+
+            if parameter_type == param_types.REPLACEMENT_PARAMETERS:
+                replacement_dict[parameter.name] = parameter.value
+            elif parameter_type == param_types.META_PARAMETERS:
+                # copy_inputs_to_history is being skipped here sort of intentionally,
+                # we wouldn't want to include this on re-run.
+                if parameter.name == "use_cached_job":
+                    use_cached_job = parameter.value == "true"
+                if parameter.name == "preferred_object_store_id":
+                    preferred_object_store_id = parameter.value
+                if parameter.name == "preferred_intermediate_object_store_id":
+                    preferred_intermediate_object_store_id = parameter.value
+                if parameter.name == "preferred_outputs_object_store_id":
+                    preferred_outputs_object_store_id = parameter.value
+            elif parameter_type == param_types.RESOURCE_PARAMETERS:
+                resource_params[parameter.name] = parameter.value
+            elif parameter_type == param_types.STEP_PARAMETERS:
+                # TODO: test subworkflows and ensure this works
+                step_id: int
+                try:
+                    step_id = int(parameter.name)
+                except TypeError:
+                    raise InconsistentDatabase("saved workflow step parameters not in the format expected")
+                step_param_map[str(steps_by_id[step_id].order_index)] = json.loads(parameter.value)
+
+        return WorkflowInvocationRequestModel(
+            history_id=history_id,
+            workflow_id=workflow_id,
+            instance=True,  # this is a workflow ID and not a stored workflow ID
+            inputs=export_inputs,
+            inputs_by=inputs_by,
+            replacement_params=None if not replacement_dict else replacement_dict,
+            resource_params=None if not resource_params else resource_params,
+            use_cached_job=use_cached_job,
+            preferred_object_store_id=preferred_object_store_id,
+            preferred_intermediate_object_store_id=preferred_intermediate_object_store_id,
+            preferred_outputs_object_store_id=preferred_outputs_object_store_id,
+            parameters_normalized=True,
+            parameters=None if not step_param_map else step_param_map,
+        )
diff --git a/lib/galaxy/webapps/galaxy/services/jobs.py b/lib/galaxy/webapps/galaxy/services/jobs.py
index 5c39175567bf0dc99ba5b576b8f8ecfa3e6509c3..c90b50068cc29bc7f03d2110f6bfc3e7ba20d231 100644
--- a/lib/galaxy/webapps/galaxy/services/jobs.py
+++ b/lib/galaxy/webapps/galaxy/services/jobs.py
@@ -58,7 +58,10 @@ class JobsService(ServiceBase):
         id: DecodedDatabaseIdField,
         full: bool = False,
     ) -> Dict[str, Any]:
-        job = self.job_manager.get_accessible_job(trans, id)
+        job = self.job_manager.get_accessible_job(
+            trans,
+            id,
+        )
         return view_show_job(trans, job, bool(full))
 
     def index(
diff --git a/lib/galaxy/webapps/galaxy/services/libraries.py b/lib/galaxy/webapps/galaxy/services/libraries.py
index 708f2bfb10f7a38f033204e9029528ff566228d1..435bac8f03934cb0ccf79a236ee7df9799c2c70b 100644
--- a/lib/galaxy/webapps/galaxy/services/libraries.py
+++ b/lib/galaxy/webapps/galaxy/services/libraries.py
@@ -16,6 +16,7 @@ from galaxy.managers.folders import FolderManager
 from galaxy.managers.libraries import LibraryManager
 from galaxy.managers.roles import RoleManager
 from galaxy.model import Role
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.schema import (
     BasicRoleModel,
@@ -170,9 +171,11 @@ class LibrariesService(ServiceBase, ConsumesModelStores):
                 trans, library, query, page, page_limit, is_library_access
             )
 
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
             return_roles = []
             for role in roles:
-                return_roles.append(BasicRoleModel(id=role.id, name=role.name, type=role.type))
+                displayed_name = private_role_emails.get(role.id, role.name)
+                return_roles.append(BasicRoleModel(id=role.id, name=displayed_name, type=role.type))
             return LibraryAvailablePermissions.model_construct(
                 roles=return_roles, page=page, page_limit=page_limit, total=total_roles
             )
diff --git a/lib/galaxy/webapps/galaxy/services/library_contents.py b/lib/galaxy/webapps/galaxy/services/library_contents.py
new file mode 100644
index 0000000000000000000000000000000000000000..971c356f56d37a8d30f00d57a10485f1ee847abb
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/services/library_contents.py
@@ -0,0 +1,303 @@
+import logging
+import shutil
+import tempfile
+from typing import (
+    cast,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+from fastapi import Path
+from starlette.datastructures import UploadFile as StarletteUploadFile
+from typing_extensions import Annotated
+
+from galaxy import exceptions
+from galaxy.actions.library import LibraryActions
+from galaxy.managers.collections import DatasetCollectionManager
+from galaxy.managers.context import (
+    ProvidesHistoryContext,
+    ProvidesUserContext,
+)
+from galaxy.managers.hdas import HDAManager
+from galaxy.model import (
+    Library,
+    tags,
+)
+from galaxy.model.base import transaction
+from galaxy.schema.fields import DecodedDatabaseIdField
+from galaxy.schema.library_contents import (
+    AnyLibraryContentsCreatePayload,
+    AnyLibraryContentsCreateResponse,
+    AnyLibraryContentsShowResponse,
+    LibraryContentsCreateDatasetCollectionResponse,
+    LibraryContentsCreateDatasetResponse,
+    LibraryContentsCreateFileListResponse,
+    LibraryContentsCreateFolderListResponse,
+    LibraryContentsDeletePayload,
+    LibraryContentsDeleteResponse,
+    LibraryContentsFileCreatePayload,
+    LibraryContentsIndexDatasetResponse,
+    LibraryContentsIndexFolderResponse,
+    LibraryContentsIndexListResponse,
+    LibraryContentsShowDatasetResponse,
+    LibraryContentsShowFolderResponse,
+    LibraryContentsUpdatePayload,
+)
+from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.webapps.base.controller import (
+    UsesExtendedMetadataMixin,
+    UsesLibraryMixinItems,
+)
+from galaxy.webapps.galaxy.services.base import ServiceBase
+
+log = logging.getLogger(__name__)
+
+MaybeLibraryFolderOrDatasetID = Annotated[
+    str,
+    Path(
+        title="The encoded ID of a library folder or dataset.",
+        example="F0123456789ABCDEF",
+        min_length=16,
+        pattern="F?[0-9a-fA-F]+",
+    ),
+]
+
+
+class LibraryContentsService(ServiceBase, LibraryActions, UsesLibraryMixinItems, UsesExtendedMetadataMixin):
+    """
+    Interface/service shared by controllers for interacting with the contents of a library contents.
+    """
+
+    def __init__(
+        self,
+        security: IdEncodingHelper,
+        hda_manager: HDAManager,
+        collection_manager: DatasetCollectionManager,
+    ):
+        super().__init__(security)
+        self.hda_manager = hda_manager
+        self.collection_manager = collection_manager
+
+    def index(
+        self,
+        trans: ProvidesUserContext,
+        library_id: DecodedDatabaseIdField,
+    ) -> LibraryContentsIndexListResponse:
+        """Return a list of library files and folders."""
+        rval: List[Union[LibraryContentsIndexFolderResponse, LibraryContentsIndexDatasetResponse]] = []
+        current_user_roles = trans.get_current_user_roles()
+        library = trans.sa_session.get(Library, library_id)
+        if not library:
+            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
+        if not (trans.user_is_admin or trans.app.security_agent.can_access_library(current_user_roles, library)):
+            raise exceptions.RequestParameterInvalidException("No library found with the id provided.")
+        # appending root folder
+        url = self._url_for(trans, library_id, library.root_folder.id, "folder")
+        rval.append(LibraryContentsIndexFolderResponse(id=library.root_folder.id, type="folder", name="/", url=url))
+        library.root_folder.api_path = ""
+        # appending all other items in the library recursively
+        for content in self._traverse(trans, library.root_folder, current_user_roles):
+            url = self._url_for(trans, library_id, content.id, content.api_type)
+            response_model: Union[LibraryContentsIndexFolderResponse, LibraryContentsIndexDatasetResponse]
+            common_args = dict(id=content.id, type=content.api_type, name=content.api_path, url=url)
+            if content.api_type == "folder":
+                response_model = LibraryContentsIndexFolderResponse(**common_args)
+            else:
+                response_model = LibraryContentsIndexDatasetResponse(**common_args)
+            rval.append(response_model)
+        return LibraryContentsIndexListResponse(root=rval)
+
+    def show(
+        self,
+        trans: ProvidesUserContext,
+        id: MaybeLibraryFolderOrDatasetID,
+    ) -> AnyLibraryContentsShowResponse:
+        """Returns information about library file or folder."""
+        class_name, content_id = self._decode_library_content_id(id)
+        if class_name == "LibraryFolder":
+            content = self.get_library_folder(trans, content_id, check_ownership=False, check_accessible=True)
+            return LibraryContentsShowFolderResponse(**content.to_dict(view="element"))
+        else:
+            content = self.get_library_dataset(trans, content_id, check_ownership=False, check_accessible=True)
+            rval_dict = content.to_dict(view="element")
+            tag_manager = tags.GalaxyTagHandler(trans.sa_session)
+            rval_dict["tags"] = tag_manager.get_tags_list(content.library_dataset_dataset_association.tags)
+            return LibraryContentsShowDatasetResponse(**rval_dict)
+
+    def create(
+        self,
+        trans: ProvidesHistoryContext,
+        library_id: DecodedDatabaseIdField,
+        payload: AnyLibraryContentsCreatePayload,
+        files: Optional[List[StarletteUploadFile]] = None,
+    ) -> AnyLibraryContentsCreateResponse:
+        """Create a new library file or folder."""
+        if trans.user_is_bootstrap_admin:
+            raise exceptions.RealUserRequiredException("Only real users can create a new library file or folder.")
+        # security is checked in the downstream controller
+        parent = self.get_library_folder(trans, payload.folder_id, check_ownership=False, check_accessible=False)
+        # The rest of the security happens in the library_common controller.
+
+        # are we copying an HDA to the library folder?
+        #   we'll need the id and any message to attach, then branch to that private function
+        if payload.create_type == "file":
+            if payload.from_hda_id:
+                rval = self._copy_hda_to_library_folder(
+                    trans, self.hda_manager, payload.from_hda_id, payload.folder_id, payload.ldda_message
+                )
+                return LibraryContentsCreateDatasetResponse(**rval)
+            elif payload.from_hdca_id:
+                rval = self._copy_hdca_to_library_folder(
+                    trans, self.hda_manager, payload.from_hdca_id, payload.folder_id, payload.ldda_message
+                )
+                return LibraryContentsCreateDatasetCollectionResponse(root=rval)
+
+        # Now create the desired content object, either file or folder.
+        if payload.create_type == "file":
+            payload = cast(LibraryContentsFileCreatePayload, payload)
+            upload_files = []
+            if files:
+                for upload_file in files:
+                    with tempfile.NamedTemporaryFile(
+                        dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
+                    ) as dest:
+                        shutil.copyfileobj(upload_file.file, dest)
+                    upload_file.file.close()
+                    upload_files.append(dict(filename=upload_file.filename, local_filename=dest.name))
+            payload.upload_files = upload_files
+            rval = self._upload_library_dataset(trans, payload)
+            return LibraryContentsCreateFileListResponse(root=self._create_response(trans, payload, rval, library_id))
+        elif payload.create_type == "folder":
+            rval = self._create_folder(trans, payload)
+            return LibraryContentsCreateFolderListResponse(root=self._create_response(trans, payload, rval, library_id))
+        elif payload.create_type == "collection":
+            rval = self._create_collection(trans, payload, parent)
+            return LibraryContentsCreateDatasetCollectionResponse(root=rval)
+        else:
+            raise exceptions.RequestParameterInvalidException("Invalid create_type specified.")
+
+    def update(
+        self,
+        trans: ProvidesUserContext,
+        id: DecodedDatabaseIdField,
+        payload: LibraryContentsUpdatePayload,
+    ) -> None:
+        """Create an ImplicitlyConvertedDatasetAssociation."""
+        if payload.converted_dataset_id:
+            content = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=False)
+            content_conv = self.get_library_dataset(
+                trans, payload.converted_dataset_id, check_ownership=False, check_accessible=False
+            )
+            assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
+                parent=content.library_dataset_dataset_association,
+                dataset=content_conv.library_dataset_dataset_association,
+                file_type=content_conv.library_dataset_dataset_association.extension,
+                metadata_safe=True,
+            )
+            trans.sa_session.add(assoc)
+            with transaction(trans.sa_session):
+                trans.sa_session.commit()
+
+    def delete(
+        self,
+        trans: ProvidesHistoryContext,
+        id: DecodedDatabaseIdField,
+        payload: LibraryContentsDeletePayload,
+    ) -> LibraryContentsDeleteResponse:
+        """Delete the LibraryDataset with the given ``id``."""
+        rval = {"id": id}
+        ld = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=True)
+        user_is_admin = trans.user_is_admin
+        can_modify = trans.app.security_agent.can_modify_library_item(trans.user.all_roles(), ld)
+        if not (user_is_admin or can_modify):
+            raise exceptions.InsufficientPermissionsException("Unauthorized to delete or purge this library dataset")
+
+        ld.deleted = True
+        if payload.purge:
+            ld.purged = True
+            trans.sa_session.add(ld)
+            with transaction(trans.sa_session):
+                trans.sa_session.commit()
+
+            # TODO: had to change this up a bit from Dataset.user_can_purge
+            dataset = ld.library_dataset_dataset_association.dataset
+            no_history_assoc = len(dataset.history_associations) == len(dataset.purged_history_associations)
+            no_library_assoc = dataset.library_associations == [ld.library_dataset_dataset_association]
+            can_purge_dataset = not dataset.purged and no_history_assoc and no_library_assoc
+
+            if can_purge_dataset:
+                try:
+                    ld.library_dataset_dataset_association.dataset.full_delete()
+                    trans.sa_session.add(ld.dataset)
+                except Exception:
+                    pass
+                # flush now to preserve deleted state in case of later interruption
+                with transaction(trans.sa_session):
+                    trans.sa_session.commit()
+            rval["purged"] = True
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+        rval["deleted"] = True
+        return LibraryContentsDeleteResponse(**rval)
+
+    def _decode_library_content_id(
+        self,
+        content_id: MaybeLibraryFolderOrDatasetID,
+    ) -> Tuple:
+        if len(content_id) % 16 == 0:
+            return "LibraryDataset", content_id
+        elif content_id.startswith("F"):
+            return "LibraryFolder", content_id[1:]
+        else:
+            raise exceptions.MalformedId(
+                f"Malformed library content id ( {str(content_id)} ) specified, unable to decode."
+            )
+
+    def _url_for(self, trans: ProvidesUserContext, library_id, id, type):
+        encoded_library_id = trans.security.encode_id(library_id)
+        encoded_id = trans.security.encode_id(id)
+        if type == "folder":
+            encoded_id = f"F{encoded_id}"
+        return (
+            trans.url_builder("library_content", library_id=encoded_library_id, id=encoded_id)
+            if trans.url_builder
+            else None
+        )
+
+    def _traverse(self, trans: ProvidesUserContext, folder, current_user_roles):
+        admin = trans.user_is_admin
+        rval = []
+        for subfolder in folder.active_folders:
+            if not admin:
+                can_access, folder_ids = trans.app.security_agent.check_folder_contents(
+                    trans.user, current_user_roles, subfolder
+                )
+            if (admin or can_access) and not subfolder.deleted:
+                subfolder.api_path = f"{folder.api_path}/{subfolder.name}"
+                subfolder.api_type = "folder"
+                rval.append(subfolder)
+                rval.extend(self._traverse(trans, subfolder, current_user_roles))
+        for ld in folder.datasets:
+            if not admin:
+                can_access = trans.app.security_agent.can_access_dataset(
+                    current_user_roles, ld.library_dataset_dataset_association.dataset
+                )
+            if (admin or can_access) and not ld.deleted:
+                ld.api_path = f"{folder.api_path}/{ld.name}"
+                ld.api_type = "file"
+                rval.append(ld)
+        return rval
+
+    def _create_response(self, trans, payload, output, library_id):
+        rval = []
+        for v in output.values():
+            if payload.extended_metadata is not None:
+                # If there is extended metadata, store it, attach it to the dataset, and index it
+                self.create_extended_metadata(trans, payload.extended_metadata)
+            if isinstance(v, trans.app.model.LibraryDatasetDatasetAssociation):
+                v = v.library_dataset
+            url = self._url_for(trans, library_id, v.id, payload.create_type)
+            rval.append(dict(id=v.id, name=v.name, url=url))
+        return rval
diff --git a/lib/galaxy/webapps/galaxy/services/library_folders.py b/lib/galaxy/webapps/galaxy/services/library_folders.py
index bc560c849238ad91e24d4e2535fce1ce4dd44a40..21b33762a31ca61a386f2c516d35c814d61e84b7 100644
--- a/lib/galaxy/webapps/galaxy/services/library_folders.py
+++ b/lib/galaxy/webapps/galaxy/services/library_folders.py
@@ -12,6 +12,7 @@ from galaxy.exceptions import (
 )
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.roles import RoleManager
+from galaxy.model.db.role import get_private_role_user_emails_dict
 from galaxy.schema.fields import LibraryFolderDatabaseIdField
 from galaxy.schema.schema import (
     BasicRoleModel,
@@ -114,9 +115,12 @@ class LibraryFoldersService(ServiceBase):
         #  Return roles that are available to select.
         elif scope == LibraryPermissionScope.available:
             roles, total_roles = trans.app.security_agent.get_valid_roles(trans, folder, query, page, page_limit)
+
+            private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
             return_roles = []
             for role in roles:
-                return_roles.append(BasicRoleModel(id=role.id, name=role.name, type=role.type))
+                displayed_name = private_role_emails.get(role.id, role.name)
+                return_roles.append(BasicRoleModel(id=role.id, name=displayed_name, type=role.type))
             return LibraryAvailablePermissions(roles=return_roles, page=page, page_limit=page_limit, total=total_roles)
         else:
             raise RequestParameterInvalidException(
diff --git a/lib/galaxy/webapps/galaxy/services/quotas.py b/lib/galaxy/webapps/galaxy/services/quotas.py
index 38b6a69fe84976ffc13675ff2ca23d6df5c2a04a..564f864d59931ac2dfc6b9bcb530e8cd5e9d7768 100644
--- a/lib/galaxy/webapps/galaxy/services/quotas.py
+++ b/lib/galaxy/webapps/galaxy/services/quotas.py
@@ -11,8 +11,8 @@ from galaxy import util
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.groups import get_group_by_name
 from galaxy.managers.quotas import QuotaManager
-from galaxy.managers.users import get_user_by_email
 from galaxy.model import Quota
+from galaxy.model.db.user import get_user_by_email
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.quota._schema import (
     CreateQuotaParams,
@@ -96,7 +96,8 @@ class QuotasService(ServiceBase):
         messages = []
         for method in methods:
             message = method(quota, params)
-            messages.append(message)
+            if message:
+                messages.append(message)
         return "; ".join(messages)
 
     def delete(
diff --git a/lib/galaxy/webapps/galaxy/services/roles.py b/lib/galaxy/webapps/galaxy/services/roles.py
new file mode 100644
index 0000000000000000000000000000000000000000..16504fb11bad923923330cdca77ca9ed69c3b0a2
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/services/roles.py
@@ -0,0 +1,71 @@
+from typing import Optional
+
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.roles import RoleManager
+from galaxy.model.db.role import get_private_role_user_emails_dict
+from galaxy.schema.fields import (
+    DecodedDatabaseIdField,
+    Security,
+)
+from galaxy.schema.schema import (
+    RoleDefinitionModel,
+    RoleListResponse,
+    RoleModelResponse,
+)
+from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.webapps.base.controller import url_for
+from galaxy.webapps.galaxy.services.base import ServiceBase
+
+
+def role_to_model(role, displayed_name: Optional[str] = None):
+    item = role.to_dict(view="element")
+    role_id = Security.security.encode_id(role.id)
+    item["url"] = url_for("role", id=role_id)
+    # If displayed_name provided, use that value in place of Role.name. It is
+    # used to disambiguate generic role names like "private role".
+    if displayed_name:
+        item["name"] = displayed_name
+    return RoleModelResponse(**item)
+
+
+class RolesService(ServiceBase):
+
+    def __init__(
+        self,
+        security: IdEncodingHelper,
+        role_manager: RoleManager,
+    ):
+        super().__init__(security)
+        self.role_manager = role_manager
+
+    def get_index(self, trans: ProvidesUserContext) -> RoleListResponse:
+        roles = self.role_manager.list_displayable_roles(trans)
+        private_role_emails = get_private_role_user_emails_dict(trans.sa_session)
+        data = []
+        for role in roles:
+            displayed_name = private_role_emails.get(role.id, role.name)
+            data.append(role_to_model(role, displayed_name))
+        return RoleListResponse(root=data)
+
+    def show(self, trans: ProvidesUserContext, id: DecodedDatabaseIdField) -> RoleModelResponse:
+        role = self.role_manager.get(trans, id)
+        return role_to_model(role)
+
+    def create(self, trans: ProvidesUserContext, role_definition_model: RoleDefinitionModel):
+        role = self.role_manager.create_role(trans, role_definition_model)
+        return role_to_model(role)
+
+    def delete(self, trans: ProvidesUserContext, id: DecodedDatabaseIdField) -> RoleModelResponse:
+        role = self.role_manager.get(trans, id)
+        role = self.role_manager.delete(trans, role)
+        return role_to_model(role)
+
+    def purge(self, trans: ProvidesUserContext, id: DecodedDatabaseIdField) -> RoleModelResponse:
+        role = self.role_manager.get(trans, id)
+        role = self.role_manager.purge(trans, role)
+        return role_to_model(role)
+
+    def undelete(self, trans: ProvidesUserContext, id: DecodedDatabaseIdField) -> RoleModelResponse:
+        role = self.role_manager.get(trans, id)
+        role = self.role_manager.undelete(trans, role)
+        return role_to_model(role)
diff --git a/lib/galaxy/webapps/galaxy/services/tools.py b/lib/galaxy/webapps/galaxy/services/tools.py
index 9e2298eae134231171baedfcb6ce5d81a19a68cd..04b03973735fe758483d74c1b16ee6e045c54908 100644
--- a/lib/galaxy/webapps/galaxy/services/tools.py
+++ b/lib/galaxy/webapps/galaxy/services/tools.py
@@ -17,6 +17,7 @@ from galaxy import (
     util,
 )
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.exceptions.utils import api_error_to_dict
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
 from galaxy.managers.context import (
     ProvidesHistoryContext,
@@ -71,7 +72,7 @@ class ToolsService(ServiceBase):
                 with tempfile.NamedTemporaryFile(
                     dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
                 ) as dest:
-                    shutil.copyfileobj(upload_file.file, dest)  # type: ignore[misc]  # https://github.com/python/mypy/issues/15031
+                    shutil.copyfileobj(upload_file.file, dest)
                     util.umask_fix_perms(dest.name, trans.app.config.umask, 0o0666)
                 upload_file.file.close()
                 files_payload[f"files_{i}|file_data"] = FilesPayload(
@@ -203,7 +204,17 @@ class ToolsService(ServiceBase):
         rval["produces_entry_points"] = tool.produces_entry_points
         if job_errors := vars.get("job_errors", []):
             # If we are here - some jobs were successfully executed but some failed.
-            rval["errors"] = job_errors
+            # TODO: We should probably alter the response status code and have a component that knows
+            # how to template in things like src and id, so we don't have to rely just on a textual error message.
+            execution_errors = [
+                (
+                    trans.security.encode_all_ids(api_error_to_dict(exception=e))
+                    if isinstance(e, exceptions.MessageException)
+                    else e
+                )
+                for e in job_errors
+            ]
+            rval["errors"] = execution_errors
 
         outputs = rval["outputs"]
         # TODO:?? poss. only return ids?
diff --git a/lib/galaxy/webapps/galaxy/services/users.py b/lib/galaxy/webapps/galaxy/services/users.py
index 4cab9d01ab122d30593a3b5d4de93e052bb571ba..1d5705b34bac7f0ed28c752f67f8b6d3d7378458 100644
--- a/lib/galaxy/webapps/galaxy/services/users.py
+++ b/lib/galaxy/webapps/galaxy/services/users.py
@@ -4,13 +4,6 @@ from typing import (
     Union,
 )
 
-from sqlalchemy import (
-    false,
-    or_,
-    select,
-    true,
-)
-
 import galaxy.managers.base as managers_base
 from galaxy import (
     exceptions as glx_exceptions,
@@ -27,6 +20,7 @@ from galaxy.managers.users import (
     UserSerializer,
 )
 from galaxy.model import User
+from galaxy.model.db.user import get_users_for_index
 from galaxy.queue_worker import send_local_control_task
 from galaxy.quota import QuotaAgent
 from galaxy.schema import APIKeyModel
@@ -36,6 +30,7 @@ from galaxy.schema.schema import (
     FlexibleUserIdType,
     LimitedUserModel,
     MaybeLimitedUserModel,
+    RoleListResponse,
     UserModel,
 )
 from galaxy.security.idencoding import IdEncodingHelper
@@ -43,6 +38,7 @@ from galaxy.webapps.galaxy.services.base import (
     async_task_summary,
     ServiceBase,
 )
+from galaxy.webapps.galaxy.services.roles import role_to_model
 
 
 class UsersService(ServiceBase):
@@ -206,31 +202,11 @@ class UsersService(ServiceBase):
         f_name: Optional[str],
         f_any: Optional[str],
     ) -> List[MaybeLimitedUserModel]:
-        rval: List[MaybeLimitedUserModel] = []
-        stmt = select(User)
-
-        if f_email and (trans.user_is_admin or trans.app.config.expose_user_email):
-            stmt = stmt.filter(User.email.like(f"%{f_email}%"))
-
-        if f_name and (trans.user_is_admin or trans.app.config.expose_user_name):
-            stmt = stmt.filter(User.username.like(f"%{f_name}%"))
-
-        if f_any:
-            if trans.user_is_admin:
-                stmt = stmt.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
-            else:
-                if trans.app.config.expose_user_email and trans.app.config.expose_user_name:
-                    stmt = stmt.filter(or_(User.email.like(f"%{f_any}%"), User.username.like(f"%{f_any}%")))
-                elif trans.app.config.expose_user_email:
-                    stmt = stmt.filter(User.email.like(f"%{f_any}%"))
-                elif trans.app.config.expose_user_name:
-                    stmt = stmt.filter(User.username.like(f"%{f_any}%"))
-
+        # check for early return conditions
         if deleted:
-            # only admins can see deleted users
             if not trans.user_is_admin:
+                # only admins can see deleted users
                 return []
-            stmt = stmt.filter(User.deleted == true())
         else:
             # special case: user can see only their own user
             # special case2: if the galaxy admin has specified that other user email/names are
@@ -244,8 +220,19 @@ class UsersService(ServiceBase):
                     return [UserModel(**trans.user.to_dict())]
                 else:
                     return []
-            stmt = stmt.filter(User.deleted == false())
-        for user in trans.sa_session.scalars(stmt).all():
+
+        users = get_users_for_index(
+            trans.sa_session,
+            deleted,
+            f_email,
+            f_name,
+            f_any,
+            trans.user_is_admin,
+            trans.app.config.expose_user_email,
+            trans.app.config.expose_user_name,
+        )
+        rval: List[MaybeLimitedUserModel] = []
+        for user in users:
             user_dict = user.to_dict()
             # If NOT configured to expose_email, do not expose email UNLESS the user is self, or
             # the user is an admin
@@ -263,3 +250,8 @@ class UsersService(ServiceBase):
             else:
                 rval.append(UserModel(**user_dict))
         return rval
+
+    def get_user_roles(self, trans, user_id):
+        user = self.get_user(trans, user_id)
+        roles = [ura.role for ura in user.roles]
+        return RoleListResponse(root=[role_to_model(r) for r in roles])
diff --git a/lib/galaxy/webapps/galaxy/services/visualizations.py b/lib/galaxy/webapps/galaxy/services/visualizations.py
index 0138de78d9ffe4eabd1fe2d0db06308e45243c9b..d2b7e681951995cdda9cf23c3af5ad688db0c474 100644
--- a/lib/galaxy/webapps/galaxy/services/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/services/visualizations.py
@@ -1,16 +1,49 @@
+import json
 import logging
-from typing import Tuple
+from typing import (
+    cast,
+    Optional,
+    Tuple,
+    Union,
+)
 
 from galaxy import exceptions
+from galaxy.managers.base import security_check
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.sharable import (
+    slug_exists,
+    SlugBuilder,
+)
 from galaxy.managers.visualizations import (
     VisualizationManager,
     VisualizationSerializer,
 )
+from galaxy.model import (
+    Visualization,
+    VisualizationRevision,
+)
+from galaxy.model.base import transaction
+from galaxy.model.item_attrs import (
+    add_item_annotation,
+    get_item_annotation_str,
+)
+from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.visualization import (
+    VisualizationCreatePayload,
+    VisualizationCreateResponse,
     VisualizationIndexQueryPayload,
+    VisualizationRevisionResponse,
+    VisualizationShowResponse,
     VisualizationSummaryList,
+    VisualizationUpdatePayload,
+    VisualizationUpdateResponse,
 )
 from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.structured_app import StructuredApp
+from galaxy.util.hash_util import md5_hash_str
+from galaxy.visualization.plugins.plugin import VisualizationPlugin
+from galaxy.visualization.plugins.registry import VisualizationsRegistry
+from galaxy.web import url_for
 from galaxy.webapps.galaxy.services.base import ServiceBase
 from galaxy.webapps.galaxy.services.notifications import NotificationService
 from galaxy.webapps.galaxy.services.sharable import ShareableService
@@ -41,7 +74,7 @@ class VisualizationsService(ServiceBase):
 
     def index(
         self,
-        trans,
+        trans: ProvidesUserContext,
         payload: VisualizationIndexQueryPayload,
         include_total_count: bool = False,
     ) -> Tuple[VisualizationSummaryList, int]:
@@ -60,3 +93,272 @@ class VisualizationsService(ServiceBase):
             VisualizationSummaryList(root=[entry.to_dict() for entry in entries]),
             total_matches,
         )
+
+    def show(
+        self,
+        trans: ProvidesUserContext,
+        visualization_id: DecodedDatabaseIdField,
+    ) -> VisualizationShowResponse:
+        """Return a dictionary containing the Visualization's details
+
+        :rtype:     dictionary
+        :returns:   Visualization details
+        """
+        # TODO: revisions should be a contents/nested controller like viz/xxx/r/xxx)?
+        # the important thing is the config
+        # TODO:?? /api/visualizations/registry -> json of registry.listings?
+        visualization = self._get_visualization(trans, visualization_id, check_ownership=False, check_accessible=True)
+        dictionary = {
+            "model_class": "Visualization",
+            "id": visualization.id,
+            "title": visualization.title,
+            "type": visualization.type,
+            "user_id": visualization.user.id,
+            "dbkey": visualization.dbkey,
+            "slug": visualization.slug,
+            # to_dict only the latest revision (allow older to be fetched elsewhere)
+            "latest_revision": (
+                self._get_visualization_revision(visualization.latest_revision)
+                if visualization.latest_revision
+                else None
+            ),
+            # need to encode ids in revisions as well
+            # NOTE: does not encode ids inside the configs
+            "revisions": [r.id for r in visualization.revisions],
+        }
+        # replace with trans.url_builder if possible
+        dictionary["url"] = url_for(
+            controller="visualization",
+            action="display_by_username_and_slug",
+            username=visualization.user.username,
+            slug=visualization.slug,
+        )
+        dictionary["username"] = visualization.user.username
+        dictionary["email_hash"] = md5_hash_str(visualization.user.email)
+        dictionary["tags"] = visualization.make_tag_string_list()
+        dictionary["annotation"] = get_item_annotation_str(trans.sa_session, trans.user, visualization)
+        app = cast(StructuredApp, trans.app)
+        if app.visualizations_registry:
+            visualizations_registry = cast(VisualizationsRegistry, app.visualizations_registry)
+            visualization_plugin = cast(VisualizationPlugin, visualizations_registry.get_plugin(dictionary["type"]))
+            dictionary["plugin"] = visualization_plugin.to_dict()
+        return VisualizationShowResponse(**dictionary)
+
+    def create(
+        self,
+        trans: ProvidesUserContext,
+        import_id: Optional[DecodedDatabaseIdField],
+        payload: VisualizationCreatePayload,
+    ) -> VisualizationCreateResponse:
+        """Returns a dictionary of the created visualization
+
+        :rtype:     dictionary
+        :returns:   dictionary containing Visualization details
+        """
+
+        if import_id:
+            visualization = self._import_visualization(trans, import_id)
+        else:
+            type = payload.type
+            title = payload.title
+            slug = payload.slug
+            dbkey = payload.dbkey
+            annotation = payload.annotation
+            config = payload.config
+
+            # generate defaults - this will err if given a weird key?
+            visualization = self._create_visualization(trans, type, title, dbkey, slug, annotation)
+
+            # Create and save first visualization revision
+            revision = VisualizationRevision(visualization=visualization, title=title, config=config, dbkey=dbkey)
+            visualization.latest_revision = revision
+
+            session = trans.sa_session
+            session.add(revision)
+            with transaction(session):
+                session.commit()
+
+        return VisualizationCreateResponse(id=str(visualization.id))
+
+    def update(
+        self,
+        trans: ProvidesUserContext,
+        visualization_id: DecodedDatabaseIdField,
+        payload: VisualizationUpdatePayload,
+    ) -> Optional[VisualizationUpdateResponse]:
+        """
+        Update a visualization
+
+        :rtype:     dictionary
+        :returns:   dictionary containing Visualization details
+        """
+        rval = None
+
+        # there's a differentiation here between updating the visualization and creating a new revision
+        # that needs to be handled clearly here or alternately, using a different controller
+        # like e.g. PUT /api/visualizations/{visualization_id}/r/{revision_id}
+
+        # TODO: consider allowing direct alteration of revisions title (without a new revision)
+        #   only create a new revsion on a different config
+
+        # only update owned visualizations
+        visualization = self._get_visualization(trans, visualization_id, check_ownership=True)
+        latest_revision = cast(VisualizationRevision, visualization.latest_revision)
+        title = payload.title or latest_revision.title
+        dbkey = payload.dbkey or latest_revision.dbkey
+        deleted = payload.deleted or visualization.deleted
+        config = payload.config or latest_revision.config
+
+        latest_config = latest_revision.config
+        if (
+            (title != latest_revision.title)
+            or (dbkey != latest_revision.dbkey)
+            or (json.dumps(config) != json.dumps(latest_config))
+        ):
+            revision = self._add_visualization_revision(trans, visualization, config, title, dbkey)
+            rval = {"id": str(visualization_id), "revision": str(revision.id)}
+
+        # allow updating vis title
+        visualization.title = title
+        visualization.deleted = deleted
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+
+        return VisualizationUpdateResponse(**rval) if rval else None
+
+    def _get_visualization(
+        self,
+        trans: ProvidesUserContext,
+        visualization_id: DecodedDatabaseIdField,
+        check_ownership=True,
+        check_accessible=False,
+    ) -> Visualization:
+        """
+        Get a Visualization from the database by id, verifying ownership.
+        """
+        visualization = trans.sa_session.get(Visualization, visualization_id)
+        if not visualization:
+            raise exceptions.ObjectNotFound("Visualization not found")
+        else:
+            return security_check(trans, visualization, check_ownership, check_accessible)
+
+    def _get_visualization_revision(
+        self,
+        revision: VisualizationRevision,
+    ) -> VisualizationRevisionResponse:
+        """
+        Return a set of detailed attributes for a visualization in dictionary form.
+        NOTE: that encoding ids isn't done here should happen at the caller level.
+        """
+        revision_dict = {
+            "model_class": "VisualizationRevision",
+            "id": revision.id,
+            "visualization_id": revision.visualization.id,
+            "title": revision.title,
+            "dbkey": revision.dbkey,
+            "config": revision.config,
+        }
+        return VisualizationRevisionResponse(**revision_dict)
+
+    def _add_visualization_revision(
+        self,
+        trans: ProvidesUserContext,
+        visualization: Visualization,
+        config: Optional[Union[dict, bytes]],
+        title: Optional[str],
+        dbkey: Optional[str],
+    ) -> VisualizationRevision:
+        """
+        Adds a new `VisualizationRevision` to the given `visualization` with
+        the given parameters and set its parent visualization's `latest_revision`
+        to the new revision.
+        """
+        # precondition: only add new revision on owned vis's
+        # TODO:?? should we default title, dbkey, config? to which: visualization or latest_revision?
+        revision = VisualizationRevision(visualization=visualization, title=title, dbkey=dbkey, config=config)
+
+        visualization.latest_revision = revision
+        # TODO:?? does this automatically add revision to visualzation.revisions?
+        trans.sa_session.add(revision)
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+        return revision
+
+    def _create_visualization(
+        self,
+        trans: ProvidesUserContext,
+        type: str,
+        title: Optional[str] = "Untitled Visualization",
+        dbkey: Optional[str] = None,
+        slug: Optional[str] = None,
+        annotation: Optional[str] = None,
+    ) -> Visualization:
+        """Create visualization but not first revision. Returns Visualization object."""
+        user = trans.get_user()
+
+        # Error checking.
+        if slug:
+            slug_err = ""
+            if not SlugBuilder.is_valid_slug(slug):
+                slug_err = (
+                    "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
+                )
+            elif slug_exists(trans.sa_session, Visualization, user, slug, ignore_deleted=True):
+                slug_err = "visualization identifier must be unique"
+            if slug_err:
+                # TODO: handle this error structure better
+                raise exceptions.RequestParameterMissingException(slug_err)
+
+        # Create visualization
+        visualization = Visualization(user=user, title=title, dbkey=dbkey, type=type)
+        if slug:
+            visualization.slug = slug
+        else:
+            slug_builder = SlugBuilder()
+            slug_builder.create_item_slug(trans.sa_session, visualization)
+        if annotation:
+            # TODO: if this is to stay in the mixin, UsesAnnotations should be added to the superclasses
+            #   right now this is depending on the classes that include this mixin to have UsesAnnotations
+            add_item_annotation(trans.sa_session, trans.user, visualization, annotation)
+
+        session = trans.sa_session
+        session.add(visualization)
+        with transaction(session):
+            session.commit()
+
+        return visualization
+
+    def _import_visualization(
+        self,
+        trans: ProvidesUserContext,
+        visualization_id: DecodedDatabaseIdField,
+    ) -> Visualization:
+        """
+        Copy the visualization with the given id and associate the copy
+        with the given user (defaults to trans.user).
+
+        Raises `ItemAccessibilityException` if `user` is not passed and
+        the current user is anonymous, and if the visualization is not `importable`.
+        Raises `ItemDeletionException` if the visualization has been deleted.
+        """
+        # default to trans.user, error if anon
+        if not trans.user:
+            raise exceptions.ItemAccessibilityException("You must be logged in to import Galaxy visualizations")
+        user = trans.user
+
+        # check accessibility
+        visualization = self._get_visualization(trans, visualization_id, check_ownership=False)
+        if not visualization.importable:
+            raise exceptions.ItemAccessibilityException(
+                "The owner of this visualization has disabled imports via this link."
+            )
+        if visualization.deleted:
+            raise exceptions.ItemDeletionException("You can't import this visualization because it has been deleted.")
+
+        # copy vis and alter title
+        # TODO: need to handle custom db keys.
+        imported_visualization = visualization.copy(user=user, title=f"imported: {visualization.title}")
+        trans.sa_session.add(imported_visualization)
+        with transaction(trans.sa_session):
+            trans.sa_session.commit()
+        return imported_visualization
diff --git a/lib/galaxy/webapps/galaxy/services/workflows.py b/lib/galaxy/webapps/galaxy/services/workflows.py
index 72414b169abfb502cbd47e6142fb71e905c2344c..f34ce0db46b2e033d8650bd6cfc674d20b0270f0 100644
--- a/lib/galaxy/webapps/galaxy/services/workflows.py
+++ b/lib/galaxy/webapps/galaxy/services/workflows.py
@@ -70,7 +70,9 @@ class WorkflowsService(ServiceBase):
         query, total_matches = self._workflows_manager.index_query(trans, payload, include_total_count)
         rval = []
         for wf in query.all():
-            item = wf.to_dict(value_mapper={"id": trans.security.encode_id})
+            item = wf.to_dict(
+                value_mapper={"id": trans.security.encode_id, "latest_workflow_id": trans.security.encode_id}
+            )
             encoded_id = trans.security.encode_id(wf.id)
             item["annotations"] = [x.annotation for x in wf.annotations]
             item["url"] = web.url_for("workflow", id=encoded_id)
@@ -131,7 +133,10 @@ class WorkflowsService(ServiceBase):
         by_stored_id = not payload.instance
         stored_workflow = self._workflows_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id)
         version = payload.version
-        workflow = stored_workflow.get_internal_version(version)
+        if version is None and payload.instance:
+            workflow = stored_workflow.get_internal_version_by_id(workflow_id)
+        else:
+            workflow = stored_workflow.get_internal_version(version)
         run_configs = build_workflow_run_configs(trans, workflow, payload.model_dump(exclude_unset=True))
         is_batch = payload.batch
         if not is_batch and len(run_configs) != 1:
diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py
index 759380d78da463a666d807bb27c5f49580020398..98b1e226d718df0ca304083ffbeb25d4b84c24dd 100644
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -24,8 +24,8 @@ from galaxy import (
     model,
     util,
 )
-from galaxy.managers.users import get_user_by_email
 from galaxy.model import Job
+from galaxy.model.db.user import get_user_by_email
 from galaxy.web.legacy_framework import grids
 from galaxy.webapps.base.controller import (
     BaseUIController,
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index 8e4fc74afc21314270209adb01729caa0359e118..801c0d9e7e7770e3f589ecc7f40960440bb6fce0 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -49,12 +49,6 @@ class WorkRequestContext(ProvidesHistoryContext):
         self.workflow_building_mode = workflow_building_mode
         self.galaxy_session = galaxy_session
 
-    def set_cache_value(self, args: Tuple[str, ...], value: Any):
-        self._short_term_cache[args] = value
-
-    def get_cache_value(self, args: Tuple[str, ...], default: Any = None) -> Any:
-        return self._short_term_cache.get(args, default)
-
     @property
     def app(self):
         return self._app
@@ -89,15 +83,23 @@ class WorkRequestContext(ProvidesHistoryContext):
 class GalaxyAbstractRequest:
     """Abstract interface to provide access to some request properties."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def base(self) -> str:
         """Base URL of the request."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
+    def url_path(self) -> str:
+        """Base with optional prefix added."""
+
+    @property
+    @abc.abstractmethod
     def host(self) -> str:
         """The host address."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def is_secure(self) -> bool:
         """Was this a secure (https) request."""
 
@@ -109,7 +111,8 @@ class GalaxyAbstractRequest:
 class GalaxyAbstractResponse:
     """Abstract interface to provide access to some response utilities."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def headers(self) -> dict:
         """The response headers."""
 
@@ -171,7 +174,7 @@ class SessionRequestContext(WorkRequestContext):
 
 def proxy_work_context_for_history(
     trans: ProvidesHistoryContext, history: Optional[History] = None, workflow_building_mode=False
-):
+) -> WorkRequestContext:
     """Create a WorkContext for supplied context with potentially different history.
 
     This provides semi-structured access to a transaction/work context with a supplied target
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index 6072f322d9cbfe1321236664b871cd5a3126060c..4e1d427d9634631f41030557398b340c9a100d85 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -116,7 +116,7 @@ def extract_steps(
         if name not in step_labels:
             step.label = name
             step_labels.add(name)
-        step.tool_inputs = dict(name=name)  # type:ignore[assignment]
+        step.tool_inputs = dict(name=name)
         hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     for i, hid in enumerate(dataset_collection_ids):
@@ -132,7 +132,7 @@ def extract_steps(
         if name not in step_labels:
             step.label = name
             step_labels.add(name)
-        step.tool_inputs = dict(name=name, collection_type=collection_type)  # type:ignore[assignment]
+        step.tool_inputs = dict(name=name, collection_type=collection_type)
         hid_to_output_pair[hid] = (step, "output")
         steps.append(step)
     # Tool steps
@@ -283,7 +283,7 @@ class WorkflowSummary:
         # just grab the implicitly mapped jobs and handle in second pass. Second pass is
         # needed because cannot allow selection of individual datasets from an implicit
         # mapping during extraction - you get the collection or nothing.
-        for content in self.history.active_contents:
+        for content in self.history.visible_contents:
             self.__summarize_content(content)
 
     def __summarize_content(self, content):
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index d0eb5025d5c4dcbfde4eefca43e7a753b442af7a..8d5e4eb479ae7f8f214e1e62ed2f8eddff7b412b 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -4,15 +4,19 @@ Modules used in building workflows
 
 import json
 import logging
+import math
 import re
 from collections import defaultdict
 from typing import (
     Any,
     cast,
     Dict,
+    get_args,
     Iterable,
     List,
+    Literal,
     Optional,
+    Tuple,
     Type,
     TYPE_CHECKING,
     Union,
@@ -30,8 +34,10 @@ from galaxy.exceptions import (
 )
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.model import (
+    Job,
     PostJobAction,
     Workflow,
+    WorkflowInvocationStep,
     WorkflowStep,
     WorkflowStepConnection,
 )
@@ -43,21 +49,24 @@ from galaxy.schema.invocation import (
     InvocationCancellationReviewFailed,
     InvocationFailureDatasetFailed,
     InvocationFailureExpressionEvaluationFailed,
+    InvocationFailureOutputNotFound,
     InvocationFailureWhenNotBoolean,
+    InvocationFailureWorkflowParameterInvalid,
 )
 from galaxy.tool_util.cwl.util import set_basename_and_derived_properties
+from galaxy.tool_util.parser import get_input_source
 from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
 from galaxy.tools import (
     DatabaseOperationTool,
     DefaultToolState,
     get_safe_version,
 )
-from galaxy.tools.actions import filter_output
 from galaxy.tools.execute import (
     execute,
     MappingParameters,
     PartialJobExecution,
 )
+from galaxy.tools.execution_helpers import filter_output
 from galaxy.tools.expressions import do_eval
 from galaxy.tools.parameters import (
     check_param,
@@ -67,7 +76,6 @@ from galaxy.tools.parameters import (
 from galaxy.tools.parameters.basic import (
     BaseDataToolParameter,
     BooleanToolParameter,
-    ColorToolParameter,
     DataCollectionToolParameter,
     DataToolParameter,
     FloatToolParameter,
@@ -81,11 +89,15 @@ from galaxy.tools.parameters.basic import (
 from galaxy.tools.parameters.grouping import (
     Conditional,
     ConditionalWhen,
+    Repeat,
 )
 from galaxy.tools.parameters.history_query import HistoryQuery
+from galaxy.tools.parameters.populate_model import populate_model
 from galaxy.tools.parameters.workflow_utils import (
     ConnectedValue,
     is_runtime_value,
+    NO_REPLACEMENT,
+    NoReplacement,
     runtime_to_json,
     workflow_building_modes,
 )
@@ -99,6 +111,7 @@ from galaxy.util.json import safe_loads
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import fill_template
 from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
+from galaxy.workflow.workflow_parameter_input_definitions import get_default_parameter
 
 if TYPE_CHECKING:
     from galaxy.schema.invocation import InvocationMessageUnion
@@ -114,13 +127,8 @@ RUNTIME_STEP_META_STATE_KEY = "__STEP_META_STATE__"
 # ones.
 RUNTIME_POST_JOB_ACTIONS_KEY = "__POST_JOB_ACTIONS__"
 
-
-class NoReplacement:
-    def __str__(self):
-        return "NO_REPLACEMENT singleton"
-
-
-NO_REPLACEMENT = NoReplacement()
+INPUT_PARAMETER_TYPES = Literal["text", "integer", "float", "boolean", "color", "directory_uri"]
+POSSIBLE_PARAMETER_TYPES: Tuple[INPUT_PARAMETER_TYPES] = get_args(INPUT_PARAMETER_TYPES)
 
 
 class ConditionalStepWhen(BooleanToolParameter):
@@ -155,6 +163,7 @@ def to_cwl(value, hda_references, step):
             properties = {
                 "class": "File",
                 "location": "step_input://%d" % len(hda_references),
+                "format": value.extension,
             }
             set_basename_and_derived_properties(
                 properties, value.dataset.created_from_basename or element_identifier or value.name
@@ -283,7 +292,7 @@ class WorkflowModule:
 
     # ---- Saving in various forms ------------------------------------------
 
-    def save_to_step(self, step, detached=False):
+    def save_to_step(self, step, detached: bool = False) -> None:
         step.type = self.type
         step.tool_inputs = self.get_state()
 
@@ -314,9 +323,14 @@ class WorkflowModule:
         the step.
         """
         if inputs := self.get_inputs():
-            return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested)
-        else:
-            return self.state.inputs
+            try:
+                return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested)
+            except ValueError:
+                log.warning("Tool state invalid for workflow module", exc_info=True)
+                # Always preferable to save unmodified and continue, I think ... we're explicit about alterations when retrieving any workflow,
+                # and it is what we do if we don't have the tool installed (assuming this is a tool).
+                pass
+        return self.state.inputs
 
     def get_export_state(self):
         return self.get_state(nested=True)
@@ -402,14 +416,11 @@ class WorkflowModule:
         """
         return {}
 
-    def compute_runtime_state(self, trans, step=None, step_updates=None):
+    def compute_runtime_state(self, trans, step=None, step_updates=None, replace_default_values=False):
         """Determine the runtime state (potentially different from self.state
         which describes configuration state). This (again unlike self.state) is
         currently always a `DefaultToolState` object.
 
-        If `step` is not `None`, it will be used to search for default values
-        defined in workflow input steps.
-
         If `step_updates` is `None`, this is likely for rendering the run form
         for instance and no runtime properties are available and state must be
         solely determined by the default runtime state described by the step.
@@ -418,6 +429,8 @@ class WorkflowModule:
         supplied by the workflow runner.
         """
         state = self.get_runtime_state()
+        if replace_default_values and step:
+            state.inputs = step.state.inputs
         step_errors = {}
 
         if step is not None:
@@ -427,8 +440,11 @@ class WorkflowModule:
                 if step_input is None:
                     return NO_REPLACEMENT
 
-                if step_input.default_value_set:
-                    return step_input.default_value
+                if replace_default_values and step_input.default_value_set:
+                    input_value = step_input.default_value
+                    if isinstance(input, BaseDataToolParameter):
+                        input_value = raw_to_galaxy(trans.app, trans.history, input_value)
+                    return input_value
 
                 return NO_REPLACEMENT
 
@@ -455,7 +471,7 @@ class WorkflowModule:
 
         return state, step_errors
 
-    def encode_runtime_state(self, step, runtime_state):
+    def encode_runtime_state(self, step, runtime_state: DefaultToolState):
         """Takes the computed runtime state and serializes it during run request creation."""
         return runtime_state.encode(Bunch(inputs=self.get_runtime_inputs(step)), self.trans.app)
 
@@ -644,7 +660,7 @@ class SubWorkflowModule(WorkflowModule):
         module.subworkflow = step.subworkflow
         return module
 
-    def save_to_step(self, step, **kwd):
+    def save_to_step(self, step, detached=False):
         step.type = self.type
         step.subworkflow = self.subworkflow
         ensure_object_added_to_session(step, object_in_session=self.subworkflow)
@@ -712,7 +728,7 @@ class SubWorkflowModule(WorkflowModule):
         if hasattr(self.subworkflow, "workflow_outputs"):
             from galaxy.managers.workflows import WorkflowContentsManager
 
-            workflow_contents_manager = WorkflowContentsManager(self.trans.app)
+            workflow_contents_manager = WorkflowContentsManager(self.trans.app, self.trans.app.trs_proxy)
             subworkflow_dict = workflow_contents_manager._workflow_to_dict_editor(
                 trans=self.trans,
                 stored=self.subworkflow.stored_workflow,
@@ -762,7 +778,7 @@ class SubWorkflowModule(WorkflowModule):
         return self.trans.security.encode_id(self.subworkflow.id)
 
     def execute(
-        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+        self, trans, progress: "WorkflowProgress", invocation_step: WorkflowInvocationStep, use_cached_job: bool = False
     ) -> Optional[bool]:
         """Execute the given workflow step in the given workflow invocation.
         Use the supplied workflow progress object to track outputs, find
@@ -822,7 +838,17 @@ class SubWorkflowModule(WorkflowModule):
             workflow_output_label = (
                 workflow_output.label or f"{workflow_output.workflow_step.order_index}:{workflow_output.output_name}"
             )
-            replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output)
+            try:
+                replacement = subworkflow_progress.get_replacement_workflow_output(workflow_output)
+            except KeyError:
+                raise FailWorkflowEvaluation(
+                    why=InvocationFailureOutputNotFound(
+                        reason=FailureReason.output_not_found,
+                        workflow_step_id=workflow_output.workflow_step_id,
+                        output_name=workflow_output.output_name,
+                        dependent_workflow_step_id=step.id,
+                    )
+                )
             outputs[workflow_output_label] = replacement
         progress.set_step_outputs(invocation_step, outputs)
         return None
@@ -897,7 +923,7 @@ class InputProxy:
         return as_dict
 
 
-def optional_param(optional):
+def optional_param(optional=None):
     bool_source = dict(name="optional", label="Optional", type="boolean", checked=optional)
     optional_value = BooleanToolParameter(None, bool_source)
     return optional_value
@@ -930,7 +956,7 @@ class InputModule(WorkflowModule):
 
     def get_runtime_state(self):
         state = DefaultToolState()
-        state.inputs = dict(input=None)
+        state.inputs = dict(input=NO_REPLACEMENT)
         return state
 
     def get_all_inputs(self, data_only=False, connectable_only=False):
@@ -942,7 +968,7 @@ class InputModule(WorkflowModule):
         invocation = invocation_step.workflow_invocation
         step = invocation_step.workflow_step
         input_value = step.state.inputs["input"]
-        if input_value is None:
+        if input_value is NO_REPLACEMENT:
             default_value = step.get_input_default_value(NO_REPLACEMENT)
             if default_value is not NO_REPLACEMENT:
                 input_value = raw_to_galaxy(trans.app, trans.history, default_value)
@@ -969,13 +995,16 @@ class InputModule(WorkflowModule):
         # everything should come in from the API and this can be eliminated.
         if not invocation.has_input_for_step(step.id):
             content = next(iter(step_outputs.values()))
-            if content:
+            if content and content is not NO_REPLACEMENT:
                 invocation.add_input(content, step.id)
         progress.set_outputs_for_input(invocation_step, step_outputs)
         return None
 
-    def recover_mapping(self, invocation_step, progress):
-        progress.set_outputs_for_input(invocation_step, already_persisted=True)
+    def recover_mapping(self, invocation_step: WorkflowInvocationStep, progress: "WorkflowProgress"):
+        super().recover_mapping(invocation_step, progress)
+        progress.set_outputs_for_input(
+            invocation_step, progress.outputs.get(invocation_step.workflow_step_id), already_persisted=True
+        )
 
     def get_export_state(self):
         return self._parse_state_into_dict()
@@ -1011,7 +1040,7 @@ class InputModule(WorkflowModule):
         state = json.dumps(state)
         return state
 
-    def save_to_step(self, step, **kwd):
+    def save_to_step(self, step, detached=False):
         step.type = self.type
         step.tool_inputs = self._parse_state_into_dict()
 
@@ -1031,15 +1060,15 @@ class InputDataModule(InputModule):
         return [dict(name="output", extensions=extensions, optional=optional)]
 
     def get_filter_set(self, connections=None):
-        filter_set = []
+        filter_set = set()  # Use a set to ensure unique extensions
         if connections:
             for oc in connections:
                 for ic in oc.input_step.module.get_data_inputs():
                     if "extensions" in ic and ic["extensions"] != "input" and ic["name"] == oc.input_name:
-                        filter_set += ic["extensions"]
+                        filter_set.update(ic["extensions"])
         if not filter_set:
-            filter_set = ["data"]
-        return ", ".join(filter_set)
+            filter_set = {"data"}
+        return ", ".join(sorted(filter_set))
 
     def get_runtime_inputs(self, step, connections: Optional[Iterable[WorkflowStepConnection]] = None):
         parameter_def = self._parse_state_into_dict()
@@ -1163,7 +1192,7 @@ class InputDataCollectionModule(InputModule):
 
 
 class InputParameterModule(WorkflowModule):
-    POSSIBLE_PARAMETER_TYPES = ["text", "integer", "float", "boolean", "color"]
+    POSSIBLE_PARAMETER_TYPES = POSSIBLE_PARAMETER_TYPES
     type = "parameter_input"
     name = "Input parameter"
     default_parameter_type = "text"
@@ -1176,7 +1205,6 @@ class InputParameterModule(WorkflowModule):
     def get_inputs(self):
         parameter_def = self._parse_state_into_dict()
         parameter_type = parameter_def["parameter_type"]
-        optional = parameter_def["optional"]
         select_source = dict(name="parameter_type", label="Parameter type", type="select", value=parameter_type)
         select_source["options"] = [
             {"value": "text", "label": "Text"},
@@ -1184,6 +1212,7 @@ class InputParameterModule(WorkflowModule):
             {"value": "float", "label": "Float"},
             {"value": "boolean", "label": "Boolean (True or False)"},
             {"value": "color", "label": "Color"},
+            {"value": "directory_uri", "label": "Directory URI"},
         ]
         input_parameter_type = SelectToolParameter(None, select_source)
         # encode following loop in description above instead
@@ -1194,61 +1223,15 @@ class InputParameterModule(WorkflowModule):
                 option[2] = True
                 input_parameter_type.static_options[i] = tuple(option)
 
-        parameter_type_cond = Conditional()
-        parameter_type_cond.name = "parameter_definition"
+        parameter_type_cond = Conditional("parameter_definition")
         parameter_type_cond.test_param = input_parameter_type
         cases = []
 
-        for param_type in ["text", "integer", "float", "boolean", "color"]:
-            default_source: Dict[str, Union[int, float, bool, str]] = dict(
-                name="default", label="Default Value", type=param_type
-            )
-            if param_type == "text":
-                if parameter_type == "text":
-                    text_default = parameter_def.get("default") or ""
-                else:
-                    text_default = ""
-                default_source["value"] = text_default
-                input_default_value: Union[
-                    TextToolParameter,
-                    IntegerToolParameter,
-                    FloatToolParameter,
-                    BooleanToolParameter,
-                    ColorToolParameter,
-                ] = TextToolParameter(None, default_source)
-            elif param_type == "integer":
-                if parameter_type == "integer":
-                    integer_default = parameter_def.get("default") or 0
-                else:
-                    integer_default = 0
-                default_source["value"] = integer_default
-                input_default_value = IntegerToolParameter(None, default_source)
-            elif param_type == "float":
-                if parameter_type == "float":
-                    float_default = parameter_def.get("default") or 0.0
-                else:
-                    float_default = 0.0
-                default_source["value"] = float_default
-                input_default_value = FloatToolParameter(None, default_source)
-            elif param_type == "boolean":
-                if parameter_type == "boolean":
-                    boolean_default = parameter_def.get("default") or False
-                else:
-                    boolean_default = False
-                default_source["value"] = boolean_default
-                default_source["checked"] = boolean_default
-                input_default_value = BooleanToolParameter(None, default_source)
-            elif param_type == "color":
-                if parameter_type == "color":
-                    color_default = parameter_def.get("default") or "#000000"
-                else:
-                    color_default = "#000000"
-                default_source["value"] = color_default
-                input_default_value = ColorToolParameter(None, default_source)
+        for param_type in POSSIBLE_PARAMETER_TYPES:
+            default_parameter = get_default_parameter(param_type)
 
-            optional_value = optional_param(optional)
-            optional_cond = Conditional()
-            optional_cond.name = "optional"
+            optional_value = optional_param()
+            optional_cond = Conditional("optional")
             optional_cond.test_param = optional_value
 
             when_this_type = ConditionalWhen()
@@ -1256,19 +1239,19 @@ class InputParameterModule(WorkflowModule):
             when_this_type.inputs = {}
             when_this_type.inputs["optional"] = optional_cond
 
-            specify_default_checked = "default" in parameter_def
             specify_default_source = dict(
-                name="specify_default", label="Specify a default value", type="boolean", checked=specify_default_checked
+                name="specify_default",
+                label="Specify a default value",
+                type="boolean",
             )
             specify_default = BooleanToolParameter(None, specify_default_source)
-            specify_default_cond = Conditional()
-            specify_default_cond.name = "specify_default"
+            specify_default_cond = Conditional("specify_default")
             specify_default_cond.test_param = specify_default
 
             when_specify_default_true = ConditionalWhen()
             when_specify_default_true.value = "true"
             when_specify_default_true.inputs = {}
-            when_specify_default_true.inputs["default"] = input_default_value
+            when_specify_default_true.inputs["default"] = default_parameter
 
             when_specify_default_false = ConditionalWhen()
             when_specify_default_false.value = "false"
@@ -1279,53 +1262,89 @@ class InputParameterModule(WorkflowModule):
 
             when_true = ConditionalWhen()
             when_true.value = "true"
-            when_true.inputs = {}
-            when_true.inputs["default"] = specify_default_cond
+            when_true.inputs = {"default": specify_default_cond}
 
             when_false = ConditionalWhen()
             when_false.value = "false"
-            when_false.inputs = {}
+            # This is only present for backwards compatibility,
+            # We don't need this conditional since you can set
+            # a default value for optional and required parameters.
+            # TODO: version the state and upgrade it to a simpler version
+            when_false.inputs = {"default": specify_default_cond}
 
             optional_cases = [when_true, when_false]
             optional_cond.cases = optional_cases
 
+            def regex_validator_definition():
+                add_validators_repeat = Repeat("validators")
+                add_validators_repeat.title = "Add validator to restrict valid input"
+                add_validators_repeat.min = 0
+                add_validators_repeat.max = math.inf
+                add_validators_repeat.inputs = {
+                    "regex_match": TextToolParameter(
+                        None,
+                        {
+                            "optional": False,
+                            "name": "regex_match",
+                            "label": "Specify regular expression",
+                            "help": "Provided [regular expression](gxhelp://programming.python.reg.ex) must match input value for input to be valid",
+                            "help_format": "markdown",
+                        },
+                    ),
+                    "regex_doc": TextToolParameter(
+                        None,
+                        {
+                            "optional": False,
+                            "name": "regex_doc",
+                            "label": "Specify a message",
+                            "help": "This message will be shown if the regular does not match the input",
+                        },
+                    ),
+                }
+
+                return add_validators_repeat
+
             if param_type == "text":
+
+                specify_multiple_source = dict(
+                    name="multiple",
+                    label="Allow multiple selection",
+                    help="Only applies when connected to multi-select parameter(s)",
+                    type="boolean",
+                )
+
+                specify_multiple = BooleanToolParameter(None, specify_multiple_source)
+
+                # Insert multiple option as first option, which is determined by dictionary insert order
+                when_this_type.inputs = {
+                    "multiple": specify_multiple,
+                    "validators": regex_validator_definition(),
+                    **when_this_type.inputs,
+                }
+
                 restrict_how_source: Dict[str, Union[str, List[Dict[str, Union[str, bool]]]]] = dict(
                     name="how", label="Restrict Text Values?", type="select"
                 )
-                if parameter_def.get("restrictions") is not None:
-                    restrict_how_value = "staticRestrictions"
-                elif parameter_def.get("restrictOnConnections") is True:
-                    restrict_how_value = "onConnections"
-                elif parameter_def.get("suggestions") is not None:
-                    restrict_how_value = "staticSuggestions"
-                else:
-                    restrict_how_value = "none"
                 restrict_how_source["options"] = [
                     {
                         "value": "none",
                         "label": "Do not specify restrictions (default).",
-                        "selected": restrict_how_value == "none",
                     },
                     {
                         "value": "onConnections",
                         "label": "Attempt restriction based on connections.",
-                        "selected": restrict_how_value == "onConnections",
                     },
                     {
                         "value": "staticRestrictions",
                         "label": "Provide list of all possible values.",
-                        "selected": restrict_how_value == "staticRestrictions",
                     },
                     {
                         "value": "staticSuggestions",
                         "label": "Provide list of suggested values.",
-                        "selected": restrict_how_value == "staticSuggestions",
                     },
                 ]
-                restrictions_cond = Conditional()
+                restrictions_cond = Conditional("restrictions")
                 restrictions_how = SelectToolParameter(None, restrict_how_source)
-                restrictions_cond.name = "restrictions"
                 restrictions_cond.test_param = restrictions_how
 
                 when_restrict_none = ConditionalWhen()
@@ -1379,11 +1398,58 @@ class InputParameterModule(WorkflowModule):
                 restrictions_cond.cases = restrictions_cond_cases
                 when_this_type.inputs["restrictions"] = restrictions_cond
 
+            if param_type == "integer":
+                when_this_type.inputs["min"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+            if param_type == "float":
+                when_this_type.inputs["min"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+            if param_type == "directory_uri":
+                when_this_type.inputs["validators"] = regex_validator_definition()
+
             cases.append(when_this_type)
 
         parameter_type_cond.cases = cases
         return {"parameter_definition": parameter_type_cond}
 
+    def get_config_form(self, step=None):
+        """Serializes input parameters of a module into input dictionaries."""
+        group_inputs: List[Dict[str, Any]] = []
+        populate_model(self.trans, self.get_inputs(), self.state.inputs, group_inputs)
+        return {"title": self.name, "inputs": group_inputs}
+
     def restrict_options(self, step, connections: Iterable[WorkflowStepConnection], default_value):
         try:
             static_options = []
@@ -1399,7 +1465,7 @@ class InputParameterModule(WorkflowModule):
 
                     def callback(input, prefixed_name, context, **kwargs):
                         if prefixed_name == connection.input_name and hasattr(input, "get_options"):  # noqa: B023
-                            static_options.append(input.get_options(self.trans, {}))
+                            static_options.append(input.get_options(self.trans, context))
 
                     visit_input_values(tool_inputs, module.state.inputs, callback)
                 elif isinstance(module, SubWorkflowModule):
@@ -1443,12 +1509,15 @@ class InputParameterModule(WorkflowModule):
         parameter_def = self._parse_state_into_dict()
         parameter_type = parameter_def["parameter_type"]
         optional = parameter_def["optional"]
+        default_value_set = "default" in parameter_def
         default_value = parameter_def.get("default", self.default_default_value)
-        if parameter_type not in ["text", "boolean", "integer", "float", "color"]:
+        if parameter_type not in ["text", "boolean", "integer", "float", "color", "directory_uri"]:
             raise ValueError("Invalid parameter type for workflow parameters encountered.")
 
         # Optional parameters for tool input source definition.
         parameter_kwds: Dict[str, Union[str, List[Dict[str, Any]]]] = {}
+        if "multiple" in parameter_def:
+            parameter_kwds["multiple"] = parameter_def["multiple"]
 
         is_text = parameter_type == "text"
         restricted_inputs = False
@@ -1485,13 +1554,16 @@ class InputParameterModule(WorkflowModule):
             parameter_kwds["options"] = _parameter_def_list_to_options(restriction_values)
             restricted_inputs = True
 
+        if parameter_def.get("validators"):
+            parameter_kwds["validators"] = parameter_def["validators"]
+
         client_parameter_type = parameter_type
         if restricted_inputs:
             client_parameter_type = "select"
 
         parameter_class = parameter_types[client_parameter_type]
 
-        if optional:
+        if default_value_set:
             if client_parameter_type == "select":
                 parameter_kwds["selected"] = default_value
             else:
@@ -1499,22 +1571,20 @@ class InputParameterModule(WorkflowModule):
             if parameter_type == "boolean":
                 parameter_kwds["checked"] = default_value
 
-        if "value" not in parameter_kwds and parameter_type in ["integer", "float"]:
-            parameter_kwds["value"] = str(0)
-
         if is_text and parameter_def.get("suggestions") is not None:
             suggestion_values = parameter_def.get("suggestions")
             parameter_kwds["options"] = _parameter_def_list_to_options(suggestion_values)
 
-        input_source = dict(
+        input_source_dict = dict(
             name="input", label=self.label, type=client_parameter_type, optional=optional, **parameter_kwds
         )
+        input_source = get_input_source(input_source_dict, trusted=False)
         input = parameter_class(None, input_source)
         return dict(input=input)
 
     def get_runtime_state(self):
         state = DefaultToolState()
-        state.inputs = dict(input=None)
+        state.inputs = dict(input=NO_REPLACEMENT)
         return state
 
     def get_all_outputs(self, data_only=False):
@@ -1528,6 +1598,7 @@ class InputParameterModule(WorkflowModule):
                 label=self.label,
                 type=parameter_def.get("parameter_type"),
                 optional=parameter_def["optional"],
+                multiple=parameter_def.get("multiple", False),
                 parameter=True,
             )
         ]
@@ -1536,8 +1607,11 @@ class InputParameterModule(WorkflowModule):
         self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
     ) -> Optional[bool]:
         step = invocation_step.workflow_step
-        input_value = step.state.inputs["input"]
-        if input_value is None:
+        if step.id in progress.inputs_by_step_id:
+            input_value = progress.inputs_by_step_id[step.id]
+        else:
+            input_value = step.state.inputs["input"]
+        if input_value is NO_REPLACEMENT:
             default_value = step.get_input_default_value(NO_REPLACEMENT)
             # TODO: look at parameter type and infer if value should be a dictionary
             # instead. Guessing only field parameter types in CWL branch would have
@@ -1545,6 +1619,16 @@ class InputParameterModule(WorkflowModule):
             if not isinstance(default_value, dict):
                 default_value = {"value": default_value}
             input_value = default_value.get("value", NO_REPLACEMENT)
+        input_param = self.get_runtime_inputs(self)["input"]
+        # TODO: raise DelayedWorkflowEvaluation if replacement not ready ? Need test
+        try:
+            input_param.validate(input_value, trans)
+        except ValueError as e:
+            raise FailWorkflowEvaluation(
+                why=InvocationFailureWorkflowParameterInvalid(
+                    reason=FailureReason.workflow_parameter_invalid, workflow_step_id=step.id, details=str(e)
+                )
+            )
         step_outputs = dict(output=input_value)
         progress.set_outputs_for_input(invocation_step, step_outputs)
         return None
@@ -1555,7 +1639,8 @@ class InputParameterModule(WorkflowModule):
         if "default" in state:
             default_set = True
             default_value = state["default"]
-            state["optional"] = True
+        multiple = state.get("multiple")
+        source_validators = state.get("validators")
         restrictions = state.get("restrictions")
         restrictOnConnections = state.get("restrictOnConnections")
         suggestions = state.get("suggestions")
@@ -1573,6 +1658,25 @@ class InputParameterModule(WorkflowModule):
                 "optional": {"optional": str(state.get("optional", False))},
             }
         }
+        if multiple is not None:
+            state["parameter_definition"]["multiple"] = multiple
+        if source_validators is not None:
+            form_validators = []
+            # the form definition can change from Galaxy to Galaxy fairly freely, but the source validators are persisted
+            # and need to be consistent - here we convert the persisted/YAML tool definition version to the "tool form" version.
+            for source_validator in source_validators:
+                source_type = source_validator["type"]
+                if source_type == "regex":
+                    form_validators.append(
+                        {
+                            "regex_doc": source_validator.get("message"),
+                            "regex_match": source_validator.get("expression"),
+                        }
+                    )
+                elif source_type == "in_range":
+                    state["parameter_definition"]["min"] = source_validator.get("min")
+                    state["parameter_definition"]["max"] = source_validator.get("max")
+            state["parameter_definition"]["validators"] = form_validators
         state["parameter_definition"]["restrictions"] = {}
         state["parameter_definition"]["restrictions"]["how"] = restrictions_how
 
@@ -1614,6 +1718,34 @@ class InputParameterModule(WorkflowModule):
                     rval["default"] = optional_state["specify_default"]["default"]
             else:
                 optional = False
+            if "multiple" in parameters_def:
+                rval["multiple"] = parameters_def["multiple"]
+            source_validators = []
+            if "min" in parameters_def or "max" in parameters_def:
+                min = parameters_def.get("min")
+                max = parameters_def.get("max")
+                source_validators.append(
+                    {
+                        "min": min,
+                        "max": max,
+                        "negate": False,
+                        "type": "in_range",
+                    }
+                )
+
+            if "validators" in parameters_def:
+                form_validators = parameters_def["validators"]
+                # convert the current tool form structure to the persisted YAML-definition style
+                for form_validator in form_validators:
+                    source_validators.append(
+                        {
+                            "message": form_validator["regex_doc"],
+                            "expression": form_validator["regex_match"],
+                            "negate": False,
+                            "type": "regex",
+                        }
+                    )
+            rval["validators"] = source_validators
             restrictions_cond_values = parameters_def.get("restrictions")
             if restrictions_cond_values:
 
@@ -1648,7 +1780,7 @@ class InputParameterModule(WorkflowModule):
             rval.update({"parameter_type": self.default_parameter_type, "optional": self.default_optional})
         return rval
 
-    def save_to_step(self, step, **kwd):
+    def save_to_step(self, step, detached=False):
         step.type = self.type
         step.tool_inputs = self._parse_state_into_dict()
 
@@ -1854,7 +1986,7 @@ class ToolModule(WorkflowModule):
         return self.tool.version if self.tool else self.tool_version
 
     def get_tooltip(self, static_path=None):
-        if self.tool and self.tool.help:
+        if self.tool and self.tool.raw_help and self.tool.raw_help.format == "restructuredtext":
             host_url = self.trans.url_builder("/")
             static_path = self.trans.url_builder(static_path) if static_path else ""
             return self.tool.help.render(host_url=host_url, static_path=static_path)
@@ -2103,13 +2235,14 @@ class ToolModule(WorkflowModule):
     def get_runtime_inputs(self, step, connections: Optional[Iterable[WorkflowStepConnection]] = None):
         return self.get_inputs()
 
-    def compute_runtime_state(self, trans, step=None, step_updates=None):
+    def compute_runtime_state(self, trans, step=None, step_updates=None, replace_default_values=False):
         # Warning: This method destructively modifies existing step state.
         if self.tool:
             step_errors = {}
             state = self.state
-            self.runtime_post_job_actions = {}
-            state, step_errors = super().compute_runtime_state(trans, step, step_updates)
+            state, step_errors = super().compute_runtime_state(
+                trans, step, step_updates, replace_default_values=replace_default_values
+            )
             if step_updates:
                 self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {})
                 step_metadata_runtime_state = self.__step_meta_runtime_state()
@@ -2136,7 +2269,11 @@ class ToolModule(WorkflowModule):
             )
 
     def execute(
-        self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
+        self,
+        trans,
+        progress: "WorkflowProgress",
+        invocation_step: "WorkflowInvocationStep",
+        use_cached_job: bool = False,
     ) -> Optional[bool]:
         invocation = invocation_step.workflow_invocation
         step = invocation_step.workflow_step
@@ -2145,7 +2282,12 @@ class ToolModule(WorkflowModule):
             # TODO: why do we even create an invocation, seems like something we could check on submit?
             message = f"Specified tool [{tool.id}] in step {step.order_index + 1} is not workflow-compatible."
             raise exceptions.MessageException(message)
+        self.state, _ = self.compute_runtime_state(
+            trans, step, step_updates=progress.param_map.get(step.id), replace_default_values=True
+        )
+        step.state = self.state
         tool_state = step.state
+        assert tool_state is not None
         tool_inputs = tool.inputs.copy()
         # Not strictly needed - but keep Tool state clean by stripping runtime
         # metadata parameters from it.
@@ -2258,19 +2400,7 @@ class ToolModule(WorkflowModule):
             param_combinations.append(execution_state.inputs)
 
         complete = False
-        completed_jobs = {}
-        for i, param in enumerate(param_combinations):
-            if use_cached_job:
-                completed_jobs[i] = tool.job_search.by_tool_input(
-                    trans=trans,
-                    tool_id=tool.id,
-                    tool_version=tool.version,
-                    param=param,
-                    param_dump=tool.params_to_strings(param, trans.app, nested=True),
-                    job_state=None,
-                )
-            else:
-                completed_jobs[i] = None
+        completed_jobs: Dict[int, Optional[Job]] = tool.completed_jobs(trans, use_cached_job, param_combinations)
         try:
             mapping_params = MappingParameters(tool_state.inputs, param_combinations)
             max_num_jobs = progress.maximum_jobs_to_schedule_or_none
@@ -2286,7 +2416,7 @@ class ToolModule(WorkflowModule):
                 mapping_params=mapping_params,
                 history=invocation.history,
                 collection_info=collection_info,
-                workflow_invocation_uuid=invocation.uuid.hex,
+                workflow_invocation_uuid=invocation.uuid.hex if invocation.uuid else None,
                 invocation_step=invocation_step,
                 max_num_jobs=max_num_jobs,
                 validate_outputs=validate_outputs,
@@ -2305,10 +2435,11 @@ class ToolModule(WorkflowModule):
             raise DelayedWorkflowEvaluation(why=delayed_why)
 
         progress.record_executed_job_count(len(execution_tracker.successful_jobs))
+        step_outputs: Dict[str, Union[model.HistoryDatasetCollectionAssociation, model.HistoryDatasetAssociation]] = {}
         if collection_info:
-            step_outputs = dict(execution_tracker.implicit_collections)
+            step_outputs.update(execution_tracker.implicit_collections)
         else:
-            step_outputs = dict(execution_tracker.output_datasets)
+            step_outputs.update(execution_tracker.output_datasets)
             step_outputs.update(execution_tracker.output_collections)
         progress.set_step_outputs(invocation_step, step_outputs, already_persisted=not invocation_step.is_new)
 
@@ -2448,23 +2579,6 @@ def load_module_sections(trans):
     is configured with.
     """
     module_sections = {}
-    module_sections["inputs"] = {
-        "name": "inputs",
-        "title": "Inputs",
-        "modules": [
-            {"name": "data_input", "title": "Input Dataset", "description": "Input dataset"},
-            {
-                "name": "data_collection_input",
-                "title": "Input Dataset Collection",
-                "description": "Input dataset collection",
-            },
-            {
-                "name": "parameter_input",
-                "title": "Parameter Input",
-                "description": "Simple inputs used for workflow logic",
-            },
-        ],
-    }
 
     if trans.app.config.enable_beta_workflow_modules:
         module_sections["experimental"] = {
@@ -2505,7 +2619,7 @@ class WorkflowModuleInjector:
         self.trans = trans
         self.allow_tool_state_corrections = allow_tool_state_corrections
 
-    def inject(self, step: WorkflowStep, step_args=None, steps=None, **kwargs):
+    def inject(self, step: WorkflowStep, step_args=None, steps=None, allow_tool_state_corrections=False, **kwargs):
         """Pre-condition: `step` is an ORM object coming from the database, if
         supplied `step_args` is the representation of the inputs for that step
         supplied via web form.
@@ -2538,7 +2652,12 @@ class WorkflowModuleInjector:
 
             subworkflow = step.subworkflow
             assert subworkflow
-            populate_module_and_state(self.trans, subworkflow, param_map=unjsonified_subworkflow_param_map)
+            populate_module_and_state(
+                self.trans,
+                subworkflow,
+                param_map=unjsonified_subworkflow_param_map,
+                allow_tool_state_corrections=allow_tool_state_corrections,
+            )
 
     def inject_all(self, workflow: Workflow, param_map=None, ignore_tool_missing_exception=False, **kwargs):
         param_map = param_map or {}
diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index 264fa843d8303c39c2593b2d731280e3b03ce865..84dabc0d388acf0f928827c095888d78b7136589 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -9,6 +9,7 @@ from galaxy.tools.parameters import visit_input_values
 from galaxy.tools.parameters.basic import contains_workflow_parameter
 from galaxy.tools.parameters.workflow_utils import (
     ConnectedValue,
+    NO_REPLACEMENT,
     runtime_to_json,
 )
 from .schema import (
@@ -43,20 +44,24 @@ from .schema import (
 )
 from ..modules import (
     InputParameterModule,
-    NO_REPLACEMENT,
+    WorkflowModuleInjector,
 )
 
 log = logging.getLogger(__name__)
 
 
 class WorkflowRefactorExecutor:
-    def __init__(self, raw_workflow_description, workflow, module_injector):
+    def __init__(self, raw_workflow_description, workflow, module_injector: WorkflowModuleInjector):
         # we mostly use the ga representation, but there may be cases where the
         # models/modules of existing workflow are more usable.
         self.raw_workflow_description = raw_workflow_description
         self.workflow = workflow
         self.module_injector = module_injector
-        self.module_injector.inject_all(workflow, ignore_tool_missing_exception=True)
+        self.module_injector.inject_all(
+            workflow,
+            ignore_tool_missing_exception=True,
+            allow_tool_state_corrections=module_injector.allow_tool_state_corrections,
+        )
 
     def refactor(self, refactor_request: RefactorActions):
         action_executions = []
@@ -462,18 +467,30 @@ class WorkflowRefactorExecutor:
     def _inject(self, step, execution):
         # compute runtime state, capture upgrade messages that result
         if not hasattr(step, "module"):
-            self.module_injector.inject(step)
+            self.module_injector.inject(step, allow_tool_state_corrections=True)
         self.module_injector.compute_runtime_state(step)
         if getattr(step, "upgrade_messages", None):
             for key, value in step.upgrade_messages.items():
-                message = RefactorActionExecutionMessage(
-                    message=value,
-                    message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,
-                    input_name=key,
-                    step_label=step.label,
-                    order_index=step.order_index,
-                )
-                execution.messages.append(message)
+                if isinstance(value, dict):
+                    for input_name, message in value.items():
+                        execution.messages.append(
+                            RefactorActionExecutionMessage(
+                                message=message,
+                                message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,
+                                input_name=input_name,
+                                step_label=step.label,
+                                order_index=step.order_index,
+                            )
+                        )
+                else:
+                    message = RefactorActionExecutionMessage(
+                        message=value,
+                        message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,
+                        input_name=key,
+                        step_label=step.label,
+                        order_index=step.order_index,
+                    )
+                    execution.messages.append(message)
         if getattr(step.module, "version_changes", None):
             for version_change in step.module.version_changes:
                 message = RefactorActionExecutionMessage(
diff --git a/lib/galaxy/workflow/reports/generators/__init__.py b/lib/galaxy/workflow/reports/generators/__init__.py
index 081155ca811b5b1c41bb5d8c9f8b6407c48a9f51..70cf73787ff29b51574eb414e4c51b030a9f440e 100644
--- a/lib/galaxy/workflow/reports/generators/__init__.py
+++ b/lib/galaxy/workflow/reports/generators/__init__.py
@@ -12,6 +12,7 @@ from galaxy.managers.markdown_util import (
     ready_galaxy_markdown_for_export,
     resolve_invocation_markdown,
 )
+from galaxy.model import WorkflowInvocation
 from galaxy.schema import PdfDocumentType
 
 
@@ -35,7 +36,7 @@ class WorkflowReportGeneratorPlugin(metaclass=ABCMeta):
 class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=ABCMeta):
     """WorkflowReportGeneratorPlugin that generates markdown as base report."""
 
-    def generate_report_json(self, trans, invocation, runtime_report_config_json=None):
+    def generate_report_json(self, trans, invocation: WorkflowInvocation, runtime_report_config_json=None):
         """ """
         workflow_manager = workflows.WorkflowsManager(trans.app)
         workflow_encoded_id = trans.app.security.encode_id(invocation.workflow_id)
@@ -44,13 +45,15 @@ class WorkflowMarkdownGeneratorPlugin(WorkflowReportGeneratorPlugin, metaclass=A
             trans, invocation, runtime_report_config_json=runtime_report_config_json
         )
         export_markdown, extra_rendering_data = ready_galaxy_markdown_for_export(trans, internal_markdown)
+        # Invocations can only be run on history, and user must exist, so this should always work
+        username = invocation.history and invocation.history.user and invocation.history.user.username
         rval = {
             "render_format": "markdown",  # Presumably the frontend could render things other ways.
             "markdown": export_markdown,
             "invocation_markdown": export_markdown,
             "model_class": "Report",
             "id": trans.app.security.encode_id(invocation.workflow_id),
-            "username": trans.user.username,
+            "username": username,
             "title": workflow.name,
         }
         rval.update(extra_rendering_data)
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 2addb711cad681767b566e3ddbea81018c8ed62c..cfda4b776eb76faa8373143c11ebfe9e72553dc6 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -1,5 +1,6 @@
 import logging
 import uuid
+from collections.abc import MutableMapping
 from typing import (
     Any,
     Dict,
@@ -37,6 +38,11 @@ from galaxy.schema.invocation import (
     WarningReason,
 )
 from galaxy.tools.parameters.basic import raw_to_galaxy
+from galaxy.tools.parameters.workflow_utils import (
+    is_runtime_value,
+    NO_REPLACEMENT,
+    NoReplacement,
+)
 from galaxy.tools.parameters.wrapped import nested_key_to_path
 from galaxy.util import ExecutionTimer
 from galaxy.workflow import modules
@@ -144,7 +150,12 @@ def queue_invoke(
         )
     workflow_invocation = workflow_run_config_to_request(trans, workflow_run_config, workflow)
     workflow_invocation.workflow = workflow
-    return trans.app.workflow_scheduling_manager.queue(workflow_invocation, request_params, flush=flush)
+    initial_state = model.WorkflowInvocation.states.NEW
+    if workflow_run_config.requires_materialization:
+        initial_state = model.WorkflowInvocation.states.REQUIRES_MATERIALIZATION
+    return trans.app.workflow_scheduling_manager.queue(
+        workflow_invocation, request_params, flush=flush, initial_state=initial_state
+    )
 
 
 class WorkflowInvoker:
@@ -252,7 +263,7 @@ class WorkflowInvoker:
                 step_delayed = delayed_steps = True
                 self.progress.mark_step_outputs_delayed(step, why=de.why)
             except Exception as e:
-                log_function = log.exception
+                log_function = log.error
                 if isinstance(e, modules.FailWorkflowEvaluation) and e.why.reason in FAILURE_REASONS_EXPECTED:
                     log_function = log.info
                 log_function(
@@ -329,6 +340,7 @@ class WorkflowInvoker:
                 )
 
     def _invoke_step(self, invocation_step: WorkflowInvocationStep) -> Optional[bool]:
+        assert invocation_step.workflow_step.module
         incomplete_or_none = invocation_step.workflow_step.module.execute(
             self.trans,
             self.progress,
@@ -427,11 +439,11 @@ class WorkflowProgress:
 
     def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[str, Any]):
         replacement: Union[
-            modules.NoReplacement,
+            NoReplacement,
             model.DatasetCollectionInstance,
             List[model.DatasetCollectionInstance],
-            "HistoryItem",
-        ] = modules.NO_REPLACEMENT
+            HistoryItem,
+        ] = NO_REPLACEMENT
         prefixed_name = input_dict["name"]
         multiple = input_dict["multiple"]
         is_data = input_dict["input_type"] in ["dataset", "dataset_collection"]
@@ -451,15 +463,18 @@ class WorkflowProgress:
                     replacement = temp
             else:
                 replacement = self.replacement_for_connection(connection[0], is_data=is_data)
-        elif step.state and (state_input := get_path(step.state.inputs, nested_key_to_path(prefixed_name), None)):
+        elif (
+            step.state
+            and (state_input := get_path(step.state.inputs, nested_key_to_path(prefixed_name), None))
+            and not is_runtime_value(state_input)
+        ):
             # workflow submitted with step parameters populates state directly
             # via populate_module_and_state
             replacement = state_input
-        else:
-            for step_input in step.inputs:
-                if step_input.name == prefixed_name and step_input.default_value_set:
-                    if is_data:
-                        replacement = raw_to_galaxy(trans.app, trans.history, step_input.default_value)
+        elif (step_input := step.inputs_by_name.get(prefixed_name)) and step_input.default_value_set:
+            replacement = step_input.default_value
+            if is_data:
+                replacement = raw_to_galaxy(trans.app, trans.history, step_input.default_value)
         return replacement
 
     def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True):
@@ -489,6 +504,8 @@ class WorkflowProgress:
                     dependent_workflow_step_id=output_step_id,
                 )
             )
+        if isinstance(replacement, MutableMapping) and replacement.get("__class__") == "NoReplacement":
+            return NO_REPLACEMENT
         if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
             if not replacement.collection.populated:
                 if not replacement.waiting_for_elements:
@@ -569,21 +586,11 @@ class WorkflowProgress:
         if self.inputs_by_step_id:
             step_id = step.id
             if step_id not in self.inputs_by_step_id and "output" not in outputs:
-                default_value = step.input_default_value
-                if default_value or step.input_optional:
-                    outputs["output"] = default_value
-                else:
-                    log.error(f"{step.log_str()} not found in inputs_step_id {self.inputs_by_step_id}")
-                    raise modules.FailWorkflowEvaluation(
-                        why=InvocationFailureOutputNotFound(
-                            reason=FailureReason.output_not_found,
-                            workflow_step_id=invocation_step.workflow_step_id,
-                            output_name="output",
-                            dependent_workflow_step_id=invocation_step.workflow_step_id,
-                        )
-                    )
+                default_value = step.get_input_default_value(NO_REPLACEMENT)
+                outputs["output"] = default_value
             elif step_id in self.inputs_by_step_id:
-                outputs["output"] = self.inputs_by_step_id[step_id]
+                if self.inputs_by_step_id[step_id] is not None or "output" not in outputs:
+                    outputs["output"] = self.inputs_by_step_id[step_id]
 
         if step.label and step.type == "parameter_input" and "output" in outputs:
             self.runtime_replacements[step.label] = str(outputs["output"])
@@ -614,7 +621,7 @@ class WorkflowProgress:
                     # Add this non-data, non workflow-output output to the workflow outputs.
                     # This is required for recovering the output in the next scheduling iteration,
                     # and should be replaced with a WorkflowInvocationStepOutputValue ASAP.
-                    if not workflow_outputs_by_name.get(output_name) and not output_object == modules.NO_REPLACEMENT:
+                    if not workflow_outputs_by_name.get(output_name) and output_object is not NO_REPLACEMENT:
                         workflow_output = model.WorkflowOutput(step, output_name=output_name)
                         step.workflow_outputs.append(workflow_output)
             for workflow_output in step.workflow_outputs:
@@ -639,6 +646,8 @@ class WorkflowProgress:
                 )
 
     def _record_workflow_output(self, step: "WorkflowStep", workflow_output: "WorkflowOutput", output: Any) -> None:
+        if output is NO_REPLACEMENT:
+            output = {"__class__": "NoReplacement"}
         self.workflow_invocation.add_output(workflow_output, step, output)
 
     def mark_step_outputs_delayed(self, step: "WorkflowStep", why: Optional[str] = None) -> None:
@@ -695,7 +704,8 @@ class WorkflowProgress:
         for input_subworkflow_step in subworkflow.input_steps:
             connection_found = False
             subworkflow_step_id = input_subworkflow_step.id
-            for input_connection in step.input_connections:
+            input_connections = step.input_connections
+            for input_connection in input_connections:
                 if input_connection.input_subworkflow_step_id == subworkflow_step_id:
                     is_data = input_connection.output_step.type != "parameter_input"
                     replacement = self.replacement_for_connection(
@@ -706,7 +716,18 @@ class WorkflowProgress:
                     connection_found = True
                     break
 
-            if not connection_found and not input_subworkflow_step.input_optional:
+            if not input_subworkflow_step.input_optional and not connection_found:
+
+                if not input_connections:
+                    # TODO: Prevent this on import / runtime !
+                    raise modules.FailWorkflowEvaluation(
+                        InvocationUnexpectedFailure(
+                            reason=FailureReason.unexpected_failure,
+                            workflow_step_id=step.id,
+                            details="Subworkflow has disconnected required input.",
+                        )
+                    )
+
                 raise modules.FailWorkflowEvaluation(
                     InvocationFailureOutputNotFound(
                         reason=FailureReason.output_not_found,
@@ -731,6 +752,7 @@ class WorkflowProgress:
         return raw_to_galaxy(self.module_injector.trans.app, self.module_injector.trans.history, value)
 
     def _recover_mapping(self, step_invocation: WorkflowInvocationStep) -> None:
+        assert step_invocation.workflow_step.module
         try:
             step_invocation.workflow_step.module.recover_mapping(step_invocation, self)
         except modules.DelayedWorkflowEvaluation as de:
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index 516c85d07eb1ca4c92537d08ceda37ba92f95213..b448050e66eb7976c4ed90d199323faf93e0e5c1 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -10,11 +10,13 @@ from typing import (
 )
 
 from galaxy import exceptions
+from galaxy.managers.hdas import dereference_input
 from galaxy.model import (
     EffectiveOutput,
     History,
     HistoryDatasetAssociation,
     HistoryDatasetCollectionAssociation,
+    InputWithRequest,
     LibraryDataset,
     LibraryDatasetDatasetAssociation,
     WorkflowInvocation,
@@ -25,7 +27,11 @@ from galaxy.model.base import (
     ensure_object_added_to_session,
     transaction,
 )
+from galaxy.tool_util.parameters import DataRequestUri
+from galaxy.tools.parameters.basic import ParameterValueError
 from galaxy.tools.parameters.meta import expand_workflow_inputs
+from galaxy.tools.parameters.workflow_utils import NO_REPLACEMENT
+from galaxy.workflow.modules import WorkflowModuleInjector
 from galaxy.workflow.resources import get_resource_mapper_function
 
 if TYPE_CHECKING:
@@ -57,6 +63,9 @@ class WorkflowRunConfig:
     :param inputs: Map from step ids to dict's containing HDA for these steps.
     :type inputs: dict
 
+    :param requires_materialization: True if an input requires materialization before
+                                     the workflow is scheduled.
+
     :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows
                       steps - by unencoded database id ('step_id'), index in workflow
                       'step_index' (independent of database), or by input name for
@@ -78,6 +87,7 @@ class WorkflowRunConfig:
         copy_inputs_to_history: bool = False,
         use_cached_job: bool = False,
         resource_params: Optional[Dict[int, Any]] = None,
+        requires_materialization: bool = False,
         preferred_object_store_id: Optional[str] = None,
         preferred_outputs_object_store_id: Optional[str] = None,
         preferred_intermediate_object_store_id: Optional[str] = None,
@@ -91,6 +101,7 @@ class WorkflowRunConfig:
         self.resource_params = resource_params or {}
         self.allow_tool_state_corrections = allow_tool_state_corrections
         self.use_cached_job = use_cached_job
+        self.requires_materialization = requires_materialization
         self.preferred_object_store_id = preferred_object_store_id
         self.preferred_outputs_object_store_id = preferred_outputs_object_store_id
         self.preferred_intermediate_object_store_id = preferred_intermediate_object_store_id
@@ -113,7 +124,9 @@ def _normalize_inputs(
             elif inputs_by_el == "step_uuid":
                 possible_input_keys.append(str(step.uuid))
             elif inputs_by_el == "name":
-                possible_input_keys.append(step.label or step.tool_inputs.get("name"))  # type:ignore[union-attr]
+                label = step.effective_label
+                if label:
+                    possible_input_keys.append(label)
             else:
                 raise exceptions.MessageException(
                     "Workflow cannot be run because unexpected inputs_by value specified."
@@ -309,8 +322,8 @@ def build_workflow_run_configs(
     add_to_history = "no_add_to_history" not in payload
     legacy = payload.get("legacy", False)
     already_normalized = payload.get("parameters_normalized", False)
-    raw_parameters = payload.get("parameters", {})
-
+    raw_parameters = payload.get("parameters") or {}
+    requires_materialization: bool = False
     run_configs = []
     unexpanded_param_map = _normalize_step_parameters(
         workflow.steps, raw_parameters, legacy=legacy, already_normalized=already_normalized
@@ -358,26 +371,42 @@ def build_workflow_run_configs(
 
         steps_by_id = workflow.steps_by_id
         # Set workflow inputs.
+        module_injector = WorkflowModuleInjector(trans, False)
         for key, input_dict in normalized_inputs.items():
             if input_dict is None:
                 continue
             step = steps_by_id[key]
             if step.type == "parameter_input":
+                module_injector.inject(step)
+                assert step.module
+                input_param = step.module.get_runtime_inputs(step.module)["input"]
+                try:
+                    input_param.validate(input_dict, trans=trans)
+                except ParameterValueError as e:
+                    raise exceptions.RequestParameterInvalidException(
+                        f"{step.label or step.order_index + 1}: {e.message_suffix}"
+                    )
                 continue
             if "src" not in input_dict:
                 raise exceptions.RequestParameterInvalidException(
                     f"Not input source type defined for input '{input_dict}'."
                 )
-            if "id" not in input_dict:
-                raise exceptions.RequestParameterInvalidException(f"Not input id defined for input '{input_dict}'.")
+            input_source = input_dict["src"]
+            if "id" not in input_dict and input_source != "url":
+                raise exceptions.RequestParameterInvalidException(f"No input id defined for input '{input_dict}'.")
+            elif input_source == "url" and not input_dict.get("url"):
+                raise exceptions.RequestParameterInvalidException(
+                    f"Supplied 'url' is empty or absent for input '{input_dict}'."
+                )
             if "content" in input_dict:
                 raise exceptions.RequestParameterInvalidException(
                     f"Input cannot specify explicit 'content' attribute {input_dict}'."
                 )
-            input_source = input_dict["src"]
-            input_id = input_dict["id"]
+            input_id = input_dict.get("id")
             try:
+                added_to_history = False
                 if input_source == "ldda":
+                    assert input_id
                     ldda = trans.sa_session.get(LibraryDatasetDatasetAssociation, trans.security.decode_id(input_id))
                     assert ldda
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
@@ -385,6 +414,7 @@ def build_workflow_run_configs(
                     )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
                 elif input_source == "ld":
+                    assert input_id
                     library_dataset = trans.sa_session.get(LibraryDataset, trans.security.decode_id(input_id))
                     assert library_dataset
                     ldda = library_dataset.library_dataset_dataset_association
@@ -394,6 +424,7 @@ def build_workflow_run_configs(
                     )
                     content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
                 elif input_source == "hda":
+                    assert input_id
                     # Get dataset handle, add to dict and history if necessary
                     content = trans.sa_session.get(HistoryDatasetAssociation, trans.security.decode_id(input_id))
                     assert trans.user_is_admin or trans.app.security_agent.can_access_dataset(
@@ -401,11 +432,21 @@ def build_workflow_run_configs(
                     )
                 elif input_source == "hdca":
                     content = app.dataset_collection_manager.get_dataset_collection_instance(trans, "history", input_id)
+                elif input_source == "url":
+                    data_request = DataRequestUri.model_validate(input_dict)
+                    hda: HistoryDatasetAssociation = dereference_input(trans, data_request, history)
+                    added_to_history = True
+                    content = InputWithRequest(
+                        input=hda,
+                        request=data_request.model_dump(mode="json"),
+                    )
+                    if not data_request.deferred:
+                        requires_materialization = True
                 else:
                     raise exceptions.RequestParameterInvalidException(
                         f"Unknown workflow input source '{input_source}' specified."
                     )
-                if add_to_history and content.history != history:
+                if not added_to_history and add_to_history and content.history != history:
                     if isinstance(content, HistoryDatasetCollectionAssociation):
                         content = content.copy(element_destination=history, flush=False)
                     else:
@@ -474,6 +515,7 @@ def build_workflow_run_configs(
                 allow_tool_state_corrections=allow_tool_state_corrections,
                 use_cached_job=use_cached_job,
                 resource_params=resource_params,
+                requires_materialization=requires_materialization,
                 preferred_object_store_id=preferred_object_store_id,
                 preferred_outputs_object_store_id=preferred_outputs_object_store_id,
                 preferred_intermediate_object_store_id=preferred_intermediate_object_store_id,
@@ -505,6 +547,7 @@ def workflow_run_config_to_request(
     for step in workflow.steps:
         steps_by_id[step.id] = step
         assert step.module
+        assert step.state
         serializable_runtime_state = step.module.encode_runtime_state(step, step.state)
 
         step_state = WorkflowRequestStepState()
@@ -559,7 +602,8 @@ def workflow_run_config_to_request(
             type=param_types.REPLACEMENT_PARAMETERS,
         )
     for step_id, content in run_config.inputs.items():
-        workflow_invocation.add_input(content, step_id)
+        if content is not NO_REPLACEMENT:
+            workflow_invocation.add_input(content, step_id)
     for step_id, param_dict in run_config.param_map.items():
         add_parameter(
             name=str(step_id),
diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py
index 3868e24c13a922f25ee13ed677b9344c7e78763b..a68f42aa8933edb6f1465b1694768b88c4cf002e 100644
--- a/lib/galaxy/workflow/scheduling_manager.py
+++ b/lib/galaxy/workflow/scheduling_manager.py
@@ -1,11 +1,22 @@
 import os
 from functools import partial
+from typing import Optional
 
 import galaxy.workflow.schedulers
 from galaxy import model
 from galaxy.exceptions import HandlerAssignmentError
 from galaxy.jobs.handler import InvocationGrabber
 from galaxy.model.base import transaction
+from galaxy.schema.invocation import (
+    FailureReason,
+    InvocationFailureDatasetFailed,
+    InvocationState,
+    InvocationUnexpectedFailure,
+)
+from galaxy.schema.tasks import (
+    MaterializeDatasetInstanceTaskRequest,
+    RequestUser,
+)
 from galaxy.util import plugin_config
 from galaxy.util.custom_logging import get_logger
 from galaxy.util.monitors import Monitors
@@ -154,8 +165,9 @@ class WorkflowSchedulingManager(ConfiguresHandlers):
         if exception:
             raise exception
 
-    def queue(self, workflow_invocation, request_params, flush=True):
-        workflow_invocation.set_state(model.WorkflowInvocation.states.NEW)
+    def queue(self, workflow_invocation, request_params, flush=True, initial_state: Optional[InvocationState] = None):
+        initial_state = initial_state or model.WorkflowInvocation.states.NEW
+        workflow_invocation.set_state(initial_state)
         workflow_invocation.scheduler = request_params.get("scheduler", None) or self.default_scheduler_id
         sa_session = self.app.model.context
         sa_session.add(workflow_invocation)
@@ -326,10 +338,54 @@ class WorkflowRequestMonitor(Monitors):
             if not self.monitor_running:
                 return
 
+    def __attempt_materialize(self, workflow_invocation, session) -> bool:
+        try:
+            inputs_to_materialize = workflow_invocation.inputs_requiring_materialization()
+            for input_to_materialize in inputs_to_materialize:
+                hda = input_to_materialize.hda
+                user = RequestUser(user_id=workflow_invocation.history.user_id)
+                task_request = MaterializeDatasetInstanceTaskRequest(
+                    user=user,
+                    history_id=workflow_invocation.history.id,
+                    source="hda",
+                    content=hda.id,
+                )
+                materialized_okay = self.app.hda_manager.materialize(task_request, in_place=True)
+                if not materialized_okay:
+                    workflow_invocation.fail()
+                    workflow_invocation.add_message(
+                        InvocationFailureDatasetFailed(
+                            workflow_step_id=input_to_materialize.input_dataset.workflow_step.id,
+                            reason=FailureReason.dataset_failed,
+                            hda_id=hda.id,
+                        )
+                    )
+                    session.add(workflow_invocation)
+                    session.commit()
+                    return False
+
+            # place back into ready and let it proceed normally on next iteration?
+            workflow_invocation.set_state(model.WorkflowInvocation.states.READY)
+            session.add(workflow_invocation)
+            session.commit()
+            return True
+        except Exception as e:
+            log.exception(f"Failed to materialize dataset for workflow {workflow_invocation.id} - {e}")
+            workflow_invocation.fail()
+            failure = InvocationUnexpectedFailure(reason=FailureReason.unexpected_failure, details=str(e))
+            workflow_invocation.add_message(failure)
+            session.add(workflow_invocation)
+            session.commit()
+        return False
+
     def __attempt_schedule(self, invocation_id, workflow_scheduler):
         with self.app.model.context() as session:
             workflow_invocation = session.get(model.WorkflowInvocation, invocation_id)
-
+            if workflow_invocation.state == workflow_invocation.states.REQUIRES_MATERIALIZATION:
+                if not self.__attempt_materialize(workflow_invocation, session):
+                    return None
+                if self.app.config.workflow_scheduling_separate_materialization_iteration:
+                    return None
             try:
                 if workflow_invocation.state == workflow_invocation.states.CANCELLING:
                     workflow_invocation.cancel_invocation_steps()
diff --git a/lib/galaxy/workflow/trs_proxy.py b/lib/galaxy/workflow/trs_proxy.py
index e465127a99ad609875e0d318868c5f0461bbbc96..bc4875b95f4bb452e38c77e19be52e9ca8100e03 100644
--- a/lib/galaxy/workflow/trs_proxy.py
+++ b/lib/galaxy/workflow/trs_proxy.py
@@ -2,15 +2,22 @@ import logging
 import os
 import re
 import urllib.parse
+from typing import List
 
 import yaml
 
-from galaxy.exceptions import MessageException
+from galaxy.config import Configuration
+from galaxy.exceptions import (
+    MessageException,
+    RequestParameterInvalidException,
+)
+from galaxy.files.uris import validate_non_local
 from galaxy.util import (
     asbool,
     DEFAULT_SOCKET_TIMEOUT,
     requests,
 )
+from galaxy.util.config_parsers import IpAllowedListEntryT
 from galaxy.util.search import parse_filters
 
 log = logging.getLogger(__name__)
@@ -53,8 +60,8 @@ def parse_search_kwds(search_query):
 
 
 class TrsProxy:
-    def __init__(self, config=None):
-        config_file = getattr(config, "trs_servers_config_file", None)
+    def __init__(self, config: Configuration):
+        config_file = config.trs_servers_config_file
         if config_file and os.path.exists(config_file):
             with open(config_file) as f:
                 server_list = yaml.safe_load(f)
@@ -62,6 +69,7 @@ class TrsProxy:
             server_list = DEFAULT_TRS_SERVERS
         self._server_list = server_list if server_list else []
         self._server_dict = {t["id"]: t for t in self._server_list}
+        self.fetch_url_allowlist_ips = config.fetch_url_allowlist_ips
 
     def get_servers(self):
         return self._server_list
@@ -73,7 +81,25 @@ class TrsProxy:
     def server_from_url(self, trs_url):
         return TrsServer(trs_url)
 
-    def match_url(self, url):
+    def get_trs_id_and_version_from_trs_url(self, trs_url):
+        parts = self.match_url(trs_url, self.fetch_url_allowlist_ips)
+        if parts:
+            return self.server_from_url(parts["trs_base_url"]), parts["tool_id"], parts["version_id"]
+        raise RequestParameterInvalidException(f"Invalid TRS URL {trs_url}.")
+
+    def get_version_from_trs_url(self, trs_url):
+        server, trs_tool_id, trs_version_id = self.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
+        return server.get_version_descriptor(trs_tool_id, trs_version_id)
+
+    def match_url(self, url, ip_allowlist: List[IpAllowedListEntryT]):
+        if url.lstrip().startswith("file://"):
+            # requests doesn't know what to do with file:// anyway, but just in case we swap
+            # out the implementation
+            raise RequestParameterInvalidException("Invalid TRS URL %s", url)
+        validate_non_local(url, ip_allowlist=ip_allowlist or [])
+        return self._match_url(url)
+
+    def _match_url(self, url):
         if matches := re.match(TRS_URL_REGEX, url):
             match_dict = matches.groupdict()
             match_dict["tool_id"] = urllib.parse.unquote(match_dict["tool_id"])
@@ -114,6 +140,9 @@ class TrsServer:
         )
         return self._get(trs_api_url)["content"]
 
+    def get_trs_url(self, tool_id: str, version_id: str):
+        return f"{self._get_tool_api_endpoint(tool_id)}/versions/{version_id}"
+
     def _quote(self, tool_id, **kwd):
         if asbool(kwd.get("tool_id_b64_encoded", False)):
             import base64
diff --git a/lib/galaxy/workflow/workflow_parameter_input_definitions.py b/lib/galaxy/workflow/workflow_parameter_input_definitions.py
new file mode 100644
index 0000000000000000000000000000000000000000..8cb3bc110b5bdf4b432829a27413127cf37db9d6
--- /dev/null
+++ b/lib/galaxy/workflow/workflow_parameter_input_definitions.py
@@ -0,0 +1,53 @@
+from typing import (
+    Dict,
+    Literal,
+    Union,
+)
+
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    ColorToolParameter,
+    DirectoryUriToolParameter,
+    FloatToolParameter,
+    IntegerToolParameter,
+    TextToolParameter,
+)
+
+param_types = Literal["text", "integer", "float", "color", "boolean", "directory_uri"]
+default_source_type = Dict[str, Union[int, float, bool, str]]
+tool_param_type = Union[
+    TextToolParameter,
+    IntegerToolParameter,
+    FloatToolParameter,
+    BooleanToolParameter,
+    ColorToolParameter,
+    DirectoryUriToolParameter,
+]
+
+
+def get_default_parameter(param_type: param_types) -> tool_param_type:
+    """
+    param_type is the type of parameter we want to build up, stored_parameter_type is the parameter_type
+    as stored in the tool state
+    """
+    default_source: default_source_type = dict(name="default", label="Default Value", type=param_type, optional=False)
+    if param_type == "text":
+        input_default_value: Union[
+            TextToolParameter,
+            IntegerToolParameter,
+            FloatToolParameter,
+            BooleanToolParameter,
+            ColorToolParameter,
+            DirectoryUriToolParameter,
+        ] = TextToolParameter(None, default_source)
+    elif param_type == "integer":
+        input_default_value = IntegerToolParameter(None, default_source)
+    elif param_type == "float":
+        input_default_value = FloatToolParameter(None, default_source)
+    elif param_type == "boolean":
+        input_default_value = BooleanToolParameter(None, default_source)
+    elif param_type == "color":
+        input_default_value = ColorToolParameter(None, default_source)
+    elif param_type == "directory_uri":
+        input_default_value = DirectoryUriToolParameter(None, default_source)
+    return input_default_value
diff --git a/lib/galaxy_test/api/conftest.py b/lib/galaxy_test/api/conftest.py
new file mode 100644
index 0000000000000000000000000000000000000000..74d8958b91585cd2a0ddcde9c0d58f67acf9f6b9
--- /dev/null
+++ b/lib/galaxy_test/api/conftest.py
@@ -0,0 +1,180 @@
+"""Fixtures for a version of API testing that relies more heavily on pytest injection."""
+
+import os
+from dataclasses import dataclass
+from typing import (
+    Any,
+    Iterator,
+    List,
+    Optional,
+)
+
+import pytest
+
+from galaxy.tool_util.verify.test_data import TestDataResolver
+from galaxy_test.base.api import (
+    AnonymousGalaxyInteractor,
+    ApiTestInteractor,
+)
+from galaxy_test.base.api_util import (
+    get_admin_api_key,
+    get_user_api_key,
+)
+from galaxy_test.base.env import setup_keep_outdir
+from galaxy_test.base.populators import (
+    check_missing_tool,
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    DescribeToolInputs,
+    get_tool_ids,
+    RequiredTool,
+    TargetHistory,
+)
+from galaxy_test.base.testcase import host_port_and_url
+
+
+@dataclass
+class ApiConfigObject:
+    host: str
+    port: Optional[str]
+    url: str
+    user_api_key: Optional[str]
+    admin_api_key: Optional[str]
+    test_data_resolver: Any
+    keepOutdir: Any
+
+
+@pytest.fixture(scope="session")
+def api_test_config_object(real_driver) -> ApiConfigObject:
+    host, port, url = host_port_and_url(real_driver)
+    user_api_key = get_user_api_key()
+    admin_api_key = get_admin_api_key()
+    test_data_resolver = TestDataResolver()
+    keepOutdir = setup_keep_outdir()
+    return ApiConfigObject(
+        host,
+        port,
+        url,
+        user_api_key,
+        admin_api_key,
+        test_data_resolver,
+        keepOutdir,
+    )
+
+
+@pytest.fixture(scope="session")
+def galaxy_interactor(api_test_config_object: ApiConfigObject) -> ApiTestInteractor:
+    return ApiTestInteractor(api_test_config_object)
+
+
+@pytest.fixture(scope="session")
+def dataset_populator(galaxy_interactor: ApiTestInteractor) -> DatasetPopulator:
+    return DatasetPopulator(galaxy_interactor)
+
+
+@pytest.fixture(scope="session")
+def dataset_collection_populator(galaxy_interactor: ApiTestInteractor) -> DatasetCollectionPopulator:
+    return DatasetCollectionPopulator(galaxy_interactor)
+
+
+@pytest.fixture(scope="session")
+def anonymous_galaxy_interactor(api_test_config_object: ApiConfigObject) -> AnonymousGalaxyInteractor:
+    return AnonymousGalaxyInteractor(api_test_config_object)
+
+
+@pytest.fixture(autouse=True, scope="session")
+def request_celery_app(celery_session_app, celery_config):
+    try:
+        yield
+    finally:
+        if os.environ.get("GALAXY_TEST_EXTERNAL") is None:
+            from galaxy.celery import celery_app
+
+            celery_app.fork_pool.stop()
+            celery_app.fork_pool.join(timeout=5)
+
+
+@pytest.fixture(autouse=True, scope="session")
+def request_celery_worker(celery_session_worker, celery_config, celery_worker_parameters):
+    yield
+
+
+@pytest.fixture(scope="session", autouse=True)
+def celery_worker_parameters():
+    return {
+        "queues": ("galaxy.internal", "galaxy.external"),
+    }
+
+
+@pytest.fixture(scope="session")
+def celery_parameters():
+    return {
+        "task_create_missing_queues": True,
+        "task_default_queue": "galaxy.internal",
+    }
+
+
+@pytest.fixture
+def history_id(dataset_populator: DatasetPopulator, request) -> Iterator[str]:
+    history_name = f"API Test History for {request.node.nodeid}"
+    with dataset_populator.test_history(name=history_name) as history_id:
+        yield history_id
+
+
+@pytest.fixture
+def target_history(
+    dataset_populator: DatasetPopulator, dataset_collection_populator: DatasetCollectionPopulator, history_id: str
+) -> TargetHistory:
+    return TargetHistory(dataset_populator, dataset_collection_populator, history_id)
+
+
+@pytest.fixture
+def required_tools(
+    dataset_populator: DatasetPopulator, history_id: str, required_tool_ids: List[str]
+) -> List[RequiredTool]:
+    tools = []
+    for tool_id in required_tool_ids:
+        tool = RequiredTool(dataset_populator, tool_id, history_id)
+        tools.append(tool)
+    return tools
+
+
+@pytest.fixture
+def required_tool(dataset_populator: DatasetPopulator, history_id: str, required_tool_ids: List[str]) -> RequiredTool:
+    if len(required_tool_ids) != 1:
+        raise AssertionError("required_tool fixture must only be used on methods that require a single tool")
+    tool_id = required_tool_ids[0]
+    tool = RequiredTool(dataset_populator, tool_id, history_id)
+    return tool
+
+
+@pytest.fixture(params=["legacy", "21.01"])
+def tool_input_format(request) -> Iterator[DescribeToolInputs]:
+    yield DescribeToolInputs(request.param)
+
+
+@pytest.fixture(autouse=True)
+def check_required_tools(anonymous_galaxy_interactor, request):
+    for marker in request.node.iter_markers():
+        if marker.name == "requires_tool_id":
+            tool_id = _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker)
+            check_missing_tool(tool_id not in get_tool_ids(anonymous_galaxy_interactor))
+
+
+@pytest.fixture
+def required_tool_ids(anonymous_galaxy_interactor, request) -> List[str]:
+    tool_ids = []
+    for marker in request.node.iter_markers():
+        if marker.name == "requires_tool_id":
+            tool_id = _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker)
+            tool_ids.append(tool_id)
+    return tool_ids
+
+
+def _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker):
+    tool_id = marker.args[0]
+    if "|" in tool_id:
+        any_of_tool_ids = tool_id.split("|")
+        all_tool_ids = get_tool_ids(anonymous_galaxy_interactor)
+        tool_id = [t for t in any_of_tool_ids if t in all_tool_ids][0]
+    return tool_id
diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py
index c9428ad84ffe5c7fe29b0ab9486db0c7cad2398a..d7710c57b2fa1fa3be61236c76329a334c436c0d 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -1,6 +1,7 @@
 import zipfile
 from io import BytesIO
 from typing import List
+from urllib.parse import quote
 
 from galaxy.util.unittest_utils import skip_if_github_down
 from galaxy_test.base.api_asserts import assert_object_id_error
@@ -189,6 +190,7 @@ class TestDatasetCollectionsApi(ApiTestCase):
             hdca_id = self.dataset_populator.fetch(payload, wait=True).json()["outputs"][0]["id"]
             create_response = self._download_dataset_collection(history_id=history_id, hdca_id=hdca_id)
             self._assert_status_code_is(create_response, 200)
+            assert quote(name, safe="") in create_response.headers["Content-Disposition"]
 
     @requires_new_user
     def test_hda_security(self):
diff --git a/lib/galaxy_test/api/test_datasets.py b/lib/galaxy_test/api/test_datasets.py
index dd9084c8c4f44ecff5c351dd274ed7c0299ad210..1bc79da81695503ee540cfca394033cc11580705 100644
--- a/lib/galaxy_test/api/test_datasets.py
+++ b/lib/galaxy_test/api/test_datasets.py
@@ -6,6 +6,7 @@ from typing import (
     Dict,
     List,
 )
+from urllib.parse import quote
 
 from galaxy.model.unittest_utils.store_fixtures import (
     deferred_hda_model_store_dict,
@@ -18,10 +19,12 @@ from galaxy_test.base.api_asserts import assert_has_keys
 from galaxy_test.base.decorators import (
     requires_admin,
     requires_new_history,
+    requires_new_library,
 )
 from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
     DatasetPopulator,
+    LibraryPopulator,
     skip_without_datatype,
     skip_without_tool,
 )
@@ -46,6 +49,7 @@ class TestDatasetsApi(ApiTestCase):
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.library_populator = LibraryPopulator(self.galaxy_interactor)
         self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
 
     def test_index(self):
@@ -705,6 +709,21 @@ class TestDatasetsApi(ApiTestCase):
         for purged_source_id in expected_purged_source_ids:
             self.dataset_populator.wait_for_purge(history_id, purged_source_id["id"])
 
+    @requires_new_library
+    def test_delete_batch_lddas(self):
+        # Create a library dataset
+        ld = self.library_populator.new_library_dataset("lda_test_library")
+        ldda_id = ld["ldda_id"]
+
+        # Delete the library dataset using the delete_batch endpoint
+        delete_payload = {"datasets": [{"id": ldda_id, "src": "ldda"}]}
+        deleted_result = self._delete_batch_with_payload(delete_payload)
+        assert deleted_result["success_count"] == 1
+
+        # Ensure the library dataset is deleted
+        library_dataset = self.library_populator.show_ldda(ldda_id=ldda_id)
+        assert library_dataset["deleted"] is True
+
     def test_delete_batch_error(self):
         num_datasets = 4
         dataset_map: Dict[int, str] = {}
@@ -840,9 +859,7 @@ class TestDatasetsApi(ApiTestCase):
 
     def test_storage_show(self, history_id):
         hda = self.dataset_populator.new_dataset(history_id, wait=True)
-        hda_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=hda)
-        dataset_id = hda_details["dataset_id"]
-        storage_info_dict = self.dataset_populator.dataset_storage_info(dataset_id)
+        storage_info_dict = self.dataset_populator.dataset_storage_info(hda["id"])
         assert_has_keys(storage_info_dict, "object_store_id", "name", "description")
 
     def test_storage_show_on_discarded(self, history_id):
@@ -897,3 +914,10 @@ class TestDatasetsApi(ApiTestCase):
         response = self._put(f"histories/{history_id}/contents/{hda_id}", data={"datatype": "tabular"}, json=True)
         self._assert_status_code_is(response, 403)
         assert response.json()["err_msg"] == "History is immutable"
+
+    def test_download_non_english_characters(self, history_id):
+        name = "دیتاست"
+        hda = self.dataset_populator.new_dataset(history_id=history_id, name=name, content="data", wait=True)
+        response = self._get(f"histories/{history_id}/contents/{hda['id']}/display?to_ext=json")
+        self._assert_status_code_is(response, 200)
+        assert quote(name, safe="") in response.headers["Content-Disposition"]
diff --git a/lib/galaxy_test/api/test_groups.py b/lib/galaxy_test/api/test_groups.py
index 8e4c5510fe989175546fb6590efcaab42fea1e04..0176bde0d21c523d1320f8d797789c43c55bcdfa 100644
--- a/lib/galaxy_test/api/test_groups.py
+++ b/lib/galaxy_test/api/test_groups.py
@@ -107,7 +107,9 @@ class TestGroupsApi(ApiTestCase):
             another_user_id = self.dataset_populator.user_id()
             another_role_id = self.dataset_populator.user_private_role_id()
         assert another_user_id is not None
-        update_response = self._put(f"groups/{group_id}", data={"user_ids": [another_user_id]}, admin=True, json=True)
+        update_response = self._put(
+            f"groups/{group_id}", data={"user_ids": [user_id, another_user_id]}, admin=True, json=True
+        )
         self._assert_status_code_is_ok(update_response)
 
         # Check if the user was added
@@ -119,7 +121,9 @@ class TestGroupsApi(ApiTestCase):
         )
 
         # Add another role to the group
-        update_response = self._put(f"groups/{group_id}", data={"role_ids": [another_role_id]}, admin=True, json=True)
+        update_response = self._put(
+            f"groups/{group_id}", data={"role_ids": [user_private_role_id, another_role_id]}, admin=True, json=True
+        )
         self._assert_status_code_is_ok(update_response)
 
         # Check if the role was added
diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 6d3ba17d87e0a4d8cda55355898b55594bc5d4ad..42fbe529ef16eead412dbb83b77ab7936390620d 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -544,6 +544,12 @@ class TestHistoriesApi(ApiTestCase, BaseHistories):
             }
             self.dataset_populator.import_history(import_data)
 
+    def test_publish_non_alphanumeric(self):
+        history_name = "تاریخچه"
+        history_id = self.dataset_populator.new_history(name=history_name)
+        response = self.dataset_populator.make_public(history_id)
+        assert history_name in response["username_and_slug"]
+
     def test_immutable_history_update_fails(self):
         history_id = self._create_history("TestHistoryForImmutability")["id"]
 
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index 50ca0d4b74da9c8c4d08017039ce4564d4e38c84..aca989ebb29d59c9ef480b417b5bf36677d12d82 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -464,6 +464,32 @@ steps:
             assert hdca["visible"]
             assert isoparse(hdca["update_time"]) > (isoparse(first_update_time))
 
+    def test_rerun_exception_handling(self):
+        with self.dataset_populator.test_history() as history_id:
+            other_run_response = self.dataset_populator.run_tool(
+                tool_id="job_properties",
+                inputs={},
+                history_id=history_id,
+            )
+            unrelated_job_id = other_run_response["jobs"][0]["id"]
+            run_response = self._run_map_over_error(history_id)
+            job_id = run_response["jobs"][0]["id"]
+            self.dataset_populator.wait_for_job(job_id)
+            failed_hdca = self.dataset_populator.get_history_collection_details(
+                history_id=history_id,
+                content_id=run_response["implicit_collections"][0]["id"],
+                assert_ok=False,
+            )
+            assert failed_hdca["visible"]
+            rerun_params = self._get(f"jobs/{job_id}/build_for_rerun").json()
+            inputs = rerun_params["state_inputs"]
+            inputs["rerun_remap_job_id"] = unrelated_job_id
+            before_rerun_items = self.dataset_populator.get_history_contents(history_id)
+            rerun_response = self._run_detect_errors(history_id=history_id, inputs=inputs)
+            assert "does not match rerun tool id" in rerun_response["err_msg"]
+            after_rerun_items = self.dataset_populator.get_history_contents(history_id)
+            assert len(before_rerun_items) == len(after_rerun_items)
+
     @skip_without_tool("empty_output")
     def test_common_problems(self):
         with self.dataset_populator.test_history() as history_id:
@@ -608,7 +634,7 @@ steps:
         assert response.status_code == 400
         assert (
             response.json()["err_msg"]
-            == "parameter 'collection': the previously selected dataset collection has elements that are deleted."
+            == "Parameter 'collection': the previously selected dataset collection has elements that are deleted."
         )
 
     @pytest.mark.require_new_history
@@ -1050,6 +1076,24 @@ steps:
         self._assert_status_code_is(empty_search_response, 200)
         assert len(empty_search_response.json()) == 0
 
+    @pytest.mark.require_new_history
+    def test_delete_job_with_message(self, history_id):
+        input_dataset_id = self.__history_with_ok_dataset(history_id)
+        inputs = json.dumps({"input1": {"src": "hda", "id": input_dataset_id}})
+        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)
+        # create a job
+        tool_response = self._post("tools", data=search_payload).json()
+        job_id = tool_response["jobs"][0]["id"]
+        output_dataset_id = tool_response["outputs"][0]["id"]
+        # delete the job with message
+        expected_message = "test message"
+        delete_job_response = self._delete(f"jobs/{job_id}", data={"message": expected_message}, json=True)
+        self._assert_status_code_is(delete_job_response, 200)
+        # Check the output dataset is deleted and the info field contains the message
+        dataset_details = self._get(f"histories/{history_id}/contents/{output_dataset_id}").json()
+        assert dataset_details["deleted"] is True
+        assert dataset_details["misc_info"] == expected_message
+
     @pytest.mark.require_new_history
     def test_destination_params(self, history_id):
         dataset_id = self.__history_with_ok_dataset(history_id)
diff --git a/lib/galaxy_test/api/test_landing.py b/lib/galaxy_test/api/test_landing.py
new file mode 100644
index 0000000000000000000000000000000000000000..53182fadae2a7af5910c95150e440ad023454945
--- /dev/null
+++ b/lib/galaxy_test/api/test_landing.py
@@ -0,0 +1,166 @@
+from base64 import b64encode
+from typing import (
+    Any,
+    Dict,
+)
+
+from galaxy.schema.schema import (
+    CreateWorkflowLandingRequestPayload,
+    WorkflowLandingRequest,
+)
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    skip_without_tool,
+    WorkflowPopulator,
+)
+from ._framework import ApiTestCase
+
+
+class TestLandingApi(ApiTestCase):
+    dataset_populator: DatasetPopulator
+    workflow_populator: WorkflowPopulator
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+
+    @skip_without_tool("cat1")
+    def test_create_public_workflow_landing_authenticated_user(self):
+        request = _get_simple_landing_payload(self.workflow_populator, public=True)
+        response = self.dataset_populator.create_workflow_landing(request)
+        assert response.workflow_id == request.workflow_id
+        assert response.workflow_target_type == request.workflow_target_type
+
+        with self._different_user():
+            # Can use without claim
+            _can_use_request(self.dataset_populator, response)
+
+        with self._different_user(anon=True):
+            # Cannot claim since can't run workflows
+            _cannot_use_request(self.dataset_populator, response)
+
+        # Should claim of public landing request be denied ?
+        # Yes, so other user cannot own workflow in between use and invocation submission
+        # No, since there's no way to delete a landing request. If you accidentally make something
+        # with a private reference public you can't delete the landing page request.
+        # TODO: allow deleting landing request, deny claiming public requests ?
+
+        with self._different_user():
+            _can_claim_request(self.dataset_populator, response)
+            _can_use_request(self.dataset_populator, response)
+
+        # Cannot use if other user claimed
+        _cannot_claim_request(self.dataset_populator, response)
+
+    @skip_without_tool("cat1")
+    def test_create_public_workflow_landing_anonymous_user(self):
+        # Anonymous user can create public landing request
+        request = _get_simple_landing_payload(self.workflow_populator, public=True)
+        with self._different_user(anon=True):
+            response = self.dataset_populator.create_workflow_landing(request)
+
+        with self._different_user():
+            # Can use without claim
+            _can_use_request(self.dataset_populator, response)
+
+        with self._different_user(anon=True):
+            # Cannot claim since can't run workflows
+            _cannot_use_request(self.dataset_populator, response)
+
+        with self._different_user():
+            _can_claim_request(self.dataset_populator, response)
+            _can_use_request(self.dataset_populator, response)
+
+        # Cannot use if other user claimed
+        _cannot_claim_request(self.dataset_populator, response)
+
+    @skip_without_tool("cat1")
+    def test_create_private_workflow_landing_authenticated_user(self):
+        request = _get_simple_landing_payload(self.workflow_populator, public=False)
+        response = self.dataset_populator.create_workflow_landing(request)
+        with self._different_user():
+            # Must be claimed first
+            _cannot_use_request(self.dataset_populator, response, expect_status_code=409)
+            _can_claim_request(self.dataset_populator, response)
+            # Can be used after claim by same user
+            _can_use_request(self.dataset_populator, response)
+
+        # other user claimed, so we can't use
+        _cannot_claim_request(self.dataset_populator, response)
+        _cannot_use_request(self.dataset_populator, response)
+
+    @skip_without_tool("cat1")
+    def test_create_private_workflow_landing_anonymous_user(self):
+        request = _get_simple_landing_payload(self.workflow_populator, public=False)
+        with self._different_user(anon=True):
+            response = self.dataset_populator.create_workflow_landing(request)
+        with self._different_user():
+            # Must be claimed first
+            _cannot_use_request(self.dataset_populator, response, expect_status_code=409)
+            _can_claim_request(self.dataset_populator, response)
+            # Can be used after claim by same user
+            _can_use_request(self.dataset_populator, response)
+
+        # other user claimed, so we can't use
+        _cannot_claim_request(self.dataset_populator, response)
+        _cannot_use_request(self.dataset_populator, response)
+
+
+def _workflow_request_state() -> Dict[str, Any]:
+    deferred = False
+    input_b64_1 = b64encode(b"1 2 3").decode("utf-8")
+    input_b64_2 = b64encode(b"4 5 6").decode("utf-8")
+    inputs = {
+        "WorkflowInput1": {"src": "url", "url": f"base64://{input_b64_1}", "ext": "txt", "deferred": deferred},
+        "WorkflowInput2": {"src": "url", "url": f"base64://{input_b64_2}", "ext": "txt", "deferred": deferred},
+    }
+    return inputs
+
+
+def _get_simple_landing_payload(workflow_populator: WorkflowPopulator, public: bool = False):
+    workflow_id = workflow_populator.simple_workflow("test_landing")
+    if public:
+        workflow_populator.make_public(workflow_id)
+    workflow_target_type = "stored_workflow"
+    request_state = _workflow_request_state()
+    return CreateWorkflowLandingRequestPayload(
+        workflow_id=workflow_id,
+        workflow_target_type=workflow_target_type,
+        request_state=request_state,
+        public=public,
+    )
+
+
+def _can_claim_request(dataset_populator: DatasetPopulator, request: WorkflowLandingRequest):
+    response = dataset_populator.claim_workflow_landing(request.uuid)
+    assert response.workflow_id == request.workflow_id
+    assert response.workflow_target_type == request.workflow_target_type
+
+
+def _cannot_claim_request(dataset_populator: DatasetPopulator, request: WorkflowLandingRequest):
+    exception_encountered = False
+    try:
+        _can_claim_request(dataset_populator, request)
+    except Exception as e:
+        assert "Request status code (403)" in str(e)
+        exception_encountered = True
+    assert exception_encountered, "Expected claim to fail"
+
+
+def _can_use_request(dataset_populator: DatasetPopulator, request: WorkflowLandingRequest):
+    response = dataset_populator.use_workflow_landing(request.uuid)
+    assert response.workflow_id == request.workflow_id
+    assert response.workflow_target_type == request.workflow_target_type
+
+
+def _cannot_use_request(
+    dataset_populator: DatasetPopulator, request: WorkflowLandingRequest, expect_status_code: int = 403
+):
+    exception_encountered = False
+    try:
+        _can_use_request(dataset_populator, request)
+    except Exception as e:
+        assert f"Request status code ({expect_status_code})" in str(e)
+        exception_encountered = True
+    assert exception_encountered, "Expected landing page usage to fail"
diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index 440d004db1467b138e4ecb9fa8487eb465b55f85..75f8f4c304521254e50f2119ce73119340a70384 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -313,9 +313,9 @@ class TestLibrariesApi(ApiTestCase):
             "upload_option": "upload_file",
             "files_0|url_paste": FILE_URL,
         }
-        create_response = self._post(f"libraries/{library['id']}/contents", payload)
+        create_response = self._post(f"libraries/{library['id']}/contents", payload, json=True)
         self._assert_status_code_is(create_response, 400)
-        assert create_response.json() == "Requested extension 'xxx' unknown, cannot upload dataset."
+        assert create_response.json()["err_msg"] == "Requested extension 'xxx' unknown, cannot upload dataset."
 
     @skip_if_github_down
     @requires_new_library
@@ -340,7 +340,6 @@ class TestLibrariesApi(ApiTestCase):
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": targets,
-            "validate_hashes": True,
         }
         tool_response = self.dataset_populator.fetch(payload, assert_ok=False)
         job = self.dataset_populator.check_run(tool_response)
@@ -447,10 +446,11 @@ class TestLibrariesApi(ApiTestCase):
             "name": "updated_name",
             "file_ext": "fasta",
             "misc_info": "updated_info",
-            "genome_build": "updated_genome_build",
+            "message": "update message",
         }
         ld_updated = self._patch_library_dataset(ld["id"], data)
-        self._assert_has_keys(ld_updated, "name", "file_ext", "misc_info", "genome_build")
+        for key, value in data.items():
+            assert ld_updated[key] == value
 
     @requires_new_library
     def test_update_dataset_tags(self):
@@ -551,7 +551,7 @@ class TestLibrariesApi(ApiTestCase):
             history_id, contents=["xxx", "yyy"], direct_upload=True, wait=True
         ).json()["outputs"][0]["id"]
         payload = {"from_hdca_id": hdca_id, "create_type": "file", "folder_id": folder_id}
-        create_response = self._post(f"libraries/{library['id']}/contents", payload)
+        create_response = self._post(f"libraries/{library['id']}/contents", payload, json=True)
         self._assert_status_code_is(create_response, 200)
 
     @requires_new_library
@@ -587,7 +587,7 @@ class TestLibrariesApi(ApiTestCase):
             create_type="folder",
             name="New Folder",
         )
-        return self._post(f"libraries/{library['id']}/contents", data=create_data)
+        return self._post(f"libraries/{library['id']}/contents", data=create_data, json=True)
 
     def _create_subfolder(self, containing_folder_id):
         create_data = dict(
@@ -604,6 +604,6 @@ class TestLibrariesApi(ApiTestCase):
         history_id = self.dataset_populator.new_history()
         hda_id = self.dataset_populator.new_dataset(history_id, content=content, wait=wait)["id"]
         payload = {"from_hda_id": hda_id, "create_type": "file", "folder_id": folder_id}
-        ld = self._post(f"libraries/{folder_id}/contents", payload)
+        ld = self._post(f"libraries/{library['id']}/contents", payload, json=True)
         ld.raise_for_status()
         return ld
diff --git a/lib/galaxy_test/api/test_library_contents.py b/lib/galaxy_test/api/test_library_contents.py
new file mode 100644
index 0000000000000000000000000000000000000000..2bc097d82a43c3572f6e6782fe939f8d2db9ea62
--- /dev/null
+++ b/lib/galaxy_test/api/test_library_contents.py
@@ -0,0 +1,228 @@
+from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    LibraryPopulator,
+)
+from ._framework import ApiTestCase
+
+
+class TestLibraryContentsApi(ApiTestCase):
+    dataset_populator: DatasetPopulator
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+        self.library_populator = LibraryPopulator(self.galaxy_interactor)
+
+        self.library = self.library_populator.new_private_library("TestLibrary")
+        self.history = self.dataset_populator.new_history()
+
+    def test_create_folder(self):
+        folder_list = self._create_library_content(type="folder")
+        assert isinstance(folder_list, list), "Expected response to be a list"
+        for folder in folder_list:
+            self._assert_has_keys(folder, "id", "name")
+
+    def test_create_file_from_hda(self):
+        file_item = self._create_library_content(type="from_hda")
+        self._assert_has_keys(file_item, "id", "name")
+
+    def test_create_file_from_hdca(self):
+        files = self._create_library_content(type="from_hdca")
+        assert isinstance(files, list), "Response should be a list of files"
+        for file_item in files:
+            self._assert_has_keys(file_item, "id", "name")
+
+    def test_create_invalid(self):
+        library_id = self.library["id"]
+        folder_id = self.library["root_folder_id"]
+
+        payload = {"folder_id": folder_id, "create_type": "invalid_type"}
+        response = self._post(f"/api/libraries/{library_id}/contents", data=payload, json=True)
+        self._assert_status_code_is(response, 400)
+
+    def test_index(self):
+        library_id = self.library["id"]
+        response = self._get(f"/api/libraries/{library_id}/contents")
+        self._assert_status_code_is(response, 200)
+
+        contents = response.json()
+        assert isinstance(contents, list), "Expected response to be a list"
+
+        for item in contents:
+            self._assert_has_keys(item, "id", "name", "type", "url")
+
+    def test_get_library_contents_invalid_id(self):
+        invalid_library_id = "invalid_id"
+        response = self._get(f"/api/libraries/{invalid_library_id}/contents")
+        self._assert_status_code_is(response, 400)
+
+    def test_get_library_folder(self):
+        library_id = self.library["id"]
+        folder_id = self._create_library_content(type="folder")[0]["id"]
+        response = self._get(f"/api/libraries/{library_id}/contents/{folder_id}")
+        self._assert_status_code_is(response, 200)
+
+        folder_info = response.json()
+        self._assert_has_keys(
+            folder_info,
+            "model_class",
+            "id",
+            "parent_id",
+            "name",
+            "description",
+            "item_count",
+            "genome_build",
+            "update_time",
+            "deleted",
+            "library_path",
+            "parent_library_id",
+        )
+
+    def test_get_library_file_from_hda(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hda")["id"]
+        response = self._get(f"/api/libraries/{library_id}/contents/{file_id}")
+        self._assert_status_code_is(response, 200)
+
+        file_info = response.json()
+        self._assert_has_keys(
+            file_info,
+            "id",
+            "ldda_id",
+            "parent_library_id",
+            "folder_id",
+            "model_class",
+            "state",
+            "name",
+            "file_name",
+            "created_from_basename",
+            "uploaded_by",
+            "message",
+            "date_uploaded",
+            "update_time",
+            "file_size",
+            "file_ext",
+            "data_type",
+            "genome_build",
+            "misc_info",
+            "misc_blurb",
+            "peek",
+            "uuid",
+            "metadata_dbkey",
+            "metadata_data_lines",
+            "tags",
+        )
+
+    def test_get_library_file_from_hdca(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hdca")[0]["id"]
+        response = self._get(f"/api/libraries/{library_id}/contents/{file_id}")
+        self._assert_status_code_is(response, 200)
+
+        file_info = response.json()
+        self._assert_has_keys(
+            file_info,
+            "id",
+            "ldda_id",
+            "parent_library_id",
+            "folder_id",
+            "model_class",
+            "state",
+            "name",
+            "file_name",
+            "created_from_basename",
+            "uploaded_by",
+            "message",
+            "date_uploaded",
+            "update_time",
+            "file_size",
+            "file_ext",
+            "data_type",
+            "genome_build",
+            "misc_info",
+            "misc_blurb",
+            "peek",
+            "uuid",
+            "metadata_dbkey",
+            "metadata_data_lines",
+            "tags",
+        )
+
+    def test_get_invalid_library_item(self):
+        library_id = self.library["id"]
+        invalid_item_id = "invalid_id"
+        response = self._get(f"/api/libraries/{library_id}/contents/{invalid_item_id}")
+        self._assert_status_code_is(response, 400)
+
+    def test_delete_library_item_from_hda(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hda")["id"]
+
+        response = self._delete(f"/api/libraries/{library_id}/contents/{file_id}")
+        self._assert_status_code_is(response, 200)
+
+    def test_delete_library_item_from_hdca(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hdca")[0]["id"]
+
+        response = self._delete(f"/api/libraries/{library_id}/contents/{file_id}")
+        self._assert_status_code_is(response, 200)
+
+    def test_delete_library_item_from_hda_purged(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hda")["id"]
+        payload = {"purged": True}
+        response = self._delete(f"/api/libraries/{library_id}/contents/{file_id}", data=payload, json=True)
+        self._assert_status_code_is(response, 200)
+
+    def test_delete_library_item_from_hdca_purged(self):
+        library_id = self.library["id"]
+        file_id = self._create_library_content(type="from_hdca")[0]["id"]
+        payload = {"purged": True}
+        response = self._delete(f"/api/libraries/{library_id}/contents/{file_id}", data=payload, json=True)
+        self._assert_status_code_is(response, 200)
+
+    def test_delete_invalid_library_item(self):
+        library_id = self.library["id"]
+        invalid_item_id = "invalid_id"
+        response_invalid = self._delete(f"/api/libraries/{library_id}/contents/{invalid_item_id}")
+        self._assert_status_code_is(response_invalid, 400)
+
+    def _create_library_content(self, type):
+        folder_id = self.library["root_folder_id"]
+        library_id = self.library["id"]
+
+        if type == "folder":
+            folder_name = "NewFolder"
+            payload = {
+                "folder_id": folder_id,
+                "create_type": "folder",
+                "name": folder_name,
+                "description": "Test",
+            }
+
+        elif type == "from_hda":
+            dataset_id = self.dataset_populator.new_dataset(self.history)["id"]
+            payload = {
+                "folder_id": folder_id,
+                "create_type": "file",
+                "from_hda_id": dataset_id,
+                "ldda_message": "Test",
+            }
+
+        elif type == "from_hdca":
+            hdca_id = self.dataset_collection_populator.create_list_in_history(
+                self.history, contents=["dataset01", "dataset02"], direct_upload=True, wait=True
+            ).json()["outputs"][0]["id"]
+            payload = {
+                "folder_id": folder_id,
+                "create_type": "file",
+                "from_hdca_id": hdca_id,
+                "ldda_message": "Test",
+            }
+
+        response = self._post(f"/api/libraries/{library_id}/contents", data=payload, json=True)
+        self._assert_status_code_is(response, 200)
+        return response.json()
diff --git a/lib/galaxy_test/api/test_tags.py b/lib/galaxy_test/api/test_tags.py
index f8908968f3b8fce790a3cb757efd538614e2cf40..cdce0a0705af39d5145dfb67557e9d73b72134bb 100644
--- a/lib/galaxy_test/api/test_tags.py
+++ b/lib/galaxy_test/api/test_tags.py
@@ -112,6 +112,13 @@ class TestLibraryDatasetTags(TagsApiTests):
         item = item_response.json()
         return item
 
+    def test_upload_file_contents_with_tags(self):
+        initial_tags = ["name:foobar", "barfoo"]
+        ld = self.library_populator.new_library_dataset(
+            name=f"test-library-dataset-{uuid4()}", tags=json.dumps(initial_tags)
+        )
+        assert ld["tags"] == initial_tags
+
 
 class TestPageTags(TagsApiTests):
     api_name = "pages"
@@ -150,12 +157,10 @@ class TestVisualizationTags(TagsApiTests):
 
         title = f"Test Visualization {uuid_str}"
         slug = f"test-visualization-{uuid_str}"
-        config = json.dumps(
-            {
-                "x": 10,
-                "y": 12,
-            }
-        )
+        config = {
+            "x": 10,
+            "y": 12,
+        }
         create_payload = {
             "title": title,
             "slug": slug,
@@ -164,7 +169,7 @@ class TestVisualizationTags(TagsApiTests):
             "annotation": "this is a test visualization for tags",
             "config": config,
         }
-        response = self._post("visualizations", data=create_payload)
+        response = self._post("visualizations", data=create_payload, json=True)
         self._assert_status_code_is(response, 200)
         viz = response.json()
         return viz["id"]
diff --git a/lib/galaxy_test/api/test_tool_execute.py b/lib/galaxy_test/api/test_tool_execute.py
new file mode 100644
index 0000000000000000000000000000000000000000..95bf43e2792175e987ff1b60f9cc9c64e14ac672
--- /dev/null
+++ b/lib/galaxy_test/api/test_tool_execute.py
@@ -0,0 +1,485 @@
+"""Test tool execution pieces.
+
+Longer term ideally we would separate all the tool tests in test_tools.py that
+describe tool execution into this file and make sure we have parallel or matching
+tests for both the legacy tool execution API and the tool request API. We would then
+keep things like testing other tool APIs in ./test_tools.py (index, search, tool test
+files, etc..).
+"""
+
+from dataclasses import dataclass
+from typing import List
+
+import pytest
+
+from galaxy_test.base.decorators import requires_tool_id
+from galaxy_test.base.populators import (
+    DescribeToolExecution,
+    DescribeToolInputs,
+    RequiredTool,
+    SrcDict,
+    TargetHistory,
+)
+
+
+@requires_tool_id("multi_data_param")
+def test_multidata_param(target_history: TargetHistory, required_tool: RequiredTool):
+    hda1 = target_history.with_dataset("1\t2\t3").src_dict
+    hda2 = target_history.with_dataset("4\t5\t6").src_dict
+    execution = required_tool.execute.with_inputs(
+        {
+            "f1": {"batch": False, "values": [hda1, hda2]},
+            "f2": {"batch": False, "values": [hda2, hda1]},
+        }
+    )
+    execution.assert_has_job(0).with_output("out1").with_contents("1\t2\t3\n4\t5\t6\n")
+    execution.assert_has_job(0).with_output("out2").with_contents("4\t5\t6\n1\t2\t3\n")
+
+
+@requires_tool_id("expression_forty_two")
+def test_galaxy_expression_tool_simplest(required_tool: RequiredTool):
+    required_tool.execute.assert_has_single_job.with_single_output.with_contents("42")
+
+
+@requires_tool_id("expression_parse_int")
+def test_galaxy_expression_tool_simple(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs({"input1": "7"})
+    execution.assert_has_single_job.with_single_output.with_contents("7")
+
+
+@requires_tool_id("expression_log_line_count")
+def test_galaxy_expression_metadata(target_history: TargetHistory, required_tool: RequiredTool):
+    hda1 = target_history.with_dataset("1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14").src_dict
+    execution = required_tool.execute.with_inputs({"input1": hda1})
+    execution.assert_has_single_job.with_single_output.with_contents("3")
+
+
+@requires_tool_id("multi_select")
+def test_multi_select_as_list(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs({"select_ex": ["--ex1", "ex2"]})
+    execution.assert_has_single_job.with_output("output").with_contents("--ex1,ex2")
+
+
+@requires_tool_id("multi_select")
+def test_multi_select_optional(required_tool: RequiredTool):
+    execution = required_tool.execute.with_inputs(
+        {
+            "select_ex": ["--ex1"],
+            "select_optional": None,
+        }
+    )
+    job = execution.assert_has_single_job
+    job.assert_has_output("output").with_contents("--ex1")
+    job.assert_has_output("output2").with_contents_stripped("None")
+
+
+@requires_tool_id("identifier_single")
+def test_identifier_outside_map(target_history: TargetHistory, required_tool: RequiredTool):
+    hda = target_history.with_dataset("123", named="Plain HDA")
+    execute = required_tool.execute.with_inputs({"input1": hda.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("Plain HDA")
+
+
+@requires_tool_id("identifier_multiple")
+def test_identifier_in_multiple_reduce(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_pair()
+    execute = required_tool.execute.with_inputs({"input1": hdca.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("identifier_in_conditional")
+def test_identifier_map_over_multiple_input_in_conditional(
+    target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
+):
+    hdca = target_history.with_pair()
+    inputs = tool_input_format.when.flat(
+        {
+            "outer_cond|input1": hdca.src_dict,
+        }
+    ).when.nested(
+        {
+            "outer_cond": {
+                "multi_input": True,
+                "input1": hdca.src_dict,
+            },
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("identifier_multiple_in_repeat")
+def test_identifier_multiple_reduce_in_repeat(
+    target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
+):
+    hdca = target_history.with_pair()
+    inputs = tool_input_format.when.nested(
+        {
+            "the_repeat": [{"the_data": {"input1": hdca.src_dict}}],
+        }
+    ).when.flat(
+        {
+            "the_repeat_0|the_data|input1": hdca.src_dict,
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("forward\nreverse")
+
+
+@requires_tool_id("output_action_change_format")
+def test_map_over_with_output_format_actions(
+    target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
+):
+    hdca = target_history.with_pair()
+    for use_action in ["do", "dont"]:
+        inputs = tool_input_format.when.flat(
+            {
+                "input_cond|dispatch": use_action,
+                "input_cond|input": {"batch": True, "values": [hdca.src_dict]},
+            }
+        ).when.nested(
+            {
+                "input_cond": {
+                    "dispatch": use_action,
+                    "input": {"batch": True, "values": [hdca.src_dict]},
+                }
+            }
+        )
+        execute = required_tool.execute.with_inputs(inputs)
+        execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+        expected_extension = "txt" if (use_action == "do") else "data"
+        execute.assert_has_job(0).with_single_output.with_file_ext(expected_extension)
+        execute.assert_has_job(1).with_single_output.with_file_ext(expected_extension)
+
+
+@requires_tool_id("output_action_change_format_paired")
+def test_map_over_with_nested_paired_output_format_actions(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_example_list_of_pairs()
+    execute = required_tool.execute.with_inputs(
+        {"input": {"batch": True, "values": [dict(map_over_type="paired", **hdca.src_dict)]}}
+    )
+    execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+    execute.assert_has_job(0).with_single_output.with_file_ext("txt")
+    execute.assert_has_job(1).with_single_output.with_file_ext("txt")
+
+
+@requires_tool_id("identifier_collection")
+def test_identifier_with_data_collection(target_history: TargetHistory, required_tool: RequiredTool):
+    contents = [("foo", "text for foo element"), ("bar", "more text for bar element")]
+    hdca = target_history.with_list(contents)
+    execute = required_tool.execute.with_inputs({"input1": hdca.src_dict})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("foo\nbar")
+
+
+@requires_tool_id("identifier_in_actions")
+def test_identifier_in_actions(target_history: TargetHistory, required_tool: RequiredTool):
+    contents = [("foo", "text for foo element"), ("bar", "more text for bar element")]
+    hdca = target_history.with_list(contents)
+
+    execute = required_tool.execute.with_inputs({"input": {"batch": True, "values": [hdca.src_dict]}})
+
+    output = execute.assert_has_job(0).assert_has_single_output
+    assert output.details["metadata_column_names"][1] == "foo", output.details
+
+    output = execute.assert_has_job(1).assert_has_single_output
+    assert output.details["metadata_column_names"][1] == "bar", output.details
+
+
+@requires_tool_id("identifier_single_in_repeat")
+def test_identifier_single_in_repeat(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_pair()
+    execute = required_tool.execute.with_inputs(
+        {"the_repeat_0|the_data|input1": {"batch": True, "values": [hdca.src_dict]}}
+    )
+    execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+    output_collection = execute.assert_creates_implicit_collection(0)
+    output_collection.assert_has_dataset_element("forward").with_contents_stripped("forward")
+    output_collection.assert_has_dataset_element("reverse").with_contents_stripped("reverse")
+
+
+@requires_tool_id("identifier_multiple_in_conditional")
+def test_identifier_multiple_in_conditional(target_history: TargetHistory, required_tool: RequiredTool):
+    hda = target_history.with_dataset("123", named="Normal HDA1")
+    execute = required_tool.execute.with_inputs(
+        {
+            "outer_cond|inner_cond|input1": hda.src_dict,
+        }
+    )
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("Normal HDA1")
+
+
+@requires_tool_id("identifier_multiple")
+def test_identifier_with_multiple_normal_datasets(target_history: TargetHistory, required_tool: RequiredTool):
+    hda1 = target_history.with_dataset("123", named="Normal HDA1")
+    hda2 = target_history.with_dataset("456", named="Normal HDA2")
+    execute = required_tool.execute.with_inputs({"input1": [hda1.src_dict, hda2.src_dict]})
+    execute.assert_has_single_job.assert_has_single_output.with_contents_stripped("Normal HDA1\nNormal HDA2")
+
+
+@requires_tool_id("cat|cat1")
+def test_map_over_empty_collection(target_history: TargetHistory, required_tool: RequiredTool):
+    hdca = target_history.with_list([])
+    inputs = {
+        "input1": {"batch": True, "values": [hdca.src_dict]},
+    }
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_n_jobs(0)
+    name = execute.assert_creates_implicit_collection(0).details["name"]
+    assert "Concatenate datasets" in name
+    assert "on collection 1" in name
+
+
+@dataclass
+class MultiRunInRepeatFixtures:
+    repeat_datasets: List[SrcDict]
+    common_dataset: SrcDict
+
+
+@pytest.fixture
+def multi_run_in_repeat_datasets(target_history: TargetHistory) -> MultiRunInRepeatFixtures:
+    dataset1 = target_history.with_dataset("123").src_dict
+    dataset2 = target_history.with_dataset("456").src_dict
+    common_dataset = target_history.with_dataset("Common").src_dict
+    return MultiRunInRepeatFixtures([dataset1, dataset2], common_dataset)
+
+
+@requires_tool_id("cat|cat1")
+def test_multi_run_in_repeat(
+    required_tool: RequiredTool,
+    multi_run_in_repeat_datasets: MultiRunInRepeatFixtures,
+    tool_input_format: DescribeToolInputs,
+):
+    inputs = tool_input_format.when.flat(
+        {
+            "input1": {"batch": False, "values": [multi_run_in_repeat_datasets.common_dataset]},
+            "queries_0|input2": {"batch": True, "values": multi_run_in_repeat_datasets.repeat_datasets},
+        }
+    ).when.nested(
+        {
+            "input1": {"batch": False, "values": [multi_run_in_repeat_datasets.common_dataset]},
+            "queries": [
+                {
+                    "input2": {"batch": True, "values": multi_run_in_repeat_datasets.repeat_datasets},
+                }
+            ],
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    _check_multi_run_in_repeat(execute)
+
+
+@requires_tool_id("cat|cat1")
+def test_multi_run_in_repeat_mismatch(
+    required_tool: RequiredTool,
+    multi_run_in_repeat_datasets: MultiRunInRepeatFixtures,
+    tool_input_format: DescribeToolInputs,
+):
+    """Same test as above but without the batch wrapper around the common dataset shared between multirun."""
+    inputs = tool_input_format.when.flat(
+        {
+            "input1": multi_run_in_repeat_datasets.common_dataset,
+            "queries_0|input2": {"batch": True, "values": multi_run_in_repeat_datasets.repeat_datasets},
+        }
+    ).when.nested(
+        {
+            "input1": multi_run_in_repeat_datasets.common_dataset,
+            "queries": [
+                {
+                    "input2": {"batch": True, "values": multi_run_in_repeat_datasets.repeat_datasets},
+                }
+            ],
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    _check_multi_run_in_repeat(execute)
+
+
+def _check_multi_run_in_repeat(execute: DescribeToolExecution):
+    execute.assert_has_n_jobs(2)
+    execute.assert_has_job(0).with_single_output.with_contents_stripped("Common\n123")
+    execute.assert_has_job(1).with_single_output.with_contents_stripped("Common\n456")
+
+
+@dataclass
+class TwoMultiRunsFixture:
+    first_two_datasets: List[SrcDict]
+    second_two_datasets: List[SrcDict]
+
+
+@pytest.fixture
+def two_multi_run_datasets(target_history: TargetHistory) -> TwoMultiRunsFixture:
+    dataset1 = target_history.with_dataset("123").src_dict
+    dataset2 = target_history.with_dataset("456").src_dict
+    dataset3 = target_history.with_dataset("789").src_dict
+    dataset4 = target_history.with_dataset("0ab").src_dict
+    return TwoMultiRunsFixture([dataset1, dataset2], [dataset3, dataset4])
+
+
+@requires_tool_id("cat|cat1")
+def test_multirun_on_multiple_inputs(
+    required_tool: RequiredTool,
+    two_multi_run_datasets: TwoMultiRunsFixture,
+    tool_input_format: DescribeToolInputs,
+):
+    inputs = tool_input_format.when.flat(
+        {
+            "input1": {"batch": True, "values": two_multi_run_datasets.first_two_datasets},
+            "queries_0|input2": {"batch": True, "values": two_multi_run_datasets.second_two_datasets},
+        }
+    ).when.nested(
+        {
+            "input1": {"batch": True, "values": two_multi_run_datasets.first_two_datasets},
+            "queries": [
+                {"input2": {"batch": True, "values": two_multi_run_datasets.second_two_datasets}},
+            ],
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_n_jobs(2)
+    execute.assert_has_job(0).with_single_output.with_contents_stripped("123\n789")
+    execute.assert_has_job(1).with_single_output.with_contents_stripped("456\n0ab")
+
+
+@requires_tool_id("cat|cat1")
+def test_multirun_on_multiple_inputs_unlinked(
+    required_tool: RequiredTool,
+    two_multi_run_datasets: TwoMultiRunsFixture,
+    tool_input_format: DescribeToolInputs,
+):
+    inputs = tool_input_format.when.flat(
+        {
+            "input1": {"batch": True, "linked": False, "values": two_multi_run_datasets.first_two_datasets},
+            "queries_0|input2": {"batch": True, "linked": False, "values": two_multi_run_datasets.second_two_datasets},
+        }
+    ).when.nested(
+        {
+            "input1": {"batch": True, "linked": False, "values": two_multi_run_datasets.first_two_datasets},
+            "queries": [
+                {"input2": {"batch": True, "linked": False, "values": two_multi_run_datasets.second_two_datasets}},
+            ],
+        }
+    )
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_n_jobs(4)
+    execute.assert_has_job(0).with_single_output.with_contents_stripped("123\n789")
+    execute.assert_has_job(1).with_single_output.with_contents_stripped("123\n0ab")
+    execute.assert_has_job(2).with_single_output.with_contents_stripped("456\n789")
+    execute.assert_has_job(3).with_single_output.with_contents_stripped("456\n0ab")
+
+
+@requires_tool_id("cat|cat1")
+def test_map_over_collection(
+    target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
+):
+    hdca = target_history.with_pair(["123", "456"])
+    inputs = tool_input_format.when.any({"input1": {"batch": True, "values": [hdca.src_dict]}})
+    execute = required_tool.execute.with_inputs(inputs)
+    execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
+    output_collection = execute.assert_creates_implicit_collection(0)
+    output_collection.assert_has_dataset_element("forward").with_contents_stripped("123")
+    output_collection.assert_has_dataset_element("reverse").with_contents_stripped("456")
+
+
+@requires_tool_id("gx_repeat_boolean_min")
+def test_optional_repeats_with_mins_filled_id(target_history: TargetHistory, required_tool: RequiredTool):
+    # we have a tool test for this but I wanted to verify it wasn't just the
+    # tool test framework filling in a default. Creating a raw request here
+    # verifies that currently select parameters don't require a selection.
+    required_tool.execute.assert_has_single_job.with_single_output.containing("false").containing("length: 2")
+
+
+@requires_tool_id("gx_select")
+@requires_tool_id("gx_select_no_options_validation")
+def test_select_first_by_default(required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs):
+    empty = tool_input_format.when.any({})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(empty).assert_has_single_job.with_output("output").with_contents_stripped(
+            "--ex1"
+        )
+
+
+@requires_tool_id("gx_select")
+@requires_tool_id("gx_select_no_options_validation")
+@requires_tool_id("gx_select_dynamic_empty")
+@requires_tool_id("gx_select_dynamic_empty_validated")
+def test_select_on_null_errors(required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs):
+    # test_select_first_by_default verifies the first option will just be selected, despite that if an explicit null
+    # is passed, an error (rightfully) occurs. This test verifies that.
+    null_parameter = tool_input_format.when.any({"parameter": None})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(null_parameter).assert_fails.with_error_containing("an invalid option")
+
+
+@requires_tool_id("gx_select_dynamic_empty")
+@requires_tool_id("gx_select_dynamic_empty_validated")
+def test_select_empty_causes_error_regardless(
+    required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs
+):
+    # despite selects otherwise selecting defaults - nothing can be done if the select option list is empty
+    empty = tool_input_format.when.any({})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(empty).assert_fails.with_error_containing("an invalid option")
+
+
+@requires_tool_id("gx_select_optional")
+@requires_tool_id("gx_select_optional_no_options_validation")
+def test_select_optional_null_by_default(required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs):
+    # test_select_first_by_default shows that required select values will pick an option by default,
+    # this test verify that doesn't occur for optional selects.
+    empty = tool_input_format.when.any({})
+    null_parameter = tool_input_format.when.any({"parameter": None})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(empty).assert_has_single_job.with_output("output").with_contents_stripped(
+            "None"
+        )
+        required_tool.execute.with_inputs(null_parameter).assert_has_single_job.with_output(
+            "output"
+        ).with_contents_stripped("None")
+
+
+@requires_tool_id("gx_select_multiple")
+@requires_tool_id("gx_select_multiple_optional")
+def test_select_multiple_does_not_select_first_by_default(
+    required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs
+):
+    # unlike single selects - no selection is forced and these serve as optional by default
+    empty = tool_input_format.when.any({})
+    null_parameter = tool_input_format.when.any({"parameter": None})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(empty).assert_has_single_job.with_output("output").with_contents_stripped(
+            "None"
+        )
+        required_tool.execute.with_inputs(null_parameter).assert_has_single_job.with_output(
+            "output"
+        ).with_contents_stripped("None")
+
+
+@requires_tool_id("gx_text")
+@requires_tool_id("gx_text_optional_false")
+def test_null_to_text_tools(required_tools: List[RequiredTool], tool_input_format: DescribeToolInputs):
+    for required_tool in required_tools:
+        execute = required_tool.execute.with_inputs(tool_input_format.when.any({}))
+        execute.assert_has_single_job.with_output("output").with_contents_stripped("")
+        execute.assert_has_single_job.with_output("inputs_json").with_json({"parameter": ""})
+
+        execute = required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": None}))
+        execute.assert_has_single_job.with_output("output").with_contents_stripped("")
+        execute.assert_has_single_job.with_output("inputs_json").with_json({"parameter": ""})
+
+
+@requires_tool_id("gx_text_optional")
+def test_null_to_optinal_text_tool(required_tool: RequiredTool, tool_input_format: DescribeToolInputs):
+    execute = required_tool.execute.with_inputs(tool_input_format.when.any({}))
+    execute.assert_has_single_job.with_output("output").with_contents_stripped("")
+    execute.assert_has_single_job.with_output("inputs_json").with_json({"parameter": None})
+
+    execute = required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": None}))
+    execute.assert_has_single_job.with_output("output").with_contents_stripped("")
+    execute.assert_has_single_job.with_output("inputs_json").with_json({"parameter": None})
+
+
+@requires_tool_id("gx_text_empty_validation")
+def test_null_to_text_tool_with_validation(required_tool: RequiredTool, tool_input_format: DescribeToolInputs):
+    required_tool.execute.with_inputs(tool_input_format.when.any({})).assert_fails()
+    required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": None})).assert_fails()
+    required_tool.execute.with_inputs(tool_input_format.when.any({"parameter": ""})).assert_fails()
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 78a4b3e05c928264454e0d7963cf1194b990834f..73f368b43345d020c8b3cddcad1c329bc5f445fe 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -8,7 +8,9 @@ from typing import (
     Any,
     Dict,
     List,
+    Optional,
 )
+from uuid import uuid4
 
 import pytest
 from requests import (
@@ -29,7 +31,6 @@ from galaxy_test.base.populators import (
     BaseDatasetCollectionPopulator,
     DatasetCollectionPopulator,
     DatasetPopulator,
-    LibraryPopulator,
     skip_without_tool,
     stage_rules_example,
 )
@@ -72,21 +73,6 @@ class TestsTools:
         hdca_id = create_response.json()["outputs"][0]["id"]
         return hdca_id
 
-    def _run_and_check_simple_collection_mapping(self, history_id, inputs):
-        create = self._run_cat(history_id, inputs=inputs, assert_ok=True)
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 2
-        assert len(outputs) == 2
-        assert len(implicit_collections) == 1
-        output1 = outputs[0]
-        output2 = outputs[1]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
-        assert output1_content.strip() == "123"
-        assert output2_content.strip() == "456"
-
     def _run_cat(self, history_id, inputs, assert_ok=False, **kwargs):
         return self._run("cat", history_id, inputs, assert_ok=assert_ok, **kwargs)
 
@@ -216,6 +202,19 @@ class TestToolsApi(ApiTestCase, TestsTools):
         self._assert_has_keys(case2_inputs[0], "name", "type", "label", "help", "argument")
         assert case2_inputs[0]["name"] == "seed"
 
+    @skip_without_tool("gx_conditional_select")
+    def test_invalid_conditional_payload_handled(self):
+        with self.dataset_populator.test_history() as history_id:
+            # Invalid request, should be `{"conditional_parameter": {"test_parameter": "A"}}`
+            response = self._run(
+                tool_id="gx_conditional_select", history_id=history_id, inputs={"conditional_parameter": "A"}
+            )
+            assert response.status_code == 400
+            assert (
+                response.json()["err_msg"]
+                == "Invalid value 'A' submitted for conditional parameter 'conditional_parameter'."
+            )
+
     @skip_without_tool("multi_data_param")
     def test_show_multi_data(self):
         tool_info = self._show_valid_tool("multi_data_param")
@@ -879,60 +878,102 @@ class TestToolsApi(ApiTestCase, TestsTools):
             output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output, wait=True)
             assert not output_details["visible"]
 
-    @skip_without_tool("multi_select")
-    def test_multi_select_as_list(self):
+    @skip_without_tool("gx_drill_down_exact")
+    @skip_without_tool("gx_drill_down_exact_multiple")
+    @skip_without_tool("gx_drill_down_recurse")
+    @skip_without_tool("gx_drill_down_recurse_multiple")
+    def test_drill_down_first_by_default(self):
+        # we have a tool test for this but I wanted to verify it wasn't just the
+        # tool test framework filling in a default. Creating a raw request here
+        # verifies that currently select parameters don't require a selection.
         with self.dataset_populator.test_history(require_new=False) as history_id:
-            inputs = {
-                "select_ex": ["--ex1", "ex2"],
-            }
-            response = self._run("multi_select", history_id, inputs, assert_ok=True)
+            inputs: Dict[str, Any] = {}
+            response = self._run("gx_drill_down_exact", history_id, inputs, assert_ok=False)
+            self._assert_status_code_is(response, 400)
+            assert "an invalid option" in response.text
+
+            response = self._run("gx_drill_down_exact_multiple", history_id, inputs, assert_ok=False)
+            self._assert_status_code_is(response, 400)
+            assert "an invalid option" in response.text
+
+            response = self._run("gx_drill_down_recurse", history_id, inputs, assert_ok=False)
+            self._assert_status_code_is(response, 400)
+            assert "an invalid option" in response.text
+
+            response = self._run("gx_drill_down_recurse_multiple", history_id, inputs, assert_ok=False)
+            self._assert_status_code_is(response, 400)
+            assert "an invalid option" in response.text
+
+            # having an initially selected value - is useful for the UI but doesn't serve
+            # as a default and doesn't make the drill down optional in a someway.
+            response = self._run("gx_drill_down_exact_with_selection", history_id, inputs, assert_ok=True)
             output = response["outputs"][0]
             output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output1_content.strip() == "parameter: aba"
+
+    def test_data_column_defaults(self):
+        for input_format in ["legacy", "21.01"]:
+            tabular_contents = "1\t2\t3\t\n4\t5\t6\n"
+            with self.dataset_populator.test_history(require_new=True) as history_id:
+                hda = dataset_to_param(
+                    self.dataset_populator.new_dataset(history_id, content=tabular_contents, file_type="tabular")
+                )
+                details = self.dataset_populator.get_history_dataset_details(history_id, dataset=hda, assert_ok=True)
+                inputs = {"ref_parameter": hda}
+                response = self._run(
+                    "gx_data_column", history_id, inputs, assert_ok=False, input_format=input_format
+                ).json()
+                output = response["outputs"]
+                details = self.dataset_populator.get_history_dataset_details(
+                    history_id, dataset=output[0], assert_ok=False
+                )
+                assert details["state"] == "ok"
 
-            assert output1_content == "--ex1,ex2"
-
-    @skip_without_tool("multi_select")
-    def test_multi_select_optional(self):
-        with self.dataset_populator.test_history(require_new=False) as history_id:
-            inputs = {
-                "select_ex": ["--ex1"],
-                "select_optional": None,
-            }
-            response = self._run("multi_select", history_id, inputs, assert_ok=True)
-            output = response["outputs"]
-            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
-            output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[1])
-            assert output1_content.strip() == "--ex1"
-            assert output2_content.strip() == "None", output2_content
-
-    @skip_without_tool("library_data")
-    def test_library_data_param(self):
-        with self.dataset_populator.test_history(require_new=False) as history_id:
-            ld = LibraryPopulator(self.galaxy_interactor).new_library_dataset("lda_test_library")
-            inputs = {"library_dataset": ld["ldda_id"], "library_dataset_multiple": [ld["ldda_id"], ld["ldda_id"]]}
-            response = self._run("library_data", history_id, inputs, assert_ok=True)
-            output = response["outputs"]
-            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
-            assert output_content == "TestData\n", output_content
-            output_multiple_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[1])
-            assert output_multiple_content == "TestData\nTestData\n", output_multiple_content
-
-    @skip_without_tool("multi_data_param")
-    def test_multidata_param(self):
-        with self.dataset_populator.test_history(require_new=False) as history_id:
-            hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="1\t2\t3"))
-            hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content="4\t5\t6"))
-            inputs = {
-                "f1": {"batch": False, "values": [hda1, hda2]},
-                "f2": {"batch": False, "values": [hda2, hda1]},
-            }
-            response = self._run("multi_data_param", history_id, inputs, assert_ok=True)
-            output1 = response["outputs"][0]
-            output2 = response["outputs"][1]
-            output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-            output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
-            assert output1_content == "1\t2\t3\n4\t5\t6\n", output1_content
-            assert output2_content == "4\t5\t6\n1\t2\t3\n", output2_content
+                bed1_contents = open(self.get_filename("1.bed")).read()
+                hda = dataset_to_param(
+                    self.dataset_populator.new_dataset(history_id, content=bed1_contents, file_type="bed")
+                )
+                details = self.dataset_populator.get_history_dataset_details(history_id, dataset=hda, assert_ok=True)
+                inputs = {"ref_parameter": hda}
+                response = self._run(
+                    "gx_data_column", history_id, inputs, assert_ok=False, input_format=input_format
+                ).json()
+                output = response["outputs"]
+                details = self.dataset_populator.get_history_dataset_details(
+                    history_id, dataset=output[0], assert_ok=False
+                )
+                assert details["state"] == "ok"
+
+            with self.dataset_populator.test_history(require_new=False) as history_id:
+                response = self._run("gx_data_column_multiple", history_id, inputs, assert_ok=False).json()
+                assert "err_msg" in response, str(response)
+                assert "Parameter 'parameter': an invalid option" in response["err_msg"]
+
+            with self.dataset_populator.test_history(require_new=True) as history_id:
+                response = self._run("gx_data_column_optional", history_id, inputs, assert_ok=True)
+                output = response["outputs"]
+                content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
+                assert "parameter: None" in content
+
+                response = self._run("gx_data_column_with_default", history_id, inputs, assert_ok=True)
+                output = response["outputs"]
+                content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
+                assert "parameter: 2" in content
+
+                response = self._run("gx_data_column_with_default_legacy", history_id, inputs, assert_ok=True)
+                output = response["outputs"]
+                content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
+                assert "parameter: 3" in content
+
+                response = self._run("gx_data_column_accept_default", history_id, inputs, assert_ok=True)
+                output = response["outputs"]
+                content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
+                assert "parameter: 1" in content
+
+                response = self._run("gx_data_column_multiple_with_default", history_id, inputs, assert_ok=True)
+                output = response["outputs"]
+                content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
+                assert "parameter: 1,2" in content
 
     @skip_without_tool("cat1")
     def test_run_cat1(self):
@@ -948,15 +989,19 @@ class TestToolsApi(ApiTestCase, TestsTools):
             output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
             assert output1_content.strip() == "Cat1Test"
 
+    def _get_cat1_inputs(self, history_id):
+        new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
+        inputs = dict(
+            input1=dataset_to_param(new_dataset),
+        )
+        return inputs
+
     @skip_without_tool("cat1")
     @requires_new_history
     def test_run_cat1_use_cached_job(self):
         with self.dataset_populator.test_history_for(self.test_run_cat1_use_cached_job) as history_id:
             # Run simple non-upload tool with an input data parameter.
-            new_dataset = self.dataset_populator.new_dataset(history_id, content="Cat1Test")
-            inputs = dict(
-                input1=dataset_to_param(new_dataset),
-            )
+            inputs = self._get_cat1_inputs(history_id)
             outputs_one = self._run_cat1(history_id, inputs=inputs, assert_ok=True, wait_for_job=True)
             outputs_two = self._run_cat1(
                 history_id, inputs=inputs, use_cached_job=False, assert_ok=True, wait_for_job=True
@@ -972,6 +1017,31 @@ class TestToolsApi(ApiTestCase, TestsTools):
             assert len(filenames) == 3, filenames
             assert len(set(filenames)) <= 2, filenames
 
+    @skip_without_tool("cat1")
+    @requires_new_history
+    def test_run_cat1_use_cached_job_from_public_history(self):
+        with self.dataset_populator.test_history_for(self.test_run_cat1_use_cached_job) as history_id:
+            # Run simple non-upload tool with an input data parameter.
+            inputs = self._get_cat1_inputs(history_id)
+            original_output = self._run_cat1(history_id, inputs=inputs, assert_ok=True, wait_for_job=True)
+            original_job = self.dataset_populator.get_job_details(original_output["jobs"][0]["id"], full=True).json()
+
+            def run_again(user_email):
+                with self._different_user_and_history(user_email=user_email) as different_history_id:
+                    cached_output = self._run_cat1(
+                        different_history_id, inputs=inputs, use_cached_job=True, assert_ok=True, wait_for_job=True
+                    )
+                    return self.dataset_populator.get_job_details(cached_output["jobs"][0]["id"], full=True).json()
+
+            job = run_again(f"{uuid4()}@test.com")
+            assert job["user_id"] != original_job["user_id"]
+            assert not job["copied_from_job_id"]
+            # publish history, now we can use cached job
+            self.dataset_populator.make_public(history_id=history_id)
+            cached_job = run_again(f"{uuid4()}@test.com")
+            assert cached_job["user_id"] != original_job["user_id"]
+            assert cached_job["copied_from_job_id"] == original_output["jobs"][0]["id"]
+
     @skip_without_tool("cat1")
     def test_run_cat1_listified_param(self):
         with self.dataset_populator.test_history_for(self.test_run_cat1_listified_param) as history_id:
@@ -1462,56 +1532,6 @@ class TestToolsApi(ApiTestCase, TestsTools):
         ]
         assert sorted(len(c.split("\n")) for c in outputs_contents) == [1, 2, 3]
 
-    @skip_without_tool("cat1")
-    def test_multirun_in_repeat(self):
-        history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
-        inputs = {
-            "input1": common_dataset,
-            "queries_0|input2": {"batch": True, "values": repeat_datasets},
-        }
-        self._check_repeat_multirun(history_id, inputs)
-
-    @skip_without_tool("cat1")
-    def test_multirun_in_repeat_mismatch(self):
-        history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
-        inputs = {
-            "input1": {"batch": False, "values": [common_dataset]},
-            "queries_0|input2": {"batch": True, "values": repeat_datasets},
-        }
-        self._check_repeat_multirun(history_id, inputs)
-
-    @skip_without_tool("cat1")
-    def test_multirun_on_multiple_inputs(self):
-        history_id, first_two, second_two = self._setup_two_multiruns()
-        inputs = {
-            "input1": {"batch": True, "values": first_two},
-            "queries_0|input2": {"batch": True, "values": second_two},
-        }
-        outputs = self._cat1_outputs(history_id, inputs=inputs)
-        assert len(outputs) == 2
-        outputs_contents = [
-            self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs
-        ]
-        assert "123\n789" in outputs_contents
-        assert "456\n0ab" in outputs_contents
-
-    @skip_without_tool("cat1")
-    def test_multirun_on_multiple_inputs_unlinked(self):
-        history_id, first_two, second_two = self._setup_two_multiruns()
-        inputs = {
-            "input1": {"batch": True, "linked": False, "values": first_two},
-            "queries_0|input2": {"batch": True, "linked": False, "values": second_two},
-        }
-        outputs = self._cat1_outputs(history_id, inputs=inputs)
-        outputs_contents = [
-            self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs
-        ]
-        assert len(outputs) == 4
-        assert "123\n789" in outputs_contents
-        assert "456\n0ab" in outputs_contents
-        assert "123\n0ab" in outputs_contents
-        assert "456\n789" in outputs_contents
-
     @skip_without_tool("dbkey_output_action")
     def test_dynamic_parameter_error_handling(self):
         # Run test with valid index once, then supply invalid dbkey and invalid table
@@ -1525,7 +1545,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
             return [
                 {
                     "inputs": inputs,
-                    "outputs": {},
+                    "outputs": [],
                     "required_files": required_files,
                     "output_collections": [],
                     "test_index": 0,
@@ -1635,101 +1655,6 @@ class TestToolsApi(ApiTestCase, TestsTools):
             for key, value in props.items():
                 assert details[key] == value
 
-    def _setup_repeat_multirun(self):
-        history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123")
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456")
-        common_dataset = self.dataset_populator.new_dataset(history_id, content="Common")
-        return (
-            history_id,
-            dataset_to_param(common_dataset),
-            [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
-        )
-
-    def _check_repeat_multirun(self, history_id, inputs):
-        outputs = self._cat1_outputs(history_id, inputs=inputs)
-        assert len(outputs) == 2
-        output1 = outputs[0]
-        output2 = outputs[1]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
-        assert output1_content.strip() == "Common\n123"
-        assert output2_content.strip() == "Common\n456"
-
-    def _setup_two_multiruns(self):
-        history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123")
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456")
-        new_dataset3 = self.dataset_populator.new_dataset(history_id, content="789")
-        new_dataset4 = self.dataset_populator.new_dataset(history_id, content="0ab")
-        return (
-            history_id,
-            [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
-            [dataset_to_param(new_dataset3), dataset_to_param(new_dataset4)],
-        )
-
-    @skip_without_tool("cat")
-    def test_map_over_collection(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-        }
-        self._run_and_check_simple_collection_mapping(history_id, inputs)
-
-    @skip_without_tool("cat1")
-    def test_map_over_empty_collection(self, history_id):
-        response = self.dataset_collection_populator.create_list_in_history(history_id, contents=[], wait=True).json()
-        hdca_id = response["output_collections"][0]["id"]
-        inputs = {
-            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-        }
-        create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 0
-        assert len(outputs) == 0
-        assert len(implicit_collections) == 1
-
-        empty_output = implicit_collections[0]
-        assert empty_output["name"] == "Concatenate datasets on collection 1", empty_output
-
-    @skip_without_tool("output_action_change_format")
-    def test_map_over_with_output_format_actions(self, history_id):
-        for use_action in ["do", "dont"]:
-            hdca_id = self._build_pair(history_id, ["123", "456"])
-            inputs = {
-                "input_cond|dispatch": use_action,
-                "input_cond|input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
-            }
-            create = self._run("output_action_change_format", history_id, inputs).json()
-            outputs = create["outputs"]
-            jobs = create["jobs"]
-            implicit_collections = create["implicit_collections"]
-            assert len(jobs) == 2
-            assert len(outputs) == 2
-            assert len(implicit_collections) == 1
-            output1 = outputs[0]
-            output2 = outputs[1]
-            output1_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1)
-            output2_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output2)
-            assert output1_details["file_ext"] == "txt" if (use_action == "do") else "data"
-            assert output2_details["file_ext"] == "txt" if (use_action == "do") else "data"
-
-    @skip_without_tool("output_action_change_format_paired")
-    def test_map_over_with_nested_paired_output_format_actions(self, history_id):
-        hdca_id = self.__build_nested_list(history_id)
-        inputs = {"input": {"batch": True, "values": [dict(map_over_type="paired", src="hdca", id=hdca_id)]}}
-        create = self._run("output_action_change_format_paired", history_id, inputs).json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 2
-        assert len(outputs) == 2
-        assert len(implicit_collections) == 1
-        for output in outputs:
-            assert output["file_ext"] == "txt", output
-
     @skip_without_tool("output_filter_with_input")
     def test_map_over_with_output_filter_no_filtering(self, history_id):
         hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, wait=True).json()["outputs"][0][
@@ -1871,85 +1796,6 @@ class TestToolsApi(ApiTestCase, TestsTools):
         build = self.dataset_populator.build_tool_state("identifier_multiple", history_id)
         assert len(build["inputs"][0]["options"]["hdca"]) == 1
 
-    @skip_without_tool("identifier_multiple")
-    def test_identifier_in_multiple_reduce(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "input1": {"src": "hdca", "id": hdca_id},
-        }
-        create_response = self._run("identifier_multiple", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward\nreverse"
-
-    @skip_without_tool("identifier_in_conditional")
-    def test_identifier_map_over_multiple_input_in_conditional(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "outer_cond|input1": {"src": "hdca", "id": hdca_id},
-        }
-        create_response = self._run("identifier_in_conditional", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward\nreverse"
-
-    @skip_without_tool("identifier_in_conditional")
-    def test_identifier_map_over_multiple_input_in_conditional_new_payload_form(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "outer_cond": {
-                "multi_input": True,
-                "input1": {"id": hdca_id, "src": "hdca"},
-            },
-        }
-        create_response = self._run("identifier_in_conditional", history_id, inputs, input_format="21.01")
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward\nreverse"
-
-    @skip_without_tool("identifier_multiple_in_repeat")
-    def test_identifier_multiple_reduce_in_repeat_new_payload_form(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "the_repeat": [{"the_data": {"input1": {"src": "hdca", "id": hdca_id}}}],
-        }
-        create_response = self._run("identifier_multiple_in_repeat", history_id, inputs, input_format="21.01")
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward\nreverse"
-
     @skip_without_tool("identifier_in_conditional")
     def test_identifier_map_over_input_in_conditional(self, history_id):
         # Run cat tool, so HDA names are different from element identifiers
@@ -1958,21 +1804,14 @@ class TestToolsApi(ApiTestCase, TestsTools):
             "outer_cond|input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
             "outer_cond|multi_input": False,
         }
-        create_response = self._run("identifier_in_conditional", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 2
-        assert len(outputs) == 2
-        assert len(implicit_collections) == 1
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward"
-        output2 = outputs[1]
-        output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
-        assert output2_content.strip() == "reverse"
+        execute = (
+            self.dataset_populator.describe_tool_execution("identifier_in_conditional")
+            .in_history(history_id)
+            .with_inputs(inputs)
+        )
+        collection = execute.assert_has_n_jobs(2).assert_creates_implicit_collection(0)
+        collection.assert_has_dataset_element("forward").with_contents_stripped("forward")
+        collection.assert_has_dataset_element("reverse").with_contents_stripped("reverse")
 
     @skip_without_tool("identifier_multiple_in_conditional")
     def test_identifier_multiple_reduce_in_conditional(self, history_id):
@@ -1993,138 +1832,6 @@ class TestToolsApi(ApiTestCase, TestsTools):
         output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
         assert output1_content.strip() == "forward\nreverse"
 
-    @skip_without_tool("identifier_multiple_in_repeat")
-    def test_identifier_multiple_reduce_in_repeat(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {
-            "the_repeat_0|the_data|input1": {"src": "hdca", "id": hdca_id},
-        }
-        create_response = self._run("identifier_multiple_in_repeat", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "forward\nreverse"
-
-    @skip_without_tool("identifier_single_in_repeat")
-    def test_identifier_single_in_repeat(self, history_id):
-        hdca_id = self._build_pair(history_id, ["123", "456"])
-        inputs = {"the_repeat_0|the_data|input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}}
-        create_response = self._run("identifier_single_in_repeat", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 2
-        assert len(implicit_collections) == 1
-        output_collection = implicit_collections[0]
-        elements = output_collection["elements"]
-        assert len(elements) == 2
-        forward_output = elements[0]["object"]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=forward_output)
-        assert output1_content.strip() == "forward", output1_content
-
-    @skip_without_tool("identifier_multiple_in_conditional")
-    def test_identifier_multiple_in_conditional(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123", name="Normal HDA1")
-        inputs = {
-            "outer_cond|inner_cond|input1": {"src": "hda", "id": new_dataset1["id"]},
-        }
-        create_response = self._run("identifier_multiple_in_conditional", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "Normal HDA1"
-
-    @skip_without_tool("identifier_multiple")
-    def test_identifier_with_multiple_normal_datasets(self, history_id):
-        new_dataset1 = self.dataset_populator.new_dataset(history_id, content="123", name="Normal HDA1")
-        new_dataset2 = self.dataset_populator.new_dataset(history_id, content="456", name="Normal HDA2")
-        inputs = {"input1": [{"src": "hda", "id": new_dataset1["id"]}, {"src": "hda", "id": new_dataset2["id"]}]}
-        create_response = self._run("identifier_multiple", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        implicit_collections = create["implicit_collections"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        assert len(implicit_collections) == 0
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "Normal HDA1\nNormal HDA2"
-
-    @skip_without_tool("identifier_collection")
-    def test_identifier_with_data_collection(self, history_id):
-        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id)
-
-        payload = dict(
-            instance_type="history",
-            history_id=history_id,
-            element_identifiers=element_identifiers,
-            collection_type="list",
-        )
-
-        create_response = self._post("dataset_collections", payload, json=True)
-        dataset_collection = create_response.json()
-
-        inputs = {
-            "input1": {"src": "hdca", "id": dataset_collection["id"]},
-        }
-
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        create_response = self._run("identifier_collection", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        jobs = create["jobs"]
-        assert len(jobs) == 1
-        assert len(outputs) == 1
-        output1 = outputs[0]
-        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
-        assert output1_content.strip() == "\n".join(d["name"] for d in element_identifiers)
-
-    @skip_without_tool("identifier_in_actions")
-    def test_identifier_in_actions(self, history_id):
-        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=["1\t2"])
-
-        payload = dict(
-            instance_type="history",
-            history_id=history_id,
-            element_identifiers=element_identifiers,
-            collection_type="list",
-        )
-
-        create_response = self._post("dataset_collections", payload, json=True)
-        dataset_collection = create_response.json()
-
-        inputs = {
-            "input": {"batch": True, "values": [{"src": "hdca", "id": dataset_collection["id"]}]},
-        }
-
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        create_response = self._run("identifier_in_actions", history_id, inputs)
-        self._assert_status_code_is(create_response, 200)
-        create = create_response.json()
-        outputs = create["outputs"]
-        output1 = outputs[0]
-
-        output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1)
-        assert output_details["metadata_column_names"][1] == "data1", output_details
-
     @skip_without_tool("cat1")
     def test_map_over_nested_collections(self, history_id):
         hdca_id = self.__build_nested_list(history_id)
@@ -2481,6 +2188,54 @@ class TestToolsApi(ApiTestCase, TestsTools):
             )
             assert output_hdca["collection_type"] == "list"
 
+    @skip_without_tool("column_multi_param")
+    def test_multi_param_column_nested_list(self):
+        with self.dataset_populator.test_history() as history_id:
+            hdca = self.dataset_collection_populator.create_list_of_list_in_history(
+                history_id, ext="tabular", wait=True
+            ).json()
+            inputs = {
+                "input1": {"src": "hdca", "id": hdca["id"]},
+                # FIXME: integers don't work here
+                "col": "1",
+            }
+            response = self._run("column_multi_param", history_id, inputs, assert_ok=True)
+            self.dataset_populator.wait_for_job(job_id=response["jobs"][0]["id"], assert_ok=True)
+
+    @skip_without_tool("column_multi_param")
+    def test_multi_param_column_nested_list_fails_on_invalid_column(self):
+        with self.dataset_populator.test_history() as history_id:
+            hdca = self.dataset_collection_populator.create_list_of_list_in_history(
+                history_id, ext="tabular", wait=True
+            ).json()
+            inputs = {
+                "input1": {"src": "hdca", "id": hdca["id"]},
+                "col": "10",
+            }
+            try:
+                self._run("column_multi_param", history_id, inputs, assert_ok=True)
+            except AssertionError as e:
+                exception_raised = e
+            assert exception_raised, "Expected invalid column selection to fail job"
+
+    @skip_without_tool("implicit_conversion_format_input")
+    def test_implicit_conversion_input_dataset_tracking(self):
+        with self.dataset_populator.test_history() as history_id:
+            compressed_path = self.test_data_resolver.get_filename("1.fastqsanger.gz")
+            with open(compressed_path, "rb") as fh:
+                dataset = self.dataset_populator.new_dataset(
+                    history_id, content=fh, file_type="fastqsanger.gz", wait=True
+                )
+            outputs = self._run(
+                "Grep1", history_id=history_id, inputs={"data": {"src": "hda", "id": dataset["id"]}}, assert_ok=True
+            )
+            job_details = self.dataset_populator.get_job_details(outputs["jobs"][0]["id"], full=True).json()
+            assert job_details["inputs"]["input"]["id"] != dataset["id"]
+            converted_input = self.dataset_populator.get_history_dataset_details(
+                history_id=history_id, content_id=job_details["inputs"]["input"]["id"]
+            )
+            assert converted_input["extension"] == "fastqsanger"
+
     @skip_without_tool("column_multi_param")
     def test_implicit_conversion_and_reduce(self):
         with self.dataset_populator.test_history() as history_id:
@@ -2493,7 +2248,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
                 self._run_implicit_collection_and_reduce(history_id=history_id, param="X")
         details = self.dataset_populator.get_history_dataset_details(history_id=history_id, hid=3, assert_ok=False)
         assert details["state"] == "error"
-        assert "parameter 'col': an invalid option" in details["misc_info"]
+        assert "Parameter 'col': an invalid option" in details["misc_info"]
 
     def _run_implicit_collection_and_reduce(self, history_id, param):
         fasta_path = self.test_data_resolver.get_filename("1.fasta")
@@ -2512,6 +2267,8 @@ class TestToolsApi(ApiTestCase, TestsTools):
                 ],
                 wait=True,
             )
+            details = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
+            assert details["extension"] == "fasta"
             self._assert_status_code_is(response, 200)
             hdca_id = response.json()["outputs"][0]["id"]
             inputs = {
@@ -2710,42 +2467,6 @@ class TestToolsApi(ApiTestCase, TestsTools):
         output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
         assert output_content.strip() == "123\n456\n456\n0ab"
 
-    @skip_without_tool("expression_forty_two")
-    def test_galaxy_expression_tool_simplest(self):
-        history_id = self.dataset_populator.new_history()
-        run_response = self._run("expression_forty_two", history_id)
-        self._assert_status_code_is(run_response, 200)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        output_content = self.dataset_populator.get_history_dataset_content(history_id)
-        assert output_content == "42"
-
-    @skip_without_tool("expression_parse_int")
-    def test_galaxy_expression_tool_simple(self):
-        history_id = self.dataset_populator.new_history()
-        inputs = {
-            "input1": "7",
-        }
-        run_response = self._run("expression_parse_int", history_id, inputs)
-        self._assert_status_code_is(run_response, 200)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        output_content = self.dataset_populator.get_history_dataset_content(history_id)
-        assert output_content == "7"
-
-    @skip_without_tool("expression_log_line_count")
-    def test_galaxy_expression_metadata(self):
-        history_id = self.dataset_populator.new_history()
-        new_dataset1 = self.dataset_populator.new_dataset(
-            history_id, content="1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n11\n12\n13\n14"
-        )
-        inputs = {
-            "input1": dataset_to_param(new_dataset1),
-        }
-        run_response = self._run("expression_log_line_count", history_id, inputs)
-        self._assert_status_code_is(run_response, 200)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-        output_content = self.dataset_populator.get_history_dataset_content(history_id)
-        assert output_content == "3"
-
     @skip_without_tool("cat1")
     def test_run_deferred_dataset(self, history_id):
         details = self.dataset_populator.create_deferred_hda(
@@ -2808,6 +2529,71 @@ class TestToolsApi(ApiTestCase, TestsTools):
         job_details = self.dataset_populator.get_job_details(job_id=job_id).json()
         assert job_details["state"] == "failed"
 
+    @skip_without_tool("gx_allow_uri_if_protocol")
+    def test_allow_uri_if_protocol_on_deferred_input(self, history_id):
+        source_uri = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/simple_line.txt"
+        deferred_hda = self.dataset_populator.create_deferred_hda(history_id, source_uri, ext="txt")
+
+        inputs = {"input1": dataset_to_param(deferred_hda)}
+        # The tool just returns the URI (or file path if it was materialized) as the output content
+        run_response = self.dataset_populator.run_tool(
+            tool_id="gx_allow_uri_if_protocol", inputs=inputs, history_id=history_id
+        )
+        output = run_response["outputs"][0]
+        output_details = self.dataset_populator.get_history_dataset_details(
+            history_id, dataset=output, wait=True, assert_ok=True
+        )
+        assert output_details["state"] == "ok"
+        output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+        assert output_content.strip() == source_uri.strip()
+
+    @skip_without_tool("gx_allow_uri_if_protocol")
+    def test_allow_uri_if_protocol_on_collection_with_deferred(self, history_id):
+        source_uris = [
+            "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/simple_line.txt",
+            "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/simple_line_alternative.txt",
+        ]
+        elements = [
+            {
+                "src": "url",
+                "url": source_uri,
+                "deferred": True,
+                "ext": "txt",
+            }
+            for source_uri in source_uris
+        ]
+        targets = [
+            {
+                "destination": {"type": "hdca"},
+                "elements": elements,
+                "collection_type": "list",
+                "name": "deferred list",
+            }
+        ]
+        payload = {
+            "history_id": history_id,
+            "targets": json.dumps(targets),
+        }
+        fetch_response = self.dataset_populator.fetch(payload, wait=True)
+        dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response)
+        hdca_id = dataset_collection["id"]
+        inputs = {
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
+        }
+        run_response = self.dataset_populator.run_tool(
+            tool_id="gx_allow_uri_if_protocol", inputs=inputs, history_id=history_id
+        )
+        hdca_id = run_response["implicit_collections"][0]["id"]
+        dataset_collection = self.dataset_populator.get_history_collection_details(history_id, id=hdca_id)
+        elements = dataset_collection["elements"]
+        assert len(elements) == 2
+        for element in elements:
+            object = element["object"]
+            assert isinstance(object, dict)
+            assert object["state"] == "ok"
+            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=object)
+            assert output_content.strip() in source_uris
+
     @skip_without_tool("cat1")
     def test_run_deferred_mapping(self, history_id: str):
         elements = [
@@ -3061,31 +2847,8 @@ class TestToolsApi(ApiTestCase, TestsTools):
         hdca_list_id = response.json()["outputs"][0]["id"]
         return hdca_list_id
 
-    def __build_nested_list(self, history_id):
-        response = self.dataset_collection_populator.upload_collection(
-            history_id,
-            "list:paired",
-            elements=[
-                {
-                    "name": "test0",
-                    "elements": [
-                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "txt"},
-                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "txt"},
-                    ],
-                },
-                {
-                    "name": "test1",
-                    "elements": [
-                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "txt"},
-                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "txt"},
-                    ],
-                },
-            ],
-            wait=True,
-        )
-        self._assert_status_code_is(response, 200)
-        hdca_list_id = response.json()["outputs"][0]["id"]
-        return hdca_list_id
+    def __build_nested_list(self, history_id: str) -> str:
+        return self.dataset_collection_populator.example_list_of_pairs(history_id)
 
     def _build_pair(self, history_id, contents, run_cat=False):
         create_response = self.dataset_collection_populator.create_pair_in_history(
@@ -3108,8 +2871,8 @@ class TestToolsApi(ApiTestCase, TestsTools):
         # assert "User does not have permission to use a dataset" in err_message, err_message
 
     @contextlib.contextmanager
-    def _different_user_and_history(self):
-        with self._different_user():
+    def _different_user_and_history(self, user_email: Optional[str] = None):
+        with self._different_user(email=user_email):
             with self.dataset_populator.test_history() as other_history_id:
                 yield other_history_id
 
diff --git a/lib/galaxy_test/api/test_tools_upload.py b/lib/galaxy_test/api/test_tools_upload.py
index 64d7e97365b938ba0c5e21824c4b2e2cd755c193..fae8cd087730668b0c6a2a06f4707bebb2034bb9 100644
--- a/lib/galaxy_test/api/test_tools_upload.py
+++ b/lib/galaxy_test/api/test_tools_upload.py
@@ -1,12 +1,17 @@
 import json
 import os
+import tempfile
 import urllib.parse
+from base64 import b64encode
+from typing import cast
 
 import pytest
 from tusclient import client
 
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.util import UNKNOWN
+from galaxy.util.compression_utils import decompress_bytes_to_directory
+from galaxy.util.hash_util import md5_hash_file
 from galaxy.util.unittest_utils import (
     skip_if_github_down,
     skip_if_site_down,
@@ -25,6 +30,17 @@ from galaxy_test.base.populators import (
 )
 from ._framework import ApiTestCase
 
+B64_FOR_1_2_3 = b64encode(b"1 2 3").decode("utf-8")
+URI_FOR_1_2_3 = f"base64://{B64_FOR_1_2_3}"
+
+EXPECTED_TAR_CONTENTS = {
+    "testdir": "Directory",
+    "testdir/c": "Directory",
+    "testdir/a": "File",
+    "testdir/b": "File",
+    "testdir/c/d": "File",
+}
+
 
 class TestToolsUpload(ApiTestCase):
     dataset_populator: DatasetPopulator
@@ -238,6 +254,7 @@ class TestToolsUpload(ApiTestCase):
                 "class": "File",
                 "format": "txt",
                 "path": "test-data/simple_line_no_newline.txt",
+                "hashes": [{"hash_function": "SHA-1", "hash_value": "f030155d3459c233efd37e13bc1061c1dc744ebf"}],
             }
         }
         inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False)
@@ -245,6 +262,8 @@ class TestToolsUpload(ApiTestCase):
         content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
         # By default this appends the newline.
         assert content == "This is a line of text.\n"
+        dataset = self.dataset_populator.get_history_dataset_details(history_id, content_id=dataset["id"])
+        assert dataset["hashes"][0]["hash_value"] == "f030155d3459c233efd37e13bc1061c1dc744ebf"
 
     def test_stage_object(self, history_id: str) -> None:
         job = {"input1": "randomstr"}
@@ -600,18 +619,11 @@ class TestToolsUpload(ApiTestCase):
         assert content.strip() == "Test123"
         extra_files = self.dataset_populator.get_history_dataset_extra_files(history_id, dataset_id=dataset["id"])
         assert len(extra_files) == 5, extra_files
-        expected_contents = {
-            "testdir": "Directory",
-            "testdir/c": "Directory",
-            "testdir/a": "File",
-            "testdir/b": "File",
-            "testdir/c/d": "File",
-        }
         found_files = set()
         for extra_file in extra_files:
             path = extra_file["path"]
-            assert path in expected_contents
-            assert extra_file["class"] == expected_contents[path]
+            assert path in EXPECTED_TAR_CONTENTS
+            assert extra_file["class"] == EXPECTED_TAR_CONTENTS[path]
             found_files.add(path)
 
         assert len(found_files) == 5, found_files
@@ -635,6 +647,75 @@ class TestToolsUpload(ApiTestCase):
             details = self.dataset_populator.get_history_dataset_details(history_id, dataset=dataset, assert_ok=False)
             assert details["state"] == "error"
 
+    def test_upload_tar_roundtrip(self, history_id):
+        testdir = TestDataResolver().get_filename("testdir.tar")
+        expected_size = os.path.getsize(testdir)
+        with open(testdir, "rb") as fh:
+            details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=True)
+        assert details["file_ext"] == "tar"
+        assert details["file_size"] == expected_size
+        content = cast(
+            bytes, self.dataset_populator.get_history_dataset_content(history_id, dataset=details, type="bytes")
+        )
+        # Make sure we got the expected content size.
+        assert len(content) == expected_size
+
+        # Make sure we get the expected contents.
+        dir_path = decompress_bytes_to_directory(content)
+        assert dir_path.endswith("testdir")
+        for path, entry_class in EXPECTED_TAR_CONTENTS.items():
+            path = os.path.join(dir_path, os.path.pardir, path)
+            if entry_class == "Directory":
+                assert os.path.isdir(path)
+            else:
+                assert os.path.isfile(path)
+
+        # Make sure the hash of the content matches the hash of the original file.
+        expected_hash = md5_hash_file(testdir)
+        assert expected_hash is not None
+        self._assert_content_matches_hash(content, expected_hash)
+
+    def _assert_content_matches_hash(self, content: bytes, expected_hash: str):
+        with tempfile.NamedTemporaryFile("wb") as temp:
+            temp.write(content)
+            temp.flush()
+            actual_hash = md5_hash_file(temp.name)
+            assert actual_hash == expected_hash
+
+    def test_upload_zip_roundtrip(self, history_id):
+        testdir = TestDataResolver().get_filename("testdir1.zip")
+        expected_size = os.path.getsize(testdir)
+        with open(testdir, "rb") as fh:
+            details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=True)
+        assert details["file_ext"] == "zip"
+        assert details["file_size"] == expected_size
+        content = cast(
+            bytes, self.dataset_populator.get_history_dataset_content(history_id, dataset=details, type="bytes")
+        )
+        # Make sure we got the expected content size.
+        assert len(content) == expected_size
+
+        # Make sure we get the expected contents.
+        dir_path = decompress_bytes_to_directory(content)
+        assert dir_path.endswith("testdir1")
+        EXPECTED_ZIP_CONTENTS = {
+            "file1": "File",
+            "file2": "File",
+            "dir1/": "Directory",
+            "dir1/file3": "File",
+        }
+        for path, entry_class in EXPECTED_ZIP_CONTENTS.items():
+            path = os.path.join(dir_path, path)
+            if entry_class == "Directory":
+                assert os.path.isdir(path)
+            else:
+                assert os.path.isfile(path)
+
+        # Make sure the hash of the content matches the hash of the original file.
+        expected_hash = md5_hash_file(testdir)
+        assert expected_hash is not None
+        self._assert_content_matches_hash(content, expected_hash)
+
     def test_upload_dbkey(self):
         with self.dataset_populator.test_history() as history_id:
             payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19")
@@ -927,6 +1008,61 @@ class TestToolsUpload(ApiTestCase):
         terminal_validated_state = self.dataset_populator.validate_dataset_and_wait(history_id, dataset_id)
         assert terminal_validated_state == "ok", terminal_validated_state
 
+    def test_upload_and_validate_hash_valid(self):
+        with self.dataset_populator.test_history() as history_id:
+            destination = {"type": "hdas"}
+            targets = [
+                {
+                    "destination": destination,
+                    "items": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [
+                                {"hash_function": "SHA-1", "hash_value": "65e9d53484d28eef5447bc06fe2d754d1090975a"}
+                            ],
+                        },
+                    ],
+                }
+            ]
+            payload = {
+                "history_id": history_id,
+                "targets": targets,
+            }
+            fetch_response = self.dataset_populator.fetch(payload)
+            self._assert_status_code_is(fetch_response, 200)
+            # history ok implies the dataset upload work
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+
+    def test_upload_and_validate_hash_invalid(self):
+        with self.dataset_populator.test_history() as history_id:
+            destination = {"type": "hdas"}
+            targets = [
+                {
+                    "destination": destination,
+                    "items": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [{"hash_function": "SHA-1", "hash_value": "invalidhash"}],
+                        },
+                    ],
+                }
+            ]
+            payload = {
+                "history_id": history_id,
+                "targets": targets,
+            }
+            fetch_response = self.dataset_populator.fetch(payload, assert_ok=True, wait=False)
+            self._assert_status_code_is(fetch_response, 200)
+            outputs = fetch_response.json()["outputs"]
+            new_dataset = outputs[0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=False)
+            dataset_details = self.dataset_populator.get_history_dataset_details(
+                history_id, dataset=new_dataset, assert_ok=False
+            )
+            assert dataset_details["state"] == "error"
+
     def _velvet_upload(self, history_id, extra_inputs):
         payload = self.dataset_populator.upload_payload(
             history_id,
diff --git a/lib/galaxy_test/api/test_users.py b/lib/galaxy_test/api/test_users.py
index 8e081fd2389bc4b503d44996514a91e43cdd73de..21c5c7fca473cde539955f6f51c7d814a481ca5b 100644
--- a/lib/galaxy_test/api/test_users.py
+++ b/lib/galaxy_test/api/test_users.py
@@ -7,6 +7,7 @@ from galaxy_test.base.decorators import (
 )
 from galaxy_test.base.populators import (
     DatasetPopulator,
+    PRIVATE_ROLE_TYPE,
     skip_without_tool,
 )
 
@@ -20,6 +21,7 @@ TEST_USER_EMAIL_SHOW = "user_for_show_test@bx.psu.edu"
 
 
 class TestUsersApi(ApiTestCase):
+
     @requires_admin
     @requires_new_user
     def test_index(self):
@@ -356,3 +358,12 @@ class TestUsersApi(ApiTestCase):
         response = self._get(f"users/{user_id}/beacon")
         user_beacon_settings = response.json()
         assert user_beacon_settings["enabled"]
+
+    @requires_admin
+    @requires_new_user
+    def test_user_roles(self):
+        user = self._setup_user(TEST_USER_EMAIL)
+        response = self._get(f"users/{user['id']}/roles", admin=True)
+        user_roles = response.json()
+        assert len(user_roles) == 1
+        assert user_roles[0]["type"] == PRIVATE_ROLE_TYPE
diff --git a/lib/galaxy_test/api/test_visualizations.py b/lib/galaxy_test/api/test_visualizations.py
index 989fc25f2489df0a80fd640b3d8b61e3590bfabf..0a2577c086ca2669f6ab7c7de5b99f858009f19f 100644
--- a/lib/galaxy_test/api/test_visualizations.py
+++ b/lib/galaxy_test/api/test_visualizations.py
@@ -1,8 +1,5 @@
-import json
 import uuid
 
-from requests import put
-
 from galaxy_test.api.sharable import SharingApiTests
 from galaxy_test.base.api_asserts import assert_has_keys
 from ._framework import ApiTestCase
@@ -89,7 +86,7 @@ class TestVisualizationsApi(ApiTestCase, SharingApiTests):
     def test_update_title(self):
         viz_id, viz = self._create_viz()
         update_url = self._api_url(f"visualizations/{viz_id}", use_key=True)
-        response = put(update_url, {"title": "New Name"})
+        response = self._put(update_url, {"title": "New Name"}, json=True)
         self._assert_status_code_is(response, 200)
         updated_viz = self._show_viz(viz_id)
         assert updated_viz["title"] == "New Name"
@@ -114,12 +111,10 @@ class TestVisualizationsApi(ApiTestCase, SharingApiTests):
         config = (
             config
             if config is not None
-            else json.dumps(
-                {
-                    "x": 10,
-                    "y": 12,
-                }
-            )
+            else {
+                "x": 10,
+                "y": 12,
+            }
         )
         create_payload = {
             "title": title,
@@ -129,7 +124,7 @@ class TestVisualizationsApi(ApiTestCase, SharingApiTests):
             "annotation": "this is a test of the emergency visualization system",
             "config": config,
         }
-        response = self._post("visualizations", data=create_payload)
+        response = self._post("visualizations", data=create_payload, json=True)
         return response
 
     def _publish_viz(self, id):
diff --git a/lib/galaxy_test/api/test_workflow_build_module.py b/lib/galaxy_test/api/test_workflow_build_module.py
new file mode 100644
index 0000000000000000000000000000000000000000..546f6192e3978db0259b4dee818973354d2cd89d
--- /dev/null
+++ b/lib/galaxy_test/api/test_workflow_build_module.py
@@ -0,0 +1,19 @@
+from galaxy_test.base.populators import (
+    skip_without_tool,
+    WorkflowPopulator,
+)
+from ._framework import ApiTestCase
+
+
+class TestBuildWorkflowModule(ApiTestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+
+    @skip_without_tool("select_from_url")
+    def test_build_module_filter_dynamic_select(self):
+        # Verify that filtering on parameters that depend on parameter and validators works
+        # fine in workflow building mode.
+        module = self.workflow_populator.build_module(step_type="tool", content_id="select_from_url")
+        assert not module["errors"], module["errors"]
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index cfb72304893420ff66500f7a340453d7075e54a6..6ceed7dea76a998039003d2eaf77be7116c93450 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -1,4 +1,5 @@
 import base64
+import io
 import json
 import os
 import shutil
@@ -208,8 +209,8 @@ class BaseWorkflowsApiTestCase(ApiTestCase, RunsWorkflowFixtures):
     def _ds_entry(self, history_content):
         return self.dataset_populator.ds_entry(history_content)
 
-    def _invocation_details(self, workflow_id, invocation_id, **kwds):
-        invocation_details_response = self._get(f"workflows/{workflow_id}/usage/{invocation_id}", data=kwds)
+    def _invocation_details(self, workflow_id: Optional[str], invocation_id: str, **kwds):
+        invocation_details_response = self._get(f"invocations/{invocation_id}", data=kwds)
         self._assert_status_code_is(invocation_details_response, 200)
         invocation_details = invocation_details_response.json()
         return invocation_details
@@ -886,6 +887,43 @@ class TestWorkflowsApi(BaseWorkflowsApiTestCase, ChangeDatatypeTests):
         workflow_dict = self.workflow_populator.download_workflow(workflow_id)
         assert workflow_dict["license"] == "AAL"
 
+    def test_update_name_for_workflow_with_subworkflows(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+label: old name
+inputs:
+  dataset: data
+steps:
+  subworkflow:
+    in:
+      dataset: dataset
+    outputs:
+      output:
+        outputSource: cat1/out_file1
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        dataset:
+          type: data
+      steps:
+        cat1:
+          tool_id: cat1
+          in:
+            input1: dataset
+  cat1:
+    tool_id: cat1
+    in:
+      input1: subworkflow/output
+"""
+        )
+        self.workflow_populator.download_workflow(workflow_id)
+        new_name = "my cool new name"
+        data = {"name": new_name}
+        self._update_workflow(workflow_id, data).raise_for_status()
+        post_update_workflow = self.workflow_populator.download_workflow(workflow_id)
+        assert post_update_workflow["name"] == new_name
+
     def test_update_name_empty(self):
         # Update doesn't allow empty names.
 
@@ -1001,6 +1039,43 @@ steps:
         refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=False)
         refactor_response.raise_for_status()
 
+    def test_refactor_subworkflow_tool_state_upgrade(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs: {}
+steps:
+  subworkflow:
+    run:
+      class: GalaxyWorkflow
+      inputs: {}
+      steps:
+        multiple_versions_changes:
+          tool_id: multiple_versions_changes
+          tool_version: "0.2"
+          state:
+            cond:
+              bool_to_select: false
+""",
+            fill_defaults=False,
+        )
+        actions = [{"action_type": "upgrade_all_steps"}]
+        refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=True)
+        assert refactor_response.status_code == 200, refactor_response.text
+        refactor_result = refactor_response.json()
+        upgrade_result = refactor_result["action_executions"][0]
+        assert upgrade_result["action"]["action_type"] == "upgrade_all_steps"
+        message_one, message_two, message_three = upgrade_result["messages"]
+        assert message_one["input_name"] == "inttest"
+        assert message_one["message"] == "No value found for 'inttest'. Using default: '1'."
+        assert message_two["message"] == "No value found for 'floattest'. Using default: '1.0'."
+        assert message_two["input_name"] == "floattest"
+        assert message_three["message"] == "The selected case is unavailable/invalid. Using default: 'b'."
+        assert message_three["input_name"] == "cond|bool_to_select"
+
+        refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=False)
+        refactor_response.raise_for_status()
+
     def test_update_no_tool_id(self):
         workflow_object = self.workflow_populator.load_workflow(name="test_import")
         upload_response = self.__test_upload(workflow=workflow_object)
@@ -1196,7 +1271,7 @@ steps:
             == "#workflow/github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow"
         )
         assert original_workflow.get("source_metadata").get("trs_version_id") == "master"
-        assert original_workflow.get("source_metadata").get("trs_server") == ""
+        assert not original_workflow.get("source_metadata").get("trs_server")
         assert original_workflow.get("source_metadata").get("trs_url") == (
             "https://dockstore.org/api/ga4gh/trs/v2/tools/"
             "%23workflow%2Fgithub.com%2Fjmchilton%2Fgalaxy-workflow-dockstore-example-1%2Fmycoolworkflow/"
@@ -1226,7 +1301,7 @@ steps:
         assert "COVID-19: variation analysis reporting" in original_workflow["name"]
         assert original_workflow.get("source_metadata").get("trs_tool_id") == "109"
         assert original_workflow.get("source_metadata").get("trs_version_id") == "5"
-        assert original_workflow.get("source_metadata").get("trs_server") == ""
+        assert not original_workflow.get("source_metadata").get("trs_server")
         assert (
             original_workflow.get("source_metadata").get("trs_url")
             == "https://workflowhub.eu/ga4gh/trs/v2/tools/109/versions/5"
@@ -1495,41 +1570,144 @@ steps:
     def test_run_workflow(self):
         self.__run_cat_workflow(inputs_by="step_id")
 
-    @skip_without_tool("multiple_versions")
-    def test_run_versioned_tools(self):
-        with self.dataset_populator.test_history() as history_01_id:
-            workflow_version_01 = self._upload_yaml_workflow(
-                """
-class: GalaxyWorkflow
-steps:
-  multiple:
-    tool_id: multiple_versions
-    tool_version: "0.1"
-    state:
-      inttest: 0
-"""
+    @skip_without_tool("cat1")
+    def test_run_workflow_by_deferred_url(self):
+        with self.dataset_populator.test_history() as history_id:
+            self.__run_cat_workflow(inputs_by="deferred_url", history_id=history_id)
+            # it did an upload of the inputs anyway - so this is a 3 is a bit of a hack...
+            # TODO fix this.
+            input_dataset_details = self.dataset_populator.get_history_dataset_details(history_id, hid=3)
+            assert input_dataset_details["state"] == "deferred"
+
+    @skip_without_tool("cat1")
+    def test_run_workflow_by_url(self):
+        with self.dataset_populator.test_history() as history_id:
+            self.__run_cat_workflow(inputs_by="url", history_id=history_id)
+            input_dataset_details = self.dataset_populator.get_history_dataset_details(
+                history_id, hid=3, assert_ok=False
             )
-            self.workflow_populator.invoke_workflow_and_wait(workflow_version_01, history_id=history_01_id)
+            assert input_dataset_details["state"] == "ok"
 
-        with self.dataset_populator.test_history() as history_02_id:
-            workflow_version_02 = self._upload_yaml_workflow(
-                """
-class: GalaxyWorkflow
-steps:
-  multiple:
-    tool_id: multiple_versions
-    tool_version: "0.2"
-    state:
-      inttest: 1
-"""
+    @skip_without_tool("cat1")
+    def test_run_workflow_with_valid_url_hashes(self):
+        with self.dataset_populator.test_history() as history_id:
+            workflow = self.workflow_populator.load_workflow(name="test_for_run_invalid_url_hashes")
+            workflow_id = self.workflow_populator.create_workflow(workflow)
+            input_b64_1 = base64.b64encode(b"1 2 3").decode("utf-8")
+            input_b64_2 = base64.b64encode(b"4 5 6").decode("utf-8")
+            deferred = False
+            hashes_1 = [{"hash_function": "MD5", "hash_value": "5ba48b6e5a7c4d4930fda256f411e55b"}]
+            hashes_2 = [{"hash_function": "MD5", "hash_value": "ad0f811416f7ed2deb9122007d649fb0"}]
+            inputs = {
+                "WorkflowInput1": {
+                    "src": "url",
+                    "url": f"base64://{input_b64_1}",
+                    "ext": "txt",
+                    "deferred": deferred,
+                    "hashes": hashes_1,
+                },
+                "WorkflowInput2": {
+                    "src": "url",
+                    "url": f"base64://{input_b64_2}",
+                    "ext": "txt",
+                    "deferred": deferred,
+                    "hashes": hashes_2,
+                },
+            }
+            workflow_request = dict(
+                history=f"hist_id={history_id}",
+            )
+            workflow_request["inputs"] = json.dumps(inputs)
+            workflow_request["inputs_by"] = "name"
+            invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, request=workflow_request
+            ).json()["id"]
+            invocation = self._invocation_details(workflow_id, invocation_id)
+            assert invocation["state"] == "scheduled", invocation
+            invocation_jobs = self.workflow_populator.get_invocation_jobs(invocation_id)
+            for job in invocation_jobs:
+                assert job["state"] == "ok"
+
+    @skip_without_tool("cat1")
+    def test_run_workflow_with_invalid_url_hashes(self):
+        with self.dataset_populator.test_history() as history_id:
+            workflow = self.workflow_populator.load_workflow(name="test_for_run_invalid_url_hashes")
+            workflow_id = self.workflow_populator.create_workflow(workflow)
+            input_b64_1 = base64.b64encode(b"1 2 3").decode("utf-8")
+            input_b64_2 = base64.b64encode(b"4 5 6").decode("utf-8")
+            deferred = False
+            hashes = [{"hash_function": "MD5", "hash_value": "abadmd5sumhash"}]
+            inputs = {
+                "WorkflowInput1": {
+                    "src": "url",
+                    "url": f"base64://{input_b64_1}",
+                    "ext": "txt",
+                    "deferred": deferred,
+                    "hashes": hashes,
+                },
+                "WorkflowInput2": {
+                    "src": "url",
+                    "url": f"base64://{input_b64_2}",
+                    "ext": "txt",
+                    "deferred": deferred,
+                    "hashes": hashes,
+                },
+            }
+            workflow_request = dict(
+                history=f"hist_id={history_id}",
             )
-            self.workflow_populator.invoke_workflow_and_wait(workflow_version_02, history_id=history_02_id)
+            workflow_request["inputs"] = json.dumps(inputs)
+            workflow_request["inputs_by"] = "name"
+            invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, request=workflow_request, assert_ok=False
+            ).json()["id"]
+            invocation_details = self._invocation_details(workflow_id, invocation_id)
+            assert invocation_details["state"] == "failed"
+            assert len(invocation_details["messages"]) == 1
+            message = invocation_details["messages"][0]
+            assert message["reason"] == "dataset_failed"
 
-    def __run_cat_workflow(self, inputs_by):
+    @skip_without_tool("cat1")
+    def test_run_workflow_with_invalid_url(self):
+        with self.dataset_populator.test_history() as history_id:
+            workflow = self.workflow_populator.load_workflow(name="test_for_run_invalid_url")
+            workflow_id = self.workflow_populator.create_workflow(workflow)
+            deferred = False
+            inputs = {
+                "WorkflowInput1": {
+                    "src": "url",
+                    "url": "gxfiles://thisurl/doesnt/work",
+                    "ext": "txt",
+                    "deferred": deferred,
+                },
+                "WorkflowInput2": {
+                    "src": "url",
+                    "url": "gxfiles://thisurl/doesnt/work",
+                    "ext": "txt",
+                    "deferred": deferred,
+                },
+            }
+            workflow_request = dict(
+                history=f"hist_id={history_id}",
+            )
+            workflow_request["inputs"] = json.dumps(inputs)
+            workflow_request["inputs_by"] = "name"
+            invocation_id = self.workflow_populator.invoke_workflow_and_wait(
+                workflow_id, request=workflow_request, assert_ok=False
+            ).json()["id"]
+            invocation_details = self._invocation_details(workflow_id, invocation_id)
+            assert invocation_details["state"] == "failed"
+            assert len(invocation_details["messages"]) == 1
+            message = invocation_details["messages"][0]
+            assert message["reason"] == "dataset_failed"
+
+    def __run_cat_workflow(self, inputs_by, history_id: Optional[str] = None):
         workflow = self.workflow_populator.load_workflow(name="test_for_run")
         workflow["steps"]["0"]["uuid"] = str(uuid4())
         workflow["steps"]["1"]["uuid"] = str(uuid4())
-        workflow_request, _, workflow_id = self._setup_workflow_run(workflow, inputs_by=inputs_by)
+        workflow_request, _, workflow_id = self._setup_workflow_run(
+            workflow, inputs_by=inputs_by, history_id=history_id
+        )
         invocation_id = self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request).json()[
             "id"
         ]
@@ -2119,6 +2297,38 @@ some_file:
         assert dataset_details["metadata_bam_index"]
         assert dataset_details["file_ext"] == "bam"
 
+    def test_expression_tool_output_in_format_source(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_workflow(
+                """class: GalaxyWorkflow
+inputs:
+  input:
+    type: data
+steps:
+  skip:
+    tool_id: cat_data_and_sleep
+    in:
+      input1: input
+    when: $(false)
+  pick_larger:
+    tool_id: expression_pick_larger_file
+    in:
+      input1: skip/out_file1
+      input2: input
+  format_source:
+    tool_id: cat_data_and_sleep
+    in:
+      input1: pick_larger/larger_file
+test_data:
+  input:
+    value: 1.fastqsanger.gz
+    type: File
+    file_type: fastqsanger.gz
+""",
+                history_id=history_id,
+            )
+            self.dataset_populator.wait_for_history(history_id=history_id, assert_ok=True)
+
     def test_run_workflow_simple_conditional_step(self):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow(
@@ -2454,6 +2664,30 @@ when:
                 if step["workflow_step_label"] == "cat1":
                     assert sum(1 for j in step["jobs"] if j["state"] == "skipped") == 1
 
+    def test_run_workflow_conditional_subworkflow_step_with_hdca_creation(self):
+        # Regression test, ensures scheduling proceeds even if a skipped step creates a collection
+        with self.dataset_populator.test_history() as history_id:
+            self._run_workflow(
+                """
+class: GalaxyWorkflow
+inputs: []
+steps:
+  conditional_subworkflow_step:
+    when: $(false)
+    run:
+      class: GalaxyWorkflow
+      inputs: []
+      steps:
+        create_collection:
+          tool_id: create_input_collection
+        flatten_collection:
+          tool_id: cat_list
+          in:
+            input1: create_collection/output
+                           """,
+                history_id=history_id,
+            )
+
     def test_run_workflow_conditional_step_map_over_expression_tool(self):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow(
@@ -2783,93 +3017,6 @@ outer_input:
             details = self.dataset_populator.get_history_dataset_details(history_id)
             assert details["name"] == "moocow suffix"
 
-    @skip_without_tool("create_2")
-    def test_placements_from_text_inputs(self):
-        with self.dataset_populator.test_history() as history_id:
-            run_def = """
-class: GalaxyWorkflow
-inputs: []
-steps:
-  create_2:
-    tool_id: create_2
-    state:
-      sleep_time: 0
-    outputs:
-      out_file1:
-        rename: "${replaceme} name"
-      out_file2:
-        rename: "${replaceme} name 2"
-test_data:
-  replacement_parameters:
-    replaceme: moocow
-"""
-
-            self._run_jobs(run_def, history_id=history_id)
-            details = self.dataset_populator.get_history_dataset_details(history_id)
-            assert details["name"] == "moocow name 2"
-
-            run_def = """
-class: GalaxyWorkflow
-inputs:
-  replaceme: text
-steps:
-  create_2:
-    tool_id: create_2
-    state:
-      sleep_time: 0
-    outputs:
-      out_file1:
-        rename: "${replaceme} name"
-      out_file2:
-        rename: "${replaceme} name 2"
-test_data:
-  replaceme:
-    value: moocow
-    type: raw
-"""
-            self._run_jobs(run_def, history_id=history_id)
-            details = self.dataset_populator.get_history_dataset_details(history_id)
-            assert details["name"] == "moocow name 2", details["name"]
-
-    def test_placements_from_text_inputs_nested(self):
-        with self.dataset_populator.test_history() as history_id:
-            run_def = """
-class: GalaxyWorkflow
-inputs:
-  replacemeouter: text
-steps:
-  nested_workflow:
-    run:
-      class: GalaxyWorkflow
-      inputs:
-        replacemeinner: text
-      outputs:
-        workflow_output_1:
-          outputSource: create_2/out_file1
-        workflow_output_2:
-          outputSource: create_2/out_file2
-      steps:
-        create_2:
-          tool_id: create_2
-          state:
-            sleep_time: 0
-          outputs:
-            out_file1:
-              rename: "${replacemeinner} name"
-            out_file2:
-              rename: "${replacemeinner} name 2"
-    in:
-      replacemeinner: replacemeouter
-
-test_data:
-  replacemeouter:
-    value: moocow
-    type: raw
-"""
-            self._run_jobs(run_def, history_id=history_id)
-            details = self.dataset_populator.get_history_dataset_details(history_id)
-            assert details["name"] == "moocow name 2", details["name"]
-
     @skip_without_tool("random_lines1")
     def test_run_runtime_parameters_after_pause(self):
         with self.dataset_populator.test_history() as history_id:
@@ -2929,111 +3076,6 @@ test_data:
 
         run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX)
 
-    @skip_without_tool("cat1")
-    @skip_without_tool("collection_paired_test")
-    def test_workflow_run_zip_collections(self):
-        with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
-class: GalaxyWorkflow
-inputs:
-  test_input_1: data
-  test_input_2: data
-steps:
-  first_cat:
-    tool_id: cat1
-    in:
-      input1: test_input_1
-  zip_it:
-    tool_id: "__ZIP_COLLECTION__"
-    in:
-      input_forward: first_cat/out_file1
-      input_reverse: test_input_2
-  concat_pair:
-    tool_id: collection_paired_test
-    in:
-      f1: zip_it/output
-"""
-            )
-            hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
-            hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
-            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-            inputs = {
-                "0": self._ds_entry(hda1),
-                "1": self._ds_entry(hda2),
-            }
-            invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id)
-            self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
-            content = self.dataset_populator.get_history_dataset_content(history_id)
-            assert content.strip() == "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0"
-
-    @skip_without_tool("collection_paired_test")
-    def test_workflow_flatten(self):
-        with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(
-                """
-class: GalaxyWorkflow
-steps:
-  nested:
-    tool_id: collection_creates_dynamic_nested
-    state:
-      sleep_time: 0
-      foo: 'dummy'
-  flatten:
-    tool_id: '__FLATTEN__'
-    state:
-      input:
-        $link: nested/list_output
-      join_identifier: '-'
-""",
-                test_data={},
-                history_id=history_id,
-            )
-            details = self.dataset_populator.get_history_collection_details(history_id, hid=14)
-            assert details["collection_type"] == "list"
-            elements = details["elements"]
-            identifiers = [e["element_identifier"] for e in elements]
-            assert len(identifiers) == 6
-            assert "oe1-ie1" in identifiers
-
-    @skip_without_tool("collection_paired_test")
-    def test_workflow_flatten_with_mapped_over_execution(self):
-        with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(
-                r"""
-class: GalaxyWorkflow
-inputs:
-  input_fastqs: collection
-steps:
-  split_up:
-    tool_id: collection_split_on_column
-    in:
-      input1: input_fastqs
-  flatten:
-    tool_id: '__FLATTEN__'
-    in:
-      input: split_up/split_output
-    join_identifier: '-'
-test_data:
-  input_fastqs:
-    collection_type: list
-    elements:
-      - identifier: samp1
-        content: "0\n1"
-""",
-                history_id=history_id,
-            )
-            history = self._get(f"histories/{history_id}/contents").json()
-            flattened_collection = history[-1]
-            assert flattened_collection["history_content_type"] == "dataset_collection"
-            assert flattened_collection["collection_type"] == "list"
-            assert flattened_collection["element_count"] == 2
-            nested_collection = self.dataset_populator.get_history_collection_details(history_id, hid=3)
-            assert nested_collection["collection_type"] == "list:list"
-            assert nested_collection["element_count"] == 1
-            assert nested_collection["elements"][0]["object"]["populated"]
-            assert nested_collection["elements"][0]["object"]["element_count"] == 2
-
     @skip_without_tool("cat")
     def test_workflow_invocation_report_1(self):
         test_data = """
@@ -3069,6 +3111,18 @@ steps:
             assert "## Workflow Outputs" in markdown_content
             assert "## Workflow Inputs" in markdown_content
             assert "## About This Report" not in markdown_content
+            with self._different_user():
+                exception_raised = False
+                try:
+                    self.workflow_populator.workflow_report_json(workflow_id, invocation_id)
+                except AssertionError as e:
+                    if "Request status code (403)" in str(e):
+                        exception_raised = True
+            assert exception_raised, "Expected workflow report request to fail, but it didn't"
+            self.dataset_populator.make_public(history_id)
+            self.workflow_populator.make_public(workflow_id)
+            with self._different_user():
+                self.workflow_populator.workflow_report_json(workflow_id, invocation_id)
 
     @skip_without_tool("cat")
     def test_workflow_invocation_report_custom(self):
@@ -3227,7 +3281,7 @@ steps:
 """,
                 test_data="""
 num_lines_param:
-  type: int
+  type: raw
   value: 2
 input collection 1:
   collection_type: list
@@ -3466,6 +3520,33 @@ input_c:
             )
             assert output_filtered["element_count"] == 2, output_filtered
 
+    def test_subworkflow_missing_input_connection_error(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow(
+                """
+class: GalaxyWorkflow
+inputs: []
+steps:
+  subworkflow_step:
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        my_input:
+          type: data
+      steps: []
+""",
+                history_id=history_id,
+                assert_ok=False,
+            )
+            workflow_details = self._invocation_details(summary.workflow_id, summary.invocation_id)
+            assert workflow_details["messages"] == [
+                {
+                    "details": "Subworkflow has disconnected required input.",
+                    "reason": "unexpected_failure",
+                    "workflow_step_id": 0,
+                }
+            ]
+
     def test_workflow_request(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_queue")
         workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)
@@ -3475,6 +3556,31 @@ input_c:
         invocation_id = run_workflow_response.json()["id"]
         self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
 
+    def test_workflow_request_recover(self):
+        workflow = self.workflow_populator.load_workflow(name="test_for_queue")
+        workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)
+        run_workflow_response = self.workflow_populator.invoke_workflow_raw(
+            workflow_id, workflow_request, assert_ok=True
+        )
+        invocation_id = run_workflow_response.json()["id"]
+        self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
+        request = self.workflow_populator.invocation_to_request(invocation_id)
+        assert request["history_id"] == history_id
+        assert request["replacement_params"] is None
+        assert request["use_cached_job"] is False
+        assert request["preferred_object_store_id"] is None
+        assert request["preferred_intermediate_object_store_id"] is None
+        assert request["preferred_outputs_object_store_id"] is None
+        assert request["parameters_normalized"] is True
+        assert request["parameters"] is None
+
+        assert request["inputs"]["WorkflowInput1"]["src"] == "hda"
+        encoded_id = request["inputs"]["WorkflowInput1"]["id"]
+        assert self.dataset_populator.get_history_dataset_content(history_id, dataset_id=encoded_id).strip() == "1 2 3"
+        assert request["inputs"]["WorkflowInput2"]["src"] == "hda"
+        encoded_id = request["inputs"]["WorkflowInput2"]["id"]
+        assert self.dataset_populator.get_history_dataset_content(history_id, dataset_id=encoded_id).strip() == "4 5 6"
+
     def test_workflow_new_autocreated_history(self):
         workflow = self.workflow_populator.load_workflow(name="test_for_new_autocreated_history")
         workflow_request, history_id, workflow_id = self._setup_workflow_run(workflow)
@@ -3489,6 +3595,39 @@ input_c:
         invocation_id = run_workflow_dict["id"]
         self.workflow_populator.wait_for_invocation_and_jobs(new_history_id, workflow_id, invocation_id)
 
+    def test_invocation_job_metrics_simple(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id=history_id, workflow_id=summary.workflow_id, invocation_id=summary.invocation_id
+            )
+            job_metrics = self._get(f"invocations/{summary.invocation_id}/metrics").json()
+            galaxy_slots = [m for m in job_metrics if m["name"] == "galaxy_slots"]
+            assert len(galaxy_slots) == 1
+
+    def test_invocation_job_metrics_map_over(self):
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow(
+                WORKFLOW_SIMPLE,
+                test_data={
+                    "input1": {
+                        "collection_type": "list",
+                        "name": "the_dataset_list",
+                        "elements": [
+                            {"identifier": "el1", "value": "1.fastq", "type": "File"},
+                            {"identifier": "el2", "value": "1.fastq", "type": "File"},
+                        ],
+                    }
+                },
+                history_id=history_id,
+            )
+            self.workflow_populator.wait_for_invocation_and_jobs(
+                history_id=history_id, workflow_id=summary.workflow_id, invocation_id=summary.invocation_id
+            )
+            job_metrics = self._get(f"invocations/{summary.invocation_id}/metrics").json()
+            galaxy_slots = [m for m in job_metrics if m["name"] == "galaxy_slots"]
+            assert len(galaxy_slots) == 2
+
     def test_workflow_output_dataset(self):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow(WORKFLOW_SIMPLE, test_data={"input1": "hello world"}, history_id=history_id)
@@ -4913,7 +5052,7 @@ test_data:
 
     def test_run_with_optional_collection_specified(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(
+            result = self._run_workflow(
                 WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION,
                 test_data="""
 input1:
@@ -4934,6 +5073,12 @@ input1:
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert "GAATTGATCAGGACATAGGACAACTGTAGGCACCAT" in content
 
+            invocation_id = result.invocation_id
+            request = self.workflow_populator.invocation_to_request(invocation_id)
+            assert request["history_id"] == history_id
+            assert request["inputs"]["input1"]["src"] == "hdca"
+            assert request["inputs"]["input1"]["id"]
+
     def test_run_with_optional_collection_unspecified(self):
         with self.dataset_populator.test_history() as history_id:
             self._run_jobs(
@@ -5023,9 +5168,14 @@ int_input:
             # self.dataset_populator.wait_for_history(history_id, assert_ok=True)
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert len(content.splitlines()) == 1, content
-            invocation = self.workflow_populator.get_invocation(run_response.invocation_id)
+            invocation_id = run_response.invocation_id
+            invocation = self.workflow_populator.get_invocation(invocation_id)
             assert invocation["input_step_parameters"]["int_input"]["parameter_value"] == 1
 
+            request = self.workflow_populator.invocation_to_request(invocation_id)
+            assert request["history_id"] == history_id
+            assert request["inputs"]["int_input"] == 1
+
             run_response = self._run_workflow(
                 WORKFLOW_PARAMETER_INPUT_INTEGER_OPTIONAL,
                 test_data="""
@@ -5298,56 +5448,6 @@ test_data: {}
         assert int(str_43) == 43
         assert abs(float(str_4point14) - 4.14) < 0.0001
 
-    @skip_without_tool("param_value_from_file")
-    def test_expression_tool_map_over(self, history_id):
-        self._run_jobs(
-            """
-class: GalaxyWorkflow
-inputs:
-  text_input1: collection
-steps:
-- label: param_out
-  tool_id: param_value_from_file
-  in:
-     input1: text_input1
-- label: consume_expression_parameter
-  tool_id: validation_default
-  in:
-    input1: param_out/text_param
-  outputs:
-    out_file1:
-      rename: "replaced_param_collection"
-test_data:
-  text_input1:
-    collection_type: list
-    elements:
-      - identifier: A
-        content: A
-      - identifier: B
-        content: B
-""",
-            history_id=history_id,
-        )
-        history_contents = self._get(f"histories/{history_id}/contents").json()
-        collection = [
-            c
-            for c in history_contents
-            if c["history_content_type"] == "dataset_collection" and c["name"] == "replaced_param_collection"
-        ][0]
-        collection_details = self._get(collection["url"]).json()
-        assert collection_details["element_count"] == 2
-        elements = collection_details["elements"]
-        assert elements[0]["element_identifier"] == "A"
-        assert elements[1]["element_identifier"] == "B"
-        element_a_content = self.dataset_populator.get_history_dataset_content(
-            history_id, dataset=elements[0]["object"]
-        )
-        element_b_content = self.dataset_populator.get_history_dataset_content(
-            history_id, dataset=elements[1]["object"]
-        )
-        assert element_a_content.strip() == "A"
-        assert element_b_content.strip() == "B"
-
     @skip_without_tool("create_input_collection")
     def test_workflow_optional_input_text_parameter_reevaluation(self):
         with self.dataset_populator.test_history() as history_id:
@@ -5424,6 +5524,10 @@ steps:
                 workflow_id, new_workflow_request, assert_ok=True
             ).json()
             invocation_id = new_workflow_response["id"]
+
+            request = self.workflow_populator.invocation_to_request(invocation_id)
+            assert request["use_cached_job"] is True
+
             self.workflow_populator.wait_for_invocation_and_jobs(history_id_two, workflow_id, invocation_id)
 
             # get_history_dataset_details defaults to last item in history, so since we've done
@@ -5623,6 +5727,9 @@ outer_input:
         content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
         assert content["name"] == "foo was replaced"
 
+        request = self.workflow_populator.invocation_to_request(invocation_id)
+        assert request["replacement_params"]["replaceme"] == "was replaced"
+
     @skip_without_tool("hidden_param")
     def test_hidden_param_in_workflow(self):
         with self.dataset_populator.test_history() as history_id:
@@ -6261,52 +6368,6 @@ fastq_input:
             name = content["name"]
             assert name == "fastq1 suffix", name
 
-    @skip_without_tool("mapper2")
-    def test_run_rename_based_on_input_collection(self):
-        with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(
-                """
-class: GalaxyWorkflow
-inputs:
-  fasta_input: data
-  fastq_inputs: data
-steps:
-  mapping:
-    tool_id: mapper2
-    state:
-      fastq_input:
-        fastq_input_selector: paired_collection
-        fastq_input1:
-          $link: fastq_inputs
-      reference:
-        $link: fasta_input
-    outputs:
-      out_file1:
-        rename: "#{fastq_input.fastq_input1 | basename} suffix"
-""",
-                test_data="""
-fasta_input:
-  value: 1.fasta
-  type: File
-  name: fasta1
-  file_type: fasta
-fastq_inputs:
-  collection_type: list
-  name: the_dataset_pair
-  elements:
-    - identifier: forward
-      value: 1.fastq
-      type: File
-    - identifier: reverse
-      value: 1.fastq
-      type: File
-""",
-                history_id=history_id,
-            )
-            content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
-            name = content["name"]
-            assert name == "the_dataset_pair suffix", name
-
     @skip_without_tool("collection_creates_pair")
     def test_run_hide_on_collection_output(self):
         with self.dataset_populator.test_history() as history_id:
@@ -6780,6 +6841,27 @@ steps:
             hda2 = self.dataset_populator.get_history_dataset_details(history_id, hid=2)
             assert hda2["validated_state"] == "invalid"
 
+    @skip_without_tool("dbkey_filter_input")
+    def test_value_restriction_with_data_meta_filter(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  select_text:
+     type: text
+     restrictOnConnections: true
+steps:
+  select:
+    tool_id: dbkey_filter_input
+    in:
+      index: select_text
+"""
+        )
+        with self.dataset_populator.test_history() as history_id:
+            run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
+        options = run_workflow["steps"][0]["inputs"][0]["options"]
+        assert len(options) >= 1
+
     def test_value_restriction_with_select_and_text_param(self):
         workflow_id = self.workflow_populator.upload_yaml_workflow(
             """
@@ -7069,12 +7151,14 @@ inputs:
   outer_input_1:
     type: int
     default: 1
+    optional: true
     position:
       left: 0
       top: 0
   outer_input_2:
     type: int
     default: 2
+    optional: true
     position:
       left: 100
       top: 0
@@ -7171,7 +7255,7 @@ outputs:
     @skip_without_tool("random_lines1")
     def test_run_replace_params_over_default(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs(
+            wf_run = self._run_workflow(
                 WORKFLOW_ONE_STEP_DEFAULT,
                 test_data="""
 step_parameters:
@@ -7189,6 +7273,13 @@ input:
             result = self.dataset_populator.get_history_dataset_content(history_id)
             assert result.count("\n") == 4
 
+            request = self.workflow_populator.invocation_to_request(wf_run.invocation_id)
+            assert request["parameters"]["1"]["num_lines"] == 4
+
+            self.workflow_populator.rerun(wf_run)
+            result = self.dataset_populator.get_history_dataset_content(history_id)
+            assert result.count("\n") == 4
+
     @skip_without_tool("random_lines1")
     def test_defaults_editor(self):
         workflow_id = self._upload_yaml_workflow(WORKFLOW_ONE_STEP_DEFAULT, publish=True)
@@ -7196,44 +7287,6 @@ input:
         put_response = self._update_workflow(workflow_id, workflow_object)
         assert put_response.status_code == 200
 
-    def test_empty_collection_sort(self, history_id):
-        self._run_workflow(
-            """class: GalaxyWorkflow
-inputs:
-  input: collection
-  filter_file: data
-steps:
-  filter_collection:
-    tool_id: __FILTER_FROM_FILE__
-    in:
-       input: input
-       how|filter_source: filter_file
-  sort_collection_1:
-    tool_id: __SORTLIST__
-    in:
-      input: filter_collection/output_filtered
-  sort_collection_2:
-    tool_id: __SORTLIST__
-    in:
-      input: filter_collection/output_discarded
-  merge_collection:
-    tool_id: __MERGE_COLLECTION__
-    in:
-      inputs_0|input: sort_collection_1/output
-      inputs_1|input: sort_collection_2/output
-test_data:
-  input:
-    collection_type: list
-    elements:
-      - identifier: i1
-        content: "0"
-  filter_file: i1
-""",
-            history_id=history_id,
-            wait=True,
-            assert_ok=True,
-        )
-
     @skip_without_tool("random_lines1")
     def test_run_replace_params_over_default_delayed(self):
         with self.dataset_populator.test_history() as history_id:
@@ -7450,6 +7503,84 @@ steps: []
 
         assert invocation_steps[1]["state"] == "ok"
 
+    def test_data_input_recovery_on_delayed_input(self):
+        self.workflow_populator.run_workflow(
+            """
+class: GalaxyWorkflow
+inputs: {}
+outputs:
+  the_output:
+    outputSource: child/output
+steps:
+  running_output:
+    tool_id: job_properties
+    tool_state:
+      failbool: false
+      sleepsecs: 3
+      thebool: false
+  child:
+    in:
+      input_dataset:
+        source: running_output/out_file1
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        input_dataset: data
+        run_step:
+          default: false
+          optional: true
+          type: boolean
+      outputs:
+        output:
+          outputSource: conditional_cat/out_file1
+      steps:
+        conditional_cat:
+          tool_id: cat
+          when: $(inputs.when)
+          in:
+            input1: input_dataset
+            when:
+              source: run_step"""
+        )
+
+    def test_subworkflow_output_not_found_fails(self):
+        # This test might start failing if we ever validate connections before attempting to schedule
+        summary = self.workflow_populator.run_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  input: data
+outputs:
+  the_output:
+    outputSource: child/output
+steps:
+  child:
+    in:
+      input_dataset:
+        source: input
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        input_dataset: data
+      outputs:
+        output:
+          outputSource: cat/out_file_that_doesnt_exist
+      steps:
+        cat:
+          tool_id: cat
+          in:
+            input1: input_dataset
+test_data:
+  input:
+    value: 1.fasta
+    type: File
+            """,
+            assert_ok=False,
+        )
+        invocation = self.workflow_populator.get_invocation(summary.invocation_id)
+        assert invocation["state"] == "failed"
+        assert invocation["messages"][0]["reason"] == "output_not_found"
+
     def _run_mapping_workflow(self):
         history_id = self.dataset_populator.new_history()
         summary = self._run_workflow(
@@ -7752,6 +7883,11 @@ outer_input:
         subworkflow = downloaded_workflow["steps"]["1"]["subworkflow"]
         assert subworkflow["tags"] == []
 
+    def test_upload_malformated_yaml(self):
+        malformated_yaml = "class: GalaxyWorkflow:\n    a-1:()"
+        r = self._post("workflows", files={"archive_file": io.StringIO(malformated_yaml)})
+        assert r.status_code == 400
+
 
 class TestAdminWorkflowsApi(BaseWorkflowsApiTestCase):
     require_admin_user = True
diff --git a/lib/galaxy_test/base/api.py b/lib/galaxy_test/base/api.py
index 63e33dd5e90a47c08480f3bb766bb337d000367d..b1881f917b63196548b5cc5a6c4f30f6f2d22aea 100644
--- a/lib/galaxy_test/base/api.py
+++ b/lib/galaxy_test/base/api.py
@@ -147,7 +147,7 @@ class UsesApiTestCaseMixin:
         return user, self._post(f"users/{user['id']}/api_key", admin=True).json()
 
     @contextmanager
-    def _different_user(self, email=OTHER_USER, anon=False):
+    def _different_user(self, email: Optional[str] = None, anon=False):
         """Use in test cases to switch get/post operations to act as new user
 
         ..code-block:: python
@@ -164,6 +164,7 @@ class UsesApiTestCaseMixin:
             self.galaxy_interactor.cookies = cookies
             new_key = None
         else:
+            email = OTHER_USER if email is None else email
             _, new_key = self._setup_user_get_key(email)
         try:
             self.user_api_key = new_key
diff --git a/lib/galaxy_test/base/api_asserts.py b/lib/galaxy_test/base/api_asserts.py
index 8e5796791e986ed724468b172afa9c33b5765aa3..fd423ee2735bff9ab1f47d3e133cc02e9a5c8aa0 100644
--- a/lib/galaxy_test/base/api_asserts.py
+++ b/lib/galaxy_test/base/api_asserts.py
@@ -24,8 +24,8 @@ def assert_status_code_is(response: Response, expected_status_code: int, failure
 def assert_status_code_is_ok(response: Response, failure_message: Optional[str] = None):
     """Assert that the supplied response is okay.
 
-    The easier alternative ``response.raise_for_status()`` might be
-    preferable generally.
+    This is an alternative to ``response.raise_for_status()`` with a more detailed
+    error message.
 
     .. seealso:: :py:meth:`requests.Response.raise_for_status()`
     """
@@ -35,6 +35,17 @@ def assert_status_code_is_ok(response: Response, failure_message: Optional[str]
         _report_status_code_error(response, "2XX", failure_message)
 
 
+def assert_status_code_is_not_ok(response: Response, failure_message: Optional[str] = None):
+    """Assert that the supplied response is not okay.
+
+    .. seealso:: :py:meth:`assert_status_code_is_ok`
+    """
+    response_status_code = response.status_code
+    is_two_hundred_status_code = response_status_code >= 200 and response_status_code <= 300
+    if is_two_hundred_status_code:
+        _report_status_code_error(response, "2XX", failure_message)
+
+
 def _report_status_code_error(
     response: Response, expected_status_code: Union[str, int], failure_message: Optional[str]
 ):
diff --git a/lib/galaxy_test/base/decorators.py b/lib/galaxy_test/base/decorators.py
index 324d6e9ea884e4fbaffcec0143f3319cc8e7e1c7..95ea1a18ab28cfd90831307d3ac1bb8876064051 100644
--- a/lib/galaxy_test/base/decorators.py
+++ b/lib/galaxy_test/base/decorators.py
@@ -67,6 +67,14 @@ def _wrap_method_with_galaxy_requirement(method, tag: KnownRequirementT):
     return wrapped_method
 
 
+def requires_tool_id(tool_id: str):
+
+    def method_wrapper(method):
+        return pytest.mark.requires_tool_id(tool_id)(method)
+
+    return method_wrapper
+
+
 def requires_new_history(method):
     return _wrap_method_with_galaxy_requirement(method, "new_history")
 
diff --git a/lib/galaxy_test/base/env.py b/lib/galaxy_test/base/env.py
index 0caee6da17f3c89bcb3b04aa45c5f24976e39117..8ad3894457016b403b23e98a35283d572580b578 100644
--- a/lib/galaxy_test/base/env.py
+++ b/lib/galaxy_test/base/env.py
@@ -10,7 +10,12 @@ from typing import (
     Tuple,
 )
 
+from galaxy.util import asbool
+
 DEFAULT_WEB_HOST = socket.gethostbyname("localhost")
+REQUIRE_ALL_NEEDED_TOOLS = asbool(os.environ.get("GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS", "0"))
+
+GalaxyTarget = Tuple[str, Optional[str], str]
 
 
 def setup_keep_outdir() -> str:
@@ -23,7 +28,7 @@ def setup_keep_outdir() -> str:
     return keep_outdir
 
 
-def target_url_parts() -> Tuple[str, Optional[str], str]:
+def target_url_parts() -> GalaxyTarget:
     host = socket.gethostbyname(os.environ.get("GALAXY_TEST_HOST", DEFAULT_WEB_HOST))
     port = os.environ.get("GALAXY_TEST_PORT")
     if port:
diff --git a/lib/galaxy_test/base/interactor.py b/lib/galaxy_test/base/interactor.py
index 45c055ce817b3d4682e0b1d9c9420ac091f05204..4dabb5963b07fabab779615c6ad5a0c71f28a177 100644
--- a/lib/galaxy_test/base/interactor.py
+++ b/lib/galaxy_test/base/interactor.py
@@ -4,9 +4,12 @@ from galaxy.tool_util.verify.interactor import GalaxyInteractorApi
 class TestCaseGalaxyInteractor(GalaxyInteractorApi):
     def __init__(self, functional_test_case, test_user=None, api_key=None):
         self.functional_test_case = functional_test_case
+        admin_api_key = getattr(functional_test_case, "master_api_key", None) or getattr(
+            functional_test_case, "admin_api_key", None
+        )
         super().__init__(
             galaxy_url=functional_test_case.url,
-            master_api_key=getattr(functional_test_case, "master_api_key", None),
+            master_api_key=admin_api_key,
             api_key=api_key or getattr(functional_test_case, "user_api_key", None),
             test_user=test_user,
             keep_outputs_dir=getattr(functional_test_case, "keepOutdir", None),
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index d373b23d389d31b9b48bbf42e79544359a5b46dc..e1261cede5eedaa703e5ea3db2d1369f6fa9cc8f 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -57,6 +57,7 @@ from operator import itemgetter
 from typing import (
     Any,
     Callable,
+    cast,
     Dict,
     Generator,
     List,
@@ -76,11 +77,22 @@ from gxformat2 import (
     convert_and_import_workflow,
     ImporterGalaxyInterface,
 )
-from gxformat2._yaml import ordered_load
+from gxformat2.yaml import ordered_load
+from pydantic import UUID4
 from requests import Response
 from rocrate.rocrate import ROCrate
-from typing_extensions import Literal
+from typing_extensions import (
+    Literal,
+    Self,
+    TypedDict,
+)
 
+from galaxy.schema.schema import (
+    CreateToolLandingRequestPayload,
+    CreateWorkflowLandingRequestPayload,
+    ToolLandingRequest,
+    WorkflowLandingRequest,
+)
 from galaxy.tool_util.client.staging import InteractorStaging
 from galaxy.tool_util.cwl.util import (
     download_output,
@@ -101,6 +113,7 @@ from galaxy.util import (
     galaxy_root_path,
     UNKNOWN,
 )
+from galaxy.util.path import StrPath
 from galaxy.util.resources import resource_string
 from galaxy.util.unittest_utils import skip_if_site_down
 from galaxy_test.base.decorators import (
@@ -110,10 +123,12 @@ from galaxy_test.base.decorators import (
 from galaxy_test.base.json_schema_utils import JsonSchemaValidator
 from . import api_asserts
 from .api import (
+    AnonymousGalaxyInteractor,
     ApiTestInteractor,
     HasAnonymousGalaxyInteractor,
 )
 from .api_util import random_name
+from .env import REQUIRE_ALL_NEEDED_TOOLS
 
 FILE_URL = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed"
 FILE_MD5 = "37b59762b59fff860460522d271bc111"
@@ -130,6 +145,8 @@ DEFAULT_TIMEOUT = 60  # Secs to wait for state to turn ok
 
 SKIP_FLAKEY_TESTS_ON_ERROR = os.environ.get("GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR", None)
 
+PRIVATE_ROLE_TYPE = "private"
+
 
 def flakey(method):
     @wraps(method)
@@ -147,6 +164,15 @@ def flakey(method):
     return wrapped_method
 
 
+def get_tool_ids(interactor: AnonymousGalaxyInteractor):
+    index = interactor.get("tools", data=dict(in_panel=False))
+    api_asserts.assert_status_code_is_ok(index, "Failed to fetch toolbox for target Galaxy.")
+    tools = index.json()
+    # In panels by default, so flatten out sections...
+    tool_ids = [itemgetter("id")(_) for _ in tools]
+    return tool_ids
+
+
 def skip_without_tool(tool_id: str):
     """Decorate an API test method as requiring a specific tool.
 
@@ -154,18 +180,10 @@ def skip_without_tool(tool_id: str):
     """
 
     def method_wrapper(method):
-        def get_tool_ids(api_test_case: HasAnonymousGalaxyInteractor):
-            interactor = api_test_case.anonymous_galaxy_interactor
-            index = interactor.get("tools", data=dict(in_panel=False))
-            api_asserts.assert_status_code_is_ok(index, "Failed to fetch toolbox for target Galaxy.")
-            tools = index.json()
-            # In panels by default, so flatten out sections...
-            tool_ids = [itemgetter("id")(_) for _ in tools]
-            return tool_ids
 
         @wraps(method)
         def wrapped_method(api_test_case, *args, **kwargs):
-            _raise_skip_if(tool_id not in get_tool_ids(api_test_case))
+            check_missing_tool(tool_id not in get_tool_ids(api_test_case.anonymous_galaxy_interactor))
             return method(api_test_case, *args, **kwargs)
 
         return wrapped_method
@@ -253,6 +271,16 @@ def _raise_skip_if(check, *args):
         raise unittest.SkipTest(*args)
 
 
+def check_missing_tool(check):
+    if check:
+        if REQUIRE_ALL_NEEDED_TOOLS:
+            raise AssertionError("Test requires a missing tool and GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS is enabled")
+        else:
+            raise unittest.SkipTest(
+                "Missing tool required to run test, skipping. If this is not intended, ensure GALAXY_TEST_TOOL_CONF if set contains the required tool_conf.xml target and the tool properly parses and loads in Galaxy's test configuration"
+            )
+
+
 def conformance_tests_gen(directory, filename="conformance_tests.yaml"):
     conformance_tests_path = os.path.join(directory, filename)
     with open(conformance_tests_path) as f:
@@ -369,7 +397,9 @@ class BasePopulator(metaclass=ABCMeta):
     galaxy_interactor: ApiTestInteractor
 
     @abstractmethod
-    def _post(self, route, data=None, files=None, headers=None, admin=False, json: bool = False) -> Response:
+    def _post(
+        self, route, data=None, files=None, headers=None, admin=False, json: bool = False, anon: bool = False
+    ) -> Response:
         """POST data to target Galaxy instance on specified route."""
 
     @abstractmethod
@@ -453,6 +483,45 @@ class BaseDatasetPopulator(BasePopulator):
             history_id, content=open(test_data_resolver.get_filename("1.bam"), "rb"), file_type="bam", wait=True
         )
 
+    def new_directory_dataset(
+        self, test_data_resolver: TestDataResolver, history_id: str, directory: str, format: str = "directory"
+    ):
+        directory_path = test_data_resolver.get_filename(directory)
+        assert os.path.isdir(directory_path)
+
+        tmp = tempfile.NamedTemporaryFile(delete=False)
+        tf = tarfile.open(fileobj=tmp, mode="w:")
+        tf.add(directory_path, ".")
+        tf.close()
+
+        with open(tmp.name, "rb") as tar_f:
+            destination = {"type": "hdas"}
+            targets = [
+                {
+                    "destination": destination,
+                    "items": [
+                        {
+                            "src": "pasted",
+                            "paste_content": "",
+                            "ext": format,
+                            "extra_files": {
+                                "items_from": "archive",
+                                "src": "files",
+                                # Prevent Galaxy from checking for a single file in
+                                # a directory and re-interpreting the archive
+                                "fuzzy_root": False,
+                            },
+                        }
+                    ],
+                }
+            ]
+            payload = {"history_id": history_id, "targets": targets, "__files": {"files_0|file_data": tar_f}}
+            fetch_response = self.fetch(payload)
+        assert fetch_response.status_code == 200, fetch_response.content
+        outputs = fetch_response.json()["outputs"]
+        assert len(outputs) == 1
+        return outputs[0]
+
     def fetch(
         self,
         payload: dict,
@@ -674,6 +743,11 @@ class BaseDatasetPopulator(BasePopulator):
     def get_job_details(self, job_id: str, full: bool = False) -> Response:
         return self._get(f"jobs/{job_id}", {"full": full})
 
+    def job_outputs(self, job_id: str) -> List[Dict[str, Any]]:
+        outputs = self._get(f"jobs/{job_id}/outputs")
+        outputs.raise_for_status()
+        return outputs.json()
+
     def compute_hash(
         self,
         dataset_id: str,
@@ -758,6 +832,41 @@ class BaseDatasetPopulator(BasePopulator):
         wait_on(_wait_for_purge, "dataset to become purged", timeout=2)
         return self._get(dataset_url)
 
+    def create_tool_landing(self, payload: CreateToolLandingRequestPayload) -> ToolLandingRequest:
+        create_url = "tool_landings"
+        json = payload.model_dump(mode="json")
+        create_response = self._post(create_url, json, json=True, anon=True)
+        api_asserts.assert_status_code_is(create_response, 200)
+        create_response.raise_for_status()
+        return ToolLandingRequest.model_validate(create_response.json())
+
+    def create_workflow_landing(self, payload: CreateWorkflowLandingRequestPayload) -> WorkflowLandingRequest:
+        create_url = "workflow_landings"
+        json = payload.model_dump(mode="json")
+        create_response = self._post(create_url, json, json=True, anon=True)
+        api_asserts.assert_status_code_is(create_response, 200)
+        assert create_response.headers["access-control-allow-origin"]
+        create_response.raise_for_status()
+        return WorkflowLandingRequest.model_validate(create_response.json())
+
+    def claim_tool_landing(self, uuid: UUID4) -> ToolLandingRequest:
+        url = f"tool_landings/{uuid}/claim"
+        claim_response = self._post(url, {"client_secret": "foobar"}, json=True)
+        api_asserts.assert_status_code_is(claim_response, 200)
+        return ToolLandingRequest.model_validate(claim_response.json())
+
+    def claim_workflow_landing(self, uuid: UUID4) -> WorkflowLandingRequest:
+        url = f"workflow_landings/{uuid}/claim"
+        claim_response = self._post(url, {"client_secret": "foobar"}, json=True)
+        api_asserts.assert_status_code_is(claim_response, 200)
+        return WorkflowLandingRequest.model_validate(claim_response.json())
+
+    def use_workflow_landing(self, uuid: UUID4) -> WorkflowLandingRequest:
+        url = f"workflow_landings/{uuid}"
+        landing_reponse = self._get(url, {"client_secret": "foobar"})
+        api_asserts.assert_status_code_is(landing_reponse, 200)
+        return WorkflowLandingRequest.model_validate(landing_reponse.json())
+
     def create_tool_from_path(self, tool_path: str) -> Dict[str, Any]:
         tool_directory = os.path.dirname(os.path.abspath(tool_path))
         payload = dict(
@@ -812,19 +921,27 @@ class BaseDatasetPopulator(BasePopulator):
     @contextlib.contextmanager
     def test_history_for(self, method) -> Generator[str, None, None]:
         require_new_history = has_requirement(method, "new_history")
-        with self.test_history(require_new=require_new_history) as history_id:
+        name = f"API Test History for {method.__name__}"
+        with self.test_history(require_new=require_new_history, name=name) as history_id:
             yield history_id
 
     @contextlib.contextmanager
-    def test_history(self, require_new: bool = True) -> Generator[str, None, None]:
+    def test_history(self, require_new: bool = True, name: Optional[str] = None) -> Generator[str, None, None]:
         with self._test_history(require_new=require_new, cleanup_callback=self._cleanup_history) as history_id:
             yield history_id
 
     @contextlib.contextmanager
     def _test_history(
-        self, require_new: bool = True, cleanup_callback: Optional[Callable[[str], None]] = None
+        self,
+        require_new: bool = True,
+        cleanup_callback: Optional[Callable[[str], None]] = None,
+        name: Optional[str] = None,
     ) -> Generator[str, None, None]:
-        history_id = self.new_history()
+        if name is not None:
+            kwds = {"name": name}
+        else:
+            kwds = {}
+        history_id = self.new_history(**kwds)
         try:
             yield history_id
         except Exception:
@@ -944,6 +1061,9 @@ class BaseDatasetPopulator(BasePopulator):
         tool_response = self._post(url, data=payload)
         return tool_response
 
+    def describe_tool_execution(self, tool_id: str) -> "DescribeToolExecution":
+        return DescribeToolExecution(self, tool_id)
+
     def materialize_dataset_instance(self, history_id: str, id: str, source: str = "hda"):
         payload: Dict[str, Any]
         if source == "ldda":
@@ -1009,14 +1129,17 @@ class BaseDatasetPopulator(BasePopulator):
         assert isinstance(transform, list)
         return {t["action"] for t in transform}
 
-    def get_history_dataset_details(self, history_id: str, **kwds) -> Dict[str, Any]:
+    def get_history_dataset_details(self, history_id: str, keys: Optional[str] = None, **kwds) -> Dict[str, Any]:
         dataset_id = self.__history_content_id(history_id, **kwds)
-        details_response = self.get_history_dataset_details_raw(history_id, dataset_id)
+        details_response = self.get_history_dataset_details_raw(history_id, dataset_id, keys=keys)
         details_response.raise_for_status()
         return details_response.json()
 
-    def get_history_dataset_details_raw(self, history_id: str, dataset_id: str) -> Response:
-        details_response = self._get_contents_request(history_id, f"/datasets/{dataset_id}")
+    def get_history_dataset_details_raw(self, history_id: str, dataset_id: str, keys: Optional[str] = None) -> Response:
+        data = None
+        if keys:
+            data = {"keys": keys}
+        details_response = self._get_contents_request(history_id, f"/datasets/{dataset_id}", data=data)
         return details_response
 
     def get_history_dataset_extra_files(self, history_id: str, **kwds) -> list:
@@ -1191,11 +1314,13 @@ class BaseDatasetPopulator(BasePopulator):
         return users[0]["id"]
 
     def user_private_role_id(self) -> str:
-        user_email = self.user_email()
-        roles = self.get_roles()
-        users_roles = [r for r in roles if r["name"] == user_email]
-        assert len(users_roles) == 1, f"Did not find exactly one role for email {user_email} - {users_roles}"
-        role = users_roles[0]
+        userid = self.user_id()
+        response = self._get(f"users/{userid}/roles", admin=True)
+        assert response.status_code == 200
+        roles = response.json()
+        private_roles = [r for r in roles if r["type"] == PRIVATE_ROLE_TYPE]
+        assert len(private_roles) == 1, f"Did not find exactly one private role for user {userid} - {private_roles}"
+        role = private_roles[0]
         assert "id" in role, role
         return role["id"]
 
@@ -1661,8 +1786,10 @@ class GalaxyInteractorHttpMixin:
     def _api_key(self):
         return self.galaxy_interactor.api_key
 
-    def _post(self, route, data=None, files=None, headers=None, admin=False, json: bool = False) -> Response:
-        return self.galaxy_interactor.post(route, data, files=files, admin=admin, headers=headers, json=json)
+    def _post(
+        self, route, data=None, files=None, headers=None, admin=False, json: bool = False, anon: bool = False
+    ) -> Response:
+        return self.galaxy_interactor.post(route, data, files=files, admin=admin, headers=headers, json=json, anon=anon)
 
     def _put(self, route, data=None, headers=None, admin=False, json: bool = False):
         return self.galaxy_interactor.put(route, data, headers=headers, admin=admin, json=json)
@@ -1689,7 +1816,10 @@ class DatasetPopulator(GalaxyInteractorHttpMixin, BaseDatasetPopulator):
 
     @contextlib.contextmanager
     def _test_history(
-        self, require_new: bool = True, cleanup_callback: Optional[Callable[[str], None]] = None
+        self,
+        require_new: bool = True,
+        cleanup_callback: Optional[Callable[[str], None]] = None,
+        name: Optional[str] = None,
     ) -> Generator[str, None, None]:
         with self.galaxy_interactor.test_history(
             require_new=require_new, cleanup_callback=cleanup_callback
@@ -1698,7 +1828,7 @@ class DatasetPopulator(GalaxyInteractorHttpMixin, BaseDatasetPopulator):
 
 
 # Things gxformat2 knows how to upload as workflows
-YamlContentT = Union[str, os.PathLike, dict]
+YamlContentT = Union[StrPath, dict]
 
 
 class BaseWorkflowPopulator(BasePopulator):
@@ -1770,7 +1900,11 @@ class BaseWorkflowPopulator(BasePopulator):
         return workflow_id
 
     def wait_for_invocation(
-        self, workflow_id: str, invocation_id: str, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True
+        self,
+        workflow_id: Optional[str],
+        invocation_id: str,
+        timeout: timeout_type = DEFAULT_TIMEOUT,
+        assert_ok: bool = True,
     ) -> str:
         url = f"invocations/{invocation_id}"
 
@@ -1809,6 +1943,8 @@ class BaseWorkflowPopulator(BasePopulator):
                 invocations = self.history_invocations(history_id)
                 if len(invocations) == expected_invocation_count:
                     return True
+                elif len(invocations) > expected_invocation_count:
+                    raise AssertionError("More than the expect number of invocations found in workflow")
 
             wait_on(invocation_count, f"{expected_invocation_count} history invocations")
         for invocation in self.history_invocations(history_id):
@@ -1818,7 +1954,7 @@ class BaseWorkflowPopulator(BasePopulator):
 
     def wait_for_workflow(
         self,
-        workflow_id: str,
+        workflow_id: Optional[str],
         invocation_id: str,
         history_id: str,
         assert_ok: bool = True,
@@ -1827,6 +1963,9 @@ class BaseWorkflowPopulator(BasePopulator):
         """Wait for a workflow invocation to completely schedule and then history
         to be complete."""
         self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout, assert_ok=assert_ok)
+        for step in self.get_invocation(invocation_id)["steps"]:
+            if step["subworkflow_invocation_id"]:
+                self.wait_for_invocation(None, step["subworkflow_invocation_id"], timeout=timeout, assert_ok=assert_ok)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=assert_ok, timeout=timeout)
 
     def get_invocation(self, invocation_id, step_details=False):
@@ -1898,7 +2037,7 @@ class BaseWorkflowPopulator(BasePopulator):
         url = f"workflows/{workflow_id}/invocations"
         invocation_response = self._post(url, data=request, json=True)
         if assert_ok:
-            invocation_response.raise_for_status()
+            api_asserts.assert_status_code_is_ok(invocation_response)
         return invocation_response
 
     def invoke_workflow(
@@ -1946,6 +2085,7 @@ class BaseWorkflowPopulator(BasePopulator):
         history_id: Optional[str] = None,
         inputs: Optional[dict] = None,
         request: Optional[dict] = None,
+        assert_ok: bool = True,
     ) -> Response:
         invoke_return = self.invoke_workflow(workflow_id, history_id=history_id, inputs=inputs, request=request)
         invoke_return.raise_for_status()
@@ -1958,7 +2098,7 @@ class BaseWorkflowPopulator(BasePopulator):
             if history_id.startswith("hist_id="):
                 history_id = history_id[len("hist_id=") :]
         assert history_id
-        self.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=True)
+        self.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok)
         return invoke_return
 
     def workflow_report_json(self, workflow_id: str, invocation_id: str) -> dict:
@@ -1986,6 +2126,11 @@ class BaseWorkflowPopulator(BasePopulator):
         else:
             return ordered_load(response.text)
 
+    def invocation_to_request(self, invocation_id: str):
+        request_response = self._get(f"invocations/{invocation_id}/request")
+        api_asserts.assert_status_code_is_ok(request_response)
+        return request_response.json()
+
     def set_tags(self, workflow_id: str, tags: List[str]) -> None:
         update_payload = {"tags": tags}
         response = self.update_workflow(workflow_id, update_payload)
@@ -2084,7 +2229,51 @@ class BaseWorkflowPopulator(BasePopulator):
             workflow_request.update(extra_invocation_kwds)
         if has_uploads:
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+
+        return self._request_to_summary(
+            history_id,
+            workflow_id,
+            workflow_request,
+            inputs=inputs,
+            wait=wait,
+            assert_ok=assert_ok,
+            invocations=invocations,
+            expected_response=expected_response,
+        )
+
+    def rerun(self, run_jobs_summary: "RunJobsSummary", wait: bool = True, assert_ok: bool = True) -> "RunJobsSummary":
+        history_id = run_jobs_summary.history_id
+        invocation_id = run_jobs_summary.invocation_id
+        inputs = run_jobs_summary.inputs
+        workflow_request = self.invocation_to_request(invocation_id)
+        workflow_id = workflow_request["workflow_id"]
+        assert workflow_request["history_id"] == history_id
+        assert workflow_request["instance"] is True
+        return self._request_to_summary(
+            history_id,
+            workflow_id,
+            workflow_request,
+            inputs=inputs,
+            wait=wait,
+            assert_ok=assert_ok,
+            invocations=1,
+            expected_response=200,
+        )
+
+    def _request_to_summary(
+        self,
+        history_id: str,
+        workflow_id: str,
+        workflow_request: Dict[str, Any],
+        inputs,
+        wait: bool,
+        assert_ok: bool,
+        invocations: int,
+        expected_response: int,
+    ):
+        workflow_populator = self
         assert invocations > 0
+
         jobs = []
         for _ in range(invocations):
             invocation_response = workflow_populator.invoke_workflow_raw(workflow_id, workflow_request)
@@ -2100,6 +2289,7 @@ class BaseWorkflowPopulator(BasePopulator):
                 if wait:
                     workflow_populator.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok)
                 jobs.extend(self.dataset_populator.invocation_jobs(invocation_id))
+
         return RunJobsSummary(
             history_id=history_id,
             workflow_id=workflow_id,
@@ -2145,23 +2335,33 @@ class BaseWorkflowPopulator(BasePopulator):
             workflow_id = self.create_workflow(workflow)
         if not history_id:
             history_id = self.dataset_populator.new_history()
-        hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
-        hda2 = self.dataset_populator.new_dataset(history_id, content="4 5 6", wait=True)
+        hda1: Optional[Dict[str, Any]] = None
+        hda2: Optional[Dict[str, Any]] = None
+        label_map: Optional[Dict[str, Any]] = None
+        if inputs_by != "url":
+            hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
+            hda2 = self.dataset_populator.new_dataset(history_id, content="4 5 6", wait=True)
+            label_map = {"WorkflowInput1": ds_entry(hda1), "WorkflowInput2": ds_entry(hda2)}
         workflow_request = dict(
             history=f"hist_id={history_id}",
         )
-        label_map = {"WorkflowInput1": ds_entry(hda1), "WorkflowInput2": ds_entry(hda2)}
         if inputs_by == "step_id":
+            assert label_map
             ds_map = self.build_ds_map(workflow_id, label_map)
             workflow_request["ds_map"] = ds_map
         elif inputs_by == "step_index":
+            assert hda1
+            assert hda2
             index_map = {"0": ds_entry(hda1), "1": ds_entry(hda2)}
             workflow_request["inputs"] = json.dumps(index_map)
             workflow_request["inputs_by"] = "step_index"
         elif inputs_by == "name":
+            assert label_map
             workflow_request["inputs"] = json.dumps(label_map)
             workflow_request["inputs_by"] = "name"
         elif inputs_by in ["step_uuid", "uuid_implicitly"]:
+            assert hda1
+            assert hda2
             assert workflow, f"Must specify workflow for this inputs_by {inputs_by} parameter value"
             uuid_map = {
                 workflow["steps"]["0"]["uuid"]: ds_entry(hda1),
@@ -2170,6 +2370,16 @@ class BaseWorkflowPopulator(BasePopulator):
             workflow_request["inputs"] = json.dumps(uuid_map)
             if inputs_by == "step_uuid":
                 workflow_request["inputs_by"] = "step_uuid"
+        elif inputs_by in ["url", "deferred_url"]:
+            input_b64_1 = base64.b64encode(b"1 2 3").decode("utf-8")
+            input_b64_2 = base64.b64encode(b"4 5 6").decode("utf-8")
+            deferred = inputs_by == "deferred_url"
+            inputs = {
+                "WorkflowInput1": {"src": "url", "url": f"base64://{input_b64_1}", "ext": "txt", "deferred": deferred},
+                "WorkflowInput2": {"src": "url", "url": f"base64://{input_b64_2}", "ext": "txt", "deferred": deferred},
+            }
+            workflow_request["inputs"] = json.dumps(inputs)
+            workflow_request["inputs_by"] = "name"
 
         return workflow_request, history_id, workflow_id
 
@@ -2288,6 +2498,12 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
         assert upload_response.status_code == 200, upload_response
         return upload_response.json()
 
+    def build_module(self, step_type: str, content_id: Optional[str] = None, inputs: Optional[Dict[str, Any]] = None):
+        payload = {"inputs": inputs or {}, "type": step_type, "content_id": content_id}
+        response = self._post("workflows/build_module", data=payload, json=True)
+        assert response.status_code == 200, response
+        return response.json()
+
     def _import_tool_response(self, tool) -> Response:
         using_requirement("admin")
         tool_str = json.dumps(tool, indent=4)
@@ -2387,6 +2603,13 @@ class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, Import
             link = f"{str(link)}/{output_name}"
         return {"$link": link}
 
+    def make_public(self, workflow_id: str) -> dict:
+        using_requirement("new_published_objects")
+        sharing_response = self._put(f"workflows/{workflow_id}/publish")
+        api_asserts.assert_status_code_is_ok(sharing_response)
+        assert sharing_response.status_code == 200
+        return sharing_response.json()
+
 
 class CwlPopulator:
     def __init__(self, dataset_populator: DatasetPopulator, workflow_populator: WorkflowPopulator):
@@ -2532,13 +2755,13 @@ class CwlPopulator:
             raise Exception("Expected run to fail but it didn't.")
 
         expected_outputs = test["output"]
-        try:
-            for key, value in expected_outputs.items():
+        for key, value in expected_outputs.items():
+            try:
                 actual_output = run.get_output_as_object(key)
                 cwltest.compare.compare(value, actual_output)
-        except Exception:
-            self.dataset_populator._summarize_history(run.history_id)
-            raise
+            except Exception:
+                self.dataset_populator._summarize_history(run.history_id)
+                raise
 
 
 class LibraryPopulator:
@@ -2598,7 +2821,6 @@ class LibraryPopulator:
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
             "targets": targets,
-            "validate_hashes": True,
         }
         return library, self.dataset_populator.fetch(payload, assert_ok=assert_ok)
 
@@ -2687,6 +2909,7 @@ class LibraryPopulator:
             "upload_option": upload_option,
             "file_type": kwds.get("file_type", "auto"),
             "db_key": kwds.get("db_key", "?"),
+            "tags": kwds.get("tags", []),
         }
         if kwds.get("link_data"):
             create_data["link_data_only"] = "link_to_files"
@@ -2718,10 +2941,9 @@ class LibraryPopulator:
         return show().json()
 
     def raw_library_contents_create(self, library_id, payload, files=None):
-        if files is None:
-            files = {}
-
         url_rel = f"libraries/{library_id}/contents"
+        if not files:
+            return self.galaxy_interactor.post(url_rel, payload, json=True)
         return self.galaxy_interactor.post(url_rel, payload, files=files)
 
     def show_ld_raw(self, library_id: str, library_dataset_id: str) -> Response:
@@ -2828,6 +3050,32 @@ class BaseDatasetCollectionPopulator:
         )
         return self.__create(payload)
 
+    def example_list_of_pairs(self, history_id: str) -> str:
+        response = self.upload_collection(
+            history_id,
+            "list:paired",
+            elements=[
+                {
+                    "name": "test0",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "123\n", "name": "forward", "ext": "txt"},
+                        {"src": "pasted", "paste_content": "456\n", "name": "reverse", "ext": "txt"},
+                    ],
+                },
+                {
+                    "name": "test1",
+                    "elements": [
+                        {"src": "pasted", "paste_content": "789\n", "name": "forward", "ext": "txt"},
+                        {"src": "pasted", "paste_content": "0ab\n", "name": "reverse", "ext": "txt"},
+                    ],
+                },
+            ],
+            wait=True,
+        )
+        api_asserts.assert_status_code_is_ok(response)
+        hdca_id = response.json()["outputs"][0]["id"]
+        return hdca_id
+
     def create_list_of_pairs_in_history(self, history_id, **kwds):
         return self.upload_collection(
             history_id,
@@ -2888,7 +3136,7 @@ class BaseDatasetCollectionPopulator:
         else:
             return self.__create_payload_collection(history_id, *args, **kwds)
 
-    def __create_payload_fetch(self, history_id: str, collection_type, **kwds):
+    def __create_payload_fetch(self, history_id: str, collection_type, ext="txt", **kwds):
         contents = None
         if "contents" in kwds:
             contents = kwds["contents"]
@@ -2910,7 +3158,7 @@ class BaseDatasetCollectionPopulator:
                     elements.append(contents_level)
                     continue
 
-                element = {"src": "pasted", "ext": "txt"}
+                element = {"src": "pasted", "ext": ext}
                 # Else older style list of contents or element ID and contents,
                 # convert to fetch API.
                 if isinstance(contents_level, tuple):
@@ -3064,8 +3312,9 @@ def load_data_dict(
 ) -> LoadDataDictResponseT:
     """Load a dictionary as inputs to a workflow (test data focused)."""
 
+    test_data_resolver = TestDataResolver()
+
     def open_test_data(test_dict, mode="rb"):
-        test_data_resolver = TestDataResolver()
         filename = test_data_resolver.get_filename(test_dict.pop("value"))
         return open(filename, mode)
 
@@ -3133,7 +3382,12 @@ def load_data_dict(
         elif is_dict and "type" in value:
             input_type = value.pop("type")
             if input_type == "File":
-                content = open_test_data(value)
+                if "value" in value:
+                    content = open_test_data(value)
+                elif "content" in value:
+                    content = value["content"]
+                else:
+                    raise ValueError(f"Invalid test_data def {test_data}")
                 new_dataset_kwds = {"content": content}
                 if "name" in value:
                     new_dataset_kwds["name"] = value["name"]
@@ -3142,6 +3396,12 @@ def load_data_dict(
                 hda = dataset_populator.new_dataset(history_id, wait=True, **new_dataset_kwds)
                 label_map[key] = dataset_populator.ds_entry(hda)
                 has_uploads = True
+            elif input_type == "Directory":
+                hda = dataset_populator.new_directory_dataset(
+                    test_data_resolver, history_id, directory=value["value"], format=value.get("file_type", "directory")
+                )
+                label_map[key] = dataset_populator.ds_entry(hda)
+                has_uploads = True
             elif input_type == "raw":
                 label_map[key] = value["value"]
                 inputs[key] = value["value"]
@@ -3150,8 +3410,6 @@ def load_data_dict(
             hda = dataset_populator.new_dataset(history_id, content=value)
             label_map[key] = dataset_populator.ds_entry(hda)
             inputs[key] = hda
-        else:
-            raise ValueError(f"Invalid test_data def {test_data}")
 
     return inputs, label_map, has_uploads
 
@@ -3176,6 +3434,7 @@ def stage_inputs(
         job=job,
         use_path_paste=use_path_paste,
         to_posix_lines=to_posix_lines,
+        resolve_data=galaxy_interactor._find_in_test_data_directories,
         **kwds,
     )
 
@@ -3217,6 +3476,7 @@ def wait_on_state(
             "queued",
             "new",
             "ready",
+            "requires_materialization",
             "stop",
             "stopped",
             "setting_metadata",
@@ -3255,6 +3515,349 @@ def _store_payload(
     return payload
 
 
+class DescribeToolExecutionOutput:
+
+    def __init__(self, dataset_populator: BaseDatasetPopulator, history_id: str, hda_id: str):
+        self._dataset_populator = dataset_populator
+        self._history_id = history_id
+        self._hda_id = hda_id
+
+    @property
+    def details(self) -> Dict[str, Any]:
+        dataset_details = self._dataset_populator.get_history_dataset_details(self._history_id, dataset_id=self._hda_id)
+        return dataset_details
+
+    @property
+    def contents(self) -> str:
+        return self._dataset_populator.get_history_dataset_content(history_id=self._history_id, dataset_id=self._hda_id)
+
+    def with_contents(self, expected_contents: str) -> Self:
+        contents = self.contents
+        if contents != expected_contents:
+            raise AssertionError(f"Output dataset had contents {contents} but expected {expected_contents}")
+        return self
+
+    def with_contents_stripped(self, expected_contents: str) -> Self:
+        contents = self.contents
+        if contents.strip() != expected_contents:
+            raise AssertionError(f"Output dataset had contents {contents} but expected {expected_contents}")
+        return self
+
+    def containing(self, expected_contents: str) -> Self:
+        contents = self.contents
+        if expected_contents not in contents:
+            raise AssertionError(
+                f"Output dataset had contents {contents} which does not contain the expected text {expected_contents}"
+            )
+        return self
+
+    def with_file_ext(self, expected_ext: str) -> Self:
+        ext = self.details["file_ext"]
+        if ext != expected_ext:
+            raise AssertionError(f"Output dataset had file extension {ext}, not the expected extension {expected_ext}")
+        return self
+
+    @property
+    def json(self) -> Any:
+        contents = self.contents
+        return json.loads(contents)
+
+    def with_json(self, expected_json: Any) -> Self:
+        json = self.json
+        if json != expected_json:
+            raise AssertionError(f"Output dataset contianed JSON {json}, not {expected_json} as expected")
+        return self
+
+    # aliases that might help make tests more like English in particular cases. Declaring them explicitly
+    # instead quick little aliases because of https://github.com/python/mypy/issues/6700
+    def assert_contains(self, expected_contents: str) -> Self:
+        return self.containing(expected_contents)
+
+    def assert_has_contents(self, expected_contents: str) -> Self:
+        return self.with_contents(expected_contents)
+
+
+class DescribeToolExecutionOutputCollection:
+
+    def __init__(self, dataset_populator: BaseDatasetPopulator, history_id: str, hdca_id: str):
+        self._dataset_populator = dataset_populator
+        self._history_id = history_id
+        self._hdca_id = hdca_id
+
+    @property
+    def details(self) -> Dict[str, Any]:
+        collection_details = self._dataset_populator.get_history_collection_details(
+            self._history_id, content_id=self._hdca_id
+        )
+        return collection_details
+
+    @property
+    def elements(self) -> List[Dict[str, Any]]:
+        return self.details["elements"]
+
+    def with_n_elements(self, n: int) -> Self:
+        count = len(self.elements)
+        if count != n:
+            raise AssertionError("Collection contained {count} elements and not the expected {n} elements")
+        return self
+
+    def with_element_dict(self, index: Union[str, int]) -> Dict[str, Any]:
+        elements = self.elements
+        if isinstance(index, int):
+            element_dict = elements[index]
+        else:
+            element_dict = [e for e in elements if e["element_identifier"] == index][0]
+        return element_dict
+
+    def with_dataset_element(self, index: Union[str, int]) -> "DescribeToolExecutionOutput":
+        element_dict = self.with_element_dict(index)
+        element_object = element_dict["object"]
+        return DescribeToolExecutionOutput(self._dataset_populator, self._history_id, element_object["id"])
+
+    def named(self, expected_name: str) -> Self:
+        name = self.details["name"]
+        if name != expected_name:
+            raise AssertionError(f"Dataset collection named {name} did not have expected name {expected_name}.")
+        return self
+
+    # aliases that might help make tests more like English in particular cases.
+    def assert_has_dataset_element(self, index: Union[str, int]) -> "DescribeToolExecutionOutput":
+        return self.with_dataset_element(index)
+
+
+class DescribeJob:
+
+    def __init__(self, dataset_populator: BaseDatasetPopulator, history_id: str, job_id: str):
+        self._dataset_populator = dataset_populator
+        self._history_id = history_id
+        self._job_id = job_id
+        self._final_details: Optional[Dict[str, Any]] = None
+
+    def _wait_for(self):
+        if self._final_details is None:
+            self._dataset_populator.wait_for_job(self._job_id, assert_ok=False)
+            self._final_details = self._dataset_populator.get_job_details(self._job_id).json()
+
+    @property
+    def final_details(self) -> Dict[str, Any]:
+        self._wait_for()
+        final_details = self._final_details
+        assert final_details
+        return final_details
+
+    @property
+    def final_state(self) -> str:
+        final_state = self.final_details["state"]
+        assert final_state
+        return final_state
+
+    def with_final_state(self, expected_state: str) -> Self:
+        final_state = self.final_state
+        if final_state != expected_state:
+            raise AssertionError(
+                f"Expected job {self._job_id} to end with state {expected_state} but it ended with state {final_state}"
+            )
+        return self
+
+    @property
+    def with_single_output(self) -> DescribeToolExecutionOutput:
+        return self.with_output(0)
+
+    def with_output(self, output: Union[str, int]) -> DescribeToolExecutionOutput:
+        self.with_final_state("ok")
+        outputs = self._dataset_populator.job_outputs(self._job_id)
+        by_name = isinstance(output, str)
+        dataset_id: Optional[str] = None
+        if by_name:
+            for output_assoc in outputs:
+                if output_assoc["name"] == output:
+                    dataset_id = output_assoc["dataset"]["id"]
+        else:
+            assert isinstance(output, int)
+            dataset_id = outputs[output]["dataset"]["id"]
+        if dataset_id is None:
+            raise AssertionError(f"Could not find job output identified by {output}")
+        return DescribeToolExecutionOutput(self._dataset_populator, self._history_id, dataset_id)
+
+    # aliases that might help make tests more like English in particular cases.
+    def assert_has_output(self, output: Union[str, int]) -> DescribeToolExecutionOutput:
+        return self.with_output(output)
+
+    @property
+    def assert_has_single_output(self) -> DescribeToolExecutionOutput:
+        return self.with_single_output
+
+
+class DescribeFailure:
+    def __init__(self, response: Response):
+        self._response = response
+
+    def __call__(self) -> Self:
+        return self
+
+    def with_status_code(self, code: int) -> Self:
+        api_asserts.assert_status_code_is(self._response, code)
+        return self
+
+    def with_error_containing(self, message: str) -> Self:
+        assert message in self._response.text
+        return self
+
+
+class RequiredTool:
+
+    def __init__(self, dataset_populator: BaseDatasetPopulator, tool_id: str, default_history_id: Optional[str]):
+        self._dataset_populator = dataset_populator
+        self._tool_id = tool_id
+        self._default_history_id = default_history_id
+
+    @property
+    def execute(self) -> "DescribeToolExecution":
+        execution = DescribeToolExecution(self._dataset_populator, self._tool_id)
+        if self._default_history_id:
+            execution.in_history(self._default_history_id)
+        return execution
+
+
+class DescribeToolInputs:
+    _input_format: str = "legacy"
+    _inputs: Optional[Dict[str, Any]]
+
+    def __init__(self, input_format: str):
+        self._input_format = input_format
+        self._inputs = None
+
+    def any(self, inputs: Dict[str, Any]) -> Self:
+        self._inputs = inputs
+        return self
+
+    def flat(self, inputs: Dict[str, Any]) -> Self:
+        if self._input_format == "legacy":
+            self._inputs = inputs
+        return self
+
+    def nested(self, inputs: Dict[str, Any]) -> Self:
+        if self._input_format == "21.01":
+            self._inputs = inputs
+        return self
+
+    # aliases for self to create silly little English sentense... inputs.when.flat().when.legacy()
+    @property
+    def when(self) -> Self:
+        return self
+
+
+class DescribeToolExecution:
+    _history_id: Optional[str] = None
+    _execute_response: Optional[Response] = None
+    _input_format: Optional[str] = None
+    _inputs: Dict[str, Any]
+
+    def __init__(self, dataset_populator: BaseDatasetPopulator, tool_id: str):
+        self._dataset_populator = dataset_populator
+        self._tool_id = tool_id
+        self._inputs = {}
+
+    def in_history(self, has_history_id: Union[str, "TargetHistory"]) -> Self:
+        if isinstance(has_history_id, str):
+            self._history_id = has_history_id
+        else:
+            self._history_id = has_history_id._history_id
+        return self
+
+    def with_inputs(self, inputs: Union[DescribeToolInputs, Dict[str, Any]]) -> Self:
+        if isinstance(inputs, DescribeToolInputs):
+            self._inputs = inputs._inputs or {}
+            self._input_format = inputs._input_format
+        else:
+            self._inputs = inputs
+            self._input_format = "legacy"
+        return self
+
+    def with_nested_inputs(self, inputs: Dict[str, Any]) -> Self:
+        self._inputs = inputs
+        self._input_format = "21.01"
+        return self
+
+    def _execute(self):
+        kwds = {}
+        if self._input_format is not None:
+            kwds["input_format"] = self._input_format
+        history_id = self._ensure_history_id
+        self._execute_response = self._dataset_populator.run_tool_raw(
+            self._tool_id, self._inputs, history_id, assert_ok=False, **kwds
+        )
+
+    @property
+    def _ensure_history_id(self) -> str:
+        history_id = self._history_id
+        if history_id is None:
+            raise AssertionError("Problem building test execution - no history ID has been specified.")
+        return history_id
+
+    def _ensure_executed(self) -> None:
+        if self._execute_response is None:
+            self._execute()
+
+    def _assert_executed_ok(self) -> Dict[str, Any]:
+        self._ensure_executed()
+        execute_response = self._execute_response
+        assert execute_response is not None
+        api_asserts.assert_status_code_is_ok(execute_response)
+        return execute_response.json()
+
+    def assert_has_n_jobs(self, n: int) -> Self:
+        response = self._assert_executed_ok()
+        jobs = response["jobs"]
+        if len(jobs) != n:
+            raise AssertionError(f"Expected tool execution to produce {n} jobs but it produced {len(jobs)}")
+        return self
+
+    def assert_creates_n_implicit_collections(self, n: int) -> Self:
+        response = self._assert_executed_ok()
+        collections = response["implicit_collections"]
+        if len(collections) != n:
+            raise AssertionError(f"Expected tool execution to produce {n} implicit but it produced {len(collections)}")
+        return self
+
+    def assert_creates_implicit_collection(self, index: Union[str, int]) -> "DescribeToolExecutionOutputCollection":
+        response = self._assert_executed_ok()
+        collections = response["implicit_collections"]
+        assert isinstance(index, int)  # TODO: implement and then prefer str.
+        history_id = self._ensure_history_id
+        return DescribeToolExecutionOutputCollection(self._dataset_populator, history_id, collections[index]["id"])
+
+    @property
+    def assert_has_single_job(self) -> DescribeJob:
+        return self.assert_has_n_jobs(1).assert_has_job(0)
+
+    def assert_has_job(self, job_index: int = 0) -> DescribeJob:
+        response = self._assert_executed_ok()
+        job = response["jobs"][job_index]
+        history_id = self._ensure_history_id
+        return DescribeJob(self._dataset_populator, history_id, job["id"])
+
+    @property
+    def that_fails(self) -> DescribeFailure:
+        self._ensure_executed()
+        execute_response = self._execute_response
+        assert execute_response is not None
+        if execute_response.status_code != 200:
+            return DescribeFailure(execute_response)
+        else:
+            response = self._assert_executed_ok()
+            jobs = response["jobs"]
+            for job in jobs:
+                final_state = self._dataset_populator.wait_for_job(job["id"])
+                assert final_state == "error"
+            return DescribeFailure(execute_response)
+
+    # alternative assert_ syntax for cases where it reads better.
+    @property
+    def assert_fails(self) -> DescribeFailure:
+        return self.that_fails
+
+
 class GiHttpMixin:
     """Mixin for adapting Galaxy testing populators helpers to bioblend."""
 
@@ -3270,11 +3873,14 @@ class GiHttpMixin:
     def _get(self, route, data=None, headers=None, admin=False) -> Response:
         return self._gi.make_get_request(self._url(route), params=data)
 
-    def _post(self, route, data=None, files=None, headers=None, admin=False, json: bool = False) -> Response:
+    def _post(
+        self, route, data=None, files=None, headers=None, admin=False, json: bool = False, anon: bool = False
+    ) -> Response:
         if headers is None:
             headers = {}
         headers = headers.copy()
-        headers["x-api-key"] = self._gi.key
+        if not anon:
+            headers["x-api-key"] = self._gi.key
         return requests.post(self._url(route), data=data, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
 
     def _put(self, route, data=None, headers=None, admin=False, json: bool = False):
@@ -3332,6 +3938,95 @@ class GiWorkflowPopulator(GiHttpMixin, BaseWorkflowPopulator):
         self.dataset_populator = GiDatasetPopulator(gi)
 
 
+ListContentsDescription = Union[List[str], List[Tuple[str, str]]]
+
+
+class TargetHistory:
+
+    def __init__(
+        self,
+        dataset_populator: DatasetPopulator,
+        dataset_collection_populator: DatasetCollectionPopulator,
+        history_id: str,
+    ):
+        self._dataset_populator = dataset_populator
+        self._dataset_collection_populator = dataset_collection_populator
+        self._history_id = history_id
+
+    @property
+    def id(self) -> str:
+        return self._history_id
+
+    def with_dataset(
+        self,
+        content: str,
+        named: Optional[str] = None,
+    ) -> "HasSrcDict":
+        kwd = {}
+        if named is not None:
+            kwd["name"] = named
+        new_dataset = self._dataset_populator.new_dataset(
+            history_id=self._history_id,
+            content=content,
+            assert_ok=True,
+            wait=True,
+            **kwd,
+        )
+        return HasSrcDict("hda", new_dataset)
+
+    def with_pair(self, contents: Optional[List[str]] = None) -> "HasSrcDict":
+        return self._fetch_response(
+            self._dataset_collection_populator.create_pair_in_history(
+                self._history_id, contents=contents, direct_upload=True, wait=True
+            )
+        )
+
+    def with_list(self, contents: Optional[ListContentsDescription] = None) -> "HasSrcDict":
+        return self._fetch_response(
+            self._dataset_collection_populator.create_list_in_history(
+                self._history_id, contents=contents, direct_upload=True, wait=True
+            )
+        )
+
+    def with_example_list_of_pairs(self) -> "HasSrcDict":
+        return HasSrcDict("hdca", self._dataset_collection_populator.example_list_of_pairs(self._history_id))
+
+    @classmethod
+    def _fetch_response(clz, response: Response) -> "HasSrcDict":
+        api_asserts.assert_status_code_is_ok(response)
+        hdca = response.json()["output_collections"][0]
+        return HasSrcDict("hdca", hdca)
+
+    def execute(self, tool_id: str) -> "DescribeToolExecution":
+        return self._dataset_populator.describe_tool_execution(tool_id).in_history(self)
+
+
+class SrcDict(TypedDict):
+    src: str
+    id: str
+
+
+class HasSrcDict:
+    api_object: Union[str, Dict[str, Any]]
+
+    def __init__(self, src_type: str, api_object: Union[str, Dict[str, Any]]):
+        self.src_type = src_type
+        self.api_object = api_object
+
+    @property
+    def id(self) -> str:
+        has_id = self.api_object
+        return has_id if isinstance(has_id, str) else cast(str, has_id["id"])
+
+    @property
+    def src_dict(self) -> SrcDict:
+        return SrcDict({"src": self.src_type, "id": self.id})
+
+    @property
+    def to_dict(self):
+        return self.api_object
+
+
 def wait_on(function: Callable, desc: str, timeout: timeout_type = DEFAULT_TIMEOUT):
     return tool_util_wait_on(function, desc, timeout)
 
diff --git a/lib/galaxy_test/base/testcase.py b/lib/galaxy_test/base/testcase.py
index 6f148d19840b72758ab01b1e094d81c02b63000c..58acf00ea4087641dbe2d6af37a7e72016a79a4f 100644
--- a/lib/galaxy_test/base/testcase.py
+++ b/lib/galaxy_test/base/testcase.py
@@ -9,6 +9,7 @@ import pytest
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.util.unittest import TestCase
 from galaxy_test.base.env import (
+    GalaxyTarget,
     setup_keep_outdir,
     target_url_parts,
 )
@@ -16,6 +17,16 @@ from galaxy_test.base.env import (
 log = logging.getLogger(__name__)
 
 
+def host_port_and_url(test_driver: Optional[Any]) -> GalaxyTarget:
+    host, port, url = target_url_parts()
+    server_wrapper = test_driver and test_driver.server_wrappers and test_driver.server_wrappers[0]
+    if server_wrapper:
+        host = server_wrapper.host
+        port = server_wrapper.port
+        url = f"http://{host}:{port}{server_wrapper.prefix.rstrip('/')}/"
+    return host, port, url
+
+
 @pytest.mark.usefixtures("embedded_driver")
 class FunctionalTestCase(TestCase):
     """Base class for tests targetting actual Galaxy servers.
@@ -34,14 +45,7 @@ class FunctionalTestCase(TestCase):
     _test_driver: Optional[Any]
 
     def setUp(self) -> None:
-        self.host, self.port, self.url = target_url_parts()
-        server_wrapper = (
-            self._test_driver and self._test_driver.server_wrappers and self._test_driver.server_wrappers[0]
-        )
-        if server_wrapper:
-            self.host = server_wrapper.host
-            self.port = server_wrapper.port
-            self.url = f"http://{self.host}:{self.port}{server_wrapper.prefix.rstrip('/')}/"
+        self.host, self.port, self.url = host_port_and_url(self._test_driver)
         self.test_data_resolver = TestDataResolver()
         self.keepOutdir = setup_keep_outdir()
 
diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py
index b736196dd63a18a8442e155d061865f6e41a3f9a..7b4eb6186b99e7e52c9d755507e85ecebc2703d6 100644
--- a/lib/galaxy_test/base/workflow_fixtures.py
+++ b/lib/galaxy_test/base/workflow_fixtures.py
@@ -617,6 +617,7 @@ inputs:
   int_input:
     type: integer
     default: 3
+    optional: true
 steps:
   random:
     tool_id: random_lines1
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index 77ab88ca068276cd713dab8be6bbd77f5ad81cc7..206a69f9e2e41ac97333c38ef034fa2020827b48 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -34,6 +34,7 @@ from galaxy.tool_util.verify.interactor import (
     GalaxyInteractorApi,
     verify_tool,
 )
+from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.util import (
     asbool,
     download_to_file,
@@ -65,6 +66,7 @@ FRAMEWORK_DATATYPES_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "sample_datatypes_c
 MIGRATED_TOOL_PANEL_CONFIG = "config/migrated_tools_conf.xml"
 INSTALLED_TOOL_PANEL_CONFIGS = [os.environ.get("GALAXY_TEST_SHED_TOOL_CONF", "config/shed_tool_conf.xml")]
 DEFAULT_LOCALES = "en"
+DEFAULT_TOOL_TEST_WAIT: int = int(os.environ.get("GALAXY_TEST_DEFAULT_WAIT", 60))
 
 log = logging.getLogger("test_driver")
 
@@ -799,7 +801,7 @@ class TestDriver:
         self.server_wrappers: List[ServerWrapper] = []
         self.temp_directories: List[str] = []
 
-    def setup(self, config_object=None) -> None:
+    def setup(self) -> None:
         """Called before tests are built."""
 
     def tear_down(self) -> None:
@@ -850,7 +852,8 @@ class GalaxyTestDriver(TestDriver):
 
         default_tool_conf: Optional[str]
         datatypes_conf_override: Optional[str]
-        if getattr(config_object, "framework_tool_and_types", False):
+        framework_tools_and_types = getattr(config_object, "framework_tool_and_types", False)
+        if framework_tools_and_types:
             default_tool_conf = FRAMEWORK_SAMPLE_TOOLS_CONF
             datatypes_conf_override = FRAMEWORK_DATATYPES_CONF
         else:
@@ -860,6 +863,7 @@ class GalaxyTestDriver(TestDriver):
         self.allow_tool_conf_override = allow_tool_conf_override
         self.default_tool_conf = default_tool_conf
         self.datatypes_conf_override = datatypes_conf_override
+        self.maxseconds = getattr(config_object, "maxseconds", DEFAULT_TOOL_TEST_WAIT)
 
     def setup(self, config_object=None):
         """Setup a Galaxy server for functional test (if needed).
@@ -959,11 +963,17 @@ class GalaxyTestDriver(TestDriver):
             "keep_outputs_dir": None,
         }
         galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
+        # Cut down default timeout to 60 seconds within tests run via
+        # GalaxyTestDriver. Does not affect tests run via galaxy-tool-util,
+        # which use a much longer timeout.
+        maxseconds = kwd.pop("maxseconds", self.maxseconds)
         verify_tool(
             tool_id=tool_id,
             test_index=index,
             galaxy_interactor=galaxy_interactor,
             resource_parameters=resource_parameters,
+            test_data_resolver=TestDataResolver(),
+            maxseconds=maxseconds,
             **kwd,
         )
 
diff --git a/lib/galaxy_test/driver/integration_setup.py b/lib/galaxy_test/driver/integration_setup.py
index b63b567247ea68db009dedbb6e92508a12ea54a7..30194e63c830c4cc26734efa47cef8ca0c764e74 100644
--- a/lib/galaxy_test/driver/integration_setup.py
+++ b/lib/galaxy_test/driver/integration_setup.py
@@ -15,7 +15,9 @@ GROUP_B = "group name with spaces"
 REQUIRED_GROUP_EXPRESSION = f"{GROUP_A} or '{GROUP_B}'"
 
 
-def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include_test_data_dir: bool) -> str:
+def get_posix_file_source_config(
+    root_dir: str, roles: str, groups: str, include_test_data_dir: bool, prefer_links: bool = False
+) -> str:
     rval = f"""
 - type: posix
   id: posix_test
@@ -26,6 +28,17 @@ def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include
   requires_roles: {roles}
   requires_groups: {groups}
 """
+    if prefer_links:
+        rval += f"""
+- type: posix
+  id: linking_source
+  label: Posix
+  doc: Files from local path to links
+  root: {root_dir}
+  writable: true
+  prefer_links: true
+"""
+
     if include_test_data_dir:
         rval += """
 - type: posix
@@ -44,9 +57,10 @@ def create_file_source_config_file_on(
     include_test_data_dir,
     required_role_expression,
     required_group_expression,
+    prefer_links: bool = False,
 ):
     file_contents = get_posix_file_source_config(
-        root_dir, required_role_expression, required_group_expression, include_test_data_dir
+        root_dir, required_role_expression, required_group_expression, include_test_data_dir, prefer_links=prefer_links
     )
     file_path = os.path.join(temp_dir, "file_sources_conf_posix.yml")
     with open(file_path, "w") as f:
@@ -67,6 +81,7 @@ class PosixFileSourceSetup:
         # Require role for access but do not require groups by default on every test to simplify them
         required_role_expression=REQUIRED_ROLE_EXPRESSION,
         required_group_expression="",
+        prefer_links: bool = False,
     ):
         temp_dir = os.path.realpath(mkdtemp())
         clazz_ = clazz_ or cls
@@ -79,6 +94,7 @@ class PosixFileSourceSetup:
             clazz_.include_test_data_dir,
             required_role_expression,
             required_group_expression,
+            prefer_links=prefer_links,
         )
         config["file_sources_config_file"] = file_sources_config_file
 
diff --git a/lib/galaxy_test/selenium/framework.py b/lib/galaxy_test/selenium/framework.py
index 310c88c880535fafac6f8dc7af2a55797ac41634..9c300dc7b0def9ea97f799cbd0b0b70e118f3859 100644
--- a/lib/galaxy_test/selenium/framework.py
+++ b/lib/galaxy_test/selenium/framework.py
@@ -744,12 +744,14 @@ class SeleniumSessionGetPostMixin:
         response = requests.get(full_url, params=data, cookies=cookies, headers=headers, timeout=DEFAULT_SOCKET_TIMEOUT)
         return response
 
-    def _post(self, route, data=None, files=None, headers=None, admin=False, json: bool = False) -> Response:
+    def _post(
+        self, route, data=None, files=None, headers=None, admin=False, json: bool = False, anon: bool = False
+    ) -> Response:
         full_url = self.selenium_context.build_url(f"api/{route}", for_selenium=False)
         cookies = None
         if admin:
             full_url = f"{full_url}?key={self._mixin_admin_api_key}"
-        else:
+        elif not anon:
             cookies = self.selenium_context.selenium_to_requests_cookies()
         request_kwd = prepare_request_params(data=data, files=files, as_json=json, headers=headers, cookies=cookies)
         response = requests.post(full_url, timeout=DEFAULT_SOCKET_TIMEOUT, **request_kwd)
diff --git a/lib/galaxy_test/selenium/jupyter/notebook_example_testing.ipynb b/lib/galaxy_test/selenium/jupyter/notebook_example_testing.ipynb
index c99aacf8802faefdf0c8c46e7732742892d666c9..065248a456edbce0d087ac3319d572ef9943f883 100644
--- a/lib/galaxy_test/selenium/jupyter/notebook_example_testing.ipynb
+++ b/lib/galaxy_test/selenium/jupyter/notebook_example_testing.ipynb
@@ -66,7 +66,6 @@
    "source": [
     "# optional step that shows how to access ActionChains\n",
     "\n",
-    "from selenium import webdriver\n",
     "from selenium.webdriver.common.action_chains import ActionChains\n",
     "ac = ActionChains(gx_selenium_context.driver)"
    ]
diff --git a/lib/galaxy_test/selenium/test_change_password.py b/lib/galaxy_test/selenium/test_change_password.py
index 7b8aae51050921d126ed3822ac35f7ae517b8ad0..8ab3e9f8e3118ad6d956c82ab4a1f505d977b93c 100644
--- a/lib/galaxy_test/selenium/test_change_password.py
+++ b/lib/galaxy_test/selenium/test_change_password.py
@@ -10,8 +10,7 @@ class TestChangePassword(SeleniumTestCase):
         self.home()
         email = self._get_random_email()
         self.register(email)
-        self.click_masthead_user()
-        self.components.masthead.preferences.wait_for_and_click()
+        self.navigate_to_user_preferences()
         self.components.preferences.change_password.wait_for_and_click()
         new_password = self._get_random_password()
         self.fill_input_fields(self.default_password, new_password, new_password)
@@ -57,8 +56,7 @@ class TestChangePassword(SeleniumTestCase):
     def register_and_change_password(self):
         self.home()
         self.register()
-        self.click_masthead_user()
-        self.components.masthead.preferences.wait_for_and_click()
+        self.navigate_to_user_preferences()
         self.components.preferences.change_password.wait_for_and_click()
 
     def fill_input_fields(self, current, password, confirm):
diff --git a/lib/galaxy_test/selenium/test_collection_builders.py b/lib/galaxy_test/selenium/test_collection_builders.py
index 1ef184dec3f61a60e723caabe0cb8d6d57a4099b..2c57e632e8b5707c855d7986cfb6f419a243a094 100644
--- a/lib/galaxy_test/selenium/test_collection_builders.py
+++ b/lib/galaxy_test/selenium/test_collection_builders.py
@@ -32,18 +32,6 @@ class TestCollectionBuilders(SeleniumTestCase):
         self.collection_builder_create()
         self._wait_for_hid_visible(3)
 
-    @selenium_test
-    @managed_history
-    def test_build_pair_simple_hidden(self):
-        self.perform_upload(self.get_filename("1.tabular"))
-        self.perform_upload(self.get_filename("2.tabular"))
-        self._wait_for_and_select([1, 2])
-        self._collection_dropdown("build pair")
-        self.collection_builder_set_name("my awesome pair")
-        self.screenshot("collection_builder_pair")
-        self.collection_builder_create()
-        self._wait_for_hid_visible(5)
-
     @selenium_test
     @managed_history
     def test_build_paired_list_simple(self):
@@ -51,7 +39,6 @@ class TestCollectionBuilders(SeleniumTestCase):
         self.perform_upload(self.get_filename("2.tabular"))
         self._wait_for_and_select([1, 2])
         self._collection_dropdown("build list of pairs")
-        self.collection_builder_clear_filters()
         self.collection_builder_click_paired_item("forward", 0)
         self.collection_builder_click_paired_item("reverse", 1)
         self.collection_builder_set_name("my awesome paired list")
@@ -73,7 +60,7 @@ class TestCollectionBuilders(SeleniumTestCase):
         self._wait_for_and_select([1, 2])
         self._collection_dropdown("build list of pairs")
         collection_builders = self.components.collection_builders
-        collection_builders.clear_filters.wait_for_and_click()
+        self.ensure_collection_builder_filters_cleared()
         forward_column = collection_builders.forward_datasets.wait_for_visible()
         first_datset_forward = forward_column.find_elements(self.by.CSS_SELECTOR, "li")[0]
         first_datset_forward.click()
diff --git a/lib/galaxy_test/selenium/test_dataset_edit.py b/lib/galaxy_test/selenium/test_dataset_edit.py
index 3859616cb81cdb1288438e9ca24db550c9fe4d0f..b6da177f42b425ce7da9313c4a9158d4d06ecfb7 100644
--- a/lib/galaxy_test/selenium/test_dataset_edit.py
+++ b/lib/galaxy_test/selenium/test_dataset_edit.py
@@ -65,3 +65,33 @@ class TestHistoryPanel(SeleniumTestCase):
 
         assert annotation_component.wait_for_value() == TEST_ANNOTATION
         assert info_component.wait_for_value() == TEST_INFO
+
+    @selenium_test
+    @managed_history
+    def test_history_dataset_auto_detect_datatype(self):
+        expected_datatype = "txt"
+        provided_datatype = "tabular"
+        history_entry = self.perform_single_upload(self.get_filename("1.txt"), ext=provided_datatype)
+        hid = history_entry.hid
+        self.wait_for_history()
+        self.history_panel_wait_for_hid_ok(hid)
+        self.history_panel_item_edit(hid=hid)
+        edit_dataset_attributes = self.components.edit_dataset_attributes
+        datatypes_tab = edit_dataset_attributes.datatypes_tab
+        datatype_component = edit_dataset_attributes.datatype_dropdown
+        datatypes_tab.wait_for_and_click()
+        assert datatype_component.wait_for_text() == provided_datatype
+
+        # click auto detect datatype button
+        edit_dataset_attributes.auto_detect_datatype_button.wait_for_and_click()
+        edit_dataset_attributes.alert.wait_for_visible()
+
+        assert edit_dataset_attributes.alert.has_class("alert-success")
+
+        # reopen and check that datatype is updated
+        self.home()
+        self.history_panel_wait_for_hid_ok(hid)
+        self.history_panel_item_edit(hid=hid)
+        datatypes_tab.wait_for_and_click()
+
+        assert datatype_component.wait_for_text() == expected_datatype
diff --git a/lib/galaxy_test/selenium/test_invocation_grid.py b/lib/galaxy_test/selenium/test_invocation_grid.py
index 32db11471280bfe484cc04fd38f575dec150609f..48c17d2e447a312935c3db3d7229a3b477139b6c 100644
--- a/lib/galaxy_test/selenium/test_invocation_grid.py
+++ b/lib/galaxy_test/selenium/test_invocation_grid.py
@@ -21,11 +21,12 @@ class TestInvocationGridSelenium(SeleniumTestCase, TestsGalaxyPagers):
             wait=True,
             invocations=30,
         )
-        gx_selenium_context.navigate_to_invocations()
+        gx_selenium_context.navigate_to_invocations_grid()
+        invocations = gx_selenium_context.components.invocations
+        invocations.invocations_table.wait_for_visible()
 
         # shows a maximum of 25 invocations per page
         self._assert_showing_n_invocations(25)
-        invocations = gx_selenium_context.components.invocations
         invocations.pager.wait_for_visible()
         self.screenshot("invocations_paginated_first_page")
         self._next_page(invocations)
diff --git a/lib/galaxy_test/selenium/test_library_contents.py b/lib/galaxy_test/selenium/test_library_contents.py
index 19b26825e1cefba7b5dfaa74e78de199036b1d41..a2b9511f6f6d568a9e36cc01c6138c6667ec817a 100644
--- a/lib/galaxy_test/selenium/test_library_contents.py
+++ b/lib/galaxy_test/selenium/test_library_contents.py
@@ -69,14 +69,14 @@ class TestLibraryContents(SeleniumTestCase, UsesLibraryAssertions):
         self.sleep_for(self.wait_types.UX_RENDER)
         self.libraries_dataset_import(self.navigation.libraries.folder.labels.from_history)
         # Click the cancel button, make sure modal is hidden.
-        self.wait_for_visible(self.navigation.libraries.folder.selectors.import_modal)
-        self.wait_for_and_click(self.navigation.libraries.folder.selectors.import_datasets_cancel_button)
-        self.wait_for_absent_or_hidden(self.navigation.libraries.folder.selectors.import_modal)
+        self.wait_for_visible(self.navigation.libraries.folder.selectors.import_datasets_from_history_modal)
+        self.wait_for_and_click(self.navigation.libraries.folder.selectors.import_datasets_from_history_modal_cancel)
+        self.wait_for_absent_or_hidden(self.navigation.libraries.folder.selectors.import_datasets_from_history_modal)
 
         self.libraries_dataset_import(self.navigation.libraries.folder.labels.from_history)
-        # Need to select the right item on the dropdown
+        # Need to search for the history and select it before we can select datasets.
         self.sleep_for(self.wait_types.UX_RENDER)
-        self._select_history_option("Unnamed history")
+        self._search_and_select_history(1, "Unnamed history")
         self.sleep_for(self.wait_types.UX_RENDER)
         self.libraries_dataset_import_from_history_select(["1.txt"])
         # Add
@@ -186,6 +186,9 @@ class TestLibraryContents(SeleniumTestCase, UsesLibraryAssertions):
         self.screenshot("libraries_show_details_done")
 
     @retry_during_transitions
-    def _select_history_option(self, label_text):
-        select = self.components.libraries.folder.add_history_items.wait_for_select()
-        select.select_by_visible_text(label_text)
+    def _search_and_select_history(self, row_index=1, label_text="Unnamed history"):
+        self.libraries_dataset_import_from_history_search_for(label_text)
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.components.libraries.folder.import_datasets_from_history_modal_select_list_item_by_index(
+            row_index=row_index
+        ).wait_for_and_click()
diff --git a/lib/galaxy_test/selenium/test_library_to_collections.py b/lib/galaxy_test/selenium/test_library_to_collections.py
index 2b2359c3088cd810f3def7000bb36c2fcd6f1f7c..e46ccc905cccef15e710df384812d0e549d2864c 100644
--- a/lib/galaxy_test/selenium/test_library_to_collections.py
+++ b/lib/galaxy_test/selenium/test_library_to_collections.py
@@ -63,7 +63,7 @@ class TestLibraryToCollections(SeleniumTestCase, UsesLibraryAssertions):
                 collection_option=collection_option
             ).wait_for_and_click()
         self.screenshot(f"libraries_to_collection_landing_is_new_history={is_new_history}")
-        self.components.libraries.folder.import_datasets_ok_button.wait_for_and_click()
+        self.components.libraries.folder.add_to_history_as_collection.wait_for_and_click()
         self.build_collection_and_assert()
         if is_new_history:
             assert self.history_panel_name_element().text == random_name
@@ -78,7 +78,7 @@ class TestLibraryToCollections(SeleniumTestCase, UsesLibraryAssertions):
             collection_option="list:paired"
         ).wait_for_and_click()
         self.screenshot(f"test_export_pairs_list={is_new_history}")
-        self.components.libraries.folder.import_datasets_ok_button.wait_for_and_click()
+        self.components.libraries.folder.add_to_history_as_collection.wait_for_and_click()
         self.components.libraries.folder.clear_filters.wait_for_and_click()
         self.collection_builder_click_paired_item("forward", 0)
         self.collection_builder_click_paired_item("reverse", 1)
diff --git a/lib/galaxy_test/selenium/test_published_pages.py b/lib/galaxy_test/selenium/test_published_pages.py
index d8813f323ba194305995816cc9af8375d9fbf334..c73495dd588f438e0409fa27d371800edd4cee86 100644
--- a/lib/galaxy_test/selenium/test_published_pages.py
+++ b/lib/galaxy_test/selenium/test_published_pages.py
@@ -7,7 +7,7 @@ from .framework import (
 class TestPublishedPagesGrid(SharedStateSeleniumTestCase):
     @selenium_test
     def test_index(self):
-        self.navigate_to_published_pages()
+        self.navigate_to_pages()
         assert len(self.get_grid_entry_names("#pages-published-grid")) == 2
 
     def setup_shared_state(self):
diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py
index 2b3a715b386ed92483b4a83f6c06e1c116922ebe..c08ed95761d52b3e5e6922a71d351be73b7fe4d9 100644
--- a/lib/galaxy_test/selenium/test_sign_out.py
+++ b/lib/galaxy_test/selenium/test_sign_out.py
@@ -11,8 +11,7 @@ class TestSignOut(SeleniumTestCase):
     def test_sign_out(self):
         email = self._get_random_email()
         self.register(email)
-        self.click_masthead_user()
-        self.components.masthead.preferences.wait_for_and_click()
+        self.navigate_to_user_preferences()
         self.components.preferences.sign_out.wait_for_and_click()
         self.components.sign_out.cancel_button.wait_for_and_click()
         assert self.is_logged_in()
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index 42740dd720440a8d61a83618dd6f4fb331d1ea72..6e11ce100130fdc72215e500522a0b6e39b139c9 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -170,6 +170,20 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         self.history_panel_wait_for_hid_ok(2)
         self._check_dataset_details_for_inttest_value(2)
 
+    @selenium_test
+    def test_rerun_with_non_latest_version(self):
+        version = "0.1+galaxy6"
+        self._run_multiple_version_test_tool(version)
+        self.history_panel_wait_for_hid_ok(1)
+        self.hda_click_primary_action_button(1, "rerun")
+        self.components.tool_form.tool_version_button.wait_for_and_click()
+        menu_element = self.wait_for_selector_visible(".dropdown-menu.show")
+        menu_options = menu_element.find_elements(By.CSS_SELECTOR, "a.dropdown-item")
+        for menu_option in menu_options:
+            if f"Selected {version}" in menu_option.text:
+                return
+        raise Exception("Tool version does not match job version")
+
     @selenium_test
     def test_rerun_deleted_dataset(self):
         # upload a first dataset that should not become selected on re-run
@@ -191,9 +205,9 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         assert (
             error_input1.text
-            == "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
+            == "Parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
         )
-        assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
+        assert error_col.text == "Parameter 'col': an invalid option ('3') was selected (valid options: 1)"
         # validate errors when inputs are missing
         self.components.tool_form.parameter_data_input_collection(parameter="input1").wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
@@ -201,8 +215,8 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         error_col_names = self.components.tool_form.parameter_error(parameter="col_names").wait_for_visible()
         assert error_input1.text == "Please provide a value for this option."
-        assert error_col.text == "parameter 'col': requires a value, but no legal values defined"
-        assert error_col_names.text == "parameter 'col_names': requires a value, but no legal values defined"
+        assert error_col.text == "Parameter 'col': requires a value, but no legal values defined"
+        assert error_col_names.text == "Parameter 'col_names': requires a value, but no legal values defined"
         # validate warnings when inputs are restored
         self.components.tool_form.parameter_data_input_single(parameter="input1").wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
@@ -210,9 +224,9 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         assert (
             error_input1.text
-            == "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
+            == "Parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
         )
-        assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
+        assert error_col.text == "Parameter 'col': an invalid option ('3') was selected (valid options: 1)"
 
     @selenium_test
     def test_rerun_dataset_collection_element(self):
@@ -314,6 +328,13 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         self.tool_set_value("inttest", inttest_value)
         self.tool_form_execute()
 
+    def _run_multiple_version_test_tool(self, version):
+        self.home()
+        self.tool_open("multiple_versions")
+        self.components.tool_form.tool_version_button.wait_for_and_click()
+        self.select_dropdown_item(f"Switch to {version}")
+        self.tool_form_execute()
+
 
 class TestLoggedInToolForm(SeleniumTestCase):
     ensure_registered = True
diff --git a/lib/galaxy_test/selenium/test_uploads.py b/lib/galaxy_test/selenium/test_uploads.py
index 6ce9607ea02e7e707b916950a2b1968c29b5b519..aa8065af60dea8b935b4de420690cf788ab19dd8 100644
--- a/lib/galaxy_test/selenium/test_uploads.py
+++ b/lib/galaxy_test/selenium/test_uploads.py
@@ -182,7 +182,7 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
         self.upload_start_click()
         self.upload_queue_local_file(self.get_filename("1.sam"))
         self.upload_paste_data("some pasted data")
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # reopen modal and check that the files are still there
         self.upload_start_click()
@@ -191,12 +191,12 @@ class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
 
         # perform upload and close modal
         self.upload_start()
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # add another pasted file, but don't upload it
         self.upload_start_click()
         self.upload_paste_data("some more pasted data")
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # reopen modal and see 2 uploaded, 1 yet to upload
         self.upload_start_click()
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 7aefe2ef269df69e803fba4e1ec4b59b28854525..ed62bb4886983ab5b9b187abe242fe805d80ca71 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -23,7 +23,6 @@ from galaxy_test.base.workflow_fixtures import (
 )
 from .framework import (
     retry_assertion_during_transitions,
-    retry_during_transitions,
     RunsWorkflows,
     selenium_test,
     SeleniumTestCase,
@@ -42,34 +41,24 @@ class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
         self.assert_wf_annotation_is(annotation)
 
         editor.canvas_body.wait_for_visible()
-        editor.tool_menu.wait_for_visible()
 
         # shouldn't have changes on fresh load
         save_button = self.components.workflow_editor.save_button
-        save_button.wait_for_visible()
-        assert save_button.has_class("disabled")
+        save_button.assert_disabled()
 
         self.screenshot("workflow_editor_blank")
 
         self.hover_over(self.components._.left_panel_drag.wait_for_visible())
-        self.components._.left_panel_collapse.wait_for_and_click()
-
-        self.sleep_for(self.wait_types.UX_RENDER)
-
-        self.screenshot("workflow_editor_left_collapsed")
-
-        self.hover_over(self.components._.right_panel_drag.wait_for_visible())
-        self.components._.right_panel_collapse.wait_for_and_click()
 
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self.workflow_editor_maximize_center_pane()
 
-        self.screenshot("workflow_editor_left_and_right_collapsed")
+        self.screenshot("workflow_editor_center_pane_maximized")
 
     @selenium_test
     def test_edit_annotation(self):
         editor = self.components.workflow_editor
         annotation = "new_annotation_test"
-        name = self.workflow_create_new(annotation=annotation)
+        name = self.create_and_wait_for_new_workflow_in_editor(annotation=annotation)
         edit_annotation = self.components.workflow_editor.edit_annotation
         self.assert_wf_annotation_is(annotation)
 
@@ -83,9 +72,7 @@ class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
 
     @selenium_test
     def test_edit_name(self):
-        editor = self.components.workflow_editor
-        name = self.workflow_create_new()
-        editor.canvas_body.wait_for_visible()
+        name = self.create_and_wait_for_new_workflow_in_editor()
         new_name = self._get_random_name()
         edit_name = self.components.workflow_editor.edit_name
         edit_name.wait_for_and_send_keys(new_name)
@@ -97,18 +84,95 @@ class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
     @selenium_test
     def test_edit_license(self):
         editor = self.components.workflow_editor
-        name = self.workflow_create_new()
-        editor.canvas_body.wait_for_visible()
+        name = self.create_and_wait_for_new_workflow_in_editor()
         editor.license_selector.wait_for_visible()
-        editor.license_selector.assert_no_axe_violations_with_impact_of_at_least("serious")
-        editor.license_selector.assert_data_value("license", "null")
+        assert "Do not specify" in editor.license_current_value.wait_for_text()
 
         self.workflow_editor_set_license("MIT")
         self.workflow_editor_click_save()
 
         self.workflow_index_open_with_name(name)
         editor.license_selector.wait_for_visible()
-        editor.license_selector.assert_data_value("license", "MIT")
+        assert "MIT" in editor.license_current_value.wait_for_text()
+
+    @selenium_test
+    def test_parameter_regex_validation(self):
+        editor = self.components.workflow_editor
+        workflow_run = self.components.workflow_run
+
+        parameter_name = "text_param"
+        name = self.create_and_wait_for_new_workflow_in_editor()
+        self.workflow_editor_add_input("parameter_input")
+        editor.label_input.wait_for_and_send_keys(parameter_name)
+        # this really should be parameterized with the repeat name
+        self.components.tool_form.repeat_insert.wait_for_and_click()
+        self.components.tool_form.parameter_input(
+            parameter="parameter_definition|validators_0|regex_match"
+        ).wait_for_and_send_keys("moocow.*")
+        self.components.tool_form.parameter_input(
+            parameter="parameter_definition|validators_0|regex_doc"
+        ).wait_for_and_send_keys("input must start with moocow")
+        self.save_after_node_form_changes()
+
+        self.workflow_run_with_name(name)
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
+        input_element.send_keys("startswrong")
+        workflow_run.run_workflow_disabled.wait_for_absent()
+        workflow_run.run_error.assert_absent_or_hidden()
+        self.workflow_run_submit()
+        element = workflow_run.run_error.wait_for_present()
+        assert "input must start with moocow" in element.text
+
+    @selenium_test
+    def test_int_parameter_minimum_validation(self):
+        editor = self.components.workflow_editor
+        workflow_run = self.components.workflow_run
+
+        parameter_name = "int_param"
+        name = self.create_and_wait_for_new_workflow_in_editor()
+        self.workflow_editor_add_input("parameter_input")
+        editor.label_input.wait_for_and_send_keys(parameter_name)
+        select_field = self.components.tool_form.parameter_select(parameter="parameter_definition|parameter_type")
+        self.select_set_value(select_field, "integer")
+        self.components.tool_form.parameter_input(parameter="parameter_definition|min").wait_for_and_send_keys("4")
+        self.save_after_node_form_changes()
+
+        self.workflow_run_with_name(name)
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
+        input_element.send_keys("3")
+        workflow_run.run_workflow_disabled.wait_for_absent()
+        workflow_run.run_error.assert_absent_or_hidden()
+        self.workflow_run_submit()
+        element = workflow_run.run_error.wait_for_present()
+        # follow up with a bigger PR to just make this (4 <= value) right? need to set default message
+        # in parameter validators
+        assert "Value ('3') must fulfill (4 <= value <= +infinity)" in element.text, element.text
+
+    @selenium_test
+    def test_float_parameter_maximum_validation(self):
+        editor = self.components.workflow_editor
+        workflow_run = self.components.workflow_run
+
+        parameter_name = "float_param"
+        name = self.create_and_wait_for_new_workflow_in_editor()
+        self.workflow_editor_add_input("parameter_input_float")
+        editor.label_input.wait_for_and_send_keys(parameter_name)
+        self.components.tool_form.parameter_input(parameter="parameter_definition|max").wait_for_and_send_keys("3.14")
+        self.save_after_node_form_changes()
+
+        self.workflow_run_with_name(name)
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        input_element = workflow_run.simplified_input(label=parameter_name).wait_for_and_click()
+        input_element.send_keys("3.2")
+        workflow_run.run_workflow_disabled.wait_for_absent()
+        workflow_run.run_error.assert_absent_or_hidden()
+        self.workflow_run_submit()
+        element = workflow_run.run_error.wait_for_present()
+        # see message in test test_int_parameter_minimum_validation about making this a little more human
+        # friendly.
+        assert "Value ('3.2') must fulfill (-infinity <= value <= 3.14)" in element.text, element.text
 
     @selenium_test
     def test_optional_select_data_field(self):
@@ -121,9 +185,7 @@ class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
         node.title.wait_for_and_click()
         self.components.tool_form.parameter_checkbox(parameter="select_single").wait_for_and_click()
         self.components.tool_form.parameter_input(parameter="select_single").wait_for_and_send_keys("parameter value")
-        # onSetData does an extra POST to build_modules, so we need to wait for that ...
-        self.sleep_for(self.wait_types.UX_RENDER)
-        self.assert_workflow_has_changes_and_save()
+        self.save_after_node_form_changes()
         workflow = self.workflow_populator.download_workflow(workflow_id)
         tool_state = json.loads(workflow["steps"]["0"]["tool_state"])
         assert tool_state["select_single"] == "parameter value"
@@ -269,6 +331,7 @@ steps:
         editor = self.components.workflow_editor
 
         tool_node = editor.node._(label="tool_exec")
+        tool_node.wait_for_and_click()
         tool_input = tool_node.input_terminal(name="inttest")
         self.hover_over(tool_input.wait_for_visible())
         tool_node.connector_destroy_callout(name="inttest").wait_for_and_click()
@@ -474,7 +537,8 @@ steps:
         self.workflow_index_open_with_name(name)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.screenshot("workflow_editor_edit_menu")
-        self.workflow_editor_click_option("Save As")
+
+        self.components.workflow_editor.save_as_activity.wait_for_and_click()
 
     @selenium_test
     def test_editor_tool_upgrade(self):
@@ -546,7 +610,7 @@ steps:
         self.components.workflows.edit_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
-        self.assert_modal_has_text("parameter 'inttest': an integer or workflow parameter is required")
+        self.assert_modal_has_text("Parameter 'inttest': an integer or workflow parameter is required")
         self.screenshot("workflow_editor_subworkflow_tool_upgrade")
         self.components.workflow_editor.modal_button_continue.wait_for_and_click()
         self.assert_workflow_has_changes_and_save()
@@ -704,6 +768,8 @@ steps:
         editor.remove_tags_input.wait_for_and_send_keys("#oldboringtag" + Keys.ENTER + Keys.ESCAPE)
         self.sleep_for(self.wait_types.UX_RENDER)
         cat_node.clone.wait_for_and_click()
+        cloned_node = editor.node.by_id(id=2)
+        cloned_node.wait_for_and_click()
         editor.label_input.wait_for_and_send_keys(Keys.BACKSPACE * 20)
         editor.label_input.wait_for_and_send_keys("cloned label")
         output_label = editor.label_output(output="out_file1")
@@ -745,9 +811,7 @@ steps:
         self.components.workflows.edit_button.wait_for_and_click()
         editor = self.components.workflow_editor
         editor.canvas_body.wait_for_visible()
-        editor.tool_menu.wait_for_visible()
-        editor.tool_menu_section_link(section_name="workflows").wait_for_and_click()
-        editor.workflow_link(workflow_title=child_workflow_name).wait_for_and_click()
+        self.workflow_editor_add_subworkflow(child_workflow_name)
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_workflow_has_changes_and_save()
         workflow = self.workflow_populator.download_workflow(parent_workflow_id)
@@ -771,9 +835,7 @@ steps:
         self.workflow_editor_add_input(item_name="data_input")
         editor = self.components.workflow_editor
         editor.canvas_body.wait_for_visible()
-        editor.tool_menu.wait_for_visible()
-        editor.tool_menu_section_link(section_name="workflows").wait_for_and_click()
-        editor.insert_steps(workflow_title=steps_to_insert).wait_for_and_click()
+        self.workflow_editor_add_steps(steps_to_insert)
         self.assert_connected("input1#output", "first_cat#input1")
         self.assert_workflow_has_changes_and_save()
         workflow_id = self.driver.current_url.split("id=")[1]
@@ -789,14 +851,15 @@ steps:
         param_type_element = editor.param_type_form.wait_for_present()
         self.switch_param_type(param_type_element, "Boolean")
         editor.label_input.wait_for_and_send_keys("param_input")
-        editor.tool_menu.wait_for_visible()
         # Insert cat tool
         self.tool_open("cat")
         self.sleep_for(self.wait_types.UX_RENDER)
         editor.label_input.wait_for_and_send_keys("downstream_step")
         # Insert head tool
         self.tool_open("head")
-        self.workflow_editor_click_option("Auto Layout")
+
+        self.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
+
         self.sleep_for(self.wait_types.UX_RENDER)
         editor.label_input.wait_for_and_send_keys("conditional_step")
         # Connect head to cat
@@ -846,7 +909,7 @@ steps:
         param_type_element = editor.param_type_form.wait_for_present()
         self.switch_param_type(param_type_element, "Boolean")
         editor.label_input.wait_for_and_send_keys("param_input")
-        self.workflow_editor_click_option("Auto Layout")
+        self.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         conditional_node = editor.node._(label=child_workflow_name)
         conditional_node.wait_for_and_click()
@@ -858,7 +921,9 @@ steps:
         self.assert_workflow_has_changes_and_save()
 
     def switch_param_type(self, element, param_type):
-        self.action_chains().move_to_element(element).click().send_keys(param_type).send_keys(Keys.ENTER).perform()
+        self.action_chains().move_to_element(element).click().pause(1).send_keys(param_type).pause(1).send_keys(
+            Keys.ENTER
+        ).perform()
 
     @selenium_test
     def test_editor_invalid_tool_state(self):
@@ -890,33 +955,6 @@ steps:
         self.assert_modal_has_text("Tool is not installed")
         self.screenshot("workflow_editor_missing_tool")
 
-    @selenium_test
-    def test_workflow_bookmarking(self):
-        @retry_during_transitions
-        def assert_workflow_bookmarked_status(target_status):
-            name_matches = [c.text == new_workflow_name for c in self.components.tool_panel.workflow_names.all()]
-            status = any(name_matches)
-            assert status == target_status
-
-        new_workflow_name = self.workflow_create_new(clear_placeholder=True)
-
-        # Assert workflow not initially bookmarked.
-        assert_workflow_bookmarked_status(False)
-
-        self.components.workflow_editor.canvas_body.wait_for_visible()
-        self.wait_for_selector_absent_or_hidden(self.modal_body_selector())
-        self.components.masthead.workflow.wait_for_and_click()
-
-        self.sleep_for(self.wait_types.UX_RENDER)
-        self.components.workflows.bookmark_link(action="add").wait_for_and_click()
-        self.components.masthead.workflow.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_TRANSITION)
-
-        # search for bookmark in tools menu
-        self.components.tool_panel.search.wait_for_and_send_keys(new_workflow_name)
-        self.sleep_for(self.wait_types.UX_RENDER)
-        assert_workflow_bookmarked_status(True)
-
     def tab_to(self, accessible_name, direction="forward"):
         for _ in range(100):
             ac = self.action_chains()
@@ -1224,8 +1262,6 @@ steps:
         self.workflow_create_new(annotation="simple workflow")
         self.sleep_for(self.wait_types.UX_RENDER)
 
-        editor.tool_menu.wait_for_visible()
-
         self.tool_open("cat")
         self.sleep_for(self.wait_types.UX_RENDER)
         editor.label_input.wait_for_and_send_keys("tool_node")
@@ -1271,6 +1307,7 @@ steps:
         self.mouse_drag(from_element=tool_node, to_element=canvas, to_offset=(0, -100))
 
         # select the node
+        editor.node_inspector_close.wait_for_and_click()
         self.action_chains().move_to_element(tool_node).key_down(Keys.SHIFT).click().key_up(Keys.SHIFT).perform()
         self.sleep_for(self.wait_types.UX_RENDER)
 
@@ -1334,6 +1371,17 @@ steps:
 
         assert editor.tool_bar.selection_count.wait_for_visible().text.find("1 comment") != -1
 
+    def create_and_wait_for_new_workflow_in_editor(self, annotation: Optional[str] = None) -> str:
+        editor = self.components.workflow_editor
+        name = self.workflow_create_new(annotation=annotation)
+        editor.canvas_body.wait_for_visible()
+        return name
+
+    def save_after_node_form_changes(self):
+        # onSetData does an extra POST to build_modules, so we need to wait for that ...
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.assert_workflow_has_changes_and_save()
+
     def get_node_position(self, label: str):
         node = self.components.workflow_editor.node._(label=label).wait_for_present()
 
@@ -1382,12 +1430,14 @@ steps:
         self.click_center()
 
     def workflow_editor_maximize_center_pane(self, collapse_left=True, collapse_right=True):
-        if collapse_left:
-            self.hover_over(self.components._.left_panel_drag.wait_for_visible())
-            self.components._.left_panel_collapse.wait_for_and_click()
-        if collapse_right:
-            self.hover_over(self.components._.right_panel_drag.wait_for_visible())
-            self.components._.right_panel_collapse.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        editor = self.components.workflow_editor
+
+        if collapse_right and not editor.node_inspector.is_absent:
+            editor.node_inspector_close.wait_for_and_click()
+        if collapse_left and not self.components._.active_nav_item.is_absent:
+            self.components._.active_nav_item.wait_for_and_click()
+
         self.sleep_for(self.wait_types.UX_RENDER)
 
     def workflow_editor_connect(self, source, sink, screenshot_partial=None):
@@ -1420,7 +1470,7 @@ steps:
         self.workflow_index_open()
         self.workflow_index_open_with_name(name)
         if auto_layout:
-            self.workflow_editor_click_option("Auto Layout")
+            self.components.workflow_editor.tool_bar.auto_layout.wait_for_and_click()
             self.sleep_for(self.wait_types.UX_RENDER)
         return name
 
@@ -1447,16 +1497,6 @@ steps:
 
         return source_id, sink_id
 
-    def workflow_editor_add_input(self, item_name="data_input"):
-        editor = self.components.workflow_editor
-
-        # Make sure we're on the workflow editor and not clicking the main tool panel.
-        editor.canvas_body.wait_for_visible()
-
-        editor.tool_menu.wait_for_visible()
-        editor.tool_menu_section_link(section_name="inputs").wait_for_and_click()
-        editor.tool_menu_item_link(item_name=item_name).wait_for_and_click()
-
     def workflow_editor_destroy_connection(self, sink):
         editor = self.components.workflow_editor
 
@@ -1485,12 +1525,6 @@ steps:
         self.workflow_index_search_for(name)
         self.components.workflows.edit_button.wait_for_and_click()
 
-    def workflow_upload_yaml_with_random_name(self, content):
-        workflow_populator = self.workflow_populator
-        name = self._get_random_name()
-        workflow_populator.upload_yaml_workflow(content, name=name)
-        return name
-
     @retry_assertion_during_transitions
     def assert_wf_name_is(self, expected_name):
         edit_name_element = self.components.workflow_editor.edit_name.wait_for_visible()
diff --git a/lib/galaxy_test/selenium/test_workflow_invocation_details.py b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
index 6d98905b852854fa54c4084f76c50b2d12cd643f..6d9f3a7acb052f4abff67d55f764947b258968c5 100644
--- a/lib/galaxy_test/selenium/test_workflow_invocation_details.py
+++ b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
@@ -16,25 +16,31 @@ class TestWorkflowInvocationDetails(SeleniumTestCase):
         gx_selenium_context.workflow_populator.run_workflow(
             WORKFLOW_WITH_OUTPUT_COLLECTION, history_id=history_id, assert_ok=True, wait=True
         )
-        gx_selenium_context.navigate_to_invocations()
+
+        # open invocations panel
+        self.home()
+        gx_selenium_context.components.invocations.activity.wait_for_and_click()
+
         invocations = gx_selenium_context.components.invocations
-        invocations.invocations_table.wait_for_visible()
+        invocations.invocations_panel_list.wait_for_visible()
 
         @retry_assertion_during_transitions
         def assert_has_row():
-            invocations.invocations_table_rows.wait_for_visible()
-            invocation_rows = invocations.invocations_table_rows.all()
+            invocations.invocations_panel_list_items.wait_for_visible()
+            invocation_rows = invocations.invocations_panel_list_items.all()
             assert len(invocation_rows) > 0
             return invocation_rows[0]
 
         assert_has_row()
 
         invocations.state_details.assert_absent()
-        invocations.toggle_invocation_details.wait_for_visible()
-        details = invocations.toggle_invocation_details.all()[0]
+        details = invocations.invocations_panel_list_items.all()[0]
         details.click()
         invocations.state_details.wait_for_visible()
 
+        # close invocations panel
+        gx_selenium_context.components.invocations.activity.wait_for_and_click()
+
         @retry_assertion_during_transitions
         def assert_progress_steps_note_contains(text):
             assert text in invocations.progress_steps_note.wait_for_visible().text
@@ -46,23 +52,16 @@ class TestWorkflowInvocationDetails(SeleniumTestCase):
         invocations.input_details_title(label="text_input").wait_for_visible()
         assert "Test_Dataset" in invocations.input_details_name(label="text_input").wait_for_visible().text
 
-        invocations.invocation_tab(label="Overview").wait_for_and_click()
-        invocations.hide_invocation_graph.wait_for_and_click()
+        invocations.invocation_tab(label="Steps").wait_for_and_click()
         assert "Step 1: text_input" in invocations.step_title(order_index="0").wait_for_visible().text
         assert "Step 2: split_up" in invocations.step_title(order_index="1").wait_for_visible().text
         assert "Step 3: paired" in invocations.step_title(order_index="2").wait_for_visible().text
 
         invocations.step_details(order_index="1").wait_for_and_click()
-        invocations.step_job_details(order_index="1").wait_for_and_click()
-        invocations.step_job_table(order_index="1").wait_for_visible()
-        invocations.step_job_table_rows(order_index="1").wait_for_visible()
-        job_rows = invocations.step_job_table_rows(order_index="1").all()
-        assert len(job_rows) == 1
-
-        invocations.step_job_information(order_index="1").assert_absent()
-        job_rows[0].click()
+        invocations.step_job_details(order_index="1").wait_for_visible()
+
         self.sleep_for(self.wait_types.UX_RENDER)
-        self.screenshot("invocations_job_table")
+        self.screenshot("invocation_step_jobs")
 
         invocations.step_job_information(order_index="1").wait_for_visible()
         assert (
@@ -70,7 +69,7 @@ class TestWorkflowInvocationDetails(SeleniumTestCase):
             in invocations.step_job_information_tool_id(order_index="1").wait_for_visible().text
         )
 
-        invocations.step_output_collection(order_index="1").wait_for_and_click()
+        invocations.step_output_collection(order_index="1").wait_for_visible()
         invocations.step_output_collection_toggle(order_index="1").wait_for_and_click()
         invocations.step_output_collection_element_identifier(element_identifier="forward").wait_for_and_click()
         datatype = invocations.step_output_collection_element_datatype(order_index="1").wait_for_text()
diff --git a/lib/galaxy_test/selenium/test_workflow_landing.py b/lib/galaxy_test/selenium/test_workflow_landing.py
new file mode 100644
index 0000000000000000000000000000000000000000..9927c383bb5efeb2deee070df840314495db457a
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_workflow_landing.py
@@ -0,0 +1,63 @@
+from typing import Literal
+
+from galaxy.schema.schema import CreateWorkflowLandingRequestPayload
+from .framework import (
+    managed_history,
+    RunsWorkflows,
+    selenium_test,
+    SeleniumTestCase,
+)
+
+
+class TestWorkflowLanding(SeleniumTestCase, RunsWorkflows):
+    ensure_registered = True
+
+    @selenium_test
+    @managed_history
+    def test_private_request(self):
+        self._create_landing_and_run(public="false")
+
+    @selenium_test
+    @managed_history
+    def test_pubblic_request(self):
+        self._create_landing_and_run(public="true")
+
+    def _create_landing_and_run(self, public: Literal["false", "true"]):
+        self.perform_upload(self.get_filename("1.txt"))
+        self.wait_for_history()
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  input_int: integer
+  input_data: data
+steps:
+  simple_constructs:
+    tool_id: simple_constructs
+    label: tool_exec
+    in:
+      inttest: input_int
+      files_0|file: input_data
+""",
+            name=self._get_random_name("landing_wf"),
+        )
+        if public == "true":
+            client_secret = None
+        else:
+            client_secret = "abcdefg"
+        landing_request_payload = CreateWorkflowLandingRequestPayload(
+            workflow_id=workflow_id,
+            workflow_target_type="stored_workflow",
+            request_state={"input_int": 321123},
+            public=public,
+            client_secret=client_secret,
+        )
+        landing_request = self.dataset_populator.create_workflow_landing(landing_request_payload)
+        self.go_to_workflow_landing(str(landing_request.uuid), public="false", client_secret=client_secret)
+        self.screenshot("workflow_run_private_landing")
+        self.workflow_run_submit()
+        output_hid = 2
+        self.workflow_run_wait_for_ok(hid=output_hid)
+        history_id = self.current_history_id()
+        content = self.dataset_populator.get_history_dataset_content(history_id, hid=output_hid)
+        assert "321123" in content, content
diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py
index 047681aa0f45528b9de9331d1a2ee82187aa6b3e..36a4a60af0802a403787a3119ab0f536f6cb024d 100644
--- a/lib/galaxy_test/selenium/test_workflow_run.py
+++ b/lib/galaxy_test/selenium/test_workflow_run.py
@@ -32,6 +32,54 @@ from .framework import (
 class TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows):
     ensure_registered = True
 
+    @selenium_test
+    @managed_history
+    def test_workflow_export_file_rocrate(self):
+        self._setup_simple_invocation_for_export_testing()
+        invocations = self.components.invocations
+        self.workflow_run_wait_for_ok(hid=2)
+        invocations.export_tab.wait_for_and_click()
+        self.screenshot("invocation_export_formats")
+        invocations.export_output_format(type="ro-crate").wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        download_option = invocations.export_destination(destination="download")
+        download_option.wait_for_present()
+        self.screenshot("invocation_export_rocrate_destinations")
+        download_option.wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        export_button = invocations.wizard_export_button
+        export_button.wait_for_present()
+        self.screenshot("invocation_export_rocrate_download_options")
+        export_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.screenshot("invocation_export_crate_preparing_download")
+        invocations.export_download_link.wait_for_present()
+        self.screenshot("invocation_export_crate_download_ready")
+
+    @selenium_test
+    @managed_history
+    def test_workflow_export_file_native(self):
+        self._setup_simple_invocation_for_export_testing()
+        invocations = self.components.invocations
+        self.workflow_run_wait_for_ok(hid=2)
+        invocations.export_tab.wait_for_and_click()
+        self.screenshot("invocation_export_formats")
+        invocations.export_output_format(type="default-file").wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        download_option = invocations.export_destination(destination="download")
+        download_option.wait_for_present()
+        self.screenshot("invocation_export_native_destinations")
+        download_option.wait_for_and_click()
+        invocations.wizard_next_button.wait_for_and_click()
+        export_button = invocations.wizard_export_button
+        export_button.wait_for_present()
+        self.screenshot("invocation_export_native_download_options")
+        export_button.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+        self.screenshot("invocation_export_native_preparing_download")
+        invocations.export_download_link.wait_for_present()
+        self.screenshot("invocation_export_native_download_ready")
+
     @selenium_test
     @managed_history
     def test_simple_execution(self):
@@ -75,6 +123,29 @@ class TestWorkflowRun(SeleniumTestCase, UsesHistoryItemAssertions, RunsWorkflows
 
         self._assert_has_3_lines_after_run(hid=2)
 
+    @selenium_test
+    @managed_history
+    def test_runtime_parameters_simple_optional(self):
+        self.workflow_run_open_workflow(
+            """
+class: GalaxyWorkflow
+inputs: {}
+steps:
+  int_step:
+    tool_id: expression_null_handling_integer
+    runtime_inputs:
+      - int_input
+"""
+        )
+        self.tool_parameter_div("int_input")
+        self._set_num_lines_to_3("int_input")
+        self.screenshot("workflow_run_optional_runtime_parameters_modified")
+        self.workflow_run_submit()
+        self.workflow_run_wait_for_ok(hid=1)
+        history_id = self.current_history_id()
+        content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
+        assert json.loads(content) == 3
+
     @selenium_test
     @managed_history
     def test_subworkflows_expanded(self):
@@ -353,3 +424,13 @@ steps: {}
         assert initial_value == "", initial_value
         input_element.clear()
         input_element.send_keys(value)
+
+    def _setup_simple_invocation_for_export_testing(self):
+        # precondition: refresh history
+        self.perform_upload(self.get_filename("1.fasta"))
+        self.wait_for_history()
+        self.workflow_run_open_workflow(WORKFLOW_SIMPLE_CAT_TWICE)
+        self.workflow_run_submit()
+        history_id = self.current_history_id()
+        self.workflow_populator.wait_for_history_workflows(history_id, expected_invocation_count=1)
+        return self.workflow_populator.history_invocations(history_id)[0]
diff --git a/lib/galaxy_test/workflow/__init__.py b/lib/galaxy_test/workflow/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..2355ab50ab9af4656574eb980e1b128ace9dffef
--- /dev/null
+++ b/lib/galaxy_test/workflow/__init__.py
@@ -0,0 +1,7 @@
+"""Framework tests for checking workflow correctness and defining expected workflow behavior.
+
+This is meant to grow into the workflow based mirror of what the framework tests are for tools.
+api/test_workflows.py is still the place to test exceptional conditions, errors, etc... but tests
+of normal operation where semantics can be verified with simple inputs and outputs can now be
+placed in here.
+"""
diff --git a/lib/galaxy_test/workflow/conftest.py b/lib/galaxy_test/workflow/conftest.py
new file mode 100644
index 0000000000000000000000000000000000000000..1075bb4a374dd21a0438003226288e9854a41739
--- /dev/null
+++ b/lib/galaxy_test/workflow/conftest.py
@@ -0,0 +1,22 @@
+import os
+
+import pytest
+
+from galaxy_test.driver.driver_util import GalaxyTestDriver
+
+
+class ConfigObject:
+    framework_tool_and_types = True
+
+
+@pytest.fixture(scope="session")
+def real_driver():
+    if not os.environ.get("GALAXY_TEST_ENVIRONMENT_CONFIGURED"):
+        driver = GalaxyTestDriver()
+        driver.setup(ConfigObject)
+        try:
+            yield driver
+        finally:
+            driver.tear_down()
+    else:
+        yield None
diff --git a/lib/galaxy_test/workflow/default_values.gxwf-tests.yml b/lib/galaxy_test/workflow/default_values.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f5f7de07fee714ff2380960509d3af4c19c22b23
--- /dev/null
+++ b/lib/galaxy_test/workflow/default_values.gxwf-tests.yml
@@ -0,0 +1,35 @@
+- doc: |
+    Test that default value doesn't need to be supplied
+  job: {}
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
+- doc: |
+    Test that explicit null is not replaced and fails
+  expect_failure: true
+  job:
+    required_int_with_default:
+      type: raw
+      value: null
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
+- doc: |
+    Test that empty string is not replaced and fails
+  expect_failure: true
+  job:
+    required_int_with_default:
+      type: raw
+      value: ""
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
diff --git a/lib/galaxy_test/workflow/default_values.gxwf.yml b/lib/galaxy_test/workflow/default_values.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..db89c2bedd7dd875afa839889fcbb2cfabb4d152
--- /dev/null
+++ b/lib/galaxy_test/workflow/default_values.gxwf.yml
@@ -0,0 +1,17 @@
+class: GalaxyWorkflow
+inputs:
+  required_int_with_default:
+    type: int
+    default: 1
+outputs:
+  out:
+    outputSource: integer_default/out_file1
+steps:
+  integer_default:
+    tool_id: integer_default
+    tool_state:
+      input1: 0
+      input2: 0
+    in:
+      input3:
+        source: required_int_with_default
diff --git a/lib/galaxy_test/workflow/default_values_optional.gxwf-tests.yml b/lib/galaxy_test/workflow/default_values_optional.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9cd1d0abc328c08df186458deed66671e34b81b7
--- /dev/null
+++ b/lib/galaxy_test/workflow/default_values_optional.gxwf-tests.yml
@@ -0,0 +1,35 @@
+- doc: |
+    Test that default value doesn't need to be supplied
+  job: {}
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
+- doc: |
+    Test that explicit null is not replaced and fails
+  expect_failure: true
+  job:
+    optional_int_with_default:
+      type: raw
+      value: null
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
+- doc: |
+    Test that empty string is not replaced and fails
+  expect_failure: true
+  job:
+    optional_int_with_default:
+      type: raw
+      value: ""
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "1"
diff --git a/lib/galaxy_test/workflow/default_values_optional.gxwf.yml b/lib/galaxy_test/workflow/default_values_optional.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4df2e2528cc539b5677d2a2ffd50b7010e232ac7
--- /dev/null
+++ b/lib/galaxy_test/workflow/default_values_optional.gxwf.yml
@@ -0,0 +1,18 @@
+class: GalaxyWorkflow
+inputs:
+  optional_int_with_default:
+    type: int
+    default: 1
+    optional: true
+outputs:
+  out:
+    outputSource: integer_default/out_file1
+steps:
+  integer_default:
+    tool_id: integer_default
+    tool_state:
+      input1: 0
+      input2: 0
+    in:
+      input3:
+        source: optional_int_with_default
diff --git a/lib/galaxy_test/workflow/directory_index.gxwf-tests.yml b/lib/galaxy_test/workflow/directory_index.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e5c74e6658a052c6fc29812ee4bd375a1db61668
--- /dev/null
+++ b/lib/galaxy_test/workflow/directory_index.gxwf-tests.yml
@@ -0,0 +1,22 @@
+- doc: |
+    Test that passing directory indexes works
+  job:
+    reference:
+      type: File
+      value: 1.fasta
+      file_type: fasta
+  outputs:
+    output:
+      class: File
+      file: 1.fasta
+- doc: |
+    Test that uploading index works
+  job:
+    reference:
+      type: Directory
+      file_type: bwa_mem2_index
+      value: bwa_mem2_index
+  outputs:
+    output:
+      class: File
+      file: 1.fasta
diff --git a/lib/galaxy_test/workflow/directory_index.gxwf.yml b/lib/galaxy_test/workflow/directory_index.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..2dbca18630d3d3922a1201a8d8748fc1f5f092fa
--- /dev/null
+++ b/lib/galaxy_test/workflow/directory_index.gxwf.yml
@@ -0,0 +1,36 @@
+class: GalaxyWorkflow
+inputs:
+  reference:
+    type: data
+    format:
+      - fasta
+      - bwa_mem2_index
+outputs:
+  output:
+    outputSource: use_index/output
+steps:
+  create_index:
+    tool_id: create_directory_index
+    when: $(inputs.reference.format != "bwa_mem2_index" )
+    in:
+      reference:
+        source: reference
+  pick_value:
+    tool_id: pick_value
+    in:
+      style_cond|type_cond|pick_from_0|value:
+        source: create_index/index
+      style_cond|type_cond|pick_from_1|value:
+        source: reference
+    tool_state:
+      style_cond:
+        pick_style: first
+        type_cond:
+          param_type: data
+          pick_from:
+          - value: create_index/index
+          - value: reference
+  use_index:
+    tool_id: use_directory_index
+    in:
+      reference: pick_value/data_param
diff --git a/lib/galaxy_test/workflow/empty_collection_sort.gxwf-tests.yml b/lib/galaxy_test/workflow/empty_collection_sort.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d5ac9d9b15b458e1da65095f7629b0fe14670e24
--- /dev/null
+++ b/lib/galaxy_test/workflow/empty_collection_sort.gxwf-tests.yml
@@ -0,0 +1,18 @@
+- doc: | 
+    Test to verify collection operations like the sort tool work fine with empty collections.
+  job:
+    input:
+      collection_type: list
+      elements:
+      - identifier: i1
+        content: "0"
+    filter_file: i1
+  outputs:
+    output:
+      class: Collection
+      collection_type: list
+      elements:
+        i1:
+          asserts:
+          - that: has_text
+            text: "0"
diff --git a/lib/galaxy_test/workflow/empty_collection_sort.gxwf.yml b/lib/galaxy_test/workflow/empty_collection_sort.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7520bcd5d68f0dfaeb25dd569b0b0b030b79c68e
--- /dev/null
+++ b/lib/galaxy_test/workflow/empty_collection_sort.gxwf.yml
@@ -0,0 +1,26 @@
+class: GalaxyWorkflow
+inputs:
+  input: collection
+  filter_file: data
+outputs:
+  output:
+    outputSource: merge_collection/output
+steps:
+  filter_collection:
+    tool_id: __FILTER_FROM_FILE__
+    in:
+       input: input
+       how|filter_source: filter_file
+  sort_collection_1:
+    tool_id: __SORTLIST__
+    in:
+      input: filter_collection/output_filtered
+  sort_collection_2:
+    tool_id: __SORTLIST__
+    in:
+      input: filter_collection/output_discarded
+  merge_collection:
+    tool_id: __MERGE_COLLECTION__
+    in:
+      inputs_0|input: sort_collection_1/output
+      inputs_1|input: sort_collection_2/output
diff --git a/lib/galaxy_test/workflow/filter_null.gxwf-tests.yml b/lib/galaxy_test/workflow/filter_null.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7572b8c5c623830996f2aefb8192b9df66e63842
--- /dev/null
+++ b/lib/galaxy_test/workflow/filter_null.gxwf-tests.yml
@@ -0,0 +1,32 @@
+- doc: |
+    Test to verify filter null tool keeps non-null datasets.
+  job:
+    input_collection:
+      collection_type: list
+      elements:
+        - identifier: first
+          content: "abc"
+    when:
+      value: true
+      type: raw
+  outputs:
+    out:
+      class: Collection
+      collection_type: list
+      element_count: 1
+- doc: |
+    Test to verify filter null tool discards null datasets.
+  job:
+    input_collection:
+      collection_type: list
+      elements:
+        - identifier: first
+          content: "abc"
+    when:
+      value: false
+      type: raw
+  outputs:
+    out:
+      class: Collection
+      collection_type: list
+      element_count: 0
diff --git a/lib/galaxy_test/workflow/filter_null.gxwf.yml b/lib/galaxy_test/workflow/filter_null.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b2e35edc36c067a6efa78cc721da3290a55a82ca
--- /dev/null
+++ b/lib/galaxy_test/workflow/filter_null.gxwf.yml
@@ -0,0 +1,22 @@
+class: GalaxyWorkflow
+inputs:
+  input_collection:
+    type: data_collection
+  when:
+    type: boolean
+outputs:
+  out:
+    outputSource: filter_null/output
+steps:
+  cat:
+    tool_id: cat
+    in:
+      input1:
+        source: input_collection
+      when:
+        source: when
+    when: $(inputs.when)
+  filter_null:
+    tool_id: '__FILTER_NULL__'
+    in:
+      input: cat/out_file1
diff --git a/lib/galaxy_test/workflow/flatten_collection.gxwf-tests.yml b/lib/galaxy_test/workflow/flatten_collection.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7af6cff256bcfd0ad8a44ecf3994d897a068053d
--- /dev/null
+++ b/lib/galaxy_test/workflow/flatten_collection.gxwf-tests.yml
@@ -0,0 +1,20 @@
+- doc: | 
+    Test to verify collection flatten collection operation in the context of a workflow.
+  job: {}
+  outputs:
+    out:
+      class: Collection
+      collection_type: list
+      elements:
+        'oe1-ie1':
+          asserts:
+          - that: has_text
+            text: "A"
+        'oe1-ie2':
+          asserts:
+          - that: has_text
+            text: "B"
+        'oe2-ie1':
+          asserts:
+          - that: has_text
+            text: "C"
diff --git a/lib/galaxy_test/workflow/flatten_collection.gxwf.yml b/lib/galaxy_test/workflow/flatten_collection.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..993bd9dac005ed4d8477bcdc22454ea5a319b7c5
--- /dev/null
+++ b/lib/galaxy_test/workflow/flatten_collection.gxwf.yml
@@ -0,0 +1,17 @@
+class: GalaxyWorkflow
+inputs: {}
+outputs:
+  out:
+    outputSource: flatten/output
+steps:
+  nested:
+    tool_id: collection_creates_dynamic_nested
+    state:
+      sleep_time: 0
+      foo: 'dummy'
+  flatten:
+    tool_id: '__FLATTEN__'
+    state:
+      join_identifier: '-'
+    in:
+      input: nested/list_output
diff --git a/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf-tests.yml b/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..85d986adbb108318767031b9104ae11496b53dad
--- /dev/null
+++ b/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf-tests.yml
@@ -0,0 +1,21 @@
+- doc: | 
+    Test to verify collection flatten collection operation mid workflow.
+  job:
+    input_fastqs:
+      collection_type: list
+      elements:
+        - identifier: samp1
+          content: "0 mycoolline\n1 mysecondline\n"
+  outputs:
+    out:
+      class: Collection
+      collection_type: list
+      elements:
+        'samp1-0':
+          asserts:
+          - that: has_text
+            text: "mycoolline"
+        'samp1-1':
+          asserts:
+          - that: has_text
+            text: "mysecondline"
diff --git a/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf.yml b/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..172eaa7d4b2669405b0df4eaa5cf1d812dfc0f6a
--- /dev/null
+++ b/lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf.yml
@@ -0,0 +1,17 @@
+class: GalaxyWorkflow
+inputs:
+  input_fastqs: collection
+outputs:
+  out:
+    outputSource: flatten/output
+steps:
+  split_up:
+    tool_id: collection_split_on_column
+    in:
+      input1: input_fastqs
+  flatten:
+    tool_id: '__FLATTEN__'
+    state:
+      join_identifier: '-'
+    in:
+      input: split_up/split_output
diff --git a/lib/galaxy_test/workflow/integer_into_data_column.gxwf-tests.yml b/lib/galaxy_test/workflow/integer_into_data_column.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..eae87aa6f314bba3a13c509711e82c453e40caf9
--- /dev/null
+++ b/lib/galaxy_test/workflow/integer_into_data_column.gxwf-tests.yml
@@ -0,0 +1,16 @@
+- doc: |
+    Test to verify text parameter can be connected to data column param
+  job:
+    input:
+      type: File
+      value: 2.tabular
+      file_type: tabular
+    column:
+      value: "2"
+      type: raw
+  outputs:
+    output:
+      class: File
+      asserts:
+        - that: has_line
+          line: "parameter: 2"
diff --git a/lib/galaxy_test/workflow/integer_into_data_column.gxwf.yml b/lib/galaxy_test/workflow/integer_into_data_column.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b665558b0a892d314b5562c02994ecc38f5edc97
--- /dev/null
+++ b/lib/galaxy_test/workflow/integer_into_data_column.gxwf.yml
@@ -0,0 +1,15 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: data
+  column:
+    type: integer
+outputs:
+  output:
+    outputSource: data_column_step/output
+steps:
+  data_column_step:
+    tool_id: gx_data_column
+    in:
+      ref_parameter: input
+      parameter: column
diff --git a/lib/galaxy_test/workflow/map_over_expression.gxwf-tests.yml b/lib/galaxy_test/workflow/map_over_expression.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..7a52cb858c285e6c58c86377cf99592f4b0c689c
--- /dev/null
+++ b/lib/galaxy_test/workflow/map_over_expression.gxwf-tests.yml
@@ -0,0 +1,23 @@
+- doc: |
+    Test to verify text parameter can be connected to data column param
+  job:
+    text_input1:
+      collection_type: list
+      elements:
+        - identifier: A
+          content: A
+        - identifier: B
+          content: B
+  outputs:
+    out1:
+      class: Collection
+      collection_type: list
+      elements:
+        A:
+          asserts:
+            - that: has_line
+              line: A
+        B:
+          asserts:
+            - that: has_line
+              line: B
diff --git a/lib/galaxy_test/workflow/map_over_expression.gxwf.yml b/lib/galaxy_test/workflow/map_over_expression.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c361b2232022c3d4578cec13ac170d6bc480256d
--- /dev/null
+++ b/lib/galaxy_test/workflow/map_over_expression.gxwf.yml
@@ -0,0 +1,18 @@
+class: GalaxyWorkflow
+inputs:
+  text_input1: collection
+outputs:
+  out1:
+    outputSource: consume_expression_parameter/out_file1
+steps:
+  param_out:
+    tool_id: param_value_from_file
+    in:
+      input1: text_input1
+  consume_expression_parameter:
+    tool_id: validation_default
+    in:
+      input1: param_out/text_param
+    outputs:
+      out_file1:
+        rename: "replaced_param_collection"
diff --git a/lib/galaxy_test/workflow/multi_select_mapping.gxwf-tests.yml b/lib/galaxy_test/workflow/multi_select_mapping.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b9857cc306426a1c3fcc91dde2337ad61ec9da6f
--- /dev/null
+++ b/lib/galaxy_test/workflow/multi_select_mapping.gxwf-tests.yml
@@ -0,0 +1,29 @@
+- doc: |
+    Test to verify that mapping a list of a multi-select parameter maps over the job.
+    Ideally there would be a way to specify that the list should be reduced into the
+    parameter. It might work to have an expression tool to combine the list into a
+    string.
+  job:
+    input:
+      type: collection
+      collection_type: list
+      elements:
+        - identifier: the_example_2
+          content: '"ex2"'
+          ext: 'expression.json'
+        - identifier: the_example_5
+          content: '"ex5"'
+          ext: 'expression.json'
+  outputs:
+    output:
+      class: Collection
+      collection_type: list
+      elements:
+        the_example_2:
+          asserts:
+          - that: has_text
+            text: 'ex2'
+        the_example_5:
+          asserts:
+          - that: has_text
+            text: 'ex5'
diff --git a/lib/galaxy_test/workflow/multi_select_mapping.gxwf.yml b/lib/galaxy_test/workflow/multi_select_mapping.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f810d022fb1a79dee48e835d1db8a81eca5fdfc3
--- /dev/null
+++ b/lib/galaxy_test/workflow/multi_select_mapping.gxwf.yml
@@ -0,0 +1,14 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: collection
+    collection_type: list
+outputs:
+  output:
+    outputSource: map_over_multi_select/output2
+steps:
+  map_over_multi_select:
+    tool_id: multi_select
+    in:
+      select_ex: input
+      select_optional: input
diff --git a/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf-tests.yml b/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..365bf7f6de1f3a12e6fb0fb884ed6de3cf0971de
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf-tests.yml
@@ -0,0 +1,16 @@
+- doc: |
+    Test to verify text parameter can be connected to data column param
+  job:
+    input:
+      type: File
+      value: 2.tabular
+      file_type: tabular
+    column:
+      value: [1, 2]
+      type: raw
+  outputs:
+    output:
+      class: File
+      asserts:
+        - that: has_text
+          text: "col 1,2"
diff --git a/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf.yml b/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9778e0aa56764e189e6c3d40c358b9a9b319ce0b
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf.yml
@@ -0,0 +1,16 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: data
+  column:
+    type: [integer]
+outputs:
+  output:
+    outputSource: column_param_list/output2
+steps:
+  column_param_list:
+    tool_id: column_param_list
+    in:
+      input1: input
+      col: column
+      col_names: column
diff --git a/lib/galaxy_test/workflow/multiple_text.gxwf-tests.yml b/lib/galaxy_test/workflow/multiple_text.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..09a7dd89e55707d0b63d4eba19ca69eb955bcbc8
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_text.gxwf-tests.yml
@@ -0,0 +1,15 @@
+- doc: |
+    Test that workflows can run with multiple text parameter fed into a multi select parameter.
+  job:
+    input:
+      value:
+        - --ex1
+        - ex2
+        - --ex3
+      type: raw
+  outputs:
+    output:
+      class: File
+      asserts:
+        - that: has_line
+          line: '--ex1,ex2,--ex3'
diff --git a/lib/galaxy_test/workflow/multiple_text.gxwf.yml b/lib/galaxy_test/workflow/multiple_text.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f62f668ba9b960fa114c79eb343b9a4fc7a5a6d2
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_text.gxwf.yml
@@ -0,0 +1,15 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: [string]
+outputs:
+  output:
+    outputSource: multi_select/output
+steps:
+  multi_select:
+    tool_id: multi_select
+    tool_version: "0.1"
+    in:
+      select_ex: input
+    tool_state:
+      select_optional: null
diff --git a/lib/galaxy_test/workflow/multiple_versions.gxwf-tests.yml b/lib/galaxy_test/workflow/multiple_versions.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bbe2eee671e1d2c047fb812a7764262ff2357336
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_versions.gxwf-tests.yml
@@ -0,0 +1,21 @@
+- doc: | 
+    Test that workflows can run with multiple versions of tools and the version specified matches the one run.
+  job:
+    input:
+      value: 1
+      type: raw
+  outputs:
+    output_1:
+      class: File
+      asserts:
+        - that: has_text
+          text: 'Version 0.1'
+        - that: not_has_text
+          text: 'Version 0.2'
+    output_2:
+      class: File
+      asserts:
+        - that: has_text
+          text: 'Version 0.2'
+        - that: not_has_text
+          text: 'Version 0.1'
diff --git a/lib/galaxy_test/workflow/multiple_versions.gxwf.yml b/lib/galaxy_test/workflow/multiple_versions.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..abcdd44e2ca8c70507497c393dfe62d4c86e1f11
--- /dev/null
+++ b/lib/galaxy_test/workflow/multiple_versions.gxwf.yml
@@ -0,0 +1,20 @@
+class: GalaxyWorkflow
+inputs:
+  input:
+    type: int
+outputs:
+  output_1:
+    outputSource: multiple_1/out_file1
+  output_2:
+    outputSource: multiple_2/out_file1
+steps:
+  multiple_1:
+    tool_id: multiple_versions
+    tool_version: "0.1"
+    in:
+      inttest: input
+  multiple_2:
+    tool_id: multiple_versions
+    tool_version: "0.2"
+    in:
+      inttest: input
diff --git a/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf-tests.yml b/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c531a2b803bbdfe03884293f257f889237435192
--- /dev/null
+++ b/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf-tests.yml
@@ -0,0 +1,12 @@
+- doc: |
+    Test that scheduling succeeds even if step needs rescheduling
+  job:
+    optional_text:
+      type: raw
+      value: null
+  outputs:
+    out:
+      class: File
+      asserts:
+      - that: has_text
+        text: "null"
diff --git a/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf.yml b/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..dbf5a4b57b64dedfaaf52ff0a7bd6385ec99bcb7
--- /dev/null
+++ b/lib/galaxy_test/workflow/optional_text_param_rescheduling.gxwf.yml
@@ -0,0 +1,30 @@
+class: GalaxyWorkflow
+inputs:
+  optional_text:
+    type: text
+    optional: true
+  when:
+    type: boolean
+    default: true
+outputs:
+  out:
+    outputSource: gx_text_optional/inputs_json
+steps:
+  pick_value:
+    tool_id: pick_value
+    tool_state:
+      style_cond:
+        pick_style: first
+        type_cond:
+          param_type: boolean
+          pick_from:
+          - value: true
+  gx_text_optional:
+    tool_id: gx_text_optional
+    # the when expression requires pick_value to execute, which recapitulates https://github.com/galaxyproject/galaxy/issues/19328
+    when: $(inputs.when)
+    in:
+      parameter:
+        source: optional_text
+      when:
+        source: pick_value/boolean_param
diff --git a/lib/galaxy_test/workflow/output_parameter.gxwf-tests.yml b/lib/galaxy_test/workflow/output_parameter.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d422d9e3d8360b93bc46f89f8b9bcf04142e19bd
--- /dev/null
+++ b/lib/galaxy_test/workflow/output_parameter.gxwf-tests.yml
@@ -0,0 +1,8 @@
+- doc: |
+    Test to verify exact output parameter verification works propery.
+  job:
+    text_int:
+      type: File
+      content: "43"
+  outputs:
+    out_int: 43
diff --git a/lib/galaxy_test/workflow/output_parameter.gxwf.yml b/lib/galaxy_test/workflow/output_parameter.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4157f894f49259dd19faada35778b59f74d758f3
--- /dev/null
+++ b/lib/galaxy_test/workflow/output_parameter.gxwf.yml
@@ -0,0 +1,13 @@
+class: GalaxyWorkflow
+inputs:
+  text_int: data
+outputs:
+  out_int:
+    outputSource: param_out/integer_param
+steps:
+  param_out:
+    tool_id: param_value_from_file
+    state:
+      param_type: integer
+    in:
+      input1: text_int
diff --git a/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf-tests.yml b/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9f76add4f57492f93b6fe060d05da9c8419b1481
--- /dev/null
+++ b/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf-tests.yml
@@ -0,0 +1,23 @@
+- doc: | 
+    Test output dataset renaming when the target basename is based on an input collection.
+  job:
+    fasta_input:
+      value: 1.fasta
+      type: File
+      name: fasta1
+      file_type: fasta
+    fastq_inputs:
+      collection_type: list
+      name: the_dataset_pair
+      elements:
+        - identifier: forward
+          value: 1.fastq
+          type: File
+        - identifier: reverse
+          value: 1.fastq
+          type: File
+  outputs:
+    output:
+      class: File
+      metadata:
+        name: 'the_dataset_pair suffix'
diff --git a/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf.yml b/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0d6a19abfdd3c010eb755f9b6a295a0a1592eb16
--- /dev/null
+++ b/lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf.yml
@@ -0,0 +1,20 @@
+class: GalaxyWorkflow
+inputs:
+  fasta_input: data
+  fastq_inputs: data
+outputs:
+  output:
+    outputSource: mapping/out_file1
+steps:
+  mapping:
+    tool_id: mapper2
+    state:
+      fastq_input:
+        fastq_input_selector: paired_collection
+        fastq_input1:
+          $link: fastq_inputs
+      reference:
+        $link: fasta_input
+    outputs:
+      out_file1:
+        rename: "#{fastq_input.fastq_input1 | basename} suffix"
diff --git a/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf-tests.yml b/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b800042dc1a42102a8db65b9f5f61b1914c0870e
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf-tests.yml
@@ -0,0 +1,14 @@
+- doc: |
+    Test to verify legacy behavior of implicit runtime parameters continues to function correctly.
+  job:
+    replacement_parameters:
+      replaceme: moocow
+  outputs:
+    out1:
+      class: File
+      metadata:
+        name: 'moocow name'
+    out2:
+      class: File
+      metadata:
+        name: 'moocow name 2'
diff --git a/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf.yml b/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..834721c3cc2bee75aebd864a65c218cc6512d7ab
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_legacy.gxwf.yml
@@ -0,0 +1,17 @@
+class: GalaxyWorkflow
+inputs: {}
+outputs:
+  out1:
+    outputSource: create_2/out_file1
+  out2:
+    outputSource: create_2/out_file2
+steps:
+  create_2:
+    tool_id: create_2
+    state:
+      sleep_time: 0
+    outputs:
+      out_file1:
+        rename: "${replaceme} name"
+      out_file2:
+        rename: "${replaceme} name 2"
diff --git a/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf-tests.yml b/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f9acae8274f11965ea04ad873f57358cab90fcb4
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf-tests.yml
@@ -0,0 +1,15 @@
+- doc: |
+    Test to verify text parameters can be implicitly used as replacement parameters in subworkflows if they are connected up.
+  job:
+    replacemeouter: 
+      value: moocow
+      type: raw
+  outputs:
+    out1:
+      class: File
+      metadata:
+        name: 'moocow name'
+    out2:
+      class: File
+      metadata:
+        name: 'moocow name 2'
diff --git a/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf.yml b/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d783195ae584f1ae672bf36149217cf5c66e7206
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_nested.gxwf.yml
@@ -0,0 +1,31 @@
+class: GalaxyWorkflow
+inputs:
+  replacemeouter: text
+outputs:
+  out1:
+    outputSource: nested_workflow/workflow_output_1
+  out2: 
+    outputSource: nested_workflow/workflow_output_2
+steps:
+  nested_workflow:
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        replacemeinner: text
+      outputs:
+        workflow_output_1:
+          outputSource: create_2/out_file1
+        workflow_output_2:
+          outputSource: create_2/out_file2
+      steps:
+        create_2:
+          tool_id: create_2
+          state:
+            sleep_time: 0
+          outputs:
+            out_file1:
+              rename: "${replacemeinner} name"
+            out_file2:
+              rename: "${replacemeinner} name 2"
+    in:
+      replacemeinner: replacemeouter
diff --git a/lib/galaxy_test/workflow/replacement_parameters_text.gxwf-tests.yml b/lib/galaxy_test/workflow/replacement_parameters_text.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..fd8dc8eb7bfcfdfac213ee96e29c6c16e7bf0dec
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_text.gxwf-tests.yml
@@ -0,0 +1,15 @@
+- doc: |
+    Test to verify text parameters can be implicitly used as replacement parameters in workflow step PJAs.
+  job:
+    replaceme: 
+      value: moocow
+      type: raw
+  outputs:
+    out1:
+      class: File
+      metadata:
+        name: 'moocow name'
+    out2:
+      class: File
+      metadata:
+        name: 'moocow name 2'
diff --git a/lib/galaxy_test/workflow/replacement_parameters_text.gxwf.yml b/lib/galaxy_test/workflow/replacement_parameters_text.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..18f73aadb699f3fb430819856c52a52c8a63e2bb
--- /dev/null
+++ b/lib/galaxy_test/workflow/replacement_parameters_text.gxwf.yml
@@ -0,0 +1,18 @@
+class: GalaxyWorkflow
+inputs:
+  replaceme: text
+outputs:
+  out1:
+    outputSource: create_2/out_file1
+  out2:
+    outputSource: create_2/out_file2
+steps:
+  create_2:
+    tool_id: create_2
+    state:
+      sleep_time: 0
+    outputs:
+      out_file1:
+        rename: "${replaceme} name"
+      out_file2:
+        rename: "${replaceme} name 2"
diff --git a/lib/galaxy_test/workflow/test_framework_workflows.py b/lib/galaxy_test/workflow/test_framework_workflows.py
new file mode 100644
index 0000000000000000000000000000000000000000..9b22877c19f14b4d1ec18dc77f0a96420818d493
--- /dev/null
+++ b/lib/galaxy_test/workflow/test_framework_workflows.py
@@ -0,0 +1,157 @@
+import glob
+import os
+import tempfile
+from pathlib import Path
+
+import pytest
+import requests
+import yaml
+from gxformat2.yaml import ordered_load
+
+from galaxy.tool_util.models import (
+    OutputChecks,
+    OutputsDict,
+    TestDicts,
+    TestJobDict,
+)
+from galaxy.tool_util.parser.interface import TestCollectionOutputDef
+from galaxy.tool_util.verify import verify_file_contents_against_dict
+from galaxy.tool_util.verify.interactor import (
+    compare_expected_metadata_to_api_response,
+    get_metadata_to_test,
+    verify_collection,
+)
+from galaxy.util import asbool
+from galaxy_test.api._framework import ApiTestCase
+from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+    RunJobsSummary,
+    WorkflowPopulator,
+)
+
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+TEST_WORKFLOW_AFTER_RERUN = asbool(os.environ.get("GALAXY_TEST_WORKFLOW_AFTER_RERUN", "0"))
+
+
+def find_workflows():
+    return [Path(p) for p in glob.glob(f"{SCRIPT_DIRECTORY}/*.gxwf.yml")]
+
+
+def pytest_generate_tests(metafunc):
+    parameter_combinations = []
+    test_ids = []
+    for workflow_path in find_workflows():
+        for index, test_job in enumerate(_test_jobs(workflow_path)):
+            parameter_combinations.append([workflow_path, test_job])
+            workflow_test_name = workflow_path.name[0 : -len(".gxwf.yml")]
+            test_ids.append(f"{workflow_test_name}_{index}")
+    if "workflow_path" in metafunc.fixturenames:
+        metafunc.parametrize("workflow_path,test_job", parameter_combinations, ids=test_ids)
+
+
+class TestWorkflow(ApiTestCase):
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super().setUp()
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+
+    @pytest.mark.workflow
+    def test_workflow(self, workflow_path: Path, test_job: TestJobDict):
+        with workflow_path.open() as f:
+            yaml_content = ordered_load(f)
+        with self.dataset_populator.test_history() as history_id:
+            exc = None
+            try:
+                run_summary = self.workflow_populator.run_workflow(
+                    yaml_content,
+                    test_data=test_job["job"],
+                    history_id=history_id,
+                )
+                if TEST_WORKFLOW_AFTER_RERUN:
+                    run_summary = self.workflow_populator.rerun(run_summary)
+                self._verify(run_summary, test_job["outputs"])
+            except Exception as e:
+                exc = e
+            if test_job.get("expect_failure"):
+                if not exc:
+                    raise Exception("Expected workflow test to fail but it passed")
+            elif exc:
+                raise exc
+
+    def _verify(self, run_summary: RunJobsSummary, output_definitions: OutputsDict):
+        for output_name, output_definition in output_definitions.items():
+            self._verify_output(run_summary, output_name, output_definition)
+
+    def _verify_output(self, run_summary: RunJobsSummary, output_name, test_properties: OutputChecks):
+        is_collection_test = isinstance(test_properties, dict) and (
+            "elements" in test_properties or test_properties.get("class") == "Collection"
+        )
+        item_label = f"Output named {output_name}"
+
+        def get_filename(name: str) -> str:
+            return self.test_data_resolver.get_filename(name)
+
+        def verify_dataset(dataset: dict, test_properties: OutputChecks):
+            output_content = self.dataset_populator.get_history_dataset_content(
+                run_summary.history_id, dataset=dataset, type="bytes"
+            )
+            verify_file_contents_against_dict(get_filename, _get_location, item_label, output_content, test_properties)
+            if isinstance(test_properties, dict):
+                metadata = get_metadata_to_test(test_properties)
+                if metadata:
+                    dataset_details = self.dataset_populator.get_history_dataset_details(
+                        run_summary.history_id, content_id=dataset["id"]
+                    )
+                    compare_expected_metadata_to_api_response(metadata, dataset_details)
+
+        if is_collection_test:
+            assert isinstance(test_properties, dict)
+            test_properties["name"] = output_name
+            output_def = TestCollectionOutputDef.from_yaml_test_format(test_properties)
+            invocation_details = self.workflow_populator.get_invocation(run_summary.invocation_id, step_details=True)
+            assert output_name in invocation_details["output_collections"]
+            test_output = invocation_details["output_collections"][output_name]
+            output_collection = self.dataset_populator.get_history_collection_details(
+                run_summary.history_id, content_id=test_output["id"]
+            )
+
+            def verify_dataset_element(element, test_properties, element_outfile):
+                hda = element["object"]
+                verify_dataset(hda, test_properties)
+
+            verify_collection(output_def, output_collection, verify_dataset_element)
+        else:
+            if isinstance(test_properties, dict):
+                test_properties["name"] = output_name
+            invocation_details = self.workflow_populator.get_invocation(run_summary.invocation_id, step_details=True)
+            assert output_name in invocation_details["outputs"]
+            test_output = invocation_details["outputs"][output_name]
+            verify_dataset(test_output, test_properties)
+
+
+def _test_jobs(workflow_path: Path) -> TestDicts:
+    test_path = _workflow_test_path(workflow_path)
+    with test_path.open() as f:
+        jobs = yaml.safe_load(f)
+    return jobs
+
+
+def _workflow_test_path(workflow_path: Path) -> Path:
+    base_name = workflow_path.name[0 : -len(".gxwf.yml")]
+    test_path = workflow_path.parent / f"{base_name}.gxwf-tests.yml"
+    return test_path
+
+
+def _get_location(location: str) -> str:
+    data_file = tempfile.NamedTemporaryFile(prefix="gx_workflow_framework_test_file_", delete=False)
+    with requests.get(location, stream=True) as r:
+        r.raise_for_status()
+
+        for chunk in r.iter_content():
+            if chunk:
+                data_file.write(chunk)
+        return data_file.name
diff --git a/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml b/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e0e4ffc5ba69b689e50c5518c3f26cee64e6616f
--- /dev/null
+++ b/lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml
@@ -0,0 +1,10 @@
+- doc: | 
+    Test simple use of __ZIP_COLLECTION__ in a workflow.
+  job:
+    test_input_1: "samp1\t10.0\nsamp2\t20.0\n"
+    test_input_2: "samp1\t20.0\nsamp2\t40.0\n"
+  outputs:
+    out:
+      asserts:
+      - that: has_text
+        text: "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0"
diff --git a/lib/galaxy_test/workflow/zip_collection.gxwf.yml b/lib/galaxy_test/workflow/zip_collection.gxwf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..151e0ffd1aa66b0042814c5413a7f6f31be18c0c
--- /dev/null
+++ b/lib/galaxy_test/workflow/zip_collection.gxwf.yml
@@ -0,0 +1,21 @@
+class: GalaxyWorkflow
+inputs:
+  test_input_1: data
+  test_input_2: data
+outputs:
+  out:
+    outputSource: concat_pair/out1
+steps:
+  first_cat:
+    tool_id: cat
+    in:
+      input1: test_input_1
+  zip_it:
+    tool_id: "__ZIP_COLLECTION__"
+    in:
+      input_forward: first_cat/out_file1
+      input_reverse: test_input_2
+  concat_pair:
+    tool_id: collection_paired_test
+    in:
+      f1: zip_it/output
diff --git a/lib/tool_shed/context.py b/lib/tool_shed/context.py
index 613c52b79a364d37cf1b9880512cc3b4cb33367c..b936a7b7bf93a4cfb666b61368d51e02fb0d2cb6 100644
--- a/lib/tool_shed/context.py
+++ b/lib/tool_shed/context.py
@@ -24,7 +24,8 @@ class ProvidesAppContext(Protocol):
     Mixed in class must provide `app` property.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def app(self) -> ToolShedApp:
         """Provide access to the shed ``app`` object."""
 
@@ -54,7 +55,8 @@ class ProvidesUserContext(ProvidesAppContext, Protocol):
     properties.
     """
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def user(self) -> Optional[User]:
         """Provide access to the user object."""
 
@@ -74,7 +76,8 @@ class ProvidesUserContext(ProvidesAppContext, Protocol):
 
 
 class ProvidesRepositoriesContext(ProvidesUserContext, Protocol):
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def repositories_hostname(self) -> str:
         """Provide access to hostname used by target mercurial server."""
 
@@ -86,16 +89,19 @@ class SessionRequestContext(ProvidesRepositoriesContext, Protocol):
     @abc.abstractmethod
     def set_galaxy_session(self, galaxy_session: GalaxySession): ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def request(self) -> GalaxyAbstractRequest: ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def response(self) -> GalaxyAbstractResponse: ...
 
     @abc.abstractmethod
     def url_builder(self): ...
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def session_csrf_token(self) -> str: ...
 
 
diff --git a/lib/tool_shed/managers/categories.py b/lib/tool_shed/managers/categories.py
index 1d418f1aa8fa0b9a360f0a890a73f1269d4f1b6a..13b09297fdbf931650f2e9c99384b575ba52487f 100644
--- a/lib/tool_shed/managers/categories.py
+++ b/lib/tool_shed/managers/categories.py
@@ -59,9 +59,7 @@ class CategoryManager:
 
     def to_dict(self, category: Category) -> Dict[str, Any]:
         category_dict = category.to_dict(view="collection", value_mapper=get_value_mapper(self.app))
-        category_dict["repositories"] = self.app.repository_registry.viewable_repositories_and_suites_by_category.get(
-            category.name, 0
-        )
+        category_dict["repositories"] = category.active_repository_count()
         category_dict["url"] = web.url_for(
             controller="categories", action="show", id=self.app.security.encode_id(category.id)
         )
diff --git a/lib/tool_shed/managers/model_cache.py b/lib/tool_shed/managers/model_cache.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ce8c205e901aeb5da7505f9455b6d6f645c5ff5
--- /dev/null
+++ b/lib/tool_shed/managers/model_cache.py
@@ -0,0 +1,64 @@
+import json
+import os
+from typing import (
+    Any,
+    Dict,
+    Optional,
+    Type,
+    TypeVar,
+)
+
+from pydantic import BaseModel
+
+from galaxy.util.hash_util import md5_hash_str
+
+RAW_CACHED_JSON = Dict[str, Any]
+
+
+def hash_model(model_class: Type[BaseModel]) -> str:
+    return md5_hash_str(json.dumps(model_class.model_json_schema()))
+
+
+MODEL_HASHES: Dict[Type[BaseModel], str] = {}
+
+
+M = TypeVar("M", bound=BaseModel)
+
+
+def ensure_model_has_hash(model_class: Type[BaseModel]) -> None:
+    if model_class not in MODEL_HASHES:
+        MODEL_HASHES[model_class] = hash_model(model_class)
+
+
+class ModelCache:
+    _cache_directory: str
+
+    def __init__(self, cache_directory: str):
+        if not os.path.exists(cache_directory):
+            os.makedirs(cache_directory)
+        self._cache_directory = cache_directory
+
+    def _cache_target(self, model_class: Type[M], tool_id: str, tool_version: str) -> str:
+        ensure_model_has_hash(model_class)
+        # consider breaking this into multiple directories...
+        cache_target = os.path.join(self._cache_directory, MODEL_HASHES[model_class], tool_id, tool_version)
+        return cache_target
+
+    def get_cache_entry_for(self, model_class: Type[M], tool_id: str, tool_version: str) -> Optional[M]:
+        cache_target = self._cache_target(model_class, tool_id, tool_version)
+        if not os.path.exists(cache_target):
+            return None
+        with open(cache_target) as f:
+            return model_class.model_validate(json.load(f))
+
+    def has_cached_entry_for(self, model_class: Type[M], tool_id: str, tool_version: str) -> bool:
+        cache_target = self._cache_target(model_class, tool_id, tool_version)
+        return os.path.exists(cache_target)
+
+    def insert_cache_entry_for(self, model_object: M, tool_id: str, tool_version: str) -> None:
+        cache_target = self._cache_target(model_object.__class__, tool_id, tool_version)
+        parent_directory = os.path.dirname(cache_target)
+        if not os.path.exists(parent_directory):
+            os.makedirs(parent_directory)
+        with open(cache_target, "w") as f:
+            json.dump(model_object.dict(), f)
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 58f2158c5cd3f6902ccdf521d90ccd4f5f978c93..e7af6ff641bf4451c4208712e40308390793159d 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -273,8 +273,7 @@ def get_repository_metadata_for_management(
     trans: ProvidesUserContext, encoded_repository_id: str, changeset_revision: str
 ) -> RepositoryMetadata:
     repository = get_repository_in_tool_shed(trans.app, encoded_repository_id)
-    if not can_manage_repo(trans, repository):
-        raise InsufficientPermissionsException("Cannot manage target repository")
+    ensure_can_manage(trans, repository, "Cannot manage target repository")
     revisions = [r for r in repository.metadata_revisions if r.changeset_revision == changeset_revision]
     if len(revisions) != 1:
         raise ObjectNotFound()
@@ -582,6 +581,12 @@ def upload_tar_and_set_metadata(
     return message
 
 
+def ensure_can_manage(trans: ProvidesUserContext, repository: Repository, error_message: Optional[str] = None) -> None:
+    if not can_manage_repo(trans, repository):
+        error_message = error_message or "You do not have permission to update this repository."
+        raise InsufficientPermissionsException(error_message)
+
+
 def _get_repository_by_name_and_owner(session: scoped_session, name: str, owner: str, user_model):
     stmt = (
         select(Repository)
diff --git a/lib/tool_shed/managers/tools.py b/lib/tool_shed/managers/tools.py
index bd648d4903a916744dcadb37036b5c5045347954..0768758fc9bb8259953ab2fa52cc87090dc483d8 100644
--- a/lib/tool_shed/managers/tools.py
+++ b/lib/tool_shed/managers/tools.py
@@ -1,8 +1,46 @@
+import os
+import tempfile
 from collections import namedtuple
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
 
 from galaxy import exceptions
-from tool_shed.context import SessionRequestContext
+from galaxy.exceptions import (
+    InconsistentApplicationState,
+    InternalServerError,
+    ObjectNotFound,
+    RequestParameterInvalidException,
+)
+from galaxy.tool_shed.metadata.metadata_generator import RepositoryMetadataToolDict
+from galaxy.tool_shed.util.basic_util import remove_dir
+from galaxy.tool_shed.util.hg_util import (
+    clone_repository,
+    get_changectx_for_changeset,
+)
+from galaxy.tool_util.models import (
+    parse_tool,
+    ParsedTool,
+)
+from galaxy.tool_util.parser import (
+    get_tool_source,
+    ToolSource,
+)
+from galaxy.tools.stock import stock_tool_sources
+from galaxy.util import relpath
+from tool_shed.context import (
+    ProvidesRepositoriesContext,
+    SessionRequestContext,
+)
+from tool_shed.util.common_util import generate_clone_url_for
+from tool_shed.webapp.model import RepositoryMetadata
 from tool_shed.webapp.search.tool_search import ToolSearch
+from .trs import trs_tool_id_to_repository_metadata
+
+STOCK_TOOL_SOURCES: Optional[Dict[str, Dict[str, ToolSource]]] = None
 
 
 def search(trans: SessionRequestContext, q: str, page: int = 1, page_size: int = 10) -> dict:
@@ -42,3 +80,108 @@ def search(trans: SessionRequestContext, q: str, page: int = 1, page_size: int =
     results = tool_search.search(trans.app, search_term, page, page_size, boosts)
     results["hostname"] = trans.repositories_hostname
     return results
+
+
+def get_repository_metadata_tool_dict(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str
+) -> Tuple[RepositoryMetadata, RepositoryMetadataToolDict]:
+    if trs_tool_id.count("~") < 2:
+        RequestParameterInvalidException(f"Invalid TRS tool id ({trs_tool_id})")
+
+    name, owner, tool_id = trs_tool_id.split("~", 3)
+    repository, metadata_by_version = trs_tool_id_to_repository_metadata(trans, trs_tool_id)
+    if tool_version not in metadata_by_version:
+        raise ObjectNotFound()
+    tool_version_repository_metadata: RepositoryMetadata = metadata_by_version[tool_version]
+    raw_metadata = tool_version_repository_metadata.metadata
+    tool_dicts: List[RepositoryMetadataToolDict] = raw_metadata.get("tools", [])
+    for tool_dict in tool_dicts:
+        if tool_dict["id"] != tool_id or tool_dict["version"] != tool_version:
+            continue
+        return tool_version_repository_metadata, tool_dict
+    raise ObjectNotFound()
+
+
+def parsed_tool_model_cached_for(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str, repository_clone_url: Optional[str] = None
+) -> ParsedTool:
+    model_cache = trans.app.model_cache
+    parsed_tool = model_cache.get_cache_entry_for(ParsedTool, trs_tool_id, tool_version)
+    if parsed_tool is not None:
+        return parsed_tool
+    parsed_tool = parsed_tool_model_for(trans, trs_tool_id, tool_version, repository_clone_url=repository_clone_url)
+    model_cache.insert_cache_entry_for(parsed_tool, trs_tool_id, tool_version)
+    return parsed_tool
+
+
+def parsed_tool_model_for(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str, repository_clone_url: Optional[str] = None
+) -> ParsedTool:
+    tool_source = tool_source_for(trans, trs_tool_id, tool_version, repository_clone_url=repository_clone_url)
+    return parse_tool(tool_source)
+
+
+def tool_source_for(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str, repository_clone_url: Optional[str] = None
+) -> ToolSource:
+    if "~" in trs_tool_id:
+        return _shed_tool_source_for(trans, trs_tool_id, tool_version, repository_clone_url)
+    else:
+        tool_source = _stock_tool_source_for(trs_tool_id, tool_version)
+        if tool_source is None:
+            raise ObjectNotFound()
+        return tool_source
+
+
+def _shed_tool_source_for(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str, tool_version: str, repository_clone_url: Optional[str] = None
+) -> ToolSource:
+    rval = get_repository_metadata_tool_dict(trans, trs_tool_id, tool_version)
+    repository_metadata, tool_version_metadata = rval
+    tool_config = tool_version_metadata["tool_config"]
+
+    repo = repository_metadata.repository.hg_repo
+    ctx = get_changectx_for_changeset(repo, repository_metadata.changeset_revision)
+    work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-tool_source")
+    if repository_clone_url is None:
+        repository_clone_url = generate_clone_url_for(trans, repository_metadata.repository)
+    try:
+        cloned_ok, error_message = clone_repository(repository_clone_url, work_dir, str(ctx.rev()))
+        if error_message:
+            raise InternalServerError("Failed to materialize target repository revision")
+        repo_files_dir = repository_metadata.repository.hg_repository_path(trans.app.config.file_path)
+        if not repo_files_dir:
+            raise InconsistentApplicationState(
+                f"Failed to resolve repository path from hgweb_config_manager for [{trs_tool_id}], inconsistent repository state or application configuration"
+            )
+        repo_rel_tool_path = relpath(tool_config, repo_files_dir)
+        path_to_tool = os.path.join(work_dir, repo_rel_tool_path)
+        if not os.path.exists(path_to_tool):
+            raise InconsistentApplicationState(
+                f"Target tool expected at [{path_to_tool}] and not found, inconsistent repository state or application configuration"
+            )
+        tool_source = get_tool_source(path_to_tool)
+        return tool_source
+    finally:
+        remove_dir(work_dir)
+
+
+def _stock_tool_source_for(tool_id: str, tool_version: str) -> Optional[ToolSource]:
+    _init_stock_tool_sources()
+    assert STOCK_TOOL_SOURCES
+    tool_version_sources = STOCK_TOOL_SOURCES.get(tool_id)
+    if tool_version_sources is None:
+        return None
+    return tool_version_sources.get(tool_version)
+
+
+def _init_stock_tool_sources() -> None:
+    global STOCK_TOOL_SOURCES
+    if STOCK_TOOL_SOURCES is None:
+        STOCK_TOOL_SOURCES = {}
+        for tool_source in stock_tool_sources():
+            tool_id = tool_source.parse_id()
+            tool_version = tool_source.parse_version()
+            if tool_id not in STOCK_TOOL_SOURCES:
+                STOCK_TOOL_SOURCES[tool_id] = {}
+            STOCK_TOOL_SOURCES[tool_id][tool_version] = tool_source
diff --git a/lib/tool_shed/managers/trs.py b/lib/tool_shed/managers/trs.py
index 3c5cfb9e89e1389769ed44c2bd6982973dbdcf75..ebb74220ccd368c4604aace7942096272b96949c 100644
--- a/lib/tool_shed/managers/trs.py
+++ b/lib/tool_shed/managers/trs.py
@@ -74,10 +74,14 @@ def tool_classes() -> List[ToolClass]:
     return [ToolClass(id="galaxy_tool", name="Galaxy Tool", description="Galaxy XML Tools")]
 
 
-def trs_tool_id_to_repository(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> Repository:
+def trs_tool_id_to_guid(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> str:
     guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
     guid = remove_protocol_and_user_from_clone_url(guid)
-    return guid_to_repository(trans.app, guid)
+    return guid
+
+
+def trs_tool_id_to_repository(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> Repository:
+    return guid_to_repository(trans.app, trs_tool_id_to_guid(trans, trs_tool_id))
 
 
 def get_repository_metadata_by_tool_version(
@@ -104,7 +108,7 @@ def get_tools_for(repository_metadata: RepositoryMetadata) -> List[Dict[str, Any
 
 def trs_tool_id_to_repository_metadata(
     trans: ProvidesRepositoriesContext, trs_tool_id: str
-) -> Optional[Tuple[Repository, Dict[str, RepositoryMetadata]]]:
+) -> Tuple[Repository, Dict[str, RepositoryMetadata]]:
     tool_guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
     tool_guid = remove_protocol_and_user_from_clone_url(tool_guid)
     _, tool_id = tool_guid.rsplit("/", 1)
@@ -112,7 +116,7 @@ def trs_tool_id_to_repository_metadata(
     app = trans.app
     versions: Dict[str, RepositoryMetadata] = get_repository_metadata_by_tool_version(app, repository, tool_id)
     if not versions:
-        return None
+        raise ObjectNotFound()
 
     return repository, versions
 
@@ -121,8 +125,6 @@ def get_tool(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> Tool:
     guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
     guid = remove_protocol_and_user_from_clone_url(guid)
     repo_metadata = trs_tool_id_to_repository_metadata(trans, trs_tool_id)
-    if not repo_metadata:
-        raise ObjectNotFound()
     repository, metadata_by_version = repo_metadata
 
     repo_owner = repository.user.username
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 31a1fc45cac0f66a32ac8d799f317f1234a13949..1f9b817e02300ed70cdbb28923e77ef7ad818cf3 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -957,9 +957,11 @@ class RepositoryMetadataManager(ToolShedMetadataGenerator):
             status = "error"
         return message, status
 
-    def set_repository(self, repository, repository_clone_url=None):
+    def set_repository(
+        self, repository, relative_install_dir: Optional[str] = None, changeset_revision: Optional[str] = None
+    ):
         super().set_repository(repository)
-        self.repository_clone_url = repository_clone_url or common_util.generate_clone_url_for(self.trans, repository)
+        self.repository_clone_url = relative_install_dir or common_util.generate_clone_url_for(self.trans, repository)
 
     def set_repository_metadata(self, host, content_alert_str="", **kwd):
         """
diff --git a/lib/tool_shed/repository_registry.py b/lib/tool_shed/repository_registry.py
index 521ae1a06c6fa74cf66d1fb9cb92e75e35306719..b49ce0b5695ad6874d8c1257750100ffadf6cda8 100644
--- a/lib/tool_shed/repository_registry.py
+++ b/lib/tool_shed/repository_registry.py
@@ -6,6 +6,7 @@ from sqlalchemy import (
     or_,
     select,
 )
+from typing_extensions import Protocol
 
 import tool_shed.repository_types.util as rt_util
 from tool_shed.util import (
@@ -18,11 +19,77 @@ from tool_shed.webapp.model import (
     Repository,
     RepositoryMetadata,
 )
+from .structured_app import ToolShedApp
 
 log = logging.getLogger(__name__)
 
 
-class Registry:
+class RegistryInterface(Protocol):
+
+    # only used in legacy controllers - can drop when drop old tool shed webapp
+    def add_category_entry(self, category): ...
+
+    def add_entry(self, repository):
+        # used when creating a repository
+        # Used in legacy add_repository_registry_entry API endpoint - already deemed not worth pulling over to 2.0
+        # used in legacy undelete_repository admin controller
+        # used in legacy deprecate controller
+        ...
+
+    def edit_category_entry(self, old_name, new_name):
+        # used in legacy admin controller
+        ...
+
+    def is_valid(self, repository) -> bool:
+        # probably not used outside this class but also not hurting anything
+        ...
+
+    def remove_category_entry(self, category): ...
+
+    def remove_entry(self, repository): ...
+
+
+# stop gap to implement the same general interface as repository_registry but do nothing,
+# I don't think this stuff is needed - outside potentially old test cases?
+class NullRepositoryRegistry(RegistryInterface):
+
+    def __init__(self, app: ToolShedApp):
+        self.app = app
+
+        # all of these are only used by repository_grids - which I think the tool shed 2.0
+        # does not use at all - but they are part of the "public interface" consumed by
+        # the full registry.
+        self.certified_level_one_viewable_repositories_and_suites_by_category: dict = {}
+        self.certified_level_one_viewable_suites_by_category: dict = {}
+        self.viewable_repositories_and_suites_by_category: dict = {}
+        self.viewable_suites_by_category: dict = {}
+        self.viewable_valid_repositories_and_suites_by_category: dict = {}
+        self.viewable_valid_suites_by_category: dict = {}
+
+    def add_category_entry(self, category):
+        # only used in legacy controllers - can drop when drop old tool shed webapp
+        pass
+
+    def add_entry(self, repository):
+        # used when creating a repository, and maybe more?
+        pass
+
+    def edit_category_entry(self, old_name, new_name):
+        pass
+
+    def is_valid(self, repository) -> bool:
+        if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions:
+            return True
+        return False
+
+    def remove_category_entry(self, category):
+        pass
+
+    def remove_entry(self, repository):
+        pass
+
+
+class Registry(RegistryInterface):
     def __init__(self, app):
         log.debug("Loading the repository registry...")
         self.app = app
@@ -32,17 +99,30 @@ class Registry:
         self.certified_level_one_suite_tuples = []
         # These category dictionaries contain entries where the key is the category and the value is the integer count
         # of viewable repositories within that category.
+
+        # only used internally to class and by repository_grids
         self.certified_level_one_viewable_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.certified_level_one_viewable_suites_by_category = {}
-        self.certified_level_two_repository_and_suite_tuples = []
-        self.certified_level_two_suite_tuples = []
-        self.certified_level_two_viewable_repositories_and_suites_by_category = {}
-        self.certified_level_two_viewable_suites_by_category = {}
+
+        # not even used in legacy shed code...
+        # self.certified_level_two_repository_and_suite_tuples = []
+        # self.certified_level_two_suite_tuples = []
+        # self.certified_level_two_viewable_repositories_and_suites_by_category = {}
+        # self.certified_level_two_viewable_suites_by_category = {}
+
+        # only used internally to class
         self.repository_and_suite_tuples = []
+        # only used internally to class
         self.suite_tuples = []
+
+        # only used internally to class and by repository_grids
         self.viewable_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_valid_repositories_and_suites_by_category = {}
+        # only used internally to class and by repository_grids
         self.viewable_valid_suites_by_category = {}
         self.load()
 
@@ -152,6 +232,7 @@ class Registry:
             self.certified_level_one_viewable_suites_by_category[new_name] = 0
 
     def get_certified_level_one_clause_list(self):
+        # only used internally to class
         clause_list = []
         for repository in get_repositories(self.sa_session):
             certified_level_one_tuple = self.get_certified_level_one_tuple(repository)
@@ -169,6 +250,7 @@ class Registry:
         """
         Return True if the latest installable changeset_revision of the received repository is level one certified.
         """
+        # only used internally to class
         if repository is None:
             return (None, False)
         if repository.deleted or repository.deprecated:
@@ -190,6 +272,7 @@ class Registry:
             return (None, False)
 
     def is_level_one_certified(self, repository_metadata):
+        # only used internally to class
         if repository_metadata:
             repository = repository_metadata.repository
             if repository:
@@ -206,12 +289,13 @@ class Registry:
                     return tuple in self.certified_level_one_repository_and_suite_tuples
         return False
 
-    def is_valid(self, repository):
+    def is_valid(self, repository) -> bool:
         if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions:
             return True
         return False
 
     def load_certified_level_one_repository_and_suite_tuple(self, repository):
+        # only used internally to class
         # The received repository has been determined to be level one certified.
         name = str(repository.name)
         owner = str(repository.user.username)
@@ -226,6 +310,7 @@ class Registry:
                     self.certified_level_one_repository_and_suite_tuples.append(certified_level_one_tuple)
 
     def load_repository_and_suite_tuple(self, repository):
+        # only used internally to class
         name = str(repository.name)
         owner = str(repository.user.username)
         for repository_metadata in repository.metadata_revisions:
@@ -238,6 +323,7 @@ class Registry:
                     self.suite_tuples.append(tuple)
 
     def load_repository_and_suite_tuples(self):
+        # only used internally to class
         # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples.
         clauses = self.get_certified_level_one_clause_list()
         for repository in get_certified_repositories_with_user(self.sa_session, clauses, model.User):
@@ -247,11 +333,12 @@ class Registry:
             self.load_repository_and_suite_tuple(repository)
 
     def load_viewable_repositories_and_suites_by_category(self):
+        # only used internally to class
         # Clear all dictionaries just in case they were previously loaded.
         self.certified_level_one_viewable_repositories_and_suites_by_category = {}
         self.certified_level_one_viewable_suites_by_category = {}
-        self.certified_level_two_viewable_repositories_and_suites_by_category = {}
-        self.certified_level_two_viewable_suites_by_category = {}
+        # self.certified_level_two_viewable_repositories_and_suites_by_category = {}
+        # self.certified_level_two_viewable_suites_by_category = {}
         self.viewable_repositories_and_suites_by_category = {}
         self.viewable_suites_by_category = {}
         self.viewable_valid_repositories_and_suites_by_category = {}
@@ -363,6 +450,7 @@ class Registry:
 
     @property
     def sa_session(self):
+        # only used internally to class
         return self.app.model.session
 
     def unload_certified_level_one_repository_and_suite_tuple(self, repository):
diff --git a/lib/tool_shed/structured_app.py b/lib/tool_shed/structured_app.py
index deb0b0ece6be320f851a9629971e17f40f3d1a4d..8a38e008fbbe1eac38b8fd027d4c4d404e7322c2 100644
--- a/lib/tool_shed/structured_app.py
+++ b/lib/tool_shed/structured_app.py
@@ -3,7 +3,8 @@ from typing import TYPE_CHECKING
 from galaxy.structured_app import BasicSharedApp
 
 if TYPE_CHECKING:
-    from tool_shed.repository_registry import Registry as RepositoryRegistry
+    from tool_shed.managers.model_cache import ModelCache
+    from tool_shed.repository_registry import RegistryInterface
     from tool_shed.repository_types.registry import Registry as RepositoryTypesRegistry
     from tool_shed.util.hgweb_config import HgWebConfigManager
     from tool_shed.webapp.model import mapping
@@ -13,6 +14,7 @@ if TYPE_CHECKING:
 class ToolShedApp(BasicSharedApp):
     repository_types_registry: "RepositoryTypesRegistry"
     model: "mapping.ToolShedModelMapping"
-    repository_registry: "RepositoryRegistry"
+    repository_registry: "RegistryInterface"
     hgweb_config_manager: "HgWebConfigManager"
     security_agent: "CommunityRBACAgent"
+    model_cache: "ModelCache"
diff --git a/lib/tool_shed/test/base/browser.py b/lib/tool_shed/test/base/browser.py
index 559ce7468cf36ecb91b10b807ccef0e279334df1..f20804eecc09c08319859dbfd663b8ca38bacb14 100644
--- a/lib/tool_shed/test/base/browser.py
+++ b/lib/tool_shed/test/base/browser.py
@@ -36,7 +36,8 @@ class ShedBrowser(metaclass=abc.ABCMeta):
     def submit_form_with_name(self, form_name: str, button="runtool_btn", **kwd):
         """Submit the target button."""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def is_twill(self) -> bool:
         """Return whether this is a twill browser."""
 
diff --git a/lib/tool_shed/test/base/driver.py b/lib/tool_shed/test/base/driver.py
index a4fa67efdfb501b5352b5359eab00cd5413c3475..5fe5280d786c17d0f38c1153f515be03ff0b40e7 100644
--- a/lib/tool_shed/test/base/driver.py
+++ b/lib/tool_shed/test/base/driver.py
@@ -66,7 +66,7 @@ def build_shed_app(simple_kwargs):
 class ToolShedTestDriver(driver_util.TestDriver):
     """Instantiate a Galaxy-style TestDriver for testing the tool shed."""
 
-    def setup(self):
+    def setup(self) -> None:
         """Entry point for test driver script."""
         self.external_shed = bool(os.environ.get("TOOL_SHED_TEST_EXTERNAL", None))
         if not self.external_shed:
diff --git a/lib/tool_shed/test/base/playwrightbrowser.py b/lib/tool_shed/test/base/playwrightbrowser.py
index 01949ff1eb9606adcfd7482ed03632eaf489f4c8..cc32cb49f2a5b577ebd47f192db6e156f3334c68 100644
--- a/lib/tool_shed/test/base/playwrightbrowser.py
+++ b/lib/tool_shed/test/base/playwrightbrowser.py
@@ -173,6 +173,7 @@ class PlaywrightShedBrowser(ShedBrowser):
         logout_locator = self._page.locator(Locators.toolbar_logout)
         if logout_locator.is_visible():
             logout_locator.click()
+            self._page.wait_for_load_state("networkidle")
         if assert_logged_out:
             self.expect_not_logged_in()
 
diff --git a/lib/tool_shed/test/base/populators.py b/lib/tool_shed/test/base/populators.py
index 01cc8eea69370188f758b93484844078ad44aa9f..642c1b76b9ac0ba2d3070895dad5d024f4ab9426 100644
--- a/lib/tool_shed/test/base/populators.py
+++ b/lib/tool_shed/test/base/populators.py
@@ -23,6 +23,7 @@ from tool_shed_client.schema import (
     Category,
     CreateCategoryRequest,
     CreateRepositoryRequest,
+    DetailedRepository,
     from_legacy_install_info,
     GetInstallInfoRequest,
     GetOrderedInstallableRevisionsRequest,
@@ -41,6 +42,7 @@ from tool_shed_client.schema import (
     ResetMetadataOnRepositoryResponse,
     ToolSearchRequest,
     ToolSearchResults,
+    UpdateRepositoryRequest,
     Version,
 )
 from .api_util import (
@@ -209,6 +211,17 @@ class ToolShedPopulator:
         )
         return response
 
+    def update_raw(self, repository: HasRepositoryId, request: UpdateRepositoryRequest) -> requests.Response:
+        repository_id = self._repository_id(repository)
+        body_json = request.model_dump(exclude_unset=True, by_alias=True)
+        put_response = self._api_interactor.put(f"repositories/{repository_id}", json=body_json)
+        return put_response
+
+    def update(self, repository: HasRepositoryId, request: UpdateRepositoryRequest) -> Repository:
+        response = self.update_raw(repository, request)
+        api_asserts.assert_status_code_is_ok(response)
+        return Repository(**response.json())
+
     def upload_revision(
         self, repository: HasRepositoryId, path: Traversable, commit_message: str = DEFAULT_COMMIT_MESSAGE
     ) -> RepositoryUpdate:
@@ -358,11 +371,14 @@ class ToolShedPopulator:
         delete_response = self._api_interactor.delete(f"repositories/{repository_id}/deprecated")
         delete_response.raise_for_status()
 
-    def is_deprecated(self, repository: HasRepositoryId) -> bool:
+    def get_repository(self, repository: HasRepositoryId) -> DetailedRepository:
         repository_id = self._repository_id(repository)
         repository_response = self._api_interactor.get(f"repositories/{repository_id}")
         repository_response.raise_for_status()
-        return Repository(**repository_response.json()).deprecated
+        return DetailedRepository(**repository_response.json())
+
+    def is_deprecated(self, repository: HasRepositoryId) -> bool:
+        return self.get_repository(repository).deprecated
 
     def get_metadata(self, repository: HasRepositoryId, downloadable_only=True) -> RepositoryMetadata:
         repository_id = self._repository_id(repository)
diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py
index f957cfe0ea2ceefaf2044277370de088ac13ee60..21f08b1451ce862ce615ee4b36067a73aa3b679d 100644
--- a/lib/tool_shed/test/base/test_db_util.py
+++ b/lib/tool_shed/test/base/test_db_util.py
@@ -9,7 +9,7 @@ from sqlalchemy import (
 import galaxy.model
 import galaxy.model.tool_shed_install
 import tool_shed.webapp.model as model
-from galaxy.managers.users import (
+from galaxy.model.db.user import (
     get_user_by_email,
     get_user_by_username,
 )
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 87eaf2c3ab8d066557db0c34514eaef6cb5be9e8..a8414ff3dc69667bc015024239baba83731e2083 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -150,11 +150,13 @@ class ToolShedInstallationClient(metaclass=abc.ABCMeta):
     ) -> Dict[str, Any]:
         """"""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def tool_data_path(self) -> str:
         """"""
 
-    @abc.abstractproperty
+    @property
+    @abc.abstractmethod
     def shed_tool_data_table_conf(self) -> str:
         """"""
 
diff --git a/lib/tool_shed/test/functional/test_shed_repositories.py b/lib/tool_shed/test/functional/test_shed_repositories.py
index fe7c4d3bac247f6f2e427fd5e83bc539d01b4ab2..bd4e88d2656720309417fc9e41b9cdb39b21d938 100644
--- a/lib/tool_shed/test/functional/test_shed_repositories.py
+++ b/lib/tool_shed/test/functional/test_shed_repositories.py
@@ -10,7 +10,10 @@ from tool_shed.test.base.populators import (
     HasRepositoryId,
     repo_tars,
 )
-from tool_shed_client.schema import RepositoryRevisionMetadata
+from tool_shed_client.schema import (
+    RepositoryRevisionMetadata,
+    UpdateRepositoryRequest,
+)
 from ..base.api import (
     ShedApiTestCase,
     skip_if_api_v1,
@@ -49,6 +52,40 @@ class TestShedRepositoriesApi(ShedApiTestCase):
         )
         assert repository_update.is_ok
 
+    def test_update_repository_info(self):
+        populator = self.populator
+        prefix = "testupdateinfo"
+        category_id = populator.new_category(prefix=prefix).id
+        repository = populator.new_repository(category_id, prefix=prefix)
+        repository_id = repository.id
+        request = UpdateRepositoryRequest(homepage_url="https://www.google.com")
+        update = populator.update(repository_id, request)
+        assert update.homepage_url == "https://www.google.com"
+        assert populator.get_repository(repository_id).homepage_url == "https://www.google.com"
+
+    def test_update_category(self):
+        populator = self.populator
+        prefix = "testupdatecategory"
+
+        old_category_id = populator.new_category(prefix=prefix).id
+        new_category_id = populator.new_category(prefix=prefix).id
+
+        populator.assert_category_has_n_repositories(old_category_id, 0)
+        populator.assert_category_has_n_repositories(new_category_id, 0)
+
+        repository = populator.new_repository(old_category_id, prefix=prefix)
+        repository_id = repository.id
+
+        populator.assert_category_has_n_repositories(old_category_id, 1)
+        populator.assert_category_has_n_repositories(new_category_id, 0)
+
+        request = UpdateRepositoryRequest(category_ids=[new_category_id])
+        populator.update(repository_id, request)
+
+        # does this mean we cannot remove categories?
+        populator.assert_category_has_n_repositories(old_category_id, 0)
+        populator.assert_category_has_n_repositories(new_category_id, 1)
+
     # used by getRepository in TS client.
     def test_metadata_simple(self):
         populator = self.populator
diff --git a/lib/tool_shed/test/functional/test_shed_tools.py b/lib/tool_shed/test/functional/test_shed_tools.py
index c54dd825e4795c7ce4a5588c5e504f2323085161..5c2a9ea4389e09ef3997206a2f6d5198df590f3c 100644
--- a/lib/tool_shed/test/functional/test_shed_tools.py
+++ b/lib/tool_shed/test/functional/test_shed_tools.py
@@ -62,9 +62,17 @@ class TestShedToolsApi(ShedApiTestCase):
         repository = populator.setup_column_maker_repo(prefix="toolstrsindex")
         tool_id = populator.tool_guid(self, repository, "Add_a_column1")
         tool_shed_base, encoded_tool_id = encode_identifier(tool_id)
-        print(encoded_tool_id)
         url = f"ga4gh/trs/v2/tools/{encoded_tool_id}"
-        print(url)
         tool_response = self.api_interactor.get(url)
         tool_response.raise_for_status()
         assert Tool(**tool_response.json())
+
+    @skip_if_api_v1
+    def test_trs_tool_parameter_json_schema(self):
+        populator = self.populator
+        repository = populator.setup_column_maker_repo(prefix="toolsparameterschema")
+        tool_id = populator.tool_guid(self, repository, "Add_a_column1")
+        tool_shed_base, encoded_tool_id = encode_identifier(tool_id)
+        url = f"tools/{encoded_tool_id}/versions/1.1.0/parameter_request_schema"
+        tool_response = self.api_interactor.get(url)
+        tool_response.raise_for_status()
diff --git a/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml b/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml
new file mode 100644
index 0000000000000000000000000000000000000000..090972695b10ce37bb06d5e62b784f1fc64dbc68
--- /dev/null
+++ b/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml
@@ -0,0 +1,19 @@
+<tool id="missing_data_ref" name="missing_data_ref" version="1.0" profile="23.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        echo $column
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="column" type="data_column" />
+    </inputs>
+    <outputs>
+        <data name="output" format="text"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help/>
+</tool>
diff --git a/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml b/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml
new file mode 100644
index 0000000000000000000000000000000000000000..608dd7aad61c854a6bbd2d69c3f8a492bfecb010
--- /dev/null
+++ b/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml
@@ -0,0 +1,19 @@
+<tool id="wrong_data_ref" name="wrong_data_ref" version="1.0" profile="23.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        echo $column
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="column" type="data_column" data_ref="nonsense" />
+    </inputs>
+    <outputs>
+        <data name="output" format="text"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help/>
+</tool>
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 9c9545c2e7f18e6b03cfb218162c0b1fed6cb873..51c9ae6d11559c5bab7bd41efc55a125579737f1 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -231,12 +231,7 @@ def create_repository(
     session = sa_session()
     with transaction(session):
         session.commit()
-    dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
-    # Define repo name inside hashed directory.
-    final_repository_path = os.path.join(dir, "repo_%d" % repository.id)
-    # Create final repository directory.
-    if not os.path.exists(final_repository_path):
-        os.makedirs(final_repository_path)
+    final_repository_path = repository.ensure_hg_repository_path(app.config.file_path)
     os.rename(repository_path, final_repository_path)
     app.hgweb_config_manager.add_entry(lhs, final_repository_path)
     # Update the repository registry.
@@ -437,17 +432,27 @@ def change_repository_name_in_hgrc_file(hgrc_file: str, new_name: str) -> None:
 def update_repository(trans: "ProvidesUserContext", id: str, **kwds) -> Tuple[Optional["Repository"], Optional[str]]:
     """Update an existing ToolShed repository"""
     app = trans.app
-    message = None
-    flush_needed = False
     sa_session = app.model.session
     repository = sa_session.get(app.model.Repository, app.security.decode_id(id))
     if repository is None:
         return None, "Unknown repository ID"
 
-    if not (trans.user_is_admin or trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
+    if not (trans.user_is_admin or app.security_agent.user_can_administer_repository(trans.user, repository)):
         message = "You are not the owner of this repository, so you cannot administer it."
         return None, message
 
+    return update_validated_repository(trans, repository, **kwds)
+
+
+def update_validated_repository(
+    trans: "ProvidesUserContext", repository: "Repository", **kwds
+) -> Tuple[Optional["Repository"], Optional[str]]:
+    """Update an existing ToolShed repository metadata once permissions have been checked."""
+    app = trans.app
+    sa_session = app.model.session
+    message = None
+    flush_needed = False
+
     # Allowlist properties that can be changed via this method
     for key in ("type", "description", "long_description", "remote_repository_url", "homepage_url"):
         # If that key is available, not None and different than what's in the model
@@ -456,10 +461,9 @@ def update_repository(trans: "ProvidesUserContext", id: str, **kwds) -> Tuple[Op
             flush_needed = True
 
     if "category_ids" in kwds and isinstance(kwds["category_ids"], list):
+
         # Remove existing category associations
-        delete_repository_category_associations(
-            sa_session, app.model.RepositoryCategoryAssociation, app.security.decode_id(id)
-        )
+        delete_repository_category_associations(sa_session, app.model.RepositoryCategoryAssociation, repository.id)
 
         # Then (re)create category associations
         for category_id in kwds["category_ids"]:
diff --git a/lib/tool_shed/util/shed_index.py b/lib/tool_shed/util/shed_index.py
index ee94d4c1a785c7c1f597e4a0dbc25e044f0777ba..11faf5d9c8c2d57f6a373e6c224097e26b542294 100644
--- a/lib/tool_shed/util/shed_index.py
+++ b/lib/tool_shed/util/shed_index.py
@@ -56,6 +56,8 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, hgweb_repo_prefix
     execution_timer = ExecutionTimer()
     with repo_index.searcher() as searcher:
         for repo in get_repos(sa_session, file_path, hgweb_config_dir, hgweb_repo_prefix, **kwargs):
+            if repo is None:
+                continue
             tools_list = repo.pop("tools_list")
             repo_id = repo["id"]
             indexed_document = searcher.document(id=repo_id)
@@ -119,9 +121,11 @@ def get_repos(sa_session, file_path, hgweb_config_dir, hgweb_repo_prefix, **kwar
         full_last_updated = repo.update_time.strftime("%Y-%m-%d %I:%M %p")
 
         # Load all changesets of the repo for lineage.
-        repo_path = os.path.join(
-            hgweb_config_dir, hgwcm.get_entry(os.path.join(hgweb_repo_prefix, repo.user.username, repo.name))
-        )
+        try:
+            entry = hgwcm.get_entry(os.path.join(hgweb_repo_prefix, repo.user.username, repo.name))
+        except Exception:
+            return None
+        repo_path = os.path.join(hgweb_config_dir, entry)
         hg_repo = hg.repository(ui.ui(), repo_path.encode("utf-8"))
         lineage = []
         for changeset in hg_repo.changelog:
diff --git a/lib/tool_shed/webapp/api/users.py b/lib/tool_shed/webapp/api/users.py
index 54f1fba3ffe754ec622d8cab7e6a9b6b76f25e78..5fb00463be2525dbd094d4e66716bcba1b241d5f 100644
--- a/lib/tool_shed/webapp/api/users.py
+++ b/lib/tool_shed/webapp/api/users.py
@@ -52,7 +52,7 @@ class UsersController(BaseShedAPIController):
         value_mapper = {"id": trans.security.encode_id}
         return value_mapper
 
-    @web.expose_api_anonymous
+    @web.expose_api_anonymous_and_sessionless
     def index(self, trans, deleted=False, **kwd):
         """
         GET /api/users
@@ -67,7 +67,7 @@ class UsersController(BaseShedAPIController):
             user_dicts.append(user_dict)
         return user_dicts
 
-    @web.expose_api_anonymous
+    @web.expose_api_anonymous_and_sessionless
     def show(self, trans, id, **kwd):
         """
         GET /api/users/{encoded_user_id}
diff --git a/lib/tool_shed/webapp/api2/repositories.py b/lib/tool_shed/webapp/api2/repositories.py
index ef510c088888a34a9e5963e911b7bf0e4729d4c0..24425bbe0239084eae15342197d6bd29c758bd76 100644
--- a/lib/tool_shed/webapp/api2/repositories.py
+++ b/lib/tool_shed/webapp/api2/repositories.py
@@ -19,7 +19,10 @@ from fastapi import (
 )
 from starlette.datastructures import UploadFile as StarletteUploadFile
 
-from galaxy.exceptions import InsufficientPermissionsException
+from galaxy.exceptions import (
+    ActionInputError,
+    InsufficientPermissionsException,
+)
 from galaxy.model.base import transaction
 from galaxy.webapps.galaxy.api import as_form
 from tool_shed.context import SessionRequestContext
@@ -28,6 +31,7 @@ from tool_shed.managers.repositories import (
     can_update_repo,
     check_updates,
     create_repository,
+    ensure_can_manage,
     get_install_info,
     get_ordered_installable_revisions,
     get_repository_metadata_dict,
@@ -42,7 +46,10 @@ from tool_shed.managers.repositories import (
     upload_tar_and_set_metadata,
 )
 from tool_shed.structured_app import ToolShedApp
-from tool_shed.util.repository_util import get_repository_in_tool_shed
+from tool_shed.util.repository_util import (
+    get_repository_in_tool_shed,
+    update_validated_repository,
+)
 from tool_shed_client.schema import (
     CreateRepositoryRequest,
     DetailedRepository,
@@ -57,6 +64,7 @@ from tool_shed_client.schema import (
     RepositoryUpdateRequest,
     ResetMetadataOnRepositoryRequest,
     ResetMetadataOnRepositoryResponse,
+    UpdateRepositoryRequest,
     ValidRepostiroyUpdateMessage,
 )
 from . import (
@@ -293,6 +301,28 @@ class FastAPIRepositories:
         repository = get_repository_in_tool_shed(self.app, encoded_repository_id)
         return to_detailed_model(self.app, repository)
 
+    @router.put(
+        "/api/repositories/{encoded_repository_id}",
+        operation_id="repositories__update_repository",
+    )
+    def update_repository(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        encoded_repository_id: str = RepositoryIdPathParam,
+        request: UpdateRepositoryRequest = Body(...),
+    ) -> DetailedRepository:
+        repository = get_repository_in_tool_shed(self.app, encoded_repository_id)
+        ensure_can_manage(trans, repository)
+
+        # may want to set some of these to null, so we're using the exclude_unset feature
+        # to just serialize the ones we want to use to a dictionary.
+        update_dictionary = request.model_dump(exclude_unset=True)
+        repo_result, message = update_validated_repository(trans, repository, **update_dictionary)
+        if repo_result is None:
+            raise ActionInputError(message)
+
+        return to_detailed_model(self.app, repository)
+
     @router.get(
         "/api/repositories/{encoded_repository_id}/permissions",
         operation_id="repositories__permissions",
@@ -323,8 +353,7 @@ class FastAPIRepositories:
         encoded_repository_id: str = RepositoryIdPathParam,
     ) -> List[str]:
         repository = get_repository_in_tool_shed(self.app, encoded_repository_id)
-        if not can_manage_repo(trans, repository):
-            raise InsufficientPermissionsException("You do not have permission to update this repository.")
+        ensure_can_manage(trans, repository)
         return trans.app.security_agent.usernames_that_can_push(repository)
 
     @router.post(
@@ -390,8 +419,7 @@ class FastAPIRepositories:
         encoded_repository_id: str = RepositoryIdPathParam,
     ):
         repository = get_repository_in_tool_shed(self.app, encoded_repository_id)
-        if not can_manage_repo(trans, repository):
-            raise InsufficientPermissionsException("You do not have permission to update this repository.")
+        ensure_can_manage(trans, repository)
         repository.deprecated = True
         trans.sa_session.add(repository)
         with transaction(trans.sa_session):
@@ -409,8 +437,7 @@ class FastAPIRepositories:
         encoded_repository_id: str = RepositoryIdPathParam,
     ):
         repository = get_repository_in_tool_shed(self.app, encoded_repository_id)
-        if not can_manage_repo(trans, repository):
-            raise InsufficientPermissionsException("You do not have permission to update this repository.")
+        ensure_can_manage(trans, repository)
         repository.deprecated = False
         trans.sa_session.add(repository)
         with transaction(trans.sa_session):
@@ -470,7 +497,7 @@ class FastAPIRepositories:
                 dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
             ) as dest:
                 upload_file_like: IO[bytes] = the_file.file
-                shutil.copyfileobj(upload_file_like, dest)  # type: ignore[misc] # https://github.com/python/mypy/issues/15031
+                shutil.copyfileobj(upload_file_like, dest)
             the_file.file.close()
             filename = dest.name
             try:
diff --git a/lib/tool_shed/webapp/api2/tools.py b/lib/tool_shed/webapp/api2/tools.py
index bd48db71ce013945c111b1bc64a12e77af5bea73..be5d04da9aebd9eb4ecd08cbf9376f544fc44a4e 100644
--- a/lib/tool_shed/webapp/api2/tools.py
+++ b/lib/tool_shed/webapp/api2/tools.py
@@ -4,10 +4,19 @@ from typing import List
 from fastapi import (
     Path,
     Request,
+    Response,
 )
 
+from galaxy.tool_util.models import ParsedTool
+from galaxy.tool_util.parameters import (
+    RequestToolState,
+    to_json_schema_string,
+)
 from tool_shed.context import SessionRequestContext
-from tool_shed.managers.tools import search
+from tool_shed.managers.tools import (
+    parsed_tool_model_cached_for,
+    search,
+)
 from tool_shed.managers.trs import (
     get_tool,
     service_info,
@@ -41,6 +50,17 @@ TOOL_ID_PATH_PARAM: str = Path(
     description="See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids",
 )
 
+TOOL_VERSION_PATH_PARAM: str = Path(
+    ...,
+    title="Galaxy Tool Wrapper Version",
+    description="The full version string defined on the Galaxy tool wrapper.",
+)
+
+
+def json_schema_response(pydantic_model) -> Response:
+    json_str = to_json_schema_string(pydantic_model)
+    return Response(content=json_str, media_type="application/json")
+
 
 @router.cbv
 class FastAPITools:
@@ -122,3 +142,31 @@ class FastAPITools:
         tool_id: str = TOOL_ID_PATH_PARAM,
     ) -> List[ToolVersion]:
         return get_tool(trans, tool_id).versions
+
+    @router.get(
+        "/api/tools/{tool_id}/versions/{tool_version}",
+        operation_id="tools__parameter_model",
+        summary="Return Galaxy's meta model description of the tool's inputs",
+    )
+    def show_tool(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        tool_id: str = TOOL_ID_PATH_PARAM,
+        tool_version: str = TOOL_VERSION_PATH_PARAM,
+    ) -> ParsedTool:
+        return parsed_tool_model_cached_for(trans, tool_id, tool_version)
+
+    @router.get(
+        "/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema",
+        operation_id="tools__parameter_request_model",
+        summary="Return a JSON schema description of the tool's inputs for the tool request API that will be added to Galaxy at some point",
+        description="The tool request schema includes validation of map/reduce concepts that can be consumed by the tool execution API and not just the request for a single execution.",
+    )
+    def tool_state(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        tool_id: str = TOOL_ID_PATH_PARAM,
+        tool_version: str = TOOL_VERSION_PATH_PARAM,
+    ) -> Response:
+        parsed_tool = parsed_tool_model_cached_for(trans, tool_id, tool_version)
+        return json_schema_response(RequestToolState.parameter_model_for(parsed_tool.inputs))
diff --git a/lib/tool_shed/webapp/app.py b/lib/tool_shed/webapp/app.py
index 58ccf206596cdc869ace6d10fa203c9199298e35..1a10551ed0f780b703347435381dc3b5a1475a0e 100644
--- a/lib/tool_shed/webapp/app.py
+++ b/lib/tool_shed/webapp/app.py
@@ -1,10 +1,7 @@
 import logging
 import sys
 import time
-from typing import (
-    Any,
-    Optional,
-)
+from typing import Optional
 
 from sqlalchemy.orm.scoping import scoped_session
 
@@ -33,6 +30,7 @@ from galaxy.security import idencoding
 from galaxy.structured_app import BasicSharedApp
 from galaxy.web_stack import application_stack_instance
 from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
+from tool_shed.managers.model_cache import ModelCache
 from tool_shed.structured_app import ToolShedApp
 from tool_shed.util.hgweb_config import hgweb_config_manager
 from tool_shed.webapp.model.migrations import verify_database
@@ -53,7 +51,7 @@ class UniverseApplication(ToolShedApp, SentryClientMixin, HaltableContainer):
         # will be overwritten when building WSGI app
         self.is_webapp = False
         # Read the tool_shed.ini configuration file and check for errors.
-        self.config: Any = config.Configuration(**kwd)
+        self.config = config.Configuration(**kwd)
         self.config.check()
         configure_logging(self.config)
         self.application_stack = application_stack_instance()
@@ -83,6 +81,7 @@ class UniverseApplication(ToolShedApp, SentryClientMixin, HaltableContainer):
         self._register_singleton(SharedModelMapping, model)
         self._register_singleton(mapping.ToolShedModelMapping, model)
         self._register_singleton(scoped_session, self.model.context)
+        self.model_cache = ModelCache(self.config.model_cache_dir)
         self.user_manager = self._register_singleton(UserManager, UserManager(self, app_type="tool_shed"))
         self.api_keys_manager = self._register_singleton(ApiKeyManager)
         # initialize the Tool Shed tag handler.
@@ -106,7 +105,10 @@ class UniverseApplication(ToolShedApp, SentryClientMixin, HaltableContainer):
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         self.hgweb_config_manager.hgweb_repo_prefix = self.config.hgweb_repo_prefix
         # Initialize the repository registry.
-        self.repository_registry = tool_shed.repository_registry.Registry(self)
+        if config.SHED_API_VERSION != "v2":
+            self.repository_registry = tool_shed.repository_registry.Registry(self)
+        else:
+            self.repository_registry = tool_shed.repository_registry.NullRepositoryRegistry(self)
         # Configure Sentry client if configured
         self.configure_sentry_client()
         #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
diff --git a/lib/tool_shed/webapp/buildapp.py b/lib/tool_shed/webapp/buildapp.py
index 6988874a6b526d308f18448cc9ff08c5722f1b04..16b47bc450b385dae4b6a1972ffc609be56a2ad0 100644
--- a/lib/tool_shed/webapp/buildapp.py
+++ b/lib/tool_shed/webapp/buildapp.py
@@ -26,8 +26,7 @@ from galaxy.webapps.base.webapp import (
     GalaxyWebTransaction,
 )
 from galaxy.webapps.util import wrap_if_allowed
-
-SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")
+from .config import SHED_API_VERSION
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 9c0e3d44964abeecc4ac4338a41556024a646448..817d85776cc230a948b6d9e297f9ffd89e1ba308 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -27,6 +27,7 @@ from galaxy.version import (
 log = logging.getLogger(__name__)
 
 TOOLSHED_APP_NAME = "tool_shed"
+SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")
 
 
 class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 2fb4015ce9f42e003862926812152d97ab741284..67fd5ed998cdcb7f53f66e19663a08d5641362cc 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -24,8 +24,8 @@ from galaxy import (
     util,
     web,
 )
-from galaxy.managers.users import get_user_by_username
 from galaxy.model.base import transaction
+from galaxy.model.db.user import get_user_by_username
 from galaxy.tool_shed.util import dependency_display
 from galaxy.tools.repositories import ValidationContext
 from galaxy.util.tool_shed import encoding_util
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index eb9a11878ebaf13c3c4cd47da77cc8af7988ae5c..63016fe8d70e9778d0391416424dcd646c096c4e 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -8,8 +8,8 @@ from galaxy import (
     web,
 )
 from galaxy.managers.api_keys import ApiKeyManager
-from galaxy.managers.users import get_user_by_email
 from galaxy.model.base import transaction
+from galaxy.model.db.user import get_user_by_email
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
diff --git a/lib/tool_shed/webapp/fast_app.py b/lib/tool_shed/webapp/fast_app.py
index ba094c74ec2c8b7a1df44363c44eebe49ce2b7f3..56f3c0e2e711551a0e98df849bf55a51b212784f 100644
--- a/lib/tool_shed/webapp/fast_app.py
+++ b/lib/tool_shed/webapp/fast_app.py
@@ -166,7 +166,7 @@ def initialize_fast_app(gx_webapp, tool_shed_app):
     app = get_fastapi_instance()
     add_exception_handler(app)
     add_request_id_middleware(app)
-    from .buildapp import SHED_API_VERSION
+    from .config import SHED_API_VERSION
 
     def mount_static(directory: Path):
         name = directory.name
diff --git a/lib/tool_shed/webapp/frontend/.eslintignore b/lib/tool_shed/webapp/frontend/.eslintignore
index b22c816bfd5e2859757e25b9b04de7cd05f46060..a220c535ece58131e598f1e0cedc70aa8c032534 100644
--- a/lib/tool_shed/webapp/frontend/.eslintignore
+++ b/lib/tool_shed/webapp/frontend/.eslintignore
@@ -3,5 +3,5 @@ node_modules
 # don't lint build output (make sure it's set to your correct build folder name)
 dist
 
-# Ignore codegen aritfacts
+# Ignore codegen artifacts
 src/gql/*.ts
diff --git a/lib/tool_shed/webapp/frontend/README.md b/lib/tool_shed/webapp/frontend/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..b164ce1dcb18667ebaa2b2774f6890f08ea6134b
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/README.md
@@ -0,0 +1,23 @@
+# Tool Shed 2.0 client
+
+You will need to start the Tool Shed backend from the galaxy root directory.
+This is required if you want to develop against a local tool shed, and if you
+plan to make changes to the graphql queries if you want to target a remote tool shed.
+
+```shell
+TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+```
+
+Start the HMR dev server **and** the graphql dev server
+
+```shell
+yarn run dev-all
+```
+
+If you want to target an external V2 tool shed API run
+
+```shell
+TOOL_SHED_URL=https://testtoolshed.g2.bx.psu.edu CHANGE_ORIGIN=true yarn vite dev
+```
+
+Note that you still need a local backend to generate the graphql schema.
diff --git a/lib/tool_shed/webapp/frontend/package.json b/lib/tool_shed/webapp/frontend/package.json
index 0050777dadbacf87e59335b7ac6db534dabc8bc2..b9a803e1fe99acc63444a16e465eaf43c3e0ea82 100644
--- a/lib/tool_shed/webapp/frontend/package.json
+++ b/lib/tool_shed/webapp/frontend/package.json
@@ -38,17 +38,16 @@
     "vue-tsc": "^1.0.16"
   },
   "dependencies": {
-    "@apollo/client": "^3.7.3",
+    "@apollo/client": "^3.8.6",
     "@quasar/extras": "^1.12.4",
     "@vue/apollo-composable": "^4.0.0-beta.1",
     "@vue/apollo-option": "^4.0.0-alpha.20",
-    "axios": "^1.2.1",
     "date-fns": "^2.29.3",
     "date-fns-tz": "^1.3.7",
     "e": "^0.2.2",
     "graphql": "^16.6.0",
     "graphql-tag": "^2.12.6",
-    "openapi-typescript-fetch": "^1.1.3",
+    "openapi-fetch": "^0.10.2",
     "pinia": "^2.0.28",
     "quasar": "^2.5.0",
     "vue": "^3.2.6",
diff --git a/lib/tool_shed/webapp/frontend/src/apiUtil.ts b/lib/tool_shed/webapp/frontend/src/apiUtil.ts
deleted file mode 100644
index 9dfa3df9109dc94e4954699527f25458dfc0c5d3..0000000000000000000000000000000000000000
--- a/lib/tool_shed/webapp/frontend/src/apiUtil.ts
+++ /dev/null
@@ -1,19 +0,0 @@
-import axios from "axios"
-import { RawAxiosRequestConfig } from "axios"
-import { components } from "@/schema"
-
-type User = components["schemas"]["UserV2"]
-
-export async function getCurrentUser(): Promise<User | null> {
-    const conf: RawAxiosRequestConfig<unknown> = {}
-    conf.validateStatus = (status: number) => {
-        const valid = status == 200 || status == 404
-        return valid
-    }
-    const { data: user, status } = await axios.get<object>("/api/users/current", conf)
-    if (status == 404) {
-        return null
-    } else {
-        return user as User
-    }
-}
diff --git a/lib/tool_shed/webapp/frontend/src/components/RecentlyCreatedRepositories.vue b/lib/tool_shed/webapp/frontend/src/components/RecentlyCreatedRepositories.vue
index 934f4e38598518775965c3331139ecd03f9c1973..f9383afb94a727d542b7361cd0528c52df785401 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RecentlyCreatedRepositories.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RecentlyCreatedRepositories.vue
@@ -8,7 +8,7 @@ import RepositoryCreation from "@/components/RepositoryCreation.vue"
 
 const query = graphql(`
     query recentlyCreatedRepositories {
-        relayRepositories(first: 10, sort: UPDATE_TIME_DESC) {
+        relayRepositories(first: 10, sort: CREATE_TIME_DESC) {
             edges {
                 node {
                     ...RepositoryCreationItem
diff --git a/lib/tool_shed/webapp/frontend/src/components/RegisterPage.vue b/lib/tool_shed/webapp/frontend/src/components/RegisterPage.vue
index a66cf394f529a34d4fe7abb4451f2053655b6b0b..dbb856522431b30e6c61b7752a9f525bad9b7f3e 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RegisterPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RegisterPage.vue
@@ -1,8 +1,8 @@
 <script setup lang="ts">
 import { ref } from "vue"
 import ModalForm from "@/components/ModalForm.vue"
-import { fetcher } from "@/schema"
-import { notify } from "@/util"
+import { ToolShedApi } from "@/schema"
+import { notifyOnCatch } from "@/util"
 import router from "@/router"
 import { AUTH_FORM_INPUT_PROPS } from "@/constants"
 
@@ -12,19 +12,25 @@ const confirm = ref("")
 const username = ref("")
 
 const title = ref("Register")
-const createFetcher = fetcher.path("/api_internal/register").method("post").create()
 // type Response = components["schemas"]["UiRegisterResponse"]
 
 async function onRegister() {
     // TODO: handle confirm and implement bear_field.
     // let data: Response
     try {
-        const { data } = await createFetcher({
-            email: email.value,
-            password: password.value,
-            username: username.value,
-            bear_field: "",
+        const { data } = await ToolShedApi().POST("/api_internal/register", {
+            body: {
+                email: email.value,
+                password: password.value,
+                username: username.value,
+                bear_field: "",
+            },
         })
+
+        if (!data) {
+            return
+        }
+
         const query = {
             activation_error: data.activation_error ? "true" : "false",
             activation_sent: data.activation_sent ? "true" : "false",
@@ -33,7 +39,7 @@ async function onRegister() {
         }
         router.push({ path: "/registration_success", query: query })
     } catch (e) {
-        notify(String(e))
+        notifyOnCatch(e)
     }
 }
 </script>
diff --git a/lib/tool_shed/webapp/frontend/src/components/RepositoriesGrid.vue b/lib/tool_shed/webapp/frontend/src/components/RepositoriesGrid.vue
index fd8ed9104b7ad7c6b8ba19aa088700e7e3c73ea6..972677babae9b1c0728d651c351ddfc877977642 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RepositoriesGrid.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RepositoriesGrid.vue
@@ -14,6 +14,7 @@ interface RepositoriesGridProps {
     rows: Array<RepositoryGridItem>
     noDataLabel?: string
     debug?: boolean
+    allowSearch?: boolean
 }
 
 interface ScrollDetails {
@@ -29,6 +30,7 @@ const compProps = withDefaults(defineProps<RepositoriesGridProps>(), {
     debug: false,
     onScroll: null as OnScroll | null,
     noDataLabel: "No repositories found",
+    allowSearch: false,
 })
 
 const pagination = { rowsPerPage: 0 }
@@ -44,7 +46,7 @@ const NAME_COLUMN: QTableColumn = {
     name: "name",
     label: "Name",
     align: "left",
-    field: "name",
+    field: "effectiveName",
 }
 
 const columns = computed(() => {
@@ -58,7 +60,6 @@ const columns = computed(() => {
 const tableLoading = ref(false)
 
 async function onVirtualScroll(details: ScrollDetails) {
-    console.log(details)
     const { to, direction } = details
     if (direction == "decrease") {
         return
@@ -72,10 +73,14 @@ async function onVirtualScroll(details: ScrollDetails) {
     }
 }
 
+const search = ref("")
+
 // Adapt the rows with doubleIndex so
 const adaptedRows = computed(() =>
     compProps.rows.map((r) => {
-        return { doubleIndex: r.index * 2, ...r }
+        // create this effective name so we are filtering on this when searching...
+        const effectiveName = r.owner + " " + r.name
+        return { doubleIndex: r.index * 2, effectiveName: effectiveName, ...r }
     })
 )
 </script>
@@ -84,10 +89,10 @@ const adaptedRows = computed(() =>
         <q-table
             v-if="loading || rows.length > 0"
             style="height: 85vh"
-            :title="title"
             :rows="adaptedRows"
             :columns="columns"
             :loading="tableLoading"
+            :filter="search"
             row-key="newIndex"
             virtual-scroll
             :virtual-scroll-item-size="48"
@@ -99,6 +104,16 @@ const adaptedRows = computed(() =>
             hide-header
             hide-bottom
         >
+            <template #top>
+                <div class="row col-12">
+                    <div class="q-table__control col-8">
+                        <div class="q-table__title">{{ title }}</div>
+                    </div>
+                    <div class="col-4 justify-end q-pa-md" v-if="allowSearch">
+                        <q-input v-model="search" autogrow label="Filter"></q-input>
+                    </div>
+                </div>
+            </template>
             <template #body="props">
                 <q-tr :props="props" :key="`m_${props.row.index}`">
                     <q-td v-for="col in props.cols" :key="col.name" :props="props">
diff --git a/lib/tool_shed/webapp/frontend/src/components/RepositoryActions.vue b/lib/tool_shed/webapp/frontend/src/components/RepositoryActions.vue
index ccd55676efbdb4f39d84b04f9bf6640b36516155..ccd07ba41aeffce8c11489229d4b4f3d18705034 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RepositoryActions.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RepositoryActions.vue
@@ -1,10 +1,12 @@
 <script setup lang="ts">
-import { fetcher } from "@/schema"
+import { ToolShedApi } from "@/schema"
 import { notify, notifyOnCatch } from "@/util"
-const resetFetcher = fetcher.path("/api/repositories/{encoded_repository_id}/reset_metadata").method("post").create()
 
 async function resetMetadata() {
-    resetFetcher({ encoded_repository_id: props.repositoryId })
+    ToolShedApi()
+        .POST("/api/repositories/{encoded_repository_id}/reset_metadata", {
+            params: { path: { encoded_repository_id: props.repositoryId } },
+        })
         .catch(notifyOnCatch)
         .then(() => {
             notify("Repository metadata reset.")
diff --git a/lib/tool_shed/webapp/frontend/src/components/RepositoryCreation.vue b/lib/tool_shed/webapp/frontend/src/components/RepositoryCreation.vue
index 8e41a409c1bdf224c692ed68f6aea59a34e62fa7..2b98257dff5d2cbf640814778016985d034c49e0 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RepositoryCreation.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RepositoryCreation.vue
@@ -1,20 +1,9 @@
 <script setup lang="ts">
 import UtcDate from "@/components/UtcDate.vue"
 
-import { graphql } from "@/gql"
 import { type FragmentType, useFragment } from "@/gql/fragment-masking"
 import { goToRepository } from "@/router"
-
-const CreateFragment = graphql(/* GraphQL */ `
-    fragment RepositoryCreationItem on RelayRepository {
-        encodedId
-        name
-        user {
-            username
-        }
-        createTime
-    }
-`)
+import { CreateFragment } from "@/gqlFragements"
 
 const props = defineProps<{
     creation: FragmentType<typeof CreateFragment>
diff --git a/lib/tool_shed/webapp/frontend/src/components/RevisionActions.vue b/lib/tool_shed/webapp/frontend/src/components/RevisionActions.vue
index 525934331e1e69e24041236614b054e8d609c97b..305821460e5e9a3972520c6f1d131b868dc8f943 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RevisionActions.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RevisionActions.vue
@@ -1,16 +1,8 @@
 <script setup lang="ts">
 import { computed } from "vue"
 import { RevisionMetadata } from "@/schema"
-import { fetcher } from "@/schema"
+import { ToolShedApi } from "@/schema"
 import { notify, notifyOnCatch } from "@/util"
-const setMaliciousFetcher = fetcher
-    .path("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious")
-    .method("put")
-    .create()
-const unsetMaliciousFetcher = fetcher
-    .path("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious")
-    .method("delete")
-    .create()
 
 interface RevisionActionsProps {
     repositoryId: string
@@ -20,27 +12,39 @@ interface RevisionActionsProps {
 const props = defineProps<RevisionActionsProps>()
 
 async function setMalicious() {
-    setMaliciousFetcher({
-        encoded_repository_id: props.repositoryId,
-        changeset_revision: props.currentMetadata.changeset_revision,
-    })
+    ToolShedApi()
+        .PUT("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious", {
+            params: {
+                path: {
+                    encoded_repository_id: props.repositoryId,
+                    changeset_revision: props.currentMetadata.changeset_revision,
+                },
+            },
+        })
         .catch(notifyOnCatch)
         .then(() => {
             notify("Marked repository as malicious")
             emits("update")
         })
 }
+
 async function unsetMalicious() {
-    unsetMaliciousFetcher({
-        encoded_repository_id: props.repositoryId,
-        changeset_revision: props.currentMetadata.changeset_revision,
-    })
+    ToolShedApi()
+        .DELETE("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious", {
+            params: {
+                path: {
+                    encoded_repository_id: props.repositoryId,
+                    changeset_revision: props.currentMetadata.changeset_revision,
+                },
+            },
+        })
         .catch(notifyOnCatch)
         .then(() => {
             notify("Un-marked repository as malicious")
             emits("update")
         })
 }
+
 const malicious = computed(() => props.currentMetadata.malicious)
 type Emits = {
     (eventName: "update"): void
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/AdminControls.vue b/lib/tool_shed/webapp/frontend/src/components/pages/AdminControls.vue
index 14744ddb64d8633fff0dbce0f375ad77a96af6ae..13f305e5a2e5adcdef5c46d783279f056d60bbf8 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/AdminControls.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/AdminControls.vue
@@ -1,16 +1,20 @@
 <script setup lang="ts">
 import { ref } from "vue"
-import { fetcher, components } from "@/schema"
+import { ToolShedApi, components } from "@/schema"
 import PageContainer from "@/components/PageContainer.vue"
+import { notifyOnCatch } from "@/util"
 
-const searchIndexer = fetcher.path("/api/tools/build_search_index").method("put").create()
 type IndexResults = components["schemas"]["BuildSearchIndexResponse"]
 
-const searchResults = ref(null as IndexResults | null)
+const searchResults = ref<IndexResults>()
 
 async function onIndex() {
-    const { data } = await searchIndexer({})
-    searchResults.value = data
+    try {
+        const { data } = await ToolShedApi().PUT("/api/tools/build_search_index")
+        searchResults.value = data
+    } catch (e) {
+        notifyOnCatch(e)
+    }
 }
 </script>
 <template>
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/ChangePassword.vue b/lib/tool_shed/webapp/frontend/src/components/pages/ChangePassword.vue
index de69706dec343d2b35bce52ed4160bfe81b8f058..267286a548482edce48bdc09d7b6e2afd8f66c72 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/ChangePassword.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/ChangePassword.vue
@@ -2,8 +2,8 @@
 import { ref } from "vue"
 import ModalForm from "@/components/ModalForm.vue"
 import { AUTH_FORM_INPUT_PROPS } from "@/constants"
-import { fetcher } from "@/schema"
-import { errorMessage } from "@/util"
+import { ToolShedApi } from "@/schema"
+import { errorMessageAsString } from "@/util"
 import ErrorBanner from "@/components/ErrorBanner.vue"
 import router from "@/router"
 
@@ -11,18 +11,20 @@ const current = ref("")
 const password = ref("")
 const confirm = ref("")
 const error = ref<string | null>(null)
-const changePasswordFetcher = fetcher.path("/api_internal/change_password").method("put").create()
 
 async function onChange() {
-    changePasswordFetcher({
-        current: current.value,
-        password: password.value,
-    })
+    ToolShedApi()
+        .PUT("/api_internal/change_password", {
+            body: {
+                current: current.value,
+                password: password.value,
+            },
+        })
         .then(() => {
             router.push("/")
         })
-        .catch((e: Error) => {
-            error.value = errorMessage(e)
+        .catch((e) => {
+            error.value = errorMessageAsString(e)
         })
 }
 
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/CitableRepositoryPage.vue b/lib/tool_shed/webapp/frontend/src/components/pages/CitableRepositoryPage.vue
index bbf717fecde44447a8784096cc3f9155503daff1..63f89714af043f104e3b885d69d843475e3f1fca 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/CitableRepositoryPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/CitableRepositoryPage.vue
@@ -1,12 +1,11 @@
 <script setup lang="ts">
 import { ref, watch } from "vue"
 import RepositoryPage from "./RepositoryPage.vue"
-import { fetcher } from "@/schema"
+import { ToolShedApi } from "@/schema"
 import type { Repository } from "@/schema/types"
 import LoadingDiv from "@/components/LoadingDiv.vue"
 import ErrorBanner from "@/components/ErrorBanner.vue"
-
-const indexFetcher = fetcher.path("/api/repositories").method("get").create()
+import { errorMessageAsString } from "@/util"
 
 interface CitableRepositoryPageProps {
     username: string
@@ -18,16 +17,28 @@ const error = ref<string | null>(null)
 
 async function update() {
     error.value = null
-    const { data } = await indexFetcher({ owner: props.username, name: props.repositoryName })
-    if (data instanceof Array) {
-        if (data.length == 0) {
-            error.value = `Repository ${props.username}/${props.repositoryName} is not found`
-        } else {
-            const repository: Repository = data[0]
-            if (repository.id != repositoryId.value) {
-                repositoryId.value = repository.id
+    try {
+        const { data } = await ToolShedApi().GET("/api/repositories", {
+            params: {
+                query: {
+                    owner: props.username,
+                    name: props.repositoryName,
+                },
+            },
+        })
+
+        if (data instanceof Array) {
+            if (data.length == 0) {
+                error.value = `Repository ${props.username}/${props.repositoryName} is not found`
+            } else {
+                const repository: Repository = data[0]
+                if (repository.id != repositoryId.value) {
+                    repositoryId.value = repository.id
+                }
             }
         }
+    } catch (e) {
+        error.value = errorMessageAsString(e)
     }
 }
 
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/ManageApiKey.vue b/lib/tool_shed/webapp/frontend/src/components/pages/ManageApiKey.vue
index 74d7c55980f9b1c13f3b5a907592d7bdd8262d37..0729f12d664e5fc8f452e089c99a93be752f257d 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/ManageApiKey.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/ManageApiKey.vue
@@ -1,15 +1,11 @@
 <script setup lang="ts">
 import { ref, computed } from "vue"
 import PageContainer from "@/components/PageContainer.vue"
-import { fetcher } from "@/schema"
-import { notify, copyAndNotify, notifyOnCatch } from "@/util"
+import { ToolShedApi } from "@/schema"
+import { notify, copyAndNotify, notifyOnCatch, errorMessageAsString } from "@/util"
 import ConfigFileContents from "@/components/ConfigFileContents.vue"
 
-const apiKeyFetcher = fetcher.path("/api/users/{encoded_user_id}/api_key").method("get").create()
-const deleteKeyFetcher = fetcher.path("/api/users/{encoded_user_id}/api_key").method("delete").create()
-const recreateKeyFetcher = fetcher.path("/api/users/{encoded_user_id}/api_key").method("post").create()
-
-const apiKey = ref(null as string | null)
+const apiKey = ref<string | null>(null)
 const planemoConfig = computed(
     () =>
         `sheds:
@@ -26,29 +22,48 @@ async function copyKey() {
 const params = { encoded_user_id: "current" }
 
 async function init() {
-    apiKeyFetcher(params)
-        .then(({ data }) => {
-            apiKey.value = data
+    try {
+        const { data } = await ToolShedApi().GET("/api/users/{encoded_user_id}/api_key", {
+            params: {
+                path: params,
+            },
         })
-        .catch(notifyOnCatch)
+        apiKey.value = data ?? null
+    } catch (e) {
+        notifyOnCatch(new Error(`Error fetching API key: ${errorMessageAsString(e)}`))
+    }
 }
 
 async function deleteKey() {
-    deleteKeyFetcher(params)
-        .then(() => {
-            apiKey.value = null
-            notify("API key deactivated")
+    try {
+        await ToolShedApi().DELETE("/api/users/{encoded_user_id}/api_key", {
+            params: {
+                path: params,
+            },
         })
-        .catch(notifyOnCatch)
+
+        apiKey.value = null
+        notify("API key deactivated")
+    } catch (e) {
+        notifyOnCatch(new Error(`Error deactivating API key: ${errorMessageAsString(e)}`))
+    }
 }
 
 async function recreateKey() {
-    recreateKeyFetcher(params)
-        .then(({ data }) => {
+    try {
+        const { data } = await ToolShedApi().POST("/api/users/{encoded_user_id}/api_key", {
+            params: {
+                path: params,
+            },
+        })
+
+        if (data) {
             apiKey.value = data
             notify("Re-generated API key")
-        })
-        .catch(notifyOnCatch)
+        }
+    } catch (e) {
+        notifyOnCatch(new Error(`Error re-generating API key: ${errorMessageAsString(e)}`))
+    }
 }
 
 void init()
@@ -76,7 +91,7 @@ void init()
             alternate means to access your account and should be treated with the same care as your login password.
         </p>
         <p>
-            Add the following block to your Planemo configuration file (typically found in
+            Add the following block to your Planemo configuration file (typically) found in
             <code>~/.planemo.yml</code> in your
         </p>
         <config-file-contents name=".planemo.yml" :contents="planemoConfig" what="Planemo configuration" />
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesByCategory.vue b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesByCategory.vue
index 868415b472415def92ecd9287f12d12991c9a9f4..cb3046247e0776c4df5d1e54d525be0b1d6a74eb 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesByCategory.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesByCategory.vue
@@ -1,8 +1,8 @@
 <script setup lang="ts">
-import { computed } from "vue"
+import { computed, ref } from "vue"
 import { useCategoriesStore } from "@/stores"
 import RepositoriesGrid from "@/components/RepositoriesGrid.vue"
-import { nodeToRow } from "@/components/RepositoriesGridInterface"
+import { nodeToRow, type RepositoryGridItem } from "@/components/RepositoriesGridInterface"
 import ErrorBanner from "@/components/ErrorBanner.vue"
 import LoadingDiv from "@/components/LoadingDiv.vue"
 import { graphql } from "@/gql"
@@ -30,7 +30,7 @@ const categoryName = computed(() => {
 
 const query = graphql(/* GraphQL */ `
     query repositoriesByCategory($categoryId: String, $cursor: String) {
-        relayRepositoriesForCategory(encodedId: $categoryId, sort: UPDATE_TIME_DESC, first: 10, after: $cursor) {
+        relayRepositoriesForCategory(encodedId: $categoryId, sort: NAME_ASC, first: 10, after: $cursor) {
             edges {
                 cursor
                 node {
@@ -67,6 +67,11 @@ const rows = computed(() => {
     <loading-div v-if="loading" />
     <error-banner error="Failed to load repository" v-else-if="error"> </error-banner>
     <q-page class="q-pa-md" v-if="categoryName">
-        <repositories-grid :title="`Repositories for ${categoryName}`" :rows="rows" :on-scroll="onScroll" />
+        <repositories-grid
+            :title="`Repositories for ${categoryName}`"
+            :rows="rows"
+            :on-scroll="onScroll"
+            :allow-search="true"
+        />
     </q-page>
 </template>
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesBySearch.vue b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesBySearch.vue
index a2a87875cc5f1b0fde78874369df90cfcc6d24bc..bf8ca25559f35c418975814aab05ad7596e49a9d 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesBySearch.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoriesBySearch.vue
@@ -3,11 +3,12 @@ import { computed, ref, watch } from "vue"
 import PageContainer from "@/components/PageContainer.vue"
 import RepositoryGrid from "@/components/RepositoriesGrid.vue"
 import { type RepositoryGridItem, type OnScroll } from "@/components/RepositoriesGridInterface"
-import { fetcher, components } from "@/schema"
-const searchFetcher = fetcher.path("/api/repositories").method("get").create()
+import { ToolShedApi, components } from "@/schema"
+import { notifyOnCatch } from "@/util"
 
 const query = ref("")
 const page = ref(1)
+const searching = ref(false)
 const fetchedLastPage = ref(false)
 const hits = ref([] as Array<RepositorySearchHit>)
 
@@ -15,23 +16,40 @@ type RepositorySearchHit = components["schemas"]["RepositorySearchHit"]
 
 async function doQuery() {
     const queryValue = query.value
-    const { data } = await searchFetcher({ q: queryValue, page: page.value, page_size: 10 })
-    if (query.value != queryValue) {
-        console.log("query changed.... not using these results...")
+    if (!queryValue) {
+        hits.value = []
         return
     }
-    if ("hits" in data) {
-        if (page.value == 1) {
-            hits.value = data.hits
-        } else {
-            data.hits.forEach((h) => hits.value.push(h))
+    searching.value = true
+    try {
+        const { data } = await ToolShedApi().GET("/api/repositories", {
+            params: {
+                query: { q: queryValue, page: page.value, page_size: 10 },
+            },
+        })
+
+        if (query.value != queryValue) {
+            console.log("query changed.... not using these results...")
+            return
         }
-        if (hits.value.length >= parseInt(data.total_results)) {
-            fetchedLastPage.value = true
+
+        if (data && "hits" in data) {
+            if (page.value == 1) {
+                hits.value = data.hits
+            } else {
+                data.hits.forEach((h) => hits.value.push(h))
+            }
+            if (hits.value.length >= parseInt(data.total_results)) {
+                fetchedLastPage.value = true
+            }
+            page.value = page.value + 1
+        } else {
+            throw Error("Server response structure error for [" + queryValue + "]")
         }
-        page.value = page.value + 1
-    } else {
-        throw Error("Server response structure error.")
+    } catch (e) {
+        notifyOnCatch(e)
+    } finally {
+        searching.value = false
     }
 }
 
@@ -77,12 +95,26 @@ function rowsFunc() {
     return rows
 }*/
 
+const noDataLabel = computed<string>(() => {
+    if (searching.value) {
+        return "Searching..."
+    } else {
+        return "No repositories matching query"
+    }
+})
+
 const rows = realRows
 </script>
 <template>
     <page-container>
         <q-input debounce="20" filled v-model="query" label="Search Repositories" />
-        <repository-grid v-if="query && query.length > 1" :rows="rows" title="Search Results" :on-scroll="OnScrollImpl">
+        <repository-grid
+            v-if="query && query.length > 1"
+            :rows="rows"
+            title="Search Results"
+            :on-scroll="OnScrollImpl"
+            :no-data-label="noDataLabel"
+        >
         </repository-grid>
     </page-container>
 </template>
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
index d337877ce8bd89d7d615532b7e1c32a088e16a9f..fc3bc5cafb7a5c9e0d20ffddcc18a018f41c12e3 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/RepositoryPage.vue
@@ -14,21 +14,10 @@ import ConfigFileContents from "@/components/ConfigFileContents.vue"
 import RepositoryLinks from "@/components/RepositoryLinks.vue"
 import RepositoryExplore from "@/components/RepositoryExplore.vue"
 import { type RevisionMetadata } from "@/schema"
-import { fetcher } from "@/schema"
+import { ToolShedApi } from "@/schema"
 import { notifyOnCatch } from "@/util"
 import { UPDATING_WITH_PLANEMO_URL, EPHEMERIS_TRAINING } from "@/constants"
 
-const readmeFetcher = fetcher
-    .path("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/readmes")
-    .method("get")
-    .create()
-
-const deprecateFetcher = fetcher.path("/api/repositories/{encoded_repository_id}/deprecated").method("put").create()
-const undeprecateFetcher = fetcher
-    .path("/api/repositories/{encoded_repository_id}/deprecated")
-    .method("delete")
-    .create()
-
 interface RepositoryProps {
     repositoryId: string
     changesetRevision?: string | null
@@ -41,14 +30,24 @@ function onUpdate() {
 async function onDeprecate() {
     const repositoryId = repository.value?.id
     if (repositoryId) {
-        deprecateFetcher({ encoded_repository_id: repositoryId }).then(onUpdate).catch(notifyOnCatch)
+        ToolShedApi()
+            .PUT("/api/repositories/{encoded_repository_id}/deprecated", {
+                params: { path: { encoded_repository_id: repositoryId } },
+            })
+            .then(onUpdate)
+            .catch(notifyOnCatch)
     }
 }
 
 async function onUndeprecate() {
     const repositoryId = repository.value?.id
     if (repositoryId) {
-        undeprecateFetcher({ encoded_repository_id: repositoryId }).then(onUpdate).catch(notifyOnCatch)
+        ToolShedApi()
+            .DELETE("/api/repositories/{encoded_repository_id}/deprecated", {
+                params: { path: { encoded_repository_id: repositoryId } },
+            })
+            .then(onUpdate)
+            .catch(notifyOnCatch)
     }
 }
 
@@ -133,10 +132,15 @@ watch(
 
 watch(currentRevision, () => {
     if (currentRevision.value) {
-        readmeFetcher({
-            encoded_repository_id: props.repositoryId,
-            changeset_revision: currentRevision.value,
-        })
+        ToolShedApi()
+            .GET("/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/readmes", {
+                params: {
+                    path: {
+                        encoded_repository_id: props.repositoryId,
+                        changeset_revision: currentRevision.value,
+                    },
+                },
+            })
             .then((response) => {
                 if (response.data) {
                     readmes.value = response.data
diff --git a/lib/tool_shed/webapp/frontend/src/gql/gql.ts b/lib/tool_shed/webapp/frontend/src/gql/gql.ts
index 0793f695985973a7955d67946898a92a8289b9a7..8faa4df3e4c24d5bfad6230436ff5bf645e22c8a 100644
--- a/lib/tool_shed/webapp/frontend/src/gql/gql.ts
+++ b/lib/tool_shed/webapp/frontend/src/gql/gql.ts
@@ -13,20 +13,20 @@ import { TypedDocumentNode as DocumentNode } from "@graphql-typed-document-node/
  * Therefore it is highly recommended to use the babel-plugin for production.
  */
 const documents = {
-    "\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: UPDATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n":
+    "\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: CREATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n":
         types.RecentlyCreatedRepositoriesDocument,
     "\n    query recentRepositoryUpdates {\n        relayRepositories(first: 10, sort: UPDATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryUpdateItem\n                }\n            }\n        }\n    }\n":
         types.RecentRepositoryUpdatesDocument,
     "\n    query repositoriesByOwner($username: String, $cursor: String) {\n        relayRepositoriesForOwner(username: $username, sort: UPDATE_TIME_DESC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n":
         types.RepositoriesByOwnerDocument,
-    "\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n":
-        types.RepositoryCreationItemFragmentDoc,
-    "\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: UPDATE_TIME_DESC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n":
+    "\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: NAME_ASC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n":
         types.RepositoriesByCategoryDocument,
     "\n    fragment RepositoryListItemFragment on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        description\n        type\n        updateTime\n        homepageUrl\n        remoteRepositoryUrl\n    }\n":
         types.RepositoryListItemFragmentFragmentDoc,
     "\n    fragment RepositoryUpdateItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        updateTime\n    }\n":
         types.RepositoryUpdateItemFragmentDoc,
+    "\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n":
+        types.RepositoryCreationItemFragmentDoc,
 }
 
 /**
@@ -47,8 +47,8 @@ export function graphql(source: string): unknown
  * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
  */
 export function graphql(
-    source: "\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: UPDATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n"
-): (typeof documents)["\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: UPDATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n"]
+    source: "\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: CREATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n"
+): (typeof documents)["\n    query recentlyCreatedRepositories {\n        relayRepositories(first: 10, sort: CREATE_TIME_DESC) {\n            edges {\n                node {\n                    ...RepositoryCreationItem\n                }\n            }\n        }\n    }\n"]
 /**
  * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
  */
@@ -65,14 +65,8 @@ export function graphql(
  * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
  */
 export function graphql(
-    source: "\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n"
-): (typeof documents)["\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n"]
-/**
- * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
- */
-export function graphql(
-    source: "\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: UPDATE_TIME_DESC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n"
-): (typeof documents)["\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: UPDATE_TIME_DESC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n"]
+    source: "\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: NAME_ASC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n"
+): (typeof documents)["\n    query repositoriesByCategory($categoryId: String, $cursor: String) {\n        relayRepositoriesForCategory(encodedId: $categoryId, sort: NAME_ASC, first: 10, after: $cursor) {\n            edges {\n                cursor\n                node {\n                    ...RepositoryListItemFragment\n                }\n            }\n            pageInfo {\n                endCursor\n                hasNextPage\n            }\n        }\n    }\n"]
 /**
  * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
  */
@@ -85,6 +79,12 @@ export function graphql(
 export function graphql(
     source: "\n    fragment RepositoryUpdateItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        updateTime\n    }\n"
 ): (typeof documents)["\n    fragment RepositoryUpdateItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        updateTime\n    }\n"]
+/**
+ * The graphql function is used to parse GraphQL queries into a document that can be used by GraphQL clients.
+ */
+export function graphql(
+    source: "\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n"
+): (typeof documents)["\n    fragment RepositoryCreationItem on RelayRepository {\n        encodedId\n        name\n        user {\n            username\n        }\n        createTime\n    }\n"]
 
 export function graphql(source: string) {
     return (documents as any)[source] ?? {}
diff --git a/lib/tool_shed/webapp/frontend/src/gql/graphql.ts b/lib/tool_shed/webapp/frontend/src/gql/graphql.ts
index f6c3433eb96be4ba929266346f06746107c0a9e5..e7a02dc13d6220b2e16515971d528f90978bc724 100644
--- a/lib/tool_shed/webapp/frontend/src/gql/graphql.ts
+++ b/lib/tool_shed/webapp/frontend/src/gql/graphql.ts
@@ -20,6 +20,27 @@ export type Scalars = {
     DateTime: any
 }
 
+export type BooleanFilter = {
+    eq?: InputMaybe<Scalars["Boolean"]>
+    in?: InputMaybe<Array<InputMaybe<Scalars["Boolean"]>>>
+    nEq?: InputMaybe<Scalars["Boolean"]>
+    notIn?: InputMaybe<Array<InputMaybe<Scalars["Boolean"]>>>
+}
+
+export type DefaultDateTimeScalarFilter = {
+    eq?: InputMaybe<Scalars["DateTime"]>
+    in?: InputMaybe<Array<InputMaybe<Scalars["DateTime"]>>>
+    nEq?: InputMaybe<Scalars["DateTime"]>
+    notIn?: InputMaybe<Array<InputMaybe<Scalars["DateTime"]>>>
+}
+
+export type IdFilter = {
+    eq?: InputMaybe<Scalars["ID"]>
+    in?: InputMaybe<Array<InputMaybe<Scalars["ID"]>>>
+    nEq?: InputMaybe<Scalars["ID"]>
+    notIn?: InputMaybe<Array<InputMaybe<Scalars["ID"]>>>
+}
+
 /** An object with an ID */
 export type Node = {
     /** The ID of the object */
@@ -61,6 +82,7 @@ export type QueryNodeArgs = {
 export type QueryRelayCategoriesArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayCategoryFilter>
     first?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
     sort?: InputMaybe<Array<InputMaybe<RelayCategorySortEnum>>>
@@ -69,6 +91,7 @@ export type QueryRelayCategoriesArgs = {
 export type QueryRelayRepositoriesArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayRepositoryFilter>
     first?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
     sort?: InputMaybe<Array<InputMaybe<RelayRepositorySortEnum>>>
@@ -78,6 +101,7 @@ export type QueryRelayRepositoriesForCategoryArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
     encodedId?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayRepositoryFilter>
     first?: InputMaybe<Scalars["Int"]>
     id?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
@@ -87,6 +111,7 @@ export type QueryRelayRepositoriesForCategoryArgs = {
 export type QueryRelayRepositoriesForOwnerArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayRepositoryFilter>
     first?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
     sort?: InputMaybe<Array<InputMaybe<RelayRepositorySortEnum>>>
@@ -96,6 +121,7 @@ export type QueryRelayRepositoriesForOwnerArgs = {
 export type QueryRelayRevisionsArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayRepositoryMetadataFilter>
     first?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
     sort?: InputMaybe<Array<InputMaybe<RelayRepositoryMetadataSortEnum>>>
@@ -104,6 +130,7 @@ export type QueryRelayRevisionsArgs = {
 export type QueryRelayUsersArgs = {
     after?: InputMaybe<Scalars["String"]>
     before?: InputMaybe<Scalars["String"]>
+    filter?: InputMaybe<RelayUserFilter>
     first?: InputMaybe<Scalars["Int"]>
     last?: InputMaybe<Scalars["Int"]>
     sort?: InputMaybe<Array<InputMaybe<RelayUserSortEnum>>>
@@ -138,6 +165,17 @@ export type RelayCategoryEdge = {
     node?: Maybe<RelayCategory>
 }
 
+export type RelayCategoryFilter = {
+    and?: InputMaybe<Array<InputMaybe<RelayCategoryFilter>>>
+    createTime?: InputMaybe<DefaultDateTimeScalarFilter>
+    deleted?: InputMaybe<BooleanFilter>
+    description?: InputMaybe<StringFilter>
+    id?: InputMaybe<IdFilter>
+    name?: InputMaybe<StringFilter>
+    or?: InputMaybe<Array<InputMaybe<RelayCategoryFilter>>>
+    updateTime?: InputMaybe<DefaultDateTimeScalarFilter>
+}
+
 /** An enumeration. */
 export enum RelayCategorySortEnum {
     CreateTimeAsc = "CREATE_TIME_ASC",
@@ -187,6 +225,20 @@ export type RelayRepositoryEdge = {
     node?: Maybe<RelayRepository>
 }
 
+export type RelayRepositoryFilter = {
+    and?: InputMaybe<Array<InputMaybe<RelayRepositoryFilter>>>
+    createTime?: InputMaybe<DefaultDateTimeScalarFilter>
+    description?: InputMaybe<StringFilter>
+    homepageUrl?: InputMaybe<StringFilter>
+    id?: InputMaybe<IdFilter>
+    longDescription?: InputMaybe<StringFilter>
+    name?: InputMaybe<StringFilter>
+    or?: InputMaybe<Array<InputMaybe<RelayRepositoryFilter>>>
+    remoteRepositoryUrl?: InputMaybe<StringFilter>
+    type?: InputMaybe<StringFilter>
+    updateTime?: InputMaybe<DefaultDateTimeScalarFilter>
+}
+
 export type RelayRepositoryMetadata = Node & {
     __typename?: "RelayRepositoryMetadata"
     changesetRevision: Scalars["String"]
@@ -217,6 +269,12 @@ export type RelayRepositoryMetadataEdge = {
     node?: Maybe<RelayRepositoryMetadata>
 }
 
+export type RelayRepositoryMetadataFilter = {
+    and?: InputMaybe<Array<InputMaybe<RelayRepositoryMetadataFilter>>>
+    id?: InputMaybe<IdFilter>
+    or?: InputMaybe<Array<InputMaybe<RelayRepositoryMetadataFilter>>>
+}
+
 /** An enumeration. */
 export enum RelayRepositoryMetadataSortEnum {
     IdAsc = "ID_ASC",
@@ -269,6 +327,13 @@ export type RelayUserEdge = {
     node?: Maybe<RelayUser>
 }
 
+export type RelayUserFilter = {
+    and?: InputMaybe<Array<InputMaybe<RelayUserFilter>>>
+    id?: InputMaybe<IdFilter>
+    or?: InputMaybe<Array<InputMaybe<RelayUserFilter>>>
+    username?: InputMaybe<StringFilter>
+}
+
 /** An enumeration. */
 export enum RelayUserSortEnum {
     IdAsc = "ID_ASC",
@@ -327,6 +392,16 @@ export type SimpleUser = {
     username: Scalars["String"]
 }
 
+export type StringFilter = {
+    eq?: InputMaybe<Scalars["String"]>
+    ilike?: InputMaybe<Scalars["String"]>
+    in?: InputMaybe<Array<InputMaybe<Scalars["String"]>>>
+    like?: InputMaybe<Scalars["String"]>
+    nEq?: InputMaybe<Scalars["String"]>
+    notIn?: InputMaybe<Array<InputMaybe<Scalars["String"]>>>
+    notlike?: InputMaybe<Scalars["String"]>
+}
+
 export type RecentlyCreatedRepositoriesQueryVariables = Exact<{ [key: string]: never }>
 
 export type RecentlyCreatedRepositoriesQuery = {
@@ -383,14 +458,6 @@ export type RepositoriesByOwnerQuery = {
     } | null
 }
 
-export type RepositoryCreationItemFragment = {
-    __typename?: "RelayRepository"
-    encodedId: string
-    name: string
-    createTime?: any | null
-    user: { __typename?: "SimpleUser"; username: string }
-} & { " $fragmentName"?: "RepositoryCreationItemFragment" }
-
 export type RepositoriesByCategoryQueryVariables = Exact<{
     categoryId?: InputMaybe<Scalars["String"]>
     cursor?: InputMaybe<Scalars["String"]>
@@ -433,12 +500,20 @@ export type RepositoryUpdateItemFragment = {
     user: { __typename?: "SimpleUser"; username: string }
 } & { " $fragmentName"?: "RepositoryUpdateItemFragment" }
 
-export const RepositoryCreationItemFragmentDoc = {
+export type RepositoryCreationItemFragment = {
+    __typename?: "RelayRepository"
+    encodedId: string
+    name: string
+    createTime?: any | null
+    user: { __typename?: "SimpleUser"; username: string }
+} & { " $fragmentName"?: "RepositoryCreationItemFragment" }
+
+export const RepositoryListItemFragmentFragmentDoc = {
     kind: "Document",
     definitions: [
         {
             kind: "FragmentDefinition",
-            name: { kind: "Name", value: "RepositoryCreationItem" },
+            name: { kind: "Name", value: "RepositoryListItemFragment" },
             typeCondition: { kind: "NamedType", name: { kind: "Name", value: "RelayRepository" } },
             selectionSet: {
                 kind: "SelectionSet",
@@ -453,18 +528,22 @@ export const RepositoryCreationItemFragmentDoc = {
                             selections: [{ kind: "Field", name: { kind: "Name", value: "username" } }],
                         },
                     },
-                    { kind: "Field", name: { kind: "Name", value: "createTime" } },
+                    { kind: "Field", name: { kind: "Name", value: "description" } },
+                    { kind: "Field", name: { kind: "Name", value: "type" } },
+                    { kind: "Field", name: { kind: "Name", value: "updateTime" } },
+                    { kind: "Field", name: { kind: "Name", value: "homepageUrl" } },
+                    { kind: "Field", name: { kind: "Name", value: "remoteRepositoryUrl" } },
                 ],
             },
         },
     ],
-} as unknown as DocumentNode<RepositoryCreationItemFragment, unknown>
-export const RepositoryListItemFragmentFragmentDoc = {
+} as unknown as DocumentNode<RepositoryListItemFragmentFragment, unknown>
+export const RepositoryUpdateItemFragmentDoc = {
     kind: "Document",
     definitions: [
         {
             kind: "FragmentDefinition",
-            name: { kind: "Name", value: "RepositoryListItemFragment" },
+            name: { kind: "Name", value: "RepositoryUpdateItem" },
             typeCondition: { kind: "NamedType", name: { kind: "Name", value: "RelayRepository" } },
             selectionSet: {
                 kind: "SelectionSet",
@@ -479,22 +558,18 @@ export const RepositoryListItemFragmentFragmentDoc = {
                             selections: [{ kind: "Field", name: { kind: "Name", value: "username" } }],
                         },
                     },
-                    { kind: "Field", name: { kind: "Name", value: "description" } },
-                    { kind: "Field", name: { kind: "Name", value: "type" } },
                     { kind: "Field", name: { kind: "Name", value: "updateTime" } },
-                    { kind: "Field", name: { kind: "Name", value: "homepageUrl" } },
-                    { kind: "Field", name: { kind: "Name", value: "remoteRepositoryUrl" } },
                 ],
             },
         },
     ],
-} as unknown as DocumentNode<RepositoryListItemFragmentFragment, unknown>
-export const RepositoryUpdateItemFragmentDoc = {
+} as unknown as DocumentNode<RepositoryUpdateItemFragment, unknown>
+export const RepositoryCreationItemFragmentDoc = {
     kind: "Document",
     definitions: [
         {
             kind: "FragmentDefinition",
-            name: { kind: "Name", value: "RepositoryUpdateItem" },
+            name: { kind: "Name", value: "RepositoryCreationItem" },
             typeCondition: { kind: "NamedType", name: { kind: "Name", value: "RelayRepository" } },
             selectionSet: {
                 kind: "SelectionSet",
@@ -509,12 +584,12 @@ export const RepositoryUpdateItemFragmentDoc = {
                             selections: [{ kind: "Field", name: { kind: "Name", value: "username" } }],
                         },
                     },
-                    { kind: "Field", name: { kind: "Name", value: "updateTime" } },
+                    { kind: "Field", name: { kind: "Name", value: "createTime" } },
                 ],
             },
         },
     ],
-} as unknown as DocumentNode<RepositoryUpdateItemFragment, unknown>
+} as unknown as DocumentNode<RepositoryCreationItemFragment, unknown>
 export const RecentlyCreatedRepositoriesDocument = {
     kind: "Document",
     definitions: [
@@ -537,7 +612,7 @@ export const RecentlyCreatedRepositoriesDocument = {
                             {
                                 kind: "Argument",
                                 name: { kind: "Name", value: "sort" },
-                                value: { kind: "EnumValue", value: "UPDATE_TIME_DESC" },
+                                value: { kind: "EnumValue", value: "CREATE_TIME_DESC" },
                             },
                         ],
                         selectionSet: {
@@ -760,7 +835,7 @@ export const RepositoriesByCategoryDocument = {
                             {
                                 kind: "Argument",
                                 name: { kind: "Name", value: "sort" },
-                                value: { kind: "EnumValue", value: "UPDATE_TIME_DESC" },
+                                value: { kind: "EnumValue", value: "NAME_ASC" },
                             },
                             {
                                 kind: "Argument",
diff --git a/lib/tool_shed/webapp/frontend/src/gqlFragements.ts b/lib/tool_shed/webapp/frontend/src/gqlFragements.ts
index 4eca9379d0daa89486e586597c76cf9f899cff43..0713fbbb344dfa4277a06c39f0d8fe25ff10239c 100644
--- a/lib/tool_shed/webapp/frontend/src/gqlFragements.ts
+++ b/lib/tool_shed/webapp/frontend/src/gqlFragements.ts
@@ -25,3 +25,14 @@ export const UpdateFragment = graphql(/* GraphQL */ `
         updateTime
     }
 `)
+
+export const CreateFragment = graphql(/* GraphQL */ `
+    fragment RepositoryCreationItem on RelayRepository {
+        encodedId
+        name
+        user {
+            username
+        }
+        createTime
+    }
+`)
diff --git a/lib/tool_shed/webapp/frontend/src/schema/client.ts b/lib/tool_shed/webapp/frontend/src/schema/client.ts
new file mode 100644
index 0000000000000000000000000000000000000000..60d79234cf97d2ee841a82d18db198539ee77d29
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/src/schema/client.ts
@@ -0,0 +1,43 @@
+import createClient, { Middleware } from "openapi-fetch"
+import type { paths as ToolShedApiPaths } from "./schema"
+import { errorMessageAsString } from "@/util"
+
+let client: ToolShedApiClient
+
+function apiClientFactory() {
+    const errorHandlingMiddleware: Middleware = {
+        async onResponse({ response }) {
+            if (!response.ok) {
+                const message = response.headers.get("content-type")?.includes("json")
+                    ? await response.clone().json()
+                    : await response.clone().text()
+                throw new Error(`Request failed with status ${response.status}`, {
+                    cause: errorMessageAsString(message),
+                })
+            }
+            return response
+        },
+    }
+
+    const client = createClient<ToolShedApiPaths>({ baseUrl: "" })
+
+    client.use(errorHandlingMiddleware)
+
+    return client
+}
+
+export type ToolShedApiClient = ReturnType<typeof apiClientFactory>
+
+/**
+ * Returns the Galaxy Tool Shed API client.
+ *
+ * It can be used to make requests to the Galaxy Tool Shed API using the OpenAPI schema.
+ *
+ * See: https://openapi-ts.dev/openapi-fetch/
+ */
+export function ToolShedApi() {
+    if (!client) {
+        client = apiClientFactory()
+    }
+    return client
+}
diff --git a/lib/tool_shed/webapp/frontend/src/schema/fetcher.ts b/lib/tool_shed/webapp/frontend/src/schema/fetcher.ts
deleted file mode 100644
index bb88f1cd5cbde5ce5ddb03b19c2bed664a8347cd..0000000000000000000000000000000000000000
--- a/lib/tool_shed/webapp/frontend/src/schema/fetcher.ts
+++ /dev/null
@@ -1,20 +0,0 @@
-import { Fetcher } from "openapi-typescript-fetch"
-import type { paths } from "./schema"
-
-/*
-import type { Middleware } from "openapi-typescript-fetch";
-import { rethrowSimple } from "@/utils/simple-error";
-const rethrowSimpleMiddleware: Middleware = async (url, init, next) => {
-    try {
-        const response = await next(url, init);
-        return response;
-    } catch (e) {
-        rethrowSimple(e);
-    }
-};
-
-use: [rethrowSimpleMiddleware]
-*/
-
-export const fetcher = Fetcher.for<paths>()
-fetcher.configure({ baseUrl: "" })
diff --git a/lib/tool_shed/webapp/frontend/src/schema/index.ts b/lib/tool_shed/webapp/frontend/src/schema/index.ts
index f334fdb0d2a290746492b9bfcd11944f4b5ec312..7af624d3c151681a87fc86a13470ef4d70a5295b 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/index.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/index.ts
@@ -1,3 +1,3 @@
-export type { components, operations, paths } from "./schema"
-export { fetcher } from "./fetcher"
+export type { components, operations, paths as ToolShedApiPaths } from "./schema"
+export { ToolShedApi } from "./client"
 export type { RepositoryTool, RevisionMetadata } from "./types"
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index 738ad268432e6ed61a2988819f27ca6ab80297b5..14aab45a3c36fd1c9394a3d89580af7e1010a388 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -5,246 +5,755 @@
 
 export interface paths {
     "/api/authenticate/baseauth": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Returns returns an API key for authenticated user based on BaseAuth headers. */
         get: operations["authenticate__baseauth"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/categories": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Index
          * @description index category
          */
         get: operations["categories__index"]
+        put?: never
         /**
          * Create
          * @description create a category
          */
         post: operations["categories__create"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/categories/{encoded_category_id}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Show
          * @description show category
          */
         get: operations["categories__show"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/categories/{encoded_category_id}/repositories": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Repositories
          * @description display repositories by category
          */
         get: operations["categories__repositories"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/ga4gh/trs/v2/service-info": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Service Info */
         get: operations["tools_trs_service_info"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/ga4gh/trs/v2/toolClasses": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Tool Classes */
         get: operations["tools__trs_tool_classes"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/ga4gh/trs/v2/tools": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Trs Index */
         get: operations["tools__trs_index"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/ga4gh/trs/v2/tools/{tool_id}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Trs Get */
         get: operations["tools__trs_get"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/ga4gh/trs/v2/tools/{tool_id}/versions": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Trs Get Versions */
         get: operations["tools__trs_get_versions"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Index
          * @description Get a list of repositories or perform a search.
          */
         get: operations["repositories__index"]
+        put?: never
         /**
          * Create
          * @description create a new repository
          */
         post: operations["repositories__create"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/get_ordered_installable_revisions": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Get Ordered Installable Revisions
          * @description Get an ordered list of the repository changeset revisions that are installable
          */
         get: operations["repositories__get_ordered_installable_revisions"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/get_repository_revision_install_info": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Legacy Install Info
          * @description Get information used by the install client to install this repository.
          */
         get: operations["repositories__legacy_install_info"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/install_info": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Install Info
          * @description Get information used by the install client to install this repository.
          */
         get: operations["repositories__install_info"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/reset_metadata_on_repository": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
+        put?: never
         /**
          * Reset Metadata On Repository Legacy
          * @description reset metadata on a repository
          */
         post: operations["repositories__reset_legacy"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/updates": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Updates */
         get: operations["repositories__update"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Show */
         get: operations["repositories__show"]
+        /** Update Repository */
+        put: operations["repositories__update_repository"]
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/allow_push": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Show Allow Push */
         get: operations["repositories__show_allow_push"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/allow_push/{username}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
+        put?: never
         /** Add Allow Push */
         post: operations["repositories__add_allow_push"]
         /** Remove Allow Push */
         delete: operations["repositories__remove_allow_push"]
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/changeset_revision": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
+        put?: never
         /**
          * Create Changeset Revision
          * @description upload new revision to the repository
          */
         post: operations["repositories__create_revision"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/deprecated": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /** Set Deprecated */
         put: operations["repositories__set_deprecated"]
+        post?: never
         /** Unset Deprecated */
         delete: operations["repositories__unset_deprecated"]
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/metadata": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Metadata
          * @description Get information about repository metadata
          */
         get: operations["repositories__metadata"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/permissions": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Permissions */
         get: operations["repositories__permissions"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/reset_metadata": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
+        put?: never
         /**
          * Reset Metadata On Repository
          * @description reset metadata on a repository
          */
         post: operations["repositories__reset"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/malicious": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /** Set Malicious */
         put: operations["repositories__set_malicious"]
+        post?: never
         /** Unset Malicious */
         delete: operations["repositories__unset_malicious"]
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/repositories/{encoded_repository_id}/revisions/{changeset_revision}/readmes": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Get Readmes
          * @description fetch readmes for repository revision
          */
         get: operations["repositories__readmes"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/tools": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Index */
         get: operations["tools__index"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/tools/build_search_index": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /**
          * Build Search Index
          * @description Not part of the stable API, just something to simplify
-         * bootstrapping tool sheds, scripting, testing, etc...
+         *     bootstrapping tool sheds, scripting, testing, etc...
          */
         put: operations["tools__build_search_index"]
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
+    }
+    "/api/tools/{tool_id}/versions/{tool_version}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        /** Return Galaxy's meta model description of the tool's inputs */
+        get: operations["tools__parameter_model"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
+    }
+    "/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        /**
+         * Return a JSON schema description of the tool's inputs for the tool request API that will be added to Galaxy at some point
+         * @description The tool request schema includes validation of map/reduce concepts that can be consumed by the tool execution API and not just the request for a single execution.
+         */
+        get: operations["tools__parameter_request_model"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/users": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Index
          * @description index users
          */
         get: operations["users__index"]
+        put?: never
         /**
          * Create
          * @description create a user
          */
         post: operations["users__create"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/users/current": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Current
          * @description show current user
          */
         get: operations["users__current"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/users/{encoded_user_id}": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Show
          * @description show a user
          */
         get: operations["users__show"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/users/{encoded_user_id}/api_key": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Return the user's API key */
         get: operations["users__get_or_create_api_key"]
+        put?: never
         /** Creates a new API key for the user */
         post: operations["users__create_api_key"]
         /** Delete the current API key of the user */
         delete: operations["users__delete_api_key"]
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api/version": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /** Version */
         get: operations["configuration__version"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api_internal/change_password": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /**
          * Change Password
          * @description reset a user
          */
         put: operations["users__internal_change_password"]
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api_internal/login": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /**
          * Internal Login
          * @description login to web UI
          */
         put: operations["users__internal_login"]
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api_internal/logout": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
         /**
          * Internal Logout
          * @description logout of web UI
          */
         put: operations["users__internal_logout"]
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api_internal/register": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        get?: never
+        put?: never
         /**
          * Register
          * @description register a user
          */
         post: operations["users__internal_register"]
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
     "/api_internal/repositories/{encoded_repository_id}/metadata": {
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         /**
          * Metadata Internal
          * @description Get information about repository metadata
          */
         get: operations["repositories__internal_metadata"]
+        put?: never
+        post?: never
+        delete?: never
+        options?: never
+        head?: never
+        patch?: never
+        trace?: never
     }
 }
-
 export type webhooks = Record<string, never>
-
 export interface components {
     schemas: {
         /** APIKeyResponse */
@@ -252,13 +761,88 @@ export interface components {
             /** Api Key */
             api_key: string
         }
+        /** BaseUrlParameterModel */
+        BaseUrlParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_baseurl
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_baseurl"
+        }
         /** Body_repositories__create_revision */
         Body_repositories__create_revision: {
             /** Commit Message */
-            commit_message?: Record<string, never>
+            commit_message?: unknown
             /** Files */
             files?: string[] | null
         }
+        /** BooleanParameterModel */
+        BooleanParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Falsevalue */
+            falsevalue?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_boolean
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_boolean"
+            /** Truevalue */
+            truevalue?: string | null
+            /**
+             * Value
+             * @default false
+             */
+            value: boolean | null
+        }
         /** BuildSearchIndexResponse */
         BuildSearchIndexResponse: {
             /** Repositories Indexed */
@@ -289,12 +873,130 @@ export interface components {
             /**
              * Type
              * @description The digest method used to create the checksum.
-             * The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://github.com/ga4gh-discovery/ga4gh-checksum/blob/master/hash-alg.csv[GA4GH Checksum Hash Algorithm Registry].
-             * Other values MAY be used, as long as implementers are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
-             * GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future.
+             *     The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://github.com/ga4gh-discovery/ga4gh-checksum/blob/master/hash-alg.csv[GA4GH Checksum Hash Algorithm Registry].
+             *     Other values MAY be used, as long as implementers are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
+             *     GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future.
              */
             type: string
         }
+        /** Citation */
+        Citation: {
+            /** Content */
+            content: string
+            /** Type */
+            type: string
+        }
+        /** ColorParameterModel */
+        ColorParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_color
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_color"
+            /** Value */
+            value?: string | null
+        }
+        /** ConditionalParameterModel */
+        ConditionalParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_conditional
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_conditional"
+            /** Test Parameter */
+            test_parameter:
+                | components["schemas"]["BooleanParameterModel"]
+                | components["schemas"]["SelectParameterModel"]
+            /** Whens */
+            whens: components["schemas"]["ConditionalWhen"][]
+        }
+        /** ConditionalWhen */
+        ConditionalWhen: {
+            /** Discriminator */
+            discriminator: boolean | string
+            /** Is Default When */
+            is_default_when: boolean
+            /** Parameters */
+            parameters: (
+                | components["schemas"]["CwlIntegerParameterModel"]
+                | components["schemas"]["CwlFloatParameterModel"]
+                | components["schemas"]["CwlStringParameterModel"]
+                | components["schemas"]["CwlBooleanParameterModel"]
+                | components["schemas"]["CwlNullParameterModel"]
+                | components["schemas"]["CwlFileParameterModel"]
+                | components["schemas"]["CwlDirectoryParameterModel"]
+                | components["schemas"]["CwlUnionParameterModel"]
+                | components["schemas"]["TextParameterModel"]
+                | components["schemas"]["IntegerParameterModel"]
+                | components["schemas"]["FloatParameterModel"]
+                | components["schemas"]["BooleanParameterModel"]
+                | components["schemas"]["HiddenParameterModel"]
+                | components["schemas"]["SelectParameterModel"]
+                | components["schemas"]["DataParameterModel"]
+                | components["schemas"]["DataCollectionParameterModel"]
+                | components["schemas"]["DataColumnParameterModel"]
+                | components["schemas"]["DirectoryUriParameterModel"]
+                | components["schemas"]["RulesParameterModel"]
+                | components["schemas"]["DrillDownParameterModel"]
+                | components["schemas"]["GroupTagParameterModel"]
+                | components["schemas"]["BaseUrlParameterModel"]
+                | components["schemas"]["GenomeBuildParameterModel"]
+                | components["schemas"]["ColorParameterModel"]
+                | components["schemas"]["ConditionalParameterModel"]
+                | components["schemas"]["RepeatParameterModel"]
+                | components["schemas"]["SectionParameterModel"]
+            )[]
+        }
         /** CreateCategoryRequest */
         CreateCategoryRequest: {
             /** Description */
@@ -321,7 +1023,7 @@ export interface components {
              * @default unrestricted
              * @enum {string}
              */
-            type?: "repository_suite_definition" | "tool_dependency_definition" | "unrestricted"
+            type: "repository_suite_definition" | "tool_dependency_definition" | "unrestricted"
         }
         /** CreateUserRequest */
         CreateUserRequest: {
@@ -332,124 +1034,1047 @@ export interface components {
             /** Username */
             username: string
         }
-        /**
-         * DescriptorType
-         * @enum {string}
-         */
-        DescriptorType: "CWL" | "WDL" | "NFL" | "GALAXY" | "SMK"
-        /**
-         * DescriptorTypeVersion
-         * @description The language version for a given descriptor type. The version should correspond to the actual declared version of the descriptor. For example, tools defined in CWL could have a version of `v1.0.2` whereas WDL tools may have a version of `1.0` or `draft-2`
-         */
-        DescriptorTypeVersion: string
-        /** DetailedRepository */
-        DetailedRepository: {
-            /** Create Time */
-            create_time: string
-            /** Deleted */
-            deleted: boolean
-            /** Deprecated */
-            deprecated: boolean
-            /** Description */
-            description: string
-            /** Homepage Url */
-            homepage_url?: string | null
-            /** Id */
-            id: string
-            /** Long Description */
-            long_description: string | null
+        /** CwlBooleanParameterModel */
+        CwlBooleanParameterModel: {
             /** Name */
             name: string
-            /** Owner */
-            owner: string
-            /** Private */
-            private: boolean
-            /** Remote Repository Url */
-            remote_repository_url?: string | null
-            /** Times Downloaded */
-            times_downloaded: number
-            /** Type */
-            type: string
-            /** Update Time */
-            update_time: string
-            /** User Id */
-            user_id: string
-        }
-        /** FailedRepositoryUpdateMessage */
-        FailedRepositoryUpdateMessage: {
-            /** Err Msg */
-            err_msg: string
-        }
-        /** HTTPValidationError */
-        HTTPValidationError: {
-            /** Detail */
-            detail?: components["schemas"]["ValidationError"][]
-        }
-        /** ImageData */
-        ImageData: {
             /**
-             * Checksum
-             * @description A production (immutable) tool version is required to have a hashcode. Not required otherwise, but might be useful to detect changes.  This exposes the hashcode for specific image versions to verify that the container version pulled is actually the version that was indexed by the registry.
+             * Parameter Type
+             * @default cwl_boolean
+             * @constant
+             * @enum {string}
              */
-            checksum?: components["schemas"]["Checksum"][] | null
+            parameter_type: "cwl_boolean"
+        }
+        /** CwlDirectoryParameterModel */
+        CwlDirectoryParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
             /**
-             * Image Name
-             * @description Used in conjunction with a registry_url if provided to locate images.
+             * Hidden
+             * @default false
              */
-            image_name?: string | null
-            image_type?: components["schemas"]["ImageType"] | null
+            hidden: boolean
             /**
-             * Registry Host
-             * @description A docker registry or a URL to a Singularity registry. Used along with image_name to locate a specific image.
+             * Is Dynamic
+             * @default false
              */
-            registry_host?: string | null
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
             /**
-             * Size
-             * @description Size of the container in bytes.
+             * Optional
+             * @default false
              */
-            size?: number | null
+            optional: boolean
             /**
-             * Updated
-             * @description Last time the container was updated.
+             * Parameter Type
+             * @default cwl_directory
+             * @constant
+             * @enum {string}
              */
-            updated?: string | null
+            parameter_type: "cwl_directory"
         }
-        /**
-         * ImageType
-         * @enum {string}
-         */
-        ImageType: "Docker" | "Singularity" | "Conda"
-        /** InstallInfo */
-        InstallInfo: {
-            metadata_info?: components["schemas"]["RepositoryMetadataInstallInfo"] | null
-            repo_info?: components["schemas"]["RepositoryExtraInstallInfo"] | null
-        }
-        /** Organization */
-        Organization: {
+        /** CwlFileParameterModel */
+        CwlFileParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
             /**
-             * Name
-             * @description Name of the organization responsible for the service
+             * Hidden
+             * @default false
              */
-            name: string
+            hidden: boolean
             /**
-             * Url
-             * Format: uri
-             * @description URL of the website of the organization (RFC 3986 format)
+             * Is Dynamic
+             * @default false
              */
-            url: string
-        }
-        /** RepositoriesByCategory */
-        RepositoriesByCategory: {
-            /** Description */
-            description: string
-            /** Id */
-            id: string
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
             /** Name */
             name: string
-            /** Repositories */
-            repositories: components["schemas"]["Repository"][]
-            /** Repository Count */
-            repository_count: number
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default cwl_file
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_file"
+        }
+        /** CwlFloatParameterModel */
+        CwlFloatParameterModel: {
+            /** Name */
+            name: string
+            /**
+             * Parameter Type
+             * @default cwl_float
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_float"
+        }
+        /** CwlIntegerParameterModel */
+        CwlIntegerParameterModel: {
+            /** Name */
+            name: string
+            /**
+             * Parameter Type
+             * @default cwl_integer
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_integer"
+        }
+        /** CwlNullParameterModel */
+        CwlNullParameterModel: {
+            /** Name */
+            name: string
+            /**
+             * Parameter Type
+             * @default cwl_null
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_null"
+        }
+        /** CwlStringParameterModel */
+        CwlStringParameterModel: {
+            /** Name */
+            name: string
+            /**
+             * Parameter Type
+             * @default cwl_string
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_string"
+        }
+        /** CwlUnionParameterModel */
+        CwlUnionParameterModel: {
+            /** Name */
+            name: string
+            /**
+             * Parameter Type
+             * @default cwl_union
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "cwl_union"
+            /** Parameters */
+            parameters: (
+                | components["schemas"]["CwlIntegerParameterModel"]
+                | components["schemas"]["CwlFloatParameterModel"]
+                | components["schemas"]["CwlStringParameterModel"]
+                | components["schemas"]["CwlBooleanParameterModel"]
+                | components["schemas"]["CwlNullParameterModel"]
+                | components["schemas"]["CwlFileParameterModel"]
+                | components["schemas"]["CwlDirectoryParameterModel"]
+                | components["schemas"]["CwlUnionParameterModel"]
+            )[]
+        }
+        /** DataCollectionParameterModel */
+        DataCollectionParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Collection Type */
+            collection_type?: string | null
+            /**
+             * Extensions
+             * @default [
+             *       "data"
+             *     ]
+             */
+            extensions: string[]
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_data_collection
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_data_collection"
+            /** Value */
+            value: Record<string, never> | null
+        }
+        /** DataColumnParameterModel */
+        DataColumnParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Multiple */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_data_column
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_data_column"
+        }
+        /** DataParameterModel */
+        DataParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /**
+             * Extensions
+             * @default [
+             *       "data"
+             *     ]
+             */
+            extensions: string[]
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Max */
+            max?: number | null
+            /** Min */
+            min?: number | null
+            /**
+             * Multiple
+             * @default false
+             */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_data
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_data"
+        }
+        /**
+         * DescriptorType
+         * @enum {string}
+         */
+        DescriptorType: "CWL" | "WDL" | "NFL" | "GALAXY" | "SMK"
+        /**
+         * DescriptorTypeVersion
+         * @description The language version for a given descriptor type. The version should correspond to the actual declared version of the descriptor. For example, tools defined in CWL could have a version of `v1.0.2` whereas WDL tools may have a version of `1.0` or `draft-2`
+         */
+        DescriptorTypeVersion: string
+        /** DetailedRepository */
+        DetailedRepository: {
+            /** Create Time */
+            create_time: string
+            /** Deleted */
+            deleted: boolean
+            /** Deprecated */
+            deprecated: boolean
+            /** Description */
+            description: string
+            /** Homepage Url */
+            homepage_url?: string | null
+            /** Id */
+            id: string
+            /** Long Description */
+            long_description: string | null
+            /** Name */
+            name: string
+            /** Owner */
+            owner: string
+            /** Private */
+            private: boolean
+            /** Remote Repository Url */
+            remote_repository_url?: string | null
+            /** Times Downloaded */
+            times_downloaded: number
+            /** Type */
+            type: string
+            /** Update Time */
+            update_time: string
+            /** User Id */
+            user_id: string
+        }
+        /** DirectoryUriParameterModel */
+        DirectoryUriParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_directory_uri
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_directory_uri"
+            /**
+             * Validators
+             * @default []
+             */
+            validators: (
+                | components["schemas"]["LengthParameterValidatorModel"]
+                | components["schemas"]["RegexParameterValidatorModel"]
+                | components["schemas"]["ExpressionParameterValidatorModel"]
+                | components["schemas"]["EmptyFieldParameterValidatorModel"]
+            )[]
+        }
+        /** DrillDownOptionsDict */
+        DrillDownOptionsDict: {
+            /** Name */
+            name: string | null
+            /** Options */
+            options: components["schemas"]["DrillDownOptionsDict"][]
+            /** Selected */
+            selected: boolean
+            /** Value */
+            value: string
+        }
+        /** DrillDownParameterModel */
+        DrillDownParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Hierarchy
+             * @enum {string}
+             */
+            hierarchy: "recurse" | "exact"
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Multiple */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /** Options */
+            options?: components["schemas"]["DrillDownOptionsDict"][] | null
+            /**
+             * Parameter Type
+             * @default gx_drill_down
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_drill_down"
+        }
+        /** EmptyFieldParameterValidatorModel */
+        EmptyFieldParameterValidatorModel: {
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Message */
+            message?: string | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default empty_field
+             * @constant
+             * @enum {string}
+             */
+            type: "empty_field"
+        }
+        /**
+         * ExpressionParameterValidatorModel
+         * @description Check if a one line python expression given expression evaluates to True.
+         *
+         *     The expression is given is the content of the validator tag.
+         */
+        ExpressionParameterValidatorModel: {
+            /** Expression */
+            expression: string
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Message */
+            message?: string | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default expression
+             * @constant
+             * @enum {string}
+             */
+            type: "expression"
+        }
+        /** FailedRepositoryUpdateMessage */
+        FailedRepositoryUpdateMessage: {
+            /** Err Msg */
+            err_msg: string
+        }
+        /** FilePatternDatasetCollectionDescription */
+        FilePatternDatasetCollectionDescription: {
+            /** Assign Primary Output */
+            assign_primary_output: boolean
+            /** Directory */
+            directory: string | null
+            /**
+             * Discover Via
+             * @constant
+             * @enum {string}
+             */
+            discover_via: "pattern"
+            /** Format */
+            format: string | null
+            /** Match Relative Path */
+            match_relative_path: boolean
+            /** Pattern */
+            pattern: string
+            /** Recurse */
+            recurse: boolean
+            /**
+             * Sort Comp
+             * @enum {string}
+             */
+            sort_comp: "lexical" | "numeric"
+            /**
+             * Sort Key
+             * @enum {string}
+             */
+            sort_key: "filename" | "name" | "designation" | "dbkey"
+            /** Visible */
+            visible: boolean
+        }
+        /** FloatParameterModel */
+        FloatParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Max */
+            max?: number | null
+            /** Min */
+            min?: number | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_float
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_float"
+            /**
+             * Validators
+             * @default []
+             */
+            validators: components["schemas"]["InRangeParameterValidatorModel"][]
+            /** Value */
+            value?: number | null
+        }
+        /** GenomeBuildParameterModel */
+        GenomeBuildParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Multiple */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_genomebuild
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_genomebuild"
+        }
+        /** GroupTagParameterModel */
+        GroupTagParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Multiple */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_group_tag
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_group_tag"
+        }
+        /** HelpContent */
+        HelpContent: {
+            /** Content */
+            content: string
+            /**
+             * Format
+             * @enum {string}
+             */
+            format: "restructuredtext" | "plain_text" | "markdown"
+        }
+        /** HiddenParameterModel */
+        HiddenParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_hidden
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_hidden"
+            /**
+             * Validators
+             * @default []
+             */
+            validators: (
+                | components["schemas"]["LengthParameterValidatorModel"]
+                | components["schemas"]["RegexParameterValidatorModel"]
+                | components["schemas"]["ExpressionParameterValidatorModel"]
+                | components["schemas"]["EmptyFieldParameterValidatorModel"]
+            )[]
+            /** Value */
+            value: string | null
+        }
+        /** ImageData */
+        ImageData: {
+            /**
+             * Checksum
+             * @description A production (immutable) tool version is required to have a hashcode. Not required otherwise, but might be useful to detect changes.  This exposes the hashcode for specific image versions to verify that the container version pulled is actually the version that was indexed by the registry.
+             */
+            checksum?: components["schemas"]["Checksum"][] | null
+            /**
+             * Image Name
+             * @description Used in conjunction with a registry_url if provided to locate images.
+             */
+            image_name?: string | null
+            image_type?: components["schemas"]["ImageType"] | null
+            /**
+             * Registry Host
+             * @description A docker registry or a URL to a Singularity registry. Used along with image_name to locate a specific image.
+             */
+            registry_host?: string | null
+            /**
+             * Size
+             * @description Size of the container in bytes.
+             */
+            size?: number | null
+            /**
+             * Updated
+             * @description Last time the container was updated.
+             */
+            updated?: string | null
+        }
+        /**
+         * ImageType
+         * @enum {string}
+         */
+        ImageType: "Docker" | "Singularity" | "Conda"
+        /** InRangeParameterValidatorModel */
+        InRangeParameterValidatorModel: {
+            /**
+             * Exclude Max
+             * @default false
+             */
+            exclude_max: boolean
+            /**
+             * Exclude Min
+             * @default false
+             */
+            exclude_min: boolean
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Max */
+            max?: number | null
+            /** Message */
+            message?: string | null
+            /** Min */
+            min?: number | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default in_range
+             * @constant
+             * @enum {string}
+             */
+            type: "in_range"
+        }
+        /** InstallInfo */
+        InstallInfo: {
+            metadata_info?: components["schemas"]["RepositoryMetadataInstallInfo"] | null
+            repo_info?: components["schemas"]["RepositoryExtraInstallInfo"] | null
+        }
+        /** IntegerParameterModel */
+        IntegerParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Max */
+            max?: number | null
+            /** Min */
+            min?: number | null
+            /** Name */
+            name: string
+            /** Optional */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_integer
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_integer"
+            /**
+             * Validators
+             * @default []
+             */
+            validators: components["schemas"]["InRangeParameterValidatorModel"][]
+            /** Value */
+            value?: number | null
+        }
+        /** LabelValue */
+        LabelValue: {
+            /** Label */
+            label: string
+            /** Selected */
+            selected: boolean
+            /** Value */
+            value: string
+        }
+        /** LengthParameterValidatorModel */
+        LengthParameterValidatorModel: {
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Max */
+            max?: number | null
+            /** Message */
+            message?: string | null
+            /** Min */
+            min?: number | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default length
+             * @constant
+             * @enum {string}
+             */
+            type: "length"
+        }
+        /** MessageExceptionModel */
+        MessageExceptionModel: {
+            /** Err Code */
+            err_code: number
+            /** Err Msg */
+            err_msg: string
+        }
+        /** NoOptionsParameterValidatorModel */
+        NoOptionsParameterValidatorModel: {
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Message */
+            message?: string | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default no_options
+             * @constant
+             * @enum {string}
+             */
+            type: "no_options"
+        }
+        /** Organization */
+        Organization: {
+            /**
+             * Name
+             * @description Name of the organization responsible for the service
+             */
+            name: string
+            /**
+             * Url
+             * Format: uri
+             * @description URL of the website of the organization (RFC 3986 format)
+             */
+            url: string
+        }
+        /** ParsedTool */
+        ParsedTool: {
+            /** Citations */
+            citations: components["schemas"]["Citation"][]
+            /** Description */
+            description: string | null
+            /** Edam Operations */
+            edam_operations: string[]
+            /** Edam Topics */
+            edam_topics: string[]
+            help: components["schemas"]["HelpContent"] | null
+            /** Id */
+            id: string
+            /** Inputs */
+            inputs: (
+                | components["schemas"]["CwlIntegerParameterModel"]
+                | components["schemas"]["CwlFloatParameterModel"]
+                | components["schemas"]["CwlStringParameterModel"]
+                | components["schemas"]["CwlBooleanParameterModel"]
+                | components["schemas"]["CwlNullParameterModel"]
+                | components["schemas"]["CwlFileParameterModel"]
+                | components["schemas"]["CwlDirectoryParameterModel"]
+                | components["schemas"]["CwlUnionParameterModel"]
+                | components["schemas"]["TextParameterModel"]
+                | components["schemas"]["IntegerParameterModel"]
+                | components["schemas"]["FloatParameterModel"]
+                | components["schemas"]["BooleanParameterModel"]
+                | components["schemas"]["HiddenParameterModel"]
+                | components["schemas"]["SelectParameterModel"]
+                | components["schemas"]["DataParameterModel"]
+                | components["schemas"]["DataCollectionParameterModel"]
+                | components["schemas"]["DataColumnParameterModel"]
+                | components["schemas"]["DirectoryUriParameterModel"]
+                | components["schemas"]["RulesParameterModel"]
+                | components["schemas"]["DrillDownParameterModel"]
+                | components["schemas"]["GroupTagParameterModel"]
+                | components["schemas"]["BaseUrlParameterModel"]
+                | components["schemas"]["GenomeBuildParameterModel"]
+                | components["schemas"]["ColorParameterModel"]
+                | components["schemas"]["ConditionalParameterModel"]
+                | components["schemas"]["RepeatParameterModel"]
+                | components["schemas"]["SectionParameterModel"]
+            )[]
+            /** License */
+            license: string | null
+            /** Name */
+            name: string
+            /** Outputs */
+            outputs: (
+                | components["schemas"]["ToolOutputDataset"]
+                | components["schemas"]["ToolOutputCollection"]
+                | components["schemas"]["ToolOutputText"]
+                | components["schemas"]["ToolOutputInteger"]
+                | components["schemas"]["ToolOutputFloat"]
+                | components["schemas"]["ToolOutputBoolean"]
+            )[]
+            /** Profile */
+            profile: string | null
+            /** Version */
+            version: string | null
+            /** Xrefs */
+            xrefs: components["schemas"]["XrefDict"][]
+        }
+        /**
+         * RegexParameterValidatorModel
+         * @description Check if a regular expression **matches** the value, i.e. appears
+         *     at the beginning of the value. To enforce a match of the complete value use
+         *     ``$`` at the end of the expression. The expression is given is the content
+         *     of the validator tag. Note that for ``selects`` each option is checked
+         *     separately.
+         */
+        RegexParameterValidatorModel: {
+            /** Expression */
+            expression: string
+            /**
+             * Implicit
+             * @default false
+             */
+            implicit: boolean
+            /** Message */
+            message?: string | null
+            /**
+             * Negate
+             * @default false
+             */
+            negate: boolean
+            /**
+             * Type
+             * @default regex
+             * @constant
+             * @enum {string}
+             */
+            type: "regex"
+        }
+        /** RepeatParameterModel */
+        RepeatParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Max */
+            max?: number | null
+            /** Min */
+            min?: number | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_repeat
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_repeat"
+            /** Parameters */
+            parameters: (
+                | components["schemas"]["CwlIntegerParameterModel"]
+                | components["schemas"]["CwlFloatParameterModel"]
+                | components["schemas"]["CwlStringParameterModel"]
+                | components["schemas"]["CwlBooleanParameterModel"]
+                | components["schemas"]["CwlNullParameterModel"]
+                | components["schemas"]["CwlFileParameterModel"]
+                | components["schemas"]["CwlDirectoryParameterModel"]
+                | components["schemas"]["CwlUnionParameterModel"]
+                | components["schemas"]["TextParameterModel"]
+                | components["schemas"]["IntegerParameterModel"]
+                | components["schemas"]["FloatParameterModel"]
+                | components["schemas"]["BooleanParameterModel"]
+                | components["schemas"]["HiddenParameterModel"]
+                | components["schemas"]["SelectParameterModel"]
+                | components["schemas"]["DataParameterModel"]
+                | components["schemas"]["DataCollectionParameterModel"]
+                | components["schemas"]["DataColumnParameterModel"]
+                | components["schemas"]["DirectoryUriParameterModel"]
+                | components["schemas"]["RulesParameterModel"]
+                | components["schemas"]["DrillDownParameterModel"]
+                | components["schemas"]["GroupTagParameterModel"]
+                | components["schemas"]["BaseUrlParameterModel"]
+                | components["schemas"]["GenomeBuildParameterModel"]
+                | components["schemas"]["ColorParameterModel"]
+                | components["schemas"]["ConditionalParameterModel"]
+                | components["schemas"]["RepeatParameterModel"]
+                | components["schemas"]["SectionParameterModel"]
+            )[]
+        }
+        /** RepositoriesByCategory */
+        RepositoriesByCategory: {
+            /** Description */
+            description: string
+            /** Id */
+            id: string
+            /** Name */
+            name: string
+            /** Repositories */
+            repositories: components["schemas"]["Repository"][]
+            /** Repository Count */
+            repository_count: number
         }
         /** Repository */
         Repository: {
@@ -537,7 +2162,7 @@ export interface components {
         }
         /** RepositoryMetadata */
         RepositoryMetadata: {
-            [key: string]: components["schemas"]["RepositoryRevisionMetadata"] | undefined
+            [key: string]: components["schemas"]["RepositoryRevisionMetadata"]
         }
         /** RepositoryMetadataInstallInfo */
         RepositoryMetadataInstallInfo: {
@@ -609,7 +2234,7 @@ export interface components {
         }
         /** RepositoryRevisionReadmes */
         RepositoryRevisionReadmes: {
-            [key: string]: string | undefined
+            [key: string]: string
         }
         /** RepositorySearchHit */
         RepositorySearchHit: {
@@ -670,7 +2295,7 @@ export interface components {
             /** Name */
             name: string
             /** Requirements */
-            requirements: Record<string, never>[]
+            requirements: unknown[]
             /** Tool Config */
             tool_config: string
             /** Tool Type */
@@ -693,6 +2318,141 @@ export interface components {
             /** Stop Time */
             stop_time: string
         }
+        /** RulesParameterModel */
+        RulesParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_rules
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_rules"
+        }
+        /** SectionParameterModel */
+        SectionParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_section
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_section"
+            /** Parameters */
+            parameters: (
+                | components["schemas"]["CwlIntegerParameterModel"]
+                | components["schemas"]["CwlFloatParameterModel"]
+                | components["schemas"]["CwlStringParameterModel"]
+                | components["schemas"]["CwlBooleanParameterModel"]
+                | components["schemas"]["CwlNullParameterModel"]
+                | components["schemas"]["CwlFileParameterModel"]
+                | components["schemas"]["CwlDirectoryParameterModel"]
+                | components["schemas"]["CwlUnionParameterModel"]
+                | components["schemas"]["TextParameterModel"]
+                | components["schemas"]["IntegerParameterModel"]
+                | components["schemas"]["FloatParameterModel"]
+                | components["schemas"]["BooleanParameterModel"]
+                | components["schemas"]["HiddenParameterModel"]
+                | components["schemas"]["SelectParameterModel"]
+                | components["schemas"]["DataParameterModel"]
+                | components["schemas"]["DataCollectionParameterModel"]
+                | components["schemas"]["DataColumnParameterModel"]
+                | components["schemas"]["DirectoryUriParameterModel"]
+                | components["schemas"]["RulesParameterModel"]
+                | components["schemas"]["DrillDownParameterModel"]
+                | components["schemas"]["GroupTagParameterModel"]
+                | components["schemas"]["BaseUrlParameterModel"]
+                | components["schemas"]["GenomeBuildParameterModel"]
+                | components["schemas"]["ColorParameterModel"]
+                | components["schemas"]["ConditionalParameterModel"]
+                | components["schemas"]["RepeatParameterModel"]
+                | components["schemas"]["SectionParameterModel"]
+            )[]
+        }
+        /** SelectParameterModel */
+        SelectParameterModel: {
+            /** Argument */
+            argument?: string | null
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Multiple */
+            multiple: boolean
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /** Options */
+            options?: components["schemas"]["LabelValue"][] | null
+            /**
+             * Parameter Type
+             * @default gx_select
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_select"
+            /** Validators */
+            validators: components["schemas"]["NoOptionsParameterValidatorModel"][]
+        }
         /** Service */
         Service: {
             /**
@@ -762,14 +2522,69 @@ export interface components {
              */
             version: string
         }
+        /** TextParameterModel */
+        TextParameterModel: {
+            /**
+             * Area
+             * @default false
+             */
+            area: boolean
+            /** Argument */
+            argument?: string | null
+            /**
+             * Default Options
+             * @default []
+             */
+            default_options: components["schemas"]["LabelValue"][]
+            /** Help */
+            help?: string | null
+            /**
+             * Hidden
+             * @default false
+             */
+            hidden: boolean
+            /**
+             * Is Dynamic
+             * @default false
+             */
+            is_dynamic: boolean
+            /** Label */
+            label?: string | null
+            /** Name */
+            name: string
+            /**
+             * Optional
+             * @default false
+             */
+            optional: boolean
+            /**
+             * Parameter Type
+             * @default gx_text
+             * @constant
+             * @enum {string}
+             */
+            parameter_type: "gx_text"
+            /**
+             * Validators
+             * @default []
+             */
+            validators: (
+                | components["schemas"]["LengthParameterValidatorModel"]
+                | components["schemas"]["RegexParameterValidatorModel"]
+                | components["schemas"]["ExpressionParameterValidatorModel"]
+                | components["schemas"]["EmptyFieldParameterValidatorModel"]
+            )[]
+            /** Value */
+            value?: string | null
+        }
         /** Tool */
         Tool: {
             /**
              * Aliases
              * @description Support for this parameter is optional for tool registries that support aliases.
-             * A list of strings that can be used to identify this tool which could be  straight up URLs.
-             * This can be used to expose alternative ids (such as GUIDs) for a tool
-             * for registries. Can be used to match tools across registries.
+             *     A list of strings that can be used to identify this tool which could be  straight up URLs.
+             *     This can be used to expose alternative ids (such as GUIDs) for a tool
+             *     for registries. Can be used to match tools across registries.
              */
             aliases?: string[] | null
             /**
@@ -837,6 +2652,143 @@ export interface components {
              */
             name?: string | null
         }
+        /** ToolOutputBoolean */
+        ToolOutputBoolean: {
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Name */
+            name: string
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "boolean"
+        }
+        /** ToolOutputCollection */
+        ToolOutputCollection: {
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Name */
+            name: string
+            structure: components["schemas"]["ToolOutputCollectionStructure"]
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "collection"
+        }
+        /** ToolOutputCollectionStructure */
+        ToolOutputCollectionStructure: {
+            /** Collection Type */
+            collection_type: string | null
+            /** Collection Type From Rules */
+            collection_type_from_rules: string | null
+            /** Collection Type Source */
+            collection_type_source: string | null
+            /** Discover Datasets */
+            discover_datasets:
+                | (
+                      | components["schemas"]["FilePatternDatasetCollectionDescription"]
+                      | components["schemas"]["ToolProvidedMetadataDatasetCollection"]
+                  )[]
+                | null
+            /** Structured Like */
+            structured_like: string | null
+        }
+        /** ToolOutputDataset */
+        ToolOutputDataset: {
+            /** Discover Datasets */
+            discover_datasets:
+                | (
+                      | components["schemas"]["FilePatternDatasetCollectionDescription"]
+                      | components["schemas"]["ToolProvidedMetadataDatasetCollection"]
+                  )[]
+                | null
+            /** Format */
+            format: string
+            /** Format Source */
+            format_source: string | null
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Metadata Source */
+            metadata_source: string | null
+            /** Name */
+            name: string
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "data"
+        }
+        /** ToolOutputFloat */
+        ToolOutputFloat: {
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Name */
+            name: string
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "float"
+        }
+        /** ToolOutputInteger */
+        ToolOutputInteger: {
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Name */
+            name: string
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "integer"
+        }
+        /** ToolOutputText */
+        ToolOutputText: {
+            /** Hidden */
+            hidden: boolean
+            /** Label */
+            label: string | null
+            /** Name */
+            name: string
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            type: "text"
+        }
+        /** ToolProvidedMetadataDatasetCollection */
+        ToolProvidedMetadataDatasetCollection: {
+            /** Assign Primary Output */
+            assign_primary_output: boolean
+            /** Directory */
+            directory: string | null
+            /**
+             * Discover Via
+             * @constant
+             * @enum {string}
+             */
+            discover_via: "tool_provided_metadata"
+            /** Format */
+            format: string | null
+            /** Match Relative Path */
+            match_relative_path: boolean
+            /** Recurse */
+            recurse: boolean
+            /** Visible */
+            visible: boolean
+        }
         /** ToolVersion */
         ToolVersion: {
             /**
@@ -859,7 +2811,7 @@ export interface components {
              * @description A map providing information about the language versions used in this tool. The keys should be the same values used in the `descriptor_type` field, and the value should be an array of all the language versions used for the given `descriptor_type`. Depending on the `descriptor_type` (e.g. CWL) multiple version values may be used in a single tool.
              */
             descriptor_type_version?: {
-                [key: string]: components["schemas"]["DescriptorTypeVersion"][] | undefined
+                [key: string]: components["schemas"]["DescriptorTypeVersion"][]
             } | null
             /**
              * Id
@@ -936,7 +2888,7 @@ export interface components {
              * Logout All
              * @default false
              */
-            logout_all?: boolean
+            logout_all: boolean
             /** Session Csrf Token */
             session_csrf_token: string
         }
@@ -959,17 +2911,34 @@ export interface components {
              * Activation Error
              * @default false
              */
-            activation_error?: boolean
+            activation_error: boolean
             /**
              * Activation Sent
              * @default false
              */
-            activation_sent?: boolean
+            activation_sent: boolean
             /** Contact Email */
             contact_email?: string | null
             /** Email */
             email: string
         }
+        /** UpdateRepositoryRequest */
+        UpdateRepositoryRequest: {
+            /** Category IDs */
+            category_ids?: string[] | null
+            /** Description */
+            description?: string | null
+            /** Homepage Url */
+            homepage_url?: string | null
+            /** Name */
+            name?: string | null
+            /** Remote Repository Url */
+            remote_repository_url?: string | null
+            /** Synopsis */
+            synopsis?: string | null
+            /** Type */
+            type?: ("repository_suite_definition" | "tool_dependency_definition" | "unrestricted") | null
+        }
         /** UserV2 */
         UserV2: {
             /** Id */
@@ -997,9 +2966,9 @@ export interface components {
             /** Name */
             name: string
             /** Requirements */
-            requirements: Record<string, never>[]
+            requirements: unknown[]
             /** Tests */
-            tests: Record<string, never>[]
+            tests: unknown[]
             /** Tool Config */
             tool_config: string
             /** Tool Type */
@@ -1009,27 +2978,25 @@ export interface components {
             /** Version String Cmd */
             version_string_cmd?: string | null
         }
-        /** ValidationError */
-        ValidationError: {
-            /** Location */
-            loc: (string | number)[]
-            /** Message */
-            msg: string
-            /** Error Type */
-            type: string
-        }
         /** Version */
         Version: {
             /**
              * Api Version
              * @default v1
              */
-            api_version?: string
+            api_version: string
             /** Version */
             version: string
             /** Version Major */
             version_major: string
         }
+        /** XrefDict */
+        XrefDict: {
+            /** Reftype */
+            reftype: string
+            /** Value */
+            value: string
+        }
     }
     responses: never
     parameters: never
@@ -1037,40 +3004,91 @@ export interface components {
     headers: never
     pathItems: never
 }
-
-export type external = Record<string, never>
-
+export type $defs = Record<string, never>
 export interface operations {
     authenticate__baseauth: {
-        /** Returns returns an API key for authenticated user based on BaseAuth headers. */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["APIKeyResponse"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     categories__index: {
-        /**
-         * Index
-         * @description index category
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["Category"][]
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["Category"][]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     categories__create: {
-        /**
-         * Create
-         * @description create a category
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["CreateCategoryRequest"]
@@ -1079,49 +3097,75 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Category"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     categories__show: {
-        /**
-         * Show
-         * @description show category
-         */
         parameters: {
-            /** @description The encoded database identifier of the category. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the category. */
                 encoded_category_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Category"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     categories__repositories: {
-        /**
-         * Repositories
-         * @description display repositories by category
-         */
         parameters: {
             query?: {
                 installable?: boolean
@@ -1129,111 +3173,242 @@ export interface operations {
                 sort_order?: string
                 page?: number | null
             }
-            /** @description The encoded database identifier of the category. */
+            header?: never
             path: {
+                /** @description The encoded database identifier of the category. */
                 encoded_category_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["RepositoriesByCategory"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     tools_trs_service_info: {
-        /** Service Info */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Service"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     tools__trs_tool_classes: {
-        /** Tool Classes */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["ToolClass"][]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     tools__trs_index: {
-        /** Trs Index */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": Record<string, never>
+                    "application/json": unknown
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     tools__trs_get: {
-        /** Trs Get */
         parameters: {
-            /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
+            query?: never
+            header?: never
             path: {
+                /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
                 tool_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Tool"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     tools__trs_get_versions: {
-        /** Trs Get Versions */
         parameters: {
-            /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
+            query?: never
+            header?: never
             path: {
+                /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
                 tool_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["ToolVersion"][]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__index: {
-        /**
-         * Index
-         * @description Get a list of repositories or perform a search.
-         */
-        parameters?: {
+        parameters: {
             query?: {
                 q?: string | null
                 page?: number | null
@@ -1242,29 +3417,50 @@ export interface operations {
                 owner?: string | null
                 name?: string | null
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json":
                         | components["schemas"]["RepositorySearchResults"]
                         | components["schemas"]["Repository"][]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__create: {
-        /**
-         * Create
-         * @description create a new repository
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["CreateRepositoryRequest"]
@@ -1273,121 +3469,204 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Repository"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__get_ordered_installable_revisions: {
-        /**
-         * Get Ordered Installable Revisions
-         * @description Get an ordered list of the repository changeset revisions that are installable
-         */
-        parameters?: {
+        parameters: {
             query?: {
                 owner?: string | null
                 name?: string | null
                 tsr_id?: string | null
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string[]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__legacy_install_info: {
-        /**
-         * Legacy Install Info
-         * @description Get information used by the install client to install this repository.
-         */
         parameters: {
-            /** @description Name of the target repository. */
-            /** @description Owner of the target repository. */
-            /** @description Changeset of the target repository. */
             query: {
+                /** @description Name of the target repository. */
                 name: string
+                /** @description Owner of the target repository. */
                 owner: string
+                /** @description Changeset of the target repository. */
                 changeset_revision: string
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": Record<string, never>[]
+                    "application/json": unknown[]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__install_info: {
-        /**
-         * Install Info
-         * @description Get information used by the install client to install this repository.
-         */
         parameters: {
-            /** @description Name of the target repository. */
-            /** @description Owner of the target repository. */
-            /** @description Changeset of the target repository. */
             query: {
+                /** @description Name of the target repository. */
                 name: string
+                /** @description Owner of the target repository. */
                 owner: string
+                /** @description Changeset of the target repository. */
                 changeset_revision: string
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["InstallInfo"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__reset_legacy: {
-        /**
-         * Reset Metadata On Repository Legacy
-         * @description reset metadata on a repository
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["ResetMetadataOnRepositoryResponse"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     repositories__update: {
-        /** Updates */
         parameters: {
             query: {
                 owner?: string | null
@@ -1395,132 +3674,266 @@ export interface operations {
                 changeset_revision: string
                 hexlify?: boolean | null
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": Record<string, never>
+                    "application/json": unknown
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__show: {
-        /** Show */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
+            path: {
+                /** @description The encoded database identifier of the repository. */
+                encoded_repository_id: string
+            }
+            cookie?: never
+        }
+        requestBody?: never
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["DetailedRepository"]
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+        }
+    }
+    repositories__update_repository: {
+        parameters: {
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
+        }
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["UpdateRepositoryRequest"]
+            }
         }
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["DetailedRepository"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__show_allow_push: {
-        /** Show Allow Push */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string[]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__add_allow_push: {
-        /** Add Allow Push */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
-            /** @description The target username. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
+                /** @description The target username. */
                 username: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string[]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__remove_allow_push: {
-        /** Remove Allow Push */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
-            /** @description The target username. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
+                /** @description The target username. */
                 username: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string[]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__create_revision: {
-        /**
-         * Create Changeset Revision
-         * @description upload new revision to the repository
-         */
         parameters: {
-            /** @description Set commit message as a query parameter. */
             query?: {
+                /** @description Set commit message as a query parameter. */
                 commit_message?: string | null
             }
-            /** @description The encoded database identifier of the repository. */
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
         requestBody?: {
             content: {
@@ -1530,263 +3943,573 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["RepositoryUpdate"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__set_deprecated: {
-        /** Set Deprecated */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__unset_deprecated: {
-        /** Unset Deprecated */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__metadata: {
-        /**
-         * Metadata
-         * @description Get information about repository metadata
-         */
         parameters: {
-            /** @description Include only downloadable repositories. */
             query?: {
+                /** @description Include only downloadable repositories. */
                 downloadable_only?: boolean
             }
-            /** @description The encoded database identifier of the repository. */
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": Record<string, never>
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__permissions: {
-        /** Permissions */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["RepositoryPermissions"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__reset: {
-        /**
-         * Reset Metadata On Repository
-         * @description reset metadata on a repository
-         */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["ResetMetadataOnRepositoryResponse"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__set_malicious: {
-        /** Set Malicious */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
-            /** @description The changeset revision corresponding to the target revision of the target repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
+                /** @description The changeset revision corresponding to the target revision of the target repository. */
                 changeset_revision: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__unset_malicious: {
-        /** Unset Malicious */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
-            /** @description The changeset revision corresponding to the target revision of the target repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
+                /** @description The changeset revision corresponding to the target revision of the target repository. */
                 changeset_revision: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__readmes: {
-        /**
-         * Get Readmes
-         * @description fetch readmes for repository revision
-         */
         parameters: {
-            /** @description The encoded database identifier of the repository. */
-            /** @description The changeset revision corresponding to the target revision of the target repository. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
+                /** @description The changeset revision corresponding to the target revision of the target repository. */
                 changeset_revision: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["RepositoryRevisionReadmes"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     tools__index: {
-        /** Index */
         parameters: {
             query: {
                 q: string
                 page?: number
                 page_size?: number
             }
+            header?: never
+            path?: never
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": Record<string, never>
+                    "application/json": unknown
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     tools__build_search_index: {
-        /**
-         * Build Search Index
-         * @description Not part of the stable API, just something to simplify
-         * bootstrapping tool sheds, scripting, testing, etc...
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["BuildSearchIndexResponse"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+        }
+    }
+    tools__parameter_model: {
+        parameters: {
+            query?: never
+            header?: never
+            path: {
+                /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
+                tool_id: string
+                /** @description The full version string defined on the Galaxy tool wrapper. */
+                tool_version: string
+            }
+            cookie?: never
+        }
+        requestBody?: never
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["ParsedTool"]
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+        }
+    }
+    tools__parameter_request_model: {
+        parameters: {
+            query?: never
+            header?: never
+            path: {
+                /** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
+                tool_id: string
+                /** @description The full version string defined on the Galaxy tool wrapper. */
+                tool_version: string
+            }
+            cookie?: never
+        }
+        requestBody?: never
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": unknown
+                }
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     users__index: {
-        /**
-         * Index
-         * @description index users
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UserV2"][]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     users__create: {
-        /**
-         * Create
-         * @description create a user
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["CreateUserRequest"]
@@ -1795,139 +4518,278 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UserV2"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__current: {
-        /**
-         * Current
-         * @description show current user
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UserV2"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     users__show: {
-        /**
-         * Show
-         * @description show a user
-         */
         parameters: {
-            /** @description The encoded database identifier of the user. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the user. */
                 encoded_user_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UserV2"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__get_or_create_api_key: {
-        /** Return the user's API key */
         parameters: {
-            /** @description The encoded database identifier of the user. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the user. */
                 encoded_user_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__create_api_key: {
-        /** Creates a new API key for the user */
         parameters: {
-            /** @description The encoded database identifier of the user. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the user. */
                 encoded_user_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": string
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__delete_api_key: {
-        /** Delete the current API key of the user */
         parameters: {
-            /** @description The encoded database identifier of the user. */
+            query?: never
+            header?: never
             path: {
+                /** @description The encoded database identifier of the user. */
                 encoded_user_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     configuration__version: {
-        /** Version */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["Version"]
                 }
             }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
         }
     }
     users__internal_change_password: {
-        /**
-         * Change Password
-         * @description reset a user
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["UiChangePasswordRequest"]
@@ -1935,20 +4797,39 @@ export interface operations {
         }
         responses: {
             /** @description Successful Response */
-            204: never
-            /** @description Validation Error */
-            422: {
+            204: {
+                headers: {
+                    [name: string]: unknown
+                }
+                content?: never
+            }
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__internal_login: {
-        /**
-         * Internal Login
-         * @description login to web UI
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["UiLoginRequest"]
@@ -1957,23 +4838,40 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UiLoginResponse"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__internal_logout: {
-        /**
-         * Internal Logout
-         * @description logout of web UI
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["UiLogoutRequest"]
@@ -1982,23 +4880,40 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UiLogoutResponse"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     users__internal_register: {
-        /**
-         * Register
-         * @description register a user
-         */
+        parameters: {
+            query?: never
+            header?: never
+            path?: never
+            cookie?: never
+        }
         requestBody: {
             content: {
                 "application/json": components["schemas"]["UiRegisterRequest"]
@@ -2007,44 +4922,73 @@ export interface operations {
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["UiRegisterResponse"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
     }
     repositories__internal_metadata: {
-        /**
-         * Metadata Internal
-         * @description Get information about repository metadata
-         */
         parameters: {
-            /** @description Include only downloadable repositories. */
             query?: {
+                /** @description Include only downloadable repositories. */
                 downloadable_only?: boolean
             }
-            /** @description The encoded database identifier of the repository. */
+            header?: never
             path: {
+                /** @description The encoded database identifier of the repository. */
                 encoded_repository_id: string
             }
+            cookie?: never
         }
+        requestBody?: never
         responses: {
             /** @description Successful Response */
             200: {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
                     "application/json": components["schemas"]["RepositoryMetadata"]
                 }
             }
-            /** @description Validation Error */
-            422: {
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown
+                }
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"]
+                }
+            }
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown
+                }
                 content: {
-                    "application/json": components["schemas"]["HTTPValidationError"]
+                    "application/json": components["schemas"]["MessageExceptionModel"]
                 }
             }
         }
diff --git a/lib/tool_shed/webapp/frontend/src/schema/types.ts b/lib/tool_shed/webapp/frontend/src/schema/types.ts
index 2e328c9cb591630e10f1c6687c644fd6f8143c15..8f54b8a8615a00ded2239a73747623ecd4a54637 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/types.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/types.ts
@@ -3,3 +3,4 @@ import type { components } from "./schema"
 export type Repository = components["schemas"]["Repository"]
 export type RevisionMetadata = components["schemas"]["RepositoryRevisionMetadata"]
 export type RepositoryTool = components["schemas"]["RepositoryTool"]
+export type ApiMessageException = components["schemas"]["MessageExceptionModel"]
diff --git a/lib/tool_shed/webapp/frontend/src/stores/auth.store.ts b/lib/tool_shed/webapp/frontend/src/stores/auth.store.ts
index 9392f9d60ba4311d6dcdf7e2b6db996a7d8c4e51..f982921240219eb7dac1c9d948d8e8107be2678c 100644
--- a/lib/tool_shed/webapp/frontend/src/stores/auth.store.ts
+++ b/lib/tool_shed/webapp/frontend/src/stores/auth.store.ts
@@ -1,11 +1,7 @@
 import { defineStore } from "pinia"
-import { ensureCookie, notifyOnCatch } from "@/util"
-import { getCurrentUser } from "@/apiUtil"
+import { ensureCookie, errorMessageAsString, notifyOnCatch } from "@/util"
 
-import { fetcher } from "@/schema"
-
-const loginFetcher = fetcher.path("/api_internal/login").method("put").create()
-const logoutFetcher = fetcher.path("/api_internal/logout").method("put").create()
+import { ToolShedApi } from "@/schema"
 
 export const useAuthStore = defineStore({
     id: "auth",
@@ -16,19 +12,25 @@ export const useAuthStore = defineStore({
     }),
     actions: {
         async setup() {
-            const user = await getCurrentUser()
-            this.user = user
-            // store user details and jwt in local storage to keep user logged in between page refreshes
-            localStorage.setItem("user", user ? JSON.stringify(user) : "null")
+            try {
+                const { data: user } = await ToolShedApi().GET("/api/users/current")
+                this.user = user
+                // store user details and jwt in local storage to keep user logged in between page refreshes
+                localStorage.setItem("user", user ? JSON.stringify(user) : "null")
+            } catch (e) {
+                console.debug(`Failed to get current user: ${errorMessageAsString(e)}`)
+            }
         },
         async login(username: string, password: string) {
             const token = ensureCookie("session_csrf_token")
-            console.log(token)
-            loginFetcher({
-                login: username,
-                password: password,
-                session_csrf_token: token,
-            })
+            ToolShedApi()
+                .PUT("/api_internal/login", {
+                    body: {
+                        login: username,
+                        password: password,
+                        session_csrf_token: token,
+                    },
+                })
                 .then(async () => {
                     // We need to do this outside the router to get updated
                     // cookies and hence csrf token.
@@ -38,9 +40,13 @@ export const useAuthStore = defineStore({
         },
         async logout() {
             const token = ensureCookie("session_csrf_token")
-            logoutFetcher({
-                session_csrf_token: token,
-            })
+            ToolShedApi()
+                .PUT("/api_internal/logout", {
+                    body: {
+                        session_csrf_token: token,
+                        logout_all: false,
+                    },
+                })
                 .then(async () => {
                     this.user = null
                     localStorage.removeItem("user")
diff --git a/lib/tool_shed/webapp/frontend/src/stores/categories.store.ts b/lib/tool_shed/webapp/frontend/src/stores/categories.store.ts
index 4038ad835f6774ead8e9b47f29e18d931506b4da..a75b59d4cc8e9400d73e9dfb9f04ec0f5ed3de60 100644
--- a/lib/tool_shed/webapp/frontend/src/stores/categories.store.ts
+++ b/lib/tool_shed/webapp/frontend/src/stores/categories.store.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia"
 
-import { fetcher, components } from "@/schema"
-const categoriesFetcher = fetcher.path("/api/categories").method("get").create()
+import { ToolShedApi, components } from "@/schema"
+import { notifyOnCatch } from "@/util"
 type Category = components["schemas"]["Category"]
 
 export const useCategoriesStore = defineStore({
@@ -13,9 +13,14 @@ export const useCategoriesStore = defineStore({
     actions: {
         async getAll() {
             this.loading = true
-            const { data: categories } = await categoriesFetcher({})
-            this.categories = categories
-            this.loading = false
+            try {
+                const { data: categories } = await ToolShedApi().GET("/api/categories")
+                this.categories = categories ?? []
+            } catch (e) {
+                notifyOnCatch(e)
+            } finally {
+                this.loading = false
+            }
         },
     },
     getters: {
diff --git a/lib/tool_shed/webapp/frontend/src/stores/repository.store.ts b/lib/tool_shed/webapp/frontend/src/stores/repository.store.ts
index 7d5f7223c12ce4e230ab637ca14ae9662f8ea44e..a131c8dac963eb5017a81d7b28d58271a4690f0b 100644
--- a/lib/tool_shed/webapp/frontend/src/stores/repository.store.ts
+++ b/lib/tool_shed/webapp/frontend/src/stores/repository.store.ts
@@ -1,24 +1,15 @@
 import { defineStore } from "pinia"
 
-import { fetcher, components } from "@/schema"
-const repositoryFetcher = fetcher.path("/api/repositories/{encoded_repository_id}").method("get").create()
-const repositoryMetadataFetcher = fetcher
-    .path("/api_internal/repositories/{encoded_repository_id}/metadata")
-    .method("get")
-    .create()
-const repositoryPermissionsFetcher = fetcher
-    .path("/api/repositories/{encoded_repository_id}/permissions")
-    .method("get")
-    .create()
-const repositoryPermissionsAdder = fetcher
-    .path("/api/repositories/{encoded_repository_id}/allow_push/{username}")
-    .method("post")
-    .create()
-const repositoryPermissionsRemover = fetcher
-    .path("/api/repositories/{encoded_repository_id}/allow_push/{username}")
-    .method("delete")
-    .create()
-const repositoryInstallInfoFetcher = fetcher.path("/api/repositories/install_info").method("get").create()
+import { ToolShedApi, components } from "@/schema"
+import { notifyOnCatch } from "@/util"
+
+function fetchRepositoryPermissions(repositoryId: string) {
+    return ToolShedApi().GET("/api/repositories/{encoded_repository_id}/permissions", {
+        params: {
+            path: { encoded_repository_id: repositoryId },
+        },
+    })
+}
 
 type DetailedRepository = components["schemas"]["DetailedRepository"]
 type InstallInfo = components["schemas"]["InstallInfo"]
@@ -38,28 +29,40 @@ export const useRepositoryStore = defineStore({
     }),
     actions: {
         async allowPush(username: string) {
-            if (this.repositoryId == null) {
-                throw Error("Logic problem in repository store")
-            }
-            const params = {
-                encoded_repository_id: this.repositoryId,
-                username: username,
+            try {
+                if (this.repositoryId == null) {
+                    throw Error("Logic problem in repository store")
+                }
+                const params = {
+                    encoded_repository_id: this.repositoryId,
+                    username: username,
+                }
+                await ToolShedApi().POST("/api/repositories/{encoded_repository_id}/allow_push/{username}", {
+                    params: { path: params },
+                })
+                const { data: _repositoryPermissions } = await fetchRepositoryPermissions(this.repositoryId)
+                this.repositoryPermissions = _repositoryPermissions ?? null
+            } catch (e) {
+                notifyOnCatch(e)
             }
-            await repositoryPermissionsAdder(params)
-            const { data: _repositoryPermissions } = await repositoryPermissionsFetcher(params)
-            this.repositoryPermissions = _repositoryPermissions
         },
         async disallowPush(username: string) {
-            if (this.repositoryId == null) {
-                throw Error("Logic problem in repository store")
-            }
-            const params = {
-                encoded_repository_id: this.repositoryId,
-                username: username,
+            try {
+                if (this.repositoryId == null) {
+                    throw Error("Logic problem in repository store")
+                }
+                const params = {
+                    encoded_repository_id: this.repositoryId,
+                    username: username,
+                }
+                await ToolShedApi().DELETE("/api/repositories/{encoded_repository_id}/allow_push/{username}", {
+                    params: { path: params },
+                })
+                const { data: _repositoryPermissions } = await fetchRepositoryPermissions(this.repositoryId)
+                this.repositoryPermissions = _repositoryPermissions ?? null
+            } catch (e) {
+                notifyOnCatch(e)
             }
-            await repositoryPermissionsRemover(params)
-            const { data: _repositoryPermissions } = await repositoryPermissionsFetcher(params)
-            this.repositoryPermissions = _repositoryPermissions
         },
         async setId(repositoryId: string) {
             this.repositoryId = repositoryId
@@ -71,41 +74,50 @@ export const useRepositoryStore = defineStore({
             }
             this.loading = true
             const params = { encoded_repository_id: this.repositoryId }
-            const metadataParams = { encoded_repository_id: this.repositoryId, downloadable_only: false }
-            const [{ data: repository }, { data: repositoryMetadata }] = await Promise.all([
-                repositoryFetcher(params),
-                repositoryMetadataFetcher(metadataParams),
-            ])
-            this.repository = repository
-            this.repositoryMetadata = repositoryMetadata
-            let repositoryPermissions = {
-                can_manage: false,
-                can_push: false,
-                allow_push: [] as string[],
-            }
             try {
-                const { data: _repositoryPermissions } = await repositoryPermissionsFetcher(params)
-                repositoryPermissions = _repositoryPermissions
-                this.repositoryPermissions = repositoryPermissions
-            } catch (e) {
-                // console.log(e)
-            }
-            const latestMetadata = Object.values(repositoryMetadata)[0]
-            if (!latestMetadata) {
-                this.empty = true
-            } else {
-                if (this.empty) {
-                    this.empty = false
+                const [{ data: repository }, { data: repositoryMetadata }] = await Promise.all([
+                    ToolShedApi().GET("/api/repositories/{encoded_repository_id}", { params: { path: params } }),
+                    ToolShedApi().GET("/api_internal/repositories/{encoded_repository_id}/metadata", {
+                        params: { path: params, query: { downloadable_only: false } },
+                    }),
+                ])
+                this.repository = repository ?? null
+                this.repositoryMetadata = repositoryMetadata ?? null
+
+                let repositoryPermissions = {
+                    can_manage: false,
+                    can_push: false,
+                    allow_push: [] as string[],
                 }
-                const installParams = {
-                    name: repository.name,
-                    owner: repository.owner,
-                    changeset_revision: latestMetadata.changeset_revision,
+                try {
+                    const { data: _repositoryPermissions } = await fetchRepositoryPermissions(this.repositoryId)
+                    repositoryPermissions = _repositoryPermissions ?? repositoryPermissions
+                    this.repositoryPermissions = repositoryPermissions
+                } catch (e) {
+                    // console.log(e)
                 }
-                const { data: repositoryInstallInfo } = await repositoryInstallInfoFetcher(installParams)
-                this.repositoryInstallInfo = repositoryInstallInfo
+                const latestMetadata = Object.values(repositoryMetadata ?? {})[0]
+                if (!latestMetadata || !repository) {
+                    this.empty = true
+                } else {
+                    if (this.empty) {
+                        this.empty = false
+                    }
+                    const installParams = {
+                        name: repository.name,
+                        owner: repository.owner,
+                        changeset_revision: latestMetadata.changeset_revision,
+                    }
+                    const { data: repositoryInstallInfo } = await ToolShedApi().GET("/api/repositories/install_info", {
+                        params: { query: installParams },
+                    })
+                    this.repositoryInstallInfo = repositoryInstallInfo ?? null
+                }
+            } catch (e) {
+                notifyOnCatch(e)
+            } finally {
+                this.loading = false
             }
-            this.loading = false
         },
     },
 })
diff --git a/lib/tool_shed/webapp/frontend/src/stores/users.store.ts b/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
index 5e32f20421785573c6bdd62d87f0bb19bc52b5ef..82d6dba3445f1422ba7d935b4036437d68f9a4d0 100644
--- a/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
+++ b/lib/tool_shed/webapp/frontend/src/stores/users.store.ts
@@ -1,7 +1,7 @@
 import { defineStore } from "pinia"
 
-import { fetcher, components } from "@/schema"
-const usersFetcher = fetcher.path("/api/users").method("get").create()
+import { ToolShedApi, components } from "@/schema"
+import { notifyOnCatch } from "@/util"
 
 type User = components["schemas"]["UserV2"]
 
@@ -14,9 +14,14 @@ export const useUsersStore = defineStore({
     actions: {
         async getAll() {
             this.loading = true
-            const { data: users } = await usersFetcher({})
-            this.users = users
-            this.loading = false
+            try {
+                const { data: users } = await ToolShedApi().GET("/api/users")
+                this.users = users ?? []
+            } catch (e) {
+                notifyOnCatch(e)
+            } finally {
+                this.loading = false
+            }
         },
     },
 })
diff --git a/lib/tool_shed/webapp/frontend/src/util.ts b/lib/tool_shed/webapp/frontend/src/util.ts
index fec1486bd948547310ee4ca85eccd59c806ac629..1717aea379c9464b5876b80b8c17666c52249b4e 100644
--- a/lib/tool_shed/webapp/frontend/src/util.ts
+++ b/lib/tool_shed/webapp/frontend/src/util.ts
@@ -1,7 +1,7 @@
 import { copyToClipboard, Notify, Cookies } from "quasar"
 import type { QNotifyCreateOptions } from "quasar"
 import { type LocationQueryValue } from "vue-router"
-import { ApiError } from "openapi-typescript-fetch"
+import { type ApiMessageException } from "./schema/types"
 
 export function getCookie(name: string): string | null {
     return Cookies.get(name)
@@ -31,18 +31,33 @@ export async function copyAndNotify(value: string, notification: string) {
     notify(notification)
 }
 
-export function errorMessage(e: Error): string {
-    if (e instanceof ApiError) {
-        return e.data.err_msg
-    } else {
-        return JSON.stringify(e)
+export function errorMessageAsString(
+    e: Error | ApiMessageException | string | unknown,
+    defaultMessage = "Request failed."
+): string {
+    if (e instanceof Error) {
+        if (e.cause) {
+            return `${e.message}: ${e.cause}`
+        }
+        return e.message
+    } else if (isApiException(e)) {
+        return e.err_msg
+    } else if (typeof e == "string") {
+        return e
     }
+
+    return defaultMessage
+}
+
+function isApiException(e: unknown): e is ApiMessageException {
+    return e instanceof Object && "err_msg" in e
 }
 
 export function queryParamToString(param: LocationQueryValue | LocationQueryValue[]): string | null {
     return Array.isArray(param) ? param[0] : param
 }
 
-export function notifyOnCatch(e: Error) {
-    notify(errorMessage(e))
+export function notifyOnCatch(e: unknown) {
+    console.debug(e)
+    notify(errorMessageAsString(e))
 }
diff --git a/lib/tool_shed/webapp/frontend/vite.config.ts b/lib/tool_shed/webapp/frontend/vite.config.ts
index ccf3705b85532e7de0b11fac23d917537152728d..e45d75d4e61abfba738674d9939bc7fd2c77af6b 100644
--- a/lib/tool_shed/webapp/frontend/vite.config.ts
+++ b/lib/tool_shed/webapp/frontend/vite.config.ts
@@ -1,23 +1,32 @@
-import { fileURLToPath } from 'url'
-import { defineConfig } from 'vite'
-import vue from '@vitejs/plugin-vue'
-import { quasar, transformAssetUrls } from '@quasar/vite-plugin'
+import { fileURLToPath } from "url"
+import { defineConfig } from "vite"
+import vue from "@vitejs/plugin-vue"
+import { quasar, transformAssetUrls } from "@quasar/vite-plugin"
 
 // https://vitejs.dev/config/
 export default defineConfig({
-  plugins: [
-    vue({
-      template: { transformAssetUrls },
-    }),
+    plugins: [
+        vue({
+            template: { transformAssetUrls },
+        }),
 
-    quasar({
-      sassVariables: 'src/quasar-variables.sass',
-    }),
-  ],
-  build: {},
-  resolve: {
-    alias: {
-      '@': fileURLToPath(new URL('./src', import.meta.url)),
+        quasar({
+            sassVariables: "src/quasar-variables.sass",
+        }),
+    ],
+    build: {},
+    resolve: {
+        alias: {
+            "@": fileURLToPath(new URL("./src", import.meta.url)),
+        },
+    },
+    server: {
+        proxy: {
+            "/api": {
+                target: process.env.TOOL_SHED_URL || "http://127.0.0.1:9009",
+                changeOrigin: process.env.CHANGE_ORIGIN ? !process.env.CHANGE_ORIGIN : true,
+                secure: !process.env.CHANGE_ORIGIN,
+            },
+        },
     },
-  },
 })
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 859b8fe2b09622aa711bab120b55d061d1fd29a6..8cd5f31d8a045397f4c3ba9d1cce64da0941f83d 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -28,6 +28,7 @@ from sqlalchemy import (
     not_,
     String,
     Table,
+    text,
     TEXT,
     true,
     UniqueConstraint,
@@ -35,6 +36,7 @@ from sqlalchemy import (
 from sqlalchemy.orm import (
     Mapped,
     mapped_column,
+    object_session,
     registry,
     relationship,
 )
@@ -524,6 +526,19 @@ class Repository(Base, Dictifiable):
             os.path.join(hgweb_config_manager.hgweb_repo_prefix, self.user.username, self.name)
         )
 
+    def hg_repository_path(self, repositories_directory: str) -> str:
+        if self.id is None:
+            raise Exception("Attempting to call hg_repository_path before id has been set on repository object")
+        dir = os.path.join(repositories_directory, *util.directory_hash_id(self.id))
+        final_repository_path = os.path.join(dir, "repo_%d" % self.id)
+        return final_repository_path
+
+    def ensure_hg_repository_path(self, repositories_directory: str) -> str:
+        final_repository_path = self.hg_repository_path(repositories_directory)
+        if not os.path.exists(final_repository_path):
+            os.makedirs(final_repository_path)
+        return final_repository_path
+
     def revision(self):
         repo = self.hg_repo
         tip_ctx = repo[repo.changelog.tip()]
@@ -605,6 +620,22 @@ class Category(Base, Dictifiable):
     dict_collection_visible_keys = ["id", "name", "description", "deleted"]
     dict_element_visible_keys = ["id", "name", "description", "deleted"]
 
+    def active_repository_count(self, session=None) -> int:
+        statement = """
+SELECT count(*) as count
+FROM repository r
+INNER JOIN repository_category_association rca on rca.repository_id = r.id
+WHERE
+    rca.category_id = :category_id
+    AND r.private = false
+    AND r.deleted = false
+    and r.deprecated = false
+"""
+        if session is None:
+            session = object_session(self)
+        params = {"category_id": self.id}
+        return session.execute(text(statement), params).scalar()
+
     def __init__(self, deleted=False, **kwd):
         super().__init__(**kwd)
         self.deleted = deleted
@@ -644,6 +675,8 @@ class Tag(Base):
 
 
 class RepositoryMetadata(Dictifiable):
+    repository: "Repository"
+
     # Once the class has been mapped, all Column items in this table will be available
     # as instrumented class attributes on RepositoryMetadata.
     table = Table(
diff --git a/lib/tool_shed_client/schema/__init__.py b/lib/tool_shed_client/schema/__init__.py
index 42c890ad4afd436b641fcbddc9df8e37207eb96a..ebf5a0a850a0b50a22e76cb1aa06fca444c1003c 100644
--- a/lib/tool_shed_client/schema/__init__.py
+++ b/lib/tool_shed_client/schema/__init__.py
@@ -123,6 +123,25 @@ class CreateRepositoryRequest(BaseModel):
     model_config = ConfigDict(populate_by_name=True)
 
 
+class UpdateRepositoryRequest(BaseModel):
+    name: Optional[str] = None
+    synopsis: Optional[str] = None
+    type_: Optional[RepositoryType] = Field(
+        None,
+        alias="type",
+        title="Type",
+    )
+    description: Optional[str] = None
+    remote_repository_url: Optional[str] = None
+    homepage_url: Optional[str] = None
+    category_ids: Optional[List[str]] = Field(
+        None,
+        alias="category_ids",
+        title="Category IDs",
+    )
+    model_config = ConfigDict(populate_by_name=True)
+
+
 class RepositoryUpdateRequest(BaseModel):
     commit_message: Optional[str] = None
 
diff --git a/mypy.ini b/mypy.ini
index 0ec6ae26998629b7848489aa9fd9abc862058e44..9048c43b80ee85350ac87311915d6177935f5ede 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,4 +1,5 @@
 [mypy]
+enable_error_code = ignore-without-code
 plugins = pydantic.mypy
 show_error_codes = True
 ignore_missing_imports = True
@@ -114,8 +115,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.phenotype_association.pagetag]
 check_untyped_defs = False
-[mypy-galaxy.tools.bundled.meme.fimo_wrapper]
-check_untyped_defs = False
 [mypy-galaxy.tools.bundled.maf.maf_to_bed]
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.filters.trimmer]
diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
index a01c8a3a25c109a99fddf76fd1de0609165a7de1..ea32e8d4b28f731e9fba0c69eaf17f28568e0579 100644
--- a/packages/app/HISTORY.rst
+++ b/packages/app/HISTORY.rst
@@ -4,11 +4,391 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private role name performance issue by `@jdavcs <https://github.com/jdavcs>`_ in `#19679 <https://github.com/galaxyproject/galaxy/pull/19679>`_
+* Fix tool directory pulsar transfer by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19799 <https://github.com/galaxyproject/galaxy/pull/19799>`_
+* Use materialized datasets in pulsar job runner by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19807 <https://github.com/galaxyproject/galaxy/pull/19807>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix conditional dependency path resolution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19723 <https://github.com/galaxyproject/galaxy/pull/19723>`_
+* Allow tool state changes in refactor actions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19730 <https://github.com/galaxyproject/galaxy/pull/19730>`_
+* Update fs.dropboxfs conditional dependency version to 1.0.3 by `@davelopez <https://github.com/davelopez>`_ in `#19741 <https://github.com/galaxyproject/galaxy/pull/19741>`_
+* Follow-up to #19651: Do not reassign: method modifies object in-place by `@jdavcs <https://github.com/jdavcs>`_ in `#19746 <https://github.com/galaxyproject/galaxy/pull/19746>`_
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+* Skip slow tests for manage_db, db_dev scripts by `@jdavcs <https://github.com/jdavcs>`_ in `#19744 <https://github.com/galaxyproject/galaxy/pull/19744>`_
+
+=============
+Other changes
+=============
+
+* Make k8s user and group ids overriddable per job by `@nuwang <https://github.com/nuwang>`_ in `#19568 <https://github.com/galaxyproject/galaxy/pull/19568>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Remove unused and broken methods by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19614 <https://github.com/galaxyproject/galaxy/pull/19614>`_
+* Raise ``RequestParameterInvalidException`` on invalid ``input_format`` parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19631 <https://github.com/galaxyproject/galaxy/pull/19631>`_
+* Raise serializable exception on invalid workflow connection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19636 <https://github.com/galaxyproject/galaxy/pull/19636>`_
+* Raise ``MessageException`` when using data provider on incompatible data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19639 <https://github.com/galaxyproject/galaxy/pull/19639>`_
+* Apply exec options to connection by `@jdavcs <https://github.com/jdavcs>`_ in `#19651 <https://github.com/galaxyproject/galaxy/pull/19651>`_
+* Initialize dictionary used to set connection execution options by `@jdavcs <https://github.com/jdavcs>`_ in `#19653 <https://github.com/galaxyproject/galaxy/pull/19653>`_
+* Fix various bugs around tool data table bundles by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19659 <https://github.com/galaxyproject/galaxy/pull/19659>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Dynamics options add library dataset by `@gagayuan <https://github.com/gagayuan>`_ in `#18198 <https://github.com/galaxyproject/galaxy/pull/18198>`_
+* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Update mercurial by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18686 <https://github.com/galaxyproject/galaxy/pull/18686>`_
+* Replace types-pkg-resources with types-setuptools by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18708 <https://github.com/galaxyproject/galaxy/pull/18708>`_
+* Fix tag processing in library upload by `@davelopez <https://github.com/davelopez>`_ in `#18714 <https://github.com/galaxyproject/galaxy/pull/18714>`_
+* Update ruff to 0.6.1 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18716 <https://github.com/galaxyproject/galaxy/pull/18716>`_
+* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
+* Fixes and tests for data fetch models. by `@jmchilton <https://github.com/jmchilton>`_ in `#18834 <https://github.com/galaxyproject/galaxy/pull/18834>`_
+* data_column params: offer same columns with and without use_header_names by `@wm75 <https://github.com/wm75>`_ in `#18879 <https://github.com/galaxyproject/galaxy/pull/18879>`_
+* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
+* Fix the bioblend test failures by `@arash77 <https://github.com/arash77>`_ in `#18991 <https://github.com/galaxyproject/galaxy/pull/18991>`_
+* Fix job directory not being cleaned up by `@davelopez <https://github.com/davelopez>`_ in `#18997 <https://github.com/galaxyproject/galaxy/pull/18997>`_
+* Fixes random job failures in kubernetes  by `@mapk-amazon <https://github.com/mapk-amazon>`_ in `#19001 <https://github.com/galaxyproject/galaxy/pull/19001>`_
+* Fix numerous issues with tool input format "21.01" by `@jmchilton <https://github.com/jmchilton>`_ in `#19030 <https://github.com/galaxyproject/galaxy/pull/19030>`_
+* Fix test_stock.py unit test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19037 <https://github.com/galaxyproject/galaxy/pull/19037>`_
+* quota: do not complain on no-change of default by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19045 <https://github.com/galaxyproject/galaxy/pull/19045>`_
+* Normalize usernames to lowercase in OIDC authentication by `@arash77 <https://github.com/arash77>`_ in `#19131 <https://github.com/galaxyproject/galaxy/pull/19131>`_
+* 2 small uv config fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19146 <https://github.com/galaxyproject/galaxy/pull/19146>`_
+* Fix invocation metrics usability by providing job context. by `@jmchilton <https://github.com/jmchilton>`_ in `#19279 <https://github.com/galaxyproject/galaxy/pull/19279>`_
+* Fix import of previously-deleted TRS workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19311 <https://github.com/galaxyproject/galaxy/pull/19311>`_
+* Fix quota usage with user object stores by `@davelopez <https://github.com/davelopez>`_ in `#19323 <https://github.com/galaxyproject/galaxy/pull/19323>`_
+* Fix workflows with optional non-default parameter input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19332 <https://github.com/galaxyproject/galaxy/pull/19332>`_
+* Backport #19001 kubernetes api client fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19338 <https://github.com/galaxyproject/galaxy/pull/19338>`_
+* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
+* Use select_from_url test data from github, not usegalaxy.org by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19352 <https://github.com/galaxyproject/galaxy/pull/19352>`_
+* Fix to only show ChatGXY when available. by `@dannon <https://github.com/dannon>`_ in `#19389 <https://github.com/galaxyproject/galaxy/pull/19389>`_
+* Fix job parameter summary for inputs without label by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19427 <https://github.com/galaxyproject/galaxy/pull/19427>`_
+* Show Keycloak provider label in UI by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19447 <https://github.com/galaxyproject/galaxy/pull/19447>`_
+* Expression tool format source backport by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19466 <https://github.com/galaxyproject/galaxy/pull/19466>`_
+* backport of defensive refresh tokens by `@martenson <https://github.com/martenson>`_ in `#19471 <https://github.com/galaxyproject/galaxy/pull/19471>`_
+* Improve relabel from file error if file doesn't contain enough lines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19480 <https://github.com/galaxyproject/galaxy/pull/19480>`_
+* Serialize message exceptions on execution error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19483 <https://github.com/galaxyproject/galaxy/pull/19483>`_
+* Fail with error message when submitting invalid request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19489 <https://github.com/galaxyproject/galaxy/pull/19489>`_
+* Fix deleting lddas in batch by `@davelopez <https://github.com/davelopez>`_ in `#19506 <https://github.com/galaxyproject/galaxy/pull/19506>`_
+* Skip token refresh without refresh token in psa by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19514 <https://github.com/galaxyproject/galaxy/pull/19514>`_
+* Downgrade 'InteractiveTools are not enabled' to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19518 <https://github.com/galaxyproject/galaxy/pull/19518>`_
+* Fix extracting workflows from purged and deleted histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19525 <https://github.com/galaxyproject/galaxy/pull/19525>`_
+* Fix error message when subworkflow input connection missing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19526 <https://github.com/galaxyproject/galaxy/pull/19526>`_
+* Fix remap for parameter called id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19532 <https://github.com/galaxyproject/galaxy/pull/19532>`_
+* Fix admin cancel job message not being displayed to the user by `@davelopez <https://github.com/davelopez>`_ in `#19537 <https://github.com/galaxyproject/galaxy/pull/19537>`_
+* Use instance wide default ``real_system_username`` if not defined on destination by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19544 <https://github.com/galaxyproject/galaxy/pull/19544>`_
+* Fix job paused on user defined object store by `@davelopez <https://github.com/davelopez>`_ in `#19578 <https://github.com/galaxyproject/galaxy/pull/19578>`_
+
+============
+Enhancements
+============
+
+* Add clean up job working directory as celery task by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#15816 <https://github.com/galaxyproject/galaxy/pull/15816>`_
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Feature - stdout live reporting by `@gecage952 <https://github.com/gecage952>`_ in `#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
+* Add Python 3.13 support by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18449 <https://github.com/galaxyproject/galaxy/pull/18449>`_
+* Add onedata templates by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18457 <https://github.com/galaxyproject/galaxy/pull/18457>`_
+* Support high-availability setups for the interactive tools proxy by `@kysrpex <https://github.com/kysrpex>`_ in `#18481 <https://github.com/galaxyproject/galaxy/pull/18481>`_
+* Add unique constraints to the email and username fields in the galaxy_user table by `@jdavcs <https://github.com/jdavcs>`_ in `#18493 <https://github.com/galaxyproject/galaxy/pull/18493>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18505 <https://github.com/galaxyproject/galaxy/pull/18505>`_
+* Improvements for K8S deployment (especially ITs) by `@almahmoud <https://github.com/almahmoud>`_ in `#18514 <https://github.com/galaxyproject/galaxy/pull/18514>`_
+* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
+* Improvements to Tool Test Parsing by `@jmchilton <https://github.com/jmchilton>`_ in `#18560 <https://github.com/galaxyproject/galaxy/pull/18560>`_
+* Group tool templating exceptions in sentry by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18570 <https://github.com/galaxyproject/galaxy/pull/18570>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18578 <https://github.com/galaxyproject/galaxy/pull/18578>`_
+* Record container id and type in core job metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18579 <https://github.com/galaxyproject/galaxy/pull/18579>`_
+* Rev pinned gxformat2. by `@jmchilton <https://github.com/jmchilton>`_ in `#18624 <https://github.com/galaxyproject/galaxy/pull/18624>`_
+* Better Typing for Tool Execution Plumbing by `@jmchilton <https://github.com/jmchilton>`_ in `#18626 <https://github.com/galaxyproject/galaxy/pull/18626>`_
+* Remove unused functions in dataset managers by `@jmchilton <https://github.com/jmchilton>`_ in `#18631 <https://github.com/galaxyproject/galaxy/pull/18631>`_
+* Parameter Model Improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#18641 <https://github.com/galaxyproject/galaxy/pull/18641>`_
+* Parse stored config details to script-based visualizations by `@guerler <https://github.com/guerler>`_ in `#18651 <https://github.com/galaxyproject/galaxy/pull/18651>`_
+* Another round of parameter model improvements. by `@jmchilton <https://github.com/jmchilton>`_ in `#18673 <https://github.com/galaxyproject/galaxy/pull/18673>`_
+* Allow access to invocation via shared or published history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18707 <https://github.com/galaxyproject/galaxy/pull/18707>`_
+* Allow specifying multi-select workflow parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18715 <https://github.com/galaxyproject/galaxy/pull/18715>`_
+* Improvements to help terms & tool help. by `@jmchilton <https://github.com/jmchilton>`_ in `#18722 <https://github.com/galaxyproject/galaxy/pull/18722>`_
+* Add a retry when deleting a k8s job by `@afgane <https://github.com/afgane>`_ in `#18744 <https://github.com/galaxyproject/galaxy/pull/18744>`_
+* More typing, docs, and decomposition around tool execution by `@jmchilton <https://github.com/jmchilton>`_ in `#18758 <https://github.com/galaxyproject/galaxy/pull/18758>`_
+* Add Workflow Title and Annotation sections by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18762 <https://github.com/galaxyproject/galaxy/pull/18762>`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Allow using tracks and groups in visualization xml by `@guerler <https://github.com/guerler>`_ in `#18779 <https://github.com/galaxyproject/galaxy/pull/18779>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
+* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18864 <https://github.com/galaxyproject/galaxy/pull/18864>`_
+* Implement Pydantic model for workflow test format.  by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
+* Remove some unused dynamic drill down options. by `@jmchilton <https://github.com/jmchilton>`_ in `#18892 <https://github.com/galaxyproject/galaxy/pull/18892>`_
+* Enable ``ignore-without-code`` mypy error code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18898 <https://github.com/galaxyproject/galaxy/pull/18898>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18904 <https://github.com/galaxyproject/galaxy/pull/18904>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
+* Remove outdated fimo wrapper and galaxy-sequence-utils dependency by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18937 <https://github.com/galaxyproject/galaxy/pull/18937>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18943 <https://github.com/galaxyproject/galaxy/pull/18943>`_
+* Allow to overwrite `real_system_username` per destination by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18945 <https://github.com/galaxyproject/galaxy/pull/18945>`_
+* Assert that `data_column` parameters have a valid `data_ref` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18949 <https://github.com/galaxyproject/galaxy/pull/18949>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18982 <https://github.com/galaxyproject/galaxy/pull/18982>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Enhance relabel_from_file to work with any column pair in mapping file by `@wm75 <https://github.com/wm75>`_ in `#19022 <https://github.com/galaxyproject/galaxy/pull/19022>`_
+* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
+* Better logging around tool loading by `@jmchilton <https://github.com/jmchilton>`_ in `#19029 <https://github.com/galaxyproject/galaxy/pull/19029>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19031 <https://github.com/galaxyproject/galaxy/pull/19031>`_
+* Silence the quota manager for updates by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19046 <https://github.com/galaxyproject/galaxy/pull/19046>`_
+* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19062 <https://github.com/galaxyproject/galaxy/pull/19062>`_
+* Annotate ``DatasetAssociationManager`` as generic type by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19063 <https://github.com/galaxyproject/galaxy/pull/19063>`_
+* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
+* Replace poetry with uv by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19075 <https://github.com/galaxyproject/galaxy/pull/19075>`_
+* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
+* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
+* Allow directory_uri workflow parameters.  by `@jmchilton <https://github.com/jmchilton>`_ in `#19093 <https://github.com/galaxyproject/galaxy/pull/19093>`_
+* Better cleanup of sharing roles on user purge by `@jdavcs <https://github.com/jdavcs>`_ in `#19096 <https://github.com/galaxyproject/galaxy/pull/19096>`_
+* Support deferred datasets in visualizations by `@davelopez <https://github.com/davelopez>`_ in `#19097 <https://github.com/galaxyproject/galaxy/pull/19097>`_
+* uv: Do not recalculate dependencies when exporting by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19099 <https://github.com/galaxyproject/galaxy/pull/19099>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Test hash validation also for upload by path by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19109 <https://github.com/galaxyproject/galaxy/pull/19109>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Add type annotations to ``JobRunnerMapper`` and related code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19115 <https://github.com/galaxyproject/galaxy/pull/19115>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19123 <https://github.com/galaxyproject/galaxy/pull/19123>`_
+* Allow a posix file source to prefer linking. by `@jmchilton <https://github.com/jmchilton>`_ in `#19132 <https://github.com/galaxyproject/galaxy/pull/19132>`_
+* Remove OpenLayers legacy files and add SVG logo by `@guerler <https://github.com/guerler>`_ in `#19135 <https://github.com/galaxyproject/galaxy/pull/19135>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19149 <https://github.com/galaxyproject/galaxy/pull/19149>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+* Workflow Inputs Activity by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#19252 <https://github.com/galaxyproject/galaxy/pull/19252>`_
+
+=============
+Other changes
+=============
+
+* Fix workflow invocation accessibility check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18746 <https://github.com/galaxyproject/galaxy/pull/18746>`_
+* Fix destentation typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19140 <https://github.com/galaxyproject/galaxy/pull/19140>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Update mercurial to non-yanked 6.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18434 <https://github.com/galaxyproject/galaxy/pull/18434>`_
+* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Don't call job_runner.stop_job on jobs in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18495 <https://github.com/galaxyproject/galaxy/pull/18495>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18559 <https://github.com/galaxyproject/galaxy/pull/18559>`_
+* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
+* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
+* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18634 <https://github.com/galaxyproject/galaxy/pull/18634>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Allow to change only the description of a quota by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18775 <https://github.com/galaxyproject/galaxy/pull/18775>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
+* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18819 <https://github.com/galaxyproject/galaxy/pull/18819>`_
+* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Skip metric collection if job working directory doesn't exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18845 <https://github.com/galaxyproject/galaxy/pull/18845>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Fix username used in invocation report by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18932 <https://github.com/galaxyproject/galaxy/pull/18932>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix job search statement building by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19010 <https://github.com/galaxyproject/galaxy/pull/19010>`_
+* Put cached jobs back into queue on handler restart by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19012 <https://github.com/galaxyproject/galaxy/pull/19012>`_
+* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
+* Create harmonized collections from correct tool outputs by `@wm75 <https://github.com/wm75>`_ in `#19222 <https://github.com/galaxyproject/galaxy/pull/19222>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
+* prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by `@ljocha <https://github.com/ljocha>`_ in `#18826 <https://github.com/galaxyproject/galaxy/pull/18826>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Update mercurial to non-yanked 6.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18434 <https://github.com/galaxyproject/galaxy/pull/18434>`_
+* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18559 <https://github.com/galaxyproject/galaxy/pull/18559>`_
+* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
+* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
+* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18634 <https://github.com/galaxyproject/galaxy/pull/18634>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Allow to change only the description of a quota by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18775 <https://github.com/galaxyproject/galaxy/pull/18775>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
+* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18819 <https://github.com/galaxyproject/galaxy/pull/18819>`_
+* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Skip metric collection if job working directory doesn't exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18845 <https://github.com/galaxyproject/galaxy/pull/18845>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Fix username used in invocation report by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18932 <https://github.com/galaxyproject/galaxy/pull/18932>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix job search statement building by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19010 <https://github.com/galaxyproject/galaxy/pull/19010>`_
+* Put cached jobs back into queue on handler restart by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19012 <https://github.com/galaxyproject/galaxy/pull/19012>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
+* prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by `@ljocha <https://github.com/ljocha>`_ in `#18826 <https://github.com/galaxyproject/galaxy/pull/18826>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18559 <https://github.com/galaxyproject/galaxy/pull/18559>`_
+* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
+* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
+* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18634 <https://github.com/galaxyproject/galaxy/pull/18634>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Allow to change only the description of a quota by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18775 <https://github.com/galaxyproject/galaxy/pull/18775>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
+* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18819 <https://github.com/galaxyproject/galaxy/pull/18819>`_
+* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Skip metric collection if job working directory doesn't exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18845 <https://github.com/galaxyproject/galaxy/pull/18845>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
+* prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by `@ljocha <https://github.com/ljocha>`_ in `#18826 <https://github.com/galaxyproject/galaxy/pull/18826>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index cb942f6718571eb99df7d93d7f267750f65c2c5a..5151db161bd2811597557fe00d95d4aaf2df23a2 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-app
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -41,7 +42,7 @@ install_requires =
     galaxy-objectstore
     galaxy-tool-util[cwl,edam]
     galaxy-tours
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     Beaker
@@ -57,23 +58,25 @@ install_requires =
     Mako
     Markdown
     MarkupSafe
+    mercurial>=6.8.2
     packaging
     paramiko!=2.9.0,!=2.9.1
     pebble
     pulsar-galaxy-lib>=0.15.0.dev0
     pydantic>=2.7.4
     pysam>=0.21
+    python-slugify
     PyJWT
     PyYAML
     refgenconf>=0.12.0
     regex
     requests
-    SQLAlchemy>=2.0,<2.1
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
     sqlitedict
     starlette
     svgwrite
     typing-extensions
-    WebOb
+    WebOb>=1.8.9
     Whoosh
 packages = find:
 python_requires = >=3.8
diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
index c0cbc0c0d8c3591ef64d24bbf51209584fe3dfd5..023b0ae4ee90f98e8b03160392b44be993b5639e 100644
--- a/packages/auth/HISTORY.rst
+++ b/packages/auth/HISTORY.rst
@@ -4,11 +4,53 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg
index 44bac91c764a16304390914af13adab25035bb62..37ab7f17ed18d043d260b34208987739d67c550b 100644
--- a/packages/auth/setup.cfg
+++ b/packages/auth/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-auth
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
index f9cf20c3f0f65b3d83674ed8a220e16beb5c1bad..6eafc2dc47d2b02eb891c3258af0bf73d6713d51 100644
--- a/packages/config/HISTORY.rst
+++ b/packages/config/HISTORY.rst
@@ -4,11 +4,179 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add rDock prm datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19783 <https://github.com/galaxyproject/galaxy/pull/19783>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix conditional dependency path resolution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19723 <https://github.com/galaxyproject/galaxy/pull/19723>`_
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Updated registration warning message by `@dannon <https://github.com/dannon>`_ in `#19598 <https://github.com/galaxyproject/galaxy/pull/19598>`_
+
+============
+Enhancements
+============
+
+* Add fastk_ktab_tar datatype required for fastk tool by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#19615 <https://github.com/galaxyproject/galaxy/pull/19615>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix loading error for built in tool `sift` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18357 <https://github.com/galaxyproject/galaxy/pull/18357>`_
+* Add gtf to auto_compressed_types by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19175 <https://github.com/galaxyproject/galaxy/pull/19175>`_
+* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
+* Fix to only show ChatGXY when available. by `@dannon <https://github.com/dannon>`_ in `#19389 <https://github.com/galaxyproject/galaxy/pull/19389>`_
+
+============
+Enhancements
+============
+
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Improve usability of Directory datatype by `@wm75 <https://github.com/wm75>`_ in `#17614 <https://github.com/galaxyproject/galaxy/pull/17614>`_
+* Add pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18419 <https://github.com/galaxyproject/galaxy/pull/18419>`_
+* Add onedata templates by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18457 <https://github.com/galaxyproject/galaxy/pull/18457>`_
+* Support high-availability setups for the interactive tools proxy by `@kysrpex <https://github.com/kysrpex>`_ in `#18481 <https://github.com/galaxyproject/galaxy/pull/18481>`_
+* Minor config documentation enhancements by `@bgruening <https://github.com/bgruening>`_ in `#18499 <https://github.com/galaxyproject/galaxy/pull/18499>`_
+* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
+* Bring your own file sources: Add the WebDAV template and configuration by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#18598 <https://github.com/galaxyproject/galaxy/pull/18598>`_
+* Add BlobToolkit to the list of interactive tools by `@Delphine-L <https://github.com/Delphine-L>`_ in `#18630 <https://github.com/galaxyproject/galaxy/pull/18630>`_
+* Remove `defaults` channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18757 <https://github.com/galaxyproject/galaxy/pull/18757>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Jupyter Interactive Tool 1.0.1/24.07 by `@natefoo <https://github.com/natefoo>`_ in `#18861 <https://github.com/galaxyproject/galaxy/pull/18861>`_
+* Allow setting a few global defaults for file source plugin types. by `@jmchilton <https://github.com/jmchilton>`_ in `#18909 <https://github.com/galaxyproject/galaxy/pull/18909>`_
+* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
+* Add hint to the tool schema about runtime conditional changes by `@martenson <https://github.com/martenson>`_ in `#18996 <https://github.com/galaxyproject/galaxy/pull/18996>`_
+* Irods ssl connection by `@pauldg <https://github.com/pauldg>`_ in `#19014 <https://github.com/galaxyproject/galaxy/pull/19014>`_
+* Add some Zarr-based datatypes by `@davelopez <https://github.com/davelopez>`_ in `#19040 <https://github.com/galaxyproject/galaxy/pull/19040>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+* Add XML based `vtk` datatype by `@tStehling <https://github.com/tStehling>`_ in `#19104 <https://github.com/galaxyproject/galaxy/pull/19104>`_
+* Allow a posix file source to prefer linking. by `@jmchilton <https://github.com/jmchilton>`_ in `#19132 <https://github.com/galaxyproject/galaxy/pull/19132>`_
+* Add bcsp datatype by `@SantaMcCloud <https://github.com/SantaMcCloud>`_ in `#19365 <https://github.com/galaxyproject/galaxy/pull/19365>`_
+* add MuData as subclass of H5 by `@pavanvidem <https://github.com/pavanvidem>`_ in `#19416 <https://github.com/galaxyproject/galaxy/pull/19416>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Strip whitespace when listifying admin users by `@jdavcs <https://github.com/jdavcs>`_ in `#18656 <https://github.com/galaxyproject/galaxy/pull/18656>`_
+* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+* More datatype deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18612 <https://github.com/galaxyproject/galaxy/pull/18612>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro <https://github.com/cat-bro>`_ in `#18784 <https://github.com/galaxyproject/galaxy/pull/18784>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Strip whitespace when listifying admin users by `@jdavcs <https://github.com/jdavcs>`_ in `#18656 <https://github.com/galaxyproject/galaxy/pull/18656>`_
+* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+* More datatype deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18612 <https://github.com/galaxyproject/galaxy/pull/18612>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro <https://github.com/cat-bro>`_ in `#18784 <https://github.com/galaxyproject/galaxy/pull/18784>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Strip whitespace when listifying admin users by `@jdavcs <https://github.com/jdavcs>`_ in `#18656 <https://github.com/galaxyproject/galaxy/pull/18656>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+* More datatype deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18612 <https://github.com/galaxyproject/galaxy/pull/18612>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro <https://github.com/cat-bro>`_ in `#18784 <https://github.com/galaxyproject/galaxy/pull/18784>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg
index 8b66d4c8be59b98224f825ae3b52b5c480d8b765..dcc0810cfbae9f5f829a22f28d6cdc8ac4a02645 100644
--- a/packages/config/setup.cfg
+++ b/packages/config/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-config
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index 5092affb1e05f8725fb49d4ebfe72a9870053a78..c7908519bfec978a0af9cec56473b96406f878ec 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -4,11 +4,258 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private role name performance issue by `@jdavcs <https://github.com/jdavcs>`_ in `#19679 <https://github.com/galaxyproject/galaxy/pull/19679>`_
+* Fix anndata metadata setting for data with integer indexes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19774 <https://github.com/galaxyproject/galaxy/pull/19774>`_
+* Fix parameter model constructions with leading underscores, fixes converter linting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19790 <https://github.com/galaxyproject/galaxy/pull/19790>`_
+
+============
+Enhancements
+============
+
+* Add rDock prm datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19783 <https://github.com/galaxyproject/galaxy/pull/19783>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix recording transform action name. by `@jmchilton <https://github.com/jmchilton>`_ in `#19672 <https://github.com/galaxyproject/galaxy/pull/19672>`_
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+=============
+Other changes
+=============
+
+* Backport #19620 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19725 <https://github.com/galaxyproject/galaxy/pull/19725>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Set content-type to text/plain if dataset not safe by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19563 <https://github.com/galaxyproject/galaxy/pull/19563>`_
+* Fail request explicitly when sqlite provider used on non-sqlite file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19630 <https://github.com/galaxyproject/galaxy/pull/19630>`_
+* Fix various bugs around tool data table bundles by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19659 <https://github.com/galaxyproject/galaxy/pull/19659>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Raise Message Exception when displaying binary data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18503 <https://github.com/galaxyproject/galaxy/pull/18503>`_
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
+* Fix migration data fixes tests by `@jdavcs <https://github.com/jdavcs>`_ in `#18885 <https://github.com/galaxyproject/galaxy/pull/18885>`_
+* Fix backend role sharing bug by `@jdavcs <https://github.com/jdavcs>`_ in `#18942 <https://github.com/galaxyproject/galaxy/pull/18942>`_
+* Add merge migration to merge 2 heads by `@jdavcs <https://github.com/jdavcs>`_ in `#19163 <https://github.com/galaxyproject/galaxy/pull/19163>`_
+* Record implicitly converted dataset as input dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19301 <https://github.com/galaxyproject/galaxy/pull/19301>`_
+* Fix quota usage with user object stores by `@davelopez <https://github.com/davelopez>`_ in `#19323 <https://github.com/galaxyproject/galaxy/pull/19323>`_
+* Fix workflows with optional non-default parameter input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19332 <https://github.com/galaxyproject/galaxy/pull/19332>`_
+* Fix importing shared workflows with deeply nested subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19335 <https://github.com/galaxyproject/galaxy/pull/19335>`_
+* Backport fix from #19396 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19399 <https://github.com/galaxyproject/galaxy/pull/19399>`_
+* Prevent cycling through failing conversion jobs in trackster by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19494 <https://github.com/galaxyproject/galaxy/pull/19494>`_
+* Fix extracting workflows from purged and deleted histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19525 <https://github.com/galaxyproject/galaxy/pull/19525>`_
+* Fix error message when subworkflow input connection missing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19526 <https://github.com/galaxyproject/galaxy/pull/19526>`_
+* Fix admin cancel job message not being displayed to the user by `@davelopez <https://github.com/davelopez>`_ in `#19537 <https://github.com/galaxyproject/galaxy/pull/19537>`_
+* Add tool_id index on job table by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19543 <https://github.com/galaxyproject/galaxy/pull/19543>`_
+* Update 24.2 db revision tags by `@jdavcs <https://github.com/jdavcs>`_ in `#19550 <https://github.com/galaxyproject/galaxy/pull/19550>`_
+* Provide guidance in case of deadlock during db migration by `@jdavcs <https://github.com/jdavcs>`_ in `#19551 <https://github.com/galaxyproject/galaxy/pull/19551>`_
+* Fix job paused on user defined object store by `@davelopez <https://github.com/davelopez>`_ in `#19578 <https://github.com/galaxyproject/galaxy/pull/19578>`_
+* Handle isatools dependency by `@jdavcs <https://github.com/jdavcs>`_ in `#19582 <https://github.com/galaxyproject/galaxy/pull/19582>`_
+
+============
+Enhancements
+============
+
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Improve usability of Directory datatype by `@wm75 <https://github.com/wm75>`_ in `#17614 <https://github.com/galaxyproject/galaxy/pull/17614>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
+* Add pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18419 <https://github.com/galaxyproject/galaxy/pull/18419>`_
+* Prepare for NumPy 2.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18422 <https://github.com/galaxyproject/galaxy/pull/18422>`_
+* Add unique constraints to the email and username fields in the galaxy_user table by `@jdavcs <https://github.com/jdavcs>`_ in `#18493 <https://github.com/galaxyproject/galaxy/pull/18493>`_
+* Improvements for K8S deployment (especially ITs) by `@almahmoud <https://github.com/almahmoud>`_ in `#18514 <https://github.com/galaxyproject/galaxy/pull/18514>`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
+* Handle compressed content in dataset preview for all sequence classes by `@PlushZ <https://github.com/PlushZ>`_ in `#18776 <https://github.com/galaxyproject/galaxy/pull/18776>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
+* Refactor migration testing setup code by `@jdavcs <https://github.com/jdavcs>`_ in `#18886 <https://github.com/galaxyproject/galaxy/pull/18886>`_
+* Allow setting a few global defaults for file source plugin types. by `@jmchilton <https://github.com/jmchilton>`_ in `#18909 <https://github.com/galaxyproject/galaxy/pull/18909>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
+* Fix extra files path type hint by `@davelopez <https://github.com/davelopez>`_ in `#18958 <https://github.com/galaxyproject/galaxy/pull/18958>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* Optimize to_history_dataset_association in create_datasets_from_library_folder by `@arash77 <https://github.com/arash77>`_ in `#18970 <https://github.com/galaxyproject/galaxy/pull/18970>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Add some Zarr-based datatypes by `@davelopez <https://github.com/davelopez>`_ in `#19040 <https://github.com/galaxyproject/galaxy/pull/19040>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+* Annotate ``DatasetAssociationManager`` as generic type by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19063 <https://github.com/galaxyproject/galaxy/pull/19063>`_
+* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
+* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
+* Better cleanup of sharing roles on user purge by `@jdavcs <https://github.com/jdavcs>`_ in `#19096 <https://github.com/galaxyproject/galaxy/pull/19096>`_
+* Add XML based `vtk` datatype by `@tStehling <https://github.com/tStehling>`_ in `#19104 <https://github.com/galaxyproject/galaxy/pull/19104>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Enable specifying dataset hash in test jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19113 <https://github.com/galaxyproject/galaxy/pull/19113>`_
+* Enhance UTF-8 support for filename handling in downloads by `@arash77 <https://github.com/arash77>`_ in `#19161 <https://github.com/galaxyproject/galaxy/pull/19161>`_
+* Backport of Workflow Editor Activity Bar by `@dannon <https://github.com/dannon>`_ in `#19212 <https://github.com/galaxyproject/galaxy/pull/19212>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+
+=============
+Other changes
+=============
+
+* Merge 24.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#18386 <https://github.com/galaxyproject/galaxy/pull/18386>`_
+* Format dev to fix linting. by `@jmchilton <https://github.com/jmchilton>`_ in `#18860 <https://github.com/galaxyproject/galaxy/pull/18860>`_
+* Add 24.2 migration tags by `@jdavcs <https://github.com/jdavcs>`_ in `#19169 <https://github.com/galaxyproject/galaxy/pull/19169>`_
+* Fix type annotations for pysam 0.23.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19571 <https://github.com/galaxyproject/galaxy/pull/19571>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Optimize/fix sqlite hid update statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19106 <https://github.com/galaxyproject/galaxy/pull/19106>`_
+* Prefer auto-decompressed datatype when picking conversion target  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19162 <https://github.com/galaxyproject/galaxy/pull/19162>`_
+* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
+* Fix bad merge conflict resolution by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19297 <https://github.com/galaxyproject/galaxy/pull/19297>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index 4d8cee887fd9bc583baf25cbe9a48c323c367a3e..c725208551d443411039b8487b96e7e8972a7358 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-data
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -36,17 +37,15 @@ install_requires =
     galaxy-objectstore
     galaxy-schema
     galaxy-tool-util
-    galaxy-util[template]
+    galaxy-util[image_util,template]
     alembic
-    alembic-utils
     bdbag>=1.6.3
     bx-python
     dnspython
     galaxy-sequence-utils
     h5grove>=1.2.1
     h5py
-    isa-rwval>=0.10.10
-    isal
+    isal>=1.7.0
     MarkupSafe
     msal
     mrcfile
@@ -58,11 +57,10 @@ install_requires =
     python-magic
     pysam>=0.21
     rocrate
-    social-auth-core[openidconnect]==4.0.3
-    SQLAlchemy>=2.0,<2.1
+    social-auth-core>=4.5.0
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
     tifffile
     typing-extensions
-    WebOb
 packages = find:
 python_requires = >=3.8
 
@@ -75,4 +73,4 @@ console_scripts =
 
 [options.packages.find]
 exclude =
-    tests*
\ No newline at end of file
+    tests*
diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
index 0827590918d1f678ea88800b39056feabcd4f877..22a2a86cf852c82f4b9bb557d3906c6923ddc424 100644
--- a/packages/files/HISTORY.rst
+++ b/packages/files/HISTORY.rst
@@ -4,11 +4,80 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private role name performance issue by `@jdavcs <https://github.com/jdavcs>`_ in `#19679 <https://github.com/galaxyproject/galaxy/pull/19679>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix RDM token access for user-defined file sources by `@davelopez <https://github.com/davelopez>`_ in `#19768 <https://github.com/galaxyproject/galaxy/pull/19768>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* Add onedata templates by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18457 <https://github.com/galaxyproject/galaxy/pull/18457>`_
+* Add missing version in the file sources and object store templates by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#18497 <https://github.com/galaxyproject/galaxy/pull/18497>`_
+* Add a new version of the production s3fs file source template with the writable configuration variable added by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#18575 <https://github.com/galaxyproject/galaxy/pull/18575>`_
+* Bring your own file sources: Add the WebDAV template and configuration by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#18598 <https://github.com/galaxyproject/galaxy/pull/18598>`_
+* Allow setting a few global defaults for file source plugin types. by `@jmchilton <https://github.com/jmchilton>`_ in `#18909 <https://github.com/galaxyproject/galaxy/pull/18909>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Allow a posix file source to prefer linking. by `@jmchilton <https://github.com/jmchilton>`_ in `#19132 <https://github.com/galaxyproject/galaxy/pull/19132>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix production_aws_private_bucket.yml by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19155 <https://github.com/galaxyproject/galaxy/pull/19155>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg
index 198052e2cc2546967a38113d61c0edcebf46be16..a2ba05108bc7d628f313d54b14594a92966644fd 100644
--- a/packages/files/setup.cfg
+++ b/packages/files/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,14 +28,13 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-files
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
 install_requires =
     galaxy-util[config_template]
     fs
-    isal
     typing-extensions
 packages = find:
 python_requires = >=3.8
diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
index c43f9b0c30dc4cfe68d51e545efe8c9faada0e41..86056de1cbef0dbacc077bd1dc6ae00be9bb83ac 100644
--- a/packages/job_execution/HISTORY.rst
+++ b/packages/job_execution/HISTORY.rst
@@ -4,11 +4,80 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Use materialized datasets in pulsar job runner by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19807 <https://github.com/galaxyproject/galaxy/pull/19807>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo <https://github.com/natefoo>`_ in `#18863 <https://github.com/galaxyproject/galaxy/pull/18863>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo <https://github.com/natefoo>`_ in `#18863 <https://github.com/galaxyproject/galaxy/pull/18863>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo <https://github.com/natefoo>`_ in `#18863 <https://github.com/galaxyproject/galaxy/pull/18863>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
index d5f7f2bf4379551e2f1f0921a57780039bdbd61d..954503ce6b81421c67e5999436bc9f1b9e6fa57a 100644
--- a/packages/job_execution/setup.cfg
+++ b/packages/job_execution/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-job-execution
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -38,7 +39,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     MarkupSafe
-    SQLAlchemy>=2.0,<2.1
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
index 76b0afce976ba6547f5eb5209fb06032ef063cf2..5e164af083b00a4fe6d9ae8c783f788e27da0f1e 100644
--- a/packages/job_metrics/HISTORY.rst
+++ b/packages/job_metrics/HISTORY.rst
@@ -4,11 +4,58 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Record container id and type in core job metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18579 <https://github.com/galaxyproject/galaxy/pull/18579>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg
index bb20a15f6637e53694f8667ac20292e5cb3565a4..3e3c45df486fe2970211c428035266c6f634c163 100644
--- a/packages/job_metrics/setup.cfg
+++ b/packages/job_metrics/setup.cfg
@@ -15,6 +15,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -28,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-job-metrics
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/meta/HISTORY.rst b/packages/meta/HISTORY.rst
index 7297421a74876874b0e0eb758e0262362b72faac..50a6be68b6627313903c771e23af36a4f084a33f 100644
--- a/packages/meta/HISTORY.rst
+++ b/packages/meta/HISTORY.rst
@@ -10,7 +10,7 @@ History
 
 
 ---------------------
-19.9.0
+19.9.0 (2019-11-21)
 ---------------------
 
 * Initial import from dev branch of Galaxy during 19.09 development cycle.
diff --git a/packages/meta/requirements.txt b/packages/meta/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg
index 260765e0f7d2b9399f9f1597942669f33ee534ae..b0d651a3eb563fd37243328ad78d8fbee745c419 100644
--- a/packages/meta/setup.cfg
+++ b/packages/meta/setup.cfg
@@ -15,6 +15,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering :: Bio-Informatics
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
@@ -29,12 +30,13 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy
 url = https://github.com/galaxyproject/galaxy
-version = 23.2.dev0
+version = 24.2.dev0
 
 [options]
 include_package_data = True
 packages = find:
 python_requires = >=3.8
+install_requires = file: requirements.txt
 
 [options.extras_require]
 postgresql =
diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst
index e1fcd22d984f03973409572a8e732d339a1aa732..6ab5fa87c329da59a33101c8308c98e2cda4de54 100644
--- a/packages/navigation/HISTORY.rst
+++ b/packages/navigation/HISTORY.rst
@@ -4,11 +4,53 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg
index 6dbcdaafcb193d4221bff63ea6966acfd90a2e00..144beabf25860e4272fffe12c105c4e93233c035 100644
--- a/packages/navigation/setup.cfg
+++ b/packages/navigation/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-navigation
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index ffcff6f795dc2654afe356f459ebad09e0e1abb9..b38877e8de24d32eaabd93c7b7342aa262efec55 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -4,11 +4,86 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix job directory not being cleaned up by `@davelopez <https://github.com/davelopez>`_ in `#18997 <https://github.com/galaxyproject/galaxy/pull/18997>`_
+* Fix quota usage with user object stores by `@davelopez <https://github.com/davelopez>`_ in `#19323 <https://github.com/galaxyproject/galaxy/pull/19323>`_
+* Fix object not found handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19468 <https://github.com/galaxyproject/galaxy/pull/19468>`_
+
+============
+Enhancements
+============
+
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* Add onedata templates by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18457 <https://github.com/galaxyproject/galaxy/pull/18457>`_
+* Add missing version in the file sources and object store templates by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#18497 <https://github.com/galaxyproject/galaxy/pull/18497>`_
+* Add a retry when deleting a k8s job by `@afgane <https://github.com/afgane>`_ in `#18744 <https://github.com/galaxyproject/galaxy/pull/18744>`_
+* Irods ssl connection by `@pauldg <https://github.com/pauldg>`_ in `#19014 <https://github.com/galaxyproject/galaxy/pull/19014>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
index 38a0e8cf40b816f5d9fe86bab796d70bef618a55..8a7e7d5206ec7a9c15cee988ea642351cb654211 100644
--- a/packages/objectstore/setup.cfg
+++ b/packages/objectstore/setup.cfg
@@ -15,6 +15,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -28,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-objectstore
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/package-dev-install.sh b/packages/package-dev-install.sh
new file mode 100755
index 0000000000000000000000000000000000000000..b22d5460e72c166bf406043123e56af55aad4b87
--- /dev/null
+++ b/packages/package-dev-install.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+#
+# Install packages in development mode, for running installed Galaxy from the source
+#
+set -euo pipefail
+
+editable=false
+
+while getopts ':e' OPTION
+do
+    case $OPTION in
+        e)
+            editable=true
+           ;;
+    esac
+done
+shift $((OPTIND - 1))
+
+up_to="${1:-}"
+
+if [ -n "$up_to" -a ! -d "$up_to" ]; then
+    echo "ERROR: package does not exist: $up_to"
+    exit 1
+fi
+
+while read package; do
+    [ -n "$package" ] || continue
+    pushd $package
+    if $editable; then
+        pip install -e .
+    else
+        pip install .
+    fi
+    popd
+    [ "$package" != "$up_to" ] || exit
+done < packages_by_dep_dag.txt
diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst
index 0fafdcb684cde6d6d9e9108144c7746bf6b8bcc1..95402274ae4a05ef81404493b13000e3a881065e 100644
--- a/packages/schema/HISTORY.rst
+++ b/packages/schema/HISTORY.rst
@@ -4,11 +4,143 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
+* Fix invocation metrics usability by providing job context. by `@jmchilton <https://github.com/jmchilton>`_ in `#19279 <https://github.com/galaxyproject/galaxy/pull/19279>`_
+
+============
+Enhancements
+============
+
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Feature - stdout live reporting by `@gecage952 <https://github.com/gecage952>`_ in `#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`_
+* Add errors fast api by `@arash77 <https://github.com/arash77>`_ in `#18093 <https://github.com/galaxyproject/galaxy/pull/18093>`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* Improve datasets permissions API schema typing by `@davelopez <https://github.com/davelopez>`_ in `#18563 <https://github.com/galaxyproject/galaxy/pull/18563>`_
+* Improve typing for archived histories API schema by `@davelopez <https://github.com/davelopez>`_ in `#18586 <https://github.com/galaxyproject/galaxy/pull/18586>`_
+* Tighten user notification API response types by `@davelopez <https://github.com/davelopez>`_ in `#18599 <https://github.com/galaxyproject/galaxy/pull/18599>`_
+* Improve update user API payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18602 <https://github.com/galaxyproject/galaxy/pull/18602>`_
+* Improve update history payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18618 <https://github.com/galaxyproject/galaxy/pull/18618>`_
+* Improve types around User in schema and client by `@davelopez <https://github.com/davelopez>`_ in `#18645 <https://github.com/galaxyproject/galaxy/pull/18645>`_
+* Improve accept header API schema by `@davelopez <https://github.com/davelopez>`_ in `#18668 <https://github.com/galaxyproject/galaxy/pull/18668>`_
+* Migrate Visualizations API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18721 <https://github.com/galaxyproject/galaxy/pull/18721>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Update Visualization FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18792 <https://github.com/galaxyproject/galaxy/pull/18792>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
+* Enable ``ignore-without-code`` mypy error code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18898 <https://github.com/galaxyproject/galaxy/pull/18898>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
+* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
+* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_
+* Remove the default `Incoming` suffix in `GenericModel` class by `@davelopez <https://github.com/davelopez>`_ in `#19174 <https://github.com/galaxyproject/galaxy/pull/19174>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
+* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
+* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
index 21987bc30fb4fb3fc94f9954a2e27bab5400b7cb..074d7363e2f5aae72688a9cbe900e4377dc46258 100644
--- a/packages/schema/setup.cfg
+++ b/packages/schema/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-schema
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
index 1b5017e4459739a41111b603c5816ab6f89d8018..81bbfd50fe75f3a7e00748176a9131b465bcd155 100644
--- a/packages/selenium/HISTORY.rst
+++ b/packages/selenium/HISTORY.rst
@@ -4,11 +4,85 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Set content-type to text/plain if dataset not safe by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19563 <https://github.com/galaxyproject/galaxy/pull/19563>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix transiently failing selenium tooltip issues by `@jmchilton <https://github.com/jmchilton>`_ in `#18847 <https://github.com/galaxyproject/galaxy/pull/18847>`_
+* release testing - UI tests for new workflow parameters by `@jmchilton <https://github.com/jmchilton>`_ in `#19182 <https://github.com/galaxyproject/galaxy/pull/19182>`_
+
+============
+Enhancements
+============
+
+* Masthead Revision by `@guerler <https://github.com/guerler>`_ in `#17927 <https://github.com/galaxyproject/galaxy/pull/17927>`_
+* Moves Libraries from Masthead to Activity Bar by `@guerler <https://github.com/guerler>`_ in `#18468 <https://github.com/galaxyproject/galaxy/pull/18468>`_
+* Replace History Dataset Picker in Library Folder by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18518 <https://github.com/galaxyproject/galaxy/pull/18518>`_
+* Workflow Invocation view improvements by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18615 <https://github.com/galaxyproject/galaxy/pull/18615>`_
+* Guide users to collection builders by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18857 <https://github.com/galaxyproject/galaxy/pull/18857>`_
+* Workflow license and creator edit keyboard access by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18936 <https://github.com/galaxyproject/galaxy/pull/18936>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Backport of Workflow Editor Activity Bar by `@dannon <https://github.com/dannon>`_ in `#19212 <https://github.com/galaxyproject/galaxy/pull/19212>`_
+* Various list of pairs builder usability fixes. by `@jmchilton <https://github.com/jmchilton>`_ in `#19248 <https://github.com/galaxyproject/galaxy/pull/19248>`_
+* Workflow Inputs Activity by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#19252 <https://github.com/galaxyproject/galaxy/pull/19252>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Persist uploaded data between Regular and Collection upload tabs by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19083 <https://github.com/galaxyproject/galaxy/pull/19083>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg
index 799669cc8903b3766a5c08ff077c2e79f5af1630..b4c5e334c06207b8593340b7d53d3c821ccd418d 100644
--- a/packages/selenium/setup.cfg
+++ b/packages/selenium/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-selenium
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/test.sh b/packages/test.sh
index d2ed377c352b418cd386190a6a77cea198bc4b13..2120ac2b922a18a18e0039ca5da837ec9e3bd605 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -49,7 +49,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
 
     # Install extras (if needed)
     if [ "$package_dir" = "util" ]; then
-        pip install '.[template,jstree,config_template]'
+        pip install '.[image_util,template,jstree,config_template]'
     elif [ "$package_dir" = "tool_util" ]; then
         pip install '.[cwl,mulled,edam,extended-assertions]'
     else
diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst
index 5e9ebad174f151af75412532383a5d657492dd7e..536247734432342dd041c91cfc4a4376a378e059 100644
--- a/packages/test_api/HISTORY.rst
+++ b/packages/test_api/HISTORY.rst
@@ -4,11 +4,166 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Allow tool state changes in refactor actions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19730 <https://github.com/galaxyproject/galaxy/pull/19730>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix tag processing in library upload by `@davelopez <https://github.com/davelopez>`_ in `#18714 <https://github.com/galaxyproject/galaxy/pull/18714>`_
+* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
+* Fix numerous issues with tool input format "21.01" by `@jmchilton <https://github.com/jmchilton>`_ in `#19030 <https://github.com/galaxyproject/galaxy/pull/19030>`_
+* Record implicitly converted dataset as input dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19301 <https://github.com/galaxyproject/galaxy/pull/19301>`_
+* Expression tool format source backport by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19466 <https://github.com/galaxyproject/galaxy/pull/19466>`_
+* Fail with error message when submitting invalid request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19489 <https://github.com/galaxyproject/galaxy/pull/19489>`_
+* Fix deleting lddas in batch by `@davelopez <https://github.com/davelopez>`_ in `#19506 <https://github.com/galaxyproject/galaxy/pull/19506>`_
+* Fix ``test_storage_show`` API test by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19522 <https://github.com/galaxyproject/galaxy/pull/19522>`_
+* Fix error message when subworkflow input connection missing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19526 <https://github.com/galaxyproject/galaxy/pull/19526>`_
+* Fix admin cancel job message not being displayed to the user by `@davelopez <https://github.com/davelopez>`_ in `#19537 <https://github.com/galaxyproject/galaxy/pull/19537>`_
+
+============
+Enhancements
+============
+
+* Improve usability of Directory datatype by `@wm75 <https://github.com/wm75>`_ in `#17614 <https://github.com/galaxyproject/galaxy/pull/17614>`_
+* Implement Declarative Testing for Workflow Behaviors by `@jmchilton <https://github.com/jmchilton>`_ in `#18542 <https://github.com/galaxyproject/galaxy/pull/18542>`_
+* More tool test typing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18590 <https://github.com/galaxyproject/galaxy/pull/18590>`_
+* Better Typing for Tool Execution Plumbing by `@jmchilton <https://github.com/jmchilton>`_ in `#18626 <https://github.com/galaxyproject/galaxy/pull/18626>`_
+* Parameter Model Improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#18641 <https://github.com/galaxyproject/galaxy/pull/18641>`_
+* Another round of parameter model improvements. by `@jmchilton <https://github.com/jmchilton>`_ in `#18673 <https://github.com/galaxyproject/galaxy/pull/18673>`_
+* Allow access to invocation via shared or published history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18707 <https://github.com/galaxyproject/galaxy/pull/18707>`_
+* Migrate Visualizations API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18721 <https://github.com/galaxyproject/galaxy/pull/18721>`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
+* Implement Pydantic model for workflow test format.  by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* More concise, readable tool execution testing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Do not skip CI tests on missing tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#19002 <https://github.com/galaxyproject/galaxy/pull/19002>`_
+* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
+* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
+* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
+* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
+* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Enable specifying dataset hash in test jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19113 <https://github.com/galaxyproject/galaxy/pull/19113>`_
+* Enhance UTF-8 support for filename handling in downloads by `@arash77 <https://github.com/arash77>`_ in `#19161 <https://github.com/galaxyproject/galaxy/pull/19161>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+
+=============
+Other changes
+=============
+
+* Fix workflow invocation accessibility check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18746 <https://github.com/galaxyproject/galaxy/pull/18746>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg
index 8fc3a5dbc3347378236f5eb5057d5effdeabe573..fb6049ffaedbe5253e667102fd9bb0395acdc534 100644
--- a/packages/test_api/setup.cfg
+++ b/packages/test_api/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-test-api
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
index 7867cc9a86860e03dfd0ed05f5092a50c109128d..a5bffa7f610700ac7b1e69c085f149f9a9acd407 100644
--- a/packages/test_base/HISTORY.rst
+++ b/packages/test_base/HISTORY.rst
@@ -4,11 +4,115 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
+* Fix tag processing in library upload by `@davelopez <https://github.com/davelopez>`_ in `#18714 <https://github.com/galaxyproject/galaxy/pull/18714>`_
+
+============
+Enhancements
+============
+
+* Mixed enhancements from CWL branch by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18539 <https://github.com/galaxyproject/galaxy/pull/18539>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
+* Implement Pydantic model for workflow test format.  by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Allow CORS requests to /api/workflow_landings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18963 <https://github.com/galaxyproject/galaxy/pull/18963>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* More concise, readable tool execution testing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+* Release testing - selenium tests for workflow invocation export. by `@jmchilton <https://github.com/jmchilton>`_ in `#19262 <https://github.com/galaxyproject/galaxy/pull/19262>`_
+
+=============
+Other changes
+=============
+
+* Fix workflow invocation accessibility check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18746 <https://github.com/galaxyproject/galaxy/pull/18746>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg
index 497247d478d5e489fcfe9cbfa3eeb87170d6830f..573ba4c25a97edffd66db2f8a5c5adaf1bf6ec9c 100644
--- a/packages/test_base/setup.cfg
+++ b/packages/test_base/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-test-base
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -35,7 +36,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     bioblend
-    cwltest
+    cwltest>=2.5.20240906231108
     gxformat2
     pytest
     PyYAML
diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
index 77740d14fb96fb63609db7e8d7f0a694270e2a7f..f472bd71f60055052a263f4d02730290a8573706 100644
--- a/packages/test_driver/HISTORY.rst
+++ b/packages/test_driver/HISTORY.rst
@@ -4,11 +4,70 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+
+============
+Enhancements
+============
+
+* Implement Declarative Testing for Workflow Behaviors by `@jmchilton <https://github.com/jmchilton>`_ in `#18542 <https://github.com/galaxyproject/galaxy/pull/18542>`_
+* Allow a posix file source to prefer linking. by `@jmchilton <https://github.com/jmchilton>`_ in `#19132 <https://github.com/galaxyproject/galaxy/pull/19132>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg
index c1de1fed8578c9fe3bbac11b58a8119805f51a5e..ab9d976f4427b47792aac75ae7039bf3e1dec68e 100644
--- a/packages/test_driver/setup.cfg
+++ b/packages/test_driver/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-test-driver
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg
index 03134c45bb19a773da0f73944389c5e0f0a5de76..def14cb2d5935e92ee1b00ee673761395c358ef0 100644
--- a/packages/test_selenium/setup.cfg
+++ b/packages/test_selenium/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-test-selenium
 url = https://github.com/galaxyproject/galaxy
-version = 23.2.dev0
+version = 24.2.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst
index efd9ed446874ed9c12a08884103636aa16754be2..c4072425659dab4b30287578fbd3be91b9e65de8 100644
--- a/packages/tool_shed/HISTORY.rst
+++ b/packages/tool_shed/HISTORY.rst
@@ -4,11 +4,65 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Skip slow tests for manage_db, db_dev scripts by `@jdavcs <https://github.com/jdavcs>`_ in `#19744 <https://github.com/galaxyproject/galaxy/pull/19744>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
+* Rip repository_registry out of tool shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18647 <https://github.com/galaxyproject/galaxy/pull/18647>`_
+* Assert that `data_column` parameters have a valid `data_ref` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18949 <https://github.com/galaxyproject/galaxy/pull/18949>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg
index bb38254a06b81d2e9e333d4684e673b80888279d..01999691c8aa51e6e8c38ef72a7de5615bc1fdeb 100644
--- a/packages/tool_shed/setup.cfg
+++ b/packages/tool_shed/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-tool-shed
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -36,7 +37,7 @@ install_requires =
     galaxy-auth
     galaxy-config
     galaxy-data
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     galaxy-web-apps
@@ -48,11 +49,11 @@ install_requires =
     graphql-core
     Mako
     MarkupSafe
-    mercurial
+    mercurial>=6.8.2
     Paste
     pydantic>=2.7.4
     Routes
-    SQLAlchemy>=2.0,<2.1
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
     starlette
     starlette-context
     starlette-graphene3
diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index 16fa70ea4b6616b950ed4e869176d409754b8020..72fb5638eacf301fb9e7214fcaf8d07b1bba0fda 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -4,11 +4,196 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix parameter model constructions with leading underscores, fixes converter linting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19790 <https://github.com/galaxyproject/galaxy/pull/19790>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* add missing linter name argument to linter report function calls by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19707 <https://github.com/galaxyproject/galaxy/pull/19707>`_
+* Assertion linter fixes by `@jmchilton <https://github.com/jmchilton>`_ in `#19715 <https://github.com/galaxyproject/galaxy/pull/19715>`_
+* Fix dataypes linter: allow auto for output tags by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19757 <https://github.com/galaxyproject/galaxy/pull/19757>`_
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix mulled tests by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19626 <https://github.com/galaxyproject/galaxy/pull/19626>`_
+* xsd: fix format by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19683 <https://github.com/galaxyproject/galaxy/pull/19683>`_
+* Fix validation of required floats specified as empty strings in tool XML. by `@jmchilton <https://github.com/jmchilton>`_ in `#19701 <https://github.com/galaxyproject/galaxy/pull/19701>`_
+* Fix container building by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19714 <https://github.com/galaxyproject/galaxy/pull/19714>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
+* Fix handling of v2 hashes by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18522 <https://github.com/galaxyproject/galaxy/pull/18522>`_
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Handle output parsing when tool is not available for tool-centric API. by `@jmchilton <https://github.com/jmchilton>`_ in `#18643 <https://github.com/galaxyproject/galaxy/pull/18643>`_
+* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
+* Fix commas that shouldn't be in biotools_mappings.tsv by `@jmchilton <https://github.com/jmchilton>`_ in `#18919 <https://github.com/galaxyproject/galaxy/pull/18919>`_
+* Allow modes `z` and `Z` for docker volumes by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18998 <https://github.com/galaxyproject/galaxy/pull/18998>`_
+* Add requirement/resource to schema docs by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19172 <https://github.com/galaxyproject/galaxy/pull/19172>`_
+* Fix mulled_hash by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19199 <https://github.com/galaxyproject/galaxy/pull/19199>`_
+* Outputs filter linter fixes by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19208 <https://github.com/galaxyproject/galaxy/pull/19208>`_
+* Replace mambaforge Docker image with miniforge3 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19327 <https://github.com/galaxyproject/galaxy/pull/19327>`_
+* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
+* Backport fix for ``test_singularity_container_test`` test by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19349 <https://github.com/galaxyproject/galaxy/pull/19349>`_
+* Remove unnecessary quoting in conda package specification by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19382 <https://github.com/galaxyproject/galaxy/pull/19382>`_
+* Fix timeout handling for planemo / galaxy-tool-util by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19384 <https://github.com/galaxyproject/galaxy/pull/19384>`_
+* Fix for empty string in regex validator message. by `@jmchilton <https://github.com/jmchilton>`_ in `#19387 <https://github.com/galaxyproject/galaxy/pull/19387>`_
+* `mulled-build-tool` fix for packages wo version by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19450 <https://github.com/galaxyproject/galaxy/pull/19450>`_
+* Fix parsing of validators with inf limits by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19459 <https://github.com/galaxyproject/galaxy/pull/19459>`_
+* Remove print statement by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19469 <https://github.com/galaxyproject/galaxy/pull/19469>`_
+* Downgrade 'InteractiveTools are not enabled' to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19518 <https://github.com/galaxyproject/galaxy/pull/19518>`_
+
+============
+Enhancements
+============
+
+* Add linters for datatypes by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17600 <https://github.com/galaxyproject/galaxy/pull/17600>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
+* Stray small changes from structured_tool_state branch. by `@jmchilton <https://github.com/jmchilton>`_ in `#18453 <https://github.com/galaxyproject/galaxy/pull/18453>`_
+* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
+* Mixed enhancements from CWL branch by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18539 <https://github.com/galaxyproject/galaxy/pull/18539>`_
+* Implement Declarative Testing for Workflow Behaviors by `@jmchilton <https://github.com/jmchilton>`_ in `#18542 <https://github.com/galaxyproject/galaxy/pull/18542>`_
+* Improvements to Tool Test Parsing by `@jmchilton <https://github.com/jmchilton>`_ in `#18560 <https://github.com/galaxyproject/galaxy/pull/18560>`_
+* More tool test typing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18590 <https://github.com/galaxyproject/galaxy/pull/18590>`_
+* Parameter Model Improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#18641 <https://github.com/galaxyproject/galaxy/pull/18641>`_
+* Another round of parameter model improvements. by `@jmchilton <https://github.com/jmchilton>`_ in `#18673 <https://github.com/galaxyproject/galaxy/pull/18673>`_
+* De-couple XML from tool interface for test collections. by `@jmchilton <https://github.com/jmchilton>`_ in `#18676 <https://github.com/galaxyproject/galaxy/pull/18676>`_
+* Another round of parameter model enhancements and tool tests by `@jmchilton <https://github.com/jmchilton>`_ in `#18678 <https://github.com/galaxyproject/galaxy/pull/18678>`_
+* Dynamic Models for Tool Test Validation by `@jmchilton <https://github.com/jmchilton>`_ in `#18679 <https://github.com/galaxyproject/galaxy/pull/18679>`_
+* Improvements to help terms & tool help. by `@jmchilton <https://github.com/jmchilton>`_ in `#18722 <https://github.com/galaxyproject/galaxy/pull/18722>`_
+* Implement tool upgrade assistant. by `@jmchilton <https://github.com/jmchilton>`_ in `#18728 <https://github.com/galaxyproject/galaxy/pull/18728>`_
+* Improvements to parameter models for test case inputs by `@jmchilton <https://github.com/jmchilton>`_ in `#18743 <https://github.com/galaxyproject/galaxy/pull/18743>`_
+* Remove `defaults` channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18757 <https://github.com/galaxyproject/galaxy/pull/18757>`_
+* Modelling for Test Assertions by `@jmchilton <https://github.com/jmchilton>`_ in `#18787 <https://github.com/galaxyproject/galaxy/pull/18787>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Add docs on indexing for filter column by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18844 <https://github.com/galaxyproject/galaxy/pull/18844>`_
+* Implement Pydantic model for workflow test format.  by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
+* Improvements to Planemo test format based on feedback/discussions. by `@jmchilton <https://github.com/jmchilton>`_ in `#18889 <https://github.com/galaxyproject/galaxy/pull/18889>`_
+* Add support for arbitrarily ordered image axes in image content assertions by `@kostrykin <https://github.com/kostrykin>`_ in `#18891 <https://github.com/galaxyproject/galaxy/pull/18891>`_
+* Remove some unused dynamic drill down options. by `@jmchilton <https://github.com/jmchilton>`_ in `#18892 <https://github.com/galaxyproject/galaxy/pull/18892>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
+* Assert that `data_column` parameters have a valid `data_ref` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18949 <https://github.com/galaxyproject/galaxy/pull/18949>`_
+* More concise, readable tool execution testing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Add hint to the tool schema about runtime conditional changes by `@martenson <https://github.com/martenson>`_ in `#18996 <https://github.com/galaxyproject/galaxy/pull/18996>`_
+* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
+* Better logging around tool loading by `@jmchilton <https://github.com/jmchilton>`_ in `#19029 <https://github.com/galaxyproject/galaxy/pull/19029>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19031 <https://github.com/galaxyproject/galaxy/pull/19031>`_
+* Integrate Tool Parameter Modeling into Linting (for Planemo) by `@jmchilton <https://github.com/jmchilton>`_ in `#19073 <https://github.com/galaxyproject/galaxy/pull/19073>`_
+* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
+* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
+* Enable specifying dataset hash in test jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19113 <https://github.com/galaxyproject/galaxy/pull/19113>`_
+* Add linter to check validity of output filters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19114 <https://github.com/galaxyproject/galaxy/pull/19114>`_
+* Also use miniforge docker for container building by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19128 <https://github.com/galaxyproject/galaxy/pull/19128>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18510 <https://github.com/galaxyproject/galaxy/pull/18510>`_
+* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18605 <https://github.com/galaxyproject/galaxy/pull/18605>`_
+* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
+* Don't check availability of shellescape by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18954 <https://github.com/galaxyproject/galaxy/pull/18954>`_
+* Backport 2 CI fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18973 <https://github.com/galaxyproject/galaxy/pull/18973>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix extra call to test_data_path that requires an admin key by `@jmchilton <https://github.com/jmchilton>`_ in `#19011 <https://github.com/galaxyproject/galaxy/pull/19011>`_
+* flip default value for use_mamba to false by `@bgruening <https://github.com/bgruening>`_ in `#19295 <https://github.com/galaxyproject/galaxy/pull/19295>`_
+* Linter: allow dynamic option definition by from_url by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19300 <https://github.com/galaxyproject/galaxy/pull/19300>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18510 <https://github.com/galaxyproject/galaxy/pull/18510>`_
+* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18605 <https://github.com/galaxyproject/galaxy/pull/18605>`_
+* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
+* Don't check availability of shellescape by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18954 <https://github.com/galaxyproject/galaxy/pull/18954>`_
+* Backport 2 CI fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18973 <https://github.com/galaxyproject/galaxy/pull/18973>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix extra call to test_data_path that requires an admin key by `@jmchilton <https://github.com/jmchilton>`_ in `#19011 <https://github.com/galaxyproject/galaxy/pull/19011>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18510 <https://github.com/galaxyproject/galaxy/pull/18510>`_
+* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18605 <https://github.com/galaxyproject/galaxy/pull/18605>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/tool_util/MANIFEST.in b/packages/tool_util/MANIFEST.in
index 3c6d371983de42dc1d9755fd842201ade0868c95..414da413053e7c5dc344d9fe8e4965c948962a64 100644
--- a/packages/tool_util/MANIFEST.in
+++ b/packages/tool_util/MANIFEST.in
@@ -5,3 +5,5 @@ include galaxy/tool_util/toolbox/filters/*.sample
 include galaxy/tool_util/verify/test_config.sample.yml
 include galaxy/tool_util/xsd/*
 include galaxy/tool_util/ontologies/*tsv
+include galaxy/tool_util/linters/datatypes_conf.xml.sample
+include galaxy/tool_util/upgrade/upgrade_codes.json
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index 194481687d6445b3b5140d03c96edc82c9e50fb5..bf638770a272834e719c2a1b8a2a04cd0c06076d 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -15,6 +15,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -28,12 +29,12 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-tool-util
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
 install_requires =
-    galaxy-util>=22.1
+    galaxy-util[image_util]>=22.1
     conda-package-streaming
     lxml!=4.2.2
     MarkupSafe
@@ -49,6 +50,9 @@ python_requires = >=3.7
 [options.entry_points]
 console_scripts =
         galaxy-tool-test = galaxy.tool_util.verify.script:main
+        galaxy-tool-test-case-validation = galaxy.tool_util.parameters.scripts.validate_test_cases:main
+        galaxy-tool-upgrade-advisor = galaxy.tool_util.upgrade.script:main
+        validate-test-format = galaxy.tool_util.validate_test_format:main
         mulled-build = galaxy.tool_util.deps.mulled.mulled_build:main
         mulled-build-channel = galaxy.tool_util.deps.mulled.mulled_build_channel:main
         mulled-build-files = galaxy.tool_util.deps.mulled.mulled_build_files:main
diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst
index ebc29d06751ac81a42295b971ee14ebdcdf45565..b2b3fdfb5b0c1b70874869aeb47f63c68ad05a23 100644
--- a/packages/tours/HISTORY.rst
+++ b/packages/tours/HISTORY.rst
@@ -4,11 +4,58 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg
index c236c2202b8b84488cd01af2b8bc4102bbaecdc1..88c735fd1f1075c8e5498c648127869fa1e57828 100644
--- a/packages/tours/setup.cfg
+++ b/packages/tours/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-tours
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst
index fed3f29e564affdf65269de9ebda98880724b14d..9d531bbb39baec337220482526fc7bca54b1c466 100644
--- a/packages/util/HISTORY.rst
+++ b/packages/util/HISTORY.rst
@@ -4,11 +4,119 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix numerous issues with tool input format "21.01" by `@jmchilton <https://github.com/jmchilton>`_ in `#19030 <https://github.com/galaxyproject/galaxy/pull/19030>`_
+* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
+* Fix config template validation for file sources and object store templates  by `@davelopez <https://github.com/davelopez>`_ in `#19414 <https://github.com/galaxyproject/galaxy/pull/19414>`_
+* Serialize message exceptions on execution error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19483 <https://github.com/galaxyproject/galaxy/pull/19483>`_
+
+============
+Enhancements
+============
+
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* Add Python 3.13 support by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18449 <https://github.com/galaxyproject/galaxy/pull/18449>`_
+* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
+* Rip repository_registry out of tool shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18647 <https://github.com/galaxyproject/galaxy/pull/18647>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
+* Raise exception if CompressedFile used on incompatible file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18888 <https://github.com/galaxyproject/galaxy/pull/18888>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+* Enhance UTF-8 support for filename handling in downloads by `@arash77 <https://github.com/arash77>`_ in `#19161 <https://github.com/galaxyproject/galaxy/pull/19161>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+
+============
+Enhancements
+============
+
+* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+
+============
+Enhancements
+============
+
+* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+
+============
+Enhancements
+============
+
+* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
index 08067a739317197db4dea1014a1ac0b4a85327cd..933b5b869404c28e487e238986ac5cf98fdef65c 100644
--- a/packages/util/setup.cfg
+++ b/packages/util/setup.cfg
@@ -15,6 +15,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -28,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-util
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -48,10 +49,13 @@ packages = find:
 python_requires = >=3.7
 
 [options.extras_require]
+image_util =
+    pillow
 jstree =
     dictobj
 template =
-    Cheetah3
+    CT3>=3.3.3
+    fissix;python_version>='3.13'
     future>=1.0.0
 config_template =
     Jinja2
diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
index a8daf79a97affa3fe2e6fa188af9ebb3f6e6e210..a6adf538cd1c988dbb2cbb86ac5c2ab200d81554 100644
--- a/packages/web_apps/HISTORY.rst
+++ b/packages/web_apps/HISTORY.rst
@@ -4,11 +4,247 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private role name performance issue by `@jdavcs <https://github.com/jdavcs>`_ in `#19679 <https://github.com/galaxyproject/galaxy/pull/19679>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix user preferences secret (without vault) lost on save by `@davelopez <https://github.com/davelopez>`_ in `#19610 <https://github.com/galaxyproject/galaxy/pull/19610>`_
+* Disable chatgxy wizard for anon users by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19628 <https://github.com/galaxyproject/galaxy/pull/19628>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
+* Fix MessageException handling in get_edit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18529 <https://github.com/galaxyproject/galaxy/pull/18529>`_
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
+* Fix response if dataset requested by display application is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18803 <https://github.com/galaxyproject/galaxy/pull/18803>`_
+* Ignore preflight options in API schema by `@jmchilton <https://github.com/jmchilton>`_ in `#18983 <https://github.com/galaxyproject/galaxy/pull/18983>`_
+* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
+* Fix auto-detect metadata from Edit Dataset Attributes panel by `@davelopez <https://github.com/davelopez>`_ in `#19025 <https://github.com/galaxyproject/galaxy/pull/19025>`_
+* Prevent purged users from logging in by `@jdavcs <https://github.com/jdavcs>`_ in `#19094 <https://github.com/galaxyproject/galaxy/pull/19094>`_
+* Restore access to saved visualizations by `@guerler <https://github.com/guerler>`_ in `#19136 <https://github.com/galaxyproject/galaxy/pull/19136>`_
+* Fix PSA Redirect by `@dannon <https://github.com/dannon>`_ in `#19247 <https://github.com/galaxyproject/galaxy/pull/19247>`_
+* Login redirect followup by `@dannon <https://github.com/dannon>`_ in `#19251 <https://github.com/galaxyproject/galaxy/pull/19251>`_
+* Fix invocation metrics usability by providing job context. by `@jmchilton <https://github.com/jmchilton>`_ in `#19279 <https://github.com/galaxyproject/galaxy/pull/19279>`_
+* Fix importing shared workflows with deeply nested subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19335 <https://github.com/galaxyproject/galaxy/pull/19335>`_
+* Show Keycloak provider label in UI by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19447 <https://github.com/galaxyproject/galaxy/pull/19447>`_
+* Serialize message exceptions on execution error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19483 <https://github.com/galaxyproject/galaxy/pull/19483>`_
+* Use visualizations api in trackster by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19495 <https://github.com/galaxyproject/galaxy/pull/19495>`_
+* Set a hard limit of 100 invocations per request in api/invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19497 <https://github.com/galaxyproject/galaxy/pull/19497>`_
+* Fix deleting lddas in batch by `@davelopez <https://github.com/davelopez>`_ in `#19506 <https://github.com/galaxyproject/galaxy/pull/19506>`_
+* Fix WSGI response status handling in controller methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19520 <https://github.com/galaxyproject/galaxy/pull/19520>`_
+* Fix saved visualization (non-trackster ones) not displaying by `@davelopez <https://github.com/davelopez>`_ in `#19561 <https://github.com/galaxyproject/galaxy/pull/19561>`_
+* Allow unused query params in ``workflows/export_to_file`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19574 <https://github.com/galaxyproject/galaxy/pull/19574>`_
+
+============
+Enhancements
+============
+
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Feature - stdout live reporting by `@gecage952 <https://github.com/gecage952>`_ in `#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`_
+* Add errors fast api by `@arash77 <https://github.com/arash77>`_ in `#18093 <https://github.com/galaxyproject/galaxy/pull/18093>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
+* Replace History Dataset Picker in Library Folder by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18518 <https://github.com/galaxyproject/galaxy/pull/18518>`_
+* Update openapi-typescript dependency to version 6.7.6 by `@davelopez <https://github.com/davelopez>`_ in `#18519 <https://github.com/galaxyproject/galaxy/pull/18519>`_
+* Improve datasets permissions API schema typing by `@davelopez <https://github.com/davelopez>`_ in `#18563 <https://github.com/galaxyproject/galaxy/pull/18563>`_
+* Drop unused datasets controller methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18568 <https://github.com/galaxyproject/galaxy/pull/18568>`_
+* Improve typing for archived histories API schema by `@davelopez <https://github.com/davelopez>`_ in `#18586 <https://github.com/galaxyproject/galaxy/pull/18586>`_
+* More tool test typing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18590 <https://github.com/galaxyproject/galaxy/pull/18590>`_
+* Improve update user API payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18602 <https://github.com/galaxyproject/galaxy/pull/18602>`_
+* Improve update history payload schema by `@davelopez <https://github.com/davelopez>`_ in `#18618 <https://github.com/galaxyproject/galaxy/pull/18618>`_
+* Parameter Model Improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#18641 <https://github.com/galaxyproject/galaxy/pull/18641>`_
+* Improve accept header API schema by `@davelopez <https://github.com/davelopez>`_ in `#18668 <https://github.com/galaxyproject/galaxy/pull/18668>`_
+* Allow access to invocation via shared or published history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18707 <https://github.com/galaxyproject/galaxy/pull/18707>`_
+* Migrate Visualizations API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18721 <https://github.com/galaxyproject/galaxy/pull/18721>`_
+* Improvements to help terms & tool help. by `@jmchilton <https://github.com/jmchilton>`_ in `#18722 <https://github.com/galaxyproject/galaxy/pull/18722>`_
+* More typing, docs, and decomposition around tool execution by `@jmchilton <https://github.com/jmchilton>`_ in `#18758 <https://github.com/galaxyproject/galaxy/pull/18758>`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Update Visualization FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18792 <https://github.com/galaxyproject/galaxy/pull/18792>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
+* Enable extra user preferences for remotely authorized users by `@maartenschermer <https://github.com/maartenschermer>`_ in `#18887 <https://github.com/galaxyproject/galaxy/pull/18887>`_
+* Enable ``ignore-without-code`` mypy error code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18898 <https://github.com/galaxyproject/galaxy/pull/18898>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Allow CORS requests to /api/workflow_landings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18963 <https://github.com/galaxyproject/galaxy/pull/18963>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* Optimize to_history_dataset_association in create_datasets_from_library_folder by `@arash77 <https://github.com/arash77>`_ in `#18970 <https://github.com/galaxyproject/galaxy/pull/18970>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19031 <https://github.com/galaxyproject/galaxy/pull/19031>`_
+* Silence the quota manager for updates by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19046 <https://github.com/galaxyproject/galaxy/pull/19046>`_
+* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
+* Better cleanup of sharing roles on user purge by `@jdavcs <https://github.com/jdavcs>`_ in `#19096 <https://github.com/galaxyproject/galaxy/pull/19096>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Backport of Workflow Editor Activity Bar by `@dannon <https://github.com/dannon>`_ in `#19212 <https://github.com/galaxyproject/galaxy/pull/19212>`_
+* Workflow Inputs Activity by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#19252 <https://github.com/galaxyproject/galaxy/pull/19252>`_
+
+=============
+Other changes
+=============
+
+* Format dev to fix linting. by `@jmchilton <https://github.com/jmchilton>`_ in `#18860 <https://github.com/galaxyproject/galaxy/pull/18860>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Check if dataset has any data before running provider checks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18526 <https://github.com/galaxyproject/galaxy/pull/18526>`_
+* Raise appropriate exception if ldda not found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18569 <https://github.com/galaxyproject/galaxy/pull/18569>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+* Fix resume_paused_jobs if no session provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18640 <https://github.com/galaxyproject/galaxy/pull/18640>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Return error when following a link to a non-ready display application by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18672 <https://github.com/galaxyproject/galaxy/pull/18672>`_
+* Only load authnz routes when oidc enabled by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18683 <https://github.com/galaxyproject/galaxy/pull/18683>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix sorting users in admin by last login by `@jdavcs <https://github.com/jdavcs>`_ in `#18694 <https://github.com/galaxyproject/galaxy/pull/18694>`_
+* Fix resume paused jobs response handling by `@dannon <https://github.com/dannon>`_ in `#18733 <https://github.com/galaxyproject/galaxy/pull/18733>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Don't use ``async def`` where not appropriate by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18944 <https://github.com/galaxyproject/galaxy/pull/18944>`_
+* Fix very slow workflow editor loading by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19068 <https://github.com/galaxyproject/galaxy/pull/19068>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
+=============
+Other changes
+=============
+
+* Fix check dataset check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18856 <https://github.com/galaxyproject/galaxy/pull/18856>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Check if dataset has any data before running provider checks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18526 <https://github.com/galaxyproject/galaxy/pull/18526>`_
+* Raise appropriate exception if ldda not found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18569 <https://github.com/galaxyproject/galaxy/pull/18569>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+* Fix resume_paused_jobs if no session provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18640 <https://github.com/galaxyproject/galaxy/pull/18640>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Return error when following a link to a non-ready display application by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18672 <https://github.com/galaxyproject/galaxy/pull/18672>`_
+* Only load authnz routes when oidc enabled by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18683 <https://github.com/galaxyproject/galaxy/pull/18683>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix sorting users in admin by last login by `@jdavcs <https://github.com/jdavcs>`_ in `#18694 <https://github.com/galaxyproject/galaxy/pull/18694>`_
+* Fix resume paused jobs response handling by `@dannon <https://github.com/dannon>`_ in `#18733 <https://github.com/galaxyproject/galaxy/pull/18733>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Don't use ``async def`` where not appropriate by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18944 <https://github.com/galaxyproject/galaxy/pull/18944>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
+=============
+Other changes
+=============
+
+* Fix check dataset check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18856 <https://github.com/galaxyproject/galaxy/pull/18856>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
+* Check if dataset has any data before running provider checks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18526 <https://github.com/galaxyproject/galaxy/pull/18526>`_
+* Raise appropriate exception if ldda not found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18569 <https://github.com/galaxyproject/galaxy/pull/18569>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+* Fix resume_paused_jobs if no session provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18640 <https://github.com/galaxyproject/galaxy/pull/18640>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Return error when following a link to a non-ready display application by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18672 <https://github.com/galaxyproject/galaxy/pull/18672>`_
+* Only load authnz routes when oidc enabled by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18683 <https://github.com/galaxyproject/galaxy/pull/18683>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix sorting users in admin by last login by `@jdavcs <https://github.com/jdavcs>`_ in `#18694 <https://github.com/galaxyproject/galaxy/pull/18694>`_
+* Fix resume paused jobs response handling by `@dannon <https://github.com/dannon>`_ in `#18733 <https://github.com/galaxyproject/galaxy/pull/18733>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+
+=============
+Other changes
+=============
+
+* Fix check dataset check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18856 <https://github.com/galaxyproject/galaxy/pull/18856>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index dfbb85e86dc06168ac1322a6a51aeafacd06a9c6..d8e8c8ea3edf6cbe57dbbe61c130519a9881df29 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-web-apps
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -42,7 +43,7 @@ install_requires =
     a2wsgi
     apispec
     Babel
-    Cheetah3
+    CT3>=3.3.3
     fastapi>=0.101.0
     gunicorn
     gxformat2
@@ -57,18 +58,21 @@ install_requires =
     PyYAML
     requests
     Routes
-    SQLAlchemy>=2.0,<2.1
-    sqlalchemy-migrate
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
     starlette
     starlette-context
     tuswsgi
     typing-extensions
     uvicorn
-    uvloop
-    WebOb
+    uvloop>=0.21.0
+    WebOb>=1.8.9
 packages = find:
 python_requires = >=3.8
 
+[options.entry_points]
+console_scripts =
+        galaxy-web = galaxy.webapps.galaxy.script:main
+
 [options.packages.find]
 exclude =
     tests*
diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
index f09158a5f388ff2cc6f098aa7b89a587d3e885b3..9e2782e0c1eb5312df0ff27c67730316ab6aa02e 100644
--- a/packages/web_framework/HISTORY.rst
+++ b/packages/web_framework/HISTORY.rst
@@ -4,11 +4,87 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix WSGI response status handling in controller methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19520 <https://github.com/galaxyproject/galaxy/pull/19520>`_
+
+============
+Enhancements
+============
+
+* Parse stored config details to script-based visualizations by `@guerler <https://github.com/guerler>`_ in `#18651 <https://github.com/galaxyproject/galaxy/pull/18651>`_
+* Enable extra user preferences for remotely authorized users by `@maartenschermer <https://github.com/maartenschermer>`_ in `#18887 <https://github.com/galaxyproject/galaxy/pull/18887>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Apply statsd arg sanitization to all pages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18509 <https://github.com/galaxyproject/galaxy/pull/18509>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Apply statsd arg sanitization to all pages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18509 <https://github.com/galaxyproject/galaxy/pull/18509>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Apply statsd arg sanitization to all pages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18509 <https://github.com/galaxyproject/galaxy/pull/18509>`_
+* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg
index 083f8622406dba92418a4511c6ea89ada9b08134..47f5cad1d5be9ac49aaa166429aeb5534137b3c5 100644
--- a/packages/web_framework/setup.cfg
+++ b/packages/web_framework/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-web-framework
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
@@ -40,7 +41,7 @@ install_requires =
     pydantic>=2.7.4
     requests
     Routes
-    SQLAlchemy>=2.0,<2.1
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
     WebOb
 
 packages = find:
diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst
index 91460bc9610d379a50d553fc5ef64999408cadbc..2d0672c24c45efd72a310de4509301ea119492a9 100644
--- a/packages/web_stack/HISTORY.rst
+++ b/packages/web_stack/HISTORY.rst
@@ -4,11 +4,58 @@ History
 .. to_doc
 
 -----------
-24.1.2.dev0
+24.2.4.dev0
 -----------
 
 
 
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+============
+Enhancements
+============
+
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 24.1.1 (2024-07-02)
 -------------------
diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg
index 2974323c3b3ffcb2f8007e9f4fee0ccc27e13b62..5f470d458dd71d70afbb8b062179b3ffea13773d 100644
--- a/packages/web_stack/setup.cfg
+++ b/packages/web_stack/setup.cfg
@@ -14,6 +14,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Software Development
     Topic :: Software Development :: Code Generators
     Topic :: Software Development :: Testing
@@ -27,14 +28,14 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-web-stack
 url = https://github.com/galaxyproject/galaxy
-version = 24.1.2.dev0
+version = 24.2.4.dev0
 
 [options]
 include_package_data = True
 install_requires =
     galaxy-data
     galaxy-util
-    SQLAlchemy>=2.0,<2.1
+    SQLAlchemy>=2.0,<2.1,!=2.0.36
 packages = find:
 python_requires = >=3.8
 
diff --git a/pyproject.toml b/pyproject.toml
index af688c2412cd9868e629ac8d40d93815c275d21f..be857e903b7fbbf0faf8a4c17c1f8bdc2f3030c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,185 @@
+[project]
+name = "galaxy"
+version = "0.1.0"  # Not the real version, which is instead defined in lib/galaxy/version.py
+description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
+authors = [
+    {name = "Galaxy Contributors"},
+]
+maintainers = [
+    {name = "Galaxy Committers", email = "galaxy-committers@lists.galaxyproject.org"}
+]
+license = {file = "LICENSE.txt"}
+readme = "README.rst"
+requires-python = ">=3.8"
+dependencies = [
+    "a2wsgi",
+    "aiofiles",
+    "alembic",
+    "apispec",
+    "Babel",
+    "bdbag>=1.6.3",
+    "Beaker",
+    "bioblend",
+    "bleach",
+    "boltons",
+    "boto",
+    "bx-python",
+    "celery",
+    "cloudauthz==0.6.0",
+    "cloudbridge",
+    "circus",
+    "conda-package-streaming",
+    "CT3>=3.3.3",  # Python 3.13 support
+    "cwltool>=3.1.20230624081518",  # save time, minimum needed by cwl-1.0 branch
+    "dictobj",
+    "dnspython",
+    "docutils!=0.17,!=0.17.1",
+    "dparse",
+    "edam-ontology",
+    "fastapi-slim>=0.111.0",
+    "fissix ; python_version>='3.13'",
+    "fs",
+    "future>=1.0.0",  # Python 3.12 support
+    "graphene",
+    "graphene-sqlalchemy>=3.0.0rc1",  # need a beta release to be compat. with starlette plugin
+    "graphql-core",
+    "gravity>=1.0.4",
+    "gunicorn",
+    "gxformat2",
+    "h5grove>=1.2.1",
+    "h5py",  # Python 3.8 support
+    "h5py>=3.12 ; python_version>='3.9'",  # Python 3.13 support
+    "importlib-resources ; python_version<'3.9'",  # for importlib.{abc.Traversable,resources.{files, Package}}
+    "isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master",  # https://github.com/ISA-tools/isa-rwval/pull/17
+    "isal>=1.7.0",  # Python 3.13 support
+    "jinja2",
+    "kombu>=5.3",  # for importlib-metadata fix
+    "lagom",
+    "Mako",
+    "Markdown",
+    "MarkupSafe",
+    "mercurial>=6.8.2",  # Python 3.13 support
+    "mrcfile",
+    "msal",
+    "nodeenv",
+    "numpy",
+    "numpy>=1.26.0 ; python_version=='3.9'",  # Python 3.12 support
+    "numpy>=2.1.0 ; python_version>='3.10'",  # Python 3.13 support
+    "packaging",
+    "paramiko!=2.9.0,!=2.9.1",  # https://github.com/paramiko/paramiko/issues/1961
+    "Parsley",
+    "Paste",
+    "pebble",
+    "pillow",
+    "psutil",
+    "pulsar-galaxy-lib>=0.15.0.dev0",
+    "pycryptodome",
+    "pydantic[email]>=2.7.4",  # https://github.com/pydantic/pydantic/pull/9639
+    "PyJWT",
+    "pykwalify",
+    "pylibmagic",
+    "pyparsing",
+    "pysam>=0.21",  # for Python 3.11 support on macOS
+    "python-dateutil",
+    "python-magic",
+    "python-multipart",  # required to support form parsing in FastAPI/Starlette
+    "python-slugify",
+    "PyYAML",
+    "refgenconf>=0.12.0",
+    "regex",
+    "requests",
+    "rocrate",
+    "Routes",
+    "s3fs>=2023.1.0",
+    "schema-salad>=8.7.20240905150001",  # Python 3.13 support
+    "social-auth-core>=4.5.0",  # to drop dependency on abandoned python-jose
+    "sortedcontainers",
+    "SQLAlchemy>=2.0,<2.1,!=2.0.36",  # https://github.com/sqlalchemy/sqlalchemy/issues/12019,
+    "sqlitedict",
+    "sqlparse",
+    "starlette",
+    "starlette-context",
+    "starlette-graphene3",
+    "svgwrite",
+    "tifffile",
+    "tuswsgi",
+    "typing-extensions",
+    "uvicorn!=0.28.0",  # https://github.com/galaxyproject/galaxy/issues/17669
+    "uvloop>=0.21.0",  # Python 3.13 support
+    "WebOb>=1.8.9",  # Python 3.13 support
+    "Whoosh",
+    "zipstream-new",
+]
+
+[project.urls]
+Homepage = "https://galaxyproject.org/"
+Documentation = "https://docs.galaxyproject.org/"
+Repository = "https://github.com/galaxyproject/galaxy"
+"Bug Tracker" = "https://github.com/galaxyproject/galaxy/issues"
+
+[dependency-groups]
+dev = [
+    "ase>=3.18.1",
+    "axe-selenium-python",
+    "black",
+    "boto3",
+    "codespell",
+    "cwltest>=2.5.20240906231108",  # Python 3.13 support
+    "darker",
+    "fluent-logger",
+    "galaxy-release-util",
+    "httpx",
+    "isort",
+    "lxml!=4.2.2",
+    "markdown-it-reporter",
+    "myst-parser",
+    "onedatafilerestclient==21.2.5.2",
+    "pkce",
+    "playwright>=1.48.0",  # Python 3.13 support
+    "pytest<8",  # https://github.com/galaxyproject/galaxy/issues/17561
+    "pytest-asyncio",
+    "pytest-cov",
+    "pytest-html",
+    "pytest-httpserver",
+    "python-irodsclient!=1.1.2",  # https://github.com/irods/python-irodsclient/issues/356
+    "pytest-json-report",
+    "pytest-mock",
+    "pytest-playwright",
+    "pytest-postgresql!=3.0.0",  # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426
+    "pytest-shard",
+    "responses",
+    "rucio-clients>=33.6.0 ; python_version>='3.9'",  # https://github.com/galaxyproject/galaxy/pull/17156
+    "selenium",
+    "seletools",
+    "Sphinx>=4.0",  # support docutils 0.17
+    "sphinx-rtd-theme",
+    "statsd",
+    "testfixtures",
+    "tuspy",
+    "twill>=3.2.5",  # Python 3.13 support
+    "watchdog",
+    "Werkzeug",
+]
+typecheck = [
+    "boto3-stubs[s3]",
+    "lxml-stubs",
+    "mypy",
+    "pydantic>=2.7.4",  # for pydantic.mypy plugin
+    "types-bleach",
+    "types-boto",
+    "types-contextvars",
+    "types-dataclasses",
+    "types-docutils",
+    "types-Markdown",
+    "types-paramiko",
+    "types-python-dateutil",
+    "types-python-slugify",
+    "types-PyYAML",
+    "types-requests",
+    "types-setuptools",
+    "types-six",
+]
+
 [tool.black]
 line-length = 120
 target-version = ['py38']
@@ -12,195 +194,17 @@ extend-exclude = '''
 [tool.darker]
 isort = true
 
-[tool.poetry]
-package-mode = false
-name = "galaxy"
-description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
-authors = ["Galaxy Contributors"]
-license = "AFL-3.0"
-readme = "README.rst"
-homepage = "https://galaxyproject.org/"
-repository = "https://github.com/galaxyproject/galaxy/"
-documentation = "https://docs.galaxyproject.org/"
-
-[[tool.poetry.source]]
-name = "galaxyproject"
-url = "https://wheels.galaxyproject.org/simple"
-priority = "primary"
-
-[[tool.poetry.source]]
-name = "PyPI"
-priority = "primary"
-
-[tool.poetry.dependencies]
-a2wsgi = "*"
-aiofiles = "*"
-alembic = "*"
-apispec = "*"
-Babel = "*"
-bdbag = ">=1.6.3"
-Beaker = "*"
-bioblend = "*"
-bleach = "*"
-boltons = "*"
-boto = "*"
-bx-python = "*"
-celery = "*"
-Cheetah3 = "*"
-cloudauthz = "==0.6.0"
-cloudbridge = "*"
-circus = "*"
-cwltool = ">=3.1.20230624081518"  # save time, minimum needed by cwl-1.0 branch
-conda-package-streaming = "*"
-dictobj = "*"
-dnspython = "*"
-docutils = "!=0.17, !=0.17.1"
-dparse = "*"
-edam-ontology = "*"
-fastapi-slim = ">=0.111.0"
-fs = "*"
-future = ">=1.0.0"  # Python 3.12 support
-galaxy_sequence_utils = "*"
-graphene = "*"
-graphene-sqlalchemy = ">=3.0.0rc1"  # need a beta release to be compat. with starlette plugin
-graphql-core = "*"
-gravity = ">=1.0.4"
-gunicorn = "*"
-gxformat2 = "*"
-h5grove = ">=1.2.1"
-h5py = "*"
-importlib-resources = { version = "*", python = "<3.9" }  # for importlib.{abc.Traversable,resources.{files, Package}}
-isa-rwval = ">=0.10.10"
-jinja2 = "*"
-kombu = ">=5.3"  # for importlib-metadata fix
-isal = "*"
-lagom = "*"
-Mako = "*"
-Markdown = "*"
-MarkupSafe = "*"
-Mercurial = "*"
-mrcfile = "*"
-msal = "*"
-nodeenv = "*"
-numpy = "*"
-packaging = "*"
-paramiko = ">=2.12.0"
-Parsley = "*"
-Paste = "*"
-pebble = "*"
-pillow = "*"
-psutil = "*"
-pulsar-galaxy-lib = ">=0.15.0.dev0"
-pycryptodome = "*"
-pydantic = {version = ">=2.7.4", extras = ["email"]}  # https://github.com/pydantic/pydantic/pull/9639
-PyJWT = "*"
-pykwalify = "*"
-pylibmagic = "*"
-pyparsing = "*"
-pysam = ">=0.21"  # for Python 3.11 support on macOS
-python = ">=3.8,<3.13"  # Keep maximum version strict to appease numpy and scipy
-python-dateutil = "*"
-python-magic = "*"
-python-multipart = "*"  # required to support form parsing in FastAPI/Starlette
-PyYAML = "*"
-refgenconf = ">=0.12.0"
-regex = "*"
-requests = "*"
-rocrate = "*"
-Routes = "*"
-schema-salad = "!=8.3.20220721194857"  # https://github.com/common-workflow-language/schema_salad/issues/575
-social-auth-core = ">=4.5.0"  # to drop dependency on abandoned python-jose
-sortedcontainers = "*"
-SQLAlchemy = "^2.0"
-sqlitedict = "*"
-sqlparse = "*"
-fs-sshfs = "*"
-starlette = "*"
-starlette-context = "*"
-starlette-graphene3 = "*"
-svgwrite = "*"
-tifffile = "*"
-tuswsgi = "*"
-typing-extensions = "*"
-uvicorn = "!=0.28.0"  # https://github.com/galaxyproject/galaxy/issues/17669
-uvloop = "*"
-WebOb = "*"
-Whoosh = "*"
-zipstream-new = "*"
-s3fs = "*"
-
-[tool.poetry.group.dev.dependencies]
-ase = ">=3.18.1"
-axe-selenium-python = "*"
-black = "*"
-boto3 = "*"
-codespell = "*"
-cwltest = "*"
-darker = "*"
-fluent-logger = "*"
-galaxy-release-util = "*"
-httpx = "*"
-isort = "*"
-lxml = "!=4.2.2"
-markdown-it-reporter = "*"
-myst-parser = "*"
-onedatafilerestclient = "==21.2.5.1"
-pkce = "*"
-playwright = "*"
-pytest = "*"
-pytest-asyncio = "*"
-pytest-cov = "*"
-pytest-html = "*"
-pytest-httpserver = "*"
-python-irodsclient = "!=1.1.2"  # https://github.com/irods/python-irodsclient/issues/356
-pytest-json-report = "*"
-pytest-mock = "*"
-pytest-playwright = "*"
-pytest-postgresql = "!=3.0.0"  # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426
-pytest-shard = "*"
-responses = "*"
-rucio-clients = {version = ">=33.6.0", python = ">=3.9"}  # https://github.com/galaxyproject/galaxy/pull/17156
-selenium = "*"
-urllib3 = "<2"  # Necessary for poetry for resolve deps for Python 3.8+
-seletools = "*"
-Sphinx = ">=4.0"  # support docutils 0.17
-sphinx-rtd-theme = "*"
-statsd = "*"
-testfixtures = "*"
-tuspy = "*"
-twill = ">=3.2.1"  # https://github.com/twill-tools/twill/issues/18
-watchdog = "*"
-Werkzeug = "*"
-
-[tool.poetry.group.typecheck.dependencies]
-mypy = "*"
-boto3-stubs = {version = "*", extras = ["s3"]}
-lxml-stubs = "*"
-pydantic = ">=2.7.4"  # for pydantic.mypy plugin
-types-bleach = "*"
-types-boto = "*"
-types-contextvars = "*"
-types-dataclasses = "*"
-types-docutils = "*"
-types-Markdown = "*"
-types-paramiko = "*"
-types-pkg-resources = "*"
-types-python-dateutil = "*"
-types-PyYAML = "*"
-types-requests = "*"
-types-six = "*"
-
 [tool.ruff]
 target-version = "py38"
 exclude = [
-  "lib/tool_shed/test/test_data/repos"
+    "lib/tool_shed/test/test_data/repos"
 ]
 
 [tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
 # flake8-comprehensions (C4), flake8-logging-format (G),
 # flake8-implicit-str-concat (ISC) and pyupgrade (UP)
-select = ["E", "F", "B", "C4", "G", "ISC", "UP"]
+select = ["E", "F", "B", "C4", "G", "ISC", "NPY", "UP"]
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings
@@ -218,6 +222,10 @@ allow-dict-calls-with-keyword-arguments = true
 combine-as-imports = true
 relative-imports-order = "closest-to-furthest"
 
+[tool.ruff.lint.pyupgrade]
+# Preserve types, even if a file imports `from __future__ import annotations`.
+keep-runtime-typing = true
+
 [tool.ruff.lint.per-file-ignores]
 # Don't check pyupgrade rules on tool scripts, which may use different Python versions
 "test/functional/tools/*" = ["UP"]
@@ -227,3 +235,12 @@ relative-imports-order = "closest-to-furthest"
 "lib/galaxy/schema/drs/*" = ["UP006", "UP007"]
 "lib/tool_shed_client/schema/trs.py" = ["UP006", "UP007"]
 "lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]
+
+[tool.uv]
+constraint-dependencies = [
+    "scipy>=1.14.1; python_version>='3.10'",  # Python 3.13 support
+]
+default-groups = []
+extra-index-url = ["https://wheels.galaxyproject.org/simple"]
+index-strategy = "unsafe-best-match"
+package = false
diff --git a/pytest.ini b/pytest.ini
index 7c1d4030631048f342af36ce196b33f38d253285..706dc325bb0342db034eed2ea208f7d6d05291f3 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,5 +1,5 @@
 [pytest]
-addopts = --doctest-continue-on-failure --verbosity=1
+addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
 # Install pytest-memray and set memray to true here to enable memory profiling of tests
@@ -10,6 +10,7 @@ markers =
   external_dependency_management: slow tests which resolves dependencies with e.g. conda
   require_new_history: test that needs to be given a new history
   tool: marks test as a tool test
+  requires_tool_id: marks API test as requiring specified tool id
   gtn_screenshot: marks test as a screenshot producer for galaxy training network
   local: mark indicates, that it is sufficient to run test locally to get relevant artifacts (e.g. screenshots)
   external: mark indicates, that test has to be run against external production server to get relevant artifacts (e.g. screenshots)
diff --git a/run_tests.sh b/run_tests.sh
index 21c7aa54f4e5b4363065e08d83ba4106ccbc47bd..6a2adab2dad40dffef9d1f9fa695c134599bd625 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -14,6 +14,8 @@ cat <<EOF
 '${0##*/} -main'                    for running tests of tools shipped with Galaxy
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
 '${0##*/} -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'
+'${0##*/} -framework-workflows'      for running through workflow tests to test correctness of workflow evaluation
+'${0##*/} -framework-workflows -id workflow_name' test single workflow framework test
 '${0##*/} -data_managers -id data_manager_id'    for testing one Data Manager with id 'data_manager_id'
 '${0##*/} -unit'                    for running all unit tests (doctests and tests in test/unit)
 '${0##*/} -unit (test_selector)'    for running unit tests on specified test path (using pytest selector syntax)
@@ -400,13 +402,19 @@ do
           export GALAXY_TEST_USER_API_KEY=$2
           shift 2
           ;;
-      -f|-framework|--framework)
+      -f|-framework|--framework|--framework-tools)
           GALAXY_TEST_TOOL_CONF="test/functional/tools/sample_tool_conf.xml"
           marker="tool"
           report_file="run_framework_tests.html"
           framework_test=1
           shift 1
           ;;
+      -w|--framework-workflows)
+          marker="workflow"
+          report_file="run_framework_workflows_tests.html"
+          framework_workflows_test=1
+          shift 1
+          ;;
       -d|-data_managers|--data_managers)
           marker="data_manager"
           report_file="run_data_managers_tests.html"
@@ -484,14 +492,15 @@ do
       -u|-unit|--unit)
           report_file="run_unit_tests.html"
           unit_extra='--doctest-modules
-			--ignore lib/galaxy/jobs/runners/chronos.py
-			--ignore lib/galaxy/model/migrations/alembic
-			--ignore lib/galaxy/tools/bundled
-			--ignore lib/galaxy/web/proxy/js/node_modules/
-			--ignore lib/galaxy_test
-			--ignore lib/tool_shed/test
-			--ignore lib/tool_shed/webapp/controllers
-			--ignore=lib/tool_shed/webapp/model/migrations/alembic/'
+            --ignore lib/galaxy/datatypes/converters/
+            --ignore lib/galaxy/jobs/runners/chronos.py
+            --ignore lib/galaxy/model/migrations/alembic
+            --ignore lib/galaxy/tools/bundled
+            --ignore lib/galaxy/web/proxy/js/node_modules/
+            --ignore lib/galaxy_test
+            --ignore lib/tool_shed/test
+            --ignore lib/tool_shed/webapp/controllers
+            --ignore=lib/tool_shed/webapp/model/migrations/alembic/'
           generate_cwl_conformance_tests=1
           if [ $# -gt 1 ]; then
               unit_extra="$unit_extra $2"
@@ -586,6 +595,13 @@ if [ -n "$framework_test" ] || [ -n "$data_managers_test" ] ; then
         selector=""
     fi
     extra_args="test/functional/test_toolbox_pytest.py $selector"
+elif [ -n "$framework_workflows_test" ]; then
+    if [ -n "$test_id" ]; then
+        selector="-k $test_id"
+    else
+        selector=""
+    fi
+    extra_args="lib/galaxy_test/workflow/test_framework_workflows.py $selector"
 elif [ -n "$selenium_script" ]; then
     extra_args="$selenium_script"
 elif [ -n "$toolshed_script" ]; then
diff --git a/scripts/bootstrap_test_shed.py b/scripts/bootstrap_test_shed.py
index aa657476bace876913f999c1a3534d2e4c7231ee..ba1268bf96bdb5219a17e1237c8dbc18b58a1f83 100644
--- a/scripts/bootstrap_test_shed.py
+++ b/scripts/bootstrap_test_shed.py
@@ -17,12 +17,10 @@ from typing import (
     Optional,
 )
 
-from galaxy.util import requests
-
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
-
 from galaxy.tool_shed.util.hg_util import clone_repository
+from galaxy.util import requests
 from tool_shed.test.base.api import ensure_user_with_email
 from tool_shed.test.base.api_util import (
     create_user,
diff --git a/scripts/check_and_update_purged_on_duplicated_uuid.py b/scripts/check_and_update_purged_on_duplicated_uuid.py
new file mode 100644
index 0000000000000000000000000000000000000000..5fbc6bc163b382e56c4df5a8681e7577e0aa4a88
--- /dev/null
+++ b/scripts/check_and_update_purged_on_duplicated_uuid.py
@@ -0,0 +1,64 @@
+"""
+This script will inspect non-purged datasets that have been re-assigned to HDAs following the duplicate uuid bug.
+If the file does not exist on disk anymore we mark the dataset and corresponding HDAs as deleted and purged.
+Activate Galaxy's virtualenv and run this script from galaxy's root directory with
+`GALAXY_CONFIG_FILE=path/to/galaxy.yml python scripts/check_and_update_purged_on_duplicated_uuid.py`
+
+This script assumes that the hda_dataset_mapping_pre_uuid_condense table created by migration 04288b6a5b25.
+"""
+
+import logging
+import os
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
+
+WARNING_MODULES = ["parso", "asyncio", "galaxy.datatypes"]
+for mod in WARNING_MODULES:
+    logger = logging.getLogger(mod)
+    logger.setLevel("WARNING")
+
+log = logging.getLogger(__name__)
+
+from sqlalchemy import text
+
+from galaxy.celery import build_app
+from galaxy.model import Dataset
+from galaxy.model.orm.scripts import get_config
+from galaxy.objectstore import ObjectStore
+
+if __name__ == "__main__":
+
+    from galaxy.celery import tasks  # noqa: F401
+
+    config = get_config(sys.argv)
+    os.environ["GALAXY_CONFIG_FILE"] = os.environ.get("GALAXY_CONFIG_FILE", config["config_file"])
+    app = build_app()
+    session = app.model.session
+    object_store: ObjectStore = app.object_store
+    SQL = """
+SELECT distinct d.id FROM hda_dataset_mapping_pre_uuid_condense as hda_pre_condense
+  JOIN history_dataset_association as hda on hda.id=hda_pre_condense.id
+  JOIN dataset as d on hda.dataset_id = d.id;
+"""
+
+    updated_hda_ids = []
+    dataset_ids = session.scalars(text(SQL)).all()
+    for i, dataset_id in enumerate(dataset_ids):
+        d = session.get(Dataset, dataset_id)
+        if not object_store.exists(d):
+            d.deleted = True
+            d.purged = True
+            for dataset_instance in d.active_history_associations:
+                dataset_instance.deleted = True
+                dataset_instance.purged = True
+                updated_hda_ids.append(dataset_instance.id)
+        if i % 100 == 0:
+            log.info(f"processed {i} of {len(dataset_ids)} datasets")
+            session.commit()
+    session.commit()
+    if updated_hda_ids:
+        log.warning(
+            "The following history dataset associations could not be found on disk and were marked as deleted and purged: %s",
+            updated_hda_ids,
+        )
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 325cd6b24b08e013fb10f7fb73e4413297cad594..97a142623ebf2818dc845487817a60cd320274bd 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -401,7 +401,8 @@ class RequiresDiskUsageRecalculation:
             statements = calculate_user_disk_usage_statements(user_id, quota_source_map)
 
             for sql, args in statements:
-                sql, _ = re.subn(r"\:([\w]+)", r"%(\1)s", sql)
+                sql = sql.replace("%", "%%")
+                sql = re.sub(r"\:([\w]+)", r"%(\1)s", sql)
                 new_args = {}
                 for key, val in args.items():
                     if isinstance(val, list):
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index e1fa46fdbac6d2b89f31006a82011989a5baabc2..20a9b0ea29c157ad86e0416ce016b17fa02a96a2 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -34,7 +34,6 @@ done
 SAMPLES="
     tool-data/shared/ucsc/builds.txt.sample
     tool-data/shared/ucsc/manual_builds.txt.sample
-    static/welcome.html.sample
 "
 
 RMFILES="
diff --git a/scripts/galaxy_main.py b/scripts/galaxy_main.py
index 02ef739286047d043cd1474f8881d48bff4dce97..85d6b954dbb722c225f2bb2add3c95146c09e02c 100755
--- a/scripts/galaxy_main.py
+++ b/scripts/galaxy_main.py
@@ -87,8 +87,15 @@ def load_galaxy_app(config_builder, config_env=False, log=None, attach_to_pools=
     kwds = config_builder.app_kwds()
     kwds = load_app_properties(**kwds)
     from galaxy.app import UniverseApplication
+    from galaxy.celery import (
+        celery_app,
+        config_celery_app,
+    )
 
     app = UniverseApplication(global_conf=config_builder.global_conf(), attach_to_pools=attach_to_pools, **kwds)
+    # Update celery app, which might not have taken into account the config file if set via the `-c` argument.
+    config_celery_app(app.config, celery_app)
+
     app.database_heartbeat.start()
     app.application_stack.log_startup()
     return app
diff --git a/static/robots.txt b/static/robots.txt
index 55bca6a57ccefdd89ed5755d240894242a6b9db0..77bcf4fa5497be1b147a1e65a63b2e1cbbdeaa5b 100644
--- a/static/robots.txt
+++ b/static/robots.txt
@@ -2,3 +2,4 @@ User-agent: *
 Disallow: /display?
 Disallow: /display_as?
 Disallow: /training-material/
+Disallow: /tool_runner?
diff --git a/static/welcome.html.sample b/static/welcome.sample.html
similarity index 100%
rename from static/welcome.html.sample
rename to static/welcome.sample.html
diff --git a/templates/webapps/galaxy/dataset/display.mako b/templates/webapps/galaxy/dataset/display.mako
index d389836b40f711c9340cd32113533f07d40a78fb..d77734acfba948924ed316d45c7bc4c9bff79921 100644
--- a/templates/webapps/galaxy/dataset/display.mako
+++ b/templates/webapps/galaxy/dataset/display.mako
@@ -82,10 +82,6 @@
     %if data.deleted:
         <div class="errormessagelarge" id="deleted-data-message">
             You are viewing a deleted dataset.
-            %if data.history and data.history.user == trans.get_user():
-                <br />
-                <a href="javascript:void(0)" role="button" onclick="$.ajax( {type: 'GET', cache: false, url: '${h.url_for( controller='dataset', action='undelete_async', dataset_id=trans.security.encode_id( data.id ) )}', dataType: 'text', contentType: 'text/html', success: function( data, textStatus, jqXHR ){ if (data == 'OK' ){ $( '#deleted-data-message' ).slideUp( 'slow' ) } else { alert( 'Undelete failed.' ) } }, error: function( data, textStatus, jqXHR ){ alert( 'Undelete failed.' ); } } );">Undelete</a>
-            %endif
         </div>
     %endif
 </%def>
diff --git a/templates/webapps/galaxy/workflow/build_from_current_history.mako b/templates/webapps/galaxy/workflow/build_from_current_history.mako
index 22770fc009415f88772cc202b911a0f0f4b92100..ff62f33f448902e0583e5bbacf9d97bb0861e392 100644
--- a/templates/webapps/galaxy/workflow/build_from_current_history.mako
+++ b/templates/webapps/galaxy/workflow/build_from_current_history.mako
@@ -88,7 +88,7 @@ into a workflow will be shown in gray.</p>
     <div class="warningmark">${warning}</div>
 %endfor
 
-<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history')}">
+<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history', history_id=trans.security.encode_id(history.id))}">
 <div class='form-row'>
     <label>Workflow name</label>
     <input name="workflow_name" type="text" value="Workflow constructed from history '${ util.unicodify( history.name )}'" size="60"/>
@@ -112,6 +112,7 @@ into a workflow will be shown in gray.</p>
     <%
     cls = "toolForm"
     tool_name = "Unknown"
+    checked_job = "checked" if any(True for d in datasets if not d[1].deleted) else ""
     if hasattr( job, 'is_fake' ) and job.is_fake:
         cls += " toolFormDisabled"
         disabled = True
@@ -142,7 +143,10 @@ into a workflow will be shown in gray.</p>
                     %if disabled:
                         <div style="font-style: italic; color: gray">${disabled_why}</div>
                     %else:
-                        <div><input type="checkbox" name="job_ids" value="${job.id}" checked="true" />Include "${tool_name}" in workflow</div>
+                        <div><input type="checkbox" name="job_ids" value="${job.id}" ${checked_job} />Include "${tool_name}" in workflow</div>
+                        %if not checked_job:
+                            ${ render_msg( "All job outputs have been deleted", status="info" ) }
+                        %endif
                         %if tool_version_warning:
                             ${ render_msg( tool_version_warning, status="warning" ) }
                         %endif
diff --git a/test-data/bwa_mem2_index/1.fasta b/test-data/bwa_mem2_index/1.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..c9ecbb612dd1722e967de63db3a078ce5ce30d93
--- /dev/null
+++ b/test-data/bwa_mem2_index/1.fasta
@@ -0,0 +1,2 @@
+>hg17
+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAGGACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAcccccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC----------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTACCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCCGAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAGCAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGCCGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGGCATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTCCTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCAGGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATTGGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGACATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCCTGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAGTAGAGGTGGGGGGAAACAAGTGTCAGGAAGA--------------------------------------------CTCAAA---------ATCTTC--------------------------------------------------------------CAGAGAAATTGT-----GCAGGGTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATGAGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAACTTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTATAGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACACTCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACAGTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAGG----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAGAGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GTGCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGGTGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGATTGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAATGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGGCAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCCCAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCCTCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAATATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGACAGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGTCTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAGGAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGCACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCATCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCCTTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGCTTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTGACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTGTTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATTTCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGGG-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---GGGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCCAGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGATGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCACATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCATTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCAAAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTTACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagatatttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttctgagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaattgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaaggcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaaccccatctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagctacttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgagccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacacacacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-tatctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCTGTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTGGTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTGTGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTGAATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGAAAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCCTGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCTCACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTCTGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAATGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCCACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAGGAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGTAGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgtgtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCCTACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTCTACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttggcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagttcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTTTGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGTTGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAACTTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGAGTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCAAATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT-------CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTGGG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAAGAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCATCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTTGTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAGGGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAACTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGCAGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTATATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatcttttttggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtgatcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcccaagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggctcaagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacacccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTTCTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GCCAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AGGGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCTCCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC--------TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAATGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACAGCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACAGCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGACTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGGACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAGTTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TGCTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGATTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCCACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctctcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatctcctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gcattggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcagccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaaaactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATAGCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACCCAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaatgcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacaaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaaggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcctatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccagctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgagccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaagaaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggaggatgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaacactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaataaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGCACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAATCAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATCCCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTGGCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATTATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtggtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGAATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTTCTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTAATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtttggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtctctcacacacacccagcacaagtccaag-------------------------accagcatggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagttgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccatatctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacgacaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttagtcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatggccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaagatattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgtgtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GATTCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATAGGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAGCTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTGGTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATTTGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGGGGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTGGAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCACTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTAACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGGAAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAAATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGGA---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc--------------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctgagccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAACATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCCTACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAATATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATTGGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtctttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccatatttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgccttccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcccattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgttgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcagtaagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAGTGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATGGGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACACCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagatagatatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatgcagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AGCATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAGCTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCTAAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGATGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTGGTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCTGTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCACTGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctgaatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTCTGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG--------------------------------------------------------TTCTAATTCTAAACCACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggctgggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcattcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaataataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggctgagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgccaccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaataaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttaggaggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggcaagacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGATTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCGATTAGCTGAGC----------CACATGCAGGCACAG------------------------CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCCTCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCTTG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------CTCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tgtagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccctttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtcttttctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaattaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaagttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA
diff --git a/test-data/im5_uint8.tif b/test-data/im5_uint8.tif
new file mode 100644
index 0000000000000000000000000000000000000000..5dca8cad973d5ebdd9df601c00ea50b4a54a90ba
Binary files /dev/null and b/test-data/im5_uint8.tif differ
diff --git a/test-data/im6_uint8.tif b/test-data/im6_uint8.tif
new file mode 100644
index 0000000000000000000000000000000000000000..5221d413ea3f2a59ec31ab738a30e62bdee0d921
Binary files /dev/null and b/test-data/im6_uint8.tif differ
diff --git a/test-data/im7_uint8.tif b/test-data/im7_uint8.tif
new file mode 100644
index 0000000000000000000000000000000000000000..c6f3d7ba20f9b4126f2c2a1102f51b880059ef8d
Binary files /dev/null and b/test-data/im7_uint8.tif differ
diff --git a/test-data/im8_uint16.tif b/test-data/im8_uint16.tif
new file mode 100644
index 0000000000000000000000000000000000000000..be4c15380cea074ed1668ef99f4dddc418a4d04a
Binary files /dev/null and b/test-data/im8_uint16.tif differ
diff --git a/test-data/new_labels_3.txt b/test-data/new_labels_3.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15233d02aaad8dea1b8308403c678c7c70107b98
--- /dev/null
+++ b/test-data/new_labels_3.txt
@@ -0,0 +1 @@
+new_i1	to_ignore	i1	to_ignore
diff --git a/test-data/selenium-test-notebook.ipynb b/test-data/selenium-test-notebook.ipynb
index 1cdb2736403d7798dbba580ee06b164102a68279..2d87460a6120006e65cd63858d91bf1b9aecf0fa 100644
--- a/test-data/selenium-test-notebook.ipynb
+++ b/test-data/selenium-test-notebook.ipynb
@@ -44,7 +44,7 @@
     }
    ],
    "source": [
-    "get(1)"
+    "get(1)  # noqa: F821"
    ]
   },
   {
@@ -85,7 +85,7 @@
    },
    "outputs": [],
    "source": [
-    "put(\"/tmp/cow\")"
+    "put(\"/tmp/cow\")  # noqa: F821"
    ]
   },
   {
@@ -115,7 +115,7 @@
    },
    "outputs": [],
    "source": [
-    "put(\"/import/ipython_galaxy_notebook.ipynb\")"
+    "put(\"/import/ipython_galaxy_notebook.ipynb\")  # noqa: F821"
    ]
   },
   {
diff --git a/test/functional/tools/create_directory_index.xml b/test/functional/tools/create_directory_index.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3c849f238fed13bb9d84dfdcf9a543ee6eba8eb0
--- /dev/null
+++ b/test/functional/tools/create_directory_index.xml
@@ -0,0 +1,20 @@
+<tool id="create_directory_index" name="Create directory index" version="1.0" profile="24.2">
+    <command><![CDATA[
+mkdir '$index.extra_files_path' &&
+cp '$reference' '$index.extra_files_path/1.fasta'
+    ]]></command>
+    <inputs>
+        <param name="reference" type="data" label="Select a genome to index" help="Build an index for this FASTA sequence." format="fasta"/>
+    </inputs>
+    <outputs>
+        <data name="index" format="bwa_mem2_index"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference" value="1.fasta"></param>
+            <output name="index" ftype="bwa_mem2_index">
+                <extra_files name="1.fasta" type="file" value="1.fasta"></extra_files>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/deprecated/simple_constructs_24_2.xml b/test/functional/tools/deprecated/simple_constructs_24_2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ce545d8161d89b120cd4f7fd0ed65124bf3363b5
--- /dev/null
+++ b/test/functional/tools/deprecated/simple_constructs_24_2.xml
@@ -0,0 +1,80 @@
+<tool id="simple_constructs_24_2" name="simple_constructs_24_2" version="1.0.0" profile="24.2">
+    <!-- just simple_constructs with newer profile - the test cases should be invalid -->
+    <command><![CDATA[
+echo '$p1.p1val'  > '$out_file1' &&
+echo $booltest  >> '$out_file1' &&
+echo $inttest   >> '$out_file1' &&
+echo $floattest >> '$out_file1' &&
+echo $radio_select >> '$out_file1' &&
+echo $check_select >> '$out_file1' &&
+echo $drop_select  >> '$out_file1' &&
+#if len($files) > 0
+    cat '$files[0].file' >> '$out_file1'
+#end if
+    ]]></command>
+    <inputs>
+        <conditional name="p1">
+            <param type="boolean" name="p1use" />
+            <when value="true">
+                <param name="p1val" value="p1used" type="text" />
+            </when>
+            <when value="false">
+                <param name="p1val" value="p1notused" type="text" />
+            </when>
+        </conditional>
+        <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="inttest" value="1" type="integer" />
+        <param name="floattest" value="1.0" type="float" />
+        <param name="radio_select" type="select" display="radio">
+            <option value="a_radio" selected="true">A Radio</option>
+            <option value="b_radio">B Radio</option>
+            <option value="c_radio">C Radio</option>
+        </param>
+        <param name="check_select" type="select" display="checkboxes" multiple="true">
+            <option value="a_check" selected="true">A Check</option>
+            <option value="b_check">B Check</option>
+            <option value="c_check">C Check</option>
+        </param>
+        <param name="drop_select" type="select">
+            <option value="a_drop" selected="true">A Drop</option>
+            <option value="b_drop">B Drop</option>
+            <option value="c_drop">C Drop</option>
+        </param>
+        <repeat name="files" title="Files">
+            <param name="file" type="data" format="txt" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="p1use" value="true" />
+            <param name="booltest" value="true" />
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <param name="file" value="simple_line.txt" /> <!-- This is a line of text. -->
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="p1used" />
+                    <has_line line="booltrue" />
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                    <has_line line="This is a line of text." />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- Again but using boolean's truevalue -->
+            <param name="p1use" value="true" />
+            <param name="booltest" value="booltrue" />
+            <param name="file" value="simple_line.txt" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="p1used" />
+                    <has_line line="booltrue" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/discover_sort_by.xml b/test/functional/tools/discover_sort_by.xml
index 4f29087f3118b1178453a34d1a3b5028b40d628c..f3ac7dcca92b3b6c32f6256830c7a88515a86f2b 100644
--- a/test/functional/tools/discover_sort_by.xml
+++ b/test/functional/tools/discover_sort_by.xml
@@ -71,7 +71,6 @@ done
     </test>
     <!-- same test with wrong order should fail  -->
     <test expect_num_outputs="4" expect_test_failure="true">
-      <param name="input1" value="tinywga.fam" />
       <output_collection name="collection_numeric_name" type="list" count="10">
         <element name="1">
           <assert_contents><has_text_matching expression="^.*$"/></assert_contents>
diff --git a/test/functional/tools/discover_sort_by_legacy_test.xml b/test/functional/tools/discover_sort_by_legacy_test.xml
index 2b62e12ea49e404b01f20c0796c275e084caf361..275e1966189d6bd63dbf2da9a1e8253281015f78 100644
--- a/test/functional/tools/discover_sort_by_legacy_test.xml
+++ b/test/functional/tools/discover_sort_by_legacy_test.xml
@@ -25,7 +25,6 @@ done
   </outputs>
   <tests>
     <test expect_num_outputs="4">
-      <param name="input1" value="tinywga.fam" />
       <output_collection name="collection_numeric_name" type="list" count="10">
         <element name="2">
           <assert_contents><has_text_matching expression="^.*$"/></assert_contents>
diff --git a/test/functional/tools/empty_select.xml b/test/functional/tools/empty_select.xml
index 76b3c9a03729c5fc637692a81654c77a35c7830c..4c1128fb08a92a269fc7472df0ee88ee859ad772 100644
--- a/test/functional/tools/empty_select.xml
+++ b/test/functional/tools/empty_select.xml
@@ -1,5 +1,4 @@
 <tool id="empty_select" name="empty_select" version="1.0.0">
-    <description>multi_select</description>
     <command><![CDATA[
 touch '$output'
 #if $select_optional:
diff --git a/test/functional/tools/expression_pick_larger_file.xml b/test/functional/tools/expression_pick_larger_file.xml
index daed2d9175eaea50b53f6910552148cc3a36e386..e624ed302f26d086ca8046532e8ca6a54dc38285 100644
--- a/test/functional/tools/expression_pick_larger_file.xml
+++ b/test/functional/tools/expression_pick_larger_file.xml
@@ -20,7 +20,7 @@
         <param name="input2" type="data" optional="true" label="Second file" />
     </inputs>
     <outputs>
-        <output name="larger_file" type="data" from="output" />
+        <output name="larger_file" type="data" from="output" format_source="input1" />
     </outputs>
     <tests>
         <test>
diff --git a/test/functional/tools/float_default.xml b/test/functional/tools/float_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a92e3db8c0093be8801e4d0f87090514e456cfc6
--- /dev/null
+++ b/test/functional/tools/float_default.xml
@@ -0,0 +1,33 @@
+<tool id="float_default" name="Test float default" version="0.1.0">
+    <command><![CDATA[
+echo ${float($input1) + float($input2) + float($input3)} > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="input1" type="float" value="0.0" label="Float with default 0.0" />
+        <param name="input2" type="float" value="" label="Float with default empty string" />
+        <!-- Not needed any more to have `value=""` when there is no good default -->
+        <param name="input3" type="float" label="Float with no default value" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.0" />
+            <param name="input2" value="2.0" />
+            <param name="input3" value="3.0" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="6.0" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test that it fails if a non-optional float param is not set -->
+        <test expect_failure="true">
+            <param name="input1" value="1.0" />
+            <param name="input2" value="2.0" />
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/galaxy_json_discover_and_sleep.xml b/test/functional/tools/galaxy_json_discover_and_sleep.xml
index 8b598bb72fa47af73a2612690f99c0cf743f3290..36f5ce5268c0b2553d6e71994ca7f190f6abf398 100644
--- a/test/functional/tools/galaxy_json_discover_and_sleep.xml
+++ b/test/functional/tools/galaxy_json_discover_and_sleep.xml
@@ -20,7 +20,6 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="7" />
             <output name="output" md5="d41d8cd98f00b204e9800998ecf8427e">
             </output>
         </test>
diff --git a/test/functional/tools/help_features_markdown.xml b/test/functional/tools/help_features_markdown.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c120812fa43afe36cc4049f134bdb0a053c5841e
--- /dev/null
+++ b/test/functional/tools/help_features_markdown.xml
@@ -0,0 +1,75 @@
+<tool id="help_features_markdown" name="help_features_markdown" version="1.0.0">
+    <command>
+        cp '$input.file_name' '$output'
+    </command>
+    <inputs>
+        <param name="input" type="data" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <help format="markdown"><![CDATA[
+----
+
+Static path images
+
+![Zipping operation](gxstatic://images/tools/collection_ops/zip.svg)
+
+----
+
+Markdown can also reference help terms like [map over](gxhelp://galaxy.collections.mapOver),
+[command line](gxhelp://unix.commandLine), [standard error](gxhelp://unix.stderr), and
+[the FASTA file format](gxhelp://galaxy.datatypes.extensions.fasta).
+
+-----
+
+Markdown extensions for tables should work...
+
+
+| this | is | a | table |
+|------|----|---|-------|
+| 1 | 2 | 3 | 4 |
+
+Some more examples from https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/organizing-information-with-tables
+
+| Command | Description |
+| --- | --- |
+| `git status` | List all *new or modified* files |
+| `git diff` | Show file differences that **haven't been** staged |
+
+
+| Left-aligned | Center-aligned | Right-aligned |
+| :---         |     :---:      |          ---: |
+| git status   | git status     | git status    |
+| git diff     | git diff       | git diff      |
+
+-----
+
+
+Text styles 
+
+**This is bold text**
+
+_This text is italicized_
+
+~~This was mistaken text~~
+
+**This text is _extremely_ important**
+
+***All this text is important***
+
+----
+
+It would be easy to turn on sub script but we haven't yet.
+
+This is a <sub>subscript</sub> text
+
+----
+
+Text that is not a quote
+
+> Text that is a quote
+
+Well... that does render with a block quote tag in Galaxy 24.2 but it isn't formatted at all.
+]]></help>
+</tool>
diff --git a/test/functional/tools/help_features_rst.xml b/test/functional/tools/help_features_rst.xml
new file mode 100644
index 0000000000000000000000000000000000000000..413272129727778fdc2432212f69312042c176ee
--- /dev/null
+++ b/test/functional/tools/help_features_rst.xml
@@ -0,0 +1,80 @@
+<tool id="help_features_rst" name="help_features_rst" version="1.0.0">
+    <command>
+        cp '$input.file_name' '$output'
+    </command>
+    <inputs>
+        <param name="input" type="data" format="txt" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <help><![CDATA[
+Header
+-------
+
+SubHeader
+---------
+
+SubSubHeader
+~~~~~~~~~~
+
+Some text here....
+
+----
+
+.. class:: warningmark
+
+'''TIP''' This tool requires *txt* format.
+
+----
+
+.. class:: infomark
+
+Here is some extra info....
+
+----
+
+Example Table from RST Docs....
+
+
+.. list-table:: Title of the table.
+   :widths: 25 25 50
+   :header-rows: 1
+
+   * - Heading row 1, column 1
+     - Heading row 1, column 2
+     - Heading row 1, column 3
+   * - Row 1, column 1
+     -
+     - Row 1, column 3
+   * - Row 2, column 1
+     - Row 2, column 2
+     - Row 2, column 3
+
+----
+
+**negative example**
+
+.. code-block::
+   :caption: Doesn't work in Galaxy
+
+       Code with captions doesn't seem to work.
+
+
+----
+
+.. code-block::
+
+       The output of this line has no spaces at the beginning.
+
+----
+
+Static path images...
+
+.. image:: ${static_path}/images/tools/collection_ops/zip.svg
+  :width: 500
+  :alt: Zipping operation
+
+
+    ]]></help>
+</tool>
diff --git a/test/functional/tools/html_output.xml b/test/functional/tools/html_output.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7558bca44ec1465d7f471c8a204164fe292505ae
--- /dev/null
+++ b/test/functional/tools/html_output.xml
@@ -0,0 +1,25 @@
+<tool id="html_output" name="html_output" version="1.0.0">
+    <command><![CDATA[
+cp '$html_file' '$output'
+    ]]></command>
+    <configfiles>
+        <configfile name="html_file"><![CDATA[
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title data-description="hello-world">Hello World</title>
+</head>
+<body>
+    <main>
+       <h1>Hello, World!</h1>
+    </main>
+</body>
+</html>
+        ]]></configfile>
+    </configfiles>
+    <outputs>
+        <data name="output" format="html" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/implicit_conversion_format_input.xml b/test/functional/tools/implicit_conversion_format_input.xml
index e93f54095592b46c952f59c4dddc7690ed1320a5..090aa474f0fca9386bd6999acd4b903bacf6e79a 100644
--- a/test/functional/tools/implicit_conversion_format_input.xml
+++ b/test/functional/tools/implicit_conversion_format_input.xml
@@ -3,7 +3,7 @@
     cut -f 1 '$input1' > '$output1'
   </command>
   <inputs>
-    <param type="data" format="fasta" name="input1" label="Input 1" />
+    <param type="data" format="txt" name="input1" label="Input 1" />
   </inputs>
   <outputs>
     <data name="output1" format="input" />
diff --git a/test/functional/tools/legacy_interpreter.xml b/test/functional/tools/legacy_interpreter.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7ca65584d3886afa891e877905c41e8e7417be11
--- /dev/null
+++ b/test/functional/tools/legacy_interpreter.xml
@@ -0,0 +1,19 @@
+<tool id="legacy_interpreter" name="legacy_interpreter" version="1.0.0">
+    <command interpreter="python"><![CDATA[
+legacy_interpreter_write_output.py
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="output1" format="xml" from_work_dir="output1" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output1">
+                <assert_contents>
+                    <has_text text="hello world" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/legacy_interpreter_write_output.py b/test/functional/tools/legacy_interpreter_write_output.py
new file mode 100644
index 0000000000000000000000000000000000000000..25791f7b3d868a757236a9ece6991a9ed07798df
--- /dev/null
+++ b/test/functional/tools/legacy_interpreter_write_output.py
@@ -0,0 +1,2 @@
+with open("output1", "w") as f:
+    f.write("hello world")
diff --git a/test/functional/tools/metadata_column_names.xml b/test/functional/tools/metadata_column_names.xml
index 918042f52426ec7957ec5203b7624b90db18c13d..5aee4b64525ff568016ffd72fbff091041d89587 100644
--- a/test/functional/tools/metadata_column_names.xml
+++ b/test/functional/tools/metadata_column_names.xml
@@ -32,6 +32,7 @@
             <param name="input" value="2.tabular" />
             <output name="output">
                 <metadata name="column_names" value="First,2.tabular"/>
+                <metadata name="column_types" value="int,int,float"/>
             </output>
             <output_collection name="paired_output" type="paired">
                 <element name="forward" ftype="tabular" value="2.tabular">
diff --git a/test/functional/tools/multiple_versions_changes_v01.xml b/test/functional/tools/multiple_versions_changes_v01.xml
index da49bbcda79485846670bae71d0a80165e129d96..a29a4388f198e1daf6fe9f9a71bd9c85d308d3c9 100644
--- a/test/functional/tools/multiple_versions_changes_v01.xml
+++ b/test/functional/tools/multiple_versions_changes_v01.xml
@@ -15,7 +15,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="intest" value="1" />
+            <param name="inttest" value="1" />
             <output name="out_file1">
                 <assert_contents>
                     <has_line line="Version 0.1" />
diff --git a/test/functional/tools/multiple_versions_changes_v02.xml b/test/functional/tools/multiple_versions_changes_v02.xml
index 14ef9dafeebc8d0a8ae62d6b533f0f25460a793e..8441a2e01b4598a1d93a22204d59dd6e1d1eabaf 100644
--- a/test/functional/tools/multiple_versions_changes_v02.xml
+++ b/test/functional/tools/multiple_versions_changes_v02.xml
@@ -20,7 +20,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="intest" value="1" />
+            <param name="inttest" value="1" />
             <output name="out_file1">
                 <assert_contents>
                     <has_line line="Version 0.2" />
diff --git a/test/functional/tools/multiple_versions_v01.xml b/test/functional/tools/multiple_versions_v01.xml
index fa72fd5f65e754210e682ff699d1beaeaf99c947..6b656cf7a5b66c75743e57a8f9a859d47618236d 100644
--- a/test/functional/tools/multiple_versions_v01.xml
+++ b/test/functional/tools/multiple_versions_v01.xml
@@ -10,7 +10,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="intest" value="1" />
+            <param name="inttest" value="1" />
             <output name="out_file1" file="multiple_versions_0.1.txt">
                 <assert_contents>
                     <has_line line="Version 0.1" />
diff --git a/test/functional/tools/multiple_versions_v01galaxy6.xml b/test/functional/tools/multiple_versions_v01galaxy6.xml
index 030b6bc70a9f362ee743f2e22bc82a2b49aa0d5f..2ee1b05f34e718316bbfc3a47b32dfed6f9b7300 100644
--- a/test/functional/tools/multiple_versions_v01galaxy6.xml
+++ b/test/functional/tools/multiple_versions_v01galaxy6.xml
@@ -10,7 +10,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="intest" value="1" />
+            <param name="inttest" value="1" />
             <output name="out_file1">
                 <assert_contents>
                     <has_line line="Version 0.1+galaxy6" />
diff --git a/test/functional/tools/multiple_versions_v02.xml b/test/functional/tools/multiple_versions_v02.xml
index 5eb00f8718d3f9a379f7b7024c0200dcbc73ff64..a32268dc0e98e578ad902eb02312619b47815e30 100644
--- a/test/functional/tools/multiple_versions_v02.xml
+++ b/test/functional/tools/multiple_versions_v02.xml
@@ -10,7 +10,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="intest" value="1"/>
+            <param name="inttest" value="1"/>
             <output name="out_file1" file="multiple_versions_0.2.txt">
                 <assert_contents>
                     <has_line line="Version 0.2"/>
diff --git a/test/functional/tools/options_from_metadata_file.xml b/test/functional/tools/options_from_metadata_file.xml
index 87e1863bbb8de31f3dbc2e6ad667773a1403f67c..d0ee9114b8be208e7645c66b7109744f10aac83c 100644
--- a/test/functional/tools/options_from_metadata_file.xml
+++ b/test/functional/tools/options_from_metadata_file.xml
@@ -22,7 +22,7 @@ echo '${species_2}' >> '${output}'
         </options>
     </param>
     <!-- test meta_file_key referring a collection to define options-->
-    <param name="input_2" type="data_collection" collection_type="list" format="maf" label="MAF Collection" multiple="true"/>
+    <param name="input_2" type="data_collection" collection_type="list" format="maf" label="MAF Collection" />
     <param name="species_2" type="select" optional="false" label="Select species for the input dataset" multiple="true">
         <options from_dataset="input_2" meta_file_key="species_chromosomes">
             <column name="name" index="0"/>
diff --git a/test/functional/tools/output_format_input.xml b/test/functional/tools/output_format_input.xml
index c346b10dedf341939c9c8ef355128bc68b6f2dd1..6080f0c21ca295124ba69bfa91ff7d85fd7b1ac3 100644
--- a/test/functional/tools/output_format_input.xml
+++ b/test/functional/tools/output_format_input.xml
@@ -1,6 +1,6 @@
 <tool id="output_format_input" name="output_format_input" version="1.0" profile="21.01">
   <!-- test format="input" for the profile version where the format is set to "input"
-       (for legacy tools, i.e. profile <16.04, the format of a ramdom input is used) -->
+       (for legacy tools, i.e. profile <16.04, the format of a random input is used) -->
   <description></description>
   <command>
     cat '$input' > '$output'
diff --git a/test/functional/tools/parameters/cwl_boolean.cwl b/test/functional/tools/parameters/cwl_boolean.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..be6150d48920d4b02ca049866d520a2840a0d0f6
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_boolean.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: boolean
+
+outputs:
+  output: boolean
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_boolean_optional.cwl b/test/functional/tools/parameters/cwl_boolean_optional.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..f05516dd5d807ffd52b25806a30f7a86d7b43fed
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_boolean_optional.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: boolean?
+
+outputs:
+  output: boolean?
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_directory.cwl b/test/functional/tools/parameters/cwl_directory.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..66d3c53530791281ff593bceb6569837718e3026
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_directory.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: Directory
+
+outputs:
+  output: Directory
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_file.cwl b/test/functional/tools/parameters/cwl_file.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ea48da6d2e8257928fb75596a8831ad16875c8aa
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_file.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: File
+
+outputs:
+  output: File
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_float.cwl b/test/functional/tools/parameters/cwl_float.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..9e7e094690556e707d4f5c12d2eeace9f3698144
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_float.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: float
+
+outputs:
+  output: float
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_float_optional.cwl b/test/functional/tools/parameters/cwl_float_optional.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..1bc34fa1bc56f6b00b5a8b4f928b006283b903f6
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_float_optional.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: float?
+
+outputs:
+  output: float?
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_int.cwl b/test/functional/tools/parameters/cwl_int.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..5ba0a8d5c76cbc0146348770a063906a2aa2ac96
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_int.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: int
+
+outputs:
+  output: int
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_int_optional.cwl b/test/functional/tools/parameters/cwl_int_optional.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..63d9c6915862e9bf2d1964b9d543b550b789caf3
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_int_optional.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: int?
+
+outputs:
+  output: int?
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_string.cwl b/test/functional/tools/parameters/cwl_string.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..571a4cefc6ec9b21287115aa0456587abdcc596d
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_string.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: string
+
+outputs:
+  output: string
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/cwl_string_optional.cwl b/test/functional/tools/parameters/cwl_string_optional.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..fecc8272d99a113525ece58c5e7b0c767afc6b69
--- /dev/null
+++ b/test/functional/tools/parameters/cwl_string_optional.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  parameter:
+    type: string?
+
+outputs:
+  output: string?
+
+expression: "$({'output': inputs.parameter})"
diff --git a/test/functional/tools/parameters/gx_allow_uri_if_protocol.xml b/test/functional/tools/parameters/gx_allow_uri_if_protocol.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b6cd4d6d42050c40f96b9d3ad374af55720f4f88
--- /dev/null
+++ b/test/functional/tools/parameters/gx_allow_uri_if_protocol.xml
@@ -0,0 +1,23 @@
+<tool id="gx_allow_uri_if_protocol" name="gx_allow_uri_if_protocol" version="1.0.0">
+    <command><![CDATA[
+        #for $input in $input1:
+            ## We should handle the case where the input must be treated as a URI with a specific protocol.
+            #if $input.is_deferred:
+                ## Here, the input is a deferred dataset which source URI has the protocol 'https'.
+                ## We append the URI to the output file.
+                echo '$input' >> '$output'
+            #else:
+                ## Here, the input is a regular dataset or a materialized dataset in case of a 
+                ## deferred dataset which source URI has a protocol different than 'https'.
+                ## We append the content of the dataset to the output file.
+                cat '$input' >> '$output'
+            #end if
+        #end for
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" allow_uri_if_protocol="https" multiple="true"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+    </outputs>
+</tool>
diff --git a/test/functional/tools/parameters/gx_boolean.xml b/test/functional/tools/parameters/gx_boolean.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d89ec53fe3ffbf3b6bac8c3b1715e1b9e319699d
--- /dev/null
+++ b/test/functional/tools/parameters/gx_boolean.xml
@@ -0,0 +1,36 @@
+<tool id="gx_boolean" name="gx_boolean" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="boolean" truevalue="mytrue" falsevalue="myfalse" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="myfalse" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="false" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="myfalse" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="true" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="mytrue" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_boolean_checked.xml b/test/functional/tools/parameters/gx_boolean_checked.xml
new file mode 100644
index 0000000000000000000000000000000000000000..de33a26e6f560019fd502d028ba218aad4222ceb
--- /dev/null
+++ b/test/functional/tools/parameters/gx_boolean_checked.xml
@@ -0,0 +1,36 @@
+<tool id="gx_boolean_checked" name="gx_boolean_checked" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="boolean" truevalue="mytrue" falsevalue="myfalse" checked="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="mytrue" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="false" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="myfalse" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="true" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="mytrue" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_boolean_optional.xml b/test/functional/tools/parameters/gx_boolean_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..57a6d6f3f1bed7798aaa7061cf770d077f28a84f
--- /dev/null
+++ b/test/functional/tools/parameters/gx_boolean_optional.xml
@@ -0,0 +1,81 @@
+<tool id="gx_boolean_optional" name="gx_boolean_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="boolean" optional="true" />
+    </inputs>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+            <!-- I wish this were null? It is somehow in expression_null_handling_boolean -->
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: false" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="null" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: null" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="false" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: false" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="true" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="true" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value="true" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="true" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value="false" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_boolean_optional_checked.xml b/test/functional/tools/parameters/gx_boolean_optional_checked.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f1c27f98ce4602ac7206db29ea5daf3999a5d4af
--- /dev/null
+++ b/test/functional/tools/parameters/gx_boolean_optional_checked.xml
@@ -0,0 +1,58 @@
+<tool id="gx_boolean_optional_checked" name="gx_boolean_optional_checked" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="boolean" optional="true" checked="true" />
+    </inputs>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="true" />
+                </assert_contents>
+            </output>
+            <!-- I wish this were null? It is somehow in expression_null_handling_boolean -->
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: true" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="null" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+            <!-- I wish this were null? It is somehow in expression_null_handling_boolean -->
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: null" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value_json="false" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="false" />
+                </assert_contents>
+            </output>
+            <output name="inputs_json">
+                <assert_contents>
+                    <has_text text="&quot;parameter&quot;: false" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_color.xml b/test/functional/tools/parameters/gx_color.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fe158d0e6fb1a29a7188bb660aaa4d5ba724c2e6
--- /dev/null
+++ b/test/functional/tools/parameters/gx_color.xml
@@ -0,0 +1,21 @@
+<tool id="gx_color" name="gx_color" version="1.0.0">
+    <command>
+        echo "$parameter"  > $out_file1;
+    </command>
+    <inputs>
+        <param name="parameter" type="color" value="#aabbcc" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="#aaaaaa" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="#aaaaaa" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_boolean.xml b/test/functional/tools/parameters/gx_conditional_boolean.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7c5feffab0eca334b36f91b963f2868032ebb0f4
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_boolean.xml
@@ -0,0 +1,101 @@
+<tool id="gx_conditional_boolean" name="gx_conditional_boolean" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="common_conditional_tags" />    
+    <inputs>
+        <conditional name="conditional_parameter">
+            <!-- boolean parameters as the test parameter are discouraged, respect linting and don't do this -->
+            <param name="test_parameter" type="boolean" />
+            <when value="true">
+                <param name="integer_parameter" type="integer" value="1" />
+            </when>
+            <when value="false">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+        </conditional>
+    </inputs>
+    <tests>
+        <test>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="false" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="True" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="False" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="false" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_boolean_checked.xml b/test/functional/tools/parameters/gx_conditional_boolean_checked.xml
new file mode 100644
index 0000000000000000000000000000000000000000..09fdbd71fe6d0733e99c9bbac79d79f12a726ad6
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_boolean_checked.xml
@@ -0,0 +1,53 @@
+<tool id="gx_conditional_boolean_checked" name="gx_conditional_boolean_checked" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="common_conditional_tags" />
+    <inputs>
+        <conditional name="conditional_parameter">
+            <!-- boolean parameters as the test parameter are discouraged, respect linting and don't do this -->
+            <param name="test_parameter" type="boolean" checked="true" />
+            <when value="true">
+                <param name="integer_parameter" type="integer" value="1" />
+            </when>
+            <when value="false">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+        </conditional>
+    </inputs>
+    <tests>
+        <test>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="false" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_boolean_discriminate_on_string_value.xml b/test/functional/tools/parameters/gx_conditional_boolean_discriminate_on_string_value.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6bc790d81ad918ae748ede97323d90025d54b149
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_boolean_discriminate_on_string_value.xml
@@ -0,0 +1,113 @@
+<tool id="gx_conditional_boolean_discriminate_on_string_value" name="gx_conditional_boolean_discriminate_on_string_value" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="common_conditional_tags" />    
+    <inputs>
+        <conditional name="conditional_parameter">
+            <!-- boolean parameters as the test parameter are discouraged, respect linting and don't do this -->
+            <param name="test_parameter" type="boolean" truevalue="a_value_that_is_t" falsevalue="a_value_that_is_f"  />
+            <when value="a_value_that_is_t">
+                <param name="integer_parameter" type="integer" value="1" />
+            </when>
+            <when value="a_value_that_is_f">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+        </conditional>
+    </inputs>
+    <tests>
+        <test>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_f" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_t" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="false" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_f" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_t" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="a_value_that_is_t" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_t" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="a_value_that_is_f" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_f" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="True" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_t" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="False" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a_value_that_is_f" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_boolean_optional.xml b/test/functional/tools/parameters/gx_conditional_boolean_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..69fa3d83049928b636a9031383059189a76d9c00
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_boolean_optional.xml
@@ -0,0 +1,79 @@
+<tool id="gx_conditional_boolean_optional" name="gx_conditional_boolean_optional" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="common_conditional_tags" />
+    <inputs>
+        <conditional name="conditional_parameter">
+            <!-- boolean parameters as the test parameter are discouraged, respect linting and don't do this -->
+            <param name="test_parameter" type="boolean" optional="true" />
+            <when value="true">
+                <param name="integer_parameter" type="integer" value="1" />
+            </when>
+            <when value="false">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+        </conditional>
+    </inputs>
+    <tests>
+        <test>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="null" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <!-- When it is a conditional test parameter - it doesn't respect the null. -->
+                <!-- These are discouraged strongly discouraged already - maybe disable for newer profile version. -->
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <!-- The disrespected null was interpreted as false though -->
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="false" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: false" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="false" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value_json="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: true" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="true" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_conditional_boolean.xml b/test/functional/tools/parameters/gx_conditional_conditional_boolean.xml
new file mode 100644
index 0000000000000000000000000000000000000000..343f3576cf6e2f35d26281ce5e4286492ac82f2a
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_conditional_boolean.xml
@@ -0,0 +1,30 @@
+<tool id="gx_conditional_conditional_boolean" name="gx_conditional_conditional_boolean" version="1.0.0">
+    <command><![CDATA[
+echo '$outer_conditional_parameter.outer_test_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <conditional name="outer_conditional_parameter">
+            <!-- boolean parameters as the test parameter are discouraged, respect linting and don't do this -->
+            <param name="outer_test_parameter" type="boolean" />
+            <when value="true">
+                <conditional name="inner_conditional_parameter">
+                    <param name="inner_test_parameter" type="boolean" />
+                    <when value="true">
+                        <param name="integer_parameter" type="integer" value="1" />
+                    </when>
+                    <when value="false">
+                        <param name="boolean_parameter" type="boolean" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="false">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_conditional_select.xml b/test/functional/tools/parameters/gx_conditional_select.xml
new file mode 100644
index 0000000000000000000000000000000000000000..51ab24b008b906c4c2a338d6b9c078c579193d47
--- /dev/null
+++ b/test/functional/tools/parameters/gx_conditional_select.xml
@@ -0,0 +1,85 @@
+<tool id="gx_conditional_select" name="gx_conditional_select" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="common_conditional_tags" />
+    <inputs>
+        <conditional name="conditional_parameter">
+            <param name="test_parameter" type="select">
+                <option value="a">A</option>
+                <option value="b">B</option>
+                <option value="c">C</option>
+            </param>
+            <when value="a">
+                <param name="integer_parameter" type="integer" value="1" />
+            </when>
+            <when value="b">
+                <param name="boolean_parameter" type="boolean" />
+            </when>
+            <when value="c">
+                <param name="color_parameter" type="color" value="#aabbcc" />
+            </when>
+        </conditional>
+    </inputs>
+    <tests>
+        <test>
+            <expand macro="assert_output">
+                <has_line line="test: a" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="&quot;a&quot;" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="b" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: b" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="&quot;b&quot;" />
+                <has_json_property_with_value property="boolean_parameter" value="false" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="a" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="&quot;a&quot;" />
+                <has_json_property_with_value property="integer_parameter" value="1" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="a" />
+                <param name="integer_parameter" value="4" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: a" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="&quot;a&quot;" />
+                <has_json_property_with_value property="integer_parameter" value="4" />
+            </expand>
+        </test>
+        <test>
+            <conditional name="conditional_parameter">
+                <param name="test_parameter" value="b" />
+                <param name="boolean_parameter" value="true" />
+            </conditional>
+            <expand macro="assert_output">
+                <has_line line="test: b" />
+            </expand>
+            <expand macro="assert_inputs_json">
+                <has_json_property_with_value property="test_parameter" value="&quot;b&quot;" />
+                <has_json_property_with_value property="boolean_parameter" value="true" />
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data.xml b/test/functional/tools/parameters/gx_data.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ea05c074c033b264c6430903c4b7a5d5eb6f5f14
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data.xml
@@ -0,0 +1,13 @@
+<tool id="gx_data" name="gx_data" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data" ext="data" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_collection.xml b/test/functional/tools/parameters/gx_data_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5669f2921f6464af7a97ff38d76f00de9f6555a5
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_collection.xml
@@ -0,0 +1,14 @@
+<tool id="gx_data_collection" name="gx_data_collection" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data_collection" ext="data" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+        <!-- TODO: -->
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_collection_optional.xml b/test/functional/tools/parameters/gx_data_collection_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9802176c4f76d0944a05c5539042a3b6950b3dac
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_collection_optional.xml
@@ -0,0 +1,14 @@
+<tool id="gx_data_collection_optional" name="gx_data_collection_optional" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data_collection" ext="data" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+        <!-- TODO: -->
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column.xml b/test/functional/tools/parameters/gx_data_column.xml
new file mode 100644
index 0000000000000000000000000000000000000000..19e44530caf3d63845467dd5bf18d50f05b66451
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column.xml
@@ -0,0 +1,36 @@
+<tool id="gx_data_column" name="gx_data_column" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="2" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 2"/>
+            </expand>
+        </test>
+        <!-- these parameters are implicitly optional -->
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_accept_default.xml b/test/functional/tools/parameters/gx_data_column_accept_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5b189f4ebda013168c445694609cfb391c7f06f8
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_accept_default.xml
@@ -0,0 +1,21 @@
+<tool id="gx_data_column_accept_default" name="gx_data_column_accept_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" accept_default="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_multiple.xml b/test/functional/tools/parameters/gx_data_column_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bd6b30a2a545cd325f9ca9868eaab9e48bd620f3
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_multiple.xml
@@ -0,0 +1,33 @@
+<tool id="gx_data_column_multiple" name="gx_data_column_multiple" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" multiple="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1,2,3" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2,3"/>
+            </expand>
+        </test>
+        <!-- these parameters are not implicitly optional! -->
+        <test expect_failure="true">
+            <param name="ref_parameter" value="2.tabular" />
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_multiple_accept_default.xml b/test/functional/tools/parameters/gx_data_column_multiple_accept_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..401d416668d2a860443fa0843c7b227d79d298f1
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_multiple_accept_default.xml
@@ -0,0 +1,21 @@
+<tool id="gx_data_column_multiple_accept_default" name="gx_data_column_multiple_accept_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" multiple="true" accept_default="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_multiple_optional.xml b/test/functional/tools/parameters/gx_data_column_multiple_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b9bb1fc0639cdaf3044430e991d6a5710d5cb6d9
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_multiple_optional.xml
@@ -0,0 +1,28 @@
+<tool id="gx_data_column_multiple_optional" name="gx_data_column_multiple_optional" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" multiple="true" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1,2,3" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2,3"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_multiple_optional_with_default.xml b/test/functional/tools/parameters/gx_data_column_multiple_optional_with_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0700e38a23a9692ca545d62fb093b18a6ebf2c28
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_multiple_optional_with_default.xml
@@ -0,0 +1,21 @@
+<tool id="gx_data_column_multiple_optional_with_default" name="gx_data_column_multiple_optional_with_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" multiple="true" optional="true" value="1, 2" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_multiple_with_default.xml b/test/functional/tools/parameters/gx_data_column_multiple_with_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fca81373d544147db38fc195fea6edfd640bfe3e
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_multiple_with_default.xml
@@ -0,0 +1,21 @@
+<tool id="gx_data_column_multiple_with_default" name="gx_data_column_multiple_with_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" multiple="true" value="1,2" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_optional.xml b/test/functional/tools/parameters/gx_data_column_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..604c2545bdc665886faede0413208039df39475c
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_optional.xml
@@ -0,0 +1,28 @@
+<tool id="gx_data_column_optional" name="gx_data_column_optional" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_optional_accept_default.xml b/test/functional/tools/parameters/gx_data_column_optional_accept_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..be893d34337fba598ffedfb0f68b899ab1625787
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_optional_accept_default.xml
@@ -0,0 +1,21 @@
+<tool id="gx_data_column_optional_accept_default" name="gx_data_column_optional_accept_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" optional="true" accept_default="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_with_default.xml b/test/functional/tools/parameters/gx_data_column_with_default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..126c4dfc8ec18b59f2182e62cd23606ab0af1d3b
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_with_default.xml
@@ -0,0 +1,22 @@
+<tool id="gx_data_column_with_default" name="gx_data_column_with_default" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" value="2" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- these parameters are implicitly optional -->
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 2"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_column_with_default_legacy.xml b/test/functional/tools/parameters/gx_data_column_with_default_legacy.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b77b546add50566a445682705ea5a86ec362501c
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_column_with_default_legacy.xml
@@ -0,0 +1,22 @@
+<tool id="gx_data_column_with_default_legacy" name="gx_data_column_with_default_legacy" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" default_value="3" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- these parameters are implicitly optional -->
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 3"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_multiple.xml b/test/functional/tools/parameters/gx_data_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8529f2c7cac98b9b4f103fe3c585ca5c0b3060f8
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_multiple.xml
@@ -0,0 +1,13 @@
+<tool id="gx_data_multiple" name="gx_data_multiple" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data" ext="data" multiple="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_multiple_optional.xml b/test/functional/tools/parameters/gx_data_multiple_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..01b63bd83692b52f6e0fbf9768f2efff88a572e5
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_multiple_optional.xml
@@ -0,0 +1,13 @@
+<tool id="gx_data_multiple_optional" name="gx_data_multiple_optional" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data" ext="data" multiple="true" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_data_optional.xml b/test/functional/tools/parameters/gx_data_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3578d4e436e75cdd1067e04128d60271b0d46839
--- /dev/null
+++ b/test/functional/tools/parameters/gx_data_optional.xml
@@ -0,0 +1,13 @@
+<tool id="gx_data_optional" name="gx_data_optional" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="data" ext="data" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_directory_uri.xml b/test/functional/tools/parameters/gx_directory_uri.xml
new file mode 100644
index 0000000000000000000000000000000000000000..49ed4f98af853d9518c2677c341718cbcdc26612
--- /dev/null
+++ b/test/functional/tools/parameters/gx_directory_uri.xml
@@ -0,0 +1,12 @@
+<tool id="gx_directory_uri" name="gx_directory_uri" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+        echo 'parameter: $parameter' > $output
+    ]]></command>
+    <inputs>
+        <param type="directory_uri" name="parameter" />
+    </inputs>
+    <expand macro="simple_text_output" />
+</tool>
diff --git a/test/functional/tools/parameters/gx_directory_uri_validation.xml b/test/functional/tools/parameters/gx_directory_uri_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7375c298b7111623841a5751a6d23c6ced7f3222
--- /dev/null
+++ b/test/functional/tools/parameters/gx_directory_uri_validation.xml
@@ -0,0 +1,16 @@
+<tool id="gx_directory_uri" name="gx_directory_uri" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+        echo 'parameter: $parameter' > $output
+    ]]></command>
+    <inputs>
+        <param type="directory_uri" name="parameter">
+            <validator type="length" min="10" max="45" />
+            <validator type="expression">'api' in value</validator>
+            <validator type="regex">^.*json$</validator>
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_code.py b/test/functional/tools/parameters/gx_drill_down_code.py
new file mode 100644
index 0000000000000000000000000000000000000000..518cb67c6a7e46afe767c5ac2930900a5260b50a
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_code.py
@@ -0,0 +1,24 @@
+def collate_table(path: str) -> list:
+    with open(path, "r") as f:
+        contents = f.read()
+    first_options = []
+    second_options = []
+    values = [
+        {"name": "First Column", "value": "first", "selected": False, "options": first_options},
+        {"name": "Second Column", "value": "second", "selected": False, "options": second_options},
+    ]
+    seen_in_column_1 = set()
+    seen_in_column_2 = set()
+    for line in contents.splitlines():
+        parts = line.split("\t")
+        if len(parts) >= 1:
+            val = parts[0]
+            if val not in seen_in_column_1:
+                first_options.append({"name": val.upper(), "value": val, "selected": False, "options": []})
+                seen_in_column_1.add(val)
+        if len(parts) >= 2:
+            val = parts[1]
+            if val not in seen_in_column_2:
+                second_options.append({"name": val.upper(), "value": val, "selected": False, "options": []})
+                seen_in_column_2.add(val)
+    return values
diff --git a/test/functional/tools/parameters/gx_drill_down_code.xml b/test/functional/tools/parameters/gx_drill_down_code.xml
new file mode 100644
index 0000000000000000000000000000000000000000..42ae442574e4deac46f2bf6beaff8a2a26f85fe3
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_code.xml
@@ -0,0 +1,38 @@
+<tool id="gx_drill_down_code" name="gx_drill_down_code" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <code file="gx_drill_down_code.py"/>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" ext="tabular" >
+        </param>
+g        <param name="parameter" type="drill_down" dynamic_options="collate_table(ref_parameter.dataset.get_file_name())">
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="1.tabular" />
+            <param name="parameter" value="chr22" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="parameter: chr22" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="ref_parameter" value="1.tabular" />
+            <param name="parameter" value="2000" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="parameter: 2000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_exact.xml b/test/functional/tools/parameters/gx_drill_down_exact.xml
new file mode 100644
index 0000000000000000000000000000000000000000..42603cc7c4c9155fb53a13023572aaf604f0cc92
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_exact.xml
@@ -0,0 +1,35 @@
+<tool id="gx_drill_down_exact" name="gx_drill_down_exact" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <!-- default drill_down, i.e. hierarchy="exact"
+            - select exacty the chosen values
+            - "inner" option nodes (non-leaves) are selectable
+        -->
+        <param name="parameter" type="drill_down" hierarchy="exact">
+            <expand macro="drill_down_static_options" />
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- select options from different levels of tree -->
+        <test>
+            <param name="parameter" value="a"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: a"/>
+            </expand>
+        </test>
+        <test>
+            <param name="parameter" value="ab"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: ab"/>
+            </expand>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_exact_multiple.xml b/test/functional/tools/parameters/gx_drill_down_exact_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..303a81089d4b0a670e7f25ae29b9ee245405ce5a
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_exact_multiple.xml
@@ -0,0 +1,35 @@
+<tool id="gx_drill_down_exact_multiple" name="gx_drill_down_exact_multiple" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <!-- default drill_down, i.e. hierarchy="exact"
+            - select exacty the chosen values
+            - "inner" option nodes (non-leaves) are selectable
+        -->
+        <param name="parameter" type="drill_down" hierarchy="exact" multiple="true">
+            <expand macro="drill_down_static_options" />
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- select options from different levels of tree -->
+        <test>
+            <param name="parameter" value="a"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: a"/>
+            </expand>
+        </test>
+        <test>
+            <param name="parameter" value="a,ab"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: a,ab"/>
+            </expand>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_exact_with_selection.xml b/test/functional/tools/parameters/gx_drill_down_exact_with_selection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7e6bb9364e1b0fa547a42c1ae3e453a8745f8626
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_exact_with_selection.xml
@@ -0,0 +1,57 @@
+<tool id="gx_drill_down_exact_with_selection" name="gx_drill_down_exact_with_selection" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <!-- default drill_down, i.e. hierarchy="exact"
+            - select exacty the chosen values
+            - "inner" option nodes (non-leaves) are selectable
+        -->
+        <param name="parameter" type="drill_down" hierarchy="exact">
+            <!-- same as gx_drill_down_exact except one of these is selected="true" -->
+            <options>
+                <option name="a" value="a">
+                    <option name="aa" value="aa"/>
+                    <option name="ab" value="ab">
+                        <option name="aba" value="aba" selected="true" />
+                        <option name="abb" value="abb"/>
+                    </option>
+                </option>
+                <option name="b" value="b">
+                    <option name="ba" value="ba"/>
+                    <option name="bb" value="bb">
+                        <option name="bba" value="bba"/>
+                        <option name="bbb" value="bbb"/>
+                    </option>
+                </option>
+            </options>
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- select options from different levels of tree -->
+        <test>
+            <param name="parameter" value="a"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: a"/>
+            </expand>
+        </test>
+        <test>
+            <param name="parameter" value="ab"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: ab"/>
+            </expand>
+        </test>
+        <test>
+            <!-- one is selected by default so we don't need to set it here -->
+            <expand macro="assert_output">
+                <has_line line="parameter: aba"/>
+            </expand>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_recurse.xml b/test/functional/tools/parameters/gx_drill_down_recurse.xml
new file mode 100644
index 0000000000000000000000000000000000000000..561bc04a955f6fa4044abaa11b286d08c85cf17d
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_recurse.xml
@@ -0,0 +1,32 @@
+<tool id="gx_drill_down_recurse" name="gx_drill_down_recurse" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="drill_down" hierarchy="recurse">
+            <expand macro="drill_down_static_options" />
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="parameter" value="bba"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: bba"/>
+            </expand>
+        </test>
+        <!-- recurse only works properly with multiple=true...
+        <test>
+            <param name="parameter" value="ab"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: aba,abb"/>
+            </expand>
+        </test>
+        -->
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_drill_down_recurse_multiple.xml b/test/functional/tools/parameters/gx_drill_down_recurse_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..22224f92312df1f22768ab11486df88a2caa279f
--- /dev/null
+++ b/test/functional/tools/parameters/gx_drill_down_recurse_multiple.xml
@@ -0,0 +1,35 @@
+<tool id="gx_drill_down_recurse_multiple" name="gx_drill_down_recurse_multiple" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <!-- default drill_down, i.e. hierarchy="exact"
+            - select exacty the chosen values
+            - "inner" option nodes (non-leaves) are selectable
+        -->
+        <param name="parameter" type="drill_down" hierarchy="recurse" multiple="true">
+            <expand macro="drill_down_static_options" />
+        </param>
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <!-- select options from different levels of tree -->
+        <test>
+            <param name="parameter" value="ab"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: aba,abb"/>
+            </expand>
+        </test>
+        <test>
+            <param name="parameter" value="aa,bb"/>
+            <expand macro="assert_output">
+                <has_line line="parameter: aa,bba,bbb"/>
+            </expand>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/parameters/gx_float.xml b/test/functional/tools/parameters/gx_float.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5da8bc9790b959f4034c352547562f11c1321c75
--- /dev/null
+++ b/test/functional/tools/parameters/gx_float.xml
@@ -0,0 +1,29 @@
+<tool id="gx_float" name="gx_float" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1.0" type="float" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value_json="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456.0" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456.0" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_float_min_max.xml b/test/functional/tools/parameters/gx_float_min_max.xml
new file mode 100644
index 0000000000000000000000000000000000000000..55a4d6fb0881f00d785407cfde57043130c23252
--- /dev/null
+++ b/test/functional/tools/parameters/gx_float_min_max.xml
@@ -0,0 +1,14 @@
+<tool id="gx_float_validation_range" name="gx_float_validation_range" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="float" min="0.1" max="9.8">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_float_optional.xml b/test/functional/tools/parameters/gx_float_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7d2ad2be396ef9d0ba410861ae2e494f952b8cad
--- /dev/null
+++ b/test/functional/tools/parameters/gx_float_optional.xml
@@ -0,0 +1,29 @@
+<tool id="gx_float_optional" name="gx_float_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="float" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value_json="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456.0" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456.0" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_float_validation_range.xml b/test/functional/tools/parameters/gx_float_validation_range.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8988e92506dfecedab4e5e9ade2b1c216f7cb89f
--- /dev/null
+++ b/test/functional/tools/parameters/gx_float_validation_range.xml
@@ -0,0 +1,15 @@
+<tool id="gx_float_validation_range" name="gx_float_validation_range" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="float">
+            <validator type="in_range" min="0.1" max="9.8" exclude_min="false" exclude_max="true" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_genomebuild.xml b/test/functional/tools/parameters/gx_genomebuild.xml
new file mode 100644
index 0000000000000000000000000000000000000000..516eb6efeca9302b7fb838301e72d6b9f9a3c61c
--- /dev/null
+++ b/test/functional/tools/parameters/gx_genomebuild.xml
@@ -0,0 +1,29 @@
+<tool id="gx_genomebuild" name="gx_genomebuild" version="1.0.0">
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="genomebuild">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="hg19" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="parameter: hg19" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="parameter: ?" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_genomebuild_multiple.xml b/test/functional/tools/parameters/gx_genomebuild_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c70e712ee2dbef1fe9f03b047d29df49dad0f735
--- /dev/null
+++ b/test/functional/tools/parameters/gx_genomebuild_multiple.xml
@@ -0,0 +1,29 @@
+<tool id="gx_genomebuild_multiple" name="gx_genomebuild_multiple" version="1.0.0">
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="genomebuild" multiple="true">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="hg19,hg18" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="parameter: hg19,hg18" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="parameter: None" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_genomebuild_optional.xml b/test/functional/tools/parameters/gx_genomebuild_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bffe9d9ff3632d57df62ee4a7143929b10fe5152
--- /dev/null
+++ b/test/functional/tools/parameters/gx_genomebuild_optional.xml
@@ -0,0 +1,29 @@
+<tool id="gx_genomebuild_optional" name="gx_genomebuild_optional" version="1.0.0">
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="genomebuild" optional="true">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="hg19" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="parameter: hg19" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="parameter: None" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_group_tag.xml b/test/functional/tools/parameters/gx_group_tag.xml
new file mode 100644
index 0000000000000000000000000000000000000000..90dd50e6ae03c2fff61a3cd99fd96b3cc30d6bc0
--- /dev/null
+++ b/test/functional/tools/parameters/gx_group_tag.xml
@@ -0,0 +1,27 @@
+<tool id="gx_group_tag" name="gx_group_tag" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_group_tag_multiple.xml b/test/functional/tools/parameters/gx_group_tag_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d26bf14b16b7216ee24f86e156e679e9159994d1
--- /dev/null
+++ b/test/functional/tools/parameters/gx_group_tag_multiple.xml
@@ -0,0 +1,39 @@
+<tool id="gx_group_tag_multiple" name="gx_group_tag_multiple" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" multiple="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single,type:split" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single,type:split"/>
+            </expand>
+        </test>
+        <test expect_failure="true">
+            <!-- interesting... this fails here but multi-selects don't -->
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_group_tag_optional.xml b/test/functional/tools/parameters/gx_group_tag_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9f06c3234f0033bea574c7e7447e882233624833
--- /dev/null
+++ b/test/functional/tools/parameters/gx_group_tag_optional.xml
@@ -0,0 +1,38 @@
+<tool id="gx_group_tag_optional" name="gx_group_tag_optional" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo "parameter: $parameter" > '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_hidden.xml b/test/functional/tools/parameters/gx_hidden.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e6da3bfb927982e3362d3e67f7c71bb53785b4ca
--- /dev/null
+++ b/test/functional/tools/parameters/gx_hidden.xml
@@ -0,0 +1,21 @@
+<tool id="gx_hidden" name="gx_hidden" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="hidden" value="moo" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_hidden_optional.xml b/test/functional/tools/parameters/gx_hidden_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e3969f2a8074952d5b858fc5d33643039a091908
--- /dev/null
+++ b/test/functional/tools/parameters/gx_hidden_optional.xml
@@ -0,0 +1,21 @@
+<tool id="gx_hidden_optional" name="gx_hidden_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="hidden" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_hidden_validation.xml b/test/functional/tools/parameters/gx_hidden_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e40a67aae964d06a0da8fbc3145f48abfc5bec50
--- /dev/null
+++ b/test/functional/tools/parameters/gx_hidden_validation.xml
@@ -0,0 +1,17 @@
+<tool id="gx_hidden_validation" name="gx_hidden_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="hidden" value="http://mycoolsource/api/index.json">
+            <validator type="length" min="10" max="45" />
+            <validator type="expression">'api' in value</validator>
+            <validator type="regex">^.*json$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int.xml b/test/functional/tools/parameters/gx_int.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e6f2e6758d26eb4f40156c06320d8ee46d86aee8
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int.xml
@@ -0,0 +1,29 @@
+<tool id="gx_int" name="gx_int" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value_json="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int_min_max.xml b/test/functional/tools/parameters/gx_int_min_max.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c826948d746caaff41930ca02594c0a94feef16c
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int_min_max.xml
@@ -0,0 +1,14 @@
+<tool id="gx_int_min_max" name="gx_int_min_max" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer" min="0" max="10">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int_optional.xml b/test/functional/tools/parameters/gx_int_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..39e985dae6091b3ed00790d5193bd54d8a7c9fea
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int_optional.xml
@@ -0,0 +1,21 @@
+<tool id="gx_int_optional" name="gx_int_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value_json="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int_required.xml b/test/functional/tools/parameters/gx_int_required.xml
new file mode 100644
index 0000000000000000000000000000000000000000..05a22fc2f3db70cb49861c0cd0b533df53907e37
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int_required.xml
@@ -0,0 +1,11 @@
+<tool id="gx_int_required" name="gx_int_required" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int_required_via_empty_string.xml b/test/functional/tools/parameters/gx_int_required_via_empty_string.xml
new file mode 100644
index 0000000000000000000000000000000000000000..26e76cb46e916638c6fe6960ccc5cf9a9156349d
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int_required_via_empty_string.xml
@@ -0,0 +1,12 @@
+<tool id="gx_int_required_via_empty_string" name="gx_int_required_via_empty_string" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <!-- https://github.com/galaxyproject/galaxy/pull/16966/files -->
+        <param name="parameter" value="" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/parameters/gx_int_validation_range.xml b/test/functional/tools/parameters/gx_int_validation_range.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5f7862497abf6c9e6ca3a92871175f17457b0d4b
--- /dev/null
+++ b/test/functional/tools/parameters/gx_int_validation_range.xml
@@ -0,0 +1,15 @@
+<tool id="gx_int_validation_range" name="gx_int_validation_range" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer">
+            <validator type="in_range" min="0" max="10" exclude_min="false" exclude_max="true" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_repeat_boolean.xml b/test/functional/tools/parameters/gx_repeat_boolean.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c57ba06b4838843abd6b742b104dc09fab1ab286
--- /dev/null
+++ b/test/functional/tools/parameters/gx_repeat_boolean.xml
@@ -0,0 +1,15 @@
+<tool id="gx_repeat_boolean" name="gx_repeat_boolean" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter[0].boolean_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <repeat name="parameter" title="Repeat Parameter">
+            <param name="boolean_parameter" type="boolean" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_repeat_boolean_min.xml b/test/functional/tools/parameters/gx_repeat_boolean_min.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ac30097e095de1ae54d500a7257f31ca01e4032e
--- /dev/null
+++ b/test/functional/tools/parameters/gx_repeat_boolean_min.xml
@@ -0,0 +1,25 @@
+<tool id="gx_repeat_boolean_min" name="gx_repeat_boolean_min" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter[0].boolean_parameter' >> '$output'
+#set $repeat_length = len($parameter)
+echo 'length: $repeat_length' >> '$output'
+    ]]></command>
+    <inputs>
+        <repeat name="parameter" title="Repeat Parameter" min="2">
+            <param name="boolean_parameter" type="boolean" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="false" />
+                    <has_text text="length: 2" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_repeat_data.xml b/test/functional/tools/parameters/gx_repeat_data.xml
new file mode 100644
index 0000000000000000000000000000000000000000..646a31eb48c4fffb9ab3649f8810cfa9ca390acb
--- /dev/null
+++ b/test/functional/tools/parameters/gx_repeat_data.xml
@@ -0,0 +1,21 @@
+<tool id="gx_repeat_data" name="gx_repeat_data" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter[0].data_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <repeat name="parameter" title="Repeat Parameter">
+            <param name="data_parameter" type="data" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="parameter">
+                <param name="data_parameter" value="1.bed" />
+            </repeat>
+            <output name="out_file1" file="1.bed" />
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_repeat_data_min.xml b/test/functional/tools/parameters/gx_repeat_data_min.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1d584ad870ac7b21a046af610726f87e7730c29d
--- /dev/null
+++ b/test/functional/tools/parameters/gx_repeat_data_min.xml
@@ -0,0 +1,24 @@
+<tool id="gx_repeat_data_min" name="gx_repeat_data_min" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter[0].data_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <repeat name="parameter" title="Repeat Parameter" min="2">
+            <param name="data_parameter" type="data" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="parameter">
+                <param name="data_parameter" value="1.bed" />
+            </repeat>
+            <repeat name="parameter">
+                <param name="data_parameter" value="1.bed" />
+            </repeat>
+            <output name="out_file1" file="1.bed" />
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_section_boolean.xml b/test/functional/tools/parameters/gx_section_boolean.xml
new file mode 100644
index 0000000000000000000000000000000000000000..af948dd3276f2d67314d08e3089adcbe98679b76
--- /dev/null
+++ b/test/functional/tools/parameters/gx_section_boolean.xml
@@ -0,0 +1,35 @@
+<tool id="gx_section_boolean" name="gx_section_boolean" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter.boolean_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <section name="parameter">
+            <param name="boolean_parameter" type="boolean" truevalue="mytrue" falsevalue="myfalse" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <section name="parameter">
+                <param name="boolean_parameter" value="true" />
+            </section>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="mytrue" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <section name="parameter">
+                <param name="boolean_parameter" value="false" />
+            </section>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="myfalse" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_section_data.xml b/test/functional/tools/parameters/gx_section_data.xml
new file mode 100644
index 0000000000000000000000000000000000000000..76e0e5734c16128d6c88e0755a0c77b05dc229b8
--- /dev/null
+++ b/test/functional/tools/parameters/gx_section_data.xml
@@ -0,0 +1,21 @@
+<tool id="gx_section_data" name="gx_section_data" version="1.0.0">
+    <command><![CDATA[
+cat '$parameter.data_parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <section name="parameter">
+            <param name="data_parameter" type="data" ext="data" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <section name="parameter">
+                <param name="data_parameter" value="1.bed" />
+            </section>
+            <output name="out_file1" file="1.bed" />
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select.xml b/test/functional/tools/parameters/gx_select.xml
new file mode 100644
index 0000000000000000000000000000000000000000..90833398af3c096b659840cdc579d0f4bda686b9
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select.xml
@@ -0,0 +1,37 @@
+<tool id="gx_select" name="gx_select" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="ex2" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="ex2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- Selects implicitly default to the first option as the default option.
+	             Additional verification in test_select_first_by_default API test in test_tools.py.
+            -->
+            <output name="output">
+                <assert_contents>
+                    <has_line line="--ex1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_dynamic.xml b/test/functional/tools/parameters/gx_select_dynamic.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8959f3d0e3d4788397c4411833407ba97b7738ff
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_dynamic.xml
@@ -0,0 +1,36 @@
+<tool id="gx_select_dynamic" name="gx_select_dynamic" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <code file="gx_select_dynamic_options.py"/>
+    <inputs>
+        <param name="ref_parameter" type="data" ext="txt" >
+        </param>
+        <param name="parameter" type="select" dynamic_options="every_other_word(ref_parameter.dataset.get_file_name())">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="ref_parameter" value="simple_line.txt" />
+            <param name="parameter" value="of" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="of" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- Selects implicitly default to the first option as the default option.
+            -->
+            <param name="ref_parameter" value="simple_line.txt" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="This" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_dynamic_empty.py b/test/functional/tools/parameters/gx_select_dynamic_empty.py
new file mode 100644
index 0000000000000000000000000000000000000000..6a79a047f3cb97fe4e4956bc7c6ad2ac7efda762
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_dynamic_empty.py
@@ -0,0 +1,8 @@
+from typing import (
+    List,
+    Tuple,
+)
+
+
+def empty_list() -> List[Tuple[str, str, bool]]:
+    return []
diff --git a/test/functional/tools/parameters/gx_select_dynamic_empty.xml b/test/functional/tools/parameters/gx_select_dynamic_empty.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7554604033fdc65499037142ad77ad6424ab813c
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_dynamic_empty.xml
@@ -0,0 +1,15 @@
+<tool id="gx_select_dynamic_empty" name="gx_select_dynamic_empty" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <code file="gx_select_dynamic_empty.py"/>
+    <inputs>
+        <param name="parameter" type="select" dynamic_options="empty_list()">
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_dynamic_empty_validated.xml b/test/functional/tools/parameters/gx_select_dynamic_empty_validated.xml
new file mode 100644
index 0000000000000000000000000000000000000000..39ffa263174eadb39ef8024afe38fcf4ef14a7ed
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_dynamic_empty_validated.xml
@@ -0,0 +1,16 @@
+<tool id="gx_select_dynamic_empty_validated" name="gx_select_dynamic_empty_validated" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <code file="gx_select_dynamic_empty.py"/>
+    <inputs>
+        <param name="parameter" type="select" dynamic_options="empty_list()">
+            <validator type="no_options" message="this is the empty message" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_dynamic_options.py b/test/functional/tools/parameters/gx_select_dynamic_options.py
new file mode 100644
index 0000000000000000000000000000000000000000..734174b6da1d781da67068b58a907260b78e4066
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_dynamic_options.py
@@ -0,0 +1,10 @@
+from typing import (
+    List,
+    Tuple,
+)
+
+
+def every_other_word(path: str) -> List[Tuple[str, str, bool]]:
+    with open(path, "r") as f:
+        contents = f.read()
+    return [(r.strip(), r.strip(), False) for (i, r) in enumerate(contents.split()) if i % 2 == 0]
diff --git a/test/functional/tools/parameters/gx_select_multiple.xml b/test/functional/tools/parameters/gx_select_multiple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..593b4187fc2ed93bf9bb77719e203d01fde97395
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_multiple.xml
@@ -0,0 +1,35 @@
+<tool id="gx_select_multiple" name="gx_select_multiple" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" multiple="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="ex2" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="ex2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- these parameters are not implicitly optional and don't select top option -->
+            <output name="output">
+                <assert_contents>
+                    <has_line line="None" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_multiple_optional.xml b/test/functional/tools/parameters/gx_select_multiple_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..22ac9259b061d06f213f70d2578054960a6c5da0
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_multiple_optional.xml
@@ -0,0 +1,34 @@
+<tool id="gx_select_multiple_optional" name="gx_select_multiple_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" multiple="true" optional="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="ex2" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="ex2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="None" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_no_options_validation.xml b/test/functional/tools/parameters/gx_select_no_options_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..217b95b5363988f07e45ab70408fd5762996c029
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_no_options_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_select_no_options_validation" name="gx_select_no_options_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+            <validator type="no_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_optional.xml b/test/functional/tools/parameters/gx_select_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..03fc045dba2a78df0524e29a7451c4811c37fad8
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_optional.xml
@@ -0,0 +1,34 @@
+<tool id="gx_select_optional" name="gx_select_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" optional="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="ex2" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="ex2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="None" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_optional_no_options_validation.xml b/test/functional/tools/parameters/gx_select_optional_no_options_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6e3e78de040072badcca488fc3cac14b154cdca2
--- /dev/null
+++ b/test/functional/tools/parameters/gx_select_optional_no_options_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_select_optional_no_options_validation" name="gx_select_optional_no_options_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" optional="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+            <validator type="no_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text.xml b/test/functional/tools/parameters/gx_text.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3b9e2e00dfbc58b64e77dc6920a86edbac2c727e
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text.xml
@@ -0,0 +1,26 @@
+<tool id="gx_text" name="gx_text" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_empty_validation.xml b/test/functional/tools/parameters/gx_text_empty_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..76374be72ded22715ff52d70aec063607477a2de
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_empty_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_text_empty_validation" name="gx_text_empty_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="empty_field" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_expression_validation.xml b/test/functional/tools/parameters/gx_text_expression_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fe5113ec8fefe321d24a4d8bb65ebbbf7289994e
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_expression_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_text_expression_validation" name="gx_text_expression_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="expression">'foobar' in value</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_length_validation.xml b/test/functional/tools/parameters/gx_text_length_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4d5434aa6c583aa2524f0c6546370055763a6166
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_length_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_text_length_validation" name="gx_text_length_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="length" min="2" max="10" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_length_validation_negate.xml b/test/functional/tools/parameters/gx_text_length_validation_negate.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4b0b835fe562bee4d3f7dc408ecfa389c4d28d6b
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_length_validation_negate.xml
@@ -0,0 +1,20 @@
+<tool id="gx_text_length_validation" name="gx_text_length_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="length" min="2" max="10" negate="true" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_optional.xml b/test/functional/tools/parameters/gx_text_optional.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ae10d327837681bebc3b612ec10282175797f93a
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_optional.xml
@@ -0,0 +1,26 @@
+<tool id="gx_text_optional" name="gx_text_optional" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="12456" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="12456" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_optional_false.xml b/test/functional/tools/parameters/gx_text_optional_false.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9e29d53fc4cada97d2953ff7e6775cff1ad0069e
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_optional_false.xml
@@ -0,0 +1,18 @@
+<tool id="gx_text_optional_false" name="gx_text_optional_false" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text" optional="false" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_text_regex_validation.xml b/test/functional/tools/parameters/gx_text_regex_validation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..2e1bd7325d8a98137ec02a88037d2dceebe70e3d
--- /dev/null
+++ b/test/functional/tools/parameters/gx_text_regex_validation.xml
@@ -0,0 +1,20 @@
+<tool id="gx_text_regex_validation" name="gx_text_regex_validation" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output';
+cat '$inputs' >> $inputs_json;
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <inputs>
+        <param name="parameter" type="text">
+            <validator type="regex">^[actg]*$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/macros.xml b/test/functional/tools/parameters/macros.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7b00d8004b34024c37e4197d6169000c09c33d71
--- /dev/null
+++ b/test/functional/tools/parameters/macros.xml
@@ -0,0 +1,56 @@
+<macros>
+  <xml name="simple_text_output">
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+  </xml>
+  <xml name="common_conditional_tags">
+    <command><![CDATA[
+echo 'test: $conditional_parameter.test_parameter' >> '$output';
+cat '$inputs' >> '$inputs_json';
+    ]]></command>
+    <configfiles>
+        <inputs name="inputs" filename="inputs.json" />
+    </configfiles>
+    <outputs>
+        <data name="output" format="txt" />
+        <data name="inputs_json" format="json" />
+    </outputs>
+    <help>
+        This is a test tool used to establish and verify the behavior of some aspect of Galaxy's
+        parameter handling.
+    </help>
+  </xml>
+  <xml name="assert_output">
+    <output name="output">
+        <assert_contents>
+            <yield />
+        </assert_contents>
+    </output>
+  </xml>
+  <xml name="assert_inputs_json">
+    <output name="inputs_json">
+        <assert_contents>
+            <yield />
+        </assert_contents>
+    </output>
+  </xml>
+  <xml name="drill_down_static_options">
+    <options>
+        <option name="a" value="a">
+            <option name="aa" value="aa"/>
+            <option name="ab" value="ab">
+                <option name="aba" value="aba"/>
+                <option name="abb" value="abb"/>
+            </option>
+        </option>
+        <option name="b" value="b">
+            <option name="ba" value="ba"/>
+            <option name="bb" value="bb">
+                <option name="bba" value="bba"/>
+                <option name="bbb" value="bbb"/>
+            </option>
+        </option>
+    </options>
+  </xml>
+</macros>
diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml
index e61be45f2e3aa285f2c29a9c5471d5c2188b4c64..534d35122ec96b719c810b1c9f1e3978779b2e15 100644
--- a/test/functional/tools/sample_datatypes_conf.xml
+++ b/test/functional/tools/sample_datatypes_conf.xml
@@ -48,6 +48,7 @@
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true" />
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true"/>
     <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
+    <datatype extension="expression.json" type="galaxy.datatypes.text:ExpressionJson" display_in_upload="true"/>
     <datatype extension="data_manager_json" type="galaxy.datatypes.text:DataManagerJson" mimetype="application/json" subclass="true" display_in_upload="false"/>
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" />
@@ -59,6 +60,7 @@
     </datatype>
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
+    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>
     <datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
   </registration>
 </datatypes>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 45eee3cc16c908d49cfb11c1c004c66a41b78409..dbae7b26ce3777e79ea73145262e8cefe78b478b 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -24,6 +24,8 @@
   <tool file="multi_repeats.xml" />
   <tool file="remove_value.xml" />
   <tool file="bibtex.xml" />
+  <tool file="help_features_rst.xml" />
+  <tool file="help_features_markdown.xml" />
   <tool file="select_from_url.xml" />
   <tool file="multi_select.xml" />
   <tool file="multi_output.xml" />
@@ -137,6 +139,7 @@
   <tool file="column_param_configfile.xml" />
   <tool file="column_param_list.xml" />
   <tool file="column_multi_param.xml" />
+  <tool file="select_optional_legacy.xml" />
   <tool file="select_optional.xml" />
   <tool file="select_dynamic.xml" />
   <tool file="hidden_param.xml" />
@@ -145,7 +148,7 @@
   <tool file="sam_to_unsorted_bam.xml" />
   <tool file="top_level_data.xml" />
   <tool file="validation_hdf5.xml" />
-  <tool file="validation_image.xml"/>
+  <tool file="validation_image.xml" />
   <tool file="validation_zip.xml" />
   <tool file="validation_tar.xml" />
   <tool file="validation_tar_gz.xml" />
@@ -176,6 +179,7 @@
   <tool file="identifier_in_actions.xml" />
   <tool file="fail_identifier.xml" />
   <tool file="fail_writing_work_dir_file.xml" />
+  <tool file="legacy_interpreter.xml" />
   <tool file="tool_directory.xml" />
   <tool file="tool_directory_docker.xml" />
   <tool file="output_action_change_format.xml" />
@@ -227,6 +231,7 @@
   <tool file="expect_num_outputs.xml" />
   <tool file="text_repeat.xml" />
   <tool file="integer_default.xml" />
+  <tool file="float_default.xml" />
   <tool file="all_output_types.xml" />
   <tool file="multiple_versions_v01.xml" />
   <tool file="multiple_versions_v01galaxy6.xml" />
@@ -239,10 +244,12 @@
 
   <tool file="multiple_versions_changes_v01.xml" />
   <tool file="multiple_versions_changes_v02.xml" />
+  <tool file="html_output.xml" />
 
   <tool file="interactivetool_simple.xml" />
   <tool file="interactivetool_two_entry_points.xml" />
   <tool file="converter_target_datatype.xml" />
+  <tool file="tool_directory_copy.xml" />
 
   <!-- Tools interesting only for building up test workflows. -->
 
@@ -265,6 +272,10 @@
   <tool file="for_workflows/count_multi_file.xml" />
   <tool file="for_workflows/create_input_collection.xml" />
   <tool file="for_workflows/randomlines.xml" />
+  <tool file="create_directory_index.xml" />
+  <tool file="use_directory_index.xml" />
+
+  <tool_dir dir="parameters/" />
 
   <section id="filter" name="For Tours">
     <tool file="for_tours/filtering.xml" />
@@ -297,6 +308,7 @@
   <tool file="${model_tools_path}/filter_failed_collection.xml" />
   <tool file="${model_tools_path}/keep_success_collection.xml" />
   <tool file="${model_tools_path}/filter_empty_collection.xml" />
+  <tool file="${model_tools_path}/filter_null.xml" />
   <tool file="${model_tools_path}/flatten_collection.xml" />
   <tool file="${model_tools_path}/sort_collection_list.xml" />
   <tool file="${model_tools_path}/harmonize_two_collections_list.xml" />
diff --git a/test/functional/tools/section_24_2.xml b/test/functional/tools/section_24_2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ec62f0fd8ee9952b8cbe99cb6fd9a4ff00711c22
--- /dev/null
+++ b/test/functional/tools/section_24_2.xml
@@ -0,0 +1,43 @@
+<tool id="section_24_2" name="section_24_2" version="1.0.0" profile="24.2">
+    <command><![CDATA[
+echo $int.inttest > '$out_file1' &&
+echo $float.floattest >> '$out_file1'
+    ]]></command>
+    <inputs>
+        <section name="int" title="Integer Section" expanded="true">
+            <param name="inttest" value="1" type="integer" />
+        </section>
+        <section name="float" title="Float Section" expanded="false">
+            <param name="floattest" value="1.0" type="float" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="int|inttest" value="12456" />
+            <param name="float|floattest" value="6.789" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <section name="int">
+                <param name="inttest" value="12456" />
+            </section>
+            <section name="float">
+                <param name="floattest" value="6.789" />
+            </section>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/select_from_url.xml b/test/functional/tools/select_from_url.xml
index 60a712e7463108138343d1e6d2b3799ba650a8b4..81aced1695d423f135f9151509b5a342acb26c4d 100644
--- a/test/functional/tools/select_from_url.xml
+++ b/test/functional/tools/select_from_url.xml
@@ -7,8 +7,14 @@ echo '$url_param_value_header_and_body' > '$param_value_header_and_body'
     ]]></command>
     <inputs>
         <param name="url_param_value" type="select">
-            <options from_url="https://usegalaxy.org/api/genomes">
+            <options from_url="https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/refs/heads/master/genomes.json"></options>
+        </param>
+        <param name="dynamic_param_filtered_with_validator" type="select">
+            <!-- tested in test_build_module_filter_dynamic_select -->
+            <options from_url="https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/refs/heads/master/genomes.json">
+                <filter type="param_value" ref="url_param_value" column="1" />
             </options>
+            <validator type="no_options" message="Need at least one option here" />
         </param>
         <!--
         <param name="url_param_value_templated" type="select">
@@ -17,14 +23,14 @@ echo '$url_param_value_header_and_body' > '$param_value_header_and_body'
         </param>
         -->
         <param name="url_param_value_postprocessed" type="select">
-            <options from_url="https://usegalaxy.org/api/genomes/dm6">
+            <options from_url="https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/refs/heads/master/dm6.json">
                 <postprocess_expression type="ecma5.1"><![CDATA[
                     $( Object.values(inputs.chrom_info).map((v) => [v.chrom, v.len]) )
                 ]]></postprocess_expression>
             </options>
         </param>
         <param name="invalid_url_param_value_postprocessed" type="select">
-            <options from_url="https://usegalaxy.or/api/genomes/dm6">
+            <options from_url="https://usegalaxy.or">
                 <postprocess_expression type="ecma5.1"><![CDATA[${
                     if (inputs) {
                         return Object.values(inputs.chrom_info).map((v) => [v.chrom, v.len])
diff --git a/test/functional/tools/select_optional.xml b/test/functional/tools/select_optional.xml
index ab809859794df1f699a050a777e329482f74fd44..fa783c7f2ff3b2e8a21262f0f13a783a7023cb84 100644
--- a/test/functional/tools/select_optional.xml
+++ b/test/functional/tools/select_optional.xml
@@ -1,4 +1,5 @@
 <tool id="select_optional" name="Optional select" version="1.0.0" profile="20.01">
+    <!-- this tool has a profile of 20.01, but has an identical behavior without it -->
     <command><![CDATA[
         echo select_opt $select_opt >> '$output1' &&
         echo select_mult_opt $select_mult_opt >> '$output1' &&
diff --git a/test/functional/tools/tool_directory_copy.xml b/test/functional/tools/tool_directory_copy.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8db6695c0a0e340ab56dfc52bc21eb19672db503
--- /dev/null
+++ b/test/functional/tools/tool_directory_copy.xml
@@ -0,0 +1,16 @@
+<tool id="tool_directory_copy" name="tool_directory_copy" version="0.1.0" profile="24.2">
+    <!-- Copy a directory to a new location. -->
+    <command><![CDATA[
+cp -r '$__tool_directory__/realtime/simple' '$output_directory.extra_files_path'
+    ]]></command>
+    <outputs>
+        <data name="output_directory" format="directory" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output_directory" ftype="directory">
+                <extra_files type="file" name="Dockerfile" md5="ed0e3613e45ca9111121f78643afbb52"></extra_files>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/use_directory_index.xml b/test/functional/tools/use_directory_index.xml
new file mode 100644
index 0000000000000000000000000000000000000000..593bc5db51b55400622187a77688969fbe6cabba
--- /dev/null
+++ b/test/functional/tools/use_directory_index.xml
@@ -0,0 +1,17 @@
+<tool id="use_directory_index" name="Uses directory index" version="1.0" profile="24.2">
+    <command><![CDATA[
+cp '$reference.extra_files_path/1.fasta' '$output'
+    ]]></command>
+    <inputs>
+        <param name="reference" type="data" label="Select an index" format="bwa_mem2_index"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference" value="bwa_mem2_index" class="Directory" ftype="bwa_mem2_index"></param>
+            <output name="output" value="1.fasta" />
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/validation_image.xml b/test/functional/tools/validation_image.xml
index a3c93ea84f67d3d6c28fff736731152f012a8f1d..c94c3581c3f18b35e6c98ba21253bb789a3f0aeb 100644
--- a/test/functional/tools/validation_image.xml
+++ b/test/functional/tools/validation_image.xml
@@ -11,7 +11,7 @@
     <tests>
         <!-- Tests with intensity images -->
         <test>
-            <param name="input" value="im1_uint8.tif" />
+            <param name="input" value="im1_uint8.tif" /><!-- axes: YX -->
             <output name="output">
                 <assert_contents>
                     <has_image_width width="32" />
@@ -22,7 +22,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_width width="30" delta="2" />
@@ -30,7 +30,7 @@
             </output>
         </test>
         <test expect_test_failure="true">
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_width width="29" delta="2" />
@@ -38,7 +38,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_width width="32" />
@@ -54,7 +54,7 @@
             </output>
         </test>
         <test expect_test_failure="true">
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_mean_intensity channel="0" mean_intensity="0.24" />
@@ -62,7 +62,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_mean_intensity channel="0" mean_intensity="0.24" eps="0.0100000001" />
@@ -70,7 +70,7 @@
             </output>
         </test>
         <test>
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_mean_intensity channel="0" min="0.24" max="0.26" />
@@ -78,7 +78,7 @@
             </output>
         </test>
         <test expect_test_failure="true">
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_mean_intensity channel="0" max="0.24" />
@@ -86,16 +86,78 @@
             </output>
         </test>
         <test expect_test_failure="true">
-            <param name="input" value="im3_b.tif" />
+            <param name="input" value="im3_b.tif" /><!-- axes: YXS -->
             <output name="output">
                 <assert_contents>
                     <has_image_mean_intensity channel="0" min="0.26" />
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input" value="im5_uint8.tif" /><!-- axes: CYX -->
+            <output name="output">
+                <assert_contents>
+                    <has_image_width width="16" />
+                    <has_image_height height="8" />
+                    <has_image_channels channels="2" />
+                    <has_image_depth depth="1" />
+                    <has_image_frames frames="1" />
+                    <has_image_mean_intensity mean_intensity="22.25" />
+                    <has_image_mean_intensity mean_intensity="12.68" channel="0" />
+                    <has_image_mean_intensity mean_intensity="31.83" channel="1" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="im7_uint8.tif" /><!-- axes: ZYX -->
+            <output name="output">
+                <assert_contents>
+                    <has_image_width width="16" />
+                    <has_image_height height="8" />
+                    <has_image_channels channels="1" />
+                    <has_image_depth depth="25" />
+                    <has_image_frames frames="1" />
+                    <has_image_mean_intensity mean_intensity="26.56" />
+                    <has_image_mean_intensity mean_intensity="12.68" slice="0" />
+                    <has_image_mean_intensity mean_intensity="9.05" slice="24" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="im6_uint8.tif" /><!-- axes: ZCYX -->
+            <output name="output">
+                <assert_contents>
+                    <has_image_width width="50" />
+                    <has_image_height height="50" />
+                    <has_image_channels channels="2" />
+                    <has_image_depth depth="25" />
+                    <has_image_frames frames="1" />
+                    <has_image_mean_intensity mean_intensity="14.18" />
+                    <has_image_mean_intensity mean_intensity="12.61" channel="0" />
+                    <has_image_mean_intensity mean_intensity="15.75" channel="1" />
+                    <has_image_mean_intensity mean_intensity="4.03" slice="0" />
+                    <has_image_mean_intensity mean_intensity="3.44" slice="0" channel="0" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="im8_uint16.tif" /><!-- axes: TYX -->
+            <output name="output">
+                <assert_contents>
+                    <has_image_width width="56" />
+                    <has_image_height height="49" />
+                    <has_image_channels channels="1" />
+                    <has_image_depth depth="1" />
+                    <has_image_frames frames="5" />
+                    <has_image_mean_intensity mean_intensity="5815.49" />
+                    <has_image_mean_intensity mean_intensity="5767.93" frame="0" />
+                    <has_image_mean_intensity mean_intensity="5844.76" frame="4" />
+                </assert_contents>
+            </output>
+        </test>
         <!-- Tests with float TIFF images -->
         <test>
-            <param name="input" value="im4_float.tif" />
+            <param name="input" value="im4_float.tif" /><!-- axes: YX -->
             <output name="output">
                 <assert_contents>
                     <has_image_width width="25" />
diff --git a/test/integration/cloudauthz/test_cloudauthz.py b/test/integration/cloudauthz/test_cloudauthz.py
deleted file mode 100644
index 6444c303d830bdc6fefaa9ad3719a19a653ca9fd..0000000000000000000000000000000000000000
--- a/test/integration/cloudauthz/test_cloudauthz.py
+++ /dev/null
@@ -1,35 +0,0 @@
-"""
-You may run this test using the following command:
-./run_tests.sh test/integration/cloudauthz/test_cloudauthz.py:TestDefineCloudAuthz.test_post_cloudauthz_without_authn -s
-"""
-
-import json
-
-from galaxy_test.driver import integration_util
-
-
-class TestDefineCloudAuthz(integration_util.IntegrationTestCase):
-    framework_tool_and_types = True
-
-    def test_post_cloudauthz_without_authn(self):
-        """
-        This test asserts if a cloudauthz object
-        can be successfully posted to the cloudauthz API
-        (i.e., api/cloud/authz).
-        """
-        provider = "azure"
-        tenant_id = "abc"
-        client_id = "def"
-        client_secret = "ghi"
-        with self._different_user("vahid@test.com"):
-            # The payload for the POST API.
-            payload = {
-                "provider": provider,
-                "config": json.dumps({"tenant_id": tenant_id, "client_id": client_id, "client_secret": client_secret}),
-            }
-
-            response = self._post(path="cloud/authz", data=payload)
-            response.raise_for_status()
-            cloudauthz = response.json()
-
-            assert cloudauthz["provider"] == provider
diff --git a/test/integration/objectstore/test_jobs.py b/test/integration/objectstore/test_jobs.py
index 30383b8e5372fb5feb628077eb067c529b5abb1e..3d1bab41e37e425b47bf374f92945c5e794493ef 100644
--- a/test/integration/objectstore/test_jobs.py
+++ b/test/integration/objectstore/test_jobs.py
@@ -3,12 +3,17 @@
 import os
 import string
 
+from galaxy_test.driver.integration_util import (
+    integration_module_instance,
+    integration_tool_runner,
+)
 from ._base import (
     BaseObjectStoreIntegrationTestCase,
     files_count,
 )
+from .test_selection_with_resource_parameters import DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
+HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
     """<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
@@ -39,7 +44,20 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
 
-class TestObjectStoreJobsIntegration(BaseObjectStoreIntegrationTestCase):
+class TestDistributedObjectStore(BaseObjectStoreIntegrationTestCase):
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        super().handle_galaxy_config_kwds(config)
+        config["metadata_strategy"] = "directory"
+        config["object_store_store_by"] = "uuid"
+        cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
+
+
+instance = integration_module_instance(TestDistributedObjectStore)
+test_tools = integration_tool_runner(["all_output_types"])
+
+
+class TestObjectStoreJobsIntegration(TestDistributedObjectStore):
     # setup by _configure_object_store
     files1_path: str
     files2_path: str
@@ -48,7 +66,7 @@ class TestObjectStoreJobsIntegration(BaseObjectStoreIntegrationTestCase):
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         super().handle_galaxy_config_kwds(config)
-        cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
+        cls._configure_object_store(HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE, config)
 
     def setUp(self):
         super().setUp()
@@ -68,7 +86,7 @@ class TestObjectStoreJobsIntegration(BaseObjectStoreIntegrationTestCase):
     def test_files_count_and_content_in_each_objectstore_backend(self):
         """
         According to the ObjectStore configuration given in the
-        `DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE` variable, datasets
+        `HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE` variable, datasets
         can be stored on three backends, named:
             -   primary/files1;
             -   primary/files2;
diff --git a/test/integration/objectstore/test_per_user.py b/test/integration/objectstore/test_per_user.py
index a7a5637fc406310be4e688dd904499dc17c5ca8a..efc20ff5d2c426df495e583a2e435018551faecf 100644
--- a/test/integration/objectstore/test_per_user.py
+++ b/test/integration/objectstore/test_per_user.py
@@ -103,6 +103,18 @@ class BaseUserObjectStoreIntegration(BaseObjectStoreIntegrationTestCase):
         object_store_id = object_store_json["object_store_id"]
         assert object_store_id.startswith("user_objects://")
 
+        response = self.dataset_populator._get(f"object_store_instances/{object_store_json['uuid']}/test")
+        response.raise_for_status()
+        from galaxy.util.config_templates import PluginStatus
+
+        status = PluginStatus.model_validate(response.json())
+        assert status.connection
+        assert not status.connection.is_not_ok
+        assert status.template_definition
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+
         object_stores = self.dataset_populator.selectable_object_stores()
         after_selectable_object_store_count = len(object_stores)
         assert after_selectable_object_store_count == before_selectable_object_store_count + 1
@@ -409,3 +421,69 @@ class TestPerUserObjectStoreUpgradesWithSecretsIntegration(
             assert object_store_json["template_version"] == 2
             assert "sec1" not in secrets
             assert "sec2" in secrets
+
+
+class TestPerUserObjectStoreQuotaIntegration(BaseUserObjectStoreIntegration):
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls._write_template_and_object_store_config(config, LIBRARY_2)
+        config["enable_quotas"] = True
+
+    def test_user_object_store_does_not_pause_jobs_over_quota(self):
+        object_store_id = self._create_simple_object_store()
+        with self.dataset_populator.test_history() as history_id:
+
+            def _run_tool(tool_id, inputs, preferred_object_store_id=None):
+                response = self.dataset_populator.run_tool(
+                    tool_id,
+                    inputs,
+                    history_id,
+                    preferred_object_store_id=preferred_object_store_id,
+                )
+                self.dataset_populator.wait_for_history(history_id)
+                return response
+
+            # Create one dataset in the default object store
+            hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3\n4 5 6\n7 8 9\n", wait=True)
+            storage_info = self.dataset_populator.dataset_storage_info(hda1["id"])
+            assert storage_info["object_store_id"] == "default"
+
+            # Set a quota of 1 byte so running a tool will pause the job
+            self._define_quota_in_bytes(1)
+
+            # Run a tool
+            hda1_input = {"src": "hda", "id": hda1["id"]}
+            response = _run_tool("multi_data_param", {"f1": hda1_input, "f2": hda1_input})
+            paused_job_id = response["jobs"][0]["id"]
+            storage_info, _ = self._storage_info_for_job_output(response)
+            assert storage_info["object_store_id"] == "default"
+
+            # The job should be paused because the default object store is over quota
+            state = self.dataset_populator.wait_for_job(paused_job_id)
+            assert state == "paused"
+
+            # Set the user object store as the preferred object store
+            self.dataset_populator.set_user_preferred_object_store_id(object_store_id)
+
+            # Run the tool again
+            response = _run_tool("multi_data_param", {"f1": hda1_input, "f2": hda1_input})
+            job_id = response["jobs"][0]["id"]
+            storage_info, _ = self._storage_info_for_job_output(response)
+            assert storage_info["object_store_id"] == object_store_id
+
+            # The job should not be paused because the user object store is not subject to quotas
+            state = self.dataset_populator.wait_for_job(job_id)
+            assert state == "ok"
+
+    def _define_quota_in_bytes(self, bytes: int):
+        quotas = self.dataset_populator.get_quotas()
+        assert len(quotas) == 0
+
+        payload = {
+            "name": "defaultquota1",
+            "description": "first default quota",
+            "amount": f"{bytes} bytes",
+            "operation": "=",
+            "default": "registered",
+        }
+        self.dataset_populator.create_quota(payload)
diff --git a/test/integration/objectstore/test_selection_with_user_preferred_object_store.py b/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
index 494bf093be72c3c3dedc2bacbf683cb1f1342a99..fee15742b8a20f51774828face726bb8f8fe8b27 100644
--- a/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
+++ b/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
@@ -244,17 +244,22 @@ class TestObjectStoreSelectionWithPreferredObjectStoresIntegration(BaseObjectSto
 
     def test_workflow_objectstore_selection(self):
         with self.dataset_populator.test_history() as history_id:
-            output_dict, intermediate_dict = self._run_workflow_get_output_storage_info_dicts(history_id)
+            output_dict, intermediate_dict, _ = self._run_workflow_get_output_storage_info_dicts(history_id)
             assert_storage_name_is(output_dict, "Default Store")
             assert_storage_name_is(intermediate_dict, "Default Store")
 
-            output_dict, intermediate_dict = self._run_workflow_get_output_storage_info_dicts(
+            output_dict, intermediate_dict, wf_run = self._run_workflow_get_output_storage_info_dicts(
                 history_id, {"preferred_object_store_id": "static"}
             )
             assert_storage_name_is(output_dict, "Static Storage")
             assert_storage_name_is(intermediate_dict, "Static Storage")
 
-            output_dict, intermediate_dict = self._run_workflow_get_output_storage_info_dicts(
+            request = self.workflow_populator.invocation_to_request(wf_run.invocation_id)
+            assert request["preferred_object_store_id"] == "static"
+            assert request["preferred_outputs_object_store_id"] is None
+            assert request["preferred_intermediate_object_store_id"] is None
+
+            output_dict, intermediate_dict, wf_run = self._run_workflow_get_output_storage_info_dicts(
                 history_id,
                 {
                     "preferred_outputs_object_store_id": "static",
@@ -264,6 +269,11 @@ class TestObjectStoreSelectionWithPreferredObjectStoresIntegration(BaseObjectSto
             assert_storage_name_is(output_dict, "Static Storage")
             assert_storage_name_is(intermediate_dict, "Dynamic EBS")
 
+            request = self.workflow_populator.invocation_to_request(wf_run.invocation_id)
+            assert request["preferred_object_store_id"] is None
+            assert request["preferred_outputs_object_store_id"] == "static"
+            assert request["preferred_intermediate_object_store_id"] == "dynamic_ebs"
+
     def test_simple_subworkflow_objectstore_selection(self):
         with self.dataset_populator.test_history() as history_id:
             output_dict, intermediate_dict = self._run_simple_nested_workflow_get_output_storage_info_dicts(
@@ -420,15 +430,14 @@ class TestObjectStoreSelectionWithPreferredObjectStoresIntegration(BaseObjectSto
     def _run_nested_workflow_with_effective_output_get_output_storage_info_dicts(
         self, history_id: str, extra_invocation_kwds: Optional[Dict[str, Any]] = None, twice_nested=False
     ):
-        worklfow_data = WORKFLOW_NESTED_OUTPUT if not twice_nested else WORKFLOW_NESTED_TWICE_OUTPUT
+        workflow_data = WORKFLOW_NESTED_OUTPUT if not twice_nested else WORKFLOW_NESTED_TWICE_OUTPUT
         wf_run = self.workflow_populator.run_workflow(
-            worklfow_data,
+            workflow_data,
             test_data=TEST_NESTED_WORKFLOW_TEST_DATA,
             history_id=history_id,
             extra_invocation_kwds=extra_invocation_kwds,
         )
         jobs = wf_run.jobs_for_tool("cat1")
-        print(jobs)
         assert len(jobs) == 2
 
         intermediate_info = self._storage_info_for_job_id(jobs[1]["id"])
@@ -448,11 +457,10 @@ class TestObjectStoreSelectionWithPreferredObjectStoresIntegration(BaseObjectSto
             extra_invocation_kwds=extra_invocation_kwds,
         )
         jobs = wf_run.jobs_for_tool("cat")
-        print(jobs)
         assert len(jobs) == 2
         output_info = self._storage_info_for_job_id(jobs[0]["id"])
         intermediate_info = self._storage_info_for_job_id(jobs[1]["id"])
-        return output_info, intermediate_info
+        return output_info, intermediate_info, wf_run
 
     def _storage_info_for_job_id(self, job_id: str) -> Dict[str, Any]:
         job_dict = self.dataset_populator.get_job_details(job_id, full=True).json()
diff --git a/test/integration/resubmission_pulsar_job_conf.xml b/test/integration/resubmission_pulsar_job_conf.xml
index da6a2cd6559f062834abd698ae24ce5e50d67b08..4b3902f2e7333d86ccd4076122e0e5fd3b0de83d 100644
--- a/test/integration/resubmission_pulsar_job_conf.xml
+++ b/test/integration/resubmission_pulsar_job_conf.xml
@@ -1,11 +1,13 @@
 <?xml version="1.0"?>
-<!-- 
+<!--
     Variant of resubmission_job_conf for testing Pulsar resubmission.
 -->
 <job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
-        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"/>
+        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">
+            <param id="transport_timeout">10</param>
+        </plugin>
     </plugins>
 
     <destinations default="initial_pulsar">
diff --git a/test/integration/resubmission_runners.py b/test/integration/resubmission_runners.py
index 73da3c2e1e7fc4aefbc9da99e2f9524d441f2d32..e516ca243b27b31a65c3449200d061e52b6d6e78 100644
--- a/test/integration/resubmission_runners.py
+++ b/test/integration/resubmission_runners.py
@@ -1,3 +1,4 @@
+import subprocess
 import time
 from typing import List
 
@@ -13,7 +14,8 @@ class FailsJobRunner(LocalJobRunner):
     def queue_job(self, job_wrapper):
         if not self._prepare_job_local(job_wrapper):
             return
-
+        command_line, _ = self._command_line(job_wrapper)
+        subprocess.run([command_line])
         resource_parameters = job_wrapper.get_resource_parameters()
         failure_state = resource_parameters.get("failure_state", None)
 
diff --git a/test/integration/test_celery_user_rate_limit.py b/test/integration/test_celery_user_rate_limit.py
index b9b832c5cddce9645f93a4cc072098fd95d43099..c36dacc880fdff807e98722b66186c3e8fed6f67 100644
--- a/test/integration/test_celery_user_rate_limit.py
+++ b/test/integration/test_celery_user_rate_limit.py
@@ -50,7 +50,7 @@ def setup_users(dburl: str, num_users: int = 2):
                 for user_id in user_ids_to_add:
                     conn.execute(
                         text("insert into galaxy_user(id, active, email, password) values (:id, :active, :email, :pw)"),
-                        [{"id": user_id, "active": True, "email": "e", "pw": "p"}],
+                        [{"id": user_id, "active": True, "email": f"e{user_id}", "pw": "p"}],
                     )
 
 
diff --git a/test/integration/test_container_resolvers.py b/test/integration/test_container_resolvers.py
index 2188cf3f9bb21175bfb86c8cfa3f13faeb444471..1d1fda4739eaac11ccd350e97518153dba62ddda 100644
--- a/test/integration/test_container_resolvers.py
+++ b/test/integration/test_container_resolvers.py
@@ -480,6 +480,11 @@ class MulledTestCase:
     mulled_hash = "mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619-0"
 
 
+class MulledTestCaseWithBuildInfo:
+    tool_id = "mulled_example_multi_2"
+    mulled_hash = "mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:a6419f25efff953fc505dbd5ee734856180bb619-0"
+
+
 class TestDefaultContainerResolvers(DockerContainerResolverTestCase, ContainerResolverTestCases, MulledTestCase):
     """
     Test default container resolvers
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index c7169ac3d5832aadbb2e155b6c5ece77b061f764..2254b79a8a5a11c157e7c6011aead955d82c30f8 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -30,32 +30,47 @@ class MulledJobTestCases:
     """
 
     dataset_populator: DatasetPopulator
+    container_type: str
+
+    def _run_and_get_contents(self, tool_id: str, history_id: str):
+        run_response = self.dataset_populator.run_tool(tool_id, {}, history_id)
+        job_id = run_response["jobs"][0]["id"]
+        self.dataset_populator.wait_for_job(job_id=job_id, assert_ok=True, timeout=EXTENDED_TIMEOUT)
+        job_metrics = self.dataset_populator._get(f"/api/jobs/{job_id}/metrics").json()
+        # would be nice if it wasn't just a list of unpredictable order ...
+        container_id = None
+        container_type = None
+        for metric in job_metrics:
+            if metric["name"] == "container_id":
+                container_id = metric["value"]
+            if metric["name"] == "container_type":
+                container_type = metric["value"]
+        assert container_id, "Job metrics did not include container_id"
+        assert container_type, "Job metrics did not include container_type"
+        assert container_type == self.container_type
+        return self.dataset_populator.get_history_dataset_content(
+            history_id, content_id=run_response["outputs"][0]["id"]
+        )
 
     def test_explicit(self, history_id: str) -> None:
         """
         tool having one package + one explicit container requirement
         """
-        self.dataset_populator.run_tool("mulled_example_explicit", {}, history_id)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True, timeout=EXTENDED_TIMEOUT)
-        output = self.dataset_populator.get_history_dataset_content(history_id)
+        output = self._run_and_get_contents("mulled_example_explicit", history_id)
         assert "0.7.15-r1140" in output
 
     def test_mulled_simple(self, history_id: str) -> None:
         """
         tool having one package requirement
         """
-        self.dataset_populator.run_tool("mulled_example_simple", {}, history_id)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True, timeout=EXTENDED_TIMEOUT)
-        output = self.dataset_populator.get_history_dataset_content(history_id)
+        output = self._run_and_get_contents("mulled_example_simple", history_id)
         assert "0.7.15-r1140" in output
 
     def test_mulled_explicit_invalid_case(self, history_id: str) -> None:
         """
         tool having one package + one (invalid? due to capitalization) explicit container requirement
         """
-        self.dataset_populator.run_tool("mulled_example_invalid_case", {}, history_id)
-        self.dataset_populator.wait_for_history(history_id, assert_ok=True, timeout=EXTENDED_TIMEOUT)
-        output = self.dataset_populator.get_history_dataset_content(history_id)
+        output = self._run_and_get_contents("mulled_example_invalid_case", history_id)
         assert "0.7.15-r1140" in output
 
 
diff --git a/test/integration/test_extended_metadata.py b/test/integration/test_extended_metadata.py
index 50c21940cfba0357a165f093aa0d90c0fb8a36bc..94240052147aa2ae29f5cceb2cce27f2e954aef1 100644
--- a/test/integration/test_extended_metadata.py
+++ b/test/integration/test_extended_metadata.py
@@ -43,6 +43,7 @@ TEST_TOOL_IDS = [
     "collection_creates_dynamic_nested_from_json_elements",
     "implicit_conversion",
     "environment_variables",
+    "all_output_types",
 ]
 
 
diff --git a/test/integration/test_extended_metadata_mapping.py b/test/integration/test_extended_metadata_mapping.py
index b4e088146492bd088264104e822ab6d87713cd4b..6dd1cbf6c747814c6323d11784e21efc834116ae 100644
--- a/test/integration/test_extended_metadata_mapping.py
+++ b/test/integration/test_extended_metadata_mapping.py
@@ -29,3 +29,18 @@ class TestExtendedMetadataMappingIntegration(integration_util.IntegrationTestCas
             "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
         }
         self._run_and_check_simple_collection_mapping(history_id, inputs)
+
+    def _run_and_check_simple_collection_mapping(self, history_id, inputs):
+        create = self._run_cat(history_id, inputs=inputs, assert_ok=True)
+        outputs = create["outputs"]
+        jobs = create["jobs"]
+        implicit_collections = create["implicit_collections"]
+        assert len(jobs) == 2
+        assert len(outputs) == 2
+        assert len(implicit_collections) == 1
+        output1 = outputs[0]
+        output2 = outputs[1]
+        output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
+        output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
+        assert output1_content.strip() == "123"
+        assert output2_content.strip() == "456"
diff --git a/test/integration/test_job_resubmission.py b/test/integration/test_job_resubmission.py
index dd6da5d423a3af08e3a0ac266c37eae8ebba86b4..a812978d96e568e84d32ff2a6bf99437e45d1147 100644
--- a/test/integration/test_job_resubmission.py
+++ b/test/integration/test_job_resubmission.py
@@ -2,6 +2,7 @@
 
 import os
 
+from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
@@ -27,15 +28,15 @@ JOB_RESUBMISSION_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubm
 class _BaseResubmissionIntegrationTestCase(integration_util.IntegrationTestCase):
     framework_tool_and_types = True
 
-    def _assert_job_passes(self, tool_id="exit_code_oom", resource_parameters=None):
+    def _assert_job_passes(self, tool_id="exit_code_oom", resource_parameters=None, history_id=None):
         resource_parameters = resource_parameters or {}
-        self._run_tool_test(tool_id, resource_parameters=resource_parameters)
+        self._run_tool_test(tool_id, resource_parameters=resource_parameters, test_history=history_id)
 
-    def _assert_job_fails(self, tool_id="exit_code_oom", resource_parameters=None):
+    def _assert_job_fails(self, tool_id="exit_code_oom", resource_parameters=None, history_id=None):
         resource_parameters = resource_parameters or {}
         exception_thrown = False
         try:
-            self._run_tool_test(tool_id, resource_parameters=resource_parameters)
+            self._run_tool_test(tool_id, resource_parameters=resource_parameters, test_history=history_id)
         except Exception:
             exception_thrown = True
 
@@ -44,6 +45,11 @@ class _BaseResubmissionIntegrationTestCase(integration_util.IntegrationTestCase)
 
 class TestJobResubmissionIntegration(_BaseResubmissionIntegrationTestCase):
     framework_tool_and_types = True
+    dataset_populator: DatasetPopulator
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -52,6 +58,9 @@ class TestJobResubmissionIntegration(_BaseResubmissionIntegrationTestCase):
         config["job_resource_params_file"] = JOB_RESUBMISSION_JOB_RESOURCES_CONFIG_FILE
         config["job_runner_monitor_sleep"] = 1
         config["job_handler_monitor_sleep"] = 1
+        config["job_metrics"] = [{"type": "core"}]
+        # Can't set job_metrics_config_file to None as default location will be used otherwise
+        config["job_metrics_config_file"] = "xxx.xml"
 
     def test_retry_tools_have_resource_params(self):
         tool_show = self._get("tools/simple_constructs", data=dict(io_details=True)).json()
@@ -74,6 +83,20 @@ class TestJobResubmissionIntegration(_BaseResubmissionIntegrationTestCase):
             }
         )
 
+    def test_failure_runner_job_metrics_collected(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._assert_job_fails(
+                resource_parameters={
+                    "test_name": "test_failure_runner",
+                    "initial_target_environment": "fails_without_resubmission",
+                },
+                history_id=history_id,
+            )
+            jobs = self.dataset_populator.history_jobs(history_id=history_id)
+            assert len(jobs) == 1
+            job_metrics = self.dataset_populator._get(f"/api/jobs/{jobs[0]['id']}/metrics").json()
+            assert job_metrics
+
     def test_walltime_resubmission(self):
         self._assert_job_passes(
             resource_parameters={"test_name": "test_walltime_resubmission", "failure_state": "walltime_reached"}
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 9748d4b497b54949d278371009e54c8c602a5bdd..56c00a3c8552cb1581ef0a9e9c9ca7f8ca2374c2 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -191,6 +191,7 @@ class TestKubernetesIntegration(BaseJobEnvironmentIntegrationTestCase, MulledJob
     jobs_directory: str
     persistent_volume_claims: List[KubeSetupConfigTuple]
     persistent_volumes: List[KubeSetupConfigTuple]
+    container_type = "docker"
 
     def setUp(self) -> None:
         super().setUp()
diff --git a/test/integration/test_materialize_dataset_instance_tasks.py b/test/integration/test_materialize_dataset_instance_tasks.py
index 7bd606cd390a0c13361132ecb9cf1e0f82068339..817098994a5fa69a3b4d4cde3330e63f3f87053c 100644
--- a/test/integration/test_materialize_dataset_instance_tasks.py
+++ b/test/integration/test_materialize_dataset_instance_tasks.py
@@ -78,6 +78,26 @@ class TestMaterializeDatasetInstanceTasaksIntegration(IntegrationTestCase, UsesC
         assert new_hda_details["state"] == "ok"
         assert not new_hda_details["deleted"]
 
+    @pytest.mark.require_new_history
+    def test_materialize_hash_failure(self, history_id: str):
+        store_dict = deferred_hda_model_store_dict(source_uri="gxfiles://testdatafiles/2.bed")
+        store_dict["datasets"][0]["file_metadata"]["hashes"][0]["hash_value"] = "invalidhash"
+        as_list = self.dataset_populator.create_contents_from_store(history_id, store_dict=store_dict)
+        assert len(as_list) == 1
+        deferred_hda = as_list[0]
+        assert deferred_hda["model_class"] == "HistoryDatasetAssociation"
+        assert deferred_hda["state"] == "deferred"
+        assert not deferred_hda["deleted"]
+
+        self.dataset_populator.materialize_dataset_instance(history_id, deferred_hda["id"])
+        self.dataset_populator.wait_on_history_length(history_id, 2)
+        new_hda_details = self.dataset_populator.get_history_dataset_details(
+            history_id, hid=2, assert_ok=False, wait=False
+        )
+        assert new_hda_details["model_class"] == "HistoryDatasetAssociation"
+        assert new_hda_details["state"] == "error"
+        assert not new_hda_details["deleted"]
+
     @pytest.mark.require_new_history
     def test_materialize_history_dataset_bam(self, history_id: str):
         as_list = self.dataset_populator.create_contents_from_store(
diff --git a/test/integration/test_notifications.py b/test/integration/test_notifications.py
index d44fcaea8da6344a636f9ee169df4d55123c063f..89077357f8246e96a6f6a3a016ca952630bec7e0 100644
--- a/test/integration/test_notifications.py
+++ b/test/integration/test_notifications.py
@@ -356,7 +356,7 @@ class NotificationsIntegrationBase(IntegrationTestCase):
             "type": "example",
             "dbkey": "hg17",
         }
-        response = self._post("visualizations", data=create_payload).json()
+        response = self._post("visualizations", data=create_payload, json=True).json()
         visualization_id = response["id"]
         payload = {"user_ids": user_ids}
         sharing_response = self._put(f"visualizations/{visualization_id}/share_with_users", data=payload, json=True)
diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
index c2d37c2652732022977143de526d523f7e9bb1c9..69d7a5efd44be464c26af6763140832e9ad3277f 100644
--- a/test/integration/test_pulsar_embedded.py
+++ b/test/integration/test_pulsar_embedded.py
@@ -23,6 +23,8 @@ instance = integration_util.integration_module_instance(EmbeddedPulsarIntegratio
 
 test_tools = integration_util.integration_tool_runner(
     [
+        "cat_default",
+        "collection_nested_default",
         "collection_creates_dynamic_nested_from_json",
         "composite",
         "simple_constructs",
@@ -38,5 +40,7 @@ test_tools = integration_util.integration_tool_runner(
         "composite_output",
         "composite_output_tests",
         "detect_errors",
+        "tool_directory_copy",
+        "metadata_columns",
     ]
 )
diff --git a/test/integration/test_pulsar_embedded_mq.py b/test/integration/test_pulsar_embedded_mq.py
index 19022a9b4b2f57b205d4afdc7b41e38edfed2d36..b9376a10a16f085fd785866838b52cbfddb7b974 100644
--- a/test/integration/test_pulsar_embedded_mq.py
+++ b/test/integration/test_pulsar_embedded_mq.py
@@ -43,7 +43,7 @@ execution:
     local_environment:
       runner: local
 tools:
-  - id: upload1
+  - id: __DATA_FETCH__
     environment: local_environment
 """
 
diff --git a/test/integration/test_quota.py b/test/integration/test_quota.py
index 07137786a353ffd872d8e28829d4b99b80598ea0..0debde6ac6275d3c28e3a3ec876150dfd10448e6 100644
--- a/test/integration/test_quota.py
+++ b/test/integration/test_quota.py
@@ -85,6 +85,26 @@ class TestQuotaIntegration(integration_util.IntegrationTestCase):
         json_response = show_response.json()
         assert json_response["name"] == new_quota_name
 
+    def test_update_description(self):
+        quota_name = "test-update-quota-description"
+        quota = self._create_quota_with_name(quota_name)
+        quota_id = quota["id"]
+
+        # update description (one needs to specify a name even if should not be changed)
+        quota_description = "description of test-updated-quota-name"
+        update_payload = {
+            "name": quota_name,
+            "description": quota_description,
+        }
+        put_response = self._put(f"quotas/{quota_id}", data=update_payload, json=True)
+        put_response.raise_for_status()
+
+        show_response = self._get(f"quotas/{quota_id}")
+        show_response.raise_for_status()
+        json_response = show_response.json()
+        assert json_response["name"] == quota_name
+        assert json_response["description"] == quota_description
+
     def test_delete(self):
         quota_name = "test-delete-quota"
         quota = self._create_quota_with_name(quota_name)
diff --git a/test/integration/test_remote_files.py b/test/integration/test_remote_files.py
index c56759bb6f73b14131fcf95e71fcf7d7016047c0..6ac53a15550636237cc77e34f4cedf18007c845f 100644
--- a/test/integration/test_remote_files.py
+++ b/test/integration/test_remote_files.py
@@ -205,6 +205,46 @@ class TestRemoteFilesIntegration(ConfiguresRemoteFilesIntegrationTestCase):
             with open(os.path.join(ftp_dir, "my_cool", "utf8_name_😻.txt")) as f:
                 assert "example content\n" == f.read()
 
+    def test_export_remote_tool_with_space(self):
+        dataset_populator = self.dataset_populator
+        ftp_dir = self.user_ftp_dir
+        _write_file_fixtures(self.root, ftp_dir)
+        dir_with_space = os.path.join(ftp_dir, "space dir")
+        os.makedirs(dir_with_space)
+        with dataset_populator.test_history() as history_id:
+            dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
+            infile = {"src": "hda", "id": dataset["id"]}
+            inputs = {
+                "d_uri": "gxftp://space dir/",
+                "export_type|export_type_selector": "datasets_named",
+                "export_type|datasets_0|infile": infile,
+                "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt",
+            }
+            response = dataset_populator.run_tool("export_remote", inputs, history_id)
+            dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
+            with open(os.path.join(ftp_dir, "space dir", "my_cool", "utf8_name_😻.txt")) as f:
+                assert "example content\n" == f.read()
+
+    def test_export_remote_tool_with_space_encoded(self):
+        dataset_populator = self.dataset_populator
+        ftp_dir = self.user_ftp_dir
+        _write_file_fixtures(self.root, ftp_dir)
+        dir_with_space = os.path.join(ftp_dir, "space%20dir")
+        os.makedirs(dir_with_space)
+        with dataset_populator.test_history() as history_id:
+            dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
+            infile = {"src": "hda", "id": dataset["id"]}
+            inputs = {
+                "d_uri": "gxftp://space%20dir/",
+                "export_type|export_type_selector": "datasets_named",
+                "export_type|datasets_0|infile": infile,
+                "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt",
+            }
+            response = dataset_populator.run_tool("export_remote", inputs, history_id)
+            dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
+            with open(os.path.join(ftp_dir, "space%20dir", "my_cool", "utf8_name_😻.txt")) as f:
+                assert "example content\n" == f.read()
+
     def test_export_remote_tool_default_duplicate_name_fails(self):
         dataset_populator = self.dataset_populator
         ftp_dir = self.user_ftp_dir
diff --git a/test/integration/test_remote_files_posix.py b/test/integration/test_remote_files_posix.py
index 7d588cdf9d25656548f54cced5cac497d9d5f103..75a449ff2e45d56b55cd82e112a5ad7df0d0bd62 100644
--- a/test/integration/test_remote_files_posix.py
+++ b/test/integration/test_remote_files_posix.py
@@ -1,8 +1,8 @@
-# Before running this test, start nginx+webdav in Docker using following command:
-# docker run -v `pwd`/test/integration/webdav/data:/media  -e WEBDAV_USERNAME=alice -e WEBDAV_PASSWORD=secret1234 -p 7083:7083 jmchilton/webdavdev
-# Apache Docker host (shown next) doesn't work because displayname not set in response.
-# docker run -v `pwd`/test/integration/webdav:/var/lib/dav  -e AUTH_TYPE=Basic -e USERNAME=alice -e PASSWORD=secret1234  -e LOCATION=/ -p 7083:80 bytemark/webdav
+import os
 
+from sqlalchemy import select
+
+from galaxy.model import Dataset
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
@@ -108,3 +108,53 @@ class TestPosixFileSourceIntegration(PosixFileSourceSetup, integration_util.Inte
 
     def _assert_access_forbidden_response(self, response):
         api_asserts.assert_status_code_is(response, 403)
+
+
+class TestPreferLinksPosixFileSourceIntegration(PosixFileSourceSetup, integration_util.IntegrationTestCase):
+    dataset_populator: DatasetPopulator
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        PosixFileSourceSetup.handle_galaxy_config_kwds(
+            config,
+            cls,
+            prefer_links=True,
+        )
+
+    def setUp(self):
+        super().setUp()
+        self._write_file_fixtures()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    def test_links_by_default(self):
+        with self.dataset_populator.test_history() as history_id:
+            element = dict(src="url", url="gxfiles://linking_source/a")
+            target = {
+                "destination": {"type": "hdas"},
+                "elements": [element],
+            }
+            targets = [target]
+            payload = {
+                "history_id": history_id,
+                "targets": targets,
+            }
+            new_dataset = self.dataset_populator.fetch(payload, assert_ok=True).json()["outputs"][0]
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset)
+            assert content == "a\n", content
+            stmt = select(Dataset).order_by(Dataset.create_time.desc()).limit(1)
+            dataset = self._app.model.session.execute(stmt).unique().scalar_one()
+            assert dataset.external_filename.endswith("/root/a")
+            assert os.path.exists(dataset.external_filename)
+            assert open(dataset.external_filename).read() == "a\n"
+            payload = self.dataset_populator.run_tool(
+                tool_id="cat",
+                inputs={
+                    "input1": {"src": "hda", "id": new_dataset["id"]},
+                },
+                history_id=history_id,
+            )
+            derived_dataset = payload["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            derived_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=derived_dataset)
+            assert derived_content.strip() == "a"
diff --git a/test/integration/test_tool_submission_errors.py b/test/integration/test_tool_submission_errors.py
new file mode 100644
index 0000000000000000000000000000000000000000..d73f621fa823c60c32e4ff23f7a1bf487b44cb7e
--- /dev/null
+++ b/test/integration/test_tool_submission_errors.py
@@ -0,0 +1,56 @@
+from sqlalchemy import select
+
+from galaxy.model import HistoryDatasetAssociation
+from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
+    DatasetPopulator,
+)
+from galaxy_test.driver import integration_util
+
+
+class TestFailJobWhenToolUnavailable(integration_util.IntegrationTestCase):
+    dataset_populator: DatasetPopulator
+    dataset_collection_populator: DatasetCollectionPopulator
+    require_admin_user = True
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
+
+    @property
+    def sa_session(self):
+        return self._app.model.session
+
+    def test_partial_job_success_error_handling(self):
+        with self.dataset_populator.test_history() as history_id:
+            create_response = self.dataset_collection_populator.create_list_in_history(
+                history_id, contents=["xxx\n", "yyy\n"], wait=True
+            ).json()
+            hdca_id = create_response["output_collections"][0]["id"]
+            first_hda_id = self.dataset_populator.get_history_collection_details(history_id, content_id=hdca_id)[
+                "elements"
+            ][0]["object"]["id"]
+            database_id = self._get(f"configuration/decode/{first_hda_id}").json()["decoded_id"]
+            hda = self.sa_session.scalar(
+                select(HistoryDatasetAssociation).where(HistoryDatasetAssociation.id == database_id)
+            )
+            assert hda
+            hda.state = HistoryDatasetAssociation.states.FAILED_METADATA
+            self.sa_session.add(hda)
+            self.sa_session.commit()
+            response = self.dataset_populator.run_tool_raw(
+                tool_id="__FILTER_NULL__",
+                inputs={"input": {"src": "hdca", "id": hdca_id}},
+                history_id=history_id,
+            ).json()
+            assert response["errors"] == [
+                {
+                    "err_code": 0,
+                    "err_msg": "Tool requires inputs to be in valid state, but "
+                    "dataset with hid 2 is in state 'failed_metadata'",
+                    "id": "eb142648ac45b77086610f67617bec2ad3808fd4409d175f",
+                    "input_name": "input1",
+                    "src": "hda",
+                }
+            ]
diff --git a/test/integration/test_user_preferences.py b/test/integration/test_user_preferences.py
index b01f4850489d5ed00006f1fa934e8a5427a58686..62e76aa108a85bf0ce9db70ba8313f2b802243a5 100644
--- a/test/integration/test_user_preferences.py
+++ b/test/integration/test_user_preferences.py
@@ -8,7 +8,7 @@ from requests import (
     put,
 )
 
-from galaxy.managers.users import get_user_by_email
+from galaxy.model.db.user import get_user_by_email
 from galaxy_test.driver import integration_util
 
 TEST_USER_EMAIL = "test_user_preferences@bx.psu.edu"
diff --git a/test/integration/test_vault_extra_prefs.py b/test/integration/test_vault_extra_prefs.py
index e3ec8fd5c7f17cb6541ab15fff35c415dffee944..583ce9d72f3044359d9984b168761cef48b0f855 100644
--- a/test/integration/test_vault_extra_prefs.py
+++ b/test/integration/test_vault_extra_prefs.py
@@ -10,7 +10,7 @@ from requests import (
     put,
 )
 
-from galaxy.managers.users import get_user_by_email
+from galaxy.model.db.user import get_user_by_email
 from galaxy_test.driver import integration_util
 
 TEST_USER_EMAIL = "vault_test_user@bx.psu.edu"
@@ -129,6 +129,89 @@ class TestExtraUserPreferences(integration_util.IntegrationTestCase, integration
             == "an_updated_secret_value"
         )
 
+    def test_extra_prefs_secret_not_in_vault(self):
+        user = self._setup_user(TEST_USER_EMAIL)
+        url = self.__url("information/inputs", user)
+        app = cast(Any, self._test_driver.app if self._test_driver else None)
+        db_user = self._get_dbuser(app, user)
+
+        # create some initial data
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "non_vault_test_section|user": "test_user",
+                    "non_vault_test_section|pass": "test_pass",
+                }
+            ),
+        )
+
+        # retrieve saved data
+        response = get(url).json()
+
+        def get_input_by_name(inputs, name):
+            return [input for input in inputs if input["name"] == name][0]
+
+        inputs = [section for section in response["inputs"] if section["name"] == "non_vault_test_section"][0]["inputs"]
+
+        # value should be what we saved
+        input_user = get_input_by_name(inputs, "user")
+        assert input_user["value"] == "test_user"
+
+        # the secret should not be stored in the vault
+        assert app.vault.read_secret(f"user/{db_user.id}/preferences/non_vault_test_section/pass") is None
+        # it should be in the user preferences model
+        app.model.session.refresh(db_user)
+        assert db_user.extra_preferences["non_vault_test_section|pass"] == "test_pass"
+
+        # secret type values should not be retrievable by the client
+        input_pass = get_input_by_name(inputs, "pass")
+        assert input_pass["value"] != "test_pass"
+        assert input_pass["value"] == "__SECRET_PLACEHOLDER__"
+
+        # changing the text property value should not change the secret property value
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "non_vault_test_section|user": "a_new_test_user",
+                    "non_vault_test_section|pass": "__SECRET_PLACEHOLDER__",
+                }
+            ),
+        )
+
+        response = get(url).json()
+        inputs = [section for section in response["inputs"] if section["name"] == "non_vault_test_section"][0]["inputs"]
+        input_user = get_input_by_name(inputs, "user")
+        assert input_user["value"] == "a_new_test_user"
+        # the secret value is not exposed to the client
+        input_pass = get_input_by_name(inputs, "pass")
+        assert input_pass["value"] == "__SECRET_PLACEHOLDER__"
+
+        # The secret value should not have changed in the internal user preferences model
+        app.model.session.refresh(db_user)
+        assert db_user.extra_preferences["non_vault_test_section|pass"] == "test_pass"
+
+        # changing the secret value should update the secret value
+        put(
+            url,
+            data=json.dumps(
+                {
+                    "non_vault_test_section|user": "a_new_test_user",
+                    "non_vault_test_section|pass": "a_new_test_pass",
+                }
+            ),
+        )
+
+        response = get(url).json()
+        inputs = [section for section in response["inputs"] if section["name"] == "non_vault_test_section"][0]["inputs"]
+        input_pass = get_input_by_name(inputs, "pass")
+        assert input_pass["value"] == "__SECRET_PLACEHOLDER__"
+
+        # the secret value should be updated in the internal user preferences model
+        app.model.session.refresh(db_user)
+        assert db_user.extra_preferences["non_vault_test_section|pass"] == "a_new_test_pass"
+
     def __url(self, action, user):
         return self._api_url(f"users/{user['id']}/{action}", params=dict(key=self.master_api_key))
 
diff --git a/test/integration/test_vault_file_source.py b/test/integration/test_vault_file_source.py
index dc39477cd2f6f1fe1309e814eebe0bb134355a61..71b8ff31dd6fbb03aa6596410b22e0b74da0ab08 100644
--- a/test/integration/test_vault_file_source.py
+++ b/test/integration/test_vault_file_source.py
@@ -1,7 +1,7 @@
 import os
 import tempfile
 
-from galaxy.managers.users import get_user_by_email
+from galaxy.model.db.user import get_user_by_email
 from galaxy.security.vault import UserVaultWrapper
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
diff --git a/test/integration/test_web_framework_config.py b/test/integration/test_web_framework_config.py
index d617eed03ae47866f288a047d965c96e2aae8e8f..23e5091e3f86ead3dce5c5c9463745846b1fa2c3 100644
--- a/test/integration/test_web_framework_config.py
+++ b/test/integration/test_web_framework_config.py
@@ -4,10 +4,14 @@ from requests import options
 
 from galaxy_test.driver import integration_util
 
+ENDPOINT_WITH_CORS = "workflow_landings"
+ENDPOINT_WITHOUT_EXPLICIT_CORS = "licenses"
+WSGI_ENDPOINT = "tools"
+
 
 class BaseWebFrameworkTestCase(integration_util.IntegrationTestCase):
-    def _options(self, headers=None):
-        url = self._api_url("licenses")
+    def _options(self, headers=None, endpoint=ENDPOINT_WITH_CORS):
+        url = self._api_url(endpoint)
         options_response = options(url, headers=headers or {})
         return options_response
 
@@ -18,8 +22,18 @@ class TestCorsDefaultIntegration(BaseWebFrameworkTestCase):
             "Access-Control-Request-Method": "GET",
             "origin": "http://192.168.0.101:8083",
         }
-        options_response = self._options(headers)
-        assert options_response.status_code == 200
+        options_response = self._options(headers, ENDPOINT_WITHOUT_EXPLICIT_CORS)
+        options_response.raise_for_status()
+        assert "access-control-allow-origin" not in options_response.headers
+
+    def test_options_wsgi(self):
+        # Tests legacy handling
+        headers = {
+            "Access-Control-Request-Method": "GET",
+            "origin": "http://192.168.0.101:8083",
+        }
+        options_response = self._options(headers, WSGI_ENDPOINT)
+        options_response.raise_for_status()
         assert "access-control-allow-origin" not in options_response.headers
 
     def test_origin_not_allowed_default(self):
@@ -28,10 +42,20 @@ class TestCorsDefaultIntegration(BaseWebFrameworkTestCase):
             "Access-Control-Request-Headers": "Authorization",
             "origin": "http://192.168.0.101:8083",
         }
-        options_response = self._options(headers)
-        assert options_response.status_code == 200
+        options_response = self._options(headers, ENDPOINT_WITHOUT_EXPLICIT_CORS)
+        options_response.raise_for_status()
         assert "access-control-allow-origin" not in options_response.headers
 
+    def test_origin_explicitly_allowed(self):
+        headers = {
+            "Access-Control-Request-Method": "GET",
+            "Access-Control-Request-Headers": "Authorization",
+            "Origin": "http://192.168.0.101:8083",
+        }
+        options_response = self._options(headers, ENDPOINT_WITH_CORS)
+        options_response.raise_for_status()
+        assert options_response.headers["access-control-allow-origin"] == "http://192.168.0.101:8083"
+
 
 class TestAllowOriginIntegration(BaseWebFrameworkTestCase):
     @classmethod
@@ -45,7 +69,7 @@ class TestAllowOriginIntegration(BaseWebFrameworkTestCase):
             "origin": "http://192.168.0.101:8083",
             "Access-Control-Request-Headers": "Authorization",
         }
-        options_response = self._options(headers)
+        options_response = self._options(headers, ENDPOINT_WITHOUT_EXPLICIT_CORS)
         options_response.raise_for_status()
         assert "access-control-allow-origin" in options_response.headers
         assert options_response.headers["access-control-allow-origin"] == "http://192.168.0.101:8083"
@@ -57,7 +81,7 @@ class TestAllowOriginIntegration(BaseWebFrameworkTestCase):
             "origin": "http://rna.galaxyproject.org",
             "Access-Control-Request-Headers": "Authorization",
         }
-        options_response = self._options(headers)
+        options_response = self._options(headers, ENDPOINT_WITHOUT_EXPLICIT_CORS)
         options_response.raise_for_status()
         assert "access-control-allow-origin" in options_response.headers
         assert options_response.headers["access-control-allow-origin"] == "http://rna.galaxyproject.org"
@@ -69,5 +93,5 @@ class TestAllowOriginIntegration(BaseWebFrameworkTestCase):
             "origin": "http://192.168.0.102:8083",  # swapped ip by one
             "Access-Control-Request-Headers": "Authorization",
         }
-        options_response = self._options(headers)
+        options_response = self._options(headers, ENDPOINT_WITHOUT_EXPLICIT_CORS)
         assert options_response.status_code == 400
diff --git a/test/integration/test_workflow_invocation.py b/test/integration/test_workflow_invocation.py
index 72276bf77979e7638ae8ba60a7d20631f9e7c31c..3ef39b06779c8fc13a9d621c0107b95c6d310520 100644
--- a/test/integration/test_workflow_invocation.py
+++ b/test/integration/test_workflow_invocation.py
@@ -69,6 +69,56 @@ class TestWorkflowInvocation(integration_util.IntegrationTestCase, UsesShedApi):
                 if step["workflow_step_label"] == "cat1":
                     assert sum(1 for j in step["jobs"] if j["state"] == "skipped") == 1
 
+    def test_pick_value_preserves_datatype_and_inheritance_chain(self):
+        self.install_repository("iuc", "pick_value", "b19e21af9c52")
+        with self.dataset_populator.test_history() as history_id:
+            summary = self.workflow_populator.run_workflow(
+                """
+class: GalaxyWorkflow
+inputs:
+  input_dataset: data
+outputs:
+  the_output:
+    outputSource: pick_value/data_param
+steps:
+  skip_step:
+    tool_id: job_properties
+    when: $(false)
+  pick_value:
+    tool_id: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
+    in:
+      style_cond|type_cond|pick_from_0|value:
+        source: skip_step/out_file1
+      style_cond|type_cond|pick_from_1|value:
+        source: input_dataset
+    tool_state:
+      style_cond:
+        pick_style: first
+        type_cond:
+          param_type: data
+          pick_from:
+          - value:
+            __class__: RuntimeValue
+          - value:
+            __class__: RuntimeValue
+test_data:
+  input_dataset:
+      value: 1.txt
+      type: File
+""",
+                history_id=history_id,
+            )
+            invocation = self.workflow_populator.get_invocation(summary.invocation_id)
+            output = self.dataset_populator.get_history_dataset_details(
+                history_id,
+                content_id=invocation["outputs"]["the_output"]["id"],
+                # copied_from_history_dataset_association_id is not in any of the default serializers
+                keys="state,extension,copied_from_history_dataset_association_id",
+            )
+            assert output["state"] == "ok"
+            assert output["extension"] == "txt"
+            assert output["copied_from_history_dataset_association_id"]
+
     def test_run_workflow_optional_data_provided_runs_step(self) -> None:
         self.install_repository("iuc", "map_param_value", "5ac8a4bf7a8d")
         with self.dataset_populator.test_history() as history_id:
diff --git a/test/integration/test_workflow_tasks.py b/test/integration/test_workflow_tasks.py
index c250b624439f87a09081b382bf9eb53d6ace22fb..3f8869dc91093e0248acacebf1815f29fc10a280 100644
--- a/test/integration/test_workflow_tasks.py
+++ b/test/integration/test_workflow_tasks.py
@@ -17,6 +17,7 @@ from galaxy_test.api.test_workflows import RunsWorkflowFixtures
 from galaxy_test.base import api_asserts
 from galaxy_test.base.api import UsesCeleryTasks
 from galaxy_test.base.populators import (
+    DatasetCollectionPopulator,
     DatasetPopulator,
     RunJobsSummary,
     WorkflowPopulator,
@@ -27,6 +28,7 @@ from galaxy_test.driver.integration_util import IntegrationTestCase
 
 class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, UsesCeleryTasks, RunsWorkflowFixtures):
     dataset_populator: DatasetPopulator
+    dataset_collection_populator: DatasetCollectionPopulator
     framework_tool_and_types = True
 
     @classmethod
@@ -37,6 +39,7 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us
     def setUp(self):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
         self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
         self._write_file_fixtures()
 
@@ -124,6 +127,47 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us
             invocation_details = self._export_and_import_workflow_invocation(summary, use_uris)
             self._rerun_imported_workflow(summary, invocation_details)
 
+    def test_export_import_invocation_with_copied_hdca_and_database_operation_tool(self):
+        with self.dataset_populator.test_history() as history_id:
+            self.dataset_collection_populator.create_list_in_history(history_id=history_id, wait=True).json()
+            new_history = self.dataset_populator.copy_history(history_id=history_id).json()
+            copied_collection = self.dataset_populator.get_history_collection_details(new_history["id"])
+            workflow_id = self.workflow_populator.upload_yaml_workflow(
+                """class: GalaxyWorkflow
+inputs:
+  input:
+    type: collection
+    collection_type: list
+steps:
+  extract_dataset:
+    tool_id: __EXTRACT_DATASET__
+    in:
+      input:
+        source: input
+"""
+            )
+            inputs = {"input": {"src": "hdca", "id": copied_collection["id"]}}
+            workflow_request = {"history": f"hist_id={new_history['id']}", "inputs_by": "name", "inputs": inputs}
+            invocation = self.workflow_populator.invoke_workflow_raw(
+                workflow_id, workflow_request, assert_ok=True
+            ).json()
+            invocation_id = invocation["id"]
+            self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
+            jobs = self.workflow_populator.get_invocation_jobs(invocation_id)
+            summary = RunJobsSummary(
+                history_id=history_id,
+                workflow_id=workflow_id,
+                invocation_id=invocation["id"],
+                inputs=inputs,
+                jobs=jobs,
+                invocation=invocation,
+                workflow_request=workflow_request,
+            )
+            imported_invocation_details = self._export_and_import_workflow_invocation(summary)
+            original_contents = self.dataset_populator.get_history_contents(new_history["id"])
+            contents = self.dataset_populator.get_history_contents(imported_invocation_details["history_id"])
+            assert len(contents) == len(original_contents) == 5
+
     def _export_and_import_workflow_invocation(
         self, summary: RunJobsSummary, use_uris: bool = True, model_store_format="tgz"
     ) -> Dict[str, Any]:
diff --git a/test/integration/user_preferences_extra_conf.yml b/test/integration/user_preferences_extra_conf.yml
index b678edeed82c8bffc69073420cc110b4a63eee38..9fe29b8f22a75160094d748897910edbc1f6a9b4 100644
--- a/test/integration/user_preferences_extra_conf.yml
+++ b/test/integration/user_preferences_extra_conf.yml
@@ -21,3 +21,15 @@ preferences:
               type: secret
               store: vault
               required: True
+
+    non_vault_test_section:
+        description: For testing Settings
+        inputs:
+            - name: user
+              label: User
+              type: text
+              required: True
+            - name: pass
+              label: Pass
+              type: secret # It's a secret but not stored in vault
+              required: True
diff --git a/test/integration_selenium/test_allowlist_sanitization.py b/test/integration_selenium/test_allowlist_sanitization.py
new file mode 100644
index 0000000000000000000000000000000000000000..109862158cb07020d904fe390e0b3022f1667c0e
--- /dev/null
+++ b/test/integration_selenium/test_allowlist_sanitization.py
@@ -0,0 +1,52 @@
+from .framework import (
+    selenium_test,
+    SeleniumIntegrationTestCase,
+)
+
+
+class TestAllowListSanitization(SeleniumIntegrationTestCase):
+    run_as_admin = True
+    axe_skip = True  # skip testing iframe contents
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        super().handle_galaxy_config_kwds(config)
+        config["sanitize_all_html"] = True
+
+    def run_html_output(self):
+        history_id = self.dataset_populator.new_history()
+        run_response = self.dataset_populator.run_tool("html_output", {}, history_id=history_id)
+        hda_id = run_response["outputs"][0]["id"]
+        self.dataset_populator.wait_for_dataset(history_id, dataset_id=hda_id)
+        return hda_id
+
+    @selenium_test
+    def test_html_output_sanitized(self):
+        self.login()
+        hda_id = self.run_html_output()
+        self.get(f"datasets/{hda_id}/preview")
+        self.wait_for_selector_visible("[data-description='sanitization warning']")
+        self.assert_selector_absent("[data-description='allowlist link']")
+        self.screenshot("sanitization warning")
+        assert self.switch_to_frame()
+        self.assert_selector_absent("[data-description='hello-world']")
+
+    @selenium_test
+    def test_html_output_sanitized_admin(self):
+        self.admin_login()
+        hda_id = self.run_html_output()
+        self.get(f"datasets/{hda_id}/preview")
+        self.wait_for_selector_visible("[data-description='sanitization warning']")
+        self.wait_for_selector_visible("[data-description='allowlist link']")
+        self.screenshot("sanitization warning admin")
+        try:
+            self._put(
+                "/api/sanitize_allow?tool_id=html_output", data={"params": {"tool_id": "html_output"}}, admin=True
+            ).raise_for_status()
+            self.driver.refresh()
+            self.assert_selector_absent("[data-description='sanitization warning']")
+            self.assert_selector_absent("[data-description='allowlist link']")
+            assert self.switch_to_frame()
+            self.wait_for_selector("[data-description='hello-world']")
+        finally:
+            self._delete("/api/sanitize_allow?tool_id=html_output", admin=True)
diff --git a/test/integration_selenium/test_edam_tool_panel_views.py b/test/integration_selenium/test_edam_tool_panel_views.py
index a98b608d2e6a31674a6bb0efc949b3306cee3d39..ac10392f87357ae426d389aff7d6073628792779 100644
--- a/test/integration_selenium/test_edam_tool_panel_views.py
+++ b/test/integration_selenium/test_edam_tool_panel_views.py
@@ -28,13 +28,14 @@ class TestEdamToolPanelViewsSeleniumIntegration(SeleniumIntegrationTestCase):
 
         editor = self.components.workflow_editor
         editor.canvas_body.wait_for_visible()
-        editor.tool_menu.wait_for_visible()
+        self.open_toolbox()
         self._assert_displaying_edam_operations()
         self.screenshot("tool_panel_view_edam_workflow_editor")
 
     @retry_during_transitions
     def _assert_displaying_edam_operations(self):
         tool_panel = self.components.tool_panel
+        tool_panel.toolbox.wait_for_visible()
         labels = tool_panel.panel_labels.all()
         assert len(labels) > 0
         label0 = labels[0]
diff --git a/test/integration_selenium/test_objectstore_selection.py b/test/integration_selenium/test_objectstore_selection.py
index 85be2f93743032ee7d54e4d2c30fd818e72a7b7e..aa7f28b0118d7f45259a1b1817e1b5d26408890f 100644
--- a/test/integration_selenium/test_objectstore_selection.py
+++ b/test/integration_selenium/test_objectstore_selection.py
@@ -136,7 +136,6 @@ class TestObjectStoreSelectionSeleniumIntegration(SeleniumIntegrationTestCase, C
         preferences = self.components.preferences
         preferences.preferred_storage.wait_for_and_click()
         self.select_storage("__null__")
-
         self.run_environment_test_tool()
         self.wait_for_hid_ok_and_open_details(1)
         details = self.components.object_store_details
diff --git a/test/integration_selenium/test_toolbox_filters.py b/test/integration_selenium/test_toolbox_filters.py
index 2c61729c0d0ebdf4a716344316d362dfa74b0b48..f23c6342c0411719313c979183e9dc0f26fd17b6 100644
--- a/test/integration_selenium/test_toolbox_filters.py
+++ b/test/integration_selenium/test_toolbox_filters.py
@@ -26,6 +26,7 @@ class TestToolboxFiltersSeleniumIntegration(SeleniumIntegrationTestCase):
         the specified section is no longer displayed in the browser.
         """
         self.register()
+        self.components.tool_panel.tool_box.wait_for_visible()
         # The tool panel section should be visible and clickable at this stage
         section = self.driver.find_element(By.LINK_TEXT, "Test Section")
         self.action_chains().move_to_element(section).click().perform()
@@ -41,6 +42,7 @@ class TestToolboxFiltersSeleniumIntegration(SeleniumIntegrationTestCase):
         self.components.toolbox_filters.submit.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.home()
+        self.components.tool_panel.tool_box.wait_for_visible()
         # But now it should raise NoSuchElementException
         with self.assertRaises(NoSuchElementException):
             self.driver.find_element(By.LINK_TEXT, "Test Section")
diff --git a/test/integration_selenium/test_user_file_source_aws_public.py b/test/integration_selenium/test_user_file_source_aws_public.py
index 668d022b97f07b1e33759f24591c98edaa6e6c51..5ec2ba12d64de73a2316c3601733294e1ec0c3f6 100644
--- a/test/integration_selenium/test_user_file_source_aws_public.py
+++ b/test/integration_selenium/test_user_file_source_aws_public.py
@@ -15,7 +15,6 @@ class TestUserFileSourceAwsPublicSeleniumIntegration(BaseUserObjectStoreSelenium
     @managed_history
     @selenium_test
     def test_create_and_use(self):
-        self.navigate_to_user_preferences()
         random_name = self._get_random_name(prefix="Encyclopedia of DNA Elements ENCODE")
         instance = FileSourceInstance(
             template_id="aws_public",
diff --git a/test/integration_selenium/test_user_library_permissions.py b/test/integration_selenium/test_user_library_permissions.py
index 328c67b84a2f463de546ecefd9e9fb77607b4458..c3c24962eff46cae0c8055b4cb4d3e5e65212b58 100644
--- a/test/integration_selenium/test_user_library_permissions.py
+++ b/test/integration_selenium/test_user_library_permissions.py
@@ -57,7 +57,7 @@ class TestUserLibraryImport(SeleniumIntegrationTestCase):
         self.wait_for_selector_absent_or_hidden(self.modal_body_selector())
 
         # assert 'user import folder was not created' warning
-        self.components.libraries.folder.toast_warning.wait_for_visible()
+        self.components.libraries.folder.alert_not_exists_user_import_dir.wait_for_visible()
 
     @selenium_test
     def test_user_library_dataset_permissions(self):
diff --git a/test/integration_selenium/test_workflow_run_target.py b/test/integration_selenium/test_workflow_run_target.py
index b078d3e0de7ae0f3464c4566daf64acdbf8d1ee8..1e47aee98d30a2326864da0f15bf033efbfb71fb 100644
--- a/test/integration_selenium/test_workflow_run_target.py
+++ b/test/integration_selenium/test_workflow_run_target.py
@@ -38,9 +38,10 @@ class TestWorkflowRunTargetNewSeleniumIntegration(BaseWorkflowRunTargetTestCase)
         workflow_run.expanded_form.wait_for_absent_or_hidden()
         self.workflow_run_submit()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        workflow_run.new_history_target_link.wait_for_and_click()
+        workflow_run.new_history_badge.wait_for_visible()
+        workflow_run.history_target_link.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        workflow_run.new_history_target_link.wait_for_absent_or_hidden()
+        workflow_run.new_history_badge.wait_for_absent_or_hidden()
         self.workflow_run_wait_for_ok(hid=2, expand=True)
         self.assert_item_summary_includes(2, "2 sequences")
 
@@ -63,7 +64,7 @@ class TestWorkflowRunTargetCurrentSeleniumIntegration(BaseWorkflowRunTargetTestC
         workflow_run.expanded_form.wait_for_absent_or_hidden()
         self.workflow_run_submit()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        workflow_run.new_history_target_link.wait_for_absent_or_hidden()
+        workflow_run.new_history_badge.wait_for_absent_or_hidden()
         self.sleep_for(self.wait_types.UX_TRANSITION)
         self.workflow_run_wait_for_ok(hid=2, expand=True)
         self.assert_item_summary_includes(2, "2 sequences")
@@ -92,8 +93,9 @@ class TestWorkflowRunTargetSelectNewSeleniumIntegration(BaseWorkflowRunTargetTes
         workflow_run.runtime_setting_target.wait_for_absent_or_hidden()
         self.workflow_run_submit()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        workflow_run.new_history_target_link.wait_for_and_click()
+        workflow_run.new_history_badge.wait_for_visible()
+        workflow_run.history_target_link.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
-        workflow_run.new_history_target_link.wait_for_absent_or_hidden()
+        workflow_run.new_history_badge.wait_for_absent_or_hidden()
         self.workflow_run_wait_for_ok(hid=2, expand=True)
         self.assert_item_summary_includes(2, "2 sequences")
diff --git a/test/unit/app/authnz/test_custos_authnz.py b/test/unit/app/authnz/test_custos_authnz.py
index 0a940f5695d79d569fe334a7243e84873a64e793..70398ec71ec175bd745cf9690350adcd72baaff0 100644
--- a/test/unit/app/authnz/test_custos_authnz.py
+++ b/test/unit/app/authnz/test_custos_authnz.py
@@ -631,7 +631,12 @@ class TestCustosAuthnz(TestCase):
         provider = custos_authnz_token.provider
         email = custos_authnz_token.user.email
 
-        success, message, redirect_uri = self.custos_authnz.disconnect(provider, self.trans, email, "/")
+        success, message, redirect_uri = self.custos_authnz.disconnect(
+            provider,
+            self.trans,
+            disconnect_redirect_url="/",
+            email=email,
+        )
 
         assert 1 == len(self.trans.sa_session.deleted)
         deleted_token = self.trans.sa_session.deleted[0]
diff --git a/test/unit/app/jobs/test_job_wrapper.py b/test/unit/app/jobs/test_job_wrapper.py
index 8102089a17494cd96cb652a7505dc33447aeed78..0a2976c0d2d5ea34ed59c45302c8d04c97f284a5 100644
--- a/test/unit/app/jobs/test_job_wrapper.py
+++ b/test/unit/app/jobs/test_job_wrapper.py
@@ -117,10 +117,7 @@ class MockEvaluator:
         pass
 
     def build(self):
-        return TEST_COMMAND, "", [], []
-
-    def populate_interactivetools(self):
-        return []
+        return TEST_COMMAND, "", [], [], []
 
 
 class MockJobQueue:
diff --git a/test/unit/app/jobs/test_mapper.py b/test/unit/app/jobs/test_mapper.py
index f2ec4cd1b87bafd665fd10547c05b474a6e9b38a..effd1fe71cd8d991594addd63266b4ec12efa89d 100644
--- a/test/unit/app/jobs/test_mapper.py
+++ b/test/unit/app/jobs/test_mapper.py
@@ -1,8 +1,11 @@
 import uuid
+from typing import cast
 
 from galaxy.jobs import (
     HasResourceParameters,
+    JobConfiguration,
     JobDestination,
+    JobWrapper,
 )
 from galaxy.jobs.mapper import (
     ERROR_MESSAGE_NO_RULE_FUNCTION,
@@ -134,10 +137,10 @@ def __assert_mapper_errors_with_message(mapper, message):
 
 
 def __mapper(tool_job_destination=TOOL_JOB_DESTINATION):
-    job_wrapper = MockJobWrapper(tool_job_destination)
-    job_config = MockJobConfig()
+    job_wrapper = cast(JobWrapper, MockJobWrapper(tool_job_destination))
+    job_config = cast(JobConfiguration, MockJobConfig())
 
-    mapper = JobRunnerMapper(job_wrapper, {}, job_config)
+    mapper = JobRunnerMapper(job_wrapper, lambda url: JobDestination(), job_config)
     mapper.rules_module = test_rules
     return mapper
 
diff --git a/test/unit/app/jobs/test_queue_limit.py b/test/unit/app/jobs/test_queue_limit.py
new file mode 100644
index 0000000000000000000000000000000000000000..ab3bfed003e64c0fcb7fad7103b956ac13e93b6e
--- /dev/null
+++ b/test/unit/app/jobs/test_queue_limit.py
@@ -0,0 +1,133 @@
+from typing import Optional
+from unittest.mock import Mock
+
+from galaxy.jobs import (
+    JobConfigurationLimits,
+    MinimalJobWrapper,
+)
+from galaxy.model import (
+    GalaxySession,
+    Job,
+)
+from galaxy.model.unittest_utils import GalaxyDataTestApp
+from galaxy.model.unittest_utils.data_app import GalaxyDataTestConfig
+
+
+class MockJobConfig:
+
+    def __init__(self) -> None:
+        self.limits = JobConfigurationLimits()
+
+    def get_destinations(self, tag):
+        return [create_mock_destination()]
+
+
+class GalaxyJobConfigApp(GalaxyDataTestApp):
+
+    def __init__(self, config: Optional[GalaxyDataTestConfig] = None, **kwd):
+        super().__init__(config, **kwd)
+        self.job_config = MockJobConfig()
+
+
+def create_mock_app():
+    return GalaxyJobConfigApp()
+
+
+def create_job_wrapper(app: GalaxyJobConfigApp, user_id=None, session_id=None):
+    if session_id:
+        session = GalaxySession(id=session_id)
+        app.model.session.add(session)
+        app.model.session.commit()
+    job = create_mock_job(app, user_id, session_id)
+    job_wrapper = MinimalJobWrapper(job, app)  # type: ignore[arg-type]
+    return job_wrapper
+
+
+def create_mock_job(app: GalaxyJobConfigApp, user_id=None, session_id=None, state="new"):
+    """Creates a mock job object."""
+    job = Job()
+    job.user_id = user_id
+    job.session_id = session_id
+    job.state = state
+    app.model.session.add(job)
+    app.model.session.commit()
+    return job
+
+
+def create_mock_destination():
+    """Creates a mock job destination."""
+    job_destination_mock = Mock()
+    job_destination_mock.id = "one"
+    job_destination_mock.params = {}
+    job_destination_mock.runner = "test_runner"
+    job_destination_mock.tags = ["one", "two"]
+    return job_destination_mock
+
+
+def test_registered_user_limit():
+    app = create_mock_app()
+    job_wrapper = create_job_wrapper(app, user_id=1)
+    job = job_wrapper.get_job()
+    job_destination_mock = create_mock_destination()
+
+    for _ in range(2):
+        create_mock_job(app, user_id=1, state="running")
+
+    # Test below limit
+    job_wrapper.app.job_config.limits.registered_user_concurrent_jobs = 3
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is True
+
+    # Test at limit
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is False
+
+
+def test_anonymous_user_limit():
+    app = create_mock_app()
+    job_wrapper = create_job_wrapper(app, session_id=1)
+    job = job_wrapper.get_job()
+    job_destination_mock = create_mock_destination()
+
+    create_mock_job(app, session_id=1, state="running")
+
+    # Test below limit
+    app.job_config.limits.anonymous_user_concurrent_jobs = 2
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is True
+
+    # Test at limit
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is False
+
+
+def test_destination_total_limit():
+    app = create_mock_app()
+    job_wrapper = create_job_wrapper(app, user_id=1)
+    job = job_wrapper.get_job()
+    job_destination_mock = create_mock_destination()
+
+    # Test below limit
+    app.job_config.limits.destination_total_concurrent_jobs["one"] = 1
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is True
+
+    # Test at limit
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is False
+
+
+def test_destination_tag_limit():
+    app = create_mock_app()
+    job_wrapper = create_job_wrapper(app, user_id=1)
+    job = job_wrapper.get_job()
+    job_destination_mock = create_mock_destination()
+
+    # Test below limit
+    app.job_config.limits.destination_total_concurrent_jobs["two"] = 1
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is True
+
+    # Test at limit
+    result = job_wrapper.queue_with_limit(job, job_destination_mock)
+    assert result is False
diff --git a/test/unit/app/jobs/test_rule_helper.py b/test/unit/app/jobs/test_rule_helper.py
index 1d1197a0dc789fa8f8e92f87d87b2a7ad476df31..f3be1cdd20c05eeee35d1bf055b21acc434a7127 100644
--- a/test/unit/app/jobs/test_rule_helper.py
+++ b/test/unit/app/jobs/test_rule_helper.py
@@ -66,7 +66,7 @@ def __setup_fixtures(app):
     # user3 has no jobs.
     user1 = model.User(email=USER_EMAIL_1, password="pass1")
     user2 = model.User(email=USER_EMAIL_2, password="pass2")
-    user3 = model.User(email=USER_EMAIL_2, password="pass2")
+    user3 = model.User(email=USER_EMAIL_3, password="pass3")
 
     app.add(user1, user2, user3)
 
diff --git a/test/unit/app/managers/test_CitationsManager.py b/test/unit/app/managers/test_CitationsManager.py
index 027ab05303801608c3922940b5e2ea62812e563f..7997067288279f4a5063b5e7081d76331d823300 100644
--- a/test/unit/app/managers/test_CitationsManager.py
+++ b/test/unit/app/managers/test_CitationsManager.py
@@ -1,10 +1,13 @@
 import os.path
 import tempfile
 
+import responses
+
 from galaxy.managers.citations import DoiCache
 from galaxy.util.bunch import Bunch
 
 
+@responses.activate
 def test_DoiCache():
     with tempfile.TemporaryDirectory() as tmp_database_dir:
         config = Bunch(
@@ -16,5 +19,7 @@ def test_DoiCache():
             citation_cache_schema_name=None,
         )
         doi_cache = DoiCache(config)
-        assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
-        assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
+        dois = (("10.1093/bioinformatics/bts252", "Jörg"), ("10.1101/2021.12.24.474111", "Özkurt"))
+        for doi, author in dois:
+            responses.add(method="GET", url=f"https://doi.org/{doi}", body=author)
+            assert author in doi_cache.get_bibtex(doi)
diff --git a/test/unit/app/managers/test_CitationsManager_db.py b/test/unit/app/managers/test_CitationsManager_db.py
index d159015949a9bd21eb47bc048abcf7462a6c4a3b..3df9673b70b3ba20cd1e58716aaf150faf70a86e 100644
--- a/test/unit/app/managers/test_CitationsManager_db.py
+++ b/test/unit/app/managers/test_CitationsManager_db.py
@@ -1,6 +1,4 @@
-from unittest import SkipTest
-
-import requests
+import responses
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
 
@@ -27,16 +25,16 @@ class MockDoiCache(DoiCache):
         self._cache.clear()
 
 
+@responses.activate
 def test_DoiCache(url_factory):  # noqa: F811
     db_url = url_factory()
     with create_and_drop_database(db_url):
         doi_cache = MockDoiCache(galaxy.config.GalaxyAppConfiguration(override_tempdir=False), db_url)
         assert is_cache_empty(db_url, "doi")
-        try:
-            assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
-            assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
-        except requests.exceptions.RequestException as e:
-            raise SkipTest(f"dx.doi failed to respond: {e}")
+        dois = (("10.1093/bioinformatics/bts252", "Jörg"), ("10.1101/2021.12.24.474111", "Özkurt"))
+        for doi, author in dois:
+            responses.add(method="GET", url=f"https://doi.org/{doi}", body=author)
+            assert author in doi_cache.get_bibtex(doi)
         assert not is_cache_empty(db_url, "doi")
         doi_cache._cache.clear()
         assert is_cache_empty(db_url, "doi")
diff --git a/test/unit/app/managers/test_DatasetManager.py b/test/unit/app/managers/test_DatasetManager.py
index 91f891829fb615c6775323e5d4a3d502d8408db3..da4468994000ab51addc43879a1e5eeb7277756f 100644
--- a/test/unit/app/managers/test_DatasetManager.py
+++ b/test/unit/app/managers/test_DatasetManager.py
@@ -31,6 +31,11 @@ class TestDatasetManager(BaseTestCase):
         super().set_up_managers()
         self.dataset_manager = DatasetManager(self.app)
 
+    def create_dataset_with_permissions(self, manage_roles=None, access_roles=None) -> model.Dataset:
+        dataset = self.dataset_manager.create(flush=False)
+        self.dataset_manager.permissions.set(dataset, manage_roles, access_roles)
+        return dataset
+
     def test_create(self):
         self.log("should be able to create a new Dataset")
         dataset1 = self.dataset_manager.create()
@@ -125,7 +130,7 @@ class TestDatasetManager(BaseTestCase):
         )
         owner = self.user_manager.create(**user2_data)
         owner_private_role = self.user_manager.private_role(owner)
-        dataset = self.dataset_manager.create(manage_roles=[owner_private_role])
+        dataset = self.create_dataset_with_permissions(manage_roles=[owner_private_role])
 
         permissions = self.dataset_manager.permissions.get(dataset)
         assert isinstance(permissions, tuple)
@@ -157,7 +162,9 @@ class TestDatasetManager(BaseTestCase):
         self.log("should be able to create a new Dataset and give it private permissions")
         owner = self.user_manager.create(**user2_data)
         owner_private_role = self.user_manager.private_role(owner)
-        dataset = self.dataset_manager.create(manage_roles=[owner_private_role], access_roles=[owner_private_role])
+        dataset = self.create_dataset_with_permissions(
+            manage_roles=[owner_private_role], access_roles=[owner_private_role]
+        )
 
         permissions = self.dataset_manager.permissions.get(dataset)
         assert isinstance(permissions, tuple)
@@ -268,7 +275,7 @@ class TestDatasetSerializer(BaseTestCase):
 
     def test_serializers(self):
         # self.user_manager.create( **user2_data )
-        dataset = self.dataset_manager.create()
+        dataset = self.dataset_manager.create(state=model.Dataset.states.NEW)
         all_keys = list(self.dataset_serializer.serializable_keyset)
         serialized = self.dataset_serializer.serialize(dataset, all_keys)
 
diff --git a/test/unit/app/managers/test_HDAManager.py b/test/unit/app/managers/test_HDAManager.py
index a868c7ce5ca352dcf23388e63facd27a1e61e633..aac4e2273c4b0603a0bcf8be1a1c72b1ebe58b9e 100644
--- a/test/unit/app/managers/test_HDAManager.py
+++ b/test/unit/app/managers/test_HDAManager.py
@@ -412,7 +412,7 @@ class TestHDASerializer(HDATestCase):
         assert isinstance(serialized["file_size"], int)
         assert isinstance(serialized["nice_size"], str)
         # TODO: these should be tested w/copy
-        self.assertNullableEncodedId(serialized["copied_from_history_dataset_association_id"])
+        assert isinstance(serialized["copied_from_history_dataset_association_id"], int)
         self.assertNullableEncodedId(serialized["copied_from_library_dataset_dataset_association_id"])
         self.assertNullableBasestring(serialized["info"])
         self.assertNullableBasestring(serialized["blurb"])
diff --git a/test/unit/app/managers/test_HistoryManager.py b/test/unit/app/managers/test_HistoryManager.py
index 021e348fc0194acaf5e1e89bda0a5f45288b69ed..8696c7ba7c6953a0a202598e6d94c4dcf24a38d6 100644
--- a/test/unit/app/managers/test_HistoryManager.py
+++ b/test/unit/app/managers/test_HistoryManager.py
@@ -66,7 +66,7 @@ class TestHistoryManager(BaseTestCase):
             == self.trans.sa_session.execute(select(model.History).filter(model.History.user == user2)).scalar_one()
         )
 
-        history2 = self.history_manager.copy(history1, user=user3)
+        history2 = history1.copy(target_user=user3)
 
         self.log("should be able to query")
         histories = self.trans.sa_session.scalars(select(model.History)).all()
@@ -108,7 +108,7 @@ class TestHistoryManager(BaseTestCase):
         self.app.tag_handler.set_tags_from_list(user=user2, item=hda, new_tags_list=hda_tags)
         self.hda_manager.annotate(hda, hda_annotation, user=user2)
 
-        history2 = self.history_manager.copy(history1, user=user3)
+        history2 = history1.copy(target_user=user3)
         assert isinstance(history2, model.History)
         assert history2.user == user3
         assert history2 == self.trans.sa_session.get(model.History, history2.id)
diff --git a/test/unit/app/managers/test_NotificationManager.py b/test/unit/app/managers/test_NotificationManager.py
index 6e0c36397c959327d904abd602d46963f44733e2..76e934cc9e6fa637c8edf9a48c6227f7e4ab2cf9 100644
--- a/test/unit/app/managers/test_NotificationManager.py
+++ b/test/unit/app/managers/test_NotificationManager.py
@@ -524,8 +524,9 @@ class TestNotificationRecipientResolver(NotificationsBaseTestCase):
         sa_session = self.trans.sa_session
         group = Group(name=name)
         sa_session.add(group)
-        self.trans.app.security_agent.set_entity_group_associations(groups=[group], roles=roles, users=users)
-        sa_session.flush()
+        user_ids = [user.id for user in users]
+        role_ids = [role.id for role in roles]
+        self.trans.app.security_agent.set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
         return group
 
     def _create_test_role(self, name: str, users: List[User], groups: List[Group]):
diff --git a/test/unit/app/managers/test_landing.py b/test/unit/app/managers/test_landing.py
new file mode 100644
index 0000000000000000000000000000000000000000..f2ccb059b4bfce2fe8d4ff96f9d2816787c28815
--- /dev/null
+++ b/test/unit/app/managers/test_landing.py
@@ -0,0 +1,184 @@
+from uuid import uuid4
+
+from galaxy.config import GalaxyAppConfiguration
+from galaxy.exceptions import (
+    InsufficientPermissionsException,
+    ItemAlreadyClaimedException,
+    ItemMustBeClaimed,
+    ObjectNotFound,
+)
+from galaxy.managers.landing import LandingRequestManager
+from galaxy.managers.workflows import WorkflowContentsManager
+from galaxy.model import (
+    StoredWorkflow,
+    Workflow,
+)
+from galaxy.model.base import transaction
+from galaxy.schema.schema import (
+    ClaimLandingPayload,
+    CreateToolLandingRequestPayload,
+    CreateWorkflowLandingRequestPayload,
+    LandingRequestState,
+    ToolLandingRequest,
+    WorkflowLandingRequest,
+)
+from galaxy.workflow.trs_proxy import TrsProxy
+from .base import BaseTestCase
+
+TEST_TOOL_ID = "cat1"
+TEST_TOOL_VERSION = "1.0.0"
+TEST_STATE = {
+    "input1": {
+        "src": "url",
+        "url": "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt",
+        "ext": "txt",
+    },
+}
+CLIENT_SECRET = "mycoolsecret"
+
+
+class TestLanding(BaseTestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.workflow_contents_manager = WorkflowContentsManager(self.app, self.app.trs_proxy)
+        self.landing_manager = LandingRequestManager(
+            self.trans.sa_session, self.app.security, self.workflow_contents_manager
+        )
+        self.trans.app.trs_proxy = TrsProxy(GalaxyAppConfiguration(override_tempdir=False))
+
+    def test_tool_landing_requests_typical_flow(self):
+        landing_request: ToolLandingRequest = self.landing_manager.create_tool_landing_request(self._tool_request)
+        assert landing_request.state == LandingRequestState.UNCLAIMED
+        assert landing_request.uuid is not None
+        uuid = landing_request.uuid
+        claim_payload = ClaimLandingPayload(client_secret=CLIENT_SECRET)
+        landing_request = self.landing_manager.claim_tool_landing_request(self.trans, uuid, claim_payload)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+        landing_request = self.landing_manager.get_tool_landing_request(self.trans, uuid)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+
+    def test_tool_landing_requests_requires_matching_client_secret(self):
+        landing_request: ToolLandingRequest = self.landing_manager.create_tool_landing_request(self._tool_request)
+        uuid = landing_request.uuid
+        claim_payload = ClaimLandingPayload(client_secret="wrongsecret")
+        exception = None
+        try:
+            self.landing_manager.claim_tool_landing_request(self.trans, uuid, claim_payload)
+        except InsufficientPermissionsException as e:
+            exception = e
+        assert exception is not None
+
+    def test_tool_landing_requests_get_requires_claim(self):
+        landing_request: ToolLandingRequest = self.landing_manager.create_tool_landing_request(self._tool_request)
+        uuid = landing_request.uuid
+        exception = None
+        try:
+            self.landing_manager.get_tool_landing_request(self.trans, uuid)
+        except ItemMustBeClaimed as e:
+            exception = e
+        assert exception is not None
+
+    def test_cannot_reclaim_tool_landing(self):
+        landing_request: ToolLandingRequest = self.landing_manager.create_tool_landing_request(self._tool_request)
+        assert landing_request.state == LandingRequestState.UNCLAIMED
+        uuid = landing_request.uuid
+        claim_payload = ClaimLandingPayload(client_secret=CLIENT_SECRET)
+        landing_request = self.landing_manager.claim_tool_landing_request(self.trans, uuid, claim_payload)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        exception = None
+        try:
+            self.landing_manager.claim_tool_landing_request(self.trans, uuid, claim_payload)
+        except ItemAlreadyClaimedException as e:
+            exception = e
+        assert exception
+
+    def test_get_tool_unknown_claim(self):
+        exception = None
+        try:
+            self.landing_manager.get_tool_landing_request(self.trans, uuid4())
+        except ObjectNotFound as e:
+            exception = e
+        assert exception
+
+    def test_stored_workflow_landing_requests_typical_flow(self):
+        landing_request: WorkflowLandingRequest = self.landing_manager.create_workflow_landing_request(
+            self._stored_workflow_request
+        )
+        assert landing_request.state == LandingRequestState.UNCLAIMED
+        assert landing_request.uuid is not None
+        assert landing_request.workflow_target_type == "stored_workflow"
+        uuid = landing_request.uuid
+        claim_payload = ClaimLandingPayload(client_secret=CLIENT_SECRET)
+        landing_request = self.landing_manager.claim_workflow_landing_request(self.trans, uuid, claim_payload)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+        assert landing_request.workflow_target_type == "stored_workflow"
+        landing_request = self.landing_manager.get_workflow_landing_request(self.trans, uuid)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+        assert landing_request.workflow_target_type == "stored_workflow"
+
+    def test_workflow_landing_requests_typical_flow(self):
+        landing_request: WorkflowLandingRequest = self.landing_manager.create_workflow_landing_request(
+            self._workflow_request
+        )
+        assert landing_request.state == LandingRequestState.UNCLAIMED
+        assert landing_request.uuid is not None
+        assert landing_request.workflow_target_type == "workflow"
+        uuid = landing_request.uuid
+        claim_payload = ClaimLandingPayload(client_secret=CLIENT_SECRET)
+        landing_request = self.landing_manager.claim_workflow_landing_request(self.trans, uuid, claim_payload)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+        assert landing_request.workflow_target_type == "workflow"
+        landing_request = self.landing_manager.get_workflow_landing_request(self.trans, uuid)
+        assert landing_request.state == LandingRequestState.CLAIMED
+        assert landing_request.uuid == uuid
+        assert landing_request.workflow_target_type == "workflow"
+
+    @property
+    def _tool_request(self) -> CreateToolLandingRequestPayload:
+        return CreateToolLandingRequestPayload(
+            tool_id=TEST_TOOL_ID,
+            tool_version=TEST_TOOL_VERSION,
+            request_state=TEST_STATE.copy(),
+            client_secret=CLIENT_SECRET,
+        )
+
+    @property
+    def _stored_workflow_request(self) -> CreateWorkflowLandingRequestPayload:
+        sa_session = self.app.model.context
+        stored_workflow = StoredWorkflow()
+        stored_workflow.user = self.trans.user
+        sa_session.add(stored_workflow)
+        with transaction(sa_session):
+            sa_session.commit()
+
+        return CreateWorkflowLandingRequestPayload(
+            workflow_id=self.app.security.encode_id(stored_workflow.id),
+            workflow_target_type="stored_workflow",
+            request_state=TEST_STATE.copy(),
+            client_secret=CLIENT_SECRET,
+        )
+
+    @property
+    def _workflow_request(self) -> CreateWorkflowLandingRequestPayload:
+        sa_session = self.app.model.context
+        stored_workflow = StoredWorkflow()
+        stored_workflow.user = self.trans.user
+        workflow = Workflow()
+        workflow.stored_workflow = stored_workflow
+        sa_session.add(stored_workflow)
+        sa_session.add(workflow)
+        with transaction(sa_session):
+            sa_session.commit()
+
+        return CreateWorkflowLandingRequestPayload(
+            workflow_id=self.app.security.encode_id(workflow.id),
+            workflow_target_type="workflow",
+            request_state=TEST_STATE.copy(),
+            client_secret=CLIENT_SECRET,
+        )
diff --git a/test/unit/app/managers/test_user_file_sources.py b/test/unit/app/managers/test_user_file_sources.py
index c0362b08bb8c46942576daa5a916b79cd5d8bcc9..bb30feed8184e62f2ba9833d76bcb0f0d5b2296f 100644
--- a/test/unit/app/managers/test_user_file_sources.py
+++ b/test/unit/app/managers/test_user_file_sources.py
@@ -5,7 +5,16 @@ from typing import (
     Optional,
     Type,
 )
+from unittest import SkipTest
+from uuid import uuid4
 
+from fs.osfs import OSFS
+
+try:
+    from fs.dropboxfs import DropboxFS
+except ImportError:
+    DropboxFS = None
+from requests.exceptions import HTTPError
 from yaml import safe_load
 
 from galaxy.exceptions import (
@@ -13,12 +22,15 @@ from galaxy.exceptions import (
     RequestParameterMissingException,
 )
 from galaxy.files import FileSourcesUserContext
+from galaxy.files.sources import dropbox
 from galaxy.files.templates import ConfiguredFileSourceTemplates
 from galaxy.files.templates.examples import get_example
 from galaxy.managers.file_source_instances import (
     CreateInstancePayload,
     FileSourceInstancesManager,
     ModifyInstancePayload,
+    TestUpdateInstancePayload,
+    TestUpgradeInstancePayload,
     UpdateInstancePayload,
     UpdateInstanceSecretPayload,
     UpgradeInstancePayload,
@@ -27,6 +39,12 @@ from galaxy.managers.file_source_instances import (
     UserDefinedFileSourcesImpl,
     UserFileSourceModel,
 )
+from galaxy.model import (
+    get_uuid,
+    UserFileSource,
+)
+from galaxy.schema.schema import OAuth2State
+from galaxy.util import config_templates
 from galaxy.util.config_templates import RawTemplateConfig
 from .base import BaseTestCase
 
@@ -205,6 +223,138 @@ class TestFileSourcesTestCase(BaseTestCase):
         assert file_source.get_scheme() == USER_FILE_SOURCES_SCHEME
         assert file_source.get_uri_root() == uri_root
 
+    def test_oauth2_flow(self, tmp_path, monkeypatch):
+
+        json = {
+            "refresh_token": "my_test_refresh_token",
+        }
+
+        def mock_get_token_from_code_raw(
+            code,
+            client_pair,
+            config,
+            redirect_uri,
+        ):
+            return MockResponse(json)
+
+        monkeypatch.setattr(config_templates, "get_token_from_code_raw", mock_get_token_from_code_raw)
+
+        self._init_dropbox_env(tmp_path, monkeypatch)
+
+        authorize_url = self.manager.template_oauth2(self.trans, "dropbox", 0).authorize_url
+        from urllib.parse import (
+            parse_qs,
+            urlparse,
+        )
+
+        parse_result = urlparse(authorize_url)
+        assert parse_result.hostname == "www.dropbox.com"
+        assert parse_result.path == "/oauth2/authorize"
+        query_params = parse_qs(parse_result.query)
+        assert "state" in query_params
+        state_param = query_params["state"]
+        state = OAuth2State.decode(state_param[0])
+        assert state.route == "file_source_instances/dropbox/0"
+        redirect_url = self.manager.handle_authorization_code(
+            self.trans,
+            "moocow",
+            state,
+        )
+        parse_result = urlparse(redirect_url)
+        query_params = parse_qs(parse_result.query)
+        assert "uuid" in query_params
+        uuid_param = query_params["uuid"]
+        uuid = uuid_param[0]
+
+        user_vault = self.trans.user_vault
+        config_secret_key = UserFileSource.vault_key_from_uuid(uuid, "_oauth2_refresh_token", None)
+        assert user_vault.read_secret(config_secret_key)
+
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="dropbox",
+            template_version=0,
+            variables={},
+            secrets={},
+            uuid=uuid,
+        )
+        user_object = self._create_instance(create_payload)
+        assert get_uuid(user_object.uuid) == get_uuid(uuid)
+
+    def test_oauth2_access_token_injection_during_verify(self, tmp_path, monkeypatch):
+        if DropboxFS is None:
+            raise SkipTest("Optional dropbpox dependency not available")
+        self._init_dropbox_env(tmp_path, monkeypatch)
+
+        uuid = uuid4().hex
+        user_vault = self.trans.user_vault
+        config_secret_key = UserFileSource.vault_key_from_uuid(uuid, "_oauth2_refresh_token", None)
+        user_vault.write_secret(config_secret_key, "test_refresh_token")
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="dropbox",
+            template_version=0,
+            variables={},
+            secrets={},
+            uuid=uuid,
+        )
+        self._create_instance(create_payload)
+        json = {
+            "access_token": "my_test_access_token",
+        }
+
+        def mock_get_token_from_refresh_raw(refresh_token, client_pair, config):
+            return MockResponse(json)
+
+        pyfilesystem_fs_init_kwd = {}
+
+        class MockDropboxFS(OSFS):
+
+            def __init__(self, **kwd):
+                pyfilesystem_fs_init_kwd.update(kwd)
+                root = tmp_path / "foobar"
+                root.mkdir()
+                super().__init__(root)
+
+        monkeypatch.setattr(config_templates, "get_token_from_refresh_raw", mock_get_token_from_refresh_raw)
+        monkeypatch.setattr(dropbox, "DropboxFS", MockDropboxFS)
+        status = self.manager.plugin_status(self.trans, create_payload)
+        assert status.oauth2_access_token_generation
+        assert not status.oauth2_access_token_generation.is_not_ok
+        assert status.connection
+        assert not status.connection.is_not_ok
+        assert pyfilesystem_fs_init_kwd["access_token"] == "my_test_access_token"
+
+    def test_report_oauth2_access_token_generation_failure(self, tmp_path, monkeypatch):
+        self._init_dropbox_env(tmp_path, monkeypatch)
+
+        uuid = uuid4().hex
+        user_vault = self.trans.user_vault
+        config_secret_key = UserFileSource.vault_key_from_uuid(uuid, "_oauth2_refresh_token", None)
+        user_vault.write_secret(config_secret_key, "test_refresh_token")
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="dropbox",
+            template_version=0,
+            variables={},
+            secrets={},
+            uuid=uuid,
+        )
+        self._create_instance(create_payload)
+        excepton_message = "There is an issue with the refresh_token"
+
+        def mock_get_token_from_refresh_raw(refresh_token, client_pair, config):
+            return MockExceptionResponse(excepton_message)
+
+        monkeypatch.setattr(config_templates, "get_token_from_refresh_raw", mock_get_token_from_refresh_raw)
+        status = self.manager.plugin_status(self.trans, create_payload)
+        assert status.oauth2_access_token_generation
+        assert status.oauth2_access_token_generation.is_not_ok
+        assert excepton_message in status.oauth2_access_token_generation.message
+
     def test_io(self, tmp_path):
         self._init_managers(tmp_path)
         user_file_source = self._create_user_file_source()
@@ -532,6 +682,100 @@ class TestFileSourcesTestCase(BaseTestCase):
         assert "Input should be a valid boolean" in status.template_settings.message
         assert status.connection is None
 
+    def test_status_existing_valid(self, tmp_path):
+        self.init_user_in_database()
+        self._init_managers(tmp_path)
+        (tmp_path / self.trans.user.username).mkdir()
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="home_directory",
+            template_version=0,
+            variables={},
+            secrets={},
+        )
+        user_file_source = self._create_instance(create_payload)
+        status = self.manager.plugin_status_for_instance(self.trans, user_file_source.uuid)
+        assert status.connection
+        assert not status.connection.is_not_ok
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+
+    def test_status_update_valid(self, tmp_path):
+        self._init_managers(tmp_path, config_dict=simple_variable_template(tmp_path))
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="simple_variable",
+            template_version=0,
+            variables={"var1": "originalvarval"},
+            secrets={},
+        )
+        user_file_source = self._create_instance(create_payload)
+
+        update = TestUpdateInstancePayload(
+            variables={
+                "var1": "newval",
+            }
+        )
+
+        status = self.manager.test_modify_instance(self.trans, user_file_source.uuid, update)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+        assert status.connection
+        assert status.connection.is_not_ok
+
+    def test_status_upgrade_valid(self, tmp_path):
+        user_file_source = self._init_upgrade_test_case(tmp_path)
+        assert "sec1" in user_file_source.secrets
+        assert "sec2" not in user_file_source.secrets
+        self._assert_secret_is(user_file_source, "sec1", "moocow")
+        self._assert_secret_absent(user_file_source, "foobarxyz")
+        self._assert_secret_absent(user_file_source, "sec2")
+        upgrade_to_1 = TestUpgradeInstancePayload(
+            template_version=1,
+            secrets={
+                "sec1": "moocow",
+                "sec2": "aftersec2",
+            },
+            variables={},
+        )
+        status = self.manager.test_modify_instance(self.trans, user_file_source.uuid, upgrade_to_1)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+        assert status.connection
+        assert status.connection.is_not_ok
+
+    def test_status_upgrade_invalid(self, tmp_path):
+        user_file_source = self._init_invalid_upgrade_test_case(tmp_path)
+        upgrade_to_1 = TestUpgradeInstancePayload(
+            template_version=1,
+            secrets={},
+            variables={},
+        )
+        status = self.manager.test_modify_instance(self.trans, user_file_source.uuid, upgrade_to_1)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert status.template_settings.is_not_ok
+        assert "Input should be a valid boolean" in status.template_settings.message
+        assert status.connection is None
+
+    def _init_invalid_upgrade_test_case(self, tmp_path) -> UserFileSourceModel:
+        version_0 = home_directory_template(tmp_path)
+        version_0["version"] = 0
+        version_1 = invalid_home_directory_template_type_error(tmp_path)
+        version_1["version"] = 1
+        version_1["id"] = version_0["id"]
+        config_dict = [
+            version_0,
+            version_1,
+        ]
+        self._init_managers(tmp_path, config_dict=config_dict)
+        return self._create_user_file_source()
+
     def _init_upgrade_test_case(self, tmp_path) -> UserFileSourceModel:
         example_yaml_str = UPGRADE_EXAMPLE
         example_yaml_str.replace("/data", str(tmp_path))
@@ -545,6 +789,13 @@ class TestFileSourcesTestCase(BaseTestCase):
         user_file_source = self._create_user_file_source()
         return user_file_source
 
+    def _init_dropbox_env(self, tmp_path, monkeypatch):
+        self.init_user_in_database()
+        self._init_managers(tmp_path, safe_load(get_example("production_dropbox.yml")))
+
+        monkeypatch.setenv("GALAXY_DROPBOX_APP_CLIENT_ID", "mock_client_id")
+        monkeypatch.setenv("GALAXY_DROPBOX_APP_CLIENT_SECRET", "mock_client_secret")
+
     def _create_user_file_source(self, template_id="home_directory") -> UserFileSourceModel:
         create_payload = CreateInstancePayload(
             name=SIMPLE_FILE_SOURCE_NAME,
@@ -608,3 +859,28 @@ class TestFileSourcesTestCase(BaseTestCase):
         manager = self.app[FileSourceInstancesManager]
         self.file_sources = file_sources
         self.manager = manager
+
+
+class MockResponse:
+    _error_checked = False
+
+    def __init__(self, json):
+        self._json = json
+
+    def raise_for_status(self):
+        self._error_checked = True
+
+    def json(self):
+        return self._json
+
+    def assert_error_checked(self):
+        assert self._error_checked
+
+
+class MockExceptionResponse:
+
+    def __init__(self, exception_msg: str):
+        self._exception_msg = exception_msg
+
+    def raise_for_status(self):
+        raise HTTPError(self._exception_msg, self._exception_msg, response=None)  # type: ignore[arg-type]
diff --git a/test/unit/app/managers/test_user_object_stores.py b/test/unit/app/managers/test_user_object_stores.py
index 96d11ee7ffc46dd01be31cf9d5d8b033ee43fd51..1ad20cc9af9127caffbbd962a59f291a1f4a03f5 100644
--- a/test/unit/app/managers/test_user_object_stores.py
+++ b/test/unit/app/managers/test_user_object_stores.py
@@ -14,6 +14,8 @@ from galaxy.managers.object_store_instances import (
     CreateInstancePayload,
     ModifyInstancePayload,
     ObjectStoreInstancesManager,
+    TestUpdateInstancePayload,
+    TestUpgradeInstancePayload,
     UpdateInstancePayload,
     UpdateInstanceSecretPayload,
     UpgradeInstancePayload,
@@ -146,9 +148,9 @@ class TestUserObjectStoreTestCase(BaseTestCase):
         assert response.variables
         assert response.variables["var1"] == "newval"
 
-        user_file_source_showed = self.manager.show(self.trans, user_object_store.uuid)
-        assert user_file_source_showed.variables
-        assert user_file_source_showed.variables["var1"] == "newval"
+        user_object_store_showed = self.manager.show(self.trans, user_object_store.uuid)
+        assert user_object_store_showed.variables
+        assert user_object_store_showed.variables["var1"] == "newval"
 
     def test_update_errors_on_extra_variables(self, tmp_path):
         self._init_managers(tmp_path, config_dict=simple_variable_template(tmp_path))
@@ -328,6 +330,25 @@ class TestUserObjectStoreTestCase(BaseTestCase):
         assert status.template_settings
         assert not status.template_settings.is_not_ok
 
+    def test_status_existing_valid(self, tmp_path):
+        self.init_user_in_database()
+        self._init_managers(tmp_path, simple_vault_template(tmp_path))
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="simple_vault",
+            template_version=0,
+            variables={},
+            secrets={"sec1": "foosec"},
+        )
+        user_object_store = self._create_instance(create_payload)
+        status = self.manager.plugin_status_for_instance(self.trans, user_object_store.uuid)
+        assert status.connection
+        assert not status.connection.is_not_ok
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+
     def test_status_invalid_settings_undefined_variable(self, tmp_path):
         self.init_user_in_database()
         self._init_managers(tmp_path, config_dict=simple_vault_template_with_undefined_jinja_problem(tmp_path))
@@ -348,6 +369,68 @@ class TestUserObjectStoreTestCase(BaseTestCase):
         )
         assert status.connection is None
 
+    def test_status_update_valid(self, tmp_path):
+        self._init_managers(tmp_path, config_dict=simple_variable_template(tmp_path))
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="simple_variable",
+            template_version=0,
+            variables={"var1": "originalvarval"},
+            secrets={},
+        )
+        user_object_store = self._create_instance(create_payload)
+
+        update = TestUpdateInstancePayload(
+            variables={
+                "var1": "newval",
+            }
+        )
+        status = self.manager.test_modify_instance(self.trans, user_object_store.uuid, update)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+        assert status.connection
+        assert not status.connection.is_not_ok
+
+    def test_status_upgrade_valid(self, tmp_path):
+        user_object_store = self._init_upgrade_test_case(tmp_path)
+        assert "sec1" in user_object_store.secrets
+        assert "sec2" not in user_object_store.secrets
+        self._assert_secret_is(user_object_store, "sec1", "moocow")
+        self._assert_secret_absent(user_object_store, "foobarxyz")
+        self._assert_secret_absent(user_object_store, "sec2")
+        upgrade_to_1 = TestUpgradeInstancePayload(
+            template_version=1,
+            secrets={
+                "sec1": "moocow",
+                "sec2": "aftersec2",
+            },
+            variables={},
+        )
+        status = self.manager.test_modify_instance(self.trans, user_object_store.uuid, upgrade_to_1)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert not status.template_settings.is_not_ok
+        assert status.connection
+        assert not status.connection.is_not_ok
+
+    def test_status_upgrade_invalid(self, tmp_path):
+        user_object_store = self._init_invalid_upgrade_test_case(tmp_path)
+        upgrade_to_1 = TestUpgradeInstancePayload(
+            template_version=1,
+            secrets={},
+            variables={},
+        )
+        status = self.manager.test_modify_instance(self.trans, user_object_store.uuid, upgrade_to_1)
+        assert not status.template_definition.is_not_ok
+        assert status.template_settings
+        assert status.template_settings.is_not_ok
+        assert (
+            "Problem with template definition causing invalid settings resolution" in status.template_settings.message
+        )
+        assert status.connection is None
+
     def _init_upgrade_test_case(self, tmp_path) -> UserConcreteObjectStoreModel:
         example_yaml_str = UPGRADE_EXAMPLE
         example_yaml_str.replace("/data", str(tmp_path))
@@ -356,6 +439,28 @@ class TestUserObjectStoreTestCase(BaseTestCase):
         user_object_store = self._create_instance(UPGRADE_INITIAL_PAYLOAD)
         return user_object_store
 
+    def _init_invalid_upgrade_test_case(self, tmp_path) -> UserConcreteObjectStoreModel:
+        version_0 = simple_vault_template(tmp_path)
+        version_0["version"] = 0
+        version_1 = simple_vault_template_with_undefined_jinja_problem(tmp_path)
+        version_1["version"] = 1
+        version_1["id"] = version_0["id"]
+        config_dict = [
+            version_0,
+            version_1,
+        ]
+        self._init_managers(tmp_path, config_dict=config_dict)
+        create_payload = CreateInstancePayload(
+            name=SIMPLE_FILE_SOURCE_NAME,
+            description=SIMPLE_FILE_SOURCE_DESCRIPTION,
+            template_id="simple_vault",
+            template_version=0,
+            variables={},
+            secrets={"sec1": "foosec"},
+        )
+        user_object_store = self._create_instance(create_payload)
+        return user_object_store
+
     def _read_secret(self, user_object_store: UserConcreteObjectStoreModel, secret_name: str) -> str:
         user_vault = self.trans.user_vault
         config_secret_key = f"object_store_config/{user_object_store.uuid}/{secret_name}"
diff --git a/test/unit/app/test_dbscript.py b/test/unit/app/test_dbscript.py
index 4b68c60d51d47dc74be949af942e310bc4197ef1..11ef77d27f4cdb38f8ae493d6bd3151617bad785 100644
--- a/test/unit/app/test_dbscript.py
+++ b/test/unit/app/test_dbscript.py
@@ -41,6 +41,9 @@ ADMIN_CMD = "manage_db.sh"
 DEV_CMD = "scripts/db_dev.sh"
 COMMANDS = [ADMIN_CMD, DEV_CMD]
 
+# Skip all but one due to slow speed. Leave one test as a "smoke test".
+SKIP_REASON = "Slow test: database migration management scripts"
+
 
 @pytest.fixture(scope="session")
 def migrations_dir() -> Traversable:
@@ -99,6 +102,7 @@ def create_alembic_branches(config: Config, gxy_versions_dir: str, tsi_versions_
     )
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestRevisionCommand:
     def test_revision_cmd(self, config):
         run_command(f"{DEV_CMD} revision --message foo1")
@@ -121,6 +125,7 @@ class TestRevisionCommand:
         assert "the following arguments are required: -m/--message" in completed.stderr
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestShowCommand:
     def test_show_cmd(self, config):
         alembic.command.revision(config, rev_id="42", head=GXY_BASE_ID)
@@ -146,6 +151,7 @@ class TestShowCommand:
         assert "the following arguments are required: revision" in completed.stderr
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestHistoryCommand:
     def test_history_cmd(self, config):
         alembic.command.revision(config, rev_id="1", head=GXY_BASE_ID)
@@ -180,6 +186,7 @@ class TestHistoryCommand:
         assert "gxy0 -> 1 (gxy)" in completed.stdout
 
 
+@pytest.mark.skip(SKIP_REASON)
 @pytest.mark.parametrize("command", COMMANDS)
 class TestVersionCommand:
     def test_version_cmd(self, config, command):
@@ -200,6 +207,7 @@ class TestVersionCommand:
         assert "Revises: 1" in completed.stdout
 
 
+@pytest.mark.skip(SKIP_REASON)
 @pytest.mark.parametrize("command", COMMANDS)
 class TestDbVersionCommand:
     def test_dbversion_cmd(self, config, command):
@@ -230,6 +238,7 @@ class TestDbVersionCommand:
 
 @pytest.mark.parametrize("command", COMMANDS)
 class TestUpgradeCommand:
+    @pytest.mark.skip(SKIP_REASON)
     def test_upgrade_cmd(self, config, command):
         alembic.command.revision(config, rev_id="1", head=GXY_BASE_ID)
         alembic.command.revision(config, rev_id="2", head="1")
@@ -271,6 +280,7 @@ class TestUpgradeCommand:
         assert "UPDATE alembic_version SET version_num='2'" in completed.stdout
         assert "UPDATE alembic_version SET version_num='3'" in completed.stdout
 
+    @pytest.mark.skip(SKIP_REASON)
     def test_upgrade_cmd_with_revision_arg(self, config, command):
         alembic.command.revision(config, rev_id="1", head=GXY_BASE_ID)
         alembic.command.revision(config, rev_id="2", head="1")
@@ -283,6 +293,7 @@ class TestUpgradeCommand:
         heads = get_db_heads(config)
         assert heads == ("1",)
 
+    @pytest.mark.skip(SKIP_REASON)
     def test_upgrade_cmd_with_relative_revision_syntax(self, config, command):
         alembic.command.revision(config, rev_id="a", head=GXY_BASE_ID)
         alembic.command.revision(config, rev_id="b", head="a")
@@ -309,6 +320,7 @@ class TestUpgradeCommand:
         heads = get_db_heads(config)
         assert heads == ("d",)
 
+    @pytest.mark.skip(SKIP_REASON)
     def test_repair_arg_available_to_dev_script_only(self, config, command):
         completed = run_command(f"{command} upgrade --repair")
         if command == DEV_CMD:
@@ -318,6 +330,7 @@ class TestUpgradeCommand:
             assert "unrecognized arguments: --repair" in completed.stderr
 
 
+@pytest.mark.skip(SKIP_REASON)
 @pytest.mark.parametrize("command", COMMANDS)
 class TestDowngradeCommand:
     def test_downgrade_cmd(self, config, command):
diff --git a/test/unit/app/tools/test_actions.py b/test/unit/app/tools/test_actions.py
index 1e6b69528ac70160a05ccb6d1de3db94b71a3fb4..a6126cfb8b323c3356679123c63601909966847c 100644
--- a/test/unit/app/tools/test_actions.py
+++ b/test/unit/app/tools/test_actions.py
@@ -14,8 +14,8 @@ from galaxy.tool_util.parser.xml import parse_change_format
 from galaxy.tools.actions import (
     DefaultToolAction,
     determine_output_format,
-    on_text_for_names,
 )
+from galaxy.tools.execution_helpers import on_text_for_names
 from galaxy.util import XML
 from galaxy.util.unittest import TestCase
 
@@ -140,7 +140,7 @@ class TestDefaultToolAction(TestCase, tools_support.UsesTools):
         if incoming is None:
             incoming = dict(param1="moo")
         self._init_tool(contents)
-        job, out_data, _ = self.action.execute(
+        job, out_data, *_ = self.action.execute(
             tool=self.tool,
             trans=self.trans,
             history=self.history,
@@ -231,7 +231,7 @@ def __assert_output_format_is(expected, output, input_extensions=None, param_con
         )
         c1.elements = [dce1, dce2]
 
-        input_collections["hdcai"] = [(hc1, False)]
+        input_collections["hdcai"] = hc1
 
     actual_format = determine_output_format(output, param_context, inputs, input_collections, last_ext)
     assert actual_format == expected, f"Actual format {actual_format}, does not match expected {expected}"
diff --git a/test/unit/app/tools/test_citations.py b/test/unit/app/tools/test_citations.py
index ab6b79292eec5397b3ace2dbf9511ee2fe6b9ed6..9f6d7943acac86a4744836e1eaaf478a91e9f6d4 100644
--- a/test/unit/app/tools/test_citations.py
+++ b/test/unit/app/tools/test_citations.py
@@ -3,6 +3,7 @@ from galaxy.managers.citations import (
     CitationCollection,
     parse_citation,
 )
+from galaxy.tool_util.parser.xml import parse_citation_elem
 from galaxy.util import parse_xml_string
 
 EXAMPLE_BIBTEX_CITATION = """<citation type="bibtex">@article{goecks2010galaxy,
@@ -19,7 +20,10 @@ EXAMPLE_BIBTEX_CITATION = """<citation type="bibtex">@article{goecks2010galaxy,
 def test_parse_citation():
     xml_text = EXAMPLE_BIBTEX_CITATION
     citation_elem = parse_xml_string(xml_text)
-    citation = parse_citation(citation_elem, None)
+    citation_model = parse_citation_elem(citation_elem)
+    assert citation_model
+    citation = parse_citation(citation_model, None)
+    assert citation
     bibtex = citation.to_bibtex()
     assert "title={Galaxy" in bibtex
 
diff --git a/test/unit/app/tools/test_data_fetch.py b/test/unit/app/tools/test_data_fetch.py
index 58e13e5d15497862ce4712c19965ea9258b89897..667e5e7ebbb18e0139330d45d77315efbed8bdf4 100644
--- a/test/unit/app/tools/test_data_fetch.py
+++ b/test/unit/app/tools/test_data_fetch.py
@@ -1,15 +1,32 @@
 import json
 import os
 import tempfile
+from base64 import b64encode
 from contextlib import contextmanager
 from shutil import rmtree
 from tempfile import mkdtemp
+from typing import Optional
+
+import pytest
 
 from galaxy.tools.data_fetch import main
 from galaxy.util.unittest_utils import skip_if_github_down
 
+B64_FOR_1_2_3 = b64encode(b"1 2 3").decode("utf-8")
+URI_FOR_1_2_3 = f"base64://{B64_FOR_1_2_3}"
+
 
-def test_simple_path_get():
+@pytest.mark.parametrize(
+    "hash_value, error_message",
+    [
+        ("471ddd37fc297fba09b893b88739ece9", None),
+        (
+            "thisisbad",
+            "Failed to validate upload with [MD5] - expected [thisisbad] got [471ddd37fc297fba09b893b88739ece9]",
+        ),
+    ],
+)
+def test_simple_path_get(hash_value: str, error_message: Optional[str]):
     with _execute_context() as execute_context:
         job_directory = execute_context.job_directory
         example_path = os.path.join(job_directory, "example_file")
@@ -21,13 +38,29 @@ def test_simple_path_get():
                     "destination": {
                         "type": "hdas",
                     },
-                    "elements": [{"src": "path", "path": example_path}],
+                    "elements": [
+                        {
+                            "src": "path",
+                            "path": example_path,
+                            "hashes": [
+                                {
+                                    "hash_function": "MD5",
+                                    "hash_value": hash_value,
+                                }
+                            ],
+                        }
+                    ],
                 }
-            ]
+            ],
         }
         execute_context.execute_request(request)
         output = _unnamed_output(execute_context)
         assert output
+        hda_result = output["elements"][0]
+        if error_message is not None:
+            assert hda_result["error_message"] == error_message
+        else:
+            assert "error_message" not in hda_result
 
 
 @skip_if_github_down
@@ -55,6 +88,130 @@ def test_simple_uri_get():
         assert hda_result["ext"] == "bed"
 
 
+def test_correct_md5():
+    with _execute_context() as execute_context:
+        request = {
+            "targets": [
+                {
+                    "destination": {
+                        "type": "hdas",
+                    },
+                    "elements": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [
+                                {
+                                    "hash_function": "MD5",
+                                    "hash_value": "5ba48b6e5a7c4d4930fda256f411e55b",
+                                }
+                            ],
+                        }
+                    ],
+                }
+            ],
+        }
+        execute_context.execute_request(request)
+        output = _unnamed_output(execute_context)
+        hda_result = output["elements"][0]
+        assert hda_result["state"] == "ok"
+        assert hda_result["ext"] == "txt"
+
+
+def test_incorrect_md5():
+    with _execute_context() as execute_context:
+        request = {
+            "targets": [
+                {
+                    "destination": {
+                        "type": "hdas",
+                    },
+                    "elements": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [
+                                {
+                                    "hash_function": "MD5",
+                                    "hash_value": "thisisbad",
+                                }
+                            ],
+                        }
+                    ],
+                }
+            ],
+        }
+        execute_context.execute_request(request)
+        output = _unnamed_output(execute_context)
+        hda_result = output["elements"][0]
+        assert (
+            hda_result["error_message"]
+            == "Failed to validate upload with [MD5] - expected [thisisbad] got [5ba48b6e5a7c4d4930fda256f411e55b]"
+        )
+
+
+def test_correct_sha1():
+    with _execute_context() as execute_context:
+        request = {
+            "targets": [
+                {
+                    "destination": {
+                        "type": "hdas",
+                    },
+                    "elements": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [
+                                {
+                                    "hash_function": "SHA-1",
+                                    "hash_value": "65e9d53484d28eef5447bc06fe2d754d1090975a",
+                                }
+                            ],
+                        }
+                    ],
+                }
+            ],
+        }
+        execute_context.execute_request(request)
+        output = _unnamed_output(execute_context)
+        hda_result = output["elements"][0]
+        assert hda_result["state"] == "ok"
+        assert hda_result["ext"] == "txt"
+
+
+def test_incorrect_sha1():
+    with _execute_context() as execute_context:
+        request = {
+            "targets": [
+                {
+                    "destination": {
+                        "type": "hdas",
+                    },
+                    "elements": [
+                        {
+                            "src": "url",
+                            "url": URI_FOR_1_2_3,
+                            "hashes": [
+                                {
+                                    "hash_function": "SHA-1",
+                                    "hash_value": "thisisbad",
+                                }
+                            ],
+                        }
+                    ],
+                }
+            ],
+        }
+        execute_context.execute_request(request)
+        output = _unnamed_output(execute_context)
+        hda_result = output["elements"][0]
+        assert (
+            hda_result["error_message"]
+            == "Failed to validate upload with [SHA-1] - expected [thisisbad] got [65e9d53484d28eef5447bc06fe2d754d1090975a]"
+        )
+
+
 @skip_if_github_down
 def test_deferred_uri_get():
     with _execute_context() as execute_context:
diff --git a/test/unit/app/tools/test_dynamic_options.py b/test/unit/app/tools/test_dynamic_options.py
index 38626d65b9919e9db164fd36a8ca194e534b5664..3de57c332e54aa9b07a2c4a35e3eb735bf4b44c7 100644
--- a/test/unit/app/tools/test_dynamic_options.py
+++ b/test/unit/app/tools/test_dynamic_options.py
@@ -1,11 +1,18 @@
 from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.tools.parameters.dynamic_options import DynamicOptions
+from galaxy.tools.parameters.options import ParameterOption
 from galaxy.util import XML
 from galaxy.util.bunch import Bunch
 from galaxy.work.context import WorkRequestContext
 
 
 def get_from_url_option():
+    tool_param = Bunch(
+        tool=Bunch(
+            app=Bunch(),
+        ),
+    )
+
     return DynamicOptions(
         XML(
             """
@@ -26,7 +33,7 @@ def get_from_url_option():
 </options>
 """
         ),
-        Bunch(),
+        tool_param,
     )
 
 
@@ -54,4 +61,4 @@ def test_dynamic_option_cache():
             "start_index": 0,
         },
     )
-    assert from_url_option.get_options(trans, {}) == [["chr2L", "23513712", False]]
+    assert from_url_option.get_options(trans, {}) == [ParameterOption("chr2L", "23513712", False)]
diff --git a/test/unit/app/tools/test_evaluation.py b/test/unit/app/tools/test_evaluation.py
index 52d25566b638a3a86745a43601a2406fbcd59a26..372f9b28b651776ee87909cd6d0a46f8d7a122c5 100644
--- a/test/unit/app/tools/test_evaluation.py
+++ b/test/unit/app/tools/test_evaluation.py
@@ -27,6 +27,7 @@ from galaxy.tools.parameters.grouping import (
     ConditionalWhen,
     Repeat,
 )
+from galaxy.tools.parameters.options import ParameterOption
 from galaxy.util import XML
 from galaxy.util.bunch import Bunch
 from galaxy.util.unittest import TestCase
@@ -57,8 +58,7 @@ class TestToolEvaluator(TestCase, UsesApp):
         assert command_line == "bwa --thresh=4 --in=/galaxy/files/dataset_1.dat --out=/galaxy/files/dataset_2.dat"
 
     def test_repeat_evaluation(self):
-        repeat = Repeat()
-        repeat.name = "r"
+        repeat = Repeat("r")
         repeat.inputs = {"thresh": self.tool.test_thresh_param()}
         self.tool.set_params({"r": repeat})
         self.job.parameters = [
@@ -85,8 +85,7 @@ class TestToolEvaluator(TestCase, UsesApp):
         select_xml = XML("""<param name="always_true" type="select"><option value="true">True</option></param>""")
         parameter = SelectToolParameter(self.tool, select_xml)
 
-        conditional = Conditional()
-        conditional.name = "c"
+        conditional = Conditional("c")
         conditional.test_param = parameter
         when = ConditionalWhen()
         when.inputs = {"thresh": self.tool.test_thresh_param()}
@@ -173,7 +172,7 @@ class TestToolEvaluator(TestCase, UsesApp):
             return ["/old/path/human"]
 
         def get_options(trans, other_values):
-            return [["", "/old/path/human", ""]]
+            return [ParameterOption("", "/old/path/human", False)]
 
         parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value, get_options=get_options)
         self.tool.set_params({"index_path": parameter})
diff --git a/test/unit/app/tools/test_metadata.py b/test/unit/app/tools/test_metadata.py
index 7e1784a84caa09ea659862f2fb5f094a74f1ab91..8f83c6b90ef66200ae2427a72a4b3fa5213388c7 100644
--- a/test/unit/app/tools/test_metadata.py
+++ b/test/unit/app/tools/test_metadata.py
@@ -18,7 +18,7 @@ class TestMetadata(TestCase, tools_support.UsesTools):
     def setUp(self):
         super().setUp()
         self.setup_app()
-        model.Dataset.object_store = self.app.object_store  # type: ignore[assignment]
+        model.Dataset.object_store = self.app.object_store
         job = model.Job()
         sa_session = self.app.model.session
         sa_session.add(job)
diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
index 842e7df91844ea77d2b4867dc6a534e43e21927d..e33e183fc962a61c46e08ac2e53aac130bfde188 100644
--- a/test/unit/app/tools/test_parameter_parsing.py
+++ b/test/unit/app/tools/test_parameter_parsing.py
@@ -452,3 +452,12 @@ class TestParameterParsing(BaseParameterTestCase):
         )
         assert param.type == "data_collection"
         assert param.collection_types == ["list", "list:paired"]
+
+    def test_data_allow_uri_if_protocol(self):
+        param = self._parameter_for(
+            xml="""
+            <param name="deferred" type="data" allow_uri_if_protocol="https,s3">
+            </param>
+        """
+        )
+        assert param.allow_uri_if_protocol == ["https", "s3"]
diff --git a/test/unit/app/tools/test_parameter_validation.py b/test/unit/app/tools/test_parameter_validation.py
index a7798927eb6587550681b9c38fd5cee13dbd5423..d2022c4cba42aa6510421b5e3ab71b4e23b7c59d 100644
--- a/test/unit/app/tools/test_parameter_validation.py
+++ b/test/unit/app/tools/test_parameter_validation.py
@@ -85,7 +85,7 @@ class TestParameterValidation(BaseParameterTestCase):
 </param>"""
         )
         p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter index: No options available for selection"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'index': No options available for selection"):
             p.validate(None)
 
         p = self._parameter_for(
@@ -95,7 +95,7 @@ class TestParameterValidation(BaseParameterTestCase):
     <validator type="no_options" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter index: Options available for selection"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'index': Options available for selection"):
             p.validate("foo")
         p.validate(None)
 
@@ -107,7 +107,7 @@ class TestParameterValidation(BaseParameterTestCase):
 </param>"""
         )
         p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Field requires a value"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field requires a value"):
             p.validate("")
 
         p = self._parameter_for(
@@ -116,7 +116,7 @@ class TestParameterValidation(BaseParameterTestCase):
     <validator type="empty_field" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Field must not set a value"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field must not set a value"):
             p.validate("foo")
         p.validate("")
 
@@ -130,14 +130,14 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate("Foo")
         p.validate("foo")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Fop' does not match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Fop' does not match regular expression '\[Ff\]oo'"
         ):
             p.validate("Fop")
 
         # test also valitation of lists (for select parameters)
         p.validate(["Foo", "foo"])
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Fop' does not match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Fop' does not match regular expression '\[Ff\]oo'"
         ):
             p.validate(["Foo", "Fop"])
 
@@ -148,16 +148,16 @@ class TestParameterValidation(BaseParameterTestCase):
 </param>"""
         )
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate("Foo")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate("foo")
         p.validate("Fop")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate(["Fop", "foo"])
         p.validate(["Fop", "fop"])
@@ -171,9 +171,9 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         p.validate("foo")
         p.validate("bar")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
             p.validate("f")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
             p.validate("foobarbaz")
 
         p = self._parameter_for(
@@ -182,9 +182,9 @@ class TestParameterValidation(BaseParameterTestCase):
     <validator type="length" min="2" max="8" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must not have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must not have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("bar")
         p.validate("f")
         p.validate("foobarbaz")
@@ -204,11 +204,11 @@ class TestParameterValidation(BaseParameterTestCase):
     <validator type="in_range" message="Doh!! %s not in range" min="10" exclude_min="true" max="20"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Doh!! 10 not in range"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 10 not in range"):
             p.validate(10)
         p.validate(15)
         p.validate(20)
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Doh!! 21 not in range"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 21 not in range"):
             p.validate(21)
 
         p = self._parameter_for(
@@ -220,12 +220,12 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate(10)
         with self.assertRaisesRegex(
             ValueError,
-            r"Parameter blah: Value \('15'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)",
+            r"Parameter 'blah': Value \('15'\) must not fulfill \(10 < value <= 20\)",
         ):
             p.validate(15)
         with self.assertRaisesRegex(
             ValueError,
-            r"Parameter blah: Value \('20'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)",
+            r"Parameter 'blah': Value \('20'\) must not fulfill \(10 < value <= 20\)",
         ):
             p.validate(20)
         p.validate(21)
@@ -253,7 +253,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate(ok_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset is still being generated, select another dataset or wait until it is completed",
+            "Parameter 'blah': The selected dataset is still being generated, select another dataset or wait until it is completed",
         ):
             p.validate(notok_hda)
         p = self._parameter_for(
@@ -262,7 +262,7 @@ class TestParameterValidation(BaseParameterTestCase):
     <validator type="dataset_ok_validator" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: The selected dataset must not be in state OK"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': The selected dataset must not be in state OK"):
             p.validate(ok_hda)
         p.validate(notok_hda)
 
@@ -288,7 +288,7 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         p.validate(full_hda)
         with self.assertRaisesRegex(
-            ValueError, "Parameter blah: The selected dataset is empty, this tool expects non-empty files."
+            ValueError, "Parameter 'blah': The selected dataset is empty, this tool expects non-empty files."
         ):
             p.validate(empty_hda)
 
@@ -299,7 +299,7 @@ class TestParameterValidation(BaseParameterTestCase):
 </param>"""
         )
         with self.assertRaisesRegex(
-            ValueError, "Parameter blah: The selected dataset is non-empty, this tool expects empty files."
+            ValueError, "Parameter 'blah': The selected dataset is non-empty, this tool expects empty files."
         ):
             p.validate(full_hda)
         p.validate(empty_hda)
@@ -329,7 +329,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate(has_extra_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input.",
+            "Parameter 'blah': The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input.",
         ):
             p.validate(has_no_extra_hda)
 
@@ -342,7 +342,7 @@ class TestParameterValidation(BaseParameterTestCase):
 
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset's extra_files_path directory is non-empty or does exist, this tool expects empty extra_files_path directories associated with the selected input.",
+            "Parameter 'blah': The selected dataset's extra_files_path directory is non-empty or does exist, this tool expects empty extra_files_path directories associated with the selected input.",
         ):
             p.validate(has_extra_hda)
         p.validate(has_no_extra_hda)
@@ -376,7 +376,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p = self._parameter_for(xml=param_xml.format(check="strandCol", skip=""))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -385,7 +385,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p = self._parameter_for(xml=param_xml.format(check="", skip="dbkey,comment_lines,column_names,nameCol"))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -398,7 +398,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p = self._parameter_for(xml=param_xml_negate.format(check="nameCol", skip=""))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: At least one of the checked metadata 'nameCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': At least one of the checked metadata 'nameCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -409,7 +409,7 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -437,7 +437,7 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate(has_dbkey_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Unspecified genome build, click the pencil icon in the history item to set the genome build",
+            "Parameter 'blah': Unspecified genome build, click the pencil icon in the history item to set the genome build",
         ):
             p.validate(has_no_dbkey_hda)
 
@@ -449,7 +449,7 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Specified genome build, click the pencil icon in the history item to remove the genome build",
+            "Parameter 'blah': Specified genome build, click the pencil icon in the history item to remove the genome build",
         ):
             p.validate(has_dbkey_hda)
         p.validate(has_no_dbkey_hda)
diff --git a/test/unit/app/tools/test_populate_state.py b/test/unit/app/tools/test_populate_state.py
new file mode 100644
index 0000000000000000000000000000000000000000..d641ff079397afd66c70ade3b39eec4c0fa462fe
--- /dev/null
+++ b/test/unit/app/tools/test_populate_state.py
@@ -0,0 +1,63 @@
+from typing import (
+    Any,
+    cast,
+    Dict,
+)
+
+from galaxy.tools.parameters import (
+    populate_state,
+    ToolInputsT,
+)
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    TextToolParameter,
+)
+from galaxy.tools.parameters.grouping import (
+    Conditional,
+    ConditionalWhen,
+    Repeat,
+)
+from galaxy.util import XML
+from galaxy.util.bunch import Bunch
+
+trans = Bunch(workflow_building_mode=False)
+
+
+def mock_when(**kwd):
+    return cast(ConditionalWhen, Bunch(**kwd))
+
+
+def test_populate_state():
+    a = TextToolParameter(None, XML('<param name="a"/>'))
+    b = Repeat("b")
+    b.min = 0
+    b.max = 1
+    c = TextToolParameter(None, XML('<param name="c"/>'))
+    d = Repeat("d")
+    d.min = 0
+    d.max = 1
+    e = TextToolParameter(None, XML('<param name="e"/>'))
+    f = Conditional("f")
+    g = BooleanToolParameter(None, XML('<param name="g"/>'))
+    h = TextToolParameter(None, XML('<param name="h"/>'))
+    i = TextToolParameter(None, XML('<param name="i"/>'))
+    b.inputs = {"c": c, "d": d}
+    d.inputs = {"e": e, "f": f}
+    f.test_param = g
+    f.cases = [mock_when(value="true", inputs={"h": h}), mock_when(value="false", inputs={"i": i})]
+    inputs = {"a": a, "b": b}
+    flat = {"a": 1, "b_0|c": 2, "b_0|d_0|e": 3, "b_0|d_0|f|h": 4, "b_0|d_0|f|g": True}
+    state: Dict[str, Any] = {}
+    populate_state(trans, cast(ToolInputsT, inputs), flat, state, check=False)
+    assert state["a"] == 1
+    assert state["b"][0]["c"] == 2
+    assert state["b"][0]["d"][0]["e"] == 3
+    assert state["b"][0]["d"][0]["f"]["h"] == 4
+    # now test with input_format='21.01'
+    nested = {"a": 1, "b": [{"c": 2, "d": [{"e": 3, "f": {"h": 4, "g": True}}]}]}
+    state_new: Dict[str, Any] = {}
+    populate_state(trans, cast(ToolInputsT, inputs), nested, state_new, check=False, input_format="21.01")
+    assert state_new["a"] == 1
+    assert state_new["b"][0]["c"] == 2
+    assert state_new["b"][0]["d"][0]["e"] == 3
+    assert state_new["b"][0]["d"][0]["f"]["h"] == 4
diff --git a/test/unit/app/tools/test_select_parameters.py b/test/unit/app/tools/test_select_parameters.py
index 656325490a954e93e4b8d0836927d268c2856503..63a56ad59e2f656f9138a364136ee3ed754eadf6 100644
--- a/test/unit/app/tools/test_select_parameters.py
+++ b/test/unit/app/tools/test_select_parameters.py
@@ -4,6 +4,7 @@ import pytest
 
 from galaxy import model
 from galaxy.model.base import transaction
+from galaxy.tools.parameters.options import ParameterOption
 from galaxy.tools.parameters.workflow_utils import RuntimeValue
 from .util import BaseParameterTestCase
 
@@ -42,15 +43,23 @@ class TestSelectToolParameter(BaseParameterTestCase):
 
     def test_filter_param_value(self):
         self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>"""
-        assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testname1"})
-        assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testname2"})
+        assert ParameterOption("testname1", "testpath1", False) in self.param.get_options(
+            self.trans, {"input_bam": "testname1"}
+        )
+        assert ParameterOption("testname2", "testpath2", False) in self.param.get_options(
+            self.trans, {"input_bam": "testname2"}
+        )
         assert len(self.param.get_options(self.trans, {"input_bam": "testname3"})) == 0
 
     def test_filter_param_value2(self):
         # Same test as above, but filtering on a different column.
         self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>"""
-        assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testpath1"})
-        assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testpath2"})
+        assert ParameterOption("testname1", "testpath1", False) in self.param.get_options(
+            self.trans, {"input_bam": "testpath1"}
+        )
+        assert ParameterOption("testname2", "testpath2", False) in self.param.get_options(
+            self.trans, {"input_bam": "testpath2"}
+        )
         assert len(self.param.get_options(self.trans, {"input_bam": "testpath3"})) == 0
 
     # TODO: Good deal of overlap here with TestDataToolParameter, refactor.
diff --git a/test/unit/app/tools/test_stock.py b/test/unit/app/tools/test_stock.py
new file mode 100644
index 0000000000000000000000000000000000000000..25aeca8753194d7adc323ff2df6ba784acaa064e
--- /dev/null
+++ b/test/unit/app/tools/test_stock.py
@@ -0,0 +1,16 @@
+from galaxy.tools.stock import (
+    stock_tool_paths,
+    stock_tool_sources,
+)
+
+
+def test_stock_tool_paths():
+    file_names = [f.name for f in list(stock_tool_paths())]
+    assert "merge_collection.xml" in file_names
+    assert "meme.xml" in file_names
+    assert "output_auto_format.xml" in file_names
+
+
+def test_stock_tool_sources():
+    tool_source = next(stock_tool_sources())
+    assert tool_source.parse_id()
diff --git a/test/unit/app/tools/test_validation_parsing.py b/test/unit/app/tools/test_validation_parsing.py
new file mode 100644
index 0000000000000000000000000000000000000000..c13b0973e6a0bcb9a9fe5ccacce87c45a4e2df63
--- /dev/null
+++ b/test/unit/app/tools/test_validation_parsing.py
@@ -0,0 +1,41 @@
+from typing import Optional
+
+from galaxy.tool_util.unittest_utils.sample_data import (
+    INVALID_XML_VALIDATORS,
+    VALID_XML_VALIDATORS,
+)
+from galaxy.tools.parameters.validation import parse_xml_validators
+from galaxy.util import XML
+
+
+class MockApp:
+
+    @property
+    def tool_data_tables(self):
+        return {"mycooltable": MockTable()}
+
+
+class MockTable:
+
+    def get_version_fields(self):
+        return (1, [])
+
+
+def test_xml_validation_valid():
+    for xml_validator in VALID_XML_VALIDATORS:
+        _validate_xml_str(xml_validator)
+
+
+def test_xml_validation_invalid():
+    for xml_validator in INVALID_XML_VALIDATORS:
+        exc: Optional[Exception] = None
+        try:
+            _validate_xml_str(xml_validator)
+        except ValueError as e:
+            exc = e
+        assert exc is not None, f"{xml_validator} - validated when it wasn't expected to"
+
+
+def _validate_xml_str(xml_str: str):
+    xml_el = XML(f"<param>{xml_str}</param>")
+    parse_xml_validators(MockApp(), xml_el)
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index f47366ad1826d49b7855cf97ebc96990a8b41cfd..e4a930287315500571f4e26eea8f023ebee67733 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -310,6 +310,7 @@ class MockDataset:
         self.extra_files_path = MOCK_DATASET_EXTRA_FILES_PATH
         self.ext = MOCK_DATASET_EXT
         self.tags = []
+        self.has_deferred_data = False
 
     def get_file_name(self, sync_cache=True, user=None):
         return MOCK_DATASET_PATH
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
index baf72fe065c826f1d81df5995263da8ae2134bab..772c54bb925e4cf432632956944c980dae2cdca4 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationPlugin.py
@@ -74,7 +74,7 @@ class TestVisualizationsPlugin(VisualizationsBase_TestCase):
         render_vars = plugin._build_render_vars(config)
         assert render_vars["visualization_name"] == plugin.name
         assert render_vars["visualization_display_name"] == plugin.config["name"]
-        assert render_vars["title"] is None
+        assert render_vars["title"] == "Unnamed Visualization"
         assert render_vars["saved_visualization"] is None
         assert render_vars["visualization_id"] is None
         assert render_vars["query"] == {}
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index 1c7f9707f047a0b5b935442aeba66630f701ba7f..6f5ce4274e70b13090a157b5a485ff0035120dde 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -15,7 +15,7 @@ from . import VisualizationsBase_TestCase
 
 glx_dir = galaxy_directory()
 template_cache_dir = os.path.join(glx_dir, "database", "compiled_templates")
-addtional_templates_dir = os.path.join(glx_dir, "config", "plugins", "visualizations", "common", "templates")
+additional_templates_dir = os.path.join(glx_dir, "config", "plugins", "visualizations", "common", "templates")
 vis_reg_path = "config/plugins/visualizations"
 
 config1 = """\
@@ -144,7 +144,7 @@ class TestVisualizationsRegistry(VisualizationsBase_TestCase):
                     <model_class>HistoryDatasetAssociation</model_class>
                 </data_source>
             </data_sources>
-            <entry_point entry_point_type="script" data-main="one" src="bler"></entry_point>
+            <entry_point entry_point_type="script" container="mycontainer" src="mysrc" css="mycss"></entry_point>
         </visualization>
         """
         )
@@ -167,11 +167,11 @@ class TestVisualizationsRegistry(VisualizationsBase_TestCase):
         assert script_entry.serves_templates
 
         trans = galaxy_mock.MockTrans()
-        script_entry._set_up_template_plugin(mock_app_dir.root_path, [addtional_templates_dir])
-        response = script_entry._render({}, trans=trans, embedded=True)
-        assert 'src="bler"' in response
-        assert 'type="text/javascript"' in response
-        assert 'data-main="one"' in response
+        script_entry._set_up_template_plugin(mock_app_dir.root_path, [additional_templates_dir])
+        response = script_entry.render(trans=trans, embedded=True)
+        assert '<script type="module" src="mysrc">' in response
+        assert '<link rel="stylesheet" href="mycss">' in response
+        assert "<div id=\"mycontainer\" data-incoming='{}'></div>" in response
         mock_app_dir.remove()
 
 
diff --git a/test/unit/config/test_config_values.py b/test/unit/config/test_config_values.py
index 2f00824839d058824bd87f13f4d0371f2cee06bd..753fbf7b1f2d5997edf33a3eb28e33191c0c6da3 100644
--- a/test/unit/config/test_config_values.py
+++ b/test/unit/config/test_config_values.py
@@ -67,6 +67,44 @@ def test_error_if_database_connection_contains_brackets(bracket):
         config.GalaxyAppConfiguration(override_tempdir=False, amqp_internal_connection=uri)
 
 
+def test_error_if_interactivetoolsproxy_map_matches_other_database_connections():
+    """
+    The setting `interactivetoolsproxy_map` allows storing the session map in a
+    database supported by SQLAlchemy. This database must be different from the Galaxy database
+    and the tool shed database.
+
+    Motivation for this constraint:
+    https://github.com/galaxyproject/galaxy/pull/18481#issuecomment-2218493956
+    """
+    database_connection = "dbscheme://user:password@host/db"
+    install_database_connection = "dbscheme://user:password@host/install_db"
+    settings = dict(
+        override_tempdir=False,
+        database_connection=database_connection,
+        install_database_connection=install_database_connection,
+    )
+
+    with pytest.raises(ConfigurationError):
+        # interactivetoolsproxy_map matches database_connection
+        config.GalaxyAppConfiguration(
+            **settings,
+            interactivetoolsproxy_map=database_connection,
+        )
+
+    with pytest.raises(ConfigurationError):
+        # interactivetoolsproxy_map matches install_database_connection
+        config.GalaxyAppConfiguration(
+            **settings,
+            interactivetoolsproxy_map=install_database_connection,
+        )
+
+    # interactivetoolsproxy_map differs from database_connection, install_database_connection
+    config.GalaxyAppConfiguration(
+        **settings,
+        interactivetoolsproxy_map="dbscheme://user:password@host/gxitproxy",
+    )
+
+
 class TestIsFetchWithCeleryEnabled:
     def test_disabled_if_celery_disabled(self, appconfig):
         appconfig.enable_celery_tasks = False
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 02f33787081f78e6b430de29609f75213d802622..77afe7333c558a0952d933929145c5234e3e31ea 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -142,7 +142,7 @@ def test_resolves_to_invalid_type(monkeypatch):
 
 
 def test_resolves_with_empty_component(monkeypatch):
-    # A path can be None (root path is never None; may be asigned elsewhere)
+    # A path can be None (root path is never None; may be assigned elsewhere)
     mock_schema = {
         "path0": {
             "type": "str",
@@ -155,7 +155,7 @@ def test_resolves_with_empty_component(monkeypatch):
         "path2": {
             "type": "str",
             "default": "value2",
-            "path_resolves_to": "path1",
+            "path_resolves_to": "path0",
         },
     }
     monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(mock_schema))
@@ -163,5 +163,5 @@ def test_resolves_with_empty_component(monkeypatch):
 
     config = BaseAppConfiguration()
     assert config.path0 == "value0"
-    assert config.path1 == "value0"
+    assert config.path1 is None
     assert config.path2 == "value0/value2"
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 97953b3d0787ffbca2b6cf33e3f68e16d5ec8e26..d7e7dd0918d605bc863ee326bc8bde629ab636e0 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -132,21 +132,21 @@ def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
 
 def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
     # Expect: use value from kwargs, strip old prefix, then resolve
-    new_path1 = "old-config"
+    new_path1 = "old-config/foo"
     config = BaseAppConfiguration(path1=new_path1)
 
-    assert config.path1 == "my-config/"  # stripped of old prefix, then resolved
+    assert config.path1 == "my-config/foo"  # stripped of old prefix, then resolved
     assert config.path2 == "my-data/my-data-files"  # stripped of old prefix, then resolved
     assert config.path3 == "my-other-files"  # no change
 
 
 def test_kwargs_set_to_null(mock_init):
-    # Expected: allow overriding with null, then resolve
+    # Expected: allow overriding with null
     # This is not a common scenario, but it does happen: one example is
     # `job_config` set to `None` when testing
     config = BaseAppConfiguration(path1=None)
 
-    assert config.path1 == "my-config"  # resolved
+    assert config.path1 is None
     assert config.path2 == "my-data/my-data-files"  # resolved
     assert config.path3 == "my-other-files"  # no change
 
diff --git a/test/unit/data/datatypes/test_bam.py b/test/unit/data/datatypes/test_bam.py
index 877851cfbbcafd04e184e5ee39ee897ae41d7b53..694c9ac405a68aa2af8205132942096776f640e6 100644
--- a/test/unit/data/datatypes/test_bam.py
+++ b/test/unit/data/datatypes/test_bam.py
@@ -1,6 +1,6 @@
 import json
 
-from pysam import (  # type: ignore[attr-defined]
+from pysam import (  # type: ignore[attr-defined, unused-ignore]
     AlignmentFile,
     view,
 )
@@ -16,8 +16,12 @@ from .util import (
 def test_merge_bam():
     with get_input_files("1.bam", "1.bam") as input_files, get_tmp_path() as outpath:
         Bam.merge(input_files, outpath)
-        alignment_count_output = int(view("-c", outpath).strip())
-        alignment_count_input = int(view("-c", input_files[0]).strip()) * 2
+        ret = view("-c", outpath)
+        assert isinstance(ret, str)
+        alignment_count_output = int(ret.strip())
+        ret = view("-c", input_files[0])
+        assert isinstance(ret, str)
+        alignment_count_input = int(ret.strip()) * 2
         assert alignment_count_input == alignment_count_output
 
 
diff --git a/test/unit/data/datatypes/test_check_required.py b/test/unit/data/datatypes/test_check_required.py
index e5f8d1c880e37ed1e69781442cf107c9ca091e14..8351f1c08bf53ea293116d393b370e61b59e59f0 100644
--- a/test/unit/data/datatypes/test_check_required.py
+++ b/test/unit/data/datatypes/test_check_required.py
@@ -22,21 +22,21 @@ class CheckRequiredInherited(CheckRequiredTrue):
 
 def test_check_required_metadata_false():
     app = GalaxyDataTestApp()
-    app.datatypes_registry.datatypes_by_extension["false"] = CheckRequiredFalse
+    app.datatypes_registry.datatypes_by_extension["false"] = CheckRequiredFalse()
     hda = HistoryDatasetAssociation(sa_session=app.model.session, extension="false")
     assert not hda.metadata.spec["columns"].check_required_metadata
 
 
 def test_check_required_metadata_true():
     app = GalaxyDataTestApp()
-    app.datatypes_registry.datatypes_by_extension["true"] = CheckRequiredTrue
+    app.datatypes_registry.datatypes_by_extension["true"] = CheckRequiredTrue()
     hda = HistoryDatasetAssociation(sa_session=app.model.session, extension="true")
     assert hda.metadata.spec["columns"].check_required_metadata
 
 
 def test_check_required_metadata_inherited():
     app = GalaxyDataTestApp()
-    app.datatypes_registry.datatypes_by_extension["inherited"] = CheckRequiredInherited
+    app.datatypes_registry.datatypes_by_extension["inherited"] = CheckRequiredInherited()
     hda = HistoryDatasetAssociation(sa_session=app.model.session, extension="inherited")
     assert hda.metadata.spec["columns"].check_required_metadata
     assert not hda.metadata.spec["something"].check_required_metadata
diff --git a/test/unit/data/datatypes/test_constructive_solid_geometry.py b/test/unit/data/datatypes/test_constructive_solid_geometry.py
new file mode 100644
index 0000000000000000000000000000000000000000..bfaa95ed804dbeb0b0c016061aa14a0f15599bc9
--- /dev/null
+++ b/test/unit/data/datatypes/test_constructive_solid_geometry.py
@@ -0,0 +1,16 @@
+from galaxy.datatypes.constructive_solid_geometry import VtkXml
+from .util import (
+    get_dataset,
+    MockDatasetDataset,
+)
+
+
+def test_vtkXml_set_meta():
+    vtkXml = VtkXml()
+    with get_dataset("data.vtu") as dataset:
+        dataset.dataset = MockDatasetDataset(dataset.get_file_name())
+        vtkXml.set_meta(dataset)
+
+    assert dataset.metadata.vtk_version == "0.1"
+    assert dataset.metadata.file_format == "XML"
+    assert dataset.metadata.dataset_type == "UnstructuredGrid"
diff --git a/test/unit/data/model/__init__.py b/test/unit/data/model/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..7d0a1eeb1f8dc19b19a4f88c3132bb4d6040342c 100644
--- a/test/unit/data/model/__init__.py
+++ b/test/unit/data/model/__init__.py
@@ -0,0 +1,10 @@
+PRIVATE_OBJECT_STORE_ID = "my_private_data"
+
+
+class MockObjectStore:
+
+    def is_private(self, object):
+        if object.object_store_id == PRIVATE_OBJECT_STORE_ID:
+            return True
+        else:
+            return False
diff --git a/test/unit/data/model/conftest.py b/test/unit/data/model/conftest.py
index 034be09e51b8deef8f14d83e141a3588be50c799..1f70263110b6bf5f140de3028da4969c69509c46 100644
--- a/test/unit/data/model/conftest.py
+++ b/test/unit/data/model/conftest.py
@@ -1,7 +1,5 @@
 import contextlib
 import os
-import random
-import string
 import tempfile
 import uuid
 
@@ -10,6 +8,10 @@ from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
 from galaxy import model as m
+from galaxy.model.unittest_utils.utils import (
+    random_email,
+    random_str,
+)
 
 
 @pytest.fixture
@@ -73,15 +75,43 @@ def make_data_manager_history_association(session):
     return f
 
 
+@pytest.fixture
+def make_dataset_collection(session):
+    def f(**kwd):
+        model = m.DatasetCollection(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_dataset_collection_element(session, make_hda):
+    def f(**kwd):
+        kwd["element"] = kwd.get("element") or make_hda()
+        model = m.DatasetCollectionElement(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_dataset_permissions(session):
+    def f(**kwd):
+        model = m.DatasetPermissions(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
 @pytest.fixture
 def make_default_history_permissions(session, make_history, make_role):
     def f(**kwd):
-        if "history" not in kwd:
-            kwd["history"] = make_history()
-        if "action" not in kwd:
-            kwd["action"] = random_str()
-        if "role" not in kwd:
-            kwd["role"] = make_role()
+        kwd["history"] = kwd.get("history") or make_history()
+        kwd["action"] = kwd.get("action") or random_str()
+        kwd["role"] = kwd.get("role") or make_role()
         model = m.DefaultHistoryPermissions(**kwd)
         write_to_db(session, model)
         return model
@@ -89,6 +119,19 @@ def make_default_history_permissions(session, make_history, make_role):
     return f
 
 
+@pytest.fixture
+def make_default_user_permissions(session, make_user, make_role):
+    def f(**kwd):
+        kwd["user"] = kwd.get("user") or make_user()
+        kwd["action"] = kwd.get("action") or random_str()
+        kwd["role"] = kwd.get("role") or make_role()
+        model = m.DefaultUserPermissions(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
 @pytest.fixture
 def make_event(session):
     def f(**kwd):
@@ -112,10 +155,8 @@ def make_galaxy_session(session):
 @pytest.fixture
 def make_galaxy_session_to_history_association(session, make_history, make_galaxy_session):
     def f(**kwd):
-        if "galaxy_session" not in kwd:
-            kwd["galaxy_session"] = make_galaxy_session()
-        if "history" not in kwd:
-            kwd["history"] = make_history()
+        kwd["galaxy_session"] = kwd.get("galaxy_session") or make_galaxy_session()
+        kwd["history"] = kwd.get("history") or make_history()
         model = m.GalaxySessionToHistoryAssociation(**kwd)
         write_to_db(session, model)
         return model
@@ -123,11 +164,51 @@ def make_galaxy_session_to_history_association(session, make_history, make_galax
     return f
 
 
+@pytest.fixture
+def make_group(session):
+    def f(**kwd):
+        model = m.Group(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_group_role_association(session):
+    def f(group, role):
+        model = m.GroupRoleAssociation(group, role)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_hda(session, make_history):
+    def f(**kwd):
+        kwd["history"] = kwd.get("history") or make_history()
+        model = m.HistoryDatasetAssociation(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_hdca(session):
+    def f(**kwd):
+        model = m.HistoryDatasetCollectionAssociation(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
 @pytest.fixture
 def make_history(session, make_user):
     def f(**kwd):
-        if "user" not in kwd:
-            kwd["user"] = make_user()
+        kwd["user"] = kwd.get("user") or make_user()
         model = m.History(**kwd)
         write_to_db(session, model)
         return model
@@ -168,10 +249,8 @@ def make_history_dataset_collection_association(session):
 @pytest.fixture
 def make_history_rating_association(session, make_user, make_history):
     def f(**kwd):
-        if "user" not in kwd:
-            kwd["user"] = make_user()
-        if "item" not in kwd:
-            kwd["item"] = make_history()
+        kwd["user"] = kwd.get("user") or make_user()
+        kwd["item"] = kwd.get("item") or make_history()
         model = m.HistoryRatingAssociation(**kwd)
         write_to_db(session, model)
         return model
@@ -229,9 +308,81 @@ def make_job_import_history_archive(session):
     return f
 
 
+@pytest.fixture
+def make_ldca(session):
+    def f(**kwd):
+        model = m.LibraryDatasetCollectionAssociation(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_ldda(session):
+    def f(**kwd):
+        model = m.LibraryDatasetDatasetAssociation(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_library(session):
+    def f(**kwd):
+        model = m.Library(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_library_folder(session):
+    def f(**kwd):
+        model = m.LibraryFolder(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_library_permissions(session, make_library, make_role):
+    def f(**kwd):
+        action = kwd.get("action") or random_str()
+        library = kwd.get("library") or make_library()
+        role = kwd.get("role") or make_role()
+        model = m.LibraryPermissions(action, library, role)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_page(session, make_user):
+    def f(**kwd):
+        kwd["user"] = kwd.get("user") or make_user()
+        model = m.Page(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
 @pytest.fixture
 def make_role(session):
     def f(**kwd):
+        # We must specify `name` because after removing the unique constraint
+        # from role.name (migration 9a5207190a4d) and setting up a default name
+        # generation for roles that do not receive a name argument that does
+        # not generate unique names, any migration unit tests that use
+        # this fixture AFTER DOWNGRADING (like # test_migrations.py::test_349dd9d9aac9)
+        # would break due to violating that constraint (restored via
+        # downgrading) without setting name.
+        kwd["name"] = kwd.get("name") or random_str()
         model = m.Role(**kwd)
         write_to_db(session, model)
         return model
@@ -240,9 +391,10 @@ def make_role(session):
 
 
 @pytest.fixture
-def make_workflow(session):
+def make_stored_workflow(session, make_user):
     def f(**kwd):
-        model = m.Workflow(**kwd)
+        kwd["user"] = kwd.get("user") or make_user()
+        model = m.StoredWorkflow(**kwd)
         write_to_db(session, model)
         return model
 
@@ -250,11 +402,13 @@ def make_workflow(session):
 
 
 @pytest.fixture
-def make_workflow_invocation(session, make_workflow):
+def make_task(session, make_job):
     def f(**kwd):
-        if "workflow" not in kwd:
-            kwd["workflow"] = make_workflow()
-        model = m.WorkflowInvocation(**kwd)
+        kwd["job"] = kwd.get("job") or make_job()
+        # Assumption: if the following args are needed, a test should supply them
+        kwd["working_directory"] = kwd.get("working_directory") or random_str()
+        kwd["prepare_files_cmd"] = kwd.get("prepare_files_cmd") or random_str()
+        model = m.Task(**kwd)
         write_to_db(session, model)
         return model
 
@@ -264,12 +418,9 @@ def make_workflow_invocation(session, make_workflow):
 @pytest.fixture
 def make_user(session):
     def f(**kwd):
-        if "username" not in kwd:
-            kwd["username"] = random_str()
-        if "email" not in kwd:
-            kwd["email"] = random_email()
-        if "password" not in kwd:
-            kwd["password"] = random_str()
+        kwd["username"] = kwd.get("username") or random_str()
+        kwd["email"] = kwd.get("email") or random_email()
+        kwd["password"] = kwd.get("password") or random_str()
         model = m.User(**kwd)
         write_to_db(session, model)
         return model
@@ -277,6 +428,86 @@ def make_user(session):
     return f
 
 
+@pytest.fixture
+def make_user_and_role(session, make_user, make_role, make_user_role_association):
+    """
+    Each user created in Galaxy is assumed to have a private role, such that role.type == Role.types.PRIVATE.
+    Since we are testing user/group/role associations here, to ensure the correct state of the test database,
+    we need to ensure that a user is never created without a corresponding private role.
+    Therefore, we use this fixture instead of make_user (which only creates a user).
+    """
+
+    def f(**kwd):
+        user = make_user(**kwd)
+        private_role = make_role(type=m.Role.types.PRIVATE, name=m.Role.default_name(m.Role.types.PRIVATE))
+        make_user_role_association(user, private_role)
+        return user, private_role
+
+    return f
+
+
+@pytest.fixture
+def make_user_item_rating_association(session):
+    def f(assoc_class, user, item, rating):
+        model = assoc_class(user, item, rating)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_user_group_association(session):
+    def f(user, group):
+        model = m.UserGroupAssociation(user, group)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_user_role_association(session):
+    def f(user, role):
+        model = m.UserRoleAssociation(user, role)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_visualization(session, make_user):
+    def f(**kwd):
+        kwd["user"] = kwd.get("user") or make_user()
+        model = m.Visualization(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_workflow(session):
+    def f(**kwd):
+        model = m.Workflow(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
+@pytest.fixture
+def make_workflow_invocation(session, make_workflow):
+    def f(**kwd):
+        kwd["workflow"] = kwd.get("workflow") or make_workflow()
+        model = m.WorkflowInvocation(**kwd)
+        write_to_db(session, model)
+        return model
+
+    return f
+
+
 # utility functions
 
 
@@ -289,17 +520,6 @@ def transaction(session):
         yield
 
 
-def random_str() -> str:
-    alphabet = string.ascii_lowercase + string.digits
-    size = random.randint(5, 10)
-    return "".join(random.choices(alphabet, k=size))
-
-
-def random_email() -> str:
-    text = random_str()
-    return f"{text}@galaxy.testing"
-
-
 def write_to_db(session, model) -> None:
     with transaction(session):
         session.add(model)
diff --git a/test/unit/data/model/db/__init__.py b/test/unit/data/model/db/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..7b083aa84acdc79ae485ef87666ccc67e8f1e4ba 100644
--- a/test/unit/data/model/db/__init__.py
+++ b/test/unit/data/model/db/__init__.py
@@ -0,0 +1,13 @@
+from collections import (
+    Counter,
+    namedtuple,
+)
+
+MockTransaction = namedtuple("MockTransaction", "user")
+
+
+def have_same_elements(items, expected_items):
+    """
+    Assert that items and expected_items contain the same elements.
+    """
+    return Counter(items) == Counter(expected_items)
diff --git a/test/unit/data/model/db/conftest.py b/test/unit/data/model/db/conftest.py
index 240268ef207f7654f8a8f86e21b9966d5b5b1c11..8cd81ed509041b6a86d2bff32d8aeb4d631ac69f 100644
--- a/test/unit/data/model/db/conftest.py
+++ b/test/unit/data/model/db/conftest.py
@@ -8,9 +8,13 @@ from sqlalchemy import (
     create_engine,
     text,
 )
+from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import Session
 
 from galaxy import model as m
+from galaxy.datatypes.registry import Registry as DatatypesRegistry
+from galaxy.model.triggers.update_audit_table import install as install_timestamp_triggers
+from .. import MockObjectStore
 
 if TYPE_CHECKING:
     from sqlalchemy.engine import Engine
@@ -32,22 +36,62 @@ def engine(db_url: str) -> "Engine":
 
 @pytest.fixture
 def session(engine: "Engine") -> Session:
-    return Session(engine)
+    session = Session(engine)
+    # For sqlite, we need to explicitly enale foreign key constraints.
+    if engine.name == "sqlite":
+        session.execute(text("PRAGMA foreign_keys = ON;"))
+    return session
 
 
 @pytest.fixture(autouse=True, scope="module")
 def init_database(engine: "Engine") -> None:
     """Create database objects."""
     m.mapper_registry.metadata.create_all(engine)
+    install_timestamp_triggers(engine)
+
+
+@pytest.fixture(autouse=True, scope="module")
+def init_object_store() -> None:
+    m.Dataset.object_store = MockObjectStore()  # type:ignore[assignment]
+
+
+@pytest.fixture(autouse=True, scope="module")
+def init_datatypes() -> None:
+    datatypes_registry = DatatypesRegistry()
+    datatypes_registry.load_datatypes()
+    m.set_datatypes_registry(datatypes_registry)
 
 
 @pytest.fixture(autouse=True)
-def clear_database(engine: "Engine") -> "Generator":
+def clear_database(engine: "Engine", session) -> "Generator":
     """Delete all rows from all tables. Called after each test."""
     yield
-    with engine.begin() as conn:
-        for table in m.mapper_registry.metadata.tables:
-            # Unless db is sqlite, disable foreign key constraints to delete out of order
-            if engine.name != "sqlite":
-                conn.execute(text(f"ALTER TABLE {table} DISABLE TRIGGER ALL"))
-            conn.execute(text(f"DELETE FROM {table}"))
+
+    # If a test left an open transaction, rollback to prevent database locking.
+    if session.in_transaction():
+        session.rollback()
+
+    with engine.connect() as conn:
+        if engine.name == "sqlite":
+            conn.execute(text("PRAGMA foreign_keys = OFF;"))
+            for table in m.mapper_registry.metadata.tables:
+                conn.execute(text(f"DELETE FROM {table}"))
+        else:
+            # For postgres, we can disable foreign key constraints with this statement:
+            #   conn.execute(text(f"ALTER TABLE {table} DISABLE TRIGGER ALL"))
+            # However, unless running as superuser, this will raise an error when trying
+            #   to disable a system trigger. Disabling USER triggers instead of ALL
+            #   won't work because the USER option excludes foreign key constraints.
+            # The following is an alternative: we do multiple passes until all tables have been cleared:
+            to_delete = list(m.mapper_registry.metadata.tables)
+            failed = []
+            while to_delete:
+                for table in to_delete:
+                    try:
+                        conn.execute(text(f"DELETE FROM {table}"))
+                    except IntegrityError:
+                        failed.append(table)
+                        conn.rollback()
+                to_delete, failed = failed, []
+
+        conn.commit()
diff --git a/test/unit/data/model/db/test_history_table_pruner.py b/test/unit/data/model/db/test_history_table_pruner.py
index 376b0c52939cfc224f13a8853f8e8fc0fd54b24c..916e3d6f162172a58f1425cca5e0faaf471afe9b 100644
--- a/test/unit/data/model/db/test_history_table_pruner.py
+++ b/test/unit/data/model/db/test_history_table_pruner.py
@@ -4,7 +4,6 @@ import pytest
 from sqlalchemy import (
     func,
     select,
-    text,
 )
 
 from galaxy import model as m
@@ -69,10 +68,6 @@ def setup_db(
     make_data_manager_history_association(history=histories[32])
     make_cleanup_event_history_association(history_id=histories[33].id)
     make_galaxy_session_to_history_association(history=histories[34])
-    # HistoryAudit is not instantiable, so created association manually.
-    stmt = text("insert into history_audit values(:history_id, :update_time)")
-    params = {"history_id": histories[35].id, "update_time": datetime.date.today()}
-    session.execute(stmt, params)
 
     # 6. Create a galaxy_session record referring to a history.
     # This cannot be deleted, but the history reference can be set to null.
@@ -86,7 +81,8 @@ def setup_db(
 
 
 def test_run(setup_db, session, db_url, engine):
-
+    # In this test we do not verify counts of rows in the HistoryAudit table since those rows are created
+    # automatically via db trigger.
     def verify_counts(model, expected):
         assert session.scalar(select(func.count()).select_from(model)) == expected
 
@@ -122,7 +118,6 @@ def test_run(setup_db, session, db_url, engine):
         m.DataManagerHistoryAssociation,
         m.CleanupEventHistoryAssociation,
         m.GalaxySessionToHistoryAssociation,
-        m.HistoryAudit,
     ]:
         verify_counts(model, 1)
     verify_counts(
@@ -162,6 +157,5 @@ def test_run(setup_db, session, db_url, engine):
         m.DataManagerHistoryAssociation,
         m.CleanupEventHistoryAssociation,
         m.GalaxySessionToHistoryAssociation,
-        m.HistoryAudit,
     ]:
         verify_counts(model, 0)
diff --git a/test/unit/data/model/db/test_libraries.py b/test/unit/data/model/db/test_libraries.py
new file mode 100644
index 0000000000000000000000000000000000000000..3bba9c03b610639b0ad5ac7e694e792eac46b11c
--- /dev/null
+++ b/test/unit/data/model/db/test_libraries.py
@@ -0,0 +1,100 @@
+from galaxy.model.db.library import (
+    get_libraries_by_name,
+    get_libraries_for_admins,
+    get_libraries_for_nonadmins,
+    get_library_ids,
+    get_library_permissions_by_role,
+)
+from . import have_same_elements
+
+
+def test_get_library_ids(session, make_library, make_library_permissions):
+    l1, l2, l3, l4 = make_library(), make_library(), make_library(), make_library()
+    make_library_permissions(library=l1, action="a")
+    make_library_permissions(library=l2, action="b")
+    make_library_permissions(library=l3, action="b")
+    make_library_permissions(library=l3, action="b")  # intentional duplicate
+    make_library_permissions(library=l4, action="c")
+
+    ids = get_library_ids(session, "b").all()
+    expected = [l2.id, l3.id]
+    have_same_elements(ids, expected)
+
+
+def test_get_library_permissions_by_role(session, make_role, make_library_permissions):
+    r1, r2 = make_role(), make_role()
+    make_library_permissions()
+    make_library_permissions()
+    make_library_permissions(role=r1)
+    make_library_permissions(role=r2)
+    lps = get_library_permissions_by_role(session, (r1.id, r2.id)).all()
+
+    lp_roles = [lp.role for lp in lps]
+    expected = [r1, r2]
+    have_same_elements(lp_roles, expected)
+
+
+def test_get_libraries_for_admins(session, make_library):
+    libs = [make_library() for _ in range(5)]
+    libs[0].deleted = True
+    libs[1].deleted = True
+    libs[2].deleted = False
+    libs[3].deleted = False
+    libs[4].deleted = False
+
+    libs_deleted = get_libraries_for_admins(session, True).all()
+    expected = [libs[0], libs[1]]
+    have_same_elements(libs_deleted, expected)
+
+    libs_not_deleted = get_libraries_for_admins(session, False).all()
+    expected = [libs[2], libs[3], libs[4]]
+    have_same_elements(libs_not_deleted, expected)
+
+    libs_all = get_libraries_for_admins(session, None).all()
+    have_same_elements(libs_all, libs)
+
+
+def test_get_libraries_for_admins__ordering(session, make_library):
+    l1 = make_library(name="c")
+    l2 = make_library(name="B")
+    l3 = make_library(name="a")
+
+    libs = get_libraries_for_admins(session, None).all()
+    assert libs == [l3, l2, l1]  # sorted by name, case insensitive
+
+
+def test_get_libraries_for_non_admins(session, make_library):
+    l1, l2, l3, l4 = (make_library() for _ in range(4))
+    restricted_ids = (l2.id, l3.id, l4.id)
+    accessible_restricted_ids = (l2.id,)
+    l2.deleted = False  # use default for l1.deleted
+    l3.deleted = False
+    l4.deleted = True
+
+    allowed = get_libraries_for_nonadmins(session, restricted_ids, accessible_restricted_ids).all()
+    # Expected:  l1 (not deleted, not restricted), l2 (not deleted, restricted but accessible)
+    # Not returned: l3 (not deleted but restricted), l4 (deleted)
+    expected = [l1, l2]
+    have_same_elements(allowed, expected)
+
+
+def test_get_libraries_for_admins_non_admins__ordering(session, make_library):
+    l1 = make_library(name="c")
+    l2 = make_library(name="B")
+    l3 = make_library(name="a")
+
+    expected = [l3, l2, l1]  # sorted by Library.name, case insensitive
+    libs = get_libraries_for_admins(session, None).all()
+    assert libs == expected
+    libs = get_libraries_for_nonadmins(session, [], []).all()
+    assert libs == expected
+
+
+def test_get_libraries_by_name(session, make_library):
+    make_library(name="a")
+    l2 = make_library(name="b")
+    l3 = make_library(name="b")  # intentional duplicate
+    l3.deleted = True  # should not be returned
+
+    libs = get_libraries_by_name(session, "b").all()
+    assert libs == [l2]
diff --git a/test/unit/data/model/db/test_misc.py b/test/unit/data/model/db/test_misc.py
new file mode 100644
index 0000000000000000000000000000000000000000..9dadda4c326ae708bc1e49405049f36dd957f04c
--- /dev/null
+++ b/test/unit/data/model/db/test_misc.py
@@ -0,0 +1,324 @@
+import random
+
+import pytest
+from sqlalchemy import inspect
+
+from galaxy import model as m
+from galaxy.model.unittest_utils.db_helpers import get_hdca_by_name
+from . import MockTransaction
+from .. import PRIVATE_OBJECT_STORE_ID
+
+
+def test_history_update(make_history, make_hda, session):
+    """
+    Verify the following behavior:
+    - history updated due to hda insert
+    - history updated due to hda update
+    - history NOT updated when hda copied
+    """
+    h1 = make_history()
+    old_update_time = h1.update_time
+
+    hda = make_hda(history=h1, create_dataset=True, sa_session=session)
+    # history updated due to hda insert
+    assert h1.update_time > old_update_time
+
+    old_update_time = h1.update_time
+    hda.name = "new name"
+    session.add(hda)
+    session.commit()
+    # history updated due to hda update
+    assert h1.update_time > old_update_time
+
+    old_update_time = h1.update_time
+    hda2 = hda.copy()
+    assert hda2
+    # history NOT updated when hda copied
+    assert h1.update_time == old_update_time
+
+
+def test_ratings(
+    make_user,
+    make_stored_workflow,
+    make_history,
+    make_page,
+    make_visualization,
+    make_hdca,
+    make_ldca,
+    make_user_item_rating_association,
+):
+    def _test_rating(assoc_class, item, assoc_class_item_attr_name):
+        user = make_user()
+        rating = random.randint(0, 100)
+        rating_assoc = make_user_item_rating_association(assoc_class, user, item, rating)
+        assert rating_assoc.user == user
+        assert getattr(rating_assoc, assoc_class_item_attr_name) == item
+        assert rating_assoc.rating == rating
+
+    _test_rating(m.StoredWorkflowRatingAssociation, make_stored_workflow(), "stored_workflow")
+    _test_rating(m.HistoryRatingAssociation, make_history(), "history")
+    _test_rating(m.PageRatingAssociation, make_page(), "page")
+    _test_rating(m.VisualizationRatingAssociation, make_visualization(), "visualization")
+    _test_rating(m.HistoryDatasetCollectionRatingAssociation, make_hdca(), "dataset_collection")
+    _test_rating(m.LibraryDatasetCollectionRatingAssociation, make_ldca(), "dataset_collection")
+
+
+def test_hda_to_library_dataset_dataset_association(session, make_user, make_history, make_hda, make_library_folder):
+    hda = make_hda(create_dataset=True, sa_session=session)
+    target_folder = make_library_folder()
+    mock_trans = MockTransaction(user=None)
+
+    ldda = hda.to_library_dataset_dataset_association(
+        trans=mock_trans,
+        target_folder=target_folder,
+    )
+    assert target_folder.item_count == 1
+    assert ldda.id
+    assert ldda.library_dataset.id
+    assert ldda.library_dataset.library_dataset_dataset_association.id
+
+    new_ldda = hda.to_library_dataset_dataset_association(
+        trans=mock_trans, target_folder=target_folder, replace_dataset=ldda.library_dataset
+    )
+    assert new_ldda.id != ldda.id
+    assert new_ldda.library_dataset_id == ldda.library_dataset_id
+    assert new_ldda.library_dataset.library_dataset_dataset_association_id == new_ldda.id
+    assert len(new_ldda.library_dataset.expired_datasets) == 1
+    assert new_ldda.library_dataset.expired_datasets[0] == ldda
+    assert target_folder.item_count == 1
+
+
+def test_hda_to_library_dataset_dataset_association_fails_if_private(
+    session, make_user, make_history, make_hda, make_library_folder
+):
+    hda = make_hda(create_dataset=True, sa_session=session)
+    hda.dataset.object_store_id = PRIVATE_OBJECT_STORE_ID
+    target_folder = make_library_folder()
+    mock_trans = MockTransaction(user=None)
+
+    with pytest.raises(Exception) as exec_info:
+        hda.to_library_dataset_dataset_association(
+            trans=mock_trans,
+            target_folder=target_folder,
+        )
+    assert m.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE in str(exec_info.value)
+
+
+def test_collection_get_interface(session, make_hda, make_dataset_collection):
+    c = make_dataset_collection(collection_type="list")
+    d = make_hda(create_dataset=True, sa_session=session)
+    elements = 100
+    dces = [
+        m.DatasetCollectionElement(collection=c, element=d, element_identifier=f"{i}", element_index=i)
+        for i in range(elements)
+    ]
+    for i in range(elements):
+        assert c[i] == dces[i]
+
+
+def test_collections_in_histories(session, make_dataset_collection, make_dataset_collection_element, make_hdca):
+    c = make_dataset_collection(collection_type="pair")
+    dce1 = make_dataset_collection_element(collection=c, element_identifier="left")
+    dce2 = make_dataset_collection_element(collection=c, element_identifier="right")
+    make_hdca(name="foo", collection=c)
+    loaded_dataset_collection = get_hdca_by_name(session, "foo").collection
+
+    assert len(loaded_dataset_collection.elements) == 2
+    assert loaded_dataset_collection.collection_type == "pair"
+    assert loaded_dataset_collection["left"] == dce1
+    assert loaded_dataset_collection["right"] == dce2
+
+
+def test_dataset_action_tuples(
+    session,
+    make_user,
+    make_history,
+    make_hda,
+    make_role,
+    make_dataset_permissions,
+    make_dataset_collection,
+    make_dataset_collection_element,
+):
+    role = make_role()
+    hda1 = make_hda(create_dataset=True, sa_session=session)
+    hda2 = make_hda(create_dataset=True, sa_session=session)
+    make_dataset_permissions(action="action1", dataset=hda1.dataset, role=role)
+    make_dataset_permissions(action=None, dataset=hda1.dataset, role=role)
+    make_dataset_permissions(action="action3", dataset=hda1.dataset, role=role)
+    c = make_dataset_collection(collection_type="type1")
+    make_dataset_collection_element(collection=c, element=hda1)
+    make_dataset_collection_element(collection=c, element=hda2)
+    assert c.dataset_action_tuples == [("action1", role.id), ("action3", role.id)]
+
+
+def test_dataset_dbkeys_and_extensions_summary(
+    session, make_hda, make_dataset_collection, make_dataset_collection_element, make_hdca
+):
+    d1 = make_hda(extension="bam", dbkey="hg19", create_dataset=True, sa_session=session)
+    d2 = make_hda(extension="txt", dbkey="hg19", create_dataset=True, sa_session=session)
+    c1 = make_dataset_collection(collection_type="paired")
+    make_dataset_collection_element(collection=c1, element=d1)
+    make_dataset_collection_element(collection=c1, element=d2)
+
+    hdca = make_hdca(collection=c1)
+    assert hdca.dataset_dbkeys_and_extensions_summary[0] == {"hg19"}
+    assert hdca.dataset_dbkeys_and_extensions_summary[1] == {"bam", "txt"}
+
+
+def test_populated_optimized_ok(session, make_dataset_collection, make_dataset_collection_element, make_hda):
+    c1 = make_dataset_collection(collection_type="paired")
+    make_dataset_collection_element(collection=c1, element=make_hda(create_dataset=True, sa_session=session))
+    make_dataset_collection_element(collection=c1, element=make_hda(create_dataset=True, sa_session=session))
+    assert c1.populated
+    assert c1.populated_optimized
+
+
+def test_populated_optimized_empty_list_list_ok(make_dataset_collection, make_dataset_collection_element):
+    c1 = make_dataset_collection(collection_type="list")
+    c2 = make_dataset_collection(collection_type="list:list")
+    make_dataset_collection_element(collection=c2, element=c1)
+    assert c1.populated
+    assert c1.populated_optimized
+    assert c2.populated
+    assert c2.populated_optimized
+
+
+def test_populated_optimized_list_list_not_populated(make_dataset_collection, make_dataset_collection_element):
+    c1 = make_dataset_collection(collection_type="list", populated=False)
+    c2 = make_dataset_collection(collection_type="list:list")
+    make_dataset_collection_element(collection=c2, element=c1)
+    assert not c1.populated
+    assert not c1.populated_optimized
+    assert not c2.populated
+    assert not c2.populated_optimized
+
+
+def test_default_disk_usage(session, make_user):
+    u = make_user()
+    u.adjust_total_disk_usage(1, None)
+    user_reload = session.get(m.User, u.id)
+    assert user_reload.disk_usage == 1
+
+
+def test_history_contents(session, make_history, make_hda):
+    h1 = make_history()
+    d1 = make_hda(history=h1, name="1")
+    d2 = make_hda(history=h1, name="2", visible=False, create_dataset=True, sa_session=session)
+    d2.dataset.object_store_id = "foobar"
+    d3 = make_hda(history=h1, name="3", deleted=True, create_dataset=True, sa_session=session)
+    d3.dataset.object_store_id = "three_store"
+    d4 = make_hda(history=h1, name="4", visible=False, deleted=True)
+
+    def contents_iter_names(**kwds):
+        history = session.get(m.History, h1.id)
+        return [h.name for h in history.contents_iter(**kwds)]
+
+    assert contents_iter_names() == ["1", "2", "3", "4"]
+    assert contents_iter_names(deleted=False) == ["1", "2"]
+    assert contents_iter_names(visible=True) == ["1", "3"]
+    assert contents_iter_names(visible=True, object_store_ids=["three_store"]) == ["3"]
+    assert contents_iter_names(visible=False) == ["2", "4"]
+    assert contents_iter_names(deleted=True, visible=False) == ["4"]
+    assert contents_iter_names(deleted=False, object_store_ids=["foobar"]) == ["2"]
+    assert contents_iter_names(deleted=False, object_store_ids=["foobar2"]) == []
+    assert contents_iter_names(ids=[d1.id, d2.id, d3.id, d4.id]) == ["1", "2", "3", "4"]
+    assert contents_iter_names(ids=[d1.id, d2.id, d3.id, d4.id], max_in_filter_length=1) == ["1", "2", "3", "4"]
+    assert contents_iter_names(ids=[d1.id, d3.id]) == ["1", "3"]
+
+
+def test_current_galaxy_session(make_user, make_galaxy_session):
+    user = make_user()
+    galaxy_session = make_galaxy_session(user=user)
+    assert user.current_galaxy_session == galaxy_session
+    new_galaxy_session = make_galaxy_session()
+    user.galaxy_sessions.append(new_galaxy_session)
+    assert user.current_galaxy_session == new_galaxy_session
+
+
+def test_next_hid(make_history):
+    h = make_history()
+    assert h.hid_counter == 1
+    h._next_hid()
+    assert h.hid_counter == 2
+    h._next_hid(n=3)
+    assert h.hid_counter == 5
+
+
+def test_history_hid_counter_is_expired_after_next_hid_call(make_history):
+    h = make_history()
+    state = inspect(h)
+    assert h.hid_counter == 1
+    assert "hid_counter" not in state.unloaded
+    assert "id" not in state.unloaded
+
+    h._next_hid()
+
+    assert "hid_counter" in state.unloaded  # this attribute has been expired
+    assert "id" not in state.unloaded  # but other attributes have NOT been expired
+    assert h.hid_counter == 2  # check this last: this causes this hid_counter to be reloaded
+
+
+def test_get_display_name(make_ldda, make_hda, make_history, make_library, make_library_folder):
+
+    def assert_display_name_converts_to_unicode(item, name):
+        assert isinstance(item.get_display_name(), str)
+        assert item.get_display_name() == name
+
+    ldda = make_ldda(name="ldda_name")
+    assert_display_name_converts_to_unicode(ldda, "ldda_name")
+
+    hda = make_hda(name="hda_name")
+    assert_display_name_converts_to_unicode(hda, "hda_name")
+
+    history = make_history(name="history_name")
+    assert_display_name_converts_to_unicode(history, "history_name")
+
+    library = make_library(name="library_name")
+    assert_display_name_converts_to_unicode(library, "library_name")
+
+    library_folder = make_library_folder(name="library_folder")
+    assert_display_name_converts_to_unicode(library_folder, "library_folder")
+
+    history = make_history(name="Hello₩◎ґʟⅾ")
+    assert isinstance(history.name, str)
+    assert isinstance(history.get_display_name(), str)
+    assert history.get_display_name() == "Hello₩◎ґʟⅾ"
+
+
+def test_metadata_spec(make_hda):
+    metadata = dict(chromCol=1, startCol=2, endCol=3)
+    d = make_hda(extension="interval", metadata=metadata)
+    assert d.metadata.chromCol == 1
+    assert d.metadata.anyAttribute is None
+    assert "items" not in d.metadata
+
+
+def test_job_metrics(make_job):
+    job = make_job()
+    job.add_metric("gx", "galaxy_slots", 5)
+    job.add_metric("system", "system_name", "localhost")
+
+    assert len(job.text_metrics) == 1
+    assert job.text_metrics[0].plugin == "system"
+    assert job.text_metrics[0].metric_name == "system_name"
+    assert job.text_metrics[0].metric_value == "localhost"
+    assert len(job.numeric_metrics) == 1
+    assert job.numeric_metrics[0].plugin == "gx"
+    assert job.numeric_metrics[0].metric_name == "galaxy_slots"
+    assert job.numeric_metrics[0].metric_value == 5
+
+
+def test_task_metrics(make_task):
+    task = make_task()
+    task.add_metric("foo", "some-name", "some-value")
+    big_value = ":".join(f"{i}" for i in range(2000))
+    task.add_metric("env", "BIG_PATH", big_value)
+
+    assert len(task.text_metrics) == 2
+    assert task.text_metrics[0].plugin == "foo"
+    assert task.text_metrics[0].metric_name == "some-name"
+    assert task.text_metrics[0].metric_value == "some-value"
+    assert task.text_metrics[1].plugin == "env"
+    assert task.text_metrics[1].metric_name == "BIG_PATH"
+    # Ensure big values truncated
+    assert len(task.text_metrics[1].metric_value) <= 1023
diff --git a/test/unit/data/model/db/test_role.py b/test/unit/data/model/db/test_role.py
new file mode 100644
index 0000000000000000000000000000000000000000..6863ec9b1f8e9fee244430260ad465e2c6d86166
--- /dev/null
+++ b/test/unit/data/model/db/test_role.py
@@ -0,0 +1,178 @@
+from galaxy.model import Role
+from galaxy.model.db.role import (
+    get_displayable_roles,
+    get_npns_roles,
+    get_private_role_user_emails_dict,
+    get_private_user_role,
+    get_roles_by_ids,
+)
+from galaxy.model.security import _get_valid_roles_exposed
+from . import have_same_elements
+
+
+def test_get_npns_roles(session, make_role):
+    make_role(deleted=True)
+    make_role(type=Role.types.PRIVATE)
+    make_role(type=Role.types.SHARING)
+    r4 = make_role()
+    r5 = make_role()
+
+    roles = get_npns_roles(session).all()
+    # Expected: r4, r5
+    # Not returned: r1: deleted, r2: private, r3: sharing
+    expected = [r4, r5]
+    have_same_elements(roles, expected)
+
+
+def test_get_private_user_role(session, make_user, make_role, make_user_role_association):
+    u1, u2 = make_user(), make_user()
+    r1 = make_role(type=Role.types.PRIVATE)
+    r2 = make_role(type=Role.types.PRIVATE)
+    r3 = make_role()
+    make_user_role_association(u1, r1)  # user1 private
+    make_user_role_association(u1, r3)  # user1 non-private
+    make_user_role_association(u2, r2)  # user2 private
+
+    role = get_private_user_role(u1, session)
+    assert role is r1
+
+
+def test_get_roles_by_ids(session, make_role):
+    roles = [make_role() for _ in range(10)]  # create roles
+    r1, r2, r3 = roles[0], roles[3], roles[7]  # select some random roles
+    ids = [r1.id, r2.id, r3.id]
+
+    roles2 = get_roles_by_ids(session, ids)
+    expected = [r1, r2, r3]
+    have_same_elements(roles2, expected)
+
+
+def test_get_valid_roles_exposed(session, make_user_and_role, make_user, make_role, make_user_role_association):
+    # Make 3 users with private roles
+    (
+        u1,
+        rp1,
+    ) = make_user_and_role(email="foo1@x.com")
+    (
+        u2,
+        rp2,
+    ) = make_user_and_role(email="foo2@x.com")
+    (
+        u3,
+        rp3,
+    ) = make_user_and_role(email="bar@x.com")
+
+    # Make 2 sharing roles
+    rs1 = make_role(type="sharing", name="sharing role for u1")
+    make_user_role_association(user=u1, role=rs1)
+    rs2 = make_role(type="sharing", name="sharing role for u2")
+    make_user_role_association(user=u2, role=rs2)
+
+    # Make 4 admin roles
+    ra1 = make_role(type="admin", name="admin role1")
+    make_user_role_association(user=u1, role=ra1)
+    make_user_role_association(user=u2, role=ra1)
+    ra2 = make_role(type="admin", name="admin role2")
+    make_user_role_association(user=u1, role=ra2)
+    make_user_role_association(user=u2, role=ra2)
+
+    limit, page, page_limit = 1000, 1, 1000
+
+    is_admin = True
+
+    search_query = None
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 7  # all roles returned
+
+    search_query = "foo%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 2
+    assert rp1 in roles
+    assert rp2 in roles
+
+    search_query = "foo1%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 1
+    assert roles[0] == rp1
+
+    search_query = "sharing%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 2
+    assert rs1 in roles
+    assert rs2 in roles
+
+    search_query = "sharing role for u1%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 1
+    assert roles[0] == rs1
+
+    search_query = "admin role%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 2
+    assert ra1 in roles
+    assert ra2 in roles
+
+    search_query = "admin role1%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 1
+    assert roles[0] == ra1
+
+    is_admin = False  # non admins should see only private roles
+
+    search_query = None
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 3
+
+    search_query = "foo%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 2
+    assert rp1 in roles
+    assert rp2 in roles
+
+    search_query = "foo1%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 1
+    assert roles[0] == rp1
+
+    search_query = "sharing%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 0
+
+    search_query = "admin role%"
+    roles = _get_valid_roles_exposed(session, search_query, is_admin, limit, page, page_limit)
+    assert len(roles) == 0
+
+
+def test_get_displayable_roles(session, make_role, make_user_and_role):
+    # make users with private roles
+    user1, private_role1 = make_user_and_role(email="user1@example.com")
+    user2, private_role2 = make_user_and_role(email="user2@example.com")
+    # make 2 non-private roles, one is deleted, so it should not be returned
+    admin_role1 = make_role(type="admin", name="admin-role-1", description="Description of admin-role1")
+    make_role(type="admin", description="Description of admin-role1", deleted=True)
+
+    user_is_admin, security_agent = True, None
+    roles = get_displayable_roles(session, user1, user_is_admin, security_agent)
+    assert len(roles) == 3
+    assert roles[0].id == private_role1.id
+    assert roles[1].id == private_role2.id
+    assert roles[2].id == admin_role1.id
+    assert roles[0].name == "private role"
+    assert roles[1].name == "private role"
+    assert roles[2].name == "admin-role-1"
+
+
+def test_get_private_role_user_emails_dict(session, make_role, make_user_and_role):
+    # make users with private roles
+    user1, private_role1 = make_user_and_role(email="user1@example.com")
+    user2, private_role2 = make_user_and_role(email="user2@example.com")
+    user3, private_role3 = make_user_and_role(email="user3@example.com")
+    # make 2 non-private roles
+    make_role(type="admin", name="admin-role-1", description="Description of admin-role1")
+    make_role(type="admin", name="admin-role-2", description="Description of admin-role2")
+
+    data = get_private_role_user_emails_dict(session)
+    assert len(data) == 3  # only private role mappings are returned
+    assert data[private_role1.id] == "user1@example.com"
+    assert data[private_role2.id] == "user2@example.com"
+    assert data[private_role3.id] == "user3@example.com"
diff --git a/test/unit/data/model/db/test_security.py b/test/unit/data/model/db/test_security.py
new file mode 100644
index 0000000000000000000000000000000000000000..a255e408048b88079f8dc714275e0858ef5c2ca8
--- /dev/null
+++ b/test/unit/data/model/db/test_security.py
@@ -0,0 +1,936 @@
+import pytest
+
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.model import (
+    Group,
+    Role,
+    User,
+)
+from galaxy.model.security import GalaxyRBACAgent
+from . import have_same_elements
+
+
+def test_private_user_role_assoc_not_affected_by_setting_user_roles(session, make_user_and_role):
+    # Create user with a private role
+    user, private_role = make_user_and_role()
+    verify_user_associations(user, [], [private_role])  # the only existing association is with the private role
+
+    # Delete user roles
+    GalaxyRBACAgent(session).set_user_group_and_role_associations(user, role_ids=[])
+    # association with private role is preserved
+    verify_user_associations(user, [], [private_role])
+
+
+def test_private_user_role_assoc_not_affected_by_setting_role_users(session, make_user_and_role):
+    # Create user with a private role
+    user, private_role = make_user_and_role()
+    verify_user_associations(user, [], [private_role])  # the only existing association is with the private role
+
+    # Update role users
+    GalaxyRBACAgent(session).set_role_user_and_group_associations(private_role, user_ids=[])
+    # association of private role with user is preserved
+    verify_role_associations(private_role, [user], [])
+
+
+def test_cannot_assign_private_roles(session, make_user_and_role, make_role):
+    user, private_role1 = make_user_and_role()
+    _, private_role2 = make_user_and_role()
+    new_role = make_role()
+    verify_user_associations(user, [], [private_role1])  # the only existing association is with the private role
+
+    # Try to assign 2 more roles: regular role + another private role
+    GalaxyRBACAgent(session).set_user_group_and_role_associations(user, role_ids=[new_role.id, private_role2.id])
+    # Only regular role has been added: other private role ignored; original private role still assigned
+    verify_user_associations(user, [], [private_role1, new_role])
+
+
+def test_get_sharing_roles(session, make_user):
+    security_agent = GalaxyRBACAgent(session)
+    user1 = make_user()
+    user2 = make_user()
+
+    # verify: no sharing roles yet
+    roles1 = security_agent.get_sharing_roles(user1)
+    assert len(roles1) == 0
+    roles2 = security_agent.get_sharing_roles(user2)
+    assert len(roles2) == 0
+
+    # create sharing role for both users, verify
+    sharing_role = security_agent._create_sharing_role([user1, user2])
+    roles1 = security_agent.get_sharing_roles(user1)
+    assert len(roles1) == 1
+    roles2 = security_agent.get_sharing_roles(user2)
+    assert len(roles2) == 1
+
+    # update user's email, retrieve sharing roles for that user again, verify
+    user1.email = f"{user1.email}-updated"
+    roles3 = security_agent.get_sharing_roles(user1)
+    assert len(roles3) == 1
+
+    # verify we've been retrieving the correct role
+    assert roles1[0] is roles2[0] is roles3[0] is sharing_role
+
+
+class TestSetGroupUserAndRoleAssociations:
+
+    def test_add_associations_to_existing_group(self, session, make_user_and_role, make_role, make_group):
+        """
+        State: group exists in database, has no user and role associations.
+        Action: add new associations.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # users and roles for creating associations
+        users_to_add = [users[0], users[2], users[4]]
+        user_ids = [u.id for u in users_to_add]
+        roles_to_add = [roles[1], roles[3]]
+        role_ids = [r.id for r in roles_to_add]
+
+        # verify no preexisting associations
+        verify_group_associations(group, [], [])
+
+        # set associations
+        GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
+
+        # verify new associations
+        verify_group_associations(group, users_to_add, roles_to_add)
+
+    def test_add_associations_to_new_group(self, session, make_user_and_role, make_role):
+        """
+        State: group does NOT exist in database, has no user and role associations.
+        Action: add new associations.
+        """
+        group = Group()
+        session.add(group)
+        assert group.id is None  # group does not exist in database
+        users = [make_user_and_role()[0] for _ in range(5)]  # type: ignore[unreachable]
+        roles = [make_role() for _ in range(5)]
+
+        # users and roles for creating associations
+        users_to_add = [users[0], users[2], users[4]]
+        user_ids = [u.id for u in users_to_add]
+        roles_to_add = [roles[1], roles[3]]
+        role_ids = [r.id for r in roles_to_add]
+
+        # set associations
+        GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
+
+        # verify new associations
+        verify_group_associations(group, users_to_add, roles_to_add)
+
+    def test_update_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_group_role_association,
+    ):
+        """
+        State: group exists in database AND has user and role associations.
+        Action: update associations (add some/drop some).
+        Expect: old associations are REPLACED by new associations.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[0], users[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for user in users_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_group_role_association(group, role)
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+        # users and roles for creating new associations
+        new_users_to_add = [users[0], users[1], users[3]]
+        user_ids = [u.id for u in new_users_to_add]
+        new_roles_to_add = [roles[2]]
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        # set associations
+        GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
+
+        # verify new associations
+        verify_group_associations(group, new_users_to_add, new_roles_to_add)
+
+    def test_drop_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_group_role_association,
+    ):
+        """
+        State: group exists in database AND has user and role associations.
+        Action: drop all associations.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[0], users[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for user in users_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_group_role_association(group, role)
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+        # drop associations
+        GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=[], role_ids=[])
+
+        # verify associations dropped
+        verify_group_associations(group, [], [])
+
+    def test_invalid_user(self, session, make_user_and_role, make_role, make_group):
+        """
+        State: group exists in database, has no user and role associations.
+        Action: try to add several associations, last one having an invalid user id.
+        Expect: no associations are added, appropriate error is raised.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+
+        # users for creating associations
+        user_ids = [users[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(group.users) == 0
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids)
+
+        # verify no change
+        assert len(group.users) == 0
+
+    def test_invalid_role(self, session, make_role, make_group):
+        """
+        state: group exists in database, has no user and role associations.
+        action: try to add several associations, last one having an invalid role id.
+        expect: no associations are added, appropriate error is raised.
+        """
+        group = make_group()
+        roles = [make_role() for _ in range(5)]
+
+        # roles for creating associations
+        role_ids = [roles[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(group.roles) == 0
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_group_user_and_role_associations(group, role_ids=role_ids)
+
+        # verify no change
+        assert len(group.roles) == 0
+
+    def test_duplicate_user(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_group_role_association,
+    ):
+        """
+        State: group exists in database and has user and role associations.
+        Action: try update user and role associations including a duplicate user
+        Expect: error raised, no change is made to group users and group roles.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[0], users[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for user in users_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_group_role_association(group, role)
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+        # users and roles for creating new associations
+        new_users_to_add = users + [users[0]]  # include a duplicate user
+        user_ids = [u.id for u in new_users_to_add]
+
+        new_roles_to_add = roles  # NO duplice roles
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
+
+        # verify associations not updated
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+    def test_duplicate_role(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_group_role_association,
+    ):
+        """
+        State: group exists in database and has user and role associations.
+        Action: try update user and role associations including a duplicate role
+        Expect: error raised, no change is made to group users and group roles.
+        """
+        group = make_group()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[0], users[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for user in users_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_group_role_association(group, role)
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+        # users and roles for creating new associations
+        new_users_to_add = users  # NO duplicate users
+        user_ids = [u.id for u in new_users_to_add]
+
+        new_roles_to_add = roles + [roles[0]]  # include a duplicate role
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_group_user_and_role_associations(group, user_ids=user_ids, role_ids=role_ids)
+
+        # verify associations not updated
+        verify_group_associations(group, users_to_load, roles_to_load)
+
+
+class TestSetUserGroupAndRoleAssociations:
+    """
+    Note: a user should always have a private role which is not affected
+    by modifying a user's group associations or role associations.
+    """
+
+    def test_add_associations_to_existing_user(self, session, make_user_and_role, make_role, make_group):
+        """
+        State: user exists in database, has no group and only one private role association.
+        Action: add new associations.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # groups and roles for creating associations
+        groups_to_add = [groups[0], groups[2], groups[4]]
+        group_ids = [g.id for g in groups_to_add]
+        roles_to_add = [roles[1], roles[3]]
+        role_ids = [r.id for r in roles_to_add]
+
+        # verify preexisting associations
+        verify_user_associations(user, [], [private_role])
+
+        # set associations
+        GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids, role_ids=role_ids)
+
+        # verify new associations
+        verify_user_associations(user, groups_to_add, roles_to_add + [private_role])
+
+    def test_add_associations_to_new_user(self, session, make_role, make_group):
+        """
+        State: user does NOT exist in database, has no group and role associations.
+        Action: add new associations.
+        """
+        user = User(email="foo@foo.com", password="password")
+        # We are not creating a private role and a user-role association with that role because that would result in
+        # adding the user to the database before calling the method under test, whereas the test is intended to verify
+        # correct processing of a user that has NOT been saved to the database.
+
+        session.add(user)
+        assert user.id is None  # user does not exist in database
+        groups = [make_group() for _ in range(5)]  # type: ignore[unreachable]
+        roles = [make_role() for _ in range(5)]
+
+        # groups and roles for creating associations
+        groups_to_add = [groups[0], groups[2], groups[4]]
+        group_ids = [g.id for g in groups_to_add]
+        roles_to_add = [roles[1], roles[3]]
+        role_ids = [r.id for r in roles_to_add]
+
+        # set associations
+        GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids, role_ids=role_ids)
+
+        # verify new associations
+        verify_user_associations(user, groups_to_add, roles_to_add)
+
+    def test_update_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_user_role_association,
+    ):
+        """
+        State: user exists in database AND has group and role associations.
+        Action: update associations (add some/drop some).
+        Expect: old associations are REPLACED by new associations.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        groups_to_load = [groups[0], groups[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for group in groups_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_user_role_association(user, role)
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+        # groups and roles for creating new associations
+        new_groups_to_add = [groups[0], groups[1], groups[3]]
+        group_ids = [g.id for g in new_groups_to_add]
+        new_roles_to_add = [roles[2]]
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        # set associations
+        GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids, role_ids=role_ids)
+        # verify new associations
+        verify_user_associations(user, new_groups_to_add, new_roles_to_add + [private_role])
+
+    def test_drop_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_user_role_association,
+    ):
+        """
+        State: user exists in database AND has group and role associations.
+        Action: drop all associations.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        groups_to_load = [groups[0], groups[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for group in groups_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_user_role_association(user, role)
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+        # drop associations
+        GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=[], role_ids=[])
+
+        # verify associations dropped
+        verify_user_associations(user, [], [private_role])
+
+    def test_invalid_group(self, session, make_user_and_role, make_group):
+        """
+        State: user exists in database, has no group and only one private role association.
+        Action: try to add several associations, last one having an invalid group id.
+        Expect: no associations are added, appropriate error is raised.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+
+        # groups for creating associations
+        group_ids = [groups[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(user.groups) == 0
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids)
+
+        # verify no change
+        assert len(user.groups) == 0
+
+    def test_invalid_role(self, session, make_user_and_role, make_role):
+        """
+        State: user exists in database, has no group and only one private role association.
+        action: try to add several associations, last one having an invalid role id.
+        expect: no associations are added, appropriate error is raised.
+        """
+        user, private_role = make_user_and_role()
+        roles = [make_role() for _ in range(5)]
+
+        # roles for creating associations
+        role_ids = [roles[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(user.roles) == 1  # one is the private role association
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_user_group_and_role_associations(user, role_ids=role_ids)
+
+        # verify no change
+        assert len(user.roles) == 1  # one is the private role association
+
+    def test_duplicate_group(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_user_role_association,
+    ):
+        """
+        State: user exists in database and has group and role associations.
+        Action: try update group and role associations including a duplicate group
+        Expect: error raised, no change is made to user groups and user roles.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        groups_to_load = [groups[0], groups[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for group in groups_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_user_role_association(user, role)
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+        # groups and roles for creating new associations
+        new_groups_to_add = groups + [groups[0]]  # include a duplicate group
+        group_ids = [g.id for g in new_groups_to_add]
+
+        new_roles_to_add = roles  # NO duplicate roles
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids, role_ids=role_ids)
+
+        # verify associations not updated
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+    def test_duplicate_role(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_group_association,
+        make_user_role_association,
+    ):
+        """
+        State: user exists in database and has group and role associations.
+        Action: try update group and role associations including a duplicate role
+        Expect: error raised, no change is made to user groups and user roles.
+        """
+        user, private_role = make_user_and_role()
+        groups = [make_group() for _ in range(5)]
+        roles = [make_role() for _ in range(5)]
+
+        # load and verify existing associations
+        groups_to_load = [groups[0], groups[2]]
+        roles_to_load = [roles[1], roles[3]]
+        for group in groups_to_load:
+            make_user_group_association(user, group)
+        for role in roles_to_load:
+            make_user_role_association(user, role)
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+        # groups and roles for creating new associations
+        new_groups_to_add = groups  # NO duplicate groups
+        group_ids = [g.id for g in new_groups_to_add]
+
+        new_roles_to_add = roles + [roles[0]]  # include a duplicate role
+        role_ids = [r.id for r in new_roles_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+        assert not have_same_elements(roles_to_load, new_roles_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_user_group_and_role_associations(user, group_ids=group_ids, role_ids=role_ids)
+
+        # verify associations not updated
+        verify_user_associations(user, groups_to_load, roles_to_load + [private_role])
+
+
+class TestSetRoleUserAndGroupAssociations:
+    """
+    Note: a user should always have a private role which is not affected
+    by modifying a user's group associations or role associations.
+    """
+
+    def test_add_associations_to_existing_role(self, session, make_user_and_role, make_role, make_group):
+        """
+        State: role exists in database, has no group and no user associations.
+        Action: add new associations.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        groups = [make_group() for _ in range(5)]
+
+        # users and groups for creating associations
+        users_to_add = [users[0], users[2], users[4]]
+        user_ids = [u.id for u in users_to_add]
+        groups_to_add = [groups[0], groups[2], groups[4]]
+        group_ids = [g.id for g in groups_to_add]
+
+        # verify preexisting associations
+        verify_role_associations(role, [], [])
+
+        # set associations
+        GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids, group_ids=group_ids)
+
+        # verify new associations
+        verify_role_associations(role, users_to_add, groups_to_add)
+
+    def test_add_associations_to_new_role(self, session, make_user_and_role, make_group):
+        """
+        State: user does NOT exist in database, has no group and role associations.
+        Action: add new associations.
+        """
+        role = Role()
+        session.add(role)
+        assert role.id is None  # role does not exist in database
+        users = [make_user_and_role()[0] for _ in range(5)]  # type: ignore[unreachable]
+        groups = [make_group() for _ in range(5)]
+
+        # users and groups for creating associations
+        users_to_add = [users[0], users[2], users[4]]
+        user_ids = [u.id for u in users_to_add]
+        groups_to_add = [groups[0], groups[2], groups[4]]
+        group_ids = [g.id for g in groups_to_add]
+
+        # set associations
+        GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids, group_ids=group_ids)
+
+        # verify new associations
+        verify_role_associations(role, users_to_add, groups_to_add)
+
+    def test_update_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_user_role_association,
+        make_group_role_association,
+    ):
+        """
+        State: role exists in database AND has user and group associations.
+        Action: update associations (add some/drop some).
+        Expect: old associations are REPLACED by new associations.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        groups = [make_group() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[1], users[3]]
+        groups_to_load = [groups[0], groups[2]]
+        for user in users_to_load:
+            make_user_role_association(user, role)
+        for group in groups_to_load:
+            make_group_role_association(group, role)
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+        # users and groups for creating new associations
+        new_users_to_add = [users[0], users[2], users[4]]
+        user_ids = [u.id for u in new_users_to_add]
+        new_groups_to_add = [groups[0], groups[2], groups[4]]
+        group_ids = [g.id for g in new_groups_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+
+        # set associations
+        GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids, group_ids=group_ids)
+        # verify new associations
+        verify_role_associations(role, new_users_to_add, new_groups_to_add)
+
+    def test_drop_associations(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_group_role_association,
+        make_user_role_association,
+    ):
+        """
+        State: role exists in database AND has user and group associations.
+        Action: drop all associations.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        groups = [make_group() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[1], users[3]]
+        groups_to_load = [groups[0], groups[2]]
+        for user in users_to_load:
+            make_user_role_association(user, role)
+        for group in groups_to_load:
+            make_group_role_association(group, role)
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+        # drop associations
+        GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=[], group_ids=[])
+
+        # verify associations dropped
+        verify_role_associations(role, [], [])
+
+    def test_invalid_user(self, session, make_role, make_user_and_role):
+        """
+        State: role exists in database, has no user and group eassociations.
+        action: try to add several associations, last one having an invalid user id.
+        expect: no associations are added, appropriate error is raised.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+
+        # users for creating associations
+        user_ids = [users[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(role.users) == 0
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids)
+
+        # verify no change
+        assert len(role.users) == 0
+
+    def test_invalid_group(self, session, make_role, make_group):
+        """
+        State: role exists in database, has no user and group eassociations.
+        Action: try to add several associations, last one having an invalid group id.
+        Expect: no associations are added, appropriate error is raised.
+        """
+        role = make_role()
+        groups = [make_group() for _ in range(5)]
+
+        # groups for creating associations
+        group_ids = [groups[0].id, -1]  # first is valid, second is invalid
+
+        # verify no preexisting associations
+        assert len(role.groups) == 0
+
+        # try to set associations
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_role_user_and_group_associations(role, group_ids=group_ids)
+
+        # verify no change
+        assert len(role.groups) == 0
+
+    def test_duplicate_user(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_group_role_association,
+        make_user_role_association,
+    ):
+        """
+        State: role exists in database and has group and user associations.
+        Action: try update group and user associations including a duplicate user
+        Expect: error raised, no change is made to role groups and role users.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        groups = [make_group() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[1], users[3]]
+        groups_to_load = [groups[0], groups[2]]
+        for user in users_to_load:
+            make_user_role_association(user, role)
+        for group in groups_to_load:
+            make_group_role_association(group, role)
+
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+        # users and groups for creating new associations
+        new_users_to_add = users + [users[0]]  # include a duplicate user
+        user_ids = [u.id for u in new_users_to_add]
+
+        new_groups_to_add = groups  # NO duplicate groups
+        group_ids = [g.id for g in new_groups_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids, group_ids=group_ids)
+
+        # verify associations not updated
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+    def test_duplicate_group(
+        self,
+        session,
+        make_user_and_role,
+        make_role,
+        make_group,
+        make_group_role_association,
+        make_user_role_association,
+    ):
+        """
+        State: role exists in database and has group and user associations.
+        Action: try update group and user associations including a duplicate group
+        Expect: error raised, no change is made to role groups and role users.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        groups = [make_group() for _ in range(5)]
+
+        # load and verify existing associations
+        users_to_load = [users[1], users[3]]
+        groups_to_load = [groups[0], groups[2]]
+        for user in users_to_load:
+            make_user_role_association(user, role)
+        for group in groups_to_load:
+            make_group_role_association(group, role)
+
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+        # users and groups for creating new associations
+        new_users_to_add = users  # NO duplicate users
+        user_ids = [u.id for u in new_users_to_add]
+
+        new_groups_to_add = groups + [groups[0]]  # include a duplicate group
+        group_ids = [g.id for g in new_groups_to_add]
+
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+        assert not have_same_elements(groups_to_load, new_groups_to_add)
+
+        with pytest.raises(RequestParameterInvalidException):
+            GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids, group_ids=group_ids)
+
+        # verify associations not updated
+        verify_role_associations(role, users_to_load, groups_to_load)
+
+    def test_delete_default_user_permissions_and_default_history_permissions(
+        self,
+        session,
+        make_role,
+        make_user_and_role,
+        make_user_role_association,
+        make_default_user_permissions,
+        make_default_history_permissions,
+        make_history,
+    ):
+        """
+        When setting role users, we check check previously associated users to:
+        - delete DefaultUserPermissions for users that are being removed from this role;
+        - delete DefaultHistoryPermissions for histories associated with users that are being removed from this role.
+        """
+        role = make_role()
+        users = [make_user_and_role()[0] for _ in range(5)]
+        # load and verify existing associations
+        user1, user2 = users[0], users[1]
+        users_to_load = [user1, user2]
+        for user in users_to_load:
+            make_user_role_association(user, role)
+        verify_role_associations(role, users_to_load, [])
+
+        # users and groups for creating new associations
+        new_users_to_add = [users[1], users[2]]  # REMOVE users[0], LEAVE users[1], ADD users[2]
+        user_ids = [u.id for u in new_users_to_add]
+        # sanity check: ensure we are trying to change existing associations
+        assert not have_same_elements(users_to_load, new_users_to_add)
+
+        # load default user permissions
+        dup1 = make_default_user_permissions(user=user1, role=role)
+        dup2 = make_default_user_permissions(user=user2, role=role)
+        assert have_same_elements(user1.default_permissions, [dup1])
+        assert have_same_elements(user2.default_permissions, [dup2])
+
+        # load and verify default history permissions for users associated with this role
+        history1, history2 = make_history(user=user1), make_history(user=user1)  # 2 histories for user 1
+        history3 = make_history(user=user2)  # 1 history for user 2
+        dhp1 = make_default_history_permissions(history=history1, role=role)
+        dhp2 = make_default_history_permissions(history=history2, role=role)
+        dhp3 = make_default_history_permissions(history=history3, role=role)
+        assert have_same_elements(history1.default_permissions, [dhp1])
+        assert have_same_elements(history2.default_permissions, [dhp2])
+        assert have_same_elements(history3.default_permissions, [dhp3])
+
+        # now update role users
+        GalaxyRBACAgent(session).set_role_user_and_group_associations(role, user_ids=user_ids)
+
+        # verify user role associations
+        verify_role_associations(role, new_users_to_add, [])
+
+        # verify default user permissions
+        assert have_same_elements(user1.default_permissions, [])  # user1 was removed from role
+        assert have_same_elements(user2.default_permissions, [dup2])  # user2 was NOT removed from role
+
+        # verify default history permissions
+        assert have_same_elements(history1.default_permissions, [])
+        assert have_same_elements(history2.default_permissions, [])
+        assert have_same_elements(history3.default_permissions, [dhp3])
+
+
+def verify_group_associations(group, expected_users, expected_roles):
+    new_group_users = [assoc.user for assoc in group.users]
+    new_group_roles = [assoc.role for assoc in group.roles]
+    assert have_same_elements(new_group_users, expected_users)
+    assert have_same_elements(new_group_roles, expected_roles)
+
+
+def verify_user_associations(user, expected_groups, expected_roles):
+    new_user_groups = [assoc.group for assoc in user.groups]
+    new_user_roles = [assoc.role for assoc in user.roles]
+    assert have_same_elements(new_user_groups, expected_groups)
+    assert have_same_elements(new_user_roles, expected_roles)
+
+
+def verify_role_associations(role, expected_users, expected_groups):
+    new_role_users = [assoc.user for assoc in role.users]
+    new_role_groups = [assoc.group for assoc in role.groups]
+    assert have_same_elements(new_role_users, expected_users)
+    assert have_same_elements(new_role_groups, expected_groups)
diff --git a/test/unit/data/model/db/test_user.py b/test/unit/data/model/db/test_user.py
new file mode 100644
index 0000000000000000000000000000000000000000..042a541eb8177871838946cff44b522b89f2b0ba
--- /dev/null
+++ b/test/unit/data/model/db/test_user.py
@@ -0,0 +1,163 @@
+import pytest
+from sqlalchemy import select
+from sqlalchemy.exc import IntegrityError
+
+from galaxy.model import (
+    Role,
+    UserRoleAssociation,
+)
+from galaxy.model.db.user import (
+    _cleanup_nonprivate_user_roles,
+    get_user_by_email,
+    get_user_by_username,
+    get_users_by_ids,
+    get_users_for_index,
+)
+from . import have_same_elements
+
+
+@pytest.fixture
+def make_random_users(session, make_user):
+    def f(count):
+        return [make_user() for _ in range(count)]
+
+    return f
+
+
+def test_get_user_by_username(session, make_user):
+    my_user = make_user(username="a")
+    make_user()  # make another user
+    make_user(email="other_username")  # make another user
+
+    user = get_user_by_username(session, "a")
+    assert user is my_user
+
+
+def test_get_user_by_email(session, make_user):
+    my_user = make_user(email="a@foo.bar")
+    make_user(email="other_email")  # make another user
+
+    user = get_user_by_email(session, "a@foo.bar")
+    assert user is my_user
+
+
+def test_get_users_by_ids(session, make_random_users):
+    users = make_random_users(10)
+    u1, u2, u3 = users[0], users[3], users[7]  # select some random users
+    ids = [u1.id, u2.id, u3.id]
+
+    users2 = get_users_by_ids(session, ids)
+    expected = [u1, u2, u3]
+    have_same_elements(users2, expected)
+
+
+def test_get_users_for_index(session, make_user):
+    u1 = make_user(email="a", username="b")
+    u2 = make_user(email="c", username="d")
+    u3 = make_user(email="e", username="f")
+    u4 = make_user(email="g", username="h")
+    u5 = make_user(email="i", username="z")
+    u6 = make_user(email="z", username="i")
+
+    users = get_users_for_index(session, False, f_email="a", expose_user_email=True)
+    have_same_elements(users, [u1])
+    users = get_users_for_index(session, False, f_email="c", is_admin=True)
+    have_same_elements(users, [u2])
+    users = get_users_for_index(session, False, f_name="f", expose_user_name=True)
+    have_same_elements(users, [u3])
+    users = get_users_for_index(session, False, f_name="h", is_admin=True)
+    have_same_elements(users, [u4])
+    users = get_users_for_index(session, False, f_any="i", is_admin=True)
+    have_same_elements(users, [u5, u6])
+    users = get_users_for_index(session, False, f_any="i", expose_user_email=True, expose_user_name=True)
+    have_same_elements(users, [u5, u6])
+    users = get_users_for_index(session, False, f_any="i", expose_user_email=True)
+    have_same_elements(users, [u5])
+    users = get_users_for_index(session, False, f_any="i", expose_user_name=True)
+    have_same_elements(users, [u6])
+
+    u1.deleted = True
+    users = get_users_for_index(session, True)
+    have_same_elements(users, [u1])
+
+
+def test_username_is_unique(make_user):
+    # Verify username model definition
+    make_user(username="a")
+    with pytest.raises(IntegrityError):
+        make_user(username="a")
+
+
+def test_cleanup_nonprivate_user_roles(session, make_user_and_role, make_role, make_user_role_association):
+    # Create 3 users with private roles
+    user1, role_private1 = make_user_and_role(email="user1@foo.com")
+    user2, role_private2 = make_user_and_role(email="user2@foo.com")
+    user3, role_private3 = make_user_and_role(email="user3@foo.com")
+
+    # Create role_sharing1 and associated it with user1 and user2
+    role_sharing1 = make_role(type=Role.types.SHARING, name="sharing role for user1@foo.com, user2@foo.com")
+    make_user_role_association(user1, role_sharing1)
+    make_user_role_association(user2, role_sharing1)
+
+    # Create role_sharing2 and associated it with user3
+    role_sharing2 = make_role(type=Role.types.SHARING, name="sharing role for user3@foo.com")
+    make_user_role_association(user3, role_sharing2)
+
+    # Create another role and associate it with all users
+    role6 = make_role()
+    make_user_role_association(user1, role6)
+    make_user_role_association(user2, role6)
+    make_user_role_association(user3, role6)
+
+    # verify number of all user role associations
+    associations = session.scalars(select(UserRoleAssociation)).all()
+    assert len(associations) == 9  # 3 private, 2 + 1 sharing, 3 with role6
+
+    # verify user1 roles
+    assert len(user1.roles) == 3
+    assert role_private1 in [ura.role for ura in user1.roles]
+    assert role_sharing1 in [ura.role for ura in user1.roles]
+    assert role6 in [ura.role for ura in user1.roles]
+
+    # run cleanup on user user1
+    _cleanup_nonprivate_user_roles(session, user1, role_private1.id)
+    session.commit()  # must commit since method does not commit
+
+    # private role not deleted, associations with role6 and with sharing role deleted, sharing role name updated
+    assert len(user1.roles) == 1
+    assert user1.roles[0].id == role_private1.id
+    assert role_sharing1.name == "sharing role for [USER PURGED], user2@foo.com"
+
+    # verify user2 roles
+    assert len(user2.roles) == 3
+    assert role_private2 in [ura.role for ura in user2.roles]
+    assert role_sharing1 in [ura.role for ura in user2.roles]
+    assert role6 in [ura.role for ura in user2.roles]
+
+    # run cleanup on user user2
+    _cleanup_nonprivate_user_roles(session, user2, role_private2.id)
+    session.commit()
+
+    # private role not deleted, association with sharing role deleted
+    assert len(user2.roles) == 1
+    assert user2.roles[0].id == role_private2.id
+    # sharing role1 deleted since it has no more users associated with it
+    roles = session.scalars(select(Role)).all()
+    assert len(roles) == 5  # 3 private, role6, sharing2
+    assert role_sharing1.id not in [role.id for role in roles]
+
+    # verify user3 roles
+    assert len(user3.roles) == 3
+    assert role_private3 in [ura.role for ura in user3.roles]
+    assert role_sharing2 in [ura.role for ura in user3.roles]
+    assert role6 in [ura.role for ura in user3.roles]
+
+    # run cleanup on user user3
+    _cleanup_nonprivate_user_roles(session, user3, role_private3.id)
+    session.commit()
+
+    # remaining: 3 private roles + 3 associations, role6
+    roles = session.scalars(select(Role)).all()
+    assert len(roles) == 4
+    associations = session.scalars(select(UserRoleAssociation)).all()
+    assert len(associations) == 3
diff --git a/test/unit/data/model/migration_fixes/__init__.py b/test/unit/data/model/migration_fixes/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test/unit/data/model/migration_fixes/conftest.py b/test/unit/data/model/migration_fixes/conftest.py
new file mode 100644
index 0000000000000000000000000000000000000000..21edbb3a49fc6e3c42fdf267ea65073f24b511b9
--- /dev/null
+++ b/test/unit/data/model/migration_fixes/conftest.py
@@ -0,0 +1,41 @@
+import tempfile
+from typing import TYPE_CHECKING
+
+import pytest
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+
+if TYPE_CHECKING:
+    from sqlalchemy.engine import Engine
+
+from galaxy.model.unittest_utils.model_testing_utils import (
+    _generate_unique_database_name,
+    _make_sqlite_db_url,
+)
+
+
+@pytest.fixture(scope="module")
+def sqlite_url_factory():
+    """Return a function that generates a sqlite url"""
+
+    def url():
+        database = _generate_unique_database_name()
+        return _make_sqlite_db_url(tmp_dir, database)
+
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        yield url
+
+
+@pytest.fixture(scope="module")
+def db_url(sqlite_url_factory):  # noqa: F811
+    return sqlite_url_factory()
+
+
+@pytest.fixture()
+def engine(db_url: str) -> "Engine":
+    return create_engine(db_url)
+
+
+@pytest.fixture
+def session(engine: "Engine") -> Session:
+    return Session(engine)
diff --git a/test/unit/data/model/migration_fixes/test_migrations.py b/test/unit/data/model/migration_fixes/test_migrations.py
new file mode 100644
index 0000000000000000000000000000000000000000..0c6c8979d8cc5ebac3daeb097fec9c4ca9ee4cfa
--- /dev/null
+++ b/test/unit/data/model/migration_fixes/test_migrations.py
@@ -0,0 +1,400 @@
+from typing import (
+    Generator,
+    TYPE_CHECKING,
+)
+
+import pytest
+from sqlalchemy import (
+    select,
+    text,
+)
+
+from galaxy import model as m
+from galaxy.model import (
+    GroupRoleAssociation,
+    User,
+    UserGroupAssociation,
+    UserRoleAssociation,
+)
+from galaxy.model.unittest_utils.migration_scripts_testing_utils import run_command
+
+if TYPE_CHECKING:
+    from sqlalchemy.engine import Engine
+
+COMMAND = "manage_db.sh"
+
+
+@pytest.fixture(autouse=True)
+def clear_database(engine: "Engine") -> "Generator":
+    """Delete all rows from all tables. Called after each test."""
+    yield
+    with engine.begin() as conn:
+        for table in m.mapper_registry.metadata.tables:
+            # Unless db is sqlite, disable foreign key constraints to delete out of order
+            if engine.name != "sqlite":
+                conn.execute(text(f"ALTER TABLE {table} DISABLE TRIGGER ALL"))
+            conn.execute(text(f"DELETE FROM {table}"))
+
+
+@pytest.fixture(autouse=True)
+def upgrade_database_after_test():
+    """Run after each test for proper cleanup"""
+    yield
+    run_command(f"{COMMAND} upgrade")
+
+
+def test_1cf595475b58(monkeypatch, session, make_user, make_history):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # STEP 0: Load pre-migration state
+    run_command(f"{COMMAND} downgrade d619fdfa6168")
+
+    # STEP 1: Load users with duplicate emails
+
+    # Duplicate group 1: users have no histories
+    # Expect: oldest user preserved
+    u1_1 = make_user(email="a")
+    u1_2 = make_user(email="a")
+    u1_3 = make_user(email="a")
+    original_email1 = u1_1.email
+    assert u1_1.email == u1_2.email == u1_3.email
+    assert u1_1.create_time < u1_2.create_time < u1_3.create_time  # u1_1 is oldest user
+
+    # Duplicate group 2: oldest user does NOT have a history, another user has a history
+    # Expect: user with history preserved
+    u2_1 = make_user(email="b")
+    u2_2 = make_user(email="b")
+    u2_3 = make_user(email="b")
+    original_email2 = u2_1.email
+    assert u2_1.email == u2_2.email == u2_3.email
+    assert u2_1.create_time < u2_2.create_time < u2_3.create_time  # u2_1 is oldest user
+
+    make_history(user=u2_2)  # u2_2 has a history
+
+    # Duplicate group 3: oldest user does NOT have a history, 2 users have a history
+    # Expect: oldest user with history preserved
+    u3_1 = make_user(email="c")
+    u3_2 = make_user(email="c")
+    u3_3 = make_user(email="c")
+    original_email3 = u3_1.email
+    assert u3_1.email == u3_2.email == u3_3.email
+    assert u3_1.create_time < u3_2.create_time < u3_3.create_time  # u2_1 is oldest user
+
+    make_history(user=u3_2)  # u3_2 has a history
+    make_history(user=u3_3)  # u3_3 has a history
+
+    # User w/o duplicate email
+    u4 = make_user()
+    original_email4 = u4.email
+
+    # STEP 2: Run migration
+
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # STEP 3: Verify deduplicated results
+
+    # Duplicate group 1:
+    u1_1_fixed = session.get(User, u1_1.id)
+    u1_2_fixed = session.get(User, u1_2.id)
+    u1_3_fixed = session.get(User, u1_3.id)
+
+    # oldest user's email is preserved; the rest are deduplicated
+    assert u1_1.email == original_email1
+    assert u1_1.email != u1_2.email != u1_3.email
+    # deduplicated users are marked as deleted
+    assert u1_1_fixed.deleted is False
+    assert u1_2_fixed.deleted is True
+    assert u1_3_fixed.deleted is True
+
+    # Duplicate group 2:
+    u2_1_fixed = session.get(User, u2_1.id)
+    u2_2_fixed = session.get(User, u2_2.id)
+    u2_3_fixed = session.get(User, u2_3.id)
+
+    # the email of the user with a history is preserved; the rest are deduplicated
+    assert u2_2.email == original_email2
+    assert u2_1.email != u1_2.email != u1_3.email
+    # deduplicated users are marked as deleted
+    assert u2_1_fixed.deleted is True
+    assert u2_2_fixed.deleted is False
+    assert u2_3_fixed.deleted is True
+
+    # Duplicate group 3:
+    u3_1_fixed = session.get(User, u3_1.id)
+    u3_2_fixed = session.get(User, u3_2.id)
+    u3_3_fixed = session.get(User, u3_3.id)
+
+    # the email of the oldest user with a history is preserved; the rest are deduplicated
+    assert u3_2.email == original_email3
+    assert u3_1.email != u3_2.email != u3_3.email
+    # deduplicated users are marked as deleted
+    assert u3_1_fixed.deleted is True
+    assert u3_2_fixed.deleted is False
+    assert u3_3_fixed.deleted is True
+
+    # User w/o duplicate email
+    u4_no_change = session.get(User, u4.id)
+    assert u4_no_change.email == original_email4
+    assert u4_no_change.deleted is False
+
+
+def test_d619fdfa6168(monkeypatch, session, make_user):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # STEP 0: Load pre-migration state
+    run_command(f"{COMMAND} downgrade d2d8f51ebb7e")
+
+    # STEP 1: Load users with duplicate usernames
+
+    # Expect: oldest user preserved
+    u1 = make_user(username="a")
+    u2 = make_user(username="a")
+    u3 = make_user(username="a")
+    original_username = u3.username
+    assert u1.username == u2.username == u3.username
+    assert u1.create_time < u2.create_time < u3.create_time  # u3 is newest user
+
+    # STEP 2: Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # STEP 3: Verify deduplicated results
+    u1_fixed = session.get(User, u1.id)
+    u2_fixed = session.get(User, u2.id)
+    u3_fixed = session.get(User, u3.id)
+
+    # oldest user's username is preserved; the rest are deduplicated
+    assert u3_fixed.username == original_username
+    assert u1.username != u2.username != u3.username
+    # deduplicated users are marked as deleted
+    assert u1_fixed.deleted is True
+    assert u2_fixed.deleted is True
+    assert u3_fixed.deleted is False
+
+
+def test_349dd9d9aac9(monkeypatch, session, make_user, make_role, make_user_role_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 1cf595475b58")
+
+    # Load duplicate records
+    u1, u2 = make_user(), make_user()
+    r1, r2 = make_role(), make_role()
+    make_user_role_association(user=u1, role=r1)
+    make_user_role_association(user=u1, role=r2)
+    make_user_role_association(user=u1, role=r2)  # duplicate
+    make_user_role_association(user=u2, role=r1)
+    make_user_role_association(user=u2, role=r1)  # duplicate
+
+    # Verify duplicates
+    assert len(u1.roles) == 3
+    assert len(u2.roles) == 2
+    all_associations = session.execute(select(UserRoleAssociation)).all()
+    assert len(all_associations) == 5
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    assert len(u1.roles) == 2
+    assert len(u2.roles) == 1
+    all_associations = session.execute(select(UserRoleAssociation)).all()
+    assert len(all_associations) == 3
+
+
+def test_56ddf316dbd0(monkeypatch, session, make_user, make_group, make_user_group_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 1fdd615f2cdb")
+
+    # Load duplicate records
+    u1, u2 = make_user(), make_user()
+    g1, g2 = make_group(), make_group()
+    make_user_group_association(user=u1, group=g1)
+    make_user_group_association(user=u1, group=g2)
+    make_user_group_association(user=u1, group=g2)  # duplicate
+    make_user_group_association(user=u2, group=g1)
+    make_user_group_association(user=u2, group=g1)  # duplicate
+
+    # Verify duplicates
+    assert len(u1.groups) == 3
+    assert len(u2.groups) == 2
+    all_associations = session.execute(select(UserGroupAssociation)).all()
+    assert len(all_associations) == 5
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    assert len(u1.groups) == 2
+    assert len(u2.groups) == 1
+    all_associations = session.execute(select(UserGroupAssociation)).all()
+    assert len(all_associations) == 3
+
+
+def test_9ef6431f3a4e(monkeypatch, session, make_group, make_role, make_group_role_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 13fe10b8e35b")
+
+    # Load duplicate records
+    g1, g2 = make_group(), make_group()
+    r1, r2 = make_role(), make_role()
+    make_group_role_association(group=g1, role=r1)
+    make_group_role_association(group=g1, role=r2)
+    make_group_role_association(group=g1, role=r2)  # duplicate
+    make_group_role_association(group=g2, role=r1)
+    make_group_role_association(group=g2, role=r1)  # duplicate
+
+    # Verify duplicates
+    assert len(g1.roles) == 3
+    assert len(g2.roles) == 2
+    all_associations = session.execute(select(GroupRoleAssociation)).all()
+    assert len(all_associations) == 5
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    assert len(g1.roles) == 2
+    assert len(g2.roles) == 1
+    all_associations = session.execute(select(GroupRoleAssociation)).all()
+    assert len(all_associations) == 3
+
+
+def test_1fdd615f2cdb(monkeypatch, session, make_user, make_role, make_user_role_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 349dd9d9aac9")
+
+    # Load records w/nulls
+    ura1 = make_user_role_association(user=make_user(), role=make_role())
+    ura2 = make_user_role_association(user=make_user(), role=make_role())
+    ura3 = make_user_role_association(user=make_user(), role=make_role())
+    ura1.user_id = None
+    ura2.role_id = None
+    ura3.user_id = None
+    ura3.role_id = None
+    session.add_all([ura1, ura2, ura3])
+    session.commit()
+
+    # Load record w/o nulls
+    make_user_role_association(user=make_user(), role=make_role())
+
+    # Verify data
+    all_associations = session.execute(select(UserRoleAssociation)).all()
+    assert len(all_associations) == 4
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    all_associations = session.execute(select(UserRoleAssociation)).all()
+    assert len(all_associations) == 1
+
+
+def test_13fe10b8e35b(monkeypatch, session, make_user, make_group, make_user_group_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 56ddf316dbd0")
+
+    # Load records w/nulls
+    uga1 = make_user_group_association(user=make_user(), group=make_group())
+    uga2 = make_user_group_association(user=make_user(), group=make_group())
+    uga3 = make_user_group_association(user=make_user(), group=make_group())
+    uga1.user_id = None
+    uga2.group_id = None
+    uga3.user_id = None
+    uga3.group_id = None
+    session.add_all([uga1, uga2, uga3])
+    session.commit()
+
+    # Load record w/o nulls
+    make_user_group_association(user=make_user(), group=make_group())
+
+    # Verify data
+    all_associations = session.execute(select(UserGroupAssociation)).all()
+    assert len(all_associations) == 4
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    all_associations = session.execute(select(UserGroupAssociation)).all()
+    assert len(all_associations) == 1
+
+
+def test_25b092f7938b(monkeypatch, session, make_group, make_role, make_group_role_association):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # Load pre-migration state
+    run_command(f"{COMMAND} downgrade 9ef6431f3a4e")
+
+    # Load records w/nulls
+    gra1 = make_group_role_association(group=make_group(), role=make_role())
+    gra2 = make_group_role_association(group=make_group(), role=make_role())
+    gra3 = make_group_role_association(group=make_group(), role=make_role())
+    gra1.group_id = None
+    gra2.role_id = None
+    gra3.group_id = None
+    gra3.role_id = None
+    session.add_all([gra1, gra2, gra3])
+    session.commit()
+
+    # Load record w/o nulls
+    make_group_role_association(group=make_group(), role=make_role())
+
+    # Verify data
+    all_associations = session.execute(select(GroupRoleAssociation)).all()
+    assert len(all_associations) == 4
+
+    # Run migration
+    run_command(f"{COMMAND} upgrade")
+    session.expire_all()
+
+    # Verify clean data
+    all_associations = session.execute(select(GroupRoleAssociation)).all()
+    assert len(all_associations) == 1
diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py
index a30410dd02079582dd929ad01fcac43d3ee67940..cbf8afa5a7e2dc9846f3c6ed7d9e3d35c26bb0c7 100644
--- a/test/unit/data/model/test_model_store.py
+++ b/test/unit/data/model/test_model_store.py
@@ -122,32 +122,80 @@ def test_import_export_history_allow_discarded_data():
     assert imported_job.output_datasets[0].dataset == datasets[1]
 
 
-def test_import_export_history_with_implicit_conversion():
+def setup_history_with_implicit_conversion():
     app = _mock_app()
 
     u, h, d1, d2, j = _setup_simple_cat_job(app)
 
+    intermediate_ext = "bam"
+    intermediate_implicit_hda = model.HistoryDatasetAssociation(
+        extension=intermediate_ext, create_dataset=True, flush=False, history=h
+    )
+    intermediate_implicit_hda.hid = d2.hid
     convert_ext = "fasta"
     implicit_hda = model.HistoryDatasetAssociation(extension=convert_ext, create_dataset=True, flush=False, history=h)
     implicit_hda.hid = d2.hid
     # this adds and flushes the result...
-    d2.attach_implicitly_converted_dataset(app.model.context, implicit_hda, convert_ext)
+    intermediate_implicit_hda.attach_implicitly_converted_dataset(app.model.context, implicit_hda, convert_ext)
+    d2.attach_implicitly_converted_dataset(app.model.context, intermediate_implicit_hda, intermediate_ext)
+
+    app.object_store.update_from_file(intermediate_implicit_hda.dataset, file_name=TEST_PATH_2_CONVERTED, create=True)
     app.object_store.update_from_file(implicit_hda.dataset, file_name=TEST_PATH_2_CONVERTED, create=True)
 
-    assert len(h.active_datasets) == 3
+    assert len(h.active_datasets) == 4
+    return app, h, implicit_hda
+
+
+def test_import_export_history_with_implicit_conversion():
+    app, h, _ = setup_history_with_implicit_conversion()
     imported_history = _import_export_history(app, h, export_files="copy", include_hidden=True)
 
-    assert len(imported_history.active_datasets) == 3
+    assert len(imported_history.active_datasets) == 4
     recovered_hda_2 = imported_history.active_datasets[1]
     assert recovered_hda_2.implicitly_converted_datasets
-    imported_conversion = recovered_hda_2.implicitly_converted_datasets[0]
-    assert imported_conversion.type == "fasta"
-    assert imported_conversion.dataset == imported_history.active_datasets[2]
+    intermediate_conversion = recovered_hda_2.implicitly_converted_datasets[0]
+    assert intermediate_conversion.type == "bam"
+    intermediate_hda = intermediate_conversion.dataset
+    assert intermediate_hda.implicitly_converted_datasets
+    final_conversion = intermediate_hda.implicitly_converted_datasets[0]
+
+    assert final_conversion.type == "fasta"
+    assert final_conversion.dataset == imported_history.active_datasets[-1]
 
     # implicit conversions have the same HID... ensure this property is recovered...
     assert imported_history.active_datasets[2].hid == imported_history.active_datasets[1].hid
 
 
+def test_import_export_history_with_implicit_conversion_parents_purged():
+    app, h, implicit_hda = setup_history_with_implicit_conversion()
+    # Purge parents
+    parent = implicit_hda.implicitly_converted_parent_datasets[0].parent_hda
+    parent.dataset.purged = True
+    grandparent = parent.implicitly_converted_parent_datasets[0].parent_hda
+    grandparent.dataset.purged = True
+    app.model.context.commit()
+    imported_history = _import_export_history(app, h, export_files="copy", include_hidden=True)
+
+    assert len(imported_history.active_datasets) == 2
+    assert len(imported_history.datasets) == 4
+    imported_implicit_hda = imported_history.active_datasets[1]
+    assert imported_implicit_hda.extension == "fasta"
+
+    # implicit conversions have the same HID... ensure this property is recovered...
+    assert imported_implicit_hda.hid == implicit_hda.hid
+    assert imported_implicit_hda.implicitly_converted_parent_datasets
+    intermediate_implicit_conversion = imported_implicit_hda.implicitly_converted_parent_datasets[0]
+    intermediate_hda = intermediate_implicit_conversion.parent_hda
+    assert intermediate_hda.hid == implicit_hda.hid
+    assert intermediate_hda.extension == "bam"
+    assert intermediate_hda.implicitly_converted_datasets
+    assert intermediate_hda.implicitly_converted_parent_datasets
+    first_implicit_conversion = intermediate_hda.implicitly_converted_parent_datasets[0]
+    source_hda = first_implicit_conversion.parent_hda
+    assert source_hda.hid == implicit_hda.hid
+    assert source_hda.extension == "txt"
+
+
 def test_import_export_history_with_implicit_conversion_and_extra_files():
     app = _mock_app()
 
@@ -1018,7 +1066,7 @@ def _setup_collection_invocation(app):
     workflow_step_1 = model.WorkflowStep()
     workflow_step_1.order_index = 0
     workflow_step_1.type = "data_collection_input"
-    workflow_step_1.tool_inputs = {}  # type:ignore[assignment]
+    workflow_step_1.tool_inputs = {}
     sa_session.add(workflow_step_1)
     workflow_1 = _workflow_from_steps(u, [workflow_step_1])
     workflow_1.license = "MIT"
@@ -1044,7 +1092,7 @@ def _setup_simple_invocation(app):
     workflow_step_1 = model.WorkflowStep()
     workflow_step_1.order_index = 0
     workflow_step_1.type = "data_input"
-    workflow_step_1.tool_inputs = {}  # type:ignore[assignment]
+    workflow_step_1.tool_inputs = {}
     sa_session.add(workflow_step_1)
     workflow = _workflow_from_steps(u, [workflow_step_1])
     workflow.license = "MIT"
@@ -1215,7 +1263,6 @@ def import_archive(archive_path, app, user, import_options=None):
     dest_dir = CompressedFile(archive_path).extract(dest_parent)
 
     import_options = import_options or store.ImportOptions()
-    new_history = None
     model_store = store.get_import_model_store_for_directory(
         dest_dir,
         app=app,
diff --git a/test/unit/data/test_dataset_materialization.py b/test/unit/data/test_dataset_materialization.py
index 9015b107539f0bb440ac25cebf2cd7668335a179..be791a047cce5de2b725732bb5096ff0d7f6e877 100644
--- a/test/unit/data/test_dataset_materialization.py
+++ b/test/unit/data/test_dataset_materialization.py
@@ -62,6 +62,69 @@ def test_deferred_hdas_basic_attached():
     _assert_2_bed_metadata(materialized_hda)
 
 
+def test_hash_validate():
+    fixture_context = setup_fixture_context_with_history()
+    store_dict = deferred_hda_model_store_dict()
+    perform_import_from_store_dict(fixture_context, store_dict)
+    deferred_hda = fixture_context.history.datasets[0]
+    assert deferred_hda
+    _assert_2_bed_metadata(deferred_hda)
+    assert deferred_hda.dataset.state == "deferred"
+    materializer = materializer_factory(True, object_store=fixture_context.app.object_store)
+    materialized_hda = materializer.ensure_materialized(deferred_hda)
+    materialized_dataset = materialized_hda.dataset
+    assert materialized_dataset.state == "ok"
+
+
+def test_hash_invalid():
+    fixture_context = setup_fixture_context_with_history()
+    store_dict = deferred_hda_model_store_dict()
+    store_dict["datasets"][0]["file_metadata"]["hashes"][0]["hash_value"] = "invalidhash"
+    perform_import_from_store_dict(fixture_context, store_dict)
+    deferred_hda = fixture_context.history.datasets[0]
+    assert deferred_hda
+    _assert_2_bed_metadata(deferred_hda)
+    assert deferred_hda.dataset.state == "deferred"
+    materializer = materializer_factory(True, object_store=fixture_context.app.object_store)
+    materialized_hda = materializer.ensure_materialized(deferred_hda)
+    materialized_dataset = materialized_hda.dataset
+    assert materialized_dataset.state == "error"
+
+
+def test_hash_validate_source_of_download():
+    fixture_context = setup_fixture_context_with_history()
+    store_dict = deferred_hda_model_store_dict()
+    store_dict["datasets"][0]["file_metadata"]["sources"][0]["hashes"] = [
+        {"model_class": "DatasetSourceHash", "hash_function": "MD5", "hash_value": "f568c29421792b1b1df4474dafae01f1"}
+    ]
+    perform_import_from_store_dict(fixture_context, store_dict)
+    deferred_hda = fixture_context.history.datasets[0]
+    assert deferred_hda
+    _assert_2_bed_metadata(deferred_hda)
+    assert deferred_hda.dataset.state == "deferred"
+    materializer = materializer_factory(True, object_store=fixture_context.app.object_store)
+    materialized_hda = materializer.ensure_materialized(deferred_hda)
+    materialized_dataset = materialized_hda.dataset
+    assert materialized_dataset.state == "ok", materialized_hda.info
+
+
+def test_hash_invalid_source_of_download():
+    fixture_context = setup_fixture_context_with_history()
+    store_dict = deferred_hda_model_store_dict()
+    store_dict["datasets"][0]["file_metadata"]["sources"][0]["hashes"] = [
+        {"model_class": "DatasetSourceHash", "hash_function": "MD5", "hash_value": "invalidhash"}
+    ]
+    perform_import_from_store_dict(fixture_context, store_dict)
+    deferred_hda = fixture_context.history.datasets[0]
+    assert deferred_hda
+    _assert_2_bed_metadata(deferred_hda)
+    assert deferred_hda.dataset.state == "deferred"
+    materializer = materializer_factory(True, object_store=fixture_context.app.object_store)
+    materialized_hda = materializer.ensure_materialized(deferred_hda)
+    materialized_dataset = materialized_hda.dataset
+    assert materialized_dataset.state == "error", materialized_hda.info
+
+
 def test_deferred_hdas_basic_attached_store_by_uuid():
     # skip a flush here so this is a different path...
     fixture_context = setup_fixture_context_with_history(store_by="uuid")
diff --git a/test/unit/data/test_dereference.py b/test/unit/data/test_dereference.py
new file mode 100644
index 0000000000000000000000000000000000000000..36527c44bc6cd75f3515dcc3a039538d41cbc92a
--- /dev/null
+++ b/test/unit/data/test_dereference.py
@@ -0,0 +1,57 @@
+from base64 import b64encode
+
+from galaxy.model.dereference import dereference_to_model
+from galaxy.tool_util.parameters import DataRequestUri
+from .model.test_model_store import setup_fixture_context_with_history
+
+B64_FOR_1_2_3 = b64encode(b"1 2 3").decode("utf-8")
+TEST_URI = "gxfiles://test/1.bed"
+TEST_BASE64_URI = f"base64://{B64_FOR_1_2_3}"
+
+
+def test_dereference():
+    app, sa_session, user, history = setup_fixture_context_with_history()
+    uri_request = DataRequestUri(url=TEST_URI, ext="bed")
+    hda = dereference_to_model(sa_session, user, history, uri_request)
+    assert hda.name == "1.bed"
+    assert hda.dataset.sources[0].source_uri == TEST_URI
+    assert hda.ext == "bed"
+
+
+def test_dereference_dbkey():
+    app, sa_session, user, history = setup_fixture_context_with_history()
+    uri_request = DataRequestUri(url=TEST_URI, ext="bed", dbkey="hg19")
+    hda = dereference_to_model(sa_session, user, history, uri_request)
+    assert hda.name == "1.bed"
+    assert hda.dataset.sources[0].source_uri == TEST_URI
+    assert hda.dbkey == "hg19"
+
+
+def test_dereference_md5():
+    app, sa_session, user, history = setup_fixture_context_with_history()
+    md5 = "f2b33fb7b3d0eb95090a16060e6a24f9"
+    uri_request = DataRequestUri.model_validate(
+        {
+            "url": TEST_BASE64_URI,
+            "name": "foobar.txt",
+            "ext": "txt",
+            "hashes": [{"hash_function": "MD5", "hash_value": md5}],
+        }
+    )
+    hda = dereference_to_model(sa_session, user, history, uri_request)
+    assert hda.name == "foobar.txt"
+    assert hda.dataset.sources[0].source_uri == TEST_BASE64_URI
+    assert hda.dataset.sources[0].hashes[0]
+    assert hda.dataset.sources[0].hashes[0].hash_function == "MD5"
+    assert hda.dataset.sources[0].hashes[0].hash_value == md5
+
+
+def test_dereference_to_posix():
+    app, sa_session, user, history = setup_fixture_context_with_history()
+    uri_request = DataRequestUri.model_validate(
+        {"url": TEST_BASE64_URI, "name": "foobar.txt", "ext": "txt", "space_to_tab": True}
+    )
+    hda = dereference_to_model(sa_session, user, history, uri_request)
+    assert hda.name == "foobar.txt"
+    assert hda.dataset.sources[0].source_uri == TEST_BASE64_URI
+    assert hda.dataset.sources[0].transform[0]["action"] == "spaces_to_tabs"
diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index 1a88a82f78ed48807a1805bda98e90d0eb20f553..83975f0e7490818727be41cd530caca813343d53 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -1,4 +1,3 @@
-import collections
 import os
 import random
 import uuid
@@ -23,6 +22,7 @@ from galaxy.model.orm.util import (
     get_object_session,
 )
 from galaxy.model.security import GalaxyRBACAgent
+from galaxy.model.unittest_utils.utils import random_email
 from galaxy.objectstore import QuotaSourceMap
 from galaxy.util.unittest import TestCase
 
@@ -77,192 +77,9 @@ class BaseModelTestCase(TestCase):
 
 
 class TestMappings(BaseModelTestCase):
-    def test_ratings(self):
-        user_email = "rater@example.com"
-        u = model.User(email=user_email, password="password")
-        self.persist(u)
-
-        def persist_and_check_rating(rating_class, item):
-            rating = 5
-            rating_association = rating_class(u, item, rating)
-            self.persist(rating_association)
-            self.expunge()
-            stored_rating = self.model.session.scalars(select(rating_class)).all()[0]
-            assert stored_rating.rating == rating
-            assert stored_rating.user.email == user_email
-
-        sw = model.StoredWorkflow()
-        add_object_to_object_session(sw, u)
-        sw.user = u
-        self.persist(sw)
-        persist_and_check_rating(model.StoredWorkflowRatingAssociation, sw)
-
-        h = model.History(name="History for Rating", user=u)
-        self.persist(h)
-        persist_and_check_rating(model.HistoryRatingAssociation, h)
-
-        d1 = model.HistoryDatasetAssociation(
-            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
-        )
-        self.persist(d1)
-        persist_and_check_rating(model.HistoryDatasetAssociationRatingAssociation, d1)
-
-        page = model.Page()
-        page.user = u
-        self.persist(page)
-        persist_and_check_rating(model.PageRatingAssociation, page)
-
-        visualization = model.Visualization()
-        visualization.user = u
-        self.persist(visualization)
-        persist_and_check_rating(model.VisualizationRatingAssociation, visualization)
-
-        dataset_collection = model.DatasetCollection(collection_type="paired")
-        history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
-        self.persist(history_dataset_collection)
-        persist_and_check_rating(model.HistoryDatasetCollectionRatingAssociation, history_dataset_collection)
-
-        library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
-        self.persist(library_dataset_collection)
-        persist_and_check_rating(model.LibraryDatasetCollectionRatingAssociation, library_dataset_collection)
-
-    def test_display_name(self):
-        def assert_display_name_converts_to_unicode(item, name):
-            assert isinstance(item.get_display_name(), str)
-            assert item.get_display_name() == name
-
-        ldda = model.LibraryDatasetDatasetAssociation(name="ldda_name")
-        assert_display_name_converts_to_unicode(ldda, "ldda_name")
-
-        hda = model.HistoryDatasetAssociation(name="hda_name")
-        assert_display_name_converts_to_unicode(hda, "hda_name")
-
-        history = model.History(name="history_name")
-        assert_display_name_converts_to_unicode(history, "history_name")
-
-        library = model.Library(name="library_name")
-        assert_display_name_converts_to_unicode(library, "library_name")
-
-        library_folder = model.LibraryFolder(name="library_folder")
-        assert_display_name_converts_to_unicode(library_folder, "library_folder")
-
-        history = model.History(name="Hello₩◎ґʟⅾ")
-
-        assert isinstance(history.name, str)
-        assert isinstance(history.get_display_name(), str)
-        assert history.get_display_name() == "Hello₩◎ґʟⅾ"
-
-    def test_hda_to_library_dataset_dataset_association(self):
-        model = self.model
-        u = self.model.User(email="mary@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        hda = model.HistoryDatasetAssociation(
-            name="hda_name", create_dataset=True, history=h1, sa_session=model.session
-        )
-        self.persist(hda)
-        trans = collections.namedtuple("trans", "user")
-        target_folder = model.LibraryFolder(name="library_folder")
-        ldda = hda.to_library_dataset_dataset_association(
-            trans=trans(user=u),
-            target_folder=target_folder,
-        )
-        assert target_folder.item_count == 1
-        assert ldda.id
-        assert ldda.library_dataset.id
-        assert ldda.library_dataset_id
-        assert ldda.library_dataset.library_dataset_dataset_association
-        assert ldda.library_dataset.library_dataset_dataset_association_id
-        library_dataset_id = ldda.library_dataset_id
-        replace_dataset = ldda.library_dataset
-        new_ldda = hda.to_library_dataset_dataset_association(
-            trans=trans(user=u), target_folder=target_folder, replace_dataset=replace_dataset
-        )
-        assert new_ldda.id != ldda.id
-        assert new_ldda.library_dataset_id == library_dataset_id
-        assert new_ldda.library_dataset.library_dataset_dataset_association_id == new_ldda.id
-        assert len(new_ldda.library_dataset.expired_datasets) == 1
-        assert new_ldda.library_dataset.expired_datasets[0] == ldda
-        assert target_folder.item_count == 1
-
-    def test_hda_to_library_dataset_dataset_association_fails_if_private(self):
-        model = self.model
-        u = model.User(email="mary2@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        hda = model.HistoryDatasetAssociation(
-            name="hda_name", create_dataset=True, history=h1, sa_session=model.session
-        )
-        hda.dataset.object_store_id = PRIVATE_OBJECT_STORE_ID
-        self.persist(hda)
-        trans = collections.namedtuple("trans", "user")
-        target_folder = model.LibraryFolder(name="library_folder")
-        with pytest.raises(Exception) as exec_info:
-            hda.to_library_dataset_dataset_association(
-                trans=trans(user=u),
-                target_folder=target_folder,
-            )
-        assert galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE in str(exec_info.value)
-
-    def test_tags(self):
-        TAG_NAME = "Test Tag"
-        my_tag = model.Tag(name=TAG_NAME)
-        u = model.User(email="tagger@example.com", password="password")
-        self.persist(my_tag, u)
-
-        def tag_and_test(taggable_object, tag_association_class):
-            q = select(tag_association_class).join(model.Tag).where(model.Tag.name == TAG_NAME)
-
-            assert len(self.model.session.execute(q).all()) == 0
-
-            tag_association = tag_association_class()
-            tag_association.tag = my_tag
-            taggable_object.tags = [tag_association]
-            self.persist(tag_association, taggable_object)
-
-            assert len(self.model.session.execute(q).all()) == 1
-
-        sw = model.StoredWorkflow(user=u)
-        tag_and_test(sw, model.StoredWorkflowTagAssociation)
-
-        h = model.History(name="History for Tagging", user=u)
-        tag_and_test(h, model.HistoryTagAssociation)
-
-        d1 = model.HistoryDatasetAssociation(
-            extension="txt", history=h, create_dataset=True, sa_session=self.model.session
-        )
-        tag_and_test(d1, model.HistoryDatasetAssociationTagAssociation)
-
-        page = model.Page(user=u)
-        tag_and_test(page, model.PageTagAssociation)
-
-        visualization = model.Visualization(user=u)
-        tag_and_test(visualization, model.VisualizationTagAssociation)
-
-        dataset_collection = model.DatasetCollection(collection_type="paired")
-        history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
-        tag_and_test(history_dataset_collection, model.HistoryDatasetCollectionTagAssociation)
-
-        library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
-        tag_and_test(library_dataset_collection, model.LibraryDatasetCollectionTagAssociation)
-
-    def test_collection_get_interface(self):
-        u = model.User(email="mary@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(
-            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        c1 = model.DatasetCollection(collection_type="list")
-        elements = 100
-        dces = [
-            model.DatasetCollectionElement(collection=c1, element=d1, element_identifier=f"{i}", element_index=i)
-            for i in range(elements)
-        ]
-        self.persist(u, h1, d1, c1, *dces, commit=False, expunge=False)
-        self.model.session.flush()
-        for i in range(elements):
-            assert c1[i] == dces[i]
 
     def test_dataset_instance_order(self) -> None:
-        u = model.User(email="mary@example.com", password="password")
+        u = model.User(email=random_email(), password="password")
         h1 = model.History(name="History 1", user=u)
         elements = []
         list_pair = model.DatasetCollection(collection_type="list:paired")
@@ -308,71 +125,6 @@ class TestMappings(BaseModelTestCase):
         assert all(d.name == f"forward_{i}" for i, d in enumerate(forward_hdas))
         assert all(d.name == f"reverse_{i}" for i, d in enumerate(reverse_hdas))
 
-    def test_collections_in_histories(self):
-        u = model.User(email="mary@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(
-            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        d2 = model.HistoryDatasetAssociation(
-            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-
-        c1 = model.DatasetCollection(collection_type="pair")
-        hc1 = model.HistoryDatasetCollectionAssociation(history=h1, collection=c1, name="HistoryCollectionTest1")
-
-        dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="left")
-        dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="right")
-
-        self.persist(u, h1, d1, d2, c1, hc1, dce1, dce2)
-
-        stmt = (
-            select(model.HistoryDatasetCollectionAssociation)
-            .filter(model.HistoryDatasetCollectionAssociation.name == "HistoryCollectionTest1")
-            .limit(1)
-        )
-        loaded_dataset_collection = self.model.session.scalars(stmt).first().collection
-        assert len(loaded_dataset_collection.elements) == 2
-        assert loaded_dataset_collection.collection_type == "pair"
-        assert loaded_dataset_collection["left"] == dce1
-        assert loaded_dataset_collection["right"] == dce2
-
-    def test_collections_in_library_folders(self):
-        u = model.User(email="mary2@example.com", password="password")
-        lf = model.LibraryFolder(name="RootFolder")
-        library = model.Library(name="Library1", root_folder=lf)
-        ld1 = model.LibraryDataset()
-        ld2 = model.LibraryDataset()
-
-        ldda1 = model.LibraryDatasetDatasetAssociation(extension="txt", library_dataset=ld1)
-        ldda2 = model.LibraryDatasetDatasetAssociation(extension="txt", library_dataset=ld1)
-
-        c1 = model.DatasetCollection(collection_type="pair")
-        dce1 = model.DatasetCollectionElement(collection=c1, element=ldda1)
-        dce2 = model.DatasetCollectionElement(collection=c1, element=ldda2)
-        self.persist(u, library, lf, ld1, ld2, c1, ldda1, ldda2, dce1, dce2)
-
-        # TODO:
-        # loaded_dataset_collection = self.query( model.DatasetCollection ).filter( model.DatasetCollection.name == "LibraryCollectionTest1" ).first()
-        # assert len(loaded_dataset_collection.datasets) == 2
-        # assert loaded_dataset_collection.collection_type == "pair"
-
-    def test_dataset_action_tuples(self):
-        u = model.User(email="foo", password="foo")
-        h1 = model.History(user=u)
-        hda1 = model.HistoryDatasetAssociation(history=h1, create_dataset=True, sa_session=self.model.session)
-        hda2 = model.HistoryDatasetAssociation(history=h1, create_dataset=True, sa_session=self.model.session)
-        r1 = model.Role()
-        dp1 = model.DatasetPermissions(action="action1", dataset=hda1.dataset, role=r1)
-        dp2 = model.DatasetPermissions(action=None, dataset=hda1.dataset, role=r1)
-        dp3 = model.DatasetPermissions(action="action3", dataset=hda1.dataset, role=r1)
-        c1 = model.DatasetCollection(collection_type="type1")
-        dce1 = model.DatasetCollectionElement(collection=c1, element=hda1)
-        dce2 = model.DatasetCollectionElement(collection=c1, element=hda2)
-        self.model.session.add_all([u, h1, hda1, hda2, r1, dp1, dp2, dp3, c1, dce1, dce2])
-        self.model.session.flush()
-        assert c1.dataset_action_tuples == [("action1", r1.id), ("action3", r1.id)]
-
     def test_nested_collection_attributes(self):
         u = model.User(email="mary2@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
@@ -461,215 +213,8 @@ class TestMappings(BaseModelTestCase):
         ]
         assert c4.dataset_elements == [dce1, dce2]
 
-    def test_dataset_dbkeys_and_extensions_summary(self):
-        u = model.User(email="mary2@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(
-            extension="bam", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        d2 = model.HistoryDatasetAssociation(
-            extension="txt", dbkey="hg19", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        c1 = model.DatasetCollection(collection_type="paired")
-        dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
-        dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
-        hdca = model.HistoryDatasetCollectionAssociation(collection=c1, history=h1)
-        self.model.session.add_all([d1, d2, c1, dce1, dce2, hdca])
-        self.model.session.flush()
-        assert hdca.dataset_dbkeys_and_extensions_summary[0] == {"hg19"}
-        assert hdca.dataset_dbkeys_and_extensions_summary[1] == {"bam", "txt"}
-
-    def test_populated_optimized_ok(self):
-        u = model.User(email="mary2@example.com", password="password")
-        h1 = model.History(name="History 1", user=u)
-        d1 = model.HistoryDatasetAssociation(
-            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        d2 = model.HistoryDatasetAssociation(
-            extension="txt", history=h1, create_dataset=True, sa_session=self.model.session
-        )
-        c1 = model.DatasetCollection(collection_type="paired")
-        dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
-        dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
-        self.model.session.add_all([d1, d2, c1, dce1, dce2])
-        self.model.session.flush()
-        assert c1.populated
-        assert c1.populated_optimized
-
-    def test_populated_optimized_empty_list_list_ok(self):
-        c1 = model.DatasetCollection(collection_type="list")
-        c2 = model.DatasetCollection(collection_type="list:list")
-        dce1 = model.DatasetCollectionElement(
-            collection=c2, element=c1, element_identifier="empty_list", element_index=0
-        )
-        self.model.session.add_all([c1, c2, dce1])
-        self.model.session.flush()
-        assert c1.populated
-        assert c1.populated_optimized
-        assert c2.populated
-        assert c2.populated_optimized
-
-    def test_populated_optimized_list_list_not_populated(self):
-        c1 = model.DatasetCollection(collection_type="list")
-        c1.populated_state = False
-        c2 = model.DatasetCollection(collection_type="list:list")
-        dce1 = model.DatasetCollectionElement(
-            collection=c2, element=c1, element_identifier="empty_list", element_index=0
-        )
-        self.model.session.add_all([c1, c2, dce1])
-        self.model.session.flush()
-        assert not c1.populated
-        assert not c1.populated_optimized
-        assert not c2.populated
-        assert not c2.populated_optimized
-
-    def test_default_disk_usage(self):
-        u = model.User(email="disk_default@test.com", password="password")
-        self.persist(u)
-        u.adjust_total_disk_usage(1, None)
-        u_id = u.id
-        self.expunge()
-        user_reload = self.model.session.get(model.User, u_id)
-        assert user_reload.disk_usage == 1
-
-    def test_basic(self):
-        original_user_count = len(self.model.session.scalars(select(model.User)).all())
-
-        # Make some changes and commit them
-        u = model.User(email="james@foo.bar.baz", password="password")
-        h1 = model.History(name="History 1", user=u)
-        h2 = model.History(name=("H" * 1024))
-        self.persist(u, h1, h2)
-        metadata = dict(chromCol=1, startCol=2, endCol=3)
-        d1 = model.HistoryDatasetAssociation(
-            extension="interval", metadata=metadata, history=h2, create_dataset=True, sa_session=self.model.session
-        )
-        self.persist(d1)
-
-        # Check
-        users = self.model.session.scalars(select(model.User)).all()
-        assert len(users) == original_user_count + 1
-        user = [user for user in users if user.email == "james@foo.bar.baz"][0]
-        assert user.email == "james@foo.bar.baz"
-        assert user.password == "password"
-        assert len(user.histories) == 1
-        assert user.histories[0].name == "History 1"
-        hists = self.model.session.scalars(select(model.History)).all()
-        hist0 = [history for history in hists if history.id == h1.id][0]
-        hist1 = [history for history in hists if history.id == h2.id][0]
-        assert hist0.name == "History 1"
-        assert hist1.name == ("H" * 255)
-        assert hist0.user == user
-        assert hist1.user is None
-        assert hist1.datasets[0].metadata.chromCol == 1
-        # The filename test has moved to objectstore
-        # id = hist1.datasets[0].id
-        # assert hist1.datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + f"/dataset_{id}.dat"
-        # Do an update and check
-        hist1.name = "History 2b"
-        self.expunge()
-        hists = self.model.session.scalars(select(model.History)).all()
-        hist0 = [history for history in hists if history.name == "History 1"][0]
-        hist1 = [history for history in hists if history.name == "History 2b"][0]
-        assert hist0.name == "History 1"
-        assert hist1.name == "History 2b"
-        # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like.
-
-    def test_metadata_spec(self):
-        metadata = dict(chromCol=1, startCol=2, endCol=3)
-        d = model.HistoryDatasetAssociation(extension="interval", metadata=metadata, sa_session=self.model.session)
-        assert d.metadata.chromCol == 1
-        assert d.metadata.anyAttribute is None
-        assert "items" not in d.metadata
-
-    def test_dataset_job_relationship(self):
-        dataset = model.Dataset()
-        job = model.Job()
-        dataset.job = job
-        self.persist(job, dataset)
-        loaded_dataset = self.model.session.execute(
-            select(model.Dataset).filter(model.Dataset.id == dataset.id)
-        ).scalar_one()
-        assert loaded_dataset.job_id == job.id
-
-    def test_jobs(self):
-        u = model.User(email="jobtest@foo.bar.baz", password="password")
-        job = model.Job()
-        job.user = u
-        job.tool_id = "cat1"
-
-        self.persist(u, job)
-
-        loaded_job = self.model.session.scalars(select(model.Job).filter(model.Job.user == u).limit(1)).first()
-        assert loaded_job.tool_id == "cat1"
-
-    def test_job_metrics(self):
-        u = model.User(email="jobtest@foo.bar.baz", password="password")
-        job = model.Job()
-        job.user = u
-        job.tool_id = "cat1"
-
-        job.add_metric("gx", "galaxy_slots", 5)
-        job.add_metric("system", "system_name", "localhost")
-
-        self.persist(u, job)
-
-        task = model.Task(job=job, working_directory="/tmp", prepare_files_cmd="split.sh")
-        task.add_metric("gx", "galaxy_slots", 5)
-        task.add_metric("system", "system_name", "localhost")
-
-        big_value = ":".join(f"{i}" for i in range(2000))
-        task.add_metric("env", "BIG_PATH", big_value)
-        self.persist(task)
-        # Ensure big values truncated
-        assert len(task.text_metrics[1].metric_value) <= 1023
-
-    def test_tasks(self):
-        u = model.User(email="jobtest@foo.bar.baz", password="password")
-        job = model.Job()
-        task = model.Task(job=job, working_directory="/tmp", prepare_files_cmd="split.sh")
-        job.user = u
-        self.persist(u, job, task)
-
-        loaded_task = self.model.session.scalars(select(model.Task).filter(model.Task.job == job).limit(1)).first()
-        assert loaded_task.prepare_input_files_cmd == "split.sh"
-
-    def test_history_contents(self):
-        u = model.User(email="contents@foo.bar.baz", password="password")
-        # gs = model.GalaxySession()
-        h1 = model.History(name="HistoryContentsHistory1", user=u)
-
-        self.persist(u, h1, expunge=False)
-
-        d1 = self.new_hda(h1, name="1")
-        d2 = self.new_hda(h1, name="2", visible=False, object_store_id="foobar")
-        d3 = self.new_hda(h1, name="3", deleted=True, object_store_id="three_store")
-        d4 = self.new_hda(h1, name="4", visible=False, deleted=True)
-
-        self.session().flush()
-
-        def contents_iter_names(**kwds):
-            history = self.model.session.scalars(
-                select(model.History).filter(model.History.name == "HistoryContentsHistory1").limit(1)
-            ).first()
-            return [hda.name for hda in history.contents_iter(**kwds)]
-
-        assert contents_iter_names() == ["1", "2", "3", "4"]
-        assert contents_iter_names(deleted=False) == ["1", "2"]
-        assert contents_iter_names(visible=True) == ["1", "3"]
-        assert contents_iter_names(visible=True, object_store_ids=["three_store"]) == ["3"]
-        assert contents_iter_names(visible=False) == ["2", "4"]
-        assert contents_iter_names(deleted=True, visible=False) == ["4"]
-        assert contents_iter_names(deleted=False, object_store_ids=["foobar"]) == ["2"]
-        assert contents_iter_names(deleted=False, object_store_ids=["foobar2"]) == []
-
-        assert contents_iter_names(ids=[d1.id, d2.id, d3.id, d4.id]) == ["1", "2", "3", "4"]
-        assert contents_iter_names(ids=[d1.id, d2.id, d3.id, d4.id], max_in_filter_length=1) == ["1", "2", "3", "4"]
-
-        assert contents_iter_names(ids=[d1.id, d3.id]) == ["1", "3"]
-
     def test_history_audit(self):
-        u = model.User(email="contents@foo.bar.baz", password="password")
+        u = model.User(email=random_email(), password="password")
         h1 = model.History(name="HistoryAuditHistory", user=u)
         h2 = model.History(name="HistoryAuditHistory", user=u)
 
@@ -723,23 +268,12 @@ class TestMappings(BaseModelTestCase):
         session.add(lf)
         session.flush()
 
-    def test_current_session(self):
-        user = model.User(email="testworkflows@bx.psu.edu", password="password")
-        galaxy_session = model.GalaxySession()
-        galaxy_session.user = user
-        self.persist(user, galaxy_session)
-        assert user.current_galaxy_session == galaxy_session
-        new_galaxy_session = model.GalaxySession()
-        user.galaxy_sessions.append(new_galaxy_session)
-        self.persist(user, new_galaxy_session)
-        assert user.current_galaxy_session == new_galaxy_session
-
     def test_flush_refreshes(self):
         # Normally I don't believe in unit testing library code, but the behaviors around attribute
         # states and flushing in SQL Alchemy is very subtle and it is good to have a executable
         # reference for how it behaves in the context of Galaxy objects.
         model = self.model
-        user = model.User(email="testworkflows@bx.psu.edu", password="password")
+        user = model.User(email=random_email(), password="password")
         galaxy_session = model.GalaxySession()
         galaxy_session_other = model.GalaxySession()
         galaxy_session.user = user
@@ -812,7 +346,7 @@ class TestMappings(BaseModelTestCase):
         assert "id" not in inspect(galaxy_model_object_new).unloaded
 
     def test_workflows(self):
-        user = model.User(email="testworkflows@bx.psu.edu", password="password")
+        user = model.User(email=random_email(), password="password")
 
         child_workflow = _workflow_from_steps(user, [])
         self.persist(child_workflow)
@@ -922,13 +456,12 @@ class TestMappings(BaseModelTestCase):
         assert counts.root["scheduled"] == 1
 
     def test_role_creation(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
 
         def check_private_role(private_role, email):
             assert private_role.type == model.Role.types.PRIVATE
             assert len(private_role.users) == 1
-            assert private_role.name == email
-            assert private_role.description == "Private Role for " + email
+            assert private_role.name == model.Role.default_name(model.Role.types.PRIVATE)
 
         email = "rule_user_1@example.com"
         u = model.User(email=email, password="password")
@@ -955,7 +488,7 @@ class TestMappings(BaseModelTestCase):
         check_private_role(role, email)
 
     def test_private_share_role(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
 
         u_from, u_to, u_other = self._three_users("private_share_role")
 
@@ -970,7 +503,7 @@ class TestMappings(BaseModelTestCase):
         assert not security_agent.can_access_dataset(u_other.all_roles(), d1.dataset)
 
     def test_make_dataset_public(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, u_other = self._three_users("make_dataset_public")
 
         h = model.History(name="History for Annotation", user=u_from)
@@ -986,7 +519,7 @@ class TestMappings(BaseModelTestCase):
         assert security_agent.can_access_dataset(u_other.all_roles(), d1.dataset)
 
     def test_set_all_dataset_permissions(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, _, u_other = self._three_users("set_all_perms")
 
         h = model.History(name="History for Annotation", user=u_from)
@@ -1007,7 +540,7 @@ class TestMappings(BaseModelTestCase):
         assert not security_agent.can_access_dataset(u_other.all_roles(), d1.dataset)
 
     def test_can_manage_privately_shared_dataset(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, u_other = self._three_users("can_manage_dataset")
 
         h = model.History(name="History for Prevent Sharing", user=u_from)
@@ -1022,7 +555,7 @@ class TestMappings(BaseModelTestCase):
         assert not security_agent.can_manage_dataset(u_to.all_roles(), d1.dataset)
 
     def test_can_manage_private_dataset(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, _, u_other = self._three_users("can_manage_dataset_ps")
 
         h = model.History(name="History for Prevent Sharing", user=u_from)
@@ -1035,33 +568,8 @@ class TestMappings(BaseModelTestCase):
         assert security_agent.can_manage_dataset(u_from.all_roles(), d1.dataset)
         assert not security_agent.can_manage_dataset(u_other.all_roles(), d1.dataset)
 
-    def test_history_hid_counter_is_expired_after_next_hid_call(self):
-        u = model.User(email="hid_abuser@example.com", password="password")
-        h = model.History(name="History for hid testing", user=u)
-        self.persist(u, h)
-        state = inspect(h)
-        assert h.hid_counter == 1
-        assert "hid_counter" not in state.unloaded
-        assert "id" not in state.unloaded
-
-        h._next_hid()
-
-        assert "hid_counter" in state.unloaded  # this attribute has been expired
-        assert "id" not in state.unloaded  # but other attributes have NOT been expired
-        assert h.hid_counter == 2  # check this last: this causes thie hid_counter to be reloaded
-
-    def test_next_hid(self):
-        u = model.User(email="hid_abuser@example.com", password="password")
-        h = model.History(name="History for hid testing", user=u)
-        self.persist(u, h)
-        assert h.hid_counter == 1
-        h._next_hid()
-        assert h.hid_counter == 2
-        h._next_hid(n=3)
-        assert h.hid_counter == 5
-
     def test_cannot_make_private_objectstore_dataset_public(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, _ = self._three_users("cannot_make_private_public")
 
         h = self.model.History(name="History for Prevent Sharing", user=u_from)
@@ -1078,7 +586,7 @@ class TestMappings(BaseModelTestCase):
         assert galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE in str(exec_info.value)
 
     def test_cannot_make_private_objectstore_dataset_shared(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, _ = self._three_users("cannot_make_private_shared")
 
         h = self.model.History(name="History for Prevent Sharing", user=u_from)
@@ -1095,7 +603,7 @@ class TestMappings(BaseModelTestCase):
         assert galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE in str(exec_info.value)
 
     def test_cannot_set_dataset_permisson_on_private(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, _ = self._three_users("cannot_set_permissions_on_private")
 
         h = self.model.History(name="History for Prevent Sharing", user=u_from)
@@ -1115,7 +623,7 @@ class TestMappings(BaseModelTestCase):
         assert galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE in str(exec_info.value)
 
     def test_cannot_make_private_dataset_public(self):
-        security_agent = GalaxyRBACAgent(self.model)
+        security_agent = GalaxyRBACAgent(self.model.session)
         u_from, u_to, u_other = self._three_users("cannot_make_private_dataset_public")
 
         h = self.model.History(name="History for Annotation", user=u_from)
diff --git a/test/unit/data/test_quota.py b/test/unit/data/test_quota.py
index 5c34ea7cb056a9811f2374b86c99ef2635226973..f06984e66113c90d5ce3ada8e43a24d4220a5144 100644
--- a/test/unit/data/test_quota.py
+++ b/test/unit/data/test_quota.py
@@ -1,6 +1,7 @@
 import uuid
 
 from galaxy import model
+from galaxy.model.unittest_utils.utils import random_email
 from galaxy.objectstore import (
     QuotaSourceInfo,
     QuotaSourceMap,
@@ -16,7 +17,7 @@ class TestPurgeUsage(BaseModelTestCase):
     def setUp(self):
         super().setUp()
         model = self.model
-        u = model.User(email="purge_usage@example.com", password="password")
+        u = model.User(email=random_email(), password="password")
         u.disk_usage = 25
         self.persist(u)
 
@@ -111,6 +112,21 @@ class TestCalculateUsage(BaseModelTestCase):
 
         assert u.calculate_disk_usage_default_source(object_store) == 10
 
+    def test_calculate_usage_with_user_provided_storage(self):
+        u = self.u
+
+        self._add_dataset(10)
+        # This dataset should not be counted towards the user's disk usage
+        self._add_dataset(30, object_store_id="user_objects://user/provided/storage")
+
+        object_store = MockObjectStore()
+        assert u.calculate_disk_usage_default_source(object_store) == 10
+        assert u.disk_usage is None
+        u.calculate_and_set_disk_usage(object_store)
+        assert u.calculate_disk_usage_default_source(object_store) == 10
+
+        self._refresh_user_and_assert_disk_usage_is(10)
+
     def test_calculate_usage_readjusts_incorrect_quota(self):
         u = self.u
 
diff --git a/test/unit/files/_util.py b/test/unit/files/_util.py
index 16ad933affa4d6c7cfb69174e0661495b72e44aa..2bf1274fcee5750a6f120f44012a145aea47aff5 100644
--- a/test/unit/files/_util.py
+++ b/test/unit/files/_util.py
@@ -2,6 +2,7 @@
 
 import os
 import tempfile
+from typing import Optional
 
 from galaxy.files import (
     ConfiguredFileSources,
@@ -156,8 +157,9 @@ def write_from(
         file_source_path.file_source.write_from(file_source_path.path, f.name, user_context=user_context)
 
 
-def configured_file_sources(conf_file):
-    file_sources_config = FileSourcePluginsConfig()
+def configured_file_sources(conf_file, file_sources_config: Optional[FileSourcePluginsConfig] = None):
+    file_sources_config = file_sources_config or FileSourcePluginsConfig()
+    assert file_sources_config
     if isinstance(conf_file, str):
         conf = ConfiguredFileSourcesConf(conf_file=conf_file)
     else:
diff --git a/test/unit/files/test_template_models.py b/test/unit/files/test_template_models.py
index 9d11069fc01d29ea4a739512d1c87de8aa1af2f9..c23b6bcf943b78616aa046e1b7c7c55e5498ffc7 100644
--- a/test/unit/files/test_template_models.py
+++ b/test/unit/files/test_template_models.py
@@ -295,11 +295,14 @@ def test_examples_parse():
     _assert_example_parses("production_aws_private_bucket.yml")
     _assert_example_parses("production_aws_public_bucket.yml")
     _assert_example_parses("production_s3fs.yml")
+    _assert_example_parses("production_dropbox.yml")
     _assert_example_parses("s3fs_by_host_and_port.yml")
     _assert_example_parses("templating_override.yml")
     _assert_example_parses("admin_secrets.yml")
     _assert_example_parses("admin_secrets_with_defaults.yml")
     _assert_example_parses("testing_multi_version_with_secrets.yml")
+    _assert_example_parses("dropbox_client_secrets_in_vault.yml")
+    _assert_example_parses("dropbox_client_secrets_explicit.yml")
 
 
 def _assert_example_parses(filename: str):
diff --git a/test/unit/files/test_webdav.py b/test/unit/files/test_webdav.py
index 071281e1bc88573efd332e5fcab537c44bf29b02..9294881ec247e4ff245edc8c9b98c04692acb105 100644
--- a/test/unit/files/test_webdav.py
+++ b/test/unit/files/test_webdav.py
@@ -1,9 +1,10 @@
 # docker run -v `pwd`/test/integration/webdav/data:/media  -e WEBDAV_USERNAME=alice -e WEBDAV_PASSWORD=secret1234 -p 7083:7083 jmchilton/webdavdev
-# GALAXY_TEST_WEBDAV=1 pytest test/unit/files/webdav.py
+# GALAXY_TEST_WEBDAV=1 pytest test/unit/files/test_webdav.py
 import os
 
 import pytest
 
+from galaxy.files.plugins import FileSourcePluginsConfig
 from ._util import (
     configured_file_sources,
     find,
@@ -17,6 +18,7 @@ from .test_posix import _download_and_check_file
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "webdav_file_sources_conf.yml")
+FILE_SOURCES_CONF_NO_USE_TEMP_FILES = os.path.join(SCRIPT_DIRECTORY, "webdav_file_sources_without_use_temp_conf.yml")
 USER_FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "webdav_user_file_sources_conf.yml")
 
 skip_if_no_webdav = pytest.mark.skipif(not os.environ.get("GALAXY_TEST_WEBDAV"), reason="GALAXY_TEST_WEBDAV not set")
@@ -62,17 +64,40 @@ def test_sniff_to_tmp():
 
 @skip_if_no_webdav
 def test_serialization():
-    # serialize the configured file sources and rematerialize them,
-    # ensure they still function. This is needed for uploading files.
-    file_sources = serialize_and_recover(configured_file_sources(FILE_SOURCES_CONF))
+    configs = [FILE_SOURCES_CONF_NO_USE_TEMP_FILES, FILE_SOURCES_CONF]
+    for config in configs:
+        # serialize the configured file sources and rematerialize them,
+        # ensure they still function. This is needed for uploading files.
+        file_sources = serialize_and_recover(configured_file_sources(config))
 
-    res = list_root(file_sources, "gxfiles://test1", recursive=True)
-    assert find_file_a(res)
+        res = list_root(file_sources, "gxfiles://test1", recursive=True)
+        assert find_file_a(res)
 
-    res = list_root(file_sources, "gxfiles://test1", recursive=False)
-    assert find_file_a(res)
+        res = list_root(file_sources, "gxfiles://test1", recursive=False)
+        assert find_file_a(res)
 
-    _download_and_check_file(file_sources)
+        _download_and_check_file(file_sources)
+
+
+@skip_if_no_webdav
+def test_config_options():
+    file_sources = configured_file_sources(FILE_SOURCES_CONF)
+    fs = file_sources._file_sources[0]
+    user_context = user_context_fixture()
+    assert fs._open_fs(user_context).use_temp_files
+
+    file_sources = configured_file_sources(FILE_SOURCES_CONF_NO_USE_TEMP_FILES)
+    fs = file_sources._file_sources[0]
+    user_context = user_context_fixture()
+    assert not fs._open_fs(user_context).use_temp_files
+
+    disable_default_use_temp = FileSourcePluginsConfig(
+        webdav_use_temp_files=False,
+    )
+    file_sources = configured_file_sources(FILE_SOURCES_CONF, disable_default_use_temp)
+    fs = file_sources._file_sources[0]
+    user_context = user_context_fixture()
+    assert not fs._open_fs(user_context).use_temp_files
 
 
 @skip_if_no_webdav
diff --git a/test/unit/files/webdav_file_sources_conf.yml b/test/unit/files/webdav_file_sources_conf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6116edd6de1f3860a3895f85f2c300d27d9164ba
--- /dev/null
+++ b/test/unit/files/webdav_file_sources_conf.yml
@@ -0,0 +1,6 @@
+- type: webdav
+  id: test1
+  doc: Test WebDAV server.
+  url: http://127.0.0.1:7083
+  login: alice
+  password: secret1234  
diff --git a/test/unit/files/webdav_file_sources_without_use_temp_conf.yml b/test/unit/files/webdav_file_sources_without_use_temp_conf.yml
new file mode 100644
index 0000000000000000000000000000000000000000..916f8068f459103b4849e03b86ef7cb798f97275
--- /dev/null
+++ b/test/unit/files/webdav_file_sources_without_use_temp_conf.yml
@@ -0,0 +1,7 @@
+- type: webdav
+  id: test1
+  doc: Test WebDAV server.
+  url: http://127.0.0.1:7083
+  login: alice
+  password: secret1234  
+  use_temp_files: false
diff --git a/test/unit/objectstore/irods_object_store_conf_logical_path.xml b/test/unit/objectstore/irods_object_store_conf_logical_path.xml
new file mode 100644
index 0000000000000000000000000000000000000000..09298ebdcb4bf01a36dff686528efcfbd93cf790
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_logical_path.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247" timeout="30" refresh_time="300" connection_pool_monitor_interval="3600"/>
+    <logical path="/tempZone/home/rods" />
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/irods_object_store_conf_ssl.xml b/test/unit/objectstore/irods_object_store_conf_ssl.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d59a55fd73b1e2bfa3a04cc19819f88ea12e9f1b
--- /dev/null
+++ b/test/unit/objectstore/irods_object_store_conf_ssl.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<object_store type="irods"> 
+    <auth username="rods" password="rods" />
+    <resource name="demoResc" />
+    <zone name="tempZone" />
+    <connection host="localhost" port="1247" timeout="30" refresh_time="300" connection_pool_monitor_interval="3600"/>
+    <ssl client_server_negotiation="request_server_negotiation" client_server_policy="CS_NEG_REQUIRE" 
+         encryption_algorithm="AES-256-CBC" encryption_key_size="32" encryption_num_hash_rounds="16" 
+         encryption_salt_size="8" ssl_verify_server="cert" ssl_ca_certificate_file="/etc/irods/ssl/irods.crt" />
+    <cache path="database/object_store_cache" size="1000" />
+    <extra_dir type="job_work" path="database/job_working_directory_irods"/>
+    <extra_dir type="temp" path="database/tmp_irods"/>
+</object_store>
diff --git a/test/unit/objectstore/test_irods.py b/test/unit/objectstore/test_irods.py
index ad6f0e689fb26ae7d2181e42bb2fe71eeb0c0fb4..8996cab29c82e56ebc272a27ebe642ccf156bc31 100644
--- a/test/unit/objectstore/test_irods.py
+++ b/test/unit/objectstore/test_irods.py
@@ -16,6 +16,12 @@ CONFIG_FILE_NO_EXTRA_DIR = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_EX
 CONFIG_FILE_NAME_NO_AUTH = "irods_object_store_conf_no_auth.xml"
 CONFIG_FILE_NO_AUTH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_NO_AUTH)
 
+CONFIG_FILE_NAME_SSL = "irods_object_store_conf_ssl.xml"
+CONFIG_FILE_SSL = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_SSL)
+
+CONFIG_FILE_NAME_LOGICAL_PATH = "irods_object_store_conf_logical_path.xml"
+CONFIG_FILE_LOGICAL_PATH = os.path.join(SCRIPT_DIRECTORY, CONFIG_FILE_NAME_LOGICAL_PATH)
+
 
 def test_parse_valid_config_xml():
     tree = parse_xml(CONFIG_FILE)
@@ -39,6 +45,29 @@ def test_parse_valid_config_xml():
     assert config["extra_dirs"][1]["path"] == "database/tmp_irods"
 
 
+def test_parse_config_xml_ssl():
+    tree = parse_xml(CONFIG_FILE_SSL)
+    root = tree.getroot()
+    config = parse_config_xml(root)
+
+    assert config["ssl"]["client_server_negotiation"] == "request_server_negotiation"
+    assert config["ssl"]["client_server_policy"] == "CS_NEG_REQUIRE"
+    assert config["ssl"]["encryption_algorithm"] == "AES-256-CBC"
+    assert config["ssl"]["encryption_key_size"] == 32
+    assert config["ssl"]["encryption_num_hash_rounds"] == 16
+    assert config["ssl"]["encryption_salt_size"] == 8
+    assert config["ssl"]["ssl_verify_server"] == "cert"
+    assert config["ssl"]["ssl_ca_certificate_file"] == "/etc/irods/ssl/irods.crt"
+
+
+def test_parse_config_xml_logical_path():
+    tree = parse_xml(CONFIG_FILE_LOGICAL_PATH)
+    root = tree.getroot()
+    config = parse_config_xml(root)
+
+    assert config["logical"]["path"] == "/tempZone/home/rods"
+
+
 def test_parse_config_xml_no_extra_dir():
     tree = parse_xml(CONFIG_FILE_NO_EXTRA_DIR)
     root = tree.getroot()
diff --git a/test/unit/objectstore/test_template_models.py b/test/unit/objectstore/test_template_models.py
index 81f0bce8068fab3c9653f79991c0975cc0b623ac..9513a6e807dc588059a9542da55c7db7c700d715 100644
--- a/test/unit/objectstore/test_template_models.py
+++ b/test/unit/objectstore/test_template_models.py
@@ -1,5 +1,7 @@
 import os
+import sys
 
+import pytest
 from yaml import safe_load
 
 from galaxy.objectstore.templates.examples import get_example
@@ -14,6 +16,10 @@ from galaxy.objectstore.templates.models import (
 )
 from galaxy.util.config_templates import VariablesDict
 
+if sys.version_info < (3, 8):  # noqa: UP036
+    pytest.skip(reason="Pydantic tool parameter models require python3.8 or higher", allow_module_level=True)
+
+
 LIBRARY_1 = """
 - id: amazon_bucket
   name: Amazon Bucket
diff --git a/test/unit/schema/test_schema.py b/test/unit/schema/test_schema.py
index 21b37096d13156c4eae197e8c8f9b355bd5af7a5..07d2cb3b3d51fb43038c0d1d00f0ec6c5adec759 100644
--- a/test/unit/schema/test_schema.py
+++ b/test/unit/schema/test_schema.py
@@ -5,6 +5,7 @@ from pydantic import BaseModel
 
 from galaxy.schema.schema import (
     DatasetStateField,
+    OAuth2State,
     TAG_ITEM_PATTERN,
 )
 from galaxy.schema.tasks import (
@@ -78,3 +79,10 @@ class TestTagPattern:
         ]
         for t in tag_strings:
             assert not re.match(TAG_ITEM_PATTERN, t)
+
+
+def test_oauth_state():
+    state_in = OAuth2State(route="/file_sources/dropbox", nonce="abcde56")
+    state_out = OAuth2State.decode(state_in.encode())
+    assert state_out.route == "/file_sources/dropbox"
+    assert state_out.nonce == "abcde56"
diff --git a/test/unit/tool_shed/_util.py b/test/unit/tool_shed/_util.py
index df50c5270ef264ddc12f1cbc671d0d1e7a05e906..03f27ce98874b872f410c58d7358e0a91e8d22ca 100644
--- a/test/unit/tool_shed/_util.py
+++ b/test/unit/tool_shed/_util.py
@@ -17,6 +17,7 @@ import tool_shed.repository_registry
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.util import safe_makedirs
 from tool_shed.context import ProvidesRepositoriesContext
+from tool_shed.managers.model_cache import ModelCache
 from tool_shed.managers.repositories import upload_tar_and_set_metadata
 from tool_shed.managers.users import create_user
 from tool_shed.repository_types import util as rt_util
@@ -32,6 +33,7 @@ from tool_shed.webapp.model import (
     Category,
     mapping,
     Repository,
+    RepositoryCategoryAssociation,
     User,
 )
 from tool_shed_client.schema import CreateCategoryRequest
@@ -80,6 +82,7 @@ class TestToolShedApp(ToolShedApp):
         self.config = TestToolShedConfig(temp_directory)
         self.security = IdEncodingHelper(id_secret=self.config.id_secret)
         self.repository_registry = tool_shed.repository_registry.Registry(self)
+        self.model_cache = ModelCache(os.path.join(temp_directory, "model_cache"))
 
     @property
     def security_agent(self):
@@ -193,3 +196,12 @@ def create_category(provides_repositories: ProvidesRepositoriesContext, create:
 
     request = CreateCategoryRequest(**create)
     return CategoryManager(provides_repositories.app).create(provides_repositories, request)
+
+
+def attach_category(provides_repositories: ProvidesRepositoriesContext, repository: Repository, category: Category):
+    assoc = RepositoryCategoryAssociation(
+        repository=repository,
+        category=category,
+    )
+    provides_repositories.sa_session.add(assoc)
+    provides_repositories.sa_session.flush()
diff --git a/test/unit/tool_shed/test_dbscript.py b/test/unit/tool_shed/test_dbscript.py
index 065c5a6213343564ff1b3ed8bd31ec39e4393a76..0d8553fc02bbb91775e40c2ac91be8922279f2a4 100644
--- a/test/unit/tool_shed/test_dbscript.py
+++ b/test/unit/tool_shed/test_dbscript.py
@@ -23,6 +23,8 @@ DbUrl = NewType("DbUrl", str)
 BASE_ID = "ts0"
 COMMAND = "manage_toolshed_db.sh"
 
+SKIP_REASON = "Slow test: database migration management scripts"
+
 
 @pytest.fixture(scope="session")
 def migrations_dir():
@@ -70,6 +72,7 @@ def create_alembic_branch(config: Config, versions_dir: str) -> None:
     alembic.command.revision(config, head="base", rev_id=BASE_ID, version_path=versions_dir)
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestVersionCommand:
     def test_version_cmd(self, config):
         alembic.command.revision(config, rev_id="1", head=BASE_ID)
@@ -89,6 +92,7 @@ class TestVersionCommand:
         assert "Revises: 1" in completed.stdout
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestDbVersionCommand:
     def test_dbversion_cmd(self, config):
         alembic.command.revision(config, rev_id="1", head=BASE_ID)
@@ -116,6 +120,7 @@ class TestDbVersionCommand:
         assert "Revises: 1" in completed.stdout
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestUpgradeCommand:
     def test_upgrade_cmd(self, config):
         alembic.command.revision(config, rev_id="1", head=BASE_ID)
@@ -185,6 +190,7 @@ class TestUpgradeCommand:
         assert heads == ("d",)
 
 
+@pytest.mark.skip(SKIP_REASON)
 class TestDowngradeCommand:
     def test_downgrade_cmd(self, config):
         alembic.command.revision(config, rev_id="1", head=BASE_ID)
diff --git a/test/unit/tool_shed/test_graphql.py b/test/unit/tool_shed/test_graphql.py
index 111dbf6fccd8dd7f1d5da89e4e25c13e8169f48e..88318c75b6b464fe74a343d8bbc96a47dd06381c 100644
--- a/test/unit/tool_shed/test_graphql.py
+++ b/test/unit/tool_shed/test_graphql.py
@@ -12,12 +12,9 @@ from tool_shed.context import (
     ProvidesUserContext,
 )
 from tool_shed.webapp.graphql.schema import schema
-from tool_shed.webapp.model import (
-    Category,
-    Repository,
-    RepositoryCategoryAssociation,
-)
+from tool_shed.webapp.model import Repository
 from ._util import (
+    attach_category,
     create_category,
     repository_fixture,
     upload_directories_to_repository,
@@ -110,15 +107,6 @@ def test_simple_repositories(provides_repositories: ProvidesRepositoriesContext,
     assert new_repository.name in repository_names
 
 
-def attach_category(provides_repositories: ProvidesRepositoriesContext, repository: Repository, category: Category):
-    assoc = RepositoryCategoryAssociation(
-        repository=repository,
-        category=category,
-    )
-    provides_repositories.sa_session.add(assoc)
-    provides_repositories.sa_session.flush()
-
-
 def test_relay_repos_by_category(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
     name = new_repository.name
     category = create_category(provides_repositories, {"name": "test_graphql_relay_categories_1"})
diff --git a/test/unit/tool_shed/test_model_cache.py b/test/unit/tool_shed/test_model_cache.py
new file mode 100644
index 0000000000000000000000000000000000000000..89ebb8d54042cd0201039d157e90a6f7762bf02e
--- /dev/null
+++ b/test/unit/tool_shed/test_model_cache.py
@@ -0,0 +1,53 @@
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+)
+
+from tool_shed.managers.model_cache import (
+    hash_model,
+    ModelCache,
+)
+
+
+class Moo(BaseModel):
+    foo: int
+
+
+class MooLike(BaseModel):
+    model_config = ConfigDict(title="Moo")
+    foo: int
+
+
+class NewMoo(BaseModel):
+    model_config = ConfigDict(title="Moo")
+    foo: int
+    new_prop: str
+
+
+def test_hash():
+    hash_moo_1 = hash_model(Moo)
+    hash_moo_2 = hash_model(Moo)
+    assert hash_moo_1 == hash_moo_2
+
+
+def test_hash_by_value():
+    hash_moo_1 = hash_model(Moo)
+    hash_moo_like = hash_model(MooLike)
+    assert hash_moo_1 == hash_moo_like
+
+
+def test_hash_different_on_updates():
+    hash_moo_1 = hash_model(Moo)
+    hash_moo_new = hash_model(NewMoo)
+    assert hash_moo_1 != hash_moo_new
+
+
+def cache_dict(tmp_path):
+    model_cache = ModelCache(tmp_path)
+    assert not model_cache.has_cached_entry_for(Moo, "moo", "1.0")
+    assert None is model_cache.get_cache_entry_for(Moo, "moo", "1.0")
+    model_cache.insert_cache_entry_for(Moo(foo=4), "moo", "1.0")
+    moo = model_cache.get_cache_entry_for(Moo, "moo", "1.0")
+    assert moo
+    assert moo.foo == 4
+    assert model_cache.has_cached_entry_for(Moo, "moo", "1.0")
diff --git a/test/unit/tool_shed/test_repository_utils.py b/test/unit/tool_shed/test_repository_utils.py
index d23388b8a8972ccbdc007212143e9fe751acb1da..c648a13104bac8230f2ba5ca02c24e46b61f67e4 100644
--- a/test/unit/tool_shed/test_repository_utils.py
+++ b/test/unit/tool_shed/test_repository_utils.py
@@ -5,6 +5,8 @@ from tool_shed.webapp.model import (
     User,
 )
 from ._util import (
+    attach_category,
+    create_category,
     repository_fixture,
     TEST_DATA_FILES,
     TestToolShedApp,
@@ -83,6 +85,27 @@ def test_upload_dry_run_ok(provides_repositories: ProvidesRepositoriesContext, n
     assert old_tip == new_tip
 
 
+def test_category_count(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
+    category = create_category(provides_repositories, {"name": "test_category_count_1"})
+    attach_category(provides_repositories, new_repository, category)
+
+    category = new_repository.categories[0].category
+    assert category.active_repository_count() == 1
+
+    tar_resource = TEST_DATA_FILES.joinpath("column_maker/column_maker.tar")
+    upload_ok, *_ = upload_tar(
+        provides_repositories,
+        new_repository.user.username,
+        new_repository,
+        tar_resource,
+        commit_message="Commit Message",
+    )
+    assert upload_ok
+
+    category = new_repository.categories[0].category
+    assert category.active_repository_count() == 1
+
+
 def test_upload_dry_run_failed(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
     tar_resource = TEST_DATA_FILES.joinpath("safetar_with_symlink.tar")
     upload_ok, message, _, _, _, _ = upload_tar(
diff --git a/test/unit/tool_shed/test_tool_source.py b/test/unit/tool_shed/test_tool_source.py
new file mode 100644
index 0000000000000000000000000000000000000000..601d4d63df54a6b3b034b7728c56ba768f1f3f03
--- /dev/null
+++ b/test/unit/tool_shed/test_tool_source.py
@@ -0,0 +1,38 @@
+from tool_shed.context import ProvidesRepositoriesContext
+from tool_shed.managers.tools import (
+    parsed_tool_model_cached_for,
+    parsed_tool_model_for,
+    tool_source_for,
+)
+from tool_shed.webapp.model import Repository
+from ._util import upload_directories_to_repository
+
+
+def test_get_tool(provides_repositories: ProvidesRepositoriesContext, new_repository: Repository):
+    upload_directories_to_repository(provides_repositories, new_repository, "column_maker")
+    owner = new_repository.user.username
+    name = new_repository.name
+    encoded_id = f"{owner}~{name}~Add_a_column1"
+
+    repo_path = new_repository.repo_path(app=provides_repositories.app)
+    tool_source = tool_source_for(provides_repositories, encoded_id, "1.2.0", repository_clone_url=repo_path)
+    assert tool_source.parse_id() == "Add_a_column1"
+    bundle = parsed_tool_model_for(provides_repositories, encoded_id, "1.2.0", repository_clone_url=repo_path)
+    assert len(bundle.inputs) == 3
+
+    cached_bundle = parsed_tool_model_cached_for(
+        provides_repositories, encoded_id, "1.2.0", repository_clone_url=repo_path
+    )
+    assert len(cached_bundle.inputs) == 3
+
+    cached_bundle = parsed_tool_model_cached_for(
+        provides_repositories, encoded_id, "1.2.0", repository_clone_url=repo_path
+    )
+    assert len(cached_bundle.inputs) == 3
+
+
+def test_stock_bundle(provides_repositories: ProvidesRepositoriesContext):
+    cached_bundle = parsed_tool_model_cached_for(
+        provides_repositories, "__ZIP_COLLECTION__", "1.0.0", repository_clone_url=None
+    )
+    assert len(cached_bundle.inputs) == 2
diff --git a/test/unit/tool_shed/test_tool_validation.py b/test/unit/tool_shed/test_tool_validation.py
index a1f421120eccaa54e237b87e04f1352d8dc6c2f5..cf538e5599a17eab35afde03addeb2f08ab87074 100644
--- a/test/unit/tool_shed/test_tool_validation.py
+++ b/test/unit/tool_shed/test_tool_validation.py
@@ -11,6 +11,8 @@ BISMARK_DIR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/rep
 BOWTIE2_INDICES = os.path.join(
     galaxy_directory(), "lib/tool_shed/test/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample"
 )
+MISSING_DATA_REF_DIR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/repos/missing_data_ref")
+WRONG_DATA_REF_DIR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/repos/wrong_data_ref")
 
 
 def test_validate_valid_tool():
@@ -64,6 +66,22 @@ def test_validate_tool_without_index():
         assert not tool.params_with_missing_index_file
 
 
+def test_validate_missing_data_ref():
+    repo_dir = MISSING_DATA_REF_DIR
+    with get_tool_validator() as tv:
+        full_path = os.path.join(repo_dir, "missing_data_ref.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
+        assert valid is False
+
+
+def test_validate_wrong_data_ref():
+    repo_dir = WRONG_DATA_REF_DIR
+    with get_tool_validator() as tv:
+        full_path = os.path.join(repo_dir, "wrong_data_ref.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
+        assert valid is False
+
+
 @contextmanager
 def get_tool_validator():
     app = MockApp()
diff --git a/test/unit/tool_util/framework_tool_checks.yml b/test/unit/tool_util/framework_tool_checks.yml
new file mode 100644
index 0000000000000000000000000000000000000000..883fd3d40ffc79e9385a47ba29a8a224bff51a49
--- /dev/null
+++ b/test/unit/tool_util/framework_tool_checks.yml
@@ -0,0 +1,62 @@
+# file format mirrors parameters_specification.yml but applies to any tool in the older
+# (and more general) test/functional/tools directory.
+
+empty_select:
+  request_valid:
+  - {}
+  request_invalid:
+  - select_optional: anyoption
+
+select_from_dataset_in_conditional:
+  request_valid:
+  - single: {src: hda, id: abcde133543d}
+  request_invalid:
+  - single: 7
+  request_internal_valid:
+  - single: {src: hda, id: 7}
+  request_internal_invalid:
+  - single: 7
+  job_internal_valid:
+  - single: {src: hda, id: 7}
+  job_internal_valid:
+  - single: {src: hda, id: 7}
+    cond:
+      cond: single
+      select_single: chr10
+      inner_cond:
+        inner_cond: single
+        select_single: chr10
+  job_internal_invalid:
+  - single: {src: hda, id: 7}
+    cond:
+      cond: single
+      select_single: chr10
+      inner_cond:
+        inner_cond: single
+        select_single: chr10
+        badoption: true
+  - single: {src: hda, id: 7}
+    cond:
+      cond: single
+      select_single: chr10
+
+column_param:
+  request_valid:
+  - input1: {src: hda, id: abcde133543d}
+    col: 1
+    col_names: 1
+  request_invalid:
+  - input1: {src: hda, id: abcde133543d}
+    col: moocow
+    col_names: moocow
+  request_internal_valid:
+  - input1: {src: hda, id: 7}
+    col: 1
+    col_names: 1
+  request_internal_invalid:
+  - input1: {src: hda, id: abcde133543d}
+    col: 1
+    col_names: 1
+
+
+
diff --git a/test/unit/tool_util/mulled/test_mulled_build.py b/test/unit/tool_util/mulled/test_mulled_build.py
index eb08e531d1fa073187fd057f2a88858930faa29d..91c0b0be702fe571efb6d93b8e2a209124deba4c 100644
--- a/test/unit/tool_util/mulled/test_mulled_build.py
+++ b/test/unit/tool_util/mulled/test_mulled_build.py
@@ -5,13 +5,13 @@ import pytest
 from galaxy.tool_util.deps.mulled.mulled_build import (
     base_image_for_targets,
     build_target,
-    CondaInDockerContext,
     DEFAULT_BASE_IMAGE,
     DEFAULT_EXTENDED_BASE_IMAGE,
     InvolucroContext,
     mull_targets,
     target_str_to_targets,
 )
+from galaxy.tool_util.deps.mulled.util import CondaInDockerContext
 from ..util import external_dependency_management
 
 
diff --git a/test/unit/tool_util/mulled/test_mulled_search.py b/test/unit/tool_util/mulled/test_mulled_search.py
index dd17ab79d0ee4435f484e194999be5b900a175ef..8fc0868eda28bbd20f25a8dd51c0a02098863ef7 100644
--- a/test/unit/tool_util/mulled/test_mulled_search.py
+++ b/test/unit/tool_util/mulled/test_mulled_search.py
@@ -25,10 +25,10 @@ def test_quay_search():
 @skip_unless_executable("conda")
 def test_conda_search():
     t = CondaSearch("bioconda")
-    search1 = t.get_json("asdfasdf")
-    search2 = t.get_json("bioconductor-gosemsim")
-    assert search1 == []
-    assert all(r["package"] == "bioconductor-gosemsim" for r in search2)
+    search = t.get_json("asdfasdf")
+    assert search == []
+    search = t.get_json("bioconductor-gosemsim")
+    assert all(r["package"] == "bioconductor-gosemsim" for r in search)
 
 
 @external_dependency_management
diff --git a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
index 728757b52f312b20b90954d7f3d9f113d6db578f..9ec4e47b44f8ce90bf10daf3168d3203811c7b7e 100644
--- a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
+++ b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
@@ -46,6 +46,6 @@ def test_singularity_container_test(tmp_path) -> None:
         "singularity",
         tmp_path,
     )
-    assert "samtools:1.0--1" in results["passed"]
-    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
-    assert "yasm:1.3.0--0" in results["notest"]
+    assert "samtools:1.0--1" in results["passed"], results
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"], results
+    assert "yasm:1.3.0--0" in results["notest"], results
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
new file mode 100644
index 0000000000000000000000000000000000000000..f444e718986971b6ea9b379eb3fbc8fb838892e9
--- /dev/null
+++ b/test/unit/tool_util/parameter_specification.yml
@@ -0,0 +1,2009 @@
+# Tools to create.
+
+# Notes on conditional boolean values...
+# - if you set truevalue/falsevalue - it doesn't look like the when can remain
+#   true/false - so go through and simplify that. means don't need to create test
+#   cases that test that. Linting also at very least warns on this.
+
+# - gx_conditional_boolean_empty_default
+# - gx_conditional_boolean_empty_else
+# - gx_conditional_select_*
+# - gx_repeat_select_required
+# - gx_repeat_repeat_select_required
+# - gx_repeat_conditional_boolean_optional
+
+# Things to verify:
+# - non optional, multi-selects require a selection (see TODO below...)
+# - https://github.com/galaxyproject/galaxy/issues/18541
+gx_int:
+  request_valid:
+    - parameter: 5
+    - parameter: 6
+    # galaxy parameters created with a value - so doesn't need to appear in request even though non-optional
+    - {}
+  request_invalid:
+    - parameter: null
+    - parameter: "null"
+    - parameter: "None"
+    - parameter: { 5 }
+    - parameter: {__class__: 'ConnectedValue'}
+  job_internal_valid:
+   - parameter: 5
+  job_internal_invalid:
+   - parameter: null
+   - {}
+  landing_request_valid:
+    - {}
+    - parameter: 5
+  landing_request_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+  landing_request_internal_valid:
+    - {}
+    - parameter: 5
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+  test_case_xml_valid:
+    - parameter: 5
+    - {}
+  test_case_xml_invalid:
+    - parameter: null
+    - parameter: "5"
+  workflow_step_valid:
+    - parameter: 5
+    - {}
+  workflow_step_invalid:
+    - parameterx: 5
+    - parameter: 'foobar'
+  workflow_step_linked_valid:
+    - parameter: 5
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: null
+    - parameter: 'foobar'
+    - parameter: {__class__: 'ConnectedValue2'}
+
+
+gx_boolean:
+  request_valid:
+    - parameter: True
+    - parameter: False
+    - {}
+  request_invalid:
+    - parameter: {}
+    - parameter: "true"
+    # This is borderline... should we allow truevalue/falsevalue in the API.
+    # Marius and John were on fence here.
+    - parameter: "mytrue"
+    - parameter: null
+    - parameter: {__class__: 'ConnectedValue'}
+  job_internal_valid:
+   - parameter: true
+   - parameter: false
+  job_internal_invalid:
+   - {}
+  landing_request_valid:
+    - {}
+    - parameter: true
+    - parameter: false
+  landing_request_invalid:
+    - parameter: "true"
+    - parameter: "5"
+  landing_request_internal_valid:
+    - {}
+    - parameter: true
+    - parameter: false
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "true"
+    - parameter: "5"
+  workflow_step_valid:
+    - parameter: True
+    - {}
+  workflow_step_invalid:
+    - parameter: "true"
+    - parameter: mytrue
+    - parameter: null
+  workflow_step_linked_valid:
+    - parameter: True
+    - {}
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: "true"
+    - parameter: {__class__: 'ConnectedValue3'}
+
+gx_int_optional:
+  request_valid:
+   - parameter: 5
+   - parameter: null
+   - {}
+  request_invalid:
+   - parameter: "5"
+   - parameter: "None"
+   - parameter: "null"
+   - parameter: [5]
+   - parameter: {__class__: 'ConnectedValue'}
+  job_internal_valid:
+   - parameter: 5
+   - parameter: null
+  job_internal_invalid:
+   - {}
+  landing_request_valid:
+    - {}
+    - parameter: 5
+    - parameter: null
+  landing_request_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+  landing_request_internal_valid:
+    - {}
+    - parameter: 5
+    - parameter: null
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+  workflow_step_valid:
+   - parameter: 5
+   - parameter: null
+   - {}
+  workflow_step_invalid:
+   - parameter: "5"
+   - parameter: "None"
+   - parameter: "null"
+   - parameter: [5]
+  workflow_step_linked_valid:
+   - parameter: 5
+   - parameter: null
+   - {}
+   - parameter: {__class__: 'ConnectedValue'}
+
+gx_int_required: &gx_int_required
+  request_valid:
+    - parameter: 5
+    - parameter: 6
+  request_invalid:
+    - {}
+    - parameter: null
+    - parameter: "null"
+    - parameter: "None"
+    - parameter: { 5 }
+    - parameter: {__class__: 'ConnectedValue'}
+  job_internal_valid:
+   - parameter: 5
+  job_internal_invalid:
+   - {}
+  # and actual request will require a value but the landing only needs to specify parameters
+  # of interest - forcing users to make the rest of the selections.
+  landing_request_valid:
+    - {}
+    - parameter: 5
+  landing_request_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+  landing_request_internal_valid:
+    - {}
+    - parameter: 5
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+
+gx_int_required_via_empty_string:
+  <<: *gx_int_required
+
+gx_int_validation_range:
+  request_valid:
+  - parameter: 1
+  - parameter: 9
+  request_invalid:
+  - parameter: {}
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: -1
+  - parameter: 11
+  - parameter: 10
+  workflow_step_linked_valid:
+   - parameter: {__class__: 'ConnectedValue'}
+
+gx_int_min_max:
+  request_valid:
+  - parameter: 1
+  - parameter: 9
+  - parameter: 10
+  request_invalid:
+  - parameter: -1
+  - parameter: 11
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+  - parameter: -1
+
+gx_text_regex_validation:
+  request_valid:
+  - parameter: acgt
+  - parameter: a
+  - parameter: aaaggttac
+  request_invalid:
+  - parameter: acgu
+  - parameter: nucleic
+  workflow_step_linked_valid:
+   - parameter: {__class__: 'ConnectedValue'}
+
+gx_text_expression_validation:
+  request_valid:
+  - parameter: the code was foobar
+  - parameter: foobar
+  request_invalid:
+  - parameter: the code was not foo bar
+  - parameter: ''
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+  - parameter: ''
+
+gx_text_empty_validation:
+  request_valid:
+  - parameter: foobar
+  - {}
+  request_invalid:
+  - parameter: ''
+  job_internal_valid:
+  - parameter: foobar
+  job_internal_invalid:
+  - {}
+  - parameter: ''
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+  - parameter: ''
+
+gx_text:
+  request_valid: &gx_text_request_valid
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - {}
+    # need to explicitly mark these as non-optional
+    - parameter: null
+  request_invalid: &gx_text_request_invalid
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+    - parameter: {__class__: 'ConnectedValue'}
+  request_internal_valid:
+    *gx_text_request_valid
+  request_internal_invalid:
+    *gx_text_request_invalid
+  request_internal_dereferenced_valid:
+    *gx_text_request_valid
+  request_internal_dereferenced_invalid:
+    *gx_text_request_invalid
+  landing_request_valid:
+    *gx_text_request_valid
+  landing_request_invalid:
+    *gx_text_request_invalid
+  landing_request_internal_valid:
+    *gx_text_request_valid
+  landing_request_internal_invalid:
+    *gx_text_request_invalid
+  job_internal_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - parameter: null
+  job_internal_invalid:
+    - {}
+    - parameter: { "moo": "cow" }
+  workflow_step_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - {}
+    - parameter: null
+  workflow_step_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - {}
+    - parameter: {__class__: 'ConnectedValue'}
+    - parameter: null
+  workflow_step_linked_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+    - parameter: {"class": 'ConnectedValue'}
+
+gx_text_optional:
+  request_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - parameter: null
+  request_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  landing_request_valid: &gx_text_optional_landing_request_valid
+    - parameter: "moo cow"
+    - {}
+    - parameter: null
+  landing_request_invalid: &gx_text_optional_landing_request_invalid
+    - parameter: 5
+    - parameter: 6
+  landing_request_internal_valid:
+    *gx_text_optional_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_text_optional_landing_request_invalid
+
+  workflow_step_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - parameter: null
+  workflow_step_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - parameter: null
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+
+gx_text_length_validation: 
+  request_valid:
+  - parameter: "mytext"
+  - parameter: "mytext123"
+  request_invalid:
+  - parameter: "s"  # too short
+  - parameter: "mytext1231231231sd"  # too long
+
+gx_text_length_validation_negate: 
+  request_valid:
+  - parameter: "m"
+  - parameter: "mytext123mocowdowees"
+  request_invalid:
+  - parameter: "goldilocks"
+
+gx_select:
+  request_valid:
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  # see API Tests -> test_tools.py -> test_select_first_by_default
+  - {}
+  request_invalid:
+  # Not allowing selecting booleans by truevalue/falsevalue - don't allow selecting
+  # selects by label.
+  - parameter: "Ex1"
+  # Do not allow lists for non-multi-selects
+  - parameter: ["ex2"]
+  - parameter: null
+  - parameter: {}
+  - parameter: 5
+  request_internal_valid: &gx_select_request_valid
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  request_internal_invalid: &gx_select_request_invalid
+  - parameter: {}
+  request_internal_dereferenced_valid:
+   *gx_select_request_valid
+  request_internal_dereferenced_invalid:
+   *gx_select_request_invalid
+  landing_request_valid: &gx_select_landing_request_valid
+    - parameter: "--ex1"
+    - parameter: "ex2"
+    - {}
+  landing_request_invalid: &gx_select_landing_request_invalid
+    - parameter: 5
+    - parameter: null
+    - parameter: "Ex1"
+  landing_request_internal_valid:
+    *gx_select_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_select_landing_request_invalid
+  job_internal_valid:
+  - parameter: '--ex1'
+  - parameter: 'ex2'
+  job_internal_invalid:
+  - {}
+  test_case_xml_valid:
+  - parameter: 'ex2'
+  - parameter: '--ex1'
+  - {}
+  test_case_xml_invalid:
+  - parameter: {}
+  - parameter: null
+  workflow_step_valid:
+  - parameter: "--ex1"
+  - {}
+  workflow_step_invalid:
+  - parameter: 'foobar'
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+  - parameter: "--ex1"
+  - parameter: {__class__: 'ConnectedValue'}
+  - {}
+  workflow_step_linked_invalid:
+  - parameter: 'foobar'
+  - parameter: null
+
+gx_select_optional:
+  request_valid:
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  - parameter: null
+  - {}
+  request_invalid:
+  # Not allowing selecting booleans by truevalue/falsevalue - don't allow selecting
+  # selects by label.
+  - parameter: "Ex1"
+  # Do not allow lists for non-multi-selects
+  - parameter: ["ex2"]
+  - parameter: {}
+  - parameter: 5
+  landing_request_valid: &gx_select_optional_landing_request_valid
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  - parameter: null
+  - {}
+  landing_request_invalid: &gx_select_optional_landing_request_invalid
+  - parameter: 5
+  - parameter: "Ex1"
+  - parameter: {}
+  landing_request_internal_valid:
+    *gx_select_optional_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_select_optional_landing_request_invalid
+  job_internal_valid:
+  - parameter: '--ex1'
+  - parameter: 'ex2'
+  - parameter: null
+  job_internal_invalid:
+  - parameter: 'invalid'
+  - {}
+  test_case_xml_valid:
+  - {}
+  workflow_step_valid:
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  - parameter: null
+  - {}
+  workflow_step_invalid:
+  - parameter: "Ex1"
+  - parameter: ["ex2"]
+  - parameter: {}
+  - parameter: 5
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+  - parameter: "--ex1"
+  - parameter: "ex2"
+  - parameter: null
+  - {}
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+  - parameter: "Ex1"
+  - parameter: ["ex2"]
+  - parameter: {}
+  - parameter: 5
+
+gx_select_multiple:
+  request_valid:
+  - parameter: ["--ex1"]
+  - parameter: ["ex2"]
+  # ugh... but these aren't optional...
+  - parameter: null
+  - {}
+  request_invalid:
+  - parameter: ["Ex1"]
+  - parameter: {}
+  - parameter: 5
+  landing_request_valid: &gx_select_multiple_landing_request_valid
+  - parameter: ["--ex1"]
+  - parameter: ["ex2"]
+  - parameter: null
+  - {}
+  landing_request_invalid: &gx_select_multiple_landing_request_invalid
+  - parameter: 5
+  - parameter: ["Ex1"]
+  - parameter: {}
+  - parameter: false
+  landing_request_internal_valid:
+    *gx_select_multiple_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_select_multiple_landing_request_invalid
+  workflow_step_valid:
+  - parameter: ["--ex1"]
+  - parameter: ["ex2"]
+  - {}  # could come in linked...
+  # ... hmmm? this should maybe be invalid right? 
+  - parameter: null
+  job_internal_valid:
+  - parameter: ["--ex1"]
+  # itd be coool if this was forced to empty list - probably breaks backward compat though...
+  - parameter: null
+  job_internal_invalid:
+  - {}
+  - parameter: "--ex1"
+  workflow_step_invalid:
+  - parameter: ["Ex1"]
+  - parameter: {}
+  - parameter: 5
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: [{__class__: 'ConnectedValue'}]
+  workflow_step_linked_valid:
+  - parameter: ["--ex1"]
+  - parameter: ["ex2"]
+  - parameter: [{__class__: 'ConnectedValue'}]
+  - {}
+  - parameter: null
+  workflow_step_linked_invalid:
+  - parameter: ["Ex1"]
+  - parameter: {}
+  - parameter: 5
+  # might be wrong? I guess we would expect the semantic of this to do like a map-over
+  # but as far as I am aware that is not implemented https://github.com/galaxyproject/galaxy/issues/18541
+  - parameter: {__class__: 'ConnectedValue'}
+
+gx_select_multiple_optional:
+  request_valid:
+  - parameter: ["--ex1"]
+  - parameter: ["ex2"]
+  - {}
+  - parameter: null
+  request_invalid:
+  - parameter: ["Ex1"]
+  - parameter: {}
+  - parameter: 5
+
+gx_select_no_options_validation:
+  job_internal_valid:
+  - parameter: "--ex1"
+  job_internal_invalid:
+  - {}
+
+gx_genomebuild:
+  request_valid:
+  - parameter: hg19
+  - parameter: hg18
+  # implicitly selects top option "?"
+  - {}
+  request_invalid:
+  - parameter: null
+  - parameter: 9
+  landing_request_valid: &gx_genomebuild_landing_request_valid
+  - parameter: hg19
+  - parameter: hg18
+  - {}
+  landing_request_invalid: &gx_genomebuild_landing_request_invalid
+  - parameter: null
+  - parameter: 9
+  landing_request_internal_valid:
+    *gx_genomebuild_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_genomebuild_landing_request_invalid
+  job_internal_valid:
+  - parameter: hg19
+  job_internal_invalid:
+  - {}
+
+gx_genomebuild_optional:
+  request_valid:
+  - parameter: hg19
+  - parameter: hg18
+  # these yield actual null parameters instead of ?
+  - {}
+  - parameter: null
+  request_invalid:
+  - parameter: 8
+  - parameter: true
+  landing_request_valid: &gx_genomebuild_optional_landing_request_valid
+  - parameter: hg19
+  - parameter: hg18
+  - {}
+  - parameter: null
+  landing_request_invalid: &gx_genomebuild_optional_landing_request_invalid
+  - parameter: 9
+  landing_request_internal_valid:
+    *gx_genomebuild_optional_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_genomebuild_optional_landing_request_invalid
+  job_internal_valid:
+  - parameter: null
+  job_internal_invalid:
+  - {}
+
+gx_genomebuild_multiple:
+  request_valid:
+  - parameter: ["hg18", hg19"]
+  request_invalid:
+  - parameter: 6
+  # DIVERGES_FROM_CURRENT_API
+  - parameter: null
+
+gx_directory_uri:
+  request_valid:
+  - parameter: "gxfiles://foobar/"
+  - parameter: "gxfiles://foobar"
+  request_invalid:
+  - parameter: "justsomestring"
+  - parameter: true
+  - parameter: null
+  landing_request_valid: &gx_directory_uri_landing_request_valid
+  - parameter: "gxfiles://foobar/"
+  - parameter: "gxfiles://foobar"
+  - {}
+  landing_request_invalid: &gx_directory_uri_landing_request_invalid
+  - parameter: true
+  - parameter: null
+  - parameter: 8
+  landing_request_internal_valid:
+    *gx_directory_uri_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_directory_uri_landing_request_invalid
+  job_internal_valid:
+  - parameter: "gxfiles://foobar/"
+  - parameter: "gxfiles://foobar"
+  job_internal_invalid:
+  - parameter: "justsomestring"
+  - parameter: true
+  - parameter: null
+
+gx_directory_uri_validation:
+  request_valid:
+  - parameter: "gxfiles://mycoolsource/api/index.json"
+  request_invalid:
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: "gxfiles://tooshort/index.json"
+  - parameter: "gxfiles://mycoolsource/api/wrongex.js"
+  - parameter: "gxfiles://mycoolsource/badexp.json"
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: "gxfiles://mycoolsource/api/index.json"
+  workflow_step_linked_invalid:
+  - parameter: "gxfiles://tooshort/index.json"
+  - parameter: "gxfiles://mycoolsource/api/wrongex.js"
+  - parameter: "gxfiles://mycoolsource/badexp.json"
+
+gx_hidden:
+  request_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    # it will use a default if value is set in definition and no value supplied (see hidden_param.xml)
+    - {}
+  request_invalid:
+    - parameter: null
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  landing_request_valid: &gx_hidden_landing_request_valid
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - {}
+  landing_request_invalid: &gx_hidden_landing_request_invalid
+    - parameter: null
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  landing_request_internal_valid:
+    *gx_hidden_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_hidden_landing_request_invalid
+  job_internal_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+  job_internal_invalid:
+    - {}
+  workflow_step_valid:
+    - parameter: moocow
+    - {}
+  workflow_step_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  workflow_step_linked_valid:
+    - parameter: moocow
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: 5
+    - parameter: null
+
+gx_hidden_optional:
+  request_valid:
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - parameter: null
+  request_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  landing_request_valid: &gx_hidden_optional_landing_request_valid
+    - parameter: moocow
+    - parameter: 'some spaces'
+    - parameter: ''
+    - {}
+    - parameter: null
+  landing_request_invalid: &gx_hidden_optional_landing_request_invalid
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  landing_request_internal_valid:
+    *gx_hidden_optional_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_hidden_optional_landing_request_invalid
+  workflow_step_valid:
+    - parameter: moocow
+    - {}
+    - parameter: null
+  workflow_step_invalid:
+    - parameter: 5
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  workflow_step_linked_valid:
+    - parameter: moocow
+    - parameter: {__class__: 'ConnectedValue'}
+    - parameter: null
+  workflow_step_linked_invalid:
+    - parameter: 5
+
+gx_hidden_validation:
+  request_valid:
+  - parameter: "http://mycoolservice.com/api/index.json"
+  request_invalid:
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: "http://mycoolservice.com/index.json"
+  - parameter: "http://mycoolservice.com/api/wrongex.js"
+  - parameter: "http://mycoolservice.com/badexp.json"
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  - parameter: "http://mycoolservice.com/api/index.json"
+  workflow_step_linked_invalid:
+  - parameter: "http://mycoolservice.com/index.json"
+  - parameter: "http://mycoolservice.com/api/wrongex.js"
+  - parameter: "http://mycoolservice.com/badexp.json"
+
+gx_float:
+  request_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - parameter: 5.0001
+    # galaxy parameters created with a value - so doesn't need to appear in request even though non-optional
+    - {}
+  request_invalid:
+    - parameter: null
+    - parameter: "5"
+    - parameter: "5.0"
+    - parameter: { "moo": "cow" }
+  job_internal_valid:
+   - parameter: 5
+   - parameter: 5.0
+  job_internal_invalid:
+   - {}
+   - parameter: "5"
+   - parameter: "5.0"
+   - parameter: null
+  landing_request_valid:
+    - {}
+    - parameter: 5
+    - parameter: 5.0
+  landing_request_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+    - parameter: "5.0"
+  landing_request_internal_valid:
+    - {}
+    - parameter: 5
+    - parameter: 5.0
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+    - parameter: "5.0"
+  test_case_xml_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - {}
+  test_case_xml_invalid:
+    - parameter: null
+    - parameter: "5.0"
+    - parameter: "5.1"
+  workflow_step_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - {}
+  workflow_step_invalid:
+    - parameterx: 5
+    - parameter: 'foobar'
+  workflow_step_linked_valid:
+    - parameter: 5
+    - parameter: 5.4
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: null
+    - parameter: 'foobar'
+    - parameter: {__class__: 'ConnectedValue2'}
+
+
+gx_float_optional:
+  request_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - parameter: 5.0001
+    - parameter: null
+    - {}
+  request_invalid:
+    - parameter: "5"
+    - parameter: "5.0"
+    - parameter: {}
+    - parameter: { "moo": "cow" }
+  job_internal_valid:
+   - parameter: 5
+   - parameter: 5.0
+   - parameter: null
+  job_internal_invalid:
+   - {}
+   - parameter: "5"
+   - parameter: "5.0"
+  landing_request_valid:
+    - {}
+    - parameter: 5
+    - parameter: 5.0
+    - parameter: null
+  landing_request_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+    - parameter: "5.0"
+  landing_request_internal_valid:
+    - {}
+    - parameter: 5
+    - parameter: 5.0
+    - parameter: null
+  landing_request_internal_invalid:
+    - parameter: "moo"
+    - parameter: "5"
+    - parameter: "5.0"
+  test_case_xml_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - {}
+    - parameter: null
+  test_case_xml_invalid:
+    - parameter: "5.0"
+    - parameter: "5.1"
+  workflow_step_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - {}
+  workflow_step_invalid:
+    - parameterx: 5
+    - parameter: 'foobar'
+  workflow_step_linked_valid:
+    - parameter: 5
+    - parameter: 5.4
+    - parameter: {__class__: 'ConnectedValue'}
+    - parameter: null
+  workflow_step_linked_invalid:
+    - parameter: 'foobar'
+    - parameter: {__class__: 'ConnectedValue2'}
+
+gx_float_validation_range:
+  request_valid:
+  - parameter: 0.1
+  - parameter: 9.7
+  - parameter: 5
+  request_invalid:
+  - parameter: 10
+  - parameter: 0
+  - parameter: 9.8  # endpoint not included because specified in validator
+
+gx_float_min_max:
+  request_valid:
+  - parameter: 0.1
+  - parameter: 9.7
+  - parameter: 5
+  - parameter: 9.8  # endpoint implicitly included when max attribute set on param
+  request_invalid:
+  - parameter: 10
+  - parameter: 0
+
+gx_color:
+  request_valid:
+   - parameter: '#aabbcc'
+   - parameter: '#000000'
+  request_invalid:
+   - parameter: null
+   - parameter: {}
+   - parameter: '#abcd'
+  workflow_step_valid:
+   - parameter: '#aabbcc'
+   - parameter: '#000000'
+   - {}
+  workflow_step_invalid:
+    - parameterx: '#aabbcc'
+    - parameter: 'foobar'
+    - parameter: 5
+  workflow_step_linked_valid:
+    - parameter: '#aabbcc'
+    - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+    - parameter: null
+    - parameter: 'foobar'
+    - parameter: 5
+    - parameter: {__class__: 'ConnectedValue2'}
+
+gx_data:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", "ext": "txt"}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: abcdabcd}]}
+  request_invalid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {src: hda, id: 7}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_valid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hda, id: 0}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}
+  request_internal_invalid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: abcdabcd}]}
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_dereferenced_valid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hda, id: 0}
+  request_internal_dereferenced_invalid:
+   # the difference between request internal and request internal dereferenced is that these have been converted
+   # to datasets.
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}
+  landing_request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", "ext": "txt"}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: abcdabcd}]}
+   - {}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", "ext": "txt"}
+  landing_request_invalid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hda, id: 0}
+  landing_request_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - {}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", "ext": "txt"}
+  landing_request_internal_invalid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: abcdabcd}]}
+  job_internal_valid:
+   - parameter: {src: hda, id: 7}
+  job_internal_invalid:
+   # valid request but after the job has been created, map/reduce concepts should have been
+   # expanded out.
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {src: hda, id: abcdabcd}
+   # url parameters should be dereferrenced into datasets by this point...
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", "ext": "txt"}
+   - {}
+  test_case_xml_valid:
+   - parameter: {class: File, path: foo.bed}
+   - parameter: {class: File, location: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt"}
+  test_case_xml_invalid:
+   - parameter: foo.bed
+   - parameter: null
+   - {}
+  workflow_step_valid:
+   - {}
+  workflow_step_invalid:
+   - {src: hda, id: abcdabcd}
+   - {src: hda, id: 7}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+   - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+   - {}
+   - {src: hda, id: abcdabcd}
+   - {src: hda, id: 7}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {__class__: 'ConnectedValueX'}
+
+
+gx_data_optional:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: null
+   - {}
+  request_invalid:
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: null
+   - {}
+  request_internal_invalid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  job_internal_valid:
+   - parameter: null
+   - parameter: {src: hda, id: 5}
+  job_internal_invalid:
+   - {}
+  workflow_step_valid:
+   - {}
+  workflow_step_invalid:
+   - {src: hda, id: abcdabcd}
+   - {src: hda, id: 7}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_valid:
+   - {}
+   - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+   - {src: hda, id: abcdabcd}
+   - {src: hda, id: 7}
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: {__class__: 'ConnectedValueX'}
+  test_case_xml_valid:
+  - {}
+  - parameter: {class: "File", path: "1.bed"}
+  test_case_xml_invalid:
+  - parameter: {class: "NotAFile", path: "1.bed"}
+
+gx_data_multiple:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: [{src: hda, id: abcdabcd}]
+   - parameter: [{src: hdca, id: abcdabcd}]
+   - parameter: [{src: hdca, id: abcdabcd}, {src: hda, id: abcdabcd}]
+  request_invalid:
+   - parameter: {src: hda, id: 5}
+   - parameter: [{src: hdca, id: 5}, {src: hda, id: 5}]
+   - parameter: null
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hdca, id: 5}
+   - parameter: [{src: hda, id: 5}]
+   - parameter: [{src: hdca, id: 5}]
+   - parameter: [{src: hdca, id: 5}, {src: hda, id: 5}]
+   - parameter: [{src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}]
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+  request_internal_invalid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: [{src: hdca, id: abcdabcd}, {src: hda, id: abcdabcd}]
+   - parameter: null
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_dereferenced_valid:
+   - parameter: {__class__: "Batch", values: [{src: hdca, id: 5}]}
+   - parameter: [{src: hda, id: 5}]
+   - parameter: [{src: hda, id: 0}]
+  request_internal_dereferenced_invalid:
+   # the difference between request internal and request internal dereferenced is that these have been converted
+   # to datasets.
+   - parameter: [{src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}]
+  landing_request_valid:
+   - parameter: [{src: hda, id: abcdabcd}]
+   - {}
+  landing_request_invalid:
+   - parameter: [{src: hda, id: 6}]
+  landing_request_internal_valid:
+   - parameter: [{src: hda, id: 6}]
+   - {}
+  landing_request_internal_invalid:
+   - parameter: [{src: hda, id: abcdabcd}]
+  job_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: [{src: hda, id: 5}, {src: hda, id: 6}]
+  job_internal_invalid:
+   - {}
+
+gx_data_multiple_optional:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: [{src: hda, id: abcdabcd}]
+   - parameter: [{src: hdca, id: abcdabcd}]
+   - parameter: [{src: hdca, id: abcdabcd}, {src: hda, id: abcdabcd}]
+   - parameter: null
+   - {}
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}
+   - parameter: [{src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}]
+  request_invalid:
+   - parameter: {src: hda, id: 5}
+   - parameter: {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: {src: hdca, id: 5}
+   - parameter: [{src: hda, id: 5}]
+   - parameter: [{src: hdca, id: 5}]
+   - parameter: [{src: hdca, id: 5}, {src: hda, id: 5}]
+   - parameter: null
+   - {}
+   - parameter: [{src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}]
+  request_internal_invalid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_dereferenced_valid:
+   - parameter: {src: hda, id: 5}
+  request_internal_dereferenced_invalid:
+   - parameter: {src: hda, id: abcdabcd}
+   - parameter: [{src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}]
+   - parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"}
+  job_internal_valid:
+   - parameter: {src: hda, id: 5}
+   - parameter: [{src: hda, id: 5}, {src: hda, id: 6}]
+   - parameter: null
+  job_internal_invalid:
+   - {}
+
+gx_data_collection:
+  request_valid:
+   - parameter: {src: hdca, id: abcdabcd}
+  request_invalid:
+   - parameter: {src: hdca, id: 7}
+   - parameter: null
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_valid:
+   - parameter: {src: hdca, id: 5}
+  request_internal_invalid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+  request_internal_dereferenced_valid:
+   - parameter: {src: hdca, id: 5}
+  request_internal_dereferenced_invalid:
+   - parameter: {src: hdca, id: abcdabcd}
+  landing_request_valid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - {}
+  landing_request_invalid:
+   - parameter: {src: hdca, id: 5}
+   - parameter: [{src: hdca, id: abcdabcd}]
+  landing_request_internal_valid:
+   - parameter: {src: hdca, id: 5}
+   - {}
+  landing_request_internal_invalid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: [{src: hdca, id: abcdabcd}]
+  workflow_step_valid:
+  - {}
+  workflow_step_invalid:
+  - parameter: {src: hdca, id: abcdabcd}
+  - parameter: 5
+  - parameter: {}  
+  workflow_step_linked_valid:
+  - parameter: {__class__: 'ConnectedValue'}
+  workflow_step_linked_invalid:
+  - {}
+  test_case_xml_valid:
+  - parameter: {class: Collection, collection_type: list, elements: []}
+  - parameter:
+     class: Collection
+     collection_type: list
+     elements:
+     - {identifier: "first", path: "1.bed", class: File}
+     - {identifier: "second", path: "2.bed", class: File}
+  - parameter:
+     name: "A nested listed with a name"
+     class: Collection
+     collection_type: "list:paired"
+     elements:
+     - class: Collection
+       collection_type: paired
+       identifier: first_el
+       elements:
+       - {identifier: "forward", path: "1_f.bed", class: File}
+       - {identifier: "reverse", path: "1_r.bed", class: File}
+  test_case_xml_invalid:
+  # collection type is required
+  - parameter: {class: Collection, elements: []}
+  - parameter:
+     class: Collection
+     collection_type: list
+     elements:
+     - {identifier: "first", path: "1.bed", class: NotAFile}
+  - parameter:
+     class: Collection
+     collection_type: list
+     elements:
+     - {identifier: "first", pathmisspelled: "1.bed", class: File}
+  - parameter:
+     name: "A nested listed with a name"
+     class: Collection
+     collection_type: "list:paired"
+     elements:
+     - class: Collection
+       collection_type: paired
+       identifier: first_el
+       elements:
+       - {identifier: "forward", path: "1_f.bed", class: File}
+       - {identifier: "reverse", path: "1_r.bed", class: FileX}
+  job_internal_valid:
+    - parameter: {src: hdca, id: 5}
+  job_internal_invalid:
+    - parameter: {src: hdca, id: abcdabcd}
+    - parameter: null
+    - {}
+
+gx_data_collection_optional:
+  request_valid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - {}
+  request_invalid:
+   - parameter: {src: hdca, id: 7}
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+   - parameter: {}
+  request_internal_valid:
+   - parameter: {src: hdca, id: 5}
+   - parameter: null
+   - {}
+  request_internal_invalid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+   - parameter: {}
+  landing_request_valid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - {}
+  landing_request_invalid:
+   - parameter: {src: hdca, id: 5}
+   - parameter: [{src: hdca, id: abcdabcd}]
+  landing_request_internal_valid:
+   - parameter: {src: hdca, id: 5}
+   - parameter: null
+   - {}
+  landing_request_internal_invalid:
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: [{src: hdca, id: abcdabcd}]
+  job_internal_valid:
+    - parameter: {src: hdca, id: 5}
+    - parameter: null
+  job_internal_invalid:
+    - parameter: {src: hdca, id: abcdabcd}
+    - {}
+
+gx_conditional_boolean:
+  request_valid:
+    - conditional_parameter:
+        test_parameter: true
+        integer_parameter: 1
+    - conditional_parameter:
+        test_parameter: true
+        integer_parameter: 2
+    - conditional_parameter:
+        test_parameter: false
+        boolean_parameter: true
+    # Test parameter has default and so does it "case" - so this should be fine
+    - {}
+    # The boolean_parameter is optional so just setting a test_parameter is fine
+    - conditional_parameter:
+        test_parameter: true
+    - conditional_parameter:
+        test_parameter: false
+    # if test parameter is missing, it should be false in this case (TODO: test inverse)
+    # so boolean_parameter or either type or missing should be fine.
+    - conditional_parameter: 
+        boolean_parameter: true
+    - conditional_parameter: 
+        boolean_parameter: false
+    - conditional_parameter: {}
+  request_invalid:
+    - conditional_parameter:
+        test_parameter: false
+        integer_parameter: 1
+    - conditional_parameter:
+        test_parameter: null
+    - conditional_parameter:
+        test_parameter: true
+        integer_parameter: "1"
+    - conditional_parameter: 
+        test_parameter: true
+        integer_parameter: null
+    # if test parameter is missing, it should be false in this case
+    # in that case having an integer_parameter is not acceptable.
+    - conditional_parameter: 
+        integer_parameter: 5
+  landing_request_valid: &gx_conditional_boolean_landing_request_valid
+    - {}
+  landing_request_invalid: &gx_conditional_boolean_landing_request_invalid
+    - conditional_parameter:
+        test_parameter: false
+        integer_parameter: 1
+  landing_request_internal_valid:
+    *gx_conditional_boolean_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_conditional_boolean_landing_request_invalid
+  job_internal_valid:
+    - conditional_parameter:
+        test_parameter: true
+        integer_parameter: 1
+    - conditional_parameter:
+        test_parameter: false
+        boolean_parameter: false
+  job_internal_invalid:
+    # missing defaults are fine in request, but job_internal records parameters used,
+    # must include defaults.
+    - {}
+    - conditional_parameter: {}
+    - conditional_parameter:
+        test_parameter: true
+    - conditional_parameter:
+        boolean_parameter: true
+
+gx_conditional_boolean_checked:
+  request_valid:
+    # if no test parameter is defined, the default is 'checked' so the test
+    # parameter is true.
+    - conditional_parameter:
+        integer_parameter: 5
+    - conditional_parameter:
+        integer_parameter: 0
+
+  request_invalid:
+    # if test parameter is missing, it should be true (it is 'checked') in this case
+    # in that case having a boolean_parameter is not acceptable.
+    - conditional_parameter: 
+        boolean_parameter: false
+
+  job_internal_invalid:
+    - conditional_parameter: {}
+    - {}
+
+gx_conditional_conditional_boolean:
+  request_valid:
+    - outer_conditional_parameter:
+        outer_test_parameter: false
+        boolean_parameter: true
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        inner_conditional_parameter: 
+          inner_test_parameter: true
+          integer_parameter: 5
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        inner_conditional_parameter:
+          inner_test_parameter: false
+          boolean_parameter: true
+    # Test parameter has default and so does it "case" - so this should be fine
+    - {}
+    - outer_conditional_parameter: {}
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        inner_conditional_parameter: {}
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+  request_invalid:
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        boolean_parameter: true
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        inner_conditional_parameter:
+          inner_test_parameter: false
+          integer_parameter: 5
+    - outer_conditional_parameter:
+        outer_test_parameter: true
+        inner_conditional_parameter:
+          inner_test_parameter: true
+          integer_parameter: true
+  job_internal_invalid:
+   - {}
+   - outer_conditional_parameter: {}
+   - outer_conditional_parameter: {}
+   - outer_conditional_parameter:
+      outer_test_parameter: true
+      inner_conditional_parameter: {}
+   - outer_conditional_parameter:
+      outer_test_parameter: true
+
+gx_conditional_select:
+  request_valid:
+    - conditional_parameter:
+        test_parameter: a
+        integer_parameter: 1
+    - conditional_parameter:
+        test_parameter: a
+        integer_parameter: 2
+    - conditional_parameter:
+        test_parameter: b
+        boolean_parameter: true
+    # Test parameter has default and so does it "case" - so this should be fine
+    - {}
+    # # The select is optional so just setting a test_parameter is fine
+    - conditional_parameter:
+        integer_parameter: 1
+  request_invalid:
+    - conditional_parameter:
+        test_parameter: b
+        integer_parameter: 1
+    - conditional_parameter:
+        test_parameter: null
+    - conditional_parameter:
+        test_parameter: a
+        integer_parameter: "1"
+    - conditional_parameter: 
+        test_parameter: b
+        integer_parameter: null
+    # if test parameter is missing, it should be false in this case
+    # in that case having an integer_parameter is not acceptable.
+    - conditional_parameter: 
+        boolean_parameter: true
+  job_internal_valid:
+  - conditional_parameter:
+      test_parameter: a
+      integer_parameter: 1
+  - conditional_parameter:
+      test_parameter: b
+      boolean_parameter: true
+  job_internal_invalid:
+  - {}
+  - conditional_parameter:
+      integer_parameter: 1
+  - conditional_parameter: null
+  - conditional_parameter: {}
+
+gx_repeat_boolean:
+  request_valid:
+    - parameter:
+      - { boolean_parameter: true }
+    - parameter: []
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+    - parameter: [{}]
+    - parameter: [{}, {}]
+  request_invalid:
+    - parameter:
+      - { boolean_parameter: 4 }
+    - parameter:
+      - { foo: 4 }
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+      - { boolean_parameter: 4 }
+    - parameter: 5
+  landing_request_valid: &gx_repeat_boolean_landing_request_valid
+    - {}
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+    - parameter: [{}]
+    - parameter: [{}, {}]
+  landing_request_invalid: &gx_repeat_boolean_landing_request_invalid
+    - parameter:
+      - { boolean_parameter: 4 }
+  landing_request_internal_valid:
+    *gx_repeat_boolean_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_repeat_boolean_landing_request_invalid
+  job_internal_valid:
+    - parameter:
+      - { boolean_parameter: true }
+    - parameter: []
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+  job_internal_invalid:
+    - parameter: [{}]
+    - parameter: [{}, {}]
+
+
+gx_repeat_boolean_min:
+  request_valid:
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+    - parameter: [{}, {}]
+    # even though a minimum is set here - each instance of the repeat does not require a value
+    # so we can skip the repeat all together and Galaxy I think will just use the defaults at
+    # each stage - see API tests -> test_tools.py -> test_optional_repeats_with_mins_filled_id
+    - {}
+  request_invalid:
+    - parameter: []
+    - parameter: [{}]
+    - parameter:
+      - { boolean_parameter: true }
+    - parameter:
+      - { boolean_parameter: 4 }
+    - parameter:
+      - { foo: 4 }
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+      - { boolean_parameter: 4 }
+    - parameter: 5
+  job_internal_valid:
+    - parameter:
+      - { boolean_parameter: true }
+      - { boolean_parameter: false }
+  job_internal_invalid:
+    - parameter: [{}, {}]
+    - parameter: []
+
+gx_repeat_data:
+  request_valid:
+    - parameter:
+      - { data_parameter: {src: hda, id: abcdabcd} }
+      - { data_parameter: {src: hda, id: abcdabcd} }
+    - parameter: []
+    - parameter:
+      - { data_parameter: {src: hda, id: abcdabcd} }
+    # an empty repeat is fine
+    - {}
+    - parameter:
+      - { data_parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"} }
+  request_invalid:
+    - parameter: [{}, {}]
+    - parameter: [{}]
+    - parameter: 5
+  request_internal_valid:
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+    - parameter:
+      - { data_parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"} }
+  request_internal_invalid:
+    - parameter:
+      - { data_parameter: { src: hda, id: abcdabcd } }
+  landing_request_valid: &gx_repeat_data_landing_request_valid
+    - {}
+    # unlike above - in landing mode all parameters are optional so it is find to have an unset data parameters
+    - parameter: [{}]
+  landing_request_invalid: &gx_repeat_data_landing_request_invalid
+    - parameter: 5
+  landing_request_internal_valid:
+    *gx_repeat_data_landing_request_valid
+  landing_request_internal_invalid:
+    *gx_repeat_data_landing_request_invalid
+  job_internal_valid:
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+  job_internal_invalid:
+    - parameter: null
+    - parameter: {}
+    - parameter:
+       - { data_parameter: {src: url, url: "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt", ext: "txt"} }
+
+gx_repeat_data_min:
+  request_valid:
+    - parameter:
+      - { data_parameter: {src: hda, id: abcdabcd} }
+      - { data_parameter: {src: hda, id: abcdabcd} }
+  request_invalid:
+    # data isn't optional and so we need at least one list element
+    - {}
+    - parameter: []
+    - parameter:
+      - { data_parameter: {src: hda, id: abcdabcd} }
+    - parameter: [{}, {}]
+    - parameter: [{}]
+    - parameter: 5
+  landing_request_valid:
+  - {}
+  # ignore the min here - can just specify the first set of parameters and I think that should work
+  - parameter:
+    - { data_parameter: {src: hda, id: abcdabcd} }
+  landing_request_invalid:
+  - parameter:
+    - { data_parameter: {src: hda, id: 5} }
+  landing_request_internal_valid:
+  - {}
+  # ignore the min here - can just specify the first set of parameters and I think that should work
+  - parameter:
+    - { data_parameter: {src: hda, id: 5} }
+  landing_request_internal_invalid:
+  - parameter:
+    - { data_parameter: {src: hda, id: abcdabcd} }
+  request_internal_valid:
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+      - { data_parameter: { src: hda, id: 5 } }
+  request_internal_invalid:
+    - parameter:
+      - { data_parameter: { src: hda, id: abcdabcd } }
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+  job_internal_valid:
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+      - { data_parameter: { src: hda, id: 6 } }
+  job_internal_invalid:
+    - parameter:
+      - { data_parameter: { src: hda, id: 5 } }
+    - parameter:
+      - {}
+    - parameter: {}
+
+
+gx_section_boolean:
+  request_valid:
+    - parameter: { boolean_parameter: true }
+    # booleans are optional in requests, so this should be fine?
+    - {}
+  request_invalid:
+    - parameter: { boolean_parameter: 4 }
+  job_internal_valid:
+    - parameter: { boolean_parameter: true }
+  job_internal_invalid:
+    - {}
+    - parameter: { boolean_parameter: 4 }
+
+
+gx_section_data:
+  request_valid:
+    - parameter: { data_parameter: { src: hda, id: abcdabcd } }
+  request_invalid:
+    - parameter: { data_parameter: 4 }
+    - parameter: { data_parameter: { src: hda, id: 5 } }
+    - {}
+  request_internal_valid:
+    - parameter: { data_parameter: { src: hda, id: 5 } }
+  request_internal_invalid:
+    - parameter: { data_parameter: { src: hda, id: abcdabcd } }
+    - {}
+  job_internal_valid:
+    - parameter: { data_parameter: { src: hda, id: 5 } }
+  job_internal_invalid:
+    - {}
+
+gx_drill_down_exact:
+  request_valid:
+  - parameter: aa
+  - parameter: bbb
+  - parameter: ba
+  # non-leaf nodes seem to be selectable in exact mode
+  - parameter: a
+  request_invalid:
+  - parameter: c
+  - parameter: {}
+  # no implicit default currently - see test_drill_down_first_by_default in API test test_tools.py.
+  - {}
+  - parameter: null
+  job_internal_valid:
+  - parameter: aa
+  job_internal_invalid:
+  - parameter: c
+  - {}
+
+gx_drill_down_exact_with_selection:
+  request_valid:
+  - parameter: aa
+  - parameter: bbb
+  - parameter: ba
+  # non-leaf nodes seem to be selectable in exact mode
+  - parameter: a
+  request_invalid:
+  - parameter: c
+  # see note above no implicit selection
+  - parameter: {}
+  - parameter: null
+  job_internal_valid:
+  - parameter: aa
+  job_internal_invalid:
+  - parameter: c
+  - parameter: null
+  - {}
+
+gx_drill_down_recurse:
+  request_valid:
+  - parameter: bba
+  request_invalid:
+  - parameter: a
+  - parameter: c
+
+gx_drill_down_recurse_multiple:
+  request_valid:
+  - parameter: [bba]
+  - parameter: [a]
+  request_invalid:
+  - parameter: c
+
+gx_data_column:
+  request_valid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: 0 }
+  request_invalid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: [ 0 ] }
+  request_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+  request_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: "0" }
+  job_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+  job_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123} }
+  - { }
+  test_case_xml_valid:
+  - { ref_parameter: {class: "File", path: "1.bed"}, parameter: 3 }
+  test_case_xml_invalid:
+  - { ref_parameter: {class: "File", path: "1.bed"}, parameter: "3" }
+  test_case_xml_invalid:
+  - { ref_parameter: {class: "File", path: "1.bed"}, parameter: "c2: With name" }
+
+gx_data_column_optional:
+  request_valid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: 0 }
+  - { ref_parameter: {src: hda, id: abcdabcd} }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: null }
+  request_invalid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: [ 0 ] }
+  job_internal_valid:
+  - { ref_parameter: {src: hda, id: 1}, parameter: 0 }
+  - { ref_parameter: {src: hda, id: 1}, parameter: null }
+  job_internal_invalid:
+  - { ref_parameter: {src: hda, id: 1} }
+  - { }
+  - { ref_parameter: {src: hda, id: 1}, parameter: "0" }
+  request_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+  request_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: "0" }
+
+gx_data_column_multiple:
+  request_valid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: [0] }
+  request_invalid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: ["0"] }
+  request_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: [0] }
+  job_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: [0] }
+  job_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: ["0"] }
+  - { ref_parameter: {src: hda, id: 123}, parameter: null }
+  request_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+
+gx_group_tag:
+  request_valid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'type:matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'matched' }
+  request_invalid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: null }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 7 }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: true }
+  - { ref_parameter: { src: hdca, id: abcdabcd} }
+  request_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 'type: matched' }
+  request_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+
+gx_group_tag_optional:
+  request_valid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'type:matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd} }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: null }
+  request_invalid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 7 }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: true }
+  request_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 'type: matched' }
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+  request_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 8 }
+  job_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+  - { ref_parameter: { src: hdca, id: 123}, parameter: "matched" }
+  job_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123} }
+
+
+gx_group_tag_multiple:
+  request_valid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['type:matched'] }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['matched'] }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['matched'] }
+  request_invalid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 7 }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: true }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: null }
+  - { ref_parameter: { src: hdca, id: abcdabcd} }
+  request_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: ['type: matched'] }
+  request_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 8 }
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+  job_internal_valid:
+  - { ref_parameter: { src: hdca, id: 123}, parameter: ['matched'] }
+  job_internal_invalid:
+  - { ref_parameter: { src: hdca, id: 123} }
+  - { ref_parameter: { src: hdca, id: 123}, parameter: null }
+
+
+
+cwl_int:
+  request_valid:
+    - parameter: 5
+  request_invalid:
+    - parameter: "5"
+    - {}
+    - parameter: null
+    - parameter: "None"
+
+
+# TODO: Not a thing perhaps?
+# cwl_null:
+#   request_valid:
+#     - parameter: null
+#     - {}
+#   request_invalid:
+#     - parameter: "5"
+#     - parameter: 5
+#     - parameter: {}
+
+cwl_int_optional:
+  request_valid:
+    - parameter: 5
+    - parameter: null
+  request_invalid:
+    - parameter: "5"
+    - {}
+    - parameter: "None"
+
+cwl_float:
+  request_valid:
+    - parameter: 5
+    - parameter: 5.0
+  request_invalid:
+    - parameter: null
+    - parameter: "5"
+    - {}
+    - parameter: "None"
+
+cwl_float_optional:
+  request_valid:
+    - parameter: 5
+    - parameter: 5.0
+    - parameter: null
+  request_invalid:
+    - parameter: "5"
+    - {}
+    - parameter: "None"
+
+cwl_string:
+  request_valid:
+    - parameter: "moo"
+    - parameter: ""
+  request_invalid:
+    - parameter: null
+    - {}
+    - parameter: 5
+
+cwl_string_optional:
+  request_valid:
+    - parameter: "moo"
+    - parameter: ""
+    - parameter: null
+  request_invalid:
+    - {}
+    - parameter: 5
+
+cwl_boolean:
+  request_valid:
+    - parameter: true
+    - parameter: false
+  request_invalid:
+    - parameter: null
+    - {}
+    - parameter: 5
+    - parameter: "true"
+    - parameter: "True"
+
+cwl_boolean_optional:
+  request_valid:
+    - parameter: true
+    - parameter: false
+    - parameter: null
+  request_invalid:
+    - {}
+    - parameter: 5
+    - parameter: "true"
+    - parameter: "True"
+
+cwl_file:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+  request_invalid:
+   - parameter: {src: hda, id: 7}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+
+cwl_directory:
+  request_valid:
+   - parameter: {src: hda, id: abcdabcd}
+  request_invalid:
+   - parameter: {src: hda, id: 7}
+   - parameter: {src: hdca, id: abcdabcd}
+   - parameter: null
+   - parameter: {src: fooda, id: abcdabcd}
+   - parameter: {id: abcdabcd}
+   - parameter: {}
+   - {}
+   - parameter: true
+   - parameter: 5
+   - parameter: "5"
+
diff --git a/test/unit/tool_util/test_assertion_models.py b/test/unit/tool_util/test_assertion_models.py
new file mode 100644
index 0000000000000000000000000000000000000000..d4b6ff8f1ed608c584b013428f3905320ed0ea66
--- /dev/null
+++ b/test/unit/tool_util/test_assertion_models.py
@@ -0,0 +1,246 @@
+import sys
+from string import Template
+
+import lxml.etree as ET
+import pytest
+from pydantic import ValidationError
+
+from galaxy.tool_util.verify.assertion_models import assertion_list
+from galaxy.tool_util.verify.codegen import galaxy_xsd_path
+from galaxy.tool_util.verify.parse import assertion_xml_els_to_models
+from galaxy.util.commands import shell
+from galaxy.util.unittest_utils import skip_unless_executable
+
+valid_assertions = [
+    {"that": "has_size", "size": "5G"},
+    {"that": "has_size", "size": 1},
+    {"that": "has_size", "size": "5Mi"},
+    {"that": "has_text", "text": "JBrowseDefaultMainPage"},
+    {"that": "has_line", "line": "'>Wildtype Staphylococcus aureus strain WT.'"},
+    {"that": "has_n_columns", "n": 2},
+    {"that": "is_valid_xml"},
+    {"that": "has_element_with_path", "path": "//el"},
+    {"that": "has_n_elements_with_path", "path": "//el", "n": 4},
+    {"that": "element_text_matches", "expression": "foob[a]r", "path": "//el"},
+    {"that": "element_text_is", "text": "foobar", "path": "//el"},
+    {
+        "that": "xml_element",
+        "path": "./elem/more[2]",
+        "children": [{"that": "has_text_matching", "expression": "foo$"}],
+    },
+    {"that": "xml_element", "path": "./elem/more[2]"},
+    {"that": "element_text", "path": "./elem/more[2]", "children": [{"that": "has_text", "text": "foo"}]},
+    {"that": "has_json_property_with_value", "property": "foobar", "value": "'6'"},
+    {"that": "has_json_property_with_text", "property": "foobar", "text": "cowdog"},
+    {"that": "has_archive_member", "path": ".*/my-file.txt"},
+    {"that": "has_archive_member", "path": ".*/my-file.txt", "children": [{"that": "has_text", "text": "1235abc"}]},
+    {"that": "has_image_width", "width": 560},
+    {"that": "has_image_width", "width": 560, "delta": 490},
+    {"that": "has_image_height", "height": 560, "delta": 490},
+    {"that": "has_image_height", "min": 45, "max": 90},
+    {"that": "has_image_channels", "channels": 3},
+    {"that": "has_image_channels", "channels": 3, "delta": 1},
+    {"that": "has_image_channels", "min": 1, "max": 4},
+    {"that": "has_image_channels", "min": 1, "max": 4, "negate": True},
+    {"that": "has_image_mean_intensity", "mean_intensity": 3.4},
+    {"that": "has_image_mean_intensity", "mean_intensity": 3.4, "eps": 0.2},
+    {"that": "has_image_mean_intensity", "mean_intensity": 3.4, "eps": 0.2, "channel": 1},
+    {"that": "has_image_mean_intensity", "min": 0.4, "max": 0.6, "channel": 1},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34"},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34", "channel": 1},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34", "channel": 1, "eps": 0.2},
+    {"that": "has_image_n_labels", "n": 85},
+    {"that": "has_image_n_labels", "labels": [1, 3, 4]},
+    {"that": "has_image_n_labels", "n": 9, "exclude_labels": [1, 3, 4]},
+    {"that": "has_image_n_labels", "n": 9, "exclude_labels": [1, 3, 4], "negate": True},
+    {"that": "has_image_mean_object_size", "mean_object_size": 9, "exclude_labels": [1, 3, 4]},
+    {"that": "has_image_mean_object_size", "mean_object_size": 9, "labels": [1, 3, 4]},
+    {"that": "has_image_mean_object_size", "mean_object_size": 9, "channel": 1, "eps": 0.2},
+    {"that": "has_json_property_with_value", "property": "skipped_columns", "value": "[1, 3, 5]"},
+    {"that": "has_json_property_with_text", "property": "color", "text": "red"},
+    {"that": "has_n_columns", "n": 30},
+    {"that": "has_n_columns", "n": 30, "delta": 4},
+    {"that": "has_n_columns", "n": 30, "delta": 4, "sep": " ", "comment": "####"},
+]
+
+valid_xml_assertions = [
+    """<has_size value="5G" />""",
+    """<has_size size="5G" />""",
+    """<has_size size="5G" />""",
+    """<has_text text="JBrowseDefaultMainPage" />""",
+    """<has_line line="'>Wildtype Staphylococcus aureus strain WT.'" />""",
+    """<xml_element path="./elem/more[2]" attribute="name"><has_text_matching expression="foo$"/></xml_element>""",
+    """<xml_element path="./elem/more[2]" attribute="name"></xml_element>""",
+    """<element_text path="./elem/more[2]"><has_text text="foo" /></element_text>""",
+    """<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />""",
+    r"""<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>""",
+    """<element_text_is path="BlastOutput_program" text="blastp" />""",
+    r"""<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />""",
+    """<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def"><not_has_text text="EDK72998.1" /></element_text>""",
+    """<has_archive_member path=".*/my-file.txt"><not_has_text text="EDK72998.1"/></has_archive_member>""",
+    """<has_archive_member path=".*/my-file.txt"></has_archive_member>""",
+    """<has_image_n_labels n="85" />""",
+    """<has_image_center_of_mass center_of_mass="511.07, 223.34" />""",
+    """<has_image_center_of_mass center_of_mass="511.07, 223.34" eps=".2" />""",
+    """<has_image_mean_intensity mean_intensity="0.83" />""",
+    """<has_image_height height="512" delta="2" />""",
+    """<has_image_width width="512" delta="2" />""",
+    """<has_image_channels channels="3" />""",
+    """<has_image_channels channels="3" delta="1" />""",
+    """<has_image_channels min="3" max="5" />""",
+    """<has_image_channels min="3" max="5" negate="true" />""",
+    """<has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />""",
+    """<has_json_property_with_text property="color" text="red" />""",
+    """<has_n_columns n="30" />""",
+    """<has_n_columns n="30" delta="4" />""",
+    """<has_n_columns n="30" delta="4" sep=" " comment="###" />""",
+    """<has_image_width min="500" />""",
+    """<has_image_height min="500" />""",
+]
+
+invalid_assertions = [
+    {"that": "has_size", "size": "5Gigabytes"},
+    # negative sizes not allowed
+    {"that": "has_size", "size": -1},
+    {"that": "has_n_columns", "n": [2]},
+    {"that": "has_n_columns", "n": -2},
+    {"that": "is_valid_xml_foo"},
+    {"that": "has_element_with_path", "path": 45},
+    {"that": "has_n_elements_with_path", "n": 4},
+    {"that": "has_n_elements_with_path", "n": -4},
+    {"that": "element_text_matches", "expression": 12, "path": "//el"},
+    # unclosed regex group
+    {"that": "element_text_matches", "expression": "[12", "path": "//el"},
+    {"that": "xml_element", "path": "./elem/more[2]", "children": [{"that": "foobar"}]},
+    {
+        "that": "xml_element",
+        "path": "./elem/more[2]",
+        "children": [{"that": "has_text_matching", "line": "invalidprop"}],
+    },
+    # must specify children for element_text
+    {"that": "element_text", "path": "./elem/more[2]"},
+    {"that": "has_json_property_with_value", "property": 42, "value": "cowdog"},
+    {"that": "has_json_property_with_text", "property": "foobar", "text": 6},
+    {"that": "has_archive_member", "path": ".*/my-file.txt", "extra": "param"},
+    {"that": "has_archive_member", "path": ".*/my-file.txt", "children": [{"that": "invalid"}]},
+    {"that": "has_image_width", "width": "560"},
+    {"that": "has_image_width", "width": -560},
+    {"that": "has_image_width", "width": 560, "delta": "wrong"},
+    {"that": "has_image_height", "height": -560},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34, foobar"},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07"},
+    {"that": "has_image_center_of_mass", "center_of_mass": "511.07, cow"},
+    # negative mean object sizes are not allowed
+    {"that": "has_image_n_labels", "n": -85},
+    {"that": "has_image_n_labels", "n": 85, "delta": -3},
+    # negative mean object sizes are not allowed
+    {"that": "has_image_mean_object_size", "mean_object_size": -9, "exclude_labels": [1, 3, 4]},
+    {"that": "has_image_mean_object_size", "mean_object_size": -9.0, "exclude_labels": [1, 3, 4]},
+    {"that": "has_image_mean_object_size", "mean_object_size": 9, "exclude_labels": [1, 3, 4], "eps": -0.2},
+    # looks a little odd in JSON but value is JSON loaded so must be a string
+    {"that": "has_json_property_with_value", "property": "skipped_columns", "value": [1, 3, 5]},
+    # missing property
+    {"that": "has_json_property_with_value", "property": "skipped_columns"},
+    {"that": "has_json_property_with_text", "property": "color"},
+    {"that": "has_n_columns", "n": 30, "delta": "wrongtype"},
+    {"that": "has_n_columns", "n": 30, "delta": -2},
+    {"that": "has_n_columns", "n": 30, "delta": 4, "sep": " ", "comment": "####", "extra": "param"},
+]
+
+invalid_xml_assertions = [
+    """<has_n_columns n="cow" />""",
+    """<has_text line="JBrowseDefaultMainPage" />""",
+    """<has_line text="JBrowseDefaultMainPage" />""",
+    # at least one child assertion is required here...
+    """<element_text path="./elem/more[2]"></element_text>""",
+    """<has_archive_member path=".*/my-file.txt"><not_has_text line="EDK72998.1"/></has_archive_member>""",
+    """<has_archive_member path=".*/my-file.txt"><foobar /></has_archive_member>""",
+    """<has_image_center_of_mass center_of_mass="511.07, 223.34" extra="param" />""",
+    """<has_image_center_of_mass center_of_mass="511.07, 223.34" eps="foobar" />""",
+    # negative numbers not allowed
+    """<has_image_n_labels n="-85" />""",
+    """<has_image_n_labels n="85" delta="-3" />""",
+    """<has_image_mean_intensity mean_intensity="not_a_number" />""",
+    """<has_image_mean_intensity mean_intensity=".83" extra="param" />""",
+    """<has_image_height height="512" delta="notanumber" />""",
+    """<has_image_width width="512" delta="2" extra="param" />""",
+    """<has_image_height height="512" delta="-2" />""",
+    """<has_image_width width="512" delta="-2" />""",
+    """<has_image_height height="-512" />""",
+    """<has_image_width width="-512" />""",
+    """<has_image_channels channels="3" exclude="wrong" />""",
+    """<has_image_channels channels="3" delta="not_a_number"  />""",
+    """<has_image_channels min="3" max="5" foo="bar" />""",
+    """<has_image_channels min="3" max="5" negate="NOTABOOLEAN" />""",
+    # missing required arguments...
+    """<has_json_property_with_value property="skipped_columns" />""",
+    """<has_json_property_with_text property="color" />""",
+    """<has_n_columns n="30" delta="wrong_type" />""",
+    """<has_n_columns n="30" delta="4" sep=" " comment="###" extra="param"/>""",
+]
+
+
+TOOL_TEMPLATE = Template(
+    """
+<tool id="gx_test" name="gx_test" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value_json="12456" />
+            <output name="output">
+                <assert_contents>
+                    $assertion_xml
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
+"""
+)
+
+
+if sys.version_info < (3, 8):  # noqa: UP036
+    pytest.skip(reason="Pydantic assertion models require python3.8 or higher", allow_module_level=True)
+
+
+def test_valid_json_models_validate():
+    assertion_list.model_validate(valid_assertions)
+
+
+def test_invalid_json_models_do_not_validate():
+    for invalid_assertion in invalid_assertions:
+        with pytest.raises(ValidationError):
+            assertion_list.model_validate([invalid_assertion])
+
+
+@skip_unless_executable("xmllint")
+def test_valid_xsd(tmp_path):
+    for assertion_xml in valid_xml_assertions:
+        tool_xml = TOOL_TEMPLATE.safe_substitute(assertion_xml=assertion_xml)
+        tool_path = tmp_path / "tool.xml"
+        tool_path.write_text(tool_xml)
+        ret = shell(["xmllint", "--nowarning", "--noout", "--schema", galaxy_xsd_path, str(tool_path)])
+        assert ret == 0, f"{assertion_xml} failed to validate"
+
+
+@skip_unless_executable("xmllint")
+def test_invalid_xsd(tmp_path):
+    for assertion_xml in invalid_xml_assertions:
+        tool_xml = TOOL_TEMPLATE.safe_substitute(assertion_xml=assertion_xml)
+        tool_path = tmp_path / "tool.xml"
+        tool_path.write_text(tool_xml)
+        ret = shell(["xmllint", "--nowarning", "--noout", "--schema", galaxy_xsd_path, str(tool_path)])
+        assert ret != 0, f"{assertion_xml} validated when error expected"
+
+
+def test_valid_xml_models_validate_after_json_transform():
+    for assertion_xml in valid_xml_assertions:
+        assertion_xml_els_to_models([ET.fromstring(assertion_xml)])
diff --git a/test/unit/tool_util/test_ontologies.py b/test/unit/tool_util/test_ontologies.py
index 3991d358c3db5ec0019d3c4eb3658625d247e6a3..5c1faca4771fb28e8bcf8c47ce7dfbed6346e0fc 100644
--- a/test/unit/tool_util/test_ontologies.py
+++ b/test/unit/tool_util/test_ontologies.py
@@ -46,6 +46,22 @@ inputs:
     type: integer
 """
 
+TOOL_YAML_NO_EXPLICIT_XREFS = """
+name: "Bowtie Mapper"
+class: GalaxyTool
+id: sort1
+version: 1.0.2
+description: "The Bowtie Mapper"
+command: "bowtie --map-the-stuff"
+outputs:
+  out1:
+    format: bam
+    from_work_dir: out1.bam
+inputs:
+  - name: input1
+    type: integer
+"""
+
 
 def test_parse_edam_empty():
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_1)
@@ -66,3 +82,17 @@ def test_parse_edam_mapping_operations_legacy():
     ontology_data = expand_ontology_data(test_source, ["sort1"], None)
     assert ontology_data.edam_operations == ["operation_3802"]
     assert ontology_data.edam_topics == []
+
+
+def test_parse_biotools_default_mapping():
+    test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
+    ontology_data = expand_ontology_data(test_source, ["cheetah_problem_unbound_var_input"], None)
+    assert ontology_data.xrefs[0]["reftype"] == "bio.tools"
+    assert ontology_data.xrefs[0]["value"] == "bwa"
+
+    test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
+    ontology_data = expand_ontology_data(test_source, ["rxlr_motifs"], None)
+    assert len(ontology_data.xrefs) == 2
+    values = [x["value"] for x in ontology_data.xrefs]
+    assert "signalp" in values
+    assert "hmmer2" in values
diff --git a/test/unit/tool_util/test_output_models.py b/test/unit/tool_util/test_output_models.py
new file mode 100644
index 0000000000000000000000000000000000000000..4f5c9269c19ed6681ecae3656588db8c1b2d0e1a
--- /dev/null
+++ b/test/unit/tool_util/test_output_models.py
@@ -0,0 +1,9 @@
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.parser.output_models import from_tool_source
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
+
+
+def test_from_tool_data_table():
+    tool_source = get_tool_source(functional_test_tool_path("dbkey_output_action.xml"))
+    # prevent regression of https://github.com/galaxyproject/galaxy/issues/18554. Tool fails without fix
+    from_tool_source(tool_source)
diff --git a/test/unit/tool_util/test_parameter_convert.py b/test/unit/tool_util/test_parameter_convert.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f5deff41e8567de72f9bafa553f4b70770a7572
--- /dev/null
+++ b/test/unit/tool_util/test_parameter_convert.py
@@ -0,0 +1,251 @@
+from typing import (
+    Any,
+    Dict,
+    Optional,
+)
+
+from galaxy.tool_util.parameters import (
+    DataRequestInternalHda,
+    DataRequestUri,
+    decode,
+    dereference,
+    encode,
+    fill_static_defaults,
+    input_models_for_tool_source,
+    landing_decode,
+    landing_encode,
+    LandingRequestToolState,
+    RequestInternalDereferencedToolState,
+    RequestInternalToolState,
+    RequestToolState,
+)
+from galaxy.tool_util.parser.util import parse_profile_version
+from .test_parameter_test_cases import tool_source_for
+
+EXAMPLE_ID_1_ENCODED = "123456789abcde"
+EXAMPLE_ID_1 = 13
+EXAMPLE_ID_2_ENCODED = "123456789abcd2"
+EXAMPLE_ID_2 = 14
+
+ID_MAP: Dict[int, str] = {
+    EXAMPLE_ID_1: EXAMPLE_ID_1_ENCODED,
+    EXAMPLE_ID_2: EXAMPLE_ID_2_ENCODED,
+}
+
+
+def test_encode_data():
+    tool_source = tool_source_for("parameters/gx_data")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState({"parameter": {"src": "hda", "id": EXAMPLE_ID_1_ENCODED}})
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"]["src"] == "hda"
+    assert decoded_state.input_state["parameter"]["id"] == EXAMPLE_ID_1
+
+
+def test_encode_collection():
+    tool_source = tool_source_for("parameters/gx_data_collection")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState({"parameter": {"src": "hdca", "id": EXAMPLE_ID_1_ENCODED}})
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"]["src"] == "hdca"
+    assert decoded_state.input_state["parameter"]["id"] == EXAMPLE_ID_1
+
+
+def test_encode_repeat():
+    tool_source = tool_source_for("parameters/gx_repeat_data")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState({"parameter": [{"data_parameter": {"src": "hda", "id": EXAMPLE_ID_1_ENCODED}}]})
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"][0]["data_parameter"]["src"] == "hda"
+    assert decoded_state.input_state["parameter"][0]["data_parameter"]["id"] == EXAMPLE_ID_1
+
+
+def test_encode_section():
+    tool_source = tool_source_for("parameters/gx_section_data")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState({"parameter": {"data_parameter": {"src": "hda", "id": EXAMPLE_ID_1_ENCODED}}})
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"]["data_parameter"]["src"] == "hda"
+    assert decoded_state.input_state["parameter"]["data_parameter"]["id"] == EXAMPLE_ID_1
+
+
+def test_encode_conditional():
+    tool_source = tool_source_for("identifier_in_conditional")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState(
+        {"outer_cond": {"multi_input": False, "input1": {"src": "hda", "id": EXAMPLE_ID_1_ENCODED}}}
+    )
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["outer_cond"]["input1"]["src"] == "hda"
+    assert decoded_state.input_state["outer_cond"]["input1"]["id"] == EXAMPLE_ID_1
+
+
+def test_multi_data():
+    tool_source = tool_source_for("parameters/gx_data_multiple")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = RequestToolState(
+        {"parameter": [{"src": "hda", "id": EXAMPLE_ID_1_ENCODED}, {"src": "hda", "id": EXAMPLE_ID_2_ENCODED}]}
+    )
+    request_state.validate(bundle)
+    decoded_state = decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"][0]["src"] == "hda"
+    assert decoded_state.input_state["parameter"][0]["id"] == EXAMPLE_ID_1
+    assert decoded_state.input_state["parameter"][1]["src"] == "hda"
+    assert decoded_state.input_state["parameter"][1]["id"] == EXAMPLE_ID_2
+
+    encoded_state = encode(decoded_state, bundle, _fake_encode)
+    assert encoded_state.input_state["parameter"][0]["src"] == "hda"
+    assert encoded_state.input_state["parameter"][0]["id"] == EXAMPLE_ID_1_ENCODED
+    assert encoded_state.input_state["parameter"][1]["src"] == "hda"
+    assert encoded_state.input_state["parameter"][1]["id"] == EXAMPLE_ID_2_ENCODED
+
+
+def test_landing_encode_data():
+    tool_source = tool_source_for("parameters/gx_data")
+    bundle = input_models_for_tool_source(tool_source)
+    request_state = LandingRequestToolState({"parameter": {"src": "hda", "id": EXAMPLE_ID_1_ENCODED}})
+    request_state.validate(bundle)
+    decoded_state = landing_decode(request_state, bundle, _fake_decode)
+    assert decoded_state.input_state["parameter"]["src"] == "hda"
+    assert decoded_state.input_state["parameter"]["id"] == EXAMPLE_ID_1
+
+    encoded_state = landing_encode(decoded_state, bundle, _fake_encode)
+    assert encoded_state.input_state["parameter"]["src"] == "hda"
+    assert encoded_state.input_state["parameter"]["id"] == EXAMPLE_ID_1_ENCODED
+
+
+def test_dereference():
+    tool_source = tool_source_for("parameters/gx_data")
+    bundle = input_models_for_tool_source(tool_source)
+    raw_request_state = {"parameter": {"src": "url", "url": "gxfiles://mystorage/1.bed", "ext": "bed"}}
+    request_state = RequestInternalToolState(raw_request_state)
+    request_state.validate(bundle)
+
+    exception: Optional[Exception] = None
+    try:
+        # quickly verify this request needs to be dereferenced
+        bad_state = RequestInternalDereferencedToolState(raw_request_state)
+        bad_state.validate(bundle)
+    except Exception as e:
+        exception = e
+    assert exception is not None
+
+    dereferenced_state = dereference(request_state, bundle, _fake_dereference)
+    assert isinstance(dereferenced_state, RequestInternalDereferencedToolState)
+    dereferenced_state.validate(bundle)
+
+
+def test_fill_defaults():
+    with_defaults = fill_state_for({}, "parameters/gx_int")
+    assert with_defaults["parameter"] == 1
+    with_defaults = fill_state_for({}, "parameters/gx_float")
+    assert with_defaults["parameter"] == 1.0
+    with_defaults = fill_state_for({}, "parameters/gx_boolean")
+    assert with_defaults["parameter"] is False
+    with_defaults = fill_state_for({}, "parameters/gx_boolean_optional")
+    # This is False unfortunately - see comments in gx_boolean_optional XML.
+    assert with_defaults["parameter"] is False
+    with_defaults = fill_state_for({}, "parameters/gx_boolean_checked")
+    assert with_defaults["parameter"] is True
+    with_defaults = fill_state_for({}, "parameters/gx_boolean_optional_checked")
+    assert with_defaults["parameter"] is True
+
+    with_defaults = fill_state_for({}, "parameters/gx_conditional_boolean")
+    assert with_defaults["conditional_parameter"]["test_parameter"] is False
+    assert with_defaults["conditional_parameter"]["boolean_parameter"] is False
+
+    with_defaults = fill_state_for({"conditional_parameter": {}}, "parameters/gx_conditional_boolean")
+    assert with_defaults["conditional_parameter"]["test_parameter"] is False
+    assert with_defaults["conditional_parameter"]["boolean_parameter"] is False
+
+    with_defaults = fill_state_for({}, "parameters/gx_repeat_boolean")
+    assert len(with_defaults["parameter"]) == 0
+    with_defaults = fill_state_for({"parameter": [{}]}, "parameters/gx_repeat_boolean")
+    assert len(with_defaults["parameter"]) == 1
+    instance_state = with_defaults["parameter"][0]
+    assert instance_state["boolean_parameter"] is False
+
+    with_defaults = fill_state_for({}, "parameters/gx_repeat_boolean_min")
+    assert len(with_defaults["parameter"]) == 2
+    assert with_defaults["parameter"][0]["boolean_parameter"] is False
+    assert with_defaults["parameter"][1]["boolean_parameter"] is False
+    with_defaults = fill_state_for({"parameter": [{}, {}]}, "parameters/gx_repeat_boolean_min")
+    assert len(with_defaults["parameter"]) == 2
+    assert with_defaults["parameter"][0]["boolean_parameter"] is False
+    assert with_defaults["parameter"][1]["boolean_parameter"] is False
+    with_defaults = fill_state_for({"parameter": [{}]}, "parameters/gx_repeat_boolean_min")
+    assert with_defaults["parameter"][0]["boolean_parameter"] is False
+    assert with_defaults["parameter"][1]["boolean_parameter"] is False
+
+    with_defaults = fill_state_for({}, "parameters/gx_section_boolean")
+    assert with_defaults["parameter"]["boolean_parameter"] is False
+
+    with_defaults = fill_state_for({}, "parameters/gx_drill_down_exact_with_selection")
+    assert with_defaults["parameter"] == "aba"
+
+    with_defaults = fill_state_for({}, "parameters/gx_hidden")
+    assert with_defaults["parameter"] == "moo"
+
+    with_defaults = fill_state_for({}, "parameters/gx_genomebuild_optional")
+    assert with_defaults["parameter"] is None
+
+    with_defaults = fill_state_for({}, "parameters/gx_select")
+    assert with_defaults["parameter"] == "--ex1"
+
+    with_defaults = fill_state_for({}, "parameters/gx_select_optional")
+    assert with_defaults["parameter"] is None
+
+    # Not ideal but matching current behavior
+    with_defaults = fill_state_for({}, "parameters/gx_select_multiple")
+    assert with_defaults["parameter"] is None
+
+    with_defaults = fill_state_for({}, "parameters/gx_select_multiple_optional")
+    assert with_defaults["parameter"] is None
+
+    # Do not fill in dynamic defaults... these require a Galaxy runtime.
+    with_defaults = fill_state_for({}, "remove_value", partial=True)
+    assert "choose_value" not in with_defaults
+
+    with_defaults = fill_state_for(
+        {"single": {"src": "hda", "id": 4}}, "select_from_dataset_in_conditional", partial=True
+    )
+    assert with_defaults["cond"]["cond"] == "single"
+    assert with_defaults["cond"]["inner_cond"]["inner_cond"] == "single"
+
+    # dynamic parameters should just stay empty - null would cause runtime to skip over population
+    with_defaults = fill_state_for({}, "parameters/gx_select_dynamic", partial=True)
+    assert "parameter" not in with_defaults
+
+    # dynamic parameters should just stay empty - null would cause runtime to skip over population
+    with_defaults = fill_state_for(
+        {"conditional_parameter": {"test_parameter": False}},
+        "parameters/gx_conditional_boolean_discriminate_on_string_value",
+    )
+    assert "conditional_parameter" in with_defaults
+    assert "boolean_parameter" in with_defaults["conditional_parameter"]
+    assert with_defaults["conditional_parameter"]["boolean_parameter"] is False
+
+
+def _fake_dereference(input: DataRequestUri) -> DataRequestInternalHda:
+    return DataRequestInternalHda(id=EXAMPLE_ID_1)
+
+
+def _fake_decode(input: str) -> int:
+    return next(key for key, value in ID_MAP.items() if value == input)
+
+
+def _fake_encode(input: int) -> str:
+    return ID_MAP[input]
+
+
+def fill_state_for(tool_state: Dict[str, Any], tool_path: str, partial: bool = False) -> Dict[str, Any]:
+    tool_source = tool_source_for(tool_path)
+    bundle = input_models_for_tool_source(tool_source)
+    profile = parse_profile_version(tool_source)
+    internal_state = fill_static_defaults(tool_state, bundle, profile, partial=partial)
+    return internal_state
diff --git a/test/unit/tool_util/test_parameter_specification.py b/test/unit/tool_util/test_parameter_specification.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed4b437449b59989c8b1cc3acb4b36489ad0bbb6
--- /dev/null
+++ b/test/unit/tool_util/test_parameter_specification.py
@@ -0,0 +1,254 @@
+import sys
+from functools import partial
+from typing import (
+    Callable,
+    List,
+    Optional,
+)
+
+import pytest
+import yaml
+
+from galaxy.exceptions import RequestParameterInvalidException
+from galaxy.tool_util.parameters import (
+    decode,
+    encode,
+    RawStateDict,
+    RequestInternalToolState,
+    RequestToolState,
+    ToolParameterBundleModel,
+    validate_internal_job,
+    validate_internal_landing_request,
+    validate_internal_request,
+    validate_internal_request_dereferenced,
+    validate_landing_request,
+    validate_request,
+    validate_test_case,
+    validate_workflow_step,
+    validate_workflow_step_linked,
+    ValidationFunctionT,
+)
+from galaxy.tool_util.parameters.json import to_json_schema_string
+from galaxy.tool_util.unittest_utils.parameters import (
+    parameter_bundle_for_file,
+    parameter_bundle_for_framework_tool,
+)
+from galaxy.util.resources import resource_string
+
+if sys.version_info < (3, 8):  # noqa: UP036
+    pytest.skip(reason="Pydantic tool parameter models require python3.8 or higher", allow_module_level=True)
+
+
+def specification_object():
+    try:
+        yaml_str = resource_string(__package__, "parameter_specification.yml")
+    except AttributeError:
+        # hack for the main() function below where this file is interpreted as part of the
+        # Galaxy tree.
+        yaml_str = open("test/unit/tool_util/parameter_specification.yml").read()
+    return yaml.safe_load(yaml_str)
+
+
+def framework_tool_checks():
+    # Extend parameter_specification with some extra tests against existing framework tools.
+    # There is something beautiful about a targeted tool for every parameter feature but realistically
+    # we've been doing a version of the for a decade with tool tests and we can leverage those also.
+    try:
+        yaml_str = resource_string(__package__, "framework_tool_checks.yml")
+    except AttributeError:
+        # hack for the main() function below where this file is interpreted as part of the
+        # Galaxy tree.
+        yaml_str = open("test/unit/tool_util/framework_tool_checks.yml").read()
+    return yaml.safe_load(yaml_str)
+
+
+def test_specification():
+    parameter_spec = specification_object()
+    for file in parameter_spec.keys():
+        _test_file(file, parameter_spec)
+
+
+def test_framework_tool_checks():
+    parameter_spec = framework_tool_checks()
+    for file in parameter_spec.keys():
+        _test_file(file, parameter_spec, parameter_bundle_for_framework_tool(f"{file}.xml"))
+
+
+def test_single():
+    # _test_file("gx_int")
+    # _test_file("gx_float")
+    # _test_file("gx_boolean")
+    # _test_file("gx_int_optional")
+    # _test_file("gx_float_optional")
+    # _test_file("gx_conditional_boolean")
+    # _test_file("gx_conditional_conditional_boolean")
+    _test_file("gx_conditional_boolean_checked")
+
+
+def _test_file(file: str, specification=None, parameter_bundle: Optional[ToolParameterBundleModel] = None):
+    spec = specification or specification_object()
+    combos = spec[file]
+    if parameter_bundle is None:
+        parameter_bundle = parameter_bundle_for_file(file)
+    assert parameter_bundle
+
+    assertion_functions = {
+        "request_valid": _assert_requests_validate,
+        "request_invalid": _assert_requests_invalid,
+        "request_internal_valid": _assert_internal_requests_validate,
+        "request_internal_invalid": _assert_internal_requests_invalid,
+        "request_internal_dereferenced_valid": _assert_internal_requests_dereferenced_validate,
+        "request_internal_dereferenced_invalid": _assert_internal_requests_dereferenced_invalid,
+        "landing_request_valid": _assert_landing_requests_validate,
+        "landing_request_invalid": _assert_landing_requests_invalid,
+        "landing_request_internal_valid": _assert_internal_landing_requests_validate,
+        "landing_request_internal_invalid": _assert_internal_landing_requests_invalid,
+        "job_internal_valid": _assert_internal_jobs_validate,
+        "job_internal_invalid": _assert_internal_jobs_invalid,
+        "test_case_xml_valid": _assert_test_cases_validate,
+        "test_case_xml_invalid": _assert_test_cases_invalid,
+        "workflow_step_valid": _assert_workflow_steps_validate,
+        "workflow_step_invalid": _assert_workflow_steps_invalid,
+        "workflow_step_linked_valid": _assert_workflow_steps_linked_validate,
+        "workflow_step_linked_invalid": _assert_workflow_steps_linked_invalid,
+    }
+
+    for valid_or_invalid, tests in combos.items():
+        assertion_function = assertion_functions[valid_or_invalid]
+        assertion_function(parameter_bundle, tests)
+
+    # Assume request validation will work here.
+    if "request_internal_valid" not in combos and "request_valid" in combos:
+        _assert_internal_requests_validate(parameter_bundle, combos["request_valid"])
+    if "request_internal_invalid" not in combos and "request_invalid" in combos:
+        _assert_internal_requests_invalid(parameter_bundle, combos["request_invalid"])
+
+
+def _for_each(test: Callable, parameters: ToolParameterBundleModel, requests: List[RawStateDict]) -> None:
+    for request in requests:
+        test(parameters, request)
+
+
+def model_assertion_function_factory(validate_function: ValidationFunctionT, what: str):
+
+    def _assert_validates(parameters: ToolParameterBundleModel, request: RawStateDict) -> None:
+        try:
+            validate_function(parameters, request)
+        except RequestParameterInvalidException as e:
+            raise AssertionError(f"Parameters {parameters} failed to validate {what} {request}. {e}")
+
+    def _assert_invalid(parameters: ToolParameterBundleModel, request: RawStateDict) -> None:
+        exc = None
+        try:
+            validate_function(parameters, request)
+        except RequestParameterInvalidException as e:
+            exc = e
+
+        if exc is None:
+            raise AssertionError(
+                f"Parameters {parameters} didn't result in validation error on {what} {request} as expected."
+            )
+
+    return _assert_validates, _assert_invalid
+
+
+_assert_request_validates, _assert_request_invalid = model_assertion_function_factory(validate_request, "request")
+_assert_internal_request_validates, _assert_internal_request_invalid = model_assertion_function_factory(
+    validate_internal_request, "internal request"
+)
+_assert_internal_request_dereferenced_validates, _assert_internal_request_dereferenced_invalid = (
+    model_assertion_function_factory(validate_internal_request_dereferenced, "dereferenced internal request")
+)
+_assert_internal_job_validates, _assert_internal_job_invalid = model_assertion_function_factory(
+    validate_internal_job, "internal job description"
+)
+_assert_test_case_validates, _assert_test_case_invalid = model_assertion_function_factory(
+    validate_test_case, "XML derived test case"
+)
+_assert_workflow_step_validates, _assert_workflow_step_invalid = model_assertion_function_factory(
+    validate_workflow_step, "workflow step tool state (unlinked)"
+)
+_assert_workflow_step_linked_validates, _assert_workflow_step_linked_invalid = model_assertion_function_factory(
+    validate_workflow_step_linked, "linked workflow step tool state"
+)
+_assert_landing_request_validates, _assert_landing_request_invalid = model_assertion_function_factory(
+    validate_landing_request, "landing request"
+)
+_assert_internal_landing_request_validates, _assert_internal_landing_request_invalid = model_assertion_function_factory(
+    validate_internal_landing_request, " internallanding request"
+)
+
+_assert_requests_validate = partial(_for_each, _assert_request_validates)
+_assert_requests_invalid = partial(_for_each, _assert_request_invalid)
+_assert_internal_requests_validate = partial(_for_each, _assert_internal_request_validates)
+_assert_internal_requests_invalid = partial(_for_each, _assert_internal_request_invalid)
+_assert_internal_requests_dereferenced_validate = partial(_for_each, _assert_internal_request_dereferenced_validates)
+_assert_internal_requests_dereferenced_invalid = partial(_for_each, _assert_internal_request_dereferenced_invalid)
+_assert_internal_jobs_validate = partial(_for_each, _assert_internal_job_validates)
+_assert_internal_jobs_invalid = partial(_for_each, _assert_internal_job_invalid)
+_assert_test_cases_validate = partial(_for_each, _assert_test_case_validates)
+_assert_test_cases_invalid = partial(_for_each, _assert_test_case_invalid)
+_assert_workflow_steps_validate = partial(_for_each, _assert_workflow_step_validates)
+_assert_workflow_steps_invalid = partial(_for_each, _assert_workflow_step_invalid)
+_assert_workflow_steps_linked_validate = partial(_for_each, _assert_workflow_step_linked_validates)
+_assert_workflow_steps_linked_invalid = partial(_for_each, _assert_workflow_step_linked_invalid)
+_assert_landing_requests_validate = partial(_for_each, _assert_landing_request_validates)
+_assert_landing_requests_invalid = partial(_for_each, _assert_landing_request_invalid)
+_assert_internal_landing_requests_validate = partial(_for_each, _assert_internal_landing_request_validates)
+_assert_internal_landing_requests_invalid = partial(_for_each, _assert_internal_landing_request_invalid)
+
+
+def decode_val(val: str) -> int:
+    assert val == "abcdabcd"
+    return 5
+
+
+def test_decode_gx_data():
+    input_bundle = parameter_bundle_for_file("gx_data")
+
+    request_tool_state = RequestToolState({"parameter": {"src": "hda", "id": "abcdabcd"}})
+    request_internal_tool_state = decode(request_tool_state, input_bundle, decode_val)
+    assert request_internal_tool_state.input_state["parameter"]["id"] == 5
+    assert request_internal_tool_state.input_state["parameter"]["src"] == "hda"
+
+
+def test_decode_gx_int():
+    input_bundle = parameter_bundle_for_file("gx_int")
+
+    request_tool_state = RequestToolState({"parameter": 5})
+    request_internal_tool_state = decode(request_tool_state, input_bundle, decode_val)
+    assert request_internal_tool_state.input_state["parameter"] == 5
+
+
+def test_json_schema_for_conditional():
+    input_bundle = parameter_bundle_for_file("gx_conditional_boolean")
+    tool_state = RequestToolState.parameter_model_for(input_bundle)
+    print(to_json_schema_string(tool_state))
+
+
+def test_encode_gx_data():
+    input_bundle = parameter_bundle_for_file("gx_data")
+
+    def encode_val(val: int) -> str:
+        assert val == 5
+        return "abcdabcd"
+
+    request_internal_tool_state = RequestInternalToolState({"parameter": {"src": "hda", "id": 5}})
+    request_tool_state = encode(request_internal_tool_state, input_bundle, encode_val)
+    assert request_tool_state.input_state["parameter"]["id"] == "abcdabcd"
+    assert request_tool_state.input_state["parameter"]["src"] == "hda"
+
+
+if __name__ == "__main__":
+    parameter_spec = specification_object()
+    parameter_models_json = {}
+    for file in parameter_spec.keys():
+        tool_parameter_model = parameter_bundle_for_file(file)
+        parameter_models_json[file] = tool_parameter_model.dict()
+    yaml_str = yaml.safe_dump(parameter_models_json)
+    with open("client/src/components/Tool/parameter_models.yml", "w") as f:
+        f.write("# auto generated file for JavaScript testing, do not modify manually\n")
+        f.write("# -----\n")
+        f.write('# PYTHONPATH="lib" python test/unit/tool_util/test_parameter_specification.py\n')
+        f.write("# -----\n")
+        f.write(yaml_str)
diff --git a/test/unit/tool_util/test_parameter_test_cases.py b/test/unit/tool_util/test_parameter_test_cases.py
new file mode 100644
index 0000000000000000000000000000000000000000..3ff5c3a0fdbf4607779f776925ff1a4ff21e15e9
--- /dev/null
+++ b/test/unit/tool_util/test_parameter_test_cases.py
@@ -0,0 +1,313 @@
+import os
+import re
+import sys
+from typing import (
+    Any,
+    List,
+    Optional,
+    Tuple,
+)
+
+import pytest
+
+from galaxy.tool_util.models import parse_tool
+from galaxy.tool_util.parameters import (
+    DataCollectionRequest,
+    DataRequestHda,
+    encode_test,
+    input_models_for_tool_source,
+)
+from galaxy.tool_util.parameters.case import (
+    test_case_state as case_state,
+    TestCaseStateAndWarnings,
+    TestCaseStateValidationResult,
+    validate_test_cases_for_tool_source,
+)
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.parser.interface import (
+    JsonTestCollectionDefDict,
+    JsonTestDatasetDefDict,
+    ToolSource,
+    ToolSourceTest,
+)
+from galaxy.tool_util.unittest_utils import functional_test_tool_directory
+from galaxy.tool_util.verify.parse import parse_tool_test_descriptions
+from .util import dict_verify_each
+
+# legacy tools allows specifying parameter and repeat parameters without
+# qualification. This was problematic and could result in ambigious specifications.
+TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS = [
+    "boolean_conditional.xml",
+    "simple_constructs.xml",
+    "section.xml",
+    "collection_paired_conditional_structured_like.xml",
+    "output_action_change_format.xml",
+    "top_level_data.xml",
+    "disambiguate_cond.xml",
+    "multi_repeats.xml",
+    "implicit_default_conds.xml",
+    "min_repeat.xml",
+]
+
+# tools that use truevalue/falsevalue in parameter setting, I think we're going to
+# forbid this for a future tool profile version. Potential ambigouity could result.
+TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION = [
+    "inputs_as_json_profile.xml",
+    "inputs_as_json_with_paths.xml",
+    "inputs_as_json.xml",
+]
+
+TOOLS_THAT_USE_SELECT_BY_VALUE = [
+    "multi_select.xml",
+]
+
+
+TEST_TOOL_THAT_DO_NOT_VALIDATE = (
+    TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS
+    + TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION
+    + TOOLS_THAT_USE_SELECT_BY_VALUE
+    + [
+        # will never handle upload_dataset
+        "upload.xml",
+    ]
+)
+
+MOCK_ID = "thisisafakeid"
+
+
+if sys.version_info < (3, 8):  # noqa: UP036
+    pytest.skip(reason="Pydantic tool parameter models require python3.8 or higher", allow_module_level=True)
+
+
+def test_parameter_test_cases_validate():
+    validation_result = validate_test_cases_for("column_param")
+    assert len(validation_result[0].warnings) == 0
+    assert len(validation_result[1].warnings) == 0
+    assert len(validation_result[2].warnings) == 1
+
+    validation_result = validate_test_cases_for("column_param", use_latest_profile=True)
+    assert validation_result[2].validation_error
+
+
+def test_legacy_features_fail_validation_with_24_2(tmp_path):
+    for filename in TOOLS_THAT_USE_UNQUALIFIED_PARAMETER_ACCESS + TOOLS_THAT_USE_TRUE_FALSE_VALUE_BOOLEAN_SPECIFICATION:
+        _assert_tool_test_parsing_only_fails_with_newer_profile(tmp_path, filename, index=None)
+
+    # column parameters need to be indexes
+    _assert_tool_test_parsing_only_fails_with_newer_profile(tmp_path, "column_param.xml", index=2)
+
+    # selection by value only
+    _assert_tool_test_parsing_only_fails_with_newer_profile(tmp_path, "multi_select.xml", index=1)
+
+
+def _assert_tool_test_parsing_only_fails_with_newer_profile(tmp_path, filename: str, index: Optional[int] = 0):
+    test_tool_directory = functional_test_tool_directory()
+    original_path = os.path.join(test_tool_directory, filename)
+    new_path = tmp_path / filename
+    with open(original_path) as rf:
+        tool_contents = rf.read()
+        tool_contents = re.sub(r'profile="[\d\.]*"', r"", tool_contents)
+        new_profile_contents = tool_contents.replace("<tool ", '<tool profile="24.2" ', 1)
+    with open(new_path, "w") as wf:
+        wf.write(new_profile_contents)
+    test_cases = list(parse_tool_test_descriptions(get_tool_source(original_path)))
+    if index is not None:
+        assert test_cases[index].to_dict()["error"] is False
+    else:
+        # just make sure there is at least one failure...
+        assert not any(c.to_dict()["error"] is True for c in test_cases)
+
+    test_cases = list(parse_tool_test_descriptions(get_tool_source(new_path)))
+    if index is not None:
+        assert (
+            test_cases[index].to_dict()["error"] is True
+        ), f"expected {filename} to have validation failure preventing loading of tools"
+    else:
+        assert any(c.to_dict()["error"] is True for c in test_cases)
+
+
+def test_validate_framework_test_tools():
+    test_tool_directory = functional_test_tool_directory()
+    for tool_name in os.listdir(test_tool_directory):
+        if tool_name in TEST_TOOL_THAT_DO_NOT_VALIDATE:
+            continue
+        if tool_name.endswith("_conf.xml"):
+            # tool conf (toolbox) files or sample datatypes
+            continue
+        tool_path = os.path.join(test_tool_directory, tool_name)
+        if not tool_path.endswith(".xml") or os.path.isdir(tool_path):
+            continue
+
+        try:
+            _validate_path(tool_path)
+        except Exception as e:
+            raise Exception(f"Failed to validate {tool_path}: {str(e)}")
+
+
+def test_test_case_state_conversion():
+    tool_source = tool_source_for("collection_nested_test")
+    test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations: List[Tuple[List[Any], Optional[Any]]]
+    expectations = [
+        (["f1", "collection_type"], "list:paired"),
+        (["f1", "class"], "Collection"),
+        (["f1", "elements", 0, "class"], "Collection"),
+        (["f1", "elements", 0, "collection_type"], "paired"),
+        (["f1", "elements", 0, "elements", 0, "class"], "File"),
+        (["f1", "elements", 0, "elements", 0, "path"], "simple_line.txt"),
+        (["f1", "elements", 0, "elements", 0, "identifier"], "forward"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    tool_source = tool_source_for("dbkey_filter_input")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations = [
+        (["inputs", "class"], "File"),
+        (["inputs", "dbkey"], "hg19"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    tool_source = tool_source_for("discover_metadata_files")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations = [
+        (["input_bam", "class"], "File"),
+        (["input_bam", "filetype"], "bam"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    tool_source = tool_source_for("remote_test_data_location")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations = [
+        (["input", "class"], "File"),
+        (
+            ["input", "location"],
+            "https://raw.githubusercontent.com/galaxyproject/planemo/7be1bf5b3971a43eaa73f483125bfb8cabf1c440/tests/data/hello.txt",
+        ),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    tool_source = tool_source_for("composite")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations = [
+        (["input", "class"], "File"),
+        (["input", "filetype"], "velvet"),
+        (["input", "composite_data", 0], "velveth_test1/Sequences"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    tool_source = tool_source_for("parameters/gx_group_tag")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[0])
+    expectations = [
+        (["ref_parameter", "class"], "Collection"),
+        (["ref_parameter", "collection_type"], "paired"),
+        (["ref_parameter", "elements", 0, "identifier"], "forward"),
+        (["ref_parameter", "elements", 0, "tags", 0], "group:type:single"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    index = 2
+    tool_source = tool_source_for("filter_param_value_ref_attribute")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[index])
+    expectations = [
+        (["data_mult", 0, "path"], "1.bed"),
+        (["data_mult", 0, "dbkey"], "hg19"),
+        (["data_mult", 1, "path"], "2.bed"),
+        (["data_mult", 0, "dbkey"], "hg19"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    index = 1
+    tool_source = tool_source_for("expression_pick_larger_file")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[index])
+    expectations = [
+        (["input1", "path"], "simple_line_alternative.txt"),
+        (["input2"], None),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    index = 2
+    state = case_state_for(tool_source, test_cases[index])
+    expectations = [
+        (["input1"], None),
+        (["input2", "path"], "simple_line.txt"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+    index = 0
+    tool_source = tool_source_for("composite_shapefile")
+    test_cases = tool_source.parse_tests_to_dict()["tests"]
+    state = case_state_for(tool_source, test_cases[index])
+    expectations = [
+        (["input", "filetype"], "shp"),
+        (["input", "composite_data", 0], "shapefile/shapefile.shp"),
+    ]
+    dict_verify_each(state.tool_state.input_state, expectations)
+
+
+def test_convert_to_requests():
+    tools = [
+        "parameters/gx_drill_down_recurse_multiple",
+        "parameters/gx_conditional_select",
+        "expression_pick_larger_file",
+        "identifier_in_conditional",
+        "column_param_list",
+        "composite_shapefile",
+    ]
+    for tool_path in tools:
+        tool_source = tool_source_for(tool_path)
+        parameters = input_models_for_tool_source(tool_source)
+        parsed_tool = parse_tool(tool_source)
+        profile = tool_source.parse_profile()
+        test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]
+
+        def mock_adapt_datasets(input: JsonTestDatasetDefDict) -> DataRequestHda:
+            return DataRequestHda(src="hda", id=MOCK_ID)
+
+        def mock_adapt_collections(input: JsonTestCollectionDefDict) -> DataCollectionRequest:
+            return DataCollectionRequest(src="hdca", id=MOCK_ID)
+
+        for test_case in test_cases:
+            if test_case.get("expect_failure"):
+                continue
+            test_case_state_and_warnings = case_state(test_case, parsed_tool.inputs, profile)
+            test_case_state = test_case_state_and_warnings.tool_state
+
+            encode_test(test_case_state, parameters, mock_adapt_datasets, mock_adapt_collections)
+
+
+def _validate_path(tool_path: str):
+    tool_source = get_tool_source(tool_path)
+    parsed_tool = parse_tool(tool_source)
+    profile = tool_source.parse_profile()
+    test_cases: List[ToolSourceTest] = tool_source.parse_tests_to_dict()["tests"]
+    for test_case in test_cases:
+        if test_case.get("expect_failure"):
+            continue
+        test_case_state_and_warnings = case_state(test_case, parsed_tool.inputs, profile)
+        tool_state = test_case_state_and_warnings.tool_state
+        assert tool_state.state_representation == "test_case_xml"
+
+
+def validate_test_cases_for(tool_name: str, **kwd) -> List[TestCaseStateValidationResult]:
+    return validate_test_cases_for_tool_source(tool_source_for(tool_name), **kwd)
+
+
+def case_state_for(tool_source: ToolSource, test_case: ToolSourceTest) -> TestCaseStateAndWarnings:
+    parsed_tool = parse_tool(tool_source)
+    profile = tool_source.parse_profile()
+    return case_state(test_case, parsed_tool.inputs, profile)
+
+
+def tool_source_for(tool_name: str) -> ToolSource:
+    test_tool_directory = functional_test_tool_directory()
+    tool_path = os.path.join(test_tool_directory, f"{tool_name}.xml")
+    tool_source = get_tool_source(tool_path)
+    return tool_source
diff --git a/test/unit/tool_util/test_parameter_validator_models.py b/test/unit/tool_util/test_parameter_validator_models.py
new file mode 100644
index 0000000000000000000000000000000000000000..17af98f2ce6c45595ebc0ed9274318d0058c882d
--- /dev/null
+++ b/test/unit/tool_util/test_parameter_validator_models.py
@@ -0,0 +1,28 @@
+from typing import Optional
+
+from galaxy.tool_util.parser.parameter_validators import parse_xml_validators
+from galaxy.tool_util.unittest_utils.sample_data import (
+    INVALID_XML_VALIDATORS,
+    VALID_XML_VALIDATORS,
+)
+from galaxy.util import XML
+
+
+def test_xml_validation_valid():
+    for xml_validator in VALID_XML_VALIDATORS:
+        _validate_xml_str(xml_validator)
+
+
+def test_xml_validation_invalid():
+    for xml_validator in INVALID_XML_VALIDATORS:
+        exc: Optional[Exception] = None
+        try:
+            _validate_xml_str(xml_validator)
+        except ValueError as e:
+            exc = e
+        assert exc is not None, f"{xml_validator} - validated when it wasn't expected to"
+
+
+def _validate_xml_str(xml_str: str):
+    xml_el = XML(f"<param>{xml_str}</param>")
+    parse_xml_validators(xml_el)
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index 7550bea601abec6c3bc5887fac67935487c4adf1..21ec92387694d6bd6db0aa9b0cba1def24304a48 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -3,9 +3,22 @@ import os.path
 import shutil
 import tempfile
 from math import isinf
-from typing import Optional
+from typing import (
+    cast,
+    List,
+    Optional,
+    Type,
+    TypeVar,
+)
 
 from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.parser.output_models import (
+    from_tool_source,
+    ToolOutput,
+    ToolOutputCollection,
+    ToolOutputDataset,
+)
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
 from galaxy.util import galaxy_directory
 from galaxy.util.unittest import TestCase
 
@@ -248,11 +261,16 @@ class BaseLoaderTestCase(TestCase):
     def _tool_source(self):
         return self._get_tool_source()
 
+    @property
+    def _output_models(self) -> List[ToolOutput]:
+        return from_tool_source(self._tool_source)
+
     def _get_tool_source(self, source_file_name=None, source_contents=None, macro_contents=None):
         if source_file_name is None:
-            source_file_name = self.source_file_name
+            source_file_name = self._get_source_file_name()
         if source_contents is None:
             source_contents = self.source_contents
+
         return get_test_tool_source(
             source_file_name,
             source_contents,
@@ -260,6 +278,10 @@ class BaseLoaderTestCase(TestCase):
             self.temp_directory,
         )
 
+    def _get_source_file_name(self) -> str:
+        assert self.source_file_name
+        return self.source_file_name
+
 
 class TestXmlExpressionLoader(BaseLoaderTestCase):
     source_file_name = "expression.xml"
@@ -350,7 +372,7 @@ class TestXmlLoader(BaseLoaderTestCase):
         assert isinf(exit[0].range_end)
 
     def test_help(self):
-        help_text = self._tool_source.parse_help()
+        help_text = self._tool_source.parse_help().content
         assert help_text.strip() == "This is HELP TEXT1!!!"
 
     def test_tests(self):
@@ -383,6 +405,16 @@ class TestXmlLoader(BaseLoaderTestCase):
         assert attributes1["compare"] == "sim_size"
         assert attributes1["lines_diff"] == 4
 
+    def test_output_models(self):
+        output_models = self._output_models
+        assert len(output_models) == 1
+        output_model = output_models[0]
+        assert output_model.name == "out1"
+        assert not output_model.hidden
+        assert output_model.label is None
+        output_dataset_model = assert_output_model_of_type(output_model, ToolOutputDataset)
+        assert output_dataset_model.metadata_source is None
+
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
         assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
@@ -547,7 +579,7 @@ class TestYamlLoader(BaseLoaderTestCase):
         assert isinf(exit[1].range_end)
 
     def test_help(self):
-        help_text = self._tool_source.parse_help()
+        help_text = self._tool_source.parse_help().content
         assert help_text.strip() == "This is HELP TEXT2!!!"
 
     def test_inputs(self):
@@ -661,6 +693,17 @@ class TestApplyRulesToolLoader(BaseLoaderTestCase):
         assert len(outputs) == 1
         assert len(output_collections) == 1
 
+    def test_output_models(self):
+        output_models = self._output_models
+        assert len(output_models) == 1
+        output_model = output_models[0]
+        assert output_model.name == "output"
+        assert not output_model.hidden
+        assert output_model.label == "${input.name} (re-organized)"
+        output_collection_model = assert_output_model_of_type(output_model, ToolOutputCollection)
+        structure = output_collection_model.structure
+        assert structure.collection_type_from_rules == "rules"
+
 
 class TestBuildListToolLoader(BaseLoaderTestCase):
     source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/build_list.xml")
@@ -672,9 +715,16 @@ class TestBuildListToolLoader(BaseLoaderTestCase):
         assert tool_module[1] == "BuildListCollectionTool"
 
 
-class TestExpressionTestToolLoader(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/expression_null_handling_boolean.xml")
-    source_contents = None
+class FunctionalTestToolTestCase(BaseLoaderTestCase):
+    test_path: str
+    source_contents: None
+
+    def _get_source_file_name(self) -> str:
+        return functional_test_tool_path(self.test_path)
+
+
+class TestExpressionTestToolLoader(FunctionalTestToolTestCase):
+    test_path = "expression_null_handling_boolean.xml"
 
     def test_test(self):
         test_dicts = self._tool_source.parse_tests_to_dict()["tests"]
@@ -700,10 +750,17 @@ class TestExpressionTestToolLoader(BaseLoaderTestCase):
         assert "object" in output0["attributes"]
         assert output0["attributes"]["object"] is None
 
+    def test_output_models(self):
+        output_models = self._output_models
+        assert len(output_models) == 1
+        output_model = output_models[0]
+        assert output_model.name == "bool_out"
+        assert not output_model.hidden
+        assert output_model.label is None
 
-class TestDefaultDataTestToolLoader(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/for_workflows/cat_default.xml")
-    source_contents = None
+
+class TestDefaultDataTestToolLoader(FunctionalTestToolTestCase):
+    test_path = "for_workflows/cat_default.xml"
 
     def test_input_parsing(self):
         input_pages = self._tool_source.parse_input_pages()
@@ -719,9 +776,8 @@ class TestDefaultDataTestToolLoader(BaseLoaderTestCase):
         assert default_dict["location"] == "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed"
 
 
-class TestDefaultCollectionDataTestToolLoader(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_paired_default.xml")
-    source_contents = None
+class TestDefaultCollectionDataTestToolLoader(FunctionalTestToolTestCase):
+    test_path = "collection_paired_default.xml"
 
     def test_input_parsing(self):
         input_pages = self._tool_source.parse_input_pages()
@@ -745,9 +801,8 @@ class TestDefaultCollectionDataTestToolLoader(BaseLoaderTestCase):
         assert element1["location"] == "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.fasta"
 
 
-class TestDefaultNestedCollectionDataTestToolLoader(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_nested_default.xml")
-    source_contents = None
+class TestDefaultNestedCollectionDataTestToolLoader(FunctionalTestToolTestCase):
+    test_path = "collection_nested_default.xml"
 
     def test_input_parsing(self):
         input_pages = self._tool_source.parse_input_pages()
@@ -774,9 +829,8 @@ class TestDefaultNestedCollectionDataTestToolLoader(BaseLoaderTestCase):
         assert elements01["identifier"] == "reverse"
 
 
-class TestExpressionOutputDataToolLoader(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/expression_pick_larger_file.xml")
-    source_contents = None
+class TestExpressionOutputDataToolLoader(FunctionalTestToolTestCase):
+    test_path = "expression_pick_larger_file.xml"
 
     def test_output_parsing(self):
         outputs, _ = self._tool_source.parse_outputs(None)
@@ -808,9 +862,8 @@ class TestSpecialToolLoader(BaseLoaderTestCase):
         assert action[1] == "ExportHistoryToolAction"
 
 
-class TestCollection(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_two_paired.xml")
-    source_contents = None
+class TestCollection(FunctionalTestToolTestCase):
+    test_path = "collection_two_paired.xml"
 
     def test_tests(self):
         tests_dict = self._tool_source.parse_tests_to_dict()
@@ -822,27 +875,24 @@ class TestCollection(BaseLoaderTestCase):
         assert len(output_collections) == 0
 
 
-class TestCollectionOutputXml(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair.xml")
-    source_contents = None
+class TestCollectionOutputXml(FunctionalTestToolTestCase):
+    test_path = "collection_creates_pair.xml"
 
     def test_tests(self):
         outputs, output_collections = self._tool_source.parse_outputs(None)
         assert len(output_collections) == 1
 
 
-class TestCollectionOutputYaml(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair_y.yml")
-    source_contents = None
+class TestCollectionOutputYaml(FunctionalTestToolTestCase):
+    test_path = "collection_creates_pair_y.yml"
 
     def test_tests(self):
         outputs, output_collections = self._tool_source.parse_outputs(None)
         assert len(output_collections) == 1
 
 
-class TestEnvironmentVariables(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/environment_variables.xml")
-    source_contents = None
+class TestEnvironmentVariables(FunctionalTestToolTestCase):
+    test_path = "environment_variables.xml"
 
     def test_tests(self):
         tests_dict = self._tool_source.parse_tests_to_dict()
@@ -850,9 +900,8 @@ class TestEnvironmentVariables(BaseLoaderTestCase):
         assert len(tests) == 1
 
 
-class TestExpectations(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/detect_errors.xml")
-    source_contents = None
+class TestExpectations(FunctionalTestToolTestCase):
+    test_path = "detect_errors.xml"
 
     def test_tests(self):
         tests_dict = self._tool_source.parse_tests_to_dict()
@@ -863,9 +912,8 @@ class TestExpectations(BaseLoaderTestCase):
         assert len(test_0["stdout"]) == 2
 
 
-class TestExpectationsCommandVersion(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/job_properties.xml")
-    source_contents = None
+class TestExpectationsCommandVersion(FunctionalTestToolTestCase):
+    test_path = "job_properties.xml"
 
     def test_tests(self):
         tests_dict = self._tool_source.parse_tests_to_dict()
@@ -875,9 +923,8 @@ class TestExpectationsCommandVersion(BaseLoaderTestCase):
         assert len(test_0["command_version"]) == 1
 
 
-class TestQcStdio(BaseLoaderTestCase):
-    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/qc_stdout.xml")
-    source_contents = None
+class TestQcStdio(FunctionalTestToolTestCase):
+    test_path = "qc_stdout.xml"
 
     def test_tests(self):
         exit, regexes = self._tool_source.parse_stdio()
@@ -885,3 +932,43 @@ class TestQcStdio(BaseLoaderTestCase):
         assert len(regexes) == 2
         regex = regexes[0]
         assert regex.error_level == 1.1
+
+
+class TestCollectionCatGroupTag(FunctionalTestToolTestCase):
+    test_path = "collection_cat_group_tag.xml"
+
+    def test_output_models(self):
+        output_models = self._output_models
+        assert len(output_models) == 1
+        output_model = output_models[0]
+        assert output_model.name == "out_file1"
+        assert not output_model.hidden
+        assert output_model.label is None
+        output_dataset_model = assert_output_model_of_type(output_model, ToolOutputDataset)
+        assert output_dataset_model.metadata_source == "input1"
+
+
+class TestToolProvidedMetadata2(FunctionalTestToolTestCase):
+    test_path = "tool_provided_metadata_2.xml"
+
+    def test_output_models(self):
+        output_models = self._output_models
+        assert len(output_models) == 1
+        output_model = output_models[0]
+        assert output_model.name == "sample"
+        assert not output_model.hidden
+        assert output_model.label is None
+        output_dataset_model = assert_output_model_of_type(output_model, ToolOutputDataset)
+        assert output_dataset_model.metadata_source is None
+        discover_datasets = output_dataset_model.discover_datasets or []
+        assert len(discover_datasets) == 1
+        discover_datasets_0 = discover_datasets[0]
+        assert discover_datasets_0.discover_via == "pattern"
+
+
+T = TypeVar("T")
+
+
+def assert_output_model_of_type(obj, clazz: Type[T]) -> T:
+    assert isinstance(obj, clazz)
+    return cast(T, obj)
diff --git a/test/unit/tool_util/test_test_definition_parsing.py b/test/unit/tool_util/test_test_definition_parsing.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed5fbdaaee91199667a3147f8aa25cd8c0c06c0a
--- /dev/null
+++ b/test/unit/tool_util/test_test_definition_parsing.py
@@ -0,0 +1,137 @@
+"""Tool test parsing to dicts logic."""
+
+import os
+from typing import (
+    Any,
+    List,
+)
+
+from pytest import skip
+
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
+from galaxy.tool_util.verify.parse import parse_tool_test_descriptions
+from galaxy.util import (
+    galaxy_directory,
+    in_packages,
+)
+from galaxy.util.unittest import TestCase
+from .util import dict_verify_each
+
+# Not the whole response, just some keys and such to test...
+SIMPLE_CONSTRUCTS_EXPECTATIONS_0 = [
+    (["inputs", "booltest"], [True]),
+    (["inputs", "inttest"], ["12456"]),
+    (["inputs", "floattest"], ["6.789"]),
+    (["inputs", "p1|p1use"], [True]),
+    (["inputs", "files_0|file"], ["simple_line.txt"]),
+    (["outputs", 0, "name"], "out_file1"),
+    (["required_files", 0, 0], "simple_line.txt"),
+    (["required_files", 0, 1, "value"], "simple_line.txt"),
+]
+# this test case covers specifying boolean parameters by string truevalue/falsevalue
+SIMPLE_CONSTRUCTS_EXPECTATIONS_1 = [
+    (["inputs", "booltest"], [True]),
+    (["inputs", "p1|p1use"], [True]),
+    (["inputs", "files_0|file"], ["simple_line.txt"]),
+    (["outputs", 0, "name"], "out_file1"),
+]
+SECTION_EXPECTATIONS = [
+    (["inputs", "int|inttest"], ["12456"]),
+    (["inputs", "float|floattest"], ["6.789"]),
+]
+MIN_REPEAT_EXPECTATIONS = [
+    (["inputs", "queries_0|input"], ["simple_line.txt"]),
+    (["inputs", "queries_1|input"], ["simple_line.txt"]),
+    (["inputs", "queries2_0|input2"], ["simple_line_alternative.txt"]),
+]
+DBKEY_FILTER_INPUT_EXPECTATIONS = [
+    (["inputs", "inputs"], ["simple_line.txt"]),
+    (["inputs", "index"], ["hg19_value"]),
+    (["required_files", 0, 1, "dbkey"], "hg19"),
+    (["required_data_tables", 0], "test_fasta_indexes"),
+]
+COLLECTION_TYPE_SOURCE_EXPECTATIONS = [
+    (["inputs", "input_collect", "model_class"], "TestCollectionDef"),
+    (["inputs", "input_collect", "collection_type"], "list"),
+]
+BIGWIG_TO_WIG_EXPECTATIONS = [
+    (["inputs", "chrom"], "chr21"),
+]
+
+
+class TestTestParsing(TestCase):
+    def _parse_tests(self):
+        return parse_tool_test_descriptions(self.tool_source)
+
+    def _init_tool_for_path(self, path):
+        tool_source = get_tool_source(path)
+        self.tool_source = tool_source
+
+    def test_maxseconds_not_filled_with_default(self):
+        self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
+        test_dicts = list(self._parse_tests())
+        assert test_dicts[0].maxseconds is None
+        assert "maxseconds" not in test_dicts[0].to_dict()
+
+    def test_maxseconds_parsed(self):
+        self._init_tool_for_path(functional_test_tool_path("maxseconds.xml"))
+        test_def = next(iter(self._parse_tests()))
+        assert test_def.maxseconds == 5
+        test_dict = test_def.to_dict()
+        print(test_dict)
+        assert "maxseconds" in test_dict
+        assert test_dict["maxseconds"] == 5
+
+    def test_simple_state_parsing(self):
+        self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
+        test_dicts = self._parse_tests()
+        self._verify_each(test_dicts[0].to_dict(), SIMPLE_CONSTRUCTS_EXPECTATIONS_0)
+        self._verify_each(test_dicts[1].to_dict(), SIMPLE_CONSTRUCTS_EXPECTATIONS_1)
+
+    def test_section_state_parsing(self):
+        self._init_tool_for_path(functional_test_tool_path("section.xml"))
+        test_dicts = self._parse_tests()
+        # without and with section tags in the tests...
+        self._verify_each(test_dicts[0].to_dict(), SECTION_EXPECTATIONS)
+        self._verify_each(test_dicts[1].to_dict(), SECTION_EXPECTATIONS)
+
+    def test_repeat_state_parsing(self):
+        self._init_tool_for_path(functional_test_tool_path("min_repeat.xml"))
+        test_dicts = self._parse_tests()
+        # without and with section tags in the tests...
+        self._verify_each(test_dicts[0].to_dict(), MIN_REPEAT_EXPECTATIONS)
+
+    def test_dynamic_options_data_table_parsing(self):
+        self._init_tool_for_path(functional_test_tool_path("dbkey_filter_input.xml"))
+        test_dicts = self._parse_tests()
+        self._verify_each(test_dicts[0].to_dict(), DBKEY_FILTER_INPUT_EXPECTATIONS)
+
+    def test_collection_type_source_parsing(self):
+        self._init_tool_for_path(functional_test_tool_path("collection_type_source.xml"))
+        test_dicts = self._parse_tests()
+        self._verify_each(test_dicts[0].to_dict(), COLLECTION_TYPE_SOURCE_EXPECTATIONS)
+
+    def test_unqualified_access_disabled_in_24_2(self):
+        self._init_tool_for_path(functional_test_tool_path("deprecated/simple_constructs_24_2.xml"))
+        test_dicts = self._parse_tests()
+        test_0 = test_dicts[0].to_dict()
+        assert test_0["error"] is True
+
+    def test_bigwigtowig_converter(self):
+        # defines
+        if in_packages():
+            skip(
+                "skipping this mode for now - we need a framework test tool that skips names and just specifies arguments"
+            )
+        tool_path = os.path.join(
+            galaxy_directory(), "lib", "galaxy", "datatypes", "converters", "bigwig_to_wig_converter.xml"
+        )
+        self._init_tool_for_path(tool_path)
+        test_dicts = self._parse_tests()
+        self._verify_each(test_dicts[1].to_dict(), BIGWIG_TO_WIG_EXPECTATIONS)
+
+    def _verify_each(self, target_dict: dict, expectations: List[Any]):
+        exception = target_dict.get("exception")
+        assert not exception, f"Test failed to generate with exception {exception}"
+        dict_verify_each(target_dict, expectations)
diff --git a/test/unit/tool_util/test_test_format_model.py b/test/unit/tool_util/test_test_format_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..986f5c12ba87d32b66d47fc52338cc7a85bdf27a
--- /dev/null
+++ b/test/unit/tool_util/test_test_format_model.py
@@ -0,0 +1,39 @@
+import os
+from pathlib import Path
+from typing import List
+
+import yaml
+
+from galaxy.tool_util.models import Tests
+from galaxy.util import galaxy_directory
+from galaxy.util.unittest_utils import skip_unless_environ
+
+TEST_WORKFLOW_DIRECTORY = os.path.join(galaxy_directory(), "lib", "galaxy_test", "workflow")
+IWC_WORKFLOWS_USING_UNVERIFIED_SYNTAX: List[str] = []
+
+
+def test_validate_workflow_tests():
+    path = Path(TEST_WORKFLOW_DIRECTORY)
+    test_files = path.glob("*.gxwf-tests.yml")
+    for test_file in test_files:
+        with open(test_file) as f:
+            json = yaml.safe_load(f)
+        Tests.model_validate(json)
+
+
+@skip_unless_environ("GALAXY_TEST_IWC_DIRECTORY")
+def test_iwc_directory():
+    path = Path(os.environ["GALAXY_TEST_IWC_DIRECTORY"])
+    test_files = path.glob("workflows/**/*-test*.yml")
+
+    for test_file in test_files:
+        print(test_file)
+        skip_file = False
+        for unverified in IWC_WORKFLOWS_USING_UNVERIFIED_SYNTAX:
+            if str(test_file).endswith(unverified):
+                skip_file = True
+        if skip_file:
+            continue
+        with open(test_file) as f:
+            json = yaml.safe_load(f)
+        Tests.model_validate(json)
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 7e6d3b62ec93837cc29be4cda7c3f53637e9491e..92de05d8ab68764db6003ab1b8b9172b25a4b41a 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -16,6 +16,7 @@ from galaxy.tool_util.lint import (
 from galaxy.tool_util.linters import (
     citations,
     command,
+    datatypes,
     general,
     help,
     inputs,
@@ -26,7 +27,9 @@ from galaxy.tool_util.linters import (
     xsd,
 )
 from galaxy.tool_util.loader_directory import load_tool_sources_from_path
+from galaxy.tool_util.parser.interface import ToolSource
 from galaxy.tool_util.parser.xml import XmlToolSource
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
 from galaxy.util import (
     ElementTree,
     submodules,
@@ -638,15 +641,31 @@ OUTPUTS_DUPLICATED_NAME_LABEL = """
         <data name="valid_name" format="fasta"/>
         <data name="valid_name" format="fasta"/>
         <data name="another_valid_name" format="fasta" label="same label may be OK if there is a filter">
-            <filter>a condition</filter>
+            <filter>a and condition</filter>
         </data>
         <data name="yet_another_valid_name" format="fasta" label="same label may be OK if there is a filter">
-            <filter>another condition</filter>
+            <filter>another or condition</filter>
         </data>
     </outputs>
 </tool>
 """
 
+# check if filters are valid python expressions
+OUTPUTS_FILTER_EXPRESSION = """
+<tool id="id" name="name">
+    <outputs>
+        <data name="another_valid_name" format="fasta" label="a label">
+            <filter>an invalid condition</filter>
+            <filter> an and condition </filter>
+        </data>
+        <collection name="yet_another_valid_name" type="list" format="fasta" label="another label">
+            <filter>another invalid condition</filter>
+            <filter>another or condition</filter>
+        </collection>
+    </outputs>
+</tool>
+"""
+
 # tool xml for repeats linter
 REPEATS = """
 <tool id="id" name="name">
@@ -698,6 +717,11 @@ STDIO_INVALID_MATCH = """
 TESTS_ABSENT = """
 <tool id="id" name="name"/>
 """
+TESTS_ABSENT_YAML = """
+class: GalaxyTool
+name: name
+id: id
+"""
 TESTS_ABSENT_DATA_SOURCE = """
 <tool id="id" name="name" tool_type="data_source"/>
 """
@@ -794,6 +818,38 @@ ASSERTS = """
     </tests>
 </tool>
 """
+INVALID_CENTER_OF_MASS = """
+<tool id="id" name="name">
+    <outputs>
+        <data name="out_image"/>
+    </outputs>
+    <tests>
+        <test>
+            <output name="out_image">
+                <assert_contents>
+                    <has_image_center_of_mass center_of_mass="511.07, 223.34, 2.3" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
+"""
+VALID_CENTER_OF_MASS = """
+<tool id="id" name="name">
+    <outputs>
+        <data name="out_image"/>
+    </outputs>
+    <tests>
+        <test>
+            <output name="out_image">
+                <assert_contents>
+                    <has_image_center_of_mass center_of_mass="511.07, 223.34" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
+"""
 TESTS_VALID = """
 <tool id="id" name="name">
     <outputs>
@@ -801,7 +857,7 @@ TESTS_VALID = """
     </outputs>
     <tests>
         <test>
-            <output name="test"/>
+            <output name="test" value="empty.txt" />
         </test>
     </tests>
 </tool>
@@ -950,6 +1006,19 @@ def get_xml_tool_source(xml_string: str) -> XmlToolSource:
     return XmlToolSource(get_xml_tree(xml_string))
 
 
+def get_tool_source(source_contents: str) -> ToolSource:
+    if "GalaxyTool" in source_contents:
+        with tempfile.NamedTemporaryFile(mode="w", suffix="tool.yml") as tmp:
+            tmp.write(source_contents)
+            tmp.flush()
+            tool_sources = load_tool_sources_from_path(tmp.name)
+            assert len(tool_sources) == 1, "Expected 1 tool source"
+            tool_source = tool_sources[0][1]
+            return tool_source
+    else:
+        return get_xml_tool_source(source_contents)
+
+
 def run_lint_module(lint_ctx, lint_module, lint_target):
     lint_tool_source_with_modules(lint_ctx, lint_target, list({lint_module, xsd}))
 
@@ -1678,6 +1747,25 @@ def test_outputs_duplicated_name_label(lint_ctx):
     assert len(lint_ctx.error_messages) == 1
 
 
+def test_outputs_filter_expression(lint_ctx):
+    """ """
+    tool_source = get_xml_tool_source(OUTPUTS_FILTER_EXPRESSION)
+    run_lint_module(lint_ctx, output, tool_source)
+    assert "2 outputs found." in lint_ctx.info_messages
+    assert len(lint_ctx.info_messages) == 1
+    assert not lint_ctx.valid_messages
+    assert (
+        "Filter 'another invalid condition' is no valid expression: invalid syntax (<unknown>, line 1)"
+        in lint_ctx.warn_messages
+    )
+    assert (
+        "Filter 'another invalid condition' is no valid expression: invalid syntax (<unknown>, line 1)"
+        in lint_ctx.warn_messages
+    )
+    assert len(lint_ctx.warn_messages) == 2
+    assert not lint_ctx.error_messages
+
+
 def test_stdio_default_for_default_profile(lint_ctx):
     tool_source = get_xml_tool_source(STDIO_DEFAULT_FOR_DEFAULT_PROFILE)
     run_lint_module(lint_ctx, stdio, tool_source)
@@ -1751,13 +1839,14 @@ def test_stdio_invalid_match(lint_ctx):
 
 
 def test_tests_absent(lint_ctx):
-    tool_source = get_xml_tool_source(TESTS_ABSENT)
-    run_lint_module(lint_ctx, tests, tool_source)
-    assert "No tests found, most tools should define test cases." in lint_ctx.warn_messages
-    assert not lint_ctx.info_messages
-    assert not lint_ctx.valid_messages
-    assert len(lint_ctx.warn_messages) == 1
-    assert not lint_ctx.error_messages
+    for test_contents in [TESTS_ABSENT, TESTS_ABSENT_YAML]:
+        tool_source = get_tool_source(test_contents)
+        run_lint_module(lint_ctx, tests, tool_source)
+        assert "No tests found, most tools should define test cases." in lint_ctx.warn_messages
+        assert not lint_ctx.info_messages
+        assert not lint_ctx.valid_messages
+        assert len(lint_ctx.warn_messages) == 1
+        assert not lint_ctx.error_messages
 
 
 def test_tests_data_source(lint_ctx):
@@ -1791,7 +1880,6 @@ def test_tests_param_output_names(lint_ctx):
     )
     assert not lint_ctx.info_messages
     assert len(lint_ctx.valid_messages) == 1
-    assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 6
 
 
@@ -1806,7 +1894,7 @@ def test_tests_expect_failure_output(lint_ctx):
     )
     assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
-    assert len(lint_ctx.warn_messages) == 1
+    assert len(lint_ctx.warn_messages) == 3
     assert len(lint_ctx.error_messages) == 2
 
 
@@ -1854,10 +1942,24 @@ def test_tests_asserts(lint_ctx):
     assert "Test 1: 'has_size' must not specify 'value' and 'size'" in lint_ctx.error_messages
     assert "Test 1: 'has_n_columns' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
     assert "Test 1: 'has_n_lines' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
-    assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 9
 
 
+def test_tests_assertion_models_valid(lint_ctx):
+    tool_source = get_xml_tool_source(VALID_CENTER_OF_MASS)
+    run_lint_module(lint_ctx, tests, tool_source)
+    assert len(lint_ctx.error_messages) == 0
+    assert len(lint_ctx.warn_messages) == 0
+
+
+def test_tests_assertion_models_invalid(lint_ctx):
+    tool_source = get_xml_tool_source(INVALID_CENTER_OF_MASS)
+    run_lint_module(lint_ctx, tests, tool_source)
+    assert len(lint_ctx.error_messages) == 0
+    assert len(lint_ctx.warn_messages) == 1
+    assert "Test 1: failed to validate assertions. Validation errors are " in lint_ctx.warn_messages
+
+
 def test_tests_output_type_mismatch(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_OUTPUT_TYPE_MISMATCH)
     run_lint_module(lint_ctx, tests, tool_source)
@@ -1869,7 +1971,6 @@ def test_tests_output_type_mismatch(lint_ctx):
         "Test 1: test collection output 'data_name' does not correspond to a 'output_collection' output, but a 'data'"
         in lint_ctx.error_messages
     )
-    assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 2
 
 
@@ -1892,7 +1993,6 @@ def test_tests_discover_outputs(lint_ctx):
         "Test 5: test collection 'collection_name' must contain nested 'element' tags and/or element children with a 'count' attribute"
         in lint_ctx.error_messages
     )
-    assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 4
 
 
@@ -1911,7 +2011,6 @@ def test_tests_compare_attrib_incompatibility(lint_ctx):
     assert 'Test 1: Attribute sort is incompatible with compare="contains".' in lint_ctx.error_messages
     assert not lint_ctx.info_messages
     assert len(lint_ctx.valid_messages) == 1
-    assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 2
 
 
@@ -1924,6 +2023,72 @@ def test_xml_order(lint_ctx):
     assert lint_ctx.error_messages == ["Invalid XML: Element 'wrong_tag': This element is not expected."]
 
 
+VALID_DATATYPES = """
+<tool id="id" name="name">
+    <inputs>
+        <param name="adata" type="data" format="txt"/>
+        <param name="bdata" type="data" format="invalid,fasta,custom"/>
+        <param name="fdata" type="data" format="fasta.gz"/>
+        <param name="auto_input" type="data" format="auto"/>
+    </inputs>
+    <outputs>
+        <data name="autoformat" format="auto"/>
+        <data name="name" format="another_invalid">
+            <change_format>
+                <when input="input_text" value="foo" format="just_another_invalid"/>
+            </change_format>
+        </data>
+        <collection name="collection_name" format="collection_format">
+            <discover_datasets format="txt"/>
+            <discover_datasets ext="invalid"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="adata" ftype="txt"/>
+            <param name="bdata" ftype="invalid"/>
+            <param name="auto_test_input" ftype="auto"/>
+        </test>
+    </tests>
+</tool>
+"""
+DATATYPES_CONF = """
+<datatypes>
+    <registration>
+        <datatype extension="custom"/>
+    </registration>
+</datatypes>
+"""
+
+
+def test_valid_datatypes(lint_ctx):
+    """
+    test datatypes linters
+    """
+    with tempfile.TemporaryDirectory() as tmp:
+        tool_path = os.path.join(tmp, "tool.xml")
+        datatypes_path = os.path.join(tmp, "datatypes_conf.xml")
+        with open(tool_path, "w") as tmpf:
+            tmpf.write(VALID_DATATYPES)
+        with open(datatypes_path, "w") as tmpf:
+            tmpf.write(DATATYPES_CONF)
+        tool_xml, _ = load_with_references(tool_path)
+        tool_source = XmlToolSource(tool_xml, source_path=tool_path)
+        run_lint_module(lint_ctx, datatypes, tool_source)
+    assert not lint_ctx.info_messages
+    assert not lint_ctx.valid_messages
+    assert "Tool uses a custom datatypes_conf.xml which is discouraged" in lint_ctx.warn_messages
+    assert len(lint_ctx.warn_messages) == 1
+    assert "Unknown datatype [invalid] used in param" in lint_ctx.error_messages
+    assert "Unknown datatype [another_invalid] used in data" in lint_ctx.error_messages
+    assert "Unknown datatype [just_another_invalid] used in when" in lint_ctx.error_messages
+    assert "Unknown datatype [collection_format] used in collection" in lint_ctx.error_messages
+    assert "Unknown datatype [invalid] used in param" in lint_ctx.error_messages
+    assert "Unknown datatype [invalid] used in discover_datasets" in lint_ctx.error_messages
+    assert "Format [auto] can not be used for tool or tool test inputs" in lint_ctx.error_messages  # 2x
+    assert len(lint_ctx.error_messages) == 8
+
+
 DATA_MANAGER = """<tool id="test_dm" name="test dm" version="1" tool_type="manage_data">
     <inputs>
         <param name="select" type="select">
@@ -2077,14 +2242,8 @@ outputs:
 
 
 def test_linting_yml_tool(lint_ctx):
-    with tempfile.TemporaryDirectory() as tmp:
-        tool_path = os.path.join(tmp, "tool.yml")
-        with open(tool_path, "w") as tmpf:
-            tmpf.write(YAML_TOOL)
-        tool_sources = load_tool_sources_from_path(tmp)
-        assert len(tool_sources) == 1, "Expected 1 tool source"
-        tool_source = tool_sources[0][1]
-        lint_tool_source_with(lint_ctx, tool_source)
+    tool_source = get_tool_source(YAML_TOOL)
+    lint_tool_source_with(lint_ctx, tool_source)
     assert "Tool defines a version [1.0]." in lint_ctx.valid_messages
     assert "Tool defines a name [simple_constructs_y]." in lint_ctx.valid_messages
     assert "Tool defines an id [simple_constructs_y]." in lint_ctx.valid_messages
@@ -2145,7 +2304,7 @@ def test_skip_by_module(lint_ctx):
 def test_list_linters():
     linter_names = Linter.list_listers()
     # make sure to add/remove a test for new/removed linters if this number changes
-    assert len(linter_names) == 132
+    assert len(linter_names) == 137
     assert "Linter" not in linter_names
     # make sure that linters from all modules are available
     for prefix in [
@@ -2164,6 +2323,23 @@ def test_list_linters():
         assert len([x for x in linter_names if x.startswith(prefix)])
 
 
+def test_linting_functional_tool_multi_select(lint_ctx):
+    tool_source = functional_test_tool_source("multi_select.xml")
+    run_lint_module(lint_ctx, tests, tool_source)
+    warn_message = lint_ctx.warn_messages[0]
+    assert (
+        "Test 2: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [5 validation errors for"
+        in str(warn_message)
+    )
+
+
+def functional_test_tool_source(name: str) -> ToolSource:
+    tool_sources = load_tool_sources_from_path(functional_test_tool_path(name))
+    assert len(tool_sources) == 1, "Expected 1 tool source"
+    tool_source = tool_sources[0][1]
+    return tool_source
+
+
 def test_linter_module_list():
     linter_modules = submodules.import_submodules(galaxy.tool_util.linters)
     linter_module_names = [m.__name__.split(".")[-1] for m in linter_modules]
diff --git a/test/unit/tool_util/upgrade/__init__.py b/test/unit/tool_util/upgrade/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/test/unit/tool_util/upgrade/test_upgrade_advice.py b/test/unit/tool_util/upgrade/test_upgrade_advice.py
new file mode 100644
index 0000000000000000000000000000000000000000..3fbd06359288ecb8b6c71fd0aa1129f328706e87
--- /dev/null
+++ b/test/unit/tool_util/upgrade/test_upgrade_advice.py
@@ -0,0 +1,174 @@
+# Not yet tested:
+# - 21_09_fix_from_work_dir_whitespace
+# - 23_0_consider_optional_text
+import os
+from typing import List
+
+import pytest
+
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
+from galaxy.tool_util.upgrade import (
+    Advice,
+    advise_on_upgrade,
+    TARGET_TOO_NEW,
+)
+
+FUTURE_GALAXY_VERSION = "29.6"
+
+
+def test_does_not_work_on_non_xml_tools():
+    simple_constructs = _tool_path("simple_constructs.yml")
+    with pytest.raises(Exception) as e:
+        advise_on_upgrade(simple_constructs, "16.04")
+    assert "XML tools" in str(e)
+
+
+def test_does_not_work_on_versions_too_new():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    with pytest.raises(Exception) as e:
+        advise_on_upgrade(simple_constructs, FUTURE_GALAXY_VERSION)
+    assert TARGET_TOO_NEW in str(e)
+
+
+def test_old_advice_does_not_appear_when_upgrading_past_it():
+    a_16_01_tool = _tool_path("tool_provided_metadata_1.xml")
+    advice = advise_on_upgrade(a_16_01_tool)
+    assert_has_advice(advice, "16_04_consider_implicit_extra_file_collection")
+
+    a_17_09_tool = _tool_path("tool_provided_metadata_6.xml")
+    advice = advise_on_upgrade(a_17_09_tool)
+    assert_not_has_advice(advice, "16_04_consider_implicit_extra_file_collection")
+
+
+def test_interpreter_advice_positive():
+    legacy_interpreter = _tool_path("legacy_interpreter.xml")
+    advice = advise_on_upgrade(legacy_interpreter, "16.04")
+    assert_has_advice(advice, "16_04_fix_interpreter")
+    assert_not_has_advice(advice, "16_04_ready_interpreter")
+
+
+def test_interpreter_advice_negative():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs, "16.04")
+    assert_not_has_advice(advice, "16_04_fix_interpreter")
+    assert_has_advice(advice, "16_04_ready_interpreter")
+
+
+def test_output_format_advice_positive():
+    output_format = _tool_path("output_format.xml")
+    advice = advise_on_upgrade(output_format, "16.04")
+    assert_has_advice(advice, "16_04_fix_output_format")
+
+
+def test_20_05_inputs_changes():
+    inputs_as_json = _tool_path("inputs_as_json.xml")
+    advice = advise_on_upgrade(inputs_as_json)
+    assert_has_advice(advice, "20_05_consider_inputs_as_json_changes")
+
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_not_has_advice(advice, "20_05_consider_inputs_as_json_changes")
+
+
+def test_output_format_advice_negative():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs, "16.04")
+    assert_not_has_advice(advice, "16_04_fix_output_format")
+
+
+def test_consider_implicit_extra_file_collection():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs, "16.04")
+    assert_has_advice(advice, "16_04_consider_implicit_extra_file_collection")
+
+
+def test_consider_stdio():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs, "16.04")
+    assert_has_advice(advice, "16_04_exit_code")
+
+    a_17_09_tool = _tool_path("tool_provided_metadata_6.xml")
+    advice = advise_on_upgrade(a_17_09_tool)
+    assert_not_has_advice(advice, "16_04_exit_code")
+
+
+def test_2009_output_collection_advice_positive():
+    collection_creates_list = _tool_path("collection_creates_list.xml")
+    advice = advise_on_upgrade(collection_creates_list)
+    assert_has_advice(advice, "20_09_consider_output_collection_order")
+
+
+def test_2009_output_collection_advice_negative():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_not_has_advice(advice, "20_09_consider_output_collection_order")
+
+
+def test_2009_consider_strict_shell_positive():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_has_advice(advice, "20_09_consider_set_e")
+
+
+def test_1801_consider_home_directory():
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_has_advice(advice, "18_01_consider_home_directory")
+
+
+def test_1801_consider_structured_like():
+    simple_constructs = _tool_path("collection_paired_conditional_structured_like.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_has_advice(advice, "18_01_consider_structured_like")
+
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_not_has_advice(advice, "18_01_consider_structured_like")
+
+
+def test_21_09_data_source_advice():
+    test_data_source = _tool_path("test_data_source.xml")
+    advice = advise_on_upgrade(test_data_source)
+    assert_has_advice(advice, "21_09_consider_python_environment")
+
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_not_has_advice(advice, "21_09_consider_python_environment")
+
+
+def test_24_0_request_cleaning():
+    test_data_source = _tool_path("test_data_source.xml")
+    advice = advise_on_upgrade(test_data_source)
+    assert_has_advice(advice, "24_0_request_cleaning")
+
+    simple_constructs = _tool_path("simple_constructs.xml")
+    advice = advise_on_upgrade(simple_constructs)
+    assert_not_has_advice(advice, "24_0_request_cleaning")
+
+
+def test_24_2_test_case_validation():
+    test_data_source = _tool_path("column_param.xml")
+    advice = advise_on_upgrade(test_data_source)
+    assert_has_advice(advice, "24_2_fix_test_case_validation")
+
+    int_param = _tool_path("parameters/gx_int.xml")
+    advice = advise_on_upgrade(int_param)
+    assert_not_has_advice(advice, "24_2_fix_test_case_validation")
+
+
+def _tool_path(tool_name: str):
+    return os.path.join(functional_test_tool_path(tool_name))
+
+
+def assert_has_advice(advice_list: List[Advice], advice_code: str):
+    for advice in advice_list:
+        if advice.advice_code["name"] == advice_code:
+            return
+
+    raise AssertionError(f"Was expecting advice {advice_code} in list of upgrade advice {advice_list}")
+
+
+def assert_not_has_advice(advice_list: List[Advice], advice_code: str):
+    for advice in advice_list:
+        if advice.advice_code["name"] == advice_code:
+            raise AssertionError(f"Was not expecting advice {advice_code} in list of upgrade advice {advice_list}")
diff --git a/test/unit/tool_util/util.py b/test/unit/tool_util/util.py
index c94345b29f5455564a9d7857f69017850db980f7..27f0ee677fbdde272bcda552bf2fd0310b78858b 100644
--- a/test/unit/tool_util/util.py
+++ b/test/unit/tool_util/util.py
@@ -1,11 +1,35 @@
+import json
 from contextlib import contextmanager
 from os import environ
+from typing import (
+    Any,
+    List,
+)
 
 import pytest
 
 external_dependency_management = pytest.mark.external_dependency_management
 
 
+def dict_verify_each(target_dict: dict, expectations: List[Any]):
+    assert_json_encodable(target_dict)
+    for path, expectation in expectations:
+        exception = target_dict.get("exception")
+        assert not exception, f"Test failed to generate with exception {exception}"
+        dict_verify(target_dict, path, expectation)
+
+
+def dict_verify(target_dict: dict, expectation_path: List[Any], expectation: Any):
+    rest = target_dict
+    for path_part in expectation_path:
+        rest = rest[path_part]
+    assert rest == expectation, f"{rest} != {expectation} for {expectation_path}"
+
+
+def assert_json_encodable(as_dict: dict):
+    json.dumps(as_dict)
+
+
 @contextmanager
 def modify_environ(values, keys_to_remove=None):
     """
diff --git a/test/unit/tool_util/verify/test_asserts.py b/test/unit/tool_util/verify/test_asserts.py
index a7f419fa4a32260bf0ed3b910055b142f9730560..2f2e9648f64b7bccf167ae91d9005d6a25ac26de 100644
--- a/test/unit/tool_util/verify/test_asserts.py
+++ b/test/unit/tool_util/verify/test_asserts.py
@@ -1259,7 +1259,7 @@ def test_has_json_property_with_text_neg():
 if h5py is not None:
     with tempfile.NamedTemporaryFile(delete=False) as tmp:
         h5name = tmp.name
-        with h5py.File(tmp.name, "w") as h5fh:
+        with h5py.File(tmp.name, "w", locking=False) as h5fh:
             h5fh.attrs["myfileattr"] = "myfileattrvalue"
             h5fh.attrs["myfileattrint"] = 1
             dset = h5fh.create_dataset("myint", (100,), dtype="i")
@@ -1315,7 +1315,7 @@ if h5py is not None:
         """test has_attribute .. negative"""
         a = run_assertions(H5_HAS_ATTRIBUTE_NEGATIVE, H5BYTES)
         assert (
-            "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', 1)]\n\n\t(myfileattr : wrong)"
+            "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', '1')]\n\n\t(myfileattr : wrong)"
             in a
         )
         assert len(a) == 1
@@ -1324,6 +1324,7 @@ if h5py is not None:
 def run_assertions(assertion_xml: str, data, decompress=False) -> Tuple:
     assertion = parse_xml_string(assertion_xml)
     assertion_description = __parse_assert_list_from_elem(assertion)
+    assert assertion_description
     try:
         asserts.verify_assertions(data, assertion_description, decompress=decompress)
     except AssertionError as e:
diff --git a/test/unit/util/test_checkers.py b/test/unit/util/test_checkers.py
index 1e30d25656cda301aeaf3463df98dfd37f2393a2..b474defc965a59567bf3624a7f966118969fd62b 100644
--- a/test/unit/util/test_checkers.py
+++ b/test/unit/util/test_checkers.py
@@ -1,6 +1,10 @@
+import os.path
 import tempfile
 
-from galaxy.util.checkers import check_html
+from galaxy.util.checkers import (
+    check_html,
+    check_image,
+)
 
 
 def test_check_html():
@@ -17,3 +21,10 @@ def test_check_html():
         tmpb.write(b"\x1f\x8b")
         tmpb.flush()
         assert not check_html(tmpb.name)
+
+
+def test_check_image():
+    for filename, expected in (("1.tiff", True), ("454Score.png", True), ("1.bam", False)):
+        path = f"test-data/{filename}"
+        assert os.path.exists(path)
+        assert check_image(path) is expected
diff --git a/test/unit/util/test_config_template_validation.py b/test/unit/util/test_config_template_validation.py
index dd388068e9ee3a256f4b714effc98fcddcc91ac1..cde93f5063ff698e7ba28361369294a77c186013 100644
--- a/test/unit/util/test_config_template_validation.py
+++ b/test/unit/util/test_config_template_validation.py
@@ -27,6 +27,7 @@ TEST_TEMPLATE_VERSION = 0
 
 class TestTemplate(StrictModel):
     id: str
+    type: str = "test"
     version: int
     variables: Optional[List[TemplateVariable]]
     secrets: Optional[List[TemplateSecret]]
diff --git a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
index 31d90e28a1299f9ff579bf9bed33dfc694fcd67f..fbe4fd9cae6d031fceab7e25677b2619fa3eb96c 100644
--- a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
+++ b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
@@ -8,7 +8,10 @@ import uuid
 import pytest
 from fastapi import FastAPI
 from fastapi.param_functions import Depends
-from httpx import AsyncClient
+from httpx import (
+    ASGITransport,
+    AsyncClient,
+)
 from starlette_context import context as request_context
 
 from galaxy.app_unittest_utils.galaxy_mock import MockApp
@@ -16,6 +19,7 @@ from galaxy.webapps.base.api import add_request_id_middleware
 
 app = FastAPI()
 add_request_id_middleware(app)
+transport = ASGITransport(app=app)
 GX_APP = None
 
 
@@ -96,7 +100,7 @@ def assert_scoped_session_is_thread_local(gx_app):
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_single_request():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         response = await client.get("/")
         assert response.status_code == 200
         assert response.json() == {"msg": "Hello World"}
@@ -106,7 +110,7 @@ async def test_request_scoped_sa_session_single_request():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_exception():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         with pytest.raises(UnexpectedException):
             await client.get("/internal_server_error")
         assert GX_APP
@@ -115,7 +119,7 @@ async def test_request_scoped_sa_session_exception():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_sync():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         awaitables = (client.get("/sync_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
@@ -129,7 +133,7 @@ async def test_request_scoped_sa_session_concurrent_requests_sync():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_async():
-    async with AsyncClient(app=app, base_url="http://test") as client:
+    async with AsyncClient(base_url="http://test", transport=transport) as client:
         awaitables = (client.get("/async_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
         uuids = []
@@ -147,7 +151,7 @@ async def test_request_scoped_sa_session_concurrent_requests_and_background_thre
     target = functools.partial(assert_scoped_session_is_thread_local, GX_APP)
     with concurrent.futures.ThreadPoolExecutor() as pool:
         background_pool = loop.run_in_executor(pool, target)
-        async with AsyncClient(app=app, base_url="http://test") as client:
+        async with AsyncClient(base_url="http://test", transport=transport) as client:
             awaitables = (client.get("/async_wait") for _ in range(10))
             result = await asyncio.gather(*awaitables)
             uuids = []
diff --git a/test/unit/webapps/test_service_base.py b/test/unit/webapps/test_service_base.py
index 993b841c133e719576f740f0465233877d5ad2ea..4a8f351af080c01dfc85c2aca7059beec2b2d327 100644
--- a/test/unit/webapps/test_service_base.py
+++ b/test/unit/webapps/test_service_base.py
@@ -13,7 +13,7 @@ class MockShortTermStorageAllocator(ShortTermStorageAllocator):
         self.expected_filename = expected_filename
         self.expected_mime_type = expected_mime_type
 
-    def new_target(self, filename, mime_type):
+    def new_target(self, filename, mime_type, duration=None, security=None):
         assert filename == self.expected_filename
         assert mime_type == self.expected_mime_type
 
diff --git a/test/unit/workflows/test_extract_summary.py b/test/unit/workflows/test_extract_summary.py
index 0d183e7ab88e4a54c58a61005fc5944771787adc..1517b9e6b806cd0d097e2fedf111e8b57411c197 100644
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -121,6 +121,10 @@ class MockHistory:
     def active_contents(self):
         return self.active_datasets
 
+    @property
+    def visible_contents(self):
+        return self.active_contents
+
 
 class MockTrans:
     def __init__(self, history):
diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py
index 9e2bf5c4516e34d9e78d7435b2e20f6f115280e7..d2e40b88138f0e618eb8f0edafaaacc408aa6dbe 100644
--- a/test/unit/workflows/test_modules.py
+++ b/test/unit/workflows/test_modules.py
@@ -14,6 +14,7 @@ import pytest
 
 from galaxy import model
 from galaxy.managers.workflows import WorkflowContentsManager
+from galaxy.tools.parameters.workflow_utils import NO_REPLACEMENT
 from galaxy.util import bunch
 from galaxy.workflow import modules
 from .workflow_support import (
@@ -57,7 +58,7 @@ def test_data_input_compute_runtime_state_default():
     state, errors = module.compute_runtime_state(module.trans, module.test_step)
     assert not errors
     assert "input" in state.inputs
-    assert state.inputs["input"] is None
+    assert state.inputs["input"] is NO_REPLACEMENT
 
 
 def test_data_input_compute_runtime_state_args():
@@ -207,7 +208,7 @@ steps:
     -   output_name: "out_file1"
 """
 
-COLLECTION_TYPE_WORKLFOW_YAML = """
+COLLECTION_TYPE_WORKFLOW_YAML = """
 steps:
   - type: "data_collection_input"
     label: "input1"
@@ -234,7 +235,7 @@ def test_subworkflow_new_inputs():
 
 
 def test_subworkflow_new_inputs_collection_type():
-    subworkflow_module = __new_subworkflow_module(COLLECTION_TYPE_WORKLFOW_YAML)
+    subworkflow_module = __new_subworkflow_module(COLLECTION_TYPE_WORKFLOW_YAML)
     inputs = subworkflow_module.get_data_inputs()
     assert inputs[0]["collection_type"] == "list:list"
 
@@ -428,7 +429,9 @@ def _output_step(step_input_def, step_output_def) -> Dict[str, Any]:
 @pytest.mark.parametrize("test_case", _construct_steps_for_map_over())
 def test_subworkflow_map_over_type(test_case):
     trans = MockTrans()
-    new_steps = WorkflowContentsManager(app=trans.app)._resolve_collection_type(test_case.steps)
+    new_steps = WorkflowContentsManager(app=trans.app, trs_proxy=trans.app.trs_proxy)._resolve_collection_type(
+        test_case.steps
+    )
     assert (
         new_steps[1]["outputs"][0].get("collection_type") == test_case.expected_collection_type
     ), "Expected collection_type '{}' for a '{}' input module, a '{}' input and a '{}' output, got collection_type '{}' instead".format(
diff --git a/test/unit/workflows/test_run_parameters.py b/test/unit/workflows/test_run_parameters.py
index 76eae89557441f2a393e611c8d9654bea431649b..5718ac923a40b0bcb4c01d6d1c582f06bbfb9078 100644
--- a/test/unit/workflows/test_run_parameters.py
+++ b/test/unit/workflows/test_run_parameters.py
@@ -1,5 +1,6 @@
 from galaxy import model
 from galaxy.model.base import transaction
+from galaxy.model.unittest_utils.utils import random_email
 from galaxy.workflow.run_request import (
     _normalize_inputs,
     _normalize_step_parameters,
@@ -89,7 +90,7 @@ def __new_input():
 
 
 def __workflow_fixure(trans):
-    user = model.User(email="testworkflow_params@bx.psu.edu", password="pass")
+    user = model.User(email=random_email(), password="pass")
     stored_workflow = model.StoredWorkflow()
     stored_workflow.user = user
     workflow = model.Workflow()
diff --git a/test/unit/workflows/test_trs_proxy.py b/test/unit/workflows/test_trs_proxy.py
index 6296dea9968878ad2a81e5b2d5ddc6cce99d37b3..0d07723a088e151108726805a0a0467b3e13caa3 100644
--- a/test/unit/workflows/test_trs_proxy.py
+++ b/test/unit/workflows/test_trs_proxy.py
@@ -4,6 +4,8 @@ from os import environ
 import pytest
 import yaml
 
+from galaxy.config import GalaxyAppConfiguration
+from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.workflow.trs_proxy import (
     GA4GH_GALAXY_DESCRIPTOR,
     parse_search_kwds,
@@ -17,8 +19,12 @@ search_test = pytest.mark.skipif(
 )
 
 
+def get_trs_proxy():
+    return TrsProxy(GalaxyAppConfiguration(fetch_url_allowlist_ips=[], override_tempdir=False))
+
+
 def test_proxy():
-    proxy = TrsProxy()
+    proxy = get_trs_proxy()
     server = proxy.get_server("dockstore")
 
     assert "dockstore" == proxy.get_servers()[0]["id"]
@@ -48,10 +54,10 @@ def test_proxy():
 
 
 def test_match_url():
-    proxy = TrsProxy()
-    valid_dockstore = proxy.match_url(
+    proxy = get_trs_proxy()
+    valid_dockstore = proxy._match_url(
         "https://dockstore.org/api/ga4gh/trs/v2/tools/"
-        "quay.io%2Fcollaboratory%2Fdockstore-tool-bedtools-genomecov/versions/0.3"
+        "quay.io%2Fcollaboratory%2Fdockstore-tool-bedtools-genomecov/versions/0.3",
     )
     assert valid_dockstore
     assert valid_dockstore["trs_base_url"] == "https://dockstore.org/api"
@@ -59,9 +65,9 @@ def test_match_url():
     assert valid_dockstore["tool_id"] == "quay.io/collaboratory/dockstore-tool-bedtools-genomecov"
     assert valid_dockstore["version_id"] == "0.3"
 
-    valid_dockstore_unescaped = proxy.match_url(
+    valid_dockstore_unescaped = proxy._match_url(
         "https://dockstore.org/api/ga4gh/trs/v2/tools/"
-        "#workflow/github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow/versions/master"
+        "#workflow/github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow/versions/master",
     )
     assert valid_dockstore_unescaped
     assert valid_dockstore_unescaped["trs_base_url"] == "https://dockstore.org/api"
@@ -71,13 +77,13 @@ def test_match_url():
     )
     assert valid_dockstore_unescaped["version_id"] == "master"
 
-    valid_workflow_hub = proxy.match_url("https://workflowhub.eu/ga4gh/trs/v2/tools/344/versions/1")
+    valid_workflow_hub = proxy._match_url("https://workflowhub.eu/ga4gh/trs/v2/tools/344/versions/1")
     assert valid_workflow_hub
     assert valid_workflow_hub["trs_base_url"] == "https://workflowhub.eu"
     assert valid_workflow_hub["tool_id"] == "344"
     assert valid_workflow_hub["version_id"] == "1"
 
-    valid_arbitrary_trs = proxy.match_url(
+    valid_arbitrary_trs = proxy._match_url(
         "https://my-trs-server.golf/stuff/ga4gh/trs/v2/tools/hello-world/versions/version-1"
     )
     assert valid_arbitrary_trs
@@ -85,29 +91,36 @@ def test_match_url():
     assert valid_arbitrary_trs["tool_id"] == "hello-world"
     assert valid_arbitrary_trs["version_id"] == "version-1"
 
-    ignore_extra = proxy.match_url(
-        "https://workflowhub.eu/ga4gh/trs/v2/tools/344/versions/1/CWL/descriptor/ro-crate-metadata.json"
+    ignore_extra = proxy._match_url(
+        "https://workflowhub.eu/ga4gh/trs/v2/tools/344/versions/1/CWL/descriptor/ro-crate-metadata.json",
     )
     assert ignore_extra
     assert ignore_extra["trs_base_url"] == "https://workflowhub.eu"
     assert ignore_extra["tool_id"] == "344"
     assert ignore_extra["version_id"] == "1"
 
-    invalid = proxy.match_url("https://workflowhub.eu/workflows/1")
+    invalid = proxy._match_url("https://workflowhub.eu/workflows/1")
     assert invalid is None
 
-    missing_version = proxy.match_url("https://workflowhub.eu/ga4gh/trs/v2/tools/344")
+    missing_version = proxy._match_url("https://workflowhub.eu/ga4gh/trs/v2/tools/344")
     assert missing_version is None
 
-    blank = proxy.match_url("")
+    blank = proxy.match_url("", [])
     assert blank is None
 
-    not_url = proxy.match_url("1234")
+    not_url = proxy.match_url("1234", [])
     assert not_url is None
 
+    expected_exception = None
+    try:
+        proxy.match_url("https://localhost", [])
+    except ConfigDoesNotAllowException as e:
+        expected_exception = e
+    assert expected_exception, "matching url against localhost should fail"
+
 
 def test_server_from_url():
-    proxy = TrsProxy()
+    proxy = get_trs_proxy()
     server = proxy.server_from_url("https://workflowhub.eu")
 
     assert "https://workflowhub.eu" == server._trs_url
@@ -136,7 +149,7 @@ def test_server_from_url():
 
 @search_test
 def test_search():
-    proxy = TrsProxy()
+    proxy = get_trs_proxy()
     server = proxy.get_server("dockstore")
 
     search_kwd = parse_search_kwds("documentation")
diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py
index d0d2f9902e79f8a0ace30dd4f0ca8dbdce9bd02d..5a63ca3f87c108a6c1e27131a4c7e3b2a642278f 100644
--- a/test/unit/workflows/test_workflow_progress.py
+++ b/test/unit/workflows/test_workflow_progress.py
@@ -100,7 +100,7 @@ class TestWorkflowProgress(TestCase):
 
             workflow_invocation_step_state = model.WorkflowRequestStepState()
             workflow_invocation_step_state.workflow_step_id = step_id
-            workflow_invocation_step_state.value = cast(bytes, True)
+            workflow_invocation_step_state.value = {"my_param": True}
             self.invocation.step_states.append(workflow_invocation_step_state)
 
     def _step(self, index):
diff --git a/test/unit/workflows/workflow_support.py b/test/unit/workflows/workflow_support.py
index 05064e722face22adab2c5f4dc084da7a4ce1c4c..a3b8374637df787c9cdb1a1e403520e87a0b4a58 100644
--- a/test/unit/workflows/workflow_support.py
+++ b/test/unit/workflows/workflow_support.py
@@ -6,12 +6,14 @@ from galaxy import model
 from galaxy.app_unittest_utils import galaxy_mock
 from galaxy.managers.workflows import WorkflowsManager
 from galaxy.model.base import transaction
+from galaxy.util.bunch import Bunch
 from galaxy.workflow.modules import module_factory
 
 
 class MockTrans:
     def __init__(self):
         self.app = MockApp()
+        self.app.trs_proxy = Bunch()
         self.sa_session = self.app.model.context
         self._user = None
 
diff --git a/tools/data_export/export_remote.py b/tools/data_export/export_remote.py
index 6574756a85f9637874c1bc17dd0b0616f5ef2cd0..f0b027e5a928d2cdc7c3383cfa2b0f2f10c590c3 100644
--- a/tools/data_export/export_remote.py
+++ b/tools/data_export/export_remote.py
@@ -35,15 +35,23 @@ def write_if_not_exists(file_sources, target_uri, real_data_path):
     file_source.write_from(file_source_path.path, real_data_path)
 
 
+def get_directory_uri(args):
+    directory_uri = args.directory_uri
+    if not directory_uri:
+        inputs = json.load(open(args.inputs, "r"))
+        directory_uri = inputs["d_uri"]
+    if not directory_uri.endswith("/"):
+        directory_uri = f"{directory_uri}/"
+    return directory_uri
+
+
 def main(argv=None):
     if argv is None:
         argv = sys.argv[1:]
     args = _parser().parse_args(argv)
     exit_code = 0
     file_sources = get_file_sources(args.file_sources)
-    directory_uri = args.directory_uri
-    if not directory_uri.endswith("/"):
-        directory_uri = f"{directory_uri}/"
+    directory_uri = get_directory_uri(args)
     export_metadata_files = args.export_metadata_files
     with open(args.files_to_export) as f:
         files_to_export = json.load(f)
@@ -68,6 +76,8 @@ def main(argv=None):
 
 def _parser():
     parser = argparse.ArgumentParser()
+    parser.add_argument("--inputs", type=str, help="galaxy inputs")
+    # post 2026.XX drop the directory-uri argument and just assume inputs always contains d_uri.
     parser.add_argument("--directory-uri", type=str, help="directory target URI")
     parser.add_argument("--file-sources", type=str, help="file sources json")
     parser.add_argument("--files-to-export", type=str, help="files to export")
diff --git a/tools/data_export/export_remote.xml b/tools/data_export/export_remote.xml
index fe544c48e200f98c57ee8845f45d814178aa431e..63f2318a6c5aa8d0a329e9b2739ee21c58a7b749 100644
--- a/tools/data_export/export_remote.xml
+++ b/tools/data_export/export_remote.xml
@@ -8,7 +8,7 @@
     <command><![CDATA[
 python '$__tool_directory__/export_remote.py'
     --file-sources '$file_sources'
-    --directory-uri '$d_uri'
+    --inputs '$inputs'
     --files-to-export '$files_to_export'
     #if $include_metadata_files:
         --export-metadata-files $include_metadata_files
@@ -17,6 +17,7 @@ python '$__tool_directory__/export_remote.py'
     ]]></command>
     <configfiles>
         <file_sources name="file_sources"/>
+        <inputs name="inputs" />
         <configfile name="files_to_export">#import json
 #from galaxy.util import filesystem_safe_string
 #if $export_type.export_type_selector == "datasets_auto":
diff --git a/tools/data_export/send.py b/tools/data_export/send.py
deleted file mode 100644
index 87270b1d8fadb371d05b7f78e50c2984c56cd257..0000000000000000000000000000000000000000
--- a/tools/data_export/send.py
+++ /dev/null
@@ -1,139 +0,0 @@
-"""
-This tool implements the logic of sending data
-from Galaxy to a cloud-based storage.
-
-This tool depends on the CloudManager for configuring
-a connection to a cloud-based resource provider. Also,
-it leverages Cloudbridge (github.com/CloudVE/cloudbridge)
-to send a dataset to a cloud-based storage.
-
-"""
-
-import argparse
-import datetime
-import json
-import os
-import sys
-import time
-
-from galaxy.exceptions import ObjectNotFound
-from galaxy.managers.cloud import CloudManager
-
-try:
-    from cloudbridge.factory import (
-        CloudProviderFactory,
-        ProviderList,
-    )
-except ImportError:
-    CloudProviderFactory = None
-    ProviderList = None
-
-NO_CLOUDBRIDGE_ERROR_MESSAGE = (
-    "Cloud ObjectStore is configured, but no CloudBridge dependency available."
-    "Please install CloudBridge or modify ObjectStore configuration."
-)
-
-
-def load_credential(credentials_file):
-    print("[1/5 {}] Reading cloud authorization.".format(datetime.datetime.now().replace(microsecond=0)))
-    with open(credentials_file) as f:
-        credentials = f.read()
-    os.remove(credentials_file)
-    return json.loads(credentials)
-
-
-def send(provider, credentials, bucket, object_label, filename, overwrite_existing):
-    start_time = time.time()
-    if not os.path.exists(filename):
-        raise Exception("The file `{}` does not exist.".format(filename))
-    if CloudProviderFactory is None:
-        raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
-
-    print("[2/5 {}] Establishing a connection to {}.".format(datetime.datetime.now().replace(microsecond=0), provider))
-    try:
-        connection = CloudManager.configure_provider(provider, credentials)
-    except Exception:
-        print("Failed to establish the connection.")
-
-    print("[3/5 {}] Accessing bucket {}.".format(datetime.datetime.now().replace(microsecond=0), bucket))
-    bucket_obj = connection.storage.buckets.get(bucket)
-    if bucket_obj is None:
-        raise ObjectNotFound("Could not find the specified bucket `{}`.".format(bucket))
-    if overwrite_existing is False and bucket_obj.objects.get(object_label) is not None:
-        object_label += "_" + datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-
-    print("[4/5 {}] Creating object {}.".format(datetime.datetime.now().replace(microsecond=0), object_label))
-    try:
-        created_obj = bucket_obj.objects.create(object_label)
-    except Exception:
-        print("Failed to create the object.")
-
-    print("[5/5 {}] Sending dataset.".format(datetime.datetime.now().replace(microsecond=0)))
-    transfer_start_time = time.time()
-    try:
-        created_obj.upload_from_file(filename)
-    except Exception:
-        print("Failed to send the dataset.")
-
-    print("Finished successfully.")
-    print("Job runtime:\t{}".format(time.time() - start_time))
-    print(
-        "Transfer ET:\t{}\tSpeed:\t{}MB/sec".format(
-            time.time() - transfer_start_time,
-            round((os.path.getsize(filename) >> 20) / (time.time() - transfer_start_time), 3),
-        )
-    )
-
-
-def parse_args(args):
-    parser = argparse.ArgumentParser()
-    parser.add_argument("-p", "--provider", type=str, required=True, help="Provider")
-
-    parser.add_argument(
-        "-b",
-        "--bucket",
-        type=str,
-        required=True,
-        help="The cloud-based storage bucket in which data should be written.",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--object_label",
-        type=str,
-        required=True,
-        help="The label of the object created on the cloud-based storage for the data to be persisted.",
-    )
-
-    parser.add_argument(
-        "-f",
-        "--filename",
-        type=str,
-        required=True,
-        help="The (absolute) filename of the data to be persisted on the cloud-based storage.",
-    )
-
-    parser.add_argument(
-        "-w",
-        "--overwrite_existing",
-        type=str,
-        required=True,
-        help="Sets if an object with the given `object_label` exists, this tool "
-        "should overwrite it (true) or append a time stamp to avoid "
-        "overwriting (false).",
-    )
-
-    parser.add_argument("--credentials_file", type=str, required=True, help="Credentials file")
-
-    return parser.parse_args(args)
-
-
-def __main__():
-    args = parse_args(sys.argv[1:])
-    overwrite_existing = args.overwrite_existing.lower() == "true"
-    credentials = load_credential(args.credentials_file)
-    send(args.provider, credentials, args.bucket, args.object_label, args.filename, overwrite_existing)
-
-
-if __name__ == "__main__":
-    sys.exit(__main__())
diff --git a/tools/data_export/send.xml b/tools/data_export/send.xml
deleted file mode 100644
index 62e5ccffd943d04d64babec3c2446caea8a0ca07..0000000000000000000000000000000000000000
--- a/tools/data_export/send.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-<?xml version="1.0"?>
-
-<tool id="send_to_cloud" name="Send to cloud" version="0.1.0" workflow_compatible="false">
-    <!--
-    <requirements>
-        <requirement type="package" version="0.3.3">cloudbridge</requirement>
-    </requirements>
-    -->
-    <command><![CDATA[
-        #try
-            #set $authz_record=$__app__.authnz_manager.try_get_authz_config($__app__.obj.model.session, int($__user_id__), $__app__.security.decode_id($authz_id.__str__()))
-            #set $credentials_file = $__app__.authnz_manager.get_cloud_access_credentials_in_file($__app__.config.new_file_path, $authz_record, $__app__.obj.model.session, int($__user_id__))
-        #except Exception as e:
-            echo '$e' >&2
-        #else
-            python $__tool_directory__/send.py
-                --provider=$authz_record.provider
-                --filename=$filename
-                --credentials_file=$credentials_file
-                --bucket=$bucket
-                --object_label=$filename.name.replace(" ", "_")
-                --overwrite_existing=$overwrite_existing
-        #end try
-    ]]></command>
-    <inputs>
-        <param name="filename" type="data" label="Datasets to be sent to a cloud-based storage:" />
-        <param name="bucket" type="text" label="Bucket" />
-        <param name="authz_id" type="text" label="Cloud Authorization ID" />
-        <param name="object_label" type="text" hidden="true" label="Object Label" />
-        <param name="overwrite_existing" type="boolean" label="Overwrite Existing" />
-    </inputs>
-    <outputs>
-        <data name="output" type="data" hidden="false"/>
-    </outputs>
-    <help>
-**What it does**
-        Send dataset(s) from Galaxy to cloud-based storage (e.g., AWS S3).
-
-        Supply a name of the target bucket where the data will be sent along
-        with an id for the desired cloud authorization. To get the list of Cloud
-        Authorization IDs available for your account, visit `/api/cloud/authz`.
-
-**Remarks**
-        This tool leverages OpenID Connect protocol and CloudAuthz (https://github.com/galaxyproject/cloudauthz)
-        to access cloud-based resources without requiring user credentials.
-
-        If selecting multiple datasets, make sure each dataset is named
-        differently; otherwise, only one copy of the selected datasets will be
-        copied.
-    </help>
-</tool>
diff --git a/tools/data_source/ebi_sra.xml b/tools/data_source/ebi_sra.xml
index 5a1e946b815eed0e615d66811ee0278be2d08ac9..316fbb7bed5d19c53c7349009775d6607bd3885a 100644
--- a/tools/data_source/ebi_sra.xml
+++ b/tools/data_source/ebi_sra.xml
@@ -9,7 +9,7 @@
 python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
     ]]></command>
     <!-- The URL where Galaxy will forwards the user when this tool is accessed from the Get Data menu -->
-    <inputs action="https://www.ebi.ac.uk/ena/data/search" check_values="false" method="get">
+    <inputs action="https://www.ebi.ac.uk/ena/browser/search" check_values="false" method="get">
         <display>go to EBI SRA server $GALAXY_URL</display>
     </inputs>
     <uihints minwidth="800"/>
diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 548b631633345db1b3ec658573be69512646b633..d8c7ace6b2ab32a9ae0e1904e8c5da133a0cc692 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -59,6 +59,7 @@
     </upload_dataset>
     <param name="force_composite" type="hidden" value="false" />
     <param name="dbkey" type="genomebuild" label="Genome" />
+    <param name="tags" type="hidden" value="" />
     <conditional name="files_metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
     <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
   </inputs>
diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index 9c67a644c8ff481fa8ce4f7baf0abab1bb1e2f83..d7bcf05bf196014c1e53a66c4c361717985cc566 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -42,9 +42,9 @@ __status__ = "beta"
 fake_sff_name = "fake_sff_name"
 
 # readname as key: lines with matches from SSAHA, one best match
-ssahapematches = {}  # type: ignore
+ssahapematches = {}  # type: ignore[var-annotated]
 # linker readname as key: length of linker sequence
-linkerlengths = {}  # type: ignore
+linkerlengths = {}  # type: ignore[var-annotated]
 
 # set to true if something really fishy is going on with the sequences
 stern_warning = False
diff --git a/tools/interactive/interactivetool_blobtoolkit.xml b/tools/interactive/interactivetool_blobtoolkit.xml
new file mode 100644
index 0000000000000000000000000000000000000000..091af7f4febd864731d53865b697824b5da26064
--- /dev/null
+++ b/tools/interactive/interactivetool_blobtoolkit.xml
@@ -0,0 +1,53 @@
+<tool id="interactive_tool_blobtoolkit" tool_type="interactive" name="Interactive BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>genome assembly QC viewer</description>
+    <macros>
+        <token name="@TOOL_VERSION@">4.1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">quay.io/galaxy/blobtoolkit-server:@TOOL_VERSION@</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Blobtoolkit View" requires_domain="True">
+            <port>80</port>
+            <url>view/all</url>
+        </entry_point>
+    </entry_points>
+    <command detect_errors="exit_code"><![CDATA[
+    ## The following is a hack. Our embedded pulsar is not respecting the Galaxy jwd-tmp dir.
+    export TEMP=\$PWD &&
+    export TMP=\$PWD &&
+    export TMPDIR=\$PWD &&
+    mkdir datasets &&
+    cd datasets &&
+    mkdir './Blobdir' &&
+    #if $blobdir:
+        #if $blobdir.is_of_type("tgz")
+            tar -zxf '${blobdir}' -C './Blobdir' &&
+        #else
+            tar -xf '${blobdir}' -C './Blobdir' &&
+        #end if
+        cd .. &&
+        export BTK_FILE_PATH=\$PWD/datasets &&
+        startup.sh
+    #else:
+        cd .. &&
+        startup.sh
+    #end if
+    ]]></command>
+    <inputs>
+        <param name="blobdir" type="data" format="tgz,tar" optional="true" label="Blobdir file" help="This file should be generated by the module create. The collection of JSON files should be packed in the tarbal file without directory structure." />
+    </inputs>
+    <outputs>
+        <data name="Interactive BlobToolKit on data ${on_string}" format="txt"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly, 
+    read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1534/g3.119.400908</citation>
+    </citations>
+</tool>
diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8f52af0b7b7bfaf06ec7c02045e5f1337aca0e76
--- /dev/null
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -0,0 +1,107 @@
+<tool id="interactive_tool_ilastik" tool_type="interactive" name="Ilastik" version="@VERSION@" profile="23.0">
+    <description>interactive learning and segmentation toolkit</description>
+    <macros>
+        <token name="@VERSION@">1.4.0</token>
+    </macros>
+    <requirements>
+        <container type="docker">quay.io/galaxy/ilastik:@VERSION@</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Ilastik" requires_domain="True">
+            <port>5800</port>
+        </entry_point>
+    </entry_points>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        ## Check inputs have no duplicated element_identifier:
+        #set labels = [input.element_identifier for input in $infiles]
+        #set duplicates = [label for label in labels if labels.count(label) > 1]
+        #if len(duplicates) > 0:
+            #set unique_duplicates = list(set(duplicates))
+            echo "Cannot run ilastik because these identifiers are present more than once:" &&
+            #for label in $unique_duplicates:
+                echo $label &&
+            #end for
+            exit 1 &&
+        #end if
+        export HOME=\$PWD &&
+        ## Create a directory where the app user has access
+        mkdir -p ./output &&
+        chown 1000:1000 ./output/ &&
+        ## Make a copy of the existing project if exists
+        #if str($input_type.existing) == "existing":
+            cp '$input_type.project' ./output/MyProject.ilp &&
+        #end if
+
+        ## Link input images to current working directory
+        #for input in $infiles:
+            ln -s '$input' ./'$input.element_identifier'.tif &&
+        #end for
+        ## Write the bash script to run:
+        #if str($input_type.existing) == "new":
+            echo "ilastik --new_project \$HOME/output/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
+        #else:
+            echo "ilastik --project \$HOME/output/MyProject.ilp" > ./ilastik_with_args &&
+        #end if
+        ## Copy it to /bin/ so it will be used by the container:
+        chmod +x ./ilastik_with_args &&
+        cp ./ilastik_with_args '/bin/' &&
+        /init
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="existing" type="select" label="Which project you want to work on?">
+                <option value="new">Start a new project</option>
+                <option value="existing">Modify an existing project</option>
+            </param>
+            <when value="new">
+                <param name="Workflow" type="select" label="Type of Workflow" >
+                    <option value="PixelClassificationWorkflow">Pixel Classification</option>
+                    <option value="AutocontextTwoStage">Autocontext (2-stage)</option>
+                    <option value="ObjectClassificationWorkflowPixel">Pixel Classification + Object Classification</option>
+                    <option value="ObjectClassificationWorkflowPrediction">Object Classification [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="ObjectClassificationWorkflowBinary">Object Classification [Inputs: Raw Data, Segmentation]</option>
+                    <option value="ConservationTrackingWorkflowFromBinary">Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="ConservationTrackingWorkflowFromPrediction">Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromBinary">Animal Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromPrediction">Animal Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="StructuredTrackingWorkflowFromBinary">Tracking with Learning [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="StructuredTrackingWorkflowFromPrediction">Tracking with Learning [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="EdgeTrainingWithMulticutWorkflow">Bounary-based Segmentation with Multicut</option>
+                    <option value="CountingWorkflow">Cell Density Counting</option>
+                    <option value="DataConversionWorkflow">Data Conversion</option>
+                    <option value="neuralNetwork.RemoteWorkflow">Neural Network Classification (Remote)</option>
+                    <option value="neuralNetwork.LocalWorkflow">Neural Network Classification (Local)</option>
+                </param>
+            </when>
+            <when value="existing">
+                <param argument="--project" type="data" format="h5" label="Existing ilastik project" />
+            </when>
+        </conditional>
+        <param name="infiles" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/>
+    </inputs>
+    
+    <outputs>
+        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="output/MyProject.ilp"/>
+    </outputs>
+    
+    <tests>
+    </tests>
+    
+    <help><![CDATA[
+        Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.
+
+        This tool has been designed uniquely to make/modify a project.
+        
+        - It requires that input images have unique identifiers.
+        - When you have trained your project, save it and quit the application. The project called 'MyProject.ilp' will be imported into your history.
+        - If you want to modify a project, make sure you use at least the same images (with the same identifiers) as the first time (but you can add more).
+
+        Please, check the documentation at https://www.ilastik.org/documentation/.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41592-019-0582-9</citation>
+    </citations>
+</tool>
diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
index 5b5e91e1614435fbecc8772a07c6abc5f520317c..870ecd19fd286602f0ca53a05098e3e2cc9cdef7 100644
--- a/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml
@@ -2,6 +2,9 @@
     <requirements>
         <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>
     </requirements>
+    <required_files>
+        <include path="default_notebook.ipynb"/>
+    </required_files>
     <entry_points>
         <entry_point name="JupyTool interactive tool" label="jupytool" requires_domain="False" requires_path_in_url="True">
             <port>8888</port>
diff --git a/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8c249e289af2f47dfdb6148a7b42ef6569d7df68
--- /dev/null
+++ b/tools/interactive/interactivetool_jupyter_notebook_1.0.1.xml
@@ -0,0 +1,271 @@
+<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyterLab Notebook" version="1.0.1" profile="23.0">
+    <requirements>
+        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:24.07</container>
+    </requirements>
+    <required_files>
+        <include path="default_notebook.ipynb"/>
+    </required_files>
+    <entry_points>
+        <entry_point name="JupyTool interactive tool" label="jupytool" requires_domain="False" requires_path_in_url="True">
+            <port>8888</port>
+            <url>ipython/lab</url>
+        </entry_point>
+    </entry_points>
+    <environment_variables>
+        <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+        <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
+        <environment_variable name="API_KEY" inject="api_key"/>
+        <environment_variable name="EP_PATH" inject="entry_point_path_for_label">jupytool</environment_variable>
+    </environment_variables>
+    <configfiles>
+        <inputs name="inputs" filename="galaxy_inputs.json" data_style="staging_path_and_source_path"/>
+        <configfile name="staging_script" filename="staging_script.py"><![CDATA[
+import json, os, shutil
+import os.path
+galaxy_inputs = "galaxy_inputs.json"
+galaxy_inputs_raw = "galaxy_inputs_raw.json"
+base_staging_path = "jupyter"
+base_data_staging_path = "galaxy_inputs"
+data_staging_path = os.path.join(base_staging_path, base_data_staging_path)
+os.makedirs(data_staging_path, exist_ok=True)
+shutil.copyfile(galaxy_inputs, os.path.join(data_staging_path, galaxy_inputs_raw))
+galaxy_input_dict = {}
+for user_input in json.load(open(galaxy_inputs, "r")).get("user_inputs", []):
+    input_values = user_input['input_type']['input_value']
+    input_name = user_input["input_name"]
+    assert input_name not in galaxy_input_dict, ValueError("Each name can only be used once, but a duplicate was found: %s" % (input_name))
+    if 'dataset' in user_input['input_type']['input_type_selector']:
+        input_values2 = []
+        if not isinstance(input_values, list):
+            input_values = [input_values]
+        for input_value_dict in input_values:
+            path, filename = os.path.split(input_value_dict['staging_path'])
+            input_value_dict2 = {"path": os.path.join(base_data_staging_path, input_name, path, filename), "metadata_files": []}
+            ## TODO: enable passing in all metadata values; ideally just handed off from original json creation
+            path = os.path.join(data_staging_path, input_name, path)
+            os.makedirs(path, exist_ok=True)
+            try:
+                os.symlink(input_value_dict['source_path'], os.path.join(path, filename))
+            except FileExistsError:
+                pass
+            for metadata_value_dict in input_value_dict['metadata_files']:
+                path, filename = os.path.split(metadata_value_dict['staging_path'])
+                input_value_dict2["metadata_files"].append(os.path.join(base_data_staging_path, input_name, path, filename))
+                path = os.path.join(data_staging_path, input_name, path)
+                os.makedirs(path, exist_ok=True)
+                try:
+                    os.symlink(metadata_value_dict['source_path'], os.path.join(path, filename))
+                except FileExistsError:
+                    pass
+            input_values2.append(input_value_dict2)
+        input_values = input_values2
+    galaxy_input_dict[input_name] = input_values
+with open(os.path.join(data_staging_path, galaxy_inputs), "w") as fh:
+    json.dump(galaxy_input_dict, fh)
+]]>
+        </configfile>
+        <configfile name="galaxy_input_startup_script"><![CDATA[
+import json, os
+from galaxy_ie_helpers import get
+from galaxy_ie_helpers import put
+from galaxy_ie_helpers import get_galaxy_connection
+HISTORY_ID = os.environ.get('HISTORY_ID', None)
+try:
+    GALAXY_INPUTS = json.load(open(os.path.join(os.environ.get("GALAXY_WORKING_DIR", ""), "jupyter", "galaxy_inputs", "galaxy_inputs.json")))
+except FileNotFoundError:
+    GALAXY_INPUTS = {}
+        ]]>
+    </configfile>
+    </configfiles>
+    <command><![CDATA[
+        python staging_script.py &&
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/collection &&
+        mkdir -p ./jupyter/galaxy_inputs &&
+        export PROXY_PREFIX=\${EP_PATH%/ipython*} &&
+
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export HOME=/home/jovyan/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
+        cp '${galaxy_input_startup_script}' /home/jovyan/.ipython/profile_default/startup/00-load.py &&
+
+        #set $output_notebook_name = 'ipython_galaxy_notebook.ipynb'
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ${output_notebook_name} &&
+            jupyter trust ${output_notebook_name} &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+        #else:
+            #import re
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            #if not $cleaned_name.endswith(".ipynb"):
+                #set $cleaned_name = "%s.ipynb" % $cleaned_name
+            #end if
+            cp '$mode.ipynb' '${cleaned_name}' &&
+            jupyter trust '${cleaned_name}' &&
+
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output '${output_notebook_name}' --allow-errors '${cleaned_name}' &&
+            #else:
+                #set $output_notebook_name = $cleaned_name
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+        #end if
+        cp '${output_notebook_name}' '$jupyter_notebook'
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="mode">
+            <param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
+                <option value="scratch">Start with a fresh notebook</option>
+                <option value="previous">Load a previous notebook</option>
+            </param>
+            <when value="scratch"/>
+            <when value="previous">
+                <param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
+                <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one." help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
+            </when>
+        </conditional>
+        <repeat name="user_inputs" title="User inputs">
+            <param name="input_name" type="text" value="" label="Name for parameter" optional="False" help="Required. ASCII letters and numbers only.">
+                <validator type="empty_field" message="Name is required"/>
+                <sanitizer>
+                    <valid initial="string.ascii_letters,string.digits"/>
+                </sanitizer>
+            </param>
+            <param name="description" type="text" label="Additional optional description" optional="true"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" type="select" label="Choose the input type">
+                    <option value="dataset" selected="true">Dataset</option>
+                    <option value="dataset_multiple">Multiple datasets</option>
+                    <option value="dataset_collection">Dataset collection</option>
+                    <option value="dataset_collection_list">Dataset collection (list)</option>
+                    <option value="dataset_collection_paired">Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired">Dataset collection (list:paired)</option>
+                    <option value="text">Text</option>
+                    <option value="integer">Integer</option>
+                    <option value="float">Floating point</option>
+                    <option value="boolean">Boolean</option>
+                    <option value="color">Color selector</option>
+                    <option value="dataset_optional" selected="true">Optional Dataset</option>
+                    <option value="dataset_multiple_optional">Optional Multiple datasets</option>
+                    <option value="dataset_collection_optional">Optional Dataset collection</option>
+                    <option value="dataset_collection_list_optional">Optional Dataset collection (list)</option>
+                    <option value="dataset_collection_paired_optional">Optional Dataset collection (paired)</option>
+                    <option value="dataset_collection_list_paired_optional">Optional Dataset collection (list:paired)</option>
+                    <option value="text_optional">Optional Text</option>
+                    <option value="integer_optional">Optional Integer</option>
+                    <option value="float_optional">Optional Floating point</option>
+                    <option value="boolean_optional">Optional Boolean</option>
+                    <option value="color_optional">Optional Color selector</option>
+                </param>
+                <when value="dataset">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="false"/>
+                </when>
+                <when value="dataset_multiple">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="false"/>
+                </when>
+                <when value="dataset_collection">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_collection_list">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="false"/>
+                </when>
+                <when value="dataset_collection_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="false"/>
+                </when>
+                <when value="dataset_collection_list_paired">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="false"/>
+                </when>
+                <when value="text">
+                    <param name="input_value" type="text" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="integer">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="float">
+                    <param name="input_value" type="float" value="" label="Select value" optional="false"/>
+                </when>
+                <when value="boolean">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="false"/>
+                </when>
+                <when value="color">
+                    <param name="input_value" type="color" label="Select value" optional="false"/>
+                </when>
+                <when value="dataset_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="false" optional="true"/>
+                </when>
+                <when value="dataset_multiple_optional">
+                    <param name="input_value" type="data" format="data" label="Select value" multiple="true" optional="true"/>
+                </when>
+                <when value="dataset_collection_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list" optional="true"/>
+                </when>
+                <when value="dataset_collection_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="paired" optional="true"/>
+                </when>
+                <when value="dataset_collection_list_paired_optional">
+                    <param name="input_value" type="data_collection" format="data" label="Select value" collection_type="list:paired" optional="true"/>
+                </when>
+                <when value="text_optional">
+                    <param name="input_value" type="text" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="integer_optional">
+                    <param name="input_value" type="integer" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="float_optional">
+                    <param name="input_value" type="float" value="" label="Select value" optional="true"/>
+                </when>
+                <when value="boolean_optional">
+                    <param name="input_value" type="boolean" truevalue="true" falsevalue="false" label="Select value" optional="true"/>
+                </when>
+                <when value="color_optional">
+                    <param name="input_value" type="color" label="Select value" optional="true"/>
+                </when>
+            </conditional>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="jupyter_notebook" format="ipynb" label="Executed JupyTool Notebook"/>
+        <data name="output_dataset" format="data">
+            <discover_datasets pattern="__designation_and_ext__" directory="jupyter/outputs" visible="true" assign_primary_output="true"/>
+        </data>
+        <collection name="output_collection" type="list" label="JupyTool output collection">
+            <discover_datasets pattern="__designation_and_ext__" directory="jupyter/outputs/collection" visible="false"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="mode" value="previous"/>
+            <param name="ipynb" value="test.ipynb"/>
+            <param name="run_it" value="true"/>
+            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
+        </test>
+    </tests>
+    <help>
+    Welcome to the **JupyTool**! Here you can create, run, and share custom Galaxy tools based upon Jupyter Notebooks.
+
+    The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
+    visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
+    machine learning, and much more.
+
+    Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
+    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
+
+    You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your colleague and execute it on your dataset.
+    You can specify any number of user-defined inputs using the repeat input, providing `name` value, selecting the type of input, and then providing values.
+
+    You can make the JupyTool reusable in a workflow, by allowing the user to specify input values for the defined input blocks.
+    Inputs can be accessed by `name` from the automatically provided `GALAXY_INPUTS` dictionary.
+    Outputs can be written automatically to the user's history by writing to the `outputs` directory for one individual file or to the `outputs/collection` directory for multiple files.
+    Using collection tools, you can parse out the individual elements from the collection, as needed.
+
+    For backwards compatibility, you can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
+    </help>
+</tool>
diff --git a/tools/interactive/interactivetool_ml_jupyter_notebook.xml b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
index 5d19185d4ef69fa0126e508214f639b580907e08..757a3fbfd9eea687dfdeb5ffafd4969e1233741a 100644
--- a/tools/interactive/interactivetool_ml_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
@@ -1,9 +1,9 @@
-<tool id="interactive_tool_ml_jupyter_notebook" tool_type="interactive" name="GPU enabled Interactive Jupyter Notebook for Machine Learning" version="@VERSION@" profile="22.01">
+<tool id="interactive_tool_ml_jupyter_notebook" tool_type="interactive" name="GPU-enabled Interactive Jupyter Notebook for Machine Learning" version="@VERSION@" profile="22.01">
     <macros>
-        <token name="@VERSION@">0.2</token>
+        <token name="@VERSION@">0.4</token>
     </macros>
     <requirements>
-        <container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-@VERSION@</container>
+        <container type="docker">quay.io/galaxy/docker-ml-jupyterlab:galaxy-integration-@VERSION@</container>
     </requirements>
     <entry_points>
         <entry_point name="GPU enabled Interactive Jupyter Notebook for Machine Learning" requires_domain="True">
@@ -80,6 +80,15 @@ except FileNotFoundError:
     </configfiles>
     
     <command><![CDATA[
+        ## Check if the node has GPU. Activate CPU or GPU version of tensorflow
+        if nvidia-smi 2> /dev/null; then
+            echo An NVDIA GPU was detected. ;
+            ln -s \$PYTHON_LIB_PATH/tensorflow-GPU-cached \$PYTHON_LIB_PATH/tensorflow ;
+        else
+            echo No compatible GPU present. ;
+            ln -s \$PYTHON_LIB_PATH/tensorflow-CPU-cached \$PYTHON_LIB_PATH/tensorflow ;
+        fi &&
+
         python staging_script.py &&
         export GALAXY_WORKING_DIR=`pwd` &&
         mkdir -p ./jupyter/outputs &&
@@ -88,6 +97,10 @@ except FileNotFoundError:
         export HOME=/home/\$NB_USER/ &&
         export PATH=/home/\$NB_USER/.local/bin:\$PATH &&
         cp '${galaxy_input_startup_script}' /home/\$NB_USER/.ipython/profile_default/startup/02-load.py &&
+
+        ## Disable popups informing that "a new release is available"
+        jupyter labextension disable "@jupyterlab/apputils-extension:announcements" &&
+
         #set $output_notebook_name = 'jupyterlab_notebook.ipynb'
         #if $mode.mode_select == 'scratch':
             cp -r /home/\$NB_USER/data ./ &&
@@ -96,6 +109,10 @@ except FileNotFoundError:
             cp -r /home/\$NB_USER/usecases ./ &&
             cp -r /home/\$NB_USER/home_page.ipynb ./ &&
             jupyter lab --no-browser --NotebookApp.shutdown_button=True
+        #elif $mode.mode_select == 'github':
+            cp /home/\$NB_USER/home_page.ipynb ./ &&
+            git clone $mode.repo_url &&
+            jupyter lab --no-browser --NotebookApp.shutdown_button=True
         #else:
             #import re
             #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
@@ -119,9 +136,13 @@ except FileNotFoundError:
         <conditional name="mode">
             <param name="mode_select" type="select" label="Do you already have a notebook?" help="Select a set of default notebooks or load an existing one.">
                 <option value="scratch">Start with default notebooks</option>
+                <option value="pull_repo">Start with a code repository</option>
                 <option value="previous">Load an existing notebook</option>
             </param>
             <when value="scratch"/>
+            <when value="pull_repo">
+                <param name="repo_url" type="text" value="" label="Online code repository (Git-based) URL" optional="False" help="Provide URL of Git-based code repository (for example: GitHub repository URL such as https://github.com/anuprulez/gpu_jupyterlab_ct_image_segmentation)"/>
+            </when>
             <when value="previous">
                 <param name="ipynb" type="data" format="ipynb" label="IPython Notebook" required="true"/>
                 <param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one." help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
diff --git a/tools/meme/fimo.xml b/tools/meme/fimo.xml
deleted file mode 100644
index 199c3bb7f2a0e2d52d53d3318df2699a6dc50c8b..0000000000000000000000000000000000000000
--- a/tools/meme/fimo.xml
+++ /dev/null
@@ -1,238 +0,0 @@
-<tool id="meme_fimo" name="FIMO" version="0.0.1">
-  <requirements><requirement type="package">meme</requirement></requirements>
-  <description>- Find Individual Motif Occurrences</description>
-  <command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
-  
-  #if str( $options_type.options_type_selector ) == 'advanced':
-  --max-seq-length "${options_type.max_seq_length}" 
-  --max-stored-scores "${options_type.max_stored_scores }" 
-  --motif-pseudo "${options_type.motif_pseudo}" 
-  ${options_type.norc} 
-  --output-pthresh "${options_type.output_pthresh}" 
-
-  
-  #for $motif in $options_type.motifs:
-    --motif "${motif.motif}"
-  #end for
-  
-  #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
-    --bgfile "motif-file"
-  #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif-file':
-    --bgfile "${options_type.bgfile_type.bgfile}"
-  #end if
-  
-  #if str( $options_type.qvalue_type.qvalue_type_selector ) == 'no-qvalue':
-    --no-qvalue
-  #else:
-    --output-qthresh "${options_type.qvalue_type.output_qthresh}"
-  #end if
-  #end if
-  
-  "${input_motifs}" 
-  
-  #if str( $fasta_type.fasta_type_selector ) == 'history':
-    "${fasta_type.input_database}"
-  #else:
-    "${fasta_type.input_database.fields.path}"
-  #end if
-
-  '
-  
-  '${html_outfile.files_path}'
-  
-  '${html_outfile}'
-  
-  '${interval_outfile}'
-  
-  '${txt_outfile}'
-  
-  '${xml_outfile}'
-  
-  '${gff_outfile}'
-    
-  </command>
-  <inputs>
-    <param format="memexml" name="input_motifs" type="data" label="'MEME output' formatted file"/>
-    
-    <conditional name="fasta_type">
-      <param name="fasta_type_selector" type="select" label="Source for sequence to search">
-        <option value="cached">Locally Cached sequences</option>
-        <option value="history" selected="true">Sequences from your history</option>
-      </param>
-      <when value="cached">
-        <param name="input_database" type="select" label="Genome to search">
-          <options from_data_table="all_fasta">
-          </options>
-        </param>
-      </when>
-      <when value="history">
-         <param format="fasta" name="input_database" type="data" label="Sequences"/>
-      </when>
-    </conditional>
-    
-      <conditional name="options_type">
-        <param name="options_type_selector" type="select" label="Options Configuration">
-          <option value="basic" selected="true">Basic</option>
-          <option value="advanced">Advanced</option>
-        </param>
-        <when value="basic">
-          <!-- do nothing here -->
-        </when>
-        <when value="advanced">
-    
-    <conditional name="bgfile_type">
-      <param name="bgfile_type_selector" type="select" label="Background file type">
-        <option value="motif-file">Use Frequencies from Motif File</option>
-        <option value="default" selected="true">Use frequencies from non-redundant database (default)</option>
-        <option value="bgfile">Use Frequencies from Background File</option>
-      </param>
-      <when value="motif-file">
-      <!-- do nothing here -->
-      </when>
-      <when value="default">
-      <!-- do nothing here -->
-      </when>
-      <when value="bgfile">
-        <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" />
-      </when>
-    </conditional>
-    
-    <repeat name="motifs" title="Limit to specified motif">
-      <param name="motif" type="text" value="" label="Specify motif by id" />
-    </repeat>
-    
-    <param name="max_seq_length" type="integer" value="250000000" label="Maximum input sequence length" />
-    <param name="max_stored_scores" type="integer" value="100000" label="Maximum score count to store" />
-    <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" />
-    <param name="norc" label="Do not check reverse complement" type="boolean" truevalue="--norc" falsevalue="" checked="False"/>
-    <param name="output_pthresh" type="float" value="1e-4" label="p-value threshold" />
-    
-    <conditional name="qvalue_type">
-      <param name="qvalue_type_selector" type="select" label="q-value options">
-        <option value="no-qvalue">Do not compute q-value</option>
-        <option value="q-value" selected="true">Compute q-value</option>
-      </param>
-      <when value="no-qvalue">
-      <!-- do nothing here -->
-      </when>
-      <when value="q-value">
-        <param name="output_qthresh" type="float" value="1.0" label="q-value threshold" />
-      </when>
-    </conditional>
-    
-      </when>
-    </conditional>
-    
-    <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
-      <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
-    </param>
-  
-  </inputs>
-  <outputs>
-    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
-      <actions>
-        <conditional name="fasta_type.fasta_type_selector">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_data_table" name="all_fasta" column="1" offset="0">
-                <filter type="param_value" column="0" value="seq" keep="True"/>
-                <filter type="param_value" ref="fasta_type.input_database" column="1"/>
-              </option>
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
-      <actions>
-        <conditional name="fasta_type.fasta_type_selector">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_data_table" name="all_fasta" column="1" offset="0">
-                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
-              </option>
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
-      <actions>
-        <conditional name="fasta_type.fasta_type_selector">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_data_table" name="all_fasta" column="1" offset="0">
-                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
-              </option>
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
-      <actions>
-        <conditional name="fasta_type.fasta_type_selector">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_data_table" name="all_fasta" column="1" offset="0">
-                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
-              </option>
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)">
-      <actions>
-        <conditional name="fasta_type.fasta_type_selector">
-          <when value="cached">
-            <action type="metadata" name="dbkey">
-              <option type="from_data_table" name="all_fasta" column="1" offset="0">
-                <filter type="param_value" ref="fasta_type.input_database" column="0"/>
-              </option>
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_motifs" value="meme/meme/meme_output_xml_1.xml" ftype="memexml"/>
-      <param name="fasta_type_selector" value="history"/>
-      <param name="input_database" value="phiX.fasta" ftype="fasta"/>
-      <param name="options_type_selector" value="basic"/>
-      <param name="non_commercial_use" value="True"/>
-      <output name="html_outfile" file="meme/fimo/fimo_output_html_1.html" lines_diff="12"/>
-      <output name="txt_outfile" file="meme/fimo/fimo_output_txt_1.txt" lines_diff="0"/>
-      <output name="gff_outfile" file="meme/fimo/fimo_output_almost-gff_1.txt" lines_diff="0"/>
-      <output name="xml_outfile" file="meme/fimo/fimo_output_xml_1.xml" lines_diff="8"/>
-      <output name="interval_outfile" file="meme/fimo/fimo_output_interval_1.txt" lines_diff="0"/>
-    </test>
-  </tests>
-  <help>
-
-.. class:: warningmark
-
-**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
-
-.. class:: infomark
-
-**To cite FIMO:**
-`Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21330290&gt;`_
-
-
-For detailed information on FIMO, click here_. To view the license_.
-
-------
-
-**Citation**
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-
-.. _here: http://meme.nbcr.net/meme/fimo-intro.html
-.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
-
-  </help>
-</tool>
diff --git a/tools/meme/fimo_wrapper.py b/tools/meme/fimo_wrapper.py
deleted file mode 100644
index 1d32ae4b34981cf23e0d3c844a6456440fc50f74..0000000000000000000000000000000000000000
--- a/tools/meme/fimo_wrapper.py
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/usr/bin/env python
-# Dan Blankenberg
-"""
-Read text output from FIMO and create an interval file.
-"""
-import os
-import shutil
-import subprocess
-import sys
-import tempfile
-
-from galaxy_utils.sequence.transform import DNA_reverse_complement
-
-buffsize = 1048576
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
-
-
-def main():
-    assert len(sys.argv) == 8, "Wrong number of arguments"
-    sys.argv.pop(0)
-    fimo_cmd = sys.argv.pop(0)
-    html_path = sys.argv.pop(0)
-    html_out = sys.argv.pop(0)
-    interval_out = sys.argv.pop(0)
-    txt_out = sys.argv.pop(0)
-    xml_out = sys.argv.pop(0)
-    gff_out = sys.argv.pop(0)
-
-    # run fimo
-    try:
-        tmp_stderr = tempfile.NamedTemporaryFile()
-        proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr)
-        returncode = proc.wait()
-        tmp_stderr.seek(0)
-        stderr = ""
-        try:
-            while True:
-                stderr += tmp_stderr.read(buffsize)
-                if not stderr or len(stderr) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-
-        if returncode != 0:
-            raise Exception(stderr)
-    except Exception as e:
-        raise Exception("Error running FIMO:\n" + str(e))
-
-    shutil.move(os.path.join(html_path, "fimo.txt"), txt_out)
-    shutil.move(os.path.join(html_path, "fimo.gff"), gff_out)
-    shutil.move(os.path.join(html_path, "fimo.xml"), xml_out)
-    shutil.move(os.path.join(html_path, "fimo.html"), html_out)
-
-    out_file = open(interval_out, "wb")
-    out_file.write(
-        "#%s\n"
-        % "\t".join(
-            ("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value")
-        )
-    )
-    for line in open(txt_out):
-        if line.startswith("#"):
-            continue
-        fields = line.rstrip("\n\r").split("\t")
-        start, end = int(fields[2]), int(fields[3])
-        sequence = fields[7]
-        if start > end:
-            start, end = end, start  # flip start and end, and set strand
-            strand = "-"
-            sequence = DNA_reverse_complement(
-                sequence
-            )  # we want sequences relative to strand; FIMO always provides + stranded sequence
-        else:
-            strand = "+"
-        start -= 1  # make 0-based start position
-        out_file.write(
-            "%s\n"
-            % "\t".join((fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]))
-        )
-    out_file.close()
-
-
-if __name__ == "__main__":
-    main()
diff --git a/tools/phenotype_association/sift.xml b/tools/phenotype_association/sift.xml
index 3654c74a053aef6c0fd6908dbe504745389625f2..14ef9512c1f4c40f7e77534426b89301bd977947 100644
--- a/tools/phenotype_association/sift.xml
+++ b/tools/phenotype_association/sift.xml
@@ -8,7 +8,7 @@
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset">
       <validator type="unspecified_build"/>
-      <validator type="dataset_metadata_in_file" filename="sift_db.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
+      <validator type="dataset_metadata_in_data_table" table_name="sift_db" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
     </param>
     <param name="chrom_col"  type="data_column" data_ref="input" label="Column with chromosome"/>
     <param name="pos_col"    type="data_column" data_ref="input" numerical="true" label="Column with position"/>
diff --git a/tox.ini b/tox.ini
index bf7909a66f1cb88abbfd519b4c9ab8057dbacf70..ab1153917d2e66fa38f35b1319aedbb26f46a185 100644
--- a/tox.ini
+++ b/tox.ini
@@ -46,6 +46,8 @@ setenv =
     first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true
     mulled: marker=external_dependency_management
     mulled,unit: GALAXY_VIRTUAL_ENV={envdir}
+    mypy,test_galaxy_packages,test_galaxy_packages_for_pulsar: PIP_INDEX_URL=https://wheels.galaxyproject.org/simple
+    mypy,test_galaxy_packages,test_galaxy_packages_for_pulsar: PIP_EXTRA_INDEX_URL=https://pypi.python.org/simple
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
     unit: marker=not external_dependency_management
 deps =